Soil Ecology Wiki - User contributions [en]

Plant Hormones

2021-05-05T20:02:42Z

Ephanrah:

==Introduction==
Plant hormones auxin and cytokinin are primarily known for their roles in vegetative (indeterminate) growth. This type of growth involves the repetition of structures in a given order once the plant has established the primary apical meristem. Auxin and cytokinin work antagonistically during the vegetative growth of plants, but synergistically in cellular regeneration [1]. Auxin is produced in the apical meristem of the plant, whereas cytokinin is produced in the leaves. Auxins are responsible for apical dominance in vegetative growth, repressing cytokinin from activating dormant axillary (lateral) buds from growing new lateral shoots. Cytokinin is responsible for creating new lateral shoots when the apical meristem is damaged or the concentration of auxin falls below the ability to repress cytokinin [1].

==Auxin==
[[File:EVS463_Auxin_Image.JPG|right|300px|thumb|Organic and synthetic Auxins [7]]]
The plant hormone auxin, produced in the apical meristem, can be found in nature as a compound known as indole-3-acetic acid (IAA), and is primarily synthesized from the well-known amino acid tryptophan [4]. There are also synthetic auxins known as 2,4-dichlorophenoxyacetic acid (2,4-D) and naphthalene acetic acid (NAA) [3].

Auxins are extremely important to plant growth as they are responsible primarily for cellular elongation, root development, and apical dominance during vegetative growth. During apical dominance, auxin produced by the apical meristem creates a downward concentration gradient, preventing axillary buds from activating through cytokinin initiation. This concentration gradient also creates a hormone sink in the roots, where auxin stimulates root development. They are widely used commercially for root induction for plant propagation [3].

Interestingly, auxins can induce epinastic and hyponastic responses through localized auxin concentrations. This causes plant bending in the process known as phototropism, where plants such as sunflowers tend to face direct sunlight to increase photosynthetic function. In this process, the plant will bend toward the localized auxin concentration. It may also induce leaf epinasty, where leaves bend downward "as result of disturbances in their growth, with greater expansion in adaxial cells as compared to abaxial surface cells" [4].

==Cytokinin==
[[File:EVS463_Cytokinin_image.JPG|right|300px|thumb|Organic and synthetic cytokinins [7]]]
The plant hormone cytokinin, produced in leaf tissues of plants, is primarily found in nature as a compound known as zeatin. Interestingly, "almost all [[organisms]] make cytokinin; for example, isopentenyl adenine derivatives found adjacent to the anticodon loop of a subset of tRNAs in most eukaryotes and bacteria" [5]. These were first discovered while searching for factors that promote cell proliferation in plant cells in concert with auxin to regulate cell division and differentiation [5].

Cytokinins are primarily responsible for cellular division and overcoming apical dominance to stimulate lateral shoot formation. If the plant apical meristem becomes damaged, the auxin concentration of the plant falls allowing cytokinin concentrations to accumulate and activate dormant axillary buds [5]. In some cases, the auxin concentration gradient falls below levels of apical dominance near the ground, causing lateral shoot formation in a Christmas-tree like effect.

==Plant Callus Formation==
[[File:EVS463_Callus_Formation.JPG|left|200px|thumb|Plant callus tissue forms as a result of wounding, followed by cellular regeneration controlled by the ratio of auxin to cytokinin [7]]]
Callus formation on plants occurs as a result of wounding, infection, or unregulated and undifferentiated cellular regeneration, controlled by concentrations of auxin and cytokinin. Studies have shown "an intermediate ratio of auxin and cytokinin promotes callus induction, while a high ratio of auxin-to-cytokinin or cytokinin-to-auxin induces root and shoot regeneration, respectively" [6]. These hormones are important for infection processes in plants such as agrobacterium where transgenes are inserted into the host genome. The agrobacterium T-DNA has oncogenes which promote production of auxin and cytokinin in order to provide a favorable environment for the bacteria to reproduce and feed. This site is typically referred to as the crown gall. Eventually the plant will die, in which the bacteria are released back into the [[soil]] to begin the infection process again.

==References==
#Su, Ying-Hua, et al. “Auxin-Cytokinin Interaction Regulates Meristem Development.” Molecular plant, vol. 4, no. 4, Elsevier Inc, 2011, pp. 616–25, doi:10.1093/mp/ssr007.
#G. Eric Schaller, et al. “The Yin-Yang of Hormones: Cytokinin and Auxin Interactions in Plant Development.” The Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 44–63, doi:10.1105/tpc.114.133595.
#Zaman, Mohammad, et al. “Enhancing Crop Yield with the Use of N‐based Fertilizers Co‐applied with Plant Hormones or Growth Regulators.” Journal of the Science of Food and Agriculture, vol. 95, no. 9, John Wiley & Sons, Ltd, 2015, pp. 1777–85, doi:10.1002/jsfa.6938.
#Sandalio, Luisa M., et al. “Leaf Epinasty and Auxin: A Biochemical and Molecular Overview.” Plant Science (Limerick), vol. 253, Elsevier Ireland Ltd, 2016, pp. 187–93, doi:10.1016/j.plantsci.2016.10.002.
#Kieber, Joseph J., and G. Eric Schaller. “Cytokinin Signaling in Plant Development.” Development (Cambridge), vol. 145, no. 4, COMPANY BIOLOGISTS LTD, 2018, p. dev149344–, doi:10.1242/dev.149344.
#Momoko Ikeuchi, et al. “Plant Callus: Mechanisms of Induction and Repression.” The Plant Cell, vol. 25, no. 9, American Society of Plant Biologists, 2013, pp. 3159–73, doi:10.1105/tpc.113.116053.
#Berry, James O. “Rec#6 Hormones and Plant Form.” 2021.

Plant Hormones

2021-05-05T19:54:56Z

Ephanrah:

==Introduction==
Plant hormones auxin and cytokinin are primarily known for their roles in vegetative (indeterminate) growth. This type of growth involves the repetition of structures in a given order once the plant has established the primary apical meristem. Auxin and cytokinin work antagonistically during the vegetative growth of plants, but synergistically in cellular regeneration [1]. Auxin is produced in the apical meristem of the plant, whereas cytokinin is produced in the leaves. Auxins are responsible for apical dominance in vegetative growth, repressing cytokinin from activating dormant axillary (lateral) buds from growing new lateral shoots. Cytokinin is responsible for creating new lateral shoots when the apical meristem is damaged or the concentration of auxin falls below the ability to repress cytokinin [1].

==Auxin==
[[File:EVS463_Auxin_Image.JPG|right|300px|thumb|Organic and synthetic Auxins [7]]]
The plant hormone auxin, produced in the apical meristem, can be found in nature as a compound known as indole-3-acetic acid (IAA), and is primarily synthesized from the well-known amino acid tryptophan [4]. There are also synthetic auxins known as 2,4-dichlorophenoxyacetic acid (2,4-D) and naphthalene acetic acid (NAA) [3].

Auxins are extremely important to plant growth as they are responsible primarily for cellular elongation, root development, and apical dominance during vegetative growth. During apical dominance, auxin produced by the apical meristem creates a downward concentration gradient, preventing axillary buds from activating through cytokinin initiation. This concentration gradient also creates a hormone sink in the roots, where auxin stimulates root development. They are widely used commercially for root induction for plant propagation [3].

Interestingly, auxins can induce epinastic responses through localized auxin concentrations, causing plant bending in a process known as phototropism. In this process, the plant will bend toward the localized auxin concentration. It may also induce leaf epinasty, where leaves bend downward "as result of disturbances in their growth, with greater expansion in adaxial cells as compared to abaxial surface cells" [4].

==Cytokinin==
[[File:EVS463_Cytokinin_image.JPG|right|300px|thumb|Organic and synthetic cytokinins [7]]]
The plant hormone cytokinin, produced in leaf tissues of plants, is primarily found in nature as a compound known as zeatin. Interestingly, "almost all [[organisms]] make cytokinin; for example, isopentenyl adenine derivatives found adjacent to the anticodon loop of a subset of tRNAs in most eukaryotes and bacteria" [5]. These were first discovered while searching for factors that promote cell proliferation in plant cells in concert with auxin to regulate cell division and differentiation [5].

Cytokinins are primarily responsible for cellular division and overcoming apical dominance to stimulate lateral shoot formation. If the plant apical meristem becomes damaged, the auxin concentration of the plant falls allowing cytokinin concentrations to accumulate and activate dormant axillary buds [5]. In some cases, the auxin concentration gradient falls below levels of apical dominance near the ground, causing lateral shoot formation in a Christmas-tree like effect.

==Plant Callus Formation==
[[File:EVS463_Callus_Formation.JPG|left|200px|thumb|Plant callus tissue forms as a result of wounding, followed by cellular regeneration controlled by the ratio of auxin to cytokinin [7]]]
Callus formation on plants occurs as a result of wounding, infection, or unregulated and undifferentiated cellular regeneration, controlled by concentrations of auxin and cytokinin. Studies have shown "an intermediate ratio of auxin and cytokinin promotes callus induction, while a high ratio of auxin-to-cytokinin or cytokinin-to-auxin induces root and shoot regeneration, respectively" [6]. These hormones are important for infection processes in plants such as agrobacterium where transgenes are inserted into the host genome. The agrobacterium T-DNA has oncogenes which promote production of auxin and cytokinin in order to provide a favorable environment for the bacteria to reproduce and feed. This site is typically referred to as the crown gall. Eventually the plant will die, in which the bacteria are released back into the [[soil]] to begin the infection process again.

==References==
#Su, Ying-Hua, et al. “Auxin-Cytokinin Interaction Regulates Meristem Development.” Molecular plant, vol. 4, no. 4, Elsevier Inc, 2011, pp. 616–25, doi:10.1093/mp/ssr007.
#G. Eric Schaller, et al. “The Yin-Yang of Hormones: Cytokinin and Auxin Interactions in Plant Development.” The Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 44–63, doi:10.1105/tpc.114.133595.
#Zaman, Mohammad, et al. “Enhancing Crop Yield with the Use of N‐based Fertilizers Co‐applied with Plant Hormones or Growth Regulators.” Journal of the Science of Food and Agriculture, vol. 95, no. 9, John Wiley & Sons, Ltd, 2015, pp. 1777–85, doi:10.1002/jsfa.6938.
#Sandalio, Luisa M., et al. “Leaf Epinasty and Auxin: A Biochemical and Molecular Overview.” Plant Science (Limerick), vol. 253, Elsevier Ireland Ltd, 2016, pp. 187–93, doi:10.1016/j.plantsci.2016.10.002.
#Kieber, Joseph J., and G. Eric Schaller. “Cytokinin Signaling in Plant Development.” Development (Cambridge), vol. 145, no. 4, COMPANY BIOLOGISTS LTD, 2018, p. dev149344–, doi:10.1242/dev.149344.
#Momoko Ikeuchi, et al. “Plant Callus: Mechanisms of Induction and Repression.” The Plant Cell, vol. 25, no. 9, American Society of Plant Biologists, 2013, pp. 3159–73, doi:10.1105/tpc.113.116053.
#Berry, James O. “Rec#6 Hormones and Plant Form.” 2021.

Plant Hormones

2021-05-05T19:54:30Z

Ephanrah:

==Introduction==
Plant hormones auxin and cytokinin are primarily known for their roles in vegetative (indeterminate) growth. This type of growth involves the repetition of structures in a given order once the plant has established the primary apical meristem. Auxin and cytokinin work antagonistically during the vegetative growth of plants, but synergistically in cellular regeneration [1]. Auxin is produced in the apical meristem of the plant, whereas cytokinin is produced in the leaves. Auxins are responsible for apical dominance in vegetative growth, repressing cytokinin from activating dormant axillary (lateral) buds from growing new lateral shoots. Cytokinin is responsible for creating new lateral shoots when the apical meristem is damaged or the concentration of auxin falls below the ability to repress cytokinin [1].

==Auxin==
[[File:EVS463_Auxin_Image.JPG|right|300px|thumb|Organic and synthetic Auxins [7]]]
The plant hormone auxin, produced in the apical meristem, can be found in nature as a compound known as indole-3-acetic acid (IAA), and is primarily synthesized from the well-known amino acid tryptophan [4]. There are also synthetic auxins known as 2,4-dichlorophenoxyacetic acid (2,4-D) and naphthalene acetic acid (NAA) [3].

Auxins are extremely important to plant growth as they are responsible primarily for cellular elongation, root development, and apical dominance during vegetative growth. During apical dominance, auxin produced by the apical meristem creates a downward concentration gradient, preventing axillary buds from activating through cytokinin initiation. This concentration gradient also creates a hormone sink in the roots, where auxin stimulates root development. They are widely used commercially for root induction for plant propagation [3].

Interestingly, auxins can induce epinastic responses through localized auxin concentrations, causing plant bending in a process known as phototropism. In this process, the plant will bend toward the localized auxin concentration. It may also induce leaf epinasty, where leaves bend downward "as result of disturbances in their growth, with greater expansion in adaxial cells as compared to abaxial surface cells" [4].

==Cytokinin==
[[File:EVS463_Cytokinin_image.JPG|right|300px|thumb|Organic and synthetic cytokinins [7]]]
The plant hormone cytokinin, produced in leaf tissues of plants, is primarily found in nature as a compound known as zeatin. Interestingly, "almost all [[organisms]] make cytokinin; for example, isopentenyl adenine derivatives found adjacent to the anticodon loop of a subset of tRNAs in most eukaryotes and bacteria" [5]. These were first discovered while searching for factors that promote cell proliferation in plant cells in concert with auxin to regulate cell division and differentiation [5].

Cytokinins are primarily responsible for cellular division and overcoming apical dominance to stimulate lateral shoot formation. If the plant apical meristem becomes damaged, the auxin concentration of the plant falls allowing cytokinin concentrations to accumulate and activate dormant axillary buds [5]. In some cases, the auxin concentration gradient falls below levels of apical dominance near the ground, causing lateral shoot formation in a Christmas-tree like effect.

==Plant Callus Formation==
[[File:EVS463_Callus_Formation.JPG|left|200px|thumb|Plant callus tissue forms as a result of wounding, followed by cellular regeneration controlled by the ratio of auxin to cytokinin [7]]]
Callus formation on plants occurs as a result of wounding, infection, or unregulated and undifferentiated cellular regeneration, controlled by concentrations of auxin and cytokinin. Studies have shown "an intermediate ratio of auxin and cytokinin promotes callus induction, while a high ratio of auxin-to-cytokinin or cytokinin-to-auxin induces root and shoot regeneration, respectively" [6]. These hormones are important for infection processes in plants such as agrobacterium where transgenes are inserted into the host genome. The agrobacterium T-DNA has oncogenes which promote production of auxin and cytokinin in order to provide a favorable environment for the bacteria to reproduce and feed. This site is typically referred to as the crown gall. Eventually the plant will die, in which the bacteria are released back into the [[soil]] to begin the infection process again.

==References==
#Su, Ying-Hua, et al. “Auxin-Cytokinin Interaction Regulates Meristem Development.” Molecular plant, vol. 4, no. 4, Elsevier Inc, 2011, pp. 616–25, doi:10.1093/mp/ssr007.
#G. Eric Schaller, et al. “The Yin-Yang of Hormones: Cytokinin and Auxin Interactions in Plant Development.” The Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 44–63, doi:10.1105/tpc.114.133595.
#Zaman, Mohammad, et al. “Enhancing Crop Yield with the Use of N‐based Fertilizers Co‐applied with Plant Hormones or Growth Regulators.” Journal of the Science of Food and Agriculture, vol. 95, no. 9, John Wiley & Sons, Ltd, 2015, pp. 1777–85, doi:10.1002/jsfa.6938.
#Sandalio, Luisa M., et al. “Leaf Epinasty and Auxin: A Biochemical and Molecular Overview.” Plant Science (Limerick), vol. 253, Elsevier Ireland Ltd, 2016, pp. 187–93, doi:10.1016/j.plantsci.2016.10.002.
#Kieber, Joseph J., and G. Eric Schaller. “Cytokinin Signaling in Plant Development.” Development (Cambridge), vol. 145, no. 4, COMPANY BIOLOGISTS LTD, 2018, p. dev149344–, doi:10.1242/dev.149344.
#Momoko Ikeuchi, et al. “Plant Callus: Mechanisms of Induction and Repression.” The Plant Cell, vol. 25, no. 9, American Society of Plant Biologists, 2013, pp. 3159–73, doi:10.1105/tpc.113.116053.
#Berry, James O. “Rec#6 Hormones and Plant Form.” 2021.

Planaria

2021-05-05T19:41:30Z

Ephanrah:

== Introduction ==
Planaria, or flatworms, which occupy the order [[Tricladida]] within the phylum [[Platyhelminthes]], are commonly inhabitants of freshwater sources such as streams or ponds, but some are terrestrial in deep soils [1]. These complex [[organisms]] are known to be scavengers, predators, and in many cases parasitic. Planarians such as ''Schmidtea mediterranea'' are known for their remarkable ability to regenerate from pluripotent stem cells scattered throughout their bodies [2]. These adult stem cells, also known as neoblasts, allow planarians to reproduce asexually as well as simply regenerating their entire body from a fragment roughly 1/279 the size of the original worm [7]. These model organisms are medically and scientifically important, as understanding the process of regeneration may carry incredible value to advanced technologies.
[[File:Image203 (2).jpg|right|300px|thumb|S. mediterranea midsection cut regeneration group]]

==Anatomy==
[[File:EVS463_Planarian_Anatomy_1.JPG |left|300px|thumb|Anatomy of Planarian gut, neurons, axons, and pharynx [9]]]
Planarians are triploblastic, involving all three germ layers (ecto-, meso-. and endoderm) and an organized nervous system composed of two anterior cephalic ganglia and two parallel nerve chords that run ventrally along the length of the body [9]. They also contain two photoreceptors which are connected to the nervous system by axons of the optic chiasm [9]. In addition, planarians contain chemoreceptors and rheoreceptors at the anterior end which send projections to the cephalic ganglia [1]. Movement is permitted through the use of motile cilia on the ventral epithelium [9]. These organisms lack a coelom, and all space between the organs and nervous system is composed of mesenchyme [1]. The body wall contains a complex of longitudinal, diagonal, and circular muscle fibers which aid in negotiating obstacles [1]. Food is ingested through an extensible pharynx, which serves as both the mouth and anus, connected to a three-branch (triclad) digestive system [1].

==Planarian Diversity and Distribution ==
Within the [[Tricladida]] exist three proposed taxonomic groups, which are based on their different habitats: [[Paludicola]] (freshwater planarians), [[Terricola]] (land planarians), and [[Maricola]] (marine planarians) [8]. These three taxonomic groups may be even further subdivided by classification of anatomical and external feature differences. "Molecular sequence data has helped to clarify the phylogenetic relationships and the evolutionary history of the Tricladida and in many cases facilitated a more natural classification. However, at certain levels resolution is still poor, thus requiring further studies" [8]. The genome of planarians is vast due to their ancient age and evolutionary processes making a difficult challenge to truly understand the depth of [[diversity]] between the proposed groups.

The distribution of planarians ranges from temperate to tropical and has been modified by introduction of species to newer continents. Climate and moisture play a large role in the distribution of these organisms as they are most vulnerable to desiccation. Terrestrial planarians are found scattered throughout temperate, tropical, and subtropical regions across the globe, whereas the majority of freshwater planarians are mainly confined to the temperate and tropical regions of North America, Europe, and Asia in which draught rarely occurs [8].

== Parasitic Behavior and Treatment ==
Over a third of the world’s population is estimated to be infected with parasitic worms" [4]. Most cases of parasitic flatworm infections are associated with unsanitary drinking water, as these organisms are typically found near the bottom of freshwater sources. Symptoms of host infection result from egg deposition within the liver, gastrointestinal tract, or urinary bladder, resulting in granuloma formation and fibrosis [4]. Drugs such as Praziquantel (PZQ), an anthelmintic, can cure fluke infection by disrupting the neoblast regeneration pattern in planarians. Specifically, the drug causes increased levels of calcium which is suspected to be the main inhibitor of proper neoblast regeneration [5]. This disruption leads to regeneration of Planaria with two heads by inhibiting posterior expression, eventually driving them out of the host.
== Stem Cells and Regeneration ==
[[File:Image212_(2).jpg|right|300px|thumb|RNAi of beta-catenin gene in S. mediterranea and regeneration following midsection cut]]
Neoblasts represent approximately 25%-30% of all planarian cells [1]. Neoblast regeneration and differentiation is activated by the WNT signaling pathway, a signal transduction pathway which specifies the anterior and posterior axis in development. "Wnt signaling directly targets the nucleus, and it is broadly used to regulate cell fate, proliferation and self-renewal of stem and progenitor cells in any tissue and at any stage of metazoan life" [6]. Specifically, this pathway specifies posterior axis development, however, in the absence of the Wnt ligand, the protein beta-catenin is degraded inhibiting posterior specification and enhancing anterior expression markers. Without the Wnt pathway properly activated, a planarian will regenerate with two anterior halves due to lack of posterior expression regulated by beta-catenin. Studies have shown how RNAi, also known as RNA silencing, can inactivate the beta-catenin gene resulting in a lack of posterior expression markers and structures in regenerated planarians [3].

== References ==
#Reddien, Peter W., and Alejandro Sánchez Alvarado. “Fundamentals of Planarian Regeneration.” Annual Review of Cell and Developmental Biology, vol. 20, no. 1, Annual Reviews, Inc, 2004, pp. 725–57, doi:10.1146/annurev.cellbio.20.010403.095114
#Rink, Jochen C., and Jochen C. Rink. “Stem Cell Systems and Regeneration in Planaria.” Development Genes and Evolution, vol. 223, no. 1, Springer-Verlag, 2013, pp. 67–84, doi:10.1007/s00427-012-0426-4.
#Kyle A. Gurley, et al. “β-Catenin Defines Head Versus Tail Identity During Planarian Regeneration and Homeostasis.” Science (American Association for the Advancement of Science), vol. 319, no. 5861, American Association for the Advancement of Science, 2008, pp. 323–27, doi:10.1126/science.1150029.
#Chan, John D., et al. “‘Death and Axes’: Unexpected Ca2+ Entry Phenologs Predict New Anti-Schistosomal Agents.” PLoS Pathogens, vol. 10, no. 2, Public Library of Science (PLoS), 2014, pp. e1003942–e1003942, doi:10.1371/journal.ppat.1003942.
#Cioli, Donato, et al. “Schistosomiasis Control: Praziquantel Forever?” Molecular and Biochemical Parasitology, vol. 195, no. 1, Elsevier B.V, 2014, pp. 23–29, doi:10.1016/j.molbiopara.2014.06.002.
#Almuedo-Castillo, Maria, et al. “Wnt Signaling in Planarians: New Answers to Old Questions.” The International Journal of Developmental Biology, vol. 56, no. 1-2-3, 2012, pp. 53–65, doi:10.1387/ijdb.113451ma.
#Alvarado, Alejandro Sánchez. “Planarians.” Current Biology, vol. 14, no. 18, Elsevier Inc, 2004, pp. R737–R738, doi:10.1016/j.cub.2004.09.005.
#Rink, Jochen C. Planarian Regeneration Methods and Protocols / Edited by Jochen C. Rink. 1st ed. 2018., Springer New York, 2018, doi:10.1007/978-1-4939-7802-1.
#Elliott, Sarah A., and Alejandro Sánchez Alvarado. “The History and Enduring Contributions of Planarians to the Study of Animal Regeneration.” Wiley Interdisciplinary Reviews. Developmental Biology, vol. 2, no. 3, John Wiley & Sons, Inc, 2013, pp. 301–26, doi:10.1002/wdev.82.

Planaria

2021-05-05T19:36:58Z

Ephanrah:

== Introduction ==
Planaria, or flatworms, which occupy the order [[Tricladida]] within the phylum [[Platyhelminthes]], are commonly inhabitants of freshwater sources such as streams or ponds, but some are terrestrial in deep soils [1]. These complex [[organisms]] are known to be scavengers, predators, and in many cases parasitic. Planarians such as ''Schmidtea mediterranea'' are known for their remarkable ability to regenerate from pluripotent stem cells scattered throughout their bodies [2]. These adult stem cells, also known as neoblasts, allow planarians to reproduce asexually as well as simply regenerating their entire body from a fragment roughly 1/279 the size of the original worm [7]. These model organisms are medically and scientifically important, as understanding the process of regeneration may carry incredible value to advanced technologies.
[[File:Image203 (2).jpg|right|300px|thumb|S. mediterranea midsection cut regeneration group]]

==Anatomy==
[[File:EVS463_Planarian_Anatomy_1.JPG |left|300px|thumb|Anatomy of Planarian gut, neurons, axons, and pharynx [9]]]
Planarians are triploblastic, involving all three germ layers (ecto-, meso-. and endoderm) and an organized nervous system composed of two anterior cephalic ganglia and two parallel nerve chords that run ventrally along the length of the body [9]. They also contain two photoreceptors which are connected to the nervous system by axons of the optic chiasm [9]. In addition, planarians contain chemoreceptors and rheoreceptors at the anterior end which send projections to the cephalic ganglia [1]. Movement is permitted through the use of motile cilia on the ventral epithelium [9]. These organisms lack a coelom, and all space between the organs and nervous system is composed of mesenchyme [1]. The body wall contains a complex of longitudinal, diagonal, and circular muscle fibers which aid in negotiating obstacles [1]. Food is ingested through an extensible pharynx, which serves as both the mouth and anus, connected to a three-branch (triclad) digestive system [1].

==Planarian Diversity and Distribution ==
Within the [[Tricladida]] exist three proposed taxonomic groups, which are based on their different habitats: [[Paludicola]] (freshwater planarians), [[Terricola]] (land planarians), and [[Maricola]] (marine planarians) [8]. These three taxonomic groups may be even further subdivided by classification of anatomical and external feature differences. "Molecular sequence data has helped to clarify the phylogenetic relationships and the evolutionary history of the Tricladida and in many cases facilitated a more natural classification. However, at certain levels resolution is still poor, thus requiring further studies" [8]. The genome of planarians is vast due to their ancient age and evolutionary processes making a difficult challenge to truly understand the depth of [[diversity]] between the proposed groups.

The distribution of planarians ranges from temperate to tropical and has been modified by introduction of species to newer continents. Climate and moisture play a large role in the distribution of these organisms as they are most vulnerable to desiccation. Terrestrial planarians are found scattered throughout temperate, tropical, and subtropical regions across the globe, whereas the majority of freshwater planarians are mainly confined to the temperate and tropical regions of North America, Europe, and Asia in which draught rarely occurs [8].

== Parasitic Behavior and Treatment ==
Over a third of the world’s population is estimated to be infected with parasitic worms" [4]. Most cases of parasitic flatworm infections are associated with unsanitary drinking water, as these organisms are typically found near the bottom of freshwater sources. Symptoms of host infection result from egg deposition within the liver, gastrointestinal tract, or urinary bladder, resulting in granuloma formation and fibrosis [4]. Drugs such as Praziquantel (PZQ), an anthelmintic, can cure fluke infection by disrupting the neoblast regeneration pattern in planarians. Specifically, the drug causes increased levels of calcium which is suspected to be the main inhibitor of proper neoblast regeneration [5]. This disruption leads to regeneration of Planaria with two heads by inhibiting posterior expression, eventually driving them out of the host.
== Stem Cells and Regeneration ==
Neoblasts represent approximately 25%-30% of all planarian cells [1]. Neoblast regeneration and differentiation is activated by the WNT signaling pathway, a signal transduction pathway which specifies the anterior and posterior axis in development. "Wnt signaling directly targets the nucleus, and it is broadly used to regulate cell fate, proliferation and self-renewal of stem and progenitor cells in any tissue and at any stage of metazoan life" [6]. Specifically, this pathway specifies posterior axis development, however, in the absence of the Wnt ligand, the protein beta-catenin is degraded inhibiting posterior specification and enhancing anterior expression markers. Without the Wnt pathway properly activated, a planarian will regenerate with two anterior halves due to lack of posterior expression regulated by beta-catenin. Studies have shown how RNAi, also known as RNA silencing, can inactivate the beta-catenin gene resulting in a lack of posterior expression markers and structures in regenerated planarians [3].
[[File:Image212_(2).jpg|right|300px|thumb|RNAi of beta-catenin gene in S. mediterranea and regeneration following midsection cut]]

== References ==
#Reddien, Peter W., and Alejandro Sánchez Alvarado. “Fundamentals of Planarian Regeneration.” Annual Review of Cell and Developmental Biology, vol. 20, no. 1, Annual Reviews, Inc, 2004, pp. 725–57, doi:10.1146/annurev.cellbio.20.010403.095114
#Rink, Jochen C., and Jochen C. Rink. “Stem Cell Systems and Regeneration in Planaria.” Development Genes and Evolution, vol. 223, no. 1, Springer-Verlag, 2013, pp. 67–84, doi:10.1007/s00427-012-0426-4.
#Kyle A. Gurley, et al. “β-Catenin Defines Head Versus Tail Identity During Planarian Regeneration and Homeostasis.” Science (American Association for the Advancement of Science), vol. 319, no. 5861, American Association for the Advancement of Science, 2008, pp. 323–27, doi:10.1126/science.1150029.
#Chan, John D., et al. “‘Death and Axes’: Unexpected Ca2+ Entry Phenologs Predict New Anti-Schistosomal Agents.” PLoS Pathogens, vol. 10, no. 2, Public Library of Science (PLoS), 2014, pp. e1003942–e1003942, doi:10.1371/journal.ppat.1003942.
#Cioli, Donato, et al. “Schistosomiasis Control: Praziquantel Forever?” Molecular and Biochemical Parasitology, vol. 195, no. 1, Elsevier B.V, 2014, pp. 23–29, doi:10.1016/j.molbiopara.2014.06.002.
#Almuedo-Castillo, Maria, et al. “Wnt Signaling in Planarians: New Answers to Old Questions.” The International Journal of Developmental Biology, vol. 56, no. 1-2-3, 2012, pp. 53–65, doi:10.1387/ijdb.113451ma.
#Alvarado, Alejandro Sánchez. “Planarians.” Current Biology, vol. 14, no. 18, Elsevier Inc, 2004, pp. R737–R738, doi:10.1016/j.cub.2004.09.005.
#Rink, Jochen C. Planarian Regeneration Methods and Protocols / Edited by Jochen C. Rink. 1st ed. 2018., Springer New York, 2018, doi:10.1007/978-1-4939-7802-1.
#Elliott, Sarah A., and Alejandro Sánchez Alvarado. “The History and Enduring Contributions of Planarians to the Study of Animal Regeneration.” Wiley Interdisciplinary Reviews. Developmental Biology, vol. 2, no. 3, John Wiley & Sons, Inc, 2013, pp. 301–26, doi:10.1002/wdev.82.

File:EVS463 Planarian Anatomy 1.JPG

2021-05-05T19:30:45Z

Ephanrah: Planarian anatomy of gut, neurons, digestive tract, and a merged photo of all together Elliott, Sarah A., and Alejandro Sánchez Alvarado. “The History and Enduring Contributions of Planarians to the Study of Animal Regeneration.” Wiley Interdisci...

Planarian anatomy of gut, neurons, digestive tract, and a merged photo of all together

Elliott, Sarah A., and Alejandro Sánchez Alvarado. “The History and Enduring Contributions of Planarians to the Study of Animal Regeneration.” Wiley Interdisciplinary Reviews. Developmental Biology, vol. 2, no. 3, John Wiley & Sons, Inc, 2013, pp. 301–26, doi:10.1002/wdev.82.

Planaria

2021-05-05T19:29:28Z

Ephanrah:

== Introduction ==
Planaria, or flatworms, which occupy the order [[Tricladida]] within the phylum [[Platyhelminthes]], are commonly inhabitants of freshwater sources such as streams or ponds, but some are terrestrial in deep soils [1]. These complex [[organisms]] are known to be scavengers, predators, and in many cases parasitic. Planarians such as ''Schmidtea mediterranea'' are known for their remarkable ability to regenerate from pluripotent stem cells scattered throughout their bodies [2]. These adult stem cells, also known as neoblasts, allow planarians to reproduce asexually as well as simply regenerating their entire body from a fragment roughly 1/279 the size of the original worm [7]. These model organisms are medically and scientifically important, as understanding the process of regeneration may carry incredible value to advanced technologies.
[[File:Image203 (2).jpg|right|300px|thumb|S. mediterranea midsection cut regeneration group]]

==Anatomy==
Planarians are triploblastic, involving all three germ layers (ecto-, meso-. and endoderm) and an organized nervous system composed of two anterior cephalic ganglia and two parallel nerve chords that run ventrally along the length of the body [9]. They also contain two photoreceptors which are connected to the nervous system by axons of the optic chiasm [9]. In addition, planarians contain chemoreceptors and rheoreceptors at the anterior end which send projections to the cephalic ganglia [1]. Movement is permitted through the use of motile cilia on the ventral epithelium [9]. These organisms lack a coelom, and all space between the organs and nervous system is composed of mesenchyme [1]. The body wall contains a complex of longitudinal, diagonal, and circular muscle fibers which aid in negotiating obstacles [1]. Food is ingested through an extensible pharynx, which serves as both the mouth and anus, connected to a three-branch (triclad) digestive system [1].

==Planarian Diversity and Distribution ==
Within the [[Tricladida]] exist three proposed taxonomic groups, which are based on their different habitats: [[Paludicola]] (freshwater planarians), [[Terricola]] (land planarians), and [[Maricola]] (marine planarians) [8]. These three taxonomic groups may be even further subdivided by classification of anatomical and external feature differences. "Molecular sequence data has helped to clarify the phylogenetic relationships and the evolutionary history of the Tricladida and in many cases facilitated a more natural classification. However, at certain levels resolution is still poor, thus requiring further studies" [8]. The genome of planarians is vast due to their ancient age and evolutionary processes making a difficult challenge to truly understand the depth of [[diversity]] between the proposed groups.

The distribution of planarians ranges from temperate to tropical and has been modified by introduction of species to newer continents. Climate and moisture play a large role in the distribution of these organisms as they are most vulnerable to desiccation. Terrestrial planarians are found scattered throughout temperate, tropical, and subtropical regions across the globe, whereas the majority of freshwater planarians are mainly confined to the temperate and tropical regions of North America, Europe, and Asia in which draught rarely occurs [8].

== Parasitic Behavior and Treatment ==
Over a third of the world’s population is estimated to be infected with parasitic worms" [4]. Most cases of parasitic flatworm infections are associated with unsanitary drinking water, as these organisms are typically found near the bottom of freshwater sources. Symptoms of host infection result from egg deposition within the liver, gastrointestinal tract, or urinary bladder, resulting in granuloma formation and fibrosis [4]. Drugs such as Praziquantel (PZQ), an anthelmintic, can cure fluke infection by disrupting the neoblast regeneration pattern in planarians. Specifically, the drug causes increased levels of calcium which is suspected to be the main inhibitor of proper neoblast regeneration [5]. This disruption leads to regeneration of Planaria with two heads by inhibiting posterior expression, eventually driving them out of the host.
== Stem Cells and Regeneration ==
Neoblasts represent approximately 25%-30% of all planarian cells [1]. Neoblast regeneration and differentiation is activated by the WNT signaling pathway, a signal transduction pathway which specifies the anterior and posterior axis in development. "Wnt signaling directly targets the nucleus, and it is broadly used to regulate cell fate, proliferation and self-renewal of stem and progenitor cells in any tissue and at any stage of metazoan life" [6]. Specifically, this pathway specifies posterior axis development, however, in the absence of the Wnt ligand, the protein beta-catenin is degraded inhibiting posterior specification and enhancing anterior expression markers. Without the Wnt pathway properly activated, a planarian will regenerate with two anterior halves due to lack of posterior expression regulated by beta-catenin. Studies have shown how RNAi, also known as RNA silencing, can inactivate the beta-catenin gene resulting in a lack of posterior expression markers and structures in regenerated planarians [3].
[[File:Image212_(2).jpg|right|300px|thumb|RNAi of beta-catenin gene in S. mediterranea and regeneration following midsection cut]]

== References ==
#Reddien, Peter W., and Alejandro Sánchez Alvarado. “Fundamentals of Planarian Regeneration.” Annual Review of Cell and Developmental Biology, vol. 20, no. 1, Annual Reviews, Inc, 2004, pp. 725–57, doi:10.1146/annurev.cellbio.20.010403.095114
#Rink, Jochen C., and Jochen C. Rink. “Stem Cell Systems and Regeneration in Planaria.” Development Genes and Evolution, vol. 223, no. 1, Springer-Verlag, 2013, pp. 67–84, doi:10.1007/s00427-012-0426-4.
#Kyle A. Gurley, et al. “β-Catenin Defines Head Versus Tail Identity During Planarian Regeneration and Homeostasis.” Science (American Association for the Advancement of Science), vol. 319, no. 5861, American Association for the Advancement of Science, 2008, pp. 323–27, doi:10.1126/science.1150029.
#Chan, John D., et al. “‘Death and Axes’: Unexpected Ca2+ Entry Phenologs Predict New Anti-Schistosomal Agents.” PLoS Pathogens, vol. 10, no. 2, Public Library of Science (PLoS), 2014, pp. e1003942–e1003942, doi:10.1371/journal.ppat.1003942.
#Cioli, Donato, et al. “Schistosomiasis Control: Praziquantel Forever?” Molecular and Biochemical Parasitology, vol. 195, no. 1, Elsevier B.V, 2014, pp. 23–29, doi:10.1016/j.molbiopara.2014.06.002.
#Almuedo-Castillo, Maria, et al. “Wnt Signaling in Planarians: New Answers to Old Questions.” The International Journal of Developmental Biology, vol. 56, no. 1-2-3, 2012, pp. 53–65, doi:10.1387/ijdb.113451ma.
#Alvarado, Alejandro Sánchez. “Planarians.” Current Biology, vol. 14, no. 18, Elsevier Inc, 2004, pp. R737–R738, doi:10.1016/j.cub.2004.09.005.
#Rink, Jochen C. Planarian Regeneration Methods and Protocols / Edited by Jochen C. Rink. 1st ed. 2018., Springer New York, 2018, doi:10.1007/978-1-4939-7802-1.
#Elliott, Sarah A., and Alejandro Sánchez Alvarado. “The History and Enduring Contributions of Planarians to the Study of Animal Regeneration.” Wiley Interdisciplinary Reviews. Developmental Biology, vol. 2, no. 3, John Wiley & Sons, Inc, 2013, pp. 301–26, doi:10.1002/wdev.82.

Planaria

2021-05-05T19:13:24Z

Ephanrah: Addition of Anatomy section

== Introduction ==
Planaria, or flatworms, which occupy the order [[Tricladida]] within the phylum [[Platyhelminthes]], are commonly inhabitants of freshwater sources such as streams or ponds, but some are terrestrial in deep soils [1]. These complex [[organisms]] are known to be scavengers, predators, and in many cases parasitic. Planarians such as ''Schmidtea mediterranea'' are known for their remarkable ability to regenerate from pluripotent stem cells scattered throughout their bodies [2]. These adult stem cells, also known as neoblasts, allow planarians to reproduce asexually as well as simply regenerating their entire body from a fragment roughly 1/279 the size of the original worm [7]. These model organisms are medically and scientifically important, as understanding the process of regeneration may carry incredible value to advanced technologies.
[[File:Image203 (2).jpg|right|300px|thumb|S. mediterranea midsection cut regeneration group]]

==Anatomy==
Planarians are triploblastic, involving all three germ layers (ecto-, meso-. and endoderm) and an organized nervous system composed of two anterior cephalic ganglia and two parallel nerve chords that run ventrally along the length of the body [9]. They also contain two photoreceptors which are connected to the nervous system by axons of the optic chiasm [9]. Movement is permitted through the use of motile cilia on the ventral-most epithelium [9]. Interestingly, these organisms contain stem cells known as neoblasts allowing regeneration following injury making them a great model organism for scientific study [1].

==Planarian Diversity and Distribution ==
Within the [[Tricladida]] exist three proposed taxonomic groups, which are based on their different habitats: [[Paludicola]] (freshwater planarians), [[Terricola]] (land planarians), and [[Maricola]] (marine planarians) [8]. These three taxonomic groups may be even further subdivided by classification of anatomical and external feature differences. "Molecular sequence data has helped to clarify the phylogenetic relationships and the evolutionary history of the Tricladida and in many cases facilitated a more natural classification. However, at certain levels resolution is still poor, thus requiring further studies" [8]. The genome of planarians is vast due to their ancient age and evolutionary processes making a difficult challenge to truly understand the depth of [[diversity]] between the proposed groups.

The distribution of planarians ranges from temperate to tropical and has been modified by introduction of species to newer continents. Climate and moisture play a large role in the distribution of these organisms as they are most vulnerable to desiccation. Terrestrial planarians are found scattered throughout temperate, tropical, and subtropical regions across the globe, whereas the majority of freshwater planarians are mainly confined to the temperate and tropical regions of North America, Europe, and Asia in which draught rarely occurs [8].

== Parasitic Behavior and Treatment ==
Over a third of the world’s population is estimated to be infected with parasitic worms" [4]. Most cases of parasitic flatworm infections are associated with unsanitary drinking water, as these organisms are typically found near the bottom of freshwater sources. Symptoms of host infection result from egg deposition within the liver, gastrointestinal tract, or urinary bladder, resulting in granuloma formation and fibrosis [4]. Drugs such as Praziquantel (PZQ), an anthelmintic, can cure fluke infection by disrupting the neoblast regeneration pattern in planarians. Specifically, the drug causes increased levels of calcium which is suspected to be the main inhibitor of proper neoblast regeneration [5]. This disruption leads to regeneration of Planaria with two heads by inhibiting posterior expression, eventually driving them out of the host.
== Stem Cells and Regeneration ==
Neoblasts represent approximately 25%-30% of all planarian cells [1]. Neoblast regeneration and differentiation is activated by the WNT signaling pathway, a signal transduction pathway which specifies the anterior and posterior axis in development. "Wnt signaling directly targets the nucleus, and it is broadly used to regulate cell fate, proliferation and self-renewal of stem and progenitor cells in any tissue and at any stage of metazoan life" [6]. Specifically, this pathway specifies posterior axis development, however, in the absence of the Wnt ligand, the protein beta-catenin is degraded inhibiting posterior specification and enhancing anterior expression markers. Without the Wnt pathway properly activated, a planarian will regenerate with two anterior halves due to lack of posterior expression regulated by beta-catenin. Studies have shown how RNAi, also known as RNA silencing, can inactivate the beta-catenin gene resulting in a lack of posterior expression markers and structures in regenerated planarians [3].
[[File:Image212_(2).jpg|right|300px|thumb|RNAi of beta-catenin gene in S. mediterranea and regeneration following midsection cut]]

== References ==
#Reddien, Peter W., and Alejandro Sánchez Alvarado. “Fundamentals of Planarian Regeneration.” Annual Review of Cell and Developmental Biology, vol. 20, no. 1, Annual Reviews, Inc, 2004, pp. 725–57, doi:10.1146/annurev.cellbio.20.010403.095114
#Rink, Jochen C., and Jochen C. Rink. “Stem Cell Systems and Regeneration in Planaria.” Development Genes and Evolution, vol. 223, no. 1, Springer-Verlag, 2013, pp. 67–84, doi:10.1007/s00427-012-0426-4.
#Kyle A. Gurley, et al. “β-Catenin Defines Head Versus Tail Identity During Planarian Regeneration and Homeostasis.” Science (American Association for the Advancement of Science), vol. 319, no. 5861, American Association for the Advancement of Science, 2008, pp. 323–27, doi:10.1126/science.1150029.
#Chan, John D., et al. “‘Death and Axes’: Unexpected Ca2+ Entry Phenologs Predict New Anti-Schistosomal Agents.” PLoS Pathogens, vol. 10, no. 2, Public Library of Science (PLoS), 2014, pp. e1003942–e1003942, doi:10.1371/journal.ppat.1003942.
#Cioli, Donato, et al. “Schistosomiasis Control: Praziquantel Forever?” Molecular and Biochemical Parasitology, vol. 195, no. 1, Elsevier B.V, 2014, pp. 23–29, doi:10.1016/j.molbiopara.2014.06.002.
#Almuedo-Castillo, Maria, et al. “Wnt Signaling in Planarians: New Answers to Old Questions.” The International Journal of Developmental Biology, vol. 56, no. 1-2-3, 2012, pp. 53–65, doi:10.1387/ijdb.113451ma.
#Alvarado, Alejandro Sánchez. “Planarians.” Current Biology, vol. 14, no. 18, Elsevier Inc, 2004, pp. R737–R738, doi:10.1016/j.cub.2004.09.005.
#Rink, Jochen C. Planarian Regeneration Methods and Protocols / Edited by Jochen C. Rink. 1st ed. 2018., Springer New York, 2018, doi:10.1007/978-1-4939-7802-1.
#Elliott, Sarah A., and Alejandro Sánchez Alvarado. “The History and Enduring Contributions of Planarians to the Study of Animal Regeneration.” Wiley Interdisciplinary Reviews. Developmental Biology, vol. 2, no. 3, John Wiley & Sons, Inc, 2013, pp. 301–26, doi:10.1002/wdev.82.

Microplastics

2021-05-05T18:32:08Z

Ephanrah: Fixed citation spacing

==Overview==
Most commonly studied for the detrimental effects caused in marine environments, the impact of '''Microplastics''' on [[soil]] ecosystems have been largely neglected. The main sources of microplastic pollution in soil is thought to be plastic mulching film and fertilizer produced through waste water irrigation [1]. "Microplastics are widely defined as synthetic polymers with an upper size limit of 5mm and without specified lower limit" [10].
‎[[File:Microplasticsfoundinsoil.jpg|center|thumb|450px| A microscopic look at plastic microfibers found in soil.]]

===Primary Microplastics===
Primary microplastics are originally manufactured to be smaller than 5mm, and are typically found in the following [10]:
*Textiles
*Medicines
*Personal care products
These may be transported through rivers, water-treatment plants, and wind or surface run-off [10].

===Secondary Microplastics===
Secondary microplastics are typically derived from the fragmentation or degradation of larger plastic debris through a few processes including photo-degradation, physical, chemical and biological interactions [10]. The majority of microplastics are categorized as secondary microplastics, and can originate from both land and ocean based sources including the following: [10]
*Fishing nets
*Industrial resin pellets
*Household items
*Other discarded plastic debris
Estimates have concluded that ocean based sources contribute approximately 20% of total plastic debris in the marine environment, whereas terrestrial based sources contribute the remaining 80% [10].

==Plastic Mulching==
[[File:20110829-FSA-XX-0028 - Flickr - USDAgov.jpg|120px|left|thumb|Plastic mulching in agriculture]]
Plastic mulch is used to conserve water and subdue weed growth in agriculture. Conventional plastic polymers are typically used as biodegradable alternatives are usually much more expensive [3]. Plastic polymers tend to accumulate in soil as it is broken down due to lack of economical and legal incentive surrounding removal of plastic mulching [1].

==Buildup of Microplastics Due to Fertilizer Application==
[[File:Shovel excavator loading the sewage sludge (6305610332).jpg|thumb|Shovel excavator loading sewage sludge fertilizer onto farmland.]]
Wastewater facilities receive a large amount of microplastic fibers emitted from industry, surface run-off, and households in urban areas. A surprisingly large amount may come through use of washer machines [4]. Most of these fibers accumulate in sewage sludge, which is often turned into a fertilizer. While there are regulatory methods on the possible pollutants in waste water sludge, there remains none regarding the accumulation of microplastics. Microplastics are able to accumulate in soil through the repeat application of this sewage sludge fertilizer[2].

==Unknown Consequences==
Studies done in Norway suggest a large portion of microplastics generated in western societies end up in the sludge found at wastewater treatment facilities [1]. In America and Europe, it is estimated that about half of total sewage sludge accumulated each year is used as fertilizer. Estimates range anywhere from 110,000 tons and 730,000 tons of microplastics being transferred to American and European soil each year [5]. There is an estimated total of 93,000 to 236,000 metric tons of microplastic entering the ocean each year [6], making soil potentially a larger reservoir than the ocean for microplastics.

==Potential Impacts on Plant and Soil Health==
[[File:Isotoma Habitus.jpg|left|200px|thumb|A [[springtail]], whose movement and ability to escape predations may be debilitated due to microplastic interference with the furcula appendage.]]
The vast potential consequences of microplastics on soil and plant [[ecology]] in generally unknown [2]. In a study conducted over five weeks, soil was exposed to a concentration of up to 2% of micro-fibrous plastics. Bulk density, water holding capacity, hydraulic conductivity, soil aggregation, and microbial activity were all measured. It was concluded that microplastics effected the bulk density of soil, water holding capacity, and the relationship between microbes and soil. The study suggests that microplastics could potentially be interfering with [[Arbuscular Mycorrhizal Fungi]], a crucial symbiotic relationship many plants rely on. In another study, it was found that microplastics actually inhibit the movement of [[springtail]], an organism that plays a part in [[Soil Ecology|soil ecology]] [8]. There is a clear and surprising knowledge gap on the effects on microplastics on soils and more research is needed in order get a better understanding of the problem and the solutions to fix it [1].

==Potential Impacts on Human Health==
"Microplastics are considered an emerging environmental contaminant, and so there is a dearth of convincing evidence on adverse human health effects" [9]. Evidence through research involving mathematic modeling, animal studies, and in vitro testing suggests that microplastics pose the following health risks [9]:
*Oxidative stress and cytotoxicity
*Altering metabolism and energy balance
*Disruption of immune function
*Translocation to distant tissues
*Neurotoxicity
*Reproductive toxicity
*Carcinogenicity

It is hypothesized that the adverse effects of microplastics on humans largely depends on the degree of exposure and the susceptibility of the individual [9].

===Routes of Exposure===
Direct routes of microplastic exposure include ingestion of contaminated food and water, inhalation, and through skin (dermal) contact of of microplastics found in a number of personal care products, textiles, or indoor dust [9].

Of these routes, the most common tends to be ingestion of microplastics through contaminated food and water sources. Microplastic ingestion based on American diet and lifestyle patterns was estimated to be between 39,000 and 52,000 particles per individual, and when combined with the inhalation route of exposure, these estimates increased to 74,000 to 121,000 particles per individual [9].

==Refrences==
[1] Lei.(2018).Microplastics in soils: Analytical methods, pollution characteristics and ecological risks.TrAC Trends in Analytical Chemistry.163-172.0165-9936.https://doi.org/10.1016/j.trac.2018.10.006.

[2] Rillig,M.C.(2012).Microplastic in Terrestrial Ecosystems and the Soil?.Environ.Sci.Technol. 46 (12), 6453– 6454, DOI: 10.1021/es302011r

[3] Nizzetto et al (2016): “A theoretical assessment of microplastic transport in river catchments and their retention by soils and river sediments” in Environ. Sci.: Processes Impacts, 2016, 18, 1050-1059. DOI: 10.1039/C6EM00206D

[4] Nizzetto, Futter, Langaas (2016): “Are Agricultural Soils Dumps for Microplastics of Urban Origin?“ in Environ. Sci. Technol. DOI: 10.1021/acs.est.6b04140

[5] Rodríguez-Seijo, Andrés & Pereira, Ruth. (2019). Chapter 3. Microplastics in Agricultural Soils: Are They a Real Environmental Hazard?. 10.1201/9781315205137.

[6] Luís Carlos de Sá, Miguel Oliveira, Francisca Ribeiro, Thiago Lopes Rocha, Martyn Norman Futter.(2018).studies of the effects of microplastics on aquatic [[organisms]]: What do we know and where should we focus our efforts in the future?.Science of The Total Environment.Volume.645.1029-1039.0048-9697.https://doi.org/10.1016/j.scitotenv.2018.07.207

[7] Anderson Abel de Souza Machado, Chung Wai Lau, Jennifer Till, Werner Kloas, Anika Lehmann, Roland Becker, and Matthias C. Rillig
Environmental Science & Technology 2018 52 (17), 9656-9665
DOI: 10.1021/acs.est.8b02212

[8] Kim, S. W., and Y.-J. An. 2019. Soil microplastics inhibit the movement of springtail species. Environment International 126:699–706.

[9] Rahman, Arifur, et al. “Potential Human Health Risks Due to Environmental Exposure to Nano- and Microplastics and Knowledge Gaps: A Scoping Review.” The Science of the Total Environment, vol. 757, Elsevier B.V, 2021, pp. 143872–143872, doi:10.1016/j.scitotenv.2020.143872.

[10] Li, Jingyi, et al. “Microplastics in Freshwater Systems: A Review on Occurrence, Environmental Effects, and Methods for Microplastics Detection.” Water Research (Oxford), vol. 137, Elsevier Ltd, 2018, pp. 362–74, doi:10.1016/j.watres.2017.12.056.

Microplastics

2021-05-05T18:31:26Z

Ephanrah: Fixed citation error for [10]

==Overview==
Most commonly studied for the detrimental effects caused in marine environments, the impact of '''Microplastics''' on [[soil]] ecosystems have been largely neglected. The main sources of microplastic pollution in soil is thought to be plastic mulching film and fertilizer produced through waste water irrigation [1]. "Microplastics are widely defined as synthetic polymers with an upper size limit of 5mm and without specified lower limit" [10].
‎[[File:Microplasticsfoundinsoil.jpg|center|thumb|450px| A microscopic look at plastic microfibers found in soil.]]

===Primary Microplastics===
Primary microplastics are originally manufactured to be smaller than 5mm, and are typically found in the following [10]:
*Textiles
*Medicines
*Personal care products
These may be transported through rivers, water-treatment plants, and wind or surface run-off [10].

===Secondary Microplastics===
Secondary microplastics are typically derived from the fragmentation or degradation of larger plastic debris through a few processes including photo-degradation, physical, chemical and biological interactions [10]. The majority of microplastics are categorized as secondary microplastics, and can originate from both land and ocean based sources including the following: [10]
*Fishing nets
*Industrial resin pellets
*Household items
*Other discarded plastic debris
Estimates have concluded that ocean based sources contribute approximately 20% of total plastic debris in the marine environment, whereas terrestrial based sources contribute the remaining 80% [10].

==Plastic Mulching==
[[File:20110829-FSA-XX-0028 - Flickr - USDAgov.jpg|120px|left|thumb|Plastic mulching in agriculture]]
Plastic mulch is used to conserve water and subdue weed growth in agriculture. Conventional plastic polymers are typically used as biodegradable alternatives are usually much more expensive [3]. Plastic polymers tend to accumulate in soil as it is broken down due to lack of economical and legal incentive surrounding removal of plastic mulching [1].

==Buildup of Microplastics Due to Fertilizer Application==
[[File:Shovel excavator loading the sewage sludge (6305610332).jpg|thumb|Shovel excavator loading sewage sludge fertilizer onto farmland.]]
Wastewater facilities receive a large amount of microplastic fibers emitted from industry, surface run-off, and households in urban areas. A surprisingly large amount may come through use of washer machines [4]. Most of these fibers accumulate in sewage sludge, which is often turned into a fertilizer. While there are regulatory methods on the possible pollutants in waste water sludge, there remains none regarding the accumulation of microplastics. Microplastics are able to accumulate in soil through the repeat application of this sewage sludge fertilizer[2].

==Unknown Consequences==
Studies done in Norway suggest a large portion of microplastics generated in western societies end up in the sludge found at wastewater treatment facilities [1]. In America and Europe, it is estimated that about half of total sewage sludge accumulated each year is used as fertilizer. Estimates range anywhere from 110,000 tons and 730,000 tons of microplastics being transferred to American and European soil each year [5]. There is an estimated total of 93,000 to 236,000 metric tons of microplastic entering the ocean each year [6], making soil potentially a larger reservoir than the ocean for microplastics.

==Potential Impacts on Plant and Soil Health==
[[File:Isotoma Habitus.jpg|left|200px|thumb|A [[springtail]], whose movement and ability to escape predations may be debilitated due to microplastic interference with the furcula appendage.]]
The vast potential consequences of microplastics on soil and plant [[ecology]] in generally unknown [2]. In a study conducted over five weeks, soil was exposed to a concentration of up to 2% of micro-fibrous plastics. Bulk density, water holding capacity, hydraulic conductivity, soil aggregation, and microbial activity were all measured. It was concluded that microplastics effected the bulk density of soil, water holding capacity, and the relationship between microbes and soil. The study suggests that microplastics could potentially be interfering with [[Arbuscular Mycorrhizal Fungi]], a crucial symbiotic relationship many plants rely on. In another study, it was found that microplastics actually inhibit the movement of [[springtail]], an organism that plays a part in [[Soil Ecology|soil ecology]] [8]. There is a clear and surprising knowledge gap on the effects on microplastics on soils and more research is needed in order get a better understanding of the problem and the solutions to fix it [1].

==Potential Impacts on Human Health==
"Microplastics are considered an emerging environmental contaminant, and so there is a dearth of convincing evidence on adverse human health effects" [9]. Evidence through research involving mathematic modeling, animal studies, and in vitro testing suggests that microplastics pose the following health risks [9]:
*Oxidative stress and cytotoxicity
*Altering metabolism and energy balance
*Disruption of immune function
*Translocation to distant tissues
*Neurotoxicity
*Reproductive toxicity
*Carcinogenicity

It is hypothesized that the adverse effects of microplastics on humans largely depends on the degree of exposure and the susceptibility of the individual [9].

===Routes of Exposure===
Direct routes of microplastic exposure include ingestion of contaminated food and water, inhalation, and through skin (dermal) contact of of microplastics found in a number of personal care products, textiles, or indoor dust [9].

Of these routes, the most common tends to be ingestion of microplastics through contaminated food and water sources. Microplastic ingestion based on American diet and lifestyle patterns was estimated to be between 39,000 and 52,000 particles per individual, and when combined with the inhalation route of exposure, these estimates increased to 74,000 to 121,000 particles per individual [9].

==Refrences==
[1] Lei.(2018).Microplastics in soils: Analytical methods, pollution characteristics and ecological risks.TrAC Trends in Analytical Chemistry.163-172.0165-9936.https://doi.org/10.1016/j.trac.2018.10.006.

[2] Rillig,M.C.(2012).Microplastic in Terrestrial Ecosystems and the Soil?.Environ.Sci.Technol. 46 (12), 6453– 6454, DOI: 10.1021/es302011r

[3] Nizzetto et al (2016): “A theoretical assessment of microplastic transport in river catchments and their retention by soils and river sediments” in Environ. Sci.: Processes Impacts, 2016, 18, 1050-1059. DOI: 10.1039/C6EM00206D

[4] Nizzetto, Futter, Langaas (2016): “Are Agricultural Soils Dumps for Microplastics of Urban Origin?“ in Environ. Sci. Technol. DOI: 10.1021/acs.est.6b04140

[5] Rodríguez-Seijo, Andrés & Pereira, Ruth. (2019). Chapter 3. Microplastics in Agricultural Soils: Are They a Real Environmental Hazard?. 10.1201/9781315205137.

[6] Luís Carlos de Sá, Miguel Oliveira, Francisca Ribeiro, Thiago Lopes Rocha, Martyn Norman Futter.(2018).studies of the effects of microplastics on aquatic [[organisms]]: What do we know and where should we focus our efforts in the future?.Science of The Total Environment.Volume.645.1029-1039.0048-9697.https://doi.org/10.1016/j.scitotenv.2018.07.207

[7] Anderson Abel de Souza Machado, Chung Wai Lau, Jennifer Till, Werner Kloas, Anika Lehmann, Roland Becker, and Matthias C. Rillig
Environmental Science & Technology 2018 52 (17), 9656-9665
DOI: 10.1021/acs.est.8b02212

[8]Kim, S. W., and Y.-J. An. 2019. Soil microplastics inhibit the movement of springtail species. Environment International 126:699–706.

[9]Rahman, Arifur, et al. “Potential Human Health Risks Due to Environmental Exposure to Nano- and Microplastics and Knowledge Gaps: A Scoping Review.” The Science of the Total Environment, vol. 757, Elsevier B.V, 2021, pp. 143872–143872, doi:10.1016/j.scitotenv.2020.143872.

[10]Li, Jingyi, et al. “Microplastics in Freshwater Systems: A Review on Occurrence, Environmental Effects, and Methods for Microplastics Detection.” Water Research (Oxford), vol. 137, Elsevier Ltd, 2018, pp. 362–74, doi:10.1016/j.watres.2017.12.056.

Microplastics

2021-05-05T18:28:35Z

Ephanrah: Addition of the definition of a microplastic, primary and secondary MPs, and human health risks

==Overview==
Most commonly studied for the detrimental effects caused in marine environments, the impact of '''Microplastics''' on [[soil]] ecosystems have been largely neglected. The main sources of microplastic pollution in soil is thought to be plastic mulching film and fertilizer produced through waste water irrigation [1]. "Microplastics are widely defined as synthetic polymers with an upper size limit of 5mm and without specified lower limit" [10].
‎[[File:Microplasticsfoundinsoil.jpg|center|thumb|450px| A microscopic look at plastic microfibers found in soil.]]

===Primary Microplastics===
Primary microplastics are originally manufactured to be smaller than 5mm, and are typically found in the following [10]:
*Textiles
*Medicines
*Personal care products
These may be transported through rivers, water-treatment plants, and wind or surface run-off [10].

===Secondary Microplastics===
Secondary microplastics are typically derived from the fragmentation or degradation of larger plastic debris through a few processes including photo-degradation, physical, chemical and biological interactions [10]. The majority of microplastics are categorized as secondary microplastics, and can originate from both land and ocean based sources including the following: [10]
*Fishing nets
*Industrial resin pellets
*Household items
*Other discarded plastic debris
Estimates have concluded that ocean based sources contribute approximately 20% of total plastic debris in the marine environment, whereas terrestrial based sources contribute the remaining 80% [10].

==Plastic Mulching==
[[File:20110829-FSA-XX-0028 - Flickr - USDAgov.jpg|120px|left|thumb|Plastic mulching in agriculture]]
Plastic mulch is used to conserve water and subdue weed growth in agriculture. Conventional plastic polymers are typically used as biodegradable alternatives are usually much more expensive [3]. Plastic polymers tend to accumulate in soil as it is broken down due to lack of economical and legal incentive surrounding removal of plastic mulching [1].

==Buildup of Microplastics Due to Fertilizer Application==
[[File:Shovel excavator loading the sewage sludge (6305610332).jpg|thumb|Shovel excavator loading sewage sludge fertilizer onto farmland.]]
Wastewater facilities receive a large amount of microplastic fibers emitted from industry, surface run-off, and households in urban areas. A surprisingly large amount may come through use of washer machines [4]. Most of these fibers accumulate in sewage sludge, which is often turned into a fertilizer. While there are regulatory methods on the possible pollutants in waste water sludge, there remains none regarding the accumulation of microplastics. Microplastics are able to accumulate in soil through the repeat application of this sewage sludge fertilizer[2].

==Unknown Consequences==
Studies done in Norway suggest a large portion of microplastics generated in western societies end up in the sludge found at wastewater treatment facilities [1]. In America and Europe, it is estimated that about half of total sewage sludge accumulated each year is used as fertilizer. Estimates range anywhere from 110,000 tons and 730,000 tons of microplastics being transferred to American and European soil each year [5]. There is an estimated total of 93,000 to 236,000 metric tons of microplastic entering the ocean each year [6], making soil potentially a larger reservoir than the ocean for microplastics.

==Potential Impacts on Plant and Soil Health==
[[File:Isotoma Habitus.jpg|left|200px|thumb|A [[springtail]], whose movement and ability to escape predations may be debilitated due to microplastic interference with the furcula appendage.]]
The vast potential consequences of microplastics on soil and plant [[ecology]] in generally unknown [2]. In a study conducted over five weeks, soil was exposed to a concentration of up to 2% of micro-fibrous plastics. Bulk density, water holding capacity, hydraulic conductivity, soil aggregation, and microbial activity were all measured. It was concluded that microplastics effected the bulk density of soil, water holding capacity, and the relationship between microbes and soil. The study suggests that microplastics could potentially be interfering with [[Arbuscular Mycorrhizal Fungi]], a crucial symbiotic relationship many plants rely on. In another study, it was found that microplastics actually inhibit the movement of [[springtail]], an organism that plays a part in [[Soil Ecology|soil ecology]] [8]. There is a clear and surprising knowledge gap on the effects on microplastics on soils and more research is needed in order get a better understanding of the problem and the solutions to fix it [1].

==Potential Impacts on Human Health==
"Microplastics are considered an emerging environmental contaminant, and so there is a dearth of convincing evidence on adverse human health effects" [9]. Evidence through research involving mathematic modeling, animal studies, and in vitro testing suggests that microplastics pose the following health risks [9]:
*Oxidative stress and cytotoxicity
*Altering metabolism and energy balance
*Disruption of immune function
*Translocation to distant tissues
*Neurotoxicity
*Reproductive toxicity
*Carcinogenicity

It is hypothesized that the adverse effects of microplastics on humans largely depends on the degree of exposure and the susceptibility of the individual [9].

===Routes of Exposure===
Direct routes of microplastic exposure include ingestion of contaminated food and water, inhalation, and through skin (dermal) contact of of microplastics found in a number of personal care products, textiles, or indoor dust [9].

Of these routes, the most common tends to be ingestion of microplastics through contaminated food and water sources. Microplastic ingestion based on American diet and lifestyle patterns was estimated to be between 39,000 and 52,000 particles per individual, and when combined with the inhalation route of exposure, these estimates increased to 74,000 to 121,000 particles per individual [9].

==Refrences==
[1] Lei.(2018).Microplastics in soils: Analytical methods, pollution characteristics and ecological risks.TrAC Trends in Analytical Chemistry.163-172.0165-9936.https://doi.org/10.1016/j.trac.2018.10.006.

[2] Rillig,M.C.(2012).Microplastic in Terrestrial Ecosystems and the Soil?.Environ.Sci.Technol. 46 (12), 6453– 6454, DOI: 10.1021/es302011r

[3] Nizzetto et al (2016): “A theoretical assessment of microplastic transport in river catchments and their retention by soils and river sediments” in Environ. Sci.: Processes Impacts, 2016, 18, 1050-1059. DOI: 10.1039/C6EM00206D

[4] Nizzetto, Futter, Langaas (2016): “Are Agricultural Soils Dumps for Microplastics of Urban Origin?“ in Environ. Sci. Technol. DOI: 10.1021/acs.est.6b04140

[5] Rodríguez-Seijo, Andrés & Pereira, Ruth. (2019). Chapter 3. Microplastics in Agricultural Soils: Are They a Real Environmental Hazard?. 10.1201/9781315205137.

[6] Luís Carlos de Sá, Miguel Oliveira, Francisca Ribeiro, Thiago Lopes Rocha, Martyn Norman Futter.(2018).studies of the effects of microplastics on aquatic [[organisms]]: What do we know and where should we focus our efforts in the future?.Science of The Total Environment.Volume.645.1029-1039.0048-9697.https://doi.org/10.1016/j.scitotenv.2018.07.207

[7] Anderson Abel de Souza Machado, Chung Wai Lau, Jennifer Till, Werner Kloas, Anika Lehmann, Roland Becker, and Matthias C. Rillig
Environmental Science & Technology 2018 52 (17), 9656-9665
DOI: 10.1021/acs.est.8b02212

[8]Kim, S. W., and Y.-J. An. 2019. Soil microplastics inhibit the movement of springtail species. Environment International 126:699–706.

[9]Rahman, Arifur, et al. “Potential Human Health Risks Due to Environmental Exposure to Nano- and Microplastics and Knowledge Gaps: A Scoping Review.” The Science of the Total Environment, vol. 757, Elsevier B.V, 2021, pp. 143872–143872, doi:10.1016/j.scitotenv.2020.143872.

[10]2. Li, Jingyi, et al. “Microplastics in Freshwater Systems: A Review on Occurrence, Environmental Effects, and Methods for Microplastics Detection.” Water Research (Oxford), vol. 137, Elsevier Ltd, 2018, pp. 362–74, doi:10.1016/j.watres.2017.12.056.

C4 Carbon Fixation

2021-05-05T01:00:11Z

Ephanrah: /* Anatomy */

==Description==
[[File:EVS463_C4_Carbon_Fixation.JPG|right|200px|thumb|Hatch-Slack pathway in C4 plants.]]
The [[Hatch-Slack pathway]], also known as the C4 plant carbon fixation pathway, involves the storing of atmospheric CO2 in bundle sheath cells. "The evolution of C4 photosynthesis ~35–40 million years ago provided a natural solution to remedy the inefficiency of Rubisco" [2]. The Hatch-Slack pathway is acknowledged for its improved efficiency, where the concentration of CO2 is increased around the enzyme Rubisco in order to reduce [[photorespiration]].

==Anatomy and Function==
[[File:BIO_370_Pep_Antibody_(2).jpg|right|200px|thumb|Amaranth mesophyll cells stained with PEP Case primary antibody.]]
[[File:BIO370_Rubisco_primary_antibody_(2).jpg|right|200px|thumb|Amaranth bundle sheath cells stained with rubisco primary antibody.]]
C4 plants exhibit a Kranz-type leaf anatomy involving two photosynthetic cells known as mesophyll cells and bundle sheath cells which differ in their CO2 assimilation functions [1]. In mesophyll cells, atmospheric carbon dioxide is converted to a C4 acid by the enzyme phosphoenolpyruvate carboxylase (PEP Case) during the carboxylation phase of carbon fixation. In this step, PEP Case catalyzes the reaction between bicarbonate, HCO3-, and phosphoenolpyruvate (PEP), a three-carbon molecule, to form the four-carbon acid oxaloacetate and inorganic phosphate [4]. The four-carbon acids are then transported to the bundle sheath cells surrounding leaf veins where rubisco (ribulose-1,5-bisphosphate carboxylase-oxygenase) fixes and assimilates CO2 into the [[Calvin Cycle]]. Once CO2 is assimilated into the cycle by RuBP and Rubisco, energy (ATP, NADPH) from the light reactions during photosynthesis is used to produce sugars such as glucose [5].

==Agricultural Significance==
C4 plants typically occupy hot, arid climates, whereas C3 plants are most frequently found in temperate, moist environments. When fixing carbon, C3 plants open their stomata to allow atmospheric gasses such as carbon dioxide and oxygen at the cost of allowing water to evaporate from the plants leaves. However, C4 plants have evolved to retain water through the ability to continue fixing carbon while the stomata are closed [6]. This adaptation allows C4 plants to survive the hot and dry climates, reducing harmful photorespiration and water losses through evaporation.

Several common agriculturally significant C4 plants include [6]:
*Maize
*Sugarcane
*Sorghum

In many subtropical, tropical, and desert climates, C4 plants are the primary economic agricultural generators due to their carbon fixation efficiency and ability to retain water. "Drought is a major agricultural problem worldwide. Therefore, selection for increased water use efficiency (WUE) in food and biofuel crop species will be an important trait in plant breeding programs" [3]. With [[climate change]] in mind, C4 plants are becoming much more favorable in agriculture as they are resilient in the face of warmer ambient temperatures and drier seasons.

==Evolution==
It has been hypothesized through evolutionary radiation analysis that C4 vegetation contributed to global cooling during the late Miocene period [7]. Researchers have proposed that low atmospheric CO2 during the late Miocene triggered C4 evolution in [[Andropogonae]] grasses roughly 17 million years ago [7]. With the help of paleontologists, recent studies have hypothesized C4 evolution began in the late Oligocene period approximately 25-30 million years ago when CO2 levels were falling below 1000ppm (parts per million) [7]. Interestingly, it is suspected that the rise of C4 plants contributed to diversification of many animal clades such as the formation of large grazing guilds in the C4 grasslands of Africa [7]. With current technological advancements, research is still uprooting the foundation of C4 plant evolution, however the previously proposed mechanisms are generally agreed upon by ecological and paleontological organizations.

==References==
#PATEL, Minesh, and James O. BERRY. “Rubisco Gene Expression in C4 Plants: Photosynthesis: CO2 Uptake and the Pathways of Carbon Fixation.” Journal of Experimental Botany, vol. 59, no. 7, Oxford University Press, 2008, pp. 1625–34.
#Sharwood, Robert E., et al. “Improved Analysis of C4 and C3 Photosynthesis via Refined in Vitro Assays of Their Carbon Fixation Biochemistry.” Journal of Experimental Botany, vol. 67, no. 10, Oxford University Press, 2016, pp. 3137–48, doi:10.1093/jxb/erw154.
#Ellsworth, Patrick Z., and Asaph B. Cousins. “Carbon Isotopes and Water Use Efficiency in C4 Plants.” Current Opinion in Plant Biology, vol. 31, no. C, Elsevier Ltd, 2016, pp. 155–61, doi:10.1016/j.pbi.2016.04.006.
#“Phosphoenolpyruvate Carboxylase.” Wikipedia, Wikimedia Foundation, 19 Oct. 2020, en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxylase.
#National Geographic Society. “Calvin Cycle.” National Geographic Society, 9 Nov. 2012, www.nationalgeographic.org/media/calvincycle/#:~:text=by%20Tim%20Gunther-,The%20Calvin%20cycle%20is%20a%20process%20that%20plants%20and%20algae,cycle%20for%20energy%20and%20food.
#“The Difference between C3 and C4 Plants.” RIPE, 18 Mar. 2020, ripe.illinois.edu/blog/difference-between-c3-and-c4-plants.
#Sage, Rowan F., et al. “Some Like It Hot: The Physiological [[Ecology]] of C4 Plant Evolution.” Oecologia, vol. 187, no. 4, Springer Berlin Heidelberg, 2018, pp. 941–66, doi:10.1007/s00442-018-4191-6.
#Berry, James O. “Exp. #10. Laser Scanning Confocal Microscopy, C4 Leaf Development.” 2021.

Polymerase Chain Reaction (PCR)

2021-05-05T00:34:06Z

Ephanrah: Undo revision 6339 by Ephanrah (talk)

=Definition=
Polymerase chain reaction (PCR) using a method used to amplify a small amount of DNA in order to allow scientist to study it in detail[1]. RNA can also be extracted from samples and converted into complimentary DNA (cDNA) for PCR amplification [4]. Primers are used to identify the location of the DNA in the sample. Enzymes that have defined segments of DNA are taken advantage of to recreate cDNA [4].
==Primers==
PCR primers are single strands of DNA used to identify the location of the DNA in the sample. This refers to a small set of nucleotides in DNA. For bacteria and [[archaebacteria]] primers that are ubiquitous to the 16s ribosomal RNA (rRNA) are used [1,2,3,5,6]
==Method==
There are three essential steps when conducting PCR.

1. The melting of the target DNA [2]

2. After the DNA has been melted the primers are combined into a synthesized DNA [2]

3. Finally, there is a primer extension by thermostable DNA polymerase [2]
[[File:Screen Shot 2021-04-15 at 3.51.44 PM.png|thumb|right|Stages of PCR and the resultant amplification of DNA copies of the target region[2]]]

==Uses==
PCR is helpful for scientist as it recreates small strands of DNA using either DNA or RNA. This is especially helpful in looking at genetic [[ecology]] studies as it allows scientists to get a closer look at DNA [5]. Pathogens among samples are able to be seen using PCR [1,4,6]. Bacterial cultures is the traditional way to sample these, but it usually only accounts for a small amount of microbial biomass [1].
==References==
1. Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborn, A.M., Strike, P., Ritchie, D.A., 1992. Amplification of DNA from native populations of [[soil]] bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413–3416. https://doi.org/10.1128/AEM.58.10.3413-3416.1992

2. Henson, J.M., French, R.C., n.d. THE POLYMERASE CHAIN REACTION AND PLANT DISEASE DIAGNOSIS 30.

3. Picard, C., Ponsonnet, C., Paget, E., Nesme, X., Simonet, P., 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717–2722. https://doi.org/10.1128/AEM.58.9.2717-2722.1992

4. Schochetman, G., Ou, C.-Y., 2021. Polymerase Chain Reaction 5

5. Tsai, Y.L., Olson, B.H., 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Applied and Environmental Microbiology 58, 754–757. https://doi.org/10.1128/AEM.58.2.754-757.1992

6. WILSONl, K.H., Blitchington, R.B., Greene, R.C., 1990. Amplification of Bacterial 16S Ribosomal DNA with Polymerase Chain Reaction. J. CLIN. MICROBIOL. 28, 5.

Polymerase Chain Reaction (PCR)

2021-05-05T00:33:22Z

Ephanrah: Undo revision 6340 by Ephanrah (talk)

=Description=
The polymerase chain reaction (PCR) is a method used to amplify a small amount of DNA in order to allow scientists to study target genes or specific DNA sequences in detail [1]. DNA is extracted from sample tissues and converted into complimentary DNA (cDNA) with the use of a reverse transcriptase [4]. Target primers identify the location of the DNA sequence(s) in the sample, in which DNA polymerases recognize and begin to synthesize the complementary strands of targeted sequences.

==Primers==
PCR primers are single strands of RNA that recognize and attach to the targeted sequence of DNA in the sample tissue. Once the targeted sequence has been located, a DNA polymerase attaches to the primer and begins synthesizing cDNA strands, amplifying the target sequence. For bacteria and [[archaebacteria]], primers that are ubiquitous to the 16s ribosomal RNA (rRNA) are used [1,2,3,5,6]

==Methods==
There are several essential steps when conducting PCR.

1. Purifying RNA from specific tissues or cells [2]

2. Amplifying cDNA copies of the purified RNA [2]

3. Analysis of copied DNA sequences [2]

[[File:Screen Shot 2021-04-15 at 3.51.44 PM.png|thumb|right|Stages of PCR and the resultant amplification of DNA copies of the target region[2]]]

==Stages of PCR==
1. '''Denaturing stage''': During this phase, the purified sample containing the double stranded (ds) DNA and reaction mixture is heated to a temperature of 94C-95C, breaking the hydrogen bonds and separating the strands to allow for future amplification [7].

2. '''Annealing stage''': During this phase, the reaction mixture is cooled to a temperature of 50C-65C, allowing specific target primers (forward and reverse) to attach to the complementary target DNA sequence through hydrogen bonding. This step is necessary, as DNA polymerases cannot extend the primers to create new copies of the DNA without a section of dsDNA to begin with [7].

3. '''Extension stage''': During this phase, the temperature is increased to 72C to enable to attachment and activity of the DNA polymerase. This specific DNA polymerase comes from the heat-loving bacteria ''Thermus aquaticus'', which is stable at higher temperatures needed for the initial denaturing of double stranded DNA from sample tissues. Once this binds to the forward or reverse primer of the target DNA sequence, it begins to synthesize new strands or copies of the sequence through addition of dNTPs in the 5' to 3' direction [7].

These phases are repeated roughly 20-40 times, producing potentially billions of copies of the targeted sequence in a short period of time.

==Uses==
Polymerase chain reactions are helpful for scientists as they enhance specific target sequences within the genome of an organism. This can allow scientists to determine the temporal and/or spatial expression of genes throughout an organism, or even the differences between mutant and wild-type plants and [[animals]]. Today, PCR is commonly used in identifying pathogens among samples, such as COVID-19 and many other life-threatening viruses [1,4,6].

==References==
1. Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborn, A.M., Strike, P., Ritchie, D.A., 1992. Amplification of DNA from native populations of [[soil]] bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413–3416. https://doi.org/10.1128/AEM.58.10.3413-3416.1992

2. Henson, J.M., French, R.C., n.d. THE POLYMERASE CHAIN REACTION AND PLANT DISEASE DIAGNOSIS 30.

3. Picard, C., Ponsonnet, C., Paget, E., Nesme, X., Simonet, P., 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717–2722. https://doi.org/10.1128/AEM.58.9.2717-2722.1992

4. Schochetman, G., Ou, C.-Y., 2021. Polymerase Chain Reaction 5

5. Tsai, Y.L., Olson, B.H., 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Applied and Environmental Microbiology 58, 754–757. https://doi.org/10.1128/AEM.58.2.754-757.1992

6. WILSONl, K.H., Blitchington, R.B., Greene, R.C., 1990. Amplification of Bacterial 16S Ribosomal DNA with Polymerase Chain Reaction. J. CLIN. MICROBIOL. 28, 5.

7. “What Is PCR (Polymerase Chain Reaction)?” Facts, The Public Engagement Team at the Wellcome Genome Campus, 25 Jan. 2016, www.yourgenome.org/facts/what-is-pcr-polymerase-chain-reaction.

Polymerase Chain Reaction (PCR)

2021-05-05T00:29:54Z

Ephanrah: Undo revision 6351 by Ephanrah (talk)

=Description=
The polymerase chain reaction (PCR) is a method used to amplify a small amount of DNA in order to allow scientists to study target genes or specific DNA sequences in detail [1]. RNA is extracted from sample tissues and converted into complimentary DNA (cDNA) with the use of a reverse transcriptase [4]. Target primers identify the location of the DNA sequence(s) in the sample, in which DNA polymerases recognize and begin to synthesize the complementary strands of targeted sequences.

==Primers==
PCR primers are single strands of RNA that recognize and attach to the targeted sequence of DNA in the sample tissue. Once the targeted sequence has been located, a DNA polymerase attaches to the primer and begins synthesizing cDNA strands, amplifying the target sequence. For bacteria and [[archaebacteria]], primers that are ubiquitous to the 16s ribosomal RNA (rRNA) are used [1,2,3,5,6]

==Methods==
There are several essential steps when conducting PCR.

1. Purifying RNA from specific tissues or cells [2]

2. Amplifying cDNA copies of the purified RNA [2]

3. Analysis of copied DNA sequences [2]

[[File:Screen Shot 2021-04-15 at 3.51.44 PM.png|thumb|right|Stages of PCR and the resultant amplification of DNA copies of the target region[2]]]

==Stages of PCR==
1. '''Denaturing stage''': During this phase, the purified sample containing the double stranded (ds) DNA and reaction mixture is heated to a temperature of 94C-95C, breaking the hydrogen bonds and separating the strands to allow for future amplification [7].

2. '''Annealing stage''': During this phase, the reaction mixture is cooled to a temperature of 50C-65C, allowing specific target primers (forward and reverse) to attach to the complementary target DNA sequence through hydrogen bonding. This step is necessary, as DNA polymerases cannot extend the primers to create new copies of the DNA without a section of dsDNA to begin with [7].

3. '''Extension stage''': During this phase, the temperature is increased to 72C to enable to attachment and activity of the DNA polymerase. This specific DNA polymerase comes from the heat-loving bacteria ''Thermus aquaticus'', which is stable at higher temperatures needed for the initial denaturing of double stranded DNA from sample tissues. Once this binds to the forward or reverse primer of the target DNA sequence, it begins to synthesize new strands or copies of the sequence through addition of dNTPs in the 5' to 3' direction [7].

These phases are repeated roughly 20-40 times, producing potentially billions of copies of the targeted sequence in a short period of time.

==Uses==
Polymerase chain reactions are helpful for scientists as they enhance specific target sequences within the genome of an organism. This can allow scientists to determine the temporal and/or spatial expression of genes throughout an organism, or even the differences between mutant and wild-type plants and [[animals]]. Today, PCR is commonly used in identifying pathogens among samples, such as COVID-19 and many other life-threatening viruses [1,4,6].

==References==
1. Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborn, A.M., Strike, P., Ritchie, D.A., 1992. Amplification of DNA from native populations of [[soil]] bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413–3416. https://doi.org/10.1128/AEM.58.10.3413-3416.1992

2. Henson, J.M., French, R.C., n.d. THE POLYMERASE CHAIN REACTION AND PLANT DISEASE DIAGNOSIS 30.

3. Picard, C., Ponsonnet, C., Paget, E., Nesme, X., Simonet, P., 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717–2722. https://doi.org/10.1128/AEM.58.9.2717-2722.1992

4. Schochetman, G., Ou, C.-Y., 2021. Polymerase Chain Reaction 5

5. Tsai, Y.L., Olson, B.H., 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Applied and Environmental Microbiology 58, 754–757. https://doi.org/10.1128/AEM.58.2.754-757.1992

6. WILSONl, K.H., Blitchington, R.B., Greene, R.C., 1990. Amplification of Bacterial 16S Ribosomal DNA with Polymerase Chain Reaction. J. CLIN. MICROBIOL. 28, 5.

7. “What Is PCR (Polymerase Chain Reaction)?” Facts, The Public Engagement Team at the Wellcome Genome Campus, 25 Jan. 2016, www.yourgenome.org/facts/what-is-pcr-polymerase-chain-reaction.

Polymerase Chain Reaction (PCR)

2021-05-05T00:29:32Z

Ephanrah: Undo revision 6352 by Ephanrah (talk)

=Description=
The polymerase chain reaction (PCR) is a method used to amplify a small amount of DNA in order to allow scientists to study target genes or specific DNA sequences in detail [1]. RNA is extracted from sample tissues and converted into complimentary DNA (cDNA) with the use of a reverse transcriptase [4]. Target primers identify the location of the DNA sequence(s) in the sample, in which DNA polymerases recognize and begin to synthesize the complementary strands of targeted sequences.

==Primers==
PCR primers are single strands of RNA that recognize and attach to the targeted sequence of DNA in the sample tissue. Once the targeted sequence has been located, a DNA polymerase attaches to the primer and begins synthesizing cDNA strands, amplifying the target sequence. For bacteria and [[archaebacteria]], primers that are ubiquitous to the 16s ribosomal RNA (rRNA) are used [1,2,3,5,6]

==Methods==
There are several essential steps when conducting Standard PCR.

1. Purifying DNA from specific tissues or cells [2]

2. Amplifying cDNA copies of the purified DNA [2]

3. Analysis of copied DNA sequences [2]

[[File:Screen Shot 2021-04-15 at 3.51.44 PM.png|thumb|right|Stages of PCR and the resultant amplification of DNA copies of the target region[2]]]

There are also a number of different types of polymerase chain reactions including endpoint, quantitative real time, reverse transcription, multiplex, and more. These have been modified to analyze different types of data, such as end point PCR where analysis of cDNA takes place after the plateau phase, or RT-PCR where cDNA is synthesized from RNA through the use of a reverse transcriptase enzyme.

==Stages of PCR==
1. '''Denaturing stage''': During this phase, the purified sample containing the double stranded (ds) DNA and reaction mixture is heated to a temperature of 94C-95C, breaking the hydrogen bonds and separating the strands to allow for future amplification [7].

2. '''Annealing stage''': During this phase, the reaction mixture is cooled to a temperature of 50C-65C, allowing specific target primers (forward and reverse) to attach to the complementary target DNA sequence through hydrogen bonding. This step is necessary, as DNA polymerases cannot extend the primers to create new copies of the DNA without a section of dsDNA to begin with [7].

3. '''Extension stage''': During this phase, the temperature is increased to 72C to enable to attachment and activity of the DNA polymerase. This specific DNA polymerase comes from the heat-loving bacteria ''Thermus aquaticus'', which is stable at higher temperatures needed for the initial denaturing of double stranded DNA from sample tissues. Once this binds to the forward or reverse primer of the target DNA sequence, it begins to synthesize new strands or copies of the sequence through addition of dNTPs in the 5' to 3' direction [7].

These phases are repeated roughly 20-40 times, producing potentially billions of copies of the targeted sequence in a short period of time.

==Uses==
Polymerase chain reactions are helpful for scientists as they enhance specific target sequences within the genome of an organism. This can allow scientists to determine the temporal and/or spatial expression of genes throughout an organism, or even the differences between mutant and wild-type plants and [[animals]]. Today, PCR is commonly used in identifying pathogens among samples, such as COVID-19 and many other life-threatening viruses [1,4,6].

==References==
1. Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborn, A.M., Strike, P., Ritchie, D.A., 1992. Amplification of DNA from native populations of [[soil]] bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413–3416. https://doi.org/10.1128/AEM.58.10.3413-3416.1992

2. Henson, J.M., French, R.C., n.d. THE POLYMERASE CHAIN REACTION AND PLANT DISEASE DIAGNOSIS 30.

3. Picard, C., Ponsonnet, C., Paget, E., Nesme, X., Simonet, P., 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717–2722. https://doi.org/10.1128/AEM.58.9.2717-2722.1992

4. Schochetman, G., Ou, C.-Y., 2021. Polymerase Chain Reaction 5

5. Tsai, Y.L., Olson, B.H., 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Applied and Environmental Microbiology 58, 754–757. https://doi.org/10.1128/AEM.58.2.754-757.1992

6. WILSONl, K.H., Blitchington, R.B., Greene, R.C., 1990. Amplification of Bacterial 16S Ribosomal DNA with Polymerase Chain Reaction. J. CLIN. MICROBIOL. 28, 5.

7. “What Is PCR (Polymerase Chain Reaction)?” Facts, The Public Engagement Team at the Wellcome Genome Campus, 25 Jan. 2016, www.yourgenome.org/facts/what-is-pcr-polymerase-chain-reaction.

Polymerase Chain Reaction (PCR)

2021-05-05T00:29:09Z

Ephanrah: Undo revision 6354 by Ephanrah (talk)

=Description=
The polymerase chain reaction (PCR) is a method used to amplify a small amount of DNA in order to allow scientists to study target genes or specific DNA sequences in detail [1]. DNA is extracted from sample tissues or cells and converted into complimentary DNA (cDNA) [4]. In some cases, RNA is extracted and converted to cDNA with the use of a reverse transcriptase. Target primers identify the location of the DNA sequence(s) in the sample, in which DNA polymerases recognize and begin to synthesize the complementary strands of targeted sequences.

==Primers==
PCR primers are single strands of RNA that recognize and attach to the targeted sequence of DNA in the sample tissue. Once the targeted sequence has been located, a DNA polymerase attaches to the primer and begins synthesizing cDNA strands, amplifying the target sequence. For bacteria and [[archaebacteria]], primers that are ubiquitous to the 16s ribosomal RNA (rRNA) are used [1,2,3,5,6]

==Methods==
There are several essential steps when conducting Standard PCR.

1. Purifying DNA from specific tissues or cells [2]

2. Amplifying cDNA copies of the purified DNA [2]

3. Analysis of copied DNA sequences [2]

[[File:Screen Shot 2021-04-15 at 3.51.44 PM.png|thumb|right|Stages of PCR and the resultant amplification of DNA copies of the target region[2]]]

There are also a number of different types of polymerase chain reactions including endpoint, quantitative real time, reverse transcription, multiplex, and more. These have been modified to analyze different types of data, such as end point PCR where analysis of cDNA takes place after the plateau phase, or RT-PCR where cDNA is synthesized from RNA through the use of a reverse transcriptase enzyme.

==Stages of PCR==
1. '''Denaturing stage''': During this phase, the purified sample containing the double stranded (ds) DNA and reaction mixture is heated to a temperature of 94C-95C, breaking the hydrogen bonds and separating the strands to allow for future amplification [7].

2. '''Annealing stage''': During this phase, the reaction mixture is cooled to a temperature of 50C-65C, allowing specific target primers (forward and reverse) to attach to the complementary target DNA sequence through hydrogen bonding. This step is necessary, as DNA polymerases cannot extend the primers to create new copies of the DNA without a section of dsDNA to begin with [7].

3. '''Extension stage''': During this phase, the temperature is increased to 72C to enable to attachment and activity of the DNA polymerase. This specific DNA polymerase comes from the heat-loving bacteria ''Thermus aquaticus'', which is stable at higher temperatures needed for the initial denaturing of double stranded DNA from sample tissues. Once this binds to the forward or reverse primer of the target DNA sequence, it begins to synthesize new strands or copies of the sequence through addition of dNTPs in the 5' to 3' direction [7].

These phases are repeated roughly 20-40 times, producing potentially billions of copies of the targeted sequence in a short period of time.

==Uses==
Polymerase chain reactions are helpful for scientists as they enhance specific target sequences within the genome of an organism. This can allow scientists to determine the temporal and/or spatial expression of genes throughout an organism, or even the differences between mutant and wild-type plants and [[animals]]. Today, PCR is commonly used in identifying pathogens among samples, such as COVID-19 and many other life-threatening viruses [1,4,6].

==References==
1. Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborn, A.M., Strike, P., Ritchie, D.A., 1992. Amplification of DNA from native populations of [[soil]] bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413–3416. https://doi.org/10.1128/AEM.58.10.3413-3416.1992

2. Henson, J.M., French, R.C., n.d. THE POLYMERASE CHAIN REACTION AND PLANT DISEASE DIAGNOSIS 30.

3. Picard, C., Ponsonnet, C., Paget, E., Nesme, X., Simonet, P., 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717–2722. https://doi.org/10.1128/AEM.58.9.2717-2722.1992

4. Schochetman, G., Ou, C.-Y., 2021. Polymerase Chain Reaction 5

5. Tsai, Y.L., Olson, B.H., 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Applied and Environmental Microbiology 58, 754–757. https://doi.org/10.1128/AEM.58.2.754-757.1992

6. WILSONl, K.H., Blitchington, R.B., Greene, R.C., 1990. Amplification of Bacterial 16S Ribosomal DNA with Polymerase Chain Reaction. J. CLIN. MICROBIOL. 28, 5.

7. “What Is PCR (Polymerase Chain Reaction)?” Facts, The Public Engagement Team at the Wellcome Genome Campus, 25 Jan. 2016, www.yourgenome.org/facts/what-is-pcr-polymerase-chain-reaction.

Polymerase Chain Reaction (PCR)

2021-05-05T00:27:45Z

Ephanrah: Undo revision 6355 by Ephanrah (talk)

[[File:EVS463_Phases_of_PCR.JPG|right|450px|thumb|The three phases of polymerase chain reactions [7]]]
=Description=
The polymerase chain reaction (PCR) is a method used to amplify a small amount of DNA in order to allow scientists to study target genes or specific DNA sequences in detail [1]. DNA is extracted from sample tissues or cells and converted into complimentary DNA (cDNA) [4]. In some cases, RNA is extracted and converted to cDNA with the use of a reverse transcriptase. Target primers identify the location of the DNA sequence(s) in the sample, in which DNA polymerases recognize and begin to synthesize the complementary strands of targeted sequences.

==Primers==
PCR primers are single strands of RNA that recognize and attach to the targeted sequence of DNA in the sample tissue. Once the targeted sequence has been located, a DNA polymerase attaches to the primer and begins synthesizing cDNA strands, amplifying the target sequence. For bacteria and [[archaebacteria]], primers that are ubiquitous to the 16s ribosomal RNA (rRNA) are used [1,2,3,5,6]

==Methods==
There are several essential steps when conducting Standard PCR.

1. Purifying DNA from specific tissues or cells [2]

2. Amplifying cDNA copies of the purified DNA [2]

3. Analysis of copied DNA sequences [2]

[[File:Screen Shot 2021-04-15 at 3.51.44 PM.png|thumb|right|Stages of PCR and the resultant amplification of DNA copies of the target region[2]]]

There are also a number of different types of polymerase chain reactions including endpoint, quantitative real time, reverse transcription, multiplex, and more. These have been modified to analyze different types of data, such as end point PCR where analysis of cDNA takes place after the plateau phase, or RT-PCR where cDNA is synthesized from RNA through the use of a reverse transcriptase enzyme.

==Stages of PCR==
1. '''Denaturing stage''': During this phase, the purified sample containing the double stranded (ds) DNA and reaction mixture is heated to a temperature of 94C-95C, breaking the hydrogen bonds and separating the strands to allow for future amplification [7].

2. '''Annealing stage''': During this phase, the reaction mixture is cooled to a temperature of 50C-65C, allowing specific target primers (forward and reverse) to attach to the complementary target DNA sequence through hydrogen bonding. This step is necessary, as DNA polymerases cannot extend the primers to create new copies of the DNA without a section of dsDNA to begin with [7].

3. '''Extension stage''': During this phase, the temperature is increased to 72C to enable to attachment and activity of the DNA polymerase. This specific DNA polymerase comes from the heat-loving bacteria ''Thermus aquaticus'', which is stable at higher temperatures needed for the initial denaturing of double stranded DNA from sample tissues. Once this binds to the forward or reverse primer of the target DNA sequence, it begins to synthesize new strands or copies of the sequence through addition of dNTPs in the 5' to 3' direction [7].

These phases are repeated roughly 20-40 times, producing potentially billions of copies of the targeted sequence in a short period of time.

==Uses==
Polymerase chain reactions are helpful for scientists as they enhance specific target sequences within the genome of an organism. This can allow scientists to determine the temporal and/or spatial expression of genes throughout an organism, or even the differences between mutant and wild-type plants and [[animals]]. Today, PCR is commonly used in identifying pathogens among samples, such as COVID-19 and many other life-threatening viruses [1,4,6].

==References==
1. Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborn, A.M., Strike, P., Ritchie, D.A., 1992. Amplification of DNA from native populations of [[soil]] bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413–3416. https://doi.org/10.1128/AEM.58.10.3413-3416.1992

2. Henson, J.M., French, R.C., n.d. THE POLYMERASE CHAIN REACTION AND PLANT DISEASE DIAGNOSIS 30.

3. Picard, C., Ponsonnet, C., Paget, E., Nesme, X., Simonet, P., 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717–2722. https://doi.org/10.1128/AEM.58.9.2717-2722.1992

4. Schochetman, G., Ou, C.-Y., 2021. Polymerase Chain Reaction 5

5. Tsai, Y.L., Olson, B.H., 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Applied and Environmental Microbiology 58, 754–757. https://doi.org/10.1128/AEM.58.2.754-757.1992

6. WILSONl, K.H., Blitchington, R.B., Greene, R.C., 1990. Amplification of Bacterial 16S Ribosomal DNA with Polymerase Chain Reaction. J. CLIN. MICROBIOL. 28, 5.

7. “What Is PCR (Polymerase Chain Reaction)?” Facts, The Public Engagement Team at the Wellcome Genome Campus, 25 Jan. 2016, www.yourgenome.org/facts/what-is-pcr-polymerase-chain-reaction.

Polymerase Chain Reaction (PCR)

2021-05-05T00:27:19Z

Ephanrah: Undo revision 6356 by Ephanrah (talk)

=Description=
The polymerase chain reaction (PCR) is a method used to amplify a small amount of DNA in order to allow scientists to study target genes or specific DNA sequences in detail [1]. DNA is extracted from sample tissues or cells and converted into complimentary DNA (cDNA) [4]. In some cases, RNA is extracted and converted to cDNA with the use of a reverse transcriptase. Target primers identify the location of the DNA sequence(s) in the sample, in which DNA polymerases recognize and begin to synthesize the complementary strands of targeted sequences. With each cycle of the reaction, cDNA begins to amplify exponentially at a point known as the cycle threshold value in which the abundance of cDNA can be measured using an instrument known as a thermocycler.

==Primers==
[[File:EVS463_Phases_of_PCR.JPG|right|450px|thumb|The three phases of polymerase chain reactions [7]]]
PCR primers are single strands of RNA that recognize and attach to the targeted sequence of DNA in the sample tissue. Once the targeted sequence has been located, a DNA polymerase attaches to the primer and begins synthesizing cDNA strands, amplifying the target sequence. For bacteria and [[archaebacteria]], primers that are ubiquitous to the 16s ribosomal RNA (rRNA) are used [1,2,3,5,6]

==Methods==
There are several essential steps when conducting Standard PCR.

1. Purifying DNA from specific tissues or cells [2]

2. Amplifying cDNA copies of the purified DNA [2]

3. Analysis of copied DNA sequences [2]

There are also a number of different types of polymerase chain reactions including endpoint, quantitative real time, reverse transcription, multiplex, and more. These have been modified to analyze different types of data, such as end point PCR where analysis of cDNA takes place after the plateau phase, or RT-PCR where cDNA is synthesized from RNA through the use of a reverse transcriptase enzyme.

==Stages of PCR==
[[File:Screen Shot 2021-04-15 at 3.51.44 PM.png|300px|thumb|right|Stages of PCR and the resultant amplification of DNA copies of the target region[2]]]
1. '''Denaturing stage''': During this phase, the purified sample containing the double stranded (ds) DNA and reaction mixture is heated to a temperature of 94C-95C, breaking the hydrogen bonds and separating the strands to allow for future amplification [7].

2. '''Annealing stage''': During this phase, the reaction mixture is cooled to a temperature of 50C-65C, allowing specific target primers (forward and reverse) to attach to the complementary target DNA sequence through hydrogen bonding. This step is necessary, as DNA polymerases cannot extend the primers to create new copies of the DNA without a section of dsDNA to begin with [7].

3. '''Extension stage''': During this phase, the temperature is increased to 72C to enable to attachment and activity of the DNA polymerase. This specific DNA polymerase comes from the heat-loving bacteria ''Thermus aquaticus'', which is stable at higher temperatures needed for the initial denaturing of double stranded DNA from sample tissues. Once this binds to the forward or reverse primer of the target DNA sequence, it begins to synthesize new strands or copies of the sequence through addition of dNTPs in the 5' to 3' direction [7].

These phases are repeated roughly 20-40 times, producing potentially billions of copies of the targeted sequence in a short period of time.

==Uses==
Polymerase chain reactions are helpful for scientists as they enhance specific target sequences within the genome of an organism. This can allow scientists to determine the temporal and/or spatial expression of genes throughout an organism, or even the differences between mutant and wild-type plants and [[animals]]. Today, PCR is commonly used in identifying pathogens among samples, such as COVID-19 and many other life-threatening viruses [1,4,6].

==References==
1. Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborn, A.M., Strike, P., Ritchie, D.A., 1992. Amplification of DNA from native populations of [[soil]] bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413–3416. https://doi.org/10.1128/AEM.58.10.3413-3416.1992

2. Henson, J.M., French, R.C., n.d. THE POLYMERASE CHAIN REACTION AND PLANT DISEASE DIAGNOSIS 30.

3. Picard, C., Ponsonnet, C., Paget, E., Nesme, X., Simonet, P., 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717–2722. https://doi.org/10.1128/AEM.58.9.2717-2722.1992

4. Schochetman, G., Ou, C.-Y., 2021. Polymerase Chain Reaction 5

5. Tsai, Y.L., Olson, B.H., 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Applied and Environmental Microbiology 58, 754–757. https://doi.org/10.1128/AEM.58.2.754-757.1992

6. WILSONl, K.H., Blitchington, R.B., Greene, R.C., 1990. Amplification of Bacterial 16S Ribosomal DNA with Polymerase Chain Reaction. J. CLIN. MICROBIOL. 28, 5.

7. “What Is PCR (Polymerase Chain Reaction)?” Facts, The Public Engagement Team at the Wellcome Genome Campus, 25 Jan. 2016, www.yourgenome.org/facts/what-is-pcr-polymerase-chain-reaction.

Polymerase Chain Reaction (PCR)

2021-05-05T00:27:10Z

Ephanrah: Undo revision 6584 by Ephanrah (talk)

=Description=
The polymerase chain reaction (PCR) is a method used to amplify a small amount of DNA in order to allow scientists to study target genes or specific DNA sequences in detail [1]. DNA is extracted from sample tissues or cells and converted into complimentary DNA (cDNA) [4]. In some cases, RNA is extracted and converted to cDNA with the use of a reverse transcriptase. Target primers identify the location of the DNA sequence(s) in the sample, in which DNA polymerases recognize and begin to synthesize the complementary strands of targeted sequences. With each cycle of the reaction, cDNA begins to amplify exponentially at a point known as the cycle threshold value in which the abundance of cDNA can be measured using an instrument known as a thermocycler.

==Primers==
[[File:EVS463_Phases_of_PCR.JPG|right|450px|thumb|The three phases of polymerase chain reactions [7]]]
PCR primers are single strands of RNA that recognize and attach to the targeted sequence of DNA in the sample tissue. Once the targeted sequence has been located, a DNA polymerase attaches to the primer and begins synthesizing cDNA strands, amplifying the target sequence. For bacteria and [[archaebacteria]], primers that are ubiquitous to the 16s ribosomal RNA (rRNA) are used [1,2,3,5,6]

==Methods==
There are several essential steps when conducting Standard PCR.

1. Purifying DNA from specific tissues or cells [2]

2. Amplifying cDNA copies of the purified DNA [2]

3. Analysis of copied DNA sequences [2]

There are also a number of different types of polymerase chain reactions including endpoint, quantitative real time, reverse transcription, multiplex, and more. These have been modified to analyze different types of data, such as end point PCR where analysis of cDNA takes place after the plateau phase, or RT-PCR where cDNA is synthesized from RNA through the use of a reverse transcriptase enzyme.

==Stages of PCR==
[[File:Screen Shot 2021-04-15 at 3.51.44 PM.png|300px|thumb|right|Stages of PCR and the resultant amplification of DNA copies of the target region[2]]]
1. '''Denaturing stage''': During this phase, the purified sample containing the double stranded (ds) DNA and reaction mixture is heated to a temperature of 94C-95C, breaking the hydrogen bonds and separating the strands to allow for future amplification [7].

2. '''Annealing stage''': During this phase, the reaction mixture is cooled to a temperature of 50C-65C, allowing specific target primers (forward and reverse) to attach to the complementary target DNA sequence through hydrogen bonding. This step is necessary, as DNA polymerases cannot extend the primers to create new copies of the DNA without a section of dsDNA to begin with [7].

3. '''Extension stage''': During this phase, the temperature is increased to 72C to enable to attachment and activity of the DNA polymerase. This specific DNA polymerase comes from the heat-loving bacteria ''Thermus aquaticus'', which is stable at higher temperatures needed for the initial denaturing of double stranded DNA from sample tissues. Once this binds to the forward or reverse primer of the target DNA sequence, it begins to synthesize new strands or copies of the sequence through addition of dNTPs in the 5' to 3' direction [7].

These phases are repeated roughly 20-40 times, producing potentially billions of copies of the targeted sequence in a short period of time.

==Uses==
Polymerase chain reactions are helpful for scientists as they enhance specific target sequences within the genome of an organism. This can allow scientists to determine the temporal and/or spatial expression of genes throughout an organism, or even the differences between mutant and wild-type plants and [[animals]]. Today, PCR is commonly used in identifying [[pathogens]] among samples, such as COVID-19 and many other life-threatening viruses [1,4,6].

==References==
1. Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborn, A.M., Strike, P., Ritchie, D.A., 1992. Amplification of DNA from native populations of [[soil]] bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413–3416. https://doi.org/10.1128/AEM.58.10.3413-3416.1992

2. Henson, J.M., French, R.C., n.d. THE POLYMERASE CHAIN REACTION AND PLANT DISEASE DIAGNOSIS 30.

3. Picard, C., Ponsonnet, C., Paget, E., Nesme, X., Simonet, P., 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717–2722. https://doi.org/10.1128/AEM.58.9.2717-2722.1992

4. Schochetman, G., Ou, C.-Y., 2021. Polymerase Chain Reaction 5

5. Tsai, Y.L., Olson, B.H., 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Applied and Environmental Microbiology 58, 754–757. https://doi.org/10.1128/AEM.58.2.754-757.1992

6. WILSONl, K.H., Blitchington, R.B., Greene, R.C., 1990. Amplification of Bacterial 16S Ribosomal DNA with Polymerase Chain Reaction. J. CLIN. MICROBIOL. 28, 5.

7. “What Is PCR (Polymerase Chain Reaction)?” Facts, The Public Engagement Team at the Wellcome Genome Campus, 25 Jan. 2016, www.yourgenome.org/facts/what-is-pcr-polymerase-chain-reaction.

Polymerase Chain Reaction (PCR)

2021-05-05T00:27:02Z

Ephanrah: Undo revision 6356 by Ephanrah (talk)

=Description=
The polymerase chain reaction (PCR) is a method used to amplify a small amount of DNA in order to allow scientists to study target genes or specific DNA sequences in detail [1]. DNA is extracted from sample tissues or cells and converted into complimentary DNA (cDNA) [4]. In some cases, RNA is extracted and converted to cDNA with the use of a reverse transcriptase. Target primers identify the location of the DNA sequence(s) in the sample, in which DNA polymerases recognize and begin to synthesize the complementary strands of targeted sequences. With each cycle of the reaction, cDNA begins to amplify exponentially at a point known as the cycle threshold value in which the abundance of cDNA can be measured using an instrument known as a thermocycler.

==Primers==
[[File:EVS463_Phases_of_PCR.JPG|right|450px|thumb|The three phases of polymerase chain reactions [7]]]
PCR primers are single strands of RNA that recognize and attach to the targeted sequence of DNA in the sample tissue. Once the targeted sequence has been located, a DNA polymerase attaches to the primer and begins synthesizing cDNA strands, amplifying the target sequence. For bacteria and [[archaebacteria]], primers that are ubiquitous to the 16s ribosomal RNA (rRNA) are used [1,2,3,5,6]

==Methods==
There are several essential steps when conducting Standard PCR.

1. Purifying DNA from specific tissues or cells [2]

2. Amplifying cDNA copies of the purified DNA [2]

3. Analysis of copied DNA sequences [2]

There are also a number of different types of polymerase chain reactions including endpoint, quantitative real time, reverse transcription, multiplex, and more. These have been modified to analyze different types of data, such as end point PCR where analysis of cDNA takes place after the plateau phase, or RT-PCR where cDNA is synthesized from RNA through the use of a reverse transcriptase enzyme.

==Stages of PCR==
[[File:Screen Shot 2021-04-15 at 3.51.44 PM.png|300px|thumb|right|Stages of PCR and the resultant amplification of DNA copies of the target region[2]]]
1. '''Denaturing stage''': During this phase, the purified sample containing the double stranded (ds) DNA and reaction mixture is heated to a temperature of 94C-95C, breaking the hydrogen bonds and separating the strands to allow for future amplification [7].

2. '''Annealing stage''': During this phase, the reaction mixture is cooled to a temperature of 50C-65C, allowing specific target primers (forward and reverse) to attach to the complementary target DNA sequence through hydrogen bonding. This step is necessary, as DNA polymerases cannot extend the primers to create new copies of the DNA without a section of dsDNA to begin with [7].

3. '''Extension stage''': During this phase, the temperature is increased to 72C to enable to attachment and activity of the DNA polymerase. This specific DNA polymerase comes from the heat-loving bacteria ''Thermus aquaticus'', which is stable at higher temperatures needed for the initial denaturing of double stranded DNA from sample tissues. Once this binds to the forward or reverse primer of the target DNA sequence, it begins to synthesize new strands or copies of the sequence through addition of dNTPs in the 5' to 3' direction [7].

These phases are repeated roughly 20-40 times, producing potentially billions of copies of the targeted sequence in a short period of time.

==Uses==
Polymerase chain reactions are helpful for scientists as they enhance specific target sequences within the genome of an organism. This can allow scientists to determine the temporal and/or spatial expression of genes throughout an organism, or even the differences between mutant and wild-type plants and [[animals]]. Today, PCR is commonly used in identifying pathogens among samples, such as COVID-19 and many other life-threatening viruses [1,4,6].

==References==
1. Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborn, A.M., Strike, P., Ritchie, D.A., 1992. Amplification of DNA from native populations of [[soil]] bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413–3416. https://doi.org/10.1128/AEM.58.10.3413-3416.1992

2. Henson, J.M., French, R.C., n.d. THE POLYMERASE CHAIN REACTION AND PLANT DISEASE DIAGNOSIS 30.

3. Picard, C., Ponsonnet, C., Paget, E., Nesme, X., Simonet, P., 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717–2722. https://doi.org/10.1128/AEM.58.9.2717-2722.1992

4. Schochetman, G., Ou, C.-Y., 2021. Polymerase Chain Reaction 5

5. Tsai, Y.L., Olson, B.H., 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Applied and Environmental Microbiology 58, 754–757. https://doi.org/10.1128/AEM.58.2.754-757.1992

6. WILSONl, K.H., Blitchington, R.B., Greene, R.C., 1990. Amplification of Bacterial 16S Ribosomal DNA with Polymerase Chain Reaction. J. CLIN. MICROBIOL. 28, 5.

7. “What Is PCR (Polymerase Chain Reaction)?” Facts, The Public Engagement Team at the Wellcome Genome Campus, 25 Jan. 2016, www.yourgenome.org/facts/what-is-pcr-polymerase-chain-reaction.

Polymerase Chain Reaction (PCR)

2021-05-04T02:54:49Z

Ephanrah: /* Uses */

=Description=
The polymerase chain reaction (PCR) is a method used to amplify a small amount of DNA in order to allow scientists to study target genes or specific DNA sequences in detail [1]. DNA is extracted from sample tissues or cells and converted into complimentary DNA (cDNA) [4]. In some cases, RNA is extracted and converted to cDNA with the use of a reverse transcriptase. Target primers identify the location of the DNA sequence(s) in the sample, in which DNA polymerases recognize and begin to synthesize the complementary strands of targeted sequences. With each cycle of the reaction, cDNA begins to amplify exponentially at a point known as the cycle threshold value in which the abundance of cDNA can be measured using an instrument known as a thermocycler.

==Primers==
[[File:EVS463_Phases_of_PCR.JPG|right|450px|thumb|The three phases of polymerase chain reactions [7]]]
PCR primers are single strands of RNA that recognize and attach to the targeted sequence of DNA in the sample tissue. Once the targeted sequence has been located, a DNA polymerase attaches to the primer and begins synthesizing cDNA strands, amplifying the target sequence. For bacteria and [[archaebacteria]], primers that are ubiquitous to the 16s ribosomal RNA (rRNA) are used [1,2,3,5,6]

==Methods==
There are several essential steps when conducting Standard PCR.

1. Purifying DNA from specific tissues or cells [2]

2. Amplifying cDNA copies of the purified DNA [2]

3. Analysis of copied DNA sequences [2]

There are also a number of different types of polymerase chain reactions including endpoint, quantitative real time, reverse transcription, multiplex, and more. These have been modified to analyze different types of data, such as end point PCR where analysis of cDNA takes place after the plateau phase, or RT-PCR where cDNA is synthesized from RNA through the use of a reverse transcriptase enzyme.

==Stages of PCR==
[[File:Screen Shot 2021-04-15 at 3.51.44 PM.png|300px|thumb|right|Stages of PCR and the resultant amplification of DNA copies of the target region[2]]]
1. '''Denaturing stage''': During this phase, the purified sample containing the double stranded (ds) DNA and reaction mixture is heated to a temperature of 94C-95C, breaking the hydrogen bonds and separating the strands to allow for future amplification [7].

2. '''Annealing stage''': During this phase, the reaction mixture is cooled to a temperature of 50C-65C, allowing specific target primers (forward and reverse) to attach to the complementary target DNA sequence through hydrogen bonding. This step is necessary, as DNA polymerases cannot extend the primers to create new copies of the DNA without a section of dsDNA to begin with [7].

3. '''Extension stage''': During this phase, the temperature is increased to 72C to enable to attachment and activity of the DNA polymerase. This specific DNA polymerase comes from the heat-loving bacteria ''Thermus aquaticus'', which is stable at higher temperatures needed for the initial denaturing of double stranded DNA from sample tissues. Once this binds to the forward or reverse primer of the target DNA sequence, it begins to synthesize new strands or copies of the sequence through addition of dNTPs in the 5' to 3' direction [7].

These phases are repeated roughly 20-40 times, producing potentially billions of copies of the targeted sequence in a short period of time.

==Uses==
Polymerase chain reactions are helpful for scientists as they enhance specific target sequences within the genome of an organism. This can allow scientists to determine the temporal and/or spatial expression of genes throughout an organism, or even the differences between mutant and wild-type plants and [[animals]]. Today, PCR is commonly used in identifying [[pathogens]] among samples, such as COVID-19 and many other life-threatening viruses [1,4,6].

==References==
1. Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborn, A.M., Strike, P., Ritchie, D.A., 1992. Amplification of DNA from native populations of [[soil]] bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413–3416. https://doi.org/10.1128/AEM.58.10.3413-3416.1992

2. Henson, J.M., French, R.C., n.d. THE POLYMERASE CHAIN REACTION AND PLANT DISEASE DIAGNOSIS 30.

3. Picard, C., Ponsonnet, C., Paget, E., Nesme, X., Simonet, P., 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717–2722. https://doi.org/10.1128/AEM.58.9.2717-2722.1992

4. Schochetman, G., Ou, C.-Y., 2021. Polymerase Chain Reaction 5

5. Tsai, Y.L., Olson, B.H., 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Applied and Environmental Microbiology 58, 754–757. https://doi.org/10.1128/AEM.58.2.754-757.1992

6. WILSONl, K.H., Blitchington, R.B., Greene, R.C., 1990. Amplification of Bacterial 16S Ribosomal DNA with Polymerase Chain Reaction. J. CLIN. MICROBIOL. 28, 5.

7. “What Is PCR (Polymerase Chain Reaction)?” Facts, The Public Engagement Team at the Wellcome Genome Campus, 25 Jan. 2016, www.yourgenome.org/facts/what-is-pcr-polymerase-chain-reaction.

Polymerase Chain Reaction (PCR)

2021-05-04T02:53:37Z

Ephanrah: Moved images and added small details

=Description=
The polymerase chain reaction (PCR) is a method used to amplify a small amount of DNA in order to allow scientists to study target genes or specific DNA sequences in detail [1]. DNA is extracted from sample tissues or cells and converted into complimentary DNA (cDNA) [4]. In some cases, RNA is extracted and converted to cDNA with the use of a reverse transcriptase. Target primers identify the location of the DNA sequence(s) in the sample, in which DNA polymerases recognize and begin to synthesize the complementary strands of targeted sequences. With each cycle of the reaction, cDNA begins to amplify exponentially at a point known as the cycle threshold value in which the abundance of cDNA can be measured using an instrument known as a thermocycler.

==Primers==
[[File:EVS463_Phases_of_PCR.JPG|right|450px|thumb|The three phases of polymerase chain reactions [7]]]
PCR primers are single strands of RNA that recognize and attach to the targeted sequence of DNA in the sample tissue. Once the targeted sequence has been located, a DNA polymerase attaches to the primer and begins synthesizing cDNA strands, amplifying the target sequence. For bacteria and [[archaebacteria]], primers that are ubiquitous to the 16s ribosomal RNA (rRNA) are used [1,2,3,5,6]

==Methods==
There are several essential steps when conducting Standard PCR.

1. Purifying DNA from specific tissues or cells [2]

2. Amplifying cDNA copies of the purified DNA [2]

3. Analysis of copied DNA sequences [2]

There are also a number of different types of polymerase chain reactions including endpoint, quantitative real time, reverse transcription, multiplex, and more. These have been modified to analyze different types of data, such as end point PCR where analysis of cDNA takes place after the plateau phase, or RT-PCR where cDNA is synthesized from RNA through the use of a reverse transcriptase enzyme.

==Stages of PCR==
[[File:Screen Shot 2021-04-15 at 3.51.44 PM.png|300px|thumb|right|Stages of PCR and the resultant amplification of DNA copies of the target region[2]]]
1. '''Denaturing stage''': During this phase, the purified sample containing the double stranded (ds) DNA and reaction mixture is heated to a temperature of 94C-95C, breaking the hydrogen bonds and separating the strands to allow for future amplification [7].

2. '''Annealing stage''': During this phase, the reaction mixture is cooled to a temperature of 50C-65C, allowing specific target primers (forward and reverse) to attach to the complementary target DNA sequence through hydrogen bonding. This step is necessary, as DNA polymerases cannot extend the primers to create new copies of the DNA without a section of dsDNA to begin with [7].

3. '''Extension stage''': During this phase, the temperature is increased to 72C to enable to attachment and activity of the DNA polymerase. This specific DNA polymerase comes from the heat-loving bacteria ''Thermus aquaticus'', which is stable at higher temperatures needed for the initial denaturing of double stranded DNA from sample tissues. Once this binds to the forward or reverse primer of the target DNA sequence, it begins to synthesize new strands or copies of the sequence through addition of dNTPs in the 5' to 3' direction [7].

These phases are repeated roughly 20-40 times, producing potentially billions of copies of the targeted sequence in a short period of time.

==Uses==
Polymerase chain reactions are helpful for scientists as they enhance specific target sequences within the genome of an organism. This can allow scientists to determine the temporal and/or spatial expression of genes throughout an organism, or even the differences between mutant and wild-type plants and [[animals]]. Today, PCR is commonly used in identifying pathogens among samples, such as COVID-19 and many other life-threatening viruses [1,4,6].

==References==
1. Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborn, A.M., Strike, P., Ritchie, D.A., 1992. Amplification of DNA from native populations of [[soil]] bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413–3416. https://doi.org/10.1128/AEM.58.10.3413-3416.1992

2. Henson, J.M., French, R.C., n.d. THE POLYMERASE CHAIN REACTION AND PLANT DISEASE DIAGNOSIS 30.

3. Picard, C., Ponsonnet, C., Paget, E., Nesme, X., Simonet, P., 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717–2722. https://doi.org/10.1128/AEM.58.9.2717-2722.1992

4. Schochetman, G., Ou, C.-Y., 2021. Polymerase Chain Reaction 5

5. Tsai, Y.L., Olson, B.H., 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Applied and Environmental Microbiology 58, 754–757. https://doi.org/10.1128/AEM.58.2.754-757.1992

6. WILSONl, K.H., Blitchington, R.B., Greene, R.C., 1990. Amplification of Bacterial 16S Ribosomal DNA with Polymerase Chain Reaction. J. CLIN. MICROBIOL. 28, 5.

7. “What Is PCR (Polymerase Chain Reaction)?” Facts, The Public Engagement Team at the Wellcome Genome Campus, 25 Jan. 2016, www.yourgenome.org/facts/what-is-pcr-polymerase-chain-reaction.

Polymerase Chain Reaction (PCR)

2021-05-04T02:42:56Z

Ephanrah: Addition of image on phases of PCR

File:EVS463 Phases of PCR.JPG

2021-05-04T02:40:22Z

Ephanrah: The three phases of Polymerase chain reactions: Denaturing, Annealing, and Extension of primers.

The three phases of Polymerase chain reactions: Denaturing, Annealing, and Extension of primers.

Polymerase Chain Reaction (PCR)

2021-05-04T02:37:37Z

Ephanrah: /* Description */

=Description=
The polymerase chain reaction (PCR) is a method used to amplify a small amount of DNA in order to allow scientists to study target genes or specific DNA sequences in detail [1]. DNA is extracted from sample tissues or cells and converted into complimentary DNA (cDNA) [4]. In some cases, RNA is extracted and converted to cDNA with the use of a reverse transcriptase. Target primers identify the location of the DNA sequence(s) in the sample, in which DNA polymerases recognize and begin to synthesize the complementary strands of targeted sequences.

==Primers==
PCR primers are single strands of RNA that recognize and attach to the targeted sequence of DNA in the sample tissue. Once the targeted sequence has been located, a DNA polymerase attaches to the primer and begins synthesizing cDNA strands, amplifying the target sequence. For bacteria and [[archaebacteria]], primers that are ubiquitous to the 16s ribosomal RNA (rRNA) are used [1,2,3,5,6]

==Methods==
There are several essential steps when conducting Standard PCR.

1. Purifying DNA from specific tissues or cells [2]

2. Amplifying cDNA copies of the purified DNA [2]

3. Analysis of copied DNA sequences [2]

[[File:Screen Shot 2021-04-15 at 3.51.44 PM.png|thumb|right|Stages of PCR and the resultant amplification of DNA copies of the target region[2]]]

There are also a number of different types of polymerase chain reactions including endpoint, quantitative real time, reverse transcription, multiplex, and more. These have been modified to analyze different types of data, such as end point PCR where analysis of cDNA takes place after the plateau phase, or RT-PCR where cDNA is synthesized from RNA through the use of a reverse transcriptase enzyme.

==Stages of PCR==
1. '''Denaturing stage''': During this phase, the purified sample containing the double stranded (ds) DNA and reaction mixture is heated to a temperature of 94C-95C, breaking the hydrogen bonds and separating the strands to allow for future amplification [7].

2. '''Annealing stage''': During this phase, the reaction mixture is cooled to a temperature of 50C-65C, allowing specific target primers (forward and reverse) to attach to the complementary target DNA sequence through hydrogen bonding. This step is necessary, as DNA polymerases cannot extend the primers to create new copies of the DNA without a section of dsDNA to begin with [7].

3. '''Extension stage''': During this phase, the temperature is increased to 72C to enable to attachment and activity of the DNA polymerase. This specific DNA polymerase comes from the heat-loving bacteria ''Thermus aquaticus'', which is stable at higher temperatures needed for the initial denaturing of double stranded DNA from sample tissues. Once this binds to the forward or reverse primer of the target DNA sequence, it begins to synthesize new strands or copies of the sequence through addition of dNTPs in the 5' to 3' direction [7].

These phases are repeated roughly 20-40 times, producing potentially billions of copies of the targeted sequence in a short period of time.

==Uses==
Polymerase chain reactions are helpful for scientists as they enhance specific target sequences within the genome of an organism. This can allow scientists to determine the temporal and/or spatial expression of genes throughout an organism, or even the differences between mutant and wild-type plants and [[animals]]. Today, PCR is commonly used in identifying pathogens among samples, such as COVID-19 and many other life-threatening viruses [1,4,6].

==References==
1. Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborn, A.M., Strike, P., Ritchie, D.A., 1992. Amplification of DNA from native populations of [[soil]] bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413–3416. https://doi.org/10.1128/AEM.58.10.3413-3416.1992

2. Henson, J.M., French, R.C., n.d. THE POLYMERASE CHAIN REACTION AND PLANT DISEASE DIAGNOSIS 30.

3. Picard, C., Ponsonnet, C., Paget, E., Nesme, X., Simonet, P., 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717–2722. https://doi.org/10.1128/AEM.58.9.2717-2722.1992

4. Schochetman, G., Ou, C.-Y., 2021. Polymerase Chain Reaction 5

5. Tsai, Y.L., Olson, B.H., 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Applied and Environmental Microbiology 58, 754–757. https://doi.org/10.1128/AEM.58.2.754-757.1992

6. WILSONl, K.H., Blitchington, R.B., Greene, R.C., 1990. Amplification of Bacterial 16S Ribosomal DNA with Polymerase Chain Reaction. J. CLIN. MICROBIOL. 28, 5.

7. “What Is PCR (Polymerase Chain Reaction)?” Facts, The Public Engagement Team at the Wellcome Genome Campus, 25 Jan. 2016, www.yourgenome.org/facts/what-is-pcr-polymerase-chain-reaction.

Polymerase Chain Reaction (PCR)

2021-05-04T02:34:35Z

Ephanrah: /* Methods */

=Description=
The polymerase chain reaction (PCR) is a method used to amplify a small amount of DNA in order to allow scientists to study target genes or specific DNA sequences in detail [1]. RNA is extracted from sample tissues and converted into complimentary DNA (cDNA) with the use of a reverse transcriptase [4]. Target primers identify the location of the DNA sequence(s) in the sample, in which DNA polymerases recognize and begin to synthesize the complementary strands of targeted sequences.

==Primers==
PCR primers are single strands of RNA that recognize and attach to the targeted sequence of DNA in the sample tissue. Once the targeted sequence has been located, a DNA polymerase attaches to the primer and begins synthesizing cDNA strands, amplifying the target sequence. For bacteria and [[archaebacteria]], primers that are ubiquitous to the 16s ribosomal RNA (rRNA) are used [1,2,3,5,6]

==Methods==
There are several essential steps when conducting Standard PCR.

1. Purifying DNA from specific tissues or cells [2]

2. Amplifying cDNA copies of the purified DNA [2]

3. Analysis of copied DNA sequences [2]

[[File:Screen Shot 2021-04-15 at 3.51.44 PM.png|thumb|right|Stages of PCR and the resultant amplification of DNA copies of the target region[2]]]

There are also a number of different types of polymerase chain reactions including endpoint, quantitative real time, reverse transcription, multiplex, and more. These have been modified to analyze different types of data, such as end point PCR where analysis of cDNA takes place after the plateau phase, or RT-PCR where cDNA is synthesized from RNA through the use of a reverse transcriptase enzyme.

==Stages of PCR==
1. '''Denaturing stage''': During this phase, the purified sample containing the double stranded (ds) DNA and reaction mixture is heated to a temperature of 94C-95C, breaking the hydrogen bonds and separating the strands to allow for future amplification [7].

2. '''Annealing stage''': During this phase, the reaction mixture is cooled to a temperature of 50C-65C, allowing specific target primers (forward and reverse) to attach to the complementary target DNA sequence through hydrogen bonding. This step is necessary, as DNA polymerases cannot extend the primers to create new copies of the DNA without a section of dsDNA to begin with [7].

3. '''Extension stage''': During this phase, the temperature is increased to 72C to enable to attachment and activity of the DNA polymerase. This specific DNA polymerase comes from the heat-loving bacteria ''Thermus aquaticus'', which is stable at higher temperatures needed for the initial denaturing of double stranded DNA from sample tissues. Once this binds to the forward or reverse primer of the target DNA sequence, it begins to synthesize new strands or copies of the sequence through addition of dNTPs in the 5' to 3' direction [7].

These phases are repeated roughly 20-40 times, producing potentially billions of copies of the targeted sequence in a short period of time.

==Uses==
Polymerase chain reactions are helpful for scientists as they enhance specific target sequences within the genome of an organism. This can allow scientists to determine the temporal and/or spatial expression of genes throughout an organism, or even the differences between mutant and wild-type plants and [[animals]]. Today, PCR is commonly used in identifying pathogens among samples, such as COVID-19 and many other life-threatening viruses [1,4,6].

==References==
1. Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborn, A.M., Strike, P., Ritchie, D.A., 1992. Amplification of DNA from native populations of [[soil]] bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413–3416. https://doi.org/10.1128/AEM.58.10.3413-3416.1992

2. Henson, J.M., French, R.C., n.d. THE POLYMERASE CHAIN REACTION AND PLANT DISEASE DIAGNOSIS 30.

3. Picard, C., Ponsonnet, C., Paget, E., Nesme, X., Simonet, P., 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717–2722. https://doi.org/10.1128/AEM.58.9.2717-2722.1992

4. Schochetman, G., Ou, C.-Y., 2021. Polymerase Chain Reaction 5

5. Tsai, Y.L., Olson, B.H., 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Applied and Environmental Microbiology 58, 754–757. https://doi.org/10.1128/AEM.58.2.754-757.1992

6. WILSONl, K.H., Blitchington, R.B., Greene, R.C., 1990. Amplification of Bacterial 16S Ribosomal DNA with Polymerase Chain Reaction. J. CLIN. MICROBIOL. 28, 5.

7. “What Is PCR (Polymerase Chain Reaction)?” Facts, The Public Engagement Team at the Wellcome Genome Campus, 25 Jan. 2016, www.yourgenome.org/facts/what-is-pcr-polymerase-chain-reaction.

Polymerase Chain Reaction (PCR)

2021-05-04T01:18:34Z

Ephanrah: /* Description */

=Description=
The polymerase chain reaction (PCR) is a method used to amplify a small amount of DNA in order to allow scientists to study target genes or specific DNA sequences in detail [1]. RNA is extracted from sample tissues and converted into complimentary DNA (cDNA) with the use of a reverse transcriptase [4]. Target primers identify the location of the DNA sequence(s) in the sample, in which DNA polymerases recognize and begin to synthesize the complementary strands of targeted sequences.

==Primers==
PCR primers are single strands of RNA that recognize and attach to the targeted sequence of DNA in the sample tissue. Once the targeted sequence has been located, a DNA polymerase attaches to the primer and begins synthesizing cDNA strands, amplifying the target sequence. For bacteria and [[archaebacteria]], primers that are ubiquitous to the 16s ribosomal RNA (rRNA) are used [1,2,3,5,6]

==Methods==
There are several essential steps when conducting PCR.

1. Purifying RNA from specific tissues or cells [2]

2. Amplifying cDNA copies of the purified RNA [2]

3. Analysis of copied DNA sequences [2]

[[File:Screen Shot 2021-04-15 at 3.51.44 PM.png|thumb|right|Stages of PCR and the resultant amplification of DNA copies of the target region[2]]]

==Stages of PCR==
1. '''Denaturing stage''': During this phase, the purified sample containing the double stranded (ds) DNA and reaction mixture is heated to a temperature of 94C-95C, breaking the hydrogen bonds and separating the strands to allow for future amplification [7].

2. '''Annealing stage''': During this phase, the reaction mixture is cooled to a temperature of 50C-65C, allowing specific target primers (forward and reverse) to attach to the complementary target DNA sequence through hydrogen bonding. This step is necessary, as DNA polymerases cannot extend the primers to create new copies of the DNA without a section of dsDNA to begin with [7].

3. '''Extension stage''': During this phase, the temperature is increased to 72C to enable to attachment and activity of the DNA polymerase. This specific DNA polymerase comes from the heat-loving bacteria ''Thermus aquaticus'', which is stable at higher temperatures needed for the initial denaturing of double stranded DNA from sample tissues. Once this binds to the forward or reverse primer of the target DNA sequence, it begins to synthesize new strands or copies of the sequence through addition of dNTPs in the 5' to 3' direction [7].

These phases are repeated roughly 20-40 times, producing potentially billions of copies of the targeted sequence in a short period of time.

==Uses==
Polymerase chain reactions are helpful for scientists as they enhance specific target sequences within the genome of an organism. This can allow scientists to determine the temporal and/or spatial expression of genes throughout an organism, or even the differences between mutant and wild-type plants and [[animals]]. Today, PCR is commonly used in identifying pathogens among samples, such as COVID-19 and many other life-threatening viruses [1,4,6].

==References==
1. Bruce, K.D., Hiorns, W.D., Hobman, J.L., Osborn, A.M., Strike, P., Ritchie, D.A., 1992. Amplification of DNA from native populations of [[soil]] bacteria by using the polymerase chain reaction. Applied and Environmental Microbiology 58, 3413–3416. https://doi.org/10.1128/AEM.58.10.3413-3416.1992

2. Henson, J.M., French, R.C., n.d. THE POLYMERASE CHAIN REACTION AND PLANT DISEASE DIAGNOSIS 30.

3. Picard, C., Ponsonnet, C., Paget, E., Nesme, X., Simonet, P., 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Applied and Environmental Microbiology 58, 2717–2722. https://doi.org/10.1128/AEM.58.9.2717-2722.1992

4. Schochetman, G., Ou, C.-Y., 2021. Polymerase Chain Reaction 5

5. Tsai, Y.L., Olson, B.H., 1992. Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction. Applied and Environmental Microbiology 58, 754–757. https://doi.org/10.1128/AEM.58.2.754-757.1992

6. WILSONl, K.H., Blitchington, R.B., Greene, R.C., 1990. Amplification of Bacterial 16S Ribosomal DNA with Polymerase Chain Reaction. J. CLIN. MICROBIOL. 28, 5.

7. “What Is PCR (Polymerase Chain Reaction)?” Facts, The Public Engagement Team at the Wellcome Genome Campus, 25 Jan. 2016, www.yourgenome.org/facts/what-is-pcr-polymerase-chain-reaction.

Polymerase Chain Reaction (PCR)

2021-05-04T01:12:20Z

Ephanrah:

C4 Carbon Fixation

2021-05-02T20:10:53Z

Ephanrah:

==Description==
[[File:EVS463_C4_Carbon_Fixation.JPG|right|200px|thumb|Hatch-Slack pathway in C4 plants.]]
The [[Hatch-Slack pathway]], also known as the C4 plant carbon fixation pathway, involves the storing of atmospheric CO2 in bundle sheath cells. "The evolution of C4 photosynthesis ~35–40 million years ago provided a natural solution to remedy the inefficiency of Rubisco" [2]. The Hatch-Slack pathway is acknowledged for its improved efficiency, where the concentration of CO2 is increased around the enzyme Rubisco in order to reduce [[photorespiration]].

==Anatomy==
[[File:BIO_370_Pep_Antibody_(2).jpg|right|200px|thumb|Amaranth mesophyll cells stained with PEP Case primary antibody.]]
[[File:BIO370_Rubisco_primary_antibody_(2).jpg|right|200px|thumb|Amaranth bundle sheath cells stained with rubisco primary antibody.]]
C4 plants exhibit a Kranz-type leaf anatomy involving two photosynthetic cells known as mesophyll cells and bundle sheath cells which differ in their CO2 assimilation functions [1]. In mesophyll cells, atmospheric carbon dioxide is converted to a C4 acid by the enzyme phosphoenolpyruvate carboxylase (PEP Case) during the carboxylation phase of carbon fixation. In this step, PEP Case catalyzes the reaction between bicarbonate, HCO3-, and phosphoenolpyruvate (PEP), a three-carbon molecule, to form the four-carbon acid oxaloacetate and inorganic phosphate [4]. The four-carbon acids are then transported to the bundle sheath cells surrounding leaf veins where rubisco (ribulose-1,5-bisphosphate carboxylase-oxygenase) fixes and assimilates CO2 into the [[Calvin Cycle]]. Once CO2 is assimilated into the cycle by RuBP and Rubisco, energy (ATP, NADPH) from the light reactions during photosynthesis is used to produce sugars such as glucose [5].

==Agricultural Significance==
C4 plants typically occupy hot, arid climates, whereas C3 plants are most frequently found in temperate, moist environments. When fixing carbon, C3 plants open their stomata to allow atmospheric gasses such as carbon dioxide and oxygen at the cost of allowing water to evaporate from the plants leaves. However, C4 plants have evolved to retain water through the ability to continue fixing carbon while the stomata are closed [6]. This adaptation allows C4 plants to survive the hot and dry climates, reducing harmful photorespiration and water losses through evaporation.

Several common agriculturally significant C4 plants include [6]:
*Maize
*Sugarcane
*Sorghum

In many subtropical, tropical, and desert climates, C4 plants are the primary economic agricultural generators due to their carbon fixation efficiency and ability to retain water. "Drought is a major agricultural problem worldwide. Therefore, selection for increased water use efficiency (WUE) in food and biofuel crop species will be an important trait in plant breeding programs" [3]. With [[climate change]] in mind, C4 plants are becoming much more favorable in agriculture as they are resilient in the face of warmer ambient temperatures and drier seasons.

==Evolution==
It has been hypothesized through evolutionary radiation analysis that C4 vegetation contributed to global cooling during the late Miocene period [7]. Researchers have proposed that low atmospheric CO2 during the late Miocene triggered C4 evolution in [[Andropogonae]] grasses roughly 17 million years ago [7]. With the help of paleontologists, recent studies have hypothesized C4 evolution began in the late Oligocene period approximately 25-30 million years ago when CO2 levels were falling below 1000ppm (parts per million) [7]. Interestingly, it is suspected that the rise of C4 plants contributed to diversification of many animal clades such as the formation of large grazing guilds in the C4 grasslands of Africa [7]. With current technological advancements, research is still uprooting the foundation of C4 plant evolution, however the previously proposed mechanisms are generally agreed upon by ecological and paleontological organizations.

==References==
#PATEL, Minesh, and James O. BERRY. “Rubisco Gene Expression in C4 Plants: Photosynthesis: CO2 Uptake and the Pathways of Carbon Fixation.” Journal of Experimental Botany, vol. 59, no. 7, Oxford University Press, 2008, pp. 1625–34.
#Sharwood, Robert E., et al. “Improved Analysis of C4 and C3 Photosynthesis via Refined in Vitro Assays of Their Carbon Fixation Biochemistry.” Journal of Experimental Botany, vol. 67, no. 10, Oxford University Press, 2016, pp. 3137–48, doi:10.1093/jxb/erw154.
#Ellsworth, Patrick Z., and Asaph B. Cousins. “Carbon Isotopes and Water Use Efficiency in C4 Plants.” Current Opinion in Plant Biology, vol. 31, no. C, Elsevier Ltd, 2016, pp. 155–61, doi:10.1016/j.pbi.2016.04.006.
#“Phosphoenolpyruvate Carboxylase.” Wikipedia, Wikimedia Foundation, 19 Oct. 2020, en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxylase.
#National Geographic Society. “Calvin Cycle.” National Geographic Society, 9 Nov. 2012, www.nationalgeographic.org/media/calvincycle/#:~:text=by%20Tim%20Gunther-,The%20Calvin%20cycle%20is%20a%20process%20that%20plants%20and%20algae,cycle%20for%20energy%20and%20food.
#“The Difference between C3 and C4 Plants.” RIPE, 18 Mar. 2020, ripe.illinois.edu/blog/difference-between-c3-and-c4-plants.
#Sage, Rowan F., et al. “Some Like It Hot: The Physiological [[Ecology]] of C4 Plant Evolution.” Oecologia, vol. 187, no. 4, Springer Berlin Heidelberg, 2018, pp. 941–66, doi:10.1007/s00442-018-4191-6.
#Berry, James O. “Exp. #10. Laser Scanning Confocal Microscopy, C4 Leaf Development.” 2021.

Plant Hormones

2021-05-02T19:54:19Z

Ephanrah:

==Introduction==
Plant hormones auxin and cytokinin are primarily known for their roles in vegetative (indeterminate) growth. This type of growth involves the repetition of structures in a given order once the plant has established the primary apical meristem. Auxin and cytokinin work antagonistically during the vegetative growth of plants, but synergistically in cellular regeneration [1]. Auxin is produced in the apical meristem of the plant, whereas cytokinin is produced in the leaves. Auxins are responsible for apical dominance in vegetative growth, repressing cytokinin from activating dormant axillary (lateral) buds from growing new lateral shoots. Cytokinin is responsible for creating new lateral shoots when the apical meristem is damaged or the concentration of auxin falls below the ability to repress cytokinin [1].

==Auxin==
[[File:EVS463_Auxin_Image.JPG|right|300px|Organic and synthetic Auxins]]
The plant hormone auxin, produced in the apical meristem, can be found in nature as a compound known as indole-3-acetic acid (IAA), and is primarily synthesized from the well-known amino acid tryptophan [4]. There are also synthetic auxins known as 2,4-dichlorophenoxyacetic acid (2,4-D) and naphthalene acetic acid (NAA) [3].

Auxins are extremely important to plant growth as they are responsible primarily for cellular elongation, root development, and apical dominance during vegetative growth. During apical dominance, auxin produced by the apical meristem creates a downward concentration gradient, preventing axillary buds from activating through cytokinin initiation. This concentration gradient also creates a hormone sink in the roots, where auxin stimulates root development. They are widely used commercially for root induction for plant propagation [3].

Interestingly, auxins can induce epinastic responses through localized auxin concentrations, causing plant bending in a process known as phototropism. Due to the hormone's cellular elongation [[properties]], it can swell the cells on one side like a balloon, bending the plant in the opposite direction from its application. It may also induce leaf epinasty, where leaves bend downward "as result of disturbances in their growth, with greater expansion in adaxial cells as compared to abaxial surface cells" [4].

==Cytokinin==
[[File:EVS463_Cytokinin_image.JPG|right|300px|Organic and synthetic cytokinins]]
The plant hormone cytokinin, produced in leaf tissues of plants, is primarily found in nature as a compound known as zeatin. Interestingly, "almost all [[organisms]] make cytokinin; for example, isopentenyl adenine derivatives found adjacent to the anticodon loop of a subset of tRNAs in most eukaryotes and bacteria" [5]. These were first discovered while searching for factors that promote cell proliferation in plant cells in concert with auxin to regulate cell division and differentiation [5].

Cytokinins are primarily responsible for cellular division and overcoming apical dominance to stimulate lateral shoot formation. If the plant apical meristem becomes damaged, the auxin concentration of the plant falls allowing cytokinin concentrations to accumulate and activate dormant axillary buds [5]. In some cases, the auxin concentration gradient falls below levels of apical dominance near the ground, causing lateral shoot formation in a Christmas-tree like effect.

==Plant Callus Formation==
[[File:EVS463_Callus_Formation.JPG|right|200px|thumb|Plant callus tissue forms as a result of wounding, followed by cellular regeneration controlled by the ratio of auxin to cytokinin]]
Callus formation on plants occurs as a result of wounding, infection, or unregulated and undifferentiated cellular regeneration, controlled by concentrations of auxin and cytokinin. Studies have shown "an intermediate ratio of auxin and cytokinin promotes callus induction, while a high ratio of auxin-to-cytokinin or cytokinin-to-auxin induces root and shoot regeneration, respectively" [6]. These hormones are important for infection processes in plants such as agrobacterium where transgenes are inserted into the host genome. The agrobacterium T-DNA has oncogenes which promote production of auxin and cytokinin in order to provide a favorable environment for the bacteria to reproduce and feed. This site is typically referred to as the crown gall. Eventually the plant will die, in which the bacteria are released back into the [[soil]] to begin the infection process again.

==References==
#Su, Ying-Hua, et al. “Auxin-Cytokinin Interaction Regulates Meristem Development.” Molecular plant, vol. 4, no. 4, Elsevier Inc, 2011, pp. 616–25, doi:10.1093/mp/ssr007.
#G. Eric Schaller, et al. “The Yin-Yang of Hormones: Cytokinin and Auxin Interactions in Plant Development.” The Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 44–63, doi:10.1105/tpc.114.133595.
#Zaman, Mohammad, et al. “Enhancing Crop Yield with the Use of N‐based Fertilizers Co‐applied with Plant Hormones or Growth Regulators.” Journal of the Science of Food and Agriculture, vol. 95, no. 9, John Wiley & Sons, Ltd, 2015, pp. 1777–85, doi:10.1002/jsfa.6938.
#Sandalio, Luisa M., et al. “Leaf Epinasty and Auxin: A Biochemical and Molecular Overview.” Plant Science (Limerick), vol. 253, Elsevier Ireland Ltd, 2016, pp. 187–93, doi:10.1016/j.plantsci.2016.10.002.
#Kieber, Joseph J., and G. Eric Schaller. “Cytokinin Signaling in Plant Development.” Development (Cambridge), vol. 145, no. 4, COMPANY BIOLOGISTS LTD, 2018, p. dev149344–, doi:10.1242/dev.149344.
#Momoko Ikeuchi, et al. “Plant Callus: Mechanisms of Induction and Repression.” The Plant Cell, vol. 25, no. 9, American Society of Plant Biologists, 2013, pp. 3159–73, doi:10.1105/tpc.113.116053.
#Berry, James O. “Rec#6 Hormones and Plant Form.” 2021.

Planaria

2021-05-02T19:53:43Z

Ephanrah:

== Introduction ==
Planaria, or flatworms, which occupy the order [[Tricladida]] within the phylum [[Platyhelminthes]], are commonly inhabitants of freshwater sources such as streams or ponds, but some are terrestrial in deep soils [1]. These complex [[organisms]] are known to be scavengers, predators, and in many cases parasitic. Planarians such as ''Schmidtea mediterranea'' are known for their remarkable ability to regenerate from pluripotent stem cells scattered throughout their bodies [2]. These adult stem cells, also known as neoblasts, allow planarians to reproduce asexually as well as simply regenerating their entire body from a fragment roughly 1/279 the size of the original worm [7]. These model organisms are medically and scientifically important, as understanding the process of regeneration may carry incredible value to advanced technologies.
[[File:Image203 (2).jpg|right|300px|thumb|S. mediterranea midsection cut regeneration group]]
==Planarian Diversity and Distribution ==
Within the [[Tricladida]] exist three proposed taxonomic groups, which are based on their different habitats: [[Paludicola]] (freshwater planarians), [[Terricola]] (land planarians), and [[Maricola]] (marine planarians) [8]. These three taxonomic groups may be even further subdivided by classification of anatomical and external feature differences. "Molecular sequence data has helped to clarify the phylogenetic relationships and the evolutionary history of the Tricladida and in many cases facilitated a more natural classification. However, at certain levels resolution is still poor, thus requiring further studies" [8]. The genome of planarians is vast due to their ancient age and evolutionary processes making a difficult challenge to truly understand the depth of [[diversity]] between the proposed groups.

The distribution of planarians ranges from temperate to tropical and has been modified by introduction of species to newer continents. Climate and moisture play a large role in the distribution of these organisms as they are most vulnerable to desiccation. Terrestrial planarians are found scattered throughout temperate, tropical, and subtropical regions across the globe, whereas the majority of freshwater planarians are mainly confined to the temperate and tropical regions of North America, Europe, and Asia in which draught rarely occurs [8].

== Parasitic Behavior and Treatment ==
Over a third of the world’s population is estimated to be infected with parasitic worms" [4]. Most cases of parasitic flatworm infections are associated with unsanitary drinking water, as these organisms are typically found near the bottom of freshwater sources. Symptoms of host infection result from egg deposition within the liver, gastrointestinal tract, or urinary bladder, resulting in granuloma formation and fibrosis [4]. Drugs such as Praziquantel (PZQ), an anthelmintic, can cure fluke infection by disrupting the neoblast regeneration pattern in planarians. Specifically, the drug causes increased levels of calcium which is suspected to be the main inhibitor of proper neoblast regeneration [5]. This disruption leads to regeneration of Planaria with two heads by inhibiting posterior expression, eventually driving them out of the host.
== Stem Cells and Regeneration ==
Neoblasts represent approximately 25%-30% of all planarian cells [1]. Neoblast regeneration and differentiation is activated by the WNT signaling pathway, a signal transduction pathway which specifies the anterior and posterior axis in development. "Wnt signaling directly targets the nucleus, and it is broadly used to regulate cell fate, proliferation and self-renewal of stem and progenitor cells in any tissue and at any stage of metazoan life" [6]. Specifically, this pathway specifies posterior axis development, however, in the absence of the Wnt ligand, the protein beta-catenin is degraded inhibiting posterior specification and enhancing anterior expression markers. Without the Wnt pathway properly activated, a planarian will regenerate with two anterior halves due to lack of posterior expression regulated by beta-catenin. Studies have shown how RNAi, also known as RNA silencing, can inactivate the beta-catenin gene resulting in a lack of posterior expression markers and structures in regenerated planarians [3].
[[File:Image212_(2).jpg|right|300px|thumb|RNAi of beta-catenin gene in S. mediterranea and regeneration following midsection cut]]

== References ==
#Reddien, Peter W., and Alejandro Sánchez Alvarado. “Fundamentals of Planarian Regeneration.” Annual Review of Cell and Developmental Biology, vol. 20, no. 1, Annual Reviews, Inc, 2004, pp. 725–57, doi:10.1146/annurev.cellbio.20.010403.095114
#Rink, Jochen C., and Jochen C. Rink. “Stem Cell Systems and Regeneration in Planaria.” Development Genes and Evolution, vol. 223, no. 1, Springer-Verlag, 2013, pp. 67–84, doi:10.1007/s00427-012-0426-4.
#Kyle A. Gurley, et al. “β-Catenin Defines Head Versus Tail Identity During Planarian Regeneration and Homeostasis.” Science (American Association for the Advancement of Science), vol. 319, no. 5861, American Association for the Advancement of Science, 2008, pp. 323–27, doi:10.1126/science.1150029.
#Chan, John D., et al. “‘Death and Axes’: Unexpected Ca2+ Entry Phenologs Predict New Anti-Schistosomal Agents.” PLoS Pathogens, vol. 10, no. 2, Public Library of Science (PLoS), 2014, pp. e1003942–e1003942, doi:10.1371/journal.ppat.1003942.
#Cioli, Donato, et al. “Schistosomiasis Control: Praziquantel Forever?” Molecular and Biochemical Parasitology, vol. 195, no. 1, Elsevier B.V, 2014, pp. 23–29, doi:10.1016/j.molbiopara.2014.06.002.
#Almuedo-Castillo, Maria, et al. “Wnt Signaling in Planarians: New Answers to Old Questions.” The International Journal of Developmental Biology, vol. 56, no. 1-2-3, 2012, pp. 53–65, doi:10.1387/ijdb.113451ma.
#Alvarado, Alejandro Sánchez. “Planarians.” Current Biology, vol. 14, no. 18, Elsevier Inc, 2004, pp. R737–R738, doi:10.1016/j.cub.2004.09.005.
#Rink, Jochen C. Planarian Regeneration Methods and Protocols / Edited by Jochen C. Rink. 1st ed. 2018., Springer New York, 2018, doi:10.1007/978-1-4939-7802-1.

C4 Carbon Fixation

2021-05-02T18:36:17Z

Ephanrah: /* Agricultural Significance */

==Description==
[[File:EVS463_C4_Carbon_Fixation.JPG|right|200px|]]
The [[Hatch-Slack pathway]], also known as the C4 plant carbon fixation pathway, involves the storing of atmospheric CO2 in bundle sheath cells. "The evolution of C4 photosynthesis ~35–40 million years ago provided a natural solution to remedy the inefficiency of Rubisco" [2]. The Hatch-Slack pathway is acknowledged for its improved efficiency, where the concentration of CO2 is increased around the enzyme Rubisco in order to reduce [[photorespiration]].

==Anatomy==
[[File:BIO_370_Pep_Antibody_(2).jpg|right|200px|Amaranth mesophyll cells stained with PEP Case primary antibody]]
[[File:BIO370_Rubisco_primary_antibody_(2).jpg|right|200px|Amaranth bundle sheath cells stained with rubisco primary antibody]]
C4 plants exhibit a Kranz-type leaf anatomy involving two photosynthetic cells known as mesophyll cells and bundle sheath cells which differ in their CO2 assimilation functions [1]. In mesophyll cells, atmospheric carbon dioxide is converted to a C4 acid by the enzyme phosphoenolpyruvate carboxylase (PEP Case) during the carboxylation phase of carbon fixation. In this step, PEP Case catalyzes the reaction between bicarbonate, HCO3-, and phosphoenolpyruvate (PEP), a three-carbon molecule, to form the four-carbon acid oxaloacetate and inorganic phosphate [4]. The four-carbon acids are then transported to the bundle sheath cells surrounding leaf veins where rubisco (ribulose-1,5-bisphosphate carboxylase-oxygenase) fixes and assimilates CO2 into the [[Calvin Cycle]]. Once CO2 is assimilated into the cycle by RuBP and Rubisco, energy (ATP, NADPH) from the light reactions during photosynthesis is used to produce sugars such as glucose [5].

==Agricultural Significance==
C4 plants typically occupy hot, arid climates, whereas C3 plants are most frequently found in temperate, moist environments. When fixing carbon, C3 plants open their stomata to allow atmospheric gasses such as carbon dioxide and oxygen at the cost of allowing water to evaporate from the plants leaves. However, C4 plants have evolved to retain water through the ability to continue fixing carbon while the stomata are closed [6]. This adaptation allows C4 plants to survive the hot and dry climates, reducing harmful photorespiration and water losses through evaporation.

Several common agriculturally significant C4 plants include [6]:
*Maize
*Sugarcane
*Sorghum

In many subtropical, tropical, and desert climates, C4 plants are the primary economic agricultural generators due to their carbon fixation efficiency and ability to retain water. "Drought is a major agricultural problem worldwide. Therefore, selection for increased water use efficiency (WUE) in food and biofuel crop species will be an important trait in plant breeding programs" [3]. With [[climate change]] in mind, C4 plants are becoming much more favorable in agriculture as they are resilient in the face of warmer ambient temperatures and drier seasons.

==Evolution==
It has been hypothesized through evolutionary radiation analysis that C4 vegetation contributed to global cooling during the late Miocene period [7]. Researchers have proposed that low atmospheric CO2 during the late Miocene triggered C4 evolution in [[Andropogonae]] grasses roughly 17 million years ago [7]. With the help of paleontologists, recent studies have hypothesized C4 evolution began in the late Oligocene period approximately 25-30 million years ago when CO2 levels were falling below 1000ppm (parts per million) [7]. Interestingly, it is suspected that the rise of C4 plants contributed to diversification of many animal clades such as the formation of large grazing guilds in the C4 grasslands of Africa [7]. With current technological advancements, research is still uprooting the foundation of C4 plant evolution, however the previously proposed mechanisms are generally agreed upon by ecological and paleontological organizations.

==References==
#PATEL, Minesh, and James O. BERRY. “Rubisco Gene Expression in C4 Plants: Photosynthesis: CO2 Uptake and the Pathways of Carbon Fixation.” Journal of Experimental Botany, vol. 59, no. 7, Oxford University Press, 2008, pp. 1625–34.
#Sharwood, Robert E., et al. “Improved Analysis of C4 and C3 Photosynthesis via Refined in Vitro Assays of Their Carbon Fixation Biochemistry.” Journal of Experimental Botany, vol. 67, no. 10, Oxford University Press, 2016, pp. 3137–48, doi:10.1093/jxb/erw154.
#Ellsworth, Patrick Z., and Asaph B. Cousins. “Carbon Isotopes and Water Use Efficiency in C4 Plants.” Current Opinion in Plant Biology, vol. 31, no. C, Elsevier Ltd, 2016, pp. 155–61, doi:10.1016/j.pbi.2016.04.006.
#“Phosphoenolpyruvate Carboxylase.” Wikipedia, Wikimedia Foundation, 19 Oct. 2020, en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxylase.
#National Geographic Society. “Calvin Cycle.” National Geographic Society, 9 Nov. 2012, www.nationalgeographic.org/media/calvincycle/#:~:text=by%20Tim%20Gunther-,The%20Calvin%20cycle%20is%20a%20process%20that%20plants%20and%20algae,cycle%20for%20energy%20and%20food.
#“The Difference between C3 and C4 Plants.” RIPE, 18 Mar. 2020, ripe.illinois.edu/blog/difference-between-c3-and-c4-plants.
#Sage, Rowan F., et al. “Some Like It Hot: The Physiological [[Ecology]] of C4 Plant Evolution.” Oecologia, vol. 187, no. 4, Springer Berlin Heidelberg, 2018, pp. 941–66, doi:10.1007/s00442-018-4191-6.
#Berry, James O. “Exp. #10. Laser Scanning Confocal Microscopy, C4 Leaf Development.” 2021.

C4 Carbon Fixation

2021-05-02T18:35:37Z

Ephanrah:

==Description==
[[File:EVS463_C4_Carbon_Fixation.JPG|right|200px|]]
The [[Hatch-Slack pathway]], also known as the C4 plant carbon fixation pathway, involves the storing of atmospheric CO2 in bundle sheath cells. "The evolution of C4 photosynthesis ~35–40 million years ago provided a natural solution to remedy the inefficiency of Rubisco" [2]. The Hatch-Slack pathway is acknowledged for its improved efficiency, where the concentration of CO2 is increased around the enzyme Rubisco in order to reduce [[photorespiration]].

==Anatomy==
[[File:BIO_370_Pep_Antibody_(2).jpg|right|200px|Amaranth mesophyll cells stained with PEP Case primary antibody]]
[[File:BIO370_Rubisco_primary_antibody_(2).jpg|right|200px|Amaranth bundle sheath cells stained with rubisco primary antibody]]
C4 plants exhibit a Kranz-type leaf anatomy involving two photosynthetic cells known as mesophyll cells and bundle sheath cells which differ in their CO2 assimilation functions [1]. In mesophyll cells, atmospheric carbon dioxide is converted to a C4 acid by the enzyme phosphoenolpyruvate carboxylase (PEP Case) during the carboxylation phase of carbon fixation. In this step, PEP Case catalyzes the reaction between bicarbonate, HCO3-, and phosphoenolpyruvate (PEP), a three-carbon molecule, to form the four-carbon acid oxaloacetate and inorganic phosphate [4]. The four-carbon acids are then transported to the bundle sheath cells surrounding leaf veins where rubisco (ribulose-1,5-bisphosphate carboxylase-oxygenase) fixes and assimilates CO2 into the [[Calvin Cycle]]. Once CO2 is assimilated into the cycle by RuBP and Rubisco, energy (ATP, NADPH) from the light reactions during photosynthesis is used to produce sugars such as glucose [5].

==Agricultural Significance==
C4 plants typically occupy hot, arid climates, whereas C3 plants are most frequently found in temperate, moist environments. When fixing carbon, C3 plants open their stomata to allow atmospheric gasses such as carbon dioxide and oxygen at the cost of allowing water to evaporate from the plants leaves. However, C4 plants have evolved to retain water through the ability to continue fixing carbon while the stomata are closed [6]. This adaptation allows C4 plants to survive the hot and dry climates, reducing harmful photorespiration and water losses through evaporation.

Several common agriculturally significant C4 plants include [6]:
*Maize
*Sugarcane
*Sorghum

In many subtropical, tropical, and desert climates, C4 plants are the primary economic agricultural generators due to their carbon fixation efficiency and ability to retain water. "Drought is a major agricultural problem worldwide. Therefore, selection for increased water use efficiency (WUE) in food and biofuel crop species will be an important trait in plant breeding programs" [3]. With [[climate change]] in mind, C4 plants are becoming much more favorable in agriculture as they are resilient in the face of warmer ambient temperatures.

==Evolution==
It has been hypothesized through evolutionary radiation analysis that C4 vegetation contributed to global cooling during the late Miocene period [7]. Researchers have proposed that low atmospheric CO2 during the late Miocene triggered C4 evolution in [[Andropogonae]] grasses roughly 17 million years ago [7]. With the help of paleontologists, recent studies have hypothesized C4 evolution began in the late Oligocene period approximately 25-30 million years ago when CO2 levels were falling below 1000ppm (parts per million) [7]. Interestingly, it is suspected that the rise of C4 plants contributed to diversification of many animal clades such as the formation of large grazing guilds in the C4 grasslands of Africa [7]. With current technological advancements, research is still uprooting the foundation of C4 plant evolution, however the previously proposed mechanisms are generally agreed upon by ecological and paleontological organizations.

==References==
#PATEL, Minesh, and James O. BERRY. “Rubisco Gene Expression in C4 Plants: Photosynthesis: CO2 Uptake and the Pathways of Carbon Fixation.” Journal of Experimental Botany, vol. 59, no. 7, Oxford University Press, 2008, pp. 1625–34.
#Sharwood, Robert E., et al. “Improved Analysis of C4 and C3 Photosynthesis via Refined in Vitro Assays of Their Carbon Fixation Biochemistry.” Journal of Experimental Botany, vol. 67, no. 10, Oxford University Press, 2016, pp. 3137–48, doi:10.1093/jxb/erw154.
#Ellsworth, Patrick Z., and Asaph B. Cousins. “Carbon Isotopes and Water Use Efficiency in C4 Plants.” Current Opinion in Plant Biology, vol. 31, no. C, Elsevier Ltd, 2016, pp. 155–61, doi:10.1016/j.pbi.2016.04.006.
#“Phosphoenolpyruvate Carboxylase.” Wikipedia, Wikimedia Foundation, 19 Oct. 2020, en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxylase.
#National Geographic Society. “Calvin Cycle.” National Geographic Society, 9 Nov. 2012, www.nationalgeographic.org/media/calvincycle/#:~:text=by%20Tim%20Gunther-,The%20Calvin%20cycle%20is%20a%20process%20that%20plants%20and%20algae,cycle%20for%20energy%20and%20food.
#“The Difference between C3 and C4 Plants.” RIPE, 18 Mar. 2020, ripe.illinois.edu/blog/difference-between-c3-and-c4-plants.
#Sage, Rowan F., et al. “Some Like It Hot: The Physiological [[Ecology]] of C4 Plant Evolution.” Oecologia, vol. 187, no. 4, Springer Berlin Heidelberg, 2018, pp. 941–66, doi:10.1007/s00442-018-4191-6.
#Berry, James O. “Exp. #10. Laser Scanning Confocal Microscopy, C4 Leaf Development.” 2021.

C4 Carbon Fixation

2021-05-02T18:32:46Z

Ephanrah: Created page with "==Description== 200px| The Hatch-Slack pathway, also known as the C4 plant carbon fixation pathway, involves the storing of at..."

==Description==
[[File:EVS463_C4_Carbon_Fixation.JPG|right|200px|]]
The [[Hatch-Slack pathway]], also known as the C4 plant carbon fixation pathway, involves the storing of atmospheric CO2 in bundle sheath cells. "The evolution of C4 photosynthesis ~35–40 million years ago provided a natural solution to remedy the inefficiency of Rubisco" [2]. The Hatch-Slack pathway is acknowledged for its improved efficiency, where the concentration of CO2 is increased around the enzyme Rubisco in order to reduce [[photorespiration]].

==Anatomy==
[[File:BIO_370_Pep_Antibody_(2).jpg|right|200px|Amaranth mesophyll cells stained with PEP Case primary antibody]]
[[File:BIO370_Rubisco_primary_antibody_(2).jpg|right|200px|Amaranth bundle sheath cells stained with rubisco primary antibody]]
C4 plants exhibit a Kranz-type leaf anatomy involving two photosynthetic cells known as mesophyll cells and bundle sheath cells which differ in their CO2 assimilation functions [1]. In mesophyll cells, atmospheric carbon dioxide is converted to a C4 acid by the enzyme phosphoenolpyruvate carboxylase (PEP Case) during the carboxylation phase of carbon fixation. In this step, PEP Case catalyzes the reaction between bicarbonate, HCO3-, and phosphoenolpyruvate (PEP), a three-carbon molecule, to form the four-carbon acid oxaloacetate and inorganic phosphate [4]. The four-carbon acids are then transported to the bundle sheath cells surrounding leaf veins where rubisco (ribulose-1,5-bisphosphate carboxylase-oxygenase) fixes and assimilates CO2 into the [[Calvin Cycle]]. Once CO2 is assimilated into the cycle by RuBP and Rubisco, energy (ATP, NADPH) from the light reactions during photosynthesis is used to produce sugars such as glucose [5].

==Agricultural Significance==
C4 plants typically occupy hot, arid climates, whereas C3 plants are most frequently found in temperate, moist environments. When fixing carbon, C3 plants open their stomata to allow atmospheric gasses such as carbon dioxide and oxygen at the cost of allowing water to evaporate from the plants leaves. However, C4 plants have evolved to retain water through the ability to continue fixing carbon while the stomata are closed [6]. This adaptation allows C4 plants to survive the hot and dry climates, reducing harmful photorespiration and water losses through evaporation.

Several common agriculturally significant C4 plants include [6]:
*Maize
*Sugarcane
*Sorghum

In many subtropical, tropical, and desert climates, C4 plants are the primary economic agricultural generators due to their carbon fixation efficiency and ability to retain water. "Drought is a major agricultural problem worldwide. Therefore, selection for increased water use efficiency (WUE) in food and biofuel crop species will be an important trait in plant breeding programs" [3]. With [[climate change]] in mind, C4 plants are becoming much more favorable in agriculture as they are resilient in the face of warmer ambient temperatures.

==Evolution==
It has been hypothesized through evolutionary radiation analysis that C4 vegetation contributed to global cooling during the late Miocene period [7]. Researchers have proposed that low atmospheric CO2 during the late Miocene triggered C4 evolution in [[Andropogonae]] grasses roughly 17 million years ago [7]. With the help of paleontologists, recent studies have hypothesized C4 evolution began in the late Oligocene period approximately 25-30 million years ago when CO2 levels were falling below 1000ppm (parts per million) [7]. Interestingly, it is suspected that the rise of C4 plants contributed to diversification of many animal clades such as the formation of large grazing guilds in the C4 grasslands of Africa [7]. With current technological advancements, research is still uprooting the foundation of C4 plant evolution, however the previously proposed mechanisms are generally agreed upon by ecological and paleontological organizations.

File:EVS463 C4 Carbon Fixation.JPG

2021-05-02T18:19:42Z

Ephanrah: C4 carbon fixation (Hatch-Slack pathway) Berry, James O. “Exp. #10. Laser Scanning Confocal Microscopy, C4 Leaf Development.” 2021.

C4 carbon fixation (Hatch-Slack pathway)

Berry, James O. “Exp. #10. Laser Scanning Confocal Microscopy, C4 Leaf Development.” 2021.

File:BIO370 Rubisco primary antibody (2).jpg

2021-05-02T18:16:50Z

Ephanrah: Confocal image of Amaranth leaf cross section stained with rubisco primary antibody attached to fluorophore

Confocal image of Amaranth leaf cross section stained with rubisco primary antibody attached to fluorophore

File:BIO 370 Pep Antibody (2).jpg

2021-05-02T18:15:29Z

Ephanrah: Confocal image of Amaranth leaf cross section stained with PEP Case primary antibody attached to fluorophore

Confocal image of Amaranth leaf cross section stained with PEP Case primary antibody attached to fluorophore

Phytoremediation

2021-05-02T14:48:04Z

Ephanrah: Corrected "ox" to "of" in sentence "The joining of xenobiotic fragments with larger...."

== Definition ==

Phytoremediation is a process that uses vascular plants as a means of extracting inorganic and organic contaminants from soils (1). The strategies used in phytoremediation can be grouped into physical, chemical and biological methods for mitigating the effect subsurface pollutants have on the [[soil]] and groundwater.

[[File:Phytodegradation.jpg|frame| Cellular pathway of xenobiotic compounds as they pass through the phases of phytodegradation (1).]]

== Phytodegradation ==

Phytodegradation utilizes the metabolic capability of plants in breaking down soil contaminants. The term “green liver” has been used to describe this process as the plant metabolizes xenobiotic compounds in an analogous way to that of the mammalian liver (2). In plants, the xenobiotic metabolism occurs over three phases; transformation, conjugation, and excretion. The result of these phases is detoxification of the xenobiotic as well as making them more inert and stored away from other cellular processes.

The first phase involves the chemical modification of the xenobiotic compound by either oxidation, reduction, or hydrolysis. This causes the xenobiotic to become more water soluble and thus be more biochemically reactive within the plant (3). Plants utilize many different enzymes to alter these compounds. Cytochrome P450 family enzymes act as mono-oxygenases towards a broad range of substrates and convert hydrophobic compounds into those which are more soluble in water (4). Carboxylesterases (CXEs) can convert carboxyl esters into carboxylic acids via hydrolysis which can go on to react with other molecules in the next phase (5).

The water soluble and reactive compounds formed from transformation are then conjugated to endogenous modules such as sugars or peptides. The joining of xenobiotic fragments with larger endogenous compounds decreases the toxicity of the xenobiotic while also making it easier to shuttle them around the cell during the last phase of compartmentalization. Glycosyltransferases are a large family of enzymes that catalyze the joining of nucleotide-diphosphate-sugars (usually in the form of Uridine diphosphate glucose or UDP-glucose) to xenobiotic compounds (6). The glycosylation of these compounds results in a higher stability of the xenobiotic fragments as well as trapping them within the vacuole and preventing them from reacting further to form harmful substances (7). Glutathione S-transferases (GSTs) is another class of enzymes that attach to xenobiotics at a tripeptide glutathione region and facilitate transfer to the vacuole or cell wall (8).

The final phase sees the xenobiotics bound to larger macromolecules sequestered to specific locations within plant cells, namely the vacuole or cell wall. Most xenobiotics are incorporated into the cell wall after being bound to lignin molecules while enzymes called ATP-binding cassette (ABC) transporters facilitate xenobiotic transfer to the vacuole (9).

== Rhizodegradation ==

[[File:Rhizodegradation.jpg|frame| A generalized schematic of the interplay between root exudates and soil microorganisms under the "rhizosphere effect" (1).]]

Rhizodegradation results from the establishment a vast variety of soil microorganisms in the region surrounds the roots known as the [[rhizosphere]]. This region serves as a favorable habitat and in turn increases the degradation of pollutants by the soil [[microorganisms]] themselves (1). Plants can lead to the induction of catabolic genes in soil microbes as well as population shifts through the release of root exudates (10). Sugars, amino acids, and organic acids are commonly released into the rhizosphere where they are readily used by microbes to grow. Along with these compounds’ plants release secondary metabolites for soil microbes, namely isoprenoids, alkaloids, and [[flavonoids]]. Normally soil microbes would not necessarily switch to using xenobiotic compounds as a source of carbon as it would be a negative return for them. However, these secondary compounds from plants mimic that of xenobiotics and are easier to break down (11). This in turn causes microbes to synthesize catabolic proteins that break down the secondary metabolites as well as the xenobiotic contaminants in the soil.

== References ==

#Reichenauer, Thomas G., and James J. Germida. “Phytoremediation of Organic Contaminants in Soil and Groundwater.” ChemSusChem, vol. 1, no. 8‐9, WILEY‐VCH Verlag, 2008, pp. 708–17, doi:10.1002/cssc.200800125.
#Sandermann H Jr. Plant metabolism of xenobiotics. Trends Biochem Sci. 1992 Feb;17(2):82-4. doi: 10.1016/0968-0004(92)90507-6. PMID: 1566333.
#Komives T, Gullner G. Phase I xenobiotic metabolic systems in plants. Z Naturforsch C J Biosci. 2005 Mar-Apr;60(3-4):179-85. PMID: 15948581. https://pubmed-ncbi-nlm-nih-gov.gate.lib.buffalo.edu/15948581.
#Bernhardt R. Cytochromes P450 as versatile biocatalysts. J Biotechnol. 2006 Jun 25;124(1):128-45. doi: 10.1016/j.jbiotec.2006.01.026. Epub 2006 Mar 3. PMID: 16516322. https://pubmed-ncbi-nlm-nih-gov.gate.lib.buffalo.edu/16516322.
#D. Werck‐Reichhart, A. Hehn, L. Didierjean, Trends Plant Sci. 2000, 5, 116–123. https://www-sciencedirect-com.gate.lib.buffalo.edu/science/article/abs/pii/S1360138500015673?via%3Dihub.
#Vogt T, Jones P. Glycosyltransferases in plant natural product synthesis: characterization of a supergene family. Trends Plant Sci. 2000 Sep;5(9):380-6. doi: 10.1016/s1360-1385(00)01720-9. PMID: 10973093. https://pubmed-ncbi-nlm-nih-gov.gate.lib.buffalo.edu/10973093.
#Kahn RA, Bak S, Svendsen I, Halkier BA, Møller BL. Isolation and reconstitution of cytochrome P450ox and in vitro reconstitution of the entire biosynthetic pathway of the cyanogenic glucoside dhurrin from sorghum. Plant Physiol. 1997 Dec;115(4):1661-70. doi: 10.1104/pp.115.4.1661. PMID: 9414567; PMCID: PMC158632. https://pubmed-ncbi-nlm-nih-gov.gate.lib.buffalo.edu/9414567.
#Edwards R, Dixon DP, Walbot V. Plant glutathione S-transferases: enzymes with multiple functions in sickness and in health. Trends Plant Sci. 2000 May;5(5):193-8. doi: 10.1016/s1360-1385(00)01601-0. PMID: 10785664. https://pubmed-ncbi-nlm-nih-gov.gate.lib.buffalo.edu/10785664.
#Philip A. Rea. “MRP Subfamily ABC Transporters from Plants and Yeast.” Journal of Experimental Botany, vol. 50, no. 90001, OXFORD UNIVERSITY PRESS, 1999, pp. 895–913, doi:10.1093/jexbot/50.suppl_1.895. https://www-jstor-org.gate.lib.buffalo.edu/stable/23696197?sid=primo&seq=1#metadata_info_tab_contents.
#Fatima, Kaneez, et al. “Bacterial Rhizosphere and Endosphere Populations Associated with Grasses and Trees to Be Used for Phytoremediation of Crude Oil Contaminated Soil.” Bulletin of Environmental Contamination and Toxicology, vol. 94, no. 3, Springer US, 2015, pp. 314–20, doi:10.1007/s00128-015-1489-5. https://web-a-ebscohost-com.gate.lib.buffalo.edu/ehost/detail/detail?vid=0&sid=241754d3-ccb3-4acc-83b9-afafa5c82bcb%40sdc-v-sessmgr03&bdata=JnNpdGU9ZWhvc3QtbGl2ZSZzY29wZT1zaXRl#AN=101049230&db=eih.
#Singer AC, Crowley DE, Thompson IP. Secondary plant metabolites in phytoremediation and biotransformation. Trends Biotechnol. 2003 Mar;21(3):123-30. doi: 10.1016/S0167-7799(02)00041-0. PMID: 12628369. https://pubmed-ncbi-nlm-nih-gov.gate.lib.buffalo.edu/12628369.

Phytoremediation

2021-05-02T14:46:45Z

Ephanrah: Undo revision 6168 by Ephanrah (talk)

== Definition ==

Phytoremediation is a process that uses vascular plants as a means of extracting inorganic and organic contaminants from soils (1). The strategies used in phytoremediation can be grouped into physical, chemical and biological methods for mitigating the effect subsurface pollutants have on the [[soil]] and groundwater.

[[File:Phytodegradation.jpg|frame| Cellular pathway of xenobiotic compounds as they pass through the phases of phytodegradation (1).]]

== Phytodegradation ==

Phytodegradation utilizes the metabolic capability of plants in breaking down soil contaminants. The term “green liver” has been used to describe this process as the plant metabolizes xenobiotic compounds in an analogous way to that of the mammalian liver (2). In plants, the xenobiotic metabolism occurs over three phases; transformation, conjugation, and excretion. The result of these phases is detoxification of the xenobiotic as well as making them more inert and stored away from other cellular processes.

The first phase involves the chemical modification of the xenobiotic compound by either oxidation, reduction, or hydrolysis. This causes the xenobiotic to become more water soluble and thus be more biochemically reactive within the plant (3). Plants utilize many different enzymes to alter these compounds. Cytochrome P450 family enzymes act as mono-oxygenases towards a broad range of substrates and convert hydrophobic compounds into those which are more soluble in water (4). Carboxylesterases (CXEs) can convert carboxyl esters into carboxylic acids via hydrolysis which can go on to react with other molecules in the next phase (5).

The water soluble and reactive compounds formed from transformation are then conjugated to endogenous modules such as sugars or peptides. The joining ox xenobiotic fragments with larger endogenous compounds decreases the toxicity of the xenobiotic while also making it easier to shuttle them around the cell during the last phase of compartmentalization. Glycosyltransferases are a large family of enzymes that catalyze the joining of nucleotide-diphosphate-sugars (usually in the form of Uridine diphosphate glucose or UDP-glucose) to xenobiotic compounds (6). The glycosylation of these compounds results in a higher stability of the xenobiotic fragments as well as trapping them within the vacuole and preventing them from reacting further to form harmful substances (7). Glutathione S-transferases (GSTs) is another class of enzymes that attach to xenobiotics at a tripeptide glutathione region and facilitate transfer to the vacuole or cell wall (8).

The final phase sees the xenobiotics bound to larger macromolecules sequestered to specific locations within plant cells, namely the vacuole or cell wall. Most xenobiotics are incorporated into the cell wall after being bound to lignin molecules while enzymes called ATP-binding cassette (ABC) transporters facilitate xenobiotic transfer to the vacuole (9).

== Rhizodegradation ==

[[File:Rhizodegradation.jpg|frame| A generalized schematic of the interplay between root exudates and soil microorganisms under the "rhizosphere effect" (1).]]

Rhizodegradation results from the establishment a vast variety of soil microorganisms in the region surrounds the roots known as the [[rhizosphere]]. This region serves as a favorable habitat and in turn increases the degradation of pollutants by the soil [[microorganisms]] themselves (1). Plants can lead to the induction of catabolic genes in soil microbes as well as population shifts through the release of root exudates (10). Sugars, amino acids, and organic acids are commonly released into the rhizosphere where they are readily used by microbes to grow. Along with these compounds’ plants release secondary metabolites for soil microbes, namely isoprenoids, alkaloids, and [[flavonoids]]. Normally soil microbes would not necessarily switch to using xenobiotic compounds as a source of carbon as it would be a negative return for them. However, these secondary compounds from plants mimic that of xenobiotics and are easier to break down (11). This in turn causes microbes to synthesize catabolic proteins that break down the secondary metabolites as well as the xenobiotic contaminants in the soil.

== References ==

#Reichenauer, Thomas G., and James J. Germida. “Phytoremediation of Organic Contaminants in Soil and Groundwater.” ChemSusChem, vol. 1, no. 8‐9, WILEY‐VCH Verlag, 2008, pp. 708–17, doi:10.1002/cssc.200800125.
#Sandermann H Jr. Plant metabolism of xenobiotics. Trends Biochem Sci. 1992 Feb;17(2):82-4. doi: 10.1016/0968-0004(92)90507-6. PMID: 1566333.
#Komives T, Gullner G. Phase I xenobiotic metabolic systems in plants. Z Naturforsch C J Biosci. 2005 Mar-Apr;60(3-4):179-85. PMID: 15948581. https://pubmed-ncbi-nlm-nih-gov.gate.lib.buffalo.edu/15948581.
#Bernhardt R. Cytochromes P450 as versatile biocatalysts. J Biotechnol. 2006 Jun 25;124(1):128-45. doi: 10.1016/j.jbiotec.2006.01.026. Epub 2006 Mar 3. PMID: 16516322. https://pubmed-ncbi-nlm-nih-gov.gate.lib.buffalo.edu/16516322.
#D. Werck‐Reichhart, A. Hehn, L. Didierjean, Trends Plant Sci. 2000, 5, 116–123. https://www-sciencedirect-com.gate.lib.buffalo.edu/science/article/abs/pii/S1360138500015673?via%3Dihub.
#Vogt T, Jones P. Glycosyltransferases in plant natural product synthesis: characterization of a supergene family. Trends Plant Sci. 2000 Sep;5(9):380-6. doi: 10.1016/s1360-1385(00)01720-9. PMID: 10973093. https://pubmed-ncbi-nlm-nih-gov.gate.lib.buffalo.edu/10973093.
#Kahn RA, Bak S, Svendsen I, Halkier BA, Møller BL. Isolation and reconstitution of cytochrome P450ox and in vitro reconstitution of the entire biosynthetic pathway of the cyanogenic glucoside dhurrin from sorghum. Plant Physiol. 1997 Dec;115(4):1661-70. doi: 10.1104/pp.115.4.1661. PMID: 9414567; PMCID: PMC158632. https://pubmed-ncbi-nlm-nih-gov.gate.lib.buffalo.edu/9414567.
#Edwards R, Dixon DP, Walbot V. Plant glutathione S-transferases: enzymes with multiple functions in sickness and in health. Trends Plant Sci. 2000 May;5(5):193-8. doi: 10.1016/s1360-1385(00)01601-0. PMID: 10785664. https://pubmed-ncbi-nlm-nih-gov.gate.lib.buffalo.edu/10785664.
#Philip A. Rea. “MRP Subfamily ABC Transporters from Plants and Yeast.” Journal of Experimental Botany, vol. 50, no. 90001, OXFORD UNIVERSITY PRESS, 1999, pp. 895–913, doi:10.1093/jexbot/50.suppl_1.895. https://www-jstor-org.gate.lib.buffalo.edu/stable/23696197?sid=primo&seq=1#metadata_info_tab_contents.
#Fatima, Kaneez, et al. “Bacterial Rhizosphere and Endosphere Populations Associated with Grasses and Trees to Be Used for Phytoremediation of Crude Oil Contaminated Soil.” Bulletin of Environmental Contamination and Toxicology, vol. 94, no. 3, Springer US, 2015, pp. 314–20, doi:10.1007/s00128-015-1489-5. https://web-a-ebscohost-com.gate.lib.buffalo.edu/ehost/detail/detail?vid=0&sid=241754d3-ccb3-4acc-83b9-afafa5c82bcb%40sdc-v-sessmgr03&bdata=JnNpdGU9ZWhvc3QtbGl2ZSZzY29wZT1zaXRl#AN=101049230&db=eih.
#Singer AC, Crowley DE, Thompson IP. Secondary plant metabolites in phytoremediation and biotransformation. Trends Biotechnol. 2003 Mar;21(3):123-30. doi: 10.1016/S0167-7799(02)00041-0. PMID: 12628369. https://pubmed-ncbi-nlm-nih-gov.gate.lib.buffalo.edu/12628369.

Talk:Phytoremediation

2021-05-02T14:45:47Z

Ephanrah: Created page with "Really good work! The visuals definitely helped in understanding the process as you were describing the steps. I fixed one small error where you accidentally wrote "ox" instea..."

Really good work! The visuals definitely helped in understanding the process as you were describing the steps. I fixed one small error where you accidentally wrote "ox" instead of "of". Overall, I really think your page is strong! Good work :) -Ethan

Phytoremediation

2021-05-02T14:42:57Z

Ephanrah: Changed "ox" to "of" in the sentence "This causes the xenobiotic fragments to become more water soluble..."

Talk:Platyhelminthes

2021-05-02T12:46:54Z

Ephanrah: Created page with "I enjoyed your page as these organisms are fascinating (also really enjoyed the pictures)! I think it would be a good idea to add a section on reproduction methods and maybe a..."

I enjoyed your page as these organisms are fascinating (also really enjoyed the pictures)! I think it would be a good idea to add a section on reproduction methods and maybe add more on the population abundances of each individual grouping for more background, but it isn't entirely necessary. Good work! :) - Ethan

Talk:Fungal farming

2021-05-02T12:37:51Z

Ephanrah:

Overall pretty good. Might want to rephrase some sentences to be more formal.

I enjoyed how in depth you went on this topic, as it provides a lot of good background information about the fungal farming systems that are established in terrestrial and aquatic systems! I agree with the statement above, as there are some areas that could maybe be reworded or rearranged for strength. For example, in the Terrestrial systems section the first sentence sounded like it ran on, so you could use a bulleted list of the insects instead of listing them within the sentence! Overall I really enjoyed your page and images! Good work :) - Ethan

Talk:Sphaeriidae

2021-04-26T19:56:43Z

Ephanrah:

Page looks really great so far, I enjoyed how in-depth your discussion of the life history and dispersal mechanisms were. Only recommendation I would offer is to possibly include a picture of their lifecycle if you are able to find one. -Niko

I enjoyed the page and fluency in topics! The pictures were great and the content was interesting. Niko mentioned a lifecycle image, and to back that up, I feel like that would be a great idea! -Ethan

Plant Hormones

2021-04-26T19:47:55Z

Ephanrah: /* Plant Callus Formation */

==Introduction==
Plant hormones auxin and cytokinin are primarily known for their roles in vegetative (indeterminate) growth. This type of growth involves the repetition of structures in a given order once the plant has established the primary apical meristem. Auxin and cytokinin work antagonistically during the vegetative growth of plants, but synergistically in cellular regeneration [1]. Auxin is produced in the apical meristem of the plant, whereas cytokinin is produced in the leaves. Auxins are responsible for apical dominance in vegetative growth, repressing cytokinin from activating dormant axillary (lateral) buds from growing new lateral shoots. Cytokinin is responsible for creating new lateral shoots when the apical meristem is damaged or the concentration of auxin falls below the ability to repress cytokinin [1].

==Auxin==
[[File:EVS463_Auxin_Image.JPG|right|300px|Organic and synthetic Auxins]]
The plant hormone auxin, produced in the apical meristem, can be found in nature as a compound known as indole-3-acetic acid (IAA), and is primarily synthesized from the well-known amino acid tryptophan [4]. There are also synthetic auxins known as 2,4-dichlorophenoxyacetic acid (2,4-D) and naphthalene acetic acid (NAA) [3].

Auxins are extremely important to plant growth as they are responsible primarily for cellular elongation, root development, and apical dominance during vegetative growth. During apical dominance, auxin produced by the apical meristem creates a downward concentration gradient, preventing axillary buds from activating through cytokinin initiation. This concentration gradient also creates a hormone sink in the roots, where auxin stimulates root development. They are widely used commercially for root induction for plant propagation [3].

Interestingly, auxins can induce epinastic responses through localized auxin concentrations, causing plant bending in a process known as phototropism. Due to the hormone's cellular elongation properties, it can swell the cells on one side like a balloon, bending the plant in the opposite direction from its application. It may also induce leaf epinasty, where leaves bend downward "as result of disturbances in their growth, with greater expansion in adaxial cells as compared to abaxial surface cells" [4].

==Cytokinin==
[[File:EVS463_Cytokinin_image.JPG|right|300px|Organic and synthetic cytokinins]]
The plant hormone cytokinin, produced in leaf tissues of plants, is primarily found in nature as a compound known as zeatin. Interestingly, "almost all organisms make cytokinin; for example, isopentenyl adenine derivatives found adjacent to the anticodon loop of a subset of tRNAs in most eukaryotes and bacteria" [5]. These were first discovered while searching for factors that promote cell proliferation in plant cells in concert with auxin to regulate cell division and differentiation [5].

Cytokinins are primarily responsible for cellular division and overcoming apical dominance to stimulate lateral shoot formation. If the plant apical meristem becomes damaged, the auxin concentration of the plant falls allowing cytokinin concentrations to accumulate and activate dormant axillary buds [5]. In some cases, the auxin concentration gradient falls below levels of apical dominance near the ground, causing lateral shoot formation in a Christmas-tree like effect.

==Plant Callus Formation==
[[File:EVS463_Callus_Formation.JPG|right|200px|Plant callus tissue forms as a result of wounding, followed by cellular regeneration controlled by the ratio of auxin to cytokinin]]
Callus formation on plants occurs as a result of wounding, infection, or unregulated and undifferentiated cellular regeneration, controlled by concentrations of auxin and cytokinin. Studies have shown "an intermediate ratio of auxin and cytokinin promotes callus induction, while a high ratio of auxin-to-cytokinin or cytokinin-to-auxin induces root and shoot regeneration, respectively" [6]. These hormones are important for infection processes in plants such as agrobacterium where transgenes are inserted into the host genome. The agrobacterium T-DNA has oncogenes which promote production of auxin and cytokinin in order to provide a favorable environment for the bacteria to reproduce and feed. This site is typically referred to as the crown gall. Eventually the plant will die, in which the bacteria are released back into the soil to begin the infection process again.

==References==
#Su, Ying-Hua, et al. “Auxin-Cytokinin Interaction Regulates Meristem Development.” Molecular plant, vol. 4, no. 4, Elsevier Inc, 2011, pp. 616–25, doi:10.1093/mp/ssr007.
#G. Eric Schaller, et al. “The Yin-Yang of Hormones: Cytokinin and Auxin Interactions in Plant Development.” The Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 44–63, doi:10.1105/tpc.114.133595.
#Zaman, Mohammad, et al. “Enhancing Crop Yield with the Use of N‐based Fertilizers Co‐applied with Plant Hormones or Growth Regulators.” Journal of the Science of Food and Agriculture, vol. 95, no. 9, John Wiley & Sons, Ltd, 2015, pp. 1777–85, doi:10.1002/jsfa.6938.
#Sandalio, Luisa M., et al. “Leaf Epinasty and Auxin: A Biochemical and Molecular Overview.” Plant Science (Limerick), vol. 253, Elsevier Ireland Ltd, 2016, pp. 187–93, doi:10.1016/j.plantsci.2016.10.002.
#Kieber, Joseph J., and G. Eric Schaller. “Cytokinin Signaling in Plant Development.” Development (Cambridge), vol. 145, no. 4, COMPANY BIOLOGISTS LTD, 2018, p. dev149344–, doi:10.1242/dev.149344.
#Momoko Ikeuchi, et al. “Plant Callus: Mechanisms of Induction and Repression.” The Plant Cell, vol. 25, no. 9, American Society of Plant Biologists, 2013, pp. 3159–73, doi:10.1105/tpc.113.116053.
#Berry, James O. “Rec#6 Hormones and Plant Form.” 2021.

File:EVS463 Callus Formation.JPG

2021-04-26T19:45:16Z

Ephanrah: Plant callus tissue forms as a result of cellular regeneration, controlled by concentrations of auxin and cytokinin. Berry, James O. “Rec#6 Hormones and Plant Form.” 2021.

Plant callus tissue forms as a result of cellular regeneration, controlled by concentrations of auxin and cytokinin.

Berry, James O. “Rec#6 Hormones and Plant Form.” 2021.

Plant Hormones

2021-04-26T19:37:48Z

Ephanrah: /* References */

==Introduction==
Plant hormones auxin and cytokinin are primarily known for their roles in vegetative (indeterminate) growth. This type of growth involves the repetition of structures in a given order once the plant has established the primary apical meristem. Auxin and cytokinin work antagonistically during the vegetative growth of plants, but synergistically in cellular regeneration [1]. Auxin is produced in the apical meristem of the plant, whereas cytokinin is produced in the leaves. Auxins are responsible for apical dominance in vegetative growth, repressing cytokinin from activating dormant axillary (lateral) buds from growing new lateral shoots. Cytokinin is responsible for creating new lateral shoots when the apical meristem is damaged or the concentration of auxin falls below the ability to repress cytokinin [1].

==Auxin==
[[File:EVS463_Auxin_Image.JPG|right|300px|Organic and synthetic Auxins]]
The plant hormone auxin, produced in the apical meristem, can be found in nature as a compound known as indole-3-acetic acid (IAA), and is primarily synthesized from the well-known amino acid tryptophan [4]. There are also synthetic auxins known as 2,4-dichlorophenoxyacetic acid (2,4-D) and naphthalene acetic acid (NAA) [3].

Auxins are extremely important to plant growth as they are responsible primarily for cellular elongation, root development, and apical dominance during vegetative growth. During apical dominance, auxin produced by the apical meristem creates a downward concentration gradient, preventing axillary buds from activating through cytokinin initiation. This concentration gradient also creates a hormone sink in the roots, where auxin stimulates root development. They are widely used commercially for root induction for plant propagation [3].

Interestingly, auxins can induce epinastic responses through localized auxin concentrations, causing plant bending in a process known as phototropism. Due to the hormone's cellular elongation properties, it can swell the cells on one side like a balloon, bending the plant in the opposite direction from its application. It may also induce leaf epinasty, where leaves bend downward "as result of disturbances in their growth, with greater expansion in adaxial cells as compared to abaxial surface cells" [4].

==Cytokinin==
[[File:EVS463_Cytokinin_image.JPG|right|300px|Organic and synthetic cytokinins]]
The plant hormone cytokinin, produced in leaf tissues of plants, is primarily found in nature as a compound known as zeatin. Interestingly, "almost all organisms make cytokinin; for example, isopentenyl adenine derivatives found adjacent to the anticodon loop of a subset of tRNAs in most eukaryotes and bacteria" [5]. These were first discovered while searching for factors that promote cell proliferation in plant cells in concert with auxin to regulate cell division and differentiation [5].

Cytokinins are primarily responsible for cellular division and overcoming apical dominance to stimulate lateral shoot formation. If the plant apical meristem becomes damaged, the auxin concentration of the plant falls allowing cytokinin concentrations to accumulate and activate dormant axillary buds [5]. In some cases, the auxin concentration gradient falls below levels of apical dominance near the ground, causing lateral shoot formation in a Christmas-tree like effect.

==Plant Callus Formation==
Callus formation on plants occurs as a result of wounding, infection, or unregulated and undifferentiated cellular regeneration, controlled by concentrations of auxin and cytokinin. Studies have shown "an intermediate ratio of auxin and cytokinin promotes callus induction, while a high ratio of auxin-to-cytokinin or cytokinin-to-auxin induces root and shoot regeneration, respectively" [6]. These hormones are important for infection processes in plants such as agrobacterium where transgenes are inserted into the host genome. The agrobacterium T-DNA has oncogenes which promote production of auxin and cytokinin in order to provide a favorable environment for the bacteria to reproduce and feed. This site is typically referred to as the crown gall. Eventually the plant will die, in which the bacteria are released back into the soil to begin the infection process again.

==References==
#Su, Ying-Hua, et al. “Auxin-Cytokinin Interaction Regulates Meristem Development.” Molecular plant, vol. 4, no. 4, Elsevier Inc, 2011, pp. 616–25, doi:10.1093/mp/ssr007.
#G. Eric Schaller, et al. “The Yin-Yang of Hormones: Cytokinin and Auxin Interactions in Plant Development.” The Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 44–63, doi:10.1105/tpc.114.133595.
#Zaman, Mohammad, et al. “Enhancing Crop Yield with the Use of N‐based Fertilizers Co‐applied with Plant Hormones or Growth Regulators.” Journal of the Science of Food and Agriculture, vol. 95, no. 9, John Wiley & Sons, Ltd, 2015, pp. 1777–85, doi:10.1002/jsfa.6938.
#Sandalio, Luisa M., et al. “Leaf Epinasty and Auxin: A Biochemical and Molecular Overview.” Plant Science (Limerick), vol. 253, Elsevier Ireland Ltd, 2016, pp. 187–93, doi:10.1016/j.plantsci.2016.10.002.
#Kieber, Joseph J., and G. Eric Schaller. “Cytokinin Signaling in Plant Development.” Development (Cambridge), vol. 145, no. 4, COMPANY BIOLOGISTS LTD, 2018, p. dev149344–, doi:10.1242/dev.149344.
#Momoko Ikeuchi, et al. “Plant Callus: Mechanisms of Induction and Repression.” The Plant Cell, vol. 25, no. 9, American Society of Plant Biologists, 2013, pp. 3159–73, doi:10.1105/tpc.113.116053.
#Berry, James O. “Rec#6 Hormones and Plant Form.” 2021.

Plant Hormones

2021-04-26T19:37:19Z

Ephanrah: /* Cytokinin */

==Introduction==
Plant hormones auxin and cytokinin are primarily known for their roles in vegetative (indeterminate) growth. This type of growth involves the repetition of structures in a given order once the plant has established the primary apical meristem. Auxin and cytokinin work antagonistically during the vegetative growth of plants, but synergistically in cellular regeneration [1]. Auxin is produced in the apical meristem of the plant, whereas cytokinin is produced in the leaves. Auxins are responsible for apical dominance in vegetative growth, repressing cytokinin from activating dormant axillary (lateral) buds from growing new lateral shoots. Cytokinin is responsible for creating new lateral shoots when the apical meristem is damaged or the concentration of auxin falls below the ability to repress cytokinin [1].

==Auxin==
[[File:EVS463_Auxin_Image.JPG|right|300px|Organic and synthetic Auxins]]
The plant hormone auxin, produced in the apical meristem, can be found in nature as a compound known as indole-3-acetic acid (IAA), and is primarily synthesized from the well-known amino acid tryptophan [4]. There are also synthetic auxins known as 2,4-dichlorophenoxyacetic acid (2,4-D) and naphthalene acetic acid (NAA) [3].

Auxins are extremely important to plant growth as they are responsible primarily for cellular elongation, root development, and apical dominance during vegetative growth. During apical dominance, auxin produced by the apical meristem creates a downward concentration gradient, preventing axillary buds from activating through cytokinin initiation. This concentration gradient also creates a hormone sink in the roots, where auxin stimulates root development. They are widely used commercially for root induction for plant propagation [3].

Interestingly, auxins can induce epinastic responses through localized auxin concentrations, causing plant bending in a process known as phototropism. Due to the hormone's cellular elongation properties, it can swell the cells on one side like a balloon, bending the plant in the opposite direction from its application. It may also induce leaf epinasty, where leaves bend downward "as result of disturbances in their growth, with greater expansion in adaxial cells as compared to abaxial surface cells" [4].

==Cytokinin==
[[File:EVS463_Cytokinin_image.JPG|right|300px|Organic and synthetic cytokinins]]
The plant hormone cytokinin, produced in leaf tissues of plants, is primarily found in nature as a compound known as zeatin. Interestingly, "almost all organisms make cytokinin; for example, isopentenyl adenine derivatives found adjacent to the anticodon loop of a subset of tRNAs in most eukaryotes and bacteria" [5]. These were first discovered while searching for factors that promote cell proliferation in plant cells in concert with auxin to regulate cell division and differentiation [5].

Cytokinins are primarily responsible for cellular division and overcoming apical dominance to stimulate lateral shoot formation. If the plant apical meristem becomes damaged, the auxin concentration of the plant falls allowing cytokinin concentrations to accumulate and activate dormant axillary buds [5]. In some cases, the auxin concentration gradient falls below levels of apical dominance near the ground, causing lateral shoot formation in a Christmas-tree like effect.

==Plant Callus Formation==
Callus formation on plants occurs as a result of wounding, infection, or unregulated and undifferentiated cellular regeneration, controlled by concentrations of auxin and cytokinin. Studies have shown "an intermediate ratio of auxin and cytokinin promotes callus induction, while a high ratio of auxin-to-cytokinin or cytokinin-to-auxin induces root and shoot regeneration, respectively" [6]. These hormones are important for infection processes in plants such as agrobacterium where transgenes are inserted into the host genome. The agrobacterium T-DNA has oncogenes which promote production of auxin and cytokinin in order to provide a favorable environment for the bacteria to reproduce and feed. This site is typically referred to as the crown gall. Eventually the plant will die, in which the bacteria are released back into the soil to begin the infection process again.

==References==
#Su, Ying-Hua, et al. “Auxin-Cytokinin Interaction Regulates Meristem Development.” Molecular plant, vol. 4, no. 4, Elsevier Inc, 2011, pp. 616–25, doi:10.1093/mp/ssr007.
#G. Eric Schaller, et al. “The Yin-Yang of Hormones: Cytokinin and Auxin Interactions in Plant Development.” The Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 44–63, doi:10.1105/tpc.114.133595.
#Zaman, Mohammad, et al. “Enhancing Crop Yield with the Use of N‐based Fertilizers Co‐applied with Plant Hormones or Growth Regulators.” Journal of the Science of Food and Agriculture, vol. 95, no. 9, John Wiley & Sons, Ltd, 2015, pp. 1777–85, doi:10.1002/jsfa.6938.
#Sandalio, Luisa M., et al. “Leaf Epinasty and Auxin: A Biochemical and Molecular Overview.” Plant Science (Limerick), vol. 253, Elsevier Ireland Ltd, 2016, pp. 187–93, doi:10.1016/j.plantsci.2016.10.002.
#Kieber, Joseph J., and G. Eric Schaller. “Cytokinin Signaling in Plant Development.” Development (Cambridge), vol. 145, no. 4, COMPANY BIOLOGISTS LTD, 2018, p. dev149344–, doi:10.1242/dev.149344.
#Momoko Ikeuchi, et al. “Plant Callus: Mechanisms of Induction and Repression.” The Plant Cell, vol. 25, no. 9, American Society of Plant Biologists, 2013, pp. 3159–73, doi:10.1105/tpc.113.116053.

Plant Hormones

2021-04-26T19:36:34Z

Ephanrah: /* Auxin */

==Introduction==
Plant hormones auxin and cytokinin are primarily known for their roles in vegetative (indeterminate) growth. This type of growth involves the repetition of structures in a given order once the plant has established the primary apical meristem. Auxin and cytokinin work antagonistically during the vegetative growth of plants, but synergistically in cellular regeneration [1]. Auxin is produced in the apical meristem of the plant, whereas cytokinin is produced in the leaves. Auxins are responsible for apical dominance in vegetative growth, repressing cytokinin from activating dormant axillary (lateral) buds from growing new lateral shoots. Cytokinin is responsible for creating new lateral shoots when the apical meristem is damaged or the concentration of auxin falls below the ability to repress cytokinin [1].

==Auxin==
[[File:EVS463_Auxin_Image.JPG|right|300px|Organic and synthetic Auxins]]
The plant hormone auxin, produced in the apical meristem, can be found in nature as a compound known as indole-3-acetic acid (IAA), and is primarily synthesized from the well-known amino acid tryptophan [4]. There are also synthetic auxins known as 2,4-dichlorophenoxyacetic acid (2,4-D) and naphthalene acetic acid (NAA) [3].

Auxins are extremely important to plant growth as they are responsible primarily for cellular elongation, root development, and apical dominance during vegetative growth. During apical dominance, auxin produced by the apical meristem creates a downward concentration gradient, preventing axillary buds from activating through cytokinin initiation. This concentration gradient also creates a hormone sink in the roots, where auxin stimulates root development. They are widely used commercially for root induction for plant propagation [3].

Interestingly, auxins can induce epinastic responses through localized auxin concentrations, causing plant bending in a process known as phototropism. Due to the hormone's cellular elongation properties, it can swell the cells on one side like a balloon, bending the plant in the opposite direction from its application. It may also induce leaf epinasty, where leaves bend downward "as result of disturbances in their growth, with greater expansion in adaxial cells as compared to abaxial surface cells" [4].

==Cytokinin==
The plant hormone cytokinin, produced in leaf tissues of plants, is primarily found in nature as a compound known as zeatin. Interestingly, "almost all organisms make cytokinin; for example, isopentenyl adenine derivatives found adjacent to the anticodon loop of a subset of tRNAs in most eukaryotes and bacteria" [5]. These were first discovered while searching for factors that promote cell proliferation in plant cells in concert with auxin to regulate cell division and differentiation [5].

Cytokinins are primarily responsible for cellular division and overcoming apical dominance to stimulate lateral shoot formation. If the plant apical meristem becomes damaged, the auxin concentration of the plant falls allowing cytokinin concentrations to accumulate and activate dormant axillary buds [5]. In some cases, the auxin concentration gradient falls below levels of apical dominance near the ground, causing lateral shoot formation in a Christmas-tree like effect.

==Plant Callus Formation==
Callus formation on plants occurs as a result of wounding, infection, or unregulated and undifferentiated cellular regeneration, controlled by concentrations of auxin and cytokinin. Studies have shown "an intermediate ratio of auxin and cytokinin promotes callus induction, while a high ratio of auxin-to-cytokinin or cytokinin-to-auxin induces root and shoot regeneration, respectively" [6]. These hormones are important for infection processes in plants such as agrobacterium where transgenes are inserted into the host genome. The agrobacterium T-DNA has oncogenes which promote production of auxin and cytokinin in order to provide a favorable environment for the bacteria to reproduce and feed. This site is typically referred to as the crown gall. Eventually the plant will die, in which the bacteria are released back into the soil to begin the infection process again.

==References==
#Su, Ying-Hua, et al. “Auxin-Cytokinin Interaction Regulates Meristem Development.” Molecular plant, vol. 4, no. 4, Elsevier Inc, 2011, pp. 616–25, doi:10.1093/mp/ssr007.
#G. Eric Schaller, et al. “The Yin-Yang of Hormones: Cytokinin and Auxin Interactions in Plant Development.” The Plant Cell, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 44–63, doi:10.1105/tpc.114.133595.
#Zaman, Mohammad, et al. “Enhancing Crop Yield with the Use of N‐based Fertilizers Co‐applied with Plant Hormones or Growth Regulators.” Journal of the Science of Food and Agriculture, vol. 95, no. 9, John Wiley & Sons, Ltd, 2015, pp. 1777–85, doi:10.1002/jsfa.6938.
#Sandalio, Luisa M., et al. “Leaf Epinasty and Auxin: A Biochemical and Molecular Overview.” Plant Science (Limerick), vol. 253, Elsevier Ireland Ltd, 2016, pp. 187–93, doi:10.1016/j.plantsci.2016.10.002.
#Kieber, Joseph J., and G. Eric Schaller. “Cytokinin Signaling in Plant Development.” Development (Cambridge), vol. 145, no. 4, COMPANY BIOLOGISTS LTD, 2018, p. dev149344–, doi:10.1242/dev.149344.
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