User:Jforson/sandbox

Wikipedia evaluation

Botany Notes

• Article is detailed with many different subsections, and includes many sources.
  • Many of the sources appear to be from textbooks; others appear to be reputable.
• Though there are a lot of sources, paragraphs 2-4 in the general executive summary are lacking in-text citations even though the text appears to be paraphrased.
• Paragraph 3: "Modern Botany" has a heavy use of jargon that does not follow the style of other paragraphs found in the article. Though the sentences are cited, further re-paraphrasing edits might be necessary to avoid plagiarism.
• Scope and Importance section: the overall section might be better placed at the end of the article. Also, edits to sentences like in line 4 of paragraph 1 might be necessary.
  • The importance of paragraph 3 in this section was very confusing to figure out. The paragraph discusses the differences in opinion of the definition of "plants;" however, the paragraph never clearly leads to a concluding point as to why understanding these differences is either important or of some major scope or the subject itself.
  • There is a portion of this section that discusses the importance of plants to indigenous people. It would be interesting, maybe even helpful/more clarifying, to discuss the role of Native Americans and plant history in the History section as opposed to keeping it in the Scope and Importance/Biochemistry sections.
• Talk section: references to edits made to references and links are noted. No other major discussions have been made.
• Overall:
  • Need for organization of sections and subsections
  • Check spelling and preposition use errors throughout article
  • Review consistency of style--mainly look at use for oxford commas and other common grammar issues

Cyanobacteria Notes

• Article is simple to understand in the introduction. As the article progresses, the lack of sources makes reading the article difficult because my attention is distracted by whether or not the facts presented are accurate or not.
  • Exceptions can be found in paragraph 1 of Nitrogen fixation section and the entire Photosynthesis section. Consequently, these are also the same paragraphs that lack citations.
• Talk section: Major discussions have apparently been occurring over various controversial cyanobacteria facts, like which chlorophyll are actually present in the species.
  • The discussions strays from discussing organization and sticks with whether or not the facts are presented correctly. It is surprising that instead of seeing authors post references to prove that the current article is incorrect, the authors are simply stating the facts are wrong. I think it would helpful to use the primary method.
• The only reason most of the material seems logical is because this species was just covered in lecture on March 21.
• Citations that are posted seem reputable/legitimate and are also varied, which means a more neutral article.
• Overall:
  • Need for citations/clarification of topics mentioned in talk section

Pinophyta Notes

• Article like Cyanobacteria article is lacking a lot of citations.
  • Citations available, some, are lacking in care and legitimacy.
• Difficult to read text knowing there are a lack of sources that act as an indicator of fact check.
• It is surprising that in the Talk section there is an author who claims to be a teacher and states that she assigned students to work on references.
• Because we have not covered this species in class it is impossible to compare the article to lecture notes.
• Many sentences have a lot of jargon, making it difficult to understand.
• Great images.
• Would it be beneficial/is it better on wikipedia to use a diagram to describe a process? For this article, the process would be the life cycle.

Edits to Red Algae Wikipedia Article

https://en.wikipedia.org/wiki/User:Marioux/sandbox

Attached above is the link to the edits reviewed and made for the group wikipedia assignment.

Edited/Final Version of Red Algae Article

Introduction

Red algae, or Rhodophyta (/roʊˈdɒfᵻtə/ roh-dof-fit-tə or /ˌroʊdəˈfaɪtə/ roh-də-fy-tə; from Ancient Greek: ῥόδον rhodon, "rose" and φυτόν phyton, "plant"), are one of the oldest and largest phyla of eukaryotic algae. ^[2] Currently, scientists recognize over 7,000 species in the red algae division; however, taxonomic revisions are ongoing.[3] The majority of those species, approximately 6,793, are found in the Florideophyceae (class), and consist of mostly multicellular, marine algae, including many notable seaweeds.^[3][4] Predominantly, most red algae species are marine, but approximately 5% of the red algae occur in freshwater environments.[5][47]

The red algae form a distinct group characterized by their lack of flagella and centrioles, lack of external endoplasmic reticulum and unstacked (stoma) thylakoids in chloroplasts, and their use of chloorphyll a, phycobilins, and carotenoids to produce their distinguishing red color. ^[6] [47] Red algae store sugars as floridean starch as food reserves outside their plastids. of This type of starch consists of highly branched amylopectin without amylose. [7] The red algal life history is typically an alternation of haploid and diploid generations.[8]

Red algae, green algae, and Glaucophytes evolved from an endosymbiotic event probably between an ancestral, photosynthetic cyanobacterium and an early eukaryotic Phagotroph. [9] The event (termed Primary endosymbiosis) caused the oldest evolutionary lineages of photosynthetic eukaryotes. [10] A secondary endosymbiosis event involving an ancestral red alga and a heterotrophic eukaryote resulted in the evolution and diversification of several other photosynthetic lineages. [10]

Habitat

Unicellular members of the Cyanidiophyceae are thermoacidophiles and are found in sulphuric hot springs and other acidic environments.^[12] The remaining taxa are found in marine and freshwater environments. Most Rhodophyta are marine species with a worldwide distribution, and are often found at greater depths compared to other marine algae because of dominance in certain pigments (i.e., phycoerythrin) within their chloroplasts.^[13] Some marine species are found on sandy shores, while most others can be found attached to rocky substrata.^[13] Moreover, red algae are important in the formation of tropical reefs because they provide resistance to movement from waves. Freshwater species account for 5% of red algal diversity, but they also have a worldwide distribution in various habitats;^[5] they generally prefer clean, high-flow streams with clear waters and rocky bottoms.^[14] A few freshwater species are found in black waters with sandy bottoms ^[15] and even fewer are found in more lentic waters.^[16] Both marine and freshwater taxa are represented by free-living macroalgal forms and smaller endo/epiphytic/zoic forms, meaning they live in or on other algae, plants, and animals. ^[6] In addition, some marine species have adopted a parasitic lifestyle and may be found on closely or more distantly related red algal hosts. ^[17][18]

Fossil Record

Recently, between 2006-2011, two kinds of fossils resembling red algae were found in well-preserved sedimentary rocks in Chitrakoot, central India. The presumed red algae was found embedded in fossil mats of cyanobacteria, called stromatolites, 1.6 billion-year-old Indian phosphorite — making them the oldest plant-like fossils ever found by about 400 million years.^[19]

Prior to this discovery, scientists believed the oldest fossilized red algae was a multicellular fossil that was found in the arctic region of Canada. The fossil, Bangiomorpha pubescens, dated to 1.2 billion years ago, and was also considered the oldest fossilized eukaryote. ^[1]

Calcite crusts that have been interpreted as the remains of coralline red algae, date to the terminal Proterozoic.^[20] Thallophytes resembling coralline red algae are known from the late Proterozoic Doushantuo formation.^[21]

Red algae are noted as being very well preserved, especially those that produce calcium carbonate. The presence of calcium carbonate in red algae allows for the creation of limestone, which in turn preserves the tissues of the organism. With these optimal preserves, scientists have been working towards solving the question of the relationship between Cyanophyta, a phylum of bacteria that show similar chemistry and morphology.

Taxonomy

In the system of Adl et al. 2005, the red algae are classified in the Archaeplastida, along with the glaucophytes and green algae plus land plants (Viridiplantae or Chloroplastida). The authors use a hierarchical arrangement where the clade names do not signify rank; the class name Rhodophyceae is used for the red algae. No subdivisions are given; the authors say, "Traditional subgroups are artificial constructs, and no longer valid."^[22]

Many studies published since Adl et al. 2005 have provided evidence that is in agreement for monophyly in the Archaeplastida (including red algae).^{[23][24][25][26]} However, other studies have suggested Archaeplastida is paraphyletic.^[27][28] As of January 2011, the situation appears unresolved.

Below are other published taxonomies of the red algae using molecular and traditional alpha taxonomic data; however, the taxonomy of the red algae is still in a state of flux (with classification above the level of order having received little scientific attention for most of the 20th century).^[29]

·      If one defines the kingdom Plantae to mean the Archaeplastida, the red algae will be part of that kingdom

·      If Plantae are defined more narrowly, to be the Viridiplantae, then the red algae might be considered their own kingdom, or part of the kingdom Protista.

A major research initiative to reconstruct the Red Algal Tree of Life (RedToL) using phylogenetic and genomic approaches is funded by the National Science Foundation as part of the Assembling the Tree of Life Program.

Species of Red Algae

Over 7,000 species are currently described for the red algae,^[3] but the taxonomy is in constant flux with new species described each year.^[29][30] The vast majority of these are marine with about 200 that live only in fresh water.

Some examples of species and genera of red algae are:

·      Cyanidioschyzon merolae, a primitive red alga

·      Atractophora hypnoides

·      Gelidiella calcicola

·      Lemanea, a freshwater genus

·      Palmaria palmata, dulse

·      Schmitzia hiscockiana

·      Chondrus crispus, Irish moss

·      Mastocarpus stellatus

·      Vanvoorstia bennettiana, became extinct in the early 20th century

·      Acrochaetium efflorescens

·      Audouinella, with freshwater as well as marine species

·      Polysiphonia ceramiaeformis, banded siphon weed

Genomes of Red Algae

Complete genome sequences are only available for 5 species of red algae, including 4 published in 2013.

·      Cyanidioschyzon merolae, Cyanidiophyceae^[32][33]

·      Galdieria sulphuraria, Cyanidiophyceae^[34]

·      Pyropia yezoensis, Bangiophyceae^[35]

·      Chondrus crispus, Florideophyceae^[36]

·      Porphyridium purpureum, Porphyridiophyceae^[37]

 Relationship to Chromalveolata chloroplasts

Chromalveolates seem to have evolved from bikonts that have acquired red algae as endosymbionts. According to this theory, over time these bikonts and their endosymbiont red algae evolved into chromalveolates and chloroplasts. This part of endosymbiotic theory is supported by various structural and genetic similarities.^[38]

Chemistry

The δ¹³C values of red algae reflect their lifestyles. The largest difference results from their photosynthetic metabolic pathway: algae that use HCO₃ as a carbon source have less negative δ¹³C values than those that only use CO₂.^[39] An additional difference of about 1.71‰ separates groups intertidal from those below the lowest tide line, which are never exposed to atmospheric carbon. The latter group uses the more ¹³C-negative CO₂ dissolved in seawater, whereas those with access to atmospheric carbon reflect the more positive signature of this reserve.

The presence of δ¹³C also reflects an important chemical and preservation process for red algae and are related toδ¹³C carbon calcification processes. Currently, it is unclear as to the function and importance of calcification. One highly agreed upon hypothesis is that calcification allows for production of carbon dioxide that is later used for photosynthesis [47].

Morphology

The molecular structure of red algae is a distinguishing factor between the species and others in the Archaeplastida supergroup. Red algae cells do not contain centrioles or flagellated cells, rather, they have specialized microtubules [47]. Red algae have double cell walls.^[40] The outer layers contain the polysaccharides agarose and agaropectin that can be extracted from the cell walls by boiling as agar ,and the internal walls are mostly cellulose.^[40]  

Red algae are red due to phycoerythrin. They contain the sulfated polysaccharide carrageenan in the amorphous sections of their cell walls, although red algae from the genus Porphyra contain porphyran. They also produce a specific type of tannin called phlorotannins, but in a lower amount than the brown algae.

Pit connections

Pit connections, or pit plugs, are unique and distinctive features of red algae that form during the process of cytokinesis following mitosis.^[41][42] In red algae, cytokinesis is incomplete. Typically, a small pore is left in the middle of the newly formed partition. The pit connection is formed where the daughter cells remain in contact.

Shortly after the pit connection is formed, cytoplasmic continuity is blocked by the generation of a pit plug, which is deposited in the wall gap that connects the cells.

Connections between cells having a common parent cell are called primary pit connections. Because apical growth is the norm in red algae, most cells have two primary pit connections, one to each adjacent cell.

Connections that exist between cells not sharing a common parent cell are labeled secondary pit connections. These connections are formed when an unequal cell division produced a nucleated daughter cell that then fuses to an adjacent cell. Patterns of secondary pit connections can be seen in Ceramiales, an order of the red algae group.^[42]

After a pit connection is formed, tubular membranes appear. A granular protein, called the plug core, then forms around the membranes. The tubular membranes eventually disappear. While some orders of red algae simply have a plug core, others have an associated membrane at each side of the protein mass, called cap membranes. The pit connection continues to exist between the cells until one of the cells dies. When this happens, the living cell produces a layer of wall material that seals off the plug [48].

Function

The pit connections have been suggested to function as structural reinforcement, or as avenues for cell-to-cell communication and transport in red algae, however there is still inadequate data to support this hypothesis.

Reproduction

The reproductive cycle of red algae may be altered by a variety of factors such as day length, light quality, temperature, season, nutrients, osmotic stress, pH, wave motion, and pollution. Plant growth regulators can also act as chemical signals that alter the reproductive cycle. The life cycles of red algae are considered to be highly complex, involving transitioning between unicellular to multicellular organisms. [49] ^[2]

Fertilization

Red algae lack motile sperm. Hence, they rely on water currents to transport their gametes to the female organs – although their sperm are capable of "gliding" to a carpogonium's trichogyne.^[2]

The trichogyne will continue to grow until it encounters a spermatium; once it has been fertilized, the cell wall at its base progressively thickens, separating it from the rest of the carpogonium at its base.^[2]

Upon their collision, the walls of the spermatium and carpogonium dissolve. The male nucleus divides and moves into the carpogonium; one half of the nucleus merges with the carpogonium's nucleus.^[2]

The polyamine spermine is produced, which triggers carpospore production.^[2]

Spermatangia may have long, delicate appendages, which increase their chances of "hooking up".^[2]

Life cycle

They display alternation of generations; in addition to gametophyte generation, many have two sporophyte generations, the carposporophyte-producing carpospores, which germinate into a tetrasporophyte – this produces spore tetrads, which dissociate and germinate into gametophytes.^[2] The gametophyte is typically (but not always) identical to the tetrasporophyte.^[44]

Carpospores may also germinate directly into thalloid gametophytes, or the carposporophytes may produce a tetraspore without going through a (free-living) tetrasporophyte phase.^[44] Tetrasporangia may be arranged in a row (zonate), in a cross (cruciate), or in a tetrad.^[2]

The carposporophyte may be enclosed within the gametophyte, which may cover it with branches to form a cystocarp.^[44]

These case studies may be helpful to understand some of the life histories algae may display:

In a simple case, such as Rhodochorton investiens:

In the Carposporophyte: a spermatium merges with a trichogyne (a long hair on the female sexual organ), which then divides to form carposporangia – which produce carpospores.

Carpospores germinate into gametophytes, which produce sporophytes. Both of these are very similar; they produce monospores from monosporangia "just below a cross wall in a filament"^[2] and their spores are "liberated through apex of sporangial cell."^[2]

The spores of a sporophyte produce either tetrasporophytes. Monospores produced by this phase germinate immediately, with no resting phase, to form an identical copy of parent. Tetrasporophytes may also produce a carpospore, which germinates to form another tetrasporophyte.^{[[[Wikipedia:Verifiability|verification needed]]][2]}

The gametophyte may replicate using monospores, but produces sperm in spermatangia, and "eggs"(?) in a carpogonium.^[2]

A rather different example is Porphyra gardneri:

In its diploid phase, a carpospore can germinate to form a filamentous "conchocelis stage", which lives inside a conch giving the shellfish flesh a pinkish color. Carpospores can also self-replicate using monospores. The conchocelis stage eventually produces conchosporangia. The resulting conchospore germinates to form a tiny prothallus with rhizoids, which develops to a cm-scale leafy thallus. This too can reproduce via monospores, which are produced inside the thallus itself.^[2] They can also reproduce via spermatia, produced internally, which are released to meet a prospective carpogonium in its conceptacle.^[2]  

^{Human consumption}

^Porphyra is commonly used as the outer wrapping of sushi.

^{Several species are important food crops, in particular members of the genus Porphyra, variously known as nori (Japan), gim (Korea), or laver (Britain). Dulse (Palmaria palmata)[45]is another important British species.[46] In East and Southeast Asia, agar is most commonly produced from Gelidium amansii. Rhodophyta are known to produce a diverse array of secondary metabolites, more so than brown or green algae. In particular, red algae mainly produce halogenated compounds such as laurenterol, halomon, and callicladol [50]. These compounds have a variety of properties, including acting as antibacterial, antifungal, anti-inflammation, cytotoxic, and insecticidal agents[51].}

Additional References

^{[48] Dawes, C. J., Scott, F. M., & Bowler, E. (1961). A light-and electron-microscopic survey of algal cell walls. I. Phaeophyta and Rhodophyta. American Journal of Botany, 925-934.}

[47] Evert, Ray F.; Eichhorn, Susan E. (2013). Biology of Plants. New York, NY: W.H. Freeman and Company    Publishers

^{[49[ García-Jiménez, P., & Robaina, R. R. (2015). On reproduction in red algae: further research needed at the        molecular level. Frontiers in plant science, 6.}

^{[50] Kasanah, N., Triyanto, T., Seto, D. S., Amelia, W., & Isnansetyo, A. (2015). Antibacterial Compounds}

^{from Red Seaweeds (Rhodophyta). Indonesian Journal of Chemistry, 15(2), 201-209.}

^{[51] Raja, A., Vipin, C., & Aiyappan, A. (2013). Biological importance of Marine Algae-An overview. Int. J.}

^{Curr.Microbiol. Appl. Sci, 2, 222-227.}