Wikipedia talk:USEP/Courses/JHU MolBio Ogg 2012/Section 83/Group 83E

Hi Group 83E, Let's try and organize how we will be tackling the articles in order to drill it down to our choice article to work on. Any ideas will be appreciated. Seguncha (talk) 15:46, 5 October 2012 (UTC)

Choosing Article

Hey Group,

I was thinking best choice for our project would be the article that has the least amount of content. Meaning we kind of have a blank canvas to work with. The more we can contribute the better our overall grade should be.

Makselrod (talk) 00:35, 8 October 2012 (UTC)

I agree. Can we start by drilling this down to the worse in content article. Then, we may want to choose the best topic that we can then expand on. Can we all look at what it out there and then provide the three worse in content article? Then if we have a consensus on the worse in content article, we can then start working to improve it. Any other thoughts?Seguncha (talk) 17:08, 8 October 2012 (UTC)

I agree as well, it will definitely be easier to contribute with a blank canvas. I'm going through some of the articles now and will provide some feedback. Skhan58 (talk) 22:35, 15 October 2012 (UTC)

Three good picks

Group,

After going through the different topics for the project I have found three that I believe would be good picks for us.

Oskar - deals w/ fruit flies, some info in our required textbook. Plenty of info available online. Topics to cover Oskar would be talking about the mRNA and proteins sides of Oskar and what else we feel is relevant.

Homeotic selector gene - PLENTY of info in the text and online.

Trans-acting siRNA - not my favorite option but the wikipedia article is pretty much blank so its an option.

PLEASE include your picks as this is a first-come-first-served basis!!! I was thinking a group chat option maybe through Yahoo or JHU if its available would be helpful in discussing the subject matter, and dividing out tasks for the group so that we can maintain a timeline to make sure we have our work completed by the due dates. Let me know what you think. 98.207.95.15 (talk) 05:47, 11 October 2012 (UTC)

Not sure why Wikipedia logged me out, and it didn't leave my name after my comments above but yea. Makselrod (talk) 05:49, 11 October 2012 (UTC)

Hi, Makselrod, I think the comment above should be a new section, because it is not indented, and you're starting a new discussion thread. So I went ahead and added a section title to it. I also turned your article names into links -- that's a nice thing to do to make it a little easier for your readers to get to the articles. Klortho (talk) 11:36, 11 October 2012 (UTC)

Hey Makselrod, I like the Homeotic selector gene topic, so far that has my vote but I am still doing some research. Skhan58

Hey Group, I narrowed my preferences down to Homeotic selector gene or DnaC. DnaC is briefly mentioned in the textbook on bage 235 and 241, and there have been various studies on it in E.Coli. Skhan58 22:30, 15 October 2012 (UTC)

Hey Group, dnaC is a good topic but I think it may be difficult to only concentrate on that one subject without talking about dnaA and dnaB all the time. Skhan58, Do you have any ideas on how we could only concentrate on dnaC? Homeotic selector gene is my pick, if you can think of a better topic please let me know. If we could pick the topic tonight that would be great. We still have to write up a one page summary by tmrw night. Makselrod (talk) 23:34, 15 October 2012 (UTC)

Hi Group 83E, do you think you will be selecting Homeotic selector gene? If so, could someone post on the 83A page if that is the case so we don't scoop you? Thank you. Aehall47 (talk) 23:46, 15 October 2012 (UTC)

Aehall47, there is a good chance that is the subject we are going with, I am waiting for the rest of my group to respond. If you could leave that subject it would be greatly appreciated, but I do understand that it is first-come-first-served basis. Makselrod (talk) 23:57, 15 October 2012 (UTC)

I say lets do Homeotic selector gene! We need the okay of our last partner! Skhan58 (talk) 00:13, 16 October 2012 (UTC)

Seguncha, by any chance have you made up your mind on the topic? Skhan58 and I have decided on Homeotic selector gene let us know if that is okay with you as a summary of why we picked this topic still needs to be done by this evening. Makselrod (talk) 19:44, 16 October 2012 (UTC)

Makselrod, I think we should select the topic now since it's 8 pm. Also, I drafted a quick rationale which needs improvement, you and Seguncha can edit and make additions. Let's have our topic selected by 9 pm hopefully. Skhan58 (talk) 23:57, 16 October 2012 (UTC)

I'm going to select the topic we picked now. I started doing research on the topic. I will add to the information that you have already provided. Makselrod (talk) 00:14, 17 October 2012 (UTC)

Make sure any edits are done on the project page and not the talk page! I just added a new section to the project page and transferred over what I wrote here onto the project page. Seguncha, feel free to email us if wikipedia isn't the best form of communication! Skhan58 (talk) 02:21, 17 October 2012 (UTC)

Unit 6 Article Selection Rationale

Hey group,

I decided to get started on the rationale, please make edits since this is just a rough draft.

Homeotic selector genes are a class of regulatory genes which are responsible for diversification of body segments in Drosophila development. Two examples of these genes include Antp, Antennapedia, and Ubx, Ultrabithorax. The Antp gene is responsible the mesothorax, the middle segment of the thorax which produces a pair of legs which are distinct from the forelegs and hindlegs. The Ubx gene codes the protein which develops the third thoracic segment, called the metathorax. Drosophila are used as a model system which expand the understanding of human genetics. The drosophila genome is easily manipulated, isolated and identified, which makes way for novel discoveries. The complement of these homeotic selector genes are known as Hox genes in Humans, which were first discovered in 1984 by William McGinnis. Studying mutations in these genes in drosophila lead to the understanding that Hox gene mutations can lead to deformed limbs. We choose to expands the topic of Homeotic selector genes are Wikipedia due to the plethora of information available both in our textbook and in various publications. There is enough knowledge on this topic which has yet to be consolidated in one webpage, such as Wikipedia. We will be able to make a significant contribution to the Wikipedia community through our research of homeotic selector genes. Skhan58 (talk) 22:06, 16 October 2012 (UTC)

I added the rationale of why we picked our topic, and what we can improve upon based on what is considered Wikipedia:Good article criteria. The info is already on the project page. Feel free to add any additional information. Makselrod (talk) 02:59, 17 October 2012 (UTC)

I did a complete write up for the article that was selected. Can I email to the two of you to have your input and edits before we officially post it online at our page. Since you worked on the rationale, I took the liberty of doing the write up and you can add to what I have written if that is okay by you. Seguncha (talk) 20:08, 27 October 2012 (UTC)

Seguncha, Since this is our talk page for the project, it may be better if we just edit all contributions here since this is how we show our contributions to the project. Makselrod (talk) 21:57, 27 October 2012 (UTC)

Article rationale assignment feedback

You should not be signing your contributions on the project page, with four tildes. Signing posts like that is exclusively for talk pages. Klortho (talk) 18:40, 17 October 2012 (UTC)

Article Draft

Here we go group, I am including the complete write up below. We can make changes and edits before we post it to the official user page. I could not get the pictures to show. Does anyone know how to include pictures?Seguncha (talk) 15:45, 29 October 2012 (UTC)

Homeotic Selector Genes

Description: The human body continues to be more complex as we develop in life and in this growing complexity there are simplifying feature that creates a better understanding of the whole developmental process. Complex structures are made by repeating a few basic themes with variations in every species and at every level of organization. There are subtle individual variations in different sites amongst basic differentiated cell types such as muscle cells or fibroblasts which are organized into a limited variety of tissue types, such as muscle or tendon which are repeated with subtle variations in the different regions of the body. An example is the fact that various tissues organs such as teeth or digits, molars and incisors are built as well as variations that arise from fingers and thumbs and toes with repeated structure variations. This process is called modulated repetition hence creating a scenario that raises a lot of questions: what are the basic construction mechanism that is similar to all the objects of the given class, and how is this mechanism changed in order to give the observed variations? The segments of the insect body provide a very clear example of such a variation and changes.

History of Homeotic Selector Genes: Through the genetic analysis of Drosophila, over 80 years ago, the homeotic gene was discovered which created some bizarre disturbances of the organization of the adult fly. This discovery provided a glimpse of a genetic answer to the question of how each segment acquires its individual identity. According to In the Antennapedia mutant, for example, legs sprout from the head in place of antennae (Figure1)1, while in the bithorax mutant, portions of an extra pair of wings appear where normally there should be the much smaller appendages called halteres1. Some homeotic genes controls the development of mouth parts and antennae from head segments while others control the formation of wings and halters from thoracic segments.

Homeotic: Mutation that transform parts of the body into structures appropriate to other positions is called homeotic.

Homeotic Genes: Homeotic selector genes are an important class of developmental regulators that causes diversification to occur in the morphology of the different body segments as depicted in Drosophila. Invertebrate genome contains about eight (8) to ten (10) homeotic genes which are located within a single complex. However, the Drosophila genome has a total of eight (8) homeotic genes which is organized in two gene clusters or complexes; the Antennapedia complex and the Bithorax Complex. Vertebrates have duplicated the ancestral Hox complex and contain four (4) clusters. Changes in the expression and function of homeotic genes are responsible for the changes in the morphology of the libs of arthropods as well as in the axial skeletons of vertebrates.

Bithorax Complex: The genes in the bithorax complex control the differences among the abdominal and thoracic segments of the body in the Drosophila fly.

Antennapedia Complex: The genes in the antennapedia complex control the differences among thoracic and head segments of the Drosophila fly. In doing comparisons with other species, it is determined that the same genes are present in essentially all animals, including humans.

Hox Complex: The Hox complex comprises of both the Antennapedia and bithorax complexes that has become split in the course of the evolution of the Drosophila fly. These complexes are both coordinated in a way that they help to exert control over the head-to-tail pattern of the body of the fly.

Figure 1 Homeotic Mutation: Antennapedia mutant is the fly that is depicted in Fig. 1. Its antennae are converted into leg structures by a mutation in the regulatory region of the Antennapedia gene that causes it to be expressed in the head.

Types of Homeotic Genes: • Antp • Ubx Antp and Ubx are homeotic genes that suppress development of Antennae and Wings in the Drosophila fly.

Antp (Antennapedia): This homeotic gene controls the development of the mesothorax which is the middle segment of the thorax. Although the mesothorax of the fly typically will produce legs that are morphologically different from the forelegs and hind legs, Antp encodes a homodomain regulatory protein (that is expressed in the mesothorax) of the developing embryo of the fly which typically is not expressed in other areas. However, in dominant Antp mutation which is caused by a chromosome inversion changes the control of Antp protein-coding sequence to be taken over by a foreign regulatory DNA that mediates gene expression in head tissues which affects the antennae. Mis-expression of the gene in the head causes a change in the fly’s morphology. I.e. Legs develop instead of antennae.

Ubx (Ultrabithorax): This homeotic gene controls encodes the homodomain regulatory protein that controls the development of the third thoracic segment called the metathorax. Ubx represses expression of genes that are responsible for the development of the mesothorax by suppressing Antp expression in the developing embryo of the fly. However, a mutant of the fly that lacks the Ubx repressor has an abnormal Antp expression which creates a situation where there is Antp expression in the mesothorax and mis-expression in the developing metathorax. The mis-expressed Antp creates the transformation of the metathorax into duplicate mesothorax (the fly has two pairs of wings rather than one set of wings and one set of halters). In the mutant strain, the halteres have been transformed by the mis-expression of Ubx into a set of wings. Mesothorax contains a pair of legs and wings while Metathorax contains a pair of legs and halteres (halteres are smaller than the wings of the fly and helps to balance the fly during a flight).

Homeotic Selector Genes Code for DNA-Binding Proteins That Interact with Other Gene Regulatory Proteins: On a visual evaluation, it seems like each homeotic selector gene is normally expressed only in the regions that develop abnormally when the gene is mutated or absent. The products of these genes may then be viewed as a molecular address label possessed by the cells of each para-segment which then seems like the physical embodiment of the cells' positional value. Then, If the address labels are changed for some reason, the para-segment will now behave as if it were located somewhere else, and deletion of the entire complex will result in a larva whose body segments look alike (see Figure 2).

Figure 2 The effect of deleting most of the genes of the bithorax complex: (A) A normal Drosophila larva shown in dark-field illumination; (B) the mutant larva with the bithorax complex largely deleted. In the mutant the para-segments posterior to P5 all have the appearance of P5. (From G. Struhl, Nature 293:36–41, 1981. © Macmillan Magazines Ltd.) Understanding how the homeotic selector gene products act on the basic segment-patterning machinery to give each para-segment its individuality. The products of the homeotic selector genes are gene regulatory proteins which all relate to one another by the possession of a highly conserved DNA-binding homeodomain which is approximately 60 amino acids long. The corresponding segment in the DNA sequence is called a homeobox from which, by abbreviation, the Hox complex takes its name. The similarity of the homeotic selector genes to their DNA-binding regions and how they exert different effects so as to make one para-segment different from the next lies largely in the parts of the proteins that do not bind directly to DNA but interact with other proteins in DNA-bound complexes. The different partners in these complexes act together with the homeotic selector proteins to dictate which DNA-binding sites will be recognized and whether the effect on transcription at those sites will be activation or repression. In this way, the products of the homeotic selector genes combine with other gene regulatory proteins and modulate their actions so as to give each para-segment its characteristic features1.

The Homeotic Selector Genes Are Expressed Sequentially According to Their Order in the Hox Complex: In order to understand how the Hox complex provides cells with positional values a consideration was given to how the expression of the Hox genes themselves is regulated. The coding sequences of the eight homeotic selector genes in the Antennapedia and bithorax complexes are interspersed amid a total of about 650,000 nucleotide pairs of regulatory DNA. The regulatory DNA in the Hox complex acts as an interpreter of the multiple items of positional information supplied to it by all these gene regulatory proteins. In response, a particular set of homeotic selector genes is transcribed, appropriate to the location. The sequence by which the genes are ordered along the chromosome, in both the Antennapedia and the bithorax complexes corresponds almost exactly to the order in which they are expressed along the axis of the body (Figure 3). This finding suggests that the genes are activated serially by some process that is graded in duration or intensity along the axis of the body, and whose action spreads gradually along the chromosome. The most “posterior” of the genes expressed in a cell generally dominates, driving down expression of the previously activated “anterior” genes and dictating the character of the segment.

Figure 3 The patterns of expression compared to the chromosomal locations of the genes of the Hox Complex: The sequence of genes in each of the two subdivisions of the chromosomal complex corresponds to the spatial sequence in which the genes are expressed. There are hundreds of other homeobox-containing genes in the genome of the fly and of other animal species but most of them are scattered and not clustered in complexes such as the Hox complex. They have many different gene regulatory functions, but a substantial proportion of them have roles akin to that of the Hox genes: they control the variations on a basic developmental theme. Different classes of neurons, for example, are often distinguished from one another by expression of specific genes of this large superfamily. The Hox Complex Carries a Permanent Record of Positional Information The spatial pattern of expression of the genes in the Hox complex is set up by signals acting early in development, but the consequences are long-lasting. Although the pattern of expression undergoes complex adjustments as development proceeds, the Hox complex behaves in each cell as though stamped with a permanent record of the anteroposterior position that the cell occupied in the early embryo. In this way, the cells of each segment are equipped with a long-term memory of their location along the anteroposterior axis of the body. (I.e. anteroposterior positional value). The memory trace imprinted on the Hox complex governs the segment-specific identity not only of the larval segments, but also of the structures of the adult fly, which are generated at a much later stage from the larval imaginal discs and other nests of imaginal precursor cells in the larva.

The molecular mechanism of the cell memory for this positional information relies on two types of regulatory inputs. One is from the homeotic selector genes themselves: many of the Hox proteins autoactivate the transcription of their own genes. Another crucial input is from two large complementary sets of transcriptional regulators called the Polycomb group and the Trithorax group. If these regulators are defective, the pattern of expression of the homeotic selector genes is set up correctly at first but is not correctly maintained as the embryo grows older. The Two Sets of Regulators Act in Opposite Ways. Trithorax Group Proteins: Trithorax group proteins are needed to maintain the transcription of Hox genes in cells where transcription has already been switched on. Polycomb Group Proteins: Polycomb group proteins form stable complexes that bind to the chromatin of the Hox complex and maintain the repressed state in cells where Hox genes have not been activated at the critical time. (Figure 4). The developmental memory involves acetylation of histone H4 at specific regulatory sites in the chromatin adjacent to the Hox genes; the proteins of the Trithorax and Polycomb groups act somehow to perpetuate the H4 state hyperacetylated if the target Hox gene has been transiently exposed at embryonic stages to an activator of gene transcription, not acetylated in this way otherwise (see Figure 8).

Figure 4 Action of Genes of the Polycomb Group: (A) Photograph of a mutant embryo defective for the gene extra sex combs (esc) and derived from a mother also lacking this gene. The gene belongs to the Polycomb group. Essentially all segments have been transformed to resemble the most posterior abdominal segment (compare with Figure 2). In the mutant the pattern of expression of the homeotic selector genes, which is roughly normal initially, is unstable in such a way that all these genes soon become switched on all along the body axis. (B) The normal pattern of binding of Polycomb protein to Drosophila giant chromosomes, visualized with an antibody against Polycomb. The protein is bound to the Antennapedia complex (ANT-C) and the bithorax complex (BX-C) as well as about 60 other sites. (from G. Struhl, Nature 293:36–41, 1981. © Macmillan Magazines Ltd; B, courtesy of B. Zink and R. Paro, Trends Genet. 6:416–421, 1990. © Elsevier.) The Anteroposterior Axis Is Controlled by Hox Selector Genes in Vertebrates Also Homologs of the Drosophila homeotic selector genes have been found in almost every animal species studied, from cnidarians (hydroids) and nematodes to molluscs and mammals. Remarkably, these genes are often grouped in complexes similar to the insect Hox complex. In the mouse there are four such complexes called the HoxA, HoxB, HoxC, and HoxD complexes each on a different chromosome. Individual genes in each complex can be recognized by their sequences as counterparts of specific members of the Drosophila set. Indeed, mammalian Hox genes can function in Drosophila as partial replacements for the corresponding Drosophila Hox genes. It appears that each of the four mammalian Hox complexes is, roughly speaking, the equivalent of a complete insect complex (that is, an Antennapedia complex plus a bithorax complex) (Figure 5).

Figure 5: The genes of the Antennapedia and bithorax complexes of Drosophila are shown in their chromosomal order in the top line; the corresponding genes of the four mammalian Hox complexes are shown below, also in chromosomal order. The gene expression domains in fly and mammal are indicated in a simplified form by color in the cartoons of animals above and below. However, the details of the patterns depend on developmental stage and vary somewhat from one mammalian Hox complex to another. Also, in many cases, genes shown here as expressed in an anterior domain are also expressed more posteriorly, overlapping the domains of more posterior Hox genes (see, for example, Figure 6). The complexes are thought to have evolved as follows: first, in some common ancestor of worms, flies, and vertebrates, a single primordial homeotic selector gene underwent repeated duplication to form a series of such genes in tandem—the ancestral Hox complex. In the Drosophila sub-lineage this single complex became split into separate Antennapedia and bithorax complexes. Meanwhile, in the lineage leading to the mammals the whole complex was repeatedly duplicated to give four Hox complexes. The parallelism is not perfect because apparently some individual genes have been duplicated, others lost, and still others coopted for different purposes (genes in parentheses in the top line) since the complexes diverged. (Based on a diagram kindly supplied by William McGinnis.) The ordering of the genes within each vertebrate Hox complex is essentially the same as in the insect Hox complex, suggesting that all four vertebrate complexes originated by duplications of a single primordial complex and have preserved its basic organization. Most tellingly, when the expression patterns of the Hox genes are examined in the vertebrate embryo by in situ hybridization, it turns out that the members of each complex are expressed in a head-to-tail series along the axis of the body, just as they are in Drosophila (Figure 6). The pattern is most clearly seen in the neural tube, but is also visible in other tissues, especially the mesoderm. With minor exceptions this anatomical ordering matches the chromosomal ordering of the genes in each complex, and corresponding genes in the four different Hox complexes have almost identical anteroposterior domains of expression.

Figure 6: The photographs show whole embryos displaying the expression domains of two genes of the HoxB complex (blue stain). These domains can be revealed by in situ hybridization or, as in these examples, by constructing transgenic mice containing the control sequence of a Hox gene coupled to a LacZ reporter gene, whose product is detected histochemically. Each gene is expressed in a long expanse of tissue with a sharply defined anterior limit. The earlier the position of the gene in its chromosomal complex, the more anterior the anatomical limit of its expression. Thus, with minor exceptions, the anatomical domains of the successive genes form a nested set, ordered according to the ordering of the genes in the chromosomal complex. (Courtesy of Robb Krumlauf) The gene expression domains define a detailed system of correspondences between insect body regions and vertebrate body regions (see Figure 5). The para-segments of the fly correspond to a similarly labeled series of segments in the anterior part of the vertebrate embryo. As shown in Figure 7, these are most clearly demarcated in the hindbrain, where they are called rhombomeres. In the tissues lateral to the hindbrain the segmentation is seen in the series of branchial arches, prominent in all vertebrate embryos—the precursors of the system of gills in fish and of the jaws and structures of the neck in mammals; each pair of rhombomeres in the hindbrain corresponds to one branchial arch (Figure 7). In the hindbrain, as in Drosophila, the boundaries of the expression domains of many of the Hox genes are aligned with the boundaries of the anatomical segments.

Figure 7: The pattern of HoxB gene expression is indicated by coloring as in Figure 5. For simplicity, the expression in tissues other than the central nervous system is not shown. In regions where the expression domains of two or more Hox genes overlap, the coloring corresponds to the most “posterior” of the genes expressed. Just as the expression domains in the fly are related to para-segments, so the expression domains in the vertebrate are related to the rhombomeres (segments in the hindbrain). Each pair of rhombomeres is associated with a branchial arch (a modified gill rudiment), to which it sends innervation. The pattern of Hox gene expression in the branchial arches (not shown) matches that in the associated rhombomeres. In the spinal cord, there are no rhombomere boundaries, and the expression domains of the different posterior Hox genes overlap. The products of the mammalian Hox genes appear to specify positional values that control the anteroposterior pattern of parts in the hindbrain, neck, and trunk. Eliminating the function of a Hox gene in the mouse leads to a defect in a body region that corresponds to the domain of expression of that gene. Sometimes the affected body region is transformed into a more anterior body region, as in Drosophila homeotic mutants; sometimes the affected body region dies or fails to grow. The transformations observed in mouse Hox mutants are often incomplete, perhaps because of a redundancy between genes in the four Hox gene clusters. But it seems clear that the fly and the mouse use essentially the same molecular machinery to give individual characters to successive regions along at least a part of their anteroposterior axis.

Cbx (Contrabithorax) Mutation: Cbx mutation disrupts the Ubx regulatory DNA that is responsible for the expression of Ubx in the different tissues of the metathorax without changing the Ubx protein encoding region. When there is Cbx mutation, Ubx is then mis-expressed in the metathorax as well as its normal site of expression in the metathorax. This means that Ubx represses the expression of Antp as well as other genes that are responsible for the development of the mesothorax. The mesothorax creates duplicate copies of metathorax whereby the fly becomes wingless but has sets of a pair of halteres instead of a pair of wings and halteres.

Causes of Arthropod Diversity: The diversity of arthropods stems in part from the fact that they have some modular architecture with a series of repeating body segments that can be modified in numerous ways.

Changes in Morphology of Crustaceans: There are different patterns of Ubx expression in isopods and branchiopods. For the isopods, the possible explanation is due to the fact that Ubx regulatory DNA of isopods was acquired by mutation which allows the Ubx enhancers to no longer mediate expression in the first thoracic segment.

Src Expressions in Branchiopods: Src expression which is limited to the head region helps in the development of feeding appendages in brachiopods. Ubx is expressed in the thorax where it controls the development of swimming limbs.

Src Expression in Isopods: Src expression is detected in both the head and the first thoracic segment (T1) in isopods and as a result, the swimming limb in T1 is transformed into a feeding appendage (the maxillipped). The posterior expansion of Src was made possible by the loss of Ubx expression in T1 because Ubx normally represses Src expression.

Reasons why insects Lack Abdominal Limbs: Some insects have limbs throughout their thoracic segment while others have six limbs representing 2 on each thoracic segment. The reason is that there is functional changes in the Ubx regulatory proteins in those insects that that do not have limbs in their entire thoracic segments.

In insects, Ubx and abd-A represses the critical gene called Distal-less (DII) that is required for the development of limbs. Drosophila: In Drosophila, embryo, Ubx is expressed in high levels in the metathorax and anterior abdominal segments, abd-A expression extends into more posterior abdominal segments. In combination, Ubx and abd-A does not allow DII to function in the first seven abdominal segments.

Crustaceans: In crustaceans, there are high levels of both Ubx and DII in all 11 thoracic segments. The expression of DII promotes the development of swimming limbs. The reason why Ubx protein does not repress DII in crustaceans is because of Ubx has diverged (functionally different) between insects and crustaceans.

Summary/Conclusion: The complexity of the adult body of an animal is built up by modulated repetition of a few basic types of structure. Thus, superimposed on the pattern of gene expression that repeats itself in every segment, there is a serial pattern of expression of homeotic selector genes that confer on each segment a different identity. The homeotic selector genes code for DNA-binding proteins of the homeodomain family. They are grouped in the Drosophila genome in two clusters, called the Antennapedia and bithorax complexes which is believed to be the two parts of a single primordial Hox complex that became split during evolution of the fly. In each complex, the genes are arranged in a sequence that matches their sequence of expression along the axis of the body. Hox gene expression is initiated in the embryo. It is maintained subsequently by the action of DNA-binding proteins of the Polycomb and Trithorax group, which stamp the chromatin of the Hox complex with a heritable record of its embryonic state of activation. Hox complexes homologous to that of Drosophila are found in virtually every type of animal that has been examined, from cnidarians to humans, and they appear to have an evolutionarily conserved role in patterning the anteroposterior axis of the body. Mammals have four Hox complexes, each showing a similar relationship between a serial arrangement of the genes in the chromosome and their serial pattern of expression along the body axis.

References: 1. Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. 2. G. Struhl, Nature 293:36–41, 1981. © Macmillan Magazines Ltd. 3. James D. Watson, Tania A. Baker, Stephen P. Bell, Alexander Gann, Michael Levine, Richard Losick. Molecular Biology of the Genes. Sixth Edition. Pages 693-701 4. http://www.ncbi.nlm.nih.gov/books/NBK26913/ 5. Watson D. James, Baker A. Tania, Bell P. Stephen, Gann Alexander, Levine Michael. Losick Richard. Molecular Biology of the Genes. Sixth Edition. Seguncha (talk) 15:45, 29 October 2012 (UTC)

Group Discussion of the Article Draft

Hey Seguncha, this looks great. We will have to make sure that we have the proper permissions for images. I will carefully go through what you have provided so far and suggest edits. Also, let's try and make sure that it's an easy read because wikipedia is pretty much where everyone goes to get the basics. I have started working on the Unit 9 Progress report and will post it here for you guys to see. great work so far Seguncha! 137.187.241.4 (talk) 18:40, 31 October 2012 (UTC)

Thanks. I will await your modification and we can proceed to post on the user page. Ideally, we should quote the source of any picture and figure. I still have the pictures when we are ready to post in the user page.Seguncha (talk) 14:21, 3 November 2012 (UTC)

Seguncha, I've reviewed your write-up, the amount of information that you have provided is awesome. I have one general critique, although the amount of information you have is great, we need references to back up the information that you were able to gather. I did see the 5 references you have provided. The following topics have no references: Reasons why insects Lack Abdominal Limbs, Src Expression in Isopods, Changes in Morphology of Crustaceans, among others. I will try to find references for the ones that are missing but if you still have them saved on your computer that will make it a lot easier. If it is OK with you and Skhan58 I would like to start transferring your write-up onto the actual Wikipedia page. We can add the references as we find them. Having the info you have provided on the actual page will let the previous editors on the subject be able to contribute resulting in a more solid article.

You mention quite a few images, figures, and diagrams, I will try to add the images to the article page, as well as the information already provided by the end of Monday.

The report that I believe Skhan58 has already started for the group needs to include the following information. Any progress made so far on improving the article - I believe we have a great level of improvement that has been made to the article. Any significant interactions you've had with other Wikipedia editors. Were they helpful? Did any edits you made get reverted? - I think we are lacking this completely right now which is why I would like to transfer Seguncha's edit to the article page. To-do list for improvements that you plan to make in the remaining weeks - One improvement is hopefully interact with other editors. - Finalize all edits, and have references to back up all the information which we add to the article. - Include pictures, diagrams; any visual aids that may help viewers of the article to better understand the subject matter. Any other problems or concerns - I don't foresee any problems or concerns as we still have plenty of time to fully complete all the requirements for the article prior to the December deadline. Makselrod (talk) 08:03, 5 November 2012 (UTC)

Okay by me to transfer the article over to the user page. I can provide the pictures for you by email to transfer to the user page. With regards to the references that Makselrod was refering to, the additional references for those topics were from Watson et al. Molecular Biology of the Genes. Please include it in the write up. Seguncha (talk) 20:58, 6 November 2012 (UTC)

Our progress report is due today. Has anyone written it yet? Seguncha (talk) 21:05, 6 November 2012 (UTC)

The progress report is already on the project page. Makselrod (talk) 04:41, 7 November 2012 (UTC)

Seguncha, can you send me the pictures that you have for the article? I will message you my email to your wiki email. Makselrod (talk) 05:05, 19 November 2012 (UTC)

Feedback on article draft

Hi, I have some feedback and a question. First, please try to follow the guidelines for this talk page a little better than you have been. Please remember to:

• Start a new section whenever you are starting a new "thread" of discussion
• Always sign your comments on this talk page with four tildes
• When you respond to someone else's comment, always indent your response one more than that person did.

These conventions exist so that others (like me) can follow the conversation that you've been having. It is not so critical on this group page, but it will become important when you interact with other Wikipedia editors. If you are still unsure about these, please go back and re-watch the tutorial video about talk pages.

Next, the question: where are you guys actively working on your article? I see a very impressive draft above -- is it being actively edited by the whole group? If so, where? I would strongly urge you to go ahead and put this content into the actual Wikipedia article page now, and then continue to edit and revise there. That is the "wiki way". Editing is a collaborative effort, and part of this assignment is to get you to start to interact with the wider Wikipedia community. You shouldn't expect to get your article perfect, and then transfer it to the real article page. Move it now, even if it has some inconsistencies and some "warts", and then keep working on it, collaboratively, from there.

Cheers! Klortho (talk) 01:59, 9 November 2012 (UTC)

Article Peer Review

Hey guys! I'm from group 83F and we have been assigned to peer review the article you are improving (Homeotic selector gene). I went to the article page and it looks like you have not yet put much of your information into the article; we are in the same boat! It does seem that you have quite an amazing draft here on your Talk page! There are many great sections and sub-sections that will provide lots of good information on the Homeotic selector gene. Well done! I guess my advice would be to go ahead and take this draft and insert it onto that actual article page. Then you could maybe get some feedback from some other Wikipedia editors and it will be easier for your whole group to make edits along the way. One thing that I did notice in your draft is that you may need to add a few more sources (references) and footnotes to go along with it. Below I have links to two really great citing tools to use for articles that have PMIDs or DOIs. You can literally just copy the PMID or DOI number and paste it into one of the tools and it will create the "coding" you need to insert on your editing page to create the footnotes. They are great!!! I would maybe recommend trying them out in your respective sandboxes first so that you know how they work. Here are the links:

http://sumsearch.org/cite/

http://reftag.appspot.com/doiweb.py?doi=10.1093%2Fhmg%2F7.2.227

Again, your draft here on the Talk page is looking really great!! I will keep checking in for the remaining weeks of the semester and try to do my part in giving you some useful review remarks! Rexsmiley (talk) 02:02, 19 November 2012 (UTC)

Rexsmiley, Thanks for the advice, I am currently transferring the article to the article page. Anything to make citing our work easier is always greatly appreciated. Makselrod (talk) 05:02, 19 November 2012 (UTC)

I just helped move the remaining parts of the draft over, we still need to move the references over as Maskelrod has said. Skhan58 (talk) 15:51, 19 November 2012 (UTC)

Skhan58, As soon as Seguncha lets me know what references go to what subject matter I can add them in. Same goes for all the figures. Makselrod (talk) 23:15, 19 November 2012 (UTC)

Hi guys! Nice job on your progress! I'm really impressed with the amount of information that you guys have already! Another helpful hint on references - when you cite your references using the 'cite journal' button, you just have to type in the doi or PMID and click on the magnifying glass - it will auto-populate the information. I'm also really impressed with how you can garner all those information from just few sources. Are you guys planning to add the figures that you're describing? Keep up the good work! Sytae (talk) 20:22, 24 November 2012 (UTC)

Hi, I just read this (usually I just glance at these comments, so I often overlook things). The prefered reference-generation tool for the WikiProject we're engaged with is Dilberri's template-filling tool. Each one formats the reference in a slightly different way, so it's nice to use this one for consistency's sake. You can just fill in the PubMed ID, and check the "Add ref tag" box, and then hit submit. Let me know if you have any problems. Klortho (talk) 15:50, 25 November 2012 (UTC)

Please move your content into the Helicase article

Hi! Why isn't your draft content, above, integrated into the Homeotic selector gene article yet? This should have been done weeks ago. Klortho (talk) 03:23, 19 November 2012 (UTC)

Just moved it over, we should make edits directly on the article page correct?Skhan58 (talk) 16:01, 19 November 2012 (UTC)

Thanks, that's correct! Klortho (talk) 22:37, 19 November 2012 (UTC)

Questions Regarding Article Draft

Seguncha,

What reference should I add to the following subjects:

Homeotic

Homeotic Genes

Bithorax Complex

Antennapedia Complex

Hox Complex

Types of Homeotic Genes

Ubx (Ultrabithorax)

Cbx (Contrabithorax) Mutation

Causes of Arthropod Diversity

Changes in Morphology of Crustaceans

Src Expressions in Branchiopods

Src Expression in Isopods

Reasons why insects Lack Abdominal Limbs

Crustaceans

Makselrod (talk) 07:20, 19 November 2012 (UTC)

Images

Wikipedia has some extreme restrictions when it comes to the use of images. The images that I received from Seguncha via email are either from a textbook or by a published article, which means we need permission to use those images. I uploaded two images, and I was told that if it is not a admissible copyright status the image will be deleted after one week. I am afraid we may have some difficulty uploading images, and having them still being on our page after a week. We may have to use the commons section for images, which all the images are already confirmed for copyrights and are good to use. Let me know if anyone has any suggestions on how to get permission to use the images. Makselrod (talk) 08:00, 26 November 2012 (UTC)

Actually, it's not Wikipedia that is extreme, it's that most other venues you've been involved with are very lax. Wikipedian's are just very diligent about enforcing copyright laws, mostly to protect themselves from lawsuits, since their pockets are not very deep. Rather than try to get permissions for particular copyrighted images, I'd suggest you'd have better luck if you try to find different images that have suitable licenses. That means CC-BY or CC-BY-SA. Two places you can find images are the Wikimedia Commons and the PMC open access subset. I'm not too sure how to search Wikimedia Commons -- you might google around for help.

For PMC, you can find the open access articles by adding "AND open access[filter]" to the end of your search, like, for example, here. I just tried that and the first hit is this article, which has some nice images. The license is CC-BY, which is good (you can see that at the top of the article, click on "Copyright and license information", and you'll see it says "This is an open-access article distributed under the terms of the Creative Commons Attribution License".) Hope that helps. Klortho (talk) 12:24, 27 November 2012 (UTC)

2nd Peer Review

Hey guys! I put the message below on your actual article (Homeotic selector gene) Talk page as well. Just wasn't sure where would be the best place for you to view it! ;-)

I'm just giving you another review to try and help out with editing the article. Great job in getting all your content transferred to the article page! It looks like it is coming together for you quite well! Congrats!

In reviewing the article, I found a few things that could use some editing/improvement. Some of the suggestions below, you may know about, and others maybe not. And keep in mind, these are my opinions, so use them at your discretion if they can be helpful at all.

1. There are several places in the text that need some grammatical corrections to make the noun match the action of the verb of the sentence. For example, from your "Description" section, "The human body continues to be more complex as we develop in life and in this growing complexity there are simplifying feature that creates a better understanding of the whole developmental process"

To make the sentence grammatically correct it should read: The human body continues to become more complex as we develop in life and in this growing complexity, there are simplifying features that create a better understanding of the whole developmental process.

This is just one example, but there are several like this throughout the article. Just give it a good (slow) read-through to make some of these minor corrections.

2. There are a few sentences that seem to run-on and/or don't seem to make sense to me. An example from the article would be "An example is the fact that various tissues organs such as teeth or digits, molars and incisors are built as well as variations that arise from fingers and thumbs and toes with repeated structure variations. This process is called modulated repetition hence creating a scenario that raises a lot of questions: what are the basic construction mechanism that is similar to all the objects of the given class, and how is this mechanism changed in order to give the observed variations?"

Again, I think just reading through the article a few times and you can catch many of these types of sentences that may need some re-structering and/or clarification.

3. Another thing I noticed is that under your "History" section you have the terms "Hox Complex, Homeotic Genes, Bithorax Complex, Antennapedia Complex, and Homeotic". I wonder if it would be a good idea to maybe include a section prior to the "History" section and simply name it "Definitions" or something similar. You could then move the aforementioned terms and their respective descriptions to that section. Just a thought. May help to understand prior to reading further into the article.

4. Another thing I noticed, is that there are several terms throughout the article that could be "wiki-linked" to other articles on Wikipedia. Just a few examples include: halteres, Antennapedia, bithorax, and Drosophila. It is pretty easy to add these types of links by simply putting brackets around them if there is a Wikipedia article relating to them.

For example: Drosophila

5. The last thing for this review that I wanted to mention is that you may need a few more sources (citations) for your article content; unless a lot of your content came from just a few scientific journals. I'm not sure if you have seen these, but the links below are two really great citing tools that basically make the in-line citations for you simply by inputting the PMID or DOI. They are as follows:

http://sumsearch.org/cite/

http://reftag.appspot.com/doiweb.py?doi=10.1093%2Fhmg%2F7.2.227

Well, that is all for now. Like I said, I hope that these suggestions can be of some value to you. I will try to take another look at your article by the end of the week to see if I can be of any more assistance. Great Job! Rexsmiley (talk) 04:39, 27 November 2012 (UTC)

Rexsmiley, you bring up a lot of good points, and I have to agree with you on the basis of grammatical errors, and run-on sentences. The limited amount of sources is definitely is a concern and is something that we are working on. Thank you for all the great advice, any additional points in improving our article are greatly appreciated. Makselrod (talk) 05:02, 27 November 2012 (UTC)

Unit 12 Progress report

I have added a progress report for unit 12 which is due today. Please add your peer review suggestions that you made to the group we are peer reviewing today. Makselrod (talk) 23:47, 1 December 2012 (UTC)

Hey I think you did a great job in covering what we have to do, I added a few things to the to do list. There are plenty of places we have to rearrange and proofread as you have highlighted in the progress report. Skhan58 (talk) 00:44, 2 December 2012 (UTC)

Hey guys, I tried adding one of the images Seguncha emailed me however it was removed by Wikipedia. Since the other images are from the same source we may not have much luck...any suggestions? Skhan58 (talk) 06:04, 6 December 2012 (UTC)

You can often find suitably licensed images by searching on Wikimedia commons. Here is a list of a few search tools that you can try to use to search Wikimedia Commons. Or, you can try looking at related Wikipedia articles, to see if any of them might have a similar figure. If it's used in one article, you can reuse it for your article. Or, you can search for open access articles in PMC, and the scan through those articles to see if they have good figures you can use. Try this search. Klortho (talk) 13:40, 9 December 2012 (UTC)

Final Week

Hey group, I'm editing the article and reorganizing somethings. Although I know the draft must have taken much time and effort, I am deleting some sections like Conclusion and Description as they are usually not found in wikipedia articles. For now, we have to find figures that we can use. I am holding off on deleting the figure headers and content underneath until we can figure out how to use them, but if we can not, I suggest we remove those sections from the page, as they make it very confusing. Let me know what you all think. Skhan58 (talk) 18:31, 10 December 2012 (UTC)

I have added images from the wikimedia commons section. Images that we can actually use, and will not get deleted. As far as the 7 or 8 figures that are referenced in the article, the best we can do is keep relevant information but delete the wording were we reference an image. I will do my best to find additional images to add to the article page. Makselrod (talk) 07:06, 14 December 2012 (UTC)

A final progress report has been added to the project page, feel free to make changes or additions to the report. Makselrod (talk) 05:15, 15 December 2012 (UTC)