Hey guys can you read this?

[425nm]

So for the term paper of my Genetics 408 class (at the UofA) I decided to write my paper on a genetic phenomenon in Octocorals!
The instructions for the paper were to write an article that anyone could read on a topic related to Genetics, so since Canreef has a diverse array of posters I was wondering if you guys could give me some feedback?
If you guys could skim through and post about anything you didn't understand or would like expanded on that'd be awesome.
Its due on Monday (I only just finished this quasi-final draft) so if I could get some feedback by Sunday evening that'd be awesome. If not I'd still be interested in knowing what people think of it.
Thanks!
Liam Brinston.


The Octocorals: a story of genetic nesting dolls



Corals capture the imagination with their bizarre appearance and their ability to photosynthesize. It is often a surprise for many to learn despite their photosynthetic abilities corals are in fact animals. The ability of Corals to photosynthesize is derived from a partnership with zooxanthellae, small algae that lives in the coral skeleton (8). These algae provide the coral with energy from photosynthesis and the coral provides the zooxanthellae with shelter and other nutrients. Corals are also considered Eukaryotes, meaning they possess mitochondria. The mitochondria are the organs of the cell, they are the power house of the cell as they generate energy for the cell. Scientists believe that mitochondria to have once been a free living bacterium that formed a partnership with a bigger organism. This partnership is similar to the partnership between corals and their zooxanthellae. Over time the mitochondria’s partnership became so close that it became part of the bigger organism, giving rise to Eukaryotes. Due to their free living past, mitochondria have retained their own set of DNA or genome, called the mitochondrial genome (mtGenome). This mtGenome contains instructions for the running of the mitochondria but not its building. As the partnership progressed many of the genes from the mtGenome were exported to the nuclear genome of its partner. The nuclear genome is what is conventionally thought of as the blue print of the cell and also contains the instructions for building mitochondria. The mtgenome is shared by all Eukaryotes but often differs somewhat in size and less often in gene order but rarely does it differ in the genes.

Corals are a sort of genetic nesting doll. Corals house zooxanthellae which is a separate organism, possessing its own genome. The Zooxanthellae themselves contain organelles similar to the plastids of plants, the photosynthetic cellular organ of plants which like mitochondria may have once been free living. Corals also possess mitochondria, which has its own genome and was once a separate organism. In one group of corals, the Octocorals which are comprised of the gorgonians, sea pens and soft corals, this nesting goes one step deeper. The mtGenome of the Octocorals possess an additional gene. The addition of a gene to the mtGenome has not been observed in any other group of organisms (1). Interestingly the Octocoral sister sub-family, the Hexacoralia: anemones, zoanthids, and the stony corals (6), lacks this gene but it has been found in every Octocoral to date. This confirms that the Octocoralia and Hexacoralia are genetically distinct from one another. The presence of this gene in all Octocorals suggests that it is providing some advantage to the Octocorals, however its absence in all other corals tells us that it is not essential for the function of coral mitochondria (1).

The gene in question is a copy of MutS. A gene originally found in E. coli, also present in Humans (refered to as MSH – MutS Homolog in humans) this gene is part of a DNA repair system. In E. coli MutS detects DNA damage, and signals to other proteins to repair it but is not able to repair the damage itself (5). The Octocorallian mitochondrial MutS (mtMutS) appears to have acquired a modification that will allow mtMutS to potentially carry out the repair process by itself (1). The presence of a gene does not necessarily mean that it is working however Bilewitch and Degnan (1) were able to detect the expression of mtMutS in three separate Octocoral species. If a working mtMutS is being produced it may explain why the mtGenome of the Octocorals appears to be evolving slower than the mtGenome of the Hexacorallia. Alternatively this slower change in the Octocoral genome can be viewed as indirect evidence of mtMutS working. Interestingly the mtMutS gene itself seems to be evolving faster than the rest of the mtGenome but not as fast as the mtGenome of the Hexacorallia. How exactly mtMutS is stabilizing the Octocoral mtGenome is unclear. It is likely that the stabilization effect is the result of mtMuts carrying out DNA repair as it retains the necessary components to do so (1). A similar stabilizing effect is seen in plants that lose a copy of the nuclear MutS that is made outside of the mitochondria then transported to the mitochondria. These plants have an increase in reshuffling of mitochondrial genes resulting from double strand breaks in mitochondrial DNA (10). It is possible that mtMutS is preventing such breaks in the DNA from occurring in the mtGenome of the Octocorals. Despite inversions, reversal of gene order, being rather rare in the Octocoral mtGenome, it has occurred at least three times (9). These inversions are speculated to have occurred by misalignment of double stranded DNA leading to a double strand break (9). This is a very similar situation to the damage suppressed by MutS in plants (10).

When mtMutS was first discovered it was thought that it was the ancestral copy of MutS from the mitochondria’s time as a free living bacterium (3). However this has recently been called into question by Ogata et al. (7) who showed that the mtMutS is more closely related to a MutS genes belonging to NucleoCytoplasmic Large DNA Viruses (NCLDV) and epsilonproteobacteria, than either the E. coli or the Human MutS. The E. coli copy of mutS would be more similar to mtMutS if it was a relic of the bacterial mitochondria MutS. Additionally the NCLDV MutS also possess the same component believed to allow mtMutS to operate independently (7). Both Bilewitch and Degnan (1) and Ogata et al. (8) showed that together the Octocoral mtMutS, NCLDV mutS, and epsilonproteobacteria mutS form a unique subfamily of mutS proteins, the mutS7. These two studies provide strong support for mtMutS having arisen from a transfer of the MutS gene from either the NCLDV or an epsilonproteobacteria to the ancestral Octocoral mitochondria. This passing of DNA from one organism to another is called a Horizontal Gene Transfer (HGT). HGT are rare however NCLDVs are highly abundant in marine environments (Claverie et al. 2009) and corals are well known for their association with a diverse array of microorganisms including the Proteobacteria (4). This viral introduction of the mtMutS gene additionally calls into question the origin of Human mutS which was until now assumed to have come from the ancestral mitochondria.

It is currently unknown if NCLDVs are able to infect Octocorals, however there is evidence that they are able to infect sponges (2). The means by which mtMutS would have made its way from an NCLDV to the mitochondria of the Octocoral is also unclear, as NCLDVs have yet to demonstrate the ability to infect mitochondria. Mitochondrial infecting viruses are known infect terrestrial fungi. This unique evolutionary event provides a tool for identifying any coral that belongs to the Octocorals. The variability of the mtMutS gene may also assist scientists in determining the species boundaries within the Octocorals, as currently morphological groupings provide an incomplete picture. The occurrence of such a rare event bears significant repercussions for the understanding of evolution. Previous to this discovery a HGT event occurring in the mitochondrial was considered so unlikely it was never considered a possibility. The role that NCLDVs have played and currently are playing in the evolution of marine organisms has yet to be fully grasped.


Literature Cited:

1. Bilewitch P. J., and Degnan M. S. 2011. A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function. BMC Evolutionary Biology. 11: 228. 1471-2148.
2. Claverie J-M., Grzela R., Lartigue A., Bernadac A., Nitsche S., Vacelet J., Ogata H., and Abergel C. 2009. Mimivirus and Mimiviridae: Giant viruses with an increasing number of potential hosts, including corals and sponges. Journal of Invertebrate Pathology. 101. 172-180.
3. Culligan M. K., Meyer-Gauen G., Lyons-Weiler J., and Hays B. J. 2000. Evolutionary origin, diversification and specialization of eukaryotic MutS homolog mismatch repair proteins. Nucleic Acids Research. 28:2. 463-471.
4. Lee O. O., Yang J., Bougouffa S., Wang Y., Batand Z., Tian R., Al-Suwailem A., and Qian P-Y. 2012. Spatial and Species Varaitions in Bacterial Communities Associated with Corals from the Red Sea Revealed by Pyrosequencing. Applied and Environmental Microbiology. 78:20. 7173-7184.
5. Malik S. H. and Henikoff S. 2000. Dual recognition-incision enzymes might be involved in mismatch repair and meiosis. TIBS 25. 414-418.
6. McFadden S. C., Sanchez A. J., and France C. S. 2010. Molecular Phylogenetic Insights into the Evolution of Octocorallia: A Review. Integrative and Comparative Biology. 50: 3. 389-410.
7. Ogata H., Ray J., Toyoda K., Sandaa R-A., Nagasaki K., Bratbak G., and Claverie J-M. 2011. Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment. International Society for Microbial Ecology. 5. 1143-1151.
8. Stat M., Baker C. A., Bourne G. D., Correa M. S. A., Forsman Z., Huggett J. M., Pochon X., Skillings D., Toonen J. R., van Oppen J. H., and Gates D. R. 2012. Molecular Delineation of Species in the Coral Holobiont. Advances in Marine Biology. 63. 1-65.
9. Uda K., Komeda Y., Koyama H., Koga K., Fujita T., Iwasaki N., and Tomohiko S. 2011. Complete mitochondrial genomes of two Japanese precious corals, Paracorallium japonicum and Corallium konojoi (Cnidaria, Octocorallia, Coralliidae): Notable differences in gene arrangement. Gene. 476. 27-37.
10. Xu Y., Arrieta-Montiel P. M., Virdri S. K., de Paula B.M. K., de Paula B.M. W., Widhalm R. J., Basset J. G., Davila I. J., Elthon E. T., Elowasky G. C., Sato J. S., Clemente E. T., and Mackenzie A. S. 2011. MutS HOMOLOG1 Is a Nucleoid Protein That Alters Mitochondrial and Plastid Properties and Plant Response to High Light. The Plant Cell. 23: 3428-3441.

[Reef_Geek]

It's a good paper. As a TA I would have given it a good grade. It reads more like a graduate level paper than undergrad.

If you feel so inclined, maybe some background info such as:
-coral phylogenies have largely focused on skeletal structures
-this is not possible with many soft corals, especially those lacking spicules
-mitochondrial DNA appears to be a better means to investigate coral phylogenies
-coral appearances can differ under different environmental conditions, for the same species
Maybe some good questions:
-what is the application? to identify species, biochemical processes that produce promising medical compounds?
-is there merit to sequencing coral genetics? biomedical applications?
-are there any ah-ha's? like all along we thought some corals were the same but in fact they are not...

It's pretty good as is, but if you want to later tweak it... I ended up publishing many of my school papers just giving them complete overhauls to suit a hobbyist audience. You can get a few hundred bucks an article from the likes of TFH, as long as you've changed it so that it's something a reader would be interested in reading. You may also want to ask the mods to pull this post. You can't submit an article that you've already submitted/posted elsewhere... as publishers are buying the "first publication rights"

[425nm]

Thanks for the feedback man
I hope to make it Grad school, some day maybe. If my GPA is high enough.
I probably should expand on how Coral phylogenetic arrangements are currently envisioned.
I'm not sure how you'd get biomedical applications out of it. Unless it turns out that the mtMutS's function turns out to be radically different from all over mutS proteins. Which is possible since no one has performed any structural or functional studies on the mtMutS7 class.
I could maybe talk more about the NCLDV. They're super super interesting. I actually found a paper that proposed that they might form the fourth domain of life. Whether or not they've got a strong enough argument it'll be years before that's recognized.

Anyone else have comments, or thoughts? Absolutely anything helps.

[Reef_Geek]

I don't think you have to make changes for the sake of making changes. It's fine for its purpose.

I meant in the broader sense... why study coral protein expression and its molecular pathways (thus linked to their genetics)? because of novel compounds with potential medical applications.

a quick search in Web of Sci found these on the first page of results:

Bioactive pregnane-type steroids from the soft coral Scleronephthya gracillimum
Author(s): Fang, HY (Fang, Hui-Yu)1; Liaw, CC (Liaw, Chih-Chuang)1,4; Chao, CH (Chao, Chih-Hua)1; Wen, ZH (Wen, Zhi-Hong)1; Wu, YC (Wu, Yang-Chang)2; Hsu, CH (Hsu, Chi-Hsin)1; Dai, CF (Dai, Chang-Feng)3; Sheu, JH (Sheu, Jyh-Horng)1,4
Source: TETRAHEDRON Volume: 68 Issue: 47 Pages: 9694-9700 Published: NOV 25 2012
Times Cited: 0 (from Web of Science)
Cited References: 36 [ view related records ] Citation Map
Abstract: Nine new steroids, sclerosteroids A-1 (1, 5, 6, 8-13), along with 18 known metabolites (2-4, 7, 14-27), were isolated from the soft coral Scleronephthya gracillimum. These structures were elucidated on the basis of detailed spectroscopic analysis. The absolute configurations of sugar moieties in steroidal glycosides 10-13 were determined by HPLC analysis of the o-tolylthiocarbamate derivatives of the liberated sugars from hydrolysis of these steroidal giycosides. Cytotoxic and anti-inflammatory activities of these compounds were measured in vitro. (c) 2012 Elsevier Ltd. All rights reserved.


Pavidolides A-E, new cembranoids from the soft coral Sinularia pavida
Author(s): Shen, S (Shen, Shi)1; Zhu, HJ (Zhu, Huajie)2; Chen, DW (Chen, Dawei)1; Liu, D (Liu, Dong)1; van Ofwegen, L (van Ofwegen, Leen)3; Proksch, P (Proksch, Peter)4; Lin, WH (Lin, Wenhan)1
Source: TETRAHEDRON LETTERS Volume: 53 Issue: 43 Pages: 5759-5762 DOI: 10.1016/j.tetlet.2012.08.049 Published: OCT 24 2012
Times Cited: 0 (from Web of Science)
Cited References: 20 [ view related records ] Citation Map
Abstract: Five new cembrane-based diterpenoids, namely pavidolides A-E (1-5) were isolated from the marine soft coral Sinularia pavida, together with sarcophytin and chatancin. The structures of new compounds were determined on the basis of extensive spectroscopic data analysis. Pavidolide B (2) possesses an unprecedented 6,5,7-tricarbocyclic nucleus, whereas pavidolide C (3) is characteristic of an unusual C-5 and C-9 conjuncted cembranoid. Pavidolides C and D showed moderate antifouling activity against the larval settlement of barnacle Balanus amphitrite, while pavidolides B and C exhibited inhibitory activity against the human leukemia cell line HL-60. (C) 2012 Elsevier Ltd. All rights reserved.

Proteomic profiling of the 11-dehydrosinulariolide-treated oral carcinoma cells Ca9-22: Effects on the cell apoptosis through mitochondrial-related and ER stress pathway.
Author(s): Liu, Chih-I; Wang, Robert Yung-Liang; Lin, Jen-Jie; Su, Jui-Hsin; Chiu, Chien-Chih; Chen, Jiing-Chuan; Chen, Jeff Yi-Fu; Wu, Yu-Jen
Source: Journal of proteomics Volume: 75 Issue: 18 Pages: 5578-89 DOI: 10.1016/j.jprot.2012.07.037 Published: 2012-Oct-22 (Epub 2012 Aug 03)
[ PubMed Related Articles ]
Abstract: An oral squamous cell carcinoma Ca9-22 cell line was treated with 11-dehydrosinulariolide, an active compound isolated from the soft coral Sinularia leptoclados, in order to evaluate the effect of this compound on cell growth and protein expression. Cell proliferation was strongly inhibited by 11-dehydrosinulariolide treatment. The 2-DE master maps of control and treated Ca9-22 cells were generated by analysis with the PDQuest software. The comparison between such maps showed up- and down-regulation of 23 proteins, of which 14 were upregulated and 9 were downregulated. The proteomic studies described here have identified some proteins, which are involved in the mitochondrial dysfunction and ER-stress pathway and imply that 11-dehydrosinulariolide induces cell apoptosis through either mitochondrial dysfunction-related or ER stress pathway. Based on this observation, several proteins related to apoptosis pathway were explored for the potential roles involved in this drug-induced cytotoxicity. Furthermore, Salubrinal, an ER stress inhibitor, is able to protect the cell from 11-dehydrosinulariolide-induced apoptosis in a physiological dosage. The significance of these studies illustrates the potential development of anticancer drugs from the natural derivatives of soft coral. Copyright 2012 Elsevier B.V. All rights reserved.

Digital Marine Bioprospecting: Mining New Neurotoxin Drug Candidates from the Transcriptomes of Cold-Water Sea Anemones
Author(s): Urbarova, I (Urbarova, Ilona)1,2; Karlsen, BO (Karlsen, Bard Ove)1,2; Okkenhaug, S (Okkenhaug, Siri)1,2; Seternes, OM (Seternes, Ole Morten)3; Johansen, SD (Johansen, Steinar D.)1,2,4; Emblem, A (Emblem, Ase)1,2
Source: MARINE DRUGS Volume: 10 Issue: 10 Pages: 2265-2279 DOI: 10.3390/md10102265 Published: OCT 2012
Times Cited: 0 (from Web of Science)
Cited References: 45 [ view related records ] Citation Map
Abstract: Marine bioprospecting is the search for new marine bioactive compounds and large-scale screening in extracts represents the traditional approach. Here, we report an alternative complementary protocol, called digital marine bioprospecting, based on deep sequencing of transcriptomes. We sequenced the transcriptomes from the adult polyp stage of two cold-water sea anemones, Bolocera tuediae and Hormathia digitata. We generated approximately 1.1 million quality-filtered sequencing reads by 454 pyrosequencing, which were assembled into approximately 120,000 contigs and 220,000 single reads. Based on annotation and gene ontology analysis we profiled the expressed mRNA transcripts according to known biological processes. As a proof-of-concept we identified polypeptide toxins with a potential blocking activity on sodium and potassium voltage-gated channels from digital transcriptome libraries.

[Reef_Geek]

I showed your article to my wife. She is a researcher in genetics, and have graded many undergraduate papers. Here's what she wrote:

Hi Liam,
Interesting article! I have a few recommendations that should help out:
General:
• Overall, try to be more concise in your writing. It will be easier to read once you remove some of the superfluous language, and it should help with the general flow of the article. For instance, in your introduction you use the word ‘cell’ three times in one sentence, when mentioning it once would be sufficient. You also spend a lot of time discussing the origins of the mitochondria throughout the article, when you really only need to mention this once in the introduction.
• Pay attention to grammar and what you capitalize. For example, sometimes you have zooxanthellae capitalized and other times you don’t. Keep this consistent throughout your article. Also be conscious of when something is plural (eg. zooxanthellae) and keep your verb tenses in agreement with that.
• In your second paragraph you mention an additional gene that the Octocorals possess. Rather than waiting until the third paragraph to name this gene, mention the name there and then go into further detail about the gene/protein in the next paragraph.
• Similar to my first point, don’t repeat information. Repeatedly mentioning that this particular gene is found in Octocorals, for example, becomes redundant.
• Pay attention to how you reference your sources, and be consistent in how you do this. For instance, use all numbers or all names to cite your sources, don’t mix them up. It’s also easier to read when you include your citation at the end of a sentence rather than in the middle of it.
The Science:
• You begin the article talking about corals as nesting dolls, corals and zooxanthellae, etc. However, reading your article the focus seems to be more the mitochondrial genome and its role in evolution, using Octocorals and the MutS gene as an example of this. It might be a good idea to introduce this somewhere in your introduction (for example, as a thesis statement) to make the article more cohesive and to set the focus of the article earlier on.
• Along the same lines, flesh out what you write about the mitochondria. Talk about how in many species, mitochondrial DNA is only inherited from the mother and the role that it plays in phylogenetics. I think that this would add some relevant background information to your introduction and perhaps help to put the importance of mitochondrial DNA and the significance of the MutS gene into perspective for your audience.
• When you mention that the mitochondrial genome is unique from the nuclear genome, give a couple of examples. What processes/pathways/proteins are unique to the mitochondria and why are they important?
• When you introduce the MutS gene, you mention that there are similar genes in humans, E.coli and plants. It would be a nice addition to include the % similarities between these genes and the gene found in the corals of interest, and it would also add perspective to how similar/dissimilar these genes are.
• When discussing the role of MutS in DNA repair, briefly mention the repair pathways that the protein is involved in. Is it involved in the repair of certain types of DNA damage? It would also be really helpful to add a figure that illustrates how MutS functions in these different pathways (eg. in E.coli vs. Octocorals would be a really nice figure because you specifically mention that they are different and that this difference is significant). You should be able to modify figures that represent this from the papers you have referenced, or from another review paper.
• You discuss a MutS subfamily. A phylogenetic tree demonstrating this subfamily would also be a really nice addition allowing the reader to visualize what you mean by a subfamily. As I mentioned before, you may be able to find something like this in a paper that you’ve already referenced or from a review paper that you can modify.
• You discuss the evolution of the Octocoral mitochondrial genome vs. the Hexacoral mitochondrial genome. Include some of the results from the papers that you reference to back up your statements.
• When you are writing gene names vs. protein names, they should be written differently. One is italicized and the other is not. You should check which is which and apply those to your article. This will help to differentiate when you are discussing the gene vs. the protein.
• Don’t say that a gene is ‘working’, say that it is expressed.
• When you mention that this gene was expressed in three species of coral, mention the names of these corals.
• You may want to include a closing paragraph that wraps up the point of your article. As it is, you conclude by talking about horizontal gene transfer and viruses which you had only recently introduced. Talk about the MutS gene, the significance of its expression in these corals and what this means in general for the science of evolution/phylogenetics etc. Start specific and end on a general note. As it is currently, I’m left wondering “what does it all mean in the bigger picture of genetics and evolution” after I finish your last paragraph.
Overall, I think that your article is interesting and I really like the subject matter. Aside from some grammatical issues that are easily corrected, I think that modifying your introduction to make it clear that the focus of your article is the mitochondrial genome and its significance in studying evolution will make a huge impact. Adding actual data from the papers you reference to support your statements and writing a good closing paragraph will make for an excellent, well-rounded paper. Good luck!