Hey guys can you read this?

[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!