Submited on: 24 Feb 2011 03:23:19 PM GMT
Published on: 25 Feb 2011 10:19:15 PM GMT
 

1 Is the subject of the article within the scope of the subject category? Yes
2 Are the interpretations / conclusions sound and justified by the data? Yes
3 Is this a new and original contribution? Yes
4 Does this paper exemplify an awareness of other research on the topic? Yes
5 Are structure and length satisfactory? Yes
6 Can you suggest brief additions or amendments or an introductory statement that will increase the value of this paper for an international audience? No
7 Can you suggest any reductions in the paper, or deletions of parts? No
8 Is the quality of the diction satisfactory? Yes
9 Are the illustrations and tables necessary and acceptable? Yes
10 Are the references adequate and are they all necessary? Yes
11 Are the keywords and abstract or summary informative? Yes
  • Other Comments:

    This is an excellent paper exploring a novel area of genomic research by examining the potential impacts of SNPs upon predicted RNA structures from transcribed regions of the human genome.

  • Competing interests:
    No
  • Invited by the author to review this article? :
    No
  • Have you previously published on this or a similar topic?:
    No
  • References:
    None
  • Experience and credentials in the specific area of science:

    Experienced in areas of comparative genomics and the use of bioinformatics to explore structure function relationships of genes and encoded proteins.

  • How to cite:  Holmes R S.Review of paper by Johnson and coworkers on the impacts of SNPs on RNA structures in transcribed regions of the human genome[Review of the article 'RNA Structures Affected By Single Nucleotide Polymorphisms In Transcribed Regions Of The Human Genome ' by Sadee W].WebmedCentral 2011;2(5):WMCRW00718
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Intersting manuscript
Posted by Dr. Ciarmiello LF on 04 Apr 2011 09:29:28 AM GMT

1 Is the subject of the article within the scope of the subject category? Yes
2 Are the interpretations / conclusions sound and justified by the data? Yes
3 Is this a new and original contribution? Yes
4 Does this paper exemplify an awareness of other research on the topic? Yes
5 Are structure and length satisfactory? Yes
6 Can you suggest brief additions or amendments or an introductory statement that will increase the value of this paper for an international audience? Yes
7 Can you suggest any reductions in the paper, or deletions of parts? Yes
8 Is the quality of the diction satisfactory? Yes
9 Are the illustrations and tables necessary and acceptable? Yes
10 Are the references adequate and are they all necessary? Yes
11 Are the keywords and abstract or summary informative? Yes
  • Other Comments:

    I'm in agreement with manuscript's content. In the article, according with other authors, Dr AD Johnson et al., suggest that there is a strongly relationship between mRNA 3D structure and biological significance. Indeed, they evidenced that the mRNA 3D structure is influenced by SNPs.

     

    I suggest to improve the quality of illustrations n. 5 and 6 and to verify the correspondence between illustration's number and legend below illustrations.

     

  • Invited by the author to review this article? :
    Yes
  • Have you previously published on this or a similar topic?:
    Yes
  • References:
    Ciarmiello L. F., Piccirillo P., Pontecorvo G., De Luca A. and Woodrow P. 2010. A PCR based SNPs marker for specific characterization of English walnut (Juglans regia L.) cultivars. Molecular Biology Reports [I.F.= 2.038]. DOI 10.1007/s11033-010-0223-y
  • Experience and credentials in the specific area of science:

    Fingerprintig analysis of plants by detection of SNPs. Prediction of RNA secondary structure and phylogenetic analysis.

  • How to cite:  LF C .Intersting manuscript[Review of the article 'RNA Structures Affected By Single Nucleotide Polymorphisms In Transcribed Regions Of The Human Genome ' by Sadee W].WebmedCentral 2011;2(4):WMCRW00640
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1 Is the subject of the article within the scope of the subject category? Yes
2 Are the interpretations / conclusions sound and justified by the data? Yes
3 Is this a new and original contribution? Yes
4 Does this paper exemplify an awareness of other research on the topic? Yes
5 Are structure and length satisfactory? Yes
6 Can you suggest brief additions or amendments or an introductory statement that will increase the value of this paper for an international audience? Yes
7 Can you suggest any reductions in the paper, or deletions of parts? Yes
8 Is the quality of the diction satisfactory? Yes
9 Are the illustrations and tables necessary and acceptable? Yes
10 Are the references adequate and are they all necessary? No
11 Are the keywords and abstract or summary informative? Yes
  • Other Comments:

    The article of Dr. Andrew D Johnson et. al. suggests, that mRNA has 3D structure and it has some biological significance. This is a simple and logical statement, it is still controversial. The “classical” view is that mRNA is like a tape which passes the translation machinery like the tape passes a tape-recorder. Any structure is only disturbing complication if you adopt this simple view of translation.  

    Biotech. industry is very liberal to introduce changes into mRNA to increase the yield of protein syntheses and the efficiency of the production and they are totally unaware of the possible biological consequences of the changes. It is completely OK for them to introduce mutations into the mRNA sequence, as far as it is silent, i.e. has no effect on the sequence of the protein product.

    Johnson’s article is very welcomed because it shows that mRNA has 3D structure and it is strongly influenced by SNPs.

    The major insufficiency of Johnson’s paper is that he never riches the most exciting consequences of the mRNA structure formation, namely that mRNA structure might provide information to protein folding. This idea, called “nucleic acid mediated protein folding” of “mRNA chaperons” was published in in 2005. Therefore the reader is kindly advised to study the following articles to fully understand the scientific value of Johnson’s article.

    Biro JC: Nucleic acid chaperons: a theory of an RNA-assisted protein folding. Theoretical Biology and Medical Modelling 2005, 2:35 (1 September 2005)

    Biro JC: Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases. Theoretical Biology and Medical Modelling 2008, 5:14 (29 July 2008)

    Biro JC: Does codon bias have an evolutionary origin? Theoretical Biology and Medical Modelling 2008, 5:16 (30 July 2008)

    The article is too long even for the most enthusiastic reader. Should be better bellow 12-15 pages incl. Figures.

  • Competing interests:
    NO
  • Invited by the author to review this article? :
    Yes
  • Have you previously published on this or a similar topic?:
    Yes
  • References:
    Biro JC: Nucleic acid chaperons: a theory of an RNA-assisted protein folding. Theoretical Biology and Medical Modelling 2005, 2:35 (1 September 2005) Biro JC: Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases. Theoretical Biology and Medical Modelling 2008, 5:14 (29 July 2008) Biro JC: Does codon bias have an evolutionary origin? Theoretical Biology and Medical Modelling 2008, 5:16 (30 July 2008) more in my book, THE PROTEOMIC CODE (SEE WWW.JANBIRO.COM)
  • Experience and credentials in the specific area of science:

    I am the scientist who discovered the PROTEOMIC CODE and NUCLEIC ACID ASSISTED PROTEIN FOLDING.

    WWW.JANBIRO.COM

  • How to cite:  Biro J C.Nice work with insufficient discussion and conclusions.[Review of the article 'RNA Structures Affected By Single Nucleotide Polymorphisms In Transcribed Regions Of The Human Genome ' by Sadee W].WebmedCentral 2011;2(3):WMCRW00593
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