Biology Direct - Latest Comments

ImRNA or RNA antibody model?

Donald Forsdyke — 2009-10-09T00:00:00Z

The author's appendix (p. 11) summarizes nine steps in the proposed "imRNA response mechanism." Two of these are weak.
Step 3: Recognition of foreign viral mRNA "possibly by host reverse transcriptases RT." But how does reverse transcriptase distinguish between self and not-self RNAs?
Step 6: Integration into host genome. But there is no distinction between somatic cells and germline cells. How is the "Weismann barrier" breached in the case of germline cells? As Koonin points out, there is Lamarckian element here.
While there is much indirect evidence, ably summarized by Flegel, that support his model (especially bacterial CRISPR systems), the above objections are overcome in the "RNA antibody" model we suggested (see Paper in Trends in Immunology [1]. The model was updated in Chapter 12 of my textbook [2].

1. Forsdyke DR, Madill CA, Smith SD: Immunity as a function of the unicellular state. Trends Immunol 2002, 23:575-579.

2. Forsdyke DR: Evolutionary Bioinformatics 2006, Springer, New York.

good idea, again

William Martin — 2009-09-24T00:00:00Z

In 2003, Ford Doolittle called this the "Genome of Eden" constraint, in Phil Trans Roy Soc Lond B. In 2007 (PNAS) and 2008 (PNAS), Tal Dagan used it to estimate LGT frequency and cumulative impact among prokaryotes. Good idea, again.

An early warning against rejection-free claim for iPS cells

Shi Liu — 2009-09-04T00:00:00Z

I have been wondering why almost all the transplantations of iPSCs (induced pluripotent stem cells) were done on SCID mice rather than on normal mice. As a matter of fact I even publicly questioned the study design of a study and asked: Why a study aimed at showing a "circumvention of the immune rejection barrier" by using iPSC-based therapy would still use sub-lethally irradiated mice as the recipients? (see publication at http://im1.biz/displayimage.php?album=84&pos=1 ).

I think the results presented here should serve as a warning against many naive claims for cell therapy. Immunity may be more tricky than we have thought of and reprogramming cells may even present or expose some antigens subject to rejection reactions.

Response from the authors

Robson Francisco De Souza — 2009-08-26T00:00:00Z

1) The sequences corressponding to the structures in PDB for the Anabaena protein are indeed different from those derived from the genomic sequence. Given that the domain is short any such change, even if at the termini, appear to distort the key structural elements. This justifies our exclusion of the Anabaena structures from further analysis.

2) This is indeed true and this observation reinforces our basic inference that there is no strict link between functions of solo ASRAH proteins and ASR-type sensory rhodopsins.

A few remarks

Leonid Brown — 2009-08-20T00:00:00Z

1) The authors claim that "Examination of the structures reveals that key structural elements of the
Anabaena representative have been mutated to obtain its crystal structure." I believe this is incorrect. There are parts of the structure which are missing due to disorder, but there are no mutations in the main sequence, with the exception of His-tags added on either of the termini.

2) Not only there are many rhodopsin-less species in which ASRT homologs are found, but there are also several bacterial species having homologs of ASR, but no ASRT.

A great example of science in action

Stephen Curry — 2009-03-30T00:00:00Z

I thought this a very interesting paper that shed important light on the difficulties inherent in predicting structure from sequence - and in correcting earlier errors. The insights derived from the exchanges between reviewers and authors were particularly illuminating. I've mentioned the paper on my blog as an example of the great value of openness in the publication procedure.

1R or 2R

Amir Abbasi — 2008-12-22T00:00:00Z

Among the "Whole genome duplication" scenario proponents there are two versions of Ohno,s hypothesis, some has suggested two round (2R) scenario (leading to octaploids), whereas others only one round (1R) of whole genome duplication (leading to tetraploids, please see Ref 25 of this manuscript, and also see Gu et al 2002 Nat.Genet.31, 205-209 and Durand Dannie TRENDS in Genetics Vol.19 No1 Jan 2003). The title of the manuscript refers to 1R. However in the text I provide a critical overview of 2R also (please see in particular the sections “Paralogy regions in the Human genome” and “HOX cluster duplication and the history of vertebrate genome evolution”. I can hope this comment will let the readers to understand the title of this manuscript. I am the author of this manuscript.

octaploids

Herman Van Eck — 2008-12-16T00:00:00Z

Two rounds of genome duplication would generate from diploids -> tetraploids and from tetraploids -> octaploids. So I do not understand the title of the paper. In fact there is a paper on this issue that indeed refers to octaploidy. TJ Gibson and J Spring (2000) Evidence in favour of ancient octaploidy in the vertebrate genome, Biochem Soc Trans 28:259–264.

Correction and citation

Dustin Holloway — 2008-10-07T00:00:00Z

Although the KEGG database is mentioned at several points within the text, readers should also note that the layout of the WNT pathway as seen in Figure 4 was modeled after that seen in the KEGG WNT Signaling Pathway(http://www.genome.jp/kegg/pathway/hsa/hsa04310.html).

Please also note that, in Figure 2, the y-axis is the Positive Predictive Value (PPV).

Finally, identifiers for several of the TFs in the bottom portion of Figure 6A are missing. The TFs should be labeled (from left to right) SRF, E2F, Mef2a, T3R, YY1, and CebpB.

We apologize for any inconvenience this may have caused the sophisticated reader.

Figure Correction

Dustin Holloway — 2008-10-07T00:00:00Z

Please note the following minor correction to Figure 1:

The small box on the bottom right hand corner of Figure 1 contains the following text: "100X Average Accuracy." This should instead read "50X Average Accuracy." (The Figure legend provides the correct number). Also, the text directly next to the box should read "Average the Accuracy Estimates Over 50 Repeats", rather than "...Over 100 Repeats."