Biology Direct - Latest Comments

Yeast Standards

Reed Cartwright — 2011-03-08T10:02:52Z

After rereading the paper in light of Dr. Wolfe's comments, I can tell that we went a bit too far with the yeast nomenclature. The actual point is that at sometime in the past, what were seen as being short and long arms were standardized as left and right arms (Hong, personal communication). As maps improved, they didn't redo the left and right designations to reflect new sizes. Even if this is also wrong, the spirit of the standardization should still be embraced.

Article mis-states the yeast convention

Ken Wolfe — 2011-03-01T12:28:56Z

The article mis-states the yeast convention. The Watson strand is the strand with its 5' end at the left telomere, but the left arm is not always the shorter arm of a yeast chromosome. In fact, the L arm is longer than the R arm for 7 of the 16 yeast chromosomes (up to 4 times longer, in the cases of chromosomes IX and XIV).

The left/right nomenclature for yeast chromosome arms dates back to the early days of yeast genetic maps, but I do not know who introduced it. Cytogenetics is not really possible for Saccharomyces because the chromosomes are too small and do not have extensive heterochromatin at centromeres, so nobody knew which arm was the shorter one until chromosome-sized genetic (and eventually genomic) maps became available. Oliver et al (Nature 357:38, 1992) then used the well established genetic conventions (chromosome numbering and L/R arm nomenclature) when they published the first yeast chromosome sequence. They chose the name Watson for the strand that has its 5' end at the left telomere.

I am suppose that PyrD polarization in this article is incorrect

Valery Anisimov — 2010-12-07T16:10:00Z

For sure this paper propose a new interesting method for the indels polarization based on the structural analysis. But on the same time we should be careful in this point because without clear rules of it implementation sometimes we can come to the wrong conclusions. I think that PyrD polarization made by authors in this paper is exactly the case of applying such muddy logic.
First of all the authors claims that polarization of the PyrD indel using HemE protein as an outgroup made by Skophammer and others is questionable. I am totally agree with this statement. But then they are also rejected polarization of the PyrD based on the consideration of HisA and HisF proteins as outgroup, claimed that "indel arguments contradict themselves". I do not see a logic in the last statement. Why if polarization based on the one outgroup is wrong it should contradict to results of the another polarization for which authors didn't provide any proof of it incorrectness? I think that most correct decision in this point was to say that probable incorrectness of the PyrD - HemE pair polarization mean that Archaea and Firmicutes can not be excluded from the root and PyrD - HisA (or HisF) polarization (which is out of questions) excluded the root from Gram-negatives and the Actinobacteria. Instead the authors switched from the indel analysis to "another line of reasoning" based on the structural analysis of the PyD proteins. But the method of such analysis in this case also not obvious at all (at least for me). In fact the main statement of the authors on which they based the logic of the final conclusion is that an evolution in the direction monomer -> homodimer -> heterotetramer with emerging a new protein-protein interface at each step is much more probable than reverse one even if indel analysis supporting the second scenario. So what is the reason to think that joining of few proteins in one protein complex during evolution is much more probable than disassembling this protein complex on few subunits? And even more than that, at least in this concrete case I believe that we have some proof that evolution really proceeded in the direction heterotetramer -> homodimer -> monomer not vice versa! In fact the authors themselves made the first step in this proof. They are investigated the distribution of the PyrD heterotetramer - PyrD 1B among bacterial taxons. Initially they said that PyrD 1B (PRK07259) protein was found across the Archaea and Firmicutes. Later on they noted that PyrD 1B is presented also in one subgroup of Chloroflexi. They explained this fact by probable HGT. But I should say that myself request to NCBI data base give me not only 6 strains in the group Chloroflexi, but also 7 strains in the group Aquificae, 9 strains in the group Bacteroides/Chlorobi, 8 strains in the group Deltaproteobacteria and 1 strain on the group Fusobacteria. It is certainly very difficult to explain such representation in the different bacterial groups only by possible HGT. So I consider this as an additional argument that PyrD protein complex was presented (as heterotetramer) already in the genome of LUCA. Or by other words this is one more egg to the bucket of the hypothesis that root of life was inside Firmicutes.

I am particularly agree with the author in some points.

Valery Anisimov — 2010-12-02T17:25:22Z

According to myself investigations based on the analysis of the percentage of the genes shared by different bacterial clades, closest clade to Archaea is Actinobacteria and for Bacillus closest one of course Clostridia but on the second place we can see again Actinobacteria. So it is quite possible that Actinobacteria, Neomura and Bacillus had the common ancestor. But based on the analysis of the genes reading directions distributions inside bacterial genomes I guess that this common ancestor was close to Clostridia clade. LUCA probably had RNA-based chromosome which in the secondary structure was organized as one huge stem. So during transcription process ribosome can move only one way. As consequence all genes had the same reading direction. Afterwards when RNA-based genome was transformed to DNA-based genome each part of the RNA steam secondary structure complemented by the second chain was converted to the half of the new circular chromosome ring. So as result all genes in the one half of the chromosome had one direction and all (initially the same) genes on it other part had an opposite direction. If this hypothesis have sense than the clade which is closer to the root should still have large degree of asymmetry in the genes directions in the two parts of the ring. And this is exactly what we can see in the Clostridia clade. Per example Acetohalobium arabaticum had more than 90% of genes which is oriented in the same direction in the each part of the chromosome. It is absolutely statistically impossible to have this distribution after the just by chance process. So based on this method I am estimate that most antic clade is Clostridia. But Bacillus, Actinobacteria and Fusobacteria also old enough. Archaea probably much younger.
This hypothesis can also explain why operons so widely distributed inside Firmucutes (probably most protein complexes in LUCA genome worked on the base of the self-assembling like per example in the the present tense bacteriophages).

GC% and AG% not independent

Donald Forsdyke — 2010-11-25T17:02:50Z

There is a reciprocal relationship between GC% and AG%.

There are two ways to modulate (G+C)% when the total number of bases is constant; either by changing the number of G’s, or by changing the number of C’s. As (G+C)% increases, trading A for G would not affect the AG%. Likewise, trading T for C would not affect the AG%. However, if T were replaced by G, the AG% would increase as (G+C)% increases. Conversely, if A were replaced with C the AG% would decrease as (G+C)% increases.

The latter inverse relationship is observed in bacteria (Lao & Forsdyke 2000; Mortimer & Forsdyke 2003) and eukaryotes (Cristillo et al 2001), and is extensively discussed in my textbook - Evolutionary Bioinformatics (Springer 2006).

Cristillo, A.D., Mortimer, J. R., Barrette, I. H., Lillicrap, T. P. & Forsdyke, D. R. (2001) Double-stranded RNA as a not-self alarm signal: to evade, most viruses purine-load their RNAs, but some (HTLV-1, Epstein-Barr) pyrimidine-load. J. Theor. Biol. 208, 475-491.

Lao PJ, Forsdyke DR (2000) Thermophilic bacteria strictly obey Szybalsky's transcription direction rule and politely purine-load RNAs with both adenine and guanine. Genome Research 10, 228-236.

Mortimer JR, Forsdyke DR (2003) Comparison of responses by bacteriophage and bacteria to pressures on the base composition of open reading frames. Applied Bioinformatics 2, 47-62.

Correction of Acknowledgement

Mark Ragan — 2010-06-07T09:17:28Z

This paper was developed from a talk I gave at ISHPSSB-2009 on the invitation of Maureen O'Malley (Exeter University). An incorrect attribution is given in the Acknowledgements.

BIO INSIPER NANOTECH: COST ACTION 2010

Paolo Manzelli — 2010-04-06T15:30:51Z

BIO-INSPIRED NANOTECH. EUROPEAN COST ACTION 2010.
Notes and suggestion by Paolo Manzelli <pmanzelli@gmail.com>

To Jean-Jacques Toulmé <jean-jacques.toulme@inserm.fr> and colleagues in address .

I would like to suggest to develop a section on Quantum Entanglement and Biological information Exhange on the basis of the following considerations.

As a matter of facts the basic question of Bio-inspired technology is focused on undestanding a physical model of self-molecular assembly, in order to create complex systems of Bio-inspired Tech.at nano scale. To understand the underlining criteria of self assembly I think that science need to overcome the traditional mechanical approach of physics and need to to develop a complete new approach focused on the physical meaning information exchange in Biology.
Genes hold information as genomic sequence ,directing linear protein synthesis. But for instance what is the information holded in Chaperone proteins, to guide newly linear sinthetized polypeptides ino their vaious functional three dimensional shapes.
Therefore because the folding process cannot be a direct consequence of the transfer of DNA-Gene sequencing, there are no chances to predict the self-assembly in proteins folding , if we do not be able to go in deeper on the question of what is a generalized information exchange in biology.
In fact, considering the self assembly in protein folding that is independent from the genetic code , we need to admit the existence of a new kind of information as a new driver of the functional folding of proteins. Besides knowing that for a polypeptide chain of 1000 amino acids there are an enormous ammount of possible different unuseful conformation, but in spite of this the functional conformation is very precisely built up by chaperonnes. Therefore we know that it is impossible to think that the protein folding can be made through a casual event bases on trial and error biological process.
Following those consiseration in brief I believe that the COST Action on Bio-Inspired Nano-technology, need to reserve a section of study oriented to build up models of unerstanding auto-organization process at nanoscale level, based on the the Quantum Entanglement no-local simultaneity of information field, that is an extended property of no classical information processing in biology , as in recent years has been fully verified by numerous experiments interpreted by innovative theory .

I hope that some collegus would like to agree to appoach this study on QUANTUMENTANGLEMENT & NO LOCAL INFORMATION EXCHANGE as a section of the BIO-INSPIRED NANOTECH. EUROPEAN COST ACTION 2010.

My best regards and cordiality's to all of you. Having a Good Easter. Paolo Manzelli
03/APRIL/10 FIRENZE .

--Biblio on Line : http://drivel.ca/writing/bio-nanotech.pdf
http://www.edscuola.it/archivio/lre/entangling_information_theory.htm
http://www.physics.drexel.edu/~bob/Term_Reports/Zhou_Di.pdf

ImRNA or RNA antibody model?

Donald Forsdyke — 2009-10-09T10:05:20Z

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 — 2009-09-24T10:33:42Z

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 — 2009-09-04T09:53:49Z

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.