416-428: Mad Biology

Thanks to Mike the Mad Biologist for this breakdown. Others are encouraged to do the same.

So it's that time again, when the Mad Biologist downloads more interesting science articles that I'll never get around to reading. As before, this is not an all-inclusive list, just some stuff I found interesting. Hopefully, Josh will get around to posting this on the Evolution Project. For those of you too dim to figure it out, evolution is really important for understanding microbiology.

Nonhomogeneous Model of Sequence Evolution Indicates Independent Origins of Primary Endosymbionts Within the Enterobacteriales (gamma-Proteobacteria), Herbeck et al. (2005) Mol. Biol. Evol. 22: 520.

This paper uses non-standard molecular models to reconstruct the evolutionary history of insect bacterial endosymbionts.

The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off, Kreft et al. (2005) Microbiology 151: 637.

One of the issues this article addresses is why bacteria haven't evolved multicellularity.

Osteocalcin protein sequences of Neanderthals and modern primates, Nielsen-Marsh (2005) PNAS 102: 4409.

So there's no microbiology. I think anytime you can do protein chemistry on 75,000 year old molecules and relate it to evolution, it's pretty cool.

Integrons in Xanthomonas: A source of species genome diversity, Gillings et al. (2005) PNAS 102: 4419.

The integration of gene cassettes into Xanthomonas has resulted in ecological differentiation within this genus.

A mechanism for the association of amino acids with their codons and the origin of the genetic code, Copley et al. (2005) PNAS 102: 4442.

This article discusses the evolution of the genetic code.

Detecting amino acid sites under positive selection and purifying selection, Massingham et al. (2005) Genetics 169: 1753.

This article describes a technique for determining which amino acids in a protein are under selection.

Evolution of genomic content in the stepwise emergence of Escherichia coli O157:H7, Wick et al. (2005) J. Bacteriology 187: 1783.

This article describes how a nice, run-of-the-mill E. coli evolved into a highly virulent pathogen (and I've mentioned O157:H7 before).

Escherichia coli strains belonging to phylogenetic group B2 have superior capacity to persist in the intestinal microflora of infants, Nowrouzian et al. (2005) Journal of Infectious Diseases 191: 1078.

One group of E. coli descended from a common ancestor persist longer in infants.

Antimicrobial-resistant and extraintestinal pathogenic Escherichia coli in retail foods, Johnson et al. (2005) Journal of Infectious Diseases 191: 1040.

Population genetic analyses indicate that retail foods are an important vehicle for community-wide dissemination of antimicrobialresistant E. coli and extra-intestinal pathogenic E. coli (such as those that cause urinary tract infections).

Evolutionary origins and sequence of the Escherichia coli O4 O-antigen gene cluster, D'Souza et al. (2005) FEMS Microbiology Letters 244: 27.

"Sequencing of the E. coli O4 O-antigen gene cluster revealed a similar gene order and high levels of similarity to that of E. coli O26; indicating a common ancestor. These lateral transfer events observed within O-antigen gene clusters may occur as part of the evolution of the pathogenic clones."

Tackling the population genetics of clonal and partially clonal organisms, Halkett et al. (2005) Trends in Ecol. and Evol. 20: 194.

A summary of how to do population genetics in clonal organisms. I have a feeling I'm going to be disappointed with this article...

Falsifications and corroborations: Karl Popper's influence on systematics, Helfenbein et al. (2005), Molecular Phylogenetics and Evolution 35: 271.

"In this paper, we provide the reader with a concise summary of Popper s ideas relevant to systematics, review the systematic literature invoking or declining Popper s importance to the field, and make a recommendation for the future course of philosophical thinking in systematics. We try to make clear various authors interpretations of Popper's work and how those interpretations have impacted systematic thought." Hey, we are supposed to doctors of philosophy after all...

Nucleotide substitution and recombination at orthologous loci in Staphylococcus aureus, Hughes et al. (2005), Journal of Bacteriology 187: 2698.

Genes related to pathogenesis have undergone recombination, suggesting that recombination plays a significant role in the evolution of pathogenesis.