Thursday, February 17, 2005

104-126: Microbiology roundup

Someone else gets it. I don't plan to read every damn thing. So the incorrigible Mike the Mad Biologist offers Microbiology and Evolution:

Microevolution and history of the plague bacillus, Yersinia pestis, Achtman, et al. (2004) PNAS 101: 17837.
The plague bacillus did not evolve from Yersinia pseudotuberculosis ~1,500 years ago, but instead arose and spread globally >10,000 years ago.

Natural Isolates of Salmonella enterica serovar Dublin carry a single nadA missense mutation, Bergthorsson et al. (2005) J. Bacteriol. 187:400.
This article tests various evolutionary hypotheses about why certain disease-causing Salmonella can not synthesize pyridine.

Phenotypic differences between Salmonella and Escherichia coli resulting from the disparate regulation of homologous genes, Winfield et al. (2004) PNAS 101: 17162.
Differences in gene regulation account for phenotypic divergence between Salmonella and E. coli.

Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation, Vinuesa et al. (2005) Molecular Phylogenetics and Evolution 34:29.
“This finding provides strong evidence for the existence of well delineated species in the bacterial world.”

Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human, Song et al. (2005) PNAS 102:2430.
Uses evolutionary analyses to determine where the SARS virus came from and what genetic changes made it dangerous to humans.

Characterization of MADS-box genes in charophycean green algae and its implication for the evolution of MADS-box genes, Tanabe et al. (2005) PNAS 102:2436.
The MADS-box genes of land plants are extensively diverged to form a superfamily and are important in various aspects of development including the specification of floral organs as homeotic selector genes....These expression patterns suggest that the precursors of land plant MADS-box genes originally functioned in haploid reproductive cell differentiation and that the haploid MADS-box genes were recruited into a diploid generation during the evolution of land plants.“

Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization, Morrell et al. (2005), PNAS 102:2442.
Inbreeding plants appear to have the same lack of linkage disequilibrium as outcrossing plants. If you really want to know why the Mad Biologist finds this very interesting you'll have to send email.

Genomic insights that advance the species definition for prokaryotes, Konstantinidis et al. (2005), PNAS 102:2567.
Compares bacterial species definitions derived from traditional methods to those derived from genome data.

Neutral microepidemic evolution of bacterial pathogens, Fraser et al. (2005). PNAS 102:1968.
”The analysis suggests the emergence of neutral bacterial population structure from overlapping microepidemics within clustered host populations and provides insight into the nature and size distribution of these clusters. These findings challenge the assumption that strains of bacterial pathogens differ markedly in relative fitness.“

A monkey's tale: The origin of Plasmodium vivax as a human malaria parasite, Escalante et al. (2005), PNAS 102:1980.
Human malaria may have evolved from malaria found in Southeast Asian macaques, not from animals in Africa.

A genomic population genetics analysis of the pathogenic enterocyte effacement island in Escherichia coli: The search for the unit of selection, Castillo et al. (2005), PNAS 102:1542.
Recombination and selection may be breaking breaking apart this genomic region so that different elements are, at best, weakly coupled in their evolution. These observations suggest that the units of selection are not the complete island, but rather, much smaller units that comprise the island.

High rate of viral evolution associated with the emergence of carnivore parvovirus, Shackleton et al. (2005), PNAS 102:379.
Carnivore parovirus is a recently emergent virus that kills dogs. Read this article or more puppies will die!

Experimental evolution of conflict mediation between genomes, Sachs et al. (2005), PNAS 102:390.
Using two bacterial viruses, the authors examine the following phenomena: evolution of reduced genomes in symbionts, cotransmission of partners, and obligate coexistence between cooperating species.

Postzygotic isolating factor in sympatric speciation in Rhagoletis flies: Reduced response of hybrids to parental host-fruit odors, Linn et al. (2005), PNAS 101:17753.
Rhagoletis is an excellent example of speciation that we have been able to observe. This paper describes a mechanism by which speciation has happened.

Extensive gene diversity in septicemic Escherichia coli strains, Mokady et al. (2005) J. Clin. Microbiol. 43:66.
This paper shows that there is extensive genome plasticity between E. coli that cause the same disease and target similar tissues. Also, gene associated with virulence are found in a variety of different animals, ”implying a high degree of zoonotic risk.“

The limits of theoretical population genetics, Wakeley (2005), Genetics 169:1.
Gee, what do you think it's about?

Lack of evidence for horizontal transfer of the lac operon into Escherichia coli, Stoebel (2005), Mol. Biol. Evol. 22:683.
The ability to use lactose by E. coli has always been cited as the prime example of horizontal gene transfer giving rise to ecological divergence. Dan blows this example away.

Evolutionary genetics of a new pathogenic Escherichia species: Escherichia albertii related Shigella boydii strains, Hyma et al. (2005), J. Bacteriol. 187:619.
There's a new species of Escherichia.

Microeconomic principles explain an optimal genome size in bacteria, Ranea et al. (2005), Trends in Genetics 21:21.
Why are bacterial genomes the sizes that they are?

A bunch of fun-guys: the whole-genome view of yeast evolution, Ochman et al. (2005), Trends in Genetics 21:1.
Genome evolution in yeasts is different than genome evolution in bacteria, largely because yeast chromosomes have stronger selective constraints.

Germs, genomes, and genealogies, Wilson et al. (2005), Trends in Ecology and Evolution 20:39.
Pathogen biology can be inferred from patterns of molecular variation.

Weighted genome trees: refinements and applications, Gophna et al. (2005), J. Bacteriol. 187:1305.
How to construct genome-level phylogenies.

I think that's enough to keep you busy...
You bet, Mike. Thanks for the help.