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Genomics in the Journals: Feb 28, 2013

NEW YORK (GenomeWeb News) – Temperature stress may prompt some bacteria to take on mutations associated with antibiotic resistance, even in the absence of such drugs, a BMC Evolutionary Biology study suggests. French and American researchers grew Escherichia coli bacteria in different combinations of temperature conditions and food sources. When they sequenced clones from the resulting populations, they discovered examples of E. coli grown at 42.2ºC (almost 108ºF) that had acquired mutations in the rpoB gene — alterations that subsequently rendered them resistant to an antibiotic called rifampicin.

Through a series of follow-up experiments, the team tracked the timing with which these mutations appeared in E. coli and looked at their effects on fitness, demonstrating that mutations associated with antibiotic exposure are not always detrimental to a bug's fitness in antibiotic-free conditions.

"Our study shows that antibiotic resistance can occur even in the absence of antibiotics and that, depending on the type of bacteria, and growth conditions, rather than being costly to maintain, can be highly beneficial," INSERM's Olivier Tenaillon, corresponding author on the study, said in a statement.

In Nature Genetics, researchers from the Chinese Academy of Sciences, the International Center for Bamboo and Rattan, and China's State Forestry described efforts to sequence and assemble a draft genome for the woody bamboo species Phyllostachys heterocycla, commonly known as moso bamboo. Within the resulting assembly — which spans more than two billion bases and an estimated 95 percent of the P. heterocycla var. pubescens genome — the team found nearly 32,000 predicted protein-coding genes, along with more than 2 million apparent heterozygous SNPs and tens of thousands of small insertions and deletions.

Together with complementary DNA sequences and RNA-sequencing data, the newly generated genome assembly offered a look at bamboo features ranging from flowering and shoot development to cell wall formation. The team's analyses also provided insights into relationships between bamboo with other grass plants and pointed to a whole-genome duplication in the bamboo lineage some seven to 12 million years back.

A study in The Lancet outlined findings from a meta-analysis of genome-wide association studies on the five psychiatric conditions: autism spectrum disorder, schizophrenia, bipolar disorder, major depressive disorder, and attention deficit-hyperactivity disorder.

Members of the Psychiatric Genomics Consortium brought together data on 33,332 cases and 27,888 controls, all of European ancestry. Across the conditions as a whole, the most strongly associated SNPs were variants in the chromosome 3 gene ITIH3, SNPs at two loci on chromosome 10, and variants in and around two genes coding for voltage-gated calcium channel subunits, the researchers reported.

Other variants showed ties to specific psychiatric conditions. Still, study authors found overlap between specific psychiatric conditions when they considered the sets of SNPs linked to each individual condition. For instance, polygenic risk profiles tended to overlap for schizophrenia, bipolar disorder, and major depressive disorder — conditions known to appear in adulthood. On the other hand, ASD shared potential genetic ties to schizophrenia and bipolar disorder but not major depressive disorder.

"This analysis provides the first genome-wide evidence that individual and aggregate molecular genetic risk factors are shared between five childhood-onset or adult-onset psychiatric disorders that are treated as distinct categories in clinical practice," corresponding author Jordan Smoller, with the Massachusetts General Hospital, said in a statement, noting that such results "may inform a move beyond descriptive syndromes in psychiatry and towards classification based on underlying causes."

An American Journal of Human Genetics study by the University of Arizona's Michael Hammer and colleagues from the US, Cameroon, and UK described the discovery and analysis of a new, apparently ancient paternal lineage. During commercial genotyping on a sample from an African American individual, investigators found that the man carried only versions of Y chromosome SNPs that are presumed to be ancestral.

Subsequent screening did not pick up this paternal lineage — dubbed A00 — in individuals from hunter-gatherer populations in sub-Saharan Africa, though it was detected at low frequency in samples from central Africa, researchers noted.

Phylogenetic analyses that incorporated this new, basal Y chromosome lineage suggested that the Y chromosome's common ancestor stretches back some 338,000 years — earlier than fossil records for modern humans and the estimated age of mitochondrial lineages. Based on such findings, the study's authors speculated that it may be necessary to evaluate Y chromosome diversity within more complicated models than those used at present.

"The extremely ancient age combined with the rarity of the A00 lineage … point to the importance of considering more complex models for the origin of Y chromosome diversity," they wrote. "These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans."

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.