In this week's PNAS Early Edition, researchers at the University of Washington, Sage Bionetworks, and Pacific Biosciences report their use of "both time-series data and genetics data to infer directionality of edges in regulatory networks: time-series data contain information about the chronological order of regulatory events and genetics data allow us to map DNA variations to variations at the RNA level." The Washington-led team generated microarray data measuring time-dependent gene-expression levels in 95 genotyped yeast segregants subjected to a drug perturbation, which it then subjected to a "Bayesian model averaging regression algorithm that incorporates external information from diverse data types to infer regulatory networks" from that time-series and genetic data. "Our algorithm is capable of generating feedback loops," the team writes, adding that its approach can also be used to "discover de novo transcription-factor binding sites."
Elsewhere in the Early Edition, investigators at Princeton University, the National Institutes of Health, and the Centers for Disease Control and Prevention report on their modeling of "rotavirus strain dynamics in developed countries to understand the potential impact of vaccination on genotype distributions." The Princeton-NIH-CDC team says its "model can explain the coexistence and cyclical pattern in the distribution of genotypes observed in most developed countries," such that the predicted frequency of cycling "depends on the relative strength of homotypic [versus] heterotypic immunity." Overall, the team says that a "better understanding of homotypic [versus] heterotypic immunity, both natural and vaccine-induced, will be critical in predicting the impact of vaccination."
A team led by researchers at North Carolina State University this week shows that a "wing-patterning gene redefines the mimetic history of Heliconius butterflies." By comparing relationships within H. erato and H. melpomene using a series of unlinked genes, those linked to color-pattern loci, and optix ("a gene recently shown to control red color-pattern variation"), the team found that the latter structured "lineages by red color patterns … supporting a single origin of red-rayed patterns within each species." The NC State-led team says that with these refined relationships among Heliconius, "we resolve a long-standing debate about the origins of the races within each species, supporting the hypothesis that the red-rayed Amazonian pattern evolved recently and expanded, causing disjunctions of more ancestral patterns."
The University of Cambridge's Krastan Blagoev says the niche proliferative potential of stem cells "is quantitatively related to the proliferative potential of the individual stem cells for different structural classes of the stem cell niche," such that those cells "at the periphery of a niche are under pressure to divide and to differentiate, as well as to maintain the stem cell niche boundary." In a paper published online in advance in PNAS this week, Blagoev says that "the geometry of the stem cell niche is expected to play a role in determining the stem cell division sequence and differentiation."