Recruitment, rewiring and deep conservation in flowering plant gene regulation.

Transcription factors (TFs) are proteins that bind DNA to control where and when genes are expressed. In plants, dozens of TF families interact with distinct sets of binding sites (TFBSs) that reflect each TF's role in organismal function and species-specific adaptations. However, defining these roles and understanding broader patterns of regulatory evolution remain challenging, as predicted TFBSs may lack a clear impact on transcription, and experimentally derived TF binding maps to date are modest in scale or restricted to model organisms.

Beneficial reversal of dominance maintains a resistance polymorphism under fluctuating insecticide selection.

Large-effect functional genetic variation is commonly found in natural populations, even though natural selection should erode such variants. Theory suggests that under fluctuating selective pressures, beneficial reversal of dominance - where alleles are dominant when beneficial and recessive when deleterious - can protect these loci from selection, allowing them to persist. However, empirical evidence for this mechanism remains elusive because testing requires direct measurements of selection and dominance in natural conditions.

pigmentation demonstrates adaptive phenotypic parallelism but genomic unpredictability over multiple timescales.

Unlabelled: Populations are capable of responding to environmental change over ecological timescales via adaptive tracking. However, the translation from patterns of allele frequency change to rapid adaptation of complex traits remains unresolved. We used abdominal pigmentation in as a model phenotype to address the nature, genetic architecture, and repeatability of rapid adaptation in the field.

Direct observation of adaptive tracking on ecological time scales in .

Direct observation of evolution in response to natural environmental change can resolve fundamental questions about adaptation, including its pace, temporal dynamics, and underlying phenotypic and genomic architecture. We tracked the evolution of fitness-associated phenotypes and allele frequencies genome-wide in 10 replicate field populations of over 10 generations from summer to late fall. Adaptation was evident over each sampling interval (one to four generations), with exceptionally rapid phenotypic adaptation and large allele frequency shifts at many independent loci.

The PathOlogist: an automated tool for pathway-centric analysis.

Background: The PathOlogist is a new tool designed to transform large sets of gene expression data into quantitative descriptors of pathway-level behavior. The tool aims to provide a robust alternative to the search for single-gene-to-phenotype associations by accounting for the complexity of molecular interactions.

Results: Molecular abundance data is used to calculate two metrics--'activity' and 'consistency'--for each pathway in a set of more than 500 canonical molecular pathways (source: Pathway Interaction Database, http://pid.

Genetic variations at loci involved in the immune response are risk factors for hepatocellular carcinoma.

Unlabelled: Primary liver cancer is the third most common cause of cancer-related death worldwide, with a rising incidence in Western countries. Little is known about the genetic etiology of this disease. To identify genetic factors associated with hepatocellular carcinoma (HCC) and liver cirrhosis (LC), we conducted a comprehensive, genome-wide variation analysis in a population of unrelated Asian individuals.