Search

Gavin Sherlock and colleagues report an experimental genome evolution study in Saccharomyces cerevisiae demonstrating adaptive evolution by clonal interference.

Thousands of centromeres were identified and tracked across two major fungal clades, showing that new centromeres spread progressively and that the kinetochore acts as a filter to determine which new centromere variants are tolerated.

Analyses of both natural and experimental evolution suggest that adaptation depends on the evolutionary past and adaptive potential decreases over time. Here, by tracking yeast adaptation with DNA barcoding, the authors show that such evolutionary phenomena can be observed even after a single adaptive step.

Helsen et al. use experimental evolution and chromosome engineering to probe the link between karyotype changes and the cell division machinery. They conclude that spindle organization dictates the available trajectories for karyotype evolution.

Lineage tracking of barcoded Saccharomyces cerevisiae growing in nutrient-limited conditions finds that a predictable increase in genetic diversity through single-mutant lineages is followed by a crash in diversity, owing to the success of highly fit double mutants.

Evolutionary theory predicts that trade-offs between traits are pervasive, yet they are rarely observed in experimental evolution. Dense sampling and precise measuring of performance of adaptive mutations in evolving yeast shows that while many such mutations result in modest improvements in multiple traits, the totality of the data reveals the existence of trade-offs even during initial adaptation.

CrAss-like phages are bacterial viruses often found in the human gut. Here, Siranosian et al. analyze gut metagenomic data to evaluate the patterns of acquisition, transmission and strain diversity of these phages in mother-infant pairs and in patients undergoing fecal microbiota transplantation.

Random DNA barcodes were used to simultaneously track hundreds of thousands of lineages in large cell populations, revealing deterministic dynamics early in their evolution.

The fungal pathogen Candida albicans can undergo a parasexual process that may contribute to genetic diversity, but its actual relevance is unclear. Here, Ropars et al. analyse the genomic sequences of 182 C. albicans isolates collected worldwide and find evidence of gene flow and thus parasexuality in nature.

Candida species are the most common cause of opportunistic fungal infection worldwide. Here, the genomes of six Candida species are sequenced and compared with each other and with related pathogens and non-pathogens; providing insight into the genetic features that underlie the diversity of Candida biology, including pathogenesis and the architecture of mating and meiotic processes.

A comprehensive microarray-based analysis of the cell cycle shows that periodic transcription of most genes is not conserved between Schizosaccharomyces pombe and Saccharomyces cerevisiae. A core group of ∼40–80 genes have conserved patterns of transcription and may have key roles in cell cycle progression.

Cell division is fundamental to life, and so might be expected to have changed little during evolution. Data from four species show that the genes involved can vary, but the regulation of complexes is a common theme.

Since the introduction of microarray technology into the biologist's arsenal, there have been concerns about the reproducibility of experimental results obtained using different microarray platforms. In this issue, three articles address this point, and show that with carefully designed and controlled experiments using standardized protocols and data analyses, reproducibility across platforms is much better than previously shown.

When normal cells are compared to cancer cells by microarray analysis, the most obvious differences occur in the expression levels of genes that control cell proliferation. Can this 'proliferation signature' be used as a biomarker for cancer research and therapy?

Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.

With a comprehensive analysis of sequencing data, DNA copy number, gene expression and DNA methylation in a large number of human glioblastomas, The Cancer Genome Atlas project initiative provides a broad overview of the genes and pathways that are altered in this cancer type.