1 and 4. Accumulation of DNA methylation
Two studies examine the accumulation of DNA methylation changes in lineages of Arabidopsis thaliana plants over 30 generations. The results demonstrate rates of new heritable methylation changes that were at least 1000-fold higher than the expected DNA mutation rate. Such differences in methylation patterns can affect transcription and morphology, driving phenotypic diversity in the absence of genetic mutations.
R.J. Schmitz et al., “Transgenerational epigenetic instability is a source of novel methylation variants,” Science, 334:369-73, 2011. Free F1000 Evaluation
C. Becker et al., “Spontaneous epigenetic variation in the Arabidopsis thaliana methylome,” Nature, doi: 10.1038/nature10555, 2011. Free F1000 Evaluation
2. Bacterial DNA to host
Both the conjugative sharing of DNA between bacteria and the [don’t know] transfer of bacterial DNA into eukaryotic host cells—a phenomenon only demonstrated in one bacterium, a plant pathogen called Agrobacterium tumefaciens—are mediated by bacterial type IV secretion systems (T4SS). Here, researchers identify another T4SS-mediated DNA transfer from bacteria to host, in this case a human bacterial pathogen Bartonella henselae into human cells, which may hold implications for the development of gene-delivery vectors for DNA-based vaccines or gene therapies.
G. Schröder et al., “Conjugative DNA transfer into human cells by the VirB/VirD4 type IV secretion system of the bacterial pathogen Bartonella henselae,” Proc Natl Acad Sci, 108:14643-48, 2011. Free F1000 Evaluation
3. Who’s the best sequencer?
The Assemblathon 1 is a genome assembly competition, in which teams from all of the major sequencing centers demonstrate the accuracy of their pipelines in an assembly challenge—sequence the genomes of two made-up species. The contest drew 41 different assemblies from 17 worldwide groups. While the results demonstrated a high level of coverage and accuracy, entries that thrived in one category often suffered from lower quality in other categories, suggesting there is room for improvement across the board.
D. Earl et al., “Assemblathon 1: A competitive assessment of de novo short read assembly methods,” Genome Res, ISSN 1088-9051/11, 2011. Free F1000 Evaluation
Whether bacteria age has been debated since 2005, when researchers first suggested that they do. A new model re-examines earlier experiments and suggests that aging may have evolved early on as a mechanism that protects new generations from damages accrued by the parent.
C.U. Rang et al., “Temporal dynamics of bacterial aging and rejuvenation,” Current Biology, 21:1813-36, 2011. Free F1000 Evaluation
6. Most common genes identified
An analysis of 10 million protein-encoding genes and gene tags from sequenced bacteria, archaea, eukaryotes, viruses, and metagenomes reveals that genes encoding transposases—enzymes that catalyze the movement of the mobile, transposable elements to another part of the genome—are the most prevalent in nature. The results suggest that transposases are advantageous to their host organisms, and are supported by their mobile nature, which drives their dissemination within and between genomes.
R.K. Aziz et al., “Transposases are the most abundant, most ubiquitous genes in nature,” Nucleic Acids Res, 38:4207-17, 2010. Free F1000 Evaluation
7. The good and bad of human evolution
Analyzing three genome-wide genomic datasets from European individuals and performing evolutionary simulations, researchers find that, compared with other organisms such as Drosophila, humans have experienced less species-wide positive selection, with weakly deleterious mutations driving much genomic change.
K.E. Lohmueller et al., “Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome,” PLoS Genetics, 7:e1002326, 2011. Free F1000 Evaluation
The F1000 Top 7 is a snapshot of the highest ranked articles from a 30-day period on Faculty of 1000 Evolutionary Biology, as calculated on November 28, 2011. Faculty Members evaluate and rate the most important papers in their field. To see the latest rankings, search the database, and read daily evaluations, visit http://f1000.com.