In PLoS Biology this week, scientists at the SUNY Upstate Medical University in Syracuse show that they can use pluripotent cells to generate a fully functioning eye in the frog. Cells from blastula stage embryos are pluripotent, but usually, they only differentiate into epidermis. In contrast, they say, when they forced expression of seven eye field transcription factor genes, "the cells differentiate into all seven retinal cell classes and eventually organize themselves into a functioning eye that can detect light and guide tadpoles in a vision-based behavior," they write.
At the University of California, San Francisco, Patricia Babbitt led work that mapped drugs according to how they interact with metabolic enzymes. The effects of small molecule drugs "may be therapeutic or toxic, but are frequently unexpected," says the abstract. To that end, she and her team created a system-wide map linking drugs to metabolism based on drug and metabolite grouping in chemical space. They applied the method to 246 known drugs classes and 385 organisms. The work appears in this week's issue of PLoS Computational Biology.
In PLoS Genetics, Spanish scientists have found that in S. cerevisiae, many genes are regulated not just at the level of transcription initiation, but also at the elongation level. Using a "combination of ChIP-on-chip and genomic run-on approaches," they found that the proportion of active RNA polymerase II throughout the genome is characteristic of some functional gene classes, like those related to ribosomes and mitochondria, they write. They also found that in vivo, depleting FACT, a chromatin-related elongation factor, also "produces a regulon-specific effect on the expression of the yeast genome."
French scientists in Marseille have published a paper in PLoS Pathogens looking at how HIV latency affects its ability to become resistant to immune responses. Here, they show that in an in vitro model and in HIV-1-infected patients, CpG methylation at the HIV-1 promoter "is important for the maintenance but not for the establishment of HIV-1 latency." From this knowledge, they say that some histone deacetylase inhibitors and cytosine methylation inhibitors "would represent an important part of HAART protocols in the future."