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This Week in Cell: Mar 12, 2014

Researchers from Harvard Medical School and Helicos BioSciences followed the half-lives of more than 21,000 messenger RNAs in yeast using the so-called anchor-away approach — a method that involves conditioning depleting cell nuclei of a polymerase II subunit component and then sequencing RNA in the cells as it became depleted. Based on their analysis of 21,248 transcript isoforms, the investigators identified variability in mRNA half-life, even amongst similar or identical isoforms. They also narrowed in on sequences and structures that appear to prompt increased or diminished transcript stability.

A California Institute of Technology-led team took a look at the gene expression consequences of dialing transcription factor copy number up or down. The researchers used time-lapse fluorescence microscopy to follow reporter gene expression in cells containing varying numbers of transcription factors carried on plasmids in Escherichia coli. In addition to developing a predictive model bringing together gene expression, transcription factor binding sites, and plasmid copy number, the team also went on to consider plasmid copy number dynamics across the cell cycle.

The metabolites mediating Caenorhabditis elegans gene expression can vary depending on the worm's bacterial diet source, according to a study by researchers at the University of Massachusetts and the University of Toronto. The group considered the metabolites formed in C. elegans following ingestion of either E. coli or another bacterial species, Comamonas aquatica, focusing on metabolites affecting the worm's gene expression and physiology. For example, the analysis uncovered a role for vitamin B12, a metabolite from Comamonas, in development, gene expression, and diminished fertility.

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.