Scientific highlights 2013
Caesarean delivery may increase susceptibility to later allergic disease through altered microbiota
Child delivery by caesarean section has been shown to delay bacterial colonisation of the infant gut, which may affect the development of immune system regulation and render individuals more prone to allergic disease in later life. Since caesarean delivery is increasing in many parts of the world, the findings of this study will be of value when determining future clinical practice in the field.
Dog domestication: a key role for brain function and starch digestion
A unique whole-genome resequencing study of dog and wolf DNA indicates that both changes in brain genes and novel adaptations that allowed the ancestors of modern dogs to thrive on a diet rich in starch constituted an important step in their domestication. The results also point to a potential striking case of parallel evolution whereby the agricultural revolution caused similar adaptive responses in both dogs and humans.
First-time in-situ sequencing of RNA fragments in preserved cells and tissue
In-situ sequencing for parallel-targeted analysis of short RNA fragments in morphologically preserved cells and tissue has now been successfully demonstrated for point mutations and multiplexed gene expression profiling in human breast cancer sections. Being better able to understand the interplay between distinct cell types in complex organ tissues opens up new prospects in basic research and clinical diagnostics.
Getting the measure of our anthropometric traits: a new body of evidence
A large genome-wide association study meta-analysis of up to 263,407 individuals identified 165 loci associated with distribution tails of body mass index, height and waist-to-hip ratio, and/or clinical classes of obesity. Eleven of these loci have not previously been associated with anthropometric traits. These findings further our knowledge about the genetic architecture of complex traits and will help design more effective and cost-efficient future genetic studies of obesity, as well as other complex traits.
High-resolution analysis of human TF specificity generates new models of DNA-binding
Our understanding of the transcriptional networks that control physiological and pathological processes has been boosted by a new high-throughput analysis of the DNA-binding specificities of most human transcription factors (TFs). Results revealed several new insights into the interactions that take place and allowed improved computational models of TF-DNA binding to be developed.
Keeping track of intracellular diffusive states and transition rates in single molecules
Combining information from thousands of short single-molecule trajectories of intra-cellularly diffusing proteins is now a reality thanks to anew analytical tool. The method has already created an objective interaction map for the Hfq protein that allowed a number of diffusive states and transition rates to be identified.
Low selective pressure on disordered protein regions allow greater protein length variation
By first analyzing length variation between homologous proteins, SciLifeLab researchers gained fresh insights into how insertion and deletion events (indels) in genes influence proteins. A surprisingly strong relationship between difference in length and difference in the number of intrinsically disordered residues was noted. It was suggested that two out of three length-different causing mutations occurs in intrinsically disordered regions. These findings suggest that indels within disordered protein regions are subject to a remarkably low purifying selection.
Mapping the spatial distribution of proteins in cells: imaging techniques still deliver
The largest investigation of its kind has confirmed the value of immunofluorescence (IF) and fluorescent-protein (FP) tagging for providing vital information about the spatial location of proteins in mammalian cells. Although certain discrepancies were noted, both techniques were considered highly complementary and indispensable. They yielded the same sub-cellular distribution for 80% of the proteins studied (more than 500) and revealed the locations of 250 previously non-localized proteins.
New method digs deep into higher eukaryotic genomes
Combining experimental pre-fractionation based on peptide isoelectric point (pI) with theoretical prediction of pI allowed full six-reading-frame translation (6FT) searches of higher eukaryotic genomes in the 3-Gb size range. Such searching, previously believed only to have been performed on the Arabidopsis thaliana 157-Mb genome, enables deep proteome coverage and unbiased proteogenomics. When applied to human and mouse genomes, the method identified 98 and 52 previously undiscovered protein coding loci, respectively.
Sprucing up our knowledge of conifer genome evolution
A draft assembly of the 20-gigabase genome of Norway spruce (Picea abies) – the first available for any gymnosperm – has enabled a much sought-after analysis of conifer gene architecture. Although the number of genes found was similar to the more than 100-fold smaller genome of the angiosperm Arabidopsis thaliana, no evidence of recent whole-genome duplication was seen. Instead, P. abies’ large genome size seems to result from the slow but steady accumulation of a diverse set of transposable elements – a ‘one-way ticket to genome obesity’. A fresh model of conifer genome evolution is proposed.