Average genome size is an important, yet often overlooked, property of microbial communities. We developed MicrobeCensus to rapidly and accurately estimate average genome size from shotgun metagenomic data and applied our tool to 1,352 human microbiome samples. We found that average genome size differs significantly within and between body sites and tracks with major functional and taxonomic differences. In the gut, average genome size is positively correlated with the abundance of Bacteroides and genes related to carbohydrate metabolism. Importantly, we found that average genome size variation can bias comparative analyses, and that normalization improves detection of differentially abundant genes.
Dmitry Alexeev's insight:
well size matters isn't it?
i enjoyed the difference in genome sizes between body habitats
MicroRNAs (miRNAs) are small regulatory RNA molecules that inhibit the expression of specific target genes by binding to and cleaving their messenger RNAs or otherwise inhibiting their translation into proteins. miRNAs are transcribed as much larger primary transcripts (pri-miRNAs), the function of which is not fully understood. Here we show that plant pri-miRNAs contain short open reading frame sequences that encode regulatory peptides. The pri-miR171b of Medicago truncatula and the pri-miR165a of Arabidopsis thaliana produce peptides, which we term miPEP171b and miPEP165a, respectively, that enhance the accumulation of their corresponding mature miRNAs, resulting in downregulation of target genes involved in root development. The mechanism of miRNA-encoded peptide (miPEP) action involves increasing transcription of the pri-miRNA. Five other pri-miRNAs of A. thaliana and M. truncatula encode active miPEPs, suggesting that miPEPs are widespread throughout the plant kingdom. Synthetic miPEP171b and miPEP165a peptides applied to plants specifically trigger the accumulation of miR171b and miR165a, leading to reduction of lateral root development and stimulation of main root growth, respectively, suggesting that miPEPs might have agronomical applications.
Brain Blogger (blog) The Brain-Gut Axis, Part 3 – The Gut Microbiota In Disease Brain Blogger (blog) In Part 2 of the brain-gut axis article series, I explained how the brain and the gut microbiota communicate.
The determination of the most central agents in complex networks is important because they are responsible for a faster propagation of information, epidemics, failures and congestion, among others. A challenging problem is to identify them in networked systems characterized by different types of interactions, forming interconnected multilayer networks. Here we describe a mathematical framework that allows us to calculate centrality in such networks and rank nodes accordingly, finding the ones that play the most central roles in the cohesion of the whole structure, bridging together different types of relations. These nodes are the most versatile in the multilayer network. We investigate empirical interconnected multilayer networks and show that the approaches based on aggregating—or neglecting—the multilayer structure lead to a wrong identification of the most versatile nodes, overestimating the importance of more marginal agents and demonstrating the power of versatility in predicting their role in diffusive and congestion processes.
Ranking in interconnected multilayer networks reveals versatile nodes Manlio De Domenico, Albert Solé-Ribalta, Elisa Omodei, Sergio Gómez & Alex Arenas
тумукBoth proteins and RNAs can misfold into non-functional conformations. Protein chaperones promote native folding of nascent polypeptides and re-folding of misfolded species, thereby buffering mutations that compromise protein structure and function. Here we show that RNA chaperones can also act as mutation buffers that enhance organismal fitness. Using competition assays, we demonstrate that overexpression of select RNA chaperones, including three DEAD box RNA helicases (CsdA, SrmB, RhlB) and the cold shock protein CspA, improves fitness of two independently evolved E. coli mutator strains that have accumulated deleterious mutations during short- and long-term laboratory evolution. We identify strain-specific mutations that are deleterious and subject to buffering when introduced individually into the ancestral genotype. For DEAD box RNA helicases we show that buffering requires helicase activity, implicating RNA structural remodelling in the buffering process. Our results suggest that RNA chaperones might play a fundamental role in RNA evolution and evolvability.
Dmitry Alexeev's insight:
never heard it before - RNA chaperones - they buffer the mutations
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