Several technical challenges in metagenomic data analysis, including assembling metagenomic sequence data or identifying operational taxonomic units, are both significant and well known. These forms of analysis are increasingly cited as conceptually flawed, given the extreme variation within traditionally defined species and rampant horizontal gene transfer. Furthermore, computational requirements of such analysis have hindered content-based organization of metagenomic data at large scale.
How can runners improve their performance, weight and fitness? Researchers have produced a mathematical model to optimize running, which could lead to personal e-coaching customized to each individual's physiological state. It also confirms a well-known fact in the sports community: runners who vary their speed spend their energy better and thus run longer. Mathematics gives them the opportunity to switch from simple statistical tools to personalized sporting advice.
Despite identifying abundant genes capable of conferring antibiotic resistance in soil microorganisms, a study finds that few are shared by human pathogens and that there is little transfer of the genes within the soil communities. See Letter p.612
The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters.
Trillions of microorganisms that inhabit the intestinal tract form a diverse and intricate ecosystem with a deeply embedded symbiotic relationship with their hosts. As more detailed information on gut microbiota complexity and functional diversity accumulates, we are learning more about how diet-microbiota interactions can influence the immune system within and outside the gut and host health in general. Heat shock proteins are a set of highly conserved proteins that are present in all types of cells, from microbes to mammals. These proteins carry out crucial intracellular housekeeping functions and unexpected extracellular immuno-regulatory features in order to maintain the mucosal barrier integrity and gut homeostasis. It is becoming evident that the enteric microbiota is one of the major determinants of heat shock protein production in intestinal epithelial cells. This review will focus on the interactions between diet, gut microbiota and their role for regulating heat shock protein production and, furthermore, how these interactions influence the immune system and the integrity of the mucosal barrier.
Dmitry Alexeev's insight:
microbiota and heatshock - some of the topics we unite in our research
Nature is the international weekly journal of science: a magazine style journal that publishes full-length research papers in all disciplines of science, as well as News and Views, reviews, news, features, commentaries, web focuses and more, covering all branches of science and how science impacts upon all aspects of society and life.
Dmitry Alexeev's insight:
having a lot of data on metaaproteomics we are out to search all the possibilities data can provide
Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions and the associated transcriptional responses are often unknown. Organism-wide modeling of network activation can reveal unique and shared mechanisms between tissues, and potentially as yet unknown processes. The same method can also be applied to cell-biological conditions in one or more tissues.
"It has been drawn to our attention that the methods described in the main text and the Supplementary Information of this Article have been considered by some researchers to be insufficient to enable them to identify enterotypes in their own data sets."
Good start for the Nature addendum - and yes we were among those researchers who were unable to identify )))