metaBIT,an integrative and automated metagenomic pipeline for analysing microbial profiles from high‐throughput sequencing shotgun data

Micro‐organisms account for most of the Earth's biodiversity and yet remain largely unknown. The complexity and diversity of microbial communities present in clinical and environmental samples can now be robustly investigated in record times and prices thanks to recent advances in high‐throughput DNA sequencing (HTS). Here, we develop metaBIT, an open‐source computational pipeline automatizing routine microbial profiling of shotgun HTS data. Customizable by the user at different stringency levels, it performs robust taxonomy‐based assignment and relative abundance calculation of microbial taxa, as well as cross‐sample statistical analyses of microbial diversity distributions. We demonstrate the versatility of metaBIT within a range of published HTS data sets sampled from the environment (soil and seawater) and the human body (skin and gut), but also from archaeological specimens. We present the diversity of outputs provided by the pipeline for the visualization of microbial profiles (barplots, heatmaps) and for their characterization and comparison (diversity indices, hierarchical clustering and principal coordinates analyses). We show that metaBIT allows an automatic, fast and user‐friendly profiling of the microbial DNA present in HTS shotgun data sets. The applications of metaBIT are vast, from monitoring of laboratory errors and contaminations, to the reconstruction of past and present microbiota, and the detection of candidate species, including pathogens.     

ECM-Regulator timp Is Required for Stem Cell Niche Organization and Cyst Production in the Drosophila Ovary

The extracellular matrix (ECM) is a pivotal component adult tissues and of many tissue-specific stem cell niches. It provides structural support and regulates niche signaling during tissue maintenance and regeneration. In many tissues, ECM remodeling depends on the regulation of MMP (matrix metalloproteinase) activity by inhibitory TIMP (tissue inhibitors of metalloproteinases) proteins. Here, we report that the only Drosophila timp gene is required for maintaining the normal organization and function of the germline stem cell niche in adult females. timp mutant ovaries show reduced levels of both Drosophila Collagen IV α chains. In addition, tissue stiffness and the cellular organization of the ovarian niche are affected in timp mutants. Finally, loss of timp impairs the ability of the germline stem cell niche to generate new cysts. Our results demonstrating a crucial role for timp in tissue organization and gamete production thus provide a link between the regulation of ECM metabolism and tissue homeostasis.     

Effects of weed harrowing frequency on beneficial arthropods,plants and crop yield

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Perspectives of surface plasmon resonance sensors for optimized biogas methanation

Biogas production is becoming significantly viable as an energy source for replacing fossil‐based fuels. The further development of the biogas production process could lead to significant improvements in its potential. Wastewater treatment currently accounts for 3% of the electrical energy load in developed countries, while it could be developed to provide a source of nitrogen and phosphorus, in addition to energy. The improvement of anaerobic digestion (AD) detection technologies is the cornerstone to reach higher methane productivities and develop fully automatized processes to decrease operational costs. New sensors are requested to automatically obtain a better interpretation of the complex and dynamical internal reactor environment. This will require detailed systematic detection in order to realize a near‐optimal production process. In this review, optical fiber‐based sensors will be discussed to assess their potential for use in AD. There is currently a disparity between the complexity of AD, and online detection. By improving the durability, sensitivity, and cost of dissolved H₂ (as well as H₂S, acetic acid, ammonia, and methane) sensor technology, further understanding of the AD process may allow the prevention of process failure. The emergence of surface plasmon resonance (SPR) sensing with optical fibers coupled with the H₂‐sensitive metal palladium, allows detection of dissolved hydrogen in liquid. By implementing these SPR sensors into AD, improvements to the biogas production process, even at small scales, may be achieved by guiding the process in the optimum direction, avoiding the collapse of the biological process. This review intends to assess the feasibility of online, cost‐effective, rapid, and efficient detection of dissolved H₂, as well as briefly assessing H₂S, acetic acid, ammonia, and methane in AD by SPR.     

Size-asymmetric root competition in deep,nutrient-poor soil

Aims There is much evidence that plant competition below ground is size symmetric, i.e. that competing plants share contested resources in proportion to their sizes. Several researchers have hypothesized that a patchy distribution of soil nutrients could result in size-asymmetric root competition. We tested this hypothesis.     

Potent inhibitors of malarial P. Falciparum protein kinase G: Improving the cell activity of a series of imidazopyridines

Development of a class of bicyclic inhibitors of the Plasmodium falciparum cyclic GMP-dependent protein kinase (PfPKG), starting from known compounds with activity against a related parasite PKG orthologue, is reported. Examination of key sub-structural elements led to new compounds with good levels of inhibitory activity against the recombinant kinase and in vitro activity against the parasite. Key examples were shown to possess encouraging in vitro ADME properties, and computational analysis provided valuable insight into the origins of the observed activity profiles.     

Autoinhibition Mechanism of the Ubiquitin-Conjugating Enzyme UBE2S by Autoubiquitination

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Surfing on the seascape: Adaptation in a changing environment

The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation‐limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an “adaptive‐walk” approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations.     

A high‐stress shelly fauna associated with sponge mud‐mounds in the Coniacian Arnager Limestone of Bornholm,Denmark

The benthic macrofaunas of the Upper Cretaceous chalk of NW Europe show characteristically high species‐richnesses and commonly high densities. They are predominated by bivalves, brachiopods, polychaetes, echinoids, crinoids, asteroids, sponges and towards the end of the Cretaceous also by bryozoans. The mound‐bedded chalk of the Coniacian Arnager Limestone on the island of Bornholm in the Baltic Sea, Denmark, differs from this general picture. It was deposited on a small fault block adjacent to the main Bornholm block, which was emerged during much of the Mesozoic and thus occupied a much more proximal position than most other Upper Cretaceous chalks in NW Europe. The Arnager Limestone contains a unique, exceptionally rich and well‐preserved fauna of mainly hexactinellid, lyssacinosan sponges. The low mud‐mounds are interpreted as formed by baffling and trapping of fine sediment particles by the dense sponge thickets. In contrast, the associated shelly fauna is unusually sparse, of very low richness and extremely low density, except for inoceramid bivalves. It represents a strongly depauparated version of the shelly faunas of contemporaneous chalks in NW Europe. The rare specimens of non‐inoceramid shelly species are interpreted to represent occasional successful spatfalls of benthic species from the deeper‐water chalk farther offshore in the Baltic area. The sponge mud‐mounds of the Arnager Limestone show remarkable resemblances with modern sponge mounds recently discovered on the continental shelf of western Canada. They form an important link between the well‐known older Mesozoic sponge mud‐mounds or ‘reefs’ and the modern mounds and are among the youngest examples of Mesozoic sponge mounds.