Quantifying the evolutionary dynamics of structure and content in closely-related E. coli genomes.

Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics of accessory genome evolution are very poorly understood, in contrast to the core genome where diversification is readily described by mutations and homologous recombination. Here, we tackle this problem for the case of very closely related genomes.

Hydrothermal vents supporting persistent plumes and microbial chemoautotrophy at Gakkel Ridge (Arctic Ocean).

Hydrothermal vents emit hot fluids enriched in energy sources for microbial life. Here, we compare the ecological and biogeochemical effects of hydrothermal venting of two recently discovered volcanic seamounts, Polaris and Aurora of the Gakkel Ridge, in the ice-covered Central Arctic Ocean. At both sites, persistent hydrothermal plumes increased up to 800 m into the deep Arctic Ocean.

High-quality draft genome of Gammaproteobacterial SUP05 cluster from non-buoyant hydrothermal plumes of ultraslow spreading Gakkel Ridge (Central Arctic Ocean).

Hydrothermal plumes are an important yet understudied component of deep-sea microbial ecosystems. We report metagenome-assembled genomes (MAGs) of three Bacteria belonging to the Gammaproteobacterial SUP05 cluster (family ), assembled from the metagenomes of two non-buoyant hydrothermal plumes in the ultraslow spreading Gakkel Ridge.

The Impact of Sea Ice Cover on Microbial Communities in Antarctic Shelf Sediments.

The area around the Antarctic Peninsula (AP) is facing rapid climatic and environmental changes, with so far unknown impacts on the benthic microbial communities of the continental shelves. In this study, we investigated the impact of contrasting sea ice cover on microbial community compositions in surface sediments from five stations along the eastern shelf of the AP using 16S ribosomal RNA (rRNA) gene sequencing. Redox conditions in sediments with long ice-free periods are characterized by a prevailing ferruginous zone, whereas a comparatively broad upper oxic zone is present at the heavily ice-covered station.

: scalable bacterial pan-genome graph construction.

The genomic diversity of microbes is commonly parameterized as SNPs relative to a reference genome of a well-characterized, but arbitrary, isolate. However, any reference genome contains only a fraction of the microbial , the set of genes observed in a given species. Reference-based approaches are thus blind to the dynamics of the accessory genome, as well as variation within gene order and copy number.

A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes.

Members of the bacterial genus Sulfurimonas (phylum Campylobacterota) dominate microbial communities in marine redoxclines and are important for sulfur and nitrogen cycling. Here we used metagenomics and metabolic analyses to characterize a Sulfurimonas from the Gakkel Ridge in the Central Arctic Ocean and Southwest Indian Ridge, showing that this species is ubiquitous in non-buoyant hydrothermal plumes at Mid Ocean Ridges across the global ocean. One Sulfurimonas species, Sulfurimonas pluma, was found to be globally abundant and active in cold (<0-4 °C), oxygen-saturated and hydrogen-rich hydrothermal plumes.

Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection.

Selection protocols such as SELEX, where molecules are selected over multiple rounds for their ability to bind to a target of interest, are popular methods for obtaining binders for diagnostic and therapeutic purposes. We show that Restricted Boltzmann Machines (RBMs), an unsupervised two-layer neural network architecture, can successfully be trained on sequence ensembles from single rounds of SELEX experiments for thrombin aptamers. RBMs assign scores to sequences that can be directly related to their fitnesses estimated through experimental enrichment ratios.

Endometrioid Cancer Associated With Endometriosis: From the Seed and Soil Theory to Clinical Practice.

Endometriosis is a benign condition characterized by the presence of ectopic endometrial tissue. It is still debated whether endometriosis is a disease that can predispose to the pathogenesis of endometrial cancer outside the uterus. Deficiencies in mismatch repair (MMR) genes are a known risk factor for developing endometrioid cancer.

Restoration experiments in polymetallic nodule areas.

Deep-seabed polymetallic nodule mining can have multiple adverse effects on benthic communities, such as permanent loss of habitat by removal of nodules and habitat modification of sediments. One tool to manage biodiversity risks is the mitigation hierarchy, including avoidance, minimization of impacts, rehabilitation and/or restoration, and offset. We initiated long-term restoration experiments at sites in polymetallic nodule exploration contract areas in the Clarion-Clipperton Zone that were (i) cleared of nodules by a preprototype mining vehicle, (ii) disturbed by dredge or sledge, (iii) undisturbed, and (iv) naturally devoid of nodules.

Impact of physical and functional fitness on mortality from all causes of physically independent older adults.

Objective: To provide reference values for functional fitness tests (PFFT) and verify the capability of these tests alone and grouped into a general index (GFFI-6), to predict mortality from all causes, during seven years of follow-up of physically independent older adults.

Methods: The sample consisted of 422 older adults, evaluated at baseline using six PFFTs, as well as sociodemographic, behavioral, anthropometric, and comorbidity variables. Mortality from all causes was followed for seven subsequent years.

Survival probability and size of lineages in antibody affinity maturation.

Affinity maturation (AM) is the process through which the immune system is able to develop potent antibodies against new pathogens it encounters, and is at the base of the efficacy of vaccines. At its core AM is analogous to a Darwinian evolutionary process, where B cells mutate and are selected on the base of their affinity for an antigen (Ag), and Ag availability tunes the selective pressure. In cases when this selective pressure is high, the number of B cells might quickly decrease and the population might risk extinction in what is known as a population bottleneck.

Comparison of Two 16S rRNA Primers (V3-V4 and V4-V5) for Studies of Arctic Microbial Communities.

Microbial communities of the Arctic Ocean are poorly characterized in comparison to other aquatic environments as to their horizontal, vertical, and temporal turnover. Yet, recent studies showed that the Arctic marine ecosystem harbors unique microbial community members that are adapted to harsh environmental conditions, such as near-freezing temperatures and extreme seasonality. The gene for the small ribosomal subunit (16S rRNA) is commonly used to study the taxonomic composition of microbial communities in their natural environment.

Quantitative modeling of the effect of antigen dosage on B-cell affinity distributions in maturating germinal centers.

Affinity maturation is a complex dynamical process allowing the immune system to generate antibodies capable of recognizing antigens. We introduce a model for the evolution of the distribution of affinities across the antibody population in germinal centers. The model is amenable to detailed mathematical analysis and gives insight on the mechanisms through which antigen availability controls the rate of maturation and the expansion of the antibody population.

Persistence of plastic debris and its colonization by bacterial communities after two decades on the abyssal seafloor.

The fate of plastic debris entering the oceans is largely unconstrained. Currently, intensified research is devoted to the abiotic and microbial degradation of plastic floating near the ocean surface for an extended period of time. In contrast, the impacts of environmental conditions in the deep sea on polymer properties and rigidity are virtually unknown.

Effects of a deep-sea mining experiment on seafloor microbial communities and functions after 26 years.

Future supplies of rare minerals for global industries with high-tech products may depend on deep-sea mining. However, environmental standards for seafloor integrity and recovery from environmental impacts are missing. We revisited the only midsize deep-sea disturbance and recolonization experiment carried out in 1989 in the Peru Basin nodule field to compare habitat integrity, remineralization rates, and carbon flow with undisturbed sites.

CO leakage can cause loss of benthic biodiversity in submarine sands.

One of the options to mitigate atmospheric CO increase is CO Capture and Storage in sub-seabed geological formations. Since predicting long-term storage security is difficult, different CO leakage scenarios and impacts on marine ecosystems require evaluation. Submarine CO vents may serve as natural analogues and allow studying the effects of CO leakage in a holistic approach.

Environmental Drivers Controlling Bacterial and Archaeal Abundance in the Sediments of a Mediterranean Lagoon Ecosystem.

The environmental factors controlling the abundance of Bacteria and Archaea in lagoon ecosystems are poorly understood. Here, an integrated physico-chemical, biogeochemical, and microbiological survey was applied in the Sacca di Goro lagoon (Po River Delta, Italy) to investigate the variation of bacterial and archaeal abundance, as assessed by Fluorescence In Situ Hybridization, along winter and summer environmental gradients. We hypothesised that bacterial and archaeal cells respond differentially to physico-chemical parameters of the sediment, which can be manifested in variations of total cells number.

CO leakage alters biogeochemical and ecological functions of submarine sands.

Subseabed CO storage is considered a future climate change mitigation technology. We investigated the ecological consequences of CO leakage for a marine benthic ecosystem. For the first time with a multidisciplinary integrated study, we tested hypotheses derived from a meta-analysis of previous experimental and in situ high-CO impact studies.

Response of Posidonia oceanica seagrass and its epibiont communities to ocean acidification.

The unprecedented rate of CO2 increase in our atmosphere and subsequent ocean acidification (OA) threatens coastal ecosystems. To forecast the functioning of coastal seagrass ecosystems in acidified oceans, more knowledge on the long-term adaptive capacities of seagrass species and their epibionts is needed. Therefore we studied morphological characteristics of Posidonia oceanica and the structure of its epibiont communities at a Mediterranean volcanic CO2 vent off Panarea Island (Italy) and performed a laboratory experiment to test the effect of OA on P.

Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems.

Bacteria and archaea dominate the biomass of benthic deep-sea ecosystems at all latitudes, playing a crucial role in global biogeochemical cycles, but their macroscale patterns and macroecological drivers are still largely unknown. We show the results of the most extensive field study conducted so far to investigate patterns and drivers of the distribution and structure of benthic prokaryote assemblages from 228 samples collected at latitudes comprising 34°N to 79°N, and from ca. 400- to 5570-m depth.

[Analysis of the influence of pharmacotherapy on the quality of life of seniors with osteoarthritis].

Aims: This study aimed to assess the influence of pharmacotherapy on health-related quality of life of elderly with ostheoartritis.

Methods: Longitudinal study involving 91 older adults from both genders (Age: 70.36±5.

Smoking status and its relationship with exercise capacity, physical activity in daily life and quality of life in physically independent, elderly individuals.

Objective: To investigate the relationship between smoking status and exercise capacity, physical activity in daily life and health-related quality of life in physically independent, elderly (≥60 years) individuals.

Design: Cross-sectional, observational study.

Setting: Community-dwelling, elderly individuals.

Large-scale distribution and activity of prokaryotes in deep-sea surface sediments of the Mediterranean Sea and the adjacent Atlantic Ocean.

The deep-sea represents a substantial portion of the biosphere and has a major influence on carbon cycling and global biogeochemistry. Benthic deep-sea prokaryotes have crucial roles in this ecosystem, with their recycling of organic matter from the photic zone. Despite this, little is known about the large-scale distribution of prokaryotes in the surface deep-sea sediments.

Reliability of CARD-FISH procedure for enumeration of Archaea in deep-sea surficial sediments.

The enumeration of Archaea in deep-sea sediment samples is still limited, although different methodological procedures have been applied. Among these, catalysed reporter deposition-fluorescence in situ hybridisation (CARD-FISH) technique is a promising tool for estimation of archaeal abundance in deep-sea sediment samples. Comparing different permeabilisation treatments, the best results obtained both on archaeal pure cultures and on natural assemblages were with hydrochloric acid (0.