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It is generally acknowledged that reactive oxygen species (ROS) play crucial roles in a variety of natural processes in cells. If increased to levels which cannot be neutralized by the defense mechanisms, they damage biological molecules, alter their functions, and also act as signaling molecules thus generating a spectrum of pathologies. In this review, we summarize current data on oxidative stress markers associated with human immunodeficiency virus type-1 (HIV-1) infection, analyze mechanisms by which this virus triggers massive ROS production, and describe the status of various defense mechanisms of the infected host cell. In addition, we have scrutinized scarce data on the effect of ROS on HIV-1 replication. Finally, we present current state of knowledge on the redox alterations as crucial factors of HIV-1 pathogenicity, such as neurotoxicity and dementia, exhaustion of CD4+/CD8+ T-cells, predisposition to lung infections, and certain side effects of the antiretroviral therapy, and compare them to the pathologies associated with the nitrosative stress.

Fibrobacter succinogenes is an important member of the rumen microbial community that converts plant biomass into nutrients usable by its host. This bacterium, which is also one of only two cultivated species in its phylum, is an efficient and prolific degrader of cellulose. Specifically, it has a particularly high activity against crystalline cellulose that requires close physical contact with this substrate. However, unlike other known cellulolytic microbes, it does not degrade cellulose using a cellulosome or by producing high extracellular titers of cellulase enzymes. To better understand the biology of F. succinogenes, we sequenced the genome of the type strain S85 to completion. A total of 3,085 open reading frames were predicted from its 3.84 Mbp genome. Analysis of sequences predicted to encode for carbohydrate-degrading enzymes revealed an unusually high number of genes that were classified into 49 different families of glycoside hydrolases, carbohydrate binding modules (CBMs), carbohydrate esterases, and polysaccharide lyases. Of the 31 identified cellulases, none contain CBMs in families 1, 2, and 3, typically associated with crystalline cellulose degradation. Polysaccharide hydrolysis and utilization assays showed that F. succinogenes was able to hydrolyze a number of polysaccharides, but could only utilize the hydrolytic products of cellulose. This suggests that F. succinogenes uses its array of hemicellulose-degrading enzymes to remove hemicelluloses to gain access to cellulose. This is reflected in its genome, as F. succinogenes lacks many of the genes necessary to transport and metabolize the hydrolytic products of non-cellulose polysaccharides. The F. succinogenes genome reveals a bacterium that specializes in cellulose as its sole energy source, and provides insight into a novel strategy for cellulose degradation.

Hepatitis C virus (HCV) is a highly pathogenic human virus associated with liver fibrosis, steatosis, and cancer. In infected cells HCV induces oxidative stress. Here, we show that HCV proteins core, E1, E2, NS4B, and NS5A activate antioxidant defense Nrf2/ARE pathway via several independent mechanisms. This was demonstrated by the analysis of transient co-expression in Huh7 cells of HCV proteins and luciferase reporters. Expression, controlled by the promoters of stress-response genes or their minimal Nrf2-responsive elements, was studied using luminescence assay, RT-qPCR and/or Western-blot analysis. All five proteins induced Nrf2 activation by protein kinase C in response to accumulation of reactive oxygen species (ROS). In addition, expression of core, E1, E2, NS4B, and NS5A proteins resulted in the activation of Nrf2 in a ROS-independent manner. The effect of core and NS5A was mediated through casein kinase 2 and phosphoinositide-3 kinase, whereas those of NS4B, E1, and E2, were not mediated by either PKC, CK2, PI3K, p38, or ERK. Altogether, on the earliest stage of expression HCV proteins induced a strong up-regulation of the antioxidant defense system. These events may underlie the harmful effects of HCV-induced oxidative stress during acute stage of hepatitis C.

Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of diversity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts. Almost 190,000 draft-quality DNA virus genomes are recovered by mining more than 11,000 deposited human stool metagenomes to improve resources for understanding the human gut virome.

This work aims to present our current best physical understanding of common-envelope evolution (CEE). We highlight areas of consensus and disagreement, and stress ideas which should point the way forward for progress in this important but long-standing and largely unconquered problem. Unusually for CEE-related work, we mostly try to avoid relying on results from population synthesis or observations, in order to avoid potentially being misled by previous misunderstandings. As far as possible we debate all the relevant issues starting from physics alone, all the way from the evolution of the binary system immediately before CEE begins to the processes which might occur just after the ejection of the envelope. In particular, we include extensive discussion about the energy sources and sinks operating in CEE, and hence examine the foundations of the standard energy formalism. Special attention is also given to comparing the results of hydrodynamic simulations from different groups and to discussing the potential effect of initial conditions on the differences in the outcomes. We compare current numerical techniques for the problem of CEE and also whether more appropriate tools could and should be produced (including new formulations of computational hydrodynamics, and attempts to include 3D processes within 1D codes). Finally we explore new ways to link CEE with observations. We compare previous simulations of CEE to the recent outburst from V1309 Sco, and discuss to what extent post-common-envelope binaries and nebulae can provide information, e.g. from binary eccentricities, which is not currently being fully exploited.

Common-envelope events (CEEs), during which two stars temporarily orbit within a shared envelope, are believed to be vital for the formation of a wide range of close binaries. For decades, the only evidence that CEEs actually occur has been indirect, based on the existence of systems that could not be otherwise explained. Here we propose a direct observational signature of CEEs arising from a physical model where emission from matter ejected in a CEE is controlled by a recombination front as the matter cools. The natural range of time scales and energies from this model, as well as the expected colors, light-curve shapes, ejection velocities, and event rate, match those of a recently recognized class of red transient outbursts.

Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called ‘microbial dark matter’. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet. Uncultivated archaeal and bacterial cells of major uncharted branches of the tree of life are targeted and sequenced using single-cell genomics; this enables resolution of many intra- and inter-phylum-level relationships, uncovers unexpected metabolic features that challenge established boundaries between the three domains of life, and leads to the proposal of two new superphyla. The genomics of uncultured microbes Currently available genome sequences give us a narrow view of the remarkable diversity of microorganisms because the vast majority of them have never been cultivated in pure culture. Here Tanja Woyke and colleagues use single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats. This information reveals numerous intra- and inter-phylum relationships and a number of unexpected metabolic features. On the basis of the new data the authors propose taxonomic revisions to the archaeal and bacterial domains, including a proposal to reorganizing the Archaea into three superphyla.

—For the first time, an approach to processing Earth remote sensing (ERS) data obtained by the Harmonized Landsat Sentinel-2 spacecraft has been applied to the northern end of the eastern slope of the Polar Urals. It consists of integrating metasomatic alteration distribution maps and lineament density schemes created based on the results of statistical processing of multispectral ERS data, as well as the Aster GDEM (Advanced Spaceborne Thermal Emission and Reflection Radiometer Global Digital Elevation Model) digital elevation model. The study has been carried out to identify morphological signs and patterns and features of the deep structure to identify areas promising for gold ore mineralization. As a result of the study, two new promising areas have been outlined and additional prediction and exploration criteria for gold mineralization have been identified: (1) it has been established that areas promising for the gold ore type of mineralization should be sought along transregional fault zones that intersect favorable horizons and structures and control ore mineralization, as well as along the periphery of a large (97 by 76 km) bowl-shaped heterogeneous volcano–plutonic structure of the first order with a long history of development localized above intracrustal magmatic chambers; (2) the morphostructure must be complicated by ring and arc structures of the second rank and higher, as well as NW- and NE-trending faults with a length of more than 10 km, or weakened zones, along which intrusions of intrusive bodies paragenetically associated with mineralization are recorded; and (3) in potentially ore-bearing volcanic structures, metasomatic halos of a significant area (more than 30 km 2 ) with increased values of iron (III) oxides (hematite), iron (II) oxides, and hydroxides (limonite), as well as (to a lesser extent) hydroxyl–(Al–OH, Mg–OH), carbonate-containing minerals, and ferrous oxides, must be manifested.

The relevance of the proposed study is due to the application of Newton’s laws on the determination of speed and acceleration, which reflects the establishment of the actual specific weights of production factors by phases (stages) of the economies’ development of the countries in the world. By applying the laws of physics, the simplest methods have been developed for decomposing the absolute growth of GDP per capita, according to the factors that determine it. A model of economic growth is determined, which is similar in content to Newton’s first law of measuring the paths traveled with uniformly accelerated motion of matter. By calculation, the forecast parameters of the Russian economy can be determined, which determine the GDP per capita until 2030. At the same time, the basic factors of development (45%), investment in fixed assets (35%) and innovative (20%) remain the main factor in the development of global competitiveness in Russia. To do this, you need to gain the proper acceleration. We propose a new approach for assessing the economic stability of socio-economic systems, based on taking into account the mutual influence of the elements of large systems on each other. The novelty of the research lies in the use of the laws of inertia in the development of the economy, since the existing forecasting activity does not provide for obtaining promising changes in the volume and structure of the forecast. As the competitiveness of the countries of the world develops, the share of basic factors such as labor, capital and natural resources decreases significantly (from 50% in the first stage to 40% in the second, and up to 30% in the third stage of economic development). In the stage of high-tech development of the countries in the world, the proportion of factors of innovative development grows up to 30% comparing with 10% in the first two stages of its development. To illustrate the applied value, Newton’s second law was applied as an alternative method for preliminary estimation of the specific weights of three groups of production factors.

Metagenomic and microbial sequence data are made easier to interpret with the addition of 1,003 genomes to the Genomic Encyclopedia of Bacteria and Archaea. We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.