Archaeal Communities of Frozen Quaternary Sediments of Marine Origin on the Coast of Western Spitsbergen

The archaeal composition of permafrost samples taken during the drilling of frozen marine sediments in the area of the Barentsburg coal mine on the east coast of Grønfjord Bay of Western Spitsbergen has been studied. This study is based on an analysis of the V4 region of the 16S rRNA gene, carried out using next-generation sequencing. The general phyla of the Archaea domain are Euryarchaeota, Bathyarchaeota, Thaumarchaeota, and Asgardarchaea. As a result of a phylogenetic analysis of the dominant operational taxonomic units, representatives of methanogenic and methane- and ammonium-oxidizing archaea, as well as heterotrophic archaea, are found. The methanogenic archaea of Euryarchaeota phylum, Methanobacteria class, are found in permafrost with controversial genesis, while the methane-oxidizing archaea of Methanomicrobia class Methanosarcinales order are found in the marine permafrost at Cape Finneset: the ANME-2a, -2b group in layers of 8.6 and 11.7 m and the ANME-2d group (Candidatus Methanoperedens) in a layer of 6.5 m. Ammonium-oxidizing archaea of phylum Thaumarchaeota is present in all types of permafrost, while the order of Nitrososphaerales is found in permafrost with controversial genesis and the order Nitrosopumilales is in permafrost with marine and controversial genesis. Representatives of phylum Bathyarchaeota are found stratigraphically in the most ancient samples under study. Asgardarchaeota superfylum is excluded in the layers of permafrost with marine genesis and is represented by the phyla Lokiarchaeota, Thorarchaeota, and an unclassified group belonging to this superphylum. The presence of methane, ethylene, and ethane in the permafrost of the first sea terrace of Cape Finneset at a depth of 11.7 m, as well as the composition of the archaeal community, give us reason to assume that, before freezing, microbiological processes of anaerobic methane oxidation took place in it, probably received from Tertiary rocks. The results of both this and previous works present the Spitsbergen permafrost as a rich archive of genetic information of little-studied prokaryotic groups

Bacterial Communities of Frozen Quaternary Sediments of Marine Origin on the Coast of Western Spitsbergen

The bacterial composition of permafrost samples taken during drilling of frozen marine sediments in the area of Barentsburg coal mine on the east coast of Grønfjord Bay of Western Spitsbergen has been studied. The study was based on the analysis of the V4 region of the 16S rRNA gene, carried out using next generation sequencing, as well as using classical microbiological methods (direct luminescence microscopy and aerobic cultivation).The total cell number in permafrost samples ranges from 6.73 ± 0.73 × 106 to 3.37 ± 0.19 107 cells per g. The number of cultivable aerobic bacteria in frozen samples on 1/5 TSA and R2A media ranges from 0 to 6.20 ± 0.45 × 104 CFU/g. Isolates of aerobic bacteria were identified by 16S rRNA gene analysis as representatives of the genera Arthrobacter, Pseudarthrobacter, Psychrobacter, and Rhodoferax. The dominant phyla of the domain Bacteria were Actinobacteria, Proteobacteria, Chloroflexi, Nitrospirae and Firmicutes. As a result of phylogenetic analysis of the dominant operational taxonomic units, representatives of methane oxidizing, sulfate reducing bacteria, as well as heterotrophic bacteria involved in the transformation of organic matter were found

A Dual-Beam Irradiation Facility for a Novel Hybrid Cancer Therapy

In this paper we present the main ideas and discuss both the feasibility and the conceptual design of a novel hybrid technique and equipment for an experimental cancer therapy based on the simultaneous and/or sequential application of two beams, namely a beam of neutrons and a CW (continuous wave) or intermittent sub-terahertz wave beam produced by a gyrotron for treatment of cancerous tumors. The main simulation tools for the development of the computer aided design (CAD) of the prospective experimental facility for clinical trials and study of such new medical technology are briefly reviewed. Some tasks for a further continuation of this feasibility analysis are formulated as well.Comment: 18 pages, 3 tables, 8 figures, 50 reference

Quantum dynamics in strong fluctuating fields

A large number of multifaceted quantum transport processes in molecular systems and physical nanosystems can be treated in terms of quantum relaxation processes which couple to one or several fluctuating environments. A thermal equilibrium environment can conveniently be modelled by a thermal bath of harmonic oscillators. An archetype situation provides a two-state dissipative quantum dynamics, commonly known under the label of a spin-boson dynamics. An interesting and nontrivial physical situation emerges, however, when the quantum dynamics evolves far away from thermal equilibrium. This occurs, for example, when a charge transferring medium possesses nonequilibrium degrees of freedom, or when a strong time-dependent control field is applied externally. Accordingly, certain parameters of underlying quantum subsystem acquire stochastic character. Herein, we review the general theoretical framework which is based on the method of projector operators, yielding the quantum master equations for systems that are exposed to strong external fields. This allows one to investigate on a common basis the influence of nonequilibrium fluctuations and periodic electrical fields on quantum transport processes. Most importantly, such strong fluctuating fields induce a whole variety of nonlinear and nonequilibrium phenomena. A characteristic feature of such dynamics is the absence of thermal (quantum) detailed balance.Comment: review article, Advances in Physics (2005), in pres

Hair Cell Bundles: Flexoelectric Motors of the Inner Ear

Microvilli (stereocilia) projecting from the apex of hair cells in the inner ear are actively motile structures that feed energy into the vibration of the inner ear and enhance sensitivity to sound. The biophysical mechanism underlying the hair bundle motor is unknown. In this study, we examined a membrane flexoelectric origin for active movements in stereocilia and conclude that it is likely to be an important contributor to mechanical power output by hair bundles. We formulated a realistic biophysical model of stereocilia incorporating stereocilia dimensions, the known flexoelectric coefficient of lipid membranes, mechanical compliance, and fluid drag. Electrical power enters the stereocilia through displacement sensitive ion channels and, due to the small diameter of stereocilia, is converted to useful mechanical power output by flexoelectricity. This motor augments molecular motors associated with the mechanosensitive apparatus itself that have been described previously. The model reveals stereocilia to be highly efficient and fast flexoelectric motors that capture the energy in the extracellular electro-chemical potential of the inner ear to generate mechanical power output. The power analysis provides an explanation for the correlation between stereocilia height and the tonotopic organization of hearing organs. Further, results suggest that flexoelectricity may be essential to the exquisite sensitivity and frequency selectivity of non-mammalian hearing organs at high auditory frequencies, and may contribute to the “cochlear amplifier” in mammals

Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3

Background: Alternative splicing (AS) of maturing mRNA can generate structurally and functionally distinct transcripts from the same gene. Recent bioinformatic analyses of available genome databases inferred a positive correlation between intron length and AS. To study the interplay between intron length and AS empirically and in more detail, we analyzed the diversity of alternatively spliced transcripts (ASTs) in the Drosophila RNA-binding Bruno-3 (Bru-3) gene. This gene was known to encode thirteen exons separated by introns of diverse sizes, ranging from 71 to 41,973 nucleotides in D. melanogaster. Although Bru-3's structure is expected to be conducive to AS, only two ASTs of this gene were previously described. Results: Cloning of RT-PCR products of the entire ORF from four species representing three diverged Drosophila lineages provided an evolutionary perspective, high sensitivity, and long-range contiguity of splice choices currently unattainable by high-throughput methods. Consequently, we identified three new exons, a new exon fragment and thirty-three previously unknown ASTs of Bru-3. All exon-skipping events in the gene were mapped to the exons surrounded by introns of at least 800 nucleotides, whereas exons split by introns of less than 250 nucleotides were always spliced contiguously in mRNA. Cases of exon loss and creation during Bru-3 evolution in Drosophila were also localized within large introns. Notably, we identified a true de novo exon gain: exon 8 was created along the lineage of the obscura group from intronic sequence between cryptic splice sites conserved among all Drosophila species surveyed. Exon 8 was included in mature mRNA by the species representing all the major branches of the obscura group. To our knowledge, the origin of exon 8 is the first documented case of exonization of intronic sequence outside vertebrates. Conclusion: We found that large introns can promote AS via exon-skipping and exon turnover during evolution likely due to frequent errors in their removal from maturing mRNA. Large introns could be a reservoir of genetic diversity, because they have a greater number of mutable sites than short introns. Taken together, gene structure can constrain and/or promote gene evolution

Mitochondrial Pseudogenes in the Nuclear Genomes of Drosophila

Mitochondrial pseudogenes in nuclear chromosomes (numts) have been detected in the genomes of a diverse range of eukaryotic species. However, the numt content of different genomes and their properties is not uniform, and study of these differences provides insight into the mechanisms and dynamics of genome evolution in different organisms. In the genus Drosophila, numts have previously only been identified on a genome-wide scale in the melanogaster subgroup. The present study extends the identification to 11 species of the Drosophila genus. We identify a total of 302 numts and show that the numt complement is highly variable in Drosophilids, ranging from just 4 in D. melanogaster to 67 in D. willistoni, broadly correlating with genome size. Many numts have undergone large-scale rearrangements in the nucleus, including interruptions, inversions, deletions and duplications of sequence of variable size. Estimating the age of the numts in the nucleus by phylogenetic tree reconstruction reveals the vast majority of numts to be recent gains, 90% having arisen on terminal branches of the species tree. By identifying paralogs and counting duplications among the extant numts we estimate that 23% of extant numts arose through post-insertion duplications. We estimate genus average rates of insertion of 0.75 per million years, and a duplication rate of 0.010 duplications per numt per million years

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world’s largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org

Intelligent control for energy-positive street lighting

The paper investigates the application of solar energy in public lighting for realizing a street lighting sub-grid with positive yearly energy balance. The focus is given to the central controller, which ensures the adaptive behavior of the overall system and provides smart city services to the end users via its web-based user interface. A functionality of the controller of special interest is the optimization of the energy management of the system, i.e., determining when to sell and buy electricity to/from the grid, in order to minimize the cost of electricity (or to maximize the profit) subject to a given, time-of-use variable energy tariff. This requires precise forecasts of the energy produced and consumed, as well as appropriate robust optimization techniques that guarantee that the system bridges potential power outages of moderate duration in island mode

The Evolution of Compact Binary Star Systems

We review the formation and evolution of compact binary stars consisting of white dwarfs (WDs), neutron stars (NSs), and black holes (BHs). Binary NSs and BHs are thought to be the primary astrophysical sources of gravitational waves (GWs) within the frequency band of ground-based detectors, while compact binaries of WDs are important sources of GWs at lower frequencies to be covered by space interferometers (LISA). Major uncertainties in the current understanding of properties of NSs and BHs most relevant to the GW studies are discussed, including the treatment of the natal kicks which compact stellar remnants acquire during the core collapse of massive stars and the common envelope phase of binary evolution. We discuss the coalescence rates of binary NSs and BHs and prospects for their detections, the formation and evolution of binary WDs and their observational manifestations. Special attention is given to AM CVn-stars -- compact binaries in which the Roche lobe is filled by another WD or a low-mass partially degenerate helium-star, as these stars are thought to be the best LISA verification binary GW sources.Comment: 105 pages, 18 figure