87 research outputs found

    The first data on methane concentrations in degassing griffins of Lake Baskunchak

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    For the first time, the distribution of methane in the brine and bottom sediments of the Ulan-Blag stream (tributary of Lake Baskunchak), fed by underground degassing springs, as well as directly in Baskunchak Lake at a distance from underground sources. The composition of the main ions in brine, acid-base and redox conditions in bottom sediments have been established. The brine mineralization in Baskunchak Lake is 312 g/dm3, which is 2.1 times higher than the mineralization of the Ulan-Blag stream. The chemical composition of the brine of both stations is classified as chloride type, sodium cationic composition. The concentration of methane in the brine of the studied underground degassing sources in the ravine stream of the Ulan-Blag reaches high values (up to 215 µl/dm3), exceeding by 1–2 orders of magnitude its concentration in the brine of Lake Baskunchak. The low concentrations of methane in the brine of the lake are probably due to its insignificant flow from the bottom sediments into the water due to the presence of a salt crust that prevents gas emission, as well as due to its small concentrations in the upper layers of sediments

    The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

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    INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

    Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers

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    Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity using small-angle X-ray scattering, cytometry, and fluorescence polarization. Using a new iterative design procedure, Interaction Based Drug Design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.peerReviewe

    Novel Hybrid Benzoazacrown Ligand as a Chelator for Copper and Lead Cations: What Difference Does Pyridine Make

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    A synthetic procedure for the synthesis of azacrown ethers with a combination of pendant arms has been developed and the synthesized ligand, characterized by various techniques, was studied. The prepared benzoazacrown ether with hybrid pendant arms and its complexes with copper and lead cations were studied in terms of biomedical applications. Similarly to a fully acetate analog, the new one binds both cations with close stability constants, despite the decrease in both constants. The calculated geometry of the complexes correlate with the data from X-ray absorption and NMR spectroscopy. Coordination of both cations differs due to the difference between the ionic radii. However, these chelation modes provide effective shielding of cations in both cases, that was shown by the stability of their complexes in the biologically relevant media towards transchelation and transmetallation

    Insights into fullerene polymerization under the high pressure: The role of endohedral Sc dimer

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    In this work, through the technology of producing endohedral metallofullerene in macroscopic quanti-ties, the process of pressure polymerization of Sc2C2@C-82 and their mechanical properties have been investigated in detail using a set of experimental and theoretical methods. The crucial role of endohedral atoms is demonstrated by comparison with pristine fullerenes. It is shown that the embedding of Sc2C2 complex inside a fullerene significantly facilitates the polymerization process which finally leads to the highly rigid material at high pressures. (C) 2021 Elsevier Ltd. All rights reserved

    Database of Ice-Rich Yedoma Permafrost Version 2 (IRYP v2)

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    Ice-rich permafrost in the circum-Arctic and sub-Arctic, such as late Pleistocene Yedoma, are especially prone to degradation due to climate change or human activity. When Yedoma deposits thaw, large amounts of frozen organic matter and biogeochemically relevant elements return into current biogeochemical cycles. Building on previous mapping efforts, the objective of this paper is to compile the first digital pan-Arctic Yedoma map and spatial database of Yedoma coverage. Therefore, we 1) synthesized, analyzed, and digitized geological and stratigraphical maps allowing identification of Yedoma occurrence at all available scales, and 2) compiled field data and expert knowledge for creating Yedoma map confidence classes. We used GIS-techniques to vectorize maps and harmonize site information based on expert knowledge. Hence, here we synthesize data on the circum-Arctic and sub-Arctic distribution and thickness of Yedoma for compiling a preliminary circum-polar Yedoma map. To harmonize the different datasets and to avoid merging artifacts, we applied map edge cleaning while merging data from different database layers. For the digitalization and spatial integration, we used Adobe Photoshop CS6 (Version: 13.0 x64), Adobe Illustrator CS6 (Version 16.0.3 x64), Avenza MAPublisher 9.5.4 (Illustrator Plug-In) and ESRI ArcGIS 10.6.1 for Desktop (Advanced License). Generally, we followed workflow of figure 2 of the related publication (IRYP Version 2, Strauss et al 2021, https://doi.org/10.3389/feart.2021.758360). We included a range of attributes for Yedoma areas based on lithological and stratigraphic information from the source maps and assigned three different confidence levels of the presence of Yedoma (confirmed, likely, or uncertain). Using a spatial buffer of 20 km around mapped Yedoma occurrences, we derived an extent of the Yedoma domain. Our result is a vector-based map of the current pan-Arctic Yedoma domain that covers approximately 2,587,000 km², whereas Yedoma deposits are found within 480,000 km² of this region. We estimate that 35% of the total Yedoma area today is located in the tundra zone, and 65% in the taiga zone. With this Yedoma mapping, we outlined the substantial spatial extent of late Pleistocene Yedoma deposits and created a unique pan-Arctic dataset including confidence estimates

    Circum-Arctic Map of the Yedoma Permafrost Domain

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    Ice-rich permafrost in the circum-Arctic and sub-Arctic (hereafter pan-Arctic), such as late Pleistocene Yedoma, are especially prone to degradation due to climate change or human activity. When Yedoma deposits thaw, large amounts of frozen organic matter and biogeochemically relevant elements return into current biogeochemical cycles. This mobilization of elements has local and global implications: increased thaw in thermokarst or thermal erosion settings enhances greenhouse gas fluxes from permafrost regions. In addition, this ice-rich ground is of special concern for infrastructure stability as the terrain surface settles along with thawing. Finally, understanding the distribution of the Yedoma domain area provides a window into the Pleistocene past and allows reconstruction of Ice Age environmental conditions and past mammoth-steppe landscapes. Therefore, a detailed assessment of the current pan-Arctic Yedoma coverage is of importance to estimate its potential contribution to permafrost-climate feedbacks, assess infrastructure vulnerabilities, and understand past environmental and permafrost dynamics. Building on previous mapping efforts, the objective of this paper is to compile the first digital pan-Arctic Yedoma map and spatial database of Yedoma coverage. Therefore, we 1) synthesized, analyzed, and digitized geological and stratigraphical maps allowing identification of Yedoma occurrence at all available scales, and 2) compiled field data and expert knowledge for creating Yedoma map confidence classes. We used GIS-techniques to vectorize maps and harmonize site information based on expert knowledge. We included a range of attributes for Yedoma areas based on lithological and stratigraphic information from the source maps and assigned three different confidence levels of the presence of Yedoma (confirmed, likely, or uncertain). Using a spatial buffer of 20 km around mapped Yedoma occurrences, we derived an extent of the Yedoma domain. Our result is a vector-based map of the current pan-Arctic Yedoma domain that covers approximately 2,587,000 km2, whereas Yedoma deposits are found within 480,000 km2 of this region. We estimate that 35% of the total Yedoma area today is located in the tundra zone, and 65% in the taiga zone. With this Yedoma mapping, we outlined the substantial spatial extent of late Pleistocene Yedoma deposits and created a unique pan-Arctic dataset including confidence estimates

    A Neural Network Technique for the Derivation of Runge-Kutta Pairs Adjusted for Scalar Autonomous Problems

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    We consider the scalar autonomous initial value problem as solved by an explicit Runge-Kutta pair of orders 6 and 5. We focus on an efficient family of such pairs, which were studied extensively in previous decades. This family comes with 5 coefficients that one is able to select arbitrarily. We set, as a fitness function, a certain measure, which is evaluated after running the pair in a couple of relevant problems. Thus, we may adjust the coefficients of the pair, minimizing this fitness function using the differential evolution technique. We conclude with a method (i.e. a Runge-Kutta pair) which outperforms other pairs of the same two orders in a variety of scalar autonomous problems

    The Role of Small-Angle X-Ray Scattering and Molecular Simulations in 3D Structure Elucidation of a DNA Aptamer Against Lung Cancer

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    Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here we present a general optimization procedure for finding most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated aptamer LC-18t was developed. A three-dimensional shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The truncated aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.peerReviewe

    Cloning and Characterization of Polyhydroxybutyrate Synthase from Methylobacterium extorquens AM1

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    В результате поиска генов, кодирующих вероятные ПГБ-синтазы в геномах бактерий рода Methylobacterium, выявлены множественные (до пяти у одного штамма) гены ПГБ-синтаз. Филогенетическим анализом показано, что белки PhaC1, PhaC2, PhaC3 относятся к I классу ПГБ-синтаз, белки PhaC4 – к ПГБ-синтазам III класса, тогда как PhaC5, по-видимому, представляет неохарактеризованный класс ПГБ-синтаз. Впервые выделена и охарактеризована рекомбинантная ПГБ-синтаза I класса (КФ 2.3.1.B2) из Methylobacterium extorquens AM1, кодируемая геном phaC1. Молекулярная масса мономера фермента составила 78 кДа. Константа Михаэлиса (Km) для PhaC1 из штамма AM1 составила 1,3 мМ, а максимальная скорость реакции (Vmax) – 0,1 мкмоль∙мин-1∙мг-1. Получен делеционный мутант Methylobacterium extorquens по гену phaC, перспективный для дальнейшего исследования особенностей биосинтеза ПГБ метилобактериямиMultiple genes encoding putative PHB synthases (up to 5 in single strain) were found in Methylobacterium genomes. As a result of phylogenetic analysis proteins PhaC1, PhaC2, PhaC3 were identified as class I PHB synthases, PhaC4 proteins were identified as class III PHB synthases, while PhaC5 apparently belongs to uncharacterized class of PHB synthases. Firstly, the recombinant class I PBH synthase (EC 2.3.1.B2) encoded by phaC1 gene from Methylobacterium extorquens AM1 was purified and characterized. Molecular mass of enzyme monomer was 78 kDa. Michaelis constant (Km) for PhaC1 was 1,3 mM and maximal reaction rate (Vmax) was 0,1 μmol∙min–1∙mg–1. The deletion mutant of Methylobacterium extorquens in the phaC gene was obtained which is promising for further study of peculiarities of methylobacteria’s PHB biosynthesi
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