Kinetics of Amyloid Formation by Different Proteins and Peptides: Polymorphism and Sizes of Folding Nuclei of Fibrils

Aggregation of peptides and proteins into amyloid structure is one of the most intensively studied biological phenomena at the moment. To date, there is no developed theory that would allow one to determine what kind of mechanism presents in the given experiment on the basis of aggregation kinetic data. Debates concerning the mechanism of the amyloid fibrils formation and, in particular, the size of the amyloidogenic nucleus are still going on. We created such a theory on the basis of the kinetics of amyloid aggregates formation. In the presented chapter, theoretical and experimental approaches were employed for studding the process of amyloid formation by different proteins and peptides. The current kinetic models described in this chapter adequately describe the key features of amyloid nucleation and growth

PRE-FLOW AND OF A NUCLEUS FORMATION OF LOCALIZED DEFORMATION BAND IN LOW-CARBON STEEL WITH DEFORMATION AGING

С использованием метода корреляции цифровых изображений изучены особенности пластического течения в ходе деформации растяжением образцов стали 08Г2Б, проявляющей эффект деформационного старения. Стандартные плоские образцы, вырезанные из листа, изготовленного по режиму контролируемой прокатки, испытаны на растяжение после термообработки: 680 °C, выдержка 30 мин, охлаждение на воздухе. Показано, что на стадии макроупругой деформации происходит как рассеянное пластическое течение в отдельных участках растягиваемого образца, так и возникновение зародышевого центра в приповерхностной области, из которой впоследствии вырастает зародыш полосы локализованной деформации.By means of digital image correlation method, the features of plastic flow during tensile deformation of 08G2B steel samples exhibiting the effect of deformation aging were studied. Standard flat samples were tested for tensile strength after heat treatment according to the mode: 680 °C, holding time 30 min, air cooling. It was shown that at the stage of macroelastic deformation, both scattered flow occurs in individual parts of the stretched sample, and the emergence of the nucleus center, the region from which the nucleus of the localized deformation band subsequently grows

Засоби розробки WebAR: огляд

Web augmented reality (WebAR) development tools aimed at improving the visual aspects of learning are far from being visual and available themselves. This causing problems of selecting and testing WebAR development tools for CS undergraduates mastering in web-design basics. The research is aimed at conducting comparative analysis of WebAR tools to select those appropriated for beginners.Інструменти розробки доповненої реальності в Інтернеті (WebAR), спрямовані на покращення візуальних аспектів навчання, далеко не візуальні та доступні самі по собі. Це викликає проблеми з вибором та тестуванням засобів розробки WebAR для CS-студентів, які опановують основи веб-дизайну. Дослідження спрямоване на проведення порівняльного аналізу інструментів WebAR для відбору інструментів, призначених для початківців

Formation of Amyloid-Like Fibrils by Y-Box Binding Protein 1 (YB-1) Is Mediated by Its Cold Shock Domain and Modulated by Disordered Terminal Domains

YB-1, a multifunctional DNA- and RNA-binding nucleocytoplasmic protein, is involved in the majority of DNA- and mRNA-dependent events in the cell. It consists of three structurally different domains: its central cold shock domain has the structure of a β-barrel, while the flanking domains are predicted to be intrinsically disordered. Recently, we showed that YB-1 is capable of forming elongated fibrils under high ionic strength conditions. Here we report that it is the cold shock domain that is responsible for formation of YB-1 fibrils, while the terminal domains differentially modulate this process depending on salt conditions. We demonstrate that YB-1 fibrils have amyloid-like features, including affinity for specific dyes and a typical X-ray diffraction pattern, and that in contrast to most of amyloids, they disassemble under nearly physiological conditions

Nanohaloarchaea as beneficiaries of xylan degradation by haloarchaea

DATA AVAILABILITY STATEMENT : All statements regarding data availability, finding resources and conflict of interest disclosure have been provided.DATA DEPOSITION : All (meta)genomic and transcriptomic information is available under GenBank BioProject ID PRJNA865582; BioSamples SAMN30630960, SAMN30630938, SAMN30630946, SAMN30631035, SAMN30630966, SAMN30631033, SAMN30120999, SAMN30121000, SAMN30121001, SAMN30121002, SAMN30121003 and SAMN30121004; genome accession no. CP104322 for Halorhabdus sp. SVX81, genome accession no. CP104395 for Ca. Nanohalococcus occultus SVXNc, genome accession nos. CP104741 (chromosome), CP104742 (plasmid 1), CP104743 (plasmid 2) and CP104744 (plasmid 3) for Haloferax lucertense SVX82; genome accession no. CP107254 for Halorhabdus sp. BNX81, genome accession no. CP107255 for Ca. Nanohalovita haloferacivicina BNXNv, genome accession nos. CP106966 (chromosome), CP106967 (plasmid 1), CP106968 (plasmid 2), CP106969 (plasmid 3) and CP106970 (plasmid 4) for Haloferax lucertense BNX82. Transcriptomic raw data are available under accession SRR21676140-SRR216761401. The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD036877.Climate change, desertification, salinisation of soils and the changing hydrology of the Earth are creating or modifying microbial habitats at all scales including the oceans, saline groundwaters and brine lakes. In environments that are saline or hypersaline, the biodegradation of recalcitrant plant and animal polysaccharides can be inhibited by salt-induced microbial stress and/or by limitation of the metabolic capabilities of halophilic microbes. We recently demonstrated that the chitinolytic haloarchaeon Halomicrobium can serve as the host for an ectosymbiont, nanohaloarchaeon ‘Candidatus Nanohalobium constans’. Here, we consider whether nanohaloarchaea can benefit from the haloarchaea-mediated degradation of xylan, a major hemicellulose component of wood. Using samples of natural evaporitic brines and anthropogenic solar salterns, we describe genome-inferred trophic relations in two extremely halophilic xylan-degrading three-member consortia. We succeeded in genome assembly and closure for all members of both xylan-degrading cultures and elucidated the respective food chains within these consortia. We provide evidence that ectosymbiontic nanohaloarchaea is an active ecophysiological component of extremely halophilic xylan-degrading communities (although by proxy) in hypersaline environments. In each consortium, nanohaloarchaea occur as ectosymbionts of Haloferax, which in turn act as scavenger of oligosaccharides produced by xylan-hydrolysing Halorhabdus. We further obtained and characterised the nanohaloarchaea–host associations using microscopy, multi-omics and cultivation approaches. The current study also doubled culturable nanohaloarchaeal symbionts and demonstrated that these enigmatic nano-sized archaea can be readily isolated in binary co-cultures using an appropriate enrichment strategy. We discuss the implications of xylan degradation by halophiles in biotechnology and for the United Nation's Sustainable Development Goals.Agence Nationale de la Recherche; Centre for Environmental Biotechnology Project, partly funded by the European Regional Development Fund via the Welsh Assembly Government European Union; H2020 Food; Ministerio de Ciencia e Innovación, Agencia Estatal de Investigación (AEI);; SYAM-Gravitation Program of the Dutch Ministry of Education, Culture and Science.https://sfamjournals.onlinelibrary.wiley.com/journal/17517915am2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-03:Good heatlh and well-beingSDG-08:Decent work and economic growthSDG-09: Industry, innovation and infrastructureSDG-11:Sustainable cities and communitiesSDG-12:Responsible consumption and productionSDG-13:Climate actionSDG-14:Life below waterSDG-15:Life on lan

Search for new particles in events with energetic jets and large missing transverse momentum in proton-proton collisions at root s=13 TeV

A search is presented for new particles produced at the LHC in proton-proton collisions at root s = 13 TeV, using events with energetic jets and large missing transverse momentum. The analysis is based on a data sample corresponding to an integrated luminosity of 101 fb(-1), collected in 2017-2018 with the CMS detector. Machine learning techniques are used to define separate categories for events with narrow jets from initial-state radiation and events with large-radius jets consistent with a hadronic decay of a W or Z boson. A statistical combination is made with an earlier search based on a data sample of 36 fb(-1), collected in 2016. No significant excess of events is observed with respect to the standard model background expectation determined from control samples in data. The results are interpreted in terms of limits on the branching fraction of an invisible decay of the Higgs boson, as well as constraints on simplified models of dark matter, on first-generation scalar leptoquarks decaying to quarks and neutrinos, and on models with large extra dimensions. Several of the new limits, specifically for spin-1 dark matter mediators, pseudoscalar mediators, colored mediators, and leptoquarks, are the most restrictive to date.Peer reviewe

Probing effective field theory operators in the associated production of top quarks with a Z boson in multilepton final states at root s=13 TeV

Peer reviewe

Structural and Functional Peculiarities of α-Crystallin

α-Crystallin is the major protein of the eye lens and a member of the family of small heat-shock proteins. Its concentration in the human eye lens is extremely high (about 450 mg/mL). Three-dimensional structure of native α-crystallin is unknown. First of all, this is the result of the highly heterogeneous nature of α-crystallin, which hampers obtaining it in a crystalline form. The modeling based on the electron microscopy (EM) analysis of α-crystallin preparations shows that the main population of the α-crystallin polydisperse complex is represented by oligomeric particles of rounded, slightly ellipsoidal shape with the diameter of about 13.5 nm. These complexes have molecular mass of about 700 kDa. In our opinion, the heterogeneity of the α-crystallin complex makes it impossible to obtain a reliable 3D model. In the literature, there is evidence of an enhanced chaperone function of α-crystallin during its dissociation into smaller components. This may indirectly indicate that the formation of heterogeneous complexes is probably necessary to preserve α-crystallin in a state inactive before stressful conditions. Then, not only the heterogeneity of the α-crystallin complex is an evolutionary adaptation that protects α-crystallin from crystallization but also the enhancement of the function of α-crystallin during its dissociation is also an evolutionary acquisition. An analysis of the literature on the study of α-crystallin in vitro led us to the assumption that, of the two α-crystallin isoforms (αA- and αB-crystallins), it is αA-crystallin that plays the role of a special chaperone for αB-crystallin. In addition, our data on X-ray diffraction analysis of α-crystallin at the sample concentration of about 170–190 mg/mL allowed us to assume that, at a high concentration, the eye lens α-crystallin can be in a gel-like stage. Finally, we conclude that, since all the accumulated data on structural-functional studies of α-crystallin were carried out under conditions far from native, they cannot adequately reflect the features of the functioning of α-crystallin in vivo

The number of domains in the ribosomal protein S1 as a hallmark of the phylogenetic grouping of bacteria.

The family of ribosomal proteins S1 contains about 20% of all bacterial proteins including the S1 domain. An important feature of this family is multiple copies of structural domains in bacteria, the number of which changes in a strictly limited range from one to six. In this study, the automated exhaustive analysis of 1453 sequences of S1 allowed us to demonstrate that the number of domains in S1 is a distinctive characteristic for phylogenetic bacterial grouping in main phyla. 1453 sequences of S1 were identified in 25 out of 30 different phyla according to the List of Prokaryotic Names with Standing in Nomenclature. About 62% of all records are identified as six-domain S1 proteins, which belong to phylum Proteobacteria. Four-domain S1 are identified mainly in proteins from phylum Firmicutes and Actinobacteria. Records belonging to these phyla are 33% of all records. The least represented two-domain S1 are about 0.6% of all records. The third and fourth domains for the most representative four- and six-domain S1 have the highest percentage of identity with the S1 domain from polynucleotide phosphorylase and S1 domains from one-domain S1. In addition, for these groups, the central part of S1 (the third domain) is more conserved than the terminal domains

Mechanism of Amyloid Gel Formation by Several Short Amyloidogenic Peptides

Under certain conditions, many proteins/peptides are capable of self-assembly into various supramolecular formations: fibrils, films, amyloid gels. Such formations can be associated with pathological phenomena, for example, with various neurodegenerative diseases in humans (Alzheimer’s, Parkinson’s and others), or perform various functions in the body, both in humans and in representatives of other domains of life. Recently, more and more data have appeared confirming the ability of many known and, probably, not yet studied proteins/peptides, to self-assemble into quaternary structures. Fibrils, biofilms and amyloid gels are promising objects for the developing field of research of nanobiotechnology. To develop methods for obtaining nanobiomaterials with desired properties, it is necessary to study the mechanism of such structure formation, as well as the influence of various factors on this process. In this work, we present the results of a study of the structure of biogels formed by four 10-membered amyloidogenic peptides: the VDSWNVLVAG peptide (AspNB) and its analogue VESWNVLVAG (GluNB), which are amyloidogenic fragments of the glucantransferase Bgl2p protein from a yeast cell wall, and amyloidogenic peptides Aβ(31–40), Aβ(33–42) from the Aβ(1–42) peptide. Based on the analysis of the data, we propose a possible mechanism for the formation of amyloid gels with these peptides