Large-scale Ferrofluid Simulations on Graphics Processing Units

We present an approach to molecular-dynamics simulations of ferrofluids on graphics processing units (GPUs). Our numerical scheme is based on a GPU-oriented modification of the Barnes-Hut (BH) algorithm designed to increase the parallelism of computations. For an ensemble consisting of one million of ferromagnetic particles, the performance of the proposed algorithm on a Tesla M2050 GPU demonstrated a computational-time speed-up of four order of magnitude compared to the performance of the sequential All-Pairs (AP) algorithm on a single-core CPU, and two order of magnitude compared to the performance of the optimized AP algorithm on the GPU. The accuracy of the scheme is corroborated by comparing the results of numerical simulations with theoretical predictions

Kombucha microbiome as a probiotic: a view from the perspective of post-genomics and synthetic ecology

Probiotics are essential for establishing and maintaining optimal immune health. The probiotic therapy is known from alternative medicine for ages; however, the recent demonstration of the normal microflora to induce innate immunity has introduced the science-based concept of therapeutic application of potentially beneficial probiotic microorganisms for a treatment of functional disorders. Traditionally, probiotics are associated with dairy products, however, novel formulations are needed, first of all, originated from naturally occurring symbiotic microbial communities as the most robust assemblages. Especially, safe and robust probiotics are needed for long-term expeditions, outposts, extraterrestrial permanently-manned bases, where humans are exposed to adverse environmental factors. Kombucha beverage is Symbiotic Culture of Bacteria and Yeast (SCOBY) and associated with health-promoting effects. Kombucha tea/mat is being in use in human livings within millennia as a probiotic drink for healing and health prophylaxis effects, however, new research opportunities promise its «renaissance», going to be used pharmacologically

МЕХАНОХИМИЧЕСКИЙ СИНТЕЗ КАРБИДА ВОЛЬФРАМА С УЧАСТИЕМ РАЗЛИЧНЫХ УГЛЕРОДНЫХ КОМПОНЕНТОВ

It has been established that the basic criteria of realization of mechano-chemical tungsten carbide synthesis are the structure of carbon modifications and the degree of their aromaticity. The prospects of application of carbon modifications obtained as a result of pyrolysis of vegetative raw materials for synthesis of tungsten carbide with minimum contents of sulfur are shown.Установлено, что основными критериями реализации механохимического синтеза карбида вольфрама являются структура углеродных модификаций и степень их ароматичности. Показана перспективность использования модификаций углерода, полученных в результате пиролиза растительного сырья, для синтеза карбида вольфрама с минимальным содержанием серы

BEAM POSITION MONITOR SYSTEM FOR 2 MEV ELECTRON COOLER FOR COSY

Abstract The 2 MEV electron cooler for COSY storage ring FZJ is assembling in BINP. Beam position monitor (BPM) system for orbit measurements has been developed and fabricated at BINP. The system contains 2 BPMs inside the cooling section and 10 BPMs in transport channels. Continuous electron beam is modulated with a 3 MHz signal for capability to get signals from pickup electrodes. The beam current modulation can be varied in the range of 0.3-1.5 mA. The BPMs inside the cooling section can measure both electron and proton beams. It is achieved by means of switching the reference signals inside the BPM electronics. The BPM electronics provides highly precise beam position measurements. Position measurement error doesn't exceed 1 micron. Design features of the BPM system, its parameters and testing results are presented in this paper

Metabarcoding of the kombucha microbial community grown in different microenvironments

Introducing of the DNA metabarcoding analysis of probiotic microbial communities allowed getting insight into their functioning and establishing a better control on safety and efficacy of the probiotic communities. In this work the kombucha poly-microbial probiotic community was analysed to study its flexibility under different growth conditions. Environmental DNA sequencing revealed a complex and flexible composition of the kombucha microbial culture (KMC) constituting more bacterial and fungal organisms in addition to those found by cultural method. The community comprised bacterial and yeast components including cultured and uncultivable microorganisms. Culturing the KMC under different conditions revealed the core part of the community which included acetobacteria of two genera Komagataeibacter (former Gluconacetobacter) and Gluconobacter, and representatives of several yeast genera among which Brettanomyces/Dekkera and Pichia (including former Issatchenkia) were dominant. Herbaspirillum spp. and Halomonas spp., which previously had not been described in KMC, were found to be minor but permanent members of the community. The community composition was dependent on the growth conditions. The bacterial component of KMC was relatively stable, but may include additional member—lactobacilli. The yeast species composition was significantly variable. High-throughput sequencing showed complexity and variability of KMC that may affect the quality of the probiotic drink. It was hypothesized that the kombucha core community might recruit some environmental bacteria, particularly lactobacilli, which potentially may contribute to the fermentative capacity of the probiotic drink. As many KMC-associated microorganisms cannot be cultured out of the community, a robust control for community composition should be provided by using DNA metabarcoding.National Academy of Sciences of Ukraine (N47/2013)http://www.amb-express.comhb201

To other planets with upgraded millennial kombucha in rhythms of sustainability and health support

Humankind has entered a new era of space exploration: settlements on other planetary bodies are foreseen in the near future. Advanced technologies are being developed to support the adaptation to extraterrestrial environments and, with a view on the longer term, to support the viability of an independent economy. Biological processes will likely play a key role and lead to the production of life-support consumables, and other commodities, in a way that is cheaper and more sustainable than exclusively abiotic processes. Microbial communities could be used to sustain the crews’ health as well as for the production of consumables, for waste recycling, and for biomining. They can self-renew with little resources from Earth, be highly productive on a per-volume basis, and be highly versatile—all of which will be critical in planetary outposts. Well-de!ned, semi-open, and stress-resistant microecosystems are particularly promising. An instance of it is kombucha, known worldwide as a microbial association that produces an eponymous, widespread soft drink that could be valuable for sustaining crews’ health or as a synbiotic (i.e., probiotic and prebiotic) after a rational assemblage of de!ned probiotic bacteria and yeasts with endemic or engineered cellulose producers. Bacterial cellulose products offer a wide spectrum of possible functions, from leather-like to innovative smart materials during long-term missions and future activities in extraterrestrial settlements. Cellulose production by kombucha is zero-waste and could be linked to bioregenerative life support system (BLSS) loops. Another advantage of kombucha lies in its ability to mobilize inorganic ions from rocks, which may help feed BLSS from local resources. Besides outlining those applications and others, we discuss needs for knowledge and other obstacles, among which is the biosafety of microbial producers

Electron Cooling Experiments in CSR

The six species heavy ion beam was accumulated with the help of electron cooling in the main ring of Cooler Storage Ring of Heavy Ion Research Facility in Lanzhou(HIRFL-CSR), the ion beam accumulation dependence on the parameters of cooler was investigated experimentally. The 400MeV/u 12C6+ and 200MeV/u 129Xe54+ was stored and cooled in the experimental ring CSRe, the cooling force was measured in different condition.Comment: 5 pages 11 figure

Deriving a mutation index of carcinogenicity using protein structure and protein interfaces

With the advent of Next Generation Sequencing the identification of mutations in the genomes of healthy and diseased tissues has become commonplace. While much progress has been made to elucidate the aetiology of disease processes in cancer, the contributions to disease that many individual mutations make remain to be characterised and their downstream consequences on cancer phenotypes remain to be understood. Missense mutations commonly occur in cancers and their consequences remain challenging to predict. However, this knowledge is becoming more vital, for both assessing disease progression and for stratifying drug treatment regimes. Coupled with structural data, comprehensive genomic databases of mutations such as the 1000 Genomes project and COSMIC give an opportunity to investigate general principles of how cancer mutations disrupt proteins and their interactions at the molecular and network level. We describe a comprehensive comparison of cancer and neutral missense mutations; by combining features derived from structural and interface properties we have developed a carcinogenicity predictor, InCa (Index of Carcinogenicity). Upon comparison with other methods, we observe that InCa can predict mutations that might not be detected by other methods. We also discuss general limitations shared by all predictors that attempt to predict driver mutations and discuss how this could impact high-throughput predictions. A web interface to a server implementation is publicly available at http://inca.icr.ac.uk/

BIOINFORMATIC SEARCH OF CRISPR/CAS SYSTEM STRUCTURES IN GENOME OF PCT281 PLASMID OF BACILLUS THURINGIENSIS SUBSP. CHINENSIS STRAIN CT-43

Background. CRISPR/Cas systems loci are one of the functionally important patterns in bacterial genome which perform the role of “adaptive immune defense” from foreign nucleic acids. The study of CRISPR/Cas systems structure in genomes of plasmids and phages provide new information about the evolution of this systems in bacterial hosts.Aims. A search of CRISPR/Cas systems structures in pCT281 plasmid from Bacillus thuringiensis subsp. chinensis strain CT-43 using bioinformatic methods.Materials and methods. Search studies using bioinformatics methods were performed with the genome of pCT281 plasmid of B. thuringiensis subsp. chinensis strain CT-43 from the RefSeq database. To search for the CRISPR/Cas system structure MacSyFinder (ver. 1.0.5) and three combined algorithms were used: CRISPRFinder; PILER-CR; CRISPR Recognition Tool (CRT). The consensus repeat sequence was generated in WebLogo 3.Results and discussion. In pCT281 plasmid we detected one locus of CRISPR/Cas system of the type I-C which contains 2 CRISPR-cassettes and 4 cas-genes located between them. The CRISPR-cassette 1 includes 10 spacers from 32 to 35 bp and 11 repeats 32bp in length. 5 spacers (33–35 bp) separated by 6 repeats 32 bp in length were detected in the CRISPR-cassette 2.Conclusions. The bioinformatic methods used in this study enable to conduct a search of CRISPR/Cas systems structures in plasmid genomes. The presence of the CRISPR-Cas locus in pCT281 plasmid confirms a possible transfer of this system from the nucleoid to this plasmid. The detected spacers provide information about phages this bacteria was encountered