Search results for "Putin"
showing 10 items of 25297 documents
SPECTR
2018
Modern high throughput sequencing platforms can produce large amounts of short read DNA data at low cost. Error correction is an important but time-consuming initial step when processing this data in order to improve the quality of downstream analyses. In this paper, we present a Scalable Parallel Error CorrecToR designed to improve the throughput of DNA error correction for Illumina reads on various parallel platforms. Our design is based on a k-spectrum approach where a Bloom filter is frequently probed as a key operation and is optimized towards AVX-512-based multi-core CPUs, Xeon Phi many-cores (both KNC and KNL), and heterogeneous compute clusters. A number of architecture-specific opt…
Visualization of Simulated Arrhythmias due to Gap Junctions
2018
New computational models are able to simulate details of cardiac cell networks. Their results allow a better understanding of the functionality of the heart and suggest possible actions to reduce non-fatal premature beats that can give rise to serious diseases. We developed a user-friendly interface to organize Neuron simulations and to present in real-time a three-dimensional representation of the electrical activity due to the gap junctions which interconnect the cells inside cardiac tissues. All physiological parameters were set according to real experimental observations and compared against different types of arrhythmias, retrieved from the Physionet Data Base.
Reconstruction of Past Dynamics of Methane-Oxidizing Bacteria in Lake Sediments Using a Quantitative PCR Method: Connecting Past Environmental Change…
2019
AbstractIn this study, a quantitative PCR (qPCR) method was applied to amplify ancient DNA (aDNA) of different methane-oxidizing bacteria (MOB) types in lake sediments and to reconstruct microbial community dynamics over the last 1200 years. We also used reconstructions of in-lake nutrients concentrations, air temperature fluctuations, and sedimentary organic matter dynamics to study impacts of past environmental and climatic changes on MOB community composition. DNA preservation in lake sediments is sufficient, and qPCR amplification was successfully applied to the analysis of MOB aDNA. Temporal changes in MOB community showed different patterns between lakes, and drivers of past MOB dynam…
Bioprospecting challenges in unusual environments
2017
Editorial: The microbiome as a source of new enterprises and job creation.
Constitutive activation of MexT by amino acid substitutions results in MexEF-OprN overproduction in clinical isolates of Pseudomonas aeruginosa
2018
ABSTRACT When overproduced, the multidrug efflux system MexEF-OprN increases the resistance of Pseudomonas aeruginosa to fluoroquinolones, chloramphenicol, and trimethoprim. In this work, we demonstrate that gain-of-function mutations in the regulatory gene mexT result in oligomerization of the LysR regulator MexT, constitutive upregulation of the efflux pump, and increased resistance in clinical isolates.
Phosphorylation of CENP-A on serine 7 does not control centromere function.
2019
CENP-A is the histone H3 variant necessary to specify the location of all eukaryotic centromeres via its CENP-A targeting domain and either one of its terminal regions. In humans, several post-translational modifications occur on CENP-A, but their role in centromere function remains controversial. One of these modifications of CENP-A, phosphorylation on serine 7, has been proposed to control centromere assembly and function. Here, using gene targeting at both endogenous CENP-A alleles and gene replacement in human cells, we demonstrate that a CENP-A variant that cannot be phosphorylated at serine 7 maintains correct CENP-C recruitment, faithful chromosome segregation and long-term cell viab…
TReND in Africa: Toward a Truly Global (Neuro)science Community
2020
TReND is a volunteer-scientist run charity dedicated to promoting research and education on the African continent. Focusing on neuroscience, we discuss approaches to address some of the factors that currently stifle Africa's scientific development and our experience in implementing them.
Role of AxyZ Transcriptional Regulator in Overproduction of AxyXY-OprZ Multidrug Efflux System in Achromobacter Species Mutants Selected by Tobramycin
2017
ABSTRACT AxyXY-OprZ is an RND-type efflux system that confers innate aminoglycoside resistance to Achromobacter spp. We investigated here a putative TetR family transcriptional regulator encoded by the axyZ gene located upstream of axyXY-oprZ . An in-frame axyZ gene deletion assay led to increased MICs of antibiotic substrates of the efflux system, including aminoglycosides, cefepime, fluoroquinolones, tetracyclines, and erythromycin, indicating that the product of axyZ negatively regulates expression of axyXY-oprZ . Moreover, we identified an amino acid substitution at position 29 of AxyZ (V29G) in a clinical Achromobacter strain that occurred during the course of chronic respiratory tract…
High-throughput sequencing for 1-methyladenosine (m1A) mapping in RNA
2016
Abstract Detection and mapping of modified nucleotides in RNAs is a difficult and laborious task. Several physico-chemical approaches based on differential properties of modified nucleotides can be used, however, most of these methods do not allow high-throughput analysis. Here we describe in details a method for mapping of rather common 1-methyladenosine (m1A) residues using high-throughput next generation sequencing (NGS). Since m1A residues block primer extension during reverse transcription (RT), the accumulation of abortive products as well as the nucleotide misincorporation can be detected in the sequencing data. The described library preparation protocol allows to capture both types …
Engineering of a DNA Polymerase for Direct m6A Sequencing
2017
Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N6-methyladenosine (m6A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody-based enrichment of m6A-containing RNA prior to sequencing, since m6A modifications are generally "erased" during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m6A sequencing. Therefore, we developed a screen to evolve an RT-active KlenTaq DNA polymerase variant that sets a mark for…