Profiling of Mycoplasma gallisepticum Ribosomes.

The development of high-throughput technologies is increasingly resulting in identification of numerous cases of low correlation between mRNA and the protein level in cells. These controversial observations were made on various bacteria, such as E. coli, Desulfovibrio vulgaris, and Lactococcus lactis.

The mystery of the fourth clone: comparative genomic analysis of four non-typeable Streptococcus pneumoniae strains with different susceptibilities to optochin.

Optochin-resistant pneumococci can be rarely caught in clinical microbiology laboratories because of the routine identification of all such strains as viridans group non-pneumococci. We were lucky to find four non-typeable Streptococcus pneumoniae clones demonstrating the different susceptibilities to optochin: one of them (Spn_13856) was resistant to optochin, while the other three (Spn_1719, Spn_27, and Spn_2298) were susceptible. Whole genome nucleotide sequences of these strains were compared to reveal the differences between the optochin-resistant and optochin-susceptible strains.

Morphology and aggregation of RADA-16-I peptide Studied by AFM, NMR and molecular dynamics simulations.

RADA-16-I is a self-assembling peptide which forms biocompatible fibrils and hydrogels. We used molecular dynamics simulations, atomic-force microscopy, NMR spectroscopy, and thioflavin T binding assay to examine size, structure, and morphology of RADA-16-I aggregates. We used the native form of RADA-16-I (H-(ArgAlaAspAla)4 -OH) rather than the acetylated one commonly used in the previous studies.

Bovine serum albumin as a universal suppressor of non-specific peptide binding in vials prior to nano-chromatography coupled mass-spectrometry analysis.

Non-specific binding (NSB) is a well-known problem for any application that deals with ultralow analyte quantities. The modern nano-flow chromatography coupled tandem mass-spectrometry (nanoLC-MS/MS) works with the lowest conceivable analyte concentrations. However, while the NSB problem is widely accepted and investigated for metabolomics and single-peptide medicine-related assays, its impact is not studied for complex peptide mixtures in proteomic applications.

Generation of recombinant destabilase-lysozyme from medicinal leeches in three different expression systems.

Destabilase-lysozyme (mlDL) is an enzyme secreted by the salivary gland cells of medicinal leeches. Destabilase-lysozyme possesses lysozyme and isopeptidase activities. We generated recombinant destabilase-lysozyme isoform 2 in three expression systems, i.

The 5'-proximal region of Potato virus X RNA involves the potential cap-dependent "conformational element" for encapsidation.

Filamentous helical Potato virus X (PVX) can be regarded as one of the well-studied viruses. Nevertheless, some aspects of the PVX assembly remained obscure. Previously, we have shown that the presence of a cap structure at the 5' end of PVX RNA is indispensable for assembly of viral ribonucleoprotein (vRNP) particles varying in length.

Recombinant fragilysin isoforms cause E-cadherin cleavage of intact cells and do not cleave isolated E-cadherin.

The fragilysin (BFT) is a protein secreted by enterotoxigenic Bacteroides fragilis strains. BFT contains zinc-binding motif which was found in the metzincins family of metalloproteinases. In this study, we generated three known recombinant isoforms of BFT using Escherichia coli, tested their activity and examined whether E-cadherin is a substrate for BFTs.

Complete Genome Sequence of an Enterotoxigenic Bacteroides fragilis Clinical Isolate.

Here we present the complete genome sequence of Bacteroides fragilis isolate BOB25. It is an enterotoxigenic isolate that was obtained from a stool sample of a patient with dysbiosis.

[Disturbance of serum albumin conformation in patients with melancholic depression].

Objective: Conformational protein changes may be an important component of the disturbance of molecular processes in the development of pathological process in the body. We studied conformations of albumin molecule in the blood of patients with depression using biophysical -nanotechnical approach.

Material And Methods: We examined 19 patients with depression and 25 healthy controls.

Quantification of autoantibodies to plasminogen in plasma of patients with cancer.

Background: The investigation of autoantibodies which may play a role in the processes of angiogenesis and tumorogenesis is important in the early diagnostis of cancer.

Objective: This study aimed to investigate the levels of autoantibodies to Glu-plasminogen (Pg) in plasma of patients with tumors.

Methods: Plasma samples from healthy volunteers were compared with samples from patients with prostate cancer using 2D electrophoresis and MALDI-TOF mass spectrometry.

Structure of the capsular polysaccharide of Acinetobacter baumannii 1053 having the KL91 capsule biosynthesis gene locus.

Acinetobacter baumannii 1053 is the type strain for the maintenance of specific bacteriophage AP22, which infects a fairly broad range of A. baumannii strains circulating in Russian clinics and hospitals. A capsular polysaccharide (CPS) was isolated from cells of strain 1053 and studied by sugar analysis along with 1D and 2D (1)H and (13)C NMR spectroscopy.

No DNA damage response and negligible genome-wide transcriptional changes in human embryonic stem cells exposed to terahertz radiation.

Terahertz (THz) radiation was proposed recently for use in various applications, including medical imaging and security scanners. However, there are concerns regarding the possible biological effects of non-ionising electromagnetic radiation in the THz range on cells. Human embryonic stem cells (hESCs) are extremely sensitive to environmental stimuli, and we therefore utilised this cell model to investigate the non-thermal effects of THz irradiation.

Visualization of fibrinogen αC regions and their arrangement during fibrin network formation by high-resolution AFM.

Background: Fibrinogen has been intensively studied with transmission electron microscopy and x-ray diffraction. But until now, a complete 3D structure of the molecule has not yet been available because the two highly flexible αC regions could not be resolved in fibrinogen crystals. This study was aimed at determining whether the αC regions can be visualized by high-resolution atomic force microscopy.

Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium.

The avian bacterial pathogen Mycoplasma gallisepticum is a good model for systems studies due to small genome and simplicity of regulatory pathways. In this study, we used RNA-Seq and MS-based proteomics to accurately map coding sequences, transcription start sites (TSSs) and transcript 3'-ends (T3Es). We used obtained data to investigate roles of TSSs and T3Es in stress-induced transcriptional responses.

Proteome-metabolome profiling of ovarian cancer ascites reveals novel components involved in intercellular communication.

Ovarian cancer ascites is a native medium for cancer cells that allows investigation of their secretome in a natural environment. This medium is of interest as a promising source of potential biomarkers, and also as a medium for cell-cell communication. The aim of this study was to elucidate specific features of the malignant ascites metabolome and proteome.

Long-term dissemination of CTX-M-5-producing hypermutable Salmonella enterica serovar typhimurium sequence type 328 strains in Russia, Belarus, and Kazakhstan.

In this paper, we present evidence of long-term circulation of cefotaxime-resistant clonally related Salmonella enterica serovar Typhimurium strains over a broad geographic area. The genetic relatedness of 88 isolates collected from multiple outbreaks and sporadic cases of nosocomial salmonellosis in various parts of Russia, Belarus, and Kazakhstan from 1996 to 2009 was established by multilocus tandem-repeat analysis (MLVA) and multilocus sequence typing (MLST). The isolates belong to sequence type 328 (ST328) and produce CTX-M-5 β-lactamase, whose gene is carried by highly related non-self-conjugative but mobilizable plasmids.

Draft Genome Sequence of Bacillus pumilus 7P, Isolated from the Soil of the Tatarstan Republic, Russia.

Here, we present a draft genome sequence of Bacillus pumilus strain 7P. This strain was isolated from soil as an extracellular RNase-producing microorganism. The RNase of B.

Comprehensive analysis of the venom gland transcriptome of the spider Dolomedes fimbriatus.

A comprehensive transcriptome analysis of an expressed sequence tag (EST) database of the spider Dolomedes fimbriatus venom glands using single-residue distribution analysis (SRDA) identified 7,169 unique sequences. Mature chains of 163 different toxin-like polypeptides were predicted on the basis of well-established methodology. The number of protein precursors of these polypeptides was appreciably numerous than the number of mature polypeptides.

[Prognostic value of left bundle brunch block in patients with acute coronary syndrome].

Aim: to assess rognostic value of ECG signs of left bundle brunch block (LBBB) using database of registries of acute coronary syndromes (ACS) RECORD 1 (2007-2008) and 2 (2009-2011).

Material And Methods: Total number of included patients was 2452, 2321 patients (94.9%) had no signs of LBBB, for 5 patients (0.

Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips.

Illumina's Infinium HumanMethylation450 BeadChip arrays were used to examine genome-wide DNA methylation profiles in 22 sample pairs from colorectal cancer (CRC) and adjacent tissues and 19 colon tissue samples from cancer-free donors. We show that the methylation profiles of tumors and healthy tissue samples can be clearly distinguished from one another and that the main source of methylation variability is associated with disease status. We used different statistical approaches to evaluate the methylation data.

Core proteome of the minimal cell: comparative proteomics of three mollicute species.

Mollicutes (mycoplasmas) have been recognized as highly evolved prokaryotes with an extremely small genome size and very limited coding capacity. Thus, they may serve as a model of a 'minimal cell': a cell with the lowest possible number of genes yet capable of autonomous self-replication. We present the results of a comparative analysis of proteomes of three mycoplasma species: A.

Influenza virus hemagglutinin spike neck architectures and interaction with model enzymes evaluated by MALDI-TOF mass spectrometry and bioinformatics tools.

Interactions between model enzymes and the influenza virus hemagglutinin (HA) homotrimeric spike were addressed. We digested influenza virions (naturally occurring strains and laboratory reassortants) with bromelain or subtilisin Carlsberg and analyzed by MALDI-TOF mass spectrometry the resulting HA2 C-terminal segments. All cleavage sites, together with (minor) sites detected in undigested HAs, were situated in the linker region that connects the transmembrane domain to the ectodomain.