The GWAS-MAP|ovis platform for aggregation and analysis of genome-wide association study results in sheep.

In recent years, the number of genome-wide association studies (GWAS) carried out for various economically important animal traits has been increasing. GWAS discoveries provide summary statistics that can be used both for targeted marker-oriented selection and for studying the genetic control of economically important traits of farm animals. In contrast to research in human genetics, GWAS on farm animals often does not meet generally accepted standards (availability of information about effect and reference alleles, the size and direction of the effect, etc.). This greatly complicates the use of GWAS results for breeding needs. Within the framework of human genetics, there are several technological solutions for researching the harmonized results of GWAS, including one of the largest, the GWAS-MAP platform. For other types of living organisms, including economically important agricultural animals, there are no similar solutions. To our knowledge, no similar solution has been proposed to date for any of the species of economically important animals. As part of this work, we focused on creating a platform similar to GWAS-MAP for working with the results of GWAS of sheep, since sheep breeding is one of the most important branches of agriculture. By analogy with the GWAS-MAP platform for storing, unifying and analyzing human GWAS, we have created the GWAS-MAP|ovis platform. The platform currently contains information on more than 34 million associations between genomic sequence variants and traits of meat production in sheep. The platform can also be used to conduct colocalization analysis, a method that allows one to determine whether the association of a particular locus with two different traits is the result of pleiotropy or whether these traits are associated with different variants that are in linkage disequilibrium. This platform will be useful for breeders to select promising markers for breeding, as well as to obtain information for the introduction of genomic breeding and for scientists to replicate the results obtained.

[Simultaneous surgery for complicated giant post-traumatic phrenic hernia in a patient with morbid obesity and diabetes mellitus type II]. / Opyt vypolneniya simul'tannoi operatsii po povodu oslozhnennoi gigantskoi posttravmaticheskoi diafragmal'noi gryzhi u patsienta s morbidnym ozhireniem i sakharnym diabetom II tipa.

Surgical treatment of post-traumatic right-sided phrenic hernia is associated with certain technical difficulties due to topographic and anatomical features. Morbid obesity combined with diabetes mellitus type II is one of the main factors complicating any surgical thoracic or abdominal surgery and further rehabilitation. We report simultaneous surgery for complicated post-traumatic right-sided phrenic hernia in a patient with morbid obesity and diabetes mellitus type II. Surgical correction of giant phrenic hernia facilitated further effective treatment of morbid obesity and concomitant diabetes mellitus type II.

CASBench: A Benchmarking Set of Proteins with Annotated Catalytic and Allosteric Sites in Their Structures.

In recent years, the phenomenon of allostery has witnessed growing attention driven by a fundamental interest in new ways to regulate the functional properties of proteins, as well as the prospects of using allosteric sites as targets to design novel drugs with lower toxicity due to a higher selectivity of binding and specificity of the mechanism of action. The currently available bioinformatic methods can sometimes correctly detect previously unknown ligand binding sites in protein structures. However, the development of universal and more efficient approaches requires a deeper understanding of the common and distinctive features of the structural organization of both functional (catalytic) and allosteric sites, the evolution of their amino acid sequences in respective protein families, and allosteric communication pathways. The CASBench benchmark set contains 91 entries related to enzymes with both catalytic and allosteric sites within their structures annotated based on the experimental information from the Allosteric Database, Catalytic Site Atlas, and Protein Data Bank. The obtained dataset can be used to benchmark the performance of existing computational approaches and develop/train perspective algorithms to search for new catalytic and regulatory sites, as well as to study the mechanisms of protein regulation on a large collection of allosteric enzymes. Establishing a relationship between the structure, function, and regulation is expected to improve our understanding of the mechanisms of action of enzymes and open up new prospects for discovering new drugs and designing more efficient biocatalysts. The CASBench can be operated offline on a local computer or online using built-in interactive tools at https://biokinet.belozersky.msu.ru/casbench.

The Preferable Binding Pose of Canonical Butyrylcholinesterase Substrates Is Unproductive for Echothiophate.

In this paper, we, for the first time, describe the interaction between the butyrylcholinesterase enzyme and echothiophate, a popular model compound and an analogue of the chemical warfare agents VX and VR, at the atomistic level. Competition between the two echothiophate conformations in the active site was found using molecular modeling techniques. The first one is close to the mode of binding of the substrates of choline series (butyrylcholine and butyrylthiocholine) and is inhibitory, since it is unable to react with the enzyme. The second one is characterized by a significantly worse estimated binding affinity and is reactive. Thus, echothiophate combines the features of two types of inhibitors: competitive and suicidal. This observation will help clarify the kinetic reaction scheme in order to accurately assess the kinetic constants, which is especially important when designing new butyrylcholinesterase variants capable of full-cycle hydrolysis of organophosphorus compounds.

Evolution of catalytic centers of antibodies by virtual screening of broad repertoire of mutants using supercomputer.

It is proposed to perform quantum mechanical/molecular dynamics calculations of chemical reactions that are planned to be catalyzed by antibodies and then conduct a virtual screening of the library of potential antibody mutants to select an optimal biocatalyst. We tested the effectiveness of this approach by the example of hydrolysis of organophosphorus toxicant paraoxon using kinetic approaches and X-ray analysis of the antibody biocatalyst designed de novo.

Population specific analysis of Yakut exomes.

We studied the genetic diversity of the Yakut population using exome sequencing. We performed comparative analysis of the Yakut population and the populations that are included in the "1000 Genomes" project and we identified the alleles specific to the Yakut population. We showed, that the Yakuts population is a separate cluster between Europeans and East Asians.

Osteopontin mediates an MZF1-TGF-ß1-dependent transformation of mesenchymal stem cells into cancer-associated fibroblasts in breast cancer.

Interactions between tumor cells and cancer-associated fibroblasts (CAFs) in the tumor microenvironment significantly influence cancer growth and metastasis. Transforming growth factor-ß (TGF-ß) is known to be a critical mediator of the CAF phenotype, and osteopontin (OPN) expression in tumors is associated with more aggressive phenotypes and poor patient outcomes. The potential link between these two pathways has not been previously addressed. Utilizing in vitro studies using human mesenchymal stem cells (MSCs) and MDA-MB231 (OPN+) and MCF7 (OPN-) human breast cancer cell lines, we demonstrate that OPN induces integrin-dependent MSC expression of TGF-ß1 to mediate adoption of the CAF phenotype. This OPN-TGF-ß1 pathway requires the transcription factor, myeloid zinc finger 1 (MZF1). In vivo studies with xenotransplant models in NOD-scid mice showed that OPN expression increases cancer growth and metastasis by mediating MSC-to-CAF transformation in a process that is MZF1 and TGF-ß1 dependent. We conclude that tumor-derived OPN engenders MSC-to-CAF transformation in the microenvironment to promote tumor growth and metastasis via the OPN-MZF1-TGF-ß1 pathway.

[Pectic polysaccharides in the stem calli of the rowan tree Sorbus aucuparia L].

The water-soluble polysaccharide fractions SAcI and SAclI were isolated from rowan tree stem calli. The SAcI fraction was shown to contain compounds belonging to the arabinogalactan II group. The SAcII fraction, termed sorban, was found to contain pectic polysaccharides that make up the protopectin complex of the cell wall callusand that had a high content of galacturonic acid residues together with neutral sugars characteristic of rhamnogalacturonan I (RG-I) polysaccharides. Using methylation assays, some structural features of the ramified region of sorban were elucidated. The backbone of sorban was found to consist of 1,4-α-D-galacto-pyranosyluronic acid residues. The neutral sugars are represented by 1,6-linked galactopyranose and 1,5-linked arabinofuranose residues as the primary constituents, as well as 1,6-linked mannopyranose and 1,4-linked glucopyranose and xylopyranose residues. Callus growth was shown to be accompanied by nearly constant quantities of galacturonic acid and neutral sugar residues in sorban (fraction SAcII) from the rowan stem callus.

[Choice of urinary tract drainage in different age groups of patients with urolithiasis].

Retro- and prospective analyses of 802 case histories of patients with nephrostomic drainage (n=272), ureteral catheter (n=27) and ureteral stent (n=503) treated for urolithiasis in the urological department of M.F. Vladimirsky Moscow Region Research Clinical Institute and Zhukovsky city hospital hospitalized in 1995 to 2009 made it possible to develop algorithms of choice of upper urinary tract drainage depending on clinical and laboratory indices. Nephrostomic drainage is preferable in a single functioning kidney, acute obstructive pyelonephritis, anuria, hyperthermia above 38 degrees C, marked supravesical urodynamic disorder, in renal failure, serum creatinine over 200 mcmol/l, urea over 10 mmol/l, blood potassium over 5 mmol/l, uric acid over 380 mcmol/l and leukocytosis over 8 x 10(9) l. Draining with ureteral stent was used primarily in elective surgery--extracorporeal shock-wave lithotripsy and transurethral operations. Stenting was better tolerated and entailed less frequent complications. In the rest cases choice of drain method should be made by the urologist. In active inflammation, before getting antibioticogram, the drain should be followed by antibiotic treatment with fluoroquinolones, cephalosporines of the third or forth generation, aminoglycosides, carbapenems in standard doses.

[Diagnosis and treatment of urolithiasis in combination with infravesical obstruction in presenile and senile patients].

The analysis of the results of examination and treatment of 510 urolithiasis patients with organic infravesical obstruction (IVO) treated in the urological clinic of M. F. Vladimirsky Moscow Regional Research Clinical Institute and in the urological department of Zhukovsky city hospital from 1995 to 2009 made it possible to arrive at the following conclusions: the above patients have obstruction symptoms in 100% cases, irritative symptoms--in more than 2/3 of the patients; combined use of low invasive, endoscopic and open methods reestablishes urodynamics of the lower urinary tract in more than 90% patients; the decision on the treatment policy and techniques depends on severity of clinical symptoms caused by IVO and urolithiasis as well as disturbance of upper and lower urinary tract urodynamics. In adequate choice of the patients and correct indications combined use of low invasive, endoscopic and open methods provides good treatment effect in patients with IVO and urolithiasis.

[Evaluation of the efficiency of use of the bed fund of a central district hospital]. / Otsenka éffektivnosti ispol'zovaniia koechnogo fonda tsentral'noi raionnoi bol'nitsy.

The paper deals with a complex sociohygienic study of the basic indices of resource provision of the public health system in the Tver Region and with an analysis of the scope of inpatient care to the population of the Torzhok District, Tver Region. Based on an in-depth examination, the efficiency of the use of the bed fund of the central district hospital (CDH) was evaluated and economic losses from inadequate use of beds and economic effects of work of daily CDH-based hospitals were calculated.

Notch-1 regulates NF-kappaB activity in hemopoietic progenitor cells.

We investigated the interaction between two elements critical for differentiation of hemopoietic cells, the Notch-1 receptor and the transcription factor NF-kappaB. These factors were studied in hemopoietic progenitor cells (HPC) using Notch-1 antisense transgenic (Notch-AS-Tg) mice. DNA binding of NF-kappaB as well as its ability to activate transcription was strongly decreased in HPC from Notch-AS-Tg mice. NF-kappaB-driven transcriptional activity was completely restored after transduction of the cells with retroviral constructs containing activated Notch-1 gene. HPC from Notch-AS-Tg mice have decreased levels of several members of the NF-kappaB family, p65, p50, RelB, and c-Rel and this is due to down-regulation of the gene expression. To investigate functional consequences of decreased NF-kappaB activity in transgenic mice, we studied LPS-induced proliferation of B cells and GM-CSF-dependent differentiation of dendritic cells from HPC. These two processes are known to be closely dependent on NF-kappaB. B cells from Notch-AS-Tg mice had almost 3-fold lower response to LPS than B cells isolated from control mice. Differentiation of dendritic cells was significantly affected in Notch-AS-Tg mice. However, it was restored by transduction of activated Notch-1 into HPC. Taken together, these data indicate that in HPC NF-kappaB activity is regulated by Notch-1 via transcriptional control of NF-kappaB.

Notch signaling as a target in multimodality cancer therapy.

Notch signaling is an extremely conserved and widely used mechanism controlling cell fate determination. Recent evidence shows that Notch receptors regulate cell differentiation, proliferation and apoptosis in many cells, including neoplastic cells. In the context of cancer experimental immunotherapy and multimodality therapy, the Notch signaling network is acquiring increasing importance for its possible roles in both neoplastic cells and the immune system. In this review, we discuss: (i) the roles of Notch signaling in cancer cells and the immune system; and (ii) strategies through which Notch-targeting biologicals may be used to increase the effectiveness of multimodality cancer treatment, including cancer vaccines.

Toward the rational design of cell fate modifiers: notch signaling as a target for novel biopharmaceuticals.

Recent advances in our understanding of highly conserved mechanisms that control cell fate determination are paving the way towards rationally designed biologics that modulate specific cell fate decisions. Cell fate decisions leading to proliferation, differentiation or apoptosis are crucial elements in the pathogenesis of countless human diseases. Biopharmaceuticals designed to regulate such processes in specific cell types in vivo or ex vivo have vast potential applications in oncology, stem cell technology, immunomodulation and neuropathology. One of the most conserved mechanisms controlling cell fate determination is based upon Notch-ligand interactions and subsequent signaling events. Recent studies have shown that this mechanism regulates cell differentiation, proliferation and apoptosis in a wide variety of cell maturation processes and in neoplastic cells. These observations identify the Notch signaling network as a promising drug target for numerous indications. In this review, we describe: 1) potential drug targets in the Notch signaling network; 2) the Notch agonists and antagonists developed so far, including recombinant proteins, antibody-based agents, synthetic peptides, antisense oligonucleotides and gene therapy approaches, as well as possible strategies to design novel Notch-targeting biopharmaceuticals; 3) the possible clinical applications of such biopharmaceuticals and 4) a model strategy for the selection and developement of a Notch-targeting biopharmaceutical.

Dopamine antagonist and "binge' cocaine effects on rat opioid and dopamine transporter mRNAs.

The modulation by selective dopamine receptor antagonists of the effects of "binge' cocaine (3 x 15 mg kg-1 day-1, i.p., for 3 days after 11 days of adaptation to saline injections) on preproenkephalin, preprodynorphin, kappa opioid receptor and dopamine transporter mRNAs was determined. Administration of cocaine was preceded by daily single injections of a D1 (SCH 23390; 2 mg kg-1) or the D2 (sulpiride; 50 mg kg-1) dopamine receptor antagonist. The D1, and not the D2, antagonist blocked cocaine-induced preprodynorphine and preproenkephalin increases in the caudate-putamen. Sulpiride alone, and sulpiride plus cocaine, increased preproenkephalin mRNA. Dopamine transporter mRNA levels showed a cocaine treatment-antagonist interaction. These data indicate that this administration paradigm elevates both preprodynorphin and preproenkephalin mRNAs by a D1-dependent mechanism not requiring D2 activation.

[The enhancement of the diagnostic reliability of immunoblot for HIV-1 antibodies by enriching the preparation for immunoblot with the HIV-1 gp120 protein]. / Uvelichenie diagnosticheskoi dostovernosti immunoblota na antitela k VICh-1 za schet obogashcheniia preparata dlia immunoblota belkom gp120 VICh-1.

The diagnostic value of original immunoblot system depends on the availability of enveloped protein GP120 because it is the antibodies to this polypeptide that frequently indicate the running virus infection. This polypeptide is lost during purification of viral material but remains free in culture medium. The extraction of GP120 from culture fluid with immunosorbent based on sepharose 4B with ligated immunoglobulins from HIV-1-infected persons enriched the preparation for immunoblot with proteins increasing its diagnostic value.

[The characteristics of human immunodeficiency virus strains isolated from HIV-infected persons on the territory of the USSR]. / Kharakteristika shtammov virusa immunodefitsita cheloveka, vydelennykh ot VICh-infitsirovannykh lits na territorii SSSR.

Fifty-seven HIV-1 strains were isolated from peripheral blood lymphocytes of 102 HIV-infected persons involved in epidemic outbreaks in different cities of the USSR. The effectiveness of isolation was 29.1% in asymptomatic infection, 51.7% in cases with generalized lymphadenopathy, and 82.6% in persons with severe clinical manifestations. Identification of the isolates by indirect immunofluorescence, ELISA, reverse transcriptase activity, Western blot, electron microscopy, and polymerase chain reaction showed them to belong to HIV-1 type. Reproduction of the isolates in cell cultures was accompanied by cytopathic effect and syncytium formation. The isolated strains can be divided into two groups: (1) the poorly growing isolates with low or negative RT and ELISA results and (2) the isolates with high infectivity, broad spectrum of cell tropism, and high levels of RT and ELISA. These data show the correlation of biological properties of HIV-1 strains isolated in the USSR with those of HIV strains previously isolated in Europe, USA, and Africa.

[Inhibitors of ADP ribosylation as antiviral agents: an experimental study in a model of HIV infection]. / Ingibitory ADF-ribozilirovaniia kak protivovirusnye sredstva: éksperimental'noe izuchenie na modeli VICh-infektsii.

The paper deals with further search for substances modifying metabolic processes, changing the conditions of virus existence in the host cell and, consequently, possessing a certain antiviral activity. The antiviral effects of aromatic carbonic acids amides including trisubstituted benzamides and nicotinamide were tested. Five out of 8 substances tested possessed antiviral activity which might be due to their capacity to inhibit the activity of the enzymes of ADP-ribosylation. By blocking cellular processes of ADP-ribosylation, the substances under study depressed DNA capacity for reparation, inhibited differentiation and transformation of cells, i.e. had an indirect effect on reproduction of viruses. The universal nature of the processes coursing with participation of NAD(+)-dependent ADP-ribosylation suggests that the range of antiviral activity of inhibitors of mono- and poly-ADP-ribosylation would not be limited to HIV infection but would be rather wide.

[A comparative analysis of the polypeptides of the the Sindbis and Karelian fever viruses]. / Sravnitel'nyi analiz polipeptidov virusov Sindbis i karel'skoi likhoradki.

In pulse-chase experiments with Karelian fever virus-infected cells, proteins were found with molecular weights of 130, 98, 78, and 62 kD of which the first, second and fourth were classified as polypeptide precursors of the structural proteins of virion. The molecular weights of proteins E1, E2 and C of 52, 47 and 34 kD, respectively, as well as isoelectric points of isolated glycoproteins (pI E1 = 6.3, pI E2 = 8.4) were similar in KFV (strain Leiv-9298) and Sindbis virus (strain AR339). The antigenic similarity of the strains under study in neutralization test with hyperimmune sera, the identity of physicochemical characteristics of the structural proteins of KFV and prototype Sindbis virus strain suggest a close relationship of the Leiv-9298 strain to the Afro-European variants of Sindbis virus.

[Monoclonal antibodies to the Karelian fever virus. The characteristics of their biological properties]. / Monoklonal'nye antitela k virusu karel'skoi likhoradki. Kharakteristika biologicheskikh svoistv.

Biological properties of 6 variants of monoclonal antibodies (MAb) to Karelian fever virus, a member of the alpha-virus serocomplex Sindbis-WEE, produced by the available hybridomas. The productivity of hybridomas of the "Karel" series in tissue culture and in cultivation as ascitic fluid was evaluated. Among the antibodies analysed, all were specific to envelope proteins, of them 2 were against protein E2 and four against protein E1. Comparison of MCA biologic activity (neutralizing, antihemagglutinating activities, participation in immunofluorescence, EIA, and immune blotting) allows one to distinguish four different hybridomas among them producing specific antibodies differing in their properties.