PhyloBench: A Benchmark for Evaluating Phylogenetic Programs.

Phylogenetic inference based on protein sequence alignment is a widely used procedure. Numerous phylogenetic algorithms have been developed, most of which have many parameters and options. Choosing a program, options, and parameters can be a nontrivial task.

Platelet glutamate dehydrogenase activity and efficacy of antipsychotic therapy in patients with schizophrenia.

Background: Evaluation of possible relationship between platelet glutamate dehydrogenase (GDH) activity and mental state of schizophrenia patients after antipsychotic pharmacotherapy.

Methods: Patients (n = 50) with chronic paranoid schizophrenia (F20.0) initially in acute psychotic state were examined before and after a treatment course with antipsychotics.

Experimental Study of Flakozid Activity in Viral Hepatitis C In Vitro.

Antiviral activity of a Russian drug flakozid towards infection caused by a cytopathogenic variant of hepatitis C virus in SPEV cells is studied. Flakozid is an individual natural flavonoid glycoside 7-O-β-D-glucopyranoside-8-(methyl-but)-2-enyl)-5,4'-dioxyflavanolol), isolated from the leaves of Phellodendron amurense Rupr. and Ph.

PQ, a new program for phylogeny reconstruction.

Background: Many algorithms and programs are available for phylogenetic reconstruction of families of proteins. Methods used widely at present use either a number of distance-based principles or character-based principles of maximum parsimony or maximum likelihood.

Results: We developed a novel program, named PQ, for reconstructing protein and nucleic acid phylogenies following a new character-based principle.

Small Molecule Inhibitor of Type Three Secretion System Belonging to a Class 2,4-disubstituted-4H-[1,3,4]-thiadiazine-5-ones Improves Survival and Decreases Bacterial Loads in an Airway Infection in Mice.

is a cause of high mortality in burn, immunocompromised, and surgery patients. High incidence of antibiotic resistance in this pathogen makes the existent therapy inefficient. Type three secretion system (T3SS) is a leading virulence system of that actively suppresses host resistance and enhances the severity of infection.

Interplay between reaction and diffusion processes in governing the dynamics of virus infections.

Spreading of viral infection in the tissues such as lymph nodes or spleen depends on virus multiplication in the host cells, their transport and on the immune response. Reaction-diffusion systems of equations with delays in cell proliferation and death by apoptosis represent an appropriate model to study this process. The properties of the cells of the immune system and the initial viral load determine the spatiotemporal regimes of infection spreading.

Lycopene Inhibits Propagation of Chlamydia Infection.

Chlamydiaceae is a family of obligate intracellular pathogenic bacteria with similar developmental cycles and cell biology responsible for a wide range of diseases in different hosts including genital and eye inflammatory diseases, arthritis, and inflammatory diseases of the respiratory and cardiovascular systems. In the present paper, we report that lycopene, one of the main dietary carotenoids, which is present in tomato and some other fruits, has a strong inhibitory effect on and infections in alveolar macrophages. This finding was documented by both immunofluorescence analysis and electron microscopy.

Two Variants of Recombinant Human Bone Morphogenetic Protein-2 (rhBMP-2) with Additional Protein Domains: Synthesis in an Escherichia coli Heterologous Expression System.

Two variants of recombinant human bone morphogenetic protein-2 (rhBMP-2) with additional N-terminal protein domains were obtained by expression in E. coli. The N-terminal domains were s-tag (15-a.

Spatiotemporal Dynamics of Virus Infection Spreading in Tissues.

Virus spreading in tissues is determined by virus transport, virus multiplication in host cells and the virus-induced immune response. Cytotoxic T cells remove infected cells with a rate determined by the infection level. The intensity of the immune response has a bell-shaped dependence on the concentration of virus, i.

Phylogeography of Crimean Congo Hemorrhagic Fever Virus.

Crimean Congo hemorrhagic fever virus (CCHFV) is one of the most severe viral zoonozes. It is prevalent throughout Africa, Asia and southern Europe. Limited availability of sequence data has hindered phylogeographic studies.

Recombinant domains III of Tick-Borne Encephalitis Virus envelope protein in combination with dextran and CpGs induce immune response and partial protectiveness against TBE virus infection in mice.

Background: E protein of tick-borne encephalitis virus (TBEV) and other flaviviruses is located on the surface of the viral particle. Domain III of this protein seems to be a promising component of subunit vaccines for prophylaxis of TBE and kits for diagnostics of TBEV.

Methods: Three variants of recombinant TBEV E protein domain III of European, Siberian and Far Eastern subtypes fused with dextran-binding domain of Leuconostoc citreum KM20 were expressed in E.

Conserved features of complexes of TATA-box binding proteins with DNA.

A comparative analysis of all available structures of complexes of TATA-box binding proteins (TBPs) with DNA is performed. Conserved features of DNA-protein interaction are described, including nine amino acid residues that form conserved hydrogen bonds, 13 residues participating in formation of two conserved hydrophobic clusters at DNA-protein interface, and four conserved water-mediated contacts. Partial symmetry of conserved contacts reflects quasi-symmetry of TBP structure.

Development of pan-phlebovirus RT-PCR assay.

This study reports the pan-phlebovirus assay capable of detecting both sandfly/mosquito- and tick-borne phleboviruses. Sensitivity and specificity of the assay was verified using a panel of arboviruses. The RT-PCR assay is simple and sensitive, and thus well suited for screening of field samples.

Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes.

Background: Avoidance of palindromic recognition sites of Type II restriction-modification (R-M) systems was shown for many R-M systems in dozens of prokaryotic genomes. However the phenomenon has not been investigated systematically for all presently available genomes and annotated R-M systems. We have studied all known recognition sites in thousands of prokaryotic genomes and found factors that influence their avoidance.

An updated version of NPIDB includes new classifications of DNA-protein complexes and their families.

The recent upgrade of nucleic acid-protein interaction database (NPIDB, http://npidb.belozersky.msu.

A small-molecule compound belonging to a class of 2,4-disubstituted 1,3,4-thiadiazine-5-ones inhibits intracellular growth and persistence of Chlamydia trachomatis.

Chlamydia trachomatis is one of the most common sexually transmitted pathogens in the world and often causes chronic inflammatory diseases that are insensitive to antibiotics. The type 3 secretion system (T3SS) of pathogenic bacteria is a promising target for therapeutic intervention aimed at bacterial virulence and can be an attractive alternative for the treatment of chronic infections. Recently, we have shown that a small-molecule compound belonging to a class of 2,4-disubstituted 1,3,4-thiadiazine-5-ones produced through the chemical modification of the thiohydrazides of oxamic acids, designated CL-55, inhibited the intracellular growth of C.

Role of Chlamydia in Multiple Sclerosis.

Chlamydia and antibodies to them were detected by serological, molecular biological, and culture methods in the sera and cerebrospinal fluid of patients with multiple sclerosis and in the reference groups of subjects without neurological diseases. Correlations between the agent presence in the biological fluids of patients and clinical characteristics of the disease were analyzed. C.