Comparative Genomic Analysis of Mycobacterium tuberculosis Drug Resistant Strains from Russia

Tuberculosis caused by multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (MTB) strains is a growing problem in many countries. The availability of the complete nucleotide sequences of several MTB genomes allows to use the comparative genomics as a tool to study the relationships of strains and differences in their evolutionary history including acquisition of drug-resistance. In our work, we sequenced three genomes of Russian MTB strains of different phenotypes – drug susceptible, MDR and XDR. Of them, MDR and XDR strains were collected in Tomsk (Siberia, Russia) during the local TB outbreak in 1998–1999 and belonged to rare KQ and KY families in accordance with IS6110 typing, which are considered endemic for Russia. Based on phylogenetic analysis, our isolates belonged to different genetic families, Beijing, Ural and LAM, which made the direct comparison of their genomes impossible. For this reason we performed their comparison in the broader context of all M. tuberculosis genomes available in GenBank. The list of unique individual non-synonymous SNPs for each sequenced isolate was formed by comparison with all SNPs detected within the same phylogenetic group. For further functional analysis, all proteins with unique SNPs were ascribed to 20 different functional classes based on Clusters of Orthologous Groups (COG). We have confirmed drug resistant status of our isolates that harbored almost all known drug-resistance associated mutations. Unique SNPs of an XDR isolate CTRI-4^XDR, belonging to a Beijing family were compared in more detail with SNPs of additional 14 Russian XDR strains of the same family. Only type specific mutations in genes of repair, replication and recombination system (COG category L) were found common within this group. Probably the other unique SNPs discovered in CTRI-4^XDR may have an important role in adaptation of this microorganism to its surrounding and in escape from antituberculosis drugs treatment.     

In search of biomarkers for autism: scientific, social and ethical challenges

There is widespread hope that the discovery of valid biomarkers for autism will both reveal the causes of autism and enable earlier and more targeted methods for diagnosis and intervention. However, growing enthusiasm about recent advances in this area of autism research needs to be tempered by an awareness of the major scientific challenges and the important social and ethical concerns arising from the development of biomarkers and their clinical application. Collaborative approaches involving scientists and other stakeholders must combine the search for valid, clinically useful autism biomarkers with efforts to ensure that individuals with autism and their families are treated with respect and understanding.     

Interaction of PARP-2 with DNA structures mimicking DNA repair intermediates and consequences on activity of base excision repair proteins

Poly(ADP-ribosyl)ation is a posttranslational protein modification significant for genomic stability and cell survival in response to DNA damage. Poly(ADP-ribosyl)ation is catalyzed by poly(ADP-ribose)polymerases (PARPs). Among the 17 members of the PARP family, PARP-1 and PARP-2 are described as enzymes whose catalytic activity is stimulated by some types of DNA damages.     

Conformational Changes in HIV-1 Reverse Transcriptase that Facilitate Its Maturation

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Genetic study of Escherichia coli K-12 mutations that affect the transposition process

Results of genetic analysis of bacterial tnm mutations influencing transposition of Tn9 are presented. Five independent tnm mutations were mapped at 90,5 min of the E. coli genetic map. The tnm mutations were 3,5 and 46,5% contransducible with metA and malB markers, respectively. Two tnm mutations tested were recessive in tnm+/tnm- merodiploids. The effect of tnm mutations on other transposons--Tn10, Tn601, Tn3 and Tn5 was examined. It was shown that tnm1 and tnm2 mutations reduced the frequency of transposition of Tn10, Tn3, Tn5 and Tn601 from the genome of phage lambda and inhibited intracellular development of the infecting Mu phage. The latter effect was probably due to the inhibition of Mu integration into bacterial chromosome. The tnm3 mutation affected the transposition of Tn9 only.     

Detection of Fluoroquinolone Resistance Single-Nucleotide Polymorphisms in <Emphasis Type="Italic">Neisseria gonorrhoeae gyr</Emphasis>A and <Emphasis Type="Italic">par</Emphasis>C Using MALDI-TOF Mass Spectrometry

Many known mechanisms of drug resistance in microorganisms have genetic markers, which are specific genomic changes, mostly single-nucleotide polymorphisms (SNPs). A search for new methods of detecting SNPs is necessary for more efficient identification of resistant strains. A new method was proposed for SNP detection on the basis of minisequencing and/or sequencing with subsequent matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry. The method was tested with a set of Neisseria gonorrhoeae clinical isolates in experiments on detecting the gyrA and parC SNPs that are markers of fluoroquinolone resistance. The results fully coincided with data previously obtained by gold-standard methods (sequencing and gel electrophoresis of sequencing products). Sequencing of short DNA fragments with MALDI-TOF mass spectrometry is of special interest. The new method considerably improves the efficiency of identification and genotyping of microorganisms and determination of their drug resistance markers.     

Apoptosis in medfly hemocytes is regulated during pupariation through FAK, Src, ERK, PI-3K p85a, and Akt survival signaling

Focal adhesion kinase (FAK) and its downstream signaling targets are implicated in the process of apoptosis induced by external stimuli, in several mammalian systems. In this report, we demonstrate, that medfly (Ceratitis capitata) hemocytes do undergo apoptosis during larval development. In particular, we show using Western blot, ELISA and flow cytometry analysis, that FAK expression silencing in transfected by FAK double-stranded RNA (dsRNA) hemocytes, enhances twofold hemocyte apoptosis, by signaling through Src, MEK/ERK, and PI-3K/Akt signaling pathways. FAK expression silencing, in response to FAK dsRNA treatment, blocks partially the phosphorylation of its downstream targets. Pre-incubation of hemocytes, with specific inhibitors of FAK downstream signaling molecules, demonstrated that all these inhibitors reduced hemocyte viability and enhanced the magnitude of apoptosis about threefold. This data suggest that these pathways contribute to hemocyte survival and/or death during development. The expression and phosphorylation of FAK, Src, PI-3K p85a, Akt, and ERK signaling molecules appear to be dependent upon developmental stages. The expression and phosphorylation of the above signaling molecules, in annexin-positive and annexin-negative hemocytes is also distinct. The maximum expression and phosphorylation of FAK, Src, PI-3K p85a, Akt, and ERK appeared in annexin-positive hemocytes, in both early and late apoptotic hemocytes. The novel aspect of this report is based on the fact that hemocytes attempt to suppress apoptosis, by increasing the expression/phosphorylation of FAK and, hence its downstream targets signaling molecules Src, ERK, PI-3K p85a, and Akt. Evidently, the basic survival pathways among insects and mammals appear to remain unchanged, during evolution.     

Advances in phytochemistry,pharmacology and biotechnology of Bulgarian <Emphasis Type="Italic">Astragalus</Emphasis> species

The genus Astragalus L., Fabaceae (Leguminosae) is presented in Bulgarian flora by 31 species including local endemics, nine of them listed in the Red Data Book. The main biologically active compounds found in the Bulgarian Astragalus plants are saponins and flavonoids with a variety of effects: immunomodulatory, hepatoprotective, cytotoxic, antioxidant, antihypoxic and others. In the recent years volatiles with cytotoxic activity have also been determined. Saponins and flavonoids are still preferably produced by plants due to their complex structures. Variable quantities and qualities of the wild plant material, plants that need to grow several years before they are ready for harvesting and over-collecting of endangered Astragalus species are just a few of the problems connected with the production of these natural products. Therefore, cultured cells are possible alternative for production of high-value secondary metabolites. This review is focused on phytochemical, pharmacological and biotechnological studies of Bulgarian Astragalus plants and includes also results from our investigations.