74 research outputs found
Primary Sequences of Protein-Like Copolymers: Levy Flight Type Long Range Correlations
We consider the statistical properties of primary sequences of two-letter HP
copolymers (H for hydrophobic and P for polar) designed to have water soluble
globular conformations with H monomers shielded from water inside the shell of
P monomers. We show, both by computer simulations and by exact analytical
calculation, that for large globules and flexible polymers such sequences
exhibit long-range correlations which can be described by Levy-flight
statistics.Comment: 4 pages, including 2 figures; several references added, some
formulations improve
RNA-Seq gene expression profiling of HepG2 cells: the influence of experimental factors and comparison with liver tissue
Genome-Wide Mycobacterium tuberculosis Variation (GMTV) Database: A New Tool for Integrating Sequence Variations and Epidemiology
Background
Tuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome sequencing data are being assessed broadly and yet there exists no comprehensive online resource that connects M. tuberculosis genome variants with geographic origin, with drug resistance or with clinical outcome. Description
Here we describe a broadly inclusive unifying Genome-wide Mycobacterium tuberculosis Variation (GMTV) database, (http://mtb.dobzhanskycenter.org) that catalogues genome variations of M. tuberculosis strains collected across Russia. GMTV contains a broad spectrum of data derived from different sources and related to M. tuberculosis molecular biology, epidemiology, TB clinical outcome, year and place of isolation, drug resistance profiles and displays the variants across the genome using a dedicated genome browser. GMTV database, which includes 1084 genomes and over 69,000 SNP or Indel variants, can be queried about M. tuberculosis genome variation and putative associations with drug resistance, geographical origin, and clinical stages and outcomes. Conclusions
Implementation of GMTV tracks the pattern of changes of M. tuberculosis strains in different geographical areas, facilitates disease gene discoveries associated with drug resistance or different clinical sequelae, and automates comparative genomic analyses among M. tuberculosis strains
Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology
No Evidence of a Common DNA Variant Profile Specific to World Class Endurance Athletes
There are strong genetic components to cardiorespiratory fitness and its
response to exercise training. It would be useful to understand the
differences in the genomic profile of highly trained endurance athletes of
world class caliber and sedentary controls. An international consortium
(GAMES) was established in order to compare elite endurance athletes and
ethnicity-matched controls in a case-control study design. Genome-wide
association studies were undertaken on two cohorts of elite endurance athletes
and controls (GENATHLETE and Japanese endurance runners), from which a panel
of 45 promising markers was identified. These markers were tested for
replication in seven additional cohorts of endurance athletes and controls:
from Australia, Ethiopia, Japan, Kenya, Poland, Russia and Spain. The study is
based on a total of 1520 endurance athletes (835 who took part in endurance
events in World Championships and/or Olympic Games) and 2760 controls. We
hypothesized that world-class athletes are likely to be characterized by an
even higher concentration of endurance performance alleles and we performed
separate analyses on this subsample. The meta-analysis of all available
studies revealed one statistically significant marker (rs558129 at GALNTL6
locus, p = 0.0002), even after correcting for multiple testing. As shown by
the low heterogeneity index (I2 = 0), all eight cohorts showed the same
direction of association with rs558129, even though p-values varied across the
individual studies. In summary, this study did not identify a panel of genomic
variants common to these elite endurance athlete groups. Since GAMES was
underpowered to identify alleles with small effect sizes, some of the
suggestive leads identified should be explored in expanded comparisons of
world-class endurance athletes and sedentary controls and in tightly
controlled exercise training studies. Such studies have the potential to
illuminate the biology not only of world class endurance performance but also
of compromised cardiac functions and cardiometabolic diseases
Matrix-Assisted Laser Desorption Ionization-Time of Flight (Mass Spectrometry) for Hepatitis C Virus Genotyping
Determination of the hepatitis C virus (HCV) genotype has become accepted as the standard procedure in laboratory practice. Genotype assignment helps in disease prognosis and assists in establishing the appropriate duration of treatment. More than 10 types and 70 subtypes of HCV have been described. In Russia the most common subtypes are 1a, 1b, 2a, and 3a, and the types 4 and 5 are relatively rare. The “gold standard” for testing is gene sequencing. However, a variety of other assays had been developed to provide more rapid and cheaper forms of testing. The aim of this study was to determine the HCV genotype by minisequencing followed by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. Fragments of 5′ untranslated region of the HCV genome were amplified. Three oligonucleotide primers were designed to detect two sets of genotype-specific single nucleotide polymorphisms. The primer extension reaction was performed using modified thermostable DNA polymerase and in the presence of dideoxynucleosides. The molecular weights of the reaction products were analyzed with MALDI-TOF mass spectrometer. The HCV genotype was determined by registering the particles of the expected molecular weights. The method was used to genotype HCV from HCV-positive blood sera or plasma. The 1a, 1b, 2a, 3a, and 4 genotype HCVs were determined in the samples examined. The data were confirmed by direct sequencing. Thus, we propose a new accurate and efficient method for HCV genotyping based on minisequencing followed by mass spectrometry
Molecular Surveillance of Clinical Neisseria gonorrhoeae Isolates in Russia â–ż â€
The choice of adequate methods for epidemiological purposes remains a challenging problem in Neisseria gonorrhoeae molecular monitoring. In this study, the collection of geographically unrelated gonococci (n = 103) isolated in Russian clinics was comparably tested by (i) a traditional serotyping scheme, (ii) por typing, (iii) Neisseria gonorrhoeae multiantigen sequence typing (NG-MAST), and (iv) multilocus sequence typing (MLST). It is shown that, according to sequencing data, a third of the strains carried new porB1 alleles, as well as tbpB ones, and more than half of the samples had new sequence types (STs) as determined by NG-MAST or MLST. The discriminatory power for each typing method was calculated by using the Hunter-Gaston discriminatory index, D. Commonly, modern nucleic acid-based typing methods (por typing, NG-MAST, and MLST) appeared to be more efficient than the classical serotyping scheme. While the traditional serotyping gave a D value of 0.82, the por typing, NG-MAST, and MLST approaches yielded D values of 0.97, 0.98, and 0.91, respectively. Each typing technique revealed the distribution of gonococci slightly correlated with their geographical sources. However, only the MLST method STs were highly associated with certain phenotypes. Although ST1594, ST1892, and ST6720 were typical for susceptible gonococci, ST1901 and ST6716 were undoubtedly associated with a multidrug-resistant phenotype. We conclude that every tested nucleic acid-based typing method is suitable for N. gonorrhoeae molecular surveillance. However, the MLST method seems to serve large-scale epidemiological purposes, whereas the NG-MAST and por typing approaches are more appropriate for the investigation of local outbreaks
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