MOTIVATION Major tumor sequencing projects have been conducted in the past few years to identify genes that contain 'driver' somatic mutations in tumor samples. These genes have been defined as those for which the non-silent mutation rate is significantly greater than a background mutation rate estimated from silent mutations. Several methods have been used for estimating the background mutatio...

We have calibrated five different molecular clocks for circulating poliovirus based upon the rates of fixation of total substitutions (K(t)), synonymous substitutions (K(s)), synonymous transitions (A(s)), synonymous transversions (B(s)), and nonsynonymous substitutions (K(a)) into the P1/capsid region (2,643 nucleotides). Rates were determined over a 10-year period by analysis of sequences of ...

To the Editor of " The Indian Medical Gazette." Sir-I shall feel obliged if you will give the following a place in your paper in reply to Dr. Clarke's criticism of my contribution in Rheumatism in August number I was indeed not very particular about the'nomenclature and took it as it was; and I considered it as a certain manifestation attended with pain, incapabilities with certa n tissue chang...

BACKGROUND It has recently been shown that levels of diversity in mitochondrial DNA are remarkably constant across animals of diverse census population sizes and ecologies, which has led to the suggestion that the effective population of mitochondrial DNA may be relatively constant. RESULTS Here we present several lines of evidence that suggest, to the contrary, that the effective population ...

Analyses of transgene expression have defined essential components of a locus control region (LCR) in the J(H)-C(mu) intron of the IgH locus. Targeted deletion of this LCR from the endogenous IgH locus of hybridoma cells results in variegated expression, i.e., cells can exist in two epigenetically inherited states in which the Ig(mu) H chain gene is either active or silent; the active or silent...

The recessive gene rymv-1, responsible for the high resistance of Oryza sativa 'Gigante' to Rice yellow mottle virus (genus Sobemovirus), was overcome by the variant CI4*, which emerged after serial inoculations of the non-resistance-breaking (nRB) isolate CI4. By comparison of the full-length sequences of CI4 and CI4*, a non-synonymous mutation was identified at position 1729, localized in the...

Mutations in the quinolone resistance-determining region of the gyrA gene from 138 ciprofloxacin-resistant (MIC, > or =4 microg/ml) and 24 ciprofloxacin-susceptible (MIC, < or =1 microg/ml) clinical Campylobacter jejuni isolates were subjected to single-strand conformation polymorphism analysis and sequencing. All of the isolates could be assigned to three genotypic clusters based on silent mut...

Viruses rely on widespread genetic variation and large population size for adaptation. Large DNA virus populations are thought to harbor little variation though natural populations may be polymorphic. To measure the genetic variation present in a dsDNA virus population, we deep sequenced a natural strain of the baculovirus Autographa californica multiple nucleopolyhedrovirus. With 124,221X aver...

A novel heterozygous non-synonymous mutation and a novel polymorphism in OMI/HTRA2 locus have been associated with Parkinson's disease (PD) in a German population. In an attempt to replicate these results in an independent population, we analyzed the entire coding region of OMI/HTRA2 in a series of 644 North American PD cases with both young- and late-onset disease and in 828 North American neu...

BACKGROUND Chagas disease patients with longstanding megaesophagus have a significantly increased risk for esophageal carcinoma. MATERIALS AND METHODS PCR-SSCP analysis and DNA sequencing of esophageal mucosa from Chagas disease patients (with or without megaesophagus) in the exons of the TP53, CDKN2A and FHIT genes were performed. RESULTS SSCP analysis showed a mobility shift in 2/20 patie...