Low-pass genome-wide sequencing and variant inference using identity-by-descent in an isolated human population.

Whole-genome sequencing in an isolated population with few founders directly ascertains variants from the population bottleneck that may be rare elsewhere. In such populations, shared haplotypes allow imputation of variants in unsequenced samples without resorting to complex statistical methods as in studies of outbred cohorts. We focus on an isolated population cohort from the Pacific Island of Kosrae, Micronesia, where we previously collected SNP array and rich phenotype data for the majority of the population. We report identification of long regions with haplotypes co-inherited between pairs of individuals and methodology to leverage such shared genetic content for imputation. Our estimates show that sequencing as few as 40 personal genomes allows for inference in up to 60% of the 3000-person cohort at the average locus. We ascertained a pilot data set of whole-genome sequences from seven Kosraean individuals, with average 5× coverage. This assay identified 5,735,306 unique sites of which 1,212,831 were previously unknown. Additionally, these variants are unusually enriched for alleles that are rare in other populations when compared to geographic neighbors (published Korean genome SJK). We used the presence of shared haplotypes between the seven Kosraen individuals to estimate expected imputation accuracy of known and novel homozygous variants at 99.6% and 97.3%, respectively. This study presents whole-genome analysis of a homogenous isolate population with emphasis on optimal rare variant inference.

Microbial genes homologous to the peptidyl-tRNA hydrolase-encoding gene of Escherichia coli.

We have cloned and determined the nucleotide (nt) sequences of the genes encoding peptidyl-tRNA hydrolase (Pth) homologues of Salmonella typhi (St) and the Lyme disease spirochaete, Borrelia burgdorferi (Bb). We also completed the nt sequence of a pth homologous gene contained in a Chlamydia trachomatis (Ct) clone identified in the databanks. The open reading frames (ORFs) of the Pth homologues encode putative polypeptides of 194 (St), 188 (Bb) and 194 (Ct) amino acids exhibiting significant identity with Escherichia coli (Ec) Pth. Together with the products of two previously unidentified ORFs from Bacillus subtilis and Saccharomyces cerevisiae, and the recently recognized Haemophilus influenzae and Mycoplasma genitalium pth genes, these seven putative polypeptides and the Ec Pth form a group of homologous basic proteins spanning eubacteria and eukaryota which can be defined by at least three conserved regions. Previously known Ec pth mutations were located in highly conserved residues.

Distance education through the Internet: the GNA-VSNS biocomputing course.

A prototype course on biocomputing was delivered via international computer networks in early summer 1995. The course lasted 11 weeks, and was offered free of charge. It was organized by the BioComputing Division of the Virtual School of Natural Sciences, which is a member school of the Globewide Network Academy. It brought together 34 students and 7 instructors from all over the world, and covered the basics of sequence analysis. Five authors from Germany and USA prepared a hypertext book which was discussed in weekly study sessions that took place in a virtual classroom at the BioMOO electronic conferencing system. The course aimed at students with backgrounds in molecular biology, biomedicine or computer science, complementing and extending their skills with an interdisciplinary curriculum. Special emphasis was placed on the use of Internet resources, and the development of new teaching tools. The hypertext book includes direct links to sequence analysis and databank search services on the Internet. A tool for the interactive visualization of unit-cost pairwise sequence alignment was developed for the course. All course material will stay accessible at the World Wide Web address (Uniform Resource Locator) http://+www.techfak.uni-bielefeld.de/bcd/welcome .html. This paper describes the aims and organization of the course, and gives a preliminary account of this novel experience in distance education.

Open reading frames flanking the peptidyl-tRNA hydrolase-encoding gene of Escherichia coli.

The nucleotide (nt) sequences flanking the peptidyl-tRNA hydrolase-encoding gene (pth) of Escherichia coli were determined and analyzed. A coding open reading frame (ORF-3), identified just downstream from pth, had a deduced amino acid (aa) sequence homologous to a family of GTP-binding proteins. We found discrepancies between the ORF-3 sequence from a plasmid clone used in previous studies and another one derived from Kohara's phage collection. Two putative genes, ORF-4 and ORF-2, were also found upstream from pth. ORF-4 could code for a 393-aa peptide homologous to membrane-bound proteins. The nt sequence between ORF-2 and pth revealed the existence of a CAP-binding site correctly positioned to regulate the expression of ORF-2.

Peptidyl-tRNA hydrolase is involved in lambda inhibition of host protein synthesis.

Escherichia coli rap mutants do not support vegetative growth of bacteriophage lambda and die upon transcription of lambda DNA bar sites. Bacteria harbouring a pth(ts) mutation synthesize thermosensitive peptidyl-tRNA hydrolase (Pth) and die at 42 degrees C from a defect in protein synthesis. We present evidence that both rap and pth(ts) mutations affect the same gene: (i) peptidyl-tRNA hydrolase activity was found to be defective in rap mutants; (ii) at a threshold temperature, pth cells, like rap mutants, prevented lambda growth and were killed by transcription of cloned bar sites; (iii) sequencing a 1600 bp DNA fragment comprising both loci revealed an ORF located within the limits set by a complementation analysis and encoding a putative polypeptide of 21 kDa; (iv) cloning and sequencing of rap and pth(ts) mutant DNAs both revealed single nucleotide transitions from the wild type ORF sequence, resulting in Arg134 to His and Gly101 to Asp changes respectively. Analysis of plasmid-directed proteins identified a polypeptide of approximately 21 kDa; the N-terminal sequence, amino acid composition and isoelectric point of this protein match those expected from the ORF nucleotide sequence. We propose that Pth activity, directly or indirectly, is the target for lambda bar RNA leading to rap cell death.

Dimethyl sulfoxide enhances lipid synthesis and secretion by long-term cultures of adult rat hepatocytes.

Dimethyl sulfoxide (DMSO) was tested for its effects on lipid metabolism of long-term cultures of adult rat hepatocytes. The addition of 1% DMSO to 3T3-hepatocyte cultures was not toxic to cells and in fact treated cultures maintained better their characteristic morphology for up to 14 days of exposure. DMSO treatment increased 2-3 fold the de novo synthesis of total lipids from[14C]acetate. The analysis by thin layer chromatography of cellular and secreted lipids revealed that DMSO increased the levels of cellular triglycerides, phospholipides and free and sterified cholesterol at 7 days of exposure while at 14 days there was also a 2-3-fold increase in medium secreted lipids. Additionally, DMSO increased the activity of glycerol-phosphate dehydrogenase, a marker enzyme of glycerolipid synthesis, by greater than 50% at either 7 or 14 days of exposure. These results show that 1% DMSO not only is not detrimental to cultured hepatocytes but also enhances lipid synthesis and secretion, both hepatic-differentiated functions.

Effects of probucol on lipid metabolism and secretion in long-term cultures of adult rat hepatocytes.

To study the effects of probucol on hepatic lipid metabolism, we used adult rat hepatocytes cultured on a feeder layer of 3T3 cells lethally treated with mitomycin C. These cultures synthesize and secrete for at least 2 weeks various lipids from [14C]acetate and [14C]oleate precursors. Treatment with 20 micrograms/ml of probucol for 7 and 14 days decreased the secretion of various radiolabeled lipid species to the culture medium and produced an intracytoplasmic accumulation of triacylglycerol droplets. The lipids whose secretion was most decreased were free and esterified cholesterol (50-70% reduction). Secretion of triacylglycerols and phospholipids was also reduced but to a lower extent. Intracytoplasmic triacylglycerols accumulated and the activity of glycerol phosphate dehydrogenase, a marker enzyme of glycerolipid synthesis, also increased (35-56%). The total incorporation of both radioactive precursors into free and esterified cholesterol and phospholipids was reduced 20-60%. Our data show that 2-week treatment of 3T3-hepatocyte cultures with pharmacological concentrations of probucol reduces significantly lipid secretion and suggest that at least part of the in vivo hypolipidemic effect of probucol could be attributed to a decrease in the secretion of lipids (i.e., lipoproteins) by hepatocytes.