A Possible Etiology of the Infertile 46XX Male Subject

We report on an infertile male patient with the predominant 46XX female karyotype. A testicular biopsy revealed widely separated testicular tubules, absence of sperm formation and large numbers of Leydig cells. Chromosome studies, including measurements of the X chromosomes, showed a significant difference between the lengths of the short arm of the 2 X chromosomes. This information lends support for an X-Y chromosome interchange as the etiology of this syndrome. The clinical features of this rare syndrome and other theories of etiology of XX male subjects are discussed

Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data

<p>Abstract</p> <p>Background</p> <p>The advent of pyrophosphate sequencing makes large volumes of sequencing data available at a lower cost than previously possible. However, the short read lengths are difficult to assemble and the large dataset is difficult to handle. During the sequencing of a virus from the tsetse fly, <it>Glossina pallidipes</it>, we found the need for tools to search quickly a set of reads for near exact text matches.</p> <p>Methods</p> <p>A set of tools is provided to search a large data set of pyrophosphate sequence reads under a "live" CD version of Linux on a standard PC that can be used by anyone without prior knowledge of Linux and without having to install a Linux setup on the computer. The tools permit short lengths of <it>de novo </it>assembly, checking of existing assembled sequences, selection and display of reads from the data set and gathering counts of sequences in the reads.</p> <p>Results</p> <p>Demonstrations are given of the use of the tools to help with checking an assembly against the fragment data set; investigating homopolymer lengths, repeat regions and polymorphisms; and resolving inserted bases caused by incomplete chain extension.</p> <p>Conclusion</p> <p>The additional information contained in a pyrophosphate sequencing data set beyond a basic assembly is difficult to access due to a lack of tools. The set of simple tools presented here would allow anyone with basic computer skills and a standard PC to access this information.</p

The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species

Genes in durophage intersection set at 15 dpf. This is a comma separated table of the genes in the 15 dpf durophage intersection set. Given are edgeR results for each pairwise comparison. Columns indicating whether a gene is included in the intersection set at a threshold of 1.5 or 2 fold are provided. (CSV 13 kb

Gene targeting in adult rhesus macaque fibroblasts

<p>Abstract</p> <p>Background</p> <p>Gene targeting in nonhuman primates has the potential to produce critical animal models for translational studies related to human diseases. Successful gene targeting in fibroblasts followed by somatic cell nuclear transfer (SCNT) has been achieved in several species of large mammals but not yet in primates. Our goal was to establish the protocols necessary to achieve gene targeting in primary culture of adult rhesus macaque fibroblasts as a first step in creating nonhuman primate models of genetic disease using nuclear transfer technology.</p> <p>Results</p> <p>A primary culture of adult male fibroblasts was transfected with hTERT to overcome senescence and allow long term <it>in vitro </it>manipulations. Successful gene targeting of the HPRT locus in rhesus macaques was achieved by electroporating S-phase synchronized cells with a construct containing a SV40 enhancer.</p> <p>Conclusion</p> <p>The cell lines reported here could be used for the production of null mutant rhesus macaque models of human genetic disease using SCNT technology. In addition, given the close evolutionary relationship and biological similarity between rhesus macaques and humans, the protocols described here may prove useful in the genetic engineering of human somatic cells.</p

Comparing De Novo Genome Assembly: The Long and Short of It

Recent advances in DNA sequencing technology and their focal role in Genome Wide Association Studies (GWAS) have rekindled a growing interest in the whole-genome sequence assembly (WGSA) problem, thereby, inundating the field with a plethora of new formalizations, algorithms, heuristics and implementations. And yet, scant attention has been paid to comparative assessments of these assemblers' quality and accuracy. No commonly accepted and standardized method for comparison exists yet. Even worse, widely used metrics to compare the assembled sequences emphasize only size, poorly capturing the contig quality and accuracy. This paper addresses these concerns: it highlights common anomalies in assembly accuracy through a rigorous study of several assemblers, compared under both standard metrics (N50, coverage, contig sizes, etc.) as well as a more comprehensive metric (Feature-Response Curves, FRC) that is introduced here; FRC transparently captures the trade-offs between contigs' quality against their sizes. For this purpose, most of the publicly available major sequence assemblers – both for low-coverage long (Sanger) and high-coverage short (Illumina) reads technologies – are compared. These assemblers are applied to microbial (Escherichia coli, Brucella, Wolbachia, Staphylococcus, Helicobacter) and partial human genome sequences (Chr. Y), using sequence reads of various read-lengths, coverages, accuracies, and with and without mate-pairs. It is hoped that, based on these evaluations, computational biologists will identify innovative sequence assembly paradigms, bioinformaticists will determine promising approaches for developing “next-generation” assemblers, and biotechnologists will formulate more meaningful design desiderata for sequencing technology platforms. A new software tool for computing the FRC metric has been developed and is available through the AMOS open-source consortium

Major prospects for exploring canine vector borne diseases and novel intervention methods using 'omic technologies

Canine vector-borne diseases (CVBDs) are of major socioeconomic importance worldwide. Although many studies have provided insights into CVBDs, there has been limited exploration of fundamental molecular aspects of most pathogens, their vectors, pathogen-host relationships and disease and drug resistance using advanced, 'omic technologies. The aim of the present article is to take a prospective view of the impact that next-generation, 'omics technologies could have, with an emphasis on describing the principles of transcriptomic/genomic sequencing as well as bioinformatic technologies and their implications in both fundamental and applied areas of CVBD research. Tackling key biological questions employing these technologies will provide a 'systems biology' context and could lead to radically new intervention and management strategies against CVBDs

Preferential in-vitro growth and expansion of leukemic T lymphoblasts

An in-vitro culture system was used to selectively grow malignant cells from the bone marrow of a patient with acute T-lymphoblastic leukemia. Molecular analysis of DNA extracted from the bone marrow cells before culture showed the presence of both rearranged and germ line patterns for the T-cell beta receptor (CT B) gene, and chromosomal analysis revealed the presence of a major and a minor abnormal clone. The cells were cultured in RPMI medium supplemented with 20% fetal calf serum, 2% lymphocyte conditioned medium, l-glutamine and antibiotics. The presence of malignant cells in the cultured population was confirmed by morphologic, molecular probing and cytogenetic analysis. After four weeks in culture, DNA extracted from the cultured cells showed only the rearranged pattern for the CT B gene. Chromosomal analysis of the same cultured sample revealed only the presence of the initially predominant abnormal close. Shortly thereafter, analysis of fresh uncultured bone marrow cells from the patient in relapse revealed that the same chromosomally abnormal clone also predominated in vivo. Thus, our resúlts demonstrate the selective nature of this culture system and its ability to amplify leukemic T-lymphoblasts. This culture system is also useful for detecting occult malignant cells in histologically normal bone marrow