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A collection of resources about NGS
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Sequencing the whole genomes of bacterial pathogens as they spread among hospital patients and health care workers could transform the control of infectious disease.
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Rescooped by Ed Rybicki from IIDMM News |
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Malaria and HIV are among the most important global health problems of our time and together are responsible for approximately 3 million deaths annually. These two diseases overlap in many regions of the world including sub-Saharan Africa, Southeast Asia and South America, leading to a higher risk of co-infection. In this study, we generated and characterized hybrid molecules to target Plasmodium falciparum and HIV simultaneously for a potential HIV/malaria combination therapy. Hybrid molecules were synthesized by the covalent fusion of azidothymidine (AZT) with dihydroartemisinin (DHA), a tetraoxane or a 4-aminoquinoline derivative; and the small library was tested for antiviral and antimalarial activity. Our data suggests that compound 7 is the most potent molecule in vitro, with antiplasmodial activity comparable to that of DHA (IC50 = 26 nM, SI >3000), a moderate activity against HIV (IC50 = 2.9 μM; SI >35) and not toxic to HeLa cells at concentrations used in the assay (CC50 >100 μM). Pharmacokinetics studies further revealed that compound 7 is metabolically unstable and is cleaved via O-dealkylation. These studies account for the lack of in vivo efficacy of compound 7 against the CQ-sensitive Plasmodium berghei N strain in mice, when administered orally at 20 mg/kg.
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"Microbes dominate most global biogeochemical cycles, and microbial metagenomics (studying the collective microbial genomes) provides invaluable new insights into microbial systems, independent of cultivation. Metagenomic approaches targeting specific genes, e.g. small subunit (ssu) ribosomal RNA (rRNA), can be used to investigate microbial community organization by efficiently showing which taxa of organisms are present, while shotgun approaches show all genes and can indicate what functions the organisms are capable of. But collecting and organizing comprehensive shotgun data is extremely challenging and costly, and, in theory, predicting functionalities from microbial identities alone would save immense effort. However, we don’t yet know to what extent such predictions are applicable."
Finally: a population-scale means of studying microbial communities. The next few years are going to be VERY illuminating.
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Rescooped by Chris Upton + helpers from Science News |
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A science website will use a $200,000 grant from the federal government to use social media to promote science to up to 250,000 young Australians.
Via Sakis Koukouvis
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Rescooped by Chris Upton + helpers from Amazing Science |
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The results support polygenic models in which spontaneous coding mutations in any of a large number of genes increases risk by 5- to 20-fold. Despite the challenge posed by such models, results from de novo events and a large parallel case–control study provide strong evidence in favour of CHD8 and KATNAL2 as genuine autism risk factors.
Three original papers are here: http://www.nature.com/nature/index.html
Via Dr. Stefan Gruenwald
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Rescooped by Chris Upton + helpers from bioinf |
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The ease of creating and distributing video tutorials instead of static content improves accessibility for researchers, annotators and curators. This article focuses on online video repositories for educational and tutorial videos provided by resource developers and users. It also describes a project in Japan named TogoTV (http://togotv.dbcls.jp/en/)
Via Mohamed Nadhir Djekidel
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Rescooped by Chris Upton + helpers from BS2064: Bioinformatics |
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Epigenetic Modifications To DNA Caused By Exercise (Medical News Today): Share With Friends: | | Top News - He...
Via Dr Richard Badge
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Rescooped by Chris Upton + helpers from Amazing Science |
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PRDM9 has evolved exceptionally rapidly between humans and chimpanzees and this rapid evolution explains a second, previously published, finding of the researchers: recombination hotspots also differ between humans and chimpanzees. Remarkably, PRDM9 is involved not just in determining mouse hotspot locations, but is also a key player in mouse speciation.
Via Dr. Stefan Gruenwald
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Slides from the talk presented at the conference "Applied Bioinformatics and Public Health" at Cambridge during 1-3 June 2011 (BG7, open-source (AGPL) bacterial genome annotation pipeline system for NGS, from #ohnosequences ...)...
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An overview and tutorial about RefSeqGene, a resource at NCBI that is the standard for reporting gene-specific sequence variation.
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Rescooped by Chris Upton + helpers from bioinf |
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Scooped by Ed Rybicki |
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Illumina shares are up today on a report that Roche is renewing its bid for the DNA sequencing leader with an offer price that has been sweetened to $8.1 billion from an earlier $6.7 billion bid. Cue Bloomberg: Illumina Inc.
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We have developed a fully automated degenerate PCR primer design system that plays a key role in the J. Craig Venter Institute's (JCVI) high-throughput viral sequencing pipeline. A consensus viral genome, or a set of consensus segment sequences in the case of a segmented virus, is specified using IUPAC ambiguity codes in the consensus template sequence to represent the allelic diversity of the target population. PCR primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the full length of the specified target region. As part of the tiling process, primer pairs are computationally screened to meet the criteria for successful PCR with one of two described amplification protocols. The actual sequencing success rates for designed primers for measles virus, mumps virus, human parainfluenza virus 1 and 3, human respiratory syncytial virus A and B and human metapneumovirus are described, where >90% of designed primer pairs were able to consistently successfully amplify >75% of the isolates.
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Background
Human papillomavirus (HPV) is the aetiological agent for cervical cancer and genital warts. Concurrent HPV and HIV infection in the South African population is high. HIV positive (+) women are often infected with multiple, rare and undetermined HPV types. Data on HPV incidence and genotype distribution are based on commercial HPV detection kits, but these kits may not detect all HPV types in HIV + women. The objectives of this study were to (i) identify the HPV types not detected by commercial genotyping kits present in a cervical specimen from an HIV positive South African woman using next generation sequencing, and (ii) determine if these types were prevalent in a cohort of HIV-infected South African women.Methods
Total DNA was isolated from 109 cervical specimens from South African HIV + women. A specimen within this cohort representing a complex multiple HPV infection, with 12 HPV genotypes detected by the Roche Linear Array HPV genotyping (LA) kit, was selected for next generation sequencing analysis. All HPV types present in this cervical specimen were identified by Illumina sequencing of the extracted DNA following rolling circle amplification. The prevalence of the HPV types identified by sequencing, but not included in the Roche LA, was then determined in the 109 HIV positive South African women by type-specific PCR.Results
Illumina sequencing identified a total of 16 HPV genotypes in the selected specimen, with four genotypes (HPV-30, 74, 86 and 90) not included in the commercial kit. The prevalence's of HPV-30, 74, 86 and 90 in 109 HIV positive South African women were found to be 14.6 %, 12.8 %, 4.6 % and 8.3 % respectively.Conclusions
Our results indicate that there are HPV types, with substantial prevalence, in HIV positive women not being detected in molecular epidemiology studies using commercial kits. The significance of these types in relation to cervical disease remains to be investigated.
Papillomavirus graphic by Russell Kightley Media
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Whole genome sequencing (WGS) promises to be transformative for the practice of clinical microbiology, and the rapidly falling cost and turnaround time mean that this will become a viable technology in diagnostic and reference laboratories in the near future. The objective of this article is to consider at a very practical level where, in the context of a modern diagnostic microbiology laboratory, WGS might be cost-effective compared to current alternatives. We propose that molecular epidemiology performed for surveillance and outbreak investigation and genotypic antimicrobial susceptibility testing for microbes that are difficult to grow represent the most immediate areas for application of WGS, and discuss the technical and infrastructure requirements for this to be implemented.
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Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ.
Three benchtop high-throughput sequencing instruments are now available. The 454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies) are laser-printer sized and offer modest set-up and running costs.
Marion Koopmans's curator insight,
February 16, 11:05 AM
Nice comparison. Whether differences matter depends on application/study question.
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Rescooped by Chris Upton + helpers from Virology and Bioinformatics from Virology.ca |
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The analysis of next-generation sequencing data from large genomes is a timely research topic. Sequencers are producing billions of short sequence fragments from newly sequenced organisms.
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Special Issue of Briefings in Functional Genomics
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Rescooped by Chris Upton + helpers from BS2064: Bioinformatics |
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Researchers from Karlsruhe Institute of Technology (KIT) in Germany and the National Tsing Hua University in Taiwan have created a DNA-based (Salmon DNA-based memory device | KurzweilAI http://t.co/utx6zx9R...
Via Dr Richard Badge
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Rescooped by Chris Upton + helpers from bioinf |
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Folding@home is a distributed computing project -- people from throughout the world download and run software to band together to make one of the largest supercomputers in the world. Every computer takes the project closer to our goals.
Via Mohamed Nadhir Djekidel
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RT @druvus: Computer Scientists' Solution to a Biologist’s Problem http://t.co/62bzZgVZ #bioinformatics #populus...
Database searching...
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Rescooped by Chris Upton + helpers from bioinf |
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"he advent of next-generation sequencing technologies is accompanied with the development of many whole-genome sequence assembly methods and software, especially for de novo fragment assembly. Due to the poor knowledge about the applicability and performance of these software tools, choosing a befitting assembler becomes a tough task. Here, we provide the information of adaptivity for each program, then above all, compare the performance of eight distinct tools against eight groups of simulated datasets from Solexa sequencing platform...."
Via Mohamed Nadhir Djekidel
Marion Koopmans's curator insight,
February 16, 11:13 AM
lots of comparisons needed, but hard to keep up!
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Researchers have completed the genome sequence for the gorilla, the last genus of the living great apes to have its genome decoded.
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