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EL SEGUNDO, CA, United States

Aislabie J.M.,Landcare Research | Lau A.,University of Auckland | Dsouza M.,University of Auckland | Shepherd C.,University of Auckland | And 2 more authors.
Extremophiles | Year: 2013

The aim of this study was to examine the bacterial composition of high latitude soils from the Darwin-Hatherton glacier region of Antarctica. Four soil pits on each of four glacial drift sheets were sampled for chemical and microbial analyses. The four drifts-Hatherton, Britannia, Danum, and Isca-ranged, respectively, from early Holocene (10 ky) to mid-Quaternary (ca 900 ky). Numbers of culturable bacteria were low, with highest levels detected in soils from the younger Hatherton drift. DNA was extracted and 16S rRNA gene clone libraries prepared from samples below the desert pavement for each of the four drift sheets. Between 31 and 262 clones were analysed from each of the Hatherton, Britannia, and Danum drifts. Bacterial sequences were dominated by members of the phyla Deinococcus-Thermus, Actinobacteria, and Bacteroidetes. Culturable bacteria, including some that clustered with soil clones (e.g., members of the genera Arthrobacter, Adhaeribacter, and Pontibacter), belonged to Actinobacteria and Bacteroidetes. The isolated bacteria are ideal model organisms for genomic and phenotypic investigations of those attributes that allow bacteria to survive and/or grow in Antarctic soils because they have close relatives that are not tolerant of these conditions. © 2013 Springer Japan.

Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 156.81K | Year: 2014

DESCRIPTION (provided by applicant): Cancers selected for the NIH's The Cancer Genome Atlas (TCGA) project have been chosen because of their poor prognosis and overall public health impact. Select tissue samples have been profiled for gene and miRNA expression, promoter methylation, DNA sequence and mutation analysis, as well as copy number variation (CNV), with total expenditures of 275 Million13. The copy number variation (CNV) information, derived from the raw array-based comparative genomic hybridization (aCGH) and SNP-array data, has been successfully utilized in specific application areas, such as identification of significant recurrent aberrations in each tumor type from population-wide, tumor- specific analysis. However, the full potential of this data has not yet been exploited. The two major obstacles have been the method used to perform the initial data processing which have somewhat limited its utility, and the lack of a comprehensive integrated data access and analytical platform for copy n

Biodiscovery, Inc. | Date: 2014-11-03

Software that is used for analysing genetic data.

Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 214.71K | Year: 2010

DESCRIPTION (provided by applicant): There is a growing demand for custom synthesis of short genes libraries coding for active peptides or regulatory RNAs. DNA microarrays can be manufactured by synthesizing oligonucleotides on solid substrate in a massively-parallel manner using a high-yield low cost chemistry. Oligonucleotides can be cleaved off the microarray surface and recovered as a pool. Our hypothesis is that we can use this technology to create custom libraries of long DNA oligonucleotides at a much reduced cost and increased complexity compared to current technologies. Our long term objectives are to implement a commercial service of affordable custom synthesis of long oligonucleotide libraries. These libraries are used as a research tools in many applications such as studies on gene silencing, protein-DNA interaction, epitope mapping or even antimicrobial peptides. There are no limits for applications than the imagination of scientists. The heath relatedness of the project resides in the facts that these applications lead to the discovery of new cellular mechanisms, diagnosis tools, drugs or even vaccines. The scope of the proposed project is 1) to demonstrate the feasibility of using an emulsion-based PCR to amplify oligonucleotide libraries; 2) to investigate the possibility to synthesize libraries of oligonucleotide up to 150 mer in length and 3) to determine the synthesis error rate and type of sequence mutations present in these libraries. We will in particular test the effect of droplet size and number of templates per droplet on the PCR amplification of oligonucleotide template in an emulsion. We wil characterize the complexity of an amplified library by deep-sequencing a PCR product. The large amount of sequence information obtained will also permit an in depth characterization the type of errors occuring during massively-parallel long oligonucleotide synthesis. PUBLIC HEALTH RELEVANCE: The unprecedented availability of affordable custom libraries of long oligonucleotides will enable new experimentations in fields such as gene silencing, protein-DNA interaction, epitope mapping or even antimicrobial peptides. This technology will undoubtedly bolster the discovery of new cellular mechanisms, diagnosis tools, drugs or even vaccines, ultimately benefiting the society.

Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 219.26K | Year: 2010

DESCRIPTION (provided by applicant): Peptides play a significant role in the defense mechanisms of the body and binding of cells, bacteria and viruses to surfaces. Combinatorial peptide chemistry has emerged as a powerful tool for mapping receptor-ligand interactions in drug discovery applications as well as epitope mapping. There is a huge, but largely unrealized, potential for peptide microarray applications in drug discovery, study of cellular pathways and treatment of tumors. There are two reasons why the peptide micro arrays have not yet reached their potential: i) the enormous diversity possible with peptide microarrays as well as ii) the high cost of peptide microarrays in comparison to DNA microarrays. In this proposal our goals are to: 1) Develop a highly flexible and fast in situ custom peptide synthesis technology which can lower the cost of peptide microarrays by at least an order of magnitude and reduce the synthesis time to less than 24 hours for peptides containing up to 15 amino acids; 2) Increase the density of peptides on a microarray by an order of magnitude to gt10,000/array; 3) Use fluorescent probes as well as high resolution mass spectroscopy to determine sequence purity and stepwise yields for addition of each of the 20 naturally occurring amino acids. We have developed a revolutionary light gated oligonucleotide microarray synthesis technology which uses off the shelf reagents and a modified projector to carry out custom microarray synthesis on open or curved surfaces with probe densities of up to 500K/glass slide for about one tenth the cost of most commercial microarrays of similar density. In this project we will modify the chemistry and instrumentation used for oligonucelotide microarray synthesis to develop a system for combinatorial peptide synthesis on open/closed slide surfaces or membranes.

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