miBLAST: scalable evaluation of a batch of nucleotide sequence queries with BLAST

A common task in many modern bioinformatics applications is to match a set of nucleotide query sequences against a large sequence dataset. Exis-ting tools, such as BLAST, are designed to evaluate a single query at a time and can be unacceptably slow when the number of sequences in the query set is large. In this paper, we present a new algorithm, called miBLAST, that evaluates such batch workloads efficiently. At the core, miBLAST employs a q-gram filtering and an index join for efficiently detecting similarity between the query sequences and database sequences. This set-oriented technique, which indexes both the query and the database sets, results in substantial performance improvements over existing methods. Our results show that miBLAST is significantly faster than BLAST in many cases. For example, miBLAST aligned 247 965 oligonucleotide sequences in the Affymetrix probe set against the Human UniGene in 1.26 days, compared with 27.27 days with BLAST (an improvement by a factor of 22). The relative performance of miBLAST increases for larger word sizes; however, it decreases for longer queries. miBLAST employs the familiar BLAST statistical model and output format, guaranteeing the same accuracy as BLAST and facilitating a seamless transition for existing BLAST users

The Compass-like Locus, Exclusive to the Ambulacrarians, Encodes a Chromatin Insulator Binding Protein in the Sea Urchin Embryo

Chromatin insulators are eukaryotic genome elements that upon binding of specific proteins display barrier and/or enhancer-blocking activity. Although several insulators have been described throughout various metazoans, much less is known about proteins that mediate their functions. This article deals with the identification and functional characterization in Paracentrotus lividus of COMPASS-like (CMPl), a novel echinoderm insulator binding protein. Phylogenetic analysis shows that the CMPl factor, encoded by the alternative spliced Cmp/Cmpl transcript, is the founder of a novel ambulacrarian-specific family of Homeodomain proteins containing the Compass domain. Specific association of CMPl with the boxB cis-element of the sns5 chromatin insulator is demonstrated by using a yeast one-hybrid system, and further corroborated by ChIP-qPCR and trans-activation assays in developing sea urchin embryos. The sns5 insulator lies within the early histone gene cluster, basically between the H2A enhancer and H1 promoter. To assess the functional role of CMPl within this locus, we challenged the activity of CMPl by two distinct experimental strategies. First we expressed in the developing embryo a chimeric protein, containing the DNA-binding domain of CMPl, which efficiently compete with the endogenous CMPl for the binding to the boxB sequence. Second, to titrate the embryonic CMPl protein, we microinjected an affinity-purified CMPl antibody. In both the experimental assays we congruently observed the loss of the enhancer-blocking function of sns5, as indicated by the specific increase of the H1 expression level. Furthermore, microinjection of the CMPl antiserum in combination with a synthetic mRNA encoding a forced repressor of the H2A enhancer-bound MBF1 factor restores the normal H1 mRNA abundance. Altogether, these results strongly support the conclusion that the recruitment of CMPl on sns5 is required for buffering the H1 promoter from the H2A enhancer activity, and this, in turn, accounts for the different level of accumulation of early linker and nucleosomal transcripts

A model-based definition of the generic remanufacturing business process

Access to the full-text thesis is no longer available at the author's request, due to 3rd party copyright restrictions. Access removed on 28.11.2016 by CS (TIS).Metadata merged with duplicate record (http://hdl.handle.net/10026.1/2829) on 20.12.2016 by CS (TIS).Remanufacturing is a process of bringing used products to a "like-new" functional state by rebuilding and replacing their component parts. The practice has a low profile in world economies, however, studies indicate that it obtains cost savings in the region of 20% to 80%, as well as quality similar to that of an equivalent "new" product. In fact, in excess of 73,000 firms are engaged in some sort of remanufacturing in the United States alone. The key remanufacturing issues are the ambiguity in its definition and the scarcity of its analytic models. The objective of the research was to address these issues, and was achieved using a 3-Phase research approach that followed Eisenhardt's (1989) case study methodology. Initially, the research examined remanufacturing operations in order to unambiguously define it. Following this, the remanufacturing business process was modelled to define remanufacturing in the context of its total system. The research contributions are a robust definition of remanufacturing and a comprehensive generic model of the remanufacturing business process. The research beneficiaries are industry and academia, because the unambiguous definition permits remanufacturing to be differentiated from alternative secondary market operations for the first time. This assists researchers to explicitly understand remanufacturing so they can undertake effective remanufacturing research and correctly disseminate their findings. The generic model is a remanufacturing-specific, analytic error-reduction tool to reduce risk in remanufacturing. The research originality is that for the first time remanufacturing has been analysed from a business process perspective, an unambiguous definition of remanufacturing is determined and a generic model of the remanufacturing business process has been established

Phylogeny of Vibrio vulnificus from the analysis of the core-genome: implications for intra-species taxonomy

Vibrio vulnificus (Vv) is a multi-host pathogenic species currently subdivided into three biotypes (Bts). The three Bts are human-pathogens, but only Bt2 is also a fish-pathogen, an ability that is conferred by a transferable virulence-plasmid (pVvbt2). Here we present a phylogenomic analysis from the core genome of 80 Vv strains belonging to the three Bts recovered from a wide range of geographical and ecological sources. We have identified five well-supported phylogenetic groups or lineages (L). LI comprises a mixture of clinical and environmental Bt1 strains, most of them involved in human clinical cases related to raw seafood ingestion. LII is linked to the aquaculture industry and includes Bt3 strains exclusively, mostly related to wound infections or secondary septicemia after farmed-fish handling. LIII is formed by a mixture of Bt1 and Bt2 strains from various sources, including diseased fish, and is also related to the aquaculture industry. Lastly, LIV and LV include a few strains of Bt1 associated with specific geographical areas. The phylogenetic trees for ChrI and II are not congruent to one another, which suggests that inter- and/or intra-chromosomal rearrangements have been produced along Vv evolution. Further, the phylogenetic trees for each chromosome and the virulence plasmid were also not congruent, which also suggests that pVvbt2 has been acquired independently by different clones, probably in fish farms. From all these clones, the one with zoonotic capabilities (Bt2-Serovar E) has successfully spread worldwide. From these results, we propose a new updated classification of the species based on phylogenetic lineages rather than on Bts, as well as the inclusion of all Bt2 strains in a pathovar with the particular ability to cause fish vibriosis, for which we suggest the name 'piscis'

Structure of the multi-subunit chloroplast RNA polymerase

Chloroplasts contain a dedicated genome that encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a plastid-encoded RNA polymerase (PEP), a nearly 1 MDa complex composed of core subunits with homology to eubacterial RNA polymerases (RNAPs) and at least 12 additional chloroplast-specific PEP-associated proteins (PAPs). However, the architecture of this complex and the functions of the PAPs remain unknown. Here, we report the cryo-EM structure of a 19-subunit PEP complex from Sinapis alba (white mustard). The structure reveals that the PEP core resembles prokaryotic and nuclear RNAPs but contains chloroplast-specific features that mediate interactions with the PAPs. The PAPs are unrelated to known transcription factors and arrange around the core in a unique fashion. Their structures suggest potential functions during transcription in the chemical environment of chloroplasts. These results reveal structural insights into chloroplast transcription and provide a framework for understanding photosynthesis gene expression

Second Aerospace Environmental Technology Conference

The mandated elimination of CFC'S, Halons, TCA, and other ozone depleting chemicals and specific hazardous materials has required changes and new developments in aerospace materials and processes. The aerospace industry has been involved for several years in providing product substitutions, redesigning entire production processes, and developing new materials that minimize or eliminate damage to the environment. These activities emphasize replacement cleaning solvents and their application, verification, compliant coatings including corrosion protection system and removal techniques, chemical propulsion effects on the environment, and the initiation of modifications to relevant processing and manufacturing specifications and standards

Investigating The Grey Field Slug

High-throughput sequencing was used to analyse cDNA generated from tissues of the grey field slug, Deroceras reticulatum, a significant invertebrate pest of agricultural and horticultural crops. Almost no sequence data is available for this organism. In this project, we performed de novo transcriptome sequencing to produce sequence dataset for the Deroceras reticulatum. A total of 132,597 and 161,419 sequencing reads between 50-600bp from the digestive gland and neural tissue were obtained through Roche 454 pyrosequencing. These reads were assembled into contiguous sequences and annotated using sequence homology search tools. Multiple sequence assemblies and annotation data was amalgamated into a biological database using BioSQL. Analysis of the dataset with predictions of probable protein function were made based on annotation data. InterPro (IPR) terms generated with InterProScan software were mapped to read counts and used to identify more frequently sequenced gene families. Digestive hydrolases were major transcripts in the digestive gland, with cysteine proteinases and cellulases being the most abundant functional classes. A Cathepsin L homologue is likely to be responsible for the proteinase activity of the digestive gland which was previously detected by biochemical analysis. Cathepsin L and several other predicted proteins were used to design RNAi experiments to assess potential for crop pest defence strategy. Further work on protein expression of a native tumour necrosis factor (TNF) ligand homologue was also conducted as an exemplar study

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De novo sequencing, assembly and analysis of the genome and transcriptome of the nematode Panagrolaimus superbus

The nematode Panagrolaimus superbus can survive for extended peri- ods of time in a desiccated state (anhydrobiosis) and is also freezing tol- erant (cryobiotic). These adaptations make it an interesting candidate for genome and transcriptome sequencing using second generation high through- put methods. In this project the transcriptome of P. superbus was sequenced using the 454 (Roche) platform. To enrich for stress-related genes, nema- todes were exposed to one of the following stresses (desiccation, cold, heat or oxidation). Equal numbers of nematodes from each stress treatment were combined with unstressed control nematodes prior to RNA extraction. Nor- malised and unnormalised cDNA libraries were prepared from this mixed population. A de novo assembly of the transcriptome was generated using a variety of assembly programs and strategies. A Sanger sequenced expressed sequence dataset comprising 3,982 unigenes was fully annotated and inte- grated into the de novo transcriptome assembly. The de novo assembly has also been annotated and putative stress response genes were identified. The haploid karyotype of P. superbus was determined to be n=4. P. superbus genomic DNA was sequenced using 454 (Roche) methods along with 50 bp and 100 bp paired end Illumina reads. Eight different gDNA assemblies were prepared, generating predicted genome sizes ranging from 87.9 kilobases to 159.7 kilobases. The longest contigs were obtained from the 454 genomic DNA assembly and the assemblies of the Illumina reads generated shorter contigs. The gene order of the P. superbus mitochondrial DNA genome was obtained and a draft assembly of the mitochondrial genome is presented. The current transcriptome assembly is a resource suitable for use as a refer- ence for aligning high throughput RNA Seq reads. Both the transcriptome and genome assemblies can be used to generate a protein reference database for the mass spectrometry based identification of the proteome of control and desiccated P. superbus for future studies