High-Throughput GRID Computing for Life Sciences

The number of fully sequenced genomes increases daily, producing an exponential explosion of the sequence, annotation and metadata databases. Data analysis on a genome-wide level or investigation within a specific data repository has become a data- and calculation-intensive process occupying single computers and even larger computer clusters for month or even years. In most cases such applications can be subdivided into many independent smaller tasks. The smaller tasks are particularly suited to distribution over a computational GRID infrastructure, which drastically reduces the time to reach the final result. In our analysis of gene ontology data and their associations to gene products of any kind of organism in a search to find gene products with similar functionalities, we developed a system to divide the full search into a large number of jobs and to submit these jobs to the GRID infrastructure as long as all jobs are processed successfully, guaranteeing an analysis of the data without missing any information.

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A Novel High-Throughput Screen Reveals Yeast Genes That Increase Secretion of Heterologous Proteins

Applied and Environmental Microbiology ◽

10.1128/aem.02427-06 ◽

2006 ◽

Vol 73 (4) ◽

pp. 1189-1198 ◽

Cited By ~ 62

Author(s):

Alane E. Wentz ◽

Eric V. Shusta

Keyword(s):

Surface Display ◽

Yeast Surface Display ◽

Gene Products ◽

Heterologous Proteins ◽

Single Chain ◽

Yeast Gene ◽

Genome Wide ◽

A Genome ◽

Yeast Surface ◽

Yeast Genes

ABSTRACT The yeast Saccharomyces cerevisiae is an attractive host for the production of heterologous proteins. However, low-yield production of many proteins (from micrograms to milligrams/liter) leaves considerable room for optimization. By engineering the yeast cell via traceable genome-wide libraries, genes that can enhance protein expression level because of their roles in protein transcription, translation, folding, and trafficking processes can be readily identified. This report details a novel approach that combines yeast cDNA overexpression libraries with yeast surface display to allow the rapid flow cytometric screening of engineered yeast for gene products that improve the display of heterologous proteins. After optimization of the screening conditions, a genome-wide scan yielded five yeast gene products that promoted increased display levels of a single-chain T-cell receptor (scTCR). The display-enhancing genes included those coding for cell wall proteins (CCW12, CWP2, and SED1), a ribosomal subunit protein (RPP0), and an endoplasmic reticulum-resident protein (ERO1). Under the premise that yeast surface display levels could be used as a predictor of secretion efficiency, each display-enhancing gene product was tested for its ability to affect secretion levels of multiple scTCR and single-chain antibodies (scFv). All of the selected yeast gene products were shown to promote increased secretion of active protein (1.5-fold to 7.9-fold), with CCW12 and ERO1 being the most generalizable enhancers of scFv/scTCR secretion.

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A novel assay provides insight into tRNAPhe retrograde nuclear import and re-export in S. cerevisiae

Nucleic Acids Research ◽

10.1093/nar/gkaa879 ◽

2020 ◽

Vol 48 (20) ◽

pp. 11577-11588

Author(s):

Regina T Nostramo ◽

Anita K Hopper

Keyword(s):

Nuclear Import ◽

Gene Products ◽

Amino Acid Deprivation ◽

Additional Gene ◽

Hsp70 Protein ◽

Genome Wide ◽

A Genome ◽

Evolutionarily Conserved ◽

Specific Manner ◽

Insight Into

Abstract In eukaryotes, tRNAs are transcribed in the nucleus and subsequently exported to the cytoplasm where they serve as essential adaptor molecules in translation. However, tRNAs can be returned to the nucleus by the evolutionarily conserved process called tRNA retrograde nuclear import, before relocalization back to the cytoplasm via a nuclear re-export step. Several important functions of these latter two trafficking events have been identified, yet the pathways are largely unknown. Therefore, we developed an assay in Saccharomyces cerevisiae to identify proteins mediating tRNA retrograde nuclear import and re-export using the unique wybutosine modification of mature tRNAPhe. Our hydrochloric acid/aniline assay revealed that the karyopherin Mtr10 mediates retrograde import of tRNAPhe, constitutively and in response to amino acid deprivation, whereas the Hsp70 protein Ssa2 mediates import specifically in the latter. Furthermore, tRNAPhe is re-exported by Crm1 and Mex67, but not by the canonical tRNA exporters Los1 or Msn5. These findings indicate that the re-export process occurs in a tRNA family-specific manner. Together, this assay provides insights into the pathways for tRNAPhe retrograde import and re-export and is a tool that can be used on a genome-wide level to identify additional gene products involved in these tRNA trafficking events.

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Treponema denticola biofilm-induced expression of a bacteriophage, toxin–antitoxin systems and transposases

Microbiology ◽

10.1099/mic.0.033654-0 ◽

2010 ◽

Vol 156 (3) ◽

pp. 774-788 ◽

Cited By ~ 34

Author(s):

Helen L. Mitchell ◽

Stuart G. Dashper ◽

Deanne V. Catmull ◽

Rita A. Paolini ◽

Steven M. Cleal ◽

...

Keyword(s):

Pcr Analysis ◽

Treponema Denticola ◽

Gene Products ◽

Planktonic Cells ◽

Biofilm Model ◽

Genome Wide ◽

A Genome ◽

Phage Dna ◽

Genes Encoding ◽

Genetic Mobility

Treponema denticola is an oral spirochaete that has been strongly associated with chronic periodontitis. The bacterium exists as part of a dense biofilm (subgingival dental plaque) accreted to the tooth. To determine T. denticola gene products important for persistence as a biofilm we developed a continuous-culture biofilm model and conducted a genome-wide transcriptomic analysis of biofilm and planktonic cells. A total of 126 genes were differentially expressed with a fold change of 1.5 or greater. This analysis identified the upregulation of putative prophage genes in the T. denticola 35405 genome. Intact bacteriophage particles were isolated from T. denticola and circular phage DNA was detected by PCR analysis. This represents the first, to our knowledge, functional bacteriophage isolated from T. denticola, which we have designated φtd1. In biofilm cells there was also an upregulation of genes encoding several virulence factors, toxin–antitoxin systems and a family of putative transposases. Together, these data indicate that there is a higher potential for genetic mobility in T. denticola when growing as a biofilm and that these systems are important for the biofilm persistence and therefore virulence of this bacterium.

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Common genetic determinants of vitamin D insufficiency: a genome-wide association study

Yearbook of Pediatrics ◽

10.1016/j.yped.2010.12.026 ◽

2012 ◽

Vol 2012 ◽

pp. 454-456

Author(s):

J.A. Stockman

Keyword(s):

Vitamin D ◽

Association Study ◽

Genome Wide Association Study ◽

Vitamin D Insufficiency ◽

Genome Wide Association ◽

Genetic Determinants ◽

Genome Wide ◽

A Genome

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Establishment of a genome-wide RNAi screen; Identification of novel genes involved in clonal maintenance of ALL

Klinische Pädiatrie ◽

10.1055/s-0034-1374830 ◽

2014 ◽

Vol 226 (03) ◽

Author(s):

F Ponthan ◽

D Pal ◽

J Vormoor ◽

O Heidenreich

Keyword(s):

Rnai Screen ◽

Novel Genes ◽

Genome Wide ◽

A Genome

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A genome-wide linkage scan for familial partial lipodystrophy susceptibility genes in a German kindreds

Clinical & Investigative Medicine ◽

10.25011/cim.v30i4.2861 ◽

2007 ◽

Vol 30 (4) ◽

pp. 86

Author(s):

M. Lanktree ◽

J. Robinson ◽

J. Creider ◽

H. Cao ◽

D. Carter ◽

...

Keyword(s):

Subcutaneous Fat ◽

Visceral Obesity ◽

Fat Distribution ◽

Dominant Negative ◽

Molecular Forms ◽

Partial Lipodystrophy ◽

Genome Wide ◽

A Genome ◽

Familial Partial Lipodystrophy ◽

Promoter Mutations

Background: In Dunnigan-type familial partial lipodystrophy (FPLD) patients are born with normal fat distribution, but subcutaneous fat from extremities and gluteal regions are lost during puberty. The abnormal fat distribution leads to the development of metabolic syndrome (MetS), a cluster of phenotypes including hyperglycemia, dyslipidemia, hypertension, and visceral obesity. The study of FPLD as a monogenic model of MetS may uncover genetic risk factors of the common MetS which affects ~30% of adult North Americans. Two molecular forms of FPLD have been identified including FPLD2, resulting from heterozygous mutations in the LMNA gene, and FPLD3, resulting from both heterozygous dominant negative and haploinsufficiency mutations in the PPARG gene. However, many patients with clinically diagnosed FPLD have no mutation in either LMNA or PPARG, suggesting the involvement of additional genes in FPLD etiology. Methods: Here, we report the results of an Affymetrix 10K GeneChip microarray genome-wide linkage analysis study of a German kindred displaying the FPLD phenotype and no known lipodystrophy-causing mutations. Results: The investigation identified three chromosomal loci, namely 1q, 3p, and 9q, with non-parametric logarithm of odds (NPL) scores >2.7. While not meeting the criteria for genome-wide significance, it is interesting to note that the 1q and 3p peaks contain the LMNA and PPARG genes respectively. Conclusions: Three possible conclusions can be drawn from these results: 1) the peaks identified are spurious findings, 2) additional genes physically close to LMNA, PPARG, or within 9q, are involved in FPLD etiology, or 3) alternative disease causing mechanisms not identified by standard exon sequencing approaches, such as promoter mutations, alternative splicing, or epigenetics, are also responsible for FPLD.

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