Project description:The long-tailed macaque, also referred to as cynomolgus monkey (Macaca fascicularis), is one of the most important non-human primate animal models in basic and applied biomedical research. To improve the predictive power of primate experiments for humans, we determined the genome sequence of a Macaca fascicularis female of Mauritian origin using a whole-genome shotgun sequencing approach. We applied a template switch strategy which employs either the rhesus or the human genome to assemble sequence reads. The 6-fold sequence coverage of the draft genome sequence enabled discovery of about 2.1 million potential single-nucleotide polymorphisms based on occurrence of a dimorphic nucleotide at a given position in the genome sequence. Homology-based annotation allowed us to identify 17,387 orthologs of human protein-coding genes in the M. fascicularis draft genome and the predicted transcripts enabled the design of a M. fascicularis-specific gene expression microarray. Using liver samples from 36 individuals of different geographic origin, we identified 718 genes with highly variable expression in liver, whereas the majority of the transcriptome shows relatively stable and comparable expression. Knowledge of the M. fascicularis draft genome is an important contribution to both the use of this animal in disease models and the safety assessment of drugs and their metabolites. In particular, this information allows high-resolution genotyping and microarray-based gene expression profiling for animal stratification, thereby allowing the use of well-characterized animals for safety testing. Finally, the genome sequence presented here is a significant contribution to the global "3R" animal welfare initiative, which has the goal to reduce, refine and replace animal experiments.
Project description:Comparative genomics and transcriptomics of the filamentous fungi Aspergillus oryzae and Aspergillus niger have opened possibilities for investigating the cellular metabolism and regulation of these fungi on a systemic level. The aim of this work was to understand how metabolism is regulated and to identify common regulatory responses between A. oryzae and A. niger. We therefore conducted batch fermentations with A. oryzae and A. niger grown on three different carbon sources (glucose, maltose, and xylose) in order to investigate their genome-wide transcription response Keywords: Two Aspergillus species and different carbon sources
Project description:Comparative genomics and transcriptomics of the filamentous fungi Aspergillus oryzae and Aspergillus niger have opened possibilities for investigating the cellular metabolism and regulation of these fungi on a systemic level. The aim of this work was to understand how metabolism is regulated and to identify common regulatory responses between A. oryzae and A. niger. We therefore conducted batch fermentations with A. oryzae and A. niger grown on three different carbon sources (glucose, maltose, and xylose) in order to investigate their genome-wide transcription response Keywords: Two Aspergillus species and different carbon sources Three conditions (glucose, maltose and xylose) with three biological replicates for A. oryzae and A. niger
Project description:Global mRNA expression profiling of HCT116 cells overexpressing miR30a-5p were collected using Agilent human whole genome array (G4845A AMADID 026652, cRNA 4x44k V2) . Two different sources of RNA were analyzed: 1.) HCT116 colon cancer cells overexpressing human mir-30a-5p together with a sponge vector expressing binding sites for the antisense sequence of sh30a-5p vector construct to compete out possible miRNAs derived from the anti-guide strand of this vector. 2.) HCT116 colon cancer cells expressing control vector (pLKO.1-LV) and the sponge vector described above.
Project description:Although the major food-borne pathogen Campylobacter jejuni has been isolated from diverse animal, human and environmental sources, our knowledge of genomic diversity in C. jejuni is based exclusively on human or human food-chain-associated isolates. Studies employing multilocus sequence typing have indicated that some clonal complexes are more commonly associated with particular sources. Using comparative genomic hybridization on a collection of 80 isolates representing diverse sources and clonal complexes, we identified a separate clade comprising a group of water/wildlife isolates of C. jejuni with multilocus sequence types uncharacteristic of human food-chain-associated isolates. By genome sequencing one representative of this diverse group (C. jejuni 1336), and a representative of the bank-vole niche specialist ST-3704 (C. jejuni 414), we identified deletions of genomic regions normally carried by human food-chain-associated C. jejuni. Several of the deleted regions included genes implicated in chicken colonization or in virulence. Novel genomic insertions contributing to the accessory genomes of strains 1336 and 414 were identified. Comparative analysis using PCR assays indicated that novel regions were common but not ubiquitous among the water/wildlife group of isolates, indicating further genomic diversity among this group, whereas all ST-3704 isolates carried the same novel accessory regions. While strain 1336 was able to colonize chicks, strain 414 was not, suggesting that regions specifically absent from the genome of strain 414 may play an important role in this common route of Campylobacter infection of humans. We suggest that the genomic divergence observed constitutes evidence of adaptation leading to niche specialization. Data is also available from <ahref=http://bugs.sgul.ac.uk/E-BUGS-95 target=_blank>BuG@Sbase</a>
2011-04-15 | E-BUGS-95 | biostudies-arrayexpress
Project description:Whole genome sequence of B. pseudomallei isolated from human, animal, and soil
Project description:We report the application of size selection of small RNA species isolated from Jjhan cells harboring the human herpesvirus 6A genome. We ammassed >3.4million reads of sequence from three different sources: Normal Brain cell total RNA, Jjhan total RNA and HHV-6A BAC transfected Jjhan total RNA. Sequences were mapped to the HHV-6A Uganda 1102 strain genome (GenBank: X83413.1) with no less than 100% match for reads >20nt and <23nt. The resulting pool of candidates was mapped to the HHV-6A genome.