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Innovations in -omics technologies have driven advances in biomedical research. However, integrating and analysing the large volumes of data generated from different high-throughput -omics technologies remain a significant challenge to basic and clinical scientists without bioinformatics skills or access to bioinformatics support. To address this demand, we have significantly updated our previous O-miner analytical suite, to incorporate several new features and data types to provide an efficient and easy-to-use Web tool for the automated analysis of data from ‘-omics’ technologies. Created from a biologist’s perspective, this tool allows for the automated analysis of large and complex transcriptomic, genomic and methylomic data sets, together with biological/clinical information, to identify significantly altered pathways and prioritize novel biomarkers/targets for biological validation. Our resource can be used to analyse both in-house data and the huge amount of publicly available information from array and sequencing platforms. Multiple data sets can be easily combined, allowing for meta-analyses. Here, we describe the analytical pipelines currently available in O-miner and present examples of use to demonstrate its utility and relevance in maximizing research output. O-miner Web server is free to use and is available at http://www.o-miner.org.

Leucaena leucocephala is a leguminous tree species accounting for one-fourth of raw material supplied to paper and pulp industry in India. Cinnamate 4-Hydroxylase (C4H, EC 1.14.13.11) is the second gene of phenylpropanoid pathway and a member of cytochrome P450 family. There is currently intense interest to alter or modify lignin content of L. leucocephala. Three highly similar C4H alleles of LlC4H1 gene were isolated and characterized. The alleles shared more than 98 % sequence identity at amino acid level to each other. Binding of partial promoter of another C4H gene LlC4H2, to varying amounts of crude nuclear proteins isolated from leaf and stem tissues of L. leucocephala formed two loose and one strong complex, respectively, suggesting that the abundance of proteins that bind with the partial C4H promoter is higher in stem tissue than in leaf tissue. Quantitative Real Time PCR study suggested that among tissues of same age, root tissues had highest level of C4H transcripts. Maximum transcript level was observed in 30 day old root tissue. Among the tissues investigated, C4H activity was highest in 60 day old root tissues. Tissue specific quantitative comparison of lignin from developing seedling stage to 1 year old tree stage indicated that Klason lignin increased in tissues with age.

Declines in brain glucose metabolism have been described early in Alzheimer's disease (AD), and there is evidence that a genetic predisposition to AD contributes to accelerate this process. The epsilon 4 (e4) allele of the apolipoprotein E (ApoE) gene has been implicated as a major risk factor in this process. The aim of this FDG-PET study was to assess the ApoE e4 dose related effect on regional cerebral glucose metabolism (METglc) in clinical AD patients, with statistical voxel based methods.Eighty six consecutive mild to moderate AD patients included in the Network for Efficiency and Standardisation of Dementia Diagnosis database underwent FDG-PET scans at rest. PCR was used to determine the ApoE genotype. Patients were grouped as e4 non-carriers (n = 46), e3/e4 (n = 27) and e4/e4 (n = 13) carriers. A voxel-based mapping program was used to compare each AD subgroup with a database of 35 sex and age matched controls (p0.001, corrected for cluster extent) and also to compare between the subgroups (p0.001, uncorrected).No difference was found as to age at examination, age at onset, sex, disease duration, educational level, or severity of dementia between AD subgroups. Compared with controls, all AD subgroups had equivalent METglc reductions in the precuneus, posterior cingulate, parietotemporal, and frontal regions. Direct comparisons between AD subgroups indicated that patients with at least one e4 allele had METglc reductions within additional associative and limbic areas compared with e4 non-carriers.The present FDG-PET study showed different metabolic phenotypes related to the ApoE genotype in clinical AD patients, as revealed with voxel based statistical methods. The results suggest a generalised disorder in e4 carriers impairing metabolism globally, in addition to the more localised changes typical of AD patients.

ObjectivesHigh throughput sequencing of bacterial DNA from clinical samples provides untargeted, open-ended information on the entire microbial community. The downside of this approach is the vulnerability to DNA contamination from other sources than the clinical sample. Here we describe contamination from sterile paper points (PPs) used in microbial sample collection.MethodsPeri-implant samples from 48 individuals were collected using sterile PPs. Control samples contained only PPs or DNA extraction blank controls. 16S rRNA gene libraries were sequenced using 454 pyrosequencing. 16S rRNA gene copy numbers were measured by quantitative PCR.ResultsNearly half of the sequencing reads belonged to two OTUs classified as Enterococcus (25% of reads) or Exiguobacterium (21%), which are not typical oral microorganisms. Of 87 peri-implant samples, only 10 samples (11%) contained neither of the two OTUs. The relative abundance of both unusual OTUs correlated with each other (p < 0.001; r = 0.828, Spearman correlation). The control samples showed that 2 of 4 (50%) of the sterile unused PPs contained bacterial DNA equivalent to 1.2 × 103 and 1.1 × 104 cells respectively, which was within the range of DNA in the clinical samples (average 1.8 × 107, SD 4.8 × 107, min 4.4 × 102, max 2.8 × 108). The microbial profile from these PPs was dominated (>83% of reads) by the two unusual OTUs.ConclusionsSterile PPs can contain contaminating bacterial DNA. The use of PPs as a sampling tool for microbial profiling of clinical samples by open-ended techniques such as sequencing or DGGE should be avoided.Clinical significanceClinicians working with PPs as sampling tools for bacterial DNA should consider using an alternative sampling tool, because sterile unused PPs can be a considerable source of foreign bacterial DNA. We recommend sterile curettes for collecting clinical samples for open-ended techniques, such as sequencing or DGGE.

This study has investigated quantification of chimerism in sex-mismatched transplantations by quantitative real time PCR (RQ-PCR) using FTA paper for blood sampling. First, we demonstrate that the quantification of DNA from EDTA-blood which has been deposit on FTA card is accurate and reproducible. Secondly, we show that fraction of recipient cells detected by RQ-PCR was concordant between the FTA and salting-out method, reference DNA extraction method. Furthermore, the sensitivity of detection of recipient cells is relatively similar with the two methods. Our results show that this innovative method can be used for MC assessment by RQ-PCR.