Project description:Paenibacillus larvae, the causal agent of American Foulbrood disease (AFB), affects honeybee health worldwide. The present study investigates the transcriptional response of this Gram-positive, endospore-forming bacterium to bodily fluids from honeybee larvae. Four different conditions were evaluated with a loop design: sampling of in vitro grown P. larvae cultures one or four hours after addition of larval fluids or BHIT-broth (C1, T1, C4, T4).
Project description:We compare the transcriptome of gnotobiotic Ae. aegypti generated by contaminating axenic (bacteria-free) larvae with bacterial isolates found in natural mosquito breeding sites. We focused on four bacterial isolates (Lysobacter, Flavobacterium, Paenibacillus and Enterobacteriaceae) and found that different gnotobiotic treatments resulted in massive transcriptomic changes throughout the mosquito development.
Project description:The Guthrie 903 card archived dried blood spots (DBS) are a unique but terminal resource amenable for individual and population wide genomic profiling. The limited amounts of DBS-derived genomic DNA (gDNA) can be whole-genome amplified (WGA) producing sufficient gDNA for genomic applications, albeit with variable success, and optimizing the isolation of high-quality DNA from these finite, low-yield specimens is essential. Visual automated fluorescence electrophoresis (VAFE) is a novel QC technology affording precise quality, quantity and molecular weight of double-stranded DNA from a single microliter of sample. The VAFE QC data were correlated with subsequent sample performance in PCR, sequencing, and high-density comparative genome hybridization array.
Project description:The following strains of Paenibacillus larvae classified as ERIC I-IV genotypes (pl1-pl4) were used in the study: ERIC I - DSM-7030; ERIC II - DSM-25430; ERIC III - LMG-16252; and ERIC IV - DSM-3615.
The 7 biological replicates (a-g) of the exoprotein fractions prepared from each ERIC genotype were used in the nanoLC-MS/MS analysis.
All 28 samples were consecutively analyzed using an OrbitrapTM FusionTM Tribrid q-OT-IT mass spectrometer.
To improve the protein identification and easy exclude contaminants from the medium, we considered the proteins that could originate from the yeast extract and Mueller-Hinton broth (contains beef fusion and casein peptone-acidic hydrolysate) in analyzing the MS data. Thus, we included the sequences related to Saccharomyces cerevisiae and Bos taurus, respectively, to the list of contaminants in MaxQuant. The contaminants.fasta file is provided. Futhermore, we provide the database (uniprot-paenibacillus+larvae.fasta) used for the identification of P. larvae proteins created of different strains of P. larvae.
The sequences were downloaded of UniProt on 12.03.2019.
Finally, the compressed (zipped) folder "combined" is provided.
The data were analyzed in MaxQuant v1.6.3.4.
Project description:Zebrafish have the remarkable ability to regenerate body parts including the heart, spinal cord and fins by a process referred to as epimorphic regeneration. Recent studies have illustrated that similar to adult zebrafish, early life stage-larvae also possess the ability to regenerate the caudal fin. A comparative genomic analysis was used to determine the degree of conservation in gene expression among the regenerating adult caudal fin, adult heart and larval fin. Results indicate that these tissues respond to amputation/injury with strikingly similar genomic responses. Comparative analysis revealed raldh2, a rate-limiting enzyme for the synthesis of Retinoic acid (RA), as one of the highly induced genes across the three regeneration platforms. Keywords: comparative genomics
Project description:Integrative multi-omic approaches have been increasingly applied to discovery and functional studies of complex human diseases. Short-term preoperative antibiotics have been adopted to reduce site infections in colorectal cancer (CRC) resections. We hypothesize that the antibiotics will impact analysis of multi-omic datasets generated from resection samples to investigate biological CRC risk factors. To assess the impact of preoperative antibiotics on integrated microbiome and human transcriptomic data generated from archived frozen CRC resection samples. Genomic DNA (gDNA) and RNA were extracted from 51 pairs of frozen sporadic CRC tumor and adjacent non-tumor mucosal samples from 50 CRC patients archived at a single medical center. 16S rRNA gene sequencing (V3V4 region, paired end (PE), 300 bp) and confirmatory quantitative polymerase chain reaction (qPCR) assays were conducted on gDNA. RNA sequencing IPE, 125bp) was performed on parallel tumor and non-tumor RNA samples with RNA Integrity Numbers (RIN) scores ≥ 6.
