Project description:Experiment was designed to study the effect of Deformed wing virus (DWV) and the mite Varroa destructor on on siRNA and miRNA composition using high-throughput sequencing of small RNA in developing worker honeybee (Apis mellifera). Newly hatched bee larvae (day 3 of bee development) were transferred from a Varroa-free colony with low DWV levels to a Varroa-infested colony with high levels of DWV in bees and Varroa mites. All transferred larvae were receiving the DWV strains present in this Varroa-infested colony with the food delivered by the nurse bees until their capping (day 8). About half of these larvae were capped with Varroa mite and were subjected to the mite piercing and feeding on their haemolymph during pupal development until sampling at purple eye stage (day 14). Exposure to the mite piercing and feeding resulted in about 1000-fold increase of the DWV levels in the majority of the mite-exposed pupae compared to the control pupae and the pupae not exposed to Varroa mites.
Project description:Interethnic variability in chemotherapy response is becoming increasingly evident, making approaches for customizing chemotherapy treatment to different ethnic populations desirable. At the same time, significant genetic variation has also been observed between ethnic groups, including many germline and somatic pharmacogenetic variants involved in chemotherapy pharmacology. Recently, based on meta-analyses of studies on germline pharmacogenetic variant frequencies and clinical trials, the investigators found that chemotherapy outcomes between Asians and Caucasians colorectal cancer (CRC) patients could potentially be inferred from the frequencies of variants between the ethnic groups and their respective biological functions. In this study, the investigators seek to further clarify the validity of using pharmacogenetic variants to customize chemotherapy between ethnicities through the following specific aims: (1) To verify the differences observed in the frequency of germline pharmacogenetic variants related to chemotherapy between Asian and Caucasian CRC patients, (2) To test whether variations in the frequency of somatic pharmacogenetic gene mutations between Asian and Caucasian CRC patients could be used to infer differences in clinical outcomes between the two ethnicities. (3) (4) For Aim 1, DNA samples from approximately 1000 Asian and Caucasian CRC patients each will be analyzed for the frequency of a panel of germline pharmacogenetic variants identified in our meta-analyses using high-throughput methodology. For Aim 2, meta-analyses will be performed on pharmacogenetic studies and clinical trials to establish the relative frequencies of somatic variants and clinical outcomes in Asian and Caucasian CRC patients. These frequencies will be verified on the same series of DNA samples used in Aim 1. The clinical outcomes inferred from the frequency differences and biological functions will then be compared to those summarized from clinical trials. This data could provide a basis for developing a rational approach to customizing chemotherapy in non-Caucasian populations and improve assessment of drug feasibility in different ethnic populations.If validated, this working hypothesis would be of high clinical interest, giving the opportunity to use this as a DNA prognosis biomarker in CRC.
Pharmacogenetic frequencies could be a potentially useful approach for predicting likely chemotherapy outcomes in non-Caucasian populations
| 2125182 | ecrin-mdr-crc
Project description:A semi-automated and high-throughput approach for the detection of honey bee viruses in bee samples
Project description:Changes in the amino acid sequences of proteins cause thousands of human genetic diseases. However, only a subset of variants in any protein is typically pathogenic, with variants having a diversity of molecular consequences. Determining which of the thousands of possible variants in any protein have similar molecular effects is very challenging, but crucial for identifying pathogenic variants, determining disease mechanisms, understanding clinical phenotypic variation, and developing targeted therapeutics. Here we present a general method to classify variants by their molecular effects that we term intramolecular genetic interaction profiling. The approach relies on the principle that variants with similar molecular consequences have similar genetic interactions with other variants in the same protein. These intramolecular genetic interactions are straightforward to quantify for any protein with a selectable function. We apply intramolecular genetic interaction profiling to amyloid beta, the protein that aggregates in Alzheimer’s disease (AD) and is mutated in familial AD (fAD). Genetic interactions identify two classes of gain-of-function variants, with all known familial Alzheimer’s disease variants having very similar genetic interaction profiles, consistent with a common gain-of-function mechanism leading to pathology. We believe that intramolecular genetic interaction profiling is a powerful approach for classifying variants in disease genes that will empower rare variant association studies and the discovery of disease mechanisms.
Project description:Experimental methods for discovering RNA Binding Protein (RBP) binding sites on target RNAs have recently emerged which employ fusions of RBPs to RNA-editing enzymes (such asAPOBEC1 or ADAR) to “label” mRNA. However, off-target editing, genetic variants and sequencing errors can lead to false positives when using data derived from such approaches, and highlight a need for a robust, statistical approach to prioritizing confident binding sites.
Project description:Experiment was designed to study the effect of Deformed wing virus (DWV) and the mite Varroa destructor on global gene expression using microarray transcriptional profiling in developing worker honeybee (Apis mellifera). Newly hatched bee larvae (day 3 of bee development) were transferred from a Varroa-free colony with low DWV levels to a Varroa-infested colony with high levels of DWV in bees and Varroa mites. All transferred larvae were receiving the DWV strains present in this Varroa-infested colony with the food delivered by the nurse bees until their capping (day 8). About half of these larvae were capped with Varroa mite and were subjected to the mite piercing and feeding on their haemolymph during pupal development until sampling at purple eye stage (day 14). Exposure to the mite piercing and feeding resulted in about 1000-fold increase of the DWV levels in the majority of the mite-exposed pupae compared to the control pupae and the pupae not exposed to Varroa mites.
Project description:Four single consecutive murine kidney tissue specimens were prepared with the direct trypsinization with RapiGest (DTR) approach or with the filter aided sample preparation (FASP) protocol using both 10k and 30k filter devices and analyzed by label-free, quantitative liquid chromatography – tandem mass spectrometry (LC-MS/MS). Furthermore, we probed compatibility of the DTR protocol for the analysis of common histological stainings, namely hematoxylin & eosin (H&E), hematoxylin, and hemalaun. These were proteomically compared to an unstained control by analyzing four human tonsil FFPE tissues per condition.
Project description:Arabidopsis seedlings were grown for 1 week in Aradishes and then subjected to 5 min to 10 h of simulated microgravity using a 2D clinostat. RNA; proteins and metabolites were extracted and analyzed by RNA.seq and label free quantitative MS.
Project description:Gene expression for NCI-H1299 cell line transfected with human DENND2D and vector (pcDNA3.1/V5-His TOPO TA vector) respectively. The microarray experiment was designed to perform four replicates for each H1299-DENND2D and H1299-vector sample. cRNA used in replication 1 and 2 was from the same label reaction to perform the hybridization replicates.