The White House Rural Doctor Assciation Of Australia
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PROVIDER: PRJNA339448 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Deep sequencing of mRNA from two macaques, crab-eating macaque and Indian rhesus macaque Analysis of ploy(A)+ RNA of different specimens:brain,ileum,kidney,liver,testes and white adipose for crab-eating macaque while brain,heart,,kidney,liver,quadriceps and testes for Indian rhesus macaque
2011-10-13 | E-GEOD-29629 | biostudies-arrayexpress
Project description:Although copper is an essential nutrient crucial for many biological processes, an excessive concentration can be toxic and lead to cell death. The metabolism of this two-faced metal must be strictly regulated at the cell level. In this study, we investigated copper homeostasis in two related unicellular organisms: nonpathogenic Naegleria gruberi and the “brain-eating amoeba” Naegleria fowleri. We identified and confirmed the function of their specific copper transporters securing the main pathway of copper acquisition. Adjusting to different environments with varying copper levels during the life cycle of these organisms requires various metabolic adaptations. Using comparative proteomic analyses, measuring oxygen consumption, and enzymatic determination of NADH dehydrogenase, we showed that both amoebas respond to copper deprivation by upregulating the components of the branched electron transport chain: the alternative oxidase and alternative NADH dehydrogenase. Interestingly, analysis of iron acquisition indicated that this system is copper-dependent in N. gruberi but not in its pathogenic relative. Importantly, we identified a potential key protein of copper metabolism of N. gruberi, the homolog of human DJ-1 protein, which is known to be linked to Parkinson’s disease. Altogether, our study reveals the mechanisms underlying copper metabolism in the model amoeba N. gruberi and the fatal pathogen N. fowleri and highlights the differences between the two amoebas.
2022-05-20 | PXD032745 | Pride
Project description:Most malaria infections in sub-Saharan Africa are acquired indoors, thus finding effective ways of preventing mosquito house entry should reduce transmission. Since most malaria mosquitoes fly less than 1 m from the ground, we tested whether raising buildings off the ground would prevent the entry of Anopheles gambiae, the principal African malaria vector, in rural Gambia. Nightly collections of mosquitoes were made using light traps from four inhabited experimental huts, each of which could be moved up or down. Mosquito house entry declined with increasing height, with a hut at 3 m reducing An. gambiae house entry by 84% when compared with huts on the ground. A propensity for malaria vectors to fly close to the ground and reduced levels of carbon dioxide, a major mosquito attractant, in elevated huts, may explain our findings. Raised buildings may help reduce malaria transmission in Africa.
| S-EPMC8150013 | biostudies-literature
Project description:204 placentas from three cohorts were processed for DNAme arrays in Vancouver, Canada. The three cohorts consisted of: (i) V-NORM, a normative population of term pregnancies recruited at BC Women’s Hospital (BCWH) in Vancouver, Canada (n=35), as part of a study on Epigenetics in Pregnancy Complications (EPIC); ii) V-SSRI, a population of pregnant individuals recruited in Vancouver, Canada in the 20th week of gestation (n=64), with/without clinical depression, and with/without the use of selective serotonin reuptake inhibitors (SSRIs); and (iii) QF-2011, a population of term pregnancies that were exposed to sudden-onset stress during gestation due to catastrophic flooding in the Australian state of Queensland in early January 2011 (n=105). DNA samples from all three cohorts were run on Illumina Infinium MethylationEPIC arrays in Vancouver, BC, Canada. Processing included DNA purification after extraction using the DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA, USA), bisulfite conversion using the EZ DNAme Kit (Zymo Research, Orange, CA, USA), and hybridization to and processing of the Illumina Infinium MethylationEPIC BeadChip arrays according to the manufacturer’s protocol (Illumina, San Diego, CA, USA). Samples from the three cohorts were randomized and run in 3 array batches across 44 eight-sample chips as illustrated in Supp Figure 5. In the case of the V-SSRI and QF-2011 cohorts, sample exposure groups (SSRI exposed/non-exposed and objective flood stress high/low) and infant sex were carefully distributed across array chips (1-44) and rows (1-8) to minimize potential batch effects. DNAme data from raw IDAT files were read into R v4.2.2(54) and annotated with the Illumina Infinium MethylationEPIC v1.0 B4 Manifest. Several data quality control checks were undertaken using the R packages minfi(55,56), wateRmelon(57,58), and ewastools(59). First, each sample was assessed at 17 Illumina control probes to evaluate bisulfite conversion efficiency and array run quality; all samples passed the manufacturer-recommended thresholds at the control probes. Next, average total (methylated + unmethylated) fluorescence intensity was assessed between samples, and between array batches. All samples had similar total fluorescence, though samples run on the EPIC array in Batch 3 had slightly higher average intensities than those in Batch 1 and 2. Sample sex was assessed with the ewastools package(59), using the mean total fluorescence intensity (methylated + unmethylated) of the X and Y chromosome probes, normalized to the per-sample mean autosomal total fluorescence intensity, and was confirmed to match the clinically-reported sex of the infant in all cases. Sample genetic identity was assessed using the 59 SNP (‘rs’) probes on the EPIC array with the call_genotypes() and enumerate_sample_donors() functions (ewastools)(59). Finally, DNAme beta value density plots of all samples were visually assessed to determine overall similarity of the beta value distributions between samples, with no outliers identified.
2023-08-08 | GSE232778 | GEO
Project description:Experiment: Expression profiling in breast cancer brain metastases (BC) compared to breast cancers (BC) and primary brain tumors (prBT). The objectives are to identify expression profiles that are specific to BCBM in order to identify new molecular biomarkers. The characterization of the BCBM samples included adjacent genetic techniques.
2017-12-29 | GSE100534 | GEO
Project description:Circadian clocks in peripheral organs are entrained by feeding. Eating in the right time is crucial to maintain metabolic health, whereas eating in the wrong time increases the susceptibility to metabolic diseases. It is unknown how change of mealtime impacts circadian transcriptomes in peripheral organs and brain. Here, we presented global circadian transcript profile of mouse tissues (i.e. skeletal muscle) entrained by inverted feeding to compile an atlas for mechanistic insights into how feed-fast cycle regulates circadian biology.
2023-04-23 | GSE194106 | GEO
Project description:19 bronchial epithelial SAGE libraries were constructed and analyzed in this study. Discussed in the study: IDENTIFICATION OF NOVEL LUNG GENES IN BRONCHIAL EPITHELIUM BY SERIAL ANALYSIS OF GENE EXPRESSION Kim M. Lonergan1, Raj Chari1, Ronald J. deLeeuw1, Ashleen Shadeo1, Bryan Chi1, Ming-Sound Tsao2, Steven Jones3, Marco Marra3, Victor Ling1, Raymond Ng1,4, Calum MacAulay5, Stephen Lam5 and Wan L. Lam1 From the 1Department of Cancer Genetics & Developmental Biology, 5Department of Cancer Imaging, 3Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, BC, Canada, 2Ontario Cancer Institute / Princess Margaret Hospital, Toronto, ON, Canada, 4the Department of Computer Science, University of British Columbia, Vancouver, BC, Canada A description of the transcriptome of human bronchial epithelium should provide a basis for studying lung diseases including cancer. We demonstrate here that minute epithelial specimens obtained by bronchial brushings afford reliable profiling by serial analysis of gene expression (SAGE) leading to lung gene discovery. We have deduced global gene expression profiles of bronchial epithelium and lung parenchyma, based upon a vast data set of nearly two million sequence tags from 21 SAGE libraries generated from individuals with a history of smoking. Cluster and linear regression analysis demonstrate the repeatability and reproducibility of bronchial SAGE libraries, and suggest that the transcriptome of the bronchial epithelium is distinct from that of lung parenchyma and other tissue types. This distinction is highlighted by the abundant expression of signature genes that reflect tissue-specific and region-specific functions. Through our analysis we have identified novel bronchial-enriched genes and a novel transcript variant for surfactant, pulmonary-associated protein B in lung parenchyma. Conspicuously, gene expression associated with ciliogenesis is evident in bronchial epithelium. Additionally, it is noted that a large number of unmapped tags awaits further investigation. This study represents a comprehensive delineation of the bronchial and parenchyma transcriptomes, identifying more than 20,000 known and hypothetical genes expressed in the human lung, constituting one of the largest human SAGE studies reported to date. Keywords: bronchial epithelium 19 bronchial epithelial SAGE libraries were constructed and analyzed in this study.
2006-07-14 | E-GEOD-3707 | biostudies-arrayexpress
Project description:The piperazine derivatives most frequently consumed for recreational purposes are 1-benzylpiperazine (BZP), 1-(3,4-methylenedioxybenzyl)piperazine (MDBP), 1-(3-trifluoromethylphenyl)piperazine (TFMPP), and 1-(4-methoxyphenyl)piperazine (MeOPP). Currently it is unclear whether piperazine designer drugs induce mechanisms of hepatotoxicity and, if so, whether they act by a common mechanism. We performed a gene array study with rat hepatocytes incubated with the four designer drugs for 24 h in order to detail the global programme of gene expression Primary rat hepatocytes were cultured in collagen sandwich and incubated with the piperazine designer drugs. After 24 h, the RNA was extracted and the Affymetrix microarray analysis was performed.
2015-05-13 | E-GEOD-68785 | biostudies-arrayexpress