How do consumers deal with stoichiometric constraints?
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ABSTRACT:
ORGANISM(S): Daphnia pulex
SUBMITTER: Jacqueline Lopez
PROVIDER: E-GEOD-27959 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Determine gene expression in daphnia exposed to biotic and abiotic stressors. Identify in Daphnia pulex unique gene regulatory patterns involved in the regulation of limited phosphorous.
2012-03-13 | GSE27959 | GEO
Project description:Comparison of miRNA expression profiles in normal and malignant prostate tissues. Keywords: microarray analysis of microRNA expression profiles MicroRNA expression was compared between normal prostate tissue from either young subjects that died of trauma, or normal adjacent to tumor, and prostatic tumors in older prostate cancer patients. RNA was isolated from frozen tissue sections, enriched for the miRNA fraction, which was subsequently labeled and hybridized to miRNA microarrays for expression profiling analysis.
2010-05-14 | E-GEOD-6636 | biostudies-arrayexpress
Project description:Intra-tumoral heterogeneity can wreak havoc on current precision medicine strategies due to challenges in sufficient sampling of geographically separated areas of biodiversity distributed across centimeter-scale tumor distances. In particular, modern tissue profiling approaches are still largely designed to only interrogate small tumor fragments; which may constitute a minute and non-representative fraction of the overall neoplasm. To address this gap, we developed a pipeline that leverages deep learning to define topographic histomorphologic fingerprints of tissue and create Histomic Atlases of Variation Of Cancers (HAVOC). Importantly, using a number of spatially-resolved readouts, including mass-spectrometry-based proteomics and immunohistochemisy, we demonstrate that these personalized atlases of histomic variation can define regional cancer boundaries with distinct biological programs. Using larger tumor specimens, we show that HAVOC can map spatial organization of cancer biodiversity spanning tissue coordinates separated by multiple centimeters. By applying this tool to guide profiling of 19 distinct geographic partitions from 6 high-grade gliomas, HAVOC revealed that distinct states of differentiation can often co-exist and be regionally distributed across individual tumors. Finally,to highlight generalizability, we further benchmark HAVOC on additional tumor types and experimental models of heterogeneity. Together, we establish HAVOC as a versatile and accessible tool to generate small-scale maps of tissue heterogeneity and guide regional deployment of molecular resources to relevant and biodiverse tumor niches.
2023-08-23 | PXD037548 | Pride
Project description:The goal of this study is the discovery of (a) meaningful phylogenomic relationships among members of this B. cereus/B. anthracis group, and (b) reliable gene-phenotype associations, e.g. recognition of links between genomic traits and the ability of certain strains to cause various forms of disease. We also tried to elucidate genome evolution aspects that may lead to the emergence of variants that are capable (or have the potential) of causing anthrax-like disease. This large-scale comparative genomics approach is unprecedented for this taxonomic group. Dr. A. Hoffmaster (CDC) provided the PFGRC with 73 B. cereus and B. anthracis isolates from the CDC culture collection. Of these, 27 were isolated from patients with severe or systemic disease; ten isolates of this group were obtained from patients (welding factory workers) with anthrax-like disease or from the environment near their workplace. Another set of 26 represented isolates from food-born illnesses. Of the 26 gastrointestinal disease isolates (GIDI), 10 were obtained from patients with diarrhea, whereas another set of 10 had been shown to harbor the emetic (vomit) toxin gene by PCR. The rest of the group consisted of 20 isolates with various phenotypes. All strains were screened for their genomic content using the B. cereus/B. anthracis species microarray. Seventy-three query strains were investigated in this study, with each query strain hybridized against the reference strain, Sterne. Dye-swap experiments were performed with all the 73 strains on both chipA and chipB of the microarray, for a total of four or more hybridizations per query strain. Each 70mer oligo spotted on the B. cereus species microarray is spotted once. Positive controls on the array consist of oligos designed from the sequenced reference genome, Sterne, and negative controls on the array consist of oligos designed from the thale cress plant, Arabidopsis thaliana.
2010-05-20 | E-GEOD-19125 | biostudies-arrayexpress
Project description:The goal of this project was to screen soil samples for bacteria that may harbor B. anthracis virulence-associated genes (VAGs). There is currently no information about the prevalence of these types of organisms in the environment. Due to increased environmental monitoring of select agents by programs such as BioWatch and biodetection systems in place at the United States Post Offices and Department of State locations, it has become critical that we not only better understand the natural range of B. anthracis but also how widespread B. anthracis virulence genes are in environmental communities. Naturally occurring isolates containing the B. anthracis virulence genes could generate false-positive results in tests that detect the anthrax toxins, capsule or their associated genes. Understanding the true diversity and pathogenic potential of Bacillus spp. and particularly the B. cereus group is crucial not only in terms of understanding data from environmental monitoring but also diagnosing patients with clinical presentations similar to anthrax in the future. Severe and fatal disease caused by strains similar to B. anthracis could unnecessarily initiate emergency responses if anthrax was incorrectly suspected. Conversely, these strains may be used as bioterror agents requiring science-based responses; presently our limited understanding of these organisms does not permit data-driven decision making. We have investigated 700 aerobic sporoform soil isolates obtained from two areas in the Southwest of the US. Soil samples from the first site had been taken from public access land approximately 50 meters across from the work site of a fatal pneumonia case in a welding factory. This took place in year 2003 when B. cereus was isolated from a metal worker. The second site was targeted because of a recent case involving a deceased mule suspected to have died of a B. anthracis infection. Soil samples were initially analyzed at the CDC. Isolates were obtained by heating the soil at 65 degrees Celcius for 30 minutes followed by plating on agar media. All isolates were screened by PCR for the presence of B. anthracis genomic traits such as toxin genes (cya, lef and pag) as well as chromosomal markers. All isolates were also tested for their hemolytic activity as well as phage sensitivity. Eighty-four query strains were investigated in this study, with each query strain hybridized against the reference strain, Sterne. Two dye-swap experiments were performed with seventeen strains, for a total of four hybridizations per query strain. The other strains have a single dye experiment, for a total of two hybridizations per query strain. Each 70mer oligo spotted on the B. cereus species microarray is spotted once. Positive controls on the array consist of oligos designed from the sequenced reference genome, Sterne, and negative controls on the array consist of oligos designed from the thale cress plant, Arabidopsis thaliana.
2010-05-19 | E-GEOD-19071 | biostudies-arrayexpress
Project description:Comparison of miRNA expression profiles in a small set of prostate needle core biopsies or fine needle aspirates. Keywords: Expression profiling of prostate needle core biopsies MicroRNA expression was compared between a pooled normal sample consisting of 10 separate normal adjacent to tumor prostate needle core biopsies, two prostate tumor cell lines (PC3 and LNCaP), two needle core biopsies, and a fine needle aspirate of a prostate tumor metastasis to the supraclavicular lymph node. MicroRNA was isolated from fresh frozen tissue sections of the needle core biopsies using the mirVana miRNA Isolation kit from Ambion per the manufacturer's instructions. MicroRNA was amplified using 10 ng input and 750 ng of amplified material was subsequently labeled for hybridization. All samples were normalized to the same normal prostate control.
2010-06-11 | E-GEOD-4574 | biostudies-arrayexpress
Project description:rs07-05_sphingolipids-cold - sphingo-1 - The cold choc response seems to be partly triggered by Sphingolipid species. To date no gene response as been associated to sphingolipid signaling pathway in plant. Our aim is to identify among the cold induced genes the ones regulated by sphingolipids and to try to define a sphingolipid pathway specific group of genes. - 7ml of 5 days-old cells suspensions were incubated in presence of different sphingolipid pathway inhibitors, 30 min to 2 hours depending in the coumpound (all were resuspended in DMSO and control were done with DMSO). Then a 30 min cold choc was applied before cells were harvested and frozen in cold nitrogen. RNA were then extracted. FB1 and DMS were from Alexis , Myr from Cayman, TSP from matreya. 6 dye-swap - treated vs untreated comparison
2012-03-27 | E-GEOD-36659 | biostudies-arrayexpress
Project description:Comparison of gene expression between L. reuteri DSM 17938 and L. reuteri DSM 17938::pocR mutant grown in semi-defined medium after 24h of growth at 37C in anaerobic condition. PocR is an AraC-like transcriptional regulator, and changes in gene expression between mutant and wild-type strains would indicate genes involved in the PocR regulon. Includes 3 biological replicates and dye-swaps for DSM 17938 versus pocR mutant. One sample includes total RNA isolated from wildtype DSM 17938 labeled with either cy3 or cy5, and total RNA isolated from the pocR mutant labeled with the opposite dye. Samples 1, 2, and 3 represent biological replicates. Samples 4, 5, and 6 represent dye-swaps of the same biological replicates.
2014-01-24 | E-GEOD-54324 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE29854: Daphnia magna exposed to narcotics and polar narcotics - aniline GSE29856: Daphnia magna exposed to narcotics and polar narcotics - 4-chloroaniline GSE29857: Daphnia magna exposed to narcotics and polar narcotics - 3,5-dichloroaniline GSE29858: Daphnia magna exposed to narcotics and polar narcotics - 2,3,4-trichloroaniline GSE29862: Daphnia magna exposed to narcotics and polar narcotics - ethanol GSE29864: Daphnia magna exposed to narcotics and polar narcotics - isopropanol GSE29867: Daphnia magna exposed to narcotics and polar narcotics - methanol Refer to individual Series
2012-02-01 | E-GEOD-29993 | biostudies-arrayexpress
Project description:MicroRNA (miRNA) is a family of small regulatory RNA that post-transcriptionally regulates many biological functions including growth and development. Chicken miR-143 and miR-10a are expressed in both the embryonic and post-hatch chick in a spatio-temporal manner. In order to study the functions of these miRNAs, loss of function and microarray approaches were employed. Spleen cells were isolated from embryonic day 18 chickens and immediately transfected with either a synthetic miR-143 inhibitor or a synthetic miR-10a inhibitor or a negative control oligo-nucleotide (Dharmacon). Cultures were maintained for 48 hrs and microarray analysis was performed using the Arizona Gallus gallus 20.7K long oligoarray (GPL6049). Differentially expressed genes were identified for each miRNA by comparing the miRNA knock-down group to the negative control group. The differentially expressed genes were functionally categorized using the DAVID Functional Annotation Tool (http://david.abcc.ncifcrf.gov/). The 3â-UTR of the up-regulated genes (de-repressed after the miRNAs knock-down) were scanned for potential miR-143 or miR-10a binding sites using the miRanda algorithm version 3.1 (http://www.microrna.org/microrna). In addition, the Chicken (Gallus gallus) Unigene database (NCBI) was also used to predict potential targets of these miRNAs. A set of predicted targets for both miRNAs was selected and validated by dual luciferase reporter gene assay. Overall, many of the identified targets for miR-143 are associated with cell proliferation, tumerigenesis and apoptosis. Many of potential targets for miR-10a are associated with immune response. A reference designed microarray was performed in which samples (Cy3) were co-hybridized with the reference RNA pool (Cy5) on the array. The microarray data set was processed using within- and across-array loess normalization method in JMP Genomics 3.0, SAS (Cary, NC). Data quality was evaluated using the MA plots process and the correlation and grouped scatter plots procedure (JMP Genomics 3.0). Differentially expressed genes were identified using ANOVA process on JMP Genomics 3.0 with fixed effect of treatments and random effect of arrays.
2010-05-16 | E-GEOD-16653 | biostudies-arrayexpress