Transcriptional profiling of P. yoelii SAP1 knockout
Ontology highlight
ABSTRACT:
ORGANISM(S): Plasmodium yoelii
SUBMITTER: Hilda Silva-Rivera
PROVIDER: E-GEOD-12397 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Microarray studies using synchronized Plasmodium falciparum parasites have revealed a ‘continuous cascade’ of gene expression. Reports vary regarding the stability in these transcriptional patterns in the presence of external stressors. Using Plasmodium yoelii 17X parasites replicating in vivo, we have examined differential gene expression in parasites isolated from individual mice, from independent infections, during ascending and peak parasitemia and in the presence and absence of host antibody responses. Across experimental conditions, transcription was surprisingly stable. Differential gene expression was greatest when comparing differences due to parasite load and/or host cell availability; however, even these changes were modest. Of genes that were differentially expressed, many are of unknown function. There was little to no differential expression of members of the yir and pyst-a multigene families, although a relatively large number of these were expressed during blood-stage infection regardless of experimental condition. Taken together, these results indicate that 1) P. yoelii gene expression remains stable in the presence of a changing host environment and 2) concurrent expression of a large number of the yir and pyst-a genes may function to divert host immune responses away from invariant protective antigens. 1. P. yoelii 17X gene expression profiles were determined in blood-stage parasites isolated from infected Balb/c mice (male, 8-12 weeks old) as follows: a. Mouse 1 (M1), Mouse 2 (M2), Mouse 3 (M3), Donor (D) mouse – three mice simultaneously infected with P. yoelii 17X iRBCs from a single donor mouse. Parasite RNA was isolated early during infection when parasitemia was ascending as follows: M1 - day 11 at 13.0% parasitemia; M2 - day 10 at 11.1% parasitemia; M3 - day 10 at 18.6% parasitemia; D – day 11 at 18.7% parasitemia. b. Infection #1 (I1), infection #2 (I2), infection #3 (I3), infection #4 (I4) – four groups of mice infected on four separate occasions using P. yoelii 17X iRBCs obtained from four separate donor mice. In each case, P. yoelii 17X RNA was isolated from iRBCs obtained on days 10-11 of infection when parasitemia was ascending and was ~15%. c. Day 10 (D10), Day 14 (D14) – P. yoelii 17X RNA isolated from iRBCs during infection #2 on day 10 (14% parasitemia, 14.4% reticulocytes) and on day 14 of infection #2 (43.5% parasitemia, 57.9% reticulocytes). d. WT and JHD - P. yoelii 17X RNA isolated from iRBCs during infection #4 from immunologically intact, wild-type Balb/c mice and B cell deficient, JHD mice on a Balb/c background (ascending infection, 15% parasitemia). e. QA and RMP - P. yoelii 17X RNA isolated from iRBCs during infection #1 from mice previously immunized with a preparation of membrane proteins isolated from P. yoelii 17X infected reticulocytes (PyRMP) (day 12, 13.3% parasitemia and Quil A immunized (QA) control mice (day 10, 15.6% parasitemia) 2. On each array, gene expression in P. yoelii 17X blood-stage parasites was evaluated relative to a standard comparator of purified P. yoelii 17XL total RNA (pooled RNA from 45 mice, mean parasitemia ~35%). Each sample was analyzed on three replicate arrays, one of which was a standard dye-flip. One exception was the infection #3 sample which was analyzed on only on two arrays. On each array, oligonucleotides were spotted in duplicate. 3. Through the use of the standard reference RNA, the following 15 pairwise comparisons across samples were made: (M1 vs M2); (M2 vs M3); (M1 vs M3); (D vs M1); (D vs M2); (D vs M3); (I1 vs I2); (I1 vs I3); (I1 vs I4); (I2 vs I3); (I2 vs I4); (I3 vs I4); (D10 vs D14); (WT vs JHD); (QA vs RMP)
2011-11-01 | E-GEOD-31274 | biostudies-arrayexpress
Project description:To study the function of gene SAP1. We knocked out SAP1 gene in P. yoelii, and compared the global gene expression profiles of the P. yoelii SAP1 knockout parasites isolated from mosquito salivary gland to that of wild type P. yoelii parasites.
2009-08-01 | GSE12397 | GEO
Project description:Field-caught permethrin-resistant Anopheles gambiae s.s. overexpress CYP6P3, a P450 that metabolizes pyrethroids
2009-01-17 | E-MTAB-52 | biostudies-arrayexpress
Project description:We present a microarray study of hemocyte-enriched transcriptome in Aedes aegypti. We directed our efforts to critically assess the transcriptomic features distinctive of hemocytes, and discussed our findings in relation to infection-responsive genes and immune-relate gene families. Specifically, our analysis examined how tissue-enriched expression patterns change with the immune status of the host, and resolved patterns of transcriptional change unique to hemocytes from those that are likely shared by other immune responsive tissues. We profiled the transcriptome of circulating hemocytes and the remaining carcass in both naM-CM-/ve and bacteria-challenged adult female mosquitoes. To examine transcriptional changes associated with hemocoelic infection in distinct tissue samples, we adopted a linear model-based framework for analyzing dual-channel hybridizations (i.e., two-color microarrays) as separate single-channels (Smyth, 2004). The biological and technical dye-swap replicates of the 2M-CM-^W3 experimental conditions consisted of forty separate single-channel intensity profiles. For each biological replication, hemolymph perfusate and the remaining carcass were collected as paired samples at 24 hours post intra-hemocoelic injection of either Escherichia coli or Micrococcus luteus overnight culture (0.5 M-BM-5l) in parallel with an age-matched naM-CM-/ve group from the same cohort. Concomitantly-collected hemocyte and carcass samples were co-hybridized on microarrays. Material for each experimental condition was generated from three (bacterial challenge) or four (naM-CM-/ve) separate generations of mosquitoes, and four separate microarray hybridizations using carcass and hemocyte material were performed. The first hybridization compared naM-CM-/ve and E. coli-challenged conditions, the second compared naM-CM-/ve and M. luteus-challenged conditions, and the third and fourth compared all three conditions.
2012-07-22 | E-GEOD-38744 | biostudies-arrayexpress
Project description:Seeds of Pisum sativum L. cv Alaska Early (purchased from the âAbundant Life Seed Foundationâ, Port Townsend, USA) were equilibrated for approximately 5 weeks in tightly sealed boxes over 300 g-1 non-saturated LiCl (Hay et al. 2008), producing 60% relative humidity, in a temperature-controlled room (20 ± 1 ºC) until their water potential was stable at 12 % MC. Relative humidity was recorded with a Rotronic AWVC-D10 Hygropalm. These equilibrated seeds are referred to as 0 day ânon-aged controlsâ. Following equilibration, accelerated ageing was carried out by placing seeds in sealed bottles at 50 °C until viability loss, thereafter referred to as âageingâ. Samples were taken at intervals after 8, 12, and 15 days of ageing. At each interval, germination tests were performed on 1 % water agar at 25 °C under warm white fluorescent light (15 micromol m-2 s-1) at a day / night cycle (8/16h). Germination was defined as radical emergence by at least 2 mm. To summarize, we have performed a transcriptional profiling of Pisum sativum seeds comparing 0 day ânon-aged controlsâ with 8, 12 and 15 days of artificially aged seeds. Four-condition experiment, 0 days, 8 days, 12 days and 15 days. Biological replicates: 3 for each comparison. Each biological replicate was independently grown and harvested.
2010-10-22 | E-GEOD-24864 | biostudies-arrayexpress
Project description:The ability to perform complex bioassays in parallel enables experiments otherwise impossible due to throughput and cost constraints. By way of example, highly parallel chemical-genetic screens using pooled collections of thousands of defined Saccharomyces cerevisiae gene deletion strains are feasible because each strain is barcoded with unique DNA sequences. It is, however, time consuming and expensive to individually barcode individual strains. To provide a simple and general method of barcoding yeast collections, we built a set of donor strains, called Barcoders, with unique barcodes that can be systematically transferred to any S. cerevisiae collection. We applied this technology by generating a collection of barcoded DAmP (Decreased Abundance by mRNA Perturbation) loss-of-function strains comprising 87.1% of all essential yeast genes. This test collection validates both the Barcoders and the DAmP collection as useful tools for genome-wide chemical genetic assays.
2008-07-03 | E-MEXP-1671 | biostudies-arrayexpress
Project description:We conducted a genome wide survey of mosquito gene expression profiles in 4 different tissues of adult Anopheles gambiae mosquitoes. The tissues included the head, the midgut, the carcass (corresponding to the remainder of the mosquito after decapitation and midgut removal) and ovaries. Ovaries were collected from adult female mosquitoes, which had been bloodfed 48h prior to dissection. To investigate mosquito expression in those tissues, we performed competitive two-dye hybridizations of experimental and standard reference RNA samples to MMC1 microarrays. MMC1 microarrays contain approximately 20,000 EST clones. Standard reference RNA was produced in vitro from the spotted ESTs and was utilized to provide consistent, non-zero reference values for almost all probes of the array. For the experiment, two biological replicates, corresponding to mosquito generations 1 and 3 (generation 2 was discarded due to probable labelling errors) and one technical (dye-swap) replicate was conducted.
2007-07-19 | E-TABM-153 | biostudies-arrayexpress
Project description:Coral populations have declined worldwide largely due to increased sea surface temperatures. Recovery of coral populations depends in part upon larval recruitment. Many corals reproduce during the warmest time of year when further increases in temperature can lead to low fertilization rates of eggs and high larval mortality. Microarray experiments were designed to capture and assess variability in the thermal stress responses of Acropora palmata larvae from Puerto Rico. Transcription profiles showed a striking acceleration of normal developmental gene expression patterns with increased temperature. The transcriptional response to heat suggested rapid depletion of larval energy stores via peroxisomal lipid oxidation and included key enzymes that indicated the activation of the glyoxylate cycle. High temperature also resulted in expression differences in key developmental signalling genes including the conserved WNT pathway that is critical for pattern formation and tissue differentiation in developing embryos. Expression of these and other important developmental and thermal stress genes such as ferritin, heat shock proteins, cytoskeletal components, cell adhesion and autophagy proteins also varied among larvae derived from different parent colonies. Disruption of normal developmental and metabolic processes will have negative impacts on larval survival and dispersal as temperatures rise. However, it appears that variation in larval response to high temperature remains despite the dramatic population declines. Further research is needed to determine whether this variation is heritable or attributable to maternal effects. Hybridization followed a dual channel loop design using two biological replicates (dye-swapped) from each treatment that maximized power to detect differential expression in contrasts between temperatures and batches (within time-points) as well as the amount of data obtained from each slide (Simon and Dobbin 2003). A total of 18 arrays on two 12 plex slides were used (Table S1). Additional samples from other sub-batches (b3/b4) were included in the microarray experiment but are not used in this analysis. Each array measures the expression level of 135,185 genes from the elkhorn coral (Acropora palmata) transcriptome (Polato et al. 2011). Two 60-mer probes were designed for each contig (n = 85,260), and a single probe was designed for each singleton sequence (n = 45,390). Two additional probes each were developed for sequences associated with annotation information relating to calcium metabolism and stress response (n = 4,798). Replicate probes for individual sequences from the assembled transcriptome were not identical; rather they represented multiple different 60-mer sequences from the original template.
2012-12-13 | E-GEOD-36983 | biostudies-arrayexpress
Project description:Hodgkin lymphoma derived cell lines (from the Deutsche Sammlung von Mikroorganismen und Zellkulturen) were cultured in RPMI 1640 medium supplemented with <br><br>20% (HDML-2) or 10% (HD-MY-Z) heat inactivated fetal calf serum. Cytoplasmic RNA was extracted according to "Cytoplasmic_RNA_CRG" protocol available at Arrayexpress
2010-12-31 | E-MEXP-2959 | biostudies-arrayexpress
Project description:Background The response of macrophages to danger signals is an important early stage in the immune response. Our understanding of this complex event has been furthered by microarray analysis, which allows the simultaneous investigation of the expression of large numbers of genes. However, the microarray resources available to study these events in livestock animals are limited. Results Here we report the development of a bovine macrophage specific (BoMP) cDNA microarray. The BoMP microarray contains 5026 sequence elements (printed in duplicate) and numerous controls. The majority of the clones incorporated on the microarray were derived from the BoMP cDNA library generated from bovine myeloid cells subjected to various stimuli, including over 900 sequences unique to the library. Additional clones representing immunologically important genes have been included on the BoMP microarray. The microarray was validated by investigating the response of bovine monocytes to stimulation with interferon-g and lipopolysaccharide using amplified RNA. At 2 and 16 hours post stimulation 695 genes exhibited statistically significant differential expression, including; 26 sequences unique to the BoMP library, interleukin 6, prion protein and toll-like receptor 4. Conclusions A 5K cDNA microarray has been successfully developed to investigate gene expression in bovine myeloid cells. The BoMP microarray is available from the ARK-Genomics facility (www.ark-genomics.org).
2006-09-20 | E-MAXD-16 | biostudies-arrayexpress