RNA-seq characterization of Physarum macroplasmodia
Ontology highlight
ABSTRACT:
ORGANISM(S): Physarum polycephalum
SUBMITTER: Israel Barrantes
PROVIDER: E-GEOD-33793 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Metals have been used for coronary artery stent materials in order to prevent stenosis caused by atherosclerosis. Degradable metallic materials (DMMs) are considered to be useful to avoid in-stent restenosis and late thrombosis. A new DMM, Fe-35Mn alloy, was fabricated through powder metallurgy in order to satisfy the ideal criteria of cardiovascular stent made of DMM. Since in-stent restenosis is mediated by the extracellular matrix production, which is mostly regulated by fibroblasts, the gene expression profile of 3T3 fibroblasts in the presence of Fe-35Mn alloy was then investigated. The mechanism of cellular responses in the presence of DMM is then expected to be clearly described through the gene profiling experiment. 3T3 fibroblast cells derived from mouse (Mus musculus) embryo (BALB/3T3 clone A31, ATTC) were put in the culture and treated with iron, manganese, and Fe-35Mn alloy for 24 hour in parallel and followed by the RNA extraction. Six technical replicates were included for treated cells as well as control cells.
2010-07-24 | E-GEOD-22794 | biostudies-arrayexpress
Project description:Phosphorus, in its orthophosphate form (Pi), is one of the most limiting macronutrients in soils for plant growth and development. However, the whole genome molecular mechanisms contributing to plant acclimation to Pi deficiency remain largely unknown. White lupin (Lupinus albus L.) has evolved unique adaptations for growth in Pi deficient soils including the development of cluster roots to increase root surface area. In this study, we utilized RNA-Seq technology to assess global gene expression in white lupin cluster roots, normal roots, and leaves in response to Pi supply. We de novo assembled 277,224,180 Illumina reads from 12 cDNA libraries to build the first white lupin gene index (LAGI 1.0). This index contains 125,821 unique sequences with an average length of 1,155 bp. Of these sequences 50,734 were transcriptionally active (RPKM = 3) representing approximately 7.8% of the Lupinus albus genome, using the predicted genome size of Lupinus angustifolius as a reference. We identified a total of 2,128 sequences differentially expressed in response to Pi deficiency with a = 2-fold change and a p-value = 0.05. Twelve sequences were consistently differentially expressed due to Pi deficiency stress in three species, making them ideal candidates to monitor the Pi status of plants. Additionally, classic physiological experiments were coupled with RNA-Seq data to examine the role of cytokinin and gibberellic acid in Pi deficiency-induced cluster root development. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to Pi deficiency. Examination of 2 different tissue types (roots and leaves) under phosphorus (P) -sufficient or P-deficient condition with 3 biological replications per condition in white lupin (Lupinus albus).
2012-11-29 | E-GEOD-31132 | biostudies-arrayexpress
Project description:Transcription factors are key components of regulatory networks that control development, as well as the response to environmental stimuli. We have established an experimental pipeline in C. elegans that permits global identification of the binding sites for transcription factors using chromatin immunoprecipitation and deep sequencing. We describe and validate this strategy, and apply it to the transcription factor PHA-4, which plays critical roles in organ development and starvation stress response. We defined binding sites for PHA-4 during formation of the embryonic pharynx, and in starved larvae. PHA-4 binds to thousands of locations throughout the genome. These sites shift dramatically between embryos and larvae, from developmentally regulated genes to genes involved in metabolism. We acquired transcriptome of wild type N2 worms at embyonic and starved L1 stages using RNA-seq method in comparing to the ChIP-seq experiment to study transcription factor binding. The wild type worms were cultured the same as the transgenic worms for transcription factor binding experiment. Keywords: Transcriptome Analysis For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Two development stages embryo and starved larvae each contains 3 technical replicates are reported
2009-06-11 | E-GEOD-16552 | biostudies-arrayexpress
Project description:In this experiment, we used advanced proteomics techniques to discern differences in energy allocation between three strains of ammonia oxidizing bacteria: Nitrosomonas europaea, Nitrosomonas ureae, and Nitrosospira multiformis, during ammonia starved and ammonia replete conditions. Replicate cultures in late log phase from the three strains were starved of ammonia for 24 hours and compared to replicate control cultures grown for the same period. All three species were grown with three biological replicates for each condition and species with the exception of two replicates from the N. ureae starved cultures due to sample processing loss. This study has, to our knowledge, produced the first complete proteomes of Nitrosospira multiformis and Nitrosomonas ureae.
2018-05-16 | PXD008954 | Pride
Project description:Twenty years since publication of the Plasmodium falciparum and P. berghei genomes one-third of their protein-coding genes lack functional annotation. In the absence of sequence and structural homology, protein-protein interactions can facilitate functional prediction of such orphan genes by mapping protein complexes in their natural cellular environment. The Plasmodium NPC (nuclear pore complex) is a case in point: it remains poorly defined; its constituents lack conservation with the 30+ proteins described in the NPC of many opisthokonts, a clade of eukaryotes that includes fungi and animals, but not Plasmodium. Here we developed a labeling methodology based on TurboID fusion proteins, which allows visualization of the berghei NPC and facilitates the identification of its components. Following affinity purification and mass spectrometry we identify four known Nups (138, 205, 221, and the bait 313) and verify interaction with the putative FG Nup637; we assign five proteins lacking annotation (and therefore meaningful homology with proteins outside the genus) to the NPC, which is confirmed by GFP tagging. Based on gene deletion attempts, all new Nups Nup176, 269, 335, 390, and 434 are essential to parasite survival. They lack primary sequence homology with proteins outside the Plasmodium genus; albeit two incorporate short domains with structural homology to human Nup155 and yeast Nup157, and the condensin SMC4. The protocols developed here showcase the power of proximity-labeling for elucidating protein complex composition and annotation in Plasmodium. It opens the door to exploring the function of the Plasmodium NPC and understanding its evolutionary position.
2022-08-21 | PXD034491 | Pride
Project description:Here we fully characterize the genomes of 14 Plasmodium falciparum patient isolates taken recently from the Iquitos regions using genome-scanning, a microarray-based technique which delineates the majority of single-base changes, indels and copy number variants distinguishing the coding regions of two clones. We show that the parasite population in the Peruvian Amazon is highly structured with a limited number of genotypes and low recombination frequencies. Despite the essentially clonal nature of some isolates, we see high frequencies of mutations in subtelomeric highly variable genes and internal var genes indicating mutations arising during self-mating or mitotic replication. The data also reveal that 1 or 2 meioses separate different isolates showing that P. falciparum clones isolated from different individuals in defined geographical regions could be useful in linkage analyses or quantitative trait locus studies. Through pair-wise comparisons of different isolates we discovered point mutations in the apicoplast genome that are close to known mutations that confer clindamycin resistance in other species but which were hitherto unknown in malaria parasites. Subsequent drug sensitivity testing revealed over 100-fold increase clindamycin EC50 in strains harboring one of these mutations. This evidence of clindamycin resistant parasites in the Amazon suggests a shift should be made in health policy away from quinine+clindamycin therapy for malaria in pregnant women and infants and that the development of new lincosamide antibiotics for malaria should be reconsidered. Genome DNA from Peruvian Isolates vs. Reference 3D7
2010-08-04 | E-GEOD-22861 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in Plasmodium falciparum 3D7 delta-PfPuf2 mutant, compared to the wild-type strain 3D7. The mutation engineered into this strain render tanslational control. The mutants analyzed in this study are further described in Miao J, Li J, Fan Q, Li X, Li X, Cui L.2010. The Puf-family RNA-binding protein PfPuf2 regulates sexual development and sex differentiation in the malaria parasite Plasmodium falciparum. J Cell Sci. 123(7):1039-49 (PMID 20197405). A 12 chip study using total RNA recovered from six separate wild-type cultures of Plasmodium falciparum 3D7 at gametocyte stage III (three cultures) and stage V (three cultures) and six separate cultures of dalta PfPuf2 mutant at gametocyte stage III (three cultures) and stage V (three cultures). Each chip measures the expression level of 5,367 genes from Plasmodium falciparum 3D7 with 45-60 mer probes with two replicates on final array of 71618 probes.
2012-07-05 | E-GEOD-39124 | biostudies-arrayexpress
Project description:In this work, changes in the proteome level during a step-wise adaptation of an adherent Madin Darby canine kidney (MDCK) cell line to suspension growth and chemically defined medium were analyzed.
2015-04-22 | PXD001306 | Pride
Project description:Most malaria drug development focuses on parasite stages detected in red-blood cells even though to achieve eradication next-generation drugs active against both erythrocytic and exo-erythrocytic forms would be preferable. We applied a multifactorial approach to a set of >4,000 commercially available compounds with previously demonstrated blood stage activity (IC50 < 1 M-BM-5M), and identified chemical scaffolds with potent activity against both forms. From this screen, we identified an imidazolopiperazine scaffold series that was highly enriched among compounds active against Plasmodium liver stages. Our orally bioavailable lead imidazolopiperazine confers complete causal prophylactic protection (15 mg/kg) in rodent models of malaria and shows potent in vivo blood-stage therapeutic activity. The open source chemical tools resulting from our effort provide starting points for future drug discovery programs, as well as opportunities for researchers to investigate the biology of exo-erythrocytic forms. Genome DNA from IP resistant strains vs. Reference 3D7 or Dd2
2011-10-31 | E-GEOD-32485 | biostudies-arrayexpress
Project description:Plasmodium ssp. are pathogens in their vertebrate hosts and also cause deleterious effects to their insect vectors. We show here, however, that Plasmodium-infected mosquitoes more efficiently accumulate energy resources (glycogen) during oocyst development, and survive better when they are starved. Microarray analysis revealed that mosquito metabolism is altered by the presence of rapidly growing oocysts in the midgut. Plasmodium infection is associated with enhanced expression of several insulin-like peptides in mosquitoes and blocking insulin-like signaling results in diminished Plasmodium development. We conclude that Plasmodium infection dramatically changes mosquito metabolism pathways, epitomized by enhanced insulin-signaling, and thereby confer a survival advantage to the insects during periods of starvation. Manipulation of this pathway may provide new strategies to influence the ability of mosquitoes to transmit the protozoa that cause malaria.
2011-12-31 | GSE32200 | GEO