The role of actin II in the mosquito stages of Plasmodium berghei
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion
ORGANISM(S): Plasmodium Berghei
TISSUE(S): Cell Culture
SUBMITTER: 
Serena Camerini
LAB HEAD: Serena Camerini
PROVIDER: PXD033378 | Pride | 2023-02-16
REPOSITORIES: Pride
Similar Datasets
Project description:The aim of the project is to develop and validate a new method to measure proNGF in the cerebrospinal fluid of living patients, and to use it as a biomarker of Alzheimer’s disease (AD). This method, a novel proNGF immunoassay, is based on molecular size separation by capillary electrophoresis and is performed with Simple Wes: this technique produces different immunoreactive peaks whose area can be calculated to search for a quantitative relation with AD. Our purpose was to confirm and validate by mass spectrometry analysis the presence of NGF in the selected peaks
2022-02-17 | PXD025883 | Pride
Project description:Hair Follicle regeneration relies on both epithelial components (bulge and hair germ cells) and a mesenchymal one (dermal papilla cells). We used microarrays to detail the global programme of gene expression underlying organ regeneration at the transition between quiescent stages (early and middle telogen) and the initiation of a new growth (late telogen). Experiment Overall Design: These microarray at the 3 different stages were designed to identify signals released by the mesenchymal dermal papilla cells to activate epithelial growth, their target genes in the hair germ and bulge compartments, and to get at gene signature differences and similarities between hair germ and bulge cells.
2009-03-25 | E-GEOD-15185 | biostudies-arrayexpress
Project description:RNA-seq of coding RNA of Streptococcus pneumoniae D39 wild type strain before and after 30 min of exposure to sub-lethal doses of 800 µM HOCl stress during the log phase of microaerophilic grown bacteria. The S. pneumoniae D39 wild type strain was cultivated in RPMI medium and treated with thiol-reactive compound NaOCl, which dissociates in aqueous solution to hypochlorous acid (HOCl) and hypochlorite (OCl−) - the concentration of HOCl was determined by absorbance measurements - here 800 µM HOC, at an OD600 of 0.4 for 30 min. Bacteria were harvested before and after treatment in ice-cold killing buffer (50 mM Tris pH 7.5, 5 mM MgCl2, 20 mM NaN3), centrifuged at 4,750 rpm for 10 min at 4°C. The pellets were immediately frozen in liquid nitrogen and stored at -80°C. RNA isolation was performed using the acidic phenol-chloroform extraction protocol. After DNase-I treatment (Zymo Research, Germany), the RNA quality was checked by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6,000 kit using an Agilent 2,100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). For RNA-seq transcriptomics, Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, United States) was applied to prepare the cDNA libraries. The cDNAs were sequenced paired end on an Illumina HiSeq 1,500 (San Diego, CA, United States) using 70 bp read length and a minimum sequencing depth of 10 million reads per library.
2022-12-06 | E-MTAB-11968 | biostudies-arrayexpress
Project description:Nanotechnology has the potential to revolutionize agriculture by developing engineered nanomaterials to be used as biostimulants, fertilizers, pesticides or smart sensors. Seed priming may represent an opportunity for nano-enabled plant technology to match economic, agronomic and environmental needs. This study investigates the effects of seed priming mediated by iron oxide magnetic nanoparticles (MNPs) in plants. We performed a multilevel integrated study to understand the basic interactions between MNPs and seeds in pepper (Capsicum annuum). Moreover, phenotypic, physiological and molecular analyses were performed to elucidate the biological impact of MNPs from seed to plant development. Interestingly, our findings show positive effects of MNPs on vegetative growth and a profound impact on pepper gene expression patterns. Indeed, we found 2,204 differentially expressed transcripts in nanoprimed seeds, most of them involved in plant defence mechanisms, potentially establishing a seed memory that might enhance the plant's capacity to counteract diverse forms of stress. In conclusion, this work provides a comprehensive investigation about nanoparticle-seed interactions with interesting implications for agricultural technology.
2023-11-08 | E-MTAB-13087 | biostudies-arrayexpress
Project description:We investigated gene expression levels in Heliconius erato butterflies with divergent wing patterns across a 656KB genomic interval linked to the red color pattern wing polymorphism. This included comparison of expression between two H. erato color pattern populations (H. e. petiverana and a H.e. etylus x H. himera hybrid) across three sections of the forewing that differed in pigmentation (the basal, mid, and distal wing sections) and five different stages of pupal development (Day 1, 3, 5 pupae and ommochrome and melanin pigmentation stages). These results allowed us to determine whether certain genes in this interval were differentially expressed between the wing pattern elements, and, therefore, potentially responsible for adaptive color pattern variation in these butterflies. Forewings from a total of 29 individuals, covering three biological replicates of five developmental time points for each of the two H. erato distinct phenotypes were dissected, with the only exception being that there were only two replicates of the day 1 hybrid phenotype. Individuals were reared at 25˚C and dissected at the following stages: a) day 1 = 12 hr after pupation; b) day 3 = 60 hr after pupation; c) day 5 = 108 hr after pupation; d) early ommochrome = ~ 156 hr after pupation when red scales in forewing partially mature, showing a pale orange color; and e) early melanin = ~ 180 hr after pupation melanic scales begin to turn black and are present primarily at the center of the wing. Using wing veins as landmarks, each forewing was cut into three sections corresponding to the color pattern boundaries: basal (F1), middle (F2), and apical (F3). A eight custom-designed Roche NimbleGen 12x135K format microarrays with probes spanning a 656,307bp genomic region (Roche NimbleGen Inc., Madison, Wisconsin, United States) were used to hybridize double stranded cDNA from 87 tissue samples. Repetitive sequence elements found more than five times across all currently available H. erato genomic sequences, including the probed region as well as additional genomic BAC sequences, were masked from the tiling region. The remaining unmasked non-repetitive genomic sequences were tiled using 60 bp probes staggered every 13 bp on average, with slight modifications to ensure probe quality, for a total of 48,547 probes. Microarry design and printing was performed by Roche NimbleGen. cDNA labeling, hybridization, and array scanning was performed by the City of Hope Microarray Facility (Duarte, California, United States). In addition to the probes from the red color pattern intervals, the arrays also include 40,763 probes across two other genomic intervals not addressed in this study, 45,046 probes representing 12450 transcripts from a recent transcriptome assembly at 1-6X coverage, and 3248 random probes. Results from the transcriptome and other color pattern intervals will be published separately, however, we analyzed all probes together for array normalization and quality control.
2011-12-02 | E-GEOD-30221 | biostudies-arrayexpress
Project description:This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a 35S:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone treatment. Tissue samples were collected immediately after the treatment, as well as subsequent timepoints. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (non-commercial; Meyerowitz Lab Arabidopsis Operon Array v4). Keywords: time course Four sets of biologically independent tissue samples were collect at 0, 2, 4 ,8, and 12 hours after the application of dexamethasone (Dex-; activation of the AP1-GR fusion protein) or a mock solution (Mock-; control). In each of the biological replicates of the time course experiments, all the samples derived from dexamethasone (Dex)-treated plants were labeled with one dye (i.e., Cy3), and all the samples derived from the corresponding Mock-treated plants were labeled with the alternative dye (i.e., Cy5). The dyes used for labeling RNA from a given treatment type (Dex and Mock) were switched for two of the replicate experiments, to reduce dye-related artifacts. Dex- and Mock-derived samples for each timepoint and biological replicate were co-hybridized. This experimental setup resulted in a total of 5 hybridizations per set (0h, 2h, 4, 8h, and 12h; Dex vs. Mock at each timepoint), and two biological replicate sets labeled with each dye polarity (Mock-Cy3/Dex-Cy5, and vice versa). The combined ratio data results are available as a supplementary file on the Series record.
2010-04-02 | E-GEOD-20182 | biostudies-arrayexpress
Project description:This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a 35S:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone treatment. Tissue samples were collected immediately after the treatment, as well as subsequent timepoints. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (non-commercial; Meyerowitz Lab Arabidopsis Operon Array v4). Keywords: time course Four sets of biologically independent tissue samples were collect at 0, 2, 4 ,8, and 12 hours after the application of dexamethasone (Dex-; activation of the AP1-GR fusion protein) or a mock solution (Mock-; control). In each of the biological replicates of the time course experiments, all the samples derived from dexamethasone (Dex)-treated plants were labeled with one dye (i.e., Cy3), and all the samples derived from the corresponding Mock-treated plants were labeled with the alternative dye (i.e., Cy5). The dyes used for labeling RNA from a given treatment type (Dex and Mock) were switched for two of the replicate experiments, to reduce dye-related artifacts. Dex- and Mock-derived samples for each timepoint and biological replicate were co-hybridized. This experimental setup resulted in a total of 5 hybridizations per set (0h, 2h, 4, 8h, and 12h; Dex vs. Mock at each timepoint), and two biological replicate sets labeled with each dye polarity (Mock-Cy3/Dex-Cy5, and vice versa). The combined ratio data results are available as a supplementary file on the Series record.
2010-04-02 | E-GEOD-20183 | biostudies-arrayexpress
Project description:P. tricornutum (Bacillariophyta, Pennatae, NEPCC640) was obtained from the Algal Center of the Institute of Oceanology of the Chinese Academy of Sciences. The cells were cultured in a modified f/2 medium (Guillard, 1975) at 20 +/- 1C, and illuminated with 120 umol photon m-2 s-1 under a 12:12 light: dark cycle. Flasks were shaken by the researchers twice a day at the fixed times. Experiments were conducted in triplicate in 3L sterilized and acid-washed Erlenmeyer flask containing 2L medium. The equipment used in this study is similar to the ones used in previous ocean acidification research (Fu et al., 2007; Hutchins et al., 2007; Wu et al., 2010). Prior to inoculation, the mediums were treated by different CO2 concentrations. The low CO2 medium was bubbled with ambient air of about 400 ppmv (low CO2, LC) and the high CO2 medium was bubbled with pre-mixed air-CO2 mixtures (1000 ppmv; high CO2, HC) from a plant growth CO2 chamber (HP400G-D, Ruihua Instrument & Equipment Ltd, Wuhan, China) with a variation of less than 5%. Semi-continuous cultures were used to maintain the pH stability during P. tricornutum growth in the present study, All the cultures were diluted to 1x104 cells mL-1 with fresh medium and pre-acclimated to the desired CO2 level every 24 h to maintain an exponential growth phase and minimize pH fluctuations of the cells. Cultures were harvested after 8 months of semi-continuous incubation. Significant differences between the carbonate systems in different cultures.
2019-11-07 | E-MTAB-8351 | biostudies-arrayexpress
Project description:Transcriptional profiling of P. falciparum comparing parasites exposed to 5% and 21% oxygen environmental conditions in the late ring stage. Two experimental conditions: 5% vs 21%. Biological replicates: 3 normoxia and 3 hyperoxia replicates
2010-06-20 | E-GEOD-18831 | biostudies-arrayexpress
Project description:R. rubrum S1H inoculated on solid minimal media was sent to the ISS in September 2006 (BASE-A experiment). After 10 days flight, R. rubrum cultures returned back to Earth. These cultures were then subjected to both transcriptomic and proteomic analysis and compared with the corresponding ground control. Whole-genome oligonucleotide microarray and high throughput proteomics, which offer the possibility to survey respectively the global transcriptional and translational response of an organism, were used to test the effect of space flight. Moreover, in an effort to identify a specific stress response of R. rubrum to space flight, ground simulation of space ionizing radiation and space gravity were performed under identical culture setup and growth conditions encountered during the actual space journey. This study is unique in combining the results from an actual space experiment with the corresponding space ionizing radiation and modeled microgravity ground simulations, which lead to a more solid dissection of the different factors contribution acting in space flight conditions. Total RNA was extracted from R. rubrum S1H grown after 10 days in space flight or after 10 days in simulated ionizing radiation or simulated microgravity. Each microarray slide contained 3 technical repeats.
2010-05-16 | E-GEOD-14241 | biostudies-arrayexpress