Plasmodium falciparum: hyperoxic vs normoxic conditions
Ontology highlight
ABSTRACT:
ORGANISM(S): Plasmodium falciparum
SUBMITTER: Yannick Lepriol
PROVIDER: E-GEOD-18831 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Microarrays have become a powerful tool for DNA-based molecular diagnostics and identification of pathogens. However, most of them target a limited range of organisms and are generally based on only one or very few genes for organism identification. Although such microarrays are proven tools for species identification, they suffer from the fact that identification is only possible for organisms for which probes were specifically pre-developed. Furthermore, this approach often leads to problems with taxonomic-level resolution with insufficient diagnostic differences between closely related taxa found in the commonly used DNA sequences. An alternative strategy is to use the hybridisation pattern generated by many different anonymous markers distributed over the entire genome for identification based on comparison to a type database. We realised this strategy using a high density microarray containing 95,000 different 13-mer probes. Here, we demonstrate the specificity of our microarray based on results obtained with nine different bacterial species and strains. The hybridisation patterns allowed clear differentiation at the strain and even variant level. The reproducibility of our system was high as shown by high correlation coefficients between replicates, despite the occurrence of mismatch hybridisation. The results indicate the potential for identification of all bacterial taxa at the subspecies level using our universal microarray. Hybridisation patterns of DNA from bacterial type strains (E. coli strains K12 and B, Pantoea agglomerans strains ATCC27155T and C9-1, Pantoea stewartii pv stewartii strain DC283, Salmonella Typhimurium strains LT2 and DT204 and Micrococcus luteus) were compared to each other. Using GeneSpring v7.3.1, cluster analyses were performed as well as ANOVA in order to determine the more discriminative probes out of our 95,000-probe panel.
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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: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.
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