Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1263476 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Despite a significant increase in genomic data, our knowledge of gene functions and their transcriptional responses to environmental stimuli remains limited. Here, we use the model keystone species Daphnia pulex to study environmental responses of genes in the context of their gene family history to better understand the relationship between genome structure and gene function in response to environmental stimuli. Daphnia were exposed to five different treatments, each consisting of a diet supplemented with one of five cyanobacterial species, and a control treatment consisting of a diet of only green algae. Differential gene expression profiles of Daphnia exposed to each of these five cyanobacterial species showed that genes with known functions are more likely to be shared by different expression profiles whereas genes specific to the lineage of Daphnia are more likely to be unique to a given expression profile. Furthermore, while only a small number of non-lineage specific genes was conserved across treatment type, there was a high degree of overlap in expression profiles at the functional level. The conservation of functional responses across the different cyanobacterial treatments can be attributed to the treatment specific expression of different paralogous genes within the same gene family. Comparison with available gene expression data in the literature suggests differences in nutritional composition in diets with cyanobacterial species compared to diets of green algae as a primary driver for cyanobacterial effects on Daphnia. We conclude that conserved functional responses in Daphnia across different cyanobacterial treatments are mediated through alternate regulation of paralogous gene families. Whole transcriptome dual color arrays were used to discover differentially expressed genes following sub-lethal exposure to five cyanobacteria in D. pulex. RNA was isolated from eight independent and concurrently replicated exposures of Daphnia to control and five cyanobacteria conditions. RNA was hybridized to microarrays using a standard, control vs. treated design that included dye swaps. Cyanobacteria were Anabaena (ANA), Aphanizomenon (Aph), Cylindrospermopsis (Cyl), Nodularia (Nod) and Oscillatoria (Osl).
2015-03-07 | E-GEOD-62763 | biostudies-arrayexpress
Project description:Plant plankton and their phages from disused school swimming pools
| PRJNA1334157 | ENA
Project description:Resistance to herbicides in weeds can be due to alteration(s) in the gene encoding the herbicide target site, or to herbicide degradation via a deviation in plant general metabolism. If target-site-based resistance is easy to study, the multigenic control of metabolism-based resistance renders it much more complex to study. Metabolism-based resistance to herbicides represents the major part of herbicide resistance in black-grass. Its most likely basis is an overexpression of genes encoding enzymes degrading herbicides. We thus seek to identify such overexpressed genes by comparing the transcriptomes of resistant and sensitive black-grass individuals belonging to an F2 line segregating for two resistance genes. Given there are no genomic tools developed for black-grass, this approach will use heterologous hybridisation onto a wheat Affymetrix microarray. Comparison using heterologous hybridisation onto a wheat whole-genome microarray of transcriptome of three pools of black-grass plants obtained 2h30 after herbicide spraying at field rate. The three pools correspond to: · Sensitive plants (killed by herbicide). · Moderately resistant plants (growth impaired by herbicide but plants still alive) · Resistant plants (growth unimpaired by herbicide)
2010-05-04 | GSE15864 | GEO
Project description:Bronchopulmonary dysplasia (BPD) is the most common chronic respiratory disease in premature infants. Recent studies have highlighted the contribution of genetic factors to BPD susceptibility. Our aim was to identify the genetic variants associated to BPD, through a genomewide association study. Two discovery series were performed, using a DNA pooling-based strategy in Caucasian and black African neonates. DNA pooling studies were performed in two discovery series. The first discovery series was made up of 22 Caucasian infants with BPD and 76 Caucasian controls. The second discovery series was composed of 21 black African infants with BPD and 86 black African controls. Equimolar amounts of each DNA sample were then added to either the case or control pool, for each series. To control for experimental errors, several independent sets of pools were constructed. Concerning the Caucasian series, 3 sets of identical pools were constructed with one made in double quantity in order to hybridize it twice, which led to 4 independent replicates. Concerning the black African series, 4 sets of identical pools were constructed and each was hybridized once, leading also to 4 independent replicates. Genotyping was performed using the Infinium II Illumina HumanHap300 Genotyping BeadChip array for the Caucasian population and the Illumina HumanHap650Y array for the black African population. Each replicate was hybridized once which led to 4 arrays for each case and control pools and for each population. A total of 16 arrays were performed. technical replicate: Sample 1, Sample 2, Sample 3, Sample 4 technical replicate: Sample 5, Sample 6, Sample 7, Sample 8 technical replicate: Sample 9, Sample 10, Sample 11, Sample 12 technical replicate: Sample 13, Sample 14, Sample 15, Sample 16
2011-11-22 | E-GEOD-22284 | biostudies-arrayexpress
Project description:Harmful algal blooms present severe environmental threats, impacting water quality, aquatic ecosystems, and human health. The frequency and intensity of these blooms are rising, largely driven by global warming and changing climatic conditions. There is an urgent need for innovative methods to monitor blue-green algae, also known as cyanobacteria, to enable the implementation of preventative measures. Here, we show that native mass spectrometry is an effective tool for detecting cyanobacteria directly from lake samples, both prior and during bloom formation. Our approach allows for the rapid characterization of cyanobacterial populations within lakes, offering valuable insights into the dynamics of cyanobacterial species associated with harmful algae blooms. Overall, we highlight the exceptional capability of native mass spectrometry in directly detecting and monitoring cyanobacterial blooms, which will support the development of more effective strategies to mitigate this growing environmental challenge.
2025-07-28 | PXD065745 | Pride
Project description:Cyanobacteria from Black Band Disease microbial mat
| PRJNA281489 | ENA
Project description:Resistance to herbicides in weeds can be due to alteration(s) in the gene encoding the herbicide target site, or to herbicide degradation via a deviation in plant general metabolism. If target-site-based resistance is easy to study, the multigenic control of metabolism-based resistance renders it much more complex to study. Metabolism-based resistance to herbicides represents the major part of herbicide resistance in black-grass. Its most likely basis is an overexpression of genes encoding enzymes degrading herbicides. We thus seek to identify such overexpressed genes by comparing the transcriptomes of resistant and sensitive black-grass individuals belonging to an F2 line segregating for two resistance genes. Given there are no genomic tools developed for black-grass, this approach will use heterologous hybridisation onto a wheat Affymetrix microarray. Comparison using heterologous hybridisation onto a wheat whole-genome microarray of transcriptome of three pools of black-grass plants obtained 2h30 after herbicide spraying at field rate. The three pools correspond to: · Sensitive plants (killed by herbicide). · Moderately resistant plants (growth impaired by herbicide but plants still alive) · Resistant plants (growth unimpaired by herbicide) 6 arrays - wheat
2010-05-27 | E-GEOD-15864 | biostudies-arrayexpress