Reef fish larvae Eilat
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB20625 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1958399_1.fastq.gz | Fastqsanger.gz | |||
| ERR1958399_2.fastq.gz | Fastqsanger.gz | |||
| ERR1987830_1.fastq.gz | Fastqsanger.gz | |||
| ERR1987830_2.fastq.gz | Fastqsanger.gz | |||
| ERR1987840_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 858 |
Similar Datasets
Project description:Prolific heterotrophic biofilm growth is a common occurrence in airport receiving streams containing deicer and anti-icer runoff. This study investigated relations of heterotrophic biofilm prevalence and community composition to environmental conditions at stream sites upstream and downstream of Milwaukee Mitchell International Airport in Milwaukee, WI, during two deicing seasons (2009–2010 and 2010–2011). Modern genetic tools (such as microarray) have not previously been applied to biofilm communities in this type of setting. We used microarray results to characterize biofilm community composition as well as the response of the biofilm community to environmental factors (i.e., organic content (using chemical oxygen demand concentration) and temperature).
2019-05-13 | GSE129990 | GEO
Project description:Grain yield and protein content were determined for six wheat cultivars grown over three years at multiple sites and at multiple N-fertilizer inputs. Although grain protein was negatively correlated with yield, some grain samples had higher protein contents than expected based on their yields, a trait referred to as grain protein deviation (GPD). We used novel statistical approaches to calculate GPD across environment and to correlate gene expression in the developing caryopsis with this trait. The yield and protein content were initially adjusted for nitrogen fertilizer inputs, and then adjusted for yield (to remove the negative correlation) resulting in environmental corrected GPD. The transcriptome data for all samples were subjected to Principal Component Analysis (PCA) and ANOVA to identify individual Principal Components (PCs) correlating with GPD alone. Scores of the selected PCs significantly related to cultivar differences and GPD but not to the yield or protein content were identified as reflecting a multivariate pattern of gene expression related to genetic variation in GPD. Sets of genes significant for these PCs and hence GPD were identified as candidate genes determining cultivar differences in GPD. Microarray profiling has been used to identify the links between gene expression and grain protein content in 6 different varietes of wheat grown at 2 different sites, 3 N levels and during 3 growth seasons. Six UK cultivars (Istabraq , Hereward, Marksman, Cordiale, Malacca and Xi 19) were grown over three seasons (2008-9, 2009-10 and 2010-11) at Rothamsted . In the present publication, data from two sites are included: Rothamsted and RAGTResearch (Harpenden, UK) and at four other sites in the south-east of the UK (RAGT, Ickleton, Cambridge; Limagrain, Woolpit, Suffolk; Syngenta, Whittlesford, Cambridge; KWS-UK, Thriplow, Hertfordshire) in 2009-10 and 2010-11 only. Three replicate plots were grown at three N levels: 100kg/ha, (N100), 200kg/ha (N200) and 350 kg/ha (N350) (see Barraclough et al., 2010, Chope at al., 2014). Developing heads (10 per plot) were tagged and caryopses were harvested from the Rothamsted (2009, 2010 and 2011) and RAGT (2010 and 2011) sites at 21 days after anthesis (mid-grain filling) to measure gene expression using Affymetrix wheat microarrays giving a total of 161 samples. Six UK cultivars (Istabraq , Hereward, Marksman, Cordiale, Malacca and Xi 19) were grown over three seasons (2008-9, 2009-10 and 2010-11) at Rothamsted Research (Harpenden, UK) and at four other sites in the south-east of the UK (RAGT, Ickleton, Cambridge; Limagrain, Woolpit, Suffolk; Syngenta, Whittlesford, Cambridge; KWS-UK, Thriplow, Hertfordshire) in 2009-10 and 2010-11 only. Three replicate plots were grown at three N levels: 100kg/ha, (N100), 200kg/ha (N200) and 350 kg/ha (N350) (see Barraclough et al., 2010, Chope at al., 2014). Developing heads (10 per plot) were tagged and caryopses were harvested from the Rothamsted (2009, 2010 and 2011) and RAGT (2010 and 2011) sites at 21 days after anthesis (mid-grain filling) to measure gene expression using Affymetrix wheat microarrays giving a total of 161 samples.
2014-07-04 | E-GEOD-59056 | biostudies-arrayexpress
Project description:We profiled gene expression from a stratified cohort of subjects to define influenza vaccine response in Young and Old Differential gene expression by human PBMCs from Healthy Adults receiving Influenza Vaccination (Fluvirin, Novartis). Healthy adults (older >65, younger 21-30 years) were recruited at seasonal Influenza Vaccination clinics organized by Yale University Health Services during October to December of 2010 M-bM-^@M-^S 2011 and 2011-2012 seasons. With informed consent, healthy individuals were recruited as per a protocol approved by Human Investigations Committee of the Yale University School of Medicine. Each subject was evaluated by a screening questionnaire determining self-reported demographic information, height, weight, medications and comorbid conditions. Participants with acute illness two weeks prior to vaccination were excluded from study. Blood samples were collected into BD Vacutainer Sodium Heparin tube at four different time points, once prior to administration of vaccine and three time points after vaccination on days 2/4, 7 and 28. Peripheral Blood Mononuclear Cells (PBMC) were isolated from heparinized blood using Histopaque 1077 in gradient centrifugation. About 1.0x10^7 freshly isolated PBMC were lysed in Triso and immediately stored in -800C. Total RNA in aqueous phase of Trisol - Chloroform was isolated in an automated QiaCube instrument using miRNeasy according to manufacturerM-bM-^@M-^Ys instructions. Integrity of RNA samples were assessed by Agilent 2100 BioAnalyser Samples were processed for cRNA generation using Illumina TotalPrep cRNA Amplification Kit and subsequently hybridized to Human HT12-V4.0 BeadChip at Yale Center for Genomic Analysis (YGCA).
2015-01-26 | E-GEOD-59635 | biostudies-arrayexpress
Project description:We profiled gene expression from a stratified cohort of subjects to define influenza vaccine response in Young and Old Differential gene expression by human PBMCs from Healthy Adults receiving Influenza Vaccination (Fluvirin, Novartis). Healthy adults (older >65, younger 21-30 years) were recruited at seasonal Influenza Vaccination clinics organized by Yale University Health Services during October to December of 2010 M-bM-^@M-^S 2011 and 2011-2012 seasons. With informed consent, healthy individuals were recruited as per a protocol approved by Human Investigations Committee of the Yale University School of Medicine. Each subject was evaluated by a screening questionnaire determining self-reported demographic information, height, weight, medications and comorbid conditions. Participants with acute illness two weeks prior to vaccination were excluded from study. Blood samples were collected into BD Vacutainer Sodium Heparin tube at four different time points, once prior to administration of vaccine and three time points after vaccination on days 2/4, 7 and 28. Peripheral Blood Mononuclear Cells (PBMC) were isolated from heparinized blood using Histopaque 1077 in gradient centrifugation. About 1.0x10^7 freshly isolated PBMC were lysed in Triso and immediately stored in -800C. Total RNA in aqueous phase of Trisol - Chloroform was isolated in an automated QiaCube instrument using miRNeasy according to manufacturerM-bM-^@M-^Ys instructions. Integrity of RNA samples were assessed by Agilent 2100 BioAnalyser Samples were processed for cRNA generation using Illumina TotalPrep cRNA Amplification Kit and subsequently hybridized to Human HT12-V4.0 BeadChip at Yale Center for Genomic Analysis (YGCA).
2015-01-26 | E-GEOD-59654 | biostudies-arrayexpress
Project description:The purpose of the study was to assess the patterns of global gene expression in peripheral blood cells and uncover the complex dynamics of host response to ARIs such as pandemic H1N1. To understand the molecular bases and network orchestration of host responses, we prospectively enrolled 1610 healthy adults in the fall of 2009 and 2010, followed the subjects with influenza-like illness (N=133) for 3 weeks, and examined changes in their peripheral blood gene expression. We discovered distinct phases of the host response spanning 6 days after infection, and identified genes that differentiate influenza from non-influenza virus infection. We examined pre- and post-infection anti-influenza antibody titers defining novel gene expression correlates. Healthy adults were invited to enroll to be followed for acute respiratory illness (ARI) through two consecutive influenza seasons 2009-2010 and 2010-2011. After subjects provided consent, baseline blood specimens were obtained during enrollment. Subjects were given thermometers and instructions to call and report for evaluation within 48 hours of ARI onset. Those persons who had a new ARI were seen within 48 hours of onset (day 0) and 2, 4, and 6 days later for repeat evaluation, blood specimen collections, and medical care (including the antiviral zanamivir if indicated) and 21 days later for collection of convalescent specimens. Nasal wash samples were collected for virus detection by RT-PCR on day 0 and day 2. Surveillance for influenza was terminated after 5.5 months; all subjects were asked to return for specimen collection and to provide a medical and ARI history in spring of next year. Serum specimens obtained at baseline, day 0 and day 21 visits for illnesses, and the terminal visit were tested simultaneously using hemagglutination-inhibition (HAI) antibody assay for Influenza H1N1, H3N2, and Influenza B strains. Peripheral blood RNA (PaxGene) obtained from blood specimens at each visit were analyzed using Illumina Human HT-12 v4. The study was repeated 2010-2011. A total of 880 arrays, corresponding to 133 individuals, passed quality control and are included in this data set.
2015-04-28 | E-GEOD-68310 | biostudies-arrayexpress
Project description:Interventions: "A group: MC followed by EUS" for diagnosis of invasion depth From February 2011 to December 2013
"B group: EUS followed by MC" for diagnosis of invasion depth From February 2011 to December 2013
Primary outcome(s): Accuracy rate for invasion depth of early colorectal cancer by MC and EUS
Study Design: Cross-over Randomized
| 2620527 | ecrin-mdr-crc
Project description:The behavior of reef fish larvae, equipped with a complex toolbox of sensory apparatus, has become a central issue in understanding their transport in the ocean. In this study pelagic reef fish larvae were monitored using an unmanned open-ocean tracking device, the drifting in-situ chamber (DISC), deployed sequentially in oceanic waters and in reef-born odor plumes propagating offshore with the ebb flow. A total of 83 larvae of two taxonomic groups of the families Pomacentridae and Apogonidae were observed in the two water masses around One Tree Island, southern Great Barrier Reef. The study provides the first in-situ evidence that pelagic reef fish larvae discriminate reef odor and respond by changing their swimming speed and direction. It concludes that reef fish larvae smell the presence of coral reefs from several kilometers offshore and this odor is a primary component of their navigational system and activates other directional sensory cues. The two families expressed differences in their response that could be adapted to maintain a position close to the reef. In particular, damselfish larvae embedded in the odor plume detected the location of the reef crest and swam westward and parallel to shore on both sides of the island. This study underlines the critical importance of in situ Lagrangian observations to provide unique information on larval fish behavioral decisions. From an ecological perspective the central role of olfactory signals in marine population connectivity raises concerns about the effects of pollution and acidification of oceans, which can alter chemical cues and olfactory responses.
| S-EPMC3755995 | biostudies-literature
Project description:Reef fish sustain populations on isolated reefs and show genetic diversity between nearby reefs even though larvae of many species are swept away from the natal site during pelagic dispersal. Retention or recruitment to natal reefs requires orientation capabilities that enable larvae to find their way. Although olfactory and acoustically based orientation has been implicated in homing when larvae are in the reef's vicinity, it is still unclear how they cope with greater distances. Here we show evidence for a sun compass mechanism that can bring the larvae to the vicinity of their natal reef. In a circular arena, pre-settlement larvae and early settlers (<24 hours) of the cardinal fish, Ostorhinchus doederleini, showed a strong SSE directional swimming response, which most likely has evolved to compensate for the locally prevailing large scale NNW current drift. When fish were clock-shifted 6 hours, they changed their orientation by ca. 180° as predicted by the tropical sun curve at One Tree Island, i.e. they used a time-compensated sun compass. Furthermore, the fish oriented most consistently at times of the day when the sun azimuth is easy to determine. Microsatellite markers showed that the larvae that had just arrived at One Tree Island genetically belonged to either the local reef population or to Fitzroy Reef located 12 kilometers to the SSE. The use of a sun compass adds a missing long-distance link to the hierarchy of other sensory abilities that can direct larvae to the region of origin, including their natal reef. Predominant local recruitment, in turn, can contribute to genetic isolation and potential speciation.
| S-EPMC3694079 | biostudies-literature
Project description:<p>The overall purpose of this study is to investigate the host genetic factors in response to influenza virus infection, with the focus on influenza vaccination in the first substudy "Adult Influenza Vaccine Genetics" and with the focus on influenza natural infection and other acute respiratory infections (ARIs) in the second substudy "Acute Viral Respiratory Infection Genetics". In the first substudy, healthy adults were enrolled in 2008 (male cohort) and 2010 (female cohort) and immunized with seasonal influenza vaccine. In the second substudy, healthy adults were invited to enroll to be followed for acute respiratory illness through two consecutive influenza seasons 2009-2010 and 2010-2011. Peripheral blood genomic DNA samples were collected from all the subjects, and time-series RNA and serum samples were obtained pre- and post- immunization/infection. Genotyping was carried out on peripheral blood genomic DNA samples using Illumina HumanOmniExpress-12 v1 arrays. Peripheral blood RNA samples obtained at each visit were analyzed using Illumina Human HT-12 (for all the samples) and HiSeq 2000 (for 130 samples in the "Acute Viral Respiratory Infection Genetics" study). Serum specimens were tested using hemagglutination-inhibition (HAI) antibody assay for Influenza H1N1, H3N2, and Influenza B strains.</p> <p>A detailed description of each substudy is provided under their own pages below and via the grouping tool in the right-hand box: <ul> <li><a href="./study.cgi?study_id=phs000635">phs000635</a> Adult Influenza Vaccine Genetics</li> <li><a href="./study.cgi?study_id=phs001031">phs001031</a> Acute Viral Respiratory Infection Genetics</li> </ul> </p>
| phs001030 | dbGaP