Hepatic gene expression in chinook salmon (Oncorhynchus tshawytscha) exposed to sewage
ABSTRACT: Hepatic transcriptional profiling of fish exposed to sewage to evaluate temporal and concentration trends. Two experiments (Year 1 and 2), each with 6 concentrations (0%, 0.05%, 0.1%, 0.7%, 2% and 5/10%) of sewage diluted in seawater at 4 timepoints (1, 4, 8 and 16 days).
Project description:Edema factor of anthrax binds to the protective antigen (PA83) which cleaves to PA63 and PA20. The role of PA20 was examined using highthroughput gene expression analysis of human peripheral blood mononuclear cells (PBMC) exposed to PA20. Keywords: Toxicity determination PBMC obtained from different individuals over 6 monthes were incubated with and without rPA20
Project description:This study presents statistical analyses of gene expression in 5, 10 and 15 day post-fertilization (dpf) embryos of the teleost Fundulus heteroclitus treated with control vehicle (DMSO) or a potent non-ortho-PCB (PCB-126; 3,3’,4,4’,5-pentachlorobiphenyl). The embryos were from two populations: a clean, reference population (SC, Scorton Creek, MA USA) and a polluted Superfund population (N, New Bedford Harbor, MA USA). For each site, eggs from 8 females (~1100 total) were fertilized using minced testes from 5 males. After non-fertile eggs were culled, embryos were exposed to vehicle (DMSO; 0.1%) or PCB-126 (50 nM) in filtered seawater (salinity 25 part per thousand, 65 embros per 20 ml in glass petri dish) for 4 hr at 20º C. After exposure, the embryos were washed in filtered seawater and incubated at 20º C under a 14-h light, 10-h dark cycle. At 5-, 10-, and 15-dpf, embryos were collected as three pools of 20 embryos from each treatment group and flash frozen in liquid nitrogen and stored at -80º C until used for RNA isolation. A loop design was used for the microarray hybridizations where each sample is hybridized to 2 arrays using both Cy3 and Cy5 labeled fluorophores. We used three loops in which each loop consisted of Cy3- and Cy5-labeled embryo aRNAs from 12 samples: one sample from each population-treatment-time combination. Within a population-treatment-time, embryos were randomly assigned to one of the three loops. In total, 36 embryos were hybridized to 36 microarrays. The loops formed were SC5C→ SC5P → NBH5C→ NBH5P →SC10C→ SC10P→ NBH10C→ NBH10P → SC15C→ SC15P → NBH15C → NBH15P → SC5C, where each arrow represents a separate hybridization (array) with the biological sample at the base of the arrow labeled with Cy3 and the biological sample at the head of the arrow labeled with Cy5. SC represents the Scorton Creek, Sandwich, MA population (reference), NBH represents the New Bedford Harbor, MA population, C represents control dose (DMSO), P represents the PCB-126 dose, 5 represents 5 dpf, 10 represents 10 dpf and 15 represents 15 dpf.
Project description:Human embryonic kidney cell (HEK293) were treated with PAR2 peptide agonist 2f-LIGRLO-NH2 (1.5h, 3h, 6h and 12h) or trypsin (6h). Comparison of genes similarly regulated by both treatments allowed better characterization of PAR2 induced response as both agonists had been reported as non-specific for PAR2. Six conditioned experiments with 3 replicates each. Individual grown and harvested.
Project description:The aim of this study was to investigate the occurrence of hepatitis E virus (HEV) in sewage samples in Shen Zhen, China. Sewage samples were collected from 152 sewage plants including livestock sewage, domestic sewage and treated sewage from May to July of 2015. Two of 152 samples were HEV positive (1.32%) from the livestock sewage plants. Partial ORF2 fragments of HEV were sequenced and a phylogenetic tree was constructed using MEGA5.1. Blast and phylogenetic analyses showed that both of these two sequences belonged to HEV Genotype 4. To the best of our knowledge, this is the first study on the molecular characterization of HEV in wastewater in China and the first time to detect Genotype 4 in the sewage. Results from this study indicate that the possibilities of sporadic infections of HEV should be emphasized because virus still has the possibility to be circulating in the sewage in China.
Project description:IntroductionThe occurrence of antibiotic resistance in faecal bacteria in sewage is likely to reflect the current local clinical resistance situation.AimThis observational study investigated the relationship between Escherichia coli resistance rates in sewage and clinical samples representing the same human populations.MethodsE. coli were isolated from eight hospital (n = 721 isolates) and six municipal (n = 531 isolates) sewage samples, over 1 year in Gothenburg, Sweden. An inexpensive broth screening method was validated against disk diffusion and applied to determine resistance against 11 antibiotics in sewage isolates. Resistance data on E. coli isolated from clinical samples from corresponding local hospital and primary care patients were collected during the same year and compared with those of the sewage isolates by linear regression.ResultsE. coli resistance rates derived from hospital sewage and hospital patients strongly correlated (r2 = 0.95 for urine and 0.89 for blood samples), as did resistance rates in E. coli from municipal sewage and primary care urine samples (r2 = 0.82). Resistance rates in hospital sewage isolates were close to those in hospital clinical isolates while resistance rates in municipal sewage isolates were about half of those measured in primary care isolates. Resistance rates in municipal sewage isolates were more stable between sampling occasions than those from hospital sewage.ConclusionOur findings provide support for development of a low-cost, sewage-based surveillance system for antibiotic resistance in E. coli, which could complement current monitoring systems and provide clinically relevant antibiotic resistance data for countries and regions where surveillance is lacking.
Project description:This study investigates sex-biased gene expression between populations of Atlantic and Pacific salmon lice, Lepeophtheirus salmonis. Two Atlantic L. salmonis populations were previously used for an array study (GSE56024) while a third dataset using Pacific L. salmonis was novel. Using all three populations, a consensus-based, meta-analysis approach was used to identify sex-biased and sex-specific genes. Two separate experiments were conducted, one for Atlantic and one for Pacific salmon lice. As the Atlantic data has been previously published for other comparisons (GSE56024), only the Pacific data is uploaded here. Lice from three populations (2 in the Atlantic and 1 in the Pacific) were collected for in vitro bioassay analysis using emamectin benzoate. After 24hrs, lice were collected as per treatment protocol below. Males and females from all populations were compared separately before forming a consensus probe list of sex-biased genes concordantly expressed across all three populations. Please note that each raw data file contains three or four 'block' data and each block data correspond to individual sample raw data. Therefore, each raw data file contains raw data for 3-4 samples (as indicated in the description field).
Project description:Larval settlement and metamorphosis is a vital transition period for marine invertebrates and can have far-reaching effects on the ecology and evolution of a species. To explore the molecular mechanisms of this critical process in a non-model organism, the tropical abalone Haliotis asinina, we employed cDNA microarray methods. By comparing gene expression profiles through mid to late larval development and metamorphosis, we identified 144 genes as likely candidates for a role in competence and/or metamorphosis. Gene characterization showed that ~60% of these were significantly similar to previously described genes from other taxa, while ~40% had no significant similarities to any known genes. A high 49.3% of genes were gastropod- or abalone-specific, but none appear to be Lophotrochozoan-specific, despite the fact that metamorphosis is thought to have had a separate origin in this group. Based on temporal expression profiles, the differentially expressed larval and postlarval genes can be clustered into 5 categories that reveal there are strikingly different transcriptional patterns occurring during this phase of development. Some classes of gene activation are contingent upon exogenous cues and correlate with the initiation of settlement and metamorphosis. Importantly, there is also extensive gene activity associated with the endogenous attainment of competence, which occurs prior to, and independent of, the exogenous induction of settlement. Our results show that as the haliotid veliger larva matures, it requires the coordinated regulation of temporally different batteries of genes involved in a wide range of physiological and developmental processes associated with colonisation of the benthos. Although the signalling pathways operating at metamorphosis may be conserved across the animal kingdom, it appears they are regulating the expression of novel genes specific to abalone, gastropods and molluscs during H. asinina metamorphosis. Keywords: timecourse; metamorphosis; marine ecology Each microarray slide contained a different combination of 2 of the 9 developmental stages used in the experiment (66 hpf, 78 hpf, 90 hpf, 108 hpf, 120 hpf, 144 hpf, 12 hpi, 24 hpi, 48 hpi). Each developmental stage was subjected to 4 hybridisations – amounting to 4 technical replicates per stage - in a loop design (Churchill 2002; Oleksiak et al. 2002). This design led to raw data consisting of 72 measurements - 9 stages with 8 replicates (including 2 replicates per chip) - for each of 5541 spots.
Project description:Microbial sewage communities consist of a combination of human fecal microorganisms and nonfecal microorganisms, which may be residents of urban sewer infrastructure or flowthrough originating from gray water or rainwater inputs. Together, these different microorganism sources form an identifiable community structure that may serve as a signature for sewage discharges and as candidates for alternative indicators specific for human fecal pollution. However, the structure and variability of this community across geographic space remains uncharacterized. We used massively parallel 454 pyrosequencing of the V6 region in 16S rRNA genes to profile microbial communities from 13 untreated sewage influent samples collected from a wide range of geographic locations in the United States. We obtained a total of 380,175 high-quality sequences for sequence-based clustering, taxonomic analyses, and profile comparisons. The sewage profile included a discernible core human fecal signature made up of several abundant taxonomic groups within Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. DNA sequences were also classified into fecal, sewage infrastructure (i.e., nonfecal), and transient groups based on data comparisons with fecal samples. Across all sewage samples, an estimated 12.1% of sequences were fecal in origin, while 81.4% were consistently associated with the sewage infrastructure. The composition of feces-derived operational taxonomic units remained congruent across all sewage samples regardless of geographic locale; however, the sewage infrastructure community composition varied among cities, with city latitude best explaining this variation. Together, these results suggest that untreated sewage microbial communities harbor a core group of fecal bacteria across geographically dispersed wastewater sewage lines and that ambient water quality indicators targeting these select core microorganisms may perform well across the United States.
Project description:Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but the gut microbiota of humans and other animals contain organisms from an array of other taxonomic groups that might provide indicators of fecal pollution sources. To discern between human and nonhuman fecal sources, we compared the V6 regions of the 16S rRNA genes detected in fecal samples from six animal hosts to those found in sewage (as a proxy for humans). We focused on 10 abundant genera and used oligotyping, which can detect subtle differences between rRNA gene sequences from ecologically distinct organisms. Our analysis showed clear patterns of differential oligotype distributions between sewage and animal samples. Over 100 oligotypes of human origin occurred preferentially in sewage samples, and 99 human oligotypes were sewage specific. Sequences represented by the sewage-specific oligotypes can be used individually for development of PCR-based assays or together with the oligotypes preferentially associated with sewage to implement a signature-based approach. Analysis of sewage from Spain and Brazil showed that the sewage-specific oligotypes identified in U.S. sewage have the potential to be used as global alternative indicators of human fecal pollution. Environmental samples with evidence of prior human fecal contamination had consistent ratios of sewage signature oligotypes that corresponded to the trends observed for sewage. Our methodology represents a promising approach to identifying new bacterial taxa for MST applications and further highlights the potential of the family Lachnospiraceae to provide human-specific markers. In addition to source tracking applications, the patterns of the fine-scale population structure within fecal taxa suggest a fundamental relationship between bacteria and their hosts.
Project description:Hepatitis E virus (HEV) is endemic in India and causes epidemics and sporadic cases. However, the exact transmission route for sporadic hepatitis E remains unclear. This study investigated HEV in sporadic hepatitis cases and sewage samples, as sewage is the major source of contamination of water in developing countries.Monthly sampling and testing for HEV in sewage samples from Vellore, India was carried out for 1 year (November 2009-October 2010) and plasma and/or fecal samples from sporadic hepatitis cases presenting to a hospital in Vellore during 2006-2010 were tested for HEV RNA. A total of 144 raw sewage samples and 94 samples from sporadic hepatitis cases were tested for HEV RNA using RT-PCR.The prevalence of HEV RNA in sewage and sporadic cases was 55.6% and 9.6%, respectively. HEV strains isolated from sewage showed 94-100% nucleotide sequence similarity with the HEV strains isolated from the sporadic hepatitis cases. HEV RNA in sewage was identified more often during the summer (81.2%) than the monsoon season (14.5%) (p < 0.001).This study indicates that sewage may be a source of contamination for sporadic hepatitis and also underscores the need for preventive measures to protect drinking water from sewage contamination, particularly in the summer. GENBANK ACCESSION NUMBERS: HEV strains isolated from this study were deposited in GenBank under accession numbers JF972766-JF972773, JN705651-JN705659 and JN705660-JN705662.