Plant health identification of Coleoptera
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NextSeq 500
ORGANISM(S): Anoplophora Glabripennis
SUBMITTER: University of Hohenheim
PROVIDER: PRJEB66443 | EVA | 2023-10-01
REPOSITORIES: EVA
Dataset's files
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Aims: To assess the virulence of multiple Aeromonas spp. using two models, a neonatal mouse assay and a mouse intestinal cell culture. Methods and Results: Transcriptional responses to both infection models were evaluated using microarrays. After artificial infection with a variety of Aeromonas spp., mRNA extracts from the two models were processed and hydridized to murine microarrays to determine host gene response. Definition of virulence was determined based on host mRNA production in murine neonatal intestinal tissue and mortality of infected animals. Infections of mouse intestinal cell cultures were then performed to determine whether this simpler model system's mRNA responses correlated to neonatal results and therefore be predictive of virulence of Aeromonas spp. Virulent aeromonads up-regulated transcripts in both models including multiple host defense gene products (chemokines, regulation of transcription and apoptosis, cell signaling). Avirulent species exhibited little or no host response in neonates. Mortality results correlated well with both bacterial dose and average fold change of up-regulated transcripts in the neonatal mice. Conclusions: Cell culture results were less discriminating but showed promise as potentially being able to be predictive of virulence. Jun oncogene up-regulation in murine cell culture is potentially predictive of Aeromonas virulence. Significance and Impact of the Study: Having the ability to determine virulence of waterborne pathogens quickly would potentially assist public health officials to rapidly assess exposure risks. Experiment Overall Design: Two infection models were assessed, live, whole animals (neonatal Swiss Webster mice) and a murine small intestinal cell culture. Biological replicates (n=5) were infected with different Aeromonas species/strains and compared to uninfected controls.
2008-06-15 | E-GEOD-6065 | biostudies-arrayexpress
Project description:The delta smelt (Hypomesus transpacificus) is a pelagic fish species endemic to the Sacramento-San Joaquin Estuary in Northern California, listed as endangered under both the USA Federal and Californian State Endangered Species Acts and acts as an indicator of ecosystem health in its habitat range. Interrogative tools are required to successfully monitor effects of contaminants upon the delta smelt, and to research potential causes of population decline in this species. We used microarray technology to investigate genome-wide effects in 47-day old larvae after a 7-day exposure to ambient water samples from the Sacramento River at a monitoring field station (Hood) situated 8 miles downstream of the Sacramento regional Wastewater Treatment Plant. Genomic assessments were carried out on surviving organisms and contrasted to laboratory controls. Microarray assessments were conducted on larvae exposed for 7-days to Sacramento River water collected at Hood and pooled laboratory controls. Assessments were carried out in quadruplicate, using 3 fish per treatment. RNA was extracted from frozen whole, individual organisms, using Trizol Reagent (Invitrogen) as per manufacturer's guidelines. Total RNA from 5 fish was pooled per treatment and cDNA was synthesized from a total of 2ug total RNA, amplified using a SuperScripttm Indirect RNA Amplification System (Invitrogen). Resulting aRNA was labeled with Alexa fluor dyes (Invitrogen) as per manufacturerM-bM-^@M-^Ys instructions. Two color microarray assessments were carried out on quadruplicate treatments, using 5M-BM-5g of aRNA for pooled controls vs exposed sample, (total 4 samples). Microarray hybridizations were performed manually, and incubated in a waterbath at 42C for 16 hours. Slides were scanned using a GenePix 4000B scanner (Axon Instruments). Data was analyzed using LIMMA GUI (Linear model for microarray analysis graphical user interface) (Smyth, 2005), written in the R-programming language available through Bioconductor http://www.Bioconductor.org. Data was normalized within using print-tip Lowess and between arrays applying average intensity quantile (Aquantile) normalization methods with background correction (Smyth, 2005). A linear model fit was computed using the duplicates on the arrays and the least-squares method, with Benjamin Hochberg false discovery rate adjustment.
2012-09-20 | E-GEOD-40991 | biostudies-arrayexpress
Project description:The delta smelt (Hypomesus transpacificus) is a pelagic fish species endemic to the Sacramento-San Joaquin Estuary in Northern California, listed as endangered under both the USA Federal and Californian State Endangered Species Acts and acts as an indicator of ecosystem health in its habitat range. Interrogative tools are required to successfully monitor effects of contaminants upon the delta smelt, and to research potential causes of population decline in this species. We used microarray technology to investigate genome-wide effects in 47-day old larvae after a 7-day exposure to ambient water samples from the Sacramento River at a monitoring field station (Hood) situated 8 miles downstream of the Sacramento regional Wastewater Treatment Plant. Genomic assessments were carried out on surviving organisms and contrasted to laboratory controls.
2012-09-20 | GSE40991 | GEO
Project description:Hispanic/Latino populations possess a complex genetic structure that reflects recent admixture among and potentially ancient substructure within Native American, European, and West African source populations. Here, we quantify genome-wide patterns of SNP and haplotype variation among 100 individuals with ancestry from Ecuador, Colombia, Puerto Rico, and the Dominican Republic genotyped using Illumina technology. To investigate variations of continental ancestry between different Hispanic/Latino groups (using self-reported country-specific identification of individual, both parents, and all four grandparents) and within them from healthy controls represented in the New York Health Project Biorepository. Genotyped on the Illumina 610-Quad, which is identical to HumanHap550-v3 SNPs plus an additional ~60,000 SNPs for CNV, no CNV data is provided or was analyzed.
2010-04-07 | E-GEOD-21248 | biostudies-arrayexpress
Project description:Background：Hepatitis B virus (HBV) infection poses a substantial threat to human health, impacting not only infected individuals but also potentially exerting adverse effects on the health of their offspring. The underlying mechanisms driving this phenomenon remain elusive. This study aims to shed light on this issue by examining alterations in paternally imprinted genes within sperm. Methods: A cohort of 35 individuals with normal semen analysis, comprising 17 hepatitis B surface antigen (HBsAg)-positive and 18 negative individuals, was recruited. Based on the previous research and the Online Mendelian Inheritance in Man database (OMIM, https://www.omim.org/), targeted promoter methylation sequencing was employed to investigate 28 paternally imprinted genes associated with various diseases. Results: Bioinformatic analyses revealed 42 differentially methylated sites across 29 CpG islands within 19 genes and four differentially methylated CpG islands within four genes. At the gene level, an increase in methylation of DNMT1 and a decrease in methylation of CUL7, PRKAG2, and TP53 were observed. DNA methylation haplotype analysis identified 51 differentially methylated haplotypes within 36 CpG islands across 22 genes. Conclusions: This is the first study to explore the effects of HBV infection on sperm DNA methylation and the potential underlying mechanisms of intergenerational influence of paternal HBV infection.
2024-07-11 | GSE270937 | GEO
Project description:Yersinia pestis (Y. pestis) is the etiologic agent of the plague, an endemic zoonotic disease of critical clinical and historic importance. The species belongs to a genus comprising eleven members, three of which are human pathogens. Y. pestis and its closest extant relative, Yersinia pseudotuberculosis, are very similar in many respects, yet there is a distinct dichotomy between these species in terms of pathogenicity. Y. pseudotuberculosis produces a relatively benign food- or water-borne gastroenteritis with rare cases of potentially fatal bacteremia. In contrast, the characteristics of high infectivity and high mortality have made Y. pestis a pathogen of historic importance with devastating effects on the human populace over the course of three major pandemics. These qualities coupled with the emergence of multi-drug resistant variants make Y. pestis an ideal candidate for use as a bioterrorism agent. Consequentially, evolutionary biology of this organism has become a priority in the counter-terrorism research effort. The flow of genetic information within the Y. pseudotuberculosis/Y. pestis group motivated us to identify novel genes for the purpose of creating a pan-genome species DNA microarray to better understand the phylogenomic relationships among its members. Based on the sequence information be generated from the novel gene discovery project conducted at the PFGRC as well as other publicly available sources regarding Yersinia spp. genome sequences, we designed a species microarray which represents the hitherto known genetic repertoire of this taxonomic group. In order to create a species microarray that represents novel genes or genes with significant sequence variation, the ArrayOligoSelector software (http://arrayoligosel.sourceforge.net/) was used to design a 70-mer oligonucleotide for each of the annotated ORFs or partial ORFs. A detailed description of the 70-mer oligo design process and filters developed by the PFGRC can be found on the PFGRC web site at (http://pfgrc.tigr.org/presentations/seminars/oligo_design_final.pdf). One hundred fifty six query strains were investigated in this study, with each query strain hybridized against the reference strain, CO92. Each strain has a single dye experiment. Each oligo is spotted on the Y. pestis species microarray once. Positive controls on the array consist of oligos designed from the sequenced reference genome, CO92, and negative controls on the array consist of oligos designed from the thale cress plant, Arabidopsis thaliana.The microarrays also had Agilent internal controls.
2010-09-02 | E-GEOD-23797 | biostudies-arrayexpress
Project description:The advent of next generation sequencing (NGS) has greatly enriched the database of miRNAs. For plants so far 8455 miRNAs sequences from 73 species and 15401 miRNAs sequences from 150 species have been deposited in miRBase 22.0 and Plant Non-coding RNA Database, respectively. The occurrence of miRNAs in such a huge number, which is still increasing, is because of the fact that the profile of miRNAs expression differs greatly from species to species, both quantitatively and qualitatively. Besides, even within a species it is expected that the miRNA expression profile would differ from cultivar to cultivar depending on the trait with regard to which the two cultivars differ. Beises, the expression of a miRNA in a plant organ may differ depending upon it spatial location. The same is reflected in the NGS data of the apical and basal spikelets of the panicle of the rice cultivar Mahalaxmi.
2019-08-10 | GSE135614 | GEO
Project description:A new cryptic species within Iris ruthenica was described
| PRJEB102172 | ENA
Project description:Multiple new species within the genus Pseudomonas Genome sequencing
| PRJNA691338 | ENA
Project description:Silicon (Si) has long been known to play a major physiological role in certain organisms, including some sponges and many diatoms and higher plants, leading to the recent identification of multiple proteins responsible for silicon transport in a range of algal and plant species. In mammals, despite several convincing studies suggesting that silicon is an important factor in bone development and connective tissue health, there is a critical lack of understanding in biochemical pathways that enable silicon homeostasis. Here we report the identification of a mammalian efflux silicon transporter, namely Slc34a2 (also known as NaPiIIb), which was upregulated in the kidneys of rats following chronic dietary silicon deprivation. When heterologously expressed in Xenopus laevis oocytes, the protein displayed marked silicon transport activity, specifically efflux, comparable to plant OsLsi2 transfected in the same fashion and independent of sodium and/or phosphate influx. This is the first evidence for a specific active transporter protein for silicon in mammals and suggests an important role for silicon in vertebrates.
2017-04-05 | GSE58404 | GEO