Dataset Information

Identifying conserved UV exposure genes and mechanisms.

ABSTRACT: Studies have been showing how changes in ultraviolet (UV) affect the terrestrial system, mostly focusing on higher plants and indirect effects, e.g. UV changed food quality/decomposition. Much less attention has been given to direct effect on terrestrial species, although the negative effects have been recognized for some earthworms. Further, the actual mechanisms of UV toxicity to soil invertebrates are even less understood. We here studied the effect of UV on the soil oligochaete Enchytraeus crypticus, and attempted to identify the possible mechanisms of toxicity using high-throughput gene expression. Applying a UV dose equivalent to UV during the winter months in northern Europe we observed an 80% decrease in reproduction. For these organisms, approximately 5% of the genes were differentially expressed. Among the observations was an activation of the DNA repair mechanisms, nucleotide excision repair, which correlated with survival of the organisms. An observed repressing of apoptosis seems to have deleterious effects (e.g. because it may lead to the accumulation of aberrant cells) leading to a decline in reproduction. The mechanisms activated by UV were similar to those mechanisms activated in humans, showing conservation across species.

SUBMITTER: Gomes SIL

PROVIDER: S-EPMC5988748 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Identifying conserved UV exposure genes and mechanisms.

Gomes Susana I L SIL Roca Carlos P CP Scott-Fordsmand Janeck J JJ Amorim Mónica J B MJB

Scientific reports 20180605 1

Studies have been showing how changes in ultraviolet (UV) affect the terrestrial system, mostly focusing on higher plants and indirect effects, e.g. UV changed food quality/decomposition. Much less attention has been given to direct effect on terrestrial species, although the negative effects have been recognized for some earthworms. Further, the actual mechanisms of UV toxicity to soil invertebrates are even less understood. We here studied the effect of UV on the soil oligochaete Enchytraeus c ...[more]

PMID: 29872144

Similar Datasets

Project description:MotivationA growing number of studies have explored the process of pre-implantation embryonic development of multiple mammalian species. However, the conservation and variation among different species in their developmental programming are poorly defined due to the lack of effective computational methods for detecting co-regularized genes that are conserved across species. The most sophisticated method to date for identifying conserved co-regulated genes is a two-step approach. This approach first identifies gene clusters for each species by a cluster analysis of gene expression data, and subsequently computes the overlaps of clusters identified from different species to reveal common subgroups. This approach is ineffective to deal with the noise in the expression data introduced by the complicated procedures in quantifying gene expression. Furthermore, due to the sequential nature of the approach, the gene clusters identified in the first step may have little overlap among different species in the second step, thus difficult to detect conserved co-regulated genes.ResultsWe propose a cross-species bi-clustering approach which first denoises the gene expression data of each species into a data matrix. The rows of the data matrices of different species represent the same set of genes that are characterized by their expression patterns over the developmental stages of each species as columns. A novel bi-clustering method is then developed to cluster genes into subgroups by a joint sparse rank-one factorization of all the data matrices. This method decomposes a data matrix into a product of a column vector and a row vector where the column vector is a consistent indicator across the matrices (species) to identify the same gene cluster and the row vector specifies for each species the developmental stages that the clustered genes co-regulate. Efficient optimization algorithm has been developed with convergence analysis. This approach was first validated on synthetic data and compared to the two-step method and several recent joint clustering methods. We then applied this approach to two real world datasets of gene expression during the pre-implantation embryonic development of the human and mouse. Co-regulated genes consistent between the human and mouse were identified, offering insights into conserved functions, as well as similarities and differences in genome activation timing between the human and mouse embryos.Availability and implementationThe R package containing the implementation of the proposed method in C ++ is available at: https://github.com/JavonSun/mvbc.git and also at the R platform https://www.r-project.org/Contactjinbo@engr.uconn.edu.

Project description:BackgroundUnderstanding complex networks that modulate development in humans is hampered by genetic and phenotypic heterogeneity within and between populations. Here we present a method that exploits natural variation in highly diverse mouse genetic reference panels in which genetic and environmental factors can be tightly controlled. The aim of our study is to test a cross-species genetic mapping strategy, which compares data of gene mapping in human patients with functional data obtained by QTL mapping in recombinant inbred mouse strains in order to prioritize human disease candidate genes.MethodologyWe exploit evolutionary conservation of developmental phenotypes to discover gene variants that influence brain development in humans. We studied corpus callosum volume in a recombinant inbred mouse panel (C57BL/6J×DBA/2J, BXD strains) using high-field strength MRI technology. We aligned mouse mapping results for this neuro-anatomical phenotype with genetic data from patients with abnormal corpus callosum (ACC) development.Principal findingsFrom the 61 syndromes which involve an ACC, 51 human candidate genes have been identified. Through interval mapping, we identified a single significant QTL on mouse chromosome 7 for corpus callosum volume with a QTL peak located between 25.5 and 26.7 Mb. Comparing the genes in this mouse QTL region with those associated with human syndromes (involving ACC) and those covered by copy number variations (CNV) yielded a single overlap, namely HNRPU in humans and Hnrpul1 in mice. Further analysis of corpus callosum volume in BXD strains revealed that the corpus callosum was significantly larger in BXD mice with a B genotype at the Hnrpul1 locus than in BXD mice with a D genotype at Hnrpul1 (F = 22.48, p<9.87*10(-5)).ConclusionThis approach that exploits highly diverse mouse strains provides an efficient and effective translational bridge to study the etiology of human developmental disorders, such as autism and schizophrenia.

Project description:Water pollution remains a major environmental concern, with increased toxic by-products being released into water bodies. Many of these chemical contaminants persist in the environment and bio-accumulate in aquatic organisms. At present, toxicological tests are mostly based on laboratory tests, and effective methods for monitoring wild aquatic environments remain lacking. In the present study, we used a well-characterized toxic chemical, 3,3',4,4',5-polychlorinated biphenyl (PCB126), as an example to try to identify common biomarker genes to be used for predictive toxicity of this toxic substance. First, we used two laboratory fish models, the zebrafish (Danio rerio) and medaka (Oryzias latipes), to expose PCB126 to obtain liver transcriptomic data by RNA-seq. Comparative transcriptomic analyses indicated generally conserved and concerted changes from the two species, thus validating the transcriptomic data for biomarker gene selection. Based on the common up- and downregulated genes in the two species, we selected nine biomarker genes to further test in other fish species. The first validation experiment was carried out using the third fish species, Mozambique tilapia (Oreochromis mossambicus), and essentially, all these biomarker genes were validated for consistent responses with the two laboratory fish models. Finally, to develop universal PCR primers suitable for potentially all teleost fish species, we designed degenerate primers and tested them in the three fish species as well as in another fish species without a genomic sequence available: guppy (Poecilia reticulata). We found all the biomarker genes showed consistent response to PCB126 exposure in at least 50% of the species. Thus, our study provides a promising strategy to identify common biomarker genes to be used for teleost fish analyses. By using degenerate PCR primers and analyzing multiple biomarker genes, it is possible to develop diagnostic PCR arrays to predict water contamination from any wild fish species sampled in different water bodies.

Dataset Information

Identifying conserved UV exposure genes and mechanisms.

Publications

Identifying conserved UV exposure genes and mechanisms.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets