Dataset Information

Emerging semantics to link phenotype and environment.

ABSTRACT: Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.

SUBMITTER: Thessen AE

PROVIDER: S-EPMC4690371 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Publications

Emerging semantics to link phenotype and environment.

Thessen Anne E AE Bunker Daniel E DE Buttigieg Pier Luigi PL Cooper Laurel D LD Dahdul Wasila M WM Domisch Sami S Franz Nico M NM Jaiswal Pankaj P Lawrence-Dill Carolyn J CJ Midford Peter E PE Mungall Christopher J CJ Ramírez Martín J MJ Specht Chelsea D CD Vogt Lars L Vos Rutger Aldo RA Walls Ramona L RL White Jeffrey W JW Zhang Guanyang G Deans Andrew R AR Huala Eva E Lewis Suzanna E SE Mabee Paula M PM

PeerJ 20151214

Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and fle ...[more]

PMID: 26713234

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Project description:During maturation oocytes undergo a recently discovered mitochondrial proteome remodeling event in flies1, frogs1, and humans2. This oocyte mitochondrial remodeling, which includes substantial changes in electron transport chain (ETC) subunit abundance1,2, is regulated by maternal insulin signaling1. Why oocytes undergo mitochondrial remodeling is unknown, with some speculating that it might be an evolutionarily conserved mechanism to protect oocytes from genotoxic damage by reactive oxygen species (ROS)2. In Caenorhabditis elegans, we previously found that maternal exposure to osmotic stress drives a 50-fold increase in offspring survival in response to future osmotic stress3. Like mitochondrial remodeling, we found that this intergenerational adaptation is also regulated by insulin signaling to oocytes3. Here, we used proteomics and genetic manipulations to show that insulin signaling to oocytes regulates offspring's ability to adapt to future stress via a mechanism that depends on ETC composition in maternal oocytes. Specifically, we found that maternally expressed mutant alleles of nduf-7 (complex I subunit) or isp-1 (complex III subunit) altered offspring's response to osmotic stress at hatching independently of offspring genotype. Furthermore, we found that expressing wild-type isp-1 in germ cells (oocytes) was sufficient to restore offspring's normal response to osmotic stress. Chemical mutagenesis screens revealed that maternal ETC composition regulates offspring's response to stress by altering AMP kinase function in offspring which in turn regulates both ATP and glycerol metabolism in response to continued osmotic stress. To our knowledge, these data are the first to show that proper oocyte ETC composition is required to link a mother's environment to adaptive changes in offspring metabolism. The data also raise the possibility that the reason diverse animals exhibit insulin regulated remodeling of oocyte mitochondria is to tailor offspring metabolism to best match the environment of their mother.

Project description:Oocytes undergo a recently discovered mitochondrial proteome remodeling event in flies1, frogs1, and humans2. This oocyte mitochondrial remodeling event, which includes substantial changes in electron transport chain (ETC) subunit abundance1,2, is regulated by maternal insulin signaling1. However, why oocytes undergo mitochondrial remodeling is unknown, with some speculating that it might be a conserved mechanism to protect oocytes from genotoxic damage by reactive oxygen species (ROS)2. In Caenorhabditis elegans, we previously found that maternal exposure to osmotic stress drives a 50-fold increase in offspring survival in response to future osmotic stress, and that this intergenerational adaptation is regulated by insulin signaling to oocytes3. Here, we used proteomics and genetic manipulations to show that insulin signaling to oocytes regulates offspring’s ability to adapt to future stress via a mechanism that depends on ETC composition in maternal germ cells/oocytes. Specifically, we found that maternally expressed mutant alleles of nduf-7 (complex I subunit) or isp-1 (complex III subunit) altered offspring’s response to osmotic stress at hatching independently of offspring genotype. Furthermore, we found that expressing wild-type isp-1 in maternal germ cells (oocytes) was sufficient to restore offspring’s normal response to osmotic stress. Chemical mutagenesis screens revealed that oocyte ETC composition regulates offspring’s response to osmotic stress by altering AMP kinase function in offspring which in turn regulates both ATP and glycerol metabolism in offspring in response to continued osmotic stress. To our knowledge, these data are the first to show that changes in oocyte mitochondrial ETC composition can affect an animal phenotype that manifests after embryonic development is complete. The data also suggest that the reason diverse animals exhibit insulin regulated remodeling of oocyte mitochondria might be to tailor offspring metabolism to best match the environment of their mother.

Dataset Information

Emerging semantics to link phenotype and environment.

Publications

Emerging semantics to link phenotype and environment.

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