Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1143189 | ENA |
REPOSITORIES: ENA
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Project description:Inherited mitochondrial DNA (mtDNA) diseases transmit maternally and cause severe phenotypes. Since no effective treatment or genetic screening is available, nuclear genome transfer between patients’ and healthy eggs to replace mutant mtDNAs holds promises. Since polar body contains very few mitochondria and share same genomic material as oocyte, here we perform polar body transfer to prevent the transmission of inherited mtDNA variants. We compare the value of different germline genome transfer (spindle-chromosome, pronuclear, first and second polar body) in a mouse model. Reconstructed embryos support normal fertilization and produce live offspring. Strikingly, genetic analysis confirms F1 generation after polar body transfer possesses minimal donor mtDNA carry-over compared with spindle-chromosome (low/medium carry-over) and pronuclear (medium/high carry-over) transfer. Moreover, mtDNA genotype remains stable in F2 generation of progeny after polar body transfer. Our preclinical model demonstrates polar body transfer holds great potential in preventing the transmission of inherited mtDNA diseases.
2014-06-19 | GSE56676 | GEO
Project description:Vibrio species represent one of the most diverse genera of marine bacteria known for their ubiquitous presence in natural aquatic systems. Several members of this genus including Vibrio harveyi are receiving increasing attention lately because they are becoming a source of health problems, especially for some marine organisms widely used in sea food industry. To learn about adaptation changes triggered by V. harveyi during its long-term persistence at elevated temperatures, we studied adaptation of this marine bacterium in sea water microcosms at 30 oC that closely mimicks the upper limits of sea surface temperatures recorded around the globe.
2019-02-05 | GSE113564 | GEO
Project description:Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high value lipid products. First success in applying reverse genetics makes Nannochloropsis species attractive models to investigate the cell and molecular biology and biochemistry of this fascinating organism group. (Principle findings) Here we present the assembly of the 28.7 Mb genome of Nannochloropsis oceanica CCMP1779. RNA sequencing data from N-replete and N-depleted growth conditions support a total of 11,973 genes, which in addition to automatic annotation were manually inspected to predict the biochemical repertoire for this organism. Among others, more than 100 genes putatively related to lipid metabolism, 114 predicted transcription factors and 109 transcriptional regulators were annotated. In addition, we provide protocols for the transformation of the sequenced strain. (Significance) The availability of genomic and transcriptomic data for Nannochloropsis oceanica CCMP1779, along with efficient transformation protocols provides a blueprint for future detailed gene functional analysis and phylogenetic comparison of Nannochloropsis species by a growing academic community focused on this genus. one sample each of nitrogen-replete and nitrogen-depleted conditions
2012-04-04 | E-GEOD-36959 | biostudies-arrayexpress
Project description:The available energy and carbon sources for prokaryotes in the deep ocean remain still largely enigmatic. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes. Shipboard experiments performed in the North Atlantic using Labrador Sea Water (~2000 m depth) amended with thiosulfate led to an enhanced prokaryotic dissolved inorganic carbon (DIC) fixation.
2021-04-30 | GSE136729 | GEO
Project description:Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS) and RNA-Seq (i.e. transcriptomics) to examine the long-term epigenomic dynamics of an experimenta evolution study under high CO2 in the marine cyanobacterium Trichodesmium. We identify m5C methylated sites that rapidly change in response to short-term high CO2 exposure, which are then maintained for 4.5 years even after adaptation (i.e. trait canalization). After 7 years of CO2 selection, high-CO2 triggered methylation levels return to ancestral, low-CO2 levels, consistent with genetic assimilation theory and observations in eukaryotic model systems. These data suggest a potential role for m5C methylation in prokaryotic trait canalization and identify genetic assimilation as an evolutionary mechanism of potential biogeochemical importance under global change factors.
2020-08-18 | GSE138174 | GEO
Project description:Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS) and RNA-Seq (i.e. transcriptomics) to examine the long-term epigenomic dynamics of an experimenta evolution study under high CO2 in the marine cyanobacterium Trichodesmium. We identify m5C methylated sites that rapidly change in response to short-term high CO2 exposure, which are then maintained for 4.5 years even after adaptation (i.e. trait canalization). After 7 years of CO2 selection, high-CO2 triggered methylation levels return to ancestral, low-CO2 levels, consistent with genetic assimilation theory and observations in eukaryotic model systems. These data suggest a potential role for m5C methylation in prokaryotic trait canalization and identify genetic assimilation as an evolutionary mechanism of potential biogeochemical importance under global change factors.
2020-08-18 | GSE138171 | GEO
Project description:Polar cod, a key fish species in the arctic marine foodweb is vulnerable to effects of pollution from offshore petroleum related activities in the Arctic and sub-arctic region. The study was conducted to map transcriptome responses to in Polar cod (Boreogadus saida) liver slice culture exposed to benzo[a]pyrene (BaP) in the presence or absence of physiological levels of ethynylestradiol (EE2). BaP is a polycyclic aromatic hydrocarbon (PAH), also found in crude oil contaminants. PAHs such as BaP are among the most toxic compounds of crude oil. Precision-cut liver slice cultures from five female polar cod (n = 5/ group, paired design) were exposed to BaP alone (10 µM), or in combination with low concentrations of EE2 (5 nM), to mimic physiological estradiol levels in early vitellogenic female fish. Transcriptome analysis (RNA-seq) was performed after 72 h exposure in culture. The results provide a global view of transcriptome responses to BaP, EE2 and their mixture. In the mixture exposure, BaP resulted attenuation of EE2 stimulated gene expression (anti-estrogenic effects). The results from this ex vivo experiment suggest that pollutants that activate the Ahr pathway such as the PAH compound BaP can result in anti-estrogenic effects that may lead to endocrine disruption in polar cod.
2021-05-24 | E-MTAB-10509 | biostudies-arrayexpress
Project description:Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high value lipid products. First success in applying reverse genetics makes Nannochloropsis species attractive models to investigate the cell and molecular biology and biochemistry of this fascinating organism group. (Principle findings) Here we present the assembly of the 28.7 Mb genome of Nannochloropsis oceanica CCMP1779. RNA sequencing data from N-replete and N-depleted growth conditions support a total of 11,973 genes, which in addition to automatic annotation were manually inspected to predict the biochemical repertoire for this organism. Among others, more than 100 genes putatively related to lipid metabolism, 114 predicted transcription factors and 109 transcriptional regulators were annotated. In addition, we provide protocols for the transformation of the sequenced strain. (Significance) The availability of genomic and transcriptomic data for Nannochloropsis oceanica CCMP1779, along with efficient transformation protocols provides a blueprint for future detailed gene functional analysis and phylogenetic comparison of Nannochloropsis species by a growing academic community focused on this genus.
2012-04-04 | GSE36959 | GEO