Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cell proliferation at 122 degrees C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation.

ABSTRACT: We have developed a technique for cultivation of chemolithoautotrophs under high hydrostatic pressures that is successfully applicable to various types of deep-sea chemolithoautotrophs, including methanogens. It is based on a glass-syringe-sealing liquid medium and gas mixture used in conjunction with a butyl rubber piston and a metallic needle stuck into butyl rubber. By using this technique, growth, survival, and methane production of a newly isolated, hyperthermophilic methanogen Methanopyrus kandleri strain 116 are characterized under high temperatures and hydrostatic pressures. Elevated hydrostatic pressures extend the temperature maximum for possible cell proliferation from 116 degrees C at 0.4 MPa to 122 degrees C at 20 MPa, providing the potential for growth even at 122 degrees C under an in situ high pressure. In addition, piezophilic growth significantly affected stable carbon isotope fractionation of methanogenesis from CO(2). Under conventional growth conditions, the isotope fractionation of methanogenesis by M. kandleri strain 116 was similar to values (-34 per thousand to -27 per thousand) previously reported for other hydrogenotrophic methanogens. However, under high hydrostatic pressures, the isotope fractionation effect became much smaller (< -12 per thousand), and the kinetic isotope effect at 122 degrees C and 40 MPa was -9.4 per thousand, which is one of the smallest effects ever reported. This observation will shed light on the sources and production mechanisms of deep-sea methane.

SUBMITTER: Takai K

PROVIDER: S-EPMC2490668 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Reactivity oscillation in the heavy-light-heavy Cl + CH4 reaction.

Project description:It has long been predicted that oscillatory behavior exists in reactivity as a function of collision energy for heavy-light-heavy (HLH) chemical reactions in which a light atom is transferred between two heavy atoms or groups of atoms, but direct observation of such a behavior in bimolecular reactions remains a challenge. Here we report a joint theoretical and crossed-molecular-beam study on the Cl + CH4 ? HCl + CH3 reaction. A distinctive peak at a collision energy of 0.15 eV for the CH3(v = 0) product was experimentally detected in the backward scattering direction. Detailed quantum-dynamics calculations on a highly accurate potential energy surface revealed that this feature originates from the reactivity oscillation in this HLH polyatomic reaction. We anticipate that such reactivity oscillations exist in many HLH reactions involving polyatomic reagents.

| S-EPMC7196785 | biostudies-literature

Microfluidic devices for cell cultivation and proliferation.

Project description:Microfluidic technology provides precise, controlled-environment, cost-effective, compact, integrated, and high-throughput microsystems that are promising substitutes for conventional biological laboratory methods. In recent years, microfluidic cell culture devices have been used for applications such as tissue engineering, diagnostics, drug screening, immunology, cancer studies, stem cell proliferation and differentiation, and neurite guidance. Microfluidic technology allows dynamic cell culture in microperfusion systems to deliver continuous nutrient supplies for long term cell culture. It offers many opportunities to mimic the cell-cell and cell-extracellular matrix interactions of tissues by creating gradient concentrations of biochemical signals such as growth factors, chemokines, and hormones. Other applications of cell cultivation in microfluidic systems include high resolution cell patterning on a modified substrate with adhesive patterns and the reconstruction of complicated tissue architectures. In this review, recent advances in microfluidic platforms for cell culturing and proliferation, for both simple monolayer (2D) cell seeding processes and 3D configurations as accurate models of in vivo conditions, are examined.

| S-EPMC3829894 | biostudies-other

Pressure- and Temperature-Induced Insertion of N2, O2 and CH4 to Ag-Natrolite.

Project description:This paper aimed to investigate the structural and chemical changes of Ag-natrolite (Ag16Al16Si24O80·16H2O, Ag-NAT) in the presence of different pressure transmitting mediums (PTMs), such as N2, O2 and CH4, up to ~8 GPa and 250 °C using in situ synchrotron X-ray powder diffraction and Rietveld refinement. Pressure-induced insertion occurs in two stages in the case of N2 and O2 runs, as opposed to the CH4 run. First changes of the unit cell volume in N2, O2 and CH4 runs are observed at 0.88(5) GPa, 1.05(5) GPa and 1.84(5) GPa with increase of 5.7(1)%, 5.5(1)% and 5.7(1)%, respectively. Subsequent volume changes of Ag-natrolite in the presence of N2 and O2 appear at 2.15(5) GPa and 5.24(5) GPa with a volume increase of 0.8(1)% and a decrease of 3.0(1)%, respectively. The bulk moduli of the Ag-NAT change from 42(1) to 49(7), from 38(1) to 227(1) and from 49(3) to 79(2) in the case of N2, O2 and CH4 runs, respectively, revealing that the Ag-NAT becomes more incompressible after each insertion of PTM molecules. The shape of the channel window of the Ag-NAT changes from elliptical to more circular after the uptake of N2, O2 and CH4. Overall, the experimental results of Ag-NAT from our previous data and this work establish that the onset pressure exponentially increases with the molecular size. The unit cell volumes of the expanded (or contracted) phases of the Ag-NAT have a linear relationship and limit to maximally expand and contract upon pressure-induced insertion.

| S-EPMC7560438 | biostudies-literature

Co-cultivation of the strictly anaerobic methanogen Methanosarcina barkeri with aerobic methanotrophs in an oxygen-limited membrane bioreactor.

Project description:Wetlands contribute to 30% of global methane emissions due to an imbalance between microbial methane production and consumption. Methanogenesis and methanotrophy have mainly been studied separately, and little is known about their potential interactions in aquatic environments. To mimic the interaction between methane producers and oxidizers in the environment, we co-cultivated the methanogenic archaeon Methanosarcina barkeri with aerobic Methylocystaceae methanotrophs in an oxygen-limited bioreactor using acetate as methanogenic substrate. Methane, acetate, dissolved oxygen, available nitrogen, pH, temperature, and cell density were monitored to follow system stability and activity. Stable reactor operation was achieved for two consecutive periods of 2 months. Fluorescence in situ hybridization micrographs indicated close association between both groups of microorganisms. This association suggests that the methanotrophs profit from direct access to the methane that is produced from acetate, while methanogens are protected by the concomitant oxygen consumption of the methanotrophs. This proof of principle study can be used to set up systems to study their responses to environmental changes.

| S-EPMC5999129 | biostudies-literature

Methanogen

Project description:Methanogens sequencing

| PRJNA669286 | ENA

methanogen

Project description:methanogen Raw sequence reads

| PRJNA353878 | ENA

Heavy-machinery traffic impacts methane emissions as well as methanogen abundance and community structure in oxic forest soils.

Project description:Temperate forest soils are usually efficient sinks for the greenhouse gas methane, at least in the absence of significant amounts of methanogens. We demonstrate here that trafficking with heavy harvesting machines caused a large reduction in CH(4) consumption and even turned well-aerated forest soils into net methane sources. In addition to studying methane fluxes, we investigated the responses of methanogens after trafficking in two different forest sites. Trafficking generated wheel tracks with different impact (low, moderate, severe, and unaffected). We found that machine passes decreased the soils' macropore space and lowered hydraulic conductivities in wheel tracks. Severely compacted soils yielded high methanogenic abundance, as demonstrated by quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes, whereas these sequences were undetectable in unaffected soils. Even after a year after traffic compression, methanogen abundance in compacted soils did not decline, indicating a stability of methanogens here over time. Compacted wheel tracks exhibited a relatively constant community structure, since we found several persisting mcrA sequence types continuously present at all sampling times. Phylogenetic analysis revealed a rather large methanogen diversity in the compacted soil, and most mcrA gene sequences were mostly similar to known sequences from wetlands. The majority of mcrA gene sequences belonged either to the order Methanosarcinales or Methanomicrobiales, whereas both sites were dominated by members of the families Methanomicrobiaceae Fencluster, with similar sequences obtained from peatland environments. The results show that compacting wet forest soils by heavy machinery causes increases in methane production and release.

| S-EPMC3165404 | biostudies-literature

HNF-4α inhibits hepatocellular carcinoma cell proliferation through mir-122-adam17 pathway.

Project description:Hepatocellular carcinoma (HCC) is one of the most common human cancers, its prevalence and severity need us to discover novel early diagnostic biomarkers and new therapeutic strategies. MicroRNA-122 is the most abundant microRNA in the liver, and acts as a tumor suppressor and represses HCC development. In our study we showed that HNF-4α and MiR-122 were down-regulated significantly in hepatocellular carcinoma. Over-expression of HNF-4α inhibit hepatocellular carcinoma cells proliferation. And miR-122 is one of the downstream effector of HNF-4α. Up-regulated miR-122 inhibited hepatocellular carcinoma cells proliferation through regulating ADAM17. Collectively, our results suggested that HNF-4α could inhibit hepatocellular carcinoma proliferation with miR-122 being a downstream target of it. And miR-122 would inhibit hepatocellular carcinoma proliferation by regulating ADAM17 signal pathway.

| S-EPMC7094838 | biostudies-literature

Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil.

Project description:In recent years, culture-independent methods have been used in preference to traditional isolation techniques for microbial community analysis. However, it is questionable whether uncultured organisms from a given sample are important for determining the impact of anthropogenic stress on indigenous communities. To investigate this, soil samples were taken from a site with patchy metal contamination, and the bacterial community structure was assessed with a variety of approaches. There were small differences in microscopic epifluorescence bacterial counts. Denaturing gradient gel electrophoresis (DGGE) profiles of 16S rRNA gene fragments (16S-DGGE) amplified directly from soil samples were highly similar. A clone library generated from the most contaminated sample revealed a diverse bacterial community, which showed similarities to pristine soil communities from other studies. However, the proportion of bacteria from the soil samples that were culturable on standard plate-counting media varied between 0.08 and 2.2%, and these values correlated negatively with metal concentrations. The culturable communities from each sample were compared by 16S-DGGE of plate washes and by fatty acid profiling of individual isolates. Each approach indicated that there were considerable differences between the compositions of the culturable communities from each sample. DGGE bands from both culture-based and culture-independent approaches were sequenced and compared. These data indicated that metal contamination did not have a significant effect on the total genetic diversity present but affected physiological status, so that the number of bacteria capable of responding to laboratory culture and their taxonomic distribution were altered. Thus, it appears that plate counts may be a more appropriate method for determining the effect of heavy metals on soil bacteria than culture-independent approaches.

| S-EPMC161537 | biostudies-literature

MiR-122 inhibits cell proliferation and tumorigenesis of breast cancer by targeting IGF1R.

Project description:miRNAs are emerging as critical regulators in carcinogenesis and tumor progression. Recently, microRNA-122 (miR-122) has been proved to play an important role in hepatocellular carcinoma, but its functions in the context of breast cancer (BC) remain unknown. In this study, we report that miR-122 is commonly downregulated in BC specimens and BC cell lines with important functional consequences. Overexpression of miR-122 not only dramatically suppressed cell proliferation, colony formation by inducing G1-phase cell-cycle arrest in vitro, but also reduced tumorigenicity in vivo. We then screened and identified a novel miR-122 target, insulin-like growth factor 1 receptor (IGF1R), and it was further confirmed by luciferase assay. Overexpression of miR-122 would specifically and markedly reduce its expression. Similar to the restoring miR-122 expression, IGF1R downregulation suppressed cell growth and cell-cycle progression, whereas IGF1R overexpression rescued the suppressive effect of miR-122. To identify the mechanisms, we investigated the Akt/mTOR/p70S6K pathway and found that the expression of Akt, mTOR and p70S6K were suppressed, whereas re-expression of IGF1R which did not contain the 3'UTR totally reversed the inhibition of Akt/mTOR/p70S6K signal pathway profile. We also identified a novel, putative miR-122 target gene, PI3CG, a member of PI3K family, which further suggests miR-122 may be a key regulator of the PI3K/Akt pathway. In clinical specimens, IGF1R was widely overexpressed and its mRNA levels were inversely correlated with miR-122 expression. Taken together, our results demonstrate that miR-122 functions as a tumor suppressor and plays an important role in inhibiting the tumorigenesis through targeting IGF1R and regulating PI3K/Akt/mTOR/p70S6K pathway. Given these, miR-122 may serve as a novel therapeutic or diagnostic/prognostic-target for treating BC.

| S-EPMC3466252 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data