Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A fully integrated isoprenoid emissions model coupling emissions to photosynthetic characteristics.

ABSTRACT: The lack of a mechanistic basis has hampered modelling isoprene emission responses to environmental drivers, in particular the simulation of isoprene emissions under different CO₂ concentrations. Here, we advance previous semi-mechanistic model formulations by introducing a model that explicitly links electron availability for other purpose than carbon assimilation (or available energy for secondary metabolism processes; supply-constraint) and enzyme activity (capacity-constraint) to emissions. We furthermore investigate the sensitivity of the model to variations in photosynthetic and emission-specific parameters. By comparing species-specific simulations with experimental data, we demonstrate that differences in photosynthetic characteristics can explain inter-species differences in emissions. Interestingly, the seasonal development of emissions could also be explained to some degree by the change in energy supply from photosynthesis throughout the season. In addition, we show that the principal responses are not limited to isoprene but can be formulated to describe the emission of other light-dependent volatile species. The proposed model is suitable for implementation into regional and global models, particularly those that already provide species-specific photosynthesis estimates.

SUBMITTER: Grote R

PROVIDER: S-EPMC4415481 | biostudies-other | 2014 Aug

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

An Overview of the Isoprenoid Emissions From Tropical Plant Species.

Project description:Terrestrial vegetation is the largest contributor of isoprenoids (a group of biogenic volatile organic compounds (BVOCs)) to the atmosphere. BVOC emission data comes mostly from temperate regions, and less is known about BVOC emissions from tropical vegetation, even though it is estimated to be responsible for >70% of BVOC emissions. This review summarizes the available data and our current understanding of isoprenoid emissions from tropical plant species and the spatial and temporal variation in emissions, which are strongly species-specific and regionally variable. Emission models lacking foliar level data for tropical species need to revise their parameters to account for seasonal and diurnal variation due to differences in dependencies on temperature and light of emissions from plants in other ecosystems. More experimental information and determining how emission capacity varies during foliar development are warranted to account for seasonal variations more explicitly.

| S-EPMC9163954 | biostudies-literature

Projecting state-level air pollutant emissions using an integrated assessment model: GCAM-USA.

Project description:Integrated Assessment Models (IAMs) characterize the interactions among human and earth systems. IAMs typically have been applied to investigate future energy, land use, and emission pathways at global to continental scales. Recent directions in IAM development include enhanced technological detail, greater spatial and temporal resolution, and the inclusion of air pollutant emissions. These developments expand the potential applications of IAMs to include support for air quality management and for coordinated environmental, climate, and energy planning. Furthermore, these IAMs could help decision makers more fully understand tradeoffs and synergies among policy goals, identify important cross-sector interactions, and, via scenarios, consider uncertainties in factors such as population and economic growth, technology development, human behavior, and climate change. A version of the Global Change Assessment Model with U.S. state-level resolution (GCAM-USA) is presented that incorporates U.S.-specific emission factors, pollutant controls, and air quality and energy regulations. Resulting air pollutant emission outputs are compared to U.S. Environmental Protection Agency 2011 and projected inventories. A Quality Metric is used to quantify GCAM-USA performance for several pollutants at the sectoral and state levels. This information provides insights into the types of applications for which GCAM-USA is currently well suited and highlights where additional refinement may be warranted. While this analysis is specific to the U.S., the results indicate more generally the importance of enhanced spatial resolution and of considering national and sub-national regulatory constraints within IAMs.

| S-EPMC6054859 | biostudies-literature

Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli

Project description:Isopentenyl pyrophosphate (IPP) is the universal C5 precursor for isoprenoids, the largest class of natural products and frequent targets for metabolic engineering. In engineered microbial systems, IPP toxicity presents a challenge since its formation is unavoidable in the production of high-value, long-chain terpenes. In this work, we develop an experimental platform to study IPP toxicity in E. coli engineered to produce isoprenol, an IPP-derived C5 alcohol. We first characterize the physiological response to IPP accumulation, demonstrating that elevated levels of IPP are linked to growth inhibition, altered morphology, and reduced cell viability. We show that IPP toxicity selects for pathway “breakage”, using proteomics to identify a reduction in phosphomevalonate kinase (PMK) as a probable recovery mechanism. Next, we demonstrate that endogenous E. coli metabolism is globally impacted by IPP accumulation, which results in inhibited nutrient uptake, reduced ATP levels, and an apparent “pause” in metabolism. Finally, we suggest that IPP toxicity is mediated by the formation of an isoprenyl-ATP analog (ApppI). The complementary data presented here represent the most comprehensive assessment of IPP stress to date and suggest potential strategies for the alleviation of IPP and prenyl diphosphate toxicity.

2018-03-14 | GSE102672 | GEO

Capturing intracellular pH dynamics by coupling its molecular mechanisms within a fully tractable mathematical model.

Project description:We describe the construction of a fully tractable mathematical model for intracellular pH. This work is based on coupling the kinetic equations depicting the molecular mechanisms for pumps, transporters and chemical reactions, which determine this parameter in eukaryotic cells. Thus, our system also calculates the membrane potential and the cytosolic ionic composition. Such a model required the development of a novel algebraic method that couples differential equations for slow relaxation processes to steady-state equations for fast chemical reactions. Compared to classical heuristic approaches based on fitted curves and ad hoc constants, this yields significant improvements. This model is mathematically self-consistent and allows for the first time to establish analytical solutions for steady-state pH and a reduced differential equation for pH regulation. Because of its modular structure, it can integrate any additional mechanism that will directly or indirectly affect pH. In addition, it provides mathematical clarifications for widely observed biological phenomena such as overshooting in regulatory loops. Finally, instead of including a limited set of experimental results to fit our model, we show examples of numerical calculations that are extremely consistent with the wide body of intracellular pH experimental measurements gathered by different groups in many different cellular systems.

| S-EPMC3894979 | biostudies-literature

Fully integrated parity-time-symmetric electronics.

Project description:Harnessing parity-time symmetry with balanced gain and loss profiles has created a variety of opportunities in electronics from wireless energy transfer to telemetry sensing and topological defect engineering. However, existing implementations often employ ad hoc approaches at low operating frequencies and are unable to accommodate large-scale integration. Here we report a fully integrated realization of parity-time symmetry in a standard complementary metal-oxide-semiconductor process technology. Our work demonstrates salient parity-time symmetry features such as phase transition as well as the ability to manipulate broadband microwave generation and propagation beyond the limitations encountered by existing schemes. The system shows 2.1 times the bandwidth and 30% noise reduction compared to conventional microwave generation in the oscillatory mode, and displays large non-reciprocal microwave transport from 2.75 to 3.10 GHz in the non-oscillatory mode due to enhanced nonlinearities. This approach could enrich integrated circuit design methodology beyond well-established performance limits and enable the use of scalable integrated circuit technology to study topological effects in high-dimensional non-Hermitian systems.

| S-EPMC8930767 | biostudies-literature

Towards fully integrated photonic displacement sensors.

Project description:The field of optical metrology with its high precision position, rotation and wavefront sensors represents the basis for lithography and high resolution microscopy. However, the on-chip integration-a task highly relevant for future nanotechnological devices-necessitates the reduction of the spatial footprint of sensing schemes by the deployment of novel concepts. A promising route towards this goal is predicated on the controllable directional emission of the fundamentally smallest emitters of light, i.e., dipoles, as an indicator. Here we realize an integrated displacement sensor based on the directional emission of Huygens dipoles excited in an individual dipolar antenna. The position of the antenna relative to the excitation field determines its directional coupling into a six-way crossing of photonic crystal waveguides. In our experimental study supported by theoretical calculations, we demonstrate the first prototype of an integrated displacement sensor with a standard deviation of the position accuracy below λ/300 at room temperature and ambient conditions.

| S-EPMC7283363 | biostudies-literature

Benthic-pelagic coupling in the Barents Sea: an integrated data-model framework.

Project description:The Barents Sea is experiencing long-term climate-driven changes, e.g. modification in oceanographic conditions and extensive sea ice loss, which can lead to large, yet unquantified disruptions to ecosystem functioning. This key region hosts a large fraction of Arctic primary productivity. However, processes governing benthic and pelagic coupling are not mechanistically understood, limiting our ability to predict the impacts of future perturbations. We combine field observations with a reaction-transport model approach to quantify organic matter (OM) processing and disentangle its drivers. Sedimentary OM reactivity patterns show no gradients relative to sea ice extent, being mostly driven by seafloor spatial heterogeneity. Burial of high reactivity, marine-derived OM is evident at sites influenced by Atlantic Water (AW), whereas low reactivity material is linked to terrestrial inputs on the central shelf. Degradation rates are mainly driven by aerobic respiration (40-75%), being greater at sites where highly reactive material is buried. Similarly, ammonium and phosphate fluxes are greater at those sites. The present-day AW-dominated shelf might represent the future scenario for the entire Barents Sea. Our results represent a baseline systematic understanding of seafloor geochemistry, allowing us to anticipate changes that could be imposed on the pan-Arctic in the future if climate-driven perturbations persist. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.

| S-EPMC7481668 | biostudies-literature

Student perspectives of preparedness characteristics for clinical learning within a fully distributed veterinary teaching model.

Project description:The transition into the clinical environment is challenging and associated with significant stress and anxiety. This study aimed to examine the perspectives of students on the characteristics important for preparedness for clinical learning and the influence of gender, age, and graduate status on those perspectives. This descriptive, questionnaire-based study of 62 characteristics categorised into six themes was conducted within the Surrey School of Veterinary Medicine completed by 139 students commencing their final clinical year. The Friedman test and post-hoc Wilcoxon signed rank sum test explored for differences in ranking across the themes. Ordinal logistic regression and Mann-Whitney U pairwise comparisons were utilised to investigate for effects of gender, age, and graduate status on theme ranking. There was a significant difference (P <0.05) between medians for themes of preparedness characteristics with comparisons revealing willingness and communication and interaction as the most highly rated characteristics. Knowledge and understanding were viewed as the least important characteristic. Regression and pairwise Mann-Whitney U comparisons confirmed no significant effects (P >0.05) of gender, age or graduate status on student rating of preparedness characteristics. Integrating learning opportunities of those preparedness characteristics in the pre-clinical curriculum may improve students' preparedness for the clinical environment.

| S-EPMC8118455 | biostudies-literature

Photosynthetic decline in aging perennial grass is not fully explained by leaf nitrogen.

Project description:Aging in perennial plants is traditionally observed in terms of changes in end-of-season biomass; however, the driving phenological and physiological changes are poorly understood. We found that 3-year-old (mature) stands of the perennial grass Miscanthus×giganteus had 19-30% lower Anet than 1-year-old M.×giganteus (juvenile) stands; 10-34% lower maximum carboxylation rates of Rubisco and 34% lower light-saturated Anet (Asat). These changes could be related to nitrogen (N) limitations, as mature plants were larger and had 14-34% lower leaf N on an area basis (Na) than juveniles. However, N fertilization restored Na to juvenile levels but compensated only 50% of the observed decline in leaf photosynthesis with age. Comparison of leaf photosynthesis per unit of leaf N (PNUE) showed that mature stands had at least 26% lower PNUE than juvenile stands across all N fertilization rates, suggesting that other factors, besides N, may be limiting photosynthesis in mature stands. We hypothesize that sink limitations in mature stands could be causing feedback inhibition of photosynthesis which is associated with the age-related decline in photosynthesis.

| S-EPMC9730795 | biostudies-literature

Characteristics and toxicant emissions of JUUL electronic cigarettes.

Project description:IntroductionJUUL is an electronic cigarette (ECIG) with a compact form factor. It is prefilled with a liquid that is advertised to contain a high concentration of nicotine salt. JUUL commands 50% of the US ECIG market share, and its wide popularity with underage users has triggered unprecedented actions by the US FDA. Apart from its nicotine salt-containing liquid and compact form, a salient advertised design feature is a control circuit that limits the heating coil temperature, presumably reducing unwanted toxicants. In this study, several tobacco-flavoured JUUL devices were reverse engineered, and their aerosol emissions were studied.MethodsTotal nicotine and its partitioning (freebase and protonated), propylene glycol/vegetable glycerin (PG/VG) ratio, and carbonyls were quantified by gas chromatography (GC) and high performance liquid chromatography (HPLC). The temperature control functionality of JUUL was investigated using a temperature-controlled bath in which the coil was submerged.ResultsThe liquid nicotine concentration was found to be 69 mg/mL, and the liquid and aerosol PG/VG ratio was found to be 30/70. In 15 puffs, JUUL emitted 2.05 (0.08) mg of nicotine, overwhelmingly in the protonated form. Carbonyl yields were significantly lower than those reported for combustible cigarettes, but similar to other closed-system ECIG devices. The heating coil resistance was 1.6 (0.66) Ohm, while the maximum power delivered by the JUUL device was 8.1 W. The control circuit limited the peak operating temperature to approximately 215C.ConclusionsJUUL emits a high-nicotine concentration aerosol predominantly in the protonated form. JUUL's nicotine-normalised formaldehyde and total aldehyde yields are lower than other previously studied ECIGs and combustible cigarettes.

| S-EPMC7341718 | 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