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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A Brief Overview of Reactive Transport Codes Used in CO 2 Applications

Reactive transport modelling consists of computational and numerical models that describe the coupled physical, chemical, mechanical, and biological processes interacting with each other over a broad range of spatial and temporal scales. This report reviews some of the reactive transport codes available in the literature for carbon dioxide (CO 2 ) applications and can assist the scientific community with the applicability of each code to solve a specific problem. Approaches implemented in these codes can be categorized in three groups: (i) continuum-scale, (ii) pore-scale, and (iii) hybrid-scale approaches. Theoretical foundations, numerical implementations, and application examples using the models are described. In the continuum approach, flow and transport are formulated in terms of a representative control volume of the medium and coupled with geochemical reactions. The medium is characterized by bulk parameters such as porosity, permeability, or reactive surface area. In the pore-scale approach, each point of space in the pore network is occupied by either a fluid or solid phase. The pore-scale approach requires an exact knowledge of the spatial and temporal phase distribution. In the hybrid-scale approach, media are described by multiple characteristic length-scales, with some regions using a pore-scale approach while others used a continuum approach.

01 COAL, LIGNITE, AND PEAT↗
NASA NTRS2004

Extracellular mass transport considerations for space flight research concerning suspended and adherent in vitro cell cultures

Conducting biological research in space requires consideration be given to isolating appropriate control parameters. For in vitro cell cultures, numerous environmental factors can adversely affect data interpretation. A biological response attributed to microgravity can, in theory, be explicitly correlated to a specific lack of weight or gravity-driven motion occurring to, within or around a cell. Weight can be broken down to include the formation of hydrostatic gradients, structural load (stress) or physical deformation (strain). Gravitationally induced motion within or near individual cells in a fluid includes sedimentation (or buoyancy) of the cell and associated shear forces, displacement of cytoskeleton or organelles, and factors associated with intra- or extracellular mass transport. Finally, and of particular importance for cell culture experiments, the collective effects of gravity must be considered for the overall system consisting of the cells, their environment and the device in which they are contained. This does not, however, rule out other confounding variables such as launch acceleration, on orbit vibration, transient acceleration impulses or radiation, which can be isolated using onboard centrifuges or vibration isolation techniques. A framework is offered for characterizing specific cause-and-effect relationships for gravity-dependent responses as a function of the above parameters.

Non-NASA Center↗
DOE OSTI2020

Micro-XRF mapping and quantitative assessment of Cd in rice ( Oryza sativa L.) roots

Understanding Cd uptake and distribution in rice roots is important for breeding varieties that do not accumulate Cd in the grain to any large extent. Here, we examined the physiological and molecular factors responsible for Cd uptake and transport differences between two japonica rice cultivars prescreened as high (zhefu7) or low (Xiangzaoxian45) accumulators of Cd in the grain. No significant differences in Cd uptake between the two cultivars were observed; however, Xiangzaoxian45 retained most of the absorbed Cd in the roots, whereas zhefu7 showed higher transport of Cd from the root to the shoot, regardless of the duration of exposure to Cd. The inability to sequester Cd into root vacuoles caused high accumulation of Cd in the grain in zhefu7, whereas inefficient transport of Cd from roots to shoots in Xiangzaoxian45 caused low accumulation of Cd in the grain. Cd sequestration in the roots and transport from the root to the shoot were greatly influenced by the expression patterns of transport-related genes OsHMA3 and OsHMA2, respectively. Further, micro-X-ray fluorescence spectroscopy mapping confirmed that more Cd was sequestered in the roots of Xiangzaoxian45 than in those of zhefu7, with a significant amount of Cd localized in the root hairs, as well as in the meristematic and elongation zones, and dermal and stele tissues. Finally, we propose that effective Cd sequestration in root vacuoles was the major determinant of divergent Cd-accumulation patterns in the two rice cultivars under study.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1989

Gravity receptors and responses

The overall process of gravity sensing and response processes in plants may be divided conveniently into at least four components or stages: Stimulus susception (a physical event, characteristically the input to the G receptor system of environmental information about the G force magnitude, its vector direction, or both); information perception (an influence of susception on some biological structure or process that can be described as the transformation of environmental information into a biologicallly meaningful change); information transport (the export, if required, of an influence (often chemical) to cells and organs other than those at the sensor location); and biological response (almost always (in plants) a growth change of some kind). Some analysts of the process identify, between information perception and information transport, an additional stage, transduction, which would emphasize the importance of a transformation from one form of information to another, for example from mechanical statolith displacement to an electric, chemical, or other alteration that was its indirect result. These four (or five) stages are temporally sequential. Even if all that occurs at each stage can not be confidently identified, it seems evident that during transduction and transport, matters dealt with are found relatively late in the information flow rather than at the perception stage. As more and more is learned about the roles played by plant hormones which condition the G responses, the mechanism(s) of perception which should be are not necessarily better understood. However, if by asking the right questions and being lucky with experiments perhaps the discovery of how some process (such as sedimentation of protoplasmic organelles) dictates what happens down stream in the information flow sequence may be made.

Brown, Allan H.↗
NASA NTRS1996

A New Generation Fiber Optic Probe: Characterization of Biological Fluids, Protein Crystals and Ophthalmic Diseases

A new fiber optic probe developed for determining transport properties of sub-micron particles in fluids experiments in a microgravity environment has been applied to characterize particulate dispersions/suspensions in various challenging environments which have been hitherto impossible. The probe positioned in front of a sample delivers a low power light (few nW - 3mW) from a laser and guides the light which is back scattered by the suspended particles through a receiving optical fiber to a photo detector and to a digital correlator. The probe provides rapid determination of macromolecular diffusivities and their respective size distributions. It has been applied to characterize various biological fluids, protein crystals, and ophthalmic diseases.

Ansari, Rafat R.↗
DOE OSTI2025

Structure and mechanism of human vesicular polyamine transporter

Polyamines play essential roles in gene expression and modulate neuronal transmission in mammals. Vesicular polyamine transporters (VPAT) from the SLC18 family exploit the transmembrane H + gradient to translocate polyamines into secretory vesicles, enabling the quantal release of polyamine neuromodulators and underpinning learning and memory formation. Here, we report the cryo-electron microscopy structures of human VPAT in complex with spermine, spermidine, H + , or tetrabenazine, elucidating discrete lumen-facing states of the antiporter and pivotal interactions between VPAT and its substrate or inhibitor. Leveraging structure-inspired mutagenesis studies and protein structure prediction, we deduce an unforeseen mechanism whereby the polyamine and H + compete for multiple acidic protein residues both directly and indirectly, and rationalize how the antidopaminergic therapeutic tetrabenazine impedes vesicular transport of polyamines. This study unravels the mechanism of an H + -coupled polyamine antiporter, reveals mechanistic diversity between VPAT and other SLC18 antiporters, and raises new prospects for combating human disorders of polyamine homeostasis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The mitochondrial Cu + transporter PiC2 (SLC25A3) is a target of MTF1 and contributes to the development of skeletal muscle in vitro

The loading of copper (Cu) into cytochrome c oxidase (COX) in mitochondria is essential for energy production in cells. Extensive studies have been performed to characterize mitochondrial cuproenzymes that contribute to the metallation of COX, such as Sco1, Sco2, and Cox17. However, limited information is available on the upstream mechanism of Cu transport and delivery to mitochondria, especially through Cu-impermeable membranes, in mammalian cells. The mitochondrial phosphate transporter SLC25A3, also known as PiC2, binds Cu + and transports the ion through these membranes in eukaryotic cells, ultimately aiding in the metallation of COX. We used the well-established differentiation model of primary myoblasts derived from mouse satellite cells, wherein Cu availability is necessary for growth and maturation, and showed that PiC2 is a target of MTF1, and its expression is both induced during myogenesis and favored by Cu supplementation. PiC2 deletion using CRISPR/Cas9 showed that the transporter is required for proliferation and differentiation of primary myoblasts, as both processes are delayed upon PiC2 knock-out. The effects of PiC2 deletion were rescued by the addition of Cu to the growth medium, implying the deleterious effects of PiC2 knockout in myoblasts may be in part due to a failure to deliver sufficient Cu to the mitochondria, which can be compensated by other mitochondrial cuproproteins. Co-localization and co-immunoprecipitation of PiC2 and COX also suggest that PiC2 may participate upstream in the copper delivery chain into COX, as verified by in vitro Cu + -transfer experiments. These data indicate an important role for PiC2 in both the delivery of Cu to the mitochondria and COX, favoring the differentiation of primary myoblasts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Redundant roles of four ZIP family members in zinc homeostasis and seed development in Arabidopsis thaliana

Zinc (Zn) is essential for normal plant growth and development. The Zn-regulated transporter, iron-regulated transporter (IRT)-like protein (ZIP) family members are involved in Zn transport and cellular Zn homeostasis throughout the domains of life. In this study, we have characterized four ZIP transporters from Arabidopsis thaliana (IRT3, ZIP4, ZIP6, and ZIP9) to better understand their functional roles. The four ZIP proteins can restore the growth defect of a yeast Zn uptake mutant and are upregulated under Zn deficiency. Single and double mutants show no phenotypes under Zn-sufficient or Zn-limited growth conditions. In contrast, triple and quadruple mutants show impaired growth irrespective of external Zn supply due to reduced Zn translocation from root to shoot. All four ZIP genes are highly expressed during seed development, and siliques from all single and higher-order mutants exhibited an increased number of abnormal seeds and decreased Zn levels in mature seeds relative to wild type. The seed phenotypes could be reversed by supplementing the soil with Zn. Finally, our data demonstrate that IRT3, ZIP4, ZIP6, and ZIP9 function redundantly in maintaining Zn homeostasis and seed development in A. thaliana.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Porin-Inspired Ionomers with sub-nm Gated Ion Channels for High Ion Conductivity and Selectivity (Final Project Report (2026))

The physiological functions of living systems heavily rely on biological ion channels, whose malfunction can lead to disease. These channels enable selective and regulated transport of water, ions, or small molecules across membranes. Analogously, ionomers used in energy conversion and storage technologies govern ion transport within membrane separators and catalyst binder layers. This DOE Office of Science Early CAREER project aimed to achieve molecular-level control over ionic conductivity and ion permselectivity by translating the functionalities of biological, gated ion channels into a novel class of ion-conducting polymers (ionomers) incorporating macrocyclic calix[4]arene-based repeat units. The overarching goal was to establish fundamental design principles and elucidate proton conduction mechanisms through strategic design of macrocyclic calix[4]arene-containing ionomers, with close relevance to energy conversion and storage devices, including proton exchange membrane fuel cells (PEMFCs). The project leveraged sub-nm-sized macrocyclic pores to facilitate exceptionally fast ion transport (beneficial to addressing sluggish ORR kinetics of PEMFC electrodes) and achieve functionalities of ionic diodes under applied electrochemical fields, beneficial for selective transport/separation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

PLAT domain protein 1 (PLAT1/PLAFP) binds to the Arabidopsis thaliana plasma membrane and inserts a lipid

Robust agricultural yields depend on the plant's ability to fix carbon amid variable environmental conditions. Over seasonal and diurnal cycles, the plant must constantly adjust its metabolism according to available resources or external stressors. The metabolic changes that a plant undergoes in response to stress are well understood, but the long-distance signaling mechanisms that facilitate communication throughout the plant are less studied. The phloem is considered the predominant conduit for the bidirectional transport of these signals in the form of metabolites, nucleic acids, proteins, and lipids. Lipid trafficking through the phloem in particular attracted our attention due to its reliance on soluble lipid-binding proteins (LBP) that generate and solubilize otherwise membrane-associated lipids. The Phloem Lipid-Associated Family Protein (PLAFP) from Arabidopsis thaliana is generated in response to abiotic stress as is its lipid-ligand phosphatidic acid (PA). PLAFP is proposed to transport PA through the phloem in response to drought stress. To understand the interactions between PLAFP and PA, nearly 100 independent systems comprised of the protein and one PA, or a plasma membrane containing varying amounts of PA, were simulated using atomistic classical molecular dynamics methods. In these simulations, PLAFP is found to bind to plant plasma membrane models independent of the PA concentration. When bound to the membrane, PLAFP adopts a binding pose where W41 and R82 penetrate the membrane surface and anchor PLAFP. This triggers a separation of the two loop regions containing W41 and R82. Subsequent simulations indicate that PA insert into the β -sandwich of PLAFP, driven by interactions with multiple amino acids besides the W41 and R82 identified during the insertion process. Finally, fine-tuning the protein-membrane and protein-PA interface by mutating a selection of these amino acids may facilitate engineering plant signaling processes by modulating the binding response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Two TonB-dependent transporters in Methylosinus trichosporium OB3b are responsible for uptake of different forms of methanobactin and are involved in the canonical ‘copper switch’

Copper is an important component of methanotrophic physiology as it controls the expression and activity of alternative forms of methane monooxygenase (MMO). To collect copper, some methanotrophs secrete a chalkophore or copper-binding compound called methanobactin (MB). MB is a ribosomally synthesized post-translationally modified polypeptide (RiPP) that, after binding copper, is collected by MbnT, a TonB-dependent transporter (TBDT). Structurally different forms of MB have been characterized, and here we show that different forms of MB are collected by specific TBDTs. Further, we report that in the model methanotroph, Methylosinus trichosporium OB3b, expression of the TBDT required for uptake of a different MB made by Methylocystis sp. strain SB2 (MB-SB2), is induced in the presence of MB-SB2, suggesting that methanotrophs have developed specific machinery and regulatory systems to actively take up MB from other methanotrophs for copper collection. Moreover, the canonical “copper-switch” in Ms. trichosporium OB3b that controls expression of alternative MMOs is apparent if one of the two TBDTs required for MB-OB3b and MB-SB2 uptake is knocked out, but is disrupted if both TBDTs are knocked out. Furthermore, these data indicate that MB uptake, including the uptake of exogenous MB, plays an important role in the copper switch in M. trichosporium OB3b and thus overall activity. Based on these data, we propose a revised model for the “copper-switch” in this methanotroph that involves MB uptake.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2000

Diversity and regulation of plant Ca2+ pumps: insights from expression in yeast

The spatial and temporal regulation of calcium concentration in plant cells depends on the coordinate activities of channels and active transporters located on different organelles and membranes. Several Ca2+ pumps have been identified and characterized by functional expression of plant genes in a yeast mutant (K616). This expression system has opened the way to a genetic and biochemical characterization of the regulatory and catalytic features of diverse Ca2+ pumps. Plant Ca(2+)-ATPases fall into two major types: AtECA1 represents one of four or more members of the type IIA (ER-type) Ca(2+)-ATPases in Arabidopsis, and AtACA2 is one of seven or more members of the type IIB (PM-type) Ca(2+)-ATPases that are regulated by a novel amino terminal domain. Type IIB pumps are widely distributed on membranes, including the PM (plasma membrane), vacuole, and ER (endoplasmic reticulum). The regulatory domain serves multiple functions, including autoinhibition, calmodulin binding, and sites for modification by phosphorylation. This domain, however, is considerably diverse among several type IIB ATPases, suggesting that the pumps are differentially regulated. Understanding of Ca2+ transporters at the molecular level is providing insights into their roles in signaling networks and in regulating fundamental processes of cell biology.

Review, Academic↗
DOE OSTI2020

Ubiquity and functional uniformity in CO2 concentrating mechanisms in multiple phyla of Bacteria is suggested by a diversity and prevalence of genes encoding candidate dissolved inorganic carbon transporters

ABSTRACT Autotrophic microorganisms catalyze the entry of dissolved inorganic carbon (DIC; = CO2 + HCO3− + CO32−) into the biological component of the global carbon cycle, despite dramatic differences in DIC abundance and composition in their sometimes extreme environments. “Cyanobacteria” are known to have CO2 concentrating mechanisms (CCMs) to facilitate growth under low CO2 conditions. These CCMs consist of carboxysomes, containing enzymes ribulose 1,5-bisphosphate oxygenase and carbonic anhydrase, partnered to DIC transporters. CCMs and their DIC transporters have been studied in a handful of other prokaryotes, but it was not known how common CCMs were beyond “Cyanobacteria”. Since it had previously been noted that genes encoding potential transporters were found neighboring carboxysome loci, α-carboxysome loci were gathered from bacterial genomes, and potential transporter genes neighboring these loci are described here. Members of transporter families whose members all transport DIC (CHC, MDT and Sbt) were common in these neighborhoods, as were members of the SulP transporter family, many of which transport DIC. 109 of 115 taxa with carboxysome loci have some form of DIC transporter encoded in their genomes, suggesting that CCMs consisting of carboxysomes and DIC transporters are widespread not only among “Cyanobacteria”, but also among members of “Proteobacteria” and “Actinobacteria”.

Scott, Kathleen M.↗
DOE OSTI2022

Advances in Genes-Encoding Transporters for Cadmium Uptake, Translocation, and Accumulation in Plants

Cadmium (Cd) is a heavy metal that is highly toxic for plants, animals, and human beings. A better understanding of the mechanisms involved in Cd accumulation in plants is beneficial for developing strategies for either the remediation of Cd-polluted soils using hyperaccumulator plants or preventing excess Cd accumulation in the edible parts of crops and vegetables. As a ubiquitous heavy metal, the transport of Cd in plant cells is suggested to be mediated by transporters for essential elements such as Ca, Zn, K, and Mn. Identification of the genes encoding Cd transporters is important for understanding the mechanisms underlying Cd uptake, translocation, and accumulation in either crop or hyperaccumulator plants. Recent studies have shown that the transporters that mediate the uptake, transport, and accumulation of Cd in plants mainly include members of the natural resistance-associated macrophage protein (Nramp), heavy metal-transporting ATPase (HMA), zinc and iron regulated transporter protein (ZIP), ATP-binding cassette (ABC), and yellow stripe-like (YSL) families. Here, we review the latest advances in the research of these Cd transporters and lay the foundation for a systematic understanding underlying the molecular mechanisms of Cd uptake, transport, and accumulation in plants.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1989

Low temperature storage container for transporting perishables to space station

Two storage containers are disclosed within which food or biological samples may be stored for transfer in a module by the space shuttle to a space station while maintaining the food or samples at very low temperatures. The container is formed in two parts, each part having an inner shell and an outer shell disposed about the inner shell. The space between the shells is filled with a continuous wrap multi-layer insulation and a getter material. The two parts of the container have interlocking members and when connected together are sealed for preventing leakage from the space between the shells. After the two parts are filled with frozen food or samples they are connected together and a vacuum is drawn in the space between the shells and the container is stored in the module. For the extremely low temperature requirements of biological samples, an internal liner having a phase change material charged by a refrigerant coil is disposed in the space between the shells, and the container is formed from glass fiber material including honeycomb structural elements. All surfaces of the glass fiber which face the vacuum space are lined with a metal foil.

Owen, James W.↗
DOE OSTI2022

Tree-inspired lignin microrods-based composite heterogeneous nanochannels for ion transport and osmotic energy harvesting

One of the key processes of tree lignification is that lignin penetrates into the cell wall and fills in the cell wall framework, thereby increasing the hardness and hydrophobic of the tree channels, which is beneficial to consolidate and support the tree cell wall and water transport. Inspired by this natural process, we demonstrated a lignin-based nanofluidic heterogeneous membrane that closely mimics the channels in tree, which can realize ion transport function and effectively capture reverse electrodialysis. The membrane was synthesized by heating dealkaline lignin and PVA at 200 °C and this formed fusiform microrods and a closed-packed membrane. Simultaneously, this membrane composited with anodized aluminum (AAO) channels membrane at 200 °C to form asymmetric heterogeneous nanochannels membrane, which can transport counter-ions and harvest osmotic energy. This membrane implements ion current rectification in 0.1 M KCl electrolyte solution at pH 3 due to the confinement of pores and opposite surface charges in lignin-based heterogeneous nanochannel. An output power density of 0.97 W m- 2 is obtained under a 50-fold salinity gradient, which can be further improved to 1.19 W m -2 by increasing the salinity gradient from 50-fold to 500-fold. Accordingly, this nanofluidic membranes were prepared by using lignin, the key component in tree, which not only mimicked a crucial process of the water and ionic transport process of channels in tree, but also had the prospect in the field of osmotic energy harvesting.

09 BIOMASS FUELS↗
DOE OSTI2023

Restricting electron flow at cytochrome b6f when downstream electron acceptors are severely limited

Abstract Photosynthetic organisms frequently experience abiotic stress that restricts their growth and development. Under such circumstances, most absorbed solar energy cannot be used for CO2 fixation and can cause the photoproduction of reactive oxygen species (ROS) that can damage the photosynthetic reaction centers of PSI and PSII, resulting in a decline in primary productivity. This work describes a biological “switch” in the green alga Chlamydomonas reinhardtii that reversibly restricts photosynthetic electron transport (PET) at the cytochrome b6f (Cyt b6f) complex when the capacity for accepting electrons downstream of PSI is severely limited. We specifically show this restriction in STARCHLESS6 (sta6) mutant cells, which cannot synthesize starch when they are limited for nitrogen (growth inhibition) and subjected to a dark-to-light transition. This restriction represents a form of photosynthetic control that causes diminished electron flow to PSI and thereby prevents PSI photodamage but does not appear to rely on a ΔpH. Furthermore, when electron flow is restricted, the plastid alternative oxidase (PTOX) becomes active, functioning as an electron valve that dissipates some excitation energy absorbed by PSII and allows the formation of a proton motive force (PMF) that would drive some ATP production (potentially sustaining PSII repair and nonphotochemical quenching [NPQ]). The restriction at the Cyt b6f complex can be gradually relieved with continued illumination. This study provides insights into how PET responds to a marked reduction in availability of downstream electron acceptors and the protective mechanisms involved.

Plant Sciences↗