Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Biological Transport”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Directional self-locomotion of active droplets enabled by nematic environment

Active matter comprised of self-propelled interacting units holds a major promise for the extraction of useful work from its seemingly chaotic dynamics. Streamlining active matter is especially important at microscale, where the viscous forces prevail over inertia and transport requires a non-reciprocal motion. Here we report that microscopic active droplets representing aqueous dispersions of swimming bacteria Bacillus subtilis become unidirectionally motile when placed in an inactive nematic liquid crystal medium. Random motion of bacteria inside the droplet is rectified into a directional self-locomotion of the droplet by the polar director structure that the droplet creates in the surrounding nematic through anisotropic molecular interactions at its surface. Droplets without active swimmers show no net displacement. The trajectory of the active droplet can be predesigned by patterning the molecular orientation of the nematic. As a result, the effect demonstrates that broken spatial symmetry of the medium can be the reason for and the means to control directional microscale transport.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Compartmental Control of UDP-Araf Supply: Golgi Lumen UDP-Arabinopyranose Mutase Depletes Plant Cell Wall Araf Linkages

L-Arabinofuranose (Araf) is a major constituent of plant cell wall polysaccharides. UDP-Araf is generated from UDP-L-arabinopyranose (UDP-Arap) by a UDP-Arap mutase (UAM) on the cytosolic face of the Golgi and then imported into the Golgi lumen for utilization by arabinosyltransferases (AraTs). Yet, a substantial fraction of UDP-Arap is synthesized in the Golgi lumen by the UDP-xylose 4-epimerase (UXE), creating a topological paradox where luminal UDP-Arap must be exported to the cytosol for conversion to UDP-Araf by UAM and then re-imported into the Golgi lumen. To test the functional significance of this compartmentation, we mislocalized Arabidopsis (Arabidopsis thaliana) UAM1 to the Golgi lumen by fusing it to the UXE1 transmembrane domain. The fusion protein was present in the Golgi, and protease-protection assays on microsomes supported its luminal orientation. In wild-type and uam1 plants, Golgi-targeted UAM1 reduced total cell wall Arabinose without consistent changes in other monosaccharides. Linkage analyses showed that this decrease reflects selective loss of Araf residues, whereas Arap remain largely unchanged, consistent with reduced UDP-Araf availability for luminal AraTs. Under salt stress, expression of Golgi-targeted UAM1 in uam1 caused root-growth inhibition and maturation-zone swelling that exogenous L-Ara failed to rescue. These results support a hypothesis that the strong thermodynamic bias of the UAM reaction toward UDP-Arap requires spatial separation of UDP-Arap production from UDP-Araf formation to sustain UDP-Araf flux into Golgi arabinosylation and avoid futile intraluminal back-conversion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Metabolic Constraints of Organic Matter Mineralization and Metal Cycling

Floodplains are poorly understood and dynamic components of the global carbon cycle that not are well represented in Earth system models. Further, they have a dominant influence on the cycling of important metals within critical transport conduits between surface waters and groundwater. The physical characteristics of floodplains make the hydrology and associated coupled biology and geochemistry particularly responsive to ongoing and impending changes in climate, river management, and land development

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Golgi-localized putative S-adenosyl methionine transporters required for plant cell wall polysaccharide methylation

Polysaccharide methylation, especially that of pectin, is a common and important feature of land plant cell walls. Polysaccharide methylation takes place in the Golgi apparatus and therefore relies on the import of S-adenosyl methionine (SAM) from the cytosol into the Golgi. However, so far, no Golgi SAM transporter has been identified in plants. Here we studied major facilitator superfamily members in Arabidopsis that we identified as putative Golgi SAM transporters (GoSAMTs). Knockout of the two most highly expressed GoSAMTs led to a strong reduction in Golgi-synthesized polysaccharide methylation. Furthermore, solid-state NMR experiments revealed that reduced methylation changed cell wall polysaccharide conformations, interactions and mobilities. Notably, NMR revealed the existence of pectin ‘egg-box’ structures in intact cell walls and showed that their formation is enhanced by reduced methyl esterification. Here, these changes in wall architecture were linked to substantial growth and developmental phenotypes. In particular, anisotropic growth was strongly impaired in the double mutant. The identification of putative transporters involved in import of SAM into the Golgi lumen in plants provides new insights into the paramount importance of polysaccharide methylation for plant cell wall structure and function.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Structural basis for inhibition of the Cation-chloride cotransporter $\mathrm{NKCC1}$ by the diuretic drug bumetanide

Cation-chloride cotransporters (CCCs) NKCC1 and NKCC2 catalyze electroneutral symport of 1 Na + , 1K + , and 2 Cl - across cell membranes. NKCC1 mediates trans-epithelial Cl - secretion and regulates excitability of some neurons and NKCC2 is critical to renal salt reabsorption. Both transporters are inhibited by the so-called loop diuretics including bumetanide, and these drugs are a mainstay for treating edema and hypertension. Here, our single-particle electron cryo-microscopy structures supported by functional studies reveal an outward-facing conformation of NKCC1, showing bumetanide wedged into a pocket in the extracellular ion translocation pathway. Based on these and the previously published inward-facing structures, we define the translocation pathway and the conformational changes necessary for ion translocation. We also identify an NKCC1 dimer with separated transmembrane domains and extensive transmembrane and C-terminal domain interactions. We further define an N-terminal phosphoregulatory domain that interacts with the C-terminal domain, suggesting a mechanism whereby (de)phosphorylation regulates NKCC1 by tuning the strength of this domain association.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Gene Amplification, Laboratory Evolution, and Biosensor Screening Reveal MucK as a Terephthalic Acid Transporter in Acinetobacter baylyi ADP1

Microbial terephthalic acid (TPA) catabolic pathways are conserved among the few bacteria known to turnover this xenobiotic aromatic compound. However, to date there are few reported cases in which this pathway has been successfully expressed in heterologous hosts to impart efficient utilization of TPA as a sole carbon source. In this work, we aimed to engineer TPA conversion in Acinetobacter baylyi ADP1 via the heterologous expression of catabolic and transporter genes from a native TPA-utilizing bacterium. Specifically, we obtained ADP1-derived strains capable of growing on TPA as the sole carbon source using chromosomal insertion and targeted amplification of the tph catabolic operon from Comamonas sp. E6. Adaptive laboratory evolution was then used to improve growth on this substrate. TPA consumption rates of the evolved strains, which retained multiple copies of the tph genes, were ~0.2 g/L/h (or ~1 g TPA/g cells/h), similar to that of Comamonas sp. E6 and almost 2-fold higher than that of Rhodococcus jostii RHA1, another native TPA-utilizing strain. To evaluate TPA transport in the evolved ADP1 strains, we engineered a TPA biosensor consisting of the transcription factor TphR and a fluorescent reporter. In combination with whole-genome sequencing, the TPA biosensor revealed that transport of TPA was not mediated by the heterologous proteins from Comamonas sp. E6. Instead, the endogenous ADP1 muconate transporter MucK, a member of the major facilitator superfamily, was responsible for TPA transport in several evolved strains in which MucK variants were found to enhance TPA uptake. Furthermore, the IclR-type transcriptional regulator DcaS was identified as a repressor of mucK expression. Overall, this work presents an unexpected function of a native protein identified through gene amplification, adaptive laboratory evolution, and a combination of screening methods. This study also provides a TPA biosensor for application in ADP1 and identifies transporter variants for use in metabolic engineering applications focused on plastic upcycling of polyesters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Geological activity shapes the microbiome in deep-subsurface aquifers by advection

Subsurface environments host diverse microorganisms in fluid-filled fractures; however, little is known about how geological and hydrological processes shape the subterranean biosphere. Here, we sampled three flowing boreholes weekly for 10 mo in a 1478-m-deep fractured rock aquifer to study the role of fracture activity (defined as seismically or aseismically induced fracture aperture change) and advection on fluid-associated microbial community composition. We found that despite a largely stable deep-subsurface fluid microbiome, drastic community-level shifts occurred after events signifying physical changes in the permeable fracture network. The community-level shifts include the emergence of microbial families from undetected to over 50% relative abundance, as well as the replacement of the community in one borehole by the earlier community from a different borehole. Null-model analysis indicates that the observed spatial and temporal community turnover was primarily driven by stochastic processes (as opposed to deterministic processes). We, therefore, conclude that the observed community-level shifts resulted from the physical transport of distinct microbial communities from other fracture(s) that outpaced environmental selection. Given that geological activity is a major cause of fracture activity and that geological activity is ubiquitous across space and time on Earth, our findings suggest that advection induced by geological activity is a general mechanism shaping the microbial biogeography and diversity in deep-subsurface habitats across the globe.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A roadmap to understanding and anticipating microbial gene transfer in soil communities

Engineered microbes are being programmed using synthetic DNA for applications in soil to overcome global challenges related to climate change, energy, food security, and pollution. However, we cannot yet predict gene transfer processes in soil to assess the frequency of unintentional transfer of engineered DNA to environmental microbes when applying synthetic biology technologies at scale. This challenge exists because of the complex and heterogeneous characteristics of soils, which contribute to the fitness and transport of cells and the exchange of genetic material within communities. Here, we describe knowledge gaps about gene transfer across soil microbiomes. Here, we propose strategies to improve our understanding of gene transfer across soil communities, highlight the need to benchmark the performance of biocontainment measures in situ, and discuss responsibly engaging community stakeholders. We highlight opportunities to address knowledge gaps, such as creating a set of soil standards for studying gene transfer across diverse soil types and measuring gene transfer host range across microbiomes using emerging technologies. By comparing gene transfer rates, host range, and persistence of engineered microbes across different soils, we posit that community-scale, environment-specific models can be built that anticipate biotechnology risks. Such studies will enable the design of safer biotechnologies that allow us to realize the benefits of synthetic biology and mitigate risks associated with the release of such technologies.

bioccontainment↗
DOE OSTI2023

The Roles of Tidal Marshes in the Estuarine Biochemical Processes: A Numerical Modeling Study

Observations suggest that the existence of tidal marsh can alter the oxygen and nutrient dynamics in adjacent water bodies, but assessing the impacts of large tidal marshes on an estuary is challenging. In this study, we use a modeling approach to investigate the roles of tidal marshes on the estuarine biochemical processes. The marsh model, which simulates the ecological functions of marshes at seasonal and annual time-scales, is embedded inside an unstructured-grid three-dimensional hydrodynamic and eutrophication model (SCHISM-ICM). This modeling system simulates the growth and metabolism of the tidal marshes and links biological processes to nutrient dynamics in the water column and sediment. This model dynamically simulates nutrient recycling and physical transport of the materials between marshes and open water through wetting-drying processes. This coupled model system is validated and successfully applied to the York River Estuary. Model results suggest that tidal marshes influence the local diurnal dissolved oxygen (DO) cycle by exporting dissolved organic carbon and high sediment oxygen demand in the marsh system through the tidal exchange. The high deposition rates of organics and diurnal DO cycle enhance the sediment release of phosphorus. On the other hand, marshes tend to decrease dissolved inorganic nitrogen in the water column by settling particulate nutrients and enhancing the denitrification process. The study demonstrates that tidal marshes exert substantial impacts on the estuarine biochemical processes. The developed tidal marsh model enhances eutrophication modeling and advances the understanding of the feedback effects between marsh biogeochemistry and estuarine eutrophication processes on a systemic scale.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.

cytochrome c oxidase↗
DOE OSTI2020

Nitrogen derived from Combined Algal Processing supports algae cultivation for biofuels

Algae biomass, a biofuel feedstock with potential to reduce global CO 2 emissions, is currently too expensive Nitrogen, a significant input and life cycle cost, requires research on recycling and additional sources to reduce costs. Integral to nitrogen recycling is the knowledge of actual nitrogen requirements in outdoor ponds, thus data from the Unified Field Studies of the Algae Testbed Public-Private Partnership was analyzed. The data showed that Nannochloropsis oceanica used 14–24 mg/L NH 4 + per harvest cycle for robust growth. Nitrogen recycled directly from the algae conversion process will likely be the primary source of nitrogen for algae cultivation. Harvested algae can be fractionated via Combined Algal Processing (CAP), where algae are pretreated, fermented, and the fuel feedstocks (e. g. ethanol, lipids) are removed leaving a nitrogen rich slurry. Chlorella vulgaris grew robustly in nitrogen-free media supplemented with CAP residues through 4 harvest cycles with no inhibition. The amount of nitrogen as free ammonium available for recycling directly without further processing was insufficient (~4% of total needed), thus the nitrogen fixing bacteria, Azotobacter vinelandii, was investigated as a means for increasing ammonium concentration in CAP residues. This organism was shown to be proficient at growth on sugars liberated from algae biomass during pretreatment and sustained algae growth using A. vinelandii supernatants was also demonstrated. Using Azotobacter to increase ammonium concentrations on-site using an inexpensive biological process to generate the necessary ammonium for outdoor algae cultivation improves sustainability of algae biofuels by avoiding the energy intensive steps of typical ammonium production and transport. Furthermore, these results show that byproducts of algae conversion begin to close nitrogen demand and, with further supplementation by diazotrophic bacteria or protein hydrolysis, may completely replace current energyintensive and costly industrial nitrogen sources offering a path to increased economic feasibility and improved life cycle analysis of algae-based biofuels.

09 BIOMASS FUELS↗
DOE OSTI2022

Proton transfer reactions in donor site mutants of ESR, a retinal protein from Exiguobacterium sibiricum

Light-driven proton transport by microbial retinal proteins such as archaeal bacteriorhodopsin involves carboxylic residues as internal proton donors to the catalytic center which is a retinal Schiff base (SB). The proton donor, Asp96 in bacteriorhodopsin, supplies a proton to the transiently deprotonated Schiff base during the photochemical cycle. Subsequent proton uptake resets the protonated state of the donor. Here this two step process became a distinctive signature of retinal based proton pumps. Similar steps are observed also in many natural variants of bacterial proteorhodopsins and xanthorhodopsins where glutamic acid residues serve as a proton donor. Recently, however, an exception to this rule was found. A retinal protein from Exiguobacterium sibiricum, ESR, contains a Lys residue in place of Asp or Glu, which facilitates proton transfer from the bulk to the SB. Lys96 can be functionally replaced with the more common donor residues, Asp or Glu. Proton transfer to the SB in the mutants containing these replacements (K96E and K96D/A47T) is much faster than in the proteins lacking the proton donor (K96A and similar mutants), and in the case of K96D/A47T, comparable with that in the wild type, indicating that carboxylic residues can replace Lys96 as proton donors in ESR. We show here that there are important differences in the functioning of these residues in ESR from the way Asp96 functions in bacteriorhodopsin. Reprotonation of the SB and proton uptake from the bulk occur almost simultaneously during the M to N transition (as in the wild type ESR at neutral pH), whereas in bacteriorhodopsin these two steps are well separated in time and occur during the M to N and N to O transitions, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Specialization Restricts the Evolutionary Paths Available to Yeast Sugar Transporters

Functional innovation at the protein level is a key source of evolutionary novelties. The constraints on functional innovations are likely to be highly specific in different proteins, which are shaped by their unique histories and the extent of global epistasis that arises from their structures and biochemistries. These contextual nuances in the sequence–function relationship have implications both for a basic understanding of the evolutionary process and for engineering proteins with desirable properties. Here, we have investigated the molecular basis of novel function in a model member of an ancient, conserved, and biotechnologically relevant protein family. These Major Facilitator Superfamily sugar porters are a functionally diverse group of proteins that are thought to be highly plastic and evolvable. By dissecting a recent evolutionary innovation in an α-glucoside transporter from the yeast Saccharomyces eubayanus, we show that the ability to transport a novel substrate requires high-order interactions between many protein regions and numerous specific residues proximal to the transport channel. To reconcile the functional diversity of this family with the constrained evolution of this model protein, we generated new, state-of-the-art genome annotations for 332 Saccharomycotina yeast species spanning ~400 My of evolution. By integrating phylogenetic and phenotypic analyses across these species, we show that the model yeast α-glucoside transporters likely evolved from a multifunctional ancestor and became subfunctionalized. The accumulation of additive and epistatic substitutions likely entrenched this subfunction, which made the simultaneous acquisition of multiple interacting substitutions the only reasonably accessible path to novelty.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Rapid organic carbon spiraling in a headwater stream linked with streamflow, biogeochemistry, and canopy phenology

Headwater streams are abundant worldwide and important to global biogeochemical cycles, serving as critical processors and transporters of C. C spiraling is a useful way to understand the retention and mineralization of organic C (OC) in streams. However, analyses of seasonal and interannual variability in OC spiraling are currently limited. In this study, we aimed to understand the temporal patterns and driving mechanisms of OC spiraling, which will inform our understanding of future OC changes under climate change. We used 7 y of daily data in a small headwater stream (Walker Branch, Tennessee, USA) to assess seasonal and interannual variability in OC spiraling length (S OC ) and mineralization velocity (v fOC ), as well as their potential related variables. On average, S OC in Walker Branch was ~10× shorter than in previously studied small streams, indicating strong connections between the water column and the benthic environment where OC mineralization mostly takes place. OC spiraling was faster during the more biologically active periods of spring and autumn compared with more elongated OC spiraling in summer and winter, when OC retention was lower and downstream transport was higher. Gross primary production (GPP) was most strongly related to S OC and v fOC . Photosynthetically active radiation (PAR) and NO 3 − were also positively and negatively related to v fOC , respectively. Trends toward earlier and longer canopy cover and reduced GPP and PAR may result in longer S OC and slower v fOC , reducing localized instream processing of OC and potentially shunting more OC downstream. However, long-term observations indicate reduced NO 3 − at Walker Branch, suggesting opposing effects to those of GPP and PAR, leading to faster v fOC and greater OC retention. Time-series analyses of OC spiraling in streams can enhance our understanding of current and future responses of OC processing and downstream transport to climate change, as well as implications for downstream OC dynamics.

biological activity↗
DOE OSTI2025

Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory

The nuclear pore complex (NPC), a channel within the nuclear envelope filled with intrinsically disordered proteins, regulates the transport of macromolecules between the nucleus and the cytoplasm. Recent studies have highlighted the NPC’s ability to adjust its diameter in response to the membrane tension, underscoring the importance of exploring how variations in pore size influence molecular transport through the NPC. In this study, we investigated the relationship between pore size and transport rate and proposed a mathematical model describing this connection. We began by theoretically analyzing how the pore size scales with the characteristic dimensions of the mesh-like structure within the pore. By introducing key assumptions about how the meshwork structure influences molecular diffusion, we derived a mathematical expression for the transport rate based on the size of the pore and the transported molecules. To validate our model, we conducted Brownian dynamics simulations using a coarse-grained representation of the NPC. These simulations, performed across a range of pore sizes, demonstrated strong agreement with our model’s predictions, confirming its accuracy and applicability. Our model is specifically tailored for small-to-medium-sized molecules, approximately 5 nanometers in size, making it relevant to a wide range of transcription factors and signaling molecules. It also extends to molecules with weak and transient interactions with FG-Nups, such as importin-β. By presenting this model formula, our study offers a quantitative framework for analyzing the effects of pore dilation on nucleocytoplasmic transport.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Sonochemical Synthesis and Ion Transport Properties of Surfactant-Stabilized Carbon Nanotube Porins

Carbon nanotube porins (CNTPs), short segments of carbon nanotubes stabilized by a lipid coating, are a promising example of artificial membrane channels that mimic a number of key behaviors of biological ion channels. While the lipid-assisted synthesis of CNTPs may facilitate their subsequent incorporation into lipid bilayers, it limits the applicability of these pores in other self-assembled membrane materials and also precludes the use of large scale purified CNT feedstocks. In this report we demonstrate that CNTPs can be synthesized by sonochemical cutting of long CNT feedstocks in the presence of different surfactants, producing CNTS with transport properties identical to those obtained by the lipid-assisted procedure. Our results open up a large variety of synthetic routes for CNTP production.

77 NANOSCIENCE AND NANOTECHNOLOGY↗