Engineering PapersSearch

SEARCH · Engineering Papers

Results for “METABOLISM”

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 91 records · Page 5

Learning from nature’s plant engineers: Hijacking metabolism and development beyond genetics

Plant metabolism underpins the food, fiber, and fuel that support our economy, driving strong interest in new strategies to rewire plant metabolism for emerging applications. While most synthetic biology efforts are reliant on genetic engineering, plants can be manipulated in many other ways that remain comparatively underexplored. Across nature, diverse organisms, including bacteria, fungi, and insects, have evolved sophisticated mechanisms to exploit plant metabolic richness, reshaping it for purposes that span from basic nutrition to the construction of complex, novel structures for shelters. These interspecies interactions and non-model systems represent unique manners in which plants can be reprogrammed or hijacked by other organisms, offering inspiration for novel approaches to engineering plant metabolism. By better understanding the basis of how organisms induce these remarkable transformations in plants, we can expand the conceptual boundaries of synthetic biology and reveal alternative routes to manipulating plants for the production of a diverse array of valuable compounds and materials. Deeper insight into these mechanisms will yield novel blueprints for rethinking the scope and breadth in which we can redesign plant metabolism across many applications.

Sarkiss, Anthony E. [University of California, Ber

Deciphering metabolic differentiation during Bacillus subtilis sporulation

Abstract The bacteriumBacillus subtilisundergoes asymmetric cell division during sporulation, producing a mother cell and a smaller forespore connected by the SpoIIQ-SpoIIIA (or Q-A) channel. The two cells differentiate metabolically, and the forespore becomes dependent on the mother cell for essential building blocks. Here, we investigate the metabolic interactions between mother cell and forespore using genome-scale metabolic and expression models as well as experiments. Our results indicate that nucleotides are synthesized in the mother cell and transported in the form of nucleoside di- or tri-phosphates to the forespore via the Q-A channel. However, if the Q-A channel is inactivated later in sporulation, then glycolytic enzymes can form an ATP and NADH shuttle, providing the forespore with energy and reducing power. Our integrated in silico and in vivo approach sheds light into the intricate metabolic interactions underlying cell differentiation inB. subtilis, and provides a foundation for future studies of metabolic differentiation.

Science & Technology - Other Topics

A constraint-based framework for exploring the impact of multireaction dependencies on metabolic functions

Abstract Metabolism operates under physico-chemical constraints that result in multireaction dependencies. Understanding how multireaction dependencies affect metabolic phenotypes remains challenging, hindering their biotechnological applications. Here, we propose the concept of a forcedly balanced complex that allows to efficiently determine the effects of specific multireaction dependencies on metabolic network functions in constrained-based models. Using this concept, we found that the fraction of multireaction dependencies induced by forcedly balanced complexes in genome-scale metabolic networks followed power law with exponential cut-off. We identified forcedly balanced complexes that are lethal in cancer but have little effect on growth in healthy tissue models. In addition, these forcedly balanced complexes are largely specific to models of particular cancer types. Therefore, multireaction dependencies resulting from forced balancing of complexes represent an innovative means to control cancers that, we argue, can be implemented via transporter engineering. The presented constraint-based approaches pave the way for using multireaction dependencies in metabolic engineering for diverse biotechnological applications.

Küken, Anika

Quantitative principles of microbial metabolism shared across scales

Metabolism is the complex network of chemical reactions occurring within every cell and organism, maintaining life, mediating ecosystem processes and affecting Earth’s climate. Experiments and models of microbial metabolism often focus on one specific scale, overlooking the connectivity between molecules, cells and ecosystems. Here we highlight quantitative metabolic principles that exhibit commonalities across scales, which we argue could help to achieve an integrated perspective on microbial life. Mass, electron and energy balance provide quantitative constraints on their flow within metabolic networks, organisms and ecosystems, shaping how each responds to its environment. The mechanisms underlying these flows, such as enzyme–substrate interactions, often involve encounter and handling stages that are represented by equations similar to those for cells and resources, or predators and prey. Here we propose that these formal similarities reflect shared principles and discuss how their investigation through experiments and models may contribute to a common language for studying microbial metabolism across scales.

59 BASIC BIOLOGICAL SCIENCES

Glyceraldehyde-3-phosphate dehydrogenase homologs as bifunctional gatekeepers of metabolic segregation in Pseudomonas putida

Metabolically versatile Pseudomonas species can assimilate various glycolytic and gluconeogenic substrates. Simultaneous assimilation is known to segregate carbons from each substrate type into different metabolic pathways. However, the mechanisms of this metabolic segregation remain unresolved. Here, we investigate Pseudomonas putida KT2440 during processing of the sugar glucose through glycolysis versus the phenolic acid ferulate through gluconeogenesis. Metabolome profiling reveals up to twofold less tricarboxylic acid cycle metabolites but up to 10-fold higher metabolites of upper glycolysis, pentose-phosphate, and Entner–Doudoroff pathways in glucose-grown cells compared to ferulate-grown cells. After 13C-substrate switching, kinetic isotopic profiling captures rapid assimilation of new substrate carbons into initial catabolic pathways, but incorporation into downstream pathways is absent or incomplete. Proteomics identifies a 22-fold higher abundance of one homolog of glyceraldehyde-3-phosphate dehydrogenase (GAPDH, GapA) in cells fed on glucose relative to ferulate, while abundance of another homolog (GapB) remains unchanged. Growth phenotypes and quantitative metabolomics for single and double knockout mutants of these GAPDH homologs indicate only GapA involvement in glycolytic flux, which can be compensated by the Entner–Doudoroff pathway, and distinct preference of GapB with minimal role of GapA for gluconeogenic flux. Accordingly, growth of triple knockout mutant with deletion of gapA, gapB, and edd is possible only when glycolytic and gluconeogenic substrates are provided together to meet metabolic demands in a segregated fashion, but metabolic tradeoffs lead to slow growth. A mathematical, experimentally constrained, model of the GAPDH node shows that tuning of GapA and GapB concentrations enables transition between flux regimes for nutritional adaptability.

Zhou, Nanqing [Northwestern University, Evanston]

Evolutionary trajectory of transcription factors and selection of targets for metabolic engineering

Transcription factors (TFs) provide potentially powerful tools for plant metabolic engineering as they often control multiple genes in a metabolic pathway. However, selecting the best TF for a particular pathway has been challenging, and the selection often relies significantly on phylogenetic relationships. Here, we offer examples where evolutionary relationships have facilitated the selection of the suitable TFs, alongside situations where such relationships are misleading from the perspective of metabolic engineering. We argue that the evolutionary trajectory of a particular TF might be a better indicator than protein sequence homology alone in helping decide the best targets for plant metabolic engineering efforts. This article is part of the theme issue ‘The evolution of plant metabolism’.

Life Sciences & Biomedicine - Other Topics

Synergy and antagonism in a genome-scale model of metabolic hijacking by bacteriophages

Bacteriophage auxiliary metabolic genes (AMGs) alter host metabolism by hijacking reactions, but previous studies mostly inferred their roles from annotations, ignoring system-wide impacts and phage production. Here we integrate AMGs and phage assembly into a genome-scale metabolic model of Prochloroccocus marinus MED4 infected by P-HM2. We show that 17 directly hijacked reactions substantially affect more than 30% of the reactions in MED4 metabolism, including carbon fixation, photosynthesis, and nucleotide synthesis, distinguishing these AMGs as either phage aligned—shifting feasible reaction velocities in accordance with maximal phage production—or phage antialigned. Pareto optimization reveals that phage-aligned reactions alter phage-host growth trade-offs, while phage-antialigned reactions do not. We experimentally validate our predictions of system-level AMG impacts by measuring the N-dependent effect of P-HM2 cp12 expression on growth in a model relative of the genetically intractable MED4, Synechococcus elongatus. We also show that AMGs’ indirect impacts are synergistically and antagonistically coupled, providing systems-level insight into AMG perturbations and highlighting how nontrivial cascading effects shape host metabolism.

Rozum, Jordan C. [Pacific Northwest National Labor

Multi-omic characterization of a soil microbial consortium reveals critical role of succinate and glutamate metabolism during calcium carbonate precipitation

Microbially induced calcium carbonate precipitation (MICP) holds potential for use in soil stabilization and carbon sequestration, with the overall efficiency of the process being a major determinant for use in many environmental and civil engineering applications. While the biogeochemical pathways and enzymes driving MICP are known, the microbial metabolic networks and community dynamics underlying such precipitation remain poorly characterized. To address this gap, we developed a four-member consortium of soil bacteria (Curtobacterium flaccumfaciens, Rhodococcus qingshengii, Microbacterium sp., and Bacillus toyonensis), termed carbon storing consortium - A (CSC-A), that is capable of MICP. Prior work shows that MICP production is higher in CSC-A compared to the sum of carbonate produced by each member, suggesting carbonate production is driven by consortium dynamics. To that end we used a multi-omic integration approach of genomics, transcriptomics, and metabolomics to investigate potential inter-species interactions that may influence the MICP phenotype. Genomic life history characterizations identified evidence of niche specialization by B. toyonensis and Microbacterium, while metatranscriptomic analysis suggests R. qingshengii is a keystone species during growth in urea. By comparing individual species’ metabolomes to the metabolic profile of a shared well of precipitated metabolites, we identified over 200 metabolites predicted to be produced or consumed by CSC-A members. Integrating both data types to search the KEGG reactome highlighted a network centered around glutamine metabolism and branched chain amino acid biosynthesis under regulation during CSC-A growth in urea. Succinate metabolism was also a major node in this network and laboratory assays confirmed that increasing the amount of succinate in the growth medium leads to increased carbonate precipitation by CSC-A, a critical confirmation of our modeling approach. By isolating and identifying the interconnected metabolic components underlying MICP in CSC-A, we identified keystone taxa, metabolites, and pathways important for future optimization of the application of this consortia to carbonate precipitation.

carbon storing consortium - A (CSC-A)

A standardized workflow for kinetic metabolic model curation and dissemination

Kinetic metabolic models provide invaluable insights into cellular metabolism, supporting applications in synthetic biology, metabolic engineering, and systems biology. However, reproducibility and utility of these models hinge on clear and rigorous documentation, standardized annotation, and accessible visualization. This paper presents a workflow for building, annotating, visualizing, and sharing kinetic metabolic models. Our method integrates community standards and open-source tools to ensure reproducibility, interoperability, and user accessibility. This procedure enables researchers to produce reusable and well-documented kinetic models, advancing their role as powerful tools in metabolic research.

Cook, Margaret [Univ. of Washington, Seattle, WA (

A common modality of action of simulated space stresses on the oxidative metabolism of ethylmorphine, aniline and p-nitroanisole by male rat liver.

High gravity, cold and starvation elicited similar responses in male Simonson rats. These responses included a decreased rate in body weight gain, increased metabolism of aniline and p-nitroanisole, and no consistent pattern of change in the metabolism of ethylmorphine. Cold and starvation increased the amount of hepatic cytochrome P-450, while hypobaric-hyperoxia caused no change in any of the parameters measured. When 1% acetone was given to the rats in their drinking water, the effects on drug metabolism were similar to those produced by food restriction in that the metabolism of aniline and p-nitroanisole was increased, and the metabolism of ethylmorphine unchanged. The type I binding spectrum of acetone suggests that it is either a substrate, inhibitor, or both for hepatitic oxidative enzymes.

Furner, R. L.

Skeletal muscle metabolism in hypokinetic rats

Muscle growth, protein metabolism, and amino acid metabolism were studied in various groups of rats. Certain groups were adrenaliectomized; some rats were suspended while others (the controls) were weight bearing. Results show that: (1) metabolic changes in the extensor digitorum longus muscle of suspended rats are due primarily to increased circulating glucocorticoids; (2) metabolic changes in the soleus muscle due to higher steroid levels are probably potentiated by greater numbers of steroid receptors; and (3) not all metabolic responses of the soleus muscle to unloading are due to the elevated levels of glucocorticoids or the increased sensitivity of this muscle to these hormones.

Tischler, M. E.

The metabolism of the Antartic crytoendolithic microbiota

The carbon metabolism of the cryptoendolithic microbiota in sandstones from the Ross Desert region of Antarctica was studied in situ and in vitro. Organic and inorganic compounds were metabolized by the microbiota, with bicarbonate being metabolized maximally in the light. There was a linear response of photosynthesis to light up to 200 to 300 micromole photons/sq m/s. The community photosynthetic response to temperature was a minimum at -5 C, two optima at +5 and +15 C and a maximum at +35 C. Photosynthetic metabolism occurred maximally in the presence of liquid water, but could occur in an environment of water vapor. Biomass of the cryptoendolithic microbiota was measured as the amount of lipid phosphate present. The in situ biomass ranged from 1.92 to 3.26 g carbon/sq m of rock and 2 orders of magnitude less than epilithic lichen microbiota from Antarctica in a location 7 degrees more north in latitude. With these data, it was possible to calculate primary production and carbon turnover in this simple microbiota. Production values ranged from 0.108 to 4.41 mg carbon/sq m/yr, while carbon turnover values ranged from 576 to 23,520 years. These values are the lowest and longest yet recorded for any ecosystem on Earth. If life did evolve on Mars to the level of prokaryotes or primitive eukaryotes, the possibility that the organisms retreated, to the protection of the inside of the rock so that metabolism could continue during planetary cooling, cannot be overlooked.

Vestal, J. Robie

Research Opportunities in Nutrition and Metabolism in Space

The objectives of the Life Sciences Research Office (LSRO) study on nutrient requirements for meeting metabolic needs in manned space flights are as follows: review extant knowledge on the subject; identify significant gaps in knowledge; formulate suggestions for possible research; and produce a documented report of the foregoing items that can be used for program planning. In accordance with NASA's request for this study, the report focuses on issues of nutrition and metabolism that relate primarily to the contemplated United States Space Station, secondarily to the Shuttle Program as an orbital test bed for operational studies, and incidentally to scenarios for future long-term space flights. Members of the LSRO ad hoc Working Group on Nutrition and Metabolism were provided with pertinent articles and summaries on the subject. At the meeting of the Working Group, presentations were made by NASA Headquarters program staff on past experiences relative to space-flight nutrition and metabolism, as well as scenarios for future flights. The discussions of the ad hoc Working Group focused on the following: (1) metabolic needs related to work and exercise; (2) nutrients required to meet such needs; (3) food types, management, and records; and (4) nutritional amelioration or prevention of space-related physiological and behavioral changes.

Altman, Philip L.

Metabolic rate measurements comparing supine with upright upper-body exercises

The ground-based study that tested the hypothesis that metabolic rates during supine and upright upper-body exercises are similar (mean value of 200 kcal/h) is presented. Six subjects each performed supine or upright exercise at three exercise stations, a hand-cycle ergometer, a rope-pull device, and a torque wrench. After a baseline measurement of the metabolic rate at rest, the metabolic rate was measured twice at each exercise station. The mean metabolic rates (kcal/h) during supine (n = 6) and upright control (n = 4) exercise stations were not significantly different except for the rope-pull station, 153.5 +/- 16.6 (supine) as compared to 247.0 +/- 21.7 (upright), p is less than 0.05. This difference may be due in part to an increased mechanical efficiency of supine exercises (15.0 +/- 0.7 percent) as compared to that of upright exercises (11.0 +/- 1.08 percent), p is less than 0.05. The net energy input was significantly smaller for the supine rope-pull exercise (64 +/- 18) as compared to upright (176 +/- 20). The relationship between best-rest exercises, metabolic rates, and the incidence of decompression sickness (DCS) should be examined to determine the true risk of DCS in spaceflight extravehicular activities.

Fortney, Suzanne M.

Effects of Space Flight, Clinorotation, and Centrifugation on the Growth and Metabolism of Escherichia Coli

Previous experiments have shown that space flight stimulates bacterial growth and metabolism. An explanation for these results is proposed, which may eventually lead to improved terrestrial pharmaceutical production efficiency. It is hypothesized that inertial acceleration affects bacterial growth and metabolism by altering the transport phenomena in the cells external fluid environment. It is believed that this occurs indirectly through changes in the sedimentation rate acting on the bacteria and buoyancy-driven convection acting on their excreted by-products. Experiments over a broad range of accelerations consistently supported this theory. Experiments at I g indicated that higher concentrations of excreted by products surrounding bacterial cells result in a shorter lag phase. Nineteen additional experiments simulated 0 g and 0.5 g using a clinostat, and achieved 50 g, 180 g, and 400 g using a centrifuge. These experiments showed that final cell density is inversely related to the level of acceleration. The experiments also consistently showed that acceleration affects the length of the lag phase in a non-monotonic, yet predictable, manner. Additional data indicated that E. coli metabolize glucose less efficiently at hypergravity, and more efficiently at hypogravity. A space-flight experiment was also performed. Samples on orbit had a statistically significant higher final cell density and more efficient metabolism than did ground controls. These results. which were similar to simulations of 0 g using a clinostat, support the theory that gravity only affects bacterial growth and metabolism indirectly, through changes in the bacteria's fluid environment.

Brown, Robert B.

Metabolic Cages for a Space Flight Model in the Rat

A variety of space flight models are available to mimic the physiologic changes seen in the rat during weightlessness. The model reported by Wronski and Morey-Holton has been widely used by many investigators, in musculoskeletal physiologic studies especially, resulting in accumulation of an extensive database that enables scientists to mimic space flight effects in the 1-g environment of Earth. However, information on nutrition or gastrointestinal and renal function in this space flight model is limited by the difficulty in acquiring uncontaminated metabolic specimens for analysis. In the Holton system, a traction tape harness is applied to the tail, and the rat's hindquarters are elevated by attaching the harness to a pulley system. Weight-bearing hind limbs are unloaded, and there is a headward fluid shift. The tail-suspended rats are able to move freely about their cages on their forelimbs and tolerate this procedure with minimal signs of stress. The cage used in Holton's model is basically a clear acrylic box set on a plastic grid floor with the pulley and tail harness system attached to the open top of the cage. Food is available from a square food cup recessed into a corner of the floor. In this system, urine, feces, and spilled food fall through the grid floor onto absorbent paper beneath the cage and cannot be separated and recovered quantitatively for analysis in metabolic balance studies. Commercially available metabolic cages are generally cylindrical and have been used with a centrally located suspension apparatus in other space flight models. The large living area, three times as large as most metabolic cages, and the free range of motion unique to Holton's model, essential for musculoskeletal investigations, were sacrificed. Holton's cages can accommodate animals ranging in weight from 70 to 600 g. Although an alternative construction of Holton's cage has been reported, it does not permit collection of separate urine and fecal samples. We describe the modifications to Holton's food delivery system, cage base, and the addition of a separator system for the collection of urine and fecal samples for metabolic and nutrition studies in the tail suspension model.

Harper, Jennifer S.

Effects of NaCl on metabolic heat evolution rates by barley roots

The effect of salinity stress on metabolic heat output of barley (Hordeum vulgare L.) root tips was measured by isothermal microcalorimetry. Several varieties differing in tolerance to salinity were compared and differences quantified. Two levels of inhibition by increasing salt were found. Following the transition from the initial rate of the first level, inhibition remained at about 50% with further increases in salt concentration up to 150 millimolar. The concentration of salt required to inhibit to this level was cultivar dependent. At highter concentrations (>150 millimolar) of salt, metabolism was further decreased. This decrease was not cultivar dependent. The decreased rate of metabolic heat output at the first transition could be correlated with decreases in uptake of NO3-, NH4+, and Pi that occurred as the salt concentration was increased. The high degree of dependence of the inhibition of metabolic heat output on NaCl concentration points to a highly cooperative reaction responsible for the general inhibition of metabolism and nutrient uptake. The time required to attain the first level of salt inhibition is less than 20 minutes. Inhibition of root tips was not reversible by washing with salt free solutions. In addition to revealing these features of salt inhibition, isothermal microcalorimetry is a promising method for convenient and rapid determination of varietal differences in response to increasing salinity.

NASA Discipline Life Support Systems

Metabolic Expenditures During Extravehicular Activity: Spaceflight versus Ground-based Simulation

In general metabolic rates tend to be higher in NBL than in flight: a) Restraint method dependent; b) Significant differences between the NBL and flight for BRT and APFR (buoyancy effects); and c) No significant difference between NBL and flight for free float and SRMS/SSRMS operations. The total metabolic energy expenditure for a given task and for the EVA as a whole are similar between NBL and flight: a) NBL metabolic rates are higher, but training EVAs are constrained to 5 hours; and b) Flight metabolic rates are lower, but the EVAs are typically an hour or more longer in duration. NBL metabolic rates provide a useful operational tool for flight planning. Quantifying differences and similarities between training and flight improves knowledge for preparation of safe and efficient EVAs.

Klein, Jill