Systems dynamics and the uncertainties of diagnostics, testing and contact tracing for COVID-19
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59 BASIC BIOLOGICAL SCIENCES↗
SEARCH · Engineering Papers
Results for “Biological science”
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.
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Genomes of eight cultured microbes from soil sites in Wellesley, MA
We present the genomes of eight cultured microbes isolated from surface soil in Wellesley, MA. The dataset is useful for exploring genomic diversity among freshwater taxa including Pedobacter, Bacillus, Paenibacillus, Streptomyces, and Flavobacterium.
59 BASIC BIOLOGICAL SCIENCES↗
Rayonix DOE SBIR Phase IIA Final Technical Report
Explore the source record for details and available documents.
36 MATERIALS SCIENCE↗
The number of catalytic cycles in an enzyme’s lifetime and why it matters to metabolic engineering
Metabolic engineering uses enzymes as parts to build biosystems for specified tasks. Although a part’s working life and failure modes are key engineering performance indicators, this is not yet so in metabolic engineering because it is not known how long enzymes remain functional in vivo or whether cumulative deterioration (wear-out), sudden random failure, or other causes drive replacement. Consequently, enzymes cannot be engineered to extend life and cut the high energy costs of replacement. Guided by catalyst engineering, we adopted catalytic cycles until replacement (CCR) as a metric for enzyme functional life span in vivo. CCR is the number of catalytic cycles that an enzyme mediates in vivo before failure or replacement, i.e., metabolic flux rate/protein turnover rate. We used estimated fluxes and measured protein turnover rates to calculate CCRs for ~100–200 enzymes each from Lactococcus lactis, yeast, and Arabidopsis. CCRs in these organisms had similar ranges (<10 3 to >10 7 ) but different median values (3–4 × 10 4 in L. lactis and yeast versus 4 × 10 5 in Arabidopsis). In all organisms, enzymes whose substrates, products, or mechanisms can attack reactive amino acid residues had significantly lower median CCR values than other enzymes. Taken with literature on mechanism-based inactivation, the latter finding supports the proposal that 1) random active-site damage by reaction chemistry is an important cause of enzyme failure, and 2) reactive noncatalytic residues in the active-site region are likely contributors to damage susceptibility. Enzyme engineering to raise CCRs and lower replacement costs may thus be both beneficial and feasible.
54 ENVIRONMENTAL SCIENCES↗
Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes
Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species (Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry–based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants.
59 BASIC BIOLOGICAL SCIENCES↗
Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins
Borgs are huge, linear extrachromosomal elements associated with anaerobic methane-oxidizing archaea. Striking features of Borg genomes are pervasive tandem direct repeat (TR) regions. Here, we present six new Borg genomes and investigate the characteristics of TRs in all ten complete Borg genomes. We find that TR regions are rapidly evolving, recently formed, arise independently, and are virtually absent in host Methanoperedens genomes. Flanking partial repeats and A-enriched character constrain the TR formation mechanism. TRs can be in intergenic regions, where they might serve as regulatory RNAs, or in open reading frames (ORFs). TRs in ORFs are under very strong selective pressure, leading to perfect amino acid TRs (aaTRs) that are commonly intrinsically disordered regions. Proteins with aaTRs are often extracellular or membrane proteins, and functionally similar or homologous proteins often have aaTRs composed of the same amino acids. We propose that Borg aaTR-proteins functionally diversify Methanoperedens and all TRs are crucial for specific Borg–host associations and possibly cospeciation.
59 BASIC BIOLOGICAL SCIENCES↗
Polymer-Infiltrated Metal–Organic Frameworks for Thin-Film Composite Mixed-Matrix Membranes with High Gas Separation Properties
Thin-film composite mixed-matrix membranes (TFC-MMMs) have potential applications in practical gas separation processes because of their high permeance (gas flux) and gas selectivity. In this study, we fabricated a high-performance TFC-MMM based on a rubbery comb copolymer, i.e., poly(2-[3-(2H-benzotriazol-2-yl)-4-hydroxyphenyl] ethyl methacrylate)-co-poly(oxyethylene methacrylate) (PBE), and metal–organic framework MOF-808 nanoparticles. The rubbery copolymer penetrates through the pores of MOF-808, thereby tuning the pore size. In addition, the rubbery copolymer forms a defect-free interfacial morphology with polymer-infiltrated MOF-808 nanoparticles. Consequently, TFC-MMMs (thickness = 350 nm) can be successfully prepared even with a high loading of MOF-808. As polymer-infiltrated MOF is incorporated into the polymer matrix, the PBE/MOF-808 membrane exhibits a significantly higher CO 2 permeance (1069 GPU) and CO 2 /N 2 selectivity (52.7) than that of the pristine PBE membrane (CO 2 permeance = 431 GPU and CO 2 /N 2 selectivity = 36.2). Therefore, the approach considered in this study is suitable for fabricating high-performance thin-film composite membranes via polymer infiltration into MOF pores.
59 BASIC BIOLOGICAL SCIENCES↗
Engineering Microbial Communities: Frontier Science for the Bioeconomy Workshop Series
In nature, biological systems are shaped by complex interactions of diverse microorganisms such as bacteria, archaea, fungi, and viruses living within communities called microbiomes (Berg et al. 2020; Prescott 2017). These collective interactions result in emergent community properties that can be leveraged for beneficial purposes such as bioenergy and biomolecule production. Given this potential and the immensity of microbial genomic diversity, the U.S. Department of Energy’s (DOE) Biological and Environmental Research (BER) program has long invested in research to better understand the biology of environmental microbes and microbiomes.
59 BASIC BIOLOGICAL SCIENCES↗
Biological and Physical Space Research Laboratory 2002 Science Review
With the International Space Station Program approaching core complete, our NASA Headquarters sponsor, the new Code U Enterprise, Biological and Physical Research, is shifting its research emphasis from purely fundamental microgravity and biological sciences to strategic research aimed at enabling human missions beyond Earth orbit. Although we anticipate supporting microgravity research on the ISS for some time to come, our laboratory has been vigorously engaged in developing these new strategic research areas.This Technical Memorandum documents the internal science research at our laboratory as presented in a review to Dr. Ann Whitaker, MSFC Science Director, in July 2002. These presentations have been revised and updated as appropriate for this report. It provides a snapshot of the internal science capability of our laboratory as an aid to other NASA organizations and the external scientific community.
Curreri, P. A.↗
Solving complex nanostructures with ptychographic atomic electron tomography
Abstract Transmission electron microscopy (TEM) is essential for determining atomic scale structures in structural biology and materials science. In structural biology, three-dimensional structures of proteins are routinely determined from thousands of identical particles using phase-contrast TEM. In materials science, three-dimensional atomic structures of complex nanomaterials have been determined using atomic electron tomography (AET). However, neither of these methods can determine the three-dimensional atomic structure of heterogeneous nanomaterials containing light elements. Here, we perform ptychographic electron tomography from 34.5 million diffraction patterns to reconstruct an atomic resolution tilt series of a double wall-carbon nanotube (DW-CNT) encapsulating a complex ZrTe sandwich structure. Class averaging the resulting tilt series images and subpixel localization of the atomic peaks reveals a Zr 11 Te 50 structure containing a previously unobserved ZrTe 2 phase in the core. The experimental realization of atomic resolution ptychographic electron tomography will allow for the structural determination of a wide range of beam-sensitive nanomaterials containing light elements.
36 MATERIALS SCIENCE↗
Environmental stress mediates groundwater microbial community assembly
Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and ‘drift’ related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. As a result, our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.
54 ENVIRONMENTAL SCIENCES↗
Cellular, molecular, and therapeutic characterization of pilocarpine-induced temporal lobe epilepsy
Animal models have expanded our understanding of temporal lobe epilepsy (TLE). However, translating these to cell-specific druggable hypotheses is not explored. Herein, we conducted an integrative insilico-analysis of an available transcriptomics dataset obtained from animals with pilocarpine-induced-TLE. A set of 119 genes with subtle-to-moderate impact predicted most forms of epilepsy with ~ 97% accuracy and characteristically mapped to upregulated homeostatic and downregulated synaptic pathways. The deconvolution of cellular proportions revealed opposing changes in diverse cell types. The proportion of nonneuronal cells increased whereas that of interneurons, except for those expressing vasoactive intestinal peptide (Vip), decreased, and pyramidal neurons of the cornu-ammonis (CA) subfields showed the highest variation in proportion. A probabilistic Bayesian-network demonstrated an aberrant and oscillating physiological interaction between nonneuronal cells involved in the blood–brain-barrier and Vip interneurons in driving seizures, and their role was evaluated insilico using transcriptomic changes induced by valproic-acid, which showed opposing effects in the two cell-types. Additionally, we revealed novel epileptic and antiepileptic mechanisms and predicted drugs using causal inference, outperforming the present drug repurposing approaches. These well-powered findings not only expand the understanding of TLE and seizure oscillation, but also provide predictive biomarkers of epilepsy, cellular and causal micro-circuitry changes associated with it, and a drug-discovery method focusing on these events.
60 APPLIED LIFE SCIENCES↗
Robotic automation of droplet microfluidics
Droplet microfluidics enables powerful analytic capabilities but often requires workflows involving macro- and microfluidic processing steps that are cumbersome to perform manually. Here, we demonstrate the automation of droplet microfluidics with commercial fluid-handling robotics. The workflows incorporate common microfluidic devices including droplet generators, mergers, and sorters and utilize the robot's native capabilities for thermal control, incubation, and plate scanning. The ability to automate microfluidic devices using commercial fluid handling will speed up the integration of these methods into biological workflows.
59 BASIC BIOLOGICAL SCIENCES↗
Novel Microbial Routes to Synthesize Industrially Significant Precursor Compounds
Ethylene is the most widely employed organic precursor compound in industry. The potential to impact ethylene formation via recently discovered microbial processes is tenable using plentiful CO2 feedstocks. The overall long-term objective of this project was to develop an industrially compatible microbial process to synthesize ethylene in high yields. The key objective of this project was to fully define and initially characterized a recently discovered and genetically regulated anaerobic pathway to produce high levels of ethylene called the Dihydroxyacetone Phosphate - Ethylene Pathway in phototrophic bacteria. This was addressed through the following specific aims: 1. Fully probe the catalytic potential of all enzymes of the DHAP ethylene pathway and determine the regulatory mechanism of DHAP-ethylene pathway gene expression. 2. Discover effective and active ethylene enzymes encoded in cultured and uncultured organisms from anoxic environments. 3.Model the thermodynamics and kinetics of ethylene synthetic pathways to guide engineering efforts in integrating best performing DHAP-ethylene pathway enzymes into model bacteria chassis for enhance ethylene yields. Through this project we discovered the initially missing genetic and enzyme component of the DHAP-ethylene pathway that directly synthesized ethylene and other important industrial compounds like methane and ethane from specific substrates. We uncovered and partially characterized a nitrogenase-like reductase that functions in DHAP-ethylene pathway specifically and in methionine synthesis in general. This nitrogenase-like system is called the Methylthio-Alkane Reductase (MAR) for its ability to cleave volatile organic sulfur compounds into methanethiol (CH3-SH) for methionine synthesis and a hydrocarbon byproduct. Key to the DHAP-ethylene pathway, MAR is the essential enzyme that cleaves 2-methylthioethanol (CH3-S-CH2-CH2-OH) into ethylene. Coordinately, we uncovered that the MAR genes and genes associated with conversion of methanethiol (CH3-SH) to methionine are under genetic control of a LysR Type Transcriptional Regulator called SalR, whose activity is dependent upon the amount of sulfate available to the cell. When sulfate as the preferred sulfur source for cell growth drops below 200 micromolar, SalR become active for expressing the MAR and methionine biosynthesis genes to enable the cell to grow from volatile organic sulfur compounds and make ethylene. Metabolic thermos-kinetic modeling revealed that these MAR reactions for ethylene and other hydrocarbon production are highly thermodynamically favorable and are one of the largest driving forces for ethylene production by the DHAP-ethylene pathway for high ethylene yields. Modeling also indicated that a key aldolase and to a lesser extent an isomerase of the DHAP-ethylene pathway for production of the ethylene precursor, 2-methylthioethanol, also would increase ethylene yields. Through metagenomic mining and gene synthesis by the JGI DNA synthesis program, over 500 aldolase and isomerase homologs were synthesized and screened. From this, variants were uncovered with substantially higher activity that increased ethylene yields 5-fold via the aldolase reaction and 1.5-fold via the isomerase reaction. Each of these elements that increase ethylene production were integrated together via plasmid under appropriate gene promoter elements in the phototrophic bacterium, Rhodospirillum rubrum, resulting in at least 3 orders of magnitude increase in ethylene yield from carbon dioxide feedstock.
10 SYNTHETIC FUELS↗
Lignocellulosic Biomass-Derived Nanocellulose Crystals as Fillers in Membranes for Water and Wastewater Treatment: A Review
The improvement of membrane applications for wastewater treatment has been a focal point of research in recent times, with a wide variety of efforts being made to enhance the performance, integrity and environmental friendliness of the existing membrane materials. Cellulose nanocrystals (CNCs) are sustainable nanomaterials derived from microorganisms and plants with promising potential in wastewater treatment. Cellulose nanomaterials offer a satisfactory alternative to other environmentally harmful nanomaterials. However, only a few review articles on this important field are available in the open literature, especially in membrane applications for wastewater treatment. This review briefly highlights the circular economy of waste lignocellulosic biomass and the isolation of CNCs from waste lignocellulosic biomass for membrane applications. The surface chemical functionalization technique for the preparation of CNC-based materials with the desired functional groups and properties is outlined. Recent uses of CNC-based materials in membrane applications for wastewater treatment are presented. In addition, the assessment of the environmental impacts of CNCs, cellulose extraction, the production techniques of cellulose products, cellulose product utilization, and their end-of-life disposal are briefly discussed. Furthermore, the challenges and prospects for the development of CNC from waste biomass for application in wastewater treatment are discussed extensively. Finally, this review unraveled some important perceptions on the prospects of CNC-based materials, especially in membrane applications for the treatment of wastewater.
59 BASIC BIOLOGICAL SCIENCES↗
Investigating the Unique Ability of Trichodesmium To Fix Carbon and Nitrogen Simultaneously Using MiMoSA
The open ocean is an extremely competitive environment, partially due to the dearth of nutrients. Trichodesmium erythraeum, a marine diazotrophic cyanobacterium, is a keystone species in the ocean due to its ability to fix nitrogen and leak 30 to 50% into the surrounding environment, providing a valuable source of a necessary macronutrient to other species. While there are other diazotrophic cyanobacteria that play an important role in the marine nitrogen cycle, Trichodesmium is unique in its ability to fix both carbon and nitrogen simultaneously during the day without the use of specialized cells called heterocysts to protect nitrogenase from oxygen. Here, we use the advanced modeling framework called multiscale multiobjective systems analysis (MiMoSA) to investigate how Trichodesmium erythraeum can reduce dimolecular nitrogen to ammonium in the presence of oxygen. Our simulations indicate that nitrogenase inhibition is best modeled as Michealis-Menten competitive inhibition and that cells along the filament maintain microaerobia using high flux through Mehler reactions in order to protect nitrogenase from oxygen. We also examined the effect of location on metabolic flux and found that cells at the end of filaments operate in distinctly different metabolic modes than internal cells despite both operating in a photoautotrophic mode. These results give us important insight into how this species is able to operate photosynthesis and nitrogen fixation simultaneously, giving it a distinct advantage over other diazotrophic cyanobacteria because they can harvest light directly to fuel the energy demand of nitrogen fixation.
09 BIOMASS FUELS↗
Supplementary table, figures and DNA sequences of sorghum gene models SbiRTx430.01G455400 and SbiRTx.02G006600 that feature primers, gRNAs and indels created
In-context promoter bashing via genome editing is a route to identify and characterize critical regulatory regions that govern expression of genes of interest. The outcomes of in-context promoter bashing can be used to inform editing strategies to modulate the expression of selected gene models in a desired fashion. Here we employed in-context promoter bashing to characterize the proximal upstream regulatory regions of sorghum genes encoding phosphoenolpyruvate carboxykinase (Sb.PEPCK.BS, SbiTx430.01G455400) and alanine aminotransferase (SbiTx430.02G006600, SbAlaAT.BS), two proteins involved in the PCK C4 pathway. Characterized germinal edits within the targeted regions upstream of these two genes ranged in size from 138 bp up to 1790 bp. A 138 bp within the Sb.PEPCK.BS upstream region and a 1643 bp element within the Sb.AlaAT.BS upstream region were determined to be important for maintenance of transcription levels. No change in development or various physiological parameters was observed in characterized lineages carrying promoter edits. However, significant changes in seed reserves and a reduction in 100 seed weight were consistently observed, under both greenhouse and field environments, in plants carrying an edit in the promoter of Sb.PEPCK.BS gene were significantly reduced in transcript accumulation for this gene.
Quach, Truyen [Center for Plant Science Innovation↗
Phoresy in animals: review and synthesis of a common but understudied mode of dispersal
Phoresy is a type of interaction in which one species, the phoront, uses another species, the dispersal host, for transportation to new habitats or resources. Despite being a widespread behaviour, little is known about the ecology and evolution of phoresy. Our goal is to provide a comprehensive review of phoretic dispersal in animals and to bring renewed attention to this subject. We surveyed literature published between 1900 and 2020 to understand the extent of known higher-level taxonomic diversity (phyla, classes, and orders) and functional aspects of animals that use phoretic dispersal. Species dispersing phoretically have been observed in at least 13 animal phyla, 25 classes, and 60 orders. The majority of known phoronts are arthropods (Phylum Euarthropoda) in terrestrial habitats, but phoronts also occur in freshwater and marine environments. Marine phoronts may be severely under-represented in the literature due to the relative difficulty of studying these systems. Phoronts are generally small with low mobility and use habitats or resources that are ephemeral and/or widely dispersed. Many phoronts are also parasites. In general, animals that engage in phoresy use a wide variety of morphological and behavioural traits for locating, attaching to, and detaching from dispersal hosts, but the exact mechanisms behind these activities are largely unknown. In addition to diversity, we discuss the evolution of phoresy including the long-standing idea that it can be a precursor to parasitism and other forms of symbioses. To conclude, we suggest several areas of future research to improve our understanding of phoresy and its ecological and evolutionary significance.
59 BASIC BIOLOGICAL SCIENCES↗