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NASA NTRSDate not supplied

Improving Data Analyses for a Biological Mission to Deep Interplanetary Space

Onboard the Artemis 1 rocket, NASA plans to launch the first deep space bioscience mission past low Earth orbit (LEO) since 1972, BioSentinel, a 6-Unit (6U) biological CubeSat. BioSentinel’s goals are to assess the effect of deep space ionizing radiation (IR) on DNA and cell damage response, using Saccharomyces cerevisiae, or budding yeast, as a model organism. BioSentinel accomplishes this by measuring Optical Density (OD) in addition to metabolic activity using the redox dye alamarBlue, both of which will be read through light emitting diode (LED) lights of differing wavelengths. With the largest and most sophisticated energy-providing solar panels utilized on a biological CubeSat to date, BioSentinel will be equipped with an IR dosimeter to identify what doses of radiation the yeast is exposed to at any point in time, in addition to a transponder to send such data back to NASA Ames’ Multi Mission Operations Center (MMOC). Biology computational programs and data processing scripts are necessary to analyze this complex data once it is received, including automated subroutines to analyze duplication rate, alamarBlue reduction, and time periods when paired against numerous other variables. Overall, we have implemented several VisualBasic biocomputational programs to analyze such data in an organized and efficient manner so that conclusions can be made rapidly. Furthermore, we showcase why efficient analysis of particular parameters is important to better understand the risks that deep space IR poses to astronauts, especially when considering the upcoming Artemis missions.

Bijan Harandi↗

NASA NTRSDate not supplied

Emulating Nature: The Future of Sustainable Design with BIDARA

BIDARA (Bio-inspired Design and Research Assistant) is a GPT-4o chatbot that was instructed to help scientists and engineers understand, learn from, and emulate the strategies used by living things to create sustainable designs and technologies. BIDARA can guide users through the Biomimicry Institute’s Design Process, a step-by-step method to propose biomimetic solutions to challenges. This process includes defining the problem, biologizing the challenge, discovering natural models, abstracting design strategies, and emulating nature's lessons.

Brandon Ruffridge↗

DOE OSTI2015

Genome Sequencing and Comparative Analysis of the Biocontrol Agent Trichoderma harzianum sensu stricto TR274

Biological control is a complex process which requires many mechanisms and a high diversity of biochemical pathways. The species of Trichoderma harzianum are well known for their biocontrol activity against many plant pathogens. To gain new insights into the biocontrol mechanism used by T. harzianum, we sequenced the isolate TR274 genome using Illumina. The assembly was performed using AllPaths-LG with a maximum coverage of 100x. The assembly resulted in 2282 contigs with a N50 of 37033bp. The genome size generated was 40.8 Mb and the GC content was 47.7%, similar to other Trichoderma genomes. Using the JGI Annotation Pipeline we predicted 13,932 genes with a high transcriptome support. CEGMA tests suggested 100% genome completeness and 97.9% of RNA-SEQ reads were mapped to the genome. The phylogenetic comparison using orthologous proteins with all Trichoderma genomes sequenced at JGI, corroborates the Trichoderma (T. asperellum and T. atroviride), Longibrachiatum (T. reesei and T. longibrachiatum) and Pachibasium (T. harzianum and T. virens) section division described previously. The comparison between two Trichoderma harzianum species suggests a high genome similarity but some strain-specific expansions. Analyses of the secondary metabolites, CAZymes, transporters, proteases, transcription factors were performed. The Pachybasium section expanded virtually all categories analyzed compared with the other sections, specially Longibrachiatum section, that shows a clear contraction. These results suggests that these proteins families have an important role in their respective phenotypes. Future analysis will improve the understanding of this complex genus and give some insights about its lifestyle and the interactions with the environment.

Steindorff, Andrei S.↗

DOE OSTI2016

Printed biofuel cells

Methods, systems, and devices are disclosed for implementing a biofuel cell device for extracting energy from a biofuel. In one aspect, a biofuel cell device includes a substrate, an anode including a catalyst to facilitate the conversion of a fuel in a biological fluid in an oxidative process that releases electrons captured at the anode, thereby extracting energy from the fuel substance, a cathode configured on the substrate adjacent to the anode and separated from the anode by a spacing region, and a load electrically coupled to the anode and cathode via electrical interconnects to obtain the extracted energy as electrical energy.

09 BIOMASS FUELS↗

DOE OSTI2016

Uranium interaction with soil minerals in the presence of co-contaminants: Case Study- subsurface sediments at or below the water table

Uranium (U) contaminated subsurface systems are common on a global scale mainly because of its essential role in the production of plutonium for nuclear weapons and other nuclear energy and research activities. Studying the behavior and fate of U in these systems is challenging because of heterogeneities of different types (i.e., physical, chemical and mineralogical) and a complex network of often time-dependent hydrological, biological and chemical reactions and processes that occur sequentially or simultaneously, affecting and/or controlling U mobility. A U contaminated site, i.e., the Integrated Field Research Challenge site in Rifle, CO, USA (a former U mill site) is the focus of this discussion. The overall objectives of this chapter are to 1) provide an overview of the contamination levels (U and other co-contaminants) at this field site; 2) review and discuss different aspects of mineral-U contaminant interactions in reduced and oxidized environments, and in the presence of co-contaminants; 3) present results from a systematic macroscopic, microscopic, and spectroscopic study as an example of the current research efforts and the state-of-knowledge in this important research area; and 4) offer insightful conclusive remarks and future research needs about reactions and processes that control U and other contaminants’ fate and behavior under hydraulically saturated conditions. The implications and applications presented in this chapter are valid for U contaminated sites across the world.

As, V, Se contamination↗

DOE OSTI2020

Optimization of the Post-Operational Phase on Two Belgian Multi-Unit Nuclear Power Plants: the Case of the Non-Fissile Irradiated Core Items - 20156

The current legal framework in Belgium foresees the progressive phase out of nuclear power between October 2022 (Doel 3) and December 2025 (Doel 2). Upon its definitive shutdown, each unit of the Tihange and Doel sites will enter a Post-Operational Phase (POP) and be prepared for its Decontamination and Decommissioning (D and D). Prior to obtaining the D and D license, the Operator Electrabel is legally required to remove any non-fissile irradiated core items stored in the deactivation pools. The non-fissile irradiated core items consist essentially of control rods, poison rods and source thimbles as well as thimble plugs and foreign materials irradiated during operation: - Their significant content in highly radiant radionuclides (up to 6 TBq of Co-60 per kg of irradiated material) renders all existing operational waste management processes inadequate due to insufficient biological shielding; - Their high concentrations in long-lived radionuclides call for their disposal in a geological repository for which no final design nor waste acceptance criteria are expected prior to 2050. Uncertainties in the Belgian energy supply and security, however, require the Operator to be prepared for a partial nuclear phase out, where one or more units would benefit from lifetime extension while the remaining units would undergo decommissioning. The present paper aims at presenting how Electrabel, in partnership with Tractebel, addressed this challenge by maximizing the use of synergies within the respective sites as well as between both sites themselves, all the while accounting for site specificities. The most recent results and state of progress of the project will be detailed and the first lessons learned will be shared. The project has been split in multiple tasks and phased as follows: - An inventory phase aimed at mapping the contents, origin, composition and history of the non-fissile irradiated core items; - A pre-characterization phase based on neutron activation models; - A waste sorting phase aimed at separating waste forms for which an evacuation route exists from those for which such route does not exist; - A feasibility phase aimed at exploring all possible scenarios for the management of non-fissile irradiated core items and identifying the optimal feasible solution for each site; - A preparation phase (currently ongoing), developing further the optimal solution and ensuring that back-up solutions are available for any foreseeable change of context (licensing issue, modification in the nuclear phase-out program, etc.) and initiating early contacts with potential subcontractors for segmentation works and cask manufacturers, as well as the Belgian regulatory body and waste management agency. This phase also foresees the investigation of destructive and non-destructive radiological measurements to support the detailed characterization of the waste forms; - A realization phase (future work). (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

NASA NTRS1975

Physical nature of the climatic and biological effects of the Peru current

Surface and depth flow processes and their effects on the behavior of the Peru current are considered in relation to climatological and biological effects for the entire western coast of South America. The mean annual coastal air temperature is from 2 deg to 6 deg below the norm and precipitation is extremely rare. An upwelling effect brings up the cold deep waters with their rich content of organic material responsible for the huge biological productivity of the region.

Gusev, A. M.↗

NASA NTRS1995

Effect of the nonlinearity of the carbonate system on partial pressure of carbon dioxide in the oceans

Partial pressure of CO2 is a nonlinear function of several seawater properties. Due to the nonlinearity in this relationship, the partial pressure of a uniform ocean would be different from that of a nonuniform ocean with the same bulk seawater properties. Assuming uniformity of seawater properties at some temporal and spatial scales in carbon models leads to systematic errors in partial pressure of CO2. In this paper we evaluate the magnitude of these errors. We partition the Geochemical Ocean Sections Study and Transient Tracers in the Oceans data according to the horizontal structure of several box models from the literature. Our results suggest that assumption of uniformity at large scales leads to understanding of underestimation of global surface ocean partial pressure of CO2 by at least 3 - 12 microatm. Nonlinear effects also introduce systematic errors in the buffer factor estimated from bulk seawater properties. We find the standard deviation of partial pressure of CO2 to be an indicator of the magnitude of the nonlinear effects. We discuss the implications of these errors for some conclusions drawn from carbon models. Biogeochemical processes, such as mixing, gas exchange, or biological activity, influence the distribution of the seawater properties. A shift in spatial or temporal patterns of these processes can modify the nonuniformity of the seawater properties and thus alter the partial pressure of the surface waters, even if the mean intensities of the processes remain constant.

Trela, Piotr↗

DOE OSTI2021

Transforming biorefinery designs with ‘Plug-In Processes of Lignin’ to enable economic waste valorization

Biological lignin valorization has emerged as a major solution for sustainable and cost-effective biorefineries. However, current biorefineries yield lignin with inadequate fractionation for bioconversion, yet substantial changes of these biorefinery designs to focus on lignin could jeopardize carbohydrate efficiency and increase capital costs. We resolve the dilemma by designing ‘plug-in processes of lignin’ with the integration of leading pretreatment technologies. Substantial improvement of lignin bioconversion and synergistic enhancement of carbohydrate processing are achieved by solubilizing lignin via lowering molecular weight and increasing hydrophilic groups, addressing the dilemma of lignin- or carbohydrate-first scenarios. The plug-in processes of lignin could enable minimum polyhydroxyalkanoate selling price at as low as $6.18/kg. The results highlight the potential to achieve commercial production of polyhydroxyalkanoates as a co-product of cellulosic ethanol. Here, we show that the plug-in processes of lignin could transform biorefinery design toward sustainability by promoting carbon efficiency and optimizing the total capital cost.

09 BIOMASS FUELS↗

NASA NTRS2011

Summer Research Paper

Certain populations such as chemotherapy patients and atomic bomb survivors have been exposed to ionizing radiation and experience tissue damage and cancer initiation and progression. One cancer that can be initiated from radiation is esophageal squamous cell carcinoma (ESCC), an epithelial cancer that has a survival rate as low as 20%. Researchers have found that when protein tyrosine kinase receptors (RPTK) activate oncogenes, they can create epithelial tumors and cause deadly cancers like ESCC. The RPTK family has one group, MET, that has only two receptors, MET and RON, present in the human body. MET s ligand is the hepatocyte growth factor (HGF) and RON's ligand is the macrophage-stimulating protein (MSP-1). Both HGF and MSP-1 have been shown to activate their receptors and are implicated in certain processes. Since radiation damages cells throughout the biological system, researchers are investigating whether or not HGF and MSP-1 protects or kills certain normal and cancerous cells by being part of cell recovery processes. One research group recently reviewed that the HGF-MET pathway has an important role in the embryonic development in the liver, migration of myogenic precursor cells, regulation of epithelial morphogenesis and growth, and regeneration and protection in tissues. In addition, since the RON receptor is more commonly expressed in cells of epithelial origin, and when activated is part of epithelial cell matrix invasion, dissociation, and migration processes, scientists conclude that RON might be one of the factors causing epithelial cancer initiation in the biological system. In order to examine HGF and MSP-1 s effect on cancer initiation and progression we used two immortalized esophageal epithelial cell lines. One is a normal human cell line (EPC2-hTERT), while the other had a p53 mutation at the 175th amino acid position (EPC2-hTERT-p53(sup R175H)). For this investigation, we used 0(control), 2, and 4 Gray doses of gamma (Cs137) radiation and selected various concentrations from 0-100 ng/mL of HGF and MSP-1 in our assays. Since the HGF and MSP-1 pathways have proliferative roles in epithelial cells, we conducted the MTT proliferation assay to see if either drug enhances or inhibits cell proliferation over time. Also, a MTT cytotoxicity assay was necessary to observe whether the drugs are protecting the cells from radiation and if a trend is occurring depending upon the amount of dose added. In addition, a wound healing assay was done since both drugs have been to known to promote cell motility. Since cell damage occurs when radiation is added, apoptosis and micronuclei assays are vital to see if HGF and MSP-1 increase or decrease cell death and damage in normal and pre-cancerous cells and by how much based on the radiation dosage. Overall, we used the MTT, wound healing, apoptosis and micronuclei assays to investigate the effects ofHGF and MSP-1 on irradiated esophageal epithelial cells.

Patel, Zarana↗

DOE OSTI2023

Synthetic Biology Toolbox for Nitrogen-Fixing Soil Microbes

The soil environment adjacent to plant roots, termed the rhizosphere, is home to a wide variety of microorganisms that can significantly affect the physiology of nearby plants. Microbes in the rhizosphere can provide nutrients, secrete signaling compounds, and inhibit pathogens. These processes could be manipulated with synthetic biology to enhance the agricultural performance of crops grown for food, energy, or environmental remediation, if methods can be implemented in these nonmodel microbes. A common first step for domesticating nonmodel organisms is the development of a set of genetic engineering tools, termed a synthetic biology toolbox. A toolbox comprises transformation protocols, replicating vectors, genome engineering (e.g., CRISPR/Cas9), constitutive and inducible promoter systems, and other gene expression control elements. Furthermore, this work validated synthetic biology toolboxes in three nitrogen-fixing soil bacteria: Azotobacter vinelandii, Stutzerimonas stutzeri (Pseudomonas stutzeri), and a new isolate of Klebsiella variicola. All three organisms were amenable to transformation and reporter protein expression, with several functional inducible systems available for each organism. S. stutzeri and K. variicola showed more reliable plasmid-based expression, resulting in successful Cas9 recombineering to create scarless deletions and insertions. Using these tools, we generated mutants with inducible nitrogenase activity and introduced heterologous genes to produce resorcinol products with relevant biological activity in the rhizosphere.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

Source Contaminant Control System Design, Operation, and Testing for the Trash Compaction and Processing System

The Trash Compaction and Processing System (TCPS) aims to reduce volume, biologically safen, physically stabilize, manage effluents, and recover resources from astronaut trash in the International Space Station (ISS). This process involves heating the trash to high temperatures, which in turn releases gaseous contaminants. Effluent management scenarios involve releasing these gases back to the ISS cabin after processing and/or directly venting these gases out to space via the Vacuum Exhaust System (VES). Concerns for recovering the gases back to cabin are crew health, safety, and spacecraft environmental impact. The Heat Melt Compactor (HMC) at NASA Ames Research Center (ARC) serves as a test system that supports TCPS development by conducting risk reduction activities associated with an ISS flight demonstration. Previous gas effluent studies were conducted on the HMC. The results consisted of contaminants from the trash exhaust to exceed Spacecraft Maximum Allowable Concentrations (SMAC), which are selected airborne contaminants that can elicit toxicity symptoms to crewmembers via exposure. The Source Contaminant Control System (SCCS) aims to reduce that risk by converting the contaminants into carbon dioxide (CO2) and water (H2O) vapor. The SCCS is composed of a carbon adsorbent bed, to avoid catalyst poisoning, and a catalytic oxidizer (CatOx), which promotes oxidation of the contaminants to CO2 and H2O. In turn, the gases coming out of the SCCS should be compatible to the ISS cabin and systems such as the Trace Contaminant Control System (TCCS). Preparation for SCCS testing alongside the HMC Gen 3 are currently underway at ARC. The main objectives are to evaluate CatOx efficiency by CO2 conversion and characterize effectiveness of removal by comparing contaminant results before and after CatOx. This paper will report on the SCCS design, operation, and testing with results.

Janine Young↗

NASA NTRSDate not supplied

Source Contaminant Control System Design, Operation, and Testing for the Trash Compaction and Processing System

The Trash Compaction and Processing System (TCPS) aims to reduce volume, biologically safen, physically stabilize, manage effluents, and recover resources from astronaut trash in the International Space Station (ISS). This process involves heating the trash to high temperatures, which in turn releases gaseous contaminants. Effluent management scenarios involve releasing these gases back to the ISS cabin after processing and/or directly venting these gases out to space via the Vacuum Exhaust System (VES). Concerns for recovering the gases back to cabin are crew health, safety, and spacecraft environmental impact. The Heat Melt Compactor (HMC) at NASA Ames Research Center (ARC) serves as a test system that supports TCPS development by conducting risk reduction activities associated with an ISS flight demonstration. Previous gas effluent studies were conducted on the HMC. The results consisted of contaminants from the trash exhaust to exceed Spacecraft Maximum Allowable Concentrations (SMAC), which are selected airborne contaminants that can elicit toxicity symptoms to crewmembers via exposure. The Source Contaminant Control System (SCCS) aims to reduce that risk by converting the contaminants into carbon dioxide (CO2) and water (H2O) vapor. The SCCS is composed of a carbon adsorbent bed, to avoid catalyst poisoning, and a catalytic oxidizer (CatOx), which promotes oxidation of the contaminants to CO2and H2O. In turn, the gases coming out of the SCCS should be compatible to the ISS cabin and systems such as the Trace Contaminant Control System (TCCS). Preparation for SCCS testing alongside the HMC Gen 3 are currently underway at ARC. The main objectives are to evaluate CatOx efficiency by CO2conversion and characterize effectiveness of removal by comparing contaminant results before and after CatOx. This paper will report on the SCCS design, operation, and testing with results.

TCPS↗

NASA NTRSDate not supplied

Updated Analysis of the Source Contaminant Control System (SCCS) for the Trash Compaction and Processing System (TCPS)

Janine Criselda Young↗

DOE OSTI2026

Understanding Adsorption and Reactions at Aqueous Oxide Interfaces with Neural Network Potential Molecular Dynamics

Chemical processes at metal oxide−water interfaces are of central importance in geochemistry, biology, and energy technologies. A better understanding of these processes would allow us to make a significant step toward optimizing and controlling them, which could in turn lead to broader impacts. Computational modeling is indispensable to accomplishing this task because complexity and disorder often make it difficult to extract atomistic information from experiments. Balancing computational cost and accuracy, simulation schemes based on efficient machine learning representations of the potential energy surface (PES) predicted by ab initio calculations have become increasingly popular over the past decade. In particular, several studies have demonstrated the ability of machine learning models to accurately reproduce the complex ab initio PESs of aqueous oxide interfaces, allowing simulations of systems and processes that are not accessible with ab initio methods. In this Account, we review our recent efforts to understand adsorption processes and reactions at aqueous oxide interfaces using deep potential molecular dynamics (DPMD), a simulation scheme employing deep neural networks (DNNs), which has proven to be quite successful in accurately describing many different systems in the condensed phase. After summarizing the DPMD methodology, we first review our work on the acid−base chemistry of oxide surfaces in contact with water, a fundamental characteristic that controls proton transfer and surface charge at the interface. We focus on the aqueous interface of rutile IrO 2 , an oxide material thus far considered the best catalyst for the oxygen evolution reaction (OER). We show that this interface is characterized by a large fraction of dissociated water and a strong Brønsted acidity of the surface sites, in good agreement with the experimentally measured value of the point of zero proton charge. In our second example, we investigate how the adsorption of organic species from ambient air or water affects the structure and wettability of the aqueous interfaces of TiO 2 , a prototypical photocatalytic material. This is a question that is relevant to understanding the UV-induced hydrophilicity of TiO 2 surfaces, a property at the basis of self-cleaning windows and related applications. Specifically focusing on formic and acetic acids, the two most common atmospheric organic acids, our simulations reveal that these acids control the wettability of TiO 2 largely through acid−base chemistry at the interface rather than chemisorption on the oxide surface, a finding that could help improve the design of self-cleaning surfaces and photocatalytic devices. Finally, we review our recent study of methanol at TiO 2 −water interfaces, a system whose interest is largely motivated by the role of methanol in enhancing photocatalytic hydrogen evolution on TiO 2 . Our simulations provide mechanistic insights into the coupled roles of the organic adsorbate and water at the TiO 2 interface, with implications for how methanol enhances the activity of H 2 evolution.

adsorption↗

DOE OSTI2020

Biosystems Design to Accelerate C 3 -to-CAM Progression

Global demand for food and bioenergy production has increased rapidly, while the area of arable land has been declining for decades due to damage caused by erosion, pollution, sea level rise, urban development, soil salinization, and water scarcity driven by global climate change. In order to overcome this conflict, there is an urgent need to adapt conventional agriculture to water-limited and hotter conditions with plant crop systems that display higher water-use efficiency (WUE). Crassulacean acid metabolism (CAM) species have substantially higher WUE than species performing C 3 or C 4 photosynthesis. CAM plants are derived from C 3 photosynthesis ancestors. However, it is extremely unlikely that the C 3 or C 4 crop plants would evolve rapidly into CAM photosynthesis without human intervention. Currently, there is growing interest in improving WUE through transferring CAM into C 3 crops. However, engineering a major metabolic plant pathway, like CAM, is challenging and requires a comprehensive deep understanding of the enzymatic reactions and regulatory networks in both C 3 and CAM photosynthesis, as well as overcoming physiometabolic limitations such as diurnal stomatal regulation. Recent advances in CAM evolutionary genomics research, genome editing, and synthetic biology have increased the likelihood of successful acceleration of C 3 -to-CAM progression. Here, we first summarize the systems biology-level understanding of the molecular processes in the CAM pathway. Then, we review the principles of CAM engineering in an evolutionary context. Lastly, we discuss the technical approaches to accelerate the C 3 -to-CAM transition in plants using synthetic biology toolboxes.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1984

Process of making medical clip

An X-ray transparent and biologically inert medical clip for treating aneurisms and the like is disclosed, as well as a process for its production. A graphite reinforced composite film is molded into a unitary structure having a pair of hourglass-like cavities which are hinged together with a pair of jaws for grasping the aneurism extending from the wall of one cavity. A silicone rubber pellet is disposed in the other cavity to exert a spring force through the hinge area to normally bias the jaws into contact with each other.

Baucom, R. M.↗

DOE OSTI2023

A modified QuEChERS sample processing method for the determination of per- and polyfluoroalkyl substances (PFAS) in environmental biological matrices

Not Available

59 BASIC BIOLOGICAL SCIENCES↗