Engineering topics

Mitchell, Julie

Publications and source records attributed to Mitchell, Julie.

14 records

DOE OSTI2024

An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments

Abstract Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa . Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances

Easy-to-use, open-source, general-purpose programs for modeling a protein structure from inter-atomic distances are needed for modeling from experimental data and refinement of predicted protein structures. OpenMDlr is an open-source Python package for modeling protein structures from pairwise distances between any atoms, and optionally, dihedral angles. Finally, we provide a user-friendly input format for harnessing modern biomolecular force fields in an easy-to-install package that can efficiently make use of multiple compute cores.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide Removal

A grand challenge facing society is climate change caused mainly by rising CO 2 concentration in Earth’s atmosphere. Terrestrial plants are linchpins in global carbon cycling, with a unique capability of capturing CO 2 via photosynthesis and translocating captured carbon to stems, roots, and soils for long-term storage. However, many researchers postulate that existing land plants cannot meet the ambitious requirement for CO 2 removal to mitigate climate change in the future due to low photosynthetic efficiency, limited carbon allocation for long-term storage, and low suitability for the bioeconomy. To address these limitations, there is an urgent need for genetic improvement of existing plants or construction of novel plant systems through biosystems design (or biodesign). Here, we summarize validated biological parts (e.g., protein-encoding genes and noncoding RNAs) for biological engineering of carbon dioxide removal (CDR) traits in terrestrial plants to accelerate land-based decarbonization in bioenergy plantations and agricultural settings and promote a vibrant bioeconomy. Specifically, we first summarize the framework of plant-based CDR (e.g., CO 2 capture, translocation, storage, and conversion to value-added products). Then, we highlight some representative biological parts, with experimental evidence, in this framework. Finally, we discuss challenges and strategies for the identification and curation of biological parts for CDR engineering in plants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Biological Carbon Sequestration for Climate and Soil Health

58 GEOSCIENCES↗

DOE OSTI2021

Biological Carbon Sequestration for Climate and Soil Health

The United States recently launched the Net Zero World Initiative on decarbonization. As temperatures and sea levels rise, strong action is needed to mitigate high atmospheric CO 2 levels. In response to this need, a joint workshop between the US Department of Energy’s Oak Ridge National Laboratory (ORNL) and Lawrence Berkeley National Laboratory (LBNL) was convened to assess the challenges and opportunities within biological carbon (C) capture. The virtual workshop on Biological Carbon Sequestration for Climate and Soil Health focused on three aspects of biological C capture research: natural systems, engineered systems, and modeling. For this workshop, the scope of natural systems included unmanaged (e.g., grasslands, wetlands, natural forests) and managed (e.g., agricultural lands, commercial forests, forest biofuels) ecosystems. The engineered systems group covered topics in genetically modified plants and microbes, synthetic microbiomes, and altered plant–microbe interactions for enhancing C capture, storage, and utilization. The modeling group focused on computational tools and data collection to predict and assess the effectiveness of new biocarbon sequestration advances. Participant expertise included plant and microbial systems biology, synthetic biology, soil biogeochemistry, and techno-economic analysis. Together, participants outlined key scientific advances in support of biological C capture and storage. Among the major findings of the meeting were the need to better measure C flux within natural, agricultural, and fabricated ecosystems for experimentation; better understand the role of soil composition, plant roots, and the rhizosphere (i.e., the soil surrounding the plant root) in the underground storage of organic C; and design plant–microbe systems for maximal C storage.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Combining Three-Dimensional Modeling with Artificial Intelligence to Increase Specificity and Precision in Peptide–MHC Binding Predictions

The reliable prediction of the affinity of candidate peptides for the MHC is important for predicting their potential antigenicity and thus influences medical applications, such as decisions on their inclusion in T cell–based vaccines. In this study, we present a rapid, predictive computational approach that combines a popular, sequence-based artificial neural network method, NetMHCpan 4.0, with three-dimensional structural modeling. We find that the ensembles of bound peptide conformations generated by the programs MODELLER and Rosetta FlexPepDock are less variable in geometry for strong binders than for low-affinity peptides. In tests on 1271 peptide sequences for which the experimental dissociation constants of binding to the well-characterized murine MHC allele H-2D b are known, by applying thresholds for geometric fluctuations the structure-based approach in a standalone manner drastically improves the statistical specificity, reducing the number of false positives. Furthermore, filtering candidates generated with NetMHCpan 4.0 with the structure-based predictor led to an increase in the positive predictive value (PPV) of the peptides correctly predicted to bind very strongly (i.e., Kd < 100 nM) from 40 to 52% (p = 0.027). The combined method also significantly improved the PPV when tested on five human alleles, including some with limited data for training. Overall, an average increase of 10% in the PPV was found over the standalone sequence-based method. The combined method should be useful in the rapid design of effective T cell–based vaccines.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

iPNHOT: a knowledge-based approach for identifying protein-nucleic acid interaction hot spots

The interaction between proteins and nucleic acids plays pivotal roles in various biological processes such as transcription, translation, and gene regulation. Hot spots are a small set of residues that contribute most to the binding affinity of a protein-nucleic acid interaction. Compared to the extensive studies of the hot spots on protein-protein interfaces, the hot spot residues within protein-nucleic acids interfaces remain less well-studied, in part because mutagenesis data for protein-nucleic acids interaction are not as abundant as that for protein-protein interactions. In this study, we built a new computational model, iPNHOT, to effectively predict hot spot residues on protein-nucleic acids interfaces. One training data set and an independent test set were collected from dbAMEPNI and some recent literature, respectively. To build our model, we generated 97 different sequential and structural features and used a two-step strategy to select the relevant features. The final model was built based only on 7 features using a support vector machine (SVM). The features include two unique features such as ΔSASsa 1/2 and esp3, which are newly proposed in this study. Based on the cross validation results, our model gave F1 score and AUROC as 0.725 and 0.807 on the subset collected from ProNIT, respectively, compared to 0.407 and 0.670 of mCSM-NA, a state-of-the art model to predict the thermodynamic effects of protein-nucleic acid interaction. The iPNHOT model was further tested on the independent test set, which showed that our model outperformed other methods. Here, by collecting data from a recently published database dbAMEPNI, we proposed a new model, iPNHOT, to predict hotspots on both protein-DNA and protein-RNA interfaces. The results show that our model outperforms the existing state-of-art models. Our model is available for users through a webserver: http://zhulab.ahu.edu.cn/iPNHOT/.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Feature Design for Protein Interface Hotspots Using KFC2 and Rosetta

Protein–protein interactions regulate many essential biological processes and play an important role in health and disease. The process of experimentally characterizing protein residues that contribute the most to protein–protein interaction affinity and specificity is laborious. Thus, developing models that accurately characterize hotspots at protein–protein interfaces provides important information about how to inhibit therapeutically relevant protein–protein interactions. During the course of the ICERM WiSDM workshop 2017, we combined the KFC2a protein–protein interaction hotspot prediction features with Rosetta scoring function terms and interface filter metrics. A two-way and three-way forward selection strategy was employed to train support vector machine classifiers, as was a reverse feature elimination strategy. From these results, we identified subsets of KFC2a and Rosetta combined features that show improved performance over KFC2a features alone.

Seeger, Franziska↗

NASA NTRS2018

NASA's Astromaterials Acquisition and Curation Office: Enabling 50 Years of Lunar and Planetary Research, Now Heading to Mars

No abstract available

Evans, Cynthia↗

NASA NTRS2018

Next Steps in Planetary Protection for Human Spaceflight

Planetary protection is defined as: a) the prevention of contamination of extraterrestrial bodies by terrestrial microorganisms, and b) biohazard containment of returned samples from bodies in the Solar System that could harbor life.1 While the majority of interplanetary missions to date have involved robotic exploration, future missions will include human explorers. Current planetary protection requirements do not address the unique challenges associated with human exploration. The purpose of this abstract is to review planetary protection efforts for crewed missions and provide a forward plan for implementing them at the systems level. Article IX of the UN Outer Space Treaty of 1967 provides the definition of planetary protection, outlined above.1 COSPAR holds the international standard in line with this treaty2, while NASA's Planetary Protection Policy (NPD 8020.7G) outlines the U.S. implementation of the COSPAR standard. 3;4 NPI 8020.7 groups future human spaceflight planetary protection studies as follows: 1) microbial monitoring, 2) contamination mitigation and control, and 3) environmental effects. Additionally, a NPI 8020.7 outlines a five-step plan for forward work: 1) a literature review, 2) community inputs, 3) completion of recommended studies, 4) developing a draft NPR, and 5) implementation with NASA teams. The literature review was published in 2016.5 Inputs from the community were gathered at the Planetary Protection Knowledge Gaps for Human Extraterrestrial Missions, held in 2015.6 Johnson and Race (2016) outlined notional requirements and prioritized studies needed before final requirements can be produced. This prior work sets the stage for completing the necessary studies and finalizing planetary protection requirements for human spaceflight. We propose a continuation of the systems engineering approach adopted thus far. The challenges associated with the implementation of notional requirements will be quantified in detailed discussions with internal stakeholders. The status and results of high-priority studies that have been completed since 2016 or are ongoing will be incorporated into discussions with stakeholders. In this way, we plan to bridge the gap between the science behind planetary protection and the engineering development that will implement it, allowing finalized planetary protection requirements to be developed for future human space missions.

Mitchell, Julie↗

NASA NTRS2015

Development of a Low Toxicity Urine Pretreatment for Water Recovery in Space

Wastewater stabilization was an essential component of the spacecraft water cycle. The purpose of stabilizing wastewater was two-fold. First, stabilization prevents the breakdown of urea into ammonia, a toxic gas at high concentrations. Second, it prevents the growth of microorganisms, thereby mitigating hardware and water quality issues due to due biofilm and planktonic growth. Current stabilization techniques involve oxidizers and strong acids (pH=2) such as chromic and sulfuric acid, which are highly toxic and pose a risk to crew health. The purpose of this effort was to explore less toxic stabilization techniques, such as food-grade and commercial care preservatives. Additionally, certain preservatives were tested in the presence of a low-toxicity organic acid. Triplicate 300-mL volumes of urine were dosed with a predetermined quantity of stabilizer and stored for two weeks. During that time, pH, total organic carbon (TOC), ammonia, and turbidity were monitored. Those preservatives that showed the lowest visible microbial growth and stable pH were further tested in a six-month stability study. The results of the six-month study are also included in this paper. Additionally, the pretreatment formulations were tested to determine if the pretreated urine could be distilled to remove 85% of the water, as would occur on the ISS. The goal of the pretreatment was to produce no solids in the resulting brine at 85% water recovery.

Adam, Niklas↗

NASA NTRS2014

Development of Low-Toxicity Wastewater Stabilization for Spacecraft Water Recovery Systems

Adam, Niklas↗

NASA NTRS2013

Ion Exchange Technology Development in Support of the Urine Processor Assembly

The urine processor assembly (UPA) on the International Space Station (ISS) recovers water from urine via a vacuum distillation process. The distillation occurs in a rotating distillation assembly (DA) where the urine is heated and subjected to sub-ambient pressure. As water is removed, the original organics, salts, and minerals in the urine become more concentrated and result in urine brine. Eventually, water removal will concentrate the urine brine to super saturation of individual constituents, and precipitation occurs. Under typical UPA DA operating conditions, calcium sulfate or gypsum is the first chemical to precipitate in substantial quantity. During preflight testing with ground urine, the UPA achieved 85% water recovery without precipitation. However, on ISS, it is possible that crewmember urine can be significantly more concentrated relative to urine from ground donors. As a result, gypsum precipitated in the DA when operating at water recovery rates at or near 85%, causing the failure and subsequent re14 NASA Tech Briefs, September 2013 placement of the DA. Later investigations have demonstrated that an excess of calcium and sulfate will cause precipitation at water recovery rates greater than 70%. The source of the excess calcium is likely physiological in nature, via crewmembers' bone loss, while the excess sulfate is primarily due to the sulfuric acid component of the urine pretreatment. To prevent gypsum precipitation in the UPA, the Precipitation Prevention Project (PPP) team has focused on removing the calcium ion from pretreated urine, using ion exchange resins as calcium removal agents. The selectivity and effectiveness of ion exchange resins are determined by such factors as the mobility of the liquid phase through the polymer matrix, the density of functional groups, type of functional groups bound to the matrix, and the chemical characteristics of the liquid phase (pH, oxidation potential, and ionic strength). Previous experience with ion exchange resins has demonstrated that the most effective implementation for an ion exchange resin is a cartridge, or column, in which the resin is contained. Based on the results of equilibrium and sub-scale dynamic column testing, a possible solution for mitigating the calcium precipitation issue on the ISS has been identified. From an original pool of 13 ion exchange resins, two candidates have been identified that demonstrate substantial calcium removal on the sub-scale. The dramatic reduction in resin performance from published calcium uptake demonstrates the need for thorough evaluation of resins at the low pH and strong oxidizing environment present in the UPA. Chemical variations in the influent (calcium concentrations and pretreatment dosing) appear to have a noticeable impact on the calcium capacity of the resin. Low calcium concentrations and high pretreatment dosing will likely result in a decrease in calcium capacity. Conversely, low pre trea t - ment dosing will likely result in an increase in calcium capacity. In contrast, investigations at a variety of flow rates, length-to-diameter ratios, resin volumes, and flow regimes (continuous versus pulsed) show that changes in physical parameters do not have substantial impacts on resin performance in the very low specific velocity ranges of interest. This result is particularly useful because most commercial applications at higher specific velocities do show a relatively strong relationship between flow and capacity. The lack of a strong relationship will allow more flexibility in the implementation of an ion exchange bed for flight. Verification of subscale tests with flight-scale resin beds is recommended prior to implementation in the on-orbit UPA.

Mitchell, Julie↗

NASA NTRS2012

Alternative Water Processor Test Development

The Next Generation Life Support Project is developing an Alternative Water Processor (AWP) as a candidate water recovery system for long duration exploration missions. The AWP consists of biological water processor (BWP) integrated with a forward osmosis secondary treatment system (FOST). The basis of the BWP is a membrane aerated biological reactor (MABR), developed in concert with Texas Tech University. Bacteria located within the MABR metabolize organic material in wastewater, converting approximately 90% of the total organic carbon to carbon dioxide. In addition, bacteria convert a portion of the ammonia-nitrogen present in the wastewater to nitrogen gas, through a combination of nitrogen and denitrification. The effluent from the BWP system is low in organic contaminants, but high in total dissolved solids. The FOST system, integrated downstream of the BWP, removes dissolved solids through a combination of concentration-driven forward osmosis and pressure driven reverse osmosis. The integrated system is expected to produce water with a total organic carbon less than 50 mg/l and dissolved solids that meet potable water requirements for spaceflight. This paper describes the test definition, the design of the BWP and FOST subsystems, and plans for integrated testing.

Pickering, Karen D.↗