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At least 505 records · Page 28

Coarse-grained resource allocation modeling for decoding and rewiring microbial metabolism

Microbial metabolism is a complex, emergent system driven by the coordinated interplay of intricate and dynamic molecular processes. To elucidate cellular behavior and enable biotechnological applications, quantitative models that address the inherent complexity of metabolism have been developed from a resource allocation perspective. Here, we synthesize recent advances in coarse-grained resource allocation frameworks and their applications in understanding microbial physiology and guiding gene circuit design. Here, these frameworks reveal global regulatory constraints and predict cellular adaptation to nutrient and environmental changes. In addition, they enable the quantification of metabolic costs, the dissection of circuit–host interactions, and the development of strategies for burden mitigation. Collectively, these modeling frameworks provide a powerful platform for uncovering quantitative principles of microbial growth and engineering robust synthetic biological systems.

coarse-grained modeling↗

Genetic diversity, population structure and anthracnose resistance response in a novel sweet sorghum diversity panel

Sweet sorghum is an attractive feedstock for the production of renewable chemicals and fuels due to the readily available fermentable sugars that can be extracted from the juice, and the additional stream of fermentable sugars that can be obtained from the cell wall polysaccharides in the bagasse. An important selection criterion for new sweet sorghum germplasm is resistance to anthracnose, a disease caused by the fungal pathogen Colletotrichum sublineolum. The identification of novel anthracnose-resistance sources present in sweet sorghum germplasm offers a fast track towards the development of new resistant sweet sorghum germplasm. We established a sweet sorghum diversity panel (SWDP) of 272 accessions from the USDA-ARS National Plant Germplasm (NPGS) collection that includes landraces from 22 countries and advanced breeding material, and that represents ~15% of the NPGS sweet sorghum collection. Genomic characterization of the SWDP identified 171,954 single nucleotide polymorphisms (SNPs) with an average of one SNP per 4,071 kb. Population structure analysis revealed that the SWDP could be stratified into four populations and one admixed group, and that this population structure could be aligned to sorghum’s racial classification. Results from a two-year replicated trial of the SWDP for anthracnose resistance response in Texas, Georgia, Florida, and Puerto Rico showed 27 accessions to be resistant across locations, while 145 accessions showed variable resistance response against local pathotypes. A genome-wide association study identified 16 novel genomic regions associated with anthracnose resistance. Four resistance loci on chromosomes 3, 6, 8 and 9 were identified against pathotypes from Puerto Rico, and two resistance loci on chromosomes 3 and 8 against pathotypes from Texas. In Georgia and Florida, three resistance loci were detected on chromosomes 4, 5, 6 and four on chromosomes 4, 5 (two loci) and 7, respectively. One resistance locus on chromosome 2 was effective against pathotypes from Texas and Puerto Rico and a genomic region of 41.6 kb at the tip of chromosome 8 was associated with resistance response observed in Georgia, Texas, and Puerto Rico. This publicly available SWDP and the extensive evaluation of anthracnose resistance represent a valuable genomic resource for the improvement of sorghum.

59 BASIC BIOLOGICAL SCIENCES↗

Frontiers of Life Sciences: The Human Exploration of the Moon and Mars

The rapid development of the productive processes after World War II extended human settlements into new ecological niches. Advances in Life Sciences played a decisive role supporting the establishment of human presence in areas of the planet where human life could have not existed otherwise. The evolution of life support systems, and the fabrication of new materials and technologies has enabled humans to inhabit Polar Regions, ocean surfaces and depths; and to leave Earth and occupy Low Earth Orbit. By the end of the 20 th Century, stations in the Antarctic and Arctic, off shore oil platforms, submarines, and space stations had become the ultimate demonstration of human ability to engineer habitats at Earth extreme environments and outer space. As we enter the 21st Century, the next development of human settlements will occur through the exploration of the Moon, Mars, and beyond. The major risks of space exploration derive from long exposure of humans and other life systems to radiation, microgravity, isolation and confinement, dependence on artificial life support systems, and unknown effects (e.g., altered magnetic fields, ultrahigh vacuum on bacteria, fungi, etc.). Countermeasures will require a complete characterization of human and other biological systems adaptation processes. To sustain life in transit and on the surface of the Moon and Mars will require a balance of spacecraft, cargo, astronaut crews, and the use of in situ resources. Limitations on the number of crewmembers, payloads, and the barrenness of the terrain require a novel design for the capabilities needed in transit and at exploration outpost sites. The planned destinations have resources that may be accessed to produce materials, food, shelter, power, and to provide an environment compatible with successful occupation of longterm exploration sites. Once more, the advancements of Life Sciences will be essential for the design of interplanetary voyages and planetary surface operations. This presentation delineates the role of Life Sciences and its frontiers, especially Cell Science, in the context of human exploration. Life support systems, food production, and medical equipment encompass many of vital aspects related to the new vision for NASA.

North, Regina M.↗

Lambayeque Water Resources: Assessing Hydrologic Patterns Using NASA Earth Observations to Address Tree Mortality in Peru’s Coastal Mesquite Forests

The mesquite (Prosopi ssp.) forests in Northwestern Peru have had a significant increase in tree mortality in the past fifty years. Within this time frame, 17% of the forest extent was lost and the forest saw an average annual declination rate of 0.33% (Ektvedt, Vetaas, & Lundberg, 2012). These habitats support the region's rich biodiversity and play an important role in local community economies. Several hydrologic causes for mesquite mortality have been hypothesized, but local researchers lack spatially comprehensive techniques to address the problem. While in situ research is currently being utilized in an attempt to explain this recent anomaly, landscape-level visualizations through remote sensing have not been produced to find connections between hydrologic trends and the health of Northwestern Peru’s mesquite forests. Climate Hazards Group InfraRed Precipitation with Station dataand Global Land Data Assimilation Systemdata were analyzed to assess hydrologic patterns pertaining to precipitation and soil moisture in the Lambayeque region of Peru. These data were then paired with vegetation indices derived from Terra Moderate Resolution Imaging Spectroradiometer (MODIS) and Suomi National Polar-orbiting Partnership (NPP) Visible Infrared Imaging Radiometer Suite (VIIRS) to display how changing hydrologic patterns relate to the health of mesquite trees. These data were then compiled on a monthly basis over the 30-year study period to create a time series product, which was later referenced with background research to find the likely causes of recent forest decline. The results will assist in the Lambayeque Regional Government’s understanding of recent biological declination and will help them design strategies to mitigate forest decline in Lambayeque, Peru and surrounding regions.

Water Resources↗

Microbiomes Reduce Their Host’s Sensitivity to Interspecific Interactions

Description of the Earth’s microbiota has recently undergone a phenomenal expansion that has challenged basic assumptions in many areas of biology, including hominid evolution, human gastrointestinal and neurodevelopmental disorders, and plant adaptation to climate change. By using the classic model system of freshwater phytoplankton that has been drawn upon for numerous foundational theories in ecology, we show that microbiomes, by facilitating their host population, can also influence between-species interactions among their eukaryotic hosts. Between-species interactions, including competition for resources, has been a central tenet in the field of ecology because of its implications for the diversity and composition of communities and how this in turn shapes ecosystem functioning.

59 BASIC BIOLOGICAL SCIENCES↗

From the bench to the reactor: engineered filamentous fungi for biochemical and biomaterial production

Filamentous fungi can convert a wide variety of naturally occurring chemical compounds, including organic biomass and waste streams, into a range of products. They have long been used for industrial organic acid production and food preparation. In this review, we will discuss production of products such as organic acids, lipids, small molecules, enzymes, materials, and foods, and highlight advances in metabolic and protein engineering, including CRISPR-Cas9-mediated strain improvements. We discuss to what extent these products are already being made on a commercial scale, as well as what is still required to make certain promising concepts industrially and commercially relevant. Despite significant progress, the systematic application of synthetic biology to filamentous fungi remains in its infancy, with many opportunities for discovery and innovation as new strains and genetic tools are developed. The integration of fungal biotechnology into circular and bio-based economies promises to address critical challenges in waste management, resource sustainability, and the development of new materials for terrestrial and extraterrestrial applications, but requires further developments in genetic engineering and process design.

09 BIOMASS FUELS↗

Intensified Flue Gas Desulfurization Water Treatment for Reuse, Solidification, and Discharge

The goal of this final project report is to summarize the work conducted on project DE-FE0031555. In accordance with the Statement of Project Objectives (SOPO), the University of Kentucky Center for Applied Energy Research (UK CAER) (Recipient) developed a hybrid electrochemical-membrane technology for treating wet flue gas desulfurization (WFGD) blowdown from coal-fired power generation plants that (1) removes government-regulated species and total suspended solids (TSS) via electrocoagulation with solid/liquid separation to avoid further treatments by a biological method specifically for selenium, and (2) reduces total dissolved solids (TDS) in a nanofiltration unit to promote water recycle and reduce freshwater intake. Additional technological configurations were pursued, including (1) nanofiltration combined with zeolite dewatering for a near-zero liquid discharge (ZLD) scenario, and (2) polishing discharge from zeolite dewatering using capacitive deionization (CDI) with 90+% salt rejection to produce water with less than 100ppm TDS for more beneficial use. Project results verified that UK CAER’s hybrid approach addressed the complexities of WFGD blowdown with simplified unit operation at relatively low capital investment by demonstrating: (1) an effective in-situ generated solid sorbent material, green-rust (GR), that specifically removes regulated dissolved species in WFGD blowdown, including selenium, arsenic, and nitrates; (2) a low-cost, high flux nanofiltration treatment that removes both monovalent and divalent species at >80% rejection to adequately provide water recycle and extend the life of FGD equipment by mitigating chloride aided pitting corrosion mechanisms; and (3) a solidification and stabilization process using pozzolanic agents that retain regulated species and satisfy the Resource Conservation and Recovery Act (RCRA) leachate requirements. UK CAER proved electrocoagulation with GR to be an intensified solution for effluent limit guidelines (ELG), and based on preliminary techno-economic analysis (TEA), in comparison to DOE’s Case 1 for Biological Wastewater Treatment that had a purchased equipment cost (PEC) of $\$$5.26 million and a Total plant cost (TPC) of $\$$30.0 million, the EC process had a PEC of $\$$2.67 million and the TPC of $\$$17.0 million. While the electricity consumption for Case 1 was 53 kW, it was 110 kW for the EC process due to dissolving iron for a three-stage reaction design. However, electricity consumption for the EC process could be significantly reduced by adopting a counter-current reactor design for at least a 6-stage chemical reaction operation.

01 COAL, LIGNITE, AND PEAT↗

Rapid Turn Around BRIC-PDFU Payload: A New Paradigm for Spaceflight Experiments

In 2009, NASA's Fundamental Space Biology program provided an opportunity for investigators to propose for a quick-turn-around multi-user spaceflight experiment that focused on the model plant species Arabidopsis thaliana. This was a passive payload with no on-orbit power or communications available. An NRA was rapidly written (8/09), released (NNH09ZTT004N; 9/09), proposals were received (11/09) and peer reviewed with 3 PI groups selected for flight (1/10): (1) A-L Paul, University of Florida, (2) E. Blancaflor, Noble Foundation, (3) J. Kiss, Miami University. The investigators flew Arabidopsis seeds or callus cultures of their choosing (plated onto 60 mm diameter Petri dishes containing agarsolidified media) on the STS-131 Space Shuttle mission (launched 4/5/10) and the resulting plant tissues returned to earth on 4/20/10. Each petri dish was placed inside its own Petri Dish Fixation Unit (PDFU), which was assembled and loaded with either formaldehyde, glutaraldehyde or RNAlater for crew-facilitated on-orbit fixation. Five PDFUs plus a temperature data logger were loaded into each of 8 BRIC-PDFUs (Biological Research In Canisters PDFU). All eight BRIC-PDFUs were loaded into a half tray along with actuator equipment that the crew used for the fixations. Pre-flight turn-over was 28 hours prior to launch. The BRIC-PDFU assemblies were removed from the orbiter and handed over to the investigator teams for processing 5-6 hours after landing. This payload demonstrated a rapid response turnaround for flying multiple peer-reviewed science investigations using previously flown hardware and minimal ISS-resources. The approach used reduced both hardware/certification and PI costs. The time waiting for a flight opportunity for the selected Pls was minimal. This new paradigm for spaceflight experiments may provide a model for future flight research opportunities. The ultimate goal is to fly as many investigators as rapidly as possible and reinvigorate the space biology community while obtaining high-quality, peer-reviewed science.

Levine, Howard G.↗

Composting on Mars or the Moon: I. Comparative evaluation of process design alternatives

As a candidate technology for treating solid wastes and recovering resources in bioregenerative Advanced Life Support, composting potentially offers such advantages as compactness, low mass, near ambient reactor temperatures and pressures, reliability, flexibility, simplicity, and forgiveness of operational error or neglect. Importantly, the interactions among the physical, chemical, and biological factors that govern composting system behavior are well understood. This article comparatively evaluates five Generic Systems that describe the basic alternatives to composting facility design and control. These are: 1) passive aeration; 2) passive aeration abetted by mechanical agitation; 3) forced aeration--O2 feedback control; 4) forced aeration--temperature feedback control; 5) forced aeration--integrated O2 and temperature feedback control. Each of the five has a distinctive pattern of behavior and process performance characteristics. Only Systems 4 and 5 are judged to be viable candidates for ALS on alien worlds, though which is better suited in this application is yet to be determined.

Review↗

Integrative teaching of metabolic modeling and flux analysis with interactive python modules

Abstract The modeling of rates of biochemical reactions—fluxes—in metabolic networks is widely used for both basic biological research and biotechnological applications. A number of different modeling methods have been developed to estimate and predict fluxes, including kinetic and constraint‐based (Metabolic Flux Analysis and flux balance analysis) approaches. Although different resources exist for teaching these methods individually, to‐date no resources have been developed to teach these approaches in an integrative way that equips learners with an understanding of each modeling paradigm, how they relate to one another, and the information that can be gleaned from each. We have developed a series of modeling simulations in Python to teach kinetic modeling, metabolic control analysis, 13C‐metabolic flux analysis, and flux balance analysis. These simulations are presented in a series of interactive notebooks with guided lesson plans and associated lecture notes. Learners assimilate key principles using models of simple metabolic networks by running simulations, generating and using data, and making and validating predictions about the effects of modifying model parameters. We used these simulations as the hands‐on computer laboratory component of a four‐day metabolic modeling workshop and participant survey results showed improvements in learners' self‐assessed competence and confidence in understanding and applying metabolic modeling techniques after having attended the workshop. The resources provided can be incorporated in their entirety or individually into courses and workshops on bioengineering and metabolic modeling at the undergraduate, graduate, or postgraduate level.

Kaste, Joshua A. M.↗

Shrub and sedge rhizosphere communities display distinct affinities toward exudates and soil organic matter degradation: a quantitative stable isotope probing analysis

Warming temperatures are accelerating permafrost thaw and changing tundra vegetation, where woody shrubs are displacing sedges. Shrubs, such as Betula nana, and sedges, such as Eriophorum vaginatum, exhibit distinct life strategies including unique root-associated, or rhizosphere microbial communities. As permafrost thaws it unlocks previously unavailable carbon and nutrient sources resulting in deeper roots and a translocation of rhizosphere communities. Because permafrost microbial communities contain lower diversity and biomass than rhizosphere communities, the coalescence of rhizosphere and permafrost microbial communities could alter soil organic matter (SOM) degradation rates and increase greenhouse gas emissions. To identify metabolic strategies across distinct rhizosphere and permafrost microbial communities we conducted an isotope tracing incubation experiment. We inoculated thawed permafrost with shrub and sedge rhizosphere communities while adding exudates or water daily and compared this to an uninoculated control. After 46 days, we spiked samples with 18O enriched water or 13C enriched exudates and measured isotope incorporation into microbial DNA with quantitative stable isotope probing (qSIP). Our results indicate that exudate additions had little effect on uninoculated permafrost communities but the addition of exudates and rhizosphere inoculants had a compounding effect on respiration rates. We found that soils inoculated with shrub rhizosphere communities contained a mixture of exudate and SOM degraders while soils inoculated with sedge rhizosphere communities contained mainly SOM degraders. Finally, we found that individual microbial taxa exhibited maximum growth rates under specific combinations of microbial inoculant communities and exudate addition treatments. Our results reveal that microbial niches are strongly influenced by substrate preferences and community context, and suggest that a reduction in sedges and an expansion of shrubs may provide a mechanism by which permafrost carbon losses are mitigated through corresponding shifts in microbial communities and their substrate preferences.

Schaefer, Sean R [Natural Resources and Earth Syst↗

G2PDeep-v2: A Web-Based Deep-Learning Framework for Phenotype Prediction and Biomarker Discovery for All Organisms Using Multi-Omics Data

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases, conditions and other biological phenotypes being studied.

59 BASIC BIOLOGICAL SCIENCES↗

Concepts, strategies and potentials using hypo-g and other features of the space environment for commercialization using higher plants

Opportunities for releasing, capturing, constructing and/or fixing the differential expressions or response potentials of the higher plant genome in the hypo-g environment for commercialization are explored. General strategies include improved plant-growing, crop and forestry production systems which conserve soil, water, labor and energy resources, and nutritional partitioning and mobilization of nutrients and synthates. Tissue and cell culture techniques of commercial potential include the growing and manipulation of cultured plant cells in vitro in a bioreactor to produce biologicals and secondary plants of economic value. The facilitation of plant breeding, the cloning of specific pathogen-free materials, the elimination of growing point or apex viruses, and the increase of plant yield are other O-g applications. The space environment may be advantageous in somatic embryogenesis, the culture of alkaloids, and the development of completely new crop plant germ plasm.

Krikorian, A. D.↗

Production of O2 on the Moon: A lab-top demonstration of ilmenite reduction with hydrogen

Estimates of the costs of transporting materials from Earth to the Moon are around $25,000 per pound. Therefore, it is imperative that we learn to utilize the resources on the Moon to partially offset these 'astronomical' expenses. The production of oxygen on the Moon utilizing indigenous materials is crucial to the establishment and development of an autonomous lunar colony. Besides obvious biologic needs, this lunar liquid oxygen (LLOX) could result in tremendous cost savings on fuel for effective transportation systems, particularly with its export to low-Earth orbit. Over 20 different process concepts were proposed and evaluated for the production of oxygen from lunar materials. Simplicity, low energy, easily attainable feedstock, and low resupply mass are the keywords for the process(es) which will ultimately be selected for the initial production of oxygen on the Moon. One of these schemes, which has received considerable study to date, is the hydrogen reduction of ilmenite. In fact, Carbotek, Inc. (Houston, TX) patented an ilmenite, hydrogen-reduction technique involving a three-stage, fluidized-bed process for the production of LLOX. A lab-top demonstration unit of the basic concepts of this oxygen generation process that was constructed by our group at the University of Tennessee is explained. It utilizes many of the principles which must be addressed in designing an effective production plant for operation on the Moon.

Taylor, Lawrence A.↗

Improving Student Achievement in Math and Science

As the new millennium approaches, a long anticipated reckoning for the education system of the United States is forthcoming, Years of school reform initiatives have not yielded the anticipated results. A particularly perplexing problem involves the lack of significant improvement of student achievement in math and science. Three "Partnership" projects represent collaborative efforts between Xavier University (XU) of Louisiana, Southern University of New Orleans (SUNO), Mississippi Valley State University (MVSU), and the National Aeronautics and Space Administration (NASA), Stennis Space Center (SSC), to enhance student achievement in math and science. These "Partnerships" are focused on students and teachers in federally designated rural and urban empowerment zones and enterprise communities. The major goals of the "Partnerships" include: (1) The identification and dissemination of key indices of success that account for high performance in math and science; (2) The education of pre-service and in-service secondary teachers in knowledge, skills, and competencies that enhance the instruction of high school math and science; (3) The development of faculty to enhance the quality of math and science courses in institutions of higher education; and (4) The incorporation of technology-based instruction in institutions of higher education. These goals will be achieved by the accomplishment of the following objectives: (1) Delineate significant ?best practices? that are responsible for enhancing student outcomes in math and science; (2) Recruit and retain pre-service teachers with undergraduate degrees in Biology, Math, Chemistry, or Physics in a graduate program, culminating with a Master of Arts in Curriculum and Instruction; (3) Provide faculty workshops and opportunities for travel to professional meetings for dissemination of NASA resources information; (4) Implement methodologies and assessment procedures utilizing performance-based applications of higher order thinking via the incorporation of Global Learning Observations To Benefit the Environment (GLOBE), Mission to Planet Earth and the use of Geographic Imaging Systems into the K-12th grade curriculum.

Sullivan, Nancy G.↗

Finding Uncertainties that Cause the Age Dependence of Dose Limits to Be Immature

Space radiation permissible exposure limits (PEL) are intended to set acceptable levels of cancer risks, and avoid any clinical significant non-cancer effects. The 1989 recommendation of the National Council of Radiation Protection and Measurements (NCRP) recommended a strong age dependence of dose limits that departed drastically from the then mature 1970 dose limits recommendations from the National Academy of Science, which were independent of age. In 2000, the NCRP recommended revised limits that showed a similar trend of risk with age to the 1989 report. In this model, the cancer risk per Sv varies by more than 2-fold for ages between 30- and 50-yr. Therefore for galactic cosmic rays exposure, astronaut age has a larger influence on risk then radiation shielding mass or material composition, vehicle propulsion method, or position in the solar cycle. For considering the control of mission costs and resources, the possibility of using astronaut age as a trade variable in mission design could be considered. However, the uncertainties in describing the age dependence on risk have not been fully explored. We discuss biological factors that influence the age dependence of radiation risks, including susceptibility, expression and latency, and radiation quality. These factors depend not only on the individual s age, but also their genetic sensitivity and interaction with other environmental factors. Epidemiological data is limited in describing the age dependence on risk. The 2005, BEIR VII report recommends an age dependence for cancer risk attributable solely to the life-table disagreeing strongly with the NCRP model. However, BEIR VII also noted the limited power of human data for concomitantly describing both age and age after exposure dependences of cancer risks. Many experimental studies have shown that high LET radiation (e.g., high charge and energy (HZE) nuclei and neutrons) display reduced latency compared to low LET radiation, suggesting distinct biological factors are important. We discuss potential molecular mechanisms that would influence the age dependence of radiation risks. A probability distribution function for the uncertainties in age-dependence of risk models is described and predictions for Mars missions discussed. Our report suggests that theoretical considerations based on new experimental studies are needed to ensure the correct age dependence in space radiation risk models and the resulting Astronaut PEL.

Cucinotta, Francis A.↗

Increasing Data Discovery and Re-Use: The Space Life Sciences Ontology

Two of the most important goals of the adoption of the FAIR principles are increasing the ability of agents to find and re-use research data. Achieving these goals for space life sciences research is even more pressing, given the relatively expensive and scarce nature of these data. We have reported in the past on the progress made by exemplar life sciences data systems towards implementing FAIR, showing gaps particularly in the “interoperability area” of the principles; the lack of common conceptual models for space life science research is one reason for this gap. There were few available resources that define, annotate, categorize or otherwise relate various kinds of metadata describing the acquisition, nature, and intent of investigational space life sciences data. To address this gap, NASA is working with the Open Biological and Biomedical Ontology Foundry (https://obofoundry.org/) to develop the Space Life Science Ontology (SLSO) that is intended to support archival and other kinds of systems that operate using these data. The scope of the ontology includes concepts regarding those aspects of investigation design and execution specific or unique to space environments, such as types of specialized equipment, operating organizations, and documentation. The ontology is continually being developed and published to the life science community (https://github.com/nasa/LSDAO/); at the time of this publication, the SLSO newly and uniquely defines 30 types (classes), 90 properties, and 14 relations specific to space life sciences metadata. In addition, the SLSO reuses (imports) some 2,360 types (classes), 49 properties, and 393 relations from other ontologies that are relevant to these kinds of metadata. In addition to its role as a common conceptualization for space biomedical research activities, the SLSO can also be used to provide automated support for traditionally difficult and expensive activities such as data curation and cross-system data integration and analysis.

fair↗