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At least 253 records · Page 14

All sources NASA NTRS DOE OSTI

DOE OSTI2021

Climate warming threatens the persistence of a community of disturbance-adapted native annual plants

With ongoing climate change, populations are expected to exhibit shifts in demographic performance that will alter where a species can persist. This presents unique challenges for managing plant populations and may require ongoing interventions, including in situ management or introduction into new locations. However, few studies have examined how climate change may affect plant demographic performance for a suite of species, or how effective management actions could be in mitigating climate change effects. Over the course of two experiments spanning 6 yr and four sites across a latitudinal gradient in the Pacific Northwest, United States, here we manipulated temperature, precipitation, and disturbance intensity, and quantified effects on the demography of eight native annual prairie species. Each year we planted seeds and monitored germination, survival, and reproduction. We found that disturbance strongly influenced demographic performance and that seven of the eight species had increasingly poor performance with warmer conditions. Across species and sites, we observed 11% recruitment (the proportion of seeds planted that survived to reproduction) following high disturbance, but just 3.9% and 2.3% under intermediate and low disturbance, respectively. Moreover, mean seed production following high disturbance was often more than tenfold greater than under intermediate and low disturbance. Importantly, most species exhibited precipitous declines in their population growth rates (λ) under warmer-than-ambient experimental conditions and may require more frequent disturbance intervention to sustain populations. Aristida oligantha, a C4 grass, was the only species to have λ increase with warmer conditions. These results suggest that rising temperatures may cause many native annual plant species to decline, highlighting the urgency for adaptive management practices that facilitate their restoration or introduction to newly suitable locations. Frequent and intense disturbances are critical to reduce competitors and promote native annuals’ persistence, but even such efforts may prove futile under future climate regimes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins

Here, we outline recent developments in artificial intelligence (AI) and machine learning (ML) techniques for integrative structural biology of intrinsically disordered proteins (IDP) ensembles. IDPs challenge the traditional protein structure-function paradigm by adapting their conformations in response to specific binding partners leading them to mediate diverse, and often complex cellular functions such as biological signaling, self-organization and compartmentalization. Obtaining mechanistic insights into their function can therefore be challenging for traditional structural determination techniques. Often, scientists have to rely on piecemeal evidence drawn from diverse experimental techniques to characterize their functional mechanisms. Multiscale simulations can help bridge critical knowledge gaps about IDP structure-function relationships - however, these techniques also face challenges in resolving emergent phenomena within IDP conformational ensembles. We posit that scalable statistical inference techniques can effectively integrate information gleaned from multiple experimental techniques as well as from simulations, thus providing access to atomistic details of these emergent phenomena.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Improving growth of Cupriavidus necator H16 on formate using adaptive laboratory evolution-informed engineering

Conversion of CO 2 to value-added products presents an opportunity to reduce GHG emissions while generating revenue. Formate, which can be generated by the electrochemical reduction of CO 2 , has been proposed as a promising intermediate compound for microbial upgrading. Here we present progress towards improving the soil bacterium Cupriavidus necator H16, which is capable of growing on formate as its sole source of carbon and energy using the Calvin-Benson-Bassham (CBB) cycle, as a host for formate utilization. Using adaptive laboratory evolution, we generated several isolates that exhibited faster growth rates on formate. The genomes of these isolates were sequenced, and resulting mutations were systematically reintroduced by metabolic engineering, to identify those that improved growth. Further, the metabolic impact of several mutations was investigated further using RNA-seq transcriptomics. We found that deletion of a transcriptional regulator implicated in quorum sensing, PhcA, reduced expression of several operons and led to improved growth on formate. Growth was also improved by deleting large genomic regions present on the extrachromosomal megaplasmid pHG1, particularly two hydrogenase operons and the megaplasmid CBB operon, one of two copies present in the genome. Based on these findings, we generated a rationally engineered ..delta..phcA and megaplasmid-deficient strain that exhibited a 24% faster maximum growth rate on formate. Moreover, this strain achieved a 7% growth rate improvement on succinate and a 19% increase on fructose, demonstrating the broad utility of microbial genome reduction. This strain has the potential to serve as an improved microbial chassis for biological conversion of formate to value-added products.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Thermodynamic Control of Activity Patterns in Cytoskeletal Networks

Biological materials, such as the actin cytoskeleton, exhibit remarkable structural adaptability to various external stimuli by consuming different amounts of energy. In this Letter, we use methods from large deviation theory to identify a thermodynamic control principle for structural transitions in a model cytoskeletal network. Specifically, we demonstrate that biasing the dynamics with respect to the work done by nonequilibrium components effectively renormalizes the interaction strength between such components, which can eventually result in a morphological transition. Further, our work demonstrates how a thermodynamic quantity can be used to renormalize effective interactions, which in turn can tune structure in a predictable manner, suggesting a thermodynamic principle for the control of cytoskeletal structure and dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1985

USSR Space Life Sciences Digest, issue 3

This is the third issue of NASA's USSR Space Life Sciences Digest. Abstracts are included for 46 Soviet periodical articles in 20 areas of aerospace medicine and space biology and published in Russian during the second third of 1985. Selected articles are illustrated with figures and tables from the original. In addition, translated introductions and tables of contents for seven Russian books on six topics related to NASA's life science concerns are presented. Areas covered are adaptation, biospherics, body fluids, botany, cardiovascular and respiratory systems, endocrinology, exobiology, gravitational biology, habitability and environmental effects, health and medical treatment, immunology, life support systems, metabolism, microbiology, musculoskeletal system; neurophysiology, nutrition, perception, personnel selection, psychology, radiobiology, and space physiology. Two book reviews translated from the Russian are included and lists of additional relevant titles available in English with pertinent ordering information are given.

Hooke, L. R.↗

DOE OSTI2021

An adaptive adversarial domain adaptation approach for corn yield prediction

Recently, statistical machine learning and deep learning methods have been widely explored for corn yield prediction. Though successful, machine learning models generated within a specific spatial domain often lose their validity when directly applied to new regions. To address this issue, we designed an unsupervised adaptive domain adversarial neural network (ADANN). Specifically, through domain adversarial training, the ADANN model reduced the impact of domain shift by projecting data from different domains into the same subspace. Also, the ADANN model was designed to be trained in an adaptive way, which guaranteed the model can learn the domain-invariant features and perform accurate yield prediction simultaneously. Informative variables including time-series vegetation indices and sequential weather observations were first collected from multiple data sources and aggregated to the county level. Then, we trained the ADANN model with the extracted features and corresponding reported county-level corn yield from the U.S. Department of Agriculture (USDA). Finally, the trained model was evaluated in four testing years 2016–2019. The U.S. corn belt was used as the study area and counties under study were grouped into two diverse ecological regions. Overall, the experimental results showed that the developed ADANN model had better performance than three other state-of-the-art machine learning models in both local experiments (train and test in the same region) and transfer experiments (train and test in different regions). As the first study using adversarial learning for crop yield prediction, this research demonstrates a novel solution for improving model transferability on crop yield prediction.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Understanding Multilevel Selection May Facilitate Management of Arbuscular Mycorrhizae in Sustainable Agroecosystems

Studies in natural ecosystems show that adaptation of arbuscular mycorrhizal (AM) fungi and other microbial plant symbionts to local environmental conditions can help ameliorate stress and optimize plant fitness. This local adaptation arises from the process of multilevel selection, which is the simultaneous selection of a hierarchy of groups. Studies of multilevel selection in natural ecosystems may inform the creation of sustainable agroecosystems through developing strategies to effectively manage crop microbiomes including AM symbioses. Field experiments show that the species composition of AM fungal communities varies across environmental gradients, and that the biomass of AM fungi and their benefits for plants generally diminish when fertilization and irrigation eliminate nutrient and water limitations. Furthermore, pathogen protection by mycorrhizas is only important in environments prone to plant damage due to pathogens. Consequently, certain agricultural practices may inadvertently select for less beneficial root symbioses because the conventional agricultural practices of fertilization, irrigation, and use of pesticides can make these symbioses superfluous for optimizing crop performance. The purpose of this paper is to examine how multilevel selection influences the flow of matter, energy, and genetic information through mycorrhizal microbiomes in natural and agricultural ecosystems, and propose testable hypotheses about how mycorrhizae may be actively managed to increase agricultural sustainability.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The molecular mechanism of load adaptation by branched actin networks

Branched actin networks are self-assembling molecular motors that move biological membranes and drive many important cellular processes, including phagocytosis, endocytosis, and pseudopod protrusion. When confronted with opposing forces, the growth rate of these networks slows and their density increases, but the stoichiometry of key components does not change. The molecular mechanisms governing this force response are not well understood, so we used single-molecule imaging and AFM cantilever deflection to measure how applied forces affect each step in branched actin network assembly. Although load forces are observed to increase the density of growing filaments, we find that they actually decrease the rate of filament nucleation due to inhibitory interactions between actin filament ends and nucleation promoting factors. The force-induced increase in network density turns out to result from an exponential drop in the rate constant that governs filament capping. The force dependence of filament capping matches that of filament elongation and can be explained by expanding Brownian Ratchet theory to cover both processes. We tested a key prediction of this expanded theory by measuring the force-dependent activity of engineered capping protein variants and found that increasing the size of the capping protein increases its sensitivity to applied forces. In summary, we find that Brownian Ratchets underlie not only the ability of growing actin filaments to generate force but also the ability of branched actin networks to adapt their architecture to changing loads.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Biologically Cooling the Planet: A BRISK Approach that Directly Connects the Ground to Deep Space

Climate change is a grave threat to our ability to thrive and prosper on Earth. Accumulation of greenhouse gases in the atmosphere stifle the Earth’s ability to cool itself, which leads to a rise of the average temperature – Global warming. The planetary cooling is exclusively radiative – thermal radiation escapes into cold outer space via a flux of photons at the low-infrared range. The penetration of these photons through Earth’s atmosphere is dictated by atmospheric transparency, which, serendipitously possesses a window centered around the peak of the Plank spectrum for a black body at about room temperature – the average temperature of Earth. This window spanning about 8 --13 μm wavelengths allows most of the photons in this range to escape into the Cosmos carrying our planet’s heat away. The efficiency of this outer heat flux – and thus planet’s cooling ability – can be controlled via emissivity – a function of wavelength which multiplies the fundamental Plank spectrum of a black body at a given temperature. In the presence of non-trivial atmospheric transparency it can be shown that radiative cooling can be enhanced with properly “designed” emissivity function. For the last 100 years, or so, people have been looking into ways to engineer materials to take advantage of such enhancement for various cooling applications, from making ice to cool clothes, and substantial progress has been achieved, including cooling in direct sunlight. The beauty if this approach is that it is entirely passive – no energy input is required. The objective of this project was to investigate whether biological systems possess such advanced cooling capacity, developed via millennia of evolution, to enhance plant’s adaptation to a hot environment, to increase cooling capability, and possibly modulate spectral emissivities on short or long time scales. We wanted to know if BRISK (Biological Radiative Sky Cooling) occurs and to what extent. It is unknown whether biological systems can perform this "spectral redistribution." It is reasonable to expect, however, that they might: in particular, desert plants under high heat stress and arid conditions might evolve this mechanism in order to maintain a tolerable internal temperature. Our intended approach was twofold: extensive literature search and supporting experimental investigations on select plants. We obtained the answers from the former, while the latter proved to be more complicated to perform with required accuracy in the timespan/budget of a small seedling project. After one year of research, we concluded that among the plant species studied there seem to be no evidence of BRISK, but it’s not the end of the story. Our planet’s biosphere is immense, and the evolution is continuing. With our preliminary results and a better understanding of what to look for further discoveries await, considering the accelerated pace of infrared imaging and spectroscopy technology development, from microscopic to satellite-based studies of plants and canopies. In the end, Earth’s energy balance is ultimately tied to radiative cooling so that further investigation into this problem is directly tied to solving the Climate Change challenge.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation

Many organisms evolved strategies to survive desiccation. Plant seeds protect dehydrated embryos from various stressors and can lay dormant for millennia. Hydration is the key trigger to initiate germination, but the mechanism by which seeds sense water remains unresolved. Here we identified an uncharacterized Arabidopsis thaliana prion-like protein we named FLOE1, which phase separates upon hydration and allows the embryo to sense water stress. We demonstrate that biophysical states of FLOE1 condensates modulate its biological function in vivo in suppressing seed germination under unfavorable environments. We find intragenic, intraspecific, and interspecific natural variation in FLOE1 expression and phase separation and show that intragenic variation is associated with adaptive germination strategies in natural populations. This combination of molecular, organismal, and ecological studies uncovers FLOE1 as a tunable environmental sensor with direct implications for the design of drought-resistant crops, in the face of climate change.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Natural transformation as a tool in Acinetobacter baylyi : Evolution by amplification of gene copy number

For many years, the natural competency of Acinetobacter baylyi ADP1 facilitated studies of bacterial metabolism, biochemistry, and physiology. With the advent of synthetic biology, new opportunities arise to exploit the remarkable transformability and chromosomal plasticity of this model organism. In this chapter, we describe a recently developed method, “Evolution by Amplification and Synthetic Biology” (EASy). EASy allows the targeted amplification of chromosomal segments that give rise to new phenotypes. Increased gene dosage regulates protein expression in a rudimentary fashion by establishing a chromosomal array in which copy number adjusts via recombination between repeated DNA sequences. Selective conditions enrich for cells within the population that confer a growth advantage. Under continuous selective pressure, beneficial mutations may accumulate in any genomic region. Such mutations favor decreases in the average copy number of the target region. Thus, the genetic flexibility afforded by transient copy number variation helps accelerate the selection of engineered strains with desired traits during laboratory evolution. As a result, thanks to the extremely simple genetic manipulation of Acinetobacter baylyi ADP1, the EASy method can be readily implemented by researchers without the need for advanced instrumentation or complex cloning techniques.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Rewiring yeast metabolism to synthesize products beyond ethanol

Saccharomyces cerevisiae, Baker's yeast, is the industrial workhorse for producing ethanol and the subject of substantial metabolic engineering research in both industry and academia. S. cerevisiae has been used to demonstrate production of a wide range of chemical products from glucose. However, in many cases, the demonstrations report titers and yields that fall below thresholds for industrial feasibility. Ethanol synthesis is a central part of S. cerevisiae metabolism, and redirecting flux to other products remains a barrier to industrialize strains for producing other molecules. Furthermore, removing ethanol producing pathways leads to poor fitness, such as impaired growth on glucose. Here, we review metabolic engineering efforts aimed at restoring growth in non-ethanol producing strains with emphasis on relieving glucose repression associated with the Crabtree effect and rewiring metabolism to provide access to critical cellular building blocks. Finally, substantial progress has been made in the past decade, but many opportunities for improvement remain.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

U2AF - Hypoxia-induced fas alternative splicing regulator

The splicing machinery heavily contributes to biological complexity and especially to the ability of cells to adapt to altered cellular conditions. Hypoxia also plays a key role in the pathophysiology of many disease states. Recent studies have revealed that tumorigenesis and hypoxia are involved in large-scale alterations in alternative pre-mRNA splicing. Fas pre-mRNA is alternatively spliced by excluding exon 6 to produce soluble Fas (sFas) protein that lacks a transmembrane domain and acts by inhibiting Fas mediated apoptosis. }In the present study we show that U2AF is involved in hypoxia dependent anti-apoptotic Fas mRNA isoform formation. Our performed studies show that U2AF-RNA interaction is reduced in hypoxic cells, leading to reduction of Fas and increased sFas mRNAs formation. Efficient U2AF-RNA interactions of both subunits are important for Fas exon 6 inclusion into forming mRNA in normoxic and hypoxic cells.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice

This study explores viral community structure and function in remote and extreme Arctic environments, including subzero brines within marine layers of permafrost and sea ice, using a modern viral ecogenomics toolkit for the first time. In addition to providing foundational data sets for these climate-threatened habitats, we found evidence that the viruses had habitat specificity, infected dominant microbial hosts, encoded host-derived metabolic genes, and mediated horizontal gene transfer among hosts. These results advance our understanding of the virosphere and how viruses influence extreme ecosystems. More broadly, the evidence that virally mediated gene transfers may be limited by host range in these extreme habitats contributes to a mechanistic understanding of genetic exchange among microbes under stressful conditions in other systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026