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All sourcesNASA NTRSDOE OSTI
NASA NTRS1995

Plant Roots: The Hidden Half: Calcium and Gravitropism - Chapter 16

Environmental signals such as light and gravity control many aspects of plant growth and development. In higher plants, the directional growth of an organ in response to stimuli such as gravity and light is considered a tropic movement. Such movement could be either positive or negative with respect to a specific stimulus. In general, stems show a positive response to light and negative response to gravity. In contrast, most roots show a positive response to gravity and a negative response to light. Investigations on plant tropism date back a century when Darwin studied the phototropic responses of maize seedlings (Darwin). Although the precise mechanism of signal perception and transduction in roots is not understood, Darwin recognized over 100 years ago that the root cap is the probable site of signal perception. He discovered that the removal of the root cap eliminates the ability of roots to respond to gravity. Other investigators have since confirmed Darwin's observation (Konings; Evans et al.). In recent years, especially with the advent of the U.S. Space Program, there has been a renewed interest in understanding how plants respond to extracellular signals such as gravity (Halstead and Dutcher). Studies on the mechanisms involved in perception and transduction of gravity signal by roots would ultimately help us to better understand gravitropism and also to grow plants under microgravity conditions as in space. In this chapter, we restrict ourselves to the role of calcium in transduction of the gravity signal. In doing so, emphasis is given to the role of calcium-modulated proteins and their role in signal transduction in gravitropism. Detailed reviews on various other aspects of gravitropism (Scott, Torrey, Wilkins, Fim and Digby, Feldman, Pickard, Moore and Evans, Halstead and Dutcher, Poovaiah et al.) and on the role of calcium as a messenger in signal transduction in general have been published (Helper and Wayne, Poovaiah and Reddy, Roberts and Hartnon, Bowler and Chua, Gilroy and Trewavas). Plant roots have been widely used to study the transduction of gravity and light signals (Poovaiah et al., Roux and Serlin). Most roots show positive gravitropic response in either dark or light. However, roots of some varieties of plants (e.g., Zea mays L., cv Merit, and Zea rwvs L., cv Golden Cross Bantam 70) show positive gravitropic response only in light (Feldman, Miyazaki et al.). Investigations from various laboratories indicate that calcium acts as a messenger in transducing gravity and light signals in plant roots(Pickard, Evans et al., Pooviah et al.).

Poovaiah, B. W.↗
NASA NTRS1995

A Unique Facility For Metabolic and Thermoregulatory Studies

A unique exercise facility has been developed and used to perform tipper body ergometry tests for space applications. Originally designed to simulate the muscular, cardiovascular and thermoregulatory responses to working in zero gravity, this facility may be used to conduct basic thermoregulatory investigations applicable to multiple sclerosis patients. An environmental chamber houses the tipper body ergometer and permits control of temperature, air now and humidify. The chamber is a closed system and recirculate-s air after conditioning if. A Cybex Lipper body ergometer has been mounted horizontally on the wall of the environmental chamber. In this configuration, the subject lies underneath the arm crank on a supine seat in order to turn the crank. The supine seat can be removed in order to introduce other equipment into the chamber such as a stool to allow upright arm cranking, or a treadmill to allow walk-run experiments. Physiological and environmental signals are fed into a Strawberry Tree data acquisition system while being monitored and logged using the Workbench software program. Physiological monitoring capabilities include 3-lead EKG using an H-P patient monitor, 5 site skin temperature and core temperature using YSI thermistors, and O2 consumption and CO2 production using AMFTFK Applied Electrochemistry analyzers and sensors. This comprehensive data acquisition set tip allows for calculation of various thermoregulatory indices including heat storage, evaporative heat loss, latent heat loss, and metabolic rate. The current system is capable of adding more data acquisition channels if needed. Some potential studies that could be carried out using the facility include: 1) An investigation into the efficiency of cooling various segments of the body to lower Tc 1-2 F. 2) A series of heat and mass balance studies comparing various LCG configurations.

Williamson, Rebecca C.↗
NASA NTRS2002

Peptides at Membrane Surfaces and their Role in Prebiotic Evolution

Protocells had to transport ions and organic matter across membranes separating the interior of the cell from the environment, capture and utilize energy and transduce environmental signals. In a series of detailed, molecular-level computer simulations we show how these peptides in contact with membranes can acquire ordered structures and functions. We have investigated the stability of a simple alpha-helical peptide containing Leucine (L) and Serine (S) of the form (LSLLLSL)3 in a model membrane system. The parallel in-plane state is the most stable configuration. The transmembrane state is metastable, and about 15 kcal/mol is required to insert the peptide into the membrane. We investigated dimes of both (LSLLLSL)3 and glycophorin A, and show how the free energy of helix association can, at least partially, offset the free energy of insertion. We have also investigated the transmembrane pore of the influenza M2 protein. This aggregate of four identical alpha-helices, each built of 25 amino acids, forms an efficient and selective voltage-gated proton channel. Our simulations explain the gating mechanism, which can involve strands of hydrogen-bonded water through the pore or proton transfer through tautomerization of protein residues. The channel can be re-engineered to act as a simple proton pump.

Pohorille, Andrew↗
NASA NTRS2002

Peptides at Membrane Surfaces and their Role in the Origin of Life

All ancestors of contemporary cells (protocells) had to transport ions and organic matter across membranous walls, capture and utilize energy and transduce environmental signals. In modern organisms, all these functions are preformed by membrane proteins. We make the parsimonious assumption that in the protobiological milieu the same functions were carried out by their simple analogs - peptides. This, however, required that simple peptides could self-organize into ordered, functional structures. In a series of detailed, molecular-level computer simulations we demonstrated how this is possible. One example is the peptide (LSLLLSL)3 which forms a trameric bundle capable of transporting protons across membranes. Another example is the transmembrane pore of the influenza M2 protein. This aggregate of four identical alpha-helices, each built of 25 amino acids, forms an efficient and selective voltage-gated proton channel. Our simulations explain the gating mechanism in this channel. The channel can be re-engineered into a simple proton pump.

Pohorille, Andrew↗
NASA NTRS2003

Membrane-Based Functions in the Origin of Cellular Life

How simple membrane peptides performed such essential proto-cellular functions as transport of ions and organic matter across membranes separating the interior of the cell from the environment, capture and utilization of energy, and transduction of environmental signals, is a key question in protobiological evolution. On the basis of detailed, molecular-level computer simulations we investigate how these peptides insert into membranes, self-assemble into higher-order structures and acquire functions. We have studied the insertion of an a-helical peptide containing leucine (L) and serine (S) of the form (LSLLLSL)S into a model membrane. The transmembrane state is metastable, and approximately 15 kcal/mol is required to insert the peptide into the membrane. Investigations of dimers formed by (LSLLLSL)S and glycophorin A demonstrate how the favorable free energy of helix association can offset the unfavorable free energy of insertion, leading to self- assembly of peptide helices in the membrane. An example of a self-assembled structure is the tetrameric transmembrane pore of the influenza virus M2 protein, which is an efficient and selective voltage-gated proton channel. Our simulations explain the gating mechanism and provide guidelines how to reengineering the channel to act as a simple proton pump. In general, emergence of integral membrane proteins appears to be quite feasible and may be easier to envision than the emergence of water-soluble proteins.

Wilson, Michael A.↗
NASA NTRS2003

Membrane peptides and their role in protobiological evolution

How simple membrane peptides performed such essential protocellular functions as transport of ions and organic matter across membranes separating the interior of the cell from the environment, capture and utilization of energy, and transduction of environmental signals, is a key question in protobiological evolution. On the basis of detailed, molecular-level computer simulations we explain how these peptides fold at water-membrane interfaces, insert into membranes, self-assemble into higher-order structures and acquire functions. We have investigated the interfacial behavior and folding of several peptides built of leucine and glutamine residues and have demonstrated that many of them tend to adopt ordered structures. Further, we have studied the insertion of an alpha-helical peptide containing leucine (L) and serine (S) of the form (LSLLLSL)3 into a model membrane. The transmembrane state is metastable, and approximately 15 kcal mol(-1) is required to insert the peptide into the membrane. Investigations of dimers formed by (LSLLLSL)3 and glycophorin A demonstrate how the favorable free energy of helix association can offset the unfavorable free energy of insertion, leading to self-assembly of peptide helices in the membrane. An example of a self-assembled structure is the tetrameric transmembrane pore of the influenza virus M2 protein, which is an efficient and selective voltage-gated proton channel. Our simulations explain the gating mechanism and provide guidelines how to re-engineer the channel to act as a simple proton pump. In general, emergence of integral membrane proteins appears to be quite feasible and may be easier to envision than the emergence of water-soluble proteins.

Models, Chemical↗
NASA NTRS2002

Microarray analysis identifies Salmonella genes belonging to the low-shear modeled microgravity regulon

The low-shear environment of optimized rotation suspension culture allows both eukaryotic and prokaryotic cells to assume physiologically relevant phenotypes that have led to significant advances in fundamental investigations of medical and biological importance. This culture environment has also been used to model microgravity for ground-based studies regarding the impact of space flight on eukaryotic and prokaryotic physiology. We have previously demonstrated that low-shear modeled microgravity (LSMMG) under optimized rotation suspension culture is a novel environmental signal that regulates the virulence, stress resistance, and protein expression levels of Salmonella enterica serovar Typhimurium. However, the mechanisms used by the cells of any species, including Salmonella, to sense and respond to LSMMG and identities of the genes involved are unknown. In this study, we used DNA microarrays to elucidate the global transcriptional response of Salmonella to LSMMG. When compared with identical growth conditions under normal gravity (1 x g), LSMMG differentially regulated the expression of 163 genes distributed throughout the chromosome, representing functionally diverse groups including transcriptional regulators, virulence factors, lipopolysaccharide biosynthetic enzymes, iron-utilization enzymes, and proteins of unknown function. Many of the LSMMG-regulated genes were organized in clusters or operons. The microarray results were further validated by RT-PCR and phenotypic analyses, and they indicate that the ferric uptake regulator is involved in the LSMMG response. The results provide important insight about the Salmonella LSMMG response and could provide clues for the functioning of known Salmonella virulence systems or the identification of uncharacterized bacterial virulence strategies.

Non-NASA Center↗
NASA NTRS2002

Isolation and characterization of a novel calmodulin-binding protein from potato

Tuberization in potato is controlled by hormonal and environmental signals. Ca(2+), an important intracellular messenger, and calmodulin (CaM), one of the primary Ca(2+) sensors, have been implicated in controlling diverse cellular processes in plants including tuberization. The regulation of cellular processes by CaM involves its interaction with other proteins. To understand the role of Ca(2+)/CaM in tuberization, we have screened an expression library prepared from developing tubers with biotinylated CaM. This screening resulted in isolation of a cDNA encoding a novel CaM-binding protein (potato calmodulin-binding protein (PCBP)). Ca(2+)-dependent binding of the cDNA-encoded protein to CaM is confirmed by (35)S-labeled CaM. The full-length cDNA is 5 kb long and encodes a protein of 1309 amino acids. The deduced amino acid sequence showed significant similarity with a hypothetical protein from another plant, Arabidopsis. However, no homologs of PCBP are found in nonplant systems, suggesting that it is likely to be specific to plants. Using truncated versions of the protein and a synthetic peptide in CaM binding assays we mapped the CaM-binding region to a 20-amino acid stretch (residues 1216-1237). The bacterially expressed protein containing the CaM-binding domain interacted with three CaM isoforms (CaM2, CaM4, and CaM6). PCBP is encoded by a single gene and is expressed differentially in the tissues tested. The expression of CaM, PCBP, and another CaM-binding protein is similar in different tissues and organs. The predicted protein contained seven putative nuclear localization signals and several strong PEST motifs. Fusion of the N-terminal region of the protein containing six of the seven nuclear localization signals to the reporter gene beta-glucuronidase targeted the reporter gene to the nucleus, suggesting a nuclear role for PCBP.

NASA Discipline Plant Biology↗
NASA NTRS1999

Genetic ablation of root cap cells in Arabidopsis

The root cap is increasingly appreciated as a complex and dynamic plant organ. Root caps sense and transmit environmental signals, synthesize and secrete small molecules and macromolecules, and in some species shed metabolically active cells. However, it is not known whether root caps are essential for normal shoot and root development. We report the identification of a root cap-specific promoter and describe its use to genetically ablate root caps by directing root cap-specific expression of a diphtheria toxin A-chain gene. Transgenic toxin-expressing plants are viable and have normal aerial parts but agravitropic roots, implying loss of root cap function. Several cell layers are missing from the transgenic root caps, and the remaining cells are abnormal. Although the radial organization of the roots is normal in toxin-expressing plants, the root tips have fewer cytoplasmically dense cells than do wild-type root tips, suggesting that root meristematic activity is lower in transgenic than in wild-type plants. The roots of transgenic plants have more lateral roots and these are, in turn, more highly branched than those of wild-type plants. Thus, root cap ablation alters root architecture both by inhibiting root meristematic activity and by stimulating lateral root initiation. These observations imply that the root caps contain essential components of the signaling system that determines root architecture.

Non-NASA Center↗
NASA NTRS2005

The Origin and Early Evolution of Membrane Proteins

Membrane proteins mediate functions that are essential to all cells. These functions include transport of ions, nutrients and waste products across cell walls, capture of energy and its transduction into the form usable in chemical reactions, transmission of environmental signals to the interior of the cell, cellular growth and cell volume regulation. In the absence of membrane proteins, ancestors of cell (protocells), would have had only very limited capabilities to communicate with their environment. Thus, it is not surprising that membrane proteins are quite common even in simplest prokaryotic cells. Considering that contemporary membrane channels are large and complex, both structurally and functionally, a question arises how their presumably much simpler ancestors could have emerged, perform functions and diversify in early protobiological evolution. Remarkably, despite their overall complexity, structural motifs in membrane proteins are quite simple, with a-helices being most common. This suggests that these proteins might have evolved from simple building blocks. To explain how these blocks could have organized into functional structures, we performed large-scale, accurate computer simulations of folding peptides at a water-membrane interface, their insertion into the membrane, self-assembly into higher-order structures and function. The results of these simulations, combined with analysis of structural and functional experimental data led to the first integrated view of the origin and early evolution of membrane proteins.

Pohorille, Andrew↗
NASA NTRS2024

Harnessing Collaborative Learning Automata to Guide Multi-objective Optimization based Inverse Analysis for Structural Damage Identification

Structural damage identification based on physical models is often transformed into an optimization problem that minimizes the difference between measurement information of structure being monitored and the model prediction in the parametric space. However, the objective function in this context often exhibits multimodality, involving high-dimensional variables due to the reliance on finite element models for damage identification. These features pose challenges to optimization algorithms, where entrapment in local solutions can lead to false positives and false negatives in damage identification. In this research, we propose a reinforcement learning based multi-swarm optimizer to tackle such challenges in pursuit of a small yet diverse solution set that can capture the true damage scenario as one of the solutions. The proposed method leverages the flexibility of the particle swarm optimizer and incorporates novel strategies of metaheuristics to realize targeted improvement. To enable the particle swarm to adaptively select the appropriate search strategy based on the current environment, we adopt the learning automata technique, which sidesteps the need for reward strategy selection that is usually ad hoc at each step of the search. The integration harnesses the automatic learning and self-adaptation capabilities of learning automata, enabling the particles to navigate based on environmental signals. This leads to accumulated probabilities tied to advantageous movements, fostering an adaptive exploration of particles in the search space. The proposed approach is first validated through implementing into benchmark test cases with comparisons. It is then applied to structural damage identification with piezoelectric admittance experimental signals. `The results highlight the capability of the algorithm to identify a small solution set with high accuracy to match the actual damage scenario.

Yang Zhang↗
DOE OSTI2025

Environmental and ecological signals predict food shortages for subtropical populations of Australian flying foxes, reservoirs of Hendra virus

Food availability determines where and how animals use space across a landscape and, therefore, affects the risk of encounters leading to zoonotic spillover. This relationship is evident in Australian flying foxes (Pteropus spp.; fruit bats), where acute food shortages precede clusters of Hendra virus spillovers. Using machine learning, we predicted months of food shortages from climatological and ecological covariates (1996–2022) in subtropical Australia. Overall accuracy in predicting months of low food availability on a test set from 2018 up to 2022 reached 93.33 and 92.59% based on climatological and bat-level features, respectively. Seasonality and the Oceanic El Niño Index were the most important environmental features, while the number of bats in rescue centres and their body weights were the most important bat-level features. These models support predictive signals up to nine months in advance, facilitating action to mitigate spillover risk.

Pteropus↗
NASA NTRS1993

Calcium and signal transduction in plants

Environmental and hormonal signals control diverse physiological processes in plants. The mechanisms by which plant cells perceive and transduce these signals are poorly understood. Understanding biochemical and molecular events involved in signal transduction pathways has become one of the most active areas of plant research. Research during the last 15 years has established that Ca2+ acts as a messenger in transducing external signals. The evidence in support of Ca2+ as a messenger is unequivocal and fulfills all the requirements of a messenger. The role of Ca2+ becomes even more important because it is the only messenger known so far in plants. Since our last review on the Ca2+ messenger system in 1987, there has been tremendous progress in elucidating various aspects of Ca(2+) -signaling pathways in plants. These include demonstration of signal-induced changes in cytosolic Ca2+, calmodulin and calmodulin-like proteins, identification of different Ca2+ channels, characterization of Ca(2+) -dependent protein kinases (CDPKs) both at the biochemical and molecular levels, evidence for the presence of calmodulin-dependent protein kinases, and increased evidence in support of the role of inositol phospholipids in the Ca(2+) -signaling system. Despite the progress in Ca2+ research in plants, it is still in its infancy and much more needs to be done to understand the precise mechanisms by which Ca2+ regulates a wide variety of physiological processes. The purpose of this review is to summarize some of these recent developments in Ca2+ research as it relates to signal transduction in plants.

NASA Program Space Biology↗
DOE OSTI2026

Microbial spies and bloggers: programming cells to convert environmental information into discernible signals

Microbes regulate their dynamic behaviors using the chemical and physical characteristics of their environment. The ability of microbes to continuously convert this physicochemical information into biochemical information and to use organic matter in the environment as a power source makes these organisms attractive as chassis for building sensors. However, most biosensors have severe limitations when considering applications in hard-to-image settings like soils, sediments, and wastewater. Emerging technologies at the interface of biomolecular design, microbiome engineering, and synthetic biology offer new tools to program cells and communities as biosensors for these settings. Here, in this review, we describe innovations in biosensor outputs that are enabling new applications in complex environments, including reporters that are read out using electrochemical, gas chromatography, hyperspectral imaging, and next-generation sequencing methods. We also discuss computational advances that are accelerating the diversification of sensing components by mining metagenomics data for new transcriptional regulators and by designing allosteric protein switches that directly regulate reporter outputs using analytes. We highlight emerging opportunities for programming undomesticated microbes in communities to function as distributed sensors in the environment. Finally, we discuss the need for responsible biosensor development and to modernize regulatory frameworks to support evidence-based assessment of environmental biosensors.

analyte↗
DOE OSTI2020

Two interacting ethylene response factors regulate heat stress response

Abstract The ethylene response factor (ERF) transcription factors are integral components of environmental stress signaling cascades, regulating a wide variety of downstream genes related to stress responses and plant development. However, the mechanisms by which ERF genes regulate the heat stress response are not well understood. Here, we uncover the positive role of ethylene signaling, ERF95 and ERF97 in basal thermotolerance of Arabidopsis thaliana. We demonstrate that ethylene signaling-defective mutants exhibit compromised basal thermotolerance, whereas plants with constitutively activated ethylene response show enhanced basal thermotolerance. EIN3 physically binds to the promoters of ERF95 and ERF97. Ectopic constitutive expression of ERF95 or ERF97 increases the basal thermotolerance of plants. In contrast, erf95 erf96 erf97 erf98 quadruple mutants exhibit decreased basal thermotolerance. ERF95 and ERF97 genetically function downstream of EIN3. ERF95 can physically interact with ERF97, and this interaction is heat inducible. ERF95 and ERF97 regulate a common set of target genes, including known heat-responsive genes and directly bind to the promoter of HSFA2. Thus, our study reveals that the EIN3-ERF95/ERF97-HSFA2 transcriptional cascade may play an important role in the heat stress response, thereby establishing a connection between ethylene and its downstream regulation in basal thermotolerance of plants.

Biochemistry & Molecular Biology↗
NASA NTRS2002

Low-Shear modeled microgravity alters the Salmonella enterica serovar typhimurium stress response in an RpoS-independent manner

We have previously demonstrated that low-shear modeled microgravity (low-shear MMG) serves to enhance the virulence of a bacterial pathogen, Salmonella enterica serovar Typhimurium. The Salmonella response to low-shear MMG involves a signaling pathway that we have termed the low-shear MMG stimulon, though the identities of the low-shear MMG stimulon genes and regulatory factors are not known. RpoS is the primary sigma factor required for the expression of genes that are induced upon exposure to different environmental-stress signals and is essential for virulence in mice. Since low-shear MMG induces a Salmonella acid stress response and enhances Salmonella virulence, we reasoned that RpoS would be a likely regulator of the Salmonella low-shear MMG response. Our results demonstrate that low-shear MMG provides cross-resistance to several environmental stresses in both wild-type and isogenic rpoS mutant strains. Growth under low-shear MMG decreased the generation time of both strains in minimal medium and increased the ability of both strains to survive in J774 macrophages. Using DNA microarray analysis, we found no evidence of induction of the RpoS regulon by low-shear MMG but did find that other genes were altered in expression under these conditions in both the wild-type and rpoS mutant strains. Our results indicate that, under the conditions of these studies, RpoS is not required for transmission of the signal that induces the low-shear MMG stimulon. Moreover, our studies also indicate that low-shear MMG can be added to a short list of growth conditions that can serve to preadapt an rpoS mutant for resistance to multiple environmental stresses.

Non-NASA Center↗
NASA NTRS2002

Hydrogen peroxide homeostasis: activation of plant catalase by calcium/calmodulin

Environmental stimuli such as UV, pathogen attack, and gravity can induce rapid changes in hydrogen peroxide (H(2)O(2)) levels, leading to a variety of physiological responses in plants. Catalase, which is involved in the degradation of H(2)O(2) into water and oxygen, is the major H(2)O(2)-scavenging enzyme in all aerobic organisms. A close interaction exists between intracellular H(2)O(2) and cytosolic calcium in response to biotic and abiotic stresses. Studies indicate that an increase in cytosolic calcium boosts the generation of H(2)O(2). Here we report that calmodulin (CaM), a ubiquitous calcium-binding protein, binds to and activates some plant catalases in the presence of calcium, but calcium/CaM does not have any effect on bacterial, fungal, bovine, or human catalase. These results document that calcium/CaM can down-regulate H(2)O(2) levels in plants by stimulating the catalytic activity of plant catalase. Furthermore, these results provide evidence indicating that calcium has dual functions in regulating H(2)O(2) homeostasis, which in turn influences redox signaling in response to environmental signals in plants.

NASA Discipline Plant Biology↗
DOE OSTI2024

Future North Atlantic tropical cyclone intensities in thermodynamically modified historical environments

Tropical cyclones (TCs) rank as the deadliest and most financially crippling natural disasters in the United States for the last half-century. It is imperative to assess potential shifts in TC intensity within the paradigm of an evolving climate. In this study, we have modeled the intensities of 620 historical TC events in the North Atlantic Basin using the Risk Analysis Framework for Tropical Cyclones (RAFT)'s deep learning intensity model. By applying a thermodynamic warming signal extrapolated from Global Climate Models, we rerun historical events under eight different future climate scenarios, providing a spectrum of potential TC intensity outcomes. One of the future simulations indicates a staggering 43% increase in the number of major hurricanes, underscoring the critical impact of climate change on TC intensity. Additionally, an interactive dashboard has been created to enable users to explore individual storm simulations and understand the influence of future climate signals on environmental conditions of TC development and resulting TC intensities. This dataset and the user-friendly tool offer invaluable resources for systematic exploration of the discrete effects that changes in the air-sea thermodynamic state have on the intensities of TCs.

Climate Change↗