Distributed Acoustic Sensing of Anthropogenic and Polar Environmental Signals
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Baker, Michael Grant↗
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Distributed Acous.c Sensing of Anthropogenic and Polar Environmental Signals.
Abstract not provided.
Abbott, Robert↗
Genomes of multicellular algal sisters to land plants illuminate signaling network evolution
Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum . We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.
59 BASIC BIOLOGICAL SCIENCES↗
Jasmonate activates secondary cell wall biosynthesis through MYC2–MYB46 module
Formation of secondary cell wall (SCW) is tightly regulated spatiotemporally by various developmental and environmental signals. Successful fine-tuning of the trade-off between SCW biosynthesis and stress responses requires a better understanding of how plant growth is regulated under environmental stress conditions. However, the current understanding of the interplay between environmental signaling and SCW formation is limited. The lipid-derived plant hormone jasmonate (JA) and its derivatives are important signaling components involved in various physiological processes including plant growth, development, and abiotic/biotic stress responses. Recent studies suggest that JA is involved in SCW formation but the signaling pathway has not been studied for how JA regulates SCW formation. We tested this hypothesis using the transcription factor MYB46, a master switch for SCW biosynthesis, and JA treatments. Both the transcript and protein levels of MYB46, a master switch for SCW formation, were significantly increased by JA treatment, resulting in the upregulation of SCW biosynthesis. We then show that this JA-induced upregulation of MYB46 is mediated by MYC2, a central regulator of JA signaling, which binds to the promoter of MYB46. We conclude that this MYC2-MYB46 module is a key component of the plant response to JA in SCW formation.
59 BASIC BIOLOGICAL SCIENCES↗
Quantifying the Environmental Sensitivity of SSTDR Signals for Monitoring PV Strings
Not provided.
Energy & Fuels↗
The lowdown on breakdown: Open questions in plant proteolysis
Abstract Proteolysis, including post-translational proteolytic processing as well as protein degradation and amino acid recycling, is an essential component of the growth and development of living organisms. In this article, experts in plant proteolysis pose and discuss compelling open questions in their areas of research. Topics covered include the role of proteolysis in the cell cycle, DNA damage response, mitochondrial function, the generation of N-terminal signals (degrons) that mark many proteins for degradation (N-terminal acetylation, the Arg/N-degron pathway, and the chloroplast N-degron pathway), developmental and metabolic signaling (photomorphogenesis, abscisic acid and strigolactone signaling, sugar metabolism, and postharvest regulation), plant responses to environmental signals (endoplasmic-reticulum-associated degradation, chloroplast-associated degradation, drought tolerance, and the growth-defense trade-off), and the functional diversification of peptidases. We hope these thought-provoking discussions help to stimulate further research.
Eckardt, Nancy A. (ORCID:0000000316581412)↗
Structural basis of cell-surface signaling by a conserved sigma regulator in Gram-negative bacteria
Cell-surface signaling (CSS) in Gram-negative bacteria involves highly conserved regulatory pathways that optimize gene expression by transducing extracellular environmental signals to the cytoplasm via inner-membrane sigma regulators. The molecular details of ferric siderophore-mediated activation of the iron import machinery through a sigma regulator are unclear. Here, we present the 1.56 Å resolution structure of the periplasmic complex of the C-terminal CSS domain (CCSSD) of PupR, the sigma regulator in the Pseudomonas capeferrum pseudobactin BN7/8 transport system, and the N-terminal signaling domain (NTSD) of PupB, an outer-membrane TonB-dependent transducer. The structure revealed that the CCSSD consists of two subdomains: a juxta-membrane subdomain, which has a novel all-β-fold, followed by a secretin/TonB, short N-terminal subdomain at the C terminus of the CCSSD, a previously unobserved topological arrangement of this domain. Using affinity pulldown assays, isothermal titration calorimetry, and thermal denaturation CD spectroscopy, we show that both subdomains are required for binding the NTSD with micromolar affinity and that NTSD binding improves CCSSD stability. Our findings prompt us to present a revised model of CSS wherein the CCSSD:NTSD complex forms prior to ferric-siderophore binding. Upon siderophore binding, conformational changes in the CCSSD enable regulated intramembrane proteolysis of the sigma regulator, ultimately resulting in transcriptional regulation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress
Abstract We present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these questions include the need to better understand how plants detect water availability, temperature, salinity, and rising carbon dioxide (CO2) levels; how environmental signals interface with endogenous signaling and development (e.g. circadian clock and flowering time); and how this integrated signaling controls downstream responses (e.g. stomatal regulation, proline metabolism, and growth versus defense balance). The plasma membrane comes up frequently as a site of key signaling and transport events (e.g. mechanosensing and lipid-derived signaling, aquaporins). Adaptation to water extremes and rising CO2 affects hydraulic architecture and transpiration, as well as root and shoot growth and morphology, in ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution and crop resilience in the face of changing and increasingly unpredictable environments. Exploration of plant diversity within and among species can help us know which of these tradeoffs represent fundamental limits and which ones can be circumvented by bringing new trait combinations together. Better defining what constitutes beneficial stress resistance in different contexts and making connections between genes and phenotypes, and between laboratory and field observations, are overarching challenges.
Biochemistry & Molecular Biology↗
A suberized exodermis is required for tomato drought tolerance
Plant roots integrate environmental signals with development using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates flow of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation but is absent in the tomato endodermis. Instead, suberin is present in the exodermis, a cell type that is absent in the model organism Arabidopsis thaliana. Here we demonstrate that the suberin regulatory network has the same parts driving suberin production in the tomato exodermis and the Arabidopsis endodermis. Despite this co-option of network components, the network has undergone rewiring to drive distinct spatial expression and with distinct contributions of specific genes. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response and that the exodermal barrier serves an equivalent function to that of the endodermis and can act in its place.
59 BASIC BIOLOGICAL SCIENCES↗
Dynamics of pectic homogalacturonan in cellular morphogenesis and adhesion, wall integrity sensing and plant development
Homogalacturonan (HG) is the most abundant pectin subtype in plant cell walls. Although it is a linear homopolymer, its modification states allow for complex molecular encoding. HG metabolism affects its structure, chemical properties, mobility and binding capacity, allowing it to interact dynamically with other polymers during wall assembly and remodelling and to facilitate anisotropic cell growth, cell adhesion and separation, and organ morphogenesis. HGs have also recently been found to function as signalling molecules that transmit information about wall integrity to the cell. Here we highlight recent advances in our understanding of the dual functions of HG as a dynamic structural component of the cell wall and an initiator of intrinsic and environmental signalling. Here, we also predict how HG might interconnect the cell wall, plasma membrane and intracellular components with transcriptional networks to regulate plant growth and development.
59 BASIC BIOLOGICAL SCIENCES↗
Conditional guide RNA deactivation by mRNA and small molecule triggers in Saccharomyces cerevisiae
CRISPR interference (CRISPRi) technologies have revolutionized bioengineering by providing precise tools for gene expression modulation, enabling targeted gene perturbation and metabolic pathway optimization. Despite these advances, achieving dynamic control over gene expression by CRISPR-based regulation remains a challenge due to its inherently static nature. Utilizing toehold-mediated strand displacement and ligand-responsive ribozymes (aptazymes), this study introduces switchable guide RNAs (gRNAs) that facilitate tunable gene expression mediated by mRNA or small molecule signals. We demonstrate complete silencing of gRNA via strategically designed 5’ or 3’ extensions that impede the gRNA spacer or the dCas9 handle, with subsequent restoration of function through sequestration or cleavage of the obstructive sequence. The resulting toehold-embedded or aptazyme-embedded gRNAs can be deactivated by specific signals, including two full-length translatable mRNAs and two small molecule triggers, thereby lifting CRISPRi repression on targeted genes. This modular approach allows for gRNA-based biocomputing through multi-layer or multi-input genetic logic gates in Saccharomyces cerevisiae . Offering a versatile strategy for post-CRISPR regulation in response to environmental signals or cellular states, this methodology expands the toolkit in eukaryotic systems for reversible control of gene expression.
Aptazyme↗
The plant cell wall—dynamic, strong, and adaptable—is a natural shapeshifter
Mythology is replete with good and evil shapeshifters, who, by definition, display great adaptability and assume many different forms—with several even turning themselves into trees. Cell walls certainly fit this definition as they can undergo subtle or dramatic changes in structure, assume many shapes, and perform many functions. In this review, we cover the evolution of knowledge of the structures, biosynthesis, and functions of the 5 major cell wall polymer types that range from deceptively simple to fiendishly complex. Along the way, we recognize some of the colorful historical figures who shaped cell wall research over the past 100 years. The shapeshifter analogy emerges more clearly as we examine the evolving proposals for how cell walls are constructed to allow growth while remaining strong, the complex signaling involved in maintaining cell wall integrity and defense against disease, and the ways cell walls adapt as they progress from birth, through growth to maturation, and in the end, often function long after cell death. We predict the next century of progress will include deciphering cell type–specific wall polymers; regulation at all levels of polymer production, crosslinks, and architecture; and how walls respond to developmental and environmental signals to drive plant success in diverse environments.
59 BASIC BIOLOGICAL SCIENCES↗
Temporal dynamics of protein and post-translational modification abundances in Populus leaf across a diurnal period
Populus spp. are dedicated woody biomass feedstocks for advanced biofuels and bioproducts. Proper growth and fitness of poplar as a sustainable feedstock depends on timely perception and response to environmental signals (e.g., light, temperature, water). Poplar leaves, like other C3 photosynthesis plants, have evolved oscillating or circadian rhythms that play important roles in synchronizing biological processes with external cues. To characterize this phenomenon at a molecular level, we employed bottom-up proteomics using high-resolution mass spectrometry and de novo-assisted database searching to identify abundance changes in proteins and post-translational modifications in poplar leaf tissue sampled across a 12/12-hour light/dark diurnal period.
09 BIOMASS FUELS↗
Heterogeneous isotope effects decouple conifer leaf and branch sugar δ 18 O and δ 13 C
Isotope ratios of tree-ring cellulose are a prominent tool to reconstruct paleoclimate and plant responses to environmental variation. Current models for cellulose isotope ratios assume a transfer of the environmental signals recorded in bulk leaf water to carbohydrates and ultimately into stem cellulose. However, the isotopic signal of carbohydrates exported from leaf to branch may deviate from mean leaf values if spatial heterogeneity in isotope ratios exists in the leaf. We tested whether the isotopic heterogeneity previously observed along the length of a ponderosa pine (Pinus ponderosa) leaf water was preserved in photosynthetic products. We observed an increase in both sugar and bulk tissue δ 18 O values along the needle, but the increase in carbohydrate δ 18 O values was dampened relative to the trend observed in leaf water. In contrast, δ 13 C values of both sugar and bulk organic matter were invariant along the needle. Additionally, phloem-exported sugar measured in the branch below the needles did not match whole-needle values of δ 18 O or δ 13 C. Instead, there was a near-constant offset observed between the branch and needle sugar δ 13 C values, while branch δ 18 O values were most similar to δ 18 O values observed for sugar at the base of the needle. The observed offset between the branch and needle sugar δ 18 O values likely arises from partial isotope oxygen exchange between sugars and water during phloem loading and transport. An improved understanding of the conditions producing differential δ 13 C and δ 18 O isotope effects between branch phloem and needle sugars could improve tree-ring-based climate reconstructions.
59 BASIC BIOLOGICAL SCIENCES↗
Transcription initiation as a control point in plastid gene expression
The extensive processing and protein-assisted stabilization of transcripts have been taken as evidence for a viewpoint that the control of gene expression had shifted entirely in evolution from transcriptional in the bacterial endosymbiont to posttranscriptional in the plastid. This suggestion is however at odds with many observations on plastid gene transcription. Chloroplasts of flowering plants and mosses contain two or more RNA polymerases with distinct promoter preference and division of labor for the coordinated synthesis of plastid RNAs. Plant and algal plastids further possess multiple nonredundant sigma factors that function as transcription initiation factors. The controlled accumulation of plastid sigma factors and modification of their activity by sigma-binding proteins and phosphorylation constitute additional transcriptional regulatory strategies. Plant and algal plastids also contain dedicated one- or two-component transcriptional regulators. Finally, transcription initiation thus continues to form a critical control point at which varied developmental and environmental signals intersect with plastid gene expression.
59 BASIC BIOLOGICAL SCIENCES↗
An uncertainty-focused database approach to extract spatiotemporal trends from qualitative and discontinuous lake-status histories
Changes in lake status are often interpreted as palaeoclimate indicators due to their dependence on precipitation and evaporation. The Global Lake Status Database (GLSDB) has since long provided a standardised synopsis of qualitative lake status over the last 30,000 14C years. Potential sources of uncertainty however are not recorded in the GLSDB. Here we present an updated and improved relational-database framework that incorporates uncertainty in both chronology and the interpretation of palaeoenvironmental data. The database uses peer-reviewed palaeolimnological studies to produce a consensus on qualitative lake-status histories, whose chronologies are revised and standardized through the recalibration of radiocarbon dates and the application of Bayesian age-depth modelling for stratigraphic archives. Quantitative information on absolute water-level elevation is preserved if available from geomorphological sources. We also propose a new probabilistic analytical framework that accounts for these uncertainties to reconstruct synoptic, integrated environmental signals. The process is based on a Monte Carlo algorithm that iteratively samples individual lake-status histories within the limits of their uncertainties to produce many possible scenarios. We then use Recursively-Subtracted Empirical Orthogonal Function analysis to extract dominant patterns of lake-status variability from these scenarios. As a proof of concept, we apply this framework to 67 sites in eastern and southern Africa whose lake-status histories cover part of the late Pleistocene and/or Holocene. We show that, despite the sometimes large temporal and interpretation uncertainties, and the inclusion of highly discontinuous lake-status time series, identifying the major known millennial-scale climatic phases during the last 20,000 years is possible. Our framework was also able to identify an antiphased response between the lake basins in eastern and interior southern Africa to these changes. Here, we propose that our new database and methodology framework serves as a template for efficient lake-status data synthesis, encourages the incorporation of lake-status data in palaeoclimate syntheses, and expands the possibilities for the use of such data in the evaluation of climate models.
58 GEOSCIENCES↗
Developing Scenario‐Based Strategies for Health, Climate, and Environmental Preparedness: The One Health, One Earth Approach
Climate change amplifies many threats to human health. Despite advances in understanding climate change dynamics and impacts, there remains a critical gap in translating scientific knowledge into equitable, and community-driven health interventions. The inaugural One Earth, One Health workshop sought to explore this gap through human-centered design exercises involving interdisciplinary researchers from climate and Earth sciences, engineering, epidemiology, microbiology, and environmental health. Although participants did not co-develop solutions with affected communities, they used stakeholder role-playing to guide ideation and lay groundwork for actionable plans. Through these methods, participants identified community needs and proposed prototype solutions to alleviate health threats exacerbated by global environmental change. Prototypes were organized around infectious diseases, extreme weather, and air quality, as illustrative themes rather than an exhaustive set of risks. Key solutions included strategies for anticipatory systems and early warning (e.g., integrating environmental signals with health data), inclusive communication and infrastructure needs for responding to extreme weather events, and integrated platforms visualizing air quality trends to support tailored, context-aware guidance beyond one-size-fits-all alerts. The workshop highlighted opportunities such as leveraging machine learning, Earth observation, and real-time surveillance to protect communities, but also noted barriers including data quality, technological redundancy, privacy, and governance challenges. Additionally, participants emphasized the need for interdisciplinary teams capable of collaborating across sectors, breaking down silos and addressing gaps in training and education. Overall, the workshop illustrates how process-driven, human-centered approaches can help surface user needs and generate testable prototype concepts, while underscoring the importance of direct community partnership for implementation.
Abadi, Azar M. [University of Alabama, Birmingham,↗