Search NASA⌕ Search

SEARCH · Search NASA

Results for “BIOLOGICAL RHYTHM”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

16 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Forest residue harvest optimization: spanning the bridge between plant biology and biorefinery performance

Forestry residues have immense potential as alternative feedstocks to petroleum, yet their inherent complexity remains a major challenge to widespread use. Pairing the temporal rhythms of plant biology with biorefinery performance is critical to industrial-scale biorefinery development. Here, we provide the first report of a techno-economic analysis (TEA) and life cycle assessment (LCA) for a model integrated reductive catalytic fractionation (RCF)–molten salt hydrolysis process for forestry residues varying in tree part, species, and phenophase. All forestry residues resulted in net-negative greenhouse gas (GHG) emissions vs. comparable petroleum feedstocks, with GHG emissions potentially reduced >4.0× through composition-based feedstock selection (e.g., harvesting American beech bark in spring vs. summer). Moreover, American beech twigs/branchlets and bark in leafed and emergence phenophases, respectively, had 7.9× lower predicted phenolic minimum selling prices (MSPs) vs. other feedstocks and MSPs within the current global phenolic market range. Hemicellulose content and RCF yield emerged as key parameters impacting GHG emissions and biorefinery revenue, identifying hardwood twigs/branchlets in the leafed phenophase as optimal biofeedstocks. Biorefinery expenses were dominated by purchased equipment, raw materials, and utility costs, highlighting essential areas for future study. Notably, RCF reactor pressures drove 85–90% of equipment costs, but sensitivity analysis revealed that decreasing the pressure 20% could reduce the phenol MSP 4-fold. Structural carbohydrate dynamics were also investigated using a two-step acid hydrolysis method to resolve tissue- and species-level patterns in biomass composition throughout the year to enable harvest optimization based on TEA/LCA findings. Ultimately, elucidating the impact of biofeedstock dynamics on biorefinery performance enables harvest optimization, informed engineering design, and progress towards an expanded bioeconomy.

Shapiro, Alison J. [University of Delaware, Newark↗
DOE OSTI2022

Photosynthetic modulation during the diurnal cycle in a unicellular diazotrophic cyanobacterium grown under nitrogen-replete and nitrogen-fixing conditions

Abstract Cyanobacteria are the only oxygenic photosynthetic organisms that can fix nitrogen. In diazotrophic cyanobacteria, the regulation of photosynthesis during the diurnal cycle is hypothesized to be linked with nitrogen fixation and involve the D1 protein isoform PsbA4. The amount of bioavailable nitrogen has a major impact on productivity in aqueous environments. In contrast to low- or nitrogen-fixing (−N) conditions, little data on photosynthetic regulation under nitrogen-replete (+ N) conditions are available. We compared the regulation of photosynthesis under −N and + N conditions during the diurnal cycle in wild type and a psbA4 deletion strain of the unicellular diazotrophic cyanobacterium Cyanothece sp. ATCC 51142. We observed common changes to light harvesting and photosynthetic electron transport during the dark in + N and −N conditions and found that these modifications occur in both diazotrophic and non-diazotrophic cyanobacteria. Nitrogen availability increased PSII titer when cells transitioned from dark to light and promoted growth. Under −N conditions, deletion of PsbA4 modified charge recombination in dark and regulation of PSII titer during dark to light transition. We conclude that darkness impacts the acceptor-side modifications to PSII and photosynthetic electron transport in cyanobacteria independently of the nitrogen-fixing status and the presence of PsbA4.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

From primordial clocks to circadian oscillators

Circadian rhythms play an essential part in many biological processes, and only three prokaryotic proteins are required to constitute a true post-translational circadian oscillator1. The evolutionary history of the three Kai proteins indicates that KaiC is the oldest member and a central component of the clock. Subsequent additions of KaiB and KaiA regulate the phosphorylation state of KaiC for time synchronization. The canonical KaiABC system in cyanobacteria is well understood but little is known about more ancient systems that only possess KaiBC. However, there are reports that they might exhibit a basic, hourglass-like timekeeping mechanism. Here we investigate the primordial circadian clock in Rhodobacter sphaeroides , which contains only KaiBC, to elucidate its inner workings despite missing KaiA. Using a combination of X-ray crystallography and cryogenic electron microscopy, we find a new dodecameric fold for KaiC, in which two hexamers are held together by a coiled-coil bundle of 12 helices. This interaction is formed by the carboxy-terminal extension of KaiC and serves as an ancient regulatory moiety that is later superseded by KaiA. A coiled-coil register shift between daytime and night-time conformations is connected to phosphorylation sites through a long-range allosteric network that spans over 140 Å. Our kinetic data identify the difference in the ATP-to-ADP ratio between day and night as the environmental cue that drives the clock. They also unravel mechanistic details that shed light on the evolution of self-sustained oscillators.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cadmium-Free QD Building Blocks for Human Centric Lighting

This project developed Cd-free quantum dot (QD) downconverters for efficacious human-centric lighting (HCL) light emitting diode (LED) devices. Solid state HCL devices address the lack of light in the cyan wavelength region (460-490 nm) in white LEDs by enhancing the melanopic daylight efficacy ratio (MDER) value. MDER is a metric that indicates the degree to which artificial lighting stimulates nonvisual biological processes in the retina responsible for regulating circadian rhythms compared with natural lighting. The peak sensitivity of melanopsin in the retina is at 479 nm, therefore artificial lighting which can fill the well-known “cyan gap” may improve human health. Due to the Restriction of Hazardous Substances (RoHS) regulations, cadmium-free core/shell/shell QDs are the primary targets for low toxicity, tunable downconverters. Cyan- and red-emitting core/shell/shell QDs were implemented in LED devices toward achieving a brightness of 210 lm/W at 4000 K, CRI 90, and MDER > 0.7. Synthetic development of Cd-free materials yielded cyan InP/ZnS QDs with a photoluminescence quantum yield (PLQY) of ~60% between 480-490 nm, and red InP/ZnSe/(ZnSeS)/ZnS QDs reaching ~80% PLQY at 620-630 nm. We successfully demonstrated that the inclusion of cyan QDs increased the MDER value to ≥0.7, but the brightness of the HCL LED devices was hindered due to low PLQY values. However, upon substitution of the Cd-free cyan QD with a low-Cd QD with >90% PLQY, brightness improved by 25% over the Cd-free device to 179 lm/W. Despite the technical obstacles remaining toward improving emission characteristics and stability of QDs under high flux, we have confirmed the promise of narrow, tunable QD emitters in SSL packages toward the goal of healthy, human-centric lighting.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2023

A crucial role for dynamic expression of components encoding the negative arm of the circadian clock

In the Neurospora circadian system, the White Collar Complex (WCC) drives expression of the principal circadian negative arm component frequency ( frq ). FRQ interacts with FRH (FRQ-interacting RNA helicase) and CKI, forming a stable complex that represses its own expression by inhibiting WCC. In this study, a genetic screen identified a gene, designated as brd-8 , that encodes a conserved auxiliary subunit of the NuA4 histone acetylation complex. Loss of brd-8 reduces H4 acetylation and RNA polymerase (Pol) II occupancy at frq and other known circadian genes, and leads to a long circadian period, delayed phase, and defective overt circadian output at some temperatures. In addition to strongly associating with the NuA4 histone acetyltransferase complex, BRD-8 is also found complexed with the transcription elongation regulator BYE-1. Expression of brd-8, bye-1, histone h2a.z , and several NuA4 subunits is controlled by the circadian clock, indicating that the molecular clock both regulates the basic chromatin status and is regulated by changes in chromatin. Taken together, our data identify auxiliary elements of the fungal NuA4 complex having homology to mammalian components, which along with conventional NuA4 subunits, are required for timely and dynamic frq expression and thereby a normal and persistent circadian rhythm.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

S. elongatus PCC 7942 Carbon Metabolism Proteomics (MC-DP2)

The purpose of this experiment was to examine the redox proteome of S. elongatus PCC 7942 CscB/SPS under different light conditions (light and dark) and culture conditions (dense and dilute optical density). Samples were processed using a resin-assisted capture (RAC) workflow with TMT labeling to enrich and quantify protein cysteines which were differentially oxidized under four conditions. The datasets were generated by a Q Exactive Plus Orbitrap Mass Spectrometer coupled with a Waters nanoAcquity UPLC, then searched by MSGF+ for downstream redox PTM analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Genomic profiles of four novel cyanobacteria MAGs from Lake Vanda, Antarctica: insights into photosynthesis, cold tolerance, and the circadian clock

Cyanobacteria in polar environments face environmental challenges, including cold temperatures and extreme light seasonality with small diurnal variation, which has implications for polar circadian clocks. However, polar cyanobacteria remain underrepresented in available genomic data, and there are limited opportunities to study their genetic adaptations to these challenges. This paper presents four new Antarctic cyanobacteria metagenome-assembled genomes (MAGs) from microbial mats in Lake Vanda in the McMurdo Dry Valleys in Antarctica. The four MAGs were classified as Leptolyngbya sp. BulkMat.35, Pseudanabaenaceae cyanobacterium MP8IB2.15, Microcoleus sp. MP8IB2.171, and Leptolyngbyaceae cyanobacterium MP9P1.79. The MAGs contain 2.76 Mbp – 6.07 Mbp, and the bin completion ranges from 74.2–92.57%. Furthermore, the four cyanobacteria MAGs have average nucleotide identities (ANIs) under 90% with each other and under 77% with six existing polar cyanobacteria MAGs and genomes. This suggests that they are novel cyanobacteria and demonstrates that polar cyanobacteria genomes are underrepresented in reference databases and there is continued need for genome sequencing of polar cyanobacteria. Analyses of the four novel and six existing polar cyanobacteria MAGs and genomes demonstrate they have genes coding for various cold tolerance mechanisms and most standard circadian rhythm genes with the Leptolyngbya sp. BulkMat.35 and Leptolyngbyaceae cyanobacterium MP9P1.79 contained kaiB3, a divergent homolog of kaiB.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Light: An Extrinsic Factor Influencing Animal-based Research

Abstract Light is an environmental factor that is extrinsic to animals themselves and that exerts a profound influence on the regulation of circadian, neurohormonal, metabolic, and neurobehavioral systems of all animals, including research animals. These widespread biologic effects of light are mediated by distinct photoreceptors—rods and cones that comprise the conventional visual system and melanopsin-containing intrinsically photosensitive retinal ganglion cells (ipRGCs) of the nonvisual system that interact with the rods and cones. The rods and cones of the visual system, along with the ipRGCs of the nonvisual system, are species distinct in terms of opsins and opsin concentrations and interact with one another to provide vision and regulate circadian rhythms of neurohormonal and neurobehavioral responses to light. Here, we review a brief history of lighting technologies, the nature of light and circadian rhythms, our present understanding of mammalian photoreception, and current industry practices and standards. We also consider the implications of light for vivarium measurement, production, and technological application and provide simple recommendations on artificial lighting for use by regulatory authorities, lighting manufacturers, designers, engineers, researchers, and research animal care staff that ensure best practices for optimizing animal health and well-being and, ultimately, improving scientific outcomes.

Veterinary Sciences↗
DOE OSTI2024

Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi

Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. In this manuscript, we present a genome for a laboratory-tractable Entomophthora muscae isolate that infects fruit flies. Our E. muscae assembly is 1.03 Gb, consists of 7810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with recent datasets from entomophthoralean fungi, we show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity. In addition, we find that E. muscae and its closest allies possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae’s species-specific, biotrophic lifestyle. Finally, we offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex that support the need for taxonomic revision within this group. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Multi-Omics Reveals Temporal Scales of Carbon Metabolism in Synechococcus Elongatus PCC 7942 Under Light Disturbance

Central carbon metabolism in model cyanobacteria involves multiple pathways to adapt to energy-light limitations across diel cycles. However, the success in mechanistic modeling for phenotypic prediction of the protein regulators in the metabolic state depends on capturing the vast possibilities emerging from multiple regulatory pathways in complex biological processes. Here, we developed a physics-informed machine learning approach based on energy-landscape concepts to predict regulatory proteins responding to cyclic circadian and unforeseen light perturbations in cyanobacterial metabolic networks. Our approach provides interpretable de novo models for inferring gene expression dynamics from Synechococcus elongatus over diel cycles and using redox proteome analysis to distinguish immediate light-responsive elements from circadian-regulated processes in carbon metabolism pathways. We identified distinct temporal signatures with the analysis of the redox proteome: there was an immediate shift in cysteine redox states accompanied by a limited change in protein abundance under constant illumination and after 2 hours of darkness. This discovery indicates that the generation of reductants coordinates photoinduced electron transport with redox metabolic pathways in two discernable molecular mechanisms: fast redox-based protein modifications occur immediately after the light disturbance, followed by slow transcriptional regulations across networks. This temporal regulation reveals how metabolic networks integrate rapid light responses with programmed circadian rhythms to maintain cellular homeostasis under the light-energy limitations over the diel cycle.

Biomolecular & subcellular processes↗
DOE OSTI2022

Rhythm of the Night (and Day): Predictive Metabolic Modeling of Diurnal Growth in Chlamydomonas

We have developed the first transient metabolic model for diurnal growth of algae based on experimental data and capable of predicting phenotype from genotype. This model enables us to evaluate the impact of genetic and environmental changes on the growth, biomass composition and intracellular fluxes of the model green alga, Chlamydomonas reinhardtii . The availability of this model will enable faster and more efficient design of cells for production of fuels, chemicals, and pharmaceuticals.

09 BIOMASS FUELS↗
DOE OSTI2025

Cyanobacterial circadian regulation enhances bioproduction under subjective nighttime through rewiring of carbon partitioning dynamics, redox balance orchestration, and cell cycle modulation

Abstract Background The industrial feasibility of photosynthetic bioproduction using cyanobacterial platforms remains challenging due to insufficient yields, particularly due to competition between product formation and cellular carbon demands across different temporal phases of growth. This study investigates how circadian clock regulation impacts carbon partitioning between storage, growth, and product synthesis in Synechococcus elongatus PCC 7942, and provides insights that suggest potential strategies for enhanced bioproduction. Results After entrainment to light-dark cycles, PCC 7942 cultures transitioned to constant light revealed distinct temporal patterns in sucrose production, exhibiting three-fold higher productivity during subjective night compared to subjective day despite moderate down-regulation of genes from the photosynthetic apparatus. This enhanced productivity coincided with reduced glycogen accumulation and halted cell division at subjective night time, suggesting temporal separation of competing processes. Transcriptome analysis revealed coordinated circadian clock-driven adjustment of the cell cycle and rewiring of energy and carbon metabolism, with over 300 genes showing differential expression across four time points. The subjective night was characterized by altered expression of cell division-related genes and reduced expression of genes involved in glycogen synthesis, while showing upregulation of glycogen degradation pathways, alternative electron flow components, the pentose phosphate pathway, and oxidative decarboxylation of pyruvate. These molecular changes created favorable conditions for product formation through enhanced availability of major sucrose precursors (glucose-1-phosphate and fructose-6-phosphate) and maintained redox balance through multiple mechanisms. Conclusions Our analysis of circadian regulatory rewiring of carbon metabolism and redox balancing suggests two potential approaches that could be developed for improving cyanobacterial bioproduction: leveraging natural circadian rhythms for optimizing cultivation conditions and timing of pathway induction, and engineering strains that mimic circadian-driven metabolic shifts through controlled carbon flux redistribution and redox rebalancing. While these strategies remain to be tested, they could theoretically improve the efficiency of photosynthetic bioproduction by enabling better temporal separation between cell growth, carbon storage accumulation, and product synthesis phases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Lighting for Health and Wellness Recommendations in Offices: A Circadian Lighting Pilot Project in Chicago, IL

In 2019 Cook County initiated a request for proposals for a pilot project aimed at designing and specifying an advanced tunable lighting system for government offices in Chicago, Illinois. The primary goal of the project was to replace the existing tubular LED (TLED) lighting system with a lighting system that supported the circadian rhythms and wellbeing their office employees. A secondary goal was to evaluate the potential impacts of the new lighting system, informing Cook County’s internal workplace design standards. Schuler Shook, a Chicago-based lighting design firm, was awarded the Circadian Lighting Pilot Project in October 2019 and invited Pacific Northwest National Laboratory (PNNL) to contribute as a research partner. Based on the initial project goals, Schuler Shook and PNNL established design objectives that would enable a human factors study in the office spaces, investigating the benefits and drawbacks of using a tunable LED lighting system to meet existing recommendations for lighting and health. The following report details the lighting design process through design development, with summaries of the relevant circadian lighting metrics, simulation tools, energy considerations, and research plan for the Circadian Lighting Pilot Project.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2026

Circadian immunometabolic states impart a temporal response to SARS-CoV-2 spike proteins in mammalian macrophages

Circadian rhythms, the 24-hour cycles that tune organismal physiology to the daily rhythms of light and dark, optimally organize cellular processes such as metabolism and mitochondrial function. In mammals, macrophage functions are regulated by these 24-hour circadian rhythms such that the immunometabolic response is coordinated across the day, consolidating macrophage physiology into temporally distinct phases to time the cellular immune response. However, while it is known that there are time-of-day specific responses to stress in a macrophage, little has been done to determine if circadian regulation coordinates the response of a macrophage to real-world pathogens. Importantly, key proteins in the response to viral infection have been found to be under circadian control, and time of day of application is known to affect the efficacy of vaccinations, including in the case of the COVID-19 virus. Therefore, to investigate if the circadian regulation of macrophage physiology imparted a time-of-day response to viral exposure, we exposed primary mouse and human macrophages to the SARS-CoV-1 and CoV-2 spike proteins at different times over the circadian day. To establish a time-of-day effect, we performed a multi-omics analysis and in vitro tissue culture assays examining macrophage responses over circadian time. We found that, conserved across the species, the timing of spike protein exposure dictated two distinct temporal responses which were characterized by hallmarks of immunometabolic suppression and modest inflammatory activation. However, these responses were primarily influenced by central metabolic and mitochondrial changes and not by classical immune activation.

Circadian Biology↗
DOE OSTI2025

Markers of mitochondrial function and oxidative metabolism in skeletal muscle do not display intrinsic circadian regulation in female mice

Mitochondria are key regulators of metabolism and ATP supply in skeletal muscle, while circadian rhythms influence many physiological processes. However, whether mitochondrial function is intrinsically regulated in a circadian manner in mouse skeletal muscle is inadequately understood. Accordingly, we measured postabsorptive transcript abundance of markers of mitochondrial autophagy, dynamics, and metabolism [extensor digitorum longus (EDL), soleus, gastrocnemius], protein abundance of electron transport chain complexes (EDL and soleus), enzymatic activity of succinate dehydrogenase (tibialis anterior and plantaris), and maximal mitochondrial respiration (tibialis anterior) in different skeletal muscles from female C57BL/6NJ mice at four zeitgeber times: 1, 7, 13, and 19. Our findings demonstrate that markers of mitochondrial function and oxidative metabolism do not display intrinsic time-of-day regulation at the gene, protein, enzymatic, or functional level. The core-clock genes Bmal1 and Dbp exhibited intrinsic circadian rhythmicity in skeletal muscle (i.e., EDL, soleus, gastrocnemius) and circadian amplitude varied by muscle type. These findings demonstrate that female mouse skeletal muscle does not display circadian regulation of markers of mitochondrial function or oxidative metabolism over 24 h.

Circadian Biology↗
DOE OSTI2024

Transcriptomic Analysis of the CAM Species Kalanchoë fedtschenkoi Under Low- and High-Temperature Regimes

Temperature stress is one of the major limiting environmental factors that negatively impact global crop yields. Kalanchoë fedtschenkoi is an obligate crassulacean acid metabolism (CAM) plant species, exhibiting much higher water-use efficiency and tolerance to drought and heat stresses than C 3 or C 4 plant species. Previous studies on gene expression responses to low- or high-temperature stress have been focused on C 3 and C 4 plants. There is a lack of information about the regulation of gene expression by low and high temperatures in CAM plants. To address this knowledge gap, we performed transcriptome sequencing (RNA-Seq) of leaf and root tissues of K. fedtschenkoi under cold (8 °C), normal (25 °C), and heat (37 °C) conditions at dawn (i.e., 2 h before the light period) and dusk (i.e., 2 h before the dark period). Our analysis revealed differentially expressed genes (DEGs) under cold or heat treatment in comparison to normal conditions in leaf or root tissue at each of the two time points. In particular, DEGs exhibiting either the same or opposite direction of expression change (either up-regulated or down-regulated) under cold and heat treatments were identified. In addition, we analyzed gene co-expression modules regulated by cold or heat treatment, and we performed in-depth analyses of expression regulation by temperature stresses for selected gene categories, including CAM-related genes, genes encoding heat shock factors and heat shock proteins, circadian rhythm genes, and stomatal movement genes. Our study highlights both the common and distinct molecular strategies employed by CAM and C 3 /C 4 plants in adapting to extreme temperatures, providing new insights into the molecular mechanisms underlying temperature stress responses in CAM species.

59 BASIC BIOLOGICAL SCIENCES↗