SEARCH · Search NASA

Results for “Biological control”

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.

SourceResearch connectionFrom yearThrough year

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

At least 73 records · Page 4

All sources NASA NTRS DOE OSTI

DOE OSTI2023

Rat bronchoalveolar lavage proteome changes following e-cigarette aerosol exposures

E-cigarette liquids are complex mixtures of chemicals consisting of humectants, such as propylene glycol (PG) and vegetable glycerin (VG), with nicotine or flavorings added. Published literature emphasizes the toxicity of e-cigarette aerosols with flavorings whereas much less attention has been given to the biologic effects of humectants. The purpose of the current study was to provide a comprehensive view of the acute biologic effects of e-cigarette aerosols on rat bronchoalveolar lavage (BAL) using mass spectrometry-based global proteomics. Sprague–Dawley rats were exposed to e-cigarette aerosol for 3 h/day for three consecutive days. Groups included: PG/VG alone, PG/VG + 2.5% nicotine (N), or PG/VG + N + 3.3% vanillin (V). Right lung lobes were lavaged for BAL and supernatants prepared for proteomics. Extracellular BAL S100A9 concentrations and BAL cell staining for citrullinated histone H3 (citH3) were also performed. From global proteomics, ~2,100 proteins were identified from rat BAL. Overall, the greatest change in number of BAL proteins occurred with PG/VG exposures alone compared with controls with biological pathways enriched for acute phase responses, extracellular trap formation, and coagulation. Extracellular BAL S100A9 concentrations and the number of citH3 + BAL cells also increased significantly in PG/VG and PG/VG + 2.5% N. In contrast to PG/VG or PG/VG + N, the addition of vanillin to PG/VG + N increased BAL neutrophilia and downregulated lipid transport proteins. In summary, global proteomics support e-cigarette aerosol exposures to PG/VG alone as having a significant biologic effect on the lung independent of nicotine or flavoring with increased markers of extracellular trap formation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Redox active plant phenolic, acetosyringone, for electrogenetic signaling

Abstract Redox is a unique, programmable modality capable of bridging communication between biology and electronics. Previous studies have shown that the E. coli redox-responsive OxyRS regulon can be re-wired to accept electrochemically generated hydrogen peroxide (H 2 O 2 ) as an inducer of gene expression. Here we report that the redox-active phenolic plant signaling molecule acetosyringone (AS) can also induce gene expression from the OxyRS regulon. AS must be oxidized, however, as the reduced state present under normal conditions cannot induce gene expression. Thus, AS serves as a “pro-signaling molecule” that can be activated by its oxidation—in our case by application of oxidizing potential to an electrode. We show that the OxyRS regulon is not induced electrochemically if the imposed electrode potential is in the mid-physiological range. Electronically sliding the applied potential to either oxidative or reductive extremes induces this regulon but through different mechanisms: reduction of O 2 to form H 2 O 2 or oxidation of AS. Fundamentally, this work reinforces the emerging concept that redox signaling depends more on molecular activities than molecular structure. From an applications perspective, the creation of an electronically programmed “pro-signal” dramatically expands the toolbox for electronic control of biological responses in microbes, including in complex environments, cell-based materials, and biomanufacturing.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Parsed synthesis of pyocyanin via co-culture enables context-dependent intercellular redox communication

Abstract Background Microbial co-cultures and consortia are of interest in cell-based molecular production and even as “smart” therapeutics in that one can take advantage of division of labor and specialization to expand both the range of available functions and mechanisms for control. The development of tools that enable coordination and modulation of consortia will be crucial for future application of multi-population cultures. In particular, these systems would benefit from an expanded toolset that enables orthogonal inter-strain communication. Results We created a co-culture for the synthesis of a redox-active phenazine signaling molecule, pyocyanin (PYO), by dividing its synthesis into the generation of its intermediate, phenazine carboxylic acid (PCA) from the first strain, followed by consumption of PCA and generation of PYO in a second strain. Interestingly, both PCA and PYO can be used to actuate gene expression in cells engineered with the soxRS oxidative stress regulon, although importantly this signaling activity was found to depend on growth media. That is, like other signaling motifs in bacterial systems, the signaling activity is context dependent. We then used this co-culture’s phenazine signals in a tri-culture to modulate gene expression and production of three model products: quorum sensing molecule autoinducer-1 and two fluorescent marker proteins, eGFP and DsRed. We also showed how these redox-based signals could be intermingled with other quorum-sensing (QS) signals which are more commonly used in synthetic biology, to control complex behaviors. To provide control over product synthesis in the tri-cultures, we also showed how a QS-induced growth control module could guide metabolic flux in one population and at the same time guide overall tri-culture function. Specifically, we showed that phenazine signal recognition, enabled through the oxidative stress response regulon soxRS, was dependent on media composition such that signal propagation within our parsed synthetic system could guide different desired outcomes based on the prevailing environment. In doing so, we expanded the range of signaling molecules available for coordination and the modes by which they can be utilized to influence overall function of a multi-population culture. Conclusions Our results show that redox-based signaling can be intermingled with other quorum sensing signaling in ways that enable user-defined control of microbial consortia yielding various outcomes defined by culture medium. Further, we demonstrated the utility of our previously designed growth control module in influencing signal propagation and metabolic activity is unimpeded by orthogonal redox-based signaling. By exploring novel multi-modal strategies for guiding communication and consortia outcome, the concepts introduced here may prove to be useful for coordination of multiple populations within complex microbial systems.

Chun, Kayla↗

DOE OSTI2023

Trichoderma harzianum transcriptome in response to the nematode Pratylenchus brachyurus

The root-lesion nematode Pratylenchus brachyurus causes extensive damage in several crops of economic importance. Fungi of Trichoderma genus have been highlighted as biopesticide agents in the control of several plant diseases. Although it is already widely used in agriculture, there are few studies, especially at the molecular level, that evaluate T. harzianum in the control of P. brachyurus . The aim of the present study was to investigate how interaction with the nematode P. brachyurus influences gene expression of T. harzianum , by using RNA-Seq analysis. Of the 13,932 predicted genes in the T. harzianum genome, 2,922 (21%) were differentially expressed in the presence of P. brachyurus , in relation to the absence of the nematode. Among the differentially expressed genes, we found genes encoding Carbohydrate Active EnZymes (CAZy), MEROPS peptidases, and proteins related to secondary metabolite synthesis. 118 pathways were identified as related to the biosynthesis of secondary metabolites. Additionally, the analysis identified 136 metabolic pathways related to these differentially expressed genes, among which we highlight: aminobenzoate degradation, xenobiotic metabolism by cytochrome P450, and sesquiterpenoid and triterpenoid biosynthesis. Our results contribute to a better understanding of the response of T. harzianum to the nematode P. bracyurus , the potential for biocontrol by this fungus.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Predicting plant attractiveness to coccinellids with plant trait profiling, citizen science, and common garden surveys

Lady beetles are key predators in agricultural systems and their impact can be enhanced by plant resources. Facilitation of lady beetles is a potentially effective pest management strategy but a lack of data on which plant species attract and nurture them limits implementation. Here we investigate which plant species might optimize lady beetle impact by developing a profile of plant characteristics most likely to attract lady beetles and testing if the subset of “potentially preferred” plant families exhibiting those characteristics are significantly more attractive to lady beetles than other families. This testing encompassed a combination of observations submitted to a citizen science program, the Lost Ladybug Project, and two repeated site surveys. Traits reported to be most attractive to lady beetles included the presence of trichomes that provide protection from predation, nutritional resources such as nectar or prey, and visual or chemical cues associated with those traits. Significantly more lady beetles were observed on the three plant families which most often exhibit these traits, Apiaceae, Asteraceae, and Rosaceae, than on other families. Furthermore, strategies for incorporating plants from these families into production systems to attract lady beetles and limit pest damage are discussed.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Capillary absorption spectroscopy for high temporal resolution measurements of stable carbon isotopes in soil and plant-based systems

Capillary Absorption Spectroscopy (CAS) is a relatively new analytical technique for performing stable isotope analysis. Here, we demonstrate the utility of CAS by recording and quantifying variation in 13C in controlled and biologically relevant applications. We calibrated CAS system response to increased 13CO2, with an observed ~4‰ increase in measured Δ13C for each 0.03 ppm shift in 13CO2 concentration. We leveraged this calibration to quantify rates of biogeochemical processes using a 13C tracer. For example, we monitored microbial respiration of 13C-glucose within an agricultural soil at 10 s quantification intervals and results demonstrated 8.6% ± 0.4 of added glucose was converted to 13CO2 within 1.5 h of incubation. We expanded the demonstration by adapting a rhizobox to permit continuous monitoring of 13CO2 in a soil (as distinct from plant) headspace to track the timing and quantify respiration rates of fresh plant photosynthate and observed a 3.5 h delay between plant exposure to a13CO2 tracer and the first signs of respiration by soil biota. These experiments highlight CAS is effective in producing high temporal resolution quantification of 13CO2 and demonstrate potential applications.

13CO2↗

DOE OSTI2022

Comparative and pangenomic analysis of the genus Streptomyces

Abstract Streptomycetes are highly metabolically gifted bacteria with the abilities to produce bioproducts that have profound economic and societal importance. These bioproducts are produced by metabolic pathways including those for the biosynthesis of secondary metabolites and catabolism of plant biomass constituents. Advancements in genome sequencing technologies have revealed a wealth of untapped metabolic potential from Streptomyces genomes. Here, we report the largest Streptomyces pangenome generated by using 205 complete genomes. Metabolic potentials of the pangenome and individual genomes were analyzed, revealing degrees of conservation of individual metabolic pathways and strains potentially suitable for metabolic engineering. Of them, Streptomyces bingchenggensis was identified as a potent degrader of plant biomass. Polyketide, non-ribosomal peptide, and gamma-butyrolactone biosynthetic enzymes are primarily strain specific while ectoine and some terpene biosynthetic pathways are highly conserved. A large number of transcription factors associated with secondary metabolism are strain-specific while those controlling basic biological processes are highly conserved. Although the majority of genes involved in morphological development are highly conserved, there are strain-specific varieties which may contribute to fine tuning the timing of cellular differentiation. Overall, these results provide insights into the metabolic potential, regulation and physiology of streptomycetes, which will facilitate further exploitation of these important bacteria.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

MOSAIC: a joint modeling methodology for combined circadian and non-circadian analysis of multi-omics data

Abstract Motivation Circadian rhythms are approximately 24-h endogenous cycles that control many biological functions. To identify these rhythms, biological samples are taken over circadian time and analyzed using a single omics type, such as transcriptomics or proteomics. By comparing data from these single omics approaches, it has been shown that transcriptional rhythms are not necessarily conserved at the protein level, implying extensive circadian post-transcriptional regulation. However, as proteomics methods are known to be noisier than transcriptomic methods, this suggests that previously identified arrhythmic proteins with rhythmic transcripts could have been missed due to noise and may not be due to post-transcriptional regulation. Results To determine if one can use information from less-noisy transcriptomic data to inform rhythms in more-noisy proteomic data, and thus more accurately identify rhythms in the proteome, we have created the Multi-Omics Selection with Amplitude Independent Criteria (MOSAIC) application. MOSAIC combines model selection and joint modeling of multiple omics types to recover significant circadian and non-circadian trends. Using both synthetic data and proteomic data from Neurospora crassa, we showed that MOSAIC accurately recovers circadian rhythms at higher rates in not only the proteome but the transcriptome as well, outperforming existing methods for rhythm identification. In addition, by quantifying non-circadian trends in addition to circadian trends in data, our methodology allowed for the recognition of the diversity of circadian regulation as compared to non-circadian regulation. Availability and implementation MOSAIC’s full interface is available at https://github.com/delosh653/MOSAIC. An R package for this functionality, mosaic.find, can be downloaded at https://CRAN.R-project.org/package=mosaic.find. Supplementary information Supplementary data are available at Bioinformatics online.

De los Santos, Hannah↗

DOE OSTI2020

Effects of cold stress on metabolic regulation in the overwintering larvae of the Chinese white pine beetle, Dendroctonus armandi

Abstract The Chinese white pine beetle, Dendroctonus armandi Tsai & Li (Coleoptera: Curculionidae, Scolytinae), is considered the most destructive forest pest in the Qinling and Bashan Mountains of China. In recent years, winter temperature has dropped in these regions, and extremely low temperatures are hard to survive for insects. Cold hardiness becomes a crucial strategy because temperature change often leads to fluctuations in insect abundance, and the metabolism rate is a key index of resistance to cold in overwintering insects. Therefore, we investigated the relationship between the change in respiratory rate and the activity of metabolism‐related mitochondrial enzymes in D. armandi larvae under cold conditions. We found that the respiratory rate decreased, and it was matched with the activity of glutamate dehydrogenase, aconitase, and lipase during overwintering. Among the various test times under cold conditions, the respiratory rate also decreased with decreasing temperature and increased under very low temperatures. At all cold stress periods, glutamate dehydrogenase and lipase showed increased activity at higher temperatures and decreased activity under lower temperatures, but the activity of NAD‐malic enzyme, NADP‐malic enzyme, mitochondrial isocitrate dehydrogenase, and aconitase were contrary. Under all low temperatures, the activity of enzymes – except for NADP‐malic enzyme, glutamate dehydrogenase, and lipase – increased in short‐term cold stress and decreased in long‐term cold stress at 4, 0, −4, −6, −8, and −10 °C. However, at −2 °C, the activity of enzymes showed a decreasing trend in short‐term treatments and an increasing trend in long‐term treatments, except for mitochondrial isocitrate dehydrogenase. The results not only improve our understanding of the metabolic mechanism of cold adaptation in D. armandi , but also provide an important experimental basis for further study and biological pest control.

Fu, Danyang↗

DOE OSTI2026

Process Optimization and Real-Time Control of Synergistic Microalgae Cultivation and Wastewater Treatment (Final Technical Report)

The overarching goal of this work was to accelerate the commercialization of high productivity, mixed community microalgal treatment technologies for the synergistic treatment of wastewater and the production of biofuel feedstocks. This project addressed a critical barrier to the financial viability and energy efficiency of algal wastewater treatment: an inability to design and operate high-rate processes that reliably achieve target effluent qualities, areal productivities, and biochemical compositions (lipid, protein, carbohydrate content) despite fluctuations in wastewater composition, weather, and microbial communities. Key outcomes from this work include an optimized and controlled Advanced Biological Nutrient Recovery (ABNR) design as well as a suite of open-source tools that include a calibrated and validated algae process simulator in QSDsan and a novel low-cost, real-time microbial monitoring tool. These tools can be leveraged by other algal cultivation and wastewater treatment technology developers in future work.

09 BIOMASS FUELS↗

DOE OSTI2024

Predictive Phenomics Initiative Project Dataset Catalog Collection

The Predictive Phenomics Science & Technology Initiative (PPI) at Pacific Northwest National Laboratory are tackling the grand challenge of understanding and predicting phenotype by identifying the molecular basis of function and enable function-driven design and control of biological systems. Research projects within this initiative are divided into three Thrust Areas (TAs): TA1) Enhancing Multi-Scale Phenomics Measurements, TA2) Identifying Molecular Patterns of Biological Function, and TA3) Computational Methods - Phenotypic Signatures. In efforts to enable discovery, reproducibility, and reuse of PPI-funded digital research data generated or used through the course of the proposed research-funded lifecycles, all corresponding digital data assets conducted under the Laboratory Directed Research and Development Program at PNNL are linked to this PPI dataset catalog collection.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Predictive Phenomics Initiative Project Dataset Catalog Collection

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Alternative Splicing Events

Inclusion levels of alternative splicing (AS) events of five different varieties (i.e. skipped exon (SE), retained intron (RI), alternative 5’ splice site (A5SS), alternative 3’ splice site (A3SS), and mutually exclusive exons (MXE)) were measured in human blood samples from two separate cohorts of patients. Cohort 1 (Training Cohort): 12 healthy controls; 12 new onset type 1 diabetic (T1D) cases cases and controls matched on biological sex, age, and body mass index (BMI) 180 million reads Cohort 2 (Testing Cohort): 12 healthy controls; 12 new onset type 1 diabetic (T1D) cases cases and controls matched on biological sex and age. BMI not recorded. 150 million reads

Webb-Robertson, Bobbie-Jo M↗

DOE OSTI2023

Human Islet Research Network (HIRN): Alternative Splicing Events

Webb-Robertson, Bobbie-Jo M↗

DOE OSTI2020

Hierarchical biota-level and taxonomic controls on the chemistry of fossil melanosomes revealed using synchrotron X-ray fluorescence

Fossil melanosomes, micron-sized granules rich in melanin in vivo, provide key information for investigations of the original coloration, taxonomy and internal anatomy of fossil vertebrates. Such studies rely, in part, on analysis of the inorganic chemistry of preserved melanosomes and an understanding of melanosome chemical taphonomy. The extent to which the preserved chemistry of fossil melanosomes is biased by biotic and abiotic factors is, however, unknown. Here we report the discovery of hierarchical controls on the inorganic chemistry of melanosomes from fossil vertebrates from nine biotas. The chemical data are dominated by a strong biota-level signal, indicating that the primary taphonomic control is the diagenetic history of the host sediment. This extrinsic control is superimposed by a biological, tissue-level control; tissue-specific chemical variation is most likely to survive in fossils where the inorganic chemistry of preserved melanosomes is distinct from that of the host sediment. Comparative analysis of our data for fossil and modern amphibians reveals that most fossil specimens show tissue-specific melanosome chemistries that differ from those of extant analogues, strongly suggesting alteration of original melanosome chemistry. Collectively, these findings form a predictive tool for the identification of fossil deposits with well-preserved melanosomes amenable to studies of fossil colour and anatomy.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Fibrous anisotropy and mineral gradients within the radula stylus of chiton: Controlled stiffness and damage tolerance in a flexible biological composite

Over hundreds of millions of years, organisms have evolved architected structures via precise control over hierarchically assembled components, including the integration of dissimilar materials. One such example is found in the radula system of chitons, intertidal mollusks that feed on algae growing on the rock. Their radula consists of multiple rows of ultrahard teeth, each integrated with a foldable belt-like substrate via a stiff, yet flexible stylus, which is essential for efficient rasping during the feeding process. Here, we investigate the nano and micro-scale components and architectures as well as regional mechanical properties of the stylus, and their subsequent role during the rasping of Cryptochiton stelleri. Three important factors were determined to contribute to the regio-specific stiffness of the stylus: the presence of mineral components, highly oriented chitinous fibers, and a chemically cross-linked protein matrix. All these factors are varied throughout the stylus. There is a high mineral content on the trailing edge close to the tooth and a cross-linked matrix on the leading edge, both with orientational specific oriented chitin fibers that provide force transduction to the tooth. Conversely, there is a significant lack of mineral or cross-linked matrix in the proximal end as well as a low degree of fiber orientation, resulting in a flexible region that can accommodate torsion and flexure during rasping. Understanding the graded composite structure of the stylus and applying this unique design to various engineering fields such as soft robotics, biotechnology, and the medical industry, can inspire the production of high-performance materials.

Lee, Jung-Eun↗

DOE OSTI2021

Kinetic, metabolic, and statistical analytics: addressing metabolic transport limitations among organelles and microbial communities

Microbial organisms engage in a variety of metabolic interactions. A crucial part of these interactions is the exchange of molecules between different organelles, cells, and the environment. The main forces mediating this metabolic exchange are transporters. This transport can be difficult to measure experimentally because several transport mechanisms remain opaque. However, theoretical calculations about the inputs and outputs of cells via metabolic exchanges have enabled the successful inference of the workings of intra-organismal and inter-organismal systems. Kinetic, metabolic, and statistical modeling approaches in combination with omics data are enhancing our knowledge and understanding about metabolic exchange and mass resource allocation. Furthermore, this model-driven analytics approach can guide effective experimental design and yield new insights into biological function and control.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Evaluating the limitations of Bayesian metabolic control analysis

AbstractBayesian Metabolic Control Analysis (BMCA) has emerged as a promising framework for inferring metabolic control coefficients in data-limited scenarios by integrating Bayesian inference with linlog rate laws. However, its predictive accuracy and limitations remain underexplored. This study systematically evaluates BMCA’s ability to infer elasticity values, flux control coefficients (FCCs), and concentration control coefficients (CCCs) under varying data availability conditions using three synthetic metabolic network models. Our findings highlight the strengths and weaknesses of BMCA, guiding its application in metabolic engineering and emphasizing the need for methodological refinements.Author summaryUnderstanding how enzymes control metabolic pathways is crucial for optimizing biomanufacturing and synthetic biology applications. Bayesian Metabolic Control Analysis (BMCA) is a promising computational method that integrates Bayesian inference with metabolic control analysis to estimate key control parameters, even in cases with limited experimental data. However, the accuracy and limitations of BMCA remain unclear. In this study, we systematically evaluate BMCA using three synthetic metabolic networks to determine how different types of physiological data impact its predictive performance. We find that BMCA requires flux and enzyme concentration data for accurate predictions, while external metabolite concentrations contribute little. Additionally, BMCA fails to predict elasticity values beyond a magnitude of 1.5 and reliably infer allosteric regulation, even when strong regulatory interactions exist. In addition, BMCA does not accurately rank metabolic control points, which may limit its utility in identifying key enzymes in engineered pathways. Our work provides practical insights into when and how BMCA can be applied, guiding future research in metabolic modeling and control analysis.

Shin, Janis (ORCID:0000000216572455)↗