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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.

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342 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Concentration-response gene expression analysis in zebrafish reveals phenotypically-anchored transcriptional responses to retene

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental contaminants and are associated with human disease. Canonically, many PAHs induce toxicity via activation of the aryl hydrocarbon receptor (AHR) pathway. While the interaction between PAHs and the AHR is well-established, understanding which AHR-regulated transcriptional effects directly result in observable phenotypes and which are adaptive or benign is important to better understand PAH toxicity. Retene is a frequently detected PAH in environmental sampling and has been associated with AHR2-dependent developmental toxicity in zebrafish, though its mechanism of toxicity has not been fully elucidated. To interrogate transcriptional changes causally associated with retene toxicity, we conducted whole-animal RNA sequencing at 48 hours post-fertilization after exposure to eight retene concentrations. The concentrations were selected to produce effects ranging from no phenotype to mortality and malformations in 100% of animals at 5 days post-fertilization. We identified a concentration-response relationship between retene teratogenicity and differential gene expression in both number of DEGs and magnitude of expression change. Elevated expression of cyp1a at retene concentrations below the threshold for teratogenicity suggested that while cyp1a expression is a sensitive biomarker of AHR activation, it may be too sensitive to serve as a biomarker of AHR-dependent teratogenicity. Genes differentially expressed at only non-teratogenic concentrations were enriched for transforming growth factor-ß (TGF-ß) signaling pathway disruption while DEGs identified at only teratogenic concentrations were significantly enriched for response to xenobiotic stimulus and reduction-oxidation reaction activity. DEGs which spanned both non-teratogenic and teratogenic concentrations showed similar disrupted biological processes to those unique to teratogenic concentrations, indicating these processes were disrupted at low exposure concentrations. Gene co-expression network analysis identified several gene modules, including those associated with PAHs and AHR2 activation. One, Module 7, was strongly enriched for AHR2-associated genes and contained the strongest responses to retene. Benchmark concentration (BMC) of Module 7 genes identified a median BMC of 7.5 µM, nearly the highest retene concentration with no associated teratogenicity, supporting the hypothesis that Module 7 genes are largely responsible for retene toxicity.

Toxin, Zebrafish, Retene, Transcriptomics, network↗
DOE OSTI2020

A new algae technical standards focus group: Summarizing and guiding the algae state of the art

The value proposition of algae technical metrics was the subject of a recent, industry-led, Focus Group interactive discussion. The interactive platform allowed for real time capturing and priority ranking of the topics that are deemed critical challenges for a future successful algae-based bioeconomy. This work ultimately sets the stage for providing guidance, methods, and standard reference materials tailored to respective algae industry segments for the cultivation, processing and marketing of high-quality and safe algae-based products. The group solicits input from the broader algae community on the value proposition and presents a case here to build a consensus around algae-specific metrics. The value proposition of technical standards to the industry is that guidance obtained through these collaborations builds producers' and consumers' trust that algae and algae-derived products are safe, reliable, and may allow for expanded market access, and increased competitiveness and international trade.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Emerging Per- and Polyfluoroalkyl Substances in Tap Water from the American Healthy Homes Survey II

Humans experience widespread exposure to anthropogenic per- and polyfluoroalkyl substances (PFAS) through various media, which can lead to a wide range of negative health impacts. Tap water is an important source of exposure in communities with any degree of contamination but routine or large-scale PFAS monitoring often depends on targeted analytical methods limited to measuring specific PFAS. We analyzed 680 tap water samples from the American Healthy Homes Survey II for PFAS using non-targeted analysis (NTA) to expand the range of detectable PFAS. Based on detection frequency and relative abundance, about half of the identified PFAS were found only by NTA. We identified (with varying degrees of confidence) 75 distinct PFAS, including 57 exclusively detected by NTA. The identified PFAS are members of seven structural subclasses differentiated by their head groups and degree of fluorination. Clustering analysis categorized the PFAS into four coabundance groups dominated by specific PFAS subclasses. One group uniquely identified by NTA contains zwitterionic PFAS and other PFAS transformation products which are likely associated with aqueous firefighting foam contaminants in a small number of spatially correlated samples. These results help further characterize the scope of exposure to emerging PFAS experienced by the U.S. population via tap water and augment nationwide targeted-PFAS monitoring programs.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2021

Structural basis for CSPG4 as a receptor for TcdB and a therapeutic target in Clostridioides difficile infection

C. difficile is a major cause of antibiotic-associated gastrointestinal infections. Two C. difficile exotoxins (TcdA and TcdB) are major virulence factors associated with these infections, and chondroitin sulfate proteoglycan 4 (CSPG4) is a potential receptor for TcdB, but its pathophysiological relevance and the molecular details that govern recognition remain unknown. Here, we determine the cryo-EM structure of a TcdB–CSPG4 complex, revealing a unique binding site spatially composed of multiple discontinuous regions across TcdB. Mutations that selectively disrupt CSPG4 binding reduce TcdB toxicity in mice, while CSPG4-knockout mice show reduced damage to colonic tissues during C. difficile infections. We further show that bezlotoxumab, the only FDA approved anti-TcdB antibody, blocks CSPG4 binding via an allosteric mechanism, but it displays low neutralizing potency on many TcdB variants from epidemic hypervirulent strains due to sequence variations in its epitopes. In contrast, a CSPG4-mimicking decoy neutralizes major TcdB variants, suggesting a strategy to develop broad-spectrum therapeutics against TcdB.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural basis for botulinum neurotoxin E recognition of synaptic vesicle protein 2

Botulinum neurotoxin E (BoNT/E) is one of the major causes of human botulism and paradoxically also a promising therapeutic agent. Here we determined the co-crystal structures of the receptor-binding domain of BoNT/E (H C E) in complex with its neuronal receptor synaptic vesicle glycoprotein 2A (SV2A) and a nanobody that serves as a ganglioside surrogate. These structures reveal that the protein-protein interactions between H C E and SV2 provide the crucial location and specificity information for H C E to recognize SV2A and SV2B, but not the closely related SV2C. At the same time, H C E exploits a separated sialic acid-binding pocket to mediate recognition of an N-glycan of SV2. Structure-based mutagenesis and functional studies demonstrate that both the protein-protein and protein-glycan associations are essential for SV2A-mediated cell entry of BoNT/E and for its potent neurotoxicity. Our studies establish the structural basis to understand the receptor-specificity of BoNT/E and to engineer BoNT/E variants for new clinical applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Legionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain

ADP-ribosylation is a reversible post-translational modification involved in various cellular activities. Removal of ADP-ribosylation requires (ADP-ribosyl)hydrolases, with macrodomain enzymes being a major family in this category. The pathogen Legionella pneumophila mediates atypical ubiquitination of host targets using the SidE effector family in a process that involves ubiquitin ADP-ribosylation on arginine 42 as an obligatory step. Here, we show that the Legionella macrodomain effector MavL regulates this pathway by reversing the arginine ADP-ribosylation, likely to minimize potential detrimental effects caused by the modified ubiquitin. We determine the crystal structure of ADP-ribose-bound MavL, providing structural insights into recognition of the ADP-ribosyl group and catalytic mechanism of its removal. Further analyses reveal DUF4804 as a class of MavL-like macrodomain enzymes whose representative members show unique selectivity for mono-ADP-ribosylated arginine residue in synthetic substrates. We find such enzymes are also present in eukaryotes, as exemplified by two previously uncharacterized (ADP-ribosyl)hydrolases in Drosophila melanogaster . Crystal structures of several proteins in this class provide insights into arginine specificity and a shared mode of ADP-ribose interaction distinct from previously characterized macrodomains. Collectively, our study reveals a new regulatory layer of SidE-catalyzed ubiquitination and expands the current understanding of macrodomain enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The endosymbiotic box of protective tricks

This month’s Genome Watch underscores how genome and transcriptome sequencing of newly identified endosymbionts helps to connect genetic information to their protective functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structural basis underlying the synergism of NADase and SLO during group A Streptococcus infection

Group A Streptococcus (GAS) is a strict human pathogen possessing a unique pathogenic trait that utilizes the cooperative activity of NAD + -glycohydrolase (NADase) and Streptolysin O (SLO) to enhance its virulence. How NADase interacts with SLO to synergistically promote GAS cytotoxicity and intracellular survival is a long-standing question. Here, the structure and dynamic nature of the NADase/SLO complex are elucidated by X-ray crystallography and small-angle scattering, illustrating atomic details of the complex interface and functionally relevant conformations. Structure-guided studies reveal a salt-bridge interaction between NADase and SLO is important to cytotoxicity and resistance to phagocytic killing during GAS infection. Furthermore, the biological significance of the NADase/SLO complex in GAS virulence is demonstrated in a murine infection model. Overall, this work delivers the structure-functional relationship of the NADase/SLO complex and pinpoints the key interacting residues that are central to the coordinated actions of NADase and SLO in the pathogenesis of GAS infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Promise of nonthermal plasmas in addressing emerging environmental and health problems: Present and future

Nonthermal atmospheric pressure plasmas transform input electrical energy efficiently into reactive species, charged particles, and photons. This “activated gas” is being investigated as solutions for a range of environmental and health problems facing society today. In this Perspective, we take a cursory look at a few of these societal problems and the reflected role that plasmas may play in charting the pathway to a solution buoyed by supporting research. Here, we survey the plasma-based opportunities in the removal of trace contaminants in water supporting methodologies such as water reuse, which addresses scarcity and pollution, the opportunity posed by plasmas-based chemical depolymerization for plastics recycling, and the application of plasmas for food security, which includes sterilization of foodstuffs and the improvement of crop yield. Finally, we also included a short review on how plasmas may help control disease spread. In each case, the scope of the problem is presented along with the potential plasma-based solution.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Fic Proteins Inhibit the Activity of Topoisomerase IV by AMPylation in Diverse Bacteria

The Fic (filamentation induced by cyclic AMP) domain is a widely distributed motif with a conserved sequence of HPFx[D/E]GN[G/K]R, some of which regulate cellular activity by catalyzing the transfer of the AMP moiety from ATP to protein substrates. Some Fic proteins, including Fic-1 from the soil bacterium Pseudomonas fluorescens strain 2P24, have been shown to inhibit bacterial DNA replication by AMPylating the subunit B of DNA gyrase (GyrB), but the biochemical activity and cellular target of most Fic proteins remain unknown. Here, we report that Fic-2, which is another Fic protein from strain 2P24 and Fic-1 AMPylate the topoisomerase IV ParE at Tyr 109 . We also examined Fic proteins from several phylogenetically diverse bacteria and found that those from Yersinia pseudotuberculosis and Staphylococcus aureus AMPylate ParE and GrlB, the counterpart of ParE in Gram-positive bacteria, respectively. Modification by Fic-1 of P. fluorescens and FicY of Y. pseudotuberculosis inhibits the relaxation activity of topoisomerase IV. Consistent with the inhibition of ParE activity, ectopic expression of these Fic proteins causes cell filamentation akin to the canonical par phenotype in which nucleoids are assembled in the center of elongated cells, a process accompanied by the induction of the SOS response. Our results establish that Fic proteins from diverse bacterial species regulate chromosome division and cell separation in bacteria by targeting ParE.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A Review of Rattlesnake Venoms

Venom components are invaluable in biomedical research owing to their specificity and potency. Many of these components exist in two genera of rattlesnakes, Crotalus and Sistrurus, with high toxicity and proteolytic activity variation. This review focuses on venom components within rattlesnakes, and offers a comparison and itemized list of factors dictating venom composition, as well as presenting their known characteristics, activities, and significant applications in biosciences. There are 64 families and subfamilies of proteins present in Crotalus and Sistrurus venom. Snake venom serine proteases (SVSP), snake venom metalloproteases (SVMP), and phospholipases A2 (PLA2) are the standard components in Crotalus and Sistrurus venom. Through this review, we highlight gaps in the knowledge of rattlesnake venom; there needs to be more information on the venom composition of three Crotalus species and one Sistrurus subspecies. We discuss the activity and importance of both major and minor components in biomedical research and drug development.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Applications in Forensic Proteomics: Protein Identification and Profiling. ACS Symposium Series

Proteomics is a mature research tool in the life sciences, and it can be a powerful addition to the forensic science toolbox. This work presents several areas in which proteomics was used to answer forensic questions. Illustrating current applications of proteomics methods, this work introduces opportunities for proteomics to answer compelling questions in forensic science and biosecurity. These "case studies" will be valuable to both practicing forensic scientists and researchers developing proteomics methods.

proteomics, forensics, mass spectrometry, toxins, ↗