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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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At least 1,621 records · Page 90
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Assessing the Ability of Developmentally Precocious Estrogen Signaling to Recapitulate Ovarian Transcriptomes and Follicle Dynamics in Alligators from a Contaminated Lake

Concern has grown in recent decades over anthropogenic contaminants that interfere with the functioning of endocrine hormones. However, mechanisms connecting developmental processes to pathologies associated with endocrine-disrupting chemical (EDC) exposure are poorly understood in naturally exposed populations. We sought to a) characterize divergence in ovarian transcriptomic and follicular profiles between alligators originating from a historically EDC-contaminated site, Lake Apopka, and a reference site; b) test the ability of developmentally precocious estrogen exposure to recapitulate site-associated patterns of divergence; and c) test whether treatment with exogenous follicle-stimulating hormone (FSH) is capable of rescuing phenotypes associated with contaminant exposure and/or embryonic estrogen treatment. Alligators eggs were collected from a contaminated site and a reference site, and a subset of eggs from the reference site were treated with estradiol (E2) during embryonic development prior to gonadal differentiation. After hatching, alligators were raised under controlled laboratory settings for 5 months. Juveniles from both sites were divided and treated with exogenous FSH. Histological analyses and RNA-sequencing were conducted to characterize divergence in ovarian follicle dynamics and transcriptomes between sites, between reference and E2-treated animals, and between FSH-treated and nontreated animals. We observed broad site-of-origin divergence in ovarian transcriptomes and reductions in ovarian follicle density between juvenile alligators from Lake Apopka and the reference site. Treating embryos from the reference site with E2 overwhelmingly recapitulated transcriptional and histological alterations observed in Lake Apopka juveniles. Ovarian phenotypes observed in Lake Apopka alligators or resulting from estrogen treatment were only partially rescued by treatment with exogenous FSH. Recapitulation of ovarian abnormalities by precocious E2 revealed a relatively simple mechanism underlying contaminant-induced pathologies in a historical example of environmental endocrine disruption. Findings reported here support a model where the developmental timing of estrogen signaling has the potential to permanently alter ovarian organization and function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Assessing Air Velocity Distribution in Three Sizes of Commercial Broiler Houses During Tunnel Ventilation

Abstract. Convective cooling is a critical management strategy for maintaining an environment that promotes production efficiency, thermal comfort, and animal well-being in commercial broiler houses. Variations in house size, design, and equipment configuration contribute greatly to the air velocity distribution within the facility. This study assessed total airflow, air velocity distribution, and quantified the floor area in three facilities experiencing insufficient air velocity for maintenance of production efficiency, thermal comfort, and animal well-being. Test facility 1 was an 18.3 × 170.7 m solid side-wall broiler house, test facility 2 was a 15.24 × 144.8 m solid side-wall broiler house, and test facility 3 was a 12.19 × 121.9 m curtain side-wall broiler house. Total airflow of each facility, measured with a Fan Assessment and Numeration System, was 512,730, 389,495, and 329,270 m 3 h -1 for test facilities 1, 2, and 3, respectively. Air velocity distribution patterns were characterized in each house with a Scalable Environment Assessment System (SEAS) and spatial statistics. The air velocity distributions within the test facilities were variable, with notable maxima immediately downstream of the tunnel inlets, which serve as a well-defined vena contracta, and local minima near the leading end of the evaporative pads and the exhaust fans. Equipment within the facilities had an impact on the air velocity distribution by creating reduced cross-sectional areas that resulted in localized increases in air velocity. The percentage of total bird-level floor area in each facility experiencing air velocities below 1.5 m s -1 was 14.3%, 20.7%, and 10.0% for test facilities 1, 2, and 3, respectively. The effective design velocity (V ed ) was calculated from total airflow using the measured building cross-sectional area. The V ed measured 2.97, 2.45, and 2.34 m s -1 for test facilities 1, 2, and 3, respectively. Mean cross-sectional air velocity (V cs ) was calculated from SEAS data and normalized using each facility’s V ed to account for differences in building size for comparison. Test facility 1, the largest of the three houses, generated substantially higher V cs /V ed than test facilities 2 and 3. Test facilities 2 and 3 maintained a larger proportion of V cs above V ed than test facility 1. Test facility 1 showed 26.5% of the total house length below V ed , while test facilities 2 and 3 had only 20.8% and 17.5%, respectively, of the total house length below V ed . The lower-velocity regions were due to the length of the evaporative cooling pad inlet and the use of tunnel doors, and the exhaust fan placement on the side-walls in test facility 1 created an additional pronounced low-velocity area. Placement of tunnel ventilation fans on the end-wall of the facility, rather than the side-wall, eliminated the low-velocity region at the exhaust end of the facility. Modifications to current practices for broiler production facility construction and evaporative cooling pad inlet installation would be required to minimize the low-velocity region at the inlet end of these facilities. Consideration of house width and physical arrangement of the air inlets, tunnel fans, and internal equipment are critical for improving the uniformity of air velocity in commercial broiler houses. Keywords: Air velocity, Anemometer, Broiler house, FANS, Tunnel ventilation.

Agriculture↗
DOE OSTI2015

Creation of Mice Bearing a Partial Duplication of HPRT Gene Marked with a GFP Gene and Detection of Revertant Cells In Situ as GFP-Positive Somatic Cells

It is becoming clear that apparently normal somatic cells accumulate mutations. Such accumulations or propagations of mutant cells are thought to be related to certain diseases such as cancer. To better understand the nature of somatic mutations, we developed a mouse model that enables in vivo detection of rare genetically altered cells via GFP positive cells. The mouse model carries a partial duplication of 3’ portion of X-chromosomal HPRT gene and a GFP gene at the end of the last exon. In addition, although HPRT gene expression was thought ubiquitous, the expression level was found insufficient in vivo to make the revertant cells detectable by GFP positivity. To overcome the problem, we replaced the natural HPRT -gene promoter with a CAG promoter. In such animals, termed HPRT-dup-GFP mouse, losing one duplicated segment by crossover between the two sister chromatids or within a single molecule of DNA reactivates gene function, producing hybrid HPRT-GFP proteins which, in turn, cause the revertant cells to be detected as GFP-positive cells in various tissues. Frequencies of green mutant cells were measured using fixed and frozen sections (liver and pancreas), fixed whole mount (small intestine), or by means of flow cytometry (unfixed splenocytes). The results showed that the frequencies varied extensively among individuals as well as among tissues. X-ray exposure (3 Gy) increased the frequency moderately (~2 times) in the liver and small intestine. Further, in two animals out of 278 examined, some solid tissues showed too many GFP-positive cells to score (termed extreme jackpot mutation). Present results illustrated a complex nature of somatic mutations occurring in vivo. While the HPRT-dup-GFP mouse may have a potential for detecting tissue-specific environmental mutagens, large inter-individual variations of mutant cell frequency cause the results unstable and hence have to be reduced. This future challenge will likely involve lowering the background mutation frequency, thus reducing inter-individual variation

Science & Technology - Other Topics↗
DOE OSTI2016

Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocols with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig ( Sus scrofa ) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. In conclusion, knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Molecular basis of surface anchored protein A deficiency in the Staphylococcus aureus strain Wood 46

Protein A in Staphylococcus aureus is encoded by the spa (staphylococcal protein A) gene and binds to immunoglobulin (Ig). The S. aureus strain Wood 46 has been variously reported as protein A-deficient and/or spa negative and used as a control in animal models of staphylococcal infections. The results of this study indicate that Wood 46 has normal spa expression but transcribes very low levels of the srtA gene which encodes the sortase A (SrtA) enzyme. This is consistent with unique mutations in the srtA promoter. In this study, a low level of sortase A explains deficient anchoring of proteins with an LPXTG motif, such as protein A, fibrinogen-binding protein and fibronectin-binding proteins A and B on to the peptidoglycan cell wall. The activity of secreted protein A is an important consideration for use of Wood 46 in functional experiments and animal models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Small-angle X-ray scattering characteristics of mouse brain: Planar imaging measurements and tomographic imaging simulations

Small-angle x-ray scattering (SAXS) imaging can differentiate tissue types based on their nanoscale molecular structure. However, characterization of the coherent scattering cross-section profile of relevant tissues is needed to optimally design SAXS imaging techniques for a variety of biomedical applications. Reported measured nervous tissue x-ray scattering cross sections under a synchrotron source have had limited agreement. We report a set of x-ray cross-section measurements obtained from planar SAXS imaging of 1 mm thick mouse brain (APP/PS1 wild-type) coronal slices using an 8 keV laboratory x-ray source. Two characteristic peaks were found at 0.96 and 1.60 nm -1 attributed to myelin. The peak intensities varied by location in the slice. We found that regions of gray matter, white matter, and corpus callosum could be segmented by their increasing intensities of myelin peaks respectively. Measured small-angle x-ray scattering cross sections were then used to define brain tissue scattering properties in a GPU-accelerated Monte Carlo simulation of SAXS computed tomography (CT) using a higher monochromatic x-ray energy (20 keV) to study design trade-offs for noninvasive in vivo SAXS imaging on a small-animal head including radiation dose, signal-to-noise ratio (SNR), and the effect of skull presence on the previous two metrics. Simulation results show the estimated total dose to the mouse head for a single SAXS-CT slice was 149.4 mGy. The pixel SNR was approximately 30.8 for white matter material whether or not a skull was present. In this early-stage proof-of-principle work, we have demonstrated our brain cross-section data and simulation tools can be used to assess optimal instrument parameters for dedicated small-animal SAXS-CT prototypes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Laboratory strains of Bacillus anthracis exhibit pervasive alteration in expression of proteins related to sporulation under laboratory conditions relative to genetically related wild strains

The spore forming pathogen Bacillus anthracis is the etiologic agent of anthrax in humans and animals. It cycles through infected hosts as vegetative cells and is eventually introduced into the environment where it generates an endospore resistant to many harsh conditions. The endospores are subsequently taken up by another host to begin the next cycle. Outbreaks of anthrax occur regularly worldwide in wildlife and livestock, and the potential for human infection exists whenever humans encounter infected animals. It is also possible to encounter intentional releases of anthrax spores, as was the case in October 2001. Consequently, it is important to be able to rapidly establish the provenance of infectious strains of B. anthracis . Here, we compare protein expression in seven low-passage wild isolates and four laboratory strains of B. anthracis grown under identical conditions using LC-MS/MS proteomic analysis. Of the 1,023 total identified proteins, 96 had significant abundance differences between wild and laboratory strains. Of those, 28 proteins directly related to sporulation were upregulated in wild isolates, with expression driven by Spo0A, CodY, and AbrB/ScoC. In addition, we observed evidence of changes in cell division and fatty acid biosynthesis between the two classes of strains, despite being grown under identical experimental conditions. These results suggest wild B. anthracis cells are more highly tuned to sporulate than their laboratory cousins, and this difference should be exploited as a method to differentiate between laboratory and low passage wild strains isolated during an anthrax outbreak. This knowledge should distinguish between intentional releases and exposure to strains in nature, providing a basis for the type of response by public health officials and investigators.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The effect of enrofloxacin on enteric Escherichia coli : Fitting a mathematical model to in vivo data

Antimicrobial drugs administered systemically may cause the emergence and dissemination of antimicrobial resistance among enteric bacteria. To develop logical, research-based recommendations for food animal veterinarians, we must understand how to maximize antimicrobial drug efficacy while minimizing risk of antimicrobial resistance. Our objective is to evaluate the effect of two approved dosing regimens of enrofloxacin (a single high dose or three low doses) on Escherichia coli in cattle. We look specifically at bacteria above and below the epidemiological cutoff (ECOFF), above which the bacteria are likely to have an acquired or mutational resistance to enrofloxacin. We developed a differential equation model for the antimicrobial drug concentrations in plasma and colon, and bacteria populations in the feces. The model was fit to animal data of drug concentrations in the plasma and colon obtained using ultrafiltration probes. Fecal E. coli counts and minimum inhibitory concentrations were measured for the week after receiving the antimicrobial drug. We predict that the antimicrobial susceptibility of the bacteria above the ECOFF pre-treatment strongly affects the composition of the bacteria following treatment. Faster removal of the antimicrobial drugs from the colon throughout the study leads to improved clearance of bacteria above the ECOFF in the low dose regimen. If we assume a fitness cost is associated with bacteria above the ECOFF, the increased fitness costs leads to reduction of bacteria above the ECOFF in the low dose study. These results suggest the initial E. coli susceptibility is a strong indicator of how steers respond to antimicrobial drug treatment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica

Ecological theories posit that heterogeneity in environmental conditions greatly affects community structure and function. However, the degree to which ecological theory developed using plant- and animal-dominated systems applies to microbiomes is unclear. Investigating the metabolic strategies found in microbiomes are particularly informative for testing the universality of ecological theories because microorganisms have far wider metabolic capacity than plants and animals. We used metagenomic analyses to explore the relationships between the energy and physicochemical gradients in Lake Fryxell and the metabolic capacity of its benthic microbiome. Statistical analysis of the relative abundance of metabolic marker genes and gene family diversity shows that oxygenic photosynthesis, carbon fixation, and flavin-based electron bifurcation differentiate mats growing in different environmental conditions. The pattern of gene family diversity points to the likely importance of temporal environmental heterogeneity in addition to resource gradients. Overall, we found that the environmental heterogeneity of photosynthetically active radiation (PAR) and oxygen concentration ([O2]) in Lake Fryxell provide the framework by which metabolic diversity and composition of the community is structured, in accordance with its phylogenetic structure. The organization of the resulting microbial ecosystems are consistent with the maximum power principle and the species sorting model.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Habitat use by female desert tortoises suggests tradeoffs between resource use and risk avoidance

Animals may select habitat to maximize the benefits of foraging on growth and reproduction, while balancing competing factors like the risk of predation or mortality from other sources. Variation in the distribution of food resources may lead animals to forage at times or in places that carry greater predation risk, with individuals in poor quality habitats expected to take greater risks while foraging. We studied Mojave desert tortoises ( Gopherus agassizii ) in habitats with variable forage availability to determine if risk aversion in their selection of habitat relative was related to abundance of forage. As a measure of risk, we examined tortoise surface activity and mortality. We also compared tortoise body size and body condition between habitats with ample forage plants and those with less forage plants. Tortoises from low forage habitats selected areas where more annual plants were nutritious herbaceous flowering plants but did not favor areas of greater perennial shrub cover that could shelter them or their burrows. In contrast, tortoises occupying high forage habitats showed no preference for forage characteristics, but used burrows associated with more abundant and larger perennial shrubs. Tortoises in high forage habitats were larger and active above ground more often but did not have better body condition. Mortality was four times higher for females occupying low forage habitat than those in high forage habitat. Our results are consistent with the idea that tortoises may minimize mortality risk where food resources are high, but may accept some tradeoff of greater mortality risk in order to forage optimally when food resources are limiting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The microbiome of a Pacific moon jellyfish Aurelia coerulea

The impact of microbiome in animal physiology is well appreciated, but characterization of animal-microbe symbiosis in marine environments remains a growing need. This study characterizes the microbial communities associated with the moon jellyfish Aurelia coerulea, first isolated from the East Pacific Ocean and has since been utilized as an experimental system. We find that the microbiome of this Pacific Aurelia culture is dominated by two taxa, a Mollicutes and Rickettsiales. The microbiome is stable across life stages, although composition varies. Mining the host sequencing data, we assembled the bacterial metagenome-assembled genomes (MAGs). The bacterial MAGs are highly reduced, and predict a high metabolic dependence on the host. Analysis using multiple metrics suggest that both bacteria are likely new species. We therefore propose the names Ca. Mariplasma lunae (Mollicutes) and Ca. Marinirickettsia aquamalans (Rickettsiales). Finally, comparison with studies of Aurelia from other geographical populations suggests the association with Ca. Mariplasma lunae occurs in Aurelia from multiple geographical locations. The low-diversity microbiome of Aurelia provides a relatively simple system to study host-microbe interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Potent, specific MEPicides for treatment of zoonotic staphylococci

Coagulase-positive staphylococci, which frequently colonize the mucosal surfaces of animals, also cause a spectrum of opportunistic infections including skin and soft tissue infections, urinary tract infections, pneumonia, and bacteremia. However, recent advances in bacterial identification have revealed that these common veterinary pathogens are in fact zoonoses that cause serious infections in human patients. The global spread of multidrug-resistant zoonotic staphylococci, in particular the emergence of methicillin-resistant organisms, is now a serious threat to both animal and human welfare. Accordingly, new therapeutic targets that can be exploited to combat staphylococcal infections are urgently needed. Enzymes of the methylerythritol phosphate pathway (MEP) of isoprenoid biosynthesis represent potential targets for treating zoonotic staphylococci. Here we demonstrate that fosmidomycin (FSM) inhibits the first step of the isoprenoid biosynthetic pathway catalyzed by deoxyxylulose phosphate reductoisomerase (DXR) in staphylococci. In addition, we have both enzymatically and structurally determined the mechanism by which FSM elicits its effect. Using a forward genetic screen, the glycerol-3-phosphate transporter GlpT that facilitates FSM uptake was identified in two zoonotic staphylococci, Staphylococcus schleiferi and Staphylococcus pseudintermedius . A series of lipophilic ester prodrugs (termed MEPicides) structurally related to FSM were synthesized, and data indicate that the presence of the prodrug moiety not only substantially increased potency of the inhibitors against staphylococci but also bypassed the need for GlpT-mediated cellular transport. Collectively, our data indicate that the prodrug MEPicides selectively and robustly inhibit DXR in zoonotic staphylococci, and further, that DXR represents a promising, druggable target for future development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Fluorescent Crimean-Congo hemorrhagic fever virus illuminates tissue tropism patterns and identifies early mononuclear phagocytic cell targets in Ifnar -/- mice

Crimean-Congo hemorrhagic fever virus (CCHFV, order Bunyavirales, family Nairoviridae, genus Orthonairovirus) is the tick-borne etiological agent of Crimean-Congo hemorrhagic fever (CCHF) in humans. Animals are generally susceptible to CCHFV infection but refractory to disease. Small animal models are limited to interferon-deficient mice, that develop acute fatal disease following infection. Here, using a ZsGreen1- (ZsG) expressing reporter virus (CCHFV/ZsG), we examine tissue tropism and dissemination of virus in interferon-α/β receptor knock-out (Ifnar -/- ) mice. We demonstrate that CCHFV/ZsG retains in vivo pathogenicity comparable to wild-type virus. Interestingly, despite high levels of viral RNA in all organs assessed, 2 distribution patterns of infection were observed by both fluorescence and immunohistochemistry (IHC), corresponding to the permissiveness of organ tissues. To further investigate viral dissemination and to temporally define cellular targets of CCHFV in vivo, mice were serially euthanized at different stages of disease. Flow cytometry was used to characterize CCHFV-associated alterations in hematopoietic cell populations and to classify infected cells in the blood, lymph node, spleen, and liver. ZsG signal indicated that mononuclear phagocytic cells in the lymphatic tissues were early targets of infection; in latestage infection, overall, the highest levels of signal were detected in the liver, and ZsG was found in both antigen-presenting and lymphocyte cell populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Long-term persistence of infectious Zika virus: Inflammation and behavioral sequela in mice

The neurodevelopmental defects associated with ZIKV infections early in pregnancy are well documented, however the potential defects and long-term consequences associated with milder infections in late pregnancy and perinatal period are less well understood. To model these, we challenged 1 day old (P1) immunocompetent C57BL/6 mice with ZIKV. The animals developed a transient neurological syndrome including unsteady gait, kinetic tremors, severe ataxia and seizures 10–15 days post-infection (dpi) but symptoms subsided after a week, and most animals survived. Despite apparent recovery, MRI of convalescent mice show reduced cerebellar volume that correlates with altered coordination and motor function as well as hyperactivity and impulsivity. Persistent mRNA levels of pro-inflammatory genes including Cd80 , Il-1α , and Ifn-γ together with Cd3 , Cd8 and perforin ( PrfA) , suggested persistence of low-grade inflammation. Surprisingly, the brain parenchyma of convalescent mice harbor multiple small discrete foci with viral antigen, active apoptotic processes in neurons, and cellular infiltrates, surrounded by activated astrocytes and microglia as late as 1-year post-infection. Detection of negative-sense strand viral RNA and isolation of infectious virus derived from these convalescent mice by blinded passage in Vero cells confirmed long-term persistence of replicating ZIKV in CNS of convalescent mice. Although the infection appears to persist in defined reservoirs within CNS, the resulting inflammation could increase the risk of neurodegenerative disorders. This raises concern regarding possible long-term effects in asymptomatic children exposed to the virus and suggests that long-term neurological and behavioral monitoring as well as anti-viral treatment to clear virus from the CNS may be useful in patients exposed to ZIKV at an early age.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

High throughput analysis of B cell dynamics and neutralizing antibody development during immunization with a novel clade C HIV-1 envelope

A protective HIV-1 vaccine has been hampered by a limited understanding of how B cells acquire neutralizing activity. Our previous vaccines expressing two different HIV-1 envelopes elicited robust antigen specific serum IgG titers in 20 rhesus macaques; yet serum from only two animals neutralized the autologous virus. Here, we used high throughput immunoglobulin receptor and single cell RNA sequencing to characterize the overall expansion, recall, and maturation of antigen specific B cells longitudinally over 90 weeks. Diversification and expansion of many B cell clonotypes occurred broadly in the absence of serum neutralization. However, in one animal that developed neutralization, two neutralizing B cell clonotypes arose from the same immunoglobulin germline and were tracked longitudinally. Early antibody variants with high identity to germline neutralized the autologous virus while later variants acquired somatic hypermutation and increased neutralization potency. The early engagement of precursors capable of neutralization with little to no SHM followed by prolonged affinity maturation allowed the two neutralizing lineages to successfully persist despite many other antigen specific B cells. The findings provide new insight into B cells responding to HIV-1 envelope during heterologous prime and boost immunization in rhesus macaques and the development of selected autologous neutralizing antibody lineages.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Immunization of cows with HIV envelope trimers generates broadly neutralizing antibodies to the V2-apex from the ultralong CDRH3 repertoire

The generation of broadly neutralizing antibodies (bnAbs) to conserved epitopes on HIV Envelope (Env) is one of the cornerstones of HIV vaccine research. The animal models commonly used for HIV do not reliably produce a potent broadly neutralizing serum antibody response, with the exception of cows. Cows have previously produced a CD4 binding site response by homologous prime and boosting with a native-like Env trimer. In small animal models, other engineered immunogens were shown to focus antibody responses to the bnAb V2-apex region of Env. Here, we immunized two groups of cows (n = 4) with two regimens of V2-apex focusing Env immunogens to investigate whether antibody responses could be generated to the V2-apex on Env. Group 1 was immunized with chimpanzee simian immunodeficiency virus (SIV)-Env trimer that shares its V2-apex with HIV, followed by immunization with C108, a V2-apex focusing immunogen, and finally boosted with a cross-clade native-like trimer cocktail. Group 2 was immunized with HIV C108 Env trimer followed by the same HIV trimer cocktail as Group 1. Longitudinal serum analysis showed that one cow in each group developed serum neutralizing antibody responses to the V2-apex. Eight and 11 bnAbs were isolated from Group 1 and Group 2 cows, respectively, and showed moderate breadth and potency. Potent and broad responses in this study developed much later than previous cow immunizations that elicited CD4bs bnAbs responses and required several different immunogens. All isolated bnAbs were derived from the ultralong CDRH3 repertoire. The finding that cow antibodies can target more than one broadly neutralizing epitope on the HIV surface reveals the generality of elongated structures for the recognition of highly glycosylated proteins. The exclusive isolation of ultralong CDRH3 bnAbs, despite only comprising a small percent of the cow repertoire, suggests these antibodies outcompete the long and short CDRH3 antibodies during the bnAb response.

Microbiology↗
DOE OSTI2020

EGS Collab Experiment 1: 3D Seismic Velocity Model and Updated Microseismic Catalog Using Transfer-Learning Aided Double-Difference Tomography

This package contains a 3D Seismic velocity model and an updated microseismic catalog associated with a proceedings paper (Chai et al., 2020) published in the 45th Workshop on Geothermal Reservoir Engineering. The 3D_seismic_velocity_model text file contains x (m), y(m), z(m), P-wave velocity (km/s), P-wave velocity quality indicator (1 for well-constrained; 0 for poorly constrained), S-wave velocity (km/s), and S-wave velocity quality indicator (1 for well-constrained; 0 for poorly constrained). The Updated_MEQ_catalog text file contains event origin time, x(m), y(m), z(m), error in x (m), error in y (m), error in z (m), and RMS misfit (millisecond). The 3D_seismic_P-wave_velocity_model animation file shows slices of the 3D P-wave velocity model. The 3D_seismic_S-wave_velocity_model animation file shows slices of the 3D S-wave velocity model. The Interactive_MEQ_locations API file is an interactive visualization of the updated microseismic event locations. The visualization allows users to view the event locations by dragging, rotating, and zooming in. References: Chai, C., Maceira, M., Santos-Villalobos, H. J., Venkatakrishnan, S. V., Schoenball, M., and EGS Collab Team, 2020, Automatic Seismic Phase Picking Using Deep Learning for the EGS Collab Project, in PROCEEDINGS, 45th Workshop on Geothermal Reservoir Engineering, edited, Stanford University, Stanford, California, 45, 1266-1276.

15 GEOTHERMAL ENERGY↗
DOE OSTI2015

Identification of a novel nematotoxic protein by challenging the model mushroom Coprinopsis cinerea with a fungivorous nematode

The dung of herbivores, the natural habitat of the model mushroom Coprinopsis cinerea, is a nutrient-rich but also very competitive environment for a saprophytic fungus. Previously we showed that C. cinerea expresses constitutive, tissue-specific armories against antagonists such as animal predators and bacterial competitors. In order to dissect the inducible armories against such antagonists, we sequenced the poly(A)-positive transcriptome of C. cinerea vegetative mycelium upon challenge with fungivorous and bacterivorous nematodes, Gram-negative and Gram-positive bacteria and mechanical damage. As a response to the fungivorous nematode Aphelenchus avenae, C. cinerea was found to specifically induce the transcription of several genes encoding previously characterized nematotoxic lectins. In addition, a previously not characterized gene encoding a cytoplasmic protein with several predicted Ricin B-fold domains, was found to be strongly up-regulated under this condition. Functional analysis of the recombinant protein revealed a high toxicity towards the bacterivorous nematode Caenorhabditis elegans. Challenge of the mycelium with A. avenae also lead to the induction of several genes encoding putative antibacterial proteins. Some of these genes were also induced upon challenge of the mycelium with the bacteria Escherichia coli and Bacillus subtilis. Lastly, these results suggest that fungi have the ability to induce specific innate defense responses similar to plants and animals.

59 BASIC BIOLOGICAL SCIENCES↗