Search NASA⌕ Search

SEARCH · Search NASA

Results for “LABORATORY ANIMALS”

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.

At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Survival, healing, and swim performance of juvenile migratory sea lamprey ( Petromyzon marinus ) implanted with a new acoustic microtransmitter designed for small eel-like fishes

Background: Little is known about the transformer stage of the parasitic lampreys, a brief but critical period that encompasses juvenile out-migration from rivers to lakes or oceans to begin parasitic feeding. Information about this life stage could have significant conservation implications for both imperiled and invasive lampreys. We investigated tag retention, survival, wound healing, and swim performance of newly transformed sea lamprey (Petromyzon marinus) implanted with a new micro-acoustic transmitter, the eel–lamprey acoustic transmitter (ELAT), in a controlled laboratory environment. Results: The 61-day survival of our tagged subjects was 71%, within the range reported in similar studies of juvenile lampreys. However, survival was significantly lower in the tagged animals (vs control), with no effect statistically attributable to measures of animal length, mass, condition, or population of origin (Great Lakes vs. Atlantic drainage). Mortality in tagged fish was concentrated in the first four days post-surgery, suggesting injury from the surgical process. An unusually long recovery time from anesthesia may have contributed to the increased mortality. In a simple burst swim assay, tagged animals swam significantly slower (– 22.5%) than untagged animals, but were not significantly different in endurance swim tests. A composite wound healing score at day four was a significant predictor of maximum burst swim speed at day 20, and wound condition was related to animal mass, but not length, at the time of tagging. Conclusions: Impairments to survival and swim performance of juvenile sea lamprey implanted with the ELAT transmitter were within currently reported ranges for telemetry studies with small, difficult to observe fishes. Our results could be improved with more refined anesthesia and surgical techniques. The ability to track migratory movements of imperiled and pest populations of parasitic lampreys will improve our ability to estimate vital rates that underlie recruitment to the adult population (growth, survival) and to investigate the environmental factors that regulate the timing and rates of movement, in wild populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Screening Analysis for the Environmental Risk Evaluation System Task 2.1.1.2: Evaluating Effects of Stressors Fiscal Year 2011 Progress Report - Environmental Effects of Marine and Hydrokinetic Energy

Potential environmental effects of marine and hydrokinetic (MHK) energy development are not well understood, and yet regulatory agencies are required to make decisions in spite of substantial uncertainty about environmental impacts and their long-term consequences. An understanding of risks associated with interactions between MHK installations and aquatic receptors, including animals, habitats, and ecosystems, can help define key uncertainties and focus regulatory actions and scientific studies on interactions of most concern. As a first step in developing the Pacific Northwest National Laboratory (PNNL) Environmental Risk Evaluation System (ERES), PNNL scientists conducted a preliminary risk screening analysis on three initial MHK cases. During FY 2011, two additional cases were added: a tidal project in the Gulf of Maine using Ocean Renewable Power Company TidGenTM turbines and a wave project planned for the coast of Oregon using Aquamarine Oyster surge devices.

Environmental Risk Evaluation System↗
DOE OSTI2011

RADIATION ECOLOGY ISSUES ASSOCIATED WITH MURINE RODENTS AND SHREWS IN THE CHERNOBYL EXCLUSION ZONE

This article describes major studies performed by the Chernobyl Center's International Radioecology Laboratory (Slavutich, Ukraine) on radioecology of murine rodents and shrews inhabiting the Chernobyl Exclusion Zone. The article addresses the long-term (1986-2005) and seasonal dynamics of radioactive contamination of animals, and reviews interspecies differences in radionuclide accumulations and factors affecting the radionuclide accumulations. It is shown that bioavailability of radionuclides in the 'soil-to-plant' chain and a trophic specialization of animals play key roles in determining their actual contamination levels. The total absorbed dose rates in small mammals significantly reduced during the years following the Chernobyl Nuclear Power Plant accident. In 1986, the absorbed dose rate reached 1.3-6.0 Gy hr{sup -1} in the central areas of the Chernobyl Exclusion Zone (the 'Red Forest'). In 1988 and 1990, the total absorbed dose rates were 1.3 and 0.42 Gy hr{sup -1}, respectively. In 1995, 2000, and 2005, according to the present study, the total absorbed dose rates rarely exceeded 0.00023, 0.00018, and 0.00015 Gy hr{sup -1}, respectively. Contributions of individual radiation sources into the total absorbed dose are described.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2016

Field application of pathogen detection technologies

Over the last 10 years there has been a significant increase in commercial products designed for field-based detection of microbial pathogens. This is due, in part, to the anthrax attacks in the United States in 2001, and the need for first responders to quickly identify the composition of suspected white powders and other potential biothreats. Demand for rapid detection is also driven by the need to ensure safe food, water, and environmental systems. From a technology perspective, rapid identification methods have largely capitalized on PCR and other molecular recognition techniques that can be deployed as robust field instrumentation. Examples of the relevant needs include the ability to: 1) declare a water distribution system free of microbial pathogens after a pipe/main break repair; 2) assess risks of contamination such as when produce production and processing plants are located near concentrated animal feeing operations; 3) evaluate the safety of ready-to-eat products; 4) determine the extent of potential serious disease outbreaks in remote and/or disaster stricken areas where access to clinical laboratories is not an immediate option; and 5) quickly assess credible biological terrorism events. Many of the principles underlying rapid detection methods are derived from methods for environmental microbiology, but there is a dearth of literature describing and evaluating field-based detection systems. Thus, the aims of this chapter are to: 1) summarize the different kinds of commercially available sampling kits and field-based biological detectors; 2) highlight some of the continued challenges of sample preparation to stimulate new research towards minimizing the impact of inhibitors on PCR-based detection systems; 3) describe our general rationale and statistically-based approach for instrument evaluation; 4) provide statistical and spatial guidelines for developing valid sampling plans; and 5) summarize some current needs and emerging technologies. This information is presented both to highlight the state of the field, and to also highlight major questions that students may wish to consider investigating further. Where possible we will cite studies that have been conducted and published either in traditional peer-reviewed or other literature (e.g., AOAC International Methods).

Straub, Tim M.↗
DOE OSTI2011

Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

Drosophila melanogaster is emerging as an important model of non-pathogenic host–microbe interactions. The genetic and experimental tractability of Drosophila has led to significant gains in our understanding of animal–microbial symbiosis. However, the full implications of these results cannot be appreciated without the knowledge of the microbial communities associated with natural Drosophila populations. In particular, it is not clear whether laboratory cultures can serve as an accurate model of host–microbe interactions that occur in the wild, or those that have occurred over evolutionary time. To fill this gap, we characterized natural bacterial communities associated with 14 species of Drosophila and related genera collected from distant geographic locations. To represent the ecological diversity of Drosophilids, examined species included fruit-, flower-, mushroom-, and cactus-feeders. In parallel, wild host populations were compared to laboratory strains, and controlled experiments were performed to assess the importance of host species and diet in shaping bacterial microbiome composition. We find that Drosophilid flies have taxonomically restricted bacterial communities, with 85% of the natural bacterial microbiome composed of only four bacterial families. The dominant bacterial taxa are widespread and found in many different host species despite the taxonomic, ecological, and geographic diversity of their hosts. Both natural surveys and laboratory experiments indicate that host diet plays a major role in shaping the Drosophila bacterial microbiome. Despite this, the internal bacterial microbiome represents only a highly reduced subset of the external bacterial communities, suggesting that the host exercises some level of control over the bacteria that inhabit its digestive tract. Finally, we show that laboratory strains provide only a limited model of natural host–microbe interactions. Bacterial taxa used in experimental studies are rare or absent in wild Drosophila populations, while the most abundant associates of natural Drosophila populations are rare in the lab.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Clusters of antibiotic resistance genes enriched together stay together in swine agriculture

Antibiotic resistance is a worldwide health risk, but the influence of animal agriculture on the genetic context and enrichment of individual antibiotic resistance alleles remains unclear. Using quantitative PCR followed by amplicon sequencing, we quantified and sequenced 44 genes related to antibiotic resistance, mobile genetic elements, and bacterial phylogeny in microbiomes from U.S. laboratory swine and from swine farms from three Chinese regions. We identified highly abundant resistance clusters: groups of resistance and mobile genetic element alleles that cooccur. For example, the abundance of genes conferring resistance to six classes of antibiotics together with class 1 integrase and the abundance of IS 6100 -type transposons in three Chinese regions are directly correlated. These resistance cluster genes likely colocalize in microbial genomes in the farms. Resistance cluster alleles were dramatically enriched (up to 1 to 10% as abundant as 16S rRNA) and indicate that multidrug-resistant bacteria are likely the norm rather than an exception in these communities. This enrichment largely occurred independently of phylogenetic composition; thus, resistance clusters are likely present in many bacterial taxa. Furthermore, resistance clusters contain resistance genes that confer resistance to antibiotics independently of their particular use on the farms. Selection for these clusters is likely due to the use of only a subset of the broad range of chemicals to which the clusters confer resistance. The scale of animal agriculture and its wastes, the enrichment and horizontal gene transfer potential of the clusters, and the vicinity of large human populations suggest that managing this resistance reservoir is important for minimizing human risk.Agricultural antibiotic use results in clusters of cooccurring resistance genes that together confer resistance to multiple antibiotics. The use of a single antibiotic could select for an entire suite of resistance genes if they are genetically linked. No links to bacterial membership were observed for these clusters of resistance genes. These findings urge deeper understanding of colocalization of resistance genes and mobile genetic elements in resistance islands and their distribution throughout antibiotic-exposed microbiomes. In addition, as governments seek to combat the rise in antibiotic resistance, a balance is sought between ensuring proper animal health and welfare and preserving medically important antibiotics for therapeutic use. Metagenomic and genomic monitoring will be critical to determine if resistance genes can be reduced in animal microbiomes, or if these gene clusters will continue to be coselected by antibiotics not deemed medically important for human health but used for growth promotion or by medically important antibiotics used therapeutically.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2012

Laboratory Studies of the Effects of Static and Variable Magnetic Fields on Freshwater Fish

There is considerable interest in the development of marine and hydrokinetic energy projects in rivers, estuaries, and coastal ocean waters of the United States. Hydrokinetic (HK) technologies convert the energy of moving water in river or tidal currents into electricity, without the impacts of dams and impoundments associated with conventional hydropower or the extraction and combustion of fossil fuels. The Federal Energy Regulatory Commission (FERC) maintains a database that displays the geographical distribution of proposed HK projects in inland and tidal waters (FERC 2012). As of March 2012, 77 preliminary permits had been issued to private developers to study HK projects in inland waters, the development of which would total over 8,000 MW. Most of these projects are proposed for the lower Mississippi River. In addition, the issuance of another 27 preliminary permits for HK projects in inland waters, and 3 preliminary permits for HK tidal projects (totaling over 3,100 MW) were under consideration by FERC. Although numerous HK designs are under development (see DOE 2009 for a description of the technologies and their potential environmental effects), the most commonly proposed projects entail arrays of rotating devices, much like submerged wind turbines, that are positioned in the high-velocity (high energy) river channels. The many diverse HK designs imply a diversity of environmental impacts, but a potential impact common to most is the effect on aquatic organisms of electromagnetic fields (EMF) created by the projects. The submerged electrical generator will emit an EMF into the surrounding water, as will underwater cables used to transmit electricity from the generator to the shore, between individual units in an array (inter-turbine cables), and between the array and a submerged step-up transformer. The electric current moving through these cables will induce magnetic fields in the immediate vicinity, which may affect the behavior or viability of fish and benthic invertebrates (Gill et al. 2005, 2009). It is known that numerous marine and freshwater organisms are sensitive to electrical and magnetic fields, often depending on them for such diverse activities as prey location and navigation (DOE 2009; Normandeau et al. 2011). Despite the wide range of aquatic organisms that are sensitive to EMF and the increasing numbers of underwater electrical transmitting cables being installed in rivers and coastal waters, little information is available to assess whether animals will be attracted, repelled, or unaffected by these new sources of EMF. This knowledge gap is especially significant for freshwater systems, where electrosensitive organisms such as paddlefish and sturgeon may interact with electrical transmission cables. We carried out a series of laboratory experiments to test the sensitivity of freshwater fish and invertebrates to the levels of EMF that are expected to be produced by HK projects in rivers. In this context, EM fields are likely to be emitted primarily by generators in the water column and by transmission cables on or buried in the substrate. The HK units will be located in areas of high-velocity waters that are used as only temporary habitats for most riverine species, so long-term exposure of fish and benthic invertebrates to EMF is unlikely. Rather, most aquatic organisms will be briefly exposed to the fields as they drift downstream or migrate upstream. Because the exposure of most aquatic organisms to EMF in a river would be relatively brief and non-lethal, we focused our investigations on detecting behavioral effects. For example, attraction to the EM fields could result in prolonged exposures to the fields or the HK rotor. On the other hand, avoidance reactions might hinder upstream migrations of fish. The experiments reported here are a continuation of studies begun in FY 2010, which focused on the potential effects of static magnetic fields on snails, clams, and fathead minnows (Cada et al. 2011). Those experiments found little indication that the behaviors of these freshwater species were altered by the static magnetic fields that would be created by submerged, direct current (DC)-transmitting electrical cables expected to be used by the HK developers. Laboratory experiments in FY 2011 examined the responses of additional fish species (sunfish, striped bass, and channel catfish) to the static magnetic fields. In addition, the effects of variable magnetic fields (that would be created by the HK generators and AC-transmitting cables) on swimming behavior of two electrosensitive fish species (paddlefish and lake sturgeon) were studied.

13 HYDRO ENERGY↗
DOE OSTI2024

DOE BSSD Performance Management Metrics Report Q1

Microbes play key roles in our biosphere, from driving global nutrient cycling to impacting plant, animal and human health and disease. Complex data from microbial genomes, proteins, and metabolites provide a window into these tiny engines that drive life on our planet. Yet these data are dispersed among researchers’ laboratories and various repositories, making it difficult to access. This calls for new ways of managing data, improving data interoperability, advancing community standards, and creating an infrastructure where data are shared efficiently. We have built the National Microbiome Data Collaborative (NMDC) to advance how scientists create, use, and reuse data to redefine the way we understand and harness the power of microbes. The vision of the National Microbiome Data Collaborative (NMDC) is to drive a microbiome data sharing network connecting data, people, and ideas to advance microbiome innovation and discovery. The NMDC was launched in 2019 and brought together DOE National Laboratories to collaborate across resources, capabilities, and expertise. The NMDC team was strategically assembled to include software developers, microbial researchers, metadata experts, and multi-omics specialists. The diversity of the NMDC team reflects the inherently interdisciplinary nature of microbiome science, and we leverage the strengths of the DOE National Laboratory system. Towards BER’s goal of advancing an iterative systems biology approach to the understanding of microbial genomes, the NMDC serves as a foundation for infrastructure, data standards, and community building. Together with the flagship DOE User Facilities, the Joint Genome Institute (JGI) and the Environmental Molecular Sciences Laboratory (EMSL), we are developing core capabilities in metadata standards for environmental descriptors and sample handling and processing; standardized bioinformatic workflows; an interface for data search and access; and robust community engagement activities. The NMDC production platform supports long-term data infrastructure and community building for BER’s bioenergy and environmental research goals. Our approach leverages lessons learned and an ambitious framework for collaborative, interdisciplinary data infrastructure to support microbiome research. The NMDC supports data, information, and knowledge access through three defined software tools – the Submission Portal, NMDC EDGE, and the Data Portal – driven by community needs. Herein, we describe the value proposition for the microbiome research community, our overarching strategy, and challenges and opportunities for developing the NMDC as both an infrastructure and community engagement program.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Ammonia Fiber Expansion (AFEX) Pretreatment of Lignocellulosic Biomass

Lignocellulosic materials are plant-derived feedstocks, such as crop residues (e.g., corn stover, rice straw, and sugar cane bagasse) and purpose-grown energy crops (e.g., miscanthus, and switchgrass) that are available in large quantities to produce biofuels, biochemicals, and animal feed. Plant polysaccharides (i.e., cellulose, hemicellulose, and pectin) embedded within cell walls are highly recalcitrant towards conversion into useful products. Ammonia fiber expansion (AFEX) is a thermochemical pretreatment that increases accessibility of polysaccharides to enzymes for hydrolysis into fermentable sugars. These released sugars can be converted into fuels and chemicals in a biorefinery. Here, we describe a laboratory-scale batch AFEX process to produce pretreated biomass on the gram-scale without any ammonia recycling. The laboratory-scale process can be used to identify optimal pretreatment conditions (e.g., ammonia loading, water loading, biomass loading, temperature, pressure, residence time, etc.) and generates sufficient quantities of pretreated samples for detailed physicochemical characterization and enzymatic/microbial analysis. The yield of fermentable sugars from enzymatic hydrolysis of corn stover pretreated using the laboratory-scale AFEX process is comparable to pilot-scale AFEX process under similar pretreatment conditions. This paper is intended to provide a detailed standard operating procedure for the safe and consistent operation of laboratory-scale reactors for performing AFEX pretreatment of lignocellulosic biomass.

09 BIOMASS FUELS↗
DOE OSTI2012

Imaging of cardiac perfusion of free-breathing small animals using dynamic phase-correlated micro-CT

Purpose:Mouse models of cardiac diseases have proven to be a valuable tool in preclinical research. The high cardiac and respiratory rates of free breathing mice prohibit conventional in vivo cardiac perfusion studies using computed tomography even if gating methods are applied. This makes a sacrification of the animals unavoidable and only allows for the application of ex vivo methods. Methods: To overcome this issue the authors propose a low dose scan protocol and an associated reconstruction algorithm that allows for in vivo imaging of cardiac perfusion and associated processes that are retrospectively synchronized to the respiratory and cardiac motion of the animal. The scan protocol consists of repetitive injections of contrast media within several consecutive scans while the ECG, respiratory motion, and timestamp of contrast injection are recorded and synchronized to the acquired projections. The iterative reconstruction algorithm employs a six-dimensional edge-preserving filter to provide low-noise, motion artifact-free images of the animal examined using the authors' low dose scan protocol. Results: The reconstructions obtained show that the complete temporal bolus evolution can be visualized and quantified in any desired combination of cardiac and respiratory phase including reperfusion phases. The proposed reconstruction method thereby keeps the administered radiation dose at a minimum and thus reduces metabolic inference to the animal allowing for longitudinal studies. Conclusions: The authors' low dose scan protocol and phase-correlated dynamic reconstruction algorithm allow for an easy and effective way to visualize phase-correlated perfusion processes in routine laboratory studies using free-breathing mice.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

ATHENA, the Desktop Human "Body"

Creating surrogate human organs, coupled with insights from highly sensitive mass spectrometry technologies, a new project is on the brink of revolutionizing the way we screen new drugs and toxic agents. ATHENA, the Advanced Tissue-engineered Human Ectypal Network Analyzer project team, is developing four human organ constructs - liver, heart, lung and kidney - that are based on a significantly miniaturized platform. Each organ component will be about the size of a smartphone screen, and the whole ATHENA "body" of interconnected organs would fit neatly on a desk. "By developing this 'homo minutus,' we are stepping beyond the need for animal or Petri dish testing: There are huge benefits in developing drug and toxicity analysis systems that can mimic the response of actual human organs," said Rashi Iyer, a senior scientist at Los Alamos National Laboratory, the lead laboratory on the five-year, $19 million multi-institutional effort. The project is supported by the Defense Threat Reduction Agency (DTRA). Some 40 percent of pharmaceuticals fail their clinical trials, Iyer noted, and there are thousands of chemicals whose effects on humans are simply unknown. Providing a realistic, cost-effective and rapid screening system such as ATHENA with high-throughput capabilities could provide major benefits to the medical field, screening more accurately and offering a greater chance of clinical trial success.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Project ATHENA Creates Surrogate Human Organ Systems

The development of miniature surrogate human organs, coupled with highly sensitive mass spectrometry technologies, could one day revolutionize the way new drugs and toxic agents are studied. “By developing this ‘homo minutus,’ we are stepping beyond the need for animal or Petri dish testing: There are huge benefits in developing drug and toxicity analysis systems that can mimic the response of actual human organs,” said Rashi Iyer, a senior scientist at Los Alamos National Laboratory. ATHENA, the Advanced Tissue-engineered Human Ectypal Network Analyzer project team, is nearing the full integration of four human organ constructs — liver, heart, lung and kidney — each organ component is about the size of a smartphone screen, and the whole ATHENA “body” of interconnected organs will fit neatly on a desk. A new video available on the Los Alamos National Laboratory YouTube channel updates the ATHENA project as it begins to integrate the various organ systems into a single system. Some 40 percent of pharmaceuticals fail their clinical trials and there are thousands of chemicals whose effects on humans are simply unknown. Providing a realistic, cost-effective and rapid screening system such as ATHENA with high-throughput capabilities could provide major benefits to the medical field, screening more accurately and offering a greater chance of clinical trial success. ATHENA is funded by the Defense Threat Reduction Agency (DTRA) and is a collaboration of Los Alamos National Laboratory, Harvard University, Vanderbilt University, Charité Universitätsmedizin, Berlin, Germany, CFD Research Corporation, and the University of California San Francisco.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

National Virtual Biotechnology Laboratory: Report on Rapid R&D Solutions to the COVID-19 Crisis

With funding from the CARES Act, the U.S Department of Energy (DOE) established the National Virtual Biotechnology Laboratory (NVBL) in March 2020 to address key challenges associated with the COVID-19 crisis. NVBL brought together the broad scientific and technical expertise and resources of DOE’s 17 national laboratories to help tackle medical supply short ages, discover potential drugs to fight the virus, develop and validate COVID-19 testing methods, model disease spread and impact across the nation, and understand virus transport in buildings and the environment. National laboratory resources leveraged for this effort include a suite of world-leading user facilities broadly available to the research community, such as light and neutron sources, nanoscale science research centers, sequencing and biocharacterization facilities, and high-performance computing facilities. Within months, NVBL teams produced innovations in materials and advanced manufacturing that mitigated shortages in test kits and personal protective equipment (PPE), creating nearly 1,000 new jobs. They used DOE’s high-performance computers and light and neutron sources to identify promising candidates for antibodies and antivirals that universities and drug companies are now evaluating. NVBL researchers also developed new diagnostic targets and sample collection approaches, and supported U.S. Food and Drug Administration (FDA), Centers for Disease Control and Prevention (CDC), and U.S. Department of Defense (DoD) efforts to establish national guidelines used in administering millions of tests. Researchers used artificial intelligence and high-performance computing to produce near-real-time data analysis to forecast disease transmission, stress on public health infrastructure, and economic impact, which supported decision-makers at the local, state, and national levels. NVBL teams also studied how to control indoor virus movement to minimize uptake and protect human health. NVBL’s accomplishments demonstrate not only the powerful resource represented by DOE’s national laboratories working together to meet national needs, but also the effectiveness of the integrated NVBL framework for rapidly responding to emergencies with research and development (R&D) solutions. As the fight against COVID continues, sustained efforts are needed to confront this pandemic as well as future threats. Examples include: 1) Establishing “supply chains on demand” to meet emergency production needs by leveraging the materials and manufacturing expertise of DOE national laboratories and developing advances in electronics, sensing, robotics, and automation capabilities; 2) Improving the speed and robustness of drug discovery by integrating experimental platforms with DOE’s computational and experimental user facilities, which provide unique resources to support the discovery of high-potential therapeutic agents; 3) Protecting public, environmental, and animal health by developing new testing protocols and instrumentation adaptable to diverse sample types (both physiological and environmental) to quickly detect a wide range of pathogens and monitor other biorisks; 4) Supporting near-real-time data needs of decision-makers at the local, regional, state, and national levels by advancing data curation, analysis, and modeling using artificial intelligence and new data science tools for managing and evaluating large diverse datasets; 5) Harnessing DOE’s expertise in environmental modeling to design rooms and air handling for offices, classrooms, restaurants, and other structures to minimize biorisk transmissions. Going forward, NVBL is poised to apply the unique capabilities and expertise of the national laboratory complex to future national and international emergencies, both natural and engineered. Through this framework, the Office of Science will continue to be an integral component of agency wide efforts to prepare for and respond to biorisks and other crises.

42 ENGINEERING↗
DOE OSTI2025

CRCNS US-France Research Proposal: Collaborative Research: Encoding reward expectation in Drosophilia

The fruit fly Drosophila melanogaster has been a valuable model for investigating the genetic and neural bases that underlie learning and memory. Early and most current studies use basic behavior conditioning protocols to study learning in controlled laboratory settings. More recently, the ability to transgenically manipulate many of the brain neurons in the fruit fly with exquisite specificity, and the recent knowledge of the synaptic ‘connectome’ of the fruit fly brain, makes these animals almost unique as a comprehensive model for studies of learning, memory and motivated behavior. In fact, the connectome has revealed many types of new connections that had until now been overlooked. Within this context, the thesis of this proposal is that studies of learning and memory will be greatly enhanced by using more sophisticated means for evaluating memory representations, such as have been developed in vertebrates, and combining those studies with information from the connectome guided by computational modelling. We propose to push beyond the boundaries of existing conditioning protocols for fruit flies to investigate more complex memory representations. In particular, we will investigate the function of reinforcement pathways in relation to the absence of expected reinforcement. More specifically, we propose a series of experiments designed to investigate the memory representations in fruit flies when an expected consequence of a Conditioned Stimulus (CS) fails to occur. Although studies have evaluated how this failure can establish extinction memory for the CS, our studies will go beyond studying extinction. Specifically, we predict that in Drosophila when a CS is associated with a failed expectation of an appetitive food reinforcement it will acquire aversive value, and vice versa for a failed expectation of an aversive reinforcer. We combine these studies with manipulations of reinforcement pathways in the CNS inspired from the connectome, iteratively knitted in with established computational models. Intellectual Merit: The concept of reinforcement expectation and incentive contrast have been influential in the development of studies of associative learning in mammals. These questions are particularly challenging to answer in vertebrates because they require exquisite cellular, temporal, and genetic specificity of experimental manipulations. The recent development of work with identified neurons and their connectomes makes the larval and adult fly brains ripe as models for pushing our understanding of neural bases for these higher- order conditioning phenomena. Broader Impacts: Public health: These analyses and the conceptual framework of prediction error processing underlying them have a profound impact on our understanding of reinforcement-related behavior in humans, including monetary rewards and the mnemonic consequences of traumatic experiences, and for pathologies of the dopamine reinforcement system. Educational: This project will provide interdisciplinary training for postdoctoral researchers, Ph.D. and undergraduate students. The PIs will act as co-supervisors or mentors of students working in the different labs via face-to-face and internet-based technologies. We will also work with ASU’s award-winning Ask- A-Biologist program. This is an online science program designed to enrich the learning experiences of students of all ages and to provide classroom material for use by K-12 teachers. We will develop an extension of a game developed under a prior NSF award, and the new game will include modules to teach K-12 students about how insects learn. We will also integrate into the AAB site a program developed by a collaborator (B Gerber) at the Leibniz Institut für Neurobiologie, Magdeburg, and now in use in schools in Germany, to teach K-12 students how to train animals using the fruit fly larval learning paradigm. Underrepresented groups: All PIs will work with their university offices of Academic Diversity and Equal Opportunity for reaching underrepresented students.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

A Review of African Swine Fever and the Potential for Introduction into the United States and the Possibility of Subsequent Establishment in Feral Swine and Native Ticks

African swine fever (ASF) is caused by African swine fever virus (ASFV), which can cause substantial morbidity and mortality events in swine. The virus can be transmitted via direct and indirect contacts with infected swine, their products, or competent vector species, especially Ornithodoros ticks. Africa and much of Eastern Europe are endemic for ASF; a viral introduction to countries that are currently ASF free could have severe economic consequences due to the loss of production from infected animals and the trade restrictions that would likely be imposed as a result of an outbreak. We identified vulnerabilities that could lead to ASFV introduction or persistence in the United States or other ASF-free regions. Both legal and illegal movements of live animals, as well as the importation of animal products, byproducts, and animal feed, pose a risk of virus introduction. Each route is described, and current regulations designed to prevent ASFV and other pathogens from entering the United States are outlined. Furthermore, existing ASFV research gaps are highlighted. Laboratory experiments to evaluate multiple species of Ornithodoros ticks that have yet to be characterized would be useful to understand vector competence, host preferences, and distribution of competent soft tick vectors in relation to high pig production areas as well as regions with high feral swine (wild boar or similar) densities. Knowledge relative to antigenic viral proteins that contribute to host response and determination of immune mechanisms that lead to protection are foundational in the quest for a vaccine. Finally, sampling of illegally imported and confiscated wild suid products for ASFV could shed light on the types of products being imported and provide a more informed perspective relative to the risk of ASFV importation.

Veterinary Sciences↗
DOE OSTI2018

Spectroscopic Chemical Sensing and Imaging: From Plants to Animals and Humans

Chemical sensing and imaging technologies are of great importance in medical diagnostics and environmental sensing due to their ability to detect and localize chemical targets and provide valuable information in real-time. Biophotonic techniques are the most promising for in vivo applications due to their minimal invasivity. Our laboratory has introduced various biophotonics-based technologies for chemical sensing and imaging for biochemical sensing, medical diagnostics, and fundamental research. Over the years, we have developed a wide variety of fluorescence and surface-enhanced Raman scattering (SERS)-based technologies for the detection of biomarkers for cancer and other diseases. This paper provides an overview of the research on chemical and biological sensors developed in our laboratory, highlighting our work on in vivo imaging and sensing, including minimally invasive detection of endogenous fluorophores associated with malignant tissue, SERS-tag localization of cancer cells and tissues, and SERS-based detection of nucleic acid biotargets and its feasibility for in vivo applications. This manuscript also presents new development on the use of Raman imaging of SERS-labeled nanoprobes incubated in leaves for use in biofuel research, laying the foundation for studies on functional imaging of nucleic acid biomarkers in plants.

Strobbia, Pietro (ORCID:0000000308846185)↗
DOE OSTI2019

Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi

The evolution of complex multicellularity has been one of the major transitions in the history of life. In contrast to simple multicellular aggregates of cells, it has evolved only in a handful of lineages, including animals, embryophytes, red and brown algae, and fungi. Despite being a key step toward the evolution of complex organisms, the evolutionary origins and the genetic underpinnings of complex multicellularity are incompletely known. The development of fungal fruiting bodies from a hyphal thallus represents a transition from simple to complex multicellularity that is inducible under laboratory conditions. We constructed a reference atlas of mushroom formation based on developmental transcriptome data of six species and comparisons of >200 whole genomes, to elucidate the core genetic program of complex multicellularity and fruiting body development in mushroom-forming fungi (Agaricomycetes). Nearly 300 conserved gene families and >70 functional groups contained developmentally regulated genes from five to six species, covering functions related to fungal cell wall remodeling, targeted protein degradation, signal transduction, adhesion, and small secreted proteins (including effector-like orphan genes). Several of these families, including F-box proteins, expansin-like proteins, protein kinases, and transcription factors, showed expansions in Agaricomycetes, many of which convergently expanded in multicellular plants and/or animals too, reflecting convergent solutions to genetic hurdles imposed by complex multicellularity among independently evolved lineages. Finally, this study provides an entry point to studying mushroom development and complex multicellularity in one of the largest clades of complex eukaryotic organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Developing and Deploying Universal Diagnostic Platforms for One-Health Biosurveillance

ObjectiveOur goal is to develop deployable strategies for infectious disease diagnosis at the point-of-care that are applicable to multiple hosts of infection - conforming to the global One Health Strategy for diagnostics. We aim to develop methods that do not require prior knowledge of the pathogen in question, and can facilitate rapid and effective decision-making and situational awareness.IntroductionThere is an urgent need for diagnostic strategies for infections which are host-independent, so as to effectively track zoonotic spread, monitor animal carriers of pathogens, and evaluate transmission dynamics. Infection of a host - pathogen or human- by an animal results in recognition by the immune response, which consequently causes release of inflammatory mediators. Many scientists have explored the use of cytokines as diagnostic indicators of disease, but the conserved nature of the immune response in humans and animals results in cross-reactivity among many pathogens, making evaluation of the results difficult, especially in high disease burden populations. Measuring the pathogen-specific signature, however, is advantageous - as it offers discrete identification of active infection, and discrimination from exposure. It also offers a universal strategy that can be applied to human and animal hosts of infection - allowing for One Health Biosurveillance. Achieving this, however, requires the development of a) tailored strategies for the measurement of biochemically disparate pathogen signatures in clinical samples and b) ultra-sensitive detection of such signatures in the host. The sensor team at Los Alamos National Laboratory is working on both of these aspects, and the development of One Health Diagnostic platforms, the focus of the work presented here.MethodsMany of the biomarkers secreted by bacterial pathogens and recognized by innate immune receptors elicit host cytokine responses that are amphiphilic (largely glycolipids, lipoproteins or lipoglycans). Based on such, our team has developed tailored methods – membrane insertion and lipoprotein capture for the capture and detection of these greasy and stealthy molecules in infected blood. Sensitivity and specificity, assay optimization, alinearity associated with lipidic molecules and assay parameter development for biomarkers associated with bacterial pathogens will be presented. Considerations for clinical sampling for amphiphile detection in blood, and clinical study design will be demonstrated. Our team has developed an ultra-sensitive biosensor for detection of biomarkers in complex matrices based on the evanescent field properties of single mode planar optical waveguides. Detection of amphiphilic biomarkers in clinical samples, using the waveguide-based biosensor and tailored methods for the detection of such molecules has allowed for the diagnosis of infection in both human and animals hosts. Herein, we present two examples of the same; 1) diagnosis of tuberculosis in humans, cattle and badgers using pathogen-based diagnostic strategies; and 2) detection of Gram-negative Lipopolysacharides in beef and in patients with Salmonella-induced sepsis.ResultsWe have developed tailored ultra-sensitive waveguide-biosensor assays for the detection of Lipoarabinomannan (and other biomarkers) from Mycobacteria and demonstrated feasibility in blinded clinical studies in humans and cattle, demonstrating one -health compatibility.We have also demonstrated detection of lipopolysacharides from eight different serotypes of Shiga-toxin carrying E. coli in beef, and Salmonella Typhimurium in pediatric patients using the same approach.ConclusionsWe have demonstrated clinical feasibility of a One Health Strategy for point-of-care diagnostics of bacterial infections in blood for tuberculosis and Gram-negative pathogens in clinical samples. The results will be demonstrated with several discussion points on the consideration of unconventional biochemistry of pathogens for diagnostics, factors influencing point-of-care deployment and integration of diagnostic platforms for biosurveillance. One Health Considerations and challenges therein will also merit discussion.ReferencesSakamuri, R; et al. Accurate Tracking of Bovine Tuberculosis Biomarkers in Infected Cattle using a Novel Biomarker Capture Strategy, Analytical Sciences, 33(4): 457-460, 2017.Noormohammed A et al. Detection of Salmonella LPS in Patient blood by Lipoprotein Capture. Proc. SPIE 10072, Optical Diagnostics and Sensing XVII: Toward Point-of-Care Diagnostics, 100720A , 2017. doi:10.1117/12.2253506Stromberg L et al. Membrane Insertion for the Detection of Lipopolysaccharides: Exploring the Dynamics of Amphiphile-in-Lipid Assays, PloS One, April 2016.Sakamuri RM et al. Association of lipoarabinomannan with high density lipoprotein in blood: implications for diagnostics.Tuberculosis (Edinb). 2013 May;93(3):301-7. doi: 10.1016/j.tube.2013.02.015. Epub 2013 Mar 16Mukundan H et al. Understanding the interaction of Lipoarabinomannan with membrane mimetic architectures. Tuberculosis, 92(1) 32-47, 2012.Mukundan H et al., Waveguide-based Sensors for Pathogen Detection, Invited Review, Sensors, 9(7), 5783-5809.

Mukundan, Harshini↗