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DOE OSTI2024

Evaluation of the Impact of Concentration and Extraction Methods on the Targeted Sequencing of Human Viruses from Wastewater

Sequencing human viruses in wastewater is challenging due to their low abundance compared to the total microbial background. This study compared the impact of four virus concentration/extraction methods (Innovaprep, Nanotrap, Promega, and Solids extraction) on probe-capture enrichment for human viruses followed by sequencing. Different concentration/extraction methods yielded distinct virus profiles. Innovaprep ultrafiltration (following solids removal) had the highest sequencing sensitivity and richness, resulting in the successful assembly of several near-complete human virus genomes. However, it was less sensitive in detecting SARS-CoV-2 by digital polymerase chain reaction (dPCR) compared to Promega and Nanotrap. Across all preparation methods, astroviruses and polyomaviruses were the most highly abundant human viruses, and SARS-CoV-2 was rare. These findings suggest that sequencing success can be increased using methods that reduce nontarget nucleic acids in the extract, though the absolute concentration of total extracted nucleic acid, as indicated by Qubit, and targeted viruses, as indicated by dPCR, may not be directly related to targeted sequencing performance. Further, using broadly targeted sequencing panels may capture viral diversity but risks losing signals for specific low-abundance viruses. Overall, this study highlights the importance of aligning wet lab and bioinformatic methods with specific goals when employing probe-capture enrichment for human virus sequencing from wastewater.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Human Host Cellular Response to HCoV-229E Infection Transcriptomics (ACS-DP1)

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Human Host Cellular Response to HCoV-229E Infection Proteomics (ACS-JM-DP2)

The purpose of this experiment was to evaluate the human host cellular response to wild-type Human coronavirus strain 229E (HCoV-229E) infection. Sample data was obtained for mock and infected immortalized human lung epithelial cells (A549) (MOI 5) nuclear extracts, immortalized human lung fibroblasts cells (MRC5) (MOI5) nuclear extracts, and primary human airway epithelial (HAE) (MOI 3) cells from lung tissue and processed for proteome analysis. Processed datasets are openly accessible from the download button and contain secondary processed proteomic results files and supporting metadata materials. Experimental proteomics samples were prepared using Limited Proteolysis (LiP) methods for Label-free quantification (LFQ) and global proteomic evaluation. Sample data was acquired using a Q-Exactive HF-X mass spectrometer and was processed and compiled using MaxQuant software (v.1.6.17.0). Processed proteomic data downloads include a sample naming key, processed MaxQuant results/parameters, and protein annotated relative abundance files. See corresponding primary data accessions below and Viral Experiment LiP Analysis source code supporting data transparency and reuse. Experimental transcriptomics samples were collected in parallel and processed for RNA sequencing (RNA-Seq) as summarized under ACS-DP1 (https://data.pnnl.gov/group/nodes/dataset/34069).

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1993

Piloting Vertical Flight Aircraft: A Conference on Flying Qualities and Human Factors

This document contains papers from a specialists' meeting entitled "Piloting Vertical Flight Aircraft. A Conference on Flying Qualities and Human Factors." The conference was co-sponsored by the American Helicopter Society--San Francisco Bay Chapter, and the NASA Ames Research Center. It was held January 20-22, 1993 at the Sheraton Hotel Fisherman's Wharf, San Francisco, California. Vertical flight aircraft, including helicopters and a variety of Vertical Takeoff and Landing (VTOL) concepts, place unique requirements on human perception, control, and performance for the conduct of their design missions. The intent of this conference was to examine, for these vehicles, advances in: (1) design of flight control systems for ADS-33C standards; (2) assessment of human factors influences of cockpit displays and operational procedures; (3) development of VTOL design and operational criteria; and (4) development of theoretical methods or models for predicting pilot-vehicle performance and mission suitability. Recognizing that human capabilities and limitations form an integral aspect of the operations for these classes of vehicles, a secondary goal of the conference was to provide an initial venue for enhanced interaction between human factors and handling qualities specialists.

Helicopter↗

NASA NTRS2002

Gene conversion is strongly induced in human cells by double-strand breaks and is modulated by the expression of BCL-x(L)

Homology-directed repair (HDR) of DNA double-strand breaks (DSBs) contributes to the maintenance of genomic stability in rodent cells, and it has been assumed that HDR is of similar importance in DSB repair in human cells. However, some outcomes of homologous recombination can be deleterious, suggesting that factors exist to regulate HDR. We demonstrated previously that overexpression of BCL-2 or BCL-x(L) enhanced the frequency of X-ray-induced TK1 mutations, including loss of heterozygosity events presumed to arise by mitotic recombination. The present study was designed to test whether HDR is a prominent DSB repair pathway in human cells and to determine whether ectopic expression of BCL-x(L) affects HDR. Using TK6-neo cells, we find that a single DSB in an integrated HDR reporter stimulates gene conversion 40-50-fold, demonstrating efficient DSB repair by gene conversion in human cells. Significantly, DSB-induced gene conversion events are 3-4-fold more frequent in TK6 cells that stably overexpress the antiapoptotic protein BCL-X(L). Thus, HDR plays an important role in maintaining genomic integrity in human cells, and ectopic expression of BCL-x(L) enhances HDR of DSBs. This is the first study to highlight a function for BCL-x(L) in modulating DSB repair in human cells.

NASA Discipline Radiation Health↗

NASA NTRS2003

Critical issues in connection with human missions to Mars: protection of and from the Martian environment

Human missions to Mars are planned to happen within this century. Activities associated therewith will interact with the environment of Mars in two reciprocal ways: (i) the mission needs to be protected from the natural environmental elements that can be harmful to human health, the equipment or to their operations; (ii) the specific natural environment of Mars should be protected so that it retains its value for scientific and other purposes. The following environmental elements need to be considered in order to protect humans and the equipment on the planetary surface: (i) cosmic ionizing radiation, (ii) solar particle events; (iii) solar ultraviolet radiation; (iv) reduced gravity; (v) thin atmosphere; (vi) extremes in temperatures and their fluctuations; and (vii) surface dust. In order to protect the planetary environment, the requirements for planetary protection as adopted by COSPAR for lander missions need to be revised in view of human presence on the planet. Landers carrying equipment for exobiological investigations require special consideration to reduce contamination by terrestrial microorganisms and organic matter to the greatest feasible extent. Records of human activities on the planet's surface should be maintained in sufficient detail that future scientific experimenters can determine whether environmental modifications have resulted from explorations. c2002 COSPAR. Published by Elsevier Science Ltd. All rights reserved.

Extraterrestrial Environment↗

NASA NTRS1992

Chromosomal changes in cultured human epithelial cells transformed by low- and high-LET radiation

For a better assessment of radiation risk in space, an understanding of the responses of human cells, especially the epithelial cells, to low- and high-LET radiation is essential. In our laboratory, we have successfully developed techniques to study the neoplastic transformation of two human epithelial cell systems by ionizing radiation. These cell systems are human mammary epithelial cells (H184B5) and human epidermal keratinocytes (HEK). Both cell lines are immortal, anchorage dependent for growth, and nontumorigenic in athymic nude mice. Neoplastic transformation was achieved by irradiating cells successively. Our results showed that radiogenic cell transformation is a multistep process and that a single exposure of ionizing radiation can cause only one step of transformation. It requires, therefore, multihits to make human epithelial cells fully tumorigenic. Using a simple karyotyping method, we did chromosome analysis with cells cloned at various stages of transformation. We found no consistent large terminal deletion of chromosomes in radiation-induced transformants. Some changes of total number of chromosomes, however, were observed in the transformed cells. These transformants provide an unique opportunity for further genetic studies at a molecular level.

NASA Discipline Number 04-10↗

NASA NTRS2000

Food and nutrition in space: application to human health

The National Aeronautics and Space Administration begins the new millennium with the hope of expanding human space exploration beyond Earth's orbit. These extended-duration missions (3-5 years) require an in-depth assessment of the critical risks (referred to as "show stoppers") to humans when exposed to the remote environment and reduced gravity conditions for such long periods of time. Food, and the nutrition it provides, is paramount to crew health. For short-duration spaceflight (30 days), the nutrient requirements pertaining to physiological adaptations are likely to be satisfied without significant impact on crew performance or health. However, prolonged exposure to reduced gravity, or microgravity, and isolation may alter human nutrient requirements as well as increase the psychosocial role of food/meals in daily activities. An outline of critical questions and related research needs in the area of food and nutrition has been drafted (1) at NASA JSC with the help of the National Space Biomedical Research Institute (http://www.nsbri.org). The research areas outlined in this plan will directly impact the success of extended-duration human space missions. Findings from this research will have direct applications to human health issues faced here on Earth.

NASA Discipline Regulatory Physiology↗

NASA NTRS2000

Measuring the spectrum of mutation induced by nitrogen ions and protons in the human-hamster hybrid cell line A(L)C

Astronauts can be exposed to charged particles, including protons, alpha particles and heavier ions, during space flights. Therefore, studying the biological effectiveness of these sparsely and densely ionizing radiations is important to understanding the potential health effects for astronauts. We evaluated the mutagenic effectiveness of sparsely ionizing 55 MeV protons and densely ionizing 32 MeV/nucleon nitrogen ions using cells of two human-hamster cell lines, A(L) and A(L)C. We have previously characterized a spectrum of mutations, including megabase deletions, in human chromosome 11, the sole human chromosome in the human-hamster hybrid cell lines A(L)C and A(L). CD59(-) mutants have lost expression of a human cell surface antigen encoded by the CD59 gene located at 11p13. Deletion of genes located on the tip of the short arm of 11 (11p15.5) is lethal to the A(L) hybrid, so that CD59 mutants that lose the entire chromosome 11 die and escape detection. In contrast, deletion of the 11p15.5 region is not lethal in the hybrid A(L)C, allowing for the detection of chromosome loss or other chromosomal mutations involving 11p15.5. The 55 MeV protons and 32 MeV/nucleon nitrogen ions were each about 10 times more mutagenic per unit dose at the CD59 locus in A(L)C cells than in A(L) cells. In the case of nitrogen ions, the mutations observed in A(L)C cells were predominantly due to chromosome loss events or 11p deletions, often containing a breakpoint in the pericentromeric region. The increase in the CD59(-) mutant fraction for A(L)C cells exposed to protons was associated with either translocation of portions of 11q onto a hamster chromosome, or discontinuous or "skipping" mutations. We demonstrate here that A(L)C cells are a powerful tool that will aid in the understanding of the mutagenic effects of different types of ionizing radiation.

Non-NASA Center↗

NASA NTRS1999

Localization of the human 64kD autoantigen D1 to myofibrils in a subset of extraocular muscle fibers

PURPOSE. To evaluate the tissue-specific expression pattern of the 64kD human autoantigen D1, a tropomodulin-related protein that may be involved in thyroid-associated ophthalmopathy. METHODS. Recombinant 64kD human autoantigen D1 was generated in a bacterial expression system and used to immunize rabbits. Specific antibodies were affinity-purified and used for Western blots on normal and hyperthyroid rat and rabbit tissue, and immunofluorescence localization on cryosections of rat tissue. RESULTS. Anti-64kD human autoantigen D1 antibodies recognize specifically a approximately 70kD polypeptide in western blots of extraocular muscle, sternothyroid muscle, and smooth muscle. Immunofluorescence staining demonstrates that the 64kD human autoantigen D1 localizes to myofibrils in slow fibers from rat extraocular and sternothyroid muscle. The level of this protein is not altered in extraocular muscles from hyperthyroid rabbits. CONCLUSIONS. The 64kD human autoantigen D1 is expressed in slow fibers of extraocular and sternothyroid muscles as a component of myofibrils, and is not upregulated in conditions of hyperthyroidism.

Proteins/genetics/immunology/metabolism↗

NASA NTRS1997

Lymphocyte trafficking and HIV infection of human lymphoid tissue in a rotating wall vessel bioreactor

The pathogenesis of HIV infection involves a complex interplay between both the infected and noninfected cells of human lymphoid tissue, the release of free viral particles, the de novo infection of cells, and the recirculatory trafficking of peripheral blood lymphocytes. To develop an in vitro model for studying these various aspects of HIV pathogenesis we have utilized blocks of surgically excised human tonsils and a rotating wall vessel (RWV) cell culture system. Here we show that (1) fragments of the surgically excised human lymphoid tissue remain viable and retain their gross cytoarchitecture for at least 3 weeks when cultured in the RWV system; (2) such lymphoid tissue gradually shows a loss of both T and B cells to the surrounding growth medium; however, this cellular migration is reversible as demonstrated by repopulation of the tissue by labeled cells from the growth medium; (3) this cellular migration may be partially or completely inhibited by embedding the blocks of lymphoid tissue in either a collagen or agarose gel matrix; these embedded tissue blocks retain most of the basic elements of a normal lymphoid cytoarchitecture; and (4) both embedded and nonembedded RWV-cultured blocks of human lymphoid tissue are capable of productive infection by HIV-1 of at least three various strains of different tropism and phenotype, as shown by an increase in both p24 antigen levels and free virus in the culture medium, and by the demonstration of HIV-1 RNA-positive cells inside the tissue identified by in situ hybridization. It is therefore reasonable to suggest that gel-embedded and nonembedded blocks of human lymphoid tissue, cocultured with a suspension of tonsillar lymphocytes in an RWV culture system, constitute a useful model for simulating normal lymphocyte recirculatory traffic and provide a new tool for testing the various aspects of HIV pathogenesis.

Tissue Culture/instrumentation/methods↗

NASA NTRS1996

Animal models and their importance to human physiological responses in microgravity

Two prominent theories to explain the physiological effects of microgravity relate to the cascade of changes associated with the cephalic shifts of fluids and the absence of tissue deformation forces. One-g experiments for humans used bed rest and the head-down tilt (HDT) method, while animal experiments have been conducted using the tail-suspended, head-down, and hindlimbs non-weightbearing model. Because of the success of the HDT approach with rats to simulate the gravitational effects on the musculoskeletal system exhibited by humans, the same model has been used to study the effects of gravity on the cardiopulmonary systems of humans and other vertebrates. Results to date indicate the model is effective in producing comparable changes associated with blood volume, erythropoiesis, cardiac mass, baroreceptor responsiveness, carbohydrate metabolism, post-flight VO2max, and post-flight cardiac output during exercise. Inherent with these results is the potential of the model to be useful in investigating responsible mechanisms. The suspension model has promise in understanding the capillary blood PO2 changes in space as well as the arterial PO2 changes in subjects participating in a HDT experiment. However, whether the model can provide insights on the up-or-down regulation of adrenoreceptors remains to be determined, and many investigators believe the HDT approach should not be followed to study gravitational influences on pulmonary function in either humans or animals. It was concluded that the tail-suspended animal model had sufficient merit to study in-flight and post-flight human physiological responses and mechanisms.

NASA Discipline Cardiopulmonary↗

NASA NTRS1994

Spaceflight and protein metabolism, with special reference to humans

Human space missions have shown that human spaceflight is associated with a loss of body protein. Specific changes include a loss of lean body mass, decreased muscle mass in the calves, decreased muscle strength, and changes in plasma proteins and amino acids. The major muscle loss is believed to be associated with the antigravity (postural) muscle. The most significant loss of protein appears to occur during the first month of flight. The etiology is believed to be multifactorial with contributions from disuse atrophy, undernutrition, and a stress type of response. This article reviews the results of American and Russian space missions to investigate this problem in humans, monkeys, and rats. The relationship of the flight results with ground-based models including bedrest for humans and hindlimb unweighting for rats is also discussed. The results suggest that humans adapt to spaceflight much better than either monkeys or rats.

Review↗

NASA NTRS2012

Avoiding Human Error in Mission Operations: Cassini Flight Experience

Operating spacecraft is a never-ending challenge and the risk of human error is ever- present. Many missions have been significantly affected by human error on the part of ground controllers. The Cassini mission at Saturn has not been immune to human error, but Cassini operations engineers use tools and follow processes that find and correct most human errors before they reach the spacecraft. What is needed are skilled engineers with good technical knowledge, good interpersonal communications, quality ground software, regular peer reviews, up-to-date procedures, as well as careful attention to detail and the discipline to test and verify all commands that will be sent to the spacecraft. Two areas of special concern are changes to flight software and response to in-flight anomalies. The Cassini team has a lot of practical experience in all these areas and they have found that well-trained engineers with good tools who follow clear procedures can catch most errors before they get into command sequences to be sent to the spacecraft. Finally, having a robust and fault-tolerant spacecraft that allows ground controllers excellent visibility of its condition is the most important way to ensure human error does not compromise the mission.

guidance and control↗

NASA NTRS2013

Human Factors Guidelines for UAS in the National Airspace System

The ground control stations (GCS) of some UAS have been characterized by less-than-adequate human-system interfaces. In some cases this may reflect a failure to apply an existing regulation or human factors standard. In other cases, the problem may indicate a lack of suitable guidance material. NASA is leading a community effort to develop recommendations for human factors guidelines for GCS to support routine beyond-line-of-sight UAS operations in the national airspace system (NAS). In contrast to regulations, guidelines are not mandatory requirements. However, by encapsulating solutions to identified problems or areas of risk, guidelines can provide assistance to system developers, users and regulatory agencies. To be effective, guidelines must be relevant to a wide range of systems, must not be overly prescriptive, and must not impose premature standardization on evolving technologies. By assuming that a pilot will be responsible for each UAS operating in the NAS, and that the aircraft will be required to operate in a manner comparable to conventionally piloted aircraft, it is possible to identify a generic set of pilot tasks and the information, control and communication requirements needed to support these tasks. Areas where guidelines will be useful can then be identified, utilizing information from simulations, operational experience and the human factors literature. In developing guidelines, we recognize that existing regulatory and guidance material will, at times, provide adequate coverage of an area. In other cases suitable guidelines may be found in existing military or industry human factors standards. In cases where appropriate existing standards cannot be identified, original guidelines will be proposed.

Guidelines↗

NASA NTRS2013

Development and Execution of Autonomous Procedures Onboard the International Space Station to Support the Next Phase of Human Space Exploration

Now that major assembly of the International Space Station (ISS) is complete, NASA's focus has turned to using this high fidelity in-space research testbed to not only advance fundamental science research, but also demonstrate and mature technologies and develop operational concepts that will enable future human exploration missions beyond low Earth orbit. The ISS as a Testbed for Analog Research (ISTAR) project was established to reduce risks for manned missions to exploration destinations by utilizing ISS as a high fidelity micro-g laboratory to demonstrate technologies, operations concepts, and techniques associated with crew autonomous operations. One of these focus areas is the development and execution of ISS Testbed for Analog Research (ISTAR) autonomous flight crew procedures intended to increase crew autonomy that will be required for long duration human exploration missions. Due to increasing communications delays and reduced logistics resupply, autonomous procedures are expected to help reduce crew reliance on the ground flight control team, increase crew performance, and enable the crew to become more subject-matter experts on both the exploration space vehicle systems and the scientific investigation operations that will be conducted on a long duration human space exploration mission. These tests make use of previous or ongoing projects tested in ground analogs such as Research and Technology Studies (RATS) and NASA Extreme Environment Mission Operations (NEEMO). Since the latter half of 2012, selected non-critical ISS systems crew procedures have been used to develop techniques for building ISTAR autonomous procedures, and ISS flight crews have successfully executed them without flight controller involvement. Although the main focus has been preparing for exploration, the ISS has been a beneficiary of this synergistic effort and is considering modifying additional standard ISS procedures that may increase crew efficiency, reduce operational costs, and raise the amount of crew time available for scientific research. The next phase of autonomous procedure development is expected to include payload science and human research investigations. Additionally, ISS International Partners have expressed interest in participating in this effort. The recently approved one-year crew expedition starting in 2015, consisting of one Russian and one U.S. Operating Segment (USOS) crewmember, will be used not only for long duration human research investigations but also for the testing of exploration operations concepts, including crew autonomy.

beyond low earth orbit (BLEO)↗

NASA NTRS2016

Advanced Technologies for Robotic Exploration Leading to Human Exploration: Results from the SpaceOps 2015 Workshop

This paper will provide a summary and analysis of the SpaceOps 2015 Workshop all-day session on "Advanced Technologies for Robotic Exploration, Leading to Human Exploration", held at Fucino Space Center, Italy on June 12th, 2015. The session was primarily intended to explore how robotic missions and robotics technologies more generally can help lead to human exploration missions. The session included a wide range of presentations that were roughly grouped into (1) broader background, conceptual, and high-level operations concepts presentations such as the International Space Exploration Coordination Group Roadmap, followed by (2) more detailed narrower presentations such as rover autonomy and communications. The broader presentations helped to provide context and specific technical hooks, and helped lay a foundation for the narrower presentations on more specific challenges and technologies, as well as for the discussion that followed. The discussion that followed the presentations touched on key questions, themes, actions and potential international collaboration opportunities. Some of the themes that were touched on were (1) multi-agent systems, (2) decentralized command and control, (3) autonomy, (4) low-latency teleoperations, (5) science operations, (6) communications, (7) technology pull vs. technology push, and (8) the roles and challenges of operations in early human architecture and mission concept formulation. A number of potential action items resulted from the workshop session, including: (1) using CCSDS as a further collaboration mechanism for human mission operations, (2) making further contact with subject matter experts, (3) initiating informal collaborative efforts to allow for rapid and efficient implementation, and (4) exploring how SpaceOps can support collaboration and information exchange with human exploration efforts. This paper will summarize the session and provide an overview of the above subjects as they emerged from the SpaceOps 2015 Workshop session.

space operations↗

NASA NTRS2017

Application of Human-Autonomy Teaming to an Advanced Ground Station for Reduced Crew Operations

Within human factors there is burgeoning interest in the "human-autonomy teaming" (HAT) concept as a way to address the challenges of interacting with complex, increasingly autonomous systems. The HAT concept comes out of an aspiration to interact with increasingly autonomous systems as a team member, rather than simply use automation as a tool. The authors, and others, have proposed core tenets for HAT that include bi-directional communication, automation and system transparency, and advanced coordination between human and automated teammates via predefined, dynamic task sequences known as "plays." It is believed that, with proper implementation, HAT should foster appropriate teamwork, thus increasing trust and reliance on the system, which in turn will reduce workload, increase situation awareness, and improve performance. To this end, HAT has been demonstrated and/or studied in multiple applications including search and rescue operations, healthcare and medicine, autonomous vehicles, photography, and aviation. The current paper presents one such effort to apply HAT. It details the design of a HAT agent, developed by Human Automation Teaming Solutions, Inc., to facilitate teamwork between the automation and the human operator of an advanced ground dispatch station. This dispatch station was developed to support a NASA project investigating a concept called Reduced Crew Operations (RCO); consequently, we have named the agent R-HATS. Part of the RCO concept involves a ground operator providing enhanced support to a large number of aircraft with a single pilot on the flight deck. When assisted by R-HATS, operators can monitor and support or manage a large number of aircraft and use plays to respond in real-time to complicated, workload-intensive events (e.g., an airport closure). A play is a plan that encapsulates goals, tasks, and a task allocation strategy appropriate for a particular situation. In the current implementation, when a play is initiated by a user, R-HATS determines what tasks need to be completed and has the ability to autonomously execute them (e.g., determining diversion options and uplinking new routes to aircraft) when it is safe and appropriate. R-HATS has been designed to both support end users and researchers in RCO and HAT. Additionally, R-HATS and its underlying architecture were developed with generalizability in mind as a modular software applicable outside of RCO/aviation domains. This paper will also discuss future further development and testing of RHATS.

automation↗