Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “human activity recognition”

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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
NASA NTRS2002

Pittsburgh Public School District / Carnegie Mellon University Robotics Team Participation in the US First Competition

FIRST, For Inspiration and Recognition of Science and Technology, is an international program designed to encourage junior and senior high school students to participate in science and technology related activities. FIRST attempts to increase enthusiasm for technology by providing a competitive environment in which to demonstrate robotics technology designed for a particular set of tasks. Carnegie Mellon University provided student members of the project the opportunity to complete the design, construction, testing, and operation of a robot. Electrical, mechanical, and programming skills were stressed, with both adult and senior students acting as mentors for more junior members. Teamwork and integration was also stressed in order to provide students with a realistic feel for project-based work. Finally, an emphasis was placed on recruiting students with greater difficulty in entering technological fields: girls and ethnic minorities and students leaning toward humanities (especially art). Carnegie Mellon built a relationship with Taylor Allderdice High School that lasted four years. For four years, the success of the project increased each year. Each term, the students successfully designed and built a working robot that could fully participate in the competition. The enthusiasm of the students has been the cornerstone of the recruit of new students, keeping the project growing and vital. Carnegie Mellon's participation with Allderdice has been an overall great success.

Stroupe, Ashley↗
NASA NTRS2006

Comprehensive Environmental Informatics System (CEIS) Integrating Crew and Vehicle Environmental Health

Integrated Vehicle Health Management (IVHM) systems have been pursued as highly integrated systems that include smart sensors, diagnostic and prognostics software for assessments of real-time and life-cycle vehicle health information. Inclusive to such a system is the requirement to monitor the environmental health within the vehicle and the occupants of the vehicle. In this regard an enterprise approach to informatics is used to develop a methodology entitled, Comprehensive Environmental Informatics System (CEIS). The hardware and software technologies integrated into this system will be embedded in the vehicle subsystems, and maintenance operations, to provide both real-time and life-cycle health information of the environment within the vehicle cabin and of its occupants. This comprehensive information database will enable informed decision making and logistics management. One key element of the CEIS is interoperability for data acquisition and archive between environment and human system monitoring. With comprehensive components the data acquired in this system will use model based reasoning systems for subsystem and system level managers, advanced on-board and ground-based mission and maintenance planners to assess system functionality. Knowledge databases of the vehicle health state will be continuously updated and reported for critical failure modes, and routinely updated and reported for life cycle condition trending. Sufficient intelligence, including evidence-based engineering practices which are analogous to evidencebased medicine practices, will be included in the CEIS to result in more rapid recognition of off-nominal operation to enable quicker corrective actions. This will result from better information (rather than just data) for improved crew/operator situational awareness, which will produce significant vehicle and crew safety improvements, as well as increasing the chance for mission success, future mission planning as well as training. Other benefits include improved reliability, increase safety in operations and cost of operations. The cost benefits stem from significantly reduced processing and operations manpower, predictive maintenance for systems and subjects. The improvements in vehicle functionality and cost will result from increased prognostic and diagnostic capability due to the detailed total human exploration system health knowledge from CEIS. A collateral benefit is that there will be closer observations of the vehicle occupants as wrist watch sized devices are worn for continuous health monitoring. Additional database acquisition will stem from activities in countermeasure practices to ensure peak performance capability by occupants of the vehicle. The CEIS will provide data from advanced sensing technologies and informatics modeling which will be useful in problem troubleshooting, and improving NASA s awareness of systems during operation.

Nall, Mark E.↗
NASA NTRS2008

Evolution of the Mobile Information SysTem (MIST)

The Mobile Information SysTem (MIST) had its origins in the need to determine whether commercial off the shelf (COTS) technologies could improve intervehicular activities (IVA) on International Space Station (ISS) crew maintenance productivity. It began with an exploration of head mounted displays (HMDs), but quickly evolved to include voice recognition, mobile personal computing, and data collection. The unique characteristic of the MIST lies within its mobility, in which a vest is worn that contains a mini-computer and supporting equipment, and a headband with attachments for a HMD, lipstick camera, and microphone. Data is then captured directly by the computer running Morae(TM) or similar software for analysis. To date, the MIST system has been tested in numerous environments such as two parabolic flights on NASA's C-9 microgravity aircraft and several mockup facilities ranging from ISS to the Altair Lunar Sortie Lander. Functional capabilities have included its lightweight and compact design, commonality across systems and environments, and usefulness in remote collaboration. Human Factors evaluations of the system have proven the MIST's ability to be worn for long durations of time (approximately four continuous hours) with no adverse physical deficits, moderate operator compensation, and low workload being reported as measured by Corlett Bishop Discomfort Scale, Cooper-Harper Ratings, and the NASA Total Workload Index (TLX), respectively. Additionally, through development of the system, it has spawned several new applications useful in research. For example, by only employing the lipstick camera, microphone, and a compact digital video recorder (DVR), we created a portable, lightweight data collection device. Video is recorded from the participants point of view (POV) through the use of the camera mounted on the side of the head. Both the video and audio is recorded directly into the DVR located on a belt around the waist. This data is then transferred to another computer for video editing and analysis. Another application has been discovered using simulated flight, in which, a kneeboard is replaced with mini-computer and the HMD to project flight paths and glide slopes for lunar ascent. As technologies evolve, so will the system and its application for research and space system operations.

Litaker, Harry L., Jr.↗
DOE OSTI2023

tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut

Protein translation is orchestrated through tRNA aminoacylation and ribosomal elongation. Among the highly conserved structure of tRNAs, they have distinguishing features which promote interaction with their cognate aminoacyl tRNA synthetase (aaRS). These key features are referred to as identity elements. In our study, we investigated the tRNA:aaRS pair that installs the 22nd amino acid, pyrrolysine (tRNAPyl:PylRS). Pyrrolysyl-tRNA synthetases (PylRSs) are naturally encoded in some archaeal and bacterial genomes to acylate tRNAPyl with pyrrolysine. Their large amino acid binding pocket and poor recognition of the tRNA anticodon have been instrumental in incorporating > 200 noncanonical amino acids. PylRS enzymes can be divided into three classes based on their genomic structure. Two classes contain both an N-terminal and C-terminal domain, however the third class (ΔpylSn) lacks the N-terminal domain. In this study we explored the tRNA identity elements for a ΔpylSn tRNAPyl from Candidatus Methanomethylophilus alvus which drives the orthogonality seen with its cognate PylRS (MaPylRS). From aminoacylation and translation assays we identified five key elements in ΔpylSn tRNAPyl necessary for MaPylRS activity. The absence of a base (position 8) and a G–U wobble pair (G28:U42) were found to affect the high-resolution structure of the tRNA, while molecular dynamic simulations led us to acknowledge the rigidity imparted from the G–C base pairs (G3:C70 and G5:C68).

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1986

Design and development of a Space Station proximity operations research and development mockup

Proximity operations (Prox-Ops) on-orbit refers to all activities taking place within one km of the Space Station. Designing a Prox-Ops control station calls for a comprehensive systems approach which takes into account structural constraints, orbital dynamics including approach/departure flight paths, myriad human factors and other topics. This paper describes a reconfigurable full-scale mock-up of a Prox-Ops station constructed at Ames incorporating an array of windows (with dynamic star field, target vehicle(s), and head-up symbology), head-down perspective display of manned and unmanned vehicles, voice- actuated 'electronic checklist', computer-generated voice system, expert system (to help diagnose subsystem malfunctions), and other displays and controls. The facility is used for demonstrations of selected Prox-Ops approach scenarios, human factors research (work-load assessment, determining external vision envelope requirements, head-down and head-up symbology design, voice synthesis and recognition research, etc.) and development of engineering design guidelines for future module interiors.

Haines, Richard F.↗
DOE OSTI2023

Water narratives in local newspapers within the United States

Sustainable use of water resources continues to be a challenge across the globe. This is in part due to the complex set of physical and social behaviors that interact to influence water management from local to global scales. Analyses of water resources have been conducted using a variety of techniques, including qualitative evaluations of media narratives. This study aims to augment these methods by leveraging computational and quantitative techniques from the social sciences focused on text analyses. Specifically, we use natural language processing methods to investigate a large corpus (approx. 1.8M) of newspaper articles spanning approximately 35 years (1982–2017) for insights into human-nature interactions with water. Focusing on local and regional United States publications, our analysis demonstrates important dynamics in water-related dialogue about drinking water and pollution to other critical infrastructures, such as energy, across different parts of the country. Our assessment, which looks at water as a system, also highlights key actors and sentiments surrounding water. Extending these analytical methods could help us further improve our understanding of the complex roles of water in current society that should be considered in emerging activities to mitigate and respond to resource conflicts and climate change.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2012

Antarctic Exploration Parallels for Future Human Planetary Exploration: Science Operations Lessons Learned, Planning, and Equipment Capabilities for Long Range, Long Duration Traverses

The purpose for this workshop can be summed up by the question: Are there relevant analogs to planetary (meaning the Moon and Mars) to be found in polar exploration on Earth? The answer in my opinion is yes or else there would be no reason for this workshop. However, I think some background information would be useful to provide a context for my opinion on this matter. As all of you are probably aware, NASA has been set on a path that, in its current form, will eventually lead to putting human crews on the surface of the Moon and Mars for extended (months to years) in duration. For the past 50 V 60 years, starting not long after the end of World War II, exploration of the Antarctic has accumulated a significant body of experience that is highly analogous to our anticipated activities on the Moon and Mars. This relevant experience base includes: h Long duration (1 year and 2 year) continuous deployments by single crews, h Established a substantial outpost with a single deployment event to support these crews, h Carried out long distance (100 to 1000 kilometer) traverses, with and without intermediate support h Equipment and processes evolved based on lessons learned h International cooperative missions This is not a new or original thought; many people within NASA, including the most recent two NASA Administrators, have commented on the recognizable parallels between exploration in the Antarctic and on the Moon or Mars. But given that level of recognition, relatively little has been done, that I am aware of, to encourage these two exploration communities to collaborate in a significant way. [Slide 4] I will return to NASA s plans and the parallels with Antarctic traverses in a moment, but I want to spend a moment to explain the objective of this workshop and the anticipated products. We have two full days set aside for this workshop. This first day will be taken up with a series of presentations prepared by individuals with experience that extends back as far as the late 1940s and includes contemporary experience. The people presenting bring a variety of points of view, including not only U.S. but international, although most, if not all, have collaborated on international teams. The second day will consist of a series of small focused group interactions centered on those elements likely to be needed for traverse missions, such as mobility, habitation, and extravehicular activity (EVA, aka space suits). Our invited participants will be talking with people that specialize in these elements so that we can foster more direct interaction and exchange of experiences between these two exploration communities. After the workshop we will be preparing a report documenting these presentations and the essence of the focused interactions.

Hoffman, Stephen J.↗
NASA NTRS2017

Legacy of the Asteroid Redirect Robotic Mission (ARRM)

NASA’s proposed Asteroid Redirect Robotic Mission (ARRM) began with the recognition in a 2010 NASA study that emerging high-power solar electric propulsion technology could be used to rendezvous with, capture, and return an entire, very small (~10,000 kg), near Earth asteroids to the International Space Station. A 2011 workshop by the Keck Institute for Space Studies (KISS) extended the earlier NASA study to asteroid masses of order 500,000 kg by returning them to cislunar space. Subsequent detailed NASA studies in 2013-2014 confirmed the feasibility of this concept. This led to the establishment of the Asteroid Redirect Mission program that consisted of a robotic mission to return multiple tons of asteroid material to cislunar space and a crewed mission to rendezvous with the robotic vehicle, perform two extra vehicular activities (EVAs), collect samples of the asteroid material, and return this material to Earth. Implementation of ARRM got midway through Phase B before being cancelled in April 2017. Although ARRM was cancelled, it has left a near-term legacy of positive impacts to the human spaceflight community, the planetary defense community, the deep space science community, and asteroid mining interests.

Brophy, John R.↗
NASA NTRS2012

Acoustical and Intelligibility Test of the Vocera(Copyright) B3000 Communication Badge

To communicate with each other or ground support, crew members on board the International Space Station (ISS) currently use the Audio Terminal Units (ATU), which are located in each ISS module. However, to use the ATU, crew members must stop their current activity, travel to a panel, and speak into a wall-mounted microphone, or use either a handheld microphone or a Crew Communication Headset that is connected to a panel. These actions unnecessarily may increase task times, lower productivity, create cable management issues, and thus increase crew frustration. Therefore, the Habitability and Human Factors and Human Interface Branches at the NASA Johnson Space Center (JSC) are currently investigating a commercial-off-the-shelf (COTS) wireless communication system, Vocera(C), as a near-term solution for ISS communication. The objectives of the acoustics and intelligibility testing of this system were to answer the following questions: 1. How intelligibly can a human hear the transmitted message from a Vocera(c) badge in three different noise environments (Baseline = 20 dB, US Lab Module = 58 dB, Russian Module = 70.6 dB)? 2. How accurate is the Vocera(C) badge at recognizing voice commands in three different noise environments? 3. What body location (chest, upper arm, or shoulder) is optimal for speech intelligibility and voice recognition accuracy of the Vocera(C) badge on a human in three different noise environments?

Archer, Ronald↗
NASA NTRS1989

Connectionist model-based stereo vision for telerobotics

Autonomous stereo vision for range measurement could greatly enhance the performance of telerobotic systems. Stereo vision could be a key component for autonomous object recognition and localization, thus enabling the system to perform low-level tasks, and allowing a human operator to perform a supervisory role. The central difficulty in stereo vision is the ambiguity in matching corresponding points in the left and right images. However, if one has a priori knowledge of the characteristics of the objects in the scene, as is often the case in telerobotics, a model-based approach can be taken. Researchers describe how matching ambiguities can be resolved by ensuring that the resulting three-dimensional points are consistent with surface models of the expected objects. A four-layer neural network hierarchy is used in which surface models of increasing complexity are represented in successive layers. These models are represented using a connectionist scheme called parameter networks, in which a parametrized object (for example, a planar patch p=f(h,m sub x, m sub y) is represented by a collection of processing units, each of which corresponds to a distinct combination of parameter values. The activity level of each unit in the parameter network can be thought of as representing the confidence with which the hypothesis represented by that unit is believed. Weights in the network are set so as to implement gradient descent in an energy function.

Hoff, William↗
NASA NTRS1997

Biochemical markers in the assessment of bone disease

As the mean age of our population increases, increasing attention has been paid to the diseases associated with aging, including diseases of the skeleton such as osteoporosis. Effective means of treating and possibly preventing such skeletal disorders are emerging, making their early recognition an important goal for the primary care physician. Although bone density measurements and skeletal imaging studies remain of primary diagnostic importance in this regard, a large number of assays for biochemical markers of bone formation and resorption are being developed that promise to complement the densitometry measurements and imaging studies, providing an assessment of the rates of bone turnover and an earlier evaluation of the effects of therapy. In this review, emphasizing the recent literature, the major biochemical markers currently in use or under active investigation are described, and their application in a number of diseases of the skeleton including osteoporosis is evaluated.

Review↗
NASA NTRS2014

Innate Immune Responses of Drosophila Melanogaster are Altered by Spaceflight

Alterations and impairment of immune responses in humans present a health risk for space exploration missions. The molecular mechanisms under pinning innate immune defense can be confounded by the complexity of the acquired immune system of humans. Drosophila (fruit fly) innate immunity is simpler, and shares many similarities with human innate immunity at the level of molecular and genetic pathways. The goals of this study were to elucidate fundamental immune processes in Drosophila affected by spaceflight and to measure host-pathogen responses post-flight. Five containers, each containing ten female and five male fruit flies, were housed and bred on the space shuttle (average orbit altitude of330.35 km) for 12 days and 18.5 hours. A new generation of flies was reared in microgravity. In larvae, the immune system was examined by analyzing plasmatocyte number and activity in culture. In adults, the induced immune responses were analyzed by bacterial clearance and quantitative real-time polymerase chain reaction (qPCR) of selected genes following infection with E. coli. The RNA levels of relevant immune pathway genes were determined in both larvae and adults by microarray analysis. The ability of larval plasmatocytes to phagocytose E. coli in culture was attenuated following spaceflight, and in parallel, the expression of genes involved in cell maturation was down regulated. In addition, the level of constitutive expression of pattern recognition receptors and opsonins that specifically recognize bacteria, and of lysozymes, antimicrobial peptide (AMP) pathway and immune stress genes, hallmarks of humoral immunity, were also reduced in larvae. In adults, the efficiency of bacterial clearance measured in vivo following a systemic infection with E. coli post-flight, remained robust. We show that spaceflight altered both cellular and humoral immune responses in Drosophila and that the disruption occurs at multiple interacting pathways.

Marcu, Oana↗
NASA NTRS2002

Stimulus-response compatibility and psychological refractory period effects: implications for response selection

The purpose of this paper was to provide insight into the nature of response selection by reviewing the literature on stimulus-response compatibility (SRC) effects and the psychological refractory period (PRP) effect individually and jointly. The empirical findings and theoretical explanations of SRC effects that have been studied within a single-task context suggest that there are two response-selection routes-automatic activation and intentional translation. In contrast, all major PRP models reviewed in this paper have treated response selection as a single processing stage. In particular, the response-selection bottleneck (RSB) model assumes that the processing of Task 1 and Task 2 comprises two separate streams and that the PRP effect is due to a bottleneck located at response selection. Yet, considerable evidence from studies of SRC in the PRP paradigm shows that the processing of the two tasks is more interactive than is suggested by the RSB model and by most other models of the PRP effect. The major implication drawn from the studies of SRC effects in the PRP context is that response activation is a distinct process from final response selection. Response activation is based on both long-term and short-term task-defined S-R associations and occurs automatically and in parallel for the two tasks. The final response selection is an intentional act required even for highly compatible and practiced tasks and is restricted to processing one task at a time. Investigations of SRC effects and response-selection variables in dual-task contexts should be conducted more systematically because they provide significant insight into the nature of response-selection mechanisms.

Review Literature↗
DOE OSTI2025

Direct writing of PVBVA/Ti 3 C 2 T x (MXene) triboelectric nanogenerators for energy harvesting and sensing applications

Triboelectric nanogenerators (TENGs) have gained recognition for their potential to convert mechanical energy into electrical energy, making them attractive for applications in healthcare, robotics, and human-device interfaces. However, many TENG devices rely on fluorinated polymers for high charge generation and involve complex fabrication processes, which limit their practicality and environmental sustainability. Here, we developed an eco-friendly composite of poly (vinyl butyral-co-vinyl alcohol-co-vinyl acetate) (PVBVA) and Ti 3 C 2 T x MXene for extrusion printing onto aluminum foil substrates, enabling the additive manufacturing of TENGs. Experimental results indicate that integrating 5.5 mg mL -1 of MXene (P-MX 5.5) into PVBVA resulted in a power density of 760 mW·m -2 , with simultaneous improvements in open-circuit voltage (129 %) and short-circuit current (250 %), demonstrating enhanced charge transfer efficiency. Beyond aluminum foil-based devices, we further explored the fully printed P-MX 5.5 TENG by utilizing silver ink electrodes, eliminating the need for aluminum foil. This fully printed, flexible TENG was successfully used for real-time human motion sensing, demonstrating its ability to detect activities such as walking, running, knee bending, and jumping. Collectively, our additively manufactured and sustainable PVBVA-MXene TENG composites, including both aluminum-based and fully printed versions, show promise for future energy harvesters, sensors, wearable electronics, healthcare, and robotic applications.

Additive manufacturing↗
NASA NTRS2000

Over-Expression, Purification and Crystallization of Human Dihydrolipoamide Dehydrogenase

Dehydrolipoamide dehydrogenase (E3; dihydrolipoan-tide:NAD+ oxidoreductase, EC 1.8.1.4) is a common catalytic component found in pyruvate dehydrogenase complex, alpha-ketoglutarate dehydrogenase complex, and branched-chain cc-keto acid dehydrogenase complex. E3 is also a component (referred to as L protein) of the glycine cleavage system in bacterial metabolism (2). Active E3 forms a homodimer with four distinctive subdomain structures (FAD binding, NAD+ binding, central and interface domains) with non-covalently but tightly bound FAD in the holoenzyme. Deduced amino acids from cloned full-length human E3 gene showed a total of 509 amino acids with a leader sequence (N-terminal 35 amino acids) that is excised (mature form) during transportation of expressed E3 into mitochondria membrane. So far, three-dimensional structure of human E3 has not been reported. Our effort to achieve the elucidation of the X-ray crystal structure of human E3 will be presented. Recombinant pPROEX-1 expression vector (from GIBCO BRL Life Technologies) having the human E3 gene without leader sequence was constructed by Polymerase Chain Reaction (PCR) and subsequent ligation, and cloned in E.coli XL1-Blue by transformation. Since pPROEX-1 vector has an internal His-tag (six histidine peptide) located at the upstream region of a multicloning site, one-step affinity purification of E3 using nickelnitriloacetic acid (Ni-NTA) agarose resin, which has a strong affinity to His-tag, was feasible. Also a seven-amino-acid spacer peptide and a recombinant tobacco etch virus protease recognition site (seven amino acids peptide) found between His-tag and first amino acid of expressed E3 facilitated the cleavage of His-tag from E3 after the affinity purification. By IPTG induction, ca. 15 mg of human E3 (mature form) was obtained from 1L LB culture with overnight incubation at 25C. Over 98% of purity of E3 from one-step Ni-NTA agarose affinity purification was confirmed by SDS-PAGE analysis. For crystallization, E3 samples were prepared with and without His-tag. To minimize the aggregation of E3, apo- and holo- forms of E3s were tested, as well as a mutated E3. Dynamic light scattering measurements revealed that the E3 preparations without His-tag and substrate are highly monodispersive with regard to homodimers. Consequent crystallization trials of this E3 preparation led to single crystals of E3 grown by the vapor diffusion method. Crystals were obtained within a few days from solution containing poly (ethylene glycol) monomethyl ether 5000 as a precipitant. Autoindexing and integration of the X-ray diffraction data showed that E3 crystals belong to an orthorhombic system with unit cell parameters a-- 123. 1, b= 165.3 and c=214.3A. Further optimization of protein preparation and crystallization experiments for the structural determination will be discussed.

Hong, Y. S.↗
NASA NTRS1997

Activation and proliferation of lymphocytes and other mammalian cells in microgravity

The experimental findings reviewed in this chapter support the following conclusions: Proliferation. Human T-lymphocytes, associated with monocytes as accessory cells, show dramatic changes in the centrifuge, in the clinostat and in space. In free-floating cells the mitogenic response is depressed by 90% in microgravity, whereas in cells attached to a substratum activation is enhanced by 100% compared to 1-G ground and inflight controls. The duration of phase G1 of the mitotic cycle of HeLa cells is reduced in hypergravity, resulting in an increased proliferation rate. Other systems like Friend cells and WI38 human embryonic lung cells do not show significant changes. Genetic expression and signal transduction. T-lymphocytes and monocytes show important changes in the expression of cytokines like interleukin-1, interleukin-2, interferon-gamma and tumor necrosis factor. The data from space experiments in Spacelab, Space Shuttle mid-deck, and Biokosmos have helped to clarify certain aspects of the mechanism of T-cell activation. Epidermoid A431 cells show changes in the genetic expression of the proto-oncogenes c-fos and c-jun in the clinostat and in sounding rockets. Membrane function, in particular the binding of ligates as first messengers of a signal, is not changed in most of the cell systems in microgravity. Morphology and Mortility. Free cells, lymphocytes in particular, are able to move and form aggregates in microgravity, indicating that cell-cell contacts and cell communications do take place in microgravity. Dramatic morphological and ultrastructural changes are not detected in cells cultured in microgravity. Important experiments with single mammalian cells, including immune cells, were carried out recently in three Spacelab flights, (SL-J, D-2, and IML-2 in 1992, 1993, and 1994, respectively). The results of the D-2 mission have been published in ref. 75; those of the IML-2 mission in ref. 76. Finally, many cell biology experiments in space have suffered in the past from a lack of adequate controls (like 1-G centrifuges) and of proper experimental conditions (like well-controlled temperature). In this respect the availability of Biorack, outfitted with proper incubators with 1-G control centrifuge as well as a glovebox with a microscope, is a great advantage. It is also desirable that cell biology experiments in space are accompanied or even preceded by a program of ground-based investigations in the fast rotating clinostat and in the centrifuge, and that preparatory experiments be done in parabolic flights and sounding rockets, whenever possible. Proper publication of the results of space experiments is another important need. A great number of data have been published in proceedings and reports that are not available to the broad scientific community. To guarantee the credibility and the international recognition of space biology it is important that the results be published in international, peer reviewed journals.

manned↗
DOE OSTI2024

A minimal complex of KHNYN and zinc-finger antiviral protein binds and degrades single-stranded RNA

Detecting viral infection is a key role of the innate immune system. The genomes of some RNA viruses have a high CpG dinucleotide content relative to most vertebrate cell RNAs, making CpGs a molecular marker of infection. The human zinc-finger antiviral protein (ZAP) recognizes CpG, mediates clearance of the foreign CpG-rich RNA, and causes attenuation of CpG-rich RNA viruses. While ZAP binds RNA, it lacks enzymatic activity that might be responsible for RNA degradation and thus requires interacting cofactors for its function. One of these cofactors, KHNYN, has a predicted nuclease domain. Using biochemical approaches, we found that the KHNYN NYN domain is a single-stranded RNA ribonuclease that does not have sequence specificity and digests RNA with or without CpG dinucleotides equivalently in vitro. We show that unlike most KH domains, the KHNYN KH domain does not bind RNA. Indeed, a crystal structure of the KH region revealed a double-KH domain with a negatively charged surface that accounts for the lack of RNA binding. Rather, the KHNYN C-terminal domain (CTD) interacts with the ZAP RNA-binding domain (RBD) to provide target RNA specificity. We define a minimal complex composed of the ZAP RBD and the KHNYN NYN-CTD and use a fluorescence polarization assay to propose a model for how this complex interacts with a CpG dinucleotide-containing RNA. In the context of the cell, this module would represent the minimum ZAP and KHNYN domains required for CpG-recognition and ribonuclease activity essential for attenuation of viruses with clusters of CpG dinucleotides.

Yeoh, Zoe C. (ORCID:0000000226949068)↗
DOE OSTI2025

Structural and functional analyses of SARS-CoV-2 Nsp3 and its specific interactions with the 5’ UTR of the viral genome

ABSTRACT Non-structural protein 3 (Nsp3) is the largest open reading frame encoded in the SARS-CoV-2 genome, essential for the formation of double-membrane vesicles (DMV) wherein viral RNA replication occurs. We conducted an extensive structure-function analysis of Nsp3 and determined the crystal structures of the ubiquitin-like 1 (Ubl1), nucleic acid binding (NAB), β-coronavirus-specific marker (βSM) domains, and a sub-region of the Y domain of this protein. We show that the Ubl1, ADP-ribose phosphatase (ADRP), human SARS Unique (HSUD), NAB, and Y domains of Nsp3 bind the 5’ UTR of the viral genome and that the Ubl1 and Y domains possess affinity for recognition of this region, suggesting high specificity. The Ubl1-Nucleocapsid (N) protein complex binds the 5’ UTR with greater affinity than the individual proteins alone. Our results suggest that multiple domains of Nsp3, particularly Ubl1 and Y, shepherd the 5’ UTR of the viral genome during translocation through the DMV membrane, priming the Ubl1 domain to load the genome onto N protein. IMPORTANCE The largest protein encoded by the SARS-CoV-2 genome is Nsp3. In infected cells, this multi-domain protein forms a pore structure in the virus-induced double-membrane vesicles (DMV). We have incomplete data on Nsp3 molecular structure, and here, we describe crystal structures for multiple domains of Nsp3. It is thought that newly replicated viral RNA transits through the DMV pore; however, we possess incomplete data on which regions of Nsp3 actually interact with RNA. Here, we present data showing that five domains of Nsp3 interact with the 5’ UTR of the SARS-CoV-2 RNA, including the Y domain for which no function has ever been discovered. These data suggest that the pore structure plays an active role in recognizing the terminal end of the genome, transiting and loading the viral RNA onto the cytoplasmic nucleocapsid protein. These data help expand our knowledge of Nsp3 structure and function and the SARS-CoV-2 replication cycle.

Microbiology↗