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At least 271 records · Page 15

In-Depth Mass Spectrometry-Based Single-Cell and Nanoscale Proteomics

Leukemic stem cells are highly dynamic and heterogeneous. Analysis of leukemic stem cells at the single cell level should provide a wealth of insights that would not be possible using bulk measurements. Mass spectrometry (MS)-based proteomic workflows can quantify hundreds or thousands of proteins from a biological sample and has proven invaluable for biomedical research, but samples comprising large numbers of cells are typically required due to limited sensitivity. Recent developments in sample processing, chromatographic separations and MS instrumentation are now extending in-depth proteome profiling to single mammalian cells. We describe specific techniques that increase the sensitivity of single-cell proteomics by orders of magnitude, enabling the promise of single cell proteomics to become a reality. We anticipate such techniques could significantly advance our understanding of leukemic stem cells.

Liang, Yiran↗

Resource for the Development of Biomedical Accelerator Mass Spectrometry (AMS) Final Report

The NIH Research Resource for Biomedical AMS was originally funded at Lawrence Livermore National Laboratory in 1999 to develop and apply the technology of accelerator mass spectrometry (AMS) in broad- based biomedical research. The Resource’s niche is to fill needs for ultra high sensitivity quantitation when isotope-labeled agents are used. The Research Resource’s Technology Research and Development (TR&D) efforts will focus on the needs of the biomedical research community in the context of seven Driving Biomedical Projects (DBPs) that will drive the Center’s technical capabilities through three core TR&Ds. We will expand our present capabilities by developing a fully integrated HPLC AMS to increase our capabilities for metabolic measurements, we will develop methods to understand cellular processes and we will develop and validate methods for the application of AMS in human studies, which is a growing area of demand by collaborators and service users. In addition, we will continue to support new and ongoing collaborative and service projects that require the capabilities of the Resource. The Center will continue to train researchers in the use of the AMS capabilities being developed, and the results of all efforts will be widely disseminated to advance progress in biomedical research. Towards these goals, our specific aims are to:1.) Increase the value and information content of AMS measurements by combining molecular speciation with quantitation of defined macromolecular isolates. Specifically, develop and validate methods for macromolecule labeling, characterization and quantitation.2.) Develop and validate methods and strategies to enable AMS to become more broadly used in human studies. Specifically, demonstrate robust methods for conducting pharmacokinetic/pharmacodynamics studies in humans and model systems.3.) Increase the accessibility of AMS to the Biomedical research community and the throughput of AMS through direct coupling to separatory instruments.4.) Provide high throughput 14C BioAMS analysis for collaborative and service clients.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA Ames Research Center R and D Services Directorate Biomedical Systems Development

The Ames Research Center R&D Services Directorate teams with NASA, other government agencies and/or industry investigators for the development, design, fabrication, manufacturing and qualification testing of space-flight and ground-based experiment hardware for biomedical and general aerospace applications. In recent years, biomedical research hardware and software has been developed to support space-flight and ground-based experiment needs including the E 132 Biotelemetry system for the Research Animal Holding Facility (RAHF), E 100 Neurolab neuro-vestibular investigation systems, the Autogenic Feedback Systems, and the Standard Interface Glove Box (SIGB) experiment workstation module. Centrifuges, motion simulators, habitat design, environmental control systems, and other unique experiment modules and fixtures have also been developed. A discussion of engineered systems and capabilities will be provided to promote understanding of possibilities for future system designs in biomedical applications. In addition, an overview of existing engineered products will be shown. Examples of hardware and literature that demonstrate the organization's capabilities will be displayed. The Ames Research Center R&D Services Directorate is available to support the development of new hardware and software systems or adaptation of existing systems to meet the needs of academic, commercial/industrial, and government research requirements. The Ames R&D Services Directorate can provide specialized support for: System concept definition and feasibility Mathematical modeling and simulation of system performance Prototype hardware development Hardware and software design Data acquisition systems Graphical user interface development Motion control design Hardware fabrication and high-fidelity machining Composite materials development and application design Electronic/electrical system design and fabrication System performance verification testing and qualification.

Pollitt, J.↗

nf-core/proteinfamilies: a scalable pipeline for the generation of protein families

The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity, and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterized sequences with the few experimentally characterized ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates nascent protein families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage scales approximately linearly with input size, and the biological benchmarks showed that the generated protein families closely resemble manually curated families in widely used databases.

Nextflow↗

Workshop summary. Biomedical and Space-Related Research with Heavy Ions at the BEVALAC

The authors provide an overview of papers presented at a workshop on Biomedical and Space-Related Research with Heavy Ions at the BEVALAC at Lawrence Berkeley Laboratory. Goals of the meeting were to determine the critical experiments using heavy ions as probes in radiation physics, radiation chemistry, macromolecular and cellular biology, evolution science, basic neurophysiology, and medical therapies; how beam lines and facilities at Lawrence Berkeley Laboratory can be improved for these experiments; and implications in priorities and funding for national policy. Workshop topics included physics and facilities, cellular and molecular biology, tissue radiobiology, and the future of heavy ion research.

NASA Discipline Radiation Health↗

Maiden Voyage of the Rodent Habitat on ISS: Opportunities for Investigating Molecular Mechanisms and Biomedical Consequences of Long Duration Spaceflight

Research using rodents is an essential tool for advancing biomedical research on Earth and in space. The National Research Counsel’s Decadal survey (1) emphasized the importance of expanding NASAs life sciences research to perform long duration, rodent experiments on the International Space Station (ISS). To accomplish this objective, flight hardware, operations, and science capabilities were developed at NASA ARC to support both commercial and government-sponsored research. In preparation for the maiden voyage of the Rodent Habitat hardware and operations system (Rodent Research-1), and in close consultation with a Science Working Group comprised of veterinarians and experienced spaceflight investigators, we modified existing Animal Enclosure Module hardware, developed new hardware, operations, and science activities, and performed a series of ground-based verification tests. Preflight, ground based hardware tests included a simulation of SpaceX Dragon launch conditions (vibration and hypergravity) using the Transporter, and also two long-term biocompatibility tests (32 and 92 days) using the Habitat developed for long term housing on the ISS. The launch simulation test showed that adult mice housed in Transporter hardware adapted well, even if launch simulation was followed by a period of simulated weightlessness (via hind limb unloading). The biocompatibility tests demonstrated that the Habitat successfully supported animal health and also provided a useful video imaging system that enables frequent monitoring of animal health and behavior by veterinary and scientific experts on the ground, independent of ISS crew intervention. At the conclusion of all tests, mice were deemed healthy and suitable for conducting biological research. Additional preflight analyses of tissues preserved by freezing or fixation for gene expression analyses revealed that spleen and liver tissues recovered under conditions that simulated on-orbit activities yielded high quality RNA (RIN values 8-10) and liver enzyme activities and protein content (e.g. catalase). In addition, new methods were developed to optimize future science return by dissecting tissues post-euthanasia and storage. Various tissues were harvested from either intact or partially dissected, frozen carcasses after storage for ~2-6 months; most of the tissues (brain, heart, kidney, eye, adrenal glands and skeletal muscle) were of high RNA quality for science return, whereas some tissues (small intestine, bone marrow and bones) were not. These data demonstrated the protocols developed for future flight experiments supported science return despite delayed preservation post-euthanasia or prolonged storage, and furthermore, that high-quality RNA samples from many different tissues can be recovered by dissection following prolonged storage of the tissue in situ at -80˚C. The first flight experiments carrying 20 mice were launched on Sept 21, 2014 in an unmanned Dragon Capsule, SpaceX4; Rodent Research-1 is dedicated to achieving both NASA validation and CASIS science objectives. Ground based control groups (housed in flight hardware or standard cages) were maintained in environmental chambers at Kennedy Space Center. Crewmembers previously trained in animal handling transferred mice from the Transporter into Habitats under simultaneous veterinary supervision by video streaming and were deemed healthy. Health and behavior of all mice on the ISS was monitored by video feed on a daily basis. The 10 mice for validation (16wk old, female C57Bl6/J) ambulated freely and actively throughout the Habitat, relying heavily on their forelimbs for locomotion. The first on-orbit dissections of mice were performed successfully on Oct 12 and 13, 2014, and the validation mice will reside on ISS for up to 30 days. In conclusion, new capability for long duration rodent research is under development, including in-flight sample collection (which avoids the complication of reentry); results obtained to date will be described. This new Rodent Research system enables achievement of both basic science and translational research objectives to advance human exploration of space.

maiden voyage↗

Advanced Refrigerator/Freezer Technology Development. Technology Assessment

The NASA Lewis Research Center, through contract with Oceaneering Space Systems, is engaged in a project to develop advanced refrigerator/freezer (R/F) technologies for future Life and Biomedical Sciences space flight missions. The first phase of this project, a technology assessment, has been completed to identify the advanced R/F technologies needed and best suited to meet the requirements for the five R/F classifications specified by Life and Biomedical Science researchers. Additional objectives of the technology assessment were to rank those technologies based on benefit and risk, and to recommend technology development activities that can be accomplished within this project. This report presents the basis, the methodology, and results of the R/F technology assessment, along with technology development recommendations.

Gaseor, Thomas↗

Countermeasures for Preventing and Treating Opioid Overdose

The only medication available currently to prevent and treat opioid overdose (naloxone) was approved by the US Food and Drug Administration (FDA) nearly 50 years ago. Due to its pharmacokinetic and pharmacodynamic properties, naloxone has limited utility under some conditions and would not be effective to counteract mass casualties involving large-scale deployment of weaponized synthetic opioids. To address shortcomings of current medical countermeasures for opioid toxicity, a trans-agency scientific meeting was convened by the US National Institute of Allergy and Infectious Diseases/National Institutes of Health (NIAID/NIH) on August 6 and 7, 2019, to explore emerging alternative approaches for treating opioid overdose in the event of weaponization of synthetic opioids. The meeting was initiated by the Chemical Countermeasures Research Program (CCRP), was organized by NIAID, and was a collaboration with the National Institute on Drug Abuse/NIH (NIDA/NIH), the FDA, the Defense Threat Reduction Agency (DTRA), and the Biomedical Advanced Research and Development Authority (BARDA). This paper provides an overview of several presentations at that meeting that discussed emerging new approaches for treating opioid overdose, including the following: (1) intranasal nalmefene, a competitive, reversible opioid receptor antagonist with a longer duration of action than naloxone; (2) methocinnamox, a novel opioid receptor antagonist; (3) covalent naloxone nanoparticles; (4) serotonin (5-HT)1A receptor agonists; (5) fentanyl-binding cyclodextrin scaffolds; (6) detoxifying biomimetic “nanosponge” decoy receptors; and (7) antibody-based strategies. These approaches could also be applied to treat opioid use disorder.

59 BASIC BIOLOGICAL SCIENCES↗

Efficient hemodynamic event detection utilizing relational databases and wavelet analysis

Development of a temporal query framework for time-oriented medical databases has hitherto been a challenging problem. We describe a novel method for the detection of hemodynamic events in multiparameter trends utilizing wavelet coefficients in a MySQL relational database. Storage of the wavelet coefficients allowed for a compact representation of the trends, and provided robust descriptors for the dynamics of the parameter time series. A data model was developed to allow for simplified queries along several dimensions and time scales. Of particular importance, the data model and wavelet framework allowed for queries to be processed with minimal table-join operations. A web-based search engine was developed to allow for user-defined queries. Typical queries required between 0.01 and 0.02 seconds, with at least two orders of magnitude improvement in speed over conventional queries. This powerful and innovative structure will facilitate research on large-scale time-oriented medical databases.

NASA Discipline Cardiopulmonary↗

Circadian and sleep-dependent regulation of hormone release in humans

Daily oscillations characterize the release of nearly every hormone. The circadian pacemaker, located in the suprachiasmatic nucleus of the hypothalamus, generates circadian, approximately 24-hour rhythms in many physiologic functions. However, the observed hormonal oscillations do not simply reflect the output of this internal clock. Instead, daily hormonal profiles are the product of a complex interaction between the output of the circadian pacemaker, periodic changes in behavior, light exposure, neuroendocrine feedback mechanisms, gender, age, and the timing of sleep and wakefulness. The interaction of these factors can affect hormonal secretory pulse frequency and amplitude, with each endocrine system differentially affected by these factors. This chapter examines recent advances in understanding the effects on endocrine rhythms of a number of these factors. Sleep exerts a profound effect on endocrine secretion. Sleep is a dynamic process that is characterized by periodic changes in electrophysiologic activity. These electrophysiologic changes, which are used to mark the state and depth of sleep, are associated with periodic, short-term variations in hormonal levels. The secretion of hormones such as renin and human growth hormone are strongly influenced by sleep or wake state, while melatonin and cortisol levels are relatively unaffected by sleep or wake state. In addition, sleep is associated with changes in posture, behavior, and light exposure, each of which is known to affect endocrine secretion. Furthermore, the tight concordance of habitual sleep and wake times with certain circadian phases has made it difficult to distinguish sleep and circadian effects on these hormones. Specific protocols, designed to extract circadian and sleep information semi-independently, have been developed and have yielded important insights into the effects of these regulatory processes. These results may help to account for changes in endocrine rhythms observed in circadian rhythm sleep disorders, including the dyssomnia of shift work and visual impairment. Yet to be fully investigated are the interactions of these factors with age and gender. Characterization of the factors governing hormone secretion is critical to understanding the temporal regulation of endocrine systems and presents many exciting areas for future research.

Non-NASA Center↗

MIMIC II: a massive temporal ICU patient database to support research in intelligent patient monitoring

Development and evaluation of Intensive Care Unit (ICU) decision-support systems would be greatly facilitated by the availability of a large-scale ICU patient database. Following our previous efforts with the MIMIC (Multi-parameter Intelligent Monitoring for Intensive Care) Database, we have leveraged advances in networking and storage technologies to develop a far more massive temporal database, MIMIC II. MIMIC II is an ongoing effort: data is continuously and prospectively archived from all ICU patients in our hospital. MIMIC II now consists of over 800 ICU patient records including over 120 gigabytes of data and is growing. A customized archiving system was used to store continuously up to four waveforms and 30 different parameters from ICU patient monitors. An integrated user-friendly relational database was developed for browsing of patients' clinical information (lab results, fluid balance, medications, nurses' progress notes). Based upon its unprecedented size and scope, MIMIC II will prove to be an important resource for intelligent patient monitoring research, and will support efforts in medical data mining and knowledge-discovery.

NASA Discipline Cardiopulmonary↗