Search NASA⌕ Search

SEARCH · Search NASA

Results for “Biomedical Research”

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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

High-Precision Zinc Isotopic Measurement of Certified Reference Materials Relevant to the Environmental, Earth, Planetary and Biomedical Sciences

The zinc (Zn) stable isotope system has emerged as a powerful tool for investigating natural and anthropogenic processes of interest to disciplines extending from the Earth and planetary sciences to biomedical research. In nature, Zn isotopes typically fractionate ( 66 Zn/ 64 Zn) within the range of –1 and +1 permil (‰), and however, analytical limitations restrict the application of the Zn isotope system. Specifically, there is a lack of well-characterised matrix-matched reference materials covering most Zn isotope applications that are essential for validating laboratory performance, particularly given the contamination prone nature of Zn. Furthermore, the increasing demand for analysis of size-limited materials and sample types displaying small, sub-permil level Zn isotope variations requires improvements in measurement procedures. To address these limitations, the δ 66 Zn values of two pure Zn solutions and eighteen reference materials including the previously uncharacterised RGM-2, BCR-279, DOLT-4, DOLT-5, NASS-7, SBC-1, SGR-1b, MESS-3 and HISS-1, and the understudied QLO-1, SDC-1, BCR-414, NASS-6 and COQ-1 materials are reported. Furthermore, a 70 Zn- 67 Zn double-spike design has been implemented that routinely achieves intermediate measurement precision better than ± 0.02‰. This represents at least a two-fold improvement when compared with other double-spike designs, providing a robust platform of δ 66 Zn values required for quality control procedures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Unravelling Magnetic Nanochain Formation in Dispersion for In Vivo Applications

Self-assembly of iron oxide nanoparticles (IONPs) into 1D chains is appealing, because of their biocompatibility and higher mobility compared to 2D/3D assemblies while traversing the circulatory passages and blood vessels for in vivo biomedical applications. In this work, parameters such as size, concentration, composition, and magnetic field, responsible for chain formation of IONPs in a dispersion as opposed to spatially confining substrates, are examined. In particular, the monodisperse 27 nm IONPs synthesized by an extended LaMer mechanism are shown to form chains at 4 mT, which are lengthened with applied field reaching 270 nm at 2.2 T. The chain lengths are completely reversible in field. Using a combination of scattering methods and reverse Monte Carlo simulations the formation of chains is directly visualized. The visualization of real-space IONPs assemblies formed in dispersions presents a novel tool for biomedical researchers. This allows for rapid exploration of the behavior of IONPs in solution in a broad parameter space and unambiguous extraction of the parameters of the equilibrium structures. Additionally, it can be extended to study novel assemblies formed by more complex geometries of IONPs.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Unveiling the nanoscale architectures and dynamics of protein assembly with in situ atomic force microscopy

Proteins play a vital role in different biological processes by forming complexes through precise folding with exclusive inter- and intra-molecular interactions. Understanding the structural and regulatory mechanisms underlying protein complex formation provides insights into biophysical processes. Furthermore, the principle of protein assembly gives guidelines for new biomimetic materials with potential applications in medicine, energy, and nanotechnology. Atomic force microscopy (AFM) is a powerful tool for investigating protein assembly and interactions across spatial scales (single molecules to cells) and temporal scales (milliseconds to days). It has significantly contributed to understanding nanoscale architectures, inter- and intra-molecular interactions, and regulatory elements that determine protein structures, assemblies, and functions. This review describes recent advancements in elucidating protein assemblies with in situ AFM. We discuss the structures, diffusions, interactions, and assembly dynamics of proteins captured by conventional and high-speed AFM in near-native environments and recent AFM developments in the multimodal high-resolution imaging, bimodal imaging, live cell imaging, and machine-learning-enhanced data analysis. These approaches show the significance of broadening the horizons of AFM and enable unprecedented explorations of protein assembly for biomaterial design and biomedical research.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Covalently-Bonded Laminar Assembly of Van der Waals Semiconductors with Polymers: Toward High-Performance Flexible Devices

Van der Waals semiconductors (vdWS) offer superior mechanical and electrical properties and are promising for flexible microelectronics when combined with polymer substrates. However, the self-passivated vdWS surfaces and their weak adhesion to polymers tend to cause interfacial sliding and wrinkling, and thus, are still challenging the reliability of vdWS-based flexible devices. Here, in this study, an effective covalent vdWS–polymer lamination method with high stretch tolerance and excellent electronic performance is reported. Using molybdenum disulfide (MoS 2 ) and polydimethylsiloxane (PDMS) as a case study, gold–chalcogen bonding and mercapto silane bridges are leveraged. The resulting composite structures exhibit more uniform and stronger interfacial adhesion. This enhanced coupling also enables the observation of a theoretically predicted tension-induced band structure transition in MoS 2 . Moreover, no obvious degradation in the devices’ structural and electrical properties is identified after numerous mechanical cycle tests. This high-quality lamination enhances the reliability of vdWS-based flexible microelectronics, accelerating their practical applications in biomedical research and consumer electronics.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Robust surfactant-assisted one-pot sample preparation for label-free single-cell and nanoscale proteomics

With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk cells. However, such bulk measurement obscures cell to cell heterogeneity, precluding proteome profiling of single cells and small numbers of cells of interest. To address this issue, in recent 5 years there are a surge of small sample preparation methods developed for robust effective collection and processing of single cells and small numbers of cells for in-depth MS-based proteome profiling. Based on their broad accessibility, they can be categorized into two types: specific device- and standard PCR tube- or multi-well plate-based methods. Herein we describe the detailed protocol of our recently developed, easily adoptable, Surfactant-assisted One-Pot (SOP) sample preparation coupled with MS method termed SOP-MS for label-free single-cell and nanoscale proteomics. SOP-MS capitalizes on the combination of a MS-compatible surfactant, DDM (n-Dodecyl-ß-D-maltoside), and standard low-bind PCR tube or multi-well plate for ‘all-in-one’ one-pot sample preparation without sample transfer. With its robust and convenient features, SOP-MS can be readily implemented in any MS laboratory for single-cell and nanoscale proteomics. With further improvements in MS detection sensitivity and sample throughput, we believe that SOP-MS could open an avenue for single-cell proteomics with broad applicability in the biological and biomedical research.

Single-cell proteomics, nanoscale proteomics, SOP-↗
DOE OSTI2021

Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track

Blockchain distributed ledger technology is just starting to be adopted in genomics and healthcare applications. Despite its increased prevalence in biomedical research applications, skepticism regarding the practicality of blockchain technology for real-world problems is still strong and there are few implementations beyond proof-of-concept. We focus on benchmarking blockchain strategies applied to distributed methods for sharing records of gene-drug interactions. We expect this type of sharing will expedite personalized medicine. We generated gene-drug interaction test datasets using the Clinical Pharmacogenetics Implementation Consortium (CPIC) resource. We developed three blockchain-based methods to share patient records on gene-drug interactions: Query Index, Index Everything, and Dual-Scenario Indexing. We achieved a runtime of about 60 s for importing 4,000 gene-drug interaction records from four sites, and about 0.5 s for a data retrieval query. Our results demonstrated that it is feasible to leverage blockchain as a new platform to share data among institutions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Artificial intelligence methods for protein structure and interaction prediction: Recent advances and challenges

Recent advances in artificial intelligence have introduced novel methods for high-accuracy prediction of protein tertiary structures, protein complex structures, and interactions between proteins and other biomolecules, such as small molecules and nucleic acids. Such advancements are accelerating biomedical research and the development of new protein design and bioengineering methods among many other important biotechnology applications. Here, in this review, we outline the recent advances in protein-centric biomolecular structure and interaction prediction, highlight some major challenges in the field, and discuss potential directions to address them.

Morehead, Alex [Lawrence Berkeley National Laborat↗
DOE OSTI2020

Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform

Top-down proteomics is a powerful tool for characterizing genetic variations and post-translational modifications at intact protein level. That being said, one significant technical gap of top-down proteomics is the inability to analyze low amount of biological samples, which limits its access to isolated rare cells, fine-needle aspiration biopsies, and tissue substructures. Herein, we developed an ultrasensitive top-down platform by incorporating a microfluidic sample preparation system, termed nanoPOTS (Nanodroplet Processing in One pot for Trace Samples), into a top-down proteomics workflow. A unique combination of a nonionic detergent dodecyl-ß-D-maltopyranoside (DDM) with urea as protein extraction buffer significantly improved both protein extraction efficiency and sample recovery. We hypothesize that the DDM detergent improves protein recovery by efficiently reducing non-specific adsorption of intact proteins on container surfaces, while urea serves as a strong denaturant to disrupt noncovalent complexes and release intact proteins for downstream analysis. The nanoPOTS-based top-down platform reproducibly and quantitatively identified ~170 to ~620 proteoforms from ~70 to ~770 HeLa cells containing ~10 to ~115 ng of total protein. A variety of post-translational modifications including acetylation, myristoylation, and iron binding were identified using only less than 800 cells. We anticipate the nanoPOTS top-down proteomics platform will be broadly applicable in biomedical researches, particularly where clinical specimens are not available in amounts amenable to standard workflows.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Label-Free Profiling of up to 200 Single-Cell Proteomes per Day Using a Dual-Column Nanoflow Liquid Chromatography Platform

Single-cell proteomics (SCP) has great potential to advance biomedical research and personalized medicine. The sensitivity of such measurements increases with low-flow separations (<100 nL/min) due to improved ionization efficiency, but the time required for sample loading, column washing, and regeneration in these systems can lead to low measurement throughput and inefficient utilization of the mass spectrometer. Herein, we developed a two-column liquid chromatography (LC) system that dramatically increases the throughput of label-free SCP using two parallel subsystems to multiplex sample loading, online desalting, analysis, and column regeneration. The integration of MS1-based feature matching increased proteome coverage when short LC gradients were used. The high-throughput LC system was reproducible between the columns, with a 4% difference in median peptide abundance and a median CV of 18% across 100 replicate analyses of a single-cell-sized peptide standard. An average of 621, 774, 952, and 1622 protein groups were identified with total analysis times of 7, 10, 15, and 30 min, corresponding to a measurement throughput of 206, 144, 96, and 48 samples per day, respectively. When applied to single HeLa cells, we identified nearly 1000 protein groups per cell using 30 min cycles and 660 protein groups per cell for 15 min cycles. Finally, we explored the possibility of measuring cancer therapeutic targets with a pilot study comparing the K562 and Jurkat leukemia cell lines. This work demonstrates the feasibility of high-throughput label-free single-cell proteomics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

DNA Origami Incorporated into Solid-State Nanopores Enables Enhanced Sensitivity for Precise Analysis of Protein Translocations

The rapidly advancing field of nanotechnology is driving the development of precise sensing methods at the nanoscale, with solid-state nanopores emerging as promising tools for biomolecular sensing. Here, this study investigates the increased sensitivity of solid-state nanopores achieved by integrating DNA origami structures, leading to the improved analysis of protein translocations. Using holo human serum transferrin (holo-hSTf) as a model protein, we compared hybrid nanopores incorporating DNA origami with open solid-state nanopores. Results show a significant enhancement in holo-hSTf detection sensitivity with DNA origami integration, suggesting a unique role of DNA interactions beyond confinement. This approach holds potential for ultrasensitive protein detection in biosensing applications, offering advancements in biomedical research and diagnostic tool development for diseases with low-abundance protein biomarkers. Further exploration of origami designs and nanopore configurations promises even greater sensitivity and versatility in the detection of a wider range of proteins, paving the way for advanced biosensing technologies.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Photophysical Properties and Electronic Structure of Hydroporphyrin Dyads Exhibiting Strong Through-Space and Through-Bond Electronic Interactions

Electronic interactions between tetrapyrroles are utilized in natural photosynthetic systems to tune the light-harvesting and energy/charge-transfer processes in these assemblies. Such interactions also can be employed to tailor the electronic properties of tetrapyrrolic dyads and larger arrays for use in materials science and biomedical research. Here we have utilized static and time-resolved optical spectroscopy to characterize the optical absorption and emission properties of a set of chlorin and bacteriochlorin dyads with varied degrees of through-bond (TB) and through-space (TS) interactions between the constituent macrocycles. The dyads consist of two chlorins or two bacteriochlorins joined by a linker that utilizes a triple-double-triple bond (enediyne) motif in which the double bond portion is a ester-substituted ethylene or o-phenylene unit. The photophysical studies are coupled with density functional theory (DFT) calculations to probe the ground-state molecular orbital (MO) characteristics of the dyads and time-dependent calculations (TDDFT) to elucidate excited-state properties. The latter include electronic characteristics of the singlet excited state manifold and the absorption transitions to these states from the electronic ground state. Comparison of the MO and calculated spectral properties of each dyad with the linker present versus disrupted (by eliminating the double-bond portion) gives insight into the relative contributions of TB versus TS interactions to the electronic properties of the dyads. The results show that the TB and TS contributions are additive (constructively interfere), which is not always the case for molecular dyads. Most of the dyads have shorter lifetimes of the lowest singlet excited state compared to the parent monomer, which derives from increased S 1 → S 0 internal conversion. The enhancement is greater for the dyads in benzonitrile than in toluene. Furthermore, the studies provide insights into the nature of the electronic interactions between the constituents in the tetrapyrrole arrays and how these interactions dictate the spectral properties and excited-state decay characteristics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

In Vitro and in Vivo Analyses of the Effects of Source, Length, and Charge on the Cytotoxicity and Immunocompatibility of Cellulose Nanocrystals

Cellulose nanocrystals (CNCs) are an emergent, sustainable nanomaterial which are bio-sourced, abundant, and biodegradable. On account of their high aspect ratio, low density, and mechanical rigidity, they have been employed in numerous areas of biomedical research including as reinforcing materials for bone or tissue scaffolds or as carriers in drug delivery systems. Given the promise of these materials for such use, characterizing and understanding their interactions with biological systems is an important step to prevent toxicity or inflammation. Reported herein are studies aimed at exploring the in-vitro and in-vivo effects that source, length, and charge of the CNCs have on cytotoxicity and immune response. In this study, CNCs from four different biosources (cotton, wood, Miscanthus x. Giganteus, and sea tunicate) were prepared and functionalized with positive or negative charges to obtain a small library of CNCs with a range of dimensions and surface charge. A method to remove endotoxic or other impurities on the CNC surface leftover from the isolation process was developed, and the biocompatibility of the CNCs was subsequently assayed in-vitro and in-vivo. After subcutaneous injection, it was found that unfunctionalized (uncharged) CNCs form aggregates at the site of injection, inducing splenomegaly and neutrophil infiltration, while charged CNCs having surface carboxylates, sulfate half-esters, or primary amines were biologically inert. No effect of particle source or length was observed in the in-vitro and in-vivo studies conducted. The lack of in-vitro or in-vivo immune response toward charged CNCs in these experiments supports their use in future biological studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Room-Temperature Optical Detection of 14 CO 2 below the Natural Abundance with Two-Color Cavity Ring-Down Spectroscopy

Radiocarbon’s natural production, radiative decay, and isotopic rarity make it a unique tool to probe carbonaceous systems in the life and earth sciences. However, the difficulty of current radiocarbon ( 14 C) detection methods limits scientific adoption. Here, two-color cavity ring-down spectroscopy detects 14 CO 2 in room-temperature samples with an accuracy of one-tenth the natural abundance in 3 min. The intracavity pump–probe measurement uses two cavity-enhanced lasers to cancel out cavity ring-down rate fluctuations and strong one-photon absorption interference (>10 000 1/s) from hot-band transitions of CO 2 isotopologues. Selective, room-temperature detection of small 14 CO 2 absorption signals (<1 1/s) reduces the technical and operational burdens for cavity-enhanced measurements of radiocarbon, which can benefit a wide range of applications like biomedical research and field-detection of combusted fossil fuels.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

An atlas of dynamic chromatin landscapes in mouse fetal development

The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP–seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC–seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The NIH Somatic Cell Genome Editing program

The move from reading to writing the human genome offers new opportunities to improve human health. The United States National Institutes of Health (NIH) Somatic Cell Genome Editing (SCGE) Consortium aims to accelerate the development of safer and more-effective methods to edit the genomes of disease-relevant somatic cells in patients, even in tissues that are difficult to reach. Here we discuss the consortium’s plans to develop and benchmark approaches to induce and measure genome modifications, and to define downstream functional consequences of genome editing within human cells. Central to this effort is a rigorous and innovative approach that requires validation of the technology through third-party testing in small and large animals. New genome editors, delivery technologies and methods for tracking edited cells in vivo, as well as newly developed animal models and human biological systems, will be assembled—along with validated datasets—into an SCGE Toolkit, which will be disseminated widely to the biomedical research community. We visualize this toolkit—and the knowledge generated by its applications—as a means to accelerate the clinical development of new therapies for a wide range of conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A compendium of human gene functions derived from evolutionary modelling

A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this goal by generating a structured body of information about gene functions, which now includes experimental findings reported in more than 175,000 publications for human genes and genes in experimentally tractable model organisms 1,2 . Here, we describe the results of a large, international effort to integrate all of these findings to create a representation of human gene functions that is as complete and accurate as possible. Specifically, we apply an expert-curated, explicit evolutionary modelling approach to all human protein-coding genes. This approach integrates available experimental information across families of related genes into models that reconstruct the gain and loss of functional characteristics over evolutionary time. The models and the resulting set of 68,667 integrated gene functions cover approximately 82% of human protein-coding genes. The functional repertoire reveals a marked preponderance of molecular regulatory functions, and the models provide insights into the evolutionary origins of human gene functions. We show that our set of descriptions of functions can improve the widely used genomic technique of Gene Ontology enrichment analysis. The experimental evidence for each functional characteristic is recorded, thereby enabling the scientific community to help review and improve the resource, which we have made publicly available.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures

The advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new era of structural biology, enabling the routine determination of large biological molecules and their complexes at atomic resolution. The high-resolution structures of biological macromolecules and their complexes significantly expedite biomedical research and drug discovery. However, automatically and accurately building atomic models from high-resolution cryo-EM density maps is still time-consuming and challenging when template-based models are unavailable. Artificial intelligence (AI) methods such as deep learning trained on limited amount of labeled cryo-EM density maps generate inaccurate atomic models. To address this issue, we created a dataset called Cryo2StructData consisting of 7,600 preprocessed cryo-EM density maps whose voxels are labelled according to their corresponding known atomic structures for training and testing AI methods to build atomic models from cryo-EM density maps. Cryo2StructData is larger than existing, publicly available datasets for training AI methods to build atomic protein structures from cryo-EM density maps. We trained and tested deep learning models on Cryo2StructData to validate its quality showing that it is ready for being used to train and test AI methods for building atomic models.

59 BASIC BIOLOGICAL SCIENCES↗