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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.

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At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Catalytically inactive, purified RNase H1: A specific and sensitive probe for RNA–DNA hybrid imaging

R-loops are three-stranded nucleic acid structures with both physiological and pathological roles in cells. R-loop imaging generally relies on detection of the RNA–DNA hybrid component of these structures using the S9.6 antibody. We show that the use of this antibody for imaging can be problematic because it readily binds to double-stranded RNA (dsRNA) in vitro and in vivo, giving rise to nonspecific signal. In contrast, purified, catalytically inactive human RNase H1 tagged with GFP (GFP-dRNH1) is a more specific reagent for imaging RNA–DNA hybrids. GFP-dRNH1 binds strongly to RNA–DNA hybrids but not to dsRNA oligonucleotides in fixed human cells and is not susceptible to binding endogenous RNA. Furthermore, we demonstrate that purified GFP-dRNH1 can be applied to fixed cells to detect hybrids after their induction, thereby bypassing the need for cell line engineering. GFP-dRNH1 therefore promises to be a versatile tool for imaging and quantifying RNA–DNA hybrids under a wide range of conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

LDBT instead of DBTL: combining machine learning and rapid cell-free testing

Synthetic biology is defined by Design-Build-Test-Learn cycles. Machine learning has yielded significant improvements in protein design; thus, we propose that “Learning” can precede “Design” to optimize engineering workflows. Additionally, shifting to cell-free platforms will further accelerate “Build” and “Test” capabilities by allowing the rapid expression of proteins and functional testing without the need for cellular transformation or isolation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Senolysis induced by 25-hydroxycholesterol targets CRYAB in multiple cell types

Cellular senescence is a driver of many age-related pathologies. There is an active search for pharmaceuticals termed senolytics that can mitigate or remove senescent cells in vivo by targeting genes that promote the survival of senescent cells. We utilized single-cell RNA sequencing to identify CRYAB as a robust senescence-induced gene and potential target for senolysis. Using chemical inhibitor screening for CRYAB disruption, we identified 25-hydroxycholesterol (25HC), an endogenous metabolite of cholesterol biosynthesis, as a potent senolytic. We then validated 25HC as a senolytic in mouse and human cells in culture and in vivo in mouse skeletal muscle. Thus, 25HC represents a potential class of senolytics, which may be useful in combating diseases or physiologies in which cellular senescence is a key driver.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Phenotypic and functional characterization of corneal endothelial cells during in vitro expansion

The advent of cell culture-based methods for the establishment and expansion of human corneal endothelial cells (CEnC) has provided a source of transplantable corneal endothelium, with a significant potential to challenge the one donor-one recipient paradigm. However, concerns over cell identity remain, and a comprehensive characterization of the cultured CEnC across serial passages has not been performed. To this end, we compared two established CEnC culture methods by assessing the transcriptomic changes that occur during in vitro expansion. In confluent monolayers, low mitogenic culture conditions preserved corneal endothelial cell state identity better than culture in high mitogenic conditions. Expansion by continuous passaging induced replicative cell senescence. Transcriptomic analysis of the senescent phenotype identified a cell senescence signature distinct for CEnC. We identified activation of both classic and new cell signaling pathways that may be targeted to prevent senescence, a significant barrier to realizing the potential clinical utility of in vitro expansion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The Calpain-7 protease functions together with the ESCRT-III protein IST1 within the midbody to regulate the timing and completion of abscission

The Endosomal Sorting Complexes Required for Transport (ESCRT) machinery mediates the membrane fission step that completes cytokinetic abscission and separates dividing cells. Filaments composed of ESCRT-III subunits constrict membranes of the intercellular bridge midbody to the abscission point. These filaments also bind and recruit cofactors whose activities help execute abscission and/or delay abscission timing in response to mitotic errors via the NoCut/Abscission checkpoint. We previously showed that the ESCRT-III subunit IST1 binds the cysteine protease Calpain-7 (CAPN7) and that CAPN7 is required for both efficient abscission and NoCut checkpoint maintenance. Here, we report biochemical and crystallographic studies showing that the tandem microtubule-interacting and trafficking (MIT) domains of CAPN7 bind simultaneously to two distinct IST1 MIT interaction motifs. Structure-guided point mutations in either CAPN7 MIT domain disrupted IST1 binding in vitro and in cells, and depletion/rescue experiments showed that the CAPN7-IST1 interaction is required for (1) CAPN7 recruitment to midbodies, (2) efficient abscission, and (3) NoCut checkpoint arrest. CAPN7 proteolytic activity is also required for abscission and checkpoint maintenance. Hence, IST1 recruits CAPN7 to midbodies, where its proteolytic activity is required to regulate and complete abscission.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2012

GERMcode: A Stochastic Model for Space Radiation Risk Assessment

A new computer model, the GCR Event-based Risk Model code (GERMcode), was developed to describe biophysical events from high-energy protons and high charge and energy (HZE) particles that have been studied at the NASA Space Radiation Laboratory (NSRL) for the purpose of simulating space radiation biological effects. In the GERMcode, the biophysical description of the passage of HZE particles in tissue and shielding materials is made with a stochastic approach that includes both particle track structure and nuclear interactions. The GERMcode accounts for the major nuclear interaction processes of importance for describing heavy ion beams, including nuclear fragmentation, elastic scattering, and knockout-cascade processes by using the quantum multiple scattering fragmentation (QMSFRG) model. The QMSFRG model has been shown to be in excellent agreement with available experimental data for nuclear fragmentation cross sections. For NSRL applications, the GERMcode evaluates a set of biophysical properties, such as the Poisson distribution of particles or delta-ray hits for a given cellular area and particle dose, the radial dose on tissue, and the frequency distribution of energy deposition in a DNA volume. By utilizing the ProE/Fishbowl ray-tracing analysis, the GERMcode will be used as a bi-directional radiation transport model for future spacecraft shielding analysis in support of Mars mission risk assessments. Recent radiobiological experiments suggest the need for new approaches to risk assessment that include time-dependent biological events due to the signaling times for activation and relaxation of biological processes in cells and tissue. Thus, the tracking of the temporal and spatial distribution of events in tissue is a major goal of the GERMcode in support of the simulation of biological processes important in GCR risk assessments. In order to validate our approach, basic radiobiological responses such as cell survival curves, mutation, chromosomal aberrations, and representative mouse tumor induction curves are implemented into the GERMcode. Extension of these descriptions to other endpoints related to non-targeted effects and biochemical pathway responses will be discussed.

Kim, Myung-Hee Y.↗
DOE OSTI2021

Chromosome compartmentalization alterations in prostate cancer cell lines model disease progression

Prostate cancer aggressiveness and metastatic potential are influenced by gene expression and genomic aberrations, features that can be influenced by the 3D structure of chromosomes inside the nucleus. Using chromosome conformation capture (Hi-C), we conducted a systematic genome architecture comparison on a cohort of cell lines that model prostate cancer progression, from normal epithelium to bone metastasis. We describe spatial compartment identity (A-open versus B-closed) changes with progression in these cell lines and their relation to gene expression changes in both cell lines and patient samples. In particular, 48 gene clusters switch from the B to the A compartment, including androgen receptor, WNT5A, and CDK14. These switches are accompanied by changes in the structure, size, and boundaries of topologically associating domains (TADs). Further, compartment changes in chromosome 21 are exacerbated with progression and may explain, in part, the genesis of the TMPRSS2-ERG translocation. These results suggest that discrete 3D genome structure changes play a deleterious role in prostate cancer progression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structural insights into transcriptional regulation by the helicase RECQL5

Abstract Transcription poses a major challenge for genome stability. The RECQL5 helicase helps safeguard genome integrity and is the only member of the human RecQ helicase family that directly binds to RNA polymerase II (Pol II) and affects its progression. While RECQL5 mitigates transcription stress in cells, the molecular mechanism underlying this phenomenon is unclear. Here, we use cryo-electron microscopy to determine the structures of stalled human Pol II elongation complexes (ECs) bound to RECQL5. Our structures reveal the molecular interactions stabilizing RECQL5 binding to the Pol II EC and highlight its role as a transcriptional roadblock. Additionally, we find that, in its nucleotide-free state, RECQL5 twists the downstream DNA in the EC and, upon nucleotide binding, undergoes a conformational change that allosterically induces Pol II toward a post-translocation state. We propose that this mechanism may help restart Pol II elongation and, therefore, contribute to reducing transcription stress.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Investigating the Interaction Between Circulating Tumor Cells and Local Hydrodynamics via Experiment and Simulations

Introduction: The biological and mechanical properties of circulating tumor cells (CTCs) in combination with the hemodynamics affect the preference of metastatic sites in the vasculature. Despite the extensive literature on the effects of biological properties on cell adhesion, the effects of hydrodynamic forces on primary attachment remains an active area of research. Here, using simulations in conjunction with experimentation, we provide new insight into the interplay of CTCs dynamics and local hydrodynamics. Methods: A flow experiment of CTC attachment was performed within a bioprinted, double branching endothelialized vessel. Simulations of fluid flow and CTC transport in the reconstructed and idealized bifurcated vessel were respectively performed by HARVEY, our in-house massively parallel computational fluid dynamics solver. HARVEY is based on the lattice Boltzmann and finite element methods to model the fluid and cells dynamics. The immersed boundary method is employed for resolving the fluid–structure interaction. Results: CTC attachment was quantified experimentally at all regions of the complex vessel. The results demonstrate a clear preference for CTCs to attach at the branch points. To elucidate the effect of the vessel topology on the location of attachment, a fluid-only simulation was performed assessing the differences in the hydrodynamics along the vessel. CTC transport in idealized bifurcated vessels was subsequently studied to examine the effects of cell deformability on the local hydrodynamics patterns and, thus, the preference of attachment sites. Conclusions: The current work provides evidence on the correlation of the hydrodynamics forces arising from the vessel topology and CTC properties on the attachment regions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

PyZebrascope: An Open-Source Platform for Brain-Wide Neural Activity Imaging in Zebrafish

Understanding how neurons interact across the brain to control animal behaviors is one of the central goals in neuroscience. Recent developments in fluorescent microscopy and genetically-encoded calcium indicators led to the establishment of whole-brain imaging methods in zebrafish, which record neural activity across a brain-wide volume with single-cell resolution. Pioneering studies of whole-brain imaging used custom light-sheet microscopes, and their operation relied on commercially developed and maintained software not available globally. Hence it has been challenging to disseminate and develop the technology in the research community. Here, we present PyZebrascope, an open-source Python platform designed for neural activity imaging in zebrafish using light-sheet microscopy. PyZebrascope has intuitive user interfaces and supports essential features for whole-brain imaging, such as two orthogonal excitation beams and eye damage prevention. Its camera module can handle image data throughput of up to 800 MB/s from camera acquisition to file writing while maintaining stable CPU and memory usage. Its modular architecture allows the inclusion of advanced algorithms for microscope control and image processing. As a proof of concept, we implemented a novel automatic algorithm for maximizing the image resolution in the brain by precisely aligning the excitation beams to the image focal plane. PyZebrascope enables whole-brain neural activity imaging in fish behaving in a virtual reality environment. Thus, PyZebrascope will help disseminate and develop light-sheet microscopy techniques in the neuroscience community and advance our understanding of whole-brain neural dynamics during animal behaviors.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

Impact of Radiation Quality on Microdosimetry Calculation

Microdosimetry consists of studying energy deposition events in irradiated targets of volume typically of the order of a cell. The probability density 𝑓(𝑧,𝐷) of energy deposition𝑧(specific energy) in a target, exposed to an irradiation dose 𝐷,can be used to correlate inhomogeneous energy deposition events at the micro-scale(track structure)with biological responses(e.g., cell injury)[1]. Microdosimetry studies allow a better understanding of basic mechanisms of the biological response, such as the origin of the increased biological effectiveness of high Linear Energy Transfer (LET) ions, partly responsible of radiation-exposure induced cancer risks of astronauts [2].

F. Poignant↗
DOE OSTI2021

Association of human T-cell leukemia virus type 1 with prevalent rheumatoid arthritis among atomic bomb survivors: A cross-sectional study

Previous studies have suggested that human T-cell leukemia virus type 1 (HTLV-1) might act as a pathogen in rheumatoid arthritis (RA), but epidemiological evidence of an association is scarce. We measured anti-HTLV-1 antibodies among Nagasaki atomic bomb survivors to determine whether HTLV-1 is related to RA and whether radiation exposure is associated with HTLV-1 and RA prevalence. This is a cross-sectional study among atomic bomb survivors who participated in biennial health examinations from 2006 to 2010. Serum levels of anti-HTLV-1 antibodies were measured using a chemiluminescent enzyme immunoassay and confirmed by Western blotting. Association between HTLV-1 and RA was analyzed by a logistic regression model. Of 2091 participants (women 61.5%; median age, 73 years), 215 (10.3%) had anti-HTLV-1 antibodies. HTLV-1 prevalence was higher among women (13.1% vs 5.8%; P<.001). Twenty-two participants (1.1%) were diagnosed with RA. HTLV-1 prevalence among RA participants was significantly higher than that among non-RA participants (27.3% vs 10.1%; P=.020). After adjustment for age, sex, and hepatitis C virus infection, HTLV-1 was significantly associated with prevalent RA (odds ratio, 2.89; 95% confidence interval, 1.06, 7.03). There was no association between radiation dose and either the prevalence of HTLV-1 or RA. This study, among a well-defined group of atomic bomb survivors, suggests that HTLV-1 is associated with RA. Abbreviations: AHS = Adult Health Study, ATL/ATLL = adult T cell leukemia/lymphoma, bioDMARDs = biological disease modifying antirheumatic drugs, CCP = cyclic citrullinated peptide, CI = confidence interval, CLEIA = chemiluminescent enzyme immunoassay, CRP = C-reactive protein, csDMARDs = conventional synthetic disease modifying antirheumatic drugs, Gy = gray, HCV = hepatitis C virus, HTLV-1 = human T-cell leukemia virus type 1, IF = immunofluorescent, RA = rheumatoid arthritis, RERF = Radiation Effects Research Foundation, RF = rheumatoid factor, SS = Sjogren syndrome.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1996

Gravitational physiology of human immune cells: a review of in vivo, ex vivo and in vitro studies

The study of the function of immune cells in microgravity has been studied for more than 20 years in several laboratories. It is clear today that the immune system is depressed in more than 50% of the astronauts during and after space flight and that the activation of T lymphocytes by mitogens in vitro changes dramatically. This article gives an overview of the gravitational studies conducted by our laboratory in Spacelab, in MIR station, in sounding rockets and on the ground in the clinostat and the centrifuge. Three experimental approaches are followed in our work: (i) Ex vivo studies are performed with blood samples drawn from astronauts; (ii) in vivo studies are based on the application of seven antigens to the skin of the astronauts; (iii) in vitro studies are carried out with immune cells purified from the blood of healthy donors (not astronauts). The data from our in vivo and ex vivo studies are in agreement with those of other laboratories and show that the immunological function is depressed in the majority of astronauts as a consequence of the stress of space flight rather than by a direct influence of gravity on the cell. Immune depression may become a critical hazard on long duration flights on space stations or to other planets. In vitro experiments show that cultures of free-floating lymphocytes and monocytes undergo a dramatic depression of activation by the mitogen concanavalin A, while activation is more than doubled when the cells are attached to microcarrier beads. Such effects may be attributed to both direct and indirect effects of gravitational unloading on basic biological mechanisms of the cell. While the in vitro data are very important to clarify certain aspects of the biological mechanism of T cells activation, they are not descriptive of the changes of the immunological function of the astronauts.

Review↗
DOE OSTI2025

An elastin-like polymer targeting vascular endothelial growth factor receptor-1 reduces survival in serum-starved endothelial cells

Peptides often exhibit biological activity that depends on the context in which they are displayed and delivered. Understanding and controlling these contextual effects on peptide function is critical for designing targeted and responsive peptide-based biomaterials and therapeutics. Genetically engineered protein polymers such as elastin-like polypeptides (ELPs) can incorporate bioactive peptide motifs and are attractive candidates for biomaterials used in tissue engineering and targeted drug delivery. They also present an opportunity for investigating and modulating cell signaling pathways by presenting a peptide ligand in various defined chemical and physical environments. Vascular endothelial growth factor receptor-1 (VEGFR1) signaling plays important and complex roles in cell survival and angiogenesis, but polymeric materials that interact with this signaling axis are scarce. In this study, a novel genetically engineered elastin-like polymer that targets VEGFR1 is characterized. This polymer, termed R1B-ELP, binds to human endothelial cells in a manner dependent on its VEGFR1-targeting motif and, based on cell proliferation and cytotoxicity assays, demonstrates activity consistent with disrupting pro-survival signaling necessary for endothelial cell function under conditions of environmental stress. Notably, these findings indicate that ELP fusion alters the functional behavior of the targeting peptide. Modulators of VEGFR1 signaling have potential applications in basic studies of angiogenesis as well as in therapeutic applications targeting vascular or inflammatory diseases.

36 MATERIALS SCIENCE↗
NASA NTRSDate not supplied

Microbial Responses to Radiation at the Single-Cell Level

Exploring the biological effects of deep space radiation is crucial for developing protective protocols for humans traveling beyond Earth’s magnetosphere. Saccharomyces cerevisiae, or budding yeast, is an ideal model organism to study the effects of radiation on eukaryotes as it shares several pathways with humans, including DNA repair mechanisms. Here, we used time-lapse imaging of colony growth on agar plates to monitor the effects of radiation exposure on individual yeast cells and their progeny.

Paola J. Maldonado Martinez↗
NASA NTRS2008

Non-DBS DNA Repair Genes Regulate Radiation-induced Cytogenetic Damage Repair and Cell Cycle Progression

Changes of gene expression profile are one of the most important biological responses in living cells after ionizing radiation (IR) exposure. Although some studies have shown that genes up-regulated by IR may play important roles in DNA damage repair, the relationship between the regulation of gene expression by IR, particularly genes not known for their roles in DSB repair, and its impact on cytogenetic responses has not been systematically studied. In the present study, the expression of 25 genes selected on the basis of their transcriptional changes in response to IR was individually knocked down by transfection with small interfering RNA in human fibroblast cells. The purpose of this study is to identify new roles of these selected genes on regulating DSB repair and cell cycle progression , as measured in the micronuclei formation and chromosome aberration. In response to IR, the formation of MN was significantly increased by suppressed expression of 5 genes: Ku70 in the DSB repair pathway, XPA in the NER pathway, RPA1 in the MMR pathway, and RAD17 and RBBP8 in cell cycle control. Knocked-down expression of 4 genes (MRE11A, RAD51 in the DSB pathway, SESN1, and SUMO1) significantly inhibited cell cycle progression, possibly because of severe impairment of DNA damage repair. Furthermore, loss of XPA, P21, or MLH1 expression resulted in both significantly enhanced cell cycle progression and increased yields of chromosome aberrations, indicating that these gene products modulate both cell cycle control and DNA damage repair. Most of the 11 genes that affected cytogenetic responses are not known to have clear roles influencing DBS repair. Nine of these 11 genes were up-regulated in cells exposed to gamma radiation, suggesting that genes transcriptionally modulated by IR were critical to regulate the biological consequences after IR.

Zhang, Ye↗