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At least 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

A Viable New Strategy for the Discovery of Peptide Proteolytic Cleavage Products in Plant-Microbe Interactions

Small peptides that are proteolytic cleavage products (PCPs) of less than 100 amino acids are emerging as key signaling molecules that mediate cell-to-cell communication and biological processes that occur between and within plants, fungi, and bacteria. Yet, the discovery and characterization of these molecules is largely overlooked. Today, selective enrichment and subsequent characterization by mass spectrometry–based sequencing offers the greatest potential for their comprehensive characterization, however qualitative and quantitative performance metrics are rarely captured. Herein, we addressed this need by benchmarking the performance of an enrichment strategy, optimized specifically for small PCPs, using state-of-the-art de novo–assisted peptide sequencing. As a case study, we implemented this approach to identify PCPs from different root and foliar tissues of the hybrid poplar Populus × canescens 717-1B4 in interaction with the ectomycorrhizal basidiomycete Laccaria bicolor . In total, we identified 1,660 and 2,870 Populus and L. bicolor unique PCPs, respectively. Qualitative results supported the identification of well-known PCPs, like the mature form of the photosystem II complex 5-kDa protein (approximately 3 kDa). A total of 157 PCPs were determined to be significantly more abundant in root tips with established ectomycorrhiza when compared with root tips without established ectomycorrhiza and extramatrical mycelium of L. bicolor . These PCPs mapped to 64 Populus proteins and 69 L. bicolor proteins in our database, with several of them previously implicated in biologically relevant associations between plant and fungus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Leveraging Topological Events in Tracking Graphs for Understanding Particle Diffusion

Abstract Single particle tracking (SPT) of fluorescent molecules provides significant insights into the diffusion and relative motion of tagged proteins and other structures of interest in biology. However, despite the latest advances in high‐resolution microscopy, individual particles are typically not distinguished from clusters of particles. This lack of resolution obscures potential evidence for how merging and splitting of particles affect their diffusion and any implications on the biological environment. The particle tracks are typically decomposed into individual segments at observed merge and split events, and analysis is performed without knowing the true count of particles in the resulting segments. Here, we address the challenges in analyzing particle tracks in the context of cancer biology. In particular, we study the tracks of KRAS protein, which is implicated in nearly 20% of all human cancers, and whose clustering and aggregation have been linked to the signaling pathway leading to uncontrolled cell growth. We present a new analysis approach for particle tracks by representing them as tracking graphs and using topological events – merging and splitting, to disambiguate the tracks. Using this analysis, we infer a lower bound on the count of particles as they cluster and create conditional distributions of diffusion speeds before and after merge and split events. Using thousands of time‐steps of simulated and in‐vitro SPT data, we demonstrate the efficacy of our method, as it offers the biologists a new, detailed look into the relationship between KRAS clustering and diffusion speeds.

McDonald, T.↗
DOE OSTI2022

SNF1-related protein kinase 1 represses Arabidopsis growth through post-translational modification of E2Fa in response to energy stress

Cellular sugar starvation and/or energy deprivation serves as an important signaling cue for the live cells to trigger the necessary stress adaptation response. When exposed to cellular energy stress (ES) conditions, the plants reconfigure metabolic pathways and rebalance energy status while restricting vegetative organ growth. Despite the vital importance of this ES-induced growth restriction, the regulatory mechanism underlying the response remains largely elusive in plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Methodology of the Extraction of Multi-Differential Cross Sections of Charged-Current $\nu_\mu$-Argon Interactions in MicroBooNE Using Wire-Cell $\nu_\mu$CC Selection

Neutrino physics experiments rely on accurate nuclear-interaction models that are in part guided by experimental observations. Multi-differential cross section measurements are particularly valuable for exploring the underlying physics described in these models, making them a significant step forward in the field. This note presents methodology in preparation to unfold neutrino flux-averaged double and triple-differential cross sections of the inclusive muon neutrino charged-current interaction on Argon. This work builds upon the existing framework and methodology presented in recent energy dependent cross section measurements at MicroBooNE using the Wire-Cell tomographic event reconstruction. The signal definition, choice of binning, and handling of estimated detector uncertainties are discussed, and the MicroBooNE simulation model is validated over the multi-dimensional phase space of muon momentum, muon polar angle, and visible hadronic energy.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Centriole and transition zone structures in photoreceptor cilia revealed by cryo-electron tomography

Primary cilia mediate sensory signaling in multiple organisms and cell types but have structures adapted for specific roles. Structural defects in them lead to devastating diseases known as ciliopathies in humans. Key to their functions are structures at their base: the basal body, the transition zone, the “Y-shaped links,” and the “ciliary necklace.” We have used cryo-electron tomography with subtomogram averaging and conventional transmission electron microscopy to elucidate the structures associated with the basal region of the “connecting cilia” of rod outer segments in mouse retina. The longitudinal variations in microtubule (MT) structures and the lumenal scaffold complexes connecting them have been determined, as well as membrane-associated transition zone structures: Y-shaped links connecting MT to the membrane, and ciliary beads connected to them that protrude from the cell surface and form a necklace-like structure. These results represent a clearer structural scaffold onto which molecules identified by genetics, proteomics, and superresolution fluorescence can be placed in our emerging model of photoreceptor sensory cilia.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1980

Fast-response atmospheric-pollutant monitor

Fast infrared spectrometer measures atmospheric C0, CH4, and HC1 over range of 1 to 12 ppm. With modifications it could measure other pollutants and use natural light as source. Cell filled with sample to be measured filters out spectral lines of interest. Infrared beam passes through rotating cell holder that produces chopped signals at two frequencies. Difference in signal amplitudes depends on amount of test gas in sample. Signal processing circuitry amplifies and separates test-gas and reference signals.

Sebacher, D. I.↗
NASA NTRS1985

Brewster-plate spoiler - A novel method for reducing the amplitude of interference fringes that limit tunable-laser absorption sensitivities

A simple method is described for substantially reducing the amplitude of interference fringes that limit the sensitivities of tunable-laser high-resolution absorption spectrometers. A lead-salt diode laser operating in the 7-micron region is used with a single Brewster-plate spoiler to reduce the fringe amplitude by a factor of 30 and also to allow the detection of absorptances 0.001 percent in a single laser scan without subtraction techniques, without complex frequency modulation, and without distortion of the molecular line-shape signals. Application to multipass-cell spectrometers is described.

Webster, C. R.↗
NASA NTRS1988

Mineralogical and geochemical anomalous data of the K-T boundary samples

Cretaceous-Tertiary boundary problem has been discussed previously from the geological research, mainly by fossil changes. Although geochemical bulk data of Ir anomaly suggest the extraterrestrial origin of the K-T boundary, the exact formation process discussed mainly by mineralogical and geochemical study has been started recently, together with noble gas contents. The K-T boundary sample at Kawaruppu River, Hokkaido was collected, in order to compare with the typical K-T boundary samples of Bubbio, Italy, Stevns Klint, Denmark, and El Kef, Tunisia. The experimental data of the silicas and calcites in these K-T boundary samples were obtained from the X-ray unit-cell dimension (i.e., density), ESR signal and total linear absorption coefficient, as well as He and Ne contents. The K-T boundary samples are usually complex mixture of the terrestrial activities after the K-T boundary event. The mineralogical and geochemical anomalous data indicate special terrestrial atmosphere at the K-T boundary formation probably induced by asteroid impact, followed the many various terrestrial activities (especially the strong role of sea-water mixture, compared with terrestrial highland impact and impact craters in the other earth-type planetary bodies).

Miura, Y.↗
NASA NTRS1988

Elimination of pressure-induced fluorescence in diamond anvils

At pressures above one megabar (100 GPa) in high-pressure diamond anvil cell experiments, the ruby fluorescence signal needed for pressure calibration is increasingly difficult to measure. A primary cause of this difficulty is the presence of an intense pressure-induced diamond fluorescence. A tentative identification of this pressure-induced fluorescence is given, a technique for the elimination of this fluorescence is reported. It is demonstrated that weak ruby signals, completely hidden by diamond fluorescence, are now easily measured with this technique.

Eggert, Jon H.↗
NASA NTRS2004

Studies of Pressure-Broadening of Alkali Atom Resonance Lines for Modeling Atmospheres of Extrasolar Giant Planets and Brown Dwarfs

In L-dwarfs and T-dwarfs the resonance lines of sodium and potassium are so profoundly pressure-broadened that their wings extend several hundred nanometers from line center. With accurate knowledge of the line profiles as a function of temperature and pressure: such lines can prove to be valuable diagnostics of the atmospheres of such objects. We have initiated a joint program of theoretical and experimental research to study the line-broadening of alkali atom resonance lines due to collisions with species such as helium and molecular hydrogen. Although potassium and sodium are the alkali species of most interest in the atmospheres of cool brown dwarfs and extrasolar giant planets, some of our theoretical focus this year has involved the calculation of pressure-broadening of lithium resonance lines by He, as a test of a newly developed suite of computer codes. In addition, theoretical calculations have been carried out to determine the leading long range van der Waals coefficients for the interactions of ground and excited alkali metal atoms with helium atoms, to within a probable error of 2%. Such data is important in determining the behavior of the resonance line profiles in the far wings. Important progress has been made on the experimental aspects of the program since the arrival of a postdoctoral fellow in September. A new absorption cell has been designed, which incorporates a number of technical improvements over the previous cell, including a larger cell diameter to enhance the signal, and fittings which allow for easier cleaning, thereby significantly reducing the instrument down-time.

Kirby, Kate↗
NASA NTRS2001

The anabolic activity of bone tissue, suppressed by disuse, is normalized by brief exposure to extremely low-magnitude mechanical stimuli

It is generally believed that mechanical signals must be large in order to be anabolic to bone tissue. Recent evidence indicates, however, that extremely low-magnitude (<10 microstrain) mechanical signals readily stimulate bone formation if induced at a high frequency. We examined the ability of extremely low-magnitude, high-frequency mechanical signals to restore anabolic bone cell activity inhibited by disuse. Adult female rats were randomly assigned to six groups: baseline control, age-matched control, mechanically stimulated for 10 min/day, disuse (hind limb suspension), disuse interrupted by 10 min/day of weight bearing, and disuse interrupted by 10 min/day of mechanical stimulation. After a 28 day protocol, bone formation rates (BFR) in the proximal tibia of mechanically stimulated rats increased compared with age-matched control (+97%). Disuse alone reduced BFR (-92%), a suppression only slightly curbed when disuse was interrupted by 10 min of weight bearing (-61%). In contrast, disuse interrupted by 10 min per day of low-level mechanical intervention normalized BFR to values seen in age-matched controls. This work indicates that this noninvasive, extremely low-level stimulus may provide an effective biomechanical intervention for the bone loss that plagues long-term space flight, bed rest, or immobilization caused by paralysis.

Non-NASA Center↗
NASA NTRS2001

Osteoblasts respond to pulsatile fluid flow with short-term increases in PGE(2) but no change in mineralization

Although there is no consensus as to the precise nature of the mechanostimulatory signals imparted to the bone cells during remodeling, it has been postulated that deformation-induced fluid flow plays a role in the mechanotransduction pathway. In vitro, osteoblasts respond to fluid shear stress with an increase in PGE(2) production; however, the long-term effects of fluid shear stress on cell proliferation and differentiation have not been examined. The goal of this study was to apply continuous pulsatile fluid shear stresses to osteoblasts and determine whether the initial production of PGE(2) is associated with long-term biochemical changes. The acute response of bone cells to a pulsatile fluid shear stress (0.6 +/- 0.5 Pa, 3.0 Hz) was characterized by a transient fourfold increase in PGE(2) production. After 7 days of static culture (0 dyn/cm(2)) or low (0.06 +/- 0.05 Pa, 0.3 Hz) or high (0.6 +/- 0.5 Pa, 3.0 Hz) levels of pulsatile fluid shear stress, the bone cells responded with an 83% average increase in cell number, but no statistical difference (P > 0.53) between the groups was observed. Alkaline phosphatase activity per cell decreased in the static cultures but not in the low- or high-flow groups. Mineralization was also unaffected by the different levels of applied shear stress. Our results indicate that short-term changes in PGE(2) levels caused by pulsatile fluid flow are not associated with long-term changes in proliferation or mineralization of bone cells.

NASA Discipline Musculoskeletal↗
NASA NTRS2001

Demonstration of prominent actin filaments in the root columella

The distribution of actin filaments within the gravity-sensing columella cells of plant roots remains poorly understood, with studies over numerous years providing inconsistent descriptions of actin organization in these cells. This uncertainty in actin organization, and thus in actin's role in graviperception and gravisignaling, has led us to investigate actin arrangements in the columella cells of Zea mays L., Medicago truncatula Gaertn., Linum usitatissiilium L. and Nicotianla benthamiana Domin. Actin organization was examined using a combination of optimized immunofluorescence techniques, and an improved fluorochrome-conjugated phalloidin labeling method reliant on 3-maleimidobenzoyl-N-hydroxy-succinimide ester (MBS) cross-linking combined with glycerol permeabilization. Confocal microscopy of root sections labeled with anti-actin antibodies revealed patterns suggestive of actin throughout the columella region. These patterns included short and fragmented actin bundles, fluorescent rings around amyloplasts and intense fluorescence originating from the nucleus. Additionally, confocal microscopy of MBS-stabilized and Alexa Fluor-phalloidin-labeled root sections revealed a previously undetected state of actin organization in the columella. Discrete actin structures surrounded the amyloplasts and prominent actin cables radiated from the nuclear surface toward the cell periphery. Furthermore, the cortex of the columella cells contained fine actin bundles (or single filaments) that had a predominant transverse orientation. We also used confocal microscopy of plant roots expressing endoplasmic reticulum (ER)-targeted green fluorescent protein to demonstrate rapid ER movements within the columella cells, suggesting that the imaged actin network is functional. The successful identification of discrete actin structures in the root columella cells forms the perception and signaling.

Non-NASA Center↗
NASA NTRS2000

Quantitative image analysis of laminin immunoreactivity in skin basement membrane irradiated with 1 GeV/nucleon iron particles

We previously reported that laminin immunoreactivity in mouse mammary epithelium is altered shortly after whole-body irradiation with 0.8 Gy from 600 MeV/nucleon iron ions but is unaffected after exposure to sparsely ionizing radiation. This observation led us to propose that the effect could be due to protein damage from the high ionization density of the ion tracks. If so, we predicted that it would be evident soon after radiation exposure in basement membranes of other tissues and would depend on ion fluence. To test this hypothesis, we used immunofluorescence, confocal laser scanning microscopy, and image segmentation techniques to quantify changes in the basement membrane of mouse skin epidermis. At 1 h after exposure to 1 GeV/nucleon iron ions with doses from 0.03 to 1.6 Gy, neither the visual appearance nor the mean pixel intensity of laminin in the basement membrane of mouse dorsal skin epidermis was altered compared to sham-irradiated tissue. This result does not support the hypothesis that particle traversal directly affects laminin protein integrity. However, the mean pixel intensity of laminin immunoreactivity was significantly decreased in epidermal basement membrane at 48 and 96 h after exposure to 0.8 Gy 1 GeV/nucleon iron ions. We confirmed this effect with two additional antibodies raised against affinity-purified laminin 1 and the E3 fragment of the long-arm of laminin 1. In contrast, collagen type IV, another component of the basement membrane, was unaffected. Our studies demonstrate quantitatively that densely ionizing radiation elicits changes in skin microenvironments distinct from those induced by sparsely ionizing radiation. Such effects may might contribute to the carcinogenic potential of densely ionizing radiation by altering cellular signaling cascades mediated by cell-extracellular matrix interactions.

Non-NASA Center↗
NASA NTRS1999

The kinetics of translocation and cellular quantity of protein kinase C in human leukocytes are modified during spaceflight

Protein kinase C (PKC) is a family of serine/threonine kinases that play an important role in mediating intracellular signal transduction in eukaryotes. U937 cells were exposed to microgravity during a space shuttle flight and stimulated with a radiolabeled phorbol ester ([3H]PDBu) to both specifically label and activate translocation of PKC from the cytosol to the particulate fraction of the cell. Although significant translocation of PKC occurred at all g levels, the kinetics of translocation in flight were significantly different from those on the ground. In addition, the total quantity of [3H]PDBu binding PKC was increased in flight compared to cells at 1 g on the ground, whereas the quantity in hypergravity (1.4 g) was decreased with respect to 1 g. Similarly, in purified human peripheral blood T cells the quantity of PKCdelta varied in inverse proportion to the g level for some experimental treatments. In addition to these novel findings, the results confirm earlier studies which showed that PKC is sensitive to changes in gravitational acceleration. The mechanisms of cellular gravisensitivity are poorly understood but the demonstrated sensitivity of PKC to this stimulus provides us with a useful means of measuring the effect of altered gravity levels on early cell activation events.

short duration↗
NASA NTRS1995

Root gravitropism

When a plant root is reoriented within the gravity field, it responds by initiating a curvature which eventually results in vertical growth. Gravity sensing occurs primarily in the root tip. It may involve amyloplast sedimentation in the columella cells of the root cap, or the detection of forces exerted by the mass of the protoplast on opposite sides of its cell wall. Gravisensing activates a signal transduction cascade which results in the asymmetric redistribution of auxin and apoplastic Ca2+ across the root tip, with accumulation at the bottom side. The resulting lateral asymmetry in Ca2+ and auxin concentration is probably transmitted to the elongation zone where differential cellular elongation occurs until the tip resumes vertical growth. The Cholodny-Went theory proposes that gravity-induced auxin redistribution across a gravistimulated plant organ is responsible for the gravitropic response. However, recent data indicate that the gravity-induced reorientation is more complex, involving both auxin gradient-dependent and auxin gradient-independent events.

NASA Discipline Plant Biology↗
NASA NTRS1992

Nystagmus induced by electrical stimulation of the vestibular and prepositus hypoglossi nuclei in the monkey: evidence for site of induction of velocity storage

Electrical stimulation of the vestibular nuclei (VN) and prepositus hypoglossi nuclei (PPH) of alert cynomolgus monkeys evoked nystagmus and eye deviation while they were in darkness. At some sites in VN, nystagmus and after-nystagmus were induced with characteristics suggesting that velocity storage had been excited. We analyzed these responses and compared them to the slow component of optokinetic nystagmus (OKN) and to optokinetic after-nystagmus (OKAN). We then recorded unit activity in VN and determined which types of nystagmus would be evoked from the sites of recording. Nystagmus and eye deviations were also elicited by electrical stimulation of PPH, and we characterized the responses where unit activity was recorded in PPH. Horizontal slow phase velocity of the VN "storage" responses was contralateral to the side of stimulation. The rising time constants and peak steady-state velocities were similar to those of OKN, and the falling time constants of the after-nystagmus and of OKAN were approximately equal. Both the induced after-nystagmus and OKAN were habituated by stimulation of the VN. When horizontal after-nystagmus was evoked with animals on their sides, it developed yaw and pitch components that tended to shift the vector of the slow phase velocity toward the spatial vertical. Similar "cross-coupling" occurs for horizontal OKAN or for vestibular post-rotatory nystagmus elicited in tilted positions. Thus, the storage component of nystagmus induced by VN stimulation had the same characteristics as the slow component of OKN and the VOR. Positive stimulus sites for inducing nystagmus with typical storage components were located in rostral portions of VN. They lay in caudal ventral superior vestibular nucleus (SVN), dorsal portions of central medial vestibular nucleus (MVN) caudal to the abducens nuclei and in adjacent lateral vestibular nucleus (LVN). More complex stimulus responses, but with contralateral after-nystagmus, were induced from surrounding regions of ventral MVN and LVN, rostral descending vestibular nucleus and the marginal zone between MVN and PPH. Vestibular-only (VO), vestibular plus saccade (VPS) and tonic vestibular pause (TVP) units were identified by extracellular recording. Stimulation near type I lateral and vertical canal-related VO units elicited typical "storage" responses with after-nystagmus in 23 of 29 tracks (79%). Stimulus responses were more complex from the region of neurons with oculomotor-related signals, i.e., TVP or VPS cells, although after-nystagmus was also elicited from these sites. Effects of vestibular nerve and nucleus stimulation were compared.(ABSTRACT TRUNCATED AT 400 WORDS).

NASA Discipline Neuroscience↗