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At least 523 records · Page 29

Ultrastructure of the Endoplasmic Reticulum in Eukaryotic Microalgae

ABSTRACT The endoplasmic reticulum (ER) is a large and highly dynamic component of the eukaryotic endomembrane system. In eukaryotic microalgae, it plays six distinct roles: (1) It envelopes the chromatin to form thenucleus. (2) It forms cisternae in the cytoplasm, some of which scaffold the synthesis of proteins destined for incorporation into membranes or for secretion. (3) It associates withGolgicisternae to scaffold the synthesis of glycosylated proteins. (4) It associates with theplasma membraneto mediate the synthesis and secretion of hydrophobic molecules. (5) It mediates the synthesis of cytoplasmiclipid bodies. (6) In lineages harboring complex plastids of red algal ancestry, it forms thechloroplast ER, which envelops the primary chloroplast envelope. In this review, these systems are illustrated using the quick‐freeze deep‐etch electron microscopy (QFDEEM) technique, which lifts up the topological configurations adopted by this gossamer system. A key finding is that in all the complex microalgae examined except dinoflagellates, the inner nuclear envelope membrane associates directly with the plastid‐contiguous membrane of the chloroplast ER at foci designated as chloroplast‐nuclear junctions. These junctions may play a role in regulating the maintenance and physiology of the complex organelles.

Microbiology↗

Protein ubiquitination in plant peroxisomes

Protein ubiquitination regulates diverse cellular processes in eukaryotic organisms, from growth and development to stress response. Proteins subjected to ubiquitination can be found in virtually all subcellular locations and organelles, including peroxisomes, single-membrane and highly dynamic organelles ubiquitous in eukaryotes. Peroxisomes contain metabolic functions essential to plants and animals such as lipid catabolism, detoxification of reactive oxygen species (ROS), biosynthesis of vital hormones and cofactors, and photorespiration. Plant peroxisomes possess a complex proteome with functions varying among different tissue types and developmental stages, and during plant response to distinct environmental cues. However, how these diverse functions are regulated at the post-translational level is poorly understood, especially in plants. Here, in this review, we summarized current knowledge of the involvement of protein ubiquitination in peroxisome protein import, remodeling, pexophagy, and metabolism, focusing on plants, and referencing discoveries from other eukaryotic systems when relevant. Based on previous ubiquitinomics studies, we compiled a list of 56 ubiquitinated Arabidopsis peroxisomal proteins whose functions are associated with all the major plant peroxisomal metabolic pathways. This discovery suggests a broad impact of protein ubiquitination on plant peroxisome functions, therefore substantiating the need to investigate this significant regulatory mechanism in peroxisomes at more depths.

59 BASIC BIOLOGICAL SCIENCES↗

Correction and calibration of atmospheric impact observations in GOES GLM data

The Earth's atmosphere is impacted daily by both meteoroids and artificial objects. Calibrated observations of the emitted light at sufficiently high sampling rates can enable or improve the estimation of impactor attributes such as size, cohesion, trajectory, and composition, but are difficult to obtain owing to the unpredictability, brevity, and high dynamic (brightness) range of impacts. Ground-based camera systems have successfully monitored small regions of the atmosphere at video frame rates and with limited radiometric capabilities, but most impacts occur over the 70% of the Earth's surface covered by water and are therefore missed by these networks. The Geostationary Lightning Mapper (GLM) instruments aboard Geostationary Operational Environmental Satellites 16 and 17 provide near-hemispherical coverage at 500 frames per second. These data have been shown to contain the signatures of many independently confirmed impacts, often from both viewing angles simultaneously, and constitute an observational resource that is currently unparalleled in the public domain. NASA's Asteroid Threat Assessment Project has implemented an automated impact detection pipeline that processes data from GLM daily. Given a detected impact, the GLM data contain a wealth of information for use in quantitative follow-up analyses. However, impact events differ from lightning in ways that violate key assumptions built into GLM's design. The result is that GLM's onboard processing introduces errors into pixel observations of impact events and the calibrated energies near the periphery of the detector may be substantially overestimated. We present methods for mitigating these and other issues to produce a data product more suitable for impact analyses than the existing GLM lightning product.

58 GEOSCIENCES↗

Redox regulation in chloroplast thylakoid lumen: The pmf changes everything, again

Abstract Photosynthesis is the foundation of life on Earth. However, if not well regulated, it can also generate excessive reactive oxygen species (ROS), which can cause photodamage. Regulation of photosynthesis is highly dynamic, responding to both environmental and metabolic cues, and occurs at many levels, from light capture to energy storage and metabolic processes. One general mechanism of regulation involves the reversible oxidation and reduction of protein thiol groups, which can affect the activity of enzymes and the stability of proteins. Such redox regulation has been well studied in stromal enzymes, but more recently, evidence has emerged of redox control of thylakoid lumenal enzymes. This review/hypothesis paper summarizes the latest research and discusses several open questions and challenges to achieving effective redox control in the lumen, focusing on the distinct environments and regulatory components of the thylakoid lumen, including the need to transport electrons across the thylakoid membrane, the effects of pH changes by the proton motive force (pmf) in the stromal and lumenal compartments, and the observed differences in redox states. These constraints suggest that activated oxygen species are likely to be major regulatory contributors to lumenal thiol redox regulation, with key components and processes yet to be discovered.

Plant Sciences↗

Implementation and Verification of Cable Bending Stiffness in MoorDyn

The relatively large motions experienced by floating wind turbines and wave energy converters pose a challenge for power cables, whose internal components provide significant bending resistance and are sensitive to deformation. The behavior and associated design considerations of power cables in these highly dynamic applications make coupled analysis relevant for design. Bending stiffness capabilities have recently been added to the lumped-mass mooring dynamics model MoorDyn to enable simulation of dynamic power cables. MoorDyn is a common modeling choice for floating wind energy simulation (often coupled with OpenFAST) and floating wave energy converter simulation (often coupled with WEC-Sim) but the model’s previous line elasticity formulation only considered axial stiffness. To properly capture the dynamics of power cables, a bending stiffness model has been added that approximates cable curvature based on the difference in tangent vectors of adjacent elements. The resulting bending moment is realized by applying forces on adjacent nodes, enabling cable modeling while leaving the underlying lumped-mass formulation unchanged. In this paper, the new bending stiffness implementation is verified in static conditions against analytical solutions and then in a dynamic power cable scenario in comparison with the commercial simulator OrcaFlex. The dynamic scenario uses prescribed motions and includes wave loadings on the cable. Results indicate correct implementation of bending stiffness and show close agreement with OrcaFlex.

50 EE - Wind and Water Power Program - Water (EE-4↗

Exploring Novel Configuration Designs Alternatives for Lazy Wave Submarine Power Cables

Floating offshore wind turbines require a complex integrated design to balance the platform response and station-keeping requirements in a highly dynamic environment. Dynamic subsea power cables are one of the critical components that have to be considered in detail to ensure both extreme, as well as repeated operational conditions do not exceed the cable design limits. This paper presents the design feasibility limits of a 66kV dynamic cable for a lazy wave configuration. The work explores an innovative staggered cable configuration that has the potential to provide additional compliance in shallow water conditions. Both configurations are evaluated using the motions of a representative floating wind platform under development for deployment in relatively shallow water depth of 150m. The assessment was conducted using the hydrodynamic software Orcaflex, incorporating a range of design inputs and design variations. Key parameters analysed include cable curvature and effective tension and bending stress. The alternative cable configuration provides a more gradual crossing of the water column, which would allow to support increased platform excursions in shallow water depths. The design uses a combined buoyancy and bend protection element, offering designers additional options for challenging operational conditions. The paper will be of interest to designers and developers of floating wind projects, providing a comparative assessment between the conventional lazy wave configuration and an innovative alternative that enables larger cable and mooring excursion envelopes in challenging conditions.

16 TIDAL AND WAVE POWER↗

Methods and apparatus for comprehensive characterization of performance attributes and damage thresholds of ultrafast laser optics

It is presently well understood that the operational performance limits of optics are determined by three fundamental attributes: the initiation of laser-induced damage, the growth of damage sites, and the transient (nondamaging) modification of optical parameters. The comprehensive characterization of the performance limitations of ultrafast optics requires consideration of all three fundamental attributes. Here, the vast majority of literature to date, however, has focused primarily on damage-initiation and testing systems that are largely focused on determining the damage-initiation threshold under single- and multipulse excitation. In this work, we discuss a testing apparatus that was designed to offer the capability to adequately characterize all three of these performance attributes under femtosecond, near-infrared laser irradiation. Key aspects of methodology are discussed, including high-dynamic-range energy control, variable beam size, wavelength tunability, B-integral management, and functional performance characterization to explore the true operational limits of the components. Example results for a metal-dielectric mirror demonstrate the test station’s operation.

42 ENGINEERING↗

On the feasibility of polyurethane based 3D dosimeters with optical CT for dosimetric verification of low energy photon brachytherapy seeds

Purpose: To investigate the feasibility of and challenges yet to be addressed to measure dose from low energy (effective energy <50 keV) brachytherapy sources (Pd-103, Cs-131, and I-125) using polyurethane based 3D dosimeters with optical CT. Methods: The authors' evaluation used the following sources: models 200 (Pd-103), CS-1 Rev2 (Cs-131), and 6711 (I-125). The authors used the Monte Carlo radiation transport code MCNP5, simulations with the ScanSim optical tomography simulation software, and experimental measurements with PRESAGE{sup ®} dosimeters/optical CT to investigate the following: (1) the water equivalency of conventional (density = 1.065 g/cm{sup 3}) and deformable (density = 1.02 g/cm{sup 3}) formulations of polyurethane dosimeters, (2) the scatter conditions necessary to achieve accurate dosimetry for low energy photon seeds, (3) the change in photon energy spectrum within the dosimeter as a function of distance from the source in order to determine potential energy sensitivity effects, (4) the optimal delivered dose to balance optical transmission (per projection) with signal to noise ratio in the reconstructed dose distribution, and (5) the magnitude and characteristics of artifacts due to the presence of a channel in the dosimeter. Monte Carlo simulations were performed using both conventional and deformable dosimeter formulations. For verification, 2.8 Gy at 1 cm was delivered in 92 h using an I-125 source to a PRESAGE{sup ®} dosimeter with conventional formulation and a central channel with 0.0425 cm radius for source placement. The dose distribution was reconstructed with 0.02 and 0.04 cm{sup 3} voxel size using the Duke midsized optical CT scanner (DMOS). Results: While the conventional formulation overattenuates dose from all three sources compared to water, the current deformable formulation has nearly water equivalent attenuation properties for Cs-131 and I-125, while underattenuating for Pd-103. The energy spectrum of each source is relatively stable within the first 5 cm especially for I-125. The inherent assumption of radial symmetry in the TG43 geometry leads to a linear increase in sample points within the 3D dosimeter as a function of distance away from the source, which partially offsets the decreasing signal. Simulations of dose reconstruction using optical CT showed the feasibility of reconstructing dose out to a radius of 10 cm without saturating projection images using an optimal dose and high dynamic range scanning; the simulations also predicted that reconstruction artifacts at the channel surface due to a small discrepancy in refractive index should be negligible. Agreement of the measured with calculated radial dose function for I-125 was within 5% between 0.3 and 2.5 cm from the source, and the median difference of measured from calculated anisotropy function was within 5% between 0.3 and 2.0 cm from the source. Conclusions: 3D dosimetry using polyurethane dosimeters with optical CT looks to be a promising application to verify dosimetric distributions surrounding low energy brachytherapy sources.

07 ISOTOPE AND RADIATION SOURCES↗

TU-D-209-06: Head and Neck Tissue Dose From X-Ray Scatter to Physicians Performing Cardiovascular Procedures

Purpose: The purpose of this work was to characterize the spatial distribution of scatter radiation to the head and neck of a physician performing an x-ray interventional procedure and assess brain, eye lens, and carotid artery dose. Methods: Radiographic x-ray beams were tuned to match the peak energy (56 to 106 keV) and HVL (3.5 to 6.5 mm Al) of x-ray scatter originating from a patient during a fluoroscopic procedure. The radiographic beam was directed upon a Rando phantom from an inferior-left location to mimic a typical patient-operator geometric relationship. A lead-equivalent protective garment was secured to the phantom. Direct exposure Gafchromic film (XRQA2) was placed between the transverse plane layers of the head and neck region of the phantom and exposed with 4 scatter-equivalent radiographic beams. A 3×3 cm{sup 2} film placed at the left collar of the phantom was used to monitor incident dose in the position of a radiation monitoring badge. The films were converted to 2D dose distribution maps using FilmQA Pro software and an Epson 11000-XL scanner. The 2D dose distributions maps were normalized by the left collar dose and the percent of left collar dose (%LCD) was calculated for select tissues. Results: The dose maps had high dynamic range (10{sub 4}) and spatial detail. Considering all transverse planes and 4 scatter beam qualities, the median %LCD values were: whole brain 8.5%, left brain 13%, right brain 5.4%, left eye lens 67%, right eye lens 25%, left carotid artery 72%, and right carotid artery 28%. Conclusion: Scatter radiation dose to an operator can be simulated using a tuned radiographic beam and used to expose a phantom and Gafchromic film, thereby creating detailed 2D dose distribution maps. This work facilitates individualized estimation of dose to select head and neck tissues based on an operator’s radiation monitoring badge value.

60 APPLIED LIFE SCIENCES↗

De Novo Design of Self-Assembling Helical Protein Filaments

We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale filaments with a wide range of geometries in vivo and in vitro. Cryo–electron microscopy structures of six designs are close to the computational design models. The filament building blocks are idealized repeat proteins, and thus the diameter of the filaments can be systematically tuned by varying the number of repeat units. The assembly and disassembly of the filaments can be controlled by engineered anchor and capping units built from monomers lacking one of the interaction surfaces. The ability to generate dynamic, highly ordered structures that span micrometers from protein monomers opens up possibilities for the fabrication of new multiscale metamaterials.

Shen, Hao↗

Quantum interference in atom-exchange reactions

Chemical reactions, in which bonds break and form, are highly dynamic quantum processes. A fundamental question is whether coherence can be preserved in chemical reactions and then harnessed to generate entangled products. Here we investigated this question by studying the 2KRb → K 2 + Rb 2 reaction at 500 nanokelvins, focusing on the nuclear spin degrees of freedom. We prepared the initial nuclear spins in KRb (potassium-rubidium) in an entangled state by lowering the magnetic field to where the spin-spin interaction dominates and characterized the preserved coherence in nuclear spin wave function after the reaction. We observed an interference pattern that is consistent with full coherence at the end of the reaction, suggesting that entanglement prepared within the reactants could be redistributed through the atom-exchange process.

Science & Technology - Other Topics↗

Drivers of stability and transience in composition-functioning links during serial propagation of litter-decomposing microbial communities

ABSTRACT Biotic factors that influence the temporal stability of microbial community functioning are an emerging research focus for the control of natural and engineered systems. The discovery of common features within community ensembles that differ in functional stability over time is a starting point to explore biotic factors. We serially propagated a suite of soil microbial communities through five generations of 28-day microcosm incubations to examine microbial community compositional and functional stability during plant litter decomposition. Using dissolved organic carbon (DOC) abundance as a target function, we hypothesized that microbial diversity, compositional stability, and associated changes in interactions would explain the relative stability of the ecosystem function between generations. Communities with initially high DOC abundance tended to converge towards a “low DOC” phenotype within two generations, but across all microcosms, functional stability between generations was highly variable. By splitting communities into two cohorts based on their relative DOC functional stability, we found that compositional shifts, diversity, and interaction network complexity were associated with the stability of DOC abundance between generations. Further, our results showed that legacy effects were important in determining compositional and functional outcomes, and we identified taxa associated with high DOC abundance. In the context of litter decomposition, achieving functionally stable communities is required to utilize soil microbiomes to increase DOC abundance and long-term terrestrial DOC sequestration as one solution to reduce atmospheric carbon dioxide concentrations. Identifying factors that stabilize function for a community of interest may improve the success of microbiome engineering applications. IMPORTANCE Microbial community functioning can be highly dynamic over time. Identifying and understanding biotic factors that control functional stability is of significant interest for natural and engineered communities alike. Using plant litter–decomposing communities as a model system, this study examined the stability of ecosystem function over time following repeated community transfers. By identifying microbial community features that are associated with stable ecosystem functions, microbial communities can be manipulated in ways that promote the consistency and reliability of the desired function, improving outcomes and increasing the utility of microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗

Equations of state and melting curve of boron carbide in the high-pressure range of shock compression

We have constructed the equations of state for crystalline boron carbide B{sub 11}C (C–B–C) and its melt under high dynamic and static pressures. A kink on the shock adiabat for boron carbide has been revealed in the pressure range near 100 GPa, and the melting curve with negative curvature in the pressure range 0–120 GPa has been calculated. The results have been used for interpreting the kinks on the shock adiabat for boron carbide in the pressure range of 0–400 GPa.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Exploiting variability for energy optimization of parallel programs

Here in this paper we present optimizations that use DVFS mechanisms to reduce the total energy usage in scientific applications. Our main insight is that noise is intrinsic to large scale parallel executions and it appears whenever shared resources are contended. The presence of noise allows us to identify and manipulate any program regions amenable to DVFS. When compared to previous energy optimizations that make per core decisions using predictions of the running time, our scheme uses a qualitative approach to recognize the signature of executions amenable to DVFS. By recognizing the "shape of variability" we can optimize codes with highly dynamic behavior, which pose challenges to all existing DVFS techniques. We validate our approach using offline and online analyses for one-sided and two-sided communication paradigms. We have applied our methods to NWChem, and we show best case improvements in energy use of 12% at no loss in performance when using online optimizations running on 720 Haswell cores with one-sided communication. With NWChem on MPI two-sided and offline analysis, capturing the initialization, we find energy savings of up to 20%, with less than 1% performance cost.

97 MATHEMATICS AND COMPUTING↗

Genetic Background Modulates lncRNA-Coordinated Tissue Response to Low Dose Ionizing Radiation

Long noncoding RNAs (lncRNAs) are emerging as key regulators of diverse cell functions and processes. However, the relevance of lncRNAs in the cell and tissue response to ionizing radiation has not yet been characterized. Here we used microarray profiling to determine lncRNA and mRNA expression in mammary glands of BALB/c and SPRET/EiJ mice after low-dose ionizing radiation (LDIR) exposure. We found that unirradiated mammary tissues of these strains differed significantly in baseline expressions of 290 lncRNAs. LDIR exposure (10 cGy) induced a significant change in the expression of many lncRNAs. The vast majority of lncRNAs identified to be differentially expressed after LDIR in either BALB/c or SPRET/EiJ had a significantly correlated expression pattern with at least one LDIR responsive mRNA. Functional analysis revealed that the response to LDIR in BALB/c mice is highly dynamic with enrichment for genes involved in tissue injury, inflammatory responses, and mammary gland development at 2, 4, and 8 weeks after LDIR, respectively. Our study demonstrates that genetic background strongly influences the expression of lncRNAs and their response to radiation and that lncRNAs may coordinate the tissue response to LDIR exposure via regulation of coding mRNAs.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Opinion: Lighting Research During and After the Pandemic

For many lighting researchers, the recent restrictions related to COVID-19 have paused most in-person laboratory or field experiments. In certain countries, regulatory institutions have allowed such experiments to resume but issued safety recommendations like pre-checking participants for disease symptoms and excluding those that are especially vulnerable. To avoid potential complications and delays, researchers are likely to resort to other research designs that enable remote research — eliminating the need for the experimenter and subjects to be in the same room. While unanticipated, this shift to remote research methods is an opportunity to revisit and further develop remote experimental techniques, which can have beneficial long-lasting implications on lighting research during and after the pandemic. Perhaps the most common type of remote research is online experiments; which can greatly benefit from improved techniques to allow for greater control or characterization of experimental conditions, like those proposed by Villa and Labayrade . These techniques require validation specific to the type of response collected and context, e.g. space type and attributes. New research techniques continue to emerge and will enable remote collection of objective measures such as gaze direction and high dynamic range images (HDRIs) without specialized equipment. In fact, many of these methods and techniques are commonly used in other disciplines, like vision science and psychology, and can be adapted for lighting research. Not all lighting studies can be conducted online, but in the age of ubiquitous and connected technologies, there is a largely missed opportunity to utilize crowdsourced responses to lighting conditions in real environments where people live and go about their daily lives without the research being limited to a certain time and laboratory locations. For instance, outdoor street luminaires can be rated by passersby using ecological momentary assessments on mobile phones. While this approach does not provide laboratory-level control over experimental conditions, it can provide more contextual responses resulting from ‘normal’ dynamic gaze, behavior, and interactions. Further, it can also reduce bias related to the experimental setting. Further development of remote research methods and their use in lighting research can improve the quality of lighting research. Given that sample sizes in most lighting research are relatively small, remote research can substantially increase sample sizes, reduce research costs, and shorten study duration, all while reducing interaction between experimenter and subjects. Another benefit is reaching a wider audience and including under-represented individuals who typically are not reachable using common recruitment methods. The pandemic has set back our plans for in-lab experiments, but can it inspire us to think of new and creative ways to expand lighting research?

Abboushi, Belal K.↗

Evaluation of sky spectra and sky models in daylighting simulations

Sky models in daylight simulations represent the luminance variation across the sky-dome for different locations, dates, times and weather conditions, but skies are typically modelled as colourless. Recent studies explore techniques for incorporating the spectral content of daylighting in simulations. This paper provides an evaluation of the existing spectral sky models in lighting simulation software. The comparisons are made between the available mathematical sky models and naturally occurring skies that were recorded using high dynamic range photography and spectrophotometric measurements. The results show that recently developed sky models present progress compared to colourless sky models, but further research is needed to accurately simulate daylight spectra.

97 MATHEMATICS AND COMPUTING↗

High resolution crystal structure of the FAK FERM domain reveals new insights on the Druggability of tyrosine 397 and the Src SH3 binding site

Focal Adhesion Kinase (FAK) is a major cancer drug target that is involved in numerous aspects of tumor progression and survival. While multiple research groups have developed ATP-competitive small molecule inhibitors that target the kinase enzyme, recent attention has been focused on the FAK FERM (Band 4.1, Ezrin, Radixin, Moesin) domain that contains key residue Y397 and contributes to many protein-protein interactions. Previous x-ray crystal structures of the FAK FERM domain gave conflicting results on the structure of the Y397 region and therefore the overall druggability. Here, we report the identification of a higher resolution crystal structure of the avian FAK FERM domain that shows conformational differences in Y397 and surrounding residues in the F1 lobe. In addition, we resolve the residues of the Src SH3 binding site, an area of the FERM domain that has previously shown limited electron density. These crystallographic data suggest that the Y397 region is highly dynamic and question the druggability of a putative pocket on the F1 lobe. In addition, new electron density data around the Src SH3 binding site provide structural insight on the FAK-Src activation cascade through a putative auto-inhibitory conformation.

60 APPLIED LIFE SCIENCES↗