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At least 163 records · Page 9

Contrasting the Biophysical and Radiative Effects of Rising CO 2 Concentrations on Ozone Dry Deposition Fluxes

Abstract The dry deposition of ozone from the atmosphere to ecosystems is an important coupling mechanism between atmospheric chemistry and terrestrial biogeochemical processes. In most Earth system models, dry deposition is simulated using a resistor‐in‐series approach that aims to parameterize the governing biological, chemical, and physical processes through a series of functional approximations. Here, we evaluate the influence of carbon cycle‐climate responses on this parameterization using the results of the Energy Exascale Earth System Model v1.1 Biogeochemistry simulation campaign. This simulation campaign was designed in part to explore the biophysical and radiative effects of rising historical CO 2 concentrations on the Earth system. We find that while the global annual ozone dry deposition is relatively insensitive to these effects, regionally the influence can be up to 10%. The strongest regional sensitivities in ozone dry deposition are predominantly in higher latitudes over land in the northern hemisphere and are dominated by the radiative effect of CO 2 , with little net influence of biophysical responses. Of all the impacts of the radiative effect of CO 2 , we point to the potential importance of accurately representing ozone deposition to snow in Earth System Models and provide recommendations for future simulation campaigns.

54 ENVIRONMENTAL SCIENCES↗

Integrating community perceptions and cultural diversity in social impact assessment in Nigeria

The Environmental Impact Assessment (EIA) Act of 1992 aimed to make the environment a central theme in development in Nigeria. Nevertheless, the extent of engagement with local cultures in the Nigerian EIA process is not statutorily guaranteed. While most EIAs in Nigeria have been for oil and gas projects in the Niger Delta, and have focused strongly on the biophysical environment, socio-economic and cultural aspects have remained marginal. The palpable neglect of community perceptions and cultural diversity in social impact assessment (SIA) in this region prone to conflict has tended to alienate the people in the decision-making process. Thus, despite claims to compliance with regulatory requirements for EIAs, and numerous purported sustainable development initiatives by international oil companies (IOCs), the region continues to face multiple sustainability challenges. This paper situates local perceptions and cultural diversity in participatory development and canvasses the integration of community perceptions and cultural diversity into SIA in the Niger Delta region. It is argued that doing this would be critical to ensuring acceptance and success of development actions within the context of local culture while also contributing to sustainable development policy in the region. - Highlights: • Nigeria EIA Act aimed to make the environment central to development in Nigeria. • Engagement with local communities in the process is not statutorily guaranteed. • SIAs in Nigeria neglect community perceptions and cultural diversity. • Article canvasses integrating community perceptions and cultural diversity in SIA. • Local acceptance in context of culture would yield sustainable development outcomes.

54 ENVIRONMENTAL SCIENCES↗

FACE-IT. A Science Gateway for Food Security Research

Progress in sustainability science is hindered by challenges in creating and managing complex data acquisition, processing, simulation, post-processing, and intercomparison pipelines. To address these challenges, we developed the Framework to Advance Climate, Economic, and Impact Investigations with Information Technology (FACE-IT) for crop and climate impact assessments. This integrated data processing and simulation framework enables data ingest from geospatial archives; data regridding, aggregation, and other processing prior to simulation; large-scale climate impact simulations with agricultural and other models, leveraging high-performance and cloud computing; and post-processing to produce aggregated yields and ensemble variables needed for statistics, for model intercomparison, and to connect biophysical models to global and regional economic models. FACE-IT leverages the capabilities of the Globus Galaxies platform to enable the capture of workflows and outputs in well-defined, reusable, and comparable forms. We describe FACE-IT and applications within the Agricultural Model Intercomparison and Improvement Project and the Center for Robust Decision-making on Climate and Energy Policy.

97 MATHEMATICS AND COMPUTING↗

High-yield recombinant bacterial expression of 13 C-, 15 N-labeled, serine-16 phosphorylated, murine amelogenin using a modified third generation genetic code expansion protocol

Amelogenin constitutes ~ 90% of the enamel matrix in the secretory stage of amelogenesis, a still poorly understood process that results in the formation of the hardest and most mineralized tissue in vertebrates – enamel. Most biophysical research with amelogenin uses recombinant protein expressed in Escherichia coli. In addition to providing copious amounts of protein, recombinant expression allows 13 C- and 15 N-labelling for detailed structural studies using NMR spectroscopy. However, native amelogenin is phosphorylated at one position, Ser-16 in murine amelogenin, and a lingering question overshadowing decades of enamel research with recombinant amelogenin is the effect of phosphorylation on its biophysical properties. Using a modified genetic code expansion protocol we have expressed and purified uniformly 13 C-, 15 N-labeled murine amelogenin (pS16M179) with ~95% of the protein being correctly phosphorylated. Homogeneous phosphorylation was achieved using commercially available, enriched, 13 C-, 15 N-labeled media and protein expression was induced with isopropyl β-D-1-thiogalactopyranoside at 310 K. Phosphoserine incorporation was verified from one-dimensional 31P NMR spectra, comparison of 1 H- 15 N HSQC spectra, Phos-tag SDS PAGE, and mass spectrometry. Phosphorus-31 NMR spectra for pS16M179 under conditions known to trigger amelogenin self-assembly into nanospheres confirm nanosphere models with buried N-termini. Lambda phosphatase treatment of these nanospheres results in the dephosphorylation of pS16M179, confirming that smaller oligomers and monomers with exposed N-termini are in equilibrium with nanospheres. Such 13 C-, 15 N-labeling of amelogenin with accurately encoded phosphoserine incorporation will accelerate biomineralization research to understand amelogenesis and stimulate the expanded use of genetic code expansion protocols to introduce phosphorylated amino acids into proteins.

31P-NMR↗

Timing is everything: Fine-tuned molecular machines orchestrate paramyxovirus entry

The Paramyxoviridae include some of the great and ubiquitous disease-causing viruses of humans and animals. In most paramyxoviruses, two viral membrane glycoproteins, fusion protein (F) and receptor binding protein (HN, H or G) mediate a concerted process of recognition of host cell surface molecules followed by fusion of viral and cellular membranes, resulting in viral nucleocapsid entry into the cytoplasm. The interactions between the F and HN, H or G viral glycoproteins and host molecules are critical in determining host range, virulence and spread of these viruses. Recently, atomic structures, together with biochemical and biophysical studies, have provided major insights into how these two viral glycoproteins successfully interact with host receptors on cellular membranes and initiate the membrane fusion process to gain entry into cells. These studies highlight the conserved core mechanisms of paramyxovirus entry that provide the fundamental basis for rational anti-viral drug design and vaccine development. - Highlights: • New structural and functional insights into paramyxovirus entry mechanisms. • Current data on paramyxovirus glycoproteins suggest a core conserved entry mechanism. • Diverse mechanisms preventing premature fusion activation exist in these viruses. • Precise spacio-temporal interplay between paramyxovirus glycoproteins initiate entry.

60 APPLIED LIFE SCIENCES↗

Soil temperature mitigation due to vegetation biophysical feedbacks

Understanding the interactions between temperature regimes and vegetation cover is one of the key scientific topics in global environmental change and land surface process research. Recently, the prominent global greening trend has inspired considerable interest in examining climate feedbacks to vegetation changes. However, the impacts of recent widespread vegetation cover changes on soil temperature have been less documented and have received insufficient attention. Here, a high-resolution regional climate model was used to examine the potential impact of vegetation cover changes over the past 37 years, obtained as satellite observational data, on regional air and soil temperatures across the Heilong-Amur River Basin. Our sensitivity experiments indicated that the 1.85% increase in the regional fractional vegetation cover (FVC) from 1982 to 2018 cooled the air temperature by 0.045°C and the soil temperature by 0.19°C and that this cooling effect would continue in the near future, from 2016-2018 to 2051-2053. We found that soil temperatures were more sensitive to vegetation cover changes than air temperatures, particularly in mid-high latitude forest ecosystems; this finding helps to explain the nonsignificant decrease in soil temperatures in forest ecosystems over the past 40 years detected in the ERA5-Land reanalysis. Further, our results also suggest that vegetation restoration in forest ecosystems could mitigate the effects of climate change on permafrost environments by increasing the number of soil freezing days.

54 ENVIRONMENTAL SCIENCES↗

A 1D–0D–3D coupled model for simulating blood flow and transport processes in breast tissue

In this work, we present mixed dimensional models for simulating blood flow and transport processes in breast tissue and the vascular tree supplying it. These processes are considered, to start from the aortic inlet to the capillaries and tissue of the breast. Large variations in biophysical properties and flow conditions exist in this system necessitating the use of different flow models for different geometries and flow regimes. In total, we consider four different model types. First, a system of 1D nonlinear hyperbolic partial differential equations (PDEs) is considered to simulate blood flow in larger arteries with highly elastic vessel walls. Second, we assign 1D linearized hyperbolic PDEs to model the smaller arteries with stiffer vessel walls. The third model type consists of ODE systems (0D models). It is used to model the arterioles and peripheral circulation. Finally, homogenized 3D porous media models are considered to simulate flow and transport in capillaries and tissue within the breast volume. Sink terms are used to account for the influence of the venous and lymphatic systems. Combining the four model types, we obtain two different 1D–0D–3D coupled models for simulating blood flow and transport processes: The first model results in a fully coupled 1D–0D–3D model covering the complete path from the aorta to the breast combining a generic arterial network with a patient specific breast network and geometry. The second model is a reduced one based on the separation of the generic and patient specific parts. The information from a calibrated fully coupled model is used as inflow condition for the patient specific sub-model allowing a significant computational cost reduction. Several numerical experiments are conducted to calibrate the generic model parameters and to demonstrate realistic flow simulations compared to existing data on blood flow in the human breast and vascular system. Moreover, we use two different breast vasculature and tissue data sets to illustrate the robustness of our reduced sub-model approach.

multiscale blood flow models↗

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.↗

Dosimetry concepts for scanner quality assurance and tissue dose assessment in micro-CT

Purpose: At present, no established methods exist for dosimetry in micro computed tomography (micro-CT). The purpose of this study was therefore to investigate practical concepts for both dosimetric scanner quality assurance and tissue dose assessment for micro-CT. Methods: The computed tomography dose index (CTDI) was adapted to micro-CT and measurements of the CTDI both free in air and in the center of cylindrical polymethyl methacrylate (PMMA) phantoms of 20 and 32 mm diameter were performed in a 6 month interval with a 100 mm pencil ionization chamber calibrated for low tube voltages. For tissue dose assessment, z-profile measurements using thermoluminescence dosimeters (TLDs) were performed and both profile and CTDI measurements were compared to Monte Carlo (MC) dose calculations to validate an existing MC tool for use in micro-CT. The consistency of MC calculations and TLD measurements was further investigated in two mice cadavers. Results: CTDI was found to be a reproducible quantity for constancy tests on the micro-CT system under study, showing a linear dependence on tube voltage and being by definition proportional to mAs setting and z-collimation. The CTDI measured free in air showed larger systematic deviations after the 6 month interval compared to the CTDI measured in PMMA phantoms. MC calculations were found to match CTDI measurements within 3% when using x-ray spectra measured at our micro-CT installation and better than 10% when using x-ray spectra calculated from semi-empirical models. Visual inspection revealed good agreement for all z-profiles. The consistency of MC calculations and TLD measurements in mice was found to be better than 10% with a mean deviation of 4.5%. Conclusions: Our results show the CTDI implemented for micro-CT to be a promising candidate for dosimetric quality assurance measurements as it linearly reflects changes in tube voltage, mAs setting, and collimation used during the scan, encouraging further studies on a variety of systems. For tissue dose assessment, MC calculations offer an accurate and fast alternative to TLD measurements allowing for dose calculations specific to any geometry and scan protocol.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

pH-dependent structural change of the extracellular sensor domain of the DraK histidine kinase from Streptomyces coelicolor

Highlights: ► We described the biochemical and biophysical properties of the extracellular sensory domain (ESD) of DraK histidine kinase. ► The ESD of DraK showed a reversible pH-dependent conformational change in a wide pH range. ► The E83 is an important residue for the pH-dependent conformational change. -- Abstract: Recently, the DraR/DraK (Sco3063/Sco3062) two-component system (TCS) of Streptomycescoelicolor has been reported to be involved in the differential regulation of antibiotic biosynthesis. However, it has not been shown that under which conditions and how the DraR/DraK TCS is activated to initiate the signal transduction process. Therefore, to understand the sensing mechanism, structural study of the sensory domain of DraK is highly required. Here, we report the biochemical and biophysical properties of the extracellular sensory domain (ESD) of DraK. We observed a reversible pH-dependent conformational change of the ESD in a pH range of 2.5–10. Size-exclusion chromatography and AUC (analytical ultracentrifugation) data indicated that the ESD is predominantly monomeric in solution and exists in equilibrium between monomer and dimer states in acidic condition. Using NMR (nuclear magnetic resonance) and CD (circular dichroism) spectroscopy, our findings suggest that the structure of the ESD at low pH is more structured than that at high pH. In particular, the glutamate at position 83 is an important residue for the pH-dependent conformational change. These results suggest that this pH-dependent conformational change of ESD may be involved in signal transduction process of DraR/DraK TCS.

60 APPLIED LIFE SCIENCES↗

X-ray scatter correction method for dedicated breast computed tomography

Purpose: To improve image quality and accuracy in dedicated breast computed tomography (BCT) by removing the x-ray scatter signal included in the BCT projections. Methods: The previously characterized magnitude and distribution of x-ray scatter in BCT results in both cupping artifacts and reduction of contrast and accuracy in the reconstructions. In this study, an image processing method is proposed that estimates and subtracts the low-frequency x-ray scatter signal included in each BCT projection postacquisition and prereconstruction. The estimation of this signal is performed using simple additional hardware, one additional BCT projection acquisition with negligible radiation dose, and simple image processing software algorithms. The high frequency quantum noise due to the scatter signal is reduced using a noise filter postreconstruction. The dosimetric consequences and validity of the assumptions of this algorithm were determined using Monte Carlo simulations. The feasibility of this method was determined by imaging a breast phantom on a BCT clinical prototype and comparing the corrected reconstructions to the unprocessed reconstructions and to reconstructions obtained from fan-beam acquisitions as a reference standard. One-dimensional profiles of the reconstructions and objective image quality metrics were used to determine the impact of the algorithm. Results: The proposed additional acquisition results in negligible additional radiation dose to the imaged breast ({approx}0.4% of the standard BCT acquisition). The processed phantom reconstruction showed substantially reduced cupping artifacts, increased contrast between adipose and glandular tissue equivalents, higher voxel value accuracy, and no discernible blurring of high frequency features. Conclusions: The proposed scatter correction method for dedicated breast CT is feasible and can result in highly improved image quality. Further optimization and testing, especially with patient images, is necessary to characterize its impact on clinical performance.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Reconstructed Historical Land Cover and Biophysical Parameters for Studies of Land-Atmosphere Interactions within the Eastern United States

The local environment where we live within the Earth's biosphere is often taken for granted. This environment can vary depending on whether the land cover is a forest, grassland, wetland, water body, bare soil, pastureland, agricultural field, village, residential suburb, or an urban complex with concrete, asphalt, and large buildings. In general, the type and characteristics of land cover influence surface temperatures, sunlight exposure and duration, relative humidity, wind speed and direction, soil moisture amount, plant life, birds, and other wildlife in our backyards. The physical and biological properties (biophysical characteristics) of land cover help to determine our surface environment because they directly affect surface radiation, heat, and soil moisture processes, and also feedback to regional weather and climate. Depending on the spatial scale and land use intensity, land cover changes can have profound impacts on our local and regional environment. Over the past 350 years, the eastern half of the United States, an area extending from the grassland prairies of the Great Plains to the Gulf and Atlantic coasts, has experienced extensive land cover and land use changes that began with land clearing in the 1600s, led to extensive deforestation and intensive land use practices by 1920, and then evolved to the present-day landscape. Determining the consequences of such land cover changes on regional and global climate is a major research issue. Such research requires detailed historical land cover data and modeling experiments simulating historical climates. Given the need to understand the effects of historical land cover changes in the eastern United States, some questions include: - What were the most important land cover transformations and how did they alter biophysical characteristics of the land cover at key points in time since the mid-1600s? - How have land cover and land use changes over the past 350 years affected the land surface environment including surface weather, hydrologic, and climatic variability? - How do the potential effects of regional human-induced land cover change on the environment compare to similar changes that are caused by the natural variations of the Earth's climate system? To help answer these questions, we reconstructed a fractional land cover and biophysical parameter dataset for the eastern United States at 1650, 1850, 1920, and 1992 time-slices. Each land cover fraction is associated with a biophysical parameter class, a suite of parameters defining the biophysical characteristics of that kind of land cover. This new dataset is designed for use in computer models of land-atmosphere interactions, to understand and quantify the effects of historical land cover changes on the water, energy, and carbon cycles

Steyaert, Louis T.↗

Integrating plant physiology into simulation of fire behavior and effects

Summary Wildfires are a global crisis, but current fire models fail to capture vegetation response to changing climate. With drought and elevated temperature increasing the importance of vegetation dynamics to fire behavior, and the advent of next generation models capable of capturing increasingly complex physical processes, we provide a renewed focus on representation of woody vegetation in fire models. Currently, the most advanced representations of fire behavior and biophysical fire effects are found in distinct classes of fine‐scale models and do not capture variation in live fuel (i.e. living plant) properties. We demonstrate that plant water and carbon dynamics, which influence combustion and heat transfer into the plant and often dictate plant survival, provide the mechanistic linkage between fire behavior and effects. Our conceptual framework linking remotely sensed estimates of plant water and carbon to fine‐scale models of fire behavior and effects could be a critical first step toward improving the fidelity of the coarse scale models that are now relied upon for global fire forecasting. This process‐based approach will be essential to capturing the influence of physiological responses to drought and warming on live fuel conditions, strengthening the science needed to guide fire managers in an uncertain future.

54 ENVIRONMENTAL SCIENCES↗

New Tech Measures Artery Health: Engevity Cuff

Jonathan Maltz, a Berkeley Lab scientist in the Molecular Biophysics and Integrated Bioimaging division, explains a new technology developed at Berkeley Lab that could soon make detecting the process of plaque buildup in vessels a routine part of a visit to the doctor and, perhaps, home healthcare settings.

59 BASIC BIOLOGICAL SCIENCES↗

Optimized Expression and Purification for High-Activity Preparations of Algal [FeFe]-Hydrogenase

Recombinant expression and purification of metallo-enzymes, including hydrogenases, at high-yields is challenging due to complex, and enzyme specific, post-translational maturation processes. Low fidelities of maturation result in preparations containing a significant fraction of inactive, apo-protein that are not suitable for biophysical or crystallographic studies. We describe the construction, overexpression and high-yield purification of a fusion protein consisting of the algal [2Fe2S]-ferredoxin PetF (Fd) and [FeFe]-hydrogenase HydA1. The maturation of Fd-HydA1 was optimized through improvements in culture conditions and media components used for expression. We also demonstrated that fusion of Fd to the N-terminus of HydA1, in comparison to the C-terminus, led to increased expression levels that were 4-fold higher. Together, these improvements led to enhanced HydA1 activity and improved yield after purification. The strong binding-affinity of Fd for DEAE allowed for two-step purification by ion exchange and StrepTactin affinity chromatography. In addition, the incorporation of a TEV protease site in the Fd-HydA1 linker allowed for the proteolytic removal of Fd after DEAE step, and purification of HydA1 alone by StrepTactin. In combination, this process resulted in HydA1 purification yields of 5 mg L{sup -1} of culture from E. coli with specific activities of 1000 U (U = 1 {micro}mol hydrogen evolved mg{sup -1} min{sup -1}). The [FeFe]-hydrogenases are highly efficient enzymes and their catalytic sites provide model structures for synthetic efforts to develop robust hydrogen activation catalysts. In order to characterize their structure-function properties in greater detail, and to use hydrogenases for biotechnological applications, reliable methods for rapid, high-yield expression and purification are required.

09 BIOMASS FUELS↗

Chemo-mechanical modeling of tumor growth in elastic epithelial tissue

We propose a multiscale chemo-mechanical model of the cancer tumor development in the epithelial tissue. The epithelium is represented by an elastic 2D array of polygonal cells with its own gene regulation dynamics. The model allows the simulation of the evolution of multiple cells interacting via the chemical signaling or mechanically induced strain. The algorithm includes the division and intercalation of cells as well as the transformation of normal cells into a cancerous state triggered by a local failure of the spatial synchronization of the cellular rhythms driven by transcription/translation processes. Both deterministic and stochastic descriptions of the system are given for chemical signaling. The transformation of cells means the modification of their respective parameters responsible for chemo-mechanical interactions. The simulations reproduce a distinct behavior of invasive and localized carcinoma. Generally, the model is designed in such a way that it can be readily modified to take account of any newly understood gene regulation processes and feedback mechanisms affecting chemo-mechanical properties of cells.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Assembly and Characterization of Biomolecular Memristors Consisting of Ion Channel-doped Lipid Membranes

The ability to recreate synaptic functionalities in synthetic circuit elements is essential for neuromorphic computing systems that seek to emulate the cognitive powers of the brain with comparable efficiency and density. To date, silicon-based three-terminal transistors and two-terminal memristors have been widely used in neuromorphic circuits, in large part due to their ability to co-locate information processing and memory. Yet these devices cannot achieve the interconnectivity and complexity of the brain because they are power-hungry, fail to mimic key synaptic functionalities, and suffer from high noise and high switching voltages. To overcome these limitations, we have developed and characterized a biomolecular memristor that mimics the composition, structure, and switching characteristics of biological synapses. Here, we describe the process of assembling and characterizing biomolecular memristors consisting of a 5 nm-thick lipid bilayer formed between lipid-functionalized water droplets in oil and doped with voltage-activated alamethicin peptides. While similar assembly protocols have been used to investigate biophysical properties of droplet-supported lipid membranes and membrane-bound ion channels, this article focuses on key modifications of the droplet interface bilayer method essential for achieving consistent memristor performance. Specifically, we describe the liposome preparation process and the incorporation of alamethicin peptides in lipid bilayer membranes, and the appropriate concentrations of each constituent as well as their impact on the overall response of the memristors. As a result, we also detail the characterization process of biomolecular memristors, including measurement and analysis of memristive current-voltage relationships obtained via cyclic voltammetry, as well as short-term plasticity and learning in response to step-wise voltage pulse trains.

97 MATHEMATICS AND COMPUTING↗