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At least 1,387 records · Page 77

Predicting the mineral composition of dust aerosols: Insights from elemental composition measured at the Izaña Observatory: PREDICTING DUST MINERAL COMPOSITION

Regional variations of dust mineral composition are fundamental to climate impacts but generally neglected in climate models. A challenge for models is that atlases of soil composition are derived from measurements following wet sieving, which destroys the aggregates potentially emitted from the soil. Aggregates are crucial to simulating the observed size distribution of emitted soil particles. We use an extension of brittle fragmentation theory in a global dust model to account for these aggregates. Our method reproduces the size-resolved dust concentration along with the approximately size-invariant fractional abundance of elements like Fe and Al in the decade-long aerosol record from the Izaña Observatory, off the coast of West Africa. By distinguishing between Fe in structural and free forms, we can attribute improved model behavior to aggregation of Fe and Al-rich clay particles. We also demonstrate the importance of size-resolved measurements along with elemental composition analysis to constrain models.

58 GEOSCIENCES↗

AgHalo: A Facile Fluorogenic Sensor to Detect Drug-Induced Proteome Stress

Drug-induced proteome stress that involves protein aggregation may cause adverse effects and undermine the safety profile of a drug. Safety of drugs is regularly evaluated using cytotoxicity assays that measure cell death. However, these assays provide limited insights into the presence of proteome stress in live cells. A fluorogenic protein sensor is reported to detect drug-induced proteome stress prior to cell death. An aggregation prone Halo-tag mutant (AgHalo) was evolved to sense proteome stress through its aggregation. Detection of such conformational changes was enabled by a fluorogenic ligand that fluoresces upon AgHalo forming soluble aggregates. Using 5 common anticancer drugs, we exemplified detection of differential proteome stress before any cell death was observed. Thus, this sensor can be used to evaluate drug safety in a regime that the current cytotoxicity assays cannot cover and be generally applied to detect proteome stress induced by other toxins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

EISA (Energy Independence and Security Act) compliant ethanol fuel from corn stover in a depot-based decentralized system

Cellulosic biofuels face significant problems of feedstock aggregation and logistics leading to poor economies of scale. The current model is based on relatively small biorefineries using locally-gathered feedstocks. Here, we examine the potential capacity of a hypothetically distributed, depot-based, biorefinery system to produce cellulosic ethanol from corn stover in the United States Midwest. The local depots serve to aggregate, pretreat and densify biomass (via pellets), which are collected, transported, and fed to a few very large, cellulosic ethanol biorefineries. We found that a corn stover-based depot system would help establish one or two very large-scale biorefineries capable of processing about 8-12% of total corn stover available in the United States Midwest. About 55-153 depots could supply the pretreated pellets to each distributed biorefinery leading to an annual production of 1.02 - 2.91 billion liters of cellulosic ethanol. Most of the participating depots would be located in Illinois and Iowa. The ethanol selling price in this depot-based biorefinery system would varys between U$S 0.67 and U$S 0.72 liter-1. The estimated range of GHG savings from cellulosic ethanol in the depot system compared to gasoline was 3.35-4.84 Tg CO2 year-1. In addition of being economically competitive, a distributed, depot-based, biorefinery system could meet the 60% GHG reduction requirement of the U.S. Energy Independence and Security Act (EISA).

Biorefinery, Cellulosic biofuel, Corn stover, Dist↗

Superoxide Dismutase 1 Folding Stability as a Target for Molecular Tweezers in SOD1-Related Amyotrophic Lateral Sclerosis

Protein misfolding and aggregation are hallmarks of many severe neurodegenerative diseases including Alzheimer's, Parkinson's and Huntington's disease. As a supramolecular ligand that binds to lysine and arginine residues, the molecular tweezer CLR01 was found to modify the aggregation pathway of disease-relevant proteins in vitro and in vivo with beneficial effects on toxicity. However, the molecular mechanisms of how tweezers exert these effects remain mainly unknown, hampering further drug development. Here, we investigate the modulation mechanism of unfolding and aggregation pathways of SOD1, which are involved in amyotrophic lateral sclerosis (ALS), by CLR01. Using a truncated version of the wildtype SOD1 protein, SOD1 bar , we show that CLR01 acts on the first step of the aggregation pathway, the unfolding of the SOD1 monomer. CLR01 increases, by ~10 °C, the melting temperatures of the A4V and G41D SOD1 mutants, which are commonly observed mutations in familial ALS. Molecular dynamics simulations and binding free energy calculations as well as native mass spectrometry and mutational studies allowed us to identify K61 and K92 as binding sites for the tweezers to mediate the stability increase. The data suggest that the modulation of SOD1 conformational stability is a promising target for future developments of supramolecular ligands against neurodegenerative diseases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational determination of the pigment binding motif in the chlorosome protein a of green sulfur bacteria

We present a molecular-scale model of Bacteriochlorophyll a (BChl a) binding to the chlorosome protein A (CsmA) of Chlorobaculum tepidum, and the aggregated pigment–protein dimer, as determined from protein–ligand docking and quantum chemistry calculations. Our calculations provide strong evidence that the BChl a molecule is coordinated to the His25 residue of CsmA, with the magnesium center of the bacteriochlorin ring situated <3 Å from the imidazole nitrogen atom of the histidine sidechain, and the phytyl tail aligned along the nonpolar residues of the α-helix of CsmA. We also confirm that the Q y band in the absorption spectra of BChl a experiences a large (+16 to +43 nm) redshift when aggregated with another BChl a molecule in the CsmA dimer, compared to the BChl a in solvent; this redshift has been previously established by experimental researchers. We propose that our model of the BChl a–CsmA binding motif, where the dimer contains parallel aligned N-terminal regions, serves as the smallest repeating unit in a larger model of the para-crystalline chlorosome baseplate protein.

59 BASIC BIOLOGICAL SCIENCES↗

Probing Conformational Dynamics of Tau Protein by Hydrogen/Deuterium Exchange Mass Spectrometry

Fibrillization of the microtubule-associated protein tau has been recognized as one of the signature pathologies of the nervous system in Alzheimer’s disease, progressive supranuclear palsy, and other tauopathies. The conformational transition of tau in the fibrillization process, tau monomer to soluble aggregates to fibrils in particular, remains unclear. Here we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) in combination with other biochemical approaches, including Thioflavin S fluorescence measurements, enzyme-linked immunosorbent assay (ELISA), and Western blotting to understand the heparin-induced tau’s fibrillization. HDX-MS studies including anti-tau antibody epitope mapping experiments provided molecular level details of the full-length tau’s conformational dynamics and its regional solvent accessibility upon soluble aggregates formation. The results demonstrate that R3 region in the full-length tau’s microtubule binding repeat region (MTBR) is stabilized in the aggregation process, leaving both N and C terminal regions to be solvent exposed in the soluble aggregates and fibrils. The findings also illustrate the practical utility of orthogonal analytical methodologies for the characterization of protein higher order structure. .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deformation heterogeneity and intragrain lattice misorientation in high strength contrast, dual-phase bridgmanite/periclase

A bridgmanite/periclase aggregate is investigated due to its prevalence in the Earth’s lower mantle and its importance for understanding geodynamic processes. In dual-phase polycrystalline aggregates, both strength contrast between phases and single crystal elastic and plastic anisotropy are known to influence the development of intragrain misorientation, and the evolution of crystallographic texture. In this study, full-field crystal plasticity simulations are performed with a finite element solution method, and applied to an aggregate of a mechanically strong orthorhombic phase with perovskite structure (bridgmanite, MgSiO 3 ), and a relatively weaker cubic phase (periclase, MgO). The relative strengths of the phases are parameterized to elucidate the effect that strength contrast has on texture evolution and single-phase simulations are performed for comparison. Altogether, results indicate that the relative strength between the two phases influences the development of plasticity, and the overall texture evolution. Results are discussed in light of trends related to the evolution of plasticity and misorientation in the aggregate, and their dependence on both the strength contrast between phases as well as the spatial distribution of grains and phases.

36 MATERIALS SCIENCE↗

How much information on precipitation is contained in satellite infrared imagery?

Satellite infrared (IR) brightness temperature providing information on the characteristics of cloud tops is one of the primary input data used for estimating precipitation from satellites. Thus, the natural questions to ask are: Does IR imagery contain more information about precipitation in some regions more than others? What are the factors that lead to such differences? Should we expect the amount of information provided by IR imagery to change with respect to temporal or spatial aggregation? Comprehensive analysis of the accuracy of satellite-based precipitation estimates obtained from any given algorithm may provide qualitative answers to the above questions. However, such an approach only offers conclusions within the limited context of the algorithm used to obtain precipitation estimates; that is, patterns caused by the inherent information content of IR imagery are inextricable from those induced by assumptions embedded in the precipitation estimation algorithm. Here, we address the abovementioned questions from a different perspective using an information-theoretic measure, free of structural assumptions and general to a wide range of relationships, to characterize the average and seasonal dependence between IR imagery provided by satellite sensors in the spectral range (10.7–11.5 μm) and precipitation rates in the contiguous United States (CONUS) across distinct temporal and spatial scales. We analyze a total of more than 1.3 billion pairs of IR and precipitation observations over CONUS, and we observe interesting patterns. First, we show that there is a strong inverse relationship (ρ = - 0.73) between the information content of IR data and the number of no-rain observations; however, its robustness varies regionally and seasonally with less significant correlation during the warm season. Second, we demonstrate that the intuitive relationship of increasing dependence between IR and precipitation as a result of temporal or spatial aggregation exhibits a diminishing returns behavior. For instance, temporal aggregation from 1 to 3 h increases the dependence approximately 7 times as much as temporal aggregation from 12 to 24 h. Furthermore, we quantitatively examine and re-confirm several statements previously reported in the literature such as the strong association between IR and precipitation in convective storms and the low association in orographic rainfall. Finally, we conclude by illustrating the potential of the analysis in diagnosis of operational algorithms for estimating precipitation from IR brightness temperature. The findings of this study pinpoint spatial domains and time scales at which IR is not an adequate proxy for estimating precipitation. Thus, they can potentially guide the development of operational algorithms that utilize satellite Infrared imagery for estimating, downscaling and data fusion of precipitation. Finally, the analysis presented here opens up the possibility of developing new methodologies for diagnosis of satellite-based precipitation estimation algorithms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Peptide concentration alters intermediate species in amyloid β fibrillation kinetics

Highlights: ► Aβ(1–40) aggregation in vitro has been monitored at different concentrations. ► Aβ(1–40) fibrillation does not always follow conventional kinetic mechanisms. ► We demonstrate non-linear features in the kinetics of Aβ(1–40) fibril formation. ► At high Aβ(1–40) concentrations secondary processes dictate fibrillation speed. ► Intermediate species may play significant roles on final amyloid fibril development. -- Abstract: The kinetic mechanism of amyloid aggregation remains to be fully understood. Investigations into the species present in the different kinetic phases can assist our comprehension of amyloid diseases and further our understanding of the mechanism behind amyloid β (Aβ) (1–40) peptide aggregation. Thioflavin T (ThT) fluorescence and transmission electron microscopy (TEM) have been used in combination to monitor Aβ(1–40) aggregation in vitro at both normal and higher than standard concentrations. The observed fibrillation behaviour deviates, in several respects, from standard concepts of the nucleation–polymerisation models and shows such features as concentration-dependent non-linear effects in the assembly mechanism. Aβ(1–40) fibrillation kinetics do not always follow conventional kinetic mechanisms and, specifically at high concentrations, intermediate structures become populated and secondary processes may further modify the fibrillation mechanism.

60 APPLIED LIFE SCIENCES↗

Cu(II) promotes amyloid pore formation

The aggregation of α-synuclein is associated with dopamine neuron death in Parkinson's disease. There is controversy in the field over the question of which species of the aggregates, fibrils or protofibrils, are toxic. Moreover, compelling evidence suggested the exposure to heavy metals to be a risk of PD. Nevertheless, the mechanism of metal ions in promoting PD remains unclear. In this research, we investigated the structural basis of Cu(II) induced aggregation of α-synuclein. Using transmission electron microscopy experiments, Cu(II) was found to promote in vitro aggregation of α-synuclein by facilitating annular protofibril formation rather than fibril formation. Furthermore, neuroprotective baicalein disaggregated annular protofibrils accompanied by considerable decrease of β-sheet content. These results strongly support the hypothesis that annular protofibrils are the toxic species, rather than fibrils, thereby inspiring us to search novel therapeutic strategies for the suppression of the toxic annular protofibril formation. - Highlights: • Cu(II) promoted the annular protofibril formation of α-synuclein in vitro. • Cu(II) postponed the in vitro fibrillization of α-synuclein. • Neuroprotective baicalein disaggregated annular protofibrils.

60 APPLIED LIFE SCIENCES↗

Ceramidase critically affects GPVI-dependent platelet activation and thrombus formation

Highlights: • Neither ceramide synthase nor serine palmitoyltransferase inhibition modifies GPVI-dependent platelet function. • Ceramidase inhibition impairs platelet aggregation, dense granule secretion and in vitro thrombus formation. • Impaired platelet function during ceramidase inhibition could be overcome by exogenous d-sphingosine. Platelet aggregation, dense granule secretion and thrombus formation are dependent on sphingolipids like ceramide and sphingosine as well as sphingosine-1 phosphate. Sphingosine/ceramide metabolism involves ceramide synthases and ceramidases. However, the role of ceramide synthase and ceramidase in the regulation of platelet function remained ill-defined. The present study determined transmission light aggregometry, employed luciferase based ATP release measurements and studied in vitro thrombus formation under high arterial shear rates in order to define the impact of pharmacological inhibition of serine palmitoyltransferase, ceramide synthase and ceramidase on platelet function. As a result, inhibition of ceramidase significantly blunted collagen related peptide (CRP) induced glyocoprotein VI (GPVI)-dependent platelet aggregation, ATP release and thrombus formation on a collagen-coated surface under shear rates of 1700{sup −sec}. Defective platelet aggregation after ceramidase inhibition could partially be overcome by exogenous sphingosine treatment reflecting a pivotal role of ceramidase-derived sphingosine in platelet function. Inhibition of serine palmitoyltransferase and ceramide synthase did not significantly modify GPVI-dependent platelet activation. In conclusion, the present study unraveled ceramidase as a crucial player in sphingosine-induced platelet activation following GPVI-dependent signaling.

60 APPLIED LIFE SCIENCES↗

An optimal serum-free defined condition for in vitro culture of kidney organoids

Kidney organoid is an emerging topic of importance for research in kidney development and regeneration. Conventional culture systems for kidney organoids reported thus far use culture media containing serum, which may compromise our understanding and the potential clinical applicability of the organoid system. In our present study, we tested two serum-free culture conditions and compared their suitability for the maintenance and growth of kidney organoids in culture. One of the serum-free culture conditions was the combination of keratinocytes serum free medium (KSFM) with knockout serum replacement (KSR) (KSFM + KSR), and the other was the combination of knockout DMEM/F12 (KD/F12) and KSR (KD/F12 + KSR). With cell aggregates derived from E12.5 mouse embryonic kidneys, we found that KD/F12 + KSR was superior to KSFM + KSR in promoting the growth of the aggregate with expansion of Six2{sup +} nephron progenitor cells (NPC) and elaborated ureteric branching morphogenesis. With KD/F12 + KSR, we found that lower concentrations of KSR at 5–10% were superior to a higher concentration (20%) in promoting the growth of aggregates without affecting the expression levels of NPC marker genes. We also found that NPC in aggregates retained their differentiation potential to develop nephron tubules through mesenchyme-to-epithelial transition (MET), after being maintained in culture under these conditions for up to 7 days. In conclusion, we have identified a defined serum-free culture condition suitable for the maintenance and growth of kidney organoids that retain the differentiation potential to develop nephron structures. This defined serum-free culture condition may serve as a useful platform for further investigation of kidney organoids in vitro.

60 APPLIED LIFE SCIENCES↗

Beta catenin is regulated by its subcellular distribution and mutant huntingtin status in Huntington's disease cell STHdhQ111/HdhQ111

Highlights: • Mutant Htt gain-of-function in Q111 cell increases miR-214 & decreases beta catenin. • Mutant Htt function in Q111 cell is aggregate independent. • Aggregate forming mutant Htt construct 83Q-DsRed increases beta catenin in Q7 cell. • Cytosolic localization of beta catenin in Q111 cell aids to its phosphorylation. Dysregulation of gene expression at RNA and protein level is a hallmark of Huntington's disease (HD). Altered levels of microRNAs and beta catenin in HD were studied earlier; however, any direct involvement of full length, basally-expressing mutant huntingtin (Htt) remained to be elusive. Here we reported that the gain-of-function mutation of full-length basally-expressing Htt in HD cell Q111 (STHdhQ111/HdhQ111) upregulated microRNA-214 and decreased beta catenin & its transcriptional activity in an aggregate-independent manner. The result was quite opposite of the function of aggregate-forming mutant Htt fragment 83Q-DsRed. Here, we also reported an elevated level of beta catenin phosphorylation in Q111 cell compared to Q7 cell (SThdhQ7/HdhQ7). We showed that in Q111 cell (compared to Q7), beta catenin was more localized in the cytosol than that of the plasma membrane. This is significant as Gsk3beta phosphorylates beta catenin in the cytosol. Hence, for the first time, our study identified beta catenin localization and mutant Htt status as two key factors of beta catenin regulation in HD.

60 APPLIED LIFE SCIENCES↗

The microstructure of laminin-111 compensates for dystroglycan loss in mammary epithelial cells in downstream expression of milk proteins

Laminin-111 (Ln-1), an extracellular matrix (ECM) glycoprotein found in the basement membrane of mammary gland epithelia, is essential for lactation. In mammary epithelial cells (MECs), dystroglycan (Dg) is believed to be necessary for polymerization of laminin-111 into networks., thus we asked whether correct polymerization could compensate for Dg loss. Artificially polymerized laminin-111 and the laminin-glycoprotein mix Matrigel, both formed branching, spread networks with fractal dimensions from 1.7 to 1.8, whereas laminin-111 in neutral buffers formed small aggregates without fractal properties (a fractal dimension of 2). In Dg knockout cells, either polymerized laminin-111 or Matrigel readily attached to the cell surface, whereas aggregated laminin-111 did not. In contrast, polymerized and aggregated laminin-111 bound similarly to Dg knock-ins. Both polymerized laminin-111 and Matrigel promoted cell rounding, clustering, formation of tight junctions, and expression of milk proteins, whereas aggregated Ln-1 did not attach to cells or promote functional differentiation. Finally, these findings support that the microstructure of Ln-1 networks in the basement membrane regulates mammary epithelial cell function.

59 BASIC BIOLOGICAL SCIENCES↗

Elucidating the speciation of extracted lanthanides by diglycolamides

Many studies over the past few decades have been devoted to addressing the application of diglycolamides (DGAs) for hydrometallurgical-based, f-element separations. Work to date has shown the molecular structure of a DGA derivative can have a significant impact on intra-lanthanide partitioning patterns. More recent studies have pushed towards probing the structure function relationship of the lanthanide-DGA complex to enable the design of more efficient lanthanide separation systems. Spectroscopic techniques, such as UV–Visible, Fourier Transformed Infrared Spectroscopy (FT-IR), Nuclear Magnetic Resonance (NMR), and Extended X-ray Absorption Fine Structure (EXAFS), provide information regarding the inner-sphere coordination of a given lanthanide-DGA complex. Scattering techniques, such as Dynamic Light Scattering (DLS), Small-Angle X-ray Scattering (SAXS), and Small-Angle Neutron Scattering (SANS), address nanoscale structures including aggregate sizes and morphology. Here, this review assesses the current state-of-knowledge regarding lanthanide-DGA hydrometallurgical (i.e., solvent extraction systems) interrogated using spectroscopic and scattering techniques to characterize the extracted Ln 3+ DGA species. Of particular interest to this review is the impact of varied diluents, inclusion and variation of phase modifiers, and DGA derivatization on system characteristics. While there has been extensive literature on the application of DGAs for f-element separations, the literature lacks a collective assessment of the speciation of Ln 3+ in the organic phase. This review provides new insights into the field of DGA separations, explicitly with an application to intra-lanthanide separations. Specifically, this review illustrates the importance of both the co-extraction anion (Cl - , NO 3 - , or ClO 4 - ) as it pertains to both the aggregate size and Ln 3+ distribution coefficient. It is evident the ability of the anion to disrupt the hydrogen bonding network limits both aggregate size and distribution coefficients according to the Hoffmeister series. This suggests the importance of the large, softer anions with a low charge-to-surface area ratio on encouraging hydrogen bond interactions. In addition, the co-extracted cation (H + vs Na + ) is important for mitigating transfer of Ln 3+ from the aqueous to the organic phase through extensive hydrogen bonding networks. These networks are responsible for forming supramolecular aggregates where a change in morphology is observed with increasing concentrations of H + and/or Ln 3+ in the organic phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Application of micro X-ray diffraction to investigate the reaction products formed by the alkali–silica reaction in concrete structures

Alkali–silica reaction (ASR) is one of the most important deterioration mechanisms in concrete leading to substantial damages of structures worldwide. Synchrotron-based micro-X-ray diffraction (micro-XRD) was employed to characterize the mineral phases formed in micro-cracks of concrete aggregates as a consequence of ASR. This high spatial resolution technique enables to directly gain structural information on ASR products formed in a 40-year old motorway bridge damaged due to ASR. Micro-X-ray-fluorescence was applied on thin sections to locate the reaction products formed in veins within concrete aggregates. Micro-XRD pattern were collected at selected points of interest along a vein by rotating the sample. Rietveld refinement determined the structure of the ASR product consisting of a new layered framework similar to mountainite and rhodesite. It is conceivable that understanding the structure of the ASR product may help developing new technical treatments inhibiting ASR.

36 MATERIALS SCIENCE↗

Microstructural effects in the simulation of creep of concrete

The influence of the microstructure on the visco-elastic properties of concrete is investigated using finite element simulations at the meso-scale. We first derive a constitutive law for the creep of the cement paste which accounts for both recoverable and permanent deformations, as well as the influence of temperature and internal relative humidity. The model is calibrated on a set of experiments at the cement paste scale, and then validated after upscaling to the concrete scale. The model is then applied to study the influence of the microstructure on the macroscopic creep of concrete. We show that materials with finer particles exhibit less creep, and that the anisotropy of creep can be explained with the shape and orientation of the aggregates. Furthermore, the acceleration of the stress relaxation in the presence of damage is explained by the micro-mechanical interaction between the aggregates, the cement paste, and the micro-cracks.

36 MATERIALS SCIENCE↗

A three-dimensional meso-scale approach to concrete fracture based on combined DEM with X-ray μCT images

Highlights: • We investigate fracture in concrete beams subjected to 3-point bending. • We use a discrete element method (DEM) to capture fracture. • Concrete is described as 4-phase material. • Evolution of micro-structural phenomena is investigated. • The 3D results are carefully compared with the 2D ones. - Abstract: The paper shows three-dimensional (3D) numerical mesoscopic results on progressive concrete fracture at aggregate level in a notched concrete beam under bending. A classical particle discrete element method was used to capture fracture in concrete. Heterogeneity was taken into account with a 4-phase concrete description: aggregate, cement matrix, macro-voids and interfacial transitional zones. Both the real shape and location of aggregate particles in concrete were assumed in DEM analyses based on X-ray μCT scans. A satisfactory agreement in terms of the vertical force versus crack mouth opening displacement evolution and crack geometry was achieved between DEM analyses and own laboratory tests. The evolution of broken contacts, contact normal forces, particle rotations, internal energies was studied at the aggregate level. The 3D results were also carefully compared with the 2D ones. The 3D model proved to be a promising simulation tool in predicting concrete fracture at the mesoscopic and macroscopic level.

36 MATERIALS SCIENCE↗