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At least 19 records

U2AF - Hypoxia-induced fas alternative splicing regulator

The splicing machinery heavily contributes to biological complexity and especially to the ability of cells to adapt to altered cellular conditions. Hypoxia also plays a key role in the pathophysiology of many disease states. Recent studies have revealed that tumorigenesis and hypoxia are involved in large-scale alterations in alternative pre-mRNA splicing. Fas pre-mRNA is alternatively spliced by excluding exon 6 to produce soluble Fas (sFas) protein that lacks a transmembrane domain and acts by inhibiting Fas mediated apoptosis. }In the present study we show that U2AF is involved in hypoxia dependent anti-apoptotic Fas mRNA isoform formation. Our performed studies show that U2AF-RNA interaction is reduced in hypoxic cells, leading to reduction of Fas and increased sFas mRNAs formation. Efficient U2AF-RNA interactions of both subunits are important for Fas exon 6 inclusion into forming mRNA in normoxic and hypoxic cells.

60 APPLIED LIFE SCIENCES↗

Enhancing the USDA FAS Crop Forecasting System Using SMAP L3 Soil Moisture Observations

One of the U.S. Department of Agriculture-Foreign Agricultural Services (USDA-FAS) mission objectives is to provide current information on global crop supply and demand estimates. Crop growth and development is especially susceptible to the amount of water present in the root-zone portion of the soil profile. Therefore, accurate knowledge of the root-zone soil moisture (RZSM) is an essential for USDA-FAS global crop assessments. This paper focusses on the possibility of enhancing the USDA-FAS's RZSM estimates through the integration of passive-based soil moisture observations derived from the Soil Moisture Active Passive (SMAP) mission into the USDA-FAS Palmer model. Lag-correlation analysis, which explores the agreement between changes in RZSM and crop status indicated that the satellite-based observations can enhance the model-only estimates.

crop growth↗

FAS multigrid calculations of three dimensional flow using non-staggered grids

Grid staggering is a well known remedy for the problem of velocity/pressure coupling in incompressible flow calculations. Numerous inconveniences occur, however, when staggered grids are implemented, particularly when a general-purpose code, capable of handling irregular three-dimensional domains, is sought. In several non-staggered grid numerical procedures proposed in the literature, the velocity/pressure coupling is achieved by either pressure or velocity (momentum) averaging. This approach is not convenient for simultaneous (block) solvers that are preferred when using multigrid methods. A new method is introduced in this paper that is based upon non-staggered grid formulation with a set of virtual cell face velocities used for pressure/velocity coupling. Instead of pressure or velocity averaging, a momentum balance at the cell face is used as a link between the momentum and mass balance constraints. The numerical stencil is limited to 9 nodes (in 2D) or 27 nodes (in 3D), both during the smoothing and inter-grid transfer, which is a convenient feature when a block point solver is applied. The results for a lid-driven cavity and a cube in a lid-driven cavity are presented and compared to staggered grid calculations using the same multigrid algorithm. The method is shown to be stable and produce a smooth (wiggle-free) pressure field.

Matovic, D.↗

Large fluxes of fatty acids from membranes to triacylglycerol and back during N-deprivation and recovery in Chlamydomonas

Abstract Microalgae accumulate triacylglycerol (TAG) during nutrient deprivation and break it down after nutrient resupply, and these processes involve dramatic shifts in cellular carbon allocation. Due to the importance of algae in the global carbon cycle, and the potential of algal lipids as feedstock for chemical and fuel production, these processes are of both ecophysiological and biotechnological importance. However, the metabolism of TAG is not well understood, particularly the contributions of fatty acids (FAs) from different membrane lipids to TAG accumulation and the fate of TAG FAs during degradation. Here, we used isotopic labeling time course experiments on Chlamydomonas reinhardtii to track FA synthesis and transfer between lipid pools during nitrogen (N)-deprivation and resupply. When cells were labeled before N-deprivation, total levels of label in cellular FAs were unchanged during subsequent N-deprivation and later resupply, despite large fluxes into and out of TAG and membrane lipid pools. Detailed analyses of FA levels and labeling revealed that about one-third of acyl chains accumulating in TAG during N-deprivation derive from preexisting membrane lipids, and in total, at least 45% of TAG FAs passed through membrane lipids at one point. Notably, most acyl chains in membrane lipids during recovery after N-resupply come from TAG. Fluxes of polyunsaturated FAs from plastidic membranes into TAG during N-deprivation were particularly noteworthy. These findings demonstrate a high degree of integration of TAG and membrane lipid metabolism and highlight a role for TAG in storage and supply of membrane lipid components.

Plant Sciences↗

Gallium isotopic constraints for the origin of the Earth-Moon system

Comparatively heavy isotopic compositions of moderately volatile elements (MVE) in lunar rocks have been advocated to reflect the loss of light isotopes during devolatilization processes from the Moon. In this study we present new gallium (Ga) isotope data for lunar highland rocks, with a focus on the Ferroan Anorthosite Suite (FAS). These are commonly thought to be direct crystallization products from the late lunar magma ocean (LMO) and should contain the majority of the Ga inventory of the Moon. As such, FAS rocks are crucial for identifying the processes that drove Ga isotope fractionation as well as for inferring the Ga isotopic composition of the bulk Moon. Our data reveal that FAS samples have a range in δ 71 Ga from -0.27 to 0.22‰ and are generally isotopically light in Ga compared to other lunar lithologies, but straddle values typical of terrestrial rocks. Although Ga is defined as an MVE, these Ga isotope variations do not correspond with concentrations of more volatile elements, indicating that Ga isotope variations in the FAS are not primarily controlled by devolatilization processes. Instead, the Ga isotopic compositions of bulk FAS rocks broadly correlate with the composition of plagioclase, with the calcium content of plagioclase decreasing as Ga becomes isotopically heavier. This suggests that fractionation of Ga isotopes in FAS rocks was caused by the preferential incorporation of isotopically light Ga into plagioclase during the later solidification stages of the LMO. The progressive crystallization and extraction of plagioclase forces the residual melt towards increasingly heavier Ga isotope ratios, corroborating similar conclusions derived from correlations between δ 71 and Eu* in the mare basalt suite. Using Ga isotope partitioning calculations, we demonstrate that an isotope fractionation coefficient between plagioclase and coexisting melt of -0.3 to -0.4‰ could explain the observed range of δ 71 values in FAS, mare basalt suite rocks, and KREEP. These calculations allow for a first order estimate of the Ga isotopic composition of the bulk silicate Moon prior to plagioclase fractionation and suggest it was close to the composition of the bulk silicate Earth. This would imply that the Moon did not lose a substantial fraction of its Ga inventory during accretion, consistent with new constraints from Rb-Sr isotope systematics that indicate the Moon's volatile deficit was primarily inherited from Theia. In conjunction with the overlap in non-mass-dependent isotope ratios, these collective observations could be reconciled if Theia and the proto-Earth formed in similar regions of the inner Solar System that were already volatile-depleted.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Time domain probabilistic seismic risk analysis using ground motion prediction equations of Fourier amplitude spectra

Modeling of Fourier amplitude spectra (FAS) of seismic motions has gained much attention in engineering seismology. In the past few years, several ground motion prediction equations (GMPEs) and inter-frequency correlation structure of FAS have been established. Due to many preferable characteristics of FAS, probabilistic seismic hazard/risk analysis is rapidly changing from ergodic, spectrum acceleration Sa(T 0 )-based approach to non-ergodic, site-specific, FAS-based approach. This paper presents time domain intrusive framework for probabilistic seismic risk analysis using GMPE of FAS. Herein, methodology for time domain stochastic ground motion modeling based on GMPEs of FAS is presented in some detail. The simulated uncertain motions are modeled as a random process and represented by polynomial chaos Karhunen-Loève expansion. The random process excitations are further propagated into the uncertain structural system using Galerkin stochastic finite element method (SFEM). Probabilistic evolution of structural response is solved, and such solution is used to develop seismic risk for any damage state. The presented framework is illustrated through seismic risk analysis of a four-story building subjected to possible earthquakes from two strike slip faults. The influences of the epistemic uncertainties in source stress drop Δσ and site attenuation κ0 on seismic risk are investigated. The need for non-ergodic seismic risk analysis with source-specific and site specific characterizations is emphasized.

58 GEOSCIENCES↗

A genetic screen for dominant chloroplast reactive oxygen species signaling mutants reveals life stage-specific singlet oxygen signaling networks

Plants employ intricate molecular mechanisms to respond to abiotic stresses, which often lead to the accumulation of reactive oxygen species (ROS) within organelles such as chloroplasts. Such ROS can produce stress signals that regulate cellular response mechanisms. One ROS, singlet oxygen ( 1 O 2 ), is predominantly produced in the chloroplast during photosynthesis and can trigger chloroplast degradation, programmed cell death (PCD), and retrograde (organelle-to-nucleus) signaling. However, little is known about the molecular mechanisms involved in these signaling pathways or how many different signaling 1 O 2 pathways may exist. The Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant conditionally accumulates chloroplast 1 O 2 , making fc2 a valuable genetic system for studying chloroplast 1 O 2 -initiated signaling. Here, we have used activation tagging in a new forward genetic screen to identify eight dominant fc2 activation-tagged (fas) mutations that suppress chloroplast 1 O 2 -initiated PCD. While 1 O 2 -triggered PCD is blocked in all fc2 fas mutants in the adult stage, such cellular degradation in the seedling stage is blocked in only two mutants. This differential blocking of PCD suggests that life-stage-specific 1 O 2 -response pathways exist. In addition to PCD, fas mutations generally reduce 1 O 2 -induced retrograde signals. Furthermore, fas mutants have enhanced tolerance to excess light, a natural mechanism to produce chloroplast 1 O 2 . However, general abiotic stress tolerance was only observed in one fc2 fas mutant (fc2 fas2). Together, this suggests that plants can employ general stress tolerance mechanisms to overcome 1 O 2 production but that this screen was mostly specific to 1 O 2 signaling. We also observed that salicylic acid (SA) and jasmonate (JA) stress hormone response marker genes were induced in 1 O 2 -stressed fc2 and generally reduced by fas mutations, suggesting that SA and JA signaling is correlated with active 1 O 2 signaling and PCD. Together, this work highlights the complexity of 1 O 2 signaling by demonstrating that multiple pathways may exist and introduces a suite of new 1 O 2 signaling mutants to investigate the mechanisms controlling chloroplast-initiated degradation, PCD, and retrograde signaling.

59 BASIC BIOLOGICAL SCIENCES↗

The X-43 Fin Actuation System Problem - Reliability in Shades of Gray

Following the loss of the first X-43 during launch, the mishap investigation board indicated the Fin Actuator System (FAS) needed to have a larger torque margin. To supply this added torque, a second actuator was added. The consequences of what seemed to be a simple modification would trouble the X-43 program. Because of the second actuator, a new computer board was required. This proved to be subject to electronic noise. This resulted in the actuator latch up in ground tests of the FAS for the second launch. Such a latch up would cause the Pegasus booster to fail, as the FAS was a single string system. The problem was corrected and the second flight was successful. The same modifications were added to the FAS for flight three. When the FAS underwent ground tests, it also latched up. The failure indicated that each computer board had a different tolerance to electronic noise. The problem with the FAS was corrected. Subsequently, another failure occurred, raising questions about the design, and the probability of failure for the X-43 Mach 10 flight. This was not simply a technical issue, but illuminated the difficulties facing both managers and engineers in assessing risk, design requirements, and probabilities in cutting edge aerospace projects.

Peebles, Curtis↗

13C-labeling reveals how membrane lipid components contribute to triacylglycerol accumulation in Chlamydomonas

Abstract Lipid metabolism in microalgae has attracted much interest due to potential utilization of lipids as feedstocks for biofuels, nutraceuticals, and other high-value compounds. Chlamydomonas reinhardtii is a model organism for characterizing the synthesis of the neutral lipid triacylglycerol (TAG), from which biodiesel is made. While much of TAG accumulation under N-deprivation is the result of de novo fatty acid (FA) synthesis, recent work has revealed that approximately one-third of FAs, especially polyunsaturated FAs (PUFAs), come from preexisting membrane lipids. Here, we used 13C-isotopic labeling and mass spectrometry to analyze the turnover of glycerol backbones, headgroups, FAs, whole molecules, and molecular fragments of individual lipids. About one-third of the glyceryl backbones in TAG are derived from preexisting membrane lipids, as are approximately one-third of FAs. The different moieties of the major galactolipids turn over synchronously, while the FAs of diacylglyceryltrimethylhomoserine (DGTS), the most abundant extraplastidial lipid, turn over independently of the rest of the molecule. The major plastidic lipid monogalactosyldiacylglycerol (MGDG), whose predominant species is 18:3α/16:4, was previously shown to be a major source of PUFAs for TAG synthesis. This study reveals that MGDG turns over as whole molecules, the 18:3α/16:4 species is present in both DAG and TAG, and the positional distribution of these PUFAs is identical in MGDG, DAG, and TAG. We conclude that headgroup removal with subsequent acylation is the mechanism by which the major MGDG species is converted to TAG during N-deprivation. This has noteworthy implications for engineering the composition of microalgal TAG for food, fuel, and other applications.

Plant Sciences↗

Evaluating the Operational Application of SMAP for Global Agricultural Drought Monitoring

Over the past two decades, remote sensing has made possible the routine global monitoring of surface soil moisture. Regionalagricultural drought monitoring is one of the most logicalapplication areas for such monitoring. However, remote sensing alone provides soil moisture information for only the top few centimetersof the soil profile, while agricultural drought monitoring requires knowledge of the amount of water present in the entireroot zone. The assimilation of remotely sensed soil moisture productsinto continuous soil water balance models provides a way ofaddressing this shortcoming. Here, we describe the assimilationof NASA's soil moisture active passive (SMAP) surface soil moisture data into the United States Department of Agriculture Foreign Agricultural Service (USDA FAS) Palmer model and assess the impactof SMAP on USDA FAS drought monitoring capabilities. Theassimilation of SMAP is specifically designed to enhance the model skill and the USDA FAS drought capabilities by correcting for randomerrors inherent in its rainfall forcing data. The performanceof this SMAP-based assimilation system is evaluated using two approaches.At global scale, the accuracy of the system is assessed by examining the lagged correlation agreement between soil moistureand the normalized difference vegetation index (NDVI). Additional regional-scale evaluation using in situ-based soil moisture estimatesis carried out at seven of the SMAP core Cal/Val sites located in theUSA. Both types of analysis demonstrate the value of assimilating SMAP into the USDA FAS Palmer model and its potential to enhance operational USDA FAS root-zone soil moisture information.

Mladenova, Iliana E.↗

Multilevel well modeling in aggregation-based nonlinear multigrid for multiphase flow in porous media

A full approximation scheme (FAS) nonlinear multigrid solver for two-phase flow and transport problems driven by wells with multiple perforations is developed here. It is an extension to our previous work on FAS solvers for diffusion and transport problems. The solver is applicable to discrete problems defined on unstructured grids as the coarsening algorithm is aggregation-based and algebraic. To construct coarse basis that can better capture the radial flow near wells, coarse grids in which perforated well cells are not near the coarse-element interface are desired. This is achieved by an aggregation algorithm proposed in this paper that makes use of the location of well cells in the cell-connectivity graph. Numerical examples in which the FAS solver is compared against Newton's method on benchmark problems are given. In particular, for a refined version of the SAIGUP model, the FAS solver is at least 35% faster than Newton's method for time steps with a CFL number greater than 10.

58 GEOSCIENCES↗

Polyketide synthase-based controlled synthesis of polycyclopropanated fuel molecules

Reducing carbon emissions from aviation and long-distance transportation sectors requires the development of sustainable biofuels with suitable energy density, freezing point, and other physical properties. We previously demonstrated biological production of high energy polycyclopropanated fatty acids (POP-FAs, class I) using an iterative polyketide synthase (iPKS) pathway in a Streptomyces host. Here, we used a computational model of fuel properties to identify chain length and cyclopropanation control as critical steps to engineer this iPKS for biofuel applications. We next explored the natural diversity of POP biosynthesis by investigating homologous pathways. Then, by in vivo gene exchange, we determined cyclopropanase (CP) catalysis to be key for POP-FA engineering. Leveraging both natural and engineered pathway product diversity, we demonstrate targeted production of improved POP-FAs, namely shortened POP-FAs with predicted superior freezing point properties for aviation, as well as fully cyclopropane-saturated POP-FAs which should have superior energy-density. These precise and controllable modifications to POP-FA structure open the door for bioproduction of designer POP fuels.

Yin, Kevin↗

Understanding the Role of Populus ECERIFERUM2-Likes in the Biosynthesis of Very-Long-Chain Fatty Acids for Cuticular Waxes

Cuticular waxes are derived from very-long-chain fatty acid (VLCFA) precursors made by the concerted action of four enzymes that form the fatty acid (FA) elongation complex. Here, the condensing enzyme of the complex confers specificity to substrates of different chain lengths, yet on its own cannot account for the biosynthesis of VLCFAs longer than 28 carbons (C28). Recent evidence from Arabidopsis thaliana points to a synergistic role of clade II BAHD acyltransferases and condensing enzymes in the elongation of VLCFAs beyond C28. In Populus trichocarpa, clade II is composed of seven uncharacterized paralogous genes (PtCER2-like1–7). In the present study, five of these genes were heterologously expressed in yeast and their respective FA profiles were determined. PtCER2-likes differentially altered the accumulation of C28 and C30 FAs when expressed in the presence of the condensing enzyme AtCER6. Among these, PtCER2-like5 produced the highest levels of C28 FAs in yeast and its expression was localized to the epidermis in β-glucuronidase-reporter poplar lines, consistent with a role in cuticular wax biosynthesis. Complementation of the A. thaliana cer2-5 mutant with PtCER2-like5 increased the levels of C28-derived cuticular waxes at the expense of C30-derived components. Together, these results demonstrate that the role of CER2-likes in cuticular wax biosynthesis is conserved in Populus clade II BAHD acyltransferases.

59 BASIC BIOLOGICAL SCIENCES↗

Different feeding patterns affect meat quality of Tibetan pigs associated with intestinal microbiota alterations

This study aimed to investigate the effects of different feeding patterns on meat quality, gut microbiota and its metabolites of Tibetan pigs. Tibetan pigs with similar body weight were fed the high energy diets ( HEP , 20 pigs) and the regular diets ( RFP , 20 pigs), and free-ranging Tibetan pigs ( FRP , 20 pigs) were selected as the reference. After 6 weeks of experiment, meat quality indexes of semitendinosus muscle ( SM ) and cecal microbiota were measured. The results of meat quality demonstrated that the shear force of pig SM in FRP group was higher than that in HEP and RFP groups ( p < 0.001); the pH-value of SM in HEP pigs was higher at 45 min ( p < 0.05) and lower at 24 h ( p < 0.01) after slaughter than that in FRP and RFP groups; the SM lightness ( L* value) of FRP pigs increased compared with RFP and HEP groups ( p < 0.001), while the SM redness ( a* value) of FRP pigs was higher than that of RFP group ( p < 0.05). The free fatty acid ( FA ) profile exhibited that the total FAs and unsaturated FAs of pig SM in HEP and RFP groups were higher than those in FRP group ( p < 0.05); the RFP pigs had more reasonable FA composition with higher n-3 polyunsaturated FAs ( PUFAs ) and lower n-6/n-3 PUFA ratio than HEP pigs ( p < 0.05). Based on that, we observed that Tibetan pigs fed high energy diets (HEP) had lower microbial α-diversity in cecum ( p < 0.05), and distinct feeding patterns exhibited a different microbial cluster. Simultaneously, the short-chain FA levels in cecum of FRP and RFP pigs were higher compared with HEP pigs ( p < 0.05). A total of 11 genera related to muscle lipid metabolism or meat quality, including Alistipes , Anaerovibrio , Acetitomaculun , etc., were identified under different feeding patterns ( p < 0.05). Spearman correlation analysis demonstrated that alterations of free FAs in SM were affected by the genera Prevotellaceae_NK3B31_group , Prevotellaceae UCG-003 and Christensenellaceae_R-7_group ( p < 0.05). Taken together, distinct feeding patterns affected meat quality of Tibetan pigs related to gut microbiota alterations.

Zhu, Yanbin↗

Biosynthesis of polycyclopropanated high energy biofuels

Cyclopropane-functionalized hydrocarbons are excellent fuels due their high energy density. However, the organic synthesis of these molecules is challenging and harmful to the environment. In this work we produced polycyclopropanated fatty acids in bacteria. These molecules can be easily converted into renewable fuels for high energy applications such as shipping, long-haul transport, aviation, and rocketry. We explored the chemical diversity encoded in the genome of thousands of bacteria to identify and repurpose naturally occurring cyclopropanated molecules. We identified a set of candidate iterative polyketide synthases (iPKSs) predicted to produce polycyclopropanated fatty acids (POP-FAs), expressed these PKSs in Streptomyces coelicolor and produced the POP-FAs. We determined the structure of the molecules and increased their production 22-fold. Polycyclopropanated fatty acid methyl esters (POP-FAMEs) were obtained by methyl esterifying the POP-FAs. Finally, we calculated that our POP fuel candidates can have energy densities of more than 50 MJ/L. Our research shows that POP-FAMEs and other polyketide derived POPs have the energetic properties for energy-demanding applications for which sustainable alternatives are scarce.

09 BIOMASS FUELS↗

A Nonergodic Ground-Motion Model for the San Francisco Bay Area for Small-Magnitude Earthquakes

ABSTRACT Recently, generative models have become a computationally efficient alternative to physics-based numerical simulations of ground motions. Neural networks can learn from existing ground-motion data to generate unobserved ground-motion data at new source and site locations. A key challenge with generative models is ensuring that predicted ground motions remain within a physically realistic range. For this purpose, we developed an empirical, nonergodic ground-motion model (GMM) for small-magnitude earthquakes in the San Francisco Bay area based on about 5000 recordings per component for Mw ≤ 4 earthquakes. The nonergodic GMM predicts spatially varying median source, site, and path effects for both the Fourier amplitude spectrum (FAS) and the Fourier phase derivative (a proxy for duration), as well as the corresponding epistemic uncertainty for each term. For FAS, our model shows above-average source and site effects in the western part of the region and below-average effects in the eastern part, with regional effects exhibiting larger spatial correlation lengths with increasing frequency. For duration, the source term is negligible for small-magnitude earthquakes, and the site term leads to site-specific variations up to 5 s. Path effects for FAS and duration depend on the source–site pair and are extrapolated spatially using recent methods for path-effect modeling. The aleatory variability of the within-site within-path residuals is similar to the variability found in previous studies for other regions. The nonergodic model provides two key contributions: first, median adjustment terms that are transferable to larger magnitude earthquakes, further reducing aleatory variability in probabilistic seismic hazard analysis; second, region-specific criteria for validating machine learning-based ground-motion generators to evaluate whether synthetic ground motions exhibit physically realistic source, site, and path effects.

Lacour, Maxime↗

A lipidomics platform to analyze the fatty acid compositions of non-polar and polar lipid molecular species from plant tissues: Examples from developing seeds and seedlings of pennycress (Thlaspi arvense)

The lipidome comprises the total content of molecular species of each lipid class, and is measured using the analytical techniques of lipidomics. Many liquid chromatography-mass spectrometry (LC-MS) methods have previously been described to characterize the lipidome. However, many lipidomic approaches may not fully uncover the subtleties of lipid molecular species, such as the full fatty acid (FA) composition of certain lipid classes. Here, we describe a stepwise targeted lipidomics approach to characterize the polar and non-polar lipid classes using complementary LC-MS methods. Our “polar” method measures 260 molecular species across 12 polar lipid classes, and is performed using hydrophilic interaction chromatography (HILIC) on a NH2 column to separate lipid classes by their headgroup. Our “non-polar” method measures 254 molecular species across three non-polar lipid classes, separating molecular species on their FA characteristics by reverse phase (RP) chromatography on a C30 column. Five different extraction methods were compared, with an MTBE-based extraction chosen for the final lipidomics workflow. A state-of-the-art strategy to determine and relatively quantify the FA composition of triacylglycerols is also described. This lipidomics workflow was applied to developing, mature, and germinated pennycress seeds/seedlings and found unexpected changes among several lipid molecular species. During development, diacylglycerols predominantly contained long chain length FAs, which contrasted with the very long chain FAs of triacylglycerols in mature seeds. Potential metabolic explanations are discussed. The lack of very long chain fatty acids in diacylglycerols of germinating seeds may indicate very long chain FAs, such as erucic acid, are preferentially channeled into beta-oxidation for energy production.

59 BASIC BIOLOGICAL SCIENCES↗