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At least 1,423 records · Page 79

Structure of the Regulator of G Protein Signaling 8 (RGS8)-Gα q Complex: Molecular Basis for Gα Selectivity

Regulator of G protein signaling (RGS) proteins interact with activated Gα subunits via their RGS domains and accelerate the hydrolysis of GTP. Although the R4 subfamily of RGS proteins generally accepts both Gα i/o and Gα q/11 subunits as substrates, the R7 and R12 subfamilies select against Gα q/11 . In contrast, only one RGS protein, RGS2, is known to be selective for Gαq/11. The molecular basis for this selectivity is not clear. Previously, the crystal structure of RGS2 in complex with Gα q revealed a non-canonical interaction that could be due to interfacial differences imposed by RGS2, the Gα subunit, or both. To resolve this ambiguity, the 2.6 Å crystal structure of RGS8, an R4 subfamily member, was determined in complex with Gα q . RGS8 adopts the same pose on Gα q as it does when bound to Gα i3 , indicating that the non-canonical interaction of RGS2 with Gα q is due to unique features of RGS2. Here, based on the RGS8-Gα q structure, residues in RGS8 that contact a unique α-helical domain loop of Gα q were converted to those typically found in R12 subfamily members, and the reverse substitutions were introduced into RGS10, an R12 subfamily member. Although these substitutions perturbed their ability to stimulate GTP hydrolysis, they did not reverse selectivity. Instead, selectivity for Gα q seems more likely determined by whether strong contacts can be maintained between α6 of the RGS domain and Switch III of Gα q , regions of high sequence and conformational diversity in both protein families.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Self-organization of S adatoms on Au(111): √3R30° rows at low coverage

Using scanning tunneling microscopy, we observe an adlayer structure that is dominated by short rows of S atoms, on unreconstructed regions of a Au(111) surface. This structure forms upon adsorption of low S coverage (less than 0.1 monolayer) on a fully reconstructed clean surface at 300 K, then cooling to 5 K for observation. The rows adopt one of three orientations that are rotated by 30° from the close-packed directions of the Au(111) substrate, and adjacent S atoms in the rows are separated by √3 times the surface lattice constant, a. Monte Carlo simulations are performed on lattice-gas models, derived using a limited cluster expansion based on density functional theory energetics. Models which include long-range pairwise interactions (extending to 5a), plus selected trio interactions, successfully reproduce the linear rows of S atoms at reasonable temperatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes

Abstract Background Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput. Results Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50–99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC–MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18 O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics. Conclusions We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.

59 BASIC BIOLOGICAL SCIENCES↗

In Situ Studies of Methanol Decomposition Over Cu(111) and Cu2O/Cu(111): Effects of Reactant Pressure, Surface Morphology, and Hot Spots of Active Sites

The dissociative adsorption of methanol was investigated on Cu(111) and ultrathin Cu 2 O films. We employed synchrotron-based Ambient Pressure X-ray Photoelectron Spectroscopy (AP-XPS) and Scanning Tunneling Microscopy (STM) to study the dynamics of gas–solid interactions, and calculations based on Density Functional Theory (DFT) were used to examine the reaction path. C 1s XPS spectra revealed that methanol underwent dissociative adsorption on plain Cu(111) to form methoxy (CH 3 O), formaldehyde (H 2 CO), and formate (HCOO) at a pressure range of 0.5–10 mTorr, with these species remaining on the surface after evacuation. This was accompanied by the appearance of a low coverage (~0.05 ML) of O ads in the O 1s which can be considered a highly active site for methanol activation. The high activity is apparent by a coverage of 0.8 ML of methoxy at room temperature. STM was unable to image these species at room temperature as they were highly mobile on metallic copper. In contrast, for CH 3 OH on Cu 2 O/Cu(111), STM showed clear hot spots for reaction and a complex array of adsorption structures. On the oxide substrate, there was decomposition of methanol to H 2 CO, CH 3 O, HCOO, and hydrocarbon species (CH x ) due to the subsequent interactions of methanol with lattice oxygen. Cu(111) remained entirely saturated with decomposition products under 10 mTorr of methanol (θ ≈ 0.97 ML), whereas the Cu 2 O overlayer was saturated at a much lower coverage (θ ≈ 0.30 ML). STM revealed rows and step edges of Cu 2 O decorated with decomposition products and metallic Cu islands ~5 nm in size. The difference in activity between Cu(111) and Cu 2 O/Cu(111) is attributed to the significant amount of O present on the oxide surface. Additionally, Density Functional theory (DFT) calculations described the XPS measurements well, showing a likely methanol dissociation to *CH 3 O and therefore a surface reduction. More importantly, the DFT results revealed that it was the chemisorbed oxygen on Cu 2 O/Cu(111) which oxidized the dissociated *CH 3 O to *HCOO and eventually CO 2 , while the reaction only involving upper oxygen on the Cu 2 O hexagonal ring led to the formation of H 2 CO.

36 MATERIALS SCIENCE↗

Confocal filtering in cathodoluminescence microscopy of nanostructures

Cathodoluminescence (CL) microscopy allows optical characterization of nanostructures at high spatial resolution. At the nanoscale, a main challenge of the technique is related to the background CL generated within the sample substrate. Here, we implement confocal detection of the CL signal to minimize the background contribution to the measurement. Nano-phosphors were used as point sources to evaluate the filtering capabilities of our confocal CL system, obtaining an axial intensity profile with 2.7 μm full width at half maximum for the central peak, in good correspondence with theoretical expectations. Considering the electron interaction volume, we found that the confocal filter becomes effective for electron energies above 20 keV, when using a 25 μm pinhole (0.86 Airy units). To illustrate our approach, we present confocal CL imaging of gold nanowires and triangular shaped plates deposited on an indium-tin oxide covered glass substrate, comparing the images with those obtained in standard unfiltered CL detection. The results show that confocal CL microscopy is a valuable tool for the investigation of nanostructures on highly cathodoluminescent substrates, widely used in biological and optical applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Removal of Fat Components in High TDS Leather Wastewater by Saline-Tolerant Lipase-Assisted Nanoporous-Activated Carbon

The present investigation was carried out for the degradation of fatty components in high TDS containing wastewater (soak liquor) discharged from leather industry, and the degradation was achieved by saline-tolerant lipase-immobilized functionalized nanoporous-activated carbon (STLNPAC). The lipase was extracted from the halophilic organism, Bacillus cereus. The optimum conditions for lipase production such as time, 60 h; temperature, 50 °C; pH, 10; and substrate concentration, 2.5% (w/v) were determined through response surface methodology (RSM). The functionalization of NPAC was done by ethylenediamine/glutaraldehyde covalent interaction technique followed by the immobilization of saline-tolerant lipase onto FNPAC. The functional properties of STLNPAC were analyzed through instrumentation techniques such as TGA-DSC, FT-IR, XRD, and SEM images. The lipid content of soak liquor was removed by > 99% at HRT of 60 min using STLNPAC-packed bed reactor. The efficiency was evaluated by using UV-visible and FT-IR spectroscopic analyses. The degradation of lipids was best obeyed by pseudo first-order rate kinetics, and the rate constant was found to be 1.6 × 10{sup −3} min{sup −1}. The biodegradability index of soak liquor was increased from 0.322 to 0.426, highly favorable for the complete removal of organic components in subsequent operations.

60 APPLIED LIFE SCIENCES↗

Understanding the Influence of Water-Soluble Compounds from Unpretreated Corn Stover Pellets on Enzymatic Hydrolysis of Cellulose

Aqueous extractives are minor and non-structural compounds in biomass that can be extracted using solvents, while contributing significantly to lignocellulose characteristics. Yet their roles in enzyme-mediated processing of lignocellulosic biomass remain elusive. Here, we examine the composition and features of extractives derived from untreated pelleted corn stover as well as their effects on enzymatic hydrolysis. Unlike the observations described in previous reports, we find that water extractable material improves the enzymatic hydrolysis of extractive-free stover by 67% with a glucose yield increase from 12% to 20% with 6 FPU cellulase per g glucan, whereas the enzyme activities are diminished when using microcrystalline cellulose as a substrate. The different behavior of corn stover and microcrystalline cellulose is likely attributed to the presence of lignin, which may interact with inhibitory compounds such as phenolics, mitigating the detrimental impacts of soluble inhibitors or insoluble lignin or both. These findings advance our fundamental understanding of the intrinsic behavior of extractives and help to optimize the schemes for efficient and cost-competitive enzymatic conversion of lignocellulose.

09 BIOMASS FUELS↗

Multi-layered heterochromatin interaction as a switch for DIM2-mediated DNA methylation

Functional crosstalk between DNA methylation, histone H3 lysine-9 trimethylation (H3K9me3) and heterochromatin protein 1 (HP1) is essential for proper heterochromatin assembly and genome stability. However, how repressive chromatin cues guide DNA methyltransferases for region-specific DNA methylation remains largely unknown. Here, we report structure-function characterizations of DNA methyltransferase Defective-In-Methylation-2 (DIM2) in Neurospora . The DNA methylation activity of DIM2 requires the presence of both H3K9me3 and HP1. Our structural study reveals a bipartite DIM2-HP1 interaction, leading to a disorder-to-order transition of the DIM2 target-recognition domain that is essential for substrate binding. Furthermore, the structure of DIM2-HP1-H3K9me3-DNA complex reveals a substrate-binding mechanism distinct from that for its mammalian orthologue DNMT1. In addition, the dual recognition of H3K9me3 peptide by the DIM2 RFTS and BAH1 domains allosterically impacts the DIM2-substrate binding, thereby controlling DIM2-mediated DNA methylation. Together, this study uncovers how multiple heterochromatin factors coordinately orchestrate an activity-switching mechanism for region-specific DNA methylation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Superhydrophobic durable coating based on UV-photoreactive silica nanoparticles

Superhydrophobic surfaces with contact angle (CA) >150 and sliding angle (SA) <10 have been aroused curiosity over the years due to their various applications. Superhydrophobicity can be obtained tailoring the chemistry and the roughness of the surface, mimicking the Lotus flower. Most superhydrophobic surfaces based on secondary bonding lose their roughness in harsh conditions and are unsuitable for practical applications. Photoreactive SiO{sub 2} nanoparticles (NPs) based on benzophenone (BP) can be a very effective tool for formation of reactive species that function as a molecular bridge by covalent bonding between the NP and any polymer matrix with C-C and C-H bonds. The present work focused on thermoset radiation curing urethane acrylate. Upon UV irradiation reactive excited nπ* triplet benzophenone species are formed and react through hydrogen abstraction to form ketyl radicals which interact with a radicals from the UV irradiated polymer matrix to yield covalent bonding. Roughness was achieved by dipping the substrate in SiO{sub 2}@BPs NPs dispersion followed by irradiation. Fluoroalkylsilane was used to obtain hydrophobic top layer. AFM nano manipulation was used to verify the immobilization of NPs. Evaluation of durability was made using air flow at 300 km/hr. Preliminary results indicate the formation of super hydrophobic surfaces (CA>150 and SA<10) with improved stability.

36 MATERIALS SCIENCE↗

Multiscale porous elastomer substrates for multifunctional on-skin electronics with passive-cooling capabilities

In addition to mechanical compliance, achieving the full potential of on-skin electronics needs the introduction of other features. For example, substantial progress has been achieved in creating biodegradable, self-healing, or breathable, on-skin electronics. However, the research of making on-skin electronics with passive-cooling capabilities, which can reduce energy consumption and improve user comfort, is still rare. Herein, we report the development of multifunctional on-skin electronics, which can passively cool human bodies without needing any energy consumption. This property is inherited from multiscale porous polystyrene-block-poly(ethylene-ran-butylene)-block-polystyrene (SEBS) supporting substrates. The multiscale pores of SEBS substrates, with characteristic sizes ranging from around 0.2 to 7 µm, can effectively backscatter sunlight to minimize heat absorption but are too small to reflect human-body midinfrared radiation to retain heat dissipation, thereby delivering around 6 °C cooling effects under a solar intensity of 840 W∙m -2 . Other desired properties, rooted in multiscale porous SEBS substrates, include high breathability and outstanding waterproofing. The proof-of-concept bioelectronic devices include electrophysiological sensors, temperature sensors, hydration sensors, pressure sensors, and electrical stimulators, which are made via spray printing of silver nanowires on multiscale porous SEBS substrates. The devices show comparable electrical performances with conventional, rigid, nonporous ones. Also, their applications in cuffless blood pressure measurement, interactive virtual reality, and human–machine interface are demonstrated. Notably, the enabled on-skin devices are dissolvable in several organic solvents and can be recycled to reduce electronic waste and manufacturing cost. Such on-skin electronics can serve as the basis for future multifunctional smart textiles with passive-cooling functionalities.

42 ENGINEERING↗

Organic-matter decomposition along a temperature gradient in a forested headwater stream

Here, we used a natural temperature gradient in Walker Branch, a spring-fed forested stream in eastern Tennessee, USA, to examine the influence of temperature on organic-matter decomposition. These upstream sites are warmer than downstream sites in winter and are cooler than downstream sites in summer. We used a cotton-strip assay to examine breakdown of a substrate of uniform quality (95% cellulose) along the temperature gradient monthly for 2 y and litter bags to examine the interactive effects of leaf-litter quality (labile red maple [Acer rubrum] and tulip poplar [Liriodendron tulipifera], and less labile white oak [Quercus alba]), invertebrates, and temperature on breakdown rates along the downstream temperature gradient for 90 d in winter. Cotton-strip tensile loss and leaf-litter breakdown rates were highly variable. Tensile-loss rates likely were driven by a combination of daily and diel temperature, discharge, streamwater nutrients that varied seasonally and spatially along the temperature gradient. Leaf litter breakdown rates tended to be faster in warmer upstream sites (red maple = 0.0452/d, tulip poplar = 0.0376/d, white oak = 0.0142/d) and slower in cooler downstream sites (red maple = 0.0312/d, tulip poplar = 0.0236/d, white oak = 0.0107/d), and breakdown rates were positively correlated with total invertebrate density. Furthermore, temperature sensitivity of decomposition was similar among the 3 litter types. These results highlight the high degree of spatial and temporal heterogeneity that can exist for ecosystem processes and their drivers. Quantifying this heterogeneity is important when scaling functional metrics to stream and watershed scales and for understanding how organic-matter processing will respond to the warmer streamwater temperatures expected as a result of global climate change.

59 BASIC BIOLOGICAL SCIENCES↗

Prediction of a measurable sign change in the Casimir force using a magnetic fluid

Here, we demonstrate quantum levitation controlled by Casimir forces acting between a polystyrene surface and a Teflon-coated metallic substrate immersed in a mixture of toluene and magnetite particles. This system experiences repulsion-attraction transitions in the Casimir interaction for distances where the effect is measurable. This Casimir trapping can be controlled by clever choices of metallic and ferrofluid materials, which are directly linked to the emergence of the trapping effect. Thermal and quantum contributions are investigated in detail, showing how the optical and magnetic properties of the ferrofluid and other materials affect the magnitude of the trapping and its distance range of observability.

Ma, Long [University of South Florida, Tampa, FL (↗

Influence of the Turing instability on the motion of domain boundaries

Turing's theory of pattern formation has provided crucial insights into the behavior of various biological, geographical, and chemical systems over the last few decades. Existing studies have focused on moving-boundary Turing systems for which the motion of the boundary is prescribed by an external agent. In this paper, we present an extension of this theory to a class of systems in which the front motion is governed by the physical processes that occur within the domain. Biological systems exhibiting apically dominant growth and corrosion of metals and alloys highlight some of the noteworthy examples of such systems. In this study, we characterize the nature of interaction between the moving front and the Turing-instability for both an activator-inhibitor and an activator-substrate model. Behavioral regimes of periodic, as well as nonperiodic (nonconstant), growth rates are obtained. Furthermore, the trends in the first show striking similarities with the cyclic-boundary-kinetics observed in experimental systems. In general, a stationary, periodic structure is also left behind the moving front. If the periodicity of the boundary kinetics agrees with the allowed range of the stable-periodic solutions, the pattern formed tends to persist. Lastly, it evolves to a nearby energy-minimum either by peak-splitting, peak-decay, or by settling down to a spatially homogeneous state.

99 GENERAL AND MISCELLANEOUS↗

Role of Outer Membrane C-Type Cytochromes MtrC and OmcA in Shewanella Oneidensis MR-1 Cell Production, Accumulation, and Detachment During Respiration on Hematite

Solid phase iron oxides are considered to be important terminal electron acceptors for microbial respiration in many anoxic environments. Besides the knowledge that cells attach to and reduce these substrates, other aspects of surface-associated cell behavior and the related cell surface components that influence cell-mineral interactions are not well understood. In the present study, wild-type cells of the dissimilatory iron-reducing bacterium Shewanella oneidensis MR-1 formed thin biofilms one-to-two cell layers in thickness when respiring on natural specular hematite under flow conditions similar to those which exist in aquatic sediments and subsurface environments. The distribution of cells within the biofilm indicated that direct contact was not required for electron transfer from cells to the mineral surface. Detached biomass in the form of single cells represented >99% of the surface-associated wild-type cell production from respiration on hematite over the biofilm life cycle. A mutant deficient in the outer membrane c35 type cytochrome OmcA, while still able to respire and replicate on hematite, established a lower steady-state cell density on the mineral surface than that of the wild-type strain. A mutant deficient in MtrC, another outer membrane c-type cytochrome, and a mutant deficient in both cytochromes were unable to reduce sufficient amounts of hematite to support detectable growth on the mineral surface. When considered in the context of previous work, the results support a growing body of evidence that the relative importance of OmcA and MtrC to cell respiration and replication depends on the form of iron oxide available as terminal electron acceptor.

Mitchell, Andrew C↗

Ion-induced effects on grain boundaries and a-Si:H tissue quality in microcrystalline silicon films

Microcrystalline silicon films have been deposited by means of the remote expanding thermal plasma. The effect of ion bombardment on the microcrystalline silicon film properties has been investigated by applying an RF bias to the deposition substrate. The application of the RF substrate bias resulted in the formation of an additional plasma in front of the substrate holder. Neither the SiH{sub 4} depletion nor the growth flux was significantly enhanced upon substrate biasing, which suggests that (the composition of) the growth precursor flux is unaffected and that the ion-film interaction mechanisms were responsible for the observed material changes. Moderate bias conditions (i.e., dc bias voltages up to {approx}70 V) led to an improved grain boundary passivation and densification of the amorphous silicon tissue, as concluded from the analysis of the infrared Si-H{sub x} stretching modes. These improvements have been ascribed to ion-induced Si surface atom displacement, which enhances the surface diffusion length of the growth precursors. More-energetic ion bombardment (i.e., under applied dc bias voltages of {approx}60 V and higher) resulted in enhanced (di)vacancy incorporation via ion-induced Si bulk atom displacement. The film crystallinity was found not to be affected by the ion bombardment, although a reduced crystallite size was observed under ion bombardment conditions where Si bulk displacement had been sufficiently activated. The extent of the ion-film interaction mechanism has been enhanced by increasing the ion-to-Si deposition flux ratio. Under specific ion bombardment conditions, i.e., dc bias voltage in the range of 40-70 V and ion/Si arrival rate {approx}0.20, microcrystalline silicon films have been obtained which, on the basis of the Si-H{sub x} stretching modes, are qualified as solar-grade, i.e., the intergranular space is filled with a dense amorphous silicon tissue which completely passivates the crystalline grain boundaries.

36 MATERIALS SCIENCE↗

Predicting Coculture Substrate Depletion (PCSD) v1

(based on Erbilgin et al., BMC Bioinformatics, 2017, 18:57). Mixed cultures of microbial species are increasingly used to carry out a specific task in lieu of engineering a single microbe to do the same task. However, knowing how different species' metabolisms will integrate to reach a desired outcome is a difficult problem that has been studied in great detail--but only using steady-state models. Mixed cultures used for biotechnology processes, as well as microbial communities that exist in nature and crop agriculture, are metabolically dynamic systems. Studying the temporal substrate utilization by individuals is individuals in mixed cultures is an important first step in developing approaches to better model these biochemical processes and microbial communities found in nature. The 2017-004 software is comprised of four custom iPython notebooks that were used for all computational tasks in the experimental work described in "Dynamic substrate preferences predict metabolic properties of a simple microbial consortium" (Erbilgin et al., BMC Bioinformatics, 2017). The results indicate that a significant portion of a model community's overall metabolism can be predicted based on the metabolism of the individuals. The results further suggest that, when the mixed culture's substrate depletion significantly deviates from such a prediction, this may highlight potential metabolic pathways affected by species-species microbial interactions, leading to hypotheses about how a particular microbial community's structure and function may be modulated to perform a particular biotechnological goal.

Bowen, Benjamin↗

PC-12 cells adhesion and differentiation on carbon aerogel scaffolds

Electrically conducting substrates have shown much promise as neuronal scaffolds and in other biologic and biomedical applications where a smart and electrically interactive material is needed. Most materials that are inherently conducting are not suitable for biomedical applications and lack biocompatibility or biostability. On the other hand, biologically stable and compatible materials must first be manipulated, modified, and treated in order to impart the necessary electrical conductivity to the material. Here, the authors have investigated the response of PC-12 cells to two types of conducting carbon-based aerogels with different surface roughness. Results show that carbon-based aerogels support cell adhesion, proliferation, and neurite extension. The effects of surface roughness have also been investigated.

carbon↗