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At least 1,387 records · Page 77

Fluorescence In Situ mRNA Hybridization for Gene Expression Detection in a Wood Decay Fungus

Wood-degrading fungi efficiently decompose wood using a series of steps that are regulated across time and space. RNA sequencing with “bulk” sampling method has indicated processes controlled at the transcription level at different decay stages and locations along hyphal networks. To further understand these regulatory mechanisms, a high-resolution technique for gene expression determination is required. In this work, Fluorescence In Situ Hybridization (FISH) of mRNA was tested and optimized in the ‘brown rot’-type (carbohydrate-selective; lignin-rich residues) model fungus Postia (Rhodonia) placenta to image gene expression at the hyphal scale, <10 micrometers. The mRNA of one housekeeping gene Tef1a and three wood-decaying genes Cel28a, Cel5b and Qrd1 were tested in hyphae grown in liquid nutrients and wood substrate. The 20 bp-long DNA probes were successfully delivered intracellularly to give sufficient hybridization signal for imaging. Ahead of hybridization, permeabilization by lyticase and proteinase K treatments proved to be the critical step to increase probe and mRNA accessibility. Tyramide signal amplification was used after hybridization to enhance signal. This gave qualitative measures of mRNA of the four target genes, which were generally in line with previous expression patterns generated from coarser-scale RNA-seq and qRT-PCR studies. These techniques were not without challenges, and future optimization using multiple probe fragments for each mRNA molecule is proposed.

Brown rot fungi, decomposition, FISH, gene express↗

Vibrational sum frequency generation spectroscopy reveals the inertness of chromium oxide (001) surfaces

Nanoengineered metal oxides such as Cr(III)-oxide (chromia) films have diverse potential applications in corrosion inhibition, remediation, energy generation, catalysis, data storage, and biological and environmental systems. Concerns about material degradation or oxidation to toxic chromate necessitate an understanding of chromia/aqueous interfaces, beginning with their hydroxylation and hydration behavior. Vibrational sum-frequency generation spectroscopy (vSFG) provides specific molecular-level information about water at the oxide/aqueous junction with high surface selectivity. To overcome the strong absorber problem typical of certain metal oxides in the UV–visible range during nonlinear optical studies, we employed molecular beam epitaxy to deposit transparent, epitaxial nanofilms of Cr 2 O 3 with (001) crystalline orientation on sapphire (Al 2 O 3 (001)) substrates, as confirmed by atomic force microscopy and X-ray diffraction. vSFG spectra of the air and water interfaces of the Cr 2 O 3 (001) films reveal hydroxyl features corresponding to both dissociated and molecular water on the surface. In contrast to the dangling hydroxyls found on the bare Al 2 O 3 (001) substrate, the hydroxyl groups on the deposited Cr 2 O 3 (001) nanofilm do not readily undergo isotopic H/D exchange when exposed to varying forms of D 2 O under ambient conditions. When considering the chemistries of the corresponding trivalent cations in aqueous solution, the finding is at variance with their similar acidities and proton exchange dynamics but consistent with markedly slower inner-sphere water ligand exchange of hexaquo Cr 3+ . This finding challenges the idea that proton and water exchange at the water/Cr₂O₃(001) interface are solely correlated, driven by the strength of metal-bridging oxygen bonds and surface hydroxyl distribution, without direct causation.

Boamah-Agyemang, Mavis D. [Pacific Northwest Natio↗

Green and cytocompatible carboxyl modified gold–lysozyme nanoantibacterial for combating multidrug-resistant superbugs

The dissemination of multi-drug resistant (MDR) superbugs in hospital environments, communities and food animals and the very dynamic bacterial mutation frequency require the development of prolonged therapeutic strategies to gain mastery over antibiotic resistance. A AuNP–lysozyme nanoantibacterial was fabricated by the conjugation of AuNPs-C 6 H 4 -4-COOH with lysozyme via green reduction of aryldiazonium gold(III) salt [HOOC-4-C 6 H 4 N≡N]AuCl 4 . Results from molecular docking calculations aimed at revealing the binding mode of benzoic acid with the lysozyme structure clearly showed the lowest energy conformation with benzoic acid bound in the deep buried hydrophobic cavity of the protein active site through strong hydrogen bonding and hydrophobic interactions, thus validating the experimental outcomes of the current study which also exhibited the binding of –COOH functional groups in the interior of the protein structure. The superiority of the lysozyme bioconjugate against superbugs was demonstrated by the enhanced and broadened lysozyme antibacterial activities of 98–99% against extended spectrum beta lactamase (ESBL) producing Escherichia coli and imipenem-resistant Pseudomonas aeruginosa clinical isolates and a selection of Gram-negative and Gram-positive standard ATCC strains. Selective toxicity against bacteria was confirmed by the high viability of HeLa and fibroblast cell lines and the outstanding hemocompatibility at the minimum bacterial inhibitory concentrations (MICs). Turbidimetric enzyme kinetic assay showed the enhancement of the lysozyme hydrolytic activity by gold nanoparticles on the Micrococcus lysodeikticus bacterial substrate. Using gel electrophoresis, the induced cell wall breakdown was confirmed by detecting the leaked-out bacterial genomic DNA. The integrity and morphology changes of the E. coli bacteria were investigated using a scanning electron microscope after one hour of contact with the lysozyme–gold bioconjugate. The antibacterial functionalities showed little or no damage to healthy human cells and can be applied to wound dressings and medical devices.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamic Tilting of Ferroelectric Domain Walls Caused by Optically Induced Electronic Screening

Optical excitation perturbs the balance of phenomena selecting the tilt orientation of domain walls within ferroelectric thin films. The high carrier density induced in a low-strain BaTiO3 thin film by an above-bandgap ultrafast optical pulse changes the tilt angle that 90° a/c domain walls form with respect to the substrate-film interface. The dynamics of the changes are apparent in time-resolved synchrotron x-ray scattering studies of the domain diffuse scattering. Tilting occurs at 298 K, a temperature at which the a/b and a/c domain phases coexist but is absent at 343 K in the better ordered single-phase a/c regime. Furthermore, phase coexistence at 298 K leads to increased domain-wall charge density, and thus a larger screening effect than in the single-phase regime. The screening mechanism points to new directions for the manipulation of nanoscale ferroelectricity.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Synthesis and electronic properties of Ruddlesden-Popper strontium iridate epitaxial thin films stabilized by control of growth kinetics

We report on the selective fabrication of high-quality Sr 2 IrO 4 and SrIrO 3 epitaxial thin films from a single polycrystalline Sr2IrO4 target by pulsed laser deposition. Using a combination of x-ray diffraction and photoemission spectroscopy characterizations, we discover that within a relatively narrow range of substrate temperature, the oxygen partial pressure plays a critical role in the cation stoichiometric ratio of the films, and triggers the stabilization of different Ruddlesden-Popper (RP) phases. Resonant x-ray absorption spectroscopy measurements taken at the Ir L edge and the O K edge demonstrate the presence of strong spin-orbit coupling, and reveal the electronic and orbital structures of both compounds. These results suggest that in addition to the conventional thermodynamics consideration, higher members of the Sr n+1 Ir n O 3n+1 series can possibly be achieved by kinetic control away from the thermodynamic limit. These findings offer an approach to the synthesis of ultrathin films of the RP series of iridates and can be extended to other complex oxides with layered structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Effects of dietary amino acids, carbohydrates, and choline on neurotransmitter synthesis

The ability of a meal to increase or decrease brain neurotransmitter synthesis has been studied. It is concluded that brain serotonin synthesis is directly controlled by the proportions of carbohydrate to protein in meals and snacks that increase or decrease brain tryptophan levels, thereby changing the substrate saturation of tryptophan hydroxylase and the rate of serotonin synthesis. The ability of serotoninergic neurons to have their output coupled to dietary macronutrients enables them to function as sensors of peripheral metabolism, and to subserve an important role in the control of appetite. The robust and selective responses of catecholaminergic and cholinergic neurons to supplemental tyrosine and choline suggest that these compounds may become useful as a new type of drug for treating deseases or conditions in which adequate quantities of the transmitter would otherwise be unavailable.

Wurtman, Richard J.↗

Water‐Based Assembly of Polymer–Metal Organic Framework (MOF) Functional Coatings

Metal organic frameworks (MOFs) have gained attention for their porosity, size selectivity, and structural diversity. There is a need for MOF‐based coatings, particularly in applications such as separations, electronics, and energy; yet forming thin, functional, conformal coatings is prohibitive because MOFs exist as a powder. Layer‐by‐layer assembly, a versatile thin film coating approach, offers a unique solution to this problem, but this approach requires MOFs that are water‐dispersible and bear a surface charge. Here, these issues are addressed by examining water‐based dispersions of MIL‐101(Cr) that facilitate the formation of robust polymer–MOF hybrid coatings. Specifically, the substrate to be coated is alternately exposed to an aqueous solution of poly(styrene sulfonate) and nano MIL‐101(Cr) dispersion, yielding linear film growth and coatings with a MOF content as high as 77 wt%. This approach is surface‐agnostic, in which the coating is successfully applied to silicon, glass, flexible plastic, and even cotton fabric, conformally coating individual fibers. By contrast, prior attempts at forming MOF‐coatings are severely limited to a handful of surfaces, require harsh chemical treatment, and are not conformal. The approach presented here unambiguously confirms that MOFs can be conformally coated onto complex and unusual surfaces, opening the door for a wide variety of applications.

De, Souvik↗

Dielectrophoresis assisted rapid, selective and single cell detection of antibiotic resistant bacteria with G-FETs

Time-consuming, expensive and low sensitivity diagnostic methods used for monitoring bacterial infections lead to unnecessary or delays in prescription of the right antibiotic treatment. Determining an optimal clinical treatment requires rapid detection and identification of pathogenic bacteria and their sensitivity to specific antimicrobials. However, diagnostic devices that meet all of these criteria have proven elusive thus far. Graphene field effect transistors (G-FET) are a promising solution, since they are highly sensitive to chemical/biological modification, can have fast detection times and can be placed on different substrates. Here, by integrating specific peptide probes over G-FETs, we present a proof-of-concept study for species and strain specific label-free detection of clinical strains of pathogenic bacteria with high specificity and sensitivity. We found that pyrene-conjugated peptides immobilized on G-FETs were capable of detecting pathogenic Staphylococcus aureus at the single-cell level and discriminate against other gram-positive and gram-negative bacterial pathogens. A similar device was able to discriminate between antibiotic resistant and sensitive strains of Acinetobacter baumannii , suggesting that these devices can also be used for detecting antibiotic resistive pathogens. Furthermore, a new means of enhancing attachment, electric-field assisted binding, reduced the detection limit to 104 cells/ml and the detection time to below 5 minutes. Here, the combination of single step attachment, inexpensive production, rapid, selective and sensitive detection suggest G-FETs plus pyrene-conjugated peptides are a new platform for solving major challenges faced in point of care diagnostics to fight infectious diseases and antimicrobial resistance.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Tuning plasma parameters to control reactive species fluxes to substrates in the context of plasma catalysis

The key reactive plasma-produced gas phase species responsible for the enhanced conversion of chemicals in plasma catalysis compared to thermal catalysis have to date not been identified. This outstanding question is mainly due to the inherent large variety of plasma-produced species and the challenge of controlling and measuring the flux of each constituent of the cocktail of reactive species to a (catalytic) substrate. In this paper, we explore the possibility to control the dominant reactive species fluxes, relevant for plasma-catalysis, to a substrate in the effluent of an RF driven Ar-O 2 plasma jet. The absolute species densities of the major reactive species (O, O 2 (a 1 Δ g ), O 3 and ions) were quantified by molecular beam mass spectrometry (MBMS) to assess the possibility of using treatment distance, O 2 admixture concentration, plasma dissipated power, RF modulation frequency and duty cycle as well as the feed gas flow rate to alter the dominant species densities. Selected experimental results were also compared with a pseudo-1D plug flow model. The short-lived and long-lived species can be effectively separated by changing the treatment distance and the RF modulation frequency. Furthermore, adjusting the O 2 admixture concentration enables to change the ratio of the O 2 (a 1 Δ g ) and O 3 density. The changes in the trend of ion and O flux were found to be very similar for nearly all investigated parameters. Nonetheless the gas flow rate was able to significantly change the ratio of the O and ion density in the plasma jet effluent. Here, the impact of the surface-dependent loss probability and boundary layer reactions on the species flux to a substrate and how this qualitatively relates to the MBMS density measurements is further addressed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Organo-mineral interactions in active layer and permafrost soils along aging Arctic landscapes

Rising temperatures are accelerating permafrost thaw, exposing large soil organic carbon (SOC) stocks to microbial decomposition with implications for global climate. Understanding how permafrost carbon is stored and protected through associations with minerals is critical for predicting its vulnerability to decomposition upon thaw. However, how landscape age, substrate chemistry, and soil depth influence mineral associations remain relatively unexplored. We investigated organo-mineral associations in active layer and permafrost soils across a landscape age and geochemical gradient on Alaska’s North Slope, spanning three glaciated (~11,500–125,000 years) and one unglaciated site. Using selective dissolution extractions, X-ray diffraction, and Mössbauer spectroscopy, we characterized minerals and their relationship with SOC. The three recently deglaciated sites had low soil pH that decreased with age and greater abundances of pyrophosphate- and oxalate-extractable Al and Fe, whereas the oldest unglaciated site exhibited near-neutral pH, greater pyrophosphate-extractable Ca, and distinct mineralogy. Across sites, SOC was positively associated with Al and Fe mineral phases, with stronger relationships in acidic soils. Pyrophosphate-extractable Ca also showed strong relationships with SOC at the acidic sites (up to ~10x greater), suggesting that Ca-mediated protection may operate beyond traditionally recognized high-pH soils. Permafrost soils showed depth-related changes in pH, SOC, and Fe mineralogy, suggesting chemically active, heterogeneous layers may shape mineral dynamics and associated carbon. Our results highlight how landscape age, parent material, and depth create distinct geochemical environments that govern mineral-organic associations. As thaw exposes soil to new conditions, these mineral-mediated protection mechanisms may be altered, potentially affecting the permafrost carbon-climate feedback.

Synthetic Biology↗

Using electron channeling contrast imaging to inform and improve the growth of high-efficiency GaAs solar cells on nanopatterned GaAs substrates

Patterned substrates provide opportunities for reducing the cost of high-efficiency III-V devices by incorporating mechanically weak layers beneficial for substrate reuse (e.g. by spalling). In this work, the functionality of electron channeling contrast imaging (ECCI) as a tool to efficiently understand and mitigate defect formation is exemplified by developing a process in which high-quality III-V material can be grown on nanopatterned GaAs substrates. Reactive ion etching used in the patterning process was found to damage the GaAs substrate surface, leading to the formation of stacking faults in the epitaxial material as observed by ECCI. Etching the patterned substrates in a 1 NH4OH: 1 H2O2: 50 DI H2O solution for 10 s prior to growth removed the substrate surface damage and stacking faults were no longer present. Growth of solar cell device structures initially produced samples with many macroscale flaws creating shunts in the devices, which complicated the assessment of material quality by device measurements. However, ECCI revealed that the epitaxial material surrounding macroscale flaws was free from any crystallographic defects such as stacking faults and threading dislocations. With this knowledge, we focused on refining the patterning process to eliminate the macroscale flaws. Solar cells were then grown on the improved nanopatterned substrates and exhibited device structures with defect densities less than 5 x 105 cm -2 and average conversion efficiency of 24.8%, nearly identical to devices grown on unpatterned epi-ready substrates (25.0%).

14 SOLAR ENERGY↗

Layered Sn-Au Thin Films for Increased Electrochemical ATR-SEIRAS Enhancement

Operando electrochemical attenuated total reflection surface-enhanced infrared absorption spectroscopy (EC ATR-SEIRAS) is a valuable method for a fundamental understanding of electrochemical interfaces under real operating conditions. The applicability of this method depends on the ability to tune the optical and catalytic properties of an electrode film, and it thus requires unique optimization for any given material. Motivated by the growing interest in Sn-based electrocatalysts for selective reduction of CO2 to formate species, we investigate several Sn thin-film synthesis routes for the resulting SEIRA signal response. We compare the SEIRA performance of thermally evaporated metallic Sn to a series of Sn-based films on top of a SEIRA-active Au substrate (metallic Sn, oxide-derived metallic Sn, and metal oxide SnOx). Using alkanethiol self-assembled monolayers as a probe, we find that electrodepositing metallic catalyst films on top of SEIRA-active Au substrates yield higher signal relative to thermal evaporation as well as higher signal than the independent SEIRA-active Au underlayer. These observations come despite the fact that thermally evaporated Sn has a significantly higher surface roughness (and thus higher adsorbate population), suggesting specific SEIRA-magnifying effects for the stacked films. Finally, we applied these films to observe the electrochemical conversion of CO2. Differences are observed in spectral features based on the composition of the electrode being either metallic or oxide-derived metallic Sn, implying differences in their respective reaction pathways.

CO2 reduction↗

Intrinsically Bifunctional and Tunable Tungsten Carbide Catalysts Enable Efficient PVC-Compatible Polyolefin Hydrocracking

Hydrocracking is a promising route for the chemical recycling of polyolefins (PO), converting them into short hydrocarbons over bifunctional catalysts with metal sites for hydrogenation and dehydrogenation, and Brønsted acid sites (BAS) for isomerization and C–C bond cleavage. However, PO feedstocks containing polyvinyl chloride (PVC) can release chlorine (Cl) under reaction conditions, deactivating conventional noble metal/zeolite catalysts. Moreover, the lack of site intimacy and the presence of micropores within conventional catalysts create challenges around the transport of high-molecular-weight, sterically encumbered polymer intermediates. Here, in this study, we report tungsten carbides (W x C) as a novel type of bifunctional catalysts that address these challenges. W/W 2 C phases on W x C offer “metal” sites, and −OH on WO x species introduces BAS in close proximity. The “metal”:BAS ratio can be tuned through carburization temperature, leading to a volcano-shaped activity trend reflecting the requirement for metal–BAS balance. Kinetic data demonstrate that each PO chain undergoes sequential cleavage, while trends in cracking ideality and selectivity follow those in short-alkane hydrocracking. On the per-BAS basis, W x C is more efficient than conventional bifunctional catalysts by more than an order of magnitude, due to enhanced polymer transport. They maintain or show increased activity with 10 wt % PVC in the substrate. This work establishes transition-metal carbides as earth-abundant bifunctional catalysts with unique site proximity and heteroatom compatibility. These features, along with the broad structure space for rational tuning, make them promising options to tackle specific challenges that polymer feedstocks present in hydrocracking.

Nwachukwu, Uchenna C. [Univ. of Akron, OH (United ↗

Mitotic regulators and the SHP2-MAPK pathway promote IR endocytosis and feedback regulation of insulin signaling

Insulin controls glucose homeostasis and cell growth through bifurcated signaling pathways. Dysregulation of insulin signaling is linked to diabetes and cancer. The spindle checkpoint controls the fidelity of chromosome segregation during mitosis. Here, we show that insulin receptor substrate 1 and 2 (IRS1/2) cooperate with spindle checkpoint proteins to promote insulin receptor (IR) endocytosis through recruiting the clathrin adaptor complex AP2 to IR. A phosphorylation switch of IRS1/2 orchestrated by extracellular signal-regulated kinase 1 and 2 (ERK1/2) and Src homology phosphatase 2 (SHP2) ensures selective internalization of activated IR. SHP2 inhibition blocks this feedback regulation and growth-promoting IR signaling, prolongs insulin action on metabolism, and improves insulin sensitivity in mice. We propose that mitotic regulators and SHP2 promote feedback inhibition of IR, thereby limiting the duration of insulin signaling. Targeting this feedback inhibition can improve insulin sensitivity.

59 BASIC BIOLOGICAL SCIENCES↗

Targeted sulfur(VI) fluoride exchange-mediated covalent modification of a tyrosine residue in the catalytic pocket of tyrosyl-DNA phosphodiesterase 1

Abstract Developing effective inhibitors of the DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (TDP1) has been challenging because of the enzyme shallow catalytic pocket and non-specific substrate binding interactions. Recently, we discovered a quinolone-binding hot spot in TDP1’s active site proximal to the evolutionary conserved Y204 and F259 residues that position DNA. Sulfur (VI) fluoride exchange (SuFEx) is a biocompatible click chemistry reaction that enables acylation of protein residues, including tyrosine. Selective protein modifications can provide insights into the biological roles of proteins and inform ligand design. As we report herein, we used SuFEx chemistries to prepare covalent TDP1-bound binders showing site-specific covalent bonds with Y204. Our work presents the first application of SuFEx chemistries to TDP1 ligands. It validates the ability to covalently modify specific TDP1 residues by designed targeting and adds to the chemical biology resource toolbox for studying TDP1.

Chemistry↗

Influence of Langasite Crystal Orientation on Hydrogen Gas Detection up to 400°C

Hydrogen gas sensors are of great importance due to the explosive nature and volatility of H 2 at concentrations above 4%. Also important is the capability of operation at high temperatures in harsh industrial environments, aerospace, automotive, and power generation applications. Surface Acoustic Wave (SAW) technology offers many desirable properties for sensor fabrication, such as the capability of wireless and battery free operation, mass-production, small size and weight. Piezoelectric substrates or thin films, such as langasite and aluminum nitrate, exist that allow SAW devices to operate at high temperatures. Langasite SAW-based devices have been previously demonstrated as temperature, strain and gas sensors. For high temperature SAW-based gas sensors, sensitive films capable to react selectively with the target species are normally used. This work presents the detection of hydrogen gas at high-temperature (up to 470 C) using SAW resonators on the commercially available LGS plane described by Euler angles {0°, 138.5°,Ψ}. The Pt-Al 2 O 3 composite thin film is used as both the electrode and sensitive layer. Devices fabricated along different crystal orientations on the same wafer revealed different sensitivities to H 2 , which were also measured as a function of temperature up to 470 C. These different sensitivities to H 2 open the possibility of using different orientations of this commercially available LGS crystal cut to fabricate sensors capable of operating as a network, and detecting different measurands at high-temperature, including hydrogen gas.

36 MATERIALS SCIENCE↗

Laboratory investigations: Low Earth orbit environment chemistry with spacecraft surfaces

Long-term space operations that require exposure of material to the low earth orbit (LEO) environment must take into account the effects of this highly oxidative atmosphere on material properties and the possible contamination of the spacecraft surroundings. Ground-based laboratory experiments at Los Alamos using a newly developed hyperthermal atomic oxygen (AO) source have shown that not only are hydrocarbon based materials effected but that inorganic materials such as MoS2 are also oxidized and that thin protective coatings such as Al2O3 can be breached, producing oxidation of the underlying substrate material. Gas-phase reaction products, such as SO2 from oxidation of MoS2 and CO and CO2 from hydrocarbon materials, have been detected and have consequences in terms of spacecraft contamination. Energy loss through gas-surface collisions causing spacecraft drag has been measured for a few select surfaces and has been found to be highly dependent on the surface reactivity.

Cross, Jon B.↗

Universal Controller for Spacecraft Mechanisms

An electronic control unit has been fabricated and tested that can be replicated as a universal interface between the electronic infrastructure of a spacecraft and a brushless-motor (or other electromechanical actuator) driven mechanism that performs a specific mechanical function within the overall spacecraft system. The unit includes interfaces to a variety of spacecraft sensors, power outputs, and has selectable actuator control parameters making the assembly a mechanism controller. Several control topologies are selectable and reconfigurable at any time. This allows the same actuator to perform different functions during the mission life of the spacecraft. The unit includes complementary metal oxide/semiconductor electronic components on a circuit board of a type called rigid flex (signifying flexible printed wiring along with a rigid substrate). The rigid flex board is folded to make the unit fit into a housing on the back of a motor. The assembly has redundant critical interfaces, allowing the controller to perform time-critical operations when no human interface with the hardware is possible. The controller is designed to function over a wide temperature range without the need for thermal control, including withstanding significant thermal cycling, making it usable in nearly all environments that spacecraft or landers will endure. A prototype has withstood 1,500 thermal cycles between 120 and +85 C without significant deterioration of its packaging or electronic function. Because there is no need for thermal control and the unit is addressed through a serial bus interface, the cabling and other system hardware are substantially reduced in quantity and complexity, with corresponding reductions in overall spacecraft mass and cost.

Levanas, Greg↗