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At least 685 records · Page 38

Crystal structure of chorismate mutase from Burkholderia phymatum

The bacterium Burkholderia phymatum is a promiscuous symbiotic nitrogen-fixating bacterium that belongs to one of the largest groups of Betaproteobacteria. Other Burkholderia species are known to cause disease in plants and animals, and some are potential agents for biological warfare. Structural genomics efforts include characterizing the structures of enzymes from pathways that can be targeted for drug development. As part of these efforts, chorismate mutase from B. phymatum was produced and crystallized, and a 1.95 Å resolution structure is reported. This enzyme shares less than 33% sequence identity with other homologs of known structure. There are two classes of chorismate mutase: AroQ and AroH. The bacterial subclass AroQγ has reported roles in virulence. Chorismate mutase from B. phymatum has the prototypical AroQγ topology and retains the characteristic chorismate mutase active site. This suggests that substrate-based chorismate mutase inhibitors will not be specific and are likely to affect beneficial bacteria such as B. phymatum .

Asojo, Oluwatoyin A. (ORCID:0000000240432700)↗

Rubis CO selection using the vigorously aerobic and metabolically versatile bacterium Ralstonia eutropha

Recapturing atmospheric CO 2 is key to reducing global warming and increasing biological carbon availability. Ralstonia eutropha is a biotechnologically useful aerobic bacterium that uses the Calvin–Benson–Bassham ( CBB ) cycle and the enzyme ribulose 1,5‐bisphosphate carboxylase/oxygenase (Rubis CO ) for CO 2 utilization, suggesting that it may be a useful host to bioselect Rubis CO molecules with improved CO 2 ‐capture capabilities. A host strain of R. eutropha was constructed for this purpose after deleting endogenous genes encoding two related Rubis CO s. This strain could be complemented for CO 2 ‐dependent growth by introducing native or heterologous Rubis CO genes. Mutagenesis and suppressor selection identified amino acid substitutions in a hydrophobic region that specifically influences Rubis CO 's interaction with its substrates, particularly O 2 , which competes with CO 2 at the active site. Unlike most Rubis CO s, the R. eutropha enzyme has evolved to retain optimal CO 2 ‐fixation rates in a fast‐growing host, despite the presence of high levels of competing O 2 . Yet its structure‐function properties resemble those of several commonly found Rubis CO s, including the higher plant enzymes, allowing strategies to engineer analogous enzymes. Because R. eutropha can be cultured rapidly under harsh environmental conditions (e.g., with toxic industrial flue gas), in the presence of near saturation levels of oxygen, artificial selection and directed evolution studies in this organism could potentially impact efforts toward improving Rubis CO ‐dependent biological CO 2 utilization in aerobic environments. Enzymes d ‐ribulose 1,5‐bisphosphate carboxylase/oxygenase, EC 4.1.1.39 ; phosphoribulokinase, EC 2.7.1.19

Satagopan, Sriram↗

Meta Biome: a multiscale model integrating agent-based and metabolic networks to reveal spatial regulation in gut mucosal microbial communities

ABSTRACT Mucosal microbial communities (MMCs) are complex ecosystems near the mucosal layers of the gut essential for maintaining health and modulating disease states. Despite advances in high-throughput omics technologies, current methodologies struggle to capture the dynamic metabolic interactions and spatiotemporal variations within MMCs. In this work, we presentMetaBiome, a multiscale model integrating agent-based modeling (ABM), finite volume methods, and constraint-based models to explore the metabolic interactions within these communities. Integrating ABM allows for the detailed representation of individual microbial agents each governed by rules that dictate cell growth, division, and interactions with their surroundings. Through a layered approach—encompassing microenvironmental conditions, agent information, and metabolic pathways—we simulated different communities to showcase the potential of the model. Using ourin-silicoplatform, we explored the dynamics and spatiotemporal patterns of MMCs in the proximal small intestine and the cecum, simulating the physiological conditions of the two gut regions. Our findings revealed how specific microbes adapt their metabolic processes based on substrate availability and local environmental conditions, shedding light on spatial metabolite regulation and informing targeted therapies for localized gut diseases.MetaBiome provides a detailed representation of microbial agents and their interactions, surpassing the limitations of traditional grid-based systems. This work marks a significant advancement in microbial ecology, as it offers new insights into predicting and analyzing microbial communities. IMPORTANCE Our study presents a novel multiscale model that combines agent-based modeling, finite volume methods, and genome-scale metabolic models to simulate the complex dynamics of mucosal microbial communities in the gut. This integrated approach allows us to capture spatial and temporal variations in microbial interactions and metabolism that are difficult to study experimentally. Key findings from our model include the following: (i) prediction of metabolic cross-feeding and spatial organization in multi-species communities, (ii) insights into how oxygen gradients and nutrient availability shape community composition in different gut regions, and (iii) identification of spatiallyregulated metabolic pathways and enzymes inE. coli. We believe this work represents a significant advance in computational modeling of microbial communities and provides new insights into the spatial regulation of gut microbiome metabolism. The multiscale modeling approach we have developed could be broadly applicable for studying other complex microbial ecosystems.

Microbiology↗

Anaerobic Degradation of Alkanes by Marine Archaea

Alkanes are saturated apolar hydrocarbons that range from their simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea.

Microbiology↗

Synthesis of Platinum-nickel Nanowires and Optimization for Oxygen Reduction Performance

Platinum-nickel (Pt-Ni) nanowires were developed as fuel cell electrocatalysts, and were optimized for the performance and durability in the oxygen reduction reaction. Spontaneous galvanic displacement was used to deposit Pt layers onto Ni nanowire substrates. The synthesis approach produced catalysts with high specific activities and high Pt surface areas. Hydrogen annealing improved Pt and Ni mixing and specific activity. Acid leaching was used to preferentially remove Ni near the nanowire surface, and oxygen annealing was used to stabilize near-surface Ni, improving durability and minimizing Ni dissolution. These protocols detail the optimization of each post-synthesis processing step, including hydrogen annealing to 250 degrees C, exposure to 0.1 M nitric acid, and oxygen annealing to 175 degrees C. Through these steps, Pt-Ni nanowires produced increased activities more than an order of magnitude than Pt nanoparticles, while offering significant durability improvements. The presented protocols are based on Pt-Ni systems in the development of fuel cell catalysts. Furthermore, these techniques have also been used for a variety of metal combinations, and can be applied to develop catalysts for a number of electrochemical processes.

36 MATERIALS SCIENCE↗

Multi-Channel Electronically Scanned Cryogenic Pressure Sensor And Method For Making Same

A miniature, multi-channel, electronically scanned pressure measuring device uses electrostatically bonded silicon dies in a multi-element array. These dies are bonded at specific sites on a glass, pre-patterned substrate. Thermal data is multiplexed and recorded on each individual pressure measuring diaphragm. The device functions in a cryogenic environment without the need of heaters to keep the sensor at constant temperatures.

Chapman, John J.↗

MEMS Microshutter Array System for James Webb Space Telescope

A complex MEMS microshutter array system has been developed at NASA Goddard Space Flight Center (GSFC) for use as a multi-object aperture array for a Near-Infrared Spectrometer (NIRSpec). The NIRSpec is one of the four major instruments carried by the James Webb Space Telescope (JWST), the next generation of space telescope after the Hubble Space Telescope retires. The microshutter arrays (MSAs) are designed for the selective transmission of light with high efficiency and high contrast. It is demonstrated in Figure 1 how a MSA is used as a multiple object selector in deep space. The MSAs empower the NIRSpec instrument simultaneously collect spectra from more than 100 targets therefore increases the instrument efficiency 100 times or more. The MSA assembly is one of three major innovations on JWST and the first major MEMS devices serving observation missions in space. The MSA system developed at NASA GSFC is assembled with four quadrant fully addressable 365x171 shutter arrays that are actuated magnetically, latched and addressed electrostatically. As shown in Figure 2, each MSA is fabricated out of a 4' silicon-on-insulator (SOI) wafer using MEMS bulk-micromachining technology. Individual shutters are close-packed silicon nitride membranes with a pixel size close to 100x200 pm (Figure 3). Shutters are patterned with a torsion flexure permitting shutters to open 90 degrees with a minimized mechanical stress concentration. In order to prevent light leak, light shields are made on to the surrounding frame of each shutter to cover the gaps between the shutters and the Game (Figure 4). Micro-ribs and sub-micron bumps are tailored on hack walls and light shields, respectively, to prevent sticktion, shown in Figures 4 and 5. JWST instruments are required to operate at cryogenic temperatures as low as 35K, though they are to be subjected to various levels of ground tests at room temperature. The shutters should therefore maintain nearly flat in the entire temperature range between 35K and 300K. Through intensive numerical simulations and experimental studies, an optically opaque and electrically conductive metal-nitride thin film was selected as a coating material deposited on the shutters with the best thermal-expansion match to silicon nitride - the shutter blade thin film material. A shutter image shown in Figure 6 was taken at room temperature, presenting shutters slightly bowing down as expected. Shutters become flat when the temperature decreases to 35K. The MSAs are then bonded to silicon substrates that are fabricated out of 6" single-silicon wafers in the thickness of 2mm. The bonding is conducted using a novel single-sided indium flip-chip bonding technology. Indium bumps fabricated on a substrate are shown in Figure 7. There are 180,000 indium bumps for bonding a flight format MSA array to its substrate. Besides a MSA, each substrate houses five customer-designed ASIC (Application Specific Integrated Circuit) multiplexer/address chips for 2-dimensional addressing, twenty capacitors, two temperature sensors, numbers of resistors and all necessary interconnects, as shown in Figure 8. Complete MSA quadrant assemblies have been successfully manufactured and fully functionally tested. The assemblies have passed a series of critical reviews required by JWST in satisfying all the design specifications. The qualification tests cover programmable 2-D addressing, life tests, optical contrast tests, and environmental tests including radiation, vibration, and acoustic tests. A 2-D addressing pattern with 'ESA' letters programmed in a MSA is shown in Figure 9. The MSAs passed 1 million cycle life tests and achieved high optical contrast over 10,000. MSA teams are now making progress in final fabrication, testing and assembly (Figure 10). The delivery of flight-format MSA system is scheduled at the end of 2008 for being integrated to the focal plane of the NIRSpec detectors.

Li, Mary J.↗

Complementary Barrier Infrared Detector

The complementary barrier infrared detector (CBIRD) is designed to eliminate the major dark current sources in the superlattice infrared detector. The concept can also be applied to bulk semiconductor- based infrared detectors. CBIRD uses two different types of specially designed barriers: an electron barrier that blocks electrons but not holes, and a hole barrier that blocks holes but not electrons. The CBIRD structure consists of an n-contact, a hole barrier, an absorber, an electron barrier, and a p-contact. The barriers are placed at the contact-absorber junctions where, in a conventional p-i-n detector structure, there normally are depletion regions that produce generation-recombination (GR) dark currents due to Shockley-Read- Hall (SRH) processes. The wider-bandgap complementary barriers suppress G-R dark current. The barriers also block diffusion dark currents generated in the diffusion wings in the neutral regions. In addition, the wider gap barriers serve to reduce tunneling dark currents. In the case of a superlattice-based absorber, the superlattice itself can be designed to suppress dark currents due to Auger processes. At the same time, the barriers actually help to enhance the collection of photo-generated carriers by deflecting the photo-carriers that are diffusing in the wrong direction (i.e., away from collectors) and redirecting them toward the collecting contacts. The contact layers are made from materials with narrower bandgaps than the barriers. This allows good ohmic contacts to be made, resulting in lower contact resistances. Previously, THALES Research and Technology (France) demonstrated detectors with bulk InAsSb (specifically InAs0.91Sb0.09) absorber lattice-matched to GaSb substrates. The absorber is surrounded by two wider bandgap layers designed to minimize impedance to photocurrent flow. The wide bandgap materials also serve as contacts. The cutoff wavelength of the InAsSb absorber is fixed. CBIRD may be considered as a modified version of the THALES double heterostructure (DH) p-i-n device, but with even wider bandgap barriers inserted at the contact layer/absorber layer interfaces. It is designed to work with either bulk semiconductors or superlattices as the absorber material. The superlattice bandgap can be adjusted to match the desired absorption cutoff wavelength. This infrared detector has the potential of high-sensitivity operation at higher operating temperatures. This would reduce cooling requirements, thereby reducing the power, mass, and volume of the equipment and allowing an increased mission science return.

Ting, David Z.↗

Method of making a hydrogen transport membrane, and article

The present invention relates to a method of manufacturing a hydrogen transport membrane and the composite article itself. More specifically, the invention relates to producing a membrane substrate, wherein the ceramic substrate is coated with a metal oxide slurry, thereby eliminating the need for an activation step prior to plating the ceramic membrane through an electroless plating process. The invention also relates to modifying the pore size and porosity of the substrate by oxidation or reduction of the particles deposited by the metal oxide slurry.

08 HYDROGEN↗

Design and development of laser damage resistant low group delay dispersion optical coatings for high reflection at 45o incidence P polarization and wavelengths from 800 to 1000 nm.

This paper describes the modelling and design development of an optical coating that is suitable for broad bandwidth high reflection (BBHR) at 45° angle of incidence (AOI), P polarization (Ppol) and fs-class laser pulses whose frequencies correspond to wavelengths from 800 to 1000 nm, and that can eventually be produced uniformly on meter-class optical substrates. The coating design process was guided by specifications of not only high reflection but also high laser-induced damage threshold (LIDT) as well as low group delay dispersion (GDD) for reflected light over the broad, 200 nm bandwidth in order to minimize temporal broadening of the fs pulses upon reflection. The coating is based on TiO 2 /SiO 2 layer pairs by means of e-beam evaporation with ion-assisted deposition (IAD). We used OptiLayer Thin Film Software to explore coating designs with a limited optimization process starting from TiO 2 /SiO 2 layer pairs with layer thicknesses in an opposite “chirp” arrangement. This approach proved to be successful, leading to a design with R > 99.5% from 801 – 999 nm and GDD < 20 fs 2 from 843 – 949 nm (45° AOI, Ppol). The GDD behaves in a smooth way that lends itself to compensation of GDD effects. Also, the electric field intensities are favorable to high LIDT in that they quench rapidly into the outer coating layers or are of moderate strength, or they are located in the higher band gap SiO 2 layers.

36 MATERIALS SCIENCE↗

Magnetic nanotube composite membranes

The invention provides a membrane comprising tubes extending through a polymer, wherein substantially all of the tubes are parallel with each other. Also provided is a method for producing a membrane, the method comprising: placing tubes on a substrate, subjecting the tubes to a magnetic field for a time and at a magnetic field strength to cause the tubes to align parallel with each other while simultaneously causing depending ends of the tubes to embed within the substrate; applying polymer to the tubes and substrate in an amount to affix the tubes relative to each other and relative to the substrate, and applying an etchant that cleaves a specific type of the bonds within the polymer to unblock the upstream ends of the nanotubes.

Chen, Xing↗

Multimodal nonlinear optical imaging via evanescent wave excitation

A system for multimodal nonlinear optical imaging is provided. Each mode uses a high NA objective to cause total internal reflection excitation at a sample-substrate interface. The system has a femtosecond oscillator to generate pulses used for two beams. The objective receives at least one beam, redirects the received at least one beam through a dielectric substrate to cause the TIR and produces corresponding evanescent waves in a portion of the sample adjacent to the sample-substrate interface, and collects a backward-propagating beam of pulses of responsive light. The portion of the sample illuminated by the evanescent waves emits responsive light. Different modes or combinations of the distinct modalities may be selected to access complementary chemical and structural information for various chemical species near the sample-substrate interface. Each mode may have mode-specific control such as selective beam blocking, power ratios and filtering.

Doughty, Benjamin L.↗

Advanced Inductively Coupled Plasma Etching Processes for Fabrication of Resonator-Quantum Well Infrared Photodetector

Resonator-quantum well infrared photodetectors (R-QWIPs) are the next generation of QWIP detectors that use resonances to increase the quantum efficiency (QE). To achieve the expected performance, the detector geometry must be produced in precise specification. In particular, the height of the diffractive elements (DE) and the thickness of the active resonator must be uniformly and accurately realized to within 0.05 lm accuracy and the substrates of the detectors have to be removed totally. To achieve these specifications, two optimized inductively coupled plasma (ICP) etching processes are developed. Using these etching techniques, we have fabricated a number of R-QWIP test detectors and FPAs with the required dimensions and completely removed the substrates of the test detectors and FPAs. Their QE spectra were tested to be in close agreement with the theoretical predictions. The operability and spectral non-uniformity of the FPA is about 99.57% and 3% respectively.

plasma etching process↗

Hydrodynamics of countercurrent flows in a structured packed column: effects of initial wetting and dynamic contact angle

The structured packed column has gained considerable attention as a prospective technology to mitigate carbon dioxide emissions from thermal power plants. The computational flow investigation of such systems is a multiscale problem, and local hydrodynamics plays a key role in overall column efficiency. Accordingly, multiphase flow studies in the representative elementary unit (REU) of a packed column can offer insights into the local flow behavior such as flow pattern, interfacial area, etc. The interfacial area plays a key role in the overall interphase mass transfer and thereby in separation efficiency. The predicted effective area matches well with corresponding ones in experiments for Mellapak 250.Y packings. The contact angle (i.e., solid substrate behavior) is one of the critical factors that dictates wettings, and thereby the interfacial area. The dynamic contact angle (DCA) was considered in order to explore the effects of contact angle hysteresis on the interfacial area. DCA has more pronounced impact on the interfacial area for a solvent possessing a higher value of surface tension and equilibrium contact angle. The interfacial area shows temporal undulation and does not achieve a pseudo steady state due to the capillary force. In contrary, the interfacial area gets a net value for a solvent having low surface tension value. Further, specification of the static contact angle at the solid substrate shows the least value of the interfacial area. We also extensively studied the effect of the initial sheet condition (dry vs wet) on the interfacial area. The initially wetted sheets show slightly higher value of the interfacial area as compared to the initially dry sheets at a fixed flow rate for a solvent having high surface tension value. Wetting hysteresis decreases with increasing liquid loads. On the other hand, wetting hysteresis does not occur for a solvent having value of low surface tension and equilibrium contact angle.

structured packings, dynamic contact angle, interf↗

Personal glucose meters for detection and quantification of a broad range of analytes

A general methodology for the development of highly sensitive and selective sensors that can achieve portable, low-cost and quantitative detection of a broad range of targets using only a personal glucose meter (PGM) is disclosed. The method uses recognition molecules that are specific for a target agent, enzymes that can convert an enzyme substrate into glucose, and PGM. Also provided are sensors, which can include a solid support to which is attached a recognition molecule that permits detection of a target agent, wherein the recognition molecule specifically binds to the target agent in the presence of the target agent but not significantly to other agents as well as an enzyme that can catalyze the conversion of a substance into glucose, wherein the enzyme is attached directly or indirectly to the recognition molecule, and wherein in the presence of the target agent the enzyme can convert the substance into glucose. The disclosed sensors can be part of a lateral flow device. Methods of using such sensors for detecting target agents are also provided.

59 BASIC BIOLOGICAL SCIENCES↗

Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1

Human flap endonuclease 1 (FEN1) and related structure-specific 5’nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5’nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually ‘locks’ protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never misses cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability.

59 BASIC BIOLOGICAL SCIENCES↗

Leveraging High-resolution Molecular Composition of Soil Organic Matter to Enhance Carbon Cycling Modeling

Soils store more carbon than the atmosphere and vegetation combined, yet Earth system models still struggle to predict how this vast reservoir will respond to environmental change. A central limitation is that most soil biogeochemical models represent organic matter using bulk conceptual pools or chemically homogeneous fractions, preventing direct use of rapidly expanding molecular-scale datasets. Here we develop and test a new soil decomposition framework that explicitly integrates high-resolution information on organic matter composition. First, we construct a molecularly informed litter decomposition module in which plant inputs are partitioned into five functional compound classes—carbohydrates, proteins, lignin-like aromatics, lipids, and carbonyls—using a molecular mixing model calibrated to solid-state 13 C Nuclear Magnetic Resonance (NMR) spectra. Class-specific kinetics, lignin-dependent physical protection, and substrate-driven microbial carbon use efficiency allow the module to capture metabolic tradeoffs associated with enzyme production and nutrient limitation. We then embed this litter module within a microbially explicit whole-soil model that tracks the transformation of these compound classes through particulate organic matter, dissolved organic matter, mineral-associated organic matter, and microbial biomass. High-resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry (FTICR-MS) data are used to link internal pools to measurable soil organic matter fractions and to constrain key process parameters. Applications at soil-core and ecosystem scales demonstrate that the new model reproduces observed soil respiration dynamics while providing mechanistic attribution of CO 2 fluxes to specific chemical classes and pools. Compared to existing frameworks such as the Community Land Model soil biogeochemistry module and the Millennial model, our approach maintains competitive predictive skill while substantially improving interpretability and opportunities for data–model integration. This work illustrates a viable pathway for leveraging molecular-scale observations to reduce structural uncertainty in soil carbon–climate feedback projections.

54 ENVIRONMENTAL SCIENCES↗