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At least 505 records · Page 28

Challenges in integrating dissolved organic matter chemodiversity into kinetic models of soil respiration

The chemodiversity of dissolved organic matter (DOM) in soil has been proposed to influence the microbial metabolism and fate of belowground organic carbon (C). However, integrating DOM chemistry into soil C cycle models to improve predictions of C stocks and fluxes—beyond simply considering DOM pool size—remains a challenge. While recent research suggests that incorporating DOM chemodiversity into models can improve predictions of microbial respiration, there is still a lack of mechanistic understanding describing how DOM chemodiversity affects microbial metabolism and soil respiration. Here, we evaluated whether DOM chemodiversity was a determinant of soil respiration using paired measurements of high-resolution DOM chemistry, obtained from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), and potential soil respiration rates from across the United States (U.S.), all data provided by the Molecular Observation Network. Our objectives were to (1) assess statistical relationships between DOM chemodiversity and microbial respiration, and (2) evaluate the ability of kinetic models to leverage DOM chemistry to explain empirical relationships found in statistical models. Statistical regressions revealed that DOM chemodiversity (alpha diversity) was nonlinearly related to potential soil respiration rates, both independently and through its interactions with DOM and total C concentrations. In soils with relatively high DOM but low total C concentrations, potential soil respiration rates were negatively correlated with DOM alpha diversity, whereas in soils with relatively low DOM and high total C concentrations showed the opposite trend. However, when metabolic transition theory kinetic models were modified to include chemodiversity, their performance was comparable to traditional Monod kinetics approaches, which simulate respiration rates as a function of DOM concentration. The inability to account for nonlinearities in DOM chemodiversity–respiration relationships highlight an opportunity to advance substrate uptake kinetics by establishing causal links between DOM chemodiversity, microbial metabolism trade-offs, and potential interactions under varied environmental conditions.

Bioenergetic model↗

Machine Learning-Driven Solvent Screening for Biobased 2,3-Butanediol Extraction

Biobased 2,3-butanediol (2,3-BDO) is a valuable biomass-derived chemical due to its versatility in being transformed into a wide variety of products. However, the separation and purification of 2,3-BDO from fermentation broth remain a significant challenge owing to its high boiling point and hydrophilic nature. Herein, we developed a machine learning (ML)-based screening workflow that uses molecular calculations as training data and requires only a small number of experimental measurements for validation to identify alternative solvent candidates for the liquid–liquid extraction (LLE) of 2,3-BDO from aqueous solution. In particular, 130 density functional theory (DFT) calculations with the implicit solvation method not only built a correlation between the computational partition coefficient and the experimental distribution coefficient of 2,3-BDO but also parameterized an Extra-Trees ML model to screen the distribution coefficient for a wider range of 6717 organic solvents. The experimental measurements of only 24 solvents were needed to validate the computational results. A list of 50 prioritized solvents was proposed for 2,3-BDO LLE, and seven additional experimental measurements were conducted to further verify our selected solvents. The impact of the extraction temperature and solvent-to-feed ratio was also investigated for selected solvents in experiments. Furthermore, this work suggested alternative solvents for 2,3-BDO LLE and proposed a versatile workflow that requires fewer experiments and can be applied to a broader range of LLE studies.

Extraction↗

Cavity-altered superconductivity

Is it feasible to alter the ground-state properties of a material by engineering its electromagnetic environment? Inspired by theoretical predictions, experimental realizations of such cavity-controlled properties without optical excitation are beginning to emerge. Here we devised and implemented a new platform to realize cavity-altered materials. Single crystals of hyperbolic van der Waals (vdW) compounds provide a resonant electromagnetic environment with enhanced density of photonic states and prominent mode confinement. We interfaced hexagonal boron nitride (hBN) with the molecular superconductor κ-(BEDT-TTF) 2 Cu[N(CN) 2 ]Br (κ-ET). The frequencies of infrared hyperbolic modes (HMs) of hBN match the infrared-active carbon–carbon (C=C) stretching molecular resonance of κ-ET implicated in superconductivity. Nano-optical data supported by first-principles molecular Langevin dynamics simulations confirm the presence of resonant coupling between the hBN hyperbolic cavity modes and the C=C stretching mode in κ-ET. Meissner-effect measurements using magnetic force microscopy (MFM) demonstrate a strong suppression of superfluid density near the hBN/κ-ET interface. Non-resonant control heterostructures, including RuCl 3 /κ-ET and hBN/Bi 2 Sr 2 CaCu 2 O 8+x (BSCCO), do not show the pronounced superfluid suppression. These observations suggest that hBN/κ-ET realizes a cavity-altered superconducting ground state. Our work highlights the potential of dark cavities devoid of external photons for engineering electronic ground-state properties of complex quantum materials.

36 MATERIALS SCIENCE↗

The 2021 update of the EPA’s adverse outcome pathway database

The EPA developed the Adverse Outcome Pathway Database (AOP-DB) to better characterize adverse outcomes of toxicological interest that are relevant to human health and the environment. Here we present the most recent version of the EPA Adverse Outcome Pathway Database (AOP-DB), version 2. AOP-DB v.2 introduces several substantial updates, which include automated data pulls from the AOP-Wiki 2.0, the integration of tissue-gene network data, and human AOP-gene data by population, semantic mapping and SPARQL endpoint creation, in addition to the presentation of the first publicly available AOP-DB web user interface. Potential users of the data may investigate specific molecular targets of an AOP, the relation of those gene/protein targets to other AOPs, cross-species, pathway, or disease-AOP relationships, or frequencies of AOP-related functional variants in particular populations, for example. Version updates described herein help inform new testable hypotheses about the etiology and mechanisms underlying adverse outcomes of environmental and toxicological concern.

59 BASIC BIOLOGICAL SCIENCES↗

ssDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD

DNA damage repair systems are critical for genomic integrity. However, they must be coordinated with DNA replication and cell division to ensure accurate genomic transmission. In most bacteria, this coordination is mediated by the SOS response through LexA, which triggers a halt in cell division until repair is completed. Recently, an SOS-independent damage response system was revealed in Caulobacter crescentus. This pathway is controlled by the transcription activator, DriD, but how DriD senses and signals DNA damage is unknown. To address this question, we performed biochemical, cellular, and structural studies. We show that DriD binds a specific promoter DNA site via its N-terminal HTH domain to activate transcription of genes, including the cell division inhibitor didA. A structure of the C-terminal portion of DriD revealed a WYL motif domain linked to a WCX dimerization domain. Strikingly, we found that DriD binds ssDNA between the WYL and WCX domains. Comparison of apo and ssDNA-bound DriD structures reveals that ssDNA binding orders and orients the DriD domains, indicating a mechanism for ssDNA-mediated operator DNA binding activation. Biochemical and in vivo studies support the structural model. Our data thus reveal the molecular mechanism underpinning an SOS-independent DNA damage repair pathway.

59 BASIC BIOLOGICAL SCIENCES↗

A new genus and species of mud crab (Crustacea, Brachyura, Panopeidae) from shoreline waters of the western Gulf of Mexico

Several specimens of a small panopeid crab from coastal waters of the western Gulf of Mexico were long suspected to represent an undescribed species and are herein designated as representatives of a new genus. While the originally collected specimens from over four decades ago were not of gene-sequence quality, later collections from the same locality produced materials that yielded sequence data for inclusion in molecular phylogenetic studies. Building on results of those analyses, the present taxonomic description draws upon morphology to support the description of a unique species in which especially the male first gonopods differ from those of all other described panopeid genera. To date, the species remains known from only two western Gulf of Mexico sites, both of which are wave-washed intertidal rocky habitats where substrates are heavily burrowed by boring bivalves and sipunculans. While we cannot exclude the possibility that the species was introduced, recurrent collections show its populations to be at very least persistent, the species most likely being a long-overlooked among a confusing hard-substrate assemblage of small panopeid crabs.

Zoology↗

Association of AK4 Protein From Stem Cell–Derived Neurons With Cognitive Reserve

Background and Objectives: Identifying protein targets that provide cognitive reserve is a strategy to prevent and treat Alzheimer disease and Alzheimer disease related dementias (AD/ADRD). Previous studies using bulk human brain tissue reported 12 proteins associated with cognitive reserve. This study examined whether the same proteins from induced neurons (iNs) are associated with cognitive reserve of their human donors. Methods: Here, induced pluripotent stem cell (iPSC) lines were generated from cryopreserved peripheral blood mononuclear cells of older adults who were autopsied as part of the Religious Orders Study or Rush Memory and Aging Project. Neurons were induced from iPSCs using a standard neurogenin2 protocol. Tandem mass tag proteomics analyses were conducted on iNs day 21. Cognitive reserve of their human donors was measured as person-specific slopes of cognitive change not accounted for by common neuropathologies. Results: The 53 human donors died at a mean age of 91 years, all were non-Latino White, and 36 (67.9%) were female. Eighteen were diagnosed with Alzheimer dementia proximate to death, and 34 had pathologic AD diagnosis at autopsy. Approximately 60% of the donors had above-average cognitive reserve such that their cognition declined slower than an average person with comparable burdens of neuropathologies. Eight of the 12 candidate proteins were quantified in iNs proteomics analyses. Higher adenylate kinase 4 (AK4) expression in iNs was associated with lower cognitive reserve, consistent with the previous report for brain AK4 expression. Discussion: By replicating cortical protein associations with cognitive reserve in human iNs, these data provide a valuable molecular readout for studying complex clinical phenotypes such as cognitive reserve in a dish.

59 BASIC BIOLOGICAL SCIENCES↗

The interstellar line spectra of zeta Ophiuchi and zeta Persei and their relation to the short wavelength microwave background radiation

Thirty-one high dispersion Coude spectrograms of zeta Ophiuchi and seven of zeta Persei were numerically synthesized to produce high resolution, low noise spectra in the interval 3650 A to 4350 that yield data on atomic and molecular absorption in well-defined regions of the interstellar medium. The detection threshold is improved by as much as a factor 5 over single plates. Several interstellar lines were discovered in the zeta Oph - 15km/sec cloud and the zeta Per + 13 km/sec cloud.

Bortolot, V. J., Jr.↗

Galactic gamma rays: Models involving variable cosmic-ray density

Mathematical models were developed to determine variable cosmic ray flux around the galactic plane. Data indicate point sources, molecular hydrogen concentration, increased cosmic ray density toward the galactic center, and neutral pion production combine to cause radiation density variables in the galactic plane.

Strong, A. W.↗

Optical observations of interstellar molecules

Recent observational data are summarized on molecular species in diffuse interstellar clouds, and a comprehensive list of all species detected or sought is included. The discussion is focussed on the use of molecular observations to determine physical conditions in clouds, and on important species which provide constraints on cloud chemistry models. Directions for new research are suggested, including intensive work on the unidentified diffuse bands, which may have a molecular origin.

Snow, T. P., Jr.↗

The large scale dust distribution in the inner galaxy

Initial results are presented from a new large-scale survey of the first quadrant of the galactic plane at wavelengths of 160, 260, and 300 microns. The submillimeter wavelength emission, interpreted as thermal radiation by dust grains, reveals an optically thin disk of angular width about 0.09 deg (FWHM) with a mean dust temperature of 23 K and significant variation of the dust mass column density. Comparison of the dust column density with the gas column density inferred from CO survey data shows a striking spatial correlation. The mean luminosity per hydrogen atom is found to be 2.5 x 10 to the -30th W/H, implying a radiant energy density in the vicinity of the dust an order of magnitude larger than in the solar neighborhood. The data favor dust in molecular clouds as the dominant submillimeter radiation source.

Hauser, M. G.↗

Shuttle/spacelab contamination environment and effects handbook

This handbook is intended to assist users of the Spacelab/Space Transportation System by providing contamination environments and effects information that may be of value in planning, designing, manufacturing, and operating a space flight experiment. A summary of available molecular and particulate contamination data on the Space Transportation System and its facilities is presented. Contamination models, contamination effects, and protection methods information are also presented. In addition to contamination, the effects of the space environments at STS altitudes on spacecraft materials are included. Extensive references, bibliographies, and contacts are provided.

Bareiss, L. E.↗

Second coefficient of viscosity in air

Acoustic attenuation measurements in air were analyzed in order to estimate the second coefficient of viscosity. Data over a temperature range of 11 C to 50 C and at relative humidities between 6 percent and 91 percent were used. This analysis showed that the second coefficient of viscosity varied between 1900 and 20,000 times larger than the dynamic or first coefficient of viscosity over the temperature and humidity range of the data. In addition, the data showed that the molecular relaxation effects, which are responsible for the magnitude of the second coefficient of viscosity, place severe limits on the use of time-independent, thermodynamic equations of state. Compressible flows containing large streamwise velocity gradients, like shock waves, which cause significant changes in particle properties to occur during time intervals shorter than hundredths of seconds, must be modeled using dynamic equations of state. The dynamic model approach is described briefly.

Ash, Robert L.↗

Condensed-matter energetics from diatomic molecular spectra

Analyses of molecular spectra and compression data from crystals show that a single function successfully describes the dependence on interatomic separation of both the potential energy of diatomic molecules and the cohesive binding energy of condensed matter. The empirical finding that one function describes interatomic energies for such diverse forms of matter and over a wide range of conditions can be used to extend condensed-matter equations of state but warrants further theoretical study.

Kim, In H.↗

Ranges of Applicability for the Continuum-beam Model in the Constitutive Analysis of Carbon Nanotubes: Nanotubes or Nano-beams?

Ranges of validity for the continuum-beam model, the length-scale effects and continuum assumptions are analyzed in the framework of scaling analysis of NT structure. Two coupled criteria for the applicability of the continuum model are presented. Scaling analysis of NT buckling and geometric parameters (e.g., diameter and length) is carried out to determine the key non-dimensional parameters that control the buckling strains and modes of NT buckling. A model applicability map, which represents two classes of NTs, is constructed in the space of non-dimensional parameters. In an analogy with continuum mechanics, a mechanical law of geometric similitude is presented for two classes of beam-like NTs having different geometries. Expressions for the critical buckling loads and strains are tailored for the distinct groups of NTs and compared with the data provided by the molecular dynamics simulations. Implications for molecular dynamics simulations and the NT-based scanning probes are discussed.

Harik, Vasyl Michael↗

Holographic Optical Storage Using Photorefractive Polymers

The task for this report is to perform the basic research and develop a prototype benchtop holographic optical storage system based on photochromic and/or photorefractive polymers so that both permanent and erasable images may be stored and retrieved in the same mixed polymer medium. The task consist of: assembly and setup of the benchtop holographic storage system, including lasers, optics, and other ancillary equipment in a laboratory setting; and research and development of a suitable polymer matrix that will allow practical storage and retrieval of digital data. This will necessitate molecular design of the matrices involved and subsequent physics test to verify the characteristics of the matrices provide practical storage and retrieval.

Hayden, L. Michael↗