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At least 433 records · Page 24

The Historical Development of Large‐Scale Paleoclimate Field Reconstructions Over the Common Era

Abstract Climate field reconstructions (CFRs) combine modern observational data with paleoclimatic proxies to estimate climate variables over spatiotemporal grids during time periods when widespread observations of climatic conditions do not exist. The Common Era (CE) has been a period over which many seasonally‐ and annually‐resolved CFRs have been produced on regional to global scales. CFRs over the CE were first produced in the 1970s using dendroclimatic records and linear regression‐based approaches. Since that time, many new CFRs have been produced using a wide range of proxy data sets and reconstruction techniques. We assess the early history of research on CFRs for the CE, which provides context for our review of advances in CFR research over the last two decades. We review efforts to derive gridded hydroclimatic CFRs over continental regions using networks of tree‐ring proxies. We subsequently explore work to produce hemispheric‐ and global‐scale CFRs of surface temperature using multi‐proxy data sets, before specifically reviewing recently‐developed data assimilation techniques and how they have been used to produce simultaneous reconstructions of multiple climatic fields globally. We then review efforts to develop standardized and digitized databases of proxy networks for use in CFR research, before concluding with some thoughts on important next steps for CFR development.

Smerdon, Jason E.↗

A common assembly module in injectisome and flagellar type III secretion sorting platforms

Translocating proteins across the double membrane of Gram-negative bacteria, type III secretion systems (T3SS) occur in two evolutionarily related forms: injectisomes, delivering virulence factors into host cells, and the flagellar system, secreting the polymeric filament used for motility. While both systems share related elements of a cytoplasmic sorting platform that facilitates the hierarchical secretion of protein substrates, its assembly and regulation remain unclear. Here we describe a module mediating the assembly of the sorting platform in both secretion systems, and elucidate the structural basis for segregation of homologous components among these divergent T3SS subtypes sharing a common cytoplasmic milieu. These results provide a foundation for the subtype-specific assembly of T3SS sorting platforms and will support further mechanistic analysis and anti-virulence drug design.

Science & Technology - Other Topics↗

Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design

Broadly neutralizing antibodies (bNAbs) against HIV-1 Env V1V2 arise in multiple donors. However, atomic-level interactions had previously been determined only with antibodies from a single donor, thus making commonalities in recognition uncertain. Here we report the cocrystal structure of V1V2 with antibody CH03 from a second donor and model Env interactions of antibody CAP256-VRC26 from a third donor. These V1V2-directed bNAbs used strand-strand interactions between a protruding antibody loop and a V1V2 strand but differed in their N-glycan recognition. Ontogeny analysis indicated that protruding loops develop early, and glycan interactions mature over time. Altogether, the multidonor information suggested that V1V2-directed bNAbs form an 'extended class', for which we engineered ontogeny-specific antigens: Env trimers with chimeric V1V2s that interacted with inferred ancestor and intermediate antibodies. As a result, the ontogeny-based design of vaccine antigens described here may provide a general means for eliciting antibodies of a desired class.

60 APPLIED LIFE SCIENCES↗

Syntrophus conductive pili demonstrate that common hydrogen-donating syntrophs can have a direct electron transfer option

Syntrophic interspecies electron exchange is necessary for the stable functioning of diverse anaerobic microbial communities. Hydrogen/formate interspecies electron transfer (HFIT), in which H 2 and/or formate function as diffusible electron carriers, has been considered to be the primary mechanism for electron transfer because most common syntrophs were thought to lack biochemical components, such as electrically conductive pili (e-pili), necessary for direct interspecies electron transfer (DIET). Herein we report that Syntrophus aciditrophicus, one of the most intensively studied microbial models for HFIT, produces e-pili and can grow via DIET. Heterologous expression of the putative S. aciditrophicus type IV pilin gene in Geobacter sulfurreducens yielded conductive pili of the same diameter (4 nm) and conductance of the native S. aciditrophicus pili and enabled long-range electron transport in G. sulfurreducens. S. aciditrophicus lacked abundant c-type cytochromes often associated with DIET. Pilin genes likely to yield e-pili were found in other genera of hydrogen/formate-producing syntrophs. The discovery that DIET is a likely option for diverse syntrophs that are abundant in many anaerobic environments necessitates a reexamination of the paradigm that HFIT is the predominant mechanism for syntrophic electron exchange within anaerobic microbial communities of biogeochemical and practical significance.

59 BASIC BIOLOGICAL SCIENCES↗

Microbial and metabolic succession on common building materials under high humidity conditions

Despite considerable efforts to characterize the microbial ecology of the built environment, the metabolic mechanisms underpinning microbial colonization and successional dynamics remain unclear, particularly at high moisture conditions. Here, we applied bacterial/viral particle counting, qPCR, amplicon sequencing of the genes encoding 16S and ITS rRNA, and metabolomics to longitudinally characterize the ecological dynamics of four common building materials maintained at high humidity. We varied the natural inoculum provided to each material and wet half of the samples to simulate a potable water leak. Wetted materials had higher growth rates and lower alpha diversity compared to non-wetted materials, and wetting described the majority of the variance in bacterial, fungal, and metabolite structure. Inoculation location was weakly associated with bacterial and fungal beta diversity. Material type influenced bacterial and viral particle abundance and bacterial and metabolic (but not fungal) diversity. Metabolites indicative of microbial activity were identified, and they too differed by material.

59 BASIC BIOLOGICAL SCIENCES↗

Phylogenetic patterns recover known HIV epidemiological relationships and reveal common transmission of multiple variants

The growth of human immunodeficiency virus (HIV) sequence databases resulting from drug resistance testing has motivated efforts using phylogenetic methods to assess how HIV spreads. Such inference is potentially both powerful and useful for tracking the epidemiology of HIV and the allocation of resources to prevention campaigns. We recently used simulation and a small number of illustrative cases to show that certain phylogenetic patterns are associated with different types of epidemiological linkage. Our original approach was later generalized for large next-generation sequencing datasets and implemented as a free computational pipeline. Previous work has claimed that direction and directness of transmission could not be established from phylogeny because one could not be sure that there were no intervening or missing links involved. We address this issue by investigating phylogenetic patterns from 272 previously identified HIV transmission chains with 955 transmission pairs representing diverse geography, risk groups, subtypes, and genomic regions. These HIV transmissions had known linkage based on epidemiological information such as partner studies, mother-to-child transmission, pairs identified by contact tracing, and criminal cases. Here, we show that the resulting phylogeny inferred from real HIV genetic sequences indeed reveals distinct patterns associated with direct transmission contra transmissions from a common source. Thus, our results establish how to interpret phylogenetic trees based on HIV sequences when tracking who-infected-whom, when and how genetic information can be used for improved tracking of HIV spread. We also investigate limitations that stem from limited sampling and genetic time-trends in the donor and recipient HIV populations.

59 BASIC BIOLOGICAL SCIENCES↗

High-throughput dataset of impurity adsorption on common catalysts in biomass upgrading applications

Abstract An extensive dataset consisting of adsorption energies of pernicious impurities present in biomass upgrading processes on common catalysts and support materials has been generated. This work aims to inform catalyst and process development for the conversion of biomass-derived feedstocks to fuels and chemicals. A high-throughput workflow was developed to execute density functional theory calculations for a diverse set of atomic (Al, B, Ca, Cl, Fe, K, Mg, Mn, N, Na, P, S, Si, Zn) and molecular (COS, H 2 S, HCl, HCN, K 2 O, KCl, NH 3 ) species on 35 unique surfaces for transition-metal (Ag, Au, Co, Cu, Fe, Ir, Ni, Pd, Pt, Re, Rh, Ru) and metal-oxide (Al 2 O 3 , MgO, anatase-TiO 2 , rutile-TiO 2 , ZnO, ZrO 2 ) catalysts and supports. Approximately 3,000 unique adsorption geometries and corresponding adsorption energies were obtained.

09 BIOMASS FUELS↗

Mechanisms of picosecond laser-induced damage in common multilayer dielectric coatings

Abstract The physical mechanisms and ensuing material modification associated with laser-induced damage in multilayer dielectric high reflectors is investigated for pulses between 0.6 and 100 ps. We explore low-loss multilayer dielectric SiO 2 /HfO 2 mirrors which are commonly employed in petawatt-class laser systems. The spatial features of damage sites are precisely characterized, enabling the direct correlation of the observed damage morphology to the location of energy deposition and the corresponding standing-wave electric-field intensities within the layer structure. The results suggest that there are three discrete damage-initiation morphologies arising from distinctly different mechanisms: the first prevailing at laser pulse lengths shorter than about 2.3 ps, while the other two are observed for longer pulses. Modeling of the thermomechanical response of the material to localized laser-energy deposition was performed for each type of damage morphology to better understand the underlying mechanisms of energy deposition and subsequent material response.

42 ENGINEERING↗

Common origin of ornithine–urea cycle in opisthokonts and stramenopiles

Eukaryotic complex phototrophs exhibit a colorful evolutionary history. At least three independent endosymbiotic events accompanied by the gene transfer from the endosymbiont to host assembled a complex genomic mosaic. Resulting patchwork may give rise to unique metabolic capabilities; on the other hand, it can also blur the reconstruction of phylogenetic relationships. The ornithine–urea cycle (OUC) belongs to the cornerstone of the metabolism of metazoans and, as found recently, also photosynthetic stramenopiles. We have analyzed the distribution and phylogenetic positions of genes encoding enzymes of the urea synthesis pathway in eukaryotes. We show here that metazoan and stramenopile OUC enzymes share common origins and that enzymes of the OUC found in primary algae (including plants) display different origins. The impact of this fact on the evolution of stramenopiles is discussed here.

59 BASIC BIOLOGICAL SCIENCES↗

Insight into different environmental niches adaptation and allergenicity from the Cladosporium sphaerospermum genome, a common human allergy-eliciting Dothideomycetes

Cladosporium sphaerospermum, a dematiaceous saprophytic fungus commonly found in diverse environments, has been reported to cause allergy and other occasional diseases in humans. However, its basic biology and genetic information are largely unexplored. A clinical isolate C. sphaerospermum genome, UM 843, was re-sequenced and combined with previously generated sequences to form a model 26.89 Mb genome containing 9,652 predicted genes. Functional annotation on predicted genes suggests the ability of this fungus to degrade carbohydrate and protein complexes. Several putative peptidases responsible for lung tissue hydrolysis were identified. These genes shared high similarity with the Aspergillus peptidases. The UM 843 genome encodes a wide array of proteins involved in the biosynthesis of melanin, siderophores, cladosins and survival in high salinity environment. In addition, a total of 28 genes were predicted to be associated with allergy. Orthologous gene analysis together with 22 other Dothideomycetes showed genes uniquely present in UM 843 that encode four class 1 hydrophobins which may be allergens specific to Cladosporium. The mRNA of these hydrophobins were detected by RT-PCR. The genomic analysis of UM 843 contributes to the understanding of the biology and allergenicity of this widely-prevalent species.

59 BASIC BIOLOGICAL SCIENCES↗

Negative linear compressibility in common materials

Negative linear compressibility (NLC) is still considered an exotic property, only observed in a few obscure crystals. The vast majority of materials compress axially in all directions when loaded in hydrostatic compression. However, a few materials have been observed which expand in one or two directions under hydrostatic compression. At present, the list of materials demonstrating this unusual behaviour is confined to a small number of relatively rare crystal phases, biological materials, and designed structures, and the lack of widespread availability hinders promising technological applications. Using improved representations of elastic properties, this study revisits existing databases of elastic constants and identifies several crystals missed by previous reviews. More importantly, several common materials-drawn polymers, certain types of paper and wood, and carbon fibre laminates-are found to display NLC. We show that NLC in these materials originates from the misalignment of polymers/fibres. Using a beam model, we propose that maximum NLC is obtained for misalignment of 26°. The existence of such widely available materials increases significantly the prospects for applications of NLC.

36 MATERIALS SCIENCE↗

Versatile common instrumentation for optical detection of pH and dissolved oxygen

The recent trend toward use of disposable and miniature bioreactors requires the use of appropriate sensors. pH and dissolved oxygen (DO) are often measured using optical chemical sensors due to their small form factor and convenience in use. These sensors are often interrogated using a specialized opto-electronic transducer that is designed around the optical sensor. In this contribution, we are presenting a new class of opto-electronic transducers that are usable with several different chemical sensors without the need to switch the optics or hardware when changing the type of the chemical sensor. This allows flexibility closer to the lab-grade devices while the size is closer to a dedicated sensor. This versatile instrumentation is capable of seamlessly switching between the pH and DO measurement modes and is capable of auto recognition of the sensor type. The principle of ratiometric fluorescence is used for pH measurements, and that of fluorescence lifetime for DO measurements. An approach to obtain identical calibrations between several devices is also presented. The described hardware constitutes common instrumentation for measuring either pH or DO and has been tested in actual bioprocesses. It has been found adequate for continuous bioprocess monitoring.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Common origin of kinetic scale turbulence and the electron halo in the solar wind – Connection to nanoflares

We summarize our recent studies on the origin of solar wind kinetic scale turbulence and electron halo in the electron velocity distribution function. Increasing observations of nanoflares and microscopic type III radio bursts strongly suggest that nanoflares and accelerated electron beams are common in the corona. Based on particle-in-cell simulations, we show that both the core-halo feature and kinetic scale turbulence observed in the solar wind can be produced by the nonlinear evolution of electron two-stream instability driven by nanoflare accelerated electron beams. The energy exchange between waves and particles reaches equilibrium in the inner corona and the key features of the turbulence and velocity distribution are preserved as the solar wind escapes into interplanetary space along open magnetic field lines. Observational tests of the model and future theoretical work are discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Level crossing analysis of chemically induced dynamic nuclear polarization: Towards a common description of liquid-state and solid-state cases

Chemically Induced Dynamic Nuclear Polarization (CIDNP) is an efficient method of creating non-equilibrium polarization of nuclear spins by using chemical reactions, which have radical pairs as intermediates. The CIDNP effect originates from (i) electron spin-selective recombination of radical pairs and (ii) the dependence of the inter-system crossing rate in radical pairs on the state of magnetic nuclei. The CIDNP effect can be investigated by using Nuclear Magnetic Resonance (NMR) methods. The gain from CIDNP is then two-fold: it allows one to obtain considerable amplification of NMR signals; in addition, it provides a very useful tool for investigating elusive radicals and radical pairs. While the mechanisms of the CIDNP effect in liquids are well established and understood, detailed analysis of solid-state CIDNP mechanisms still remains challenging; likewise a common theoretical frame for the description of CIDNP in both solids and liquids is missing. Difficulties in understanding the spin dynamics that lead to the CIDNP effect in the solid-state case are caused by the anisotropy of spin interactions, which increase the complexity of spin evolution. In this work, we propose to analyze CIDNP in terms of level crossing phenomena, namely, to attribute features in the CIDNP magnetic field dependence to Level Crossings (LCs) and Level Anti-Crossings (LACs) in a radical pair. This approach allows one to describe liquid-state CIDNP; the same holds for the solid-state case where anisotropic interactions play a significant role in CIDNP formation. In solids, features arise predominantly from LACs, since in most cases anisotropic couplings result in perturbations, which turn LCs into LACs. We have interpreted the CIDNP mechanisms in terms of the LC/LAC concept. This consideration allows one to find analytical expressions for a wide magnetic field range, where several different mechanisms are operative; furthermore, the LAC description gives a way to determine CIDNP sign rules. Thus, LCs/LACs provide a consistent description of CIDNP in both liquids and solids with the prospect of exploiting it for the analysis of short-lived radicals and for optimizing the polarization level.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High-sensitivity plasma density retrieval in a common-path second-harmonic interferometer through simultaneous group and phase velocity measurement

Precise measurements of the plasma density in ionized gas cells and discharged capillaries are critical to the design and operation of plasma-based accelerators, active plasma lenses, and plasma-based radiation sources. In this manuscript, a spectral-domain common-path second-harmonic interferometer is upgraded with the simultaneous measurement of the group and phase velocity, allowing for high-sensitivity density characterization (from the phase velocity advance) without the need for phase tracking from zero-density (enabled by the group velocity delay). The technique is applied to 1.5-cm-long plasma structures, without density ambiguity in parameter scans with >2π phase jumps. Finally, the single-shot sensitivity in phase retrieval is demonstrated at 63 mrad, equivalent to a density-length product of 1.8·10 15 cm -2 . This is an improvement of ×45 compared to group velocity analysis alone.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Solvation at metal/water interfaces: An ab initio molecular dynamics benchmark of common computational approaches

Determining the influence of the solvent on electrochemical reaction energetics is a central challenge in our understanding of electrochemical interfaces. To date, it is unclear how well existing methods predict solvation energies at solid/liquid interfaces, since they cannot be assessed experimentally. Ab initio molecular dynamics (AIMD) simulations present a physically highly accurate, but also a very costly approach. In this work, we employ extensive AIMD simulations to benchmark solvation at charge-neutral metal/water interfaces against commonly applied continuum solvent models. We consider a variety of adsorbates including *CO, *CHO, *COH, *OCCHO, *OH, and *OOH on Cu, Au, and Pt facets solvated by water. The surfaces and adsorbates considered are relevant, among other reactions, to electrochemical CO 2 reduction and the oxygen redox reactions. We determine directional hydrogen bonds and steric water competition to be critical for a correct description of solvation at the metal/water interfaces. As a consequence, we find that the most frequently applied continuum solvation methods, which do not yet capture these properties, do not presently provide more accurate energetics over simulations in vacuum. We find most of the computed benchmark solvation energies to linearly scale with hydrogen bonding or competitive water adsorption, which strongly differ across surfaces. Furthermore, we determine solvation energies of adsorbates to be non-transferable between metal surfaces, in contrast to standard practice.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Estimating canopy fuel characteristics for predicting crown fire potential in common forest types of the Atlantic Coastal Plain, USA

We computed four stand-level canopy stratum variables important for crown fire modelling – canopy cover, stand height, canopy base height and canopy bulk density – from forest inventory data. We modelled the relationship between the canopy variables and a set of common inventory parameters – site index, stem density, basal area, stand age or stand height – and number of prescribed burns. We used a logistic model to estimate canopy cover, a linear model to estimate the other canopy variables, and the information theoretic approach for model selection. Coefficients of determination across five forest groups were 0.72–0.91 for stand height, 0.36–0.83 for canopy base height, 0.39–0.80 for canopy cover, and 0.63–0.78 for canopy bulk density. We assessed crown fire potential (1) for several sets of environmental conditions in all seasons, and (2) with increasing age, density and number of prescribed burns using our modelled canopy bulk density and canopy base height variables and local weather data to populate the Crown Fire Initiation and Spread model. Results indicated that passive crown fire is possible in any season in Atlantic coastal plain pine stands with heavy surface fuel loads and active crown fire is most probable in infrequently burned, dense stands at low fuel moistures.

Forestry↗