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At least 865 records · Page 48

Microbial models with minimal mineral protection can explain long-term soil organic carbon persistence

Soil organic carbon (SOC) models currently in widespread use omit known microbial processes, and assume the existence of a SOC pool whose intrinsic properties confer persistence for centuries to millennia, despite evidence from priming and aggregate turnover that cast doubt on the existence of SOC with profound intrinsic stability. Here we show that by including microbial interactions in a SOC model, persistence can be explained as a feedback between substrate availability, mineral protection and microbial population size, without invoking an unproven pool that is intrinsically stable for centuries. The microbial SOC model based on this concept reproduces long-term data (r 2 = 0.92; n = 90), global SOC distribution (rmse = 4.7 +/– 0.6 kg C m –2 ), and total global SOC in the top 0.3 m (822 Pg C) accurately. SOC dynamics based on a microbial feedback without stable pools are thus consistent with global SOC distribution. This has important implications for carbon management, suggesting that relatively fast cycling, rather than recalcitrant, SOC must form the primary target of efforts to build SOC stocks.

59 BASIC BIOLOGICAL SCIENCES↗

Ecosystem-bedrock interaction changes nutrient compartmentalization during early oxidative weathering

Ecosystem-bedrock interactions power the biogeochemical cycles of Earth’s shallow crust, supporting life, stimulating substrate transformation, and spurring evolutionary innovation. While oxidative processes have dominated half of terrestrial history, the relative contribution of the biosphere and its chemical fingerprints on Earth’s developing regolith are still poorly constrained. Here, we report results from a two-year incipient weathering experiment. We found that the mass release and compartmentalization of major elements during weathering of granite, rhyolite, schist and basalt was rock-specific and regulated by ecosystem components. A tight interplay between physiological needs of different biota, mineral dissolution rates, and substrate nutrient availability resulted in intricate elemental distribution patterns. Biota accelerated CO 2 mineralization over abiotic controls as ecosystem complexity increased, and significantly modified the stoichiometry of mobilized elements. Microbial and fungal components inhibited element leaching (23.4% and 7%), while plants increased leaching and biomass retention by 63.4%. All biota left comparable biosignatures in the dissolved weathering products. Nevertheless, the magnitude and allocation of weathered fractions under abiotic and biotic treatments provide quantitative evidence for the role of major biosphere components in the evolution of upper continental crust, presenting critical information for large-scale biogeochemical models and for the search for stable in situ biosignatures beyond Earth.

54 ENVIRONMENTAL SCIENCES↗

Lipid sponge droplets as programmable synthetic organelles

Living cells segregate molecules and reactions in various subcellular compartments known as organelles. Spatial organization is likely essential for expanding the biochemical functions of synthetic reaction systems, including artificial cells. Many studies have attempted to mimic organelle functions using lamellar membrane-bound vesicles. However, vesicles typically suffer from highly limited transport across the membranes and an inability to mimic the dense membrane networks typically found in organelles such as the endoplasmic reticulum. Here, we describe programmable synthetic organelles based on highly stable nonlamellar sponge phase droplets that spontaneously assemble from a single-chain galactolipid and nonionic detergents. Due to their nanoporous structure, lipid sponge droplets readily exchange materials with the surrounding environment. In addition, the sponge phase contains a dense network of lipid bilayers and nanometric aqueous channels, which allows different classes of molecules to partition based on their size, polarity, and specific binding motifs. The sequestration of biologically relevant macromolecules can be programmed by the addition of suitably functionalized amphiphiles to the droplets. We demonstrate that droplets can harbor functional soluble and transmembrane proteins, allowing for the colocalization and concentration of enzymes and substrates to enhance reaction rates. Droplets protect bound proteins from proteases, and these interactions can be engineered to be reversible and optically controlled. Our results show that lipid sponge droplets permit the facile integration of membrane-rich environments and self-assembling spatial organization with biochemical reaction systems.

59 BASIC BIOLOGICAL SCIENCES↗

Ab initio study of cross-interface electron-phonon couplings in FeSe thin films on SrTiO 3 and BaTiO 3

We study the electron-phonon coupling strength near the interface of monolayer and bilayer FeSe thin films on SrTiO 3 , BaTiO 3 , and oxygen-vacant SrTiO 3 substrates, using ab initio methods. The calculated total electron-phonon coupling strength λ = 0.2 – 0.3 cannot account for the high T c ~ 70 K observed in these systems through the conventional phonon-mediated pairing mechanism. In all of these systems, however, we find that the coupling constant of a polar oxygen branch peaks at q = 0 with negligible coupling elsewhere, while the energy of this mode coincides with the offset energy of the replica bands measured recently by angle-resolved photoemission spectroscopy experiments. However, the integrated coupling strength for this mode from our current calculations is still too small to produce the observed high T c , even through the more efficient pairing mechanism provided by the forward scattering. Also, we arrive at the same qualitative conclusion when considering a checkerboard antiferromagnetic configuration in the Fe layer. In light of the experimental observations of the replica band feature and the relatively high T c of FeSe monolayers on polar substrates, our results point towards a cooperative role for the electron-phonon interaction, where the cross-interface interaction acts in conjunction with a purely electronic interaction. Finally, we discuss a few scenarios where the coupling strength obtained here may be enhanced.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Sierpinski Structure and Electronic Topology in Bi Thin Films on InSb(111)B Surfaces

Deposition of Bi on InSb(111)B reveals a striking Sierpinski-triangle (ST)-like structure in Bi thin films. Such a fractal geometric topology is further shown to turn off the intrinsic electronic topology in a thin film. Relaxation of a huge misfit strain of about 30 to 40% between Bi adlayer and substrate is revealed to drive the ST-like island formation. A Frenkel-Kontrova model is developed to illustrate the enhanced strain relief in the ST islands offsetting the additional step energy cost. Besides a sufficiently large tensile strain, forming ST-like structures also requires larger adlayer-substrate and intra-adlayer elastic stiffnesses, and weaker intra-adlayer interatomic interactions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Development Status of the KIPM Detector Consortium

A kinetic inductance phonon-mediated detector is a calorimeter that uses kinetic inductance detectors (KIDs) to read out phonon signals from the device substrate. We have established a consortium comprising university and national lab groups dedicated to advancing the state of the art in these detectors, with the ultimate goal of designing a detector with sub-eV threshold on energy deposited in the substrate, enabling searches for both light dark matter and low-energy neutrino interactions. This consortium brings together experts in KID design, phonon and quasi-particle dynamics, and noise modeling, along with specialized fabrication facilities, test platforms, and unique calibration capabilities. Recently, our consortium has demonstrated a resolution on energy absorbed by the sensor of 2.1 eV, the current record for phonon-sensitive KIDs. However, due to ∼ 1% phonon collection efficiency, the overall detector resolution was limited to 320 eV. Finally, the current focus of the consortium is modeling and improving the phonon collection efficiency and implementing low-T c superconductors, both of which serve to improve the overall energy resolution and threshold of the detectors.

Temples, Dylan J. [Fermi National Accelerator Labo↗

Zooming in on protons: Neutron structure of protein kinase A trapped in a product complex

The question vis-à-vis the chemistry of phosphoryl group transfer catalyzed by protein kinases remains a major challenge. The neutron diffraction structure of the catalytic subunit of cAMP-dependent protein kinase (PKA-C) provides a more complete chemical portrait of key proton interactions at the active site. By using a high-affinity protein kinase substrate (PKS) peptide, we captured the reaction products, dephosphorylated nucleotide [adenosine diphosphate (ADP)] and phosphorylated PKS (pPKS), bound at the active site. In the complex, the phosphoryl group of the peptide is protonated, whereas the carboxyl group of the catalytic Asp 166 is not. Our structure, including conserved waters, shows how the peptide links the distal parts of the cleft together, creating a network that engages the entire molecule. By comparing slow-exchanging backbone amides to those determined by the NMR analysis of PKA-C with ADP and inhibitor peptide (PKI), we identified exchangeable amides that likely distinguish catalytic and inhibited states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The KIPM Detector Consortium

Kinetic Inductance Phonon-Mediated (KIPM) Detectors, microcalorimeters that leverage kinetic inductance detectors (KIDs) to read out phonon signals from the device substrate, are an attractive architecture for low-threshold rare-event searches due to their large response to small changes in quasiparticle density and native multiplexability, enabling scalability. We have established a consortium comprising university and national lab groups dedicated to advancing the state-of-the-art in these detectors, with the ultimate goal of designing a detector with a kg-scale target mass and sub-eV threshold on energy deposited in the substrate, enabling searches for both light dark matter and low-energy neutrino interactions. This consortium brings together experts in KID design, phonon and quasiparticle dynamics, and noise modeling, along with specialized fabrication facilities, test platforms, and unique calibration capabilities. Recently, our consortium has demonstrated a sensor resolution (i.e., resolution in the quasiparticle channel) of 2.1 eV, the current record for such devices. The current focus of the consortium is modeling and improving the phonon collection efficiency and implementing low-Tc superconductors, both of which serve to improve the overall energy resolution and threshold of the detectors. In this talk, I will provide an overview of the consortium and its capabilities, highlight some recent results from its member groups, and discuss near term plans toward reaching the ultimate goal.

Temples, Dylan J. [Fermilab]↗

Role of the flocculus of the cerebellum in motor learning of the vestibulo-ocular reflex

Structure-function studies at the systems level are an effective method for understanding the relationship of the central nervous system to behavior. Motor learning or adaptation of the vestibulo-ocular reflex is a clear example wherein this approach has been productive. During a vestibulo-ocular reflex the brain converts a head velocity signal, transduced through the vestibular semicircular canals, into an eye movement command delivered to the extraocular muscles. If the viewed target remains on the fovea of the retina, the reflex is compensatory, and its gain, eye velocity/head velocity, is one. When the image of the viewed object slips across the retina, visual acuity decreases, and the gain of the reflex, which is no longer one, is plastically adapted or adjusted until retinal stability is restored. The anatomic substrate for this plasticity thus involves brain structures in which visual-vestibular interaction can potentially occur, as well as vestibular and visual sensory and oculomotor motor structures. Further, it has been known for many years that removal of the flocculus of the cerebellum permanently precludes further vestibulo-ocular reflex adaptation, demonstrating the involvement of the cerebellum in this behavior. Maekawa and Simpson (J Neurophysiol 1973;36: 649-66) discovered that one visual input to the flocculus involved the accessory optic system and the inferior olive. Ensuing work has demonstrated that the visual signals used to adapt the vestibulo-ocular reflex are transmitted by this accessory optic system to the flocculus and subsequently to brain stem structures involved in vestibulo-ocular reflex plasticity. Presently the inclusive list of anatomic sites involved in vestibulo-ocular reflex circuitry and its adaptive plasticity is small. Our laboratory continues to believe that this behavior should be caused by interactions within this small class of neurons. By studying each class of identified neuron and its interactions with others within the list, we hope to ultimately understand the mechanisms used by the brain in the expression of this behavior.

Non-NASA Center↗

Wafer-scale remote epitaxy of III-V semiconductors and applications

In conventional epitaxy of single-crystalline semiconductor materials, it is challenging to separate the grown layer with the substrate due to the strong bonding at the interface. Remote epitaxy is a recently discovered method to grow single-crystalline thin films on graphene, wherein the grown film can be exfoliated at the graphene interface to form freestanding membranes. Here, we present our recent development on remote epitaxy of III-V semiconductors. We show that directly growing 2D materials on III-V substrates as a remote epitaxy template is an ideal pathway that can eliminate transfer process-related defects and can realize wafer-scale process of remote epitaxy and substrate reuse. We present the strategies to grow 2D materials on the surface of III-V materials, which is much more challenging than thermally robust substrates such as SiO2/Si or sapphire. The nucleation of III-V on 2D material-coated III-V platforms via remote interaction is investigated both experimentally and theoretically. Lastly, we show advanced remote epitaxial platforms and optoelectronic applications enabled by remote epitaxy, and the capability to recycle the III-V substrates for repeated remote epitaxy and production of freestanding III-V thin films.

Kim, Hyunseok↗

Wafer-scale remote epitaxy of III-V semiconductors and applications

In conventional epitaxy of single-crystalline semiconductor materials, it is challenging to separate the grown layer with the substrate due to the strong bonding at the interface. Remote epitaxy is a recently discovered method to grow single-crystalline thin films on graphene, wherein the grown film can be exfoliated at the graphene interface to form freestanding membranes. Here, we present our recent development on remote epitaxy of III-V semiconductors. We show that directly growing 2D materials on III-V substrates as a remote epitaxy template is an ideal pathway that can eliminate transfer process-related defects and can realize wafer-scale process of remote epitaxy and substrate reuse. We present the strategies to grow 2D materials on the surface of III-V materials, which is much more challenging than thermally robust substrates such as SiO2/Si or sapphire. The nucleation of III-V on 2D material-coated III-V platforms via remote interaction is investigated both experimentally and theoretically. Lastly, we show advanced remote epitaxial platforms and optoelectronic applications enabled by remote epitaxy, and the capability to recycle the III-V substrates for repeated remote epitaxy and production of freestanding III-V thin films.

Kim, Hyunseok↗

Pit rim decomposition into multiple quantum dots on surfaces of epitaxial thin films grown on pit-patterned substrates

Here, we report results of dynamical simulations according to an experimentally validated surface morphological evolution model on the formation of regular arrays of quantum dot molecules (QDMs) consisting of 1D arrays of smaller interacting quantum dots (QDs). These QD arrays form along the sides of each pit rim on the surface of a coherently strained thin film epitaxially deposited on a semiconductor substrate, the surface of which consists of a periodic pattern of inverted prismatic pits with rectangular pit openings. We find that this complex QDM pattern results from the decomposition of the pit rim from a “quantum fortress” with four elongated QDs into four 1D arrays of multiple smaller QDs arranged along each side of the pit rim. Systematic parametric analysis indicates that varying the pit opening dimensions and the pit wall inclination directly impacts the number of QDs in the resulting QDM pattern, while varying the pit depth only affects the dimensions of the QDs in the nanostructure pattern. Therefore, the number, arrangement, and sizes of QDs in the resulting pattern of QDMs on the film surface can be engineered precisely by proper tuning of the pit design parameters. Our simulation results are supported by predictions of morphological stability analysis, which explains the pit rim decomposition into multiple QDs as the outcome of a tip-splitting instability and provides a fundamental characterization of the post-instability nanostructure pattern. Our theoretical findings can play a vital role in designing optimal semiconductor surface patterns toward enabling future nanofabrication technologies.

36 MATERIALS SCIENCE↗

Directional locking effects for active matter particles coupled to a periodic substate

Directional locking occurs when a particle moving over a periodic substrate becomes constrained to travel along certain substrate symmetry directions. Such locking effects arise for colloids and superconducting vortices moving over ordered substrates when the direction of the external drive is varied. Here we study the directional locking of run-and-tumble active matter particles interacting with a periodic array of obstacles. In the absence of an external biasing force, we find that the active particle motion locks to various symmetry directions of the substrate when the run time between tumbles is large. The number of possible locking directions depends on the array density and on the relative sizes of the particles and the obstacles. For a square array of large obstacles, the active particle only locks to the x, y, and 45° directions, while for smaller obstacles, the number of locking angles increases. Each locking angle satisfies θ = arctan (p/q) , where p and q are integers, and the angle of motion can be measured using the ratio of the velocities or the velocity distributions in the x and y directions. When a biasing driving force is applied, the directional locking behavior is affected by the ratio of the self-propulsion force to the biasing force. For large biasing, the behavior resembles that found for directional locking in passive systems. For large obstacles under biased driving, a trapping behavior occurs that is nonmonotonic as a function of increasing run length or increasing self-propulsion force, and the trapping diminishes when the run length is sufficiently large.

36 MATERIALS SCIENCE↗

Pyridine-containing substrate analogs are restricted from accessing the human cytochrome P450 8B1 active site by tryptophan 281

The human oxysterol 12α-hydroxylase cytochrome P450 8B1 (CYP8B1) is a validated drug target for both type 2 diabetes and nonalcoholic fatty liver disease, but effective selective inhibitors are not yet available. Herein, steroidal substrate-mimicking compounds with a pyridine ring appended to the C12 site of metabolism were designed as inhibitors, synthesized, and evaluated in terms of their functional and structural interactions with CYP8B1. While the pyridine nitrogen was intended to coordinate the CYP8B1 active site heme iron, none of these compounds elicited shifts in the CYP8B1 Soret absorbance consistent with this type of interaction. However, when CYP8B1 was cocrystallized with the pyridine-containing compound with the 3-keto-Δ4 steroid backbone most similar to the endogenous substrate, it was apparent that this ligand was bound in a channel leading to the active site, instead of near the heme iron. Inspection of this structure suggested that tryptophan 281 directly above the heme might restrict active site binding of potential inhibitors with this design. This hypothesis was supported when a CYP8B1 W281F mutation did allow all three compounds to coordinate the heme iron as designed. These results indicated that the design of next-generation CYP8B1 inhibitors should be compatible with the low-ceiling tryptophan immediately above the heme iron.

59 BASIC BIOLOGICAL SCIENCES↗

Spontaneous Inward Opening of the Dopamine Transporter Is Triggered by PIP 2 -Regulated Dynamics of the N-Terminus

We present the dynamic mechanism of concerted motions in a full-length molecular model of the human dopamine transporter (hDAT), a member of the neurotransmitter/sodium symporter (NSS) family, involved in state-to-state transitions underlying function. The findings result from an analysis of unbiased atomistic molecular dynamics simulation trajectories (totaling >14 μs) of the hDAT molecule immersed in lipid membrane environments with or without phosphatidylinositol 4,5-biphosphate (PIP2) lipids. The N-terminal region of hDAT (N-term) is shown to have an essential mechanistic role in correlated rearrangements of specific structural motifs relevant to state-to-state transitions in the hDAT. The mechanism involves PIP2-mediated electrostatic interactions between the N-term and the intracellular loops of the transporter molecule. Quantitative analyses of collective motions in the trajectories reveal that these interactions correlate with the inward-opening dynamics of hDAT and are allosterically coupled to the known functional sites of the transporter. The observed large-scale motions are enabled by specific reconfiguration of the network of ionic interactions at the intracellular end of the protein. The isomerization to the inward-facing state in hDAT is accompanied by concomitant movements in the extracellular vestibule and results in the release of an Na+ ion from the Na2 site and destabilization of the substrate dopamine in the primary substrate binding S1 site. The dynamic mechanism emerging from the findings highlights the involvement of the PIP2-regulated interactions between the N-term and the intracellular loop 4 in the functionally relevant conformational transitions that are also similar to those found to underlie state-to-state transitions in the leucine transporter (LeuT), a prototypical bacterial homologue of the NSS.

Biochemistry & Molecular Biology↗

The KYxxL motif in Rad17 protein is essential for the interaction with the 9–1–1 complex

ATR-dependent DNA damage checkpoint is the major DNA damage checkpoint against UV irradiation and DNA replication stress. The Rad17–RFC and Rad9–Rad1–Hus1 (9–1–1) complexes interact with each other to contribute to ATR signaling, however, the precise regulatory mechanism of the interaction has not been established. Here, we identified a conserved sequence motif, KYxxL, in the AAA+ domain of Rad17 protein, and demonstrated that this motif is essential for the interaction with the 9–1–1 complex. We also show that UV-induced Rad17 phosphorylation is increased in the Rad17 KYxxL mutants. These data indicate that the interaction with the 9–1–1 complex is not required for Rad17 protein to be an efficient substrate for the UV-induced phosphorylation. Our data also raise the possibility that the 9–1–1 complex plays a negative regulatory role in the Rad17 phosphorylation. We also show that the nucleotide-binding activity of Rad17 is required for its nuclear localization. - Highlights: • We have identified a conserved KYxxL motif in Rad17 protein. • The KYxxL motif is crucial for the interaction with the 9–1–1 complex. • The KYxxL motif is dispensable or inhibitory for UV-induced Rad17 phosphorylation. • Nucleotide binding of Rad17 is required for its nuclear localization.

60 APPLIED LIFE SCIENCES↗

Thermo-hydrologic processes in maar eruptions: The role of vapor transport and condensation

Phreatomagmatic eruptions occur when magma interacts directly with water or slurries, commonly from groundwater in the shallow crust, resulting in rapid conversion of thermal energy to mechanical energy in a set of processes known as molten fuel-coolant interaction (MFCI). The efficiency of MFCI is controlled by properties of the magma and coolant, contact surface geometry, and system conditions, such as pressure and temperature; phreatomagmatic behavior can range from passive thermal granulation to violent thermohydraulic explosions (Zimanowski et al., 2015). Maar-diatreme eruptions, characterized by repetitive phreatomagmatic explosions, can form in a wide range of near-surface environments, from soft sediment substrate (e.g., Tecuitlapa, Mexico, Ort and Carrasco-Núñez, 2009; Hopi Buttes, AZ, Lefebvre et al., 2013) to hard, fractured country rock (e.g., West Eifel volcanic field, Germany and Massif Central, France, Lorenz, 2003). Country-rock structure, including faults and joints, rock type, and shallow crustal hydrologic properties, can influence an eruption’s behavior by controlling how much and at what rate water can be supplied to the magma (hydraulic flow rate), and determining the sediment: water ratio in the case of soft-sediment substrate eruptions. In a “soft” substrate environment, volcanic tremor can lead to liquefaction of saturated sediment, producing a slurry that may then interact with magma in unique ways (White, 1996; Auer, et al., 2006).

58 GEOSCIENCES↗

Investigating the human Calcineurin Interaction Network using the π$\phi$LxVP SLiM

Ser/thr phosphorylation is the primary reversible covalent modification of proteins in eukaryotes. As a consequence, it is the reciprocal actions of kinases and phosphatases that act as key molecular switches to fine tune cellular events. It has been well documented that ~400 human ser/thr kinases engage substrates via consensus phosphosite sequences. Strikingly, we know comparatively little about the mechanism by which ~40 human protein ser/thr phosphatases (PSPs) dephosphorylate ~15000 different substrates with high specificity. The identification of substrates of the essential PSP calcineurin (CN) has been exceptionally challenging and only a small fraction has been biochemically confirmed. It is now emerging that CN binds regulators and substrates via two short linear motifs (SLiMs), the well-studied PxIxIT SLiM and the LxVP SLiM, which remains controversial at the molecular level. Here we describe the crystal structure of CN in complex with its substrate NFATc1 and show that the LxVP SLiM is correctly defined as π$\phi$LxVP. Bioinformatics studies using the π$\phi$LxVP SLiM resulted in the identification of 567 potential CN substrates; a small subset was experimentally confirmed. This combined structural-bioinformatics approach provides a powerful method for dissecting the CN interaction network and for elucidating the role of CN in human health and disease.

Science & Technology - Other Topics↗