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Moisture modulates soil reservoirs of active DNA and RNA viruses
Abstract Soil is known to harbor viruses, but the majority are uncharacterized and their responses to environmental changes are unknown. Here, we used a multi-omics approach (metagenomics, metatranscriptomics and metaproteomics) to detect active DNA viruses and RNA viruses in a native prairie soil and to determine their responses to extremes in soil moisture. The majority of transcribed DNA viruses were bacteriophage, but some were assigned to eukaryotic hosts, mainly insects. We also demonstrated that higher soil moisture increased transcription of a subset of DNA viruses. Metaproteome data validated that the specific viral transcripts were translated into proteins, including chaperonins known to be essential for virion replication and assembly. The soil viral chaperonins were phylogenetically distinct from previously described marine viral chaperonins. The soil also had a high abundance of RNA viruses, with highest representation of Reoviridae . Leviviridae were the most diverse RNA viruses in the samples, with higher amounts in wet soil. This study demonstrates that extreme shifts in soil moisture have dramatic impacts on the composition, activity and potential functions of both DNA and RNA soil viruses.
Nucleoporin downregulation modulates progenitor differentiation independent of nuclear pore numbers
Nucleoporins (NUPs) comprise nuclear pore complexes, gateways for nucleocytoplasmic transport. As primary human keratinocytes switch from the progenitor state towards differentiation, most NUPs are strongly downregulated, with NUP93 being the most downregulated NUP in this process. To determine if this NUP downregulation is accompanied by a reduction in nuclear pore numbers, we leveraged Stochastic Optical Reconstruction Microscopy. No significant changes in nuclear pore numbers were detected using three independent NUP antibodies; however, NUP reduction in other subcellular compartments such as the cytoplasm was identified. To investigate how NUP reduction influences keratinocyte differentiation, we knocked down NUP93 in keratinocytes in the progenitor-state culture condition. NUP93 knockdown diminished keratinocytes’ clonogenicity and epidermal regenerative capacity, without drastically affecting nuclear pore numbers or permeability. Using transcriptome profiling, we identified that NUP93 knockdown induces differentiation genes related to both mechanical and immune barrier functions, including the activation of known NF-κB target genes. Consistently, keratinocytes with NUP93 knockdown exhibited increased nuclear localization of the NF-κB p65/p50 transcription factors, and increased NF-κB reporter activity. Taken together, these findings highlight the gene regulatory roles contributed by differential NUP expression levels in keratinocyte differentiation, independent of nuclear pore numbers.
Geologic stress modulates fluid mixing at fracture intersections
Fracture intersections are critical links that enable flow and transport in subsurface fracture networks, and their behavior strongly influences fluid mixing in a network. Although all subsurface fractures are subjected to geological stress, we lack a fundamental understanding of how fracture intersection geometry evolves under stress and how these changes influence fluid mixing. Here, we combine 3D printing, 3D X-ray tomographic imaging, and 3D pore-scale numerical simulations to reveal stress-induced changes in intersection geometry and their impact on mixing. Mixing is found to be strongly affected by partial closure of an intersection under stress. As an intersection closes, the void area for fluid flow and diffusion decreases leading to substantial deviations between conventional mixing models and full pore-scale modeling. To address this, we propose a modified mixing model that accounts for intersection deformation, which is essential for accurate modeling of solute transport and mixing through fracture networks.
Modulating multi-hole reaction pathways for photoelectrochemical water oxidation on gold nanocatalysts
Catechol stabilizes photo-generated holes on metal nanoparticles to create a new multi-hole reaction pathway for oxidizing water under visible light.
Fragmentation of polymer nanocomposites: modulation by dry and wet weathering, fractionation, and nanomaterial filler
Weathering and fragmentation of polymer nanocomposites.
Modulation of CO 2 adsorption in novel pillar-layered MOFs based on carboxylate–pyrazole flexible linker
Metal–organic frameworks (MOFs) have attracted significant attention as sorbents due to their high surface area, tunable pore volume and pore size, coordinatively unsaturated metal sites, and ability to install desired functional groups by post-synthetic modification. Herein, we report three new MOFs with pillar–paddlewheel structures that have been synthesized solvothermally from the mixture of the carboxylate–pyrazole flexible linker (H 2 L), 4,4-bipyridine (BPY)/triethylenediamine (DABCO), and Zn(II)/Cu(II) ions. The MOFs obtained, namely [Zn II (L)BPY], [Cu II (L)BPY], and [Cu II (L)DABCO], exhibit two-fold interpenetration and dinuclear paddle–wheel nodes. The Zn(II)/Cu(II) cations are coordinated by two equatorial L linkers that result in two-dimensional sheets which in turn are pillared by BPY or DABCO in the perpendicular direction to obtain a neutral three-dimensional framework that shows one-dimensional square channels. The three pillar-layered MOFs were characterized as microporous materials showing high crystalline stability after activation at 120 °C and CO 2 adsorption. All MOFs contain uncoordinated Lewis basic pyrazole nitrogen atoms in the framework which have an affinity toward CO 2 and hence could potentially serve as CO 2 adsorption material. The CO 2 uptake capacity was initially enhanced by replacing Zn with Cu and then replacing the pillar, going from BPY to DABCO. Overall, all the MOFs exhibit low isosteric heat (Q st ) of adsorption which signifies an advantage due to the energy required for the adsorption and regeneration processes.
Carbohydrate-binding module O -mannosylation alters binding selectivity to cellulose and lignin
Improved understanding of the effect of protein glycosylation is expected to provide the foundation for the design of protein glycoengineering strategies.
Modulation of H + /H - exchange in iridium-hydride 2-hydroxypyridine complexes by remote Lewis acids
In this study, a series of iridium hydride complexes featuring dihydrogen bonding are presented and shown to undergo rapid H + /H - exchange (1240 s -1 at 25 °C). We demonstrate that the H + /H - exchange rate can be modified by post-synthetic modification at a remote site using BH 3 , Zn(C 6 F 5 ) 2 , and [Me 3 O][BF 4 ]. This route provides a complementary strategy to traditional methods that rely on pre-metalation modifications to a metal's primary sphere.
Backbone-driven host–dopant miscibility modulates molecular doping in NDI conjugated polymers
Molecular doping is the key to enabling organic electronic devices, however, the design strategies to maximize doping efficiency demands further clarity and comprehension.
Force-modulated reductive elimination from platinum( ii ) diaryl complexes
The influence of mechanical force on the rates of model reductive elimination reactions depends on the structure of the force-transducing ligand and provides a measure of geometry changes upon reaching the transition state.
Sodium dodecyl sulfate modulates the structure and rheological properties of Pluronic F108–poly(acrylic acid) coacervates)
Micelles formed within coacervate phases can impart functional properties, but it is unclear if this micellization provides mechanical reinforcement of the coacervate whereby the micelles act as high functionality crosslinkers. Here, we examine how sodium dodecyl sulfate (SDS) influences the structure and properties of Pluronic F108–polyacrylic acid (PAA) coacervates as SDS is known to decrease the aggregation number of Pluronic micelles. Increasing the SDS concentration leads to larger water content in the coacervate and an increase in the relative concentration of PAA to the other solids. Rheological characterization with small angle oscillatory shear (SAOS) demonstrates that these coacervates are viscoelastic liquids with the moduli decreasing with the addition of the SDS. The loss factor (tan δ) initially increases linearly with the addition of SDS, but a step function increase in the loss factor occurs near the reported CMC of SDS. However, this change in rheological properties does not appear to be correlated with any large scale structural differences in the coacervate as determined by small angle X-ray scattering (SAXS) with no signature of Pluronic micelles in the coacervate when SDS concentration is >4 mM during formation of the coacervate, which is less than that observed (6 mM SDS) in initial Pluronic F108 solution despite the higher polymer concentration in the coacervate. Finally, these results suggest that the mechanical properties of polyelectrolyte-non-ionic surfactant coacervates are driven by the efficicacy of binding between the complexing species driving the coacervate, which can be disrupted by competitive binding of the SDS to the Pluronic.
Finely modulated asymmetric nonfullerene acceptors enabling simultaneously improved voltage and current for efficient organic solar cells
An asymmetric acceptor 5T-2C8-2Cl has been designed and an efficiency of 13.02% with simultaneously improved J sc and V oc has been achieved.
Thermal modulation of reaction equilibria controls mass transfer in CO 2 -binding organic liquids
CO 2 BOLs are promising CCS solvents, whose mass transfer rates improve upon cooling. We show this unintuitive behavior is due to slow transport of reaction products from the gas–liquid interface, caused by shifts in reaction equilibria.
A framework for comparing the energy production of photovoltaic modules using 2-, 3-, and 4-terminal tandem cells
Energy production, rather than efficiency, is the most important metric for comparing different configurations of tandem solar cells (2T, 3T, 4T), as each interconnection technique has its own advantages and disadvantages.
Modulation of the coordination environment enhances the electrocatalytic efficiency of Mo single atoms toward water splitting
Here, enhancing the catalytic efficiency through engineering active site environments is expected to work pronouncedly for single atom catalysts (SACs) because of intense atomic scale interactions involved between SAs and their coordination environments. Taking Mo SACs for catalyzation of the hydrogen evolution reaction (HER) as an example, three SACs of different coordination environments, namely Mo-O 2 N 2 , Mo-O 2 N 1 C 1 , and Mo-O 2 C 2 , were successfully created for demonstration. The HER performances are in an increasing order of Mo-O 2 N 2 , Mo-O 2 N 1 C 1 , and Mo-O 2 C 2 , exhibiting η 10 of 98, 71, and 61 mV, η 500 of 340, 248, and 200 mV, Tafel slopes of 95.8, 39.6, and 33.8 mV dec -1 , and current density decays of 9, 6, and 6% after a 50 hour operation at an initial current density of 100 mA cm -2 , respectively. Substituting C with N in the coordination environment results in inferior HER catalytic efficiency and stability. Density functional theory calculations reveal that replacing carbon with nitrogen for coordination with the Mo SA on a carbon substrate of a higher N-doping level shifts the d-band center of Mo more negatively from the Fermi level, thereby increasing the hydrogen adsorption energy and thus decelerating the hydrogen desorption kinetics, giving consequent inferior HER activities.
Mycobacterium tuberculosis CitA activity is modulated by cysteine oxidation and pyruvate binding
As an adaptation for survival during infection, Mycobacterium tuberculosis becomes dormant, reducing its metabolism and growth. Two types of citrate synthases have been identified in Mycobacterium tuberculosis, GltA2 and CitA. Previous work shows that overexpression of CitA, the secondary citrate synthase, stimulates the growth of Mycobacterium tuberculosis under hypoxic conditions without showing accumulation of triacylglycerols and makes mycobacteria more sensitive to antibiotics, suggesting that CitA may play a role as a metabolic switch during infection and may be an interesting TB drug target. To assess the druggability and possible mechanisms of targeting CitA with small-molecule compounds, the CitA crystal structure was solved to 2.1 Å by X-ray crystallography. The solved structure shows that CitA lacks an NADH binding site that would afford allosteric regulation, which is atypical of most citrate synthases. However, a pyruvate molecule is observed within the analogous domain, suggesting pyruvate may instead be the allosteric regulator for CitA. Further, the R149 and R153 residues forming the charged portion of the pyruvate binding pocket were mutated to glutamate and methionine, respectively, to assess the effect of mutations on activity. Protein thermal shift assay shows thermal stabilization of CitA in the presence of pyruvate compared to the two CitA variants designed to decrease pyruvate affinity. Solved crystal structures of both variants show no significant structural changes. However, the catalytic efficiency of the R153M variant increases by 2.6-fold. Additionally, we show that covalent modification of C143 of CitA by Ebselen completely arrests enzyme activity. Similar inhibition is observed using two spirocyclic Michael acceptor containing compounds, which inhibit CitA with IC app 50 values of 6.6 and 10.9 μM. A crystal structure of CitA modified by Ebselen was solved, but significant structural changes were lacking. Considering that covalent modification of C143 inactivates CitA and the proximity of C143 to the pyruvate binding site, this suggests that structural and/or chemical changes in this sub-domain are responsible for regulating CitA enzymatic activity.