Host specificity of plant-associated bacteria is negatively associated with genome size and host abundance along a latitudinal gradient.

Host specialization plays a critical role in the ecology and evolution of plant-microbe symbiosis. Theory predicts that host specialization is associated with microbial genome streamlining and is influenced by the abundance of host species, both of which can vary across latitudes, leading to a latitudinal gradient in host specificity. Here, we quantified the host specificity and composition of plant-bacteria symbioses on leaves across 329 tree species spanning a latitudinal gradient. Our analysis revealed a predominance of host-specialized leaf bacteria. The degree of host specificity was negatively correlated with bacterial genome size and the local abundance of host plants. Additionally, we found an increased host specificity at lower latitudes, aligning with the high prevalence of small bacterial genomes and rare host species in the tropics. These findings underscore the importance of genome streamlining and host abundance in the evolution of host specificity in plant-associated bacteria along the latitudinal gradient.

Impact of mandatory indications for outpatient antibiotic orders on accurate tracking of antibiotic indications.

OBJECTIVE: We sought to evaluate whether implementing mandatory indications for outpatient electronic antibiotic orders or using encounter International Classification of Diseases, Tenth Revision (ICD10) codes more accurately reflected clinicians' charted diagnosis in encounter notes. Secondarily, we examined the appropriateness of antibiotic prescriptions. DESIGN: Cross-sectional study. METHODS: Mandatory indications were added to all outpatient electronic antibiotic orders on May 18, 2022. A randomly selected convenience sample of 1300 outpatient encounters with antibiotics from walk-in clinics was reviewed. Adjusted logistic regression was used to compare the congruence between encounter ICD10 code and charted diagnosis for encounters from July 15 to September 15, 2021 (pre-implementation period) to the congruence between encounter ICD10 code, charted diagnosis, and mandatory indication for encounters from July 15 to September 15, 2022 (post-implementation period). Antibiotic appropriateness based on charted diagnosis was also evaluated. RESULTS: Among 1300 outpatient encounters, congruence between charted diagnosis and ICD10 code significantly increased in the post-implementation period (87.7% (565/644)) versus pre-implementation (83.3% (540/648), adjusted odds ratio (aOR) 1.52; 95% CI 1.03-2.25). Congruence between charted diagnosis and mandatory indication during post-implementation was 95.2% (613/644) and >5 times more likely to be congruent than charted diagnosis and ICD10 code during pre-implementation (aOR 5.45; 95% CI 3.26-9.11). Antibiotic prescribing based on charted diagnosis was twice as likely to be appropriate in the post-implementation period (aOR1.99; 95% CI 1.32-2.98). CONCLUSIONS: Mandatory indications within antibiotic orders show better congruence with charted diagnosis than ICD10 codes and may increase antibiotic appropriateness and congruence between ICD10 code and charted diagnosis.

Reaction mechanism of the ethynylation of formaldehyde on copper terminated Cu2O(100) surfaces: a DFT study.

1,4-Butanediol (BDO) is an important chemical raw material for a series of high-value-added products. And the ethynylation of formaldehyde is the key step for the production of BDO by the Reppe process. However, little work has been done to reveal the reaction mechanism. In this work, the reaction mechanism for the ethynylation of formaldehyde process on copper-terminated Cu2O(100) surfaces was investigated with density functional theory (DFT). The reaction network of the ethynylation of formaldehyde was constructed first and the adsorption properties of the related species were calculated. Then the energy barrier and reaction energy of the related reactions and the geometric configuration were calculated. It is a consecutive reaction including two processes. For the propargyl alcohol (PA) formation process, the most favorable pathway is the direct addition of acetylene to formaldehyde followed by a hydrogen transfer reaction. And the rate control step is the hydrogen transfer reaction with an energy barrier of 1.43 eV. For the 1,4-butynediol (BYD) formation process, the most competitive pathway is the addition of PA to CH2OH, including formaldehyde hydrogenation to form CH2OH, coupling addition, and dehydrogenation reaction. The rate control step of this pathway is the dehydrogenation reaction with an energy barrier of 1.51 eV.

Cryo-EM structure and molecular mechanism of abscisic acid transporter ABCG25.

Abscisic acid (ABA) is one of the plant hormones that regulate various physiological processes, including stomatal closure, seed germination and development. ABA is synthesized mainly in vascular tissues and transported to distal sites to exert its physiological functions. Many ABA transporters have been identified, however, the molecular mechanism of ABA transport remains elusive. Here we report the cryogenic electron microscopy structure of the Arabidopsis thaliana adenosine triphosphate-binding cassette G subfamily ABA exporter ABCG25 (AtABCG25) in inward-facing apo conformation, ABA-bound pre-translocation conformation and outward-facing occluded conformation. Structural and biochemical analyses reveal that the ABA bound with ABCG25 adopts a similar configuration as that in ABA receptors and that the ABA-specific binding is dictated by residues from transmembrane helices TM1, TM2 and TM5a of each protomer at the transmembrane domain interface. Comparison of different conformational structures reveals conformational changes, especially those of transmembrane helices and residues constituting the substrate translocation pathway during the cross-membrane transport process. Based on the structural data, a 'gate-flipper' translocation model of ABCG25-mediated ABA cross-membrane transport is proposed. Our structural data on AtABCG25 provide new clues to the physiological study of ABA and shed light on its potential applications in plants and agriculture.

Theoretical Insights into Midchain Radicals and Branching Characteristics in Solution Copolymerization of Ethylene and Vinyl Acetate.

The kinetics of intermolecular chain transfer to polymer (CTP) and chain transfer to monomer (CTM), as well as backbiting in solution copolymerization of ethylene and vinyl acetate (VAc), are calculated by density functional theory. An intrinsic rate coefficient for each reaction type, whose Arrhenius parameters are expressed as functions of unreacted monomer composition, is extracted from calculated elementary reactions, and hence it applies to a wide range of fragment compositions of EVA. Backbiting controls the generation of midchain radicals (MCRs) on the backbone, and its rate maximizes at a medium fraction of VAc in the unreacted monomers. CTP plays an insignificant role in MCR generation even at high conversion rates due to its low pre-exponential factor. The concentration of MCRs is quantified and is close to that of ECRs at high conversions and high fractions of VAc in monomers. Additionally, branching characteristics are explored; concentrations of short-chain branching (SCB) and long-chain branching (LCB) are about 0.7-2.5 and 0.1-0.4%, respectively, and drop with VAc fraction rapidly. The role of the migration of MCRs is highlighted, which transforms about 10% of SCB points into LCB points. Disagreeing with insights from laboratory experiments, it is the migration, rather than CTP, which increases the LCB concentration at high conversions.

Diversity and biogeography of plant phyllosphere bacteria are governed by latitude-dependent mechanisms.

Predicting and managing the structure and function of plant microbiomes requires quantitative understanding of community assembly and predictive models of spatial distributions at broad geographic scales. Here, we quantified the relative contribution of abiotic and biotic factors to the assembly of phyllosphere bacterial communities, and developed spatial distribution models for keystone bacterial taxa along a latitudinal gradient, by analyzing 16S rRNA gene sequences from 1453 leaf samples taken from 329 plant species in China. We demonstrated a latitudinal gradient in phyllosphere bacterial diversity and community composition, which was mostly explained by climate and host plant factors. We found that host-related factors were increasingly important in explaining bacterial assembly at higher latitudes while nonhost factors including abiotic environments, spatial proximity and plant neighbors were more important at lower latitudes. We further showed that local plant-bacteria associations were interconnected by hub bacteria taxa to form metacommunity-level networks, and the spatial distribution of these hub taxa was controlled by hosts and spatial factors with varying importance across latitudes. For the first time, we documented a latitude-dependent importance in the driving factors of phyllosphere bacteria assembly and distribution, serving as a baseline for predicting future changes in plant phyllosphere microbiomes under global change and human activities.

Adding Konjac Glucomannan for Enhancing the Whole Spraying Performance on Superhydrophobic and Hydrophilic Surfaces.

Spraying is a common way to coat solutions onto surfaces evenly. Improving spraying effectiveness can avoid wasting solutions and reduce pollution. In this study, a trace amount of natural polysaccharide, konjac glucomannan (KGM), was added into solutions to regulate the spraying performances including the breakup of liquid jets, size of produced droplets, and collision and spreading of droplets on both superhydrophobic and hydrophilic surfaces. The shear viscosity, extensive viscosity, and surface tension of the KGM solutions were tested. The results of spraying experiments showed that adding KGM inhibited the liquid jet from breaking into small droplets, avoided the breakage of droplets on superhydrophobic surfaces, and promoted the spreading of liquid films on hydrophilic surfaces. The numerical simulation showed the stretching of single macromolecules and quantified the energy stored in molecular chains in a shear-dominated flow field during the spreading of droplets on surfaces and an elongational-dominated flow field during the breakage of a liquid bridge. The storage and dissipation of energy during the stretching and relaxing of KMG macromolecules were important origins of the increase in the colloid viscosity and molecular mechanisms of the effect of the KGM additive on spraying performances. This study provided an understanding and a strategy for optimization and application of spraying additives.

Structural basis of the substrate recognition and inhibition mechanism of Plasmodium falciparum nucleoside transporter PfENT1.

By lacking de novo purine biosynthesis enzymes, Plasmodium falciparum requires purine nucleoside uptake from host cells. The indispensable nucleoside transporter ENT1 of P. falciparum facilitates nucleoside uptake in the asexual blood stage. Specific inhibitors of PfENT1 prevent the proliferation of P. falciparum at submicromolar concentrations. However, the substrate recognition and inhibitory mechanism of PfENT1 are still elusive. Here, we report cryo-EM structures of PfENT1 in apo, inosine-bound, and inhibitor-bound states. Together with in vitro binding and uptake assays, we identify that inosine is the primary substrate of PfENT1 and that the inosine-binding site is located in the central cavity of PfENT1. The endofacial inhibitor GSK4 occupies the orthosteric site of PfENT1 and explores the allosteric site to block the conformational change of PfENT1. Furthermore, we propose a general "rocker switch" alternating access cycle for ENT transporters. Understanding the substrate recognition and inhibitory mechanisms of PfENT1 will greatly facilitate future efforts in the rational design of antimalarial drugs.

The Effects of Species Abundance, Spatial Distribution, and Phylogeny on a Plant-Ectomycorrhizal Fungal Network.

Plant and root fungal interactions are among the most important belowground ecological interactions, however, the mechanisms underlying pairwise interactions and network patterns of rhizosphere fungi and host plants remain unknown. We tested whether neutral process or spatial constraints individually or jointly best explained quantitative plant-ectomycorrhizal fungal network assembly in a subtropical forest in southern China. Results showed that the observed plant-ectomycorrhizal fungal network had low connectivity, high interaction evenness, and an intermediate level of specialization, with nestedness and modularity both greater than random expectation. Incorporating information on the relative abundance and spatial overlap of plants and fungi well predicted network nestedness and connectance, but not necessarily explained other network metrics such as specificity. Spatial overlap better predicted pairwise species interactions of plants and ectomycorrhizal fungi than species abundance or a combination of species abundance and spatial overlap. There was a significant phylogenetic signal on species degree and interaction strength for ectomycorrhizal fungal but not for plant species. Our study suggests that neutral processes (species abundance matching) and niche/dispersal-related processes (implied by spatial overlap and phylogeny) jointly drive the shaping of a plant-ectomycorrhizal fungal network.

Comparison of the Unfolded Protein Response in Cellobiose Utilization of Recombinant Angel- and W303-1A-Derived Yeast Expressing ß-Glucosidase.

The unfolded protein response (UPR) is one of the most important protein quality control mechanisms in cells. At least, three factors are predicted to activate the UPR in yeast cells during fermentation. Using UPRE-lacZ as a reporter, we constructed two indicator strains, KZ and WZ, based on Angel-derived K-a and W303-1A strains, respectively, and investigated their UPR response to tunicamycin, ethanol, and acetic acid. Then, four strains carrying plasmids BG-cwp2 and BG were obtained to realize the displaying and secretion of ß-glucosidase, respectively. The results of cellobiose utilization assays indicated interactions between the UPR and the metabolic burden between the strain source, anchoring moiety, oxygen supply, and cellobiose concentration. Meanwhile, as expected, growth (OD600), ß-glucosidase, and ß-galactosidase activities were shown to have a positive inter-relationship, in which the values of the KZ-derived strains were far lower than those of the WZ-derived strains. Additionally, extra metabolic burden by displaying over secreting was also much more serious in strain KZ than in strain WZ. The maximum ethanol titer of the four strains (KZ (BG-cwp2), KZ (BG), WZ (BG-cwp2), and WZ (BG)) in oxygen-limited 10% cellobiose fermentation was 3.173, 5.307, 5.495, and 5.486% (v/v), respectively, and the acetic acid titer ranged from 0.038 to 0.060% (v/v). The corresponding maximum values of the ratio of ß-galactosidase activity to that of the control were 3.30, 5.29, 6.45, and 8.72, respectively. Under aerobic conditions with 2% cellobiose, those values were 3.79, 4.97, 6.99, and 7.67, respectively. A comparison of the results implied that ß-glucosidase expression durably induced the UPR, and the effect of ethanol and acetic acid depended on the titer produced. Further study is necessary to identify ethanol- or acid-specific target gene expression. Taken together, our results indicated that the host strain W303-1A is a better secretory protein producer, and the first step to modify strain K-a for cellulosic ethanol fermentation would be to relieve the bottleneck of UPR capacity. The results of the present study will help to identify candidate host strains and optimize expression and fermentation by quantifying UPR induction.

An effective AKT inhibitor-PARP inhibitor combination therapy for recurrent ovarian cancer.

BACKGROUND: Although the use of PARP inhibitor has received considerable amount of attention in ovarian cancer, PARP inhibitor resistance still emerges with disease progression. PI3K/AKT pathway inhibitors have been proposed to synergize with PARP inhibition to slow tumor growth, but the exact molecular mechanisms are still elusive. METHODS: Utilizing tumor samples from recurrent EOC patients with platinum resistance and prior PARP inhibitor use, Mini PDX and PDX models were established to study the anti-tumor effect of AKT inhibitor (LAE003) and LAE003/PARP inhibitor (Olaparib) in combination. Five ovarian cancer cell lines were treated with Olaparib or LAE003 or in combination in vitro. Cell viability and apoptosis rate were measured after the treatments. Combination index by the Chou-Talalay was used to evaluate in vitro combination effect of Olaparib and LAE003. The protein expression level of PARP1 and PAR was measured by Western blot in cell lines and by immunohistochemistry in PDX tumor tissues. RESULTS: Tumor cells from two out of five platinum-resistant ovarian cancer patients previously treated with PARP inhibitor were sensitive to AKT inhibition in Mini-PDX study. Inhibition of AKT further increased the response of tumor cells to Olaparib in a PDX model derived from a recurrent platinum-resistant ovarian cancer patient. Additive anti-proliferation effect of LAE003 and Olaparib was also observed in three ovarian cancer cell lines with high PARP1 protein level. Interestingly, mechanism study revealed that AKT inhibition decreased PARP enzyme activity as measured by PAR level and/or reduced PARP1 protein level in the tumor cell lines and PDX tumor tissues, which may explain the observed combined anti-tumor effect of LAE003 and Olaparib. CONCLUSION: Collectively, our results suggest that the combination of AKT inhibitor and PARP inhibitor could be a viable approach for clinical testing in recurrent ovarian cancer patients.

Circulating Cell-Free DNA-Based Detection of Tumor Suppressor Gene Copy Number Loss and Its Clinical Implication in Metastatic Prostate Cancer.

Current liquid biopsy assays lack sufficient sensitivity to detect copy number loss, which limits the interrogation of critical tumor suppressor gene deletions during cancer progression and treatment. Here we describe a liquid biopsy assay with improved sensitivity for detection of copy number loss in blood samples with low levels of circulating tumor DNA, and demonstrate its utility by profiling PTEN, RB1, and TP53 genetic loss in metastatic prostate cancer patients.

Dual-cation-doped MoS2nanosheets accelerating tandem alkaline hydrogen evolution reaction.

Molybdenum disulfide (MoS2) nanosheets are promising candidates as earth-abundant and low-cost catalyst for hydrogen evolution reaction (HER). Nevertheless, compared with the benchmark Pt/C catalyst, the application of MoS2nanosheets is limited to its relatively low catalytic activity, especially in alkaline environments. Here, we developed a dual-cation doping strategy to improve the alkaline HER performance of MoS2nanosheets. The designed Ni, Co co-doped MoS2nanosheets can promote the tandem HER steps simultaneously, thus leading to a much enhanced catalytic activity in alkaline solution. Density functional theory calculations revealed the individual roles of Ni and Co dopants in the catalytic process. The doped Ni is uncovered to be the active site for the initial water-cleaving step, while the Co dopant is conducive to the H desorbing by regulating the electronic structure of neighboring edge-S in MoS2. The synergistic effect resulted by the dual-cation doping thus facilitates the tandem HER steps, providing an effective route to raise the catalytic performance of MoS2materials in alkaline solution.

Molecular mechanism underlying transport and allosteric inhibition of bicarbonate transporter SbtA.

SbtA is a high-affinity, sodium-dependent bicarbonate transporter found in the cyanobacterial CO2-concentrating mechanism (CCM). SbtA forms a complex with SbtB, while SbtB allosterically regulates the transport activity of SbtA by binding with adenyl nucleotides. The underlying mechanism of transport and regulation of SbtA is largely unknown. In this study, we report the three-dimensional structures of the cyanobacterial Synechocystis sp. PCC 6803 SbtA-SbtB complex in both the presence and absence of HCO3- and/or AMP at 2.7 Å and 3.2 Å resolution. An analysis of the inward-facing state of the SbtA structure reveals the HCO3-/Na+ binding site, providing evidence for the functional unit as a trimer. A structural comparison found that SbtA adopts an elevator mechanism for bicarbonate transport. A structure-based analysis revealed that the allosteric inhibition of SbtA by SbtB occurs mainly through the T-loop of SbtB, which binds to both the core domain and the scaffold domain of SbtA and locks it in an inward-facing state. T-loop conformation is stabilized by the AMP molecules binding at the SbtB trimer interfaces and may be adjusted by other adenyl nucleotides. The unique regulatory mechanism of SbtA by SbtB makes it important to study inorganic carbon uptake systems in CCM, which can be used to modify photosynthesis in crops.

The application of the Chinese version of the Body Image Disturbance Questionnaire in patients with systemic lupus erythematosus.

ABSTRACT: This study aimed to translate the Body Image Disturbance Questionnaire (BIDQ) into Chinese and evaluate its reliability and validity in a sample of patients with systemic lupus erythematosus (SLE).Following the translation and revision of the Chinese version of the BIDQ, 169 patients with SLE were chosen as respondents to test the questionnaire's reliability and validity. We tested the content's validity through expert group evaluation. It is structural validity was examined through exploratory factor analysis and confirmatory factor analysis, and reliability was evaluated using Cronbach's α and test-retest reliability.The Chinese version of the BIDQ showed a content validity of .92. A two-factor structure was revealed by exploratory factor analysis, which explained 67.83% of the variance and proved by confirmatory factor analysis. Its overall Cronbach's α was .82 (P  < .001), and the Cronbach's α for each item ranged from .76 to .83. The test-retest reliability was .82, with the Cronbach's α for each item ranging from .76 to .84.Thus, adequate reliability and validity of the Chinese version of the BIDQ were demonstrated for use in patients with SLE.

Plant breeding systems influence the seasonal dynamics of plant-pollinator networks in a subtropical forest.

Temporal dynamics of plant-pollinator interactions inform the mechanisms of community assembly and stability. However, most studies on the dynamics of pollination networks do not consider plant reproductive traits thus offering poor understanding of the mechanism of how networks maintain stable structure under seasonal changes in flower community. We studied seasonal dynamics of pollination networks in a subtropical monsoon forest in China with a clear rainy season (April-September) and dry season (October-March) over 2 consecutive years. We constructed dioecy-ignored networks (combining visitations to dioecious male and female plants by ignoring the difference between dioecious and hermaphroditic plants) and dioecy-considered networks (excluding those visitations that only occurred either on dioecious male or female plants) for eight sampling sessions for each season. Although flower richness and flower abundance were higher in the rainy season than in the dry season, no pronounced seasonal difference was found in network specialization, nestedness and modularity for both networks. There were only significant differences in plant community robustness and pollinator specialization between seasons for dioecy-considered networks but not for dioecy-ignored networks. Furthermore, we found the flower abundance of dioecious and hermaphrodite plants mostly showed trade-off variation between rainy and dry seasons. Our results suggest various plant reproductive traits affect the temporal dynamics of pollination networks, which should be considered for conservation of plant-pollinator interactions in forest communities.

Repetitive δ-integration of a cellulase-encoding gene into the chromosome of an industrial Angel Yeast-derived strain by URA3 recycling.

Genetic modification of industrial yeast strains often faces more difficulties than that of laboratory strains. Thus, new approaches are still required. In this research, the Angel Yeast-derived haploid strain Kα was genetically modified by multiple rounds of δ-integration, which was achieved via URA3 recycling. Three δ-integrative plasmids, pGδRU, pGδRU-BGL, and pGδRU-EG, were first constructed with two 167 bp δ sequences and a repeat-URA3-repeat fragment. Then, the δ-integrative strains containing the bgl1 or egl2 gene were successfully obtained by one-time transformation of the linearized pGδRU-BGL or pGδRU-EG fragment, respectively. Their counterparts in which the URA3 gene was looped out were also easily isolated by selection for growth on 5´-fluoroorotic acid plates, although the ratio of colonies lacking URA3 to the total number of colonies decreased with increasing copy number of the corresponding integrated cellulase-encoding gene. Similar results were observed during the second round of δ-integration, in which the δ-integration strain Kα(δ::bgl1-repeat) obtained from the first round was transformed with a linearized pGδRU-EG fragment. After 10 rounds of cell growth and transfer to fresh medium, the doubling times and enzyme activities of Kα(δ::bgl1-repeat), Kα(δ::egl2-repeat), and Kα(δ::bgl1-repeat)(δ::egl2-repeat) showed no significant change and were stable. Further, their maximum ethanol concentrations during simultaneous saccharification and fermentation of pretreated corncob over a 7-day period were 46.35, 33.13, and 51.77 g/L, respectively, which were all substantially higher than the parent Kα strain. Thus, repetitive δ-integration with URA3 recycling can be a feasible and valuable method for genetic engineering of Angel Yeast. These results also provide clues about some important issues related to δ-integration, such as the structural stability of δ-integrated genes and the effects of individual integration-site locations on gene expression. Further be elucidation of these issues should help to fully realize the potential of δ-integration-based methods in industrial yeast breeding.

Mechanistic insight into methane dry reforming over cobalt: a density functional theory study.

Cobalt-based catalysts are a potential candidate among non-noble metal catalysts in dry reformation of methane (DRM), while the detailed mechanism of the DRM reaction is still largely unknown. In this contribution, the rather complicated reaction network for DRM is explored by density functional theory calculations. The most favorable adsorption structures of all species involved in the DRM reaction over Co(0001) have been identified. For CO2 activation, its direct dissociation to generate CO and O is the dominant reaction pathway. For CH4 direct dissociation, CH dehydrogenation into atomic C and H is the rate-determining step (RDS). It is predicted that the CH is the most abundant species among CHx (x = 0-3) over Co(0001). O acts as an oxidant and reacts with CH to produce CHO, and subsequently, CHO decomposes into CO and H. Atomic C may directly react with O to produce CO, or be oxidized by OH to COH, followed by the COH decomposition to CO and H. Thus, three possible pathways for DRM over the Co(0001) surface are proposed in our study, and the oxidation step is suggested as the RDS. The dominant route is identified as CH4 successive dissociation into CH, and CH oxidizing by O to form CHO, then CHO decomposition to CO and H.

A DFT study for CO2 hydrogenation on W(111) and Ni-doped W(111) surfaces.

The first-step hydrogenation of CO2 to methanol via a HCOO route, COOH route, and RWGS + CO-hydro route on NixW(111) (x = 0, 1, 3) has been studied using density functional theory (DFT) calculations. CO2 and H could be chemically adsorbed on Ni-doped W(111) surfaces with relatively high adsorption energy, due to the synergistic effect of W that helps anchoring CO2 and Ni that facilitates the adsorption of H. The HCOO route is the main path for the first-step hydrogenation of CO2 with lower barriers on all three surfaces. Besides, competition between the HCOO route and RWGS + CO-hydro route could be enhanced with the increase in doped Ni on the W(111) surface. Furthermore, the first-step hydrogenation of CO2 hardly undergoes the COOH pathway because of the higher barriers, although the doping of Ni has slightly reduced the barrier of COOH formation. Our calculated results indicate that the W(111) and Ni-doped W(111) surface are potential candidate surfaces for CO2 hydrogenation to methanol, and Ni doping could influence the selectivity of reduction pathways.