Robust Gaussian Process Regression Method for Efficient Tunneling Pathway Optimization: Application to Surface Processes.

Simulation of surface processes is a key part of computational chemistry that offers atomic-scale insights into mechanisms of heterogeneous catalysis, diffusion dynamics, and quantum tunneling phenomena. The most common theoretical approaches involve optimization of reaction pathways, including semiclassical tunneling pathways (called instantons). The computational effort can be demanding, especially for instanton optimizations with an ab initio electronic structure. Recently, machine learning has been applied to accelerate reaction-pathway optimization, showing great potential for a wide range of applications. However, previous methods still suffer from numerical and efficiency issues and were not designed for condensed-phase reactions. We propose an improved framework based on Gaussian process regression for general transformed coordinates, which has improved efficiency and numerical stability, and we propose a descriptor that combines internal and Cartesian coordinates suitable for modeling surface processes. We demonstrate with 11 instanton optimizations in three representative systems that the improved approach makes ab initio instanton optimization significantly cheaper, such that it becomes not much more expensive than a classical transition-state theory rate calculation.

Unravelling the impacts of soluble Mn(III)-NOM on arsenic immobilization by ferrihydrite or goethite under aquifer conditions.

The environmental fate of arsenic (As) relies substantially on its speciation, which occurs frequently coupled to the redox transformation of manganese. While trivalent manganese (Mn(III)), which is known for its high reactivity, is believed to play a role in As mobilization by iron (oxyhydr)oxides in dynamic aquifers, the exact roles and underlying mechanisms are still poorly understood. Using increasingly complex batch experiments that mimick As-affected aquifer conditions in combination with time-resolved characterization, we demonstrate that Mn(III)-NOM complexes play a crucial role in the manganese-mediated immobilization of As(III) by ferrihydrite and goethite. Under anaerobic condition, Mn(III)-fulvic acid (FA) rapidly oxidized 31.8% of aqueous As(III) and bound both As(III) and As(V). Furthermore, Mn(III)-FA exerted significantly different effects on the adsorption of As by ferrihydrite and goethite. Mn(III)-FA increased the adsorption of As by 6-16% due to the higher affinity of oxidation-produced As(V) for ferrihydrite under circumneutral conditions. In contrast, As adsorption by crystalline goethite was eventually inhibited due to the competitive effect of Mn(III)-FA. To summarize, our results reveal that Mn(III)-NOM complexes play dual roles in As retention by iron oxides, depending on the their crystallization. This highlights the importance of Mn(III) for the fate of As particularly in redox fluctuating groundwater environments.

Determination of concerted or stepwise mechanism of hydrogen tunneling from isotope effects: Departure between experiment and theory.

Isotope substitution is an important experimental technique that offers deep insight into reaction mechanisms, as the measured kinetic isotope effects (KIEs) can be directly compared with theory. For multiple proton transfer processes, there are two types of mechanisms: stepwise transfer and concerted transfer. The Bell-Limbach model provides a simple theory to determine whether the proton transfer mechanism is stepwise or concerted from KIEs. Recent scanning tunneling microscopy (STM) experiments have studied the proton switching process in water tetramers on NaCl(001). Theoretical studies predict that this process occurs via a concerted mechanism; however, the experimental KIEs resemble the Bell-Limbach model for stepwise tunneling, raising questions on the underlying mechanism or the validity of the model. We study this system using ab initio instanton theory, and in addition to thermal rates, we also considered microcanonical rates, as well as tunneling splittings. The instanton theory predicts a concerted mechanism, and the KIEs for tunneling rates (both thermal and microcanonical) upon deuteration are consistent with the Bell-Limbach model for concerted tunneling but could not explain the experiments. For tunneling splittings, partial and full deuteration change the size of it in a similar fashion to how they change the rates. We further examined the Bell-Limbach model in another system, porphycene, which has both stepwise and concerted tunneling pathways. The KIEs predicted by instanton theory are again consistent with the Bell-Limbach model. This study highlights differences between KIEs in stepwise and concerted tunneling and the discrepancy between theory and recent STM experiments. New theory/experiments are desired to settle this problem.

Unraveling the impact of iron oxides-organic matter complexes on iodine mobilization in alluvial-lacustrine aquifers from central Yangtze River Basin.

The biodegradation of organic matter triggers the reductive dissolution of iron oxides with the transformation among iodine species has been mostly accepted as the key iodine mobilization process in groundwater system. However, molecular characteristics of natural organic matter (NOM) and their interaction with iron oxides on geogenic iodine enrichment remain unclear. We used Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to characterize the molecular composition of both dissolved organic matter (DOM) in groundwater and water-soluble organic matter (WSOM) in aquifer sediments being depth-matched with groundwater from monitoring wells in typical iodine-affected aquifers within the central Yangtze River Basin. The results show that WSOM in high-iodine sediments contains more high molecular weight (HMW) organic compounds with higher aromaticity and nominal oxidation state of carbon (NOSC), including polycyclic aromatics, polyphenols and highly unsaturated compounds. These compounds are mostly positively associated with amorphous iron oxides (Feox1) in aquifer sediments. The association between iodine and WSOM is highly consistent with that between amorphous Feox1 and WSOM, but is contrary to that between crystalline iron oxides (Feox2) and WSOM. DOM in groundwater with higher iodine concentration contains more aliphatic compounds and less polyphenols. The complexation of HMW organic compounds of WSOM to iodine-bearing amorphous Feox1 plays an important role in iodine mobilization, which could inhibit the amorphous Feox1 transformation to crystalline Feox2. These observations indicate the biodegradation of HMW organic matter (polycyclic aromatics, polyphenols and highly unsaturated compounds) in WSOM fueling the reductive dissolution of amorphous Feox1 predominantly promotes the release of iodine from aquifer sediments into groundwater. This research provides new insights into the mobilization mechanisms of iodine in alluvial-lacustrine groundwater system controlled by the Fe-OM complexation at the molecular level.

Point mutation of V252 in neomycin C epimerase enlarges substrate-binding pocket and improves neomycin B accumulation in Streptomyces fradiae.

Neomycin, an aminoglycoside antibiotic with broad-spectrum antibacterial resistance, is widely used in pharmaceutical and agricultural fields. However, separation and purification of neomycin B as an active substance from Streptomyces fradiae are complicated. Although NeoN can catalyze conversion of neomycin C to neomycin B, the underlying catalytic mechanism is still unclear. In this study, the genomic information of high-yielding mutant S. fradiae SF-2 was elucidated using whole-genome sequencing. Subsequently, the mechanism of NeoN in catalyzing conversion of neomycin C to neomycin B was resolved based on NeoN-SAM-neomycin C ternary complex. Mutant NeoNV252A showed improved NeoN activity, and the recombinant strain SF-2-NeoNV252A accumulated 16,766.6 U/mL neomycin B, with a decrease in neomycin C ratio from 16.1% to 6.28%, when compared with the parental strain SF-2. In summary, this study analyzed the catalytic mechanism of NeoN, providing significant reference for rational design of NeoN to improve neomycin B production and weaken the proportion of neomycin C.

Hypermethylation and reduced expression of Gtl2, Rian and Mirg at the Dlk1-Dio3 imprinted locus as a marker for poor developmental potential of mouse embryonic stem cells.

Mouse embryonic stem cells (ESCs) have played a crucial role in biomedical research where they can be used to elucidate gene function through the generation of genetically modified mice. A critical requirement for the success of this technology is the ability of ESCs to contribute to viable chimaeras with germ-line transmission of the genetically modified allele. We have identified several ESC clones that cause embryonic death of chimaeras at mid to late gestation stages. These clones had a normal karyotype, were pathogen free and their in vitro differentiation potential was not compromised. Chimaeric embryos developed normally up to E13.5 but showed a significant decrease in embryo survival by E17.5 with frequent haemorrhaging. We investigated the relationship between the ESCs transcriptional and epigenomic state and their ability to contribute to viable chimaeras. RNA sequencing identified four genes (Gtl2, Rian, Mirg and Rtl1as) located in the Dlk1-Dio3 imprinted locus that were expressed at lower levels in the compromised ESC clones and this was confirmed by qRT-PCR. Bisulphite sequencing analysis showed significant hypermethylation at the Dlk1-Dio3 imprinted locus with no consistent differences in methylation patterns at other imprinted loci. Treatment of the compromised ESCs with 5-azacytidine reactivated stable expression of Gtl2 and rescued the lethal phenotype but only gave low level chimaeras.

Spatial-temporal variation characteristics and evolution of the global industrial robot trade: A complex network analysis.

Industrial robots are a strategic future technology and an important part of the development of artificial intelligence, and they are a necessary means for the intelligent transformation of manufacturing industry. Based on global industrial robot trade data from 1998 to 2017, this paper applies the dynamic complex network analysis method to reveal the spatial and temporal variation characteristics and trade status evolution of the global industrial robot trade network. The results show that the global industrial robot network density has steadily increased, and the industrial robot trade has been characterized by 'diversification'. The number of major industrial robot exporters in the world is increasing, and the import market is increasingly diversified. The export market structure is relatively tight, the centrality of the global industrial robot trade network shows a downward trend, and the dissimilarity of the 'core-edge' clusters decreases year by year. The trade status of 'catch-up' countries represented by China has rapidly increased. However, Japan, Germany, and Italy are still in the central position of the industrial robot trade. Moreover, trade of the 'catch-up' countries' is dominated by imports, and exports of industrial robot products are insufficient. Finally, policy suggestions are provided according to the results.

Atrial fibrillation in Indigenous and non-Indigenous Australians: a cross-sectional study.

OBJECTIVE: To examine the prevalence of atrial fibrillation (AF) and cardiac structural characteristics in Indigenous and non-Indigenous Australians. DESIGN: Retrospective cross-sectional study linking clinical, echocardiography and administrative databases over a 10-year period. SETTING: A tertiary, university teaching hospital in Adelaide, Australia. PARTICIPANTS: Indigenous and non-Indigenous Australians. MAIN OUTCOME MEASURES: AF prevalence and echocardiographic characteristics. RESULTS: Indigenous Australians with AF were significantly younger compared to non-Indigenous Australians (55±13 vs 75±13 years, p<0.001). As a result, racial differences in AF prevalence and left atrial diameter varied according to age. In those under 60 years of age, Indigenous Australians had a significantly greater AF prevalence (2.57 vs1.73%, p<0.001) and left atrial diameters (39±7 vs 37±7 mm, p<0.001) compared to non-Indigenous Australians. In those aged 60 years and above, however, non-Indigenous Australians had significantly greater AF prevalence (9.26 vs 4.61%, p<0.001) and left atrial diameters (39±7 vs 37±7 mm, p<0.001). Left ventricular ejection fractions were less in Indigenous Australians under 60 years of age (49±14 vs 55±11%, p<0.001) and not statistically different in those aged 60 years and above (47±11 vs 52±13, p=0.074) compared to non-Indigenous Australians. Despite their younger age, Indigenous Australians with AF had similar or greater rates of cardiovascular comorbidities than non-Indigenous Australians with AF. CONCLUSIONS: Young Indigenous Australians have a significantly greater prevalence of AF than their non-Indigenous counterparts. In contrast, older non-Indigenous Australians have a greater prevalence of AF compared to their Indigenous counterparts. These observations may be mediated by age-based differences in comorbid cardiovascular conditions, left atrial diameter and left ventricular ejection fraction. Our findings suggest that AF is likely to be contributing to the greater burden of morbidity and mortality experienced by young Indigenous Australians. Further study is required to elucidate whether strategies to prevent and better manage AF in Indigenous Australians may reduce this burden.

Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses.

Comprehensive analysis of cis-regulatory elements is key to understanding the dynamic gene regulatory networks that control embryonic development. While transgenic animals represent the gold standard assay, their generation is costly, entails significant animal usage, and in utero development complicates time-course studies. As an alternative, embryonic stem (ES) cells can readily be differentiated in a process that correlates well with developing embryos. Here, we describe a highly effective platform for enhancer assays using an Hsp68/Venus reporter cassette that targets to the Hprt locus in mouse ES cells. This platform combines the flexibility of Gateway® cloning, live cell trackability of a fluorescent reporter, low background and the advantages of single copy insertion into a defined genomic locus. We demonstrate the successful recapitulation of tissue-specific enhancer activity for two cardiac and two haematopoietic enhancers. In addition, we used this assay to dissect the functionality of the highly conserved Ets/Ets/Gata motif in the Scl+19 enhancer, which revealed that the Gata motif is not required for initiation of enhancer activity. We further confirmed that Gata2 is not required for endothelial activity of the Scl+19 enhancer using Gata2(-/-) Scl+19 transgenic embryos. We have therefore established a valuable toolbox to study gene regulatory networks with broad applicability.

LIF-independent JAK signalling to chromatin in embryonic stem cells uncovered from an adult stem cell disease.

Activating mutations in the tyrosine kinase Janus kinase 2 (JAK2) cause myeloproliferative neoplasms, clonal blood stem cell disorders with a propensity for leukaemic transformation. Leukaemia inhibitory factor (LIF) signalling through the JAK-signal transducer and activator of transcription (STAT) pathway enables self-renewal of embryonic stem (ES) cells. Here we show that mouse ES cells carrying the human JAK2V617F mutation were able to self-renew in chemically defined conditions without cytokines or small-molecule inhibitors, independently of JAK signalling through the STAT3 or phosphatidylinositol-3-OH kinase pathways. Phosphorylation of histone H3 tyrosine 41 (H3Y41) by JAK2 was recently shown to interfere with binding of heterochromatin protein 1α (HP1α). Levels of chromatin-bound HP1α were lower in JAK2V617F ES cells but increased following inhibition of JAK2, coincident with a global reduction in histone H3Y41 phosphorylation. JAK2 inhibition reduced levels of the pluripotency regulator Nanog, with a reduction in H3Y41 phosphorylation and concomitant increase in HP1α levels at the Nanog promoter. Furthermore, Nanog was required for factor independence of JAK2V617F ES cells. Taken together, these results uncover a previously unrecognized role for direct signalling to chromatin by JAK2 as an important mediator of ES cell self-renewal.

Gfi1 expression is controlled by five distinct regulatory regions spread over 100 kilobases, with Scl/Tal1, Gata2, PU.1, Erg, Meis1, and Runx1 acting as upstream regulators in early hematopoietic cells.

The growth factor independence 1 (Gfi1) gene was originally discovered in the hematopoietic system, where it functions as a key regulator of stem cell homeostasis, as well as neutrophil and T-cell development. Outside the blood system, Gfi1 is essential for inner-ear hair and intestinal secretory cell differentiation. To understand the regulatory hierarchies within which Gfi1 operates to control these diverse biological functions, we used a combination of comparative genomics, locus-wide chromatin immunoprecipitation assays, functional validation in cell lines, and extensive transgenic mouse assays to identify and characterize the complete ensemble of Gfi1 regulatory elements. This concerted effort identified five distinct regulatory elements spread over 100kb each driving expression in transgenic mice to a subdomain of endogenous Gfi1. Detailed characterization of an enhancer 35 kb upstream of Gfi1 demonstrated activity in the dorsal aorta region and fetal liver in transgenic mice, which was bound by key stem cell transcription factors Scl/Tal1, PU.1/Sfpi1, Runx1, Erg, Meis1, and Gata2. Taken together, our results reveal the regulatory regions responsible for Gfi1 expression and importantly establish that Gfi1 expression at the sites of hematopoietic stem cell (HSC) emergence is controlled by key HSC regulators, thus integrating Gfi1 into the wider HSC regulatory networks.