Crystal structure of a GDP-6-OMe-4-keto-L-xylo-heptose reductase from Campylobacter jejuni.

Carbohydrates play a major role in infection strategies of various enteric pathogens. In Campylobacter jejuni, the most common cause of gastroenteritis, uniquely modified heptoses found in surface carbohydrates are synthesized by specific pathways. Owing to the importance of such pathways for the infectious potential of pathogens and/or their virulence, these biosynthesis pathways present potential targets for therapeutic intervention. Here, we determined the crystal structure of GDP-6-OMe-4-keto-L-xylo-heptose reductase (MlghC), an enzyme within the L-gluco-heptose synthesis pathway of C. jejuni strain NCTC 11168. This enzyme lacks the canonical tyrosine residue of the conserved catalytic Ser-Lys-Tyr triad commonly found among functionally related reductases. Despite adopting the overall two-domain fold shared with other short-chain dehydrogenase/reductase family members, subtle structural differences in the interface between the cofactor- and substrate-binding domains explain the absence of epimerase activity and different substrate specificity of this reductase. Modeling of the product-bound complex based on the crystal structure presented here suggests that a tyrosine residue unique to MlghC replaces the missing canonical residue of the catalytic triad.

Fractional Flow Reserve and Cardiac Events in Coronary Artery Disease: Data From a Prospective IRIS-FFR Registry (Interventional Cardiology Research Incooperation Society Fractional Flow Reserve).

BACKGROUND: We evaluated the prognosis of deferred and revascularized coronary stenoses after fractional flow reserve (FFR) measurement to assess its revascularization threshold in clinical practice. METHODS: The IRIS-FFR registry (Interventional Cardiology Research In-cooperation Society Fractional Flow Reserve) prospectively enrolled 5846 patients with ≥1coronary lesion with FFR measurement. Revascularization was deferred in 6468 lesions and performed in 2165 lesions after FFR assessment. The primary end point was major adverse cardiac events (cardiac death, myocardial infarction, and repeat revascularization) at a median follow-up of 1.9 years and analyzed on a per-lesion basis. A marginal Cox model accounted for correlated data in patients with multiple lesions, and a model to predict per-lesion outcomes was adjusted for confounding factors. RESULTS: For deferred lesions, the risk of major adverse cardiac events demonstrated a significant, inverse relationship with FFR (adjusted hazard ratio, 1.06; 95% confidence interval, 1.05-1.08; P<0.001). However, this relationship was not observed in revascularized lesions (adjusted hazard ratio, 1.00; 95% confidence interval, 0.98-1.02; P=0.70). For lesions with FFR ≥0.76, the risk of major adverse cardiac events was not significantly different between deferred and revascularized lesions. Conversely, in lesions with FFR ≤0.75, the risk of major adverse cardiac events was significantly lower in revascularized lesions than in deferred lesions (for FFR 0.71-0.75, adjusted hazard ratio, 0.47; 95% confidence interval, 0.24-0.89; P=0.021; for FFR ≤0.70, adjusted hazard ratio 0.47; 95% confidence interval, 0.26-0.84; P=0.012). CONCLUSIONS: This large, prospective registry showed that the FFR value was linearly associated with the risk of cardiac events in deferred lesions. In addition, revascularization for coronary artery stenosis with a low FFR (≤0.75) was associated with better outcomes than the deferral, whereas for a stenosis with a high FFR (≥0.76), medical treatment would be a reasonable and safe treatment strategy. CLINICAL TRIAL REGISTRATION: URL: http://www.clinicaltrials.gov. Unique identifier: NCT01366404.

Valorization of single-carbon chemicals by using carboligases as key enzymes.

Single-carbon (C1) biorefinery plays a key role in the consumption of global greenhouse gases and a circular carbon economy. Thereby, we have focused on the valorization of C1 compounds (e.g. methanol, formaldehyde, and formate) into multicarbon products, including bioplastic monomers, glycolate, and ethylene glycol. For instance, methanol, derived from the oxidation of CH4, can be converted into glycolate, ethylene glycol, or erythrulose via formaldehyde and glycolaldehyde, employing C1 and/or C2 carboligases as essential enzymes. Escherichia coli was engineered to convert formate, produced from CO via CO2 or from CO2 directly, into glycolate. Recent progress in the design of biotransformation pathways, enzyme discovery, and engineering, as well as whole-cell biocatalyst engineering for C1 biorefinery, was addressed in this review.

Structural characterization of the type I-B CRISPR Cas7 from Thermobaculum terrenum.

Clustered regularly interspaced short palindromic repeats (CRISPR) in many prokaryotes functions as an adaptive immune system against mobile genetic elements. A heterologous ribonucleoprotein silencing complex composed of CRISPR-associated (Cas) proteins and a CRISPR RNA (crRNA) neutralizes the incoming mobile genetic elements. The type I and III silencing complexes commonly include a protein-helical backbone of several copies of identical subunits, for example, Cas7 in the type I silencing complex. In this study, we structurally characterized type I-B Cas7 (Csh2 from Thermobaculum terrenum; TterCsh2). The revealed crystal structure of TterCsh2 shows a typical glove-like architecture of Cas7, which consists of a palm, a thumb, and a finger domain. Csh2 proteins have 5 conserved sequence motifs that are arranged to form a presumable crRNA-binding site in the TterCsh2 structure. This crRNA binding site of TterCsh2 is structurally and potentially comparable to those observed in helix-forming Cas7 structures in other sub-types. Analysis of the reported Cas7 structures and their sequences suggests that Cas7s can be divided into at least two sub-classes. These data will broaden our understanding on the Cascade complex of CRISPR/Cas systems.

Engineering of two thiamine diphosphate-dependent enzymes for the regioselective condensation of C1-formaldehyde into C4-erythrulose.

A number of carboligases, which catalyze condensation of C1- and/or C2-aldehydes into multi-carbon products, have been reported. However, their catalytic activities and/or regioselectivities remained rather low. Thereby, this study has focused on engineering of C1 and C2 carboligases for the regioselective condensation of C1-formaldehyde into C4-erythrulose via C2-glycolaldehyde. The crystal structure of the glyoxylate carboligase from Escherichia coli (EcGCL) was elucidated in complex with glycolaldehyde. A structure-guided rationale generated several mutants, one of whose catalytic activity reached 15.6 M-1·s-1, almost 10 times greater than the wild-type enzyme. Another variant (i.e., EcGCL_R484M/N283Q/L478M/M488L/R284K) has shown significantly increased stability to the glycolaldehyde toxicity, enabling production of glycolaldehyde to 31 mM from 75 mM formaldehyde (conversion: 83 %). Besides, the E1 subunit of α-ketoglutarate dehydrogenase complex from Vibrio vulnificus (VvSucA) was engineered as a regiospecific C2 carboligase for condensation of glycolaldehyde into erythrulose. The combination of EcGCL_R484M/N283Q/L478M/M488L/R284K and VvSucA_K228L led to the cascade production of erythrulose to 8 mM from 90 mM formaldehyde via glycolaldehyde without byproduct formation. This study will contribute to valorization of C1 gases into industrially relevant multi-carbon products in an environment-friendly way.

Impact of Atrial Fibrillation on Patients Undergoing Transcatheter Aortic Valve Implantation (TAVI): The K-TAVI Registry.

PURPOSE: The incidence and prognostic implications of atrial fibrillation (AF) in patients with severe aortic stenosis (AS) undergoing transcatheter aortic valve implantation (TAVI) are controversial, especially for Korean patients. Furthermore, the pattern of antithrombotic therapy for these patients is unknown. The present study sought to identify the impact of AF on Korean patients undergoing TAVI and demonstrate the status of antithrombotic therapy for these patients. MATERIALS AND METHODS: A total of 660 patients who underwent TAVI for severe AS were recruited from the nationwide K-TAVI registry in Korea. The enrolled patients were stratified into sinus rhythm (SR) and AF groups. The primary endpoint was all-cause death at 1-year. RESULTS: AF was recorded in 135 patients [pre-existing AF 108 (16.4%) and new-onset AF 27 (4.1%)]. The rate of all-cause death at 1 year was significantly higher in patients with AF than in those with SR [16.2% vs. 6.4%, adjusted hazard ratio (HR): 2.207, 95% confidence interval (CI): 1.182-4.120, p=0.013], regardless of the onset timing of AF. The rate of new pacemaker insertion at 1 year was also significantly higher in patients with AF than in those with SR (14.0% vs. 5.5%, adjusted HR: 3.137, 95%CI: 1.621-6.071, p=0.001). Among AF patients, substantial number of patients received the combination of multiple antithrombotic agents (77.8%), and the most common combination was that of aspirin and clopidogrel (38.1%). CONCLUSION: AF was an independent predictor of 1-year mortality and new pacemaker insertion in Korean patients undergoing TAVI.

Optimization of FFR prediction algorithm for gray zone by hemodynamic features with synthetic model and biometric data.

BACKGROUND: Recent attempts on adopting artificial intelligence algorithm on coronary diagnosis had limitations on data quantity and quality. While most of previous studies only used vessel image as input data, flow features and biometric features should be also considered. Moreover, the accuracy should be optimized within gray zone as the purpose is to decide stent insertion with estimated fractional flow reserve. OBJECTIVES: The main purpose of this study is to develop an artificial intelligence-based coronary vascular diagnosis system focused on performance in the gray zone, from CT image extraction to FFR estimation. Three main issues should be considered for an algorithm to be used for pre-screening: algorithm optimization in the gray zone, minimization of labor during image processing, and consideration of flow and biometric features. This paper introduces a full FFR pre-screening system from automatic image extraction to an algorithm for estimating the FFR value. METHOD: The main techniques used in this study are an automatic image extraction algorithm, lattice Boltzmann method based computational fluid dynamics analysis of a synthetic model and patient data, and an AI algorithm optimization. For feature extraction, this study focused on an automatic process to reduce manual labor. The algorithm consisted of two steps: the first algorithm calculates flow features from geometrical features, and the second algorithm estimates the FFR value from flow features and patient biometric features. Algorithm selection, outlier elimination, and k-fold selection were included to optimize the algorithm. CONCLUSION: Eight types of algorithms including two neural network models and six machine learning models were optimized and tested. The random forest model shows the highest performance before optimization, whereas the multilayer perceptron regressor shows the highest gray zone accuracy after optimization.

Structural features of a minimal intact methyltransferase of a type I restriction-modification system.

Type I restriction-modification enzymes are oligomeric proteins composed of methylation (M), DNA sequence-recognition (S), and restriction (R) subunits. The different bipartite DNA sequences of 2-4 consecutive bases are recognized by two discerned target recognition domains (TRDs) located at the two-helix bundle of the two conserved regions (CRs). Two M-subunits and a single S-subunit form an oligomeric protein that functions as a methyltransferase (M2S1 MTase). Here, we present the crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH). This MTase includes the M-domain with a helix tail (M-tail helix) and the S1/2-domain of a TRD and a CR α-helix. The Ocr binds to the cleft of the TRD surface and SAH is located in the pocket within the M-domain. The solution- and negative-staining electron microscopy-based reconstructed (M1S1/2)2 structure reveals a symmetric (S1/2)2 assembly using two CR-helices and two M-tail helices as a pivot, which is plausible for recognizing two DNA regions of same sequence. The conformational flexibility of the minimal M1S1/2 MTase dimer indicates a particular state resembling the structure of M2S1 MTases.

Characterisation of trehalose-6-phosphate phosphatases from bacterial pathogens.

The trehalose biosynthesis pathway has recently received attention for therapeutic intervention combating infectious diseases caused by bacteria, helminths or fungi. Trehalose-6-phosphate phosphatase (TPP) is a key enzyme of the most common trehalose biosynthesis pathway and a particularly attractive target owing to the toxicity of accumulated trehalose-6-phosphate in pathogens. Here, we characterised TPP-like proteins from bacterial pathogens implicated in nosocomial infections in terms of their steady-state kinetics as well as pH- and metal-dependency of their enzymatic activity. Analysis of the steady-state kinetics of recombinantly expressed enzymes from Acinetobacter baumannii, Corynebacterium diphtheriae and Pseudomonas stutzeri yielded similar kinetic parameters as those of other reported bacterial TPPs. In contrast to nematode TPPs, the divalent metal ion appears to be bound only weakly in the active site of bacterial TPPs, allowing the exchange of the resident magnesium ion with other metal ions. Enzymatic activity comparable to the wild-type enzyme was observed for the TPP from P. stutzeri with manganese, cobalt and nickel. Analysis of the enzymatic activity of S. maltophilia TPP active site mutants provides evidence for the involvement of four canonical aspartate residues as well as a strictly conserved histidine residue of TPP-like proteins from bacteria in the enzyme mechanism. That histidine residue is a member of an interconnected network of five conserved residues in the active site of bacterial TPPs which likely constitute one or more functional units, directly or indirectly cooperating to enhance different aspects of the catalytic activity.

Diagnosis of obstructive sleep apnea with prediction of flow characteristics according to airway morphology automatically extracted from medical images: Computational fluid dynamics and artificial intelligence approach.

BACKGROUND: Obstructive sleep apnea syndrome (OSAS) is being observed in an increasing number of cases. It can be diagnosed using several methods such as polysomnography. OBJECTIVES: To overcome the challenges of time and cost faced by conventional diagnostic methods, this paper proposes computational fluid dynamics (CFD) and machine-learning approaches that are derived from the upper-airway morphology with automatic segmentation using deep learning. METHOD: We adopted a 3D UNet deep-learning model to perform medical image segmentation. 3D UNet prevents the feature-extraction loss that may occur by concatenating layers and extracts the anteroposterior coordination and width of the airway morphology. To create flow characteristics of the upper airway training data, we analyzed the changes in flow characteristics according to the upper-airway morphology using CFD. A multivariate Gaussian process regression (MVGPR) model was used to train the flow characteristic values. The trained MVGPR enables the prompt prediction of the aerodynamic features of the upper airway without simulation. Unlike conventional regression methods, MVGPR can be trained by considering the correlation between the flow characteristics. As a diagnostic step, a support vector machine (SVM) with predicted aerodynamic and biometric features was used in this study to classify patients as healthy or suffering from moderate OSAS. SVM is beneficial as it is easy to learn even with a small dataset, and it can diagnose various flow characteristics as factors while enhancing the feature via the kernel function. As the patient dataset is small, the Monte Carlo cross-validation was used to validate the trained model. Furthermore, to overcome the imbalanced data problem, the oversampling method was applied. RESULT: The segmented upper-airway results of the high-resolution and low-resolution models present overall average dice coefficients of 0.76±0.041 and 0.74±0.052, respectively. Furthermore, the classification accuracy, sensitivity, specificity, and F1-score of the diagnosis algorithm were 81.5%, 89.3%, 86.2%, and 87.6%, respectively. CONCLUSION: The convenience and accuracy of sleep apnea diagnosis are improved using deep learning and machine learning. Further, the proposed method can aid clinicians in making appropriate decisions to evaluate the possible applications of OSAS.

Using Social Network Methods to Test for Assortment of Prosociality among Korean High School Students.

Assortative interaction among altruistic individuals is a necessary condition for the evolution of cooperation. The requirement for assortment holds regardless of whether a meta-population is subdivided into distinct and isolated subgroups or has ephemeral boundaries with a high migration rate. The assumption, however, is rarely tested directly. In this paper, we develop a method to test for assortment of prosociality in network-structured data. The method is applied to a friendship network collected from 238 Korean students attending the same high school. A mixing matrix was used to explore the presence of assortative friendship among more prosocial individuals. An exponential random graph model of network structure that accounts for additional observed relational propensities (higher-than-expected number of people nominating no friends) and sampling constraints (upper bound on friendship nominations) found that individual prosociality predicted friendship propensity, and that individuals with higher prosocial scores had a higher probability of befriending other more prosocial individuals. The results reveal that a considerable level of assortment of prosociality characterizes this population.

Experimental evidence for convergent evolution of maternal care heuristics in industrialized and small-scale populations.

Maternal care decision rules should evolve responsiveness to factors impinging on the fitness pay-offs of care. Because the caretaking environments common in industrialized and small-scale societies vary in predictable ways, we hypothesize that heuristics guiding maternal behaviour will also differ between these two types of populations. We used a factorial vignette experiment to elicit third-party judgements about likely caretaking decisions of a hypothetical mother and her child when various fitness-relevant factors (maternal age and access to resources, and offspring age, sex and quality) were varied systematically in seven populations-three industrialized and four small-scale. Despite considerable variation in responses, we found that three of five main effects, and the two severity effects, exhibited statistically significant industrialized/ small-scale population differences. All differences could be explained as adaptive solutions to industrialized versus small-scale caretaking environments. Further, we found gradients in the relationship between the population-specific estimates and national-level socio-economic indicators, further implicating important aspects of the variation in industrialized and small-scale caretaking environments in shaping heuristics. Although there is mounting evidence for a genetic component to human maternal behaviour, there is no current evidence for interpopulation variation in candidate genes. We nonetheless suggest that heuristics guiding maternal behaviour in diverse societies emerge via convergent evolution in response to similar selective pressures.

Extra-stent vascular remodeling in in-stent restenosis after 188Re-MAG3 radiation therapy.

BACKGROUND: The effect of beta-radiation on extra-stent vascular remodeling in patients with in-stent restenosis has not been studied. The correlation between the extent of extra-stent plaque proliferation and that of intimal hyperplasia (IH) in in-stent restenosis in patients who received beta-radiation therapy as well as conventional therapy has also not been studied. METHODS: We evaluated the extra-stent remodeling in diffuse in-stent restenosis between a beta-radiation therapy patient group (188Re-MAG3, n=50) and a control group (n=9) by applying serial intravascular ultrasound (IVUS) analysis. Matching (post-intervention and follow-up) images were acquired at the follow-up lesion site and were available in 44 of 50 patients who received radiation therapy and in seven of nine control patients. RESULTS: There was a significant increase of the external elastic membrane (EEM) area in both groups: 16.4 +/- 3.3 mm2 post-intervention to 17.1 +/- 3.3 mm2 at follow-up, P=0.001 in the radiation therapy group, and 16.8 +/- 4.0 mm2 post-intervention to 17.4 +/- 4.1 mm2 at follow-up, P=0.008 in the control group. There were no statistically significant differences of the Delta EEM area between the two groups: 0.7 +/- 0.4 mm2 in the radiation therapy group vs. 0.6 +/- 0.4 mm2 in the control group, P=0.389. The Delta IH area correlated with the Delta EEM area in the control group (r=0.826, P=0.022), but not in the radiation therapy group (r=0.016, P=0.919). CONCLUSIONS: The findings of this IVUS study were that positive remodeling (increased EEM area) occurred equally in both control and irradiated patients with in-stent restenosis. The extent of remodeling was directly in proportion to IH in the control group, but no such relationship existed in the irradiated patient group.

The role of sensation seeking, perceived peer pressure, and harmful alcohol use in riding with an alcohol-impaired driver.

Alcohol-related motor vehicle collisions have been the top of policy agenda for more than three decades in Korea. Despite implementation of various traffic safety measures, some drivers' alcohol use and abuse has resulted in a high number of alcohol-impaired traffic fatalities every year. This paper presents the association of theoretical factors with behavior of riding with an alcohol-impaired driver (RAID) among all age groups in the Korean adult sample. The theoretical factors of the drivers are personality factor, socio-psychological factor, and alcohol-related behavioral risk factor. We utilized national survey data from 1007 respondents consisting of 703 males and 304 females aged 20-66 collected by Korean Institute of Criminology (KIC) to test our theorized model. Our results indicated that there were three major predictors of RAID involvement: sensation seeking propensity, perceived peer pressure, and frequent harmful drinking. Overall, prediction of RAID behavior by gender was mediated entirely through these predictors. The issue of males' higher risk of RAID involvements was addressed for effective communication strategies such as campaigns.

Determination of molecular structures of HIV envelope glycoproteins using cryo-electron tomography and automated sub-tomogram averaging.

Since its discovery nearly 30 years ago, more than 60 million people have been infected with the human immunodeficiency virus (HIV) (www.usaid.gov). The virus infects and destroys CD4+ T-cells thereby crippling the immune system, and causing an acquired immunodeficiency syndrome (AIDS) (2). Infection begins when the HIV Envelope glycoprotein "spike" makes contact with the CD4 receptor on the surface of the CD4+ T-cell. This interaction induces a conformational change in the spike, which promotes interaction with a second cell surface co-receptor (5,9). The significance of these protein interactions in the HIV infection pathway makes them of profound importance in fundamental HIV research, and in the pursuit of an HIV vaccine. The need to better understand the molecular-scale interactions of HIV cell contact and neutralization motivated the development of a technique to determine the structures of the HIV spike interacting with cell surface receptor proteins and molecules that block infection. Using cryo-electron tomography and 3D image processing, we recently demonstrated the ability to determine such structures on the surface of native virus, at ˜20 Šresolution (9,14). This approach is not limited to resolving HIV Envelope structures, and can be extended to other viral membrane proteins and proteins reconstituted on a liposome. In this protocol, we describe how to obtain structures of HIV envelope glycoproteins starting from purified HIV virions and proceeding stepwise through preparing vitrified samples, collecting, cryo-electron microscopy data, reconstituting and processing 3D data volumes, averaging and classifying 3D protein subvolumes, and interpreting results to produce a protein model. The computational aspects of our approach were adapted into modules that can be accessed and executed remotely using the Biowulf GNU/Linux parallel processing cluster at the NIH (http://biowulf.nih.gov). This remote access, combined with low-cost computer hardware and high-speed network access, has made possible the involvement of researchers and students working from school or home.