Faecalibacterium taiwanense sp. nov., isolated from human faeces.

Two Gram-stain-negative, straight rods, non-motile, asporogenous, catalase-negative and obligately anaerobic butyrate-producing strains, HLW78T and CYL33, were isolated from faecal samples of two healthy Taiwanese adults. Phylogenetic analyses of 16S rRNA and DNA mismatch repair protein MutL (mutL) gene sequences revealed that these two novel strains belonged to the genus Faecalibacterium. On the basis of 16S rRNA and mutL gene sequence similarities, the type strains Faecalibacterium butyricigenerans AF52-21T(98.3-98.1 % and 79.0-79.5 % similarity), Faecalibacterium duncaniae A2-165T(97.8-97.9 % and 70.9-80.1 %), Faecalibacterium hattorii APC922/41-1T(97.1-97.3 % and 80.3-80.5 %), Faecalibacterium longum CM04-06T(97.8-98.0% and 78.3 %) and Faecalibacterium prausnitzii ATCC 27768T(97.3-97.4 % and 82.7-82.9 %) were the closest neighbours to the novel strains HLW78T and CYL33. Strains HLW78T and CYL33 had 99.4 % both the 16S rRNA and mutL gene sequence similarities, 97.9 % average nucleotide identity (ANI), 96.3 % average amino acid identity (AAI), and 80.5 % digital DNA-DNA hybridization (dDDH) values, indicating that these two strains are members of the same species. Phylogenomic tree analysis indicated that strains HLW78T and CYL33 formed an independent robust cluster together with F. prausnitzii ATCC 27768T. The ANI, AAI and dDDH values between strain HLW78T and its closest neighbours were below the species delineation thresholds of 77.6-85.1 %, 71.4-85.2 % and 28.3-30.9 %, respectively. The two novel strains could be differentiated from the type strains of their closest Faecalibacterium species based on their cellular fatty acid compositions, which contained C18 : 1 ω7c and lacked C15 : 0 and C17 : 1 ω6c, respectively. Phenotypic, chemotaxonomic and genotypic test results demonstrated that the two novel strains HLW78T and CYL33 represented a single, novel species within the genus Faecalibacterium, for which the name Faecalibacterium taiwanense sp. nov. is proposed. The type strain is HLW78T (=BCRC 81397T=NBRC 116372T).

5NosoAE: a web server for nosocomial bacterial antibiogram investigation and epidemiology survey.

5NosoAE is a webserver that can be used for nosocomial bacterial analysis including the identification of similar strains based on antimicrobial resistance profiles (antibiogram) and the spatiotemporal distribution visualization and phylogenetic analysis of identified strains with similar antibiograms. The extensive use of antibiotics has caused many pathogenic bacteria to develop multiple drug resistance, resulting in clinical infection treatment challenges and posing a major threat to global public health. Relevant studies have investigated the key determinants of antimicrobial resistance in the whole-genome sequence of bacteria. However, a web server is currently not available for performing large-scale strain searches according to antimicrobial resistance profiles and visualizing epidemiological information including the spatiotemporal distribution, antibiogram heatmap, and phylogeny of identified strains. Here, we implemented these functions in the new server, referred to as 5NosoAE. This server accepts the genome sequence file in the FASTA format of five nosocomial bacteria, namely Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumoniae, Enterococcus faecium and Staphylococcus aureus for query. All visualizations are implemented in JavaScript and PHP. This server will be useful for physicians and epidemiologists involved in research on infectious disease. The 5NosoAE platform is available at https://nosoae.imst.nsysu.edu.tw.

MIB2: metal ion-binding site prediction and modeling server.

MOTIVATION: MIB2 (metal ion-binding) attempts to overcome the limitation of structure-based prediction approaches, with many proteins lacking a solved structure. MIB2 also offers more accurate prediction performance and more metal ion types. RESULTS: MIB2 utilizes both the (PS)2 method and the AlphaFold Protein Structure Database to acquire predicted structures to perform metal ion docking and predict binding residues. MIB2 offers marked improvements over MIB by collecting more MIB residue templates and using the metal ion type-specific scoring function. It offers a total of 18 types of metal ions for binding site predictions. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://bioinfo.cmu.edu.tw/MIB2/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Optimizing Blood Culture Volumes by Implementing PDCA Cycle Management.

BACKGROUND: The aim of this study was to optimize the mean volume of blood drawn by nurses to a level that is recommended by our hospital through the implementation of PDCA cycle management. The purpose of the current study was to match the mean volumes of blood drawn with the volume recommended by the manufacturer. METHODS: The adequacy of blood volume in a bottle of aerobic blood culture per venipuncture was evaluated for every month from January 2021 to March 2022 by using the Becton Dickinson BD blood volume monitoring system. Furthermore, the study compared changes in the mean blood volumes before and after the PDCA cycle management was implemented. RESULTS: The mean blood volumes calculated for Q1 2021 (January 2021 to March 2021) before the PDCA cycle management was 6.3 mL per culture bottle. After PDCA cycle management was implemented, the mean blood volumes for Q1 2022 (January 2022 to March 2022) were calculated as 8.6 mL (p < 0.01). In addition, the positive culture rate increased from 13% to 15%. CONCLUSIONS: Implementing the PDCA cycle management can improve the mean blood culture volumes effectively and match the volume recommended by the manufacturer. Additionally, our study indicated that a higher blood volume yielded a culture rate that was significantly positive.

Performance Evaluation of the VIDAS® D-Dimer Exclusion™ II Assay and the Beckman Coulter D-Dimer Assay.

BACKGROUND: The breakdown of fibrinogen and fibrin during the process of fibrinolysis creates D-dimer. A D-dimer analysis is crucial for the diagnosis of pulmonary embolism, deep vein thrombosis, and disseminated intravascular coagulation. The aim of this study is to evaluate the validity of two different D-dimer assays. METHODS: To analyze the D-dimer, venous blood taken in a vacuette containing 3.2% sodium citrate was used. Peripheral whole blood specimens were collected from 89 subjects, and plasma was separated from these specimens. VIDAS® D-dimer Exclusion™ II and the Beckman Coulter D-dimer assays were used for the quantitative detection of D-dimer levels. The analytical performance of the two different D-dimer assays was compared. RESULTS: The plasma values of D-dimer ranged from 89.2 to 7,452.9 ng/mL (FEU) when tested on the VIDAS® platform and from 20 to 7,770 ng/mL (FEU) when tested on the Beckman Coulter platform. Our results showed that the agreement between the two methods was acceptable and Pearson's correlation coefficient (r) was 0.93 (p < 0.001). CONCLUSIONS: A high correlation exists between quantitative D-dimer measurements conducted with the VIDAS® D-dimer Exclusion™ II and the Beckman Coulter D-dimer assays.

Sialic-Acid-Related Enzymes of B Cells and Monocytes as Novel Markers to Discriminate Improvement Categories and to Fulfill Two Remission Definitions in Rheumatoid Arthritis.

The enzymes α-2,6-sialyltransferase 1 (ST6Gal1), neuraminidase 1 (Neu1), α-2,3-sialyltransferase 1 (ST3Gal1), and neuraminidase 3 (Neu3) are known to affect immune cell function. However, it is not known whether the levels of these enzymes relate to remission definitions or differentiate American College of Rheumatology (ACR), European League Against Rheumatism (EULAR), and Simplified Disease Activity Index (SDAI) responses in patients with rheumatoid arthritis (RA). We measured the ST6Gal1, Neu1, ST3Gal1, and Neu3 levels of B cells and monocytes in RA patients and correlated the cells' enzyme levels/ratios with the improvement in the ACR, EULAR and SDAI responses and with the two remission definitions. The difference in the B-cell Neu1 levels differed between the ACR 70% improvement and non-improvement groups (p = 0.043), between the EULAR good major response (improvement) and non-good response groups (p = 0.014), and also between the SDAI 50% or 70% improvement and non-improvement groups (p = 0.001 and 0.018, respectively). The same held true when the RA patients were classified by positive rheumatoid factor or the use of biologics. The B-cell Neu1 levels significantly indicated 2005 modified American Rheumatism Association and 2011 ACR/EULAR remission definitions (area under the curve (AUC) = 0.674 with p = 0.001, and AUC = 0.682 with p < 0.001, respectively) in contrast to the CRP and ESR (all AUCs < 0.420). We suggest that B-cell Neu1 is superior for discriminating ACR, EULAR, and SDAI improvement and is good for predicting two kinds of remission definitions.

Detection of the SARS-CoV-2 D614G Mutation Using VirSNiP SARS-CoV-2 Spike D614G Assay.

BACKGROUND: At the end of 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapidly spread worldwide. Until recently, over 190 million cases and nearly four million deaths have been reported globally due to the virus. A point mutation in the SARS-CoV-2 spike protein, the D614G variant, was identified in late February 2020. Studies showed that the D614G mutation is related to higher infectivity. The current study was conducted to determine the validity of VirSNiP SARS-CoV-2 Spike D614G assay to detect the SARS-CoV-2 D614G mutation. METHODS: In this study, the detection of the SARS-CoV-2 D614G mutation was performed using VirSNiP SARS-CoV-2 Spike D614G assay (TIB Molbiol) and by Sanger sequencing. Two plasmids carrying A allele (wild-type) and G allele (mutant type) were designed using GenScript's OptimumGene gene design tool (GenScript Inc., Piscataway, NJ, USA). RESULTS: It was found that VirSNiP SARS-CoV-2 Spike D614G assay could detect the SARS-CoV-2 D614G mutation. The specific mutation is easily distinguishable in the melting peaks. All of the samples were confirmed using Sanger sequencing. CONCLUSIONS: In summary, it was shown that VirSNiP SARS-CoV-2 Spike D614G assay is a rapid, accurate, and reliable method for identifying the SARS-CoV-2 D614G mutation. In contrast, Sanger sequencing is time consuming and labor intensive. We strongly believe that VirSNiP SARS-CoV-2 Spike D614G assay will provide more information on the prevalence of the D614G mutation in Taiwanese populations.

CirPred, the first structure modeling and linker design system for circularly permuted proteins.

BACKGROUND: This work aims to help develop new protein engineering techniques based on a structural rearrangement phenomenon called circular permutation (CP), equivalent to connecting the native termini of a protein followed by creating new termini at another site. Although CP has been applied in many fields, its implementation is still costly because of inevitable trials and errors. RESULTS: Here we present CirPred, a structure modeling and termini linker design method for circularly permuted proteins. Compared with state-of-the-art protein structure modeling methods, CirPred is the only one fully capable of both circularly-permuted modeling and traditional co-linear modeling. CirPred performs well when the permutant shares low sequence identity with the native protein and even when the permutant adopts a different conformation from the native protein because of three-dimensional (3D) domain swapping. Linker redesign experiments demonstrated that the linker design algorithm of CirPred achieved subangstrom accuracy. CONCLUSIONS: The CirPred system is capable of (1) predicting the structure of circular permutants, (2) designing termini linkers, (3) performing traditional co-linear protein structure modeling, and (4) identifying the CP-induced occurrence of 3D domain swapping. This method is supposed helpful for broadening the application of CP, and its web server is available at http://10.life.nctu.edu.tw/CirPred/ and http://lo.life.nctu.edu.tw/CirPred/ .

Increased APOE glycosylation plays a key role in the atherogenicity of L5 low-density lipoprotein.

Low-density lipoprotein (LDL) is heterogeneous, composed of particles with variable atherogenicity. Electronegative L5 LDL exhibits atherogenic properties in vitro and in vivo, and its levels are elevated in patients with increased cardiovascular risk. Apolipoprotein E (APOE) content is increased in L5, but what role APOE plays in L5 function remains unclear. Here, we characterized the contributions of APOE posttranslational modification to L5's atherogenicity. Using two-dimensional electrophoresis and liquid chromatography-mass spectrometry, we studied APOE's posttranslational modification in L5 from human plasma. APOE structures with various glycan residues were predicted. Molecular docking and molecular dynamics simulation were performed to examine the functional changes of APOE resulting from glycosylation. We also examined the effects of L5 deglycosylation on endothelial cell apoptosis. The glycan sequence N-acetylgalactosamine, galactose, and sialic acid was consistently expressed on serine 94, threonine 194, and threonine 289 of APOE in L5 and was predicted to contribute to L5's negative surface charge and hydrophilicity. The electrostatic force between the negatively charged sialic acid-containing glycan residue of APOE and positively charged amino acids at the receptor-binding area suggested that glycosylation interferes with APOE's attraction to receptors, lipid-binding ability, and lipid transportation and metabolism functions. Importantly, L5 containing glycosylated APOE induced apoptosis in cultured endothelial cells through lectin-like oxidized LDL receptor-1 (LOX-1) signaling, and glycosylation removal from L5 attenuated L5-induced apoptosis. APOE glycosylation may contribute to the atherogenicity of L5 and be a useful biomarker for rapidly quantifying L5.

A Comparison of Two Molecular Methods for Detecting CALR Mutations in Myeloproliferative Neoplasms.

BACKGROUND: Myeloproliferative neoplasms (MPN) are hematopoietic disorders characterized by abnormal proliferation of the myeloid lineage. Three classic subtypes are polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). These disorders are well known for their association with the JAK2 V617F mutation, in addition to mutations in MPL exon 10, and JAK2 exon 12. CALR mutations were detected in approximately 20% to 25% of patients with ET and PMF and not in patients with PV. Most CALR mutations were deletions and insertions in exon 9, which caused frameshift mutations. METHODS: This study included 60 Taiwanese patients with MPN. We identified CALR mutations in patients with MPN using the high-resolution melting (HRM) analysis. Additionally, the HRM analysis was compared with ipsogen CALR RGQ PCR. To confirm the results of HRM and ipsogen CALR RGQ PCR, sequencing analysis was also conducted all the samples. RESULTS: Up to 6.25% of CALR mutations were successfully detected in patients with MPN using HRM analysis. Eight out of 65 patients (12.3%) were positive for the presence of CALR mutation, including p.L367fs*46 and p.K385fs*47. The results proved 100% comparable to those obtained using ipsogen CALR RGQ PCR. CONCLUSIONS: The HRM analysis and ipsogen CALR RGQ PCR are feasible and reliable techniques for the detection of CALR mutation. Furthermore, HRM offers several benefits, for example, it is time-saving, inexpensive, and does not require many personnel.

Benzyl isothiocyanate ameliorates high-fat/cholesterol/cholic acid diet-induced nonalcoholic steatohepatitis through inhibiting cholesterol crystal-activated NLRP3 inflammasome in Kupffer cells.

Incidence of nonalcoholic fatty liver disease is increasing worldwide. Activation of the NLRP3 inflammasome is central to the development of diet-induced nonalcoholic steatohepatitis (NASH). We investigated whether benzyl isothiocyanate (BITC) ameliorates diet-induced NASH and the mechanisms involved. C57BL/6 J mice fed a high-fat diet containing cholesterol and cholic acid (HFCCD) and Kupffer cells stimulated with LPS and cholesterol crystals (CC) were studied. LPS/CC increased the expression of the active form of caspase 1 (p20) and the secretion of IL-1ß by Kupffer cells, and these changes were reversed by MCC950, an NLRP3 inflammasome inhibitor. LPS/CC-induced NLRP3 inflammasome activation and IL-1ß production were dose-dependently attenuated by BITC. BITC decreased cathepsin B release from lysosomes and binding to NLRP3 induced by LPS/CC. Compared with a normal diet, the HFCCD increased serum levels of ALT, AST, total cholesterol, and IL-1ß and hepatic contents of triglycerides and total cholesterol. BITC administration (0.1% in diet) reversed the increase in AST and hepatic triglycerides in the HFCCD group. Moreover, BITC suppressed lipid accumulation, macrophage infiltration, fibrosis, crown-like structure formation, and p20 caspase 1 and p17 IL-1ß expression in liver in the HFCCD group. These results suggest that BITC ameliorates HFCCD-induced steatohepatitis by inhibiting the activation of NLRP3 inflammasome in Kupffer cells and may protect against diet-induced NASH.

Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae.

Taxonomic relationships between Lactobacillus casei, Lactobacillus paracasei and Lactobacillus zeae have long been debated. Results of previous analyses have shown that overall genome relatedness indices (such as average nucleotide identity and core nucleotide identity) between the type strains L. casei ATCC 393T and L. zeae ATCC 15820T were 94.6 and 95.3 %, respectively, which are borderline for species definition. However, the digital DNA‒DNA hybridization value was 57.3 %, which was clearly lower than the species delineation threshold of 70 %, and hence raised the possibility that L. casei could be reclassified into two species. To re-evaluate the taxonomic relationship of these taxa, multilocus sequence analysis (MLSA) based on the concatenated five housekeeping gene (dnaJ, dnaK, mutL, pheS and yycH) sequences, phylogenomic and core genome multilocus sequence typing analyses, gene presence and absence profiles using pan-genome analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling analysis, cellular fatty acid compositions, and phenotype analysis were carried out. The results of phenotypic characterization, MLSA, whole-genome sequence-based analyses and MALDI-TOF MS profiling justified an independent species designation for the L. zeae strains, and supported an emended the description of the name of Lactobacillus zeae (ex Kuznetsov 1956) Dicks et al. 1996, with ATCC 15820T (=DSM 20178T=BCRC 17942T) as the type strain.

Prevotella hominis sp. nov., isolated from human faeces.

A strictly anaerobic predominant bacterium, designated as strain gm001T, was isolated from a freshly voided faecal sample collected from a healthy Taiwanese adult. Cells were Gram-stain-negative rods, non-motile and non-spore-forming. Strain gm001T was identified as a member of the genus Prevotella, and a comparison of 16S rRNA and hsp60 gene sequences revealed sequence similarities of 98.5 and 93.3 %, respectively, demonstrating that it was most closely related to the type strain of Prevotella copri. Phylogenomic tree analysis indicated that the gm001T cluster is an independent lineage of P. copri DSM 18205T. The average nucleotide identity, digital DNA‒DNA hybridization and average amino acid identity values between strain gm001T and P. copri DSM 18205T were 80.9, 28.6 and 83.8 %, respectively, which were clearly lower than the species delineation thresholds. The species-specific genes of this novel species were also identified on the basis of pan-genomic analysis. The predominant menaquinones were MK-11 and MK-12, and the predominant fatty acids were anteiso-C15 : 0, C15 : 0 and iso-C15 : 0. Acetate and succinate were produced from glucose as metabolic end products. Taken together, the results indicate that strain gm001T represents a novel species of the genus Prevotella, for which the name Prevotella hominis sp. nov. is proposed. The type strain is gm001T (=BCRC 81118T=JCM 33280T).

Development of respirable virtual-cyclone samplers.

Health-based aerosol sampling should reflect how particles penetrate and deposit in various regions of the human respiratory system. Therefore, size-selective sampling should be adopted when monitoring aerosol concentration in the atmosphere. However, cyclone samplers, the most commonly used respirable sampler type in the workplace, show specific particle size-dependent bias toward the international respirable convention. Additionally, cyclone samplers are vulnerable to the dust loading effect resulting in an underestimation of respirable particulate matter. In the previous study, a virtual cyclone has been employed to overcome the dust loading effect, but still had the disadvantage of high aerosol penetration of large particle sizes. Therefore, in this work, the effects of key dimensions of virtual cyclones including chamber width (or inlet width), chamber size and inlet height on the separation performance were further studied and the configurations of virtual cyclones were modified to best fit the ISO/CEN/ACGIH respirable convention. Experimental results demonstrated that a better match with the ISO/CEN/ACGIH respirable convention curve can be achieved by increasing the chamber width to over 20 mm. Moreover, the new virtual cyclones can operate at a flow rate up to 21.5 L/min to collect more respirable particulate matter for the increasingly stringent respirable dust standards. The new virtual cyclones demonstrate accurate and constant measurement of the respirable dust for exposure assessment.

Quality of life at 6 years after occupational injury.

PURPOSE: Occupational injuries have considerable impact on workers' lives. However, data regarding workers' health-related quality of life (HRQOL) at several years after the injury are lacking. This study assessed workers' HRQOL at 6 years after occupational injury and determined related factors in each HRQOL domain. METHODS: Workers who sustained an occupational injury in 2009 and who responded to a previous survey at 3 or 12 months after their injury were followed up in 2015. A total of 1715 participants were candidates for this study. The Taiwanese version of the World Health Organization Quality of Life scale-abbreviated version (WHOQOL-BREF) was used to assess their HRQOL. Multiple linear regression analysis identified predictive factors for HRQOL at 6 years after occupational injury. RESULTS: A total of 563 workers completed the questionnaire (response rate, 32.8%). Adverse life events and additional severe occupational injuries that occurred within the follow-up period, and decreased salary after the injury were significant factors for low scores in all domains of the WHOQOL-BREF. In addition, unmarried participants had low scores in the social relationship domain. Workers with family members requiring care scored low in the physical and environment domains. Workers whose injuries had major effects on their physical appearance had low scores in the physical and psychological domains. Workers with unstable employment had low scores in physical, psychological, and environment domains. CONCLUSION: At 6 years after occupational injury, workers' HRQOL was poor among those whose salaries decreased after the injury, after adjustment for other factors.

Interactive Effect of Corticosterone and Lactate on Regulation of Testosterone Production in Rat Leydig Cells.

The increasing intensity of exercise enhanced corticosterone and lactate production in both humans and rodents. Our previous studies also demonstrated that lactate could stimulate testosterone production in vivo and in vitro. However, the production of testosterone in response to combined corticosterone and lactate on Leydig cells, and underlying molecular mechanisms are remained unclear. This study investigated the changes in testosterone levels of Leydig cells upon exposure to lactate, corticosterone or combination of both, and revealed the detailed mechanisms. Leydig cells were isolated from rat testes, and treated with different concentrations of lactate (2.5-20 mM), cortiosterone (10-9 -10-4 M) and lactate plus corticosterone. The production of testosterone were assayed by radioimmunoassay, and the key molecular proteins, including luteinizing hormone receptor (LHR), protein kinase A (PKA), steroidogenic acute regulatory protein (StAR), and cholesterol P450 side-chain cleavage enzyme (P450scc) involved in testosterone production were performed by Western blot. Results showed that testosterone levels were significantly increased with lactate, while decresed with corticosterone and lactate plus corticosterone treatment. Protein expressions of LHR and P450scc were upregulated with lactate treatment. However, PKA and P450scc were downregulated by lactate plus corticosterone treatment. This downregulation was followed by decreased testoterone levels in Leydig cells. Furthermore, acetylated cAMP, which activates testosterone production was increased with lactate, but not altered by conrtiosterone. Our findings conclude that corticosterone may interfere with lactate, and restrict lactate-stimulated testosterone production in Leydig cells. J. Cell. Physiol. 232: 2135-2144, 2017. © 2016 Wiley Periodicals, Inc.

Depressive, anxiety and post-traumatic stress disorders at six years after occupational injuries.

The aim of this study is to determine the prevalence rates of depressive, anxiety and PTSDs, and the risk factors for psychological symptoms at 6 years after occupational injury. This longitudinal study followed workers who were occupationally injured in 2009. Psychological symptoms and return to work were assessed at 3 and 12 months after injury. Injured workers who had completed the initial questionnaire survey at 3 or 12 months after injury were recruited. A self-administered questionnaire was mailed to the participants. For workers with high Brief Symptom Rating Scale and Post-traumatic Symptom Checklist scores, an in-depth psychiatric evaluation was performed using the Mini-international Neuropsychiatric Interview. A total of 570 workers completed the questionnaire (response rate, 28.7%). Among them, 243 (42.6%) had high psychological symptom scores and were invited for a phone interview; 135 (55.6%) completed the interview. The estimated rates of major depression and post-traumatic stress disorder (PTSD)/partial PTSD were 9.2 and 7.2%, respectively, and both these rates were higher at 6 years after injury than at 12 months after injury (2.0 and 5.1%). After adjustment for family and social factors, the risk factors for high psychological scores were length of hospitalization immediately after injury, affected physical appearance, repeated occupational injuries, unemployment, and number of quit jobs after the injury. At 6 years after occupational injury, the re-emergence of psychiatric disorders was observed. Relevant factors for poor psychological health were severity of injury and instability of work. Periodic monitoring of psychological and physical health and economic stability are warranted.

(PS)2: protein structure prediction server version 3.0.

Protein complexes are involved in many biological processes. Examining coupling between subunits of a complex would be useful to understand the molecular basis of protein function. Here, our updated (PS)(2) web server predicts the three-dimensional structures of protein complexes based on comparative modeling; furthermore, this server examines the coupling between subunits of the predicted complex by combining structural and evolutionary considerations. The predicted complex structure could be indicated and visualized by Java-based 3D graphics viewers and the structural and evolutionary profiles are shown and compared chain-by-chain. For each subunit, considerations with or without the packing contribution of other subunits cause the differences in similarities between structural and evolutionary profiles, and these differences imply which form, complex or monomeric, is preferred in the biological condition for the subunit. We believe that the (PS)(2) server would be a useful tool for biologists who are interested not only in the structures of protein complexes but also in the coupling between subunits of the complexes. The (PS)(2) is freely available at http://ps2v3.life.nctu.edu.tw/.

Pro-arrhythmogenic Effects of the V141M KCNQ1 Mutation in Short QT Syndrome and Its Potential Therapeutic Targets: Insights from Modeling.

Gain-of-function mutations in the pore-forming subunit of IKs channels, KCNQ1, lead to short QT syndrome (SQTS) and lethal arrhythmias. However, how mutant IKs channels cause SQTS and the possibility of IKs-specific pharmacological treatment remain unclear. V141M KCNQ1 is a SQTS associated mutation. We studied its effect on IKs gating properties and changes in the action potentials (AP) of human ventricular myocytes. Xenopus oocytes were used to study the gating mechanisms of expressed V141M KCNQ1/KCNE1 channels. Computational models were used to simulate human APs in endocardial, mid-myocardial, and epicardial ventricular myocytes with and without ß-adrenergic stimulation. V141M KCNQ1 caused a gain-of-function in IKs characterized by increased current density, faster activation, and slower deactivation leading to IKs accumulation. V141M KCNQ1 also caused a leftward shift of the conductance-voltage curve compared to wild type (WT) IKs (V1/2 = 33.6 ± 4.0 mV for WT, and 24.0 ± 1.3 mV for heterozygous V141M). A Markov model of heterozygous V141M mutant IKs was developed and incorporated into the O'Hara-Rudy model. Compared to the WT, AP simulations demonstrated marked rate-dependent shortening of AP duration (APD) for V141M, predicting a SQTS phenotype. Transmural electrical heterogeneity was enhanced in heterozygous V141M AP simulations, especially under ß-adrenergic stimulation. Computational simulations identified specific IK1 blockade as a beneficial pharmacologic target for reducing the transmural APD heterogeneity associated with V141M KCNQ1 mutation. V141M KCNQ1 mutation shortens ventricular APs and enhances transmural APD heterogeneity under ß-adrenergic stimulation. Computational simulations identified IK1 blockers as a potential antiarrhythmic drug of choice for SQTS.

Interplay between CRP, Atherogenic LDL, and LOX-1 and Its Potential Role in the Pathogenesis of Atherosclerosis.

BACKGROUND: Studies have shown that the classic acute-phase protein C-reactive protein (CRP) has proinflammatory effects on vascular cells and may play a causal role in the pathogenesis of coronary artery disease. A growing body of evidence has suggested that interplay between CRP, lectin-like oxidized LDL receptor-1 (LOX-1), and atherogenic LDL may underlie the mechanism of endothelial dysfunction that leads to atherosclerosis. CONTENT: We review the biochemical evidence for an association of CRP, LOX-1, and either oxidized LDL (OxLDL) or electronegative L5 LDL with the pathogenesis of coronary artery disease. Artificially oxidized OxLDL has been studied extensively for its role in atherogenesis, as has electronegative L5 LDL, which is present at increased levels in patients with increased cardiovascular risks. OxLDL and L5 have been shown to stimulate human aortic endothelial cells to produce CRP, indicating that CRP is synthesized locally in the endothelium. The ligand-binding face (B-face) of CRP has been shown to bind the LOX-1 scavenger receptor and increase LOX-1 expression in endothelial cells, thereby promoting the uptake of OxLDL or L5 by LOX-1 into endothelial cells to induce endothelial dysfunction. SUMMARY: CRP and LOX-1 may form a positive feedback loop with OxLDL or L5 in atherogenesis, whereby increased levels of atherogenic LDL in patients with cardiovascular risks induce endothelial cells to express CRP, which may in turn increase the expression of LOX-1 to promote the uptake of atherogenic LDL into endothelial cells. Further research is needed to confirm a causal role for CRP in atherogenesis.