The CRL3gigaxonin ubiquitin ligase-USP15 pathway governs the destruction of neurofilament proteins.

Giant axonal neuropathy (GAN) is caused by mutations in the GAN gene encoding for gigaxonin (GIG), which functions as an adaptor of the CUL3-RBX1-GIG (CRL3GIG) E3 ubiquitin ligase complex. The pathological hallmark of GAN is characterized by the accumulation of densely packed neurofilaments (NFs) in the axons. However, there are fundamental knowledge gaps in our understanding of the molecular mechanisms by which the ubiquitin-proteasome system controls the homeostasis of NF proteins. Recently, the deubiquitylating enzyme USP15 was reported to play a crucial role in regulating ubiquitylation and proteasomal degradation of CRL4CRBN substrate proteins. Here, we report that the CRL3GIG-USP15 pathway governs the destruction of NF proteins NEFL and INA. We identified a specific degron called NEFLL12 degron for CRL3GIG. Notably, mutations in the C-terminal Kelch domain of GIG, represented by L309R, R545C, and C570Y, disrupted the binding of GIG to NEFL and INA, leading to the accumulation of these NF proteins. This accounts for the loss-of-function mutations in GAN patients. In addition to regulating NFs, CRL3GIG also controls actin filaments by directly targeting actin-filament-binding regulatory proteins TPM1, TPM2, TAGLN, and CNN2 for proteasomal degradation. Thus, our findings broadly impact the field by providing fundamental mechanistic insights into regulating extremely long-lived NF proteins NEFL and INA by the CRL3GIG-USP15 pathway and offering previously unexplored therapeutic opportunities to treat GAN patients and other neurodegenerative diseases by explicitly targeting downstream substrates of CRL3GIG.

Distant residues modulate conformational opening in SARS-CoV-2 spike protein.

Infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) involves the attachment of the receptor-binding domain (RBD) of its spike proteins to the ACE2 receptors on the peripheral membrane of host cells. Binding is initiated by a down-to-up conformational change in the spike protein, the change that presents the RBD to the receptor. To date, computational and experimental studies that search for therapeutics have concentrated, for good reason, on the RBD. However, the RBD region is highly prone to mutations, and is therefore a hotspot for drug resistance. In contrast, we here focus on the correlations between the RBD and residues distant to it in the spike protein. This allows for a deeper understanding of the underlying molecular recognition events and prediction of the highest-effect key mutations in distant, allosteric sites, with implications for therapeutics. Also, these sites can appear in emerging mutants with possibly higher transmissibility and virulence, and preidentifying them can give clues for designing pan-coronavirus vaccines against future outbreaks. Our model, based on time-lagged independent component analysis (tICA) and protein graph connectivity network, is able to identify multiple residues that exhibit long-distance coupling with the RBD opening. Residues involved in the most ubiquitous D614G mutation and the A570D mutation of the highly contagious UK SARS-CoV-2 variant are predicted ab initio from our model. Conversely, broad-spectrum therapeutics like drugs and monoclonal antibodies can target these key distant-but-conserved regions of the spike protein.

Feruloyl Esterase (LaFae) from Lactobacillus acidophilus: Structural Insights and Functional Characterization for Application in Ferulic Acid Production.

Ferulic acid and related hydroxycinnamic acids, used as antioxidants and preservatives in the food, cosmetic, pharmaceutical and biotechnology industries, are among the most abundant phenolic compounds present in plant biomass. Identification of novel compounds that can produce ferulic acid and hydroxycinnamic acids, that are safe and can be mass-produced, is critical for the sustainability of these industries. In this study, we aimed to obtain and characterize a feruloyl esterase (LaFae) from Lactobacillus acidophilus. Our results demonstrated that LaFae reacts with ethyl ferulate and can be used to effectively produce ferulic acid from wheat bran, rice bran and corn stalks. In addition, xylanase supplementation was found to enhance LaFae enzymatic hydrolysis, thereby augmenting ferulic acid production. To further investigate the active site configuration of LaFae, crystal structures of unliganded and ethyl ferulate-bound LaFae were determined at 2.3 and 2.19 Å resolutions, respectively. Structural analysis shows that a Phe34 residue, located at the active site entrance, acts as a gatekeeper residue and controls substrate binding. Mutating this Phe34 to Ala produced an approximately 1.6-fold increase in LaFae activity against p-nitrophenyl butyrate. Our results highlight the considerable application potential of LaFae to produce ferulic acid from plant biomass and agricultural by-products.

A Multicenter Study of Clinicopathology and Immunohistochemical Distinction between Adult and Pediatric Large B-Cell Lymphoma.

Introduction: Pediatric DLBCL is considered a homogenous group and has superior outcomes compared to adults. This study investigated the clinical pathology and immunohistochemical distinction between adult and pediatric large B-cell lymphoma. Methods: A cross-sectional study of 314 NHLs with the morphology of diffuse pattern, large B-cell, and CD20 expression was investigated. Results: Of 314 cases, there were 6 cases of pleomorphic MCL (all in adults), 19 cases of Burkitt lymphoma (all in children), and 289 cases of DLBCL. Pediatric DLBCL had many striking differences: More frequency in extra-nodal sites; a higher proportion of centroblastic morphology; a predominance of GCB-type; a high proliferation rate; an infrequency of Bcl2 protein expression, and a lack of double-expresser lymphoma. Conclusions: Our study demonstrated the significant biological differences between adult and pediatric DLBCL.

Measurement of anti-suprabasin antibodies, multiple cytokines and chemokines as potential predictive biomarkers for neuropsychiatric systemic lupus erythematosus.

Neuropsychiatric systemic lupus erythematosus (NPSLE) varies in presentation and is one of the leading causes of morbidity and mortality among patients with SLE. This study determined the most critical serum biomarkers for the development of NPSLE as they may have clinical utility prior to the onset of neuropsychiatric symptoms. We retrospectively analyzed 35 NPSLE patients, 34 SLE patients, 20 viral meningitis (VM) patients, and 16 relapsing-remitting multiple sclerosis (MS) patients. We measured anti-suprabasin antibodies concentrations in serum by using Luciferase immunoprecipitation system (LIPS) assay. The serum concentrations of cytokines/chemokines were measured by using multiplex bead-based assay. We found serum FGF-2 level was significantly higher in the NPSLE group compared to the SLE group and the healthy control group. The anti-suprabasin antibody relative concentration (SRC) has high positive predictive values for the development of NPSLE. The most essential biomarkers are VEGF, anti-suprabasin antibodies, sCD40L, IL-10, GRO, MDC, IL-8, IL-9, TNF-α, MIP-1α.

iANP-EC: Identifying Anticancer Natural Products Using Ensemble Learning Incorporated with Evolutionary Computation.

Cancer is one of the most deadly diseases that annually kills millions of people worldwide. The investigation on anticancer medicines has never ceased to seek better and more adaptive agents with fewer side effects. Besides chemically synthetic anticancer compounds, natural products are scientifically proved as a highly potential alternative source for anticancer drug discovery. Along with experimental approaches being used to find anticancer drug candidates, computational approaches have been developed to virtually screen for potential anticancer compounds. In this study, we construct an ensemble computational framework, called iANP-EC, using machine learning approaches incorporated with evolutionary computation. Four learning algorithms (k-NN, SVM, RF, and XGB) and four molecular representation schemes are used to build a set of classifiers, among which the top-four best-performing classifiers are selected to form an ensemble classifier. Particle swarm optimization (PSO) is used to optimise the weights used to combined the four top classifiers. The models are developed by a set of curated 997 compounds which are collected from the NPACT and CancerHSP databases. The results show that iANP-EC is a stable, robust, and effective framework that achieves an AUC-ROC value of 0.9193 and an AUC-PR value of 0.8366. The comparative analysis of molecular substructures between natural anticarcinogens and nonanticarcinogens partially unveils several key substructures that drive anticancerous activities. We also deploy the proposed ensemble model as an online web server with a user-friendly interface to support the research community in identifying natural products with anticancer activities.

iCYP-MFE: Identifying Human Cytochrome P450 Inhibitors Using Multitask Learning and Molecular Fingerprint-Embedded Encoding.

The human cytochrome P450 (CYP) superfamily holds responsibilities for the metabolism of both endogenous and exogenous compounds such as drugs, cellular metabolites, and toxins. The inhibition exerted on the CYP enzymes is closely associated with adverse drug reactions encompassing metabolic failures and induced side effects. In modern drug discovery, identification of potential CYP inhibitors is, therefore, highly essential. Alongside experimental approaches, numerous computational models have been proposed to address this biochemical issue. In this study, we introduce iCYP-MFE, a computational framework for virtual screening on CYP inhibitors toward 1A2, 2C9, 2C19, 2D6, and 3A4 isoforms. iCYP-MFE contains a set of five robust, stable, and effective prediction models developed using multitask learning incorporated with molecular fingerprint-embedded features. The results show that multitask learning can remarkably leverage useful information from related tasks to promote global performance. Comparative analysis indicates that iCYP-MFE achieves three predominant tasks, one equivalent task, and one less effective task compared to state-of-the-art methods. The area under the receiver operating characteristic curve (AUC-ROC) and the area under the precision-recall curve (AUC-PR) were two decisive metrics used for model evaluation. The prediction task for CYP2D6-inhibition achieves the highest AUC-ROC value of 0.93 while the prediction task for CYP1A2-inhibition obtains the highest AUC-PR value of 0.92. The substructural analysis preliminarily explains the nature of the CYP-inhibitory activity of compounds. An online web server for iCYP-MFE with a user-friendly interface was also deployed to support scientific communities in identifying CYP inhibitors.

Digital Health Technologies to Improve Medication Adherence and Treatment Outcomes in Patients With Tuberculosis: Systematic Review of Randomized Controlled Trials.

BACKGROUND: Nonadherence to medication in tuberculosis (TB) hampers optimal treatment outcomes. Digital health technology (DHT) seems to be a promising approach to managing problems of nonadherence to medication and improving treatment outcomes. OBJECTIVE: This paper systematically reviews the effect of DHT in improving medication adherence and treatment outcomes in patients with TB. METHODS: A literature search in PubMed and Cochrane databases was conducted. Randomized controlled trials (RCTs) that analyzed the effect of DHT interventions on medication adherence outcomes (treatment completion, treatment adherence, missed doses, and noncompleted rate) and treatment outcomes (cure rate and smear conversion) were included. Adult patients with either active or latent TB infection were included. The Jadad score was used for evaluating the study quality. The PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guideline was followed to report study findings. RESULTS: In all, 16 RCTs were selected from 552 studies found, and 6 types of DHT interventions for TB were identified: 3 RCTs examined video directly observed therapy (VDOT), 1 examined video-observed therapy (VOT), 1 examined an ingestible sensor, 1 examined phone call reminders, 2 examined medication monitor boxes, and 8 examined SMS text message reminders. The outcomes used were treatment adherence, including treatment completion, treatment adherence, missed dose, and noncompleted rate, as well as clinical outcomes, including cure rate and smear conversion. In treatment completion, 4 RCTs (VDOT, VOT, ingestible sensor, SMS reminder) found significant effects, with odds ratios and relative risks (RRs) ranging from 1.10 to 7.69. Treatment adherence was increased in 1 study by SMS reminders (RR 1.05; 95% CI 1.04-1.06), and missed dose was reduced in 1 study by a medication monitor box (mean ratio 0.58; 95% CI 0.42-0.79). In contrast, 3 RCTs of VDOT and 3 RCTs of SMS reminders did not find significant effects for treatment completion. Moreover, no improvement was found in treatment adherence in 1 RCT of VDOT, missed dose in 1 RCT of SMS reminder, and noncompleted rate in 1 RCT of a monitor box, and 2 RCTs of SMS reminders. For clinical outcomes such as cure rate, 2 RCTs reported that phone calls (RR 1.30; 95% CI 1.07-1.59) and SMS reminders (OR 2.47; 95% CI 1.13-5.43) significantly affected cure rates. However, 3 RCTs found that SMS reminders did not have a significant impact on cure rate or smear conversion. CONCLUSIONS: It was found that DHT interventions can be a promising approach. However, the interventions exhibited variable effects regarding effect direction and the extent of improving TB medication adherence and clinical outcomes. Developing DHT interventions with personalized feedback is required to have a consistent and beneficial effect on medication adherence and outcomes among patients with TB.

Development and Validation of a Scoring System to Predict Severe Acute Lower Gastrointestinal Bleeding in Vietnamese.

BACKGROUND/AIMS: The prevalence of acute lower gastrointestinal bleeding (ALGIB) has progressively increased worldwide but there are few studies in Asian populations. This study aimed to develop and validate a scoring system to predict severe ALGIB in Vietnamese. METHODS: Risk factors for severe ALGIB were identified by multiple logistic regression analysis using data from a retrospective cohort of 357 patients admitted to a tertiary hospital. These factors were weighted to develop the severe acute lower gastrointestinal bleeding (SALGIB) score to predict severe ALGIB. The performance of SALGIB was validated in a prospective cohort of 324 patients admitted to 6 other hospitals using area under the receiver operating characteristics curve (AUC) analysis. RESULTS: There were four factors at admission independently associated with severe ALGIB in the derivation cohort: heart rate ≥ 100/min, systolic blood pressure < 100 mmHg, hematocrit < 35%, and platelets ≤ 150 × 103/µL. The SALGIB score determined severe ALGIB with AUC values of 0.91 and 0.86 in the derivation and validation cohorts, respectively. A SALGIB score < 2 associated with low risk of severe ALGIB in both cohorts (3.7% and 1.2%; respectively). CONCLUSIONS: The SALGIB score has good performance in discriminating risk of severe ALGIB in Vietnamese.

Na+ and/or Cl- Toxicities Determine Salt Sensitivity in Soybean (Glycine max (L.) Merr.), Mungbean (Vigna radiata (L.) R. Wilczek), Cowpea (Vigna unguiculata (L.) Walp.), and Common Bean (Phaseolus vulgaris L.).

Grain legumes are important crops, but they are salt sensitive. This research dissected the responses of four (sub)tropical grain legumes to ionic components (Na+ and/or Cl-) of salt stress. Soybean, mungbean, cowpea, and common bean were subjected to NaCl, Na+ salts (without Cl-), Cl- salts (without Na+), and a "high cation" negative control for 57 days. Growth, leaf gas exchange, and tissue ion concentrations were assessed at different growing stages. For soybean, NaCl and Na+ salts impaired seed dry mass (30% of control), more so than Cl- salts (60% of control). All treatments impaired mungbean growth, with NaCl and Cl- salt treatments affecting seed dry mass the most (2% of control). For cowpea, NaCl had the greatest adverse impact on seed dry mass (20% of control), while Na+ salts and Cl- salts had similar intermediate effects (~45% of control). For common bean, NaCl had the greatest adverse effect on seed dry mass (4% of control), while Na+ salts and Cl- salts impaired seed dry mass to a lesser extent (~45% of control). NaCl and Na+ salts (without Cl-) affected the photosynthesis (Pn) of soybean more than Cl- salts (without Na+) (50% of control), while the reverse was true for mungbean. Na+ salts (without Cl-), Cl- salts (without Na+), and NaCl had similar adverse effects on Pn of cowpea and common bean (~70% of control). In conclusion, salt sensitivity is predominantly determined by Na+ toxicity in soybean, Cl- toxicity in mungbean, and both Na+ and Cl- toxicity in cowpea and common bean.

Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease.

The novel coronavirus (SARS-CoV-2) has infected several million people and caused thousands of deaths worldwide since December 2019. As the disease is spreading rapidly all over the world, it is urgent to find effective drugs to treat the virus. The main protease (Mpro) of SARS-CoV-2 is one of the potential drug targets. Therefore, in this context, we used rigorous computational methods, including molecular docking, fast pulling of ligand (FPL), and free energy perturbation (FEP), to investigate potential inhibitors of SARS-CoV-2 Mpro. We first tested our approach with three reported inhibitors of SARS-CoV-2 Mpro, and our computational results are in good agreement with the respective experimental data. Subsequently, we applied our approach on a database of ∼4600 natural compounds, as well as 8 available HIV-1 protease (PR) inhibitors and an aza-peptide epoxide. Molecular docking resulted in a short list of 35 natural compounds, which was subsequently refined using the FPL scheme. FPL simulations resulted in five potential inhibitors, including three natural compounds and two available HIV-1 PR inhibitors. Finally, FEP, the most accurate and precise method, was used to determine the absolute binding free energy of these five compounds. FEP results indicate that two natural compounds, cannabisin A and isoacteoside, and an HIV-1 PR inhibitor, darunavir, exhibit a large binding free energy to SARS-CoV-2 Mpro, which is larger than that of 13b, the most reliable SARS-CoV-2 Mpro inhibitor recently reported. The binding free energy largely arises from van der Waals interaction. We also found that Glu166 forms H-bonds to all of the inhibitors. Replacing Glu166 by an alanine residue leads to ∼2.0 kcal/mol decreases in the affinity of darunavir to SARS-CoV-2 Mpro. Our results could contribute to the development of potential drugs inhibiting SARS-CoV-2.

Plant Metabolite Databases: From Herbal Medicines to Modern Drug Discovery.

Traditional herbal medicine has been an inseparable part of the traditional medical science in many countries throughout history. Nowadays, the popularity of using herbal medicines in daily life, as well as clinical practices, has gradually expanded to numerous Western countries with positive impacts and acceptance. The continuous growth of the herbal consumption market has promoted standardization and modernization of herbal-derived products with present pharmacological criteria. To store and extensively share this knowledge with the community and serve scientific research, various herbal metabolite databases have been developed with diverse focuses under the support of modern advances. The advent of these databases has contributed to accelerating research on pharmaceuticals of natural origins. In the scope of this study, we critically review 30 herbal metabolite databases, discuss different related perspectives, and provide a comparative analysis of 18 accessible noncommercial ones. We hope to provide you with fundamental information and multidimensional perspectives from herbal medicines to modern drug discovery.

Gold nanorod/molybdenum sulfide core-shell nanostructures synthesized by a photo-induced reduction process.

Coupling of plasmonic nanostructures and semiconductors gives promising hybrid nanostructures that can be used in different applications such as photosensing and energy conversion. In this report, we describe an approach for fabricating a new hybrid material by coupling a gold nanorod (Au NR) core and amorphous molybdenum sulfide (MoSx) shell. The Au NR/MoSx core-shell structure is achieved by exploiting the hot electrons generated in the plasmonic excitation of Au NRs to drive the reduction of [MoS4]2-, which is pre-adsorbed on the Au NR surface, producing a thin MoSx layer. This approach allows us to control the thickness of the MoSx coating layer on the Au NR surface. The resultant Au NR/MoSx hybrid is characterized by absorption spectroscopy, scanning electron microscopy, transmission electron microscopy, energy-dispersive x-ray spectroscopy elemental mapping, x-ray diffraction and x-ray photoelectron spectroscopy.

Structural and functional analysis of a dimeric fumarylacetoacetate hydrolase (EaFAH) from psychrophilic Exiguobacterium antarcticum.

Fumarylacetoacetate hydrolase (FAH) is essential for the degradation of aromatic amino acids as well as for the cleavage of carbon-carbon bonds in metabolites or small organic compounds. Here, the X-ray crystal structure of EaFAH, a dimeric fumarylacetoacetate hydrolase from Exiguobacterium antarcticum, was determined, and its functional properties were investigated using biochemical methods. EaFAH adopts a mixed ß-sandwich roll fold with a highly flexible lid region (Val73-Leu94), and an Mg2+ ion is bound at the active site by coordinating to the three carboxylate oxygen atoms of Glu124, Glu126, and Asp155. The hydrolytic activity of EaFAH toward various substrates, including linalyl acetate was investigated using native polyacrylamide gel electrophoresis, activity staining, gel filtration, circular dichroism spectroscopy, fluorescence, and enzyme assays.

Insights into the Electrochemical Polymerization of [Mo3 S13 ]2- Generating Amorphous Molybdenum Sulfide.

Amorphous molybdenum sulfide is an attractive electrode material for Li/Mg batteries and an efficient Pt-free catalyst for the hydrogen evolution reaction in water. By using the electrochemical quartz crystal microbalance (EQCM) analysis, new insights were gained into the electrochemical polymerization of the [Mo3 S13 ]2- cluster, which generates amorphous molybdenum sulfide thin films. In this work, it is shown that, at the anodic potential, a two-electron oxidative elimination of the terminal disulfide ligand within the [Mo3 S13 ]2- cluster induces the polymerization. A reductive elimination of the terminal disulfide ligand also occurs at the cathodic potential, inducing the polymerization. However, in sharp contrast to the anodic polymerization, according to which the film growth is rapid, the cathodic polymerization competes with the electrochemical reductive corrosion of the readily grown film, therefore occurring at a significant lower growth rate.

Characterization and mutation anaylsis of a cold-active bacterial hormone-sensitive lipase from Salinisphaera sp. P7-4.

In mammals, hormone sensitive lipase (EC 3.1.1.79, HSL) catalyzes the hydrolysis of triacylglycerols as well as the modifications of a broad range of hydrophobic substrates containing ester linkages. HSLs are composed of an N-terminal ligand-binding domain and a C-terminal catalytic domain. Bacterial hormone-sensitive lipases (bHSLs), which are homologous to the C-terminal domain of mammalian HSLs, have a catalytic triad composed of Ser, His, and Asp. Here, a novel cold-active hormone-sensitive lipase (SaHSL) from Salinisphaera sp. P7-4 was identified, functionally characterized, and subjected to site-directed mutations. The enzymatic properties of SaHSL were investigated using several biochemical and biophysical methods. Interestingly, SaHSL exhibited the ability to act on a broad range of substrates including glyceryl tributyrate and glucose pentaacetate. Homology modeling and site-directed mutagenesis indicated that hydrophobic residues (Leu156, Phe164, and Val204) around the substrate-binding pocket were involved in substrate recognition. In addition, highly conserved amino acids (Glu201, Arg207, Leu208, and Asp227) in the regulatory regions were found to be responsible for substrate specificity, thermostability, and enantioselectivity. In summary, this work provides new insights into the understanding of the C-terminal domain of HSL family and evidence that SaHSL can be used in a wide range of industrial applications.

Structural and functional characterization of a novel cold-active S-formylglutathione hydrolase (SfSFGH) homolog from Shewanella frigidimarina, a psychrophilic bacterium.

BACKGROUND: S-Formylglutathione is hydrolyzed to glutathione and formate by an S-formylglutathione hydrolase (SFGH) (3.1.2.12). This thiol esterase belongs to the esterase family and is also known as esterase D. SFGHs contain highly conserved active residues of Ser-Asp-His as a catalytic triad at the active site. Characterization and investigation of SFGH from Antarctic organisms at the molecular level is needed for industrial use through protein engineering. RESULTS: A novel cold-active S-formylglutathione hydrolase (SfSFGH) from Shewanella frigidimarina, composed of 279 amino acids with a molecular mass of ~ 31.0 kDa, was characterized. Sequence analysis of SfSFGH revealed a conserved pentapeptide of G-X-S-X-G found in various lipolytic enzymes along with a putative catalytic triad of Ser148-Asp224-His257. Activity analysis showed that SfSFGH was active towards short-chain esters, such as p-nitrophenyl acetate, butyrate, hexanoate, and octanoate. The optimum pH for enzymatic activity was slightly alkaline (pH 8.0). To investigate the active site configuration of SfSFGH, we determined the crystal structure of SfSFGH at 2.32 Å resolution. Structural analysis shows that a Trp182 residue is located at the active site entrance, allowing it to act as a gatekeeper residue to control substrate binding to SfSFGH. Moreover, SfSFGH displayed more than 50% of its initial activity in the presence of various chemicals, including 30% EtOH, 1% Triton X-100, 1% SDS, and 5 M urea. CONCLUSIONS: Mutation of Trp182 to Ala allowed SfSFGH to accommodate a longer chain of substrates. It is thought that the W182A mutation increases the substrate-binding pocket and decreases the steric effect for larger substrates in SfSFGH. Consequently, the W182A mutant has a broader substrate specificity compared to wild-type SfSFGH. Taken together, this study provides useful structure-function data of a SFGH family member and may inform protein engineering strategies for industrial applications of SfSFGH.

VIETHERB: A Database for Vietnamese Herbal Species.

Vietnam carries a highly diverse practice of traditional medicine in which various combinations of herbs have been widely used as remedies for many types of diseases. Poor hand-written records and current text-based databases, however, perplex the process of conventionalizing and evaluating canonical therapeutic effects. In efforts to reorganize the valuable information, we provide the VIETHERB database ( http://vietherb.com.vn/ ) for herbs documented in Vietnamese traditional medicines. This database is constructed with confidence to provide users with information on herbs and other side information including metabolites, diseases, morphologies, and geographical locations for each individual species. Our data in this release consist of 2,881 species, 10,887 metabolites, 458 geographical locations, and 8,046 therapeutic effects. The numbers of species-metabolite, species-therapeutic effect, species-morphology, and species-distribution binary relationships are 17,602, 2,718, 11,943, and 16,089, respectively. The information on Vietnamese herbal species can be easily accessed or queried using their scientific names. Searching for species sharing side information can be simply done by clicking on the data. The database primarily serves as an open source facilitating users in studies of modernizing traditional medicine, computer-aided drug design, conservation of endangered plants, and other relevant experimental sciences.

Effects of inter-organism interactions in biofouling on microtopographic surfaces.

An extended model of the surface energetic attachment (SEA) model is introduced to study the fouling of marine organisms on microtopographic surfaces, taking into account the excluded volume interaction and the attraction between the organisms. It is shown that the excluded volume interaction leads to changes in the site-typed attachment probabilities which increase with the average spore density on the surface. As a result of these changes, the spore density map is flattened under very high density fouling. The attractive interaction on the other hand leads to aggregation of spores and the average aggregate size increased with the strength of attraction. The model can be mapped to a specific experiment to determine the attachment energy parameters. In contrast to various prior empirical approaches, the extended SEA model is rigorous from the statistical mechanics viewpoint, thus it provides a reliable tool for studying complex attachment behaviors of microorganisms on topographic surfaces.

Characterization and Immobilization of a Novel SGNH Family Esterase (LaSGNH1) from Lactobacillus acidophilus NCFM.

The SGNH family esterases are highly effective biocatalysts due to their strong catalytic efficiencies, great stabilities, relatively small sizes, and ease of immobilization. Here, a novel SGNH family esterase (LaSGNH1) from Lactobacillus acidophilus NCFM, which has homologues in many Lactobacillus species, was identified, characterized, and immobilized. LaSGNH1 is highly active towards acetate- or butyrate-containing compounds, such as p-nitrophenyl acetate or 1-naphthyl acetate. Enzymatic properties of LaSGNH1, including thermal stability, optimum pH, chemical stability, and urea stability, were investigated. Interestingly, LaSGNH1 displayed a wide range of substrate specificity that included glyceryl tributyrate, tert-butyl acetate, and glucose pentaacetate. Furthermore, immobilization of LaSGNH1 by crosslinked enzyme aggregates (CLEAs) showed enhanced thermal stability and efficient recycling property. In summary, this work paves the way for molecular understandings and industrial applications of a novel SGNH family esterase (LaSGNH1) from Lactobacillus acidophilus.