Ligand Binding Enhances Millisecond Conformational Exchange in Xylanase B2 from Streptomyces lividans.

Xylanases catalyze the hydrolysis of xylan, an abundant carbon and energy source with important commercial ramifications. Despite tremendous efforts devoted to the catalytic improvement of xylanases, success remains limited because of our relatively poor understanding of their molecular properties. Previous reports suggested the potential role of atomic-scale residue dynamics in modulating the catalytic activity of GH11 xylanases; however, dynamics in these studies was probed on time scales orders of magnitude faster than the catalytic time frame. Here, we used nuclear magnetic resonance titration and relaxation dispersion experiments ((15)N-CPMG) in combination with X-ray crystallography and computational simulations to probe conformational motions occurring on the catalytically relevant millisecond time frame in xylanase B2 (XlnB2) and its catalytically impaired mutant E87A from Streptomyces lividans 66. Our results show distinct dynamical properties for the apo and ligand-bound states of the enzymes. The apo form of XlnB2 experiences conformational exchange for residues in the fingers and palm regions of the catalytic cleft, while the catalytically impaired E87A variant displays millisecond dynamics only in the fingers, demonstrating the long-range effect of the mutation on flexibility. Ligand binding induces enhanced conformational exchange of residues interacting with the ligand in the fingers and thumb loop regions, emphasizing the potential role of residue motions in the fingers and thumb loop regions for recognition, positioning, processivity, and/or stabilization of ligands in XlnB2. To the best of our knowledge, this work represents the first experimental characterization of millisecond dynamics in a GH11 xylanase family member. These results offer new insights into the potential role of conformational exchange in GH11 enzymes, providing essential dynamic information to help improve protein engineering and design applications.

Prevalence and risk factors for carriage of antimicrobial-resistant Escherichia coli on household and small-scale chicken farms in the Mekong Delta of Vietnam.

OBJECTIVES: To describe the prevalence of antimicrobial resistance among commensal Escherichia coli isolates on household and small-scale chicken farms, common in southern Vietnam, and to investigate the association of antimicrobial resistance with farming practices and antimicrobial usage. METHODS: We collected data on farming and antimicrobial usage from 208 chicken farms. E. coli was isolated from boot swab samples using MacConkey agar (MA) and MA with ceftazidime, nalidixic acid or gentamicin. Isolates were tested for their susceptibility to 11 antimicrobials and for ESBL production. Risk factor analyses were carried out, using logistic regression, at both the bacterial population and farm levels. RESULTS: E. coli resistant to gentamicin, ciprofloxacin and third-generation cephalosporins was detected on 201 (96.6%), 191 (91.8%) and 77 (37.0%) of the farms, respectively. Of the 895 E. coli isolates, resistance to gentamicin, ciprofloxacin and third-generation cephalosporins was detected in 178 (19.9%), 291 (32.5%) and 29 (3.2%) of the isolates, respectively. Ciprofloxacin resistance was significantly associated with quinolone usage (OR = 2.26) and tetracycline usage (OR = 1.70). ESBL-producing E. coli were associated with farms containing fish ponds (OR = 4.82). CONCLUSIONS: Household and small farms showed frequent antimicrobial usage associated with a high prevalence of resistance to the most commonly used antimicrobials. Given the weak biocontainment, the high prevalence of resistant E. coli could represent a risk to the environment and to humans.

An Integrative Explainable Artificial Intelligence Approach to Analyze Fine-Scale Land-Cover and Land-Use Factors Associated with Spatial Distributions of Place of Residence of Reported Dengue Cases.

Dengue fever is a prevalent mosquito-borne disease that burdens communities in subtropical and tropical regions. Dengue transmission is ecologically complex; several environmental conditions are critical for the spatial and temporal distribution of dengue. Interannual variability and spatial distribution of dengue transmission are well-studied; however, the effects of land cover and use are yet to be investigated. Therefore, we applied an explainable artificial intelligence (AI) approach to integrate the EXtreme Gradient Boosting and Shapley Additive Explanation (SHAP) methods to evaluate spatial patterns of the residences of reported dengue cases based on various fine-scale land-cover land-use types, Shannon's diversity index, and household density in Kaohsiung City, Taiwan, between 2014 and 2015. We found that the proportions of general roads and residential areas play essential roles in dengue case residences with nonlinear patterns. Agriculture-related features were negatively associated with dengue incidence. Additionally, Shannon's diversity index showed a U-shaped relationship with dengue infection, and SHAP dependence plots showed different relationships between various land-use types and dengue incidence. Finally, landscape-based prediction maps were generated from the best-fit model and highlighted high-risk zones within the metropolitan region. The explainable AI approach delineated precise associations between spatial patterns of the residences of dengue cases and diverse land-use characteristics. This information is beneficial for resource allocation and control strategy modification.

Role of SnO2 Nanoparticles for a Self-Forming Barrier Layer on a Mild Steel Surface in Hydrochloric Acid Medium Containing Piper betle Leaf Extract.

The self-formation of a porous organic thin-film via corrosion inhibitor supports wide applications of carbon steel in industry. Unfortunately, serious damages could be concentrated to the pinhole and/or pore locations in the porous organic film, resulting in the localized corrosion even when an optimal concentration of organic corrosion inhibitors is used. In this work, SnO2 nanoparticles are used for producing the more robust barrier layer via the self-migration of nanoparticles, resulting in a higher corrosion resistance, smooth and uniform protective layer, as well as the existence of SnO2 in the protective layer that could directly affect the high inhibition performance. Therefore, the work suggests a new way to make a more robust thin film that could extend the use of organic corrosion inhibitors.

Onion-Ring-like Carbon and Nitrogen from ZIF-8 on TiO2/Fe2O3 Nanostructure for Overall Electrochemical Water Splitting.

The carbon and nitrogen derived from ZIF-8 embedded in TiO2/Fe2O3 (i.e., C,N-ZIF/TiFe) nanostructures exhibit superior electrocatalytic performance toward oxygen evolution reactions (OER), hydrogen evolution reactions (HER), and overall H2O splitting. The results showed that the C,N-ZIF/TiFe nanostructure was the best catalyst in comparison to ZIF/TiFe and TiFe nanostructures toward HER and OER. These results revealed that combining the highly active carbon and nitrogen from ZIF-8 with a TiO2/Fe2O3 semiconductor enriched the overall H2O splitting. A possible OER mechanism is attributed to some groups that support the surface active site of the catalyst and adsorbent intermediate species. Finally, this inexpensive electrocatalyst was synthesized without noble metals and showed superior electrocatalytic activity and great stability with the potential to achieve ground-breaking and novel applications in fuel cells.

Report on Unusual Sites of Lymph Node Metastases in Nasopharyngeal Carcinoma.

Nasopharyngeal carcinoma (NPC) is amongst the most common malignancies of head and neck cancers. Most patients are admitted to the hospital with advanced disease. NPC has a tendency toward early metastatic spread to cervical lymph nodes, and levels II and III are most commonly involved. A few reports have indicated specific metastatic sites of nasopharyngeal cancer, including lymph node metastasis and distant metastasis. Evidence of histopathology and immunohistochemistry is required to prove NPC origin. In many cases, surgery can be performed to obtain accurate evidence of the pathology. However, surgery can also affect the overall treatment plan and strategy for NPC and should be considered in the specific circumstances of the disease. Multidisciplinary consultation is required for these uncommonly specific metastases. Paying attention to the specific lymph node metastasis sites of NPC plays an important role in accurately diagnosing the stage, thereby giving an appropriate treatment strategy. It is also important in determining radiotherapy volumes because radiotherapy is the standard therapy for this disease. Herein, we are reporting 2 cases of NPC with clinical metastasis to unusual lymph node sites such as the parotid salivary gland and the cheek. Histological analyses from the resected specimens confirmed its nasopharyngeal origin. Lymph node metastases in the parotid gland and the cheek are unusual. In diagnosis and follow-up, it is necessary to evaluate carefully to make an accurate diagnosis and appropriate treatment plans for patients as well as early detect recurrent metastases at uncommon sites of lymph nodes.

Pyridinedicarboxylate-Tb(III) Complex-Based Luminescent Probes for ATP Monitoring.

The pyridinedicarboxylate-Tb(III) complexes, TbPDC and Tb(PDC)3, as luminescent probes for ATP monitoring have been conveniently prepared and characterized by FT-IR, 1H-NMR, ESI-MS, UV-Vis, excitation, and emission spectroscopy. Interestingly, these two Tb(III) complexes were quenched by ATP by a similar mechanism via π-π stacking interaction between the chelating ligand and adenine moiety. The ability of luminescent probes applied for the determination of ATP in aqueous solution has been investigated. The dynamic ranges for the quantification of ATP are within 10-90 µM and 10-100 µM with detection limits of 7.62 and 11.20 µM for TbPDC and Tb(PDC)3, respectively. The results demonstrated that these luminescent probes would be a potential candidate assay for ATP monitoring in hygiene assessment.

Combining chitinase C and N-acetylhexosaminidase from Streptomyces coelicolor A3(2) provides an efficient way to synthesize N-acetylglucosamine from crystalline chitin.

The enzymatic bioconversion of chitin is of considerable interest for the natural production of bioactive compounds such as chitooligosaccharides and N-acetyl-d-glucosamine (GlcNAc). Key enzymes are involved in the natural processing of chitin, hydrolyzing this abundant biopolymer to yield chitooligosaccharides with substantial value to the medicinal and biotechnological fields. In this study, chitinase C (ScChiC) from the soil bacterium and chitin decomposer Streptomyces coelicolor A3(2) was expressed, purified and characterized. We also optimized a Streptomyces lividans system generating ScChiC expression yields nearly 500-fold higher than the previously reported heterologous expression in Escherichia coli. The purified enzyme was found to be stable below 55°C for a broad range of pH values (pH 3.5-9) and exhibited high activity against chitin and chitooligosaccharides to form chitobiose (C2) as main product. Crab shell chitin hydrolysis profiles also revealed that ScChiC catalyzes the bioconversion of chitopolysaccharides through an endo-nonprocessive mode of action. When combining ScChiC with an N-acetylhexosaminidase from S. coelicolor A3(2) (ScHEX) in an assay using crude extracts and crystalline chitin as substrate, GlcNAc was generated as final product with a yield over 90% after 8h incubation. This chitin hydrolysis yield represents one of the most efficient enzyme bioconversion of chitopolysaccharides to GlcNAc characterized to date, making the S. coelicolor ScChiC-ScHEX pair a potentially suitable contender for the viable industrial production of this important bioactive compound.