Structural and Biochemical Analysis of Butanol Dehydrogenase From Thermotoga maritima.

Butanol dehydrogenase (BDH) plays a crucial role in butanol biosynthesis by catalyzing the conversion of butanal to butanol using the coenzyme NAD(P)H. In this study, we observed that BDH from Thermotoga maritima (TmBDH) exhibits dual coenzyme specificity and catalytic activity with NADPH as the coenzyme under highly alkaline conditions. Additionally, a thermal stability analysis on TmBDH demonstrated its excellent activity retention even at elevated temperatures of 80°C. These findings demonstrate the superior thermal stability of TmBDH and suggest that it is a promising candidate for large-scale industrial butanol production. Furthermore, we discovered that TmBDH effectively catalyzes the conversion of aldehydes to alcohols and exhibits a wide range of substrate specificities toward aldehydes, while excluding alcohols. The dimeric state of TmBDH was observed using rapid online buffer exchange native mass spectrometry. Additionally, we analyzed the coenzyme-binding sites and inferred the possible locations of the substrate-binding sites. These results provide insights that improve our understanding of BDHs.

Deciphering vimentin assembly: Bridging theoretical models and experimental approaches.

The intricate assembly process of vimentin intermediate filaments (IFs), key components of the eukaryotic cytoskeleton, has yet to be elucidated. In this work, we investigated the transition from soluble tetrameric vimentin units to mature 11-nm tubular filaments, addressing a significant gap in the understanding of IF assembly. Through a combination of theoretical modeling and analysis of experimental data, we propose a novel assembly sequence, emphasizing the role of helical turns and gap filling by soluble tetramers. Our findings shed light on the unique structural dynamics of vimentin and suggest broader implications for the general principles of IF formation.

Large-area grown ultrathin molybdenum oxides for label-free sensitive biomarker detection.

The rise of two-dimensional (2D) materials has provided a confined geometry and yielded methods for guiding electrons at the nanoscale level. 2D material-enabled electronic devices can interact and transduce the subtle charge perturbation and permit significant advancement in molecule discrimination technology with high accuracy, sensitivity, and specificity, leaving a significant impact on disease diagnosis and health monitoring. However, high-performance biosensors with scalable fabrication ability and simple protocols have yet to be fully realized due to the challenges in wafer-scale 2D film synthesis and integration with electronics. Here, we propose a molybdenum oxide (MoOx)-interdigitated electrode (IDE)-based label-free biosensing chip, which stands out for its wafer-scale dimension, tunability, ease of integration and compatibility with the complementary metal-oxide-semiconductor (CMOS) fabrication. The device surface is biofunctionalized with monoclonal anti-carcinoembryonic antigen antibodies (anti-CEA) via the linkage agent (3-aminopropyl)triethoxysilane (APTES) for carcinoembryonic antigen (CEA) detection and is characterized step-by-step to reveal the working mechanism. A wide range and real-time response of the CEA concentration from 0.1 to 100 ng mL-1 and a low limit of detection (LOD) of 0.015 ng mL-1 were achieved, meeting the clinical requirements for cancer diagnosis and prognosis in serum. The MoOx-IDE biosensor also demonstrates strong surface affinity towards molecules and high selectivity using L-cysteine (L-Cys), glycine (Gly), glucose (Glu), bovine serum albumin (BSA), and immunoglobulin G (IgG). This study showcases a simple, scalable, and low-cost strategy to create a nanoelectronic biosensing platform to achieve high-performance cancer biomarker discrimination capabilities.

The NADPH oxidase inhibitor diphenyleneiodonium suppresses Ca2+ signaling and contraction in rat cardiac myocytes.

Diphenyleneiodonium (DPI) has been widely used as an inhibitor of NADPH oxidase (Nox) to discover its function in cardiac myocytes under various stimuli. However, the effects of DPI itself on Ca2+ signaling and contraction in cardiac myocytes under control conditions have not been understood. We investigated the effects of DPI on contraction and Ca2+ signaling and their underlying mechanisms using video edge detection, confocal imaging, and whole-cell patch clamp technique in isolated rat cardiac myocytes. Application of DPI suppressed cell shortenings in a concentration-dependent manner (IC50 of ≅0.17 µM) with a maximal inhibition of ~70% at ~100 µM. DPI decreased the magnitude of Ca2+ transient and sarcoplasmic reticulum Ca2+ content by 20%-30% at 3 µM that is usually used to remove the Nox activity, with no effect on fractional release. There was no significant change in the half-decay time of Ca2+ transients by DPI. The L-type Ca2+ current (ICa) was decreased concentration-dependently by DPI (IC50 of ≅40.3 µM) with ≅13.1%-inhibition at 3 µM. The frequency of Ca2+ sparks was reduced by 3 µM DPI (by ~25%), which was resistant to a brief removal of external Ca2+ and Na+. Mitochondrial superoxide level was reduced by DPI at 3-100 µM. Our data suggest that DPI may suppress L-type Ca2+ channel and RyR, thereby attenuating Ca2+-induced Ca2+ release and contractility in cardiac myocytes, and that such DPI effects may be related to mitochondrial metabolic suppression.

The prevalence of Pfk13 polymorphism in malaria patients treated with artemisinin-based therapy: a systematic review and meta-analysis.

Artemisinin (ART) combination therapy is the main treatment for malaria. Pfk13 mutations (or K13 mutations, Kelch 13) are associated with ART resistance. This study aims to conduct a systematic review and meta-analysis of the prevalence of K13 mutations with ART resistance in malaria-endemic countries. An electronic search of studies in 2018 and a manual search in 2020 were performed to identify relevant studies. The risk of bias was assessed using the National Institutes of Health (NIH) quality assessment tool for observational cohort and cross-sectional studies. Data analysis was performed using R 4.1.0. Heterogeneity was estimated using the statistic I2 and Cochran Q test. A total of 170 studies were included in our review. Of these, 55 studies investigated the prevalence of K13 mutations in Southeast Asia. The meta-analysis showed that Southeast Asia had the highest prevalence of K13 mutations, whereas Africa, South America, Oceania, and other Asian countries outside Southeast Asia had a low prevalence of K13 mutations. The C580Y mutation was the most common in Southeast Asia with 35.5% (95%CI: 25.4-46.4%), whereas the dominant mutation in Africa was K189T (22.8%, 95%CI: 7.6-43.2%). This study revealed the emergence of ART resistance associated with K13 mutations in Southeast Asia. The diversity of each type of K13 mutation in other regions was also reported.

Complementary hydrophobic interaction of the redox enzyme maturation protein NarJ with the signal peptide of the respiratory nitrate reductase NarG.

In bacteria, NarJ plays an essential role as a redox enzyme maturation protein in the assembly of the nitrate reductase NarGHI by interacting with the N-terminal signal peptide of NarG to facilitate cofactor incorporation into NarG. The purpose of our research was to elucidate the exact mechanism of NarG signal peptide recognition by NarJ. We determined the structures of NarJ alone and in complex with the signal peptide of NarG via X-ray crystallography and verified the NarJ-NarG interaction through mutational, binding, and molecular dynamics simulation studies. NarJ adopts a curved α-helix bundle structure with a U-shaped hydrophobic groove on its concave side. This groove accommodates the signal peptide of NarG via a dual binding mode in which the left and right parts of the NarJ groove each interact with two consecutive hydrophobic residues from the N- and C-terminal regions of the NarG signal peptide, respectively, through shape and chemical complementarity. This binding is accompanied by unwinding of the helical structure of the NarG signal peptide and by stabilization of the NarG-binding loop of NarJ. We conclude that NarJ recognizes the NarG signal peptide through a complementary hydrophobic interaction mechanism that mediates a structural rearrangement.

LiOtBu-promoted synthesis of bis(3-indolyl)methanes by the alkylation of indoles with alcohols under air.

Bis(3-indolyl)methanes (BIMs) are known for their important bioactivities, which include anti-cancer, anti-inflammatory, antibacterial, and antioxidant properties. In this study, we are disclosing a metal catalyst-free synthesis of BIMs in high yields via the alkylation reaction of indoles and alcohols in the presence of lithium tert-butoxide base. Notably, oxygen in air played an important role as an oxidant for the facilitation of this transformation. Interestingly, unactivated aliphatic alcohols could be successfully used as alkylating reagents in the alkylation reactions of indole. Especially, several chemical intermediates detected by GC-MS gave important information about the mechanism insights. This method demonstrated cost and environmental advantages for the development of green processes.

CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs.

Analyzing the interactions of circular RNAs (circRNAs) is a crucial step in understanding their functional impacts. While there are numerous visualization tools available for investigating circRNA interaction networks, these tools are typically limited to known circRNAs from specific databases. Moreover, these existing tools usually require complex installation procedures which can be time-consuming and challenging for users. There is a lack of a user-friendly web application that facilitates interactive exploration and visualization of circRNA interaction networks. CircNetVis is an interactive online web application to enhance the analysis of human/mouse circRNA interactions. The tool allows three different input formats of circRNAs including circRNA IDs from CircBase, circRNA coordinates (chromosome, start position, end position), and circRNA sequences in the FASTA format. It integrates multiple interaction networks for visualization and investigation of the interplay between circRNA, microRNAs, mRNAs and RNA binding proteins. CircNetVis also enables users to interactively explore the interactions of unknown circRNAs which are not reported from previous databases. The tool can generate interactive plots and allows users to save results as output files for offline usage. CircNetVis is implemented as a web application using R-shiny and freely available for academic use at https://www.meb.ki.se/shiny/truvu/CircNetVis/ .

The discriminative role of PROX-1 immunohistochemistry between venous malformation and lymphatic malformation of the deep type with no visible diagnostic surface skin lesion.

BACKGROUND: Venous malformations (VMs) are distinguished from lymphatic malformations (LMs) when specific diagnostic skin lesions are present. In the deep type, this is difficult by clinico-radiologic evaluation alone. We aimed to investigate the usefulness of lymphatic vessel endothelial cell (LEC) markers for the differential diagnosis of the deep VMs and LMs. METHODS: A retrospective study was conducted based on the medical records of patients with VMs and LMs who underwent biopsy with both D2-40 and PROX-1 immunohistochemistry. We compared the initial clinico-radiological diagnosis with the final pathological diagnosis and identified which ones showed a difference. RESULTS: From 261 patients who had VMs and LMs, 111 remained after the exclusion of those who showed definite surface diagnostic features. After pathological diagnosis with the expressions of D2-40 and PROX-1, 38 of 111 (34.2%) patients' final diagnoses were changed. Among these 38 cases, diagnosis was not changed by D2-40 positivity alone, but changed by PROX-1 positivity alone (52.6%) or by both (47.4%). The diagnostic changes were more frequent in the deep category (43.7%) than in the superficial category. CONCLUSIONS: Identifying the expression of D2-40, and especially PROX-1, in the differential diagnosis of VMs and LMs may provide important treatment guidelines and understanding their natural course.

Long-term water level dynamics in the Red River basin in response to anthropogenic activities and climate change.

Understanding the regular variations in water levels and identifying the potential drivers under the combined pressures of anthropogenic activities and climate change can offer valuable insights into riverine management. In this study, we analyzed long-term daily observational data, including water levels and water discharge, spanning from the ~1950s to 2021 at seven gauging stations within the Red River basin. We investigated the spatiotemporal variation in mean water levels using standard analytical tools, including the Mann-Kendall (MK) test, rating curves, and Empirical Orthogonal Function (EOF). Specifically, we observed a notable and substantial decline in water levels downstream of the major tributaries, including Da, Red, and Lo Rivers, as well as at their confluence, starting at the end of 2008. Notably, a strong correlation between water levels and discharge is found, highlighting the pivotal role of discharge in influencing water levels. Surprisingly, relationships between water levels and climatic factors such as rainfall and air temperature proved less influential. This suggests that water levels are predominantly shaped by discharge and anthropogenic activities, rather than climate change. The study emphasized the substantial impact of human-induced activities, particularly dam operation and sand mining, on downstream water levels in the Red River basin. An intriguing finding revealed that upstream dynamics, particularly at the Hoa Binh dam, led to significant water level increases with the same discharge, attributed to channel deposition and reservoir water storage. The research's novelty is the comprehensive evaluation of long-term water level trends and its elucidation of the combined effects of anthropogenic activities and climate change, offering valuable insights for riverine management and emphasizing the influence of anthropogenic factors, notably dam regulation and sand mining, in driving shifts in water levels.

Structural and Functional Analyses of the Flavoprotein Disulfide Reductase FN0820 of Fusobacterium nucleatum.

Escherichia coli RclA and Staphylococcus aureus MerA are part of the Group I flavoprotein disulfide reductase (FDR) family and have been implicated in the contribution to bacterial pathogenesis by defending against the host immune response. Fusobacterium nucleatum is a pathogenic, anaerobic Gram-negative bacterial species commonly found in the human oral cavity and gastrointestinal tract. In this study, we discovered that the F. nucleatum protein FN0820, belonging to the Group I FDR family, exhibited a higher activity of a Cu2+-dependent NADH oxidase than E. coli RclA. Moreover, FN0820 decreased the dissolved oxygen level in the solution with higher NADH oxidase activity. We found that L-tryptophan and its analog 5-hydroxytryptophan inhibit the FN0820 activities of NADH oxidase and the concomitant reduction of oxygen. Our results have implications for developing new treatment strategies against pathogens that defend the host immune response with Group I FDRs.

A novel hydrogel-based moisturizing cream composed of hyaluronic acid for patients with xerosis: An intraindividual comparative analysis.

BACKGROUND: Hyaluronic acid (HA) is mainly used to treat xerosis. It also exerts wound-healing, moisturizing, and antiaging effects. Although HA is considered an effective and safe ingredient in cosmetics, there is a constant demand for a more money-saving and effective formulation. This study aimed to evaluate the safety and efficacy of a novel hydrogel-based moisturizer containing HA cross-linked with silicone polymers, produced solely through irradiation without the use of cross-linking agents. MATERIALS AND METHODS: A safety study enrolled 30 participants with healthy skin to perform patch and photopatch tests while recording adverse events. For the efficacy study, 30 participants with xerosis were compared before and after using the novel hydrogel, evaluating the cutaneous barrier function, xerosis severity scale (XSS) score, participant's satisfaction, and Investigator's Global Assessment (IGA). Furthermore, the efficacy of the novel hydrogel-based moisturizer was evaluated by comparing it with a conventional moisturizer, Physiogel, in another 30 participants with xerosis. RESULTS: In the safety study, no serious adverse events were observed. In the efficacy study before and after use, skin hydration and skin surface lipid increased (p < 0.05) whereas the XSS scores decreased (p < 0.05) with time. In the comparative efficacy study with Physiogel, skin hydration increased whereas the XSS scores decreased (p < 0.05) over time in both groups. Furthermore, IGA improved in 100% of participants in both groups. Also, 100% and 93% of participants were satisfied with the novel hydrogel-based moisturizer and Physiogel, respectively. CONCLUSIONS: The novel hydrogel-based moisturizer proved to be safe and effective for xerosis, showing comparable results to the conventional moisturizer.

In depth characterization of midbrain organoids derived from wild type iPSC lines.

The ability to model human neurological tissues in vitro has been a major hurdle to effective drug development for neurological disorders. iPSC-derived brain organoids have emerged as a compelling solution to this problem as they have the potential to relevantly model the protein expression pattern and physiology of specific brain regions. Although many protocols now exist for the production of brain organoids, few attempts have been made to do an in-depth kinetic evaluation of expression of mature regiospecific markers of brain organoids. To address this, we differentiated midbrain-specific brain organoids from iPSC-lines derived from three apparently healthy individuals using a matrix-free, bioreactor method. We monitored the expression of midbrain-specific neuronal markers from 7 to 90-days using immunofluorescence and immunohistology. The organoids were further characterized using electron microscopy and RNA-seq. In addition to serving as a potential benchmark for the future evaluation of other differentiation protocols, the markers observed in this study can be useful as control parameters to identify and evaluate the disease phenotypes in midbrain organoid derived from patient iPSC-lines with genetic neurological disorders.

Copper Oxide Spike Grids for Enhanced Solution Transfer in Cryogenic Electron Microscopy.

The formation of uniform vitreous ice is a crucial step in the preparation of samples for cryogenic electron microscopy (cryo-EM). Despite the rapid technological progress in EM, controlling the thickness of vitreous ice on sample grids with reproducibility remains a major obstacle to obtaining high-quality data in cryo-EM imaging. The commonly employed classical blotting process faces the problem of excess water that cannot be absorbed by the filter paper, resulting in the formation of thick and heterogeneous ice. In this study, we propose a novel approach that combines the recently developed nanowire self-wicking technique with the classical blotting method to effectively control the thickness and homogeneity of vitrified ice. With simple procedures, we generated a copper oxide spike (COS) grid by inducing COSs on commercially available copper grids, which can effectively remove excess water during the blotting procedure without damaging the holey carbon membrane. The ice thickness could be controlled with good reproducibility compared to non-oxidized grids. Incorporated into other EM techniques, our new modification method is an effective option for obtaining high-quality data during cryo-EM imaging.

Analysis of human invasive cytotrophoblasts demonstrates mosaic aneuploidy.

A total of 24 chromosome-specific fluorescence in situ hybridization probes for interphase nucleus analysis were developed to determine the chromosomal content of individual human invasive cytotrophoblasts derived from in vitro cultured assays. At least 75% of invasive cytotrophoblasts were hyperdiploid and the total number of chromosomes ranged from 47 to 61. The results also demonstrated that these hyperdiploid invasive cytotrophoblasts showed significant heterogeneity. The most copy number gains were observed for chromosomes 13, 14, 15, 19, 21, and 22 with average copy number greater than 2.3. A parallel study using primary invasive cytotrophoblasts also showed a similar trend of copy number changes. Conclusively, 24-chromosome analysis of human non-proliferating cytotrophoblasts (interphase nuclei) was achieved. Hyperdiploidy and chromosomal heterogeneity without endoduplication in invasive cytotrophoblasts may suggest a selective advantage for invasion and short lifespan during normal placental development.

Staphylococcus equorum plasmid pKS1030-3 encodes auxiliary biofilm formation and trans-acting gene mobilization systems.

The foodborne bacterium Staphylococcus equorum strain KS1030 harbours plasmid pSELNU1, which encodes a lincomycin resistance gene. pSELNU1 undergoes horizontal transfer between bacterial strains, thus spreading antibiotic resistance. However, the genes required for horizontal plasmid transfer are not encoded in pSELNU1. Interestingly, a relaxase gene, a type of gene related to horizontal plasmid transfer, is encoded in another plasmid of S. equorum KS1030, pKS1030-3. The complete genome of pKS1030-3 is 13,583 bp long and encodes genes for plasmid replication, biofilm formation (the ica operon), and horizontal gene transfer. The replication system of pKS1030-3 possesses the replication protein-encoding gene repB, a double-stranded origin of replication, and two single-stranded origins of replication. The ica operon, relaxase gene, and a mobilization protein-encoding gene were detected in pKS1030-3 strain-specifically. When expressed in S. aureus RN4220, the ica operon and relaxase operon of pKS1030-3 conferred biofilm formation ability and horizontal gene transfer ability, respectively. The results of our analyses show that the horizontal transfer of pSELNU1 of S. equorum strain KS1030 depends on the relaxase encoded by pKS1030-3, which is therefore trans-acting. Genes encoded in pKS1030-3 contribute to important strain-specific properties of S. equorum KS1030. These results could contribute to preventing the horizontal transfer of antibiotic resistance genes in food.

Lamin Filament Assembly Derived from the Atomic Structure of the Antiparallel Four-Helix Bundle.

The nucleoskeletal protein lamin is primarily responsible for the mechanical stability of the nucleus. The lamin assembly process requires the A11, A22, and ACN binding modes of the coiled-coil dimers. Although X-ray crystallography and chemical cross-linking analysis of lamin A/C have provided snapshots of A11 and ACN binding modes, the assembly mechanism of the entire filament remains to be explained. Here, we report a crystal structure of a coil 2 fragment, revealing the A22 interaction at the atomic resolution. The structure showed detailed structural features, indicating that two coiled-coil dimers of the coil 2 subdomain are separated and then re-organized into the antiparallel-four-helix bundle. Furthermore, our findings suggest that the ACN binding mode between coil 1a and the C-terminal part of coil 2 when the A11 tetramers are arranged by the A22 interactions. We propose a full assembly model of lamin A/C with the curvature around the linkers, reconciling the discrepancy between the in situ and in vitro observations. Our model accounts for the balanced elasticity and stiffness of the nuclear envelopes, which is essential in protecting the cellular nucleus from external pressure.