Hasil untuk "Biotechnology"

Anirudh R. Urs, Varshini Ganesan Selvi, Ananya Sreekumar et al.

Abstract In silico toxicity prediction tools have become indispensable in early drug development for assessing safety risks. However, their reported predictive performance is rarely evaluated against independent experimental datasets. In this study, we systematically benchmark four widely used free, web-based toxicity predictors– ProTox, pkCSM, ADMETLab, and vNN-ADMET across experimentally validated hepatotoxicity, cardiotoxicity (hERG inhibition), nephrotoxicity, blood–brain barrier (BBB) permeability, and mutagenicity (AMES) endpoints using gold-standard datasets, including DILIrank, hERG Central, DIRIL, B3DB, and the ISSTOX Chemical Toxicity database. Tool-reported endpoint-specific performance metrics were first analyzed and subsequently compared against externally benchmarked predictions generated on independent compound sets. Model performance was evaluated using accuracy, precision, recall, F1 score, specificity, and Matthews Correlation Coefficient (MCC). Our results reveal pronounced discrepancies between tool-reported and benchmarked performance across multiple endpoints, indicating limited generalizability of several models beyond their original training and validation domains. While ProTox and vNN-ADMET demonstrated strong reported performance across endpoints, only mutagenicity predictions remained consistently robust under benchmarking conditions (F1 > 0.89; MCC > 0.80). ProTox achieved the highest benchmarked performance for hepatotoxicity (F1 = 0.92; MCC = 0.84), whereas ADMETLab showed balanced recall-driven performance for nephrotoxicity and cardiotoxicity but exhibited reduced specificity for hepatotoxicity, suggesting overprediction. In contrast, BBB permeability and nephrotoxicity emerged as the most challenging endpoints, with substantial performance degradation relative to reported metrics and consistently low MCC values across tools. Overall, no single tool demonstrated uniform reliability across all toxicity endpoints when evaluated on independent datasets. These findings underscore the limitations of relying solely on tool reported performance and highlight the necessity of endpoint aware benchmarking in in-silico toxicity screening. This study provides actionable guidance for tool selection in early drug discovery and supports future development of ensemble and applicability domain aware models to improve predictive robustness and translational relevance.

K.B. Baidakova, Y.P. Kucheryavyi, D.S. Korolova

Aim. To develop collagen matrices with increased hemostatic properties and to evaluate their effectiveness in comparison with commercial products. Methods. Collagen was obtained from calfskin by acid hydrolysis, identified by SDS-PAGE, and sterilized in an autoclave. The enzymatic clotting activator was purified from Echis multisquamatis venom by ion exchange chromatography. The activity of the activator was evaluated with the chromogenic substrate S2302. Ready-made modified matrices were obtained by lyophilization. Hemostatic efficacy was tested in the Wistar Han rat hepatic hemorrhage model, compared with commercial materials. Results. Optimal concentrations of collagen (300 μg/cm²) and enzyme activator (10 μg/cm²) were selected for the manufacture of collagen matrices with increased hemostatic properties. Studies on the rat parenchymal bleeding model showed that these matrices provide faster bleeding control compared to commercial hemostatic materials. After the removal of collagen matrices, bleeding did not resume. Conclusions. The developed collagen matrices with increased hemostatic properties demonstrate high efficiency, stable clot formation, and minimal risk of rebleeding, which confirms their prospects in surgery.

Zaher Abdel Baki, Sahar H. Abourida, Adnan Badran et al.

Bread is an indispensable staple food and a great source of complex carbohydrates, making it a potential product for fortification. The purpose of this study was to investigate the sensory, antioxidant, and nutritional properties of bread fortified with sumac (Rhus coriaria) and cactus (Opuntia ficus-indica L.) seed powder. Different levels (4, 6, and 8% w/w flour replacement) of the powdered seeds were used. Fortified bread samples were compared to control (unfortified) bread and evaluated for their moisture, nutritional composition (protein, fat, fiber, ash, carbohydrates, and energy value), sensory preference, total phenolic content (TPC), and antioxidant activity (2,2-diphenyl-1-picrylhydrazyl assay). The antioxidant capacity and TPC were significantly higher (p<0.05) for sumac- and cactus-fortified bread samples compared to the control. Nutritionally, fortification significantly increased fiber and fat content while decreasing carbohydrate content and energy value (p<0.05); protein content remained relatively stable. Sensory evaluation showed a preference for sumac-fortified bread, particularly at lower concentrations. Moisture content was significantly lower in fortified samples. This study demonstrates that fortification, particularly with 8% sumac, yielded favorable results concerning antioxidant activity, phenolic content, and sensory preference, alongside notable changes in nutritional composition.

Brandi Brown, Mark Wilkins, Rajib Saha

Ana Sosa-Fajardo, Cristian Díaz-Muñoz, David Van der Veken et al.

Abstract Background Staphylococcus shinii appears as an umbrella species encompassing several strains of Staphylococcus pseudoxylosus and Staphylococcus xylosus. Given its phylogenetic closeness to S. xylosus, S. shinii can be found in similar ecological niches, including the microbiota of fermented meats where the species may contribute to colour and flavour development. In addition to these conventional functionalities, a biopreservation potential based on the production of antagonistic compounds may be available. Such potential, however, remains largely unexplored in contrast to the large body of research that is available on the biopreservative properties of lactic acid bacteria. The present study outlines the exploration of the genetic basis of competitiveness and antimicrobial activity of a fermented meat isolate, S. shinii IMDO-S216. To this end, its genome was sequenced, de novo assembled, and annotated. Results The genome contained a single circular chromosome and eight plasmid replicons. Focus of the genomic exploration was on secondary metabolite biosynthetic gene clusters coding for ribosomally synthesized and posttranslationally modified peptides. One complete cluster was coding for a bacteriocin, namely lactococcin 972; the genes coding for the pre-bacteriocin, the ATP-binding cassette transporter, and the immunity protein were also identified. Five other complete clusters were identified, possibly functioning as competitiveness factors. These clusters were found to be involved in various responses such as membrane fluidity, iron intake from the medium, a quorum sensing system, and decreased sensitivity to antimicrobial peptides and competing microorganisms. The presence of these clusters was equally studied among a selection of multiple Staphylococcus species to assess their prevalence in closely-related organisms. Conclusions Such factors possibly translate in an improved adaptation and competitiveness of S. shinii IMDO-S216 which are, in turn, likely to improve its fitness in a fermented meat matrix.

Tung Nguyen-Thanh, Phuong-Thao Nguyen-Vu, Quy-Anh Le-Thi et al.

The objective of this meta-analysis was to evaluate the association between maternal and fetal genetic variants and the risk of preeclampsia, a pregnancy-related condition that affects women. Despite the unclear role of these genetic factors in the development of preeclampsia, this analysis aimed to provide insights into the potential contributing factors. An electronic search of online databases was conducted to identify relevant studies. Stata SE software was used for the meta-analysis. A random-effects model was used to establish the association between the genetic variants and preeclampsia risk. Egger’s test was utilized to evaluate publication bias. Ten observational studies were selected from databases that met the inclusion criteria and included seven genes and twenty polymorphisms to analyze preeclampsia susceptibility influenced by the genetic background of both the mother and fetus. Our meta-analysis revealed that both the maternal and fetal polymorphisms, FLT1 rs4769613, were significantly associated with the risk of preeclampsia. However, the association between the maternal ACE rs4646994 polymorphism and preeclampsia risk was not statistically significant. Nevertheless, a significant association was observed between the fetal ACE rs4646994 polymorphism and preeclampsia in a dominant genetic model. In this study, the associations between maternal and fetal polymorphisms in ERAP2, VEGF, VDR, REN, and MMP were not statistically significant. According to the available evidence, maternal and fetal polymorphisms can impact the likelihood of developing preeclampsia. Additional research is required to fully understand the underlying mechanisms connecting maternal and fetal polymorphisms to preeclampsia, and to formulate recommendations for screening pregnant women based on these genetic variations.

Ekaterina Petushkova, Makhmadyusuf Khasimov, Ekaterina Mayorova et al.

The purple sulfur bacterium <i>Thiocapsa roseopersicina</i> BBS is interesting from both fundamental and practical points of view. It possesses a thermostable HydSL hydrogenase, which is involved in the reaction of reversible hydrogen activation and a unique reaction of sulfur reduction to hydrogen sulfide. It is a very promising enzyme for enzymatic hydrogenase electrodes. There are speculations that HydSL hydrogenase of purple bacteria is closely related to sulfur metabolism, but confirmation is required. For that, the full genome sequence is necessary. Here, we sequenced and assembled the complete genome of this bacterium. The analysis of the obtained whole genome, through an integrative approach that comprised estimating the Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (DDH) parameters, allowed for validation of the systematic position of <i>T. roseopersicina</i> as <i>T. bogorovii</i> BBS. For the first time, we have assembled the whole genome of this typical strain of a new bacterial species and carried out its functional description against another purple sulfur bacterium: <i>Allochromatium vinosum</i> DSM 180T. We refined the automatic annotation of the whole genome of the bacteria <i>T. bogorovii</i> BBS and localized the genomic positions of several studied genes, including those involved in sulfur metabolism and genes encoding the enzymes required for the TCA and glyoxylate cycles and other central metabolic pathways. Eleven additional genes coding proteins involved in pigment biosynthesis was found.

Abida Abida, Mikhlid H. Almutairi, Nadia Mushtaq et al.

Melissa H. Pecundo, Tao Chen, Thomas Edison E. dela Cruz et al.

Heterocyte-forming cyanobacteria form symbiotic relationships with several lineages of plants. Here, twenty (20) strains of endosymbiotic cyanobacteria (cyanobionts) with <i>Nostoc</i>-like morphologies were isolated from the highly specialized coralloid roots of five host species in Cycadales—<i>Cycas debaoensis</i>, <i>C. fairylakea</i>, <i>C. elongata</i>, <i>Ceratozamia robusta</i>, and <i>Macrozamia moorei</i>. Molecular phylogeny based on the 16S rRNA gene placed these strains into seven different taxa within the Nostocaceae, specifically under the genera <i>Desmonostoc</i> and <i>Dendronalium</i>. The percent dissimilarity and unique patterns in the secondary structures of the D1-D1′, Box-B, V2, and V3 helices, which were based on the 16S–23S rRNA internal transcribed spacer (ITS) regions, supported three distinct species in <i>Desmonostoc</i>. These three morphologically distinct novel species are described in this report: <i>Desmonostoc debaoense</i> sp. nov., <i>Desmonostoc meilinense</i> sp. nov., and <i>Desmonostoc xianhuense</i> sp. nov. Other investigated strains were phylogenetically identified as members of the recently discovered genus <i>Dendronalium</i> and represent the first report of association of that genus with cycads. Our findings suggest that the order Cycadales hosts diverse species of cyanobionts in their coralloid roots and that many potential unreported or novel taxa are present in cycads occurring in their natural habitat and await discovery.

Marian O. Pacho, Dylan Deeney, Emily A. Johnson et al.

There has been profound growth in the use of 3D printed materials in dentistry in general, including orthodontics. The opportunity to impart antimicrobial properties to 3D printed parts from existing resins requires the capability of forming a stable colloid incorporating antimicrobial fillers. The objective of this research was to characterize a colloid consisting of a 3D printable resin mixed with Ag-ion releasing zeolites and fumed silica to create 3D printed parts with antiviral properties. The final composite was tested for antiviral properties against SARS-CoV-2 and HIV-1. Antiviral activity was measured in terms of the half-life of SARS-CoV-2 and HIV-1 on the composite surface. The inclusion of the zeolite did not interfere with the kinetics measured on the surface of the ATR crystal. While the depth of cure, measured following ISO4049 guidelines, was reduced from 3.8 mm to 1.4 mm in 5 s, this greatly exceeded the resolution required for 3D printing. The colloid was stable for at least 6 months and the rheological behavior was dependent upon the fumed silica loading. The inclusion of zeolites and fumed silica significantly increased the flexural strength of the composite as measured by a 3 point bend test. The composite released approximately 2500 μg/L of silver ion per gram of composite as determined by potentiometry. There was a significant reduction of the average half-life of SARS-CoV-2 (1.9 fold) and HIV-1 (2.7 fold) on the surface of the composite. The inclusion of Ag-ion releasing zeolites into 3D-printable resin can result in stable colloids that generate composites with improved mechanical properties and antiviral properties.

Wei Li, Ruixin Du, Chuanhui Xia et al.

Gonadotropin-releasing hormone (GnRH), as a vital hypothalamic neuropeptide, was a key regulator for pituitary luteinizing hormone (LH) and follicle-stimulating hormone (FSH) in the vertebrate. However, little is known about the other pituitary actions of GnRH in teleost. In the present study, two GnRH variants (namely, GnRH2 and GnRH3) and four GnRH receptors (namely, GnRHR1, GnRHR2, GnRHR3, and GnRHR4) had been isolated from grass carp. Tissue distribution displayed that GnRHR4 was more highly detected in the pituitary than the other three GnRHRs. Interestingly, ligand–receptor selectivity showed that GnRHR4 displayed a similar and high binding affinity for grass carp GnRH2 and GnRH3. Using primary culture grass carp pituitary cells as model, we found that both GnRH2 and GnRH3 could not only significantly induce pituitary reproductive hormone gene (GtHα, LHβ, FSHβ, INHBa, secretogranin-2) mRNA expression mediated by AC/PKA, PLC/IP3/PKC, and Ca2+/CaM/CaMK-II pathways but also reduce dopamine receptor 2 (DRD2) mRNA expression via the Ca2+/CaM/CaMK-II pathway. Interestingly, GnRH2 and GnRH3 could also stimulate anorexigenic peptide (POMCb, CART2, UTS1, NMBa, and NMBb) mRNA expression via AC/PKA, PLC/IP3/PKC, and Ca2+/CaM/CaMK-II pathways in grass carp pituitary cells. In addition, food intake could significantly induce brain GnRH2 mRNA expression. These results indicated that GnRH should be the coupling factor to integrate the feeding metabolism and reproduction in teleost.

Bhaskar Jyoti Borah, Chi-Kuang Sun

Summary: A resonant-scanning multiphoton optical microscope (MPM) with a millimeter-scale field-of-view (FOV) often encounters a poor Nyquist figure-of-merit (NFOM), leading to an aliasing effect owing to limited effective voxel-sampling rate. In this protocol, we provide a design guideline to enable high-NFOM MPM imaging while simultaneously securing a large FOV/digital-resolution ratio and a fast resonant raster-scanning speed. We further provide a free version of our custom acquisition software to assist with a smooth and easy construction process.For complete details on the use and execution of this protocol, please refer to Borah et al. (2021).

Verónica Marcillo-Parra, Mayra Anaguano, Maritza Molina et al.

Mango peel is gaining recognition for its nutritional and functional value. This by-product shows variable composition depending on different factors such as variety, stage maturity, and geographic site of production. This work sought to evaluate mango peel composition, bioactive compound content, antioxidant activity, and carotenoid and phenolic profiles for the three most commercial varieties of the equatorial region using UV–Vis spectroscopy, HPLC, and UPLC. Significant differences (p < 0.05) were found between all varieties regarding the content of bioactive compounds. Total phenolic, flavonoid, and carotenoid content ranged from 2930 to 6624 mg GAE/100 g, 502–795 mg CE/100 g, and 3.7–5.7 mg/100 g, respectively. A high positive correlation (r = 0.961) between the phenolic content and ABTS radical-scavenging activity was found for all samples. β-Carotene and lutein were identified and quantified, the samples of cvs. Haden and Kent showed the highest β-carotene content (8 mg/100 g). Gallic acid and rutin were identified in all samples, whereas mangiferin had the highest amount (314 mg/100 g) in cv. Tommy Atkins. The results suggest that mango peel has bioactive compounds with significant antioxidant properties, which can be used as functional ingredients in different industrial products.

An-Ni Zhang, Jeffry M. Gaston, Chengzhen L. Dai et al.

Antibiotic resistance genes are common but not all are of high risk to human health. Here, the authors develop an omics-based framework for ranking genes by risk that incorporates level of enrichment in human associated environments, gene mobility, and host pathogenicity.

Leenu Reinsalu, Leenu Reinsalu, Marju Puurand et al.

Metabolic plasticity is the ability of the cell to adjust its metabolism to changes in environmental conditions. Increased metabolic plasticity is a defining characteristic of cancer cells, which gives them the advantage of survival and a higher proliferative capacity. Here we review some functional features of metabolic plasticity of colorectal cancer cells (CRC). Metabolic plasticity is characterized by changes in adenine nucleotide transport across the outer mitochondrial membrane. Voltage-dependent anion channel (VDAC) is the main protein involved in the transport of adenine nucleotides, and its regulation is impaired in CRC cells. Apparent affinity for ADP is a functional parameter that characterizes VDAC permeability and provides an integrated assessment of cell metabolic state. VDAC permeability can be adjusted via its interactions with other proteins, such as hexokinase and tubulin. Also, the redox conditions inside a cancer cell may alter VDAC function, resulting in enhanced metabolic plasticity. In addition, a cancer cell shows reprogrammed energy transfer circuits such as adenylate kinase (AK) and creatine kinase (CK) pathway. Knowledge of the mechanism of metabolic plasticity will improve our understanding of colorectal carcinogenesis.

Ling Gao, Xiaodan Wu, Xiaole Xia et al.

Summary The very high concentrations required for industrial production of free acetic acid create toxicity and low pH values, which usually conflict with the host cell growth, leading to a poor productivity. Achieving a balance between cell fitness and product synthesis is the key challenge to improving acetic acid production efficiency in metabolic engineering. Here, we show that the synergistic regulation of alcohol/aldehyde dehydrogenase expression and cofactor PQQ level could not only efficiently relieve conflict between increased acetic acid production and compromised cell fitness, but also greatly enhance acetic acid tolerance of Acetobacter pasteurianus to a high initial concentration (3% v/v) of acetic acid. Combinatorial expression of adhA and pqqABCDE greatly shortens the duration of starting‐up process from 116 to 99 h, leading to a yield of 69 g l‐1 acetic acid in semi‐continuous fermentation. As a final result, average acetic acid productivity has been raised to 0.99 g l‐1 h‐1, which was 32% higher than the parental A. pasteurianus. This study is of great significance for decreasing cost of semi‐continuous fermentation for producing high‐strength acetic acid industrially. We envisioned that this strategy will be useful for production of many other desired organic acids, especially those involving cofactor reactions.

Subin Kim, Jinhyo Chung, Sang Hyun Lee et al.

Abstract Influenza, one of the most contagious and infectious diseases, is predominantly transmitted through aerosols, leading to the development of filter-based protective equipment. Though the currently available filters are effective at removing submicron-sized particulates, filter materials with enhanced virus-capture efficiency are still in demand. Coating or chemically modifying filters with molecules capable of binding influenza viruses has received attention as a promising approach for the production of virus-capturing filters. For this purpose, tannic acid (TA), a plant-derived polyphenol, is a promising molecule for filter functionalization because of its antiviral activities and ability to serve as a cost-efficient adhesive for various materials. This study demonstrates the facile preparation of TA-functionalized high-efficiency particulate air (HEPA) filter materials and their efficiency in influenza virus capture. Polypropylene HEPA filter fabrics were coated with TA via a dipping/washing process. The TA-functionalized HEPA filter (TA-HF) exhibits a high in-solution virus capture efficiency of up to 2,723 pfu/mm2 within 10 min, which is almost two orders of magnitude higher than that of non-functionalized filters. This result suggests that the TA-HF is a potent anti-influenza filter that can be used in protective equipment to prevent the spread of pathogenic viruses.

Jerica Sabotič, Jože Brzin, Jana Erjavec et al.

Ralstonia solanaceraum is the quarantine plant pathogenic bacterium that causes bacterial wilt in over 200 host plants, which include economically important crops such as potato, tomato, tobacco, banana, and ginger. Alternative biological methods of disease control that can be used in integrated pest management are extensively studied. In search of new proteins with antibacterial activity against R. solanacearum, we identified L-amino acid oxidases (LAOs) from fruiting bodies of Amanita phalloides (ApLAO) and Infundibulicybe geotropa (CgLAO). We describe an optimized isolation procedure for their biochemical characterization, and show that they are dimeric proteins with estimated monomer molecular masses of 72 and 66 kDa, respectively, with isoelectric point of pH 6.5. They have broad substrate specificities for hydrophobic and charged amino acids, with highest Km for L-Leu, and broad pH optima at pH 5 and pH 6, respectively. An enzyme with similar properties is also characterized from the mycelia of I. geotropa (CgmycLAO). Fractionated aqueous extracts of 15 species of mushrooms show that LAO activity against L-Leu correlates with antibacterial activity. We confirm that the LAO activities mediate the antibacterial actions of ApLAO, CgLAO, and CgmycLAO. Their antibacterial activities are greater against Gram-negative versus Gram-positive bacteria, with inhibition of growth rate, prolongation of lag-phase, and decreased endpoint biomass. In Gram-positive bacteria, they mainly prolong the lag phase. These in vitro antibacterial activities of CgLAO and CgmycLAO are confirmed in vivo in tomato plants, while ApLAO has no effect on disease progression in planta. Transmission electron microscopy shows morphological changes of R. solanacearum upon LAO treatments. Finally, broad specificity of the antibacterial activities of these purified LAOs were seen for in vitro screening against 14 phytopathogenic bacteria. Therefore, these fungal LAOs show great potential as new biological phytoprotective agents and show the fruiting bodies of higher fungi to be a valuable source of antimicrobials with unique features.