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The mechanical properties and bioactive motif densities of extracellular matrix materials play crucial roles in regulating cell behaviors, such as cell adhesion, migration, proliferation, and differentiation. However, current studies on cellular responses to ECM predominantly concentrated on polymer hydrogels featuring a single factor, such as the mechanical strength, the types of bioactive motifs, and the morphology of the polymers. This limited focus may overlook the complex interplay of multiple factors. Here, we developed dual gradient peptide Q 3 GT-I 3 K hydrogels with tunable mechanical strength (0.3–4.0 kPa) and different density of bioactive motif (0.45–3.67 mM) by enzymatic crosslinking. These hydrogels can mimic the viscoelasticity of natural soft tissues. The properties of mechanical strength and cell responsive motif density could be controlled by modulating the proportion of the substrates in the enzymatic reaction. MC3T3 cells significantly differentiated into osteoblasts after seeded on the Q 3 GT-I 3 K hydrogel (2.8 kPa, 1.83 mM Q 3 GT) for 21 days, identifying from the elevated expression of alkaline phosphatase and substantial calcium nodule formation. Importantly, the engineered hydrogels exert a synergistic effect on the cell behaviors such as early adhesion, late proliferation, and differentiation of MC3T3-E1 cells. This paper introduces a new strategy for designing tissue engineering scaffold materials with specific functions. • Q 3 GT-I 3 K hydrogel with adjustable mechanical strength and bioactive density were prepared by TGase crosslinking. • Q 3 GT-I 3 K hydrogel have similar viscoelastic properties to natural soft tissues, control osteoblast differentiation. • Mechanical strength and bioactive density of Q 3 GT-I 3 K hydrogel exhibit a synergistic effect on MC3T3-E1 cell differentiation. [ABSTRACT FROM AUTHOR]

[Display omitted] • Covers the principles, benefits and drawbacks of three commonly used phage display systems. • Highlights the phage display derived probes in biosensing. • Summarizes the more recently foodborne detection techniques based on phage-displayed biosensors. • Discusses the current status and further research opportunities of on phage display-based biosensing systems. Food-and water-borne pathogens play a significant role in food safety concerns. Detecting a low quantity of pathogens in food presents a challenge due to the limited availability of recognition molecules. Consequently, there is a pressing necessity to diversify the range of bio-recognition elements. Phage display technology (PDT) allows for the screening of probes, such as antibodies, peptides, and nanobodies, with high affinity and specificity for the target, enabling brilliant nanoprobes for a wide range of diagnostic or biosensing scaffolds. Moreover, by engaging methods such as chemical modification, microfluidic technology, high-throughput pipeline design, and genetic engineering, it is possible to effectively functionalize these ligands for use in detecting pathogenic bacteria with enhanced sensitivity and selectivity. This study primarily summaries the essential principles of phage biology that are frequently utilized in phage display vectors, expands the structure procedure of phage display nanobody library, phage display antibody library, and phage display peptide library. From the perspective of analytes, this paper outlines the innovative phage display-based biosensors developed between 2022 and 2024 for detecting various microorganisms in food products. Ultimately, some challenges and perspectives are offered in this field. [ABSTRACT FROM AUTHOR]

Coregonus peled is rich in protein and is a plentiful resource of bioactive peptides. This study was aimed at extracting novel Angiotensin I-converting enzyme (ACE) inhibitory peptides from Coregonus peled and revealing their potential hypotensive mechanisms. This paper screened six ACE inhibitory peptides with high bioactivity, good water solubility, and ADMET properties by computerized enzyme digestion of myosin-heavy chain from Coregonus peled , and LCYPR had the greatest ACE inhibition activity (IC 50 = 47.8782 μM). There were 47 potentially critical targets of LCYPR for hypertension treatment, involving 135 biological processes (BP), 30 cellular components (CC), and 30 molecular functions (MF). The results of KEGG pathway analyse showed that the LCYPR participated in 50 pathways including the renin-angiotensin system, renin secretion, lipid and atherosclerosis, relaxin signaling pathway, IL-17 signaling pathway, atherosclerosis, fluid shear stress, and others, through the key targets such as AGT, AKT1, ACE, REN, CTSB, STAT3, PLG, SRC, MMP2, and F2 to regulate the blood pressure of organisms. In conclusion, the study obtained a novel ACE inhibitory peptide from the myosin-heavy chain of Coregonus peled and revealed the potential target and pathway of LCYPR to improve hypertension. The study provides new ideas and methods for developing novel antihypertensive peptides. The results provide a theoretical basis for developing functional foods of the Xinjiang specialty cold-water fish. [ABSTRACT FROM AUTHOR]

The global public health risk posed by Salmonella Kentucky (S. Kentucky) is rising, particularly due to the dissemination of antimicrobial resistance genes in human and animal populations. This serovar, widespread in Africa, has emerged as a notable cause of non-typhoidal gastroenteritis in humans. In this study, we used a bioinformatics approach to develop a peptide-based vaccine targeting epitopes from the outer membrane proteins A, C, and F of S. Kentucky. Additionally, we employed flagellin protein (fliC) from Salmonella Typhimurium (S. Typhimurium) as an adjuvant to enhance the vaccine's effectiveness. Through this approach, we identified 14 CD8+ and 7 CD4+ T-cell epitopes, which are predicted to be restricted by various MHC class I and MHC class II alleles. The predicted epitopes are expected to achieve a population coverage of 94.91% when used in vaccine formulations. Furthermore, we identified seven highly immunogenic linear B-cell epitopes and three conformational B-cell epitopes. These T-cell and B-cell epitopes were then linked using appropriate linkers to create a multi-epitope vaccine (MEV). To boost the immunogenicity of the peptide construct, fliC from S. Typhimurium was included at the N-terminal. The resulting MEV construct demonstrated high structural quality and favorable physicochemical properties. Molecular docking studies with Toll-like receptors 1, 2, 4, and 5, followed by molecular dynamic simulations, suggested that the vaccine-receptor complexes are energetically feasible, stable, and robust. Immune simulation results showed that the MEV elicited significant responses, including IgG, IgM, CD8+ T-cells, CD4+ T-cells, and various cytokines (IFN-γ, TGF-β, IL-2, IL-10, and IL-12), along with a noticeable reduction in antigen levels. Despite these promising in-silico findings, further validation through preclinical and clinical trials is required to confirm the vaccine's efficacy and safety. [ABSTRACT FROM AUTHOR]

Cyclic compounds are generally preferred over linear compounds for functional studies due to their enhanced bioavailability, stability towards metabolic degradation, and selective receptor binding. This has led to a need for effective cyclization strategies for compound synthesis and hence increased interest in macrocyclization mediated by thioesterase (TE) domains, which naturally boost the chemical diversity and bioactivities of cyclic natural products. Many non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) derived natural products are assembled to form cyclodimeric compounds, with these molecules possessing diverse structures and biological activities. There is significant interest in identifying the biosynthetic pathways that produce such molecules given the challenge that cyclodimerization represents from a biosynthetic perspective. In the last decade, many groups have pursued the characterization of TE domains and have provided new insights into this biocatalytic machinery: however, the enzymes involved in formation of cyclodimeric compounds have proven far more elusive. In this review we focus on natural products that involve macrocyclization in their biosynthesis and chemical synthesis, with an emphasis on the function and biosynthetic investigation on the special family of TE domains responsible for forming cyclodimeric natural products. We also introduce additional macrocyclization catalysts, including butelase and the CT-mediated cyclization of peptides, alongside the formation of cyclodipeptides mediated by cyclodipeptide synthases (CDPS) and single-module NRPSs. Due to the interdisciplinary nature of biosynthetic research, we anticipate that this review will prove valuable to synthetic chemists, drug discovery groups, enzymologists, and the biosynthetic community in general, and inspire further efforts to identify and exploit these biocatalysts for the formation of novel bioactive molecules. [ABSTRACT FROM AUTHOR]

Background: Jianwei Xiaoshi oral liquid (JWXS), a classical traditional prescription comprising various edible medicinal plants, has demonstrated significant efficacy in treating paediatric indigestion. It originates from Jianpi Pill, which is developed in the Ming Dynasty and nourishes the spleen and regulates gastrointestinal function. However, the specific molecular mechanisms involved remain unclear. Methods: To elucidate the material base of JWXS and its underlying mechanism in treating dyspepsia, the UHPLC–Q–Orbitrap HRMS method and network pharmacology were utilized. This was followed by pharmacological experiments, transcriptomics analyses and gut microbiota studies to further investigate the effects of JWXS on dyspepsia. Results: A total of 105 compounds, mainly flavonoids, alkaloids, organic acids and cyclic peptides, were identified. According to the five principles of generic drug properties, 43 candidate compounds were screened out. Their efficacy was verified through gastric emptying and intestinal propulsion experiments. Transcriptomic analysis revealed that JWXS primarily alleviated dyspepsia symptoms by regulating the secretion of 8 key proteins in the pancreatic secretion pathway. The differences in the gut microbiota, as identified through 16S rRNA and ITS2 sequencing, were subsequently more pronounced than those observed in the bacterial microbiota of the model group. In total, 15 differential bacteria and 16 differential fungi were identified. Targeted metabolomics analysis of SCFAs revealed a significant decrease in valeric acid (VA), acetic acid (AA), and isovaleric acid (IVA) levels in the model group, which were restored to the corresponding levels after the administration of JWXS. Correlation analysis revealed that VA, AA, and IVA were positively correlated with Lactobacillus and Bacteroides, and negatively correlated with Aspergillus and Candida. This further suggested that JWXS might alleviate symptoms of indigestion by regulating the composition of the microbiota, increasing the variety and quantity of beneficial bacteria, reducing fungal contamination, and further increasing the levels of SCFAs in the body. Conclusion: JWXS improved functional dyspepsia in immature rats via a mechanism involving the regulation of the secretion of 8 key proteins in the pancreatic secretion pathway and the amelioration of flora disorders. [ABSTRACT FROM AUTHOR]

Methodological developments in biomedical research are currently moving towards single-cell approaches. This allows for a much better spatial and functional characterization of, for example, the deterioration of cells within a tissue in response to noxae. However, subcellular resolution is also essential to elucidate whether observed impairments are driven by an explicit organelle. Here, we use the Single Cellome™ System SS2000 (Yokogawa) to investigate the local effects of Aβ plaque-like deposits (characteristic for Alzheimer's disease) on mitochondria in the mouse microglial cell line SIM-A9. First, the specificity of subcellular extraction is demonstrated by detecting subcellular staining and RT-qPCR concerning marker genes by comparing nuclear and mitochondrial samples. Oxygen consumption and gene expression is then assessed in cells near and far from peptide deposits. Mostly, all analyses confirm the high specificity and integrity of the sampled material. In addition, impact of the peptide deposits occur concerning spatial distribution of the cells: e.g., oxygen consumption is only reduced in cells close to Aβ deposits but not in proximity to deposits of biologically inactive Aβ (scrambled) or in far distance. Moreover, a distance-related gene expression pattern occurs, demonstrating the local initiation of mitochondrial changes of microglia when approaching toxic peptide deposits. Aspiration of cellular content accompanied by confocal microscope-usage within the SS2000 allows investigation of organelle-enriched fractions and sheds light on selective effects of Aβ peptides. [ABSTRACT FROM AUTHOR]

The antimicrobial peptide (AMP) circularized bacteriocin enterocin AS-48 produced by Enterococcus sp. exhibits broad-spectrum antibacterial activity via dimer insertion into the plasma membrane to form membrane pore structures, compromising membrane integrity and leading to bactericidal activity. A specific alpha-helical region of enterocin AS-48 has been shown to be responsible for the membrane-penetrating activity of the peptide. The canon syn-enterocin peptide library, generated using rational design techniques to have ninety-five synthetic peptide variants from the truncated, linearized, membrane-interacting domain of enterocin AS-48, was screened against three clinically relevant fungal strains: Cryptococcus neoformans , Candida albicans , and Candida auris for potential antifungal activity. Twelve peptides exhibited antifungal activity against C. neoformans , and two peptides exhibited activity against C. albicans. The fourteen active antifungal peptides were minimally cytotoxic to an immortalized human keratinocyte cell line (HaCats). Four select peptides were identified with minimum inhibitory concentrations (MICs) below 8 µM against C. neoformans. In 36-hour cell growth tests with these fungicidal peptides, fungicidal peptide no. 32 displayed inhibitory properties comparable to the leading antifungal medication fluconazole against C. neoformans. Screening of peptide no. 32 against a deletion library of C. neoformans mutants revealed that the mechanism of action of peptide no. 32 may relate to multivesicular bodies (MVBs) or polysaccharide capsule targeting. These findings importantly demonstrate that naturally derived AMPs produced by bacteria can be sourced, engineered, and modified to exhibit potent antifungal activity. Our results will contribute to the development of broad treatment alternatives to fungal infections and lend themselves to direct implications for possible treatment options for C. neoformans infections. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has exposed a number of key challenges that need to be urgently addressed. Mass spectrometric studies of blood plasma proteomics provide a deep understanding of the relationship between the severe course of infection and activation of specific pathophysiological pathways. Analysis of plasma proteins in whole blood may also be relevant for the pandemic as it requires minimal sample preparation. The frozen whole blood samples were used to analyze 203 plasma proteins using multiple reaction monitoring (MRM) mass spectrometry and stable isotope-labeled peptide standards (SIS). A total of 131 samples (FRCC, Russia) from patients with mild (n=41), moderate (n=39) and severe (n=19) COVID-19 infection and healthy controls (n=32) were analyzed. Levels of 94 proteins were quantified and compared. Significant differences between all of the groups were revealed for 44 proteins. Changes in the levels of 61 reproducible COVID-19 markers (SERPINA3, SERPING1, ORM1, HRG, LBP, APOA1, AHSG, AFM, ITIH2, etc.) were consistent with studies performed with serum/plasma samples. The best-performing classifier built with 10 proteins achieved the best combination of ROC-AUC (0.97–0.98) and accuracy (0.90–0.93) metrics and distinguished patients from controls, as well as patients by severity. Here, for the first time, frozen whole blood samples were used for proteomic analysis and assessment of the status of patients with COVID-19. The results obtained with frozen whole blood samples are consistent with those from plasma and serum. [ABSTRACT FROM AUTHOR]