Search Results (28,289)

Community detection in complex networks plays a pivotal role in modern scientific research, including in social network analysis and protein structure analysis. Traditional community detection methods face challenges in integrating heterogeneous multi-source information, capturing global semantic relationships, and adapting to dynamic network evolution. This paper proposes a novel unsupervised multimodal community detection algorithm (UMM) based on fractal iteration. The core idea is to design a dual-channel encoder that comprehensively considers node semantic features and network topological structures. Initially, node representation vectors are derived from structural information (using feature vectors when available, or singular value decomposition to obtain feature vectors for nodes without attributes). Subsequently, a parameter-free graph convolutional encoder (PFGC) is developed based on fractal iteration principles to extract high-order semantic representations from structural encodings without requiring any training process. Furthermore, a semantic–structural dual-channel encoder (DC-SSE) is designed, which integrates semantic encodings—reduced in dimensionality via UMAP—with structural features extracted by PFGC to obtain the final node embeddings. These embeddings are then clustered using the K-means algorithm to achieve community partitioning. Experimental results demonstrate that the UMM outperforms existing methods on multiple real-world network datasets. Full article

The use of Botulinum Neurotoxin A (BoNT/A) to treat peripheral neuropathic pain from nerve injury has garnered interest for its long-lasting effects and safety. This study examined the effects of IncobotulinumtoxinA (Inco/A), a BoNT/A variant without accessory proteins, on nerve regeneration in rats using the chronic constriction injury (CCI) model. Inco/A was administered perineurally at two time points: on days 0 and 21 post CCI. Functional and histological assessments were conducted to evaluate the effect of Inco/A on nerve regeneration. Sciatic Functional Index (SFI) measurements and Compound Muscle Action Potential (CMAP) recordings were conducted at different time points following CCI. Inco/A-treated animals exhibited a 65% improved SFI and 22% reduction in CMAP onset latencies compared to the vehicle-treated group, suggesting accelerated functional nerve recovery. Tissue analysis revealed enhanced remyelination in Inco/A-treated animals and 60% reduction in CGRP and double S100β signal expression compared to controls. Strikingly, 30% reduced immune cell influx into the injury site was observed following Inco/A treatment, suggesting that its anti-inflammatory effect contributes to nerve regeneration. These findings show that two injections of Inco/A promote functional recovery by enhancing neuroregeneration and modulating inflammatory processes, supporting the hypothesis that Inco/A has a neuroprotective and restorative role in nerve injury conditions. Full article

Long non-coding RNAs (lncRNAs) interact with a variety of biomolecules, including DNA, mRNAs, microRNA, and proteins, to regulate various cellular processes. Recently, their interactions with lipids have gained increasing attention as an emerging research area. Both lipids and lncRNAs play central roles in cellular regulation, and growing evidence reveals a complex interplay between these molecules. These interactions contribute to key biological functions, such as cancer progression, lipid droplet transport, autophagy, liquid−liquid phase separation, and the formation of organelles without membranes. Understanding the lipid−lncRNA interface opens new avenues for unraveling cellular regulation and disease mechanisms, holding great potential not only for elucidating the fundamental aspects of cellular biology but also for identifying innovative therapeutic targets for metabolic disorders and cancer. This review highlights the biological relevance of lipid–lncRNA interactions by exploring their roles in cellular organization, regulation, and diseases, including metabolic and cancer-related disorders. Full article

Cardiovascular disease encompasses a wide group of conditions that affect the heart and blood vessels. Of these diseases, cardiomyopathies and arrhythmias specifically have been well-studied in their relationship to cardiac dyads, nanoscopic structures that connect electrical signals to muscle contraction. The proper development and positioning of dyads is essential in excitation–contraction (EC) coupling and, thus, beating of the heart. Three proteins, namely CMYA5, JPH2, and BIN1, are responsible for maintaining the dyadic cleft between the T-tubule and junctional sarcoplasmic reticulum (jSR). Various other dyadic proteins play integral roles in the primary function of the dyad—translating a propagating action potential (AP) into a myocardial contraction. Ca²⁺, a secondary messenger in this process, acts as an allosteric activator of the sarcomere, and its cytoplasmic concentration is regulated by the dyad. Loss-of-function mutations have been shown to result in cardiomyopathies and arrhythmias. Adeno-associated virus (AAV) gene therapy with dyad components can rescue dyadic dysfunction, which results in cardiomyopathies and arrhythmias. Overall, the dyad and its components serve as essential mediators of calcium homeostasis and excitation–contraction coupling in the mammalian heart and, when dysfunctional, result in significant cardiac dysfunction, arrhythmias, morbidity, and mortality. Full article

Over the past decade, the number and diversity of identified protein post-translational modifications (PTMs) have grown significantly. However, most PTMs occur at relatively low abundance, making selective enrichment of modified peptides essential. To address this, we developed a thermodynamic model describing the free beads enrichment in suspension enrichment process and derived a theoretical relationship between material dosage and analyte recovery. The model predicts a non-linear trend, with enrichment efficiency increasing up to an optimal dosage and declining thereafter—a pattern confirmed by experimental data. We validated the model using centrifugation-based enrichment for glycosylated peptides and magnetic-based enrichment for phosphorylated peptides. In both cases, the results aligned with theoretical predictions. Additionally, the optimal dosage varied among peptides with the same modification type, highlighting the importance of tailoring enrichment strategies. This study provides a solid theoretical and experimental basis for optimizing PTMs enrichment and advancing more sensitive, accurate, and efficient mass spectrometry-based proteomic workflows. Full article

The plant-based oil industry contributes significantly to food waste/by-products in the form of underutilized biomass, including oil pomace, cake/meal, seeds, peels, wastewater, etc. These waste/by-products contain a significant quantity of nutritious and bioactive compounds (phenolics, lignans, flavonoids, dietary fiber, proteins, and essential minerals) with proven health-promoting effects. The utilization of them as natural, cost-effective, and food-grade functional ingredients in novel food formulations holds considerable potential. This review highlights the potential of waste/by-products generated during plant-based oil processing as a promising source of bioactive compounds and covers systematic research, including recent studies focusing on innovative extraction and processing techniques. It also sheds light on their promising potential for valorization as food ingredients, with a focus on specific examples of food fortification. Furthermore, the potential for value creation in the food industry is emphasized, taking into account associated challenges and limitations, as well as future perspectives. Overall, the current information suggests that the valorization of plant-based oil industry waste and by-products for use in the food industry could substantially reduce malnutrition and poverty, generate favorable health outcomes, mitigate environmental concerns, and enhance economic profit in a sustainable way by developing health-promoting, environmentally sustainable food systems. Full article

Perturbations in the tightly regulated processes of VLDL biosynthesis and secretion can directly impact both liver and cardiovascular health. Patients with metabolic disorders have an increased risk of developing hepatic steatosis, which can lead to cirrhosis. These associated metabolic risks underscore the importance of discerning the role of different cellular proteins involved in VLDL biogenesis, transport, and secretion. Small VCP-Interacting Protein (SVIP) has been identified as a component of VLDL transport vesicles and VLDL secretion. This study evaluates the cellular effects stemming from the CRISPR-Cas9-mediated depletion of SVIP in rat hepatocytes. The SVIP-knockout (KO) cells display an increased VLDL retention with elevated intracellular levels of ApoB100 and neutral lipid staining. RNA sequencing studies reveal an impaired PPARα and Nrf2 signaling in the SVIP KO cells, implying a state of metabolic reprograming, with a shift from fatty acid uptake, synthesis, and oxidation to cells favoring the activation of glucose by impaired glycogen storage and increased glucose release. Additionally, SVIP KO cells exhibit a transcriptional profile indicative of acute phase response (APR) in hepatocytes. Many inflammatory markers and genes associated with APR are upregulated in the SVIP KO hepatocytes. In accordance with an APR-like response, the cells also demonstrate an increase in mRNA expression of genes associated with protein synthesis. Together, our data demonstrate that SVIP is critical in maintaining hepatic lipid homeostasis and metabolic balance by regulating key pathways such as PPARα, Nrf2, and APR. Full article

Consumer interest in vegetarian, ethical, and clean-label foods is reviving the use of plant-derived milk coagulants. Cardosins from Cynara cardunculus (“thistle”) are aspartic proteases with strong clotting activity, yet their technological impact in cheese remains under-explored. This study compared a commercial thistle extract (PC) with traditional bovine rennet rich in chymosin (AC) during manufacture and 60-day ripening of Caciotta cheese. Classical compositional assays (ripening index, texture profile, color, solubility) were integrated with scanning electron microscopy, three-dimensional surface reconstruction, and descriptive sensory analysis. AC cheeses displayed slower but sustained proteolysis, yielding a higher and more linear ripening index, softer body, greater solubility, and brighter, more yellow appearance. Imaging revealed a continuous protein matrix with uniformly distributed, larger pores, consistent with a dairy-like sensory profile dominated by milky and umami notes. Conversely, PC cheeses underwent rapid early proteolysis that plateaued, producing firmer, chewier curds with lower solubility and darker color. Micrographs showed a fragmented matrix with smaller, heterogeneous pores; sensory evaluation highlighted vegetal, bitter, and astringent attributes. The data demonstrate that thistle coagulant can successfully replace animal rennet but generates cheeses with distinct structural and sensory fingerprints. The optimization of process parameters is therefore required when targeting specific product styles. Full article

Soil salinization severely limits plant growth and productivity. Mulberry (Morus alba L.), an economically and ecologically important tree, is widely cultivated, yet its salt-tolerance mechanisms at the seedling stage remain insufficiently understood. This study investigated the physiological and biochemical responses of two-year-old mulberry (‘Tailai Sang’) seedlings subjected to six NaCl treatments (0, 50, 100, 150, 200, and 300 mmol L⁻¹) for 28 days. Results showed that growth parameters and photosynthetic gas exchange exhibited dose-dependent declines. The reduction in net photosynthetic rate (Pn) was attributed to both stomatal limitations (decreased stomatal conductance) and non-stomatal limitations, as evidenced by a significant decrease in the maximum quantum efficiency of photosystem II (Fv/Fm) under high salinity. To cope with osmotic stress, seedlings accumulated compatible solutes, including soluble sugars, proteins, and proline. Critically, mulberry seedlings demonstrated effective ion homeostasis by sequestering Na⁺ in the roots to maintain a high K⁺/Na⁺ ratio in leaves, a mechanism that was compromised above 150 mmol L⁻¹. Concurrently, indicators of oxidative stress—malondialdehyde (MDA) and H₂O₂—rose significantly with salinity, inducing the activities of antioxidant enzymes (SOD, CAT, APX, and GR), which peaked at 150 mmol L⁻¹ before declining under extreme stress. A biomass-based LC₅₀ of 179 mmol L⁻¹ NaCl was determined. These findings elucidate that mulberry salt tolerance is a coordinated process involving three key mechanisms: osmotic adjustment, selective ion distribution, and a robust antioxidant defense system. This study establishes an indicative tolerance threshold under controlled conditions and provides a physiological basis for further field-based evaluations of ‘Tailai Sang’ mulberry for cultivation on saline soils. Full article

An increasing global population, rising energy demands, and the shift toward a circular bioeconomy are driving the need for more resource-efficient waste management. The increase in the world population—now exceeding 8 billion as of 2024—results in an increased need for alternative proteins, both human and feed grade proteins, as well as for biopolymers and bioenergy. As such, agricultural, forest, and marine waste biomass represent a valuable feedstock for production of food and feed ingredients, biopolymers, and bioenergy. However, the lack of integrated and efficient valorization strategies for these diverse biomass sources remains a major challenge. This literature review aims to give a systematic approach on the recent research status of agricultural, forest, and marine waste biomass valorization, focusing on cascade processing (a sequential combination of processes such as pretreatment, extraction, and conversion methods). Potential products will be identified that create the most economic value over multiple lifetimes, to maximize resource efficiency. It highlights the challenges associated with cascade processing of waste biomass and proposes technological synergies for waste biomass valorization. Moreover, this review will provide a comprehensive understanding of the potential of waste biomass valorization in the context of sustainable and circular bioeconomy. Full article

It is believed that caspases may play a significant role in the development of cancer, and the expression levels of genes encoding these proteins may influence the prognosis and clinical course of cancer. Taking into account the information presented, we examined the expression profiles of 11 genes from the caspase family in patients diagnosed with triple-negative breast cancer (TNBC). We qualified 29 patients with TNBC. A fragment of the tumor and a fragment of normal tissue surrounding the tumor were collected from each patient. Then, RNA was isolated, and the reverse transcription process was performed. The expression levels of caspase family genes were determined using the real-time PCR method. The obtained data were correlated with clinical data and compared with data from the Cancer Genome Atlas database using the Breast Cancer Gene Expression Miner v4.8 and Ualcan. Based on the results of the conducted research, it can be assumed that the levels of expression of caspase family genes may be correlated with the clinical course of cancer in patients with TNBC, and further research may indicate that profiling the expression levels of these genes may be used in selecting personalized treatment methods. Full article

The habenula (Hb) of the epithalamus is formed of the medial (MHb) and lateral (LHb) parts. The improper functioning of the Hb may lead to depression and anxiety. The glutamate excitotoxicity is accompanied by astroglia reactivity and leads to the damage of nervous system structures. The aim of the study was to assess the influence of monosodium glutamate (MSG) administrated subcutaneously to rats in doses of 2 g/kg b.w. (I) and 4 g/kg b.w. (II), on astroglia in the MHb and LHb. Based on immunohistochemical reactions, the morphology, number of astrocytes immunoreactive for glial fibrillary acidic protein (GFAP-IR) and S100β protein (S100β-IR), and their surface area, perimeter, number and length of processes, and cytoplasmic-nuclear immunostaining intensity for the studied proteins were assessed. In the MHb of animals receiving MSG, especially at a high dose, hypertrophy and an increase in the number of GFAP-IR and S100β-IR cells were demonstrated. In the LHb, only hypertrophy of processes in S100β-positive glia was observed. The immunostaining intensity increased in GFAP-IR glia and decreased in S100β-IR cells only in animals from group I. The results revealed that astroglia respond to MSG depending on its dose and the Hb part. This different behavior of glia may indicate their different sensitivity and resistance to damaging factors. Full article

The drying process plays a crucial role in enhancing the shelf life of food products by reducing moisture content. As climate change contributes to rising temperatures, alternative drying methods, such as solar drying, offer promising solutions for sustainable food preservation. This study investigates the solar drying of eggplant (Solanum melongena L.) slices, with a focus on the effect of salting pretreatment on drying efficiency. Eggplant slices were subjected to salting pretreatment for partial moisture removal prior to drying. Drying kinetics were monitored to construct the characteristic drying curve. The dried eggplant slices were evaluated for their proximate composition and rehydration capacity, as well as textural and thermal properties. The results showed that salting pretreatment significantly enhanced the solar drying process by accelerating moisture removal. Notably, water activity (aw) decreased significantly from 0.978 to 0.554 for the control sample and to 0.534 for the saltedsample. Significant differences were observed between the dried and salted dried slices, particularly in rehydration capacity, which decreased following salting. Additionally, the salted dried samples showedreductions in protein, carbohydrate, and potassium contents. In contrast, ash content and hardness increased as a result ofosmotic pretreatment. These findings suggest that while dry salting pretreatment effectively reduces solar drying time, it may adversely affect several nutritional and textural properties. Full article

This study aimed to optimize the inoculation dosage and fermentation duration to enhance the protein content and reduce soluble oligosaccharides in soybean meal using Aspergillus oryzae and assessed its performance in dog food extrusion. A 3 × 5 factorial design was used to determine the optimal fermentation conditions. These conditions were applied to ferment soybean meal in bulk for nutritional analysis. Finally, the impact of fermentation on extrusion processing was assessed by formulating and extruding four diets: SBM (30% soybean meal), AMF (30% soybean meal with 1% Amaferm^®—A. oryzae biomass), FSBM (30% fermented soybean meal), and SPI (18% soy protein isolate). Diets were extruded with a single-screw extruder, and physical characteristics of kibbles, particle size distribution, and viscosity of raw mixes were analyzed. The optimal fermentation conditions were 1 × 10⁴ spore/g substrate for 36 h, which increased the crude protein content by 4.63% DM, methionine and cysteine total content by 0.15% DM, and eliminated sucrose, while significantly reducing stachyose, raffinose, and verbascose (95.22, 87.37, and 41.82%, respectively). The extrusion results showed that FSBM had intermediate specific mechanical energy (SME), in-barrel moisture requirements, and sectional expansion index (198.7 kJ/kg, 28.2%, and 1.80, respectively) compared with SBM (83.7 kJ/kg, 34.5%, and 1.30, respectively) and SPI (305.3 kJ/kg, 33.5%, and 2.55, respectively). The FSBM also exhibited intermediate particle size distribution and the least raw mix viscosity. These findings demonstrate that A. oryzae fermentation enhances the nutrient profile of soybean meal while improving extrusion efficiency and kibble quality, supporting its potential use as a sustainable pet food ingredient. Full article

Biocatalysis is one of the oldest fields that has been used in industrial applications, with one of the earliest purposeful examples being the mass production of acetic acid from an immobilized Acinetobacter strain in the year 1815. Efficiency, specificity, reduced reaction times, lower overall costs, and environmental friendliness are some advantages biocatalysis has over conventional chemical synthesis, which has made biocatalysis increasingly used in industry. We highlight three necessary fields that are fundamental to advancing industrial biocatalysis, including biocatalyst engineering, solvent engineering, and mechanistic engineering. However, the fundamental mechanism of enzyme function is often overlooked or given less attention, which can limit the engineering process. In this review, we describe how mechanistic enzymology benefits industrial biocatalysis by elucidating key fundamental principles, including the k_cat and k_cat/K_m parameters. Mechanistic enzymology presents a unique field that provides in-depth insights into the molecular mechanisms of enzyme activity and includes areas such as reaction kinetics, catalytic mechanisms, structural analysis, substrate specificity, and protein dynamics. In line with the objective of protein engineering to optimize enzyme activity, we summarize a range of strategies reported in the literature aimed at improving the product release rate, the chemical step of catalysis, and the overall catalytic efficiency of enzymes. Further into this review, we delineate kinetic solvent viscosity effects (KSVEs) as a very efficient, cost-effective, and easy-to-perform method to probe different aspects of enzyme reaction mechanisms, including diffusion-dependent kinetic steps and rate-limiting steps. KSVEs are cost-effective because simple kinetic enzyme assays, such as the Michaelis–Menten kinetic approach, can be combined with them without the need for specialized and costly equipment. Other techniques in protein engineering and genetic engineering are also covered in this review. Additionally, we provide information on solvent systems in enzymatic reactions, details on immobilized biocatalysts, and common misconceptions that misguide enzyme design and optimization processes. Full article