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20 pages, 2267 KiB  
Article
Mechanical Properties of Collagen Implant Used in Neurosurgery Towards Industry 4.0/5.0 Reflected in ML Model
by Marek Andryszczyk, Izabela Rojek and Dariusz Mikołajewski
Appl. Sci. 2025, 15(15), 8630; https://doi.org/10.3390/app15158630 (registering DOI) - 4 Aug 2025
Abstract
Collagen implants in neurosurgery are widely used due to their biocompatibility, biodegradability, and ability to support tissue regeneration, but their mechanical properties, such as low tensile strength and susceptibility to enzymatic degradation, remain challenging. Current technologies are improving these implants through cross-linking, synthetic [...] Read more.
Collagen implants in neurosurgery are widely used due to their biocompatibility, biodegradability, and ability to support tissue regeneration, but their mechanical properties, such as low tensile strength and susceptibility to enzymatic degradation, remain challenging. Current technologies are improving these implants through cross-linking, synthetic reinforcements, and advanced manufacturing techniques such as 3D bioprinting to improve durability and predictability. Industry 4.0 is contributing to this by automating production, using data analytics and machine learning to optimize implant properties and ensure quality control. In Industry 5.0, the focus is shifting to personalization, enabling the creation of patient-specific implants through human–machine collaboration and advanced biofabrication. eHealth integrates digital monitoring systems, enabling real-time tracking of implant healing and performance to inform personalized care. Despite progress, challenges such as cost, material property variability, and scalability for mass production remain. The future lies in smart biomaterials, AI-driven design, and precision biofabrication, which could mean the possibility of creating more effective, accessible, and patient-specific collagen implants. The aim of this article is to examine the current state and determine the prospects for the development of mechanical properties of collagen implant used in neurosurgery towards Industry 4.0/5.0, including ML model. Full article
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28 pages, 2414 KiB  
Review
Breaking Down Osteoarthritis: Exploring Inflammatory and Mechanical Signaling Pathways
by Wafa Ali Batarfi, Mohd Heikal Mohd Yunus, Adila A. Hamid, Manira Maarof and Rizal Abdul Rani
Life 2025, 15(8), 1238; https://doi.org/10.3390/life15081238 - 4 Aug 2025
Abstract
Osteoarthritis (OA) is a chronic progressive joint disease characterized by cartilage degradation, subchondral bone remodeling, and synovial inflammation. This complex disorder arises from the interplay between mechanical stress and inflammatory processes, which is mediated by interconnected molecular signaling pathways. This review explores the [...] Read more.
Osteoarthritis (OA) is a chronic progressive joint disease characterized by cartilage degradation, subchondral bone remodeling, and synovial inflammation. This complex disorder arises from the interplay between mechanical stress and inflammatory processes, which is mediated by interconnected molecular signaling pathways. This review explores the dual roles of inflammatory and mechanical signaling in OA pathogenesis, focusing on crucial pathways such as NF-kB, JAK/STAT, and MAPK in inflammation, as well as Wnt/β-catenin, Integrin-FAK, and Hippo-YAP/TAZ in mechanotransduction. The interplay between these pathways highlights a vicious cycle wherein mechanical stress exacerbates inflammation, and inflammation weakens cartilage, increasing its vulnerability to mechanical damage. Additionally, we discuss emerging therapeutic strategies targeting these pathways, including inhibitors of cartilage-degrading enzymes, anti-inflammatory biologics, cell-based regenerative approaches, and non-pharmacological mechanical interventions. By dissecting the molecular mechanisms underlying OA, this review aims to provide insights into novel interventions that address both inflammatory and mechanical components of the disease, paving the way for precision medicine in OA management. Full article
(This article belongs to the Special Issue Current Views on Knee Osteoarthritis: 3rd Edition)
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14 pages, 1567 KiB  
Article
Determining the Benzo[a]pyrene Degradation, Tolerance, and Adsorption Mechanisms of Kefir-Derived Bacterium Bacillus mojavensis TC-5
by Zhixian Duo, Haohao Li, Zeyu Wang, Zhiwei Zhang, Zhuonan Yang, Aofei Jin, Minwei Zhang, Rui Zhang and Yanan Qin
Foods 2025, 14(15), 2727; https://doi.org/10.3390/foods14152727 - 4 Aug 2025
Abstract
Microbial detoxification, as an environmentally friendly strategy, has been widely applied for benzo[a]pyrene (BaP) degradation. Within this approach, food-derived microbial strains offer unique advantages in safety, specificity, and sustainability for detoxifying food-borne BaP. In this study, we aimed to explore the potential of [...] Read more.
Microbial detoxification, as an environmentally friendly strategy, has been widely applied for benzo[a]pyrene (BaP) degradation. Within this approach, food-derived microbial strains offer unique advantages in safety, specificity, and sustainability for detoxifying food-borne BaP. In this study, we aimed to explore the potential of such strains in BaP degradation. Bacillus mojavensis TC-5, a strain that degrades BaP, was isolated from kefir grains. Surprisingly, 12 genes encoding dehydrogenases, synthases, and oxygenases, including betB, fabHB, qdoI, cdoA, and bioI, which are related to BaP degradation, were up-regulated by 2.01-fold to 4.52-fold in TC-5. Two potential degradation pathways were deduced. In pathway I, dioxygenase, betaine aldehyde dehydrogenase, and beta-ketoacyl-ACP synthase III FabHB act sequentially on BaP to form 4H-pyran-4-one,2,3-dihydro-3,5-dihydroxy-6-methyl via the phthalic acid pathway. In the presence of the cytochrome P450 enzyme, BaP progressively mediates ring cleavage via the anthracene pathway, eventually forming 3-methyl-5-propylnonane in pathway II. Notably, TC-5 achieved an impressive BaP removal efficiency of up to 63.94%, with a degradation efficiency of 32.89%. These results suggest that TC-5 has significant potential for application in addressing food-borne BaP contamination. Moreover, our findings expand the application possibilities of Xinjiang fermented milk products and add to the available green strategies for BaP degradation in food systems. Full article
(This article belongs to the Section Nutraceuticals, Functional Foods, and Novel Foods)
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23 pages, 470 KiB  
Systematic Review
Current Understanding and Future Research Direction for Estimating the Postmortem Interval: A Systematic Review
by Gabriela Strete, Andreea Sălcudean, Adina-Alexandra Cozma and Carmen-Corina Radu
Diagnostics 2025, 15(15), 1954; https://doi.org/10.3390/diagnostics15151954 - 4 Aug 2025
Abstract
Background: Accurate estimation of the postmortem interval (PMI) is critical in forensic death investigations. Traditional signs of death—algor mortis, livor mortis, and rigor mortis—are generally reliable only within the first two to three days after death, with their accuracy decreasing as decomposition [...] Read more.
Background: Accurate estimation of the postmortem interval (PMI) is critical in forensic death investigations. Traditional signs of death—algor mortis, livor mortis, and rigor mortis—are generally reliable only within the first two to three days after death, with their accuracy decreasing as decomposition progresses. This paper presents a systematic review conducted in accordance with PRISMA guidelines, aiming to evaluate and compare current methods for estimating the PMI. Specifically, the study identifies both traditional and modern techniques, analyzes their advantages, limitations, and applicable timeframes, critically synthesizes the literature, and highlights the importance of combining multiple approaches to improve accuracy. Methods: A systematic search was conducted in the PubMed, Scopus, and Web of Science databases, following the PRISMA guidelines. The review included original articles and reviews that evaluated PMI estimation methods (through thanatological signs, entomology, microbial succession, molecular, imaging, and omics approaches). Extracted data included study design, methodology, PMI range, and accuracy information. Out of the 1245 identified records, 50 studies met the inclusion criteria for qualitative synthesis. Results: Emerging methods, such as molecular markers, microbial succession, omics technologies, and advanced imaging show improved accuracy across extended postmortem intervals. RNA degradation methods demonstrated higher accuracy within the first 72 h, while entomology and microbial analysis are more applicable during intermediate and late decomposition stages. Although no single method is universally reliable, combining traditional and modern approaches tailored to case-specific factors improves overall PMI estimation accuracy. Conclusions: This study supports the use of an integrative, multidisciplinary, and evidence-based approach to improve time-since-death estimation. Such a strategy enhances forensic outcomes by enabling more precise PMI estimates in complex or delayed cases, increasing legal reliability, and supporting court-admissible expert testimony based on validated, multi-method protocols. Full article
(This article belongs to the Section Pathology and Molecular Diagnostics)
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24 pages, 2171 KiB  
Review
Induction of Autophagy as a Therapeutic Breakthrough for NAFLD: Current Evidence and Perspectives
by Yanke Liu, Mingkang Zhang and Yazhi Wang
Biology 2025, 14(8), 989; https://doi.org/10.3390/biology14080989 (registering DOI) - 4 Aug 2025
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a clinicopathological syndrome characterised by hepatic steatosis in the absence of significant alcohol consumption or other specific causes of liver injury. It has become one of the leading causes of liver dysfunction worldwide. However, the precise pathophysiological [...] Read more.
Nonalcoholic fatty liver disease (NAFLD) is a clinicopathological syndrome characterised by hepatic steatosis in the absence of significant alcohol consumption or other specific causes of liver injury. It has become one of the leading causes of liver dysfunction worldwide. However, the precise pathophysiological mechanisms underlying NAFLD remain unclear, and effective therapeutic strategies are still under investigation. Autophagy, a vital intracellular process in eukaryotic cells, enables the degradation and recycling of cytoplasmic components through a membrane trafficking pathway. Recent studies have demonstrated a strong association between impaired or deficient autophagy and the development and progression of NAFLD. Restoring autophagic function may represent a key approach to mitigating hepatocellular injury. Nevertheless, due to the complexity of autophagy regulation and its context-dependent effects on cellular function, therapeutic strategies targeting autophagy in NAFLD remain limited. This review aims to summarise the relationship between autophagy and NAFLD, focusing on autophagy as a central mechanism. We discuss the latest research advances regarding interventions such as diet and exercise, pharmacological therapies (including modern pharmacological therapy and plant-derived compounds), and other approaches (such as hormones, nanoparticles, gut microbiota, and vitamins). Furthermore, we briefly highlight potential autophagy-related molecular targets that may offer novel therapeutic insights for NAFLD management. Full article
(This article belongs to the Section Medical Biology)
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16 pages, 5537 KiB  
Article
Different Light Wavelengths Differentially Influence the Progression of the Hypersensitive Response Induced by Pathogen Infection in Tobacco
by Bao Quoc Tran, Anh Trung Nguyen and Sunyo Jung
Antioxidants 2025, 14(8), 954; https://doi.org/10.3390/antiox14080954 (registering DOI) - 3 Aug 2025
Viewed by 45
Abstract
Using light-emitting diodes (LEDs), we examined how different light wavelengths influence the hypersensitive response (HR) in tobacco plants infected with Pseudomonas syringae pv. tomato (Pst). Pst-infiltrated plants exhibited greater resistance to Pst infection under green and blue light compared to white and red [...] Read more.
Using light-emitting diodes (LEDs), we examined how different light wavelengths influence the hypersensitive response (HR) in tobacco plants infected with Pseudomonas syringae pv. tomato (Pst). Pst-infiltrated plants exhibited greater resistance to Pst infection under green and blue light compared to white and red light, as indicated by reduced HR-associated programmed cell death, lower H2O2 production, and up to 64% reduction in membrane damage. During the late stage of HR, catalase and ascorbate peroxidase activities peaked under green and blue LEDs, with 5- and 10-fold increases, respectively, while superoxide dismutase activity was higher under white and red LEDs. Defense-related genes CHS1, PALa, PR1, and PR2 were more strongly induced by white and red light. The plants treated with green or blue LEDs during Pst infection prompted faster degradation of phototoxic Mg-porphyrins and exhibited smaller declines in Fv/Fm, electron transport rate, chlorophyll content, and LHCB expression compared to those treated with white or red LEDs. By contrast, the induction of the chlorophyll catabolic gene SGR was 54% and 77% lower in green and blue LEDs, respectively, compared to white LEDs. This study demonstrates that light quality differentially affects Pst-mediated HR, with green and blue light more effectively suppressing HR progression, mainly by reducing oxidative stress through enhanced antioxidative capacity and mitigation of photosynthetic impairments. Full article
(This article belongs to the Special Issue Oxidative Stress and Antioxidant Defense in Crop Plants, 2nd Edition)
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26 pages, 956 KiB  
Review
Natural Flavonoids for the Prevention of Sarcopenia: Therapeutic Potential and Mechanisms
by Ye Eun Yoon, Seong Hun Ju, Yebean Kim and Sung-Joon Lee
Int. J. Mol. Sci. 2025, 26(15), 7458; https://doi.org/10.3390/ijms26157458 - 1 Aug 2025
Viewed by 124
Abstract
Sarcopenia, characterized by progressive skeletal muscle loss and functional decline, represents a major public heath challenge in aging populations. Despite increasing awareness, current management strategies—primarily resistance exercise and nutritional support—remain limited by accessibility, adherence, and inconsistent outcomes. This underscores the urgent need for [...] Read more.
Sarcopenia, characterized by progressive skeletal muscle loss and functional decline, represents a major public heath challenge in aging populations. Despite increasing awareness, current management strategies—primarily resistance exercise and nutritional support—remain limited by accessibility, adherence, and inconsistent outcomes. This underscores the urgent need for novel, effective, and scalable therapeutics. Flavonoids, a diverse class of plant-derived polyphenolic compounds, have attracted attention for their muti-targeted biological activities, including anti-inflammatory, antioxidant, metabolic, and myogenic effects. This review aims to evaluate the anti-sarcopenic potential of selected flavonoids—quercetin, rutin, kaempferol glycosides, baicalin, genkwanin, isoschaftoside, naringin, eriocitrin, and puerarin—based on recent preclinical findings and mechanistic insights. These compounds modulate key pathways involved in muscle homeostasis, such as NF-κB and Nrf2 signaling, AMPK and PI3K/Akt activation, mitochondrial biogenesis, proteosomal degradation, and satellite cell function. Importantly, since muscle wasting also features prominently in cancer cachexia—a distinct but overlapping syndrome—understanding flavonoid action may offer broader therapeutic relevance. By targeting shared molecular axes, flavonoids may provide a promising, biologically grounded approach to mitigating sarcopenia and the related muscle-wasting conditions. Further translational studies and clinical trials are warranted to assess their efficacy and safety in human populations. Full article
(This article belongs to the Special Issue Role of Natural Products in Human Health and Disease)
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22 pages, 4043 KiB  
Article
Research Progress and Typical Case of Open-Pit to Underground Mining in China
by Shuai Li, Wencong Su, Tubing Yin, Zhenyu Dan and Kang Peng
Appl. Sci. 2025, 15(15), 8530; https://doi.org/10.3390/app15158530 (registering DOI) - 31 Jul 2025
Viewed by 247
Abstract
As Chinese open-pit mines progressively transition to deeper operations, challenges such as rising stripping ratios, declining slope stability, and environmental degradation have become increasingly pronounced. The sustainability of traditional open-pit mining models faces substantial challenges. Underground mining, offering higher resource recovery rates and [...] Read more.
As Chinese open-pit mines progressively transition to deeper operations, challenges such as rising stripping ratios, declining slope stability, and environmental degradation have become increasingly pronounced. The sustainability of traditional open-pit mining models faces substantial challenges. Underground mining, offering higher resource recovery rates and minimal environmental disruption, is emerging as a pivotal technological pathway for the green transformation of mining. Consequently, the transition from open-pit to underground mining has emerged as a central research focus within mining engineering. This paper provides a comprehensive review of key technological advancements in this transition, emphasizing core issues such as mine development system selection, mining method choices, slope stability control, and crown pillar design. A typical case study of the Anhui Xinqiao Iron Mine is presented to analyze its engineering approaches and practical experiences in joint development, backfilling mining, and ecological restoration. The findings indicate that the mine has achieved multi-objective optimization of resource utilization, environmental coordination, and operational capacity while ensuring safety and recovery efficiency. This offers a replicable and scalable technological demonstration for the green transformation of similar mines around the world. Full article
(This article belongs to the Topic New Advances in Mining Technology)
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17 pages, 666 KiB  
Review
Three Major Deficiency Diseases Harming Mankind (Protein, Retinoid, Iron) Operate Under Tryptophan Dependency
by Yves Ingenbleek
Nutrients 2025, 17(15), 2505; https://doi.org/10.3390/nu17152505 - 30 Jul 2025
Viewed by 173
Abstract
This story began half a century ago with the discovery of an unusually high presence of tryptophan (Trp, W) in transthyretin (TTR), one of the three carrier proteins of thyroid hormones. With the Trp-rich retinol-binding protein (RBP), TTR forms a plasma complex implicated [...] Read more.
This story began half a century ago with the discovery of an unusually high presence of tryptophan (Trp, W) in transthyretin (TTR), one of the three carrier proteins of thyroid hormones. With the Trp-rich retinol-binding protein (RBP), TTR forms a plasma complex implicated in the delivery of retinoid compounds to body tissues. W has the lowest concentration among all AAs involved in the sequencing of human body proteins. The present review proposes molecular maps focusing on the ratio of W/AA residues found in the sequence of proteins involved in immune events, allowing us to ascribe the guidance of inflammatory processes as fully under the influence of W. Under the control of cytokine stimulation, plasma biomarkers of protein nutritional status work in concert with major acute-phase reactants (APRs) and with carrier proteins to release, in a free and active form, their W and hormonal ligands, interacting to generate hot spots affecting the course of acute stress disorders. The prognostic inflammatory and nutritional index (PINI) scoring formula contributes to identifying the respective roles played by each of the components prevailing during the progression of the disease. Glucagon demonstrates ambivalent properties, remaining passive under steady-state conditions while displaying stronger effects after cytokine activation. In developing countries, inappropriate weaning periods lead to toddlers eating W-deficient cereals as a staple, causing a dramatic reduction in the levels of W-rich biomarkers in plasma, constituting a novel nutritional deficiency at the global scale. Appropriate counseling should be set up using W implementations to cover the weaning period and extended until school age. In adult and elderly subjects, the helpful immune protections provided by W may be hindered by the surge in harmful catabolites with the occurrence of chronic complications, which can have a significant public health impact but lack the uncontrolled surges in PINI observed in young infants and teenagers. Biomarkers of neurodegenerative and neoplastic disorders measured in elderly patients indicate the slow-moving elevation of APRs due to rampant degradation processes. Full article
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36 pages, 9312 KiB  
Review
Current Progress in the Biosynthesis of Metal Sulfide Nanomaterials for the Degradation of Dyes: A Review
by Carol D. Langa, Nonhlangabezo Mabuba and Nomso C. Hintsho-Mbita
Catalysts 2025, 15(8), 727; https://doi.org/10.3390/catal15080727 - 30 Jul 2025
Viewed by 246
Abstract
The contamination of water bodies by industrial dyes poses a significant environmental challenge on a global scale. Conventional wastewater treatment methods often suffer from limitations related to high cost, limited efficiency, and potential secondary environmental impacts. Recent advances in photocatalytic technologies have highlighted [...] Read more.
The contamination of water bodies by industrial dyes poses a significant environmental challenge on a global scale. Conventional wastewater treatment methods often suffer from limitations related to high cost, limited efficiency, and potential secondary environmental impacts. Recent advances in photocatalytic technologies have highlighted the potential of metal sulfide-based photocatalysts, particularly those synthesized through environmentally friendly, plant-mediated approaches, as promising alternatives for efficient and sustainable dye degradation. However, despite their promising potential, metal sulfide photocatalysts often suffer from limitations such as photocorrosion, low stability under irradiation, and rapid recombination of charge carriers, which restrict their long-term applicability. In light of these challenges, this review provides a comprehensive examination of the physicochemical characteristics, synthetic strategies, and photocatalytic applications of metal sulfides. Particular emphasis is placed on green synthesis routes employing plant-derived extracts, which offer environmentally benign and sustainable alternatives to conventional methods. Moreover, the review elucidates various modification approaches, most notably, the formation of heterostructures, as viable strategies to enhance photocatalytic efficiency and mitigate the aforementioned drawbacks. The green synthesis of metal sulfides, aligned with the principles of green chemistry, offers a promising route toward the development of sustainable and environmentally friendly water treatment technologies. Full article
(This article belongs to the Special Issue Recent Advances in Photocatalysis for Environmental Applications)
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19 pages, 4279 KiB  
Article
Identification of Anticancer Target Combinations to Treat Pancreatic Cancer and Its Associated Cachexia Using Constraint-Based Modeling
by Feng-Sheng Wang, Ching-Kai Wu and Kuang-Tse Huang
Molecules 2025, 30(15), 3200; https://doi.org/10.3390/molecules30153200 - 30 Jul 2025
Viewed by 222
Abstract
Pancreatic cancer is frequently accompanied by cancer-associated cachexia, a debilitating metabolic syndrome marked by progressive skeletal muscle wasting and systemic metabolic dysfunction. This study presents a systems biology framework to simultaneously identify therapeutic targets for both pancreatic ductal adenocarcinoma (PDAC) and its associated [...] Read more.
Pancreatic cancer is frequently accompanied by cancer-associated cachexia, a debilitating metabolic syndrome marked by progressive skeletal muscle wasting and systemic metabolic dysfunction. This study presents a systems biology framework to simultaneously identify therapeutic targets for both pancreatic ductal adenocarcinoma (PDAC) and its associated cachexia (PDAC-CX), using cell-specific genome-scale metabolic models (GSMMs). The human metabolic network Recon3D was extended to include protein synthesis, degradation, and recycling pathways for key inflammatory and structural proteins. These enhancements enabled the reconstruction of cell-specific GSMMs for PDAC and PDAC-CX, and their respective healthy counterparts, based on transcriptomic datasets. Medium-independent metabolic biomarkers were identified through Parsimonious Metabolite Flow Variability Analysis and differential expression analysis across five nutritional conditions. A fuzzy multi-objective optimization framework was employed within the anticancer target discovery platform to evaluate cell viability and metabolic deviation as dual criteria for assessing therapeutic efficacy and potential side effects. While single-enzyme targets were found to be context-specific and medium-dependent, eight combinatorial targets demonstrated robust, medium-independent effects in both PDAC and PDAC-CX cells. These include the knockout of SLC29A2, SGMS1, CRLS1, and the RNF20–RNF40 complex, alongside upregulation of CERK and PIKFYVE. The proposed integrative strategy offers novel therapeutic avenues that address both tumor progression and cancer-associated cachexia, with improved specificity and reduced off-target effects, thereby contributing to translational oncology. Full article
(This article belongs to the Special Issue Innovative Anticancer Compounds and Therapeutic Strategies)
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23 pages, 2300 KiB  
Article
Electrodegradation of Selected Water Contaminants: Efficacy and Transformation Products
by Borislav N. Malinović, Tatjana Botić, Tijana Đuričić, Aleksandra Borković, Katarina Čubej, Ivan Mitevski, Jasmin Račić and Helena Prosen
Appl. Sci. 2025, 15(15), 8434; https://doi.org/10.3390/app15158434 - 29 Jul 2025
Viewed by 208
Abstract
The electrooxidation (EO) of three important environmental contaminants, anticorrosive 1H-benzotriazole (BTA), plasticizer dibutyl phthalate (DBP), and non-ionic surfactant Triton X-100 (tert-octylphenoxy[poly(ethoxy)] ethanol, t-OPPE), was studied as a possible means to improve their elimination from wastewaters, which are an important [...] Read more.
The electrooxidation (EO) of three important environmental contaminants, anticorrosive 1H-benzotriazole (BTA), plasticizer dibutyl phthalate (DBP), and non-ionic surfactant Triton X-100 (tert-octylphenoxy[poly(ethoxy)] ethanol, t-OPPE), was studied as a possible means to improve their elimination from wastewaters, which are an important emission source. EO was performed in a batch reactor with a boron-doped diamond (BDD) anode and a stainless steel cathode. Different supporting electrolytes were tested: NaCl, H2SO4, and Na2SO4. Results were analysed from the point of their efficacy in terms of degradation rate, kinetics, energy consumption, and transformation products. The highest degradation rate, shortest half-life, and lowest energy consumption was observed in the electrolyte H2SO4, followed by Na2SO4 with only slightly less favourable characteristics. In both cases, degradation was probably due to the formation of persulphate or sulphate radicals. Transformation products (TPs) were studied mainly in the sulphate media and several oxidation products were identified with all three contaminants, while some evidence of progressive degradation, e.g., ring-opening products, was observed only with t-OPPE. The possible reasons for the lack of further degradation in BTA and DBP are too short of an EO treatment time and perhaps a lack of detection due to unsuitable analytical methods for more polar TPs. Results demonstrate that BDD-based EO is a robust method for the efficient removal of structurally diverse organic contaminants, making it a promising candidate for advanced water treatment technologies. Full article
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27 pages, 15511 KiB  
Review
Recent Advances in the Structural Studies of the Proteolytic ClpP/ClpX Molecular Machine
by Astrid Audibert, Jerome Boisbouvier and Annelise Vermot
Biomolecules 2025, 15(8), 1097; https://doi.org/10.3390/biom15081097 - 29 Jul 2025
Viewed by 196
Abstract
AAA+ ATPases are ring-shaped hexameric protein complexes that operate as elaborate macromolecular motors, driving a variety of ATP-dependent cellular processes. AAA+ ATPases undergo large-scale conformational changes that lead to the conversion of chemical energy from ATP into mechanical work to perform a wide [...] Read more.
AAA+ ATPases are ring-shaped hexameric protein complexes that operate as elaborate macromolecular motors, driving a variety of ATP-dependent cellular processes. AAA+ ATPases undergo large-scale conformational changes that lead to the conversion of chemical energy from ATP into mechanical work to perform a wide range of functions, such as unfolding and translocation of the protein substrate inside a proteolysis chamber of an AAA+-associated protease. Despite extensive biochemical studies on these macromolecular assemblies, the mechanism of substrate unfolding and degradation has long remained elusive. Indeed, until recently, structural characterization of AAA+ protease complexes remained hampered by the size and complexity of the machinery, harboring multiple protein subunits acting together to process proteins to be degraded. Additionally, the major structural rearrangements involved in the mechanism of this complex represent a crucial challenge for structural biology. Here, we report the main advances in deciphering molecular details of the proteolytic reaction performed by AAA+ proteases, based on the remarkable progress in structural biology techniques. Particular emphasis is placed on the latest findings from high-resolution structural analysis of the ClpXP proteolytic complex, using crystallographic and cryo-EM investigations. In addition, this review presents some additional dynamic information obtained using solution-state NMR. This information provides molecular details that help to explain the protein degradation process by such molecular machines. Full article
(This article belongs to the Special Issue Structural Biology of Protein)
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20 pages, 770 KiB  
Review
Histamine Metabolism in IBD: Towards Precision Nutrition
by Dimitra Kanta, Eleftherios Katsamakas, Anna Maia Berg Gudiksen and Mahsa Jalili
Nutrients 2025, 17(15), 2473; https://doi.org/10.3390/nu17152473 - 29 Jul 2025
Viewed by 371
Abstract
Patients with Inflammatory Bowel Disease (IBD) exhibit a dysregulated immune response that may be further exacerbated by bioactive compounds, such as histamine. Current dietary guidelines for IBD primarily focus on symptom management and flare-up prevention, yet targeted nutritional strategies addressing histamine metabolism remain [...] Read more.
Patients with Inflammatory Bowel Disease (IBD) exhibit a dysregulated immune response that may be further exacerbated by bioactive compounds, such as histamine. Current dietary guidelines for IBD primarily focus on symptom management and flare-up prevention, yet targeted nutritional strategies addressing histamine metabolism remain largely unexplored. This narrative review aims to summarize the existing literature on the complex interplay between IBD and histamine metabolism and propose a novel dietary framework for managing IBD progression in patients with histamine intolerance (HIT). Relevant studies were identified through a comprehensive literature search of PubMed/MEDLINE, Google Scholar, ScienceDirect, Scopus, and Web of Science. The proposed low-histamine diet (LHD) aims to reduce the overall histamine burden in the body through two primary strategies: (1) minimizing exogenous intake by limiting high-histamine and histamine-releasing foods and (2) reducing endogenous histamine production by modulating gut microbiota composition, specifically targeting histamine-producing bacteria. In parallel, identifying individuals who are histamine-intolerant and understanding the role of histamine-degrading enzymes, such as diamine oxidase (DAO) and histamine-N-methyltransferase (HNMT), are emerging as important areas of focus. Despite growing interest in the role of histamine and mast cell activation in gut inflammation, no clinical trials have investigated the effects of a low-histamine diet in IBD populations. Therefore, future research should prioritize the implementation of LHD interventions in IBD patients to evaluate their generalizability and clinical applicability. Full article
(This article belongs to the Special Issue Precise Nutrition Therapy to Inflammatory Bowel Diseases)
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21 pages, 5917 KiB  
Article
Cyanobacterial Assemblages Inhabiting the Apatity Thermal Power Plant Fly Ash Dumps in the Russian Arctic
by Denis Davydov and Anna Vilnet
Microorganisms 2025, 13(8), 1762; https://doi.org/10.3390/microorganisms13081762 - 28 Jul 2025
Viewed by 197
Abstract
In the process of the work of a coal power station is formed ash and slag, which, along with process water, are deposited in the dumps. Coal ash waste dumps significantly degrade the surrounding environment due to their unprotected surfaces, which are highly [...] Read more.
In the process of the work of a coal power station is formed ash and slag, which, along with process water, are deposited in the dumps. Coal ash waste dumps significantly degrade the surrounding environment due to their unprotected surfaces, which are highly susceptible to wind and water erosion. This results in the dispersion of contaminants into adjacent ecosystems. Pollutants migrate into terrestrial and aquatic systems, compromising soil quality and water resources, and posing documented risks to the environment and human health. Primary succession on the coal ash dumps of the Apatity thermal power plant (Murmansk Region, NW Russia) was initiated by cyanobacterial colonization. We studied cyanobacterial communities inhabiting three spoil sites that varied in time since decommissioning. These sites are characterized by exceptionally high concentrations of calcium and magnesium oxides—levels approximately double those found in the region’s natural soils. A total of 18 cyanobacterial taxa were identified in disposal sites. Morphological analysis of visible surface crusts revealed 16 distinct species. Furthermore, 24 cyanobacterial strains representing 11 species were successfully isolated into unialgal culture and tested with a molecular genetic approach to confirm their identification from 16S rRNA. Three species were determined with molecular evidence. Cyanobacterial colonization of coal fly ash disposal sites begins immediately after deposition. Primary communities initially exhibit low species diversity (four taxa) and do not form a continuous ground cover in the early years. However, as succession progresses—illustrated by observations from a 30-year-old deposit—spontaneous surface revegetation occurs, accompanied by a marked increase in cyanobacterial diversity, reaching 12 species. Full article
(This article belongs to the Special Issue Microbial Diversity Research in Different Environments)
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