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10 pages, 1191 KiB  
Article
RNA Sequencing on Muscle Biopsies from Exertional Rhabdomyolysis Patients Revealed Down-Regulation of Mitochondrial Function and Enhancement of Extracellular Matrix Composition
by Mingqiang Ren, Luke P. Michaelson, Ognoon Mungunsukh, Peter Bedocs, Liam Friel, Kristen Cofer, Carolyn E. Dartt, Nyamkhishig Sambuughin and Francis G. O’Connor
Genes 2025, 16(8), 930; https://doi.org/10.3390/genes16080930 (registering DOI) - 2 Aug 2025
Abstract
Background/Objective: Exertional rhabdomyolysis (ER) is primarily driven by mechanical stress on muscles during strenuous or unaccustomed exercise, often exacerbated by environmental factors like heat and dehydration. While the general cellular pathway involving energy depletion and calcium overload is understood in horse ER models, [...] Read more.
Background/Objective: Exertional rhabdomyolysis (ER) is primarily driven by mechanical stress on muscles during strenuous or unaccustomed exercise, often exacerbated by environmental factors like heat and dehydration. While the general cellular pathway involving energy depletion and calcium overload is understood in horse ER models, the underlying mechanisms specific to the ER are not universally known within humans. This study aimed to evaluate whether patients with ER exhibited transcriptional signatures that were significantly different from those of healthy individuals. Methods: This study utilized RNA sequencing on skeletal muscle samples from 19 human patients with ER history, collected at a minimum of six months after the most recent ER event, and eight healthy controls to investigate the transcriptomic landscape of ER. To identify any alterations in biological processes between the case and control groups, functional pathway analyses were conducted. Results: Functional pathway enrichment analyses of differentially expressed genes revealed strong suppression of mitochondrial function. This suppression included the “aerobic electron transport chain” and “oxidative phosphorylation” pathways, indicating impaired energy production. Conversely, there was an upregulation of genes associated with adhesion and extracellular matrix-related pathways, indicating active restoration of muscle function in ER cases. Conclusions: The study demonstrated that muscle tissue exhibited signs of suppressed mitochondrial function and increased extracellular matrix development. Both of these facilitate muscle recovery within several months after an ER episode. Full article
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30 pages, 4011 KiB  
Article
Multitarget Design of Steroidal Inhibitors Against Hormone-Dependent Breast Cancer: An Integrated In Silico Approach
by Juan Rodríguez-Macías, Oscar Saurith-Coronell, Carlos Vargas-Echeverria, Daniel Insuasty Delgado, Edgar A. Márquez Brazón, Ricardo Gutiérrez De Aguas, José R. Mora, José L. Paz and Yovanni Marrero-Ponce
Int. J. Mol. Sci. 2025, 26(15), 7477; https://doi.org/10.3390/ijms26157477 (registering DOI) - 2 Aug 2025
Abstract
Hormone-dependent breast cancer, particularly in its treatment-resistant forms, remains a significant therapeutic challenge. In this study, we applied a fully computational strategy to design steroid-based compounds capable of simultaneously targeting three key receptors involved in disease progression: progesterone receptor (PR), estrogen receptor alpha [...] Read more.
Hormone-dependent breast cancer, particularly in its treatment-resistant forms, remains a significant therapeutic challenge. In this study, we applied a fully computational strategy to design steroid-based compounds capable of simultaneously targeting three key receptors involved in disease progression: progesterone receptor (PR), estrogen receptor alpha (ER-α), and HER2. Using a robust 3D-QSAR model (R2 = 0.86; Q2_LOO = 0.86) built from 52 steroidal structures, we identified molecular features associated with high anticancer potential, specifically increased polarizability and reduced electronegativity. From a virtual library of 271 DFT-optimized analogs, 31 compounds were selected based on predicted potency (pIC50 > 7.0) and screened via molecular docking against PR (PDB 2W8Y), HER2 (PDB 7JXH), and ER-α (PDB 6VJD). Seven candidates showed strong binding affinities (ΔG ≤ −9 kcal/mol for at least two targets), with Estero-255 emerging as the most promising. This compound demonstrated excellent conformational stability, a robust hydrogen-bonding network, and consistent multitarget engagement. Molecular dynamics simulations over 100 nanoseconds confirmed the structural integrity of the top ligands, with low RMSD values, compact radii of gyration, and stable binding energy profiles. Key interactions included hydrophobic contacts, π–π stacking, halogen–π interactions, and classical hydrogen bonds with conserved residues across all three targets. These findings highlight Estero-255, alongside Estero-261 and Estero-264, as strong multitarget candidates for further development. By potentially disrupting the PI3K/AKT/mTOR signaling pathway, these compounds offer a promising strategy for overcoming resistance in hormone-driven breast cancer. Experimental validation, including cytotoxicity assays and ADME/Tox profiling, is recommended to confirm their therapeutic potential. Full article
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8 pages, 2132 KiB  
Proceeding Paper
Impact of Current Variations on Weld Bead Properties During the Cold Metal Transfer (CMT) Welding of 7075 Aluminium Using an ER4043 Filler Wire
by Vishal Bhardwaj, Siddharth Garg and Qasim Murtaza
Eng. Proc. 2025, 93(1), 22; https://doi.org/10.3390/engproc2025093022 (registering DOI) - 1 Aug 2025
Abstract
This study investigated into how different current input levels during cold metal transfer (CMT) welding affected the characteristics of the weld bead. For the current variation, three input values were taken: 80 A, 90 A, and 100 A. Weld beads fabricated from all [...] Read more.
This study investigated into how different current input levels during cold metal transfer (CMT) welding affected the characteristics of the weld bead. For the current variation, three input values were taken: 80 A, 90 A, and 100 A. Weld beads fabricated from all three current inputs were compared by analysing their microstructure, microhardness, tensile strength, and residual stress. The microhardness of the weld bead decreased when the current parameter was increased from 80 A to 100 A. The average tensile strength increased from 80 A to 90 A. The lowest residual stress calculated was −135 MPa with 100 A current. Full article
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14 pages, 5672 KiB  
Article
Multiplex Immunofluorescence Reveals Therapeutic Targets EGFR, EpCAM, Tissue Factor, and TROP2 in Triple-Negative Breast Cancer
by T. M. Mohiuddin, Wenjie Sheng, Chaoyu Zhang, Marwah Al-Rawe, Svetlana Tchaikovski, Felix Zeppernick, Ivo Meinhold-Heerlein and Ahmad Fawzi Hussain
Int. J. Mol. Sci. 2025, 26(15), 7430; https://doi.org/10.3390/ijms26157430 (registering DOI) - 1 Aug 2025
Abstract
Triple-negative breast cancer (TNBC) is a clinically and molecularly heterogeneous subtype defined by the absence of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) expression. In this study, tumor specimens from 104 TNBC patients were analyzed to [...] Read more.
Triple-negative breast cancer (TNBC) is a clinically and molecularly heterogeneous subtype defined by the absence of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) expression. In this study, tumor specimens from 104 TNBC patients were analyzed to characterize molecular and clinicopathological features and to assess the expression and therapeutic potential of four key surface markers: epidermal growth factor receptor (EGFR), epithelial cell adhesion molecule (EpCAM), tissue factor (TF), and trophoblast cell surface antigen (TROP2). Multiplex immunofluorescence (mIF) demonstrated elevated EGFR and TROP2 expression in the majority of samples. Significant positive correlations were observed between EGFR and TF, as well as between TROP2 and both TF and EpCAM. Expression analyses revealed increased EGFR and TF levels with advancing tumor stage, whereas EpCAM expression declined in advanced-stage tumors. TROP2 and TF expression were significantly elevated in higher-grade tumors. Additionally, EGFR and EpCAM levels were significantly higher in patients with elevated Ki-67 indices. Binding specificity assays using single-chain variable fragment (scFv-SNAP) fusion proteins confirmed robust targeting efficacy, particularly for EGFR and TROP2. These findings underscore the therapeutic relevance of EGFR and TROP2 as potential biomarkers and targets in TNBC. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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20 pages, 3979 KiB  
Article
Theoretical Study of CO Oxidation on Pt Single-Atom Catalyst Decorated C3N Monolayers with Nitrogen Vacancies
by Suparada Kamchompoo, Yuwanda Injongkol, Nuttapon Yodsin, Rui-Qin Zhang, Manaschai Kunaseth and Siriporn Jungsuttiwong
Sci 2025, 7(3), 101; https://doi.org/10.3390/sci7030101 - 1 Aug 2025
Abstract
Carbon monoxide (CO) is a major toxic gas emitted from vehicle exhaust, industrial processes, and incomplete fuel combustion, posing serious environmental and health risks. Catalytic oxidation of CO into less harmful CO2 is an effective strategy to reduce these emissions. In this [...] Read more.
Carbon monoxide (CO) is a major toxic gas emitted from vehicle exhaust, industrial processes, and incomplete fuel combustion, posing serious environmental and health risks. Catalytic oxidation of CO into less harmful CO2 is an effective strategy to reduce these emissions. In this study, we investigated the catalytic performance of platinum (Pt) single atoms doped on C3N monolayers with various vacancy defects, including single carbon (CV) and nitrogen (NV) vacancies, using density functional theory (DFT) calculations. Our results demonstrate that Pt@NV-C3N exhibited the most favorable catalytic properties, with the highest O2 adsorption energy (−3.07 eV). This performance significantly outperforms Pt atoms doped at other vacancies. It can be attributed to the strong binding between Pt and nitrogen vacancies, which contributes to its excellent resistance to Pt aggregation. CO oxidation on Pt@NV-C3N proceeds via the Eley–Rideal (ER2) mechanism with a low activation barrier of 0.41 eV for the rate-determining step, indicating high catalytic efficiency at low temperatures. These findings suggest that Pt@NV-C3N is a promising candidate for CO oxidation, contributing to developing cost-effective and environmentally sustainable catalysts. The strong binding of Pt atoms to the nitrogen vacancies prevents aggregation, ensuring the stability and durability of the catalyst. The kinetic modeling further revealed that the ER2 mechanism offers the highest reaction rate constants over a wide temperature range (273–700 K). The low activation energy barrier also facilitates CO oxidation at lower temperatures, addressing critical challenges in automotive and industrial pollution control. This study provides valuable theoretical insights for designing advanced single-atom catalysts for environmental remediation applications. Full article
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34 pages, 4436 KiB  
Article
Structure of the Secretory Compartments in Goblet Cells in the Colon and Small Intestine
by Alexander A. Mironov, Irina S. Sesorova, Pavel S. Vavilov, Roberto Longoni, Paola Briata, Roberto Gherzi and Galina V. Beznoussenko
Cells 2025, 14(15), 1185; https://doi.org/10.3390/cells14151185 (registering DOI) - 31 Jul 2025
Abstract
The Golgi of goblet cells represents a specialized machine for mucin glycosylation. This process occurs in a specialized form of the secretory pathway, which remains poorly examined. Here, using high-resolution three-dimensional electron microscopy (EM), EM tomography, serial block face scanning EM (SBF-SEM) and [...] Read more.
The Golgi of goblet cells represents a specialized machine for mucin glycosylation. This process occurs in a specialized form of the secretory pathway, which remains poorly examined. Here, using high-resolution three-dimensional electron microscopy (EM), EM tomography, serial block face scanning EM (SBF-SEM) and immune EM we analyzed the secretory pathway in goblet cells and revealed that COPII-coated buds on the endoplasmic reticulum (ER) are extremely rare. The ERES vesicles with dimensions typical for the COPII-dependent vesicles were not found. The Golgi is formed by a single cisterna organized in a spiral with characteristics of the cycloid surface. This ribbon has a shape of a cup with irregular perforations. The Golgi cup is filled with secretory granules (SGs) containing glycosylated mucins. Their diameter is close to 1 µm. The cup is connected with ER exit sites (ERESs) with temporal bead-like connections, which are observed mostly near the craters observed at the externally located cis surface of the cup. The craters represent conus-like cavities formed by aligned holes of gradually decreasing diameters through the first three Golgi cisternae. These craters are localized directly opposite the ERES. Clusters of the 52 nm vesicles are visible between Golgi cisternae and between SGs. The accumulation of mucin, started in the fourth cisternal layer, induces distensions of the cisternal lumen. The thickness of these distensions gradually increases in size through the next cisternal layers. The spherical distensions are observed at the edges of the Golgi cup, where they fuse with SGs and detach from the cisternae. After the fusion of SGs located just below the apical plasma membrane (APM) with APM, mucus is secreted. The content of this SG becomes less osmiophilic and the excessive surface area of the APM is formed. This membrane is eliminated through the detachment of bubbles filled with another SG and surrounded with a double membrane or by collapse of the empty SG and transformation of the double membrane lacking a visible lumen into multilayered organelles, which move to the cell basis and are secreted into the intercellular space where the processes of dendritic cells are localized. These data are evaluated from the point of view of existing models of intracellular transport. Full article
22 pages, 2422 KiB  
Article
A Conserved N-Terminal Di-Arginine Motif Stabilizes Plant DGAT1 and Modulates Lipid Droplet Organization
by Somrutai Winichayakul, Hong Xue and Nick Roberts
Int. J. Mol. Sci. 2025, 26(15), 7406; https://doi.org/10.3390/ijms26157406 (registering DOI) - 31 Jul 2025
Abstract
Diacylglycerol-O-acyltransferase 1 (DGAT1, EC 2.3.1.20) is a pivotal enzyme in plant triacylglycerol (TAG) biosynthesis. Previous work identified conserved di-arginine (R) motifs (R-R, R-X-R, and R-X-X-R) in its N-terminal cytoplasmic acyl-CoA binding domain. To elucidate their functional significance, we engineered R-rich sequences in the [...] Read more.
Diacylglycerol-O-acyltransferase 1 (DGAT1, EC 2.3.1.20) is a pivotal enzyme in plant triacylglycerol (TAG) biosynthesis. Previous work identified conserved di-arginine (R) motifs (R-R, R-X-R, and R-X-X-R) in its N-terminal cytoplasmic acyl-CoA binding domain. To elucidate their functional significance, we engineered R-rich sequences in the N-termini of Tropaeolum majus and Zea mays DGAT1s. Comparative analysis with their respective non-mutant constructs showed that deleting or substituting R with glycine in the N-terminal region of DGAT1 markedly reduced lipid accumulation in both Camelina sativa seeds and Saccharomyces cerevisiae cells. Immunofluorescence imaging revealed co-localization of non-mutant and R-substituted DGAT1 with lipid droplets (LDs). However, disruption of an N-terminal di-R motif destabilizes DGAT1, alters LD organization, and impairs recombinant oleosin retention on LDs. Further evidence suggests that the di-R motif mediates DGAT1 retrieval from LDs to the endoplasmic reticulum (ER), implicating its role in dynamic LD–ER protein trafficking. These findings establish the conserved di-R motifs as important regulators of DGAT1 function and LD dynamics, offering insights for the engineering of oil content in diverse biological systems. Full article
(This article belongs to the Special Issue Modern Plant Cell Biotechnology: From Genes to Structure, 2nd Edition)
33 pages, 2423 KiB  
Review
Chaperone-Mediated Responses and Mitochondrial–Endoplasmic Reticulum Coupling: Emerging Insight into Alzheimer’s Disease
by Manish Kumar Singh, Minghao Fu, Sunhee Han, Jyotsna S. Ranbhise, Wonchae Choe, Sung Soo Kim and Insug Kang
Cells 2025, 14(15), 1179; https://doi.org/10.3390/cells14151179 - 31 Jul 2025
Abstract
Alzheimer’s disease (AD) is increasingly recognized as a multifactorial disorder driven by a combination of disruptions in proteostasis and organelle communication. The 2020 Lancet commission reported that approximately 10 million people worldwide were affected by AD in the mid-20th century. AD is the [...] Read more.
Alzheimer’s disease (AD) is increasingly recognized as a multifactorial disorder driven by a combination of disruptions in proteostasis and organelle communication. The 2020 Lancet commission reported that approximately 10 million people worldwide were affected by AD in the mid-20th century. AD is the most prevalent cause of dementia. By early 2030, the global cost of dementia is projected to rise by USD 2 trillion per year, with up to 85% of that cost attributed to daily patient care. Several factors have been implicated in the progression of neurodegeneration, including increased oxidative stress, the accumulation of misfolded proteins, the formation of amyloid plaques and aggregates, the unfolded protein response (UPR), and mitochondrial–endoplasmic reticulum (ER) calcium homeostasis. However, the exact triggers that initiate these pathological processes remain unclear, in part because clinical symptoms often emerge gradually and subtly, complicating early diagnosis. Among the early hallmarks of neurodegeneration, elevated levels of reactive oxygen species (ROS) and the buildup of misfolded proteins are believed to play pivotal roles in disrupting proteostasis, leading to cognitive deficits and neuronal cell death. The accumulation of amyloid-β (Aβ) plaques and tau neurofibrillary tangles is a characteristic feature of AD. These features contribute to chronic neuroinflammation, which is marked by the release of pro-inflammatory cytokines and chemokines that exacerbate oxidative stress. Given these interconnected mechanisms, targeting stress-related signaling pathways, such as oxidative stress (ROS) generated in the mitochondria and ER, ER stress, UPR, and cytosolic chaperones, represents a promising strategy for therapeutic intervention. This review focuses on the relationship between stress chaperone responses and organelle function, particularly the interaction between mitochondria and the ER, in the development of new therapies for AD and related neurodegenerative disorders. Full article
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20 pages, 2382 KiB  
Article
The Impact of the Injected Mass of the Gastrin-Releasing Peptide Receptor Antagonist on Uptake in Breast Cancer: Lessons from a Phase I Trial of [99mTc]Tc-DB8
by Olga Bragina, Vladimir Chernov, Mariia Larkina, Ruslan Varvashenya, Roman Zelchan, Anna Medvedeva, Anastasiya Ivanova, Liubov Tashireva, Theodosia Maina, Berthold A. Nock, Panagiotis Kanellopoulos, Jens Sörensen, Anna Orlova and Vladimir Tolmachev
Pharmaceutics 2025, 17(8), 1000; https://doi.org/10.3390/pharmaceutics17081000 - 31 Jul 2025
Abstract
Background/Objectives: Gastrin-releasing peptide receptor (GRPR) is overexpressed in breast cancer and might be used as a theranostics target. The expression of GRPR strongly correlates with estrogen receptor (ER) expression. Visualization of GRPR-expressing breast tumors might help to select the optimal treatment. Developing GRPR-specific [...] Read more.
Background/Objectives: Gastrin-releasing peptide receptor (GRPR) is overexpressed in breast cancer and might be used as a theranostics target. The expression of GRPR strongly correlates with estrogen receptor (ER) expression. Visualization of GRPR-expressing breast tumors might help to select the optimal treatment. Developing GRPR-specific probes for SPECT would permit imaging-guided therapy in regions with restricted access to PET facilities. In this first-in-human study, we evaluated the safety, biodistribution, and dosimetry of the [99mTc]Tc-DB8 GRPR-antagonistic peptide. We also addressed the important issue of finding the optimal injected peptide mass. Methods: Fifteen female patients with ER-positive primary breast cancer were enrolled and divided into three cohorts receiving [99mTc]Tc-DB8 (corresponding to three distinct doses of 40, 80, or 120 µg DB8) comprising five patients each. Additionally, four patients with ER-negative primary tumors were injected with 80 µg [99mTc]Tc-DB8. The injected activity was 360 ± 70 MBq. Planar scintigraphy was performed after 2, 4, 6, and 24 h, and SPECT/CT scans followed planar imaging 2, 4, and 6 h after injection. Results: No adverse events were associated with [99mTc]Tc-DB8 injections. The effective dose was 0.009–0.014 mSv/MBq. Primary tumors and all known lymph node metastases were visualized irrespective of injected peptide mass. The highest uptake in the ER-positive tumors was 2 h after injection of [99mTc]Tc-DB8 at a 80 µg DB8 dose (SUVmax 5.3 ± 1.2). Injection of [99mTc]Tc-DB8 with 80 µg DB8 provided significantly (p < 0.01) higher uptake in primary ER-positive breast cancer lesions than injection with 40 µg DB8 (SUVmax 2.0 ± 0.3) or 120 µg (SUVmax 3.2 ± 1.4). Tumor-to-contralateral breast ratio after injection of 80 μg was also significantly (p < 0.01, ANOVA test) higher than ratios after injection of other peptide masses. The uptake in ER-negative lesions was significantly lower (SUVmax 2.0 ± 0.3) than in ER-positive tumors. Conclusions: Imaging using [99mTc]Tc-DB8 is safe, tolerable, and associated with low absorbed doses. The tumor uptake is dependent on the injected peptide mass. The injection of an optimal mass (80 µg) provides the highest uptake in ER-positive tumors. At optimal dosing, the uptake was significantly higher in ER-positive than in ER-negative lesions. Full article
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18 pages, 300 KiB  
Review
Genetic Dissection of Energy Deficiency in Autism Spectrum Disorder
by John Jay Gargus
Genes 2025, 16(8), 923; https://doi.org/10.3390/genes16080923 (registering DOI) - 31 Jul 2025
Viewed by 44
Abstract
Background/Objectives: An important new consideration when studying autism spectrum disorder (ASD) is the bioenergetic mechanisms underlying the relatively recent rapid evolutionary expansion of the human brain, which pose fundamental risks for mitochondrial dysfunction and calcium signaling abnormalities and their potential role in [...] Read more.
Background/Objectives: An important new consideration when studying autism spectrum disorder (ASD) is the bioenergetic mechanisms underlying the relatively recent rapid evolutionary expansion of the human brain, which pose fundamental risks for mitochondrial dysfunction and calcium signaling abnormalities and their potential role in ASD, as recently highlighted by insights from the BTBR mouse model of ASD. The rapid brain expansion taking place as Homo sapiens evolved, particularly in the parietal lobe, led to increased energy demands, making the brain vulnerable to such metabolic disruptions as are seen in ASD. Methods: Mitochondrial dysfunction in ASD is characterized by impaired oxidative phosphorylation, elevated lactate and alanine levels, carnitine deficiency, abnormal reactive oxygen species (ROS), and altered calcium homeostasis. These dysfunctions are primarily functional, rather than being due to mitochondrial DNA mutations. Calcium signaling plays a crucial role in neuronal ATP production, with disruptions in inositol 1,4,5-trisphosphate receptor (ITPR)-mediated endoplasmic reticulum (ER) calcium release being observed in ASD patient-derived cells. Results: This impaired signaling affects the ER–mitochondrial calcium axis, leading to mitochondrial energy deficiency, particularly in high-energy regions of the developing brain. The BTBR mouse model, with its unique Itpr3 gene mutation, exhibits core autism-like behaviors and metabolic syndromes, providing valuable insights into ASD pathophysiology. Conclusions: Various interventions have been tested in BTBR mice, as in ASD, but none have directly targeted the Itpr3 mutation or its calcium signaling pathway. This review presents current genetic, biochemical, and neurological findings in ASD and its model systems, highlighting the need for further research into metabolic resilience and calcium signaling as potential diagnostic and therapeutic targets for ASD. Full article
(This article belongs to the Section Neurogenomics)
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23 pages, 11314 KiB  
Article
Transcriptomic Analysis Reveals Opposing Roles of CEL1B in Sophorose- and Lactose-Induced Cellulase Expression in Trichoderma reesei Rut C30
by Lu Wang, Junping Fan, Xiao He, Jian Cheng, Xinyan Zhang, Tian Tian and Yonghao Li
Fermentation 2025, 11(8), 439; https://doi.org/10.3390/fermentation11080439 (registering DOI) - 31 Jul 2025
Viewed by 142
Abstract
The β-glucosidase CEL1B has been linked to regulating cellulase expression in Trichoderma reesei, yet its inducer-specific functions and broader regulatory roles remain poorly characterized. In this study, CRISPR-Cas9-mediated gene knockout was applied in the industrial high-producing T. reesei Rut C30 to investigate [...] Read more.
The β-glucosidase CEL1B has been linked to regulating cellulase expression in Trichoderma reesei, yet its inducer-specific functions and broader regulatory roles remain poorly characterized. In this study, CRISPR-Cas9-mediated gene knockout was applied in the industrial high-producing T. reesei Rut C30 to investigate CEL1B function without the confounding effects of KU70 deletion. Unlike previous studies focused solely on cellulose or lactose induction, transcriptomic analysis of the CEL1B knockout strain revealed its regulatory roles under both lactose- and sophorose-rich conditions, with sophorose representing the most potent natural inducer of cellulase expression. Under lactose induction, CEL1B deletion resulted in a 52.4% increase in cellulase activity (p < 0.05), accompanied by transcriptome-wide upregulation of β-glucosidase genes (CEL3A: 729%, CEL3D: 666.8%, CEL3C: 110.9%), cellulose-sensing receptors (CRT1: 203.0%, CRT2: 105.8%), and key transcription factors (XYR1: 2.7-fold, ACE3: 2.8-fold, VIB1: 2.1-fold). Expression of ER proteostasis genes was significantly upregulated (BIP1: 3.3-fold, HSP70: 6.2-fold), contributing to enhanced enzyme secretion. Conversely, under sophorose induction, CEL1B deletion reduced cellulase activity by 25.7% (p < 0.05), which was associated with transcriptome profiling showing significant downregulation of β-glucosidase CEL3H (66.6%) and cellodextrin transporters (TrireC30_91594: 79.3%, TrireC30_127980: 76.3%), leading to reduced cellobiohydrolase expression (CEL7A: 57.8%, CEL6A: 67.8%). This first transcriptomic characterization of the CEL1B knockout strain reveals its dual opposing roles in modulating cellulase expression in response to lactose versus sophorose, providing new strategies for optimizing inducer-specific enzyme production in T. reesei. Full article
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24 pages, 17531 KiB  
Article
Efficient Unsupervised Clustering of Hyperspectral Images via Flexible Multi-Anchor Graphs
by Yihong Li, Ting Wang, Zhe Cao, Haonan Xin and Rong Wang
Remote Sens. 2025, 17(15), 2647; https://doi.org/10.3390/rs17152647 - 30 Jul 2025
Viewed by 99
Abstract
Unsupervised hyperspectral image (HSI) clustering is a fundamental yet challenging task due to high dimensionality and complex spectral–spatial characteristics. In this paper, we propose a novel and efficient clustering framework centered on adaptive and diverse anchor graph modeling. First, we introduce a parameter-free [...] Read more.
Unsupervised hyperspectral image (HSI) clustering is a fundamental yet challenging task due to high dimensionality and complex spectral–spatial characteristics. In this paper, we propose a novel and efficient clustering framework centered on adaptive and diverse anchor graph modeling. First, we introduce a parameter-free construction strategy that employs Entropy Rate Superpixel (ERS) segmentation to generate multiple anchor graphs of varying sizes from a single HSI, overcoming the limitation of fixed anchor quantities and enhancing structural expressiveness. Second, we propose an anchor-to-pixel label propagation mechanism to transfer anchor-level cluster labels back to the pixel level, reinforcing spatial coherence and spectral discriminability. Third, we perform clustering directly at the anchor level, which substantially reduces computational cost while retaining structure-aware accuracy. Extensive experiments on three benchmark datasets (Trento, Salinas, and Pavia Center) demonstrate the effectiveness and efficiency of our approach. Full article
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21 pages, 2028 KiB  
Article
Graphene Oxide-Supported QuEChERS Extraction Coupled with LC-MS/MS for Trace-Level Analysis of Wastewater Pharmaceuticals
by Weronika Rogowska and Piotr Kaczyński
Appl. Sci. 2025, 15(15), 8441; https://doi.org/10.3390/app15158441 - 30 Jul 2025
Viewed by 204
Abstract
Detecting pharmaceuticals in environmental matrices, particularly in wastewater, is crucial due to their potential environmental occurrence and unpredictable ecological and health-related consequences. These substances, often present in trace amounts, require highly sensitive and selective analytical methods for effective monitoring. A modified version of [...] Read more.
Detecting pharmaceuticals in environmental matrices, particularly in wastewater, is crucial due to their potential environmental occurrence and unpredictable ecological and health-related consequences. These substances, often present in trace amounts, require highly sensitive and selective analytical methods for effective monitoring. A modified version of the QuEChERS (Quick, Easy, Cheap, Effective, Rugged, and Safe) method was evaluated to evaluate 18 pharmaceuticals and 2 metabolites in wastewater samples using liquid chromatography with tandem mass spectrometry (LC-MS/MS). The method’s performance was assessed using linearity, recovery, precision, limits of quantification (LOQ) and detection (LOD), and the matrix effect (ME). The final method was based on acetonitrile, Na2EDTA, citrate buffer, and graphene oxide (GO). Finally, the calibration curves prepared in acetonitrile and the matrix extract showed a correlation coefficient of 0.99. Most of the compounds had LOQ values lower than 0.5 μg⋅mL−1. Recoveries were achieved in the 70–98% range, with RSD lower than 13%. GO allowed the elimination of the ME, which occurred in the range of −11% to 15%. The results indicate that a low-cost and straightforward method is suitable for routinely monitoring pharmaceuticals in wastewater, which is crucial for minimizing the impact of pollutants on aquatic ecosystems. Full article
(This article belongs to the Section Green Sustainable Science and Technology)
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21 pages, 937 KiB  
Article
LAI: Label Annotation Interaction-Based Representation Enhancement for End to End Relation Extraction
by Rongxuan Lai, Wenhui Wu, Li Zou, Feifan Liao, Zhenyi Wang and Haibo Mi
Big Data Cogn. Comput. 2025, 9(8), 198; https://doi.org/10.3390/bdcc9080198 - 29 Jul 2025
Viewed by 238
Abstract
End-to-end relation extraction (E2ERE) generally performs named entity recognition and relation extraction either simultaneously or sequentially. While numerous studies on E2ERE have centered on enhancing span representations to improve model performance, challenges remain due to the gaps between subtasks (named entity recognition and [...] Read more.
End-to-end relation extraction (E2ERE) generally performs named entity recognition and relation extraction either simultaneously or sequentially. While numerous studies on E2ERE have centered on enhancing span representations to improve model performance, challenges remain due to the gaps between subtasks (named entity recognition and relation extraction) and the modeling discrepancies between entities and relations. In this paper, we propose a novel Label Annotation Interaction-based representation enhancement method for E2ERE, which institutes a two-phase semantic interaction to augment representations. Specifically, we firstly feed label annotations that are easy to manually annotate into a language model, and conduct the first-round interaction between three types of tokens with a partial attention mechanism; Then we construct a latent multi-view graph to capture various possible links between label and entity (pair) nodes, facilitating the second-round interaction between entities and labels. A series of comparative experiments with methods of various transformer-based architectures currently in use show that LAI-Net can maintain performance on par with the current SOTA in terms of NER task, and achieves significant improvements over existing SOTA models in terms of RE task. Full article
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28 pages, 8135 KiB  
Article
Drastically Accelerating Fatigue Life Assessment: A Dual-End Multi-Station Spindle Approach for High-Throughput Precision Testing
by Abdurrahman Doğan, Kürşad Göv and İbrahim Göv
Machines 2025, 13(8), 665; https://doi.org/10.3390/machines13080665 - 29 Jul 2025
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Abstract
This study introduces a time-efficient rotating bending fatigue testing system featuring 11 dual-end spindles, enabling simultaneous testing of 22 specimens. Designed for high-throughput fatigue life (S–N curve) assessment, the system theoretically allows over 93% reduction in total test duration, with 87.5% savings demonstrated [...] Read more.
This study introduces a time-efficient rotating bending fatigue testing system featuring 11 dual-end spindles, enabling simultaneous testing of 22 specimens. Designed for high-throughput fatigue life (S–N curve) assessment, the system theoretically allows over 93% reduction in total test duration, with 87.5% savings demonstrated in validation experiments using AISI 304 stainless steel. The PLC-based architecture provides autonomous operation, real-time failure detection, and automatic cycle logging. ER16 collet holders are easily replaceable within one minute, and all the components are selected from widely available industrial-grade parts to ensure ease of maintenance. The modular design facilitates straightforward adaptation to different station counts. The validation results confirmed an endurance limit of 421 MPa, which is consistent with the established literature and within ±5% deviation. Fractographic analysis revealed distinct crack initiation and propagation zones, supporting the observed fatigue behavior. This high-throughput methodology significantly improves testing efficiency and statistical reliability, offering a practical solution for accelerated fatigue life evaluation in structural, automotive, and aerospace applications. Full article
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