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Search Results (3,043)

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Keywords = molecular dynamics analysis

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20 pages, 1828 KiB  
Review
Improving Replication in Endometrial Omics: Understanding the Influence of the Menstrual Cycle
by Jessica Chung and Peter Adrian Rogers
Int. J. Mol. Sci. 2025, 26(2), 857; https://doi.org/10.3390/ijms26020857 (registering DOI) - 20 Jan 2025
Abstract
The dynamic nature of human endometrial tissue presents unique challenges in analysis. Despite extensive research into endometrial disorders such as endometriosis and infertility, recent systematic reviews have highlighted concerning issues with the reproducibility of omics studies attempting to identify biomarkers. This review examines [...] Read more.
The dynamic nature of human endometrial tissue presents unique challenges in analysis. Despite extensive research into endometrial disorders such as endometriosis and infertility, recent systematic reviews have highlighted concerning issues with the reproducibility of omics studies attempting to identify biomarkers. This review examines factors contributing to poor reproducibility in endometrial omics research. Hormonal fluctuations in the menstrual cycle lead to widespread molecular changes in the endometrium, most notably in gene expression profiles. In this review, we examine the variability in omics data due to the menstrual cycle and highlight the importance of accurate menstrual cycle dating for effective statistical modelling. The current standards of endometrial dating lack precision and we make the case for using molecular-based modelling methods to estimate menstrual cycle time for endometrium tissue samples. Additionally, we discuss statistical considerations such as confounding and interaction effects, as well as the importance of recording the detailed and accurate clinical information of patients. By addressing these methodological challenges, we aim to establish more robust and reproducible research practises, increasing the reliability of endometrial omics research and biomarker discovery. Full article
(This article belongs to the Special Issue Molecular Studies of Endometriosis and Associated Diseases)
27 pages, 3101 KiB  
Article
Development of a Sustainable Flexible Humidity Sensor Based on Tenebrio molitor Larvae Biomass-Derived Chitosan
by Ezekiel Edward Nettey-Oppong, Riaz Muhammad, Emmanuel Ackah, Hojun Yang, Ahmed Ali, Hyun-Woo Jeong, Seong-Wan Kim, Young-Seek Seok and Seung Ho Choi
Sensors 2025, 25(2), 575; https://doi.org/10.3390/s25020575 - 20 Jan 2025
Viewed by 138
Abstract
This study presents the fabrication of a sustainable flexible humidity sensor utilizing chitosan derived from mealworm biomass as the primary sensing material. The chitosan-based humidity sensor was fabricated by casting chitosan and polyvinyl alcohol (PVA) films with interdigitated copper electrodes, forming a laminate [...] Read more.
This study presents the fabrication of a sustainable flexible humidity sensor utilizing chitosan derived from mealworm biomass as the primary sensing material. The chitosan-based humidity sensor was fabricated by casting chitosan and polyvinyl alcohol (PVA) films with interdigitated copper electrodes, forming a laminate composite suitable for real-time, resistive-type humidity detection. Comprehensive characterization of the chitosan film was performed using Fourier-transform infrared (FTIR) spectroscopy, contact angle measurements, and tensile testing, which confirmed its chemical structure, wettability, and mechanical stability. The developed sensor exhibited a broad range of measurements from 6% to 97% relative humidity (RH), a high sensitivity of 2.43 kΩ/%RH, and a rapid response time of 18.22 s with a corresponding recovery time of 22.39 s. Moreover, the chitosan-based humidity sensor also demonstrated high selectivity for water vapor when tested against various volatile organic compounds (VOCs). The superior performance of the sensor is attributed to the structural properties of chitosan, particularly its ability to form reversible hydrogen bonds with water molecules. This mechanism was further elucidated through molecular dynamics simulations, revealing that the conductivity in the sensor is modulated by proton mobility, which operates via the Grotthuss mechanism under high-humidity and the packed-acid mechanism under low-humidity conditions. Additionally, the chitosan-based humidity sensor was further seamlessly integrated into an Internet of Things (IoT) framework, enabling wireless humidity monitoring and real-time data visualization on a mobile device. Comparative analysis with existing polymer-based resistive-type sensors further highlighted the superior sensing range, rapid dynamic response, and environmental sustainability of the developed sensor. This eco-friendly, biomass-derived, eco-friendly sensor shows potential for applications in environmental monitoring, smart agriculture, and industrial process control. Full article
(This article belongs to the Special Issue Humidity Sensors Based on Spectroscopy)
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14 pages, 6236 KiB  
Article
Characterization of Macromolecular Structure and Molecular Dynamics Optimization of Gas Coal: A Case Study of Hongdunzi Coal
by Lin Hong, Xingzhu Che, Dan Zheng and Dameng Gao
Processes 2025, 13(1), 275; https://doi.org/10.3390/pr13010275 - 19 Jan 2025
Viewed by 466
Abstract
To investigate the molecular structure characteristics and chemical reaction mechanisms of gas coal from the Hong II coal mine of the Ningxia Hongdunzi Coal Industry, this study explores its elemental composition, structural features, and methods for constructing and optimizing molecular models. The basic [...] Read more.
To investigate the molecular structure characteristics and chemical reaction mechanisms of gas coal from the Hong II coal mine of the Ningxia Hongdunzi Coal Industry, this study explores its elemental composition, structural features, and methods for constructing and optimizing molecular models. The basic properties of the coal were determined through proximate and elemental analyses. The carbon structure was characterized using 13C-NMR nuclear magnetic resonance, the N and S chemical states were analyzed with XPS, and the distribution of hydroxyl, aliphatic hydrocarbons, aromatic rings, and oxygen-containing functional groups was characterized by FT-IR. Based on the analysis results, a molecular structure model of Hongdunzi gas coal was constructed with the molecular formula C204H117O17NS, and the calculated results of the model showed high consistency with the experimental spectra of 13C-NMR. The macromolecular model of gas coal was constructed using the Materials Studio 2020 software, and its structure was optimized through geometric optimization and dynamic simulations. After optimization, the total energy of the model was significantly reduced from 8525.12 kcal·mol−1 to 3966.16 kcal·mol−1, highlighting the enhanced stability of the coal molecular structure. This optimization indicates that torsional energy plays a dominant role in molecular stability, while van der Waals forces and electrostatic interactions were significantly improved during the optimization process. Full article
(This article belongs to the Topic Energy Extraction and Processing Science)
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22 pages, 955 KiB  
Review
Hallmarks of DNA Damage Response in Germination Across Model and Crop Species
by Federico Sincinelli, Shraddha Shridhar Gaonkar, Sri Amarnadh Gupta Tondepu, Conrado Jr Dueñas and Andrea Pagano
Genes 2025, 16(1), 95; https://doi.org/10.3390/genes16010095 (registering DOI) - 17 Jan 2025
Viewed by 323
Abstract
DNA damage response (DDR) contributes to seed quality by guarding genome integrity in the delicate phases of pre- and post-germination. As a key determinant of stress tolerance and resilience, DDR has notable implications on the wider scale of the agroecosystems challenged by harsh [...] Read more.
DNA damage response (DDR) contributes to seed quality by guarding genome integrity in the delicate phases of pre- and post-germination. As a key determinant of stress tolerance and resilience, DDR has notable implications on the wider scale of the agroecosystems challenged by harsh climatic events. The present review focuses on the existing and documented links that interconnect DDR efficiency with an array of molecular hallmarks with biochemical, molecular, and physiological valence within the seed metabolic networks. The expression of genes encoding DDR sensors, transducers, mediators, and effectors is interpreted as a source of conserved hallmarks, along with markers of oxidative damage reflecting the seed’s ability to germinate. Similarly, the accumulation patterns of proteins and metabolites that contribute to DNA stability are predictive of seed quality traits. While a list of candidates is presented from multiple models and crop species, their interaction with chromatin dynamics, cell cycle progression, and hormonal regulation provides further levels of analysis to investigate the seed stress response holistically. The identification of novel hallmarks of DDR in seeds constitutes a framework to prompt validation with different experimental systems, to refine the current models of pre-germinative metabolism, and to promote targeted approaches for seed quality evaluation. Full article
(This article belongs to the Special Issue DNA Damage Repair and Plant Stress Response)
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11 pages, 347 KiB  
Article
An Investigation of the Entropy Associated with a Collapsing Molecular Cloud
by Gemechu Muleta Kumssa
Astronomy 2025, 4(1), 1; https://doi.org/10.3390/astronomy4010001 - 17 Jan 2025
Viewed by 297
Abstract
The investigation of entropy variation during the star formation process within collapsing molecular clouds represents a significant field of inquiry in astrophysics. As the cloud contracts, the presence of gaseous components contributes to an increase in entropy; however, the degree of this entropy [...] Read more.
The investigation of entropy variation during the star formation process within collapsing molecular clouds represents a significant field of inquiry in astrophysics. As the cloud contracts, the presence of gaseous components contributes to an increase in entropy; however, the degree of this entropy change is contingent upon the spatial constraints imposed on the gases. In this research endeavor, I perform a comprehensive analysis of entropy dynamics on a microcosmic level within the contracting cloud, adhering to the tenets of the second law of thermodynamics. The initial focus centers on a turbulent cloud consisting of N particles, each with a mass of M, which succumbs to gravitational forces. It becomes evident that for the collapse to transpire, the gravitational energy must surpass the opposing pressure forces, resulting in the swift movement of particles throughout the cloud and ultimately facilitating a shift in entropy. Full article
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7 pages, 3141 KiB  
Proceeding Paper
A Computational Investigation of Potential 5-HT 2C Receptor Inhibitors for Treating Schizophrenia by ADMET Profile Analysis, Molecular Docking, DFT, Network Pharmacology, and Molecular Dynamic Simulation
by Mohammed Raihan Uddin, Mahira Rahman, Mosammad Jannatun Nayem Rafin and Joya Datta Ripa
Chem. Proc. 2024, 16(1), 69; https://doi.org/10.3390/ecsoc-28-20242 - 16 Jan 2025
Viewed by 148
Abstract
Background: Schizophrenia manifests through behavioral abnormalities, suicidal ideation, and neuropsychological deficits. Hence, this study focused on 5-hydroxytryptamine (5-HT 2C) which influenced the modulation of the series of events that lead to schizophrenia. Methodology: Based on the computational study, the potential 5-HT 2C inhibitors [...] Read more.
Background: Schizophrenia manifests through behavioral abnormalities, suicidal ideation, and neuropsychological deficits. Hence, this study focused on 5-hydroxytryptamine (5-HT 2C) which influenced the modulation of the series of events that lead to schizophrenia. Methodology: Based on the computational study, the potential 5-HT 2C inhibitors such as Ephemeranthoquinone from Arundina graminifolia and Actinodaphnine from Litsea polyantha were determined. The candidate ligands were optimized using the Gaussian 16 software package and the DFT 6-31g (d,p) basis set. The interaction between the ligands and proteins was examined with PyRx 0.8. Additionally, pharmacokinetics was assessed using SwissADME, and Protox II for toxicity prediction. The network pharmacology study was examined by using the STRING database and the Cytoscape 3.10.1 tool. Moreover, a 100-nanosecond molecular dynamics simulation analysis using Desmond to ensure the stability of these two compounds was carried out. Result: This computational research observed that ephemeranthoquinone and actinodaphnine are the most selective 5-HT 2C inhibitors due to their docking score, optimization, and molecular dynamics simulation results. Conclusions: These compounds are required to be studied further to develop a useful 5-HT 2C inhibitors for the treatment of schizophrenia. Full article
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14 pages, 3874 KiB  
Article
Mechanism and Characterization of Bicomponent-Filler-Reinforced Natural Rubber Latex Composites: Experiment and Molecular Dynamics (MD)
by Zhipeng Feng, Hongzhou Zhu, Bo Hu, Huabin Chen and Yong Yan
Molecules 2025, 30(2), 349; https://doi.org/10.3390/molecules30020349 - 16 Jan 2025
Viewed by 324
Abstract
The incorporation of reinforcing fillers into natural rubber latex (NR) to achieve superior elasticity and mechanical properties has been widely applied across various fields. However, the tendency of reinforcing fillers to agglomerate within NR limits their potential applications. In this study, multi-walled carbon [...] Read more.
The incorporation of reinforcing fillers into natural rubber latex (NR) to achieve superior elasticity and mechanical properties has been widely applied across various fields. However, the tendency of reinforcing fillers to agglomerate within NR limits their potential applications. In this study, multi-walled carbon nanotube (MWCNT)–silica (SiO2)/NR composites were prepared using a solution blending method, aiming to enhance the performance of NR composites through the synergistic effects of dual-component fillers. The mechanical properties, dispersion behavior, and Payne effect of three types of composites—SiO2/NR (SNR), MWCNT/NR (MNR), and MWCNT-SiO2/NR (MSNR)—were investigated. In addition, the mean square displacement (MSD), fractional free volume (FFV), and binding energy of the three composites were simulated using molecular dynamics (MD) models. The results showed that the addition of a two-component filler increased the tensile strength, elongation at break, and Young’s modulus of NR composites by 56.4%, 72.41%, and 34.44%, respectively. The Payne effect of MSNR was reduced by 4.5% compared to MNR and SNR. In addition, the MD simulation results showed that the MSD and FFV of MSNR were reduced by 21% and 17.44%, respectively, and the binding energy was increased by 69 times, which was in agreement with the experimental results. The underlying mechanisms between the dual-component fillers were elucidated through dynamic mechanical analysis (DMA), a rubber process analyzer (RPA), and field emission scanning electron microscopy (SEM). This study provides an effective reference for broadening the application fields of NR. Full article
(This article belongs to the Section Materials Chemistry)
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16 pages, 7403 KiB  
Article
Tidal Effects on Dissolved Organic Matter Dynamics in a Brackish Water Front Adjacent to Yangtze River Estuary
by Yasong Wang, Niting Peng, Zhiliang Liu, Liang Liu, Sishang Pan, Dayu Duan and Yunping Xu
Water 2025, 17(2), 226; https://doi.org/10.3390/w17020226 - 15 Jan 2025
Viewed by 469
Abstract
A brackish water front, where river water meets seawater, is a hotspot for biogeochemical processes. In this study, we examined the quantity and composition of dissolved organic matter (DOM) over a 24 h tidal cycle at a brackish water front near the Yangtze [...] Read more.
A brackish water front, where river water meets seawater, is a hotspot for biogeochemical processes. In this study, we examined the quantity and composition of dissolved organic matter (DOM) over a 24 h tidal cycle at a brackish water front near the Yangtze River estuary. Utilizing elemental analysis, fluorescence and ultraviolet spectroscopy, and ultra-high-resolution mass spectrometry, we observed rapid fluctuations in DOM throughout the tidal cycle. The dissolved organic carbon (DOC) and total nitrogen (TN) concentrations ranged from 0.70 to 1.5 mg/L and 0.43 to 0.94 mg/L, respectively. Water samples during low tide exhibited a higher fractional abundance of CHON (17.2 ± 0.1% vs. 14.6 ± 0.4%), CHOS (14.6 ± 4.5% vs. 9.1 ± 3.1%), and CHONS (1.6 ± 0.5% vs. 0.5 ± 0.3%) formulas, and a higher aromatization and average molecular weight, which is consistent with a stronger terrestrial influence. In contrast, at high tide, the water samples contained a greater abundance of CHO compounds (75.7 ± 3.8% vs. 66.5 ± 4.1%), a humic-like fluorescent C1 component, and carboxyl-rich alicyclic molecules (CRAMs), indicating a greater release of refractory DOM from resuspended sediments. However, variations in the DOC concentrations and several optical spectral parameters did not correlate with the changes in the salinity and tidal height. The results of the principal component analysis revealed different controls on specific fractions of DOM that are related to variable DOM sources or biogeochemical processes. The complexity of DOM dynamics underscores the necessity of elucidating DOM compositions at varying levels to enhance our understanding of carbon cycling in estuarine and coastal ecosystems. Full article
(This article belongs to the Section Oceans and Coastal Zones)
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22 pages, 23356 KiB  
Article
Conformational Dynamics of Mitochondrial Inorganic Pyrophosphatase hPPA2 and Its Changes Caused by Pathogenic Mutations
by Ekaterina Bezpalaya, Svetlana Kurilova, Nataliya Vorobyeva and Elena Rodina
Life 2025, 15(1), 100; https://doi.org/10.3390/life15010100 - 15 Jan 2025
Viewed by 285
Abstract
Inorganic pyrophosphatases, or PPases, are ubiquitous enzymes whose activity is necessary for a large number of biosynthetic reactions. The catalytic function of PPases is dependent on certain conformational changes that have been previously characterized based on the comparison of the crystal structures of [...] Read more.
Inorganic pyrophosphatases, or PPases, are ubiquitous enzymes whose activity is necessary for a large number of biosynthetic reactions. The catalytic function of PPases is dependent on certain conformational changes that have been previously characterized based on the comparison of the crystal structures of various complexes. The current work describes the conformational dynamics of a structural model of human mitochondrial pyrophosphatase hPPA2 using molecular dynamics simulation, all-atom principal component analysis, and coarse-grained normal mode analysis. In addition to the wild-type enzyme, four mutant variants of hPPA2 were characterized that correspond to the natural pathogenic variants causing severe mitochondrial dysfunction and cardio pathologies. As a result, we identified the global type of flexible motion that seems to be shared by other dimeric PPases. This motion is discussed in terms of the allosteric behavior of the protein. Analysis of the observed conformational dynamics revealed the formation of a binding site for anionic ligands in the active site that could be relevant to enzyme catalysis. Based on the comparison of the wild-type and mutant PPases dynamics, we suggest the possible molecular mechanisms of the functional incompetence of hPPA2 caused by mutations. The results of this work allow for deeper insight into the structural basis of PPase function and the possible effects of pathogenic mutations on the protein structure and function. Full article
(This article belongs to the Special Issue Applications of Molecular Dynamics to Biological Systems)
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19 pages, 5929 KiB  
Article
Vertical Profile Characteristics of Dissolved Organic Matter Biochemistry in the Tropical Reservoir Shaped by Hydrodynamic Forces
by Zongyue Liu, Miao Chen, Huiran Liu, Han Wang, Ziyu Ning, Wen Zhang, Yuqin Liu and Min Tang
Water 2025, 17(2), 203; https://doi.org/10.3390/w17020203 - 14 Jan 2025
Viewed by 408
Abstract
Dissolved organic matter (DOM) exerts a crucial role in biogeochemical processes and ascertaining water quality in reservoirs, where it is vulnerable to the dynamic impacts of surface water inflows. However, understanding how DOM quantity and biochemical features responds to hydrodynamic forces in tropical [...] Read more.
Dissolved organic matter (DOM) exerts a crucial role in biogeochemical processes and ascertaining water quality in reservoirs, where it is vulnerable to the dynamic impacts of surface water inflows. However, understanding how DOM quantity and biochemical features responds to hydrodynamic forces in tropical reservoirs remains limited. To enhance our understanding of the vertical profiles of DOM characteristics under varying hydrodynamic forces (strong, moderate, and weak regions) in the Chitian Reservoir (18°43′–18°42′ N, 109°68′–109°70′ E), in December 2023, we investigated the concentrations and biochemical characteristics of water column DOM samples using multispectral techniques, a parallel factor model, and two-dimensional correlation analysis. Our results indicated that DOM concentrations (4.34 ± 0.36 mg/L) are the highest in the reservoir center, whereas total nitrogen (0.52 ± 0.04 mg/L), total phosphorus (0.02 ± 0.03 mg/L), and nitrate nitrogen (1.01 ± 0.07 mg/L) present their highest values in the inlet region. As hydrodynamic force decreases, microbial activity increases, whereas DOM’s humification degree and molecular weight decline. DOM in the Chitian Reservoir comprises humic-like components, including three terrestrial sources (accounting for 85.38%~87.03%) and one microbial source, with dominant characteristics of allochthonous origin. The relative abundance of microbial components decreased from 14.62% to 12.97% with the increasing hydrodynamic force and increased with depth. DOM functional groups in the strong hydrodynamic force region and the reservoir’s upper layer show high consistency and uniformity. Phenolic O–H is the most reactive functional group concerning changes in water depth across all hydrodynamic areas, followed by polysaccharide C–O, owing to its high photoactivity. In contrast, aromatic C–H demonstrates the weakest reactivity. DOM’s spectral features are closely linked to nutrient form concentrations (N and P). Full article
(This article belongs to the Special Issue Advance in Hydrology and Hydraulics of the River System Research 2025)
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33 pages, 2203 KiB  
Article
Predicting the Anti-SARS-CoV-2 Potential of Isoquinoline Alkaloids from Brazilian Siparunaceae Species Using Chemometric Tools
by Brendo Araujo Gomes, Diégina Araújo Fernandes, Simony Carvalho Mendonça, Mariana Freire Campos, Thamirys Silva da Fonseca, Larissa Esteves Carvalho Constant, Natalia Ferreira de Sousa, Renata Priscila Barros de Menezes, Beatriz Albuquerque Custódio de Oliveira, Stephany da Silva Costa, Giovanna Barbosa Frensel, Alice Santos Rosa, Thamara Kelcya Fonseca Oliveira, Amanda Resende Tucci, Júlia Nilo Henrique Lima, Vivian Neuza Santos Ferreira, Milene Dias Miranda, Diego Allonso, Marcus Tullius Scotti, Suzana Guimarães Leitão and Gilda Guimarães Leitãoadd Show full author list remove Hide full author list
Int. J. Mol. Sci. 2025, 26(2), 633; https://doi.org/10.3390/ijms26020633 - 13 Jan 2025
Viewed by 756
Abstract
The COVID-19 pandemic has caused over 7 million deaths globally in the past four years. Siparuna spp. (Siparunaceae), which is used in Brazilian folk medicine, is considered a genus with potential antiviral alternatives. This study explored the correlation between phytochemicals in Siparuna leaf [...] Read more.
The COVID-19 pandemic has caused over 7 million deaths globally in the past four years. Siparuna spp. (Siparunaceae), which is used in Brazilian folk medicine, is considered a genus with potential antiviral alternatives. This study explored the correlation between phytochemicals in Siparuna leaf extracts (S. ficoides, S. decipiens, S. glycycarpa, S. reginae, and S. cymosa) and their potential against various SARS-CoV-2 targets. In vitro assays examined interactions between the spike protein and the ACE2 receptor, protease activity, and viral replication inhibition in Calu-3 cell models. UHPLC-MS/MS analysis, processed with MZmine and evaluated chemometrically, revealed isoquinoline alkaloids with bulbocapnine, showing promising therapeutic potential. Predictions regarding absorption, distribution, metabolism, excretion, and toxicity were conducted, along with molecular docking and dynamics simulations, to evaluate protein−ligand interaction stability. The results confirmed the antiviral activity of the Siparuna genus against SARS-CoV-2 targets, with 92% of the extracts maintaining over 70% cellular viability at 200 μg·mL−1 and 80% achieving more than 50% viral activity suppression at 50 μg·mL−1. These findings highlight the potential of isoquinoline alkaloids as novel anti-coronavirus agents and support the need for further exploration, isolation, and testing of Siparuna compounds in the fight against COVID-19. Full article
43 pages, 2331 KiB  
Review
Molecular Mechanisms of Dietary Compounds in Cancer Stem Cells from Solid Tumors: Insights into Colorectal, Breast, and Prostate Cancer
by Alexandru Filippi, Teodora Deculescu-Ioniță, Ariana Hudiță, Oana Baldasici, Bianca Gălățeanu and Maria-Magdalena Mocanu
Int. J. Mol. Sci. 2025, 26(2), 631; https://doi.org/10.3390/ijms26020631 - 13 Jan 2025
Viewed by 448
Abstract
Cancer stem cells (CSC) are known to be the main source of tumor relapse, metastasis, or multidrug resistance and the mechanisms to counteract or eradicate them and their activity remain elusive. There are different hypotheses that claim that the origin of CSC might [...] Read more.
Cancer stem cells (CSC) are known to be the main source of tumor relapse, metastasis, or multidrug resistance and the mechanisms to counteract or eradicate them and their activity remain elusive. There are different hypotheses that claim that the origin of CSC might be in regular stem cells (SC) and, due to accumulation of mutations, these normal cells become malignant, or the source of CSC might be in any malignant cell that, under certain environmental circumstances, acquires all the qualities to become CSC. Multiple studies indicate that lifestyle and diet might represent a source of wellbeing that can prevent and ameliorate the malignant phenotype of CSC. In this review, after a brief introduction to SC and CSC, we analyze the effects of phenolic and non-phenolic dietary compounds and we highlight the molecular mechanisms that are shown to link diets to CSC activation in colon, breast, and prostate cancer. We focus the analysis on specific markers such as sphere formation, CD surface markers, epithelial–mesenchymal transition (EMT), Oct4, Nanog, Sox2, and aldehyde dehydrogenase 1 (ALDH1) and on the major signaling pathways such as PI3K/Akt/mTOR, NF-κB, Notch, Hedgehog, and Wnt/β-catenin in CSC. In conclusion, a better understanding of how bioactive compounds in our diets influence the dynamics of CSC can raise valuable awareness towards reducing cancer risk. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Dietary Compounds in Cancer Management)
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22 pages, 4827 KiB  
Article
Synthesis of Anti-Inflammatory Drugs’ Chalcone Derivatives and a Study of Their Conformational Properties Through a Combination of Nuclear Magnetic Resonance Spectroscopy and Molecular Modeling
by Nikitas Georgiou, Andromachi Tzani, Kyriaki Vavougyiou, Christos Papadopoulos, Nikolaos Eleftheriadis, Primož Šket, Demeter Tzeli, Tuomas Niemi-Aro, Anastasia Detsi and Thomas Mavromoustakos
Pharmaceuticals 2025, 18(1), 88; https://doi.org/10.3390/ph18010088 - 13 Jan 2025
Viewed by 345
Abstract
Background: In this study, two chalcone analogs were synthesized through in silico and experimental methods, and their potential to inhibit the lipoxygenase enzyme, which plays a role in the inflammation pathway, was assessed. Specifically, this study is a continuation of previous research in [...] Read more.
Background: In this study, two chalcone analogs were synthesized through in silico and experimental methods, and their potential to inhibit the lipoxygenase enzyme, which plays a role in the inflammation pathway, was assessed. Specifically, this study is a continuation of previous research in which chalcone derivatives were synthesized and characterized. Objectives/Methods: In the current work, we present the re-synthesis of two chalcones, with a focus on their docking studies, NMR analysis, and dynamic simulations. The structure of each chalcone was elucidated through a combination of Nuclear Magnetic Resonance (NMR) and Density Functional Theory (DFT). The substituent effect on the absorption spectrum of the two chalcone derivatives was studied. Results: A “LOX–chalcone” complex, predicted by docking studies, was further examined using molecular dynamics (MD) simulations to evaluate the stability of the complex. After fully characterizing the “LOX–chalcone” complexes in silico, the atomic details of each chalcone’s interaction with LOX-1 and 5-LOX were revealed through Saturation Transfer Difference (STD) NMR (Nuclear Magnetic Resonance). Finally, their selectivity profile was investigated against human 15-LOX-1 and general Lipoxidase activity. Conclusions: The in silico methods suggest that chalcones could be promising lead compounds for drug designs targeting the LOX enzyme. Full article
(This article belongs to the Special Issue Chalcones: Structure, Function, and Applications)
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25 pages, 12422 KiB  
Article
Effects of Machining Parameters on Abrasive Flow Machining of Single Crystal γ-TiAl Alloy Based on Molecular Dynamics
by Junye Li, Chao Song, Xin Du, Hongcai Xie, Jinghe Zhao and Ying Chen
Micromachines 2025, 16(1), 84; https://doi.org/10.3390/mi16010084 - 13 Jan 2025
Viewed by 419
Abstract
Observing the intricate microstructure changes in abrasive flow machining with traditional experimental methods is difficult. Molecular dynamics simulations are used to look at the process of abrasive flow processing from a microscopic scale in this work. A molecular dynamics model for micro-cutting a [...] Read more.
Observing the intricate microstructure changes in abrasive flow machining with traditional experimental methods is difficult. Molecular dynamics simulations are used to look at the process of abrasive flow processing from a microscopic scale in this work. A molecular dynamics model for micro-cutting a single crystal γ-TiAl alloy with a rough surface in a fluid medium environment is constructed, which is more realistic. The evolution of material removal, cutting force, temperature, energy, and dislocation during micro-cutting are analyzed. The impact of cutting depth, abrasive particle sizes, and abrasive material on the micro-cutting process are analyzed. The analysis shows that the smaller cutting depth and abrasive particle sizes are beneficial to obtain a better machining surface, and the cubic boron nitride (CBN) abrasive is an effective substitute material for diamonds. The purpose of this study is to provide unique insights for improving the material removal rate and subsurface quality by adjusting machining parameters in actual abrasive flow precision machining. Full article
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22 pages, 3795 KiB  
Article
Dynamics and Insights into the Unique Ecological Guild of Fungi in Bacteria-Bioaugmented Anaerobic Digesters
by Linda U. Obi, Ashira Roopnarain, Memory Tekere, Jun Zhou, Heng Li, Yuanpeng Wang, Yanlong Zhang and Rasheed A. Adeleke
J. Fungi 2025, 11(1), 56; https://doi.org/10.3390/jof11010056 - 13 Jan 2025
Viewed by 393
Abstract
Anaerobic digesters host a variety of microorganisms, and they work together to produce biogas. While bacterial and archaeal communities have been well explored using molecular techniques, fungal community structures remain relatively understudied. The present study aims to investigate the dynamics and potential ecological [...] Read more.
Anaerobic digesters host a variety of microorganisms, and they work together to produce biogas. While bacterial and archaeal communities have been well explored using molecular techniques, fungal community structures remain relatively understudied. The present study aims to investigate the dynamics and potential ecological functions of the predominant fungi in bacteria-bioaugmented anaerobic digesters. Eight different anaerobic digesters that contained chopped water hyacinth and cow dung as feedstock at 2% total solids were respectively inoculated with eight different bacterial strains and digested anaerobically in controlled conditions. The diversity and dynamics of the fungal community of the digesters before and after digestion were monitored using high-throughput sequencing of the fungal ITS2 sub-region of the ribosomal gene. The functional potential of the fungal community was predicted using ecological guild analysis. The dominant fungal phyla were (with relative abundance ≥1%) Ascomycota and Neocallimastigomycota. Ascomycota exhibited over 90% dominance in all treatments after anaerobic digestion (AD). Aspergillus sp. was consistently dominant across treatments during AD, while prominent anaerobic fungal genera Anaeromyces, Cyllamyces, and Caeomyces decreased. Ecological guild analysis at genus level showed that the majority of the identified fungi were saprophytes, and diversity indices indicated decreased richness and diversity after AD, suggesting a negative impact of AD on fungal communities in the anaerobic digesters. The multivariate structure of the fungal communities showed clustering of treatments with similar fungal taxa. The findings from this study provide insights into the fungal ecological guild of different bacteria-bioaugmented anaerobic digesters, highlighting their potentials in bacteria-augmented systems. Identification of an anaerobic fungal group within the phylum Ascomycota, beyond the well-known fungal phylum Neocallimastigomycota, offers a new perspective in optimizing the AD processes in specialized ecosystems. Full article
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