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19 pages, 947 KB  
Article
Valorization of Camelina Cake by Fractionation: Characterization of Nutritional and Functional Properties
by Slađana Rakita, Nedeljka Spasevski, Strahinja Vidosavljević, Zorica Tomičić, Ivan M. Savić, Ivana M. Savić Gajić, Olivera Đuragić and Ana Marjanović Jeromela
Foods 2025, 14(19), 3437; https://doi.org/10.3390/foods14193437 - 8 Oct 2025
Viewed by 223
Abstract
The objective of this study was to investigate the effects of fractionation by sieving on cold-pressed camelina cake by separating it into particle-sized fractions and evaluating their nutritional and functional properties. Two Camelina sativa varieties, NS Zlatka and NS Slatka, were mechanically cold-pressed [...] Read more.
The objective of this study was to investigate the effects of fractionation by sieving on cold-pressed camelina cake by separating it into particle-sized fractions and evaluating their nutritional and functional properties. Two Camelina sativa varieties, NS Zlatka and NS Slatka, were mechanically cold-pressed using a screw press then ground into flour. The resulting material was fractionated into three particle-sized fractions, >250 µm, 250–180 µm, and <180 µm, using a laboratory dry sieving system. Both the whole cake and the separated fractions were analyzed for proximate composition, amino acid and fatty acid profiles, tocopherol content, antioxidant potential, color characteristics, and water and oil absorption capacities. The results indicated that the finest cake fraction (<180 µm) from both camelina varieties contained the highest content of protein (~40%), fat (17–19%), essential amino acids (~17 g/100 g), γ-tocopherols (254–266 mg/kg), and the lowest content of condensed tannins (0.5–0.9 g/kg). It also displayed a lighter color and increased yellowness. However, it contained the highest concentrations of glucosinolates (24–27 μmol/g) and phytic acid (38–41 g/kg). In contrast, the coarsest fraction (>250 µm) had increased crude fiber content (13–15%), higher antioxidant potential, the greatest water absorption capacity, and a darker color with a more pronounced reddish color. It also contained the lowest levels of glucosinolates (19–21 μmol/g) and phytic acid (17–20 g/kg). In conclusion, whole camelina cake and its fractions demonstrate considerable potential for use in animal feed and a variety of human nutritional products, due to their favorable nutritional composition and functional properties. Fine fractions with high levels of antinutritional compounds could be used as a substrate for the extraction of bioactive compounds and may find further application in the cosmetic and pharmaceutical industries. Full article
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18 pages, 1975 KB  
Article
Solvent-Assisted Vapor Condensation: A Strategy to Enhance Bio-Oil Yield and Quality from the Pyrolysis of Agro-Industrial Waste
by Jelena Isailović, Emilija Vukićević, Jan Schwarzbauer, Steva Lević, Mališa Antić, Ilija Brčeski, Branimir Jovančićević and Vesna Antić
Molecules 2025, 30(19), 3945; https://doi.org/10.3390/molecules30193945 - 1 Oct 2025
Viewed by 235
Abstract
The paper presents the effect of an organic solvent on the efficiency of vapor condensation from pyrolysis processes applied to agricultural waste, with the intention of optimizing the trapping procedure for more volatile components. Therefore, the effect of the use of acetone in [...] Read more.
The paper presents the effect of an organic solvent on the efficiency of vapor condensation from pyrolysis processes applied to agricultural waste, with the intention of optimizing the trapping procedure for more volatile components. Therefore, the effect of the use of acetone in the vapor trapping system on the yield and composition of liquid fractions (bio-oils) obtained from the pyrolysis of selected agricultural waste, including corn, tomato, and tobacco, was investigated. The focus was placed on evaluating how solvents influence the quality, yield, and composition of bio-oil, as well as whether they are necessary in the pyrolysis process. Acetone, a polar solvent with low human toxicity and the possibility of regeneration after pyrolysis, was selected for bio-oil condensation due to its effectiveness in dissolving polar compounds formed during the pyrolysis of lignocellulosic biomass. Pyrolysis was conducted at 400 and 500 °C for 30 min, to collect light and heavy fractions, which were subsequently analyzed to assess acetone’s influence. The results showed that acetone positively affected corn bio-oil yield (from 44.57% without acetone to 52.13% with acetone) and improved quality by reducing moisture (from 61.82% to 12.83%) and oxygen content (from 86.50% to 47.10%). An increase in calorific value was also observed in both corn varieties, while the effect was minimal in tobacco and nearly negligible in tomato. The obtained parameter values indicated that satisfactory results can also be achieved without the use of a solvent, representing a step toward simplified pyrolysis. GC-MS analysis confirmed that phenols and their derivatives were the dominant compounds, while FTIR analysis verified the presence of functional groups of the identified compounds. Increasing the temperature generally increased both the yield and calorific value of most samples. Light and heavy fractions were separated during condensation to improve collection efficiency and enable better quality control. Although this step adds complexity and potential contamination risks, it allows more effective utilization of the fractions. These results provide a valuable foundation for optimizing the valorization of agricultural waste through pyrolysis-based biofuel production. Full article
(This article belongs to the Special Issue Advances in Lignocellulosic Biomass)
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15 pages, 1841 KB  
Article
A Hybrid UA–CG Force Field for Aggregation Simulation of Amyloidogenic Peptide via Liquid-like Intermediates
by Hang Zheng, Shu Li and Wei Han
Molecules 2025, 30(19), 3946; https://doi.org/10.3390/molecules30193946 - 1 Oct 2025
Viewed by 192
Abstract
Elucidating amyloid formation inside biomolecular condensates requires models that resolve (i) local, chemistry specific contacts controlling β registry and (ii) mesoscale phase behavior and cluster coalescence on microsecond timescales—capabilities beyond single resolution models. We present a hybrid united atom/coarse grained (UA–CG) force field [...] Read more.
Elucidating amyloid formation inside biomolecular condensates requires models that resolve (i) local, chemistry specific contacts controlling β registry and (ii) mesoscale phase behavior and cluster coalescence on microsecond timescales—capabilities beyond single resolution models. We present a hybrid united atom/coarse grained (UA–CG) force field coupling a PACE UA peptide model with the MARTINI CG framework. Cross resolution nonbonded parameters are first optimized against all atom side chain potentials of mean force to balance the relative strength between different types of interactions and then refined through universal parameter scaling by matching radius of gyration distributions for specific systems using. We applied this approach to simulate a recently reported model system comprising the LVFFAR9 peptide that can co-assemble into amyloid fibrils via liquid–liquid phase separation. Our ten-microsecond simulations reveal rapid droplet formation populated by micelle like nanostructures with its inner core composed of LVFF clusters. The nanostructures can further fuse but the fusion is reaction-limited due to an electrostatic coalescence barrier. β structures emerge once clusters exceed ~10 peptides, and the LVFFAR9 fraction modulates amyloid polymorphism, reversing parallel versus antiparallel registry at lower LVFFAR9. These detailed insights generated from long simulations highlight the promise of our hybrid UA–CG strategy in investigating the molecular mechanism of condensate aging. Full article
(This article belongs to the Special Issue Development of Computational Approaches in Chemical Biology)
37 pages, 4235 KB  
Article
Optimization-Based Exergoeconomic Assessment of an Ammonia–Water Geothermal Power System with an Elevated Heat Source Temperature
by Asli Tiktas
Energies 2025, 18(19), 5195; https://doi.org/10.3390/en18195195 - 30 Sep 2025
Viewed by 352
Abstract
Geothermal energy has been recognized as a promising renewable resource for sustainable power generation; however, the efficiency of conventional geothermal power plants has remained relatively low, and high investment costs have limited their competitiveness with other renewable technologies. In this context, the present [...] Read more.
Geothermal energy has been recognized as a promising renewable resource for sustainable power generation; however, the efficiency of conventional geothermal power plants has remained relatively low, and high investment costs have limited their competitiveness with other renewable technologies. In this context, the present study introduced an innovative geothermal electricity generation system aimed at enhancing energy efficiency, cost-effectiveness, and sustainability. Unlike traditional configurations, the system raised the geothermal source temperature passively by employing advanced heat transfer mechanisms, eliminating the need for additional energy input. Comprehensive energy, exergy, and exergoeconomic analyses were carried out, revealing a net power output of 43,210 kW and an energy efficiency of 30.03%, notably surpassing the conventional Kalina cycle’s typical 10.30–19.48% range. The system’s annual electricity generation was 11,138.53 MWh, with an initial investment of USD 3.04 million and a short payback period of 3.20 years. A comparative assessment confirmed its superior thermoeconomic performance. In addition to its technoeconomic advantages, the environmental performance of the proposed configuration was quantified. A streamlined life cycle assessment (LCA) was performed with a functional unit of 1 MWh of net electricity. The proposed system exhibited a carbon footprint of 20–60 kg CO2 eq MWh−1 (baseline: 45 kg CO2 eq MWh−1), corresponding to annual emissions of 0.22–0.67 kt CO2 eq for the simulated output of 11,138.53 MWh. Compared with coal- and gas-fired plants of the same capacity, avoided emissions of approximately 8.6 kt and 5.0 kt CO2 eq per year were achieved. The water footprint was determined as ≈0.10 m3 MWh−1 (≈1114 m3 yr−1), which was substantially lower than the values reported for fossil technologies. These findings confirmed that the proposed system offered a sustainable alternative to conventional geothermal and fossil-based electricity generation. Multi-objective optimization using NSGA-II was carried out to maximize energy and exergy efficiencies while minimizing total cost. Key parameters such as turbine inlet temperature (459–460 K) and ammonia concentration were tuned for performance stability. A sensitivity analysis identified the heat exchanger, the first condenser (Condenser 1), and two separators (Separator 1, Separator 2) as influential on both performance and cost. The exergoeconomic results indicated Separator 1, Separator 2, and the turbine as primary locations of exergy destruction. With an LCOE of 0.026 USD/kWh, the system emerged as a cost-effective and scalable solution for sustainable geothermal power production without auxiliary energy demand. Full article
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18 pages, 1539 KB  
Review
Transcriptional Condensates: Epigenetic Reprogramming and Therapeutic Targets in Hematologic Malignancies
by Kevin Qiu, Qing Yin, Chongzhi Zang and Jianguo Tao
Cancers 2025, 17(19), 3148; https://doi.org/10.3390/cancers17193148 - 27 Sep 2025
Viewed by 437
Abstract
Transcription is a core hallmark of cancer, wherein many different proteins assemble at specific sites in the nucleus and act in concert to transcribe functionally relevant genes. Central to this process are transcription factors that bind to their cognate DNA motifs on enhancers [...] Read more.
Transcription is a core hallmark of cancer, wherein many different proteins assemble at specific sites in the nucleus and act in concert to transcribe functionally relevant genes. Central to this process are transcription factors that bind to their cognate DNA motifs on enhancers and super-enhancers to recruit cofactors, coactivators, and epigenetic modifiers, thereby inducing or repressing gene expression. Super-enhancers drive oncogenic transcription, to which cancer cells become highly addicted and confer tumor dependencies on super-enhancer-driven transcription machinery. Transcriptional condensates (TCs) are nuclear membrane-less assemblies of DNA-binding transcription factors, transcription co-activators, and the transcriptional machinery (such as RNA polymerases, non-coding RNAs) formed through liquid–liquid phase separation (LLPS). The function of transcriptionally active oncogenic proteins and their interplay with nucleic acids are carried out within these biomolecular condensates, allowing them to spatiotemporally regulate oncogene expression and lead to the induction and maintenance of cancer. With this growing understanding, specific inhibitors and strategies targeting TC assembly and activation should be considered promising therapeutic opportunities for treating various tumors, including hematological malignancies. Full article
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19 pages, 4753 KB  
Article
Exploring the Green Synthesis Process of 2-Mercaptobenzothiazole for Industrial Production
by Yan Zhang, Qi Zhang, Xiansuo Li, Ruiguo Dong, Xiaolai Zhang and Qinggang Sun
Processes 2025, 13(10), 3071; https://doi.org/10.3390/pr13103071 - 25 Sep 2025
Viewed by 297
Abstract
This study outlines a high-yield green method for synthesizing MBT using aniline, carbon disulfide and sulfur as raw materials via a one-step reaction combined with high–low-temperature extraction. The process is supported by experimental results and lab-scale tests, and the operating conditions of the [...] Read more.
This study outlines a high-yield green method for synthesizing MBT using aniline, carbon disulfide and sulfur as raw materials via a one-step reaction combined with high–low-temperature extraction. The process is supported by experimental results and lab-scale tests, and the operating conditions of the amplification process are evaluated using Aspen Plus simulation software, supplemented with Gaussian09 calculations. The sensitivity analysis results indicate that the MBT yield reaches its maximum value when the feed mass ratio of S:CS2:C6H7N:C7H8 is 6:17:20:90. Additionally, setting the reaction temperature to 240 °C and pressure to 10 MPa improves the MBT synthesis yield from 58% to 82.5%. Optimal condensation and extraction conditions are achieved at −30 °C and 1 atm, followed by a separation step at 40 °C. The simulation results provide valuable guidance for the industrial production of MBT. Full article
(This article belongs to the Section Chemical Processes and Systems)
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28 pages, 4706 KB  
Article
Comparative Performance Analysis of Machine Learning-Based Annual and Seasonal Approaches for Power Output Prediction in Combined Cycle Power Plants
by Asiye Aslan and Ali Osman Büyükköse
Energies 2025, 18(19), 5110; https://doi.org/10.3390/en18195110 - 25 Sep 2025
Viewed by 457
Abstract
This study develops an innovative framework that utilizes real-time operational data to forecast electrical power output (EPO) in Combined Cycle Power Plants (CCPPs) by employing a temperature segmentation-based modeling approach. Instead of using a single general prediction model, which is commonly seen in [...] Read more.
This study develops an innovative framework that utilizes real-time operational data to forecast electrical power output (EPO) in Combined Cycle Power Plants (CCPPs) by employing a temperature segmentation-based modeling approach. Instead of using a single general prediction model, which is commonly seen in the literature, three separate prediction models were created to explicitly capture the nonlinear effect of ambient temperature (AT) on efficiency (AT < 12 °C, 12 °C ≤ AT < 20 °C, AT ≥ 20 °C). Linear Ridge, Medium Tree, Rational Quadratic Gaussian Process Regression (GPR), Support Vector Machine (SVM) Kernel, and Neural Network methods were applied. In the modeling, the variables considered were AT, relative humidity (RH), atmospheric pressure (AP), and condenser vacuum (V). The highest performance was achieved with the Rational Quadratic GPR method. In this approach, the weighted average Mean Absolute Error (MAE) was found to be 2.225 with seasonal segmentation, while it was calculated as 2.417 in the non-segmented model. By applying seasonal prediction models, the hourly EPO prediction error was reduced by 192 kW, achieving a 99.77% average convergence of the predicted power output values to the actual values. This demonstrates the contribution of the proposed approach to enhancing operational efficiency. Full article
(This article belongs to the Section F1: Electrical Power System)
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23 pages, 2713 KB  
Review
Phase Separation-Regulated Fungal Growth, Sexual Development, Adaptation and Synthetic Biology Applications
by Xinxin Tong, Daixi Zhang and Zhenhong Zhu
J. Fungi 2025, 11(9), 680; https://doi.org/10.3390/jof11090680 - 17 Sep 2025
Viewed by 555
Abstract
Liquid–liquid phase separation (LLPS) is a fundamental biophysical process in which proteins and nucleic acids dynamically demix from the cellular milieu to form membraneless organelles (MLO) with liquid-like properties. Environmental cues, such as light, temperature fluctuations, and pathogen interactions, induce LLPS of fungal [...] Read more.
Liquid–liquid phase separation (LLPS) is a fundamental biophysical process in which proteins and nucleic acids dynamically demix from the cellular milieu to form membraneless organelles (MLO) with liquid-like properties. Environmental cues, such as light, temperature fluctuations, and pathogen interactions, induce LLPS of fungal proteins with intrinsically disordered regions (IDRs) or multimerization domains, thereby regulating fungal hyphal growth, sexual reproduction, pathogenesis, and adaptation. Recently, LLPS has emerged as a powerful tool for biomolecular research, innovative biotechnological application, biosynthesis and metabolic engineering. This review focuses on the current advances in environmental cue-triggered fungal condensates assembled by LLPS, with a focus on their roles in regulating the fungal physical biology and cellular processes including transcription, RNA modification, translation, posttranslational modification process (PTM), transport, and stress response. It further discusses the strategies of engineering synthetic biomolecular condensates in microbial cell factories to enhance production and metabolic efficiency. Full article
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16 pages, 636 KB  
Review
Stress-Induced Membraneless Organelles in Neurons: Bridging Liquid–Liquid Phase Separation and Neurodevelopmental Dysfunction
by Norbert Bencsik, Daniel Kimsanaliev, Krisztián Tárnok and Katalin Schlett
Int. J. Mol. Sci. 2025, 26(18), 9068; https://doi.org/10.3390/ijms26189068 - 17 Sep 2025
Viewed by 760
Abstract
Liquid–liquid phase separation (LLPS) in cell biology has revolutionized our understanding of how cells organize biochemical reactions and structures through dynamic, membraneless organelles (MLOs). In neurons, LLPS-driven processes are particularly important for regulating synaptic plasticity, RNA metabolism, and responses to environmental stressors. Over [...] Read more.
Liquid–liquid phase separation (LLPS) in cell biology has revolutionized our understanding of how cells organize biochemical reactions and structures through dynamic, membraneless organelles (MLOs). In neurons, LLPS-driven processes are particularly important for regulating synaptic plasticity, RNA metabolism, and responses to environmental stressors. Over the past decade, LLPS has gained increasing attention in neurobiology as a framework to interpret altered synaptic functions in various neurodevelopmental disorders (NDDs). These diseases comprise a diverse spectrum of clinical and pathological symptoms (e.g., global developmental delay, impaired cognitive and mental functions, as well as social withdrawal). Recent studies have highlighted how mutations in proteins containing intrinsically disordered regions (IDRs)—key drivers of LLPS—can alter condensate properties, resulting in persistent or defective MLO formation. These aberrant assemblies may disrupt RNA transport, splicing, and translation in developing neurons, thereby contributing to disorder pathology. IDRs are known to be enriched in membraneless components, such as stress granules, nuclear paraspeckles, and P-bodies, where they play crucial role in the formation, maintenance, and function of protein–RNA networks. This review explores the role of stress-induced MLOs in the nervous system, the molecular principles governing their formation, and how their dysfunction bridges the gap between environmental stress responses and neurodevelopmental impairment. Full article
(This article belongs to the Special Issue Role of Glia in Human Health and Disease)
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16 pages, 500 KB  
Review
The Skin Barrier: A System Driven by Phase Separation
by Fengjiao Yu, Lu Leng, Haowen Wang, Mengmeng Du, Liang Wang and Wenhua Xu
Cells 2025, 14(18), 1438; https://doi.org/10.3390/cells14181438 - 15 Sep 2025
Viewed by 684
Abstract
The mammalian epidermis forms a critical barrier against environmental insults and water loss. The formation of its outermost layer, the stratum corneum, involves a rapid terminal differentiation process that has traditionally been explained by the “bricks and mortar” model. Recent advances reveal a [...] Read more.
The mammalian epidermis forms a critical barrier against environmental insults and water loss. The formation of its outermost layer, the stratum corneum, involves a rapid terminal differentiation process that has traditionally been explained by the “bricks and mortar” model. Recent advances reveal a more dynamic mechanism governed by intracellular liquid–liquid phase separation (LLPS). This review proposes that the lifecycle of the granular layer is orchestrated by LLPS. Evidence is synthesized showing that keratohyalin granules (KGs) are biomolecular condensates formed by the phase separation of the intrinsically disordered protein filaggrin (FLG). The assembly, maturation, and pH-triggered dissolution of these condensates are essential for cytoplasmic remodeling and the programmed flattening of keratinocytes, a process known as corneoptosis. In parallel, an LLPS-based signaling pathway is described in which the kinase RIPK4 forms condensates that activate the Hippo pathway, promoting transcriptional reprogramming and differentiation. Together, these structural and signaling condensates drive skin barrier formation. This review further reinterprets atopic dermatitis, ichthyosis vulgaris, and Bartsocas-Papas syndrome as diseases of aberrant phase behavior, in which pathogenic mutations alter condensate formation or material properties. This integrative framework offers new insight into skin biology and suggests novel opportunities for therapeutic intervention through biophysics-informed biomaterial and regenerative design. Full article
(This article belongs to the Section Cellular Biophysics)
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24 pages, 495 KB  
Review
Dynamical Transitions in Trapped Superfluids Excited by Alternating Fields
by Vyacheslav I. Yukalov and Elizaveta P. Yukalova
Physics 2025, 7(3), 41; https://doi.org/10.3390/physics7030041 - 12 Sep 2025
Viewed by 336
Abstract
The paper presents a survey of some dynamical transitions in nonequilibrium trapped Bose-condensed systems subject to the action of alternating fields. Nonequilibrium states of trapped systems can be implemented in two ways: resonant and nonresonant. Under resonant excitation, several coherent modes are generated [...] Read more.
The paper presents a survey of some dynamical transitions in nonequilibrium trapped Bose-condensed systems subject to the action of alternating fields. Nonequilibrium states of trapped systems can be implemented in two ways: resonant and nonresonant. Under resonant excitation, several coherent modes are generated by external alternating fields with the frequencies been tuned to resonance with some transition frequencies of the trapped system. A Bose system of trapped atoms with Bose–Einstein condensate can display two types of the Josephson effect, the standard one, when the system is separated into two or more parts in different locations, or the internal Josephson effect, when there are no any separation barriers but the system becomes nonuniform due to the coexistence of several coherent modes interacting one with another. The mathematics in both these cases is similar. We focus on the internal Josephson effect. Systems with nonlinear coherent modes demonstrate rich dynamics, including Rabi oscillations, the Josephson effect, and chaotic motion. Under the Josephson effect, there exist dynamic transitions that are similar to phase transitions in equilibrium systems. The bosonic Josephson effect is shown to be implementable not only for quite weakly interacting systems, but also in superfluids with not necessarily as weak interactions. Sufficiently strong nonresonant excitation can generate several types of nonequilibrium states comprising vortex germs, vortex rings, vortex lines, vortex turbulence, droplet turbulence, and wave turbulence. Nonequilibrium states are shown to be characterized and distinguished by effective temperature, effective Fresnel number, and dynamic scaling laws. Full article
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16 pages, 1473 KB  
Review
Lipid-Mediated Assembly of Biomolecular Condensates: Mechanisms, Regulation, and Therapeutic Implications
by Shijie Ma, Zheng Yang, Chang Du, Binjie Gan and Tong Tang
Biology 2025, 14(9), 1232; https://doi.org/10.3390/biology14091232 - 10 Sep 2025
Viewed by 844
Abstract
Cellular organization relies on both membrane-bound organelles and membraneless biomolecular condensates formed through liquid–liquid phase separation. Recent discoveries reveal intricate coupling between lipid membrane organization and condensate assembly, reshaping our understanding of cellular compartmentalization. This review synthesizes multidisciplinary research using advanced techniques including [...] Read more.
Cellular organization relies on both membrane-bound organelles and membraneless biomolecular condensates formed through liquid–liquid phase separation. Recent discoveries reveal intricate coupling between lipid membrane organization and condensate assembly, reshaping our understanding of cellular compartmentalization. This review synthesizes multidisciplinary research using advanced techniques including super-resolution microscopy, fluorescence recovery after photobleaching, and in vitro reconstitution to examine lipid-condensate interactions. Lipid membranes serve as nucleation platforms that reduce critical concentrations for condensate formation by orders of magnitude through membrane anchoring and thermodynamic coupling, creating specialized microenvironments that substantially enhance enzymatic activities. Key regulatory mechanisms include phosphorylation-driven assembly and disassembly, membrane composition effects from cholesterol content and fatty acid saturation, and environmental factors such as calcium and pH. These interactions drive signal transduction through receptor clustering, membrane trafficking via organized domains, and stress responses through protective condensate formation. Dysregulation of lipid-condensate coupling, including aberrant phase transitions and membrane dysfunction, underlies metabolic disorders and neurodegenerative diseases. This coupling represents a fundamental organizing principle with significant therapeutic potential. Current challenges include developing quantitative methods for characterizing condensate dynamics in complex cellular environments and translating molecular mechanisms into clinical applications. Future progress requires interdisciplinary approaches combining advanced experimental techniques, computational modeling, and standardized protocols to advance both fundamental understanding and therapeutic innovations. Full article
(This article belongs to the Section Biochemistry and Molecular Biology)
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23 pages, 15647 KB  
Article
Theoretical Methods for Assessing the Density of Protein Nanodroplets
by Midhun Mohan Anila, Michał Wojciechowski, Mateusz Chwastyk and Bartosz Różycki
Int. J. Mol. Sci. 2025, 26(17), 8631; https://doi.org/10.3390/ijms26178631 - 4 Sep 2025
Viewed by 943
Abstract
Many intrinsically disordered proteins (IDPs) are known to undergo liquid–liquid phase separation (LLPS), which is a physical process that drives the formation of biomolecular condensates and membraneless organelles in biological cells. Molecular dynamics (MD) simulations provide valuable tools to explore both the molecular [...] Read more.
Many intrinsically disordered proteins (IDPs) are known to undergo liquid–liquid phase separation (LLPS), which is a physical process that drives the formation of biomolecular condensates and membraneless organelles in biological cells. Molecular dynamics (MD) simulations provide valuable tools to explore both the molecular mechanisms of LLPS and the physical properties of biomolecular condensates. However, a direct comparison of MD simulation results with phase diagrams obtained experimentally is normally prevented not only by the high computational costs of simulating large biomacromolecular systems on sufficient timescales but also by conceptual challenges. Specifically, there currently seems to be no standard or unambiguous method of defining and determining volumes occupied by coexisting phases at the nanoscale, with typically no more than a few hundred biomacromolecules in the simulation box. The goal of this work is to fill in this gap in the methodology. Focusing on α-synuclein as a model IDP, we test and compare three methods for determining the molecular density of protein nanodroplets, or clusters, generated in MD simulations or using other molecular modeling approaches. Two of the methods are based on approximating nanodroplets with homogeneous spheres and ellipsoids, respectively. The third method, which is expected to yield the most physically accurate results, is based on the SPACEBALL algorithm, with optimized, cluster-specific radii for volume probes. Our results contribute to the construction of accurate phase diagrams on the basis of MD simulations of IDP systems. Full article
(This article belongs to the Collection Feature Papers Collection in Biochemistry)
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13 pages, 2522 KB  
Article
Construction of Sulfur-Doped and Cyanide-Modified Carbon Nitride Photocatalysts with High Photocatalytic Hydrogen Production and Organic Pollutant Degradation
by Yihan Tang, Yichi Zhang, Ning Jian, Luxi Han, Huage Lin and Weinan Xing
Catalysts 2025, 15(9), 849; https://doi.org/10.3390/catal15090849 - 3 Sep 2025
Viewed by 602
Abstract
Element doping and functional group modification engineering serve as efficient approaches that contribute to the improvement of the functional efficiency in graphitic carbon nitride (CN) materials. A CN photocatalyst co-modified with sulfur (S) and cyano moieties was prepared through thermal condensation polymerization. The [...] Read more.
Element doping and functional group modification engineering serve as efficient approaches that contribute to the improvement of the functional efficiency in graphitic carbon nitride (CN) materials. A CN photocatalyst co-modified with sulfur (S) and cyano moieties was prepared through thermal condensation polymerization. The introduced S species modulated the band structure, increased charge carrier mobility, and significantly promoted charge separation and transport. Additionally, the introduction of cyano groups extended light absorption range and improved the material’s selective adsorption of reactant molecules. The as-prepared sulfur-modified CN photocatalyst obtained after a 6 h thermal treatment, which was capable of degrading organic pollutants and producing hydrogen (H2) efficiently and stably, exhibited excellent catalytic performance. The photocatalyst’s photocatalyst exhibited a significantly enhanced photocatalytic activity, with a Rhodamine B (RhB) removal efficiency reaching 97.3%. Meanwhile, the H2 production level reached 1221.47 μmol h−1g−1. Based on four-cycle experiments, the photocatalyst exhibited excellent recyclability and stability in both H2 production processes and photocatalytic organic pollutant degradation. In addition, mechanistic studies confirmed the dominant role of ·OH and ·O2 as active species responsible for the reaction system’s performance. This study highlights that the co-decoration of heteroatoms and functional groups can markedly enhance the photocatalytic performance of CN-based materials, offering considerable potential for future applications in energy conversion and environmental remediation. Full article
(This article belongs to the Special Issue Environmentally Friendly Catalysis for Green Future)
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25 pages, 2263 KB  
Article
Effects of Tannin-Rich Supplements on Immune Response in Goats and Beef Cattle: A Collection of Controlled Feeding Trials
by Sebastian P. Schreiber, Rebecca D. Burson, Cody B. Scott and Corey J. Owens
Agriculture 2025, 15(17), 1863; https://doi.org/10.3390/agriculture15171863 - 31 Aug 2025
Viewed by 625
Abstract
Emerging research evokes selection for various plant secondary compounds as a potential driver of ruminant diet selection, through animals’ evident ability to rectify deficiencies and even self-medicate. This idea was assessed by comparing physiological responses to vaccination challenges of animals fed diets of [...] Read more.
Emerging research evokes selection for various plant secondary compounds as a potential driver of ruminant diet selection, through animals’ evident ability to rectify deficiencies and even self-medicate. This idea was assessed by comparing physiological responses to vaccination challenges of animals fed diets of differing phytochemical composition. In the first of three separate trials, goats were placed in individual pens and fed one of three treatments in a completely randomized design. Treatments in Trial 1 consisted of redberry juniper (50 g) and shin oak (50 g). In Trial 2, goats were fed rations containing grape and blueberry pomace at an inclusion rate of 20%. In Trial 3, black Angus heifers were fed rations containing grape and blueberry pomace at an as-fed inclusion rate of 6%. Average daily gain, intake, and blood chemistry were assessed following vaccination health challenges. In Trial 1, goats fed shin oak had higher (p < 0.05) blood globulins. Trial 2 revealed no treatment group differences in average daily gain (ADG), intake, or blood parameters evaluated. In Trial 3, no difference occurred in blood parameters; however, intake following inoculation was significantly greater (p < 0.05) for heifers with grape/blueberry pomace included in their rations. In conclusion, phytochemicals, specifically condensed tannins, may have the ability to enhance immune response in ruminants, but further research is required, and these effects likely depend upon the source, structure, and dose of tannins or parent plant materials offered. Full article
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