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20 pages, 4765 KiB  
Article
Ultrasonic EDM for External Cylindrical Surface Machining with Graphite Electrodes: Horn Design and Hybrid NSGA-II–AHP Optimization of MRR and Ra
by Van-Thanh Dinh, Thu-Quy Le, Duc-Binh Vu, Ngoc-Pi Vu and Tat-Loi Mai
Machines 2025, 13(8), 675; https://doi.org/10.3390/machines13080675 (registering DOI) - 1 Aug 2025
Abstract
This study presents the first investigation into the application of ultrasonic vibration-assisted electrical discharge machining (UV-EDM) using graphite electrodes for external cylindrical surface machining—an essential surface in the production of tablet punches and sheet metal-forming dies. A custom ultrasonic horn was designed and [...] Read more.
This study presents the first investigation into the application of ultrasonic vibration-assisted electrical discharge machining (UV-EDM) using graphite electrodes for external cylindrical surface machining—an essential surface in the production of tablet punches and sheet metal-forming dies. A custom ultrasonic horn was designed and fabricated using 90CrSi material to operate effectively at a resonant frequency of 20 kHz, ensuring stable vibration transmission throughout the machining process. A Box–Behnken experimental design was employed to explore the effects of five process parameters—vibration amplitude (A), pulse-on time (Ton), pulse-off time (Toff), discharge current (Ip), and servo voltage (SV)—on two key performance indicators: material removal rate (MRR) and surface roughness (Ra). The optimization process was conducted in two stages: single-objective analysis to maximize MRR while ensuring Ra < 4 µm, followed by a hybrid multi-objective approach combining NSGA-II and the Analytic Hierarchy Process (AHP). The optimal solution achieved a high MRR of 9.28 g/h while maintaining Ra below the critical surface finish threshold, thus meeting the practical requirements for punch surface quality. The findings confirm the effectiveness of the proposed horn design and hybrid optimization strategy, offering a new direction for enhancing productivity and surface integrity in cylindrical EDM applications using graphite electrodes. Full article
(This article belongs to the Section Advanced Manufacturing)
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18 pages, 4863 KiB  
Article
Evaluation of Explainable, Interpretable and Non-Interpretable Algorithms for Cyber Threat Detection
by José Ramón Trillo, Felipe González-López, Juan Antonio Morente-Molinera, Roberto Magán-Carrión and Pablo García-Sánchez
Electronics 2025, 14(15), 3073; https://doi.org/10.3390/electronics14153073 (registering DOI) - 31 Jul 2025
Abstract
As anonymity-enabling technologies such as VPNs and proxies become increasingly exploited for malicious purposes, detecting traffic associated with such services emerges as a critical first step in anticipating potential cyber threats. This study analyses a network traffic dataset focused on anonymised IP addresses—not [...] Read more.
As anonymity-enabling technologies such as VPNs and proxies become increasingly exploited for malicious purposes, detecting traffic associated with such services emerges as a critical first step in anticipating potential cyber threats. This study analyses a network traffic dataset focused on anonymised IP addresses—not direct attacks—to evaluate and compare explainable, interpretable, and opaque machine learning models. Through advanced preprocessing and feature engineering, we examine the trade-off between model performance and transparency in the early detection of suspicious connections. We evaluate explainable ML-based models such as k-nearest neighbours, fuzzy algorithms, decision trees, and random forests, alongside interpretable models like naïve Bayes, support vector machines, and non-interpretable algorithms such as neural networks. Results show that neural networks achieve the highest performance, with a macro F1-score of 0.8786, but explainable models like HFER offer strong performance (macro F1-score = 0.6106) with greater interpretability. The choice of algorithm depends on project-specific needs: neural networks excel in accuracy, while explainable algorithms are preferred for resource efficiency and transparency, as stated in this work. This work underscores the importance of aligning cybersecurity strategies with operational requirements, providing insights into balancing performance with interpretability. Full article
(This article belongs to the Special Issue Network Security and Cryptography Applications)
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18 pages, 5970 KiB  
Article
Isotonic Protein Solution Supplementation Enhances Growth Performance, Intestinal Immunity, and Beneficial Microbiota in Suckling Piglets
by Changliang Gong, Zhuohang Hao, Xinyi Liao, Robert J. Collier, Yao Xiao, Yongju Zhao and Xiaochuan Chen
Vet. Sci. 2025, 12(8), 715; https://doi.org/10.3390/vetsci12080715 - 30 Jul 2025
Viewed by 188
Abstract
Suckling is crucial for piglet intestinal development and gut health, as it improves resilience during the challenging weaning phase and promotes subsequent growth. IPS, comprising Na+/K+ ions, whey protein, and glucose, has been shown to have positive effects on animal [...] Read more.
Suckling is crucial for piglet intestinal development and gut health, as it improves resilience during the challenging weaning phase and promotes subsequent growth. IPS, comprising Na+/K+ ions, whey protein, and glucose, has been shown to have positive effects on animal growth and intestinal health. The objectives of this study were to assess the impact of IPS consumption on the growth performance, immunity, intestinal growth and development, and microbiota structure of suckling piglets. A total of 160 newborn piglets were randomly divided into control and IPS groups, with IPS supplementation starting from 2 to 8 days after birth and continuing until 3 days before weaning. The findings revealed that IPS boosted the body weight at 24 days by 3.6% (p < 0.05) and improved the body weight gain from 16 to 24 days by 15.7% (p < 0.05). Additionally, the jejunal villus height and villus height to crypt depth ratio in the IPS group were notably increased to 1.08 and 1.31 times (p < 0.05), respectively, compared to the control group. Furthermore, IPS elevated the plasma levels of IgA and IgM, reduced the plasma levels of blood urea nitrogen (BUN), and enhanced the content of secretory immunoglobulin A (SIgA) in the jejunal mucosa of suckling piglets. Furthermore, IPS upregulated the mRNA expression of tight junction proteins GLP-2, ZO-1, and Claudin-1 in jejunal tissue, while downregulating the regulatory genes in the Toll-like pathway, including MyD88 and TLR-4 (p < 0.05). The analysis of gut microbiota indicated that IPS altered the relative abundance of gut microbes, with an increase in beneficial bacteria like Alloprevotella and Bacteroides. In conclusion, this study demonstrates that IPS supplementation enhances weaning weight, growth performance, immune function, and intestinal development in piglets, supporting the integration of IPS supplementation in the management of pre-weaning piglets. Full article
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22 pages, 3429 KiB  
Article
Indoor Positioning and Tracking System in a Multi-Level Residential Building Using WiFi
by Elmer Magsino, Joshua Kenichi Sim, Rica Rizabel Tagabuhin and Jan Jayson Tirados
Information 2025, 16(8), 633; https://doi.org/10.3390/info16080633 - 24 Jul 2025
Viewed by 271
Abstract
The implementation of an Indoor Positioning System (IPS) in a three-storey residential building employing WiFi signals that can also be used to track indoor movements is presented in this study. The movement of inhabitants is monitored through an Android smartphone by detecting the [...] Read more.
The implementation of an Indoor Positioning System (IPS) in a three-storey residential building employing WiFi signals that can also be used to track indoor movements is presented in this study. The movement of inhabitants is monitored through an Android smartphone by detecting the Received Signal Strength Indicator (RSSI) signals from WiFi Anchor Points (APs).Indoor movement is detected through a successive estimation of a target’s multiple positions. Using the K-Nearest Neighbors (KNN) and Particle Swarm Optimization (PSO) algorithms, these RSSI measurements are trained for estimating the position of an indoor target. Additionally, the Density-based Spatial Clustering of Applications with Noise (DBSCAN) has been integrated into the PSO method for removing RSSI-estimated position outliers of the mobile device to further improve indoor position detection and monitoring accuracy. We also employed Time Reversal Resonating Strength (TRRS) as a correlation technique as the third method of localization. Our extensive and rigorous experimentation covers the influence of various weather conditions in indoor detection. Our proposed localization methods have maximum accuracies of 92%, 80%, and 75% for TRRS, KNN, and PSO + DBSCAN, respectively. Each method also has an approximate one-meter deviation, which is a short distance from our targets. Full article
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14 pages, 2087 KiB  
Article
A 28-nm CMOS Low-Power/Low-Voltage 60-GHz LNA for High-Speed Communication
by Minoo Eghtesadi, Andrea Ballo, Gianluca Giustolisi, Salvatore Pennisi and Egidio Ragonese
Electronics 2025, 14(14), 2819; https://doi.org/10.3390/electronics14142819 - 13 Jul 2025
Viewed by 463
Abstract
This paper presents a wideband low-power/low-voltage 60-GHz low-noise amplifier (LNA) in a 28-nm bulk CMOS technology. The LNA has been designed for high-speed millimeter-wave (mm-wave) communications. It consists of two pseudo-differential amplifying stages and a buffer stage included for 50-Ohm on-wafer measurements. Two [...] Read more.
This paper presents a wideband low-power/low-voltage 60-GHz low-noise amplifier (LNA) in a 28-nm bulk CMOS technology. The LNA has been designed for high-speed millimeter-wave (mm-wave) communications. It consists of two pseudo-differential amplifying stages and a buffer stage included for 50-Ohm on-wafer measurements. Two integrated input/output baluns guarantee both simultaneous 50-ohm input–noise/output matching at input/output radio frequency (RF) pads. A power-efficient design strategy is adopted to make the LNA suitable for low-power applications, while minimizing the noise figure (NF). Thanks to the adopted design strategy, the post-layout simulation results show an excellent trade-off between power gain and 3-dB bandwidth (BW3dB) with 13.5 dB and 7 GHz centered at 60 GHz, respectively. The proposed LNA consumes only 11.6 mA from a 0.9-V supply voltage with an NF of 8.4 dB at 60 GHz, including the input transformer loss. The input 1 dB compression point (IP1dB) of −15 dBm at 60 GHz confirms the first-rate linearity of the proposed amplifier. Human body model (HBM) electrostatic discharge (ESD) protection is guaranteed up to 2 kV at the RF input/output pads thanks to the input/output integrated transformers. Full article
(This article belongs to the Special Issue 5G Mobile Telecommunication Systems and Recent Advances, 2nd Edition)
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21 pages, 10550 KiB  
Article
Quinoa–Peanut Relay Intercropping Promotes Peanut Productivity Through the Temporal Optimization of Soil Physicochemical Properties and Microbial Community Composition in Saline Soil
by Xiaoyan Liang, Rao Fu, Jiajia Li, Yinyu Gu, Kuihua Yi, Meng Li, Chuanjie Chen, Haiyang Zhang, Junlin Li, Lan Ma, Yanjing Song, Xiangyu Wang, Jialei Zhang, Shubo Wan and Hongxia Zhang
Plants 2025, 14(14), 2102; https://doi.org/10.3390/plants14142102 - 8 Jul 2025
Cited by 1 | Viewed by 372
Abstract
Peanut productivity is severely restricted by soil salinization and associated nutrient deficiency in saline soil. The quinoa–peanut relay intercrop pattern (IP) is a promising planting system that utilizes the biological advantages of quinoa to improve soil ecological functions and productivity. However, the effects [...] Read more.
Peanut productivity is severely restricted by soil salinization and associated nutrient deficiency in saline soil. The quinoa–peanut relay intercrop pattern (IP) is a promising planting system that utilizes the biological advantages of quinoa to improve soil ecological functions and productivity. However, the effects of IP on soil physicochemical and biological properties and the yield formation of the combined peanut crop are still unclear. Two-year field experiments in coastal saline soil were conducted to explore the effects of IP on peanut growth and pod yield, soil physicochemical properties, and microbial community characterization at different growth stages of peanut based on the traditional monocrop pattern (MP). The results show that IP promoted peanut pod yield, although there was the disadvantage of plant growth at an early stage. Soil water content, electrical conductivity (EC), and Na+ content in the peanut rhizosphere were lower, whereas K+, NH4+, and total organic carbon (TOC) contents were higher in IP systems at both the vegetative and reproductive stages. The pod yield of peanut was significantly negatively correlated with soil EC and Na+ contents at the vegetative stage, but positively correlated with K+, NO3, NH4+, PO43−, and TOC contents at the reproductive stage. IP rebuilt the composition of the soil bacterial community in the peanut rhizosphere and increased the abundance of the beneficial bacterial community, which were positively correlated with soil TOC, K+, NH4+, NO3, and PO43− contents. These findings suggest that IP can increase peanut pod yield through optimizing soil physicochemical properties and microbial community composition, and it is a promising planting system for improving agricultural production in coastal saline lands. Full article
(This article belongs to the Section Crop Physiology and Crop Production)
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18 pages, 3172 KiB  
Article
Characterization of the Binding and Inhibition Mechanisms of a Novel Neutralizing Monoclonal Antibody Targeting the Stem Helix Region in the S2 Subunit of the Spike Protein of SARS-CoV-2
by Selene Si Ern Tan, Ee Hong Tam, Kah Man Lai, Yanjun Wu, Tianshu Xiao and Yee-Joo Tan
Vaccines 2025, 13(7), 688; https://doi.org/10.3390/vaccines13070688 - 26 Jun 2025
Viewed by 612
Abstract
Background/Objectives: For viral entry into host cells, the spike (S) protein of coronavirus (CoV) uses its S1 domain to bind to the host receptor and S2 domain to mediate the fusion between virion and cellular membranes. The S1 domain acquired multiple mutations as [...] Read more.
Background/Objectives: For viral entry into host cells, the spike (S) protein of coronavirus (CoV) uses its S1 domain to bind to the host receptor and S2 domain to mediate the fusion between virion and cellular membranes. The S1 domain acquired multiple mutations as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolved to give rise to Variant of Concerns (VOCs) but the S2 domain has limited changes. In particular, the stem helix in S2 did not change significantly and it is fairly well-conserved across multiple beta-CoVs. In this study, we generated a murine mAb 7B2 binding to the stem helix of SARS-CoV-2. Methods: MAb 7B2 was isolated from immunized mouse and its neutralization activity was evaluated using microneutralization, plaque reduction and cell–cell fusion assays. Bio-layer interferometry was used to measure binding affinity and AlphaFold3 was used to model the antibody–antigen interface. Results: MAb 7B2 has lower virus neutralizing and membrane block activities when compared to a previously reported stem helix-binding human mAb S2P6. Alanine scanning and AlphaFold3 modeling reveals that residues K1149 and D1153 in S form a network of polar interactions with the heavy chain of 7B2. Conversely, S2P6 binding to S is not affected by alanine substitution at K1149 and D1153 as indicated by the high ipTM scores in the predicted S2P6-stem helix structure. Conclusions: Our detailed characterization of the mechanism of inhibition of 7B2 reveals its distinctive binding model from S2P6 and yields insights on multiple neutralizing and highly conserved epitopes in the S2 domain which could be key components for pan-CoV vaccine development. Full article
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19 pages, 4790 KiB  
Article
A Comprehensive Investigation on Shell Hydroforming of AA5052 Through Numerical Modeling and Experimental Analysis
by Arun Achuthankutty, Karthik Narayanan, Ajith Ramesh and Ratna Kishore Velamati
Symmetry 2025, 17(7), 989; https://doi.org/10.3390/sym17070989 - 23 Jun 2025
Viewed by 271
Abstract
This study investigates the shell hydroforming of 1.2 mm-thick AA5052 aluminum alloy sheets to produce hemispherical domes which possess inherent spatial symmetry about their central axis. Shell hydroforming is widely used in fabricating lightweight, high-strength components for aerospace, automotive, and energy applications. The [...] Read more.
This study investigates the shell hydroforming of 1.2 mm-thick AA5052 aluminum alloy sheets to produce hemispherical domes which possess inherent spatial symmetry about their central axis. Shell hydroforming is widely used in fabricating lightweight, high-strength components for aerospace, automotive, and energy applications. The forming process was driven by a spatially symmetrical internal pressure distribution applied uniformly across the blank to maintain balanced deformation and minimize geometrical distortion. Experimental trials aimed at achieving a dome depth of 50 mm revealed wrinkle formation at the blank periphery caused by circumferential compressive stresses symmetrical in nature with respect to the dome’s central axis. To better understand the forming behavior, a validated 3D finite element (FE) model was developed, capturing key phenomena such as material flow, strain rate evolution, hydrostatic stress distribution, and wrinkle development under symmetric boundary conditions. The effects of the internal pressure (IP), blank holding force (BHF), coefficient of friction (CoF), and flange radius (FR) were systematically studied. A strain rate of 0.1 s−1 in the final stage improved material flow, while a symmetric tensile hydrostatic stress of 160 MPa facilitated dome expansion. Although tensile stresses can induce void growth, the elevated strain rate helped suppress it. An optimized parameter set of IP = 5.43 MPa, BHF = 140 kN, CoF = 0.04, and FR = 5.42 mm led to successful formation of the 50 mm dome with 19.38% thinning at the apex. Internal pressure was identified as the most critical factor influencing symmetric formability. A process window was established to predict symmetric failure modes such as wrinkling and bursting. Full article
(This article belongs to the Section Engineering and Materials)
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12 pages, 1296 KiB  
Article
In Vitro Evaluation of the Ovicidal Potential of Proteases from Beauveria bassiana Against Eurytrema pancreaticum Eggs
by Lisseth Bibiana Puentes Figueroa, Amanda do Carmo Alves, Adriane Toledo da Silva, Debora Castro de Souza, Nivia Kelly Lima Sales, Lorrana Verdi Flores, Tiago Facury Moreira, Fabio Ribeiro Braga and Filippe Elias de Freitas Soares
Microbiol. Res. 2025, 16(6), 127; https://doi.org/10.3390/microbiolres16060127 - 13 Jun 2025
Viewed by 411
Abstract
In the search for new alternatives for controlling parasitic agents, proteases from Beauveria bassiana stand out. The aim of this study was to evaluate in silico and in vitro the ovicidal potential of B. bassiana proteases on Eurytrema pancreaticum Janson, 1889 (Dicrocoeliidae) eggs. [...] Read more.
In the search for new alternatives for controlling parasitic agents, proteases from Beauveria bassiana stand out. The aim of this study was to evaluate in silico and in vitro the ovicidal potential of B. bassiana proteases on Eurytrema pancreaticum Janson, 1889 (Dicrocoeliidae) eggs. Beauveria bassiana Bals. -Criv., 1835 (Cordycipitaceae) (IP 361) was cultivated for enzymatic production. Proteins were precipitated with acetone (1:4 ratio), and specific activity was determined. Protease profiles were assessed via zymography, and inhibition by phenylmethylsulfonyl fluoride (PMSF) and ethylenediaminetetraacetic acid (EDTA) was tested. Three-dimensional models of the proteases were generated. Eurytrema pancreaticum eggs were used for the in vitro anthelmintic evaluation of the proteases. The results showed that precipitation significantly concentrated proteolytic activity (p < 0.01) compared to the crude extract. However, no chitinase activity was detected. The proteolytic profile of the precipitate revealed five bands with molecular weights from 25.6 to 66.9 kDa. In the in vitro tests, the proteases significantly (p < 0.01) reduced the number of intact E. pancreaticum eggs by 53% compared to the control with denatured enzymes. These findings highlight the ovicidal potential of B. bassiana proteases, though further studies are needed to confirm their application in parasite control. Full article
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19 pages, 4558 KiB  
Article
Genome-Wide Characterization and Expression Profile of the Jumonji-C Family Genes in Populus alba × Populus glandulosa Reveal Their Potential Roles in Wood Formation
by Zhenghao Geng, Rui Liu and Xiaojing Yan
Int. J. Mol. Sci. 2025, 26(12), 5666; https://doi.org/10.3390/ijms26125666 - 13 Jun 2025
Viewed by 436
Abstract
The Jumonji C (JMJ-C) domain-containing gene family regulates epigenetic and developmental processes in plants. We identified 55 JMJ-C genes in Populus alba × Populus glandulosa using HMM and BLASTp analyses. Chromosomal mapping revealed an asymmetric distribution with conserved synteny. Phylogenetic reconstruction revealed that [...] Read more.
The Jumonji C (JMJ-C) domain-containing gene family regulates epigenetic and developmental processes in plants. We identified 55 JMJ-C genes in Populus alba × Populus glandulosa using HMM and BLASTp analyses. Chromosomal mapping revealed an asymmetric distribution with conserved synteny. Phylogenetic reconstruction revealed that PagJMJ genes segregate into five evolutionarily conserved subfamilies, exhibiting classification patterns identical to those of Arabidopsis thaliana and Populus trichocarpa. Synteny analysis indicated a closer relationship with P. trichocarpa than with A. thaliana. Motif and promoter analyses highlighted subfamily-specific features and diverse cis-elements, particularly light-responsive motifs. Expression profiling revealed tissue-specific patterns, with key genes enriched in roots, vascular tissues, and leaves. Developmental analysis in cambium and xylem identified four expression clusters related to wood formation. Co-expression analysis identified six key PagJMJ genes (PagJMJ6, 29, 34, 39, 53, and 55) strongly associated with wood formation-related transcription factors. ChIP-qPCR analysis revealed that key genes co-expressed with PagJMJ genes were marked by H3K4me3 and H3K9me2 modifications. These findings provide insights into the evolutionary and functional roles of PagJMJ genes in poplar vascular development and wood formation. Full article
(This article belongs to the Section Molecular Plant Sciences)
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16 pages, 2053 KiB  
Article
The Impact of Seasonality on Air Quality in Terms of Pollution with Substances Hazardous to the Environment
by Małgorzata Kida and Sabina Ziembowicz
Appl. Sci. 2025, 15(12), 6551; https://doi.org/10.3390/app15126551 - 10 Jun 2025
Viewed by 452
Abstract
The study presents an analysis of the concentrations of polycyclic aromatic hydrocarbons (PAHs) and particulate matter with a diameter of less than 10 µm (PM10) in the air across various locations, as well as their impact on human health. Research in [...] Read more.
The study presents an analysis of the concentrations of polycyclic aromatic hydrocarbons (PAHs) and particulate matter with a diameter of less than 10 µm (PM10) in the air across various locations, as well as their impact on human health. Research in this area was conducted at eight stations as part of the national environmental monitoring system run in Poland by the Chief Inspectorate for Environmental Protection. Daily measurement data of PM10 and the concentrations of PAHs associated with these particles were analyzed for the period from January to December 2023. The results showed that pollutant concentrations in the atmosphere vary depending on location, season, and meteorological conditions. The highest concentrations were observed during the winter season, when the combustion of solid fuels increases, while the lowest concentrations were recorded in the summer. The total concentration of PAHs ranged from 0.35 to 34.50 ng/m3. The annual average concentration of PM10 at the analyzed stations was 19.29 ± 3.01 µg/m3. Principal component analysis indicated that PAHs in the air primarily originate from emissions related to transportation, biomass combustion, and industry. Furthermore, the estimated health risk, considering the Incremental Lifetime Cancer Risk (ILCR) index, showed that the risk of cancer associated with inhaling PAHs by children and adults did not exceed the permissible limits. The main contributor to the total carcinogenic activity of the PAH mixture was benzo(b)fluorantene (BbF) (31.5%), followed by benzo(a)pyrene (BaP) (5.5%), indeno(1,2,3-cd)pyrene (IP) (18.2%), benzo(j)fluorantene (BjF) (12.9%), benzo(k)fluorantene (BkF) (8.5%), benzo(a)anthracene (BaA) (2.5%), and dibenzo(a,h)anthracene (DBahA) (1.0%). Full article
(This article belongs to the Special Issue Advances in Air Pollution Detection and Air Quality Research)
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20 pages, 5336 KiB  
Article
GCN5 Is a Master Regulator of Gene Expression in the Malaria Parasite Plasmodium falciparum
by Amuza Byaruhanga Lucky, Ahmad Rushdi Shakri, Xiaoying Liang, Hui Min, Xiao-Lian Li, Swamy Rakesh Adapa, Rays H. Y. Jiang, Liwang Cui, Chengqi Wang and Jun Miao
Cells 2025, 14(12), 876; https://doi.org/10.3390/cells14120876 - 10 Jun 2025
Viewed by 664
Abstract
GCN5-containing SAGA complex is evolutionarily conserved across yeast, plants, and humans and acts as a general transcription coactivator in the genome-wide regulation of genes. In Plasmodium falciparum, PfGCN5 forms a divergent complex, and the mis-localization of this complex by deleting the PfGCN5 [...] Read more.
GCN5-containing SAGA complex is evolutionarily conserved across yeast, plants, and humans and acts as a general transcription coactivator in the genome-wide regulation of genes. In Plasmodium falciparum, PfGCN5 forms a divergent complex, and the mis-localization of this complex by deleting the PfGCN5 bromodomain (ΔBrd) causes a plethora of growth defects. To directly test the PfGCN5 function, we performed conditional knockdown (KD) of PfGCN5. Whereas PfGCN5 KD phenotypically recapitulated the ΔBrd growth defects, it caused fewer transcriptional alterations compared to ΔBrd. To decipher the mechanism by which PfGCN5 regulates gene expression, we applied a new chromatin landscape analysis tool, CUT&Tag-seq, to map the chromatin localization of PfGCN5 and its deposited histone mark H3K9ac. Compared to ChIP-seq, CUT&Tag-seq identified substantially more H3K9ac peaks in the promoters of its target genes, with the peak intensity positively correlated with the levels of gene expression. CUT&Tag-seq analysis was remarkably more sensitive in mapping chromatin positions of PfGCN5, which colocalized with H3K9ac. The genes enriched with PfGCN5/H3K9ac signals at their promoters are involved in broad biological processes. Notably, PfGCN5′s positions overlapped with sequence motifs recognized by multiple apetela2 (AP2)-domain-containing transcription factors (AP2 TFs), suggesting that they recruited PfGCN5 to these promoters. Additionally, PfGCN5 was also colocalized with AP2-LT, further validating that AP2-LT is an integral component of the PfGCN5 complex. Collectively, these findings establish PfGCN5 as a master gene regulator in controlling general and parasite-specific cellular processes in this low-branching parasitic protist. Full article
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19 pages, 3372 KiB  
Article
iDNS3IP: Identification and Characterization of HCV NS3 Protease Inhibitory Peptides
by Hui-Ju Kao, Tzu-Hsiang Weng, Chia-Hung Chen, Chen-Lin Yu, Yu-Chi Chen, Chen-Chen Huang, Kai-Yao Huang and Shun-Long Weng
Int. J. Mol. Sci. 2025, 26(11), 5356; https://doi.org/10.3390/ijms26115356 - 3 Jun 2025
Viewed by 578
Abstract
Hepatitis C virus (HCV) infection remains a significant global health burden, driven by the emergence of drug-resistant strains and the limited efficacy of current antiviral therapies. A promising strategy for therapeutic intervention involves targeting the NS3 protease, a viral enzyme essential for replication. [...] Read more.
Hepatitis C virus (HCV) infection remains a significant global health burden, driven by the emergence of drug-resistant strains and the limited efficacy of current antiviral therapies. A promising strategy for therapeutic intervention involves targeting the NS3 protease, a viral enzyme essential for replication. In this study, we present the first computational model specifically designed to identify NS3 protease inhibitory peptides (NS3IPs). Using amino acid composition (AAC) and K-spaced amino acid pair composition (CKSAAP) features, we developed machine learning classifiers based on support vector machine (SVM) and random forest (RF), achieving accuracies of 98.85% and 97.83%, respectively, validated through 5-fold cross-validation and independent testing. To support the accessibility of the strategy, we implemented a web-based tool, iDNS3IP, which enables real-time prediction of NS3IPs. In addition, we performed feature space analyses using PCA, t-SNE, and LDA based on AAindex descriptors. The resulting visualizations showed a distinguishable clustering between NS3IPs and non-inhibitory peptides, suggesting that inhibitory activity may correlate with characteristic physicochemical patterns. This study provides a reliable and interpretable platform to assist in the discovery of therapeutic peptides and supports continued research into peptide-based antiviral strategies for drug-resistant HCV. To enhance its flexibility, the iDNS3IP web tool also incorporates a BLAST-based similarity search function, enabling users to evaluate inhibitory candidates from both predictive and homology-based perspectives. Full article
(This article belongs to the Section Molecular Informatics)
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12 pages, 690 KiB  
Article
Determination of the Activity Coefficients of Components in a Di-2-ethylhexylphosphoric Acid–n-Hexane Binary System Using Gas Chromatography
by Vladimir Glebovich Povarov, Olga Vladimirovna Cheremisina, Daria Artemovna Alferova and Aleksandr Tomasovich Fedorov
Chemistry 2025, 7(3), 92; https://doi.org/10.3390/chemistry7030092 - 1 Jun 2025
Viewed by 586
Abstract
The thermodynamic properties of di-2-ethylhexylphosphoric acid (D2EHPA) in organic solvents are critical for optimizing metal extraction processes in hydrometallurgy, necessitating precise determination of activity coefficients in binary systems such as D2EHPA–n-hexane. This study was devoted to the determination of n-hexane’s concentrations in the [...] Read more.
The thermodynamic properties of di-2-ethylhexylphosphoric acid (D2EHPA) in organic solvents are critical for optimizing metal extraction processes in hydrometallurgy, necessitating precise determination of activity coefficients in binary systems such as D2EHPA–n-hexane. This study was devoted to the determination of n-hexane’s concentrations in the vapor phase over D2EHPA solutions at 293.0 K using gas chromatography (GC) and isopiestic (IP) methods. Comparison with literature data confirmed the superior reliability of GC measurements at low n-hexane concentrations. The experimentally determined activity coefficients of hexane, obtained via GC, served as the initial input parameters for UNIFAC modeling. The optimized interaction parameters were 1144 ± 25 (CH2-HPO4) and 228 ± 50 (HPO4-CH2), with the infinite dilution activity coefficient for D2EHPA γ=22.1. These results experimentally clarify the non-ideal behavior of D2EHPA–n-hexane mixtures, establishing a validated thermodynamic modeling framework for organophosphorus extractant systems. This work establishes a fundamental basis for investigating ternary systems, such as D2EHPA–aliphatic solvent–aromatic solvent and D2EHPA–metal complex–solvent systems, paving the way for enhanced liquid–liquid extraction efficiency. Full article
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16 pages, 2495 KiB  
Article
A Comprehensive Screening of the Interactors of Areca Palm Necrotic Ringspot Virus (ANRSV) HCPro2 Highlights the Proviral Roles of eIF4A and PGK in Viral Infection
by Li Qin, Peilan Liu, Wentao Shen, Zhaoji Dai and Hongguang Cui
Plants 2025, 14(11), 1673; https://doi.org/10.3390/plants14111673 - 30 May 2025
Viewed by 475
Abstract
The areca palm (Areca catechu L.), a medicinal tropical crop, hosts three novel viruses, areca palm necrotic ringspot virus (ANRSV), areca palm necrotic spindle-spot virus (ANSSV), and ANRSV2, which form a new genus Arepavirus in the family Potyviridae. Both viruses feature [...] Read more.
The areca palm (Areca catechu L.), a medicinal tropical crop, hosts three novel viruses, areca palm necrotic ringspot virus (ANRSV), areca palm necrotic spindle-spot virus (ANSSV), and ANRSV2, which form a new genus Arepavirus in the family Potyviridae. Both viruses feature a unique tandem leader protease arrangement (HCPro1-HCPro2). To elucidate HCPro2’s role, this study identified its interaction partners in infected cells using affinity purification coupled with liquid chromatography-tandem mass spectrometry, a yeast two-hybrid system, and co-immunoprecipitation. Thirteen host proteins and five viral factors (HCPro1, 6K2, VPg, NIa-Pro, NIb) were validated as HCPro2 interactors. Among the host proteins interacting with HCPro2, the expression of five genes (NbeIF4A, NbSAMS1α, NbTEF1α, NbUEP1, and NbRan2) was upregulated under the condition of viral infection, while the expression of another five genes (NbpsbS1, NbPGK, NbchIP, NbClpC1A, and NbCysPrx) was downregulated. Functional assays showed that silencing NbeIF4A or NbPGK significantly reduced viral accumulation in Nicotiana benthamiana. These findings reveal HCPro2’s network of virus-host interaction, highlighting its critical role in viral pathogenesis. Further exploration of these interactions may clarify the evolutionary significance of tandem leader proteases and inform novel plant antiviral strategies. Full article
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