Sign in to use this feature.

Years

Between: -

Subjects

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Journals

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Article Types

Countries / Regions

remove_circle_outline
remove_circle_outline
remove_circle_outline

Search Results (302)

Search Parameters:
Keywords = protein partitioning

Order results
Result details
Results per page
Select all
Export citation of selected articles as:
19 pages, 3398 KiB  
Article
Synthesis and Evaluation of [18F]AlF-NOTA-iPD-L1 as a Potential Theranostic Pair for [177Lu]Lu-DOTA-iPD-L1
by Guillermina Ferro-Flores, Myrna Luna-Gutiérrez, Blanca Ocampo-García, Nallely Jiménez-Mancilla, Nancy Lara-Almazán, Rigoberto Oros-Pantoja, Clara Santos-Cuevas, Erika Azorín-Vega and Laura Meléndez-Alafort
Pharmaceutics 2025, 17(7), 920; https://doi.org/10.3390/pharmaceutics17070920 - 16 Jul 2025
Viewed by 59
Abstract
Background/Objective: Programmed cell death ligand-1 (PD-L1), which is overexpressed in certain tumors, inhibits the body’s natural immune response by providing an “off” signal that enables cancer cells to evade the immune system. It has been demonstrated that [177Lu]Lu-DOTA-iPD-L1 (PD-L1 inhibitor [...] Read more.
Background/Objective: Programmed cell death ligand-1 (PD-L1), which is overexpressed in certain tumors, inhibits the body’s natural immune response by providing an “off” signal that enables cancer cells to evade the immune system. It has been demonstrated that [177Lu]Lu-DOTA-iPD-L1 (PD-L1 inhibitor cyclic peptide) promotes immune responses. This study aimed to synthesize and evaluate [18F]AlF-NOTA-iPD-L1 as a novel radiotracer for PD-L1 positron emission tomography (PET) imaging and as a potential theranostic pair for [177Lu]Lu-DOTA-iPD-L1. Methods: The NOTA-iPD-L1 peptide conjugate was synthesized and characterized by U.V.-vis, I.R.-FT, and UPLC-mass spectroscopies. Radiolabeling was performed using [18F]AlF as the precursor, and the radiochemical purity (HPLC), partition coefficient, and serum stability were assessed. Cellular uptake and internalization (in 4T1 triple-negative breast cancer cells), binding competition, immunofluorescence, and Western blot assays were applied for the radiotracer in vitro characterization. Biodistribution in mice bearing 4T1 tumors was performed, and molecular imaging (Cerenkov images) of [18F]AlF-NOTA-iPD-L1 and [177Lu]Lu-DOTA-iPD-L1 in the same mouse was obtained. Results: [18F]AlF-NOTA-iPD-L1 was prepared with a radiochemical purity greater than 97%, and it demonstrated high in vitro and in vivo stability, as well as specific recognition by the PD-L1 protein (IC50 = 9.27 ± 2.69 nM). Biodistribution studies indicated a tumor uptake of 6.4% ± 0.9% ID/g at 1-hour post-administration, and Cerenkov images showed a high tumor uptake of both [18F]AlF-NOTA-iPD-L1 and 177Lu-iPD-L1 in the same mouse. Conclusions: These results warrant further studies to evaluate the clinical usefulness of [18F]AlF-NOTA-iPD-L1/[177Lu]Lu-DOTA-iPD-L1 as a radiotheranostic pair in combination with anti-PD-L1/PD1 immunotherapy. Full article
Show Figures

Figure 1

20 pages, 3835 KiB  
Article
Host RhoA Signaling Controls Filamentous vs. Spherical Morphogenesis and Cell-to-Cell Spread of RSV via Lipid Raft Localization: Host-Directed Antiviral Target
by Manoj K. Pastey, Lewis H. McCurdy and Barney S. Graham
Microorganisms 2025, 13(7), 1599; https://doi.org/10.3390/microorganisms13071599 - 7 Jul 2025
Viewed by 281
Abstract
Respiratory syncytial virus (RSV) is a major human respiratory pathogen, particularly affecting infants, the elderly, and immunocompromised individuals. RSV exists in both spherical and filamentous forms, with the filamentous morphology associated with enhanced infectivity and cell-to-cell spread. Here, we demonstrate that RhoA, a [...] Read more.
Respiratory syncytial virus (RSV) is a major human respiratory pathogen, particularly affecting infants, the elderly, and immunocompromised individuals. RSV exists in both spherical and filamentous forms, with the filamentous morphology associated with enhanced infectivity and cell-to-cell spread. Here, we demonstrate that RhoA, a small GTPase involved in cytoskeletal regulation, is essential for filamentous RSV morphogenesis through its role in organizing lipid raft microdomains. Rhosin, a selective RhoA inhibitor developed through structure-guided screening, disrupts GEF–RhoA interactions to block RhoA activation. The pharmacological inhibition of RhoA with Rhosin significantly reduced filamentous virion formation, disrupted RSV fusion (F) protein colocalization with lipid rafts, and diminished cell-to-cell fusion, without affecting overall viral replication. Scanning electron microscopy revealed that Rhosin-treated infected HEp-2 cells exhibited fewer and shorter filamentous projections compared to the extensive filament formation seen in untreated cells. β-galactosidase-based fusion assays confirmed that reduced filamentation corresponded with decreased cell-to-cell fusion. The biophysical separation of RSV spherical and filamentous particles by sucrose gradient velocity sedimentation, coupled with fluorescence and transmission electron microscopy, showed that Rhosin treatment shifted virion morphology toward spherical forms. This suggests that RhoA activity is critical for filamentous virion assembly, which may enhance viral spread. Immunofluorescence microscopy using lipid raft-selective dyes (DiIC16) and fusion protein-specific antibodies revealed the strong co-localization of RSV proteins with lipid rafts. Importantly, the pharmacological inhibition of RhoA with Rhosin disrupted F protein partitioning into raft domains, underscoring the requirement for intact lipid rafts in assembly. These findings highlight a novel role for host RhoA signaling in regulating viral assembly through raft microdomain organization, offering a potential target for host-directed antiviral intervention aimed at altering RSV structural phenotypes and limiting pathogenesis. Full article
(This article belongs to the Special Issue Viral Diseases: Current Research and Future Directions)
Show Figures

Figure 1

17 pages, 306 KiB  
Article
Inclusion of Sub-Antarctic Macroalgae (Gigartina skosttsbergii) as Feed Ingredient for Grazing Sheep
by Cinthya Glucevic, Navid Ghavipanje, Lizbeth E. Robles-Jimenez, Sergio Radic-Schilling and Manuel Gonzalez Ronquillo
Animals 2025, 15(13), 1976; https://doi.org/10.3390/ani15131976 - 4 Jul 2025
Viewed by 266
Abstract
Two experiments were carried out to evaluate the inclusion impacts of macroalgae Gigartina skottsbergii (Gs) for grazing sheep. Experiment (Exp.) 1 studied the effect of Gs on in vitro gas production (IVGP), dry matter (DM) digestibility (IVDMD), and methane (CH4) emission [...] Read more.
Two experiments were carried out to evaluate the inclusion impacts of macroalgae Gigartina skottsbergii (Gs) for grazing sheep. Experiment (Exp.) 1 studied the effect of Gs on in vitro gas production (IVGP), dry matter (DM) digestibility (IVDMD), and methane (CH4) emission using three fistulated sheep and 96 h incubation of samples. In Exp. 2, ten Dohne Merino ewes [5-year-old; 47 ± 0.14 kg body weight (BW)] were randomly assigned to dietary treatments supplemented with Gs at 0 or 450 g DM/d per animal. The study lasted 31 days and was preceded by an adaptation period of 9 days. The BW, body conditional score (BCS), and blood were sampled at the first and the last day of the trial. The results of Exp. 1 showed that Gs supplementation reduced (MCP, p = 0.026) gas production (A), lag time (p = 0.013), and IVDMD (p = 0.071), while it enhanced partition factor (PF96; p = 0.004) and microbial crude protein (MCP) (p = 0.054). The concentration of CH4 decreased after 3 h (p = 0.0002), 6 h (p = 0.013), and 12 h (p = 0.010) with a tendency at 9 h (p = 0.109) and 24 h (p = 0.068). In Exp. 2, there were no diet effects on the initial BW (IBW, p = 0.77), final BW (FBW, p = 0.91), and average daily gain (ADG, p = 0.24) of ewes; however, Gs supplementation decreased BCS (p = 0.004). Of all blood parameters, only the concentration of glucose (p = 0.021) and albumin (p = 0.011) decreased in the Gs group. Overall, our results revealed that the dietary inclusion of Gs (at 450 g DM/d) affected neither the BW nor ADG of ewes; however, Gs was accompanied by lesser IVGP and CH4 emission. Full article
14 pages, 578 KiB  
Article
Food–Drug Interactions: Effect of Propolis on the Pharmacokinetics of Enrofloxacin and Its Active Metabolite Ciprofloxacin in Rabbits
by Ali Sorucu, Cengiz Gokbulut, Busra Aslan Akyol and Osman Bulut
Pharmaceuticals 2025, 18(7), 967; https://doi.org/10.3390/ph18070967 - 27 Jun 2025
Viewed by 330
Abstract
Propolis is a natural resinous substance produced by honeybees that has many biological activities. For thousands of years, it has been widely used as a dietary supplement and traditional medicine to treat a variety of ailments due to its antimicrobial, anti-inflammatory, antioxidant, immunomodulatory, [...] Read more.
Propolis is a natural resinous substance produced by honeybees that has many biological activities. For thousands of years, it has been widely used as a dietary supplement and traditional medicine to treat a variety of ailments due to its antimicrobial, anti-inflammatory, antioxidant, immunomodulatory, and wound-healing properties. Nutritional supplements and foods may interact with drugs both pharmacodynamically and pharmacokinetically, which could raise clinical concerns. Background/Objectives: This study aimed to investigate the effect of propolis on the plasma disposition of enrofloxacin and to assess the potential pharmacokinetic interaction in rabbits. Methods: In this study, enrofloxacin was applied per os (20 mg/kg) and IM (10 mg/kg) and with propolis (100 mg resin/kg) administration in four groups of rabbits (each of six individuals). Heparinized blood samples were collected at 0, 0.1, 0.3, 0.5, 1, 2, 4, 8, 12, and 24 h post-administration. HPLC-FL was used to analyze the plasma concentrations of enrofloxacin and its active metabolite ciprofloxacin following liquid–liquid phase extraction, i.e., protein precipitation with acetonitrile and partitioning with sodium sulfate. Results: The results revealed that propolis coadministration significantly affected the plasma disposition of enrofloxacin and its active metabolite after both per os and intramuscular administration routes. Significantly greater AUC (48.91 ± 11.53 vs. 26.11 ± 12.44 µg.h/mL), as well as longer T1/2λz (11.75 ± 3.20 vs. 5.93 ± 2.51 h) and MRT (17.26 ± 4.55 vs. 8.96 ± 3.82 h) values of enrofloxacin and its metabolite ciprofloxacin, were observed after the coadministration of propolis compared to enrofloxacin alone following both per os and IM routes in rabbits. Conclusions: The concurrent use of propolis and prescription medications may prolong the half-life (T1/2λz) and increase the systemic availability of chronically used drugs with narrow therapeutic indices. The repeated use of drugs such as antibiotics, heart medications, and antidepressants, or drugs with a narrow therapeutic index such as antineoplastic and anticoagulant agents, can cause toxic effects by raising blood plasma levels. Considering the varied metabolism of rabbits and humans, further validation of this study may require thorough clinical trials in humans. Full article
(This article belongs to the Section Pharmacology)
Show Figures

Graphical abstract

15 pages, 7294 KiB  
Article
Evolutionary Dynamics and Functional Bifurcation of the C2H2 Gene Family in Basidiomycota
by Chao Duan and Jie Yang
J. Fungi 2025, 11(7), 487; https://doi.org/10.3390/jof11070487 - 27 Jun 2025
Viewed by 313
Abstract
This study performed a phylogenomic analysis of the C2H2 gene family across 30 Basidiomycota species, identifying 1032 genes distributed across six evolutionary clades (Groups I–VI). Functional diversification and lineage-specific expansions were observed: Group II (37.1%) formed a conserved core, while wood decayers (e.g., [...] Read more.
This study performed a phylogenomic analysis of the C2H2 gene family across 30 Basidiomycota species, identifying 1032 genes distributed across six evolutionary clades (Groups I–VI). Functional diversification and lineage-specific expansions were observed: Group II (37.1%) formed a conserved core, while wood decayers (e.g., Schizophyllum commune) and edible fungi (e.g., Pleurotus ostreatus) exhibited clade-specific expansions in Groups III and V, respectively. Physicochemical profiling revealed an acidic bias in Agaricomycotina proteins (pI 4.3–5.8) compared to alkaline trends in pathogens (Ustilaginomycotina/Pucciniomycotina; pI 8.3–8.6). Comparative genomics indicated that saprotrophs retained long genes (12.4 kb) with abundant introns (mean = 6.2/gene), whereas pathogens exhibited genomic streamlining (introns ≤ 2). Synteny network analysis revealed high ancestral conservation in core clusters (Cluster_1–2: 58% homologs) under strong purifying selection (Ka/Ks = 0.18–0.22), while peripheral clusters (Cluster_Mini) approached neutral evolution (Ka/Ks = 0.73). This study reveals stage-specific expression dynamics of 17 C2H2 zinc finger genes in Sarcomyxa edulis, highlighting their roles in coordinating developmental transitions (e.g., SeC2H2_1 in low-temperature adaptation, SeC2H2_7/12 in primordia initiation, and SeC2H2_8/9/13 in fruiting body maturation) through temporally partitioned regulatory programs, providing insights into fungal morphogenesis and stress-responsive adaptation. These findings underscore the dual role of C2H2 genes in sustaining conserved regulatory networks and facilitating ecological adaptation, providing new insights into fungal genome evolution. Full article
Show Figures

Figure 1

22 pages, 4788 KiB  
Article
Genome-Wide Identification, Plasma Membrane Localization, and Functional Validation of the SUT Gene Family in Yam (Dioscorea cayennensis subsp. rotundata)
by Na Li, Yanfang Zhang, Xiuwen Huo, Linan Xing, Mingran Ge and Ningning Suo
Int. J. Mol. Sci. 2025, 26(12), 5756; https://doi.org/10.3390/ijms26125756 - 16 Jun 2025
Viewed by 306
Abstract
Yam (Dioscorea cayennensis subsp. rotundata,hereafter referred to as Dioscorea rotundata) is a staple tropical tuber crop with notable nutritional and economic value. Its development and yield depend on efficient sucrose allocation from source tissues. Sucrose transporters (SUTs), a conserved family [...] Read more.
Yam (Dioscorea cayennensis subsp. rotundata,hereafter referred to as Dioscorea rotundata) is a staple tropical tuber crop with notable nutritional and economic value. Its development and yield depend on efficient sucrose allocation from source tissues. Sucrose transporters (SUTs), a conserved family of membrane proteins, mediate sucrose loading, translocation, and unloading. Although well-studied in model plants and cereals, SUTs in yam remain largely uncharacterized. This study aims to identify and characterize the SUT gene family in yam and explore their roles in sucrose transport and tuber development. We conducted a genome-wide analysis of yam SUT genes, including gene structure, subcellular localization, and phylogeny. Molecular docking was used to predict sucrose-binding residues, and qRT-PCR assessed gene expression across tissues and tuber developmental stages. Eight SUT genes were identified and classified based on sequence similarity and domain structure. Docking analysis revealed key residues involved in sucrose binding and possible conformational shifts influencing transport. Expression profiling showed that most SUT genes, especially in the tuber apex, were progressively upregulated during development, suggesting roles in sucrose unloading and cell expansion. Additionally, functional validation of DrSUT1 in Arabidopsis thaliana confirmed its involvement in sucrose transport, supporting its role in yam sucrose partitioning. Yam SUT genes, especially those highly expressed in sink tissues, are involved in sucrose partitioning and tuber development. These findings provide structural and functional insights into SUT-mediated sugar transport and lay a foundation for improving sucrose utilization and yield in yam and other tuber crops. Full article
(This article belongs to the Section Molecular Plant Sciences)
Show Figures

Figure 1

15 pages, 6405 KiB  
Article
Integrative Single-Cell Transcriptomics and Network Modeling Reveal Modular Regulators of Sheep Zygotic Genome Activation
by Xiaopeng Li, Peng Niu, Kai Hu, Xueyan Wang, Fei Huang, Pengyan Song, Qinghua Gao and Di Fang
Biology 2025, 14(6), 676; https://doi.org/10.3390/biology14060676 - 11 Jun 2025
Viewed by 814
Abstract
Zygotic genome activation (ZGA) marks the critical transition from reliance on maternal transcripts to the initiation of embryonic transcription early in development. Despite extensive characterization in model species, the regulatory framework of ZGA in sheep remains poorly defined. Here, we applied single-cell RNA [...] Read more.
Zygotic genome activation (ZGA) marks the critical transition from reliance on maternal transcripts to the initiation of embryonic transcription early in development. Despite extensive characterization in model species, the regulatory framework of ZGA in sheep remains poorly defined. Here, we applied single-cell RNA sequencing (Smart-seq2) to in vivo- and in vitro-derived sheep embryos at the 8-, 16-, and 32-cell stages. Differential expression analysis revealed 114, 1628, and 1465 genes altered in the 8- vs. 16-, 16- vs. 32-, and 8- vs. 32-cell transitions, respectively, with the core pluripotency factors SOX2, NANOG, POU5F1, and KLF4 upregulated during major ZGA. To uncover coordinated regulatory modules, we constructed a weighted gene co-expression network using WGCNA, identifying the MEred module as most tightly correlated with developmental progression (r = 0.48, p = 8.6 × 10−14). The integration of MERed genes into the STRING v11 protein–protein interaction network furnished a high-confidence scaffold for community detection. Louvain partitioning delineated two discrete communities: Community 0 was enriched in ER–Golgi vesicle-mediated transport, transmembrane transport, and cytoskeletal dynamics, suggesting roles in membrane protein processing, secretion, and early signaling; Community 1 was enriched in G2/M cell-cycle transition and RNA splicing/processing, indicating a coordinated network for accurate post-ZGA cell division and transcript maturation. Together, these integrated analyses reveal a modular regulatory architecture underlying sheep ZGA and provide a framework for dissecting early embryonic development in this species. Full article
Show Figures

Figure 1

18 pages, 1650 KiB  
Article
A Compressed Sequence Tag Index for Fast Peptide Retrieval and Efficient Storage in Protein Identification Search Engines
by Xiaoyu Xie, Yuyue Feng, Piyu Zhou, Di Zhang, Lijin Yao and Haipeng Wang
Appl. Sci. 2025, 15(12), 6482; https://doi.org/10.3390/app15126482 - 9 Jun 2025
Viewed by 311
Abstract
Proteins regulate various cellular processes and are of great biological interest. The protein search engine is a crucial tool in proteomics research, used to analyze high-throughput tandem mass spectrometry data and to identify protein sequence information. A core step in protein search engines [...] Read more.
Proteins regulate various cellular processes and are of great biological interest. The protein search engine is a crucial tool in proteomics research, used to analyze high-throughput tandem mass spectrometry data and to identify protein sequence information. A core step in protein search engines is constructing sequence tag indexes and performing the rapid retrieval of protein databases. However, as the scale of protein sequence data continues to grow, traditional protein search engines face the dual challenges of the high storage cost of sequence tag indexes and low retrieval efficiency. To address these issues, we propose a sequence tag index scheme named STIP, which is based on an inverted index and compression techniques. Based on STIP, we design a peptide retrieval algorithm named STIP-Search. This algorithm utilizes the sequence tag index constructed by STIP for peptide sequence retrieval. STIP uses the greedy algorithm to partition the tag index into blocks; in this way, STIP can generate tag indexes for very large protein databases, such as NCBI-nr. Compared to the current four mainstream tag index generation algorithms used in Open-pFind, MODplus, TIIP and PIPI2, STIP has the lowest storage and time consumption. It utilizes delta encoding, index reduction, and dynamic bit width encoding to compress the tag index, reducing the storage cost by 76.2%. Compared to TIIP, which is currently the algorithm with the lowest time complexity, the time cost of the peptide sequence retrieval of STIP-Search is reduced by 8.94% to 23.31%. Full article
Show Figures

Figure 1

18 pages, 3819 KiB  
Article
Melatonin Promotes Muscle Growth and Redirects Fat Deposition in Cashmere Goats via Gut Microbiota Modulation and Enhanced Antioxidant Capacity
by Di Han, Zibin Zheng, Zhenyu Su, Xianliu Wang, Shiwei Ding, Chunyan Wang, Liwen He and Wei Zhang
Antioxidants 2025, 14(6), 645; https://doi.org/10.3390/antiox14060645 - 27 May 2025
Viewed by 544
Abstract
Liaoning cashmere goats is a dual-purpose breed valued for premium cashmere fiber and meat yields, and there is currently a lack of optimized strategies for meat quality, including skeletal muscle development and lipid partitioning. This investigation systematically examines how melatonin administration modulates gastrointestinal [...] Read more.
Liaoning cashmere goats is a dual-purpose breed valued for premium cashmere fiber and meat yields, and there is currently a lack of optimized strategies for meat quality, including skeletal muscle development and lipid partitioning. This investigation systematically examines how melatonin administration modulates gastrointestinal microbiota and antioxidant capacity to concurrently enhance skeletal muscle hypertrophy and redirect lipid deposition patterns, ultimately improving meat quality and carcass traits in Liaoning cashmere goats. Thirty female half-sibling kids were randomized into control and melatonin-treated groups (2 mg/kg live weight with subcutaneous implants). Postmortem analyses at 8 months assessed carcass traits, meat quality, muscle histology, plasma metabolites, and gut microbiota (16S rRNA sequencing). Melatonin supplementation decreased visceral adiposity (perirenal, omental, and mesenteric fat depots with a p < 0.05) while inducing muscle fiber hypertrophy (longissimus thoracis et lumborum (LTL) and biceps femoris (BF) with p < 0.05). The melatonin-treated group demonstrated elevated postmortem pH24h values, attenuated muscle drip loss, enhanced intramuscular protein deposition, and improved systemic antioxidant status (characterized by increased catalase and glutathione levels with concomitant reduction in malondialdehyde with p < 0.05). Melatonin reshaped gut microbiota, increasing α-diversity (p < 0.05) and enriching beneficial genera (Prevotella, Romboutsia, and Akkermansia), while suppressing lipogenic Desulfovibrio populations, and concomitant with improved intestinal morphology as evidenced by elevated villus height-to-crypt depth ratios. These findings establish that melatonin-mediated gastrointestinal microbiota remodeling drives anabolic muscle protein synthesis while optimizing fat deposition, providing a scientifically grounded strategy to enhance meat quality. Full article
(This article belongs to the Special Issue Oxidative Stress in Livestock and Poultry—3rd Edition)
Show Figures

Figure 1

20 pages, 1833 KiB  
Article
Subcellular Partitioning of Trace Elements Is Related to Metal Ecotoxicological Classes in Livers of Fish (Esox lucius; Coregonus clupeaformis) from the Yellowknife Area (Northwest Territories, Canada)
by Aymeric Rolland, Mike Palmer, John Chételat, Marc Amyot and Maikel Rosabal
Toxics 2025, 13(5), 410; https://doi.org/10.3390/toxics13050410 - 19 May 2025
Viewed by 483
Abstract
The subcellular partitioning of trace elements (TEs) may depend on their binding preferences, although few field data are available from mining-impacted areas. Northern pike and lake whitefish were collected from different aquatic systems located in the Yellowknife mining area (Northwest Territories, Canada) to [...] Read more.
The subcellular partitioning of trace elements (TEs) may depend on their binding preferences, although few field data are available from mining-impacted areas. Northern pike and lake whitefish were collected from different aquatic systems located in the Yellowknife mining area (Northwest Territories, Canada) to examine the subcellular partitioning of TEs in liver cells. Elements belonging to metal classes based on binding affinities were considered: A (Ce, La), borderline (As, Pb), and class B (Ag, Cd). Measurements in the metal-detoxified fractions (granule-like structures and heat-stable proteins and peptides) and in the putative metal-sensitive fractions (heat-denatured proteins, mitochondria and microsomes, and lysosomes) revealed marked differences among metal classes. In both fish species, Cd and Ag accumulated more as detoxified forms (higher than 50%, likely bound to metallothionein-like proteins) than La and Ce (not more than 20%). The two borderline TEs (As and Pb) showed an intermediate behavior between classes A and B. Similar proportions were found in the “sensitive” subcellular fractions for all TEs, where quantitative ion character-activity relationships (QICARs) indicated the covalent index and electronegativity as predictors of the TE contribution in this compartment. This study supports the use of classes of metals to predict the toxicological risk of data-poor metals in mining areas. Full article
(This article belongs to the Special Issue Understanding the Trafficking of Toxic Metal(loid)s within Cells)
Show Figures

Graphical abstract

23 pages, 2849 KiB  
Article
Comprehensive Genomic Analysis of Klebsiella pneumoniae and Its Temperate N-15-like Phage: From Isolation to Functional Annotation
by Reham Yahya, Aljawharah Albaqami, Amal Alzahrani, Suha M. Althubaiti, Moayad Alhariri, Eisa T. Alrashidi, Nada Alhazmi, Mohammed A. Al-Matary and Najwa Alharbi
Microorganisms 2025, 13(4), 908; https://doi.org/10.3390/microorganisms13040908 - 15 Apr 2025
Viewed by 1351
Abstract
Antibiotic resistance to Klebsiella pneumoniae poses a major public health threat, particularly in intensive care unit (ICU) settings. The emergence of extensively drug-resistant (XDR) strains complicates treatment options, requiring a deeper understanding of their genetic makeup and potential therapeutic targets. This research delineated [...] Read more.
Antibiotic resistance to Klebsiella pneumoniae poses a major public health threat, particularly in intensive care unit (ICU) settings. The emergence of extensively drug-resistant (XDR) strains complicates treatment options, requiring a deeper understanding of their genetic makeup and potential therapeutic targets. This research delineated an extensively drug-resistant (XDR) Klebsiella pneumoniae strain obtained from an ICU patient and telomeric temperate phage derived from hospital effluent. The bacteria showed strong resistance to multiple antibiotics, including penicillin (≥16 μg/mL), ceftriaxone (≥32 μg/mL), and meropenem (≥8 μg/mL), which was caused by SHV-11 beta-lactamase, NDM-1 carbapenemase, and porin mutations (OmpK37, MdtQ). The strain was categorized as K46 and O2a types and carried virulence genes involved in iron acquisition, adhesion, and immune evasion, as well as plasmids (IncHI1B_1_pNDM-MAR, IncFIB) and eleven prophage regions, reflecting its genetic adaptability and resistance dissemination. The 172,025 bp linear genome and 46.3% GC content of the N-15-like phage showed strong genomic similarities to phages of the Sugarlandvirus genus, especially those that infect K. pneumoniae. There were structural proteins (11.8%), DNA replication and repair enzymes (9.3%), and a toxin–antitoxin system (0.4%) encoded by the phage genome. A protelomerase and ParA/B partitioning proteins indicate that the phage is replicating and maintaining itself in a manner similar to the N15 phage, which is renowned for maintaining a linear plasmid prophage throughout lysogeny. Understanding the dynamics of antibiotic resistance and pathogen development requires knowledge of phages like this one, which are known for their temperate nature and their function in altering bacterial virulence and resistance profiles. The regulatory and structural proteins of the phage also provide a model for research into the biology of temperate phages and their effects on microbial communities. The importance of temperate phages in bacterial genomes and their function in the larger framework of microbial ecology and evolution is emphasized in this research. Full article
(This article belongs to the Section Medical Microbiology)
Show Figures

Figure 1

21 pages, 2503 KiB  
Article
Optimization of Nanoencapsulation of Codium tomentosum Extract and Its Potential Application in Yogurt Fortification
by Micaela Costa, Cristina Soares, Aurora Silva, Maria Fátima Barroso, Pedro Simões, Mariana Ferreira, Paula Gameiro, Clara Grosso and Cristina Delerue-Matos
Mar. Drugs 2025, 23(4), 147; https://doi.org/10.3390/md23040147 - 28 Mar 2025
Cited by 1 | Viewed by 679
Abstract
Marine macroalgae are excellent sources of bioactive compounds recognized by their pharmaceutical and biomedical potential. A subcritical water extraction (SWE) was applied to the macroalga Codium tomentosum, and the extract was used to prepare phytosomes. A Box–Behnken design was applied to optimize [...] Read more.
Marine macroalgae are excellent sources of bioactive compounds recognized by their pharmaceutical and biomedical potential. A subcritical water extraction (SWE) was applied to the macroalga Codium tomentosum, and the extract was used to prepare phytosomes. A Box–Behnken design was applied to optimize the entrapment efficiency. These phytosomes were further modified with DSPE-PEG (2000)-maleimide and apolipoprotein E and characterized by dynamic light scattering, UV spectrophotometry, octanol/water partition coefficient, differential scanning calorimetry, and Fourier transform infrared spectroscopy. As proof of concept, prototypes of functional food tailored to the elderly were produced. Yogurts were fortified with seaweed extract or phytosomes, and physicochemical properties and proximal composition (pH, acidity, syneresis, moisture, peroxides, proteins, total lipids, sugar content, ash, and mineral composition) were analyzed. The antioxidant and the inhibition capacity of two brain enzymes, cholinesterases (AChE and BuChE), involved in the pathogenesis of Alzheimer’s disease, were also evaluated in the final prototypes. Despite their unappealing sensory characteristics, the results are promising for integrating marine extracts with potential neuroprotective effects into functional foods. Full article
(This article belongs to the Special Issue The Extraction and Application of Functional Components in Algae)
Show Figures

Figure 1

25 pages, 2869 KiB  
Article
Anthocyanin-Rich Fraction from Kum Akha Black Rice Attenuates NLRP3 Inflammasome-Driven Lung Inflammation In Vitro and In Vivo
by Sonthaya Umsumarng, Warathit Semmarath, Punnida Arjsri, Kamonwan Srisawad, Intranee Intanil, Sansanee Jamjod, Chanakan Prom-u-thai and Pornngarm Dejkriengkraikul
Nutrients 2025, 17(7), 1186; https://doi.org/10.3390/nu17071186 - 28 Mar 2025
Viewed by 1054
Abstract
Background/Objectives: Chronic lower respiratory tract inflammation can result from exposure to bacterial particles, leading to the activation of the NLRP3 inflammasome pathway. These effects may cause irreversible respiratory damage, contributing to persistent lung injury and chronic obstructive pulmonary disease (COPD), as observed in [...] Read more.
Background/Objectives: Chronic lower respiratory tract inflammation can result from exposure to bacterial particles, leading to the activation of the NLRP3 inflammasome pathway. These effects may cause irreversible respiratory damage, contributing to persistent lung injury and chronic obstructive pulmonary disease (COPD), as observed in long COVID or bacterial pneumonia in older adults’ patients. Given its profound impact, the NLRP3 inflammasome has emerged as a key therapeutic target for mitigating aberrant inflammatory responses. Methods: In this study, we investigated the anti-inflammatory effects of Kum Akha black rice, a functional food, on the attenuation of NLRP3 inflammasome pathway using lipopolysaccharide-induced A549 lung epithelial cells and a C57BL/6NJcl mouse model. The anthocyanin-rich fraction from Kum Akha black rice germ and bran extract (KA1-P1) was obtained using a solvent-partitioned extraction technique. Results: KA1-P1 exhibited a high anthocyanin content (74.63 ± 1.66 mg/g extract) as determined by the pH differential method. The HPLC analysis revealed cyanidin-3-O-glucoside (C3G: 45.58 ± 0.48 mg/g extract) and peonidin-3-O-glucoside (P3G: 6.92 ± 0.29 mg/g extract) as its anthocyanin’s active compounds. Additionally, KA1-P1 demonstrated strong antioxidant activity, as assessed by DPPH and ABTS assays. KA1-P1 (12.5–100 μg/mL) possessed inhibitory effects on LPS + ATP-induced A549 lung cells inflammation through the significant suppressions of NLRP3, IL-6, IL-1β, and IL-18 mRNA levels and the inhibition of cytokine secretions in a dose-dependent manner (p < 0.05). Mechanistic analysis revealed that KA1-P1 downregulated key proteins in the NLRP3 inflammasome pathway (NLRP3, ASC, pro-caspase-1, and cleaved-caspase-1). Furthermore, in vivo studies demonstrated that KA1-P1 significantly diminished LPS-induced lower respiratory inflammation in C57BL/6NJcl mice, as evidenced by the reduced bronchoalveolar lavage fluid and blood levels of inflammatory cytokines (IL-6, IL-1β, and IL-18) and diminished histopathological inflammatory lung lesions. Conclusions: Overall, our findings suggest that the anti-inflammatory properties of KA1-P1 may support its application as a functional supplement or promote the consumption of pigmented rice among the elderly to mitigate chronic lower respiratory tract inflammation mediated by the NLRP3 inflammasome pathway. Full article
Show Figures

Figure 1

12 pages, 1854 KiB  
Article
Reaction Dynamics of Plant Phenols in Regeneration of Tryptophan from Its Radical Cation Formed via Photosensitized Oxidation
by Yuqian Li, Yiming Zhou, Danhong Li and Jianping Zhang
Appl. Sci. 2025, 15(7), 3524; https://doi.org/10.3390/app15073524 - 24 Mar 2025
Viewed by 403
Abstract
Photooxidation imposes structural damage on proteins, and the amino acid tryptophan (Trp) is a key target for protein oxidation. The Trp radical cation (Trp⁺), as an oxidative product, can be reduced by plant phenols (φ-OH), a category of dietary phytochemicals essential [...] Read more.
Photooxidation imposes structural damage on proteins, and the amino acid tryptophan (Trp) is a key target for protein oxidation. The Trp radical cation (Trp⁺), as an oxidative product, can be reduced by plant phenols (φ-OH), a category of dietary phytochemicals essential for human health. This work is intended to investigate the efficacy of φ-OH regeneration of Trp from Trp⁺ as a function of φ-OH concentration and environmental pH. We have examined, by using laser flash photolysis, six different kinds of φ-OH in the aqueous system consisting of Trp and riboflavin as a photosensitizer. Taking syringic acid (Syr) as an example, upon systematically varying the pH from 2 to 10, the partition of Syr phenolate, Syr-O2−, increases from 0% to 70% and, accordingly, the rate of Trp regeneration increases from 4.8 × 106 M−1·s−1 to 1.7 × 108 M−1·s−1. It is found that the regeneration rate correlates with the driving force of the electron transfer (ET) reaction between φ-OH and Trp•+, which can be well accounted for by Marcus’s ET theory (R² = 0.89). The λ = 0.43 ± 0.08 eV for the reorganization energy for ET from the plant phenols to the Trp⁺. The effects of φ-OH concentration, environmental pH, and ET driving force on the Trp regeneration reaction herein revealed are significant for enlightening further study of protein (anti)oxidation. Full article
Show Figures

Figure 1

23 pages, 4706 KiB  
Article
Bridging the Gap Between hiPSC-CMs Cardiotoxicity Assessment and Clinical LVEF Decline Risk: A Case Study of 21 Tyrosine Kinase Inhibitors
by Zhijie Wan, Chenyu Wang, Shizheng Luo, Jinwei Zhu, Hua He and Kun Hao
Pharmaceuticals 2025, 18(4), 450; https://doi.org/10.3390/ph18040450 - 23 Mar 2025
Viewed by 475
Abstract
Objectives: There is growing concern over tyrosine kinase inhibitor (TKI)-induced cardiotoxicity, particularly regarding left ventricular dysfunction and heart failure in clinical treatment. These adverse effects often lead to treatment discontinuation, severely impacting patient outcomes. Therefore, there is an urgent need for more [...] Read more.
Objectives: There is growing concern over tyrosine kinase inhibitor (TKI)-induced cardiotoxicity, particularly regarding left ventricular dysfunction and heart failure in clinical treatment. These adverse effects often lead to treatment discontinuation, severely impacting patient outcomes. Therefore, there is an urgent need for more precise risk assessment methods. This study aimed to assess the cardiotoxicity of TKIs, refine in vitro to in vivo extrapolation (IVIVE) methodologies to improve predictive accuracy, and identify critical in vitro parameters for assessment. Methods: By leveraging high-throughput cardiotoxicity screening with human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), a mechanism-based toxicodynamic (TD) model for TKIs was constructed. A QSP-PK-TD model was developed by integrating pharmacokinetic (PK) and quantitative systems pharmacology (QSP) models. This model incorporates critical drug exposure factors, such as plasma protein binding, tissue–plasma partitioning, and drug distribution heterogeneity to enhance extrapolation accuracy. Results: The QSP-PK-TD model validated the reliability of IVIVE and identified the area under the curve of drug effects on mitochondrial membrane potential (AEMMP) and cardiomyocyte contractility (AEAAC) as key in vitro parameters for assessing TKI-induced cardiotoxicity. Incorporating critical drug exposure factors obviously improved qualitative and quantitative extrapolation accuracy. Conclusions: This study established a framework for predicting in vivo cardiotoxicity from in vitro parameters, enabling efficient translation of preclinical data into clinical risk assessment. These findings provide valuable insights for drug development and regulatory decision-making, offering a powerful tool for evaluating TKI-induced cardiotoxicity. Full article
(This article belongs to the Section Pharmacology)
Show Figures

Figure 1

Back to TopTop