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Search Results (377)

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Keywords = freshness markers

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16 pages, 1258 KiB  
Article
Genome-Wide Association Analysis of Traits Related to Nitrogen Deficiency Stress in Potato
by Carmen Iribar, Alba Alvarez-Morezuelas, Leire Barandalla and Jose Ignacio Ruiz de Galarreta
Horticulturae 2025, 11(8), 889; https://doi.org/10.3390/horticulturae11080889 (registering DOI) - 1 Aug 2025
Viewed by 193
Abstract
Potato (Solanum tuberosum L.) crop yields may be reduced by nitrogen deficiency stress tolerance. An evaluation of 144 tetraploid potato genotypes was carried out during two consecutive seasons (2019 and 2020), with the objective of characterizing their variability in key physiological and [...] Read more.
Potato (Solanum tuberosum L.) crop yields may be reduced by nitrogen deficiency stress tolerance. An evaluation of 144 tetraploid potato genotypes was carried out during two consecutive seasons (2019 and 2020), with the objective of characterizing their variability in key physiological and agronomic parameters. Physiological parameters included chlorophyll content and fluorescence, stomatal conductance, NDVI, leaf area, and perimeter, while agronomic characteristics such as yield, tuber fresh weight, tuber number, starch content, dry matter, and reducing sugars were evaluated. To genotype the population, the GGP V3 Potato array was used, generating 18,259 high-quality SNP markers. Marker–trait association analysis was conducted using the GWASpoly package in R, applying Q + K linear mixed models to enhance precision. This methodology enabled the identification of 18 SNP markers that exhibited statistically significant associations with the traits analyzed in both trials and periods, relating them to genes whose functional implication has already been described. Genetic loci associated with chlorophyll content and tuber number were detected across non-stress and stress treatments, while markers linked to leaf area and leaf perimeter were identified specifically under nitrogen deficiency stress. The genomic distribution of these markers revealed that genetic markers or single-nucleotide polymorphisms (SNPs) correlated with phenotypic traits under non-stress conditions were predominantly located on chromosome 11, whereas SNPs linked to stress responses were mainly identified on chromosomes 2 and 3. These findings contribute to understanding the genetic mechanisms underlying potato tolerance to nitrogen deficiency stress, offering valuable insights for the development of future marker-assisted selection programs aimed at improving nitrogen use efficiency and stress resilience in potato breeding. Full article
(This article belongs to the Special Issue Genetics, Genomics and Breeding of Vegetable Crops)
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18 pages, 1711 KiB  
Article
Genome-Wide Association Analysis of Fresh Maize
by Suying Guo, Rengui Zhao and Jinhao Lan
Int. J. Mol. Sci. 2025, 26(15), 7431; https://doi.org/10.3390/ijms26157431 - 1 Aug 2025
Viewed by 104
Abstract
This study measured eight key phenotypic traits across 259 fresh maize inbred lines, including plant height and spike length. A total of 82 single nucleotide polymorphisms (SNPs) significantly associated with these phenotypes were identified by applying a mixed linear model to calculate the [...] Read more.
This study measured eight key phenotypic traits across 259 fresh maize inbred lines, including plant height and spike length. A total of 82 single nucleotide polymorphisms (SNPs) significantly associated with these phenotypes were identified by applying a mixed linear model to calculate the best linear unbiased prediction (BLUP) values and integrating genome-wide genotypic data through genome-wide association analysis (GWAS). A further analysis of significant SNPs contributed to the identification of 63 candidate genes with functional annotations. Notably, 11 major candidate genes were identified from multi-trait association loci, all of which exhibited highly significant P-values (<0.0001) and explained between 7.21% and 12.78% of phenotypic variation. These 11 genes, located on chromosomes 1, 3, 4, 5, 6, and 9, were functionally involved in signaling, metabolic regulation, structural maintenance, and stress response, and are likely to play crucial roles in the growth and physiological processes of fresh maize inbred lines. The functional genes identified in this study have significant implications for the development of molecular markers, the optimization of breeding strategies, and the enhancement of quality in fresh maize. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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13 pages, 4134 KiB  
Communication
An Improved Agrobacterium-Mediated Transformation Method for an Important Fresh Fruit: Kiwifruit (Actinidia deliciosa)
by Chun-Lan Piao, Mengdou Ding, Yongbin Gao, Tao Song, Ying Zhu and Min-Long Cui
Plants 2025, 14(15), 2353; https://doi.org/10.3390/plants14152353 - 31 Jul 2025
Viewed by 273
Abstract
Genetic transformation is an essential tool for investigating gene function and editing genomes. Kiwifruit, recognized as a significant global fresh fruit crop, holds considerable economic and nutritional importance. However, current genetic transformation techniques for kiwifruit are impeded by low efficiency, lengthy culture durations [...] Read more.
Genetic transformation is an essential tool for investigating gene function and editing genomes. Kiwifruit, recognized as a significant global fresh fruit crop, holds considerable economic and nutritional importance. However, current genetic transformation techniques for kiwifruit are impeded by low efficiency, lengthy culture durations (a minimum of six months), and substantial labor requirements. In this research, we established an efficient system for shoot regeneration and the stable genetic transformation of the ‘Hayward’ cultivar, utilizing leaf explants in conjunction with two strains of Agrobacterium that harbor the expression vector pBI121-35S::GFP, which contains the green fluorescent protein (GFP) gene as a visible marker within the T-DNA region. Our results show that 93.3% of leaf explants responded positively to the regeneration medium, producing multiple independent adventitious shoots around the explants within a six-week period. Furthermore, over 71% of kanamycin-resistant plantlets exhibited robust GFP expression, and the entire transformation process was completed within four months of culture. Southern blot analysis confirmed the stable integration of GFP into the genome, while RT-PCR and fluorescence microscopy validated the sustained expression of GFP in mature plants. This efficient protocol for regeneration and transformation provides a solid foundation for micropropagation and the enhancement of desirable traits in kiwifruit through overexpression and gene silencing techniques. Full article
(This article belongs to the Special Issue Plant Transformation and Genome Editing)
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24 pages, 9486 KiB  
Article
StMAPKK1 Enhances Thermotolerance in Potato (Solanum tuberosum L.) by Enhancing Antioxidant Defense and Photosynthetic Efficiency Under Heat Stress
by Xi Zhu, Yasir Majeed, Kaitong Wang, Xiaoqin Duan, Nengkang Guan, Junfu Luo, Haifei Zheng, Huafen Zou, Hui Jin, Zhuo Chen and Yu Zhang
Plants 2025, 14(15), 2289; https://doi.org/10.3390/plants14152289 - 24 Jul 2025
Viewed by 297
Abstract
The functional role of MAPKK genes in potato (Solanum tuberosum L.) under high-temperature stress remains unexplored, despite their critical importance in stress signaling and yield protection. We characterized StMAPKK1, a novel group D MAPKK localized to plasma membrane/cytoplasm. Quantitative real-time polymerase chain [...] Read more.
The functional role of MAPKK genes in potato (Solanum tuberosum L.) under high-temperature stress remains unexplored, despite their critical importance in stress signaling and yield protection. We characterized StMAPKK1, a novel group D MAPKK localized to plasma membrane/cytoplasm. Quantitative real-time polymerase chain reaction (qRT-PCR) revealed cultivar-specific upregulation in potato (‘Atlantic’ and ‘Desiree’) leaves under heat stress (25 °C, 30 °C, and 35 °C). Transgenic lines overexpressing (OE) StMAPKK1 exhibited elevated antioxidant enzyme activity, including ascorbate peroxidase (APX), catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD), mitigating oxidative damage. Increased proline and chlorophyll accumulation and reduced oxidative stress markers, hydrogen peroxide (H2O2) and malondialdehyde (MDA), indicate improved cellular redox homeostasis. The upregulation of key antioxidant and heat stress-responsive genes (StAPX, StCAT1/2, StPOD12/47, StFeSOD2/3, StMnSOD, StCuZnSOD1/2, StHSFA3 and StHSP20/70/90) strengthened the enzymatic defense system, enhanced thermotolerance, and improved photosynthetic efficiency, with significant improvements in net photosynthetic rate (Pn), transpiration rate (E), and stomatal conductance (Gs) under heat stress (35 °C) in StMAPKK1-OE plants. Superior growth and biomass (plant height, plant and its root fresh and dry weights, and tuber yield) accumulation, confirming the positive role of StMAPKK1 in thermotolerance. Conversely, RNA interference (RNAi)-mediated suppression of StMAPKK1 led to a reduction in enzymatic activity, proline content, and chlorophyll levels, exacerbating oxidative stress. Downregulation of antioxidant-related genes impaired ROS scavenging capacity and declines in photosynthetic efficiency, growth, and biomass, accompanied by elevated H2O2 and MDA accumulation, highlighting the essential role of StMAPKK1 in heat stress adaptation. These findings highlight StMAPKK1’s potential as a key genetic target for breeding heat-tolerant potato varieties, offering a foundation for improving crop resilience in warming climates. Full article
(This article belongs to the Special Issue Cell Physiology and Stress Adaptation of Crops)
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19 pages, 3265 KiB  
Article
Biofortified Calcium Phosphate Nanoparticles Elicit Secondary Metabolite Production in Carob Callus via Biosynthetic Pathway Activation
by Doaa E. Elsherif, Fatmah A. Safhi, Mai A. El-Esawy, Alaa T. Mohammed, Osama A. Alaziz, Prasanta K. Subudhi and Abdelghany S. Shaban
Plants 2025, 14(14), 2093; https://doi.org/10.3390/plants14142093 - 8 Jul 2025
Viewed by 347
Abstract
Plant callus cultures are a sustainable alternative for producing bioactive secondary metabolites, but their low yields limit industrial applications. Carob (Ceratonia siliqua L.) is rich in medicinally valuable compounds, yet conventional cultivation faces challenges. To address this, we use biofortified calcium phosphate [...] Read more.
Plant callus cultures are a sustainable alternative for producing bioactive secondary metabolites, but their low yields limit industrial applications. Carob (Ceratonia siliqua L.) is rich in medicinally valuable compounds, yet conventional cultivation faces challenges. To address this, we use biofortified calcium phosphate nanoparticles, which refer to CaP-NPs that have been enriched with bioactive compounds via green synthesis using Jania rubens extract, thereby enhancing their functional properties as elicitors in carob callus. CaP-NPs were green-synthesized using Jania rubens extract and applied to 7-week-old callus cultures at 0, 25, 50, and 75 mg/L concentrations. At the optimal concentration (50 mg/L), CaP-NPs increased callus fresh weight by 23.9% and dry weight by 35.1%. At 50 mg/L CaP-NPs, phenolic content increased by 95.7%, flavonoids by 34.4%, tannins by 131.8%, and terpenoids by 211.9% compared to controls. Total antioxidant capacity rose by 76.2%, while oxidative stress markers malondialdehyde (MDA) and hydrogen peroxide (H2O2) decreased by 34.8% and 14.1%, respectively. Gene expression analysis revealed upregulation of PAL (4-fold), CHI (3.15-fold), FLS (1.16-fold), MVK (8.3-fold), and TA (3.24-fold) at 50 mg/L CaP-NPs. Higher doses (75 mg/L) induced oxidative damage, demonstrating a hormetic threshold. These findings indicate that CaP-NPs effectively enhance secondary metabolite production in carob callus by modulating biosynthetic pathways and redox balance, offering a scalable, eco-friendly approach for pharmaceutical and nutraceutical applications. Full article
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24 pages, 3140 KiB  
Article
Physicochemical and Sensory Evaluation of Romanian Monofloral Honeys from Different Supply Chains
by Elena Daniela Bratosin, Delia Mirela Tit, Manuela Bianca Pasca, Anamaria Lavinia Purza, Gabriela Bungau, Ruxandra Cristina Marin, Andrei Flavius Radu and Daniela Gitea
Foods 2025, 14(13), 2372; https://doi.org/10.3390/foods14132372 - 4 Jul 2025
Viewed by 398
Abstract
Honey quality and authenticity are influenced by floral origin, processing, and storage, with implications for composition and sensory appeal. This study offers a comparative assessment of eight monofloral honey samples, representing five botanical varieties: acacia, linden, rapeseed, lavender, and thyme. For acacia, linden, [...] Read more.
Honey quality and authenticity are influenced by floral origin, processing, and storage, with implications for composition and sensory appeal. This study offers a comparative assessment of eight monofloral honey samples, representing five botanical varieties: acacia, linden, rapeseed, lavender, and thyme. For acacia, linden, and rapeseed, both producer-sourced and commercial honeys were analyzed, while lavender and thyme samples were available only from local beekeepers. The botanical origin of each sample was confirmed using morphological markers of pollen grains. Physicochemical characterization included acidity, pH, moisture content, refractive index, hydroxymethyl furfural (HMF), proline concentration, and carbohydrate profiling by HPLC-RID. Acacia honey exhibited the lowest acidity and HMF levels, alongside the highest fructose/glucose (F/G) ratios, indicating superior freshness, lower crystallization risk, and a sweeter flavor profile. In contrast, rapeseed honey showed elevated glucose levels and the lowest F/G ratio, confirming its tendency to crystallize rapidly. All samples recorded proline concentrations well above the quality threshold (180 mg/kg), supporting their authenticity and proper maturation. The estimated glycemic index (eGI) varied between 43.91 and 62.68 and was strongly inversely correlated with the F/G ratio (r = −0.98, p < 0.001). Sensory evaluation highlighted acacia honey from producers as the most appreciated across visual, tactile, and flavor attributes. Correlation analyses further revealed consistent links between sugar composition and both physical and sensory properties. Overall, the findings reinforce the value of integrated analytical and sensory profiling in assessing honey quality and authenticity. Full article
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18 pages, 2296 KiB  
Article
An SSR-Base Linkage Map Reveals QTLs for Floral-Related Traits in Nightlily (Hemerocallis citrina)
by Yuting Su, Zhonghao Liang, Xinyu Zhao, Lijing Shi, Yang Liu, Yang Gao, Xiaojing Cheng, Guoming Xing and Sen Li
Agronomy 2025, 15(7), 1599; https://doi.org/10.3390/agronomy15071599 - 30 Jun 2025
Viewed by 406
Abstract
Nightlily (Hemerocallis citrina Baroni) is mainly cultivated for bud consumption with medicinal, nutritional, and economic value. Enhancing nightlily yield is one of the most significant breeding goals of modern agriculture of H. citrina breeding objective, but it also faces great [...] Read more.
Nightlily (Hemerocallis citrina Baroni) is mainly cultivated for bud consumption with medicinal, nutritional, and economic value. Enhancing nightlily yield is one of the most significant breeding goals of modern agriculture of H. citrina breeding objective, but it also faces great challenges. In this study, an intraspecific hybridization population crossed between two varieties, ‘Liuyuehua’ and ‘Datong Huanghua’ of Hemerocallis, was used to establish 715 F1 individuals. Phenotypic data for eight floral traits, including scape number, bud number, scape length, scape diameter, bud length, bud diameter, fresh flower bud weight, and dry flower bud weight, were collected from 715 F1 individuals over a three-year period (2022, 2023, and 2024). The Simple Repeat Sequence (SSR) markers were validated to genotype the 116 random F1 individuals and to construct a linkage map. The intraspecific hybridization map contained 11 linkage groups. A total of 169 SSR markers were used to construct a linkage map, spanning a total map length of 1605.3 cM, with an average marker interval of 9.50 cM. The linkage map revealed 11 floral QTLs from 7.21% to 24.29% of phenotypic variation. Through collinearity analysis, it was found that 122 markers could be aligned to the published genome sequence of H. citrina. A total of five candidate genes for floral traits were predicted. The linkage map is essential for mapping and marker-assisted progeny selection that will accelerate the pace of nightlily breeding. Full article
(This article belongs to the Section Horticultural and Floricultural Crops)
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18 pages, 3095 KiB  
Article
A Transcriptomics Approach to Unveil the Antioxidant Effects of Tryptophan on Oocyte Quality Under Oxidative Stress in Pigs
by Zhekun Zhu, Yanlong Li, Xinyin Fan, Shuang Cai, Siyu Li, Yutian Wang, Xinyu Wang and Fengjuan Yang
Biomolecules 2025, 15(7), 949; https://doi.org/10.3390/biom15070949 - 30 Jun 2025
Viewed by 291
Abstract
This study investigates the effect of tryptophan treatment on aged pig oocytes, focusing on its potential to reduce oxidative stress and improve oocyte quality. An oxidative stress model was induced using hydrogen peroxide (H2O2) to mimic aging effects on [...] Read more.
This study investigates the effect of tryptophan treatment on aged pig oocytes, focusing on its potential to reduce oxidative stress and improve oocyte quality. An oxidative stress model was induced using hydrogen peroxide (H2O2) to mimic aging effects on oocytes. Fresh ovaries from young sows were collected, and oocytes were aspirated and cultured for in vitro maturation. Oocytes in the H2O2 and the H2O2+Trp groups were exposed to 100 µM H2O2 for 30 min, with the H2O2+Trp group receiving an additional 50 µM tryptophan supplementation. RNA-sequencing was performed to study the underlying mechanism through which tryptophan mitigated the H2O2-induced oxidative stress in oocytes. The results demonstrated that tryptophan supplementation significantly reduced oxidative stress markers such as H2O2 and malonaldehyde (MDA) while restoring key antioxidant enzymes such as superoxide dismutase (SOD), and catalase (CAT) confirming its antioxidant role. Furthermore, tryptophan improved cumulus cell expansion, and oocyte quality, which were compromised by oxidative stress. Transcriptomics study revealed the enrichment of several KEGG pathways, such as P13K-Akt signaling pathways as a critical regulator of cell survival and function, emphasizing the protective effects of tryptophan on oocyte integrity. Moreover, the protein–protein interaction (PPI) network identified several hub genes in the tryptophan-treated group compared with H2O2, including TIMP1, CCN2, and MMP12 as key players in ECM remodeling and cellular adhesion, which are critical for restoring oocyte quality. These findings suggest that tryptophan supplementation not only mitigated oxidative stress but also modulated gene expression related to cellular functions and stress response. These results propose that tryptophan could be a valuable therapeutic strategy for improving reproductive outcomes in aging sows and other mammals facing age-related oocyte dysfunction. Full article
(This article belongs to the Special Issue Placental-Related Disorders of Pregnancy: 2nd Edition)
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16 pages, 3303 KiB  
Article
Assessment of Genetic Diversity by Morphological, Biochemical, and Molecular Markers in Gloriosa superba Ecotypes Collected from Different Agro-Climatic Zones in India
by Moumita Majumdar, Rakesh Arya, Soumya Prakash Sahu, Archana Tiwari and Jong-Joo Kim
Horticulturae 2025, 11(7), 723; https://doi.org/10.3390/horticulturae11070723 - 21 Jun 2025
Viewed by 347
Abstract
Background: Gloriosa superba L., commonly known as Glory Lily, is a medicinally valuable perennial climber native to tropical and subtropical regions of India. It is known for its rich alkaloid content, including colchicine and colchicoside, which contribute to its therapeutic potential in treating [...] Read more.
Background: Gloriosa superba L., commonly known as Glory Lily, is a medicinally valuable perennial climber native to tropical and subtropical regions of India. It is known for its rich alkaloid content, including colchicine and colchicoside, which contribute to its therapeutic potential in treating various ailments. Despite its pharmacological significance, genomic research on G. superba remains limited due to the lack of genetic markers, hindering molecular studies and breeding advancements. Methods: This study utilized a previously reported de novo transcriptome assembly of G. superba, identifying 14,672 EST-SSRs as genomic markers to assess genetic variations across different accessions. Genetic diversity was examined using SSR markers, while 20 morphological traits were systematically evaluated across 19 G. superba accessions from diverse geographic regions to provide insights into trait variability. Results: The most highly variable traits included plant height, number of leaves per plant, number of branches per plant, fresh pod yield, fresh seed yield, dry seed yield, number of pods per plant, leaf width, and internodal length, with coefficients of variation (CV) ranging from 63.53% to 22.45%. Intermediate CV values (10.05% to 18.75%) were observed in eight traits, while three traits (days to flowering, days to 50% flowering, and colchicine content) had low variation (<5%). Principal component analysis (PCA) accounted for 51.3% of phenotypic variation, with PC1 and PC2 contributing 29.4% and 21.9%, respectively. Clustering analysis grouped the 19 G. superba accessions into two main clusters and four sub-clusters, highlighting significant genetic divergence, with the highest dissimilarity (81.45%) observed between accessions from Arrupukottai and Pachmarhi. SSR analysis using 112 markers revealed high polymorphism but a relatively low heterozygosity index (H = 0.277) and PIC values of individual SSRs ranged from 0.26069 in RGM-51635 to 0.4534 in RGM-24219. Conclusions: The genetic divergence observed among the collected G. superba ecotypes provides valuable insights for future breeding programs aimed at enhancing cultivation efficiency and developing superior varieties with improved yield and colchicine content. Full article
(This article belongs to the Special Issue Novel Insights into the Phenology of Medicinal and Aromatic Plants)
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17 pages, 1663 KiB  
Article
Role of Mediterranean Diet and Ultra-Processed Foods on Sperm Parameters: Data from a Cross-Sectional Study
by Gabriel Cosmin Petre, Francesco Francini-Pesenti, Luca De Toni, Andrea Di Nisio, Asia Mingardi, Ilaria Cosci, Nicola Passerin, Alberto Ferlin and Andrea Garolla
Nutrients 2025, 17(13), 2066; https://doi.org/10.3390/nu17132066 - 21 Jun 2025
Viewed by 1431
Abstract
Background/Objectives: Male infertility is multifactorial, involving genetic, environmental, lifestyle, and medical factors. Recent research has underscored the influence of lifestyle choices, such as dietary habits, smoking, alcohol abuse, and metabolic disturbances, on sperm quality. In this context, nutrition plays a pivotal role: adherence [...] Read more.
Background/Objectives: Male infertility is multifactorial, involving genetic, environmental, lifestyle, and medical factors. Recent research has underscored the influence of lifestyle choices, such as dietary habits, smoking, alcohol abuse, and metabolic disturbances, on sperm quality. In this context, nutrition plays a pivotal role: adherence to a healthy diet like the Mediterranean Diet (MD), which emphasizes seasonal, fresh, and whole foods, has been linked to improved sperm performance. Conversely, a high intake of ultra-processed foods (UPFs), characterized by additives, high levels of sugars, fats, and salt, and a nutrient-poor profile, may impair sperm quality. Methods: Based on data supporting the reproductive health benefits of the MD, this observational cross-sectional study aimed at evaluating the possible relationship between MD adherence, assessed using the 14-point a priori Mediterranean Diet Adherence Screener (MEDAS) and intake of ultra-processed foods (UPFs), based on the NOVA classification, and sperm quality in 358 individuals (mean age 34.6 ± 9.3 years) who spontaneously referred to our center of reproductive medicine. Semen analyses were performed according to the WHO 2021 criteria. Hormonal profiles (FSH, LH, testosterone, SHBG, bioavailable testosterone, and calculated free testosterone) were also determined. Results: MD adherence score was significantly and positively correlated with semen parameters, whilst negatively correlated with FSH and LH levels. In contrast, UPF intake was correlated with poor semen parameters, whilst no association was observed with hormonal levels. Multivariate analyses confirmed these associations and showed the independency from age and BMI. Notably, among men with FSH levels < 8 IU/mL, higher quartiles of UPF intake had lower markers of sperm quality, particularly for viability and typical morphology. Differently, high MD adherence scores were associated with high quality sperm parameters even when FSH levels were >8 IU/mL. Conclusions: This study provides evidence that the adherence to MD, and conversely reduced intake of ultra-processed foods, is associates with a better semen profile. These findings suggest the possible role of dietary interventions as a modifiable factor in the management of male infertility. Full article
(This article belongs to the Section Nutrition and Public Health)
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26 pages, 2501 KiB  
Article
The Role of Genetic Variation in Modulating the Effects of Blended Fruits and Vegetables Versus Fruit- and Vegetable-Coated Food Products on Antioxidant Capacity, DNA Protection, and Vascular Health: A Randomized Controlled Trial
by Julia N. DeBenedictis, Na Xu, Theo M. de Kok and Simone G. van Breda
Nutrients 2025, 17(12), 2036; https://doi.org/10.3390/nu17122036 - 18 Jun 2025
Viewed by 500
Abstract
Background/Objectives: Fruits and vegetables (F&Vs) are major dietary sources of phytochemicals, crucial for preventing non-communicable diseases. However, barriers such as preparation inconvenience and a short shelf life hinder their consumption. F&V-coated foods have emerged as an alternative. This human nutrition intervention study [...] Read more.
Background/Objectives: Fruits and vegetables (F&Vs) are major dietary sources of phytochemicals, crucial for preventing non-communicable diseases. However, barriers such as preparation inconvenience and a short shelf life hinder their consumption. F&V-coated foods have emerged as an alternative. This human nutrition intervention study assessed the effects of a blended F&Vs mixture versus an F&V-coated food on phytochemical absorption and chronic disease risk markers. It also explored how genetic variation influences physiological responses to these F&V products. Methods: In this randomized-controlled trial, participants were assigned to one of three dietary interventions: a blended F&V mixture (“F&V Blend”), a rice-based cereal product coated with this blend (“Coated Pearl”), or the same product without the F&V mixture (“Uncoated Pearl”). The four-week study included a two-week run-in and a two-week intervention phase, each followed by a test day. Measurements included DNA damage resistance (comet assay), plasma antioxidant status (Trolox capacity and superoxide levels), microvasculature health (retinal analysis), and plasma phytochemical concentrations (colorimetric analyses or HPLC). To assess group differences, a linear mixed model was used. Fifteen polymorphic genes related to phytochemical metabolism and oxidative stress were tested using TaqMan and PCR, with outcomes analyzed via ANOVA. Results: The F&V Blend and Coated Pearl products increased plasma carotenoid levels versus the Uncoated Pearl product. Only the F&V Blend improved retinal dilation and DNA resistance. Surprisingly, the Uncoated Pearl product enhanced antioxidant capacity, lowered superoxide levels, and improved retinal microvasculature. Genotype effects were minimal, except for HNF1A, where wildtypes in the Uncoated Pearl group showed a higher antioxidant capacity. Conclusions: Fresh F&Vs were more effective than coated alternatives in improving vascular health and DNA protection. Full article
(This article belongs to the Special Issue Fruits and Vegetable Bioactive Substances and Nutritional Value)
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21 pages, 2429 KiB  
Article
Phospholipid-Rich DC-Vesicles with Preserved Immune Fingerprints: A Stable and Scalable Platform for Precision Immunotherapy
by Ramon Gutierrez-Sandoval, Francisco Gutierrez-Castro, Natalia Muñoz-Godoy, Ider Rivadeneira, Adolay Sobarzo, Luis Alarcón, Wilson Dorado, Andy Lagos, Diego Montenegro, Ignacio Muñoz, Rodrigo Aguilera, Jordan Iturra, Francisco Krakowiak, Cristián Peña-Vargas and Andres Toledo
Biomedicines 2025, 13(6), 1299; https://doi.org/10.3390/biomedicines13061299 - 26 May 2025
Cited by 2 | Viewed by 988
Abstract
Despite the progress in cancer immunotherapy, therapeutic responses in solid tumors remain suboptimal due to the immunosuppressive nature of the tumor microenvironment (TME), limited immune cell infiltration, and inefficient delivery of immune-activating agents. Dendritic cell-based therapies possess strong immunological potential but face challenges [...] Read more.
Despite the progress in cancer immunotherapy, therapeutic responses in solid tumors remain suboptimal due to the immunosuppressive nature of the tumor microenvironment (TME), limited immune cell infiltration, and inefficient delivery of immune-activating agents. Dendritic cell-based therapies possess strong immunological potential but face challenges in viability, standardization, and scalability. Likewise, exosomes and CAR-T cells are hindered by instability, production complexity, and limited efficacy in immune-excluded tumor settings. Objective: This study evaluates dendritic cell-derived vesicles (DC-Vesicles), embedded in a phospholipid-rich structural scaffold, as a multi-functional and scalable platform for immune modulation and therapeutic delivery. We aimed to assess their structural stability, immune marker preservation under clinical processing conditions, and potential to reprogram the TME. Methods and Results: DC-Vesicles were generated and analyzed using bottom-up proteomics via nanoLC–MS/MS on a timsTOF Pro 2 system under three conditions: fresh, concentrated, and cryopreserved. A consistent proteomic profile of over 400 proteins was identified, with cryopreserved samples retaining >90% of immune-relevant markers. Differential expression analysis confirmed stability of key immunological proteins such as HLA-A, QSOX1, ICAM1, NAMPT, TIGAR, and Galectin-9. No significant degradation was observed post-cryopreservation. Visualization through heatmaps, PCA, and volcano plots supported inter-condition consistency. In silico modeling suggested preserved capacity for M1 macrophage polarization and CD8+ T cell activation. Conclusions: DC-Vesicles demonstrate structural resilience and functional retention across storage conditions. Their cold-chain-independent compatibility, immune-targeting profile, and potential regulatory classification as Non-New Chemical Entities (NCEs) support their advancement as candidates for precision immunotherapy in resistant solid tumors. Full article
(This article belongs to the Section Immunology and Immunotherapy)
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18 pages, 3132 KiB  
Article
Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of Lithocarpus Species (Fagaceae) in South China
by Shi Shi, Ziyan Zhang, Xinhao Lin, Linjing Lu, Keyi Fu, Miaoxin He, Shiou Yih Lee, Hui Yin and Jingwei Yu
Genes 2025, 16(6), 616; https://doi.org/10.3390/genes16060616 - 22 May 2025
Viewed by 605
Abstract
Background/Objectives: In South China, Lithocarpus species dominate mixed evergreen broadleaf forests, forming symbiotic relationships with ectomycorrhizal fungi and serving as food resources for diverse fauna, including frugivorous birds and mammals. The limited understanding of chloroplast genomes in this genus restricts our insights [...] Read more.
Background/Objectives: In South China, Lithocarpus species dominate mixed evergreen broadleaf forests, forming symbiotic relationships with ectomycorrhizal fungi and serving as food resources for diverse fauna, including frugivorous birds and mammals. The limited understanding of chloroplast genomes in this genus restricts our insights into its species diversity. This study investigates the chloroplast genome (cp genome) sequences from seven Lithocarpus species, aims to elucidate their structural variation, evolutionary relationships, and functional gene content to provide effective support for future genetic conservation and breeding efforts. Methods: We isolated total DNA from fresh leaves and sequenced the complete cp genomes of these samples. To develop a genomic resource and clarify the evolutionary relationships within Lithocarpus species, comparative chloroplast genome studies and phylogenetic investigations were performed. Results: All studied species exhibited a conserved quadripartite chloroplast genome structure, with sizes ranging from 161,495 to 163,880 bp. Genome annotation revealed 130 functional genes and a GC content of 36.72–37.76%. Codon usage analysis showed a predominance of leucine-encoding codons. Our analysis identified 322 simple sequence repeats (SSRs), which were predominantly palindromic in structure (82.3%). All eight species exhibited the same 19 SSR categories in similar proportions. Eight highly variable regions (ndhF, ycf1, trnS-trnG-exon1, trnk(exon1)-rps16(exon2), rps16(exon2), rbcL-accD, and ccsA-ndh) have been identified, which could be valuable as molecular markers in future studies on the population genetics and phylogeography of this genus. The phylogeny tree provided critical insights into the evolutionary trajectory of Fagaceae, suggesting that Lithocarpus was strongly supported as monophyletic, while Quercus was inferred to be polyphyletic, showing a significant cytonuclear discrepancy. Conclusions: We characterized and compared the chloroplast genome features across eight Lithocarpus species, followed by comprehensive phylogenetic analyses. These findings provide critical insights for resolving taxonomic uncertainties and advancing systematic research in this genus. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Adaptive Evolution in Trees)
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20 pages, 3276 KiB  
Article
Harnessing Genomics for Breeding Lantana camara L.: Genotyping and Ploidy Testing of Clonal Lines Through ddRADseq Applications
by Angelo Betto, Fabio Palumbo, Damiano Riommi, Alessandro Vannozzi and Gianni Barcaccia
Int. J. Mol. Sci. 2025, 26(10), 4898; https://doi.org/10.3390/ijms26104898 - 20 May 2025
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Abstract
Lantana camara L. is sold worldwide for ornamental purposes, although it is also characterized by high invasiveness potential. Genetic and molecular data available for L. camara are still poor, and breeding is performed through conventional methods. This study focused on a molecular genotyping [...] Read more.
Lantana camara L. is sold worldwide for ornamental purposes, although it is also characterized by high invasiveness potential. Genetic and molecular data available for L. camara are still poor, and breeding is performed through conventional methods. This study focused on a molecular genotyping analysis through the ddRADseq method on an experimental collection of lantana clonal lines to evaluate the potential of molecular techniques in performing marker-assisted breeding, in favour of variety registration and in guaranteeing plant variety protection for the species. Although high genetic uniformity was observed in the population, a unique molecular profile was assigned to every line, indicating the effectiveness of the approach used. Interestingly, low degrees of heterozygosity were observed. In addition, the possibility of inferring ploidy levels through SNP profiles was assessed since it would avoid the necessity of previous biological knowledge and the use of fresh materials. Ploidy analysis is of high interest for lantana breeding to obtain less invasive triploids. Flow cytometry and chromosome counting were used for inference assessment. An nQuack framework provided correct results for the majority of the clonal lines, confirming its effectiveness. These findings encourage the adoption of molecular systems to help breed minor species such as L. camara. Full article
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17 pages, 3057 KiB  
Article
Evaluation of Freezing-Induced Changes in Aroma Profiles of Pomegranate Juice by Quantitative Descriptive Sensory Analysis, Gas Chromatography–Mass Spectrometry/Olfactometry, Odor Activity Values, Orthogonal Partial Least Squares–Discriminant Analysis, and Odorant Addition Experiment
by Yixiu Chen, Peng Wang, Wanying He, Honglei Tian, Jingzhang Geng, Runguang Zhang and Ping Zhan
Foods 2025, 14(10), 1811; https://doi.org/10.3390/foods14101811 - 20 May 2025
Viewed by 585
Abstract
Freezing is employed to preserve the quality of pomegranate juice (PJ) for producing nutritious ready-to-drink beverages. However, the aroma compounds of PJ undergo significant alterations post-freezing. This study aimed to examine the impacts of different freezing temperatures (−20 °C, −40 °C, and −80 [...] Read more.
Freezing is employed to preserve the quality of pomegranate juice (PJ) for producing nutritious ready-to-drink beverages. However, the aroma compounds of PJ undergo significant alterations post-freezing. This study aimed to examine the impacts of different freezing temperatures (−20 °C, −40 °C, and −80 °C) on the flavor profiles of PJ, using fresh PJ as a control. The quantitative descriptive sensory analysis (QDA) results showed that grassy, woody, and fruity attributes of PJ were notably diminished following the freezing treatment. In total, 34 volatiles were identified by gas chromatography–mass spectrometry (GC-MS), of which 14 were perceived by GC–olfactometry (GC-O). Together with orthogonal partial least squares–discriminant analysis (OPLS-DA) and OAV tests, five volatiles were determined as key differential markers, and three (hexanol, (Z)-3-hexen-1-ol and β-myrcene) were selected for further odorant addition experiments. The results verified that (Z)-3-hexen-1-ol was the primary odorant for enhancing the grassy and fruity notes of PJ, while hexanol and β-myrcene were crucial for enhancing grassy and woody attributes, respectively. Full article
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