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14 pages, 3725 KiB  
Article
Gut Hormones and Postprandial Metabolic Effects of Isomaltulose vs. Saccharose Consumption in People with Metabolic Syndrome
by Jiudan Zhang, Dominik Sonnenburg, Stefan Kabisch, Stephan Theis, Margrit Kemper, Olga Pivovarova-Ramich, Domenico Tricò, Sascha Rohn and Andreas F. H. Pfeiffer
Nutrients 2025, 17(15), 2539; https://doi.org/10.3390/nu17152539 (registering DOI) - 1 Aug 2025
Abstract
Background: Low-glycemic index (GI) carbohydrates like isomaltulose (ISO) are known to enhance incretin release and to improve postprandial glucose control at the following meal (an effect known as second meal effect, or SME), which is particularly beneficial for individuals with metabolic syndrome (MetS). [...] Read more.
Background: Low-glycemic index (GI) carbohydrates like isomaltulose (ISO) are known to enhance incretin release and to improve postprandial glucose control at the following meal (an effect known as second meal effect, or SME), which is particularly beneficial for individuals with metabolic syndrome (MetS). This study aimed to assess the most effective preprandial interval of ISO- or saccharose (SUC) snacks (1 h vs. 3 h preload) to enhance prandial incretin responses to a subsequent meal. Methods: In a randomized crossover design, 15 participants with MetS completed four experimental conditions on four non-consecutive days, combining two preload types (ISO or SUC) and two preload timings (Intervention A: 3 h preload; Intervention B: 1 h preload). Specifically, the four conditions were (1) ISO + Intervention A, (2) SUC + Intervention A, (3) ISO + Intervention B, and (4) SUC + Intervention B. The order of conditions was randomized and separated by a 3–7-day washout period to minimize carryover effects. On each study day, participants consumed two mixed meal tests (MMT-1 and MMT-2) with a standardized preload (50 g ISO or SUC) administered either 3 h or 1 h prior to MMT-2. Blood samples were collected over 9 h at 15 predefined time points for analysis of glucose, insulin, C-peptide, and incretin hormones (GLP-1, GIP, and PYY). Results: The unique digestion profile of ISO resulted in a blunted glucose ascent rate (ΔG/Δt: 0.28 vs. 0.53 mmol/L/min for SUC, p < 0.01), paralleled by synonyms PYY elevation over 540 min monitoring, compared with SUC. ISO also led to higher and more sustained GLP-1 and PYY levels, while SUC induced a stronger GIP response. Notably, the timing of ISO consumption significantly influenced PYY secretion, with the 3 h preload showing enhanced PYY responses and a more favorable SME compared to the 1 h preload. Conclusions: ISO, particularly when consumed 3 h before a meal (vs. 1 h), offers significant advantages over SUC by elevating PYY levels, blunting the glucose ascent rate, and sustaining GLP-1 release. This synergy enhances the second meal effect, suggesting ISO’s potential for managing postprandial glycemic excursions in MetS. Full article
(This article belongs to the Section Nutrition and Metabolism)
15 pages, 492 KiB  
Article
Head-to-Head Comparison of Etest, MICRONAUT-AM EUCAST and Reference Broth Microdilution-Based CLSI Results for Candida kefyr Antifungal Susceptibility Testing: Implications for Detection of Reduced Susceptibility to Amphotericin B
by Mohammad Asadzadeh, Suhail Ahmad, Jacques F. Meis, Josie E. Parker and Wadha Alfouzan
J. Fungi 2025, 11(8), 570; https://doi.org/10.3390/jof11080570 - 30 Jul 2025
Viewed by 117
Abstract
Invasive infections with rare yeasts are increasing worldwide and are associated with higher mortality rates due to their resistance to antifungal drugs. Accurate antifungal susceptibility testing (AFST) is crucial for proper management of rare yeast infections. We performed AFST of 74 Candida kefyr [...] Read more.
Invasive infections with rare yeasts are increasing worldwide and are associated with higher mortality rates due to their resistance to antifungal drugs. Accurate antifungal susceptibility testing (AFST) is crucial for proper management of rare yeast infections. We performed AFST of 74 Candida kefyr isolates by Etest, EUCAST-based MICRONAUT-AM assay (MCN-AM) and reference Clinical and Laboratory Standards Institute broth microdilution method (CLSI). Essential agreement (EA, ±1 two-fold dilution), categorical agreement (CA), major errors (MEs) and very-major errors (VmEs) were determined using epidemiological cut-off values of ≤1.0 µg/mL, ≤0.03 µg/mL, ≤0.5 µg/mL and ≤1 µg/mL, defining wild-type isolates for fluconazole, voriconazole, micafungin and amphotericin B (AMB), respectively. Results for AMB susceptibility were correlated with ERG2/ERG3 mutations and total-cell sterols. CA of ≥97% was recorded between any two methods while EA varied between 72 and 82%, 87 and 92%, and 49 and 76% for fluconazole, voriconazole and micafungin, respectively. For AMB, CAs between CLSI and Etest; CLSI and MCN-AM; MCN-AM and Etest were 95% (4 ME, 0 VmE), 96% (3 ME, 0 VmE) and 99%, respectively, while EA varied from 32% to 69%. Non-synonymous ERG2/ERG3 mutations and no ergosterol were found in seven of eight isolates of non-wild types for AMB by Etest. Our data show that Etest, CLSI and MCN-AM methods are suitable for AFST of C. kefyr for fluconazole, voriconazole and micafungin. Excellent CAs for AMB between Etest and MCN-AM with concordant sterol profiles but not with CLSI suggest that Etest is also an excellent alternative for the detection of C. kefyr isolates with reduced susceptibility to AMB. Full article
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14 pages, 1678 KiB  
Article
The Identification of a New Gene KRTAP 6-3 in Capra hircus and Its Potential for the Diameter Improvement of Cashmere Fibers
by Jian Cao, Zhanzhao Chen, Jianmin Zhang, Liang Cao and Shaobin Li
Genes 2025, 16(6), 721; https://doi.org/10.3390/genes16060721 - 19 Jun 2025
Viewed by 497
Abstract
Background: Cashmere is one of the important economic products of goats, and the KRTAP gene family, as an important family of regulatory genes in the growth process of cashmere fiber, largely affects the quality of cashmere. Methods: In this study, the KRTAP6-3 gene [...] Read more.
Background: Cashmere is one of the important economic products of goats, and the KRTAP gene family, as an important family of regulatory genes in the growth process of cashmere fiber, largely affects the quality of cashmere. Methods: In this study, the KRTAP6-3 gene was identified and located on goat chromosome 1 using a goat genome homology search combined with a phylogenetic tree approach. The Longdong cashmere goat KRTAP6-3 gene variation and its effect on cashmere quality were explored by using the polymerase chain reaction single-stranded conformation polymorphism (PCR-SSCP) technique, in situ hybridization, and the allele presence/absence model. Results: The results identified a total of six SNPs in KRTAP6-3, three of which were located in the coding region and two of which were synonymous mutations, in addition to 45- bp deletion sequences detected in alleles C and F. Moreover, the KRTAP6-3 mRNA showed a strong expression signal in the cortical layer of the primary and secondary follicles in the inner root sheaths, as well as in the cells of the hair papillae and the matrices during the anagen phase, and signaling at the sites described above is attenuated during the telogen phase. The presence of allele C was associated with increased MFD (mean fiber diameter) (p < 0.01). The MFD of goats with allele C genotype (genotype AC) was significantly higher (p < 0.05) than that of goats without allele C genotype (genotypes AA and AB). Conclusions: This indicates that genetic variation in the KRTAP6-3 gene in goats is significantly associated with cashmere traits and can serve as a candidate gene for molecular markers of cashmere traits. Full article
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35 pages, 2692 KiB  
Article
The Liverworts of the Murmansk Region (North-West Russia): Providing an Annotated Checklist as a Basis for the Monitoring and Further Study of Liverwort Flora
by Nadezhda A. Konstantinova, Evgeny A. Borovichev and Anna A. Vilnet
Plants 2025, 14(11), 1590; https://doi.org/10.3390/plants14111590 - 23 May 2025
Viewed by 493
Abstract
An annotated list of liverworts of the Murmansk Region is compiled based on a critical compilation of publications and label data available in the information system CRIS (L.). It includes 210 species, 2 subspecies and 8 varieties, which is 59 species more than [...] Read more.
An annotated list of liverworts of the Murmansk Region is compiled based on a critical compilation of publications and label data available in the information system CRIS (L.). It includes 210 species, 2 subspecies and 8 varieties, which is 59 species more than in the list of species published in 1982. Ten taxa were excluded through comparison with the previous list and later publications, due to misidentifications or new taxonomical treatments. Annotations for each species include the synonyms under which they were listed for the region; the category of threat in the Red Data Books of Europe, Russia and the Murmansk Region; links to the most representative publications on occurrence in each of nine accepted biogeographic provinces of the region; and at least one specimen number of the KPABG or INEP herbaria in the case of the absence of published data. In total, we provide 259 new records for different provinces based on herbaria KPABG (205 records) and INEP (52 records). Additionally, there are links to publications on the nucleotide sequence data of 149 specimens obtained for 82 species and for 1 variety from the Murmansk Region, including 14 specimens (11 species), published here for the first time. Species threatened in Europe, Russia and the Murmansk Region are discussed and future perspectives of liverwort study in the Murmansk Region are outlined. Full article
(This article belongs to the Special Issue Diversity, Distribution and Conservation of Bryophytes)
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33 pages, 7586 KiB  
Article
Origin and Possible Members of the ‘Malvasia’ Family: The New Fuencaliente de La Palma Hypothesis on the True ‘Malvasia’
by Francesca Fort, Luis Ricardo Suárez-Abreu, Qiying Lin-Yang, Juancho Asenjo, Leonor Deis, Joan Miquel Canals and Fernando Zamora
Horticulturae 2025, 11(6), 561; https://doi.org/10.3390/horticulturae11060561 - 22 May 2025
Cited by 1 | Viewed by 1196
Abstract
The name ‘Malvasia’ and its various spellings has historically been associated with a type of sweet and/or aromatic wine. However, a definitive association with a specific grape variety remains unconfirmed. In fact, up to 413 different grape variety names (cultivar name (synonym name) [...] Read more.
The name ‘Malvasia’ and its various spellings has historically been associated with a type of sweet and/or aromatic wine. However, a definitive association with a specific grape variety remains unconfirmed. In fact, up to 413 different grape variety names (cultivar name (synonym name) and/or first name) are related to the term “Malvasia”. The question arises: are all of these truly Malvasia? To answer this question, our research group presents a hypothesis. We worked with 43 genetic profiles that various scientific groups have published over decades and that are stored in the world’s largest grape database, the Vitis International Variety Catalogue (VIVC). The known molecular profiles were obtained using the SSR (Simple Sequence Repeats) or microsatellite technique. Various population structure programs were applied, information on the possible origin or area where each of the varieties was mostly grown was used, and historical information was used to explain the results obtained. Therefore, it can be concluded that the current varieties best positioned to define the concept of grape and/or wine variety “Malvasia” would be (1) Malvasia Dubrovacka, Malvasia bianca lunga, and Malvasia del Cilento, by genetic proximity; (2) Malvasia volcanica, Malvasia babosa, Malvasia nera di Basilicata, Malvasia nera di Brindisi, Vitovska, Pelena, Prunesta (false), and Lagorthi, by crosses; and (3) Malvasia di Sardegna Rosada, by mutation. The rest of the candidate varieties to be part of the ‘Malvasia’ family are dismissed because they result from crosses with members of the Muscat family or crosses with other varieties (known or unknown) that, in any case, are not related historically, genetically, or geographically (with the exception of Malvasia istriana and Malvasia Župska) to the hypothetical members of the ‘Malvasia’ family. Full article
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18 pages, 5016 KiB  
Article
Characterization of the Complete Mitochondrial Genome of Angulyagra polyzonata and Its Phylogenetic Status in Viviparidae
by Shengjie Zhang, Kangqi Zhou, Xianhui Pan, Yong Lin, Jinxia Peng, Junqi Qin, Zhenlin Ke, Yaoquan Han, Zhong Chen, Xuesong Du, Wenhong Li, Pinyuan Wei and Dapeng Wang
Animals 2025, 15(9), 1284; https://doi.org/10.3390/ani15091284 - 30 Apr 2025
Viewed by 329
Abstract
Angulyagra polyzonata is an economically important mollusk in China, but detailed insights into its mitochondrial genome remain scarce. In this study, we sequenced and comprehensively analyzed the structural features and selection pressures of the A. polyzonata mitochondrial genome. The maximum likelihood method and [...] Read more.
Angulyagra polyzonata is an economically important mollusk in China, but detailed insights into its mitochondrial genome remain scarce. In this study, we sequenced and comprehensively analyzed the structural features and selection pressures of the A. polyzonata mitochondrial genome. The maximum likelihood method and Bayesian phylogenetic inference method were used to construct a phylogenetic tree of A. polyzonata with 21 other species, including gastropods and bivalves. The full-length mitochondrial genome of 17,379 bp was found to include 22 transfer RNA genes, 2 ribosomal RNA genes, and 13 protein-coding genes, exhibiting similarity to the composition and arrangement of mitochondrial genes in other gastropod species. Notably, the Ka/Ks ratios of mitochondrial protein-coding genes (nad5, cox3, nad3, nad2, cox1, cox2, atp8, atp6, nadl, nad6, cob, nad4l, and nad4) were <1, which indicates that the snail genes of the three genera of the family may have been subjected to strong natural selection pressure during the evolutionary process, so that the number of synonymous mutations (ks) in genes was much more than that of nonsynonymous mutations (ka). Comparative genomic analysis indicated that, apart from the absence of trnW and trnQ, the gene composition of A. polyzonata shares a high degree of homology with other members of the conical snail family. Phylogenetic analysis demonstrated that the selected species could be classified into two primary clades in which A. polyzonata clustered with the Viviparidae family. This study bridges the knowledge gap regarding the mitochondrial genome of A. polyzonata and offers valuable insights into the systematic relationships within the Viviparidae family. Full article
(This article belongs to the Section Aquatic Animals)
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16 pages, 4042 KiB  
Article
Unraveling the Mitochondrial Blueprint: Genome Characterization and Phylogenetic Insights of the Endemic Fish Onychostoma virgulatum (Teleostei: Cyprinidae)
by Yuting Hu, Guoqing Duan, Huaxing Zhou, Huan Wang and Amei Liu
Genes 2025, 16(5), 541; https://doi.org/10.3390/genes16050541 - 30 Apr 2025
Viewed by 466
Abstract
Background: Onychostoma virgulatum is an endemic freshwater fish in South China, first described as a new species in 2009. However, little is known about this species and no complete mitochondrial genomes of O. virgulatum has been reported to date. This study seeks [...] Read more.
Background: Onychostoma virgulatum is an endemic freshwater fish in South China, first described as a new species in 2009. However, little is known about this species and no complete mitochondrial genomes of O. virgulatum has been reported to date. This study seeks to elucidate the characteristics of the mitochondrial genome of O. virgulatum and investigate the phylogenetic relationships within the Acrossocheilinae subfamily, particularly among the genera Onychostoma, Acrossocheilus, and Folifer. Methods: The mitochondrial genome of O. virgulatum was sequenced and assembled. We analyzed its sequence length, nucleotide composition, and evolutionary relationships within the Acrossocheilinae by incorporate data from 58 previously published mitochondrial genomes. Results: The complete circular sequence is 16,606 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a typical control region (D-loop), all arranged in a typical order. The genomic base composition is biased toward A+T content (56.5%), with 31.4% A, 25.1% T, 27.4% C, and 16.1% G. Among about 30 Acrossocheilina species, the nonsynonymous (Ka) to synonymous substitutions (Ks) for all 13 protein-coding genes (PCGs) are significantly less than 1, suggesting strong negative or purifying selection in these species. The phylogenetic trees inferred from the mitogenome and 13 PCGs of 58 Acrossocheilinae sequences consistently indicate that: (1) O. virgulatum shares the closest genetic relationship with Onychostoma barbatulum; (2) Acrossocheilinae species are clustered into three major clades, with neither Acrossocheilus nor Onychostoma forming monophyletic groups. Conclusions: This study provides new insights into the taxonomy and phylogenetic relationships of Acrossocheilinae, particularly O. virgulatum, contributing to a better understanding of the systematics, origin, and evolution of this subfamily. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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13 pages, 1752 KiB  
Article
The Identification of a Single-Base Mutation in the Maize Dwarf 1 Gene Responsible for Reduced Plant Height in the Mutant 16N125
by Ping Wang, Bingbing Liang, Zhengjun Li, Huaiyu Dong, Lixia Zhang and Xiaochun Lu
Plants 2025, 14(8), 1217; https://doi.org/10.3390/plants14081217 - 15 Apr 2025
Viewed by 573
Abstract
Maize (Zea mays L.) is a globally vital crop for food, feed, and biofuel production, with plant height (PH) being a key agronomic trait that significantly influences yield, lodging resistance, and stress tolerance. This study identified a single-base mutation in the D1 [...] Read more.
Maize (Zea mays L.) is a globally vital crop for food, feed, and biofuel production, with plant height (PH) being a key agronomic trait that significantly influences yield, lodging resistance, and stress tolerance. This study identified a single-base mutation in the D1 (Dwarf 1) gene responsible for the dwarf phenotype in the maize mutant 16N125. Through genetic analysis and fine mapping, the candidate region was localized to chromosome 3, narrowing it down to an interval containing three genes. Sequencing revealed a non-synonymous mutation in D1, which encodes a gibberellin 3-beta-dioxygenase, leading to amino acid substitutions at positions 61 and 123. Genetic analysis of F2 populations confirmed that the mutation at position 61 was responsible for the dwarf trait. Furthermore, the mutation was detected in several Chinese inbred lines, indicating its potential role in dwarfing under specific conditions. These findings provide critical insights into the genetic mechanisms regulating maize plant height, offering valuable information for breeding programs focused on improving crop architecture and yield to address the challenges of global food security and climate change. Full article
(This article belongs to the Special Issue Maize Cultivation and Improvement)
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18 pages, 3506 KiB  
Article
Genetic Variations of Three Kazakhstan Strains of the SARS-CoV-2 Virus
by Bekbolat Usserbayev, Kulyaisan T. Sultankulova, Yerbol Burashev, Aibarys Melisbek, Meirzhan Shirinbekov, Balzhan S. Myrzakhmetova, Asankadir Zhunushov, Izat Smekenov, Aslan Kerimbaev, Sergazy Nurabaev, Olga Chervyakova, Nurlan Kozhabergenov and Lesbek B. Kutumbetov
Viruses 2025, 17(3), 415; https://doi.org/10.3390/v17030415 - 14 Mar 2025
Viewed by 753
Abstract
Prompt determination of the etiological agent is important in an outbreak of pathogens with pandemic potential, particularly for dangerous infectious diseases. Molecular genetic methods allow for arriving at an accurate diagnosis, employing timely preventive measures, and controlling the spread of the disease-causing agent. [...] Read more.
Prompt determination of the etiological agent is important in an outbreak of pathogens with pandemic potential, particularly for dangerous infectious diseases. Molecular genetic methods allow for arriving at an accurate diagnosis, employing timely preventive measures, and controlling the spread of the disease-causing agent. In this study, whole-genome sequencing of three SARS-CoV-2 strains was performed using the Sanger method, which provides high accuracy in determining nucleotide sequences and avoids errors associated with multiple DNA amplification. Complete nucleotide sequences of samples, KAZ/Britain/2021, KAZ/B1.1/2021, and KAZ/Delta020/2021 were obtained, with sizes of 29.751 bp, 29.815 bp, and 29.840 bp, respectively. According to the COVID-19 Genome Annotator, 127 mutations were detected in the studied samples compared to the reference strain. The strain KAZ/Britain/2021 contained 3 deletions, 7 synonymous mutations, and 27 non-synonymous mutations, the second strain KAZ/B1.1/2021 contained 1 deletion, 5 synonymous mutations, and 31 non-synonymous mutations, and the third strain KAZ/Delta020/2021 contained 1 deletion, 5 synonymous mutations, and 37 non-synonymous mutations, respectively. The variations C241T, F106F, P314L, and D614G found in the 5′ UTR, ORF1ab, and S regions were common to all three studied samples, respectively. According to PROVEAN data, the loss-of-function mutations identified in strains KAZ/Britain/2021, KAZ/B1.1/2021, and KAZ/Delta020/2021 include 5 mutations (P218L, T716I, W149L, R52I, and Y73C), 2 mutations (S813I and Q992H), and 8 mutations (P77L, L452R, I82T, P45L, V82A, F120L, F120L, and R203M), respectively. Phylogenetic analysis showed that the strains studied (KAZ/Britain/2021, KAZ/B1.1/2021, and KAZ/Delta020/2021) belong to different SARS-CoV-2 lineages, which are closely related to samples from Germany (OU141323.1 and OU365922.1), Mexico (OK432605.1), and again Germany (OV375251.1 and OU375174.1), respectively. The nucleotide sequences of the studied SARS-CoV-2 virus strains were registered in the Genbank database with the accession numbers: ON692539.1, OP684305, and OQ561548.1. Full article
(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2, 3rd Edition)
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16 pages, 24261 KiB  
Article
The Mutations in RcMYB114 Affect Anthocyanin Glycoside Accumulation in Rose
by Maofu Li, Yuan Yang, Hua Wang, Pei Sun, Shuting Zhou, Yanhui Kang, Xiangyi Sun, Min Jin and Wanmei Jin
Biology 2025, 14(3), 258; https://doi.org/10.3390/biology14030258 - 4 Mar 2025
Viewed by 1030
Abstract
In plants, the R2R3-MYB transcription factors are one of the largest MYB gene families. These MYB transcription factors are very important for regulating plant growth and development. RcMYB114, RcbHLH, and RcWD40 promote anthocyanin accumulation by forming the MBW (MYB-bHLH-WD40) complex and determine the [...] Read more.
In plants, the R2R3-MYB transcription factors are one of the largest MYB gene families. These MYB transcription factors are very important for regulating plant growth and development. RcMYB114, RcbHLH, and RcWD40 promote anthocyanin accumulation by forming the MBW (MYB-bHLH-WD40) complex and determine the rose flower’s color. RcMYB114 genomic sequences differ between the red petal and white varieties. Two non-synonymous substitutions were found in the open reading frame. It leads to a change in amino acids. Here, the anthocyanin content showed that there was no anthocyanin in white petals, while the anthocyanin content in red petals increased firstly at stage 2, decreased slightly at stage 4, and then increased again at stage 5. The spatiotemporal expression pattern analysis showed that RcMYB114 was not expressed in all petals and tissues of white petals at different flower development stages. In red petal varieties, RcMYB114 was highly expressed in petals, followed by styles, and not expressed in stems, young leaves, and stage 1 of flower development. However, RcMYB114 has the highest expression level at the blooming stage. The RcMYB114 sequence contains 9 SNPs in the coding region, 7 of which were synonymous substitutions that had no effect on the translation product and 2 of which were non-synonymous substitutions that resulted in amino acid alteration at positions 116 and 195, respectively. The RcMYB114 gene in red rose was named RcMYB114a, and in white rose was RcMYB114b. RcMYB114c was mutated into leucine via artificial mutation; it was valine at position 116 of RcMYB114a, and Glycine mutated into Arginine at position 195 of RcMYB114a was RcMYB114d. RcMYB114b was the double mutation at positions 116 and 195 of RcMYB114a. The results of yeast two-hybrid experiments showed that RcMYB114a and its missense mutations RcMYB114b, RcMYB114c, and RcMYB114d could both interact with RcbHLH and RcWD40 to form the MYB-bHLH-WD40 complex. A transient transformation experiment in tobacco confirmed that RcMYB114a and its missense mutations RcMYB114b, RcMYB114c, and RcMYB114d could significantly promote the high expression of related structural genes in tobacco, together with the RcbHLH gene, which led to the accumulation of anthocyanins and produced the red color of the leaves. The RcMYB114a gene and its missense mutations RcMYB114b, RcMYB114c, and RcMYB114d interacted with the RcbHLH gene and significantly regulated the accumulation of anthocyanins. The two non-synonymous mutations of RcMYB114 do not affect the function of the gene itself, but the content of the anthocyanins accumulated was different. This study should provide clues and references for further research on the molecular mechanism underlying the determination of rose petal color. Full article
(This article belongs to the Special Issue Recent Advances in Biosynthesis and Degradation of Plant Anthocyanin)
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32 pages, 4595 KiB  
Article
Integrative In Silico Analysis to Identify Functional and Structural Impacts of nsSNPs on Programmed Cell Death Protein 1 (PD-1) Protein and UTRs: Potential Biomarkers for Cancer Susceptibility
by Hakeemah Al-Nakhle, Retaj Al-Shahrani, Jawanah Al-Ahmadi, Wesal Al-Madani and Rufayda Al-Juhani
Genes 2025, 16(3), 307; https://doi.org/10.3390/genes16030307 - 4 Mar 2025
Viewed by 1629
Abstract
Background: Programmed cell death protein 1 (PD-1), encoded by the PDCD1 gene, is critical in immune checkpoint regulation and cancer immune evasion. Variants in PDCD1 may alter its function, impacting cancer susceptibility and disease progression. Objectives: This study evaluates the structural, functional, and [...] Read more.
Background: Programmed cell death protein 1 (PD-1), encoded by the PDCD1 gene, is critical in immune checkpoint regulation and cancer immune evasion. Variants in PDCD1 may alter its function, impacting cancer susceptibility and disease progression. Objectives: This study evaluates the structural, functional, and regulatory impacts of non-synonymous single-nucleotide polymorphisms (nsSNPs) in the PDCD1 gene, focusing on their pathogenic and oncogenic roles. Methods: Computational tools, including PredictSNP1.0, I-Mutant2.0, MUpro, HOPE, MutPred2, Cscape, Cscape-Somatic, GEPIA2, cBioPortal, and STRING, were used to analyze 695 nsSNPs in the PD1 protein. The analysis covered structural impacts, stability changes, regulatory effects, and oncogenic potential, focusing on conserved domains and protein–ligand interactions. Results: The analysis identified 84 deleterious variants, with 45 mapped to conserved regions like the Ig V-set domain essential for ligand-binding interactions. Stability analyses identified 78 destabilizing variants with significant protein instability (ΔΔG values). Ten nsSNPs were identified as potential cancer drivers. Expression profiling showed differential PDCD1 expression in tumor versus normal tissues, correlating with improved survival in skin melanoma but limited value in ovarian cancer. Regulatory SNPs disrupted miRNA-binding sites and transcriptional regulation, affecting PDCD1 expression. STRING analysis revealed key PD-1 protein partners within immune pathways, including PD-L1 and PD-L2. Conclusions: This study highlights the significance of PDCD1 nsSNPs as potential biomarkers for cancer susceptibility, advancing the understanding of PD-1 regulation. Experimental validation and multi-omics integration are crucial to refine these findings and enhance theraputic strategies. Full article
(This article belongs to the Special Issue Molecular Diagnostic and Prognostic Markers of Human Cancers)
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16 pages, 1891 KiB  
Article
Mitochondrial COX3 and tRNA Gene Variants Associated with Risk and Prognosis of Idiopathic Pulmonary Fibrosis
by Li-Na Lee, I-Shiow Jan, Wen-Ru Chou, Wei-Lun Liu, Yen-Liang Kuo, Chih-Yueh Chang, Hsiu-Ching Chang, Jia-Luen Liu, Chia-Lin Hsu, Chia-Nan Lin, Ke-Yun Chao, Chi-Wei Tseng, I-Hsien Lee, Jann-Tay Wang and Jann-Yuan Wang
Int. J. Mol. Sci. 2025, 26(3), 1378; https://doi.org/10.3390/ijms26031378 - 6 Feb 2025
Viewed by 1102
Abstract
Idiopathic pulmonary fibrosis (IPF) has been associated with mitochondrial dysfunction. We investigated whether mitochondrial DNA variants in peripheral blood leukocytes (PBLs), which affect proteins of the respiratory chain and mitochondrial function, could be associated with an increased risk and poor prognosis of IPF. [...] Read more.
Idiopathic pulmonary fibrosis (IPF) has been associated with mitochondrial dysfunction. We investigated whether mitochondrial DNA variants in peripheral blood leukocytes (PBLs), which affect proteins of the respiratory chain and mitochondrial function, could be associated with an increased risk and poor prognosis of IPF. From 2020 to 2022, we recruited 36 patients (age: 75.3 ± 8.5; female: 19%) with IPF, and 80 control subjects (age: 72.3 ± 9.0; female: 27%). The mitochondrial genome of peripheral blood leukocytes was determined using next-generation sequencing. During a 45-month follow-up, 10 (28%) patients with IPF remained stable and the other 26 (72%) progressed, with 12 (33%) mortalities. IPF patients had more non-synonymous (NS) variants (substitution/deletion/insertion) in mitochondrial COX3 gene (coding for subunit 3 of complex IV of the respiratory chain), and more mitochondrial tRNA variants located in the anticodon (AC) stem, AC loop, variable loop, T-arm, and T-loop of the tRNA clover-leaf structure in PBLs than the control group. The succumbed IPF patients were older, had lower initial diffusion capacity, and higher initial fibrosis score on high-resolution computerized tomography (HRCT) than the alive group. NS variants in mitochondrial COX3 gene and tRNA variants in PBLs were associated with shorter survival. Our study shows that (1) leukocyte mitochondrial COX3 NS variants are associated with risk and prognosis of IPF; (2) leukocyte mitochondrial tRNA variants located in the AC stem, AC loop, variable loop, T-arm, and T-loop of the tRNA clover-leaf structure are associated with risk, and the presence of tRNA variants is associated with poor prognosis of IPF. Full article
(This article belongs to the Special Issue Advanced Molecular Research in Lung Diseases)
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12 pages, 8499 KiB  
Article
Taxonomic Revision of the Relationship Between Coproptilia and Nosphistica (Lepidoptera: Lecithoceridae) with Descriptions of Two New Species and a New Record from China
by Haotian Li and Shuai Yu
Animals 2025, 15(3), 426; https://doi.org/10.3390/ani15030426 - 4 Feb 2025
Cited by 2 | Viewed by 661
Abstract
The family Lecithoceridae represents one of the most diverse yet understudied groups within Lepidoptera, with numerous unresolved taxonomic issues requiring urgent attention. Among these, the genus Coproptilia Snellen, a small genus within Lecithoceridae, has traditionally been distinguished from its closely related genus, Nosphistica [...] Read more.
The family Lecithoceridae represents one of the most diverse yet understudied groups within Lepidoptera, with numerous unresolved taxonomic issues requiring urgent attention. Among these, the genus Coproptilia Snellen, a small genus within Lecithoceridae, has traditionally been distinguished from its closely related genus, Nosphistica Meyrick, primarily by the presence of vein R1 in the forewing. However, Nosphistica exhibits considerable interspecific variation in wing venation, complicating clear differentiation between these genera. In this study, we conducted a molecular phylogenetic analysis of Lecithoceridae based on a concatenated dataset of 5350 bp, comprising one mitochondrial marker and six nuclear markers from 28 Lecithoceridae individuals. The result shows that (1) the topological results of both Maximum Likelihood (ML) and Bayesian Inference (BI) trees show the Coproptilia branch embedded within the Nosphistica branch, so Nosphistica Meyrick should be synonymized with Coproptilia Snellen. (2) Two new species are described from China: Coproptilia uniformis Yu, sp. nov. and C. funiuensis Yu, sp. nov. (3) Coproptilia tawiensis Park, 2009, is newly recorded from China, with the first description of its female. Finally, we integrated molecular and morphological evidence to examine the taxonomic relationship between Coproptilia and Nosphistica. Additional molecular data will be needed to further clarify the subfamily affiliation of Coproptilia sensu nov. Full article
(This article belongs to the Section Ecology and Conservation)
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17 pages, 7597 KiB  
Article
Comparative Genomics and Characterisation of the Role of Saccharomyces cerevisiae Respiration in the Fermentation of Chinese Steamed Bread
by Yawen Gao, Yufeng Guo, Jianing Pang, Mingkai Liu, Tengdan Yuan, Qinhong Wang and Jingsheng Liu
J. Fungi 2025, 11(2), 114; https://doi.org/10.3390/jof11020114 - 3 Feb 2025
Viewed by 1507
Abstract
The genetic composition of Saccharomyces cerevisiae and its various phenotypes during fermentation significantly correlate to the quality of Chinese steamed bread (CSB). However, the systematic correlation between different S. cerevisiae and CSB has not been fully elucidated. Herein, we characterised CSBs prepared with [...] Read more.
The genetic composition of Saccharomyces cerevisiae and its various phenotypes during fermentation significantly correlate to the quality of Chinese steamed bread (CSB). However, the systematic correlation between different S. cerevisiae and CSB has not been fully elucidated. Herein, we characterised CSBs prepared with 36 isolates of S. cerevisiae (designated S1–S36) to comparatively evaluate their correlations. CSBs 1, 2, 13, 21, 25 and 33 exhibited suitable total titratable acidity (TTA) values, pH values and large specific volumes. Texture analysis showed that CSBs 1, 25 and 33 exhibited higher springiness and cohesiveness values. CSBs 8, 25 and 33 exhibited low hardness, gumminess and chewiness values. At the micro level, CSBs 1, 25 and 33 showed a loose reticular structure with large holes and in which starch particles wrapped into gluten protein. Fifty-nine volatile flavour compounds belonging to six categories were determined in 10 selected CSBs, and CSBs 1, 25 and 33 contained more flavour and balanced substance categories. In addition, comparative genomic analysis revealed 33 non-synonymous mutations in the three strains with strong fermentation ability (S1, S25 and S33) and the three strains with weak fermentation ability (S18, S20 and S35) involving 19 genes, including: the respiration-related genes COS5, COS8 and COX10; the starch metabolism transcription factor MSS11; the general transcription factor SPT8; the cell aggregation-related gene FLO1 and the transporter gene SEO1. Other genes with different genotypes were also enriched in respiration-related gene ontology terms. These data offer preliminary experimental evidence regarding the application of S. cerevisiae S1, S25 and S33 in fermented foods derived from grains. Full article
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57 pages, 13137 KiB  
Article
Compositional and Numerical Geomorphology Along a Basement–Foreland Transition, SE Germany, with Special Reference to Landscape-Forming Indices and Parameters in Genetic and Applied Terrain Analyses
by Harald G. Dill, Andrei Buzatu, Sorin-Ionut Balaban and Christopher Kleyer
Geosciences 2025, 15(2), 37; https://doi.org/10.3390/geosciences15020037 - 23 Jan 2025
Viewed by 1169
Abstract
The Münchberg Gneiss Complex (Central European Variscides, Germany) is separated by a deep-seated lineamentary fault zone, the Franconian Lineamentary Fault Zone, from its Mesozoic foreland. The study area offers insight into a great variety of landforms created by fluvial and mass wasting processes [...] Read more.
The Münchberg Gneiss Complex (Central European Variscides, Germany) is separated by a deep-seated lineamentary fault zone, the Franconian Lineamentary Fault Zone, from its Mesozoic foreland. The study area offers insight into a great variety of landforms created by fluvial and mass wasting processes together with their bedrocks, covering the full range from unmetamorphosed sediments to high-grade regionally metamorphic rocks. It renders the region an ideal place to conduct a study of compositional and numerical geomorphology and their landscape-forming indices and parameters. The landforms under consideration are sculpted out of the bedrocks (erosional landforms) and overlain by depositional landforms which are discussed by means of numerical landform indices (LFIs), all of which are coined for the first time in the current paper. They are designed to be suitable for applied geosciences such as extractive/economic geology as well as environmental geology. The erosional landform series are subdivided into three categories: (1) The landscape roughness indices, e.g., VeSival (vertical sinuosity—valley of landform series) and the VaSlAnalti (variation in slope angle altitude), which are used for a first order classification of landscapes into relief generations. The second order classification LFIs are devoted to the material properties of the landforms’ bedrocks, such as the rock strength (VeSilith) and the bedrock anisotropy (VaSlAnnorm). The third order scheme describes the hydrography as to its vertical changes by the inclination of the talweg and the different types of knickpoints (IncTallith/grad) and horizontal sinuosity (HoSilith/grad). The study area is subjected to a tripartite zonation into the headwater zone, synonymous with the paleoplain which undergoes some dissection at its edge, the step-fault plain representative of the track zone which undergoes widespread fluvial piracy, and the foreland plains which act as an intermediate sedimentary trap named the deposition zone. The area can be described in space and time with these landform indices reflecting fluvial and mass wasting processes operative in four different stages (around 17 Ma, 6 to 4 Ma, <1.7 Ma, and <0.4 Ma). The various groups of LFIs are a function of landscape maturity (pre-mature, mature, and super-mature). The depositional landforms are numerically defined in the same way and only differ from each other by their subscripts. Their set of LFIs is a mirror image of the composition of depositional landforms in relation to their grain size. The leading part of the acronym, such as QuantSanheav and QuantGravlith, refers to the process of quantification, the second part to the grain size, such as sand and gravel, and the subscript to the material, such as heavy minerals or lithological fragments. The three numerical indices applicable to depositional landforms are a direct measurement of the hydrodynamic and gravity-driven conditions of the fluvial and mass wasting processes using granulometry, grain morphology, and situmetry (clast orientation). Together with the previous compositional indices, the latter directly translate into the provenance analysis which can be used for environmental analyses and as a tool for mineral exploration. It creates a network between numerical geomorphology, geomorphometry, and the E&E issue disciplines (economic/extractive geology vs. environmental geology). The linguistics of the LFIs adopted in this publication are designed so as to be open for individual amendments by the reader. An easy adaptation to different landform suites worldwide, irrespective of their climatic conditions, geodynamic setting, and age of formation, is feasible due to the use of a software and a database available on a global basis. Full article
(This article belongs to the Section Sedimentology, Stratigraphy and Palaeontology)
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