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
remove_circle_outline
remove_circle_outline
remove_circle_outline

Article Types

Countries / Regions

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Search Results (520)

Search Parameters:
Keywords = repetitive protein

Order results
Result details
Results per page
Select all
Export citation of selected articles as:
13 pages, 1058 KiB  
Article
A Machine Learning-Based Guide for Repeated Laboratory Testing in Pediatric Emergency Departments
by Adi Shuchami, Teddy Lazebnik, Shai Ashkenazi, Avner Herman Cohen, Yael Reichenberg and Vered Shkalim Zemer
Diagnostics 2025, 15(15), 1885; https://doi.org/10.3390/diagnostics15151885 - 28 Jul 2025
Viewed by 315
Abstract
Background/Objectives: Laboratory tests conducted in community settings are occasionally repeated within hours of presentation to pediatric emergency departments (PEDs). Reducing unnecessary repetitions can ease child discomfort and alleviate the healthcare burden without compromising the diagnostic process or quality of care. The aim [...] Read more.
Background/Objectives: Laboratory tests conducted in community settings are occasionally repeated within hours of presentation to pediatric emergency departments (PEDs). Reducing unnecessary repetitions can ease child discomfort and alleviate the healthcare burden without compromising the diagnostic process or quality of care. The aim of this study was to develop a decision tree (DT) model to guide physicians in minimizing unnecessary repeat blood tests in PEDs. The minimal decision tree (MDT) algorithm was selected for its interpretability and capacity to generate optimally pruned classification trees. Methods: Children aged 3 months to 18 years with community-based complete blood count (CBC), electrolyte (ELE), and C-reactive protein (CRP) measurements obtained between 2016 and 2023 were included. Repeat tests performed in the pediatric emergency department within 12 h were evaluated by comparing paired measurements, with tests considered justified when values transitioned from normal to abnormal ranges or changed by ≥20%. Additionally, sensitivity analyses were conducted for absolute change thresholds of 10% and 30% and for repeat intervals of 6, 18, and 24 h. Results: Among 7813 children visits in this study, 6044, 1941, and 2771 underwent repeated CBC, ELE, and CRP tests, respectively. The mean ages of patients undergoing CRP, ELE, and CBC testing were 6.33 ± 5.38, 7.91 ± 5.71, and 5.08 ± 5.28 years, respectively. The majority were of middle socio-economic class, with 66.61–71.24% living in urban areas. Pain was the predominant presented complaint (83.69–85.99%), and in most cases (83.69–85.99%), the examination was conducted by a pediatrician. The DT model was developed and evaluated on training and validation cohorts, and it demonstrated high accuracy in predicting the need for repeat CBC and ELE tests but not CRP. Performance of the DT model significantly exceeded that of the logistic regression model. Conclusions: The data-driven guide derived from the DT model provides clinicians with a practical, interpretable tool to minimize unnecessary repeat laboratory testing, thereby enhancing patient care and optimizing healthcare resource utilization. Full article
(This article belongs to the Special Issue Artificial Intelligence for Health and Medicine)
Show Figures

Figure 1

12 pages, 782 KiB  
Review
Primary Sequence-Intrinsic Immune Evasion by Viral Proteins Guides CTL-Based Vaccine Strategies
by Li Wan, Masahiro Shuda, Yuan Chang and Patrick S. Moore
Viruses 2025, 17(8), 1035; https://doi.org/10.3390/v17081035 - 24 Jul 2025
Viewed by 476
Abstract
Viruses use a range of sophisticated strategies to evade detection by cytotoxic T-lymphocytes (CTLs) within host cells. Beyond elaborating dedicated viral proteins that disrupt the MHC class I antigen-presentation machinery, some viruses possess intrinsic, cis-acting genome-encoded elements that interfere with antigen processing and [...] Read more.
Viruses use a range of sophisticated strategies to evade detection by cytotoxic T-lymphocytes (CTLs) within host cells. Beyond elaborating dedicated viral proteins that disrupt the MHC class I antigen-presentation machinery, some viruses possess intrinsic, cis-acting genome-encoded elements that interfere with antigen processing and display. These protein features, including G-quadruplex motifs, repetitive peptide sequences, and rare-codon usage, counterintuitively limit production of proteins critical to virus survival, particularly during latency. By slowing viral protein synthesis, these features reduce antigen production and proteosomal degradation, ultimately limiting the generation of peptides for MHC I presentation. These built-in evasion tactics enable viruses to remain “invisible” to CTLs during latency. While these primary sequence intrinsic immune evasion (PSI) mechanisms are well-described in select herpesviruses, emerging evidence suggests that they may also play a critical role in RNA viruses. How these proteins are made, rather than what they functionally target, determines their immune evasion properties. Understanding PSI mechanisms could rationally inform the design of engineered viral antigens with altered or removed evasion elements to restore antigen CTL priming and activation. Such vaccine strategies have the potential to enhance immune recognition, improve clearance of chronically infected cells, and contribute to the treatment of persistent viral infections and virus-associated cancers. Full article
(This article belongs to the Special Issue 15-Year Anniversary of Viruses)
Show Figures

Figure 1

22 pages, 3350 KiB  
Article
De Novo Hybrid Assembly of the Tripterygium wilfordii Mitochondrial Genome Provides the Chromosomal Mitochondrial DNA Structure and RNA Editing Events
by Yisha Cai, Suxin Yang, Haimei Chen, Yang Ni, Jingling Li, Jinghong Zhang and Chang Liu
Int. J. Mol. Sci. 2025, 26(15), 7093; https://doi.org/10.3390/ijms26157093 - 23 Jul 2025
Viewed by 194
Abstract
Tripterygium wilfordii has extremely important pharmaceutical value in both traditional and modern medicine. The mitogenome of T. wilfordii was subjected to assembly and annotation with Nanopore long reads and Illumina short reads in this study. The mitogenome is 720,306 bp in length and [...] Read more.
Tripterygium wilfordii has extremely important pharmaceutical value in both traditional and modern medicine. The mitogenome of T. wilfordii was subjected to assembly and annotation with Nanopore long reads and Illumina short reads in this study. The mitogenome is 720,306 bp in length and is responsible for encoding 55 specific genes, including 35 protein-coding genes (PCGs), 17 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Upon repetitive sequence analysis, 223 simple sequence repeats (SSRs), 24 long tandem repeats (LTRs), and 47 dispersed repetitive sequences (DRSs) were identified. The 24 common PCGs were used for phylogenetic analysis, which revealed that T. wilfordii is more closely related to Euonymus alatus. Moreover, mitochondrial plastid DNA (MTPT) analysis revealed eight MTPTs in the mitochondrial genome. Furthermore, 600 RNA-editing sites were detected in the protein-coding genes according to RNA-seq results. Among these genes, the ccmB gene contained the greatest number of sites, followed by the nad4 gene. This is the first study to report the T. wilfordii mitogenome and illustrate its linear structure. The findings of this study will help elucidate the evolution of the T. wilfordii mitogenome and facilitate its potential application in genetic breeding. Full article
(This article belongs to the Collection Feature Papers in Molecular Informatics)
Show Figures

Figure 1

14 pages, 4833 KiB  
Article
A High-Quality Chromosome-Level Genome Assembly and Comparative Analyses Provide Insights into the Adaptation of Chrysomya megacephala (Fabricius, 1794) (Diptera: Calliphoridae)
by Dan Zhang, Liangliang Li, Junchao Ma, Jianfeng Jin, Chunli Ding, Qiang Fang, Jianjun Jin, Zhulidezi Aishan and Xuebo Li
Biology 2025, 14(8), 913; https://doi.org/10.3390/biology14080913 - 22 Jul 2025
Viewed by 174
Abstract
Chrysomya megacephala, as one of the common blowflies, displays biological characteristics, such as ovoviviparity and carrion-feeding adaptation. Thus, this species is generally considered of significant ecological, medical, and forensic importance. However, without a high-quality pseudo-chromosome genome for C. megacephala, elucidating its [...] Read more.
Chrysomya megacephala, as one of the common blowflies, displays biological characteristics, such as ovoviviparity and carrion-feeding adaptation. Thus, this species is generally considered of significant ecological, medical, and forensic importance. However, without a high-quality pseudo-chromosome genome for C. megacephala, elucidating its evolutionary trajectory proved difficult. Herein, we assembled and analyzed a high-quality chromosome-level genome assembly of the C. megacephala, combined with PacBio HiFi long reads, Hi-C data, and Illumina reads. The pseudo-chromosomes assembly of C. megacephala spans 629.44 Mb, with 97.05% anchored to five chromosomes. Final assembly includes 1056 contigs (N50 = 1.68 Mb), and 97 scaffolds (N50 = 121.37 Mb), achieving 98.90% BUSCO completeness (n = 1367). Gene annotation predicted 17,071 protein-coding genes (95.60% BUSCO completeness), while repeat masking identified 244.26 Mb (38.82%) as repetitive elements. Additionally, 3740 non-coding RNAs were characterized. Gene family analyses resulted in 10,579 gene families, containing 151 gene families that experienced rapid evolution. Comparative genomic analyses showed that the expanded genes are related to reproduction and necrophagous habits. In addition, we annotated the gene family P450s, CCEs, IRs, GRs, and ORs, all of which represent remarkable expansion, playing a crucial role in the mechanism of locating the hosts for forensic insects. Our research establishes a high-quality genome sequence to facilitate subsequent molecular investigations into significant species within forensic entomology. Full article
Show Figures

Figure 1

19 pages, 12441 KiB  
Article
Mitogenome Characteristics and Intracellular Gene Transfer Analysis of Four Adansonia Species
by Tingting Hu, Fengjuan Zhou, Lisha Wang, Xinwei Hu, Zhongxiang Li, Xinzeng Li, Daoyuan Zhou and Hui Wang
Genes 2025, 16(7), 846; https://doi.org/10.3390/genes16070846 - 21 Jul 2025
Viewed by 276
Abstract
Adansonia L. (1753) belongs to the family Malvaceae and is commonly known as the baobab tree. This species holds significant cultural and ecological value and is often referred to as the ‘tree of life.’ Although its nuclear genome has been reported, the mitogenome [...] Read more.
Adansonia L. (1753) belongs to the family Malvaceae and is commonly known as the baobab tree. This species holds significant cultural and ecological value and is often referred to as the ‘tree of life.’ Although its nuclear genome has been reported, the mitogenome has not yet been studied. Mitogenome research is crucial for understanding the evolution of the entire genome. In this study, we assembled and analyzed the mitogenomes of four Adansonia species by integrating short-read and long-read data. The results showed that the mitogenomes of all four Adansonia species were resolved as single circular sequences. Their total genome lengths ranged from 507,138 to 607,344 bp and contained a large number of repetitive sequences. Despite extensive and complex rearrangements between the mitogenomes of Adansonia and other Malvaceae species, a phylogenetic tree constructed based on protein-coding genes clearly indicated that Adansonia is more closely related to the Bombax. Selection pressure analysis suggests that the rps4 gene in Adansonia may have undergone positive selection compared to other Malvaceae species, indicating that this gene may play a significant role in the evolution of Adansonia. Additionally, by analyzing intracellular gene transfer between the chloroplast, mitochondria, and nuclear genomes, we found that genes from the chloroplast and mitochondria can successfully transfer to each chromosome of the nuclear genome, and the psbJ gene from the chloroplast remains intact in both the mitochondrial and nuclear genomes. This study enriches the genetic information of Adansonia and provides important evidence for evolutionary research in the family Malvaceae. Full article
(This article belongs to the Section Plant Genetics and Genomics)
Show Figures

Figure 1

22 pages, 3024 KiB  
Article
Effects of Ginger Supplementation on Markers of Inflammation and Functional Capacity in Individuals with Mild to Moderate Joint Pain
by Jacob Broeckel, Landry Estes, Megan Leonard, Broderick L. Dickerson, Drew E. Gonzalez, Martin Purpura, Ralf Jäger, Ryan J. Sowinski, Christopher J. Rasmussen and Richard B. Kreider
Nutrients 2025, 17(14), 2365; https://doi.org/10.3390/nu17142365 - 18 Jul 2025
Viewed by 1684
Abstract
Background: Ginger contains gingerols, shagaols, paradols, gingerdiones, and terpenes, which have been shown to display anti-inflammatory properties and inhibit pain receptors. For this reason, ginger has been marketed as a natural analgesic. This study examined whether a specialized ginger extract obtained through supercritical [...] Read more.
Background: Ginger contains gingerols, shagaols, paradols, gingerdiones, and terpenes, which have been shown to display anti-inflammatory properties and inhibit pain receptors. For this reason, ginger has been marketed as a natural analgesic. This study examined whether a specialized ginger extract obtained through supercritical CO2 extraction and subsequent fermentation affects pain perception, functional capacity, and markers of inflammation. Methods: Thirty men and women (56.0 ± 9.0 years, 164.4 ± 14 cm, 86.5 ± 20.9 kg, 31.0 ± 7.5 kg/m2) with a history of mild to severe joint and muscle pain as well as inflammation participated in a placebo-controlled, randomized, parallel-arm study. Participants donated fasting blood, completed questionnaires, rated pain in the thighs to standardized pressure, and then completed squats/deep knee bends, while holding 30% of body mass, for 3 sets of 10 repetitions on days 0, 30, and 56 of supplementation. Participants repeated tests after 2 days of recovery following each testing session. Participants were matched by demographics and randomized to ingest 125 mg/d of a placebo or ginger (standardized to contain 10% total gingerols and no more than 3% total shogaols) for 58 days. Data were analyzed by a general linear model (GLM) analysis of variance with repeated measures, mean changes from the baseline with 95% confidence intervals, and chi-squared analysis. Results: There was evidence that ginger supplementation attenuated perceptions of muscle pain in the vastus medialis; improved ratings of pain, stiffness, and functional capacity; and affected several inflammatory markers (e.g., IL-6, INF-ϒ, TNF-α, and C-Reactive Protein concentrations), particularly following two days of recovery from resistance exercise. There was also evidence that ginger supplementation increased eosinophils and was associated with less frequent but not significantly different use of over-the-counter analgesics. Conclusions: Ginger supplementation (125 mg/d, providing 12.5 mg/d of gingerols) appears to have some favorable effects on perceptions of pain, functional capacity, and inflammatory markers in men and women experiencing mild to moderate muscle and joint pain. Registered clinical trial #ISRCTN74292348. Full article
(This article belongs to the Section Phytochemicals and Human Health)
Show Figures

Figure 1

21 pages, 3456 KiB  
Article
Precision in 3D: A Fast and Accurate Algorithm for Reproducible Motoneuron Structure and Protein Expression Analysis
by Morgan Highlander, Shelby Ward, Bradley LeHoty, Teresa Garrett and Sherif Elbasiouny
Bioengineering 2025, 12(7), 761; https://doi.org/10.3390/bioengineering12070761 - 14 Jul 2025
Viewed by 306
Abstract
Structural analysis of motoneuron somas and their associated proteins via immunohistochemistry (IHC) remains tedious and subjective, requiring costly software or adapted 2D manual methods that lack reproducibility and analytical rigor. Yet, neurodegenerative disease and aging research demands precise structural comparisons to elucidate mechanisms [...] Read more.
Structural analysis of motoneuron somas and their associated proteins via immunohistochemistry (IHC) remains tedious and subjective, requiring costly software or adapted 2D manual methods that lack reproducibility and analytical rigor. Yet, neurodegenerative disease and aging research demands precise structural comparisons to elucidate mechanisms driving neuronal degeneration. To address this need, we developed a novel algorithm that automates repetitive and subjective IHC analysis tasks, enabling thorough, objective, blinded, order-agnostic, and reproducible 3D batch analysis. With no manual tracing, the algorithm produces 3D Cartesian reconstructions of motoneuron somas from 60× IHC images of mouse lumbar spinal tissue. From these reconstructions, it measures 3D soma volume and efficiently quantitates net somatic protein expression and macro-cluster size. In this validation study, we applied the algorithm to assess soma size and C-bouton expression in various healthy control mice, comparing its measurements against manual measurements and across multiple algorithm users to confirm its accuracy and reproducibility. This novel, customizable tool enables efficient and high-fidelity 3D motoneuron analysis, replacing tedious, qualitative, cell-by-cell manual tuning with automatic threshold adaptation and quantified batch settings. For the first time, we attain reproducible results with quantifiable accuracy, exhaustive sampling, and a high degree of objectivity. Full article
(This article belongs to the Special Issue Data Modeling and Algorithms in Biomedical Applications)
Show Figures

Figure 1

24 pages, 3598 KiB  
Article
Comprehensive Analysis of the Complete Mitochondrial Genome of Paeonia ludlowii Reveals a Dual-Circular Structure and Extensive Inter-Organellar Gene Transfer
by Zhefei Zeng, Zhengyan Zhang, Ngawang Norbu, Ngawang Bonjor, Xin Tan, Shutong Zhang, Norzin Tso, Junwei Wang and La Qiong
Biology 2025, 14(7), 854; https://doi.org/10.3390/biology14070854 - 14 Jul 2025
Viewed by 285
Abstract
Paeonia ludlowii, a critically endangered species endemic to Tibet, China, possesses significant ornamental, culinary, and medicinal value. However, its mitochondrial genome remains understudied, limiting insights into its evolutionary mechanisms and constraining conservation genetics applications and molecular breeding programs. We present the first [...] Read more.
Paeonia ludlowii, a critically endangered species endemic to Tibet, China, possesses significant ornamental, culinary, and medicinal value. However, its mitochondrial genome remains understudied, limiting insights into its evolutionary mechanisms and constraining conservation genetics applications and molecular breeding programs. We present the first complete assembly and comprehensive analysis of the P. ludlowii mitochondrial genome. Most remarkably, we discovered that the P. ludlowii mitogenome exhibits an atypical dual-circular structure, representing the first documented occurrence of this architectural feature within the genus Paeonia. The assembled genome spans 314,371 bp and encodes 42 tRNA genes, 3 rRNA genes, and 31 protein-coding genes, with a pronounced adenine–thymine bias. This multipartite genome structure is characterized by abundant repetitive elements (112 functionally annotated SSRs, 33 tandem repeats, and 945 dispersed repeats), which potentially drive genome rearrangements and facilitate adaptive evolution. Analyses of codon usage bias and nucleotide diversity revealed highly conserved gene expression regulation with limited variability. Phylogenetic reconstruction confirms that P. ludlowii, P. suffruticosa, and P. lactiflora form a monophyletic clade, reflecting close evolutionary relationships, while extensive syntenic collinearity with other Paeonia species underscores mitochondrial genome conservation at the genus level. Extensive inter-organellar gene transfer events, particularly from chloroplast to mitochondrion, suggest that such DNA exchanges enhance genetic diversity and promote environmental adaptation. The discovery of the dual-circular architecture provides novel insights into plant mitochondrial genome evolution and structural plasticity. This study elucidates the unique structural characteristics of the P. ludlowii mitochondrial genome and establishes a crucial genetic foundation for developing targeted conservation strategies and facilitating molecular-assisted breeding programs for this endangered species. Full article
Show Figures

Figure 1

28 pages, 2579 KiB  
Review
Telomere Maintenance and DNA Repair: A Bidirectional Relationship in Cancer Biology and Therapy
by Nina Rembiałkowska, Mikołaj Sędzik, Monika Kisielewska, Wiktoria Łuniewska, Kamil Sebastianka, Klaudia Molik, Katarzyna Skinderowicz, Jacek Kuźnicki, Joanna Tunikowska and Julita Kulbacka
Cancers 2025, 17(14), 2284; https://doi.org/10.3390/cancers17142284 - 9 Jul 2025
Viewed by 618
Abstract
Telomeres are repetitive DNA sequences at the ends of chromosomes that protect against genomic instability and prevent unwanted DNA damage responses. In most somatic cells, telomeres progressively shorten with each division, limiting cellular lifespan. However, cancer cells bypass this limitation by activating telomerase [...] Read more.
Telomeres are repetitive DNA sequences at the ends of chromosomes that protect against genomic instability and prevent unwanted DNA damage responses. In most somatic cells, telomeres progressively shorten with each division, limiting cellular lifespan. However, cancer cells bypass this limitation by activating telomerase or the alternative lengthening of telomeres, enabling unchecked proliferation and tumor progression. This review examines the molecular mechanisms underlying telomere maintenance and their intricate relationship with DNA repair pathways. We discuss how telomere-associated proteins regulate genomic stability and explore therapeutic strategies targeting telomerase and alternative lengthening of telomeres. Challenges such as resistance mechanisms and off-target effects are also considered, highlighting the need for precision approaches in telomere-based cancer therapies. Full article
(This article belongs to the Section Molecular Cancer Biology)
Show Figures

Figure 1

15 pages, 8861 KiB  
Article
The Complete Chloroplast Genome of Purdom’s Rhododendron (Rhododendron purdomii Rehder & E. H. Wilson): Genome Structure and Phylogenetic Analysis
by Lu Yuan, Ningning Zhang, Shixin Zhu and Yang Lu
Forests 2025, 16(7), 1120; https://doi.org/10.3390/f16071120 - 7 Jul 2025
Viewed by 318
Abstract
Rhododendron purdomii Rehder & E. H. Wilson (Ericaceae) is a threatened ornamental and medicinal shrub or small tree species primarily distributed in the Qinling-Daba Mountains of Central China. To facilitate its conservation and utilization, the complete chloroplast genome of Rh. purdomii was sequenced, [...] Read more.
Rhododendron purdomii Rehder & E. H. Wilson (Ericaceae) is a threatened ornamental and medicinal shrub or small tree species primarily distributed in the Qinling-Daba Mountains of Central China. To facilitate its conservation and utilization, the complete chloroplast genome of Rh. purdomii was sequenced, assembled, and characterized. The cp genome exhibited a typical quadripartite structure with a total length of 208,062 bp, comprising a large single copy (LSC) region of 110,618 bp, a small single copy (SSC) region of 2606 bp, and two inverted repeat (IR) regions of 47,419 bp each. The overall GC content was 35.81%. The genome contained 146 genes, including 96 protein-coding genes, 42 transfer RNA genes, and 8 ribosomal RNA genes. Structure analysis identified 67,354 codons, 96 long repetitive sequences, and 171 simple sequence repeats. Comparative genomic analysis across Rhododendron species revealed hypervariable coding regions (accD, rps9) and non-coding regions (trnK-UUU-ycf3, trnI-CAU-rpoB, trnT-GGU-accD, rpoA-psbL, rpl20-trnC-GCA, trnI-CAU-rrn16, and trnI-CAU-rps16), which may serve as potential molecular markers for genetic identification. Phylogenetic reconstruction confirmed the monophyly of Rhododendron species and highlighted a close relationship between Rh. purdomii and Rh. henanense subsp. lingbaoense. These results provide essential genomic resources for advancing taxonomic, evolutionary, conservation, and breeding studies of Rh. purdomii and other species within the genus Rhododendron. Full article
(This article belongs to the Section Genetics and Molecular Biology)
Show Figures

Figure 1

16 pages, 7142 KiB  
Article
Unveiling the Genome of the Diploid Wild Sugarcane Relative Narenga porphyrocoma (Hance) Bor
by Haibi Li, Yiyun Gui, Jinju Wei, Kai Zhu, Hui Zhou, Ronghua Zhang, Dongliang Huang, Sijie Huang, Shuangcai Li, Jisen Zhang, Yangrui Li and Xihui Liu
Int. J. Mol. Sci. 2025, 26(13), 6124; https://doi.org/10.3390/ijms26136124 - 26 Jun 2025
Viewed by 346
Abstract
Narenga porphyrocoma (Hance) Bor is a close relative of sugarcane, with traits such as drought resistance, robustness, early maturity, and disease resistance. In this study, we report the first genome assembly of N. porphyrocoma (Hance) Bor GXN1, a diploid species with a chromosomal [...] Read more.
Narenga porphyrocoma (Hance) Bor is a close relative of sugarcane, with traits such as drought resistance, robustness, early maturity, and disease resistance. In this study, we report the first genome assembly of N. porphyrocoma (Hance) Bor GXN1, a diploid species with a chromosomal count of 2n = 30. We assembled the genome into 15 pseudochromosomes with an N50 of 128.80 Mp, achieving a high level of completeness (99.0%) using benchmarking universal single-copy orthologs (BUSCO) assessment. The genome was approximately 1.8 Gb. Our analysis identified a substantial proportion of repetitive sequences, primarily long terminal repeats (LTRs), contributing to 69.12% of the genome. In total, 70,680 protein-coding genes were predicted and annotated, focusing on genes related to drought resistance. Transcriptome analysis under drought stress revealed the key gene families involved in plant physiological rhythms and hormone signal transduction, including aquaporins, late embryogenesis abundant proteins, and heat shock proteins. This research reveals the genome of the diploid wild sugarcane relative N. porphyrocoma (Hance) Bor, encouraging future studies on gene function, genome evolution, and genetic improvement of sugarcane. Full article
(This article belongs to the Special Issue Crop Stress Biology and Molecular Breeding: 5th Edition)
Show Figures

Figure 1

18 pages, 7517 KiB  
Article
Characteristics and Phylogenetic Analysis of the Complete Plastomes of Anthogonium gracile and Eleorchis japonica (Epidendroideae, Orchidaceae)
by Xuyong Gao, Yuming Chen, Xiaowei Xu, Hongjiang Chen, Bingcong Xing, Jianli Pan, Minghe Li and Zhuang Zhou
Horticulturae 2025, 11(6), 698; https://doi.org/10.3390/horticulturae11060698 - 17 Jun 2025
Viewed by 979
Abstract
Phylogenetic relationships within the subtribe Arethusinae (Arethuseae: Epidendroideae: Orchidaceae) remain unresolved, with particular uncertainty surrounding the phylogenetic positions of Anthogonium gracile and Eleorchis japonica. The monophyly of this subtribe remains contentious, making it one of the challenging taxa in Orchidaceae phylogenetics. In [...] Read more.
Phylogenetic relationships within the subtribe Arethusinae (Arethuseae: Epidendroideae: Orchidaceae) remain unresolved, with particular uncertainty surrounding the phylogenetic positions of Anthogonium gracile and Eleorchis japonica. The monophyly of this subtribe remains contentious, making it one of the challenging taxa in Orchidaceae phylogenetics. In this study, we sequenced and analyzed the complete plastome sequences of A. gracile and E. japonica for the first time, aiming to elucidate their plastome characteristics and phylogenetic relationships. Both plastomes exhibited a conserved quadripartite structure, with 158,358 bp in A. gracile and 152,432 bp in E. japonica, and GC contents of 37.1% and 37.3%, respectively. Comparative analyses revealed strong structural conservation, but notable gene losses: E. japonica lacked seven ndh genes (ndhC/D/F/G/H/I/K), whereas A. gracile retained a complete ndh gene set. Repetitive sequence analysis identified an abundance of simple sequence repeats (68 and 77), tandem repeats (43 and 30), and long repeats (35 and 40). Codon usage displayed a bias toward the A/U termination, with leucine and isoleucine being the most frequent. Selection pressure analysis indicated that 68 protein-coding genes underwent purifying selection (Ka/Ks < 1), suggesting evolutionary conservation of plastome protein-coding genes. Nucleotide diversity analysis highlighted six hypervariable regions (rps8-rpl14, rps16-trnQUUG, psbB-psbT, trnTUGU-trnLUAA, trnFGAA-ndhJ, and ycf1), suggesting their potential as molecular markers. Phylogenomic reconstruction, using complete plastome sequences, (ML, MP, and BI) indicated that Arethusinae was non-monophyletic. A. gracile formed a sister relationship with Mengzia foliosa and E. japonica, whereas Arundina graminifolia exhibited a sister relationship with Coelogyninae members. These results shed new light on the plastome characteristics and phylogenetic relationships of Arethusinae. Full article
(This article belongs to the Special Issue Orchids: Advances in Propagation, Cultivation and Breeding)
Show Figures

Figure 1

20 pages, 4522 KiB  
Article
Establishment of a Stable BK Polyomavirus-Secreting Cell Line: Characterization of Viral Genome Integration and Replication Dynamics Through Comprehensive Analysis
by Tamara Löwenstern, David Vecsei, David Horner, Robert Strassl, Anil Bozdogan, Michael Eder, Franco Laccone, Markus Hengstschläger, Farsad Eskandary and Ludwig Wagner
Int. J. Mol. Sci. 2025, 26(12), 5745; https://doi.org/10.3390/ijms26125745 - 15 Jun 2025
Viewed by 793
Abstract
Polyomaviruses have the potential to cause significant morbidity not only in transplant medicine, but also in other forms of disease or variants of immunosuppression. In kidney transplant recipients or recipients of human stem cell transplants, the BK-Virus is the major proponent of manifestations [...] Read more.
Polyomaviruses have the potential to cause significant morbidity not only in transplant medicine, but also in other forms of disease or variants of immunosuppression. In kidney transplant recipients or recipients of human stem cell transplants, the BK-Virus is the major proponent of manifestations such as BKPyV-associated nephropathy or hemorrhagic cystitis. As no polyomavirus-specific drug with proven in vivo effects has been developed so far, methods to screen for such drugs are important. This work describes the establishment of a virus-secreting cell line. By infecting a pre-established monkey kidney cell line (COS-1) with a non-rearranged human BK polyomavirus isolated from a kidney transplant patient suffering from BKPyV-associated nephropathy, a continuously replicating cell type with consistent virus secretion could be established and was termed COSSA. Measurements of BKPyV replication, virion production, and secretion were performed both intracellularly and in the cell supernatant. Viral proteins such as VP1 and LTAg were accurately tracked by confocal microscopy, as well as by immunoblot and qPCR. An intracellular flow cytometry (FACS) assay detecting VP1 protein was established and revealed an expanded range of positive intracellular signals. The viruses produced proved to be infectious in human tubular epithelial cell lines. Long-range sequencing of the COSSA genome using Oxford Nanopore Technology revealed a total of five distinct BKPyV integration events. One integration of a partial BKPyV genome was located upstream of the epidermal growth factor receptor gene. The second and third, both truncated forms of integration, were close to histocompatibility gene locuses, while the fourth was characterized by a ninefold and the fifth by a fourfold tandem repeat of the BKPyV genome. From both of the repeat forms, virus replicates were derived showing deletions/duplications on early and late genes and inversions within the non-coding control region (NCCR). This pattern of repetitive viral genome integration is a potential key driver of enhanced viral replication and increased virion assembly, ultimately supporting efficient virus egress. Quantitative PCR analysis confirmed the release of approximately 108/mL viral units per 48 h from 2 × 105 COSSA cells into the culture supernatant. Notably, the NCCR region of the most frequent copies of circular virus and the integrated tetrameric tandem repeat exhibited a rearranged configuration, which may contribute to the observed high replication dynamics. The establishment of a consistent methodology to generate and secrete BKPyV from a cell line is expected to significantly facilitate antiviral drug development. Full article
(This article belongs to the Special Issue Host Responses to Virus Infection)
Show Figures

Figure 1

16 pages, 3047 KiB  
Article
Chromosome-Level Genome and Variation Map of Eri Silkworm Samia cynthia ricini
by Kunpeng Lu, Jianghong Shen, Wengong Huang, Chengyu Zhan, Zhengqing Li, Shubo Liang, Kerui Lai, Qun Luo, Minjin Han, Xiaoling Tong and Fangyin Dai
Biology 2025, 14(6), 698; https://doi.org/10.3390/biology14060698 - 14 Jun 2025
Viewed by 581
Abstract
The eri silkworm Samia cynthia ricini (S. ricini) is an economically and scientifically significant lepidopteran species, though its genomic resources have remained limited. Here, we present a chromosome-level genome assembly for S. ricini generated through integrated long-read, short-read, and Hi-C sequencing [...] Read more.
The eri silkworm Samia cynthia ricini (S. ricini) is an economically and scientifically significant lepidopteran species, though its genomic resources have remained limited. Here, we present a chromosome-level genome assembly for S. ricini generated through integrated long-read, short-read, and Hi-C sequencing data. The final 456.16 Mb assembly spans 14 chromosomes, exhibiting 98.5% BUSCO completeness and a 48.51% repetitive content. Functional annotation of the 15,729 protein-coding genes against five major databases (NR, SwissProt, Pfam, GO, and KEGG) revealed a maximum annotation rate of 92.71%, demonstrating high gene set quality. Comparative genomics with B. mori uncovered conserved syntenic blocks interspersed with chromosomal fusion/fission events and inversions. We further identified 4.27 million SNPs, 1.02 million InDels, and 53,367 SVs, establishing the first comprehensive variation map for this species. These genomic variations provide a foundation for marker-assisted breeding programs and trait association studies. All the genomic resources and interactive visualization tools were integrated into the SilkMeta database. This study establishes S. ricini as a pivotal resource for comparative lepidopteran genomics and accelerates molecular breeding programs for this agriculturally valuable insect. Full article
Show Figures

Figure 1

43 pages, 1769 KiB  
Review
The Role of LAIR1 as a Regulatory Receptor of Antitumor Immune Cell Responses and Tumor Cell Growth and Expansion
by Alessandro Poggi, Serena Matis, Chiara Rosa Maria Uras, Lizzia Raffaghello, Roberto Benelli and Maria Raffaella Zocchi
Biomolecules 2025, 15(6), 866; https://doi.org/10.3390/biom15060866 - 13 Jun 2025
Viewed by 829
Abstract
It is becoming evident that the therapeutic effect of reawakening the immune response is to limit tumor cell growth and expansion. The use of immune checkpoint inhibitors, like blocking antibodies against programmed cell death receptor (PD) 1 and/or cytotoxic T lymphocyte antigen (CTLA) [...] Read more.
It is becoming evident that the therapeutic effect of reawakening the immune response is to limit tumor cell growth and expansion. The use of immune checkpoint inhibitors, like blocking antibodies against programmed cell death receptor (PD) 1 and/or cytotoxic T lymphocyte antigen (CTLA) 4 alone or in combination with other drugs, has led to unexpected positive results in some tumors but not all. Several other molecules inhibiting lymphocyte antitumor effector subsets have been discovered in the last 30 years. Herein, we focus on the leukocyte-associated immunoglobulin (Ig)-like receptor 1 (LAIR1/CD305). LAIR1 represents a typical immunoregulatory molecule expressed on almost all leukocytes, unlike other regulatory receptors expressed on discrete leukocyte subsets. It bears two immunoreceptor tyrosine-based inhibitory motifs (ITIMs) in the intracytoplasmic protein domain involved in the downregulation of signals mediated by activating receptors. LAIR1 binds to several ligands, such as collagen I and III, complement component 1Q, surfactant protein D, adiponectin, and repetitive interspersed families of polypeptides expressed by erythrocytes infected with Plasmodium malariae. This would suggest LAIR1 involvement in several cell-to-cell interactions and possibly in metabolic regulation. The presence of both cellular and soluble forms of LAIR would indicate a fine regulation of the immunoregulatory activity, as happens for the soluble/exosome-associated forms of PD1 and CTLA4 molecules. As a consequence, LAIR1 appears to play a role in some autoimmune diseases and the immune response against tumor cells. The finding of LAIR1 expression on hematological malignancies, but also on some solid tumors, could open a rationale for the targeting of this molecule to treat neoplasia, either alone or in combination with other therapeutic options. Full article
Show Figures

Figure 1

Back to TopTop