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11 pages, 1904 KB  
Article
Development of Reverse Transcriptase Recombinase Polymerase Amplification Combined with Lateral Flow Dipstick for Rapid Detection of Tilapia Lake Virus (TiLV): Pilot Study
by Saralee Srivorakul, Thunyamas Guntawang, Tidaratt Sittisak, Thanchanok Gordsueb, Kittikorn Boonsri, Rutch Khattiya, Nattawooti Sthitmatee and Kidsadagon Pringproa
Vet. Sci. 2025, 12(9), 845; https://doi.org/10.3390/vetsci12090845 (registering DOI) - 1 Sep 2025
Abstract
Tilapia Lake Virus (TiLV) is well known as a highly contagious viral infection in aquaculture, particularly affecting Tilapia worldwide. Until recently, various TiLV diagnostic methods have been used for rapid and accurate diagnostic procedures that are crucial for timely disease detection and reducing [...] Read more.
Tilapia Lake Virus (TiLV) is well known as a highly contagious viral infection in aquaculture, particularly affecting Tilapia worldwide. Until recently, various TiLV diagnostic methods have been used for rapid and accurate diagnostic procedures that are crucial for timely disease detection and reducing losses. In this study, we developed an alternative method for investigating TiLV diagnosis using Reverse Transcriptase Recombinase Polymerase Amplification (RT-RPA) assay combined with a lateral flow dipstick (LFD). The test was generated by specific anti-FITC and anti-Biotin capture antibodies that are compatible with the TiLV-specific primers tagged with FITC and Biotin. The test was conducted by the reverse transcriptase of target TiLV RNA and RPA amplification at 39 °C for 20 min. The products were then determined by a positive band signal via LFD. The RT-RPA-LFD assay detected the plasmid of TiLV (pTiLV) with a Limit of Detection (LOD) of 3.19 copies/µL, while the RT-PCR-LFD assay detected it with an LOD of 319 copies/µL. Our findings demonstrate that RT-RPA-LFD represents a possible alternative to RT-PCR for the rapid and sensitive detection of TiLV, especially in areas with limited infrastructure. Full article
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17 pages, 4401 KB  
Article
Correlation of TP53 Genetic Alterations with p53 Immunohistochemical Expression and Their Prognostic Significance in DLBCL
by Chen Chen, Zijuan Hu, Min Ren, Longlong Bao, Ran Wei, Tian Tian, Xiaoli Zhu, Qianming Bai, Baohua Yu, Xiaoqiu Li and Xiaoyan Zhou
Curr. Oncol. 2025, 32(9), 488; https://doi.org/10.3390/curroncol32090488 (registering DOI) - 31 Aug 2025
Abstract
TP53 genetic alterations represent a critical molecular feature in diffuse large B-cell lymphoma (DLBCL), with well-established associations with aggressive disease behavior and therapeutic resistance. However, significant controversy persists regarding the clinical utility of p53 immunohistochemical (IHC) expression as a surrogate marker. This study [...] Read more.
TP53 genetic alterations represent a critical molecular feature in diffuse large B-cell lymphoma (DLBCL), with well-established associations with aggressive disease behavior and therapeutic resistance. However, significant controversy persists regarding the clinical utility of p53 immunohistochemical (IHC) expression as a surrogate marker. This study presents a thorough investigation of TP53 genetic alterations and their correlation with p53 protein expression in 664 cases of DLBCL. Using targeted next-generation sequencing (tNGS), we identified TP53 alterations (mutations and/or copy number losses (CNLs)) in 170 cases (25.6%). Among them, 161 cases had mutations. Concurrent analysis of copy number variations (CNVs) in 109 cases revealed TP53 CNLs in 17.4% (19/109), with 68.4% (13/19) of these showing coexisting mutations. Immunohistochemical evaluation of p53 expression in 371 cases demonstrated strong positivity (≥65% cells) in 21% (78/371), complete negativity (<1%) in 5.7% (21/371), and wild-type pattern (1–65%) in 73.3% (272/371) of cases. The p53 IHC laboratory-developed test (LDT) showed 79.2% sensitivity and 91.6% specificity for detecting TP53 alterations overall, though sensitivity varied significantly by mutation type: 86.2% for missense mutations but only 14.3% for nonsense mutations. Clinically, cases with TP53 alterations exhibited more aggressive disease characteristics, including higher ECOG performance scores, increased frequency of B symptoms, and poorer initial treatment responses (complete response rate 68.3% vs. 82.5% in wild-type cases). Most importantly, TP53 genetic alterations, but not p53 protein expression patterns, emerged as an independent prognostic factor for progression-free survival. Our findings demonstrate that tNGS effectively identifies most TP53 alterations and complementary CNV analysis enhances detection of copy number losses. The p53 IHC LDT serves as a useful but imperfect screening tool, with high specificity but variable sensitivity depending on mutation types. These results have important implications for molecular diagnostics in DLBCL, supporting the necessity for comprehensive genetic testing rather than reliance on protein expression analysis alone for accurate risk stratification and treatment planning. Full article
(This article belongs to the Section Oncology Biomarkers)
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12 pages, 416 KB  
Article
High RAS Allele Frequency Signals Increased Risk of TERT Promoter Mutations in Thyroid Tumors
by Coralie Lefebvre, Hannah Greenspoon, Kayla E. Payne, Emily Steinberg, Felicia Tewfik, Gianluca Savoia, Sabrina Daniela da Silva, Marc Pusztaszeri, Véronique-Isabelle Forest and Richard J. Payne
Cancers 2025, 17(17), 2851; https://doi.org/10.3390/cancers17172851 - 30 Aug 2025
Viewed by 41
Abstract
Background/Objectives: RAS mutations are among the most common genetic alterations in thyroid cancer and are generally associated with less aggressive behavior. However, when co-occurring with TERT (telomerase reverse transcriptase) promoter mutations, known markers of poor prognosis, tumors exhibit markedly more aggressive features. The [...] Read more.
Background/Objectives: RAS mutations are among the most common genetic alterations in thyroid cancer and are generally associated with less aggressive behavior. However, when co-occurring with TERT (telomerase reverse transcriptase) promoter mutations, known markers of poor prognosis, tumors exhibit markedly more aggressive features. The allele frequency (AF) of RAS may serve as a potential indicator of clonal dominance and the likelihood of additional high-risk mutations, such as TERT mutation. This study aims to assess whether a high RAS AF correlates with the presence of coexisting TERT promoter mutations and other molecular alterations. Methods: A retrospective chart review was performed on 111 patients with thyroid nodules harboring RAS mutations, either alone or in combination with TERT promoter mutations. All patients underwent molecular testing with ThyroSeq v3 and subsequent thyroidectomy at McGill University teaching hospitals. RAS AF was analyzed in relation to TERT mutation status, nodule size, and other molecular alterations including copy number alterations (CNA) and gene expression profiles (GEP). Results: The mean RAS AF was significantly higher in nodules with both RAS and TERT mutations (38.1%) compared to those with RAS mutations alone (22.1%) (p = 0.002). Nodules with coexisting TERT mutations were also significantly larger (mean size: 3.7 cm vs. 2.4 cm; p = 0.005). Malignant nodules, regardless of TERT status, showed a trend toward higher RAS AF than benign nodules (23.0% vs. 16.3%; p = 0.052). Higher RAS AF was also associated with the presence of CNA and/or GEP positivity. Notably, GEP was positive in 100% of nodules with both RAS and TERT mutations, compared to 37.5% in RAS-only nodules (p = 0.002). Conclusions: A high RAS AF increases the likelihood of a TERT promoter mutation and other genetic alterations, highlighting the importance of RAS AF in optimizing patient care and management. Full article
(This article belongs to the Section Molecular Cancer Biology)
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18 pages, 339 KB  
Review
Genetics of Retinoblastoma: An Overview and Significance of Genetic Testing in Clinical Practice
by Khaled K. Abu-Amero, Altaf A. Kondkar, Naif A. M. Almontashiri, Abdullah M. Khan, Azza M. Y. Maktabi, Syed Hameed and Saleh AlMesfer
Genes 2025, 16(9), 1031; https://doi.org/10.3390/genes16091031 - 29 Aug 2025
Viewed by 175
Abstract
Retinoblastoma is a rare but malignant pediatric retinal tumor, affecting 1 in 15,000–20,000 live births annually. It arises from biallelic mutations in the RB1 tumor suppressor gene (chromosome 13q14.2), leading to uncontrolled cell cycle progression. Clinically, it presents as unilateral (60%) or bilateral [...] Read more.
Retinoblastoma is a rare but malignant pediatric retinal tumor, affecting 1 in 15,000–20,000 live births annually. It arises from biallelic mutations in the RB1 tumor suppressor gene (chromosome 13q14.2), leading to uncontrolled cell cycle progression. Clinically, it presents as unilateral (60%) or bilateral (40%) disease, with leukocoria and strabismus as hallmark signs. Untreated, retinoblastoma is fatal due to metastatic spread. The disease follows Knudson’s two-hit model: heritable forms (30–40% of cases) involve a germline RB1 mutation (M1) and a somatic second hit (M2), predisposing to bilateral/multifocal tumors and secondary cancers. Non-heritable cases (60–70%) result from somatic RB1 mutations or, rarely, MYCN amplification (2%). Genetic testing is critical to classify risk (H0, H1, and HX categories), guide surveillance, and inform family counseling. Bilateral cases almost always harbor germline mutations, while 15% of unilateral cases may carry germline/mosaic RB1 defects. Advanced techniques (Sanger/NGS sequencing for mutation detection, NGS for copy number alterations, and methylation assays) detect RB1 mutations, CNVs, and epigenetic silencing. Tumor DNA analysis resolves ambiguous cases. H1 patients require intensive ocular and brain MRI surveillance, while H0 cases need no follow-up. Prenatal/preimplantation genetic diagnosis (PGD) can prevent transmission in high-risk families. Emerging research explores additional genes (BCOR, CREBBP) and MYCN-amplified subtypes. Genetic counseling addresses recurrence risks, reproductive options, and long-term cancer monitoring. Integrating genetic insights into clinical practice enhances precision medicine, reducing morbidity and healthcare costs. Future directions include whole-genome sequencing and functional studies to refine therapeutic strategies. Full article
(This article belongs to the Section Genetic Diagnosis)
31 pages, 3096 KB  
Article
Pathoadapative Genomic Determinants of Staphylococcus aureus Community Skin Infections and Nasal Colonization
by Cody A. Black, Wonhee So, Raymond Benavides, Julianne A. Mercer, Steven S. Dallas, James F. Shurko, Sarah M. Bandy, Benjamin A. Encino, Justina S. Lipscomb, Adriana Vargus, Christopher R. Frei and Grace C. Lee
Microorganisms 2025, 13(9), 2023; https://doi.org/10.3390/microorganisms13092023 - 29 Aug 2025
Viewed by 90
Abstract
Staphylococcus aureus is a leading cause of skin and soft tissue infections (SSTIs), yet the bacterial genomic adaptations underlying the transition from nasal colonization to invasive infection remain incompletely defined. We sequenced and analyzed 157 S. aureus isolates (126 from SSTIs and 31 [...] Read more.
Staphylococcus aureus is a leading cause of skin and soft tissue infections (SSTIs), yet the bacterial genomic adaptations underlying the transition from nasal colonization to invasive infection remain incompletely defined. We sequenced and analyzed 157 S. aureus isolates (126 from SSTIs and 31 from asymptomatic nasal colonization) from a primary care network in South Texas. Using genome-wide association studies, non-synonymous single-nucleotide variant (NSNV) profiling, and machine learning, we identified strain-specific adaptations in metabolic and regulatory pathways. SSTI isolates exhibited significant enrichment of nitrogen assimilation, purine biosynthesis, menaquinone production, and anaerobic respiration genes. Elevated copy number and colocalization of phage-linked metabolic genes—including nirB, narH, and nifR3—suggest a pathoadaptive genomic island supporting infection-specific energy generation. The enrichment of α/β-hydrolase domain-encoding genes was associated with clinical severity. To quantify severity, we developed the Purulent Ulcer Skin (PUS) score, which integrates wound size, drainage, and erythema. The α/β-hydrolase and lipoprotein genes were significantly associated with higher PUS scores (higher SSTI severity) and phage-encoded virulence gene products were linked to larger wound size. Machine learning prioritized purL and other metabolic loci as key infection classifiers. NSNVs and unitig-level changes co-localized within nutrient transport, stress resistance, and cytolytic genes, supporting a model of multi-layered genomic selection. Metagenomic assemblies of nasal microbiota were enriched for Staphylococcus, Enterococcus, and Micrococcus species, core metabolic pathways, and taxon-specific virulence determinants. This underscores the roles of metabolic and virulent co-networks within nasal commensals and their adaptive capacity for pathogenic transition. These findings provide a potential genomic blueprint of S. aureus pathoadaptation during SSTI and are a step towards the development of novel therapeutic targets. Full article
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21 pages, 909 KB  
Article
Modeling How the Different Parts of the Immune System Fight Viruses
by Benito Chen-Charpentier
Algorithms 2025, 18(9), 544; https://doi.org/10.3390/a18090544 - 29 Aug 2025
Viewed by 81
Abstract
Viruses cause a large number of diseases. After penetrating into a host, the virus starts infecting healthy cells. Then it uses the RNA or DNA of the cell to replicate and afterward it explodes the infected cell, letting out many copies of the [...] Read more.
Viruses cause a large number of diseases. After penetrating into a host, the virus starts infecting healthy cells. Then it uses the RNA or DNA of the cell to replicate and afterward it explodes the infected cell, letting out many copies of the virus that can infect new cells. The innate and adaptive parts of the immune system defend the body by eliminating both the free viruses and the infected cells. Neutrophils, macrophages, natural killer cells, helper T cells (CD4+) and cytotoxic T lymphocytes (CD8+) are among the participating immune cells. The interactions are complex and not fully understood. In this paper, we present and study three mathematical models based on ordinary differential equations of virus and immune system interactions with different complexities, and also introduce possible treatments. We discuss the advantages and disadvantages of each model. We do global sensitivity analysis and numerical simulations. Finally, we present conclusions including comments about the complexity of mathematical models. Full article
24 pages, 6304 KB  
Article
Revisiting Particle-Stranding Ellipsis: A Critical Comparison of Two Analyses
by Ryuta Ono
Languages 2025, 10(9), 216; https://doi.org/10.3390/languages10090216 - 29 Aug 2025
Viewed by 216
Abstract
This paper presents novel evidence that particle-stranding ellipsis in Japanese is best accounted for by PF-deletion rather than by its theoretical competitor, LF-copying. I begin by examining a central prediction of the LF-copying analysis, which states that overt extraction is categorically ruled out, [...] Read more.
This paper presents novel evidence that particle-stranding ellipsis in Japanese is best accounted for by PF-deletion rather than by its theoretical competitor, LF-copying. I begin by examining a central prediction of the LF-copying analysis, which states that overt extraction is categorically ruled out, and show that this prediction is not supported by the empirical data. Additional evidence comes from covert across-the-board movement, as I demonstrate that particle-stranding ellipsis can occur in environments that are argued to involve this type of movement. This finding presents a serious derivational challenge to the LF-copying theory, given the widely accepted view that covert across-the-board movement is not permitted in the grammar. In addition to these syntactic observations, I present previously unreported prosodic evidence showing that particle-stranding ellipsis involving the negative polarity item -sika can exhibit focus intonation. As the LF-copying analysis cannot account for this prosodic pattern, the data provide strong support for the PF-deletion account. Finally, I show that these findings are well explained by the phonology-based deletion model that was originally proposed in the literature. Full article
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52 pages, 827 KB  
Article
The Consonant Inventory of Proto-Tsonga-Copi
by Isaac Eaton
Languages 2025, 10(9), 215; https://doi.org/10.3390/languages10090215 - 29 Aug 2025
Viewed by 412
Abstract
Recent studies have greatly furthered our understanding of the Southern Bantu languages, but questions about the internal relationships of the Southern Bantu language subgroups and the validity of the clade as a whole still remain. This study attempts to reconstruct the consonant inventory [...] Read more.
Recent studies have greatly furthered our understanding of the Southern Bantu languages, but questions about the internal relationships of the Southern Bantu language subgroups and the validity of the clade as a whole still remain. This study attempts to reconstruct the consonant inventory of one proposed genetic clade, that of Tsonga-Copi (S50–S60). Using published dictionaries and reference works for each language of the subgrouping, a corpus of cognate vocabulary was assembled. Each term was then matched, where possible, to a reconstruction in the Bantu Lexical Reconstructions 3 (BLR3) database. Sound correspondences were identified and used to reconstruct the consonant inventory of Proto-Tsonga-Copi. In addition to the discovery of several typologically unusual sound changes, the results of this study also lend support to existing and developing hypotheses about both the internal relationships of Southern Bantu clades, as well as the nature of language contact in (pre)historic Southern Africa, particularly the influence of Khoisan and other Bantu languages. Full article
(This article belongs to the Special Issue Recent Developments on the Diachrony and Typology of Bantu Languages)
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21 pages, 602 KB  
Article
Exploring Copy Number Variants in a Cohort of Children Affected by ADHD: Clinical Investigation and Translational Insights
by Federica Mirabella, Valentina Finocchiaro, Mariagrazia Figura, Ornella Galesi, Maurizio Elia, Serafino Buono, Rita Barone and Renata Rizzo
Genes 2025, 16(9), 1020; https://doi.org/10.3390/genes16091020 - 28 Aug 2025
Viewed by 250
Abstract
Background/Objectives: Attention Deficit Hyperactivity Disorder (ADHD) is a common neurodevelopmental disorder frequently associated with other neuropsychiatric conditions, characterized by high clinical heterogeneity and a complex genetic background. Recent studies suggest that copy number variations (CNVs) may contribute to ADHD susceptibility, particularly when involving [...] Read more.
Background/Objectives: Attention Deficit Hyperactivity Disorder (ADHD) is a common neurodevelopmental disorder frequently associated with other neuropsychiatric conditions, characterized by high clinical heterogeneity and a complex genetic background. Recent studies suggest that copy number variations (CNVs) may contribute to ADHD susceptibility, particularly when involving genes related to brain development, attention regulation, and impulse control. This study investigated the association between CNVs and ADHD phenotype by identifying patients with and without potential pathogenic CNVs. Methods: We evaluated 152 well-characterized ADHD pediatric patients through comprehensive clinical assessments, including dysmorphic features, brain MRI, EEG patterns, and cognitive testing. CNVs were identified using array Comparative Genomic Hybridization (array-CGH). Participants were classified as carrying potentially causative CNVs (PC-CNVs), non-causative CNVs (NC-CNVs), or without CNVs (W-CNVs) and statistically compared across clinical and neurodevelopmental measures. Results: CNVs were identified in 81 participants (53%), comprising 13 with PC-CNVs (8.5%) and 68 with NC-CNVs (44.7%). ADHD symptoms were pronounced across all groups, but PC-CNVs showed a higher burden of comorbidities, suggesting a stronger genetic contribution to ADHD complexity. Significant differences were observed in oppositional behavior, inattentive symptoms, brain MRI findings, and developmental language anomalies. Several CNVs involved genes previously implicated in neurodevelopmental disorders, supporting a potential genetic contribution to the clinical complexity of ADHD. Conclusions: This exploratory study supports the role of CNVs in ADHD susceptibility and highlights the value of genetic screening for understanding clinical variability. Larger studies are needed to clarify genotype–phenotype correlations in ADHD and to guide personalized clinical management. Full article
(This article belongs to the Section Neurogenomics)
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25 pages, 14188 KB  
Article
Assessment of Accuracy in Geometry Reconstruction, CAD Modeling, and MEX Additive Manufacturing for Models Characterized by Axisymmetry and Primitive Geometries
by Paweł Turek, Piotr Bielarski, Alicja Czapla, Hubert Futoma, Tomasz Hajder and Jacek Misiura
Designs 2025, 9(5), 101; https://doi.org/10.3390/designs9050101 - 28 Aug 2025
Viewed by 215
Abstract
Due to the rapid advancements in coordinate measuring systems, data processing software, and additive manufacturing (AM) techniques, it has become possible to create copies of existing models through the reverse engineering (RE) process. However, the lack of precise estimates regarding the accuracy of [...] Read more.
Due to the rapid advancements in coordinate measuring systems, data processing software, and additive manufacturing (AM) techniques, it has become possible to create copies of existing models through the reverse engineering (RE) process. However, the lack of precise estimates regarding the accuracy of the RE process—particularly at the measurement, reconstruction, and computer-aided design (CAD) modeling stages—poses significant challenges. Additionally, the assessment of dimensional and geometrical errors during the manufacturing stage using AM techniques limits the practical implementation of product replicas in the industry. This paper provides an estimation of the errors encountered in the RE process and the AM stage of various models. It includes examples of an electrical box, a lampshade for a standing lamp, a cover for a vacuum unit, and a battery cover. The geometry of these models was measured using a GOM Scan 1 (Carl Zeiss AG, Jena, Germany). Following the measurement process, data processing was performed, along with CAD modeling, which involved primitive detection, profile extraction, and auto-surface methods using Siemens NX 2406 software (Siemens Digital Industries, Plano, TX, USA). The models were produced using a Fortus 360-mc 3D printer (Stratasys, Eden Prairie, MN, USA) with ABS-M30 material. After fabrication, the models were scanned using a GOM Scan 1 scanner to identify any manufacturing errors. The research findings indicated that overall, 95% of the points representing reconstruction errors are within the maximum deviation range of ±0.6 mm to ±1 mm. The highest errors in CAD modeling were attributed to the auto-surfacing method, overall, 95% of the points are within the average range of ±0.9 mm. In contrast, the lowest errors occurred with the detect primitives method, averaging ±0.6 mm. Overall, 95% of the points representing the surface of a model made using the additive manufacturing technology fall within the deviation range ±0.2 mm on average. The findings provide crucial insights for designers utilizing RE and AM techniques in creating functional model replicas. Full article
(This article belongs to the Special Issue Design Process for Additive Manufacturing)
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15 pages, 10472 KB  
Article
Establishment of a CRISPR/dCas9 Activation Library for Screening Transcription Factors Co-Regulating OCT4 with GATA4 in Pig Cells
by Xiaoxia Yao, Mingjie Feng, Chengbo Sun, Sijia Yang, Zhongyu Yuan, Xueqing Liu, Qinjian Li, Chaoqian Jiang, Xiaogang Weng, Jun Song and Yanshuang Mu
Cells 2025, 14(17), 1330; https://doi.org/10.3390/cells14171330 - 28 Aug 2025
Viewed by 200
Abstract
OCT4 is a critical transcription factor for early embryonic development and pluripotency. Previous studies have shown that the regulation of OCT4 by the transcription factor GATA4 is species-specific in pigs. This study aimed to further investigate whether there are other transcription factors that [...] Read more.
OCT4 is a critical transcription factor for early embryonic development and pluripotency. Previous studies have shown that the regulation of OCT4 by the transcription factor GATA4 is species-specific in pigs. This study aimed to further investigate whether there are other transcription factors that co-regulate the transcription of OCT4 with GATA4 in pigs. A CRISPR activation (CRISPRa) sgRNA library was designed and constructed, containing 5056 sgRNAs targeting the promoter region of 1264 transcription factors in pigs. Then, a pig PK15 cell line was engineered with a single-copy OCT4 promoter-driven EGFP reporter at the ROSA26 locus, combined with the dCas9-SAM system for transcriptional activation. The CRISPRa sgRNA lentiviral library was used to screen for transcription factors, with or without GATA4 overexpression. Flow cytometry combined with high-throughput sequencing identified MYC, SOX2, and PRDM14 as activators and OTX2 and CDX2 as repressors of OCT4. In the presence of GATA4, transcription factors such as SALL4 and STAT3 showed synergistic activation. Functional validation confirmed that HOXD13 upregulates OCT4, while OTX2 inhibits it. GATA4 and SALL4 synergistically enhance OCT4 expression. These findings provide new insights into combinatorial mechanisms that control the transcriptional regulation of OCT4 in pigs. Full article
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13 pages, 3091 KB  
Article
Identification of Novel Gene Cluster Potentially Associated with Insecticide Resistance in Anopheles gambiae s.l.
by Hyacinthe Dipina Ki, Mahamadi Kientega, Sabéré O. G. Yemien, Hamidou Maiga, Nouhoun Traoré, Koama Bayili, Moussa Namountougou and Abdoulaye Diabaté
Genes 2025, 16(9), 1018; https://doi.org/10.3390/genes16091018 - 28 Aug 2025
Viewed by 197
Abstract
Background/Objectives: Despite the increasing emergence of resistance, insecticide-based tools remain the primary method for malaria vector control in Africa. To maintain the effectiveness of these interventions, continuous monitoring and identification of novel resistance mechanisms is essential. This study aimed to investigate potential new [...] Read more.
Background/Objectives: Despite the increasing emergence of resistance, insecticide-based tools remain the primary method for malaria vector control in Africa. To maintain the effectiveness of these interventions, continuous monitoring and identification of novel resistance mechanisms is essential. This study aimed to investigate potential new insecticide resistance genes in the Anopheles gambiae complex. Methods: We analyzed whole-genome sequencing data from the An. gambiae 1000 Genomes Project. A broad range of genomic analysis techniques and tools were used to identify and explore genetic variation in the candidate resistance genes. Results: High haplotype homozygosity values, indicative of positive selection, were detected in a 2L chromosomal region corresponding to an aldehyde oxidase gene cluster (AGAP006220, AGAP006221, AGAP006224, AGAP006225, AGAP006226). Single nucleotide polymorphisms (SNPs) have been identified in these genes with frequencies up to 100%, including 569, 691, 1433, 978, and 811 non-synonymous SNPs in AGAP006220, AGAP006221, AGAP006224, AGAP006225, and AGAP006226, respectively. Copy number variations (CNVs) such as deletions and amplifications were also identified at low frequencies (<12%). Population structure analyses revealed adaptive and geographic gene flow between An. gambiae and An. coluzzii. Conclusions: This study provides evidence that aldehyde oxidase genes may contribute to insecticide resistance in An. gambiae s.l. populations. These results highlight the importance of genomic surveillance for detecting novel resistance loci and guiding the development of improved vector control strategies under changing ecological and evolutionary conditions. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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18 pages, 3217 KB  
Article
Complete Chloroplast Genome of Nine Anoectochilus (Orchidaceae) Species from China: Comparative Analysis and Phylogenetic Significance
by Jianru Xiao, Kaifeng Tao, Dong Ma, Yanqiong Xia, Yan Luo and Lu Li
Horticulturae 2025, 11(9), 1017; https://doi.org/10.3390/horticulturae11091017 - 28 Aug 2025
Viewed by 379
Abstract
Members of Anoectochilus Blume (Goodyerinae, Orchidaceae) are terrestrial and perennial herbs, which possess highly medicinal and ornamental values. The intergeneric relationship and species delimitation of Anoectochilus have been controversial and needed further evidence for clarification. Therefore, complete chloroplast (cp) genomes of nine Anoectochilus [...] Read more.
Members of Anoectochilus Blume (Goodyerinae, Orchidaceae) are terrestrial and perennial herbs, which possess highly medicinal and ornamental values. The intergeneric relationship and species delimitation of Anoectochilus have been controversial and needed further evidence for clarification. Therefore, complete chloroplast (cp) genomes of nine Anoectochilus species from China were analyzed and compared; three of these were sequenced and assembled here, and the other six species were downloaded from the GenBank. The cp genomes from nine species possessed conserved quadripartite structures. Genome sizes varied between 151,414 bp and 152,976 bp, exhibiting GC contents of 36.8–37.0% and possessing 133 genes. Comparative analysis of these cp genomes indicated higher variation in the single-copy regions. Based on coding sequences (CDSs) from complete cp genomes, phylogenetic analysis revealed that the nine Anoectochilus species formed a monophyletic clade, being a sister group to Rhomboda Lindl., but distant from two species of Odontochilus Blume that was presumed to be related for a long time. Meanwhile, the nine Anoectochilus species were divided into two subclades with strong supports, providing new evidence for the delimitation of some easily confused species. Full article
(This article belongs to the Section Genetics, Genomics, Breeding, and Biotechnology (G2B2))
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14 pages, 3164 KB  
Article
Chloroplast Genome Evolution and Codon Usage In the Medicinal Plant Pothos chinensis (Araceae)
by Hua Chen and Jisi Zhang
Genes 2025, 16(9), 1017; https://doi.org/10.3390/genes16091017 - 28 Aug 2025
Viewed by 217
Abstract
Background/Objectives: Pothos chinensis is commonly used as traditional medicine in China and India. Codon usage analysis is a good way to understand plants’ evolution. However, there is no report about the codon usage bias of chloroplast genomes in P. chinensis. Methods: In [...] Read more.
Background/Objectives: Pothos chinensis is commonly used as traditional medicine in China and India. Codon usage analysis is a good way to understand plants’ evolution. However, there is no report about the codon usage bias of chloroplast genomes in P. chinensis. Methods: In this study, the chloroplast genome of the medicinal plant P. chinensis was newly obtained. Comparative analyses, DNA barcoding investigation, codon usage bias, and phylogenetic reconstruction were conducted to reveal the chloroplast genome characteristics of P. chinensis. Results: The length of the chloroplast genome of P. chinensis was 165,165 bp. A total of 134 genes were annotated, i.e., 90 protein-coding genes, 36 transfer RNA genes, and eight ribosomal RNA genes. Compared to its sister group Anthurium andraeanum, the length of the large single-copy region (LSC) had been expanded, while the small single-copy region (SSC) had been contracted. Within P. chinensis and P. scandens there were no obvious differences in the length of LSC, SSC, and two inverted repeat regions. Based on Pi values, seven hypervariable regions of whole plastomes were identified. The analysis of codons showed that an average frequency of the 50 candidate genes was 35.30%, and these genes preferred A/U-ending codons. The average effective number of codon (ENC) value was 45.49, which indicated weak codon usage bias. ENCs had a highly significant positive correlation with GC3. Fourteen optimal codons had been identified, 11 of which ended with A/U. The results of the neutrality plot, ENC-plot, and PR2-plot analysis indicated that natural selection might have a significant impact on codon usage patterns. Conclusions: Taken together, our study unraveled the codon usage patterns in P. chinensis and provided valuable genetic information for the genus Pothos. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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18 pages, 5952 KB  
Article
Exploring the Complete Chloroplast Genome of Pyrola decorata Andres: Structure, Variability, Phylogenetic Relationship
by Rong Kang, Shuai Kang, Kunzi Yu, Yuan Jiang, Zeliang Qin, Yuying Hu, Xianlong Cheng and Feng Wei
Curr. Issues Mol. Biol. 2025, 47(9), 688; https://doi.org/10.3390/cimb47090688 - 26 Aug 2025
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Abstract
Pyrola decorata Andres (P. decorata) is a traditional medicinal plant in China. However, its chloroplast genome and the deep evolutionary relationships among its genus remain unexplored. This study identified the samples as P. decorata using morphological observations from Flora of China [...] Read more.
Pyrola decorata Andres (P. decorata) is a traditional medicinal plant in China. However, its chloroplast genome and the deep evolutionary relationships among its genus remain unexplored. This study identified the samples as P. decorata using morphological observations from Flora of China (FOC) and ITS sequences. It is the first to analyze the complete chloroplast genome of P. decorata using Illumina and Nanopore sequencing technologies, confirming a typical chloroplast dumbbell structure. The chloroplast DNA (cpDNA) of P. decorata is 179,999 bp in length, consisting of a large single copy (LSC) (62.3% of total length (112,150 bp)), a small single copy (SSC) (6.5% of total length (11,701 bp)), and two inverted repeat regions (IRA and IRB) (31.2% combined (28,074 bp × 2)). Functional annotation revealed 128 genes: 77 conserved coding sequences (CDS) genes, 43 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Phylogenetic analysis placed P. decorata, Pyrola atropurpurea (P. atropurpurea), Pyrola rotundifolia (P. rotundifolia), and Chimaphila japonica within Group I, with P. decorata exhibiting the closest chloroplast genomic affinity to P. atropurpurea. These findings integrate morphological and molecular evidence to facilitate further identification, classification, and evolutionary analysis of this genus. Full article
(This article belongs to the Section Molecular Plant Sciences)
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