Genes

10 pages, 235 KiB

Open AccessArticle

Fitting of Growth Curves and Estimation of Genetic Relationship between Growth Parameters of Qianhua Mutton Merino

by Jiarong Li, Xuesong Shan, Yang Chen, Chongshun Xu, Lin Tang and Huaizhi Jiang

Genes 2024, 15(3), 390; https://doi.org/10.3390/genes15030390 - 21 Mar 2024

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Qianhua Mutton Merino is a dual-purpose (meat and wool) breed of sheep that has been newly developed in China. In this study, we assessed the growth and development of the Qianhua Mutton Merino sheep breed under house feeding conditions by measuring the body [...] Read more.

Qianhua Mutton Merino is a dual-purpose (meat and wool) breed of sheep that has been newly developed in China. In this study, we assessed the growth and development of the Qianhua Mutton Merino sheep breed under house feeding conditions by measuring the body weight and chest circumference of 2300 rams and ewes of this breed aged 0–24 months. Based on the fitting results of three nonlinear growth models, namely Logistic, Gompertz, and von Bertalanffy, in Qianhua Mutton Merino, we selected the von Bertalanffy model because of its highest fitting degree among all models (R² > 0.977). The significant analysis of the combined fixation of each sheep body’s weight and bust took place (A: mature body weight, B: adjustment parameter, K: instant relative growth rate). The results revealed that parameters A, B, and K of body weight and chest circumference have high heritability and thus could be used as target traits for genetic improvement. Moreover, the correlation strength among A, B, and K suggested that these parameters can be used as a reference to adjust the genetic parameters in the growth model to genetically improve the body size of Qianhua Mutton Merino during breeding. Full article

(This article belongs to the Special Issue Genetics and Genomics of Sheep and Goat)

17 pages, 858 KiB

Open AccessArticle

Cyto-Histological Profile of MicroRNAs as Diagnostic Biomarkers in Differentiated Thyroid Carcinomas

by Maria de Lurdes Matos, Mafalda Pinto, Marta Alves, Sule Canberk, Ana Gonçalves, Maria João Bugalho, Ana Luísa Papoila and Paula Soares

Genes 2024, 15(3), 389; https://doi.org/10.3390/genes15030389 - 21 Mar 2024

Viewed by 1550

Abstract

Introduction: The repertoire of microRNAs (miRNAs) in thyroid carcinomas starts to be elucidated. Among differentiated thyroid carcinomas (DTCs), papillary thyroid carcinoma (PTC) is the most frequent. The assessment of miRNAs expression may contribute to refine the pre-surgical diagnosis in order to obtain a [...] Read more.

Introduction: The repertoire of microRNAs (miRNAs) in thyroid carcinomas starts to be elucidated. Among differentiated thyroid carcinomas (DTCs), papillary thyroid carcinoma (PTC) is the most frequent. The assessment of miRNAs expression may contribute to refine the pre-surgical diagnosis in order to obtain a personalized and more effective treatment for patients. Aims: This study aims to evaluate (1) the miRNAs in a series of DTCs, and their association with the presence of selected genetic mutations in order to improve diagnosis and predict the biologic behavior of DTC/PTC. (2) The reliability of molecular tests in Ultrasound-guided Fine Needle Aspiration Cytology (US-FNAC) for a more precise preoperative diagnosis. Material and Methods: This series includes 176 samples (98 cytology and 78 histology samples) obtained from 106 patients submitted to surgery, including 13 benign lesions (controls) and 93 DTCs (cases). The microRNA expression was assessed for miR-146b, miR-221, miR-222, and miR-15a through quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). The results were analyzed by the 2^−ΔΔCT method, using miR16 as an endogenous control. Regarding PTC diagnosis, the discriminative ability of miRNAs expression was assessed by the area under the Receiver Operating Characteristic Curve (AUC). In PTCs, the association of miRNAs expression, clinicopathological features, and genetic mutations (BRAF, RAS, and TERTp) was evaluated. Results/Discussion: All the analyzed miRNAs presented a tendency to be overexpressed in DTCs/PTCs when compared with benign lesions, both in cytology and histology samples. In cytology, miRNAs expression levels were higher in malignant tumors than in benign tumors. In histology, the discriminative abilities regarding PTC diagnosis were as follows: miR-146b (AUC 0.94, 95% CI 0.87–1), miR-221 (AUC 0.79, 95% CI 0.68–0.9), miR-222 (AUC 0.76, 95% CI 0.63–0.89), and miR-15a (AUC 0.85, 95% CI 0.74–0.97). miR-146b showed 89% sensitivity (se) and 87% specificity (sp); miR-221 se = 68.4, sp = 90; miR-222 se = 73, sp = 70; and mi-R15a se = 72, sp = 80. MicroRNAs were associated with worst-prognosis clinicopathological characteristics in PTCs (p < 0.05), particularly for miR-222. Our data reveal a significant association between higher expression levels of miR-146b, miR-221, and miR-222 in the presence of the BRAF mutation (p < 0.001) and miR-146b (p = 0.016) and miR-221 (p = 0.010) with the RAS mutation, suggesting an interplay of these mutations with miRNAs expression. Despite this study having a relatively small sample size, overexpression of miRNAs in cytology may contribute to a more precise preoperative diagnosis. The miRNAs presented a good discriminative ability in PTC diagnosis. The association between the miRNAs expression profile and genetic alterations can be advantageous for an accurate diagnosis of DTCs/PTCs in FNAC. Full article

(This article belongs to the Special Issue Feature Papers: Molecular Genetics and Genomics 2024)

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13 pages, 2184 KiB

Open AccessArticle

by Ricardo Castro-Camba, Jesús Mª Vielba, Saleta Rico, Purificación Covelo, Mª José Cernadas, Nieves Vidal and Conchi Sánchez

Genes 2024, 15(3), 388; https://doi.org/10.3390/genes15030388 - 21 Mar 2024

Viewed by 1159

Abstract

Wounding and exogenous auxin are needed to induce adventitious roots in chestnut microshoots. However, the specific inductive role of wounding has not been characterized in this species. In the present work, two main goals were established: First, we prompted to optimize exogenous auxin [...] Read more.

Wounding and exogenous auxin are needed to induce adventitious roots in chestnut microshoots. However, the specific inductive role of wounding has not been characterized in this species. In the present work, two main goals were established: First, we prompted to optimize exogenous auxin treatments to improve the overall health status of the shoots at the end of the rooting cycle. Second, we developed a time-series transcriptomic analysis to compare gene expression in response to wounding alone and wounding plus auxin, focusing on the early events within the first days after treatments. Results suggest that the expression of many genes involved in the rooting process is under direct or indirect control of both stimuli. However, specific levels of expression of relevant genes are only attained when both treatments are applied simultaneously, leading to the successful development of roots. In this sense, we have identified four transcription factors upregulated by auxin (CsLBD16, CsERF113, Cs22D and CsIAA6), with some of them also being induced by wounding. The highest expression levels of these genes occurred when wounding and auxin treatments were applied simultaneously, correlating with the rooting response of the shoots. The results of this work clarify the genetic nature of the wounding response in chestnut, its relation to adventitious rooting, and might be helpful in the development of more specific protocols for the vegetative propagation of this species. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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Graphical abstract

16 pages, 2461 KiB

Open AccessArticle

In Vitro Low-Bortezomib Doses Induce Apoptosis and Independently Decrease the Activities of Glutathione S-Transferase and Glutathione Peroxidase in Multiple Myeloma, Taking into Account the GSTT1 and GSTM1 Gene Variants

by Szymon Zmorzynski, Sylwia Popek-Marciniec, Beata Biernacka, Aneta Szudy-Szczyrek, Sylwia Chocholska, Wojciech Styk, Joanna Czerwik-Marcinkowska and Grazyna Swiderska-Kolacz

Genes 2024, 15(3), 387; https://doi.org/10.3390/genes15030387 - 21 Mar 2024

Viewed by 1343

Abstract

Background: Multiple myeloma (MM) is a malignancy derived from plasma cells. Bortezomib affects the concentration of reduced glutathione (GSH) and the activity of glutathione enzymes. The aim of our study was to analyze deletion (null/present) variants of GSTT1 and GSTM1 genes and their [...] Read more.

Background: Multiple myeloma (MM) is a malignancy derived from plasma cells. Bortezomib affects the concentration of reduced glutathione (GSH) and the activity of glutathione enzymes. The aim of our study was to analyze deletion (null/present) variants of GSTT1 and GSTM1 genes and their association with the levels of glutathione and its enzymes in bortezomib-treated cell cultures derived from MM patients. Materials and Methods: This study included 180 individuals (80 MM patients and 100 healthy blood donors) who were genotyped via multiplex PCR (for the GSTT1/GSTM1 genes). Under in vitro conditions, MM bone marrow cells were treated with bortezomib (1–4 nM) to determine apoptosis (via fluorescence microscopy), GSH concentration, and activity of glutathione enzymes (via ELISA). Results: Bortezomib increased the number of apoptotic cells and decreased the activity of S-glutathione transferase (GST) and glutathione peroxidase (GPx). We found significant differences in GST activity between 1 nM (GSTT1-null vs. GSTT1-present), 2 nM (GSTT1-null vs. GSTT1-present), and 4 nM (GSTM1-null vs. GSTM1-present) bortezomib: 0.07 vs. 0.12, p = 0.02; 0.06 vs. 0.10, p = 0.02; and 0.03 vs. 0.08, p = 0.01, respectively. Conclusions: Bortezomib affects the activities of GST and GPx. GST activity was associated with GSTT1 and GSTM1 variants but only at some bortezomib doses. Full article

(This article belongs to the Section Human Genomics and Genetic Diseases)

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14 pages, 1612 KiB

Open AccessArticle

ACTN3 XX Genotype Negatively Affects Running Performance and Increases Muscle Injury Incidence in LaLiga Football Players

by Juan Del Coso, Gil Rodas, Aitor Soler-Aguinaga, Roberto López-Del Campo, Ricardo Resta, Joaquín González-Rodenas, Jordi Ferrandis and Víctor Moreno-Pérez

Genes 2024, 15(3), 386; https://doi.org/10.3390/genes15030386 - 21 Mar 2024

Cited by 1 | Viewed by 2537

Abstract

The aim of this study was to investigate the association of the ACTN3 rs1815739 polymorphism with match running performance and injury incidence in top-level professional football players. A total of 315 top-level professional football players from the first division of Spanish football (i.e., [...] Read more.

The aim of this study was to investigate the association of the ACTN3 rs1815739 polymorphism with match running performance and injury incidence in top-level professional football players. A total of 315 top-level professional football players from the first division of Spanish football (i.e., LaLiga) participated in this prospective and descriptive study. The ACTN3 rs1815739 genotype was identified for each player using genomic DNA samples. During LaLiga 2021–2022, players’ performance was obtained through a validated camera system in all official matches. Additionally, the incidence of non-contact injuries was obtained by each team’s medical staff according to the International Olympic Committee (IOC) statement. From the study sample, 116 (36.8%) players had the RR genotype, 156 (49.5%) had the RX genotype, and 43 (13.7%) had the XX genotype. The anthropometric characteristics of the players were similar across genotypes. However, the total running distance (p = 0.046), the distance at 21.0–23.9 km/h (p = 0.042), and the number of sprints (p = 0.042) were associated with the ACTN3 genotype. In all these variables, XX players had lower match performance values than RR players. Additionally, total and match injury incidences were higher in XX players than in RR players (p = 0.026 and 0.009, respectively). The rate of muscle injuries was also higher in XX players (p = 0.016). LaLiga football players with the ACTN3 XX genotype had lower match running performance and a higher incidence of non-contact injuries over the season. Full article

(This article belongs to the Special Issue Genetic Variation and Human Population Evolution)

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11 pages, 5373 KiB

Open AccessBrief Report

Olfactory Receptor OR2K2 Expression in Human Choroid Plexus as a Potential Marker in Early Sporadic Alzheimer’s Disease

by Victoria Cunha Alves, Joana Figueiro-Silva, Ramon Trullas, Isidre Ferrer and Eva Carro

Genes 2024, 15(3), 385; https://doi.org/10.3390/genes15030385 - 21 Mar 2024

Viewed by 1658

Abstract

Epithelial cells comprising the choroid plexus (CP) form a crucial barrier between the blood and the cerebrospinal fluid, thereby assuming a central position in brain homeostasis and signaling. Mounting evidence suggests that the impairment of CP function may be a significant contributor to [...] Read more.

Epithelial cells comprising the choroid plexus (CP) form a crucial barrier between the blood and the cerebrospinal fluid, thereby assuming a central position in brain homeostasis and signaling. Mounting evidence suggests that the impairment of CP function may be a significant contributor to Alzheimer’s disease (AD) pathogenesis. CP function relies on the expression of specific receptors, and the potential involvement of olfactory receptors (ORs) and taste receptors (TASRs) in chemical surveillance within the CP is being investigated. Previous studies have implicated ORs and TASRs in neurodegenerative disorders like AD, although the direct evidence of their expression in the human CP remains to be established. In this study, we conducted a transcriptomic analysis encompassing eleven ORs and TASRs in the CP, comparing samples from healthy age-matched controls to those from patients with AD spanning Braak stages I to VI. Among these receptors, a striking finding emerged—OR2K2 exhibited robust expression, with a statistically significant upregulation noted at Braak stage I. Surprisingly, at the protein level, OR2K2 showed a significant decrease in both Braak stage I and VI. Additionally, we identified CP epithelial cells as the source of OR2K2 expression, where it colocalized with autophagy markers LC3 and p62. We postulate that OR2K2 could be subjected to degradation by autophagy in the early stages of AD, triggering a compensatory mechanism that leads to increased OR2K2 mRNA transcription. This study uncovers a potential role for OR2K2 in AD pathogenesis, offering a novel perspective on the intricate dynamics at play in this neurodegenerative disorder. Full article

(This article belongs to the Special Issue Genetic and Molecular Bases of Neurodegeneration)

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10 pages, 515 KiB

Open AccessArticle

The Health History of First-Degree Relatives’ Dyslipidemia Can Affect Preferences and Intentions following the Return of Genomic Results for Monogenic Familial Hypercholesterolemia

by Tomoharu Tokutomi, Akiko Yoshida, Akimune Fukushima, Kayono Yamamoto, Yasushi Ishigaki, Hiroshi Kawame, Nobuo Fuse, Fuji Nagami, Yoichi Suzuki, Mika Sakurai-Yageta, Akira Uruno, Kichiya Suzuki, Kozo Tanno, Hideki Ohmomo, Atsushi Shimizu, Masayuki Yamamoto and Makoto Sasaki

Genes 2024, 15(3), 384; https://doi.org/10.3390/genes15030384 - 21 Mar 2024

Viewed by 1956

Abstract

Genetic testing is key in modern healthcare, particularly for monogenic disorders such as familial hypercholesterolemia. This Tohoku Medical Megabank Project study explored the impact of first-degree relatives’ dyslipidemia history on individual responses to familial hypercholesterolemia genomic results. Involving 214 participants and using Japan’s [...] Read more.

Genetic testing is key in modern healthcare, particularly for monogenic disorders such as familial hypercholesterolemia. This Tohoku Medical Megabank Project study explored the impact of first-degree relatives’ dyslipidemia history on individual responses to familial hypercholesterolemia genomic results. Involving 214 participants and using Japan’s 3.5KJPN genome reference panel, the study assessed preferences and intentions regarding familial hypercholesterolemia genetic testing results. The data revealed a significant inclination among participants with a family history of dyslipidemia to share their genetic test results, with more than 80% of participants intending to share positive results with their partners and children and 98.1% acknowledging the usefulness of positive results for personal health management. The study underscores the importance of family health history in genetic-testing perceptions, highlighting the need for family-centered approaches in genetic counseling and healthcare. Notable study limitations include the regional scope and reliance on questionnaire data. The study results emphasize the association between family health history and genetic-testing attitudes and decisions. Full article

(This article belongs to the Topic Advances in Genetics and Precision Medicine in Human Diseases)

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17 pages, 10945 KiB

Open AccessArticle

Mining Heat-Resistant Key Genes of Peony Based on Weighted Gene Co-Expression Network Analysis

by Xingyu Yang, Yu Huang, Yiping Yao, Wenxuan Bu, Minhuan Zhang, Tangchun Zheng, Xiaoning Luo, Zheng Wang, Weiqun Lei, Jianing Tian, Lujie Chen and Liping Qin

Genes 2024, 15(3), 383; https://doi.org/10.3390/genes15030383 - 21 Mar 2024

Cited by 1 | Viewed by 1244

Abstract

The RNA-Seq and gene expression data of mature leaves under high temperature stress of Paeonia suffruticosa ‘Hu Hong’ were used to explore the key genes of heat tolerance of peony. The weighted gene co-expression network analysis (WGCNA) method was used to construct the [...] Read more.

The RNA-Seq and gene expression data of mature leaves under high temperature stress of Paeonia suffruticosa ‘Hu Hong’ were used to explore the key genes of heat tolerance of peony. The weighted gene co-expression network analysis (WGCNA) method was used to construct the network, and the main modules and core genes of co-expression were screened according to the results of gene expression and module function enrichment analysis. According to the correlation of gene expression, the network was divided into 19 modules. By analyzing the expression patterns of each module gene, Blue, Salmon and Yellow were identified as the key modules of peony heat response related functions. GO and KEGG functional enrichment analysis was performed on the genes in the three modules and a network diagram was constructed. Based on this, two key genes PsWRKY53 (TRINITY_DN60998_c1_g2, TRINITY_DN71537_c0_g1) and PsHsfB2b (TRINITY_DN56794_c0_g1) were excavated, which may play a key role in the heat shock response of peony. The three co-expression modules and two key genes were helpful to further elucidate the heat resistance mechanism of P. suffruticosa ‘Hu Hong’. Full article

(This article belongs to the Section Plant Genetics and Genomics)

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13 pages, 796 KiB

Open AccessArticle

Genome-Wide Association Analysis of Semen Characteristics in Piétrain Boars

by Henry Reyer, Ibrahim Abou-Soliman, Martin Schulze, Hubert Henne, Norbert Reinsch, Jennifer Schoen and Klaus Wimmers

Genes 2024, 15(3), 382; https://doi.org/10.3390/genes15030382 - 20 Mar 2024

Cited by 2 | Viewed by 1791

Abstract

Since artificial insemination is common practice in pig breeding, the quality and persistence of the semen are decisive for the usability of individual boars. In the current study, genome-wide association analyses were performed to investigate the genetic variability underlying phenotypic variations in semen [...] Read more.

Since artificial insemination is common practice in pig breeding, the quality and persistence of the semen are decisive for the usability of individual boars. In the current study, genome-wide association analyses were performed to investigate the genetic variability underlying phenotypic variations in semen characteristics. These traits comprise sperm morphology and sperm motility under different temporal and thermal storage conditions, in addition to standard semen quality parameters. Two consecutive samples of the fourth and fifth ejaculates from the same boar were comprehensively analyzed in a genotyped Piétrain boar population. A total of 13 genomic regions on different chromosomes were identified that contain single-nucleotide polymorphisms significantly associated with these traits. Subsequent analysis of the genomic regions revealed candidate genes described to be involved in spermatogenesis, such as FOXL3, GPER1, PDGFA, PRKAR1B, SNRK, SUN1, and TSPO, and sperm motility, including ARRDC4, CEP78, DNAAF5, and GPER1. Some of these genes were also associated with male fertility or infertility in mammals (e.g., CEP78, GPER1). The analyses based on these laboriously determined and valuable phenotypes contribute to a better understanding of the genetic background of male fertility traits in pigs and could prospectively contribute to the improvement of sperm quality through breeding approaches. Full article

(This article belongs to the Special Issue Advances in Pig Breeding and Genetics (Volume II))

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9 pages, 1232 KiB

Open AccessCase Report

Novel MYH7 Variant in the Neonate of a Mother with Gestational Diabetes Mellitus Showing Left Ventricular Hypertrophy and Noncompaction

by Sayaka W Ozawa, Satomi Inomata, Yukiko Hata, Shinya Takarada, Mako Okabe, Hideyuki Nakaoka, Keijiro Ibuki, Naoki Nishida, Fukiko Ichida and Keiichi Hirono

Genes 2024, 15(3), 381; https://doi.org/10.3390/genes15030381 - 20 Mar 2024

Cited by 1 | Viewed by 1393

Abstract

Background: Left ventricular hypertrophy (LVH) is a well-recognized cardiac dysfunction in infants of mothers with gestational diabetes mellitus (GDM). Left ventricular noncompaction (LVNC) is a cardiomyopathy that is morphologically characterized by numerous prominent trabeculations and deep intertrabecular recesses on cardiovascular imaging. However, there [...] Read more.

Background: Left ventricular hypertrophy (LVH) is a well-recognized cardiac dysfunction in infants of mothers with gestational diabetes mellitus (GDM). Left ventricular noncompaction (LVNC) is a cardiomyopathy that is morphologically characterized by numerous prominent trabeculations and deep intertrabecular recesses on cardiovascular imaging. However, there have been no case reports on neonates of mothers with GDM showing LVH and LVNC. Case presentation: A patient, with LVH of a mother with GDM, was delivered at 36 weeks of gestation. Prominent trabeculations in the LV, suggesting LVNC, instead of LVH, were apparent 1 week after birth. A heterozygous deletion variant in the MYH7 gene (NM_000257.4: c.1090T>C, p.Phe364Leu) was discovered through genetic testing using a cardiomyopathy-associated gene panel in the patient and his father and the older brother who had LVNC. The patient is now 5 years old and does not have major cardiac events, although LVNC persisted. This is the first case of LVH secondary to a mother with GDM and LVNC with a novel variant in the MYH7 gene. Conclusion: Genetic testing should be conducted to obtain an accurate outcome and medical care in a patient with LVH and subsequently prominent hypertrabeculation in the LV. Full article

(This article belongs to the Special Issue Genetics, Genomics and Precision Medicine in Heart Diseases)

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16 pages, 4644 KiB

Open AccessArticle

First Record of Comparative Plastid Genome Analysis and Phylogenetic Relationships among Corylopsis Siebold & Zucc. (Hamamelidaceae)

by Tae-Hee Kim, Young-Ho Ha, Hiroaki Setoguchi, Kyung Choi, Sang-Chul Kim and Hyuk-Jin Kim

Genes 2024, 15(3), 380; https://doi.org/10.3390/genes15030380 - 20 Mar 2024

Cited by 1 | Viewed by 1257

Abstract

Corylopsis Siebold & Zucc. (Hamamelidaceae) is widely used as a horticultural plant and comprises approximately 25 species in East Asia. Molecular research is essential to distinguish Corylopsis species, which are morphologically similar. Molecular research has been conducted using a small number of genes [...] Read more.

Corylopsis Siebold & Zucc. (Hamamelidaceae) is widely used as a horticultural plant and comprises approximately 25 species in East Asia. Molecular research is essential to distinguish Corylopsis species, which are morphologically similar. Molecular research has been conducted using a small number of genes but not in Corylopsis. Plastid genomes of Corylopsis species (Corylopsis gotoana, Corylopsis pauciflora, and Corylopsis sinensis) were sequenced using next-generation sequencing techniques. Repeats and nucleotide diversity that could be used as DNA markers were also investigated. A phylogenetic investigation was carried out using 79 protein-coding genes to infer the evolutionary relationships within the genus Corylopsis. By including new plastomes, the overall plastid genome structure of Corylopsis was similar. Simple sequence repeats of 73–106 SSRs were identified in the protein-coding genes of the plastid genomes, and 33–40 long repeat sequences were identified in the plastomes. The Pi value of the rpl33_rps18 region, an intergenic spacer, was the highest. Phylogenetic analysis demonstrated that Corylopsis is a monophyletic group and Loropetalum is closely related to Corylopsis. C. pauciflora, C. gotoana, and C. spicata formed a clade distributed in Japan, whereas C. sinensis, C. glandulifera, and C. velutina formed a clade that was distributed in China. Full article

(This article belongs to the Special Issue Plant Plastid Genome and Phylogenetics)

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22 pages, 1580 KiB

Open AccessReview

Pediatric Beta Blocker Therapy: A Comprehensive Review of Development and Genetic Variation to Guide Precision-Based Therapy in Children, Adolescents, and Young Adults

by Mollie Walton and Jonathan B. Wagner

Genes 2024, 15(3), 379; https://doi.org/10.3390/genes15030379 - 20 Mar 2024

Viewed by 2910

Abstract

Beta adrenergic receptor antagonists, known as beta blockers, are one of the most prescribed medications in both pediatric and adult cardiology. Unfortunately, most of these agents utilized in the pediatric clinical setting are prescribed off-label. Despite regulatory efforts aimed at increasing pediatric drug [...] Read more.

Beta adrenergic receptor antagonists, known as beta blockers, are one of the most prescribed medications in both pediatric and adult cardiology. Unfortunately, most of these agents utilized in the pediatric clinical setting are prescribed off-label. Despite regulatory efforts aimed at increasing pediatric drug labeling, a majority of pediatric cardiovascular drug agents continue to lack pediatric-specific data to inform precision dosing for children, adolescents, and young adults. Adding to this complexity is the contribution of development (ontogeny) and genetic variation towards the variability in drug disposition and response. In the absence of current prospective trials, the purpose of this comprehensive review is to illustrate the current knowledge gaps regarding the key drivers of variability in beta blocker drug disposition and response and the opportunities for investigations that will lead to changes in pediatric drug labeling. Full article

(This article belongs to the Special Issue Genetics, Genomics and Precision Medicine in Heart Diseases)

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15 pages, 2552 KiB

Open AccessArticle

Fingerprint Finder: Identifying Genomic Fingerprint Sites in Cotton Cohorts for Genetic Analysis and Breeding Advancement

by Shang Liu, Hailiang Cheng, Youping Zhang, Man He, Dongyun Zuo, Qiaolian Wang, Limin Lv, Zhongxv Lin and Guoli Song

Genes 2024, 15(3), 378; https://doi.org/10.3390/genes15030378 - 19 Mar 2024

Viewed by 1271

Abstract

Genomic data in Gossypium provide numerous data resources for the cotton genomics community. However, to fill the gap between genomic analysis and breeding field work, detecting the featured genomic items of a subset cohort is essential for geneticists. We developed FPFinder v1.0 software [...] Read more.

Genomic data in Gossypium provide numerous data resources for the cotton genomics community. However, to fill the gap between genomic analysis and breeding field work, detecting the featured genomic items of a subset cohort is essential for geneticists. We developed FPFinder v1.0 software to identify a subset of the cohort’s fingerprint genomic sites. The FPFinder was developed based on the term frequency–inverse document frequency algorithm. With the short-read sequencing of an elite cotton pedigree, we identified 453 pedigree fingerprint genomic sites and found that these pedigree-featured sites had a role in cotton development. In addition, we applied FPFinder to evaluate the geographical bias of fiber-length-related genomic sites from a modern cotton cohort consisting of 410 accessions. Enriching elite sites in cultivars from the Yangtze River region resulted in the longer fiber length of Yangze River-sourced accessions. Apart from characterizing functional sites, we also identified 12,536 region-specific genomic sites. Combining the transcriptome data of multiple tissues and samples under various abiotic stresses, we found that several region-specific sites contributed to environmental adaptation. In this research, FPFinder revealed the role of the cotton pedigree fingerprint and region-specific sites in cotton development and environmental adaptation, respectively. The FPFinder can be applied broadly in other crops and contribute to genetic breeding in the future. Full article

(This article belongs to the Special Issue Cotton Genes, Genetics, and Genomics)

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12 pages, 608 KiB

Open AccessArticle

Genome and Epigenome Disorders and Male Infertility: Feedback from 15 Years of Clinical and Research Experience

by Debbie Montjean, Marion Beaumont, Abdelhafid Natiq, Noureddine Louanjli, Andre Hazout, Pierre Miron, Thomas Liehr, Rosalie Cabry, Ilham Ratbi and Moncef Benkhalifa

Genes 2024, 15(3), 377; https://doi.org/10.3390/genes15030377 - 19 Mar 2024

Cited by 1 | Viewed by 2423

Abstract

Infertility affects around 20% of couples of reproductive age; however, in some societies, as many as one-third of couples are unable to conceive. Different factors contribute to the decline of male fertility, such us environmental and professional exposure to endocrine disruptors, oxidative stress, [...] Read more.

Infertility affects around 20% of couples of reproductive age; however, in some societies, as many as one-third of couples are unable to conceive. Different factors contribute to the decline of male fertility, such us environmental and professional exposure to endocrine disruptors, oxidative stress, and life habits with the risk of de novo epigenetics dysregulation. Since the fantastic development of new “omes and omics” technologies, the contribution of inherited or de novo genomes and epigenome disorders to male infertility have been further elucidated. Many other techniques have become available to andrology laboratories for the investigation of genome and epigenome integrity and the maturation and the competency of spermatozoa. All these new methods of assessment are highlighting the importance of genetics and epigenetics investigation for assisted reproduction pathology and for supporting professionals in counselling patients and proposing different management strategies for male infertility. This aims to improve clinical outcomes while minimizing the risk of genetics or health problems at birth. Full article

(This article belongs to the Special Issue Genetic Causes of Human Infertility)

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13 pages, 4560 KiB

Open AccessArticle

Expression, Polymorphism, and Potential Functional Sites of the BMPR1A Gene in the Sheep Horn

by Guoqing Zhang, Mingxing Chu, Hao Yang, Hao Li, Jianxin Shi, Pingjie Feng, Shoufeng Wang and Zhangyuan Pan

Genes 2024, 15(3), 376; https://doi.org/10.3390/genes15030376 - 19 Mar 2024

Cited by 1 | Viewed by 1748

Abstract

Sheep horns are composed of bone and sheaths, and the BMPR1A gene is required for cartilage and osteogenic differentiation. Therefore, the BMPR1A gene may have a function related to the sheep horn, but its relationship with the sheep horn remains unclear. In this [...] Read more.

Sheep horns are composed of bone and sheaths, and the BMPR1A gene is required for cartilage and osteogenic differentiation. Therefore, the BMPR1A gene may have a function related to the sheep horn, but its relationship with the sheep horn remains unclear. In this study, we first utilized RNA sequencing (RNA-seq) data to investigate the expression of the BMPR1A gene in different tissues and breeds of sheep. Second, whole-genome sequencing (WGS) data were used to explore the functional sites of the BMPR1A gene. Lastly, the allele-specific expression of the BMPR1A gene was explored. Our results indicate that BMPR1A gene expression is significantly higher in the normal horn groups than in the scurred groups. Importantly, this trend is consistent across several sheep breeds. Therefore, this finding suggests that the BMPR1A gene may be related to horn type. A total of 43 Single-Nucleotide Polymorphisms (SNPs) (F-statistics > 0.15) and 10 allele-specific expressions (ASEs) exhibited difference between the large and small horn populations. It is probable that these sites significantly impact the size of sheep horns. Compared to other polled species, we discovered ten amino acid sites that could influence horn presence. By combining RNA-seq and WGS functional loci results, we identified a functional site at position 40574836 on chromosome 25 that is both an SNP and exhibits allele-specific expression. In conclusion, we demonstrated that the BMPR1A gene is associated with horn type and identified some important functional sites which can be used as molecular markers in the breeding of sheep horns. Full article

(This article belongs to the Special Issue Genetic Mechanism Analysis and Application of Important Economic Traits in Sheep and Goats)

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17 pages, 952 KiB

Open AccessArticle

Transferability of Human and Environmental Microbiome on Clothes as a Tool for Forensic Investigations

by Noemi Procopio, Giulia Sguazzi, Emma V. Eriksson, Nengi Ogbanga, Frazer C. McKell, Eleanor P. Newton, Paola A. Magni, Andrea Bonicelli and Sarah Gino

Genes 2024, 15(3), 375; https://doi.org/10.3390/genes15030375 - 19 Mar 2024

Viewed by 2522

Abstract

Considering the growing importance of microbiome analyses in forensics for identifying individuals, this study explores the transfer of the skin microbiome onto clothing, its persistence on fabrics over time, and its transferability from the environment and between different garments. Furthermore, this project compares [...] Read more.

Considering the growing importance of microbiome analyses in forensics for identifying individuals, this study explores the transfer of the skin microbiome onto clothing, its persistence on fabrics over time, and its transferability from the environment and between different garments. Furthermore, this project compares three specific QIAGEN microbiome extraction kits to test their extraction efficiency on fabric samples. Additionally, this study aims to check if these extracts contain human DNA, providing a chance to obtain more information from the same evidence for personal identification. The results obtained show: (1) variations in the skin microbiome between the volunteers, potentially due to their different sex; (2) differences in microbial composition between worn and unworn clothing; (3) the influence of the environment on the microbial signature of unworn clothing; (4) the potential use of certain phyla as biomarkers to differentiate between worn and unworn garments, even over extended periods; (5) a tendency towards extraction biases in the QIAampMP^® DNA microbiome kit among the three tested ones; and (6) none of the extraction kits allow for the typing of human genetic profiles suitable for comparison. In conclusion, our study offers supplementary insights into the potential utility of time-transferred microbiome analysis on garments for forensic applications. Full article

(This article belongs to the Special Issue State-of-the-Art in Forensic Genetics Volume II)

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21 pages, 667 KiB

Open AccessReview

Beyond the Anticodon: tRNA Core Modifications and Their Impact on Structure, Translation and Stress Adaptation

by Marcel-Joseph Yared, Agathe Marcelot and Pierre Barraud

Genes 2024, 15(3), 374; https://doi.org/10.3390/genes15030374 - 19 Mar 2024

Cited by 6 | Viewed by 3132

Abstract

Transfer RNAs (tRNAs) are heavily decorated with post-transcriptional chemical modifications. Approximately 100 different modifications have been identified in tRNAs, and each tRNA typically contains 5–15 modifications that are incorporated at specific sites along the tRNA sequence. These modifications may be classified into two [...] Read more.

Transfer RNAs (tRNAs) are heavily decorated with post-transcriptional chemical modifications. Approximately 100 different modifications have been identified in tRNAs, and each tRNA typically contains 5–15 modifications that are incorporated at specific sites along the tRNA sequence. These modifications may be classified into two groups according to their position in the three-dimensional tRNA structure, i.e., modifications in the tRNA core and modifications in the anticodon-loop (ACL) region. Since many modified nucleotides in the tRNA core are involved in the formation of tertiary interactions implicated in tRNA folding, these modifications are key to tRNA stability and resistance to RNA decay pathways. In comparison to the extensively studied ACL modifications, tRNA core modifications have generally received less attention, although they have been shown to play important roles beyond tRNA stability. Here, we review and place in perspective selected data on tRNA core modifications. We present their impact on tRNA structure and stability and report how these changes manifest themselves at the functional level in translation, fitness and stress adaptation. Full article

(This article belongs to the Special Issue Transfer RNA Modification)

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12 pages, 2611 KiB

Open AccessBrief Report

Long-Term Tissue Preservation at Ambient Temperature for Post-Mass Fatality Incident DNA-Based Victim Identification

by Xavier Liang Shun Chan, Shumei Michelle Lai, Danial Asyraaf bin Hamdan, Yee Bin Ng, Onn Siong Yim and Christopher Kiu Choong Syn

Genes 2024, 15(3), 373; https://doi.org/10.3390/genes15030373 - 19 Mar 2024

Viewed by 1260

Abstract

In a mass fatality incident (MFI), effective preservation of tissue samples is the cornerstone for downstream DNA-based identification of victims. This is commonly achieved through freezing of tissue samples excised from bodies/fragmented remains which may be buried or stored in refrigerated containers. This [...] Read more.

In a mass fatality incident (MFI), effective preservation of tissue samples is the cornerstone for downstream DNA-based identification of victims. This is commonly achieved through freezing of tissue samples excised from bodies/fragmented remains which may be buried or stored in refrigerated containers. This may, however, not be possible depending on the nature of the MFI; in particular, during armed conflict/war where extended periods of electrical outages would be expected. The present study compared the effectiveness of long-term tissue preservation at ambient temperatures using two commercial products (non-iodized kitchen salt and a 40% alcoholic beverage) against a chemical preservative (Allprotect™ Tissue Reagent (Qiagen, Germantown, MD, USA)) and freezing at −20 °C. Bovine muscle tissue, used as a proxy for human tissue, was treated with the four preservation methods and sampled at six different time-points over a 24-month period. All four methods were able to preserve the bovine tissue, generally yielding STR-PCR (Short Tandem Repeat-Polymerase Chain Reaction) amplicons > 200 bp in size even at the end of 24 months. Gel electrophoresis, however, indicated that salt was more effective in preserving DNA integrity with high-molecular-weight DNA clearly visible as compared to the low-molecular-weight DNA smears observed in the other methods. This study also proposes a simple process for the rapid and low-cost preservation of tissue samples for long-term storage at ambient temperatures in support of post-incident victim identification efforts. Full article

(This article belongs to the Special Issue Identification of Human Remains for Forensic and Humanitarian Purposes: From Molecular to Physical Methods)

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15 pages, 3377 KiB

Open AccessReview

Extraction of Innate Immune Genes in Dairy Cattle and the Regulation of Their Expression in Early Embryos

by Xue Wang, Lili Guo and Wenguang Zhang

Genes 2024, 15(3), 372; https://doi.org/10.3390/genes15030372 - 18 Mar 2024

Viewed by 1603

Abstract

As more and more of the available genomic data have been published, several databases have been developed for deciphering early mammalian embryogenesis; however, less research has been conducted on the regulation of the expression of natural immunity genes during early embryonic development in [...] Read more.

As more and more of the available genomic data have been published, several databases have been developed for deciphering early mammalian embryogenesis; however, less research has been conducted on the regulation of the expression of natural immunity genes during early embryonic development in dairy cows. To this end, we explored the regulatory mechanism of innate immunity genes at the whole-genome level. Based on comparative genomics, 1473 innate immunity genes in cattle were obtained by collecting the latest reports on human innate immunity genes and updated bovine genome data for comparison, and a preliminary database of bovine innate immunity genes was constructed. In order to determine the regulatory mechanism of innate immune genes in dairy cattle early embryos, we conducted weighted co-expression network analysis of the innate immune genes at different developmental stages of dairy cattle early embryos. The results showed that specific module-related genes were significantly enriched in the MAPK signaling pathway. Protein–protein interaction (PPI) analysis showed gene interactions in each specific module, and 10 of the highest connectivity genes were chosen as potential hub genes. Finally, combined with the results for differential expressed genes (DEGs), ATF3, IL6, CD8A, CD69, CD86, HCK, ERBB3, LCK, ITGB2, LYN, and ERBB2 were identified as the key genes of innate immunity in dairy cattle early embryos. In conclusion, the bovine innate immunity gene set was determined and the co-expression network of innate immunity genes in the early embryonic stage of dairy cattle was constructed by comparing and analyzing the whole genome of bovines and humans. The findings in this study provide the basis for exploring the involvement and regulation of innate immune genes in the early embryonic development of dairy cattle. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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15 pages, 1627 KiB

Open AccessReview

Karyotype Diversification and Chromosome Rearrangements in Squamate Reptiles

by Marcello Mezzasalma, Rachele Macirella, Gaetano Odierna and Elvira Brunelli

Genes 2024, 15(3), 371; https://doi.org/10.3390/genes15030371 - 18 Mar 2024

Cited by 3 | Viewed by 1878

Abstract

Karyotype diversification represents an important, yet poorly understood, driver of evolution. Squamate reptiles are characterized by a high taxonomic diversity which is reflected at the karyotype level in terms of general structure, chromosome number and morphology, and insurgence of differentiated simple or multiple-sex-chromosome [...] Read more.

Karyotype diversification represents an important, yet poorly understood, driver of evolution. Squamate reptiles are characterized by a high taxonomic diversity which is reflected at the karyotype level in terms of general structure, chromosome number and morphology, and insurgence of differentiated simple or multiple-sex-chromosome systems with either male or female heterogamety. The potential of squamate reptiles as unique model organisms in evolutionary cytogenetics has been recognised in recent years in several studies, which have provided novel insights into the chromosome evolutionary dynamics of different taxonomic groups. Here, we review and summarize the resulting complex, but promising, general picture from a systematic perspective, mapping some of the main squamate karyological characteristics onto their phylogenetic relationships. We highlight how all the major categories of balanced chromosome rearrangements contributed to the karyotype evolution in different taxonomic groups. We show that distinct karyotype evolutionary trends may occur, and coexist, with different frequencies in different clades. Finally, in light of the known squamate chromosome diversity and recent research advances, we discuss traditional and novel hypotheses on karyotype evolution and propose a scenario of circular karyotype evolution. Full article

(This article belongs to the Section Cytogenomics)

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11 pages, 6171 KiB

Open AccessTechnical Note

Enhancing Variant Prioritization in VarFish through On-Premise Computational Facial Analysis

by Meghna Ahuja Bhasin, Alexej Knaus, Pietro Incardona, Alexander Schmid, Manuel Holtgrewe, Miriam Elbracht, Peter M. Krawitz and Tzung-Chien Hsieh

Genes 2024, 15(3), 370; https://doi.org/10.3390/genes15030370 - 17 Mar 2024

Viewed by 1476

Abstract

Genomic variant prioritization is crucial for identifying disease-associated genetic variations. Integrating facial and clinical feature analyses into this process enhances performance. This study demonstrates the integration of facial analysis (GestaltMatcher) and Human Phenotype Ontology analysis (CADA) within VarFish, an open-source variant analysis framework. [...] Read more.

Genomic variant prioritization is crucial for identifying disease-associated genetic variations. Integrating facial and clinical feature analyses into this process enhances performance. This study demonstrates the integration of facial analysis (GestaltMatcher) and Human Phenotype Ontology analysis (CADA) within VarFish, an open-source variant analysis framework. Challenges related to non-open-source components were addressed by providing an open-source version of GestaltMatcher, facilitating on-premise facial analysis to address data privacy concerns. Performance evaluation on 163 patients recruited from a German multi-center study of rare diseases showed PEDIA’s superior accuracy in variant prioritization compared to individual scores. This study highlights the importance of further benchmarking and future integration of advanced facial analysis approaches aligned with ACMG guidelines to enhance variant classification. Full article

(This article belongs to the Special Issue Molecular and Genetic Diagnosis of Rare Diseases)

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15 pages, 1078 KiB

Open AccessArticle

PDE4 Gene Family Variants Are Associated with Response to Apremilast Treatment in Psoriasis

by Kalliopi Liadaki, Efterpi Zafiriou, Themistoklis Giannoulis, Sofia Alexouda, Kleoniki Chaidaki, Polyxeni Gidarokosta, Angeliki-Viktoria Roussaki-Schulze, Sotirios G. Tsiogkas, Athina Daponte, Zissis Mamuris, Dimitrios P. Bogdanos, Nicholas K. Moschonas and Theologia Sarafidou

Genes 2024, 15(3), 369; https://doi.org/10.3390/genes15030369 - 17 Mar 2024

Cited by 1 | Viewed by 2578

Abstract

Moderate-to-severe psoriasis (Ps) treatment includes systemic drugs and biological agents. Apremilast, a small molecule primarily metabolized by cytochrome CYP3A4, modulates the immune system by specifically inhibiting phosphodiesterase type 4 (PDE4) isoforms and is currently used for the treatment of Ps and psoriatic arthritis [...] Read more.

Moderate-to-severe psoriasis (Ps) treatment includes systemic drugs and biological agents. Apremilast, a small molecule primarily metabolized by cytochrome CYP3A4, modulates the immune system by specifically inhibiting phosphodiesterase type 4 (PDE4) isoforms and is currently used for the treatment of Ps and psoriatic arthritis (PsA). Clinical trials and real-world data showed variable efficacy in response among Ps patients underlying the need for personalized therapy. This study implements a candidate-gene and a network-based approach to identify genetic markers associated with apremilast response in forty-nine Greek Ps patients. Our data revealed an association of sixty-four SNPs within or near PDE4 and CYP3A4 genes, four SNPs in ncRNAs ANRIL, LINC00941 and miR4706, which influence the abundance or function of PDE4s, and thirty-three SNPs within fourteen genes whose protein products either interact directly with PDE4 proteins or constitute components of the cAMP signaling pathway which is modulated by PDE4s. Notably, fifty-six of the aforementioned SNPs constitute eQTLs for the respective genes in relevant to psoriasis tissues/cells implying that these variants could be causal. Our analysis provides a number of novel genetic variants that, upon validation in larger cohorts, could be utilized as predictive markers regarding the response of Ps patients to apremilast treatment. Full article

(This article belongs to the Special Issue Feature Papers in Human Genomics and Genetic Diseases 2023)

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14 pages, 10671 KiB

Open AccessArticle

Selection Signatures Reveal Candidate Genes for the Cornish Rex Breed-Specific Phenotype

by Minja Zorc, Tajda Horvat, Anja Tanšek, Tamara Ferme and Peter Dovč

Genes 2024, 15(3), 368; https://doi.org/10.3390/genes15030368 - 16 Mar 2024

Viewed by 2079

Abstract

Many coat color, behavioral and morphological traits are specific and fixed across cat breeds, with several variants influencing these traits being common among different breeds. In the domestic cat, rexoid mutations have been documented in several breeds. In the Cornish Rex, four bp [...] Read more.

Many coat color, behavioral and morphological traits are specific and fixed across cat breeds, with several variants influencing these traits being common among different breeds. In the domestic cat, rexoid mutations have been documented in several breeds. In the Cornish Rex, four bp deletion in the LPAR6 gene has been found to cause a frame shift and a premature stop codon. In addition to the rexoid coat, Cornish Rex cats also have a characteristic head, ear shape and body type. Analysis of the selection signatures in the Cornish Rex genome revealed several regions that are under selective pressure. One of these is located in CFA B4, in the region where the ALX1 gene is located. The ALX1 gene in Burmese cats disrupts the cranial morphogenesis and causes brachycephaly in the heterozygous state. In our study, we confirmed the presence of a deletion in LPAR6 in 20 Cornish Rex and in four F1 hybrids between Cornish Rex and domestic cat. However, we did not confirm the presence of the deletion in ALX1 in Cornish Rex cats. Genome-wide selection signature analysis was performed using ROH islands and integrated haplotype score (iHS) statistics based on publicly available SNP array data of 11 Cornish Rex cats. The selection signatures were detected on chromosomes A1, A3, C2, B1, B4 and D1. Full article

(This article belongs to the Special Issue Companion Animal Genetics and Genomics)

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18 pages, 3434 KiB

Open AccessArticle

Dynamics of Mitochondrial DNA Copy Number and Membrane Potential in Mouse Pre-Implantation Embryos: Responses to Diverse Types of Oxidative Stress

by Yasmyn E. Winstanley, Jun Liu, Deepak Adhikari, Macarena B. Gonzalez, Darryl L. Russell, John Carroll and Rebecca L. Robker

Genes 2024, 15(3), 367; https://doi.org/10.3390/genes15030367 - 16 Mar 2024

Cited by 1 | Viewed by 1976

Abstract

Mitochondria undergo a myriad of changes during pre-implantation embryo development, including shifts in activity levels and mitochondrial DNA (mtDNA) replication. However, how these distinct aspects of mitochondrial function are linked and their responsiveness to diverse stressors is not well understood. Here, we show [...] Read more.

Mitochondria undergo a myriad of changes during pre-implantation embryo development, including shifts in activity levels and mitochondrial DNA (mtDNA) replication. However, how these distinct aspects of mitochondrial function are linked and their responsiveness to diverse stressors is not well understood. Here, we show that mtDNA content increased between 8-cell embryos and the blastocyst stage, with similar copy numbers per cell in the inner cell mass (ICM) and trophectoderm (TE). In contrast, mitochondrial membrane potential (MMP) was higher in TE than ICM. Culture in ambient oxygen (20% O₂) altered both aspects of mitochondrial function: the mtDNA copy number was upregulated in ICM, while MMP was diminished in TE. Embryos cultured in 20% O₂ also exhibited delayed development kinetics, impaired implantation, and reduced mtDNA levels in E18 fetal liver. A model of oocyte mitochondrial stress using rotenone showed only a modest effect on on-time development and did not alter the mtDNA copy number in ICM; however, following embryo transfer, mtDNA was higher in the fetal heart. Lastly, endogenous mitochondrial dysfunction, induced by maternal age and obesity, altered the blastocyst mtDNA copy number, but not within the ICM. These results demonstrate that mitochondrial activity and mtDNA content exhibit cell-specific changes and are differentially responsive to diverse types of oxidative stress during pre-implantation embryogenesis. Full article

(This article belongs to the Special Issue Genetics and Genomics of Female Reproduction)

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19 pages, 3509 KiB

Open AccessArticle

Overexpression of NtGPX8a Improved Cadmium Accumulation and Tolerance in Tobacco (Nicotiana tabacum L.)

by Xiang Peng, Tengfei Ma, Kejin Song, Xue Ji, Lien Xiang, Nan Chen, Ronglei Zu, Wenyi Xu, Shunqin Zhu and Wanhong Liu

Genes 2024, 15(3), 366; https://doi.org/10.3390/genes15030366 - 15 Mar 2024

Cited by 1 | Viewed by 1404

Abstract

Cadmium (Cd)-induced oxidative stress detrimentally affects hyperaccumulator growth, thereby diminishing the efficacy of phytoremediation technology aimed at Cd pollution abatement. In the domain of plant antioxidant mechanisms, the role of glutathione peroxidase (GPX) in conferring Cd tolerance to tobacco (Nicotiana tabacum) [...] Read more.

Cadmium (Cd)-induced oxidative stress detrimentally affects hyperaccumulator growth, thereby diminishing the efficacy of phytoremediation technology aimed at Cd pollution abatement. In the domain of plant antioxidant mechanisms, the role of glutathione peroxidase (GPX) in conferring Cd tolerance to tobacco (Nicotiana tabacum) remained unclear. Our investigation employed genome-wide analysis to identify 14 NtGPX genes in tobacco, revealing their organization into seven subgroups characterized by analogous conserved domain patterns. Notably, qPCR analysis highlighted NtGPX8a as markedly responsive to Cd²⁺ stress. Subsequent exploration through yeast two-hybridization unveiled NtGPX8a’s utilization of thioredoxins AtTrxZ and AtTrxm2 as electron donors, and without interaction with AtTrx5. Introduction of NtGPX8a into Escherichia coli significantly ameliorated Cd-induced adverse effects on bacterial growth. Transgenic tobacco overexpressing NtGPX8a demonstrated significantly augmented activities of GPX, SOD, POD, and CAT under Cd²⁺ stress compared to the wild type (WT). Conversely, these transgenic plants exhibited markedly reduced levels of MDA, H₂O₂, and proline. Intriguingly, the expression of NtGPX8a in both E. coli and transgenic tobacco led to increased Cd accumulation, confirming its dual role in enhancing Cd tolerance and accumulation. Consequently, NtGPX8a emerges as a promising candidate gene for engineering transgenic hyperaccumulators endowed with robust tolerance for Cd-contaminated phytoremediation. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Molecular Genetics and Genomics)

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13 pages, 5456 KiB

Open AccessArticle

Characterization and Functional Analysis of Fads Reveals Δ5 Desaturation Activity during Long-Chain Polyunsaturated Fatty Acid Biosynthesis in Dwarf Surf Clam Mulinia lateralis

by Tianhao Teng, Zhenghua Zheng, Wenqian Jiao, Na Liu, Ao Wang, Mengjiao Liu, Le Xie, Zujing Yang, Jingjie Hu and Zhenmin Bao

Genes 2024, 15(3), 365; https://doi.org/10.3390/genes15030365 - 15 Mar 2024

Viewed by 1822

Abstract

Fatty acid desaturases (Fads), as key enzymes in the biosynthesis of long-chain polyunsaturated fatty acids (LC-PUFAs), catalyze the desaturation between defined carbons of fatty acyl chains and control the degree of unsaturation of fatty acids. In the present study, two Fads genes, designated [...] Read more.

Fatty acid desaturases (Fads), as key enzymes in the biosynthesis of long-chain polyunsaturated fatty acids (LC-PUFAs), catalyze the desaturation between defined carbons of fatty acyl chains and control the degree of unsaturation of fatty acids. In the present study, two Fads genes, designated MulFadsA and MulFadsB, were identified from the genome of the dwarf surf clam Mulinia lateralis (Mollusca, Mactridae), and their spatiotemporal expression was examined. MulFadsA and MulFadsB contained the corresponding conserved functional domains and clustered closely with their respective orthologs from other mollusks. Both genes were expressed in the developmental stages and all tested adult tissues of M. lateralis, with MulFadsA exhibiting significantly higher expression levels in adult tissues than MulFadsB. Subsequently, the effects of dietary microalgae on Fads expressions in the dwarf surf clam were investigated by feeding clams with two types of unialgal diets varying in fatty acid content, i.e., Chlorella pyrenoidosa (Cp) and Platymonas helgolandica (Ph). The results show that the expressions of MulFads were significantly upregulated among adult tissues in the Cp group compared with those in the Ph group. In addition, we observed the desaturation activity of MulFadsA via heterologous expression in yeasts, revealing Δ5 desaturation activity toward PUFA substrates. Taken together, these results provide a novel perspective on M. lateralis LC-PUFA biosynthesis, expanding our understanding of fatty acid synthesis in marine mollusks. Full article

(This article belongs to the Section Animal Genetics and Genomics)

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18 pages, 301 KiB

Open AccessReview

Advancements in Viral Gene Therapy for Gaucher Disease

by Akhil Kulkarni, Tiffany Chen, Ellen Sidransky and Tae-Un Han

Genes 2024, 15(3), 364; https://doi.org/10.3390/genes15030364 - 15 Mar 2024

Cited by 5 | Viewed by 2892

Abstract

Gaucher disease, an autosomal recessively inherited lysosomal storage disorder, results from biallelic mutations in the GBA1 gene resulting in deficient activity of the enzyme glucocerebrosidase. In Gaucher disease, the reduced levels and activity of glucocerebrosidase lead to a disparity in the rates of [...] Read more.

Gaucher disease, an autosomal recessively inherited lysosomal storage disorder, results from biallelic mutations in the GBA1 gene resulting in deficient activity of the enzyme glucocerebrosidase. In Gaucher disease, the reduced levels and activity of glucocerebrosidase lead to a disparity in the rates of formation and breakdown of glucocerebroside and glucosylsphingosine, resulting in the accumulation of these lipid substrates in the lysosome. This gives rise to the development of Gaucher cells, engorged macrophages with a characteristic wrinkled tissue paper appearance. There are both non-neuronopathic (type 1) and neuronopathic (types 2 and 3) forms of Gaucher disease, associated with varying degrees of severity. The visceral and hematologic manifestations of Gaucher disease respond well to both enzyme replacement therapy and substrate reduction therapy. However, these therapies do not improve the neuronopathic manifestations, as they cannot cross the blood–brain barrier. There is now an established precedent for treating lysosomal storage disorders with gene therapy strategies, as many have the potential to cross into the brain. The range of the gene therapies being employed is broad, but this review aimed to discuss the progress, advances, and challenges in developing viral gene therapy as a treatment for Gaucher disease. Full article

(This article belongs to the Special Issue Genetics and Genomics of Inherited Metabolic Diseases)

11 pages, 1325 KiB

Open AccessBrief Report

The Risk Genes for Neuropsychiatric Disorders negr1 and opcml Are Expressed throughout Zebrafish Brain Development

by Judith Habicher, Ilaria Sanvido, Anja Bühler, Samuele Sartori, Giovanni Piccoli and Matthias Carl

Genes 2024, 15(3), 363; https://doi.org/10.3390/genes15030363 - 14 Mar 2024

Viewed by 1881

Abstract

The immunoglobulin LAMP/OBCAM/NTM (IgLON) family of cell adhesion molecules comprises five members known for their involvement in establishing neural circuit connectivity, fine-tuning, and maintenance. Mutations in IgLON genes result in alterations in these processes and can lead to neuropsychiatric disorders. The two IgLON [...] Read more.

The immunoglobulin LAMP/OBCAM/NTM (IgLON) family of cell adhesion molecules comprises five members known for their involvement in establishing neural circuit connectivity, fine-tuning, and maintenance. Mutations in IgLON genes result in alterations in these processes and can lead to neuropsychiatric disorders. The two IgLON family members NEGR1 and OPCML share common links with several of them, such as schizophrenia, autism, and major depressive disorder. However, the onset and the underlying molecular mechanisms have remained largely unresolved, hampering progress in developing therapies. NEGR1 and OPCML are evolutionarily conserved in teleosts like the zebrafish (Danio rerio), which is excellently suited for disease modelling and large-scale screening for disease-ameliorating compounds. To explore the potential applicability of zebrafish for extending our knowledge on NEGR1- and OPCML-linked disorders and to develop new therapeutic strategies, we investigated the spatio-temporal expression of the two genes during early stages of development. negr1 and opcml are expressed maternally and subsequently in partially distinct domains of conserved brain regions. Other areas of expression in zebrafish have not been reported in mammals to date. Our results indicate that NEGR1 and OPCML may play roles in neural circuit development and function at stages earlier than previously anticipated. A detailed functional analysis of the two genes based on our findings could contribute to understanding the mechanistic basis of related psychiatric disorders. Full article

(This article belongs to the Special Issue The Genetic Basis of Mental Disorders)

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14 pages, 3506 KiB

Open AccessArticle

Dissecting the Genetic Diversity of USDA Cowpea Germplasm Collection Using Kompetitive Allele Specific PCR-Single Nucleotide Polymorphism Markers

by Jesse Potts, Vincent N. Michael, Geoffrey Meru, Xingbo Wu and Matthew W. Blair

Genes 2024, 15(3), 362; https://doi.org/10.3390/genes15030362 - 14 Mar 2024

Cited by 2 | Viewed by 1663

Abstract

Cowpea (Vigna unguiculata L. Walp) is an important grain legume crop of the subtropics, particularly in West Africa, where it contributes to the livelihoods of small-scale farmers. Despite being a drought-resilient crop, cowpea production is hampered by insect pests, diseases, parasitic weeds, [...] Read more.

Cowpea (Vigna unguiculata L. Walp) is an important grain legume crop of the subtropics, particularly in West Africa, where it contributes to the livelihoods of small-scale farmers. Despite being a drought-resilient crop, cowpea production is hampered by insect pests, diseases, parasitic weeds, and various abiotic stresses. Genetic improvement can help overcome these limitations, and exploring diverse cowpea genetic resources is crucial for cowpea breeding. This study evaluated the genetic diversity of 361 cowpea accessions from the USDA core collection for the species using 102 Kompetitive Allele Specific PCR (KASP) single nucleotide polymorphism (SNP) markers. A total of 102 KASP-SNP was validated in the germplasm panel, and 72 showed polymorphism across the germplasm panel. The polymorphism information content (PIC) of all SNPs ranged from 0.1 to 0.37, with an average of 0.29, while the mean observed heterozygosity was 0.52. The population structure revealed three distinct populations that clustered into two major groups after phylogenetic analysis. Analysis of molecular variance (AMOVA) indicated greater genetic variation within populations than among populations. Although cowpea generally has a narrow genetic diversity, the accessions used in this study exhibited considerable variation across geographical regions, sub-species, and improvement status. These results indicated that the selected KASP genotyping assay can provide robust and accurate genotyping data for application in the selection and management of cowpea germplasm in breeding programs and genebanks. Full article

(This article belongs to the Special Issue Genetics and Breeding of Legume Crops)

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13 pages, 873 KiB

Open AccessArticle

Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania

by Jemila Deida, Nasserdine Papa Mze, Mamadou Beye, Sidi Mohamed Ahmed, Ahmed El Bara, Mohamed Abdallahi Bollahi, Leonardo Basco, Ali Ould Mohamed Salem Boukhary and Pierre-Edouard Fournier

Genes 2024, 15(3), 361; https://doi.org/10.3390/genes15030361 - 14 Mar 2024

Viewed by 3264

Abstract

The rapid genetic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic has greatly challenged public health authorities worldwide, including in Mauritania. Despite the presence of the virus in Mauritania, only one study described its [...] Read more.

The rapid genetic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic has greatly challenged public health authorities worldwide, including in Mauritania. Despite the presence of the virus in Mauritania, only one study described its genomic variation during the course of the epidemic. The purpose of the present study was to document the genomic pattern of SARS-CoV-2 variants from clinical isolates during the COVID-19 outbreak in Mauritania, from September to November 2021. The whole genomes from 54 SARS-CoV-2 strains detected in nasopharyngeal swabs with a cycle threshold value ≤ 30 were successfully sequenced using next-generation sequencing (NGS) and the Illumina protocol. The mean genome coverage (±standard deviation) was 96.8% (±3.7). The most commonly identified clade was 21J (57.4%), followed by 21D (16.7%), 20A (11.1%), and 20B (9.2%). At the level of lineages, the majority of the samples were Delta variants with the sub-lineage AY.34 (or B.1.617.2.34). Among the 54 SARS-CoV-2 isolates that were successfully sequenced, 33 (61.1%) came from vaccinated individuals, and 21 (38.9%) were from unvaccinated individuals. Several SARS-CoV-2 variants were present in Mauritania between September and November 2021. As Mauritania, like many West African countries, is resource-limited regarding viral genome sequencing facilities, establishment of mutualized sub-regional sequencing platforms will be necessary to ensure continuous monitoring of mutations in viral genomes and track potential reduction in COVID-19 vaccine efficacy, increased transmissibility, and disease severity. Full article

(This article belongs to the Section Viral Genomics)

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