Genes

15 pages, 2158 KB

Open AccessEditor’s ChoiceArticle

Exploring the Potential of Genome-Wide Hybridization Capture Enrichment for Forensic DNA Profiling of Degraded Bones

by Christian Haarkötter, Xavier Roca-Rada, María Saiz, Diana C. Vinueza-Espinosa, Xiomara Gálvez, María Isabel Medina-Lozano, Daniel Díaz-Ruiz, Juan Carlos Álvarez, Bastien Llamas, Jose Antonio Lorente and Jeremy Austin

Genes 2025, 16(1), 23; https://doi.org/10.3390/genes16010023 - 26 Dec 2024

Cited by 3 | Viewed by 2070

Abstract

In many human rights and criminal contexts, skeletal remains are often the only available samples, and they present a significant challenge for forensic DNA profiling due to DNA degradation. Ancient DNA methods, particularly capture hybridization enrichment, have been proposed for dealing with severely [...] Read more.

In many human rights and criminal contexts, skeletal remains are often the only available samples, and they present a significant challenge for forensic DNA profiling due to DNA degradation. Ancient DNA methods, particularly capture hybridization enrichment, have been proposed for dealing with severely degraded bones, given their capacity to yield results in ancient remains. Background/Objectives: This paper aims to test the efficacy of genome-wide capture enrichment on degraded forensic human remains compared to autosomal STRs analysis. Methods: Six highly degraded human bones from the Spanish Civil War (1936–1939) were quantified with Quantifiler^™ Trio and amplified with GlobalFiler^™. Independently, partially UDG-treated double-stranded DNA libraries were generated and shotgun sequenced to screen for endogenous human DNA content. Subsequently, libraries were enriched with the Twist Bioscience “Twist Ancient DNA” reagent enrichment kit, which had not been previously tested for forensic purposes. Results: The results show that the samples behave similarly with both approaches (well-preserved samples yield good results). However, capture enrichment provides some new relevant insights, suggesting that its implementation in current NGS forensic platforms could be beneficial. Conclusions: Shotgun results show that the analyzed samples exhibit the same characteristics as ancient DNA samples in terms of DNA fragmentation and molecular damage, which may enhance the value of this approach when authenticating the endogenous DNA of forensic samples. Full article

(This article belongs to the Special Issue Identification of Human Remains for Forensic and Humanitarian Purposes: From Molecular to Physical Methods, 2nd Edition)

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18 pages, 2505 KB

Open AccessEditor’s ChoiceReview

From Species to Varieties: How Modern Sequencing Technologies Are Shaping Medicinal Plant Identification

by Mingcheng Wang, Haifeng Lin, Hongqiang Lin, Panyue Du and Shuqiao Zhang

Genes 2025, 16(1), 16; https://doi.org/10.3390/genes16010016 - 26 Dec 2024

Cited by 21 | Viewed by 2203

Abstract

Background/Objectives: Modern sequencing technologies have transformed the identification of medicinal plant species and varieties, overcoming the limitations of traditional morphological and chemical approaches. This review explores the key DNA-based techniques, including molecular markers, DNA barcoding, and high-throughput sequencing, and their contributions to enhancing [...] Read more.

Background/Objectives: Modern sequencing technologies have transformed the identification of medicinal plant species and varieties, overcoming the limitations of traditional morphological and chemical approaches. This review explores the key DNA-based techniques, including molecular markers, DNA barcoding, and high-throughput sequencing, and their contributions to enhancing the accuracy and reliability of plant identification. Additionally, the integration of multi-omics approaches is examined to provide a comprehensive understanding of medicinal plant identity. Methods: The literature search for this review was conducted across databases such as Google Scholar, Web of Science, and PubMed, using keywords related to plant taxonomy, genomics, and biotechnology. Inclusion criteria focused on peer-reviewed studies closely related to plant identification methods and techniques that contribute significantly to the field. Results: The review highlights that while sequencing technologies offer substantial improvements, challenges such as high costs, technical expertise, and the lack of standardized protocols remain barriers to widespread adoption. Potential solutions, including AI-driven data analysis and portable sequencers, are discussed. Conclusions: This review provides a comprehensive overview of molecular techniques, their transformative impact, and future perspectives for more accurate and efficient medicinal plant identification. Full article

(This article belongs to the Special Issue Advances in Genetics and Genomics of Plants: 2nd Edition)

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35 pages, 570 KB

Open AccessEditor’s ChoiceReview

Epigenetic Mechanisms in Aging: Extrinsic Factors and Gut Microbiome

by Alejandro Borrego-Ruiz and Juan J. Borrego

Genes 2024, 15(12), 1599; https://doi.org/10.3390/genes15121599 - 14 Dec 2024

Cited by 7 | Viewed by 3683

Abstract

Background/Objectives: Aging is a natural physiological process involving biological and genetic pathways. Growing evidence suggests that alterations in the epigenome during aging result in transcriptional changes, which play a significant role in the onset of age-related diseases, including cancer, cardiovascular disease, diabetes, and [...] Read more.

Background/Objectives: Aging is a natural physiological process involving biological and genetic pathways. Growing evidence suggests that alterations in the epigenome during aging result in transcriptional changes, which play a significant role in the onset of age-related diseases, including cancer, cardiovascular disease, diabetes, and neurodegenerative disorders. For this reason, the epigenetic alterations in aging and age-related diseases have been reviewed, and the major extrinsic factors influencing these epigenetic alterations have been identified. In addition, the role of the gut microbiome and its metabolites as epigenetic modifiers has been addressed. Results: Long-term exposure to extrinsic factors such as air pollution, diet, drug use, environmental chemicals, microbial infections, physical activity, radiation, and stress provoke epigenetic changes in the host through several endocrine and immune pathways, potentially accelerating the aging process. Diverse studies have reported that the gut microbiome plays a critical role in regulating brain cell functions through DNA methylation and histone modifications. The interaction between genes and the gut microbiome serves as a source of adaptive variation, contributing to phenotypic plasticity. However, the molecular mechanisms and signaling pathways driving this process are still not fully understood. Conclusions: Extrinsic factors are potential inducers of epigenetic alterations, which may have important implications for longevity. The gut microbiome serves as an epigenetic effector influencing host gene expression through histone and DNA modifications, while bidirectional interactions with the host and the underexplored roles of microbial metabolites and non-bacterial microorganisms such as fungi and viruses highlight the need for further research. Full article

(This article belongs to the Section Epigenomics)

26 pages, 1476 KB

Open AccessEditor’s ChoiceReview

From Omics to Multi-Omics: A Review of Advantages and Tradeoffs

by C. Nelson Hayes, Hikaru Nakahara, Atsushi Ono, Masataka Tsuge and Shiro Oka

Genes 2024, 15(12), 1551; https://doi.org/10.3390/genes15121551 - 29 Nov 2024

Cited by 17 | Viewed by 7199

Abstract

Bioinformatics is a rapidly evolving field charged with cataloging, disseminating, and analyzing biological data. Bioinformatics started with genomics, but while genomics focuses more narrowly on the genes comprising a genome, bioinformatics now encompasses a much broader range of omics technologies. Overcoming barriers of [...] Read more.

Bioinformatics is a rapidly evolving field charged with cataloging, disseminating, and analyzing biological data. Bioinformatics started with genomics, but while genomics focuses more narrowly on the genes comprising a genome, bioinformatics now encompasses a much broader range of omics technologies. Overcoming barriers of scale and effort that plagued earlier sequencing methods, bioinformatics adopted an ambitious strategy involving high-throughput and highly automated assays. However, as the list of omics technologies continues to grow, the field of bioinformatics has changed in two fundamental ways. Despite enormous success in expanding our understanding of the biological world, the failure of bulk methods to account for biologically important variability among cells of the same or different type has led to a major shift toward single-cell and spatially resolved omics methods, which attempt to disentangle the conflicting signals contained in heterogeneous samples by examining individual cells or cell clusters. The second major shift has been the attempt to integrate two or more different classes of omics data in a single multimodal analysis to identify patterns that bridge biological layers. For example, unraveling the cause of disease may reveal a metabolite deficiency caused by the failure of an enzyme to be phosphorylated because a gene is not expressed due to aberrant methylation as a result of a rare germline variant. Conclusions: There is a fine line between superficial understanding and analysis paralysis, but like a detective novel, multi-omics increasingly provides the clues we need, if only we are able to see them. Full article

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

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12 pages, 1022 KB

Open AccessEditor’s ChoiceArticle

Genome-Wide Association Studies Revealed Several Candidate Genes of Meat Productivity in Saryarka Fat-Tailed Coarse-Wool Sheep Breed

by Kairat Dossybayev, Makpal Amandykova, Ainur Orakbayeva, Sholpan Adylkanova, Altynay Kozhakhmet, Kanagat Yergali, Temirlan Kulboldin, Beibit Kulataev and Aibyn Torekhanov

Genes 2024, 15(12), 1549; https://doi.org/10.3390/genes15121549 - 29 Nov 2024

Cited by 5 | Viewed by 1490

Abstract

Background: Saryarka sheep belong to fat-tailed coarse-wool sheep breed. This breed is distinguished by increased meat productivity while being competitive in young lamb production. Live weight and body indices are relevant data for assessing sheep body constitution, which directly affects the breeding characteristics [...] Read more.

Background: Saryarka sheep belong to fat-tailed coarse-wool sheep breed. This breed is distinguished by increased meat productivity while being competitive in young lamb production. Live weight and body indices are relevant data for assessing sheep body constitution, which directly affects the breeding characteristics and meat productivity of animals. Objectives: This study aimed to find associations with SNPs and nine phenotypic characteristics of the Saryarka fat-tailed coarse-wool sheep breed including live weight and eight body indices (wither height, rump height, bicoastal diameter, body depth, body length, rump width, heart girth, and cannon bone circumference), and find candidate genes related to these characteristics. Methods: A total of 100 animals from the Karaganda region of Kazakhstan were used in this study. Live weight and eight body indices of sheep were measured using tape and electronic scales. The blood samples of the animals were used for DNA extraction. DNA samples were genotyped with the OvineSNP50 Genotyping BeadChip and analyzed using GWAS. Statistically significant SNPs were identified for each characteristic trait referencing the genome of Ovis aries (Oar_v3.1) using BioMart. Results: The GWAS results demonstrated a substantial chromosomal-level correlation between 32 chromosome-wide significant and suggestively significant SNPs in the studied sheep breed. Overall, seven SNPs located in seven different genes were revealed as candidates for live weight and four body indices: s20793.1 SNP in the IGFBP6 gene for live weight, OAR4_54217431.1 SNP in the ST7 gene for bicoastal diameter, s25229.1 in the SCD5 gene, and s01175.1 SNP in the DTNBP1 gene for rump width, OAR2_175574781.1 SNP in the KYNU gene for heart girth, and OAR1_209022621.1 SNP in the FGF12 gene and s15415.1 SNP in the FTO gene for cannon bone circumference. Some of these genes were previously reported to be involved in body constitution and fat deposit in other sheep breeds. Conclusions: The results of the present study open up new opportunities for targeted sheep breeding for meat and fat productivity. Full article

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

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13 pages, 1986 KB

Open AccessEditor’s ChoiceReview

Loss of Heterozygosity (LOH) Affecting HLA Genes in Breast Cancer: Clinical Relevance and Therapeutic Opportunities

by María Antonia Garrido, Alba Navarro-Ocón, Víctor Ronco-Díaz, Nicolás Olea and Natalia Aptsiauri

Genes 2024, 15(12), 1542; https://doi.org/10.3390/genes15121542 - 28 Nov 2024

Cited by 2 | Viewed by 3120

Abstract

Major histocompatibility complex (MHC) class-I molecules (or Human Leucocyte Antigen class-I) play a key role in adaptive immunity against cancer. They present specific tumor neoantigens to cytotoxic T cells and provoke an antitumor cytotoxic response. The total or partial loss of HLA molecules [...] Read more.

Major histocompatibility complex (MHC) class-I molecules (or Human Leucocyte Antigen class-I) play a key role in adaptive immunity against cancer. They present specific tumor neoantigens to cytotoxic T cells and provoke an antitumor cytotoxic response. The total or partial loss of HLA molecules can inhibit the immune system’s ability to detect and destroy cancer cells. Loss of heterozygosity (LOH) is a common irreversible genetic alteration that occurs in the great majority of human tumors, including breast cancer. LOH at chromosome 6, which involves HLA genes (LOH-HLA), leads to the loss of an HLA haplotype and is linked to cancer progression and a weak response to cancer immunotherapy. Therefore, the loss of genes or an entire chromosomal region which are critical for antigen presentation is of particular importance in the search for novel prognostic and clinical biomarkers in breast cancer. Here, we review the role of LOH-HLA in breast cancer, its contribution to an understanding of cancer immune escape and tumor progression, and discuss how it can be targeted in cancer therapy. Full article

(This article belongs to the Special Issue Genetic and Genomic Abnormalities in Cancer)

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27 pages, 16059 KB

Open AccessEditor’s ChoiceReview

Advances in Understanding Drought Stress Responses in Rice: Molecular Mechanisms of ABA Signaling and Breeding Prospects

by Yingying Ma, Mingyue Tang, Mingyang Wang, Yanchun Yu and Banpu Ruan

Genes 2024, 15(12), 1529; https://doi.org/10.3390/genes15121529 - 27 Nov 2024

Cited by 6 | Viewed by 3200

Abstract

Drought stress is a pivotal environmental factor impacting rice production and presents a significant challenge to sustainable agriculture worldwide. This review synthesizes the latest research advancements in the regulatory mechanisms and signaling pathways that rice employs in response to drought stress. It elaborates [...] Read more.

Drought stress is a pivotal environmental factor impacting rice production and presents a significant challenge to sustainable agriculture worldwide. This review synthesizes the latest research advancements in the regulatory mechanisms and signaling pathways that rice employs in response to drought stress. It elaborates on the adaptive changes and molecular regulatory mechanisms that occur in rice under drought conditions. The review highlights the perception and initial transmission of drought signals, key downstream signaling networks such as the MAPK and Ca²⁺ pathways, and their roles in modulating drought responses. Furthermore, the discussion extends to hormonal signaling, especially the crucial role of abscisic acid (ABA) in drought responses, alongside the identification of drought-resistant genes and the application of gene-editing technologies in enhancing rice drought resilience. Through an in-depth analysis of these drought stress regulatory signaling pathways, this review aims to offer valuable insights and guidance for future rice drought resistance breeding and agricultural production initiatives. Full article

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

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10 pages, 893 KB

Open AccessEditor’s ChoiceArticle

MIR27A rs895819 CC Genotype Severely Reduces miR-27a Plasma Expression Levels

by Georgia Ragia, Myria Pallikarou, Chrysoula Michou and Vangelis G. Manolopoulos

Genes 2024, 15(11), 1491; https://doi.org/10.3390/genes15111491 - 20 Nov 2024

Cited by 2 | Viewed by 1130

Abstract

Background/Objectives: MIR27A rs895819 polymorphism has emerged as a potential additional pharmacogenomic marker of fluoropyrimidine response. Current evidence on its potential effect on miR-27a expression, which represses DPD activity, leading to DPD deficiency and increased fluoropyrimidine-associated toxicity risk, is scarce and inconsistent. We [...] Read more.

Background/Objectives: MIR27A rs895819 polymorphism has emerged as a potential additional pharmacogenomic marker of fluoropyrimidine response. Current evidence on its potential effect on miR-27a expression, which represses DPD activity, leading to DPD deficiency and increased fluoropyrimidine-associated toxicity risk, is scarce and inconsistent. We have analyzed the effect of MIR27A rs895819 polymorphism on miR-27a-3p plasma expression levels under different models of inheritance to contribute further evidence on its plausible biological role in miR-27a expression. Methods: A total of 59 individuals with no medical history of cancer were included in this study. MIR27A rs895819 genotyping and miR-27a-3p expression were analyzed by using predesigned TaqMan assays. Results: The frequency of TT, TC, and CC genotypes was present at a prevalence of 50.8%, 44.1%, and 5.1%, respectively. Individuals carrying the CC genotype presented with decreased miR-27a-3p expression (0.422 fold-change versus TT, p = 0.041; 0.461 fold-change versus TC, p = 0.064), whereas no differences were present between TT and TC individuals (1.092 fold-change, p = 0.718). miR-27a-3p expression was decreased in CC individuals under a recessive model of inheritance (0.440 fold-change, p = 0.047). No differences were found in dominant (TT vs. TC+CC, 0.845 fold-change, p = 0.471) or over dominant (TT+CC vs. TC, 0.990 fold-change, p = 0.996) models of inheritance. Conclusions: MIR27A rs895819CC genotype leads to severely reduced miR-27a-3p expression in plasma. Further study of this association is warranted in cancer patients to apply MIR27A genotyping in therapeutics to identify fluoropyrimidine-treated patients who are at a decreased risk of experiencing fluoropyrimidine-induced severe toxicity. Full article

(This article belongs to the Special Issue MicroRNA in Cancers)

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17 pages, 5992 KB

Open AccessEditor’s ChoiceArticle

Characterization of HSP70 and HSP90 Gene Family in Takifugu fasciatus and Their Expression Profiles on Biotic and Abiotic Stresses Response

by Wenwen Zhang, Ziang Qian, Jie Ji, Tao Wang, Shaowu Yin and Kai Zhang

Genes 2024, 15(11), 1445; https://doi.org/10.3390/genes15111445 - 8 Nov 2024

Cited by 6 | Viewed by 1643

Abstract

Background: Heat shock proteins (HSPs) play crucial roles in response to temperature changes and biotic stresses. However, the HSP gene family in the pufferfish (Takifugu fasciatus) herring has not been comprehensively investigated. Methods and Results: This study presents a systematic analysis [...] Read more.

Background: Heat shock proteins (HSPs) play crucial roles in response to temperature changes and biotic stresses. However, the HSP gene family in the pufferfish (Takifugu fasciatus) herring has not been comprehensively investigated. Methods and Results: This study presents a systematic analysis of the HSP70 and HSP90 gene families in T. fasciatus, focusing on gene characterization, conserved structural domains, molecular evolutionary history, and expression patterns of the HSP gene family under stress conditions. The findings reveal that 16 HSP genes are evolutionarily conserved, while hspa4 and hsp90aa appear specific to teleost fish. HSP genes exhibit widespread expression across 11 examined tissues, with most demonstrating high expression levels in the heart, brain, and liver. Furthermore, T. fasciatus was subjected to cryogenic and biotic stresses, revealing distinct expression patterns of HSPs under various stress conditions. The response of HSPs to cold stress and Aeromonas hydrophila infection was sustained. In contrast, gene expression of HSPs significantly changed only in the pre-infection period following Ichthyophthirius multifiliis infection, gradually returning to normal levels in the later stages. Conclusions: These experimental results provide a foundation for further in-depth investigations into the characteristics and functions of HSPs in T. fasciatus. Full article

(This article belongs to the Special Issue Genetics and Molecular Breeding in Fisheries and Aquaculture)

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24 pages, 1393 KB

Open AccessEditor’s ChoiceReview

The Role of Female and Male Genes in Regulating Pollen Tube Guidance in Flowering Plants

by Siyuan Zheng, Feng Wang, Zehui Liu, Hongbin Zhang, Liangsheng Zhang and Dan Chen

Genes 2024, 15(11), 1367; https://doi.org/10.3390/genes15111367 - 24 Oct 2024

Cited by 3 | Viewed by 2997

Abstract

In flowering plants, fertilization is a complex process governed by precise communication between the male and female gametophytes. This review focuses on the roles of various female gametophyte cells—synergid, central, and egg cells—in facilitating pollen tube guidance and ensuring successful fertilization. Synergid cells [...] Read more.

In flowering plants, fertilization is a complex process governed by precise communication between the male and female gametophytes. This review focuses on the roles of various female gametophyte cells—synergid, central, and egg cells—in facilitating pollen tube guidance and ensuring successful fertilization. Synergid cells play a crucial role in attracting the pollen tube, while the central cell influences the direction of pollen tube growth, and the egg cell is responsible for preventing polyspermy, ensuring correct fertilization. The review also examines the role of the pollen tube in this communication, highlighting the mechanisms involved in its growth regulation, including the importance of pollen tube receptors, signal transduction pathways, cell wall dynamics, and ion homeostasis. The Ca²⁺ concentration gradient is identified as a key factor in guiding pollen tube growth toward the ovule. Moreover, the review briefly compares these communication processes in angiosperms with those in non-flowering plants, such as mosses, ferns, and early gymnosperms, providing evolutionary insights into gametophytic signaling. Overall, this review synthesizes the current understanding of male–female gametophyte interactions and outlines future directions for research in plant reproductive biology. Full article

(This article belongs to the Special Issue Genetics and Genomics in Horticultural Plants)

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13 pages, 7132 KB

Open AccessEditor’s ChoiceArticle

Molecular Characterization of Peroxidase (PRX) Gene Family in Cucumber

by Weirong Luo, Junjun Liu, Wenchen Xu, Shenshen Zhi, Xudong Wang and Yongdong Sun

Genes 2024, 15(10), 1245; https://doi.org/10.3390/genes15101245 - 25 Sep 2024

Cited by 2 | Viewed by 1298

Abstract

Background: The Peroxidase (PRX) gene family is essential for plant growth and significantly contributes to defense against stresses. However, information about PRX genes in cucumber (Cucumis sativus L.) remains limited. Methods: In this present study, CsPRX genes were [...] Read more.

Background: The Peroxidase (PRX) gene family is essential for plant growth and significantly contributes to defense against stresses. However, information about PRX genes in cucumber (Cucumis sativus L.) remains limited. Methods: In this present study, CsPRX genes were identified and characterized using bioinformatics analysis. The expression pattern analysis of CsPRX genes were examined utilizing the RNA-seq data of cucumber from public databases and real-time quantitative PCR (qRT-PCR) analysis. Results: Here, we identified 60 CsPRX genes and mapped them onto seven chromosomes of cucumber. The CsPRX proteins exhibited the presence of 10 conserved motifs, with motif 8, motif 2, motif 5, and motif 3 consistently appearing across all 60 CsPRX protein sequences, indicating the conservation of CsPRX proteins. Furthermore, RNA-seq analysis revealed that differential expression of CsPRX genes in various tissues. Notably, a majority of the CsPRX genes exhibited significantly higher expression levels in the root compared to the other plant tissues, suggesting a potential specialization of these genes in root function. In addition, qRT-PCR analysis for four selected CsPRX genes under different stress conditions indicated that these selected CsPRX genes demonstrated diverse expression levels when subjected to NaCl, CdCl₂, and PEG treatments, and the CsPRX17 gene was significantly induced by NaCl, CdCl₂, and PEG stresses, suggesting a vital role of the CsPRX17 gene in response to environmental stresses. Conclusions: These findings will contribute valuable insights for future research into the functions and regulatory mechanisms associated with CsPRX genes in cucumber. Full article

(This article belongs to the Special Issue Molecular Biology of Crop Abiotic Stress Resistance)

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32 pages, 4213 KB

Open AccessEditor’s ChoiceReview

The Past, Present, and Future of Plant Activators Targeting the Salicylic Acid Signaling Pathway

by Misbah Naz, Dongqin Zhang, Kangcen Liao, Xulong Chen, Nazeer Ahmed, Delu Wang, Jingjiang Zhou and Zhuo Chen

Genes 2024, 15(9), 1237; https://doi.org/10.3390/genes15091237 - 23 Sep 2024

Cited by 8 | Viewed by 4072

Abstract

Plant activators have emerged as promising alternatives to conventional crop protection chemicals for managing crop diseases due to their unique mode of action. By priming the plant’s innate immune system, these compounds can induce disease resistance against a broad spectrum of pathogens without [...] Read more.

Plant activators have emerged as promising alternatives to conventional crop protection chemicals for managing crop diseases due to their unique mode of action. By priming the plant’s innate immune system, these compounds can induce disease resistance against a broad spectrum of pathogens without directly inhibiting their proliferation. Key advantages of plant activators include prolonged defense activity, lower effective dosages, and negligible risk of pathogen resistance development. Among the various defensive pathways targeted, the salicylic acid (SA) signaling cascade has been extensively explored, leading to the successful development of commercial activators of systemic acquired resistance, such as benzothiadiazole, for widespread application in crop protection. While the action sites of many SA-targeting activators have been preliminarily mapped to different steps along the pathway, a comprehensive understanding of their precise mechanisms remains elusive. This review provides a historical perspective on plant activator development and outlines diverse screening strategies employed, from whole-plant bioassays to molecular and transgenic approaches. We elaborate on the various components, biological significance, and regulatory circuits governing the SA pathway while critically examining the structural features, bioactivities, and proposed modes of action of classical activators such as benzothiadiazole derivatives, salicylic acid analogs, and other small molecules. Insights from field trials assessing the practical applicability of such activators are also discussed. Furthermore, we highlight the current status, challenges, and future prospects in the realm of SA-targeting activator development globally, with a focus on recent endeavors in China. Collectively, this comprehensive review aims to describe existing knowledge and provide a roadmap for future research toward developing more potent plant activators that enhance crop health. Full article

(This article belongs to the Special Issue Genetic Insights into Plant-Pathogen Interactions)

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11 pages, 1540 KB

Open AccessEditor’s ChoiceReview

The Desmoplakin Phenotype Spectrum: Is the Inflammation the “Fil Rouge” Linking Myocarditis, Arrhythmogenic Cardiomyopathy, and Uncommon Autoinflammatory Systemic Disease?

by Saverio D’Elia, Adriano Caputo, Francesco Natale, Enrica Pezzullo, Giuseppe Limongelli, Paolo Golino, Giovanni Cimmino and Francesco S. Loffredo

Genes 2024, 15(9), 1234; https://doi.org/10.3390/genes15091234 - 22 Sep 2024

Cited by 3 | Viewed by 2997

Abstract

Myocarditis is an inflammatory condition of cardiac tissue presenting significant variability in clinical manifestations and outcomes. Its etiology is diverse, encompassing infectious agents (primarily viruses, but also bacteria, protozoa, and helminths) and non-infectious factors (autoimmune responses, toxins, and drugs), though often the specific [...] Read more.

Myocarditis is an inflammatory condition of cardiac tissue presenting significant variability in clinical manifestations and outcomes. Its etiology is diverse, encompassing infectious agents (primarily viruses, but also bacteria, protozoa, and helminths) and non-infectious factors (autoimmune responses, toxins, and drugs), though often the specific cause remains unidentified. Recent research has highlighted the potential role of genetic susceptibility in the development of myocarditis (and in some cases the development of inflammatory dilated cardiomyopathy, i.e., the condition in which there is chronic inflammation (>3 months) and left ventricular dysfunction\dilatation), with several studies indicating a correlation between myocarditis and genetic backgrounds. Notably, pathogenic genetic variants linked to dilated or arrhythmic cardiomyopathy are found in 8–16% of myocarditis patients. Genetic predispositions can lead to recurrent myocarditis and a higher incidence of ventricular arrhythmias and heart failure. Moreover, the presence of DSP mutations has been associated with distinct pathological patterns and clinical outcomes in arrhythmogenic cardiomyopathy (hot phases). The interplay between genetic factors and environmental triggers, such as viral infections and physical stress, is crucial in understanding the pathogenesis of myocarditis. Identifying these genetic markers can improve the diagnosis, risk stratification, and management of patients with myocarditis, potentially guiding tailored therapeutic interventions. This review aims to synthesize current knowledge on the genetic underpinnings of myocarditis, with an emphasis on desmoplakin-related arrhythmogenic cardiomyopathy, to enhance clinical understanding and inform future research directions. Full article

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

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17 pages, 9424 KB

Open AccessEditor’s ChoiceArticle

Flavonoid Synthesis Pathway Response to Low-Temperature Stress in a Desert Medicinal Plant, Agriophyllum Squarrosum (Sandrice)

by Pengshu Zhao, Xia Yan, Chaoju Qian, Guorong Ma, Xingke Fan, Xiaoyue Yin, Yuqiu Liao, Tingzhou Fang, Shanshan Zhou, Ibrahim Awuku and Xiao-Fei Ma

Genes 2024, 15(9), 1228; https://doi.org/10.3390/genes15091228 - 20 Sep 2024

Cited by 9 | Viewed by 1923

Abstract

Background/Objectives: Agriophyllum squarrosum (L.) Moq. (A. squarrosum), also known as sandrice, is an important medicinal plant widely distributed in dunes across all the deserts of China. Common garden trials have shown content variations in flavonoids among the ecotypes of sandrice, [...] Read more.

Background/Objectives: Agriophyllum squarrosum (L.) Moq. (A. squarrosum), also known as sandrice, is an important medicinal plant widely distributed in dunes across all the deserts of China. Common garden trials have shown content variations in flavonoids among the ecotypes of sandrice, which correlated with temperature heterogeneity in situ. However, there have not been any environmental control experiments to further elucidate whether the accumulation of flavonoids was triggered by cold stress; Methods: This study conducted a four-day ambient 4 °C low-temperature treatment on three ecotypes along with an in situ annual mean temperature gradient (Dulan (DL), Aerxiang (AEX), and Dengkou (DK)); Results: Target metabolomics showed that 12 out of 14 flavonoids in sandrice were driven by cold stress. Among them, several flavonoids were significantly up-regulated, such as naringenin and naringenin chalcone in all three ecotypes; isorhamnetin, quercetin, dihydroquercetin, and kaempferol in DL and AEX; and astragalin in DK. They were accompanied by 19 structural genes of flavonoid synthesis and 33 transcription factors were markedly triggered by cold stress in sandrice. The upstream genes, AsqAEX006535−CHS, AsqAEX016074−C4H, and AsqAEX004011−4CL, were highly correlated with the enrichment of naringenin, which could be fine-tuned by AsqAEX015868−bHLH62, AsqAEX001711−MYB12, and AsqAEX002220−MYB1R1; Conclusions: This study sheds light on how desert plants like sandrice adapt to cold stress by relying on a unique flavonoid biosynthesis mechanism that regulating the accumulation of naringenin. It also supports the precise development of sandrice for the medicinal industry. Specifically, quercetin and isorhamnetin should be targeted for development in DL and AEX, while astragalin should be precisely developed in DK. Full article

(This article belongs to the Special Issue Molecular Genetics and Multi-omics in Medicinal Plants)

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16 pages, 1402 KB

Open AccessEditor’s ChoiceReview

Research Progress on miRNAs and Artificial miRNAs in Insect and Disease Resistance and Breeding in Plants

by Zengfeng Ma, Jianyu Wang and Changyan Li

Genes 2024, 15(9), 1200; https://doi.org/10.3390/genes15091200 - 12 Sep 2024

Cited by 9 | Viewed by 2686

Abstract

MicroRNAs (miRNAs) are small, non-coding RNAs that are expressed in a tissue- and temporal-specific manner during development. They have been found to be highly conserved during the evolution of different species. miRNAs regulate the expression of several genes in various organisms, with some [...] Read more.

MicroRNAs (miRNAs) are small, non-coding RNAs that are expressed in a tissue- and temporal-specific manner during development. They have been found to be highly conserved during the evolution of different species. miRNAs regulate the expression of several genes in various organisms, with some regulating the expression of multiple genes with similar or completely unrelated functions. Frequent disease and insect pest infestations severely limit agricultural development. Thus, cultivating resistant crops via miRNA-directed gene regulation in plants, insects, and pathogens is an important aspect of modern breeding practices. To strengthen the application of miRNAs in sustainable agriculture, plant endogenous or exogenous miRNAs have been used for plant breeding. Consequently, the development of biological pesticides based on miRNAs has become an important avenue for future pest control methods. However, selecting the appropriate miRNA according to the desired target traits in the target organism is key to successfully using this technology for pest control. This review summarizes the progress in research on miRNAs in plants and other species involved in regulating plant disease and pest resistance pathways. We also discuss the molecular mechanisms of relevant target genes to provide new ideas for future research on pest and disease resistance and breeding in plants. Full article

(This article belongs to the Special Issue Plant Small RNAs: Biogenesis and Functions)

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12 pages, 491 KB

Open AccessEditor’s ChoiceArticle

DTVF: A User-Friendly Tool for Virulence Factor Prediction Based on ProtT5 and Deep Transfer Learning Models

by Jiawei Sun, Hongbo Yin, Chenxiao Ju, Yongheng Wang and Zhiyuan Yang

Genes 2024, 15(9), 1170; https://doi.org/10.3390/genes15091170 - 5 Sep 2024

Cited by 3 | Viewed by 2260

Abstract

Virulencefactors (VFs) are key molecules that enable pathogens to evade the immune systems of the host. These factors are crucial for revealing the pathogenic processes of microbes and drug discovery. Identification of virulence factors in microbes become an important problem in the field [...] Read more.

Virulencefactors (VFs) are key molecules that enable pathogens to evade the immune systems of the host. These factors are crucial for revealing the pathogenic processes of microbes and drug discovery. Identification of virulence factors in microbes become an important problem in the field of bioinformatics. To address this problem, this study proposes a novel model DTVF (Deep Transfer Learning for Virulence Factor Prediction), which integrates the ProtT5 protein sequence extraction model with a dual-channel deep learning model. In the dual-channel deep learning model, we innovatively integrate long short-term memory (LSTM) with convolutional neural networks (CNNs), creating a novel integrated architecture. Furthermore, by incorporating the attention mechanism, the accuracy of VF detection was significantly enhanced. We evaluated the DTVF model against other excellent-performing models in the field. DTVF demonstrates superior performance, achieving an accuracy rate of 84.55% and an AUROC of 92.08% on the benchmark dataset. DTVF shows state-of-the-art performance in this field, surpassing the existing models in nearly all metrics. To facilitate the use of biologists, we have also developed an interactive web-based user interface version of DTVF based on Gradio. Full article

(This article belongs to the Section Bioinformatics)

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11 pages, 433 KB

Open AccessEditor’s ChoiceArticle

Feeding and Nutritional Key Features of Crisponi/Cold-Induced Sweating Syndrome

by Roberta Onesimo, Elisabetta Sforza, Federica Palermo, Valentina Giorgio, Chiara Leoni, Donato Rigante, Valentina Trevisan, Cristiana Agazzi, Domenico Limongelli, Francesco Proli, Eliza Maria Kuczynska, Laura Crisponi, Giangiorgio Crisponi and Giuseppe Zampino

Genes 2024, 15(9), 1109; https://doi.org/10.3390/genes15091109 - 23 Aug 2024

Cited by 2 | Viewed by 1662

Abstract

Feeding difficulties are constantly present in patients with Crisponi/cold-induced sweating syndrome type 1 (CS/CISS1). The aim of our study was to describe their prevalence and evolution from birth to adult age. We performed an observational study at the Department of Life Sciences and [...] Read more.

Feeding difficulties are constantly present in patients with Crisponi/cold-induced sweating syndrome type 1 (CS/CISS1). The aim of our study was to describe their prevalence and evolution from birth to adult age. We performed an observational study at the Department of Life Sciences and Public Health, Rome. Fourteen patients were included in this study (six M; mean age: 18 years; SD: 10.62 years; median age: 15 years; age range: 6–44 years); six were adults (43%). Data on oral motor abilities from birth were collected. Meal duration, presence of swallowing reflex, dysphagia symptoms, difficulty chewing, and drooling management were assessed. At birth, all patients needed enteral feeding. Introduction of solid food was postponed beyond the age of 18 months in 43% of patients. During childhood and adolescence, mealtime was characterized by increased duration (43%) accompanied by fatigue during chewing (43%), food spillage from the nasal cavities (21%), sialorrhea (86%), and poor/reduced appetite (57%). A mature rotatory chewing skill was never achieved. This report expands the phenotype description of CS/CISS1 and also improves the overall management and prevention of complications in this ultra-rare disease. Full article

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

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20 pages, 28009 KB

Open AccessEditor’s ChoiceArticle

Integration of Bioinformatics and Machine Learning to Identify CD8+ T Cell-Related Prognostic Signature to Predict Clinical Outcomes and Treatment Response in Breast Cancer Patients

by Baoai Wu, Longpeng Li, Longhui Li, Yinghua Chen, Yue Guan and Jinfeng Zhao

Genes 2024, 15(8), 1093; https://doi.org/10.3390/genes15081093 - 19 Aug 2024

Cited by 2 | Viewed by 2311

Abstract

The incidence of breast cancer (BC) continues to rise steadily, posing a significant burden on the public health systems of various countries worldwide. As a member of the tumor microenvironment (TME), CD8+ T cells inhibit cancer progression through their protective role. This study [...] Read more.

The incidence of breast cancer (BC) continues to rise steadily, posing a significant burden on the public health systems of various countries worldwide. As a member of the tumor microenvironment (TME), CD8+ T cells inhibit cancer progression through their protective role. This study aims to investigate the role of CD8+ T cell-related genes (CTRGs) in breast cancer patients. Methods: We assessed the abundance of CD8+ T cells in the TCGA and METABRIC datasets and obtained CTRGs through WGCNA. Subsequently, a prognostic signature (CTR score) was constructed from CTRGs screened by seven machine learning algorithms, and the relationship between the CTR score and TME, immunotherapy, and drug sensitivity was analyzed. Additionally, CTRGs’ expression in different cells within TME was identified through single-cell analysis and spatial transcriptomics. Finally, the expression of CTRGs in clinical tissues was verified via RT-PCR. Results: The CD8+ T cell-related prognostic signature consists of two CTRGs. In the TCGA and METABRIC datasets, the CTR score appeared to be negatively linked to the abundance of CD8+ T cells, and BC patients with higher risk score show a worse prognosis. The low CTR score group exhibits higher immune infiltration levels, closely associated with inhibiting the tumor microenvironment. Compared with the high CTR score group, the low CTR score group shows better responses to chemotherapy and immune checkpoint therapy. Single-cell analysis and spatial transcriptomics reveal the heterogeneity of two CTRGs in different cells. Compared with the adjacent tissues, CD163L1 and KLRB1 mRNA are downregulated in tumor tissues. Conclusions: This study establishes a robust CD8+ T cell-related prognostic signature, providing new insights for predicting the clinical outcomes and treatment responses of breast cancer patients. Full article

(This article belongs to the Section Bioinformatics)

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23 pages, 1609 KB

Open AccessEditor’s ChoiceReview

A Comprehensive Review of Bioinformatics Tools for Genomic Biomarker Discovery Driving Precision Oncology

by Alexis J. Clark and James W. Lillard, Jr.

Genes 2024, 15(8), 1036; https://doi.org/10.3390/genes15081036 - 6 Aug 2024

Cited by 26 | Viewed by 13632

Abstract

The rapid advancement of high-throughput technologies, particularly next-generation sequencing (NGS), has revolutionized cancer research by enabling the investigation of genetic variations such as SNPs, copy number variations, gene expression, and protein levels. These technologies have elevated the significance of precision oncology, creating a [...] Read more.

The rapid advancement of high-throughput technologies, particularly next-generation sequencing (NGS), has revolutionized cancer research by enabling the investigation of genetic variations such as SNPs, copy number variations, gene expression, and protein levels. These technologies have elevated the significance of precision oncology, creating a demand for biomarker identification and validation. This review explores the complex interplay of oncology, cancer biology, and bioinformatics tools, highlighting the challenges in statistical learning, experimental validation, data processing, and quality control that underpin this transformative field. This review outlines the methodologies and applications of bioinformatics tools in cancer genomics research, encompassing tools for data structuring, pathway analysis, network analysis, tools for analyzing biomarker signatures, somatic variant interpretation, genomic data analysis, and visualization tools. Open-source tools and repositories like The Cancer Genome Atlas (TCGA), Genomic Data Commons (GDC), cBioPortal, UCSC Genome Browser, Array Express, and Gene Expression Omnibus (GEO) have emerged to streamline cancer omics data analysis. Bioinformatics has significantly impacted cancer research, uncovering novel biomarkers, driver mutations, oncogenic pathways, and therapeutic targets. Integrating multi-omics data, network analysis, and advanced ML will be pivotal in future biomarker discovery and patient prognosis prediction. Full article

(This article belongs to the Special Issue Bioinformatics and Computational Biology for Cancer Prediction and Prognosis)

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14 pages, 4279 KB

Open AccessEditor’s ChoiceArticle

A Comprehensive Systematic Review Coupled with an Interacting Network Analysis Identified Candidate Genes and Biological Pathways Related to Bovine Temperament

by Gilberto Ruiz-De-La-Cruz, Thomas H. Welsh, Jr., Ronald D. Randel and Ana María Sifuentes-Rincón

Genes 2024, 15(8), 981; https://doi.org/10.3390/genes15080981 - 25 Jul 2024

Cited by 2 | Viewed by 1642

Abstract

Comprehension of the genetic basis of temperament has been improved by recent advances in the identification of genes and genetic variants. However, due to the complexity of the temperament traits, the elucidation of the genetic architecture of temperament is incomplete. A systematic review [...] Read more.

Comprehension of the genetic basis of temperament has been improved by recent advances in the identification of genes and genetic variants. However, due to the complexity of the temperament traits, the elucidation of the genetic architecture of temperament is incomplete. A systematic review was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement to analyze candidate genes related to bovine temperament, using bovine as the population, SNPs and genes as the exposure, and temperament test as the outcome, as principal search terms for population, exposure, and outcome (PEO) categories to define the scope of the search. The search results allowed the selection of 36 articles after removing duplicates and filtering by relevance. One hundred-two candidate genes associated with temperament traits were identified. The genes were further analyzed to construct an interaction network using the STRING database, resulting in 113 nodes and 346 interactions and the identification of 31 new candidate genes for temperament. Notably, the main genes identified were SST and members of the Kelch family. The candidate genes displayed interactions with pathways associated with different functions such as AMPA receptors, hormones, neuronal maintenance, protein signaling, neuronal regulation, serotonin synthesis, splicing, and ubiquitination activities. These new findings demonstrate the complexity of interconnected biological processes that regulate behavior and stress response in mammals. This insight now enables our targeted analysis of these newly identified temperament candidate genes in bovines. Full article

(This article belongs to the Special Issue Advances in Cattle, Sheep, and Goats Molecular Genetics and Breeding)

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11 pages, 5149 KB

Open AccessEditor’s ChoiceArticle

The Role of IRF9 Upregulation in Modulating Sensitivity to Olaparib and Platinum-Based Chemotherapies in Breast Cancer

by SeokGyeong Choi, Han-Gyu Bae, Dong-Gyu Jo and Woo-Young Kim

Genes 2024, 15(7), 959; https://doi.org/10.3390/genes15070959 - 22 Jul 2024

Cited by 3 | Viewed by 2349

Abstract

Poly(ADP-ribose) polymerase (PARP) inhibitors are targeted therapies that accumulate DNA damage by interfering with DNA repair mechanisms and are approved for treating several cancers with BRCA1/2 mutations. In this study, we utilized CRISPR-dCas9 interference screening to identify genes regulating sensitivity to PARP inhibitors [...] Read more.

Poly(ADP-ribose) polymerase (PARP) inhibitors are targeted therapies that accumulate DNA damage by interfering with DNA repair mechanisms and are approved for treating several cancers with BRCA1/2 mutations. In this study, we utilized CRISPR-dCas9 interference screening to identify genes regulating sensitivity to PARP inhibitors in breast cancer cell lines. Our findings indicated that the interferon (IFN) signaling gene IRF9 was critically involved in modulating sensitivity to these inhibitors. We revealed that the loss of IRF9 leads to increased resistance to the PARP inhibitor in MDA-MB-468 cells, and a similar desensitization was observed in another breast cancer cell line, MDA-MB-231. Further analysis indicated that while the basal expression of IRF9 did not correlate with the response to the PARP inhibitor olaparib, its transcriptional induction was significantly associated with increased sensitivity to the DNA-damaging agent cisplatin in the NCI-60 cell line panel. This finding suggests a mechanistic link between IRF9 induction and cellular responses to DNA damage. Additionally, data from the METABRIC patient tissue study revealed a complex network of IFN-responsive gene expressions postchemotherapy, with seven upregulated genes, including IRF9, and three downregulated genes. These findings underscore the intricate role of IFN signaling in the cellular response to chemotherapy. Collectively, our CRISPR screening data and subsequent bioinformatic analyses suggest that IRF9 is a novel biomarker for sensitivity to DNA-damaging agents, such as olaparib and platinum-based chemotherapeutic agents. Our findings for IRF9 not only enhance our understanding of the genetic basis of drug sensitivity, but also elucidate the role of IRF9 as a critical effector within IFN signaling pathways, potentially influencing the association between the host immune system and chemotherapeutic efficacy. Full article

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

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10 pages, 2029 KB

Open AccessEditor’s ChoiceArticle

Genetic Variations of MSTN and Callipyge in Tibetan Sheep: Implications for Early Growth Traits

by Kai Zhao, Xue Li, Dehui Liu, Lei Wang, Quanbang Pei, Buying Han, Zian Zhang, Dehong Tian, Song Wang, Jincai Zhao, Bin Huang and Fuqiang Zhang

Genes 2024, 15(7), 921; https://doi.org/10.3390/genes15070921 - 15 Jul 2024

Cited by 3 | Viewed by 1474

Abstract

Tibetan sheep are vital to the ecosystem and livelihood of the Tibetan Plateau; however, traditional breeding methods limit their production and growth. Modern molecular breeding techniques are required to improve these traits. This study identified a single nucleotide polymorphism (SNP) in myostatin ( [...] Read more.

Tibetan sheep are vital to the ecosystem and livelihood of the Tibetan Plateau; however, traditional breeding methods limit their production and growth. Modern molecular breeding techniques are required to improve these traits. This study identified a single nucleotide polymorphism (SNP) in myostatin (MSTN) and Callipyge in Tibetan sheep. The findings indicated notable associations between MSTN genotypes and growth traits including birth weight (BW), body length (BL), chest width (ChW), and chest circumference (ChC), as well as a particularly strong association with cannon circumference (CaC) at 2 months of age. Conversely, Callipyge polymorphisms did not have a significant impact on Tibetan sheep. Moreover, the analyses revealed a significant association between sex and BW or hip width (HW) at 2 months of age and ChW, ChC, and CaC at 4 months of age. Furthermore, the study’s results suggested that the genotype of MSTN as a GA was associated with a notable sex effect on BW, while the genotype of Callipyge (CC) showed a significant impact of sex on CaC at 2 months of age. These results indicated that the SNP of MSTN could potentially serve as a molecular marker for early growth traits in Tibetan sheep. Full article

(This article belongs to the Special Issue Genetics and Breeding in Sheep and Goats)

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15 pages, 1824 KB

Open AccessEditor’s ChoiceReview

A Comprehensive Review of HER2 in Cancer Biology and Therapeutics

by Xiaoqing Cheng

Genes 2024, 15(7), 903; https://doi.org/10.3390/genes15070903 - 11 Jul 2024

Cited by 58 | Viewed by 23607

Abstract

Human epidermal growth factor receptor 2 (HER2), a targetable transmembrane glycoprotein receptor of the epidermal growth factor receptor (EGFR) family, plays a crucial role in cell proliferation, survival, and differentiation. Aberrant HER2 signaling is implicated in various cancers, particularly in breast and gastric [...] Read more.

Human epidermal growth factor receptor 2 (HER2), a targetable transmembrane glycoprotein receptor of the epidermal growth factor receptor (EGFR) family, plays a crucial role in cell proliferation, survival, and differentiation. Aberrant HER2 signaling is implicated in various cancers, particularly in breast and gastric cancers, where HER2 overexpression or amplification correlates with aggressive tumor behavior and poor prognosis. HER2-activating mutations contribute to accelerated tumorigenesis and metastasis. This review provides an overview of HER2 biology, signaling pathways, mechanisms of dysregulation, and diagnostic approaches, as well as therapeutic strategies targeting HER2 in cancer. Understanding the intricate details of HER2 regulation is essential for developing effective targeted therapies and improving patient outcomes. Full article

(This article belongs to the Special Issue Signaling Pathway of Cancer)

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17 pages, 1008 KB

Open AccessEditor’s ChoiceReview

SARS-CoV-2 Genomic Epidemiology Dashboards: A Review of Functionality and Technological Frameworks for the Public Health Response

by Nikita Sitharam, Houriiyah Tegally, Danilo de Castro Silva, Cheryl Baxter, Tulio de Oliveira and Joicymara S. Xavier

Genes 2024, 15(7), 876; https://doi.org/10.3390/genes15070876 - 3 Jul 2024

Cited by 3 | Viewed by 3420

Abstract

During the coronavirus disease 2019 (COVID-19) pandemic, the number and types of dashboards produced increased to convey complex information using digestible visualizations. The pandemic saw a notable increase in genomic surveillance data, which genomic epidemiology dashboards presented in an easily interpretable manner. These [...] Read more.

During the coronavirus disease 2019 (COVID-19) pandemic, the number and types of dashboards produced increased to convey complex information using digestible visualizations. The pandemic saw a notable increase in genomic surveillance data, which genomic epidemiology dashboards presented in an easily interpretable manner. These dashboards have the potential to increase the transparency between the scientists producing pathogen genomic data and policymakers, public health stakeholders, and the public. This scoping review discusses the data presented, functional and visual features, and the computational architecture of six publicly available SARS-CoV-2 genomic epidemiology dashboards. We found three main types of genomic epidemiology dashboards: phylogenetic, genomic surveillance, and mutational. We found that data were sourced from different databases, such as GISAID, GenBank, and specific country databases, and these dashboards were produced for specific geographic locations. The key performance indicators and visualization used were specific to the type of genomic epidemiology dashboard. The computational architecture of the dashboards was created according to the needs of the end user. The genomic surveillance of pathogens is set to become a more common tool used to track ongoing and future outbreaks, and genomic epidemiology dashboards are powerful and adaptable resources that can be used in the public health response. Full article

(This article belongs to the Special Issue Genomics and Bioinformatics in Microbial Science)

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14 pages, 1740 KB

Open AccessEditor’s ChoiceArticle

Genomic Regions Associated with Resistance to Gastrointestinal Parasites in Australian Merino Sheep

by Brenda Vera, Elly A. Navajas, Pablo Peraza, Beatriz Carracelas, Elize Van Lier and Gabriel Ciappesoni

Genes 2024, 15(7), 846; https://doi.org/10.3390/genes15070846 - 27 Jun 2024

Cited by 3 | Viewed by 2246

Abstract

The objective of this study was to identify genomic regions and genes associated with resistance to gastrointestinal nematodes in Australian Merino sheep in Uruguay, using the single-step GWAS methodology (ssGWAS), which is based on genomic estimated breeding values (GEBVs) obtained from a combination [...] Read more.

The objective of this study was to identify genomic regions and genes associated with resistance to gastrointestinal nematodes in Australian Merino sheep in Uruguay, using the single-step GWAS methodology (ssGWAS), which is based on genomic estimated breeding values (GEBVs) obtained from a combination of pedigree, genomic, and phenotypic data. This methodology converts GEBVs into SNP effects. The analysis included 26,638 animals with fecal egg count (FEC) records obtained in two independent parasitic cycles (FEC1 and FEC2) and 1700 50K SNP genotypes. The comparison of genomic regions was based on genetic variances (gVar(%)) explained by non-overlapping regions of 20 SNPs. For FEC1 and FEC2, 18 and 22 genomic windows exceeded the significance threshold (gVar(%) ≥ 0.22%), respectively. The genomic regions with strong associations with FEC1 were located on chromosomes OAR 2, 6, 11, 21, and 25, and for FEC2 on OAR 5, 6, and 11. The proportion of genetic variance attributed to the top windows was 0.83% and 1.9% for FEC1 and FEC2, respectively. The 33 candidate genes shared between the two traits were subjected to enrichment analysis, revealing a marked enrichment in biological processes related to immune system functions. These results contribute to the understanding of the genetics underlying gastrointestinal parasite resistance and its implications for other productive and welfare traits in animal breeding programs. Full article

(This article belongs to the Special Issue Advances in Cattle, Sheep, and Goats Molecular Genetics and Breeding)

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12 pages, 567 KB

Open AccessEditor’s ChoiceReview

Preparing for Patient-Customized N-of-1 Antisense Oligonucleotide Therapy to Treat Rare Diseases

by Harry Wilton-Clark, Eric Yan and Toshifumi Yokota

Genes 2024, 15(7), 821; https://doi.org/10.3390/genes15070821 - 21 Jun 2024

Cited by 10 | Viewed by 5733

Abstract

The process of developing therapies to treat rare diseases is fraught with financial, regulatory, and logistical challenges that have limited our ability to build effective treatments. Recently, a novel type of therapy called antisense therapy has shown immense potential for the treatment of [...] Read more.

The process of developing therapies to treat rare diseases is fraught with financial, regulatory, and logistical challenges that have limited our ability to build effective treatments. Recently, a novel type of therapy called antisense therapy has shown immense potential for the treatment of rare diseases, particularly through single-patient N-of-1 trials. Several N-of-1 antisense therapies have been developed recently for rare diseases, including the landmark study of milasen. In response to the success of N-of-1 antisense therapy, the Food and Drug Administration (FDA) has developed unique guidelines specifically for the development of antisense therapy to treat N-of-1 rare diseases. This policy change establishes a strong foundation for future therapy development and addresses some of the major limitations that previously hindered the development of therapies for rare diseases. Full article

(This article belongs to the Special Issue Molecular Genetics of Neurodegenerative Diseases and Neuromuscular Diseases)

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13 pages, 2561 KB

Open AccessEditor’s ChoiceArticle

A Small Auxin-Up RNA Gene, IbSAUR36, Regulates Adventitious Root Development in Transgenic Sweet Potato

by Yuanyuan Zhou, Aixian Li, Taifeng Du, Zhen Qin, Liming Zhang, Qingmei Wang, Zongyun Li and Fuyun Hou

Genes 2024, 15(6), 760; https://doi.org/10.3390/genes15060760 - 10 Jun 2024

Cited by 6 | Viewed by 1807

Abstract

Small auxin-upregulated RNAs (SAURs), as the largest family of early auxin-responsive genes, play important roles in plant growth and development processes, such as auxin signaling and transport, hypocotyl development, and tolerance to environmental stresses. However, the functions of few SAUR genes [...] Read more.

Small auxin-upregulated RNAs (SAURs), as the largest family of early auxin-responsive genes, play important roles in plant growth and development processes, such as auxin signaling and transport, hypocotyl development, and tolerance to environmental stresses. However, the functions of few SAUR genes are known in the root development of sweet potatoes. In this study, an IbSAUR36 gene was cloned and functionally analyzed. The IbSAUR36 protein was localized to the nucleus and plasma membrane. The transcriptional level of this gene was significantly higher in the pencil root and leaf.This gene was strongly induced by indole-3-acetic acid (IAA), but it was downregulated under methyl-jasmonate(MeJA) treatment. The promoter of IbSAUR36 contained the core cis-elements for phytohormone responsiveness. Promoter β-glucuronidase (GUS) analysis in Arabidopsis showed that IbSAUR36 is highly expressed in the young tissues of plants, such as young leaves, roots, and buds. IbSAUR36-overexpressing sweet potato roots were obtained by an efficient Agrobacterium rhizogenes-mediated root transgenic system. We demonstrated that overexpression of IbSAUR36 promoted the accumulation of IAA, upregulated the genes encoding IAA synthesis and its signaling pathways, and downregulated the genes encoding lignin synthesis and JA signaling pathways. Taken together, these results show that IbSAUR36 plays an important role in adventitious root (AR) development by regulating IAA signaling, lignin synthesis, and JA signaling pathways in transgenic sweet potatoes. Full article

(This article belongs to the Special Issue Advances in Genetic Breeding of Sweetpotato)

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18 pages, 1617 KB

Open AccessEditor’s ChoiceReview

Gene Therapy for Non-Hereditary Retinal Disease: Age-Related Macular Degeneration, Diabetic Retinopathy, and Beyond

by Lucas W. Rowe and Thomas A. Ciulla

Genes 2024, 15(6), 720; https://doi.org/10.3390/genes15060720 - 1 Jun 2024

Cited by 15 | Viewed by 7257

Abstract

Gene therapy holds promise as a transformative approach in the treatment landscape of age-related macular degeneration (AMD), diabetic retinopathy (DR), and diabetic macular edema (DME), aiming to address the challenges of frequent intravitreal anti-vascular endothelial growth factor (VEGF) injections. This manuscript reviews ongoing [...] Read more.

Gene therapy holds promise as a transformative approach in the treatment landscape of age-related macular degeneration (AMD), diabetic retinopathy (DR), and diabetic macular edema (DME), aiming to address the challenges of frequent intravitreal anti-vascular endothelial growth factor (VEGF) injections. This manuscript reviews ongoing gene therapy clinical trials for these disorders, including ABBV-RGX-314, ixoberogene soroparvovec (ixo-vec), and 4D-150. ABBV-RGX-314 utilizes an adeno-associated virus (AAV) vector to deliver a transgene encoding a ranibizumab-like anti-VEGF antibody fragment, demonstrating promising results in Phase 1/2a and ongoing Phase 2b/3 trials. Ixo-vec employs an AAV2.7m8 capsid for intravitreal delivery of a transgene expressing aflibercept, showing encouraging outcomes in Phase 1 and ongoing Phase 2 trials. 4D-150 utilizes an evolved vector to express both aflibercept and a VEGF-C inhibitory RNAi, exhibiting positive interim results in Phase 1/2 studies. Other therapies reviewed include EXG102-031, FT-003, KH631, OLX10212, JNJ-1887, 4D-175, and OCU410. These therapies offer potential advantages of reduced treatment frequency and enhanced safety profiles, representing a paradigm shift in management towards durable and efficacious cellular-based biofactories. These advancements in gene therapy hold promise for improving outcomes in AMD and addressing the complex challenges of DME and DR, providing new avenues for the treatment of diabetic eye diseases. Full article

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

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17 pages, 3167 KB

Open AccessEditor’s ChoiceArticle

Biodiversity of Demersal Fish Communities in the Cosmonaut Sea Revealed by DNA Barcoding Analyses

by Hai Li, Xing Miao, Rui Wang, Yuzhuo Liao, Yilin Wen, Ran Zhang and Longshan Lin

Genes 2024, 15(6), 691; https://doi.org/10.3390/genes15060691 - 26 May 2024

Cited by 4 | Viewed by 1583

Abstract

The Cosmonaut Sea is one of the least accessed regions in the Southern Ocean, and our knowledge about the fish biodiversity in the region is sparse. In this study, we provided a description of demersal fish diversity in the Cosmonaut Sea by analysing [...] Read more.

The Cosmonaut Sea is one of the least accessed regions in the Southern Ocean, and our knowledge about the fish biodiversity in the region is sparse. In this study, we provided a description of demersal fish diversity in the Cosmonaut Sea by analysing cytochrome oxidase I (COI) barcodes of 98 fish samples that were hauled by trawling during the 37th and 38th Chinese National Antarctic Research Expedition (CHINARE) cruises. Twenty-four species representing 19 genera and 11 families, namely, Artedidraconidae, Bathydraconidae, Bathylagidae, Channichthyidae, Liparidae, Macrouridae, Muraenolepididae, Myctophidae, Nototheniidae, Paralepididae and Zoarcidae, were discriminated and identified, which were largely identical to local fish occurrence records and the general pattern of demersal fish communities at high Antarctic shelf areas. The validity of a barcoding gap failed to be detected and confirmed across all species due to the indicative signals of two potential cryptic species. Nevertheless, DNA barcoding still demonstrated to be a very efficient and sound method for the discrimination and classification of Antarctic fishes. In the future, various sampling strategies that cover all geographic sections and depth strata of the Cosmonaut Sea are encouraged to enhance our understanding of local fish communities, within which DNA barcoding can play an important role in either molecular taxonomy or the establishment of a dedicated local reference database for eDNA metabarcoding analyses. Full article

(This article belongs to the Special Issue DNA Taxonomy, Molecular Phylogeny and Population Genetics of Cartilaginous Fishes and Teleost Fishes)

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27 pages, 2477 KB

Open AccessEditor’s ChoiceReview

Mitochondrial DNA: Inherent Complexities Relevant to Genetic Analyses

by Tomas Ferreira and Santiago Rodriguez

Genes 2024, 15(5), 617; https://doi.org/10.3390/genes15050617 - 12 May 2024

Cited by 18 | Viewed by 9735

Abstract

Mitochondrial DNA (mtDNA) exhibits distinct characteristics distinguishing it from the nuclear genome, necessitating specific analytical methods in genetic studies. This comprehensive review explores the complex role of mtDNA in a variety of genetic studies, including genome-wide, epigenome-wide, and phenome-wide association studies, with a [...] Read more.

Mitochondrial DNA (mtDNA) exhibits distinct characteristics distinguishing it from the nuclear genome, necessitating specific analytical methods in genetic studies. This comprehensive review explores the complex role of mtDNA in a variety of genetic studies, including genome-wide, epigenome-wide, and phenome-wide association studies, with a focus on its implications for human traits and diseases. Here, we discuss the structure and gene-encoding properties of mtDNA, along with the influence of environmental factors and epigenetic modifications on its function and variability. Particularly significant are the challenges posed by mtDNA’s high mutation rate, heteroplasmy, and copy number variations, and their impact on disease susceptibility and population genetic analyses. The review also highlights recent advances in methodological approaches that enhance our understanding of mtDNA associations, advocating for refined genetic research techniques that accommodate its complexities. By providing a comprehensive overview of the intricacies of mtDNA, this paper underscores the need for an integrated approach to genetic studies that considers the unique properties of mitochondrial genetics. Our findings aim to inform future research and encourage the development of innovative methodologies to better interpret the broad implications of mtDNA in human health and disease. Full article

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

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30 pages, 6195 KB

Open AccessEditor’s ChoiceArticle

Comprehensive Bioinformatic Investigation of TP53 Dysregulation in Diverse Cancer Landscapes

by Ruby Khan, Bakht Pari and Krzysztof Puszynski

Genes 2024, 15(5), 577; https://doi.org/10.3390/genes15050577 - 30 Apr 2024

Cited by 7 | Viewed by 6316

Abstract

P53 overexpression plays a critical role in cancer pathogenesis by disrupting the intricate regulation of cellular proliferation. Despite its firmly established function as a tumor suppressor, elevated p53 levels can paradoxically contribute to tumorigenesis, influenced by factors such as exposure to carcinogens, genetic [...] Read more.

P53 overexpression plays a critical role in cancer pathogenesis by disrupting the intricate regulation of cellular proliferation. Despite its firmly established function as a tumor suppressor, elevated p53 levels can paradoxically contribute to tumorigenesis, influenced by factors such as exposure to carcinogens, genetic mutations, and viral infections. This phenomenon is observed across a spectrum of cancer types, including bladder (BLCA), ovarian (OV), cervical (CESC), cholangiocarcinoma (CHOL), colon adenocarcinoma (COAD), diffuse large B-cell lymphoma (DLBC), esophageal carcinoma (ESCA), head and neck squamous cell carcinoma (HNSC), kidney chromophobe (KICH), kidney renal clear cell carcinoma (KIRC), liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), and uterine corpus endometrial carcinoma (UCEC). This broad spectrum of cancers is often associated with increased aggressiveness and recurrence risk. Effective therapeutic strategies targeting tumors with p53 overexpression require a comprehensive approach, integrating targeted interventions aimed at the p53 gene with conventional modalities such as chemotherapy, radiation therapy, and targeted drugs. In this extensive study, we present a detailed analysis shedding light on the multifaceted role of TP53 across various cancers, with a specific emphasis on its impact on disease-free survival (DFS). Leveraging data from the TCGA database and the GTEx dataset, along with GEPIA, UALCAN, and STRING, we identify TP53 overexpression as a significant prognostic indicator, notably pronounced in prostate adenocarcinoma (PRAD). Supported by compelling statistical significance (p < 0.05), our analysis reveals the distinct influence of TP53 overexpression on DFS outcomes in PRAD. Additionally, graphical representations of overall survival (OS) underscore the notable disparity in OS duration between tumors exhibiting elevated TP53 expression (depicted by the red line) and those with lower TP53 levels (indicated by the blue line). The hazard ratio (HR) further emphasizes the profound impact of TP53 on overall survival. Moreover, our investigation delves into the intricate TP53 protein network, unveiling genes exhibiting robust positive correlations with TP53 expression across 13 out of 27 cancers. Remarkably, negative correlations emerge with pivotal tumor suppressor genes. This network analysis elucidates critical proteins, including SIRT1, CBP, p300, ATM, DAXX, HSP 90-alpha, Mdm2, RPA70, 14-3-3 protein sigma, p53, and ASPP2, pivotal in regulating cell cycle dynamics, DNA damage response, and transcriptional regulation. Our study underscores the paramount importance of deciphering TP53 dynamics in cancer, providing invaluable insights into tumor behavior, disease-free survival, and potential therapeutic avenues. Full article

(This article belongs to the Special Issue Bioinformatics and Computational Biology for Cancer Prediction and Prognosis)

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25 pages, 1644 KB

Open AccessEditor’s ChoiceReview

Insights into Salinity Tolerance in Wheat

by Zechao Zhang, Zelin Xia, Chunjiang Zhou, Geng Wang, Xiao Meng and Pengcheng Yin

Genes 2024, 15(5), 573; https://doi.org/10.3390/genes15050573 - 29 Apr 2024

Cited by 20 | Viewed by 4904

Abstract

Salt stress has a detrimental impact on food crop production, with its severity escalating due to both natural and man-made factors. As one of the most important food crops, wheat is susceptible to salt stress, resulting in abnormal plant growth and reduced yields; [...] Read more.

Salt stress has a detrimental impact on food crop production, with its severity escalating due to both natural and man-made factors. As one of the most important food crops, wheat is susceptible to salt stress, resulting in abnormal plant growth and reduced yields; therefore, damage from salt stress should be of great concern. Additionally, the utilization of land in coastal areas warrants increased attention, given diminishing supplies of fresh water and arable land, and the escalating demand for wheat. A comprehensive understanding of the physiological and molecular changes in wheat under salt stress can offer insights into mitigating the adverse effects of salt stress on wheat. In this review, we summarized the genes and molecular mechanisms involved in ion transport, signal transduction, and enzyme and hormone regulation, in response to salt stress based on the physiological processes in wheat. Then, we surveyed the latest progress in improving the salt tolerance of wheat through breeding, exogenous applications, and microbial pathways. Breeding efficiency can be improved through a combination of gene editing and multiple omics techniques, which is the fundamental strategy for dealing with salt stress. Possible challenges and prospects in this process were also discussed. Full article

(This article belongs to the Special Issue Breeding and Genetics in Wheat)

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12 pages, 1241 KB

Open AccessEditor’s ChoiceReview

Genetic Mechanisms Driving Uterine Leiomyoma Pathobiology, Epidemiology, and Treatment

by Malini S. Ramaiyer, Eslam Saad, Irem Kurt and Mostafa A. Borahay

Genes 2024, 15(5), 558; https://doi.org/10.3390/genes15050558 - 27 Apr 2024

Cited by 10 | Viewed by 4884

Abstract

Uterine leiomyomas (ULs) are the most common benign tumor of the uterus. They can be associated with symptoms including abnormal uterine bleeding, pelvic pain, urinary frequency, and pregnancy complications. Despite the high prevalence of UL, its underlying pathophysiology mechanisms have historically been poorly [...] Read more.

Uterine leiomyomas (ULs) are the most common benign tumor of the uterus. They can be associated with symptoms including abnormal uterine bleeding, pelvic pain, urinary frequency, and pregnancy complications. Despite the high prevalence of UL, its underlying pathophysiology mechanisms have historically been poorly understood. Several mechanisms of pathogenesis have been suggested, implicating various genes, growth factors, cytokines, chemokines, and microRNA aberrations. The purpose of this study is to summarize the current research on the relationship of genetics with UL. Specifically, we performed a literature review of published studies to identify how genetic aberrations drive pathophysiology, epidemiology, and therapeutic approaches of UL. With regards to pathophysiology, research has identified MED12 mutations, HMGA2 overexpression, fumarate hydratase deficiency, and cytogenetic abnormalities as contributors to the development of UL. Additionally, epigenetic modifications, such as histone acetylation and DNA methylation, have been identified as contributing to UL tumorigenesis. Specifically, UL stem cells have been found to contain a unique DNA methylation pattern compared to more differentiated UL cells, suggesting that DNA methylation has a role in tumorigenesis. On a population level, genome-wide association studies (GWASs) and epidemiologic analyses have identified 23 genetic loci associated with younger age at menarche and UL growth. Additionally, various GWASs have investigated genetic loci as potential drivers of racial disparities in UL incidence. For example, decreased expression of Cytohesin 4 in African Americans has been associated with increased UL risk. Recent studies have investigated various therapeutic options, including ten-eleven translocation proteins mediating DNA methylation, adenovirus vectors for drug delivery, and “suicide gene therapy” to induce apoptosis. Overall, improved understanding of the genetic and epigenetic drivers of UL on an individual and population level can propel the discovery of novel therapeutic options. Full article

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

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22 pages, 1376 KB

Open AccessEditor’s ChoiceReview

Oxidative Stress Biomarkers in Male Infertility: Established Methodologies and Future Perspectives

by Filomena Mottola, Ilaria Palmieri, Maria Carannante, Angela Barretta, Shubhadeep Roychoudhury and Lucia Rocco

Genes 2024, 15(5), 539; https://doi.org/10.3390/genes15050539 - 25 Apr 2024

Cited by 13 | Viewed by 3040

Abstract

Male fertility can be affected by oxidative stress (OS), which occurs when an imbalance between the production of reactive oxygen species (ROS) and the body’s ability to neutralize them arises. OS can damage cells and influence sperm production. High levels of lipid peroxidation [...] Read more.

Male fertility can be affected by oxidative stress (OS), which occurs when an imbalance between the production of reactive oxygen species (ROS) and the body’s ability to neutralize them arises. OS can damage cells and influence sperm production. High levels of lipid peroxidation have been linked to reduced sperm motility and decreased fertilization ability. This literature review discusses the most commonly used biomarkers to measure sperm damage caused by ROS, such as the high level of OS in seminal plasma as an indicator of imbalance in antioxidant activity. The investigated biomarkers include 8-hydroxy-2-deoxyguanosine acid (8-OHdG), a marker of DNA damage caused by ROS, and F2 isoprostanoids (8-isoprostanes) produced by lipid peroxidation. Furthermore, this review focuses on recent methodologies including the NGS polymorphisms and differentially expressed gene (DEG) analysis, as well as the epigenetic mechanisms linked to ROS during spermatogenesis along with new methodologies developed to evaluate OS biomarkers. Finally, this review addresses a valuable insight into the mechanisms of male infertility provided by these advances and how they have led to new treatment possibilities. Overall, the use of biomarkers to evaluate OS in male infertility has supplied innovative diagnostic and therapeutic approaches, enhancing our understanding of male infertility mechanisms. Full article

(This article belongs to the Section Cytogenomics)

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13 pages, 1381 KB

Open AccessEditor’s ChoiceArticle

Resistome, Virulome, and Clonal Variation in Methicillin-Resistant Staphylococcus aureus (MRSA) in Healthy Swine Populations: A Cross-Sectional Study

by Vanessa Silva, Adriana Silva, Raquel Barbero, Mario Romero, Rosa del Campo, Manuela Caniça, Rui Cordeiro, Gilberto Igrejas and Patricia Poeta

Genes 2024, 15(5), 532; https://doi.org/10.3390/genes15050532 - 24 Apr 2024

Cited by 2 | Viewed by 1897

Abstract

This cross-sectional study investigates the methicillin-resistant Staphylococcus aureus (MRSA): its prevalence, antimicrobial resistance, and molecular characteristics in healthy swine populations in central Portugal. A total of 213 samples were collected from pigs on twelve farms, and MRSA prevalence was assessed using selective agar [...] Read more.

This cross-sectional study investigates the methicillin-resistant Staphylococcus aureus (MRSA): its prevalence, antimicrobial resistance, and molecular characteristics in healthy swine populations in central Portugal. A total of 213 samples were collected from pigs on twelve farms, and MRSA prevalence was assessed using selective agar plates and confirmed via molecular methods. Antimicrobial susceptibility testing and whole genome sequencing (WGS) were performed to characterize resistance profiles and genetic determinants. Among the 107 MRSA-positive samples (83.1% prevalence), fattening pigs and breeding sows exhibited notably high carriage rates. The genome of 20 isolates revealed the predominance of the ST398 clonal complex, with diverse spa types identified. Antimicrobial susceptibility testing demonstrated resistance to multiple antimicrobial agents, including penicillin, cefoxitin, and tetracycline. WGS analysis identified a diverse array of resistance genes, highlighting the genetic basis of antimicrobial resistance. Moreover, virulence gene profiling revealed the presence of genes associated with pathogenicity. These findings underscore the significant prevalence of MRSA in swine populations and emphasize the need for enhanced surveillance and control measures to mitigate zoonotic transmission risks. Implementation of prudent antimicrobial use practices and targeted intervention strategies is essential to reducing MRSA prevalence and safeguarding public health. Continued research efforts are warranted to elucidate transmission dynamics and virulence potential, ultimately ensuring food safety and public health protection. Full article

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

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24 pages, 6666 KB

Open AccessEditor’s ChoiceArticle

Impact of Vanadium–Titanium–Magnetite Mining Activities on Endophytic Bacterial Communities and Functions in the Root Systems of Local Plants

by Zhuang Xiong, Yunfeng Zhang, Xiaodie Chen, Ajia Sha, Wenqi Xiao, Yingyong Luo, Lianxin Peng, Liang Zou and Qiang Li

Genes 2024, 15(5), 526; https://doi.org/10.3390/genes15050526 - 23 Apr 2024

Cited by 13 | Viewed by 1762

Abstract

This study utilized 16S rRNA high-throughput sequencing technology to analyze the community structure and function of endophytic bacteria within the roots of three plant species in the vanadium–titanium–magnetite (VTM) mining area. The findings indicated that mining activities of VTM led to a notable [...] Read more.

This study utilized 16S rRNA high-throughput sequencing technology to analyze the community structure and function of endophytic bacteria within the roots of three plant species in the vanadium–titanium–magnetite (VTM) mining area. The findings indicated that mining activities of VTM led to a notable decrease in both the biodiversity and abundance of endophytic bacteria within the root systems of Eleusine indica and Carex (p < 0.05). Significant reductions were observed in the populations of Nocardioides, concurrently with substantial increments in the populations of Pseudomonas (p < 0.05), indicating that Pseudomonas has a strong adaptability to this environmental stress. In addition, β diversity analysis revealed divergence in the endophytic bacterial communities within the roots of E. indica and Carex from the VTM mining area, which had diverged to adapt to the environmental stress caused by mining activity. Functional enrichment analysis revealed that VTM mining led to an increase in polymyxin resistance, nicotinate degradation I, and glucose degradation (oxidative) (p < 0.05). Interestingly, we found that VTM mining did not notably alter the endophytic bacterial communities or functions in the root systems of Dodonaea viscosa, indicating that this plant can adapt well to environmental stress. This study represents the primary investigation into the influence of VTM mining activities on endophytic bacterial communities and the functions of nearby plant roots, providing further insight into the impact of VTM mining activities on the ecological environment. Full article

(This article belongs to the Special Issue Genomics of Microbial Diversity, Evolution and Function)

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8 pages, 1764 KB

Open AccessEditor’s ChoiceCase Report

A TMEM63A Nonsense Heterozygous Variant Linked to Infantile Transient Hypomyelinating Leukodystrophy Type 19?

by Dimitra Siori, Dimitrios Vlachakis, Periklis Makrythanasis, Joanne Traeger-Synodinos, Danai Veltra, Afrodite Kampouraki and George P. Chrousos

Genes 2024, 15(5), 525; https://doi.org/10.3390/genes15050525 - 23 Apr 2024

Cited by 3 | Viewed by 2581

Abstract

Infantile onset transient hypomyelination (IOTH) is a rare form of leukodystrophy that is associated with transient motor impairment and delayed central nervous system myelination. Here, we report a case of a new mutation in the transmembrane protein 63A (TMEM63A) gene identified [...] Read more.

Infantile onset transient hypomyelination (IOTH) is a rare form of leukodystrophy that is associated with transient motor impairment and delayed central nervous system myelination. Here, we report a case of a new mutation in the transmembrane protein 63A (TMEM63A) gene identified using Whole-Exome Sequencing (WES) in an 8.5-year-old boy with clinical symptoms similar to IOTH. The patient exhibited a mild developmental delay, including hypotonia and delayed motor milestones, as well as some notable phenotypic characteristics, such as macrocephaly and macrosomia. Despite the absence of early neuroimaging, genetic testing revealed a paternally inherited variant in TMEM63A (NM_14698.3:c.220A>T;p:(Arg74*)), potentially linked to infantile transient hypomyelinating leukodystrophy type 19. Our findings in this study and the patient’s favorable clinical course underscore the potential for successful myelination even with delayed initiation and may contribute to a better understanding of the genotype–phenotype correlation in IOTH, emphasizing the importance of genetic analysis in unresolved developmental delay cases and providing critical insights for accurate diagnosis, prognosis and potential therapeutic strategies in rare leukodystrophies. Full article

(This article belongs to the Special Issue Head and Neck Genetics)

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27 pages, 3462 KB

Open AccessEditor’s ChoiceReview

Principles in the Management of Glioblastoma

by Domingos Roda, Pedro Veiga, Joana Barbosa Melo, Isabel Marques Carreira and Ilda Patrícia Ribeiro

Genes 2024, 15(4), 501; https://doi.org/10.3390/genes15040501 - 17 Apr 2024

Cited by 29 | Viewed by 8413

Abstract

Glioblastoma, the most aggressive and common malignant primary brain tumour, is characterized by infiltrative growth, abundant vascularization, and aggressive clinical evolution. Patients with glioblastoma often face poor prognoses, with a median survival of approximately 15 months. Technological progress and the subsequent improvement in [...] Read more.

Glioblastoma, the most aggressive and common malignant primary brain tumour, is characterized by infiltrative growth, abundant vascularization, and aggressive clinical evolution. Patients with glioblastoma often face poor prognoses, with a median survival of approximately 15 months. Technological progress and the subsequent improvement in understanding the pathophysiology of these tumours have not translated into significant achievements in therapies or survival outcomes for patients. Progress in molecular profiling has yielded new omics data for a more refined classification of glioblastoma. Several typical genetic and epigenetic alterations in glioblastoma include mutations in genes regulating receptor tyrosine kinase (RTK)/rat sarcoma (RAS)/phosphoinositide 3-kinase (PI3K), p53, and retinoblastoma protein (RB) signalling, as well as mutation of isocitrate dehydrogenase (IDH), methylation of O⁶-methylguanine-DNA methyltransferase (MGMT), amplification of epidermal growth factor receptor vIII, and codeletion of 1p/19q. Certain microRNAs, such as miR-10b and miR-21, have also been identified as prognostic biomarkers. Effective treatment options for glioblastoma are limited. Surgery, radiotherapy, and alkylating agent chemotherapy remain the primary pillars of treatment. Only promoter methylation of the gene MGMT predicts the benefit from alkylating chemotherapy with temozolomide and it guides the choice of first-line treatment in elderly patients. Several targeted strategies based on tumour-intrinsic dominant signalling pathways and antigenic tumour profiles are under investigation in clinical trials. This review explores the potential genetic and epigenetic biomarkers that could be deployed as analytical tools in the diagnosis and prognostication of glioblastoma. Recent clinical advancements in treating glioblastoma are also discussed, along with the potential of liquid biopsies to advance personalized medicine in the field of glioblastoma, highlighting the challenges and promises for the future. Full article

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

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15 pages, 3832 KB

Open AccessEditor’s ChoiceReview

Neurofilaments in Sporadic and Familial Amyotrophic Lateral Sclerosis: A Systematic Review and Meta-Analysis

by Pashtun Shahim, Gina Norato, Ninet Sinaii, Henrik Zetterberg, Kaj Blennow, Leighton Chan and Christopher Grunseich

Genes 2024, 15(4), 496; https://doi.org/10.3390/genes15040496 - 16 Apr 2024

Cited by 11 | Viewed by 4597

Abstract

Background: Neurofilament proteins have been implicated to be altered in amyotrophic lateral sclerosis (ALS). The objectives of this study were to assess the diagnostic and prognostic utility of neurofilaments in ALS. Methods: Studies were conducted in electronic databases (PubMed/MEDLINE, Embase, Web of Science, [...] Read more.

Background: Neurofilament proteins have been implicated to be altered in amyotrophic lateral sclerosis (ALS). The objectives of this study were to assess the diagnostic and prognostic utility of neurofilaments in ALS. Methods: Studies were conducted in electronic databases (PubMed/MEDLINE, Embase, Web of Science, and Cochrane CENTRAL) from inception to 17 August 2023, and investigated neurofilament light (NfL) or phosphorylated neurofilament heavy chain (pNfH) in ALS. The study design, enrolment criteria, neurofilament concentrations, test accuracy, relationship between neurofilaments in cerebrospinal fluid (CSF) and blood, and clinical outcome were recorded. The protocol was registered with PROSPERO, CRD42022376939. Results: Sixty studies with 8801 participants were included. Both NfL and pNfH measured in CSF showed high sensitivity and specificity in distinguishing ALS from disease mimics. Both NfL and pNfH measured in CSF correlated with their corresponding levels in blood (plasma or serum); however, there were stronger correlations between CSF NfL and blood NfL. NfL measured in blood exhibited high sensitivity and specificity in distinguishing ALS from controls. Both higher levels of NfL and pNfH either measured in blood or CSF were correlated with more severe symptoms as assessed by the ALS Functional Rating Scale Revised score and with a faster disease progression rate; however, only blood NfL levels were associated with shorter survival. Discussion: Both NfL and pNfH measured in CSF or blood show high diagnostic utility and association with ALS functional scores and disease progression, while CSF NfL correlates strongly with blood (either plasma or serum) and is also associated with survival, supporting its use in clinical diagnostics and prognosis. Future work must be conducted in a prospective manner with standardized bio-specimen collection methods and analytical platforms, further improvement in immunoassays for quantification of pNfH in blood, and the identification of cut-offs across the ALS spectrum and controls. Full article

(This article belongs to the Special Issue Advances in Genetics of Motor Neuron Diseases)

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11 pages, 2470 KB

Open AccessEditor’s ChoiceArticle

The Effect of Short-Term Artificial Feed Domestication on the Expression of Oxidative-Stress-Related Genes and Antioxidant Capacity in the Liver and Gill Tissues of Mandarin Fish (Siniperca chuatsi)

by Zhou Zhang, Xiping Yuan, Hao Wu, Jinwei Gao, Jiayu Wu, Zhenzhen Xiong, Zhifeng Feng, Min Xie, Shaoming Li, Zhonggui Xie and Guoqing Zeng

Genes 2024, 15(4), 487; https://doi.org/10.3390/genes15040487 - 12 Apr 2024

Cited by 8 | Viewed by 2046

Abstract

To investigate whether Mandarin fish developed oxidative stress after being domesticated with artificial feed, we conducted a series of experiments. Oxidative stress is an important factor leading to diseases and aging in the body. The liver integrates functions such as digestion, metabolism, detoxification, [...] Read more.

To investigate whether Mandarin fish developed oxidative stress after being domesticated with artificial feed, we conducted a series of experiments. Oxidative stress is an important factor leading to diseases and aging in the body. The liver integrates functions such as digestion, metabolism, detoxification, coagulation, and immune regulation, while the gills are important respiratory organs that are sensitive to changes in the water environment. Therefore, we used the liver and gills of Mandarin fish as research materials. The aim of this study was to investigate the effects of short-term artificial feed domestication on the expression of oxidative stress genes and the changes in oxidative-stress-related enzyme activity in the liver and gills of Mandarin fish. We divided the Mandarin fish into two groups for treatment. The control group was fed with live bait continuously for 14 days, while the experimental group was fed with half artificial feed and half live bait from 0 to 7 days (T-7 d), followed by solely artificial feed from 7 to 14 days (T-14 d). The experimental results showed that there was no difference in the body weight, length, and standard growth rate of the Mandarin fish between the two groups of treatments; after two treatments, there were differences in the expression of genes related to oxidative stress in the gills (keap1, kappa, gsta, gstt1, gstk1, SOD, and CAT) and in the liver (GPx, keap1, kappa, gsta, gstt1, gr, and SOD). In the liver, GPx activity and the content of MDA were significantly upregulated after 7 days of domestication, while in the gills, SOD activity was significantly upregulated after 7 days of domestication and GPx activity was significantly downregulated after 14 days of domestication. These results suggest that artificial feed domestication is associated with oxidative stress. Moreover, these results provide experimental basic data for increasing the production of aquaculture feed for Mandarin fish. Full article

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

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18 pages, 6581 KB

Open AccessEditor’s ChoiceArticle

Transcriptomic Changes and Regulatory Networks Associated with Resistance to Mastitis in Xinjiang Brown Cattle

by Dan Wang, Haiyan Yang, Shengchao Ma, Tingting Liu, Mengjie Yan, Mingming Dong, Menghua Zhang, Tao Zhang, Xiaoxue Zhang, Lei Xu, Xixia Huang and Hong Chen

Genes 2024, 15(4), 465; https://doi.org/10.3390/genes15040465 - 7 Apr 2024

Cited by 4 | Viewed by 1772

Abstract

Xinjiang brown cattle are highly resistant to disease and tolerant of roughage feeding. The identification of genes regulating mastitis resistance in Xinjiang brown cattle is a novel means of genetic improvement. In this study, the blood levels of IL-1β, IL-6, IL-10, TNF-α, and [...] Read more.

Xinjiang brown cattle are highly resistant to disease and tolerant of roughage feeding. The identification of genes regulating mastitis resistance in Xinjiang brown cattle is a novel means of genetic improvement. In this study, the blood levels of IL-1β, IL-6, IL-10, TNF-α, and TGF-β in Xinjiang brown cattle with high and low somatic cell counts (SCCs) were investigated, showing that cytokine levels were higher in cattle with high SCCs. The peripheral blood transcriptomic profiles of healthy and mastitis-affected cattle were constructed by RNA-seq. Differential expression analysis identified 1632 differentially expressed mRNAs (DE-mRNAs), 1757 differentially expressed lncRNAs (DE-lncRNAs), and 23 differentially expressed circRNAs (DE-circRNAs), which were found to be enriched in key pathways such as PI3K/Akt, focal adhesion, and ECM-receptor interactions. Finally, ceRNA interaction networks were constructed using the differentially expressed genes and ceRNAs. It was found that keynote genes or mRNAs were also enriched in pathways such as PI3K-Akt, cholinergic synapses, cell adhesion molecules, ion binding, cytokine receptor activity, and peptide receptor activity, suggesting that the key genes and ncRNAs in the network may play an important role in the regulation of bovine mastitis. Full article

(This article belongs to the Special Issue Advances in Cattle, Sheep, and Goats Molecular Genetics and Breeding)

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22 pages, 2125 KB

Open AccessEditor’s ChoiceReview

PCR in Forensic Science: A Critical Review

by Caitlin McDonald, Duncan Taylor and Adrian Linacre

Genes 2024, 15(4), 438; https://doi.org/10.3390/genes15040438 - 29 Mar 2024

Cited by 18 | Viewed by 17495

Abstract

The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The introduction of PCR into forensic science marked the beginning of a new era of DNA profiling. This [...] Read more.

The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The introduction of PCR into forensic science marked the beginning of a new era of DNA profiling. This era has pushed PCR to its limits and allowed genetic data to be generated from trace DNA. Trace samples contain very small amounts of degraded DNA associated with inhibitory compounds and ions. Despite significant development in the PCR process since it was first introduced, the challenges of profiling inhibited and degraded samples remain. This review examines the evolution of the PCR from its inception in the 1980s, through to its current application in forensic science. The driving factors behind PCR evolution for DNA profiling are discussed along with a critical comparison of cycling conditions used in commercial PCR kits. Newer PCR methods that are currently used in forensic practice and beyond are examined, and possible future directions of PCR for DNA profiling are evaluated. Full article

(This article belongs to the Section Bioinformatics)

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18 pages, 892 KB

Open AccessEditor’s ChoiceReview

Innovations in Medicine: Exploring ChatGPT’s Impact on Rare Disorder Management

by Stefania Zampatti, Cristina Peconi, Domenica Megalizzi, Giulia Calvino, Giulia Trastulli, Raffaella Cascella, Claudia Strafella, Carlo Caltagirone and Emiliano Giardina

Genes 2024, 15(4), 421; https://doi.org/10.3390/genes15040421 - 28 Mar 2024

Cited by 13 | Viewed by 3875

Abstract

Artificial intelligence (AI) is rapidly transforming the field of medicine, announcing a new era of innovation and efficiency. Among AI programs designed for general use, ChatGPT holds a prominent position, using an innovative language model developed by OpenAI. Thanks to the use of [...] Read more.

Artificial intelligence (AI) is rapidly transforming the field of medicine, announcing a new era of innovation and efficiency. Among AI programs designed for general use, ChatGPT holds a prominent position, using an innovative language model developed by OpenAI. Thanks to the use of deep learning techniques, ChatGPT stands out as an exceptionally viable tool, renowned for generating human-like responses to queries. Various medical specialties, including rheumatology, oncology, psychiatry, internal medicine, and ophthalmology, have been explored for ChatGPT integration, with pilot studies and trials revealing each field’s potential benefits and challenges. However, the field of genetics and genetic counseling, as well as that of rare disorders, represents an area suitable for exploration, with its complex datasets and the need for personalized patient care. In this review, we synthesize the wide range of potential applications for ChatGPT in the medical field, highlighting its benefits and limitations. We pay special attention to rare and genetic disorders, aiming to shed light on the future roles of AI-driven chatbots in healthcare. Our goal is to pave the way for a healthcare system that is more knowledgeable, efficient, and centered around patient needs. Full article

(This article belongs to the Collection Genetics and Genomics of Rare Disorders)

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18 pages, 10173 KB

Open AccessEditor’s ChoiceArticle

Heterochromatin Is Not the Only Place for satDNAs: The High Diversity of satDNAs in the Euchromatin of the Beetle Chrysolina americana (Coleoptera, Chrysomelidae)

by José M. Rico-Porras, Pablo Mora, Teresa Palomeque, Eugenia E. Montiel, Diogo C. Cabral-de-Mello and Pedro Lorite

Genes 2024, 15(4), 395; https://doi.org/10.3390/genes15040395 - 22 Mar 2024

Cited by 19 | Viewed by 2174

Abstract

The satellitome of the beetle Chrysolina americana Linneo, 1758 has been characterized through chromosomal analysis, genomic sequencing, and bioinformatics tools. C-banding reveals the presence of constitutive heterochromatin blocks enriched in A+T content, primarily located in pericentromeric regions. Furthermore, a comprehensive satellitome analysis unveils [...] Read more.

The satellitome of the beetle Chrysolina americana Linneo, 1758 has been characterized through chromosomal analysis, genomic sequencing, and bioinformatics tools. C-banding reveals the presence of constitutive heterochromatin blocks enriched in A+T content, primarily located in pericentromeric regions. Furthermore, a comprehensive satellitome analysis unveils the extensive diversity of satellite DNA families within the genome of C. americana. Using fluorescence in situ hybridization techniques and the innovative CHRISMAPP approach, we precisely map the localization of satDNA families on assembled chromosomes, providing insights into their organization and distribution patterns. Among the 165 identified satDNA families, only three of them exhibit a remarkable amplification and accumulation, forming large blocks predominantly in pericentromeric regions. In contrast, the remaining, less abundant satDNA families are dispersed throughout euchromatic regions, challenging the traditional association of satDNA with heterochromatin. Overall, our findings underscore the complexity of repetitive DNA elements in the genome of C. americana and emphasize the need for further exploration to elucidate their functional significance and evolutionary implications. Full article

(This article belongs to the Special Issue Commemorating the Launch of the Section "Cytogenomics")

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21 pages, 667 KB

Open AccessEditor’s ChoiceReview

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 20 | Viewed by 5738

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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18 pages, 301 KB

Open AccessEditor’s ChoiceReview

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 12 | Viewed by 5314

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, 2173 KB

Open AccessEditor’s ChoiceArticle

Population Structure and Selection Signal Analysis of Nanyang Cattle Based on Whole-Genome Sequencing Data

by Yan Zhang, Zhitong Wei, Man Zhang, Shiwei Wang, Tengyun Gao, Hetian Huang, Tianliu Zhang, Hanfang Cai, Xian Liu, Tong Fu and Dong Liang

Genes 2024, 15(3), 351; https://doi.org/10.3390/genes15030351 - 11 Mar 2024

Cited by 11 | Viewed by 2751

Abstract

With a rich breeding history, Nanyang cattle (NY cattle) have undergone extensive natural and artificial selection, resulting in distinctive traits such as high fertility, excellent meat quality, and disease resistance. This makes them an ideal model for studying the mechanisms of environmental adaptability. [...] Read more.

With a rich breeding history, Nanyang cattle (NY cattle) have undergone extensive natural and artificial selection, resulting in distinctive traits such as high fertility, excellent meat quality, and disease resistance. This makes them an ideal model for studying the mechanisms of environmental adaptability. To assess the population structure and genetic diversity of NY cattle, we performed whole-genome resequencing on 30 individuals. These data were then compared with published whole-genome resequencing data from 432 cattle globally. The results indicate that the genetic structure of NY cattle is significantly different from European commercial breeds and is more similar to North–Central Chinese breeds. Furthermore, among all breeds, NY cattle exhibit the highest genetic diversity and the lowest population inbreeding levels. A genome-wide selection signal analysis of NY cattle and European commercial breeds using Fst, θπ-ratio, and θπ methods revealed significant selection signals in genes associated with reproductive performance and immunity. Our functional annotation analysis suggests that these genes may be responsible for reproduction (MAP2K2, PGR, and GSE1), immune response (NCOA2, HSF1, and PAX5), and olfaction (TAS1R3). We provide a comprehensive overview of sequence variations in the NY cattle genome, revealing insights into the population structure and genetic diversity of NY cattle. Additionally, we identify candidate genes associated with important economic traits, offering valuable references for future conservation and breeding efforts of NY cattle. Full article

(This article belongs to the Special Issue Research on Genetics and Genomics of Cattle)

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13 pages, 7064 KB

Open AccessEditor’s ChoiceArticle

A Single-Cell Transcriptome of Bovine Milk Somatic Cells

by Minja Zorc, Mateja Dolinar and Peter Dovč

Genes 2024, 15(3), 349; https://doi.org/10.3390/genes15030349 - 10 Mar 2024

Cited by 10 | Viewed by 3124

Abstract

The production of milk by dairy cows far exceeds the nutritional needs of the calf and is vital for the economical use of dairy cattle. High milk yield is a unique production trait that can be effectively enhanced through traditional selection methods. The [...] Read more.

The production of milk by dairy cows far exceeds the nutritional needs of the calf and is vital for the economical use of dairy cattle. High milk yield is a unique production trait that can be effectively enhanced through traditional selection methods. The process of lactation in cows serves as an excellent model for studying the biological aspects of lactation with the aim of exploring the mechanistic base of this complex trait at the cellular level. In this study, we analyzed the milk transcriptome at the single-cell level by conducting scRNA-seq analysis on milk samples from two Holstein Friesian cows at mid-lactation (75 and 93 days) using the 10× Chromium platform. Cells were pelleted and fat was removed from milk by centrifugation. The cell suspension from each cow was loaded on separate channels, resulting in the recovery of 9313 and 14,544 cells. Library samples were loaded onto two lanes of the NovaSeq 6000 (Illumina) instrument. After filtering at the cell and gene levels, a total of 7988 and 13,973 cells remained, respectively. We were able to reconstruct different cell types (milk-producing cells, progenitor cells, macrophages, monocytes, dendritic cells, T cells, B cells, mast cells, and neutrophils) in bovine milk. Our findings provide a valuable resource for identifying regulatory elements associated with various functions of the mammary gland such as lactation, tissue renewal, native immunity, protein and fat synthesis, and hormonal response. Full article

(This article belongs to the Collection Feature Papers in ‘Animal Genetics and Genomics’)

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25 pages, 1834 KB

Open AccessEditor’s ChoiceReview

Role of Post-Transcriptional Regulation in Learning and Memory in Mammals

by Carlo Maria Di Liegro, Gabriella Schiera, Giuseppe Schirò and Italia Di Liegro

Genes 2024, 15(3), 337; https://doi.org/10.3390/genes15030337 - 5 Mar 2024

Cited by 4 | Viewed by 3169

Abstract

After many decades, during which most molecular studies on the regulation of gene expression focused on transcriptional events, it was realized that post-transcriptional control was equally important in order to determine where and when specific proteins were to be synthesized. Translational regulation is [...] Read more.

After many decades, during which most molecular studies on the regulation of gene expression focused on transcriptional events, it was realized that post-transcriptional control was equally important in order to determine where and when specific proteins were to be synthesized. Translational regulation is of the most importance in the brain, where all the steps of mRNA maturation, transport to different regions of the cells and actual expression, in response to specific signals, constitute the molecular basis for neuronal plasticity and, as a consequence, for structural stabilization/modification of synapses; notably, these latter events are fundamental for the highest brain functions, such as learning and memory, and are characterized by long-term potentiation (LTP) of specific synapses. Here, we will discuss the molecular bases of these fundamental events by considering both the role of RNA-binding proteins (RBPs) and the effects of non-coding RNAs involved in controlling splicing, editing, stability and translation of mRNAs. Importantly, it has also been found that dysregulation of mRNA metabolism/localization is involved in many pathological conditions, arising either during brain development or in the adult nervous system. Full article

(This article belongs to the Special Issue Post-transcriptional Regulation in Mammals)

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11 pages, 248 KB

Open AccessEditor’s ChoiceReview

miRNA as a Biomarker for the Early Detection of Colorectal Cancer

by David Coleman and Scott Kuwada

Genes 2024, 15(3), 338; https://doi.org/10.3390/genes15030338 - 5 Mar 2024

Cited by 21 | Viewed by 6302

Abstract

MicroRNAs (miRNAs) are short, non-coding RNA segments that can be detected in a variety of clinical samples, including serum, stool, and urine. While miRNAs were initially known for their effect on post-translational gene expression, the last decade of research has shown them to [...] Read more.

MicroRNAs (miRNAs) are short, non-coding RNA segments that can be detected in a variety of clinical samples, including serum, stool, and urine. While miRNAs were initially known for their effect on post-translational gene expression, the last decade of research has shown them to be promising biomarkers for the detection of many types of cancer. This paper explores the use of miRNA detection as a tool for colorectal cancer (CRC) screening. We discuss the current state of miRNA detection, compare it to the existing CRC screening tools, and highlight the advantages and drawbacks of this approach from a clinical and logistical perspective. Our research finds that miRNA-based tests for CRC show great potential, but that widespread clinical adoption will be conditional on future research overcoming key hurdles. Full article

(This article belongs to the Special Issue MicroRNA in Cancers)

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