Journal Description
Genes
Genes
is a peer-reviewed, open access journal of genetics and genomics published monthly online by MDPI. The Spanish Society for Biochemistry and Molecular Biology (SEBBM) is affiliated with Genes and their members receive discounts on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, MEDLINE, PMC, Embase, PubAg, and other databases.
- Journal Rank: JCR - Q2 (Genetics & Heredity) / CiteScore - Q2 (Genetics (clinical))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 16.5 days after submission; acceptance to publication is undertaken in 2.3 days (median values for papers published in this journal in the second half of 2023).
- Recognition of Reviewers: Reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
3.5 (2022);
5-Year Impact Factor:
3.9 (2022)
Latest Articles
Y Chromosome Story—Ancient Genetic Data as a Supplementary Tool for the Analysis of Modern Croatian Genetic Pool
Genes 2024, 15(6), 748; https://doi.org/10.3390/genes15060748 (registering DOI) - 6 Jun 2024
Abstract
Due to its turbulent demographic history, marked by extensive settlement and gene flow from diverse regions of Eurasia, Southeastern Europe (SEE) has consistently served as a genetic crossroads between East and West and a junction for the migrations that reshaped Europe’s population. SEE,
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Due to its turbulent demographic history, marked by extensive settlement and gene flow from diverse regions of Eurasia, Southeastern Europe (SEE) has consistently served as a genetic crossroads between East and West and a junction for the migrations that reshaped Europe’s population. SEE, including modern Croatian territory, was a crucial passage from the Near East and even more distant regions and human populations in this region, as almost any other European population represents a remarkable genetic mixture. Modern humans have continuously occupied this region since the Upper Paleolithic era, and different (pre)historical events have left a distinctive genetic signature on the historical narrative of this region. Our views of its history have been mostly renewed in the last few decades by extraordinary data obtained from Y-chromosome studies. In recent times, the international research community, bringing together geneticists and archaeologists, has steadily released a growing number of ancient genomes from this region, shedding more light on its complex past population dynamics and shaping the genetic pool in Croatia and this part of Europe.
Full article
(This article belongs to the Section Population and Evolutionary Genetics and Genomics)
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Open AccessArticle
Cytogenetic and Molecular Effects of Kaolin’s Foliar Application in Grapevine (Vitis vinifera L.) under Summer’s Stressful Growing Conditions
by
Ana Carvalho, Lia-Tânia Dinis, Ana Luzio, Sara Bernardo, José Moutinho-Pereira and José Lima-Brito
Genes 2024, 15(6), 747; https://doi.org/10.3390/genes15060747 - 6 Jun 2024
Abstract
Grapevine varieties from “Douro Superior” (NE Portugal) experience high temperatures, solar radiation, and water deficit during the summer. This summer’s stressful growing conditions induce nucleic acids, lipids, and protein oxidation, which cause cellular, physiological, molecular, and biochemical changes. Cell cycle anomalies, mitosis delay,
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Grapevine varieties from “Douro Superior” (NE Portugal) experience high temperatures, solar radiation, and water deficit during the summer. This summer’s stressful growing conditions induce nucleic acids, lipids, and protein oxidation, which cause cellular, physiological, molecular, and biochemical changes. Cell cycle anomalies, mitosis delay, or cell death may occur at the cellular level, leading to reduced plant productivity. However, the foliar application of kaolin (KL) can mitigate the impact of abiotic stress by decreasing leaf temperature and enhancing antioxidant defence. Hence, this study hypothesised that KL-treated grapevine plants growing in NE Portugal would reveal, under summer stressful growing conditions, higher progression and stability of the leaf mitotic cell cycle than the untreated (control) plants. KL was applied after veraison for two years. Leaves, sampled 3 and 5 weeks later, were cytogenetically, molecularly, and biochemically analysed. Globally, integrating these multidisciplinary data confirmed the decreased leaf temperature and enhanced antioxidant defence of the KL-treated plants, accompanied by an improved regularity and completion of the leaf cell cycle relative to the control plants. Nevertheless, the KL efficacy was significantly influenced by the sampling date and/or variety. In sum, the achieved results confirmed the hypothesis initially proposed.
Full article
(This article belongs to the Special Issue DNA Damage Repair and Plant Stress Response)
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Open AccessReview
Unraveling the Genetic Foundations of Broiler Meat Quality: Advancements in Research and Their Impact
by
Tian Lu, Bahareldin Ali Abdalla Gibril, Jiguo Xu and Xinwei Xiong
Genes 2024, 15(6), 746; https://doi.org/10.3390/genes15060746 - 6 Jun 2024
Abstract
As societal progress elevates living standards, the focus on meat consumption has shifted from quantity to quality. In broiler production, optimizing meat quality has become paramount, prompting efforts to refine various meat attributes. Recent advancements in sequencing technologies have revealed the genome’s complexity,
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As societal progress elevates living standards, the focus on meat consumption has shifted from quantity to quality. In broiler production, optimizing meat quality has become paramount, prompting efforts to refine various meat attributes. Recent advancements in sequencing technologies have revealed the genome’s complexity, surpassing previous conceptions. Through experimentation, numerous genetic elements have been linked to crucial meat quality traits in broiler chickens. This review synthesizes the current understanding of genetic determinants associated with meat quality attributes in broilers. Researchers have unveiled the pivotal insights detailed herein by employing diverse genomic methodologies such as QTL-based investigations, candidate gene studies, single-nucleotide polymorphism screening, genome-wide association studies, and RNA sequencing. These studies have identified numerous genes involved in broiler meat quality traits, including meat lightness (COL1A2 and ACAA2), meat yellowness (BCMO1 and GDPD5), fiber diameter (myostatin and LncIRS1), meat pH (PRDX4), tenderness (CAPN1), and intramuscular fat content (miR-24-3p and ANXA6). Consequently, a comprehensive exploration of these genetic elements is imperative to devise novel molecular markers and potential targets, promising to revolutionize strategies for enhancing broiler meat quality.
Full article
(This article belongs to the Special Issue Poultry Breeding: Genetics and Genomics)
Open AccessReview
Human Endogenous Retroviruses in Neurodegenerative Diseases
by
Gabrielle L. Adler, Kelvin Le, YuHong Fu and Woojin Scott Kim
Genes 2024, 15(6), 745; https://doi.org/10.3390/genes15060745 - 5 Jun 2024
Abstract
Human endogenous retroviruses (HERVs) are DNA transposable elements that have integrated into the human genome via an ancestral germline infection. The potential importance of HERVs is underscored by the fact that they comprise approximately 8% of the human genome. HERVs have been implicated
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Human endogenous retroviruses (HERVs) are DNA transposable elements that have integrated into the human genome via an ancestral germline infection. The potential importance of HERVs is underscored by the fact that they comprise approximately 8% of the human genome. HERVs have been implicated in the pathogenesis of neurodegenerative diseases, a group of CNS diseases characterized by a progressive loss of structure and function of neurons, resulting in cell death and multiple physiological dysfunctions. Much evidence indicates that HERVs are initiators or drivers of neurodegenerative processes in multiple sclerosis and amyotrophic lateral sclerosis, and clinical trials have been designed to target HERVs. In recent years, the role of HERVs has been explored in other major neurodegenerative diseases, including frontotemporal dementia, Alzheimer’s disease and Parkinson’s disease, with some interesting discoveries. This review summarizes and evaluates the past and current research on HERVs in neurodegenerative diseases. It discusses the potential role of HERVs in disease manifestation and neurodegeneration. It critically reviews antiretroviral strategies used in the therapeutic intervention of neurodegenerative diseases.
Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
Open AccessArticle
The Usefulness of qPCR Data for Sample Pre-Assessment and Interpretation of Genetic Typing Results
by
Martina Onofri, Simona Severini, Federica Tommolini, Massimo Lancia, Cristiana Gambelunghe, Luigi Carlini and Eugenia Carnevali
Genes 2024, 15(6), 744; https://doi.org/10.3390/genes15060744 - 5 Jun 2024
Abstract
DNA quantification is a crucial step in the STR typing workflow for human identification purposes. Given the reaction’s nature, qPCR assays may be subjected to the same stochastic effects of traditional PCR for low-input concentrations. The study aims to evaluate the precision of
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DNA quantification is a crucial step in the STR typing workflow for human identification purposes. Given the reaction’s nature, qPCR assays may be subjected to the same stochastic effects of traditional PCR for low-input concentrations. The study aims to evaluate the precision of the PowerQuant® (Promega) kit assay measurements and the degree of variability for DNA templates falling below the optimal threshold of the PowerPlex® ESX-17 Fast STR typing kit (Promega). Five three-fold dilutions of the 2800 M control DNA (Promega) were set up. Each dilution (concentrations: 0.05, 0.0167, 0.0055, 0.00185, and 0.000617 ng/µL) was quantified and amplified in four replicates. Variability for qPCR results, STR profile completeness, and EPGs’ peak height were evaluated. The qPCR-estimated concentration of casework samples was correlated with profile completeness and peak intensity, to assess the predictive value of qPCR results for the successful STR typing of scarce samples. qPCR was subjected to stochastic effects, of which the degree was inversely proportional to the initial input template. Quantitation results and the STR profile’s characteristics were strongly correlated. Due to the intrinsic nature of real casework samples, a qPCR-derived DNA concentration threshold for correctly identifying probative STR profiles may be difficult to establish. Quantitation data may be useful in interpreting and corroborating STR typing results and for clearly illustrating them to the stakeholders.
Full article
(This article belongs to the Special Issue Genetic Tools and Techniques in Forensic Science—an In-Depth Look at the Process of Quantification of Forensic Samples)
Open AccessArticle
Effects of Environmental Hypoxia on Serum Hematological and Biochemical Parameters, Hypoxia-Inducible Factor (hif) Gene Expression and HIF Pathway in Hybrid Sturgeon (Acipenser schrenckii ♂ × Acipenser baerii ♀)
by
Yuanyuan Ren, Yuan Tian, Bo Cheng, Yang Liu and Huanhuan Yu
Genes 2024, 15(6), 743; https://doi.org/10.3390/genes15060743 - 5 Jun 2024
Abstract
Hypoxia is a globally pressing environmental problem in aquatic ecosystems. In the present study, a comprehensive analysis was performed to evaluate the effects of hypoxia on physiological responses (hematology, cortisol, biochemistry, hif gene expression and the HIF pathway) of hybrid sturgeons (Acipenser
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Hypoxia is a globally pressing environmental problem in aquatic ecosystems. In the present study, a comprehensive analysis was performed to evaluate the effects of hypoxia on physiological responses (hematology, cortisol, biochemistry, hif gene expression and the HIF pathway) of hybrid sturgeons (Acipenser schrenckii ♂ × Acipenser baerii ♀). A total of 180 hybrid sturgeon adults were exposed to dissolved oxygen (DO) levels of 7.00 ± 0.2 mg/L (control, N), 3.5 ± 0.2 mg/L (moderate hypoxia, MH) or 1.00 ± 0.1 mg/L (severe hypoxia, SH) and were sampled at 1 h, 6 h and 24 h after hypoxia. The results showed that the red blood cell (RBC) counts and the hemoglobin (HGB) concentration were significantly increased 6 h and 24 h after hypoxia in the SH group. The serum cortisol concentrations gradually increased with the decrease in the DO levels. Moreover, several serum biochemical parameters (AST, AKP, HBDB, LDH, GLU, TP and T-Bil) were significantly altered at 24 h in the SH group. The HIFs are transcription activators that function as master regulators in hypoxia. In this study, a complete set of six hif genes were identified and characterized in hybrid sturgeon for the first time. After hypoxia, five out of six sturgeon hif genes were significantly differentially expressed in gills, especially hif-1α and hif-3α, with more than 20-fold changes, suggesting their important roles in adaptation to hypoxia in hybrid sturgeon. A meta-analysis indicated that the HIF pathway, a major pathway for adaptation to hypoxic environments, was activated in the liver of the hybrid sturgeon 24 h after the hypoxia challenge. Our study demonstrated that hypoxia, particularly severe hypoxia (1.00 ± 0.1 mg/L), could cause considerable stress for the hybrid sturgeon. These results shed light on their adaptive mechanisms and potential biomarkers for hypoxia tolerance, aiding in aquaculture and conservation efforts.
Full article
(This article belongs to the Special Issue Genetic Studies of Fish)
Open AccessArticle
Mitogenomic Insights into the Evolution, Divergence Time, and Ancestral Ranges of Coturnix Quails
by
Prateek Dey, Swapna Devi Ray, Venkata Hanumat Sastry Kochiganti, Budhan S. Pukazhenthi, Klaus-Peter Koepfli and Ram Pratap Singh
Genes 2024, 15(6), 742; https://doi.org/10.3390/genes15060742 - 5 Jun 2024
Abstract
The Old-World quails, Coturnix coturnix (common quail) and Coturnix japonica (Japanese quail), are morphologically similar yet occupy distinct geographic ranges. This study aimed to elucidate their evolutionary trajectory and ancestral distribution patterns through a thorough analysis of their mitochondrial genomes. Mitogenomic analysis revealed
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The Old-World quails, Coturnix coturnix (common quail) and Coturnix japonica (Japanese quail), are morphologically similar yet occupy distinct geographic ranges. This study aimed to elucidate their evolutionary trajectory and ancestral distribution patterns through a thorough analysis of their mitochondrial genomes. Mitogenomic analysis revealed high structural conservation, identical translational mechanisms, and similar evolutionary pressures in both species. Selection analysis revealed significant evidence of positive selection across the Coturnix lineage for the nad4 gene tree owing to environmental changes and acclimatization requirements during its evolutionary history. Divergence time estimations imply that diversification among Coturnix species occurred in the mid-Miocene (13.89 Ma), and their current distributions were primarily shaped by dispersal rather than global vicariance events. Phylogenetic analysis indicates a close relationship between C. coturnix and C. japonica, with divergence estimated at 2.25 Ma during the Pleistocene epoch. Ancestral range reconstructions indicate that the ancestors of the Coturnix clade were distributed over the Oriental region. C. coturnix subsequently dispersed to Eurasia and Africa, and C. japonica to eastern Asia. We hypothesize that the current geographic distributions of C. coturnix and C. japonica result from their unique dispersal strategies, developed to evade interspecific territoriality and influenced by the Tibetan Plateau’s geographic constraints. This study advances our understanding of the biogeographic and evolutionary processes leading to the diversification of C. coturnix and C. japonica, laying important groundwork for further research on this genus.
Full article
(This article belongs to the Section Animal Genetics and Genomics)
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Open AccessBrief Report
Utilization of qPCR to Determine Duration and Environmental Drivers Contributing to the Persistence of Human DNA in Soil
by
Hannah L. Noel, Rebecca L. George, Brittania Bintz, Maureen Peters Hickman and Frankie West
Genes 2024, 15(6), 741; https://doi.org/10.3390/genes15060741 - 5 Jun 2024
Abstract
Little is known about the underlying mechanisms that contribute to the persistence and degradation of DNA within soil. The goals of this study are to determine the duration of mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) persistence in soils enriched by surface-level human
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Little is known about the underlying mechanisms that contribute to the persistence and degradation of DNA within soil. The goals of this study are to determine the duration of mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) persistence in soils enriched by surface-level human decomposition and to better understand the contribution of environmental factors. The surface-level decomposition of three human cadavers was documented over 11 weeks. Based on quantitative PCR results, we found nuDNA to persist in soils six weeks post-placement, while mtDNA was recoverable for the entire 11-week decomposition period. Principle components analyses and Spearman’s rank correlations revealed that (1) time, (2) total body score, and (3) weekly average air temperature were significantly correlated with concentrations of nuDNA and mtDNA in soil, suggesting these factors play a role in the degradation of DNA in soils.
Full article
(This article belongs to the Special Issue Genetic Tools and Techniques in Forensic Science—an In-Depth Look at the Process of Quantification of Forensic Samples)
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Open AccessArticle
Dual-model GWAS Analysis and Genomic Selection of Maize Flowering Time-Related Traits
by
Zehui Fan, Shaohang Lin, Jiale Jiang, Yukang Zeng, Yao Meng, Jiaojiao Ren and Penghao Wu
Genes 2024, 15(6), 740; https://doi.org/10.3390/genes15060740 - 4 Jun 2024
Abstract
An appropriate flowering period is an important selection criterion in maize breeding. It plays a crucial role in the ecological adaptability of maize varieties. To explore the genetic basis of flowering time, GWAS and GS analyses were conducted using an associating panel consisting
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An appropriate flowering period is an important selection criterion in maize breeding. It plays a crucial role in the ecological adaptability of maize varieties. To explore the genetic basis of flowering time, GWAS and GS analyses were conducted using an associating panel consisting of 379 multi-parent DH lines. The DH population was phenotyped for days to tasseling (DTT), days to pollen-shedding (DTP), and days to silking (DTS) in different environments. The heritability was 82.75%, 86.09%, and 85.26% for DTT, DTP, and DTS, respectively. The GWAS analysis with the FarmCPU model identified 10 single-nucleotide polymorphisms (SNPs) distributed on chromosomes 3, 8, 9, and 10 that were significantly associated with flowering time-related traits. The GWAS analysis with the BLINK model identified seven SNPs distributed on chromosomes 1, 3, 8, 9, and 10 that were significantly associated with flowering time-related traits. Three SNPs 3_198946071, 9_146646966, and 9_152140631 showed a pleiotropic effect, indicating a significant genetic correlation between DTT, DTP, and DTS. A total of 24 candidate genes were detected. A relatively high prediction accuracy was achieved with 100 significantly associated SNPs detected from GWAS, and the optimal training population size was 70%. This study provides a better understanding of the genetic architecture of flowering time-related traits and provides an optimal strategy for GS.
Full article
(This article belongs to the Section Plant Genetics and Genomics)
Open AccessArticle
A Nonsynonymous Substitution of Lhx3 Leads to Changes in Body Size in Dogs and Mice
by
Wanyi Dang, Dali Gao, Guangqi Lyu, David M. Irwin, Songyang Shang, Junnan Chen, Junpeng Zhang, Shuyi Zhang and Zhe Wang
Genes 2024, 15(6), 739; https://doi.org/10.3390/genes15060739 - 4 Jun 2024
Abstract
Lhx3 is a LIM-homeodomain transcription factor that affects body size in mammals by regulating the secretion of pituitary hormones. Akita, Shiba Inu, and Mame Shiba Inu dogs are Japanese native dog breeds that have different body sizes. To determine whether Lhx3 plays a
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Lhx3 is a LIM-homeodomain transcription factor that affects body size in mammals by regulating the secretion of pituitary hormones. Akita, Shiba Inu, and Mame Shiba Inu dogs are Japanese native dog breeds that have different body sizes. To determine whether Lhx3 plays a role in the differing body sizes of these three dog breeds, we sequenced the Lhx3 gene in the three breeds, which led to the identification of an SNP in codon 280 (S280N) associated with body size. The allele frequency at this SNP differed significantly between the large Akita and the two kinds of smaller Shiba dogs. To validate the function of this SNP on body size, we introduced this change into the Lhx3 gene of mice. Homozygous mutant mice (S279N+/+) were found to have significantly increased body lengths and weights compared to heterozygous mutant (S279N+/−) and wild-type (S279N−/−) mice several weeks after weaning. These results demonstrate that a nonsynonymous substitution in Lhx3 plays an important role in regulating body size in mammals.
Full article
(This article belongs to the Section Animal Genetics and Genomics)
Open AccessReview
Effects of Pathogenic Mutants of the Neuroprotective RNase 5-Angiogenin in Amyotrophic Lateral Sclerosis (ALS)
by
Giovanni Gotte
Genes 2024, 15(6), 738; https://doi.org/10.3390/genes15060738 - 4 Jun 2024
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease that affects the motoneurons. More than 40 genes are related with ALS, and amyloidogenic proteins like SOD1 and/or TDP-43 mutants are directly involved in the onset of ALS through the formation of polymorphic fibrillogenic
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Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease that affects the motoneurons. More than 40 genes are related with ALS, and amyloidogenic proteins like SOD1 and/or TDP-43 mutants are directly involved in the onset of ALS through the formation of polymorphic fibrillogenic aggregates. However, efficacious therapeutic approaches are still lacking. Notably, heterozygous missense mutations affecting the gene coding for RNase 5, an enzyme also called angiogenin (ANG), were found to favor ALS onset. This is also true for the less-studied but angiogenic RNase 4. This review reports the substrate targets and illustrates the neuroprotective role of native ANG in the neo-vascularization of motoneurons. Then, it discusses the molecular determinants of many pathogenic ANG mutants, which almost always cause loss of function related to ALS, that results in failures in angiogenesis and motoneuron protection. In addition, ANG mutations are sometimes combined with variants of other factors, thereby potentiating ALS effects. However, the activity of the native ANG enzyme should be finely balanced, and not excessive, to avoid possible harmful effects. Considering the interplay of these angiogenic RNases in many cellular processes, this review aims to stimulate further investigations to better elucidate the consequences of mutations in ANG and/or RNase 4 genes, in order to achieve early diagnosis and, possibly, successful therapies against ALS.
Full article
(This article belongs to the Special Issue Research Strategies to Unveil the Genetic and Molecular Basis of ALS)
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Open AccessArticle
A Divergent Platelet Transcriptome in Patients with Lipedema and Lymphedema
by
Alliefair Scalise, Anu Aggarwal, Naseer Sangwan, Annelise Hamer, Suman Guntupalli, Huijun Edelyn Park, Jose O. Aleman and Scott J. Cameron
Genes 2024, 15(6), 737; https://doi.org/10.3390/genes15060737 - 4 Jun 2024
Abstract
Lipedema and lymphedema are physically similar yet distinct diseases that are commonly misdiagnosed. We previously reported that lipedema and lymphedema are associated with increased risk for venous thromboembolism (VTE). The underlying etiology of the prothrombotic profile observed in lipedema and lymphedema is unclear,
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Lipedema and lymphedema are physically similar yet distinct diseases that are commonly misdiagnosed. We previously reported that lipedema and lymphedema are associated with increased risk for venous thromboembolism (VTE). The underlying etiology of the prothrombotic profile observed in lipedema and lymphedema is unclear, but may be related to alterations in platelets. Our objective was to analyze the platelet transcriptome to identify biological pathways that may provide insight into platelet activation and thrombosis. The platelet transcriptome was evaluated in patients with lymphedema and lipedema, then compared to control subjects with obesity. Patients with lipedema were found to have a divergent transcriptome from patients with lymphedema. The platelet transcriptome and impacted biological pathways in lipedema were surprisingly similar to weight-matched comparators, yet different when compared to overweight individuals with a lower body mass index (BMI). Differences in the platelet transcriptome for patients with lipedema and lymphedema were found in biological pathways required for protein synthesis and degradation, as well as metabolism. Key differences in the platelet transcriptome for patients with lipedema compared to BMI-matched subjects involved metabolism and glycosaminoglycan processing. These inherent differences in the platelet transcriptome warrant further investigation, and may contribute to the increased risk of thrombosis in patients with lipedema and lymphedema.
Full article
(This article belongs to the Special Issue Genetics of Obesity)
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Open AccessArticle
Polymorphisms in the Dopaminergic Receptor D3 Gene Correlate with Disease Progression Rate in Relapsing–Remitting Multiple Sclerosis Patients
by
Marco Ferrari, Domizia Vecchio, Sandra D’Alfonso, Alessandra Gemma, Franca Marino, Cristoforo Comi and Marco Cosentino
Genes 2024, 15(6), 736; https://doi.org/10.3390/genes15060736 - 3 Jun 2024
Abstract
Background: Multiple sclerosis (MS) is a common chronic autoimmune disease of the central nervous system. In MS, disability progresses unpredictably. Dopamine (DA) is a modulator of immune functions, and compelling evidence supports its involvement in both pathogenesis and treatment of MS. Although single
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Background: Multiple sclerosis (MS) is a common chronic autoimmune disease of the central nervous system. In MS, disability progresses unpredictably. Dopamine (DA) is a modulator of immune functions, and compelling evidence supports its involvement in both pathogenesis and treatment of MS. Although single nucleotide polymorphisms (SNPs) in dopaminergic receptor (DR) genes have been extensively studied, their role in MS progression remains unexplored. Therefore, the aim of this explorative study is to investigate the potential association between functional SNPs in DR genes and MS progression. Methods: Caucasian patients with relapsing–remitting (RR) MS were enrolled, and disease progression assessed by the Multiple Sclerosis Severity Score (MSSS). Results: Out of the 59 RRMS patients enrolled, those with the G/G genotype for rs6280 and rs1800828 SNPs in DRD3 showed significantly higher MSSSs compared to those with ancestral and heterozygous genotypes. Conclusions: If confirmed in a larger prospective study, the reported findings could contribute to a better understanding of MS pathophysiological mechanisms, opening the way for the identification of marker(s) for assessing MS progression as well as novel therapeutic strategies. A personalized approach to MS management has the potential to improve the overall well-being of MS patients and alleviate the burden on their caregivers.
Full article
(This article belongs to the Topic Advances in Genetics and Precision Medicine in Human Diseases)
Open AccessArticle
Extracellular Vesicles from NSC-34 MN-like Cells Transfected with Mutant SOD1 Modulate Inflammatory Status of Raw 264.7 Macrophages
by
Elisabetta Carata, Marco Muci, Stefania Mariano, Simona Di Giulio, Annamaria Nigro, Alessandro Romano and Elisa Panzarini
Genes 2024, 15(6), 735; https://doi.org/10.3390/genes15060735 - 3 Jun 2024
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease targeting the brain and spinal cord. Non-neuronal cells, including macrophages, may contribute to the disruption of motor neurons (MNs), neuromuscular junction dismantling and clinical signs of ALS. Understanding the modality and the effect of MNs–macrophage
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Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease targeting the brain and spinal cord. Non-neuronal cells, including macrophages, may contribute to the disruption of motor neurons (MNs), neuromuscular junction dismantling and clinical signs of ALS. Understanding the modality and the effect of MNs–macrophage communication is pivotal. Here, we focus on extracellular vesicle (EVS)-mediated communication and, in particular, we analyze the response of macrophages. NSC-34 cells transfected with mutant SOD1 (G93A, A4V, G85R, G37R) and differentiated towards MN-like cells, and Raw 264.7 macrophages are the cellular models of the study. mSOD1 NSC-34 cells release a high number of vesicles, both large-lEVs (300 nm diameter) and small-sEVs (90 nm diameter), containing inflammation-modulating molecules, and are efficiently taken up by macrophages. RT-PCR analysis of inflammation mediators demonstrated that the conditioned medium of mSOD1 NSC-34 cells polarizes Raw 264.7 macrophages towards both pro-inflammatory and anti-inflammatory phenotypes. sEVs act on macrophages in a time-dependent manner: an anti-inflammatory response mediated by TGFβ firstly starts (12 h); successively, the response shifts towards a pro-inflammation IL-1β-mediated (48 h). The response of macrophages is strictly dependent on the SOD1 mutation type. The results suggest that EVs impact physiological and behavioral macrophage processes and are of potential relevance to MN degeneration.
Full article
(This article belongs to the Special Issue Research Strategies to Unveil the Genetic and Molecular Basis of ALS)
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Open AccessArticle
Genetic Differentiation of Reed Canarygrass (Phalaris arundinacea L.) within Eastern Europe and Eurasia
by
Neil O. Anderson, Edvina Krokaitė-Kudakienė, Lina Jocienė, Tomas Rekašius, Olga A. Chernyagina, Algimantas Paulauskas and Eugenija Kupčinskienė
Genes 2024, 15(6), 734; https://doi.org/10.3390/genes15060734 - 3 Jun 2024
Abstract
Worldwide molecular research of economically important Phalaris arundinacea (Poaceae) is mainly focused on the invasions of this species from Europe to North America. Until the present study, the genetic diversity of the P. arundinacea had not been studied across the Baltic countries. The
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Worldwide molecular research of economically important Phalaris arundinacea (Poaceae) is mainly focused on the invasions of this species from Europe to North America. Until the present study, the genetic diversity of the P. arundinacea had not been studied across the Baltic countries. The objective of this research is to evaluate the diversity of Lithuanian populations of P. arundinacea at simple sequence repeat (SSR) loci comparatively among populations of the Baltic countries, Luxembourg, and the Russian Far East (Eurasian), evaluating differentiation between Lithuanian populations and ornamental accessions, and relating these with environmental features. For six selected Lithuanian river basin populations, GBS low density SNPs were used to determine genetic diversity. Bayesian analysis showed that Eurasian populations of Phalaris arundinacea consist of two gene clusters. Statistically significant genetic differentiation among European and Eurasian populations was documented. Lithuanian genotypes growing naturally along rivers are genetically distinct from cultivated ornamentals. GBS-SNPs divided the six selected Nemunas river basins into three distinct groups with one, two, or three rivers in separate groupings for genetic diversity. Genetic diversity is primarily within, rather than among, Lithuanian, eastern European, and Eurasian populations of P. arundinacea across the continent. Thus, restoration efforts would benefit from local population seed origination.
Full article
(This article belongs to the Section Genes & Environments)
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Open AccessPerspective
Hope on the Horizon? Aptamers in Diagnosis of Invasive Fungal Infections
by
Sadegh Khodavaisy and Jianping Xu
Genes 2024, 15(6), 733; https://doi.org/10.3390/genes15060733 - 3 Jun 2024
Abstract
Despite remarkable advances in the diagnosis of invasive fungal infections (IFIs), rapid, specific, sensitive, and cost-effective detection methods remain elusive. Due to their stability, ease of production, and specificity to signature molecules of fungal pathogens, short single-stranded sequences of DNA, RNA, and XNA,
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Despite remarkable advances in the diagnosis of invasive fungal infections (IFIs), rapid, specific, sensitive, and cost-effective detection methods remain elusive. Due to their stability, ease of production, and specificity to signature molecules of fungal pathogens, short single-stranded sequences of DNA, RNA, and XNA, collectively called aptamers, have emerged as promising diagnostic markers. In this perspective, we summarize recent progress in aptamer-based diagnostic tools for IFIs and discuss how these tools could potentially meet the needs and provide economical and simple solutions for point-of-care for better management of IFIs.
Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics in 2024)
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Open AccessArticle
Prognostic Role of Human Leukocyte Antigen Alleles and Cytokine Single-Nucleotide Polymorphisms in Patients with Chronic Myeloid Leukemia Treated with Tyrosine Kinase Inhibitor Drugs
by
Samuel Birru Kinde, Ilias Doxiadis, Rawleigh Howe, Tsehayneh Kelemu, Saifu Hailu Chala, Abdulaziz Sherif, Fisihatsion Tadesse, Aster Tsegaye, Amha Gebremedhin and Claudia Lehmann
Genes 2024, 15(6), 732; https://doi.org/10.3390/genes15060732 - 2 Jun 2024
Abstract
Tyrosine kinase inhibitor (TKI) drugs have significantly improved chronic myeloid leukemia (CML) outcomes. Neopeptides from CML cells may induce specific immune responses, which are crucial for deep molecular (DMR) and treatment-free remission (TFR). In this study of Ethiopian patients with CML (n =
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Tyrosine kinase inhibitor (TKI) drugs have significantly improved chronic myeloid leukemia (CML) outcomes. Neopeptides from CML cells may induce specific immune responses, which are crucial for deep molecular (DMR) and treatment-free remission (TFR). In this study of Ethiopian patients with CML (n = 162), the HLA alleles and single-nucleotide polymorphisms of five cytokines revealed significant associations with clinical outcomes. Clinically unfavorable outcomes correlated with HLA alleles A*03:01/02, A*23:17:01, B*57:01/02/03, and HLA-DRB4*01:01 (p-value = 0.0347, p-value = 0.0285, p-value = 0.037, and p-value = 0.0127, respectively), while HLA-DRB4*01:03:01 was associated with favorable outcomes (p-value = 0.0058). After assigning values for the ‘low,’ ‘intermediate,’ and ‘high’ gene expression of the SNPs’ respective cytokine genes, Kaplan–Meier estimates for relapse-free survival, adjusted for age, treatment duration, and relapse risk among patients after the administration of TKIs, indicated that a gene expression ratio above the overall median of TNF-α, IL-6, and the combination of TGF-β1/IL-10, IFNγ, and IL-6/IL-10 TGF-β1 was correlated with a higher likelihood of treatment failure ((RR: 3.01; 95% CI: 1.1–8.3; p-value = 0.0261) and (RR: 2.4; 95% CI: 1.1–5.2; p-value = 0.022), respectively). Multi-SNPs, surpassing single-SNPs, and HLA allele polymorphisms showed promise in predicting outcomes of patients with CML during TKI treatment, prompting further exploration into their potential utility.
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(This article belongs to the Special Issue Genetic Analyses of Immune Genes in Human and Animals)
Open AccessArticle
Transcriptional Comparison Reveals Differential Resistance Mechanisms between CMV-Resistant PBC688 and CMV-Susceptible G29
by
Guangjun Guo, Baogui Pan, Chengsheng Gong, Shubin Wang, Jinbing Liu, Changzhou Gao and Weiping Diao
Genes 2024, 15(6), 731; https://doi.org/10.3390/genes15060731 - 2 Jun 2024
Abstract
The Cucumber mosaic virus (CMV) presents a significant threat to pepper cultivation worldwide, leading to substantial yield losses. We conducted a transcriptional comparative study between CMV-resistant (PBC688) and -susceptible (G29) pepper accessions to understand the mechanisms of CMV resistance. PBC688 effectively suppressed CMV
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The Cucumber mosaic virus (CMV) presents a significant threat to pepper cultivation worldwide, leading to substantial yield losses. We conducted a transcriptional comparative study between CMV-resistant (PBC688) and -susceptible (G29) pepper accessions to understand the mechanisms of CMV resistance. PBC688 effectively suppressed CMV proliferation and spread, while G29 exhibited higher viral accumulation. A transcriptome analysis revealed substantial differences in gene expressions between the two genotypes, particularly in pathways related to plant–pathogen interactions, MAP kinase, ribosomes, and photosynthesis. In G29, the resistance to CMV involved key genes associated with calcium-binding proteins, pathogenesis-related proteins, and disease resistance. However, in PBC688, the crucial genes contributing to CMV resistance were ribosomal and chlorophyll a–b binding proteins. Hormone signal transduction pathways, such as ethylene (ET) and abscisic acid (ABA), displayed distinct expression patterns, suggesting that CMV resistance in peppers is associated with ET and ABA. These findings deepen our understanding of CMV resistance in peppers, facilitating future research and variety improvement.
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(This article belongs to the Special Issue Vegetable Genetic Breeding)
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Open AccessArticle
Phylogeny, Genetic Diversity and Population Structure of Fritillaria cirrhosa and Its Relatives Based on Chloroplast Genome Data
by
Jiao Huang, Xia Hu, Yong Zhou, Yan-Jie Peng and Zhong Liu
Genes 2024, 15(6), 730; https://doi.org/10.3390/genes15060730 - 2 Jun 2024
Abstract
Fritillaria cirrhosa and its relatives have been utilized in traditional Chinese medicine for many years and are under priority protection in China. Despite their medicinal and protective value, research on their phylogeny, genetic diversity, and divergence remains limited. Here, we investigate the chloroplast
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Fritillaria cirrhosa and its relatives have been utilized in traditional Chinese medicine for many years and are under priority protection in China. Despite their medicinal and protective value, research on their phylogeny, genetic diversity, and divergence remains limited. Here, we investigate the chloroplast genome variation architecture of 46 samples of F. cirrhosa and its relatives collected from various regions, encompassing the majority of wild populations across diverse geographical areas. The results indicate abundant variations in 46 accessions including 1659 single-nucleotide polymorphisms and 440 indels. Six variable markers (psbJ, ndhD, ycf1, ndhG, trnT-trnL, and rpl32-trnL) were identified. Phylogenetic and network analysis, population structure analysis, and principal component analysis showed that the 46 accessions formed five clades with significant divergence, which were related to their geographical distribution. The regions spanning from the southern Hengduan Mountains to the Qinghai–Tibet Plateau exhibited the highest levels of genetic diversity. F. cirrhosa and its relatives may have suffered a genetic bottleneck and have a relatively low genetic diversity level. Moreover, geographical barriers and discrete patches may have accelerated population divergence. The study offers novel perspectives on the phylogeny, genetic diversity, and population structure of F. cirrhosa and its relatives, information that can inform conservation and utilization strategies in the future.
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(This article belongs to the Section Plant Genetics and Genomics)
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Open AccessArticle
Gut Microbiota, Human Blood Metabolites, and Esophageal Cancer: A Mendelian Randomization Study
by
Xiuzhi Li, Bingchen Xu, Han Yang and Zhihua Zhu
Genes 2024, 15(6), 729; https://doi.org/10.3390/genes15060729 - 2 Jun 2024
Abstract
Background: Unbalances in the gut microbiota have been proposed as a possible cause of esophageal cancer (ESCA), yet the exact causal relationship remains unclear. Purpose: To investigate the potential causal relationship between the gut microbiota and ESCA with Mendelian randomization (MR) analysis. Methods:
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Background: Unbalances in the gut microbiota have been proposed as a possible cause of esophageal cancer (ESCA), yet the exact causal relationship remains unclear. Purpose: To investigate the potential causal relationship between the gut microbiota and ESCA with Mendelian randomization (MR) analysis. Methods: Genome-wide association studies (GWASs) of 207 gut microbial taxa (5 phyla, 10 classes, 13 orders, 26 families, 48 genera, and 105 species) and 205 gut microbiota metabolic pathways conducted by the Dutch Microbiome Project (DMP) and a FinnGen cohort GWAS of esophageal cancer specified the summary statistics. To investigate the possibility of a mediation effect between the gut microbiota and ESCA, mediation MR analyses were performed for 1091 blood metabolites and 309 metabolite ratios. Results: MR analysis indicated that the relative abundance of 10 gut microbial taxa was associated with ESCA but all the 12 gut microbiota metabolic pathways with ESCA indicated no statistically significant association existing. Two blood metabolites and a metabolite ratio were discovered to be mediating factors in the pathway from gut microbiota to ESCA. Conclusion: This research indicated the potential mediating effects of blood metabolites and offered genetic evidence in favor of a causal correlation between gut microbiota and ESCA.
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(This article belongs to the Section Microbial Genetics and Genomics)
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