Genes

19 pages, 12488 KiB

Open AccessArticle

Transcriptome Analysis Identifies Key Genes Involved in Response and Recovery to High Heat Stress Induced by Fire in Schima superba

by Shujing Wei, Yingxia Zhong, Wen Wen, Chong Yu, Ruisen Lu and Sisheng Luo

Genes 2024, 15(8), 1108; https://doi.org/10.3390/genes15081108 - 22 Aug 2024

Cited by 1 | Viewed by 780

Abstract

Fire-resistant tree species play a crucial role in forest fire prevention, utilizing several physiological and molecular mechanisms to respond to extreme heat stress. Many transcription factors (TFs) and genes are known to be involved in the regulatory network of heat stress response in [...] Read more.

Fire-resistant tree species play a crucial role in forest fire prevention, utilizing several physiological and molecular mechanisms to respond to extreme heat stress. Many transcription factors (TFs) and genes are known to be involved in the regulatory network of heat stress response in plants. However, their roles in response to high temperatures induced by fire remain less understood. In this study, we investigated Schima superba, a fire-resistant tree, to elucidate these mechanisms. Leaves of S. superba seedlings were exposed to fire stimulation for 10 s, 30 s, and 1 min, followed by a 24-h recovery period. Fifteen transcriptomes were assembled to identify key molecular and biological pathways affected by high temperatures. Differentially expressed genes (DEGs) analysis revealed essential candidate genes and TFs involved in the heat stress response, including members of the ethylene-responsive factors, WRKY, MYB, bHLH, and Nin-like families. Genes related to heat shock proteins/factors, lipid metabolism, antioxidant enzymes, dehydration responses, and hormone signal transduction were differentially expressed after heat stress and recovery, underscoring their roles in cellular process and recovery after heat stress. This study advances our understanding of plant response and defense strategies against extreme abiotic stresses. Full article

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

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13 pages, 874 KiB

Open AccessArticle

Clinical Features and Disease Progression in Older Individuals with Rett Syndrome

by Jeffrey L. Neul, Timothy A. Benke, Eric D. Marsh, Bernhard Suter, Cary Fu, Robin C. Ryther, Steven A. Skinner, David N. Lieberman, Timothy Feyma, Arthur Beisang, Peter Heydemann, Sarika U. Peters, Amitha Ananth and Alan K. Percy

Genes 2024, 15(8), 1107; https://doi.org/10.3390/genes15081107 - 22 Aug 2024

Viewed by 965

Abstract

Although long-term survival in Rett syndrome (RTT) has been observed, limited information on older people with RTT exists. We hypothesized that increased longevity in RTT would be associated with genetic variants in MECP2 associated with milder severity, and that clinical features would not [...] Read more.

Although long-term survival in Rett syndrome (RTT) has been observed, limited information on older people with RTT exists. We hypothesized that increased longevity in RTT would be associated with genetic variants in MECP2 associated with milder severity, and that clinical features would not be static in older individuals. To address these hypotheses, we compared the distribution of MECP2 variants and clinical severity between younger individuals with Classic RTT (under 30 years old) and older individuals (over 30 years old). Contrary to expectation, enrichment of a severe MECP2 variant (R106W) was observed in the older cohort. Overall severity was not different between the cohorts, but specific clinical features varied between the cohorts. Overall severity from first to last visit increased in the younger cohort but not in the older cohort. While some specific clinical features in the older cohort were stable from the first to the last visit, others showed improvement or worsening. These data do not support the hypothesis that mild MECP2 variants or less overall severity leads to increased longevity in RTT but demonstrate that clinical features change with increasing age in adults with RTT. Additional work is needed to understand disease progression in adults with RTT. Full article

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

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22 pages, 4485 KiB

Open AccessArticle

Genome-Wide Identification and Functional Analysis of the Genes of the ATL Family in Maize during High-Temperature Stress in Maize

by Haiping Ding, Xiaohu Li, Shilin Zhuge, Jiyuan Du, Min Wu, Wenlong Li, Yujing Li, Haoran Ma, Peng Zhang, Xingyu Wang, Guihua Lv, Zhiming Zhang and Fazhan Qiu

Genes 2024, 15(8), 1106; https://doi.org/10.3390/genes15081106 - 22 Aug 2024

Viewed by 958

Abstract

Maize is a significant food and feed product, and abiotic stress significantly impacts its growth and development. Arabidopsis Toxicosa en Levadura (ATL), a member of the RING-H2 E3 subfamily, modulates various physiological processes and stress responses in Arabidopsis. However, the [...] Read more.

Maize is a significant food and feed product, and abiotic stress significantly impacts its growth and development. Arabidopsis Toxicosa en Levadura (ATL), a member of the RING-H2 E3 subfamily, modulates various physiological processes and stress responses in Arabidopsis. However, the role of ATL in maize remains unexplored. In this study, we systematically identified the genes encoding ATL in the maize genome. The results showed that the maize ATL family consists of 77 members, all predicted to be located in the cell membrane and cytoplasm, with a highly conserved RING domain. Tissue-specific expression analysis revealed that the expression levels of ATL family genes were significantly different in different tissues. Examination of the abiotic stress data revealed that the expression levels of ATL genes fluctuated significantly under different stress conditions. To further understand the biological functions of maize ATL family genes under high-temperature stress, we studied the high-temperature phenotypes of the maize ZmATL family gene ZmATL10 and its homologous gene AtATL27 in Arabidopsis. The results showed that overexpression of the ZmATL10 and AtATL27 genes enhanced resistance to high-temperature stress. Full article

(This article belongs to the Special Issue Maize Molecular Genetics and Functional Genomics in 2024)

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13 pages, 593 KiB

Open AccessArticle

A Heuristic Approach to Analysis of the Genetic Susceptibility Profile in Patients Affected by Airway Allergies

by Domenico Lio, Gabriele Di Lorenzo, Ignazio Brusca, Letizia Scola, Chiara Bellia, Simona La Piana, Maria Barrale, Manuela Bova, Loredana Vaccarino, Giusi Irma Forte and Giovanni Pilato

Genes 2024, 15(8), 1105; https://doi.org/10.3390/genes15081105 - 22 Aug 2024

Viewed by 1001

Abstract

Allergic respiratory diseases such as asthma might be considered multifactorial diseases, having a complex pathogenesis that involves environmental factors and the activation of a large set of immune response pathways and mechanisms. In addition, variations in genetic background seem to play a central [...] Read more.

Allergic respiratory diseases such as asthma might be considered multifactorial diseases, having a complex pathogenesis that involves environmental factors and the activation of a large set of immune response pathways and mechanisms. In addition, variations in genetic background seem to play a central role. The method developed for the analysis of the complexities, as association rule mining, nowadays may be applied to different research areas including genetic and biological complexities such as atopic airway diseases to identify complex genetic or biological markers and enlighten new diagnostic and therapeutic targets. A total of 308 allergic patients and 205 controls were typed for 13 single nucleotide polymorphisms (SNPs) of cytokine and receptors genes involved in type 1 and type 2 inflammatory response (IL-4 rs2243250 C/T, IL-4R rs1801275A/G, IL-6 rs1800795 G/C, IL-10 rs1800872 A/C and rs1800896 A/G, IL-10RB rs2834167A/G, IL-13 rs1800925 C/T, IL-18 rs187238G/C, IFNγ rs 24030561A/T and IFNγR2 rs2834213G/A), the rs2228137C/T of CD23 receptor gene and rs577912C/T and rs564481C/T of Klotho genes, using KASPar SNP genotyping method. Clinical and laboratory data of patients were analyzed by formal statistic tools and by a data-mining technique—market basket analysis—selecting a minimum threshold of 90% of rule confidence. Formal statistical analyses show that IL-6 rs1800795GG, IL-10RB rs2834167G positive genotypes, IL-13 rs1800925CC, CD23 rs2228137TT Klotho rs564481TT, might be risk factors for allergy. Applying the association rule methodology, we identify 10 genotype combination patterns associated with susceptibility to allergies. Together these data necessitate being confirmed in further studies, indicating that the heuristic approach might be a straightforward and useful tool to find predictive and diagnostic molecular patterns that might be also considered potential therapeutic targets in allergy. Full article

(This article belongs to the Special Issue Bioinformatics of Disease Research)

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22 pages, 339 KiB

Open AccessReview

Leveraging Functional Genomics for Understanding Beef Quality Complexities and Breeding Beef Cattle for Improved Meat Quality

by Rugang Tian, Maryam Mahmoodi, Jing Tian, Sina Esmailizadeh Koshkoiyeh, Meng Zhao, Mahla Saminzadeh, Hui Li, Xiao Wang, Yuan Li and Ali Esmailizadeh

Genes 2024, 15(8), 1104; https://doi.org/10.3390/genes15081104 - 22 Aug 2024

Viewed by 1649

Abstract

Consumer perception of beef is heavily influenced by overall meat quality, a critical factor in the cattle industry. Genomics has the potential to improve important beef quality traits and identify genetic markers and causal variants associated with these traits through genomic selection (GS) [...] Read more.

Consumer perception of beef is heavily influenced by overall meat quality, a critical factor in the cattle industry. Genomics has the potential to improve important beef quality traits and identify genetic markers and causal variants associated with these traits through genomic selection (GS) and genome-wide association studies (GWAS) approaches. Transcriptomics, proteomics, and metabolomics provide insights into underlying genetic mechanisms by identifying differentially expressed genes, proteins, and metabolic pathways linked to quality traits, complementing GWAS data. Leveraging these functional genomics techniques can optimize beef cattle breeding for enhanced quality traits to meet high-quality beef demand. This paper provides a comprehensive overview of the current state of applications of omics technologies in uncovering functional variants underlying beef quality complexities. By highlighting the latest findings from GWAS, GS, transcriptomics, proteomics, and metabolomics studies, this work seeks to serve as a valuable resource for fostering a deeper understanding of the complex relationships between genetics, gene expression, protein dynamics, and metabolic pathways in shaping beef quality. Full article

(This article belongs to the Special Issue Breeding and Functional Genomics in Animals)

11 pages, 996 KiB

Open AccessArticle

Identification of Nonsynonymous SNPs in Immune-Related Genes Associated with Pneumonia Severity in Pigs

by Hiroki Shinkai, Kasumi Suzuki, Tomohito Itoh, Gou Yoshioka, Takato Takenouchi, Haruki Kitazawa and Hirohide Uenishi

Genes 2024, 15(8), 1103; https://doi.org/10.3390/genes15081103 - 21 Aug 2024

Viewed by 901

Abstract

We previously showed that several polymorphisms in genes encoding pattern recognition receptors that cause amino acid substitutions alter pathogen recognition ability and disease susceptibility in pigs. In this study, we expanded our analysis to a wide range of immune-related genes and investigated polymorphism [...] Read more.

We previously showed that several polymorphisms in genes encoding pattern recognition receptors that cause amino acid substitutions alter pathogen recognition ability and disease susceptibility in pigs. In this study, we expanded our analysis to a wide range of immune-related genes and investigated polymorphism distribution and its influence on pneumonia in multiple commercial pig populations. Among the polymorphisms in 42 genes causing 634 amino acid substitutions extracted from the swine genome database, 80 in 24 genes were found to have a minor allele frequency of at least 10% in Japanese breeding stock pigs via targeted resequencing. Of these, 62 single nucleotide polymorphisms (SNPs) in 23 genes were successfully genotyped in 862 pigs belonging to four populations with data on pneumonia severity. Association analysis using a generalized linear mixed model revealed that 12 SNPs in nine genes were associated with pneumonia severity. In particular, SNPs in the cellular receptor for immunoglobulin G FCGR2B and the intracellular nucleic acid sensors IFI16 and LRRFIP1 were found to be associated with mycoplasmal pneumonia of swine or porcine pleuropneumonia in multiple populations and may therefore have wide applications in the improvement of disease resistance in pigs. Functional analyses at the cellular and animal levels are required to clarify the mechanisms underlying the effects of these SNPs on disease susceptibility. Full article

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

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13 pages, 2981 KiB

Open AccessArticle

Transcriptome Analysis of Ethylene-Related Genes in Chlorine Dioxide-Treated Fresh-Cut Cauliflower

by Weiwei Jin, Qiaojun Jiang, Haijun Zhao, Fengxian Su, Yan Li and Shaolan Yang

Genes 2024, 15(8), 1102; https://doi.org/10.3390/genes15081102 - 21 Aug 2024

Cited by 1 | Viewed by 670

Abstract

Chlorine dioxide (ClO₂) is widely used for the quality preservation of postharvest horticultural plants. However, the molecular mechanism of how ClO₂ works is not clear. The purpose of this study was to understand ethylene-related molecular signaling in ClO₂-treated [...] Read more.

Chlorine dioxide (ClO₂) is widely used for the quality preservation of postharvest horticultural plants. However, the molecular mechanism of how ClO₂ works is not clear. The purpose of this study was to understand ethylene-related molecular signaling in ClO₂-treated fresh-cut cauliflower florets. Transcriptome analysis was used to investigate ethylene-related gene regulation. A total of 182.83 Gb clean data were acquired, and the reads of each sample to the unique mapped position of the reference genome could reach more than 85.51%. A sum of 2875, 3500, 4582 and 1906 differential expressed genes (DEGs) were identified at 0 d, 4 d, 8 d and 16 d between the control group and ClO₂-treated group, respectively. DEGs were enriched in functions such as ‘response to oxygen-containing compounds’ and ‘phosphorylation’, as well as MAPK signaling pathway, plant hormone transduction pathway and so on. Genes, including OXI1, MPK3, WRKY22 and ERF1, which are located at the junction of wounding, pathogen attack, pathogen infection or ethylene signal transduction pathways, were up-regulated in response to stress. ETR and CTR1 (both up-regulated), as well as three down-regulated genes, including BolC5t34953H (a probable NAC), BolC1t05767H (a probable NAC) and BolC2t06548H (a probable ERF13), might work as negative regulators for ethylene signal transduction. In conclusion, ethylene-related genes and pathways are involved in ClO₂ treatment, which might enhance stress resistance and have a negative feedback mechanism. Full article

(This article belongs to the Special Issue Gene Regulation of Ripening, Senescence and Stress Resistance in Horticultural Crops)

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18 pages, 2904 KiB

Open AccessArticle

Relationship between Capillaroscopic Architectural Patterns and Different Variant Subgroups in Fabry Disease: Analysis of Cases from a Multidisciplinary Center

by Denise Cristiana Faro, Francesco Lorenzo Di Pino, Margherita Stefania Rodolico, Luca Costanzo, Valentina Losi, Luigi Di Pino and Ines Paola Monte

Genes 2024, 15(8), 1101; https://doi.org/10.3390/genes15081101 - 21 Aug 2024

Viewed by 899

Abstract

Anderson–Fabry disease (AFD) is a genetic lysosomal storage disorder caused by mutations in the α-galactosidase A gene, leading to impaired lysosomal function and resulting in both macrovascular and microvascular alterations. AFD patients often exhibit increased intima-media thickness (IMT) and reduced flow-mediated dilation (FMD), [...] Read more.

Anderson–Fabry disease (AFD) is a genetic lysosomal storage disorder caused by mutations in the α-galactosidase A gene, leading to impaired lysosomal function and resulting in both macrovascular and microvascular alterations. AFD patients often exhibit increased intima-media thickness (IMT) and reduced flow-mediated dilation (FMD), indicating non-atherosclerotic arterial thickening and the potential for cardiovascular events. Nailfold capillaroscopy, a non-invasive diagnostic tool, has shown potential in diagnosing and monitoring microcirculatory disorders in AFD, despite limited research. This study evaluates nailfold capillaroscopy findings in AFD patients, exploring correlations with GLA gene variant subgroups (associated with classical or late-onset phenotypes and variants of uncertain significance (VUSs)), and assessing morpho-functional differences between sexes. It aims to determine whether capillaroscopy can assist in the early identification of individuals with multiorgan vascular involvement. A retrospective observational study was conducted with 25 AFD patients from AOUP “G. Rodolico-San Marco” in Catania (2020–2023). Patients underwent genetic testing, enzyme activity evaluation, and nailfold capillaroscopy using Horus basic HS 200 videodermatoscopy. Parameters like angiotectonic disorder, vascular areas, capillary density, and intimal thickening were assessed. The study identified significant differences in capillaroscopy findings among patients with different GLA gene variant subgroups. Classic AFD variant patients showed reduced capillary length and signs of erythrocyte aggregation and dilated subpapillary plexus. No correlation was found between enzymatic activity and capillaroscopy parameters. However, Lyso-Gb3 levels were positively correlated with average capillary length (ῤ = 0.453; p = 0.059). Sex-specific differences in capillaroscopy findings were observed in neoangiogenesis and average capillary length, with distinct implications for men and women. This study highlights the potential of nailfold capillaroscopy in the diagnostic process and clinical management of AFD, particularly in relation to specific GLA gene mutations, as a valuable tool for the early diagnosis and monitoring of AFD. Full article

(This article belongs to the Special Issue Advances in Genetic Counseling and Genetic Testing in Precision Medicine)

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11 pages, 2386 KiB

Open AccessFeature PaperArticle

Comparative Analysis of Two NGS-Based Platforms for Product-of-Conception Karyotyping

by Yuri Murase, Yui Shichiri, Hidehito Inagaki, Tatsuya Nakano, Yoshiharu Nakaoka, Yoshiharu Morimoto, Tomoko Ichikawa, Haruki Nishizawa, Eiji Sugihara and Hiroki Kurahashi

Genes 2024, 15(8), 1100; https://doi.org/10.3390/genes15081100 - 21 Aug 2024

Viewed by 837

Abstract

Cytogenetic information about the product of conception (POC) is important to determine the presence of recurrent chromosomal abnormalities that are an indication for preimplantation genetic testing for aneuploidy or structural rearrangements. Although microscopic examination by G-staining has long been used for such an [...] Read more.

Cytogenetic information about the product of conception (POC) is important to determine the presence of recurrent chromosomal abnormalities that are an indication for preimplantation genetic testing for aneuploidy or structural rearrangements. Although microscopic examination by G-staining has long been used for such an evaluation, detection failures are relatively common with this method, due to cell-culture-related issues. The utility of low-coverage whole-genome sequencing (lcWGS) using short-read next-generation sequencing (NGS) has been highlighted recently as an alternative cytogenomic approach for POC analysis. We, here, performed comparative analysis of two NGS-based protocols for this purpose based on different short-read sequencers (the Illumina VeriSeq system using a MiSeq sequencer and the Thermo Fisher ReproSeq system using an Ion S5 sequencer). The cytogenomic diagnosis obtained with each NGS method was equivalent in each of 20 POC samples analyzed. Notably, X chromosome sequence reads were reduced in some female samples with both systems. The possibility of low-level mosaicism for monosomy X as an explanation for this was excluded by FISH analysis. Additional data from samples with various degrees of X chromosome aneuploidy suggested that it was a technical artifact related to X chromosome inactivation. Indeed, subsequent nanopore sequencing indicated that the DNA in the samples showing the artifact was predominantly unmethylated. Our current findings indicate that although X chromosome data must be interpreted with caution, both the systems we tested for NGS-based lcWGS are useful alternatives for the karyotyping of POC samples. Full article

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

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14 pages, 4217 KiB

Open AccessArticle

Local Ancestry Inference Based on Population-Specific Single-Nucleotide Polymorphisms—A Study of Admixed Populations in the 1000 Genomes Project

by Haoyue Fu and Gang Shi

Genes 2024, 15(8), 1099; https://doi.org/10.3390/genes15081099 - 21 Aug 2024

Viewed by 1093

Abstract

Human populations have interacted throughout history, and a considerable portion of modern human populations show evidence of admixture. Local ancestry inference (LAI) is focused on detecting the genetic ancestry of chromosomal segments in admixed individuals and has wide applications. In this work, we [...] Read more.

Human populations have interacted throughout history, and a considerable portion of modern human populations show evidence of admixture. Local ancestry inference (LAI) is focused on detecting the genetic ancestry of chromosomal segments in admixed individuals and has wide applications. In this work, we proposed a new LAI method based on population-specific single-nucleotide polymorphisms (SNPs) and applied it in the analysis of admixed populations in the 1000 Genomes Project (1KGP). Based on population-specific SNPs in a sliding window, we computed local ancestry information vectors, which are moment estimators of local ancestral proportions, for two haplotypes of an admixed individual and inferred the local ancestral origins. Then we used African (AFR), East Asian (EAS), European (EUR) and South Asian (SAS) populations from the 1KGP and indigenous American (AMR) populations from the Human Genome Diversity Project (HGDP) as reference populations and conducted the proposed LAI analysis on African American populations and American populations in the 1KGP. The results were compared with those obtained by RFMix, G-Nomix and FLARE. We demonstrated that the existence of alleles in a chromosomal region that are specific to a particular reference population and the absence of alleles specific to the other reference populations provide reasonable evidence for determining the ancestral origin of the region. Contemporary AFR, AMR and EUR populations approximate ancestral populations of the admixed populations well, and the results from RFMix, G-Nomix and FLARE largely agree with those from the Ancestral Spectrum Analyzer (ASA), in which the proposed method was implemented. When admixtures are ancient and contemporary reference populations do not satisfactorily approximate ancestral populations, the performances of RFMix, G-Nomix and FLARE deteriorate with increased error rates and fragmented chromosomal segments. In contrast, our method provides fair results. Full article

(This article belongs to the Special Issue The Genetic Diversification of Human Populations)

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12 pages, 4168 KiB

Open AccessArticle

Genotype-First Approach Identifies an Association between rs28374544/FOG2^S657G and Liver Disease through Alterations in mTORC1 Signaling

by Donna M. Conlon, Siri Kanakala, Tess Cherlin, Yi-An Ko, Cecilia Vitali, Sharavana Gurunathan, Rasika Venkatesh, Jakob Woerner, Lindsay A. Guare, Penn Medicine Biobank, Anurag Verma, Shefali S. Verma and Marie A. Guerraty

Genes 2024, 15(8), 1098; https://doi.org/10.3390/genes15081098 - 21 Aug 2024

Viewed by 1036

Abstract

Metabolic dysfunction-associated Fatty Liver Disease (MAFLD) has emerged as one of the leading cardiometabolic diseases. Friend of GATA2 (FOG2) is a transcriptional co-regulator that has been shown to regulate hepatic lipid metabolism and accumulation. Using meta-analysis from several different biobank datasets, we identified [...] Read more.

Metabolic dysfunction-associated Fatty Liver Disease (MAFLD) has emerged as one of the leading cardiometabolic diseases. Friend of GATA2 (FOG2) is a transcriptional co-regulator that has been shown to regulate hepatic lipid metabolism and accumulation. Using meta-analysis from several different biobank datasets, we identified a coding variant of FOG2 (rs28374544, A1969G, S657G) predominantly found in individuals of African ancestry (minor allele frequency~20%), which is associated with liver failure/cirrhosis phenotype and liver injury. To gain insight into potential pathways associated with this variant, we interrogated a previously published genomics dataset of 38 human induced pluripotent stem cell (iPSCs) lines differentiated into hepatocytes (iHeps). Using Differential Gene Expression Analysis and Gene Set Enrichment Analysis, we identified the mTORC1 pathway as differentially regulated between iHeps from individuals with and without the variant. Transient lipid-based transfections were performed on the human hepatoma cell line (Huh7) using wild-type FOG2 and FOG2^S657G and demonstrated that FOG2S^657G increased mTORC1 signaling, de novo lipogenesis, and cellular triglyceride synthesis and mass. In addition, we observed a significant downregulation of oxidative phosphorylation in FOG2^S657G cells in fatty acid-loaded cells but not untreated cells, suggesting that FOG2^S657G may also reduce fatty acid to promote lipid accumulation. Taken together, our multi-pronged approach suggests a model whereby the FOG2^S657G may promote MAFLD through mTORC1 activation, increased de novo lipogenesis, and lipid accumulation. Our results provide insights into the molecular mechanisms by which FOG2^S657G may affect the complex molecular landscape underlying MAFLD. Full article

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

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16 pages, 2951 KiB

Open AccessArticle

Fine Mapping and Candidate Gene Analysis of Two Major Quantitative Trait Loci, qFW2.1 and qFW3.1, Controlling Fruit Weight in Pepper (Capsicum annuum)

by Congcong Guan, Yuan Jin, Zhenghai Zhang, Yacong Cao, Huamao Wu, Daiyuan Zhou, Wenqi Shao, Chuangchuang Yang, Guoliang Ban, Lingling Ma, Xin Wen, Lei Chen, Shanhan Cheng, Qin Deng, Hailong Yu and Lihao Wang

Genes 2024, 15(8), 1097; https://doi.org/10.3390/genes15081097 - 20 Aug 2024

Cited by 1 | Viewed by 893

Abstract

Fruit weight is an important agronomic trait in pepper production and is closely related to yield. At present, many quantitative trait loci (QTL) related to fruit weight have been found in pepper; however, the genes affecting fruit weight remain unknown. We analyzed the [...] Read more.

Fruit weight is an important agronomic trait in pepper production and is closely related to yield. At present, many quantitative trait loci (QTL) related to fruit weight have been found in pepper; however, the genes affecting fruit weight remain unknown. We analyzed the fruit weight-related quantitative traits in an intraspecific Capsicum annuum cross between the cultivated species blocky-type pepper, cv. Qiemen, and the bird pepper accession, “129−1” (Capsicum annuum var. glatriusculum), which was the wild progenitor of C. annuum. Using the QTL-seq combined with the linkage-based QTL mapping approach, QTL detection was performed; and two major effects of QTL related to fruit weight, qFW2.1 and qFW3.1, were identified on chromosomes 2 and 3. The qFW2.1 maximum explained 12.28% of the phenotypic variance observed in two F₂ generations, with the maximum LOD value of 11.02, respectively; meanwhile, the qFW3.1 maximum explained 15.50% of the observed phenotypic variance in the two F₂ generations, with the maximum LOD value of 11.36, respectively. qFW2.1 was narrowed down to the 1.22 Mb region using homozygous recombinant screening from BC₂S₂ and BC₂S₃ populations, while qFW3.1 was narrowed down to the 4.61Mb region. According to the transcriptome results, a total of 47 and 86 differentially expressed genes (DEGs) in the candidate regions of qFW2.1 and qFW3.1 were identified. Further, 19 genes were selected for a qRT-PCR analysis based on sequence difference combined with the gene annotation. Finally, Capana02g002938 and Capana02g003021 are the most likely candidate genes for qFW2.1, and Capana03g000903 may be a candidate gene for qFW3.1. Taken together, our results identified and fine-mapped two major QTL for fruit weight in pepper that will facilitate marker-assistant breeding for the manipulation of yield in pepper. Full article

(This article belongs to the Special Issue Pepper Genetic Breeding and Germplasm Innovation)

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14 pages, 10954 KiB

Open AccessArticle

PLEKHG1: New Potential Candidate Gene for Periventricular White Matter Abnormalities

by Francesco Calì, Mirella Vinci, Simone Treccarichi, Carla Papa, Angelo Gloria, Antonino Musumeci, Concetta Federico, Girolamo Aurelio Vitello, Antonio Gennaro Nicotera, Gabriella Di Rosa, Luigi Vetri, Salvatore Saccone and Maurizio Elia

Genes 2024, 15(8), 1096; https://doi.org/10.3390/genes15081096 - 20 Aug 2024

Viewed by 889

Abstract

Hypoxic-ischemic brain damage presents a significant neurological challenge, often manifesting during the perinatal period. Specifically, periventricular leukomalacia (PVL) is emerging as a notable contributor to cerebral palsy and intellectual disabilities. It compromises cerebral microcirculation, resulting in insufficient oxygen or blood flow to the [...] Read more.

Hypoxic-ischemic brain damage presents a significant neurological challenge, often manifesting during the perinatal period. Specifically, periventricular leukomalacia (PVL) is emerging as a notable contributor to cerebral palsy and intellectual disabilities. It compromises cerebral microcirculation, resulting in insufficient oxygen or blood flow to the periventricular region of the brain. As widely documented, these pathological conditions can be caused by several factors encompassing preterm birth (4–5% of the total cases), as well single cotwin abortion and genetic variants such as those associated with GTPase pathways. Whole exome sequencing (WES) analysis identified a de novo causative variant within the pleckstrin homology domain-containing family G member 1 (PLEKHG1) gene in a patient presenting with PVL. The PLEKHG1 gene is ubiquitously expressed, showing high expression patterns in brain tissues. PLEKHG1 is part of a family of Rho guanine nucleotide exchange factors, and the protein is essential for cell division control protein 42 (CDC42) activation in the GTPase pathway. CDC42 is a key small GTPase of the Rho-subfamily, regulating various cellular functions such as cell morphology, migration, endocytosis, and cell cycle progression. The molecular mechanism involving PLEKHG1 and CDC42 has an intriguing role in the reorientation of cells in the vascular endothelium, thus suggesting that disruption responses to mechanical stress in endothelial cells may be involved in the formation of white matter lesions. Significantly, CDC42 association with white matter abnormalities is underscored by its MIM phenotype number. In contrast, although PLEKHG1 has been recently associated with patients showing white matter hyperintensities, it currently lacks a MIM phenotype number. Additionally, in silico analyses classified the identified variant as pathogenic. Although the patient was born prematurely and subsequently to dichorionic gestation, during which its cotwin died, we suggest that the variant described can strongly contribute to PVL. The aim of the current study is to establish a plausible association between the PLEKHG1 gene and PVL. Full article

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

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15 pages, 843 KiB

Open AccessReview

Genetic and Pathophysiological Basis of Cardiac and Skeletal Muscle Laminopathies

by Shruti Bhide, Sahaana Chandran, Namakkal S. Rajasekaran and Girish C. Melkani

Genes 2024, 15(8), 1095; https://doi.org/10.3390/genes15081095 - 20 Aug 2024

Viewed by 1045

Abstract

Nuclear lamins, a type V intermediate filament, are crucial components of the nuclear envelope’s inner layer, maintaining nuclear integrity and mediating interactions between the nucleus and cytoplasm. Research on human iPSC-derived cells and animal models has demonstrated the importance of lamins in cardiac [...] Read more.

Nuclear lamins, a type V intermediate filament, are crucial components of the nuclear envelope’s inner layer, maintaining nuclear integrity and mediating interactions between the nucleus and cytoplasm. Research on human iPSC-derived cells and animal models has demonstrated the importance of lamins in cardiac and skeletal muscle development and function. Mutations in lamins result in laminopathies, a group of diseases including muscular dystrophies, Hutchison–Gilford progeria syndrome, and cardiomyopathies with conduction defects. These conditions have been linked to disrupted autophagy, mTOR, Nrf2-Keap, and proteostasis signaling pathways, indicating complex interactions between the nucleus and cytoplasm. Despite progress in understanding these pathways, many questions remain about the mechanisms driving lamin-induced pathologies, leading to limited therapeutic options. This review examines the current literature on dysregulated pathways in cardiac and skeletal muscle laminopathies and explores potential therapeutic strategies for these conditions. Full article

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

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13 pages, 30771 KiB

Open AccessArticle

Transcriptome Analysis Reveals Novel Inflammatory Signalings to Glaesserella parasuis Infection

by Jingwen Lei, Xuexue Chen, Huanhuan Zhou, Zekai Zhang, Zhong Xu, Ke Xu and Hongbo Chen

Genes 2024, 15(8), 1094; https://doi.org/10.3390/genes15081094 - 20 Aug 2024

Viewed by 890

Abstract

Glaesserella parasuis (GPS) can cause severe systemic inflammation in pigs, resulting in huge economic losses to the pig industry. At present, no effective method is available for the prevention and control of GPS infection. Molecular breeding for disease resistance is imminent, but disease-resistance [...] Read more.

Glaesserella parasuis (GPS) can cause severe systemic inflammation in pigs, resulting in huge economic losses to the pig industry. At present, no effective method is available for the prevention and control of GPS infection. Molecular breeding for disease resistance is imminent, but disease-resistance genes have not been identified. To study the mechanism of systemic acute inflammation caused by GPS, we established three in vitro infection models (3D4/21 cells, PK15 cells, and PAVEC cells) according to its infection path. There was no significant difference in apoptosis among the three kinds of cells after 12 h of continuous GPS stimulation, while inflammatory factors were significantly upregulated. Subsequent transcriptome analysis revealed 1969, 1207, and 3564 differentially expressed genes (DEGs) in 3D4/21 cells, PK15 cells, and PAVEC cells, respectively, after GPS infection. Many of the DEGs were predicted to be associated with inflammatory responses (C3, CD44, etc.); cell proliferation, growth and apoptosis; gene expression; and protein phosphorylation. Key signaling pathways, including S100 family signaling, bacteria and virus recognition, and pathogen-induced cytokine storm signaling, were enriched based on Ingenuity Pathway Analysis (IPA). Furthermore, a total of three putative transmembrane receptors and two putative G-protein-coupled receptors, namely F3, ICAM1, PLAUR, ACKR3, and GPRC5A, were identified by IPA among the three types of cells. ACKR3 and GPRC5A play pivotal roles in bacterial adhesion, invasion, host immune response and inflammatory response through the S100 family signaling pathway. Our findings provide new insights into the pathological mechanisms underlying systemic inflammation caused by GPS infection in pigs, and they lay a foundation for further research on disease-resistance breeding to GPS. Full article

(This article belongs to the Special Issue Breeding and Functional Genomics in Animals)

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20 pages, 28009 KiB

Open AccessArticle

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

Viewed by 1239

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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10 pages, 592 KiB

Open AccessArticle

Novel Loss-of-Function SYCP2 Variants in Infertile Males Upgrade the Gene–Disease Clinical Validity Classification for SYCP2 and Male Infertility to Strong

by Jinli Li, Samantha L.P. Schilit, Shanshan Liang, Ningxin Qin, Xiaoming Teng and Junyu Zhang

Genes 2024, 15(8), 1092; https://doi.org/10.3390/genes15081092 - 19 Aug 2024

Viewed by 1189

Abstract

Male infertility affects approximately 7% of the male population, and about 15% of these cases are predicted to have a genetic etiology. One gene implicated in autosomal dominant male infertility, SYCP2, encodes a protein critical for the synapsis of homologous chromosomes during [...] Read more.

Male infertility affects approximately 7% of the male population, and about 15% of these cases are predicted to have a genetic etiology. One gene implicated in autosomal dominant male infertility, SYCP2, encodes a protein critical for the synapsis of homologous chromosomes during meiosis I, resulting in impaired spermatogenesis. However, the clinical validity of the gene–disease pair was previously categorized as on the border of limited and moderate due to few reported cases. This study investigates the genetic cause of infertility for three unrelated Chinese patients with oligoasthenozoospermia. Whole exome sequencing (WES) and subsequent Sanger sequencing revealed novel heterozygous loss-of-function (LOF) variants in SYCP2 (c.89dup, c.946_947del, and c.4378_4379del). These cases, combined with the previously reported cases, provide strong genetic evidence supporting an autosomal dominant inheritance pattern. The experimental evidence also demonstrates a critical role for SYCP2 in spermatogenesis. Collectively, this updated assessment of the genetic and experimental evidence upgrades the gene–disease association strength of SYCP2 and autosomal dominant male infertility from on the border of limited and moderate to strong. The reclassification improves SYCP2 variant interpretation and qualifies it for the inclusion on diagnostic male infertility gene panels and prioritization in whole exome or genome studies for related phenotypes. These findings therefore improve the clinical interpretation of SYCP2 LOF variants. Full article

(This article belongs to the Special Issue Genetic and Phenotypic Correlation: Gene–Disease Validation Series II)

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12 pages, 6050 KiB

Open AccessArticle

Nanoparticle-Mediated Genetic Transformation in a Selaginella Species

by Madhavi A. Ariyarathne, Beate Wone, Nisitha Wijewantha and Bernard W. M. Wone

Genes 2024, 15(8), 1091; https://doi.org/10.3390/genes15081091 - 19 Aug 2024

Cited by 1 | Viewed by 1156

Abstract

The genus Selaginella holds a key phylogenetic position as a sister species to vascular plants, encompassing desiccation-tolerant members. Some Selaginella species thrive in extremely arid conditions, enduring significant water loss and recovering upon rehydration. Consequently, Selaginella has emerged as a model system for [...] Read more.

The genus Selaginella holds a key phylogenetic position as a sister species to vascular plants, encompassing desiccation-tolerant members. Some Selaginella species thrive in extremely arid conditions, enduring significant water loss and recovering upon rehydration. Consequently, Selaginella has emerged as a model system for studying desiccation tolerance in plant science. However, the absence of an efficient genetic transformation system has limited the utility of Selaginella species as a model. To address this constraint, we developed a nanoparticle-mediated transformation tool utilizing arginine-functionalized nanohydroxyapatites. This biocompatible system enabled the transient expression of the GFP, GUS, and eYGFPuv reporter genes in Selaginella moellendorffii. Establishing a stable genetic transformation technique for S. moellendorffii holds promise for application to other Selaginella species. This tool could be instrumental in identifying genetic resources for crop improvement and understanding genome-level regulatory mechanisms governing desiccation tolerance in Selaginella species. Furthermore, this tool might aid in identifying key regulatory genes associated with desiccation tolerance, offering potential applications in enhancing drought-sensitive crops and ensuring sustainable food production. Full article

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

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21 pages, 1860 KiB

Open AccessReview

Advances in the Application of Protein Language Modeling for Nucleic Acid Protein Binding Site Prediction

by Bo Wang and Wenjin Li

Genes 2024, 15(8), 1090; https://doi.org/10.3390/genes15081090 - 18 Aug 2024

Viewed by 1389

Abstract

Protein and nucleic acid binding site prediction is a critical computational task that benefits a wide range of biological processes. Previous studies have shown that feature selection holds particular significance for this prediction task, making the generation of more discriminative features a key [...] Read more.

Protein and nucleic acid binding site prediction is a critical computational task that benefits a wide range of biological processes. Previous studies have shown that feature selection holds particular significance for this prediction task, making the generation of more discriminative features a key area of interest for many researchers. Recent progress has shown the power of protein language models in handling protein sequences, in leveraging the strengths of attention networks, and in successful applications to tasks such as protein structure prediction. This naturally raises the question of the applicability of protein language models in predicting protein and nucleic acid binding sites. Various approaches have explored this potential. This paper first describes the development of protein language models. Then, a systematic review of the latest methods for predicting protein and nucleic acid binding sites is conducted by covering benchmark sets, feature generation methods, performance comparisons, and feature ablation studies. These comparisons demonstrate the importance of protein language models for the prediction task. Finally, the paper discusses the challenges of protein and nucleic acid binding site prediction and proposes possible research directions and future trends. The purpose of this survey is to furnish researchers with actionable suggestions for comprehending the methodologies used in predicting protein–nucleic acid binding sites, fostering the creation of protein-centric language models, and tackling real-world obstacles encountered in this field. Full article

(This article belongs to the Section Bioinformatics)

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7 pages, 1991 KiB

Open AccessCase Report

Application of Metagenomics Sequencing in a Patient with Dementia: A New Case Report

by Maria Minelli, Federico Anaclerio, Dario Calisi, Marco Onofrj, Ivana Antonucci, Valentina Gatta and Liborio Stuppia

Genes 2024, 15(8), 1089; https://doi.org/10.3390/genes15081089 - 18 Aug 2024

Viewed by 810

Abstract

(1) Background: The study of the microbiome is crucial for its role in major systemic diseases, in particular the oral and gut microbiota. In recent years, the study of microorganisms correlated, for example, with neurodegenerative disease has increased the prospect of a possible [...] Read more.

(1) Background: The study of the microbiome is crucial for its role in major systemic diseases, in particular the oral and gut microbiota. In recent years, the study of microorganisms correlated, for example, with neurodegenerative disease has increased the prospect of a possible link between gut microbiota and the brain. Here, we report a new case concerning a patient who was initially evaluated genetically for dementia and late-onset dyskinesia, and later tested with 16S metagenomics sequencing. (2) Methods: Starting from a buccal swab, we extracted bacterial DNA and then we performed NGS metagenomics sequencing based on the amplification of the hypervariable regions of the 16S rRNA gene in bacteria. (3) Results: The sequencing revealed the presence of the Spirochaetes phylum, a pathogenic bacterium generally known to be capable of migrating to the Central Nervous System. (4) Conclusions: Oral infections, as our results suggest, could be possible contributing factors to various neurodegenerative conditions. Full article

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

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15 pages, 2974 KiB

Open AccessArticle

Circulating miRNA Signaling for Fatty Acid Metabolism in Response to a Maximum Endurance Test in Elite Long-Distance Runners

by Dailson Paulucio, Carlos Ramirez-Sanchez, Rodolfo Velasque, Raphael Xavier, Gustavo Monnerat, Adrieli Dill, Juliano Silveira, Gabriella M. Andrade, Flavio Meirelles, Marcos Dornelas-Ribeiro, Benedikt Kirchner, Michael W. Pfaffl, Fernando Pompeu and Caleb G. M. Santos

Genes 2024, 15(8), 1088; https://doi.org/10.3390/genes15081088 - 17 Aug 2024

Viewed by 1022

Abstract

Maximal oxygen uptake (VO₂max) is a determining indicator for cardiorespiratory capacity in endurance athletes, and epigenetics is crucial in its levels and variability. This initial study examined a broad plasma miRNA profile of twenty-three trained elite endurance athletes with similar training [...] Read more.

Maximal oxygen uptake (VO₂max) is a determining indicator for cardiorespiratory capacity in endurance athletes, and epigenetics is crucial in its levels and variability. This initial study examined a broad plasma miRNA profile of twenty-three trained elite endurance athletes with similar training volumes but different VO₂max in response to an acute maximal graded endurance test. Six were clustered as higher/lower levels based on their VO₂max (75.4 ± 0.9 and 60.1 ± 5.0 mL.kg⁻¹.min⁻¹). Plasma was obtained from athletes before and after the test and 15 ng of total RNA was extracted and detected using an SYBR-based 1113 miRNA RT-qPCR panel. A total of 51 miRNAs were differentially expressed among group comparisons. Relative amounts of miRNA showed a clustering behavior among groups regarding distinct performance/time points. Significantly expressed miRNAs were used to perform functional bioinformatic analysis (DIANA tools). Fatty acid metabolism pathways were strongly targeted for the significantly different miRNAs in all performance groups and time points (p < 0.001). Although this pathway does not solely determine endurance performance, their significant contribution is certainly achieved through the involvement of miRNAs. A highly genetically dependent gold standard variable for performance evaluation in a homogeneous group of elite athletes allowed genetic/epigenetic aspects related to fatty acid pathways to emerge. Full article

(This article belongs to the Section RNA)

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20 pages, 4342 KiB

Open AccessArticle

Genome-Wide Identification of a Maize Chitinase Gene Family and the Induction of Its Expression by Fusarium verticillioides (Sacc.) Nirenberg (1976) Infection

by Jesús Eduardo Cazares-Álvarez, Paúl Alán Báez-Astorga, Analilia Arroyo-Becerra and Ignacio Eduardo Maldonado-Mendoza

Genes 2024, 15(8), 1087; https://doi.org/10.3390/genes15081087 - 17 Aug 2024

Cited by 1 | Viewed by 1074

Abstract

Maize chitinases are involved in chitin hydrolysis. Chitinases are distributed across various organisms including animals, plants, and fungi and are grouped into different glycosyl hydrolase families and classes, depending on protein structure. However, many chitinase functions and their interactions with other plant proteins [...] Read more.

Maize chitinases are involved in chitin hydrolysis. Chitinases are distributed across various organisms including animals, plants, and fungi and are grouped into different glycosyl hydrolase families and classes, depending on protein structure. However, many chitinase functions and their interactions with other plant proteins remain unknown. The economic importance of maize (Zea mays L.) makes it relevant for studying the function of plant chitinases and their biological roles. This work aims to identify chitinase genes in the maize genome to study their gene structure, family/class classification, cis-related elements, and gene expression under biotic stress, such as Fusarium verticillioides infection. Thirty-nine chitinase genes were identified and found to be distributed in three glycosyl hydrolase (GH) families (18, 19 and 20). Likewise, the conserved domains and motifs were identified in each GH family member. The identified cis-regulatory elements are involved in plant development, hormone response, defense, and abiotic stress response. Chitinase protein-interaction network analysis predicted that they interact mainly with cell wall proteins. qRT-PCR analysis confirmed in silico data showing that ten different maize chitinase genes are induced in the presence of F. verticillioides, and that they could have several roles in pathogen infection depending on chitinase structure and cell wall localization. Full article

(This article belongs to the Section Bioinformatics)

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11 pages, 7084 KiB

Open AccessArticle

Carboxypeptidase Inhibitor LXN Expression in Endometrial Tissue Is Menstrual Cycle Phase-Dependent and Is Upregulated in Endometriotic Lesions

by Meruert Sarsenova, Artjom Stepanjuk, Merli Saare, Sergo Kasvandik, Pille Soplepmann, Iveta Mikeltadze, Martin Götte, Andres Salumets and Maire Peters

Genes 2024, 15(8), 1086; https://doi.org/10.3390/genes15081086 - 17 Aug 2024

Viewed by 1004

Abstract

Endometriosis is a chronic hormone-dependent disease characterized by the spread of endometrial cells outside the uterus, which form endometriotic lesions and disrupt the functions of the affected organs. The etiopathogenesis of endometriosis is still unclear, and thus it is important to examine the [...] Read more.

Endometriosis is a chronic hormone-dependent disease characterized by the spread of endometrial cells outside the uterus, which form endometriotic lesions and disrupt the functions of the affected organs. The etiopathogenesis of endometriosis is still unclear, and thus it is important to examine the genes that may contribute to the establishment of endometriotic lesions. The aim of this study was to investigate the expression of new potential candidate gene latexin (LXN), an inhibitor of carboxypeptidases, in endometrium and endometriotic lesions to elucidate its possible role in endometriosis development. LXN expression in tissues was assessed using quantitative reverse transcription PCR (qRT–PCR) analysis and immunohistochemical staining (IHC). The functions of LXN were examined using Transwell and MTT assays. qRT–PCR analysis revealed that LXN expression in endometrium was menstrual cycle-dependent, being lowest in the early-secretory phase and highest in the late-secretory phase and was significantly upregulated in endometriotic lesions. IHC confirmed LXN expression in endometrial stromal cells, and in vitro assays demonstrated that knockdown of LXN effectively reduced the migratory capacity of endometrial stromal cells while promoting cell viability. In conclusion, our results showed that LXN can be involved in the pathogenesis of endometriosis by regulating the proliferation and migration activity of endometriotic stromal cells. Full article

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

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21 pages, 3243 KiB

Open AccessArticle

Genome-Wide Identification, Characterization, and Transcriptional Profile of the HECT E3 Ubiquitin Ligase Gene Family in the Hard-Shelled Mussel Mytilus coruscus Gould

by Feng Guo, Zhenqi Xin, Zhenyu Dong and Yingying Ye

Genes 2024, 15(8), 1085; https://doi.org/10.3390/genes15081085 - 16 Aug 2024

Viewed by 941

Abstract

The homologous E6-AP carboxy-terminal structural domain (HECT) contained in E3 ubiquitin ligases (E3s) is a key factor in protein degradation and maintenance of cellular homeostasis in animals. However, the functional roles and evolutionary aspects of the HECT gene family in bivalve mussels remain [...] Read more.

The homologous E6-AP carboxy-terminal structural domain (HECT) contained in E3 ubiquitin ligases (E3s) is a key factor in protein degradation and maintenance of cellular homeostasis in animals. However, the functional roles and evolutionary aspects of the HECT gene family in bivalve mussels remain unclear and warrant further investigation. In this study, we identified 22 HECT genes within the genome of Mytilus coruscus Gould, all containing a conserved HECT structural domain derived from dispersed repeats, distributed unevenly across 11 chromosomes. Phylogenetic analysis classified M. coruscus HECT genes into six major classes, with amino acid sequences within the same evolutionary clade displaying similar conserved motifs. Homology analysis with HECT genes of four bivalve species revealed that M. coruscus and Mytilus galloprovincialis possessed the largest number of homologous gene pairs, showing a significant correlation between the two in the evolution of the HECT gene family. Homology analysis with HECT genes of four bivalve species revealed that M. coruscus and M. galloprovincialis possessed the largest number of homologous gene pairs, showing a significant correlation between the two in the evolution of the HECT gene family. M. coruscus exhibited pronounced and specific expression in gills and blood tissues. Notably, Mco_UPL3 gene expression was significantly upregulated after 12 h of acute heat stress (33 °C) and 24 h of Vibrio injection (0.4 OD). Gene ontology analysis of the HECT genes in M. coruscus revealed that it is primarily enriched in protein modification and degradation functions. This suggests that HECT genes may play a key role in protein degradation and immunomodulation in M. coruscus. These findings offer valuable insights for the breeding of stress-tolerant traits in M. coruscus. In summary, our data shed light on the potential functions of HECT E3 ligases in response to heat stress and Vibrio infection, providing practical guidance for enhancing resilience through breeding in M. coruscus. Full article

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

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12 pages, 880 KiB

Open AccessArticle

No Evidence That Vitamin D Levels or Deficiency Are Associated with the Risk of Open-Angle Glaucoma in Individuals of European Ancestry: A Mendelian Randomisation Analysis

by Nour Kanso, Munisa Hashimi, Hasnat A. Amin, Alexander C. Day and Fotios Drenos

Genes 2024, 15(8), 1084; https://doi.org/10.3390/genes15081084 - 16 Aug 2024

Viewed by 1071

Abstract

Background: Glaucoma is the second leading cause of blindness worldwide, with intraocular pressure as the only known modifiable risk factor. Vitamin D has been proposed to influence intraocular pressure and decrease retinal ganglion cell degeneration. Based on these findings, vitamin D has been [...] Read more.

Background: Glaucoma is the second leading cause of blindness worldwide, with intraocular pressure as the only known modifiable risk factor. Vitamin D has been proposed to influence intraocular pressure and decrease retinal ganglion cell degeneration. Based on these findings, vitamin D has been suggested to prevent or reduce the severity of primary open-angle glaucoma (POAG), which is the most common form. Methods: We applied two-sample Mendelian randomisation (MR) analyses to data from the SUNLIGHT consortium and the UK Biobank to assess the causal effect of vitamin D levels and vitamin D deficiency on primary open-angle glaucoma (POAG). MR analysis, including sensitivity tests using other GWAS summary statistics from FinnGen, was also performed. We also investigated the association between single nucleotide polymorphisms (SNPs) on genes involved in vitamin D metabolic pathways and POAG. Results: We found no statistical evidence that vitamin D levels (OR = 1.146, 95% CI 0.873 to 1.504, p = 0.326) or vitamin D deficiency (OR = 0.980 (95% CI 0.928 to 1.036, p = 0.471) causally affect the risk of developing POAG. Sensitivity analyses, including the use of a more relaxed p-value threshold, and use of winter-measured samples only, replication in the FinnGen dataset, and exploration of specific genetic markers also showed no evidence of association between SNPs for genes involved in key steps of vitamin D metabolism and POAG. Conclusions: These results indicate that vitamin D may not be a significant factor in modifying POAG risk, challenging the hypothesis that vitamin D supplementation could be effective in reducing POAG risk. Further research should focus on identifying other potential risk factors for POAG prevention strategies. Full article

(This article belongs to the Section Bioinformatics)

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15 pages, 3729 KiB

Open AccessArticle

Integrating ATAC-Seq and RNA-Seq Reveals the Signal Regulation Involved in the Artemia Embryonic Reactivation Process

by Anqi Li, Zhentao Song, Mingzhi Zhang, Hu Duan, Liying Sui, Bin Wang and Tong Hao

Genes 2024, 15(8), 1083; https://doi.org/10.3390/genes15081083 - 16 Aug 2024

Viewed by 771

Abstract

Embryonic diapause is a common evolutionary adaptation observed across a wide range of organisms. Artemia is one of the classic animal models for diapause research. The current studies of Artemia diapause mainly focus on the induction and maintenance of the embryonic diapause, with [...] Read more.

Embryonic diapause is a common evolutionary adaptation observed across a wide range of organisms. Artemia is one of the classic animal models for diapause research. The current studies of Artemia diapause mainly focus on the induction and maintenance of the embryonic diapause, with little research on the molecular regulatory mechanism of Artemia embryonic reactivation. The first 5 h after embryonic diapause breaking has been proved to be most important for embryonic reactivation in Artemia. In this work, two high-throughput sequencing methods, ATAC-seq and RNA-seq, were integrated to study the signal regulation process in embryonic reactivation of Artemia at 5 h after diapause breaking. Through the GO and KEGG enrichment analysis of the high-throughput datasets, it was showed that after 5 h of diapause breaking, the metabolism and regulation of Artemia cyst were quite active. Several signal transduction pathways were identified in the embryonic reactivation process, such as G-protein-coupled receptor (GPCR) signaling pathway, cell surface receptor signaling pathway, hormone-mediated signaling pathway, Wnt, Notch, mTOR signaling pathways, etc. It indicates that embryonic reactivation is a complex process regulated by multiple signaling pathways. With the further protein structure analysis and RT-qPCR verification, 11 GPCR genes were identified, in which 5 genes function in the embryonic reactivation stage and the other 6 genes contribute to the diapause stage. The results of this work reveal the signal transduction pathways and GPCRs involved in the embryonic reactivation process of Artemia cysts. These findings offer significant clues for in-depth research on the signal regulatory mechanisms of the embryonic reactivation process and valuable insights into the mechanism of animal embryonic diapause. Full article

(This article belongs to the Special Issue Genetic and Genomic Studies of Marine Animals)

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22 pages, 825 KiB

Open AccessSystematic Review

Structural Variations Identified in Patients with Autism Spectrum Disorder (ASD) in the Chinese Population: A Systematic Review of Case-Control Studies

by Sek-Ying Chair, Ka-Ming Chow, Cecilia Wai-Ling Chan, Judy Yuet-Wa Chan, Bernard Man-Hin Law and Mary Miu-Yee Waye

Genes 2024, 15(8), 1082; https://doi.org/10.3390/genes15081082 - 15 Aug 2024

Viewed by 1208

Abstract

Autistic spectrum disorder (ASD) is a neurodevelopmental disability characterised by the impairment of social interaction and communication ability. The alarming increase in its prevalence in children urged researchers to obtain a better understanding of the causes of this disease. Genetic factors are considered [...] Read more.

Autistic spectrum disorder (ASD) is a neurodevelopmental disability characterised by the impairment of social interaction and communication ability. The alarming increase in its prevalence in children urged researchers to obtain a better understanding of the causes of this disease. Genetic factors are considered to be crucial, as ASD has a tendency to run in families. In recent years, with technological advances, the importance of structural variations (SVs) in ASD began to emerge. Most of these studies, however, focus on the Caucasian population. As a populated ethnicity, ASD shall be a significant health issue in China. This systematic review aims to summarise current case-control studies of SVs associated with ASD in the Chinese population. A list of genes identified in the nine included studies is provided. It also reveals that similar research focusing on other genetic backgrounds is demanded to manifest the disease etiology in different ethnic groups, and assist the development of accurate ethnic-oriented genetic diagnosis. Full article

(This article belongs to the Special Issue Genetics of Complex Human Disease 2024)

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14 pages, 6815 KiB

Open AccessArticle

Meta-Genomic Analysis of Different Bacteria and Their Genomes Found in Raw Buffalo Milk Obtained in Various Farms Using Different Milking Methods

by Ling Li, Wenhao Miao, Zhipeng Li, Li Huang, Enghuan Hau, Muhammad Farhan Khan, Qingyou Liu, Qingkun Zeng and Kuiqing Cui

Genes 2024, 15(8), 1081; https://doi.org/10.3390/genes15081081 - 15 Aug 2024

Viewed by 1054

Abstract

Milking methods have significant impacts on the microbiological composition, which could affect the quality of raw buffalo milk. Hence, the current study was conducted on the impact of milking methods on microorganisms in buffalo tank raw milk from 15 farms in Guangxi, China. [...] Read more.

Milking methods have significant impacts on the microbiological composition, which could affect the quality of raw buffalo milk. Hence, the current study was conducted on the impact of milking methods on microorganisms in buffalo tank raw milk from 15 farms in Guangxi, China. The farms were divided into two groups based on the milking method: mechanical milking (MM, n = 6) and hand milking (HM, n = 9). Somatic cell counts, bacterial cell counts and nutrients of the raw buffalo milk samples were analyzed. The comparison of raw buffalo milk samples was analyzed using metagenomic sequencing to detect any differences between the two groups. There was no significant difference in the basic nutritional compositions and somatic cell count of raw buffalo milk between the two milking methods. However, the HM samples had significantly higher bacterial counts and diversity compared to the MM samples. The results showed that Staphylococcus spp., Klebsiella spp., Streptococcus spp., and Pseudomonas spp. were the major microbes present in canned raw buffalo milk. However, the differences between the two milking methods were the relative abundance of core microorganisms and their potential mastitis-causing genera, including the content of antibiotic-resistance genes and virulence genes. Our study revealed that Staphylococcus spp. and Streptococcus spp. were significantly more abundant in the MM group, while Klebsiella spp. was more abundant in the HM group. Regardless of the milking method used, Pseudomonas spp. was identified as the primary genus contributing to antibiotic resistance and virulence genes in canned raw buffalo milk. These findings affirm that there are differences in the microbial and genomic levels in canned raw milk. To prove the functional roles of the discovered genes and how these genes affect milk quality, further research and experimental validation are necessary. Full article

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

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21 pages, 2018 KiB

Open AccessArticle

Activation of the CDK7 Gene, Coding for the Catalytic Subunit of the Cyclin-Dependent Kinase (CDK)-Activating Kinase (CAK) and General Transcription Factor II H, by the Trans-Activator Protein Tax of Human T-Cell Leukemia Virus Type-1

by Mashiro Shirasawa, Rinka Nakajima, Yaxuan Zhou, Lin Zhao, Mariana Fikriyanti, Ritsuko Iwanaga, Andrew P. Bradford, Kenta Kurayoshi, Keigo Araki and Kiyoshi Ohtani

Genes 2024, 15(8), 1080; https://doi.org/10.3390/genes15081080 - 15 Aug 2024

Viewed by 816

Abstract

Human T-cell leukemia virus type-1 (HTLV-1) is the etiological agent of adult T-cell leukemia (ATL). The trans-activator protein Tax of HTLV-1 plays crucial roles in leukemogenesis by promoting proliferation of virus-infected cells through activation of growth-promoting genes. However, critical target genes are yet [...] Read more.

Human T-cell leukemia virus type-1 (HTLV-1) is the etiological agent of adult T-cell leukemia (ATL). The trans-activator protein Tax of HTLV-1 plays crucial roles in leukemogenesis by promoting proliferation of virus-infected cells through activation of growth-promoting genes. However, critical target genes are yet to be elucidated. We show here that Tax activates the gene coding for cyclin-dependent kinase 7 (CDK7), the essential component of both CDK-activating kinase (CAK) and general transcription factor TFIIH. CAK and TFIIH play essential roles in cell cycle progression and transcription by activating CDKs and facilitating transcriptional initiation, respectively. Tax induced CDK7 gene expression not only in human T-cell lines but also in normal peripheral blood lymphocytes (PHA-PBLs) along with increased protein expression. Tax stimulated phosphorylation of CDK2 and RNA polymerase II at sites reported to be mediated by CDK7. Tax activated the CDK7 promoter through the NF-κB pathway, which mainly mediates cell growth promotion by Tax. Knockdown of CDK7 expression reduced Tax-mediated induction of target gene expression and cell cycle progression. These results suggest that the CDK7 gene is a crucial target of Tax-mediated trans-activation to promote cell proliferation by activating CDKs and transcription. Full article

(This article belongs to the Special Issue Feature Papers in Human Genomics and Genetic Diseases 2024)

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14 pages, 10653 KiB

Open AccessCommunication

Proteomic and Phosphoproteomic Analyses during Plant Regeneration Initiation in Cotton (Gossypium hirsutum L.)

by Haixia Guo, Jin Wang, Xuehui Huo, Xiwang Cui, Li Zhang, Xiushan Qi, Xiaoying Wu, Junchen Liu, Aijuan Wang, Jialin Liu, Xiangyu Chen, Fanchang Zeng and Huihui Guo

Genes 2024, 15(8), 1079; https://doi.org/10.3390/genes15081079 - 15 Aug 2024

Viewed by 766

Abstract

Somatic embryogenesis (SE) is a biotechnological tool used to generate new individuals and is the preferred method for rapid plant regeneration. However, the molecular basis underlying somatic cell regeneration through SE is not yet fully understood, particularly regarding interactions between the proteome and [...] Read more.

Somatic embryogenesis (SE) is a biotechnological tool used to generate new individuals and is the preferred method for rapid plant regeneration. However, the molecular basis underlying somatic cell regeneration through SE is not yet fully understood, particularly regarding interactions between the proteome and post-translational modifications. Here, we performed association analysis of high-throughput proteomics and phosphoproteomics in three representative samples (non-embryogenic calli, NEC; primary embryogenic calli, PEC; globular embryos, GE) during the initiation of plant regeneration in cotton, a pioneer crop for genetic biotechnology applications. Our results showed that protein accumulation is positively regulated by phosphorylation during SE, as revealed by correlation analyses. Of the 1418 proteins that were differentially accumulated in the proteome and the 1106 phosphoproteins that were differentially regulated in the phosphoproteome, 115 proteins with 229 phosphorylation sites overlapped (co-differential). Furthermore, seven dynamic trajectory patterns of differentially accumulated proteins (DAPs) and the correlated differentially regulated phosphoproteins (DRPPs) pairs with enrichment features were observed. During the initiation of plant regeneration, functional enrichment analysis revealed that the overlapping proteins (DAPs-DRPPs) were considerably enriched in cellular nitrogen metabolism, spliceosome formation, and reproductive structure development. Moreover, 198 DRPPs (387 phosphorylation sites) were specifically regulated at the phosphorylation level and showed four patterns of stage-enriched phosphorylation susceptibility. Furthermore, enrichment annotation analysis revealed that these phosphoproteins were significantly enriched in endosomal transport and nucleus organization processes. During embryogenic differentiation, we identified five DAPs-DRPPs with significantly enriched characteristic patterns. These proteins may play essential roles in transcriptional regulation and signaling events that initiate plant regeneration through protein accumulation and/or phosphorylation modification. This study enriched the understanding of key proteins and their correlated phosphorylation patterns during plant regeneration, and also provided a reference for improving plant regeneration efficiency. Full article

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

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Genes, Volume 15, Issue 8 (August 2024) – 143 articles

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