Genes

17 pages, 14250 KiB

Open AccessEditor’s ChoiceReview

Melatonin Function and Crosstalk with Other Phytohormones under Normal and Stressful Conditions

by Murtaza Khan, Sajid Ali, Hakim Manghwar, Saddam Saqib, Fazal Ullah, Asma Ayaz and Wajid Zaman

Genes 2022, 13(10), 1699; https://doi.org/10.3390/genes13101699 - 22 Sep 2022

Cited by 41 | Viewed by 3507

Abstract

Melatonin was discovered in plants in the late nineties, but its role, signaling, and crosstalk with other phytohormones remain unknown. Research on melatonin in plants has risen dramatically in recent years and the role of this putative plant hormone under biotic and abiotic [...] Read more.

Melatonin was discovered in plants in the late nineties, but its role, signaling, and crosstalk with other phytohormones remain unknown. Research on melatonin in plants has risen dramatically in recent years and the role of this putative plant hormone under biotic and abiotic stress conditions has been reported. In the present review, we discuss the main functions of melatonin in the growth and development of plants, its role under abiotic stresses, such as water stress (waterlogging and drought), extreme temperature (low and high), salinity, heavy metal, and light-induced stress. Similarly, we also discuss the role of melatonin under biotic stresses (antiviral, antibacterial, and antifungal effects). Moreover, the present review meticulously discusses the crosstalk of melatonin with other phytohormones such as auxins, gibberellic acids, cytokinins, ethylene, and salicylic acid under normal and stressful conditions and reports melatonin receptors and signaling in plants. All these aspects of melatonin suggest that phytomelatonin is a key player in crop improvement and biotic and abiotic stress regulation. Full article

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

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22 pages, 798 KiB

Open AccessEditor’s ChoiceReview

Recent Developments in Autism Genetic Research: A Scientometric Review from 2018 to 2022

by Mengyu Lim, Alessandro Carollo, Dagmara Dimitriou and Gianluca Esposito

Genes 2022, 13(9), 1646; https://doi.org/10.3390/genes13091646 - 14 Sep 2022

Cited by 14 | Viewed by 4331

Abstract

Genetic research in Autism Spectrum Disorder (ASD) has progressed tremendously in recent decades. Dozens of genetic loci and hundreds of alterations in the genetic sequence, expression, epigenetic transformation, and interactions with other physiological and environmental systems have been found to increase the likelihood [...] Read more.

Genetic research in Autism Spectrum Disorder (ASD) has progressed tremendously in recent decades. Dozens of genetic loci and hundreds of alterations in the genetic sequence, expression, epigenetic transformation, and interactions with other physiological and environmental systems have been found to increase the likelihood of developing ASD. There is therefore a need to represent this wide-ranging yet voluminous body of literature in a systematic manner so that this information can be synthesised and understood at a macro level. Therefore, this study made use of scientometric methods, particularly document co-citation analysis (DCA), to systematically review literature on ASD genetic research from 2018 to 2022. A total of 14,818 articles were extracted from Scopus and analyzed with CiteSpace. An optimized DCA analysis revealed that recent literature on ASD genetic research can be broadly organised into 12 major clusters representing various sub-topics. These clusters are briefly described in the manuscript and potential applications of this study are discussed. Full article

(This article belongs to the Special Issue Genetic and Epigenetic Factors and Their Interactions in the Susceptibility to Multifactorial Diseases)

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16 pages, 2904 KiB

Open AccessEditor’s ChoiceReview

Bridging Disciplines to Form a New One: The Emergence of Forensic Genetic Genealogy

by Claire L. Glynn

Genes 2022, 13(8), 1381; https://doi.org/10.3390/genes13081381 - 01 Aug 2022

Cited by 15 | Viewed by 9160

Abstract

Forensic Genetic Genealogy (FGG) has fast become a popular tool in criminal investigations since it first emerged in 2018. FGG is a novel investigatory tool that has been applied to hundreds of unresolved cold cases in the United States to generate investigative leads [...] Read more.

Forensic Genetic Genealogy (FGG) has fast become a popular tool in criminal investigations since it first emerged in 2018. FGG is a novel investigatory tool that has been applied to hundreds of unresolved cold cases in the United States to generate investigative leads and identify unknown individuals. Consumer DNA testing and the public’s increased curiosity about their own DNA and genetic ancestry, have greatly contributed to the availability of human genetic data. Genetic genealogy has been a field of study/interest for many years as both amateur and professional genetic genealogists use consumer DNA data to explore genetic connections in family trees. FGG encompasses this knowledge by applying advanced sequencing technologies to forensic DNA evidence samples and by performing genetic genealogy methods and genealogical research, to produce possible identities of unknown perpetrators of violent crimes and unidentified human remains. This combination of forensic genetics, genetic genealogy, and genealogical research has formed a new subdiscipline within the forensic sciences. This paper will summarize the individual disciplines that led to the emergence of FGG, its practice in forensic investigations, and current/future considerations for its use. Full article

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

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30 pages, 4002 KiB

Open AccessEditor’s ChoiceArticle

Nrf2/HO-1 Signaling Stimulation through Acetyl-11-Keto-Beta-Boswellic Acid (AKBA) Provides Neuroprotection in Ethidium Bromide-Induced Experimental Model of Multiple Sclerosis

by Shubham Upadhayay, Sidharth Mehan, Aradhana Prajapati, Pranshul Sethi, Manisha Suri, Ayat Zawawi, Majed N. Almashjary and Shams Tabrez

Genes 2022, 13(8), 1324; https://doi.org/10.3390/genes13081324 - 25 Jul 2022

Cited by 16 | Viewed by 2759

Abstract

Multiple sclerosis (MS) is a severe immune-mediated neurological disease characterized by neuroinflammation, demyelination, and axonal degeneration in the central nervous system (CNS). This is frequently linked to motor abnormalities and cognitive impairments. The pathophysiological hallmarks of MS include inflammatory demyelination, axonal injury, white [...] Read more.

Multiple sclerosis (MS) is a severe immune-mediated neurological disease characterized by neuroinflammation, demyelination, and axonal degeneration in the central nervous system (CNS). This is frequently linked to motor abnormalities and cognitive impairments. The pathophysiological hallmarks of MS include inflammatory demyelination, axonal injury, white matter degeneration, and the development of CNS lesions that result in severe neuronal degeneration. Several studies suggested downregulation of nuclear factor erythroid-2-related factor-2 (Nrf2)/Heme oxygenase-1 (HO-1) signaling is a causative factor for MS pathogenesis. Acetyl-11-keto-β-boswellic acid (AKBA) is an active pentacyclictriterpenoid obtained from Boswellia serrata, possessing antioxidant and anti-inflammatory properties. The present study explores the protective potential of AKBA on behavioral, molecular, neurochemical, and gross pathological abnormalitiesandhistopathological alterations by H&E and LFB staining techniques in an experimental model of multiple sclerosis, emphasizing the increase inNrf2/HO-1 levels in the brain. Moreover, we also examine the effect of AKBA on the intensity of myelin basic protein (MBP) in CSF and rat brain homogenate. Specific apoptotic markers (Bcl-2, Bax, andcaspase-3) were also estimated in rat brain homogenate. Neuro behavioralabnormalities in rats were examined using an actophotometer, rotarod test, beam crossing task (BCT),and Morris water maze (MWM). AKBA 50 mg/kg and 100 mg/kg were given orally from day 8 to 35 to alleviate MS symptoms in the EB-injected rats. Furthermore, cellular, molecular, neurotransmitter, neuroinflammatory cytokine, and oxidative stress markers in rat whole brain homogenate, blood plasma, and cerebral spinal fluid were investigated. This study shows that AKBA upregulates the level of antioxidant proteins such as Nrf2 and HO-1 in the rat brain. AKBA restores altered neurochemical levels, potentially preventing gross pathological abnormalities during MS progression. Full article

(This article belongs to the Special Issue Genetic and Molecular Mechanisms in Multiple Sclerosis)

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9 pages, 771 KiB

Open AccessEditor’s ChoiceArticle

Old and New Systemic Immune-Inflammation Indexes Are Associated with Overall Survival of Glioblastoma Patients Treated with Radio-Chemotherapy

by Francesco Pasqualetti, Celeste Giampietro, Nicola Montemurro, Noemi Giannini, Giovanni Gadducci, Paola Orlandi, Eleonora Natali, Paolo Chiarugi, Alessandra Gonnelli, Martina Cantarella, Cristian Scatena, Giuseppe Nicolò Fanelli, Antonio Giuseppe Naccarato, Paolo Perrini, Gaetano Liberti, Riccardo Morganti, Maria Franzini, Aldo Paolicchi, Giovanni Pellegrini, Guido Bocci and Fabiola Paiar Show full author list Hide full author list

Genes 2022, 13(6), 1054; https://doi.org/10.3390/genes13061054 - 13 Jun 2022

Cited by 16 | Viewed by 1880

Abstract

Background. Systemic immunity and inflammation indexes (SI) derived from blood cells have gained increasing attention in clinical oncology as potential biomarkers that are associated with survival. Materials and methods. We tested 12 different SI using blood tests from patients with isocitrate [...] Read more.

Background. Systemic immunity and inflammation indexes (SI) derived from blood cells have gained increasing attention in clinical oncology as potential biomarkers that are associated with survival. Materials and methods. We tested 12 different SI using blood tests from patients with isocitrate dehydrogenase 1 and 2 wild-type glioblastomas, treated with radio-chemotherapy. The primary endpoint was their overall survival. Results. A total of 77 patients, comprising 43 males and 34 females, with a median age of 64 years (age range 26–84), who were treated between October 2010 and July 2020, were included in the present analysis (approved by a local ethics committee). In the univariate Cox regression analysis, all the indexes except two showed a statistically significant impact on OS. In the multivariate Cox regression analysis, neutrophil × platelet × leukocyte/(lymphocyte × monocyte) (NPW/LM) and neutrophil × platelet × monocyte/lymphocyte (NPM/L) maintained their statistically significant impact value. Conclusions. This univariate analysis confirms the potential of systemic inflammation indexes in patients with glioblastoma, while the multivariate analysis verifies the prognostic value of NPW/LM and NPM/L. Full article

(This article belongs to the Special Issue The Genomics of Glioblastoma)

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29 pages, 1264 KiB

Open AccessEditor’s ChoiceReview

Mesenchymal Stem Cell Mechanisms of Action and Clinical Effects in Osteoarthritis: A Narrative Review

by Vilim Molnar, Eduard Pavelić, Kristijan Vrdoljak, Martin Čemerin, Emil Klarić, Vid Matišić, Roko Bjelica, Petar Brlek, Ivana Kovačić, Carlo Tremolada and Dragan Primorac

Genes 2022, 13(6), 949; https://doi.org/10.3390/genes13060949 - 26 May 2022

Cited by 22 | Viewed by 6504

Abstract

With the insufficient satisfaction rates and high cost of operative treatment for osteoarthritis (OA), alternatives have been sought. Furthermore, the inability of current medications to arrest disease progression has led to rapidly growing clinical research relating to mesenchymal stem cells (MSCs). The availability [...] Read more.

With the insufficient satisfaction rates and high cost of operative treatment for osteoarthritis (OA), alternatives have been sought. Furthermore, the inability of current medications to arrest disease progression has led to rapidly growing clinical research relating to mesenchymal stem cells (MSCs). The availability and function of MSCs vary according to tissue source. The three primary sources include the placenta, bone marrow, and adipose tissue, all of which offer excellent safety profiles. The primary mechanisms of action are trophic and immunomodulatory effects, which prevent the further degradation of joints. However, the function and degree to which benefits are observed vary significantly based on the exosomes secreted by MSCs. Paracrine and autocrine mechanisms prevent cell apoptosis and tissue fibrosis, initiate angiogenesis, and stimulate mitosis via growth factors. MSCs have even been shown to exhibit antimicrobial effects. Clinical results incorporating clinical scores and objective radiological imaging have been promising, but a lack of standardization in isolating MSCs prevents their incorporation in current guidelines. Full article

(This article belongs to the Special Issue Genetics and Stem Cell Research)

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13 pages, 1689 KiB

Open AccessEditor’s ChoiceArticle

Gut Microbiota as a Potential Predictive Biomarker in Relapsing-Remitting Multiple Sclerosis

by Vicente Navarro-López, María Ángeles Méndez-Miralles, Rosa Vela-Yebra, Ana Fríes-Ramos, Pedro Sánchez-Pellicer, Beatriz Ruzafa-Costas, Eva Núñez-Delegido, Humberto Gómez-Gómez, Sara Chumillas-Lidón, Jose A. Picó-Monllor and Laura Navarro-Moratalla

Genes 2022, 13(5), 930; https://doi.org/10.3390/genes13050930 - 23 May 2022

Cited by 11 | Viewed by 2818

Abstract

Background: The influence of the microbiome on neurological diseases has been studied for years. Recent findings have shown a different composition of gut microbiota detected in patients with multiple sclerosis (MS). The role of this dysbiosis is still unknown. Objective: We analyzed the [...] Read more.

Background: The influence of the microbiome on neurological diseases has been studied for years. Recent findings have shown a different composition of gut microbiota detected in patients with multiple sclerosis (MS). The role of this dysbiosis is still unknown. Objective: We analyzed the gut microbiota of 15 patients with active relapsing-remitting multiple sclerosis (RRMS), comparing with diet-matched healthy controls. Method: To determine the composition of the gut microbiota, we performed high-throughput sequencing of the 16S ribosomal RNA gene. The specific amplified sequences were in the V3 and V4 regions of the 16S ribosomal RNA gene. Results: The gut microbiota of RRMS patients differed from healthy controls in the levels of the Lachnospiraceae, Ezakiella, Ruminococcaceae, Hungatella, Roseburia, Clostridium, Shuttleworthia, Poephyromonas, and Bilophila genera. All these genera were included in a logistic regression analysis to determine the sensitivity and the specificity of the test. Finally, the ROC (receiver operating characteristic) and AUC with a 95% CI were calculated and best-matched for Ezakiella (AUC of 75.0 and CI from 60.6 to 89.4) and Bilophila (AUC of 70.2 and CI from 50.1 to 90.4). Conclusions: There is a dysbiosis in the gut microbiota of RRMS patients. An analysis of the components of the microbiota suggests the role of some genera as a predictive factor of RRMS prognosis and diagnosis. Full article

(This article belongs to the Special Issue When Genes Meet Microbial Ecology and Evolution)

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10 pages, 2329 KiB

Open AccessEditor’s ChoiceReview

m¹A RNA Modification in Gene Expression Regulation

by Hao Jin, Chunxiao Huo, Tianhua Zhou and Shanshan Xie

Genes 2022, 13(5), 910; https://doi.org/10.3390/genes13050910 - 19 May 2022

Cited by 25 | Viewed by 3579

Abstract

N¹-methyladenosine (m¹A) is a prevalent and reversible post-transcriptional RNA modification that decorates tRNA, rRNA and mRNA. Recent studies based on technical advances in analytical chemistry and high-throughput sequencing methods have revealed the crucial roles of m¹A RNA [...] Read more.

N¹-methyladenosine (m¹A) is a prevalent and reversible post-transcriptional RNA modification that decorates tRNA, rRNA and mRNA. Recent studies based on technical advances in analytical chemistry and high-throughput sequencing methods have revealed the crucial roles of m¹A RNA modification in gene regulation and biological processes. In this review, we focus on progress in the study of m¹A methyltransferases, m¹A demethylases and m¹A-dependent RNA-binding proteins and highlight the biological mechanisms and functions of m¹A RNA modification, as well as its association with human disease. We also summarize the current understanding of detection approaches for m¹A RNA modification. Full article

(This article belongs to the Special Issue Regulation of Gene Expression: RNA Modification of Genes)

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16 pages, 7751 KiB

Open AccessEditor’s ChoiceArticle

A Novel Cuproptosis-Related Prognostic Gene Signature and Validation of Differential Expression in Clear Cell Renal Cell Carcinoma

by Zilong Bian, Rong Fan and Lingmin Xie

Genes 2022, 13(5), 851; https://doi.org/10.3390/genes13050851 - 10 May 2022

Cited by 164 | Viewed by 14724

Abstract

Clear cell renal cell carcinoma (ccRCC) is the most prevalent subtype of renal cell carcinoma, which is characterized by metabolic reprogramming. Cuproptosis, a novel form of cell death, is highly linked to mitochondrial metabolism and mediated by protein lipoylation. However, the clinical impacts [...] Read more.

Clear cell renal cell carcinoma (ccRCC) is the most prevalent subtype of renal cell carcinoma, which is characterized by metabolic reprogramming. Cuproptosis, a novel form of cell death, is highly linked to mitochondrial metabolism and mediated by protein lipoylation. However, the clinical impacts of cuproptosis-related genes (CRGs) in ccRCC largely remain unclear. In the current study, we systematically evaluated the genetic alterations of cuproptosis-related genes in ccRCC. Our results revealed that CDKN2A, DLAT, DLD, FDX1, GLS, PDHA1 and PDHB exhibited differential expression between ccRCC and normal tissues (|log₂(fold change)| > 2/3 and p < 0.05). Utilizing an iterative sure independence screening (SIS) method, we separately constructed the prognostic signature of CRGs for predicting the overall survival (OS) and progression-free survival (PFS) in ccRCC patients. The prognostic score of CRGs yielded an area under the curve (AUC) of 0.658 and 0.682 for the prediction of 5-year OS and PFS, respectively. In the Kaplan−Meier survival analysis of OS, a higher risk score of cuproptosis-related gene signature was significantly correlated with worse overall survival (HR = 2.72 (2.01–3.68), log-rank p = 1.76 × 10⁻⁷). Patients with a higher risk had a significantly shorter PFS (HR = 2.83 (2.08–3.85), log-rank p = 3.66 × 10⁻⁷). Two independent validation datasets (GSE40435 (N = 101), GSE53757 (N = 72)) were collected for meta-analysis, suggesting that CDKN2A (log₂(fold change) = 1.46, 95%CI: 1.75–2.35) showed significantly higher expression in ccRCC tissues while DLAT (log₂(fold change) = −0.54, 95%CI: −0.93–−0.15) and FDX1 (log₂(fold change) = −1.01, 95%CI: −1.61–−0.42) were lowly expressed. The expression of CDKN2A and FDX1 in ccRCC was also significantly associated with immune infiltration levels and programmed cell death protein 1 (PD-1) expression (CDKN2A: r = 0.24, p = 2.14 × 10⁻⁸; FDX1: r = −0.17, p = 1.37 × 10⁻⁴). In conclusion, the cuproptosis-related gene signature could serve as a potential prognostic predictor for ccRCC patients and may offer novel insights into the cancer treatment. Full article

(This article belongs to the Topic Big Data in Healthcare, Bioinformatics and Precision Medicine)

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10 pages, 1508 KiB

Open AccessEditor’s ChoiceReview

Macrophage Polarization in Atherosclerosis

by Sahar Eshghjoo, Da Mi Kim, Arul Jayaraman, Yuxiang Sun and Robert C. Alaniz

Genes 2022, 13(5), 756; https://doi.org/10.3390/genes13050756 - 25 Apr 2022

Cited by 36 | Viewed by 8532

Abstract

The implication of the heterogeneous spectrum of pro- and anti-inflammatory macrophages (Macs) has been an important area of investigation over the last decade. The polarization of Macs alters their functional phenotype in response to their surrounding microenvironment. Macs are the major immune cells [...] Read more.

The implication of the heterogeneous spectrum of pro- and anti-inflammatory macrophages (Macs) has been an important area of investigation over the last decade. The polarization of Macs alters their functional phenotype in response to their surrounding microenvironment. Macs are the major immune cells implicated in the pathogenesis of atherosclerosis. A hallmark pathology of atherosclerosis is the accumulation of pro-inflammatory M1-like macrophages in coronary arteries induced by pro-atherogenic stimuli; these M1-like pro-inflammatory macrophages are incapable of digesting lipids, thus resulting in foam cell formation in the atherosclerotic plaques. Recent findings suggest that the progression and stability of atherosclerotic plaques are dependent on the quantity of infiltrated Macs, the polarization state of the Macs, and the ratios of different types of Mac populations. The polarization of Macs is defined by signature markers on the cell surface, as well as by factors in intracellular and intranuclear compartments. At the same time, pro- and anti-inflammatory polarized Macs also exhibit different gene expression patterns, with differential cellular characteristics in oxidative phosphorylation and glycolysis. Macs are reflective of different metabolic states and various types of diseases. In this review, we discuss the major differences between M1-like Macs and M2-like Macs, their associated metabolic pathways, and their roles in atherosclerosis. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Immune Cell Function in Obesity and Related Diseases)

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9 pages, 278 KiB

Open AccessEditor’s ChoiceArticle

Circulating miRNAs Are Associated with Inflammation Biomarkers in Children with Overweight and Obesity: Results of the I.Family Study

by Fabio Lauria, Giuseppe Iacomino, Paola Russo, Antonella Venezia, Pasquale Marena, Wolfgang Ahrens, Stefaan De Henauw, Gabriele Eiben, Ronja Foraita, Antje Hebestreit, Yiannis Kourides, Dénes Molnár, Luis A. Moreno, Toomas Veidebaum and Alfonso Siani

Genes 2022, 13(4), 632; https://doi.org/10.3390/genes13040632 - 01 Apr 2022

Cited by 10 | Viewed by 2292

Abstract

Increasing data suggest that overnutrition-induced obesity may trigger an inflammatory process in adipose tissue and upturn in the innate immune system. Numerous players have been involved in governing the inflammatory response, including epigenetics. Among epigenetic players, miRNAs are emerging as crucial regulators of [...] Read more.

Increasing data suggest that overnutrition-induced obesity may trigger an inflammatory process in adipose tissue and upturn in the innate immune system. Numerous players have been involved in governing the inflammatory response, including epigenetics. Among epigenetic players, miRNAs are emerging as crucial regulators of immune cell development, immune responses, autoimmunity, and inflammation. In this study, we aimed at identifying the involvement of candidate miRNAs in relation to inflammation-associated biomarkers in a subsample of European children with overweight and obesity participating in the I.Family study. The study sample included individuals with increased adiposity since this condition contributes to the early occurrence of chronic low-grade inflammation. We focused on the acute-phase reagent C-reactive protein (CRP) as the primary outcome and selected cytokines as plausible biomarkers of inflammation. We found that chronic low-grade CRP elevation shows a highly significant association with miR-26b-3p and hsa-miR-576-5p in boys. Furthermore, the association of CRP with hsa-miR-10b-5p and hsa-miR-31-5p is highly significant in girls. We also observed major sex-related associations of candidate miRNAs with selected cytokines. Except for IL-6, a significant association of hsa-miR-26b-3p and hsa-miR-576-5p with TNF-α, IL1-Ra, IL-8, and IL-15 levels was found exclusively in boys. The findings of this exploratory study suggest sex differences in the association of circulating miRNAs with inflammatory response biomarkers, and indicate a possible role of miRNAs among the candidate epigenetic mechanisms related to the process of low-grade inflammation in childhood obesity. Full article

(This article belongs to the Special Issue The Ins and Outs of miRNAs as Biomarkers)

24 pages, 14798 KiB

Open AccessEditor’s ChoiceArticle

Genome-Wide Analysis of the Protein Phosphatase 2C Genes in Tomato

by Jianfang Qiu, Lei Ni, Xue Xia, Shihao Chen, Yan Zhang, Min Lang, Mengyu Li, Binman Liu, Yu Pan, Jinhua Li and Xingguo Zhang

Genes 2022, 13(4), 604; https://doi.org/10.3390/genes13040604 - 28 Mar 2022

Cited by 15 | Viewed by 3101

Abstract

The plant protein phosphatase 2C (PP2C) plays an irreplaceable role in phytohormone signaling, developmental processes, and manifold stresses. However, information about the PP2C gene family in tomato (Solanum lycopersicum) is relatively restricted. In this study, a genome-wide investigation of the SlPP2C [...] Read more.

The plant protein phosphatase 2C (PP2C) plays an irreplaceable role in phytohormone signaling, developmental processes, and manifold stresses. However, information about the PP2C gene family in tomato (Solanum lycopersicum) is relatively restricted. In this study, a genome-wide investigation of the SlPP2C gene family was performed. A total of 92 SlPP2C genes were identified, they were distributed on 11 chromosomes, and all the SlPP2C proteins have the type 2C phosphatase domains. Based on phylogenetic analysis of PP2C genes in Arabidopsis, rice, and tomato, SlPP2C genes were divided into eight groups, designated A–H, which is also supported by the analyses of gene structures and protein motifs. Gene duplication analysis revealed that the duplication of whole genome and chromosome segments was the main cause of SLPP2Cs expansion. A total of 26 cis-elements related to stress, hormones, and development were identified in the 3 kb upstream region of these SlPP2C genes. Expression profile analysis revealed that the SlPP2C genes display diverse expression patterns in various tomato tissues. Furthermore, we investigated the expression patterns of SlPP2C genes in response to Ralstonia solanacearum infection. RNA-seq and qRT-PCR data reveal that nine SlPP2Cs are correlated with R. solanacearum. The above evidence hinted that SlPP2C genes play multiple roles in tomato and may contribute to tomato resistance to bacterial wilt. This study obtained here will give an impetus to the understanding of the potential function of SlPP2Cs and lay a solid foundation for tomato breeding and transgenic resistance to plant pathogens. Full article

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

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18 pages, 2604 KiB

Open AccessEditor’s ChoiceArticle

Differential Expression Profiles and Bioinformatics Analysis of tRNA-Derived Small RNAs in Muscle-Invasive Bladder Cancer in a Chinese Population

by Chuan Qin, Zheng-Hao Chen, Rui Cao, Ming-Jun Shi and Ye Tian

Genes 2022, 13(4), 601; https://doi.org/10.3390/genes13040601 - 28 Mar 2022

Cited by 10 | Viewed by 2622

Abstract

Muscle-invasive bladder cancer (MIBC) leads to a large societal burden. Recently, tRNA-derived small RNAs (tsRNAs), a novel type of noncoding RNA (ncRNAs), have been identified. However, the expression patterns and functions of tsRNAs in MIBC have not yet been identified. Here, RNA sequencing, [...] Read more.

Muscle-invasive bladder cancer (MIBC) leads to a large societal burden. Recently, tRNA-derived small RNAs (tsRNAs), a novel type of noncoding RNA (ncRNAs), have been identified. However, the expression patterns and functions of tsRNAs in MIBC have not yet been identified. Here, RNA sequencing, bioinformatics, and quantitative reverse transcription- polymerase chain reaction (qRT-PCR) were used to screen the expression profiles and predict the potential roles of tsRNAs in MIBC. Of 406 tsRNAs differentially expressed in MIBC tissues, 91 tsRNAs were significantly differentially expressed. Then, four candidate tsRNAs, tiRNA-1:34-Val-CAC-2, tiRNA-1:33-Gly-GCC-1, tRF-1:32-Gly-GCC-1, and tRF-+1:T20-Ser-TGA-1, were selected. Next, a bioinformatics analysis showed the potential target genes and tsRNA–mRNA network. The most significant and meaningful terms of gene ontology were the positive regulation of the phosphate metabolic process, lamellipodium, and protein-cysteine S-acyltransferase activity in the biological process, cellular component, and molecular function, respectively. In addition, the top four pathways were predicted by the Kyoto Encyclopedia of Genes and Genomes database (KEGG). Finally, qRT-PCR demonstrated a similar expression pattern compared to sequencing data for the candidate tsRNAs. In short, we find differential expression profiles and predict that tiRNA-1:33-Gly-GCC-1, tRF-1:32-Gly-GCC-1, and tRF-+1:T20-Ser-TGA-1 are very likely to engage in the pathophysiological process of MIBC via regulating the target genes in the key pathways. Full article

(This article belongs to the Special Issue Non-coding RNAs in Human Health and Diseases)

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20 pages, 687 KiB

Open AccessEditor’s ChoiceReview

HSF1-Activated Non-Coding Stress Response: Satellite lncRNAs and Beyond, an Emerging Story with a Complex Scenario

by Claire Vourc’h, Solenne Dufour, Kalina Timcheva, Daphné Seigneurin-Berny and André Verdel

Genes 2022, 13(4), 597; https://doi.org/10.3390/genes13040597 - 27 Mar 2022

Cited by 10 | Viewed by 2827

Abstract

In eukaryotes, the heat shock response is orchestrated by a transcription factor named Heat Shock Factor 1 (HSF1). HSF1 is mostly characterized for its role in activating the expression of a repertoire of protein-coding genes, including the heat shock protein (HSP) genes. Remarkably, [...] Read more.

In eukaryotes, the heat shock response is orchestrated by a transcription factor named Heat Shock Factor 1 (HSF1). HSF1 is mostly characterized for its role in activating the expression of a repertoire of protein-coding genes, including the heat shock protein (HSP) genes. Remarkably, a growing set of reports indicate that, upon heat shock, HSF1 also targets various non-coding regions of the genome. Focusing primarily on mammals, this review aims at reporting the identity of the non-coding genomic sites directly bound by HSF1, and at describing the molecular function of the long non-coding RNAs (lncRNAs) produced in response to HSF1 binding. The described non-coding genomic targets of HSF1 are pericentric Satellite DNA repeats, (sub)telomeric DNA repeats, Short Interspersed Nuclear Element (SINE) repeats, transcriptionally active enhancers and the NEAT1 gene. This diverse set of non-coding genomic sites, which already appears to be an integral part of the cellular response to stress, may only represent the first of many. Thus, the study of the evolutionary conserved heat stress response has the potential to emerge as a powerful cellular context to study lncRNAs, produced from repeated or unique DNA regions, with a regulatory function that is often well-documented but a mode of action that remains largely unknown. Full article

(This article belongs to the Special Issue Satellite DNA Genomics)

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17 pages, 2918 KiB

Open AccessEditor’s ChoiceArticle

Complex Changes in the Efficiency of the Expression of Many Genes in Monogenic Diseases, Mucopolysaccharidoses, May Arise from Significant Disturbances in the Levels of Factors Involved in the Gene Expression Regulation Processes

by Zuzanna Cyske, Lidia Gaffke, Karolina Pierzynowska and Grzegorz Węgrzyn

Genes 2022, 13(4), 593; https://doi.org/10.3390/genes13040593 - 26 Mar 2022

Cited by 10 | Viewed by 1879

Abstract

Monogenic diseases are primarily caused by mutations in a single gene; thus, they are commonly recognized as genetic disorders with the simplest mechanisms. However, recent studies have indicated that the molecular mechanisms of monogenic diseases can be unexpectedly complicated, and their understanding requires [...] Read more.

Monogenic diseases are primarily caused by mutations in a single gene; thus, they are commonly recognized as genetic disorders with the simplest mechanisms. However, recent studies have indicated that the molecular mechanisms of monogenic diseases can be unexpectedly complicated, and their understanding requires complex studies at the molecular level. Previously, we have demonstrated that in mucopolysaccharidoses (MPS), a group of monogenic lysosomal storage diseases, several hundreds of genes reveal significant changes in the expression of various genes. Although the secondary effects of the primary biochemical defect and the inefficient degradation of glycosaminoglycans (GAGs) might be considered, the scale of the changes in the expression of a large fraction of genes cannot be explained by a block in one biochemical pathway. Here, we demonstrate that in cellular models of 11 types of MPS, the expression of genes coding for proteins involved in the regulation of the expression of many other genes at various stages (such as signal transduction, transcription, splicing, RNA degradation, translation, and others) is significantly disturbed relative to the control cells. This conclusion was based on transcriptomic studies, supported by biochemical analyses of levels of selected proteins encoded by genes revealing an especially high level of dysregulation in MPS (EXOSC9, SRSF10, RPL23, and NOTCH3 proteins were investigated). Interestingly, the reduction in GAGs levels, through the inhibition of their synthesis normalized the amounts of EXOSC9, RPL23, and NOTCH3 in some (but not all) MPS types, while the levels of SRSF10 could not be corrected in this way. These results indicate that different mechanisms are involved in the dysregulation of the expression of various genes in MPS, pointing to a potential explanation for the inability of some therapies (such as enzyme replacement therapy or substrate reduction therapy) to fully correct the physiology of MPS patients. We suggest that the disturbed expression of some genes, which appears as secondary or tertiary effects of GAG storage, might not be reversible, even after a reduction in the amounts of the storage material. Full article

(This article belongs to the Special Issue Molecular Basis of Rare Diseases)

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20 pages, 2049 KiB

Open AccessEditor’s ChoiceArticle

Genomic Predictions for Common Bunt, FHB, Stripe Rust, Leaf Rust, and Leaf Spotting Resistance in Spring Wheat

by Kassa Semagn, Muhammad Iqbal, Diego Jarquin, José Crossa, Reka Howard, Izabela Ciechanowska, Maria Antonia Henriquez, Harpinder Randhawa, Reem Aboukhaddour, Brent D. McCallum, Anita L. Brûlé-Babel, Alireza Navabi, Amidou N’Diaye, Curtis Pozniak and Dean Spaner

Genes 2022, 13(4), 565; https://doi.org/10.3390/genes13040565 - 23 Mar 2022

Cited by 13 | Viewed by 1996

Abstract

Some studies have investigated the potential of genomic selection (GS) on stripe rust, leaf rust, Fusarium head blight (FHB), and leaf spot in wheat, but none of them have assessed the effect of the reaction norm model that incorporated GE interactions. In addition, [...] Read more.

Some studies have investigated the potential of genomic selection (GS) on stripe rust, leaf rust, Fusarium head blight (FHB), and leaf spot in wheat, but none of them have assessed the effect of the reaction norm model that incorporated GE interactions. In addition, the prediction accuracy on common bunt has not previously been studied. Here, we investigated within-population prediction accuracies using the baseline M1 model and two reaction norm models (M2 and M3) with three random cross-validation (CV1, CV2, and CV0) schemes. Three Canadian spring wheat populations were evaluated in up to eight field environments and genotyped with 3158, 5732, and 23,795 polymorphic markers. The M3 model that incorporated GE interactions reduced residual variance by an average of 10.2% as compared with the main effect M2 model and increased prediction accuracies on average by 2–6%. In some traits, the M3 model increased prediction accuracies up to 54% as compared with the M2 model. The average prediction accuracies of the M3 model with CV1, CV2, and CV0 schemes varied from 0.02 to 0.48, from 0.25 to 0.84, and from 0.14 to 0.87, respectively. In both CV2 and CV0 schemes, stripe rust in all three populations, common bunt and leaf rust in two populations, as well as FHB severity, FHB index, and leaf spot in one population had high to very high (0.54–0.87) prediction accuracies. This is the first comprehensive genomic selection study on five major diseases in spring wheat. Full article

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

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20 pages, 355 KiB

Open AccessEditor’s ChoiceArticle

Assessment of Genetic Variability and Bran Oil Characters of New Developed Restorer Lines of Rice (Oryza sativa L.)

by Mamdouh M. A. Awad-Allah, Azza H. Mohamed, Mohamed A. El-Bana, Samira A. F. El-Okkiah, Mohamed F. M. Abdelkader, Mohamed H. Mahmoud, Mohamed Z. El-Diasty, Manal M. Said, Sahar A. M. Shamseldin and Mohamed A. Abdein

Genes 2022, 13(3), 509; https://doi.org/10.3390/genes13030509 - 13 Mar 2022

Cited by 7 | Viewed by 2557

Abstract

Rice is one of the most important crops in Egypt. Due to the gap between the demand and the availability of the local edible oils, there is need to raise the nutritional value of rice and, therefore, to improve the nutritional value of [...] Read more.

Rice is one of the most important crops in Egypt. Due to the gap between the demand and the availability of the local edible oils, there is need to raise the nutritional value of rice and, therefore, to improve the nutritional value of the consumer. This research was carried out at the Experimental Farm of Sakha Agricultural Research Station, Sakha, Kafr El-Sheikh, Egypt, during the 2019 and 2020 seasons. Five newly developed genotypes of rice, namely NRL 63, NRL 64, NRL 65, NRL 66, and Giza 178 as check variety (control), were used to evaluate the analytical characterization of raw rice bran and rice bran oil from rice bran, study the genetic variability and genetic advance for various quantitative and qualitative traits in rice as well as, rice bran oil. The genotypes were evaluated in a randomized complete block design (RCBD) with three replications. Analysis of variance revealed highly significant variations among the genotypes for all the studied characters. Data revealed that high estimates of the phenotypic coefficient of variance (PCV%) and genotypic coefficient of variance (GCV%) were observed for amylose content percentage, peroxide value (meq/kg oil), myristic C14:0, and arachidic C20:0, indicating that they all interacted with the environment to some extent. The line NRL66 and NRL64 showed the highest and high values of mean performance for grain yield (t/h), grain type (shape), amylose content percentage, crude protein, ether extract and ash of milled rice, crude protein, ether extract, ash, phosphorus, magnesium, manganese, zinc, and iron of stabilized rice bran oil. Genetic advance as a percentage of mean was high for most of the studied traits. It indicates that most likely, the heritability is due to additive gene effects, and selection may be effective. The percentage of advantage over the Giza 178 as the commercial variety was significant and highly significant among the genotypes for all the characters studied in the two years, indicating that the selection is effective in the genetic improvements for these traits. Full article

(This article belongs to the Special Issue Plant Genomics and Epigenomics in Breeding for Yield, Quality, and Sustainability)

13 pages, 971 KiB

Open AccessEditor’s ChoiceReview

Clinical and Genetic Aspects of Phelan–McDermid Syndrome: An Interdisciplinary Approach to Management

by Francisco Cammarata-Scalisi, Michele Callea, Diego Martinelli, Colin Eric Willoughby, Antonio Cárdenas Tadich, Maykol Araya Castillo, María Angelina Lacruz-Rengel, Marco Medina, Piercesare Grimaldi, Enrico Bertini and Julián Nevado

Genes 2022, 13(3), 504; https://doi.org/10.3390/genes13030504 - 12 Mar 2022

Cited by 8 | Viewed by 3484

Abstract

Phelan–McDermid syndrome (PMS) is a rare, heterogeneous, and complex neurodevelopmental disorder. It is generally caused by a heterozygous microdeletion of contiguous genes located in the distal portion of the long arm of chromosome 22, including the SHANK3 gene. Sequence variants of SHANK3, [...] Read more.

Phelan–McDermid syndrome (PMS) is a rare, heterogeneous, and complex neurodevelopmental disorder. It is generally caused by a heterozygous microdeletion of contiguous genes located in the distal portion of the long arm of chromosome 22, including the SHANK3 gene. Sequence variants of SHANK3, including frameshift, nonsense mutations, small indels and splice site mutations also result in PMS. Furthermore, haploinsufficiency in SHANK3 has been suggested as the main cause of PMS. SHANK3 is also associated with intellectual disability, autism spectrum disorder and schizophrenia. The phenotype of PMS is variable, and lacks a distinctive phenotypic characteristic, so the clinical diagnosis should be confirmed by genetic analysis. PMS is a multi-system disorder, and clinical care must encompass various specialties and therapists. The role of risperidone, intranasal insulin, insulin growth factor 1, and oxytocin as potential therapeutic options in PMS will be discussed in this review. The diagnosis of PMS is important to provide an appropriate clinical evaluation, treatment, and genetic counseling. Full article

(This article belongs to the Special Issue Genetic Basis of Sensory and Neurological Disorders)

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13 pages, 20372 KiB

Open AccessEditor’s ChoiceArticle

Genome-Wide Association Study of Salt Tolerance at the Seed Germination Stage in Flax (Linum usitatissimum L.)

by Xiao Li, Dongliang Guo, Min Xue, Gongze Li, Qingcheng Yan, Haixia Jiang, Huiqing Liu, Jiaxun Chen, Yanfang Gao, Lepeng Duan and Liqiong Xie

Genes 2022, 13(3), 486; https://doi.org/10.3390/genes13030486 - 10 Mar 2022

Cited by 12 | Viewed by 2639

Abstract

Soil salinization seriously affects the growth and distribution of flax. However, there is little information about the salt tolerance of flax. In this study, the salt tolerance of 200 diverse flax accessions during the germination stage was evaluated, and then the Genome-wide Association [...] Read more.

Soil salinization seriously affects the growth and distribution of flax. However, there is little information about the salt tolerance of flax. In this study, the salt tolerance of 200 diverse flax accessions during the germination stage was evaluated, and then the Genome-wide Association Study (GWAS) was carried out based on the relative germination rate (RGR), relative shoot length (RSL) and relative root length (RRL), whereby quantitative trait loci (QTLs) related to salt tolerance were identified. The results showed that oil flax had a better salt tolerance than fiber flax. A total of 902 single nucleotide polymorphisms (SNPs) were identified on 15 chromosomes. These SNPs were integrated into 64 QTLs, explaining 14.48 to 29.38% (R²) of the phenotypic variation. In addition, 268 candidate genes were screened by combining previous transcriptome data and homologous gene annotation. Among them, Lus10033213 is a single-point SNP repeat mapping gene, which encodes a Glutathione S-transferase (GST). This study is the first to use GWAS to excavate genes related to salt tolerance during the germination stage of flax. The results of this study provide important information for studying the genetic mechanism of salt tolerance of flax, and also provide the possibility to improve the salt tolerance of flax. Full article

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

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19 pages, 2415 KiB

Open AccessEditor’s ChoiceArticle

Pleiotropic Effects of Common and Rare GCKR Exonic Mutations on Cardiometabolic Traits

by Kuan-Hung Yeh, Lung-An Hsu, Ming-Sheng Teng, Semon Wu, Hsin-Hua Chou and Yu-Lin Ko

Genes 2022, 13(3), 491; https://doi.org/10.3390/genes13030491 - 10 Mar 2022

Cited by 12 | Viewed by 2261

Abstract

Background: The common non-synonymous mutation of the glucokinase regulator (GCKR) gene, namely rs1260326, is widely reported to have pleiotropic effects on cardio-metabolic traits and hematological parameters. Objective: This study aimed to identify whether other GCKR variants may have pleiotropic effects independent [...] Read more.

Background: The common non-synonymous mutation of the glucokinase regulator (GCKR) gene, namely rs1260326, is widely reported to have pleiotropic effects on cardio-metabolic traits and hematological parameters. Objective: This study aimed to identify whether other GCKR variants may have pleiotropic effects independent of the rs1260326 genotypes. Methods: In total, 81,097 Taiwan Biobank participants were enrolled for the regional plot association studies and candidate variant analysis of the region around the GCKR gene. Results: The initial candidate variant approach showed the significant association of the rs1260326 genotypes with multiple phenotypes. Regional plot association analysis of the GCKR gene region further revealed genome-wide significant associations between GCKR variants and serum total and low-density lipoprotein cholesterol; triglyceride, uric acid, creatinine, aspartate aminotransferase, γ-Glutamyl transferase, albumin, and fasting plasma glucose levels; estimated glomerular filtration rate; leukocyte and platelet counts; microalbuminuria, and metabolic syndrome, with rs1260326 being the most common lead polymorphism. Serial conditional analysis identified genome-wide significant associations of two low-frequency exonic mutations, rs143881585 and rs8179206, with high serum triglyceride and albumin levels. In five rare GCKR exonic non-synonymous or nonsense mutations available for analysis, GCKR rs146175795 showed an independent association with serum triglyceride and albumin levels and rs150673460 showed an independent association with serum triglyceride levels. Weighted genetic risk scores from the combination of GCKR rs143881585 and rs146175795 revealed a significant association with metabolic syndrome. Conclusion: In addition to the rs1260326 variant, low-frequency and rare GCKR exonic mutations exhibit pleiotropic effects on serum triglyceride and albumin levels and the risk of metabolic syndrome. These results provide evidence that both common and rare GCKR variants may play a critical role in predicting the risk of cardiometabolic disorders. Full article

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

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25 pages, 737 KiB

Open AccessEditor’s ChoiceReview

Monogenic Parkinson’s Disease: Genotype, Phenotype, Pathophysiology, and Genetic Testing

by Fangzhi Jia, Avi Fellner and Kishore Raj Kumar

Genes 2022, 13(3), 471; https://doi.org/10.3390/genes13030471 - 07 Mar 2022

Cited by 41 | Viewed by 8684

Abstract

Parkinson’s disease may be caused by a single pathogenic variant (monogenic) in 5–10% of cases, but investigation of these disorders provides valuable pathophysiological insights. In this review, we discuss each genetic form with a focus on genotype, phenotype, pathophysiology, and the geographic and [...] Read more.

Parkinson’s disease may be caused by a single pathogenic variant (monogenic) in 5–10% of cases, but investigation of these disorders provides valuable pathophysiological insights. In this review, we discuss each genetic form with a focus on genotype, phenotype, pathophysiology, and the geographic and ethnic distribution. Well-established Parkinson’s disease genes include autosomal dominant forms (SNCA, LRRK2, and VPS35) and autosomal recessive forms (PRKN, PINK1 and DJ1). Furthermore, mutations in the GBA gene are a key risk factor for Parkinson’s disease, and there have been major developments for X-linked dystonia parkinsonism. Moreover, atypical or complex parkinsonism may be due to mutations in genes such as ATP13A2, DCTN1, DNAJC6, FBXO7, PLA2G6, and SYNJ1. Furthermore, numerous genes have recently been implicated in Parkinson’s disease, such as CHCHD2, LRP10, TMEM230, UQCRC1, and VPS13C. Additionally, we discuss the role of heterozygous mutations in autosomal recessive genes, the effect of having mutations in two Parkinson’s disease genes, the outcome of deep brain stimulation, and the role of genetic testing. We highlight that monogenic Parkinson’s disease is influenced by ethnicity and geographical differences, reinforcing the need for global efforts to pool large numbers of patients and identify novel candidate genes. Full article

(This article belongs to the Special Issue Parkinson's Disease: Genetics and Pathogenesis)

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16 pages, 3770 KiB

Open AccessEditor’s ChoiceArticle

Genome-Wide Identification of YABBY Gene Family in Cucurbitaceae and Expression Analysis in Cucumber (Cucumis sativus L.)

by Shuai Yin, Sen Li, Yiming Gao, Ezra S. Bartholomew, Ruijia Wang, Hua Yang, Chang Liu, Xiaofeng Chen, Ying Wang, Xingwang Liu and Huazhong Ren

Genes 2022, 13(3), 467; https://doi.org/10.3390/genes13030467 - 07 Mar 2022

Cited by 11 | Viewed by 3074

Abstract

YABBY transcription factors play important roles in plant growth and development. However, little is known about YABBY genes in Cucurbitaceae. Here, we identified 59 YABBY genes from eight cucurbit species, including cucumber (C. sativus L.), melon (C. melon L.), watermelon [...] Read more.

YABBY transcription factors play important roles in plant growth and development. However, little is known about YABBY genes in Cucurbitaceae. Here, we identified 59 YABBY genes from eight cucurbit species, including cucumber (C. sativus L.), melon (C. melon L.), watermelon (C. lanatus), wax gourd (B. hispida), pumpkin (C. maxima), zucchini (C. pepo L.), silver-seed gourd (C. argyrosperma), and bottle gourd (L. siceraria). The 59 YABBY genes were clustered into five subfamilies wherein the gene structures and motifs are conserved, suggesting similar functions within each subfamily. Different YABBY gene numbers in eight cucurbit species indicated that gene loss or duplication events exist in an evolutionary process across Cucurbitaceae. The cis-acting elements analysis implied that the YABBYs may be involved in plant development, and phytohormone, stress, and light responses. Importantly, YABBY genes exhibited organ-specific patterns in expression in cucumber. Furthermore, a gene CsaV3_6G038650 was constitutively expressed at higher levels at different fruit development stages and might play a crucial role in cucumber fruit development. Collectively, our work will provide a better understanding for further function identifications of YABBY genes in Cucurbitaceae. Full article

(This article belongs to the Collection Feature Papers: 'Plant Genetics and Genomics' Section)

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18 pages, 1177 KiB

Open AccessEditor’s ChoiceArticle

Comparative Chloroplast Genome Analysis of Wax Gourd (Benincasa hispida) with Three Benincaseae Species, Revealing Evolutionary Dynamic Patterns and Phylogenetic Implications

by Weicai Song, Zimeng Chen, Li He, Qi Feng, Hongrui Zhang, Guilin Du, Chao Shi and Shuo Wang

Genes 2022, 13(3), 461; https://doi.org/10.3390/genes13030461 - 04 Mar 2022

Cited by 21 | Viewed by 2763

Abstract

Benincasa hispida (wax gourd) is an important Cucurbitaceae crop, with enormous economic and medicinal importance. Here, we report the de novo assembly and annotation of the complete chloroplast genome of wax gourd with 156,758 bp in total. The quadripartite structure of the chloroplast [...] Read more.

Benincasa hispida (wax gourd) is an important Cucurbitaceae crop, with enormous economic and medicinal importance. Here, we report the de novo assembly and annotation of the complete chloroplast genome of wax gourd with 156,758 bp in total. The quadripartite structure of the chloroplast genome comprises a large single-copy (LSC) region with 86,538 bp and a small single-copy (SSC) region with 18,060 bp, separated by a pair of inverted repeats (IRa and IRb) with 26,080 bp each. Comparison analyses among B. hispida and three other species from Benincaseae presented a significant conversion regarding nucleotide content, genome structure, codon usage, synonymous and non-synonymous substitutions, putative RNA editing sites, microsatellites, and oligonucleotide repeats. The LSC and SSC regions were found to be much more varied than the IR regions through a divergent analysis of the species within Benincaseae. Notable IR contractions and expansions were observed, suggesting a difference in genome size, gene duplication and deletion, and the presence of pseudogenes. Intronic gene sequences, such as trnR-UCU–atpA and atpH–atpI, were observed as highly divergent regions. Two types of phylogenetic analysis based on the complete cp genome and 72 genes suggested sister relationships between B. hispida with the Citrullus, Lagenaria, and Cucumis. Variations and consistency with previous studies regarding phylogenetic relationships are discussed. The cp genome of B. hispida provides valuable genetic information for the detection of molecular markers, research on taxonomic discrepancies, and the inference of the phylogenetic relationships of Cucurbitaceae. Full article

(This article belongs to the Special Issue Advances in Evolution of Plant Organelle Genome)

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22 pages, 2960 KiB

Open AccessEditor’s ChoiceArticle

Development of New Restorer Lines Carrying Some Restoring Fertility Genes with Flowering, Yield and Grains Quality Characteristics in Rice (Oryza sativa L.)

by Mamdouh M. A. Awad-Allah, Nehal M. Elekhtyar, Mohamed Abd-El-Moaty El-Abd, Mohamed F. M. Abdelkader, Mohamed H. Mahmoud, Azza H. Mohamed, Mohamed Z. El-Diasty, Manal M. Said, Sahar A. M. Shamseldin and Mohamed A. Abdein

Genes 2022, 13(3), 458; https://doi.org/10.3390/genes13030458 - 03 Mar 2022

Cited by 13 | Viewed by 2771

Abstract

This study was carried out using 22 promising restorer lines of rice and their parental lines to study genetic variability and genetic advance for yield and yield-associated grain quality traits and floral traits. These genotypes are evaluated in a replicated trial using Randomized [...] Read more.

This study was carried out using 22 promising restorer lines of rice and their parental lines to study genetic variability and genetic advance for yield and yield-associated grain quality traits and floral traits. These genotypes are evaluated in a replicated trial using Randomized Complete Block Design (RCBD) with three replications at the Experimental Farm of Sakha Agricultural Research Station, Sakha, Kafr El-Sheikh, Egypt, during the seasons from 2012 to 2020. Analysis of variance revealed that highly significant variations were observed among the genotypes for all the studied characters. Both GCV% and PCV% were high for the number of spikelets per panicle, the number of filled grains per panicle, and panicle weight. The genetic advance in the percentage of mean was high for days to plant height, panicle length, number of spikelets per panicle, number of filled grains per panicle, panicle weight, grain yield per plant, anther length, anther breadth, duration of floret opening, and head rice percentage. Mean performance of the rice genotypes indicated that the genotypes NRL 59, NRL 55, NRL 62, NRL 63, NRL 66, and NRL 54-2 were promising for grain yield and associated desirable traits. Thus, some of these promising lines can be promoted as a new rice variety and could be used as a source for developing new hybrid combinations in hybrid rice breeding programs. The percentage of advantage over better parent and Giza 178 as the commercial variety was significant and there were highly significant desirable values among the genotypes for all the studied traits in the two years, indicating that the selection is effective in the genetic improvements for these traits. Full article

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

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10 pages, 1257 KiB

Open AccessEditor’s ChoiceReview

Mucopolysaccharidosis-Plus Syndrome, a Rapidly Progressive Disease: Favorable Impact of a Very Prolonged Steroid Treatment on the Clinical Course in a Child

by Martha Caterina Faraguna, Francesca Musto, Viola Crescitelli, Maria Iascone, Luigina Spaccini, Davide Tonduti, Tiziana Fedeli, Gaia Kullmann, Francesco Canonico, Alessandro Cattoni, Fabiola Dell’Acqua, Carmelo Rizzari and Serena Gasperini

Genes 2022, 13(3), 442; https://doi.org/10.3390/genes13030442 - 28 Feb 2022

Cited by 8 | Viewed by 3007

Abstract

Mucopolysaccharidosis-plus syndrome (MPS-PS) is a novel autosomal recessive disorder caused by a mutation in the VPS33A gene. This syndrome presents with typical symptoms of mucopolysaccharidosis, as well as congenital heart defects, renal, and hematopoietic system disorders. To date, twenty-four patients have been described. [...] Read more.

Mucopolysaccharidosis-plus syndrome (MPS-PS) is a novel autosomal recessive disorder caused by a mutation in the VPS33A gene. This syndrome presents with typical symptoms of mucopolysaccharidosis, as well as congenital heart defects, renal, and hematopoietic system disorders. To date, twenty-four patients have been described. There is no specific therapy for MPS-PS; clinical management is therefore limited to symptoms management. The clinical course is rapidly progressive, and most patients die before 1–2 years of age. We describe a currently 6-year-old male patient with MPS-PS presenting with multiorgan involvement. Symptoms started at four months of age when he progressively suffered from numerous acute and potentially life-threatening events. When he was two years old, he developed secondary hemophagocytic lymphohistiocytosis (HLH), which was successfully treated with steroids. To date, this child represents the oldest patient affected by MPS-PS described in the literature and the first one presenting with a life-threatening secondary HLH. The prolonged steroid treatment allowed a stabilization of his general and hematological conditions and probably determined an improvement of his psychomotor milestones and new neurological acquisitions with an improvement of quality of life. HLH should be suspected and adequately treated in MPS-PS patients presenting with suggestive symptoms of the disease. The usefulness of a prolonged steroid treatment to improve the clinical course of children with MPS-PS deserves further investigation. Full article

(This article belongs to the Special Issue Genetic Research in Metabolic Diseases)

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30 pages, 1757 KiB

Open AccessEditor’s ChoiceReview

Role of miRNAs in Neurodegeneration: From Disease Cause to Tools of Biomarker Discovery and Therapeutics

by Bidisha Roy, Erica Lee, Teresa Li and Maria Rampersaud

Genes 2022, 13(3), 425; https://doi.org/10.3390/genes13030425 - 25 Feb 2022

Cited by 35 | Viewed by 4796

Abstract

Neurodegenerative diseases originate from neuronal loss in the central nervous system (CNS). These debilitating diseases progress with age and have become common due to an increase in longevity. The National Institute of Environmental Health Science’s 2021 annual report suggests around 6.2 million Americans [...] Read more.

Neurodegenerative diseases originate from neuronal loss in the central nervous system (CNS). These debilitating diseases progress with age and have become common due to an increase in longevity. The National Institute of Environmental Health Science’s 2021 annual report suggests around 6.2 million Americans are living with Alzheimer’s disease, and there is a possibility that there will be 1.2 million Parkinson’s disease patients in the USA by 2030. There is no clear-cut universal mechanism for identifying neurodegenerative diseases, and therefore, they pose a challenge for neurobiology scientists. Genetic and environmental factors modulate these diseases leading to familial or sporadic forms. Prior studies have shown that miRNA levels are altered during the course of the disease, thereby suggesting that these noncoding RNAs may be the contributing factor in neurodegeneration. In this review, we highlight the role of miRNAs in the pathogenesis of neurodegenerative diseases. Through this review, we aim to achieve four main objectives: First, we highlight how dysregulation of miRNA biogenesis led to these diseases. Second, we highlight the computational or bioinformatics tools required to identify the putative molecular targets of miRNAs, leading to biological molecular pathways or mechanisms involved in these diseases. Third, we focus on the dysregulation of miRNAs and their target genes leading to several neurodegenerative diseases. In the final section, we highlight the use of miRNAs as potential diagnostic biomarkers in the early asymptomatic preclinical diagnosis of these age-dependent debilitating diseases. Additionally, we discuss the challenges and advances in the development of miRNA therapeutics for brain targeting. We list some of the innovative strategies employed to deliver miRNA into target cells and the relevance of these viral and non-viral carrier systems in RNA therapy for neurodegenerative diseases. In summary, this review highlights the relevance of studying brain-enriched miRNAs, the mechanisms underlying their regulation of target gene expression, their dysregulation leading to progressive neurodegeneration, and their potential for biomarker marker and therapeutic intervention. This review thereby highlights ways for the effective diagnosis and prevention of these neurodegenerative disorders in the near future. Full article

(This article belongs to the Special Issue Non-coding RNAs in Human Health and Diseases)

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11 pages, 1237 KiB

Open AccessEditor’s ChoiceReview

Alternative Splicing and Isoforms: From Mechanisms to Diseases

by Qi Liu, Leiming Fang and Chengjun Wu

Genes 2022, 13(3), 401; https://doi.org/10.3390/genes13030401 - 24 Feb 2022

Cited by 27 | Viewed by 12464

Abstract

Alternative splicing of pre-mRNA is a key mechanism for increasing the complexity of proteins in humans, causing a diversity of expression of transcriptomes and proteomes in a tissue-specific manner. Alternative splicing is regulated by a variety of splicing factors. However, the changes and [...] Read more.

Alternative splicing of pre-mRNA is a key mechanism for increasing the complexity of proteins in humans, causing a diversity of expression of transcriptomes and proteomes in a tissue-specific manner. Alternative splicing is regulated by a variety of splicing factors. However, the changes and errors of splicing regulation caused by splicing factors are strongly related to many diseases, something which represents one of this study’s main interests. Further understanding of alternative splicing regulation mediated by cellular factors is also a prospective choice to develop specific drugs for targeting the dynamic RNA splicing process. In this review, we firstly concluded the basic principle of alternative splicing. Afterwards, we showed how splicing isoforms affect physiological activities through specific disease examples. Finally, the available treatment methods relative to adjusting splicing activities have been summarized. Full article

(This article belongs to the Special Issue Alternative Splicing in Human Physiology and Disease)

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24 pages, 1188 KiB

Open AccessEditor’s ChoiceReview

Epigenetic and Epitranscriptomic Control in Prostate Cancer

by Judith López, Ana M. Añazco-Guenkova, Óscar Monteagudo-García and Sandra Blanco

Genes 2022, 13(2), 378; https://doi.org/10.3390/genes13020378 - 18 Feb 2022

Cited by 14 | Viewed by 3740

Abstract

The initiation of prostate cancer has been long associated with DNA copy-number alterations, the loss of specific chromosomal regions and gene fusions, and driver mutations, especially those of the Androgen Receptor. Non-mutational events, particularly DNA and RNA epigenetic dysregulation, are emerging as key [...] Read more.

The initiation of prostate cancer has been long associated with DNA copy-number alterations, the loss of specific chromosomal regions and gene fusions, and driver mutations, especially those of the Androgen Receptor. Non-mutational events, particularly DNA and RNA epigenetic dysregulation, are emerging as key players in tumorigenesis. In this review we summarize the molecular changes linked to epigenetic and epitranscriptomic dysregulation in prostate cancer and the role that alterations to DNA and RNA modifications play in the initiation and progression of prostate cancer. Full article

(This article belongs to the Special Issue Epigenomics and Epitranscriptomics Crosstalk)

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18 pages, 3348 KiB

Open AccessEditor’s ChoiceArticle

Altered Mitochondrial Quality Control in Rats with Metabolic Dysfunction-Associated Fatty Liver Disease (MAFLD) Induced by High-Fat Feeding

by Federica Cioffi, Antonia Giacco, Giuseppe Petito, Rita de Matteis, Rosalba Senese, Assunta Lombardi, Pieter de Lange, Maria Moreno, Fernando Goglia, Antonia Lanni and Elena Silvestri

Genes 2022, 13(2), 315; https://doi.org/10.3390/genes13020315 - 08 Feb 2022

Cited by 19 | Viewed by 2504

Abstract

Metabolic dysfunction-associated fatty liver disease (MAFLD) is defined as the presence of hepatic steatosis in addition to one of three metabolic conditions: overweight/obesity, type 2 diabetes mellitus, or metabolic dysregulation. Chronic exposure to excess dietary fatty acids may cause hepatic steatosis and metabolic [...] Read more.

Metabolic dysfunction-associated fatty liver disease (MAFLD) is defined as the presence of hepatic steatosis in addition to one of three metabolic conditions: overweight/obesity, type 2 diabetes mellitus, or metabolic dysregulation. Chronic exposure to excess dietary fatty acids may cause hepatic steatosis and metabolic disturbances. The alteration of the quality of mitochondria is one of the factors that could contribute to the metabolic dysregulation of MAFDL. This study was designed to determine, in a rodent model of MAFLD, the effects of a long-term high-fat diet (HFD) on some hepatic processes that characterize mitochondrial quality control, such as biogenesis, dynamics, and mitophagy. To mimic the human manifestation of MAFLD, the rats were exposed to both an HFD and a housing temperature within the rat thermoneutral zone (28–30 °C). After 14 weeks of the HFD, the rats showed significant fat deposition and liver steatosis. Concomitantly, some important factors related to the hepatic mitochondrial quality were markedly affected, such as increased mitochondrial reactive oxygen species (ROS) production and mitochondrial DNA (mtDNA) damage; reduced mitochondrial biogenesis, mtDNA copy numbers, mtDNA repair, and mitochondrial fusion. HFD-fed rats also showed an impaired mitophagy. Overall, the obtained data shed new light on the network of different processes contributing to the failure of mitochondrial quality control as a central event for mitochondrial dysregulation in MAFLD. Full article

(This article belongs to the Collection Genotype-Phenotype Study in Disease)

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19 pages, 862 KiB

Open AccessEditor’s ChoiceReview

A Review on CYP11A1, CYP17A1, and CYP19A1 Polymorphism Studies: Candidate Susceptibility Genes for Polycystic Ovary Syndrome (PCOS) and Infertility

by Roozbeh Heidarzadehpilehrood, Maryam Pirhoushiaran, Rasoul Abdollahzadeh, Malina Binti Osman, Maryam Sakinah, Norshariza Nordin and Habibah Abdul Hamid

Genes 2022, 13(2), 302; https://doi.org/10.3390/genes13020302 - 05 Feb 2022

Cited by 40 | Viewed by 4814

Abstract

Polycystic ovary syndrome is a multifactorial condition associated with reproductive and endocrine organs and might cause infertility and metabolic abnormalities in childbearing age. PCOS seems to be a multifactorial disorder resulting from the combination of several genetic and environmental factors. Little research has [...] Read more.

Polycystic ovary syndrome is a multifactorial condition associated with reproductive and endocrine organs and might cause infertility and metabolic abnormalities in childbearing age. PCOS seems to be a multifactorial disorder resulting from the combination of several genetic and environmental factors. Little research has been conducted to date on the impact of polymorphisms in infertility. We aim to review the appearance of polymorphisms in females of diverse ethnicities and their effect on infertility in the population with polycystic ovary syndrome. There have been numerous reports of the importance of the steroidogenesis pathway and genetic variants in PCOS pathogenesis. The most important genes that play a role in the aetiology of PCOS are CYP11A1, CYP17A1, and CYP19A1. We evaluated the occurrence of polymorphisms in various ethnicities in the CYP11A1, CYP17A1, and CYP19A1 genes and their efficacy on increasing PCOS risk with infertility. Our findings revealed that polymorphisms in various ethnicities are associated with the risk of PCOS with infertility. Although conflicting results regarding CYP11A1, CYP17A1, and CYP19A1 polymorphisms and their influence on PCOS with infertility have been reported in a small number of papers, the authors feel this may be attributable to the sample size and ethnic composition of the examined populations. In conclusion, our study strongly suggests that the CYP11A1, CYP17A1, and CYP19A1 genes might significantly enhance the probability of developing PCOS with infertility. Full article

(This article belongs to the Special Issue Genetics and Genomics in Hereditary Endocrine Disorders)

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15 pages, 7536 KiB

Open AccessEditor’s ChoiceArticle

Expanding Phenotype of Poirier–Bienvenu Syndrome: New Evidence from an Italian Multicentrical Cohort of Patients

by Alessandro Orsini, Andrea Santangelo, Francesca Bravin, Alice Bonuccelli, Diego Peroni, Roberta Battini, Thomas Foiadelli, Veronica Bertini, Angelo Valetto, Michele Iacomino, Vincenzo Nigro, Anna Laura Torella, Marcello Scala, Valeria Capra, Maria Stella Vari, Anna Fetta, Veronica Di Pisa, Francesca Montanari, Roberta Epifanio, Paolo Bonanni, Roberto Giorda, Francesca Operto, Grazia Pastorino, Esra Sarigecili, Esra Sardaroglu, Cetin Okuyaz, Sevgan Bozdogan, Luciana Musante, Flavio Faletra, Caterina Zanus, Alessandro Ferretti, Federico Vigevano, Pasquale Striano and Duccio Maria Cordelli Show full author list Hide full author list

Genes 2022, 13(2), 276; https://doi.org/10.3390/genes13020276 - 30 Jan 2022

Cited by 10 | Viewed by 4197

Abstract

Background: Poirier–Bienvenu Neurodevelopmental Syndrome (POBINDS) is a rare disease linked to mutations of the CSNK2B gene, which encodes for a subunit of caseinkinase CK2 involved in neuronal growth and synaptic transmission. Its main features include early-onset epilepsy and intellectual disability. Despite the lack [...] Read more.

Background: Poirier–Bienvenu Neurodevelopmental Syndrome (POBINDS) is a rare disease linked to mutations of the CSNK2B gene, which encodes for a subunit of caseinkinase CK2 involved in neuronal growth and synaptic transmission. Its main features include early-onset epilepsy and intellectual disability. Despite the lack of cases described, it appears that POBINDS could manifest with a wide range of phenotypes, possibly related to the different mutations of CSNK2B. Methods: Our multicentric, retrospective study recruited nine patients with POBINDS, detected using next-generation sequencing panels and whole-exome sequencing. Clinical, laboratory, and neuroimaging data were reported for each patient in order to assess the severity of phenotype, and eventually, a correlation with the type of CSNK2B mutation. Results: We reported nine unrelated patients with heterozygous de novo mutations of the CSNK2B gene. All cases presented epilepsy, and eight patients were associated with a different degree of intellectual disability. Other features detected included endocrinological and vascular abnormalities and dysmorphisms. Genetic analysis revealed six new variants of CSNK2B that have not been reported previously. Conclusion: Although it was not possible to assess a genotype–phenotype correlation in our patients, our research further expands the phenotype spectrum of POBINDS patients, identifying new mutations occurring in the CSNK2B gene. Full article

(This article belongs to the Collection Study on Genotypes and Phenotypes of Pediatric Clinical Rare Diseases)

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17 pages, 638 KiB

Open AccessEditor’s ChoiceReview

Antisense and Gene Therapy Options for Duchenne Muscular Dystrophy Arising from Mutations in the N-Terminal Hotspot

by Harry Wilton-Clark and Toshifumi Yokota

Genes 2022, 13(2), 257; https://doi.org/10.3390/genes13020257 - 28 Jan 2022

Cited by 16 | Viewed by 5807

Abstract

Duchenne muscular dystrophy (DMD) is a fatal genetic disease affecting children that is caused by a mutation in the gene encoding for dystrophin. In the absence of functional dystrophin, patients experience progressive muscle deterioration, leaving them wheelchair-bound by age 12 and with few [...] Read more.

Duchenne muscular dystrophy (DMD) is a fatal genetic disease affecting children that is caused by a mutation in the gene encoding for dystrophin. In the absence of functional dystrophin, patients experience progressive muscle deterioration, leaving them wheelchair-bound by age 12 and with few patients surviving beyond their third decade of life as the disease advances and causes cardiac and respiratory difficulties. In recent years, an increasing number of antisense and gene therapies have been studied for the treatment of muscular dystrophy; however, few of these therapies focus on treating mutations arising in the N-terminal encoding region of the dystrophin gene. This review summarizes the current state of development of N-terminal antisense and gene therapies for DMD, mainly focusing on exon-skipping therapy for duplications and deletions, as well as microdystrophin therapy. Full article

(This article belongs to the Special Issue Genetics of Muscular Disorders)

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19 pages, 16013 KiB

Open AccessEditor’s ChoiceArticle

Genomic Analysis of Resistance to Fall Armyworm (Spodoptera frugiperda) in CIMMYT Maize Lines

by Isaac Kamweru, Bruce Y. Anani, Yoseph Beyene, Dan Makumbi, Victor O. Adetimirin, Boddupalli M. Prasanna and Manje Gowda

Genes 2022, 13(2), 251; https://doi.org/10.3390/genes13020251 - 28 Jan 2022

Cited by 12 | Viewed by 3152

Abstract

The recent invasion, rapid spread, and widescale destruction of the maize crop by the fall armyworm (FAW; Spodoptera frugiperda (J.E. Smith)) is likely to worsen the food insecurity situation in Africa. In the present study, a set of 424 maize lines were screened [...] Read more.

The recent invasion, rapid spread, and widescale destruction of the maize crop by the fall armyworm (FAW; Spodoptera frugiperda (J.E. Smith)) is likely to worsen the food insecurity situation in Africa. In the present study, a set of 424 maize lines were screened for their responses to FAW under artificial infestation to dissect the genetic basis of resistance. All lines were evaluated for two seasons under screen houses and genotyped with the DArTseq platform. Foliar damage was rated on a scale of 1 (highly resistant) to 9 (highly susceptible) and scored at 7, 14, and 21 days after artificial infestation. Analyses of variance revealed significant genotypic and genotype by environment interaction variances for all traits. Heritability estimates for leaf damage scores were moderately high and ranged from 0.38 to 0.58. Grain yield was negatively correlated with a high magnitude to foliar damage scores, ear rot, and ear damage traits. The genome-wide association study (GWAS) revealed 56 significant marker–trait associations and the predicted functions of the putative candidate genes varied from a defense response to several genes of unknown function. Overall, the study revealed that native genetic resistance to FAW is quantitative in nature and is controlled by many loci with minor effects. Full article

(This article belongs to the Special Issue Research on Tropical Food Crop Genomics)

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15 pages, 2838 KiB

Open AccessEditor’s ChoiceReview

MicroRNA Interrelated Epithelial Mesenchymal Transition (EMT) in Glioblastoma

by Botle Precious Setlai, Rodney Hull, Rui Manuel Reis, Cyril Agbor, Melvin Anyasi Ambele, Thanyani Victor Mulaudzi and Zodwa Dlamini

Genes 2022, 13(2), 244; https://doi.org/10.3390/genes13020244 - 27 Jan 2022

Cited by 15 | Viewed by 4434

Abstract

MicroRNAs (miRNA) are small non-coding RNAs that are 20–23 nucleotides in length, functioning as regulators of oncogenes or tumor suppressor genes. They are molecular modulators that regulate gene expression by suppressing gene translation through gene silencing/degradation, or by promoting translation of messenger RNA [...] Read more.

MicroRNAs (miRNA) are small non-coding RNAs that are 20–23 nucleotides in length, functioning as regulators of oncogenes or tumor suppressor genes. They are molecular modulators that regulate gene expression by suppressing gene translation through gene silencing/degradation, or by promoting translation of messenger RNA (mRNA) into proteins. Circulating miRNAs have attracted attention as possible prognostic markers of cancer, which could aid in the early detection of the disease. Epithelial to mesenchymal transition (EMT) has been implicated in tumorigenic processes, primarily by promoting tumor invasiveness and metastatic activity; this is a process that could be manipulated to halt or prevent brain metastasis. Studies show that miRNAs influence the function of EMT in glioblastomas. Thus, miRNA-related EMT can be exploited as a potential therapeutic target in glioblastomas. This review points out the interrelation between miRNA and EMT signatures, and how they can be used as reliable molecular signatures for diagnostic purposes or targeted therapy in glioblastomas. Full article

(This article belongs to the Special Issue Non-coding RNAs in Human Health and Diseases)

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18 pages, 6584 KiB

Open AccessEditor’s ChoiceArticle

Identification of a Four-Gene Signature Associated with the Prognosis Prediction of Lung Adenocarcinoma Based on Integrated Bioinformatics Analysis

by Yuan Wu, Lingge Yang, Long Zhang, Xinjie Zheng, Huan Xu, Kai Wang and Xianwu Weng

Genes 2022, 13(2), 238; https://doi.org/10.3390/genes13020238 - 27 Jan 2022

Cited by 14 | Viewed by 2833

Abstract

Lung adenocarcinoma (LUAD) is often diagnosed at an advanced stage, so it is necessary to identify potential biomarkers for the early diagnosis and prognosis of LUAD. In our study, a gene co-expression network was constructed using weighted gene co-expression network analysis (WGCNA) in [...] Read more.

Lung adenocarcinoma (LUAD) is often diagnosed at an advanced stage, so it is necessary to identify potential biomarkers for the early diagnosis and prognosis of LUAD. In our study, a gene co-expression network was constructed using weighted gene co-expression network analysis (WGCNA) in order to obtain the key modules and genes correlated with LUAD prognosis. Four hub genes (HLF, CHRDL1, SELENBP1, and TMEM163) were screened out using least absolute shrinkage and selection operator (LASSO)–Cox regression analysis; then, a prognostic model was established for predicting overall survival (OS) based on these four hub genes..Furthermore, the prognostic values of this four-gene signature were verified in four validation sets (GSE26939, GSE31210, GSE72094, and TCGA-LUAD) as well as in the GEPIA database. To assess the prognostic values of hub genes, receiver operating characteristic (ROC) curves were constructed and a nomogram was created. We found that a higher expression of four hub genes was associated with a lower risk of patient death. In a training set, it was demonstrated that this four-gene signature was a better prognostic factor than clinical factors such as age and stage of disease. Moreover, our results revealed that these four genes were suppressor factors of LUAD and that their high expression was associated with a lower risk of death. In summary, we demonstrated that this four-gene signature could be a potential prognostic factor for LUAD patients. These findings provide a theoretical basis for exploring potential biomarkers for LUAD prognosis prediction in the future. Full article

(This article belongs to the Section Bioinformatics)

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18 pages, 1282 KiB

Open AccessEditor’s ChoiceArticle

miRNome Profiling Detects miR-101-3p and miR-142-5p as Putative Blood Biomarkers of Frailty Syndrome

by Giulia Carini, Jessica Mingardi, Francesco Bolzetta, Alberto Cester, Andrea Bolner, Giampietro Nordera, Luca La Via, Alessandro Ieraci, Isabella Russo, Stefania Maggi, Stefano Calza, Maurizio Popoli, Nicola Veronese, Laura Musazzi and Alessandro Barbon

Genes 2022, 13(2), 231; https://doi.org/10.3390/genes13020231 - 26 Jan 2022

Cited by 10 | Viewed by 3633

Abstract

Frailty is an aging-related pathology, defined as a state of increased vulnerability to stressors, leading to a limited capacity to meet homeostatic demands. Extracellular microRNAs (miRNAs) were proposed as potential biomarkers of various disease conditions, including age-related pathologies. The primary objective of this [...] Read more.

Frailty is an aging-related pathology, defined as a state of increased vulnerability to stressors, leading to a limited capacity to meet homeostatic demands. Extracellular microRNAs (miRNAs) were proposed as potential biomarkers of various disease conditions, including age-related pathologies. The primary objective of this study was to identify blood miRNAs that could serve as potential biomarkers and candidate mechanisms of frailty. Using the Fried index, we enrolled 22 robust and 19 frail subjects. Blood and urine samples were analysed for several biochemical parameters. We observed that sTNF-R was robustly upregulated in the frail group, indicating the presence of an inflammatory state. Further, by RNA-seq, we profiled 2654 mature miRNAs in the whole blood of the two groups. Expression levels of selected differentially expressed miRNAs were validated by qPCR, and target prediction analyses were performed for the dysregulated miRNAs. We identified 2 miRNAs able to significantly differentiate frail patients from robust subjects. Both miR-101-3p and miR-142-5p were found to be downregulated in the frail vs. robust group. Finally, using bioinformatics targets prediction tools, we explored the potential molecular mechanisms and cellular pathways regulated by the two miRNAs and potentially involved in frailty. Full article

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

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21 pages, 3129 KiB

Open AccessEditor’s ChoiceReview

The Ecology and Evolution of the Baker’s Yeast Saccharomyces cerevisiae

by Feng-Yan Bai, Da-Yong Han, Shou-Fu Duan and Qi-Ming Wang

Genes 2022, 13(2), 230; https://doi.org/10.3390/genes13020230 - 26 Jan 2022

Cited by 15 | Viewed by 8455

Abstract

The baker’s yeast Saccharomyces cerevisiae has become a powerful model in ecology and evolutionary biology. A global effort on field survey and population genetics and genomics of S. cerevisiae in past decades has shown that the yeast distributes ubiquitously in nature with clearly [...] Read more.

The baker’s yeast Saccharomyces cerevisiae has become a powerful model in ecology and evolutionary biology. A global effort on field survey and population genetics and genomics of S. cerevisiae in past decades has shown that the yeast distributes ubiquitously in nature with clearly structured populations. The global genetic diversity of S. cerevisiae is mainly contributed by strains from Far East Asia, and the ancient basal lineages of the species have been found only in China, supporting an ‘out-of-China’ origin hypothesis. The wild and domesticated populations are clearly separated in phylogeny and exhibit hallmark differences in sexuality, heterozygosity, gene copy number variation (CNV), horizontal gene transfer (HGT) and introgression events, and maltose utilization ability. The domesticated strains from different niches generally form distinct lineages and harbor lineage-specific CNVs, HGTs and introgressions, which contribute to their adaptations to specific fermentation environments. However, whether the domesticated lineages originated from a single, or multiple domestication events is still hotly debated and the mechanism causing the diversification of the wild lineages remains to be illuminated. Further worldwide investigations on both wild and domesticated S. cerevisiae, especially in Africa and West Asia, will be helpful for a better understanding of the natural and domestication histories and evolution of S. cerevisiae. Full article

(This article belongs to the Special Issue Population Genetics of Fungi)

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15 pages, 2210 KiB

Open AccessEditor’s ChoiceArticle

Evaluation and Genetic Analysis of Parthenocarpic Germplasms in Cucumber

by Chenxing Gou, Pinyu Zhu, Yongjiao Meng, Fan Yang, Yan Xu, Pengfei Xia, Jinfeng Chen and Ji Li

Genes 2022, 13(2), 225; https://doi.org/10.3390/genes13020225 - 25 Jan 2022

Cited by 10 | Viewed by 3525

Abstract

Parthenocarpy is an important agronomic trait in cucumber (Cucumis sativus L.) production. However, the systematic identification of parthenocarpic germplasms from national gene banks for cucumber improvement remains an international challenge. In this study, 201 cucumber lines were investigated, including different ecotypes. The [...] Read more.

Parthenocarpy is an important agronomic trait in cucumber (Cucumis sativus L.) production. However, the systematic identification of parthenocarpic germplasms from national gene banks for cucumber improvement remains an international challenge. In this study, 201 cucumber lines were investigated, including different ecotypes. The percentages of parthenocarpic fruit set (PFS) and parthenocarpic fruit expansion (PFE) were evaluated in three experiments. In natural populations, the PFS rates fit a normal distribution, while PFE rates showed a skewed distribution, suggesting that both PFS and PFE rates are typical quantitative traits. Genetic analysis showed that parthenocarpy in different ecotypes was inherited in a similar incompletely dominant manner. A total of 5324 single nucleotide polymorphisms (SNPs) associated with parthenocarpy were detected in a Genome-wide association study (GWAS) of parthenocarpy in the 31 cucumber lines, from which six parthenocarpic loci, including two novel loci (Pfs1.1 and Pfs4.1), were identified. Consequently, fifteen of the elite lines that were screened presented relatively stronger parthenocarpy ability (PFS > 90%, PFE > 50%), among which six cucumber lines (18007s, 18008s, 18022s, 18076s, 18099s, and 18127s) exhibited weak first-fruit inhibition. Three lines (18011s, 18018s, and 18019s) were screened for super ovary parthenocarpy, which showed more attractive performance. Four low-temperature-enhanced parthenocarpy lines (18018s, 18022s, 18029s, and 18012s) were identified, which were suited for breeding for counter-season production. Our approaches could help increase efficiency and lead to parthenocarpy improvements for modern cucumber cultivars. Full article

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

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15 pages, 1946 KiB

Open AccessEditor’s ChoiceReview

Rec8 Cohesin: A Structural Platform for Shaping the Meiotic Chromosomes

by Takeshi Sakuno and Yasushi Hiraoka

Genes 2022, 13(2), 200; https://doi.org/10.3390/genes13020200 - 22 Jan 2022

Cited by 12 | Viewed by 5748

Abstract

Meiosis is critically different from mitosis in that during meiosis, pairing and segregation of homologous chromosomes occur. During meiosis, the morphology of sister chromatids changes drastically, forming a prominent axial structure in the synaptonemal complex. The meiosis-specific cohesin complex plays a central role [...] Read more.

Meiosis is critically different from mitosis in that during meiosis, pairing and segregation of homologous chromosomes occur. During meiosis, the morphology of sister chromatids changes drastically, forming a prominent axial structure in the synaptonemal complex. The meiosis-specific cohesin complex plays a central role in the regulation of the processes required for recombination. In particular, the Rec8 subunit of the meiotic cohesin complex, which is conserved in a wide range of eukaryotes, has been analyzed for its function in modulating chromosomal architecture during the pairing and recombination of homologous chromosomes in meiosis. Here, we review the current understanding of Rec8 cohesin as a structural platform for meiotic chromosomes. Full article

(This article belongs to the Special Issue Genetics of Meiotic Chromosome Dynamics)

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16 pages, 4221 KiB

Open AccessEditor’s ChoiceArticle

Oligo-FISH Can Identify Chromosomes and Distinguish Hippophaë rhamnoides L. Taxa

by Xiaomei Luo, Juncheng Liu and Zhoujian He

Genes 2022, 13(2), 195; https://doi.org/10.3390/genes13020195 - 22 Jan 2022

Cited by 9 | Viewed by 2659

Abstract

Oligo-fluorescence in situ hybridization (FISH) facilitates precise chromosome identification and comparative cytogenetic analysis. Detection of autosomal chromosomes of Hippophaë rhamnoides has not been achieved using oligonucleotide sequences. Here, the chromosomes of five H. rhamnoides taxa in the mitotic metaphase and mitotic metaphase to [...] Read more.

Oligo-fluorescence in situ hybridization (FISH) facilitates precise chromosome identification and comparative cytogenetic analysis. Detection of autosomal chromosomes of Hippophaë rhamnoides has not been achieved using oligonucleotide sequences. Here, the chromosomes of five H. rhamnoides taxa in the mitotic metaphase and mitotic metaphase to anaphase were detected using the oligo-FISH probes (AG₃T₃)₃, 5S rDNA, and (TTG)₆. In total, 24 small chromosomes were clearly observed in the mitotic metaphase (0.89–3.03 μm), whereas 24–48 small chromosomes were observed in the mitotic metaphase to anaphase (0.94–3.10 μm). The signal number and intensity of (AG₃T₃)₃, 5S rDNA, and (TTG)₆ in the mitotic metaphase to anaphase chromosomes were nearly consistent with those in the mitotic metaphase chromosomes when the two split chromosomes were integrated as one unit. Of note, 14 chromosomes (there is a high chance that sex chromosomes are included) were exclusively identified by (AG₃T₃)₃, 5S rDNA, and (TTG)₆. The other 10 also showed a terminal signal with (AG₃T₃)₃. Moreover, these oligo-probes were able to distinguish one wild H. rhamnoides taxon from four H. rhamnoides taxa. These chromosome identification and taxa differentiation data will help in elucidating visual and elaborate physical mapping and guide breeders’ utilization of wild resources of H. rhamnoides. Full article

(This article belongs to the Special Issue Tree Genetics and Improvement)

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9 pages, 3104 KiB

Open AccessEditor’s ChoiceArticle

Evaluation of Different Cleaning Strategies for Removal of Contaminating DNA Molecules

by Martina Nilsson, Hanne De Maeyer and Marie Allen

Genes 2022, 13(1), 162; https://doi.org/10.3390/genes13010162 - 17 Jan 2022

Cited by 15 | Viewed by 6278

Abstract

Decontamination strategies and their efficiencies are crucial when performing routine forensic analysis, and many factors influence the choice of agent to use. In this study, the effects of ten different cleaning strategies were evaluated to compare their ability to remove contaminating DNA molecules. [...] Read more.

Decontamination strategies and their efficiencies are crucial when performing routine forensic analysis, and many factors influence the choice of agent to use. In this study, the effects of ten different cleaning strategies were evaluated to compare their ability to remove contaminating DNA molecules. Cell-free DNA or blood was deposited on three surfaces (plastic, metal, and wood) and decontaminated with various treatments. The quantities of recovered DNA, obtained by swabbing the surfaces after cleaning using the different strategies, was analyzed by real-time PCR. Large differences in the DNA removal efficiencies were observed between different cleaning strategies, as well as between different surfaces. The most efficient cleaning strategies for cell-free DNA were the different sodium hypochlorite solutions and Trigene^®, for which a maximum of 0.3% DNA was recovered on all three surfaces. For blood, a maximum of 0.8% of the deposited DNA was recovered after using Virkon^® for decontamination. The recoveries after using these cleaning strategies correspond to DNA from only a few cells, out of 60 ng of cell-free DNA or thousands of deposited blood cells. Full article

(This article belongs to the Special Issue Advances in Forensic Genetics)

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18 pages, 1900 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Drought, Low Nitrogen Stress, and Ultraviolet-B Radiation Effects on Growth, Development, and Physiology of Sweetpotato Cultivars during Early Season

by Purushothaman Ramamoorthy, Raju Bheemanahalli, Stephen L. Meyers, Mark W. Shankle and Kambham Raja Reddy

Genes 2022, 13(1), 156; https://doi.org/10.3390/genes13010156 - 16 Jan 2022

Cited by 15 | Viewed by 2908

Abstract

Drought, ultraviolet-B (UV-B), and nitrogen stress are significant constraints for sweetpotato productivity. Their impact on plant growth and development can be acute, resulting in low productivity. Identifying phenotypes that govern stress tolerance in sweetpotatoes is highly desirable to develop elite cultivars with better [...] Read more.

Drought, ultraviolet-B (UV-B), and nitrogen stress are significant constraints for sweetpotato productivity. Their impact on plant growth and development can be acute, resulting in low productivity. Identifying phenotypes that govern stress tolerance in sweetpotatoes is highly desirable to develop elite cultivars with better yield. Ten sweetpotato cultivars were grown under nonstress (100% replacement of evapotranspiration (ET)), drought-stress (50% replacement of ET), UV-B (10 kJ), and low-nitrogen (20% LN) conditions. Various shoot and root morphological, physiological, and gas-exchange traits were measured at the early stage of the crop growth to assess its performance and association with the storage root number. All three stress factors caused significant changes in the physiological and root- and shoot-related traits. Drought stress reduced most shoot developmental traits (29%) to maintain root growth. UV-B stress increased the accumulation of plant pigments and decreased the photosynthetic rate. Low-nitrogen treatment decreased shoot growth (11%) and increased the root traits (18%). The highly stable and productive cultivars under all four treatments were identified using multitrait stability index analysis and weighted average of absolute scores (WAASB) analyses. Further, based on the total stress response indices, ‘Evangeline’, ‘O’Henry’, and ‘Beauregard B-14’ were identified as vigorous under drought; ‘Evangeline’, ‘Orleans’, and ‘Covington’ under UV-B; and ‘Bonita’, ‘Orleans’, and ‘Beauregard B-14’ cultivars showed greater tolerance to low nitrogen. The cultivars ‘Vardaman’ and ‘NC05-198’ recorded a low tolerance index across stress treatments. This information could help determine which plant phenotypes are desirable under stress treatment for better productivity. The cultivars identified as tolerant, sensitive, and well-adapted within and across stress treatments can be used as source materials for abiotic stress tolerance breeding programs. Full article

(This article belongs to the Special Issue Genetic Diversity of Plant Tolerance to Environmental Restraints)

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13 pages, 2058 KiB

Open AccessEditor’s ChoiceReview

LncRNAs and the Angiogenic Switch in Cancer: Clinical Significance and Therapeutic Opportunities

by Peace Mabeta, Rodney Hull and Zodwa Dlamini

Genes 2022, 13(1), 152; https://doi.org/10.3390/genes13010152 - 15 Jan 2022

Cited by 16 | Viewed by 2506

Abstract

Angiogenesis is one of the hallmarks of cancer, and the establishment of new blood vessels is vital to allow for a tumour to grow beyond 1–2 mm in size. The angiogenic switch is the term given to the point where the number or [...] Read more.

Angiogenesis is one of the hallmarks of cancer, and the establishment of new blood vessels is vital to allow for a tumour to grow beyond 1–2 mm in size. The angiogenic switch is the term given to the point where the number or activity of the pro-angiogenic factors exceeds that of the anti-angiogenic factors, resulting in the angiogenic process proceeding, giving rise to new blood vessels accompanied by increased tumour growth, metastasis, and potential drug resistance. Long noncoding ribonucleic acids (lncRNAs) have been found to play a role in the angiogenic switch by regulating gene expression, transcription, translation, and post translation modification. In this regard they play both anti-angiogenic and pro-angiogenic roles. The expression levels of the pro-angiogenic lncRNAs have been found to correlate with patient survival. These lncRNAs are also potential drug targets for the development of therapies that will inhibit or modify tumour angiogenesis. Here we review the roles of lncRNAs in regulating the angiogenic switch. We cover specific examples of both pro and anti-angiogenic lncRNAs and discuss their potential use as both prognostic biomarkers and targets for the development of future therapies. Full article

(This article belongs to the Special Issue Non-coding RNAs in Human Health and Diseases)

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28 pages, 5592 KiB

Open AccessEditor’s ChoiceArticle

Effects of BPA, BPS, and BPF on Oxidative Stress and Antioxidant Enzyme Expression in Bovine Oocytes and Spermatozoa

by Mimi Nguyen, Reem Sabry, Ola S. Davis and Laura A. Favetta

Genes 2022, 13(1), 142; https://doi.org/10.3390/genes13010142 - 14 Jan 2022

Cited by 22 | Viewed by 3235

Abstract

Bisphenol A (BPA) and its analogs, bisphenol S (BPS) and bisphenol F (BPF), might impact fertility by altering oxidative stress pathways. Here, we hypothesize that bisphenols-induced oxidative stress is responsible for decreased gamete quality. In both female (cumulus-oocyte-complexes—COCs) and male (spermatozoa), oxidative stress [...] Read more.

Bisphenol A (BPA) and its analogs, bisphenol S (BPS) and bisphenol F (BPF), might impact fertility by altering oxidative stress pathways. Here, we hypothesize that bisphenols-induced oxidative stress is responsible for decreased gamete quality. In both female (cumulus-oocyte-complexes—COCs) and male (spermatozoa), oxidative stress was measured by CM-H₂DCFDA assay and key ROS scavengers (SOD1, SOD2, GPX1, GPX4, CAT) were quantified at the mRNA and protein levels using qPCR and Western blot (COCs)/immunofluorescence (sperm). Either gamete was treated in five groups: control, vehicle, and 0.05 mg/mL of BPA, BPS, or BPF. Our results show elevated ROS in BPA-treated COCs but decreased production in BPS- and BPF-treated spermatozoa. Additionally, both mRNA and protein expression of SOD2, GPX1, and GPX4 were decreased in BPA-treated COCs (p < 0.05). In sperm, motility (p < 0.03), but not morphology, was significantly altered by bisphenols. SOD1 mRNA expression was significantly increased, while GPX4 was significantly reduced. These results support BPA’s ability to alter oxidative stress in oocytes and, to a lesser extent, in sperm. However, BPS and BPF likely act through different mechanisms. Full article

(This article belongs to the Special Issue Effect of Toxicants on Oocyte Quality and Embryo Development)

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17 pages, 4295 KiB

Open AccessEditor’s ChoiceArticle

Identification and Characterization of Wall-Associated Kinase (WAK) and WAK-like (WAKL) Gene Family in Juglans regia and Its Wild Related Species Juglans mandshurica

by Mengdi Li, Jiayu Ma, Hengzhao Liu, Mengwei Ou, Hang Ye and Peng Zhao

Genes 2022, 13(1), 134; https://doi.org/10.3390/genes13010134 - 12 Jan 2022

Cited by 17 | Viewed by 2590

Abstract

Wall-associated kinase (WAK) and WAK-like kinase (WAKL) are receptor-like kinases (RLKs), which play important roles in signal transduction between the cell wall and the cytoplasm in plants. WAK/WAKLs have been studied in many plants, but were rarely studied in the important economic walnut [...] Read more.

Wall-associated kinase (WAK) and WAK-like kinase (WAKL) are receptor-like kinases (RLKs), which play important roles in signal transduction between the cell wall and the cytoplasm in plants. WAK/WAKLs have been studied in many plants, but were rarely studied in the important economic walnut tree. In this study, 27 and 14 WAK/WAKL genes were identified in Juglans regia and its wild related species Juglans mandshurica, respectively. We found tandem duplication might play a critical role in the expansion of WAK/WAKL gene family in J. regia, and most of the WAK/WAKL homologous pairs underwent purified selection during evolution. All WAK/WAKL proteins have the extracellular WAK domain and the cytoplasmic protein kinase domain, and the latter was more conserved than the former. Cis-acting elements analysis showed that WAK/WAKL might be involved in plant growth and development, plant response to abiotic stress and hormones. Gene expression pattern analysis further indicated that most WAK/WAKL genes in J. regia might play a role in the development of leaves and be involved in plant response to biotic stress. Our study provides a new perspective for the evolutionary analysis of gene families in tree species and also provides potential candidate genes for studying WAK/WAKL gene function in walnuts. Full article

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

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19 pages, 402 KiB

Open AccessEditor’s ChoiceReview

Role of Actionable Genes in Pursuing a True Approach of Precision Medicine in Monogenic Diabetes

by Antonella Marucci, Irene Rutigliano, Grazia Fini, Serena Pezzilli, Claudia Menzaghi, Rosa Di Paola and Vincenzo Trischitta

Genes 2022, 13(1), 117; https://doi.org/10.3390/genes13010117 - 09 Jan 2022

Cited by 9 | Viewed by 2967

Abstract

Monogenic diabetes is a genetic disorder caused by one or more variations in a single gene. It encompasses a broad spectrum of heterogeneous conditions, including neonatal diabetes, maturity onset diabetes of the young (MODY) and syndromic diabetes, affecting 1–5% of patients with diabetes. [...] Read more.

Monogenic diabetes is a genetic disorder caused by one or more variations in a single gene. It encompasses a broad spectrum of heterogeneous conditions, including neonatal diabetes, maturity onset diabetes of the young (MODY) and syndromic diabetes, affecting 1–5% of patients with diabetes. Some of these variants are harbored by genes whose altered function can be tackled by specific actions (“actionable genes”). In suspected patients, molecular diagnosis allows the implementation of effective approaches of precision medicine so as to allow individual interventions aimed to prevent, mitigate or delay clinical outcomes. This review will almost exclusively concentrate on the clinical strategy that can be specifically pursued in carriers of mutations in “actionable genes”, including ABCC8, KCNJ11, GCK, HNF1A, HNF4A, HNF1B, PPARG, GATA4 and GATA6. For each of them we will provide a short background on what is known about gene function and dysfunction. Then, we will discuss how the identification of their mutations in individuals with this form of diabetes, can be used in daily clinical practice to implement specific monitoring and treatments. We hope this article will help clinical diabetologists carefully consider who of their patients deserves timely genetic testing for monogenic diabetes. Full article

(This article belongs to the Special Issue Pharmacogenomics: Precision Medicine and Drug Response)

14 pages, 2034 KiB

Open AccessEditor’s ChoiceArticle

Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum Spruceanum, Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species

by Carla L. Saldaña, Pedro Rodriguez-Grados, Julio C. Chávez-Galarza, Shefferson Feijoo, Juan Carlos Guerrero-Abad, Héctor V. Vásquez, Jorge L. Maicelo, Jorge H. Jhoncon and Carlos I. Arbizu

Genes 2022, 13(1), 113; https://doi.org/10.3390/genes13010113 - 07 Jan 2022

Cited by 9 | Viewed by 3150

Abstract

Capirona (Calycophyllum spruceanum Benth.) belongs to subfamily Ixoroideae, one of the major lineages in the Rubiaceae family, and is an important timber tree. It originated in the Amazon Basin and has widespread distribution in Bolivia, Peru, Colombia, and Brazil. In this study, [...] Read more.

Capirona (Calycophyllum spruceanum Benth.) belongs to subfamily Ixoroideae, one of the major lineages in the Rubiaceae family, and is an important timber tree. It originated in the Amazon Basin and has widespread distribution in Bolivia, Peru, Colombia, and Brazil. In this study, we obtained the first complete chloroplast (cp) genome of capirona from the department of Madre de Dios located in the Peruvian Amazon. High-quality genomic DNA was used to construct libraries. Pair-end clean reads were obtained by PE 150 library and the Illumina HiSeq 2500 platform. The complete cp genome of C. spruceanum has a 154,480 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (84,813 bp) and a small single-copy (SSC) region (18,101 bp), separated by two inverted repeat (IR) regions (25,783 bp). The annotation of C. spruceanum cp genome predicted 87 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, and one pseudogene. A total of 41 simple sequence repeats (SSR) of this cp genome were divided into mononucleotides (29), dinucleotides (5), trinucleotides (3), and tetranucleotides (4). Most of these repeats were distributed in the noncoding regions. Whole chloroplast genome comparison with the other six Ixoroideae species revealed that the small single copy and large single copy regions showed more divergence than inverted regions. Finally, phylogenetic analyses resolved that C. spruceanum is a sister species to Emmenopterys henryi and confirms its position within the subfamily Ixoroideae. This study reports for the first time the genome organization, gene content, and structural features of the chloroplast genome of C. spruceanum, providing valuable information for genetic and evolutionary studies in the genus Calycophyllum and beyond. Full article

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

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18 pages, 499 KiB

Open AccessEditor’s ChoicePerspective

Genome Chaos, Information Creation, and Cancer Emergence: Searching for New Frameworks on the 50th Anniversary of the “War on Cancer”

by Julie Heng and Henry H. Heng

Genes 2022, 13(1), 101; https://doi.org/10.3390/genes13010101 - 31 Dec 2021

Cited by 25 | Viewed by 4350

Abstract

The year 2021 marks the 50th anniversary of the National Cancer Act, signed by President Nixon, which declared a national “war on cancer.” Powered by enormous financial support, this past half-century has witnessed remarkable progress in understanding the individual molecular mechanisms of cancer, [...] Read more.

The year 2021 marks the 50th anniversary of the National Cancer Act, signed by President Nixon, which declared a national “war on cancer.” Powered by enormous financial support, this past half-century has witnessed remarkable progress in understanding the individual molecular mechanisms of cancer, primarily through the characterization of cancer genes and the phenotypes associated with their pathways. Despite millions of publications and the overwhelming volume data generated from the Cancer Genome Project, clinical benefits are still lacking. In fact, the massive, diverse data also unexpectedly challenge the current somatic gene mutation theory of cancer, as well as the initial rationales behind sequencing so many cancer samples. Therefore, what should we do next? Should we continue to sequence more samples and push for further molecular characterizations, or should we take a moment to pause and think about the biological meaning of the data we have, integrating new ideas in cancer biology? On this special anniversary, we implore that it is time for the latter. We review the Genome Architecture Theory, an alternative conceptual framework that departs from gene-based theories. Specifically, we discuss the relationship between genes, genomes, and information-based platforms for future cancer research. This discussion will reinforce some newly proposed concepts that are essential for advancing cancer research, including two-phased cancer evolution (which reconciles evolutionary contributions from karyotypes and genes), stress-induced genome chaos (which creates new system information essential for macroevolution), the evolutionary mechanism of cancer (which unifies diverse molecular mechanisms to create new karyotype coding during evolution), and cellular adaptation and cancer emergence (which explains why cancer exists in the first place). We hope that these ideas will usher in new genomic and evolutionary conceptual frameworks and strategies for the next 50 years of cancer research. Full article

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

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15 pages, 300 KiB

Open AccessEditor’s ChoiceReview

Ischemic Stroke Genetics: What Is New and How to Apply It in Clinical Practice?

by Aleksandra Ekkert, Aleksandra Šliachtenko, Julija Grigaitė, Birutė Burnytė, Algirdas Utkus and Dalius Jatužis

Genes 2022, 13(1), 48; https://doi.org/10.3390/genes13010048 - 24 Dec 2021

Cited by 26 | Viewed by 7544

Abstract

The etiology of ischemic stroke is multifactorial. Although receiving less emphasis, genetic causes make a significant contribution to ischemic stroke genesis, especially in early-onset stroke. Several stroke classification systems based on genetic information corresponding to various stroke phenotypes were proposed. Twin and family [...] Read more.

The etiology of ischemic stroke is multifactorial. Although receiving less emphasis, genetic causes make a significant contribution to ischemic stroke genesis, especially in early-onset stroke. Several stroke classification systems based on genetic information corresponding to various stroke phenotypes were proposed. Twin and family history studies, as well as candidate gene approach, are common methods to discover genetic causes of stroke, however, both have their own limitations. Genome-wide association studies and next generation sequencing are more efficient, promising and increasingly used for daily diagnostics. Some monogenic disorders, despite covering only about 7% of stroke etiology, may cause well-known clinical manifestations that include stroke. Polygenic disorders are more frequent, causing about 38% of all ischemic strokes, and their identification is a rapidly developing field of modern stroke genetics. Current advances in human genetics provide opportunity for personalized prevention of stroke and novel treatment possibilities. Genetic risk scores (GRS) and extended polygenic risk scores (PRS) estimate cumulative contribution of known genetic factors to a specific outcome of stroke. Combining those scores with clinical information and risk factor profiles might result in better primary stroke prevention. Some authors encourage the use of stroke gene panels for stroke risk evaluation and further stroke research. Moreover, new biomarkers for stroke genetic causes and novel targets for gene therapy are on the horizon. In this article, we summarize the latest evidence and perspectives of ischemic stroke genetics that could be of interest to the practitioner and useful for day-to-day clinical work. Full article

(This article belongs to the Special Issue Gene Expression and Chromatin Modification in the Brain)

17 pages, 959 KiB

Open AccessEditor’s ChoiceReview

Two-Component Systems of S. aureus: Signaling and Sensing Mechanisms

by Lisa Bleul, Patrice Francois and Christiane Wolz

Genes 2022, 13(1), 34; https://doi.org/10.3390/genes13010034 - 23 Dec 2021

Cited by 26 | Viewed by 5816

Abstract

Staphylococcus aureus encodes 16 two-component systems (TCSs) that enable the bacteria to sense and respond to changing environmental conditions. Considering the function of these TCSs in bacterial survival and their potential role as drug targets, it is important to understand the exact mechanisms [...] Read more.

Staphylococcus aureus encodes 16 two-component systems (TCSs) that enable the bacteria to sense and respond to changing environmental conditions. Considering the function of these TCSs in bacterial survival and their potential role as drug targets, it is important to understand the exact mechanisms underlying signal perception. The differences between the sensing of appropriate signals and the transcriptional activation of the TCS system are often not well described, and the signaling mechanisms are only partially understood. Here, we review present insights into which signals are sensed by histidine kinases in S. aureus to promote appropriate gene expression in response to diverse environmental challenges. Full article

(This article belongs to the Special Issue Genetics, Genomics and Pathogenesis of Staphylococcus aureus)

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