Special Issue "Genes at Ten"

A special issue of Genes (ISSN 2073-4425).

Deadline for manuscript submissions: 31 October 2020.

Special Issue Editors

Prof. Dr. J. Peter W. Young
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Guest Editor
Department of Biology, University of York, Heslington, York YO10 5DD, UK
Interests: bacterial genomes; population genetics; phylogenomics; phylogenetics; genome projects; genetic diversity
Special Issues and Collections in MDPI journals
Dr. Paolo Cinelli
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Guest Editor
Center for Clinical Research, Clinic for Trauma Surgery, University Hospital Zurich, Sternwartstrasse 14, CH-8091 Zurich, Switzerland
Interests: transcriptomics; microarrays; gene expression analysis; genotyping; molecular genetics; mouse genetics; transgenic technologies; embryonic stem cells; pluripotency
Special Issues and Collections in MDPI journals
Prof. Dr. Montserrat Corominas
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Guest Editor
Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, Diagonal, 643, 08028 Barcelona, Catalonia, Spain
Interests: development; regeneration epigenetics; chromatin; Drosophila; transcription
Dr. Elaine Ostrander
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Guest Editor
Cancer Genetics Branch, National Human Genome Research Institute/National Institute of Health. Bethesda, Maryland, USA
Interests: dog breeds; canine genetics; prostate cancer; domestic dog
Special Issues and Collections in MDPI journals
Prof. Dr. Selvarangan Ponnazhagan
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Guest Editor
Experimental Cancer Therapeutics, The University of Alabama at Birmingham, 1825 University Blvd., SHEL 814 Birmingham, AL 35294-2182, USA
Interests: adeno-associated virus (AAV)-mediated gene therapy for cancer; AAV-mediated gene therapy for metabolic diseases; development of targeted-AAV for human gene therapy; biology, life cycle and molecular virology of adeno-associated virus
Prof. Dr. Roberto Tuberosa
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Guest Editor
Department of Agricultural Sciences, University of Bologna Viale Fanin, 44 40127-Bologna Italy
Interests: Quantitative Trait Loci mapping; drought resistance; root system architecture; phenotyping; maize; durum wheat; barley
Prof. Dr. Nico M. Van Straalen
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Guest Editor
Department of Ecological Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
Interests: evolution; molecular ecology; ecological genomics; zoology; toxicology
Prof. Dr. Thierry Wirth
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Guest Editor
Muséum National d'Histoire Naturelle - EPHE, Department of Systematics and Evolution, UMR-CNRS 7205, 16, rue Buffon, 75231 Paris cedex 05, France
Interests: evolution; population genetics and genomics; evolutionary microbiology; molecular epidemiology

Special Issue Information

Dear Colleagues,

In 2020, we will be celebrating the tenth anniversary of Genes, and we would be happy if you join us on this wonderful occasion.

The very first issue of Genes was released in June 2010. Since those early days, the journal has established a solid reputation and has recently attracted a remarkable increase in the number of publications as well as citations, while maintaining good quality, which is reflected in each year’s Impact Factor. The continuing success of the journal would not have been possible without the work of the journal’s professional staff, the oversight of the editors, and the quality of the authors who have chosen to publish with us.

Ten years later, we are editing this Special Issue commemorating this remarkable milestone. We will include invited articles related to the field and within the scope of each of the journal sections. We have invited those who have contributed to Genes and its prosperity over these 10 years: our top authors, but also our Editorial Board Members. In other words, the people who have made the journal successful.

Please consider submitting an article for this very Special Issue. I hope that you will agree that this is a good way to celebrate our first decade and start the next.

Thank you all for the work you are doing to keep our journal vigorous.

Prof. Dr. J. Peter W. Young
Dr. Paolo Cinelli
Prof. Dr. Montserrat Corominas
Dr. Elaine Ostrander
Prof. Dr. Selvarangan Ponnazhagan
Prof. Roberto Tuberosa
Prof. Dr. Nico M. Van Straalen
Prof. Dr. Thierry Wirth
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (9 papers)

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Research

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Open AccessArticle
Evaluation of the VISAGE Basic Tool for Appearance and Ancestry Prediction Using PowerSeq Chemistry on the MiSeq FGx System
Genes 2020, 11(6), 708; https://doi.org/10.3390/genes11060708 - 26 Jun 2020
Abstract
The study of DNA to predict externally visible characteristics (EVCs) and the biogeographical ancestry (BGA) from unknown samples is gaining relevance in forensic genetics. Technical developments in Massively Parallel Sequencing (MPS) enable the simultaneous analysis of hundreds of DNA markers, which improves successful [...] Read more.
The study of DNA to predict externally visible characteristics (EVCs) and the biogeographical ancestry (BGA) from unknown samples is gaining relevance in forensic genetics. Technical developments in Massively Parallel Sequencing (MPS) enable the simultaneous analysis of hundreds of DNA markers, which improves successful Forensic DNA Phenotyping (FDP). The EU-funded VISAGE (VISible Attributes through GEnomics) Consortium has developed various targeted MPS-based lab tools to apply FDP in routine forensic analyses. Here, we present an evaluation of the VISAGE Basic tool for appearance and ancestry prediction based on PowerSeq chemistry (Promega) on a MiSeq FGx System (Illumina). The panel consists of 153 single nucleotide polymorphisms (SNPs) that provide information about EVCs (41 SNPs for eye, hair and skin color from HIrisPlex-S) and continental BGA (115 SNPs; three overlap with the EVCs SNP set). The assay was evaluated for sensitivity, repeatability and genotyping concordance, as well as its performance with casework-type samples. This targeted MPS assay provided complete genotypes at all 153 SNPs down to 125 pg of input DNA and 99.67% correct genotypes at 50 pg. It was robust in terms of repeatability and concordance and provided useful results with casework-type samples. The results suggest that this MPS assay is a useful tool for basic appearance and ancestry prediction in forensic genetics for users interested in applying PowerSeq chemistry and MiSeq for this purpose. Full article
(This article belongs to the Special Issue Genes at Ten)
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Open AccessCommunication
Senescence and Longevity of Sea Urchins
Genes 2020, 11(5), 573; https://doi.org/10.3390/genes11050573 - 20 May 2020
Abstract
Sea urchins are a minor class of marine invertebrates that share genetic similarities with humans. For example, the sea urchin species Strongylocentrotus purpuratus is estimated to have 23,300 genes in which the majority of vertebrate gene families are enveloped. Some of the sea [...] Read more.
Sea urchins are a minor class of marine invertebrates that share genetic similarities with humans. For example, the sea urchin species Strongylocentrotus purpuratus is estimated to have 23,300 genes in which the majority of vertebrate gene families are enveloped. Some of the sea urchin species can demonstrate extreme longevity, such as Mesocentrotus franciscanus, living for well over 100 years. Comparing human to sea urchin aging suggests that the latter do not fit within the classic understanding of biological aging, as both long- and short-lived sea urchin species demonstrate negligible senescence. Sea urchins are highly regenerative organisms. Adults can regenerate external appendages and can maintain their regenerative abilities throughout life. They grow indeterminately and reproduce throughout their entire adult life. Both long- and short-lived species do not exhibit age-associated telomere shortening and display telomerase activity in somatic tissues regardless of age. Aging S. purpuratus urchins show changes in expression patterns of protein coding genes that are involved in several fundamental cellular functions such as the ubiquitin-proteasome system, signaling pathways, translational regulation, and electron transport chain. Sea urchin longevity and senescence research is a new and promising field that holds promise for the understanding of aging in vertebrates and can increase our understanding of human longevity and of healthy aging. Full article
(This article belongs to the Special Issue Genes at Ten)
Open AccessArticle
Efficient Generation and Correction of Mutations in Human iPS Cells Utilizing mRNAs of CRISPR Base Editors and Prime Editors
Genes 2020, 11(5), 511; https://doi.org/10.3390/genes11050511 - 06 May 2020
Cited by 1
Abstract
In contrast to CRISPR/Cas9 nucleases, CRISPR base editors (BE) and prime editors (PE) enable predefined nucleotide exchanges in genomic sequences without generating DNA double strand breaks. Here, we employed BE and PE mRNAs in conjunction with chemically synthesized sgRNAs and pegRNAs for efficient [...] Read more.
In contrast to CRISPR/Cas9 nucleases, CRISPR base editors (BE) and prime editors (PE) enable predefined nucleotide exchanges in genomic sequences without generating DNA double strand breaks. Here, we employed BE and PE mRNAs in conjunction with chemically synthesized sgRNAs and pegRNAs for efficient editing of human induced pluripotent stem cells (iPSC). Whereas we were unable to correct a disease-causing mutation in patient derived iPSCs using a CRISPR/Cas9 nuclease approach, we corrected the mutation back to wild type with high efficiency utilizing an adenine BE. We also used adenine and cytosine BEs to introduce nine different cancer associated TP53 mutations into human iPSCs with up to 90% efficiency, generating a panel of cell lines to investigate the biology of these mutations in an isogenic background. Finally, we pioneered the use of prime editing in human iPSCs, opening this important cell type for the precise modification of nucleotides not addressable by BEs and to multiple nucleotide exchanges. These approaches eliminate the necessity of deriving disease specific iPSCs from human donors and allows the comparison of different disease-causing mutations in isogenic genetic backgrounds. Full article
(This article belongs to the Special Issue Genes at Ten)
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Open AccessFeature PaperArticle
Ecological Processes Affecting Long-Term Eukaryote and Prokaryote Biofilm Persistence in Nitrogen Removal from Sewage
Genes 2020, 11(4), 449; https://doi.org/10.3390/genes11040449 - 20 Apr 2020
Abstract
The factors affecting long-term biofilm stability in sewage treatment remain largely unexplored. We therefore analyzed moving bed bioreactors (MBBRs) biofilm composition and function two years apart from four reactors in a nitrogen-removal sewage treatment plant. Multivariate ANOVA revealed a similar prokaryote microbiota composition [...] Read more.
The factors affecting long-term biofilm stability in sewage treatment remain largely unexplored. We therefore analyzed moving bed bioreactors (MBBRs) biofilm composition and function two years apart from four reactors in a nitrogen-removal sewage treatment plant. Multivariate ANOVA revealed a similar prokaryote microbiota composition on biofilm carriers from the same reactors, where reactor explained 84.6% of the variance, and year only explained 1.5%. Eukaryotes showed a less similar composition with reactor explaining 56.8% of the variance and year 9.4%. Downstream effects were also more pronounced for eukaryotes than prokaryotes. For prokaryotes, carbon source emerged as a potential factor for deterministic assembly. In the two reactors with methanol as a carbon source, the bacterial genus Methylotenera dominated, with M. versatilis as the most abundant species. M. versatilis showed large lineage diversity. The lineages mainly differed with respect to potential terminal electron acceptor usage (nitrogen oxides and oxygen). Searches in the Sequence Read Archive (SRA) database indicate a global distribution of the M. versatilis strains, with methane-containing sediments as the main habitat. Taken together, our results support long-term prokaryote biofilm persistence, while eukaryotes were less persistent. Full article
(This article belongs to the Special Issue Genes at Ten)
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Open AccessArticle
A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder
Genes 2020, 11(4), 407; https://doi.org/10.3390/genes11040407 - 09 Apr 2020
Abstract
Protein tandem repeats (TRs) are often associated with immunity-related functions and diseases. Since that last census of protein TRs in 1999, the number of curated proteins increased more than seven-fold and new TR prediction methods were published. TRs appear to be enriched with [...] Read more.
Protein tandem repeats (TRs) are often associated with immunity-related functions and diseases. Since that last census of protein TRs in 1999, the number of curated proteins increased more than seven-fold and new TR prediction methods were published. TRs appear to be enriched with intrinsic disorder and vice versa. The significance and the biological reasons for this association are unknown. Here, we characterize protein TRs across all kingdoms of life and their overlap with intrinsic disorder in unprecedented detail. Using state-of-the-art prediction methods, we estimate that 50.9% of proteins contain at least one TR, often located at the sequence flanks. Positive linear correlation between the proportion of TRs and the protein length was observed universally, with Eukaryotes in general having more TRs, but when the difference in length is taken into account the difference is quite small. TRs were enriched with disorder-promoting amino acids and were inside intrinsically disordered regions. Many such TRs were homorepeats. Our results support that TRs mostly originate by duplication and are involved in essential functions such as transcription processes, structural organization, electron transport and iron-binding. In viruses, TRs are found in proteins essential for virulence. Full article
(This article belongs to the Special Issue Genes at Ten)
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Open AccessArticle
Fetal Hypoxia Impacts on Proliferation and Differentiation of Sca-1+ Cardiac Progenitor Cells and Maturation of Cardiomyocytes: A Role of MicroRNA-210
Genes 2020, 11(3), 328; https://doi.org/10.3390/genes11030328 - 20 Mar 2020
Abstract
Hypoxia is one of the most frequent and severe stresses to an organism’s homeostatic mechanisms, and hypoxia during gestation has profound adverse effects on the heart development increasing the occurrence of congenital heart defects (CHDs). Cardiac progenitor cells (CPCs) are responsible for early [...] Read more.
Hypoxia is one of the most frequent and severe stresses to an organism’s homeostatic mechanisms, and hypoxia during gestation has profound adverse effects on the heart development increasing the occurrence of congenital heart defects (CHDs). Cardiac progenitor cells (CPCs) are responsible for early heart development and the later occurrence of heart disease. However, the mechanism of how hypoxic stress affects CPC fate decisions and contributes to CHDs remains a topic of debate. Here we examined the effect of hypoxic stress on the regulations of CPC fate decisions and the potential mechanism. We found that experimental induction of hypoxic responses compromised CPC function by regulating CPC proliferation and differentiation and restraining cardiomyocyte maturation. In addition, echocardiography indicated that fetal hypoxia reduced interventricular septum thickness at diastole and the ejection time, but increased the heart rate, in mouse young adult offspring with a gender-related difference. Further study revealed that hypoxia upregulated microRNA-210 expression in Sca-1+ CPCs and impeded the cell differentiation. Blockage of microRNA-210 with LNA-anti-microRNA-210 significantly promoted differentiation of Sca-1+ CPCs into cardiomyocytes. Thus, the present findings provide clear evidence that hypoxia alters CPC fate decisions and reveal a novel mechanism of microRNA-210 in the hypoxic effect, raising the possibility of microRNA-210 as a potential therapeutic target for heart disease. Full article
(This article belongs to the Special Issue Genes at Ten)
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Open AccessArticle
YARS2 Missense Variant in Belgian Shepherd Dogs with Cardiomyopathy and Juvenile Mortality
Genes 2020, 11(3), 313; https://doi.org/10.3390/genes11030313 - 14 Mar 2020
Abstract
Dog puppy loss by the age of six to eight weeks after normal development is relatively uncommon. Necropsy findings in two spontaneously deceased Belgian Shepherd puppies indicated an abnormal accumulation of material in several organs. A third deceased puppy exhibited mild signs of [...] Read more.
Dog puppy loss by the age of six to eight weeks after normal development is relatively uncommon. Necropsy findings in two spontaneously deceased Belgian Shepherd puppies indicated an abnormal accumulation of material in several organs. A third deceased puppy exhibited mild signs of an inflammation in the central nervous system and an enteritis. The puppies were closely related, raising the suspicion of a genetic cause. Pedigree analysis suggested a monogenic autosomal recessive inheritance. Combined linkage and homozygosity mapping assigned the most likely position of a potential genetic defect to 13 genome segments totaling 82 Mb. The genome of an affected puppy was sequenced and compared to 645 control genomes. Three private protein changing variants were found in the linked and homozygous regions. Targeted genotyping in 96 Belgian Shepherd dogs excluded two of these variants. The remaining variant, YARS2:1054G>A or p.Glu352Lys, was perfectly associated with the phenotype in a cohort of 474 Belgian Shepherd dogs. YARS2 encodes the mitochondrial tyrosyl-tRNA synthetase 2 and the predicted amino acid change replaces a negatively charged and evolutionary conserved glutamate at the surface of the tRNA binding domain of YARS2 with a positively charged lysine. Human patients with loss-of-function variants in YARS2 suffer from myopathy, lactic acidosis, and sideroblastic anemia 2, a disease with clinical similarities to the phenotype of the studied dogs. The carrier frequency was 27.2% in the tested Belgian Shepherd dogs. Our data suggest YARS2:1054G>A as the candidate causative variant for the observed juvenile mortality. Full article
(This article belongs to the Special Issue Genes at Ten)
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Open AccessArticle
Shared Molecular Genetic Mechanisms Underlie Endometriosis and Migraine Comorbidity
Genes 2020, 11(3), 268; https://doi.org/10.3390/genes11030268 - 29 Feb 2020
Abstract
Observational epidemiological studies indicate that endometriosis and migraine co-occur within individuals more than expected by chance. However, the aetiology and biological mechanisms underlying their comorbidity remain unknown. Here we examined the relationship between endometriosis and migraine using genome-wide association study (GWAS) data. Single [...] Read more.
Observational epidemiological studies indicate that endometriosis and migraine co-occur within individuals more than expected by chance. However, the aetiology and biological mechanisms underlying their comorbidity remain unknown. Here we examined the relationship between endometriosis and migraine using genome-wide association study (GWAS) data. Single nucleotide polymorphism (SNP) effect concordance analysis found a significant concordance of SNP risk effects across endometriosis and migraine GWAS. Linkage disequilibrium score regression analysis found a positive and highly significant genetic correlation (rG = 0.38, P = 2.30 × 10−25) between endometriosis and migraine. A meta-analysis of endometriosis and migraine GWAS data did not reveal novel genome-wide significant SNPs, and Mendelian randomisation analysis found no evidence for a causal relationship between the two traits. However, gene-based analyses identified two novel loci for migraine. Also, we found significant enrichment of genes nominally associated (Pgene < 0.05) with both traits (Pbinomial-test = 9.83 × 10−6). Combining gene-based p-values across endometriosis and migraine, three genes, two (TRIM32 and SLC35G6) of which are at novel loci, were genome-wide significant. Genes having Pgene < 0.1 for both endometriosis and migraine (Pbinomial-test = 1.85 ×10°3) were significantly enriched for biological pathways, including interleukin-1 receptor binding, focal adhesion-PI3K-Akt-mTOR-signaling, MAPK and TNF-α signalling. Our findings further confirm the comorbidity of endometriosis and migraine and indicate a non-causal relationship between the two traits, with shared genetically-controlled biological mechanisms underlying the co-occurrence of the two disorders. Full article
(This article belongs to the Special Issue Genes at Ten)
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Review

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Open AccessFeature PaperReview
Utility of Common Marmoset (Callithrix jacchus) Embryonic Stem Cells in Liver Disease Modeling, Tissue Engineering and Drug Metabolism
Genes 2020, 11(7), 729; https://doi.org/10.3390/genes11070729 (registering DOI) - 30 Jun 2020
Abstract
The incidence of liver disease is increasing significantly worldwide and, as a result, there is a pressing need to develop new technologies and applications for end-stage liver diseases. For many of them, orthotopic liver transplantation is the only viable therapeutic option. Stem cells [...] Read more.
The incidence of liver disease is increasing significantly worldwide and, as a result, there is a pressing need to develop new technologies and applications for end-stage liver diseases. For many of them, orthotopic liver transplantation is the only viable therapeutic option. Stem cells that are capable of differentiating into all liver cell types and could closely mimic human liver disease are extremely valuable for disease modeling, tissue regeneration and repair, and for drug metabolism studies to develop novel therapeutic treatments. Despite the extensive research efforts, positive results from rodent models have not translated meaningfully into realistic preclinical models and therapies. The common marmoset Callithrix jacchus has emerged as a viable non-human primate model to study various human diseases because of its distinct features and close physiologic, genetic and metabolic similarities to humans. C. jacchus embryonic stem cells (cjESC) and recently generated cjESC-derived hepatocyte-like cells (cjESC-HLCs) could fill the gaps in disease modeling, liver regeneration and metabolic studies. They are extremely useful for cell therapy to regenerate and repair damaged liver tissues in vivo as they could efficiently engraft into the liver parenchyma. For in vitro studies, they would be advantageous for drug design and metabolism in developing novel drugs and cell-based therapies. Specifically, they express both phase I and II metabolic enzymes that share similar substrate specificities, inhibition and induction characteristics, and drug metabolism as their human counterparts. In addition, cjESCs and cjESC-HLCs are advantageous for investigations on emerging research areas, including blastocyst complementation to generate entire livers, and bioengineering of discarded livers to regenerate whole livers for transplantation. Full article
(This article belongs to the Special Issue Genes at Ten)
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