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Volume 11
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Genes, Volume 11, Issue 5 (May 2020) – 119 articles

Cover Story (view full-size image): Llamas are invaluable genetic resources of Peru. They are pack animals, and their fiber is used for clothing. Despite their importance, their population is decreasing. In this context, the Camelid Germplasm Bank—Quimsachata shelters a collection of llamas from their two phenotypes, Ch'aku and Q'ara, from different regions of Peru. Assessing the genetic variability and differentiation of the llama population from the Germplasm Bank, a high genetic variation was found among individuals, hence evidencing an adequate genetic management to conserve and maintain llama diversity. View this paper.
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28 pages, 10296 KiB  
Article
Climate Change and Green Sea Turtle Sex Ratio—Preventing Possible Extinction
by Jana Blechschmidt, Meike J. Wittmann and Chantal Blüml
Genes 2020, 11(5), 588; https://doi.org/10.3390/genes11050588 - 25 May 2020
Cited by 36 | Viewed by 15007
Abstract
Climate change poses a threat to species with temperature-dependent sex determination (TSD). A recent study on green sea turtles (Chelonia mydas) at the northern Great Barrier Reef (GBR) showed a highly female-skewed sex ratio with almost all juvenile turtles being female. This [...] Read more.
Climate change poses a threat to species with temperature-dependent sex determination (TSD). A recent study on green sea turtles (Chelonia mydas) at the northern Great Barrier Reef (GBR) showed a highly female-skewed sex ratio with almost all juvenile turtles being female. This shortage of males might eventually cause population extinction, unless rapid evolutionary rescue, migration, range shifts, or conservation efforts ensure a sufficient number of males. We built a stochastic individual-based model inspired by C. mydas but potentially transferrable to other species with TSD. Pivotal temperature, nest depth, and shading were evolvable traits. Additionally, we considered the effect of crossbreeding between northern and southern GBR, nest site philopatry, and conservation efforts. Among the evolvable traits, nest depth was the most likely to rescue the population, but even here the warmer climate change scenarios led to extinction. We expected turtles to choose colder beaches under rising temperatures, but surprisingly, nest site philopatry did not improve persistence. Conservation efforts promoted population survival and did not preclude trait evolution. Although extra information is needed to make reliable predictions for the fate of green sea turtles, our results illustrate how evolution can shape the fate of long lived, vulnerable species in the face of climate change. Full article
(This article belongs to the Special Issue Rapid Evolution)
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25 pages, 1177 KiB  
Review
Genetics of Omega-3 Long-Chain Polyunsaturated Fatty Acid Metabolism and Meat Eating Quality in Tattykeel Australian White Lambs
by Shedrach Benjamin Pewan, John Roger Otto, Roger Huerlimann, Alyssa Maree Budd, Felista Waithira Mwangi, Richard Crawford Edmunds, Benjamin William Behrens Holman, Michelle Lauren Elizabeth Henry, Robert Tumwesigye Kinobe, Oyelola Abdulwasiu Adegboye and Aduli Enoch Othniel Malau-Aduli
Genes 2020, 11(5), 587; https://doi.org/10.3390/genes11050587 - 25 May 2020
Cited by 32 | Viewed by 10245
Abstract
Meat eating quality with a healthy composition hinges on intramuscular fat (IMF), fat melting point (FMP), tenderness, juiciness, flavour and omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) content. These health-beneficial n-3 LC-PUFA play significant roles in optimal cardiovascular, retinal, maternal and childhood brain [...] Read more.
Meat eating quality with a healthy composition hinges on intramuscular fat (IMF), fat melting point (FMP), tenderness, juiciness, flavour and omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) content. These health-beneficial n-3 LC-PUFA play significant roles in optimal cardiovascular, retinal, maternal and childhood brain functions, and include alpha linolenic (ALA), eicosapentaenoic (EPA), docosahexaenoic (DHA) and docosapentaenoic (DPA) acids. The primary objective of this review was to access, retrieve, synthesise and critically appraise the published literature on the synthesis, metabolism and genetics of n-3 LC-PUFA and meat eating quality. Studies on IMF content, FMP and fatty acid composition were reviewed to identify knowledge gaps that can inform future research with Tattykeel Australian White (TAW) lambs. The TAW is a new sheep breed exclusive to MARGRA brand of lamb with an outstanding low fat melting point (28–39°C), high n-3 LC-PUFA EPA+DHA content (33–69mg/100g), marbling (3.4–8.2%), tenderness (20.0–38.5N) and overall consumer liking (7.9–8.5). However, correlations between n-3 LC-PUFA profile, stearoyl-CoA desaturase (SCD), fatty acid binding protein 4 (FABP4), fatty acid synthase (FASN), other lipogenic genes and meat quality traits present major knowledge gaps. The review also identified research opportunities in nutrition–genetics interactions aimed at a greater understanding of the genetics of n-3 LC-PUFA, feedlot finishing performance, carcass traits and eating quality in the TAW sheep. It was concluded that studies on IMF, FMP and n-3 LC-PUFA profiles in parental and progeny generations of TAW sheep will be foundational for the genetic selection of healthy lamb eating qualities and provide useful insights into their correlations with SCD, FASN and FABP4 genes. Full article
(This article belongs to the Special Issue Genetics and Genomics Applied to Livestock Production)
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16 pages, 295 KiB  
Article
Association Analysis and Meta-Analysis of Multi-Allelic Variants for Large-Scale Sequence Data
by Yu Jiang, Sai Chen, Xingyan Wang, Mengzhen Liu, William G. Iacono, John K. Hewitt, John E. Hokanson, Kenneth Krauter, Markku Laakso, Kevin W. Li, Sharon M. Lutz, Matthew McGue, Anita Pandit, Gregory J.M. Zajac, Michael Boehnke, Goncalo R. Abecasis, Scott I. Vrieze, Bibo Jiang, Xiaowei Zhan and Dajiang J. Liu
Genes 2020, 11(5), 586; https://doi.org/10.3390/genes11050586 - 25 May 2020
Cited by 5 | Viewed by 4111
Abstract
There is great interest in understanding the impact of rare variants in human diseases using large sequence datasets. In deep sequence datasets of >10,000 samples, ~10% of the variant sites are observed to be multi-allelic. Many of the multi-allelic variants have been shown [...] Read more.
There is great interest in understanding the impact of rare variants in human diseases using large sequence datasets. In deep sequence datasets of >10,000 samples, ~10% of the variant sites are observed to be multi-allelic. Many of the multi-allelic variants have been shown to be functional and disease-relevant. Proper analysis of multi-allelic variants is critical to the success of a sequencing study, but existing methods do not properly handle multi-allelic variants and can produce highly misleading association results. We discuss practical issues and methods to encode multi-allelic sites, conduct single-variant and gene-level association analyses, and perform meta-analysis for multi-allelic variants. We evaluated these methods through extensive simulations and the study of a large meta-analysis of ~18,000 samples on the cigarettes-per-day phenotype. We showed that our joint modeling approach provided an unbiased estimate of genetic effects, greatly improved the power of single-variant association tests among methods that can properly estimate allele effects, and enhanced gene-level tests over existing approaches. Software packages implementing these methods are available online. Full article
(This article belongs to the Special Issue Statistical Genetics)
24 pages, 3300 KiB  
Review
The FANC/BRCA Pathway Releases Replication Blockades by Eliminating DNA Interstrand Cross-Links
by Xavier Renaudin and Filippo Rosselli
Genes 2020, 11(5), 585; https://doi.org/10.3390/genes11050585 - 25 May 2020
Cited by 27 | Viewed by 6299
Abstract
DNA interstrand cross-links (ICLs) represent a major barrier blocking DNA replication fork progression. ICL accumulation results in growth arrest and cell death—particularly in cell populations undergoing high replicative activity, such as cancer and leukemic cells. For this reason, agents able to induce DNA [...] Read more.
DNA interstrand cross-links (ICLs) represent a major barrier blocking DNA replication fork progression. ICL accumulation results in growth arrest and cell death—particularly in cell populations undergoing high replicative activity, such as cancer and leukemic cells. For this reason, agents able to induce DNA ICLs are widely used as chemotherapeutic drugs. However, ICLs are also generated in cells as byproducts of normal metabolic activities. Therefore, every cell must be capable of rescuing lCL-stalled replication forks while maintaining the genetic stability of the daughter cells in order to survive, replicate DNA and segregate chromosomes at mitosis. Inactivation of the Fanconi anemia/breast cancer-associated (FANC/BRCA) pathway by inherited mutations leads to Fanconi anemia (FA), a rare developmental, cancer-predisposing and chromosome-fragility syndrome. FANC/BRCA is the key hub for a complex and wide network of proteins that—upon rescuing ICL-stalled DNA replication forks—allows cell survival. Understanding how cells cope with ICLs is mandatory to ameliorate ICL-based anticancer therapies and provide the molecular basis to prevent or bypass cancer drug resistance. Here, we review our state-of-the-art understanding of the mechanisms involved in ICL resolution during DNA synthesis, with a major focus on how the FANC/BRCA pathway ensures DNA strand opening and prevents genomic instability. Full article
(This article belongs to the Special Issue Protective Mechanisms Against DNA Replication Stress)
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15 pages, 1083 KiB  
Article
Sequence Analysis and FISH Mapping of Four Satellite DNA Families among Cervidae
by Miluse Vozdova, Svatava Kubickova, Halina Cernohorska, Jan Fröhlich, Natália Martínková and Jiri Rubes
Genes 2020, 11(5), 584; https://doi.org/10.3390/genes11050584 - 24 May 2020
Cited by 5 | Viewed by 2985
Abstract
Centromeric and pericentromeric chromosome regions are occupied by satellite DNA. Satellite DNAs play essential roles in chromosome segregation, and, thanks to their extensive sequence variability, to some extent, they can also be used as phylogenetic markers. In this paper, we isolated and sequenced [...] Read more.
Centromeric and pericentromeric chromosome regions are occupied by satellite DNA. Satellite DNAs play essential roles in chromosome segregation, and, thanks to their extensive sequence variability, to some extent, they can also be used as phylogenetic markers. In this paper, we isolated and sequenced satellite DNA I-IV in 11 species of Cervidae. The obtained satellite DNA sequences and their chromosomal distribution were compared among the analysed representatives of cervid subfamilies Cervinae and Capreolinae. Only satI and satII sequences are probably present in all analysed species with high abundance. On the other hand, fluorescence in situ hybridisation (FISH) with satIII and satIV probes showed signals only in a part of the analysed species, indicating interspecies copy number variations. Several indices, including FISH patterns, the high guanine and cytosine (GC) content, and the presence of centromere protein B (CENP-B) binding motif, suggest that the satII DNA may represent the most important satellite DNA family that might be involved in the centromeric function in Cervidae. The absence or low intensity of satellite DNA FISH signals on biarmed chromosomes probably reflects the evolutionary reduction of heterochromatin following the formation of chromosome fusions. The phylogenetic trees constructed on the basis of the satellite I-IV DNA relationships generally support the present cervid taxonomy. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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14 pages, 2174 KiB  
Article
Distinct Tumor Microenvironments Are a Defining Feature of Strain-Specific CRISPR/Cas9-Induced MPNSTs
by Amanda Scherer, Victoria R. Stephens, Gavin R. McGivney, Wade R. Gutierrez, Emily A. Laverty, Vickie Knepper-Adrian and Rebecca D. Dodd
Genes 2020, 11(5), 583; https://doi.org/10.3390/genes11050583 - 23 May 2020
Cited by 14 | Viewed by 3578
Abstract
The tumor microenvironment plays important roles in cancer biology, but genetic backgrounds of mouse models can complicate interpretation of tumor phenotypes. A deeper understanding of strain-dependent influences on the tumor microenvironment of genetically-identical tumors is critical to exploring genotype–phenotype relationships, but these interactions [...] Read more.
The tumor microenvironment plays important roles in cancer biology, but genetic backgrounds of mouse models can complicate interpretation of tumor phenotypes. A deeper understanding of strain-dependent influences on the tumor microenvironment of genetically-identical tumors is critical to exploring genotype–phenotype relationships, but these interactions can be difficult to identify using traditional Cre/loxP approaches. Here, we use somatic CRISPR/Cas9 tumorigenesis approaches to determine the impact of mouse background on the biology of genetically-identical malignant peripheral nerve sheath tumors (MPNSTs) in four commonly-used inbred strains. To our knowledge, this is the first study to systematically evaluate the impact of host strain on CRISPR/Cas9-generated mouse models. Our data identify multiple strain-dependent phenotypes, including changes in tumor onset and the immune microenvironment. While BALB/c mice develop MPNSTs earlier than other strains, similar tumor onset is observed in C57BL/6, 129X1 and 129/SvJae mice. Indel pattern analysis demonstrates that indel frequency, type and size are similar across all genetic backgrounds. Gene expression and IHC analysis identify multiple strain-dependent differences in CD4+ T cell infiltration and myeloid cell populations, including M2 macrophages and mast cells. These data highlight important strain-specific phenotypes of genomically-matched MPNSTs that have implications for the design of future studies using similar in vivo gene editing approaches. Full article
(This article belongs to the Special Issue Genomics and Models of Nerve Sheath Tumors)
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9 pages, 1590 KiB  
Article
Comparative Analysis of ANDE 6C Rapid DNA Analysis System and Traditional Methods
by Michele Ragazzo, Stefano Melchiorri, Laura Manzo, Valeria Errichiello, Giulio Puleri, Fabio Nicastro and Emiliano Giardina
Genes 2020, 11(5), 582; https://doi.org/10.3390/genes11050582 - 22 May 2020
Cited by 15 | Viewed by 4336
Abstract
Rapid DNA analysis is an ultrafast and fully automated DNA-typing system, which can produce interpretable genetic profiles from biological samples within 90 minutes. This “swab in—profile out” method comprises DNA extraction, amplification by PCR multiplex, separation and detection of DNA fragments by capillary [...] Read more.
Rapid DNA analysis is an ultrafast and fully automated DNA-typing system, which can produce interpretable genetic profiles from biological samples within 90 minutes. This “swab in—profile out” method comprises DNA extraction, amplification by PCR multiplex, separation and detection of DNA fragments by capillary electrophoresis. The aim of study was the validation of the Accelerated Nuclear DNA Equipment (ANDE) 6C system as a typing method for reference samples according to the ISO/IEC 17025 standard. Here, we report the evaluation of the validity and reproducibility of results by the comparison of the genetic profiles generated by the ANDE 6C System with those generated by standard technologies. A quantity of 104 buccal swabs were analyzed both through the ANDE 6C technology and the traditional method (DNA extraction and quantification, amplification and separation by capillary electrophoresis). Positive typing was observed in 97% of cases for ANDE 6C technology with only three buccal swabs failing to reveal interpretable signals. Concordance was determined by comparing the allele calls generated by ANDE 6C and conventional technology. Comparison of 2800 genotypes revealed a concordance rate of 99.96%. These results met the ISO/IEC 17025 requirements, enabling us to receive the accreditation for this method. Finally, rapid technology has certainly reached a level of reliability which has made its use in laboratories of forensic genetics a reality. Full article
(This article belongs to the Special Issue Forensic Genetics and Genomics)
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23 pages, 3580 KiB  
Article
MYB43 in Oilseed Rape (Brassica napus) Positively Regulates Vascular Lignification, Plant Morphology and Yield Potential but Negatively Affects Resistance to Sclerotinia sclerotiorum
by Jiayi Jiang, Xueli Liao, Xiaoyun Jin, Li Tan, Qifeng Lu, Chenglong Yuan, Yufei Xue, Nengwen Yin, Na Lin and Yourong Chai
Genes 2020, 11(5), 581; https://doi.org/10.3390/genes11050581 - 22 May 2020
Cited by 29 | Viewed by 4015
Abstract
Arabidopsis thaliana MYB43 (AtMYB43) is suggested to be involved in cell wall lignification. PtrMYB152, the Populus orthologue of AtMYB43, is a transcriptional activator of lignin biosynthesis and vessel wall deposition. In this research, MYB43 genes from Brassica napus (rapeseed) and its parental [...] Read more.
Arabidopsis thaliana MYB43 (AtMYB43) is suggested to be involved in cell wall lignification. PtrMYB152, the Populus orthologue of AtMYB43, is a transcriptional activator of lignin biosynthesis and vessel wall deposition. In this research, MYB43 genes from Brassica napus (rapeseed) and its parental species B. rapa and B. oleracea were molecularly characterized, which were dominantly expressed in stem and other vascular organs and showed responsiveness to Sclerotinia sclerotiorum infection. The BnMYB43 family was silenced by RNAi, and the transgenic rapeseed lines showed retardation in growth and development with smaller organs, reduced lodging resistance, fewer silique number and lower yield potential. The thickness of the xylem layer decreased by 28%; the numbers of sclerenchymatous cells, vessels, interfascicular fibers, sieve tubes and pith cells in the whole cross section of the stem decreased by 28%, 59%, 48%, 34% and 21% in these lines, respectively. The contents of cellulose and lignin decreased by 17.49% and 16.21% respectively, while the pectin content increased by 71.92% in stems of RNAi lines. When inoculated with S. sclerotiorum, the lesion length was drastically decreased by 52.10% in the stems of transgenic plants compared with WT, implying great increase in disease resistance. Correspondingly, changes in the gene expression patterns of lignin biosynthesis, cellulose biosynthesis, pectin biosynthesis, cell cycle, SA- and JA-signals, and defensive pathways were in accordance with above phenotypic modifications. These results show that BnMYB43, being a growth-defense trade-off participant, positively regulates vascular lignification, plant morphology and yield potential, but negatively affects resistance to S. sclerotiorum. Moreover, this lignification activator influences cell biogenesis of both lignified and non-lignified tissues of the whole vascular organ. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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19 pages, 6588 KiB  
Article
Cytosolic/Plastid Glyceraldehyde-3-Phosphate Dehydrogenase Is a Negative Regulator of Strawberry Fruit Ripening
by Ya Luo, Cong Ge, Min Yang, Yu Long, Mengyao Li, Yong Zhang, Qing Chen, Bo Sun, Yan Wang, Xiaorong Wang and Haoru Tang
Genes 2020, 11(5), 580; https://doi.org/10.3390/genes11050580 - 21 May 2020
Cited by 14 | Viewed by 3326
Abstract
Cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPC) and plastid glyceraldehyde-3-phosphate dehydrogenase (GAPCp) are key enzymes in glycolysis. Besides their catalytic function, GAPC/GAPCp participates in the regulation of plant stress response and growth and development. However, the involvement of GAPC/GAPCp in the regulation of fruit ripening is [...] Read more.
Cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPC) and plastid glyceraldehyde-3-phosphate dehydrogenase (GAPCp) are key enzymes in glycolysis. Besides their catalytic function, GAPC/GAPCp participates in the regulation of plant stress response and growth and development. However, the involvement of GAPC/GAPCp in the regulation of fruit ripening is unclear. In this study, FaGAPC2 and FaGAPCp1 in strawberries were isolated and analyzed. FaGAPC2 and FaGAPCp1 transcripts showed high transcript levels in the fruit. Transient overexpression of FaGAPC2 and FaGAPCp1 delayed fruit ripening, whereas RNA interference promoted fruit ripening and affected fruit anthocyanins and sucrose levels. Change in the expression patterns of FaGAPC2 and FaGAPCp1 also influenced the expression of several glycolysis-related and ripening-related genes such as CEL1, CEL2, SS, ANS, MYB5, NCED1, ABI1, ALDO, PK, and G6PDH, and H2O2 level and reduced glutathione (GSH)/glutathione disulfide (GSSG) redox potential. Meanwhile, metabolomics experiments showed that transient overexpression of FaGAPCp1 resulted in a decrease in anthocyanins, flavonoids, organic acid, amino acids, and their derivatives. In addition, abscisic acid (ABA) and sucrose treatment induced the production of large amounts of H2O2 and inhibited the expression of FaGAPC2/FaGAPCp1 in strawberry fruit. These results revealed that FaGAPC2/FaGAPCp1 is a negative regulator of ABA and sucrose mediated fruit ripening which can be regulated by oxidative stress. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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9 pages, 490 KiB  
Article
Hepatic DNA Methylation in Response to Early Stimulation of Microbiota with Lactobacillus Synbiotics in Broiler Chickens
by Aleksandra Dunislawska, Anna Slawinska and Maria Siwek
Genes 2020, 11(5), 579; https://doi.org/10.3390/genes11050579 - 21 May 2020
Cited by 19 | Viewed by 3074
Abstract
DNA methylation inhibits DNA transcription by the addition of methyl residues to cysteine within the CpG islands of gene promoters. The process of DNA methylation can be modulated by environmental factors such as intestinal microbiota. In poultry, the composition of the intestinal microbiota [...] Read more.
DNA methylation inhibits DNA transcription by the addition of methyl residues to cysteine within the CpG islands of gene promoters. The process of DNA methylation can be modulated by environmental factors such as intestinal microbiota. In poultry, the composition of the intestinal microbiota can be stimulated by in ovo delivery of synbiotics. The present study aims to determine the effect of Lactobacillus synbiotics delivered in ovo on the level of hepatic DNA methylation in broiler chickens. In ovo stimulation was performed on day 12 of egg incubation. Bioactive compounds delivered in ovo included (S1)—Lactobacillus salivarius with GOS and (S2)—Lactobacillus plantarum with RFO. Samples were collected from six individuals from each group on day 42 post-hatching. DNA methylation of five genes selected on the basis of the transcriptome data were analyzed using the qMSP method. Significant changes were observed in DNA methylation of genes in liver including ANGPTL4 and NR4A3, after S2 delivery. The obtained results confirm that the downregulation of metabolic gene expression in the liver mediated by in ovo stimulation had epigenetic characteristics. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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10 pages, 889 KiB  
Review
Genome Maintenance by DNA Helicase B
by Lindsey Hazeslip, Maroof Khan Zafar, Muhammad Zain Chauhan and Alicia K. Byrd
Genes 2020, 11(5), 578; https://doi.org/10.3390/genes11050578 - 21 May 2020
Cited by 12 | Viewed by 4161
Abstract
DNA Helicase B (HELB) is a conserved helicase in higher eukaryotes with roles in the initiation of DNA replication and in the DNA damage and replication stress responses. HELB is a predominately nuclear protein in G1 phase where it is involved in [...] Read more.
DNA Helicase B (HELB) is a conserved helicase in higher eukaryotes with roles in the initiation of DNA replication and in the DNA damage and replication stress responses. HELB is a predominately nuclear protein in G1 phase where it is involved in initiation of DNA replication through interactions with DNA topoisomerase 2-binding protein 1 (TOPBP1), cell division control protein 45 (CDC45), and DNA polymerase α-primase. HELB also inhibits homologous recombination by reducing long-range end resection. After phosphorylation by cyclin-dependent kinase 2 (CDK2) at the G1 to S transition, HELB is predominately localized to the cytosol. However, this cytosolic localization in S phase is not exclusive. HELB has been reported to localize to chromatin in response to replication stress and to localize to the common fragile sites 16D (FRA16D) and 3B (FRA3B) and the rare fragile site XA (FRAXA) in S phase. In addition, HELB is phosphorylated in response to ionizing radiation and has been shown to localize to chromatin in response to various types of DNA damage, suggesting it has a role in the DNA damage response. Full article
(This article belongs to the Special Issue DNA Helicases: Mechanisms, Biological Pathways, and Disease Relevance)
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14 pages, 1419 KiB  
Article
Genome-Wide Patterns of Homozygosity and Relevant Characterizations on the Population Structure in Piétrain Pigs
by Huiwen Zhan, Saixian Zhang, Kaili Zhang, Xia Peng, Shengsong Xie, Xinyun Li, Shuhong Zhao and Yunlong Ma
Genes 2020, 11(5), 577; https://doi.org/10.3390/genes11050577 - 21 May 2020
Cited by 11 | Viewed by 3265
Abstract
Investigating the patterns of homozygosity, linkage disequilibrium, effective population size and inbreeding coefficients in livestock contributes to our understanding of the genetic diversity and evolutionary history. Here we used Illumina PorcineSNP50 Bead Chip to identify the runs of homozygosity (ROH) and estimate the [...] Read more.
Investigating the patterns of homozygosity, linkage disequilibrium, effective population size and inbreeding coefficients in livestock contributes to our understanding of the genetic diversity and evolutionary history. Here we used Illumina PorcineSNP50 Bead Chip to identify the runs of homozygosity (ROH) and estimate the linkage disequilibrium (LD) across the whole genome, and then predict the effective population size. In addition, we calculated the inbreeding coefficients based on ROH in 305 Piétrain pigs and compared its effect with the other two types of inbreeding coefficients obtained by different calculation methods. A total of 23,434 ROHs were detected, and the average length of ROH per individual was about 507.27 Mb. There was no regularity on how those runs of homozygosity distributed in genome. The comparisons of different categories suggested that the formation of long ROH was probably related with recent inbreeding events. Although the density of genes located in ROH core regions is lower than that in the other genomic regions, most of them are related with Piétrain commercial traits like meat qualities. Overall, the results provide insight into the way in which ROH is produced and the identified ROH core regions can be used to map the genes associated with commercial traits in domestic animals. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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15 pages, 1848 KiB  
Communication
Long-Term Adaption to High Osmotic Stress as a Tool for Improving Enological Characteristics in Industrial Wine Yeast
by Gabriela Betlej, Ewelina Bator, Bernadetta Oklejewicz, Leszek Potocki, Anna Górka, Magdalena Slowik-Borowiec, Wojciech Czarny, Wojciech Domka and Aleksandra Kwiatkowska
Genes 2020, 11(5), 576; https://doi.org/10.3390/genes11050576 - 20 May 2020
Cited by 16 | Viewed by 4144
Abstract
Industrial wine yeasts owe their adaptability in constantly changing environments to a long evolutionary history that combines naturally occurring evolutionary events with human-enforced domestication. Among the many stressors associated with winemaking processes that have potentially detrimental impacts on yeast viability, growth, and fermentation [...] Read more.
Industrial wine yeasts owe their adaptability in constantly changing environments to a long evolutionary history that combines naturally occurring evolutionary events with human-enforced domestication. Among the many stressors associated with winemaking processes that have potentially detrimental impacts on yeast viability, growth, and fermentation performance are hyperosmolarity, high glucose concentrations at the beginning of fermentation, followed by the depletion of nutrients at the end of this process. Therefore, in this study, we subjected three widely used industrial wine yeasts to adaptive laboratory evolution under potassium chloride (KCl)-induced osmotic stress. At the end of the evolutionary experiment, we evaluated the tolerance to high osmotic stress of the evolved strains. All of the analyzed strains improved their fitness under high osmotic stress without worsening their economic characteristics, such as growth rate and viability. The evolved derivatives of two strains also gained the ability to accumulate glycogen, a readily mobilized storage form of glucose conferring enhanced viability and vitality of cells during prolonged nutrient deprivation. Moreover, laboratory-scale fermentation in grape juice showed that some of the KCl-evolved strains significantly enhanced glycerol synthesis and production of resveratrol-enriched wines, which in turn greatly improved the wine sensory profile. Altogether, these findings showed that long-term adaptations to osmotic stress can be an attractive approach to develop industrial yeasts. Full article
(This article belongs to the Special Issue Genetic Aspects of Yeast: Cell Biology, Ecology and Biotechnology)
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12 pages, 4106 KiB  
Article
Characterization of POU2F1 Gene and Its Potential Impact on the Expression of Genes Involved in Fur Color Formation in Rex Rabbit
by Naisu Yang, Bohao Zhao, Shuaishuai Hu, Zhiyuan Bao, Ming Liu, Yang Chen and Xinsheng Wu
Genes 2020, 11(5), 575; https://doi.org/10.3390/genes11050575 - 20 May 2020
Cited by 7 | Viewed by 3514
Abstract
The naturally colorful fur of the Rex rabbit is becoming increasingly popular in the modern textile market. Our previous study found that POU class 2 homeobox 1 gene (POU2F1) potentially affects the expression of genes involved in fur color formation in [...] Read more.
The naturally colorful fur of the Rex rabbit is becoming increasingly popular in the modern textile market. Our previous study found that POU class 2 homeobox 1 gene (POU2F1) potentially affects the expression of genes involved in fur color formation in the Rex rabbit, but the function and regulation of POU2F1 has not been reported. In this study, the expression patterns of POU2F1 in Rex rabbits of various colors, as well as in different organs, were analyzed by RT-qPCR. Interference and overexpression of POU2F1 were used to identify the potential effects of POU2F1 on other genes related to fur color formation. The results show that the levels of POU2F1 expression were significantly higher in the dorsal skin of the brown and protein yellow Rex rabbits, compared with that of the black one. POU2F1 mRNAs were widespread in the tissues examined in this study and showed the highest level in the lungs. By transfecting rabbit melanocytes with an POU2F1-overexpression plasmid, we found that the POU2F1 protein was located at the nucleus, and the protein showed the classic characteristics of a transcription factor. In addition, abnormal expression of POU2F1 significantly affected the expression of pigmentation-related genes, including SLC7A11, MITF, SLC24A5, MC1R, and ASIP, revealing the regulatory roles of POU2F1 on pigmentation. The results provide the basis for further exploration of the role of POU2F1 in fur color formation of the Rex rabbit. Full article
(This article belongs to the Special Issue Coat Color Genetics)
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14 pages, 1417 KiB  
Article
Quantifying the Genetic Basis of Marfan Syndrome Clinical Variability
by Thomas Grange, Mélodie Aubart, Maud Langeois, Louise Benarroch, Pauline Arnaud, Olivier Milleron, Ludivine Eliahou, Marie-Sylvie Gross, Nadine Hanna, Catherine Boileau, Laurent Gouya and Guillaume Jondeau
Genes 2020, 11(5), 574; https://doi.org/10.3390/genes11050574 - 20 May 2020
Cited by 15 | Viewed by 4857
Abstract
Marfan syndrome (MFS) is an autosomal dominant connective tissue disorder with considerable inter- and intra-familial clinical variability. The contribution of inherited modifiers to variability has not been quantified. We analyzed the distribution of 23 clinical features in 1306 well-phenotyped MFS patients carrying FBN1 [...] Read more.
Marfan syndrome (MFS) is an autosomal dominant connective tissue disorder with considerable inter- and intra-familial clinical variability. The contribution of inherited modifiers to variability has not been quantified. We analyzed the distribution of 23 clinical features in 1306 well-phenotyped MFS patients carrying FBN1 mutations. We found strong correlations between features within the same system (i.e., ophthalmology vs. skeletal vs. cardiovascular) suggesting common underlying determinants, while features belonging to different systems were largely uncorrelated. We adapted a classical quantitative genetics model to estimate the heritability of each clinical feature from phenotypic correlations between relatives. Most clinical features showed strong familial aggregation and high heritability. We found a significant contribution by the major locus on the phenotypic variance only for ectopia lentis using a new strategy. Finally, we found evidence for the “Carter effect” in the MFS cardiovascular phenotype, which supports a polygenic model for MFS cardiovascular variability and indicates additional risk for children of MFS mothers with an aortic event. Our results demonstrate that an important part of the phenotypic variability in MFS is under the control of inherited modifiers, widely shared between features within the same system, but not among different systems. Further research must be performed to identify genetic modifiers of MFS severity. Full article
(This article belongs to the Special Issue Marfan Syndrome and Related Disorders: Genetic Basis, Molecular Mechanisms, and Genotype–Phenotype Correlations)
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6 pages, 232 KiB  
Communication
Senescence and Longevity of Sea Urchins
by Yam Amir, Maayan Insler, Abram Giller, Danielle Gutman and Gil Atzmon
Genes 2020, 11(5), 573; https://doi.org/10.3390/genes11050573 - 20 May 2020
Cited by 10 | Viewed by 7043
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)
16 pages, 2091 KiB  
Article
MicroRNA-1253 Regulation of WASF2 (WAVE2) and its Relevance to Racial Health Disparities
by Mercy A. Arkorful, Nicole Noren Hooten, Yongqing Zhang, Amirah N. Hewitt, Lori Barrientos Sanchez, Michele K. Evans and Douglas F. Dluzen
Genes 2020, 11(5), 572; https://doi.org/10.3390/genes11050572 - 20 May 2020
Cited by 4 | Viewed by 3833
Abstract
The prevalence of hypertension among African Americans (AAs) in the US is among the highest of any demographic and affects over two-thirds of AA women. Previous data from our laboratory suggest substantial differential gene expression (DGE) of mRNAs and microRNAs (miRNAs) exists within [...] Read more.
The prevalence of hypertension among African Americans (AAs) in the US is among the highest of any demographic and affects over two-thirds of AA women. Previous data from our laboratory suggest substantial differential gene expression (DGE) of mRNAs and microRNAs (miRNAs) exists within peripheral blood mononuclear cells (PBMCs) isolated from AA and white women with or without hypertension. We hypothesized that DGE by race may contribute to racial differences in hypertension. In a reanalysis of our previous dataset, we found that the Wiskott–Aldrich syndrome protein Verprolin-homologous protein 2 (WASF2 (also known as WAVE2)) is differentially expressed in AA women with hypertension, along with several other members of the actin cytoskeleton signaling pathway that plays a role in cell shape and branching of actin filaments. We performed an in silico miRNA target prediction analysis that suggested miRNA miR-1253 regulates WASF2. Transfection of miR-1253 mimics into human umbilical vein endothelial cells (HUVECs) and human aortic endothelial cells (HAECs) significantly repressed WASF2 mRNA and protein levels (p < 0.05), and a luciferase reporter assay confirmed that miR-1253 regulates the WASF2 3′ UTR (p < 0.01). miR-1253 overexpression in HUVECs significantly increased HUVEC lamellipodia formation (p < 0.01), suggesting the miR-1253–WASF2 interaction may play a role in cell shape and actin cytoskeleton function. Together, we have identified novel roles for miR-1253 and WASF2 in a hypertension-related disparities context. This may ultimately lead to the discovery of additional actin-related genes which are important in the vascular-related complications of hypertension and influence the disproportionate susceptibility to hypertension among AAs in general and AA women in particular. Full article
(This article belongs to the Special Issue Selected Papers From the Advanced Genetics Conference 2019)
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7 pages, 1120 KiB  
Case Report
Clinical and Molecular Data Define a Diagnosis of Arrhythmogenic Cardiomyopathy in a Carrier of a Brugada-Syndrome-Associated PKP2 Mutation
by Simone Persampieri, Chiara Assunta Pilato, Elena Sommariva, Angela Serena Maione, Ilaria Stadiotti, Antonio Ranalletta, Margherita Torchio, Antonio Dello Russo, Cristina Basso, Giulio Pompilio, Claudio Tondo and Michela Casella
Genes 2020, 11(5), 571; https://doi.org/10.3390/genes11050571 - 20 May 2020
Cited by 3 | Viewed by 2863
Abstract
Plakophilin-2 (PKP2) is the most frequently mutated desmosomal gene in arrhythmogenic cardiomyopathy (ACM), a disease characterized by structural and electrical alterations predominantly affecting the right ventricular myocardium. Notably, ACM cases without overt structural alterations are frequently reported, mainly in the early [...] Read more.
Plakophilin-2 (PKP2) is the most frequently mutated desmosomal gene in arrhythmogenic cardiomyopathy (ACM), a disease characterized by structural and electrical alterations predominantly affecting the right ventricular myocardium. Notably, ACM cases without overt structural alterations are frequently reported, mainly in the early phases of the disease. Recently, the PKP2 p.S183N mutation was found in a patient affected by Brugada syndrome (BS), an inherited arrhythmic channelopathy most commonly caused by sodium channel gene mutations. We here describe a case of a patient carrier of the same BS-related PKP2 p.S183N mutation but with a clear diagnosis of ACM. Specifically, we report how clinical and molecular investigations can be integrated for diagnostic purposes, distinguishing between ACM and BS, which are increasingly recognized as syndromes with clinical and genetic overlaps. This observation is fundamentally relevant in redefining the role of genetics in the approach to the arrhythmic patient, progressing beyond the concept of “one mutation, one disease”, and raising concerns about the most appropriate approach to patients affected by structural/electrical cardiomyopathy. The merging of genetics, electroanatomical mapping, and tissue and cell characterization summarized in our patient seems to be the most complete diagnostic algorithm, favoring a reliable diagnosis. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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17 pages, 1710 KiB  
Article
A Reference Genome of Bursaphelenchus mucronatus Provides New Resources for Revealing Its Displacement by Pinewood Nematode
by Shuangyang Wu, Shenghan Gao, Sen Wang, Jie Meng, Jacob Wickham, Sainan Luo, Xinyu Tan, Haiying Yu, Yujia Xiang, Songnian Hu, Lilin Zhao and Jianghua Sun
Genes 2020, 11(5), 570; https://doi.org/10.3390/genes11050570 - 19 May 2020
Cited by 9 | Viewed by 3649
Abstract
The Bursaphelenchus mucronatus, which was highly similar with Bursaphelenchus xylophilus in terms of morphological characteristics and biological properties—but had weaker pathogenicity to forests—was a native species often displaced by B. xylophilus when occupying the same niche. Since the draft genome of the [...] Read more.
The Bursaphelenchus mucronatus, which was highly similar with Bursaphelenchus xylophilus in terms of morphological characteristics and biological properties—but had weaker pathogenicity to forests—was a native species often displaced by B. xylophilus when occupying the same niche. Since the draft genome of the invasive B. xylophilus has been published, the absence of a reference genome of B. mucronatus still prevents us from understanding the molecular evidences behind competitive displacement. In this study, we employed Single Molecule, Real-Time (SMRT) sequencing and a Hi-C scaffolding approach to yield a near chromosome-level assembly of B. mucronatus, including six pseudo-chromosomes. The assembly size is 73 Mb, with scaffold N50 of 11.50 Mb and contig N50 of 1.48 Mb. Comparative genomics results showed high similarity between B. xylophilus and B. mucronatus. However, the losing of orphan genes and species-specific orthologous genes in B. mucronatus may indicate weaker adaptability to the environment. The gene family contractions of GPCRs (G Protein-Coupled Receptors) and cellulases in B. mucronatus may jointly contribute to its displacement by B. xylophilus. Overall, we introduced a valuable genomic resource for molecular and evolutionary studies of B. mucronatus, especially for studying the competitive displacement by the pinewood nematode, which could help us control the pathogenicity of pine wilt diseases. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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12 pages, 2322 KiB  
Article
Haplotypes of the Mutated SIRT2 Promoter Contributing to Transcription Factor Binding and Type 2 Diabetes Susceptibility
by Xiao Zheng, Jiajun Li, Jie Sheng, Yang Dai, Yue Wang, Jinbiao Liu and Yao Xu
Genes 2020, 11(5), 569; https://doi.org/10.3390/genes11050569 - 19 May 2020
Cited by 5 | Viewed by 2676
Abstract
Genetic variability is an important causative factor for susceptibility and pathogenesis of type 2 diabetes (T2D). Histone deacetylase, sirtuin 2 (SIRT2), plays regulatory roles in glucose metabolism and insulin sensitivity. However, whether the SIRT2 variants or haplotypes contribute to T2D risk remain to [...] Read more.
Genetic variability is an important causative factor for susceptibility and pathogenesis of type 2 diabetes (T2D). Histone deacetylase, sirtuin 2 (SIRT2), plays regulatory roles in glucose metabolism and insulin sensitivity. However, whether the SIRT2 variants or haplotypes contribute to T2D risk remain to be elucidated. In this study, we first detected three novel polymorphisms (P-MU1, P-MU2, and P-MU3) in the promoter of SIRT2 in the Chinese population. All pairwise sets of the three loci were strongly in linkage disequilibrium. Next, we constructed the haplotype block structure, and found H1-GGC and H2-CCA accounted for the most (total 91.8%) in T2D. The haplotype combination H1-H1-GGGGCC displayed a high risk for T2D (OR = 2.03, 95% CI = 1.12–3.72). By association analysis, we found the individuals carrying H1-H1-GGGGCC had significantly higher fasting plasma glucose and glycated hemoglobin. The haplotype H1-GGC presented a 6.74-fold higher promoter activity than H2-CCA, which was consistent with the correlation results. Furthermore, we clarified the mechanism whereby the C allele of both the P-MU1 and P-MU2 loci disrupted the signal transducer and activator of transcription 1 (STAT1) binding sites, leading to the attenuation of the SIRT2 transcription. Together, these data suggest that the linked haplotype GGC could be considered as a promising marker for T2D diagnosis and therapy assessment. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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18 pages, 3724 KiB  
Article
Molecular Characterization of a Date Palm Vascular Highway 1-Interacting Kinase (PdVIK) under Abiotic Stresses
by Ibtisam Al-Harrasi, Himanshu V. Patankar, Rashid Al-Yahyai, Ramanjulu Sunkar, Pannaga Krishnamurthy, Prakash P. Kumar and Mahmoud W. Yaish
Genes 2020, 11(5), 568; https://doi.org/10.3390/genes11050568 - 19 May 2020
Cited by 9 | Viewed by 2915
Abstract
The date palm (Khalas) is an extremophile plant that can adapt to various abiotic stresses including drought and salinity. Salinity tolerance is a complex trait controlled by numerous genes. Identification and functional characterization of salt-responsive genes from the date palm is [...] Read more.
The date palm (Khalas) is an extremophile plant that can adapt to various abiotic stresses including drought and salinity. Salinity tolerance is a complex trait controlled by numerous genes. Identification and functional characterization of salt-responsive genes from the date palm is fundamental to understand salinity tolerance at the molecular level in this plant species. In this study, a salt-inducible vascular highway 1-interacting kinase (PdVIK) that is a MAP kinase kinase kinase (MAPKKK) gene from the date palm, was functionally characterized using in vitro and in vivo strategies. PdVIK, one of the 597 kinases encoded by the date palm genome possesses an ankyrin repeat domain and a kinase domain. The recombinant PdVIK protein exhibited phosphotyrosine activity against myelin basic protein (MBP) substrate. Overexpression of PdVIK in yeast significantly improved its tolerance to salinity, LiCl, and oxidative stresses. Transgenic Arabidopsis seedlings overexpressing PdVIK displayed improved tolerance to salinity, osmotic, and oxidative stresses as assessed by root growth assay. The transgenic lines grown in the soil also displayed modulated salt response, compared to wild-type controls as evaluated by the overall plant growth and proline levels. Likewise, the transgenic lines exhibited drought tolerance by maintaining better relative water content (RWC) compared to non-transgenic control plants. Collectively, these results implicate the involvement of PdVIK in modulating the abiotic stress response of the date palm. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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13 pages, 1871 KiB  
Article
NOX4 Deficiency Exacerbates the Impairment of Cystatin C-Dependent Hippocampal Neurogenesis by a Chronic High Fat Diet
by Piyanart Jiranugrom, Ik Dong Yoo, Min Woo Park, Ji Hwan Ryu, Jong-Seok Moon and Sun Shin Yi
Genes 2020, 11(5), 567; https://doi.org/10.3390/genes11050567 - 19 May 2020
Cited by 5 | Viewed by 3318
Abstract
Hippocampal neurogenesis is linked with a cognitive process under a normal physiological condition including learning, memory, pattern separation, and cognitive flexibility. Hippocampal neurogenesis is altered by multiple factors such as the systemic metabolic changes. NADPH oxidase 4 (NOX4) has been implicated in the [...] Read more.
Hippocampal neurogenesis is linked with a cognitive process under a normal physiological condition including learning, memory, pattern separation, and cognitive flexibility. Hippocampal neurogenesis is altered by multiple factors such as the systemic metabolic changes. NADPH oxidase 4 (NOX4) has been implicated in the regulation of brain function. While the role of NOX4 plays in the brain, the mechanism by which NOX4 regulates hippocampal neurogenesis under metabolic stress is unclear. In this case, we show that NOX4 deficiency exacerbates the impairment of hippocampal neurogenesis by inhibiting neuronal maturation by a chronic high fat diet (HFD). NOX4 deficiency resulted in less hippocampal neurogenesis by decreasing doublecortin (DCX)-positive neuroblasts, a neuronal differentiation marker, and their branched-dendrites. Notably, NOX4 deficiency exacerbates the impairment of hippocampal neurogenesis by chronic HFD. Moreover, NOX4 deficiency had a significant reduction of Cystatin C levels, which is critical for hippocampal neurogenesis, under chronic HFD as well as normal chow (NC) diet. Furthermore, the reduction of Cystatin C levels was correlated with the impairment of hippocampal neurogenesis in NOX4 deficient and wild-type (WT) mice under chronic HFD. Our results suggest that NOX4 regulates the impairment of Cystatin C-dependent hippocampal neurogenesis under chronic HFD. Full article
(This article belongs to the Special Issue Recent Advances in the Interaction between Metabolism and Inflammation)
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9 pages, 4273 KiB  
Communication
Characterizing Y-STRs in the Evaluation of Population Differentiation Using the Mean of Allele Frequency Difference between Populations
by Yuxiang Zhou, Yining Yao, Baonian Liu, Qinrui Yang, Zhihan Zhou, Chengchen Shao, Shilin Li, Qiqun Tang and Jianhui Xie
Genes 2020, 11(5), 566; https://doi.org/10.3390/genes11050566 - 19 May 2020
Cited by 3 | Viewed by 2930
Abstract
Y-chromosomal short tandem repeats (Y-STRs) are widely used in human research for the evaluation of population substructure or population differentiation. Previous studies show that several haplotype sets can be used for the evaluation of population differentiation. However, little is known about whether each [...] Read more.
Y-chromosomal short tandem repeats (Y-STRs) are widely used in human research for the evaluation of population substructure or population differentiation. Previous studies show that several haplotype sets can be used for the evaluation of population differentiation. However, little is known about whether each Y-STR in these sets performs well during this procedure. In this study, a total of 20,927 haplotypes of a Yfiler Plus set were collected from 41 global populations. Different configurations were observed in multidimensional scaling (MDS) plots based on pairwise genetic distances evaluated using a Yfiler set and a Yfiler Plus set, respectively. Subsequently, 23 single-copy Y-STRs were characterized in the evaluation of population differentiation using the mean of allele frequency difference (mAFD) between populations. Our results indicated that DYS392 had the largest mAFD value (0.3802) and YGATAH4 had the smallest value (0.1845). On the whole, larger pairwise genetic distances could be obtained using the set with the top fifteen markers from these 23 single-copy Y-STRs, and clear clustering or separation of populations could be observed in the MDS plot in comparison with those using the set with the minimum fifteen markers. In conclusion, the mAFD value is reliable to characterize Y-STRs for efficiency in the evaluation of population differentiation. Full article
(This article belongs to the Special Issue Forensic Genetics and Genomics)
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12 pages, 2678 KiB  
Article
Overcoming Immunological Challenges to Helper-Dependent Adenoviral Vector-Mediated Long-Term CFTR Expression in Mouse Airways
by Huibi Cao, Rongqi Duan and Jim Hu
Genes 2020, 11(5), 565; https://doi.org/10.3390/genes11050565 - 18 May 2020
Cited by 2 | Viewed by 2714
Abstract
Cystic Fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, and CF patients require life-long treatment. Although CFTR modulators show a great potential for treating most CF patients, some individuals may not tolerate the treatment. [...] Read more.
Cystic Fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, and CF patients require life-long treatment. Although CFTR modulators show a great potential for treating most CF patients, some individuals may not tolerate the treatment. In addition, there is no effective therapy for patients with some rare CFTR mutations, such as class I CF mutations, which lead to a lack of CFTR protein production. Therefore, other therapeutic strategies, such as gene therapy, have to be investigated. Currently, immune responses to gene therapy vectors and transgene products are a major obstacle to applying CF gene therapy to clinical applications. In this study, we examined the effects of cyclophosphamide on the modulation of host immune responses and for the improvement of the CFTR transgene expression in the repeated delivery of helper-dependent adenoviral (HD-Ad) vectors to mouse lungs. We have found that cyclophosphamide significantly decreased the expression of T cell genes, such as CD3 (cluster of differentiation 3) and CD4, and reduced their infiltration into mouse lung tissues. We have also found that the levels of the anti-adenoviral antibody and neutralizing activity as well as B-cell infiltration into the mouse lung tissues were significantly reduced with this treatment. Correspondingly, the expression of the human CFTR transgene has been significantly improved with cyclophosphamide administration compared to the group with no treatment. These data suggest that the sustained expression of the human CFTR transgene in mouse lungs through repeated vector delivery can be achieved by transient immunosuppression. Full article
(This article belongs to the Special Issue Molecular Basis and Gene Therapies of Cystic Fibrosis)
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12 pages, 1246 KiB  
Article
Joint Genetic Analyses of Mitochondrial and Y-Chromosome Molecular Markers for a Population from Northwest China
by Yuxin Guo, Zhiyu Xia, Wei Cui, Chong Chen, Xiaoye Jin and Bofeng Zhu
Genes 2020, 11(5), 564; https://doi.org/10.3390/genes11050564 - 18 May 2020
Cited by 4 | Viewed by 9098
Abstract
The genetic markers on mitochondria DNA (mtDNA) and Y-chromosome can be applied as a powerful tool in population genetics. We present a study to reveal the genetic background of Kyrgyz group, a Chinese ethnic group living in northwest China, and genetic polymorphisms of [...] Read more.
The genetic markers on mitochondria DNA (mtDNA) and Y-chromosome can be applied as a powerful tool in population genetics. We present a study to reveal the genetic background of Kyrgyz group, a Chinese ethnic group living in northwest China, and genetic polymorphisms of 60 loci on maternal inherited mtDNA and 24 loci on paternal inherited Y-chromosome short tandem repeats (Y-STRs) were investigated. The relationship between the two systems was tested, and the result indicated that they were statistically independent from each other. The genetic distances between Kyrgyz group and 11 reference populations for mtDNA, and 13 reference populations for Y-STRs were also calculated, respectively. The present results demonstrated that the Kyrgyz group was genetically closer to East Asian populations than European populations based on the mtDNA loci but the other way around for the Y-STRs. The genetic analyses could largely strengthen the understanding for the genetic background of the Kyrgyz group. Full article
(This article belongs to the Special Issue Forensic Genetics and Genomics)
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23 pages, 1278 KiB  
Review
Mitochondrial Protein Quality Control Mechanisms
by Pooja Jadiya and Dhanendra Tomar
Genes 2020, 11(5), 563; https://doi.org/10.3390/genes11050563 - 18 May 2020
Cited by 54 | Viewed by 9693
Abstract
Mitochondria serve as a hub for many cellular processes, including bioenergetics, metabolism, cellular signaling, redox balance, calcium homeostasis, and cell death. The mitochondrial proteome includes over a thousand proteins, encoded by both the mitochondrial and nuclear genomes. The majority (~99%) of proteins are [...] Read more.
Mitochondria serve as a hub for many cellular processes, including bioenergetics, metabolism, cellular signaling, redox balance, calcium homeostasis, and cell death. The mitochondrial proteome includes over a thousand proteins, encoded by both the mitochondrial and nuclear genomes. The majority (~99%) of proteins are nuclear encoded that are synthesized in the cytosol and subsequently imported into the mitochondria. Within the mitochondria, polypeptides fold and assemble into their native functional form. Mitochondria health and integrity depend on correct protein import, folding, and regulated turnover termed as mitochondrial protein quality control (MPQC). Failure to maintain these processes can cause mitochondrial dysfunction that leads to various pathophysiological outcomes and the commencement of diseases. Here, we summarize the current knowledge about the role of different MPQC regulatory systems such as mitochondrial chaperones, proteases, the ubiquitin-proteasome system, mitochondrial unfolded protein response, mitophagy, and mitochondria-derived vesicles in the maintenance of mitochondrial proteome and health. The proper understanding of mitochondrial protein quality control mechanisms will provide relevant insights to treat multiple human diseases. Full article
(This article belongs to the Special Issue Mitochondrial Calcium Signaling, Mitochondrial Dynamics, and Mitophagy)
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15 pages, 1755 KiB  
Article
Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.)
by Jeonghwan Seo, So-Myeong Lee, Jae-Hyuk Han, Na-Hyun Shin, Yoon Kyung Lee, Backki Kim, Joong Hyoun Chin and Hee-Jong Koh
Genes 2020, 11(5), 562; https://doi.org/10.3390/genes11050562 - 18 May 2020
Cited by 3 | Viewed by 3425
Abstract
The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the [...] Read more.
The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the four non-HYVs. The Next-Generation Sequencing (NGS) mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of japonica-originated alleles. Interestingly, the HYVs shared japonica-originated genomic regions on nine chromosomes, although they were developed through different breeding programs. A panel of 94 varieties was classified into four varietal groups with 38 single nucleotide polymorphism (SNP) markers from 38 genes residing in the japonica-originated genomic regions and 16 additional trait-specific SNPs. As expected, the japonica-originated genomic regions were only present in the japonica (JAP) and HYV groups, except for Chr4-1 and Chr4-2. The Wx gene, located within Chr6-1, was present in the HYV and JAP variety groups, while the yield-related genes were conserved as indica alleles in HYVs. The japonica-originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs to further develop the HYVs in temperate rice. Full article
(This article belongs to the Special Issue Recent Advances in Genetics and Breeding of Major Staple Food Crops)
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12 pages, 1507 KiB  
Article
Exome-Wide Analysis of the DiscovEHR Cohort Reveals Novel Candidate Pharmacogenomic Variants for Clinical Pharmacogenomics
by Maria-Theodora Pandi, Marc S. Williams, Peter van der Spek, Maria Koromina and George P. Patrinos
Genes 2020, 11(5), 561; https://doi.org/10.3390/genes11050561 - 18 May 2020
Cited by 4 | Viewed by 3423
Abstract
Recent advances in next-generation sequencing technology have led to the production of an unprecedented volume of genomic data, thus further advancing our understanding of the role of genetic variation in clinical pharmacogenomics. In the present study, we used whole exome sequencing data from [...] Read more.
Recent advances in next-generation sequencing technology have led to the production of an unprecedented volume of genomic data, thus further advancing our understanding of the role of genetic variation in clinical pharmacogenomics. In the present study, we used whole exome sequencing data from 50,726 participants, as derived from the DiscovEHR cohort, to identify pharmacogenomic variants of potential clinical relevance, according to their occurrence within the PharmGKB database. We further assessed the distribution of the identified rare and common pharmacogenomics variants amongst different GnomAD subpopulations. Overall, our findings show that the use of publicly available sequence data, such as the DiscovEHR dataset and GnomAD, provides an opportunity for a deeper understanding of genetic variation in pharmacogenes with direct implications in clinical pharmacogenomics. Full article
(This article belongs to the Special Issue Translational Bioinformatics: From Prediction to Validation)
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11 pages, 716 KiB  
Article
The Q223R Polymorphism of the Leptin Receptor Gene as a Predictor of Weight Gain in Childhood Obesity and the Identification of Possible Factors Involved
by Helena Marcos-Pasero, Elena Aguilar-Aguilar, Gonzalo Colmenarejo, Ana Ramírez de Molina, Guillermo Reglero and Viviana Loria-Kohen
Genes 2020, 11(5), 560; https://doi.org/10.3390/genes11050560 - 17 May 2020
Cited by 8 | Viewed by 3539
Abstract
(1) Background: Childhood rapid weight gain during development has been postulated as a predictor of obesity. The objective of this study was to investigate the effect of single nucleotide polymorphisms (SNPs) on the annual weight gain and height growth, as well as identifying [...] Read more.
(1) Background: Childhood rapid weight gain during development has been postulated as a predictor of obesity. The objective of this study was to investigate the effect of single nucleotide polymorphisms (SNPs) on the annual weight gain and height growth, as well as identifying possible lifestyle factors involved. (2) Methods: As part of the GENYAL study, 221 children (6–8 years old) of Madrid (Spain) were enrolled. A total of 11 SNPs associated with high childhood body mass indexes (BMIs) were assessed. Anthropometric measurements, dietary and physical activity data, were collected in 2017 and 2018. Bonferroni-corrected linear models were used to fit the data. (3) Results: A significant association between the Q223R LEPR and the weight growth was found, showing a different behavior between GA and GG genotypes (p = 0.001). Regarding lifestyle factors, an interaction between Q223R genotypes and total active weekly hours/week to predict the weight growth (kg/year) was observed (p = 0.023). In all the genotypes, a beneficial effect against rapid weight growth was observed, but the effect size of the interaction was much more significant in homozygous (GG) minor homozygous (β = −0.61 (−0.95, −0.26) versus heterozygous (AG) and wild-type homozygous (AA) genotypes (β = −0.07 (−0.24, 0.09) and β = −0.12 (−0.32, 0.08), respectively). (4) Conclusions: These results may contribute to more personalized recommendations to prevent childhood obesity. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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15 pages, 1137 KiB  
Article
Differences in Gene Expression Profiles of Seven Target Proteins in Third-Stage Larvae of Anisakis simplex (Sensu Stricto) by Sites of Infection in Blue Whiting (Micromesistius poutassou)
by Marialetizia Palomba, Paolo Cipriani, Lucilla Giulietti, Arne Levsen, Giuseppe Nascetti and Simonetta Mattiucci
Genes 2020, 11(5), 559; https://doi.org/10.3390/genes11050559 - 17 May 2020
Cited by 15 | Viewed by 3623
Abstract
The third-stage larvae of the parasitic nematode genus Anisakis tend to encapsulate in different tissues including the musculature of fish. Host tissue penetration and degradation involve both mechanic processes and the production of proteins encoded by an array of genes. Investigating larval gene [...] Read more.
The third-stage larvae of the parasitic nematode genus Anisakis tend to encapsulate in different tissues including the musculature of fish. Host tissue penetration and degradation involve both mechanic processes and the production of proteins encoded by an array of genes. Investigating larval gene profiles during the fish infection has relevance in understanding biological traits in the parasite’s adaptive ability to cope with the fish hosts’ defense responses. The present study aimed to investigate the gene expression levels of some proteins in L3 of A. simplex (s.s.) infecting different tissues of blue whiting Micromesistius poutassou, a common fish host of the parasite in the NE Atlantic. The following genes encoding for Anisakis spp. proteins were studied: Kunitz-type trypsin inhibitor (TI), hemoglobin (hb), glycoprotein (GP), trehalase (treh), zinc metallopeptidase 13 (nas 13), ubiquitin-protein ligase (hyd) and sideroflexin 2 (sfxn 2). Significant differences in gene transcripts (by quantitative real-time PCR, qPCR) were observed in larvae located in various tissues of the fish host, with respect to the control. ANOVA analysis showed that relative gene expression levels of the seven target genes in the larvae are linked to the infection site in the fish host. Genes encoding some of the target proteins seem to be involved in the host tissue migration and survival of the parasite in the hostile target tissues of the fish host. Full article
(This article belongs to the Special Issue Novel Omics Studies on Anisakid Nematodes)
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