Genes

9 pages, 1737 KiB

Open AccessArticle

Danio Rerio as Model Organism for Adenoviral Vector Evaluation

by Paola Gulías, Jorge Guerra-Varela, Manuela Gonzalez-Aparicio, Ana Ricobaraza, Africa Vales, Gloria Gonzalez-Aseguinolaza, Rubén Hernandez-Alcoceba and Laura Sánchez

Genes 2019, 10(12), 1053; https://doi.org/10.3390/genes10121053 - 17 Dec 2019

Cited by 7 | Viewed by 3556

Abstract

Viral vector use is wide-spread in the field of gene therapy, with new clinical trials starting every year for different human pathologies and a growing number of agents being approved by regulatory agencies. However, preclinical testing is long and expensive, especially during the [...] Read more.

Viral vector use is wide-spread in the field of gene therapy, with new clinical trials starting every year for different human pathologies and a growing number of agents being approved by regulatory agencies. However, preclinical testing is long and expensive, especially during the early stages of development. Nowadays, the model organism par excellence is the mouse (Mus musculus), and there are few investigations in which alternative models are used. Here, we assess the possibility of using zebrafish (Danio rerio) as an in vivo model for adenoviral vectors. We describe how E1/E3-deleted adenoviral vectors achieve efficient transduction when they are administered to zebrafish embryos via intracranial injection. In addition, helper-dependent (high-capacity) adenoviral vectors allow sustained transgene expression in this organism. Taking into account the wide repertoire of genetically modified zebrafish lines, the ethical aspects, and the affordability of this model, we conclude that zebrafish could be an efficient alternative for the early-stage preclinical evaluation of adenoviral vectors. Full article

(This article belongs to the Special Issue Zebrafish Animal Models)

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14 pages, 1607 KiB

Open AccessArticle

Autism in Fragile X Syndrome; A Functional MRI Study of Facial Emotion-Processing

by Andrew G. McKechanie, Sonya Campbell, Sarah E. A. Eley and Andrew C. Stanfield

Genes 2019, 10(12), 1052; https://doi.org/10.3390/genes10121052 - 17 Dec 2019

Cited by 5 | Viewed by 3293

Abstract

Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability and autism spectrum disorder, and among those with fragile X syndrome, approximately 1/3rd meet a threshold for an autism spectrum disorder (ASD) diagnosis. Previous functional imaging studies of fragile X [...] Read more.

Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability and autism spectrum disorder, and among those with fragile X syndrome, approximately 1/3rd meet a threshold for an autism spectrum disorder (ASD) diagnosis. Previous functional imaging studies of fragile X syndrome have typically focused on those with fragile X syndrome compared to either neurotypical or autism spectrum disorder control groups. Further, the majority of previous studies have tended to focus on those who are more intellectually able than is typical for fragile X syndrome. In this study, we examine the impact of autistic traits in individuals with fragile X syndrome on a paradigm looking at facial emotion processing. The study included 17 individuals with fragile X syndrome, of whom 10 met criteria for autism as measured by the Autism Diagnostic Observation Schedule (ADOS). Prior to the scan, participants rehearsed on a mock scanner to help acclimatize to the scanner environment and thus allow more severely affected individuals to participate. The task examined the blood-oxygen-level-dependent (BOLD) response to fearful and neutral faces taken from the Ekman faces series. Individuals in the autism group had a region of significantly reduced activity centered on the left superior temporal gyrus, compared to those with FXS alone, in response to the fearful faces. We suggest that autism in individuals with fragile X syndrome is associated with similar changes in the neurobiology of facial emotion processing as seen in idiopathic autism. Full article

(This article belongs to the Special Issue Selected Papers from the International Workshop on Fragile X and Other Neurodevelopmental Disorders)

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9 pages, 214 KiB

Open AccessArticle

A 24-Month Follow-Up Study of the Effect of Intra-Articular Injection of Autologous Microfragmented Fat Tissue on Proteoglycan Synthesis in Patients with Knee Osteoarthritis

by Igor Borić, Damir Hudetz, Eduard Rod, Željko Jeleč, Trpimir Vrdoljak, Andrea Skelin, Ozren Polašek, Mihovil Plečko, Irena Trbojević-Akmačić, Gordan Lauc and Dragan Primorac

Genes 2019, 10(12), 1051; https://doi.org/10.3390/genes10121051 - 17 Dec 2019

Cited by 43 | Viewed by 4460

Abstract

Osteoarthritis (OA) is a widely prevalent disease worldwide, and with an increasingly ageing society, it has become a challenge for the field of regenerative medicine. OA is a disease process involving multiple joint tissues, including those not visible on radiography, and is a [...] Read more.

Osteoarthritis (OA) is a widely prevalent disease worldwide, and with an increasingly ageing society, it has become a challenge for the field of regenerative medicine. OA is a disease process involving multiple joint tissues, including those not visible on radiography, and is a complex disease process with multiple phenotypes that require evaluation by a multimodality imaging assessment. The purpose of this study was to evaluate the effect of micro-fragmented fat tissue intra-articular injection 24 months after application in two ways: Indirectly using functional magnetic resonance imaging (MRI) assessment analyzing the glycosaminoglycans (GAG) content in cartilage by means of delayed gadolinium (Gd)-enhanced magnetic resonance imaging of cartilage (dGEMRIC), as well as clinical outcome on observed level of GAG using standard orthopedic physical examination including VAS assessment. In our previous study assessing comprehensive results after 12 months, the dGEMRIC results have drawn attention. The present study explores the long-term effect of intra-articular injection of autologous microfragmented adipose tissue to host chondrocytes and cartilage proteoglycans in patients with knee OA. A prospective, non-randomized, interventional, single-center, open-label clinical trial was conducted from January 2016 to April 2018. A total of 17 patients were enrolled in the study, and 32 knees were assessed in a 12-month follow-up, but only 10 patients of them with 18 knees are included in a 24-month follow-up. The rest of the seven patients dropped out of the study 12 months after follow-up: three patients underwent knee arthroplasty, and the remaining four did not fulfil the basic criteria of 24 months involvement in the study. Surgical intervention (lipoaspiration), followed by tissue processing and intra-articular injection of the final microfragmented adipose tissue product into the affected knee(s), was performed in all patients. Patients were assessed for a visual analog scale (VAS), dGEMRIC at the baseline, three, six, 12 and 24 months after the treatment. A magnetic resonance sequence in dGEMRIC due to infiltration of the anionic, negatively-charged contrast gadopentetate dimeglumine (Gd-DTPA2) into the cartilage indicated that the contents of cartilage glycosaminoglycans significantly increased in specific areas of the treated knee joint. Our results suggest that this method of single intra-articular injection of autologous microfragmented adipose tissue improves GAG content on a significant scale, with over half of the measurements suggesting relevant improvement 24 months after intra-articular injection opposed to the expected GAG decrease over the natural course of the disease. Full article

(This article belongs to the Special Issue Stem Cells Application in Clinical Practice: Advances and Challenges)

22 pages, 2391 KiB

Open AccessReview

The Spectrum of PAX6 Mutations and Genotype-Phenotype Correlations in the Eye

by Dulce Lima Cunha, Gavin Arno, Marta Corton and Mariya Moosajee

Genes 2019, 10(12), 1050; https://doi.org/10.3390/genes10121050 - 17 Dec 2019

Cited by 95 | Viewed by 13452

Abstract

The transcription factor PAX6 is essential in ocular development in vertebrates, being considered the master regulator of the eye. During eye development, it is essential for the correct patterning and formation of the multi-layered optic cup and it is involved in the developing [...] Read more.

The transcription factor PAX6 is essential in ocular development in vertebrates, being considered the master regulator of the eye. During eye development, it is essential for the correct patterning and formation of the multi-layered optic cup and it is involved in the developing lens and corneal epithelium. In adulthood, it is mostly expressed in cornea, iris, and lens. PAX6 is a dosage-sensitive gene and it is highly regulated by several elements located upstream, downstream, and within the gene. There are more than 500 different mutations described to affect PAX6 and its regulatory regions, the majority of which lead to PAX6 haploinsufficiency, causing several ocular and systemic abnormalities. Aniridia is an autosomal dominant disorder that is marked by the complete or partial absence of the iris, foveal hypoplasia, and nystagmus, and is caused by heterozygous PAX6 mutations. Other ocular abnormalities have also been associated with PAX6 changes, and genotype-phenotype correlations are emerging. This review will cover recent advancements in PAX6 regulation, particularly the role of several enhancers that are known to regulate PAX6 during eye development and disease. We will also present an updated overview of the mutation spectrum, where an increasing number of mutations in the non-coding regions have been reported. Novel genotype-phenotype correlations will also be discussed. Full article

(This article belongs to the Special Issue Recent Advances in Inherited Eye Disease)

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13 pages, 898 KiB

Open AccessReview

Exploring Mammalian Genome within Phase-Separated Nuclear Bodies: Experimental Methods and Implications for Gene Expression

by Annick Lesne, Marie-Odile Baudement, Cosette Rebouissou and Thierry Forné

Genes 2019, 10(12), 1049; https://doi.org/10.3390/genes10121049 - 17 Dec 2019

Cited by 13 | Viewed by 5704

Abstract

The importance of genome organization at the supranucleosomal scale in the control of gene expression is increasingly recognized today. In mammals, Topologically Associating Domains (TADs) and the active/inactive chromosomal compartments are two of the main nuclear structures that contribute to this organization level. [...] Read more.

The importance of genome organization at the supranucleosomal scale in the control of gene expression is increasingly recognized today. In mammals, Topologically Associating Domains (TADs) and the active/inactive chromosomal compartments are two of the main nuclear structures that contribute to this organization level. However, recent works reviewed here indicate that, at specific loci, chromatin interactions with nuclear bodies could also be crucial to regulate genome functions, in particular transcription. They moreover suggest that these nuclear bodies are membrane-less organelles dynamically self-assembled and disassembled through mechanisms of phase separation. We have recently developed a novel genome-wide experimental method, High-salt Recovered Sequences sequencing (HRS-seq), which allows the identification of chromatin regions associated with large ribonucleoprotein (RNP) complexes and nuclear bodies. We argue that the physical nature of such RNP complexes and nuclear bodies appears to be central in their ability to promote efficient interactions between distant genomic regions. The development of novel experimental approaches, including our HRS-seq method, is opening new avenues to understand how self-assembly of phase-separated nuclear bodies possibly contributes to mammalian genome organization and gene expression. Full article

(This article belongs to the Special Issue Disentangling Mechanisms of Genomic Regulation of Cell Functions at the Gene Level)

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12 pages, 1223 KiB

Open AccessArticle

A Novel Arsenate-Resistant Determinant Associated with ICEpMERPH, a Member of the SXT/R391 Group of Mobile Genetic Elements

by Michael P. Ryan, Shannon Slattery and J. Tony Pembroke

Genes 2019, 10(12), 1048; https://doi.org/10.3390/genes10121048 - 16 Dec 2019

Cited by 6 | Viewed by 3236

Abstract

ICEpMERPH, the first integrative conjugative element (ICE) of the SXT/R391 family isolated in the United Kingdom and Europe, was analyzed to determine the nature of its adaptive functions, its genetic structure, and its homology to related elements normally found in pathogenic Vibrio or [...] Read more.

ICEpMERPH, the first integrative conjugative element (ICE) of the SXT/R391 family isolated in the United Kingdom and Europe, was analyzed to determine the nature of its adaptive functions, its genetic structure, and its homology to related elements normally found in pathogenic Vibrio or Proteus species. Whole genome sequencing of Escherichia coli (E. coli) isolate K802 (which contains the ICEpMERPH) was carried out using Illumina sequencing technology. ICEpMERPH has a size of 110 Kb and 112 putative open reading frames (ORFs). The “hotspot regions” of the element were found to contain putative restriction digestion systems, insertion sequences, and heavy metal resistance genes that encoded resistance to mercury, as previously reported, but also surprisingly to arsenate. A novel arsenate resistance system was identified in hotspot 4 of the element, unrelated to other SXT/R391 elements. This arsenate resistance system was potentially linked to two genes: orf69, encoding an organoarsenical efflux major facilitator superfamily (MFS) transporter-like protein related to ArsJ, and orf70, encoding nicotinamide adenine dinucleotide (NAD)-dependent glyceraldehyde-3-phosphate dehydrogenase. Phenotypic analysis using isogenic strains of Escherichia coli strain AB1157 with and without the ICEpMERPH revealed resistance to low levels of arsenate in the range of 1–5 mM. This novel, low-level resistance may have an important adaptive function in polluted environments, which often contain low levels of arsenate contamination. A bioinformatic analysis on the novel determinant and the phylogeny of ICEpMERPH was presented. Full article

(This article belongs to the Special Issue Genomic Islands)

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16 pages, 3058 KiB

Open AccessArticle

Next Generation Sequencing Identifies Five Novel Mutations in Lebanese Patients with Bardet–Biedl and Usher Syndromes

by Lama Jaffal, Wissam H Joumaa, Alexandre Assi, Charles Helou, George Cherfan, Kazem Zibara, Isabelle Audo, Christina Zeitz and Said El Shamieh

Genes 2019, 10(12), 1047; https://doi.org/10.3390/genes10121047 - 16 Dec 2019

Cited by 8 | Viewed by 3314

Abstract

Aim: To identify disease-causing mutations in four Lebanese families: three families with Bardet–Biedl and one family with Usher syndrome (BBS and USH respectively), using next generation sequencing (NGS). Methods: We applied targeted NGS in two families and whole exome sequencing (WES) in two [...] Read more.

Aim: To identify disease-causing mutations in four Lebanese families: three families with Bardet–Biedl and one family with Usher syndrome (BBS and USH respectively), using next generation sequencing (NGS). Methods: We applied targeted NGS in two families and whole exome sequencing (WES) in two other families. Pathogenicity of candidate mutations was evaluated according to frequency, conservation, in silico prediction tools, segregation with disease, and compatibility with inheritance pattern. The presence of pathogenic variants was confirmed via Sanger sequencing followed by segregation analysis. Results: Most likely disease-causing mutations were identified in all included patients. In BBS patients, we found (M1): c.2258A > T, p. (Glu753Val) in BBS9, (M2): c.68T > C; p. (Leu23Pro) in ARL6, (M3): c.265_266delTT; p. (Leu89Valfs*11) and (M4): c.880T > G; p. (Tyr294Asp) in BBS12. A previously known variant (M5): c.551A > G; p. (Asp184Ser) was also detected in BBS5. In the USH patient, we found (M6): c.188A > C, p. (Tyr63Ser) in CLRN1. M2, M3, M4, and M6 were novel. All of the candidate mutations were shown to be likely disease-causing through our bioinformatic analysis. They also segregated with the corresponding phenotype in available family members. Conclusion: This study expanded the mutational spectrum and showed the genetic diversity of BBS and USH. It also spotlighted the efficiency of NGS techniques in revealing mutations underlying clinically and genetically heterogeneous disorders. Full article

(This article belongs to the Special Issue Molecular Genetics of Retinal Dystrophies)

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9 pages, 676 KiB

Open AccessArticle

Increased Overall Mortality Even after Risk Reducing Surgery for BRCA-Positive Women in Western Sweden

by Anna Öfverholm, Zakaria Einbeigi, Antonia Wigermo, Erik Holmberg and Per Karsson

Genes 2019, 10(12), 1046; https://doi.org/10.3390/genes10121046 - 16 Dec 2019

Cited by 3 | Viewed by 2680

Abstract

Women with BRCA variants have a high lifetime risk of developing breast and ovarian cancer. The aim of this study was to investigate the standard incidence ratios (SIR) for breast and ovarian cancer and standard mortality ratios (SMR) in a population-based cohort of [...] Read more.

Women with BRCA variants have a high lifetime risk of developing breast and ovarian cancer. The aim of this study was to investigate the standard incidence ratios (SIR) for breast and ovarian cancer and standard mortality ratios (SMR) in a population-based cohort of women in Western Sweden, under surveillance and after risk reducing surgery. Women who tested positive for a BRCA variant between 1995–2016 (n = 489) were prospectively registered and followed up for cancer incidence, risk reducing surgery and mortality. The Swedish Cancer Register was used to compare breast and ovarian cancer incidence and mortality with and without risk reducing surgery for women with BRCA variants in comparison to women in the general population. SIR for breast cancer under surveillance until risk-reducing mastectomy (RRM) was 14.0 (95% CI 9.42–20.7) and decreased to 1.93 (95% CI 0.48–7.7) after RRM. The SIR for ovarian cancer was 124.6 (95% CI 59.4–261.3) under surveillance until risk reducing salpingo-oophorectomy (RRSO) and decreased to 13.5 (95% CI 4.34–41.8) after RRSO. The SMR under surveillance before any risk reducing surgery was 5.56 (95% 2.09–14.8) and after both RRM and RRSO 4.32 (95% CI 1.62–11.5). Women with cancer diagnoses from the pathology report after risk reducing surgery were excluded from the analyses. Risk reducing surgery reduced the incidence of breast and ovarian cancer in women with BRCA variants. However, overall mortality was significantly increased in comparison to the women in the general population and remained elevated even after risk reducing surgery. These findings warrant further research regarding additional measures for these women. Full article

(This article belongs to the Special Issue Functional Role of BRCA 1 and 2 in Tissue Maintenance and Neoplasia)

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14 pages, 3186 KiB

Open AccessArticle

Expression Profile of Laccase Gene Family in White-Rot Basidiomycete Lentinula edodes under Different Environmental Stresses

by Lianlian Yan, Ruiping Xu, Yinbing Bian, Hongxian Li and Yan Zhou

Genes 2019, 10(12), 1045; https://doi.org/10.3390/genes10121045 - 16 Dec 2019

Cited by 16 | Viewed by 2945

Abstract

Laccases belong to ligninolytic enzymes and play important roles in various biological processes of filamentous fungi, including fruiting-body formation and lignin degradation. The process of fruiting-body development in Lentinula edodes is complex and is greatly affected by environmental conditions. In this paper, 14 [...] Read more.

Laccases belong to ligninolytic enzymes and play important roles in various biological processes of filamentous fungi, including fruiting-body formation and lignin degradation. The process of fruiting-body development in Lentinula edodes is complex and is greatly affected by environmental conditions. In this paper, 14 multicopper oxidase-encoding (laccase) genes were analyzed in the draft genome sequence of L. edodes strain W1-26, followed by a search of multiple stress-related Cis-elements in the promoter region of these laccase genes, and then a transcription profile analysis of 14 laccase genes (Lelcc) under the conditions of different carbon sources, temperatures, and photoperiods. All laccase genes were significantly regulated by varying carbon source materials. The expression of only two laccase genes (Lelcc5 and Lelcc6) was induced by sodium-lignosulphonate and the expression of most laccase genes was specifically upregulated in glucose medium. Under different temperature conditions, the expression levels of most laccase genes decreased at 39 °C and transcription was significantly increased for Lelcc1, Lelcc4, Lelcc5, Lelcc9, Lelcc12, Lelcc13, and Lelcc14 after induction for 24 h at 10 °C, indicating their involvement in primordium differentiation. Tyrosinase, which is involved in melanin synthesis, was clustered with the same group as Lelcc4 and Lelcc7 in all the different photoperiod treatments. Meanwhile, five laccase genes (Lelcc8, Lelcc9, Lelcc12, Lelcc13, and Lelcc14) showed similar expression profiles to that of two blue light receptor genes (LephrA and LephrB) in the 12 h light/12 h dark treatment, suggesting the involvement of laccase genes in the adaptation process of L. edodes to the changing environment and fruiting-body formation. This study contributes to our understanding of the function of the different Lelcc genes and facilitates the screening of key genes from the laccase gene family for further functional research. Full article

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

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8 pages, 1246 KiB

Open AccessArticle

Real-Time Quantitative PCR Analysis of the Expression Pattern of the Hypoglycemic Polypeptide-P Gene in Momordica charantia

by Yi-Shuai Wang, Xiang-Qing Zeng, Xu-Zhong Yang, Wei Liu, Peng-Fei Li, Fu-Jun Wang and Jian Zhao

Genes 2019, 10(12), 1044; https://doi.org/10.3390/genes10121044 - 16 Dec 2019

Cited by 1 | Viewed by 2817

Abstract

This study was designed to establish a real-time quantitative polymerase chain reaction (qPCR) method to rapidly and reliably analyze the hypoglycemic polypeptide-P gene expression pattern in Momordica charantia (MC) and to examine its expression changes in different MC accessions, harvesting seasons, and tissue [...] Read more.

This study was designed to establish a real-time quantitative polymerase chain reaction (qPCR) method to rapidly and reliably analyze the hypoglycemic polypeptide-P gene expression pattern in Momordica charantia (MC) and to examine its expression changes in different MC accessions, harvesting seasons, and tissue types. The qPCR results were further verified by using Western blotting (WB). A total of 10 MCs with different accessions were collected and tested in this study. Among the tested accessions, RU5H showed the highest expression level of the polypeptide-P gene. The expression level of the polypeptide-P gene was not only season-related (with the highest in early July) but also tissue-related (with the highest in the seed tissue). In addition, the expression characteristic of the polypeptide-P gene was maturity-related, with the highest expression level in the tender MC. The WB results show that the transcription level of this gene shows an almost similar trend to the corresponding protein expression level. In conclusion, the established qPCR method can rapidly and effectively detect the expression levels of the polypeptide-P gene in MCs with different accessions; furthermore, various factors, including the accessions, harvesting seasons, and tissue types can affect the expression level. Full article

(This article belongs to the Special Issue Biotechnology Tools and Genetic Medicine)

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5 pages, 413 KiB

Open AccessEditorial

Genetic and Epigenetic Modulation of Cell Functions by Physical Exercise

by Italia Di Liegro

Genes 2019, 10(12), 1043; https://doi.org/10.3390/genes10121043 - 16 Dec 2019

Cited by 6 | Viewed by 4265

Abstract

Since ancient times, the importance of physical activity (PA) and of a wholesome diet for human health has been clearly recognized. However, only recently, it has been acknowledged that PA can reverse at least some of the unwanted effects of a sedentary lifestyle, [...] Read more.

Since ancient times, the importance of physical activity (PA) and of a wholesome diet for human health has been clearly recognized. However, only recently, it has been acknowledged that PA can reverse at least some of the unwanted effects of a sedentary lifestyle, contributing to the treatment of pathologies such as hypertension and diabetes, to the delay of aging and neurodegeneration, and even to the improvement of immunity and cognitive processes. At the same time, the cellular and molecular bases of these effects are beginning to be uncovered. The original research articles and reviews published in this Special Issue on “Genetic and Epigenetic Modulation of Cell Functions by Physical Exercise” focus on different aspects of the genetics and molecular biology of PA effects on health and, in addition, on the effects of different genotypes on the ability to perform PA. All authors have read and agreed to the published version of the manuscript. Full article

(This article belongs to the Special Issue Genetic and Epigenetic Modulation of Cell Functions by Physical Exercise)

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Graphical abstract

19 pages, 3063 KiB

Open AccessArticle

RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49

by Karina B. Ruiz, Jonathan Maldonado, Stefania Biondi and Herman Silva

Genes 2019, 10(12), 1042; https://doi.org/10.3390/genes10121042 - 16 Dec 2019

Cited by 17 | Viewed by 4008

Abstract

Quinoa (Chenopodium quinoa Willd.), a model halophytic crop species, was used to shed light on salt tolerance mechanisms at the transcriptomic level. An RNA-sequencing analysis of genotype R49 at an early vegetative stage was performed by Illumina paired-ends method comparing high salinity [...] Read more.

Quinoa (Chenopodium quinoa Willd.), a model halophytic crop species, was used to shed light on salt tolerance mechanisms at the transcriptomic level. An RNA-sequencing analysis of genotype R49 at an early vegetative stage was performed by Illumina paired-ends method comparing high salinity and control conditions in a time-course pot experiment. Genome-wide transcriptional salt-induced changes and expression profiling of relevant salt-responsive genes in plants treated or not with 300 mM NaCl were analyzed after 1 h and 5 days. We obtained up to 49 million pairs of short reads with an average length of 101 bp, identifying a total of 2416 differentially expressed genes (DEGs) based on the treatment and time of sampling. In salt-treated vs. control plants, the total number of up-regulated and down-regulated genes was 945 and 1471, respectively. The number of DEGs was higher at 5 days than at 1 h after salt treatment, as reflected in the number of transcription factors, which increased with time. We report a strong transcriptional reprogramming of genes involved in biological processes like oxidation-reduction, response to stress and response to abscisic acid (ABA), and cell wall organization. Transcript analyses by real-time RT- qPCR supported the RNA-seq results and shed light on the contribution of roots and shoots to the overall transcriptional response. In addition, it revealed a time-dependent response in the expression of the analyzed DEGs, including a quick (within 1 h) response for some genes, suggesting a “stress-anticipatory preparedness” in this highly salt-tolerant genotype. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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27 pages, 5264 KiB

Open AccessArticle

Transcriptome Profiling, Biochemical and Physiological Analyses Provide New Insights towards Drought Tolerance in Nicotiana tabacum L.

by Rayyan Khan, Peilu Zhou, Xinghua Ma, Lei Zhou, Yuanhua Wu, Zia Ullah and Shusheng Wang

Genes 2019, 10(12), 1041; https://doi.org/10.3390/genes10121041 - 15 Dec 2019

Cited by 22 | Viewed by 4288

Abstract

Drought stress is one of the main factors limiting crop production, which provokes a number of changes in plants at physiological, anatomical, biochemical and molecular level. To unravel the various mechanisms underpinning tobacco (Nicotiana tabacum L.) drought stress tolerance, we conducted a [...] Read more.

Drought stress is one of the main factors limiting crop production, which provokes a number of changes in plants at physiological, anatomical, biochemical and molecular level. To unravel the various mechanisms underpinning tobacco (Nicotiana tabacum L.) drought stress tolerance, we conducted a comprehensive physiological, anatomical, biochemical and transcriptome analyses of three tobacco cultivars (i.e., HongHuaDaJinYuan (H), NC55 (N) and Yun Yan-100 (Y)) seedlings that had been exposed to drought stress. As a result, H maintained higher growth in term of less reduction in plant fresh weight, dry weight and chlorophyll content as compared with N and Y. Anatomical studies unveiled that drought stress had little effect on H by maintaining proper leaf anatomy while there were significant changes in the leaf anatomy of N and Y. Similarly, H among the three varieties was the least affected variety under drought stress, with more proline content accumulation and a powerful antioxidant defense system, which mitigates the negative impacts of reactive oxygen species. The transcriptomic analysis showed that the differential genes expression between HongHuaDaJinYuan, NC55 and Yun Yan-100 were enriched in the functions of plant hormone signal transduction, starch and sucrose metabolism, and arginine and proline metabolism. Compared to N and Y, the differentially expressed genes of H displayed enhanced expression in the corresponding pathways under drought stress. Together, our findings offer insights that H was more tolerant than the other two varieties, as evidenced at physiological, biochemical, anatomical and molecular level. These findings can help us to enhance our understanding of the molecular mechanisms through the networks of various metabolic pathways mediating drought stress adaptation in tobacco. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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12 pages, 2252 KiB

Open AccessArticle

Skim-Sequencing Reveals the Likely Origin of the Enigmatic Endangered Sunflower Helianthus schweinitzii

by Justin Anderson, Michael Kantar, Dan Bock, Kunsiri Chaw Grubbs, Edward Schilling and Loren Rieseberg

Genes 2019, 10(12), 1040; https://doi.org/10.3390/genes10121040 - 15 Dec 2019

Cited by 2 | Viewed by 3073

Abstract

Resolving the origin of endangered taxa is an essential component of conservation. This information can be used to guide efforts of bolstering genetic diversity, and also enables species recovery and future evolutionary studies. Here, we used low-coverage whole genome sequencing to clarify the [...] Read more.

Resolving the origin of endangered taxa is an essential component of conservation. This information can be used to guide efforts of bolstering genetic diversity, and also enables species recovery and future evolutionary studies. Here, we used low-coverage whole genome sequencing to clarify the origin of Helianthus schweinitzii, an endangered tetraploid sunflower that is endemic to the Piedmont Plateau in the eastern United States. We surveyed four accessions representing four populations of H. schweinitzii and 38 accessions of six purported parental species. Using de novo approaches, we assembled 87,004 bp of the chloroplast genome and 6770 bp of the nuclear 35S rDNA. Phylogenetic reconstructions based on the chloroplast genome revealed no reciprocal monophyly of taxa. In contrast, nuclear rDNA data strongly supported the currently accepted sections of the genus Helianthus. Information from combined cpDNA and rDNA provided evidence that H. schweinitzii is likely an allo-tetraploid that formed as a result of hybridization between the diploids Helianthus giganteus and Helianthus microcephalus. Full article

(This article belongs to the Special Issue Sunflower Genetics)

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22 pages, 3733 KiB

Open AccessArticle

Transcriptomic Profiling Identifies Candidate Genes Involved in the Salt Tolerance of the Xerophyte Pugionium cornutum

by Yan-Nong Cui, Fang-Zhen Wang, Cheng-Hang Yang, Jian-Zhen Yuan, Huan Guo, Jin-Lin Zhang, Suo-Min Wang and Qing Ma

Genes 2019, 10(12), 1039; https://doi.org/10.3390/genes10121039 - 12 Dec 2019

Cited by 13 | Viewed by 2521

Abstract

The xerophyte Pugionium cornutum adapts to salt stress by accumulating inorganic ions (e.g., Cl⁻) for osmotic adjustment and enhancing the activity of antioxidant enzymes, but the associated molecular basis remains unclear. In this study, we first found that P. cornutum could [...] Read more.

The xerophyte Pugionium cornutum adapts to salt stress by accumulating inorganic ions (e.g., Cl⁻) for osmotic adjustment and enhancing the activity of antioxidant enzymes, but the associated molecular basis remains unclear. In this study, we first found that P. cornutum could also maintain cell membrane stability due to its prominent ROS-scavenging ability and exhibits efficient carbon assimilation capacity under salt stress. Then, the candidate genes associated with the important physiological traits of the salt tolerance of P. cornutum were identified through transcriptomic analysis. The results showed that after 50 mM NaCl treatment for 6 or 24 h, multiple genes encoding proteins facilitating Cl⁻ accumulation and NO₃⁻ homeostasis, as well as the transport of other major inorganic osmoticums, were significantly upregulated in roots and shoots, which should be favorable for enhancing osmotic adjustment capacity and maintaining the uptake and transport of nutrient elements; a large number of genes related to ROS-scavenging pathways were also significantly upregulated, which might be beneficial for mitigating salt-induced oxidative damage to the cells. Meanwhile, many genes encoding components of the photosynthetic electron transport pathway and carbon fixation enzymes were significantly upregulated in shoots, possibly resulting in high carbon assimilation efficiency in P. cornutum. Additionally, numerous salt-inducible transcription factor genes that probably regulate the abovementioned processes were found. This work lays a preliminary foundation for clarifying the molecular mechanism underlying the adaptation of xerophytes to harsh environments. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants: Current Challenges and Perspectives)

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19 pages, 3305 KiB

Open AccessArticle

Regulation of AMH, AMHR-II, and BMPs (2,6) Genes of Bovine Granulosa Cells Treated with Exogenous FSH and Their Association with Protein Hormones

by Saqib Umer, Abdul Sammad, Huiying Zou, Adnan Khan, Bahlibi Weldegebriall Sahlu, Haisheng Hao, Xueming Zhao, Yachun Wang, Shanjiang Zhao and Huabin Zhu

Genes 2019, 10(12), 1038; https://doi.org/10.3390/genes10121038 - 12 Dec 2019

Cited by 17 | Viewed by 4228

Abstract

Anti-Mullerian hormone (AMH) is an important reproductive marker of ovarian reserve produced by granulosa cells (GCs) of pre-antral and early-antral ovarian follicles in several species, including cattle. This hormone plays a vital role during the recruitment of primordial follicles and follicle stimulating hormone [...] Read more.

Anti-Mullerian hormone (AMH) is an important reproductive marker of ovarian reserve produced by granulosa cells (GCs) of pre-antral and early-antral ovarian follicles in several species, including cattle. This hormone plays a vital role during the recruitment of primordial follicles and follicle stimulating hormone (FSH)-dependent follicular growth. However, the regulatory mechanism of AMH expression in follicles is still unclear. In this study, we compared the expression of AMH, AMHR-II, BMP2, BMP6, FSHR, and LHCGR genes during follicular development. In-vitro expression study was performed with and without FSH for AMH, AMHR-II, BMP2, and BMP6 genes in bovine GCs which were isolated from 3–8 mm follicles. Association among the mRNA expression and hormone level was estimated. GCs were collected from small (3–8 mm), medium (9–12 mm) and large size (13 to 24 mm) follicles before, during onset, and after deviation, respectively. Further, mRNA expression, hormones (AMH, FSH, and LH), apoptosis of GCs, and cell viability were detected by qRT-PCR, ELISA, flow cytometry, and spectrophotometry. AMH, AMHR-II, BMP2, and FSHR genes were highly expressed in small and medium follicles as compared to large ones. In addition, the highest level of AMH protein (84.14 ± 5.41 ng/mL) was found in medium-size follicles. Lower doses of FSH increased the viability of bovine GCs while higher doses repressed them. In-vitro cultured GCs treated with FSH significantly increased the AMH, AMHR-II, and BMP2 expression levels at lower doses, while expression levels decreased at higher doses. We found an optimum level of FSH (25 ng/mL) which can significantly enhance AMH and BMP2 abundance (p < 0.05). In summary, AMH, AMHR-II, and BMP2 genes showed a higher expression in follicles developed in the presence of FSH. However, lower doses of FSH demonstrated a stimulatory effect on AMH and BMP2 expression, while expression started to decline at the maximum dose. In this study, we have provided a better understanding of the mechanisms regulating AMH, AMHR II, and BMP2 signaling in GCs during folliculogenesis, which would improve the outcomes of conventional assisted reproductive technologies (ARTs), such as superovulation and oestrus synchronization in bovines. Full article

(This article belongs to the Special Issue Genomics of Sexual Development and Reproduction in Mammals)

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20 pages, 6072 KiB

Open AccessArticle

Structural and Functional Dissection of the 5′ Region of the Notch Gene in Drosophila melanogaster

by Elena I. Volkova, Natalya G. Andreyenkova, Oleg V. Andreyenkov, Darya S. Sidorenko, Igor F. Zhimulev and Sergey A. Demakov

Genes 2019, 10(12), 1037; https://doi.org/10.3390/genes10121037 - 12 Dec 2019

Cited by 3 | Viewed by 3584

Abstract

Notch is a key factor of a signaling cascade which regulates cell differentiation in all multicellular organisms. Numerous investigations have been directed mainly at studying the mechanism of Notch protein action; however, very little is known about the regulation of activity of the [...] Read more.

Notch is a key factor of a signaling cascade which regulates cell differentiation in all multicellular organisms. Numerous investigations have been directed mainly at studying the mechanism of Notch protein action; however, very little is known about the regulation of activity of the gene itself. Here, we provide the results of targeted 5′-end editing of the Drosophila Notch gene in its native environment and genetic and cytological effects of these changes. Using the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9 (CRISPR/Cas9) system in combination with homologous recombination, we obtained a founder fly stock in which a 4-kb fragment, including the 5′ nontranscribed region, the first exon, and a part of the first intron of Notch, was replaced by an attachment Phage (attP) site. Then, fly lines carrying a set of six deletions within the 5′untranscribed region of the gene were obtained by ΦC31-mediated integration of transgenic constructs. Part of these deletions does not affect gene activity, but their combinations with transgenic construct in the first intron of the gene cause defects in the Notch target tissues. At the polytene chromosome level we defined a DNA segment (~250 bp) in the Notch5′-nontranscribed region which when deleted leads to disappearance of the 3C6/C7 interband and elimination of CTC-Factor (CTCF) and Chromator (CHRIZ) insulator proteins in this region. Full article

(This article belongs to the Special Issue Chromosome-Centric View of the Genome Organization and Evolution)

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11 pages, 400 KiB

Open AccessArticle

High Prevalence of Staphylococcus aureus Enterotoxin Gene Cluster Superantigens in Cystic Fibrosis Clinical Isolates

by Anthony J. Fischer, Samuel H. Kilgore, Sachinkumar B. Singh, Patrick D. Allen, Alexis R. Hansen, Dominique H. Limoli and Patrick M. Schlievert

Genes 2019, 10(12), 1036; https://doi.org/10.3390/genes10121036 - 12 Dec 2019

Cited by 24 | Viewed by 3173

Abstract

Background: Staphylococcus aureus is a highly prevalent respiratory pathogen in cystic fibrosis (CF). It is unclear how this organism establishes chronic infections in CF airways. We hypothesized that S. aureus isolates from patients with CF would share common virulence properties that enable chronic [...] Read more.

Background: Staphylococcus aureus is a highly prevalent respiratory pathogen in cystic fibrosis (CF). It is unclear how this organism establishes chronic infections in CF airways. We hypothesized that S. aureus isolates from patients with CF would share common virulence properties that enable chronic infection. Methods: 77 S. aureus isolates were obtained from 45 de-identified patients with CF at the University of Iowa. We assessed isolates phenotypically and used genotyping assays to determine the presence or absence of 18 superantigens (SAgs). Results: We observed phenotypic diversity among S. aureus isolates from patients with CF. Genotypic analysis for SAgs revealed 79.8% of CF clinical isolates carried all six members of the enterotoxin gene cluster (EGC). MRSA and MSSA isolates had similar prevalence of SAgs. We additionally observed that EGC SAgs were prevalent in S. aureus isolated from two geographically distinct CF centers. Conclusions: S. aureus SAgs belonging to the EGC are highly prevalent in CF clinical isolates. The greater prevalence in these SAgs in CF airway specimens compared to skin isolates suggests that these toxins confer selective advantage in the CF airway. Full article

(This article belongs to the Special Issue Molecular Basis and Gene Therapies of Cystic Fibrosis)

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18 pages, 3633 KiB

Open AccessArticle

Comparative Transcriptome Analysis of Gonads for the Identification of Sex-Related Genes in Giant Freshwater Prawns (Macrobrachium Rosenbergii) Using RNA Sequencing

by Jianping Jiang, Xiang Yuan, Qingqing Qiu, Guanghua Huang, Qinyang Jiang, Penghui Fu, Yu Zhang, Yinhai Jia, Xiurong Yang and Hesheng Jiang

Genes 2019, 10(12), 1035; https://doi.org/10.3390/genes10121035 - 11 Dec 2019

Cited by 24 | Viewed by 3621

Abstract

The giant freshwater prawn (Macrobrachium rosenbergii) exhibits sex dimorphism between the male and female individuals. To date, the molecular mechanism governing gonadal development was unclear, and limited data were available on the gonad transcriptome of M. rosenbergii. Here, we conducted [...] Read more.

The giant freshwater prawn (Macrobrachium rosenbergii) exhibits sex dimorphism between the male and female individuals. To date, the molecular mechanism governing gonadal development was unclear, and limited data were available on the gonad transcriptome of M. rosenbergii. Here, we conducted comprehensive gonadal transcriptomic analysis of female (ZW), super female (WW), and male (ZZ) M. rosenbergii for gene discovery. A total of 70.33 gigabases (Gb) of sequences were generated. There were 115,338 unigenes assembled with a mean size of 1196 base pair (bp) and N50 of 2195 bp. Alignment against the National Center for Biotechnology Information (NCBI) non-redundant nucleotide/protein sequence database (NR and NT), the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, SwissProt database, Protein family (Pfam), Gene ontology (GO), and the eukaryotic orthologous group (KOG) database, 36,282 unigenes were annotated at least in one database. Comparative transcriptome analysis observed that 10,641, 16,903, and 3393 genes were significantly differentially expressed in ZW vs. ZZ, WW vs. ZZ, and WW vs. ZW samples, respectively. Enrichment analysis of differentially expressed genes (DEGs) resulted in 268, 153, and 42 significantly enriched GO terms, respectively, and a total of 56 significantly enriched KEGG pathways. Additionally, 23 putative sex-related genes, including Gtsf1, IR, HSP21, MRPINK, Mrr, and other potentially promising candidate genes were identified. Moreover, 56,241 simple sequence repeats (SSRs) were identified. Our findings provide a valuable archive for further functional analyses of sex-related genes and future discoveries of underlying molecular mechanisms of gonadal development and sex determination. Full article

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

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15 pages, 9172 KiB

Open AccessArticle

Identification of Shoot Differentiation-Related Genes in Populus euphratica Oliv.

by Yaru Fu, Tianyu Dong, Lizhi Tan, Danni Yin, Miaomiao Zhang, Guomiao Zhao, Meixia Ye and Rongling Wu

Genes 2019, 10(12), 1034; https://doi.org/10.3390/genes10121034 - 11 Dec 2019

Cited by 4 | Viewed by 2958

Abstract

De novo shoot regeneration is one of the important manifestations of cell totipotency in organogenesis, which reflects a survival strategy organism evolved when facing natural selection. Compared with tissue regeneration, and somatic embryogenesis, de novo shoot regeneration denotes a shoot regeneration process directly [...] Read more.

De novo shoot regeneration is one of the important manifestations of cell totipotency in organogenesis, which reflects a survival strategy organism evolved when facing natural selection. Compared with tissue regeneration, and somatic embryogenesis, de novo shoot regeneration denotes a shoot regeneration process directly from detatched or injured tissues of plant. Studies on plant shoot regeneration had identified key genes mediating shoot regeneration. However, knowledge was derived from Arabidopsis; the regeneration capacity is hugely distinct among species. To achieve a comprehensive understanding of the shoot regeneration mechanism from tree species, we select four genetic lines of Populus euphratica from a natural population to be sequenced at transcriptome level. On the basis of the large difference of differentiation capacity, between the highly differentiated (HD) and low differentiated (LD) groups, the analysis of differential expression identified 4920 differentially expressed genes (DEGs), which were revealed in five groups of expression patterns by clustering analysis. Enrichment showed crucial pathways involved in regulation of regeneration difference, including “plant hormone signal transduction”, “cell differentiation”, "cellular response to auxin stimulus", and “auxin-activated signaling pathway”. The expression of nine genes reported to be associated with shoot regeneration was validated using quantitative real-time PCR (qRT-PCR). For the specificity of regeneration mechanism with P. euphratica, large amount of DEGs involved in "plant-pathogen interaction", ubiquitin-26S proteosome mediated proteolysis pathway, stress-responsive DEGs, and senescence-associated DEGs were summarized to possibly account for the differentiation difference with distinct genotypes of P. euphratica. The result in this study helps screening of key regulators in mediating the shoot differentiation. The transcriptomic characteristic in P. euphratica further enhances our understanding of key processes affecting the regeneration capacity of de novo shoots among distinct species. Full article

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14 pages, 3295 KiB

Open AccessArticle

Labeling of Monilinia fructicola with GFP and Its Validation for Studies on Host-Pathogen Interactions in Stone and Pome Fruit

by Silvia Rodríguez-Pires, Eduardo Antonio Espeso, Nuria Baró-Montel, Rosario Torres, Paloma Melgarejo and Antonieta De Cal

Genes 2019, 10(12), 1033; https://doi.org/10.3390/genes10121033 - 11 Dec 2019

Cited by 3 | Viewed by 3310

Abstract

To compare in vivo the infection process of Monilinia fructicola on nectarines and apples using confocal microscopy it is necessary to transform a pathogenic strain with a construct expressing a fluorescent chromophore such as GFP. Thus, germinated conidia of the pathogen were transformed [...] Read more.

To compare in vivo the infection process of Monilinia fructicola on nectarines and apples using confocal microscopy it is necessary to transform a pathogenic strain with a construct expressing a fluorescent chromophore such as GFP. Thus, germinated conidia of the pathogen were transformed with Agrobacterium tumefaciens carrying the plasmid pPK2-hphgfp that allowed the expression of a fluorescent Hph-GFP chimera. The transformants were selected according to their resistance to hygromycin B, provided by the constitutive expression of the hph-gfp gene driven by the glyceraldehyde 3P dehydrogenase promoter of Aspergillus nidulans. The presence of T-DNA construct in the genomic DNA was confirmed by PCR using a range of specific primers. Subsequent PCR-mediated analyses proved integration of the transgene at a different genomic location in each transformant and the existence of structural reorganizations at these insertion points. The expression of Hph-GFP in three independent M. fructicola transformants was monitored by immunodetection and epifluorescence and confocal microscopy. The Atd9-M. fructicola transformant displayed no morphological defects and showed growth and pathogenic characteristics similar to the wild type. Microscopy analysis of the Atd9 transformant evidenced that nectarine infection by M. fructicola was at least three times faster than on apples. Full article

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

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10 pages, 1132 KiB

Open AccessReview

Next-Generation Technologies and Strategies for the Management of Retinoblastoma

by Harini V. Gudiseva, Jesse L. Berry, Ashley Polski, Santa J. Tummina and Joan M. O’Brien

Genes 2019, 10(12), 1032; https://doi.org/10.3390/genes10121032 - 11 Dec 2019

Cited by 20 | Viewed by 6251

Abstract

Retinoblastoma (RB) is an inherited retinal disorder (IRD) caused by the mutation in the RB1 gene or, rarely, by alterations in the MYCN gene. In recent years, new treatment advances have increased ocular and visual preservation in the developed world. The management of [...] Read more.

Retinoblastoma (RB) is an inherited retinal disorder (IRD) caused by the mutation in the RB1 gene or, rarely, by alterations in the MYCN gene. In recent years, new treatment advances have increased ocular and visual preservation in the developed world. The management of RB has improved significantly in recent decades, from the use of external beam radiation to recently, more localized treatments. Determining the underlying genetic cause of RB is critical for timely management decisions. The advent of next-generation sequencing technologies have assisted in understanding the molecular pathology of RB. Liquid biopsy of the aqueous humor has also had significant potential implications for tumor management. Currently, patients’ genotypic information, along with RB phenotypic presentation, are considered carefully when making treatment decisions aimed at globe preservation. Advances in molecular testing that improve our understanding of the molecular pathology of RB, together with multiple directed treatment options, are critical for developing precision medicine strategies to treat this disease. Full article

(This article belongs to the Special Issue Recent Advances in Inherited Eye Disease)

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8 pages, 1733 KiB

Open AccessCommunication

Delineation of Homozygous Variants Associated with Prelingual Sensorineural Hearing Loss in Pakistani Families

by Muhammad Noman, Rafaqat Ishaq, Shazia A. Bukhari, Zubair M. Ahmed and Saima Riazuddin

Genes 2019, 10(12), 1031; https://doi.org/10.3390/genes10121031 - 10 Dec 2019

Cited by 14 | Viewed by 3053

Abstract

Hearing loss is a genetically heterogeneous disorder affecting approximately 360 million people worldwide and is among the most common sensorineural disorders. Here, we report a genetic analysis of seven large consanguineous families segregating prelingual sensorineural hearing loss. Whole-exome sequencing (WES) revealed seven different [...] Read more.

Hearing loss is a genetically heterogeneous disorder affecting approximately 360 million people worldwide and is among the most common sensorineural disorders. Here, we report a genetic analysis of seven large consanguineous families segregating prelingual sensorineural hearing loss. Whole-exome sequencing (WES) revealed seven different pathogenic variants segregating with hearing loss in these families, three novel variants (c.1204G>A, c.322G>T, and c.5587C>T) in TMPRSS3, ESRRB, and OTOF, and four previously reported variants (c.208C>T, c.6371G>A, c.226G>A, and c.494C>T) in LRTOMT, MYO15A, KCNE1, and LHFPL5, respectively. All identified variants had very low frequencies in the control databases and were predicted to have pathogenic effects on the encoded proteins. In addition to being familial, we also found intersibship locus heterogeneity in the evaluated families. The known pathogenic c.226C>T variant identified in KCNE1 only segregates with the hearing loss phenotype in a subset of affected members of the family GCNF21. This study further highlights the challenges of identifying disease-causing variants for highly heterogeneous disorders and reports the identification of three novel and four previously reported variants in seven known deafness genes. Full article

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

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14 pages, 1567 KiB

Open AccessReview

Alternative Lengthening of Telomeres (ALT) in Tumors and Pluripotent Stem Cells

by Shuang Zhao, Feng Wang and Lin Liu

Genes 2019, 10(12), 1030; https://doi.org/10.3390/genes10121030 - 10 Dec 2019

Cited by 23 | Viewed by 8821

Abstract

A telomere consists of repeated DNA sequences (TTAGGG)n as part of a nucleoprotein structure at the end of the linear chromosome, and their progressive shortening induces DNA damage response (DDR) that triggers cellular senescence. The telomere can be maintained by telomerase activity (TA) [...] Read more.

A telomere consists of repeated DNA sequences (TTAGGG)n as part of a nucleoprotein structure at the end of the linear chromosome, and their progressive shortening induces DNA damage response (DDR) that triggers cellular senescence. The telomere can be maintained by telomerase activity (TA) in the majority of cancer cells (particularly cancer stem cells) and pluripotent stem cells (PSCs), which exhibit unlimited self-proliferation. However, some cells, such as telomerase-deficient cancer cells, can add telomeric repeats by an alternative lengthening of the telomeres (ALT) pathway, showing telomere length heterogeneity. In this review, we focus on the mechanisms of the ALT pathway and potential clinical implications. We also discuss the characteristics of telomeres in PSCs, thereby shedding light on the therapeutic significance of telomere length regulation in age-related diseases and regenerative medicine. Full article

(This article belongs to the Special Issue ALT: From Telomere Maintenance Mechanisms to Proposed Therapies)

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17 pages, 731 KiB

Open AccessReview

Common Features of the Pericentromere and Nucleolus

by Colleen J. Lawrimore and Kerry Bloom

Genes 2019, 10(12), 1029; https://doi.org/10.3390/genes10121029 - 10 Dec 2019

Cited by 16 | Viewed by 5645

Abstract

Both the pericentromere and the nucleolus have unique characteristics that distinguish them amongst the rest of genome. Looping of pericentromeric DNA, due to structural maintenance of chromosome (SMC) proteins condensin and cohesin, drives its ability to maintain tension during metaphase. Similar loops are [...] Read more.

Both the pericentromere and the nucleolus have unique characteristics that distinguish them amongst the rest of genome. Looping of pericentromeric DNA, due to structural maintenance of chromosome (SMC) proteins condensin and cohesin, drives its ability to maintain tension during metaphase. Similar loops are formed via condensin and cohesin in nucleolar ribosomal DNA (rDNA). Condensin and cohesin are also concentrated in transfer RNA (tRNA) genes, genes which may be located within the pericentromere as well as tethered to the nucleolus. Replication fork stalling, as well as downstream consequences such as genomic recombination, are characteristic of both the pericentromere and rDNA. Furthermore, emerging evidence suggests that the pericentromere may function as a liquid–liquid phase separated domain, similar to the nucleolus. We therefore propose that the pericentromere and nucleolus, in part due to their enrichment of SMC proteins and others, contain similar domains that drive important cellular activities such as segregation, stability, and repair. Full article

(This article belongs to the Special Issue Chromosome Segregation Defects in the Origin of Genomic Instability)

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19 pages, 1613 KiB

Open AccessReview

DNA Helicases as Safekeepers of Genome Stability in Plants

by Annika Dorn and Holger Puchta

Genes 2019, 10(12), 1028; https://doi.org/10.3390/genes10121028 - 10 Dec 2019

Cited by 11 | Viewed by 4636

Abstract

Genetic information of all organisms is coded in double-stranded DNA. DNA helicases are essential for unwinding this double strand when it comes to replication, repair or transcription of genetic information. In this review, we will focus on what is known about a variety [...] Read more.

Genetic information of all organisms is coded in double-stranded DNA. DNA helicases are essential for unwinding this double strand when it comes to replication, repair or transcription of genetic information. In this review, we will focus on what is known about a variety of DNA helicases that are required to ensure genome stability in plants. Due to their sessile lifestyle, plants are especially exposed to harmful environmental factors. Moreover, many crop plants have large and highly repetitive genomes, making them absolutely dependent on the correct interplay of DNA helicases for safeguarding their stability. Although basic features of a number of these enzymes are conserved between plants and other eukaryotes, a more detailed analysis shows surprising peculiarities, partly also between different plant species. This is additionally of high relevance for plant breeding as a number of these helicases are also involved in crossover control during meiosis and influence the outcome of different approaches of CRISPR/Cas based plant genome engineering. Thus, gaining knowledge about plant helicases, their interplay, as well as the manipulation of their pathways, possesses the potential for improving agriculture. In the long run, this might even help us cope with the increasing obstacles of climate change threatening food security in completely new ways. Full article

(This article belongs to the Special Issue DNA Helicases: Mechanisms, Biological Pathways, and Disease Relevance)

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18 pages, 2407 KiB

Open AccessArticle

The Genetic Basis of Scale-Loss Phenotype in the Rapid Radiation of Takifugu Fishes

by Dong In Kim, Wataru Kai, Sho Hosoya, Mana Sato, Aoi Nozawa, Miwa Kuroyanagi, Yuka Jo, Satoshi Tasumi, Hiroaki Suetake, Yuzuru Suzuki and Kiyoshi Kikuchi

Genes 2019, 10(12), 1027; https://doi.org/10.3390/genes10121027 - 10 Dec 2019

Cited by 7 | Viewed by 4391

Abstract

Rapid radiation associated with phenotypic divergence and convergence provides an opportunity to study the genetic mechanisms of evolution. Here we investigate the genus Takifugu that has undergone explosive radiation relatively recently and contains a subset of closely-related species with a scale-loss phenotype. By [...] Read more.

Rapid radiation associated with phenotypic divergence and convergence provides an opportunity to study the genetic mechanisms of evolution. Here we investigate the genus Takifugu that has undergone explosive radiation relatively recently and contains a subset of closely-related species with a scale-loss phenotype. By using observations during development and genetic mapping approaches, we show that the scale-loss phenotype of two Takifugu species, T. pardalis Temminck & Schlegel and T. snyderi Abe, is largely controlled by an overlapping genomic segment (QTL). A search for candidate genes underlying the scale-loss phenotype revealed that the QTL region contains no known genes responsible for the evolution of scale-loss phenotype in other fishes. These results suggest that the genes used for the scale-loss phenotypes in the two Takifugu are likely the same, but the genes used for the similar phenotype in Takifugu and distantly related fishes are not the same. Meanwhile, Fgfrl1, a gene predicted to function in a pathway known to regulate bone/scale development was identified in the QTL region. Since Fgfr1a1, another memebr of the Fgf signaling pathway, has been implicated in scale loss/scale shape in fish distantly related to Takifugu, our results suggest that the convergence of the scale-loss phenotype may be constrained by signaling modules with conserved roles in scale development. Full article

(This article belongs to the Special Issue A Tale of Genes and Genomes)

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16 pages, 2111 KiB

Open AccessArticle

Nanopore Targeted Sequencing for Rapid Gene Mutations Detection in Acute Myeloid Leukemia

by Cosimo Cumbo, Crescenzio Francesco Minervini, Paola Orsini, Luisa Anelli, Antonella Zagaria, Angela Minervini, Nicoletta Coccaro, Luciana Impera, Giuseppina Tota, Elisa Parciante, Maria Rosa Conserva, Orietta Spinelli, Alessandro Rambaldi, Giorgina Specchia and Francesco Albano

Genes 2019, 10(12), 1026; https://doi.org/10.3390/genes10121026 - 09 Dec 2019

Cited by 23 | Viewed by 6484

Abstract

Acute myeloid leukemia (AML) clinical settings cannot do without molecular testing to confirm or rule out predictive biomarkers for prognostic stratification, in order to initiate or withhold targeted therapy. Next generation sequencing offers the advantage of the simultaneous investigation of numerous genes, but [...] Read more.

Acute myeloid leukemia (AML) clinical settings cannot do without molecular testing to confirm or rule out predictive biomarkers for prognostic stratification, in order to initiate or withhold targeted therapy. Next generation sequencing offers the advantage of the simultaneous investigation of numerous genes, but these methods remain expensive and time consuming. In this context, we present a nanopore-based assay for rapid (24 h) sequencing of six genes (NPM1, FLT3, CEBPA, TP53, IDH1 and IDH2) that are recurrently mutated in AML. The study included 22 AML patients at diagnosis; all data were compared with the results of S5 sequencing, and discordant variants were validated by Sanger sequencing. Nanopore approach showed substantial advantages in terms of speed and low cost. Furthermore, the ability to generate long reads allows a more accurate detection of longer FLT3 internal tandem duplications and phasing double CEBPA mutations. In conclusion, we propose a cheap, rapid workflow that can potentially enable all basic molecular biology laboratories to perform detailed targeted gene sequencing analysis in AML patients, in order to define their prognosis and the appropriate treatment. Full article

(This article belongs to the Special Issue Genetics and Genomics of Acute Myeloid Leukemia)

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14 pages, 1381 KiB

Open AccessConcept Paper

Defining Mental and Behavioural Disorders in Genetically Determined Neurodevelopmental Syndromes with Particular Reference to Prader-Willi Syndrome

by Anthony J. Holland, Lucie C.S. Aman and Joyce E. Whittington

Genes 2019, 10(12), 1025; https://doi.org/10.3390/genes10121025 - 09 Dec 2019

Cited by 20 | Viewed by 3624

Abstract

Genetically determined neurodevelopmental syndromes are frequently associated with a particular developmental trajectory, and with a cognitive profile and increased propensity to specific mental and behavioural disorders that are particular to, but not necessarily unique to the syndrome. How should these mental and behavioural [...] Read more.

Genetically determined neurodevelopmental syndromes are frequently associated with a particular developmental trajectory, and with a cognitive profile and increased propensity to specific mental and behavioural disorders that are particular to, but not necessarily unique to the syndrome. How should these mental and behavioural disorders best be conceptualised given that similar symptoms are included in the definition of different mental disorders as listed in DSM-5 and ICD-10? In addition, a different conceptual framework, that of applied behavioural analysis, has been used to inform interventions for what are termed ‘challenging behaviours’ in contrast to types of interventions for those conditions meeting diagnostic criteria for a ‘mental disorder’. These syndrome-specific developmental profiles and associated co-morbidities must be a direct or indirect consequence of the genetic abnormality associated with that syndrome, but the genetic loci associated with the syndrome may not be involved in the aetiology of similar symptoms in the general population. This being so, should we expect underlying brain mechanisms and treatments for specific psychopathology in one group to be effective in the other? Using Prader-Willi syndrome as an example, we propose that the conceptual thinking that informed the development of the Research Domain Criteria provides a model for taxonomy of psychiatric and behavioural disorders in genetically determined neurodevelopmental syndromes. This model brings together diagnostic, psychological and developmental approaches with the aim of matching specific behaviours to identifiable neural mechanisms. Full article

(This article belongs to the Special Issue Genetics of Prader-Willi syndrome)

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19 pages, 3884 KiB

Open AccessArticle

iTRAQ-Based Protein Profiling Provides Insights into the Mechanism of Light-Induced Anthocyanin Biosynthesis in Chrysanthemum (Chrysanthemum × morifolium)

by Yan Hong, Mengling Li and Silan Dai

Genes 2019, 10(12), 1024; https://doi.org/10.3390/genes10121024 - 09 Dec 2019

Cited by 12 | Viewed by 2938

Abstract

The generation of chrysanthemum (Chrysanthemum × morifolium) flower color is mainly attributed to the accumulation of anthocyanins. Light is one of the key environmental factors that affect the anthocyanin biosynthesis, but the deep molecular mechanism remains elusive. In our previous study, [...] Read more.

The generation of chrysanthemum (Chrysanthemum × morifolium) flower color is mainly attributed to the accumulation of anthocyanins. Light is one of the key environmental factors that affect the anthocyanin biosynthesis, but the deep molecular mechanism remains elusive. In our previous study, a series of light-induced structural and regulatory genes involved in the anthocyanin biosynthetic pathway in the chrysanthemum were identified using RNA sequencing. In the present study, differentially expressed proteins that are in response to light with the capitulum development of the chrysanthemum ‘Purple Reagan’ were further identified using isobaric tags for relative and absolute quantification (iTRAQ) technique, and correlation between the proteomic and the transcriptomic libraries was analyzed. In general, 5106 raw proteins were assembled based on six proteomic libraries (three capitulum developmental stages × two light treatments). As many as 160 proteins were differentially expressed between the light and the dark libraries with 45 upregulated and 115 downregulated proteins in response to shading. Comparative analysis between the pathway enrichment and the gene expression patterns indicated that most of the proteins involved in the anthocyanin biosynthetic pathway were downregulated after shading, which was consistent with the expression patterns of corresponding encoding genes; while five light-harvesting chlorophyll a/b-binding proteins were initially downregulated after shading, and their expressions were enhanced with the capitulum development thereafter. As revealed by correlation analysis between the proteomic and the transcriptomic libraries, GDSL esterase APG might also play an important role in light signal transduction. Finally, a putative mechanism of light-induced anthocyanin biosynthesis in the chrysanthemum was proposed. This study will help us to clearly identify light-induced proteins associated with flower color in the chrysanthemum and to enrich the complex mechanism of anthocyanin biosynthesis for use in cultivar breeding. Full article

(This article belongs to the Special Issue Genetic and Molecular Mechanisms in Plant-Derived Compounds for Industrial Purposes)

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