Genes, Vol. 10, Pages 835: Transcriptomic Revelation of Phenolic Compounds Involved in Aluminum Toxicity Responses in Roots of Cunninghamia lanceolata (Lamb.) Hook
Lin : Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is one of the most important coniferous evergreen tree species in South China due to its desirable attributes of fast growth and production of strong and hardy wood. However, the yield of Chinese fir is often inhibited by aluminum (Al) toxicity in acidic soils of South China. Understanding the molecular mechanisms of Chinese fir root responses to Al toxicity might help to further increase its productivity. Here we used the Illumina Hiseq4000 platform to carry out transcriptome analysis of Chinese fir roots subjected to Al toxicity conditions. A total of 88.88 G...
Source: Genes - October 23, 2019 Category: Genetics & Stem Cells Authors: Ma Lin Tags: Article Source Type: research

Genes, Vol. 10, Pages 836: Deregulated Adhesion Program in Palatal Keratinocytes of Orofacial Cleft Patients
Von den Hoff Orofacial clefts (OFCs) are the most frequent craniofacial birth defects. An orofacial cleft (OFC) occurs as a result of deviations in palatogenesis. Cell proliferation, differentiation, adhesion, migration and apoptosis are crucial in palatogenesis. We hypothesized that deregulation of these processes in oral keratinocytes contributes to OFC. We performed microarray expression analysis on palatal keratinocytes from OFC and non-OFC individuals. Principal component analysis showed a clear difference in gene expression with 24% and 17% for the first and second component, respectively. In OFC cells, 228 g...
Source: Genes - October 23, 2019 Category: Genetics & Stem Cells Authors: Mammadova Carels Zhou Gilissen Helmich Bian Zhou Von den Hoff Tags: Article Source Type: research

Genes, Vol. 10, Pages 837: Efficient Gene Disruption via Base Editing Induced Stop in Newt Pleurodeles waltl
This study not only presented the high efficiency of single base editing in a gigantic animal genome (>20 G), but also provided new tools for interrogating gene function in other salamander species. (Source: Genes)
Source: Genes - October 23, 2019 Category: Genetics & Stem Cells Authors: Cai Peng Ren Wang Tags: Technical Note Source Type: research

Genes, Vol. 10, Pages 832: Germline-Specific Repetitive Elements in Programmatically Eliminated Chromosomes of the Sea Lamprey (Petromyzon marinus)
Smith The sea lamprey (Petromyzon marinus) is one of few vertebrate species known to reproducibly eliminate large fractions of its genome during normal embryonic development. This germline-specific DNA is lost in the form of large fragments, including entire chromosomes, and available evidence suggests that DNA elimination acts as a permanent silencing mechanism that prevents the somatic expression of a specific subset of “germline” genes. However, reconstruction of eliminated regions has proven to be challenging due to the complexity of the lamprey karyotype. We applied an integrative appro...
Source: Genes - October 22, 2019 Category: Genetics & Stem Cells Authors: Vladimir A. Timoshevskiy Nataliya Y. Timoshevskaya Jeramiah J. Smith Tags: Article Source Type: research

Genes, Vol. 10, Pages 833: Likely Pathogenic Variants in One Third of Non-Syndromic Discontinuous Cleft Lip and Palate Patients
chelle Bénédicte Bayet Miikka Vikkula Oral clefts are composed of cleft of the lip, cleft of the lip and palate, or cleft of the palate, and they are associated with a wide range of expression and severity. When cleft of the palate is associated with cleft of the lip with preservation of the primary palate, it defines an atypical phenotype called discontinuous cleft. Although this phenotype may represent 5% of clefts of the lip and/or palate (CLP), it is rarely specifically referred to and its pathophysiology is unknown. We conducted whole exome sequencing (WES) and apply a candidate gene approach to ...
Source: Genes - October 22, 2019 Category: Genetics & Stem Cells Authors: B énédicte Demeer Nicole Revencu Raphael Helaers Cica Gbaguidi St éphanie Dakpe Genevi ève François Bernard Devauchelle B énédicte Bayet Miikka Vikkula Tags: Article Source Type: research

Genes, Vol. 10, Pages 834: A Method for the Structure-Based, Genome-Wide Analysis of Bacterial Intergenic Sequences Identifies Shared Compositional and Functional Features
sio Mengoni In this paper, we propose a computational strategy for performing genome-wide analyses of intergenic sequences in bacterial genomes. Following similar directions of a previous paper, where a method for genome-wide analysis of eucaryotic Intergenic sequences was proposed, here we developed a tool for implementing similar concepts in bacteria genomes. This allows us to (i) classify intergenic sequences into clusters, characterized by specific global structural features and (ii) draw possible relations with their functional features. (Source: Genes)
Source: Genes - October 22, 2019 Category: Genetics & Stem Cells Authors: Leonardo Lenzini Francesca Di Patti Roberto Livi Marco Fondi Renato Fani Alessio Mengoni Tags: Article Source Type: research

Genes, Vol. 10, Pages 829: A Genome-Wide Association Study Revealed Key SNPs/Genes Associated With Salinity Stress Tolerance In Upland Cotton
Xiongming Du Millions of hectares of land are too saline to produce economically valuable crop yields. Salt tolerance in cotton is an imperative approach for improvement in response to ever-increasing soil salinization. Little is known about the genetic basis of salt tolerance in cotton at the seedling stage. To address this issue, a genome-wide association study (GWAS) was conducted on a core collection of a genetically diverse population of upland cotton (Gossypium hirsutum L.) comprising of 419 accessions, representing various geographic origins, including China, USA, Pakistan, the former Soviet Union, Chad, Aust...
Source: Genes - October 21, 2019 Category: Genetics & Stem Cells Authors: Muhammad Yasir Shoupu He Gaofei Sun Xiaoli Geng Zhaoe Pan Wenfang Gong Yinhua Jia Xiongming Du Tags: Article Source Type: research

Genes, Vol. 10, Pages 830: Molecular Characterization of Leishmania RNA virus 2 in Leishmania major from Uzbekistan
lav Yurchenko Here we report sequence and phylogenetic analysis of two new isolates of Leishmania RNA virus 2 (LRV2) found in Leishmania major isolated from human patients with cutaneous leishmaniasis in south Uzbekistan. These new virus-infected flagellates were isolated in the same region of Uzbekistan and the viral sequences differed by only nineteen SNPs, all except one being silent mutations. Therefore, we concluded that they belong to a single LRV2 species. New viruses are closely related to the LRV2-Lmj-ASKH documented in Turkmenistan in 1995, which is congruent with their shared host (L. major) and common geogr...
Source: Genes - October 21, 2019 Category: Genetics & Stem Cells Authors: Yuliya Kleschenko Danyil Grybchuk Nadezhda S. Matveeva Diego H. Macedo Evgeny N. Ponirovsky Alexander N. Lukashev Vyacheslav Yurchenko Tags: Article Source Type: research

Genes, Vol. 10, Pages 831: The Mechanisms of Mating in Pathogenic Fungi —A Plastic Trait
Genes, Vol. 10, Pages 831: The Mechanisms of Mating in Pathogenic Fungi—A Plastic Trait Genes doi: 10.3390/genes10100831 Authors: Jane Usher The impact of fungi on human and plant health is an ever-increasing issue. Recent studies have estimated that human fungal infections result in an excess of one million deaths per year and plant fungal infections resulting in the loss of crop yields worth approximately 200 million per annum. Sexual reproduction in these economically important fungi has evolved in response to the environmental stresses encountered by the pathogens as a method to target DNA damage. Meiosis...
Source: Genes - October 21, 2019 Category: Genetics & Stem Cells Authors: Jane Usher Tags: Review Source Type: research

Genes, Vol. 10, Pages 827: Comparative Study of Gut Microbiota in Wild and Captive Giant Pandas (Ailuropoda melanoleuca)
ao Zhao Ying Li Captive breeding has been used as an effective approach to protecting endangered animals but its effect on the gut microbiome and the conservation status of these species is largely unknown. The giant panda is a flagship species for the conservation of wildlife. With integrated efforts including captive breeding, this species has been recently upgraded from “endangered” to “vulnerable” (IUCN 2016). Since a large proportion (21.8%) of their global population is still captive, it is critical to understand how captivity changes the gut microbiome of...
Source: Genes - October 20, 2019 Category: Genetics & Stem Cells Authors: Wei Guo Sudhanshu Mishra Chengdong Wang Hemin Zhang Ruihong Ning Fanli Kong Bo Zeng Jiangchao Zhao Ying Li Tags: Article Source Type: research

Genes, Vol. 10, Pages 828: i6mA-DNCP: Computational Identification of DNA N6-Methyladenine Sites in the Rice Genome Using Optimized Dinucleotide-Based Features
ang DNA N6-methyladenine (6mA) plays an important role in regulating the gene expression of eukaryotes. Accurate identification of 6mA sites may assist in understanding genomic 6mA distributions and biological functions. Various experimental methods have been applied to detect 6mA sites in a genome-wide scope, but they are too time-consuming and expensive. Developing computational methods to rapidly identify 6mA sites is needed. In this paper, a new machine learning-based method, i6mA-DNCP, was proposed for identifying 6mA sites in the rice genome. Dinucleotide composition and dinucleotide-based DNA properties were fir...
Source: Genes - October 20, 2019 Category: Genetics & Stem Cells Authors: Liang Kong Lichao Zhang Tags: Article Source Type: research

Genes, Vol. 10, Pages 826: Frameshift Variant in MFSD12 Explains the Mushroom Coat Color Dilution in Shetland Ponies
do Rebecca R. Bellone Mushroom is a unique coat color phenotype in Shetland Ponies characterized by the dilution of the chestnut coat color to a sepia tone and is hypothesized to be a recessive trait. A genome wide association study (GWAS), utilizing the Affymetrix 670K array (MNEc670k) and a single locus mixed linear model analysis (EMMAX), identified a locus on ECA7 for further investigation (Pcorrected = 2.08 × 10−10). This locus contained a 3 Mb run of homozygosity in the 12 mushroom ponies tested. Analysis of high throughput Illumina sequencing data from one mushroom Shetland pony com...
Source: Genes - October 19, 2019 Category: Genetics & Stem Cells Authors: Jocelyn Tanaka Tosso Leeb James Rushton Thomas R. Famula Maura Mack Vidhya Jagannathan Christine Flury Iris Bachmann John Eberth Sue M. McDonnell Maria Cecilia T. Penedo Rebecca R. Bellone Tags: Article Source Type: research

Genes, Vol. 10, Pages 821: Non-Coding RNA Sequencing of Equine Endometrium During Maternal Recognition of Pregnancy
This study is the first to describe ncRNA transcriptome in equine endometrium. Identifying targets of these ncRNAs could lead to determining MRP. (Source: Genes)
Source: Genes - October 18, 2019 Category: Genetics & Stem Cells Authors: Kristin M. Klohonatz Stephen J. Coleman Ashley D. Cameron Ann M. Hess Kailee J. Reed Angela Canovas Juan F. Medrano Alma D. Islas-Trejo Ted Kalbfleisch Gerrit J. Bouma Jason E. Bruemmer Tags: Article Source Type: research

Genes, Vol. 10, Pages 822: Genetic Diversity Assessed by Genotyping by Sequencing (GBS) in Watermelon Germplasm
The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and population structure using STRUCTURE and discriminant analysis of principal components (DAPC) in watermelon accessions. Two groups of watermelons were used: 1) highly utilized 41 watermelon accessions at the National Agrobiodiversity Center (NAC) at the Rural Development Administration in South Korea; and 2) 27 Korean commercial watermelons. Results revealed the presence of four clusters within the p...
Source: Genes - October 18, 2019 Category: Genetics & Stem Cells Authors: Kyung Jun Lee Jung-Ro Lee Raveendar Sebastin Myoung-Jae Shin Seong-Hoon Kim Gyu-Taek Cho Do Yoon Hyun Tags: Article Source Type: research

Genes, Vol. 10, Pages 823: Dissecting the Genome-Wide Evolution and Function of R2R3-MYB Transcription Factor Family in Rosa chinensis
In this study, 121 predicted R2R3-MYB gene sequences were identified in the rose genome. Additionally, a phylogenomic synteny network (synnet) was applied for the R2R3-MYB gene families in 35 complete plant genomes. We also analyzed the R2R3-MYB genes regarding their genomic locations, Ka/Ks ratio, encoded conserved motifs, and spatiotemporal expression. Our results indicated that R2R3-MYBs have multiple synteny clusters. The RcMYB114a gene was included in the Rosaceae-specific Cluster 54, with independent evolutionary patterns. On the basis of these results and an analysis of RcMYB114a-overexpressing tobacco leaf samples,...
Source: Genes - October 18, 2019 Category: Genetics & Stem Cells Authors: Yu Han Jiayao Yu Tao Zhao Tangren Cheng Jia Wang Weiru Yang Huitang Pan Qixiang Zhang Tags: Article Source Type: research

Genes, Vol. 10, Pages 824: Implications of Gene Inheritance Patterns on the Heterosis of Abdominal Fat Deposition in Chickens
Chen Yang Heterosis, a phenomenon characterized by the superior performance of hybrid individuals relative to their parents, has been widely utilized in livestock and crop breeding, while the underlying genetic basis remains elusive in chickens. Here, we performed a reciprocal crossing experiment with broiler and layer chickens and conducted RNA sequencing on liver tissues for reciprocal crosses and their parental lines to identify inheritance patterns of gene expression. Our results showed that heterosis of the abdominal fat percentage was 69.28%–154.71% in reciprocal crosses. Over-dominant genes of r...
Source: Genes - October 18, 2019 Category: Genetics & Stem Cells Authors: Mai Wen Sun Xu Chen Yang Tags: Article Source Type: research

Genes, Vol. 10, Pages 825: Rare Genetic Variants in Jewish Patients Suffering from Age-Related Macular Degeneration
Conclusions: Rare, high-penetrance variants have a profound contribution to early-AMD pathogenesis. Utilization of WES in genetic research of multifactorial diseases as AMD, allows a thorough comprehensive analysis with the identification of previously unreported rare variants. (Source: Genes)
Source: Genes - October 18, 2019 Category: Genetics & Stem Cells Authors: Shoshany Weiner Safir Einan-Lifshitz Pokroy Kol Modai Shomron Pras Tags: Article Source Type: research

Genes, Vol. 10, Pages 820: The Complete Mitogenome of Pyrrhocoris tibialis (Hemiptera: Pyrrhocoridae) and Phylogenetic Implications
Ming-Long Yuan We determined the complete mitogenome of Pyrrhocoris tibialis (Hemiptera: Heteroptera: Pyrrhocoridae) to better understand the diversity and phylogeny within Pentatomomorpha, which is the second largest infra-order of Heteroptera. Gene content, gene arrangement, nucleotide composition, codon usage, ribosomal RNA (rRNA) structures, and sequences of the mitochondrial transcription termination factor were well conserved in Pyrrhocoroidea. Different protein-coding genes have been subject to different evolutionary rates correlated with the G + C content. The size of control regions (CRs) was highly variable ...
Source: Genes - October 18, 2019 Category: Genetics & Stem Cells Authors: Qi-Lin Zhang Run-Qiu Feng Min Li Zhong-Long Guo Li-Jun Zhang Fang-Zhen Luo Ya Cao Ming-Long Yuan Tags: Article Source Type: research

Genes, Vol. 10, Pages 817: Detection of Microaneurysms in Fundus Images Based on an Attention Mechanism
isong Liu Microaneurysms (MAs) are the earliest detectable diabetic retinopathy (DR) lesions. Thus, the ability to automatically detect MAs is critical for the early diagnosis of DR. However, achieving the accurate and reliable detection of MAs remains a significant challenge due to the size and complexity of retinal fundus images. Therefore, this paper presents a novel MA detection method based on a deep neural network with a multilayer attention mechanism for retinal fundus images. First, a series of equalization operations are performed to improve the quality of the fundus images. Then, based on the attention mechan...
Source: Genes - October 17, 2019 Category: Genetics & Stem Cells Authors: Lizong Zhang Shuxin Feng Guiduo Duan Ying Li Guisong Liu Tags: Article Source Type: research

Genes, Vol. 10, Pages 819: Erratum: The MAPKKK CgMck1 Is Required for Cell Wall Integrity, Appressorium Development, and Pathogenicity in Colletotrichum gloeosporioides (Genes 2018, 9, 543).
Ye Huang The authors wish to make the following correction to this paper [...] (Source: Genes)
Source: Genes - October 17, 2019 Category: Genetics & Stem Cells Authors: Fang Xia Wang Zhu Ye Huang Tags: Erratum Source Type: research

Genes, Vol. 10, Pages 818: Morphological Characterization of Flower Buds Development and Related Gene Expression Profiling at Bud Break Stage in Heterodichogamous Cyclocarya paliurus (Batal.) lljinskaja
Fang Cyclocarya paliurus (Batal.) Iljinskaja, a unique species growing in southern China, is a multi-function tree species with medicinal, healthcare, material, and ornamental values. So far, sexual reproduction is the main method for extensive cultivation of C. paliurus plantations, but this is limited by low seed plumpness resulted from the character of heterodichogamy. Phenological observations have revealed the asynchronism of flower development in this species. However, its molecular mechanism remains largely unknown. To reveal molecular mechanism of heterodichogamy in C. paliurus, transcriptome of female (F) ...
Source: Genes - October 17, 2019 Category: Genetics & Stem Cells Authors: Chen Mao Huang Fang Tags: Article Source Type: research

Genes, Vol. 10, Pages 816: TRIM39-RPP21 Variants ( ∆19InsCCC) Are Not Associated with Juvenile Idiopathic Epilepsy in Egyptian Arabian Horses
Genes, Vol. 10, Pages 816: TRIM39-RPP21 Variants (∆19InsCCC) Are Not Associated with Juvenile Idiopathic Epilepsy in Egyptian Arabian Horses Genes doi: 10.3390/genes10100816 Authors: Victor N. Rivas Monica Aleman Janel A. Peterson Anna R. Dahlgren Erin N. Hales Carrie J. Finno Juvenile idiopathic epilepsy (JIE) is an inherited disease characterized by recurrent seizures during the first year of life in Egyptian Arabian horses. Definitive diagnosis requires an electroencephalogram (EEG) performed by a veterinary specialist. A recent study has suggested that a 19 base-pair deletion, along with a triple-C ...
Source: Genes - October 16, 2019 Category: Genetics & Stem Cells Authors: Victor N. Rivas Monica Aleman Janel A. Peterson Anna R. Dahlgren Erin N. Hales Carrie J. Finno Tags: Brief Report Source Type: research

Genes, Vol. 10, Pages 815: Ubiquitin Ligases Involved in the Regulation of Wnt, TGF- β, and Notch Signaling Pathways and Their Roles in Mouse Development and Homeostasis
Genes, Vol. 10, Pages 815: Ubiquitin Ligases Involved in the Regulation of Wnt, TGF-β, and Notch Signaling Pathways and Their Roles in Mouse Development and Homeostasis Genes doi: 10.3390/genes10100815 Authors: Nikol Baloghova Tomas Lidak Lukas Cermak The Wnt, TGF-β, and Notch signaling pathways are essential for the regulation of cellular polarity, differentiation, proliferation, and migration. Differential activation and mutual crosstalk of these pathways during animal development are crucial instructive forces in the initiation of the body axis and the development of organs and tissues. Due...
Source: Genes - October 16, 2019 Category: Genetics & Stem Cells Authors: Nikol Baloghova Tomas Lidak Lukas Cermak Tags: Review Source Type: research

Genes, Vol. 10, Pages 811: Comprehensive Insight into Gibberellin- and Jasmonate-Mediated Stamen Development
czek In flowering plants, proper development of male generative organs is required for successful sexual reproduction. Stamen primordia arise in the third whorl of floral organs and subsequently differentiate into filaments and anthers. The early phase of stamen development, in which meiosis occurs, is followed by a late developmental phase, which consists of filament elongation coordinated with pollen maturation, anther dehiscence and finally viable pollen grain release. Stamen development and function are modulated by phytohormones, with a key role of gibberellins (GAs) and jasmonates (JAs). Long-term, extensive inve...
Source: Genes - October 15, 2019 Category: Genetics & Stem Cells Authors: Marciniak Przedniczek Tags: Review Source Type: research

Genes, Vol. 10, Pages 812: Identification of Key Genes for the Precise Classification between Solenopsis invicta and S. geminata Facilitating the Quarantine Process
ng Jae Kang One of the 100 worst invasive exotic species, Solenopsis invicta (red imported fire ant), has the possibility to induce an allergic reaction that may eventually cause death from its aggressive stinging. In 2017, S. invicta was found at a container yard in Gamman Port, Busan, South Korea for the first time. It may result in an infestation of fire ants in the Korean environment. After this incident, sensitive quarantine procedures are required to detect possible contamination of fire ants in imported containers. However, currently, fire ant identification relies on phenotypic characteristics. This requires hi...
Source: Genes - October 15, 2019 Category: Genetics & Stem Cells Authors: Kil-Hyun Kim Ji-Su Kim Hyun-Ji Cho Jong-Ho Lee Tae-Hwan Jun Yang Jae Kang Tags: Article Source Type: research

Genes, Vol. 10, Pages 813: Experimental Modeling of Myeloproliferative Neoplasms
rchal Myeloproliferative neoplasms (MPN) are genetically very complex and heterogeneous diseases in which the acquisition of a somatic driver mutation triggers three main myeloid cytokine receptors, and phenotypically expresses as polycythemia vera (PV), essential thrombocytosis (ET), and primary myelofibrosis (PMF). The course of the diseases may be influenced by germline predispositions, modifying mutations, their order of acquisition and environmental factors such as aging and inflammation. Deciphering these contributory elements, their mutual interrelationships, and their contribution to MPN pathogenesis brings imp...
Source: Genes - October 15, 2019 Category: Genetics & Stem Cells Authors: Lucie Lanikova Olga Babosova Josef T. Prchal Tags: Review Source Type: research

Genes, Vol. 10, Pages 814: Genomics of Avian Viral Infections
th The poultry industry currently accounts for the production of around 118 million metric tons of meat and around 74 million metric tons of eggs annually. As the global population continues to increase, so does our reliance on poultry as a food source. It is therefore of vital importance that we safeguard this valuable resource and make the industry as economically competitive as possible. Avian viral infections, however, continue to cost the poultry industry billions of dollars annually. This can be in terms of vaccination costs, loss of birds and decreased production. With a view to improving the health and welfare ...
Source: Genes - October 15, 2019 Category: Genetics & Stem Cells Authors: Smith Tags: Editorial Source Type: research

Genes, Vol. 10, Pages 805: Upregulated microRNA-106a Promotes Porcine Preadipocyte Proliferation and Differentiation by Targeting Different Genes
In this study, preadipocytes were isolated from the neck subcutaneous deposits of 3–5-day old Chinese native Guanzhong black pigs using 5-ethynyl-20-deoxyuridine (EdU) staining and a CCK-8 assay to detect the number of proliferous cells and real-time qPCR (RT-qPCR) and western blot analysis to detect gene expression, as well as Oil Red O and BODIPY staining dye lipid droplets and flow cytometry (FCM) to detect cell cycles. We also used the double luciferase method to detect the relative luciferase activities. Upregulated miR-106a increased the number of proliferous cells and enhanced the expression of cell pr...
Source: Genes - October 14, 2019 Category: Genetics & Stem Cells Authors: Kuilong Huang Xin ’e Shi Jie Wang Ying Yao Ying Peng Xiaochang Chen Xiao Li Gongshe Yang Tags: Article Source Type: research

Genes, Vol. 10, Pages 806: A TAC3 Missense Variant in a Domestic Shorthair Cat with Testicular Hypoplasia and Persistent Primary Dentition
so Leeb A single male domestic shorthair cat that did not complete puberty was reported. At four years of age, it still had primary dentition, testicular hypoplasia, and was relatively small for its age. We hypothesized that the phenotype might have been due to an inherited form of hypogonadotropic hypogonadism (HH). We sequenced the genome of the affected cat and compared the data to 38 genomes from control cats. A search for private variants in 40 candidate genes associated with human HH revealed a single protein-changing variant in the affected cat. It was located in the TAC3 gene encoding tachykinin 3, a precursor ...
Source: Genes - October 14, 2019 Category: Genetics & Stem Cells Authors: Petra Hug Patricia Kern Vidhya Jagannathan Tosso Leeb Tags: Article Source Type: research

Genes, Vol. 10, Pages 807: D-GPM: A Deep Learning Method for Gene Promoter Methylation Inference
ng Li Li Whole-genome bisulfite sequencing generates a comprehensive profiling of the gene methylation levels, but is limited by a high cost. Recent studies have partitioned the genes into landmark genes and target genes and suggested that the landmark gene expression levels capture adequate information to reconstruct the target gene expression levels. This inspired us to propose that the methylation level of the promoters in landmark genes might be adequate to reconstruct the promoter methylation level of target genes, which would eventually reduce the cost of promoter methylation profiling. Here, we propose a d...
Source: Genes - October 14, 2019 Category: Genetics & Stem Cells Authors: Pan Liu Wen Liu Zhang Li Li Tags: Article Source Type: research

Genes, Vol. 10, Pages 808: Spatial Transcriptomic and miRNA Analyses Revealed Genes Involved in the Mesometrial-Biased Implantation in Pigs
In this study, the histological features of the entire uterine cross-section from gestational days 12 (pre-attachment stage) and 15 (post-attachment stage) were investigated and the differences in histological features between the mesometrial and anti-mesometrial side of the uterus were observed. Then, transcriptomic and miRNA analyses were performed on mesometrial and anti-mesometrial endometrium obtained from gestational days 12 and 15, respectively. Differentially expressed genes (DEGs) and miRNAs (DE-miRs) that were common to both or unique to either of the two anatomical locations of uterus were identified, respective...
Source: Genes - October 14, 2019 Category: Genetics & Stem Cells Authors: Huang Yang Tian Deng Yu Tags: Article Source Type: research

Genes, Vol. 10, Pages 809: Overexpression of OsPT8 Increases Auxin Content and Enhances Tolerance to High-Temperature Stress in Nicotiana tabacum
In this study, we showed that high temperatures could significantly reduce tobacco biomass and change its root architecture, probably through changes in auxin content and distribution. Overexpression of the OsPT8 phosphate transporter enhanced tobacco tolerance to high-temperature stress by changing the root architecture and increased the antioxidant ability. Molecular assays suggested that overexpression of OsPT8 in tobacco significantly increased the expression of auxin synthesis genes NtYUCCA 6, 8 and auxin efflux carriers genes NtPIN 1,2 under high-temperature stress. We also found that the expression levels of auxin r...
Source: Genes - October 14, 2019 Category: Genetics & Stem Cells Authors: Song Fan Jiao Liu Wang Jia Tags: Article Source Type: research

Genes, Vol. 10, Pages 810: Correction: Berner, D. Allele Frequency Difference AFD —An Intuitive Alternative to FST for Quantifying Genetic Population Differentiation. Genes 2019, 10, 308
Genes, Vol. 10, Pages 810: Correction: Berner, D. Allele Frequency Difference AFD—An Intuitive Alternative to FST for Quantifying Genetic Population Differentiation. Genes 2019, 10, 308 Genes doi: 10.3390/genes10100810 Authors: Berner This note is to correct an error in my paper, concerning the Shannon differentiation metric (DShannon) (Reference [43] in the paper). The paper states that DShannon is undefined mathematically whenever one or both populations are monomorphic, that is, fixed for a single allele. Accordingly, the DShannon curve in Figure 1a, showing population differentiation in relation to allel...
Source: Genes - October 14, 2019 Category: Genetics & Stem Cells Authors: Berner Tags: Correction Source Type: research

Genes, Vol. 10, Pages 804: Transcriptional Analysis of Masson Pine (Pinus massoniana) under High CO2 Stress
Kongshu Ji To explore the molecular mechanism of the response of Masson pine (Pinus massoniana), the main coniferous tree in southern China, to high CO2 stress, transcriptome sequencing was carried out to analyze the genome-wide responses of annual seedlings under different durations (0 h, 6 h, 12 h and 24 h) of high CO2 stress. The results showed that a total of 3080/1908, 3110/2115 and 2684/1483 genes were up-/down-regulated after 6 h, 12 h and 24 h of treatment, respectively, compared with control check group (CK, 0 h). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that most of these differential...
Source: Genes - October 13, 2019 Category: Genetics & Stem Cells Authors: Fan Wu Xiaobo Sun Bingzhang Zou Peihuang Zhu Nengqing Lin Jingquan Lin Kongshu Ji Tags: Article Source Type: research

Genes, Vol. 10, Pages 792: NGS Analysis for Molecular Diagnosis of Retinitis Pigmentosa (RP): Detection of a Novel Variant in PRPH2 Gene
In conclusion, PRPH2_c.668T > A provided a molecular explanation of RP symptomatology, highlighting the clinical utility of NGS panels to facilitate genotype–phenotype correlations. (Source: Genes)
Source: Genes - October 12, 2019 Category: Genetics & Stem Cells Authors: Claudia Strafella Valerio Caputo Giulia Pagliaroli Nicola Iozzo Giulia Campoli Stefania Carboni Cristina Peconi Rosaria Maria Galota Stefania Zampatti Giulietta Minozzi Giuseppe Novelli Emiliano Giardina Raffaella Cascella Tags: Article Source Type: research

Genes, Vol. 10, Pages 793: An SNP-Based Genetic Map and QTL Mapping for Growth Traits in the Red-Spotted Grouper (Epinephelus akaara)
In this study, a high-density genetic map was constructed using 3435 single nucleotide polymorphisms (SNPs) from 142 first generation (F1) full-sib offspring and two parents of a red-spotted grouper population. The total genetic length of the map was 2300.12 cM with an average intermarker distance of 0.67 cM. Seventeen genome-wide significant quantitative trait loci (QTLs) for growth-related traits were detected on 24 linkage groups, including 5 QTLs for full length, 7 QTLs for body length, and 5 QTLs for body weight. The contribution values of explained phenotypic variance ranged from 10.7% to 12.9%. Moreover, 13 potentia...
Source: Genes - October 12, 2019 Category: Genetics & Stem Cells Authors: Wang Jiang Zheng Xiao Zhang Wang Li Shi Wu Lin You Zhang Tags: Article Source Type: research

Genes, Vol. 10, Pages 794: Transcription Factors That Govern Development and Disease: An Achilles Heel in Cancer
charjee Development requires the careful orchestration of several biological events in order to create any structure and, eventually, to build an entire organism. On the other hand, the fate transformation of terminally differentiated cells is a consequence of erroneous development, and ultimately leads to cancer. In this review, we elaborate how development and cancer share several biological processes, including molecular controls. Transcription factors (TF) are at the helm of both these processes, among many others, and are evolutionarily conserved, ranging from yeast to humans. Here, we discuss four families of TFs...
Source: Genes - October 12, 2019 Category: Genetics & Stem Cells Authors: Dhananjay Huilgol Prabhadevi Venkataramani Saikat Nandi Sonali Bhattacharjee Tags: Review Source Type: research

Genes, Vol. 10, Pages 796: Characterization of GLOD4 in Leydig Cells of Tibetan Sheep During Different Stages of Maturity
Zhao Ma We have previously reported that glyoxalase domain-containing protein 4 (GLOD4) is expressed in sheep testes by proteome analysis, but its roles during testicular development remain unclear. The aim of this study was to understand the expression characteristics and biological functions of the GLOD4 gene in developmental Tibetan sheep testes. The cDNA sequence of the Tibetan sheep GLOD4 gene was cloned by the RT-PCR method, and the structural characteristics of the GLOD4 protein were analyzed using relevant bioinformatics software, including ProtParam, TMHMM, Signal P 4.1, SOPMA, and phyre2. The expression ...
Source: Genes - October 12, 2019 Category: Genetics & Stem Cells Authors: Wang Li Liu Zhang Zhao Ma Tags: Article Source Type: research

Genes, Vol. 10, Pages 797: Biological Network Approaches and Applications in Rare Disease Studies
tan Network biology has the capability to integrate, represent, interpret, and model complex biological systems by collectively accommodating biological omics data, biological interactions and associations, graph theory, statistical measures, and visualizations. Biological networks have recently been shown to be very useful for studies that decipher biological mechanisms and disease etiologies and for studies that predict therapeutic responses, at both the molecular and system levels. In this review, we briefly summarize the general framework of biological network studies, including data resources, network construction...
Source: Genes - October 12, 2019 Category: Genetics & Stem Cells Authors: Peng Zhang Yuval Itan Tags: Review Source Type: research

Genes, Vol. 10, Pages 798: Transcriptional Networks of Microglia in Alzheimer ’s Disease and Insights into Pathogenesis
Genes, Vol. 10, Pages 798: Transcriptional Networks of Microglia in Alzheimer’s Disease and Insights into Pathogenesis Genes doi: 10.3390/genes10100798 Authors: Chew Petretto Microglia, the main immune cells of the central nervous system, are increasingly implicated in Alzheimer’s disease (AD). Manifold transcriptomic studies in the brain have not only highlighted microglia’s role in AD pathogenesis, but also mapped crucial pathological processes and identified new therapeutic targets. An important component of many of these transcriptomic studies is the investigation of gene e...
Source: Genes - October 12, 2019 Category: Genetics & Stem Cells Authors: Chew Petretto Tags: Review Source Type: research

Genes, Vol. 10, Pages 795: Identification of Long Non-Coding RNA-Associated Competing Endogenous RNA Network in the Differentiation of Chicken Preadipocytes
Wang Wu Dai Emerging evidence indicates that long noncoding RNAs (lncRNAs) play important roles in the regulation of cell differentiation by acting as competing endogenous RNA (ceRNA). However, the regulatory mechanisms of lncRNA and the lncRNA-associated ceRNA network involved in adipogenic differentiation of chicken preadipocytes remain elusive. Here, we first constructed the chicken preadipocyte in vitro induction model. Then, we identified differentially expressed lncRNAs (DELs), miRNAs (DEMis), and mRNAs (DEMs) between differentiated and undifferentiated preadipocytes. Furthermore, we constructed the lncRNA...
Source: Genes - October 12, 2019 Category: Genetics & Stem Cells Authors: Chen Zhang Zhang Huang Zhang Xie Wang Wu Dai Tags: Article Source Type: research

Genes, Vol. 10, Pages 799: Severe Peripheral Joint Laxity is a Distinctive Clinical Feature of Spondylodysplastic-Ehlers-Danlos Syndrome (EDS)-B4GALT7 and Spondylodysplastic-EDS-B3GALT6
Superti-Furga Garavelli Variations in genes encoding for the enzymes responsible for synthesizing the linker region of proteoglycans may result in recessive conditions known as “linkeropathies”. The two phenotypes related to mutations in genes B4GALT7 and B3GALT6 (encoding for galactosyltransferase I and II respectively) are similar, characterized by short stature, hypotonia, joint hypermobility, skeletal features and a suggestive face with prominent forehead, thin soft tissue and prominent eyes. The most outstanding feature of these disorders is the combination of severe connective t...
Source: Genes - October 12, 2019 Category: Genetics & Stem Cells Authors: Caraffi Maini Ivanovski Pollazzon Giangiobbe Valli Rossi Sassi Faccioli Rocco Magnani Campos-Xavier Unger Superti-Furga Garavelli Tags: Article Source Type: research

Genes, Vol. 10, Pages 801: Transcriptomics of Tasmanian Devil (Sarcophilus Harrisii) Ear Tissue Reveals Homogeneous Gene Expression Patterns across a Heterogeneous Landscape
er Joanna L. Kelley In an era of unprecedented global change, exploring patterns of gene expression among wild populations across their geographic range is crucial for characterizing adaptive potential. RNA-sequencing studies have successfully characterized gene expression differences among populations experiencing divergent environmental conditions in a wide variety of taxa. However, few of these studies have identified transcriptomic signatures to multivariate, environmental stimuli among populations in their natural environments. Herein, we aim to identify environmental and sex-driven patterns of gene expression i...
Source: Genes - October 12, 2019 Category: Genetics & Stem Cells Authors: Alexandra K. Fraik Corey Quackenbush Mark J. Margres Sebastien Comte David G. Hamilton Christopher P. Kozakiewicz Menna Jones Rodrigo Hamede Paul A. Hohenlohe Andrew Storfer Joanna L. Kelley Tags: Article Source Type: research

Genes, Vol. 10, Pages 802: Transcription Factor CEBPB Inhibits the Expression of the Human HTR1A by Binding to 5 ’ Regulatory Region in Vitro
This study identified a transcription factor that might bind to the 5’ regulatory region of the HTR1A and explored the potential effect on 5-HT1A receptor expression. Based on JASPAR predictions, the binding of the transcription factor was demonstrated using the electrophoretic mobility shift assay (EMSA). Vectors over-expressing the transcription factor were co-transfected into HEK-293 and SK-N-SH cells with the recombinant pGL3 vector, and relative fluorescence intensity was measured to determine regulatory activity. Additionally, the qRT-PCR and Western blot were also used to identify whether the transcrip...
Source: Genes - October 12, 2019 Category: Genetics & Stem Cells Authors: Liu Wu Meng Ding Xu Zhang Yao Wang Tags: Article Source Type: research

Genes, Vol. 10, Pages 800: Pollination Drop Proteome and Reproductive Organ Transcriptome Comparison in Gnetum Reveals Entomophilous Adaptation
This study compared the proteome in the pollination drops of these two species using label-free quantitative techniques. The transcriptomes of fertile reproductive units (FRUs) and sterile reproductive units (SRUs) for each species were furthermore compared using Illumina Hiseq sequencing, and integrated proteomic and transcriptomic analyses were subsequently performed. Our results show that the differentially expressed proteins between FRUs and SRUs were involved in carbohydrate metabolism, the biosynthesis of amino acids and ovule defense. In addition, the differentially expressed genes between the FRUs and SRUs (e.g., M...
Source: Genes - October 12, 2019 Category: Genetics & Stem Cells Authors: Chen Hou Richard M. K. Saunders Nan Deng Tao Wan Yingjuan Su Tags: Article Source Type: research

Genes, Vol. 10, Pages 803: GWAS Discovery Of Candidate Genes for Yield-Related Traits in Peanut and Support from Earlier QTL Mapping Studies
n Sun Shan Peanut (Arachis hypogaea L.) is one of the most important oil crops worldwide, and its yet increasing market demand may be met by genetic improvement of yield related traits, which may be facilitated by a good understanding of the underlying genetic base of these traits. Here, we have carried out a genome-wide association study (GWAS) with the aim to identify genomic regions and the candidate genes within these regions that may be involved in determining the phenotypic variation at seven yield-related traits in peanut. For the GWAS analyses, 195 peanut accessions were phenotyped and/or genotyped; the l...
Source: Genes - October 12, 2019 Category: Genetics & Stem Cells Authors: Wang Yan Li Li Zhao Yuan Sun Shan Tags: Article Source Type: research

Genes, Vol. 10, Pages 791: Broken by the Cut: A Journey into the Role of Topoisomerase II in DNA Fragility
We describe the repair processes that follow removal of TOP2 adducts and the resultant broken DNA ends, and present how these processes can contribute to disease-associated mutations. Furthermore, we examine the involvement of TOP2-induced breaks in the formation of oncogenic translocations of leukemia and papillary thyroid cancer, as well as the role of TOP2 and proteins which repair TOP2 adducts in other diseases. The participation of TOP2 in generating persistent DNA breaks and leading to diseases such as cancer, could have an impact on disease treatment and prevention. (Source: Genes)
Source: Genes - October 12, 2019 Category: Genetics & Stem Cells Authors: Naomi D. Atkin Heather M. Raimer Yuh-Hwa Wang Tags: Review Source Type: research

Genes, Vol. 10, Pages 788: Human Colorectal Cancer from the Perspective of Mouse Models
r Korinek Colorectal cancer (CRC) is a heterogeneous disease that includes both hereditary and sporadic types of tumors. Tumor initiation and growth is driven by mutational or epigenetic changes that alter the function or expression of multiple genes. The genes predominantly encode components of various intracellular signaling cascades. In this review, we present mouse intestinal cancer models that include alterations in the Wnt, Hippo, p53, epidermal growth factor (EGF), and transforming growth factor β (TGFβ) pathways; models of impaired DNA mismatch repair and chemically induced tumorigenes...
Source: Genes - October 11, 2019 Category: Genetics & Stem Cells Authors: Monika Stastna Lucie Janeckova Dusan Hrckulak Vitezslav Kriz Vladimir Korinek Tags: Review Source Type: research

Genes, Vol. 10, Pages 789: Transcriptome-Based SNP Discovery and Validation in the Hybrid Zone of the Neotropical Annual Fish Genus Austrolebias
Sebastián Serra Marcelo Loureiro The genus Austrolebias (Cyprinodontiformes: Rivulidae) represents a specious group of taxa following annual life cycles in the neotropical ichthyofauna. They live in temporary ponds and each generation must be completed in a few months, depending on environmental stochasticity. Annual fish survive the dry season through diapausing eggs buried in the substrate of these ponds. A hypothesized bimodal hybrid zone between two taxa of the genus, A. charrua and A. reicherti from Dos Patos Merin lagoon system, was recently proposed based on genetics and morphological analyses. However,...
Source: Genes - October 11, 2019 Category: Genetics & Stem Cells Authors: Graciela Garc ía N éstor Ríos Ver ónica Gutiérrez Sebasti án Serra Marcelo Loureiro Tags: Article Source Type: research

Genes, Vol. 10, Pages 790: The G119S Acetylcholinesterase (Ace-1) Target Site Mutation Confers Carbamate Resistance in the Major Malaria Vector Anopheles gambiae from Cameroon: A Challenge for the Coming IRS Implementation
ene-Fossog Wondji Growing resistance is reported to carbamate insecticides in malaria vectors in Cameroon. However, the contribution of acetylcholinesterase (Ace-1) to this resistance remains uncharacterised. Here, we established that the G119S mutation is driving resistance to carbamates in Anopheles gambiae populations from Cameroon. Insecticide bioassay on field-collected mosquitoes from Bankeng, a locality in southern Cameroon, showed high resistance to the carbamates bendiocarb (64.8% ± 3.5% mortality) and propoxur (55.71% ± 2.9%) but a full susceptibility to the organophosphate fe...
Source: Genes - October 11, 2019 Category: Genetics & Stem Cells Authors: Elanga-Ndille Nouage Ndo Binyang Assatse Nguiffo-Nguete Djonabaye Irwing Tene-Fossog Wondji Tags: Article Source Type: research