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Molecular Genetics and Genomics: MGG

Chao Wu, Jun Yang, Shiyu Zhang, Jun Li, Hongzhong Jin, Xue Zhang
Acne inversa (AI) is a chronic inflammatory disease of hair follicles. The pathogenesis of AI remains unclear. Haploinsufficiency of genes encoding γ-secretase components is the genetic basis for a subset of familial AI. Idiopathic guttate hypomelanosis (IGH) is a leukoderma characterized by multiple porcelain-white macules. Familial AI associated with IGH has not been reported previously. Herein, we present the pathogenic variation in a Chinese Han family with AI and IGH. Peripheral blood samples were collected from 16 members of the entire family...
July 20, 2018: Molecular Genetics and Genomics: MGG
Craig D Soutar, John Stavrinides
For many pathogenic members of the Enterobacterales, siderophores play an important role in virulence, yet the siderophores of the host-associating members of the genus Pantoea remain unexplored. We conducted a genome-wide survey of environmental and host-associating strains of Pantoea to identify known and candidate siderophore biosynthetic clusters. Our analysis identified three clusters homologous to those of enterobactin, desferrioxamine, and aerobactin that were prevalent among Pantoea species. Using both phylogenetic and comparative genomic approaches, we demonstrate that the enterobactin-like cluster was present in the common ancestor of all Pantoea, with evidence for three independent losses of the cluster in P...
July 19, 2018: Molecular Genetics and Genomics: MGG
Ran Zhou, David Macaya-Sanz, Eli Rodgers-Melnick, Craig H Carlson, Fred E Gouker, Luke M Evans, Jeremy Schmutz, Jerry W Jenkins, Juying Yan, Gerald A Tuskan, Lawrence B Smart, Stephen P DiFazio
Dioecy has evolved numerous times in plants, but heteromorphic sex chromosomes are apparently rare. Sex determination has been studied in multiple Salix and Populus (Salicaceae) species, and P. trichocarpa has an XY sex determination system on chromosome 19, while S. suchowensis and S. viminalis have a ZW system on chromosome 15. Here we use whole genome sequencing coupled with quantitative trait locus mapping and a genome-wide association study to characterize the genomic composition of the non-recombining portion of the sex determination region...
July 18, 2018: Molecular Genetics and Genomics: MGG
Russell Reinke, Suk-Man Kim, Bo-Kyeong Kim
Yield losses as a result of biotic stresses by fungi, bacteria, viruses, and insects are a key challenge in most rice cultivation areas. The development of resistant cultivars is considered an efficient and sustainable approach to mitigate rice yield reduction. In the present study, we describe the development of japonica rice introgression lines with multiple resistance genes (MR lines), resistant to four different types of biotic stresses, and compare the agronomic performance, yield, and grain quality parameters of these lines with those of the recurrent parent...
July 5, 2018: Molecular Genetics and Genomics: MGG
Tengyue Wang, Lintao Hou, Hongju Jian, Feifei Di, Jiana Li, Liezhao Liu
Seed aging is an inevitable problem in the germplasm conservation of oil crops. Thus, clarifying the genetic mechanism of seed aging is important for rapeseed breeding. In this study, Brassica napus seeds were exposed to an artificial aging environment (40 °C and 90% relative humidity). Using a population of 172 recombinant inbred lines, 13 QTLs were detected on 8 chromosomes, which explained ~ 9.05% of the total phenotypic variation. The QTLs q2015AGIA-C08 and q2016AGI-C08-2 identified in the two environments were considered the same QTL...
July 4, 2018: Molecular Genetics and Genomics: MGG
Lin Chen, Muhammad Qasim Shahid, Jinwen Wu, Zhixiong Chen, Lan Wang, Xiangdong Liu
Autotetraploid rice is a useful germplasm that has four chromosome sets and strong biological advantages; however, low fertility limits its commercial utilization. Little information is available about the DNA variation and differential gene expressions associated with low fertility in autotetraploid rice. In the present study, 81 SNPs and 182 InDels were identified in T449 (an autotetraploid rice line with low fertility) compared to E249 (diploid counterpart) by whole-genome re-sequencing. We detected only three non-synonymous SNPs and six large-effect InDels, which were associated with three and six genes, respectively...
July 4, 2018: Molecular Genetics and Genomics: MGG
Z Juhász, E Dudás, Horolma Pamjav
We present a new self-learning computational method searching for footprints of early migration processes determining the genetic compositions of recent human populations. The data being analysed are 26- and 18-dimensional mitochondrial and Y-chromosomal haplogroup distributions representing 50 recent and 34 ancient populations in Eurasia and America. The algorithms search for associations of haplogroups jointly propagating in a significant subset of these populations. Joint propagations of Hgs are detected directly by similar ranking lists of populations derived from Hg frequencies of the 50 Hg distributions...
July 4, 2018: Molecular Genetics and Genomics: MGG
Lilin Xu, Chao Wang, Wen Cao, Shengmao Zhou, Tao Wu
Dwarf mutations have played vital roles in elucidating the regulatory molecular mechanisms of plant height. In this study, we identified a mutant named Csdw, whose mutagenesis was induced by ethyl methyl sulfonate in cucumber, and this mutant exhibited a dwarf phenotype with a reduced internode length because of the reduction of cell division in the main stem. The dwarf phenotype of Csdw could be partially rescued through GA3 application, and endogenous GA3 levels from the stem of Csdw decreased distinctly...
July 3, 2018: Molecular Genetics and Genomics: MGG
Luis Diaz-Garcia, Brandon Schlautman, Giovanny Covarrubias-Pazaran, Andrew Maule, Jennifer Johnson-Cicalese, Edward Grygleski, Nicholi Vorsa, Juan Zalapa
Because of its known phytochemical activity and benefits for human health, American cranberry (Vaccinium macrocarpon L.) production and commercialization around the world has gained importance in recent years. Flavonoid compounds as well as the balance of sugars and acids are key quality characteristics of fresh and processed cranberry products. In this study, we identified novel QTL that influence total anthocyanin content (TAcy), titratable acidity (TA), proanthocyanidin content (PAC), Brix, and mean fruit weight (MFW) in cranberry fruits...
July 2, 2018: Molecular Genetics and Genomics: MGG
Huitong Shi, Tao Zhou, Xiaozhu Wang, Yujia Yang, Chenglong Wu, Shikai Liu, Lisui Bao, Ning Li, Zihao Yuan, Yulin Jin, Suxu Tan, Wenwen Wang, Xiaoxiao Zhong, Guyu Qin, Xin Geng, Dongya Gao, Rex Dunham, Zhanjiang Liu
Disease resistance is one of the most important traits for aquaculture industry. For catfish industry, enteric septicemia of catfish (ESC), caused by the bacterial pathogen Edwardsiella ictaluri, is the most severe disease, causing enormous economic losses every year. In this study, we used three channel catfish families with 900 individuals (300 fish per family) and the 690K catfish SNP array, and conducted a genome-wide association study to detect the quantitative trait loci (QTL) associated with ESC resistance...
July 2, 2018: Molecular Genetics and Genomics: MGG
Zhe-Xin Li, Yan-Ru Fan, Shao-Fei Dang, Wan-Feng Li, Li-Wang Qi, Su-Ying Han
Somatic embryogenesis (SE) involves complex molecular signalling pathways. Understanding molecular mechanism of SE in Larix leptolepis (L. leptolepis) can aid research on genetic improvement of gymnosperms. Previously, we obtained five LaMIR166a (miR166a precursor) -overexpression embryonic cell lines in the gymnosperm Larix leptolepis. The proliferation rates of pro-embryogenic masses in transgenic and wild-type lines were calculated. Overexpression of the miR166a precursor LaMIR166a led to slower proliferation...
June 26, 2018: Molecular Genetics and Genomics: MGG
Mengjie Cui, Chen Wang, Wenying Zhang, Tariq Pervaiz, Muhammad Salman Haider, Wei Tang, Jinggui Fang
SPL is a plant-specific transcription factor family. Many researchers reported that SPL members targeted by miR156s could play crucial roles in the modulation of plant growth and development. Although there are similar reports on grapes, till now little is known about grape berry development and ripening. To gain more insight into how grape miR156s (Vv-miR156s) modulated the above given processes of grape berries by mediating their target gene Vv-SPLs, here we identified the precise sequences of Vv-miR156s in 'Giant Rose' grape berries, predicted their potential targets, and revealed that the matching degree of various Vv-miR156: Vv-SPL pairs exhibited some discrepancy, implying the divergence of their interaction...
June 25, 2018: Molecular Genetics and Genomics: MGG
Yinzhen Zheng, Junjie Yan, Shuzhen Wang, Meiling Xu, Keke Huang, Guanglong Chen, Yi Ding
Pectate lyase catalyses the eliminative cleavage of de-esterified pectin, which is a major component of primary cell walls in many higher plants. Pectate lyase-like (PLL) genes have been identified in various plant species and are involved in a broad range of physiological processes associated with pectin degradation. Previous studies have functionally identified two PLL genes in rice (Oryza sativa. L). However, the knowledge concerning genome-wide analysis of this family remains limited, and functions of the other PLL genes have not been thoroughly elucidated to date...
June 25, 2018: Molecular Genetics and Genomics: MGG
Hao Zheng, Xiong Wang, Feifei Ren, Shenglong Zou, Min Feng, Liangliang Xu, Lunguang Yao, Jingchen Sun
The classical baculovirus display system (BDS) has often recruited fields including gene delivery, gene therapy, and the genetic engineering of vaccines, as it is capable of presenting foreign polypeptides on the membranes of recombinant baculovirus through a transmembrane protein. However, classical BDS's high cost, complicated operation, low display efficiency and its inability to simultaneously display multiple gene products impede its practicality. In this study, we present a novel and highly efficient display system based on ires-dependent gp64 for rescuing gp64-null Bacmid of baculovirus construction without affecting the viral replication cycle, which we name the baculovirus multigene display system (BMDS)...
June 19, 2018: Molecular Genetics and Genomics: MGG
Ling-Xiang Wang, Yan Lu, Chao Zhang, Lan-Hai Wei, Shi Yan, Yun-Zhi Huang, Chuan-Chao Wang, Swapan Mallick, Shao-Qing Wen, Li Jin, Shu-Hua Xu, Hui Li
Diffusion of Tibeto-Burman populations across the Tibetan Plateau led to the largest human community in a high-altitude environment and has long been a focus of research on high-altitude adaptation, archeology, genetics, and linguistics. However, much uncertainty remains regarding the origin, diversification, and expansion of Tibeto-Burman populations. In this study, we analyzed a 7.0M bp region of 285 Y-chromosome sequences, including 81 newly reported ones, from male samples from Tibeto-Burman populations and other related Eastern Asian populations...
June 19, 2018: Molecular Genetics and Genomics: MGG
Rencia van der Sluis
Benzoate (found in milk and widely used as preservative), salicylate (present in fruits and the active component of aspirin), dietary polyphenols produced by gut microbiota, metabolites from organic acidemias, and medium-chain fatty acids (MCFAs) are all metabolised/detoxified by the glycine conjugation pathway. Xenobiotics are first activated to an acyl-CoA by the mitochondrial xenobiotic/medium-chain fatty acid: CoA ligases (ACSMs) and subsequently conjugated to glycine by glycine N-acyltransferase (GLYAT)...
June 14, 2018: Molecular Genetics and Genomics: MGG
Katy Sánchez-Pozos, María Guadalupe Ortíz-López, Bárbara I Peña-Espinoza, María de Los Ángeles Granados-Silvestre, Verónica Jiménez-Jacinto, Jérôme Verleyen, Fasil Tekola-Ayele, Alejandro Sanchez-Flores, Marta Menjivar
It has been presumed that increased susceptibility in Mexicans to type 2 diabetes (T2D) is attributed to the Native American genetic ancestry. Nonetheless, it is not known if there are private genetic variants that confer susceptibility to develop T2D in our population. The Maya indigenous group has the highest proportion of Native American ancestry (98%) which makes it a representative group of the original peoples of Mexico. Thus, the aim of the present study is to identify new genetic variants associated with T2D in Maya families...
June 11, 2018: Molecular Genetics and Genomics: MGG
Baoyu Li, Shunsheng Wang, Shumei Wang
MicroRNAs (miRNAs) are a novel class of diagnostic and therapeutic target in cancer. Here, we aimed to explore the effects and mechanism of miR-195 regulation in colon cancer. The expressions of several putative miRNAs in colon tumors, compared to those in normal tissues, were investigated by bioinformatical analysis of a Gene Expression Omnibus database. Quantitative real-time PCR analysis (qRT-PCR) was used to validate the identified changes in normal tissues, primary tumors, and metastatic tumors. MTT, soft agar colony formation, and transwell assays were used to evaluate the effects of miR-195 overexpression or inhibition on cell viability, proliferation, migration, and invasion...
June 9, 2018: Molecular Genetics and Genomics: MGG
Boris Malyarchuk, Miroslava Derenko, Galina Denisova, Andrey Litvinov, Urszula Rogalla, Katarzyna Skonieczna, Tomasz Grzybowski, Klára Pentelényi, Zsuzsanna Guba, Tamás Zeke, Mária Judit Molnár
Complete mitochondrial genomics is an effective tool for studying the demographic history of human populations, but there is still a deficit of mitogenomic data in European populations. In this paper, we present results of study of variability of 80 complete mitochondrial genomes in two Hungarian populations from eastern part of Hungary (Szeged and Debrecen areas). The genetic diversity of Hungarian mitogenomes is remarkably high, reaching 99.9% in a combined sample. According to the analysis of molecular variance (AMOVA), European populations showed a low, but statistically significant level of between-population differentiation (Fst = 0...
June 9, 2018: Molecular Genetics and Genomics: MGG
Sakrapee Paisitkriangkrai, Kelly Quek, Eva Nievergall, Anissa Jabbour, Andrew Zannettino, Chung Hoow Kok
Recurrent oncogenic fusion genes play a critical role in the development of various cancers and diseases and provide, in some cases, excellent therapeutic targets. To date, analysis tools that can identify and compare recurrent fusion genes across multiple samples have not been available to researchers. To address this deficiency, we developed Co-occurrence Fusion (Co-fuse), a new and easy to use software tool that enables biologists to merge RNA-seq information, allowing them to identify recurrent fusion genes, without the need for exhaustive data processing...
June 7, 2018: Molecular Genetics and Genomics: MGG
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