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Molecular Genetics and Genomics: MGG

Furong Qi, Airong Yang, Sadaf Ambreen, Xue Bai, Yali Hou, Xuemei Lu
Gene duplication and amino acid substitution are two types of genetic innovations of antiviral genes in inhibiting the emerging pathogens in different species. Mx proteins are well known for inhibiting negative-stranded RNA viruses and have evolved a number of paralogs or orthologs, showing distinct antiviral activities or capacities within or between species. The presence of upstream genes in the signaling pathway(s) that activates Mx genes (upstream regulators of Mx gene) also exhibits variety across species...
September 20, 2018: Molecular Genetics and Genomics: MGG
Line Katrine Klastrup, Stine Thorhauge Bak, Anders Lade Nielsen
The risk of developing metabolic diseases is conferred by genetic predisposition from risk genes and by environmental exposures that can manifest in epigenetic changes. The global rise in obesity and type II diabetes has motivated a search for the epigenetic factors underlying these diseases. The possibility of transgenerational inheritance of epigenetic changes raises questions regarding how spermatozoa transmit acquired epigenetic changes that affect the metabolic health of the next generation. The purpose of this review is to describe current key literature concerning small non-coding RNA (sncRNA), specifically (1) the effects of high-fat or low-protein diets on sncRNA presence in spermatozoa; (2) sncRNA transmission from father to offspring; and (3) the functional effects of inherited sncRNA on offspring metabolic phenotype...
September 18, 2018: Molecular Genetics and Genomics: MGG
Hao Zheng, Feifei Ren, Qiuyuan Lu, Zhenming Cao, Jichen Song, Min Feng, Jisheng Liu, Jingchen Sun
Bombyx mori Nucleopolyhedrovirus (BmNPV), which is a member of the Baculoviridae family, is a significant pathogen of the silkworm. The infection of BmNPV is often lethal and causes about 20% loss of cocoon in the silk industry annually. To explore the effects of different gene inhibition strategies on the replication cycle of baculovirus, we constructed the mutant virus to infect BmN cells directly and further identified ie0, ie1, and gp64 as the essential viral genes of BmNPV. To elucidate the significance of the inhibition effect of different interference strategies, we characterized and constructed the recombinant BmNPV that carried a single or multigene-interfering cassette...
September 18, 2018: Molecular Genetics and Genomics: MGG
Xiaoyong Pan, XiaoHua Hu, Yu-Hang Zhang, Lei Chen, LiuCun Zhu, ShiBao Wan, Tao Huang, Yu-Dong Cai
Breast cancer is a common and threatening malignant disease with multiple biological and clinical subtypes. It can be categorized into subtypes of luminal A, luminal B, Her2 positive, and basal-like. Copy number variants (CNVs) have been reported to be a potential and even better biomarker for cancer diagnosis than mRNA biomarkers, because it is considerably more stable and robust than gene expression. Thus, it is meaningful to detect CNVs of different cancers. To identify the CNV biomarker for breast cancer subtypes, we integrated the CNV data of more than 2000 samples from two large breast cancer databases, METABRIC and The Cancer Genome Atlas (TCGA)...
September 10, 2018: Molecular Genetics and Genomics: MGG
Xiaomei Tang, Jiying Jiang, Jinbao Zhu, Nan He, Jinlong Tan
Many non-small cell lung cancer (NSCLC) patients initially benefiting from gefitinib are confronted with acquired resistance. MiR-138 was previously stated as a growth inhibitor of several cancer cell lines including NSCLC cells and its expression level was significantly lower in gefitinib-resistant cells. The role of miR-138 in NSCLC cell lines PC9 and A549 was verified using methyl thiazolyl tetrazolium (MTT) assay and colony formation assay. Quantitative real-time PCR (RT-PCR) was employed to assess the level of miR-138 in gefitinib-sensitive PC9 cells and gefitinib-resistant PC9GR cells...
September 8, 2018: Molecular Genetics and Genomics: MGG
Md Siddiqur Rahman, Usma Aktar, Md Rafsan Jani, Swakkhar Shatabda
In bacterial DNA, there are specific sequences of nucleotides called promoters that can bind to the RNA polymerase. Sigma70 ([Formula: see text]) is one of the most important promoter sequences due to its presence in most of the DNA regulatory functions. In this paper, we identify the most effective and optimal sequence-based features for prediction of [Formula: see text] promoter sequences in a bacterial genome. We used both short-range and long-range DNA sequences in our proposed method. A very small number of effective features are selected from a large number of the extracted features using multi-window of different sizes within the DNA sequences...
September 5, 2018: Molecular Genetics and Genomics: MGG
Jimmy Obala, Rachit K Saxena, Vikas K Singh, C V Sameer Kumar, K B Saxena, Pangirayi Tongoona, Julia Sibiya, Rajeev K Varshney
Pigeonpea is an important source of dietary protein to over a billion people globally, but genetic enhancement of seed protein content (SPC) in the crop has received limited attention for a long time. Use of genomics-assisted breeding would facilitate accelerating genetic gain for SPC. However, neither genetic markers nor genes associated with this important trait have been identified in this crop. Therefore, the present study exploited whole genome re-sequencing (WGRS) data of four pigeonpea genotypes (~ 12X coverage) to identify sequence-based markers and associated candidate genes for SPC...
September 1, 2018: Molecular Genetics and Genomics: MGG
Qiyue Zhang, Yixuan Cao, Jianhua Chen, Jiawei Shen, Dandan Ke, Xiaofei Wang, Jue Ji, Yufeng Xu, Weijie Zhang, Yinhuan Shen, Dong Wang, Dun Pan, Zhuo Wang, Yongyong Shi, Shulin Cheng, Ying Zhao, Dajiang Lu
The ACTN3 gene locates on 11q13-q14 and encodes the α-actinin-3 protein, which is only expressed in human skeletal muscle and influenced muscle function and metabolism. The previous studies reported that SNP rs1815739 is associated with elite power athletes' performance. In this study, we investigated the association between five SNPs within the ACTN3 gene and Chinese children physical fitness. We recruited 2244 Han Chinese children participants, and measured their 25-m run, stand broad jump, 10-m shuttle run, handgrip, BMI (calculated by weight and height) data...
August 30, 2018: Molecular Genetics and Genomics: MGG
Chunxia Ge, Xin Ai, Shengfeng Jia, Yinqing Yang, Lu Che, Zili Yi, Cuixia Chen
Miscanthus is recognized as a promising lignocellulosic crop for the production of bioethanol and bioproducts worldwide. To facilitate the identification of agronomical important traits and establish genetics knowledge, two genetic maps were developed from a controlled interspecific cross between M. floridulus and M. sacchariflorus. A total of 650 SSR markers were mapped in M. floridulus, spanning 19 linkage groups and 2053.31 cM with an average interval of 3.25 cM. The map of M. sacchariflorus comprised 495 SSR markers in 19 linkage groups covering 1684...
August 29, 2018: Molecular Genetics and Genomics: MGG
Haron Salih, Wenfang Gong, Shoupu He, Nada S Mustafa, Xiongming Du
Transcripts of uncertain coding potential (TUCP) are part of the LncRNAs, which encode some polypeptides. However, the abundance of TUCP transcripts and their roles in Ligon-linless-1 (Li-1) cotton mutant during the early termination of fiber development are still not documented. Li-1 mutant is one of the excellent modules for investigating fiber elongation processes due to its unique fiber developmental stages. To examine the function of TUCP in cotton fiber development, it is important to identify TUCPs and their involvement in fiber development...
August 29, 2018: Molecular Genetics and Genomics: MGG
Ilya G Kichigin, Artem P Lisachov, Massimo Giovannotti, Alex I Makunin, Marsel R Kabilov, Patricia C M O'Brien, Malcolm A Ferguson-Smith, Alexander S Graphodatsky, Vladimir A Trifonov
Supernumerary elements of the genome are often called B chromosomes. They usually consist of various autosomal sequences and, because of low selective pressure, are mostly pseudogenized and contain many repeats. There are numerous reports on B chromosomes in mammals, fish, invertebrates, plants, and fungi, but only a few of them have been studied using sequencing techniques. However, reptilian supernumerary chromosomes have been detected only cytogenetically and never sequenced or analyzed at the molecular level...
August 27, 2018: Molecular Genetics and Genomics: MGG
Ming Tan, Guofang Li, Xiaojie Liu, Fang Cheng, Juanjuan Ma, Caiping Zhao, Dong Zhang, Mingyu Han
Although gibberellin (GA) has been reported to control branching, little is known about how GA mediates signals regulating the outgrowth of axillary buds (ABs). In the current study, the effect of the exogenous application of 5.0 mM GA3 on ABs outgrowth on 1-year-old 'Nagafu No. 2'/T337/M. robusta Rehd. apple trees was investigated and compared to the bud-activating treatments, 5 mM BA or decapitation. Additionally, the expression of genes related to bud-regulating signals and sucrose levels in ABs was examined...
August 16, 2018: Molecular Genetics and Genomics: MGG
Yiheng Wang, Shengnan Huang, Zhiyong Liu, Xiaoyan Tang, Hui Feng
Polyploidization is considered as the major force that drives plant species evolution and biodiversity. The leaves of Chinese cabbage, an important vegetable crop valued for its nutritional quality, constitute the main edible organ. In this study, we found that autotetraploid Chinese cabbage (Brassica rapa ssp. pekinensis) generated from a doubled haploid (DH) line via isolated microspore culture exhibits a dwarf phenotype, along with thick leaves and delayed flowering. Abscisic acid (ABA) and brassinosteroid (BR) levels were significantly lower in autotetraploids compared to DHs...
August 16, 2018: Molecular Genetics and Genomics: MGG
Ya Hu, Yan-Fang Zhu, Ai-Xia Guo, Xu-Mei Jia, Li Cheng, Tong Zhao, Yan-Xiu Wang
Iron (Fe) deficiency is a frequent nutritional problem limiting apple production in calcareous soils. The utilization of rootstock that is resistant to Fe deficiency is an effective way to solve this problem. Malus halliana is an Fe deficiency-tolerant rootstock; however, few molecular studies have been conducted on M. halliana. In the present work, a transcriptome analysis was combined with qRT-PCR and sugar measurements to investigate Fe deficiency responses in M. halliana roots at 0 h (T1), 12 h (T2) and 72 h (T3) after Fe deficiency stress...
August 12, 2018: Molecular Genetics and Genomics: MGG
Kayla K Pennerman, Johanny Gonzalez, Lydia R Chenoweth, Joan W Bennett, Guohua Yin, Sui Sheng T Hua
Aflatoxins are toxic secondary metabolites produced by members of the genus Aspergillus, most notably A. flavus. Non-aflatoxigenic strains of A. flavus are commonly used for biocontrol of the aflatoxigenic strains to reduce aflatoxins in corn, cotton, peanuts and tree nuts. However, genomic differences between aflatoxigenic strains and non-aflatoxigenic strains have not been reported in detail, though such differences may further elucidate the evolutionary histories of certain biocontrol strains and help guide development of other useful strains...
August 11, 2018: Molecular Genetics and Genomics: MGG
Suvendhu S Dutta, Wricha Tyagi, Gratify Pale, Judith Pohlong, C Aochen, Avinash Pandey, Arunava Pattanayak, Mayank Rai
Light intensity is a crucial environmental factor that affects photosynthesis and ultimately, grain yield in rice. However, no gene or marker directly associated with improved performance under low-light intensity under field conditions has been identified till date. With an aim of identifying genes and markers associated with improved performance (measured in terms of better yields) under low-light intensity, an integrated field screening, in silico and wet lab validation analysis was performed. Field-based screening of a diverse set of 110 genotypes led to the identification of two physiological and three morphological parameters critical for low-light tolerance in rice...
August 7, 2018: Molecular Genetics and Genomics: MGG
Ratan Chopra, Charles E Simpson, Andrew Hillhouse, Paxton Payton, Jyotsna Sharma, Mark D Burow
QTL mapping of important architectural traits was successfully applied to an A-genome diploid population using gene-specific variations. Peanut wild species are an important source of resistance to biotic and possibly abiotic stress; because these species differ from the cultigen in many traits, we have undertaken to identify QTLs for several plant architecture-related traits. In this study, we took recently identified SNPs, converted them into markers, and identified QTLs for architectural traits. SNPs from RNASeq data distinguishing two parents, A...
August 1, 2018: 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
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