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Molecular Genetics and Genomics: MGG

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https://www.readbyqxmd.com/read/29752548/highly-preserved-roles-of-brassica-mir172-in-polyploid-brassicas-ectopic-expression-of-variants-of-brassica-mir172-accelerates-floral-transition
#1
S M Shivaraj, Aditi Jain, Anandita Singh
Functional characterization of regulatory genes governing flowering time is a research priority for breeding earliness in crop Brassicas. Highly polyploid genomes of Brassicas pose challenges in unraveling homeolog gene function. In Arabidopsis, five MIR172 paralogs control flowering time and floral organ identity by down-regulating AP2 and AP2-like genes. The impact of homeolog diversification on MIR172 loci, however, needs to be examined in morphologically diverse Brassicas. Herein, we analyze fractionation status and phylogeny of MIR172 and target AP2 from Brassicas and compare functionality of MIR172 variants representing distinct sub-genomes and progenitor genomes...
May 11, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29752547/the-phosphatidylinositol-synthase-gene-ghpis-contributes-to-longer-stronger-and-finer-fibers-in-cotton
#2
Qin Long, Fang Yue, Ruochen Liu, Shuiqing Song, Xianbi Li, Bo Ding, Xingying Yan, Yan Pei
Cotton fibers are the most important natural raw material used in textile industries world-wide. Fiber length, strength, and fineness are the three major traits which determine the quality and economic value of cotton. It is known that exogenous application of phosphatidylinositols (PtdIns), important structural phospholipids, can promote cotton fiber elongation. Here, we sought to increase the in planta production of PtdIns to improve fiber traits. Transgenic cotton plants were generated in which the expression of a cotton phosphatidylinositol synthase gene (i...
May 11, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29752546/mir-514-attenuates-proliferation-and-increases-chemoresistance-by-targeting-atp-binding-cassette-subfamily-in-ovarian-cancer
#3
Sha Xiao, Ming Zhang, Chang Liu, Deling Wang
Cisplatin is one of the most popular chemotherapeutic drugs in treating ovarian cancer. Resistance to cisplatin is a common clinical challenge that needs to be solved to increase its anti-tumor effects. The relation of miR-514 expression with prognosis in ovarian cancer patients was analyzed based on GSE73584 datasets. The regulation of miR-514 on proliferation and cisplatin chemosensitivity of ovarian cells was examined by MTT assay, colony-formation assay and soft-agar colony-formation assay. Dual luciferase assay was performed to detect the direct interaction of miR-514 with its downstream targets...
May 11, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29744589/a-new-snp-in-cyosppdk-gene-is-associated-with-floury-endosperm-in-suweon-542
#4
Heng Wang, Young-Jun Mo, Da-Eun Im, Seong-Gyu Jang, Tae-Ho Ham, Joohyun Lee, Ji-Ung Jeung, Soon-Wook Kwon
Pyruvate orthophosphate dikinase (PPDK) is a component of glycolysis to mediate endosperm energy charge by adjusting the ratio of ATP to ADP and AMP that proposed to balance the flow of carbon into starch, protein, fatty acid and amino acid biosynthesis. However, these were inconsistent with the first report of a T-DNA insertional knockout mutant of the rice PPDK gene (flo4) showed that rice with inactivated PPDK gene failed to produce a opaque seeds. Therefore, the PPDK might have multifaceted functions in grain filling stage, which in some ways might depend on the direction of the reversible catalysis...
May 9, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29737402/gwas-analysis-using-interspecific-backcross-progenies-reveals-superior-blue-catfish-alleles-responsible-for-strong-resistance-against-enteric-septicemia-of-catfish
#5
Suxu Tan, Tao Zhou, Wenwen Wang, Yulin Jin, Xiaozhu Wang, Xin Geng, Jian Luo, Zihao Yuan, Yujia Yang, Huitong Shi, Dongya Gao, Rex Dunham, Zhanjiang Liu
Infectious diseases pose significant threats to the catfish industry. Enteric septicemia of catfish (ESC) caused by Edwardsiella ictaluri is the most devastating disease for catfish aquaculture, causing huge economic losses annually. Channel catfish and blue catfish exhibit great contrast in resistance against ESC, with channel catfish being highly susceptible and blue catfish being highly resistant. As such, the interspecific backcross progenies provide an ideal system for the identification of quantitative trait locus (QTL)...
May 8, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29721721/sorghum-ccoaomt-and-ccoaomt-like-gene-evolution-structure-expression-and-the-role-of-conserved-amino-acids-in-protein-activity
#6
M Rakoczy, I Femiak, M Alejska, M Figlerowicz, J Podkowinski
Sorghum is a crop plant that is grown for seeds, sucrose, forage and biofuel production. In all these applications, lignin is a superfluous component that decreases the efficiency of technological processes. Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) is an enzyme involved in monolignol synthesis that affects the efficiency of lignification and lignin composition. The sorghum genome harbors one CCoAOMT gene and six closely related CCoAOMT-like genes. The structures of four sorghum CCoAOMT-like enzymes suggest that these proteins might methylate caffeoyl coenzyme A and contribute to monolignol synthesis...
May 2, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29705936/microsatellite-analysis-and-marker-development-in-garlic-distribution-in-est-sequence-genetic-diversity-analysis-and-marker-transferability-across-alliaceae
#7
Karina Barboza, Vanesa Beretta, Perla C Kozub, Cecilia Salinas, Mauro M Morgenfeld, Claudio R Galmarini, Pablo F Cavagnaro
Allium vegetables, such as garlic and onion, have understudied genomes and limited molecular resources, hindering advances in genetic research and breeding of these species. In this study, we characterized and compared the simple sequence repeats (SSR) landscape in the transcriptomes of garlic and related Allium (A. cepa, A. fistulosum, and A. tuberosum) and non-Allium monocot species. In addition, 110 SSR markers were developed from garlic ESTs, and they were characterized-along with 112 previously developed SSRs-at various levels, including transferability across Alliaceae species, and their usefulness for genetic diversity analysis...
April 28, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29704047/genome-wide-evolutionary-characterization-and-expression-analyses-of-major-latex-protein-mlp-family-genes-in-vitis-vinifera
#8
Ningbo Zhang, Ruimin Li, Wei Shen, Shuzhen Jiao, Junxiang Zhang, Weirong Xu
The major latex protein/ripening-related protein (MLP/RRP) subfamily is known to be involved in a wide range of biological processes of plant development and various stress responses. However, the biological function of MLP/RRP proteins is still far from being clear and identification of them may provide important clues for understanding their roles. Here, we report a genome-wide evolutionary characterization and gene expression analysis of the MLP family in European Vitis species. A total of 14 members, was found in the grape genome, all of which are located on chromosome 1, where are predominantly arranged in tandem clusters...
April 27, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29696375/genomic-characterization-of-nitrospirillum-amazonense-strain-cbamc-a-nitrogen-fixing-bacterium-isolated-from-surface-sterilized-sugarcane-stems
#9
Stefan Schwab, Leonardo Araujo Terra, José Ivo Baldani
Nitrospirillum amazonense is a nitrogen-fixing bacterium that shows potential to promote plant growth when inoculated into sugarcane and rice plants. This microorganism has been the subject of biochemical and genetic characterization to elucidate important functions related to host plant interaction and growth promotion, including the determination of draft genome sequences of two strains, Y2 and CBAmC, the second of which is the aim of the present study. CBAmC has been isolated from sugarcane (Saccharum spp...
April 25, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29687157/hnmda-heterogeneous-network-based-mirna-disease-association-prediction
#10
Li-Hong Peng, Chuan-Neng Sun, Na-Na Guan, Jian-Qiang Li, Xing Chen
Recently, accumulating evidences have shown that microRNAs (miRNAs) could play key roles in the development and progression of multiple important human diseases. Nonetheless, due to the shortcoming of being expensive and time-consuming existing in experimental approaches, computational methods are needed for the prediction of potential miRNA-disease associations. In our study, we proposed a computational model named Heterogeneous Network-based MiRNA-Disease Association prediction (HNMDA) for the latent miRNA-disease association prediction by integrating known miRNA-disease associations, miRNA functional similarity, disease semantic similarity and Gaussian interaction profile kernel similarity...
April 23, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29671068/intracellular-generation-of-single-strand-template-increases-the-knock-in-efficiency-by-combining-crispr-cas9-with-aav
#11
Qing Xiao, Taishan Min, Shuangping Ma, Lingna Hu, Hongyan Chen, Daru Lu
Targeted integration of transgenes facilitates functional genomic research and holds prospect for gene therapy. The established microhomology-mediated end-joining (MMEJ)-based strategy leads to the precise gene knock-in with easily constructed donor, yet the limited efficiency remains to be further improved. Here, we show that single-strand DNA (ssDNA) donor contributes to efficient increase of knock-in efficiency and establishes a method to achieve the intracellular linearization of long ssDNA donor. We identified that the CRISPR/Cas9 system is responsible for breaking double-strand DNA (dsDNA) of palindromic structure in inverted terminal repeats (ITRs) region of recombinant adeno-associated virus (AAV), leading to the inhibition of viral second-strand DNA synthesis...
April 18, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29611056/cis-regulated-additively-expressed-genes-play-a-fundamental-role-in-the-formation-of-triploid-loquat-eriobotrya-japonica-thunb-lindl-heterosis
#12
Chao Liu, Di Wu, Lingli Wang, Jiangbo Dang, Qiao He, Qigao Guo, Guolu Liang
Triploid loquat (Eriobotrya japonica (Thunb.) Lindl.) has greater vigor than their respective diploid and tetraploid parents, but the molecular basis of this triploid heterosis remains unclear. Recent studies have suggested that DNA methylation is involved in heterosis, which is a recognized method of suppressing gene expression. However, our previous studies revealed a trend of increased DNA methylation in triploid loquat hybrids compared to their parents. To elucidate the mechanism of triploid loquat heterosis, we investigated the levels and regulation of relative gene expression between hybrid and parental lines using RNA-Seq technology...
April 2, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29594496/pdhs-elm-computational-predictor-for-plant-dnase-i-hypersensitive-sites-based-on-extreme-learning-machines
#13
Shanxin Zhang, Minjun Chang, Zhiping Zhou, Xiaofeng Dai, Zhenghong Xu
DNase I hypersensitive sites (DHSs) are hallmarks of chromatin zones containing transcriptional regulatory elements, making them critical in understanding the regulatory mechanisms of gene expression. Although large amounts of DHSs in the plant genome have been identified by high-throughput techniques, current DHSs obtained from experimental methods cover only a fraction of plant species and cell processes. Furthermore, these experimental methods are both time-consuming and expensive. Hence, it is urgent to develop automated computational means to efficiently and accurately predict DHSs in the plant genome...
March 29, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29589160/hla-c-06-02-independent-gender-related-association-of-psors1c3-and-psors1c1-cdsn-single-nucleotide-polymorphisms-with-risk-and-severity-of-psoriasis
#14
Andrzej Wiśniewski, Łukasz Matusiak, Aneta Szczerkowska-Dobosz, Izabela Nowak, Piotr Kuśnierczyk
Psoriasis vulgaris (PsV) is a common, chronic skin disease with a complex genetic and environmental etiology. We investigated, in 461 psoriatic patients and 454 healthy controls, the associations with psoriasis of four single-nucleotide polymorphisms (SNPs) from the psoriasis susceptibility 1 (PSORS1) interval: rs1062470 (PSORS1C1/CDSN), rs887466 (PSORS1C3), rs2894207 and rs10484554 (LOC105375015). The minor alleles of three SNPs (rs1062470A, rs2894207C and rs10484554T) strongly increased the disease risk (OR = 2...
March 27, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29589159/ten-alien-chromosome-additions-of-gossypium-hirsutum-gossypium-bickii-developed-by-integrative-uses-of-gish-and-species-specific-ssr-markers
#15
Dong Tang, Shouli Feng, Sai Li, Yu Chen, Baoliang Zhou
Gossypium bickii: (2n = 26, G1 G1 ), a wild diploid cotton, carries many favourable traits. However, these favourable traits cannot be directly transferred into G. hirsutum (2n = 52, AADD) cultivars due to the differences in genomes. Monosomic alien addition lines (MAALs) are considered an invaluable tool for the introgression of genes of interest from wild relatives into cultivated crops. In this study, the G. hirsutum-G. bickii amphidiploid (2n = 78, AADDG1 G1 ) was backcrossed with G. hirsutum to develop alien additions containing individual G...
March 27, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29572661/identification-and-functional-analysis-of-the-nlp-encoding-genes-from-the-phytopathogenic-oomycete-phytophthora-capsici
#16
Xiao-Ren Chen, Shen-Xin Huang, Ye Zhang, Gui-Lin Sheng, Yan-Peng Li, Feng Zhu
Phytophthora capsici is a hemibiotrophic, phytopathogenic oomycete that infects a wide range of crops, resulting in significant economic losses worldwide. By means of a diverse arsenal of secreted effector proteins, hemibiotrophic pathogens may manipulate plant cell death to establish a successful infection and colonization. In this study, we described the analysis of the gene family encoding necrosis- and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) in P. capsici, and identified 39 real NLP genes and 26 NLP pseudogenes...
March 23, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29557500/incidental-and-clinically-actionable-genetic-variants-in-1005-whole-exomes-and-genomes-from-qatar
#17
Abhinav Jain, Shrey Gandhi, Remya Koshy, Vinod Scaria
Incidental findings in genomic data have been studied in great detail in the recent years, especially from population-scale data sets. However, little is known about the frequency of such findings in ethnic groups, specifically the Middle East, which were not previously covered in global sequencing studies. The availability of whole exome and genome data sets for a highly consanguineous Arab population from Qatar motivated us to explore the incidental findings in this population-scale data. The sequence data of 1005 Qatari individuals were systematically analyzed for incidental genetic variants in the 59 genes suggested by the American College of Medical Genetics and Genomics...
March 20, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29549432/mexef-oprn-multidrug-efflux-pump-transporter-negatively-controls-n-acyl-homoserine-lactone-accumulation-in-pseudomonas-syringae-pv-tabaci-6605
#18
Takahiro Sawada, Miho Eguchi, Seiya Asaki, Ryota Kashiwagi, Kousuke Shimomura, Fumiko Taguchi, Hidenori Matsui, Mikihiro Yamamoto, Yoshiteru Noutoshi, Kazuhiro Toyoda, Yuki Ichinose
Our previous studies revealed that flagellar-motility-defective mutants such as ∆fliC of Pseudomonas syringae pv. tabaci 6605 (Pta6605) have remarkably reduced production of N-acyl-homoserine lactones (AHL), quorum-sensing molecules. To investigate the reason of loss of AHL production in ∆fliC mutant, we carried out transposon mutagenesis. Among approximately 14,000 transconjugants, we found 11 AHL production-recovered (APR) strains. In these APR strains, a transposon was inserted into either mexE or mexF, genes encoding for the multidrug efflux pump transporter MexEF-OprN, and mexT, a gene encoding a putative transcriptional activator for mexEF-oprN...
March 16, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29546464/chromosome-wide-gene-dosage-rebalance-may-benefit-tumor-progression
#19
Honglei Zhang, Xing Yang, Xu Feng, Haibo Xu, Qin Yang, Li Zou, Mei Yan, Dequan Liu, Xiaosan Su, Baowei Jiao
The high-risk of tumor initiation in patients with Turner syndrome (TS) characterized by X chromosome monosomy in women has been well established and aneuploidy, defined as an abnormal number of chromosomes, is a common feature in human cancer. However, the underlying mechanisms of X chromosome aneuploidy promoting tumorigenesis remain obscure. We propose that chromosome-wide gene dosage imbalance (CDI) may serve as an important mechanism. Here, we assess the relative expression ratios of X chromosome and autosomes (expression ratios of X:AA) between tumor samples and adjacent normal samples across 16 tumor types using expression datasets from The Cancer Genome Atlas (TCGA) project...
March 15, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29536180/downregulation-of-microrna-17-5p-improves-cardiac-function-after-myocardial-infarction-via-attenuation-of-apoptosis-in-endothelial-cells
#20
Shuo Yang, Tao Fan, Qi Hu, Weipan Xu, Jian Yang, Changwu Xu, Bofang Zhang, Jing Chen, Hong Jiang
MicroRNA-17-5p (miR-17-5p) was indicated to suppress the formation of blood vessels, which is associated with cardiac function after myocardial infarction. In this study, the relationship between miR-17-5p and cardiac function was researched. Human umbilical vein endothelial cells were infected with adenoviruses. Apoptosis was determined by Annexin V-7AAD/PI. Real-time RT-PCR was used to evaluate miR-17-5p and ERK levels. Western blotting was used to determine the levels of ERK, the anti-apoptosis protein bcl-2 and apoptosis proteins, including bax, caspase 3, and caspase 9...
March 13, 2018: Molecular Genetics and Genomics: MGG
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