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https://www.readbyqxmd.com/read/30103093/mismatch-tolerance-during-homologous-recombination-in-mammalian-cells
#1
Shen Li, Bryan Wehrenberg, Barbara C Waldman, Alan S Waldman
We investigated the homology dependency of recombination in thymidine kinase (tk)-deficient mouse fibroblasts. Cells were transfected with DNA constructs harboring a herpes tk gene (the "recipient") rendered non-functional by an oligonucleotide containing the recognition site for endonuclease I-SceI. Constructs also contained a "donor" tk sequence that could restore function to the recipient gene through spontaneous gene conversion or via repair of a double-strand break (DSB) at the I-SceI site...
August 1, 2018: DNA Repair
https://www.readbyqxmd.com/read/30102599/construction-of-signaling-pathways-with-rnai-data-and-multiple-reference-networks
#2
Md Abdul Alim, Ahmet Ay, Md Mahmudul Hasan, My T Thai, Tamer Kahveci
Signaling networks are involved in almost all major diseases such as cancer. As a result of this, understanding how signaling networks function is vital for finding new treatments for many diseases. Using gene knockdown assays such as RNA interference (RNAi) technology, many genes involved in these networks can be identified. However, determining the interactions between these genes in the signaling networks using only experimental techniques is very challenging, as performing extensive experiments is very expensive and sometimes, even impractical...
July 2018: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/30102306/branch-pcr-constructed-tp53-gene-nanovector-for-potential-cancer-therapy
#3
Longhuai Cheng, Huiting Deng, Dejun Ma, Beibei Zhai, Qiangzhe Zhang, Luyuan Li, Zhen Xi
A novel and efficient branch PCR strategy has been used to construct a TP53 gene nanovector based on a pair of trimers as primers, which showed unique advantages compared to other existing systems for gene delivery and effective potential cancer therapy.
August 13, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/30101711/analyzing-of-molecular-networks-for-human-diseases-and-drug-discovery
#4
Tong Hao, Qian Wang, Lingxuan Zhao, Dan Wu, Edwin Wang, Jinsheng Sun
Molecular networks represent the interactions and relations of genes/proteins, and also encode molecular mechanisms of biological processes, development and diseases. Among the molecular networks, protein-protein interaction networks (PINs) have become effective platforms for uncovering the molecular mechanisms of diseases and drug discovery. PINs have been constructed for various organisms and utilized to solve many biological problems. In human, most proteins present their complex functions by interactions with other proteins, and the sum of these interactions represents the human protein interactome...
August 13, 2018: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/30100898/selection-of-pof-saccharomyces-eubayanus-variants-for-the-construction-of-s-cerevisiae-%C3%A3-s-eubayanus-hybrids-with-reduced-4-vinyl-guaiacol-formation
#5
Jasper A Diderich, Susan M Weening, Marcel van den Broek, Jack T Pronk, Jean-Marc G Daran
Saccharomyces pastorianus is an interspecies hybrid between S. cerevisiae and S. eubayanus . The identification of the parental species of S. pastorianus enabled the de novo reconstruction of hybrids that could potentially combine a wide array of phenotypic traits. Lager yeasts are characterized by their inability to decarboxylate ferulic acid present in wort, a phenotype also known as Pof - (phenolic off-flavor). However, all known S. eubayanus strains characterized so far produce clove-like aroma specific of 4-vinyl guaiacol, a decarboxylated form of ferulic acid...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30100882/dysfunction-of-sister-chromatids-separation-promotes-progression-of-hepatocellular-carcinoma-according-to-analysis-of-gene-expression-profiling
#6
Baozhen Sun, Guibo Lin, Degang Ji, Shuo Li, Guonan Chi, Xingyi Jin
Despite studying the various molecular mechanisms of hepatocellular carcinoma (HCC), effective drugs and biomarkers in HCC therapy are still scarce. The present study was designed to investigate dysregulated pathways, novel biomarkers and therapeutic targets for HCC. The gene expression dataset of GSE14520, which included 362 tumor and their paired non-tumor tissues of HCC, was extracted for processing by the Robust multi-array average (RMA) algorithm in the R environment. SAM methods were leveraged to identify differentially expressed genes (DEGs)...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/30100805/genome-re-sequencing-snp-analysis-and-genetic-mapping-of-the-parental-lines-of-a-commercial-f-1-hybrid-cultivar-of-chinese-cabbage
#7
Daniel J Shea, Motoki Shimizu, Etsuko Itabashi, Naomi Miyaji, Junji Miyazaki, Kenji Osabe, Makoto Kaji, Keiichi Okazaki, Ryo Fujimoto
The genome-wide characterization of single nucleotide polymorphism (SNP) between cultivars or between inbred lines contributes to the creation of genetic markers that are important for plant breeding. Functional markers derived from polymorphisms within genes that affect phenotypic variation are especially valuable in plant breeding. Here, we report on the genome re-sequencing and analysis of the two parental inbred lines of the commercial F1 hybrid Chinese cabbage cultivar "W77". Through the genome-wide identification and classification of the SNPs and indels present in each parental line, we identified about 1,500 putative non-functional genes in each parent...
June 2018: Breeding Science
https://www.readbyqxmd.com/read/30100738/identification-of-prognostic-risk-factors-for-esophageal-adenocarcinoma-using-bioinformatics-analysis
#8
Zhiyu Dong, Junwen Wang, Tingting Zhan, Shuchang Xu
Purpose: Esophageal adenocarcinoma (EAC) is the most common type of esophageal cancer in Western countries. It is usually detected at an advanced stage and has a poor prognosis. The aim of this study was to identify key genes and miRNAs in EAC. Methods: The mRNA microarray data sets GSE1420, GSE26886, and GSE92396 and miRNA data set GSE16456 were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were obtained using R software...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/30100472/comparison-of-quantitative-methods-based-on-sybr-green-real-time-qpcr-to-estimate-pork-meat-adulteration-in-processed-beef-products
#9
Tae Sun Kang, Takuji Tanaka
Quantitative real-time PCR (qPCR) is a modern technique that has been widely used for the detection of species used in meat products. For obtaining accurate and reliable qPCR results, we assessed two common DNA quantification methods for isolated DNA and five quantification approaches for qPCR products. DNA dilution based on spectrofluorometric results showed better qPCR results than those based on spectrophotometry in terms of linear correlation, amplification efficiency, and linear dynamic range. Binary pork-beef mixtures were used to construct standard curves of SYBR Green-based qPCR products using five quantification approaches, and they were validated and compared using in-house pork models...
December 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/30099537/construction-of-a-selectable-marker-recycling-system-and-the-use-in-epitope-tagging-and-disruption-of-multiple-nuclear-genes-in-the-unicellular-red-alga-cyanidioschyzon-merolae
#10
Tokiaki Takemura, Sousuke Imamura, Yuki Kobayashi, Kan Tanaka
The nuclear genome of the unicellular red alga Cyanidioschyzon merolae can be modified by homologous recombination with exogenously introduced DNA. However, it is presently difficult to modify multiple chromosome loci because of the limited number of available positive selectable markers. In this study, we constructed a modified URA5.3 gene (URA5.3T), which can be repeatedly used for nuclear genome transformation, as well as two plasmid vectors for 3 × FLAG- or 3 × Myc-epitope tagging of nuclear-encoded proteins using URA5...
August 7, 2018: Plant & Cell Physiology
https://www.readbyqxmd.com/read/30099455/profiles-and-bioinformatics-analysis-of-differentially-expressed-circrnas-in-taxol-resistant-non-small-cell-lung-cancer-cells
#11
Ning Xu, Shaomu Chen, Yufeng Liu, Wei Li, Zeyi Liu, Xiaojie Bian, Chunhua Ling, Min Jiang
BACKGROUND/AIMS: Circular RNAs (circRNAs) act as microRNA (miRNA) sponges that regulate gene expression and are involved in physiological and pathological processes. In this study, we evaluated the roles of circRNAs in the chemoresistance of non-small cell lung cancer (NSCLC) to taxol. METHODS: High-throughput circRNA microarrays were employed to investigate the circRNA profiles of parental A549 and taxol-resistant A549/Taxol cells. We predicted the miRNA targets of differentially expressed circRNAs via miRNA prediction software and then constructed a circRNA/miRNA network using Cytoscape...
August 10, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/30099452/11%C3%AE-hydroxysteroid-dehydrogenase-type-1-inhibitor-development-by-lentiviral-screening-based-on-computational-modeling
#12
Haifeng Liu, Lingyu Li, Chunlei Zhang, Hongzhi Li, Jieting Liu, Chunyin Tang, Yufei Zhang, Dan Wu, Yanhui Chu, Yan Wu, Xiaohuan Yuan
In this study, rat and human 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) have been cloned by lentiviral transduction and expressed by CHO-K1 cells. The results showed that recombinant plasmids contained R11bhsd1 or H11bhsd1 have been constructed, which is consistent with the gene bank respectively. A clone cell was selected with G418 and cultivated to express 11β-HSD1. 11β-HSD1 catalytic activity of rat and human were 99.5 and 98.7%, respectively, determined by scanning radiometer. And the cloned CHO-K1 cells expressed the protein of 11β-HSD1 in a long-term and stable manner, which makes it suitable for screening 11β-HSD1 inhibitor...
August 10, 2018: Pharmacology
https://www.readbyqxmd.com/read/30099343/cathepsin-b-contributes-to-radioresistance-by-enhancing-homologous-recombination-in-glioblastoma
#13
Xin Zhang, Xuehai Wang, Shujun Xu, Xingang Li, Xiangyu Ma
Resistance to adjuvant radiotherapy is a major cause of treatment failure in patients with glioblastoma (GBM). Recently, the role of lysosome, especially lysosomal proteases, in radioresistance is being paid more and more attention to. Here, we investigated the radioresistant role of Cathepsin B (CTSB), one important member of cysteine proteases, in GBM cell lines. A protease array kit was used to test GBM cells before and after irradiation. Nude mice were implanted with GBM cells to generate orthotopic xenografts for in vivo studies...
August 9, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/30099025/transcriptional-analysis-identifies-major-pathways-as-response-components-to-sporisorium-scitamineum-stress-in-sugarcane
#14
Ning Huang, Hui Ling, Yachun Su, Feng Liu, Liping Xu, Weihua Su, Qibin Wu, Jinlong Guo, Shiwu Gao, Youxiong Que
BACKGROUND: Sugarcane smut, which is caused by Sporisorium scitamineum, is a severe fungal disease affecting sugarcane. However, the major pathways involved in the interaction between sugarcane and S. scitamineum remains unclear. RESULTS: In the present study, suppression subtractive hybridization (SSH) library construction, together with reverse northern blotting, was conducted on the most prevalent sugarcane genotype ROC22 challenged with S. scitamineum. After alignment and homologous expressed sequence tag (EST) assembly, a total of 155 differentially expressed unigenes were identified from SSH libraries...
August 9, 2018: Gene
https://www.readbyqxmd.com/read/30099020/mechanism-of-men1-gene-in-radiation-induced-pulmonary-fibrosis-in-mice
#15
Wei Wei, Hai-Yang Zhang, Xin-Kou Gong, Zhuo Dong, Zhi-Yuan Chen, Rui Wang, Jun-Xuan Yi, Yan-Nan Shen, Shun-Zi Jin
OBJECTIVE: To investigate the regulatory mechanism of MEN1 gene in radiation-induced lung fibrosis in mice and provide a new theoretical basis for the clinical treatment of radiation pulmonary fibrosis. METHODS: First, 80 C57BL/6 mice aged 8 weeks and weighing 18-22 g were selected, half of them were male and the other half were female. The mice were divided into control group and irradiation group (40 mice in each group) according to the method of the random number table...
August 9, 2018: Gene
https://www.readbyqxmd.com/read/30098414/expression-purification-and-biological-activity-of-monomeric-insulin-precursors-from-methylotrophic-yeasts
#16
Sawanan Thongyoo, Tanapati Phakham, Nanthika Khongchareonporn, Onrapak Reamtong, Aphichart Karnchanatat, Songchan Phutong, Thanaporn Wichai, Sajee Noitang, Sarintip Sooksai
The methylotrophic yeasts Pichia pastoris and Hansenula polymorpha have been used for the production of recombinant monomeric insulin precursor (MIP). Recombinant plasmids with one, two and four cassettes of the MIP gene have been successfully constructed in the pPICZαA expression vector to study the effects of gene copy number on MIP production. The MIP protein can be detected by dot-blot analysis from the culture broth of P. pastoris KM71H 24 h after placement in MMH induction medium. The secretion levels of MIP protein in culture broth at 72 h after induction indicated that P...
August 8, 2018: Protein Expression and Purification
https://www.readbyqxmd.com/read/30097905/a-network-pharmacology-based-analysis-of-multi-target-multi-pathway-multi-compound-treatment-for-ovarian-serous-cystadenocarcinoma
#17
Dan-Dan Xiong, Yue Qin, Wen-Qing Xu, Rong-Quan He, Hua-Yu Wu, Dan-Min Wei, Jing-Jing Zeng, Yi-Wu Dang, Gang Chen
BACKGROUND AND OBJECTIVES: Pharmacological control against ovarian serous cystadenocarcinoma has received increasing attention. The purpose of this study was to investigate multi-drug treatments as synergetic therapy for ovarian serous cystadenocarcinoma and to explore their mechanisms of action by the network pharmacology method. METHODS: Genes acting on ovarian serous cystadenocarcinoma were first collected from GEPIA and DisGeNET. Gene Ontology annotation, Kyoto Encyclopedia of Genes and Genomes pathway, Reactome pathway, and Disease Ontology analyses were then conducted...
August 10, 2018: Clinical Drug Investigation
https://www.readbyqxmd.com/read/30097746/high-degree-and-broad-spectrum-resistance-mediated-by-a-combination-of-nib-sirna-and-mirna-suppresses-replication-of-necrotic-and-common-strains-of-potato-virus-y
#18
Ru Yu, Caixia Chen, Weilin Cao, Hongmei Liu, Shumei Zhou, Yunzhi Song, Changxiang Zhu
In plants, viral replication can be inhibited through gene silencing, which is mediated by short interfering RNA (siRNA) or microRNA (miRNA). However, under natural conditions, viruses are extremely susceptible to mutations that may decrease the efficiency of cleavage of these small RNAs (sRNAs). Therefore, a single sRNA may not provide a sufficient degree of viral resistance to transgenic plants. Potato virus Y necrotic strain (PVYN ) and Potato virus Y common strain (PVYO ) are the two major PVY strains that cause systemic necrosis and mottling, respectively, in tobacco...
August 10, 2018: Archives of Virology
https://www.readbyqxmd.com/read/30097448/orthologues-of-bacillus-subtilis-spore-crust-proteins-have-a-structural-role-in-the-bacillus-megaterium-qm-b1551-spore-exosporium
#19
Julia Manetsberger, Abhinaba Ghosh, Elizabeth A H Hall, Graham Christie
The exosporium of Bacillus megaterium QM B1551 spores is morphologically distinct to exosporia observed in spores of many other species. Previous work has demonstrated that unidentified genes encoded on one of the large indigenous plasmids are required for the assembly of the Bacillus megaterium exosporium. Here we provide evidence that pBM600-encoded orthologues of the Bacillus subtilis CotW and CotX proteins, which form the crust layer in spores of that species, are structural components of the Bacillus megaterium QM B1551 spore exosporium...
August 10, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/30096983/spectral-library-search-improves-assignment-of-tmt-labeled-ms-ms-spectra
#20
Jianqiao Shen, Vishwajeeth Reddy Pagala, Alex Michael Breuer, Junmin Peng, Bin Ma, Xusheng Wang
Tandem mass tag (TMT)-based liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a proven approach for large-scale multiplexed protein quantification. However, the identification of TMT-labeled peptides is compromised by the labeling during traditional sequence database search. In this study, we aim to use spectral library search to increase the sensitivity and specificity of peptide identification for TMT-based MS data. Compared to MS/MS spectra of unlabeled peptides, the spectra of TMT-labeled counterparts usually display intensified b ions, suggesting that TMT labeling can alter product ion patterns during MS/MS fragementation...
August 10, 2018: Journal of Proteome Research
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