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Expression genomic integration

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https://www.readbyqxmd.com/read/29331932/cnv-biology-in-neurodevelopmental-disorders
#1
REVIEW
Toru Takumi, Kota Tamada
Copy number variants (CNVs), characterized in recent years by cutting-edge technology, add complexity to our knowledge of the human genome. CNVs contribute not only to human diversity but also to different kinds of diseases including neurodevelopmental delay, autism spectrum disorder and neuropsychiatric diseases. Interestingly, many pathogenic CNVs are shared among these diseases. Studies suggest that pathophysiology of disease may not be simply attributed to a single driver gene within a CNV but also that multifactorial effects may be important...
January 10, 2018: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/29330186/effect-of-plasmid-design-and-type-of-integration-event-on-recombinant-protein-expression-in-pichia-pastoris
#2
Thomas Vogl, Leigh Gebbie, Robin W Palfreyman, Robert Speight
Pichia pastoris (syn. Komagataella phaffii) is one of the most common eukaryotic expression systems for heterologous protein production. Expression cassettes are typically integrated in the genome to obtain stable expression strains. In contrast to Saccharomyces cerevisiae, where short overhangs are sufficient to target highly specific integration, long overhangs are more efficient in P. pastoris and ectopic integration of foreign DNA can occur. Here, we aimed to elucidate the influence of ectopic integration by high throughput screening of >700 transformants and whole genome sequencing of 27 transformants...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29330178/development-of-an-efficient-genome-editing-tool-in-bacillus-licheniformis-using-crispr-cas9-nickase
#3
Kaifeng Li, Dongbo Cai, Zhangqian Wang, Zhili He, Shouwen Chen
Bacillus strains are important industrial bacteria that can produce various biochemical products. However, low transformation efficiencies and a lack of effective genome editing tools have hindered its widespread application. Recently, clustered regularly interspaced short palindromic repeat (CRISPR)/cas9 techniques have been utilized in many organisms as genome editing tools because of their high efficiency and easy manipulation. In this study, an efficient genome editing method was developed for Bacillus licheniformis using a CRISPR-Cas9 nickase integrated into the genome of B...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29329368/discovering-personalized-driver-mutation-profiles-of-single-samples-in-cancer-by-network-control-strategy
#4
Wei-Feng Guo, Shao-Wu Zhang, Li-Li Liu, Fei Liu, Qian-Qian Shi, Lei Zhang, Ying Tang, Tao Zeng, Luonan Chen
Motivation: It is a challenging task to discover personalized driver genes that provide crucial information on disease risk and drug sensitivity for individual patients. However, few methods have been proposed to identify the personalized-sample driver genes from the cancer omics data due to the lack of samples for each individual. To circumvent this problem, here we present a novel single-sample controller strategy (SCS) to identify personalized driver mutation profiles from network controllability perspective...
January 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29328472/combined-analysis-of-gene-expression-and-genome-binding-profiles-identified-potential-therapeutic-targets-of-ciclopirox-in-ewing-sarcoma
#5
Baisheng Yuan, Wei Ji, Haipeng Xia, Jianmin Li
Ciclopirox (CPX) is a synthetic antifungal drug that is mainly used to treat dermatomycoses. The aim of the present study was to determine whether CPX could influence Ewing sarcoma progression. The present study suggested that CPX treatment may inhibit Ewing sarcoma (ES) progression through Ewing sarcoma breakpoint region 1‑Friend leukemia integration 1 (EWS‑FLI1), a common fusion transcript structure in patients with ES. To determine the underlying mechanisms of ES progression, cross analysis was conducted on three high‑throughput genome or transcript me datasets from the Gene Expression Omnibus...
January 10, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29328442/identification-of-differentially-expressed-genes-and-regulatory-relationships-in-huntington-s-disease-by-bioinformatics-analysis
#6
Xiaoyu Dong, Shuyan Cong
Huntington's disease (HD) is an inherited, progressive neurodegenerative disease caused by a CAG expansion in the huntingtin (HTT) gene; various dysfunctions of biological processes in HD have been proposed. However, at present the exact pathogenesis of HD is not fully understood. The present study aimed to explore the pathogenesis of HD using a computational bioinformatics analysis of gene expression. GSE11358 was downloaded from the Gene Expression Omnibus andthe differentially expressed genes (DEGs) in the mutant HTT knock‑in cell model STHdhQ111/Q111 were predicted...
January 9, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29328363/support-vector-machine-classifier-for-prediction-of-the-metastasis-of-colorectal-cancer
#7
Jiajun Zhi, Jiwei Sun, Zhongchuan Wang, Wenjun Ding
Colorectal cancer (CRC) is one of the most common cancers and a major cause of mortality. The present study aimed to identify potential biomarkers for CRC metastasis and uncover the mechanisms underlying the etiology of the disease. The five datasets GSE68468, GSE62321, GSE22834, GSE14297 and GSE6988 were utilized in the study, all of which contained metastatic and non-metastatic CRC samples. Among them, three datasets were integrated via meta-analysis to identify the differentially expressed genes (DEGs) between the two types of samples...
January 2, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29327725/whole-genome-sequencing-reveals-principles-of-brain-retrotransposition-in-neurodevelopmental-disorders
#8
Jasmine Jacob-Hirsch, Eran Eyal, Binyamin A Knisbacher, Jonathan Roth, Karen Cesarkas, Chen Dor, Sarit Farage-Barhom, Vered Kunik, Amos J Simon, Moran Gal, Michal Yalon, Sharon Moshitch-Moshkovitz, Rick Tearle, Shlomi Constantini, Erez Y Levanon, Ninette Amariglio, Gideon Rechavi
Neural progenitor cells undergo somatic retrotransposition events, mainly involving L1 elements, which can be potentially deleterious. Here, we analyze the whole genomes of 20 brain samples and 80 non-brain samples, and characterized the retrotransposition landscape of patients affected by a variety of neurodevelopmental disorders including Rett syndrome, tuberous sclerosis, ataxia-telangiectasia and autism. We report that the number of retrotranspositions in brain tissues is higher than that observed in non-brain samples and even higher in pathologic vs normal brains...
January 12, 2018: Cell Research
https://www.readbyqxmd.com/read/29327492/a-five-gene-signature-may-predict-sunitinib-sensitivity-and-serve-as-prognostic-biomarkers-for-renal-cell-carcinoma
#9
Yuan-Lei Chen, Guang-Ju Ge, Chao Qi, Huan Wang, Huai-Lan Wang, Li-Yang Li, Gong-Hui Li, Li-Qun Xia
Sunitinib resistance is, nowadays, the major challenge for advanced renal cell carcinoma patients. Illuminating the potential mechanisms and exploring effective strategies to overcome sunitinib resistance are highly desired. We constructed a reliable gene signature which may function as biomarkers for prediction of sunitinib sensitivity and clinical prognosis. The gene expression profiles were obtained from The Cancer Genome Atlas database. By performing GEO2R analysis, numerous differentially expressed genes (DEGs) were found to be associated with sunitinib resistance...
January 12, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29327352/ultrasound-findings-provide-clues-to-investigate-founder-mutations-expressed-as-runs-of-homozygosity-in-chromosomal-microarray-studies
#10
Hagit Daum, Israela Lerer, Ayala Frumkin, Daniel Rosenak, Nili Yanai, Shay Porat, Simcha Yagel, Vardiella Meiner
OBJECTIVES: Chromosomal microarray (CMA) analysis is effectively applied prenatally to detect copy number changes. SNP probes included in the microarray platform can detect regions of excessive homozygosity (ROH) and identical-by-descent genomic stretches. The utility of the latter as part of prenatal diagnosis is not well established. Recessive founder mutations are well recognized within distinct ethnic groups. Combining these data with prenatal sonography provides accurate focused molecular diagnoses quickly...
January 11, 2018: Prenatal Diagnosis
https://www.readbyqxmd.com/read/29325141/lncmap-pan-cancer-atlas-of-long-noncoding-rna-mediated-transcriptional-network-perturbations
#11
Yongsheng Li, Lili Li, Zishan Wang, Tao Pan, Nidhi Sahni, Xiyun Jin, Guangjuan Wang, Junyi Li, Xiangyi Zheng, Yunpeng Zhang, Juan Xu, Song Yi, Xia Li
Gene regulatory network perturbations contribute to the development and progression of cancer, however, molecular determinants that mediate transcriptional perturbations remain a fundamental challenge for cancer biology. We show that transcriptional perturbations are widely mediated by long noncoding RNAs (lncRNAs) via integration of genome-wide transcriptional regulation with paired lncRNA and gene expression profiles. Systematic construction of an LncRNA Modulator Atlas in Pan-cancer (LncMAP) reveals distinct types of lncRNA regulatory molecules, which are expressed in multiple tissues, exhibit higher conservation...
January 9, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29323249/probabilistic-data-integration-identifies-reliable-gametocyte-specific-proteins-and-transcripts-in-malaria-parasites
#12
Lisette Meerstein-Kessel, Robin van der Lee, Will Stone, Kjerstin Lanke, David A Baker, Pietro Alano, Francesco Silvestrini, Chris J Janse, Shahid M Khan, Marga van de Vegte-Bolmer, Wouter Graumans, Rianne Siebelink-Stoter, Taco W A Kooij, Matthias Marti, Chris Drakeley, Joseph J Campo, Teunis J P van Dam, Robert Sauerwein, Teun Bousema, Martijn A Huynen
Plasmodium gametocytes are the sexual forms of the malaria parasite essential for transmission to mosquitoes. To better understand how gametocytes differ from asexual blood-stage parasites, we performed a systematic analysis of available 'omics data for P. falciparum and other Plasmodium species. 18 transcriptomic and proteomic data sets were evaluated for the presence of curated "gold standards" of 41 gametocyte-specific versus 46 non-gametocyte genes and integrated using Bayesian probabilities, resulting in gametocyte-specificity scores for all P...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29323243/expression-of-cry2ah1-and-two-domain-ii-mutants-in-transgenic-tobacco-confers-high-resistance-to-susceptible-and-cry1ac-resistant-cotton-bollworm
#13
Shengyan Li, Zeyu Wang, Yiyao Zhou, Changhui Li, Guiping Wang, Hai Wang, Jie Zhang, Gemei Liang, Zhihong Lang
To improve the novel Bacillus thuringiensis insecticidal gene cry2Ah1 toxicity, two mutants cry2Ah1-vp (V354VP) and cry2Ah1-sp (V354SP) were performed. SWISS-MODEL analysis showed two mutants had a longer loop located between β-4 and β-5 of domain II, resulting in higher binding affinity with brush border membrane vesicles (BBMV) of Helicoverpa armigera comparing with Cry2Ah1. The cry2Ah1, cry2Ah1-vp, and cry2Ah1-sp were optimized codon usage according to plant codon bias, and named mcry2Ah1, mcry2Ah1-vp, and mcry2Ah1-sp...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322933/integrating-transcriptional-activity-in-genome-scale-models-of-metabolism
#14
Daniel Trejo Banos, Pauline Trébulle, Mohamed Elati
BACKGROUND: Genome-scale metabolic models provide an opportunity for rational approaches to studies of the different reactions taking place inside the cell. The integration of these models with gene regulatory networks is a hot topic in systems biology. The methods developed to date focus mostly on resolving the metabolic elements and use fairly straightforward approaches to assess the impact of genome expression on the metabolic phenotype. RESULTS: We present here a method for integrating the reverse engineering of gene regulatory networks into these metabolic models...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29322925/subtype-identification-from-heterogeneous-tcga-datasets-on-a-genomic-scale-by-multi-view-clustering-with-enhanced-consensus
#15
Menglan Cai, Limin Li
BACKGROUND: The Cancer Genome Atlas (TCGA) has collected transcriptome, genome and epigenome information for over 20 cancers from thousands of patients. The availability of these diverse data types makes it necessary to combine these data to capture the heterogeneity of biological processes and phenotypes and further identify homogeneous subtypes for cancers such as breast cancer. Many multi-view clustering approaches are proposed to discover clusters across different data types. The problem is challenging when different data types show poor agreement of clustering structure...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29322302/the-superiority-of-sucrose-cushion-centrifugation-to-ultrafiltration-and-pegylation-in-generating-high-titer-lentivirus-particles-and-transducing-stem-cells-with-enhanced-efficiency
#16
Mahdi Eskandarian Boroujeni, Mossa Gardaneh
Viral gene delivery is hailed as a great milestone in gene-based therapeutic approaches. The human immunodeficiency virus-derived lentiviral vectors (LVs) are advantageous in infecting both dividing and non-dividing cells leading to continuous expression of transgenes. A variety of protocols are available for concentration of LVs. We primarily generated our internal ribosome entry site (IRES)-based LVs. Virus titration and transduction efficiency were compared between various strategies that included sucrose cushion centrifugation (SCC), protein column ultrafiltration and polyethylene glycol precipitation...
January 10, 2018: Molecular Biotechnology
https://www.readbyqxmd.com/read/29321305/arabidopsis-rna-polymerase-v-mediates-enhanced-compaction-and-silencing-of-geminivirus-and-transposon-chromatin-during-host-recovery-from-infection
#17
Tami Coursey, Elizabeth Regedanz, David M Bisaro
Plants employ RNA-directed DNA methylation (RdDM) and dimethylation of histone 3 lysine 9 (H3K9me2) to silence geminiviruses and transposable elements (TEs). We previously showed that canonical RdDM (Pol IV-RdDM) involving RNA polymerases IV and V (Pol IV and Pol V) is required for Arabidopsis thaliana to recover from infection with Beet curly top virus lacking a suppressor protein that inhibits methylation (BCTV L2-). Recovery, which is characterized by reduced viral DNA levels and symptom remission, allows normal floral development...
January 10, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29321052/asgdb-a-specialised-genomic-resource-for-interpreting-anopheles-sinensis-insecticide%C3%A2-resistance
#18
Dan Zhou, Yang Xu, Cheng Zhang, Meng-Xue Hu, Yun Huang, Yan Sun, Lei Ma, Bo Shen, Chang-Liang Zhu
BACKGROUND: Anopheles sinensis is an important malaria vector in Southeast Asia. The widespread emergence of insecticide resistance in this mosquito species poses a serious threat to the efficacy of malaria control measures, particularly in China. Recently, the whole-genome sequencing and de novo assembly of An. sinensis (China strain) has been finished. A series of insecticide-resistant studies in An. sinensis have also been reported. There is a growing need to integrate these valuable data to provide a comprehensive database for further studies on insecticide-resistant management of An...
January 10, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29320986/revealing-alzheimer-s-disease-genes-spectrum-in-the-whole-genome-by-machine-learning
#19
Xiaoyan Huang, Hankui Liu, Xinming Li, Liping Guan, Jiankang Li, Laurent Christian Asker M Tellier, Huanming Yang, Jian Wang, Jianguo Zhang
BACKGROUND: Alzheimer's disease (AD) is an important, progressive neurodegenerative disease, with a complex genetic architecture. A key goal of biomedical research is to seek out disease risk genes, and to elucidate the function of these risk genes in the development of disease. For this purpose, expanding the AD-associated gene set is necessary. In past research, the prediction methods for AD related genes has been limited in their exploration of the target genome regions. We here present a genome-wide method for AD candidate genes predictions...
January 10, 2018: BMC Neurology
https://www.readbyqxmd.com/read/29317676/predicting-inhibitory-and-activatory-drug-targets-by-chemically-and-genetically-perturbed-transcriptome-signatures
#20
Ryusuke Sawada, Michio Iwata, Yasuo Tabei, Haruka Yamato, Yoshihiro Yamanishi
Genome-wide identification of all target proteins of drug candidate compounds is a challenging issue in drug discovery. Moreover, emerging phenotypic effects, including therapeutic and adverse effects, are heavily dependent on the inhibition or activation of target proteins. Here we propose a novel computational method for predicting inhibitory and activatory targets of drug candidate compounds. Specifically, we integrated chemically-induced and genetically-perturbed gene expression profiles in human cell lines, which avoided dependence on chemical structures of compounds or proteins...
January 9, 2018: Scientific Reports
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