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https://www.readbyqxmd.com/read/29140462/data-portal-for-the-library-of-integrated-network-based-cellular-signatures-lincs-program-integrated-access-to-diverse-large-scale-cellular-perturbation-response-data
#1
Amar Koleti, Raymond Terryn, Vasileios Stathias, Caty Chung, Daniel J Cooper, John P Turner, Dušica Vidovic, Michele Forlin, Tanya T Kelley, Alessandro D'Urso, Bryce K Allen, Denis Torre, Kathleen M Jagodnik, Lily Wang, Sherry L Jenkins, Christopher Mader, Wen Niu, Mehdi Fazel, Naim Mahi, Marcin Pilarczyk, Nicholas Clark, Behrouz Shamsaei, Jarek Meller, Juozas Vasiliauskas, John Reichard, Mario Medvedovic, Avi Ma'ayan, Ajay Pillai, Stephan C Schürer
The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and extensive reference library of cell-based perturbation-response signatures, along with novel data analytics tools to improve our understanding of human diseases at the systems level. In contrast to other large-scale data generation efforts, LINCS Data and Signature Generation Centers (DSGCs) employ a wide range of assay technologies cataloging diverse cellular responses...
November 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29124958/streptomyces-sp-is-a-powerful-biotechnological-tool-for-the-biodegradation-of-hch-isomers-biochemical-and-molecular-basis
#2
S A Cuozzo, P E Sineli, J Davila Costa, G Tortella
Actinobacteria are well-known degraders of toxic materials that have the ability to tolerate and remove organochloride pesticides; thus, they are used for bioremediation. The biodegradation of organochlorines by actinobacteria has been demonstrated in pure and mixed cultures with the concomitant production of metabolic intermediates including γ-pentachlorocyclohexene (γ-PCCH); 1,3,4,6-tetrachloro-1,4-cyclohexadiene (1,4-TCDN); 1,2-dichlorobenzene (1,2-DCB), 1,3-dichlorobenzene (1,3-DCB), or 1,4-dichlorobenzene (1,4-DCB); 1,2,3-trichlorobenzene (1,2,3-TCB), 1,2,4-trichlorobenzene (1,2,4-TCB), or 1,3,5-trichlorobenzene (1,3,5-TCB); 1,3-DCB; and 1,2-DCB...
November 10, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/29122012/drug-target-ontology-to-classify-and-integrate-drug-discovery-data
#3
Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J Yang, Cristian G Bologa, Tudor I Oprea, Stephan C Schürer
BACKGROUND: One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research and development resources. The Illuminating the Druggable Genome (IDG) project develops resources to catalyze the development of likely targetable, yet currently understudied prospective drug targets. A central component of the IDG program is a comprehensive knowledge resource of the druggable genome...
November 9, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29078818/the-human-lncrna-linc-pint-inhibits-tumor-cell-invasion-through-a-highly-conserved-sequence-element
#4
Oskar Marín-Béjar, Aina M Mas, Jovanna González, Dannys Martinez, Alejandro Athie, Xabier Morales, Mikel Galduroz, Ivan Raimondi, Elena Grossi, Shuling Guo, Ana Rouzaut, Igor Ulitsky, Maite Huarte
BACKGROUND: It is now obvious that the majority of cellular transcripts do not code for proteins, and a significant subset of them are long non-coding RNAs (lncRNAs). Many lncRNAs show aberrant expression in cancer, and some of them have been linked to cell transformation. However, the underlying mechanisms remain poorly understood and it is unknown how the sequences of lncRNA dictate their function. RESULTS: Here we characterize the function of the p53-regulated human lncRNA LINC-PINT in cancer...
October 27, 2017: Genome Biology
https://www.readbyqxmd.com/read/29065900/grcalculator-an-online-tool-for-calculating-and-mining-dose-response-data
#5
Nicholas A Clark, Marc Hafner, Michal Kouril, Elizabeth H Williams, Jeremy L Muhlich, Marcin Pilarczyk, Mario Niepel, Peter K Sorger, Mario Medvedovic
BACKGROUND: Quantifying the response of cell lines to drugs or other perturbagens is the cornerstone of pre-clinical drug development and pharmacogenomics as well as a means to study factors that contribute to sensitivity and resistance. In dividing cells, traditional metrics derived from dose-response curves such as IC 50 , AUC, and E max , are confounded by the number of cell divisions taking place during the assay, which varies widely for biological and experimental reasons. Hafner et al...
October 24, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29051223/crispr-cas9-based-screening-of-long-noncoding-rnas-lncrnas-in-macrophages-with-an-nf-kappa-b-reporter
#6
Sergio Covarrubias, Elektra K Robinson, Barbara Shapleigh, Apple Vollmers, Solomon Katzman, Nicole Hanley, Nicholas Fong, Michael T McManus, Susan Carpenter
The innate immune system protects against infections by initiating an inducible inflammatory response. NF-kappa B (NF-KB) is one of the critical transcription factors controlling this complex response, but some aspects of its regulation remain unclear. For example, although long noncoding RNAs (lncRNAs) have been shown to critically regulate gene expression, only a fraction of these have been functionally characterized, and the extent to which lncRNAs control NF-KB expression is unknown. Here, we describe the generation of a GFP-based NF-KB reporter system in immortalized murine bone marrow-derived macrophages (iBMDMs)...
October 19, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29050257/linc-ror-induces-epithelial-to-mesenchymal-transition-in-ovarian-cancer-by-increasing-wnt-%C3%AE-catenin-signaling
#7
Yanhui Lou, Huanhuan Jiang, Zhumei Cui, Lingzhi Wang, Xiangyu Wang, Tian Tian
Long intergenic non-protein coding RNA, regulator of reprogramming (linc-ROR) is an intergenic long non-coding RNA (lncRNA) previously shown to contribute to tumorigenesis in several malignancies. However, little is known about whether linc-ROR has a role in ovarian cancer progression. In this study, we found that linc-ROR expression was increased in high-grade ovarian serous cancer tissues compared with normal ovarian tissues or normal fallopian tube tissues. Furthermore, the level of linc-ROR expression was associated with ovarian cancer International Federation of Gynecology and Obstetrics stage and lymph node metastasis...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29041978/linc-ror-promotes-mapk-erk-signaling-and-confers-estrogen-independent-growth-of-breast-cancer
#8
Wan-Xin Peng, Jian-Guo Huang, Liu Yang, Ai-Hua Gong, Yin-Yuan Mo
BACKGROUND: The conversion from estrogen-dependent to estrogen-independent state of ER+ breast cancer cells is the key step to promote resistance to endocrine therapies. Although the crucial role of MAPK/ERK signaling pathway in estrogen-independent breast cancer cell growth is well established, the underlying mechanism is not fully understood. METHODS: In this study, we profiled lncRNA expression against a focused group of lncRNAs selected from lncRNA database...
October 17, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/29040414/luma-is-not-essential-for-murine-cardiac-development-and-function
#9
Matthew John Stroud, Xi Fang, Jianlin Zhang, Nuno Guimarães-Camboa, Jennifer Veevers, Nancy D Dalton, Yusu Gu, William H Bradford, Kirk L Peterson, Sylvia M Evans, Larry Gerace, Ju Chen
Aims: Luma is a recently discovered, evolutionarily conserved protein expressed in mammalian heart that is associated with the LInker of Nucleoskeleton and Cytoskeleton (LINC) complex. The LINC complex structurally integrates the nucleus and the cytoplasm, and plays a critical role in mechanotransduction across the nuclear envelope. Mutations in several LINC components in both humans and mice result in various cardiomyopathies, implying they play essential, non-redundant roles. A single amino acid substitution of serine 358 to leucine (S358L) in LUMA is the unequivocal cause of a distinct form of arrhythmogenic cardiomyopathy...
October 12, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/29028092/long-non-coding-rna-ror-is-a-novel-prognosis-factor-associated-with-non-small-cell-lung-cancer-progression
#10
C-H Qu, Q-Y Sun, F-M Zhang, Y-M Jia
OBJECTIVE: The aim of the present study was to determine the expression levels of long intergenic non-protein coding RNA, regulator of reprogramming (linc-ROR) in non-small-cell lung cancer (NSCLC) patients and to further explore the prognostic value of this lncRNA. PATIENTS AND METHODS: In our investigation, we determined the expression of linc-ROR in human NSCLC tissues and matched normal lung tissues by quantitative Real-time-PCR analysis. Also, correlations between linc-ROR expression and the clinicopathological features were evaluated...
September 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29021110/collaborative-care-from-the-emergency-department-for-injured-patients-with-prescription-drug-misuse-an-open-feasibility-study
#11
Lauren K Whiteside, Doyanne Darnell, Karlee Jackson, Jin Wang, Joan Russo, Dennis M Donovan, Douglas F Zatzick
Collaborative Care is a comprehensive longitudinal care management strategy. The purpose of this pilot effectiveness-implementation hybrid study was to determine the feasibility of a Collaborative Care intervention initiated from the Emergency Department and proceeding longitudinally for six months for injured patients with prescription drug misuse (PDM). Adult patients presenting to an urban ED with an injury were screened for eligibility from 2/2015-8/2015. Eligible participants with a positive screen for PDM were enrolled in the 'ED-LINC' intervention which included the following elements: 1) active care coordination and linkage, 2) medication safety and utilization of opioid guidelines 3) longitudinal care management and 4) utilization of Electronic Medical Record (EMR) innovations such as the statewide Emergency Department Information Exchange (EDIE) and statewide prescription monitoring program information for assessment and follow-up...
November 2017: Journal of Substance Abuse Treatment
https://www.readbyqxmd.com/read/28988861/centrifugal-displacement-of-nuclei-reveals-multiple-linc-complex-mechanisms-for-homeostatic-nuclear-positioning
#12
Ruijun Zhu, Susumu Antoku, Gregg G Gundersen
Nuclear movement is critical for developmental events, cell polarity, and migration and is usually mediated by linker of nucleoskeleton and cytoskeleton (LINC) complexes connecting the nucleus to cytoskeletal elements. Compared to active nuclear movement, relatively little is known about homeostatic positioning of nuclei, including whether it is an active process. To explore homeostatic nuclear positioning, we developed a method to displace nuclei in adherent cells using centrifugal force. Nuclei displaced by centrifugation rapidly recentered by mechanisms that depended on cell context...
October 23, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28986964/escaping-braf-inhibition-a-linc-with-non-coding-rnas
#13
Eleonora Leucci
No abstract text is available yet for this article.
October 6, 2017: Pigment Cell & Melanoma Research
https://www.readbyqxmd.com/read/28973463/paragsea-a-scalable-approach-for-large-scale-gene-expression-profiling
#14
Shaoliang Peng, Shunyun Yang, Xiaochen Bo, Fei Li
More studies have been conducted using gene expression similarity to identify functional connections among genes, diseases and drugs. Gene Set Enrichment Analysis (GSEA) is a powerful analytical method for interpreting gene expression data. However, due to its enormous computational overhead in the estimation of significance level step and multiple hypothesis testing step, the computation scalability and efficiency are poor on large-scale datasets. We proposed paraGSEA for efficient large-scale transcriptome data analysis...
September 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28930145/to-wnt-or-lose-the-missing-non-coding-linc-in-colorectal-cancer
#15
REVIEW
Peng Shen, Martin Pichler, Meng Chen, George A Calin, Hui Ling
Colorectal cancer (CRC) is the third most frequent cancer and one of the leading causes for cancer-related mortality. Aberrant activation of the Wnt signaling is an essential initiating factor in colon carcinogenesis, and a driving force of CRC progression. Recently, long non-coding RNAs (lncRNAs) have emerged as significant players in CRC pathogenesis through diversified mechanisms. Although both Wnt signaling and lncRNAs represent interesting research areas for CRC, an effort of directly connecting these two areas is lacking...
September 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28922869/genome-organization-of-sphingobium-indicum-b90a-an-archetypal-hexachlorocyclohexane-hch-degrading-genotype
#16
Helianthous Verma, Abhay Bajaj, Roshan Kumar, Jasvinder Kaur, Shailly Anand, Namita Nayyar, Akshita Puri, Yogendra Singh, Jitendra P Khurana, Rup Lal
Among sphingomonads, Sphingobium indicum B90A is widely investigated for its ability to degrade a manmade pesticide, γ-hexachlorocyclohexane (γ-HCH) and its isomers (α-, β-, δ-, and ε-HCH). In this study, complete genome of strain B90A was constructed using Single Molecule Real Time Sequencing (SMRT) and Illumina platform. The complete genome revealed that strain B90A harbors four replicons: one chromosome (3,654,322 bp) and three plasmids designated as pSRL1 (139,218 bp), pSRL2 (108,430 bp) and pSRL3 (43,761 bp)...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28885863/long-noncoding-rna-bladder-cancer-associated-transcript-1-promotes-the-proliferation-migration-and-invasion-of-nonsmall-cell-lung-cancer-through-sponging-mir-144
#17
Ji-Ru Ye, Liang Liu, Feng Zheng
Nonsmall cell lung cancer (NSCLC) is a type of malignant tumor, accounting for 80% of all lung cancer morbidity. Long noncoding RNA (lncRNA) BLACAT1 (bladder cancer associated transcript 1), also known as linc-UBC1, has been tested to be an oncogenic lncRNA in other cancers. However, the role of BLACAT1 in NSCLC is still unknown. In clinical study, BLACAT1 expression was significantly upregulated in 48 cases of NSCLC tissues compared with adjacent normal tissues, especially in pathological TNM III samples. In NSCLC cells, BLACAT1 expression was also upregulated...
October 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28874676/linc-ing-circulating-long-non-coding-rnas-to-the-diagnosis-and-malignant-prediction-of-intraductal-papillary-mucinous-neoplasms-of-the-pancreas
#18
Jennifer B Permuth, Dung-Tsa Chen, Sean J Yoder, Jiannong Li, Andrew T Smith, Jung W Choi, Jongphil Kim, Yoganand Balagurunathan, Kun Jiang, Domenico Coppola, Barbara A Centeno, Jason Klapman, Pam Hodul, Florian A Karreth, Jose G Trevino, Nipun Merchant, Anthony Magliocco, Mokenge P Malafa, Robert Gillies
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease that lacks effective biomarkers for early detection. We hypothesized that circulating long non-coding RNAs (lncRNAs) may act as diagnostic markers of incidentally-detected cystic PDAC precursors known as intraductal papillary mucinous neoplasms (IPMNs) and predictors of their pathology/histological classification. Using NanoString nCounter® technology, we measured the abundance of 28 candidate lncRNAs in pre-operative plasma from a cohort of pathologically-confirmed IPMN cases of various grades of severity and non-diseased controls...
September 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28869448/large-intergenic-non-coding-rna-ror-as-a-potential-biomarker-for-the-diagnosis-and-dynamic-monitoring-of-breast-cancer
#19
Tianhe Zhao, Lichun Wu, Xinyang Li, Huangmei Dai, Zunzhen Zhang
BACKGROUND: Recent study has revealed that large intergenic non-coding RNA-ROR (linc-ROR) is aberrantly expressed in a number of cancers including breast cancer. However, whether circulating linc-ROR in plasma could be used for breast cancer diagnosis and dynamic monitoring is not clear. OBJECTIVE: The objective of this study is to determine if plasma linc-ROR could be applied as a biomarker for the diagnosis and dynamic monitoring of breast cancer. METHODS: We tested the expression levels of linc-ROR in 24 pairs of tissue samples and 96 plasma samples from breast cancer patients by quantitative real time-polymerase chain reaction (qRT-PCR), and analyzed the correlation between plasma linc-ROR levels and clinico-pathological characteristics...
August 23, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28860661/long-intergenic-non-coding-rna-galmd3-in-chicken-marek-s-disease
#20
Bo Han, Yanghua He, Li Zhang, Yi Ding, Ling Lian, Chunfang Zhao, Jiuzhou Song, Ning Yang
Long intergenic non-coding RNAs (lincRNAs) are transcribed from non-coding DNA sequences. Studies have revealed that aberrant expressions of lincRNAs are associated with various types of cancers and neurological disorders. Marek's disease (MD) is a highly contagious T-cell lymphoid neoplasia of chicken induced by Marek's disease virus (MDV). In this study, we first identified and validated linc-GALMD3 highly expressed in MDV-infected CD4+ T cells by RNA-Seq and qRT-PCR. By RNA-Seq analysis in MDCC-MSB1 cells after loss of function of linc-GALMD3 by shRNA, we found that linc-GALMD3 could positively cis-regulate its downstream gga-miR-223 gene expression...
August 31, 2017: Scientific Reports
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