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https://www.readbyqxmd.com/read/28432618/the-identification-of-key-genes-and-pathways-in-hepatocellular-carcinoma-by-bioinformatics-analysis-of-high-throughput-data
#1
Chaoyang Zhang, Li Peng, Yaqin Zhang, Zhaoyang Liu, Wenling Li, Shilian Chen, Guancheng Li
Liver cancer is a serious threat to public health and has fairly complicated pathogenesis. Therefore, the identification of key genes and pathways is of much importance for clarifying molecular mechanism of hepatocellular carcinoma (HCC) initiation and progression. HCC-associated gene expression dataset was downloaded from Gene Expression Omnibus database. Statistical software R was used for significance analysis of differentially expressed genes (DEGs) between liver cancer samples and normal samples. Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, based on R software, were applied for the identification of pathways in which DEGs significantly enriched...
June 2017: Medical Oncology
https://www.readbyqxmd.com/read/28431975/liposomal-curcumin-alters-chemosensitivity-of-breast-cancer-cells-to-adriamycin-via-regulating-microrna-expression
#2
Siying Zhou, Jian Li, Hanzi Xu, Sijie Zhang, Xiu Chen, Wei Chen, Sujin Yang, Shanliang Zhong, Jianhua Zhao, Jinhai Tang
BACKGROUND: Emerging evidence suggests that curcumin can overcome drug resistance to classical chemotherapies, but poor bioavailability and low absorption have limited its clinical use and the mechanisms remain unclear. Also, Adriamycin (Adr) is one of the most active cytotoxic agents in breast cancer; however, the high resistant rate of Adr leads to a poor prognosis. METHODS: We utilized encapsulation in liposomes as a strategy to improve the bioavailability of curcumin and demonstrated that liposomal curcumin altered chemosensitivity of Adr-resistant MCF-7 human breast cancer (MCF-7/Adr) by MTT assay...
April 18, 2017: Gene
https://www.readbyqxmd.com/read/28430779/a-coevolution-analysis-for-identifying-protein-protein-interactions-by-fourier-transform
#3
Changchuan Yin, Stephen S-T Yau
Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees...
2017: PloS One
https://www.readbyqxmd.com/read/28429838/pyrophosphate-as-substrate-for-alkaline-phosphatase-activity-a-convenient-flow-injection-chemiluminescence-assay
#4
Qingfeng Zhang, Cuiyun Zhang, Meiding Yang, Donghong Yu, Cong Yu
A sensitive and convenient flow-injection chemiluminescence (FI-CL) turn-on assay for alkaline phosphatase (ALP) activity without any label and synthesis is developed. Cu(2+) can catalyze the luminol-H2 O2 CL reaction. Pyrophosphate (PPi) can chelate Cu(2+) and therefore the Cu(2+) -mediated luminol-H2 O2 CL reaction is inhibited. The addition of ALP can catalyze the hydrolysis of PPi into phosphate ions, Cu(2+) is released and the chemiluminescence recovers. A detection limit of 1 mU/mL ALP is obtained.
April 21, 2017: Luminescence: the Journal of Biological and Chemical Luminescence
https://www.readbyqxmd.com/read/28429201/how-to-approach-lymphocytic-esophagitis
#5
REVIEW
Anh D Nguyen, Kerry B Dunbar
PURPOSE OF REVIEW: Lymphocytic esophagitis (LE) is an unusual esophageal condition defined by an increased number of lymphocytes in the esophageal epithelium. With few published studies of LE available, it is unclear whether LE is a truly distinct clinical entity or a histological manifestation of other known gastrointestinal disorders. This review summarizes recent studies of lymphocytic esophagitis. RECENT FINDINGS: Studies have suggested that LE may be related to eosinophilic esophagitis (EoE) or a manifestation of gastroesophageal reflux disease (GERD)...
June 2017: Current Gastroenterology Reports
https://www.readbyqxmd.com/read/28428828/bioinformatics-analysis-of-key-genes-and-latent-pathway-interactions-based-on-the-anaplastic-thyroid-carcinoma-gene-expression-profile
#6
Yun Huang, Yiming Tao, Xinying Li, Shi Chang, Bo Jiang, Feng Li, Zhi-Ming Wang
Anaplastic thyroid carcinoma (ATC) is an aggressive malignant disease in older adults with a high mortality rate. The present study aimed to examine several key genes and pathways, which are associated with ATC. The GSE33630 gene expression profile was downloaded from the Gene Expression Omnibus database, which included 11 ATC and 45 normal thyroid samples. The differentially expressed genes (DEGs) in ATC were identified using the Limma package in R. The Gene Ontology functions and Kyoto Encyclopedia of Genes and Genomes pathways of the selected DEGs were enriched using the Database for Annotation, Visualization and Integrated Discovery...
January 2017: Oncology Letters
https://www.readbyqxmd.com/read/28426652/cheminformatics-aided-discovery-of-small-molecule-protein-protein-interaction-ppi-dual-inhibitors-of-tumor-necrosis-factor-tnf-and-receptor-activator-of-nf-%C3%AE%C2%BAb-ligand-rankl
#7
Georgia Melagraki, Evangelos Ntougkos, Vagelis Rinotas, Christos Papaneophytou, Georgios Leonis, Thomas Mavromoustakos, George Kontopidis, Eleni Douni, Antreas Afantitis, George Kollias
We present an in silico drug discovery pipeline developed and applied for the identification and virtual screening of small-molecule Protein-Protein Interaction (PPI) compounds that act as dual inhibitors of TNF and RANKL through the trimerization interface. The cheminformatics part of the pipeline was developed by combining structure-based with ligand-based modeling using the largest available set of known TNF inhibitors in the literature (2481 small molecules). To facilitate virtual screening, the consensus predictive model was made freely available at: http://enalos...
April 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28425585/eosinophilic-esophagitis-unclear-roles-of-ige-and-eosinophils
#8
C Blanchard, D Simon, A Schoepfer, A Straumann, H-U Simon
Eosinophilic esophagitis (EoE) is a chronic inflammatory disease of the oesophagus. Recognized as a distinct entity only two decades ago, the emergence of the disease along with the availability of new technologies has rapidly opened new research avenues and outlined the main features of the pathogenesis of EoE. Yet, each advance in our understanding of the disease has raised new questions about the previous consensus. Currently, new subsets of the disease challenge our diagnostic criteria. For instance, it was believed that EoE did not respond to proton pump inhibitor (PPI) therapy; however, it has now been shown that a substantial proportion of EoE patients indeed respond to PPIs...
May 2017: Journal of Internal Medicine
https://www.readbyqxmd.com/read/28425497/single-dose-memantine-improves-cortical-oscillatory-response-dynamics-in-patients-with-schizophrenia
#9
Gregory A Light, Wen Zhang, Yash B Joshi, Savita Bhakta, Jo A Talledo, Neal R Swerdlow
Aberrant gamma band (30-80 Hz) oscillations may underlie cognitive deficits in schizophrenia (SZ). Gamma oscillations and their regulation by NMDA receptors can be studied via their evoked power (γEP) and phase locking (γPL) in response to auditory steady state stimulation; these Auditory Steady State Responses (ASSRs) may be biomarkers for target engagement and early therapeutic effects. We previously reported that memantine, an NMDA receptor antagonist, enhanced 2 biomarkers of early auditory information processing: prepulse inhibition (PPI) and mismatch negativity (MMN) in SZ patients and healthy subjects (HS)...
April 20, 2017: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28424965/assessment-of-drug-drug-interaction-potential-between-ceritinib-and-proton-pump-inhibitors-in-healthy-subjects-and-in-patients-with-alk-positive-non-small-cell-lung-cancer
#10
Yvonne Y Lau, Wen Gu, Tiffany Lin, Kalyanee Viraswami-Appanna, Can Cai, Jeffrey W Scott, Michael Shi
PURPOSE: The impact of proton pump inhibitors (PPIs) on the pharmacokinetics (PK) and efficacy of ceritinib was evaluated. METHODS: A healthy subject drug-drug interaction (DDI) study was conducted to assess the effect of esomeprazole on the PK of a single 750 mg dose of ceritinib. To further investigate the impact of PPIs on the PK and efficacy of ceritinib in ALK-positive cancer patients, two subgroup analyses were performed. Analysis 1 evaluated ceritinib steady-state trough concentration (Ctrough,ss) and overall response rate (ORR) by concomitant use of PPIs in patients from the ASCEND-1, -2, and -3 studies; analysis 2 evaluated ceritinib single-dose and steady-state AUC0-24h and C max by concomitant PPI use in patients from ASCEND-1 using a definition of PPI usage similar to that used in the healthy subject study...
April 19, 2017: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/28424527/unified-alignment-of-protein-protein-interaction-networks
#11
Noël Malod-Dognin, Kristina Ban, Nataša Pržulj
Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28422722/the-clinical-value-regulatory-mechanisms-and-gene-network-of-the-cancer-testis-gene-stk31-in-pancreatic-cancer
#12
Kai Zhang, Zipeng Lu, Yi Zhu, Lei Tian, Jingjing Zhang, Chunhua Xi, Wentao Gao, Kuirong Jiang, Yi Miao
We aimed to identify STK31 as a cancer-testis (CT) gene and to explore its potential clinical value, regulatory mechanisms, and gene network in pancreatic cancer (PC). Gene expression data were generated from normal organ samples and pancreatic cancer samples from three public databases. STK31 expression patterns in normal and PC tissues were identified, and we explored its regulatory mechanisms. Gene ontology (GO) and pathway analyses of STK31-related genes were performed and an STK31 protein-protein interaction (PPI) network was constructed...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422503/predicting-protein-interactions-of-concentrated-globular-protein-solutions-using-colloidal-models
#13
Mahlet Asfaw Woldeyes, Cesar Calero-Rubio, Eric M Furst, Christopher J Roberts
Protein interactions of α-chymotrypsinogen A (aCgn) were quantified using light scattering from low to high protein concentrations. Static light scattering (SLS) was used to determine the excess Rayleigh ratio (R(ex)) and osmotic second virial coefficients (B22) as a function of pH and total ionic strength (TIS). Repulsive (attractive) protein-protein interactions (PPI) were observed at pH 5 (pH 7), with decreasing repulsions (attractions) upon increasing TIS. Simple colloidal potential-of-mean force models (PMF) that account for short-range non-electrostatic attractions and screened electrostatic interactions were used to fit model parameters from data for B22 vs TIS at both pH values...
April 19, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28417025/dorsal-phalloplasty-to-preserve-penis-length-after-penile-prosthesis-implantation
#14
Osama Shaeer, Kamal Shaeer, Islam A Rahman
OBJECTIVES: Following penile prosthesis implantation (PPI), patients may complain of a decrease in visible penis length. A dorsal phalloplasty defines the penopubic junction by tacking pubic skin to the pubis, revealing the base of the penis. This study aimed to evaluate the efficacy of a dorsal phalloplasty in increasing the visible penis length following PPI. METHODS: An inflatable penile prosthesis was implanted in 13 patients with severe erectile dysfunction (ED) at the Kamal Shaeer Hospital, Cairo, Egypt, from January 2013 to May 2014...
February 2017: Sultan Qaboos University Medical Journal
https://www.readbyqxmd.com/read/28416300/pyrophosphate-supplementation-prevents-chronic-and-acute-calcification-in-abcc6-deficient-mice
#15
Viola Pomozi, Christopher Brampton, Koen van de Wetering, Janna Zoll, Bianca Calio, Kevin Pham, Jesse B Owens, Joel Marh, Stefan Moisyadi, András Váradi, Ludovic Martin, Carolin Bauer, Jeanette Erdmann, Zouhair Aherrahrou, Olivier Le Saux
Soft tissue calcification occurs in several common acquired pathologies, such as diabetes and hypercholesterolemia, or can result from genetic disorders. ABCC6, a transmembrane transporter primarily expressed in liver and kidneys, initiates a molecular pathway inhibiting ectopic calcification. ABCC6 facilitates the cellular efflux of ATP, which is rapidly converted into pyrophosphate (PPi), a major calcification inhibitor. Heritable mutations in ABCC6 underlie the incurable calcification disorder pseudoxanthoma elasticum and some cases of generalized arterial calcification of infancy...
April 14, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28415685/identification-of-molecular-targets-for-esophageal-carcinoma-diagnosis-using-mirna-seq-and-rna-seq-data-from-the-cancer-genome-atlas-a-study-of-187-cases
#16
Jiang-Hui Zeng, Dan-Dan Xiong, Yu-Yan Pang, Yu Zhang, Rui-Xue Tang, Dian-Zhong Luo, Gang Chen
Esophageal carcinoma (ESCA) is one of the most common malignancies worldwide, and its pathogenesis is complex. In this study, we identified differentially expressed miRNAs (DEMs) and genes (DEGs) of ESCA from The Cancer Genome Atlas (TCGA) database. The diagnostic values of DEMs were determined by receiver operating characteristic (ROC) analyses and validated based on data from Gene Expression Omnibus (GEO). The top five DEMs with the best diagnostic values were selected, and their potential targets were predicted by various in silico methods...
March 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28414898/does-my-patient-still-have-reflux-when-ppi-therapy-does-not-work
#17
REVIEW
M F Vaezi
Gastroesophageal reflux disease (GERD) is a common condition around the world. The management of this disease is less than satisfying given complexity of patient presentation and suboptimal diagnostic testing when employed for those poorly responsive to acid suppressive therapy. In this mini review, we discuss some new strategies employed for patients with suspected GERD to better understand disease pathophysiology. We compare the strategies and outline a clinically relevant approach in this difficult group of patients...
May 2017: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
https://www.readbyqxmd.com/read/28414710/using-the-pimeloyl-coa-synthetase-adenylation-fold-to-synthesize-fatty-acid-thioesters
#18
Menglu Wang, Lucile Moynié, Peter J Harrison, Van Kelly, Andrew Piper, James H Naismith, Dominic J Campopiano
Biotin is an essential vitamin in plants and mammals, functioning as the carbon dioxide carrier within central lipid metabolism. Bacterial pimeloyl-CoA synthetase (BioW) acts as a highly specific substrate-selection gate, ensuring the integrity of the carbon chain in biotin synthesis. BioW catalyzes the condensation of pimelic acid (C7 dicarboxylic acid) with CoASH in an ATP-dependent manner to form pimeloyl-CoA, the first dedicated biotin building block. Multiple structures of Bacillus subtilis BioW together capture all three substrates, as well as the intermediate pimeloyl-adenylate and product pyrophosphate (PPi), indicating that the enzyme uses an internal ruler to select the correct dicarboxylic acid substrate...
April 17, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28414464/mechanisms-of-internalization-of-maltose-modified-poly-propylene-imine-glycodendrimers-into-leukemic-cell-lines
#19
Maciej Studzian, Aleksandra Szulc, Anna Janaszewska, Dietmar Appelhans, Łukasz Pułaski, Barbara Klajnert-Maculewicz
Poly(propylene imine) dendrimers of 4th generation partially modified with maltose (open shell structure, PPI-m OS) have been proposed as carriers for nucleotide anticancer drugs. The aim of this work was to provide basic insight into interactions between fluorescently labeled PPI-m dendrimer and two distinct leukemia cell models: CCRF-1301 lymphoid cell line and HL-60 myeloid cell line. We applied qualitative confocal imaging and quantitative flow cytometry, as well as trypan blue quenching and pharmacological inhibition, to investigate the course, kinetics and molecular mechanisms of internalization of nanoparticles...
April 17, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28414290/-the-effect-of-isatin-on-protein-protein-interactions-between-cytochrome-b5-and-cytochromes-p450
#20
P V Ershov, E O Yablokov, Yu V Mezentsev, L A Kalushskiy, A V Florinskaya, A V Veselovsky, O V Gnedenko, A A Gilep, S A Usanov, A E Medvedev, A S Ivanov
Cytochromes P450 (CYP) are involved in numerous biochemical processes including metabolism of xenobiotics, biosynthesis of cholesterol, steroid hormones etc. Since some CYP catalyze indol oxidation to isatin, we have hypothesized that isatin can regulate protein-protein interactions (PPI) between components of the CYP system thus representing a (negative?) feedback mechanism. The aim of this study was to investigate a possible effect of isatin on interaction of human CYP with cytochrome b5 (CYB5A). Using the optical biosensor test system employing surface plasmon resonance (SPR) we have investigated interaction of immobilized CYB5A with various CYP in the absence and in the presence of isatin...
March 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
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