keyword
MENU ▼
Read by QxMD icon Read
search

In silico

keyword
https://www.readbyqxmd.com/read/28343162/mesothelin-promoter-variants-are-associated-with-increased-soluble-mesothelin-related-peptide-levels-in-asbestos-exposed-individuals
#1
Chiara De Santi, Perla Pucci, Alessandra Bonotti, Ombretta Melaiu, Monica Cipollini, Roberto Silvestri, Veronika Vymetalkova, Elisa Barone, Elisa Paolicchi, Alda Corrado, Irene Lepori, Irene Dell'Anno, Lucia Pellè, Pavel Vodicka, Luciano Mutti, Rudy Foddis, Alfonso Cristaudo, Federica Gemignani, Stefano Landi
BACKGROUND: Soluble mesothelin-related peptide (SMRP) is a promising diagnostic biomarker for malignant pleural mesothelioma (MPM), but various confounders hinder its usefulness in surveillance programmes. We previously showed that a single nucleotide polymorphism (SNP) within the 3'untranslated region (3'UTR) of the mesothelin (MSLN) gene could affect the levels of SMRP. OBJECTIVES: To focus on SNPs located within MSLN promoter as possible critical genetic variables in determining SMRP levels...
March 25, 2017: Occupational and Environmental Medicine
https://www.readbyqxmd.com/read/28343125/structural-modeling-of-human-organic-cation-transporters
#2
Tikam Chand Dakal, Rajender Kumar, Dindial Ramotar
Human organic cation transporters (hOCTs) belong to solute carriers (SLC) 22 family of membrane proteins that play a central role in transportation of chemotherapeutic drugs for several clinical and pathological conditions, including cancer and diabetes. These transporters mediate drug transport; however, the precise mechanism of drug-binding and transport by them is not fully uncovered yet, partly due to unavailability of any crystal structure record. In this work, we performed a multi-phasic approach to compute the 3D structural models of seven human organic cation transporters (hOCTs) starting from primary protein sequence...
March 18, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28343034/bioactivities-of-achillea-phrygia-and-bupleurum-croceum-based-on-the-composition-of-phenolic-compounds-in-vitro-and-in-silico-approaches
#3
Gokhan Zengin, Gizem Bulut, Adriano Mollica, Mehmet Zeki Haznedaroglu, Ahmet Dogan, Abdurrahman Aktumsek
This study presents the effects of the Achillea phrygia Boiss. et Bal. and Bupleurum croceum Fenzl. extracts obtained by different solvents (ethyl acetate, methanol and water) on selected enzyme inhibitory effects and antioxidant ability with screening bioactive compounds. Total and individual bioactive compounds were detected by spectrophotometric and HPLC-DAD techniques. Antioxidant abilities were evaluated by different methods including free radical scavenging (ABTS and DPPH), reducing power (CUPRAC and FRAP), phosphomolybdenum and metal chelating...
March 22, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28342755/mutation-analysis-of-the-interactions-between-mycobacterium-tuberculosis-caseinolytic-protease-c1-clpc1-and-ecumicin
#4
In-Pil Jung, Na-Reum Ha, A-Ru Kim, Sang-Heon Kim, Moon-Young Yoon
Ecumicin is a well-known and potent inhibitor of Mycobacterium tuberculosis. Although the target of ecumicin is caseinolytic protease C1 (ClpC1), the exact mechanism by which ecumicin inhibits ClpC1 has not been identified. To analyze ecumicin's action on ClpC1, site-directed mutagenesis was performed on its binding site. The estimated binding residues within ClpC1 to ecumicin were selected via in silico analysis using molecular docking. The selected residues were mutated by site-directed mutagenesis and the effects on ecumicin binding were analyzed...
March 22, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28341520/in-silico-prediction-of-the-effects-of-mutations-in-the-human-triose-phosphate-isomerase-gene-towards-a-predictive-framework-for-tpi-deficiency
#5
Conor Oliver, David J Timson
Triose phosphate isomerase (TPI) deficiency is a rare, but highly debilitating, inherited metabolic disease. Almost all patients suffer severe neurological effects and the most severely affected are unlikely to live beyond early childhood. Here, we describe an in silico study into well-characterised variants which are associated with the disease alongside an investigation into 79 currently uncharacterised TPI variants which are known to occur in the human population. The majority of the disease-associated mutations affected amino acid residues close to the dimer interface or the active site...
March 21, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28340489/mir-34a-3p-alters-proliferation-and-apoptosis-of-meningioma-cells-in-vitro-and-is-directly-targeting-smad4-frat1-and-bcl2
#6
Tamara V Werner, Martin Hart, Ruth Nickels, Yoo-Jin Kim, Michael D Menger, Rainer M Bohle, Andreas Keller, Nicole Ludwig, Eckart Meese
Micro (mi)RNAs are short, noncoding RNAs and deregulation of miRNAs and their targets are implicated in tumor generation and progression in many cancers. Meningiomas are mostly benign, slow growing tumors of the central nervous system with a small percentage showing a malignant phenotype.Following in silico prediction of potential targets of miR-34a-3p, SMAD4, FRAT1, and BCL2 have been confirmed as targets by dual luciferase assays with co-expression of miR-34a-3p and reporter gene constructs containing the respective 3'UTRs...
March 23, 2017: Aging
https://www.readbyqxmd.com/read/28339466/in-silico-search-for-modifier-genes-associated-with-pancreatic-and-liver-disease-in-cystic-fibrosis
#7
Pascal Trouvé, Emmanuelle Génin, Claude Férec
Cystic Fibrosis is the most common lethal autosomal recessive disorder in the white population, affecting among other organs, the lung, the pancreas and the liver. Whereas Cystic Fibrosis is a monogenic disease, many studies reveal a very complex relationship between genotype and clinical phenotype. Indeed, the broad phenotypic spectrum observed in Cystic Fibrosis is far from being explained by obvious genotype-phenotype correlations and it is admitted that Cystic Fibrosis disease is the result of multiple factors, including effects of the environment as well as modifier genes...
2017: PloS One
https://www.readbyqxmd.com/read/28339201/high-throughput-in-silico-structure-validation-and-revision-of-halogenated-natural-products-is-enabled-by-parametric-corrections-to-dft-computed-13-c-nmr-chemical-shifts-and-spin-spin-coupling-constants
#8
Andrei G Kutateladze, D Sai Reddy
Halogenated natural products constitute diverse and promising feedstock for molecular pharmaceuticals. However, their solution-structure elucidation by NMR presents several challenges, including the lack of fast methods to compute (13)C chemical shifts for carbons bearing heavy atoms. We show that parametric corrections to DFT-computed chemical shifts in conjunction with rff-computed spin-spin coupling constants allow for fast and reliable screening of a large number of reported halogenated natural products, resulting in expedient structure validation or revision...
March 24, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28339071/direct-interaction-between-caffeic-acid-phenethyl-ester-and-human-neutrophil-elastase-inhibits-the-growth-and-migration-of-panc-1-cells
#9
Jianhui Duan, Yilixiati Xiaokaiti, Shengjun Fan, Yan Pan, Xin Li, Xuejun Li
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignant tumors of the digestive system, but the mechanisms of its development and progression are unclear. Inflammation is thought to be fundamental to pancreatic cancer development and caffeic acid phenethyl ester (CAPE) is an active component of honey bee resin or propolis with anti-inflammatory and anticancer activities. We investigated the inhibitory effects of CAPE on cell growth and migration induced by human neutrophil elastase (HNE) and report that HNE induced cancer cell migration at low doses and growth at higher doses...
March 21, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28338931/evolutionary-dynamics-of-pathoadaptation-revealed-by-three-independent-acquisitions-of-the-virb-d4-type-iv-secretion-system-in-bartonella
#10
Alexander Harms, Francisca H I D Segers, Maxime Quebatte, Claudia Mistl, Pablo Manfredi, Jonas Körner, Bruno B Chomel, Michael Kosoy, Soichi Maruyama, Philipp Engel, Christoph Dehio
The α-proteobacterial genus Bartonella comprises a group of ubiquitous mammalian pathogens that are studied as a model for the evolution of bacterial pathogenesis. Vast abundance of two particular phylogenetic lineages of Bartonella had been linked to enhanced host adaptability enabled by lineage-specific acquisition of a VirB/D4 type IV secretion system (T4SS) and parallel evolution of complex effector repertoires. However, the limited availability of genome sequences from one of those lineages as well as other, remote branches of Bartonella has so far hampered comprehensive understanding of how the VirB/D4 T4SS and its effectors called Beps have shaped Bartonella evolution...
March 7, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338834/comparative-genomics-of-microsporidian-genomes-reveals-a-minimal-non-coding-rna-set-and-new-insights-for-transcription-in-minimal-eukaryotic-genomes
#11
Abdel Belkorchia, Jean-François Pombert, Valérie Polonais, Nicolas Parisot, Frédéric Delbac, Jean-François Brugère, Pierre Peyret, Christine Gaspin, Eric Peyretaillade
Microsporidia are ubiquitous intracellular pathogens whose opportunistic nature led to their increased recognition with the rise of the AIDS pandemic. As the RNA world was largely unexplored in this parasitic lineage, we developed a dedicated in silico methodology to carry out exhaustive identification of ncRNAs across the Encephalitozoon and Nosema genera. Thus, the previously missing U1 small nuclear RNA (snRNA) and small nucleolar RNAs (snoRNAs) targeting only the LSU rRNA were highlighted and were further validated using 5' and 3'RACE-PCR experiments...
February 28, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338805/deciphering-the-genetic-control-of-fruit-texture-in-apple-by-multiple-family-based-analysis-and-genome-wide-association
#12
Mario Di Guardo, Marco C A M Bink, Walter Guerra, Thomas Letschka, Lidia Lozano, Nicola Busatto, Lara Poles, Alice Tadiello, Luca Bianco, Richard G F Visser, Eric van de Weg, Fabrizio Costa
Fruit texture is a complex feature composed of mechanical and acoustic properties relying on the modifications occurring in the cell wall throughout fruit development and ripening. Apple is characterized by a large variation in fruit texture behavior that directly impacts both the consumer's appreciation and post-harvest performance. To decipher the genetic control of fruit texture comprehensively, two complementing quantitative trait locus (QTL) mapping approaches were employed. The first was represented by a pedigree-based analysis (PBA) carried out on six full-sib pedigreed families, while the second was a genome-wide association study (GWAS) performed on a collection of 233 apple accessions...
February 24, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338762/redox-and-reactive-oxygen-species-network-in-acclimation-for-salinity-tolerance-in-sugar-beet
#13
M Sazzad Hossain, Abdelaleim Ismail ElSayed, Marten Moore, Karl-Josef Dietz
Fine-tuned and coordinated regulation of transport, metabolism and redox homeostasis allows plants to acclimate to osmotic and ionic stress caused by high salinity. Sugar beet is a highly salt tolerant crop plant and is therefore an interesting model to study sodium chloride (NaCl) acclimation in crops. Sugar beet plants were subjected to a final level of 300 mM NaCl for up to 14 d in hydroponics. Plants acclimated to NaCl stress by maintaining its growth rate and adjusting its cellular redox and reactive oxygen species (ROS) network...
February 18, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338626/in-silico-and-in-vitro-analysis-of-interaction-between-ximelagatran-and-human-leukocyte-antigen-hla-drb1-07-01
#14
Makoto Hirasawa, Katsunobu Hagihara, Koji Abe, Osamu Ando, Noriaki Hirayama
Idiosyncratic ximelagatran-induced hepatotoxicity has been reported to be associated with human leukocyte antigen (HLA)-DRB1*07:01 and ximelagatran has been reported to inhibit the binding of the ligand peptide to HLA-DRB1*07:01 in vitro. In order to predict the possible interaction modes of ximelagatran with HLA-DR molecules, in silico docking simulations were performed. Molecular dynamics (MD) simulations were also performed to predict the effect of ximelagatran on the binding mode of the ligand peptide to HLA-DRB1*07:01...
March 24, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28338331/an-in-silico-study-on-the-isomers-of-pentacene-the-case-for-air-stable-and-alternative-c22h14-acenes-for-organic-electronics
#15
Leighton Jones, Long Lin
Pentacene is one of the most investigated candidates for organic thin film transistor (OTFT) applications over the last few decades even though it unstable in air (Eg = 1.80 eV), owing in part to its planar nature and high charge-transfer mobilities as both a single crystal (35 cm2 V 1 s 1) and as a thin-film (3.0 cm2 V 1 s 1). Until now, picene is the only isomer of pentacene to be investigated for organic electronic applications, due to its greater stability (Eg = 4.21 eV) and high charge transfer mobility (3...
March 24, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28337978/microrna-filters-hox-temporal-transcription-noise-to-confer-boundary-formation-in-the-spinal-cord
#16
Chung-Jung Li, Tian Hong, Ying-Tsen Tung, Ya-Ping Yen, Ho-Chiang Hsu, Ya-Lin Lu, Mien Chang, Qing Nie, Jun-An Chen
The initial rostrocaudal patterning of the neural tube leads to differential expression of Hox genes that contribute to the specification of motor neuron (MN) subtype identity. Although several 3' Hox mRNAs are expressed in progenitors in a noisy manner, these Hox proteins are not expressed in the progenitors and only become detectable in postmitotic MNs. MicroRNA biogenesis impairment leads to precocious expression and propagates the noise of Hoxa5 at the protein level, resulting in an imprecise Hoxa5-Hoxc8 boundary...
March 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/28337567/novel-16s-rdna-primers-revealed-the-diversity-and-habitats-related-community-structure-of-sphingomonads-in-10-different-niches
#17
Yili Huang, Hao Feng, Hang Lu, Yanhua Zeng
It is believed that sphingomonads are ubiquitously distributed in environments. However detailed information about their community structure and their co-relationship with environmental parameters remain unclear. In this study, novel sphingomonads-specific primers based on the 16S rRNA gene were designed to investigate the distribution of sphingomonads in 10 different niches. Both in silico and in-practice tests on pure cultures and environmental samples showed that Sph384f/Sph701r was an efficient primer set...
March 23, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28336364/mechanisms-and-roles-by-which-irf-3-mediates-the-regulation-of-ormdl3-transcription-in-respiratory-syncytial-virus-infection
#18
Xiao-Hua Wang, Jin Shu, Chun-Ming Jiang, Li-Li Zhuang, Wei-Xia Yang, Hui-Weng Zhang, Lu-Lu Wang, Lin Li, Xiao-Qing Chen, Rui Jin, Guo-Ping Zhou
Respiratory syncytial virus (RSV) is the leading cause of bronchiolitis in infancy, which is a major risk factor for recurrent wheezing and asthma. Orosomucoid 1-Like Protein 3 (ORMDL3) has been reported to associate with virus-triggered recurrent wheezing and asthma in children. However, little is known about how ORMDL3 is involved into RSV infection. In this study, we showed that the mRNA expression of ORMDL3 is significantly increased in the peripheral blood lymphocytes of infants with RSV-induced bronchiolitis compared with uninfected controls, also increased in bronchial epithelial cells and lung fibroblasts following RSV infection in vitro...
March 20, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28336342/pharmacological-assessments-of-potent-a2a-receptor-antagonist-idpu-1-7-imino-3-propyl-2-3-dihydrothiazolo-4-5-d-pyrimidin-6-7h-yl-urea-in-rodent-model-of-haloperidol-induced-parkinson-like-symptoms
#19
Namrata Kumari, Saurabh Agrawal, Pratibha Mehta Luthra
A2A receptor antagonists emerged as potential candidate for management of Parkinson's disease. Earlier we had reported the therapeutic potential of 1-(7-imino-3-propyl-2,3-dihydrothiazolo[4,5-d]pyrimidin-6(7H)-yl) urea (IDPU) as A2A receptor antagonist. Herein, we have investigated the effect of IDPU in attenuation of haloperidol induced Parkinson like symptoms in rats. It has successfully restored hypo-locomotion induced by haloperidol and NECA. IDPU also displayed protective effect against oxidative stress induced by chronic haloperidol treatment in rats...
March 20, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28336271/helminth-secretomes-reflect-different-lifestyles-and-parasitized-hosts
#20
Yesid Cuesta-Astroz, Francislon Silva de Oliveira, Laila Alves Nahum, Guilherme Oliveira
Helminths cause a number of medical and agricultural problems and are a major cause of parasitic infections in humans, animals and plants. Comparative analysis of helminth genes and genomes are important to understand the genomic biodiversity and evolution of parasites and their hosts in terms of different selective pressures in their habitats. The interactions between the infective organisms and their hosts are mediated in large part by secreted proteins, known collectively as the "secretome". Proteins secreted by parasites are able to modify a host's environment and modulate their immune system...
March 20, 2017: International Journal for Parasitology
keyword
keyword
32035
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"