keyword
MENU ▼
Read by QxMD icon Read
search

In silico

keyword
https://www.readbyqxmd.com/read/29457221/association-of-stat6-gene-variants-with-food-allergy-diagnosed-by-double-blind-placebo-controlled-food-challenges
#1
C D van Ginkel, M E Pettersson, A E J Dubois, G H Koppelman
This study describes the role of two STAT6 gene variants in food allergy using data of patients and their parents who underwent double-blind placebo-controlled food challenges (DBPCFCs). After quality control, 369 trios were analyzed including 262 children (71.0%) with food allergy. Associations were tested by family based association testing (FBAT). The A alleles of both SNPs were associated with food allergy (p=0.036 and p=0.013 for rs324015 and rs1059513, respectively). Furthermore, these A alleles were associated with peanut allergy, higher sIgE levels to both peanut and cow's milk, more severe symptoms and higher eliciting doses during peanut and cow's milk DBPCFCs (all p<0...
February 19, 2018: Allergy
https://www.readbyqxmd.com/read/29456971/molecular-biochemical-and-kinetic-analysis-of-a-novel-thermostable-lipase-lipsm-from-stenotrophomonas-maltophilia-psi-1-the-first-member-of-a-new-bacterial-lipase-family-xviii
#2
Maria Parapouli, Athanasios Foukis, Panagiota-Yiolanda Stergiou, Maria Koukouritaki, Panagiotis Magklaras, Olga A Gkini, Emmanuel M Papamichael, Amalia-Sofia Afendra, Efstathios Hatziloukas
Background: Microbial lipases catalyze a broad spectrum of reactions and are enzymes of considerable biotechnological interest. The focus of this study was the isolation of new lipase genes, intending to discover novel lipases whose products bear interesting biochemical and structural features and may have a potential to act as valuable biocatalysts in industrial applications. Results: A novel lipase gene ( lipSm ), from a new environmental Stenotrophomonas maltophilia strain, Psi-1, originating from a sludge sample from Psittaleia (Greece), was cloned and sequenced...
December 2018: Journal of Biological Research
https://www.readbyqxmd.com/read/29456689/inhibition-of-the-ras-raf-extracellular-signal-regulated-kinase-1-2-signaling-pathway-by-compounds-of-natural-origin-for-possible-treatment-of-spinal-cord-injury-an-in-silico-approach
#3
Shilei Yan, Li Zhang, Shuai Wang, Tianhao Wu, Zhixin Gong
Spinal cord injury (SCI) is a severe disease associated with permanent neurological deficit. Recent studies in the treatment of SCI have demonstrated that the Ras/Raf/extracellular signal-regulated kinase 1/2 (ERK1/2) signaling pathway serves an important role in the disease etiology, and that upregulation of this signaling pathway is associated with the development of SCI. In the present study, inhibition of Ras protein was employed in order to downregulate the Ras/Raf/ERK1/2 signaling pathway using compounds of natural origin from the Interbioscreen natural compound database...
March 2018: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29456625/alignment-of-microbial-fitness-with-engineered-product-formation-obligatory-coupling-between-acetate-production-and-photoautotrophic-growth
#4
Wei Du, Joeri A Jongbloets, Coco van Boxtel, Hugo Pineda Hernández, David Lips, Brett G Oliver, Klaas J Hellingwerf, Filipe Branco Dos Santos
Background: Microbial bioengineering has the potential to become a key contributor to the future development of human society by providing sustainable, novel, and cost-effective production pipelines. However, the sustained productivity of genetically engineered strains is often a challenge, as spontaneous non-producing mutants tend to grow faster and take over the population. Novel strategies to prevent this issue of strain instability are urgently needed. Results: In this study, we propose a novel strategy applicable to all microbial production systems for which a genome-scale metabolic model is available that aligns the production of native metabolites to the formation of biomass...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29456552/identification-of-single-nucleotide-non-coding-driver-mutations-in-cancer
#5
REVIEW
Kok A Gan, Sebastian Carrasco Pro, Jared A Sewell, Juan I Fuxman Bass
Recent whole-genome sequencing studies have identified millions of somatic variants present in tumor samples. Most of these variants reside in non-coding regions of the genome potentially affecting transcriptional and post-transcriptional gene regulation. Although a few hallmark examples of driver mutations in non-coding regions have been reported, the functional role of the vast majority of somatic non-coding variants remains to be determined. This is because the few driver variants in each sample must be distinguished from the thousands of passenger variants and because the logic of regulatory element function has not yet been fully elucidated...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29456393/-in-vitro-h-k-atpase-inhibition-antiradical-effects-of-a-flavonoid-rich-fraction-of-dissotis-rotundifolia-and-in-silico-pass-prediction-of-its-isolated-compounds
#6
Michael Buenor Adinortey, Charles Ansah, Cynthia Ayefoumi Adinortey, Justine McGiboney, Alexander Nyarko
Background: Dissotis rotundifolia , commonly referred to as pink lady, has several medicinal uses including peptic ulcer. This study investigated the inhibitory effects of D. rotundifolia extract on H+ /K+ -ATPase and also assessed its antiradical activity. In silico study of some isolated compounds of this plant was also carried out to affirm the suspected binding properties of extract to H+ /K+ -ATPase enzyme. Materials and Methods: D. rotundifolia whole plant extract was obtained after extraction process and then assessed for its ability to scavenge free radicals in four in vitro test models...
January 2018: Journal of Natural Science, Biology, and Medicine
https://www.readbyqxmd.com/read/29456028/polyphasic-characterization-of-a-novel-species-in-the-lactobacillus-casei-group-from-cow-manure-of-taiwan-description-of-l-chiayiensis-sp-nov
#7
Chien-Hsun Huang, Jong-Shian Liou, Ai-Yun Lee, Min Tseng, Mika Miyashita, Lina Huang, Koichi Watanabe
Two Gram-stain-positive, rod-shaped, non-motile, catalase-negative and facultative anaerobic strains, NCYUAST and BCRC 18859 (=NRIC 1947), were isolated from cow manure of Taiwan and coconut juice of Philippines, respectively. Comparative sequence analysis of 16S rRNA gene revealed that the novel strains were members of the genus Lactobacillus. These two strains had 100% of 16S rRNA gene sequence similarity and 98.6% of average nucleotide identity (ANI) value based on whole genome sequences. On the basis of 16S rRNA gene sequence similarity, the type strains of Lactobacillus casei (99...
February 7, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29455637/molecular-dynamics-of-interaction-of-sesamin-and-related-compounds-with-the-cancer-marker-%C3%AE-catenin-an-in-silico-study
#8
Bindu Madhuri Cavuturu, Vishwambar Vishnu Bhandare, Amutha Ramaswamy, Neelakantan Arumugam
By virtue of their regulatory role in the biological process, certain protein-protein complexes form potential targets for designing and discovery of drugs. Alteration set in the controlled formation of such complexes results in dysregulation of several metabolic processes, leading to diseased condition. β-catenin/Tcf4 complex is one such protein-protein complex found altered in colorectal epithelial cells resulting in activation of target genes leading to cancer. Recently certain lignans from seeds of the oil crop sesame were found inhibiting initiation and progression of this type of cancer...
February 18, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29455435/dna-methylation-regulated-micrornas-in-hpv-16-induced-head-and-neck-squamous-cell-carcinoma-hnscc
#9
M K Sannigrahi, Rajni Sharma, Varinder Singh, Naresh K Panda, Vidya Rattan, Madhu Khullar
INTRODUCTION: Epigenetic modifications have been reported to play an important role in regulating gene expression and these modifications become critical when they have a role in controlling another important layer of epigenetic regulation namely microRNAs. In the present study, we have identified the microRNAs that may be regulated by promoter DNA methylation and histone acetylation in Human papilloma virus-positive head and neck squamous cell carcinoma. METHODOLOGY: HPV-negative cell line (UPCI:SCC-116) and HPV-16 +ve cell line (UPCI:SCC-090) were treated with methylation inhibitor (5-aza-2'-deoxycytidine, AZA) and acetylation inhibitor (Trichostatin-A, TSA), followed by micro-array analysis...
February 17, 2018: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/29454918/design-synthesis-and-biological-evaluation-of-novel-amide-and-hydrazide-based-thioether-analogs-targeting-histone-deacteylase-hdac-enzymes
#10
Ayman B Farag, Heba A Ewida, Mahmoud Salama Ahmed
Development of HDAC inhibitors have become an ultimate need targeting different types of cancer. In silico virtual screening was applied to screen novel scaffolds via scaffold hopping strategy to develop different acrylamide and aryl/heteroaryl hydrazide based analogs merged with thioether moiety. The acrylamide based analogs showed significant hydrophobic interaction within binding pocket in addition to co-ordination with Zn+2 via carbonyl group, however the aryl/heteroaryl hydrazide based analogs showed binding towards Zn+2 via thiol moiety...
February 10, 2018: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29454915/synthesis-of-n-1-6-acetamido-5-phenylpyrimidin-4-yl-piperidin-3-yl-amide-derivatives-as-potential-inhibitors-for-mitotic-kinesin-spindle-protein
#11
P Muthuraja, M Himesh, S Prakash, U Venkatasubramanian, P Manisankar
Kinesin Spindle Protein (KSP) or Eg5 is an essential kinesin that is involved in spindle separation process during mitosis and also unregulated in certain cancer cells. Inhibitors of this enzyme have proved to be effective to block spindle separation followed by mitotic arrest and apoptosis of the cancer cells. Since this enzyme has two allosteric inhibitor binding sites, it's an excellent target for developing drugs for cancer chemotherapy. Many pyrimidine derivatives have been proved to be active against cancer and other enzymes...
February 10, 2018: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29454619/delineation-of-the-functional-properties-and-the-mechanism-of-action-of-aa29504-an-allosteric-agonist-and-positive-allosteric-modulator-of-gaba-a-receptors
#12
Emma Rie Olander, Nawid Madjroh, Lennart Bunch, Pella Cecilia Söderhielm, Anders A Jensen
The retigabine analog 2-amino-4-(2,4,6-trimethylbenzylamino)-phenyl]-carbamic acid ethyl ester (AA29504) is a positive allosteric modulator (PAM) of γ-aminobutyric acidA receptors (GABAA Rs), and the modulator has been used in ex vivo/in vivo studies to probe the physiological roles of native δ-containing GABAA Rs. In this study, the functional properties and mode of action of AA29504 were investigated at human GABAA Rs expressed in Xenopus oocytes by two-electrode voltage clamp electrophysiology. AA29504 was found to be an allosteric GABAA R agonist displaying low intrinsic activities at 3-30 μM...
February 15, 2018: Biochemical Pharmacology
https://www.readbyqxmd.com/read/29454310/in-vitro-and-in-silico-validation-of-ca3-and-fhl1-downregulation-in-oral-cancer
#13
Cláudia Maria Pereira, Ana Carolina de Carvalho, Felipe Rodrigues da Silva, Matias Eliseo Melendez, Roberta Cardim Lessa, Valéria Cristina C Andrade, Luiz Paulo Kowalski, André L Vettore, André Lopes Carvalho
BACKGROUND: Aberrant methylation is a frequent event in oral cancer. METHODS: In order to better characterize these alterations, a search for genes downregulated by aberrant methylation in oral squamous cell carcinoma (OSCC) was conducted through the mining of ORESTES dataset. Findings were further validated in OSCC cell lines and patients' samples and confirmed using TCGA data. Differentially expressed genes were identified in ORESTES libraries and validated in vitro using RT-PCR in HNSCC cell-lines and OSCC tumor samples...
February 17, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29454190/potholing-of-the-hydrophobic-heme-oxygenase-1-western-region-for-the-search-of-potent-and-selective-imidazole-based-inhibitors
#14
Loredana Salerno, Emanuele Amata, Giuseppe Romeo, Agostino Marrazzo, Orazio Prezzavento, Giuseppe Floresta, Valeria Sorrenti, Ignazio Barbagallo, Antonio Rescifina, Valeria Pittalà
Here we report the design, synthesis, and molecular modeling of new potent and selective imidazole-based HO-1 inhibitors in which the imidazole nucleus and the hydrophobic groups are linked by a phenylethanolic spacer. Most of the tested compounds showed a good inhibitor activity with IC 50 values in the low micromolar range, with two of them (1b and 1j) exhibiting also high selectivity toward HO-2. These results were obtained by the idea of potholing the entire volume of the principal hydrophobic western region with an appropriate ligand volume...
February 9, 2018: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29454005/a-quest-to-find-good-primers-for-gene-expression-analysis-of-candida-albicans-from-clinical-samples
#15
Gabriela C Alonso, Ana C Pavarina, Tábata V Sousa, Marlise I Klein
Biofilm production contributes to several human diseases, including oral candidiasis. Among the Candida species, Candida albicans is the most prevalent. The expression of virulence genes is implicated in the pathogenic potential of Candida biofilms. However, the evaluation of microbial gene expression from in vivo biofilm samples is not trivial, specifically, assessment via quantitative PCR (qPCR) can be a challenge because of several species present in clinical samples. Hence, the necessity of primers specificity...
February 14, 2018: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29453813/association-between-two-common-transitions-of-h2bfwt-gene-and-male-infertility-a-case-control-meta-and-structural-analysis
#16
M Teimouri, H Najaran, A Hosseinzadeh, T Mazoochi
H2BFWT is one of the testis-specific histones that plays a fundamental role in spermatogenesis, and single nucleotide polymorphisms (SNPs) in this gene may result in male infertility. This study aimed to investigate the association between -9C>T and 368A>G transitions of H2BFWT gene and male infertility through a case-control, meta-analysis, and a bioinformatics approach. In this case-control study, 490 subjects including 240 idiopathic infertile men and 250 healthy controls were included. The -9C>T and 368A>G SNPs genotyping were performed by a PCR-RFLP method...
February 17, 2018: Andrology
https://www.readbyqxmd.com/read/29453635/monitoring-of-erlotinib-in-pancreatic-cancer-patients-during-long-time-administration-and-comparison-to-a-physiologically-based-pharmacokinetic-model
#17
Andrea Gruber, Martin Czejka, Philipp Buchner, Marie Kitzmueller, Nairi Kirchbaumer Baroian, Christian Dittrich, Azra Sahmanovic Hrgovcic
PURPOSE: In this study, a therapeutic drug monitoring (TDM) of erlotinib in pancreatic cancer patients was performed over 50 weeks to reveal possible alterations in erlotinib plasma concentrations. Additionally, a physiologically based pharmacokinetic (PBPK) model was created to assess such variations in silico. METHODS: Patients with advanced pancreatic cancer received a chemotherapeutic combination of 100 mg erlotinib q.d., 500-900 mg capecitabine b.d. and 5 mg/kg bevacizumab q...
February 16, 2018: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/29453395/the-genes-of-the-sulphoquinovose-catabolism-in-escherichia-coli-are-also-associated-with-a-previously-unknown-pathway-of-lactose-degradation
#18
Anna Kaznadzey, Pavel Shelyakin, Evgeniya Belousova, Aleksandra Eremina, Uliana Shvyreva, Darya Bykova, Vera Emelianenko, Anastasiya Korosteleva, Maria Tutukina, Mikhail S Gelfand
Comparative genomics analysis of conserved gene cassettes demonstrated resemblance between a recently described cassette of genes involved in sulphoquinovose degradation in Escherichia coli K-12 MG1655 and a Bacilli cassette linked with lactose degradation. Six genes from both cassettes had similar functions related to carbohydrate metabolism, namely, hydrolase, aldolase, kinase, isomerase, transporter, and transcription factor. The Escherichia coli sulphoglycolysis cassette was thus predicted to be associated with lactose degradation...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29453370/a-multitarget-approach-to-drug-discovery-inhibiting-mycobacterium-tuberculosis-pyrg-and-pank
#19
Laurent R Chiarelli, Giorgia Mori, Beatrice Silvia Orena, Marta Esposito, Thomas Lane, Ana Luisa de Jesus Lopes Ribeiro, Giulia Degiacomi, Júlia Zemanová, Sára Szádocka, Stanislav Huszár, Zuzana Palčeková, Marcello Manfredi, Fabio Gosetti, Joël Lelièvre, Lluis Ballell, Elena Kazakova, Vadim Makarov, Emilio Marengo, Katarina Mikusova, Stewart T Cole, Giovanna Riccardi, Sean Ekins, Maria Rosalia Pasca
Mycobacterium tuberculosis, the etiological agent of the infectious disease tuberculosis, kills approximately 1.5 million people annually, while the spread of multidrug-resistant strains is of great global concern. Thus, continuous efforts to identify new antitubercular drugs as well as novel targets are crucial. Recently, two prodrugs activated by the monooxygenase EthA, 7947882 and 7904688, which target the CTP synthetase PyrG, were identified and characterized. In this work, microbiological, biochemical, and in silico methodologies were used to demonstrate that both prodrugs possess a second target, the pantothenate kinase PanK...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29453256/structural-characterization-and-directed-evolution-of-a-novel-acetyl-xylan-esterase-reveals-thermostability-determinants-of-the-carbohydrate-esterase-7-family
#20
Fiyinfoluwa A Adesioye, Thulani P Makhalanyane, Surendra Vikram, Bryan T Sewell, Wolf-Dieter Schubert, Don A Cowan
A hot desert hypolith metagenomic DNA sequence dataset was screened in-silico for genes annotated as acetyl xylan esterases (AcXEs). One of the genes identified encoded a ∼36 kDa protein (Axe1 NaM1 ). The synthesised gene was cloned, expressed and the resulting protein, purified. NaM1 was optimally active at pH 8.5 and 30°C, and functionally stable at salt concentrations up to 5 M. The specific activity and catalytic efficiency were 488.9 Umg -1 and 3.26x10 6 M -1 s -1 , respectively. The crystal structure of wild type NaM1 was solved at a resolution of 2...
February 16, 2018: Applied and Environmental Microbiology
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"