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https://www.readbyqxmd.com/read/28743116/the-role-of-tumoral-foxp3-on-cell-proliferation-migration-and-invasion-in-gastric-cancer
#1
Lu Zhang, Jianghao Xu, Xuan Zhang, Yi Zhang, Lu Wang, Xiaoxu Huang, Zekuan Xu
BACKGROUND/AIMS: There is little published data on the role of FOXP3 in gastric cancer. METHODS: FOXP3 expression and localization in gastric cancer tissues and cells were examined by immunohistochemistry, RT-PCR, flow cytometry, western blot, and laser confocal microscopy. CCK8, plate clone, wound healing, and transwell insert assays were performed for gastric cancer cells. Potential molecules and signaling pathways were screened using high-throughput transcriptome sequencing...
July 25, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28743095/a-rapid-and-reliable-method-for-discriminating-rice-products-from-different-regions-using-mcx-based-solid-phase-extraction-and-di-ms-ms-based-metabolomics-approach
#2
Dong Kyu Lim, Changyeun Mo, Nguyen Phuoc Long, Jongguk Lim, Sung Won Kwon
The expansion of the global rice marketplace ultimately raises concerns about authenticity control. Several analytical methods for differentiating the geographical origin of rice have been developed, yet a high-throughput method is still in demand. In this study, we developed a rapid approach using direct infusion-mass spectrometry (DI-MS) to distinguish rice products from different countries. Specifically, the elimination of the matrix effect by a polytetrafluoroethylene (PTFE) filter, a mixed-mode cation exchange (MCX) solid-phase extraction (SPE) with 20% methanol, and an MCX SPE with 100% methanol were measured...
July 18, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28742937/models-for-discovery-of-targeted-therapy-in-genetic-epileptic-encephalopathies
#3
REVIEW
Snezana Maljevic, Christopher A Reid, Steven Petrou
Epileptic encephalopathies are severe disorders emerging in the first days to years of life that commonly include refractory seizures, various types of movement disorders, and different levels of developmental delay. In recent years, many de novo occurring variants have been identified in individuals with these devastating disorders. To unravel disease mechanisms the functional impact of detected variants associated with epileptic encephalopathies is investigated in a range of cellular and animal models. This review addresses efforts to advance and use such models to identify specific molecular and cellular targets for the development of novel therapies...
July 25, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28742374/high-throughput-analysis-identifying-drugs-that-regulate-apolipoprotein-a-i-synthesis
#4
Michael J Haas, Luisa Onstead-Haas, William Kurban, Harshit Shah, Monica Plazarte, Ayham Chamseddin, Arshag D Mooradian
Apolipoprotein A-I (apo A-I) is the primary antiatherogenic protein in high-density lipoprotein (HDL). Despite the controversy as to the clinical effectiveness of raising HDL, the search is ongoing for safe and effective drugs that increase HDL and apo A-I levels. To identify novel compounds that can increase hepatic apo A-I production, two drug libraries were screened. The NIH clinical collection (NCC) and the NIH clinical collection 2 (NCC2) were purchased from Evotec (San Francisco, CA). The NCC library contains 446 compounds and the NCC2 library contains 281 compounds, all dissolved in dimethylsulfoxide at a concentration of 10 mM...
July 25, 2017: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/28742351/materials-screening-for-the-discovery-of-new-half-heuslers-machine-learning-versus-ab-initio-methods
#5
Fleur Legrain, Jesús Carrete, Ambroise van Roekeghem, Georg K H Madsen, Natalio Mingo
Machine learning (ML) is increasingly becoming a helpful tool in the search for novel functional compounds. Here we use classification via random forests to predict the stability of half-Heusler (HH) compounds, using only experimentally reported compounds as a training set. Cross-validation yields an excellent agreement between the fraction of compounds classified as stable and the actual fraction of truly stable compounds in the ICSD. The ML model is then employed to screen 71,178 different 1:1:1 compositions, yielding 481 likely stable candidates...
July 25, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28742318/development-of-a-virtual-cell-model-to-predict-cell-response-to-substrate-topography
#6
Tiam Heydari, Maziar Heidari, Omid Mashinchian, Michal Wojcik, Ke Xu, Matthew John Dalby, Morteza Mahmoudi, Mohammad Reza Ejtehadi
Cells can sense and respond to changes in the topographical, chemical, and mechanical information in their environment. Engineered substrates are increasingly being developed that exploit these physical attributes to direct cell responses (most notably mesenchymal stem cells) and therefore control cell behavior toward desired applications. However, there are very few methods available for robust and accurate modeling that can predict cell behavior prior to experimental evaluations and this typically means that many cell test iterations are needed to identify best material features...
July 25, 2017: ACS Nano
https://www.readbyqxmd.com/read/28742258/metabolite-profiling-of-non-sterile-rhizosphere-soil
#7
Pierre Pétriacq, Alex Williams, T E Anne Cotton, Alexander E McFarlane, Stephen A Rolfe, Jurriaan Ton
Rhizosphere chemistry is the sum of root exudation chemicals, their breakdown products and microbial products of soil-derived chemicals. To date, most studies about root exudation chemistry are based on sterile cultivation systems, which limits the discovery of microbial breakdown products that act as semiochemicals and shape microbial rhizosphere communities. Here, we present a method for untargeted metabolic profiling of non-sterile rhizosphere soil. We have developed an experimental growth system that enables collection and analysis of rhizosphere chemicals from different plant species...
July 25, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28742153/reconstructing-the-regulatory-circuit-of-cell-fate-determination-in-yeast-mating-response
#8
Bin Shao, Haiyu Yuan, Rongfei Zhang, Xuan Wang, Shuwen Zhang, Qi Ouyang, Nan Hao, Chunxiong Luo
Massive technological advances enabled high-throughput measurements of proteomic changes in biological processes. However, retrieving biological insights from large-scale protein dynamics data remains a challenging task. Here we used the mating differentiation in yeast Saccharomyces cerevisiae as a model and developed integrated experimental and computational approaches to analyze the proteomic dynamics during the process of cell fate determination. When exposed to a high dose of mating pheromone, the yeast cell undergoes growth arrest and forms a shmoo-like morphology; however, at intermediate doses, chemotropic elongated growth is initialized...
July 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28742090/t-dna-genome-junctions-form-early-after-infection-and-are-influenced-by-the-chromatin-state-of-the-host-genome
#9
Shay Shilo, Pooja Tripathi, Cathy Melamed-Bessudo, Oren Tzfadia, Theodore R Muth, Avraham A Levy
Agrobacterium tumefaciens mediated T-DNA integration is a common tool for plant genome manipulation. However, there is controversy regarding whether T-DNA integration is biased towards genes or randomly distributed throughout the genome. In order to address this question, we performed high-throughput mapping of T-DNA-genome junctions obtained in the absence of selection at several time points after infection. T-DNA-genome junctions were detected as early as 6 hours post-infection. T-DNA distribution was apparently uniform throughout the chromosomes, yet local biases toward AT-rich motifs and T-DNA border sequence micro-homology were detected...
July 24, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28742070/growth-arrest-and-a-persister-state-enable-resistance-to-osmotic-shock-and-facilitate-dissemination-of-vibrio-cholerae
#10
Cecilia A Silva-Valenzuela, David W Lazinski, Shoshanna C Kahne, Y Nguyen, Roberto C Molina-Quiroz, Andrew Camilli
Vibrio cholerae is a water-borne bacterial pathogen and causative agent of cholera. Although V. cholerae is a halophile, it can survive in fresh water, and this has a major role in cholera epidemics through consumption of contaminated water and subsequent fecal-oral spread. After dissemination from humans back into fresh water, V. cholerae encounters limited nutrient availability and an abrupt drop in conductivity but little is known about how V. cholerae adapts to, and survives in this environment. In this work, by abolishing or altering the expression of V...
July 25, 2017: ISME Journal
https://www.readbyqxmd.com/read/28741488/extraordinary-cancer-epigenomics-thinking-outside-the-classical-coding-and-promoter-box
#11
REVIEW
Matthew Murtha, Manel Esteller
The advent of functional genomics powered by high-throughput sequencing has given us a new appreciation of the genomic sequences that lie outside the canonical promoter-coding sequence box. These regions harbor distant regulatory elements, enhancers, super-enhancers, insulators, alternative promoters, and sequences that transcribe as noncoding RNAs (ncRNAs) such as miRNAs and long ncRNAs. These functional genomics studies have also enabled a clearer understanding of the role of the 3D structure of the genome in epigenetic regulation...
October 2016: Trends in Cancer
https://www.readbyqxmd.com/read/28741359/evaluation-of-parameters-for-confident-phosphorylation-site-localization-using-an-orbitrap-fusion-tribrid-mass-spectrometer
#12
Samantha Ferries, Simon Perkins, Philip J Brownridge, Amy Campbell, Patrick A Eyers, Andrew R Jones, Claire E Eyers
Confident identification of sites of protein phosphorylation by mass spectrometry (MS) is essential to advance understanding of phosphorylation-mediated signaling events. However, development of novel instrumentation requires that methods for MS data acquisition and its interrogation be evaluated and optimized for high throughput phosphoproteomics. Here, we compare and contrast eight MS acquisition methods on the novel tribrid Orbitrap Fusion MS platform, using both a synthetic phosphopeptide library and a complex phosphopeptide-enriched cell lysate...
July 25, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28741265/mechanisms-of-type-2-diabetes-risk-loci
#13
REVIEW
Kyle J Gaulton
PURPOSE OF REVIEW: Deciphering the mechanisms of type 2 diabetes (T2DM) risk loci can greatly inform on disease pathology. This review discusses current knowledge of mechanisms through which genetic variants influence T2DM risk and considerations for future studies. RECENT FINDINGS: Over 100 T2DM risk loci to date have been identified. Candidate causal variants at risk loci map predominantly to non-coding sequence. Physiological, epigenomic and gene expression data suggest that variants at many known T2DM risk loci affect pancreatic islet regulation, although variants at other loci also affect protein function and regulatory processes in adipose, pre-adipose, liver, skeletal muscle and brain...
September 2017: Current Diabetes Reports
https://www.readbyqxmd.com/read/28741142/proteomic-expression-changes-in-large-cerebral-arteries-after-experimental-subarachnoid-hemorrhage-in-rat-are-regulated-by-the-mek-erk1-2-pathway
#14
Anne H Müller, Alistair V G Edwards, Martin R Larsen, Janne Nielsen, Karin Warfvinge, Gro K Povlsen, Lars Edvinsson
Subarachnoid hemorrhage (SAH) is a serious clinical condition where leakage of blood into the subarachnoid space causes an acute rise in intracranial pressure and reduces cerebral blood flow, which may lead to delayed cerebral ischemia and poor outcome. In experimental SAH, we have previously shown that the outcome can be significantly improved by early inhibition of the MAPK/ERK kinase/extracellular signal-regulated kinase (MEK/ERK1/2) pathway. The aim of this study was to apply mass spectrometry to investigate the overall late effects of experimental SAH on cerebrovascular protein expression...
July 24, 2017: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/28740754/the-time-course-of-broiler-intestinal-microbiota-development-after-administration-of-cecal-contents-to-incubating-eggs
#15
Erin E Donaldson, Dragana Stanley, Robert J Hughes, Robert J Moore
BACKGROUND: The microbial populations that inhabit the gastrointestinal tract (GIT) are known to influence the health and growth performance of the host. Clean hatcheries and machine-based incubation practices in the commercial poultry industry can lead to the acquisition of aberrant microbiota in the GIT of chickens and a very high level of bird-to-bird variation. The lack of microbial profile flock uniformity presents challenges for harnessing and manipulating intestinal bacteria to better serve the host...
2017: PeerJ
https://www.readbyqxmd.com/read/28739675/identification-of-the-regulon-of-aphb-and-its-essential-roles-in-luxr-and-exotoxin-asp-expression-in-the-pathogen-vibrio-alginolyticus
#16
Xiating Gao, Yang Liu, Huan Liu, Zhen Yang, Qin Liu, Yuanxing Zhang, Qiyao Wang
In Vibrios, AphB is essential to activate virulence cascades by sensing low pH and anaerobiosis signals. However, its regulon remains largely unknown. Here, AphB is found as a key virulence regulator in V. alginolyticus, a pathogen for marine animals and humans. Chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) enabled the detection of 20 loci in the V. alginolyticus genome that contain AphB-binding peaks. An AphB-specific binding consensus was confirmed by electrophoretic mobility shift assays (EMSA), and the regulation of genes flanking such binding sites was demonstrated using quantitative real-time PCR analysis...
July 24, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28739598/sequence-based-mapping-and-genome-editing-reveal-mutations-in-stickleback-hps5-cause-oculocutaneous-albinism-and-the-casper-phenotype
#17
Craig T Miller, James C Hart
Here we present and characterize the spontaneous X-linked recessive mutation casper, which causes oculocutaneous albinism in threespine sticklebacks (Gasterosteus aculeatus). In humans, Hermansky-Pudlak syndrome results in pigmentation defects due to disrupted formation of the melanin-containing lysosomal-related organelle (LRO), the melanosome. casper mutants display not only reduced pigmentation of melanosomes in melanophores, but also reductions in the iridescent silver color from iridophores, while the yellow pigmentation from xanthophores appears unaffected...
July 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28739118/single-cell-based-automated-quantification-of-therapy-response-of-invasive-cancer-spheroids-in-organotypic-3d-culture
#18
Cornelia Veelken, Gert-Jan Bakker, David Drell, Peter Friedl
Organotypic in vitro culture of 3D spheroids in extracellular matrix represent a promising cancer therapy prediction model for personalized medicine screens, due to their controlled experimental conditions and physiological similarities to in vivo models. As in tumors in vivo, 3D invasion cultures identify intratumor heterogeneity of growth, invasion and apoptosis induction by cytotoxic therapy. We here combine in vitro 3D spheroid invasion culture with irradiation and automated nucleus-based segmentation for single cell analysis to quantify growth, survival, apoptosis and invasion response during experimental radiation therapy...
July 21, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28738804/oncogenic-long-noncoding-rna-landscape-in-breast-cancer
#19
Shouping Xu, Dejia Kong, Qianlin Chen, Yanyan Ping, Da Pang
BACKGROUND: Few long noncoding RNAs (lncRNAs) that act as oncogenic genes in breast cancer have been identified. METHODS: Oncogenic lncRNAs associated with tumourigenesis and worse survival outcomes were examined and validated in Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), respectively. Then, the potential biological functions and expression regulation of these lncRNAs were studied via bioinformatics and genome data analysis. Moreover, progressive breast cancer subtype-specific lncRNAs were investigated via high-throughput sequencing in our cohort and TCGA validation...
July 24, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28738772/molecular-docking-and-drug-discovery-in-%C3%AE-adrenergic-receptors
#20
Santiago Vilar, Eduardo Sobarzo-Sánchez, Lourdes Santana, Eugenio Uriarte
Evolution in computer engineering, availability of increasing amounts of data and the development of new and fast docking algorithms and software have led to improved molecular simulations with crucial applications in virtual high-throughput screening and drug discovery. Moreover, analysis of protein-ligand recognition through molecular docking has become a valuable tool in drug design. In this review, we focus on the applicability of molecular docking on a particular class of G protein-coupled receptors: the β-adrenergic receptors, which are relevant targets in clinic for the treatment of asthma and cardiovascular diseases...
July 24, 2017: Current Medicinal Chemistry
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