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https://www.readbyqxmd.com/read/28092941/21st-century-cell-culture-for-21st-century-toxicology
#1
David Pamies, Thomas Hartung
There is no good science in bad models. Cell culture is especially prone to artifacts. A number of novel cell culture technologies have become more broadly available in the 21st century, which allow overcoming limitations of traditional culture and are more physiologically relevant. These include the use of stem-cell derived human cells, cocultures of different cell types, scaffolds and extracellular matrices, perfusion platforms (such as microfluidics), 3D culture, organ-on-chip technologies, tissue architecture, and organ functionality...
January 17, 2017: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/28092382/a-vascularized-and-perfused-organ-on-a-chip-platform-for-large-scale-drug-screening-applications
#2
Duc T T Phan, Xiaolin Wang, Brianna M Craver, Agua Sobrino, Da Zhao, Jerry C Chen, Lilian Y N Lee, Steven C George, Abraham P Lee, Christopher C W Hughes
There is a growing awareness that complex 3-dimensional (3D) organs are not well represented by monolayers of a single cell type - the standard format for many drug screens. To address this deficiency, and with the goal of improving screens so that drugs with good efficacy and low toxicity can be identified, microphysiological systems (MPS) are being developed that better capture the complexity of in vivo physiology. We have previously described an organ-on-a-chip platform that incorporates perfused microvessels, such that survival of the surrounding tissue is entirely dependent on delivery of nutrients through the vessels...
January 16, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28092380/chromatin-immunoprecipitation-in-microfluidic-droplets-towards-fast-and-cheap-analyses
#3
Bruno Teste, Jerome Champ, Arturo Londono-Vallejo, Stéphanie Descroix, Laurent Malaquin, Jean-Louis Viovy, Irena Draskovic, Guillaume Mottet
Genetic organization is governed by the interaction of DNA with histone proteins, and differential modifications of these proteins is a fundamental mechanism of gene regulation. Histone modifications are primarily studied through chromatin immunoprecipitation (ChIP) assays, however conventional ChIP procedures are time consuming, laborious and require a large number of cells. Here we report for the first time the development of ChIP in droplets based on a microfluidic platform combining nanoliter droplets, magnetic beads (MB) and magnetic tweezers (MT)...
January 16, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28088094/organ-on-a-chip-for-assessing-environmental-toxicants
#4
REVIEW
Soohee Cho, Jeong-Yeol Yoon
Man-made xenobiotics, whose potential toxicological effects are not fully understood, are oversaturating the already-contaminated environment. Due to the rate of toxicant accumulation, unmanaged disposal, and unknown adverse effects to the environment and the human population, there is a crucial need to screen for environmental toxicants. Animal models and in vitro models are ineffective models in predicting in vivo responses due to inter-species difference and/or lack of physiologically-relevant 3D tissue environment...
January 11, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28078768/microphysiological-systems-organs-on-chips-for-drug-efficacy-and-toxicity-testing
#5
Lucie A Low, Danilo A Tagle
No abstract text is available yet for this article.
January 11, 2017: Clinical and Translational Science
https://www.readbyqxmd.com/read/28078514/the-molecular-basis-of-the-organization-of-repetitive-dna-containing-constitutive-heterochromatin-in-mammals
#6
REVIEW
Gohei Nishibuchi, Jérôme Déjardin
Constitutive heterochromatin is composed mainly of repetitive elements and represents the typical inert chromatin structure in eukaryotic cells. Approximately half of the mammalian genome is made of repeat sequences, such as satellite DNA, telomeric DNA, and transposable elements. As essential genes are not present in these regions, most of these repeat sequences were considered as junk DNA in the past. However, it is now clear that these regions are essential for chromosome stability and the silencing of neighboring genes...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28072793/merit-based-incentive-payment-system-meaningful-changes-in-the-final-rule-brings-cautious-optimism
#7
Laxmaiah Manchikanti, Standiford Helm Ii, Aaron K Calodney, Joshua A Hirsch
The Medicare Access and CHIP Reauthorization Act of 2015 (MACRA) eliminated the flawed Sustainable Growth Rate (SGR) act formula - a longstanding crucial issue of concern for health care providers and Medicare beneficiaries. MACRA also included a quality improvement program entitled, "The Merit-Based Incentive Payment System, or MIPS." The proposed rule of MIPS sought to streamline existing federal quality efforts and therefore linked 4 distinct programs into one. Three existing programs, meaningful use (MU), Physician Quality Reporting System (PQRS), value-based payment (VBP) system were merged with the addition of Clinical Improvement Activity category...
January 2017: Pain Physician
https://www.readbyqxmd.com/read/28069205/study-of-a-laboratory-scaled-new-method-for-the-accelerated-continuous-ageing-of-wine-spirits-by-applying-ultrasound-energy
#8
M J Delgado-González, M M Sánchez-Guillén, M V García-Moreno, M C Rodríguez-Dodero, C García-Barroso, D A Guillén-Sánchez
During the ageing of brandies, many physicochemical processes take place involving the distilled spirit and the wood of the casks. Because of these reactions, the polyphenolic content of brandies and their content of organic acids increase with the ageing. These reactions are slow, and the ageing of high-quality brandies takes several years. In this paper, the development of a system that uses the circulation of the wine distillate through encapsulated American oak chips and the application of ultrasound energy with the aim of producing aged wine spirits has been carried out, and the influences of the operation variables over the characteristics of the produced drink have been measured...
May 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28066511/biomass-waste-to-energy-valorisation-technologies-a-review-case-for-banana-processing-in-uganda
#9
REVIEW
Robert Gumisiriza, Joseph Funa Hawumba, Mackay Okure, Oliver Hensel
BACKGROUND: Uganda's banana industry is heavily impeded by the lack of cheap, reliable and sustainable energy mainly needed for processing of banana fruit into pulp and subsequent drying into chips before milling into banana flour that has several uses in the bakery industry, among others. Uganda has one of the lowest electricity access levels, estimated at only 2-3% in rural areas where most of the banana growing is located. In addition, most banana farmers have limited financial capacity to access modern solar energy technologies that can generate sufficient energy for industrial processing...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28064247/genome-wide-analysis-of-the-distinct-types-of-chromatin-interactions-in-arabidopsis-thaliana
#10
Jingjing Wang, Yincong Zhou, Xue Li, Xianwen Meng, Miao Fan, Hongjun Chen, Jitong Xue, Ming Chen
The three-dimensional shapes of chromosomes regulate gene expression and genome function. Our knowledge of the role of chromatin interaction is evolving rapidly. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. High-throughput experimental techniques have been developed to map long-range interactions within chromatin. We have integrated data from multiple experimental sources including Hi-C, BS-seq, ChIP-chip and ChIP-seq data for 17 epigenetic marks and 35 transcription factors...
November 15, 2016: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28061365/primer-design-for-snp-genotyping-based-on-allele-specific-amplification-application-to-organ-transplantation-pharmacogenomics
#11
Luis A Tortajada-Genaro, Rosa Puchades, Ángel Maquieira
Diagnostic methods based on single nucleotide polymorphism (SNP) biomarkers are essential for the real adoption of personalized medicine. Allele specific amplification in a homogeneous format or combined to microarray hybridization are powerful approaches for SNP genotyping. However, primers must be properly selected to minimize cross-reactivity, dimer formation and nonspecific hybridization. This study presents a design workflow diagram for the selection of required oligonucleotides for multiplex assays. Based on thermodynamic restrictions, the oligonucleotide sets are chosen for a specific amplification of wild- and mutant-type templates...
December 29, 2016: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28060339/the-chip-exo-method-identifying-protein-dna-interactions-with-near-base-pair-precision
#12
Andrea A Perreault, Bryan J Venters
Chromatin immunoprecipitation (ChIP) is an indispensable tool in the fields of epigenetics and gene regulation that isolates specific protein-DNA interactions. ChIP coupled to high throughput sequencing (ChIP-seq) is commonly used to determine the genomic location of proteins that interact with chromatin. However, ChIP-seq is hampered by relatively low mapping resolution of several hundred base pairs and high background signal. The ChIP-exo method is a refined version of ChIP-seq that substantially improves upon both resolution and noise...
December 23, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28054980/an-integrated-microfabricated-chip-with-double-functions-as-an-ion-source-and-air-pump-based-on-liga-technology
#13
Hua Li, Linxiu Jiang, Chaoqun Guo, Jianmin Zhu, Yongrong Jiang, Zhencheng Chen
The injection and ionization of volatile organic compounds (VOA) by an integrated chip is experimentally analyzed in this paper. The integrated chip consists of a needle-to-cylinder electrode mounting on the Polymethyl Methacrylate (PMMA) substrate. The needle-to-cylinder electrode is designed and fabricated by Lithographie, Galvanoformung and Abformung (LIGA) technology. In this paper, the needle is connected to a negative power supply of -5 kV and used as the cathode; the cylinder electrodes are composed of two arrays of cylinders and serve as the anode...
January 4, 2017: Sensors
https://www.readbyqxmd.com/read/28045119/the-molecular-structure-of-human-red-blood-cell-membranes-from-highly-oriented-solid-supported-multi-lamellar-membranes
#14
Sebastian Himbert, Richard J Alsop, Markus Rose, Laura Hertz, Alexander Dhaliwal, Jose M Moran-Mirabal, Chris P Verschoor, Dawn M E Bowdish, Lars Kaestner, Christian Wagner, Maikel C Rheinstädter
We prepared highly oriented, multi-lamellar stacks of human red blood cell (RBC) membranes applied on silicon wafers. RBC ghosts were prepared by hemolysis and applied onto functionalized silicon chips and annealed into multi-lamellar RBC membranes. High resolution X-ray diffraction was used to determine the molecular structure of the stacked membranes. We present direct experimental evidence that these RBC membranes consist of nanometer sized domains of integral coiled-coil peptides, as well as liquid ordered (lo) and liquid disordered (ld) lipids...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28045091/ctcf-interacts-with-the-lytic-hsv-1-genome-to-promote-viral-transcription
#15
Fengchao Lang, Xin Li, Olga Vladimirova, Benxia Hu, Guijun Chen, Yu Xiao, Vikrant Singh, Danfeng Lu, Lihong Li, Hongbo Han, J M A S P Wickramasinghe, Sheryl T Smith, Chunfu Zheng, Qihan Li, Paul M Lieberman, Nigel W Fraser, Jumin Zhou
CTCF is an essential chromatin regulator implicated in important nuclear processes including in nuclear organization and transcription. Herpes Simplex Virus-1 (HSV-1) is a ubiquitous human pathogen, which enters productive infection in human epithelial and many other cell types. CTCF is known to bind several sites in the HSV-1 genome during latency and reactivation, but its function has not been defined. Here, we report that CTCF interacts extensively with the HSV-1 DNA during lytic infection by ChIP-seq, and its knockdown results in the reduction of viral transcription, viral genome copy number and virus yield...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28045076/phf14-an-innate-inhibitor-against-the-progression-of-renal-fibrosis-following-folic-acid-induced-kidney-injury
#16
Bo Yang, Sixiu Chen, Ming Wu, Lin Zhang, Mengna Ruan, Xujiao Chen, Zhengjun Chen, Changlin Mei, Zhiguo Mao
PHF14 is a newly identified regulator of mesenchyme growth in embryonic tissues. Previous studies have shown that phf14-null mutants die just after birth due to interstitial tissue hyperplasia in major organs, including the kidneys. The aim of this study was to investigate PHF14 function in renal fibrosis. By studying the chronic kidney injury mouse model, we found that PHF14 was upregulated in fibrotic kidneys after renal insults induced by folic acid administration. Compared with wild-type mice, PHF14-null mice showed more severe renal fibrosis after pro-fibrotic stimuli...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28036380/two-component-signaling-system-vgrrs-directly-senses-extracytoplasmic-and-intracellular-iron-to-control-bacterial-adaptation-under-iron-depleted-stress
#17
Li Wang, Yue Pan, Zhi-Hui Yuan, Huan Zhang, Bao-Yu Peng, Fang-Fang Wang, Wei Qian
Both iron starvation and excess are detrimental to cellular life, especially for animal and plant pathogens since they always live in iron-limited environments produced by host immune responses. However, how organisms sense and respond to iron is incompletely understood. Herein, we reveal that in the phytopathogenic bacterium Xanthomonas campestris pv. campestris, VgrS (also named ColS) is a membrane-bound receptor histidine kinase that senses extracytoplasmic iron limitation in the periplasm, while its cognate response regulator, VgrR (ColR), detects intracellular iron excess...
December 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/28031399/neurons-derived-from-different-brain-regions-are-inherently-different-in-vitro-a-novel-multiregional-brain-on-a-chip
#18
Stephanie Dauth, Ben M Maoz, Sean P Sheehy, Matthew A Hemphill, Tara Murty, Mary Kate Macedonia, Angie M Greer, Bogdan Budnik, Kevin Kit Parker
Brain in vitro models are critically important to developing our understanding of basic nervous system cellular physiology, potential neurotoxic effects of chemicals, and specific cellular mechanisms of many disease states. In this study, we sought to address key shortcomings of current brain in vitro models: The scarcity of comparative data for cells originating from distinct brain regions and the lack of multiregional brain in vitro models. We demonstrated that rat neurons from different brain regions exhibit unique profiles regarding their cell composition, protein expression, metabolism, and electrical activity in vitro...
December 28, 2016: Journal of Neurophysiology
https://www.readbyqxmd.com/read/28029625/comparison-of-classifier-architectures-for-online-neural-spike-sorting
#19
Maryam Saeed, Amir A Khan, Awais M Kamboh
High-density, intracranial recordings from micro-electrode arrays need to undergo Spike Sorting in order to associate the recorded neuronal spikes to particular neurons. This involves spike detection, feature extraction, and classification. To reduce the data transmission and power requirements, on-chip real-time processing is becoming very popular. However, high computational resources are required for classifiers in on-chip spike-sorters, making scalability a great challenge. In this review paper, we analyze several popular classifiers to propose five new hardware architectures using the off-chip training with on-chip classification approach...
December 19, 2016: IEEE Transactions on Neural Systems and Rehabilitation Engineering
https://www.readbyqxmd.com/read/28028025/genomics-of-chronic-neutrophilic-leukemia
#20
Julia E Maxson, Jeffrey W Tyner
Chronic neutrophilic leukemia (CNL) is a distinct myeloproliferative neoplasm with a high prevalence (>80%) of mutations in the Colony Stimulating Factor 3 Receptor (CSF3R). These mutations activate the receptor, leading to the proliferation of neutrophils that are a hallmark of CNL. Recently, the World Health Organization (WHO) guidelines have been updated to include CSF3R mutations as a part of the diagnostic criteria for CNL. Due to the high prevalence of CSF3R mutations in CNL, it is tempting to think of this disease as being solely driven by this genetic lesion...
December 27, 2016: Blood
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