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https://www.readbyqxmd.com/read/29222512/improving-gene-regulatory-network-inference-by-incorporating-rates-of-transcriptional-changes
#1
Jigar S Desai, Ryan C Sartor, Lovely Mae Lawas, S V Krishna Jagadish, Colleen J Doherty
Organisms respond to changes in their environment through transcriptional regulatory networks (TRNs). The regulatory hierarchy of these networks can be inferred from expression data. Computational approaches to identify TRNs can be applied in any species where quality RNA can be acquired, However, ChIP-Seq and similar validation methods are challenging to employ in non-model species. Improving the accuracy of computational inference methods can significantly reduce the cost and time of subsequent validation experiments...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29214789/microrna-183-is-essential-for-hair-cell-regeneration-after-neomycin-injury-in-zebrafish
#2
Chang Woo Kim, Ji Hyuk Han, Ling Wu, Jae Young Choi
PURPOSE: microRNAs (miRNAs) are non-coding RNAs composed of 20 to 22 nucleotides that regulate development and differentiation in various organs by silencing specific RNAs and regulating gene expression. In the present study, we show that the microRNA (miR)-183 cluster is upregulated during hair cell regeneration and that its inhibition reduces hair cell regeneration following neomycin-induced ototoxicity in zebrafish. MATERIALS AND METHODS: miRNA expression patterns after neomycin exposure were analyzed using microarray chips...
January 2018: Yonsei Medical Journal
https://www.readbyqxmd.com/read/29214585/microphysiological-systems-tissue-chips-and-their-utility-for-rare-disease-research
#3
Lucie A Low, Danilo A Tagle
The scientific and technological development of microphysiological systems (MPS) modeling organs-on-chips, or "tissue chips" (TCs), has progressed rapidly over the past decade. Stem cell research and microfluidic concepts have combined to lead to the development of microphysiological platforms representing an ever-expanding list of different human organ systems. In the context of rare diseases, these bioengineered microfluidics platforms hold promise for modeling of disorders and could prove useful in the screening and efficacy testing of existing therapeutics...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29214530/microfluidic-systems-for-studying-dynamic-function-of-adipocytes-and-adipose-tissue
#4
REVIEW
Xiangpeng Li, Christopher J Easley
Recent breakthroughs in organ-on-a-chip and related technologies have highlighted the extraordinary potential for microfluidics to not only make lasting impacts in the understanding of biological systems but also to create new and important in vitro culture platforms. Adipose tissue (fat), in particular, is one that should be amenable to microfluidic mimics of its microenvironment. While the tissue was traditionally considered important only for energy storage, it is now understood to be an integral part of the endocrine system that secretes hormones and responds to various stimuli...
December 6, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29211860/changes-in-the-epigenome-and-transcriptome-of-the-poplar-shoot-apical-meristem-in-response-to-water-availability-affect-preferentially-hormone-pathways
#5
Clément Lafon-Placette, Anne-Laure Le Gac, Didier Chauveau, Vincent Segura, Alain Delaunay, Marie-Claude Lesage-Descauses, Irène Hummel, David Cohen, Béline Jesson, Didier Le Thiec, Marie-Béatrice Bogeat-Triboulot, Franck Brignolas, Stéphane Maury
The adaptive capacity of long-lived organisms such as trees to the predicted climate changes, including severe and successive drought episodes, will depend on the presence of genetic diversity and phenotypic plasticity. Here, the involvement of epigenetic mechanisms in phenotypic plasticity toward soil water availability was examined in Populus×euramericana. This work aimed at characterizing (i) the transcriptome plasticity, (ii) the genome-wide plasticity of DNA methylation, and (iii) the function of genes affected by a drought-rewatering cycle in the shoot apical meristem...
December 2, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29207466/evaluation-of-poly-lactic-co-glycolic-acid-alone-or-in-combination-with-hydroxyapatite-on-human-periosteal-cells-bone-differentiation-and-in-sinus-lift-treatment
#6
Gabriele Ceccarelli, Rossella Presta, Saturnino Marco Lupi, Nefele Giarratana, Nora Bloise, Laura Benedetti, Maria Gabriella Cusella De Angelis, Ruggero Rodriguez Y Baena
Most recent advances in tissue engineering in the fields of oral surgery and dentistry have aimed to restore hard and soft tissues. Further improvement of these therapies may involve more biological approaches and the use of dental tissue stem cells in combination with inorganic/organic scaffolds. In this study, we analyzed the osteoconductivity of two different inorganic scaffolds based on poly (lactic-co-glycolic) acid alone (PLGA-Fisiograft) or in combination with hydroxyapatite (PLGA/HA-Alos) in comparison with an organic material based on equine collagen (PARASORB Sombrero) both in vitro and in vivo...
December 2, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29205920/multiorgan-microphysiological-systems-for-drug-development-strategies-advances-and-challenges
#7
REVIEW
Ying I Wang, Carlos Carmona, James J Hickman, Michael L Shuler
Traditional cell culture and animal models utilized for preclinical drug screening have led to high attrition rates of drug candidates in clinical trials due to their low predictive power for human response. Alternative models using human cells to build in vitro biomimetics of the human body with physiologically relevant organ-organ interactions hold great potential to act as "human surrogates" and provide more accurate prediction of drug effects in humans. This review is a comprehensive investigation into the development of tissue-engineered human cell-based microscale multiorgan models, or multiorgan microphysiological systems for drug testing...
December 4, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/29204837/current-technologies-based-on-the-knowledge-of-the-stem-cells-microenvironments
#8
Damia Mawad, Gemma Figtree, Carmine Gentile
The stem cell microenvironment or niche plays a critical role in the regulation of survival, differentiation and behavior of stem cells and their progenies. Recapitulating each aspect of the stem cell niche is therefore essential for their optimal use in in vitro studies and in vivo as future therapeutics in humans. Engineering of optimal conditions for three-dimensional stem cell culture includes multiple transient and dynamic physiological stimuli, such as blood flow and tissue stiffness. Bioprinting and microfluidics technologies, including organs-on-a-chip, are among the most recent approaches utilized to replicate the three-dimensional stem cell niche for human tissue fabrication that allow the integration of multiple levels of tissue complexity, including blood flow...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29203210/indoxyl-sulfate-upregulates-the-cannabinoid-type-1-receptor-gene-via-an-atf3-c-jun-complex-mediated-signaling-pathway-in-the-model-of-uremic-cardiomyopathy
#9
Yu-Juei Hsu, Shih-Che Hsu, Yung-Lung Chang, Shih-Ming Huang, Chun-Che Shih, Chien-Sung Tsai, Chih-Yuan Lin
BACKGROUND: The risk of cardiovascular disease is notably increased in patients with chronic kidney disease (CKD) and cannabinoid receptor type 1 (CB1R) plays an important role in the development of uremic cardiomyopathy. However, the molecular mechanism underlying the uremic toxin-induced upregulation of CB1R remains elusive. METHODS: The expression of the ATF3/c-Jun complex and CB1R in both in vivo and in vitro models of CKD were measured. We also determined the impact of the ATF3/c-Jun complex on CB1R expression by transfecting H9c2 cells with dominant negative mutants of ATF3 or c-Jun...
December 1, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/29202460/human-liver-kidney-model-elucidates-the-mechanisms-of-aristolochic-acid-nephrotoxicity
#10
Shih-Yu Chang, Elijah J Weber, Viktoriya S Sidorenko, Alenka Chapron, Catherine K Yeung, Chunying Gao, Qingcheng Mao, Danny Shen, Joanne Wang, Thomas A Rosenquist, Kathleen G Dickman, Thomas Neumann, Arthur P Grollman, Edward J Kelly, Jonathan Himmelfarb, David L Eaton
Environmental exposures pose a significant threat to human health. However, it is often difficult to study toxicological mechanisms in human subjects due to ethical concerns. Plant-derived aristolochic acids are among the most potent nephrotoxins and carcinogens discovered to date, yet the mechanism of bioactivation in humans remains poorly understood. Microphysiological systems (organs-on-chips) provide an approach to examining the complex, species-specific toxicological effects of pharmaceutical and environmental chemicals using human cells...
November 16, 2017: JCI Insight
https://www.readbyqxmd.com/read/29192191/viscous-fingering-in-multiport-hele-shaw-cell-for-controlled-shaping-of-fluids
#11
Tanveer Ul Islam, Prasanna S Gandhi
The pursuit of mimicking complex multiscale systems has been a tireless effort with many successes but a daunting task ahead. A new perspective to engineer complex cross-linked meshes and branched/tree-like structures at different scales is presented here. Control over Saffman-Taylor instability which otherwise randomly rearranges viscous fluid in a 'lifted Hele-Shaw cell' is proposed for the same. The proposed control employs multiple-ports or source-holes in this cell, to spontaneously shape a stretched fluid film into a network of well defined webs/meshes and ordered multiscale tree-like patterns...
November 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29186514/permissive-zones-for-the-centromere-binding-protein-parb-on-the-caulobacter-crescentus-chromosome
#12
Ngat T Tran, Clare E Stevenson, Nicolle F Som, Anyarat Thanapipatsiri, Adam S B Jalal, Tung B K Le
Proper chromosome segregation is essential in all living organisms. In Caulobacter crescentus, the ParA-ParB-parS system is required for proper chromosome segregation and cell viability. The bacterial centromere-like parS DNA locus is the first to be segregated following chromosome replication. parS is bound by ParB protein, which in turn interacts with ParA to partition the ParB-parS nucleoprotein complex to each daughter cell. Here, we investigated the genome-wide distribution of ParB on the Caulobacter chromosome using a combination of in vivo chromatin immunoprecipitation (ChIP-seq) and in vitro DNA affinity purification with deep sequencing (IDAP-seq)...
November 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29184959/a-multi-throughput-multi-organ-on-a-chip-system-on-a-plate-formatted-pneumatic-pressure-driven-medium-circulation-platform
#13
T Satoh, S Sugiura, K Shin, R Onuki-Nagasaki, S Ishida, K Kikuchi, M Kakiki, T Kanamori
This paper reports a multi-throughput multi-organ-on-a-chip system formed on a pneumatic pressure-driven medium circulation platform with a microplate-sized format as a novel type of microphysiological system. The pneumatic pressure-driven platform enabled parallelized multi-organ experiments (i.e. simultaneous operation of multiple multi-organ culture units) and pipette-friendly liquid handling for various conventional cell culture experiments, including cell seeding, medium change, live/dead staining, cell growth analysis, gene expression analysis of collected cells, and liquid chromatography-mass spectrometry analysis of chemical compounds in the culture medium...
November 29, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/29175062/organ-body-on-a-chip-based-on-microfluidic-technology-for-drug-discovery
#14
REVIEW
Hiroshi Kimura, Yasuyuki Sakai, Teruo Fujii
Although animal experiments are indispensable for preclinical screening in the drug discovery process, various issues such as ethical considerations and species differences remain. To solve these issues, cell-based assays using human-derived cells have been actively pursued. However, it remains difficult to accurately predict drug efficacy, toxicity, and organs interactions, because cultivated cells often do not retain their original organ functions and morphologies in conventional in vitro cell culture systems...
November 13, 2017: Drug Metabolism and Pharmacokinetics
https://www.readbyqxmd.com/read/29174673/surface-self-assembly-of-colloidal-crystals-for-micro-and-nano-patterning
#15
REVIEW
Ryan van Dommelen, Paola Fanzio, Luigi Sasso
The controlled patterning of polymeric surfaces at the micro- and nanoscale offers potential in the technological development of small-scale devices, particularly within the fields of photovoltaics, micro-optics and lab- and organ-on-chip, where the topological arrangement of the surface can influence a system's power generation, optical properties or biological function - such as, in the latter case, biomimicking surfaces or topological control of cellular differentiation. One of the most promising approaches in reducing manufacturing costs and complexity is by exploitation of the self-assembling properties of colloidal particles...
November 8, 2017: Advances in Colloid and Interface Science
https://www.readbyqxmd.com/read/29171900/beating-bias-in-directed-evolution-of-proteins-combining-high-fidelity-on-chip-solid-phase-gene-synthesis-with-efficient-gene-assembly-for-combinatorial-library-construction
#16
Manfred T Reetz, Aitao Li, Carlos G Acevedo-Rocha, Zhoutong Sun, Tony Cox, Jia Lucy Xu
Saturation mutagenesis (SM) constitutes a widely used technique in directed evolution of selective enzymes as catalysts in organic chemistry and in the manipulation of metabolic paths and genomes, but the quality of the libraries is far from optimal due to the inherent amino acid bias. Here we show how this fundamental problem can be solved by applying high-fidelity solid-phase chemical gene synthesis on Silicon-chips followed by efficient gene assembly. Limonene epoxide hydrolase was chosen as the catalyst in the model desymmetrization of cyclohexene oxide with stereoselective formation of (R,R)- and (S,S)-cyclohexane-1,2-diol...
November 24, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29168876/a-compartmentalized-microfluidic-chip-with-crisscross-microgrooves-and-electrophysiological-electrodes-for-modeling-the-blood-retinal-barrier
#17
Jose Yeste, Marta García-Ramírez, Xavi Illa, Anton Guimerà, Cristina Hernández, Rafael Simó, Rosa Villa
The interconnection of different tissue-tissue interfaces may extend organ-on-chips to a new generation of sophisticated models capable of recapitulating more complex organ-level functions. Single interfaces are largely recreated in organ-on-chips by culturing the cells on opposite sides of a porous membrane that splits a chamber in two or by connecting the cells of two adjacent compartments through microchannels. However, it is difficult to interconnect more than one interface using these approaches. To address this challenge, we present a novel microfluidic device where cells are arranged in parallel compartments and are highly interconnected through a grid of microgrooves, which facilitates paracrine signaling and heterotypic cell-cell contact between multiple tissues...
November 23, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/29167886/payment-reform-to-enhance-collaboration-of-primary-care-and-cardiology-a-review
#18
Steven A Farmer, Paul N Casale, Linda D Gillam, John S Rumsfeld, Shari Erickson, Neil M Kirschner, Kevin de Regnier, Bruce R Williams, R Shawn Martin, Mark B McClellan
Importance: The US health care system faces an unsustainable trajectory of high costs and inconsistent outcomes. The fee-for-service payment model has contributed to inefficiency, and new payment methods are a promising approach to improving value. Health reforms are needed to increase patient access, reduce costs, and improve health care quality, and the landmark Medicare Access and CHIP Reauthorization Act presents a roadmap for reform. The product of a collaboration between primary care and cardiology clinicians, this review describes a conceptual approach to delivery and payment reforms that aim to better support primary care-cardiology comanagement of chronic cardiovascular disease (CVD)...
November 22, 2017: JAMA Cardiology
https://www.readbyqxmd.com/read/29165984/on-chip-lipid-extraction-using-super-absorbent-polymers-for-mass-spectrometry
#19
Geul Bang, Young Hwan Kim, Junghyo Yoon, Yeong Jun Yu, Seok Chung, Jeong Ah Kim
Pre-treatment of samples is the one of most important steps in analytical methods for efficient and accurate results. Typically, an extraction method used for lipid analysis with mass spectrometry is accompanied by complex liquid-liquid extraction. We have devised a simple, rapid, and efficient lipid extraction method using super absorbent polymers (SAPs) and developed a high-throughput lipid extraction platform based on a microfluidic system. Since SAPs can rapidly absorb an aqueous solution from a raw sample and convert it into the gel, the lipid extraction process can be remarkably simplified...
November 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29164853/microfluidic-free-flow-electrophoresis-based-solvent-exchanger-for-continuously-operating-lab-on-chip-applications
#20
Franziska D Zitzmann, Heinz-Georg Jahnke, Simon Pfeiffer, Ronny Frank, Felix Nitschke, Laura Mauritz, Bernd Abel, Detlev Belder, Andrea A Robitzki
For miniaturization and integration of chemical synthesis and analytics on small length scales, the development of complex lab on chip (LOC) systems is in the focus of many current research projects. While application specific synthesis and analytic modules and LOC devices are widely described, the combination and integration of different modules is intensively investigated. Problems for in-line processes such as solvent incompatibilities, e.g., for a multistep synthesis or the combination of an organic drug synthesis with a cell-based biological activity testing system, require a solvent exchange between serialized modules...
November 22, 2017: Analytical Chemistry
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