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Organs chips

Daniil A Maksimov, Petr P Laktionov, Stepan N Belyakin
Analysis of gene expression regulation typically requires identification of genomic sites bound by regulatory proteins. For this purpose, chromatin immunoprecipitation (ChIP) and Dam identification (DamID) methods can be applied to cell lines, whole organisms, or enriched cell populations. In this work, we present modifications to the experimental DamID protocol, as well as a custom data processing algorithm, that allow to confidently identify genomic sites enriched with the proteins of interest. This algorithm is implemented in Perl and is also available as executable files, thereby making DamID analysis relatively straightforward...
October 21, 2016: Chromosome Research
Chuanguang Yao, Hongxin Song, Ying Wan, Kefeng Ma, Chenyu Zheng, Hongda Cui, Peng Xin, Xubo Ji, Sheng-Yuan Deng
A porphyrin-based electro-photodynamic imaging system was fabricated for monitoring the concentration of oxygen. Distinct from the electrochemiluminescent (ECL) inability of numerous organic species in aqueous solutions, a strong and stable red irradiation at 634 nm could be stimulated electrochemically on zinc(II) meso-tetra(4-carboxyphenyl) porphine (ZnTCPP)/tetraoctylammonium bromide (TOAB) in the physiological condition. In terms of in situ electron paramagnetic resonance and ECL spectroscopies, the nature of ECL was thoroughly investigated, being exactly the chemiluminescence from singlet oxygen (1O2) produced during the successive electro-reduction of ZnTCPP...
October 20, 2016: ACS Applied Materials & Interfaces
Colleen E Dugan, James P Grinias, Sebastian D Parlee, Mahmoud El-Azzouny, Charles R Evans, Robert T Kennedy
Microfluidics is an enabling technology for both cell biology and chemical analysis. We combine these attributes with a microfluidic device for on-line solid-phase extraction (SPE) and mass spectrometry (MS) analysis of secreted metabolites from living cells in culture on the chip. The device was constructed with polydimethylsiloxane (PDMS) and contains a reversibly sealed chamber for perfusing cells. A multilayer design allowed a series of valves to control an on-chip 7.5 μL injection loop downstream of the cell chamber with operation similar to a six-port valve...
October 19, 2016: Analytical and Bioanalytical Chemistry
Olivier Duverger, Takahiro Ohara, Paul W Bible, Angela Zah, Maria I Morasso
Patients with Tricho-Dento-Osseous syndrome, an ectodermal dysplasia caused by mutations in the homeodomain transcription factor DLX3, exhibit enamel hypoplasia and hypomineralization. Here we used a conditional knockout mouse model to investigate the developmental and molecular consequences of Dlx3 deletion in the dental epithelium in vivo. Dlx3 deletion in the dental epithelium resulted in the formation of chalky hypomineralized enamel in all teeth. Interestingly, transcriptomic analysis revealed that major enamel matrix proteins and proteases known to be involved in enamel secretion and maturation were not affected significantly by Dlx3 deletion in the enamel organ...
October 19, 2016: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
Philippe Chouvarine, Lutz Wiehlmann, Patricia Moran Losada, David S DeLuca, Burkhard Tümmler
Ever-increasing affordability of next-generation sequencing makes whole-metagenome sequencing an attractive alternative to traditional 16S rDNA, RFLP, or culturing approaches for the analysis of microbiome samples. The advantage of whole-metagenome sequencing is that it allows direct inference of the metabolic capacity and physiological features of the studied metagenome without reliance on the knowledge of genotypes and phenotypes of the members of the bacterial community. It also makes it possible to overcome problems of 16S rDNA sequencing, such as unknown copy number of the 16S gene and lack of sufficient sequence similarity of the "universal" 16S primers to some of the target 16S genes...
2016: PloS One
Khaled J Saleh, William O Shaffer
In 2015, the US Congress passed legislation entitled the Medicare Access and CHIP [Children's Health Insurance Program] Reauthorization Act (MACRA), which led to the formation of two reimbursement paradigms: the merit-based incentive payment system (MIPS) and alternative payment models (APMs). The MACRA effectively repealed the Centers for Medicare and Medicaid Services (CMS) sustainable growth rate (SGR) formula while combining several CMS quality-reporting programs. As such, MACRA represents an unparalleled acceleration toward reimbursement models that recognize value rather than volume...
November 2016: Journal of the American Academy of Orthopaedic Surgeons
Adama Creppy, Franck Plouraboué, Olivier Praud, Xavier Druart, Sébastien Cazin, Hui Yu, Pierre Degond
New experimental evidence of self-motion of a confined active suspension is presented. Depositing fresh semen sample in an annular shaped microfluidic chip leads to a spontaneous vortex state of the fluid at sufficiently large sperm concentration. The rotation occurs unpredictably clockwise or counterclockwise and is robust and stable. Furthermore, for highly active and concentrated semen, richer dynamics can occur such as self-sustained or damped rotation oscillations. Experimental results obtained with systematic dilution provide a clear evidence of a phase transition towards collective motion associated with local alignment of spermatozoa akin to the Vicsek model...
October 2016: Journal of the Royal Society, Interface
Yad Ghavi-Helm, Bingqing Zhao, Eileen E M Furlong
Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is an invaluable technique to assess transcription factor binding and histone modifications in a genome-wide manner, an essential step towards understanding the mechanisms that govern embryonic development. Here, we provide a detailed protocol for all steps involved in generating a ChIP-seq library, starting from embryo collection, fixation, chromatin preparation, immunoprecipitation, and finally library preparation. The protocol is optimized for Drosophila embryos, but can be easily adapted for any model organism...
2016: Methods in Molecular Biology
Kimberly A Homan, David B Kolesky, Mark A Skylar-Scott, Jessica Herrmann, Humphrey Obuobi, Annie Moisan, Jennifer A Lewis
Three-dimensional models of kidney tissue that recapitulate human responses are needed for drug screening, disease modeling, and, ultimately, kidney organ engineering. Here, we report a bioprinting method for creating 3D human renal proximal tubules in vitro that are fully embedded within an extracellular matrix and housed in perfusable tissue chips, allowing them to be maintained for greater than two months. Their convoluted tubular architecture is circumscribed by proximal tubule epithelial cells and actively perfused through the open lumen...
October 11, 2016: Scientific Reports
Onur Kilic, David Pamies, Emily Lavell, Paula Schiapparelli, Yun Feng, Thomas Hartung, Anna Bal-Price, Helena T Hogberg, Alfredo Quinones-Hinojosa, Hugo Guerrero-Cazares, Andre Levchenko
Migration of neural progenitors in the complex tissue environment of the central nervous system is not well understood. Progress in this area has the potential to drive breakthroughs in neuroregenerative therapies, brain cancer treatments, and neurodevelopmental studies. To a large extent, advances have been limited due to a lack of controlled environments recapitulating characteristics of the central nervous system milieu. Reductionist cell culture models are frequently too simplistic, and physiologically more relevant approaches such as ex vivo brain slices or in situ experiments provide little control and make information extraction difficult...
October 18, 2016: Lab on a Chip
C Wyatt Shields Iv, Jeffrey L Wang, Korine A Ohiri, Eric D Essoyan, Benjamin B Yellen, Andrew J Armstrong, Gabriel P López
Liquid biopsies hold enormous promise for the next generation of medical diagnoses. At the forefront of this effort, many are seeking to capture, enumerate and analyze circulating tumor cells (CTCs) as a means to prognosticate and develop individualized treatments for cancer. Capturing these rare cells, however, represents a major engineering challenge due to their low abundance, morphology and heterogeneity. A variety of microfluidic tools have been developed to isolate CTCs from drawn blood samples; however, few of these approaches offer a means to separate and analyze cells in an integrated system...
September 21, 2016: Lab on a Chip
Yu Shrike Zhang, Andrea Arneri, Simone Bersini, Su-Ryon Shin, Kai Zhu, Zahra Goli-Malekabadi, Julio Aleman, Cristina Colosi, Fabio Busignani, Valeria Dell'Erba, Colin Bishop, Thomas Shupe, Danilo Demarchi, Matteo Moretti, Marco Rasponi, Mehmet Remzi Dokmeci, Anthony Atala, Ali Khademhosseini
Engineering cardiac tissues and organ models remains a great challenge due to the hierarchical structure of the native myocardium. The need of integrating blood vessels brings additional complexity, limiting the available approaches that are suitable to produce integrated cardiovascular organoids. In this work we propose a novel hybrid strategy based on 3D bioprinting, to fabricate endothelialized myocardium. Enabled by the use of our composite bioink, endothelial cells directly bioprinted within microfibrous hydrogel scaffolds gradually migrated towards the peripheries of the microfibers to form a layer of confluent endothelium...
December 2016: Biomaterials
Francesco S Pasqualini, Maximillian Y Emmert, Kevin Kit Parker, Simon P Hoerstrup
No abstract text is available yet for this article.
October 6, 2016: Clinical Pharmacology and Therapeutics
J Stephen Dumler, Sara H Sinclair, Valeria Pappas-Brown, Amol C Shetty
Anaplasma phagocytophilum, an obligate intracellular prokaryote, infects neutrophils, and alters cardinal functions via reprogrammed transcription. Large contiguous regions of neutrophil chromosomes are differentially expressed during infection. Secreted A. phagocytophilum effector AnkA transits into the neutrophil or granulocyte nucleus to complex with DNA in heterochromatin across all chromosomes. AnkA binds to gene promoters to dampen cis-transcription and also has features of matrix attachment region (MAR)-binding proteins that regulate three-dimensional chromatin architecture and coordinate transcriptional programs encoded in topologically-associated chromatin domains...
2016: Frontiers in Cellular and Infection Microbiology
Hyun Jung Kim, Jaewon Lee, Jin-Ha Choi, Anthony Bahinski, Donald E Ingber
Here, we describe a protocol to perform long-term co-culture of multi-species human gut microbiome with microengineered intestinal villi in a human gut-on-a-chip microphysiological device. We recapitulate the intestinal lumen-capillary tissue interface in a microfluidic device, where physiological mechanical deformations and fluid shear flow are constantly applied to mimic peristalsis. In the lumen microchannel, human intestinal epithelial Caco-2 cells are cultured to form a 'germ-free' villus epithelium and regenerate small intestinal villi...
2016: Journal of Visualized Experiments: JoVE
Mauro Sassi, Nunzio Buccheri, Myles Rooney, Chiara Botta, Francesco Bruni, Umberto Giovanella, Sergio Brovelli, Luca Beverina
Organic light emitting diodes (OLEDs) operating in the near-infrared spectral region are gaining growing relevance for emerging photonic technologies, such as lab-on-chip platforms for medical diagnostics, flexible self-medicated pads for photodynamic therapy, night vision and plastic-based telecommunications. The achievement of efficient near-infrared electroluminescence from solution-processed OLEDs is, however, an open challenge due to the low photoluminescence efficiency of most narrow-energy-gap organic emitters...
September 28, 2016: Scientific Reports
Sumantra Chatterjee, Petra Kraus, V Sivakamasundari, Sook Peng Yap, Vibhor Kumar, Shyam Prabhakar, Thomas Lufkin
This work pertains to GEO submission GSE36672, in vivo and in vitro genome wide binding (ChIP-Seq) of Bapx1/Nkx3.2 and Sox9 proteins. We have previously shown that data from a genome wide binding assay combined with transcriptional profiling is an insightful means to divulge the mechanisms directing cell type specification and the generation of tissues and subsequent organs [1]. Our earlier work identified the role of the DNA-binding homeodomain containing protein Bapx1/Nkx3.2 in midgestation murine embryos...
December 2016: Genomics Data
Sofia P Rebelo, Eva-Maria Dehne, Catarina Brito, Reyk Horland, Paula M Alves, Uwe Marx
Equipment and device qualification and test assay validation in the field of tissue engineered human organs for substance assessment remain formidable tasks with only a few successful examples so far. The hurdles seem to increase with the growing complexity of the biological systems, emulated by the respective models. Controlled single tissue or organ culture in bioreactors improves the organ-specific functions and maintains their phenotypic stability for longer periods of time. The reproducibility attained with bioreactor operations is, per se, an advantage for the validation of safety assessment...
2016: Advances in Experimental Medicine and Biology
Jinumary Mathai, Smriti P K Mittal, Aftab Alam, Payal Ranade, Devraj Mogare, Sonal Patel, Smita Saxena, Suvankar Ghorai, Abhijeet P Kulkarni, Samit Chattopadhyay
Chromatin architecture and dynamics are regulated by various histone and non-histone proteins. The matrix attachment region binding proteins (MARBPs) play a central role in chromatin organization and function through numerous regulatory proteins. In the present study, we demonstrate that nuclear matrix protein SMAR1 orchestrates global gene regulation as determined by massively parallel ChIP-sequencing. The study revealed that SMAR1 binds to T(C/G) repeat and targets genes involved in diverse biological pathways...
September 27, 2016: Scientific Reports
Laura Iannetti, Giovanna D'Urso, Gioacchino Conoscenti, Elena Cutrì, Rocky S Tuan, Manuela T Raimondi, Riccardo Gottardi, Paolo Zunino
Next generation bioreactors are being developed to generate multiple human cell-based tissue analogs within the same fluidic system, to better recapitulate the complexity and interconnection of human physiology [1, 2]. The effective development of these devices requires a solid understanding of their interconnected fluidics, to predict the transport of nutrients and waste through the constructs and improve the design accordingly. In this work, we focus on a specific model of bioreactor, with multiple input/outputs, aimed at generating osteochondral constructs, i...
2016: PloS One
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