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https://www.readbyqxmd.com/read/29665865/integrative-analysis-reveals-functional-and-regulatory-roles-of-h3k79me2-in-mediating-alternative-splicing
#1
Tianbao Li, Qi Liu, Nick Garza, Steven Kornblau, Victor X Jin
BACKGROUND: Accumulating evidence suggests alternative splicing (AS) is a co-transcriptional splicing process not only controlled by RNA-binding splicing factors, but also mediated by epigenetic regulators, such as chromatin structure, nucleosome density, and histone modification. Aberrant AS plays an important role in regulating various diseases, including cancers. METHODS: In this study, we integrated AS events derived from RNA-seq with H3K79me2 ChIP-seq data across 34 different normal and cancer cell types and found the higher enrichment of H3K79me2 in two AS types, skipping exon (SE) and alternative 3' splice site (A3SS)...
April 17, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29657657/engineering-small-tubes-with-changes-in-diameter-for-the-study-of-kidney-cell-organization
#2
Bastien Venzac, Randa Madoun, Taous Benarab, Sylvain Monnier, Fanny Cayrac, Sarah Myram, Ludovic Leconte, François Amblard, Jean-Louis Viovy, Stéphanie Descroix, Sylvie Coscoy
Multicellular tubes are structures ubiquitously found during development and in adult organisms. Their topologies (diameter, direction or branching), together with their mechanical characteristics, play fundamental roles in organ function and in the emergence of pathologies. In tubes of micrometric range diameters, typically found in the vascular system, renal tubules or excretory ducts, cells are submitted to a strong curvature and confinement effects in addition to flow. Then, small tubes with change in diameter are submitted to a local gradient of shear stress and curvature, which may lead to complex mechanotransduction responses along tubes, and may be involved in the onset or propagation of cystic or obstructive pathologies...
March 2018: Biomicrofluidics
https://www.readbyqxmd.com/read/29656649/wetting-behavior-of-metal-catalyzed-cvd-grown-one-dimensional-cubic-sic-nanostructures
#3
Afzal Khan, Kun Huang, Ming Hu, Xuegong Yu, Deren Yang
Superhydrophobic surfaces can be fabricated by using the self-assembled nano-architecture of 3C-SiC one-dimensional (1D) nanostructures as they are capable of forming a dense network of micro/nano air pockets without any help from external sources. Herein, metal catalyzed growth of 3C-SiC nanowires/nanorods on Si substrates via vapor-liquid-solid (VLS) mechanism using five different catalysts, i.e. chemically synthesized Au nanoparticles and direct current (DC) sputtered thin films of Au, Cu, Ni and Ti are reported...
April 15, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29656459/desktop-stereolithography-3d-printing-of-a-poly-dimethylsiloxane-based-material-with-sylgard-184-properties
#4
Nirveek Bhattacharjee, Cesar Parra-Cabrera, Yong Tae Kim, Alexandra P Kuo, Albert Folch
The advantageous physiochemical properties of poly(dimethylsiloxane) (PDMS) have made it an extremely useful material for prototyping in various technological, scientific, and clinical areas. However, PDMS molding is a manual procedure and requires tedious assembly steps, especially for 3D designs, thereby limiting its access and usability. On the other hand, automated digital manufacturing processes such as stereolithography (SL) enable true 3D design and fabrication. Here the formulation, characterization, and SL application of a 3D-printable PDMS resin (3DP-PDMS) based on commercially available PDMS-methacrylate macromers, a high-efficiency photoinitiator and a high-absorbance photosensitizer, is reported...
April 14, 2018: Advanced Materials
https://www.readbyqxmd.com/read/29656237/vascularized-microfluidic-organ-chips-for-drug-screening-disease-models-and-tissue-engineering
#5
REVIEW
Tatsuya Osaki, Vivek Sivathanu, Roger D Kamm
Vascularization of micro-tissues in vitro has enabled formation of tissues larger than those limited by diffusion with appropriate nutrient/gas exchange as well as waste elimination. Furthermore, angiocrine signaling from the vasculature may be essential in mimicking organ-level functions in these micro-tissues. In drug screening applications, the presence of an appropriate blood-organ barrier in the form of a vasculature and its supporting cells (pericytes, appropriate stromal cells) may be essential to reproducing organ-scale drug delivery pharmacokinetics...
April 12, 2018: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29651473/microfluidic-lung-airway-on-a-chip-with-arrayable-suspended-gels-for-studying-epithelial-and-smooth-muscle-cell-interactions
#6
Mouhita Humayun, Chung-Wai Chow, Edmond W K Young
Chronic lung diseases (CLDs) are regulated by complex interactions between many different cell types residing in lung airway tissues. Specifically, interactions between airway epithelial cells (ECs) and airway smooth muscle cells (SMCs) have been shown in part to play major roles in the pathogenesis of CLDs, but the underlying molecular mechanisms are not well understood. To advance our understanding of lung pathophysiology and accelerate drug development processes, new innovative in vitro tissue models are needed that can reconstitute the complex in vivo microenvironment of human lung tissues...
April 13, 2018: Lab on a Chip
https://www.readbyqxmd.com/read/29649981/in-silico-cancer-research-towards-3r
#7
Claire Jean-Quartier, Fleur Jeanquartier, Igor Jurisica, Andreas Holzinger
BACKGROUND: Improving our understanding of cancer and other complex diseases requires integrating diverse data sets and algorithms. Intertwining in vivo and in vitro data and in silico models are paramount to overcome intrinsic difficulties given by data complexity. Importantly, this approach also helps to uncover underlying molecular mechanisms. Over the years, research has introduced multiple biochemical and computational methods to study the disease, many of which require animal experiments...
April 12, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29648668/widespread-enhancer-activation-via-er%C3%AE-mediates-estrogen-response-in-vivo-during-uterine-development
#8
Wendy N Jefferson, H Karimi Kinyamu, Tianyuan Wang, Adam X Miranda, Elizabeth Padilla-Banks, Alisa A Suen, Carmen J Williams
Little is known regarding how steroid hormone exposures impact the epigenetic landscape in a living organism. Here, we took a global approach to understanding how exposure to the estrogenic chemical, diethylstilbestrol (DES), affects the neonatal mouse uterine epigenome. Integration of RNA- and ChIP-sequencing data demonstrated that ∼80% of DES-altered genes had higher H3K4me1/H3K27ac signal in close proximity. Active enhancers, of which ∼3% were super-enhancers, had a high density of estrogen receptor alpha (ERα) binding sites and were correlated with alterations in nearby gene expression...
April 10, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29626551/microfluidics-in-nanoparticle-drug-delivery-from-synthesis-to-pre-clinical-screening
#9
Jungho Ahn, Jihoon Ko, Somin Lee, James Yu, YongTae Kim, Noo Li Jeon
Microfluidic technologies employ nano and microscale fabrication techniques to develop highly controllable and reproducible fluidic microenvironments. Utilizing microfluidics, lead compounds can be produced with the controlled physicochemical properties, characterized in a high-throughput fashion, and evaluated in in vitro biomimetic models of human organs; organ-on-a-chip. As a step forward from conventional in vitro culture methods, microfluidics shows promise in effective preclinical testing of nanoparticle-based drug delivery...
April 4, 2018: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/29619452/microsensor-systems-for-cell-metabolism-from-2d-culture-to-organ-on-chip
#10
REVIEW
Jochen Kieninger, Andreas Weltin, Hubert Flamm, Gerald A Urban
Microsensor systems for cell metabolism are essential tools for investigation and standardization in cell culture. Electrochemical and optical read-out schemes dominate, which enable the marker-free, continuous, online recording of transient effects and deliver information beyond microscopy and end-point tests. There has been much progress in microfluidics and microsensors, but the translation of both into standard cell culture procedures is still limited. Within this critical review, we discuss different cell culture formats ranging from standard culture vessels to dedicated microfluidic platforms...
April 5, 2018: Lab on a Chip
https://www.readbyqxmd.com/read/29614840/detection-of-metallothionein-in-javanese-medaka-oryzias-javanicus-using-a-scfv-immobilized-protein-chip
#11
Euiyeon Lee, Hyunjin Jeon, Chungwon Kang, Seonock Woo, Seungshic Yum, Youngeun Kwon
Environmental pollution by various industrial chemicals and biological agents poses serious risks to human health. Especially, marine contamination by potentially toxic elements (PTEs) has become a global concern in recent years. Many efforts have been undertaken to monitor the PTE contamination of the aquatic environment. However, there are few approaches available to assess the PTE exposure of aquatic organisms. In this research, we developed a strategy to evaluate the heavy metal exposure of marine organisms, by measuring the expression levels of metallothionein protein derived from Oryzias javanicus (OjaMT)...
April 2, 2018: Sensors
https://www.readbyqxmd.com/read/29610087/acoustic-characterization-of-a-vessel-on-a-chip-microfluidic-system-for-ultrasound-mediated-drug-delivery
#12
Ines Beekers, Tom van Rooij, Martin D Verweij, Michel Versluis, Nico de Jong, Sebastiaan J Trietsch, Klazina Kooiman
Ultrasound in the presence of gas-filled microbubbles can be used to enhance local uptake of drugs and genes. To study the drug delivery potential and its underlying physical and biological mechanisms, an in vitro vessel model should ideally include 3-D cell culture, perfusion flow, and membrane-free soft boundaries. Here, we propose an organ-on-a-chip microfluidic platform to study ultrasound-mediated drug delivery: the OrganoPlate. The acoustic propagation into the OrganoPlate was determined to assess the feasibility of controlled microbubble actuation, which is required to study the microbubble-cell interaction for drug delivery...
April 2018: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/29603422/3d-printing-of-bioinspired-liquid-superrepellent-structures
#13
Xiaojiang Liu, Hongcheng Gu, Min Wang, Xin Du, Bingbing Gao, Abdelrahman Elbaz, Liangdong Sun, Julong Liao, Pengfeng Xiao, Zhongze Gu
Bioinspired re-entrant structures have been proved to be effective in achieving liquid superrepellence (including anti-penetration, anti-adhesion, and anti-spreading). However, except for a few reports relying on isotropic etching of silicon wafers, most fluorination-dependent surfaces are still unable to repel liquids with extreme low surface energy (i.e., γ < 15 mN m-1 ), especially those fluorinated solvents. Herein, triply re-entrant structures, possessing superrepellence to water (with surface tension γ of 72...
March 30, 2018: Advanced Materials
https://www.readbyqxmd.com/read/29595596/accredited-health-department-partnerships-to-improve-health-an-analysis-of-community-health-assessments-and-improvement-plans
#14
Jessica Kronstadt, Chinecherem Chime, Bulbul Bhattacharya, Nicole Pettenati
CONTEXT: The Public Health Accreditation Board (PHAB) Standards & Measures require the development and updating of collaborative community health assessments (CHAs) and community health improvement plans (CHIPs). OBJECTIVE: The goal of this study was to analyze the CHAs and CHIPs of PHAB-accredited health departments to identify the types of partners engaged, as well as the objectives selected to measure progress toward improving community health. DESIGN: The study team extracted and coded data from documents from 158 CHA/CHIP processes submitted as part of the accreditation process...
May 2018: Journal of Public Health Management and Practice: JPHMP
https://www.readbyqxmd.com/read/29594114/microenvironment-cell-nucleus-relationship-in-the-context-of-oxidative-stress
#15
REVIEW
Shirisha Chittiboyina, Yunfeng Bai, Sophie A Lelièvre
The microenvironment is a source of reactive oxygen species (ROS) that influence cell phenotype and tissue homeostasis. The impact of ROS on redox pathways as well as directly on epigenetic mechanisms and the DNA illustrate communication with the cell nucleus. Changes in gene transcription related to redox conditions also influence the content and structure of the extracellular matrix. However, the importance of microenvironmental ROS for normal progression through life and disease development still needs to be thoroughly understood...
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29581424/a-comprehensive-map-coupling-histone-modifications-with-gene-regulation-in-adult-dopaminergic-and-serotonergic-neurons
#16
Erik Södersten, Konstantinos Toskas, Vilma Rraklli, Katarina Tiklova, Åsa K Björklund, Markus Ringnér, Thomas Perlmann, Johan Holmberg
The brain is composed of hundreds of different neuronal subtypes, which largely retain their identity throughout the lifespan of the organism. The mechanisms governing this stability are not fully understood, partly due to the diversity and limited size of clinically relevant neuronal populations, which constitute a technical challenge for analysis. Here, using a strategy that allows for ChIP-seq combined with RNA-seq in small neuronal populations in vivo, we present a comparative analysis of permissive and repressive histone modifications in adult midbrain dopaminergic neurons, raphe nuclei serotonergic neurons, and embryonic neural progenitors...
March 26, 2018: Nature Communications
https://www.readbyqxmd.com/read/29578568/a-facile-modular-approach-to-the-2d-oriented-assembly-mof-electrode-for-non-enzymatic-sweat-biosensors
#17
Zhengyun Wang, Mengxi Gui, Muhammad Asif, Yang Yu, Shuang Dong, Haitao Wang, Wei Wang, Feng Wang, Fei Xiao, Hongfang Liu
The preparation of ordered metal organic frameworks (MOFs) will be a critical process for MOF-based nanoelectrodes in the future. In this work, we develop a novel approach to fabricating a type of MOF electrode based on flexible amino-functionalized graphene paper modified with 2D oriented assembly of Cu3(btc)2 nanocubes via facile interfacial synthesis and an effective dip-coating method. One interesting finding is that 2D arrays of Cu3(btc)2 nanocubes at oil-water interfaces can be transferred on amino-functionalized graphene paper, leading to a densely packed monolayer of Cu3(btc)2 nanocubes with a uniform size loaded on the paper electrode...
March 26, 2018: Nanoscale
https://www.readbyqxmd.com/read/29578509/real-time-analysis-of-transcription-factor-binding-transcription-translation-and-turnover-to-display-global-events-during-cellular-activation
#18
Kathrin Davari, Johannes Lichti, Caroline C Friedel, Elke Glasmacher
Upon activation, cells rapidly change their functional programs and, thereby, their gene expression profile. Massive changes in gene expression occur, for example, during cellular differentiation, morphogenesis, and functional stimulation (such as activation of immune cells), or after exposure to drugs and other factors from the local environment. Depending on the stimulus and cell type, these changes occur rapidly and at any possible level of gene regulation. Displaying all molecular processes of a responding cell to a certain type of stimulus/drug is one of the hardest tasks in molecular biology...
March 7, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29578448/laser-bioprinting-of-human-induced-pluripotent-stem-cells-the-effect-of-printing-and-biomaterials-on-cell-survival-pluripotency-and-differentiation
#19
Lothar Koch, Andrea Deiwick, Annika Franke, Kristin Schwanke, Axel Haverich, Robert Zweigerdt, Boris N Chichkov
Research on human induced pluripotent stem cells (hiPSCs) is one of the fastest growing fields in biomedicine. Generated from patient's own somatic cells, hiPSCs can be differentiated towards all functional cell types and returned to the patient without immunological concerns. 3D printing of hiPSCs could enable generation of functional organs for replacement therapies or realization of organ-on-chip systems for individualized medicine. &#13; Printing of living cells was demonstrated with immortalized cell lines, primary cells, and adult stem cells with different printing technologies and biomaterials...
March 26, 2018: Biofabrication
https://www.readbyqxmd.com/read/29576540/human-ipsc-derived-endothelial-cells-and-microengineered-organ-chip-enhance-neuronal-development
#20
Samuel Sances, Ritchie Ho, Gad Vatine, Dylan West, Alex Laperle, Amanda Meyer, Marlesa Godoy, Paul S Kay, Berhan Mandefro, Seigo Hatata, Chris Hinojosa, Norman Wen, Dhruv Sareen, Geraldine A Hamilton, Clive N Svendsen
Human stem cell-derived models of development and neurodegenerative diseases are challenged by cellular immaturity in vitro. Microengineered organ-on-chip (or Organ-Chip) systems are designed to emulate microvolume cytoarchitecture and enable co-culture of distinct cell types. Brain microvascular endothelial cells (BMECs) share common signaling pathways with neurons early in development, but their contribution to human neuronal maturation is largely unknown. To study this interaction and influence of microculture, we derived both spinal motor neurons and BMECs from human induced pluripotent stem cells and observed increased calcium transient function and Chip-specific gene expression in Organ-Chips compared with 96-well plates...
March 21, 2018: Stem Cell Reports
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