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Fibroblast topology

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https://www.readbyqxmd.com/read/29662163/polymer-physics-predicts-the-effects-of-structural-variants-on-chromatin-architecture
#1
Simona Bianco, Darío G Lupiáñez, Andrea M Chiariello, Carlo Annunziatella, Katerina Kraft, Robert Schöpflin, Lars Wittler, Guillaume Andrey, Martin Vingron, Ana Pombo, Stefan Mundlos, Mario Nicodemi
Structural variants (SVs) can result in changes in gene expression due to abnormal chromatin folding and cause disease. However, the prediction of such effects remains a challenge. Here we present a polymer-physics-based approach (PRISMR) to model 3D chromatin folding and to predict enhancer-promoter contacts. PRISMR predicts higher-order chromatin structure from genome-wide chromosome conformation capture (Hi-C) data. Using the EPHA4 locus as a model, the effects of pathogenic SVs are predicted in silico and compared to Hi-C data generated from mouse limb buds and patient-derived fibroblasts...
April 16, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29550426/deciphering-synergistic-regulatory-networks-of-micrornas-in-hescs-and-fibroblasts
#2
Mousumi Sahu, Bibekanand Mallick
MicroRNAs (miRNAs) play crucial roles in pluripotency and differentiation of human Embryonic Stem Cells (hESCs). However, synergism among multiple miRNAs and their regulatory effects on stem cells are largely unknown. We investigated the synergistic regulations among miRNAs, which are differentially expressed in hESCs and fibroblasts (Fibs) to gain deeper insights into the regulatory mechanisms of miRNA-miRNA synergism in differentiation of hESCs into Fibs. In this study, we identified miRNA targets incorporating differential expression profiles of miRNAs and genes in hESCs-Fibs as well as miRNA targeting information followed by enrichment analysis...
March 14, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29511118/inflammatory-but-not-mitogenic-contexts-prime-synovial-fibroblasts-for-compensatory-signaling-responses-to-p38-inhibition
#3
Douglas S Jones, Anne P Jenney, Brian A Joughin, Peter K Sorger, Douglas A Lauffenburger
Rheumatoid arthritis (RA) is a chronic inflammatory disorder that causes joint pain, swelling, and loss of function. Development of effective new drugs has proven challenging in part because of the complexities and interconnected nature of intracellular signaling networks that complicate the effects of pharmacological interventions. We characterized the kinase signaling pathways that are activated in RA and evaluated the multivariate effects of targeted inhibitors. Synovial fluids from RA patients activated the kinase signaling pathways JAK, JNK, p38, and MEK in synovial fibroblasts (SFs), a stromal cell type that promotes RA progression...
March 6, 2018: Science Signaling
https://www.readbyqxmd.com/read/29398113/circuit-design-features-of-a-stable-two-cell-system
#4
Xu Zhou, Ruth A Franklin, Miri Adler, Jeremy B Jacox, Will Bailis, Justin A Shyer, Richard A Flavell, Avi Mayo, Uri Alon, Ruslan Medzhitov
Cell communication within tissues is mediated by multiple paracrine signals including growth factors, which control cell survival and proliferation. Cells and the growth factors they produce and receive constitute a circuit with specific properties that ensure homeostasis. Here, we used computational and experimental approaches to characterize the features of cell circuits based on growth factor exchange between macrophages and fibroblasts, two cell types found in most mammalian tissues. We found that the macrophage-fibroblast cell circuit is stable and robust to perturbations...
January 30, 2018: Cell
https://www.readbyqxmd.com/read/29289958/regulatory-variants-of-foxg1-in-the-context-of-its-topological-domain-organisation
#5
Mana M Mehrjouy, Ana Carolina S Fonseca, Nadja Ehmke, Giorgio Paskulin, Antonio Novelli, Francesco Benedicenti, Maria Antonietta Mencarelli, Alessandra Renieri, Tiffany Busa, Chantal Missirian, Claus Hansen, Kikue Terada Abe, Carlos Eduardo Speck-Martins, Angela M Vianna-Morgante, Mads Bak, Niels Tommerup
FOXG1 syndrome is caused by FOXG1 intragenic point mutations, or by long-range position effects (LRPE) of intergenic structural variants. However, the size of the FOXG1 regulatory landscape is uncertain, because the associated topologically associating domain (TAD) in fibroblasts is split into two domains in embryonic stem cells (hESC). Indeed, it has been suggested that the pathogenetic mechanism of deletions that remove the stem-cell-specific TAD boundary may be enhancer adoption due to ectopic activity of enhancer(s) located in the distal hESC-TAD...
February 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29123635/er-yag-laser-and-cyclosporin-a-effect-on-cell-cycle-regulation-of-human-gingival-fibroblast-cells
#6
Hojjat-Allah Abbaszadeh, Ali Asghar Peyvandi, Yousef Sadeghi, Akram Safaei, Mona Zamanian-Azodi, Maryam Sadat Khoramgah, Mostafa Rezaei-Tavirani
Introduction: Periodontitis is a set of inflammatory disorders characterized by periodontal attachment loss and alveolar bone resorption. Because of deficiency in periodontitis mechanical therapy, this study was aimed to explore the molecular influence of the erbiumdoped: yttrium aluminum garnet (Er:YAG) laser and cyclosporin A (CsA) on human gingival fibroblasts (HGFs) for improvement in periodontal diseases therapy. Methods: We focused on articles that studied the proteome profiles of HGFs after treatment with laser irradiation and application of CsA...
2017: Journal of Lasers in Medical Sciences
https://www.readbyqxmd.com/read/29078370/algorithm-for-cellular-reprogramming
#7
Scott Ronquist, Geoff Patterson, Lindsey A Muir, Stephen Lindsly, Haiming Chen, Markus Brown, Max S Wicha, Anthony Bloch, Roger Brockett, Indika Rajapakse
The day we understand the time evolution of subcellular events at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our understanding of cell biology. With data-guided frameworks we can develop better predictions about, and methods for, control over specific biological processes and system-wide cell behavior. Here we describe an approach for optimizing the use of transcription factors (TFs) in cellular reprogramming, based on a device commonly used in optimal control...
November 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29070488/effects-of-parameters-plasmid-dosages-and-topological-structures-on-transfection-efficiency-of-porcine-fetal-fibroblasts-using-different-electroporators
#8
Cui-Li Zhong, Guo-Ling Li, Jian-Xin Mo, Rong Quan, Hao-Qiang Wang, Zi-Cong Li, Zhen-Fang Wu, Xian-Wei Zhang
To obtain an ideal transfection efficiency of porcine fetal fibroblasts, fluorescence activated cell sorting (FACS) was used to optimize parameters for transfection of porcine fetal fibroblasts (PFFs) with ECM? 830, NEPA 21 and Nucleofector? 2b in different conditions such as electroporation parameters, plasmid dosages and topological structures. The results show that the optimum poring pulse parameter of NEPA 21 is voltage 200 V, continuous 3 ms, interval 50 ms, 3 times, voltage attenuation range of 10%; and the transfection efficiency of Nucleofector? 2b is highest under U-023 program...
October 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28884679/the-integration-of-a-macrophage-adapted-live-vaccine-strain-of-equine-infectious-anaemia-virus-eiav-in-the-horse-genome
#9
Qiang Liu, Xue-Feng Wang, Cheng Du, Yue-Zhi Lin, Jian Ma, Yu-Hong Wang, Jian-Hua Zhou, Xiaojun Wang
Integration is an important feature of retroviruses and retrovirus-based therapeutic transfection vectors. The non-primate lentivirus equine infectious anaemia virus (EIAV) primarily targets macrophages/monocytes in vivo. Investigation of the integration features of EIAVDLV121 strains, which are adapted to donkey monocyte-derived macrophages (MDMs), is of great interest. In this study, we analysed the integration features of EIAVDLV121 in equine MDMs during in vitro infection. Our previously published integration sites (IS) for EIAVFDDV13 in fetal equine dermal (FED) cells were also analysed in parallel as references...
September 7, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28792773/easy-to-apply-polyoxazoline-based-coating-for-precise-and-long-term-control-of-neural-patterns
#10
Serge Weydert, Stefan Zürcher, Stefanie Tanner, Ning Zhang, Rebecca Ritter, Thomas Peter, Mathias J Aebersold, Greta Thompson-Steckel, Csaba Forró, Markus Rottmar, Flurin Stauffer, Irene A Valassina, Giulia Morgese, Edmondo M Benetti, Samuele Tosatti, János Vörös
Arranging cultured cells in patterns via surface modification is a tool used by biologists to answer questions in a specific and controlled manner. In the past decade, bottom-up neuroscience emerged as a new application, which aims to get a better understanding of the brain via reverse engineering and analyzing elementary circuitry in vitro. Building well-defined neural networks is the ultimate goal. Antifouling coatings are often used to control neurite outgrowth. Because erroneous connectivity alters the entire topology and functionality of minicircuits, the requirements are demanding...
August 9, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28644625/chemically-modified-surface-having-a-dual-structured-hierarchical-topography-for-controlled-cell-growth
#11
Lun Peng, Shenglin Zhou, Bo Yang, Meimei Bao, Gaojian Chen, Xiaohua Zhang
This report describes a technique for fabricating dual-structured hierarchical surface topography on the surface of polydimethylsiloxane (PDMS) films through simply replicating prefabricated patterns and wrinkling PDMS films. To enhance the biocompatibility of PDMS films, we synthesize a biocompatible dopamine-glycopolymer, which is utilized to modify the chemical feature of the PDMS surface. Dopamine component in this copolymer is introduced for the formation of a carbohydrate layer on the surface of PDMS films because of its excellent adhesion...
July 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28424523/cohesin-is-positioned-in-mammalian-genomes-by-transcription-ctcf-and-wapl
#12
Georg A Busslinger, Roman R Stocsits, Petra van der Lelij, Elin Axelsson, Antonio Tedeschi, Niels Galjart, Jan-Michael Peters
Mammalian genomes are spatially organized by CCCTC-binding factor (CTCF) and cohesin into chromatin loops and topologically associated domains, which have important roles in gene regulation and recombination. By binding to specific sequences, CTCF defines contact points for cohesin-mediated long-range chromosomal cis-interactions. Cohesin is also present at these sites, but has been proposed to be loaded onto DNA elsewhere and to extrude chromatin loops until it encounters CTCF bound to DNA. How cohesin is recruited to CTCF sites, according to this or other models, is unknown...
April 27, 2017: Nature
https://www.readbyqxmd.com/read/28371268/aging-of-the-skeletal-muscle-extracellular-matrix-drives-a-stem-cell-fibrogenic-conversion
#13
Kristen M Stearns-Reider, Antonio D'Amore, Kevin Beezhold, Benjamin Rothrauff, Loredana Cavalli, William R Wagner, David A Vorp, Alkiviadis Tsamis, Sunita Shinde, Changqing Zhang, Aaron Barchowsky, Thomas A Rando, Rocky S Tuan, Fabrisia Ambrosio
Age-related declines in skeletal muscle regeneration have been attributed to muscle stem cell (MuSC) dysfunction. Aged MuSCs display a fibrogenic conversion, leading to fibrosis and impaired recovery after injury. Although studies have demonstrated the influence of in vitro substrate characteristics on stem cell fate, whether and how aging of the extracellular matrix (ECM) affects stem cell behavior has not been investigated. Here, we investigated the direct effect of the aged muscle ECM on MuSC lineage specification...
June 2017: Aging Cell
https://www.readbyqxmd.com/read/28349474/graph-theory-based-analysis-of-the-lymph-node-fibroblastic-reticular-cell-network
#14
Mario Novkovic, Lucas Onder, Gennady Bocharov, Burkhard Ludewig
Secondary lymphoid organs have developed segregated niches that are able to initiate and maintain effective immune responses. Such global organization requires tight control of diverse cellular components, specifically those that regulate lymphocyte trafficking. Fibroblastic reticular cells (FRCs) form a densely interconnected network in lymph nodes and provide key factors necessary for T cell migration and retention, and foster subsequent interactions between T cells and dendritic cells. Development of integrative systems biology approaches has made it possible to elucidate this multilevel complexity of the immune system...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28340537/study-on-a-3d-hydrogel-based-culture-model-for-characterizing-growth-of-fibroblasts-under-viral-infection-and-drug-treatment
#15
Xiaolu Zhu, Xianting Ding
Three-dimensional (3D) in vitro tissue models provide an approach for the systematic, repetitive, and quantitative study of drugs. In this study, we constructed an in vitro 3D acrylated hyaluronic acid (AHA) hydrogel model encapsulating fibroblasts, performed long-period 3D culture, and tested cellular topological changes and proliferation variation in the presence of herpes simplex virus-1 (HSV-1) as an infecting virus and acyclovir (ACV) as the treatment drug. The AHA hydrogels were formed by using Michael addition chemistry of bis-cysteine containing MMP-degradable cross-linker onto AHA prefunctionalized with cell adhesion peptides (RGD)...
June 2017: SLAS Discovery
https://www.readbyqxmd.com/read/28331312/investigation-of-silk-fibroin-nanoparticle-decorated-poly-l-lactic-acid-composite-scaffolds-for-osteoblast-growth-and-differentiation
#16
Biao-Qi Chen, Ranjith Kumar Kankala, Ai-Zheng Chen, Ding-Zhu Yang, Xiao-Xia Cheng, Ni-Na Jiang, Kai Zhu, Shi-Bin Wang
Attempts to reflect the physiology of organs is quite an intricacy during the tissue engineering process. An ideal scaffold and its surface topography can address and manipulate the cell behavior during the regeneration of targeted tissue, affecting the cell growth and differentiation significantly. Herein, silk fibroin (SF) nanoparticles were incorporated into poly(l-lactic acid) (PLLA) to prepare composite scaffolds via phase-inversion technique using supercritical carbon dioxide (SC-CO2). The SF nanoparticle core increased the surface roughness and hydrophilicity of the PLLA scaffolds, leading to a high affinity for albumin attachment...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/28068057/topological-control-of-extracellular-matrix-growth-a-native-like-model-for-cell-morphodynamics-studies
#17
David Caballero, Josep Samitier
The interaction of cells with their natural environment influences a large variety of cellular phenomena, including cell adhesion, proliferation, and migration. The complex extracellular matrix network has challenged the attempts to replicate in vitro the heterogeneity of the cell environment and has threatened, in general, the relevance of in vitro studies. In this work, we describe a new and extremely versatile approach to generate native-like extracellular matrices with controlled morphologies for the in vitro study of cellular processes...
February 1, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/27995750/keloid-progression-a-stiffness-gap-hypothesis
#18
Chenyu Huang, Longwei Liu, Zhifeng You, Bingjie Wang, Yanan Du, Rei Ogawa
Keloids are fibroproliferative skin disorders characterised clinically by continuous horizontal progression and post-surgical recurrence and histologically by the accumulation of collagen and fibroblast ingredients. Till now, their aetiology remains clear, which may cover genetic, environmental and metabolic factors. Evidence in the involvement of local mechanics (e.g. predilection site and typical shape) and the progress in mechanobiology have incubated our stiffness gap hypotheses in illustrating the chronic but constant development in keloid...
December 19, 2016: International Wound Journal
https://www.readbyqxmd.com/read/27917883/comparison-of-cell-behavior-on-pva-pva-gelatin-electrospun-nanofibers-with-random-and-aligned-configuration
#19
Chen-Yu Huang, Keng-Hsiang Hu, Zung-Hang Wei
Electrospinning technique is able to create nanofibers with specific orientation. Poly(vinyl alcohol) (PVA) have good mechanical stability but poor cell adhesion property due to the low affinity of protein. In this paper, extracellular matrix, gelatin is incorporated into PVA solution to form electrospun PVA-gelatin nanofibers membrane. Both randomly oriented and aligned nanofibers are used to investigate the topography-induced behavior of fibroblasts. Surface morphology of the fibers is studied by optical microscopy and scanning electron microscopy (SEM) coupled with image analysis...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27579918/meta-analysis-of-transcriptome-regulation-during-induction-to-cardiac-myocyte-fate-from-mouse-and-human-fibroblasts
#20
Shima Rastegar-Pouyani, Niusha Khazaei, Ping Wee, Moein Yaqubi, Abdulshakour Mohammadnia
Ectopic expression of a defined set of transcription factors (TFs) can directly convert fibroblasts into a cardiac myocyte cell fate. Beside inefficiency in generating induced cardiomyocytes (iCMs), the molecular mechanisms that regulate this process remained to be well defined. The main purpose of this study was to provide better insight on the transcriptome regulation and to introduce a new strategy for candidating TFs for the transdifferentiation process. Eight mouse and three human high quality microarray data sets were analyzed to find differentially expressed genes (DEGs), which we integrated with TF-binding sites and protein-protein interactions to construct gene regulatory and protein-protein interaction networks...
August 2017: Journal of Cellular Physiology
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