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Tissue specific network

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https://www.readbyqxmd.com/read/28535504/long-non-coding-rna-kcnq1ot1-promotes-cataractogenesis-via-mir-214-and-activation-of-the-caspase-1-pathway
#1
Xin Jin, Hao Jin, Yan Shi, Yiyuan Guo, Hong Zhang
BACKGROUND/AIMS: KCNQ1OT1 regulates the expression of tissue-specific imprinted genes within the Kcnq1 domain. Imprinted genes are positive regulators of apoptosis, one of the forms of cell death related to cataract formation, and thus may provide novel therapeutic targets for cataract treatment. Here, we studied the role of non-coding RNAs(ncRNA) in cataract formation. METHODS: Human lens epithelium cells (HLECs) were treated with H2O2, and the expression of KCNQ1OT1 and miR-214 was detected by qRT-PCR...
May 25, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28535188/molecular-heterogeneity-at-the-network-level-high-dimensional-testing-clustering-and-a-tcga-case-study
#2
Nicolas Städler, Frank Dondelinger, Steven M Hill, Rehan Akbani, Yiling Lu, Gordon B Mills, Sach Mukherjee
Motivation: Molecular pathways and networks play a key role in basic and disease biology. An emerging notion is that networks encoding patterns of molecular interplay may themselves differ between contexts, such as cell type, tissue or disease (sub)type. However, while statistical testing of differences in mean expression levels has been extensively studied, testing of network differences remains challenging. Furthermore, since network differences could provide important and biologically interpretable information to identify molecular subgroups, there is a need to consider the unsupervised task of learning subgroups and networks that define them...
May 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28529082/rice-expression-database-red-an-integrated-rna-seq-derived-gene-expression-database-for-rice
#3
Lin Xia, Dong Zou, Jian Sang, Xingjian Xu, Hongyan Yin, Mengwei Li, Shuangyang Wu, Songnian Hu, Lili Hao, Zhang Zhang
Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community. Here, we present RED (Rice Expression Database; http://expression.ic4r.org), an integrated database of rice gene expression profiles derived entirely from RNA-Seq data. RED features a comprehensive collection of 284 high-quality RNA-Seq experiments, integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments. Based on massive expression profiles, RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene(s) of interest...
May 4, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28527696/essential-roles-of-g9a-in-cell-proliferation-and-differentiation-during-tooth-development
#4
Taichi Kamiunten, Hisashi Ideno, Akemi Shimada, Yoshinori Arai, Tatsuo Terashima, Yasuhiro Tomooka, Yoshiki Nakamura, Kazuhisa Nakashima, Hiroshi Kimura, Yoichi Shinkai, Makoto Tachibana, Akira Nifuji
Teeth develop through interactions between epithelial and mesenchymal tissues mediated by a signaling network comprised of growth factors and transcription factors However, little is known about how epigenetic modifiers affect signaling pathways and thereby regulate tooth formation. We previously reported that the histone 3 lysine 9 (H3K9) methyltransferase (MTase) G9a is specifically enriched in the tooth mesenchyme during mouse development. In this study, we investigated the functions of G9a in tooth development using G9a conditional knockout (KO) mice...
May 17, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28526583/the-connexin-43-c-terminus-a-tail-of-many-tales
#5
REVIEW
Edward Leithe, Marc Mesnil, Trond Aasen
Connexins are chordate gap junction channel proteins that, by enabling direct communication between the cytosols of adjacent cells, create a unique cell signalling network. Gap junctional intercellular communication (GJIC) has important roles in controlling cell growth and differentiation and in tissue development and homeostasis. Moreover, several non-canonical connexin functions unrelated to GJIC have been discovered. Of the 21 members of the human connexin family, connexin 43 (Cx43) is the most widely expressed and studied...
May 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28525313/a-tunable-three-dimensional-in-vitro-culture-model-of-growth-plate-cartilage-using-alginate-hydrogel-scaffolds
#6
Alek G Erickson, Taylor D Laughlin, Sarah M Romereim, Catherine N Sargus-Patino, Angela K Pannier, Andrew T Dudley
Defining the final size and geometry of engineered tissues through precise control of the scalar and vector components of tissue growth is a necessary benchmark for regenerative medicine, but it has proved to be a significant challenge for tissue engineers. The growth plate cartilage that promotes elongation of the long bones is a good model system for studying morphogenetic mechanisms because cartilage is composed of a single cell type, the chondrocyte; chondrocytes are readily maintained in culture; and growth trajectory is predominately in a single vector...
May 18, 2017: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/28525280/self-healing-self-assembled-%C3%AE-sheet-peptide-poly-%C3%AE-glutamic-acid-hybrid-hydrogels
#7
David E Clarke, E Thomas Pashuck, Sergio Bertazzo, Jonathan V M Weaver, Molly M Stevens
Self-assembled biomaterials are an important class of materials that can be injected and formed in situ. However, they often are not able to meet the mechanical properties necessary for many biological applications, losing mechanical properties at low strains. We synthesized hybrid hydrogels consisting of a poly(γ-glutamic acid) polymer network physically cross-linked via grafted self-assembling β-sheet peptides to provide non-covalent cross-linking through β-sheet assembly, reinforced with a polymer backbone to improve strain stability...
May 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28520732/differential-gene-expression-along-the-animal-vegetal-axis-in-the-ascidian-embryo-is-maintained-by-a-dual-functional-protein-foxd
#8
Shin-Ichi Tokuhiro, Miki Tokuoka, Kenji Kobayashi, Atsushi Kubo, Izumi Oda-Ishii, Yutaka Satou
In many animal embryos, a specific gene expression pattern is established along the animal-vegetal axis soon after zygotic transcription begins. In the embryo of the ascidian Ciona intestinalis, soon after the division that separates animal and vegetal hemispheres into distinct blastomeres, maternal Gata.a and β-catenin activate specific genes in the animal and vegetal blastomeres, respectively. On the basis of these initial distinct gene expression patterns, gene regulatory networks promote animal cells to become ectodermal tissues and vegetal cells to become endomesodermal tissues and a part of the nerve cord...
May 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28512793/5-azacytidine-mediated-hmsc-behaviour-on-electrospun-scaffolds-for-skeletal-muscle-regeneration
#9
Ines Fasolino, Vincenzo Guarino, Valentina Cirillo, Luigi Ambrosio
Incomplete regeneration after trauma or muscular dysfunction is a common problem in muscle replacement therapies. Recent approaches in tissue engineering allow for the replication of skeletal muscle structure and function in vitro and in vivo by molecular therapies and implantable scaffolds which properly address muscle cells towards myotube differentiation and maturation. Here, we investigate the in vitro response of human Mesenchymal Stem Cells (hMSC) on electrospun fibres made of Polycaprolactone (PCL) in the presence of 5-azacytidine (5-AZA) to evaluate how fibrous network may influence the therapeutic effect of drug during in vitro myogenesis...
May 16, 2017: Journal of Biomedical Materials Research. Part A
https://www.readbyqxmd.com/read/28512021/statin-use-after-diagnosis-of-colon-cancer-and-patient-survival
#10
Philip W Voorneveld, Marlies S Reimers, Esther Bastiaannet, Rutger J Jacobs, Ronald van Eijk, Marjolein M J Zanders, Ron M C Herings, Myrthe P P van Herk-Sukel, Liudmila L Kodach, Tom van Wezel, Peter J K Kuppen, Hans Morreau, Cornelis J H van de Velde, James C H Hardwick, Gerrit Jan Liefers
BACKGROUND & AIMS: Statin use has been associated with a reduced incidence of colorectal cancer, and might also affect survival of patients diagnosed with colon cancer. Statins are believed to inhibit Ras signaling, and also activate the bone morphogenetic protein (BMP) signaling pathway in colorectal cancer cells. We investigated the effects of statins on overall survival of patients with a diagnosis of colon cancer, and whether their effects were associated with changes in KRAS or the BMP signaling pathways...
May 13, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28511181/1-cmdb-a-curated-database-of-genomic-variations-of-the-one-carbon-metabolism-pathway
#11
Manoj K Bhat, Veerendra P Gadekar, Aditya Jain, Bobby Paul, Padmalatha S Rai, Kapaettu Satyamoorthy
BACKGROUND: The one-carbon metabolism pathway is vital in maintaining tissue homeostasis by driving the critical reactions of folate and methionine cycles. A myriad of genetic and epigenetic events mark the rate of reactions in a tissue-specific manner. Integration of these to predict and provide personalized health management requires robust computational tools that can process multiomics data. The DNA sequences that may determine the chain of biological events and the endpoint reactions within one-carbon metabolism genes remain to be comprehensively recorded...
May 17, 2017: Public Health Genomics
https://www.readbyqxmd.com/read/28508297/adaptation-to-stochastic-temporal-variations-in-intratumoral-blood-flow-the-warburg-effect-as-a-bet-hedging-strategy
#12
Curtis A Gravenmier, Miriam Siddique, Robert A Gatenby
While most cancers promote ingrowth of host blood vessels, the resulting vascular network usually fails to develop a mature organization, resulting in abnormal vascular dynamics with stochastic variations that include slowing, cessation, and even reversal of flow. Thus, substantial spatial and temporal variations in oxygen concentration are commonly observed in most cancers. Cancer cells, like all living systems, are subject to Darwinian dynamics such that their survival and proliferation are dependent on developing optimal phenotypic adaptations to local environmental conditions...
May 15, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28507987/pitx2-in-embryonic-and-adult-myogenesis
#13
REVIEW
Francisco Hernandez-Torres, Lara Rodríguez-Outeiriño, Diego Franco, Amelia E Aranega
Skeletal muscle is a heterogeneous tissue that represents between 30 and 38% of the human body mass and has important functions in the organism, such as maintaining posture, locomotor impulse, or pulmonary ventilation. The genesis of skeletal muscle during embryonic development is a process controlled by an elaborate regulatory network combining the interplay of extrinsic and intrinsic regulatory mechanisms that transform myogenic precursor cells into functional muscle fibers through a finely tuned differentiation program...
2017: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/28507022/loss-of-e-cadherin-dependent-cell-cell-adhesion-and-the-development-and-progression-of-cancer
#14
Heather C Bruner, Patrick W B Derksen
Classical cadherins are the key molecules that control cell-cell adhesion. Notwithstanding this function, it is also clear that classical cadherins are more than just the "glue" that keeps the cells together. Cadherins are essential regulators of tissue homeostasis that govern multiple facets of cellular function and development, by transducing adhesive signals to a complex network of signaling effectors and transcriptional programs. In cancer, cadherins are often inactivated or functionally inhibited, resulting in disease development and/or progression...
May 15, 2017: Cold Spring Harbor Perspectives in Biology
https://www.readbyqxmd.com/read/28505478/dose-assessment-in-environmental-radiological-protection-state-of-the-art-and-perspectives
#15
REVIEW
Karolina Stark, José M Goméz-Ros, Jordi Vives I Batlle, Elisabeth Lindbo Hansen, Karine Beaugelin-Seiller, Lawrence A Kapustka, Michael D Wood, Clare Bradshaw, Almudena Real, Corynne McGuire, Thomas G Hinton
Exposure to radiation is a potential hazard to humans and the environment. The Fukushima accident reminded the world of the importance of a reliable risk management system that incorporates the dose received from radiation exposures. The dose to humans from exposure to radiation can be quantified using a well-defined system; its environmental equivalent, however, is still in a developmental state. Additionally, the results of several papers published over the last decade have been criticized because of poor dosimetry...
May 12, 2017: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/28504698/dendritic-cells-enter-lymph-vessels-by-hyaluronan-mediated-docking-to-the-endothelial-receptor-lyve-1
#16
Louise A Johnson, Suneale Banerji, William Lawrance, Uzi Gileadi, Gennaro Prota, Kayla A Holder, Yaowaluck M Roshorm, Tomáš Hanke, Vincenzo Cerundolo, Nicholas W Gale, David G Jackson
Trafficking of tissue dendritic cells (DCs) via lymph is critical for the generation of cellular immune responses in draining lymph nodes (LNs). In the current study we found that DCs docked to the basolateral surface of lymphatic vessels and transited to the lumen through hyaluronan-mediated interactions with the lymph-specific endothelial receptor LYVE-1, in dynamic transmigratory-cup-like structures. Furthermore, we show that targeted deletion of the gene Lyve1, antibody blockade or depletion of the DC hyaluronan coat not only delayed lymphatic trafficking of dermal DCs but also blunted their capacity to prime CD8(+) T cell responses in skin-draining LNs...
May 15, 2017: Nature Immunology
https://www.readbyqxmd.com/read/28503705/mri-in-neutral-lipid-storage-disease-nlsd
#17
Matteo Garibaldi, Giorgio Tasca, Jordi Diaz-Manera, Pierfancesco Ottaviani, Francesco Laschena, Donatella Pantoli, Simonetta Gerevini, Chiara Fiorillo, Lorenzo Maggi, Elisabetta Tasca, Adele D'Amico, Olimpia Musumeci, Antonio Toscano, Claudio Bruno, Roberto Massa, Corrado Angelini, Enrico Bertini, Giovanni Antonini, Elena Maria Pennisi
Neutral lipid storage disease (NLSD) is a rare inherited disorder of lipid metabolism resulting in lipid droplets accumulation in different tissues. Skeletal muscle could be affected in both two different form of disease: NLSD with myopathy (NLSD-M) and NLSD with ichthyosis (NLSD-I). We present the muscle imaging data of 12 patients from the Italian Network for NLSD: ten patients presenting NLSD-M and two patients with NLSD-I. In NLSD-M gluteus minimus, semimembranosus, soleus and gastrocnemius medialis in the lower limbs and infraspinatus in the upper limbs were the most affected muscles...
May 13, 2017: Journal of Neurology
https://www.readbyqxmd.com/read/28501625/circular-rnas-roll-into-the-regulatory-network-of-plants
#18
Quan-Feng Li, Yu-Chan Zhang, Yue-Qin Chen, Yang Yu
As a novel class of endogenous non-coding RNAs, circular RNAs (circRNAs) have become a new research hotspot in recent years. The wide distribution of circRNAs in different plant species has been proven. Furthermore, circRNAs show significant tissue-specific expression patterns in plant development and are responsive to a variety of biotic and abiotic stresses, indicating that circRNAs might have important biological functions in plant development. Here, we summarize the current knowledge of plant circRNAs in recent years and discuss views and perspectives on the possible regulatory roles of plant circRNAs, including the function of miRNA sponges, regulating the expression of their parental genes or linear mRNAs, translating into peptides or proteins and responses to different stresses...
May 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28501478/osr1-functions-downstream-of-hedgehog-pathway-to-regulate-foregut-development
#19
Lu Han, Jingyue Xu, Emily Grigg, Megan Slack, Praneet Chaturvedi, Rulang Jiang, Aaron M Zorn
During early fetal development, paracrine Hedgehog (HH) ligands secreted from the foregut epithelium activate Gli transcription factors in the surrounding mesenchyme to coordinate formation of the respiratory system, digestive track and the cardiovascular network. Although disruptions to this process can lead to devastating congenital defects, the underlying mechanisms and downstream targets, are poorly understood. We show that the zinc finger transcription factor Osr1 is a novel HH target as Osr1 expression in the foregut mesenchyme depends on HH signaling and the effector of HH pathway Gli3 binds to a conserved genomic loci near Osr1 promoter region...
May 10, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28499866/identification-and-characterization-of-novel-lncrnas-in-arabidopsis-thaliana
#20
Zhaogeng Lu, Xiao Xia, Bei Jiang, Kaibiao Ma, Likui Zhu, Li Wang, Biao Jin
Long noncoding RNAs (lncRNAs) are important regulators of various biological processes, but few studies have identified lncRNAs in plants; genome-wide discovery of novel lncRNAs is thus required. We used deep strand-specific sequencing (ssRNA-seq) to obtain approximately 62 million reads from all developmental stages of Arabidopsis thaliana and identified 156 novel lncRNAs that we classified according to their localization. These novel identified lncRNAs showed low expression levels and sequence conservation...
May 9, 2017: Biochemical and Biophysical Research Communications
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