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Tissue-specific network

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https://www.readbyqxmd.com/read/28106823/integrated-microrna-mrna-profiling-identifies-oncostatin-m-as-a-marker-of-mesenchymal-like-er-negative-her2-negative-breast-cancer
#1
Giulia Bottai, Lixia Diao, Keith A Baggerly, Laura Paladini, Balázs Győrffy, Carlotta Raschioni, Lajos Pusztai, George A Calin, Libero Santarpia
MicroRNAs (miRNAs) simultaneously modulate different oncogenic networks, establishing a dynamic system of gene expression and pathway regulation. In this study, we analyzed global miRNA and messenger RNA (mRNA) expression profiles of 17 cell lines representing different molecular breast cancer subtypes. Spearman's rank correlation test was used to evaluate the correlation between miRNA and mRNA expression. Hierarchical clustering and pathway analysis were also performed. Publicly available gene expression profiles (n = 699) and tumor tissues (n = 80) were analyzed to assess the relevance of key miRNA-regulated pathways in human breast cancer...
January 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28105929/a-compendium-of-human-genes-regulating-feeding-behavior-and-body-weight-its-functional-characterization-and-identification-of-gwas-genes-involved-in-brain-specific-ppi-network
#2
Elena V Ignatieva, Dmitry A Afonnikov, Olga V Saik, Evgeny I Rogaev, Nikolay A Kolchanov
BACKGROUND: Obesity is heritable. It predisposes to many diseases. The objectives of this study were to create a compendium of genes relevant to feeding behavior (FB) and/or body weight (BW) regulation; to construct and to analyze networks formed by associations between genes/proteins; and to identify the most significant genes, biological processes/pathways, and tissues/organs involved in BW regulation. RESULTS: The compendium of genes controlling FB or BW includes 578 human genes...
December 22, 2016: BMC Genetics
https://www.readbyqxmd.com/read/28101869/fibrin-formation-structure-and-properties
#3
John W Weisel, Rustem I Litvinov
Fibrinogen and fibrin are essential for hemostasis and are major factors in thrombosis, wound healing, and several other biological functions and pathological conditions. The X-ray crystallographic structure of major parts of fibrin(ogen), together with computational reconstructions of missing portions and numerous biochemical and biophysical studies, have provided a wealth of data to interpret molecular mechanisms of fibrin formation, its organization, and properties. On cleavage of fibrinopeptides by thrombin, fibrinogen is converted to fibrin monomers, which interact via knobs exposed by fibrinopeptide removal in the central region, with holes always exposed at the ends of the molecules...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28101863/lessons-from-animal-models-of-cytoplasmic-intermediate-filament-proteins
#4
Jamal-Eddine Bouameur, Thomas M Magin
Cytoplasmic intermediate filaments (IFs) represent a major cytoskeletal network contributing to cell shape, adhesion and migration as well as to tissue resilience and renewal in numerous bilaterians, including mammals. The observation that IFs are dispensable in cultured mammalian cells, but cause tissue-specific, life-threatening disorders, has pushed the need to investigate their function in vivo. In keeping with human disease, the deletion or mutation of murine IF genes resulted in highly specific pathologies...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28100648/multi-scale-structural-analysis-of-plant-er-pm-contact-sites
#5
Heather E McFarlane, Eun Kyoung Lee, Laura S van Bezouwen, Bradford Ross, Abel Rosado, A Lacey Samuels
Membrane contact sites (MCS) are recognized across eukaryotic systems as important nanostructures. Endoplasmic reticulum (ER)-plasma membrane (PM) contact sites (EPCS) are involved in excitation-contraction coupling, signalling, and plant responses to stress. In this report, we perform a multi-scale structural analysis of Arabidopsis EPCS that combine live cell imaging, quantitative transmission electron microscopy (TEM), and electron tomography over a developmental gradient. To place EPCS in the context of the entire cortical ER, we examined GFP-HDEL in living cells over a developmental gradient, then SYT1-GFP was used as a specific marker of EPCS...
January 18, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28092502/capacity-evaluation-of-a-quantum-based-channel-in-a-biological-context
#6
Valeria Loscri, Anna Maria Vegni
Nanotechnology, as enabler of the miniaturization of devices in a scale ranging from 1 to few hundreds of nm , represents a viable solution for " alternative" communication paradigms that could be effective in complex networked systems, as body area networks. Traditional communication paradigms are not effective in the context of joint body and nano-networked systems, for several reasons, and then novel approaches have been investigated such as nanomechanical, electromagnetic, acoustic, molecular, etc. On the other hand, quantum phenomena represent a natural direction for developing nanotechnology, since it has to be considered as a new scale where new phenomena can occur and can be exploited for information purpose...
December 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28090603/spatial-clockwork-recurrent-neural-network-for-muscle-perimysium-segmentation
#7
Yuanpu Xie, Zizhao Zhang, Manish Sapkota, Lin Yang
Accurate segmentation of perimysium plays an important role in early diagnosis of many muscle diseases because many diseases contain different perimysium inflammation. However, it remains as a challenging task due to the complex appearance of the perymisum morphology and its ambiguity to the background area. The muscle perimysium also exhibits strong structure spanned in the entire tissue, which makes it difficult for current local patch-based methods to capture this long-range context information. In this paper, we propose a novel spatial clockwork recurrent neural network (spatial CW-RNN) to address those issues...
October 2016: Medical Image Computing and Computer-assisted Intervention: MICCAI ..
https://www.readbyqxmd.com/read/28089250/pathology-of-behavior-in-pd-what-is-known-and-what-is-not
#8
REVIEW
Kaylena A Ehgoetz Martens, Simon J G Lewis
Abnormal behavior in Parkinson's disease (PD) stems from a complex orchestration of impaired neural networks that result from PD-related neurodegeneration across multiple levels. Typically, cellular and tissue abnormalities generate neurochemical changes and disrupt specific regions of the brain, in turn creating impaired neural circuits and dysfunctional global networks. The objective of this chapter is to provide an overview of the array of pathological changes that have been linked to different behavioral symptoms of PD such as depression, anxiety, apathy, fatigue, impulse control disorders, psychosis, sleep disorders and dementia...
December 29, 2016: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28088579/the-microrna-449-family-inhibits-tgf-%C3%AE-mediated-liver-cancer-cell-migration-by-targeting-sox4
#9
Maria Sandbothe, Reena Buurman, Nicole Reich, Luisa Greiwe, Beate Vajen, Engin Gürlevik, Vera Schäffer, Marlies Eilers, Florian Kühnel, Alejandro Vaquero, Thomas Longerich, Stephanie Roessler, Peter Schirmacher, Michael P Manns, Thomas Illig, Brigitte Schlegelberger, Britta Skawran
BACKGROUND & AIMS: Modulation of microRNA expression is considered for treatment of hepatocellular carcinoma (HCC). Therefore, we characterized the epigenetically regulated microRNA-449 family (miR-449a, miR-449b, miR-449c) with regards to its functional effects and target genes in HCC. METHODS: After transfection of miR-449a, miR-449b, and/or miR-449c, tumor-relevant functional effects were analyzed using in vitro assays and a xenograft mouse model. Binding specificities, target genes, and regulated pathways of each microRNA were identified by microarray analyses...
January 11, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28087776/seed-plant-specific-gene-lineages-involved-in-carpel-development
#10
Kai C Pfannebecker, Matthias Lange, Oliver Rupp, Annette Becker
Evolutionary innovations are important drivers of speciation and some are the defining characters of entire phyla. One such major innovation is the carpel, the unifying character and most complex plant organ, composed of many clearly distinct tissue types to ensure reproductive success. The origin of the carpel is unknown, but many components of the gene regulatory network (GRN) governing carpel development and their genetic interactions are known from the core eudicot Arabidopsis thaliana To unravel the evolution of the carpel GRN and to discriminate between "early" and "late" steps in carpel evolution we calculated thorough phylogeny reconstructions based on sequenced genomes...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087714/dlg5-connects-cell-polarity-and-hippo-signaling-protein-networks-by-linking-par-1-with-mst1-2
#11
Julian Kwan, Anna Sczaniecka, Emad Heidary Arash, Liem Nguyen, Chia-Chun Chen, Srdjana Ratkovic, Olga Klezovitch, Liliana Attisano, Helen McNeill, Andrew Emili, Valeri Vasioukhin
Disruption of apical-basal polarity is implicated in developmental disorders and cancer; however, the mechanisms connecting cell polarity proteins with intracellular signaling pathways are largely unknown. We determined previously that membrane-associated guanylate kinase (MAGUK) protein discs large homolog 5 (DLG5) functions in cell polarity and regulates cellular proliferation and differentiation via undefined mechanisms. We report here that DLG5 functions as an evolutionarily conserved scaffold and negative regulator of Hippo signaling, which controls organ size through the modulation of cell proliferation and differentiation...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28087637/retinoic-acid-receptor-regulation-of-epimorphic-and-homeostatic-regeneration-in-the-axolotl
#12
Matthew Nguyen, Pankhuri Singhal, Judith Piet, Sandra J Shefelbine, Malcolm Maden, S Randal Voss, James R Monaghan
Salamanders are capable of regenerating amputated limbs by generating a mass of lineage-restricted cells called a blastema. Blastemas only generate structures distal to their origin unless treated with retinoic acid (RA), which results in proximodistal (PD) limb duplications. Little is known about the transcriptional network that regulates PD duplication. In this study, we target specific retinoic acid receptors (RARs) to either PD duplicate (RA treatment or RARγ agonist) or truncate (RARβ antagonist) regenerating limbs...
January 13, 2017: Development
https://www.readbyqxmd.com/read/28087487/bioprinting-for-vascular-and-vascularized-tissue-biofabrication
#13
REVIEW
Pallab Datta, Bugra Ayan, Ibrahim T Ozbolat
: Bioprinting is a promising technology to fabricate design-specific tissue constructs due to its ability to create complex, heterocellular structures with anatomical precision. Bioprinting enables the deposition of various biologics including growth factors, cells, genes, neo-tissues and extra-cellular matrix-like hydrogels. Benefits of bioprinting have started to make a mark in the fields of tissue engineering, regenerative medicine and pharmaceutics. Specifically, in the field of tissue engineering, the creation of vascularized tissue constructs has remained a principal challenge till date...
January 10, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28087439/cerebrovascular-heterogeneity-and-neuronal-excitability
#14
REVIEW
Laura Librizzi, Marco de Curtis, Damir Janigro, Leonie Runtz, Frederic deBock, Emmanuel L Barbier, Nicola Marchi
The cerebral vasculature is a complex tridimensional network of arterial and venous vessels which are anatomically in proximity of and functionally coupled to neurons. Depending on the cellular composition of the vascular wall and its anatomical arrangement, cerebral vessels control regional blood flow, define interstitial homeostasis or cerebrospinal fluid circulation and influence immune cell patrolling. Pathological deviations from these functions promote or are a consequence of brain diseases, directly impacting neuronal firing...
January 10, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28087239/on-going-mechanical-damage-from-mastication-drives-homeostatic-th17-cell-responses-at-the-oral-barrier
#15
Nicolas Dutzan, Loreto Abusleme, Hayley Bridgeman, Teresa Greenwell-Wild, Tamsin Zangerle-Murray, Mark E Fife, Nicolas Bouladoux, Holly Linley, Laurie Brenchley, Kelly Wemyss, Gloria Calderon, Bo-Young Hong, Timothy J Break, Dawn M E Bowdish, Michail S Lionakis, Simon A Jones, Giorgio Trinchieri, Patricia I Diaz, Yasmine Belkaid, Joanne E Konkel, Niki M Moutsopoulos
Immuno-surveillance networks operating at barrier sites are tuned by local tissue cues to ensure effective immunity. Site-specific commensal bacteria provide key signals ensuring host defense in the skin and gut. However, how the oral microbiome and tissue-specific signals balance immunity and regulation at the gingiva, a key oral barrier, remains minimally explored. In contrast to the skin and gut, we demonstrate that gingiva-resident T helper 17 (Th17) cells developed via a commensal colonization-independent mechanism...
January 17, 2017: Immunity
https://www.readbyqxmd.com/read/28076377/comparative-analysis-of-vertebrate-diurnal-circadian-transcriptomes
#16
Greg Boyle, Kerstin Richter, Henry D Priest, David Traver, Todd C Mockler, Jeffrey T Chang, Steve A Kay, Ghislain Breton
From photosynthetic bacteria to mammals, the circadian clock evolved to track diurnal rhythms and enable organisms to anticipate daily recurring changes such as temperature and light. It orchestrates a broad spectrum of physiology such as the sleep/wake and eating/fasting cycles. While we have made tremendous advances in our understanding of the molecular details of the circadian clock mechanism and how it is synchronized with the environment, we still have rudimentary knowledge regarding its connection to help regulate diurnal physiology...
2017: PloS One
https://www.readbyqxmd.com/read/28074264/nacl-stress-induces-cssams-gene-expression-in-cucumis-sativus-by-mediating-the-binding-of-csgt-3b-to-the-gt-1-element-within-the-cssams-promoter
#17
Li-Wei Wang, Mei-Wen He, Shi-Rong Guo, Min Zhong, Sheng Shu, Jin Sun
The CsSAMs promoter is a salt-stress-inducible promoter containing three GT-1 elements that are sufficient for the salt-stress response. The transcription factor CsGT-3b was found to bind to the GT-1 element. The S-adenosyl-L-methionine synthase (SAMs) gene is among the functional genes induced during environmental stress. However, little is known about the regulatory mechanism and upstream regulators of this salt-inducible gene in cucumber plants. Thus, it is necessary to understand the characteristics of the SAMs gene by analyzing its promoter and transcription factors...
January 10, 2017: Planta
https://www.readbyqxmd.com/read/28071661/neuronal-sflt1-and-vegfaa-determine-venous-sprouting-and-spinal-cord-vascularization
#18
Raphael Wild, Alina Klems, Masanari Takamiya, Yuya Hayashi, Uwe Strähle, Koji Ando, Naoki Mochizuki, Andreas van Impel, Stefan Schulte-Merker, Janna Krueger, Laetitia Preau, Ferdinand le Noble
Formation of organ-specific vasculatures requires cross-talk between developing tissue and specialized endothelial cells. Here we show how developing zebrafish spinal cord neurons coordinate vessel growth through balancing of neuron-derived Vegfaa, with neuronal sFlt1 restricting Vegfaa-Kdrl mediated angiogenesis at the neurovascular interface. Neuron-specific loss of flt1 or increased neuronal vegfaa expression promotes angiogenesis and peri-neural tube vascular network formation. Combining loss of neuronal flt1 with gain of vegfaa promotes sprout invasion into the neural tube...
January 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28063987/a-mathematical-model-for-the-determination-of-forming-tissue-moduli-in-needled-nonwoven-scaffolds
#19
Joao S Soares, Will Zhang, Michael S Sacks
Formation of engineering tissues (ET) remains an important scientific area of investigation for both clinical translational and mechanobiological studies. Needled-nonwoven (NNW) scaffolds represent one of the most ubiquitous biomaterials based on their well-documented capacity to sustain tissue formation and the unique property of substantial construct stiffness amplification, the latter allowing for very sensitive determination of forming tissue modulus. Yet, their use in more fundamental studies is hampered by the lack of (1) substantial understanding of the mechanics of the NNW scaffold itself under finite deformations and means to model the complex mechanical interactions between scaffold fibers, cells, and de novo tissue; and (2) rational models with reliable predictive capabilities describing their evolving mechanical properties and their response to mechanical stimulation...
January 4, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28063054/high-dimensional-cytometry-of-central-nervous-system-leukocytes-during-neuroinflammation
#20
Dunja Mrdjen, Felix J Hartmann, Burkhard Becher
Autoimmune diseases like multiple sclerosis (MS) develop from the activation and complex interactions of a wide network of immune cells, which penetrate the central nervous system (CNS) and cause tissue damage and neurological deficits. Experimental autoimmune encephalomyelitis (EAE) is a model used to study various aspects of MS, including the infiltration of autoaggressive T cells and pathogenic, inflammatory myeloid cells into the CNS. Various signature landscapes of immune cell infiltrates have proven useful in shedding light on the causes of specific EAE symptoms in transgenic mice...
2017: Methods in Molecular Biology
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