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Tissue specific network

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https://www.readbyqxmd.com/read/27930646/retinal-expression-of-the-drosophila-eyes-absent-gene-is-controlled-by-several-cooperatively-acting-cis-regulatory-elements
#1
Bonnie M Weasner, Brandon P Weasner, Sarah D Neuman, Arash Bashirullah, Justin P Kumar
The eyes absent (eya) gene of the fruit fly, Drosophila melanogaster, is a member of an evolutionarily conserved gene regulatory network that controls eye formation in all seeing animals. The loss of eya leads to the complete elimination of the compound eye while forced expression of eya in non-retinal tissues is sufficient to induce ectopic eye formation. Within the developing retina eya is expressed in a dynamic pattern and is involved in tissue specification/determination, cell proliferation, apoptosis, and cell fate choice...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27928505/collagen-a-network-for-regenerative-medicine
#2
REVIEW
K M Pawelec, S M Best, R E Cameron
The basic building block of the extra-cellular matrix in native tissue is collagen. As a structural protein, collagen has an inherent biocompatibility making it an ideal material for regenerative medicine. Cellular response, mediated by integrins, is dictated by the structure and chemistry of the collagen fibers. Fiber formation, via fibrillogenesis, can be controlled in vitro by several factors: pH, ionic strength, and collagen structure. After formation, fibers are stabilized via cross-linking. The final bioactivity of collagen scaffolds is a result of both processes...
October 28, 2016: Journal of Materials Chemistry. B, Materials for Biology and Medicine
https://www.readbyqxmd.com/read/27923776/establishment-of-expression-in-the-shortroot-scarecrow-transcriptional-cascade-through-opposing-activities-of-both-activators-and-repressors
#3
Erin E Sparks, Colleen Drapek, Allison Gaudinier, Song Li, Mitra Ansariola, Ning Shen, Jessica H Hennacy, Jingyuan Zhang, Gina Turco, Jalean J Petricka, Jessica Foret, Alexander J Hartemink, Raluca Gordân, Molly Megraw, Siobhan M Brady, Philip N Benfey
Tissue-specific gene expression is often thought to arise from spatially restricted transcriptional cascades. However, it is unclear how expression is established at the top of these cascades in the absence of pre-existing specificity. We generated a transcriptional network to explore how transcription factor expression is established in the Arabidopsis thaliana root ground tissue. Regulators of the SHORTROOT-SCARECROW transcriptional cascade were validated in planta. At the top of this cascade, we identified both activators and repressors of SHORTROOT...
December 5, 2016: Developmental Cell
https://www.readbyqxmd.com/read/27922611/genetic-and-epigenomic-mechanisms-of-mammalian-circadian-transcription
#4
REVIEW
Romeo Papazyan, Yuxiang Zhang, Mitchell A Lazar
The mammalian molecular clock comprises a complex network of transcriptional programs that integrates environmental signals with physiological pathways in a tissue-specific manner. Emerging technologies are extending knowledge of basic clock features by uncovering their underlying molecular mechanisms, thus setting the stage for a 'systems' view of the molecular clock. Here we discuss how recent data from genome-wide genetic and epigenetic studies have informed the understanding of clock function. In addition to its importance in human physiology and disease, the clock mechanism provides an ideal model to assess general principles of dynamic transcription regulation in vivo...
December 6, 2016: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27922122/identification-of-critical-paralog-groups-with-indispensable-roles-in-the-regulation-of-signaling-flow
#5
Dezso Modos, Johanne Brooks, David Fazekas, Eszter Ari, Tibor Vellai, Peter Csermely, Tamas Korcsmaros, Katalin Lenti
Extensive cross-talk between signaling pathways is required to integrate the myriad of extracellular signal combinations at the cellular level. Gene duplication events may lead to the emergence of novel functions, leaving groups of similar genes - termed paralogs - in the genome. To distinguish critical paralog groups (CPGs) from other paralogs in human signaling networks, we developed a signaling network-based method using cross-talk annotation and tissue-specific signaling flow analysis. 75 CPGs were found with higher degree, betweenness centrality, closeness, and 'bowtieness' when compared to other paralogs or other proteins in the signaling network...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922056/identification-and-functional-analysis-of-long-intergenic-noncoding-rna-genes-in-porcine-pre-implantation-embryonic-development
#6
Jingyu Li, Zhengling Gao, Xingyu Wang, Hongbo Liu, Yan Zhang, Zhonghua Liu
Genome-wide transcriptome studies have identified thousands of long intergenic noncoding RNAs (lincRNAs), some of which play important roles in pre-implantation embryonic development (PED). Pig is an ideal model for reproduction, however, porcine lincRNAs are still poorly characterized and it is unknown if they are associated with porcine PED. Here we reconstructed 195,531 transcripts in 122,007 loci, and identified 7,618 novel lincRNAs from 4,776 loci based on published RNA-seq data. These lincRNAs show low exon number, short length, low expression level, tissue-specific expression and cis-acting, which is consistent with previous reports in other species...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27921285/spatiotemporal-distribution-modeling-of-pet-tracer-uptake-in-solid-tumors
#7
Madjid Soltani, Mostafa Sefidgar, Hossein Bazmara, Michael E Casey, Rathan M Subramaniam, Richard L Wahl, Arman Rahmim
OBJECTIVE: Distribution of PET tracer uptake is elaborately modeled via a general equation used for solute transport modeling. This model can be used to incorporate various transport parameters of a solid tumor such as hydraulic conductivity of the microvessel wall, transvascular permeability as well as interstitial space parameters. This is especially significant because tracer delivery and drug delivery to solid tumors are determined by similar underlying tumor transport phenomena, and quantifying the former can enable enhanced prediction of the latter...
December 5, 2016: Annals of Nuclear Medicine
https://www.readbyqxmd.com/read/27920798/evolutionary-and-functional-features-of-copy-number-variation-in-the-cattle-genome
#8
Brittney N Keel, Amanda K Lindholm-Perry, Warren M Snelling
Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27920729/transcriptional-network-architecture-of-breast-cancer-molecular-subtypes
#9
Guillermo de Anda-Jáuregui, Tadeo E Velázquez-Caldelas, Jesús Espinal-Enríquez, Enrique Hernández-Lemus
Breast cancer heterogeneity is evident at the clinical, histological and molecular level. High throughput technologies allowed the identification of intrinsic subtypes that capture transcriptional differences among tumors. A remaining question is whether said differences are associated to a particular transcriptional program which involves different connections between the same molecules. In other words, whether particular transcriptional network architectures can be linked to specific phenotypes. In this work we infer, construct and analyze transcriptional networks from whole-genome gene expression microarrays, by using an information theory approach...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27920338/the-plethora-gene-regulatory-network-guides-growth-and-cell-differentiation-in-arabidopsis-roots
#10
Luca Santuari, Gabino Sanchez-Perez, Marijn Luijten, Bas Rutjens, Inez Terpstra, Lidija Berke, Maartje Gorte, Kalika Prasad, Dongping Bao, Johanna L P M Timmermans-Hereijgers, Kenichiro Maeo, Kenzo Nakamura, Akie Shimotohno, Ales Pencik, Ondřej Novák, Karin Ljung, Sebastiaan van Heesch, Ewart de Bruijn, Edwin Cuppen, Viola Willemsen, Ari Pekka Mähönen, Wolfgang Lukowitz, Berend Snel, Dick de Ridder, Ben Scheres, Renze Heidstra
Organ formation in animals and plants relies on precise control of cell state transitions to turn stem cell daughters into fully differentiated cells. In plants, cells cannot rearrange due to shared cell walls. Thus, differentiation progression and the accompanying cell expansion must be tightly coordinated across tissues. PLETHORA (PLT) transcription factor gradients are unique in their ability to guide the progression of cell differentiation at different positions in the growing Arabidopsis root, which contrasts with well-described transcription factor gradients in animals specifying distinct cell fates within an essentially static context...
December 5, 2016: Plant Cell
https://www.readbyqxmd.com/read/27915976/strategies-to-strike-survival-networks-in-cancer
#11
Marzia Pennati, Graziella Cimino-Reale, Laura Gatti, Giuliana Cassinelli
The machinery that maintains cellular and tissue homeostasis in a healthy individual is recruited and hijacked by cancer cells to support tumor growth and progression. Activation of often unpredictable alternative or complementary signaling pathways allows cancer cells to bypass the intrinsic self-destructive machinery and the limited replicative potential present in every cell for correct homeostasis maintenance. Therefore, evasion/resistance to apoptosis/cell death, self-sufficiency in growth/survival signals, and limitless replicative potential remain undoubted hallmarks of cancer, contributing to drug resistance...
2016: Critical Reviews in Oncogenesis
https://www.readbyqxmd.com/read/27913189/construction-and-analysis-of-a-human-testis-sperm-enriched-interaction-network-unraveling-the-ppp1cc2-interactome
#12
Joana Vieira Silva, Sooyeon Yoon, Pieter-Jan De Bock, Alexander V Goltsev, Kris Gevaert, José Fernando F Mendes, Margarida Fardilha
BACKGROUND: Phosphoprotein phosphatase 1 catalytic subunit gamma 2 (PPP1CC2), a PPP1CC tissue-specific alternative splice restricted to testicular germ cells and spermatozoa, is essential for spermatogenesis and spermatozoa motility. The key to understand PPP1CC2 regulation lies on the characterization of its interacting partners. METHODS: We construct a testis/sperm-enriched protein interaction network and analyzed the topological properties and biological context of the network...
November 29, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27909803/evolutionary-origin-of-endochondral-ossification-the-transdifferentiation-hypothesis
#13
REVIEW
Fret Cervantes-Diaz, Pedro Contreras, Sylvain Marcellini
The vertebrate endoskeleton results from the piecemeal assembly of bone and cartilage as well as additional types of calcified extracellular matrices produced by seemingly hybrid cell types of intermediate phenotypes between osteoblasts and chondrocytes. Hence, shedding light on the emergence and subsequent diversification of skeletal tissues represents a major challenge in vertebrate evolutionary developmental biology. A 150-year-old debate in the field was recently solved by lineage tracing experiments demonstrating that, during mouse endochondral bone development, a subset of chondrocytes evades apoptosis and transdifferentiate into osteoblasts at the chondro-osseous junction...
December 1, 2016: Development Genes and Evolution
https://www.readbyqxmd.com/read/27908912/a-deep-proteome-analysis-identifies-the-complete-secretome-as-the-functional-unit-of-human-cardiac-progenitor-cells
#14
Sudhish Sharma, Rachana Mishra, Grace E Bigham, Brody Wehman, Mohd M Khan, Huichun Xu, Progyaparamita Saha, Young Ah Goo, Srinivisa R Datla, Ling Chen, Mohan E Tulapurkar, Bradley S Taylor, Peixin Yang, Sotirios K Karathanasis, David R Goodlett, Sunjay Kaushal
RATIONALE: Cardiac progenitor cells are an attractive cell type for tissue regeneration but their mechanism for myocardial remodeling is still unclear. OBJECTIVE: This investigation determines how chronological age influences the phenotypic characteristics and the secretome of human cardiac progenitor cells (CPCs), as well as their potential to recover injured myocardium. METHODS AND RESULTS: Adult (aCPCs) and neonatal (nCPCs) cells were derived from patients more than 40 years or less than one month of age, respectively, and their functional potential was determined in a rodent myocardial infarction (MI) model...
December 1, 2016: Circulation Research
https://www.readbyqxmd.com/read/27899616/the-tissuenet-v-2-database-a-quantitative-view-of-protein-protein-interactions-across-human-tissues
#15
Omer Basha, Ruth Barshir, Moran Sharon, Eugene Lerman, Binyamin F Kirson, Idan Hekselman, Esti Yeger-Lotem
Knowledge of the molecular interactions of human proteins within tissues is important for identifying their tissue-specific roles and for shedding light on tissue phenotypes. However, many protein-protein interactions (PPIs) have no tissue-contexts. The TissueNet database bridges this gap by associating experimentally-identified PPIs with human tissues that were shown to express both pair-mates. Users can select a protein and a tissue, and obtain a network view of the query protein and its tissue-associated PPIs...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899510/identification-and-in-silico-modeling-of-enhancers-reveals-new-features-of-the-cardiac-differentiation-network
#16
Denis Seyres, Yad Ghavi-Helm, Guillaume Junion, Ouarda Taghli-Lamallem, Céline Guichard, Laurence Röder, Charles Girardot, Eileen E M Furlong, Laurent Perrin
Developmental patterning and tissue formation are regulated through complex gene regulatory networks (GRNs) driven through the action of transcription factors (TFs) converging on enhancer elements. Here, as a point of entry to dissect the poorly defined GRN underlying cardiomyocyte differentiation, we apply an integrated approach to identify active enhancers and TFs involved in Drosophila heart development. The Drosophila heart consists of 104 cardiomyocytes, representing less than 0.5% of all cells in the embryo...
December 1, 2016: Development
https://www.readbyqxmd.com/read/27898171/hormesis-cellular-stress-response-and-neuroinflammation-in-schizophrenia-early-onset-versus-late-onset-state
#17
REVIEW
Vittorio Calabrese, James Giordano, Rosalia Crupi, Rosanna Di Paola, Martino Ruggieri, Rio Bianchini, Maria Laura Ontario, Salvatore Cuzzocrea, Edward J Calabrese
Abnormal redox homeostasis and oxidative stress have been proposed to play a role in the etiology of several neuropsychiatric spectrum disorders. Emerging interest has recently focused on markers of oxidative stress and neuroinflammation in schizophrenic spectrum disorders, at least in particular subgroups of patients. Altered expression of genes related to oxidative stress, oxidative damage to DNA, protein and lipids, as well as reduced glutathione levels in central and peripheral tissues could act synergistically, and contribute to the course of the disease...
November 29, 2016: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/27893402/a-convolutional-neural-network-for-automatic-characterization-of-plaque-composition-in-carotid-ultrasound
#18
Karim Lekadir, Alfiia Galimzianova, Angels Betriu, Maria Del Mar Vila, Laura Igual, Daniel Rubin, Elvira Fernandez, Petia Radeva, Sandy Napel
Characterization of carotid plaque composition, more specifically the amount of lipid core, fibrous tissue, and calcified tissue, is an important task for the identification of plaques that are prone to rupture, and thus for early risk estima-tion of cardiovascular and cerebrovascular events. Due to its low costs and wide availability, carotid ultrasound has the potential to become the modality of choice for plaque characterization in clinical practice. However, its significant image noise, coupled with the small size of the plaques and their complex appearance, makes it difficult for automated techniques to discriminate be-tween the different plaque constituents...
November 22, 2016: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/27890800/metabolic-responses-of-haliotis-diversicolor-to-vibrio-parahaemolyticus-infection
#19
Jie Lu, Yanyan Shi, Shuhui Cai, Jianghua Feng
Vibrio parahemolyticus is a devastating bacterial pathogen that often causes outbreak of vibriosis in abalone Haliotis diversicolor. Elucidation of metabolic mechanisms of abalones in responding to V. parahemolyticus infection is essential for controlling the epidemic. In this work, (1)H NMR-based metabolomic techniques along with correlation and network analyses are used to investigate characteristic metabolites, as well as corresponding disturbed pathways in hepatopancreas and gill of H. diversicolor after V...
November 25, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27890679/evaluation-of-non-supervised-maldi-mass-spectrometry-imaging-combined-with-microproteomics-for-glioma-grade-iii-classification
#20
Emilie Le Rhun, Marie Duhamel, Maxence Wisztorski, Jean-Pascal Gimeno, Fahed Zairi, Fabienne Escande, Nicolas Reyns, Firas Kobeissy, Claude-Alain Maurage, Michel Salzet, Isabelle Fournier
An integrated diagnosis using molecular features is recommended in the 2016 World Health Organization (WHO) classification. Our aim was to explore non-targeted molecular classification using MALDI mass spectrometry imaging (MALDI MSI) associated to microproteomics in order to classify anaplastic glioma by integration of clinical data. We used fresh-frozen tissue sections to perform MALDI MSI of proteins based on their digestion peptides after in-situ trypsin digestion of the tissue sections and matrix deposition by micro-spraying...
November 23, 2016: Biochimica et Biophysica Acta
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