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Tissue-specific network

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https://www.readbyqxmd.com/read/28719334/precisely-tracking-childhood-death
#1
Tamer H Farag, Jeffrey P Koplan, Robert F Breiman, Shabir A Madhi, Penny M Heaton, Trevor Mundel, Jaume Ordi, Quique Bassat, Clara Menendez, Scott F Dowell
Little is known about the specific causes of neonatal and under-five childhood death in high-mortality geographic regions due to a lack of primary data and dependence on inaccurate tools, such as verbal autopsy. To meet the ambitious new Sustainable Development Goal 3.2 to eliminate preventable child mortality in every country, better approaches are needed to precisely determine specific causes of death so that prevention and treatment interventions can be strengthened and focused. Minimally invasive tissue sampling (MITS) is a technique that uses needle-based postmortem sampling, followed by advanced histopathology and microbiology to definitely determine cause of death...
July 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28717181/discovery-of-novel-human-gene-regulatory-modules-from-gene-co-expression-and-promoter-motif-analysis
#2
Shisong Ma, Michael Snyder, Savithramma P Dinesh-Kumar
Deciphering gene regulatory networks requires identification of gene expression modules. We describe a novel bottom-up approach to identify gene modules regulated by cis-regulatory motifs from a human gene co-expression network. Target genes of a cis-regulatory motif were identified from the network via the motif's enrichment or biased distribution towards transcription start sites in the promoters of co-expressed genes. A gene sub-network containing the target genes was extracted and used to derive gene modules...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716713/n-myc-regulates-growth-and-fiber-cell-differentiation-in-lens-development
#3
Gabriel R Cavalheiro, Gabriel E Matos-Rodrigues, Yilin Zhao, Anielle L Gomes, Deepti Anand, Danilo Predes, Silmara de Lima, Jose G Abreu, Deyou Zheng, Salil A Lachke, Ales Cvekl, Rodrigo A P Martins
Myc proto-oncogenes regulate diverse cellular processes during development, but their roles during morphogenesis of specific tissues are not fully understood. We found that c-myc regulates cell proliferation in mouse lens development and previous genome-wide studies suggested functional roles for N-myc in developing lens. Here, we examined the role of N-myc in mouse lens development. Genetic inactivation of N-myc in the surface ectoderm or lens vesicle impaired eye and lens growth, while "late" inactivation in lens fibers had no effect...
July 14, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28713244/regulatory-roles-of-long-non-coding-rnas-in-the-central-nervous-system-and-associated-neurodegenerative-diseases
#4
REVIEW
Zhenzhen Quan, Da Zheng, Hong Qing
Accumulating studies have revealed that the human genome encodes tens of thousands of long non-coding RNAs (lncRNAs), which participate in multiple biological networks modulating gene expression via transcriptional, post-transcriptional and epigenetic regulation. Strikingly, a large fraction of tissue-specific lncRNAs are expressed in the Central Nervous System (CNS) with precisely regulated temporal and spatial expression patterns. These brain-specific lncRNAs are also featured with the cell-type specificity, the highest signals of evolutionary conservation, and their preferential location adjacent to brain-expressed protein-coding genes...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28711779/hyperactive-foxo1-results-in-lack-of-tip-stalk-identity-and-deficient-microvascular-regeneration-during-kidney-injury
#5
Lan T H Dang, Takahide Aburatani, Graham A Marsh, Bryce G Johnson, Stella Alimperti, Christine J Yoon, Angela Huang, Suzanne Szak, Naoki Nakagawa, Ivan Gomez, Shuyu Ren, Sarah K Read, Chris Sparages, Alfred C Aplin, Roberto F Nicosia, Chris Chen, Giovanni Ligresti, Jeremy S Duffield
Loss of the microvascular (MV) network results in tissue ischemia, loss of tissue function, and is a hallmark of chronic diseases. The incorporation of a functional vascular network with that of the host remains a challenge to utilizing engineered tissues in clinically relevant therapies. We showed that vascular-bed-specific endothelial cells (ECs) exhibit differing angiogenic capacities, with kidney microvascular endothelial cells (MVECs) being the most deficient, and sought to explore the underlying mechanism...
July 7, 2017: Biomaterials
https://www.readbyqxmd.com/read/28711757/cxcr4-and-cxcr7-play-distinct-roles-in-cardiac-lineage-specification-and-pharmacologic-%C3%AE-adrenergic-response
#6
Delaine K Ceholski, Irene C Turnbull, Venu Pothula, Laura Lecce, Andrew A Jarrah, Changwon Kho, Ahyoung Lee, Lahouaria Hadri, Kevin D Costa, Roger J Hajjar, Sima T Tarzami
CXCR4 and CXCR7 are prominent G protein-coupled receptors (GPCRs) for chemokine stromal cell-derived factor-1 (SDF-1/CXCL12). This study demonstrates that CXCR4 and CXCR7 induce differential effects during cardiac lineage differentiation and β-adrenergic response in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Using lentiviral vectors to ablate CXCR4 and/or CXCR7 expression, hiPSC-CMs were tested for phenotypic and functional properties due to gene knockdown. Gene expression and flow cytometry confirmed the pluripotent and cardiomyocyte phenotype of undifferentiated and differentiated hiPSCs, respectively...
July 8, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28707887/full-characterization-of-localization-diversity-in-human-protein-interactome
#7
Lixin Cheng, Kaili Fan, Yan Huang, Dong Wang, Kwong-Sak Leung
Spatial-temporal regulation amongst proteins forms dynamic networks in cells. Co-existence in common cell compartments can improve biological reliability of the protein-protein interactions. However, this is usually overlooked by most proteomic studies and leads to unrealistic discoveries. In this paper, we systematically characterize the interaction localization diversity in human protein interactome using localization coefficient, a novel metric proposed for assessing how diversely the interactions localize among cell compartments...
July 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28706507/epigenetics-and-autoimmune-thyroid-diseases
#8
REVIEW
Fabio Coppedè
Increasing evidence suggests that epigenetic modifications, including changes in DNA methylation, covalent modifications of histone tails, and gene silencing mediated by non-coding RNA molecules, play a substantial role in the pathogenesis of autoimmune disorders and might be seen as the result of environmental insults that trigger these conditions. Studies in cells and tissues of patients with autoimmune thyroid diseases (AITD), and particularly in Graves' disease (GD) and Hashimoto's thyroiditis (HT), are increasingly revealing altered epigenetic marks and resultant deregulation of gene expression levels, but the available data are still limited to be translated into the clinical settings...
2017: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/28702670/lmna-knockout-mouse-embryonic-fibroblasts-are-less-contractile-than-their-wild-type-counterparts
#9
I A E W van Loosdregt, M A F Kamps, C W J Oomens, S Loerakker, J L V Broers, C V C Bouten
In order to maintain tissue homeostasis and functionality, adherent cells need to sense and respond to environmental mechanical stimuli. An important ability that adherent cells need in order to properly sense and respond to mechanical stimuli is the ability to exert contractile stress onto the environment via actin stress fibers. The actin stress fibers form a structural chain between the cells' environment via focal adhesions and the nucleus via the nuclear lamina. In case one of the links in this chain is missing or aberrant, contractile stress generation will be affected...
July 12, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28702038/neofusicoccum-parvum-colonization-of-the-grapevine-woody-stem-triggers-asynchronous-host-responses-at-the-site-of-infection-and-in-the-leaves
#10
Mélanie Massonnet, Rosa Figueroa-Balderas, Erin R A Galarneau, Shiho Miki, Daniel P Lawrence, Qiang Sun, Christopher M Wallis, Kendra Baumgartner, Dario Cantu
Grapevine trunk diseases cause important economic losses in vineyards worldwide. Neofusicoccum parvum, one of the most aggressive causal agents of the trunk disease Botryosphaeria dieback, colonizes cells and tissues of the grapevine wood, leading to the formation of an internal canker. Symptoms then extend to distal shoots, with wilting of leaves and bud mortality. Our aim was to characterize the transcriptional dynamics of grapevine genes in the woody stem and in the leaves during Neofusicoccum parvum colonization...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28701923/cell-polarity-in-cerebral-cortex-development-cellular-architecture-shaped-by-biochemical-networks
#11
REVIEW
Andi H Hansen, Christian Duellberg, Christine Mieck, Martin Loose, Simon Hippenmeyer
The human cerebral cortex is the seat of our cognitive abilities and composed of an extraordinary number of neurons, organized in six distinct layers. The establishment of specific morphological and physiological features in individual neurons needs to be regulated with high precision. Impairments in the sequential developmental programs instructing corticogenesis lead to alterations in the cortical cytoarchitecture which is thought to represent the major underlying cause for several neurological disorders including neurodevelopmental and psychiatric diseases...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28701763/free-of-acrylamide-sds-based-tissue-clearing-fastclear-for-three-dimensional-visualization-of-myocardial-tissue
#12
Filippo Perbellini, Alan K L Liu, Samuel A Watson, Ifigeneia Bardi, Stephen M Rothery, Cesare M Terracciano
Several pathologic conditions of the heart lead to cardiac structural remodelling. Given the high density and the opaque nature of the myocardium, deep three dimensional (3D) imaging is difficult to achieve and structural analysis of pathological myocardial structure is often limited to two dimensional images and of thin myocardial sections. Efficient methods to obtain optical clearing of the tissue for 3D visualisation are therefore needed. Here we describe a rapid, simple and versatile Free-of-Acrylamide SDS-based Tissue Clearing (FASTClear) protocol specifically designed for cardiac tissue...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28701484/sirt1-regulates-macrophage-self-renewal
#13
Francesco Imperatore, Julien Maurizio, Stephanie Vargas Aguilar, Clara J Busch, Jérémy Favret, Elisabeth Kowenz-Leutz, Wilfried Cathou, Rebecca Gentek, Pierre Perrin, Achim Leutz, Carole Berruyer, Michael H Sieweke
Mature differentiated macrophages can self-maintain by local proliferation in tissues and can be extensively expanded in culture under specific conditions, but the mechanisms of this phenomenon remain only partially defined. Here, we show that SIRT1, an evolutionary conserved regulator of life span, positively affects macrophage self-renewal ability in vitro and in vivo Overexpression of SIRT1 during bone marrow-derived macrophage differentiation increased their proliferative capacity. Conversely, decrease of SIRT1 expression by shRNA inactivation, CRISPR/Cas9 mediated deletion and pharmacological inhibition restricted macrophage self-renewal in culture...
July 12, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28701038/micellear-gold-nanoparticle-as-delivery-vehicle-for-dual-tyrosine-kinase-inhibitor-zd6474-for-metastatic-breast-cancer-treatment
#14
Siddik Sarkar, Suraj Konar, Nagaprasad Puvvada, Shashi Rajput, Bn Prashanth Kumar, Raj R Rao, Amita Pathak, Paul B Fisher, Mahitosh Mandal
Therapeutic index of poorly water soluble drugs are often hampered due to poor pharmokinetics, reduced blood retention and lack of effective drug concentrations in the tumor region. In order to overcome these issues, drugs are often delivered using delivery vehicles to provide an enhanced therapeutic index. Gold nanoparticles synthesized in micellar networks of amphiphilic block copolymer (AuNM) provide an efficient nanocarrier for tissue- and site-specific drug delivery owing to their low cytotoxicity and immunogenicity...
July 12, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28700469/microarray-analysis-of-copy-number-variations-and-gene-expression-profiles-in-prostate-cancer
#15
Yuping Han, Xuefei Jin, Hongyan Li, Kaichen Wang, Ji Gao, Lide Song, Yanting Lv
BACKGROUND: This study aimed to identify potential prostate cancer (PC)-related variations in gene expression profiles. METHODS: Microarray data from the GSE21032 dataset that contained the whole-transcript and exon-level expression profile (GSE21034) and Agilent 244K array-comparative genomic hybridization data (GSE21035) were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and copy-number variations (CNVs) were identified between PC and normal tissue samples...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28698603/identification-of-differentially-methylated-brca1-and-crisp2-dna-regions-as-blood-surrogate-markers-for-cardiovascular-disease
#16
Geoffrey Istas, Ken Declerck, Maria Pudenz, Katarzyna Szarc Vel Szic, Veronica Lendinez-Tortajada, Montserrat Leon-Latre, Karen Heyninck, Guy Haegeman, Jose A Casasnovas, Maria Tellez-Plaza, Clarissa Gerhauser, Christian Heiss, Ana Rodriguez-Mateos, Wim Vanden Berghe
Genome-wide Illumina InfiniumMethylation 450 K DNA methylation analysis was performed on blood samples from clinical atherosclerosis patients (n = 8) and healthy donors (n = 8) in the LVAD study (NCT02174133, NCT01799005). Multiple differentially methylated regions (DMR) could be identified in atherosclerosis patients, related to epigenetic control of cell adhesion, chemotaxis, cytoskeletal reorganisations, cell proliferation, cell death, estrogen receptor pathways and phagocytic immune responses...
July 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28698227/comparative-transcriptomics-of-hepatic-differentiation-of-human-pluripotent-stem-cells-and-adult-human-liver-tissue
#17
Nidal Ghosheh, Barbara Küppers-Munther, Annika Asplund, Josefina Edsbagge, Benjamin Ulfenborg, Tommy B Andersson, Petter Björquist, Christian X Andersson, Helena Carén, Stina Simonsson, Peter Sartipy, Jane Synnergren
Hepatocyte derived from human pluripotent stem cells (hPSC-HEP) have the potential to replace presently used hepatocyte sources applied in liver disease treatment and models of drug discovery and development. Established hepatocyte differentiation protocols are effective and generate hepatocytes, which recapitulate some key features of their in vivo counterparts. However, generating mature hPSC-HEP remains a challenge. In this study, we applied transcriptomics to investigate the progress of in vitro hepatic differentiation of hPSCs at the developmental stages, definitive endoderm (DE), hepatoblasts, early hPSC-HEP, and mature hPSC-HEP, to identify functional targets that enhance efficient hepatocyte differentiation...
July 10, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28695958/identification-and-characterization-of-the-autophagy-related-genes-atg12-and-atg5-in-hydra
#18
Nishikant S Dixit, Bhupendra V Shravage, Surendra Ghaskadbi
Autophagy is an evolutionarily conserved process in eukaryotic cells that is involved in the degradation of cytoplasmic contents including organelles via the lysosome. Hydra is an early metazoan which exhibits simple tissue grade organization, a primitive nervous system, and is one of the classical non-bilaterian models extensively used in evo-devo research. Here, we describe the characterization of two core autophagy genes, Atg12 and Atg5, from hydra. In silico analyses including sequence similarity, domain analysis, and phylogenetic analysis demonstrate the conservation of these genes across eukaryotes...
2017: International Journal of Developmental Biology
https://www.readbyqxmd.com/read/28694817/tissue-specific-regulation-of-gma-mir396-family-on-coordinating-development-and-low-water-availability-responses
#19
Weican Liu, Yonggang Zhou, Xiaowei Li, Xingchao Wang, Yuanyuan Dong, Nan Wang, Xiuming Liu, Huan Chen, Na Yao, Xiyan Cui, Aysha Jameel, Fawei Wang, Haiyan Li
Previously, it was reported that miR396s interact with growth-regulating factors (GRFs) to modulate plant growth, development, and stress resistance. In soybean, 11 gma-miR396 precursors (Pre-miR396a-k) were found, and 24 GmGRFs were predicted as targets of seven mature gma-miR396s (gma-miR396a/b/c/e/h/i/k). To explore the roles of the miR396-GRF module in low water availability response of soybean, we analyzed the expression of Pre-miR396a-k, and found that Pre-miR396a/i/bdgk/e/h were up-regulated in leaves and down-regulated in roots; on the contrary, GmGRF5/6/7/8/15/17/21 were down-regulated in leaves and GmGRF1/2/17/18/19/20/21/22/23/24 were up-regulated in roots of low water potential stressed soybean...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28693578/first-detection-of-european-bat-lyssavirus-type-2-eblv-2-in-norway
#20
Torfinn Moldal, Turid Vikøren, Florence Cliquet, Denise A Marston, Jeroen van der Kooij, Knut Madslien, Irene Ørpetveit
BACKGROUND: In Europe, bat rabies is primarily attributed to European bat lyssavirus type 1 (EBLV-1) and European bat lyssavirus type 2 (EBLV-2) which are both strongly host-specific. Approximately thirty cases of infection with EBLV-2 in Daubenton's bats (Myotis daubentonii) and pond bats (M. dasycneme) have been reported. Two human cases of rabies caused by EBLV-2 have also been confirmed during the last thirty years, while natural spill-over to other non-flying mammals has never been reported...
July 11, 2017: BMC Veterinary Research
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