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Tissue-specific network

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https://www.readbyqxmd.com/read/29152379/interplay-of-neuronal-and-non-neuronal-genes-regulates-intestinal-daf-16-mediated-immune-response-during-fusarium-infection-of-caenorhabditis-elegans
#1
Papri Nag, Pooja Rani Aggarwal, Sudip Ghosh, Kanika Narula, Rajul Tayal, Nidhi Maheshwari, Niranjan Chakraborty, Subhra Chakraborty
Although precisely controlled innate immune response is governed by conserved cellular events in phylogenetically diverse hosts, the underlying molecular mechanisms by which this process is regulated against a multi-host pathogen remain unknown. Fusarium oxysporum is a model multi-host pathogen, known to be associated with neuronal stress in humans and vascular wilt in plants. The interaction between innate immune and neuronal pathways is the basis of many diverse biological responses. How these processes are coordinated in response to fungal disease is not well understood...
2017: Cell Death Discovery
https://www.readbyqxmd.com/read/29151593/gene-expression-profiles-indicate-tissue-specific-obesity-regulation-changes-and-strong-obesity-relevant-tissues
#2
R-H Hao, T-L Yang, Y Rong, S Yao, S-S Dong, H Chen, Y Guo
BACKGROUND: With the growing evidence that other tissues, apart from adipose, could have strong relevance to obesity, it is necessary to comprehensively understand the relationship between obesity and other tissues, and to point out the most relevant tissues. METHODS: There were 549 participants with 20 different tissue types involved in this study. We firstly employed both Spearman's correlation test and weighted correlation network analysis (WGCNA) to identify BMI-related genes...
November 20, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29150823/metabolic-dynamics-and-physiological-adaptation-of-panax-ginseng-during-development
#3
Yu-Jin Kim, Sung Chul Joo, Jianxin Shi, Chaoyang Hu, Sheng Quan, Jianping Hu, Johan Sukweenadhi, Padmanaban Mohanan, Deok-Chun Yang, Dabing Zhang
The dynamics of metabolites from leaves to roots of Panax ginseng during development has revealed the tissue-specific and year-specific metabolic networks. Being an essential Oriental medicinal plant, ginseng (Panax ginseng Meyer) is a slow-growing perennial herb-accumulating pharmaceutically active metabolites such as ginsenosides in roots during growth. However, little is known about how ginseng plants survive in the harsh environments such as winter cold and summer heat for a longer period and accumulates those active metabolites as the plant grows...
November 17, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29150558/branched-pectic-galactan-in-phloem-sieve-element-cell-walls-implications-for-cell-mechanics
#4
Thomas A Torode, Rachel E O'Neill, Susan E Marcus, Valerie Cornuault, Sara Pose-Albacete, Rebecca P Lauder, Stjepan Kresimir Kracun, Maja Gro Rydahl, Mathias C F Andersen, William George Tycho Willats, Siobhan Ariel Braybrook, Belinda J Townsend, Mads H Clausen, J Paul Knox
A major question in plant biology concerns the specification and functional differentiation of cell types. This is in the context of constraints imposed by networks of cell walls that both adhere cells and contribute to the form and function of developing organs. Here, we report the identification of a glycan epitope that is specific to phloem sieve element cell walls in several systems. A monoclonal antibody, designated LM26, binds to the cell wall of phloem sieve elements in stems of Arabidopsis thaliana, Miscanthus x giganteus and notably sugar beet (Beta vulgaris) roots where phloem identification is an important factor for the study of phloem unloading of sucrose...
November 17, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29149681/mechanistic-insight-into-contextual-tgf-%C3%AE-signaling
#5
REVIEW
Ying E Zhang
Transforming growth factor-β (TGF-β) controls a wide range of cellular functions by activating both SMADs and non-SMAD pathways. In different tissue or physiological environment, cellular responses to TGF-β can be diverse, even opposite. Complex regulations at the level of ligand mobilization, receptor presentation, and the network of intracellular signal transducers afford the TGF-β pathway with versatile means to induce precise cellular responses in accordance to specific contextual demands. This article summarizes recent development in how cells manage their responses to TGF-β through ligand activation, receptor abundance, as well as SMAD-dependent and SMAD-independent mechanisms...
November 14, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/29146595/the-cartilage-specific-lectin-c-type-lectin-domain-family-3-member-a-clec3a-enhances-tissue-plasminogen-activator-mediated-plasminogen-activation
#6
Daniela Lau, Dzemal Elezagic, Gabriele Hermes, Matthias Mörgelin, Alexander P Wohl, Manuel Koch, Ursula Hartmann, Stefan Höllriegl, Raimund Wagener, Mats Paulsson, Thomas Streichert, Andreas R Klatt
C-type lectin domain family 3 member A (CLEC3A) is a poorly characterized protein belonging to the superfamily of C-type lectins. Its closest homologue tetranectin binds to the kringle 4 domain of plasminogen and enhances its association with tissue plasminogen activator (tPA) thereby enhancing plasmin production, but whether CLEC3A contributes to plasminogen activation is unknown. Here, we recombinantly expressed murine and human full-length CLEC3As as well as truncated forms of CLEC3A in HEK-293 EBNA cells...
November 16, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29143621/identification-and-characterization-of-regulatory-network-components-for-anthocyanin-synthesis-in-barley-aleurone
#7
Ksenia V Strygina, Andreas Börner, Elena K Khlestkina
BACKGROUND: Among natural populations, there are different colours of barley (Hordeum vulgare L.). The colour of barley grains is directly related to the accumulation of different pigments in the aleurone layer, pericarp and lemma. Blue grain colour is due to the accumulation of anthocyanins in the aleurone layer, which is dependent on the presence of five Blx genes that are not sequenced yet (Blx1, Blx3 and Blx4 genes clustering on chromosome 4HL and Blx2 and Blx5 on 7HL). Due to the health benefits of anthocyanins, blue-grained barley can be considered as a source of dietary food...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29139535/contribution-of-cranial-neural-crest-cells-to-mouse-skull-development
#8
Taofen Wu, Guiqian Chen, Fei Tian, Hong-Xiang Liu
The mammalian skull vault is a highly regulated structure that evolutionally protects brain growth during vertebrate development. It consists of several membrane bones with different tissue origins (e.g. neural crest-derived frontal bone and mesoderm-derived parietal bone). Although membrane bones are formed through intramembranous ossification, the neural crest-derived frontal bone has superior capabilities for osteoblast activities and bone regeneration via TGF, BMP, Wnt, and FGF signaling pathways. Neural crest (NC) cells are multipotent, and once induced, will follow specific paths to migrate to different locations of the body where they give rise to a diverse array of cell types and tissues...
2017: International Journal of Developmental Biology
https://www.readbyqxmd.com/read/29137924/nasal-and-otic-placode-specific-regulation-of-sox2-involves-both-activation-by-sox-sall4-synergism-and-multiple-repression-mechanisms
#9
Satoko Sugahara, Tooru Fujimoto, Hisato Kondoh, Masanori Uchikawa
Transcription factor gene Sox2 is expressed throughout sensory development, but the enhancers that regulate the gene vary depending on the developmental stages and tissues. To gain new insights into the gene regulatory network in sensory placode specification, regulation of the nasal-otic bispecific NOP1 enhancer of Sox2 was investigated in chicken embryos. Deletion and mutational analyses using electroporation showed that transcriptional repression mechanisms in combination with activation mechanisms determine placodal specificity...
November 11, 2017: Developmental Biology
https://www.readbyqxmd.com/read/29137387/infrequently-expressed-mirnas-influence-survival-after-diagnosis-with-colorectal-cancer
#10
Martha L Slattery, Andrew J Pellatt, Frances Y Lee, Jennifer S Herrick, Wade S Samowitz, John R Stevens, Roger K Wolff, Lila E Mullany
Half of miRNAs expressed in colorectal tissue are expressed < 50% of the population. Many infrequently expressed miRNAs have low levels of expression. We hypothesize that less frequently expressed miRNAs, when expressed at higher levels, influence both disease stage and survival after diagnosis with colorectal cancer (CRC); low levels of expression may be background noise. We examine 304 infrequently expressed miRNAs in 1893 population-based cases of CRC with paired carcinoma and normal mucosa miRNA profiles...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137180/metabolomic-modularity-analysis-mma-to-quantify-human-liver-perfusion-dynamics
#11
Gautham Vivek Sridharan, Bote Bruinsma, Shyam Sundhar Bale, Anandh Swaminathan, Nima Saeidi, Martin L Yarmush, Korkut Uygun
Large-scale -omics data are now ubiquitously utilized to capture and interpret global responses to perturbations in biological systems, such as the impact of disease states on cells, tissues, and whole organs. Metabolomics data, in particular, are difficult to interpret for providing physiological insight because predefined biochemical pathways used for analysis are inherently biased and fail to capture more complex network interactions that span multiple canonical pathways. In this study, we introduce a nov-el approach coined Metabolomic Modularity Analysis (MMA) as a graph-based algorithm to systematically identify metabolic modules of reactions enriched with metabolites flagged to be statistically significant...
November 13, 2017: Metabolites
https://www.readbyqxmd.com/read/29128541/a-pegylated-platelet-free-plasma-hydrogel-based-composite-scaffold-enables-stable-vascularization-and-targeted-cell-delivery-for-volumetric-muscle-loss
#12
Amit Aurora, Nicole Wrice, Thomas J Walters, Robert J Christy, Shanmugasundaram Natesan
Extracellular matrix (ECM) scaffolds are being used for the clinical repair of soft tissue injuries. Although improved functional outcomes have been reported, ECM scaffolds show limited tissue specific remodeling response with concomitant deposition of fibrotic tissue. One plausible explanation is the regression of blood vessels which may be limiting the diffusion of oxygen and nutrients across the scaffold. Herein we develop a composite scaffold as a vasculo-inductive platform by integrating PEGylated platelet free plasma (PFP) hydrogel with a muscle derived ECM scaffold (m-ECM)...
November 8, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/29128515/injectable-network-biomaterials-via-molecular-or-colloidal-self-assembly
#13
Jugal Kishore Sahoo, Michael A VandenBerg, Matthew J Webber
Self-assembly is a powerful tool to create functional materials. A specific application for which self-assembled materials are ideally suited is in creating injectable biomaterials. Contrasting with traditional biomaterials that are implanted through surgical means, injecting biomaterials through the skin offers numerous advantages, expanding the scope and impact for biomaterials in medicine. In particular, self-assembled biomaterials prepared from molecular or colloidal interactions have been frequently explored...
November 8, 2017: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/29128506/proteoglycans-remodeling-in-cancer-underlying-molecular-mechanisms
#14
REVIEW
Achilleas D Theocharis, Nikos K Karamanos
Extracellular matrix is a highly dynamic macromolecular network. Proteoglycans are major components of extracellular matrix playing key roles in its structural organization and cell signaling contributing to the control of numerous normal and pathological processes. As multifunctional molecules, proteoglycans participate in various cell functions during morphogenesis, wound healing, inflammation and tumorigenesis. Their interactions with matrix effectors, cell surface receptors and enzymes enable them with unique properties...
November 8, 2017: Matrix Biology: Journal of the International Society for Matrix Biology
https://www.readbyqxmd.com/read/29126216/pager-2-0-an-update-to-the-pathway-annotated-list-and-gene-signature-electronic-repository-for-human-network-biology
#15
Zongliang Yue, Qi Zheng, Michael T Neylon, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, Jake Y Chen
Integrative Gene-set, Network and Pathway Analysis (GNPA) is a powerful data analysis approach developed to help interpret high-throughput omics data. In PAGER 1.0, we demonstrated that researchers can gain unbiased and reproducible biological insights with the introduction of PAGs (Pathways, Annotated-lists and Gene-signatures) as the basic data representation elements. In PAGER 2.0, we improve the utility of integrative GNPA by significantly expanding the coverage of PAGs and PAG-to-PAG relationships in the database, defining a new metric to quantify PAG data qualities, and developing new software features to simplify online integrative GNPA...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29122912/top-down-microproteomics-bridged-to-maldi-ms-imaging-reveals-the-molecular-physiome-of-brain-regions
#16
Vivian Delcourt, Julien Franck, Jusal Quanico, Jean-Pascal Gimeno, Maxence Wisztorski, Antonella Raffo Romero, Firas Kobeissy, Xavier Roucou, Michel Salzet, Isabelle Fournier
Tissue top-down microproteomics was performed on 3 brain regions, leading to the characterization of 123 reference proteins. Moreover, 8 alternative proteins from alternative open reading frames (AltORF) were identified. Some proteins display specific post-translational modification profiles or truncation linked to the brain regions and their functions. Systems biology analysis performed on the microproteome identified in each region allowed to associate sub-networks with the functional physiology of each brain region...
November 9, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29122012/drug-target-ontology-to-classify-and-integrate-drug-discovery-data
#17
Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J Yang, Cristian G Bologa, Tudor I Oprea, Stephan C Schürer
BACKGROUND: One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research and development resources. The Illuminating the Druggable Genome (IDG) project develops resources to catalyze the development of likely targetable, yet currently understudied prospective drug targets. A central component of the IDG program is a comprehensive knowledge resource of the druggable genome...
November 9, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29119508/endogenous-molecular-cellular-network-cancer-theory-a-systems-biology-approach
#18
Gaowei Wang, Ruoshi Yuan, Xiaomei Zhu, Ping Ao
In light of ever apparent limitation of the current dominant cancer mutation theory, a quantitative hypothesis for cancer genesis and progression, endogenous molecular-cellular network hypothesis has been proposed from the systems biology perspective, now for more than 10 years. It was intended to include both the genetic and epigenetic causes to understand cancer. Its development enters the stage of meaningful interaction with experimental and clinical data and the limitation of the traditional cancer mutation theory becomes more evident...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29118400/differential-transcriptome-regulation-by-3-5-t2-and-3-3-5-t3-in-brain-and-liver-uncovers-novel-roles-for-thyroid-hormones-in-tilapia
#19
A Olvera, C J Martyniuk, N Buisine, V Jiménez-Jacinto, A Sanchez-Flores, L M Sachs, A Orozco
Although 3,5,3'-triiodothyronine (T3) is considered to be the primary bioactive thyroid hormone (TH) due to its high affinity for TH nuclear receptors (TRs), new data suggest that 3,5-diiodothyronine (T2) can also regulate transcriptional networks. To determine the functional relevance of these bioactive THs, RNA-seq analysis was conducted in the cerebellum, thalamus-pituitary and liver of tilapia treated with equimolar doses of T2 or T3. We identified a total of 169, 154 and 2863 genes that were TH-responsive (FDR < 0...
November 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29116592/varicella-zoster-virus-orf7-interacts-with-orf53-and-plays-a-role-in-its-trans-golgi-network-localization
#20
Wei Wang, Wenkun Fu, Dequan Pan, Linli Cai, Jianghui Ye, Jian Liu, Che Liu, Yuqiong Que, Ningshao Xia, Hua Zhu, Tong Cheng
Varicella-zoster virus (VZV) is a neurotropic alphaherpesvirus that causes chickenpox and shingles. ORF7 is an important virulence determinant of VZV in both human skin and nerve tissues, however, its specific function and involved molecular mechanism in VZV pathogenesis remain largely elusive. Previous yeast two-hybrid studies on intraviral protein-protein interaction network in herpesviruses have revealed that VZV ORF7 may interact with ORF53, which is a virtually unstudied but essential viral protein. The aim of this study is to identify and characterize VZV ORF53, and to investigate its relationship with ORF7...
October 2017: Virologica Sinica
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