keyword
MENU ▼
Read by QxMD icon Read
search

Tissue specific gene network

keyword
https://www.readbyqxmd.com/read/28227099/a-large-scale-detailed-neuronal-model-of-electrical-stimulation-of-the-dentate-gyrus-and-perforant-path-as-a-platform-for-electrode-design-and-optimization
#1
Clayton S Bingham, Kyle Loizos, Gene Yu, Andrew Gilbert, Jean-Marie Bouteiller, Dong Song, Gianluca Lazzi, Theodore W Berger, Clayton S Bingham, Kyle Loizos, Gene Yu, Andrew Gilbert, Jean-Marie Bouteiller, Dong Song, Gianluca Lazzi, Theodore W Berger, Kyle Loizos, Gene Yu, Theodore W Berger, Gianluca Lazzi, Jean-Marie Bouteiller, Clayton S Bingham, Dong Song, Andrew Gilbert
Owing to the dramatic rise in treatment of neurological disorders with electrical micro-stimulation it has become apparent that the major technological limitation in deploying effective devices lies in the process of designing efficient, safe, and outcome specific electrode arrays. The time-consuming and low-fidelity nature of gathering test data using experimental means and the immense control and flexibility of computational models, has prompted us and others to build models of electrical stimulation of neural networks that can be simulated in a computer...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28221369/chemistry-based-molecular-signature-underlying-the-atypia-of-clozapine
#2
T Cardozo, E Shmelkov, K Felsovalyi, J Swetnam, T Butler, D Malaspina, S V Shmelkov
The central nervous system is functionally organized as a dynamic network of interacting neural circuits that underlies observable behaviors. At higher resolution, these behaviors, or phenotypes, are defined by the activity of a specific set of biomolecules within those circuits. Identification of molecules that govern psychiatric phenotypes is a major challenge. The only organic molecular entities objectively associated with psychiatric phenotypes in humans are drugs that induce psychiatric phenotypes and drugs used for treatment of specific psychiatric conditions...
February 21, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28216162/genome-wide-identification-of-glabra3-downstream-genes-for-anthocyanin-biosynthesis-and-trichome-formation-in-arabidopsis
#3
Chenhao Gao, Dong Li, Changyu Jin, Shaowei Duan, Shuanghui Qi, Kaige Liu, Hanchen Wang, Haoli Ma, Jiangbo Hai, Mingxun Chen
GLABRA3 (GL3), a bHLH transcription factor, has previously proved to be involved in anthocyanin biosynthesis and trichome formation in Arabidopsis, however, its downstream targeted genes are still largely unknown. Here, we found that GL3 was widely present in Arabidopsis vegetative and reproductive organs. New downstream targeted genes of GL3 for anthocyanin biosynthesis and trichome formation were identified in young shoots and expanding true leaves by RNA sequencing. GL3-mediated gene expression was tissue specific in the two biological processes...
February 16, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28199418/analysis-of-long-noncoding-rna-and-mrna-using-rna-sequencing-during-the-differentiation-of-intramuscular-preadipocytes-in-chicken
#4
Tao Zhang, Xiangqian Zhang, Kunpeng Han, Genxi Zhang, Jinyu Wang, Kaizhou Xie, Qian Xue, Xiaomei Fan
Long noncoding RNAs (lncRNAs) regulate metabolic tissue development and function, including adipogenesis. However, little is known about the function and profile of lncRNAs in intramuscular preadipocyte differentiation in chicken. Here, we identified lncRNAs in chicken intramuscular preadipocytes at different differentiation stages using RNA sequencing. A total of 1,311,382,604 clean reads and 25,435 lncRNAs were obtained from 12 samples. In total, 7,433 differentially expressed genes (4,698 lncRNAs and 2,735 mRNAs) were identified by pairwise comparison...
2017: PloS One
https://www.readbyqxmd.com/read/28195124/pervasive-translational-regulation-of-the-cell-signalling-circuitry-underlies-mammalian-development
#5
Kotaro Fujii, Zhen Shi, Olena Zhulyn, Nicolas Denans, Maria Barna
The degree and dynamics of translational control during mammalian development remain poorly understood. Here we monitored translation of the mammalian genome as cells become specified and organize into tissues in vivo. This identified unexpected and pervasive translational regulation of most of the core signalling circuitry including Shh, Wnt, Hippo, PI3K and MAPK pathways. We further identify and functionally characterize a complex landscape of upstream open reading frames (uORFs) across 5'-untranslated regions (UTRs) of key signalling components...
February 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28193895/p53-regulates-the-cardiac-transcriptome
#6
Tak W Mak, Ludger Hauck, Daniela Grothe, Filio Billia
The tumor suppressor Trp53 (p53) inhibits cell growth after acute stress by regulating gene transcription. The mammalian genome contains hundreds of p53-binding sites. However, whether p53 participates in the regulation of cardiac tissue homeostasis under normal conditions is not known. To examine the physiologic role of p53 in adult cardiomyocytes in vivo, Cre-loxP-mediated conditional gene targeting in adult mice was used. Genome-wide transcriptome analyses of conditional heart-specific p53 knockout mice were performed...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28192080/evo-engineering-and-the-cellular-and-molecular-origins-of-the-vertebrate-spinal-cord
#7
REVIEW
Ben Steventon, Alfonso Martinez Arias
The formation of the spinal cord during early embryonic development in vertebrate embryos is a continuous process that begins at gastrulation and continues through to the completion of somitogenesis. Despite the conserved usage of patterning mechanisms and gene regulatory networks that act to generate specific spinal cord progenitors, there now exists two seemingly disparate models to account for their action. In the first, a posteriorly localized signalling source transforms previously anterior-specified neural plate into the spinal cord...
February 9, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28191769/suppression-of-transforming-growth-factor-%C3%AE-signaling-delays-cellular-senescence-and-preserves-the-function-of-endothelial-cells-derived-from-human-pluripotent-stem-cells
#8
Hao Bai, Yongxing Gao, Dixie L Hoyle, Tao Cheng, Zack Z Wang
Transplantation of vascular cells derived from human pluripotent stem cells (hPSCs) offers an attractive noninvasive method for repairing the ischemic tissues and for preventing the progression of vascular diseases. Here, we found that in a serum-free condition, the proliferation rate of hPSC-derived endothelial cells is quickly decreased, accompanied with an increased cellular senescence, resulting in impaired gene expression of endothelial nitric oxide synthase (eNOS) and impaired vessel forming capability in vitro and in vivo...
February 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28187709/the-drosophila-gene-expression-tool-dget-for-expression-analyses
#9
Yanhui Hu, Aram Comjean, Norbert Perrimon, Stephanie E Mohr
BACKGROUND: Next-generation sequencing technologies have greatly increased our ability to identify gene expression levels, including at specific developmental stages and in specific tissues. Gene expression data can help researchers understand the diverse functions of genes and gene networks, as well as help in the design of specific and efficient functional studies, such as by helping researchers choose the most appropriate tissue for a study of a group of genes, or conversely, by limiting a long list of gene candidates to the subset that are normally expressed at a given stage or in a given tissue...
February 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28187708/incorporating-prior-biological-knowledge-for-network-based-differential-gene-expression-analysis-using-differentially-weighted-graphical-lasso
#10
Yiming Zuo, Yi Cui, Guoqiang Yu, Ruijiang Li, Habtom W Ressom
BACKGROUND: Conventional differential gene expression analysis by methods such as student's t-test, SAM, and Empirical Bayes often searches for statistically significant genes without considering the interactions among them. Network-based approaches provide a natural way to study these interactions and to investigate the rewiring interactions in disease versus control groups. In this paper, we apply weighted graphical LASSO (wgLASSO) algorithm to integrate a data-driven network model with prior biological knowledge (i...
February 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28187158/role-of-the-long-non-coding-rna-pvt1-in-the-dysregulation-of-the-cerna-cerna-network-in-human-breast-cancer
#11
Federica Conte, Giulia Fiscon, Matteo Chiara, Teresa Colombo, Lorenzo Farina, Paola Paci
Recent findings have identified competing endogenous RNAs (ceRNAs) as the drivers in many disease conditions, including cancers. The ceRNAs indirectly regulate each other by reducing the amount of microRNAs (miRNAs) available to target messenger RNAs (mRNAs). The ceRNA interactions mediated by miRNAs are modulated by a titration mechanism, i.e. large changes in the ceRNA expression levels either overcome, or relieve, the miRNA repression on competing RNAs; similarly, a very large miRNA overexpression may abolish competition...
2017: PloS One
https://www.readbyqxmd.com/read/28186107/blubber-transcriptome-response-to-acute-stress-axis-activation-involves-transient-changes-in-adipogenesis-and-lipolysis-in-a-fasting-adapted-marine-mammal
#12
J I Khudyakov, C D Champagne, L M Meneghetti, D E Crocker
Stress can compromise an animal's ability to conserve metabolic stores and participate in energy-demanding activities that are critical for fitness. Understanding how wild animals, especially those already experiencing physiological extremes (e.g. fasting), regulate stress responses is critical for evaluating the impacts of anthropogenic disturbance on physiology and fitness, key challenges for conservation. However, studies of stress in wildlife are often limited to baseline endocrine measurements and few have investigated stress effects in fasting-adapted species...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28185577/artificial-neural-network-classifier-predicts-neuroblastoma-patients-outcome
#13
Davide Cangelosi, Simone Pelassa, Martina Morini, Massimo Conte, Maria Carla Bosco, Alessandra Eva, Angela Rita Sementa, Luigi Varesio
BACKGROUND: More than fifty percent of neuroblastoma (NB) patients with adverse prognosis do not benefit from treatment making the identification of new potential targets mandatory. Hypoxia is a condition of low oxygen tension, occurring in poorly vascularized tissues, which activates specific genes and contributes to the acquisition of the tumor aggressive phenotype. We defined a gene expression signature (NB-hypo), which measures the hypoxic status of the neuroblastoma tumor. We aimed at developing a classifier predicting neuroblastoma patients' outcome based on the assessment of the adverse effects of tumor hypoxia on the progression of the disease...
November 8, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28179101/molecular-phylogenomic-study-and-the-role-of-exogenous-spermidine-in-the-metabolic-adjustment-of-endogenous-polyamine-in-two-rice-cultivars-under-salt-stress
#14
Jayita Saha, Kalyan Giri
Compelling evidences anticipated the well acclamation of involvement of exogenous and endogenous polyamines (PAs) in conferring salt tolerance in plants. Intracellular PA's anabolism and catabolism should have contributed to maintain endogenous PAs homeostasis to induce stress signal networks. In this report, the evolutionary study has been conducted to reveal the phylogenetic relationship of genes encoding enzymes of the anabolic and catabolic pathway of PAs among the five plant lineages including green algae, moss, lycophyte, dicot and monocot along with their respective exon-intron structural patterns...
April 20, 2017: Gene
https://www.readbyqxmd.com/read/28153094/a-synthetic-biology-inspired-therapeutic-strategy-for-targeting-and-treating-hepatogenous-diabetes
#15
Shuai Xue, Jianli Yin, Jiawei Shao, Yuanhuan Yu, Linfeng Yang, Yidan Wang, Mingqi Xie, Martin Fussenegger, Haifeng Ye
Hepatogenous diabetes is a complex disease that is typified by the simultaneous presence of type 2 diabetes and many forms of liver disease. The chief pathogenic determinant in this pathophysiological network is insulin resistance (IR), an asymptomatic disease state in which impaired insulin signaling in target tissues initiates a variety of organ dysfunctions. However, pharmacotherapies targeting IR remain limited and are generally inapplicable for liver disease patients. Oleanolic acid (OA) is a plant-derived triterpenoid that is frequently used in Chinese medicine as a safe but slow-acting treatment in many liver disorders...
February 1, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28143946/cellular-proteomes-drive-tissue-specific-regulation-of-the-heat-shock-response
#16
Jian Ma, Christopher E Grant, Rosemary N Plagens, Lindsey N Barrett, Karen S Kim Guisbert, Eric Guisbert
The heat shock response (HSR) is a cellular stress response that senses protein misfolding and restores protein folding homeostasis, or proteostasis. We previously identified an HSR regulatory network in Caenorhabditis elegans consisting of highly conserved genes that have important cellular roles in maintaining proteostasis. Unexpectedly, the effects of these genes on the heat shock response are distinctly tissue-specific. Here, we explore this apparent discrepancy and find that muscle-specific regulation of the HSR by the TRiC/CCT chaperonin is not driven by an enrichment of TRiC/CCT in muscle, but rather by the levels of one of its most abundant substrates, actin...
January 30, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28141819/graph-theoretical-model-of-global-human-interactome-reveals-enhanced-long-range-communicability-in-cancer-networks
#17
Evgeny Gladilin
Malignant transformation is known to involve substantial rearrangement of the molecular genetic landscape of the cell. A common approach to analysis of these alterations is a reductionist one and consists of finding a compact set of differentially expressed genes or associated signaling pathways. However, due to intrinsic tumor heterogeneity and tissue specificity, biomarkers defined by a small number of genes/pathways exhibit substantial variability. As an alternative to compact differential signatures, global features of genetic cell machinery are conceivable...
2017: PloS One
https://www.readbyqxmd.com/read/28131833/fluid-shear-stress-stimulates-mate2-k-expression-via-nrf2-pathway-activation
#18
Yasunori Fukuda, Misato Kaishima, Toshiyuki Ohnishi, Kimio Tohyama, Ikumi Chisaki, Yusuke Nakayama, Mari Ogasawara-Shimizu, Yuji Kawamata
Accurate prediction of drug-induced renal toxicity is necessary for development of safer drugs for patients. Cellular assay systems that recapitulate physiologically relevant microenvironments have been proposed for correct estimation of drug responses in the human body. However, establishment of such assay systems for accurate prediction of renal toxicity is challenging because of the lack of readily available in vitro assay systems. In this study, we investigated the cellular response to fluid shear stress, which is a characteristic of the environment in the kidney proximal tubules, using microfluidic devices...
January 25, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28131826/the-core-regulatory-network-in-human-cells
#19
Man-Sun Kim, Dongsan Kim, Nam Sook Kang, Jeong-Rae Kim
In order to discover the common characteristics of various cell types in the human body, many researches have been conducted to find the set of genes commonly expressed in various cell types and tissues. However, the functional characteristics of a cell is determined by the complex regulatory relationships among the genes rather than by expressed genes themselves. Therefore, it is more important to identify and analyze a core regulatory network where all regulatory relationship between genes are active across all cell types to uncover the common features of various cell types...
January 26, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28125282/phloem-mobile-rnas-as-systemic-signaling-agents
#20
Byung-Kook Ham, William J Lucas
The plant vascular system plays a central role in coordinating physiological and developmental events through delivery of both essential nutrients and long-distance signaling agents. The enucleate phloem sieve tube system of the angiosperms contains a broad spectrum of RNA species. Grafting and transcriptomics studies have indicated that several thousand mRNAs move long distances from source organs to meristematic sink tissues. Ribonucleoprotein complexes play a pivotal role as stable RNA-delivery systems for systemic translocation of cargo RNA...
January 11, 2017: Annual Review of Plant Biology
keyword
keyword
6880
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"