keyword
MENU ▼
Read by QxMD icon Read
search

transcriptional network

keyword
https://www.readbyqxmd.com/read/28231333/molecular-mechanisms-of-cooperative-binding-of-transcription-factors-runx1-cbf%C3%AE-ets1-on-the-tcr%C3%AE-gene-enhancer
#1
Kota Kasahara, Masaaki Shiina, Ikuo Fukuda, Kazuhiro Ogata, Haruki Nakamura
Ets1 is an essential transcription factor (TF) for several important physiological processes, including cell proliferation and differentiation. Its recognition of the enhancer region of the TCRα gene is enhanced by the cooperative binding of the Runx1-CBFβ heterodimer, with the cancelation of phosphorylation-dependent autoinhibition. The detailed mechanism of this interesting cooperativity between Ets1 and the Runx1-CBFβ heterodimer is still largely unclear. Here, we investigated the molecular mechanisms of this cooperativity, by using molecular dynamics simulations...
2017: PloS One
https://www.readbyqxmd.com/read/28231299/exploration-of-inhibitory-mechanisms-of-curcumin-in-lung-cancer-metastasis-using-a-mirna-transcription-factor-target-gene-network
#2
De-Min Jiao, Li Yan, Li-Shan Wang, Hui-Zhen Hu, Xia-Li Tang, Jun Chen, Jian Wang, You Li, Qing-Yong Chen
The present study was aimed to unravel the inhibitory mechanisms of curcumin for lung cancer metastasis via constructing a miRNA-transcription factor (TF)-target gene network. Differentially expressed miRNAs between human high-metastatic non-small cell lung cancer 95D cells treated with and without curcumin were identified using a TaqMan human miRNA array followed by real-time PCR, out of which, the top 6 miRNAs (miR-302b-3p, miR-335-5p, miR-338-3p, miR-34c-5p, miR-29c-3p and miR-34a-35p) with more verified target genes and TFs than other miRNAs as confirmed by a literature review were selected for further analysis...
2017: PloS One
https://www.readbyqxmd.com/read/28230276/dissection-of-regulatory-elements-during-direct-conversion-of-somatic-cells-into-neurons
#3
Tahereh Soleimani, Nafiseh Falsafi, Hossein Fallahi
A revolutionary approach that involves direct conversion of somatic cells into almost any other types of cells showed promising results for regenerative medicine. Currently, producing valuable cell types including neurons, cardiomyocytes and hepatocytes through direct conversion of somatic cells appear to be a feasible option for regenerative medicine. The process involves inducing the cells by chemical cocktails or by expression of different types of transcription factors. In this concept, in vitro neurogenesis considered to be able to produce neuron cells to replace damaged neurons especially in Alzheimer and Parkinson disease...
February 23, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28229088/glutathione-induces-gaba-release-through-p2x7r-activation-on-m%C3%A3-ller-glia
#4
Hércules Rezende Freitas, Ricardo A de Melo Reis
The retinal tissue of warm-blooded vertebrates performs surprisingly complex and accurate transduction of visual information. To achieve precision, a multilayered neuroglia structure is established throughout the embryonic development, and the presence of radial Müller (glial) cells ensure differentiation, growth and survival for the neuronal elements within retinal environment. It is assumed that Müller cells serve as a dynamic reservoir of progenitors, capable of expressing transcription factors, differentiating and proliferating as either neuronal or glial cells depending on extrinsic cues...
2017: Neurogenesis (Austin, Tex.)
https://www.readbyqxmd.com/read/28227255/multi-omic-approaches-for-characterization-of-hepatocellular-carcinoma
#5
Habtom W Ressom, Cristina Di Poto, Alessia Ferrarini, Yunli Hu, Mohammad R Nezami Ranjbar, Ehwang Song, Rency S Varghese, Minkun Wang, Shiyue Zhou, Rui Zhu, Yiming Zuo, Mahlet G Tadesse, Yehia Mechref, Habtom W Ressom, Cristina Di Poto, Alessia Ferrarini, Yunli Hu, Mohammad R Nezami Ranjbar, Ehwang Song, Rency S Varghese, Minkun Wang, Shiyue Zhou, Rui Zhu, Yiming Zuo, Mahlet G Tadesse, Yehia Mechref, Mahlet G Tadesse, Shiyue ZhOU, Rui Zhu, Yehia Mechref, Alessia Ferrarini, Cristina Di Poto, Yiming Zuo, Habtom W Ressom, Mohammad R Nezami Ranjbar, Ehwang Song, Minkun Wang, Rency S Varghese, Yunli Hu
Multi-omic approaches offer the opportunity to characterize complex diseases such as cancer at various molecular levels. In this paper, we present transcriptomic, proteomic/glycoproteomic, glycomic, and metabolomic (TPGM) data we acquired by analysis of liver tissues from hepatocellular carcinoma (HCC) cases and patients with liver cirrhosis. We evaluated changes in the levels of transcripts, proteins, glycans, and metabolites between tumor and cirrhotic tissues by statistical methods. We demonstrated the potential of multi-omic approaches and network analysis to investigate the interactions among these biomolecules in the progression of liver cirrhosis to HCC...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28224498/differential-gene-expression-dex-and-alternative-splicing-events-ase-for-temporal-dynamic-processes-using-hmms-and-hierarchical-bayesian-modeling-approaches
#6
Sunghee Oh, Seongho Song
In gene expression profile, data analysis pipeline is categorized into four levels, major downstream tasks, i.e., (1) identification of differential expression; (2) clustering co-expression patterns; (3) classification of subtypes of samples; and (4) detection of genetic regulatory networks, are performed posterior to preprocessing procedure such as normalization techniques. To be more specific, temporal dynamic gene expression data has its inherent feature, namely, two neighboring time points (previous and current state) are highly correlated with each other, compared to static expression data which samples are assumed as independent individuals...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28223918/rpph1-upregulates-cdc42-expression-and-promotes-hippocampal-neuron-dendritic-spine-formation-by-competing-with-mir-330-5p
#7
Yifei Cai, Ziling Sun, Huizhen Jia, Hongxue Luo, Xiaoyang Ye, Qi Wu, Yi Xiong, Wei Zhang, Jun Wan
Alzheimer's disease (AD) is a heterogeneous neurodegenerative disease. Recent studies employing microRNA-seq and genome-wide sequencing have identified some non-coding RNAs that are influentially involved in AD pathogenesis. Non-coding RNAs can compete with other endogenous RNAs by microRNA response elements (MREs) and manipulate biological processes, such as tumorigenesis. However, only a few non-coding RNAs have been reported in the pathogenesis of AD. In this study, we constructed the first competing endogenous RNA (ceRNA) network leveraging whole transcriptome sequencing and a previously studied microRNA-seq of APPswe/PS1ΔE9 transgenic mice...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28223714/comparative-physiological-and-transcriptomic-analyses-provide-integrated-insight-into-osmotic-cold-and-salt-stress-tolerance-mechanisms-in-banana
#8
Wei Hu, Zehong Ding, Weiwei Tie, Yan Yan, Yang Liu, Chunlai Wu, Juhua Liu, Jiashui Wang, Ming Peng, Biyu Xu, Zhiqiang Jin
The growth, development, and production of banana plants are constrained by multiple abiotic stressors. However, it remains elusive for the tolerance mechanisms of banana responding to multiple abiotic stresses. In this study, we found that Fen Jiao (FJ) was more tolerant to osmotic, cold, and salt stresses than BaXi Jiao (BX) by phenotypic and physiological analyses. Comparative transcriptomic analyses highlighted stress tolerance genes that either specifically regulated in FJ or changed more than twofold in FJ relative to BX after treatments...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28223135/cell-physiology-regulation-by-hypoxia-inducible-factor-1-targeting-oxygen-related-nanomachineries-of-hypoxic-cells
#9
REVIEW
Morteza Eskandani, Somayeh Vandghanooni, Jaleh Barar, Hossein Nazemiyeh, Yadollah Omidi
Any dysfunctionality in maintaining the oxygen homeostasis by mammalian cells may elicit hypoxia/anoxia, which results in inescapable oxidative stress and possible subsequent detrimental impacts on certain cells/tissues with high demands to oxygen molecules. The ischemic damage in turn can trigger initiation of a number of diseases including organs ischemia, metabolic disorders, inflammatory diseases, different types of malignancies, and alteration in wound healing process. Thus, full comprehension of molecular mechanism(s) and cellular physiology of the oxygen homeostasis is the cornerstone of the mammalian cells metabolism, energetic pathways and health and disease conditions...
February 13, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28222515/meta-analysis-of-parkinson-s-disease-and-alzheimer-s-disease-revealed-commonly-impaired-pathways-and-dysregulation-of-nrf2-dependent-genes
#10
Qian Wang, Wen-Xing Li, Shao-Xing Dai, Yi-Cheng Guo, Fei-Fei Han, Jun-Juan Zheng, Gong-Hua Li, Jing-Fei Huang
Many lines of evidence suggest that Parkinson's disease (PD) and Alzheimer's disease (AD) have common characteristics, such as mitochondrial dysfunction and oxidative stress. As the underlying molecular mechanisms are unclear, we perform a meta-analysis with 9 microarray datasets of PD studies and 7 of AD studies to explore it. Functional enrichment analysis revealed that PD and AD both showed dysfunction in the synaptic vesicle cycle, GABAergic synapses, phagosomes, oxidative phosphorylation, and TCA cycle pathways, and AD had more enriched genes...
February 7, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28222153/dissecting-nutrient-related-co-expression-networks-in-phosphate-starved-poplars
#11
Mareike Kavka, Andrea Polle
Phosphorus (P) is an essential plant nutrient, but its availability is often limited in soil. Here, we studied changes in the transcriptome and in nutrient element concentrations in leaves and roots of poplars (Populus × canescens) in response to P deficiency. P starvation resulted in decreased concentrations of S and major cations (K, Mg, Ca), in increased concentrations of N, Zn and Al, while C, Fe and Mn were only little affected. In roots and leaves >4,000 and >9,000 genes were differently expressed upon P starvation...
2017: PloS One
https://www.readbyqxmd.com/read/28219524/the-function-and-transcriptome-analysis-of-a-bzip-transcription-factor-cgap1-in-colletotrichum-gloeosporioides
#12
Xiaoyu Li, Yateng Wu, Zhiqiang Liu, Chenghui Zhang
Colletotrichum gloeosporioides is an important pathogen of anthracnose, which is able to infect numerous crops in tropical and subtropical regions, causing great economic losses. To investigate the fungal response to host-generated reactive oxygen species (ROS), we cloned and characterized the CgAP1 gene of C. gloeosporioides. CgAP1 encoded a bZIP transcription factor which had a bZIP DNA-binding domain and two cysteine-rich domains structurally and functionally related to Saccharomyces cerevisiae YAP1. Deletion of CgAP1 in C...
April 2017: Microbiological Research
https://www.readbyqxmd.com/read/28218277/mir-203-enhances-let-7-biogenesis-by-targeting-lin28b-to-suppress-tumor-growth-in-lung-cancer
#13
Yong Zhou, Hongwei Liang, Zhicong Liao, Yanbo Wang, Xiuting Hu, Xi Chen, Lin Xu, Zhibin Hu
Human cancers often exhibit increased microRNA (miRNA) biogenesis and global aberrant expression of miRNAs; thus, targeting the miRNA biogenesis pathway represents a novel strategy for cancer therapy. Here, we report that miR-203 enhances the biogenesis of tumor suppressor let-7 in lung cancer by directly targeting LIN28B. Specially, we found that the LIN28B protein levels were dramatically increased in lung cancer tissues, but its mRNA levels did not differ significantly, suggesting that a post-transcriptional mechanism is involved in LIN28B regulation...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28217809/-generation-and-phenotype-analysis-of-zebrafish-mutations-of-obesity-related-genes-lepr-and-mc4r
#14
Fei Fei, Shao-Yang Sun, Yu-Xiao Yao, Xu Wang
Obesity has become a severe public health problem across the world, and seriously affects the health and life quality of human beings. Here we generated lepr and mc4r mutant zebrafish via the CRISPR/Cas9 technique, and performed morphological and functional characterizations of those mutants. We observed that there was no significant phenotypic difference between homozygous mutants and wild-type controls before 2.5 months post-fertilization (mpf). However, the adult lepr(-/-) and mc4r(-/-) individuals displayed increased food intake, heavier weight, and higher body fat percentage, the characteristics of obesity phenotypes...
February 25, 2017: Sheng Li Xue Bao: [Acta Physiologica Sinica]
https://www.readbyqxmd.com/read/28217746/integrated-regulatory-and-metabolic-networks-of-the-marine-diatom-phaeodactylum-tricornutum-predict-the-response-to-rising-co2-levels
#15
Jennifer Levering, Christopher L Dupont, Andrew E Allen, Bernhard O Palsson, Karsten Zengler
Diatoms are eukaryotic microalgae that are responsible for up to 40% of the ocean's primary productivity. How diatoms respond to environmental perturbations such as elevated carbon concentrations in the atmosphere is currently poorly understood. We developed a transcriptional regulatory network based on various transcriptome sequencing expression libraries for different environmental responses to gain insight into the marine diatom's metabolic and regulatory interactions and provide a comprehensive framework of responses to increasing atmospheric carbon levels...
January 2017: MSystems
https://www.readbyqxmd.com/read/28217744/effect-of-tcdr-mutation-on-sporulation-in-the-epidemic-clostridium-difficile-strain-r20291
#16
Brintha P Girinathan, Marc Monot, Daniel Boyle, Kathleen N McAllister, Joseph A Sorg, Bruno Dupuy, Revathi Govind
Clostridium difficile is an important nosocomial pathogen and the leading cause of hospital-acquired diarrhea. Antibiotic use is the primary risk factor for the development of C. difficile-associated disease because it disrupts normally protective gut flora and enables C. difficile to colonize the colon. C. difficile damages host tissue by secreting toxins and disseminates by forming spores. The toxin-encoding genes, tcdA and tcdB, are part of a pathogenicity locus, which also includes the tcdR gene that codes for TcdR, an alternate sigma factor that initiates transcription of tcdA and tcdB genes...
January 2017: MSphere
https://www.readbyqxmd.com/read/28217689/multiple-roles-of-myc-in-integrating-regulatory-networks-of-pluripotent-stem-cells
#17
REVIEW
Luca Fagnocchi, Alessio Zippo
Pluripotent stem cells (PSCs) are defined by their self-renewal potential, which permits their unlimited propagation, and their pluripotency, being able to generate cell of the three embryonic lineages. These properties render PSCs a valuable tool for both basic and medical research. To induce and stabilize the pluripotent state, complex circuitries involving signaling pathways, transcription regulators and epigenetic mechanisms converge on a core transcriptional regulatory network of PSCs, thus determining their cell identity...
2017: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/28217095/endogenous-protein-interactome-of-human-udp-glucuronosyltransferases-exposed-by-untargeted-proteomics
#18
Michèle Rouleau, Yannick Audet-Delage, Sylvie Desjardins, Mélanie Rouleau, Camille Girard-Bock, Chantal Guillemette
The conjugative metabolism mediated by UDP-glucuronosyltransferase enzymes (UGTs) significantly influences the bioavailability and biological responses of endogenous molecule substrates and xenobiotics including drugs. UGTs participate in the regulation of cellular homeostasis by limiting stress induced by toxic molecules, and by controlling hormonal signaling networks. Glucuronidation is highly regulated at genomic, transcriptional, post-transcriptional and post-translational levels. However, the UGT protein interaction network, which is likely to influence glucuronidation, has received little attention...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28217086/increased-sparsity-of-hippocampal-ca1-neuronal-ensembles-in-a-mouse-model-of-down-syndrome-assayed-by-arc-expression
#19
Constance L Smith-Hicks, Peiling Cai, Alena V Savonenko, Roger H Reeves, Paul F Worley
Down syndrome (DS) is the leading chromosomal cause of intellectual disability, yet the neural substrates of learning and memory deficits remain poorly understood. Here, we interrogate neural networks linked to learning and memory in a well-characterized model of DS, the Ts65Dn mouse. We report that Ts65Dn mice exhibit exploratory behavior that is not different from littermate wild-type (WT) controls yet behavioral activation of Arc mRNA transcription in pyramidal neurons of the CA1 region of the hippocampus is altered in Ts65Dn mice...
2017: Frontiers in Neural Circuits
https://www.readbyqxmd.com/read/28217005/chromatin-based-epigenetic-regulation-of-plant-abiotic-stress-response
#20
Garima Pandey, Namisha Sharma, Pranav Pankaj Sahu, Manoj Prasad
Plants are continuously exposed to various abiotic and biotic factors limiting their growth and reproduction. In response, they need various sophisticated ways to adapt to adverse environmental conditions without compromising their proper development, reproductive success and eventually survival. This requires an intricate network to regulate gene expression at transcriptional and post-transcriptional levels, including epigenetic switches. Changes in chromatin modifications such as DNA and histone methylation have been observed in plants upon exposure to several abiotic stresses...
December 2016: Current Genomics
keyword
keyword
85408
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"