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https://www.readbyqxmd.com/read/28526138/gata-factors-master-regulators-of-gene-expression-in-trophoblast-progenitors
#1
Soumen Paul, Pratik Home, Bhaswati Bhattacharya, Soma Ray
Mammalian reproduction is critically dependent on trophoblast cells, which ensure embryo implantation and placentation. Development of trophoblast cell lineages is a multi-step process and relies upon proper spatial and temporal gene expression, which is regulated by multiple transcription factors. However, most of the transcription factors that are implicated in trophoblast development regulate gene expression at a specific developmental stage or in a specific trophoblast subtype. In contrast, recent studies from our group and other laboratories indicate that conserved GATA family of transcription factors, GATA2 and GATA3, are important to regulate gene expression at multiple stages of trophoblast development...
May 10, 2017: Placenta
https://www.readbyqxmd.com/read/28525642/dynamics-of-sequestration-based-gene-regulatory-cascades
#2
Tatenda Shopera, William R Henson, Tae Seok Moon
Gene regulatory cascades are ubiquitous in biology. Because regulatory cascades are integrated within complex networks, their quantitative analysis is challenging in native systems. Synthetic biologists have gained quantitative insights into the properties of regulatory cascades by building simple circuits, but sequestration-based regulatory cascades remain relatively unexplored. Particularly, it remains unclear how the cascade components collectively control the output dynamics. Here, we report the construction and quantitative analysis of the longest sequestration-based cascade in Escherichia coli...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28523539/the-role-of-noncoding-rnas-in-neurodevelopmental-disorders-the-case-of-rett-syndrome
#3
Aida Obiols-Guardia, Sònia Guil
Current technologies have demonstrated that only a small fraction of our genes encode for protein products. The vast majority of the human transcriptome corresponds to noncoding RNA (ncRNA) of different size, localization, and expression profile. Despite the fact that a biological function remains yet to be determined for most ncRNAs, growing evidence points to their crucial regulatory roles at all stages in gene expression regulation, including transcriptional and posttranscriptional control, so that proper cell homeostasis seems to depend largely on a variety of ncRNA-mediated regulatory networks...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28522458/a-key-role-for-apoplastic-h2o2-in-norway-spruce-phenolic-metabolism
#4
Teresa Laitinen, Kris Morreel, Nicolas Delhomme, Adrien Gauthier, Bastian Schiffthaler, Kaloian Nickolov, Günter Brader, Kean-Jin Lim, Teemu H Teeri, Nathaniel R Street, Wout A Boerjan, Anna Karkonen
Apoplastic events such as monolignol oxidation and lignin polymerization are difficult to study in intact trees. To investigate the role of apoplastic H2O2 in gymnosperm phenolic metabolism, an extracellular lignin-forming cell culture of Norway spruce (Picea abies) was used as a research model. Scavenging of apoplastic H2O2 by KI repressed lignin formation, in line with peroxidases activating monolignols for lignin polymerization. Time course analyses coupled to candidate substrate product pair network propagation revealed differential accumulation of low-molecular-weight phenolics, including (glycosylated) oligolignols, (glycosylated) flavonoids and proanthocyanidins, in lignin-forming and H2O2-scavenging cultures, and supported that monolignols are oxidatively coupled not only in the cell wall, but also in the cytoplasm where they are coupled to other monolignols and proanthocyanidins...
May 18, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28521446/candidate-mirnas-and-pathogenesis-investigation-for-hepatocellular-carcinoma-based-on-bioinformatics-analysis
#5
Wenbin Ding, Haixia Yang, Shenchu Gong, Weixiang Shi, Jing Xiao, Jinhua Gu, Yilang Wang, Bosheng He
The present study aimed to explore the mechanisms behind the development and progression of hepatocellular carcinoma (HCC) and identify information regarding HCC-related microRNAs (miRNAs) or marker genes for the gene therapy of HCC. Gene expression profile of GSE67882, generated from 4 hepatitis B virus infected HCC tissue samples (HCC group) and 8 chronic hepatitis B tissue samples with no fibrosis (control group) were downloaded from the Gene Expression Omnibus database. The differentially expressed miRNAs functional enrichment and pathway analyses of HCC were revealed, followed by transcription factor-miRNA interaction network construction and analyses...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28521423/molecular-dysexpression-in-gastric-cancer-revealed-by-integrated-analysis-of-transcriptome-data
#6
Xiaomei Li, Weiwei Dong, Xueling Qu, Huixia Zhao, Shuo Wang, Yixin Hao, Qiuwen Li, Jianhua Zhu, Min Ye, Wenhua Xiao
Gastric cancer (GC) is often diagnosed in the advanced stages and is associated with a poor prognosis. Obtaining an in depth understanding of the molecular mechanisms of GC has lagged behind compared with other cancers. This study aimed to identify candidate biomarkers for GC. An integrated analysis of microarray datasets was performed to identify differentially expressed genes (DEGs) between GC and normal tissues. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were then performed to identify the functions of the DEGs...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28521415/bioinformatics-analysis-of-dysregulated-micrornas-in-the-nipple-discharge-of-patients-with-breast-cancer
#7
Kai Zhang, Ya-Wen Wang, Rong Ma
MicroRNAs (miRNAs/miRs) have been reported to be associated with the tumorigenesis and progression of various types of human cancer; however, the underlying mechanisms of this association remain unclear. The aim of the present study was to explore the potential functions of miRNAs in the development of breast cancer using bioinformatics analysis, based on the miRNA expression profile in nipple discharge. A previous study demonstrated the upregulation of miR-3646 and miR-4484, and the downregulation of miR-4732-5p in the nipple discharge of patients with breast cancer, compared with patients with benign breast lesions...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28521404/silencing-tak1-alters-gene-expression-signatures-in-bladder-cancer-cells
#8
Jimin Chen, Nan Zhang, Jiaming Wen, Zhewei Zhang
The aim of the present study was to identify the differentially expressed genes (DEGs) that are induced by the silencing of transforming growth factor-β-activated kinase 1 (TAK1) in bladder cancer cells and to analyze the potential biological effects. Dataset GSE52452 from mutant fibroblast growth factor receptor 3 (FGFR3) bladder cancer cells transfected with control siRNA or TAK1-specific siRNA was downloaded from Gene Expression Omnibus. The DEGs between the two groups were identified using Limma package following data pre-processing by Affy in Bioconductor...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28521289/role-of-transgelin-2-in-diabetes-associated-pancreatic-ductal-adenocarcinoma
#9
Yan Sun, Weiwei He, Man Luo, Yuhong Zhou, Guilin Chang, Weiying Ren, Kefen Wu, Xi Li, Jiping Shen, Xiaoping Zhao, Yu Hu
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with poor prognosis. Diabetes is a significant risk factor for PDAC and >50% of PDAC patients have concomitant diabetes. How diabetes influences the initiation and progression of PDAC remains elusive. Here, we show that transgelin-2 is dominantly expressed in PDAC tissues compared with adjacent normal tissues. The high level of transgelin-2 indicates poor survival of patients with PDAC. Remarkably, transgelin-2 expression is correlated with diabetic status...
April 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28521110/ethanol-induced-stress-response-of-staphylococcus-aureus
#10
Jasmine M Pando, Richard F Pfeltz, Jesus A Cuaron, Vijayaraj Nagarajan, Mukti N Mishra, Nathanial J Torres, Mohamed O Elasri, Brian J Wilkinson, John E Gustafson
Transcriptional profiles of two unrelated clinical methicillin-resistant S. aureus (MRSA) isolates were analyzed following 10 % v/v ethanol challenge (15 min), which arrested growth but did not reduce viability. Ethanol-induced stress (EIS) resulted in differential gene expression of 1091 genes, 600 common to both strains, of which 291 were up-regulated. With the exception of the down-regulation of genes involved with osmotic stress functions, EIS resulted in the up-regulation of genes that contribute to stress response networks, notably those altered by oxidative stress, protein quality control in general, and heat shock in particular...
May 18, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28520736/the-bantam-microrna-acts-through-numb-to-exert-cell-growth-control-and-feedback-regulation-of-notch-in-tumor-forming-stem-cells-in-the-drosophila-brain
#11
Yen-Chi Wu, Kyu-Sun Lee, Yan Song, Stephan Gehrke, Bingwei Lu
Notch (N) signaling is central to the self-renewal of neural stem cells (NSCs) and other tissue stem cells. Its deregulation compromises tissue homeostasis and contributes to tumorigenesis and other diseases. How N regulates stem cell behavior in health and disease is not well understood. Here we show that N regulates bantam (ban) microRNA to impact cell growth, a process key to NSC maintenance and particularly relied upon by tumor-forming cancer stem cells. Notch signaling directly regulates ban expression at the transcriptional level, and ban in turn feedback regulates N activity through negative regulation of the Notch inhibitor Numb...
May 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28520732/differential-gene-expression-along-the-animal-vegetal-axis-in-the-ascidian-embryo-is-maintained-by-a-dual-functional-protein-foxd
#12
Shin-Ichi Tokuhiro, Miki Tokuoka, Kenji Kobayashi, Atsushi Kubo, Izumi Oda-Ishii, Yutaka Satou
In many animal embryos, a specific gene expression pattern is established along the animal-vegetal axis soon after zygotic transcription begins. In the embryo of the ascidian Ciona intestinalis, soon after the division that separates animal and vegetal hemispheres into distinct blastomeres, maternal Gata.a and β-catenin activate specific genes in the animal and vegetal blastomeres, respectively. On the basis of these initial distinct gene expression patterns, gene regulatory networks promote animal cells to become ectodermal tissues and vegetal cells to become endomesodermal tissues and a part of the nerve cord...
May 17, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28520713/combining-inferred-regulatory-and-reconstructed-metabolic-networks-enhances-phenotype-prediction-in-yeast
#13
Zhuo Wang, Samuel A Danziger, Benjamin D Heavner, Shuyi Ma, Jennifer J Smith, Song Li, Thurston Herricks, Evangelos Simeonidis, Nitin S Baliga, John D Aitchison, Nathan D Price
Gene regulatory and metabolic network models have been used successfully in many organisms, but inherent differences between them make networks difficult to integrate. Probabilistic Regulation Of Metabolism (PROM) provides a partial solution, but it does not incorporate network inference and underperforms in eukaryotes. We present an Integrated Deduced And Metabolism (IDREAM) method that combines statistically inferred Environment and Gene Regulatory Influence Network (EGRIN) models with the PROM framework to create enhanced metabolic-regulatory network models...
May 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28518152/stat5-alters-the-state-of-transcriptional-networks-driving-aggressive-leukemia
#14
Sinisa Dovat, Kimberly J Payne
No abstract text is available yet for this article.
May 18, 2017: Nature Immunology
https://www.readbyqxmd.com/read/28515486/prognostic-significance-of-tcf21-mrna-expression-in-patients-with-lung-adenocarcinoma
#15
Jian Xiao, Aibin Liu, Xiaoxiao Lu, Xi Chen, Wei Li, Shuya He, Bixiu He, Qiong Chen
Several prognostic indicators have shown inconsistencies in patients of different genders with lung adenocarcinoma, indicating that these variations may be due to the different genetic background of males and females with lung adenocarcinoma. In this study, we first used the Gene-Cloud of Biotechnology Information (GCBI) bioinformatics platform to identify differentially expressed genes (DEGs) that eliminated gender differences between lung adenocarcinoma and normal lung tissues. Then, we screened out that transcription factor 21 (TCF21) is a hub gene among these DEGs by creating a gene co-expression network on the GCBI platform...
May 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28515341/bet-bromodomain-inhibition-suppresses-innate-inflammatory-and-profibrotic-transcriptional-networks-in-heart-failure
#16
Qiming Duan, Sarah McMahon, Priti Anand, Hirsh Shah, Sean Thomas, Hazel T Salunga, Yu Huang, Rongli Zhang, Aarathi Sahadevan, Madeleine E Lemieux, Jonathan D Brown, Deepak Srivastava, James E Bradner, Timothy A McKinsey, Saptarsi M Haldar
Despite current standard of care, the average 5-year mortality after an initial diagnosis of heart failure (HF) is about 40%, reflecting an urgent need for new therapeutic approaches. Previous studies demonstrated that the epigenetic reader protein bromodomain-containing protein 4 (BRD4), an emerging therapeutic target in cancer, functions as a critical coactivator of pathologic gene transactivation during cardiomyocyte hypertrophy. However, the therapeutic relevance of these findings to human disease remained unknown...
May 17, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28515146/transcriptome-of-wheat-inflorescence-development-from-spikelet-initiation-to-floral-patterning
#17
Nan Feng, Gaoyuan Song, Jiantao Guan, Kai Chen, Meiling Jia, Dehua Huang, Jiajie Wu, Lichao Zhang, Xiuying Kong, Shuaifeng Geng, Jun Liu, Aili Li, Long Mao
Early reproductive development in cereals is crucial for final grain number per spike, and hence the yield potential of the crop. To date, however, no systematic analyses of gene expression profiles during this important process have been conducted for common wheat (Triticum aestivum). Here, we studied the transcriptome profiles at four stages of early wheat reproductive development, from spikelet initiation to floral organ differentiation. K-means clustering and stage-specific transcript identification detected dynamically expressed homoeologs of important transcription regulators in spikelet and floral meristems that may be involved in spikelet initiation, floret meristem specification, and floral organ patterning, as inferred from their homologs in model plants...
May 17, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28514762/novel-circular-rna-expression-profiles-reflect-progression-of-patients-with-hypopharyngeal-squamous-cell-carcinoma
#18
Shengda Cao, Dongmin Wei, Xu Li, Jieyu Zhou, Wenming Li, Ye Qian, Zhanwang Wang, Guojun Li, Xinliang Pan, Dapeng Lei
Circular RNAs (circRNAs), a novel class of endogenous noncoding RNAs, have been shown to have important roles in a number of diseases, including several types of cancers. We hypothesized that circRNAs are involved in the pathogenesis of hypopharyngeal squamous cell carcinoma (HSCC). To test our hypothesis, we initially compared the expression profiles of circRNAs in 4 paired HSCC and adjacent normal tissue samples by using a circRNA microarray. The microarray data showed that 2392 circRNAs, including 1304 upregulated and 1088 downregulated circRNA transcripts, were significantly dysregulated in the HSCC tissues...
April 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28512473/vitamin-c-in-stem-cell-biology-impact-on-extracellular-matrix-homeostasis-and-epigenetics
#19
REVIEW
Cristina D'Aniello, Federica Cermola, Eduardo Jorge Patriarca, Gabriella Minchiotti
Transcription factors and signaling molecules are well-known regulators of stem cell identity and behavior; however, increasing evidence indicates that environmental cues contribute to this complex network of stimuli, acting as crucial determinants of stem cell fate. l-Ascorbic acid (vitamin C (VitC)) has gained growing interest for its multiple functions and mechanisms of action, contributing to the homeostasis of normal tissues and organs as well as to tissue regeneration. Here, we review the main functions of VitC and its effects on stem cells, focusing on its activity as cofactor of Fe(+2)/αKG dioxygenases, which regulate the epigenetic signatures, the redox status, and the extracellular matrix (ECM) composition, depending on the enzymes' subcellular localization...
2017: Stem Cells International
https://www.readbyqxmd.com/read/28512462/de-novo-transcriptome-profiling-of-flowers-flower-pedicels-and-pods-of-lupinus-luteus-yellow-lupine-reveals-complex-expression-changes-during-organ-abscission
#20
Paulina Glazinska, Waldemar Wojciechowski, Milena Kulasek, Wojciech Glinkowski, Katarzyna Marciniak, Natalia Klajn, Jacek Kesy, Jan Kopcewicz
Yellow lupine (Lupinus luteus L., Taper c.), a member of the legume family (Fabaceae L.), has an enormous practical importance. Its excessive flower and pod abscission represents an economic drawback, as proper flower and seed formation and development is crucial for the plant's productivity. Generative organ detachment takes place at the basis of the pedicels, within a specialized group of cells collectively known as the abscission zone (AZ). During plant growth these cells become competent to respond to specific signals that trigger separation and lead to the abolition of cell wall adhesion...
2017: Frontiers in Plant Science
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