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Regulatory network

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https://www.readbyqxmd.com/read/29050308/the-lncrna-hoxa11-as-functions-as-a-competing-endogenous-rna-to-regulate-padi2-expression-by-sponging-mir-125a-5p-in-liver-metastasis-of-colorectal-cancer
#1
Dong Chen, Qiang Sun, Lufei Zhang, Xiaohu Zhou, Xiaofei Cheng, Dongkai Zhou, Feng Ye, Jianjiang Lin, Weilin Wang
Several long non-coding RNAs (lncRNAs) play important roles in the regulation of liver metastasis in colorectal cancer (CRC) patients. We previously described the potential involvement of HOMEOBOX A11 (HOXA11) antisense RNA (HOXA11-AS), miR-125a-5p, and peptidyl arginine deiminase 2 (PADI2) in promoting liver metastasis in CRC patients. In the present study, we verified the significant upregulation of HOXA11-AS and PADI2, as well as the downregulation of miR-125a-5p, in CRC patients with liver metastasis. Overexpression and knockdown studies of HOXA11-AS or PADI2, as well as gain-/loss-of-function studies of miR-125a-5p, revealed a positive correlation between HOXA11-AS and PADI2 and a negative correlation with miR-125a-5p in the regulation of liver metastasis in CRC cell lines...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29049397/the-transcriptional-regulator-lysg-rv1985c-of-mycobacterium-tuberculosis-activates-lyse-rv1986-in-a-lysine-dependent-manner
#2
Marie Schneefeld, Tobias Busche, Robert Geffers, Jörn Kalinowski, Franz-Christoph Bange
The Mycobacterium tuberculosis protein encoded by the Rv1986 gene is a target for memory T cells in patients with tuberculosis, and shows strong similarities to a lysine exporter LysE of Corynebacterium glutamicum. During infection, the pathogen Mycobacterium tuberculosis adapts its metabolism to environmental changes. In this study, we found that the expression of Rv1986 is controlled by Rv1985c. Rv1985c is located directly upstream of Rv1986 with an overlapping promoter region between both genes. Semiquantitative reverse transcription PCR using an isogenic mutant of Mycobacterium tuberculosis lacking Rv1985c showed that in the presence of lysine, Rv1985c protein positively upregulated the expression of Rv1986...
2017: PloS One
https://www.readbyqxmd.com/read/29048388/regulatory-t-cells-and-tumor-associated-macrophages-in-the-tumor-microenvironment-in-non-muscle-invasive-bladder-cancer-treated-with-intravesical-bacille-calmette-gu%C3%A3-rin-a-long-term-follow-up-study-of-a-japanese-cohort
#3
Makito Miyake, Yoshihiro Tatsumi, Daisuke Gotoh, Sayuri Ohnishi, Takuya Owari, Kota Iida, Kenta Ohnishi, Shunta Hori, Yosuke Morizawa, Yoshitaka Itami, Yasushi Nakai, Takeshi Inoue, Satoshi Anai, Kazumasa Torimoto, Katsuya Aoki, Keiji Shimada, Noboru Konishi, Nobumichi Tanaka, Kiyohide Fujimoto
The clinical significance of regulatory T cells (Treg) and tumor-associated macrophages (TAM) in the tumor microenvironment of human bladder cancer remains unclear. The aim of this study is to explore their relevance to oncological features in non-muscle invasive bladder cancer (NMIBC). We carried out immunohistochemical analysis of forkhead box P3 (FOXP3, Treg maker), CD204 (TAM marker), and interleukin-6 (IL6) using surgical specimens obtained from 154 NMIBC patients. The Treg and TAM counts surrounding the cancer lesion and IL6-positive cancer cell counts were evaluated against clinicopathological variables...
October 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29046998/metabolite-profiling-and-associated-gene-expression-reveal-two-metabolic-shifts-during-the-seed-to-seedling-transition-in-arabidopsis-thaliana
#4
Anderson Tadeu Silva, Wilco Ligterink, Henk W M Hilhorst
Metabolic and transcriptomic correlation analysis identified two distinctive profiles involved in the metabolic preparation for seed germination and seedling establishment, respectively. Transcripts were identified that may control metabolic fluxes. The transition from a quiescent metabolic state (dry seed) to the active state of a vigorous seedling is crucial in the plant's life cycle. We analysed this complex physiological trait by measuring the changes in primary metabolism that occur during the transition in order to determine which metabolic networks are operational...
October 18, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29046437/modulation-of-global-transcriptional-regulatory-networks-as-a-strategy-for-increasing-kanamycin-resistance-of-the-translational-elongation-factor-g-mutants-in-escherichia-coli
#5
Aalap Mogre, Reshma T V, Aswin Sai Narain Seshasayee
Evolve and resequence experiments have provided us a tool to understand bacterial adaptation to antibiotics. In our previous work, we had used short term evolution to isolate mutants resistant to the ribosome targeting antibiotic kanamycin, and reported that Escherichia coli develops low cost resistance to kanamycin via  different point mutations in the translation Elongation Factor-G (EF-G). Furthermore, we had shown that the resistance of EF-G mutants could be increased by second site mutations in the genes rpoD / cpxA / topA / cyaA Mutations in three of these genes had been discovered in earlier screens for aminoglycoside resistance...
October 18, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29046401/reconstructing-the-molecular-function-of-genetic-variation-in-regulatory-networks
#6
Roni Wilentzik, Chun Jimmie Ye, Irit Gat-Viks
During the past decade, genetic studies have recognized hundreds of polymorphic DNA loci ('reQTLs') as potential contributors to inter-individual variation in transcriptional response to stimulations. Such reQTLs commonly affect the transduction of signals along the regulatory network that controls gene transcription. Identifying the pathways through which reQTLs perturb the underlying network has been a major challenge. Here we present GEVIN, a methodology that simultaneously identifies a reQTL and the particular pathway at which the reQTL affects downstream signal transduction along the network...
October 18, 2017: Genetics
https://www.readbyqxmd.com/read/29045542/bacterial-artificial-chromosomes-as-recombinant-reporter-constructs-to-investigate-gene-expression-and-regulation-in-echinoderms
#7
Katherine M Buckley, Ping Dong, R Andrew Cameron, Jonathan P Rast
Genome sequences contain all the necessary information-both coding and regulatory sequences-to construct an organism. The developmental process translates this genomic information into a three-dimensional form. One interpretation of this translation process can be described using gene regulatory network (GRN) models, which are maps of interactions among regulatory gene products in time and space. As high throughput investigations reveal increasing complexity within these GRNs, it becomes apparent that efficient methods are required to test the necessity and sufficiency of regulatory interactions...
October 17, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29043977/a-protein-phosphatase-network-controls-the-temporal-and-spatial-dynamics-of-differentiation-commitment-in-human-epidermis
#8
Ajay Mishra, Benedicte Oules, Angela Oliveira Pisco, Tony Ly, Kifayathullah Liakath-Ali, Gernot Walko, Priyalakshmi Viswanathan, Matthieu Tihy, Jagdeesh Nijjher, Sara-Jane Dunn, Angus I Lamond, Fiona M Watt
Epidermal homeostasis depends on a balance between stem cell renewal and terminal differentiation. The transition between the two cell states, termed commitment, is poorly understood. Here we characterise commitment by integrating transcriptomic and proteomic data from disaggregated primary human keratinocytes held in suspension to induce differentiation. Cell detachment induces several protein phosphatases, five of which - DUSP6, PPTC7, PTPN1, PTPN13 and PPP3CA - promote differentiation by negatively regulating ERK MAPK and positively regulating AP1 transcription factors...
October 18, 2017: ELife
https://www.readbyqxmd.com/read/29042584/the-role-of-chromatin-density-in-cell-population-heterogeneity-during-stem-cell-differentiation
#9
Mahdi Golkaram, Jiwon Jang, Stefan Hellander, Kenneth S Kosik, Linda R Petzold
We incorporate three-dimensional (3D) conformation of chromosome (Hi-C) and single-cell RNA sequencing data together with discrete stochastic simulation, to explore the role of chromatin reorganization in determining gene expression heterogeneity during development. While previous research has emphasized the importance of chromatin architecture on activation and suppression of certain regulatory genes and gene networks, our study demonstrates how chromatin remodeling can dictate gene expression distribution by folding into distinct topological domains...
October 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29042395/nuclear-receptor-profiling-in-prostatospheroids-and-castration-resistant-prostate-cancer
#10
Zhu Wang, Dinglan Wu, Chi-Fai Ng, Jeremy Yuen-Chun Teoh, Shan Yu, Yuliang Wang, Franky Leung Chan
Nuclear receptors (NRs), which belong to a superfamily of transcription factors and consist of a total of 48 members in humans, govern the expression of genes involved in a board range of developmental, reproductive, metabolic and immunological programs. Given the significant importance of androgen receptor and a few known NRs in the progression of prostate cancer, we surveyed the expression profiles of the entire NR superfamily in three-dimensional (3D) cultured prostatospheroids derived from different prostate cancer cell lines and a tumor xenograft model of castration-resistant prostate cancer VCaP-CRPC by quantitative real-time RT-PCR...
October 17, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/29042082/the-proto-oncogene-tyrosine-protein-kinase-src-is-essential-for-macrophage-myofibroblast-transition-during-renal-scarring
#11
Patrick Ming-Kuen Tang, Shuang Zhou, Chun-Jie Li, Jinyue Liao, Jun Xiao, Qing-Ming Wang, Guang-Yu Lian, Jinhong Li, Xiao-Ru Huang, Ka-Fai To, Chi-Fai Ng, Charing Ching-Ning Chong, Ronald Ching-Wa Ma, Tin-Lap Lee, Hui-Yao Lan
Src activation has been associated with fibrogenesis after kidney injury. Macrophage-myofibroblast transition is a newly identified process to generate collagen-producing myofibroblasts locally in the kidney undergoing fibrosis in a TGF-β/Smad3-dependent manner. The potential role of the macrophage-myofibroblast transition in Src-mediated renal fibrosis is unknown. In studying this by RNA sequencing at single-cell resolution, we uncovered a unique Src-centric regulatory gene network as a key underlying mechanism of macrophage-myofibroblast transition...
October 14, 2017: Kidney International
https://www.readbyqxmd.com/read/29041960/substantial-contribution-of-genetic-variation-in-the-expression-of-transcription-factors-to-phenotypic-variation-revealed-by-erd-gwas
#12
Hung-Ying Lin, Qiang Liu, Xiao Li, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J Scanlon, Dan Nettleton, Patrick S Schnable
BACKGROUND: There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits. RESULTS: The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expression variation across tissues or genotypes. Transcription factors are enriched among genes with the most variation in expression across tissues, as well as among genes with higher-than-median levels of variation in expression across genotypes...
October 17, 2017: Genome Biology
https://www.readbyqxmd.com/read/29041935/a-long-non-coding-rna-hottip-expression-is-associated-with-disease-progression-and-predicts-outcome-in-small-cell-lung-cancer-patients
#13
Yanqin Sun, Yuanyuan Zhou, Yifeng Bai, Qiongyao Wang, Jiarong Bao, Yingshan Luo, Ying Guo, Linlang Guo
BACKGROUND: Despite progress in treatment of small cell lung cancer (SCLC), the biology of the tumor still remains poorly understood. Recently, we globally investigated the contributions of lncRNA in SCLC with a special focus on sponge regulatory network. Here we report lncRNA HOTTIP, which is specifically amplified in SCLC, is associated with SCLC proliferation and poor prognosis of patients. METHODS: RT-qPCR was used to investigate the expression of HOTTIP in SCLC tissues and cell lines...
October 17, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/29041906/from-provocation-to-aggression-the-neural-network
#14
Jonathan Repple, Christina M Pawliczek, Bianca Voss, Steven Siegel, Frank Schneider, Nils Kohn, Ute Habel
BACKGROUND: In-vivo observations of neural processes during human aggressive behavior are difficult to obtain, limiting the number of studies in this area. To address this gap, the present study implemented a social reactive aggression paradigm in 29 healthy men, employing non-violent provocation in a two-player game to elicit aggressive behavior in fMRI settings. RESULTS: Participants responded more aggressively after high provocation reflected in taking more money from their opponents...
October 17, 2017: BMC Neuroscience
https://www.readbyqxmd.com/read/29040739/papaya-cpein3a-and-cpnac2-cooperatively-regulate-carotenoid-biosynthesis-related-genes-cppds2-4-cplcy-e-and-cpchy-b-during-fruit-ripening
#15
Chang-Chun Fu, Yan-Chao Han, Jian-Fei Kuang, Jian-Ye Chen, Wang-Jin Lu
Papaya is an important tropical fruit with a rich source of carotenoids. The ripening of papaya is a physiological and metabolic process with remarkable changes including carotenoids accumulation, which depends primarily on the action of ethylene. Ethylene response is mediated by a transcriptional cascade involving the transcription factor families of EIN3/EILs and ERFs. Although ERF members have been reported to control carotenoids production in Arabidopsis and tomato, whether EIN3/EILs are also involved in carotenoid biosynthesis during fruit ripening remains unclear...
October 12, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29040639/the-medical-science-dmz-a-network-design-pattern-for-data-intensive-medical-science
#16
Sean Peisert, Eli Dart, William Barnett, Edward Balas, James Cuff, Robert L Grossman, Ari Berman, Anurag Shankar, Brian Tierney
Objective: We describe a detailed solution for maintaining high-capacity, data-intensive network flows (eg, 10, 40, 100 Gbps+) in a scientific, medical context while still adhering to security and privacy laws and regulations. Materials and Methods: High-end networking, packet-filter firewalls, network intrusion-detection systems. Results: We describe a "Medical Science DMZ" concept as an option for secure, high-volume transport of large, sensitive datasets between research institutions over national research networks, and give 3 detailed descriptions of implemented Medical Science DMZs...
October 6, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29040437/sperm-release-at-spermiation-is-regulated-by-changes-in-the-organization-of-actin-and-microtubule-based-cytoskeletons-at-the-apical-ectoplasmic-specialization-a-study-using-the-adjudin-model
#17
Linxi Li, Elizabeth I Tang, Haiqi Chen, Qingquan Lian, Renshan Ge, Bruno Silvestrini, C Yan Cheng
The mechanism that regulates sperm release at spermiation is unknown. Herein, we utilized an animal model wherein rats were treated with adjudin, 1-(2,4-dichlorobenzyl)-1H-indazole-3-carbohydrazide, via oral gavage to induce premature release of elongating/elongated spermatid, followed by round spermatids and spermatocytes. Spermatid release mimicking spermiation occurred within 6-12 h following adjudin treatment and by 96 h, virtually all tubules were devoid of spermatids. Using this model, we tracked the organization of F-actin and microtubules (MTs) by immunofluorescence microscopy, and the association of actin or MT regulatory proteins that either promote or demolish cytoskeletal integrity through changes in the organization of actin-microfilaments or MTs by co-immunoprecipitation...
October 12, 2017: Endocrinology
https://www.readbyqxmd.com/read/29040384/selansi-a-toolbox-for-simulation-of-stochastic-gene-regulatory-networks
#18
Manuel Pájaro, Irene Otero-Muras, Carlos Vázquez, Antonio A Alonso
Motivation: Gene regulation is inherently stochastic. In many applications concerning Systems and Synthetic Biology such as the reverse engineering and the de novo design of genetic circuits, stochastic effects (yet potentially crucial) are often neglected due to the high computational cost of stochastic simulations. With advances in these fields there is an increasing need of tools providing accurate approximations of the stochastic dynamics of gene regulatory networks (GRNs) with reduced computational effort...
October 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29040382/generalized-correlation-measure-using-count-statistics-for-gene-expression-data-with-ordered-samples
#19
Y X Rachel Wang, Ke Liu, Elizabeth Theusch, Jerome I Rotter, Marisa W Medina, Michael S Waterman, Haiyan Huang
Motivation: Capturing association patterns in gene expression levels under different conditions or time points is important for inferring gene regulatory interactions. In practice, temporal changes in gene expression may result in complex association patterns that require more sophisticated detection methods than simple correlation measures. For instance, the effect of regulation may lead to time-lagged associations and interactions local to a subset of samples. Furthermore, expression profiles of interest may not be aligned or directly comparable (e...
October 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29040362/prediction-of-protein-protein-interactions-between-fungus-magnaporthe-grisea-and-rice-oryza-sativa-l
#20
Shiwei Ma, Qi Song, Huan Tao, Andrew Harrison, Shaobo Wang, Wei Liu, Shoukai Lin, Ziding Zhang, Yufang Ai, Huaqin He
Rice blast disease caused by the fungus Magnaporthe grisea (M. grisea) is one of the most serious diseases for the cultivated rice Oryza sativa (O. sativa). A key factor causing rice blast disease and defense might be protein-protein interactions (PPIs) between rice and fungus. In this research, we have developed a computational pipeline to predict PPIs between blast fungus and rice. After cross-prediction by interolog-based and domain-based method, we achieved 532 potential PPIs between 27 fungus proteins and 236 rice proteins...
October 11, 2017: Briefings in Bioinformatics
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