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https://www.readbyqxmd.com/read/28324652/positive-feedback-genetic-circuit-incorporating-a-constitutively-active-mutant-gal3-into-yeast-gal-induction-system
#1
Shintaro Ryo, Jun Ishii, Toshihide Matsuno, Yasuyuki Nakamura, Daiki Matsubara, Masahiro Tominaga, Akihiko Kondo
The GAL expression system is the most frequently used induction technique in the yeast Saccharomyces cerevisiae. Here we report a simple but powerful genetic circuit for use with the GAL induction system. Briefly, an artificial positive feedback circuit was incorporated into the GAL regulatory network. We selected green fluorescent protein (GFP) as a reporter of GAL1 induction, and designed a strain that expressed a constitutively active Gal3 mutant protein (Gal3(c)) under control of the GAL10 promoter. In the resulting strain, GAL1 and GAL10 promoters regulate the expression of GFP and GAL3(c), respectively...
March 21, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28323865/the-microrna-302b-inhibited-insulin-like-growth-factor-binding-protein-2-signaling-pathway-induces-glioma-cell-apoptosis-by-targeting-nuclear-factor-ia
#2
Chin-Cheng Lee, Peng-Hsu Chen, Kuo-Hao Ho, Chwen-Ming Shih, Chia-Hsiung Cheng, Cheng-Wei Lin, Kur-Ta Cheng, Ann-Jeng Liu, Ku-Chung Chen
MicroRNAs are small noncoding RNAs that post-transcriptionally control the expression of genes involved in glioblastoma multiforme (GBM) development. Although miR-302b functions as a tumor suppressor, its role in GBM is still unclear. Therefore, this study comprehensively explored the roles of miR-302b-mediated gene networks in GBM cell death. We found that miR-302b levels were significantly higher in primary astrocytes than in GBM cell lines. miR-302b overexpression dose dependently reduced U87-MG cell viability and induced apoptosis through caspase-3 activation and poly(ADP ribose) polymerase degradation...
2017: PloS One
https://www.readbyqxmd.com/read/28319747/integration-of-in-silico-methods-and-computational-systems-biology-to-explore-endocrine-disrupting-chemical-binding-with-nuclear-hormone-receptors
#3
P Ruiz, A Sack, M Wampole, S Bobst, M Vracko
Thousands of potential endocrine-disrupting chemicals present difficult regulatory challenges. Endocrine-disrupting chemicals can interfere with several nuclear hormone receptors associated with a variety of adverse health effects. The U.S. Environmental Protection Agency (U.S. EPA) has released its reviews of Tier 1 screening assay results for a set of pesticides in the Endocrine Disruptor Screening Program (EDSP), and recently, the Collaborative Estrogen Receptor Activity Prediction Project (CERAPP) data...
March 9, 2017: Chemosphere
https://www.readbyqxmd.com/read/28319593/profiles-of-long-noncoding-rnas-in-hypertensive-rats-long-noncoding-rna-xr007793-regulates-cyclic-strain-induced-proliferation-and-migration-of-vascular-smooth-muscle-cells
#4
Qing-Ping Yao, Zhi-Wei Xie, Kai-Xuan Wang, Ping Zhang, Yue Han, Ying-Xin Qi, Zong-Lai Jiang
BACKGROUND: Long noncoding RNAs (lncRNAs) are being discovered in multiple diseases at a rapid pace. However, the contribution of lncRNAs to hypertension remains largely unknown. In hypertension, the vascular walls are exposed to abnormal mechanical cyclic strain, which leads to vascular remodelling. Here, we investigated the mechanobiological role of lncRNAs in hypertension. METHODS AND RESULTS: Differences in the lncRNAs and mRNAs between spontaneously hypertensive rats and Wistar-Kyoto rats were screened using a gene microarray...
March 17, 2017: Journal of Hypertension
https://www.readbyqxmd.com/read/28319331/morphogen-interpretation-concentration-time-competence-and-signaling-dynamics
#5
REVIEW
Andreas Sagner, James Briscoe
Tissue patterning during animal development is orchestrated by a handful of inductive signals. Most of these developmental cues act as morphogens, meaning they are locally produced secreted molecules that act at a distance to govern tissue patterning. The iterative use of the same signaling molecules in different developmental contexts demands that signal interpretation occurs in a highly context-dependent manner. Hence the interpretation of signal depends on the specific competence of the receiving cells. Moreover, it has become clear that the differential interpretation of morphogens depends not only on the level of signaling but also the signaling dynamics, particularly the duration of signaling...
March 20, 2017: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/28316977/microrna-mediating-networks-in-granulosa-cells-associated-with-ovarian-follicular-development
#6
Baoyun Zhang, Long Chen, Guangde Feng, Wei Xiang, Ke Zhang, Mingxing Chu, Pingqing Wang
Ovaries, which provide a place for follicular development and oocyte maturation, are important organs in female mammals. Follicular development is complicated physiological progress mediated by various regulatory factors including microRNAs (miRNAs). To demonstrate the role of miRNAs in follicular development, this study analyzed the expression patterns of miRNAs in granulosa cells through investigating three previous datasets generated by Illumina miRNA deep sequencing. Furthermore, via bioinformatic analyses, we dissected the associated functional networks of the observed significant miRNAs, in terms of interacting with signal pathways and transcription factors...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28316886/identification-of-dysregulated-genes-in-rheumatoid-arthritis-based-on-bioinformatics-analysis
#7
Ruihu Hao, Haiwei Du, Lin Guo, Fengde Tian, Ning An, Tiejun Yang, Changcheng Wang, Bo Wang, Zihao Zhou
BACKGROUND: Rheumatoid arthritis (RA) is a chronic auto-inflammatory disorder of joints. The present study aimed to identify the key genes in RA for better understanding the underlying mechanisms of RA. METHODS: The integrated analysis of expression profiling was conducted to identify differentially expressed genes (DEGs) in RA. Moreover, functional annotation, protein-protein interaction (PPI) network and transcription factor (TF) regulatory network construction were applied for exploring the potential biological roles of DEGs in RA...
2017: PeerJ
https://www.readbyqxmd.com/read/28316353/cassava-postharvest-physiological-deterioration-a-complex-phenomenon-involving-calcium-signaling-reactive-oxygen-species-and-programmed-cell-death
#8
REVIEW
Astride S M Djabou, Luiz J C B Carvalho, Qing X Li, Nicolas Niemenak, Songbi Chen
Postharvest physiological deterioration (PPD) of cassava (Manihot esculenta) storage roots is a complex physiological and biochemical process which involve many regulatory networks linked with specific proteins modulation and signaling transduction pathways. However, it is poorly understood regarding biological regulation, and the interactions among protein groups and signals to determine PPD syndrome in cassava storage roots. This review sheds some light on the possible molecular mechanisms involved in reactive oxygen species (ROS), calcium signaling transduction, and programmed cell death (PCD) in cassava PPD syndrome...
2017: Acta Physiologiae Plantarum
https://www.readbyqxmd.com/read/28316065/identification-of-key-genes-and-construction-of-microrna-mrna-regulatory-networks-in-multiple-myeloma-by-integrated-multiple-geo-datasets-using-bioinformatics-analysis
#9
Hongyu Gao, Huihan Wang, Wei Yang
Multiple myeloma (MM) is a common hematological malignancy. To identify key genes and microRNAs in MM, we downloaded two gene expression profiles (GSE16558 and GSE47552) and two microRNA expression profiles (GSE17498 and GSE16558) from the Gene Expression Omnibus (GEO) database. A total of 596 differentially expressed genes (DEGs) and 39 differentially expressed microRNAs (DEMs) were screened out. Pathway analysis showed that upregulated genes were mainly enriched in the "B cell receptor signaling pathway", "Cell cycle" and "NF-kappa B signaling pathway", whereas downregulated genes were mainly enriched in the "Ribosome", "FoxO signaling pathway" and "p53 signaling pathway"...
March 18, 2017: International Journal of Hematology
https://www.readbyqxmd.com/read/28315769/the-regulation-of-lipid-metabolism-by-a-hypothetical-p-loop-ntpase-and-its-impact-on-fecundity-of-the-brown-planthopper
#10
Rui Pang, Jieqi Qiu, Tengchao Li, Pan Yang, Lei Yue, Yixin Pan, Wenqing Zhang
BACKGROUND: Insect fecundity can be regulated by multiple genes in several important signaling pathways which form an extremely complicated regulatory network. However, there are still many genes that have significant impact on insect fecundity but their action mode are still unknown. METHODS: Quantitative real-time PCR (qRT-PCR), immunofluorescence and western blot were used to study the expression profile of Nl23867 in the brown planthopper, Nilaparvata lugens...
March 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28315266/sigma-1-receptors-fine-tune-the-neuronal-networks
#11
Shang-Yi Anne Tsai, Tsung-Ping Su
The endoplasmic reticular (ER) protein sigma-1 receptor (Sig-1R) has been implicated in CNS disorders including but not limited to neurodegenerative diseases, depression , amnesia, and substance abuse. Sig-1Rs are particularly enriched in the specific domain where ER membranes make contacts with the mitochondria (MAM). Within that specific domain, Sig-1Rs play significant roles governing calcium signaling and reactive oxygen species homeostasis to maintain proper neuronal functions. Studies showed that the Sig-1R is pivotal to regulate neuroplasticity and neural survival via multiple aspects of mechanism...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28314196/governance-and-management-dynamics-of-landscape-restoration-at-multiple-scales-learning-from-successful-environmental-managers-in-sweden
#12
Lucas Dawson, Marine Elbakidze, Per Angelstam, Johanna Gordon
Due to a long history of intensive land and water use, habitat networks for biodiversity conservation are generally degraded in Sweden. Landscape restoration (LR) is an important strategy for achieving representative and functional green infrastructures. However, outcomes of LR efforts are poorly studied, particularly the dynamics of LR governance and management. We apply systems thinking methods to a series of LR case studies to analyse the causal structures underlying LR governance and management in Sweden...
March 14, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28303958/sophisticated-clean-air-strategies-required-to-mitigate-against-particulate-organic-pollution
#13
T Grigas, J Ovadnevaite, D Ceburnis, E Moran, F M McGovern, S G Jennings, C O'Dowd
Since the 1980's, measures mitigating the impact of transboundary air pollution have been implemented successfully as evidenced in the 1980-2014 record of atmospheric sulphur pollution over the NE-Atlantic, a key region for monitoring background northern-hemisphere pollution levels. The record reveals a 72-79% reduction in annual-average airborne sulphur pollution (SO4 and SO2, respectively) over the 35-year period. The NE-Atlantic, as observed from the Mace Head research station on the Irish coast, can be considered clean for 64% of the time during which sulphate dominates PM1 levels, contributing 42% of the mass, and for the remainder of the time, under polluted conditions, a carbonaceous (organic matter and Black Carbon) aerosol prevails, contributing 60% to 90% of the PM1 mass and exhibiting a trend whereby its contribution increases with increasing pollution levels...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28303791/integer-programming-based-method-for-observability-of-singleton-attractors-in-boolean-networks
#14
Xiaoqing Cheng, Yushan Qiu, Wenpin Hou, Wai-Ki Ching
Boolean network (BN) is a popular mathematical model for revealing the behaviour of a genetic regulatory network. Furthermore, observability, an important network feature, plays a significant role in understanding the underlying network. Several studies have been done on analysis of observability of BNs and complex networks. However, the observability of attractor cycles, which can serve as biomarker detection, has not yet been addressed in the literature. This is an important, interesting and challenging problem that deserves a detailed study...
February 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28303467/mir-9-5p-down-regulates-pit2-but-not-pit1-in-human-embryonic-kidney-293-cells
#15
D P Paiva, M Keasey, J R M Oliveira
Inorganic phosphate (Pi) is an essential component for structure and metabolism. PiT1 (SLC20A1) and PiT2 (SLC20A2) are members of the mammalian type-III inorganic phosphate transporters. SLC20A2 missense variants are associated with primary brain calcification. MicroRNAs (miRNAs) are endogenous noncoding regulatory RNAs, which play important roles in post-transcriptional gene regulation. MicroRNA-9 (miR-9) acts at different stages of neurogenesis, is deeply rooted in gene networks controlling the regulation of neural progenitor proliferation, and is also linked with cancers outside the nervous system...
March 16, 2017: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/28303132/mycobacterium-abscessus-subsp-abscessus-is-capable-of-degrading-pseudomonas-aeruginosa-quinolone-signals
#16
Franziska S Birmes, Timo Wolf, Thomas A Kohl, Kai Rüger, Franz Bange, Jörn Kalinowski, Susanne Fetzner
Pseudomonas aeruginosa employs 2-heptyl-3-hydroxy-4(1H)-quinolone (the Pseudomonas quinolone signal, PQS) and 2-heptyl-4(1H)-quinolone (HHQ) as quorum sensing signal molecules, which contribute to a sophisticated regulatory network controlling the production of virulence factors and antimicrobials. We demonstrate that Mycobacterium abscessus(T) and clinical M. abscessus isolates are capable of degrading these alkylquinolone signals. Genome sequences of 50 clinical M. abscessus isolates indicated the presence of aqdRABC genes, contributing to fast degradation of HHQ and PQS, in M...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28303103/multipronged-therapeutic-effects-of-chinese-herbal-medicine-qishenyiqi-in-the-treatment-of-acute-myocardial-infarction
#17
Yong Wang, Weili Lin, Chun Li, Sarita Singhal, Gaurav Jain, Lixin Zhu, Linghui Lu, Ruixin Zhu, Wei Wang
Background: Based on global gene expression profile, therapeutic effects of Qishenyiqi (QSYQ) on acute myocardial infarction (AMI) were investigated by integrated analysis at multiple levels including gene expression, pathways involved and functional group. Methods: Sprague-Dawley (SD) rats were randomly divided into 3 groups: Sham-operated, AMI model (left anterior descending coronary artery ligation) and QSYQ-treated group. Cardiac tissues were obtained for analysing digital gene expression. Sequencing and transcriptome analyses were performed collaboratively, including analyses of differential gene expression, gene co-expression network, targeted attack on network and functional grouping...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28302728/a-high-and-phosphatidylinositol-4-phosphate-pi4p-dependent-atpase-activity-for-the-drs2p-cdc50p-flippase-after-removal-of-its-n-and-c-terminal-extensions
#18
Hassina Azouaoui, Cédric Montigny, Thibaud Dieudonné, Philippe Champeil, Aurore Jacquot, José Luis Vázquez-Ibar, Pierre Le Maréchal, Jakob Ulstrup, Miriam-Rose Ash, Joseph A Lyons, Poul Nissen, Guillaume Lenoir
P4-ATPases, also known as phospholipid flippases, are responsible for creating and maintaining transbilayer lipid asymmetry in eukaryotic cell membranes. Here, we use limited proteolysis to investigate the role of the N- and C-termini in ATP hydrolysis and auto-inhibition of the yeast flippase Drs2p/Cdc50p. We show that limited proteolysis of the detergent-solubilized and purified yeast flippase may result in more than one order of magnitude increase of its ATPase activity, which remains dependent on phosphatidylinositol-4-phosphate (PI4P), a regulator of this lipid flippase, and specific to a phosphatidylserine substrate...
March 16, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28302717/regulatory-signatures-of-liver-regeneration-distilled-by-integrative-analysis-of-mrna-histone-methylation-and-proteomics
#19
Yoshihiro Sato, Yasutake Katoh, Mitsuyo Matsumoto, Masaki Sato, Masayuki Ebina, Ari Itoh-Nakadai, Ryo Funayama, Keiko Nakayama, Michiaki Unno, Kazuhiko Igarashi
The capacity of the liver to regenerate is likely to be encoded as a plasticity of molecular networks within the liver. By applying a combination of comprehensive analyses of the epigenome, transcriptome and proteome, we herein depict the molecular landscape of liver regeneration. We demonstrated that histone H3K4 was tri-methylated at the promoter regions of many loci, among which only a fraction including cell-cycle-related genes were transcriptionally up-regulated. A cistrome analysis guided by the histone methylation patterns and the transcriptome identified FOXM1 as the key transcription factor promoting liver regeneration, which was confirmed in vitro using a hepatocarcinoma cell line...
March 16, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28302471/the-expanding-targetome-of-small-rnas-in-salmonella-typhimurium
#20
REVIEW
Daniel Ryan, Mohana Mukherjee, Mrutyunjay Suar
The enterobacterial pathogen Salmonella has long served as a model for bacterial pathogenesis, stress response, gene expression and regulation with extensive investigation involving protein function. With the advent of high-throughput sequencing technologies and their applications in genomics and transcriptomics, a wealth of data particularly with respect to small RNAs (sRNAs) is being generated. These molecules serve as regulators of major stress response and virulence networks in diverse species including Salmonella enterica subsp...
March 13, 2017: Biochimie
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