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https://www.readbyqxmd.com/read/29656417/mirna-regulation-of-innate-immunity
#1
REVIEW
Fatemeh Momen-Heravi, Shashi Bala
MicroRNAs (miRNAs) are small noncoding RNA and are pivotal posttranscriptional regulators of both innate and adaptive immunity. They act by regulating the expression of multiple immune genes, thus, are the important elements to the complex immune regulatory network. Deregulated expression of specific miRNAs can lead to potential autoimmunity, immune tolerance, hyper-inflammatory phenotype, and cancer initiation and progression. In this review, we discuss the contributory pathways and mechanisms by which several miRNAs influence the development of innate immunity and fine-tune immune response...
April 14, 2018: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/29653362/the-long-noncoding-rna-zfas1-facilitates-bladder-cancer-tumorigenesis-by-sponging-mir-329
#2
Jin-Shan Wang, Qing-Hong Liu, Xiao-Hua Cheng, Wen-Yuan Zhang, Yong-Chao Jin
The incidence and mortality rate of bladder cancer have dramatically expanded, so it's urgent to discover new biomarker and therapeutic target for bladder cancer. Recently, lncRNA has been identified as oncogene or tumor suppressor to regulate the tumorigenesis. LncRNA ZFAS1 has been confirmed as oncogene in various tumors. However, the expression, function, and underlying mechanism of ZFAS1 in bladder carcinogenesis have yet to be totally clarified. In the current study, our data demonstrated that ZFAS1 expression was significantly upregulated in bladder cancer tissues and cell lines...
April 10, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29653230/regulatory-network-analysis-of-high-expressed-long-non-coding-rna-linc00941-in-gastric-cancer
#3
Cong Luo, Yang Tao, Yuwei Zhang, Yinyin Zhu, Derry Ng Minyao, Maria Haleem, Changzheng Dong, Lina Zhang, Xiaohong Zhang, Jinshun Zhao, Qi Liao
Accumulating evidence suggests that the aberrant expression of long non-coding RNAs is closely related to the carcinogenesis and progression of gastric cancer (GC), which is a type of prevalent tumor with a high incidence and mortality rate. However, it is still a challenge to find reliable biomarkers and to understand their molecular mechanisms in GC. In this study, we first confirmed that LINC00941was up-regulated in GC tumor tissues compared with adjacent normal tissues by RT-PCR, and found that the expression level of LINC00941 was correlated with invasion depth, lymphatic metastasis, and the TNM stage of patients with GC...
April 10, 2018: Gene
https://www.readbyqxmd.com/read/29653196/transcription-factors-in-regulatory-and-protein-subnetworks-during-generation-of-neural-stem-cells-and-neurons-from-direct-reprogramming-of-non-fibroblastic-cell-sources
#4
Mohammad Reza Omrani, Moein Yaqubi, Abdulshakour Mohammadnia
Direct reprogramming of non-fibroblastic cells to the neuronal cell types including induced neurons (iNs) and induced neural stem cells (iNSCs) has provided an alternative approach for the direct reprogramming of fibroblasts to those cells. However, to increase the efficiency of the reprogramming process the underlaying mechanisms should be clarified. In the current study, we analyzed the gene expression profiles of five different cellular conversions to understand the most significant molecular mechanisms and transcription factors (TFs) underlying each conversion...
April 10, 2018: Neuroscience
https://www.readbyqxmd.com/read/29652073/the-iron-regulatory-proteins-are-defective-in-repressing-translation-via-exogenous-5-iron-responsive-elements-despite-their-relative-abundance-in-leukemic-cellular-models
#5
Emmanuel Pourcelot, Marine Lénon, Peggy Charbonnier, Fiona Louis, Pascal Mossuz, Jean-Marc Moulis
In animal cells the specific translational control of proteins contributing to iron homeostasis is mediated by the interaction between the Iron Regulatory Proteins (IRP1 and IRP2) and the Iron Responsive Elements (IRE) located in the untranslated regions (UTR) of regulated messengers, such as those encoding ferritin or the transferrin receptor. The absolute concentrations of the components of this regulatory system in hematopoietic cells and the ability of the endogenous IRP to regulate exogenous IRE have been measured...
April 13, 2018: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/29650590/coordination-of-meristem-and-boundary-functions-by-transcription-factors-in-the-shoot-meristemless-regulatory-network
#6
S Scofield, A Murison, A Jones, J Fozard, M Aida, L R Band, M Bennett, J A H Murray
The Arabidopsis homeodomain transcription factor SHOOT MERISTEMLESS (STM) is critical for shoot apical meristem (SAM) function, yet the components and structure of the STM gene regulatory network (GRN) are largely unknown. Here we show that transcriptional regulators are overrepresented amongst STM-regulated genes, and using these as GRN components in Bayesian network analysis we infer STM GRN associations and reveal regulatory relationships between STM and factors involved in multiple aspects of SAM function, including hormone regulation, TCP-mediated control of cell differentiation, AIL/PLT-mediated regulation of pluripotency and phyllotaxis, and specification of meristem-organ boundary zones via CUC1...
April 12, 2018: Development
https://www.readbyqxmd.com/read/29649445/chromatin-accessibility-based-characterization-of-the-gene-regulatory-network-underlying-plasmodium-falciparum-blood-stage-development
#7
Christa Geeke Toenhake, Sabine Anne-Kristin Fraschka, Mahalingam Shanmugiah Vijayabaskar, David Robert Westhead, Simon Jan van Heeringen, Richárd Bártfai
Underlying the development of malaria parasites within erythrocytes and the resulting pathogenicity is a hardwired program that secures proper timing of gene transcription and production of functionally relevant proteins. How stage-specific gene expression is orchestrated in vivo remains unclear. Here, using the assay for transposase accessible chromatin sequencing (ATAC-seq), we identified ∼4,000 regulatory regions in P. falciparum intraerythrocytic stages. The vast majority of these sites are located within 2 kb upstream of transcribed genes and their chromatin accessibility pattern correlates positively with abundance of the respective mRNA transcript...
April 11, 2018: Cell Host & Microbe
https://www.readbyqxmd.com/read/29648622/deep-learning-of-genomic-variation-and-regulatory-network-data
#8
Amalio Telenti, Christoph Lippert, Pi-Chuan Chang, Mark DePristo
The human genome is now investigated through high throughput functional assays, and through the generation of population genomic data. These advances support the identification of functional genetic variants and the prediction of traits (eg. deleterious variants and disease). This review summarizes lessons learned from the large-scale analyses of genome and exome datasets, modeling of population data and machine learning strategies to solve complex genomic sequence regions. The review also portrays the rapid adoption of artificial intelligence/deep neural networks in genomics; in particular, deep learning approaches are well suited to model the complex dependencies in the regulatory landscape of the genome, and to provide predictors for genetic variant calling and interpretation...
April 10, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29648592/yeast-2-0-connecting-the-dots-in-the-construction-of-the-world-s-first-functional-synthetic-eukaryotic-genome
#9
I S Pretorius, J D Boeke
Historians of the future may well describe 2018 as the year that the world's first functional synthetic eukaryotic genome became a reality. Without the benefit of hindsight, it might be hard to completely grasp the long-term significance of a breakthrough moment in the history of science like this. The role of synthetic biology in the imminent birth of a budding Saccharomyces cerevisiae yeast cell carrying 16 man-made chromosomes causes the world of science to teeter on the threshold of a future-defining scientific frontier...
June 1, 2018: FEMS Yeast Research
https://www.readbyqxmd.com/read/29644403/the-putative-pectin-methylesterase-gene-bcmf23a-is-required-for-microspore-development-and-pollen-tube-growth-in-brassica-campestris
#10
Xiaoyan Yue, Sue Lin, Youjian Yu, Li Huang, Jiashu Cao
BcMF23a contributes to pollen wall development via influencing intine construction, which, in turn, influences pollen tube growth. Pollen wall, the morphological out face of pollen, surrounds male gametophyte and plays an important role in plant reproduction. Pectin methylesterases (PMEs) are involved in pollen wall construction by de-esterifying pectin of the intine. In this study, the function of a putative pectin methylesterase gene, Brassica campestris Male Fertility 23a (BcMF23a), was investigated. Knockdown of BcMF23a by artificial microRNA (amiRNA) technology resulted in abnormal pollen intine formation outside of the germinal furrows at the binucleate stage...
April 11, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29644074/acquisition-of-pluripotency-in-the-chick-embryo-occurs-during-intrauterine-embryonic-development-via-a-unique-transcriptional-network
#11
Jae Yong Han, Hyo Gun Lee, Young Hyun Park, Young Sun Hwang, Sang Kyung Kim, Deivendran Rengaraj, Byung Wook Cho, Jeong Mook Lim
Background: Acquisition of pluripotency by transcriptional regulatory factors is an initial developmental event that is required for regulation of cell fate and lineage specification during early embryonic development. The evolutionarily conserved core transcriptional factors regulating the pluripotency network in fishes, amphibians, and mammals have been elucidated. There are also species-specific maternally inherited transcriptional factors and their intricate transcriptional networks important in the acquisition of pluripotency...
2018: Journal of Animal Science and Biotechnology
https://www.readbyqxmd.com/read/29643765/mirna-long-term-response-to-early-metabolic-environmental-challenge-in-hypothalamic-arcuate-nucleus
#12
Charlotte Benoit, Soraya Doubi-Kadmiri, Xavier Benigni, Delphine Crepin, Laure Riffault, Ghislaine Poizat, Claire-Marie Vacher, Mohammed Taouis, Anne Baroin-Tourancheau, Laurence Amar
Epidemiological reports and studies using rodent models indicate that early exposure to nutrient and/or hormonal challenges can reprogram metabolism at adulthood. Hypothalamic arcuate nucleus (ARC) integrates peripheral and central signals to adequately regulate energy homeostasis. microRNAs (miRNAs) participate in the control of gene expression of large regulatory networks including many signaling pathways involved in epigenetics regulations. Here, we have characterized and compared the miRNA population of ARC of adult male rats continuously exposed to a balanced metabolic environment to the one of adult male rats exposed to an unbalanced high-fat/high-carbohydrate/moderate-protein metabolic environment during the perinatal period and/or at adulthood that consequently displayed hyperinsulinemia and/or hyperleptinemia...
2018: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29643462/environment-dependent-striatal-gene-expression-in-the-bachd-rat-model-for-huntington-disease
#13
Arianna Novati, Thomas Hentrich, Zinah Wassouf, Jonasz J Weber, Libo Yu-Taeger, Nicole Déglon, Huu Phuc Nguyen, Julia M Schulze-Hentrich
Huntington disease (HD) is an autosomal dominant neurodegenerative disorder caused by a mutation in the huntingtin (HTT) gene which results in progressive neurodegeneration in the striatum, cortex, and eventually most brain areas. Despite being a monogenic disorder, environmental factors influence HD characteristics. Both human and mouse studies suggest that mutant HTT (mHTT) leads to gene expression changes that harbor potential to be modulated by the environment. Yet, the underlying mechanisms integrating environmental cues into the gene regulatory program have remained largely unclear...
April 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29642893/q-a-how-do-gene-regulatory-networks-control-environmental-responses-in-plants
#14
Ying Sun, José R Dinneny
A gene regulatory network (GRN) describes the hierarchical relationship between transcription factors, associated proteins, and their target genes. Studying GRNs allows us to understand how a plant's genotype and environment are integrated to regulate downstream physiological responses. Current efforts in plants have focused on defining the GRNs that regulate functions such as development and stress response and have been performed primarily in genetically tractable model plant species such as Arabidopsis thaliana...
April 11, 2018: BMC Biology
https://www.readbyqxmd.com/read/29642857/structure-and-transcriptional-regulation-of-the-major-intrinsic-protein-gene-family-in-grapevine
#15
Darren Chern Jan Wong, Li Zhang, Isabelle Merlin, Simone D Castellarin, Gregory A Gambetta
BACKGROUND: The major intrinsic protein (MIP) family is a family of proteins, including aquaporins, which facilitate water and small molecule transport across plasma membranes. In plants, MIPs function in a huge variety of processes including water transport, growth, stress response, and fruit development. In this study, we characterize the structure and transcriptional regulation of the MIP family in grapevine, describing the putative genome duplication events leading to the family structure and characterizing the family's tissue and developmental specific expression patterns across numerous preexisting microarray and RNAseq datasets...
April 11, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29642837/approximate-inference-of-gene-regulatory-network-models-from-rna-seq-time-series-data
#16
Thomas Thorne
BACKGROUND: Inference of gene regulatory network structures from RNA-Seq data is challenging due to the nature of the data, as measurements take the form of counts of reads mapped to a given gene. Here we present a model for RNA-Seq time series data that applies a negative binomial distribution for the observations, and uses sparse regression with a horseshoe prior to learn a dynamic Bayesian network of interactions between genes. We use a variational inference scheme to learn approximate posterior distributions for the model parameters...
April 11, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29628952/approximation-of-state-variables-for-discrete-time-stochastic-genetic-regulatory-networks-with-leakage-distributed-and-probabilistic-measurement-delays-a-robust-stability-problem
#17
S Pandiselvi, R Raja, Jinde Cao, G Rajchakit, Bashir Ahmad
This work predominantly labels the problem of approximation of state variables for discrete-time stochastic genetic regulatory networks with leakage, distributed, and probabilistic measurement delays. Here we design a linear estimator in such a way that the absorption of mRNA and protein can be approximated via known measurement outputs. By utilizing a Lyapunov-Krasovskii functional and some stochastic analysis execution, we obtain the stability formula of the estimation error systems in the structure of linear matrix inequalities under which the estimation error dynamics is robustly exponentially stable...
2018: Advances in Difference Equations
https://www.readbyqxmd.com/read/29628141/pseudouridylation-of-trna-derived-fragments-steers-translational-control-in-stem-cells
#18
Nicola Guzzi, Maciej Cieśla, Phuong Cao Thi Ngoc, Stefan Lang, Sonali Arora, Marios Dimitriou, Kristyna Pimková, Mikael N E Sommarin, Roberto Munita, Michal Lubas, Yiting Lim, Kazuki Okuyama, Shamit Soneji, Göran Karlsson, Jenny Hansson, Göran Jönsson, Anders H Lund, Mikael Sigvardsson, Eva Hellström-Lindberg, Andrew C Hsieh, Cristian Bellodi
Pseudouridylation (Ψ) is the most abundant and widespread type of RNA epigenetic modification in living organisms; however, the biological role of Ψ remains poorly understood. Here, we show that a Ψ-driven posttranscriptional program steers translation control to impact stem cell commitment during early embryogenesis. Mechanistically, the Ψ "writer" PUS7 modifies and activates a novel network of tRNA-derived small fragments (tRFs) targeting the translation initiation complex. PUS7 inactivation in embryonic stem cells impairs tRF-mediated translation regulation, leading to increased protein biosynthesis and defective germ layer specification...
April 4, 2018: Cell
https://www.readbyqxmd.com/read/29626602/protective-properties-of-combined-fungal-polysaccharides-from-cordyceps-sinensis-and-ganoderma-atrum-on-colon-immune-dysfunction
#19
Song-Tao Fan, Shao-Ping Nie, Xiao-Jun Huang, Sunan Wang, Jie-Lun Hu, Jun-Hua Xie, Qi-Xing Nie, Ming-Yong Xie
In vivo an ecological network of polysaccharides utilization by gut microbiota is not only an intense competition but also an impressive cooperation pattern. The present study evaluated the in vivo protective effect of combined fungal polysaccharides (CFP) from Cordyceps sinensis and Ganoderma atrum on colon immune dysfunction, induced by 150 mg/kg cyclophosphamide (CP). The results showed that C. sinensis polysaccharides (CSP) significantly promoted microbial-derived butyrate to improve histone h3 acetylation mediating regulatory T (Treg) cell specific Foxp3, as well as significantly restored CP-induced elevation of interleukin (IL)-17 and IL-21...
April 4, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29626560/bioelectrical-control-of-positional-information-in-development-and-regeneration-a-review-of-conceptual-and-computational-advances
#20
REVIEW
Alexis Pietak, Michael Levin
Positional information describes pre-patterns of morphogenetic substances that alter spatio-temporal gene expression to instruct development of growth and form. A wealth of recent data indicate bioelectrical properties, such as the transmembrane potential (Vmem ), are involved as instructive signals in the spatiotemporal regulation of morphogenesis. However, the mechanistic relationships between Vmem and molecular positional information are only beginning to be understood. Recent advances in computational modeling are assisting in the development of comprehensive frameworks for mechanistically understanding how endogenous bioelectricity can guide anatomy in a broad range of systems...
April 4, 2018: Progress in Biophysics and Molecular Biology
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