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Modeling gene regulation

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https://www.readbyqxmd.com/read/29475039/genes-and-micrornas-associated-with-mouse-cleft-palate-a-systematic-review-and-bioinformatics-analysis
#1
Akiko Suzuki, Nada Abdallah, Mona Gajera, Goo Jun, Peilin Jia, Zhongming Zhao, Junichi Iwata
Cleft palate (CP) is the most prevalent craniofacial deformity, with ethnic and geographic variation in prevalence in humans. Mice have been used as an animal model to study the cause(s) of CP by several approaches, including genetic and chemical-induced approaches. Mouse genetic approaches revealed that significant amounts of genes are involved in the CP pathology. The aim of this study was to identify common features of CP-associated genes and to explore the roles of microRNAs (miRNAs) as important post-transcriptional regulators that may be involved in the regulation of CP genes...
February 20, 2018: Mechanisms of Development
https://www.readbyqxmd.com/read/29475025/protein-anchoring-therapy-to-target-extracellular-matrix-proteins-to-their-physiological-destinations
#2
REVIEW
Mikako Ito, Kinji Ohno
Endplate acetylcholinesterase (AChE) deficiency is a form of congenital myasthenic syndrome (CMS) caused by mutations in COLQ, which encodes collagen Q (ColQ). ColQ is an extracellular matrix (ECM) protein that anchors AChE to the synaptic basal lamina. Biglycan, encoded by BGN, is another ECM protein that binds to the dystrophin-associated protein complex (DAPC) on skeletal muscle, which links the actin cytoskeleton and ECM proteins to stabilize the sarcolemma during repeated muscle contractions. Upregulation of biglycan stabilizes the DPAC...
February 20, 2018: Matrix Biology: Journal of the International Society for Matrix Biology
https://www.readbyqxmd.com/read/29474875/rig-i-is-involved-in-inflammation-through-the-ips-1-traf-6-pathway-in-astrocytes-under-chemical-hypoxia
#3
Lei Li, Rongli Yang, Meijiang Feng, YiChen Guo, YuXuan Wang, Jun Guo, Xiang Lu
The retinoic acid-inducible gene I (RIG-I) is a crucial cytoplasmic pathogen recognition receptor involved in neuroinflammation in degenerative diseases. In the present study, in vitro human astrocytes were subjected to a chemical hypoxia model using cobalt chloride pretreatment. Chemical hypoxia induces the up-regulation of RIG-I in astrocytes and results in the expression of inflammatory cytokines IL-1β, IL-6, and TNF-α in an NF-κB dependent manner. Elevated RIG-I modulates the interaction of interferon-β promoter stimulator-1 (IPS-1) and TNF receptor-associated factor 6 (TRAF6) following chemical hypoxia...
February 20, 2018: Neuroscience Letters
https://www.readbyqxmd.com/read/29474860/pharmacological-targeting-of-the-mammalian-clock-reveals-a-novel-analgesic-for-osteoarthritis-induced-pain
#4
Vaskar Das, Ranjan Kc, Xin Li, Disha Varma, Sujun Qiu, Jeffrey S Kroin, Christopher B Forsyth, Ali Keshavarzian, Andre J van Wijnen, Thomas J Park, Gary S Stein, Insug O-Sullivan, Thomas P Burris, Hee-Jeong Im
Environmental disruption of the circadian rhythm is linked with increased pain due to osteoarthritis (OA). We aimed to characterize the role of the clock gene in OA-induced pain more systemically using both genetic and pharmacological approaches. Genetically modified mice, (bmal1f/fNav1.8CreERT mice), generated by deleting the critical clock gene, bmal1, from Nav1.8 sensory neurons, were resistant to the development of mechanical hyperalgesia associated with OA induced by partial medial meniscectomy (PMM) of the knee...
February 20, 2018: Gene
https://www.readbyqxmd.com/read/29474442/dysregulation-of-the-ifn-%C3%AE-stat1-signaling-pathway-in-a-cell-line-model-of-large-granular-lymphocyte-leukemia
#5
Paige M Kulling, Kristine C Olson, Cait E Hamele, Mariella F Toro, Su-Fern Tan, David J Feith, Thomas P Loughran
T cell large granular lymphocyte leukemia (T-LGLL) is a rare incurable disease that is characterized by defective apoptosis of cytotoxic CD8+ T cells. Chronic activation of the Janus Kinase-Signal Transducer and Activator of Transcription (JAK-STAT) pathway is a hallmark of T-LGLL. One manifestation is the constitutive phosphorylation of tyrosine 701 of STAT1 (p-STAT1). T-LGLL patients also exhibit elevated serum levels of the STAT1 activator, interferon-γ (IFN-γ), thus contributing to an inflammatory environment...
2018: PloS One
https://www.readbyqxmd.com/read/29473882/on-the-metal-cofactor-in-the-tyrosinase-family
#6
REVIEW
Francisco Solano
The production of pigment in mammalian melanocytes requires the contribution of at least three melanogenic enzymes, tyrosinase and two other accessory enzymes called the tyrosinase-related proteins (Trp1 and Trp2), which regulate the type and amount of melanin. The last two proteins are paralogues to tyrosinase, and they appeared late in evolution by triplication of the tyrosinase gene. Tyrosinase is a copper-enzyme, and Trp2 is a zinc-enzyme. Trp1 has been more elusive, and the direct identification of its metal cofactor has never been achieved...
February 23, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29473817/na-h-exchanger-isoform-1-induced-osteopontin-expression-facilitates-cardiac-hypertrophy-through-p90-ribosomal-s6-kinase
#7
Nabeel Abdulrahman, Béatrice Jaspard Vinassa, Larry Fliegel, Ayesha Jabeen, Sadaf Riaz, Alain-Pierre Gadeau, Fatima Mraiche
Cardiovascular diseases are the leading cause of death worldwide. One in three cases of heart failure is due to dilated cardiomyopathy. The Na+ /H+ exchanger isoform 1 (NHE1), a multifunctional protein and the key pH regulator in the heart, has been demonstrated to be increased in this condition. We have previously demonstrated that elevated NHE1 activity induced cardiac hypertrophy in vivo. Furthermore, the overexpression of active NHE1 elicited modulation of gene expression in cardiomyocytes including an upregulation of myocardial osteopontin (OPN) expression...
February 23, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29473500/crispr-cas-system-as-a-genome-engineering-platform-applications-in-biomedicine-and-biotechnology
#8
Atieh Hashemi
Genome editing mediated by clustered regularly interspaced palindromic repeats (CRISPR) and its associated proteins (Cas) has recently been considered to be used as efficient, rapid and site-specific tools in the modification of endogenous genes in biomedically important cell types and whole organisms. It has become a predictable and precise method of choice for genome engineering by specifying a 20-nt targeting sequence within its guide RNA. First, this review aims to describe the biology of CRISPR system...
February 20, 2018: Current Gene Therapy
https://www.readbyqxmd.com/read/29473362/-effects-of-electroacupuncture-on-expression-of-cd36-in-peritoneal-macrophages-of-rabbits-with-atherosclerosis
#9
Zedong Cheng, Yulou Ning, Rui Wang
OBJECTIVE: To observe the effect of electroacupuncture (EA) on the expressions of CD36 gene and protein in peritoneal macrophages of atherosclerotic rabbits, and to explore the mechanism of acupuncture regulation of atherosclerosis. METHODS: A total of 26 male New Zealand rabbits were randomly divided into a blank group (7 rabbits) and a model group (19 rabbits). The rabbits in the blank group were fed with common feedstuff, and those in the model group were applied with high fat diet and arteria carotis communis bullon injury...
February 12, 2018: Zhongguo Zhen Jiu, Chinese Acupuncture & Moxibustion
https://www.readbyqxmd.com/read/29473182/the-androgen-receptor-malignancy-shift-in-prostate-cancer
#10
REVIEW
Ben T Copeland, Sumanta K Pal, Eric C Bolton, Jeremy O Jones
BACKGROUND: Androgens and the androgen receptor (AR) are necessary for the development, function, and homeostatic growth regulation of the prostate gland. However, once prostate cells are transformed, the AR is necessary for the proliferation and survival of the malignant cells. This change in AR function appears to occur in nearly every prostate cancer. We have termed this the AR malignancy shift. METHODS: In this review, we summarize the current knowledge of the AR malignancy shift, including the DNA-binding patterns that define the shift, the transcriptome changes associated with the shift, the putative drivers of the shift, and its clinical implications...
February 23, 2018: Prostate
https://www.readbyqxmd.com/read/29473025/dynamics-and-control-of-flagella-assembly-in-salmonella-typhimurium
#11
Chandrani Das, Chaitanya Mokashi, Sharmila S Mande, Supreet Saini
The food-borne pathogen Salmonella typhimurium is a common cause of infections and diseases in a wide range of hosts. One of the major virulence factors associated to the infection process is flagella, which helps the bacterium swim to its preferred site of infection inside the host, the M-cells (Microfold cells) lining the lumen of the small intestine. The expression of flagellar genes is controlled by an intricate regulatory network. In this work, we investigate two aspects of flagella regulation and assembly: (a) distribution of the number of flagella in an isogenic population of bacteria and (b) dynamics of gene expression post cell division...
2018: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29472869/phosphorylated-and-non-phosphorylated-leucine-rich-amelogenin-peptide-differentially-affect-ameloblast-mineralization
#12
Elvire Le Norcy, Julie Lesieur, Jeremy Sadoine, Gaël Y Rochefort, Catherine Chaussain, Anne Poliard
The Leucine Rich Amelogenin Peptide (LRAP) is a product of alternative splicing of the amelogenin gene. As full length amelogenin, LRAP has been shown, in precipitation experiments, to regulate hydroxyapatite (HAP) crystal formation depending on its phosphorylation status. However, very few studies have questioned the impact of its phosphorylation status on enamel mineralization in biological models. Therefore, we have analyzed the effect of phosphorylated (+P) or non-phosphorylated (-P) LRAP on enamel formation in ameloblast-like cell lines and ex vivo cultures of murine postnatal day 1 molar germs...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29472715/desumoylation-switches-kaiso-from-activator-to-repressor-upon-hyperosmotic-stress
#13
Svetlana Zhenilo, Igor Deyev, Ekaterina Litvinova, Nadezhda Zhigalova, Daria Kaplun, Alexey Sokolov, Alexander Mazur, Egor Prokhortchouk
Kaiso is a member of the BTB/POZ zinc finger family, which is involved in cancer progression, cell cycle control, apoptosis, and WNT signaling. Depending on promoter context, it may function as either a transcriptional repressor or activator. Previous studies found that Kaiso might be SUMOylated due to heat shock, but the biological significance of Kaiso SUMOylation is unclear. Here, we find that K42 is the only amino acid within Kaiso that is modified with SUMO. Kaiso is monoSUMOylated at lysine 42 in cell lines of kidney origin under normal physiological conditions...
February 22, 2018: Cell Death and Differentiation
https://www.readbyqxmd.com/read/29472639/transcription-factor-target-gene-network-governs-the-logical-abstraction-analysis-of-the-synthetic-circuit-in-leishmaniasis
#14
Milsee Mol, Dipali Kosey, Ramanamurthy Boppana, Shailza Singh
With the advent of synthetic biology in medicine many synthetic or engineered proteins have made their way to therapeutics and diagnostics. In this paper, the downstream gene network of CD14-TNF-EGFR pathway in leishmaniasis, a tropical disease, is reconstructed. Network analysis showed that NFkB links the signaling and gene network, used as a point of intervention through a synthetic circuit embedded within the negative autoregulatory feedback loop. A chimeric protein kinase C (PKC) is incorporated in the synthetic circuit, under the transcriptional regulation of Lac repressor and IPTG, as an inducer...
February 22, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29472582/p2x7-receptor-regulates-osteoclast-function-and-bone-loss-in-a-mouse-model-of-osteoporosis
#15
Ning Wang, Ankita Agrawal, Niklas Rye Jørgensen, Alison Gartland
Post-menopausal osteoporosis is a condition that affects millions worldwide and places a huge socio-economic burden on society. Previous research has shown an association of loss of function SNPs in the gene for the purinergic receptor P2X7R with low bone mineral density, increased rates of bone loss and vertebral fractures in post-menopausal women. In this study we use a mouse model of oestrogen deficiency-induced bone loss and the BALB/cJ P2X7R-/- to show that absence of the P2X7R resulted in increased bone loss...
February 22, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29472543/dznep-inhibits-h3k27me3-deposition-and-delays-retinal-degeneration-in-the-rd1-mice
#16
Shijie Zheng, Lirong Xiao, Yu Liu, Yujiao Wang, Lin Cheng, Junjun Zhang, Naihong Yan, Danian Chen
Retinitis pigmentosa (RP) is a group of inherited retinal degenerative diseases causing progressive loss of photoreceptors. Numerous gene mutations are identified to be related with RP, but epigenetic modifications may also be involved in the pathogenesis. Previous studies suggested that both DNA methylation and histone acetylation regulate photoreceptor cell death in RP mouse models. However, the role of histone methylation in RP has never been investigated. In this study, we found that trimethylation of several lysine sites of histone H3, including lysine 27 (H3K27me3), increased in the retinas of rd1 mice...
February 22, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29472387/class-iia-histone-deacetylases-link-camp-signaling-to-the-myelin-transcriptional-program-of-schwann-cells
#17
Clara Gomis-Coloma, Sergio Velasco-Aviles, Jose A Gomez-Sanchez, Angeles Casillas-Bajo, Johannes Backs, Hugo Cabedo
Schwann cells respond to cyclic adenosine monophosphate (cAMP) halting proliferation and expressing myelin proteins. Here we show that cAMP signaling induces the nuclear shuttling of the class IIa histone deacetylase (HDAC)-4 in these cells, where it binds to the promoter and blocks the expression of c-Jun , a negative regulator of myelination. To do it, HDAC4 does not interfere with the transcriptional activity of MEF2. Instead, by interacting with NCoR1, it recruits HDAC3 and deacetylates histone 3 in the promoter of c-Jun , blocking gene expression...
February 22, 2018: Journal of Cell Biology
https://www.readbyqxmd.com/read/29471939/tet2-mediated-clonal-hematopoiesis-accelerates-heart-failure-through-a-mechanism-involving-the-il-1%C3%AE-nlrp3-inflammasome
#18
Soichi Sano, Kosei Oshima, Ying Wang, Susan MacLauchlan, Yasufumi Katanasaka, Miho Sano, María A Zuriaga, Minoru Yoshiyama, David Goukassian, Matthew A Cooper, José J Fuster, Kenneth Walsh
BACKGROUND: Recent studies have shown that hematopoietic stem cells can undergo clonal expansion secondary to somatic mutations in leukemia-related genes, thus leading to an age-dependent accumulation of mutant leukocytes in the blood. This somatic mutation-related clonal hematopoiesis is common in healthy older individuals, but it has been associated with an increased incidence of future cardiovascular disease. The epigenetic regulator TET2 is frequently mutated in blood cells of individuals exhibiting clonal hematopoiesis...
February 27, 2018: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/29471858/tumor-promoting-properties-of-mir-8084-in-breast-cancer-through-enhancing-proliferation-suppressing-apoptosis-and-inducing-epithelial-mesenchymal-transition
#19
Yujing Gao, Hongning Ma, Chanchan Gao, Ye Lv, XueHua Chen, Rongrong Xu, Miao Sun, Xinrui Liu, Xiaohong Lu, Xiuying Pei, Pu Li
BACKGROUND: Breast cancer is one of the most frequent malignancies and the second leading cause of cancer-related mortality in women. MicroRNAs play a key role in breast cancer development and progression. microRNA(miR)-8084 has been observed an aberrant expression in breast cancer. However, the functions and regulatory axes of miR-8084, particularly in breast cancer, were not entirely clear. METHODS: miR-8084 expression in breast cancer were investigated in a GEO dataset by in silico analysis and in 42 paired tumor tissues by qPCR...
February 23, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29471801/a-maximum-likelihood-algorithm-for-reconstructing-3d-structures-of-human-chromosomes-from-chromosomal-contact-data
#20
Oluwatosin Oluwadare, Yuxiang Zhang, Jianlin Cheng
BACKGROUND: The development of chromosomal conformation capture techniques, particularly, the Hi-C technique, has made the analysis and study of the spatial conformation of a genome an important topic in bioinformatics and computational biology. Aided by high-throughput next generation sequencing techniques, the Hi-C technique can generate genome-wide, large-scale intra- and inter-chromosomal interaction data capable of describing in details the spatial interactions within a genome. These data can be used to reconstruct 3D structures of chromosomes that can be used to study DNA replication, gene regulation, genome interaction, genome folding, and genome function...
February 23, 2018: BMC Genomics
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