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https://www.readbyqxmd.com/read/28341446/pkr-induces-the-expression-of-nlrp3-by-regulating-the-nf-%C3%AE%C2%BAb-pathway-in-porphyromonas-gingivalis-infected-osteoblasts
#1
Kaya Yoshida, Hirohiko Okamura, Yuka Hiroshima, Kaori Abe, Jun-Ichi Kido, Yasuo Shinohara, Kazumi Ozaki
The double-stranded RNA-dependent kinase (PKR), which is activated by double stranded RNA, induces inflammation by regulating NF-κB signaling. The NLR family pyrin domain-containing 3 (NLRP3) inflammasome also modulates inflammation in response to infection. Porphyromonas gingivalis (P.gingivalis) is an oral bacterium which is implicated in the pathogenesis of periodontal diseases. We previously reported that PKR is a key modulator of bone metabolism and inflammation in the periodontal tissue. PKR was also reported to induce inflammation in response to microbes by regulating the NLRP3 inflammasome, suggesting that PKR could affect inflammation along with NLRP3 in periodontal diseases...
March 21, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28337393/development-and-validation-of-est-ssr-markers-for-fokienia-hodginsii-cupressaceae
#2
Mingyan Ding, Kaikai Meng, Qiang Fan, Weizheng Tan, Wenbo Liao, Sufang Chen
PREMISE OF THE STUDY: Fokienia hodginsii (Cupressaceae) is a Tertiary relict evergreen conifer of the monotypic genus Fokienia. Polymorphic microsatellite markers were developed to investigate its genetic diversity and population structure. METHODS AND RESULTS: RNA transcripts of F. hodginsii were sequenced and de novo assembled into 85,818 unigenes, and 1892 simple sequence repeat (SSR) markers were detected from the unigenes. A total of 273 expressed sequence tag-SSR primer pairs were designed and tested, and 129 successfully amplified...
March 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28330315/characterization-and-development-of-est-ssr-markers-in-sweet-potato-ipomoea-batatas-l-lam
#3
Jin-Hee Kim, Jun-Hoi Kim, Won-Sam Jo, Jeong-Gwan Ham, Il Kyung Chung, Kyung-Min Kim
In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag-simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The lengths of the developed EST-SSR markers ranged from 100 to 499 bp (average length 238 bp). Their motif sequence types were varied, with most being dinucleotides and pentanucleotides, and the most commonly found motifs were CAGAAT (29...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28324612/quantitative-image-analysis-of-single-molecule-mrna-dynamics-in-living-cells
#4
José Rino, Ana C de Jesus, Maria Carmo-Fonseca
Single mRNA molecules can be imaged in living cells by a method that consists in genetically inserting binding sites for a bacteriophage protein in the gene of interest. The resulting reporter transgene is then integrated in the genome of cells that express the phage protein fused to a fluorescent tag. Upon transcription, binding of the fluorescent protein to its target sequence makes the RNA visible. With this approach it is possible to track, in real time, the life cycle of a precursor mRNA at the site of transcription in the nucleus and transport of mature mRNA to the cytoplasm...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28320202/identification-and-expression-of-equine-mer-derived-mirnas
#5
Jeong-An Gim, Heui-Soo Kim
MicroRNAs (miRNAs) are single-stranded, small RNAs (21-23 nucleotides) that function in gene silencing and translational inhibition via the RNA interference mechanism. Most miRNAs originate from host genomic regions, such as intergenic regions, introns, exons, and transposable elements (TEs). Here, we focused on the palindromic structure of medium reiteration frequencies (MERs), which are similar to precursor miRNAs. Five MER consensus sequences (MER5A1, MER53, MER81, MER91C, and MER117) were matched with paralogous transcripts predicted to be precursor miRNAs in the horse genome (equCab2) and located in either intergenic regions or introns...
March 21, 2017: Molecules and Cells
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
#6
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/28301688/multiplex-single-cell-quantification-of-rare-rna-transcripts-from-protoplasts-in-a-model-plant-system
#7
Ulhas S Kadam, Burkhard Schulz, Joseph M K Irudayaraj
Here we demonstrate multiplex and simultaneous detection of four different rare RNA species from plant, Arabidopsis thaliana, using surface enhanced Raman spectroscopy and gold nanoprobes at single cell resolution. We show the applicability of nanoparticle-based Raman spectroscopic sensor to study intracellular RNA copies. First, we demonstrate that gold-nanoparticles decorate with Raman probes and carrying specific nucleic acid probe sequences can be uptaken by the protoplasts. We confirm the internalization of gold nanoprobes by TEM, ICP-MS, and fluorescence imaging...
March 16, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28300641/genome-editing-using-crispr-cas9-based-knock-in-approaches-in-zebrafish
#8
REVIEW
Shahad Albadri, Filippo Del Bene, Céline Revenu
With its variety of applications, the CRISPR/Cas9 genome editing technology has been rapidly evolving in the last few years. In the zebrafish community, knock-out reports are constantly increasing but insertion studies have been so far more challenging. With this review, we aim at giving an overview of the homologous directed repair (HDR)-based knock-in generation in zebrafish. We address the critical points and limitations of the procedure such as cutting efficiency of the chosen single guide RNA, use of cas9 mRNA or Cas9 protein, homology arm size etc...
March 11, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28300561/nucleolin-is-a-nuclear-target-of-heparan-sulfate-derived-from-glypican-1
#9
Fang Cheng, Mattias Belting, Lars-Åke Fransson, Katrin Mani
The recycling, S-nitrosylated heparan sulfate (HS) proteoglycan glypican-1 releases anhydromannose (anMan)-containing HS chains by a nitrosothiol-catalyzed cleavage in endosomes that can be constitutive or induced by ascorbate. The HS-anMan chains are then transported to the nucleus. A specific nuclear target for HS-anMan has not been identified. We have monitored endosome-to-nucleus trafficking of HS-anMan by deconvolution and confocal immunofluorescence microscopy using an anMan-specific monoclonal antibody in non-growing, ascorbate-treated, and growing, untreated, wild-type mouse embryonic fibroblasts and hypoxia-exposed Alzheimer mouse Tg2576 fibroblasts and human U87 glioblastoma cells...
March 12, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28298224/transcriptional-reprogramming-in-yeast-using-dcas9-and-combinatorial-grna-strategies
#10
Emil D Jensen, Raphael Ferreira, Tadas Jakočiūnas, Dushica Arsovska, Jie Zhang, Ling Ding, Justin D Smith, Florian David, Jens Nielsen, Michael K Jensen, Jay D Keasling
BACKGROUND: Transcriptional reprogramming is a fundamental process of living cells in order to adapt to environmental and endogenous cues. In order to allow flexible and timely control over gene expression without the interference of native gene expression machinery, a large number of studies have focused on developing synthetic biology tools for orthogonal control of transcription. Most recently, the nuclease-deficient Cas9 (dCas9) has emerged as a flexible tool for controlling activation and repression of target genes, by the simple RNA-guided positioning of dCas9 in the vicinity of the target gene transcription start site...
March 15, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28296173/snail-acetylation-by-histone-acetyltransferase-p300-in-lung-cancer
#11
Rui Chang, Yinjie Zhang, Peng Zhang, Qinghua Zhou
BACKGROUND: Epithelial to mesenchymal transition (EMT) is a complex and dynamic molecular event in lung cancer metastasis that has not yet been thoroughly investigated. EMT transcriptional factors, such as Snail, play a central role in regulation of the EMT process. In this study, we sought to identify an association between p300 and Snail in lung cancer, as well as the engagement of p300 in Snail acetylation. METHODS: We transfected p300 small interfering RNA into lung cancer cells to detect Snail and E-cadherin expression levels by real time-PCR...
March 13, 2017: Thoracic Cancer
https://www.readbyqxmd.com/read/28288683/chromatin-landscapes-and-genetic-risk-for-juvenile-idiopathic-arthritis
#12
Lisha Zhu, Kaiyu Jiang, Karstin Webber, Laiping Wong, Tao Liu, Yanmin Chen, James N Jarvis
BACKGROUND: The transcriptomes of peripheral blood cells in children with juvenile idiopathic arthritis (JIA) have distinct transcriptional aberrations that suggest impairment of transcriptional regulation. To gain a better understanding of this phenomenon, we studied known JIA genetic risk loci, the majority of which are located in non-coding regions, where transcription is regulated and coordinated on a genome-wide basis. We examined human neutrophils and CD4 primary T cells to identify genes and functional elements located within those risk loci...
March 14, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28287811/two-triacylglycerol-pathway-genes-ctdnep1-and-lpin1-are-down-regulated-by-hsa-mir-122-5p-in-hepatocytes
#13
Mahmood Naderi, Abdolreza Pazouki, Ehsan Arefian, Seyed Mahmoud Hashemi, Fatemeh Jamshidi-Adegani, Omid Gholamalamdari, Sara Soudi, Kayhan Azadmanesh, Siamak Mirab Samiee, Shahin Merat, Mohammad Gholami Fesharaki, Mahdieh Mondanizadeh, Mohammad Vasei, Masoud Soleimani
BACKGROUND: Expression of miR-122 is highly specific to hepatocytes of the liver.  This miRNA is involved in lipid hemostasis of the tissue; however, there is no comprehensive understanding of its function in lipid hemostasis. MATERIALS AND METHODS: Since hepatocytes are responsible for part of Triacylglycerol (TAG) synthesis in the body, we hypothesized that miR-122, as the most abundant miRNA in the tissue, might regulate TAG metabolism by targeting key enzymes that are involved in its production pathway...
March 2017: Archives of Iranian Medicine
https://www.readbyqxmd.com/read/28276850/associations-between-period-3-gene-polymorphisms-and-sleep-chronotype-related-variables-in-patients-with-late-life-insomnia
#14
Hader A Mansour, Joel Wood, Kodavali V Chowdari, Divya Tumuluru, Mikhil Bamne, Timothy H Monk, Martica H Hall, Daniel J Buysse, Vishwajit L Nimgaonkar
A variable number tandem repeat polymorphism (VNTR) in the period 3 (PER3) gene has been associated with heritable sleep and circadian variables, including self-rated chronotypes, polysomnographic (PSG) variables, insomnia and circadian sleep-wake disorders. This report describes novel molecular and clinical analyses of PER3 VNTR polymorphisms to better define their functional consequences. As the PER3 VNTR is located in the exonic (protein coding) region of PER3, we initially investigated whether both alleles (variants) are transcribed into messenger RNA in human fibroblasts...
February 27, 2017: Chronobiology International
https://www.readbyqxmd.com/read/28273364/a-multidomain-enzyme-with-glycerol-3-phosphate-dehydrogenase-and-phosphatase-activities-is-involved-in-a-chloroplastic-pathway-for-glycerol-synthesis-in-chlamydomonas-reinhardtii
#15
Daniela Morales-Sánchez, Yeongho Kim, Ee Leng Terng, Laura Peterson, Heriberto Cerutti
Understanding the unique features of algal metabolism may be necessary to realize the full potential of algae as feedstock for the production of biofuels and biomaterials. Under nitrogen deprivation, the green alga C. reinhardtii showed substantial triacylglycerol (TAG) accumulation and up-regulation of a gene, GPD2, encoding a multidomain enzyme with a putative phosphoserine phosphatase (PSP) motif fused to glycerol-3-phosphate dehydrogenase (GPD) domains. Canonical GPD enzymes catalyze the synthesis of glycerol-3-phosphate (G3P) by reduction of dihydroxyacetone phosphate (DHAP)...
March 8, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28271383/global-protein-expression-profile-response-of-planktonic-aeromonas-hydrophila-exposed-to-chlortetracycline
#16
Wanxin Li, Zujie Yao, Xiangyu Zhang, Fang Huang, Wenxiong Lin, Xiangmin Lin
The antibiotics resistance phenomena of Aeromonas hydrophila has become serious economic and public health problems for the world aquaculture industry and human health care. In this study, to investigate the instinct antibiotics adaptive mechanism of this pathogen, iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) based quantitative proteomics technologies were performed to compare the differential expression of A. hydrophila in planktonic status in response to chlortetracycline (CTC) stress and then identified total 1552 proteins including 285 altered proteins with 90 increasing and 195 decreasing abundance proteins...
April 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28267773/a-self-perpetuating-repressive-state-of-a-viral-replication-protein-blocks-superinfection-by-the-same-virus
#17
Xiao-Feng Zhang, Rong Sun, Qin Guo, Shaoyan Zhang, Tea Meulia, Randal Halfmann, Dawei Li, Feng Qu
Diverse animal and plant viruses block the re-infection of host cells by the same or highly similar viruses through superinfection exclusion (SIE), a widely observed, yet poorly understood phenomenon. Here we demonstrate that SIE of turnip crinkle virus (TCV) is exclusively determined by p28, one of the two replication proteins encoded by this virus. p28 expressed from a TCV replicon exerts strong SIE to a different TCV replicon. Transiently expressed p28, delivered simultaneously with, or ahead of, a TCV replicon, largely recapitulates this repressive activity...
March 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28267627/stop-codon-mutagenesis-for-homogenous-expression-of-human-papillomavirus-l1-protein-in-escherichia-coli
#18
Daning Wang, Fei Fan, Zhihai Li, Xinlin Liu, Shuo Song, Shuangping Wei, Maozhou He, Yahua Lin, Zhongyi Li, Minxi Wei, Hai Yu, Ying Gu, Shaowei Li, Ningshao Xia
Human papillomavirus (HPV) is widely accepted to be the major causative pathogen of cervical cancer, warts, and other epithelial tumors. Virus infection and subsequent disease development can be prevented by vaccination with HPV vaccines derived from eukaryotic expression systems. Here, we report the soluble expression of the major capsid protein L1 of HPV31, a dominant carcinogenic HPV genotype, in Escherichia coli. HPV31 L1 protein and its elongated form (L1+) were observed in SDS-PAGE and CE-SDS analysis, generated by the native HPV31 L1 gene with a TAA stop codon...
March 4, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28261684/evaluation-of-zinc-finger-e-box-binding-homeobox-1-and-transforming-growth-factor-beta2-expression-in-bladder-cancer-tissue-in-comparison-with-healthy-adjacent-tissue
#19
Ali Mahdavinezhad, Reza Yadegarazari, Seyed Habibollah Mousavi-Bahar, Jalal Poorolajal, Mohammad Jafari, Mohammad Ali Amirzargar, Hosein Effatpanah, Massoud Saidijam
PURPOSE: The fifth most common cancer is allocated to bladder cancer (BC) worldwide. Understanding the molecular mechanisms of BC invasion and metastasis to identify target therapeutic strategies will improve disease survival. So the aim of this study was to measure expression rate of zinc finger E-box binding homeobox 1 (ZEB1) and transforming growth factor-beta2 (TGF-β2) mRNA in tissue samples of patients with BC and its healthy adjacent tissue samples and their association with muscle invasion, size and grade of the tumor...
March 2017: Investigative and Clinical Urology
https://www.readbyqxmd.com/read/28254804/gene-editing-with-crispr-cas9-rna-directed-nuclease
#20
REVIEW
Thomas Doetschman, Teodora Georgieva
Genetic engineering of model organisms and cultured cells has for decades provided important insights into the mechanisms underlying cardiovascular development and disease. In the past few years the development of several nuclease systems has broadened the range of model/cell systems that can be engineered. Of these, the CRISPR (clustered regularly interspersed short palindromic repeats)/Cas9 (CRISPR-associated protein 9) system has become the favorite for its ease of application. Here we will review this RNA-guided nuclease system for gene editing with respect to its usefulness for cardiovascular studies and with an eye toward potential therapy...
March 3, 2017: Circulation Research
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