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https://www.readbyqxmd.com/read/28436945/adar1-controls-apoptosis-of-stressed-cells-by-inhibiting-staufen1-mediated-mrna-decay
#1
Masayuki Sakurai, Yusuke Shiromoto, Hiromitsu Ota, Chunzi Song, Andrew V Kossenkov, Jayamanna Wickramasinghe, Louise C Showe, Emmanuel Skordalakes, Hsin-Yao Tang, David W Speicher, Kazuko Nishikura
Both p150 and p110 isoforms of ADAR1 convert adenosine to inosine in double-stranded RNA (dsRNA). ADAR1p150 suppresses the dsRNA-sensing mechanism that activates MDA5-MAVS-IFN signaling in the cytoplasm. In contrast, the biological function of the ADAR1p110 isoform, which is usually located in the nucleus, is largely unknown. Here, we show that stress-activated phosphorylation of ADAR1p110 by MKK6-p38-MSK MAP kinases promotes its binding to Exportin-5 and its export from the nucleus. After translocating to the cytoplasm, ADAR1p110 suppresses apoptosis in stressed cells by protecting many antiapoptotic gene transcripts that contain 3'-untranslated-region dsRNA structures primarily comprising inverted Alu repeats...
April 24, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28423240/biochemical-cellular-physiological-and-pathological-consequences-of-human-loss-of-n-glycolylneuraminic-acid
#2
Jonathan Okerblom, Ajit Varki
About 2-3 million years ago, Alu-mediated deletion of a critical exon in the CMAH gene became fixed in the hominin lineage ancestral to humans, possibly through a stepwise process of selection by pathogen targeting of the CMAH product (the sialic acid Neu5Gc), followed by reproductive isolation via female anti-Neu5Gc antibodies. Loss of CMAH has occurred independently in some other lineages, but is functionally intact in Old World primates, including our closest relatives, the chimpanzees. While the biophysical and biochemical ramifications of losing tens of millions of Neu5Gc hydroxyl groups at most cell surfaces remains poorly understood, there are multi-scale effects functionally relevant to both sides of the host-pathogen interface...
April 19, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28417465/effects-of-rare-sugar-d-allulose-on-heat-induced-gelation-of-surimi-prepared-from-marine-fish
#3
Masahiro Ogawa, Masaki Inoue, Shigeru Hayakawa, Siwaporn O'Charoen, Makiko Ogawa
BACKGROUND: d-allulose (Alu), the C3-epimer of D-fructose, is noncalorie sweetener (0.39 kcal g(-1) ) with a suppressive effect on postprandial blood glucose elevation. The aim of this study was to investigate the effects of Alu used as sweetener and gel improver instead of sucrose on heat-induced gelation of surimi. RESULTS: The puncture test of a heat-induced surimi gel showed that the surimi gel with 50 g kg(-1) . Alu had 15 and 6 % higher gel strength than the counterpart gel with sucrose (Suc) and that with sorbitol (Sor), respectively...
April 18, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28415677/selective-elimination-of-long-interspersed-element-1-expressing-tumour-cells-by-targeted-expression-of-the-hsv-tk-suicide-gene
#4
Mariam Chendeb, Robert Schneider, Irwin Davidson, Anas Fadloun
In gene therapy, effective and selective suicide gene expression is crucial. We exploited the endogenous Long INterspersed Element-1 (L1) machinery often reactivated in human cancers to integrate the Herpes Simplex Virus Thymidine Kinase (HSV-TK) suicide gene selectively into the genome of cancer cells. We developed a plasmid-based system directing HSV-TK expression only when reverse transcribed and integrated in the host genome via the endogenous L1 ORF1/2 proteins and an Alu element. Delivery of these new constructs into cells followed by Ganciclovir (GCV) treatment selectively induced mortality of L1 ORF1/2 protein expressing cancer cells, but had no effect on primary cells that do not express L1 ORF1/2...
March 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28413449/links-between-dna-methylation-and-nucleosome-occupancy-in-the-human-genome
#5
Clayton K Collings, John N Anderson
BACKGROUND: DNA methylation is an epigenetic modification that is enriched in heterochromatin but depleted at active promoters and enhancers. However, the debate on whether or not DNA methylation is a reliable indicator of high nucleosome occupancy has not been settled. For example, the methylation levels of DNA flanking CTCF sites are higher in linker DNA than in nucleosomal DNA, while other studies have shown that the nucleosome core is the preferred site of methylation. In this study, we make progress toward understanding these conflicting phenomena by implementing a bioinformatics approach that combines MNase-seq and NOMe-seq data and by comprehensively profiling DNA methylation and nucleosome occupancy throughout the human genome...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28391141/development-and-validation-of-a-novel-multiplexed-dna-analysis-system-innotyper-%C3%A2-21
#6
Hiromi Brown, Robyn Thompson, Gina Murphy, Dixie Peters, Bobby La Rue, Jonathan King, Anne H Montgomery, Marion Carroll, James Baus, Sid Sinha, Frank R Wendt, Bing Song, Ranajit Chakraborty, Bruce Budowle, Sudhir K Sinha
We report here a novel multiplexed DNA analysis system consisting of 20 Alu markers and Amelogenin for analysis of highly degraded forensic biological samples. The key to the success of the system in obtaining results from degraded samples is the primer design yielding small amplicon size (60-125bp) for all 20 markers. The markers included in the InnoTyper(®) 21 system are bi-allelic, having two possible allelic states (insertion or null) and thus termed INNULs. The markers are short interspersed nuclear elements (SINEs), a category of retrotransposable elements (REs) which are non-coding genomic DNA repeat sequences, or "mobile insertion elements," comprising approximately 40% of the human genome...
March 18, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28381046/correction-of-spherical-aberration-in-multi-focal-multiphoton-microscopy-with-spatial-light-modulator
#7
Naoya Matsumoto, Alu Konno, Yasushi Ohbayashi, Takashi Inoue, Akiyuki Matsumoto, Kenji Uchimura, Kenji Kadomatsu, Shigetoshi Okazaki
We demonstrate that high-quality images of the deep regions of a thick sample can be obtained from its surface by multi-focal multiphoton microscopy (MMM). The MMM system incorporates a spatial light modulator to separate the excitation beam into a multi-focal excitation beam and modulate the pre-distortion wavefront to correct spherical aberration (SA) caused by a refractive index mismatch between the immersion medium and the biological sample. When fluorescent beads in transparent epoxy resin were observed using four SA-corrected focal beams, the fluorescence signal of the obtained images was ~52 times higher than that obtained without SA correction until a depth of ~1100 μm, similar to the result for single-focal multiphoton microscopy (SMM)...
March 20, 2017: Optics Express
https://www.readbyqxmd.com/read/28377526/the-r263k-dolutegravir-resistance-associated-substitution-progressively-decreases-hiv-1-integration
#8
Thibault Mesplède, Jing Leng, Hanh Thi Pham, Jiaming Liang, Yudong Quan, Yingshan Han, Mark A Wainberg
Human immunodeficiency virus (HIV) infection persists despite decades of active antiretroviral therapy (ART), effectively preventing viral eradication. Treatment decreases plasma viral RNA, but viral DNA persists, mostly integrated within the genome of nucleated blood cells. Viral DNA blood levels correlate with comorbidities and the rapidity of viral rebound following treatment interruption. To date, no intervention aiming at decreasing HIV DNA levels below those attained through ART has been successful. This includes use of some integrase inhibitors either as part of ART or in treatment intensification studies...
April 4, 2017: MBio
https://www.readbyqxmd.com/read/28371479/alu-mediated-deletion-of-pigl-in-a-patient-with-chime-syndrome
#9
Amy Knight Johnson, Gerald Bradley Schaefer, Jennifer Lee, Ying Hu, Daniela Del Gaudio
CHIME syndrome is a rare autosomal recessive neuroectodermal disorder associated with biallelic mutations in PIGL. To date, six molecularly confirmed cases of CHIME syndrome have been reported. Here, we report the seventh patient with biallelic PIGL mutations associated with CHIME syndrome and describe the first characterization of an intragenic deletion in PIGL. Our characterization of the deletion breakpoint junction demonstrated that the breakpoints occurred within Alu repeats and the deletion was most likely mediated by a microhomology event...
March 28, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28357596/combined-sense-antisense-alu-elements-activate-the-egfp-reporter-gene-when-stable-transfection
#10
Zhihong Ma, Xianglong Kong, Shufeng Liu, Shuxian Yin, Yuehua Zhao, Chao Liu, Zhanjun Lv, Xiufang Wang
Alu elements in the human genome are present in more than one million copies, accounting for 10% of the genome. However, the biological functions of most Alu repeats are unknown. In this present study, we detected the effects of Alu elements on EGFP gene expression using a plasmid system to find the roles of Alu elements in human genome. We inserted 5'-4TMI-Alus-CMV promoter-4TMI-Alus (or antisense Alus)-3' sequences into the pEGFP-C1 vector to construct expression vectors. We altered the copy number of Alus, the orientation of the Alus, and the presence of an enhancer (4TMI) in the inserted 5'-4TMI-Alus-CMV promoter-4TMI-Alus (or antisense Alus)-3' sequences...
March 29, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28355180/dhx9-suppresses-rna-processing-defects-originating-from-the-alu-invasion-of-the-human-genome
#11
Tuğçe Aktaş, İbrahim Avşar Ilık, Daniel Maticzka, Vivek Bhardwaj, Cecilia Pessoa Rodrigues, Gerhard Mittler, Thomas Manke, Rolf Backofen, Asifa Akhtar
Transposable elements are viewed as 'selfish genetic elements', yet they contribute to gene regulation and genome evolution in diverse ways. More than half of the human genome consists of transposable elements. Alu elements belong to the short interspersed nuclear element (SINE) family of repetitive elements, and with over 1 million insertions they make up more than 10% of the human genome. Despite their abundance and the potential evolutionary advantages they confer, Alu elements can be mutagenic to the host as they can act as splice acceptors, inhibit translation of mRNAs and cause genomic instability...
April 6, 2017: Nature
https://www.readbyqxmd.com/read/28347230/inhibition-of-microrna-21-via-locked-nucleic-acid-anti-mir-suppressed-metastatic-features-of-colorectal-cancer-cells-through-modulation-of-programmed-cell-death-4
#12
Reza Nedaeinia, Mohammadreza Sharifi, Amir Avan, Mohammad Kazemi, Abdolreza Nabinejad, Gordon A Ferns, Majid Ghayour-Mobarhan, Rasoul Salehi
Colorectal cancer is among the most lethal of malignancies, due to its propensity to metastatic spread and multifactorial-chemoresistance. The latter property supports the need to identify novel therapeutic approaches for the treatment of colorectal cancer. MicroRNAs are endogenous non-coding small RNA molecules that function as post-transcriptional regulators of gene expression. Recently, programmed cell death 4 has been identified as a protein that increases during apoptosis. This gene is among the potential targets of miR-21 (OncomiR)...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28345016/-by-slapping-their-laps-the-patient-will-know-that-you-truly-care-for-her-a-qualitative-study-on-social-norms-and-acceptability-of-the-mistreatment-of-women-during-childbirth-in-abuja-nigeria
#13
Meghan A Bohren, Joshua P Vogel, Özge Tunçalp, Bukola Fawole, Musibau A Titiloye, Akinpelu Olanrewaju Olutayo, Agnes A Oyeniran, Modupe Ogunlade, Loveth Metiboba, Olubunmi R Osunsan, Hadiza A Idris, Francis E Alu, Olufemi T Oladapo, A Metin Gülmezoglu, Michelle J Hindin
BACKGROUND: Many women experience mistreatment during childbirth in health facilities across the world. However, limited evidence exists on how social norms and attitudes of both women and providers influence mistreatment during childbirth. Contextually-specific evidence is needed to understand how normative factors affect how women are treated. This paper explores the acceptability of four scenarios of mistreatment during childbirth. METHODS: Two facilities were identified in Abuja, Nigeria...
December 2016: SSM—Population Health
https://www.readbyqxmd.com/read/28343765/human-cardiac-progenitor-cells-with-regenerative-potential-can-be-isolated-and-characterized-from-3d-electro-anatomic-guided-endomyocardial-biopsies
#14
Domenico D'Amario, Antonio Maria Leone, Maria Lucia Narducci, Costantino Smaldone, Dalgisio Lecis, Frediano Inzani, Marco Luciani, Andrea Siracusano, Federica La Neve, Melissa Manchi, Gemma Pelargonio, Francesco Perna, Piergiorgio Bruno, Massimo Massetti, Dario Pitocco, Donato Cappetta, Grazia Esposito, Konrad Urbanek, Antonella De Angelis, Francesco Rossi, Roberto Piacentini, Giulia Angelini, Domenica Donatella Li Puma, Claudio Grassi, Elisa De Paolis, Ettore Capoluongo, Valentina Silvestri, Biagio Merlino, Riccardo Marano, Filippo Crea
AIMS: In the present study, we aimed to develop a percutaneous approach and a reproducible methodology for the isolation and expansion of Cardiac Progenitor Cells (CPCs) from EndoMyocardial Biopsies (EMB) in vivo. Moreover, in an animal model of non-ischemic heart failure (HF), we would like to test whether CPCs obtained by this methodology may engraft the myocardium and differentiate. METHODS AND RESULTS: EMB were obtained using a preformed sheath and a disposable bioptome, advanced via right femoral vein in 12 healthy mini pigs, to the right ventricle...
March 1, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/28333464/quantification-of-thermodynamic-hydridicity-of-hydride-complexes-of-mn-re-mo-and-w-using-the-molecular-electrostatic-potential
#15
K S Sandhya, Cherumuttathu H Suresh
The molecular electrostatic potential (MESP) at the hydride nucleus, VH, is proposed as a powerful measure of the hydride donor ability (hydridicity) of metal hydride complexes. VH values have been determined for several group VI and group VII octahedral metal hydride complexes of Mo, W, Mn, and Re at the B3LYP level of DFT. Further, the hydridicity, defined by the thermodynamic parameter ΔG°H(-) is determined for all of these complexes using a thermodynamic cycle that describes hydride abstraction reactions by H3O(+) ions...
March 30, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28303792/toward-theoretical-synthesis-of-biocomputer
#16
Ting-Yu Kuo, Chun-Liang Lin, Natdanai Charoenkit, Yang-Yi Chen, Chakkrit Preuksakarn
Increasing applications of fundamental biological gates have been successfully built during this decade. Proceeding to the current development, this study presents a genetic arithmetic and logical unit (ALU) design based on a series of genetic logic gates. The system level's architecture consists of three parts: temp register, ALU and accumulator register. Using the concept of the ALU on the digital computer, the authors present the fundamental function of the genetic ALU via full adder register and also build the bio-storage devices to store data generated from the genetic ALU...
February 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28277746/genetic-variation-of-mhc-class-i-polymorphic-alu-insertions-poalins-in-three-subpopulations-of-the-east-midlands-uk
#17
Sarabjit S Mastana, Jasvinder S Bhatti, Puneetpal Singh, Adam Wiles, Jonathan Holland
BACKGROUND: Alu elements are highly researched due to their useful nature as markers in the study of human population genetics. Recently discovered Major Histocompatibility Complex (MHC) polymorphic Alu insertions (POALINs) have not been examined extensively for genetic variation and their HLA associations. AIMS: The aim of this study is to assess the genetic variation between three populations using five recently discovered POALINs. METHODS AND SUBJECTS: The study examined 190 healthy, unrelated subjects from three different populations in the East Midlands (UK) for the presence or absence of five Alu elements (AluHG, AluMICB, AluHJ, AluTF and AluHF) via the polymerase chain reaction followed by gel electrophoresis...
March 5, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/28259415/evaluation-of-horn-bud-wound-healing-following-cautery-disbudding-of-preweaned-dairy-calves-treated-with-aluminum-based-aerosol-bandage
#18
K L Huebner, A K Kunkel, C S McConnel, R J Callan, R P Dinsmore, L S Caixeta
Pain management during and following disbudding procedures has been studied extensively, though few studies have evaluated wound healing following cautery disbudding in dairy calves. The purpose of this study was to observe wound healing following cautery disbudding with or without treatment using a topical aluminum-based aerosol bandage (ALU) in preweaned dairy calves. Dairy calves were disbudded within the first 3 wk of life using a standard cautery disbudding protocol. The ALU treatment was randomly allocated to the right or left horn bud within each animal...
May 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28253503/xp22-31-microdeletion-due-to-microhomology-mediated-break-induced-replication-in-a-boy-with-contiguous-gene-deletion-syndrome
#19
Koki Nagai, Hirohito Shima, Miki Kamimura, Junko Kanno, Erina Suzuki, Akira Ishiguro, Satoshi Narumi, Shigeo Kure, Ikuma Fujiwara, Maki Fukami
The Xp22.31 region is characterized by a low frequency of interspersed repeats and a low GC content. Submicroscopic deletions at Xp22.31 involving STS and ANOS1 (alias KAL1) underlie X-linked ichthyosis and Kallmann syndrome, respectively. Of the known microdeletions at Xp22.31, a common approximately 1.5-Mb deletion encompassing STS was ascribed to nonallelic homologous recombination, while 2 ANOS1-containing deletions were attributed to nonhomologous end-joining. However, the genomic bases of other microdeletions within the Xp22...
2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28251877/genomic-landscape-of-cpg-rich-elements-in-human
#20
Vladimir N Babenko, Irina V Chadaeva, Yuriy L Orlov
BACKGROUND: The studies on CpG islands (CGI) and Alu elements functions, evolution, and distribution in the genome started since the discovery in nineteen eighties (1981, 1986, correspondingly). Their highly skewed genome wide distribution implies the non-random retrotransposition pattern. Besides CGIs in gene promoters, CGIs clusters were observed in the homeobox gene regions and in the macrosatellites, but the whole picture of their distribution specifics was not grasped. Attempts to identify any causative features upon their (genome wide) distribution, such as the DNA context mediated preferred insertion sites of Alu repeats, have been made to ascribe their clusters location...
February 7, 2017: BMC Evolutionary Biology
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