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https://www.readbyqxmd.com/read/28209632/high-resolution-profiling-of-nmd-targets-in-yeast-reveals-translational-fidelity-as-a-basis-for-substrate-selection
#1
Alper Celik, Richard Baker, Feng He, Allan Jacobson
Nonsense-mediated mRNA decay (NMD) plays an important role in eukaryotic gene expression yet the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we re-evaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. Our new RNA-Seq analyses confirm previous results of microarray studies, but also uncover hundreds of new NMD-regulated transcripts that had escaped previous detection, including many intron-containing pre-mRNAs and several non-coding RNAs...
February 16, 2017: RNA
https://www.readbyqxmd.com/read/28188954/comparative-glandular-trichome-transcriptome-based-gene-characterization-reveals-reasons-for-differential-menthol-biosynthesis-in-mentha-species
#2
Md Qussen Akhtar, Nida Qamar, Pallavi Yadav, Pallavi Kulkarni, Ajay Kumar, Ajit Kumar Shasany
The genes involved in menthol biosynthesis are reported earlier in Mentha × piperita. But the information on these genes is not available in Mentha arvensis. To bridge the gap in knowledge on differential biosynthesis of monoterpenes leading to compositional variation in the essential oil of these species, a comparative transcriptome analysis of the glandular trichome was carried out. In addition to the MVA and MEP pathway genes, about 210 and 196 different terpene synthases (TPS) transcripts were identified from annotation in M...
February 11, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/28188297/alternative-splicing-in-the-cytochrome-p450-superfamily-expands-protein-diversity-to-augment-gene-function-and-redirect-human-drug-metabolism
#3
Andrew J Annalora, Craig B Marcus, Patrick L Iversen
The human genome encodes 57 cytochrome P450 (CYP) genes whose enzyme products metabolize hundreds of drugs, thousands of xenobiotics and unknown numbers of endogenous compounds including steroids, retinoids and icosinoids. Indeed, CYP genes are the first line of defense against daily environmental chemical challenges in a manner that parallels the immune system. Several databases, including PubMed, AceView, and Ensembl, were queried to establish a comprehensive analysis of the full human CYP transcriptome. This review describes a remarkable diversification of the 57 human CYP genes, which may be alternatively processed into nearly 1000 distinct mRNA transcripts to shape an individual's CYP proteome...
February 10, 2017: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/28175989/predictors-of-health-related-quality-of-life-in-boys-with-duchenne-muscular-dystrophy-from-six-european-countries
#4
Christiane Otto, Birgit F Steffensen, Ann-Lisbeth Højberg, Claus Barkmann, Jes Rahbek, Ulrike Ravens-Sieberer, Annette Mahoney, Julia Vry, Kathrin Gramsch, Rachel Thompson, Sunil Rodger, Kate Bushby, Hanns Lochmüller, Janbernd Kirschner
Duchenne muscular dystrophy (DMD) is a progressive, genetically determined neuromuscular disease that affects males and leads to severe physical disability in early teenage years. Over the last decades, patient-reported outcomes such as Health-Related Quality of Life (HRQoL) gained great interest in clinical research. However, little is known about factors affecting HRQoL in boys with DMD. Data from the multi-center CARE-NMD project of boys with DMD from six European countries collected between 2011 and 2012 were analyzed (8-17 years old; n = 321)...
February 7, 2017: Journal of Neurology
https://www.readbyqxmd.com/read/28166811/pathogenic-variant-burden-in-the-exac-database-an-empirical-approach-to-evaluating-population-data-for-clinical-variant-interpretation
#5
Yuya Kobayashi, Shan Yang, Keith Nykamp, John Garcia, Stephen E Lincoln, Scott E Topper
BACKGROUND: The frequency of a variant in the general population is a key criterion used in the clinical interpretation of sequence variants. With certain exceptions, such as founder mutations, the rarity of a variant is a prerequisite for pathogenicity. However, defining the threshold at which a variant should be considered "too common" is challenging and therefore diagnostic laboratories have typically set conservative allele frequency thresholds. METHODS: Recent publications of large population sequencing data, such as the Exome Aggregation Consortium (ExAC) database, provide an opportunity to characterize with accuracy and precision the frequency distributions of very rare disease-causing alleles...
February 6, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28155073/nimodipine-ophthalmic-formulations-for-management-of-glaucoma
#6
Doaa Nabih Maria, Abd-Elgawad Helmy Abd-Elgawad, Osama Abd-Elazeem Soliman, Marwa Salah El-Dahan, Monica M Jablonski
PURPOSE: Preparation and evaluation of topical ophthalmic formulations containing nimodipine-CD complexes prepared using HP-β-CD, SBE-β-CD and M-β-CD for the management of glaucoma. METHODS: Nimodipine-CD complexes were prepared using a freeze-drying method. Two different molar ratios (NMD:CD) were used for each cyclodextrin. The inclusion complexes were characterized using DSC, FTIR, yield (%), drug content and in vitro release characteristics. NMD-CD complexes incorporated into chitosan eye drops and a temperature-triggered in situ gelling system were evaluated for their pH, viscosity and in vitro release characteristics...
February 2, 2017: Pharmaceutical Research
https://www.readbyqxmd.com/read/28153460/prognostic-value-of-nocturnal-hypoventilation-in-neuromuscular-patients
#7
David Orlikowski, Helene Prigent, Maria-Antonia Quera Salva, Nicholas Heming, Cendrine Chaffaut, Sylvie Chevret, Djillali Annane, Frederic Lofaso, Adam Ogna
In neuromuscular disease (NMD) patients, current guidelines recommend the initiation of home mechanical ventilation (HMV) in case of daytime hypercapnia or nocturnal desaturation as an indirect sign of hypoventilation. Transcutaneous capno-oximetry (TcCO2) enables the direct assessment of nocturnal hypercapnia; however the best cut-off value remains to be defined. We aimed to compare the prognostic value of several published definitions of nocturnal hypercapnia in a cohort of NMD patients. All consecutive TcCO2 recordings performed between 2010 and 2014 in unventilated adult NMD patients in a tertiary reference centre were retrospectively collected...
December 21, 2016: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/28145797/characterisation-of-new-generation-aminoglycoside-promoting-premature-termination-codon-readthrough-in-cancer-cells
#8
Laure Bidou, Olivier Bugaud, Valery Belakhov, Timor Baasov, Olivier Namy
Nonsense mutations, generating premature termination codons (PTCs), account for 10% to 30% of the mutations in tumour suppressor genes. Nonsense translational suppression, induced by small molecules including gentamicin and G418, has been suggested as a potential therapy to counteract the deleterious effects of nonsense mutations in several genetic diseases and cancers. We describe here that NB124, a synthetic aminoglycoside derivative recently developed especially for PTC suppression, strongly induces apoptosis in human tumour cells by promoting high level of PTC readthrough...
February 1, 2017: RNA Biology
https://www.readbyqxmd.com/read/28144752/novel-fam134b-mutations-and-their-clinicopathological-significance-in-colorectal-cancer
#9
Farhadul Islam, Vinod Gopalan, Riajul Wahab, Katherine Ting-Wei Lee, Md Hakimul Haque, Afraa Mamoori, Cu-Tai Lu, Robert A Smith, Alfred K-Y Lam
FAM134B is a putative tumour suppressor gene and no mutations in FAM134B have been reported in colorectal cancer (CRC) to date. This study aims to identify FAM134B mutation sites and the clinicopathological significance of the gene in patients with CRC. Eighty-eight colorectal cancers were studied for FAM134B mutations by Sanger sequencing. The mutations in these cancers were then tested for correlations with the clinical and pathological parameters of the studied cancers. In addition, mRNA and protein expression of FAM134B in colorectal cancers was examined by polymerase chain reaction, Western blots, and immunofluorescence analysis...
January 31, 2017: Human Genetics
https://www.readbyqxmd.com/read/28144257/treatment-of-denture-related-stomatitis-improves-endothelial-function-assessed-by-flow-mediated-vascular-dilation
#10
Grzegorz Osmenda, Joanna Maciąg, Grzegorz Wilk, Anna Maciąg, Daniel Nowakowski, Jolanta Loster, Elżbieta Dembowska, Douglas Robertson, Tomasz Guzik, Marta Cześnikiewicz-Guzik
INTRODUCTION: The presence of oral inflammation has recently been linked with the pathogenesis of cardiovascular diseases. While numerous studies have described links between periodontitis and endothelial dysfunction, little is known about the influence of denture-related stomatitis (DRS) on cardiovascular risk. Therefore, the aim of this study was to determine whether the treatment of DRS can lead to improvement of the clinical measures of vascular dysfunction. MATERIAL AND METHODS: The DRS patients were treated with a local oral antifungal agent for 3 weeks...
February 1, 2017: Archives of Medical Science: AMS
https://www.readbyqxmd.com/read/28128343/rna-sequencing-of-synaptic-and-cytoplasmic-upf1-bound-transcripts-supports-contribution-of-nonsense-mediated-decay-to-epileptogenesis
#11
Claire M Mooney, Eva M Jimenez-Mateos, Tobias Engel, Catherine Mooney, Mairead Diviney, Morten T Venø, Jørgen Kjems, Michael A Farrell, Donncha F O'Brien, Norman Delanty, David C Henshall
The nonsense mediated decay (NMD) pathway is a critical surveillance mechanism for identifying aberrant mRNA transcripts. It is unknown, however, whether the NMD system is affected by seizures in vivo and whether changes confer beneficial or maladaptive responses that influence long-term outcomes such the network alterations that produce spontaneous recurrent seizures. Here we explored the responses of the NMD pathway to prolonged seizures (status epilepticus) and investigated the effects of NMD inhibition on epilepsy in mice...
January 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28124995/virus-escape-and-manipulation-of-cellular-nonsense-mediated-mrna-decay
#12
REVIEW
Giuseppe Balistreri, Claudia Bognanni, Oliver Mühlemann
Nonsense-mediated mRNA decay (NMD), a cellular RNA turnover pathway targeting RNAs with features resulting in aberrant translation termination, has recently been found to restrict the replication of positive-stranded RNA ((+)RNA) viruses. As for every other antiviral immune system, there is also evidence of viruses interfering with and modulating NMD to their own advantage. This review will discuss our current understanding of why and how NMD targets viral RNAs, and elaborate counter-defense strategies viruses utilize to escape NMD...
January 23, 2017: Viruses
https://www.readbyqxmd.com/read/28115162/nonstop-mrna-decay-machinery-is-involved-in-the-clearance-of-mrna-5-fragments-produced-by-rnai-and-nmd-in-drosophila-melanogaster-cells
#13
Yoshifumi Hashimoto, Masaki Takahashi, Eri Sakota, Yoshikazu Nakamura
When translating mRNAs are cleaved in protein-coding regions, 5' fragments of mRNAs are detached from stop codons (i.e., nonstop mRNAs) and protected from 3'-5' exonucleases by ribosomes stalled at the 3' termini. It has been shown in yeast that the nonstop mRNA decay (NSD) machinery triggers nonstop mRNA degradation by removing stalled ribosomes in the artificial reporter mRNAs. However, it is not known well whether NSD is involved in the degradation of endogenous nonstop mRNAs in higher eukaryotes. In this work, we addressed the question of whether 5'-nonstop-mRNA fragments generated by siRNA cleavage or nonsense-mediated-mRNA decay (NMD) are degraded by the NSD pathway in Drosophila melanogaster cells by knocking down three NSD components, Pelota (a yeast Dom34 homolog), Hbs1 and ABCE1 (a ribosome-recycling factor)...
January 20, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28115040/nonsense-mediated-mrna-decay-at-the-crossroads-of-many-cellular-pathways
#14
Fabrice Lejeune
Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism ensuring the fast decay of mRNAs harboring a premature termination codon (PTC). As a quality control mechanism, NMD distinguishes PTCs from normal termination codons in order to degrade PTC-carrying mRNAs only. For this, NMD is connected to various other cell processes which regulate or activate it under specific cell conditions or in response to mutations, mis-regulations, stresses, or particular cell programs. These cell processes and their connections with NMD are the focus of this review, which aims both to illustrate the complexity of the NMD mechanism and its regulation and to highlight the cellular consequences of NMD inhibition...
January 24, 2017: BMB Reports
https://www.readbyqxmd.com/read/28097850/-a-regenerative-anemia-in-infants-2-cases-of-pearson%C3%A2-s-syndrome
#15
José M Martínez de Zabarte Fernández, Carmen Rodríguez-Vigil Iturrate, Cristina Martínez Faci, Inmaculada García Jiménez, Laura Murillo Sanjuan, Ascensión Muñoz Mellado
Anemia is very common in infants. Although its causes are usually not severe and treatable, proper etiologic diagnosis should be established. When anemia is non-regenerative, it can be caused by aplastic anemia, myelodysplastic syndrome, bone marrow infiltration or hematopoietic factors deficiencies. Another possible cause is Pearson's syndrome, a rare mitochondrial disease that causes non-regenerative anemia associated with other cytopenias, pancreatic insufficiency, lactic acidosis and great variability in clinical presentation conditioned by heteroplasmy...
1, 2017: Archivos Argentinos de Pediatría
https://www.readbyqxmd.com/read/28093036/combining-nanoscale-magnetic-nimodipine-liposomes-with-magnetic-resonance-image-for-parkinson-s-disease-targeting-therapy
#16
Bingshuo Ji, Meili Wang, Dawei Gao, Shanshan Xing, Lei Li, Lanxiang Liu, Min Zhao, Ximing Qi, Kun Dai
AIM: To enhance drug targeting and blood-brain barrier penetration for Parkinson's disease (PD), a novel nanoscale magnetic nimodipine (NMD) delivery system was designed and prepared. MATERIALS & METHODS: The PD rats were established and treated with free NMD or Fe3O4-modified NMD liposomes (Fe3O4-NMD-lips). Then, factional anisotropy values were measured by MRI to evaluate therapy efficacy. RESULTS: Fe3O4-NMD-lips showed the best neuroprotective effect, and the NMD concentration of lesions was 2...
January 17, 2017: Nanomedicine
https://www.readbyqxmd.com/read/28090303/genotype-phenotype-effects-of-bmpr2-mutations-on-disease-severity-in-mouse-models-of-pulmonary-hypertension
#17
Andrea L Frump, Arunima Datta, Sampa Ghose, James West, Mark P de Caestecker
More than 350 mutations in the type-2 BMP (bone morphogenetic protein) receptor, BMPR2, have been identified in patients with heritable pulmonary arterial hypertension (HPAH). However, only 30% of BMPR2 mutation carriers develop PAH, and we cannot predict which of these carriers will develop clinical disease. One possibility is that the nature of the BMPR2 mutation affects disease severity. This hypothesis has been difficult to test clinically, given the rarity of HPAH and the complexity of the confounding genetic and environmental risk factors...
December 2016: Pulmonary Circulation
https://www.readbyqxmd.com/read/28077099/a-prospective-study-on-the-characteristics-and-subjects-of-pediatric-palliative-care-case-management-provided-by-a-hospital-based-palliative-care-team
#18
Charissa T Jagt-van Kampen, Marijke C Kars, Derk A Colenbrander, Diederik K Bosman, Martha A Grootenhuis, Huib N Caron, Antoinette Y N Schouten-van Meeteren
BACKGROUND: Case management is a subject of interest within pediatric palliative care. Detailed descriptions of the content of this type of case management are lacking. We aim to describe the contents of care provided, utilization of different disciplines, and times of usage of a pediatric palliative care case management program compared for patients with malignant disease (MD) and non-malignant disease (NMD). METHODS: A three-month prospective study, with questionnaires filled in by members of a pediatric palliative care team (PPCT) for each contact with parents...
January 12, 2017: BMC Palliative Care
https://www.readbyqxmd.com/read/28062855/expression-of-the-erf1-translation-termination-factor-is-controlled-by-an-autoregulatory-circuit-involving-readthrough-and-nonsense-mediated-decay-in-plants
#19
Tünde Nyikó, Andor Auber, Levente Szabadkai, Anna Benkovics, Mariann Auth, Zsuzsanna Mérai, Zoltán Kerényi, Andrea Dinnyés, Ferenc Nagy, Dániel Silhavy
When a ribosome reaches a stop codon, the eukaryotic Release Factor 1 (eRF1) binds to the A site of the ribosome and terminates translation. In yeasts and plants, both over- and underexpression of eRF1 lead to altered phenotype indicating that eRF1 expression should be strictly controlled. However, regulation of eRF1 level is still poorly understood. Here we show that expression of plant eRF1 is controlled by a complex negative autoregulatory circuit, which is based on the unique features of the 3'untranslated region (3'UTR) of the eRF1-1 transcript...
January 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28054750/somatic-med12-nonsense-mutation-escapes-mrna-decay-and-reveals-a-motif-required-for-nuclear-entry
#20
Tuomas Heikkinen, Kati Kämpjärvi, Salla Keskitalo, Pernilla von Nandelstadh, Xiaonan Liu, Ville Rantanen, Esa Pitkänen, Matias Kinnunen, Heikki Kuusanmäki, Mika Kontro, Mikko Turunen, Netta Mäkinen, Jussi Taipale, Caroline Heckman, Kaisa Lehti, Satu Mustjoki, Markku Varjosalo, Pia Vahteristo
MED12 is a key component of the transcription-regulating Mediator complex. Specific missense and in-frame insertion/deletion mutations in exons 1 and 2 have been identified in uterine leiomyomas, breast tumors, and chronic lymphocytic leukemia. Here, we characterize the first MED12 5' end nonsense mutation (c.97G>T, p.E33X) identified in acute lymphoblastic leukemia and show that it escapes nonsense-mediated mRNA decay (NMD) by using an alternative translation initiation site. The resulting N-terminally truncated protein is unable to enter the nucleus due to the lack of identified nuclear localization signal (NLS)...
March 2017: Human Mutation
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