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Sleep genomics

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https://www.readbyqxmd.com/read/27913727/regulated-complex-assembly-safeguards-the-fidelity-of-sleeping-beauty-transposition
#1
Yongming Wang, Diana Pryputniewicz-Dobrinska, Enikö Éva Nagy, Christopher D Kaufman, Manvendra Singh, Steve Yant, Jichang Wang, Anna Dalda, Mark A Kay, Zoltán Ivics, Zsuzsanna Izsvák
The functional relevance of the inverted repeat structure (IR/DR) in a subgroup of the Tc1/mariner superfamily of transposons has been enigmatic. In contrast to mariner transposition, where a topological filter suppresses single-ended reactions, the IR/DR orchestrates a regulatory mechanism to enforce synapsis of the transposon ends before cleavage by the transposase occurs. This ordered assembly process shepherds primary transposase binding to the inner 12DRs (where cleavage does not occur), followed by capture of the 12DR of the other transposon end...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898092/transposon-mediated-generation-of-cellular-and-mouse-models-of-splicing-mutations-to-assess-the-efficacy-of-snrna-based-therapeutics
#2
Elena Barbon, Mattia Ferrarese, Laetitia van Wittenberghe, Peggy Sanatine, Giuseppe Ronzitti, Fanny Collaud, Pasqualina Colella, Mirko Pinotti, Federico Mingozzi
Disease-causing splicing mutations can be rescued by variants of the U1 small nuclear RNA (U1snRNAs). However, the evaluation of the efficacy and safety of modified U1snRNAs as therapeutic tools is limited by the availability of cellular and animal models specific for a given mutation. Hence, we exploited the hyperactive Sleeping Beauty transposon system (SB100X) to integrate human factor IX (hFIX) minigenes into genomic DNA in vitro and in vivo. We generated stable HEK293 cell lines and C57BL/6 mice harboring splicing-competent hFIX minigenes either wild type (SChFIX-wt) or mutated (SChFIXex5-2C)...
November 29, 2016: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/27855737/genetic-basis-of-chronotype-in-humans-insights-from-three-landmark-gwas
#3
David A Kalmbach, Logan D Schneider, Joseph Cheung, Sarah J Bertrand, Thiruchelvam Kariharan, Allan I Pack, Philip R Gehrman
Chronotype, or diurnal preference, refers to behavioral manifestations of the endogenous circadian system that governs preferred timing of sleep and wake. As variations in circadian timing and system perturbations are linked to disease development, the fundamental biology of chronotype has received attention for its role in the regulation and dysregulation of sleep and related medical and psychiatric illnesses. Twin and family studies have shown that chronotype is a heritable trait, thus directing attention toward its genetic basis...
October 28, 2016: Sleep
https://www.readbyqxmd.com/read/27832434/monitoring-of-venus-transgenic-cell-migration-during-pregnancy-in-non-transgenic-rabbits
#4
N Lipták, O I Hoffmann, A Kerekes, G Iski, D Ernszt, K Kvell, L Hiripi, Z Bősze
Cell transfer between mother and fetus were demonstrated previously in several species which possess haemochorial placenta (e.g. in humans, mice, rats, etc.). Here we report the assessment of fetal and maternal microchimerism in non-transgenic (non-TG) New Zealand white rabbits which were pregnant with transgenic (TG) fetuses and in non-TG newborns of TG does. The TG construct, including the Venus fluorophore cDNA driven by a ubiquitous cytomegalovirus enhancer, chicken ß-actin promoter (CAGGS), was previously integrated into the rabbit genome by Sleeping Beauty transposon system...
November 10, 2016: Transgenic Research
https://www.readbyqxmd.com/read/27815038/phenotypes-in-obstructive-sleep-apnea-a-definition-examples-and-evolution-of-approaches
#5
REVIEW
Andrey V Zinchuk, Mark J Gentry, John Concato, Henry K Yaggi
Obstructive sleep apnea (OSA) is a complex and heterogeneous disorder and the apnea hypopnea index alone can not capture the diverse spectrum of the condition. Enhanced phenotyping can improve prognostication, patient selection for clinical trials, understanding of mechanisms, and personalized treatments. In OSA, multiple condition characteristics have been termed "phenotypes." To help classify patients into relevant prognostic and therapeutic categories, an OSA phenotype can be operationally defined as: "A category of patients with OSA distinguished from others by a single or combination of disease features, in relation to clinically meaningful attributes (symptoms, response to therapy, health outcomes, quality of life)...
October 12, 2016: Sleep Medicine Reviews
https://www.readbyqxmd.com/read/27807620/genetic-background-of-enhanced-radioresistance-in-an-anhydrobiotic-insect-transcriptional-response-to-ionizing-radiations-and-desiccation
#6
Alina Ryabova, Kyosuke Mukae, Alexander Cherkasov, Richard Cornette, Elena Shagimardanova, Tetsuya Sakashita, Takashi Okuda, Takahiro Kikawada, Oleg Gusev
It is assumed that resistance to ionizing radiation, as well as cross-resistance to other abiotic stresses, is a side effect of the evolutionary-based adaptation of anhydrobiotic animals to dehydration stress. Larvae of Polypedilum vanderplanki can withstand prolonged desiccation as well as high doses of ionizing radiation exposure. For a further understanding of the mechanisms of cross-tolerance to both types of stress exposure, we profiled genome-wide mRNA expression patterns using microarray techniques on the chironomid larvae collected at different stages of desiccation and after exposure to two types of ionizing radiation-70 Gy of high-linear energy transfer (LET) ions ((4)He) and the same dose of low-LET radiation (gamma rays)...
November 2, 2016: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/27801667/transposon-mediated-generation-of-bcr-abl1-expressing-transgenic-cell-lines-for-unbiased-sensitivity-testing-of-tyrosine-kinase-inhibitors
#7
Konstantin Byrgazov, Chantal Blanche Lucini, Bettina Berkowitsch, Margit Koenig, Oskar A Haas, Gregor Hoermann, Peter Valent, Thomas Lion
Point mutations in the ABL1 kinase domain are an important mechanism of resistance to tyrosine kinase inhibitors (TKI) in BCR-ABL1-positive and, as recently shown, BCR-ABL1-like leukemias. The cell line Ba/F3 lentivirally transduced with mutant BCR-ABL1 constructs is widely used for in vitro sensitivity testing and response prediction to tyrosine kinase inhibitors. The transposon-based Sleeping Beauty system presented offers several advantages over lentiviral transduction including the absence of biosafety issues, faster generation of transgenic cell lines, and greater efficacy in introducing large gene constructs...
October 27, 2016: Oncotarget
https://www.readbyqxmd.com/read/27801296/removal-of-unwanted-variation-reveals-novel-patterns-of-gene-expression-linked-to-sleep-homeostasis-in-murine-cortex
#8
Jason R Gerstner, John N Koberstein, Adam J Watson, Nikolai Zapero, Davide Risso, Terence P Speed, Marcos G Frank, Lucia Peixoto
BACKGROUND: Why we sleep is still one of the most perplexing mysteries in biology. Strong evidence indicates that sleep is necessary for normal brain function and that sleep need is a tightly regulated process. Surprisingly, molecular mechanisms that determine sleep need are incompletely described. Moreover, very little is known about transcriptional changes that specifically accompany the accumulation and discharge of sleep need. Several studies have characterized differential gene expression changes following sleep deprivation...
October 25, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27799067/identification-of-a-rai1-associated-disease-network-through-integration-of-exome-sequencing-transcriptomics-and-3d-genomics
#9
Maria Nicla Loviglio, Christine R Beck, Janson J White, Marion Leleu, Tamar Harel, Nicolas Guex, Anne Niknejad, Weimin Bi, Edward S Chen, Isaac Crespo, Jiong Yan, Wu-Lin Charng, Shen Gu, Ping Fang, Zeynep Coban-Akdemir, Chad A Shaw, Shalini N Jhangiani, Donna M Muzny, Richard A Gibbs, Jacques Rougemont, Ioannis Xenarios, James R Lupski, Alexandre Reymond
BACKGROUND: Smith-Magenis syndrome (SMS) is a developmental disability/multiple congenital anomaly disorder resulting from haploinsufficiency of RAI1. It is characterized by distinctive facial features, brachydactyly, sleep disturbances, and stereotypic behaviors. METHODS: We investigated a cohort of 15 individuals with a clinical suspicion of SMS who showed neither deletion in the SMS critical region nor damaging variants in RAI1 using whole exome sequencing. A combination of network analysis (co-expression and biomedical text mining), transcriptomics, and circularized chromatin conformation capture (4C-seq) was applied to verify whether modified genes are part of the same disease network as known SMS-causing genes...
November 1, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27792857/sudden-infant-death-syndrome-insights-and-future-directions-from-a-utah-population-database-analysis
#10
Erik D Christensen, Justin Berger, Mouied M Alashari, Hilary Coon, Cynthia Robison, Hsu-Tso Ho, David R Adams, Willian A Gahl, Ken R Smith, John M Opitz, Dennis R Johnson
"Sudden Infant Death syndrome" (SIDS) represents the commonest category of infant death after the first month of life. As genome scale sequencing greatly facilitates the identification of new candidate disease variants, the challenges of ascribing causation to these variants persists. In order to determine the extent to which SIDS occurs in related individuals and their pedigree structure we undertook an analysis of SIDS using the Utah Population Database, recording, for example, evidence of enrichment for genetic causation following the back-to-sleep recommendations of 1992 and 1994...
October 28, 2016: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/27790711/transposon-mutagenesis-identifies-candidate-genes-that-cooperate-with-loss-of-transforming-growth-factor-beta-signaling-in-mouse-intestinal-neoplasms
#11
Shelli M Morris, Jerry Davison, Kelly T Carter, Rachele M O'Leary, Patty Trobridge, Sue E Knoblaugh, Lois L Myeroff, Sanford D Markowitz, Benjamin T Brett, Todd E Scheetz, Adam J Dupuy, Timothy K Starr, William M Grady
Colorectal cancer (CRC) results from the accumulation of gene mutations and epigenetic alterations in colon epithelial cells, which promotes CRC formation through deregulating signaling pathways. One of the most commonly deregulated signaling pathways in CRC is the transforming growth factor β (TGF-β) pathway. Importantly, the effects of TGF-β signaling inactivation in CRC are modified by concurrent mutations in the tumor cell, and these concurrent mutations determine the ultimate biological effects of impaired TGF-β signaling in the tumor...
October 28, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27788568/a-cross-sectional-study-of-the-association-between-mobile-phone-use-and-symptoms-of-ill-health
#12
Yong Min Cho, Hee Jin Lim, Hoon Jang, Kyunghee Kim, Jae Wook Choi, Chol Shin, Seung Ku Lee, Jong Hwa Kwon, Nam Kim
OBJECTIVES: This study analyzed the associations between mobile phone call frequency and duration with non-specific symptoms. METHODS: This study was conducted with a population group including 532 non-patient adults established by the Korean Genome and Epidemiology Study. The pattern of phone call using a mobile phone was investigated through face-to-face interview. Structured methods applied to quantitatively assess health effects are Headache Impact Test-6 (HIT-6), Psychosocial Well-being Index-Short Form, Beck Depression Inventory, Korean-Instrumental Activities of Daily Living, Perceived Stress Scale (PSS), Pittsburgh Sleep Quality Index, and 12-item Short Form Health Survey where a higher score represents a higher greater health effect...
2016: Environmental Health and Toxicology
https://www.readbyqxmd.com/read/27748236/common-genetic-variation-near-melatonin-receptor-1a-gene-linked-to-job-related-exhaustion-in-shift-workers
#13
Sonja Sulkava, Hanna M Ollila, Jukka Alasaari, Sampsa Puttonen, Mikko Härmä, Katriina Viitasalo, Alexandra Lahtinen, Jaana Lindström, Auli Toivola, Raimo Sulkava, Mika Kivimäki, Jussi Vahtera, Timo Partonen, Kaisa Silander, Tarja Porkka-Heiskanen, Tiina Paunio
STUDY OBJECTIVES: Tolerance to shift work varies; only some shift workers suffer from disturbed sleep, fatigue, and job-related exhaustion. Our aim was to explore molecular genetic risk factors for intolerance to shift work. METHODS: We assessed intolerance to shift work with job-related exhaustion symptoms in shift workers using the emotional exhaustion subscale of the Maslach Burnout Inventory - General Survey, and carried out a genome-wide association study (GWAS) using Illumina's Human610-Quad BeadChip (n = 176)...
October 10, 2016: Sleep
https://www.readbyqxmd.com/read/27739237/hyperactivity-and-male-specific-sleep-deficits-in-the-16p11-2-deletion-mouse-model-of-autism
#14
Christopher C Angelakos, Adam J Watson, W Timothy O'Brien, Kyle S Krainock, Thomas Nickl-Jockschat, Ted Abel
Sleep disturbances and hyperactivity are prevalent in several neurodevelopmental disorders, including autism spectrum disorders (ASDs) and attention deficit-hyperactivity disorder (ADHD). Evidence from genome-wide association studies indicates that chromosomal copy number variations (CNVs) are associated with increased prevalence of these neurodevelopmental disorders. In particular, CNVs in chromosomal region 16p11.2 profoundly increase the risk for ASD and ADHD, disorders that are more common in males than females...
October 14, 2016: Autism Research: Official Journal of the International Society for Autism Research
https://www.readbyqxmd.com/read/27729044/retroviral-vectors-and-transposons-for-stable-gene-therapy-advances-current-challenges-and-perspectives
#15
José Eduardo Vargas, Leonardo Chicaybam, Renato Tetelbom Stein, Amilcar Tanuri, Andrés Delgado-Cañedo, Martin H Bonamino
Gene therapy protocols require robust and long-term gene expression. For two decades, retrovirus family vectors have offered several attractive properties as stable gene-delivery vehicles. These vectors represent a technology with widespread use in basic biology and translational studies that require persistent gene expression for treatment of several monogenic diseases. Immunogenicity and insertional mutagenesis represent the main obstacles to a wider clinical use of these vectors. Efficient and safe non-viral vectors are emerging as a promising alternative and facilitate clinical gene therapy studies...
October 12, 2016: Journal of Translational Medicine
https://www.readbyqxmd.com/read/27699083/oxidative-stress-induced-telomere-length-shortening-of-circulating-leukocyte-in-patients-with-obstructive-sleep-apnea
#16
Kyung Soo Kim, Jin Wook Kwak, Su Jin Lim, Yong Kyun Park, Hoon Shik Yang, Hyun Jik Kim
The main mechanism of pathogenesis which causes systemic complications in obstructive sleep apnea (OSA) patients is believed to be intermittent hypoxia-induced intermediary effect and it depends on the burden of oxidative stress during sleep. We aimed to search the predictive markers which reflect the burden of systemic oxidative stress in patients with OSA and whether excessive telomere length shortening is a characteristic feature that can assess oxidative stress levels. We used quantitative PCR to measure telomere length using peripheral blood genomic DNA...
October 2016: Aging and Disease
https://www.readbyqxmd.com/read/27696897/sleeping-beauty-transposition-from-biology-to-applications
#17
Suneel A Narayanavari, Shreevathsa S Chilkunda, Zoltán Ivics, Zsuzsanna Izsvák
Sleeping Beauty (SB) is the first synthetic DNA transposon that was shown to be active in a wide variety of species. Here, we review studies from the last two decades addressing both basic biology and applications of this transposon. We discuss how host-transposon interaction modulates transposition at different steps of the transposition reaction. We also discuss how the transposon was translated for gene delivery and gene discovery purposes. We critically review the system in clinical, pre-clinical and non-clinical settings as a non-viral gene delivery tool in comparison with viral technologies...
October 4, 2016: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/27692059/cntnap2-knockout-rats-and-mice-exhibit-epileptiform-activity-and-abnormal-sleep-wake-physiology
#18
Alexia M Thomas, Michael D Schwartz, Michael D Saxe, Thomas S Kilduff
STUDY OBJECTIVES: Although recent innovations have enabled modification of the rat genome, it is unclear whether enhanced utility of rodents as human disease models will result. We compared EEG and behavioral phenotypes of rats and mice with homozygous deletion of Cntnap2, a gene associated with cortical dysplasia-focal epilepsy (CDFE) and autism spectrum disorders (ASD). METHODS: Male Cntnap2 knockout (KO) and wild-type (WT) rats and male Cntnap2 KO and WT mice were implanted with telemeters to record EEG, EMG, body temperature and locomotor activity...
September 26, 2016: Sleep
https://www.readbyqxmd.com/read/27689706/genome-wide-association-studies-in-obstructive-sleep-apnea-will-we-catch-a-black-cat-in-a-dark-room
#19
Luu V Pham, Vsevolod Y Polotsky
No abstract text is available yet for this article.
October 1, 2016: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/27684378/obstructive-sleep-apnea-is-associated-with-elevated-high-sensitivity-c-reactive-protein-levels-independent-of-obesity-korean-genome-and-epidemiology-study
#20
Jinkwan Kim, Seok Jun Lee, Kyung-Mee Choi, Seung Ku Lee, Dae Wui Yoon, Seung Gwan Lee, Chol Shin
Obstructive sleep apnea syndrome (OSA) has been recognized as a common health problem, and increasing obesity rates have led to further remarkable increases in the prevalence of OSA, along with more prominent cardiovascular morbidities. Though previous studies have reported an independent relationship between elevated high sensitivity C-reactive protein (hsCRP) levels and OSA, the issue remains controversial owing to inadequate consideration of obesity and various confounding factors. So far, few population based studies of association between OSA and hsCRP levels have been published...
2016: PloS One
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