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https://www.readbyqxmd.com/read/28717665/identification-of-an-alu-element-mediated-deletion-in-the-promoter-region-of-gne-in-siblings-with-gne-myopathy
#1
Jennifer Garland, Joshi Stephen, Bradley Class, Angela Gruber, Carla Ciccone, Aaron Poliak, Christina P Hayes, Vandana Singhal, Christina Slota, John Perreault, Ralitza Gavrilova, Joseph A Shrader, Prashant Chittiboina, Galen Joe, John Heiss, William A Gahl, Marjan Huizing, Nuria Carrillo, May Christine V Malicdan
BACKGROUND: GNE myopathy is a rare genetic disease characterized by progressive muscle atrophy and weakness. It is caused by biallelic mutations in the GNE gene that encodes for the bifunctional enzyme, uridine diphosphate (UDP)-N-acetylglucosamine (GlcNAc) 2-epimerase/N-acetylmannosamine (ManNAc) kinase. Typical characteristics of GNE myopathy include progressive myopathy, first involving anterior tibialis muscle and sparing the quadriceps, and rimmed vacuoles on muscle biopsy. Identifying biallelic mutations by sequencing of the GNE gene confirms the diagnosis of GNE myopathy...
July 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28715334/exploring-the-feasibility-of-a-dna-computer-design-of-an-alu-using-sticker-based-dna-model
#2
Mayukh Sarkar, Prasun Ghosal, Saraju P Mohanty
Since its inception, DNA computing has advanced to offer an extremely powerful, energy-efficient emerging technology for solving hard computational problems with its inherent massive parallelism and extremely high data density. This would be much more powerful and general purpose when combined with other existing well known algorithmic solutions that exist for conventional computing architectures using a suitable ALU. Thus, a specifically designed DNA ALU that can address operations suitable for both domains can mitigate the gap between these two...
July 13, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28695890/dual-loss-of-human-polq-and-lig4-abolishes-random-integration
#3
Shinta Saito, Ryo Maeda, Noritaka Adachi
Homologous recombination-mediated gene targeting has greatly contributed to genetic analysis in a wide range of species, but is highly inefficient in human cells because of overwhelmingly frequent random integration events, whose molecular mechanism remains elusive. Here we show that DNA polymerase θ, despite its minor role in chromosomal DNA repair, substantially contributes to random integration, and that cells lacking both DNA polymerase θ and DNA ligase IV, which is essential for non-homologous end joining (NHEJ), exhibit 100% efficiency of spontaneous gene targeting by virtue of undetectable levels of random integration...
July 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/28686707/molecular-characterization-of-occult-hepatitis-b-virus-infection-in-patients-with-end-stage-liver-disease-in-colombia
#4
Julio Cesar Rendon, Fabian Cortes-Mancera, Juan Carlos Restrepo-Gutierrez, Sergio Hoyos, Maria-Cristina Navas
BACKGROUND: Hepatitis B virus (HBV) occult infection (OBI) is a risk factor to be taken into account in transfusion, hemodialysis and organ transplantation. The aim of this study was to identify and characterize at the molecular level OBI cases in patients with end-stage liver disease. METHODS: Sixty-six liver samples were obtained from patients with diagnosis of end-stage liver disease submitted to liver transplantation in Medellin (North West, Colombia). Samples obtained from patients who were negative for the surface antigen of HBV (n = 50) were tested for viral DNA detection by nested PCR for ORFs S, C, and X and confirmed by Southern-Blot...
2017: PloS One
https://www.readbyqxmd.com/read/28673292/effect-of-pharmacogenetics-on-plasma-lumefantrine-pharmacokinetics-and-malaria-treatment-outcome-in-pregnant-women
#5
Ritah F Mutagonda, Appolinary A R Kamuhabwa, Omary M S Minzi, Siriel N Massawe, Muhammad Asghar, Manijeh V Homann, Anna Färnert, Eleni Aklillu
BACKGROUND: Pregnancy has considerable effects on the pharmacokinetic properties of drugs used to treat uncomplicated Plasmodium falciparum malaria. The role of pharmacogenetic variation on anti-malarial drug disposition and efficacy during pregnancy is not well investigated. The study aimed to examine the effect of pharmacogenetics on lumefantrine (LF) pharmacokinetics and treatment outcome in pregnant women. METHODS: Pregnant women with uncomplicated falciparum malaria were enrolled and treated with artemether-lumefantrine (ALu) at Mkuranga and Kisarawe district hospitals in Coast Region of Tanzania...
July 3, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28672131/association-between-serum-persistent-organic-pollutants-and-dna-methylation-in-korean-adults
#6
Mi Hwa Lee, Eo Rin Cho, Jung-Eun Lim, Sun Ha Jee
BACKGROUND: Exposure to persistent organic pollutants (POPs) has been associated with epigenetic changes such as DNA methylation, which can influence human health. However, the association between POPs and DNA methylation by sex was not shown in previous studies. OBJECTIVES: We investigated the association between POPs and DNA methylation in men and women using a larger population. METHODS: A cross-sectional study was conducted using the data of 444 Koreans (253 men and 191 women)...
June 30, 2017: Environmental Research
https://www.readbyqxmd.com/read/28653984/multiple-isoforms-of-anril-in-melanoma-cells-structural-complexity-suggests-variations-in-processing
#7
Debina Sarkar, Ali Oghabian, Pasani K Bodiyabadu, Wayne R Joseph, Euphemia Y Leung, Graeme J Finlay, Bruce C Baguley, Marjan E Askarian-Amiri
The long non-coding RNA ANRIL, antisense to the CDKN2B locus, is transcribed from a gene that encompasses multiple disease-associated polymorphisms. Despite the identification of multiple isoforms of ANRIL, expression of certain transcripts has been found to be tissue-specific and the characterisation of ANRIL transcripts remains incomplete. Several functions have been associated with ANRIL. In our judgement, studies on ANRIL functionality are premature pending a more complete appreciation of the profusion of isoforms...
June 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28652572/cascaded-exciton-energy-transfer-in-a-monolayer-semiconductor-lateral-heterostructure-assisted-by-surface-plasmon-polariton
#8
Jinwei Shi, Meng-Hsien Lin, I-Tung Chen, Nasim Mohammadi Estakhri, Xin-Quan Zhang, Yanrong Wang, Hung-Ying Chen, Chun-An Chen, Chih-Kang Shih, Andrea Alù, Xiaoqin Li, Yi-Hsien Lee, Shangjr Gwo
Atomically thin lateral heterostructures based on transition metal dichalcogenides have recently been demonstrated. In monolayer transition metal dichalcogenides, exciton energy transfer is typically limited to a short range (~1 μm), and additional losses may be incurred at the interfacial regions of a lateral heterostructure. To overcome these challenges, here we experimentally implement a planar metal-oxide-semiconductor structure by placing a WS2/MoS2 monolayer heterostructure on top of an Al2O3-capped Ag single-crystalline plate...
June 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28637190/evolution-of-the-sperm-methylome-of-primates-is-associated-with-retrotransposon-insertions-and-genome-instability
#9
Kei Fukuda, Yukihiro Inoguchi, Kenji Ichiyanagi, Tomoko Ichiyanagi, Yasuhiro Go, Masashi Nagano, Yojiro Yanagawa, Noboru Takaesu, Yasuyuki Ohkawa, Hiroo Imai, Hiroyuki Sasaki
Changes in gene expression resulting from epigenetic and/or genetic changes play an important role in the evolutionary divergence of phenotypes. To explore how epigenetic and genetic changes are linked during primate evolution, we have compared the genome-wide DNA methylation profiles (methylomes) of humans and chimpanzees, which have a 1.2% DNA sequence divergence, of sperm, the frontal cortices, B cells, and neutrophils. We revealed that species-specific differentially methylated regions (S-DMRs), ranging from several hundred bp to several kb, were frequently associated with sequence changes in transcription factor binding sites and insertions of Alu and SVA retrotransposons...
June 20, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28631163/evaluation-of-streck-bct-and-paxgene-stabilised-blood-collection-tubes-for-cell-free-circulating-dna-studies-in-plasma
#10
Kristina Warton, Nicole L Yuwono, Mark J Cowley, Mark J McCabe, Alwin So, Caroline E Ford
INTRODUCTION: Blood samples for studies of circulating DNA in disease are often collected in clinical settings where prompt processing of samples is not possible. In order to avoid problems associated with leukocyte lysis after prolonged blood storage, stabilised blood tubes have been developed containing preservatives that prevent cell lysis. We evaluated Streck BCT tubes and PAXgene ccfDNA tubes, as well as standard EDTA blood collection tubes, in terms of DNA yield and fragment size...
June 19, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28624226/transcriptome-wide-investigation-of-mrna-circrna-in-mir-184-and-its-r-57c-u-mutant-type-treatment-of-human-lens-epithelial-cells
#11
Yueqiu Luo, Siyu Liu, Ke Yao
m-miR-184 (mutant miR-184, r.57c > u) appears in familial hereditary ocular diseases, including keratoconus, cataracts, EDICT (endothelial dystrophy, iris hypoplasia, congenital cataract, and stromal thinning) syndrome, severe keratoconus, and non-ectatic corneal thinning. The biological function of m-miR-184 in these ocular diseases remains unclear. With the emergence of high-throughput sequencing, it is now possible to discover many different biological components simultaneously. Using two different RNA libraries, we sequenced the complete transcriptome of HLE cells treated with miR-184, m-miR-184, and a negative control...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28623187/control-of-box-c-d-snornp-assembly-by-n-6-methylation-of-adenine
#12
Lin Huang, Saira Ashraf, Jia Wang, David Mj Lilley
N(6)-methyladenine is the most widespread mRNA modification. A subset of human box C/D snoRNA species have target GAC sequences that lead to formation of N(6)-methyladenine at a key trans Hoogsteen-sugar A·G base pair, of which half are methylated in vivo The GAC target is conserved only in those that are methylated. Methylation prevents binding of the 15.5-kDa protein and the induced folding of the RNA Thus, the assembly of the box C/D snoRNP could in principle be regulated by RNA methylation at its critical first stage...
June 16, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28620890/identification-and-characterization-of-a-new-brca2-rearrangement-in-an-italian-family-with-hereditary-breast-and-ovarian-cancer-syndrome
#13
Paola Concolino, Roberta Rizza, Karl Hackmann, Angelo Minucci, Giovanni Luca Scaglione, Maria De Bonis, Alessandra Costella, Cecilia Zuppi, Evelin Schrock, Ettore Capoluongo
INTRODUCTION: Many studies document the involvement of BRCA1/2 gene rearrangements in genetic predisposition to breast and ovarian cancer. Large genomic rearrangements (LGRs) of BRCA1 account for 0-27% of all disease-causing mutations in various populations, while LGRs in BRCA2 are rarer. Here, we describe a novel BRCA2 LGR, involving the duplication of exons 4-26, in an Italian family with hereditary breast and ovarian cancer (HBOC) syndrome. OBJECTIVE: Our purpose was to provide an effective characterization of this variant using a combination of different methods able to establish the exact breakpoints of the duplication...
June 15, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28620780/a-novel-large-fragment-deletion-in-pls3-causes-rare-x-linked-early-onset-osteoporosis-and-response-to-zoledronic-acid
#14
F Lv, M Ma, W Liu, X Xu, Y Song, L Li, Y Jiang, O Wang, W Xia, X Xing, Z Qiu, M Li
We identified a novel large fragment deletion from intron 9 to 3'UTR in PLS3 (E10-E16del) in one Chinese boy with X-linked early-onset osteoporosis and vertebral fractures, which expanded the pathogenic spectrum of X-linked early-onset osteoporosis. Treatment with zoledronic acid was beneficial for increasing BMD and reshaping the vertebral bodies of this patient. INTRODUCTION: X-linked early-onset osteoporosis is a rare disease, which is characterized by low bone mineral density (BMD), vertebral compression fractures (VCFs), and/or long bone fractures...
June 16, 2017: Osteoporosis International
https://www.readbyqxmd.com/read/28619647/using-crispr-cas9-to-generate-gene-corrected-autologous-ipscs-for-the-treatment-of-inherited-retinal-degeneration
#15
Erin R Burnight, Manav Gupta, Luke A Wiley, Kristin R Anfinson, Audrey Tran, Robinson Triboulet, Jeremy M Hoffmann, Darcey L Klaahsen, Jeaneen L Andorf, Chunhua Jiao, Elliott H Sohn, Malavika K Adur, Jason W Ross, Robert F Mullins, George Q Daley, Thorsten M Schlaeger, Edwin M Stone, Budd A Tucker
Patient-derived induced pluripotent stem cells (iPSCs) hold great promise for autologous cell replacement. However, for many inherited diseases, treatment will likely require genetic repair pre-transplantation. Genome editing technologies are useful for this application. The purpose of this study was to develop CRISPR-Cas9-mediated genome editing strategies to target and correct the three most common types of disease-causing variants in patient-derived iPSCs: (1) exonic, (2) deep intronic, and (3) dominant gain of function...
June 12, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28611924/pcs-mva-syndrome-caused-by-an-alu-insertion-in-the-bub1b-gene
#16
Maki Kato, Takema Kato, Eriko Hosoba, Masanao Ohashi, Midori Fujisaki, Mamoru Ozaki, Masatoshi Yamaguchi, Hiroshi Sameshima, Hiroki Kurahashi
We report a case of premature chromatid separation/mosaic variegated aneuploidy syndrome identified by microcephaly on fetal ultrasound and confirmed by cytogenetic analysis of amniotic fluid. Initial mutational analysis of the entire coding region of the BUB1B gene failed to identify any causative mutations. However, further analysis revealed a known compound heterozygous mutation in the upstream region of this gene and a novel Alu insertion mutation in the intron.
2017: Human Genome Variation
https://www.readbyqxmd.com/read/28599390/fructose-1-6-bisphosphatase-deficiency-caused-by-a-novel-homozygous-alu-element-insertion-in-the-fbp1-gene-and-delayed-diagnosis
#17
Somashekara Hosaagrahara Ramakrishna, Siddaramappa Jagdish Patil, Anusha Aladakatte Jagadish, Anil Kumar Sapare, Hiremath Sagar, Subramanian Kannan
Fructose-1,6-bisphosphatase (FBPase) enzyme deficiency is one of the treatable autosomal recessive inherited metabolic disorders. If diagnosed early, FBPase deficiency has a favorable prognosis. We report the clinical and biochemical findings of a 9.5-year-old female child with FBPase deficiency. FBPase deficiency is caused by a homozygous Arthrobacter luteus (Alu) insertion in the FBP1 gene, reported for the first time.
May 23, 2017: Journal of Pediatric Endocrinology & Metabolism: JPEM
https://www.readbyqxmd.com/read/28586325/distinct-mechanisms-obviate-the-potentially-toxic-effects-of-inverted-repeat-alu-elements-on-cellular-rna-metabolism
#18
Reyad A Elbarbary, Lynne E Maquat
No abstract text is available yet for this article.
June 6, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28566750/mutation-spectrum-in-the-cacna1a-gene-in-49-patients-with-episodic-ataxia
#19
Cèlia Sintas, Oriel Carreño, Noèlia Fernàndez-Castillo, Roser Corominas, Marta Vila-Pueyo, Claudio Toma, Ester Cuenca-León, Isabel Barroeta, Carles Roig, Víctor Volpini, Alfons Macaya, Bru Cormand
Episodic ataxia is an autosomal dominant ion channel disorder characterized by episodes of imbalance and incoordination. The disease is genetically heterogeneous and is classified as episodic ataxia type 2 (EA2) when it is caused by a mutation in the CACNA1A gene, encoding the α1A subunit of the P/Q-type voltage-gated calcium channel Cav2.1. The vast majority of EA2 disease-causing variants are loss-of-function (LoF) point changes leading to decreased channel currents. CACNA1A exonic deletions have also been reported in EA2 using quantitative approaches...
May 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28562730/-socio-epidemiological-and-cultural-aspects-of-cutaneous-leishmaniasis-conceptions-attitudes-and-practices-in-the-populations-of-tierralta-and-valencia-cordoba-colombia
#20
Sandra Yaneth Patiño-Londoño, Lina Marcela Salazar, Catalina Tovar Acero, Iván Darío Vélez Bernal
This article focuses on the conceptions, attitudes and practices of the inhabitants from four villages (veredas) in Tierralta and Valencia (Cordoba, Colombia), who have suffered from or are aware of the existence of cutaneous leishmaniasis. A mixed methodology was implemented based in a qualitative design using interviews and focus groups (n=45) and an epidemiological design which included applying the Montenegro test (n=251), uncovering suspected cases of cutaneous leishmaniasis in humans, (n=5) and applying epidemiological surveys (n=409)...
January 2017: Salud Colectiva
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