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https://www.readbyqxmd.com/read/28637190/evolution-of-the-sperm-methylome-of-primates-is-associated-with-retrotransposon-insertions-and-genome-instability
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/28554225/lutein-improves-cell-viability-and-reduces-alu-rna-accumulation-in-hydrogen-peroxide-challenged-retinal-pigment-epithelial-cells
#13
You Sheng Chong, Chun Wai Mai, Chee Onn Leong, Lai Chun Wong
PURPOSE: Dysfunction of the microRNA (miRNA)-processing enzyme DICER1 and Alu RNA accumulation are linked to the pathogenesis of age-related macular degeneration (AMD). This study determined the optimal dose of lutein (LUT) and zeaxanthin (ZEA) to protect human retinal pigment epithelium (RPE) cells against hydrogen peroxide (H2O2). The effect of the optimal dose of LUT and ZEA as DICER1 and Alu RNA modulators in cultured human RPE cells challenged with H2O2 was investigated. MATERIALS AND METHODS: ARPE-19 cells were pre-treated with LUT, ZEA or both for 24 hours before 200 µM H2O2 challenge...
May 29, 2017: Cutaneous and Ocular Toxicology
https://www.readbyqxmd.com/read/28549544/genetic-dissection-of-five-ethnic-groups-from-punjab-north-west-india-a-study-based-on-autosomal-markers
#14
Gagandeep Singh, Indu Talwar, Harkirat Singh Sandhu, Kawaljit Matharoo, A J S Bhanwer
The present study assessed the applicability of Alu insertion elements and Single Nucleotide Polymorphisms (SNPs) in forensic identification and estimated the extent of genetic variation in five major ethnic groups of Punjab, North-West India. A total of 1012 unrelated samples belonging to Banias, Brahmins, Jat Sikhs, Khatris and Scheduled Castes were genotyped for four Alu elements (ACE, APO, PLAT, D1) and six Single Nucleotide Polymorphisms [ESR (PvuII), LPL (PvuII), HTR2A (MspI), DRD2 Taq1A, Taq1B, Taq1D]...
May 2017: Legal Medicine
https://www.readbyqxmd.com/read/28542625/the-identification-of-switch-like-alternative-splicing-exons-among-multiple-samples-with-rna-seq-data
#15
Zhiyi Qin, Xuegong Zhang
Alternative splicing is an ubiquitous phenomenon in most human genes and has important functions. The switch-like exon is the type of exon that has a high level of usage in some tissues, but has a low level of usage in the other tissues. They usually undergo strong tissue-specific regulations. There is still a lack a systematic method to identify switch-like exons from multiple RNA-seq samples. We proposed a novel method called iterative Tertile Absolute Deviation around the mode (iTAD) to profile the distribution of exon relative usages among multiple samples and to identify switch-like exons and other types of exons using a robust statistic estimator...
2017: PloS One
https://www.readbyqxmd.com/read/28542129/adar1-mediated-3-utr-editing-and-expression-control-of-antiapoptosis-genes-fine-tunes-cellular-apoptosis-response
#16
Chang-Ching Yang, Yi-Tung Chen, Yi-Feng Chang, Hsuan Liu, Yu-Ping Kuo, Chieh-Tien Shih, Wei-Chao Liao, Hui-Wen Chen, Wen-Sy Tsai, Bertrand Chin-Ming Tan
Adenosine-to-inosine RNA editing constitutes a crucial component of the cellular transcriptome and critically underpins organism survival and development. While recent high-throughput approaches have provided comprehensive documentation of the RNA editome, its functional output remains mostly unresolved, particularly for events in the non-coding regions. Gene ontology analysis of the known RNA editing targets unveiled a preponderance of genes related to apoptosis regulation, among which proto-oncogenes XIAP and MDM2 encode two the most abundantly edited transcripts...
May 25, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28533011/effect-of-surface-treatments-on-repair-with-composite-resin-of-a-partially-monoclinic-phase-transformed-yttrium-stabilized-tetragonal-zirconia
#17
Beatriz Regalado Galvão Ribeiro, Marilia Regalado Galvão Rabelo Caldas, Antonio Alves Almeida, Renata Garcia Fonseca, Gelson Luis Adabo
STATEMENT OF PROBLEM: Studies of composite resin repairs of yttrium-tetragonal zirconia polycrystal (Y-TZP) are usually performed in its tetragonal phase, but it may be partially transformed into a monoclinic phase in a clinical fracture. PURPOSE: The purpose of this in vitro study was to evaluate the effect of airborne-particle abrasion (APA) and a bonding agent on the shear bond strength (SBS) between a composite resin and hydrothermally aged Y-TZP. MATERIAL AND METHODS: Specimens (7...
May 20, 2017: Journal of Prosthetic Dentistry
https://www.readbyqxmd.com/read/28513612/insertion-of-alu-elements-at-a-pten-hotspot-in-cowden-syndrome
#18
Louise Crivelli, Virginie Bubien, Natalie Jones, Jennifer Chiron, Françoise Bonnet, Emmanuelle Barouk-Simonet, Patrice Couzigou, Nicolas Sevenet, Frédéric Caux, Michel Longy
Cowden syndrome (CS) is an inherited autosomal dominant disorder associated with germline pathogenic variants of the PTEN tumor suppressor gene. Its phenotypical expression is highly variable and the existence of patients with a CS suggestive phenotype without pathogenic PTEN variant may be related to genetic heterogeneity. In order to explore this hypothesis through the detection of potentially deleterious variants enabling us to identify a new candidate gene, we performed whole-exome sequencing (WES) in a series of 22 CS patients without detectable PTEN pathogenic variant using conventional methods for mutation screening...
May 17, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28502204/alu-insertion-polymorphisms-in-the-african-sahel-and-the-origin-of-fulani-pastoralists
#19
Martina Čížková, Zuzana Hofmanová, Mohammed G Mokhtar, Václav Janoušek, Issa Diallo, Pavel Munclinger, Viktor Černý
BACKGROUND: The origin of Western African pastoralism, represented today by the Fulani nomads, has been a highly debated issue for the past decades, and has not yet been conclusively resolved. AIM: This study focused on Alu polymorphisms in sedentary and nomadic populations across the African Sahel to investigate patterns of diversity that can complement the existing results and contribute to resolving issues concerning the origin of West African pastoralism. SUBJECTS AND METHODS: A new dataset of 21 Alu biallelic markers covering a substantial part of the African Sahel has been analysed jointly with several published North African populations...
May 31, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/28502002/pcr-identification-of-genetic-polymorphisms
#20
Amanda M Harbison, Jenny Ngoc Tran Nguyen
Polymerase chain reaction (PCR) enables the amplification of a specific sequence of deoxyribonucleic acid (DNA) through the process of three main steps: template DNA denaturation, annealing of the primers to complementary sequences, and primer extension to synthesize DNA strands. By using this method, the target sequence will be copied and amplified at an exponential rate. PCR provides a qualitative method for identifying DNA from fresh or dried cells/body fluids, formalin-fixed archival tissue specimens, and ancient specimens...
2017: Methods in Molecular Biology
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