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https://www.readbyqxmd.com/read/28719667/assessing-intragenomic-variation-of-the-internal-transcribed-spacer-two-adapting-the-illumina-metagenomics-protocol
#1
Lo'ai Alanagreh, Caitlin Pegg, Amritha Harikumar, Mark Buchheim
Primary and secondary structural data from the internal transcribed spacer two (ITS2) have been used extensively for diversity studies of many different eukaryotic organisms, including the green algae. Ease of amplification is due, at least in part, to the fact that ITS2 is part of the tandemly-repeated rRNA array. The potential confounding influence of intragenomic variability has yet to be addressed except in a few organisms. Moreover, few of the assessments of intragenomic variation have taken advantage of the deep sequencing capacity of sequence-by-synthesis protocols...
2017: PloS One
https://www.readbyqxmd.com/read/28719561/arterial-topographic-anatomy-near-the-femoral-head-neck-perforation-with-surgical-relevance
#2
Paulo Rego, Vasco Mascarenhas, Diego Collado, Ana Coelho, Luis Barbosa, Reinhold Ganz
BACKGROUND: Knowledge of the vascular supply of the femoral head is crucial for hip-preserving surgical procedures. The critical area for reshaping cam deformity is at the retinacular vessel penetration, an area with ill-defined topographic anatomy. We performed a cadaver study of the extension of the lateral retinaculum near the head-neck junction, distribution of the arterial vascular foramina, and initial intracapital course of these vessels. METHODS: In 16 fresh proximal parts of the femur without head-neck deformities, the deep branch of the medial femoral circumflex artery was injected with gadolinium for magnetic resonance imaging (MRI) sequences to identify arterial structures...
July 19, 2017: Journal of Bone and Joint Surgery. American Volume
https://www.readbyqxmd.com/read/28718617/initial-reduction-of-co2-on-pd-ru-and-cu-doped-ceo2-111-surfaces-effects-of-surface-modification-on-catalytic-activity-and-selectivity
#3
Chen Guo, Shuxian Wei, Sainan Zhou, Tian Zhang, Zhaojie Wang, Siu Pang Ng, Xiaoqing Lu, Chi-Man Lawrence Wu, Wenyue Guo
Surface modification by metal doping is an effective treatment technique for improving surface properties for CO2 reduction. Herein, the effects of doped Pd, Ru, and Cu on the adsorption, activation, and reduction selectivity of CO2 on CeO2(111) were investigated by periodic density functional theory. The doped metals distorted the configuration of a perfect CeO2(111) by weakening the adjacent Ce-O bond strength, and Pd doping was beneficial for generating a highly active O vacancy. The analyses of adsorption energy, charge density difference, and density of states confirmed that the doped metals were conducive for enhancing CO2 adsorption, especially for Cu/CeO2(111)...
July 18, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28717665/identification-of-an-alu-element-mediated-deletion-in-the-promoter-region-of-gne-in-siblings-with-gne-myopathy
#4
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/28717203/genome-wide-identification-and-characterization-of-circular-rnas-by-high-throughput-sequencing-in-soybean
#5
Wei Zhao, Yihui Cheng, Chi Zhang, Qingbo You, Xinjie Shen, Wei Guo, Yongqing Jiao
Circular RNAs (circRNAs) arise during pre-mRNA splicing, in which the 3' and 5' ends are linked to each other by a covalent bond. Soybean is an ancient tetraploid, which underwent two whole genome duplications. Most of soybean genes are paralogous genes with multiple copies. Although many circRNAs have been identified in animals and plants, little is known about soybean circRNAs, especially about circRNAs derived from paralogous genes. Here, we used deep sequencing technology coupled with RNase R enrichment strategy and bioinformatic approach to uncover circRNAs in soybean...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716668/incomplete-penetrance-in-mitochondrial-optic-neuropathies
#6
Leonardo Caporali, Alessandra Maresca, Mariantonietta Capristo, Valentina Del Dotto, Francesca Tagliavini, Maria Lucia Valentino, Chiara La Morgia, Valerio Carelli
Incomplete penetrance characterizes the two most frequent inherited optic neuropathies, Leber's Hereditary Optic Neuropathy (LHON) and dominant optic atrophy (DOA), due to genetic errors in the mitochondrial DNA (mtDNA) and the nuclear DNA (nDNA), respectively. For LHON, compelling evidence has accumulated on the complex interplay of mtDNA haplogroups and environmental interacting factors, whereas the nDNA remains essentially non informative. However, a compensatory mechanism of activated mitochondrial biogenesis and increased mtDNA copy number, possibly driven by a permissive nDNA background, is documented in LHON; when successful it maintains unaffected the mutation carriers, but in some individuals it might be hampered by tobacco smoking or other environmental factors, resulting in disease onset...
July 14, 2017: Mitochondrion
https://www.readbyqxmd.com/read/28715249/durable-molecular-remissions-in-chronic-lymphocytic-leukemia-treated-with-cd19-specific-chimeric-antigen-receptor-modified-t-cells-after-failure-of-ibrutinib
#7
Cameron J Turtle, Kevin A Hay, Laïla-Aïcha Hanafi, Daniel Li, Sindhu Cherian, Xueyan Chen, Brent Wood, Arletta Lozanski, John C Byrd, Shelly Heimfeld, Stanley R Riddell, David G Maloney
Purpose We evaluated the safety and feasibility of anti-CD19 chimeric antigen receptor-modified T (CAR-T) cell therapy in patients with chronic lymphocytic leukemia (CLL) who had previously received ibrutinib. Methods Twenty-four patients with CLL received lymphodepleting chemotherapy and anti-CD19 CAR-T cells at one of three dose levels (2 × 10(5), 2 × 10(6), or 2 × 10(7) CAR-T cells/kg). Nineteen patients experienced disease progression while receiving ibrutinib, three were ibrutinib intolerant, and two did not experience progression while receiving ibrutinib...
July 17, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28713353/functional-characterization-of-novel-faecalibacterium-prausnitzii-strains-isolated-from-healthy-volunteers-a-step-forward-in-the-use-of-f-prausnitzii-as-a-next-generation-probiotic
#8
Rebeca Martín, Sylvie Miquel, Leandro Benevides, Chantal Bridonneau, Véronique Robert, Sylvie Hudault, Florian Chain, Olivier Berteau, Vasco Azevedo, Jean M Chatel, Harry Sokol, Luis G Bermúdez-Humarán, Muriel Thomas, Philippe Langella
Faecalibacterium prausnitzii is a major member of the Firmicutes phylum and one of the most abundant bacteria in the healthy human microbiota. F. prausnitzii depletion has been reported in several intestinal disorders, and more consistently in Crohn's disease (CD) patients. Despite its importance in human health, only few microbiological studies have been performed to isolate novel F. prausnitzii strains in order to better understand the biodiversity and physiological diversity of this beneficial commensal species...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28713347/generic-amplicon-deep-sequencing-to-determine-ilarvirus-species-diversity-in-australian-prunus
#9
Wycliff M Kinoti, Fiona E Constable, Narelle Nancarrow, Kim M Plummer, Brendan Rodoni
The distribution of Ilarvirus species populations amongst 61 Australian Prunus trees was determined by next generation sequencing (NGS) of amplicons generated using a genus-based generic RT-PCR targeting a conserved region of the Ilarvirus RNA2 component that encodes the RNA dependent RNA polymerase (RdRp) gene. Presence of Ilarvirus sequences in each positive sample was further validated by Sanger sequencing of cloned amplicons of regions of each of RNA1, RNA2 and/or RNA3 that were generated by species specific PCRs and by metagenomic NGS...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28712841/long-term-impact-of-subthalamic-stimulation-on-cognitive-function-in-patients-with-advanced-parkinson-s-disease
#10
M Acera, A Molano, B Tijero, G Bilbao, I Lambarri, R Villoria, J Somme, E Ruiz de Gopegui, I Gabilondo, J C Gomez-Esteban
OBJECTIVE: The aim of this study was to evaluate the effects of deep brain stimulation of the subthalamic nucleus (DBS-SN) on cognitive function in patients with Parkinson's disease (PD) 5 years after surgery. MATERIAL AND METHODS: We conducted a prospective study including 50 patients with PD who underwent DBS-SN (62.5% were men; mean age of 62.2±8.2 years; mean progression time of 14.1±6.3 years). All patients were assessed before the procedure and at one year after surgery; 40 patients were further followed up until the 5-year mark...
July 13, 2017: Neurología: Publicación Oficial de la Sociedad Española de Neurología
https://www.readbyqxmd.com/read/28712340/deep-sequencing-reveals-the-mitochondrial-dna-variation-landscapes-of-breast-to-brain-metastasis-blood-samples
#11
Rhiannon E McGeehan, Lewis A Cockram, D Timothy J Littlewood, Kathleen Keatley, Diana M Eccles, Qian An
Breast-to-brain metastasis (BBM) often represents a terminal event, due to the inability of many systemic treatments to cross the blood-brain barrier (BBB), rendering the brain a sanctuary site for tumour cells. Identifying genetic variations that can predict the patients who will develop BBM would allow targeting of adjuvant treatments to reduce risk while disease bulk is minimal. Germ-line genetic variations may contribute to whether a BBM forms by influencing the primary tumour subtype that presents, or by influencing the host response to the tumour or treatment regimen, or by facilitating transition of tumour cells across the BBB and establish a viable brain metastasis...
July 15, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28711297/the-nitrogen-removal-performance-and-microbial-communities-in-a-two-stage-deep-sequencing-constructed-wetland-for-advanced-treatment-of-secondary-effluent
#12
Shuang He, Yingmu Wang, Chuansong Li, Yancheng Li, Jian Zhou
The advanced treatment of secondary effluent was conducted in a two-stage deep sequencing constructed wetland (DSCW) which comprised a denitrification chamber (W1) and a nitrification chamber (W2). The results showed that a superior NO3(-)-N removal rate was observed in W1 with a C/N ratio of 6.5, and a high NH4(+)-N removal rate was obtained when the W2 was operated with 6-h duration of idle. In the long-term operation for 45days, the two-stage DSCW pilot system achieved high and stable removal of TN, NH4(+)-N and NO3(-)-N, which were 92...
June 29, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28710374/metadiffusers-deep-subwavelength-sound-diffusers
#13
Noé Jiménez, Trevor J Cox, Vicent Romero-García, Jean-Philippe Groby
We present deep-subwavelength diffusing surfaces based on acoustic metamaterials, namely metadiffusers. These sound diffusers are rigidly backed slotted panels, with each slit being loaded by an array of Helmholtz resonators. Strong dispersion is produced in the slits and slow sound conditions are induced. Thus, the effective thickness of the panel is lengthened introducing its quarter wavelength resonance in the deep-subwavelength regime. By tuning the geometry of the metamaterial, the reflection coefficient of the panel can be tailored to obtain either a custom reflection phase, moderate or even perfect absorption...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28710104/genomic-analysis-detects-recurrent-promoter-mutations-in-breast-cancer
#14
(no author information available yet)
Deep sequencing of 360 primary breast tumors identified 9 genes with recurrently mutated promoters.
July 14, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28710005/cationic-microbubbles-and-antibiotic-free-miniplasmid-for-sustained-ultrasound-mediated-transgene-expression-in-liver
#15
Simona Manta, Gilles Renault, Anthony Delalande, Olivier Couture, Isabelle Lagoutte, Johanne Seguin, Franck Lager, Pascal Houzé, Patrick Midoux, Michel Bessodes, Daniel Scherman, Michel-Francis Bureau, Corinne Marie, Chantal Pichon, Nathalie Mignet
Despite the increasing number of clinical trials in gene therapy, no ideal methods still allow non-viral gene transfer in deep tissues such as the liver. We were interested in ultrasound (US)-mediated gene delivery to provide long term liver expression. For this purpose, new positively charged microbubbles were designed and complexed with pFAR4, a highly efficient small length miniplasmid DNA devoid of antibiotic resistance sequence. Sonoporation parameters, such as insonation time, acoustic pressure and duration of plasmid injection were controlled under ultrasound imaging guidance...
July 11, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28707270/profiling-of-cellular-microrna-responses-during-the-early-stages-of-kshv-infection
#16
Hosni A M Hussein, Shaw M Akula
Kaposi's sarcoma-associated herpesvirus (KSHV) causes a variety of cancers, including Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), and multicentric Castleman disease (MCD). Host cellular microRNAs (miRNAs) play important post-transcriptional regulatory roles in gene expression and can greatly influence virus-host cell interactions. This study investigated cellular miRNA expression profiles operating in response to early stages of KSHV infection of human Burkitt lymphoma B cells (BJAB). We employed deep sequencing to analyze miRNA expression in KSHV-infected BJAB cells 15 min post infection (PI) and compared this to uninfected BJAB cells...
July 13, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28707269/complete-genomic-sequence-of-common-reed-chlorotic-stripe-virus-a-novel-member-of-the-family-potyviridae
#17
Wen Yuan, Kaitong Du, Zaifeng Fan, Tao Zhou
Common reed (Phragmites australis) plants showing chlorotic stripe symptoms on leaves were found in Gansu Province, China. Deep sequencing of small RNAs from symptomatic leaves identified a putative potyvirus, which was named common reed chlorotic stripe virus (CRCSV). The full genome sequence was determined by reverse transcription PCR, rapid amplification of cDNA ends (RACE) PCR, and sequencing. It consists of 9,426 nucleotides, excluding the poly(A) tail, and contains a large open reading frame encoding a polyprotein of 3,014 amino acids...
July 13, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28706524/evaluation-of-wild-lentil-species-as-genetic-resources-to-improve-drought-tolerance-in-cultivated-lentil
#18
Linda Y Gorim, Albert Vandenberg
Increasingly unpredictable annual rainfall amounts and distribution patterns have far reaching implications for pulse crop biology. Seedling and whole plant survival will be affected given that water is a key factor in plant photosynthesis and also influences the evolving disease spectrum that affects crops. The wild relatives of cultivated lentil are native to drought prone areas, making them good candidates for the evaluation of drought tolerance traits. We evaluated root and shoot traits of genotypes of cultivated lentil and five wild species grown under two water deficit regimes as well as fully watered conditions over a 13 week period indoors...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28706299/findings-of-a-1303-korean-whole-exome-sequencing-study
#19
Soo Heon Kwak, Jeesoo Chae, Seongmin Choi, Min Jung Kim, Murim Choi, Jong-Hee Chae, Eun-Hae Cho, Tai Ju Hwang, Se Song Jang, Jong-Il Kim, Kyong Soo Park, Yung-Jue Bang
Ethnically specific data on genetic variation are crucial for understanding human biology and for clinical interpretation of variant pathogenicity. We analyzed data obtained by deep sequencing 1303 Korean whole exomes; the data were generated by three independent whole exome sequencing projects (named the KOEX study). The primary focus of this study was to comprehensively analyze the variant statistics, investigate secondary findings that may have clinical actionability, and identify loci that should be cautiously interpreted for pathogenicity...
July 14, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/28705883/assessing-genome-wide-copy-number-variation-in-the-han-chinese-population
#20
Jianqi Lu, Haiyi Lou, Ruiqing Fu, Dongsheng Lu, Feng Zhang, Zhendong Wu, Xi Zhang, Changhua Li, Baijun Fang, Fangfang Pu, Jingning Wei, Qian Wei, Chao Zhang, Xiaoji Wang, Yan Lu, Shi Yan, Yajun Yang, Li Jin, Shuhua Xu
BACKGROUND: Copy number variation (CNV) is a valuable source of genetic diversity in the human genome and a well-recognised cause of various genetic diseases. However, CNVs have been considerably under-represented in population-based studies, particularly the Han Chinese which is the largest ethnic group in the world. OBJECTIVES: To build a representative CNV map for the Han Chinese population. METHODS: We conducted a genome-wide CNV study involving 451 male Han Chinese samples from 11 geographical regions encompassing 28 dialect groups, representing a less-biased panel compared with the currently available data...
July 13, 2017: Journal of Medical Genetics
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