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https://www.readbyqxmd.com/read/28449399/comparative-transcriptomic-analysis-of-bombyx-mori-fat-body-tissue-following-dietary-restriction
#1
Ye Pan, Peng Lü, Qinyun Wang, Feifei Zhu, Chengjun Li, Yuanqing He, Keping Chen
Dietary restriction (DR) refers to a reduction in food intake to induce undernutrition but not malnutrition, which extends the lifespan of multiple species. Although there are invertebrate aging models, such as the Caenorhabditis elegans and Drosophila melanogaster, aging studies in Lepidoptera are few in number and the underlying life-extending molecular mechanisms are not clear. Research on a broader range of animals is necessary to support generalizations on mechanisms of aging and rates of aging. The aim of this study was to further investigate genes and pathways associated with DR in Bombyx mori...
May 2017: Archives of Insect Biochemistry and Physiology
https://www.readbyqxmd.com/read/28449382/current-use-of-chromosomal-microarray-by-australian-paediatricians-and-implications-for-the-implementation-of-next-generation-sequencing
#2
Victoria McKay, Daryl Efron, Elizabeth E Palmer, Susan M White, Chris Pearson, Margie Danchin
AIM: Chromosomal microarray (CMA) is an important diagnostic test for children with multiple congenital anomalies or certain developmental behavioural problems suggestive of an underlying genetic diagnosis. However, there are medical and ethical complexities to its use and few Australian policies to guide practice. We aimed to describe the current practice of Australian paediatricians in relation to CMA testing. We hypothesised that there are knowledge gaps in their use of CMA. METHODS: Online survey completed between September 2015 and January 2016 by paediatricians in secondary care settings...
April 27, 2017: Journal of Paediatrics and Child Health
https://www.readbyqxmd.com/read/28449322/a-bacterium-with-close-genetic-identity-to-pseudomonas-mandelii-associated-with-spring-fish-kills-in-wild-bluegill-lepomis-macrochirus-rafinesque-and-pumpkinseed-sunfish-lepomis-gibbosus-linnaeus
#3
J Lovy, D Dicarlo-Emery, J M Hutcheson
Pseudomonas fluorescens are known bacterial pathogens in fish. The P. fluorescens group contains at least nine different bacterial species, although species from fish have rarely been differentiated. Two isolated fish kills affecting wild bluegills, Lepomis macrochirus Rafinesque, and pumpkinseed sunfish, Lepomis gibbosus (Linnaeus), occurred in the spring of 2015 during cool water temperatures (12.5°C-15.5°C). Disease signs included severe bacteraemia with rare gross external signs. Pure bacterial cultures isolated from kidneys of all affected fish were identified as P...
April 27, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/28449315/panelcn-mops-copy-number-detection-in-targeted-ngs-panel-data-for-clinical-diagnostics
#4
Gundula Povysil, Antigoni Tzika, Julia Vogt, Verena Haunschmid, Ludwine Messiaen, Johannes Zschocke, Günter Klambauer, Sepp Hochreiter, Katharina Wimmer
Targeted next-generation-sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy number variations (CNVs) in addition to single-nucleotide-variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control, incidental findings, and user-friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn...
April 27, 2017: Human Mutation
https://www.readbyqxmd.com/read/28449304/a-case-of-familial-transmission-of-the-newly-described-dnmt3a-overgrowth-syndrome
#5
Gabrielle Lemire, Julie Gauthier, Jean-François Soucy, Marie-Ange Delrue
DNMT3A-Overgrowth Syndrome (also known as Tatton-Brown-Rahman Syndrome) (MIM 615879) has recently been described in 13 individuals with de novo heterozygous mutations in DNMT3A gene. This autosomal dominant condition is characterized by overgrowth, dysmorphic facial features and moderate intellectual disability. Missense and truncating point mutations, a small in-frame deletion, as well as microdeletion 2p23 have been reported. Moreover, DNMT3A is commonly somatically mutated in acute myeloid leukemia. We herein report a family with two siblings and their father affected by the syndrome...
April 27, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28449274/a-dna-barcode-library-for-germany-s-mayflies-stoneflies-and-caddisflies-ephemeroptera-plecoptera-trichoptera
#6
Jérôme Morinière, Lars Hendrich, Michael Balke, Arne J Beermann, Tobias König, Monika Hess, Stefan Koch, Reinhard Müller, Florian Leese, Paul D N Hebert, Axel Hausmann, Christoph F Schubart, Gerhard Haszprunar
Mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) are prominent representatives of aquatic macroinvertebrates, commonly used as indicator organisms for water quality and ecosystem assessments. However, unambiguous morphological identification of EPT species, especially their immature life stages, is a challenging, yet fundamental task. However, a comprehensive DNA barcode library based upon taxonomically well-curated specimens can overcome the problematic identification. Once available, this library will support the implementation of fast, cost-efficient, and reliable DNA-based identifications and assessments of ecological status...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28449233/an-evaluation-of-the-international-society-for-animal-genetics-recommended-parentage-and-identification-panel-for-the-domestic-pigeon-columba-livia-domestica
#7
M de Groot, W A van Haeringen
In this study, the International Society for Animal Genetics (ISAG) recommended panel for the identification of the domestic pigeon (Columba livia domestica) is characterized based on commonly used statistical parameters. The marker panel is based on 16 short tandem repeat (STR) loci (PIGN15, PIGN10, PIGN57, PIGN26, CliμD16, CliμD19, PIGN12, CliμD17, CliμT17, PIGN04, CliμD01, CliμD11, CliμD35, CliμT02, CliμT13, CliμT43). The alleles of the 16 loci consist of a mixture of tri-, tetra-, penta- and hexameric repeat patterns...
April 27, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28449169/analysis-of-liver-tumors-using-preoperative-and-intraoperative-contrast-enhanced-ultrasound-ceus-ioceus-by-radiologists-in-comparison-to-magnetic%C3%A2-resonance-imaging-and-histopathology
#8
Severin Huf, Natascha Platz Batista da Silva, Isabel Wiesinger, Matthias Hornung, Marcus N Scherer, Sven Lang, Christian Stroszczynski, Thomas Fischer, Ernst Michael Jung
Purpose To evaluate the diagnostic significance of preoperatively and intraoperatively performed contrast-enhanced ultrasound (CEUS/IOCEUS) in the diagnosis of liver tumors in comparison to magnetic resonance imaging (MRI) and histopathology. Materials and Methods Retrospective analysis of 70/317 patients who underwent surgery for liver tumors between January 2012 and October 2015. Findings of CEUS and IOCEUS were compared to MRI. CEUS and IOCEUS were performed using multifrequency linear probes (1 - 5, 6 - 15 MHz) after bolus injection of 1 - 5 ml sulfur hexafluoride microbubbles...
May 2017: RöFo: Fortschritte Auf Dem Gebiete der Röntgenstrahlen und der Nuklearmedizin
https://www.readbyqxmd.com/read/28449168/mri-sequences-in-head-neck-radiology-state-of-the-art
#9
Gerlig Widmann, Benjamin Henninger, Christian Kremser, Werner Jaschke
Background Magnetic resonance imaging (MRI) has become an essential imaging modality for the evaluation of head & neck pathologies. However, the diagnostic power of MRI is strongly related to the appropriate selection and interpretation of imaging protocols and sequences. The aim of this article is to review state-of-the-art sequences for the clinical routine in head & neck MRI and to describe the evidence for which medical question these sequences and techniques are useful. Method Literature review of state-of-the-art sequences in head & neck MRI...
May 2017: RöFo: Fortschritte Auf Dem Gebiete der Röntgenstrahlen und der Nuklearmedizin
https://www.readbyqxmd.com/read/28449136/-alpha-2-macroglobulin-serum-level-in-patients-with-alpha-1-antitrypsin-deficiency
#10
V Kotke, S Wiedmann, C Nell, C Vogelmeier, R Bals, T Greulich, A Klemmer
Background and objectives Alpha-2 Macroglobulin (A2M) is a plasma protein with proteolytic effects on many proteases. In patients with an inborn alpha-1 antitrypsin deficiency (AATD) the homeostasis between proteases and antiproteases is disturbed. The aim of this study was to compare the levels of AAT and A2 M in patients and controls. We hypothesized that in patients with AATD A2 M levels are elevated. Methods Patients with AATD (polymorphism Pi*ZZ, Pi*SZ, Pi*MZ and rare gene variants) as well as healthy volunteers (Pi*MM) were tested for A2 M and AAT levels...
April 27, 2017: Pneumologie
https://www.readbyqxmd.com/read/28449120/sigseeker-a-peak-calling-ensemble-approach-for-constructing-epigenetic-signatures
#11
Jens Lichtenberg, Laura Elnitski, David M Bodine
Motivation: Epigenetic data are invaluable when determining the regulatory programs governing a cell. Based on use of next-generation sequencing data for characterizing epigenetic marks and transcription factor binding, numerous peak-calling approaches have been developed to determine sites of genomic significance in these data. Such analyses can produce a large number of false positive predictions, suggesting that sites supported by multiple algorithms provide a stronger foundation for inferring and characterizing regulatory programs associated with the epigenetic data...
April 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28449119/mutations-in-thap11-cause-an-inborn-error-of-cobalamin-metabolism-and-developmental-abnormalities
#12
Anita M Quintana, Hung-Chun Yu, Alison Brebner, Mihaela Pupavac, Elizabeth A Geiger, Abigail Watson, Victoria L Castro, Warren Cheung, Shu-Huang Chen, David Watkins, Tomi Pastinen, Flemming Skovby, Bruce Appel, David S Rosenblatt, Tamim H Shaikh
CblX (MIM309541) is an X-linked recessive disorder characterized by defects in cobalamin (vitamin B12) metabolism and other developmental defects. Mutations in HCFC1, a transcriptional co-regulator which interacts with multiple transcription factors, have been associated with cblX. HCFC1 regulates cobalamin metabolism via the regulation of MMACHC expression through its interaction with THAP11, a THAP domain-containing transcription factor. The HCFC1/THAP11 complex potentially regulates genes involved in diverse cellular functions including cell cycle, proliferation, and transcription...
April 25, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28449108/poly-a-clickseq-click-chemistry-for-next-generation-3%C3%AE-end-sequencing-without-rna-enrichment-or-fragmentation
#13
Andrew Routh, Ping Ji, Elizabeth Jaworski, Zheng Xia, Wei Li, Eric J Wagner
The recent emergence of alternative polyadenylation (APA) as an engine driving transcriptomic diversity has stimulated the development of sequencing methodologies designed to assess genome-wide polyadenylation events. The goal of these approaches is to enrich, partition, capture and ultimately sequence poly(A) site junctions. However, these methods often require poly(A) enrichment, 3΄ linker ligation steps, and RNA fragmentation, which can necessitate higher levels of starting RNA, increase experimental error and potentially introduce bias...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449106/microbiomeanalyst-a-web-based-tool-for-comprehensive-statistical-visual-and-meta-analysis-of-microbiome-data
#14
Achal Dhariwal, Jasmine Chong, Salam Habib, Irah L King, Luis B Agellon, Jianguo Xia
The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449102/enhancing-expression-of-ssu1-genes-in-saccharomyces-uvarum-leads-to-an-increase-in-sulfite-tolerance-and-transcriptome-profiles-change
#15
X Z Liu, M Sang, X A Zhang, T K Zhang, H Y Zhang, X He, S X Li, X D Sun, Z M Zhang
Saccharomyces uvarum is a good wine yeast species which may have great potential for the future. However, sulfur tolerance of most S. uvarum strains is very poor. In addition there is still little information about the SSU1 gene of S. uvarum. In order to analyze the function of SSU1 genes, two expression vectors which contained different SSU1 genes were constructed and transferred into a sulfite-tolerant S. uvarum strain A9. Then sulfite tolerance, PCR analysis, sequencing analysis, SO2 output production analysis, RT-qPCR analysis and transcriptome analysis were used to access the function of the S...
April 25, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28449100/integrated-analysis-of-individual-codon-contribution-to-protein-biosynthesis-reveals-a-new-approach-to-improving-the-basis-of-rational-gene-design
#16
Juan C Villada, Otávio José Bernardes Brustolini, Wendel Batista da Silveira
Gene codon optimization may be impaired by the misinterpretation of frequency and optimality of codons. Although recent studies have revealed the effects of codon usage bias (CUB) on protein biosynthesis, an integrated perspective of the biological role of individual codons remains unknown. Unlike other previous studies, we show, through an integrated framework that attributes of codons such as frequency, optimality and positional dependency should be combined to unveil individual codon contribution for protein biosynthesis...
April 24, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28449092/genome-wide-dna-methylomes-from-discrete-developmental-stages-reveal-the-predominance-of-non-cpg-methylation-in-tribolium-castaneum
#17
Xiaowen Song, Fei Huang, Juanjuan Liu, Chengjun Li, Shanshan Gao, Wei Wu, Mengfan Zhai, Xiaojuan Yu, Wenfeng Xiong, Jia Xie, Bin Li
Cytosine DNA methylation is a vital epigenetic regulator of eukaryotic development. Whether this epigenetic modification occurs in Tribolium castaneum has been controversial, its distribution pattern and functions have not been established. Here, using bisulphite sequencing (BS-Seq), we confirmed the existence of DNA methylation and described the methylation profiles of the four life stages of T. castaneum. In the T. castaneum genome, both symmetrical CpG and non-CpG methylcytosines were observed. Symmetrical CpG methylation, which was catalysed by DNMT1 and occupied a small part in T...
April 25, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28449085/guanine-quadruplex-monoclonal-antibody-1h6-cross-reacts-with-restrained-thymidine-rich-single-stranded-dna
#18
Hinke G Kazemier, Katrin Paeschke, Peter M Lansdorp
Previously we reported the production and characterization of monoclonal antibody 1H6 raised against (T4G4)2 intermolecular guanine quadruplex (G4) DNA structures (Henderson A. et al. (2014) Nucleic Acids Res., 42, 860-869; Hoffmann R.F. et al. (2016) Nucleic Acids Res., 44, 152-163). It was shown that 1H6 strongly stains nuclei and has exquisite specificity for heterochromatin by immuno-electron microscopy. Here we extend our studies of 1H6 reactivity using enzyme-linked immunosorbent assay (ELISA) and microscale thermophoresis (MST)...
April 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449067/using-high-throughput-barcode-sequencing-to-efficiently-map-connectomes
#19
Ian D Peikon, Justus M Kebschull, Vasily V Vagin, Diana I Ravens, Yu-Chi Sun, Eric Brouzes, Ivan R Corrêa, Dario Bressan, Anthony M Zador
The function of a neural circuit is determined by the details of its synaptic connections. At present, the only available method for determining a neural wiring diagram with single synapse precision-a 'connectome'-is based on imaging methods that are slow, labor-intensive and expensive. Here, we present SYNseq, a method for converting the connectome into a form that can exploit the speed and low cost of modern high-throughput DNA sequencing. In SYNseq, each neuron is labeled with a unique random nucleotide sequence-an RNA 'barcode'-which is targeted to the synapse using engineered proteins...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449065/a-homozygous-missense-mutation-in-eral1-encoding-a-mitochondrial-rrna-chaperone-causes-perrault-syndrome
#20
Iliana A Chatzispyrou, Marielle Alders, Sergio Guerrero-Castillo, Ruben Zapata Perez, Martin A Haagmans, Laurent Mouchiroud, Janet Koster, Rob Ofman, Frank Baas, Hans R Waterham, Johannes N Spelbrink, Johan Auwerx, Marcel M Mannens, Riekelt H Houtkooper, Astrid S Plomp
Perrault syndrome (PS) is a rare recessive disorder characterized by ovarian dysgenesis and sensorineural deafness. It is clinically and genetically heterogeneous, and previously mutations have been described in different genes, mostly related to mitochondrial proteostasis. We diagnosed three unrelated females with PS and set out to identify the underlying genetic cause using exome sequencing. We excluded mutations in the known PS genes, but identified a single homozygous mutation in the ERAL1 gene (c.707A>T; p...
April 25, 2017: Human Molecular Genetics
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