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Xiaojun Zhang, Lina Sun, Jianbo Yuan, Yamin Sun, Yi Gao, Libin Zhang, Shihao Li, Hui Dai, Jean-François Hamel, Chengzhang Liu, Yang Yu, Shilin Liu, Wenchao Lin, Kaimin Guo, Songjun Jin, Peng Xu, Kenneth B Storey, Pin Huan, Tao Zhang, Yi Zhou, Jiquan Zhang, Chenggang Lin, Xiaoni Li, Lili Xing, Da Huo, Mingzhe Sun, Lei Wang, Annie Mercier, Fuhua Li, Hongsheng Yang, Jianhai Xiang
Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers...
October 2017: PLoS Biology
Nicholas J Schurch, Christian Cole, Alexander Sherstnev, Junfang Song, Céline Duc, Kate G Storey, W H Irwin McLean, Sara J Brown, Gordon G Simpson, Geoffrey J Barton
The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct and complete annotation in addition to the underlying genomic sequence is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study...
2014: PloS One
David Chagné, Ross N Crowhurst, Massimo Pindo, Amali Thrimawithana, Cecilia Deng, Hilary Ireland, Mark Fiers, Helge Dzierzon, Alessandro Cestaro, Paolo Fontana, Luca Bianco, Ashley Lu, Roy Storey, Mareike Knäbel, Munazza Saeed, Sara Montanari, Yoon Kyeong Kim, Daniela Nicolini, Simone Larger, Erika Stefani, Andrew C Allan, Judith Bowen, Isaac Harvey, Jason Johnston, Mickael Malnoy, Michela Troggio, Laure Perchepied, Greg Sawyer, Claudia Wiedow, Kyungho Won, Roberto Viola, Roger P Hellens, Lester Brewer, Vincent G M Bus, Robert J Schaffer, Susan E Gardiner, Riccardo Velasco
We present a draft assembly of the genome of European pear (Pyrus communis) 'Bartlett'. Our assembly was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffolds greater than 499 bases (maximum scaffold length of 1.2 Mb) and covers a total of 577.3 Mb, representing most of the expected 600 Mb Pyrus genome. A total of 829,823 putative single nucleotide polymorphisms (SNPs) were detected using re-sequencing of 'Louise Bonne de Jersey' and 'Old Home'...
2014: PloS One
Troels T Marstrand, John D Storey
A problem of substantial interest is to systematically map variation in chromatin structure to gene-expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for determining the existence, strength, and type of relationship between high-resolution chromatin structure in terms of DNaseI hypersensitivity and genome-wide gene-expression levels in 20 diverse human cell types. We show that ∼25% of genes show cell-type-specific expression explained by alterations in chromatin structure...
February 11, 2014: Proceedings of the National Academy of Sciences of the United States of America
K W Lau, C D Chen, H L Lee, A A Izzul, M Asri-Isa, M Zulfadli, M Sofian-Azirun
The aim of the present study was to determine the vertical distribution and abundance of Aedes mosquitoes in multiple storey buildings in Selangor and Kuala Lumpur, Malaysia. Ovitrap surveillance was conducted for 4 continuous weeks in multiple storey buildings in 4 residential areas located in Selangor [Kg. Baiduri (KB)] and Kuala Lumpur [Student Hostel of University of Malaya (UM), Kg. Kerinchi (KK) and Hang Tuah (HT)]. The results implied that Aedes mosquitoes could be found from ground floor to highest floor of multiple storey buildings and data from different elevation did not show significant difference...
March 2013: Tropical Biomedicine
Elsdon Storey, R J McKinlay Gardner
Spinocerebellar ataxia type 20 (SCA20), first reported in 2004, is a slowly progressive dominantly inherited disorder so far reported in a single Anglo-Celtic family from Australia. It is characterized by dentate calcification from an early stage of the illness. Dysarthria without ataxia is the first symptom in the majority - an unusual feature amongst the SCAs. In addition to ataxia, examination often reveals spasmodic dysphonia and palatal tremor, but the syndrome is otherwise fairly pure. The responsible genetic abnormality has been tentatively identified as a 260-kb duplication in the pericentric region of chromosome 11, but confirmation will necessarily await description of further families...
2012: Handbook of Clinical Neurology
Melanie A Knight, Dena Hernandez, Scott J Diede, Hans G Dauwerse, Ian Rafferty, Joyce van de Leemput, Susan M Forrest, R J McKinlay Gardner, Elsdon Storey, Gert-Jan B van Ommen, Stephen J Tapscott, Kenneth H Fischbeck, Andrew B Singleton
Spinocerebellar ataxia type 20 (SCA20) has been linked to chromosome 11q12, but the underlying genetic defect has yet to be identified. We applied single-nucleotide polymorphism genotyping to detect structural alterations in the genomic DNA of patients with SCA20. We found a 260 kb duplication within the previously linked SCA20 region, which was confirmed by quantitative polymerase chain reaction and fiber fluorescence in situ hybridization, the latter also showing its direct orientation. The duplication spans 10 known and 2 unknown genes, and is present in all affected individuals in the single reported SCA20 pedigree...
December 15, 2008: Human Molecular Genetics
K B Storey, M E Dent, J M Storey
A cDNA library constructed from liver of 2-month estivating female spadefoot toads, Scaphiopus couchii, was differentially screened to reveal genes that were induced or upregulated during estivation. After two rounds of screening a clone was isolated that showed 60% higher expression in liver of estivating, versus control, toads. The clone possessed a 1.0 kb insert which annealed to a single 0.7 kb band on Northern blots. Sequencing revealed a 1053 nucleotide full-length cDNA; the largest potential open reading frame was 708 nucleotides which encoded a protein of 235 amino acids...
August 1, 1999: Journal of Experimental Zoology
P A Sokol, M Z Luan, D G Storey, P Thirukkumaran
The conversion of Pseudomonas aeruginosa PAO to the mucoid phenotype has been reported for a chronic pulmonary infection model in rats (D. E. Woods, P. A. Sokol, L. E. Bryan, D. G. Storey, S. J. Mattingly, H. J. Vogel, and H. Ceri, J. Infect. Dis. 163:143-149, 1991). This conversion was associated with a genetic rearrangement upstream of the exotoxin A gene. To characterize the genetic rearrangement, the region upstream of the toxA gene was cloned from PAO, PAO-muc (a mucoid strain), and PAO-rev (a nonmucoid revertant strain)...
February 1994: Journal of Bacteriology
M Lusher, C C Storey, S J Richmond
Examination of 12 Chlamydia psittaci strains recovered from nine different host species (three avian and six mammalian) revealed the presence of a 7.5 kb plasmid in all isolates except two ovine abortion strains, the human strain IOL207 and the Cal 10 strain. Restriction mapping analysis distinguished four different plasmids that were associated with avian, feline, equine and guinea-pig C. psittaci isolates, respectively. The restriction maps of these four C. psittaci plasmid types all differed from that of the plasmid recovered from C...
May 1989: Journal of General Microbiology
A G Templeton, J Macmillan, J C McGrath, N D Storey, V G Wilson
1. The postjunctional alpha-adrenoceptors mediating contractions in the isolated vascular bed of the perfused rat tail have been investigated, in the presence and absence of an increase in perfusion pressure by arginine vasopressin (AVP). 2. In the absence of AVP, bolus doses of noradrenaline (NA) and phenylephrine produced pressor responses of similar time course, while UK-14,304 was practically inactive. Responses to noradrenaline were inhibited more by 0.05 microM prazosin than by 1 microM rauwolscine, suggesting the presence of alpha1-adrenoceptors...
June 1989: British Journal of Pharmacology
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