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101.
Fei Yao Pramila N. Ariyaratne Axel M. Hillmer Wah Heng Lee Guoliang Li Audrey S. M. Teo Xing Yi Woo Zhenshui Zhang Jieqi P. Chen Wan Ting Poh Kelson F. B. Zawack Chee Seng Chan See Ting Leong Say Chuan Neo Poh Sum D. Choi Song Gao Niranjan Nagarajan Hervé Thoreau Atif Shahab Xiaoan Ruan Valère Cacheux-Rataboul Chia-Lin Wei Guillaume Bourque Wing-Kin Sung Edison T. Liu Yijun Ruan 《PloS one》2012,7(9)
Structural variations (SVs) contribute significantly to the variability of the human genome and extensive genomic rearrangements are a hallmark of cancer. While genomic DNA paired-end-tag (DNA-PET) sequencing is an attractive approach to identify genomic SVs, the current application of PET sequencing with short insert size DNA can be insufficient for the comprehensive mapping of SVs in low complexity and repeat-rich genomic regions. We employed a recently developed procedure to generate PET sequencing data using large DNA inserts of 10–20 kb and compared their characteristics with short insert (1 kb) libraries for their ability to identify SVs. Our results suggest that although short insert libraries bear an advantage in identifying small deletions, they do not provide significantly better breakpoint resolution. In contrast, large inserts are superior to short inserts in providing higher physical genome coverage for the same sequencing cost and achieve greater sensitivity, in practice, for the identification of several classes of SVs, such as copy number neutral and complex events. Furthermore, our results confirm that large insert libraries allow for the identification of SVs within repetitive sequences, which cannot be spanned by short inserts. This provides a key advantage in studying rearrangements in cancer, and we show how it can be used in a fusion-point-guided-concatenation algorithm to study focally amplified regions in cancer. 相似文献
102.
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104.
Transformation of Soybean (Glycine max) by Infecting Germinating Seeds with Agrobacterium tumefaciens 总被引:8,自引:1,他引:8 下载免费PDF全文
The transfer of genetic material into soybean tissue was accomplished by using an avirulent strain of Agrobacterium tumefaciens which contained the binary vector pGA482. The method used for transformation requires no tissue culture steps as it involves the inoculation of the plumule, cotyledonary node, and adjacent cotyledon tissues of germinating seeds. The identification of neomycin phosphotransferase (NPT) II enzyme activity in the tissues of 16 (R0) soybean plants indicated that the plant expressible Nos-NPT II gene, contained within the T-DNA region from pGA482, had been transferred at least into somatic tissues. Putative transformed R0 soybean plants were advanced to produce R1 plants which were also assayed for the presence of the transferred Nos-NPT II gene. The combined results of these assays indicated that about 0.7% of the surviving inoculated seeds yielded transformed tissues in the R0 plant, and that about 1/10 of these plants yielded transformed R1 plants. The presence of the Nos-NPT II gene in DNAs isolated from both R0 and R1 plant was demonstrated by using genomic blot hybridization and polymerase chain reaction methods. Integration of this gene into the soybean genome was demonstrated for three R1 soybean plants. 相似文献
105.
Chee MJ Mörl K Lindner D Merten N Zamponi GW Light PE Beck-Sickinger AG Colmers WF 《The Journal of biological chemistry》2008,283(48):33337-33346
Constitutively active G-protein-coupled receptors (GPCRs) can signal even in the absence of ligand binding. Most Class I GPCRs are stabilized in the resting conformation by intramolecular interactions involving transmembrane domain (TM) 3 and TM6, particularly at loci 6.30 and 6.34 of TM6. Signaling by Gi/Go-coupled receptors such as the Neuropeptide Y1 receptor decreases already low basal metabolite levels. Thus, we examined constitutive activity using a biochemical assay mediated by a Gi/Gq chimeric protein and a more direct electrophysiological assay. Wild-type (WT-Y1) receptors express no measurable, agonist-independent activation, while mu-opioid receptors (MOR) and P2Y12 purinoceptors showed clear evidence of constitutive activation, especially in the electrophysiological assay. Neither point mutations at TM6 (T6.30A or N6.34A) nor substitution of the entire TM3 and TM6 regions from the MOR into the Y1 receptor increased basal WT-Y1 activation. By contrast, chimeric substitution of the third intracellular loop (ICL3) generated a constitutively active, Y1-ICL3-MOR chimera. Furthermore, the loss of stabilizing interactions from the native ICL3 enhanced the role of surrounding residues to permit basal receptor activation; because constitutive activity of the Y1-ICL3-MOR chimera was further increased by point mutation at locus 6.34, which did not alter WT-Y1 receptor activity. Our results indicate that the ICL3 stabilizes the Y1 receptor in the inactive state and confers structural properties critical for regulating Y receptor activation and signal transduction. These studies reveal the active participation of the ICL3 in the stabilization and activation of Class I GPCRs. 相似文献
106.
Garima Singhal ffolliott Martin Fisher Melissa J. Chee Tze Guan Tan Abdelfattah El Ouaamari Andrew C. Adams Robert Najarian Rohit N. Kulkarni Christophe Benoist Jeffrey S. Flier Eleftheria Maratos-Flier 《PloS one》2016,11(2)
Fibroblast growth factor 21 (FGF21) is an important endocrine metabolic regulator expressed in multiple tissues including liver and adipose tissue. Although highest levels of expression are in pancreas, little is known about the function of FGF21 in this tissue. In order to understand the physiology of FGF21 in the pancreas, we analyzed its expression and regulation in both acinar and islet tissues. We found that acinar tissue express 20-fold higher levels than that observed in islets. We also observed that pancreatic FGF21 is nutritionally regulated; a marked reduction in FGF21 expression was noted with fasting while obesity is associated with 3–4 fold higher expression. Acinar and islet cells are targets of FGF21, which when systemically administered, leads to phosphorylation of the downstream target ERK 1/2 in about half of acinar cells and a small subset of islet cells. Chronic, systemic FGF21 infusion down-regulates its own expression in the pancreas. Mice lacking FGF21 develop significant islet hyperplasia and periductal lymphocytic inflammation when fed with a high fat obesogenic diet. Inflammatory infiltrates consist of TCRb+ Thy1+ T lymphocytes with increased levels of Foxp3+ regulatory T cells. Increased levels of inflammatory cells were coupled with elevated expression of cytokines such as TNFα, IFNγ and IL1β. We conclude that FGF21 acts to limit islet hyperplasia and may also prevent pancreatic inflammation. 相似文献
107.
To investigate the extent of exposure and routes of Cry1Ac1 protein through the food chain, we collected Bt cabbage leaves and arthropods that occurred in the field during two trials. Protein levels in the transgenic leaves were significantly higher during the early stages of plant growth, ranging from 209.1 to 553.6?ng?g?1 in spring and from 208.2 to 402.8?ng?g?1 in autumn. Enzyme-linked immunosorbent assays were used to measure protein levels in the arthropods. Among the 16 taxa collected in the field, Cry1Ac1 was detected in the bodies of 10. Concentrations were higher in lepidopteran larvae than in the other taxa. In particular, we found a significant correlation between Cry1Ac1 protein levels in cabbage leaves and in Pieris rapae and Mamestra brassicae. Furthermore, this protein was detected in five out of nine taxa of predators (spiders and coleopterans) and parasitoids. These results will be useful as we identify the arthropods that are directly or indirectly exposed to Bt toxin within the food web and the degree to which they are exposed during the cultivation of Bt cabbage. 相似文献
108.
Paula P. Chee 《Plant cell reports》1995,14(12):753-757
Summary Results obtained from using root inducing compounds on Taxus species cuttings suggested that rooting could be significantly enhanced by the presence of thiamine. This observation was verified using a root inducing solution containing a set concentration of IBA (0.2%), NAA (0.1%), and supplemented with various concentrations of thiamine. The best rooting response for Taxus cuspidata stem cuttings was found using this solution supplemented with 0.08% thiamine. Rooted cuttings were easily established and developed into vigorous plants. In addition, Taxus brevifolia shoots obtained from tissue cultures via in vitro organogenesis also responded favorably to this 0.08% thiamine supplemented rooting solution. 相似文献
109.
The SHC gene encodes a protein that is thought to act as an adapter in many signal transduction pathways; the SHC protein probably facilitates the activation of RAS proteins in response to a variety of factors. We have mapped the human SHC gene and have identified a new SHC-related sequence. We have sequenced the region corresponding to the SHC 3 UTR from both loci and have mapped cosmids by fluorescence in situ hybridization. The human SHC gene maps to the proximal long arm of chromosome 1 and the SHC-related sequence maps to the proximal long arm of chromosome 17. A number of cancers have been positioned in the proximal long arm of chromosome 1; this is of interest given the oncogenic potential of the SHC protein. 相似文献
110.
Yang Yang Yu-Zhi Shi Ning Zhang Shuo Wang Gabor S. Ungvari Chee H. Ng Yi-Long Wang Xing-Quan Zhao Yong-Jun Wang Chun-Xue Wang Yu-Tao Xiang 《PloS one》2016,11(11)
Few studies on long-term functional outcome have been conducted in post-stroke patients in China. The objective of this study was to conduct a nationwide survey in China to investigate the 5-year prevalence of post-stroke disability and its correlation factors. A total of 893 patients with ischemic stroke were included. Demographic, clinical and neuro-imaging information were collected with standardized instruments that assessed stroke severity, depression, cognitive impairment, stroke recurrence and physical disability. Disability was assessed with the modified Ranking Score (mRS), of which a cutoff score ≥2 indicates disability. Statistical analysis included chi-square tests, two independent samples t-tests, Mann-Whitney U test and multiple logistic regression analysis. The frequency of disability in this study population was 45%. Multivariate analyses revealed that older age, lower education level, previous history of stroke, stroke severity at admission, depression, cognitive impairment at 3 months, and stroke recurrence within 5 years follow up were all significantly associated with post-stroke disability. The disability rate in 5-year post-stroke was high in Chinese patients. Treatment of depression, secondary prevention of stroke and rehabilitation may benefit disabled patients with stroke in China. 相似文献