Bio Center

Heslington, United Kingdom

Bio Center

Heslington, United Kingdom
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Shin S.Y.,National Institute of Ecology NIE | Jo B.-H.,Bio Center | Moon J.C.,National Institute of Ecology NIE | Lee J.R.,National Institute of Ecology NIE | And 4 more authors.
Journal of Plant Biotechnology | Year: 2016

Living modified (LM) crops are imported each year to South Korea as food and feeds, LM canola being one of the imported crops. The cultivation of LM crops is not permitted in South Korea but the import of these crops is increasing. In this study, we surveyed the environmental risk of imported LM canola at 9 provinces, from March 2009 to June 2013. Monitoring of canola was conducted around feed factories, roadsides, harbors, farmhouses, and flower festival regions. From the total of 595 canola samples collected from 1850 monitoring sites, we identified 6 LM canola samples. The LM canola samples were subjected to protein and DNA based analysis. PCR analyses using approved 5 single event primers (T45, MS8, RT73, Rf3 and Topas 19-2) revealed that two crops were glyphosate-resistant LM canolas, and four were glufosinate-resistant LM canolas. This study suggested that environmental monitoring is a useful research tool to manage LM crops unintentionally introduced into the environment in South Korea. This result can be used as a basis for future post-management of canola crops. © Korean Society for Plant Biotechnology.


Mickiewicz B.,Bio Center | Shin S.Y.,University of Calgary | Pozzi A.,Vanderbilt University | Pozzi A.,Veterans Affairs Hospital | And 3 more authors.
Journal of Proteome Research | Year: 2016

The risk of developing post-traumatic osteoarthritis (PTOA) following joint injury is high. Furthering our understanding of the molecular mechanisms underlying PTOA and/or identifying novel biomarkers for early detection may help to improve treatment outcomes. Increased expression of integrin α1β1 and inhibition of epidermal growth factor receptor (EGFR) signaling protect the knee from spontaneous OA; however, the impact of the integrin α1β1/EGFR axis on PTOA is currently unknown. We sought to determine metabolic changes in serum samples collected from wild-type and integrin α1-null mice that underwent surgery to destabilize the medial meniscus and were treated with the EGFR inhibitor erlotinib. Following 1H nuclear magnetic resonance spectroscopy, we generated multivariate statistical models that distinguished between the metabolic profiles of erlotinib- versus vehicle-treated mice and the integrin α1-null versus wild-type mouse genotype. Our results show the sex-dependent effects of erlotinib treatment and highlight glutamine as a metabolite that counteracts this treatment. Furthermore, we identified a set of metabolites associated with increased reactive oxygen species production, susceptibility to OA, and regulation of TRP channels in α1-null mice. Our study indicates that systemic pharmacological and genetic factors have a greater effect on serum metabolic profiles than site-specific factors such as surgery. © 2016 American Chemical Society.


Gruner S.M.,Stanford University | Gruner S.M.,Cornell University | Lattman E.E.,Hauptman Woodward Medical Research Institute | Lattman E.E.,State University of New York at Buffalo | Lattman E.E.,Bio Center
Annual Review of Biophysics | Year: 2015

Next-generation synchrotron radiation sources, such as X-ray free-electron lasers, energy recovery linacs, and ultra-low-emittance storage rings, are catalyzing novel methods of biomolecular microcrystallography and solution scattering. These methods are described and future trends are predicted. Importantly, there is a growing realization that serial microcrystallography and certain cutting-edge solution scattering experiments can be performed at existing storage ring sources by utilizing new technology. In this sense, next-generation sources are serving two distinct functions, namely, provision of new capabilities that require the newer sources and inspiration of new methods that can be performed at existing sources. © Copyright ©2015 by Annual Reviews. All rights reserved.


Sarell C.J.,University College London | Karamanos T.K.,University of Leeds | White S.J.,University of Leeds | Bunka D.H.J.,Bio Center | And 5 more authors.
Journal of Biological Chemistry | Year: 2014

Background: Altering the co-polymerization of proteins into amyloid fibrils provides an opportunity for manipulating fibril assembly.Results: NMR and kinetic analysis showed that an RNA aptamer distinguishes between two highly similar co-aggregating proteins.Conclusion: RNA aptamers are specific and discriminatory probes able to modulate amyloid formation.Significance: Aptamers can be used as tools to differentiate amyloid precursors that are closely related and alter assembly. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.


Park K.H.,Korea Basic Science Institute | Kim M.S.,Korea Basic Science Institute | Baek S.J.,Korea Basic Science Institute | Bae I.H.,Korea Basic Science Institute | And 6 more authors.
Plant Methods | Year: 2013

Background: Plant extracts are a reservoir of pharmacologically active substances; however, conventional analytical methods can analyze only a small portion of an extract. Here, we report a high-throughput analytical method capable of determining most phytochemicals in a plant extract and of providing their molecular formulae from a single experiment using ultra-high-resolution electrospray ionization mass spectrometry (UHR ESI MS). UHR mass profiling was used to analyze natural compounds in a 70% ethanol ginseng extract, which was directly infused into a 15 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer for less than 10 min without a separation process.Results: The UHR FT-ICR MS yielded a mass accuracy of 0.5 ppm and a mass resolving power (m/Δm) of 1,000,000-270,000 for the range m/z 290-1,100. The mass resolution was sufficient to resolve the isotopic fine structure (IFS) of many compounds in the extract. After noise removal from 1,552 peaks, 405 compounds were detected. The molecular formulae of 123 compounds, including 33 ginsenosides, were determined using the observed IFS, exact monoisotopic mass, and exact mass difference. Liquid chromatography (LC)/FT-ICR MS of the extract was performed to compare the high-throughput performance of UHR ESI FT-ICR MS. The LC/FT-ICR MS detected only 129 compounds, including 19 ginsenosides. The result showed that UHR ESI FT-ICR MS identified three times more compounds than LC/FT-ICR MS and in a relatively shorter time. The molecular formula determination by UHR FT-ICR MS was validated by LC and tandem MS analyses of three known ginsenosides.Conclusions: UHR mass profiling of a plant extract by 15 T FT-ICR MS showed that multiple compounds were simultaneously detected and their molecular formulae were decisively determined by a single experiment with ultra-high mass resolution and mass accuracy. Simultaneous molecular determination of multiple natural products by UHR ESI FT-ICR MS would be a powerful method to profile a wide range of natural compounds. © 2013 Park et al.; licensee BioMed Central Ltd.


Hong S.W.,South Korean National Institute of Animal Science | Kwon S.-W.,South Korean National Institute of Animal Science | Kim S.-J.,South Korean National Institute of Animal Science | Kim S.Y.,Bio Center | And 5 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2014

A Gram-stain-positive, aerobic, endospore-forming, moderately halophilic rod, designated strain R1T, was isolated from rice husks and subjected to a taxonomic study using a polyphasic approach. Strain R1T produced spherical or ellipsoidal endospores at a subterminal position in swollen sporangia, and was catalase- and oxidase-positive. The isolate grew optimally at 37 °C and pH 6.0-7.0, and could grow in the presence of up to 9 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R1T belongs to the genus Bacillus. The closest relatives of strain R1T were Bacillus subtilis subsp. subtilis NCIB 3610T, Bacillus aquimaris TF-12T, and Bacillus marisflavi TF-11T, with 16S rRNA gene sequence similarities of 96.0 %, 98.4 %, and 98.7 %, respectively. DNA-DNA relatedness values between the isolate and the reference strains were ≤42±3 %. The predominant menaquinones were MK-5 (50 %) and MK-7 (50 %). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethanolamine. The major cellular fatty acids were iso-C15: 0 (48.6 %) and anteiso-C15: 0 (20.6 %), and the cell-wall diamino acid was meso-diaminopimelic acid. On the basis of 16S rRNA gene sequence analyses and chemotaxonomic and phenotypic characteristics, it is concluded that strain R1T represents a novel species of the genus Bacillus, for which we propose the name Bacillus oryzaecorticis sp. nov. The type strain is R1T (= KACC 17217T = KCCM 90231T = JCM 19602T). © 2014 IUMS.


Duggan G.E.,Bio Center | Hittel D.S.,University of Calgary | Sensen C.W.,University of Calgary | Weljie A.M.,Bio Center | And 2 more authors.
Journal of Applied Physiology | Year: 2011

Exercise training is a common therapeutic approach known to antagonize the metabolic consequences of obesity. The aims of the present study were to examine 1) whether short-term, moderate-intensity exercise training alters the basal metabolite profile and 2) if 10 days of mild exercise training can correct obesity-induced shifts in metabolic spectra. After being weaned, male C57BL/6J littermates were randomly divided into two diet groups: low fat (LF) or high fat (HF). After 12 wk of dietary manipulation, HF animals were obese and hyperglycemic compared with LF animals. Mice from each group were further divided into sedentary or exercise treatments. Exercise training consisted of wheel running exercise (2 h/day, 10 days, 5.64 m/min). After exercise training, animals were rested (36 h) and fasted (6 h) before serum collection. Samples were analyzed by highresolution one-dimensional proton NMR. Fifty high- and mediumconcentration metabolites were identified. Pattern recognition algorithms and multivariate modeling were used to identify and isolate significant metabolites changing in response to HF and exercise training. The results showed that while exercise can mitigate some of the abnormal patterns in metabolic spectra induced by HF diet feeding, they cannot negate it. In fact, when the effects of diet and exercise were compared, diet was a stronger predictor and had the larger influence on the metabolic profile. External validation of models showed that diet could be correctly classified with an accuracy of 89%, whereas exercise training could be classified 73% of the time. The results demonstrate metabolomics to effectively characterize obesity-induced perturbations in metabolism and support the concept that exercise is beneficial for this condition. © 2011 the American Physiological Society.


Shin S.H.,Chungbuk National University | Shin S.H.,Bio Center | Kang S.S.,Chungbuk National University
Open Biochemistry Journal | Year: 2013

The transfer of acetyl groups from acetyl coenzyme A to the ε amino group of internal lysine residues is catalyzed by Tip60, which is in the MYST family of nuclear histone acetyltransferases (HATs). The tyrosine phosphorylation of Tip60 seems to be a unique modification. We present evidence that Tip60 is modified on tyrosine 327 by Abl kinase. We show that this causes functional changes in HAT activity and the subcellular localization of TIP60, which forms a complex with Abl kinase. The Tip60 mutation Y327F abolished tyrosine phosphorylation, reduced the inhibition of Tip60 HAT activity, and caused G0-G1 arrest and association with FE65. Thus, our findings for the first time suggested a novel regulation mechanism of Tip60. Regulation was through phosphorylation of tyrosine 327 by Abl tyrosine kinase and depended on environmental conditions, suggesting that the tyrosine residue of Tip60 is important for the activation process. © Shin and Kang.


PubMed | Chungbuk National University, Korea Basic Science Institute and Bio Center
Type: | Journal: Plant methods | Year: 2014

Plant extracts are a reservoir of pharmacologically active substances; however, conventional analytical methods can analyze only a small portion of an extract. Here, we report a high-throughput analytical method capable of determining most phytochemicals in a plant extract and of providing their molecular formulae from a single experiment using ultra-high-resolution electrospray ionization mass spectrometry (UHR ESI MS). UHR mass profiling was used to analyze natural compounds in a 70% ethanol ginseng extract, which was directly infused into a 15T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer for less than 10min without a separation process.The UHR FT-ICR MS yielded a mass accuracy of 0.5ppm and a mass resolving power (m/m) of 1,000,000-270,000 for the range m/z 290-1,100. The mass resolution was sufficient to resolve the isotopic fine structure (IFS) of many compounds in the extract. After noise removal from 1,552 peaks, 405 compounds were detected. The molecular formulae of 123 compounds, including 33 ginsenosides, were determined using the observed IFS, exact monoisotopic mass, and exact mass difference. Liquid chromatography (LC)/FT-ICR MS of the extract was performed to compare the high-throughput performance of UHR ESI FT-ICR MS. The LC/FT-ICR MS detected only 129 compounds, including 19 ginsenosides. The result showed that UHR ESI FT-ICR MS identified three times more compounds than LC/FT-ICR MS and in a relatively shorter time. The molecular formula determination by UHR FT-ICR MS was validated by LC and tandem MS analyses of three known ginsenosides.UHR mass profiling of a plant extract by 15T FT-ICR MS showed that multiple compounds were simultaneously detected and their molecular formulae were decisively determined by a single experiment with ultra-high mass resolution and mass accuracy. Simultaneous molecular determination of multiple natural products by UHR ESI FT-ICR MS would be a powerful method to profile a wide range of natural compounds.

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