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Tharatipyakul A.,National Center for Genetic Engineering and Biotechnology
BMC bioinformatics | Year: 2012

Manual chemical data curation from publications is error-prone, time consuming, and hard to maintain up-to-date data sets. Automatic information extraction can be used as a tool to reduce these problems. Since chemical structures usually described in images, information extraction needs to combine structure image recognition and text mining together. We have developed ChemEx, a chemical information extraction system. ChemEx processes both text and images in publications. Text annotator is able to extract compound, organism, and assay entities from text content while structure image recognition enables translation of chemical raster images to machine readable format. A user can view annotated text along with summarized information of compounds, organism that produces those compounds, and assay tests. ChemEx facilitates and speeds up chemical data curation by extracting compounds, organisms, and assays from a large collection of publications. The software and corpus can be downloaded from http://www.biotec.or.th/isl/ChemEx. Source

Chareonlimkun A.,King Mongkuts University of Technology Thonburi | Champreda V.,National Center for Genetic Engineering and Biotechnology | Shotipruk A.,Chulalongkorn University | Laosiripojana N.,King Mongkuts University of Technology Thonburi
Bioresource Technology | Year: 2010

The simultaneous hydrolysis/dehydration reaction of sugarcane bagasse, rice husk and corncob was studied under hot compressed water in the presence of TiO2, ZrO2 and TiO2-ZrO2 at 473-673 K. Among them, the reaction of corncob at 573 K in the presence of TiO2-ZrO2 produced the highest furfural and 5-hydroxymethylfurfural (HMF) yields (10.3% and 8.6%) with less by-products (i.e. glucose, fructose, xylose, and 1,6-anhydroglucose) selectivities. It was found that the catalyst preparation procedure and calcination temperature strongly affected its reactivity. Catalysts prepared by (co-) precipitation method gained higher reactivity than those prepared by sol-gel and physical mixing methods. The suitable calcination temperature for TiO2 and ZrO2 was at 773 K, whereas that for TiO2-ZrO2 was at 873 K; the XRD patterns revealed that different portions of phase formation were observed over catalysts with different calcination temperature. The portion of these phase formations affected the acidity-basicity of catalyst and thus the catalyst reactivity. © 2010 Elsevier Ltd. All rights reserved. Source

Kuhnert E.,Helmholtz Center for Infection Research | Fournier J.,Las Muros | Persoh D.,University of Bayreuth | Luangsa-Ard J.J.D.,National Center for Genetic Engineering and Biotechnology | Stadler M.,Helmholtz Center for Infection Research
Fungal Diversity | Year: 2014

Three new species of Hypoxylon (Xylariaceae) collected from Martinique in the French Caribbean are recognised by new combinations of morphological characters. Their status as undescribed taxa was supported by secondary metabolite profiling based on High performance liquid chromatography with diode array and mass spectrometric detection (HPLC/DAD-MS) as well as by comparison of ITS and partial ß-tubulin DNA sequences with related taxa. In the course of this study, the teleomorph of Nodulisporium griseobrunneum was found, and this species could be transferred to Hypoxylon. Moreover, several names in Hypoxylon are epitypified by selecting recently collected specimens from the same geographic areas as the holotypes came from. Despite the fact that our study used the hitherto most extensive taxon sampling, the phylogenetic analyses inferred from ITS and ß-tubulin sequences remain contradictory to each other, and neither genealogy was found fully in agreement with phenotype-derived traits. We conclude that the right gene (or multi-gene genealogies) to reflect the phylogeny and evolution of Hypoxylon still remains to be found. For the time being, we recommend that the application of polyphasic taxonomic concepts should be continued in taxonomic studies of Hypoxylon. © 2013 Mushroom Research Foundation. Source

Dedsuksophon W.,King Mongkuts University of Technology Thonburi | Faungnawakij K.,National Nanotechnology Center | Champreda V.,National Center for Genetic Engineering and Biotechnology | Laosiripojana N.,King Mongkuts University of Technology Thonburi
Bioresource Technology | Year: 2011

Hydrolysis/dehydration/aldol-condensation/hydrogenation of lignocellulosic-biomass (corncobs) and biomass-derived carbohydrates (tapioca flour) to produce water-soluble C5-C15 compounds was developed in a single reactor system. WO3-ZrO2 efficiently catalyzed the hydrolysis/dehydration of these feedstocks to 5-hydroxymethylfurfural and furfural, while the impregnation of WO3-ZrO2 with Pd allowed sequential aldolcondensation/hydrogenation of these furans to C5-C15 compounds. The highest C5-C15 yields of 14.8-20.3% were observed at a hydrolysis/dehydration temperature of 573K for 5min, an aldol-condensation temperature of 353K for 30h, and a hydrogenation temperature of 393K for 6h. The C5-C15 yield from tapioca flour was higher than that from corncobs (20.3% compared to 14.8%). Tapioca flour produced more C6/C9/C15, whereas corncobs generated more C5/C8/C13 compounds due to the presence of hemicellulose in the corncobs. These water-soluble organic compounds can be further converted to liquid alkanes with high cetane numbers for replacing diesel fuel in transportation applications. © 2010 Elsevier Ltd. Source

Raita M.,King Mongkuts University of Technology Thonburi | Champreda V.,National Center for Genetic Engineering and Biotechnology | Laosiripojana N.,King Mongkuts University of Technology Thonburi
Process Biochemistry | Year: 2010

Biocatalytic synthesis is a promising environmentally friendly process for the production of biodiesel, a sustainable alternative fuel from renewable plant resources. In order to develop an economical heterogeneous biocatalyst, protein-coated microcrystals (PCMCs) were prepared from a commercial enzyme preparation from a recombinant Aspergillus strain expressing Thermomyces lanuginosus lipase and used for synthesis of biodiesel from palm olein by ethanolysis. Reaction parameters, including catalyst loading, temperature, and oil/alcohol molar ratio have been systematically optimized. Addition of tert-butanol was found to markedly increase the biocatalyst activity and stability resulting in improved product yield. Optimized reactions (20%, w/w PCMC-lipase to triacylglycerol and 1:4 fatty acid equivalence/ethanol molar ratio) led to the production of alkyl esters from palm olein at 89.9% yield on molar basis after incubation at 45 °C for 24 h in the presence of tert-butanol at a 1:1 molar ratio to triacylglycerol. Crude palm oil and palm fatty acid distillate were also efficiently converted to biodiesel with 82.1 and 75.5% yield, respectively, with continual dehydration by molecular sieving. Operational stability of PCMC-lipase could be improved by treatment with tert-butanol allowing recycling of the biocatalyst for at least 8 consecutive batches with only slight reduction in activity. This work thus shows a promising approach for biodiesel synthesis with microcrystalline lipase which could be further developed for cost-efficient industrial production of biodiesel. © 2010 Elsevier Ltd. All rights reserved. Source

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