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Chareonlimkun A.,King Mongkut's University of Technology Thonburi | Champreda V.,National Center for Genetic Engineering and Biotechnology | Shotipruk A.,Chulalongkorn University | Laosiripojana N.,King Mongkut's 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.

Unrean P.,King Mongkut's University of Technology Thonburi | Unrean P.,National Center for Genetic Engineering and Biotechnology | Nguyen N.H.A.,King Mongkut's University of Technology Thonburi
Applied Microbiology and Biotechnology | Year: 2012

Elementary mode analysis (EMA) identifies all possible metabolic states of the cell metabolic network. Investigation of these states can provide a detailed insight into the underlying metabolism in the cell. In this study, the flux states of Scheffersomyces (Pichia) stipitis metabolism were examined. It was shown that increasing oxygen levels led to a decrease of ethanol synthesis. This trend was confirmed by experimental evaluation of S. stipitis in glucose-xylose fermentation. The oxygen transfer rate for an optimal ethanol production was 1.8 mmol/l/h, which gave the ethanol yield of 0.40 g/g and the ethanol productivity of 0.25 g/l/h. For a better understanding of the cell's regulatory mechanism in response to oxygenation levels, EMA was used to examine metabolic flux patterns under different oxygen levels. Up- and downregulation of enzymes in the network during the change of culturing condition from oxygen limitation to oxygen sufficiency were identified. The results indicated the flexibility of S. stipitis metabolism to cope with oxygen availability. In addition, relevant genetic targets towards improved ethanol-producing strains under all oxygenation levels were identified. These targeted genes limited the metabolic functionality of the cell to function according to the most efficient ethanol synthesis pathways. The presented approach is promising and can contribute to the development of culture optimization and strain engineers for improved lignocellulosic ethanol production by S. stipitis. © Springer-Verlag 2012.

Raita M.,King Mongkut's University of Technology Thonburi | Champreda V.,National Center for Genetic Engineering and Biotechnology | Laosiripojana N.,King Mongkut's 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.

Unrean P.,King Mongkut's University of Technology Thonburi | Unrean P.,National Center for Genetic Engineering and Biotechnology
Biotechnology Progress | Year: 2014

This research rationally analyzes metabolic pathways of Pichia pastoris to study the metabolic flux responses of this yeast under methanol metabolism. A metabolic model of P. pastoris was constructed and analyzed by elementary mode analysis (EMA). EMA was used to comprehensively identify the cell's metabolic flux profiles and its underlying regulation mechanisms for the production of recombinant proteins from methanol. Change in phenotypes and flux profiles during methanol adaptation with varying feed mixture of glycerol and methanol was examined. EMA identified increasing and decreasing fluxes during the glycerol-methanol metabolic shift, which well agreed with experimental observations supporting the validity of the metabolic network model. Analysis of all the identified pathways also led to the determination of the metabolic capacities as well as the optimum metabolic pathways for recombinant protein synthesis during methanol induction. The network sensitivity analysis revealed that the production of proteins can be improved by manipulating the flux ratios at the pyruvate branch point. In addition, EMA suggested that protein synthesis is optimum under hypoxic culture conditions. The metabolic modeling and analysis presented in this study could potentially form a valuable knowledge base for future research on rational design and optimization of P. pastoris by determining target genes, pathways, and culture conditions for enhanced recombinant protein synthesis. The metabolic pathway analysis is also of considerable value for production of therapeutic proteins by P. pastoris in biopharmaceutical applications. © 2013 American Institute of Chemical Engineers.

Dedsuksophon W.,King Mongkut's University of Technology Thonburi | Faungnawakij K.,National Nanotechnology Center | Champreda V.,National Center for Genetic Engineering and Biotechnology | Laosiripojana N.,King Mongkut's 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.

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.

Piriyapongsa J.,National Center for Genetic Engineering and Biotechnology
BMC genomics | Year: 2012

Genome-wide association studies (GWAS) do not provide a full account of the heritability of genetic diseases since gene-gene interactions, also known as epistasis are not considered in single locus GWAS. To address this problem, a considerable number of methods have been developed for identifying disease-associated gene-gene interactions. However, these methods typically fail to identify interacting markers explaining more of the disease heritability over single locus GWAS, since many of the interactions significant for disease are obscured by uninformative marker interactions e.g., linkage disequilibrium (LD). In this study, we present a novel SNP interaction prioritization algorithm, named iLOCi (Interacting Loci). This algorithm accounts for marker dependencies separately in case and control groups. Disease-associated interactions are then prioritized according to a novel ranking score calculated from the difference in marker dependencies for every possible pair between case and control groups. The analysis of a typical GWAS dataset can be completed in less than a day on a standard workstation with parallel processing capability. The proposed framework was validated using simulated data and applied to real GWAS datasets using the Wellcome Trust Case Control Consortium (WTCCC) data. The results from simulated data showed the ability of iLOCi to identify various types of gene-gene interactions, especially for high-order interaction. From the WTCCC data, we found that among the top ranked interacting SNP pairs, several mapped to genes previously known to be associated with disease, and interestingly, other previously unreported genes with biologically related roles. iLOCi is a powerful tool for uncovering true disease interacting markers and thus can provide a more complete understanding of the genetic basis underlying complex disease. The program is available for download at http://www4a.biotec.or.th/GI/tools/iloci.

Wichadakul D.,National Center for Genetic Engineering and Biotechnology
BMC genomics | Year: 2012

The microRNA-based gene-silencing machinery has been recognized as a promising approach to control viral replication and used for improving safety for the live attenuated virus vaccines. The effective host microRNA response elements (MREs) have been incorporated into a virus sequence mainly based on the experimental trials for identifying both microRNA binding sites and effective mutations. The design of MREs for viral genomes or with multiple host microRNAs of interest, then, will be time and cost consuming. In this paper, we introduced a computational flow that could be used to design MREs of human microRNAs within Influenza A H1N1 virus gene segments. The main steps of the flow includes locating possible binding sites; MREs, of human microRNAs within the viral sequences using a miRNA target prediction tool (miranda), performing various mutations among mismatched binding positions, calculating the binding energy, score, identity, and the effects of changed physical properties of amino acids according to the changed bases in RNA level, and prioritizing the mutated binding sites. The top ranked MREs of human microRNA hsa-miR-93 is consistent with previous literature while other results waited to be experimentally verified. To make the computational flow easily accessible by virologists, we also developed MicroLive, a web server version of the MRE design flow together with the database of miranda-predicted MREs within gene sequences of seven RNA viruses including Influenza A, dengue, hepatitis C, measles, mumps, poliovirus, and rabies. Users may design MREs of specific human microRNAs for their input viral sequences using MRE design tool or optimize the miranda-predicted MREs of seven viruses available on the system. Also, users could design varied number of MREs for multiple human microRNAs to modulate the degree of live vaccine attenuation and reduce the likelihood of escape mutants. The computational design of MREs helps reduce time and cost for experimental trials. While the flow was demonstrated using human microRNAs and Influenza A H1N1 virus, it could be flexibly applied to other hosts (e.g., animals) and viruses of interest for constructing host-specific live attenuated vaccines. Also, it could be deployed for engineering tissue-specific oncolytic viruses in cancer virotherapeutics. The MicroLive web server is freely accessible at http://www.biotec.or.th/isl/microlive.

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.

Numnark S.,National Center for Genetic Engineering and Biotechnology
BMC genomics | Year: 2012

MicroRNAs (miRNAs) have been known to play an important role in several biological processes in both animals and plants. Although several tools for miRNA and target identification are available, the number of tools tailored towards plants is limited, and those that are available have specific functionality, lack graphical user interfaces, and restrict the number of input sequences. Large-scale computational identifications of miRNAs and/or targets of several plants have been also reported. Their methods, however, are only described as flow diagrams, which require programming skills and the understanding of input and output of the connected programs to reproduce. To overcome these limitations and programming complexities, we proposed C-mii as a ready-made software package for both plant miRNA and target identification. C-mii was designed and implemented based on established computational steps and criteria derived from previous literature with the following distinguishing features. First, software is easy to install with all-in-one programs and packaged databases. Second, it comes with graphical user interfaces (GUIs) for ease of use. Users can identify plant miRNAs and targets via step-by-step execution, explore the detailed results from each step, filter the results according to proposed constraints in plant miRNA and target biogenesis, and export sequences and structures of interest. Third, it supplies bird's eye views of the identification results with infographics and grouping information. Fourth, in terms of functionality, it extends the standard computational steps of miRNA target identification with miRNA-target folding and GO annotation. Fifth, it provides helper functions for the update of pre-installed databases and automatic recovery. Finally, it supports multi-project and multi-thread management. C-mii constitutes the first complete software package with graphical user interfaces enabling computational identification of both plant miRNA genes and miRNA targets. With the provided functionalities, it can help accelerate the study of plant miRNAs and targets, especially for small and medium plant molecular labs without bioinformaticians. C-mii is freely available at http://www.biotec.or.th/isl/c-mii for both Windows and Ubuntu Linux platforms.

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