Zheng H.-Q.,National Cheng Kung University |
Chiang-Hsieh Y.-F.,National Cheng Kung University |
Chien C.-H.,National Cheng Kung University |
Hsu B.-K.J.,BioScience Company |
And 3 more authors.
BMC Genomics | Year: 2014
Background: Algae are important non-vascular plants that have many research applications, including high species diversity, biofuel sources, and adsorption of heavy metals and, following processing, are used as ingredients in health supplements. The increasing availability of next-generation sequencing (NGS) data for algae genomes and transcriptomes has made the development of an integrated resource for retrieving gene expression data and metabolic pathway essential for functional analysis and systems biology. In a currently available resource, gene expression profiles and biological pathways are displayed separately, making it impossible to easily search current databases to identify the cellular response mechanisms. Therefore, in this work the novel AlgaePath database was developed to retrieve transcript abundance profiles efficiently under various conditions in numerous metabolic pathways.Description: AlgaePath is a web-based database that integrates gene information, biological pathways, and NGS datasets for the green algae Chlamydomonas reinhardtii and Neodesmus sp. UTEX 2219-4. Users can search this database to identify transcript abundance profiles and pathway information using five query pages (Gene Search, Pathway Search, Differentially Expressed Genes (DEGs) Search, Gene Group Analysis, and Co-expression Analysis). The transcript abundance data of 45 and four samples from C. reinhardtii and Neodesmus sp. UTEX 2219-4, respectively, can be obtained directly on pathway maps. Genes that are differentially expressed between two conditions can be identified using Folds Search. The Gene Group Analysis page includes a pathway enrichment analysis, and can be used to easily compare the transcript abundance profiles of functionally related genes on a map. Finally, the Co-expression Analysis page can be used to search for co-expressed transcripts of a target gene. The results of the searches will provide a valuable reference for designing further experiments and for elucidating critical mechanisms from high-throughput data.Conclusions: AlgaePath is an effective interface that can be used to clarify the transcript response mechanisms in different metabolic pathways under various conditions. Importantly, AlgaePath can be mined to identify critical mechanisms based on high-throughput sequencing. To our knowledge, AlgaePath is the most comprehensive resource for integrating numerous databases and analysis tools in algae. The system can be accessed freely online at http://algaepath.itps.ncku.edu.tw. © 2014 Zheng et al.; licensee BioMed Central Ltd.
Tai H.-M.,Providence University |
Tai H.-M.,BioScience Company |
Yin L.-J.,National Kaohsiung Marine University |
Chen W.-C.,National Taiwan Ocean University |
And 2 more authors.
Journal of Agricultural and Food Chemistry | Year: 2013
To obtain a Pichia pastoris mutant with an Escherichia coli phytase gene, which was synthesized according to P. pastoris codon preference, a mature phytase cDNA of E. coli being altered according to the codons usage preference of P. pastoris was artificially synthesized and cloned into an expression vector of pGAPZαC. The final extracellular phytase activity was 112.5 U/mL after 72 h of cultivation. The phytase, with a molecular mass of 46 kDa, was purified to electrophoretical homogeneity after Ni Sepharose 6 Fast Flow chromatography. The yield, purification fold, and specific activity were 63.97%, 26.17, and 1.57 kU/mg, respectively. It had an optimal pH and temperature of 4.0-6.0 and 50 C, respectively, and was stable at pH 3.0-8.0 and 25-40 C. The purified recombinant phytase was resistant to trypsin, highly inhibited by Cu 2+, Zn2+, Hg2+, Fe2+, Fe 3+, phenylmethylsulfonyl fluoride, and N-tosyl-l-lysine chloromethyl ketone, but activated by Mg2+, Ca2+, Sr2+, Ba2+, glutathione, ethylenediaminetetraacetic acid, and N-ethylmaleimide. It revealed higher affinity to calcium phytate than to other phosphate conjugates. © 2013 American Chemical Society.
Lungu L.,Institute of Organic Chemistry |
Popa C.-V.,University of Bucharest |
Morris J.,BioScience Company |
Savoiu M.,Institute of Organic Chemistry
Romanian Biotechnological Letters | Year: 2011
Phytotoxic effects of aqueous and alcoholic extracts obtained from different parts (leaves, leaves & wood mix, fruits) of Melia azedarach L. on germination and growth of Lactuca sativa L. seeds were investigated under laboratory conditions. Ultrasonic and classic reflux methods were used for obtaining extracts from the vegetable material. The inhibitory effect on the germination of lettuce seeds as well as on seedling growth varied with concentration and extract type. Thus, fruit extract showed the most pronounced inhibitory effect followed by leaves extract and leaves and wood mix extract. The 5% w/v ethanolic extracts obtained by using reflux method showed a significant inhibitory effect on lettuce seeds germination and on seedlings. © 2011 University of Bucharest.
Yin L.-J.,National Kaohsiung Marine University |
Huang P.-S.,Providence University |
Lin H.-H.,BioScience Company
Journal of Agricultural and Food Chemistry | Year: 2010
A cellulase-producing bacterium was isolated from soil and identified as Cellulomonas sp. YJ5. Maximal cellulase activity was obtained after 48 h of incubation at 30 °C in a medium containing 1.0% carboxymethyl cellulose (CMC), 1.0% algae powder, 1.0% peptone, 0.24% (NH4) 2SO4, 0.20% K2HPO4, and 0.03% MgSO4 7H2O. The cellulase was purified after Sephacryl S-100 chromatography twice with a recovery of 27.9% and purification fold of 17.5. It was, with N-terminal amino acids of AGTKTPVAK, stable at pH 7.5-10.5 and 20-50 °C with optimal pH and temperature of 7.0 and 60 °C, respectively. Cu2+, Fe2+, Hg2+, Cr 3+, and SDS highly inhibited, but cysteine and β-mercaptoethanol activated, its activity. Substrate specificity indicated it to be an endo-β-1,4-glucanase. © 2010 American Chemical Society.
BioScience Company | Date: 2016-04-21
Abrasive paste; Air fragrancing preparations; Cleaning preparations; Cleansing milk; Cosmetics; Cosmetics for animals; Essential oils; Incense; Polishing preparations; Tooth paste.