Journal of biotechnology
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Journal of biotechnology · Oct 2014
Correction of gene expression data: Performance-dependency on inter-replicate and inter-treatment biases.
This report investigates for the first time the potential inter-treatment bias source of cell number for gene expression studies. Cell-number bias can affect gene expression analysis when comparing samples with unequal total cellular RNA content or with different RNA extraction efficiencies. For maximal reliability of analysis, therefore, comparisons should be performed at the cellular level. ⋯ Analyses of RNA sequencing and microarray data showed that the efficiencies of correction methods are influenced by the inter-treatment bias as well as the inter-replicate variance. Therefore, we recommend inspecting both of the bias sources in order to apply the most efficient correction method. As an alternative correction strategy, sequential application of different correction approaches is also advised.
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Journal of biotechnology · Sep 2013
RecA-mediated SOS response provides a geraniol tolerance in Escherichia coli.
Geraniol is an important industrial material and a potential candidate of advanced biofuels. One challenge of microbial geraniol production is the toxicity to hosts. However, the poor understanding on geraniol tolerance mechanism is an obstacle for developing geraniol tolerant host. ⋯ Based on our data, it was deciphered that recA provided tolerance through SOS response network responding to DNA damage caused by geraniol. RecA-mediated SOS response activates the homologous recombinational repair by RecB and RecN for corrective DNA maintenance. This protection mechanism suggests an effective strategy to combat geraniol toxicity in E. coli.
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Journal of biotechnology · Mar 2010
A novel multivalent vaccine based on secretary antigen-delivery induces protective immunity against Vibrio anguillarum and Aeromonas hydrophila.
In our previous work, four secretory antigen-delivery systems based on different signal peptides (SPs) (SP(hlyA), SP(rtxA), SP(vah3) and SP(empA)) have been successfully established in attenuated Vibrio anguillarum. To investigate the potential application of the antigen-delivery systems in V. anguillarum multivalent vector vaccine, the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from pathogenic Aeromonas hydrophila, as a putative protective antigen, was fused to the four delivery systems, respectively, and introduced into attenuated V. anguillarum strain MVAV6203 to get four GAPDH-delivery strains in this work. Immunodetection of GAPDH indicated that among the four constructs, the SP(empA)-mediated GAPDH-delivery strain AV(pGap-empA) showed the highest level of GAPDH expression and secretion, and was determined as the multivalent vaccine candidate. Further immune protection evaluation of AV(pGap-empA) in turbot (Scophtalmus maximus) demonstrated that the vaccine candidate could induce efficient protection against V. anguillarum and A. hydrophila, suggesting that this vector vaccine had great potential in serving as a valuable multivalent live vaccine.
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Journal of biotechnology · Aug 2006
ReviewOMICS-driven biomarker discovery in nutrition and health.
While traditional nutrition research has dealt with providing nutrients to nourish populations, it nowadays focuses on improving health of individuals through diet. Modern nutritional research is aiming at health promotion and disease prevention and on performance improvement. As a consequence of these ambitious objectives, the disciplines "nutrigenetics" and "nutrigenomics" have evolved. ⋯ The Omics disciplines applied in the context of nutrition and health have the potential to deliver biomarkers for health and comfort, reveal early indicators for disease disposition, assist in differentiating dietary responders from non-responders, and, last but not least, discover bioactive, beneficial food components. This paper reviews the state-of-the-art of the three Omics platforms, discusses their implication in nutrigenomics and elaborates on applications in nutrition and health such as digestive health, allergy, diabetes and obesity, nutritional intervention and nutrient bioavailability. Proteomic developments, applications and potential in the field of nutrition have been specifically addressed in another review issued by our group.
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Journal of biotechnology · Mar 2005
Adaptive multiscale principal component analysis for on-line monitoring of a sequencing batch reactor.
In recent years, multiscale monitoring approaches, which combine principal component analysis (PCA) and multi-resolution analysis (MRA), have received considerable attention. These approaches are potentially very efficient for detecting and analyzing diverse ranges of faults and disturbances in chemical and biochemical processes. In this work, multiscale PCA is proposed for fault detection and diagnosis of batch processes. ⋯ Process monitoring by a unifying adaptive multiscale MPCA involves combining only those scales where significant disturbances are detected. This multiscale approach facilitates diagnosis of the detected fault as it hints to the time-scale under which the fault affects the process. The proposed adaptive multiscale method is successfully applied to a pilot-scale sequencing batch reactor for biological wastewater treatment.