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Sophorolipids (SLs) are amphiphilic compounds produced from a variety of saccharides and vegetable oils by the yeast Starmerella bombicola and related strains, and they have commercial uses as detergents. In the present study, SL production was investigated using a corncob hydrolysate (CCH) medium derived from lignocellulosic feedstocks as a source of hydrophilic carbon substrates. Excess sulfuric acid concentrations during pretreatment of the corncobs increased the furfural concentrations and turned the CCH dark brown. The optimal sulfuric acid concentration was 1% (w/v), and the treated CCH, containing 45 g/l glucose, allowed the production of 33.7 g/l of SLs following 4 days of cultivation. Additional autoclaving (121°C, 20 min) inhibited SL production and cell growth by 36% and 40%, respectively. Ammonium nitrate (0.1 g-N/l) restored SL production to the autoclaved CCH. Finally, a cost-effective SL production of 49.2 g/l, with a volumetric productivity of 12.3 g/l/day, was achieved using CCH medium during batch cultivation in a jar fermentor., (Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.)

The selective production of lactic acid by anaerobic acidogenesis with low pH control was examined using a chemostat culture. By decreasing culture pH to 3.5 in a chemostat culture containing mixed microbial populations for anaerobic acidogenesis, heterolactic fermentation became dominant, resulting in the selective production of lactic acid and ethanol. This phenomenon was reversible between the acidic and neutral conditions, and was not affected by the dilution rate. The extremely low pH operation was effective for selective lactic acid production in anaerobic acidogenesis., (Copyright © 2012 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.)

Computational prediction of polyadenylation signals (PASes) is essential for analysis of alternative polyadenylation that plays crucial roles in gene regulations by generating heterogeneity of 3'-UTR of mRNAs. To date, several algorithms that are mostly based on machine learning methods have been developed to predict PASes. Accuracies of predictions by those algorithms have improved significantly for the last decade. However, they are designed primarily for prediction of the most canonical AAUAAA and its common variant AUUAAA whereas other variants have been ignored in their predictions despite recent studies indicating that non-canonical variants of AAUAAA are more important in the polyadenylation process than commonly recognized. Here we present a new algorithm "PolyF" employing fuzzy logic to confer an advance in computational PAS prediction--enable prediction of the non-canonical variants, and improve the accuracies for the canonical A(A/U)UAAA prediction. PolyF is a simple computational algorithm that is composed of membership functions defining sequence features of downstream sequence element (DSE) and upstream sequence element (USE), together with an inference engine. As a result, PolyF successfully identified the 10 single-nucleotide variants with approximately the same or higher accuracies compared to those for A(A/U)UAAA. PolyF also achieved higher accuracies for A(A/U)UAAA prediction than those by commonly known PAS finder programs, Polyadq and Erpin. Incorporating the USE into the PolyF algorithm was found to enhance prediction accuracies for all the 12 PAS hexamers compared to those using only the DSE, suggesting an important contribution of the USE in the polyadenylation process.

Microbial production of xylitol from corn cobs using Candida magnoliae was experimentally investigated. Approximately 25 g-xylose/l solution was obtained from 100 g-corn cobs/l solution by hydrolysis using 1.0% sulfuric acid at 121 degrees C for 60 min. To remove inhibitors from the hydrolysates, charcoal pellets were found to be effective in selectively removing the inhibitors from the hydrolysates without affecting xylose concentration. C. magnoliae was successfully cultivated using the treated corn cob hydrolysate, resulting in the production of 18.7 g-xylitol/l from 25 g-xylose/l within 36 h.

An effective method for cell harvesting of the halotolerant microalga, Dunaliella tertiolecta ATCC30929, was investigated. By increasing the pH of the culture broth using NaOH solution, suspended D. terfolecta cells rapidly coagulated and settled within a few minutes, which allowed simple harvesting of the concentrated cells from the culture broth. The pHs for successful coagulation were between 8.6 and 10.5 and more than 90% of cells was recovered from the culture broth. Clarified culture broth could be reused for the successive cultivation of D. tertiolecta simply by supplying fresh medium and neutralizing alkali with HCl without the requirement for an additional inoculum.

Fuzzy modeling and control based on the fuzzy sets theory have been used in the biotechnology field for the last two decades. Recent studies on fuzzy modeling and control of various biological processes are reviewed. In addition, five applications of fuzzy control to industrial biological processes are summarized, compared and discussed in terms of the system features, control purpose, input and output variables, development of fuzzy rules and effectiveness. Fuzzy modeling and control are regarded as promising methods for automating the bioprocesses in which experienced operators play significant roles in their successful operation.

The performance of a partially packed charcoal pellet bioreactor was compared to that of a fully packed bioreactor for aerobic acetic acid production. In the fully packed charcoal pellet bioreactor, it was considered that the shortening of an actual retention time of the culture broth limited the bioreactor performance under high dilution rate and high aeration conditions. By reducing the filling ratio of charcoal pellets to 44%, which increased the actual retention time of the culture broth, the maximum productivity increased from 3.9 g/l/h in the fully packed bed bioreactor to 5.7 g/l/h in the partially packed bioreactor without affecting the operational stability.

A packed bed bioreactor using charcoal pellets produced from waste mushroom medium by thermal carbonization was developed and applied to continuous acetic acid production. The pellets were characterized by their high specific surface area (200 m2/g) with numerous micropores (2-10 microm). The continuous acetic acid fermentation started up smoothly after seeding and was successfully operated for about 180 d under various retention times. The maximum acetic acid productivity was about 3.9 g/l/h using normal aeration and 6.5 g/l/h using air enriched with 40% O2. The pellets are expected to prove useful as a new packing material for bioreactor in terms of their bacterial affinity, high specific surface area with appropriate pore sizes for bacteria, as well as the operational stability of the system and the low production cost.

A two-step fermentation system combining a repeated batch process using a flocculating yeast with a charcoal pellet bioreactor was developed for onion vinegar production. Juice from the red onion R-3, which contained 67.3 g/l total sugar, was smoothly converted to onion alcohol containing 30.6 g/l ethanol by repeated batch operation using the flocculating yeast Saccharomyces cerevisiae strain IR-2. Stable operation was possible and the maximum productivity was about 8.0 g/l/h. A packed bed bioreactor containing charcoal pellets produced from waste mushroom medium was then applied to continuous onion vinegar production from the onion alcohol. Onion vinegar was successfully produced, with a maximum productivity and acetic acid concentration of about 3.3 g/l/h and 37.9 g/l, respectively. The total acetic acid yield calculated from the amount of sugar consumed was 0.86. The two-step system was operated for 50 d and proved to be competitive with other systems in terms of its high productivity, high acetic acid yield, operational stability and low production costs.

The possibility of producing a new type of vinegar from worthless onions, which fail to meet the quality standards required for marketing, was investigated. Several kinds of onion were initially tested as raw material for vinegar production, and vinegar was successfully produced from the juice of a red onion, the cultivar Kurenai, by batch culture using yeast and Acetobacter aceti. Nutritional analysis revealed that the potassium content of onion vinegar was extremely high, while the amount of sodium was lower than that in conventional vinegars. It was also shown that the total amino acid and total organic acid contents of the onion vinegar were respectively 1.6-6.9 times and 3.5-11.5 times those in other kinds of vinegars.

A fuzzy control system featuring the identification of culture phases by fuzzy logic was applied to the large-scale recombinant vitamin B2 (VB2) production at the Fukuroi factory of Nippon Roche, Fukuroi. Prior to actual operation, the knowledge base for fuzzy control was tuned and verified by a simulation system. Only four rules, formulated as IF approximately THEN instructions and membership functions for state variables, are employed to control the feed rate and pH of the fed-batch culture. By applying fuzzy control, total VB2 production and VB2 yield was increased by 6-16% and 4-11% compared with conventional control, respectively. Operating stability was also improved. The large-scale fermentor used for VB2 production has been successfully operated under the control of the fuzzy system for more than 2 years.