Metabolic flux estimation--a self-adaptive evolutionary algorithm with singular value decomposition

Metabolic flux analysis is important for metabolic system regulation and intracellular pathway identification. A popular approach for intracellular flux estimation involves using ¹³C tracer experiments to label states that can be measured by nuclear magnetic resonance spectrometry or gas chromatography mass spectrometry. However, the bilinear balance equations derived from ¹³C tracer experiments and the noisy measurements require a nonlinear optimization approach to obtain the optimal solution. In this paper, the flux quantification problem is formulated as an error-minimization problem with equality and inequality constraints through the ¹³C balance and stoichiometric equations. The stoichiometric constraints are transformed to a null space by singular value decomposition. Self-adaptive evolutionary algorithms are then introduced for flux quantification. The performance of the evolutionary algorithm is compared with ordinary least squares estimation by the simulation of the central pentose phosphate pathway. The proposed algorithm is also applied to the central metabolism of Corynebacterium glutamicum under lysine-producing conditions. A comparison between the results from the proposed algorithm and data from the literature is given. The complexity of a metabolic system with bidirectional reactions is also investigated by analyzing the fluctuations in the flux estimates when available measurements are varied.     

Cananginones A-I, linear acetogenins from the stem bark of Cananga latifolia

Nine linear C23 and C21 acetogenins, named cananginones A–I (1–9), were isolated from stem bark of Cananga latifolia. Their structures were established by spectroscopic methods. These compounds showed cytotoxicity against three cancer cell lines (KB, MCF7 and NCI-H187) with IC₅₀ values in the range 16.6–129.7 μM. Only 5 showed weak antimalarial activity against Plasmodium falciparum. In addition, 8 and 9 exhibited weak antifungal activity against Candida albicans.     

Semi-defined Medium for in vitro Cultivation of the Fastidious Insect Pathogenic Fungus Cordyceps unilateralis

Cordyceps unilateralis is a fastidious fungal pathogen affecting ants. Up to now, only the complex and expensive Grace’s insect cell culture medium has been used for in vitro cultivation (as blastospores and mycelium) of this fungus. To obtain an inexpensive and less complicated medium, the effects of carbon and nitrogen sources, salt solution and carbon-to-nitrogen (C:N) ratio on the growth of this fungus were examined. Glucose was the most important factor for blastospore formation, and yeast extract could be used as a nitrogen source for blastospore formation and mycelial growth. A suitable C:N ratio (glucose: yeast extract) was 33.3:1. As a result, a new semi-defined medium was achieved, composed of 26.68 g L⁻¹ glucose, 3.3 g L⁻¹ yeast extract and salt solution. This medium supported blastospore formation and mycelial growth of all tested C. unilateralis isolates.     

Optimization of culture conditions for production of antimalarial menisporopsin A by the seed fungus Menisporopsis theobromae BCC 4162

AIMS: The aim of this work was to optimize the production of a novel antimaralial menisporopsin A by the seed fungus Menisporopsis theobromae BCC 4162. METHODS AND RESULTS: Fungal cultures were grown in shake flasks at 25 degrees C in the basal medium with varying carbon and nitrogen sources, aeration rates and initial pH levels. The optimal carbon and nitrogen sources that improved the production of menisporopsin A were 1% fructose and 2.5% meat extract respectively. The production was further enhanced when the culture incubated on a shaker at 200 rev min(-1) with an initial pH of 8. The yield of menisporopsin A cultured under the optimized conditions was increased from 348.30 (obtained from basal medium) to 889.02 mg l(-1), and the cultivation time was reduced from 28 to only 4 days. As a result, the productivity of menisporopsin A was greatly enhanced to 222.26 mg l(-1) day(-1) which is 18-fold higher than that of basal conditions. Larger scale production in a fermenter was also achieved, yielding menisporopsin A at a maximal level of 594.32 mg l(-1) in 4 days. CONCLUSIONS: The optimized culture conditions for menisporopsin A production by M. theobromae BCC 4162 was the cultivation under shaking or agitation at 25 degrees C in fructose-meat extract medium with an initial pH of 8. SIGNIFICANCE AND IMPACT OF THE STUDY: The production of menisporopsin A in a fermenter with a relatively short incubation period could be valuable for further utilization for chemical structure modification and derivatization.     

Production of red pigments by the insect pathogenic fungus Cordyceps unilateralis BCC 1869

Production of red pigments (naphthoquinones) by the insect pathogenic fungus Cordyceps unilateralis BCC 1869 was investigated in this study. Cultivation conditions, including temperature, intitial pH of medium, and aeration, were optimised to improve the yield of total naphthoquinones in shake-flask culture of C. unilateralis. The highest yield of total naphthoquinones (3 g L^–1) was obtained from a 28-day culture grown in potato dextrose broth with an initial pH of 7.0, at 28°C with shaking-induced aeration at 200 rpm. An extraction process for isolation of the targeted naphthoquinone, 3,5,8-trihydroxy-6-methoxy-2-(5-oxohexa-1,3-dienyl)-1,4-naphthoquinone (3,5,8-TMON), from a culture of C. unilateralis, was also developed. The yield of 3,5,8-TMON obtained was about 1.2 g L^–1 or 40% of total naphthoquinones. The stability of 3,5,8-TMON was very high, even upon exposure to strong sunlight (70,000 lx), high temperature up to 200°C, and acid and alkali solutions at concentrations of 0.1 M     

Isolation and Characterization of Novel Strains of <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> and <Emphasis Type="Italic">Serratia marcescens</Emphasis> Possessing High Efficiency to Degrade Gasoline,Kerosene, Diesel Oil,and Lubricating Oil

Bacteria possessing high capacity to degrade gasoline, kerosene, diesel oil, and lubricating oil were screened from several areas of Hokkaido, Japan. Among isolates, two strains, WatG and HokM, which were identified as new strains of Pseudomonas aeruginosa and Serratia marcescens species, respectively, showed relatively high capacity and wide spectrum to degrade the hydrocarbons in gasoline, kerosene, diesel, and lubricating oil. About 90-95% of excess amount of total diesel oil and kerosene added to mineral salts media as a sole carbon source could be degraded by WatG within 2 and 3 weeks, respectively. The same amount of lubricating oil was 60% degraded within 2 weeks. Strain HokM was more capable than WatG in degrading aromatic compounds in gasoline. This strain could also degrade kerosene, diesel, and lubricating oil with a capacity of 50-60%. Thus, these two isolates have potential to be useful for bioremediation of sites highly contaminated with petroleum hydrocarbons.     

Association of comorbidity between Opisthorchis viverrini infection and diabetes mellitus in the development of cholangiocarcinoma among a high-risk population,northeastern Thailand

BackgroundCholangiocarcinoma (CCA) is a category of lethal hepatobiliary malignancies. Previous studies have found that Opisthorchis viverrini infection and diabetes mellitus (DM) are closely correlated with CCA. However, few studies have discussed the association of CCA with a combination of both O. viverrini infection and DM. This study aimed to assess the correlation of CCA with various combinations of O. viverrini infection and DM among a high-risk population in northeastern Thailand.MethodologyThis study included participants from 20 provinces in northeastern Thailand who had been screened for CCA in the Cholangiocarcinoma Screening and Care Program (CASCAP) between 2013 and 2019. Histories of O. viverrini infection and DM diagnosis were obtained using a health questionnaire. CCA screening used ultrasonography with a definitive diagnosis based on histopathology. Multilevel mixed-effects logistic regression was performed to quantify the association, which is presented as adjusted odds ratios (aOR) and their 95% confidence intervals (CI).Principal findingsOverall, 263,776 participants were included, of whom 32.4% were infected with O. viverrini, 8.2% were diagnosed with DM, and 2.9% had a history of both O. viverrini infection and DM. The overall rate of CCA was 0.36%. Of those infected with O. viverrini, 0.47% had CCA; among those with DM, 0.59% had CCA and among those infected with O. viverrini and had DM, 0.73% had CCA. Compared with participants who were not infected with O. viverrini and were non-DM, the aOR for those infected with O. viverrini and with DM was 2.36 (95% CI: 1.74–3.21; p-value <0.001).ConclusionsThe combination of O. viverrini infection and DM was highly associated with CCA, and these two conditions had a combined effect on this association that was greater than that of either alone. These findings suggest that CCA screening should have a strong focus on people with a combination of O. viverrini infection and DM.     

Modification of culture conditions for production of the anti-tubercular hirsutellones by the insect pathogenic fungus Hirsutella nivea BCC 2594

Aims:  This work aimed to improve the production of anti-tubercular hirsutellones by the insect pathogenic fungus Hirsutella nivea BCC 2594.
Methods and Results:  The fungus was cultivated under different carbon/nitrogen sources and aerations (shake vs static flasks) to improve the production of the anti-tubercular alkaloids, hirsutellones A–D. Under the basal conditions, static cultivation at 25°C in minimum salt medium, only hirsutellone B and C were detected with maximum concentrations of 139·00 and 18·27 mg l⁻¹. Substitution of fructose for glucose and peptone for yeast extract increased the titres of hirsutellones A, B and C about two- to threefold. However, hirsutellone D was not detected in this medium. Culture agitation induced the production of hirsutellone D. As a result, the significant amounts of hirsutellones A–D were obtained with the concentration of 29·93, 169·63, 22·65 and 15·71 mg l⁻¹ within 15 days.
Conclusions:  Improved titres of hirsutellones in H. nivea BCC 2549 were achieved with an agitated (200 rev min⁻¹) fructose–peptone medium at 25°C.
Significance and Impact of the Study:  Improved yields of hirsutellones B–D will enable medicinal chemistry modifications leading to a development of a potential candidate for tuberculosis therapy.     

Optimization of culture conditions for production of the anti-tubercular alkaloid hirsutellone A by Trichoderma gelatinosum BCC 7579

AIMS: This work aimed to optimize the culture conditions for production of a novel and potent anti-tubercular alkaloid, hirsutellone A, by the saprophytic soil fungus Trichoderma gelatinosum BCC 7579. METHODS AND RESULTS: The fungus was initially cultured in shake flasks at 25 degrees C in the potato dextrose broth (PDB) supplemented with various carbon and nitrogen sources and mineral salts to select suitable medium for mycelial growth and hirsutellone A production. Cultivation conditions were further optimized by adjusting initial pH and changing temperature levels to maximize the production of hirsutellone A. The optimal condition that increased the production of hirsutellone A from 19.04 mg l(-1), obtained from basal condition, to 610.55 mg l(-1) and reduced the cultivation time from 40 to 6 days was to cultivate in a shaker at 200 rev min(-1) at 25 degrees C in PDB plus 20 g l(-1) soluble starch, 10 g l(-1) peptone and 2.5% (v/v) salt solution with initial pH of 7. Production of hirsutellone A in larger-scale using a 5-l batch fermenter was also completed yielding 958 mg l(-1) of hirsutellone A within 6 days. CONCLUSIONS: The suitable culture conditions for hirsutellone A production by T. gelatinosum BCC 7579 was the cultivation in 5-l fermenter at 25 degrees C in PDB plus 20 g l(-1) soluble starch, 10 g l(-1) peptone and 2.5% (v/v) salt solution with an initial pH of 7. SIGNIFICANCE AND IMPACT OF THE STUDY: The production of hirsutellone A in a fermenter to obtain a high yield and reduce an incubation period will become very useful in anti-tubercular drug development process in the future.