• Interdisciplinary Bio Central
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• v.3 no.3
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• pp.10.1-10.8
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• 2011

Introduction: Hash functions are computer algorithms that protect information and secure transactions. In response to the NIST's "International Call for Hash Function", we developed a biological hash function using the computing capabilities of bacteria. We designed a DNA-based XOR logic gate that allows bacterial colonies arranged in a series on an agar plate to perform hash function calculations. Results and Discussion: In order to provide each colony with adequate time to process inputs and perform XOR logic, we designed and successfully demonstrated a system for time-delayed bacterial growth. Our system is based on the diffusion of ${\ss}$-lactamase, resulting in destruction of ampicillin. Our DNA-based XOR logic gate design is based on the op-position of two promoters. Our results showed that $P_{lux}$ and $P_{OmpC}$ functioned as expected individually, but $P_{lux}$ did not behave as expected in the XOR construct. Our data showed that, contrary to literature reports, the $P_{lux}$ promoter is bidirectional. In the absence of the 3OC6 inducer, the LuxR activator can bind to the $P_{lux}$ promoter and induce backwards transcription. Conclusion and Prospects: Our system of time delayed bacterial growth allows for the successive processing of a bacterial hash function, and is expected to have utility in other synthetic biology applications. While testing our DNA-based XOR logic gate, we uncovered a novel function of $P_{lux}$. In the absence of autoinducer 3OC6, LuxR binds to $P_{lux}$ and activates backwards transcription. This result advances basic research and has important implications for the widespread use of the $P_{lux}$ promoter.

• The Plant Pathology Journal
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• v.34 no.1
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• pp.78-84
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• 2018

Peroxyacetic acid mixture Perosan, composed of peroxyacetic acid, hydrogen peroxide and acetic acid, was evaluated for eco-friendly management of tomato bacterial wilt by Ralstonia pseudosolanacearum. Perosan drastically suppressed in vitro growth of R. pseudosolanacearum in liquid cultures in dose- and incubation time-dependent manners. Higher perosan doses (0.1 and 1%) caused lowered pH and phytotoxicity to detached leaves of two tomato cultivars Cupirang and Benekia 220 in aqueous solution. Treatment with 0.01% of Perosan delayed wilting symptom significantly in the detached leaves of two cultivars inoculated with R. pseudosolanacearum ($10^7cfu/ml$). Soil drenching of 5% Perosan solution in pots caused severe tissue collapse of tomato seedlings at the four-week-old stage of two tomato cultivars. Treatment with 1% Perosan by soil-drenching significantly reduced bacterial wilt in the tomato seedlings of two cultivars. These findings suggest that Perosan treatment can be applied to suppress bacterial wilt during tomato production.

• Journal of Mushroom
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• v.3 no.4
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• pp.140-144
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• 2005

This study was conducted to verify the cause of suppression symptom in mycelial growth during summer and to be able to establish a countermeasure. Cultivation of Flammulina velutipes was experimented with varying elapsed time of 0, 3, 6, 9 hours after mixing the sawdust media and two kinds of water temperature (normal water, $24^{\circ}C$ and cold water, $6^{\circ}C$) for mixing sawdust media. There were trends of increased media temperature from $24^{\circ}C$ to $31^{\circ}C$ and decreased pH from 6.5 to 5.2~5.6 with varying elapsed time from mixing the media to sterilization. Bacterial density also increased with bacterial density in Medium $24^{\circ}C$ being 1.9~4.1 times higher than that in Medium 6. Growth of F. velutipes was delayed with dual culture of bacteria isolated from sawdust media. Total nitrogen content of sawdust media was lowered by elapsed time from mixing the media to sterilization. The use of normal water($24^{\circ}C$) delayed mushroom growth by 1~2 days compared with that of cold water($6^{\circ}C$). Furthermore, mycelial growth of F. velutipes in the bottle cultivation ceased 9 hours after mixing the media. Primordia formation of F. velutipes was delayed by 1~3 days by elapsed time after mixing sawdust media, while fruit-body yield decreased by 7~12% 6 hours after mixing the media. Fruit-body yield was more stabilized with the use of cold water($6^{\circ}C$) than with that of normal water($24^{\circ}C$). Results showed that it is effective to use cold water as low as $6^{\circ}C$ in mixing media for F. velutipes cultivation, especially during summer when environmental temperature is high, high pressure sterilization after bottling work can prevent bacterial propagation in the media and can stabilize media ingredient.

• Journal of Microbiology and Biotechnology
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• v.19 no.12
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• pp.1635-1643
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• 2009

The aim of this study was to provide new insight into the mechanism whereby the housekeeping enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) locates to cell walls of Lactobacillus plantarum 299v. After purification, cytosolic and cell wall GAPDH (cw-GAPDH) forms were characterized and shown to be identical homotetrameric active enzymes. GAPDH concentration on cell walls was growth-time dependent. Free GAPDH was not observed on the culture supernatant at any time during growth, and provoked cell lysis was not concomitant with any reassociation of GAPDH onto the cell surface. Hence, with the possibility of cw-GAPDH resulting from autolysis being unlikely, entrapment of intracellular GAPDH on the cell wall after a passive efflux through altered plasma membrane was investigated. Flow cytometry was used to assess L. plantarum 299v membrane permeabilization after labeling with propidium iodide (PI). By combining PI uptake and cw-GAPDH activity measurements, we demonstrate here that the increase in cw-GAPDH concentration from the early exponential phase to the late stationary phase is closely related to an increase in plasma membrane permeability during growth. Moreover, we observed that increases in both plasma membrane permeability and cw-GAPDH activity were delayed when glucose was added during L. plantarum 299v growth. Using a double labeling of L. plantarum 299v cells with anti-GAPDH antibodies and propidium iodide, we established unambiguously that cells with impaired membrane manifest five times more cw-GAPDH than unaltered cells. Our results show that plasma membrane permeability appears to be closely related to the efflux of GAPDH on the bacterial cell surface, offering new insight into the understanding of the cell wall location of this enzyme.

• Korean Journal of Food Science and Technology
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• v.28 no.5
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• pp.987-993
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• 1996

This study was attempted to prepare milk and soymilk containing high number of viable cells of bifidobacteria during the fermentation as well as to establish the optimum condition for bacteria growth. Activity of ${\alpha}$- and ${\beta}-galactosidase$ produced by bifidobacteria was also determined. Milk and soymilk inoculated with Bifidobacterium longum ATCC 15707 were incubated in a nitrogen-carbon dioxide atmosphere at $37^{\circ}C$ for two days. and time courses of pH, acidity, viable cells and effect of growth factors were determined. After two days, pH of milk gradually decreased from 6.81 to 4.84 and pH of soymilk changed from 7.02 to 3.89. The viable cell numbers of bifidobacteria increased constantly in soymilk, while bacterial growth in milk appeared to be delayed after storage of two days. Both of ${\alpha}$- and ${\beta}-galactosidase$ activities were detected in soymilk, but activity of ${\beta}-galactosidase$ was predominant in milk. Fucosyllactose appeared to be a good growth factor in soymilk. During the fermentation of milk, L-cysteine HCl enhanced growth of bifidobacteria at the early stage and fucosyllactose was a good growth factor in the propagations of bifidobacteria from middle stage.

• Journal of Microbiology and Biotechnology
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• v.18 no.6
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• pp.1024-1032
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• 2008

Efficient expression of the Salmonella Typhimurium tdc ABCDEG operon involved in the degradation of L-serine and L-threonine requires TdcA, the transcriptional activator of the tdc operon. We found that the tdcA gene was transiently activated when the bacterial growth condition was changed from aerobic to anaerobic, but this was not observed if Salmonella was grown anaerobically from the beginning of the culture. Expression kinetics of six tdc genes after anaerobic shock demonstrated by a real-time PCR assay showed that the tdc CDEG genes were not induced in the tdcA mutant but tdcB maintained its inducibility by anaerobic shock even in the absence of tdcA, suggesting that an additional unknown transcriptional regulation may be working for the tdcB expression. We also investigated the effects of nucleoid-associated proteins by primer extension analysis and found that H-NS repressed tdcA under anaerobic shock conditions, and fis mutation delayed the peak expression time of the tdc operon. DNA microarray analysis of genes regulated by TdcA revealed that the genes involved in N-acetylmannosamine, maltose, and propanediol utilization were significantly induced in a tdcA mutant. These findings suggest that Tdc enzymes may playa pivotal role in energy metabolism under a sudden change of oxygen tension.

• Journal of the Korean Society of Food Science and Nutrition
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• v.42 no.4
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• pp.615-620
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• 2013

To extend the shelf-life of salted Chinese cabbages, electrolyzed water (EW) was used to wash raw Chinese cabbages before the salting process (to control microbial growth), and different storage temperatures evaluated (0, 4, and $10^{\circ}C$). A tap water washing group (TW) was used for comparison. The initial total bacterial population was 5.36 log CFU/g in the TW treatment and 3.50 log CFU/g in the EW treatment. The EW treatment decreased bacterial numbers by approximately 2 log CFU/g compared to the TW treatment and kept this initial population number for 32 days at $0^{\circ}C$. The salinity had no difference during storage. In general, several factors (pH, reducing sugars, hardness, and transmittance) decreased over time, and decreased slowly with EW treatment and $0^{\circ}C$ storage. Overall, the salted Chinese cabbages with EW treatment showed lower bacterial populations compared to TW treatment, and when stored at $0^{\circ}C$, delayed decreases in quality.