• Research in Plant Disease
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• v.29 no.2
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• pp.174-183
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• 2023

The limited effectiveness of current plant disease management treatments necessitates the development of new methods for controlling diseases using beneficial microbes. Demanding sustainable agriculture is increasingly highlighted as a biocontrol approach, particularly Streptomyces species known to produce a variety of antibiotic compounds and secondary metabolites. The Streptomyces globisporus SP6C4 strain and Streptomyces sp. S8 have been reported as potent antifungal agents and are gaining attention for improving crop growth in sustainable agriculture. In this study, we investigated the use of Streptomyces species formulations to enhance bacterial growth with nitrogen sources. Specifically, the addition of L-glutamic acid and L-cysteine resulted in earlier sporulation and bacterial growth in Streptomyces strains, respectively. This approach could expand the range of fermentation techniques in agriculture and be useful for controlling plant growth-promoting bacteria.

• Journal of the Institute of Electronics Engineers of Korea SP
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• v.43 no.6 s.312
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• pp.28-35
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• 2006

Statistical models of shape variability based on active shape models (ASMs) have been successfully utilized to perform segmentation and recognition tasks in two-dimensional (2D) images. Three-dimensional (3D) model-based approaches are more promising than 2D approaches since they can bring in more realistic shape constraints for recognizing and delineating the object boundary. For 3D model-based approaches, however, building the 3D shape model from a training set of segmented instances of an object is a major challenge and currently it remains an open problem in building the 3D shape model, one essential step is to generate a point distribution model (PDM). Corresponding landmarks must be selected in all1 training shapes for generating PDM, and manual determination of landmark correspondences is very time-consuming, tedious, and error-prone. In this paper, we propose a novel automatic method for generating 3D statistical shape models. Given a set of training 3D shapes, we generate a 3D model by 1) building the mean shape fro]n the distance transform of the training shapes, 2) utilizing a tetrahedron method for automatically selecting landmarks on the mean shape, and 3) subsequently propagating these landmarks to each training shape via a distance labeling method. In this paper, we investigate the accuracy and compactness of the 3D model for the human liver built from 50 segmented individual CT data sets. The proposed method is very general without such assumptions and can be applied to other data sets.

• Journal of Applied Biological Chemistry
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• v.61 no.1
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• pp.83-91
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• 2018

Advances in bacterial and fungal genome mining uncover a plethora of cryptic secondary metabolite biosynthetic gene clusters. Guided by the genome information, targeted transcriptional derepression could be employed to determine the product of a cryptic gene cluster and to explore its biological role. Monascus spp. are food grade filamentous fungi popular in eastern Asia and several genome data belong to them are now available. We achieved transcription activation of a cryptic fungal polyketide synthase-nonribosomal peptide synthase gene Mpfus1 in Monascus purpureus ${\Delta}MpPKS5$ by inserting Aspergillus gpdA promoter at the upstream of Mpfus1 through double crossover gene replacement. The gene cluster with Mpfus1 show a high similarity to those for the biosynthesis of conjugated polyene derivatives with 2-pyrrolidone ring and the mycotoxin fusarin is the representative member of this group. The ${\Delta}MpPKS5$ is incapable of producing azaphilone pigment, providing an excellent background to identify chromogenic and UV-absorbing compounds. Activation of Mpfus1 resulted in a yellow hue on mycelia and its methanol extract exhibit a maximum absorption at 365 nm. HPLC analysis of the organic extracts indicated the presence of a variety of yellow compounds in the extract. This implies that the product of MpFus1 is metabolically or chemically unstable. LC-MS analysis guided us to predict the MpFus1 product and to propose that the Mpfus1-containing gene cluster encode the biosynthesis of a desmethyl analogue of fusarin. This study showcases the genome mining in Monascus and the possibility to unveil new biological activities embedded in it.

• Microbiology and Biotechnology Letters
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• v.49 no.1
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• pp.111-119
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• 2021

A bacterial strain isolated from a Malva verticillata leaf was identified as Bacillus velezensis MV2 based on the 16S rRNA sequencing results. Complete genome sequencing revealed that B. velezensis MV2 possessed a single 4,191,702-bp contig with 45.57% GC content. Generally, Bacillus spp. are known to produce diverse antimicrobial compounds including bacteriocins, polyketides, and non-ribosomal peptides. Antimicrobial compounds in the B. velezensis MV2 were extracted from culture supernatants using hydrophobic interaction chromatography. The crude extracts showed antimicrobial activity against both gram-positive bacteria and gram-negative bacteria; however, they were more effective against gram-positive bacteria. The extracts also showed antifungal activity against phytopathogenic fungi such as Fusarium fujikuroi and F. graminearum. In time-kill assays, these antimicrobial compounds showed bactericidal activity against Bacillus cereus, used as indicator strain. To predict the type of antimicrobial compounds produced by this strain, we used the antiSMASH algorithm. Forty-seven secondary metabolites were predicted to be synthesized in MV2, and among them, fourteen were identified with a similarity of 80% or more with those previously identified. Based on the antimicrobial properties, the antimicrobial compounds may be nonribosomal peptides or polyketides. These compounds possess the potential to be used as biopesticides in the food and agricultural industry as an alternative to antibiotics.

• Korean Journal of Microbiology
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• v.49 no.2
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• pp.156-164
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• 2013

Actinomycetes produce diverse secondary metabolites which have the primary importance in medicine, agriculture and food production, and key to this is their ability to interact with other organisms in natural habitats. In this study, we have investigated the taxonomical and functional diversity of actinomycetes in fecal sample of rhinoceros beetle larvae (Allomyrina dichotoma L.) by using culture-dependent and -independent approaches. For the culture-independent approach, the community DNA was extracted from the sample and 16S rRNA genes of actinomycetes were amplified using actinomycetes-specific PCR primers. Thirty-seven clones were classified into 15 genera and 24 species of actinomycetes. For the culture-dependent approach, 53 strains were isolated from larval feces, of which 27 isolates were selected based on morphological characteristics. The isolates were classified into 4 genera and 14 species, and 24 isolates (89%) were identified as the genus Streptomyces. Many of the representative isolates had antimicrobial activities against plant pathogenic fungi and Gram-positive bacteria. In addition, most of the isolates (78%) showed biochemical properties to hydrolyze cellulose and casein. The results demonstrated that diverse and valuable actinomycetes could be isolated from insect fecal samples, indicating that insect guts can be rich sources for novel bioactive compounds.

• The Korean Journal of Mycology
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• v.43 no.1
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• pp.33-39
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• 2015

In filamentous fungi, velvet complex associated with the veA gene plays pivotal roles in development and secondary metabolism. In a model fungus Aspergillus nidulans, many proteins that can interact with VeA, including two methyltransferases VipB and VipC, have been isolated and characterized. In this study, we isolated homologs of the vipB and vipC genes in the human opportunistic pathogenic fungus Aspergillus fumigatus and named AfuvipB and AfuvipC. The AfuvipB gene, annotated as Afu3g14920 in the Aspergillus Genome Database (AspGD) database, consists of 1,510 bp interrupted with 10 introns yielding 336 amino acid-long putative methyltransferase protein. Similarly, AfuvipC, which is Afu8g01930, has 10 introns and encodes a polypeptide with 339 amino acids having a methyltransferase domain in the middle of the protein. To characterize the function of the genes in A. fumigatus, knock-out mutants were generated and the phenotypes were observed. Deletion of AfuvipB gene caused no obvious phenotypic change on point inoculation but showed smaller colony than wild-type when the mutant was subjected to culture on single spore-driven culture condition. However, AfuvipC deletion mutant demonstrated no phenotypic difference from wild type both in point inoculation and streaking cultures. These results indicate that the two methyltransfereases might have a redundant role and could be dispensable in normal culture conditions.

• KSBB Journal
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• v.21 no.5
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• pp.384-388
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• 2006

The production stability of high-yielding mutants of Streptomyces lincolnensis immobilized on celite beads was examined in repeated batch cultures. We also explored the feasibility of immobilization of vegetative mycelial cells on pre-wetted celite beads, which is practical method for cell immobilization. Repeated transfer of immobilized cells into fresh medium every 10 days increased productivity of immobilized cells and maximum concentration of lincomycin, 1007 $({\pm}256)$ mg/L, was obtained at the end of the ninth cycle. A 1.4-fold higher productivity was obtained in immobilized-cell culture than that obtained by suspended-cell culture. When pre-wetted beads were inoculated with vegetative mycelia and cultured a slightly higher amount of immobilized cells and lincomycin was obtained more than those obtained by culture of spores immobilized on dry beads. This result indicates that immobilization of mycelial cells on pre-wetted beads was readily available. This technique is simple and no additional facilities are required for cell immobilization.

• KSBB Journal
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• v.16 no.5
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• pp.516-522
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• 2001

The large-scale production of antibiotics by filamentous mycelial organism requires and adequate supply of dissolved oxygen. In terms of productivity, it means that oxygen transfer is the rate-limiting step. Therefore, the oxygen transfer coefficients(K$\_$L/A) were determined in a broth involving a filamentous mycelial organism such as Streptomyces avermitilis for use in fermentations. To determine (K$\_$L/A) inn a stirred vessel, a great deal of effort is required to provide all the cells with a sufficient oxygen supply. To overcome the oxygen limitation in a batch culture, a fed-batch culture was applied to control the growth rate by an intermittent supply of nutrients. Thus, it was possible to maintain a suitable dissolved oxygen concentration at a low agitation rate. The optimal agitation speed was 350 rpm at low cell concentrations (below 7 g/L) by considering the efficiency of agitation and shear stress. The (K$\_$L/A) was found to decrease from 64.26 to 29.21h.$\^$-1/ when the biomass concentration was increased from 9.82 to 12.06 g/L. In addition, and increase in viscosity was also observed during the growth phase. By comparing the (K$\_$L/A) values for the various agitation and aeration rates, it was found that the effect of an increase in (K$\_$L/A) by aeration was reduced dramatically at high biomass concentrations. However, this effect was not observed when altering the agitation rate. This suggests that controlling the dissolved oxygen concentration by altering the agitation rate was more efficient than increase the aeration rate.

• KSBB Journal
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• v.16 no.1
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• pp.87-94
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• 2001

The biosynthesis of Lovastatin, a cholesterol lowering agent formed by the filamentous fungus, cerulenin-resistant Aspergillus terreus mutant was studied in shake flasks and bioreactors. The lovastatin production could be improved by fed-batch under the limited condition of carbon source. The relationship between the fungal morphology and the lovastatin production was also examined during the fed-batch cultures. The fed-batch studies in shake flasks were carried out to find the optimum glucose feeding method, and the pulsed feeding of glucose from 3 days onward at 24 hours intervals was found to be optimal to increase the lovastatin production and reduce the average pellet size. When the pH was controlled at around 5.8 during the whole fermentation period, the lovastatin concentration reached 384 mg/L, which is much higher than the values obtained pH-uncontrolled and pH 7.4. The optimal glucose feeding strategies was found that 30 g/L of glucose was added initially in batch mode, and then fed-batch was conducted by continuous addition of glucose solution(180 g/L) from 72 to 240 hr at a rate of 1.2 mL/hr at $28^{\circ}C$, pH 5.8, 400 rpm, and 1.0 vvm. The lovastatin concentration of 547 mg/L was obtained in 168 hr. It was about 1.5 times higher than the value of the batch fermentation.

• Korean Journal of Food Science and Technology
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• v.42 no.3
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• pp.257-262
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• 2010

Patulin, a secondary metabolite of mold, is commonly found in rotten apples. Many countries regulate patulin at levels ranging from 30 to $50\;{\mu}g/L$. Most analytical methods for removing patulin from apple juice include liquid-liquid extraction (LLE), which is time and labor intensive. To replace the LLE method, a solid-phase extraction (SPE) method has been developed for apple juice and unfiltered apple juice. A portion of the test sample was applied to a macroporous copolymer cartridge and washed with 5 mL of 1% sodium bicarbonate, followed by 5 mL of 1% acetic acid. Patulin was eluted with 5 mL of 2% acetonitrile in anhydrous ethyl ether. The mobile phase was tetrahydrofuran in water (0.8:99.2) and was detected with a UV detector at 276 nm. Recoveries ranged from 95 to 101% in test samples, and the minimum detectable level was 30 ppb. Because this SPE method is fast, easy, reliable, and inexpensive, it could be applicable for companies or analytical agencies to analyze patulin concentrations in apple juice.