• Microbiology and Biotechnology Letters
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• v.19 no.1
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• pp.31-36
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• 1991

A 7.5 kilobases hybrid plasmid, designated as pCE1301, was constructed by combining Eschurichia cwli plasmid pBELl which carries the kanamycin resistance gene of Tn5 with a cryptic plasmid, pSRl of Corynebacterium glutamicum. pCE1301 was transformed C. glutaicum by PEG-mediated protoplast method and its transformation efficiency was about $3.0\times 10^3$ transformants per $\mu g$ of the hybrid plasmid DNA. The physical map reveals that pCE1301 has single restriction sites for SalI and EcoRl, respectively. 'The kanamycin resistance of pCE1301 was stably maintained in C. glutamicum up to 25 generations and any segregation was not detected. pCI31301 was also introduced into Brevibacterium flavum and E coil, and replicated in those strains. pCE1301 was proved to be useiul in cloning the homoscrine dehydrogenase gene from C. glutamicum.

• ALGAE
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• v.33 no.2
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• pp.157-166
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• 2018

Cryptic species complexes are increasingly recognized in phycological research, obscuring taxonomy and raising questions about factors influencing speciation. A recent exploration of kelp genetic diversity on Haida Gwaii, British Columbia revealed the existence of a new species, Saccharina druehlii, which is cryptic with Saccharina sessilis. This suggests that molecular investigations further north may be required to elucidate the taxonomy and evolutionary history of this lineage. Although, for several decades, S. sessilis was considered a single highly variable species, its taxonomy has been far from straightforward. In particular, Hedophyllum subsessile (Areschoug) Setchell is now recognized as a synonym of S. sessilis in North America, but as a growth form of Saccharina bongardiana in Far East Russia. To resolve this taxonomic confusion, we sequenced mitochondrial (CO1-5P) and nuclear (internal transcribed spacer) markers of S. sessilis populations from the Aleutian Islands, Alaska, USA. Interestingly, none of our sequences matched S. sessilis sensu stricto. Instead, CO1-5P sequences from populations in the central and eastern Aleutians matched exactly S. druehlii with increasing sequence divergence occurring westward. Samples from Attu, the western-most island, composed a genetic group that clearly represents Kjellman's concept of Hafgygia bongardiana f. subsessilis and is distinct enough from S. druehlii and S. sessilis to potentially constitute a distinct species. Therefore, Saccharina subsessilis comb. nov. is proposed for this entity. Our results suggest the existence of a species complex at the crown node of S. sessilis and thus further investigation of Saccharina in Alaskan waters should be conducted to reconstruct the evolutionary history of this fascinating lineage.

• Journal of Life Science
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• v.11 no.6
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• pp.530-536
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• 2001

Several bacterial strains utilizing crude oil as their sole carbon and energy source were isolated from marine environment polluted by crude oil. Among them, the selected strain 4A3 showed strong degradation activity for crude oil. This strain was identified as a Provindencia rettgeri 4A3 based on the morphological, biochemical, and physiological characteristics. The optimum cultural conditions was as follows; 26$^{\circ}C$ for temperature and 7.0 for initial pH. Additionally, the optimal concentration of sodium chloride was 2.0%, indicating that this strain was derived from sea water. The emulsifying activity of 4A3 was the highest after 3 days of cultivation under the condition of 2.0% sodium chloride, pH 7.0 and 26$^{\circ}C$. This strain had one cryptic plasmid in 7.0kb size.

• 한국균학회소식:학술대회논문집
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• 2014.10a
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• pp.29-29
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• 2014

Since Darwin and Wallace introduced the concept on the evolution of species, scientists have been furiously debating what species are, and how to define them. This basic yet intriguing question has bothered us ever since, as communicating to fellow biologists about fungal species is the very cornerstone of mycology. For the species presently known, this has largely been accomplished via Latin binomials linked to morphology in the absence of DNA barcodes. In recent years mycologists have embraced the ribosomal ITS as official barcode region for Fungi, and this locus is also mainly used in environmental pyrosequencing studies. Furthermore, DNA data can now also be used to describe sterile species in the absence or lack of distinct morphological structures. Recent developments such as the registration of names in MycoBank, and linking the phenotype to the genotype, have significantly changed the face of fungal systematics. By employing the Consolidated Species Concept, incorporating genealogical concordance, ecology and morphology, robust species recognition is now possible. Several international initiatives have since built on these developments, such as the DNA barcoding of holdings of Biological Resource Centres, followed by the Genera of Fungi Project, aiming to recollect, and epitypify all type species of all genera. What these data have revealed, is that most genera are poly- and paraphyletic, and that morphological species normally encompass several genetic entities, which may be cryptic species. Once we provide a stable genetic backbone capturing our existing knowledge of the past 250 years, we will be able to accommodate novelties obtained via environmental sequencing platforms. Being able to communicate these species to other biologists in a clear manner that is DNA-based, will enable scientists to elucidate the importance, role and ecological interactions that these fungi have on our planet.

• Journal of the Mineralogical Society of Korea
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• v.18 no.1
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• pp.61-72
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• 2005

Modal and chemical compositions of clinopyroxnes in spinel peridotites from the Baegryeong Island and the Boeun, enclosed in Miocene alkali basalt, are important for understanding the pre-eruptive temperature condition and chemical processes such as mantle depletion and enrichment. All spinel peridotites show transitional texture between protogranular and porphyroclastic textures. Temperature ranges of spinel peridotites from the Baegryeong Island and the Boeun at 15 kb are 773∼1188℃ and 705∼1106℃, respectively. The spinel peridotites from the Baegryeong Island and the Boeun have undergone the 1∼10% and 1∼4% fractional melting, which were determined by using primitive mantle-normalized Y and Yb of clinopyroxenes. LREE enrichment patterns of clinopyroxene indicate that these rocks from both areas have undergone cryptic mantle metasomatism without new minerals.

• Korean Journal of Microbiology
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• v.24 no.1
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• pp.7-11
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• 1986

We screened lysates of the laboratory strains of pseudomonads utilizing hydrocarbon by agarose gel electrophoresis and cesium chloride-ethidium bromide equilibrium centrifugation, to find an intrinsic plasmid as a vector and to examine the relationship between the plasmid and hydrocarbon degradation. Only one strain from the examined strains, Pseudomonas putida KU190, contained a plasmid. We named the plasmid pKU41. The molecular size of pKU41 was determined as 41kb, using covalently closed circular forms of RP4 and pSY343 as standard size markers. The restriction sites of pKU41 for BamHI, BglII, EcoRI, HindIII, and SalI were 3, 1, 3, 6 and more than 13, respectively. With double or triple digestion, restriction map of pKU41 was constructed for BamHI, BglII and HindIII. For elucidation on the biological function of the plasmid, test was conducted on the ability of hydrocarbon utilization of the host strain but no apparent relationship was observed.

• Journal of Plant Biotechnology
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• v.49 no.3
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• pp.193-206
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• 2022

Astringent persimmon (Diospyros kaki Thunb.) is an important fruit crop in Korea; it possesses significant medicinal potential. However, knowledge regarding the pathogens affecting this crop, particularly, viruses and viroids, is limited. In the present study, reverse transcription-polymerase chain reaction (RT-PCR) and high-throughput transcriptome sequencing (HTS) were used to investigate the viruses and viroids infecting astringent persimmons cultivated in Korea. A one-step multiplex RT-PCR (mRT-PCR) method for the simultaneous detection of the pathogens was developed by designing species-specific primers and selecting the primer pairs via combination and detection limit testing. Seven of the sixteen cultivars tested were found to be infection-free. The RT-PCR and HTS analyses identified two viruses and one viroid in the infected samples (n = 51/100 samples collected from 16 cultivars). The incidence of single infections (n = 39/51) was higher than that of mixed infections (n = 12/51); the infection rate of the Persimmon cryptic virus was the highest (n = 31/39). Comparison of the monoplex and mRT-PCR results using randomly selected samples confirmed the efficiency of mRT-PCR for the identification of pathogens. Collectively, the present study provides useful resources for developing disease-free seedlings; further, the developed mRT-PCR method can be extended to investigate pathogens in other woody plants.

• Journal of Microbiology and Biotechnology
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• v.33 no.2
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• pp.211-218
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• 2023

A cryptic plasmid (pTH32) was characterized from Tetragenococcus halophilus 32, an isolate from jeotgal, Korean traditional fermented seafood. pTH32 is 3,198 bp in size with G+C content of 35.84%, and contains 4 open reading frames (ORFs). orf1 and orf2 are 456 bp and 273 bp in size, respectively, and their translation products showed 65.16% and 69.35% similarities with RepB family plasmid replication initiators, respectively, suggesting the rolling-circle replication (RCR) mode of pTH32. orf3 and orf4 encodes putative hypothetical protein of 186 and 76 amino acids, respectively. A novel Tetragenococcus-Escherichia coli shuttle vector, pMJ32E (7.3 kb, Em^r), was constructed by ligation of pTH32 with pBluescript II KS(+) and an erythromycin resistance gene (ErmC). pMJ32E successfully replicated in Enterococcus faecalis 29212 and T. halophilus 31 but not in other LAB species. A pepA gene, encoding aminopeptidase A (PepA) from T. halophilus CY54, was successfully expressed in T. halophilus 31 using pMJ32E. The transformant (TF) showed higher PepA activity (49.8 U/mg protein) than T. halophilus 31 cell (control). When T. halophilus 31 TF was subculturd in MRS broth without antibiotic at 48 h intervals, 53.8% of cells retained pMJ32E after 96 h, and only 2.4% of cells retained pMJ32E after 14 days, supporting the RCR mode of pTH32. pMJ32E could be useful for the genetic engineering of Tetragenococcus and Enterococcus species.

• Journal of Microbiology and Biotechnology
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• v.33 no.11
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• pp.1437-1447
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• 2023

A recently bioinformatic analysis of genomic sequences of fungi indicated that fungi are able to produce more secondary metabolites than expected. Despite their potency, many biosynthetic pathways are silent in the absence of specific culture conditions or chemical cues. To access cryptic metabolism, 108 fungal strains isolated from various sites were cultured with or without Streptomyces sp. 13F051 which mainly produces trichostatin analogues, followed by comparison of metabolic profiles using LC-MS. Among the 108 fungal strains, 14 produced secondary metabolites that were not recognized or were scarcely produced in mono-cultivation. Of these two fungal strains, Myrmecridium schulzeri 15F098 and Scleroconidioma sphagnicola 15S058 produced four new compounds (1-4) along with a known compound (5), demonstrating that all four compounds were produced by physical interaction with Streptomyces sp. 13F051. Bioactivity evaluation indicated that compounds 3-5 impede migration of MDA-MB-231 breast cancer cells.

• The Plant Pathology Journal
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• v.40 no.2
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• pp.171-191
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• 2024

Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.