• ALGAE
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• 제22권3호
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• pp.147-152
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• 2007

We described two brownish freshwater Cryptomonas species, C. marssonii Skuja and C. pyrenoidifera Geitler as first records in Korea. The identification was based on light microscopy, scanning electron microscopy, and nuclear SSU rDNA sequences analysis. Cryptomonas marssonii is characterized by its sigmoid shape with a sharply pointed and dorsally curved antapex, dorso-ventrally flattened cell, two lateral plastids without pyrenoid, and its dimension of 18-25 μm in length and 8-13 μm in width. Cryptomonas pyrenoidifera is characterized by ovoid to elliptical shape with a partially twisted or rounded antapex, dorso-ventrally biconvex cell, lateral plastids with two pyrenoids, and the dimensions of 15-22 μm in length and 10-14 μm in width. Nuclear SSU rDNA sequences between C. marssonii WCK01 from Korea and CCAC0086 from Gernmay, and between C. pyrenoidifera WCK02 from Korea and CCMP152 from Australia were identical, respectively.

• 한국정보과학회논문지:컴퓨팅의 실제 및 레터
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• 제16권3호
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• pp.275-280
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• 2010

지역정렬(local alignment) 알고리즘은 주어진 두 서열에서 서로 유사한 부분 문자열을 찾아내는 알고리즘이다. DNA 서열은 A, C, G, T 외에 N과 X도 가질 수 있는데, N과 X는 DNA로부터 염기배열 정보를 뽑아낼 때 실험적인 이유로 혹은 다른 이유로 일부 배열 정보를 잃어버린 경우에 사용된다. 본 논문에서는 A, C, G, T 이외에 N과 X를 모두 갖는 DNA 서열의 affine gap penalty metric에 대한 지역정렬을 찾는 효율적인 알고리즘을 제시한다. 이는 N만 처리할 수 있는 Kim-Park 알고리즘을 N과 X를 모두 처리할 수 있도록 성공적으로 확장한 결과이며, 더불어 새로운 문자가 추가되더라도 바로 적용이 가능한 일반화된 결과이다.

• 한국양식학회:학술대회논문집
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• 한국양식학회 2003년도 추계학술발표대회 논문요약집
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• pp.42-42
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• 2003

The far eastern catfish (Silurus asotus) growth hormone (GH) gene was cloned and characterized. The complete nucleotide sequences of genomic GH gene sequences as well as a catfish GH cDNA were obtained by RT-PCR and gene filter screening. The GH cDNA and genomic gene span 1.0 and 1.8 kb from the start codon to the polyadenylation signal, respectively. Both on cDNA and gDNA GH genes, the sequence polymorphism was detected including various silence mutations. The genomic GH gene comprised of only four exons and three introns, which was novel type of fish GH gene structure. The evolutionary relation of the catfish GH gene was inferred based on the comparative phylogenic analysis using the gene structures and sequences.

• Asian-Australasian Journal of Animal Sciences
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• 제18권4호
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• pp.483-489
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• 2005

To understand the molecular mechanisms that regulate intramuscular fat deposition and its release, cDNA clones expressed in adipose tissues of Korean cattle were identified by differential screening from adipose tissue cDNA library. By partial nucleotide sequencing of 486 clones and a search for sequence similarity in NCBI nucleotide databases, 245 clones revealed unique clones. By a functional grouping of the clones, 14% of the clones were categorized to metabolism and enzyme-related group (stearoyl CoA desaturase, lactate dehydrogenase, fatty acid synthase, ATP citrate lyase, lipoprotein lipase, acetyl CoA synthetase, etc), and 6% to signal transduction/cell cycle-related group (C/EBP, cAMP-regulated phosphoprotein, calmodulin, cyclin G1, cyclin H, etc), and 4% to cytoskeleton and extracellular matrix components (vimentin, ankyrin 2, gelosin, syntenin, talin, prefoldin 5). The obtained 245 clones will be useful to study lipid metabolism and signal transduction pathway in adipose tissues and to study obesity in human. Some clones were subjected to full-sequencing containing open reading frame. The cDNA clone of bovine homolog of human prefoldin 5 gene had a total length of 959 nucleotides coding for 139 amino acids. Comparison of the deduced amino acid sequences of bovine prefoldin 5 with those of human and mouse showed over 95% identity. The cDNA clone of bovine homolog of human ubiquitin-like/S30 ribosomal fusion protein gene had a total length of 484 nucleotides coding for 133 amino acids. Comparison of the deduced amino acid sequences of bovine ubiquitin-like/S30 ribosomal fusion protein gene with those of human, rat and mouse showed over 97% identity. The cDNA clone of bovine homolog of human proteolipid protein 2 mRNA had a total length of 928 nucleotides coding for 152 amino acids. Comparison of the deduced amino acid sequences of bovine proteolipid protein 2 with those of human and mouse showed 87.5% similarity. The cDNA clone of bovine homolog of rat thymosin beta 4 had a total length of 602 nucleotides coding for 44 amino acids. Comparison of the deduced amino acid sequences of bovine thymosin beta 4 gene with those of human, mouse and rat showed 93.1% similarity. The cDNA clone of bovine homolog of human myotrophin mRNA had a total length of 790 nucleotides coding for 118 amino acids. Comparison of the deduced amino acid sequences of bovine myotrophin gene with those of human, mouse and rat showed 83.9% similarity. The functional role of these clones in adipose tissues needs to be established.

• 생명과학회지
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• 제13권4호
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• pp.400-411
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• 2003

5.8S rDNA를 포함한 ITS부위에 대한 염기서열 분석결과, 종에 따라 다양한 염기서열을 가지고 있어 분류에 이용될 수 있었으며, 특히 ITS2부위보다 ITS1부위에서 종에 대한 변이율이 높은 것으로 나타났다. 아울러 균종에 따라 정도의 차이는 있으나 사용된 모든 종들이 서로 계통분류학적 거리가 멀어서 종간의 구분이 명확하게 나타났다. P. tenuipes, I. japonica, P. japonicus는 multiple alignment분석에서 매우 유사한 염기서열을 가지고 있어, 이들 세종은 같은 종이지만 다른 이름으로 불리고 있는 것으로 나타났으며, 아울러 Paecilomyces sp. KACC 40220과 KACC 40656도 동일한 염기서열을 가지고 있어 p. tenuipes로 판단된다. 국내에서 유통되는 동충하초제품 35건과 중국산 1건에 대해 실험한 결과 23건은 P. tenuipes / japonica로, 11건은 C. militaris로, 1건은 B. bassiana로 분류되었으며, 중국산 제품 1건은 C. multiaxialis로 분류되었다.

• The Plant Pathology Journal
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• 제40권2호
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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.

• International Journal of Industrial Entomology and Biomaterials
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• 제6권2호
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• pp.157-162
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• 2003

The glutathione S-transferase (GSTs) are enzymes responsible for the protection of cells from chemical toxicants and oxidative stress. We describe here the cDNA sequence and mRNA expression of a putative GST from the mole cricket, Gryllotalpa orientalis. The G. orientalis GST cDNA sequences comprised of 621 bp encoding 207 amino acid residues. The multiple sequence alignment of G. orientalis GST gene with other known insect GSTs showed several conserved residues that may be essential for the enzymatic activity of the protein. Phylogenetic analysis of the deduced amino acid sequences of G. orientalis GST gene with other insect GST sequences revealed that the G. orientalis GST gene belongs to class I GST, forming a strong monophyletic group (100% bootstrap value) exclusively for class I GSTs from a diverse insect species. Northern blot analysis confirmed midgut-specific expression at transcriptional level, evidencing the midgut as a site for GST synthesis.

• 대한본초학회지
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• 제28권3호
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• pp.75-84
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• 2013

Objectives : The origin of Breeae Herba (So-gye) and Cirsii Herba (Dae-gye) is differently prescribed in Korean and Chinese modern pharmacopoeia. Since the similar morphological characteristics and chaotic plant names, moreover, the aerial part of Carduus crispus have been used as the Cirsii Herba. To develop a reliable method for correct identification of these herbal medicines and to evaluate the genetic relationship of these closely related plant species, we analyzed sequences of DNA barcode regions. Methods : Thirty-one samples of 6 medicinal plants (B. segeta, B. setosa, C. japonicum var. maackii, C. setidens, C. chanroenicum, and C. crispus) were collected from different habitate and nucleotide sequences of DNA barcode regions (rDNA-ITS, matK, and rbcL) were analyzed after amplification using appropriate primers reported in previous studies. The nucleotides of species-specific authentic marker and phylogenetic relations were estimated based on the entire sequences of DNA barcodes by the analysis of ClastalW and UPGMA, respectively. Results : In comparative analysis of DNA barcode sequences, we obtained specific nucleotides to discriminate the medicinal plant of Breeae/Cirsii Herba in species level and evaluated the phylogenetic relationship of these species. Futhermore, we identified distinct marker nucleotides enough to authenticate respective species. These sequence differences at corresponding positions were avaliable genetic markers to determine the botanical origins of Breeae Herbal as well as Cirsii Herba. Conclusions : These marker nucleotides would be useful to identify the official herbal medicines by providing of definitive information that can identify each plant species and distinguish from unauthentic adulterants and substitutes.

• Journal of Plant Biology
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• 제39권1호
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• pp.49-55
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• 1996

본 연구는 마늘(Allium sativum L.)의 기초적인 유전적 특성을 파악하기 위해, 단양마늘을 대상으로 염색체 DNA의 반복서열의 양상을 확인하고, 고반복서열이 매우 빠르게 reassociation되는 특성을 이용하여 이들에 해당되는 부분을 분리하고, 클로닝하였다. 이들 고반복서열 클론의 게놈 내의 copy수는 대체적으로 $10^{5}~10^{7}$이었다. 이 중 일부 클론의 염기서열과 분석한 결과, G/C 함량은 25~40% 정도로 낮았고, 일부서열의 내부에서는 소단위의 염기서열이 반복배열되어 있었다. 단양을 비롯한 문경, 서산, 의성 품종 사이에서 해당 반복서열의 변이정도를 조사하기 위하여, 다섯종류의 고반복서열을 탐침으로 이들 품종 마늘에 대한 RELP(restriction fragment length polymorphism)분석을 한 결과 이들 서열의 유전적변이는 거의 나타나지 않았다.

• The Plant Pathology Journal
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• 제30권1호
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• pp.68-74
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• 2014

Chrysanthemum stunt viroid (CSVd), a noncoding infectious RNA molecule, causes seriously economic losses of chrysanthemum for 3 or 4 years after its first infection. Monomeric cDNA clones of CSVd isolate SK1 (CSVd-SK1) were constructed in the plasmids pGEM-T easy vector and pUC19 vector. Linear positive-sense transcripts synthesized in vitro from the full-length monomeric cDNA clones of CSVd-SK1 could infect systemically tomato seedlings and chrysanthemum plants, suggesting that the linear CSVd RNA transcribed from the cDNA clones could be replicated as efficiently as circular CSVd in host species. However, direct inoculation of plasmid cDNA clones containing full-length monomeric cDNA of CSVd-SK1 failed to infect tomato and chrysanthemum and linear negative-sense transcripts from the plasmid DNAs were not infectious in the two plant species. The cDNA sequences of progeny viroid in systemically infected tomato and chrysanthemum showed a few substitutions at a specific nucleotide position, but there were no deletions and insertions in the sequences of the CSVd progeny from tomato and chrysanthemum plants.