• 생명과학회지
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• 제19권3호
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• pp.311-316
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• 2009

갈조류 모자반과 Pelvetia속은 다세포 조류로 많은 해조류를 포함하고 있으며 북반구 태평양과 대서양에 분포되어 있다. Pelvetia속에 속하는 우리나라의 동종 및 근연한 같은 속내 종에 대해 유전자은행을 통해 밝혀진 ITS에 의한 서열을 이용하여 계통관계를 조사하였다. 한국의 P. babingtonii은 북미의 P. babingtonii AF102957과 유사한 핵산서열로 계통도 분석에서 같은 분지군을 형성하였다. 한국의 P. siliquosa은 역시 북미의 P. siliquosa AF102958과 유사한 핵산서열로 계통도 분석에서 같은 분지군을 형성하였다. Pelvetia 속 내 여러 종간은 결실이나 삽입에 의한 indel이 많은 반면 같은 종내 계통은 치환에 의한 차이가 현저하였다. 이 속은 NJ분석에서 크게 두 분지군으로 나뉘는데 한 그룹은 P. canaliculata와 P. limitata이며 나머지 그룹은 P. siliquosa, P. compressa, P. babingtonii을 포함하고 있었다. ITS 서열로 한국 내 분류군과 북미 간 분류군이 잘 구분되었다. MP 분석에서도 높은 지지도로 잘 구분되었다. 따라서 ITS 서열로 종 동정에 이용할 수 있었으며, 종의 보전이나 생식질 보전에 기초로 이용될 수 있을 것으로 사료된다.

• Asian-Australasian Journal of Animal Sciences
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• 제20권2호
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• pp.283-294
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• 2007

Conventional culture-based methods of enumerating rumen microorganisms (bacteria, archaea, protozoa, and fungi) are being rapidly replaced by nucleic acid-based techniques which can be used to characterise complex microbial communities without incubation. The foundation of these techniques is 16S/18S rDNA sequence analysis which has provided a phylogenetically based classification scheme for enumeration and identification of microbial community members. While these analyses are very informative for determining the composition of the microbial community and monitoring changes in population size, they can only infer function based on these observations. The next step in functional analysis of the ecosystem is to measure how specific and, or, predominant members of the ecosystem are operating and interacting with other groups. It is also apparent that techniques which optimise the analysis of complex microbial communities rather than the detection of single organisms will need to address the issues of high throughput analysis using many primers/probes in a single sample. Nearly all the molecular ecological techniques are dependant upon the efficient extraction of high quality DNA/RNA representing the diversity of ruminal microbial communities. Recent reviews and technical manuals written on the subject of molecular microbial ecology of animals provide a broad perspective of the variety of techniques available and their potential application in the field of animal science which is beyond the scope of this treatise. This paper will focus on nucleic acid based molecular methods which have recently been developed for studying major functional groups (cellulolytic bacteria, protozoa, fungi and methanogens) of microorganisms that are important in nutritional studies, as well as, novel methods for studying microbial diversity and function from a genomics perspective.

• Parasites, Hosts and Diseases
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• 제54권6호
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• pp.777-786
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• 2016

Raillietina species are prevalent in domestic chickens (Gallus gallus domesticus) in Phayao province, northern Thailand. Their infection may cause disease and death, which affects the public health and economic situation in chicken farms. The identification of Raillietina has been based on morphology and molecular analysis. In this study, morphological observations using light (LM) and scanning electron microscopies (SEM) coupled with molecular analysis of the internal transcribed spacer 2 (ITS2) region and the nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1) gene were employed for precise identification and phylogenetic relationship studies of Raillietina spp. Four Raillietina species, including R. echinobothrida, R. tetragona, R. cesticillus, and Raillietina sp., were recovered in domestic chickens from 4 districts in Phayao province, Thailand. LM and SEM observations revealed differences in the morphology of the scolex, position of the genital pore, number of eggs per egg capsule, and rostellar opening surface structures in all 4 species. Phylogenetic relationships were found among the phylogenetic trees obtained by the maximum likelihood and distance-based neighbor-joining methods. ITS2 and ND1 sequence data recorded from Raillietina sp. appeared to be monophyletic. The query sequences of R. echinobothrida, R. tetragona, R. cesticillus, and Raillietina sp. were separated according to the different morphological characters. This study confirmed that morphological studies combined with molecular analyses can differentiate related species within the genus Raillietina in Thailand.

• The Plant Pathology Journal
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• 제21권1호
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• pp.47-54
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• 2005

Identification of host genes involved in disease progresses and/or defense responses is one of the most critical steps leading to the elucidation of disease resistance mechanisms in plants. Soybean mosaic virus (SMV) is one of the most prevalent pathogen of soybean (Glycine max). Although the soybeans are placed one of many important crops, relatively little is known about defense mechanism. In order to obtain host genes involved in SMV disease progress and host defense especially for virus resistance, two different cloning strategies (DD RT-PCR and Subtractive hybridization) were employed to identify pathogenesis- and defenserelated genes (PRs and DRs) from susceptible (Geumjeong 1) and resistant (Geumjeong 2) cultivars against SMV strain G7H. Using these approaches, we obtained 570 genes that expressed differentially during SMV infection processes. Based upon sequence analyses, differentially expressed host genes were classified into five groups, i.e. metabolism, genetic information processing, environmental information processing, cellular processes and unclassified group. A total of 11 differentially expressed genes including protein kinase, transcription factor, other potential signaling components and resistant-like gene involved in host defense response were selected to further characterize and determine expression profiles of each selected gene. Functional characterization of these genes will likely facilitate the elucidation of defense signal transduction and biological function in SMV-infected soybean plants.

• 원예과학기술지
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• 제29권2호
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• pp.116-122
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• 2011

본 연구에서는 지리산에서 자생하는 한국 특산종인 노각나무(Stewartia koreana Nakai)의 EST library를 제작하고 서열을 분석하였다. 노각나무의 유엽을 재료로 cDNA library 만들었고 1,392개의 cDNA에 대한 부분 서열 분석을 진행하였다. EST와 unigene 서열의 분석은 컴퓨터를 기반으로한 filtering과 수작업 그리고 NCBI의 BLAST 분석을 통해 수행하였다. 벡터 서열과 100bp 이하의 서열을 제거한 후 1,301개의 EST를 분석하였다. 전체 150개의 contig와 743개의 singleton을 분리하여 총 893개의 unigene을 분리해냈으며 서열 분석을 통해 95개의 microsatellite를 확인하였다. NCBI 데이터베이스의 BLASTX로 상동성을 검색한 결과 EST의 65%는 기능을 알고 있는 유전자와 11.6%의 EST는 아직까지 기능이 보고되지 않은 유전자와 높은 상동성을 보였다. 남아 있는 23.2%의 EST는 기존에 데이터베이스에 보고된 유전자와 상동성을 보이지 않는 유전자로 밝혀졌다. 다양한 데이터베이스를 기반으로 한 유사성 기반 기능 분석은 노각나무의 EST가 포도나무와 포플러와 높은 유사성을 보인 것을 확인하였다. 기능에 따른 분류에 있어 molecular function은 nucleotide binding, biological process는 transport, cellular component는 plastid가 가장 높은 비율로 나왔다. 본 연구를 통해 얻어진 EST 자료는 노각나무의 새로운 유전자원에 대한 연구의 기본 자료로 유용하게 활용될 것이다.

• Journal of Microbiology
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• 제45권2호
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• pp.105-112
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• 2007

The objective of this study was to analyze the phylogenetic composition of bacterial community in the soil of an earth-cave (Niu Cave) using a culture-independent molecular approach. 16S rRNA genes were amplified directly from soil DNA with universally conserved and Bacteria-specific rRNA gene primers and cloned. The clone library was screened by restriction fragment length polymorphism (RFLP), and representative rRNA gene sequences were determined. A total of 115 bacterial sequence types were found in 190 analyzed clones. Phylogenetic sequence analyses revealed novel 16S rRNA gene sequence types and a high diversity of putative bacterial community. Members of these bacteria included Proteobacteria (42.6%), Acidobacteria (18.6%), Planctomycetes (9.0 %), Chloroflexi (Green nonsulfur bacteria, 7.5%), Bacteroidetes (2.1%), Gemmatimonadetes (2.7%), Nitrospirae (8.0%), Actinobacteria (High G+C Gram-positive bacteria, 6.4%) and candidate divisions (including the OP3, GN08, and SBR1093, 3.2%). Thirty-five clones were affiliated with bacteria that were related to nitrogen, sulfur, iron or manganese cycles. The comparison of the present data with the data obtained previously from caves based on 16S rRNA gene analysis revealed similarities in the bacterial community components, especially in the high abundance of Proteobacteria and Acidobacteria. Furthermore, this study provided the novel evidence for presence of Gemmatimonadetes, Nitrosomonadales, Oceanospirillales, and Rubrobacterales in a karstic hypogean environment.

• 한국약용작물학회지
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• 제13권5호
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• pp.249-253
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• 2005

This study was carried out to develop convenient and reproducible methods for identifying the genetic relationship among germplasms of Panax species based on molecular genetics. Using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) analyses, genetic polymorphism of the Panax species was investigated with following cultivars and accessions, such as Chunpoong, Yunpoong, Kopoong, Sunpoong, and Kumpoong in domestic cultivars, Hwangsuk, Jakyung and Suckju in domestic accessions, and Panax quinquefolius L. and Panax japonicus C.A. Meyer in foreign introduced accessions, respectively. Specific DNA fragments ranging from 200 to 3,000 base pairs in size could be obtained with various ISSR and RAPD primers under the optimized PCR conditions. The dissimilarity coefficients among the genetic polymorphisms of ginseng cultivars and accessions were calculated from 0.26 to 0.90 in RAPD and from 0.12 to 0.89 in ISSR analysis, respectively. Eleven plant samples were grouped siblings together with cultivars and parents based on cluster analysis of genetic distance depending on genetic property such as origin of the species. In results, both RAPD and ISSR analyses were useful for identifying the genetic relationship among cultivars and accessions of Panax species at DNA level.

• ALGAE
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• 제34권4호
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• pp.277-288
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• 2019

Freshwater red algae of the order Batrachospermales are poorly studied in India and Nepal, especially on a molecular basis. During a survey in northeast India and east Nepal, six populations of the genus Sheathia were found and analyzed using molecular and morphological evidence. Phylogenetic analyses based on the rbcL gene sequences grouped all populations in a large clade including our S. arcuata specimens and others from several regions. Sheathia arcuata represents a species complex with a high sequence divergence and several smaller clades. Samples from India and Nepal were grouped in three distinct clades with high support and representing new cryptic species: a clade formed by two samples from India, which was named Sheathia assamica sp. nov.; one sample from India and one from Nepal formed another clade, named Sheathia indonepalensis sp. nov.; two samples from Nepal grouped with sequences from Hawaii and Indonesia (only 'Chantransia' stages) and gametophytes from Taiwan, named Sheathia dispersa sp. nov. Morphological characters of the specimens from these three species overlap one another and with the general circumscription of S. arcuata, which lacks the heterocortication (presence of bulbous cells in the cortical filaments) present in other species of the genus Sheathia. Although the region sampled is relatively restricted, the genetic diversity among specimens of these three groups was high and not closely related in the phylogenetic relationship with the other clades of S. arcuata. These data corroborate information from other groups of organisms (e.g., land and aquatic plants) that indicates this region (Eastern Himalaya) as a hotspot of biodiversity.

• 한국동물번식학회:학술대회논문집
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• 한국동물번식학회 2003년도 학술발표대회 발표논문초록집
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• pp.97-97
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• 2003

For many animals the centrosome consists of a pair of centrioles and surrounding pericentriolar materials (PCMs). PCMs have been known to play roles during cell division. It is known that centrioles are necessary to assemble centrosomal components. However, many types of oocytes undergo meiosis without centrioles. It is known that in nonmurine mammalian species, the sperm introduces an intact proximal centriole unlike sea urchin where two centrioles are introduced. In case of mouse sperm, the presence of centrosome is not clear In this study, a monoclonal antibody was developed to investigate centrosome during mouse germ cell and early embryo development. Results of immunostaining and Western blotting in CHO cells suggest that the monoclonal antibody recognizes a nuclear and centrosomal protein, thus called NCP. The NCP monoclonal antibody was used to screen a cDNA expression library prepared from 12.5 mouse brain to isolate NCP gene. Nucleotide size of NCP gene obtained from immunoscreening was about 5.5kb. It is determined that the NCP may be closely related with pericentriolar material -1 gene (Pcm-1) from the result of sequencing analysis. The molecular weight, 66kDa, calculated by known DNA sequence in database is consistent with that of detected from Western blotting using CHO cell lysates. Therefore, it is assumed that NCP may be alternative splicing form of Pcm-1 of which molecular weight is 228kDa. In mouse oocytes, NCP was distributed in nucleus as in CHO cells. It was shown that the NCP was localized around neck region, probably the centrosome in mouse neck region. Interestingly, dramatic change in distribution of NCP was also shown in male germ cell development. Finally, we observed the cellular distribution of NCP during early embryo development. NCP was detected in nucleus as well as centrosome foci. It is suggested that the centrioles reassembly we occurring in blastocysts and then affects the distribution of NCP.

• Animal cells and systems
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• 제5권3호
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• pp.163-177
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• 2001

Most, if not all, aphids harbor intracellular bacterial symbionts, called Buchnera, in their bacteriocytes, huge cells differentiated for this purpose. The association between Buchnera and aphids is so intimate, mutualistic and obligate that neither of them can any longer reproduce independently. Buchnera are vertically transmitted through generations of the host insects. Evidence suggests that Buchnera were acquired by a common ancestor of aphids 160-280 million years ago, and have been diversified, since then, in parallel with their aphid hosts. Molecular phylogenetic analyses indicate that Buchnera belong to the g subdivision of the Proteobacteria. Although Buchnera are close relatives of Escherichia coli, they contain move than 100 genomic copies per cell, and their genome size is only one seventh that of E. coli. The complete genome sequence of Buchnera revealed that their gene repertoire is quite different from those of parasitic bacteria such as Mycoplasma, Rickettsia and Chlamydia, though their genome sizes have been reduced to a similar extent. Whereas these parasitic bacteria have lost most genes for the biosynthesis of amino acids, Buchnera retain many of them. In particular, Buchnera's gene repertoire is characteristic in the richness of the genes for the biosynthesis of essential amino acids that the eukaryotic hosts are not able to synthesize, reflecting a nutritional role played by these symbionts. Buchnera, when housed in the bacteriocyte, selectively synthesize a large amount of symbionin, which is a homolog of GroEL, the major stress protein of E. coli. Symbionin not only functions as molecular chaperone, like GroEL, but also has evolutionarily acquired the phosphotransferase activity through amino acid substitutions. Aphids usually profit from Buchnera's fuction as a nutritional supplier and, when faced with an emergency, consume the biomass of Buchnera cells as nutrient reserves.