• Ocean and Polar Research
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• 제27권2호
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• pp.205-214
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• 2005

From ancient Antarctic glacier ice, we extracted total genomic DNA that was suitable for prokaryotic 16S rDNA gene cloning and sequencing, and bacterial artificial chromosome (BAC) library and end-sequencing. The ice samples were from the Dry Valley region. Age dating by $^{40}Ar/^{39}Ar$ analysis on the volcanic ashes deposited in situ indicated the ice samples are minimum 100,000-300,000 yr (sample DLE) and 8 million years (sample EME) old. Further assay proved the ice survived freeze-thaw cycles or other re-working processes. EME, which was from a small lobe of the basal Taylor glacier, is the oldest known ice on Earth. Microorganisms, preserved frozen in glacier ice and isolated from the rest of the world over a geological time scale, can provide valuable data or insight for the diversity, distribution, survival strategy, and evolutionary relationships to the extant relatives. From the 16S gene cloning study, we detected no PCR amplicons with Archaea-specific primers, however we found many phylotypes belonging to Bacteria divisions, such as Actinobacteria, Acidobacteria, Proteobacteria $({\alpha},\;{\beta},\;and\;{\gamma})$, Firmicutes, and Cytophaga-Flavobacterium-Bacteroid$. BAC cloning and sequencing revealed protein codings highly identical to phenylacetic acid degradation protein paaA, chromosome segregation ATPases, or cold shock protein B of present day bacteria. Throughput sequencing of the BAC clones is underway. Viable and culturable cells were recovered from the DLE sample, and characterized by their 16S rDNA sequences. Further investigation on the survivorship and functional genes from the past should help unveil the evolution of life on Earth, or elsewhere, if any.

• Journal of Microbiology and Biotechnology
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• 제20권11호
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• pp.1500-1505
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• 2010

The novel swine-origin influenza A/H1N1 virus (S-OIV) first detected in April 2009 has been identified to transmit from humans to humans directly and is the cause of the currently emerged pandemic. In this study, nucleotide and deduced amino acid sequences of the hemagglutinin (HA) and neuraminidase (NA) of the S-OIV and other influenza A viruses were analyzed through bioinformatic tools for phylogenetic analysis, genetic recombination, and point mutation to investigate the emergence and adaptation of the S-OIV in humans. The phylogenetic analysis showed that the HA comes from triple reassortant influenza A/H1N2 and the NA from Eurasian swine influenza A/H1N1, indicating that HA and NA descend from different lineages during the genesis of the S-OIV. Recombination analysis ified the possibility of occurrence of recombination in HA and NA, denoting the role of reassortment in the outbreak. Several conservative mutations were observed in the amino acid sequences of the HA and NA, and these mutated residues were identical in the S-OIV. The results reported herein suggest the notion that the recent pandemic is the result of reassortment of different genes from different lineages of two envelope proteins, HA and NA, which are responsible for the antigenic activity of the virus. This study further suggests that the adaptive capability of the S-OIV in humans is acquired by the unique mutations generated during emergence.

• 대한바이러스학회지
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• 제29권2호
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• pp.65-74
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• 1999

Reovirus was found to inhabit both the respiratory and the enteric tract of human and animals. The genome of reovirus comprises 10 segments of double-stranded RNA, total size 24 kbp. Nine strains of reovirus were isolated from human and field mice in Korea. Aseptically collected sera from human and lung tissues from field mice were used for virus isolation. For serotype determination, hemagglutination inhibition test was used, and three strains were confirmed to type 2 and six strains to type 3. To determine the genomic diversity and molecular phylogeny of reoviruses isolated in Korea, part of S4 genomic segment of reovirus was enzymatically amplified and directly sequenced. In nucleotide level, Apo98-35 strain showed 15.4%, 19.3%, and 14.4% differences compared to type 1 (T1L, Lang), type 2 (T2J), and type 3 reference strains, respectively. In amino acid level, Apo98-35 strain showed 10.5%, 13.7%, and 9.5% differences compared to type 1, type 2, and type 3 reference strains, respectively. Using the maximum parsimony method based on 285 bp spaning region of the S4 genomic segment, phylogenetic analysis indicated that Apo98-35 from Korea formed different phylogenetic branch. Our data obtained by sequence and phylogenetic analyses of reoviruses are consistent with the distinct geographically dependent evolution of reoviruses in Korea.

• Biomolecules & Therapeutics
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• 제20권5호
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• pp.433-445
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• 2012

During the course of evolution, animals encountered the harmful effects of fungi, which are strong pathogens. Therefore, they have developed powerful mechanisms to protect themselves against these fungal invaders. ${\beta}$-Glucans are glucose polymers of a linear ${\beta}$(1,3)-glucan backbone with ${\beta}$(1,6)-linked side chains. The immunostimulatory and antitumor activities of ${\beta}$-glucans have been reported; however, their mechanisms have only begun to be elucidated. Fungal and particulate ${\beta}$-glucans, despite their large size, can be taken up by the M cells of Peyer's patches, and interact with macrophages or dendritic cells (DCs) and activate systemic immune responses to overcome the fungal infection. The sampled ${\beta}$-glucans function as pathogen-associated molecular patterns (PAMPs) and are recognized by pattern recognition receptors (PRRs) on innate immune cells. Dectin-1 receptor systems have been incorporated as the PRRs of ${\beta}$-glucans in the innate immune cells of higher animal systems, which function on the front line against fungal infection, and have been exploited in cancer treatments to enhance systemic immune function. Dectin-1 on macrophages and DCs performs dual functions: internalization of ${\beta}$-glucan-containing particles and transmittance of its signals into the nucleus. This review will depict in detail how the physicochemical nature of ${\beta}$-glucan contributes to its immunostimulating effect in hosts and the potential uses of ${\beta}$-glucan by elucidating the dectin-1 signal transduction pathway. The elucidation of ${\beta}$-glucan and its signaling pathway will undoubtedly open a new research area on its potential therapeutic applications, including as immunostimulants for antifungal and anti-cancer regimens.

• Molecules and Cells
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• 제28권2호
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• pp.111-117
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• 2009

The CHRM3 gene is a member of the muscarinic acetylcholine receptor family that plays important roles in the regulation of fundamental physiological functions. The evolutionary mechanism of exon-acquisition and alternative splicing of the CHRM3 gene in relation to transposable elements (TEs) were analyzed using experimental approaches and in silico analysis. Five different transcript variants (T1, T2, T3, T3-1, and T4) derived from three distinct promoter regions (T1: L1HS, T2, T4: original, T3, T3-1: THE1C) were identified. A placenta (T1) and testis (T3 and T3-1)-dominated expression pattern appeared to be controlled by different TEs (L1HS and THE1C) that were integrated into the common ancestor genome during primate evolution. Remarkably, the T1 transcript was formed by the integration event of the human specific L1HS element. Among the 12 different brain regions, the brain stem, olfactory region, and cerebellum showed decreased expression patterns. Evolutionary analysis of splicing sites and alternative splicing suggested that the exon-acquisition event was determined by a selection and conservation mechanism. Furthermore, continuous integration events of transposable elements could produce lineage specific alternative transcripts by providing novel promoters and splicing sites. Taken together, exon-acquisition and alternative splicing events of CHRM3 genes were shown to have occurred through the continuous integration of transposable elements following conservation.

• Molecules and Cells
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• 제40권10호
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• pp.714-730
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• 2017

Pre-mRNA splicing further increases protein diversity acquired through evolution. The underlying driving forces for this phenomenon are unknown, especially in terms of gene expression. A rice alternatively spliced transcript detection microarray (ASDM) and RNA sequencing (RNA-Seq) were applied to differentiate the transcriptome of 4 representative organs of Oryza sativa L. cv. Ilmi: leaves, roots, 1-cm-stage panicles and young seeds at 21 days after pollination. Comparison of data obtained by microarray and RNA-Seq showed a bell-shaped distribution and a co-lineation for highly expressed genes. Transcripts were classified according to the degree of organ enrichment using a coefficient value (CV, the ratio of the standard deviation to the mean values): highly variable (CVI), variable (CVII), and constitutive (CVIII) groups. A higher index of the portion of loci with alternatively spliced transcripts in a group (IAST) value was observed for the constitutive group. Genes of the highly variable group showed the characteristics of the examined organs, and alternatively spliced transcripts tended to exhibit the same organ specificity or less organ preferences, with avoidance of 'organ distinctness'. In addition, within a locus, a tendency of higher expression was found for transcripts with a longer coding sequence (CDS), and a spliced intron was the most commonly found type of alternative splicing for an extended CDS. Thus, pre-mRNA splicing might have evolved to retain maximum functionality in terms of organ preference and multiplicity.

• Animal Systematics, Evolution and Diversity
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• 제7권2호
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• pp.179-188
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• 1991

한국의 제주도에 서식하고 있는 등줄쥐의 한 아종인 Apodemus agrarius chejuensis의 분류학적 위치의 파악을 위하여, 아시아에 서식하는 등줄쥐중에 터키,중국,대만,만주 및 한국에서 채칩된 8아종(agrarius, ningpoensis, pallidior, chevrieri, insulaemus, manchuricus, coreae 및 chejuensis), 311마리의 표본들을 사용하였다. 4개 외부형질과 27개 두골형질들을 측정하였고 cluster, principal components 및 discriminant 분석등의 다변량분석을 수행하였다. 4개형(form)으로 나뉘어졌는데, chejuensis는 가장 큰 형이었고, 큰 형인 chevrieri는 Wang(1985)에 의하여 종으로도 기술된 바가 있다. 중간 크기의 형과 작은 크기의 형은 각각 coreae와 나머지 5개 아종(agrarius, ningpoensis, pallidior, in-sulaemus 및 manchuricus)이었으며, 연속적 변이를 나타냈다. 제주도의 chejuensis(가장 큰 형)는 등줄쥐의 다른 6개 아종(중간과 작은 크기의 형들)과 형태적 형질에 있어서 불연속적 차이를 보였으므로 신종으로 판단되지만, 신종으로서의 기재를 위해서는 연구가 더 필요하다고 결론지었다.

• 대한수의학회지
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• 제56권2호
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• pp.125-127
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• 2016

Gradual mortality of look down fish (Selene vomer) was observed in a private aquarium in Seoul, showing abnormal swimming behavior and lethargy. A bacterial pathogen from kidney was cultured, identified, and confirmed as Vibrio harveyi using Vitek System 2 and 16S rRNA gene sequencing. A predominant bacterial strain, SNUVh-LW2 was proved to be most closely related to isolates from China by phylogenetic analysis with minimum evolution method. Also, tetracycline was considered as the most sensitive antibiotic agent via antibiotic susceptibility test. The group of fish was treated according to the diagnostic result and no more mortality was observed.

• 공업화학
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• 제5권4호
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• pp.609-615
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• 1994

기체크로마토그래프에 직접 연결한 펄스 반응장치를 이용하여 10wt% $Ag/{\alpha}-Al_2O_3$ 촉매상에서 에틸렌 부분산화반응을 수행하였다. 산소가 분자흡착상태로 존재하기 어려운 실험온도에서 산소를 주입한 후 에틸렌을 주입하였을 때 산화에틸렌이 발생하였으며, 이 결과로부터 원자상태의 흡착산소가 산화에틸렌 생성에 관여함을 알 수 있었다. 흡착산소량과 몸체산소량을 감소시키면 산화에틸렌의 선택도는 감소하였다. 생성된 산화에틸렌은 에틸렌과 흡착산소로 분해되거나 아세트알데히드로 이성질화되었으나, 아세트알데히드로의 이성질화반응은 먼저 흡착된 산소에 의해서 크게 억제되었다.

• 대한의생명과학회지
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• 제24권3호
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• pp.221-229
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• 2018

Trichophyton rubrum is one of the well-known pathogenic fungi and causes dermatophytosis and cutaneous mycosis in human world widely. However, there are not an available sequence type (ST) classification methods and previous studies for T. rubrum until now. Therefore, currently, molecular biological tools using their DNA sequences are used for genotype identification and classification. In the present study, in order to characterize the genetic diversity and the phylogenetic relation of T. rubrum clinical isolates, five different housekeeping genes, such as actin (ACT), calmodulin (CAL), RNA polymerase II (RPB2), superoxide dismutase 2 (SOD2), and ${\beta}$-tubulin (BT2) were analyzed using by multilocus sequence typing (MLST). Also, DNA sequence analysis was performed to examine the differences between the sequences of Trichophyton strains and the identified genetic variations sequence. As a result, most of the sequences were shown to have highly matched rates in their housekeeping genes. However, genetic variations were found on three different positions of ${\beta}$-tubulin gene and were shown to have changed from $C{\rightarrow}G$ (1766), $G{\rightarrow}T$ (1876), and $C{\rightarrow}A$ (1886). To confirm the association with T. rubrum inheritance, a phylogenetic tree analysis was performed. It was classified as four clusters, but there was little significant correlation. Even so, MLST analysis is believed to be helpful for determining the genetic variations of T. rubrum in cases where there is more large-scale data accumulation. In conclusion, the present study demonstrated the first MLST analysis of T. rubrum in Korea and explored the possibility that MLST could be a useful tool for studying the epidemiology and evolution of T. rubrum through further studies.