• ALGAE
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• 제22권2호
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• pp.57-67
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• 2007

We analyzed the nuclear-encoded large subunit ribosomal RNA gene (LSU rDNA) sequences of 19 dinoflagellates occurring in costal waters off Korea and reconstructed a phylogenetic tree containing 74 representative species from 37 distinct genera. Of these, the LSU rDNA sequences of Amylax triacantha (Jörgensen) Sournia, Gonyaulax verior Sournia (= Amylax diacantha Meunier), Gyrodinium fissum (Levander) Kofoid et Swezy, Katodinium glaucum (Lebour) Lebour III, Noctiluca scintillans (Macartney) Kofoid et Swezy, Oxyphysis oxytoxoides Kofoid, and Pyrophacus steinii (Schiller) Wall et Dale are reported for the first time. Our LSU rDNA tree consistently placed Oxyrrhis marina Dujardin and N. scintillans at the most primitive positions, giving rise to a strongly supported monophyletic group of typical dinoflagellate species belonging to the Dinophyceae. The phylogenetic relationships among the typical dinoflagellates, however, were not resolved in the higher taxonomic levels in general. Only genera at terminal branches were usually supported with high confidence. The Dinophysiales, represented by Dinophysis species and O. oxytoxoides, formed a strongly supported monophyletic assemblage. The Gymnodiniales and Peridiniales were recovered as polyphyletic groupings. Members of the Gonyaulacales were consistently grouped together, but lacked statistical support. Within this order, the Ceratiaceae and Goniodomataceae each formed a monophyletic group, but the Gonyaulacaceae was polyphyletic. The phylogenetic relationships of the Gonyaulacaceae were generally congruent with differences in the combinations of the apical pore complex, hypothecal organization and thecal formula.

• 한국미생물·생명공학회지
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• 제32권2호
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• pp.195-198
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• 2004

Molec-ular analysis was performed on the microflora found In the necrotic pulpal tissue collected from 5 infected root canals that were diagnosed as a periapical abscess. 16S rRNA coding gene (rDNA) library construction and sequencing were performed in order to identify the microflora, The 16S rDNA sequences from 278 clones were identified by a comparison with the database sequence in GenBank. Three phylum and 31 species, which were related to the oral microflora, were identified from the 3 samples (No. 87, 105, and 115). Dialister invisus (5.6％), Peptostreptococcus micron (18.3％), and Veillonella sp. (3.3％) were the organism present in all tee samples. Lac-tobacillusfementum (2.8％),Eubacterumsp./E. infirmum (6.7％), Shuttleworthiasatelles (3.9％), Psudorarnihacfer alactoiyticus (13.3％), Bulleidia moorei (2.8％), and Prevotella denticola (1.1％) were found in two samples. Two phylum and low species of environmental microflora were identified from 2 samples (No.95 and 101). The reason for this might be contamination of the samples with dental water. These results showed that molecular analysis could reveal more diverse microflora that are associated with endodontic infections than that revealed by conventional cultural methods. In addition, these results may of for the basic data to epidemiological studies related with endodontic infection.

• Asian-Australasian Journal of Animal Sciences
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• 제19권3호
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• pp.335-340
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• 2006

A large number of toxicological substances and pharmacological and physical agents can cause reproductive intervention at the cellular and molecular level. The present study was designed to assess the effect of mercury ($HgCl_2$) at 50 to $550{\mu}M$ concentration ranges, in vitro, on the sperm membrane and DNA integrity, viability, and acrosomal status of normal bull spermatozoa. The samples were processed for sperm analyses using semen-diluting fluid (PBS, pH 7.2). We recorded a sharp increase in the lipid peroxidation/LPO rate; the highest was at $550{\mu}M$ mercury concentration, indicating a deleterious effect of mercury on the sperm membrane intactness. There was also a strong negative correlation between LPO rate and % viable spermatozoa (R = 0.987, p<0.001). Data obtained from a comet assay technique revealed that mercury is capable of inducing DNA breaks in the sperm nuclei. Interestingly, 92% of DNA breaks were double-stranded. The correlation between LPO rate and % DNA breaks was 0.984. Performing the gelatin test indicates that mercury is able to alter the integrity of acrosomal membranes showing an abnormal acrosome reaction. In this regard, a strong link was found between LPO rate and % halos (R = 0.990, p<0.001). Collectively, mercury proved to be a potent oxidant in the category of environmental factors affecting bull spermatozoa. Hence, considering the wide spread use of mercury and its compounds, these metals should be regarded with more concern.

• 한국자기공명학회논문지
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• 제20권2호
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• pp.36-40
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• 2016

MRA1997 is a highly conserved protein from mycobacterial strains. However, no structural and functional information is associated with it. Thus, to obtain details about structure and function of this protein, we have utilized NMR spectroscopy. The recombinant MRA1997 was highly purified and its DNA binding mode was characterized. The tertiary structure of MRA1997 was modeled on the basis of our NMR chemical shift data combined with the webserver CS23D. The binding of MRA1997 with DNA was first monitored by electrophoresis mobility shift assays. The residues involved in DNA binding are identified using NMR chemical shift perturbation experiments. Based on our study, we suggest that MRA1997 interacts with DNA and may play an important role in Mycobacterium tuberculosis physiology.

• BMB Reports
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• 제43권11호
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• pp.732-737
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• 2010

RNA interference is a post-transcriptional silencing mechanism triggered by the bioavailability and/or exogenous introduction of double-stranded RNA (dsRNA) into cells. Here we describe a novel method for the synthesis of siRNA in a single vessel. The method employs in vitro transcription and a single-stranded DNA (ssDNA) template and design, which incorporates upon self-annealing, two promoters, two templates, and three loop regions. Using this method of synthesis we generated efficacious siRNAs designed to silence both exogenous and endogenous genes in mammalian cells. Due to its unique design the single-stranded template is easily amenable to adaptation for attachment to surface platforms for synthesis of siRNAs. A siRNA synthesis platform was generated using a 3' end-biotinylated ssDNA template tethered to a streptavidin coated surface that generates stable siRNAs under multiple cycles of production. Together these data demonstrate a unique and robust method for scalable siRNA synthesis with potential application in RNAi-based array systems.

• Journal of Plant Biotechnology
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• 제37권2호
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• pp.133-143
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• 2010

Rice (Oryza sativa) is a major cereal crop that has been developed as a monocot model species. In past decades rice researchers have established valuable resources for functional genomics in rice, such as complete genome sequencing, high-density genetic maps, a full length cDNA database, genome-wide transcriptome data, and a large number of mutants. Of these, rice mutant lines are very important to definitively determine functions of genes associated with valuable agronomic traits. In this review we summarize the progress of functional genomics approaches in rice using T-DNA mutants.

• Animal cells and systems
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• 제5권3호
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• pp.231-236
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• 2001

SINE-R retroposons have been derived from human endogenous retrovirus HERV-K family and found to be hominoid specific. Both SINE-R retroposons and HERV-K family are potentially capable of affecting the expression of closely located genes. From cDNA library of human fetal brain, we identified seven SINE-R retroposons and compared them with sequences derived from GenBank database. The SINE-R retroposons from human feta1 brain showed 85∼97% sequence similarities with the human-specific retroposon SINE-R.C2. They also showed 88∼96% sequence similarities with the sequence of the schizo-cDNA clone that derived from postmortem frontal cortex tissue of a schizophrenic patient. Phylogenetic analysis using the neiqhbor-joining method revealed that the seven new SINE-R retroposons from cDNA library of the human feta1 brain have proliferated independently during human evolution. The data indicate that such SINE-R retroposons are expressed in human fetal brain and deserve further investigation as potential leads to understanding of neuropsychiatric diseases.

• 한국잠사학회:학술대회논문집
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• 한국잠사학회 2003년도 제46회 춘계 학술연구 발표회
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• pp.47-48
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• 2003

The development of cDNA microarray has permitted the analysis of thousands of genes simultaneously. cDNA microarray has been used to analyze gene expression profiles during developmental stage in both single and multicellular organisms. Two significant factors contributing to the limitation of the development of cDNA microarray in the Bombyx mori are the shortage of accessible repositories of cDNA clones and ESTs and the relative scarcity of facilities to produce microarrays and analyze the data generated. (omitted)

• 미생물학회지
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• 제33권2호
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• pp.118-124
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• 1997

이전의 연구에서 우리는 CheY-OmpR 융합단백질인 'Chp'을 제조하여 ompF와 ompC 유전자에 미치는 영향을 조사하였다(6). 본 연구에서는 Chp의 활성 및 작용기작을 in vivo와 in vitro 실험을 통해 알아보았다. 융합단백질 Chp은 OmpR과 마찬가지로 DNA에 염기서열 특이적인 결합을 하지만, 유전자의 전사 활성 기능은 나타내지 않았다. 따라서 Chp의 ompF/C 유전자의 발현에 대한 효과는 DNA 결합 부위에 대한 OmpR과의 경쟁에 의해 나타나는 것으로 결론지을 수 있다. 그러나, in vivo와 in vitro 실험에서 Chp의 인산화에 따른 DNA 결합력 변화는 관찰할 수 없었다. Chp이 ompR 유전자의 발현을 증가시키는 것이 관찰되었는데, OmpR도 이와 같은 효과를 나타내었으며, 배지의 삼투압을 변화시켰을 때와 EnvZ 돌연변이체에서도 ompR 유전자의 발현변화가 관찰되었다.

• 한국자기공명학회논문지
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• 제10권2호
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• pp.175-187
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• 2006

Binding interactions between a positively charged porphyrin derivative TMAP(meso-tetra(p-trimethylanilinium-4-yl)porphyrin) and triple helical $(dT)_{12}{\cdot}(dA)_{12}{\cdot}(dT)_{12}$, as well as double helical $(dA)_{12}{\cdot}(dT)_{12}$ have been studied with NMR, UV and CD spectroscopy to obtain the detailed information about the binding mode and binding site. UV melting studies showed both DNA duplex and triple helix represented very similar UV absorption patterns upon binding TMAP, but the presence of third strand of triple helical $(dT)_{12}{\cdot}(dA)_{12}{\cdot}(dT)_{12}$, inhibited improvement in thermal stability in terms of melting temperature, $T_m$. In addition, the TMAP molecule is thought to bind to the major groove, according to CD and NMR data. But absence of the clear isosbestic point in UV absorption spectra represented that binding of TMAP to DNA duplex as well as DNA triplex did not show a single binding mode, rather complex binding modes.