• BMB Reports
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• v.34 no.3
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• pp.230-236
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• 2001

dTDP-rhamnose is synthesized from dTTP and glucose-1-phosphate by four enzymatic steps in the gram-negative bacteria. By using a homologous PCR product, a gene cluster encoding four genes (rfbA, rfbB, rfbC, rfbD) involved in L-rhamnose biosynthesis by Acinetobacter calcoaceticus was isolated and sequenced. The four genes were clustered on the biosynthetic operon in the order of rfbB, D, A, C. A gene, rfbA, encoding glucose-l-phosphate thymidylyltransferase (RfbA), was cloned from A. calcoaceticus pathogenic and encapsulated in the gram-negative bacterium. This enzyme catalyzes the formation of dTDP-D-glucose From $\alpha$-D-glucose-1-phosphate and dTTP.RfbA was amplified by PCR and inserted into the $T_7$ expression system. The activity of RfbA was determined by the capillary electrophoresis. The $K_m$ values for dTTP and $\alpha$-D-glucose-1-phosphate were calculated to be 1.27 mM and 0.80 mM, respectively by using the Line-Weaver Burk plot. RfbA is inactivated by diethylpyrocarbonate.

• Journal of Soil and Groundwater Environment
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• v.21 no.5
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• pp.16-24
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• 2016

A new strain of Pseudomonas sp. was isolated from mercury (Hg)-contaminated sites in Taiwan. This bacterium removed more than 80% of Hg present in the culture medium at 12 h incubation and was chosen for further analysis of the molecular mechanisms of Hg tolerance/removal abilities in this Pseudomonas sp. We used RNA-seq, one of the next-generation sequencing methods, to investigate the transcriptomic responses of the Pseudomonas sp. exposed to 60 mg/L of Hg²⁺. We de novo assembled 4,963 contigs, of which 10,533 up-regulated genes and 5,451 down-regulated genes were found to be regulated by Hg. The 40 genes most altered in expression levels were associated with tolerance to Hg stress and metabolism. Functional analysis showed that some Hg-tolerant genes were related to the mer operon, sulfate uptake and assimilation, the enzymatic antioxidant system, the HSP gene family, chaperones, and metal transporters. The transcriptome were analyzed further with Gene Ontology (GO) and Cluster of Orthologous Groups (COGs) of proteins and showed diverse biological functions and metabolic pathways under Hg stress.

• The Bulletin of The Korean Astronomical Society
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• v.41 no.2
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• pp.36.1-36.1
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• 2016

This is a presentation of the paper published as Kimm et al. 2016, ApJ, 823, 52. We investigate the formation of metal-poor globular clusters (GCs) at the center of two dark matter halos with $Mhalo{\sim}4{\times}107Msun$ at z>10 using cosmological radiation-hydrodynamics simulations. We find that very compact (${\leq}1$ pc) and massive (${\sim}6{\times}105Msun$) clusters form rapidly when pristine gas collapses isothermally with the aid of efficient $Ly{\alpha}$ emission during the transition from molecular-cooling halos to atomic-cooling halos. Because the local free-fall time of dense star-forming gas is very short (${\ll}1Myr$), a large fraction of the collapsed gas is turned into stars before stellar feedback processes blow out the gas and shut down star formation. Although the early stage of star formation is limited to a small region of the central star-forming disk, we find that the disk quickly fragments due to metal enrichment from supernovae. Sub-clusters formed in the fragmented clouds eventually merge with the main cluster at the center. The simulated clusters closely resemble the local GCs in mass and size but show a metallicity spread that is much wider than found in the local GCs. We discuss a role of pre-enrichment by Pop III and II stars as a potential solution to the latter issue. Although not without shortcomings, it is encouraging that a naive blind (not tuned) cosmological simulation presents a possible channel for the formation of at least some massive GCs.

• Journal of The Korean Astronomical Society
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• v.53 no.3
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• pp.77-85
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• 2020

In the molecular cloud G33.92+0.11A, massive stars are forming sequentially in dense cores, probably due to interaction with accreted gas. Cold dense gas, which is likely the pristine gas of the cloud, is traced by DCN line and dust continuum emission. Clear chemical differences were observed in different source locations and for different velocity components in the same line of sight. Several distinct gas components coexist in the cloud: the pristine cold gas, the accreted dense gas, and warm turbulent gas, in addition to the star-forming dense clumps. Filaments of accreted gas occur in the northern part of the A1 and A5 clumps, and the velocity gradient along these features suggests that the gas is falling toward the cloud and may have triggered the most recent star formation. The large concentration of turbulent gas in the A2 clump seems to have formed mainly through disturbances from the outside.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.296-306
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• 2004

LC/MS를 이용하여 펩타이드 혹은 단백질 같은 물질을 분석하는 실험이 급격히 늘어남에 따라 LC/MS 데이터를 자동으로 처리하는 기술에 대한 요구가 커지고 있다. 이러한 LC/MS 데이터의 자동 분석 기술에 대한 연구는 현재 활발히 진행되어 왔고, 이를 직접 구현한 여러 상용 소프트웨어들이 개발되어 있는 상태이다. LC/MS 데이터는 noise 제거, background 데이터 제거, deconvolution 알고리즘을 적용한 분자량(molecular weight) 할당 등의 작업을 거쳐 분석하게 된다. 이러한 과정을 거쳐 얻어진 분자량에 대한 데이터가 올바른 값인지 검증하는 작업이 필요하다. 본 논문에서는 이러한 검증 작업과 관련하여 Peak Clustering and Fitting(이하 PC&F)에 대한 알고리즘을 제안한다. PC&F은 peak 데이터들이 지니고 있는 속성에 대한 Mahalanobis distance를 이용하여 peak 데이터를 각 retention time에 따라 clustering 분석을 하는 작업이다. 본 논문에서 제안하는 PC&F 알고리즘을 Microsoft Visual C++ 6.0 MFC 환경에서 직접 개발한 소프트웨어(PeakClusterFitLCMS)로 실험하였다. 실험결과 PC&F 작업을 통해 동일한 구성물질로부터 발생한 peak 데이터를 모아서 보다 신뢰할 수 있는 분자량을 구할 수 있었고, 구성물질에 의해 발생되지 않은 noise peak 데이터를 찾아 제거시킬 수 있음을 확인할 수 있었다.

• Korean Journal of Agricultural Science
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• v.23 no.1
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• pp.99-107
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• 1996

Eighteen nuclear probes were used to examine RFLP(restriction fragment length polymorphism) between six species of Artemisia spp. of Korea. Total DNA from six different species of Artemisia was separately cut with three restrict enzymes. The PstI enzyme was showed to reduce the variation of polymorphisms than the other two enzymes(EcoRl and BamHI). The genetic variation of polymorphism was similar between the Dhewegiki-ssug and Cham-ssug. RAPD analysis was applied to the same six species of Artemisia spp. in order to assess the degree of DNA polymorphism within the Artemisia genus. Six species of Artemisia were evaluated for variation using a set of 11 random 10-mer primers. Nine out of the eleven primers revealed scorable polymorphisms between six species of Artemisia spp. Genetic distances between each of the species were calculated and cluster analysis was used to generate a dendrogram showing phylogenetic relationships between them This result indicates that molecular markers will be more usable in intraspecific study of Artemisia spp. than isoenzyme markers.

• The Plant Pathology Journal
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• v.30 no.1
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• pp.10-24
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• 2014

Genetic diversity and differentiation of 50 Colletotrichum spp. isolates from legume crops studied through multigene loci, RAPD and ISSR analysis. DNA sequence comparisons by six genes (ITS, ACT, Tub2, CHS-1, GAPDH, and HIS3) verified species identity of C. truncatum, C. dematium and C. gloeosporiodes and identity C. capsici as a synonym of C. truncatum. Based on the matrix distance analysis of multigene sequences, the Colletotrichum species showed diverse degrees of intera and interspecific divergence (0.0 to 1.4%) and (15.5-19.9), respectively. A multilocus molecular phylogenetic analysis clustered Colletotrichum spp. isolates into 3 well-defined clades, representing three distinct species; C. truncatum, C. dematium and C. gloeosporioides. The ISSR and RAPD and cluster analysis exhibited a high degree of variability among different isolates and permitted the grouping of isolates of Colletotrichum spp. into three distinct clusters. Distinct populations of Colletotrichum spp. isolates were genetically in accordance with host specificity and inconsistent with geographical origins. The large population of C. truncatum showed greater amounts of genetic diversity than smaller populations of C. dematium and C. gloeosporioides species. Results of ISSR and RAPD markers were congruent, but the effective maker ratio and the number of private alleles were greater in ISSR markers.

• Journal of Forest and Environmental Science
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• v.25 no.1
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• pp.57-65
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• 2009

Ficus deltoidea Jack is an important and popular medicinal plant species found in the Malaysia. Plants are being collected and used based on morphology and authentication to prevent adulteration is not in practice. In this study, twenty-six accessions of F. deltoidea Jack were collected from Kelantan and Terengganu states of Peninsular Malaysia to examine their genetic similarities and differences using randomly amplified polymorphic DNA (RAPD) technique. Out of 20 arbitrary primers, two primers (D-10 and D-11) were selected which produced reliable DNA polymorphism. D-10 and D-11 primers generated 138 RAPD bands ranging from 250 bp to 3000 bp. Ninety-nine of them were polymorphic loci (72%) and thirty-nine were nonpolymorphic loci (28%). A total of 56 bands with polymorphic loci were amplified with primer D-10 and analyzed by cluster analysis and UPGMA to present a dendrogram depicting the degree of genetic relationship among 26 accessions. Eight RAPD markers were sequenced to determine their identity. RAPD analysis showed the genetic diversity among 26 accessions of F. deltoidea Jack. The RAPD profile and RAPD marker sequences reported in this paper could be used in plant and/or plant material authentication. This study also suggested that RAPD can be a useful technique to study DNA polymorphism in F. deltoidea Jack.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.12
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• pp.1783-1790
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• 2007

The genetic diversity of domestic quail and two wild quail species, Japanese （Coturnix coturnix）and Common quail (Coturnix japonica), found in China was studied using microsatellite DNA markers. According to a comparison of the corresponding genetic indices in the three quail populations, such as Polymorphism Information Content (PIC), Mean Heterozygosity ($\bar{H}$) and Fixation Index, wild Common quail possessed rich genetic diversity with 4.67 alleles per site. Its values for PIC and $\bar{H}$ were the highest, 0.5732 and 0.6621, respectively. Domestic quail had the lowest values, 0.5467 and 0.5933, respectively. Wild Japanese quail had little difference in genetic diversity from domestic quail. In addition, from analyses of the fuzzy cluster based on standard genetic distance, the similarity relationship matrix coefficient between wild Japanese quail and domestic quail was 0.937, and that between wild Common quail and domestic quail was 0.783. All of these results showed that the wild Japanese quail were closer to the domestic quail for phylogenetic relationship than wild Common quail. These results at the molecular level provide useful data about quail's genetic background and further supported the hypothesis that the domestic quail originated from the wild Japanese quail.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.6
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• pp.751-757
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• 2012

In order to develop specific genetic markers and determine the genetic diversity of Bangladeshi native cattle (Pabna, Red Chittagong) and exotic breeds (Sahiwal), randomly amplified polymorphic DNA (RAPD) analysis was performed using 12 primers. Genomic DNA was extracted from 20 cattle (local and exotic) blood samples and extracted DNA was observed by gel electrophoresis. Among the random primers three were matched and found to be polymorphic. Genetic relations between cattle's were determined by RAPD polymorphisms from a total of 66.67%. Statistical analysis of the data, estimating the genetic distances between cattle and sketching the cluster trees were estimated by using MEGA 5.05 software. Comparatively highest genetic distance (0.834) was found between RCC-82 and SL-623. The lowest genetic distance (0.031) was observed between M-1222 and M-5730. The genetic diversity of Red Chittagong and Sahiwal cattle was relatively higher for a prescribed breed. Adequate diversity in performance and adaptability can be exploited from the study results for actual improvement accruing to conservation and development of indigenous cattle resources.