• Journal of Life Science
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• v.31 no.1
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• pp.83-89
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• 2021

Uu-ilys, an i-type lysozyme from spoon worm (Urechis unicinctus), is an innate immune factor that plays an important role in the defense against pathogens. It also possesses non-enzymatic antibacterial activity. Thus, there is a possibility to develop an antimicrobial model peptide from Uu-ilys. In this study, we report the design, production, and antibacterial activity of an Uu-ilys analog that exhibits antibacterial activity. The Uu-ilys structure was fragmented according to its secondary structures to predict the regions with antimicrobial activity using antimicrobial peptide (AMP) prediction tools from different AMP databases. A peptide containing the C-terminal fragment was predicted to exert antimicrobial activity. The chosen fragment was designated as an Uu-ilys analog containing the C-terminal fragment, Uu-ilys-CF. To examine the possibility of developing an AMP using the sequence of Uu-ilys-CF, recombinant fusion protein (TrxA-Uu-ilys-CF) was produced in an expression system that was heterologous. The produced fusion protein was cleaved after methionine leaving Uu-ilys-CF free from the fusion protein. This was then isolated through high performance liquid chromatography and reverse phase column, CapCell-Pak C18. The antibacterial activity of Uu-ilys-CF against different microbial strains (four gram-positive, six gram-negative, and one fungal strain) were assessed through the ultrasensitive radial diffusion assay (URDA). Among the bacterial strains tested, Salmonella enterica was the most susceptible. While the fungal strain tested was not susceptible to Uu-ilys-CF, broad spectrum antibacterial activity was observed.

• Journal of Life Science
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• v.22 no.12
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• pp.1644-1650
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• 2012

The aim of this study was to screen the polymorphisms and distribution of each genotype of insertion/ deletion (indel) markers which were found in a preliminary comparative study of bovine genomic sequence databases. Comparative bioinformatic analyses were first performed between the nucleotide sequences of Bovine Genome Project and those of expressed sequence tag (EST) database, and a total of fifty-one species of indel markers were screened. Of these, forty-two indel markers were evaluated, and nine informative indel markers were ultimately selected for population analysis. Nucleotide sequences of each marker were re-sequenced and their polymorphic patterns were typed in six cattle breeds: Holstein, Angus, Charolais, Hereford, and two Korean native cattle breeds (Hanwoo and Jeju Black cattle). Cattle breeds tested in this study showed polymorphic patterns in eight indel markers but not in the Indel-15 marker in Charolais and Holstein. The results of analysis for Jeju Black cattle (JBC) population indicated an observed heterozygosity (Ho) that was highest in HW_G1 (0.600) and the lowest in Indel_29 (0.274). The PIC value was the highest in HW_G4 (0.373) and lowest in Indel_6 (0.305). These polymorphic indel markers will be useful in supplying genetic information for parentage tests and traceability and to develop a molecular breeding system for improvement of animal production in cattle breeds as well as in the JBC population.

• Radiation Oncology Journal
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• v.19 no.4
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• pp.389-396
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• 2001

Purpose : To detect differentially expressed genes in the patients with uterine cervical cancer during the radiation therapy. Materials and Methods : In patients with biopsy proven uterine cervical cancer, we took tumor tissue just before radiation therapy and at 40 minutes after external irradiation of 1.8 Gy. Total RNAs isolated from non-irradiated and irradiated tumor tissue samples were analyzed using the differential-display reverse transcription-polymerase chain reaction (DDRT-PCR). Complementary DNA (cDNA) fragments corresponding to differentially expressed messenger RNAs(mRNAs) were eluted, and cloned. The differential expression of the corresponding mRNAs was confirmed by reverse northern blot. Differentially expressed cDNA bands were sequenced. Nucleotide sequence data were analyzed in the Gene Bank and EMBL databases via the BLAST network sewer to identify homologies to known genes or cDNA fragments. Expression pattern of down-regulated clone was examined using RT-PCR in S patients undergoing radiotherapy. Results : We identified 18 differentially expressed bands by DDRT-PCR, which were eluted and cloned. There were 10 up-regulated clones and 1 down-regulated clone in reverse northern blot. One cDNA fragment had homology to chemokine receptor CXCR4, four were identified as Human ESTs in the EMBL database in EST clones. Down-regulated CxCa-11 was also down regulated in all patients. Conclusion : Using the DDRT-PCR, we have identified 10 up-regulated and 1 down-regulated clone(s) in the patients with uterine cervical cancer during the radiation therapy. The clinical relevance and the functions of these genes will be further investigated.

• Journal of KIISE:Databases
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• v.28 no.4
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• pp.529-544
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• 2001

Prefetching is an effective method to minimize the number of roundtrips between the client and the server in database management systems. In this paper we propose new notions of the type-level access pattern and the type-level access locality and developed an efficient prefetchin policy based on the notions. The type-level access patterns is a sequence of attributes that are referenced in accessing the objects: the type-level access locality a phenomenon that regular and repetitive type-level access patterns exist. Existing prefetching methods are based on object-level or page-level access patterns, which consist of object0ids of page-ids of the objects accessed. However, the drawback of these methods is that they work only when exactly the same objects or pages are accessed repeatedly. In contrast, even though the same objects are not accessed repeatedly, our technique effectively prefetches objects if the same attributes are referenced repeatedly, i,e of there is type-level access locality. Many navigational applications in Object-Relational Database Management System(ORDBMs) have type-level access locality. Therefore our technique can be employed in ORDBMs to effectively reduce the number of roundtrips thereby significantly enhancing the performance. We have conducted extensive experiments in a prototype ORDBMS to show the effectiveness of our algorithm. Experimental results using the 007 benchmark and a real GIS application show that our technique provides orders of magnitude improvements in the roundtrips and several factors of improvements in overall performance over on-demand fetching and context-based prefetching, which a state-of the art prefetching method. These results indicate that our approach significantly and is a practical method that can be implemented in commercial ORDMSs.