• ALGAE
• /
• v.28 no.1
• /
• pp.31-43
• /
• 2013

This review provides a comprehensive summary of the PCR primers and profiles currently in use in our laboratory for red algal DNA barcoding and phylogenetic research. While work focuses on florideophyte taxa, many of the markers have been applied successfully to the Bangiales, as well as other lineages previously assigned to the Bangiophyceae sensu lato. All of the primers currently in use with their respective amplification profiles and strategies are provided, which can include full fragment, overlapping fragments and what might best be called "informed overlapping fragments", i.e., a fragment for a marker is amplified and sequenced for a taxon and those sequence data are then used to identify the best primers to amplify the remaining fragment(s) for that marker. We extend this strategy for the more variable markers with sequence from the external PCR primers used to "inform" the selection of internal sequencing primers. This summary will hopefully serve as a useful resource to systematists in the red algal community.

• Proceedings of the Korean Society of Plant Pathology Conference
• /
• 2003.10a
• /
• pp.130-130
• /
• 2003

Gummy stem blight pathogen is very difficult not only to monitor the inoculum levels prior to host infection, and also it is destructive and hard to control in field condition. We have applied RAPD technique to elucidate the genetic diversity of the genomic DNA of Didymella bryoniae and also to generate specific diagnostic DNA probe useful for identification and detection. The 40 primers produced clear bands consistently from the genomic DNA of twenty isolates of Didymella bryoniae, and two hundred seventy-three amplified fragments were produced with 40 primers. The combined data from 273 bands was analyzed by a cluster analysis using UPGMA method with an arithmetic average program of NTSYS-PC (Version 1.80) to generate a dendrogram. At the distance level of 0.7, two major RAPD groups were differentiated among 20 strains. RAPD group (RG) I included 8 isolates from watermelon except one isolate from melon. RAPD group (RG) IV included 12 isolates from squash, cucumber, watermelon and melon.. In amplification experiment with SCAR specific primer RG1F-RG1R resulted in a single band of 650bp fragment only for 8 isolates out of 20 isolates that should be designated as RAPD Group 1. However, same set of experiment done with RGIIF-RGIIR did not result in any amplified product.. Our attempts to detect intraspecific diversity of ITS region of rDNA by amplifying ITS region and 17s rDNA region for 20 isolates and restriction digestion of amplified fragment with 12 enzymes did not reveal polymorphic band. In order to develop RAPD markers for RGIV specific primer, a candidate PCR fragment( ≒1.4kb) was purified and Southern hybridized to the amplified fragment RGIV isolates. This promising candidate probe recognized only RGIV isolates

• Geomechanics and Engineering
• /
• v.14 no.2
• /
• pp.151-159
• /
• 2018

Annually, the global production of construction aggregates reaches over 40 billion tons, making aggregates the largest mining sector by volume and value. Currently, the aggregate industry is shifting from sand to hard rock as a result of legislation limiting the extraction of natural sands and gravels. A major implication of this change in the aggregate industry is the need for understanding rock fragmentation and energy absorption to produce more cost-effective aggregates. In this paper, we focused on incorporating dynamic rock and soil mechanics to understand the effects of loading rate and water saturation on the rock fragmentation and energy absorption of three different sandstones (Red, Berea and Buff) with different pore sizes. Rock core samples were prepared in accordance to the ASTM standards for compressive strength testing. Saturated and dry samples were subsequently prepared and fragmented via fast and dynamic compressive strength tests. The particle size distributions of the resulting fragments were subsequently analyzed using mechanical gradation tests. Our results indicate that the rock fragment size generally decreased with increasing loading rate and water content. In addition, the fragment sizes in the larger pore size sample (Buff sandstone) were relatively smaller those in the smaller pore size sample (Red sandstone). Notably, energy absorption decreased with increased loading rate, water content and rock pore size. These results support the conclusion that rock fragment size is positively correlated with the energy absorption of rocks. In addition, the rock fragment size increases as the energy absorption increases. Thus, our data provide insightful information for improving cost-effective aggregate production methods.

• The KIPS Transactions:PartD
• /
• v.16D no.1
• /
• pp.27-42
• /
• 2009

In realizing ubiquitous computing, techniques of efficiently using the limited resource at client such as mobile devices are required. With a mobile device with limited amount of memory, the techniques of XML stream query processing should be employed to process queries over a large volume of XML data. Recently, several techniques were proposed which fragment XML documents into XML fragments and stream them for query processing at client. During query processing, there could be great difference in resource usage (query processing time and memory usage) depending on how the source XML documents are fragmented. As such, an efficient fragmentation technique is needed. In this paper, we propose an XML fragmentation technique whereby resource efficiency in query processing at client could be enhanced. For this, we first present a cost model of query processing over XML fragment stream. Then, we propose an algorithm for resource-efficient XML fragmentation. Through implementation and experiments, we showed that our fragmentation technique outperformed previous techniques both in processing time and memory usage. The contribution of this paper is to have made the techniques of query processing over XML fragment stream more feasible for practical use.

• Journal of the Korean Society of Food Science and Nutrition
• /
• v.30 no.5
• /
• pp.802-805
• /
• 2001

The dapD gene of Brevibacterium lactofermentum encoding tetrahydrodipicolinate N-succinyl transferase, one of the enzymes involved in lysine biosynthesis, was cloned by complementation of Escherichia coli dapD mutnat. The recombinant plasmid pLS1 was found to contain a 3.6 kb DNA fragment. Southern hybridization analysis confirmed that the cloned DNA fragment originated from B. lactofermentum. The data of L-lysine production showed that the B. lactofermentum dapD gene was expressed in E. coli.

• Journal of KIISE:Databases
• /
• v.35 no.1
• /
• pp.67-83
• /
• 2008

In order to realize ubiquitous computing, it is essential to efficiently use the resources and the computing power of mobile devices. Among others, memory efficiency, energy efficiency, and processing efficiency are required in executing the softwares embedded in mobile devices. In this paper, query processing over XML data in a mobile device where resources are limited is addressed. In a device with limited amount of memory, the techniques of XML. stream query processing need to be employed to process queries over a large volume of XML data Recently, a technique Galled XFrag was proposed whereby XML data is fragmented with the hole-filler model and streamed in fragments for processing. With XFrag, query processing is possible in the mobile device with limited memory without reconstructing the XML data out of its fragment stream. With the hole-filler model, however, memory efficiency is not high because the additional information on holes and fillers needs to be stored. In this paper, we propose a new technique called XFLab whereby XML data is fragmented with the XML labeling scheme which is for representing the structural relationship in XML data, and streamed in fragments for processing. Through implementation and experiments, XML showed that our XFLab outperformed XFrag both in memory usage and processing time.

• Korean Journal of Veterinary Research
• /
• v.41 no.4
• /
• pp.571-578
• /
• 2001

To evaluate if the apoptotic fragment assay could be used to estimate the dose prediction after radiation exposure, we examined apoptotic mouse crypt cells per 1,000 cells after whole body $^{60}Co$ $\gamma$-rays and 50MeV ($p{\rightarrow}Be^+$) cyclotron fast neutron irradiation in the range of 0.25 to 1 Gy, respectively. The incidence of apoptotic cell death rose steeply at very low doses up to 1 Gy, and radiation at all doses tigger rapid changes in crypt cells in stem cell region. These data suggest that apoptosis may play an important role in homeostasis of damaged radiosensitive target organ by removing damaged cells. The curve of dose-effect relationship for the data of apoptotic fragments was obtained by the linear-quadratic model $y=0.18+(9.728{\pm}0.887)D+(-4.727{\pm}1.033)D^2$ ($r^2=0.984$) after $\gamma$-rays irradiation, while $y=0.18+(5.125{\pm}0.601)D+(-2.652{\pm}0.7000)D^2$ ($r^2=0.970$) after neutrons in mice. The dose-response curves were linear-quadratic, and a significant dose-response relationship was found between the frequency of apoptotic cell and dose. These data show a trend towards increase of the numbers of apoptotic crypt cells with increasing dose. Both the time course and the radiation dose-response curve for high and low linear energy transfer (LET) radiation modalities were similar. The relative biological effectiveness (RBE) value for crypt cells was 2.072. In addition, there were significant peaks on apoptosis induction at 4 and 6h after irradiation, and the morpholoigcal findings of the irradiated groups were typical apoptotic fragments in crypt cells that were hardly observed in the control group. Thus, apoptosis in crypt cells could be a useful in vivo model for studying radio-protective drug sensitivity or screening test, microdosimetric indicator and radiation-induced target organ injury. Since the apoptotic fragment assay is simple, rapid and reproducible in the range of 0.25 to 1 Gy, it will also be a good tool for evaluating the dose response of radiation-induced organ damage in vivo and provide a potentially valuable biodosimetry for the early dose prediction after accidental exposure.

• Korean Journal of Microbiology
• /
• v.32 no.4
• /
• pp.258-263
• /
• 1994

Genomic Southern hybridization of Frankia EuIKl strain, a nitrogen fixing symbiont of Elaeagnus umbellate root nodules, with nifH,D of K. pneumoniae as a probe, showed that 3.2 Kb and 5.5 Kb of BamHI fragments and 15 Kb PstI fragment were strongly hybridized with the probe, indicating nifH,D are located on these fragments. Using the same probe, one clone(pEuNIF) was isolated from the genomic library constructed into pWE15 cosmid vector by colony hybridization. The 3.2 Kb and 5.5 Kb BamHI fragments of this clone were hybridized with the same probe and this result corresponds to the genomic Southern hybridization data. However, using nifH of Frankia FaCl strain as a probe, only the 3.2 Kb BamHI fragment showed hybridization signal. Amino acid sequence deduced from nucleotide sequence of 3' terminus of the 3.2 Kb and 5' terminus of the 5.5 Kb fragments showed that the former was highly homologous with that of ArI3 nifD from 182nd to 240th amino acids, while the latter was from 241st to 282nd amino acids. These results show that nifH and partial nifD sequences are located on the 3.2 Kb fragment and residual sequences of nifH on the 5.5 Kb fragment which is contiguous to the 3.2 Kb fragment.

• Korean Journal of Microbiology
• /
• v.32 no.4
• /
• pp.264-270
• /
• 1994

A gene coding for a novel putative $\sigma$ factor of RNA polymerase has been identified from Streptomyces coelicolor A3(2) using Escherichia coli rpoS gene fragment as a probe. The 486 bp rpoS gene fragment was amplified from E. coli genomic DNA by PCR with two synthetic oligonucleotides, the sequences of which were deduced from the amino acid sequences in the regions 2.3 and 4.2 conserved among various bacterial factors. When E. coli genomic DNA fragments were hybridized with cloned rpoS probe, only one band corresponding to rpoS gene (3.2 kb PvuII fragment or 2.3 kb KpnI fragment) was detected. In S. coelicolor, however, two bands were detected both in PvuII digested DNA and SalI digested DNA. 3.5 kb PvuII fragment which binds the rpoS gene probe was cloned (pMS1) from the sublibrary, and the nucleotide sequences of 1.0 kb BamH'/HincII subclone (pBH2) was partially determined. The nucleotide sequences revealed extensive similarity to other $\sigma$ factor genes of S. coelicolor (hrdA, hrdB, hrdC, hrdD), S. aureofaciens (hrdA, hrdB, hrdC, hrdD), Synechococcus species, Pseudomonas aeruginosa, Stigmatella aurantiaca, and Anabaena species. The nucleotide sequences in regions 1.2 and 4 were compared with the corresponding regions of 5 known ${\sigma}$ factor genes of S. coelicolor by multiple alignment. It turned out that the cloned gene is most closely related to hrdA showing 88% amino acid similarity in region 1.2 and 75% in region 4.

• Journal of the Korea Institute of Information and Communication Engineering
• /
• v.10 no.8
• /
• pp.1414-1421
• /
• 2006

This paper proposes a consistency algorithm that is able to serve streaming data efficiently in VOD system. The media data is stripping into several pieces of data by the Round Robin method in order to media data service. The barrier mechanism is changed into the minimum data factor(SH. GOP) in this paper. The shared memory is allocated at one host with one fragment size. Data is combined with RTP packet transmission data format using barrier mechanism. I experiment and program the suggested algorithm on the VOD system.