• Journal of Life Science
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• v.27 no.1
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• pp.72-77
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• 2017

Inorganic iron is essential for various metabolic processes, including RNA synthesis, electron transport, and oxygen detoxification in microorganisms. Many bacterial pathogens compete for iron acquisition in diverse environmental condition such as host. Salmonella Typhimurium SL1344 also requires inorganic iron as a cofactor for growth. When a M9 minimal liquid medium was supplemented with ethylenediamine di-o-hydroxyphenylactic acid (EDDA) which acts as an iron-chelating agent, growth of Salmonella Typhimurium SL1344 in the supplemented medium was completely arrested by deficient of useful iron under iron-depleted condition. However, a number of siderophores, which are small, high-affinity iron chelating compounds secreted by microorganisms such as bacteria and fungi, were produced for utilization of restricted iron under iron-depleted condition. A M9 minimal liquid medium complemented with human transferrin (hTf)-iron complex turned completely off production of siderophores, but growth of Salmonella Typhimurium SL1344 maintained level similar to compare one complemented with iron (III) chloride (FeCl3). This means that human transferrin (hTf)-bound iron can utilize via directly interaction with Salmonella Typhimurium SL1344 without productions of siderophores. Through construction and analysis of negative mutant for utilization of human transferrin (hTf)-bound iron, we confirm that the bacterium can directly use human transferrin (hTf)-bound iron without extracellularly intermediated carriers such as siderophores.

• The KIPS Transactions:PartA
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• v.12A no.1 s.91
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• pp.53-58
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• 2005

The use of computers for control and monitoring of industrial process has expanded greatly in recent years. The computer used in such applications is shared between a certain number of time-critical control and monitor function and non time-critical batch processing job stream. Embedded systems encompass a variety of hardware and software components which perform specific function in host computer. Many embedded system must respond to external events under certain timing constraints. Failure to respond to certain events on time may either seriously degrade system performance or even result in a catastrophe. In the design of real-time embedded system, decisions made at the architectural design phase greatly affect the final implementation and performance of the system. Flexibility indicates how well a particular system architecture can tolerate with respect to satisfying real-time requirements. The degree of flexibility of real-time system architecture indicates the capability of the system to tolerate perturbations in timing related specifications. Given degree of flexibility, one may compare and rank different implementations. A system with a higher degree of flexibility is more desirable. Flexibility is also an important factor in the trade-off studies between cost and performance. In this paper, it is identified the need for flexibility function and shows that the existing real-time analysis result can be effective. This paper motivated the need for a flexibility for the efficient analysis of potential design candidates in the architectural design exploration or real time embedded system.

• Microbiology and Biotechnology Letters
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• v.32 no.3
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• pp.199-205
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• 2004

The nucleotide sequence of 8.6-kb EcoRI fragment containing sucrose phosphorylase gene isolated from Bifidobacterium longum SJ32 was determined. It was found that the fragment contained five open reading frames including the gene cluster for sucrose utilization such as a sucrose phosphorylase (ScrP), a sucrose transporter (ScrT), and a GalR-LacI-type transcriptional regulator (ScrR) identified by amino acid homology. Each gene showed over 94% amino acid homology among various B. longum strains. Genomic organization of the gene cluster is the same as those of other strains of B. longum but different from that of B. lactis. In spite of high homology of each gene among B. longum strains, the difference of flanking sequences of the gene cluster between strains SJ32 and NCC2705 insinuates the horizontal transfer of scrPTR between B. longum strains. The increase of sucrose phosphorylase activity in heterologous E. coli system by the co-expression of scrT with scrP against the single expression of scrP was measured. It seems to be the result of sucrose uptake increment by scrT in the host and is an indirect evidence that scrT is the gene for sucrose transport. The existence of multiple sucrose uptake systems in B. longum is supposed from the findings of several genes besides scrPTR involved in sucrose uptake in the genome of B. longum NCC2705.

• Food Science of Animal Resources
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• v.33 no.4
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• pp.522-530
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• 2013

The ability of probiotics to adhere to the intestinal epithelium likely plays an important role in their colonization of the gastrointestinal tract. Here, we performed high-throughput screening (HTS) for suitable characteristics of potential probiotic bacteria using attachment and colonization ability through a C. elegans surrogate in vivo model. A total of 100 strains of lactic acid bacteria (LAB) isolated from infant feces were subjected to the colonization assay using C. elegans intestine. Based on colonization ability, we showed that nine isolates have a high attachment ability during whole experimental periods (up to 168 h), compared to Lactobacillus rhamnosus strain GG as a control. Also, through the use of an in vitro cell attachment model, nine isolates revealed highly binding activity to the mucus layer. Next, the selected 9 isolates were assayed for their survival ability when exposed to acidic and bile conditions as well as cholesterol reduction and the utilization of prebiotic substrates. As a result, the isolated nine strains were determined to be highly resistant to acid and bile conditions. In addition, they have significant activity for the reduction of cholesterol and utilization of several prebiotic substrates as a carbon source. Finally, the selected nine strains were identified by either L. rhamnosus or L. plantarum (4 strains for L. rhamnosus and 5 strains for L. plantarum, respectively). Taken together, we propose that the direct colonization of probiotics using C. elegans may be applicable to the rapid screening of valuable probiotic strains in vivo.

• Journal of KIISE
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• v.44 no.9
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• pp.878-886
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• 2017

This paper discusses performance bottlenecks that may occur when executing high-performance computing MPI applications in the Intel's next generation many-core processor called Knights Landing(KNL), as well as effective resource allocation techniques to solve this problem. KNL is composed of a host processor to enable self-booting in addition to an existing accelerator consisting of a many-core processor, and it was released with a new type of on-package memory with improved bandwidth on top of existing DDR4 based memory. We empirically verified an improvement of the execution performance of multiple MPI applications and the overall system utilization ratio by studying a resource allocation method optimized for such new many-core processor architectures.

• Journal of KIISE
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• v.44 no.2
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• pp.124-131
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• 2017

The emerging next-generation manycore processors for high-performance computing are equipped with a high-bandwidth on-package memory along with the traditional host memory. The Multi-Channel DRAM (MCDRAM), for example, is the on-package memory of the Intel Xeon Phi Knights Landing (KNL) processor, and theoretically provides a four-times-higher bandwidth than the conventional DDR4 memory. In this paper, we suggest a mechanism to exploit MCDRAM for improving the performance of MPI intra-node communication. The experiment results show that the MPI intra-node communication performance can be improved by up to 272 % compared with the case where the DDR4 is utilized. Moreover, we analyze not only the performance impact of different MCDRAM-utilization mechanisms, but also that of core affinity for processes.

• BMB Reports
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• v.28 no.3
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• pp.243-248
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• 1995

Cholesteryl ester transfer protein (CETP), a hydrophobic glycoprotein promoting transfer of cholesteryl esters (CE) from high-density lipoproteins (HDL) to lower-density lipoproteins in the plasma, has been recognized a potent atherogenic factor during the development of coronary artery diseases. This study demonstrated a possible utilization of antisense RNA to inhibit expression of the CETP gene using vaccinia virus as an expression system. The CETP cDNA was inserted into a transfer vector (pSC11) in sense and antisense orientations and used to generate recombinant viruses. Recombinants containing sense or antisense orientations of the CETP cDNA were isolated by $TK^-$ selection and X-gal test. The inserted CETP cDNAs in the recombinants were identified by Southern blot analysis and allowed to transcribe in host cells (CV-1). Expressions of the exogenous CETP mRNA, extracted from the CV-1 cells coinfected with viruses containing sense and antisense DNAs, were monitored by Northern blot analysis using the CETP cDNA probe, by Western blot analysis using monoclonal antibody against the C-terminal active region of the CETP and by the CETP assay. Decreased expressions of the exogenous CETP cDNA were clearly evident in the Northern and Western blot analyses as the dose of antisense expression increased. In the CETP assay, the CETP activities decreased compared to the activity obtained from the cell extracts infected with sense construct only.

• Applied Biological Chemistry
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• v.30 no.4
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• pp.293-299
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• 1987

Bradyrhizobium japonicum spheroplasts were prepared by culturing cells in the presence of glycine, follwed by treatment with lysozyme. The cells were examined by electron microscopy during the formation of spheroplast. Then Ti plasmid from Agrobacterium tumefaciens 15955 was introduced into Bradyrhizobium japonicum by glycine-lysozyme induced spheroplast transformation. After cell wall regeneration, transformants were selected by the ability of utilization of octopine. Transformation were received at a frequency of $1{\times}10^{-7}$. The transformants obtained from spheroplast transformation harbored the introduced Ti plasmid, which was identified by agarose gel electrophoresis. Furthermore, the differences in their gene products were observed between the transformant and the recipient cell by two-dimensional polyacrylamide gel electrophoresis. The transformants which still possessed the same ability nodulate soybean (Glycine max.) as that of the original host strain, acquired the ability to induce tumor on Petunia hybrida like Agrobacterium, but formed the small crown galls in size compared to those of Agrobacterium tumefaciens.

• Journal of Korean Medicine for Obesity Research
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• v.9 no.1
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• pp.1-14
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• 2009

Complex microbial communities play an important role in the human health and co-evolved with human in the form of symbiosis. Many literatures provide new evidences that the increased prevalence of obesity cannot be attributed solely to changes in the human genome, nutritional habits, or reduction of physical activity in our daily lives. The intestinal flora was recently proposed as an environmental factor responsible for the control of body weight and energy metabolism. A number of studies suggest that the modulation of gut microbiota affects host metabolism and has an impact on energy storage and demonstrated a role for the gut microbiota in weight gain, fat increase, and insulin resistance. Variations in microbiota composition are found in obese humans and mice and the microbiota from an obese mouse confers an obese phenotype when transferred to an axenic mouse. As well, the gut microbial flora plays a role in converting nutrients into calories. Specific strategies for modifying gut microbiota may be a useful means to treat or prevent obesity. Dietary modulations of gut microbiota with a view to increasing bifidobacteria have demonstrated to reduce endotoxemia and improve metabolic diseases such as obesity. The fermentation of medicinal herbs is intended to exert a favorable influence on digestability, bioavailability and pharmacological activity of herbal extract. Therefore we also expect that the fermented herbal extracts may open up a new area to treat obesity through modulating gut microbiota.

• JSTS:Journal of Semiconductor Technology and Science
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• v.2 no.2
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• pp.132-140
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• 2002

This paper presents an ARM-based SOC bus transaction verification IP and the usage experiences in SOC designs. The verification IP is an AMBA AHB protocol checker, which captures legal AHB transactions in FSM-style signal sequence checking routines. This checker can be considered as a reusable verification IP since it does not change unless the bus protocol changes. Our AHB protocol checker is designed to be scalable to any number of AHB masters and reusable for various AMBA-based SOC designs. The keys to the scalability and the reusability are Object-Oriented Programming (OOP), virtual port, and bind operation. This paper describes how OOP, virtual port, and bind features are used to implement AHB protocol checker. Using the AHB protocol checker, an AHB simulation monitor is constructed. The monitor checks the legal bus arbitration and detects the first cycle of an AHB transaction. Then it calls AHB protocol checker to check the expected AHB signal sequences. We integrate the AHB bus monitor into Verilog simulation environment to replace time-consuming visual waveform inspection, and it allows us to find design bugs quickly. This paper also discusses AMBA AHB bus transaction coverage metrics and AHB transaction coverage analysis. Test programs for five AHB masters of an SOC, four channel DMAs and a host interface unit are executed and transaction coverage for DMA verification is collected during simulation. These coverage results can be used to determine the weak point of test programs in terms of the number of bus transactions occurred and guide to improve the quality of the test programs. Also, the coverage results can be used to obtain bus utilization statistics since the bus cycles occupied by each AHB master can be obtained.