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KORDI S&T : ·: : : 2011. 3 :
KORDI, in quest of the world’s best ocean science and technology!
CO2
A method of extracting biodiesel from microalgae / Do-Hyung Kang Trawl Fishing Gear / Sung Kim Photographing Method for Marine Organism / Sung Kim Active Emergency Control System / Hee-jin Kang Support system of tugboat based network / Yeon-Gyu Kim Capsizeing warning method for tugboat / Sun-Young Kim Auto Pilot System of Super / Myung-Soo Shin Vessel identification system / Ki-Yeol Seo Velocity measuring method / Chan-Su Yang Tow-fish lose prevention system / Hai-Soo Yoo Monitoring System for Pollution Protecting Boom / Moon jin Lee Underwater acoustic communication system / Jong-Won Park Master System for Underwater Manipulators / Bong-Huan Jun GNSS augmentation system / Deuk-Jae Cho Constant velocint joint / Sang-Bum Chi Vibration apparatus for VIV experiments / Jong-Su Choi
Kinetic resolution of GPH / Sung Gyun Kang Synoptic eddy feedback and Polar climate changes / Jong Seong Kug Snapping shrimp sound / Bong-Chae Kim A simple two-way coupling method / Sang Ho Kim Analysis of unstable vortical structure / Bu-Geun Paik Estimation of soil weathering degree / Myoung Hak Oh Ration Size Restriction on Compensatory Growth / Sung-Yong Oh Intertidal sediment characteristics / Joo-Hyung Ryu Infrasonic Noise Measurements / Seongwook Lee Synthetic analogs of indole-containing natural produests / Yeon Ju Lee Novel [NiFe]-Hydrogenases / Hyun Sook Lee Crystal structure of Lon protease / Sun-Shin Cha Protective effect against oxidative stress / Soo-Jin Heo Temporal trend, spatial distribution / Sang Hee Hong
Mechanism for formate-driven growth
I Excellence Article Review I
Formate-driven growth coupled with H2 production Yun Jae Kim I Hyun Sook Lee I Jung-Hyun Lee I Sung Gyun Kang
[ NATURE I VOL.467/16 September 2010 ]
Contents Articles
Patents
Biocatalytic resolution of glycidyl phenyl ether using a novel epoxide hydrolase from a marine bacterium, Maritimibacter alkaliphilus KCCM 42376
Role of synoptic eddy feedback on polar climate responses to the anthropogenic forcing
Snapping shrimp sound measured under laboratory conditions
Asimple two-way coupling method of BEM and VOF model for random wave calculations
Analysis of unstable vortical structure in a propeller wake affected by a simulated hull wake
Estimation of soil weathering degree using electrical resistivity
Effect of Ration Size Restriction on Compensatory Growth and Proximate Composition of Dark-banded Rockfish, Sebastes inermis
Quantitative estimation of intertidal sediment characteristics using remote sensing and GIS
Infrasonic Noise Measurements in Ocean Using Screened Hydrophones
Synthetic analogs of indole-containing natural products as inhibitors of sortase A and isocitrate lyase
Identification of a Novel Class of Membrane-Bound [NiFe]-Hydrogenases in Thermococcus onnurineus NA1 by In Silico Analysis
Crystal structure of Lon protease: Molecular architecture of gated entry to a sequestered degradation chamber
Protective effect of diphlorethohydroxycarmalol isolated from Ishige okamurae against high glucose-induced-oxidative stress in human umbilical vein endothelial cells
Temporal trend, spatial distribution, and terrestrial sources of PBDEs and PCBs in Masan Bay, Korea
A method of extracting triglyceride or fatty acid methyl esters from microalgal lipid of microalgae of heterokontophyta or haptophyta, and manufacturing biodiesel using it’s extractsf
Trawl fishing gear
Apparatus and method for photographing marine organism specimen
Active Emergency Control System Based on Real Time Location System and Sensor Network
Capsizing warning method for tug boat due to excessive tension
Support system of tugboat and method based network
Auto Pilot System of Super High-Speed Crafts
Vessel identification system interoperable with heterogenous wireless communication methods
Velocity measuring method of moving object using synthesized apperture radar
Two-fish lose prevention system
Monitoring system for position and deployed shape of pollution protecting boom, and it's application methodology
Underwater acoustic communication system and method thereof
A Master System for Workspace-Operated and Automatic control of Tele-Operated Underwater Manipulators
GNSS augmentation system
Vibration Apparatus
Patents
Biocatalytic resolution of glycidyl phenyl ether using a novel epoxide hydrolase from a marine bacterium, Maritimibacter alkaliphilus KCCM 42376
Role of synoptic eddy feedback on polar climate responses to the anthropogenic forcing
Snapping shrimp sound measured under laboratory conditions
Asimple two-way coupling method of BEM and VOF model for random wave calculations
Analysis of unstable vortical structure in a propeller wake affected by a simulated hull wake
Estimation of soil weathering degree using electrical resistivity
Effect of Ration Size Restriction on Compensatory Growth and Proximate Composition of Dark-banded Rockfish, Sebastes inermis
Quantitative estimation of intertidal sediment characteristics using remote sensing and GIS
Infrasonic Noise Measurements in Ocean Using Screened Hydrophones
Synthetic analogs of indole-containing natural products as inhibitors of sortase A and isocitrate lyase
Identification of a Novel Class of Membrane-Bound [NiFe]-Hydrogenases in Thermococcus onnurineus NA1 by In Silico Analysis
Crystal structure of Lon protease: Molecular architecture of gated entry to a sequestered degradation chamber
Protective effect of diphlorethohydroxycarmalol isolated from Ishige okamurae against high glucose-induced-oxidative stress in human umbilical vein endothelial cells
Temporal trend, spatial distribution, and terrestrial sources of PBDEs and PCBs in Masan Bay, Korea
A method of extracting triglyceride or fatty acid methyl esters from microalgal lipid of microalgae of heterokontophyta or haptophyta, and manufacturing biodiesel using it’s extractsf
Trawl fishing gear
Apparatus and method for photographing marine organism specimen
Active Emergency Control System Based on Real Time Location System and Sensor Network
Capsizing warning method for tug boat due to excessive tension
Support system of tugboat and method based network
Auto Pilot System of Super High-Speed Crafts
Vessel identification system interoperable with heterogenous wireless communication methods
Velocity measuring method of moving object using synthesized apperture radar
Two-fish lose prevention system
Monitoring system for position and deployed shape of pollution protecting boom, and it's application methodology
Underwater acoustic communication system and method thereof
A Master System for Workspace-Operated and Automatic control of Tele-Operated Underwater Manipulators
GNSS augmentation system
Vibration Apparatus
Yun Jae Kim Marine Biotechnology Research Center
[email protected]
bicarbonate and H2 (HCOO- + H2O HCO3 - + H2, Go = +1.3
kJ/mol) has not been considered energetic enough to support
growth of microorganisms. Recently, experimental evidence
for growth on formate was reported for syntrophic
communities of Moorella sp. strain AMP and a hydrogen-
consuming Methanothermobacter species and of
Desulfovibrio sp. strain G11 and Methanobrevibacter
arboriphilus AZ1. The basis of the sustainable growth of the
formate-utilizers is explained by H2 consumption by the
methanogens, which lowers the H2 partial pressure, thus
making the pathway exergonic2. However, it has never been
shown before that a single strain can grow on formate by
catalyzing its conversion to bicarbonate and H2. Here we
report that several hyperthermophilic archaea belonging to
the Thermococcus genus are capable of formate-oxidizing,
H2-producing growth. The actual G values for the formate
metabolism were calculated to range between -8 and -20
kJ/mol under the physiological conditions where
Thermococcus onnurineus NA1 were grown. Furthermore,
we detected ATP synthesis in the presence of formate as a
sole energy source. Gene expression profiling and disruption
identified the gene cluster encoding formate hydrogen lyase,
cation/proton antiporter and formate transporter, which were
responsible for growth of T. onnurineus NA1 on formate. This
work represents the first demonstration of formate-driven
growth by a single microorganism with protons as the
electron acceptor and demonstrates the biochemical basis of
this ability.
1Korea Ocean Research & Development Institute, PO Box 29, Ansan 425-600, Korea. 2Department of Marine Biotechnology, University of Science and Technology, Daejeon 305-333, Korea. 3Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan. 4Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, 117312, Moscow, Russia. *These authors contributed equally to this work.
Formate-dependent H2 production is dependent upon
formate hydrogen lyase systems composed of the
formate dehydrogenase and membrane-associated
litoralis formate is oxidized to CO2 by formate
dehydrogenase (HCOO- → CO2 + H+ + 2e-) and protons are
reduced to H2 by hydrogenase (2H+ + 2e- → H2) in response to
the accumulation of formate during fermentation to
maintain cytoplasmic pH4-7. The formate hydrogen lyase
systems in Methanococcus maripaludis and
Methanobacterium formicicum consisting of formate
dehydrogenase and F420-hydrogenase provide reductant to
methanogenesis and may play a role in maintaining the
redox balance during formate-growth8-11. However, it has
never been shown that formate oxidation with H2 production
can be coupled to ATP generation leading to growth.
We were concerned that Thermococcus onnurineus
NA1 genome contains many copies of genes coding for the
formate dehydrogenases and hydrogenases12, which might
form formate oxidizing, hydrogen-evolving formate hydrogen
lyases. Three copies of formate dehydrogenase genes
(fdhA), TON_0281, TON_1563 and TON_0539, are located in
three separate gene clusters and possess 48-61% amino
acid sequence identity with each other. Among eight copies
of hydrogenase gene clusters, three clusters were found
proximate to the formate dehydrogenase genes (Fig. 1). The
functional annotation revealed that the two large gene
clusters (fdh1-mfh1-mnh1, fdh2-mfh2-mnh2) include three
modular subclusters encoding for formate dehydrogenases,
multimeric membrane-bound hydrogenases and
sulfI) lacks one subcluster and the hydrogenase genes code
for a cytoplasmic hydrogenase.
using formate, we performed anaerobic batch culturing in
media containing formate at 80°C and investigated the cell
growth and H2 production. As shown in Fig. 2a, the strain
was able to grow efficiently by oxidation of formate as well
as to produce H2 and CO2 (mostly in the form of bicarbonate).
No growth or H2 production was detected in the control
culture lacking formate. Under these conditions, the actual
Gibbs energy values of the conversion of formate to H2 and
bicarbonate ranged between -8 and -20 kJ/mol (Fig. 2b).
Therefore, formate-dependent metabolism could yield
energy to support cell growth of T. onnurineus NA1,
although they would only allow the production of less than 1
mol ATP (ADP + Pi → ATP + H2O; G = +70 kJ/mol)13,14.
KORDI S&T No. 3 March 2011
NatureExcellence Article Review
2010 Macmillan Publishers Limited. All rights reserved 2010 Macmillan Publishers Limited. All rights reserved
LETTERS
[email protected]
[email protected]
[email protected]
[Figure 1] Gene organization of formate dehydrogenase gene clusters from
T. onnurineus NA1.
Yun Jae Kim Marine Biotechnology Research Center
[email protected]
bicarbonate and H2 (HCOO- + H2O HCO3 - + H2, Go = +1.3
kJ/mol) has not been considered energetic enough to support
growth of microorganisms. Recently, experimental evidence
for growth on formate was reported for syntrophic
communities of Moorella sp. strain AMP and a hydrogen-
consuming Methanothermobacter species and of
Desulfovibrio sp. strain G11 and Methanobrevibacter
arboriphilus AZ1. The basis of the sustainable growth of the
formate-utilizers is explained by H2 consumption by the
methanogens, which lowers the H2 partial pressure, thus
making the pathway exergonic2. However, it has never been
shown before that a single strain can grow on formate by
catalyzing its conversion to bicarbonate and H2. Here we
report that several hyperthermophilic archaea belonging to
the Thermococcus genus are capable of formate-oxidizing,
H2-producing growth. The actual G values for the formate
metabolism were calculated to range between -8 and -20
kJ/mol under the physiological conditions where
Thermococcus onnurineus NA1 were grown. Furthermore,
we detected ATP synthesis in the presence of formate as a
sole energy source. Gene expression profiling and disruption
identified the gene cluster encoding formate hydrogen lyase,
cation/proton antiporter and formate transporter, which were
responsible for growth of T. onnurineus NA1 on formate. This
work represents the first demonstration of formate-driven
growth by a single microorganism with protons as the
electron acceptor and demonstrates the biochemical basis of
this ability.
1Korea Ocean Research & Development Institute, PO Box 29, Ansan 425-600, Korea. 2Department of Marine Biotechnology, University of Science and Technology, Daejeon 305-333, Korea. 3Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan. 4Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, 117312, Moscow, Russia. *These authors contributed equally to this work.
Formate-dependent H2 production is dependent upon
formate hydrogen lyase systems composed of the
formate dehydrogenase and membrane-associated
litoralis formate is oxidized to CO2 by formate
dehydrogenase (HCOO- → CO2 + H+ + 2e-) and protons are
reduced to H2 by hydrogenase (2H+ + 2e- → H2) in response to
the accumulation of formate during fermentation to
maintain cytoplasmic pH4-7. The formate hydrogen lyase
systems in Methanococcus maripaludis and
Methanobacterium formicicum consisting of formate
dehydrogenase and F420-hydrogenase provide reductant to
methanogenesis and may play a role in maintaining the
redox balance during formate-growth8-11. However, it has
never been shown that formate oxidation with H2 production
can be coupled to ATP generation leading to growth.
We were concerned that Thermococcus onnurineus
NA1 genome contains many copies of genes coding for the
formate dehydrogenases and hydrogenases12, which might
form formate oxidizing, hydrogen-evolving formate hydrogen
lyases. Three copies of formate dehydrogenase genes
(fdhA), TON_0281, TON_1563 and TON_0539, are located in
three separate gene clusters and possess 48-61% amino
acid sequence identity with each other. Among eight copies
of hydrogenase gene clusters, three clusters were found
proximate to the formate dehydrogenase genes (Fig. 1). The
functional annotation revealed that the two large gene
clusters (fdh1-mfh1-mnh1, fdh2-mfh2-mnh2) include three
modular subclusters encoding for formate dehydrogenases,
multimeric membrane-bound hydrogenases and
sulfI) lacks one subcluster and the hydrogenase genes code
for a cytoplasmic hydrogenase.
using formate, we performed anaerobic batch culturing in
media containing formate at 80°C and investigated the cell
growth and H2 production. As shown in Fig. 2a, the strain
was able to grow efficiently by oxidation of formate as well
as to produce H2 and CO2 (mostly in the form of bicarbonate).
No growth or H2 production was detected in the control
culture lacking formate. Under these conditions, the actual
Gibbs energy values of the conversion of formate to H2 and
bicarbonate ranged between -8 and -20 kJ/mol (Fig. 2b).
Therefore, formate-dependent metabolism could yield
energy to support cell growth of T. onnurineus NA1,
although they would only allow the production of less than 1
mol ATP (ADP + Pi → ATP + H2O; G = +70 kJ/mol)13,14.
NatureExcellence Article Review
LETTERS
[email protected]
[email protected]
[email protected]
[Figure 1] Gene organization of formate dehydrogenase gene clusters from
T. onnurineus NA1.
were monitored upon the addition of formate to the cell
suspensions of T. onnurineus NA1 in the absence of any other
exogenous energy source. Indeed, ATP was newly
synthesized upon the addition of formate to the cell
suspensions (Fig. 3). No ATP production was detected in a
control lacking formate (data not shown). Each mole of
formate consumption led to the production of one mole of
CO2 and one mole of H2. The production of other gases
formed during well established anaerobic respirations, such
as CH4, CO or H2S, was not detected. Thus, the detection of
ATP biosynthesis in response to the addition of formate
provided strong evidence that formate-dependent proton
reduction could conserve energy in T. onnurineus NA1.
To identify the gene cluster to which the growth on
formate is attributed, gene expression profiling of three
formate dehydrogenase gene clusters of T. onnurineus NA1
was performed using a DNA microarray. Relative expression
ratios were derived by comparing mRNA abundance levels in
cells grown on medium containing formate alone relative to
those in cells grown on sulfur-containing medium. The
largest changes were found in the fdh2-mfh2-mnh2 gene
cluster, with 72% (13/18) of the genes up-regulated more
than two-fold (Fig. 4). On the other hand, the fdh1-mfh1-
mnh1 and fdh3-sulfI gene clusters were only slightly down-
and up-regulated, respectively.
dehydrogenase, a formate transporter can be a prerequisite
for growth on formate. In T. onnurineus NA1, three sets of
formate dehydrogenase proteins were predicted to be
localized in the cytoplasm by using PSORTb and TMHMM
online software15,16. We searched, therefore, the genome
sequence of T. onnurineus NA1 for formate transporter
genes and found two separate genes, TON_1573 and
TON_0538, in fdh2-mfh2-mnh2 and fdh3-sulfI gene clusters,
respectively; TON_1573 and TON_0538 were 56% identical.
The transcriptomic analysis showed that transcription of
TON_1573 was strongly up-regulated by 4-fold when formate
was supplied while TON_0538 was slightly down-regulated
1.3-fold, indicating that only TON_1573 contributes to growth
on formate.
cluster for growth on formate was assessed by quantitative
RT-PCR and gene disruption of the large subunits of the
hydrogenases, mfh1, mfh2 and sulfI (data not shown),
suggesting that the hydrogenase encoded by mfh2 is solely
responsible for growth on exogenous formate.
Based on the gene organization of the fdh2-mfh2-mnh2
gene cluster, we propose a mechanism for the coupling of
formate oxidation to energy conservation in T. onnurineus
NA1 (Fig. 5). We hypothesize that a formate transporter
imports formate into the cytoplasm, and the formate
hydrogen lyase complex (composed of formate
dehydrogenase (Fdh2) and hydrogenase (Mfh2)) mediates
electrogenic H+-translocation during formate oxidation. The
putative cation/proton antiporter may be involved in the
transformation of the proton gradient to a sodium gradient,
which is utilized for ATP synthesis. An understanding of the
mechanism involved in the coupling of formate oxidation to
the energy conservation will have to await the determination
of the roles of the components in the gene cluster17-19.
In summary, this work presents the first evidence for the
ability of a single microorganism alone to grow on formate
along with H2 evolution and ATP generation via a formate
dehydrogenase and an energy-conserving hydrogenase. As
such, it represents one of the simplest anaerobic respirations
described so far.
NatureNATURE | VOL. 467 | 16 September 2010NATURE | VOL. 467 | 16 September 2010Nature
[Figure 6] Proposed mechanism of coupling of formate oxidation to CO2 and H2 with
the synthesis of ATP in T. onnurineus NA1.
[Figure 2] Growth of T. onnurineus NA1 on formate. a,
T. onnurineus NA1 was inoculated into minimal medium containing 1 g/l of yeast
extract in the presence (closed symbols) or absence (open symbols) of 10 g/l
formate. Changes in cell mass (squares), formate (circles), H2 (diamonds) and CO2
(triangles) were determined at the times indicated (mean ± s.d.; n=2). b, Actual
Gibbs energy values for formate degradation to H2 and bicarbonate at 80°C.
[Figure 3] ATP synthesis from cell suspensions. ATP content (squares), formate
(circles), H2 (diamonds) and CO2 (triangles) were analyzed by the addition of 150
mM sodium formate using cell suspensions (1 mg protein) at the times indicated
mean ± s.d.; n=3).
[Figure 4] Gene expression analysis in T. onnurineus NA1.
Transcript levels of the fdh1-mfh1-mnh1, fdh2-mfh2-mnh2 and fdh3-sulfI gene
clusters in cells cultured in formate-containing medium were compared with those
from cells cultured in sulfur-containing medium. The colors of genes represent the
fold-change in expression. Asterisks indicate the target genes for RT-PCR and gene
disruption (see Fig. 5).
[Figure 5] Quantitative RT-PCR analysis and gene disruption in T. onnurineus NA1.
a, Quantitative RT-PCR analysis of the large subunits of the mfh1 (TON_0276), mfh2
(TON_1569) and sulfI (TON_0534) hydrogenases in sulfur- (1) and formate-
containing (2) medium. cha, a chaperonin-encoding gene from T. onnurineus NA1,
was used as a control to normalize expression levels. b, Growth and H2 production
of wild-type and mutant strains on formate-containing medium (mean ± s.d.; n=2).
Wild-type (squares), Δƒmfh1 (circles), Δƒmfh2 (diamonds) and ΔƒsulfI (triangles).
To test this hypothesis, H2 production and ATP content
were monitored upon the addition of formate to the cell
suspensions of T. onnurineus NA1 in the absence of any other
exogenous energy source. Indeed, ATP was newly
synthesized upon the addition of formate to the cell
suspensions (Fig. 3). No ATP production was detected in a
control lacking formate (data not shown). Each mole of
formate consumption led to the production of one mole of
CO2 and one mole of H2. The production of other gases
formed during well established anaerobic respirations, such
as CH4, CO or H2S, was not detected. Thus, the detection of
ATP biosynthesis in response to the addition of formate
provided strong evidence that formate-dependent proton
reduction could conserve energy in T. onnurineus NA1.
To identify the gene cluster to which the growth on
formate is attributed, gene expression profiling of three
formate dehydrogenase gene clusters of T. onnurineus NA1
was performed using a DNA microarray. Relative expression
ratios were derived by comparing mRNA abundance levels in
cells grown on medium containing formate alone relative to
those in cells grown on sulfur-containing medium. The
largest changes were found in the fdh2-mfh2-mnh2 gene
cluster, with 72% (13/18) of the genes up-regulated more
than two-fold (Fig. 4). On the other hand, the fdh1-mfh1-
mnh1 and fdh3-sulfI gene clusters were only slightly down-
and up-regulated, respectively.
dehydrogenase, a formate transporter can be a prerequisite
for growth on formate. In T. onnurineus NA1, three sets of
formate dehydrogenase proteins were predicted to be
localized in the cytoplasm by using PSORTb and TMHMM
online software15,16. We searched, therefore, the genome
sequence of T. onnurineus NA1 for formate transporter
genes and found two separate genes, TON_1573 and
TON_0538, in fdh2-mfh2-mnh2 and fdh3-sulfI gene clusters,
respectively; TON_1573 and TON_0538 were 56% identical.
The transcriptomic analysis showed that transcription of
TON_1573 was strongly up-regulated by 4-fold when formate
was supplied while TON_0538 was slightly down-regulated
1.3-fold, indicating that only TON_1573 contributes to growth
on formate.
cluster for growth on formate was assessed by quantitative
RT-PCR and gene disruption of the large subunits of the
hydrogenases, mfh1, mfh2 and sulfI (data not shown),
suggesting that the hydrogenase encoded by mfh2 is solely
responsible for growth on exogenous formate.
Based on the gene organization of the fdh2-mfh2-mnh2
gene cluster, we propose a mechanism for the coupling of
formate oxidation to energy conservation in T. onnurineus
NA1 (Fig. 5). We hypothesize that a formate transporter
imports formate into the cytoplasm, and the formate
hydrogen lyase complex (composed of formate
dehydrogenase (Fdh2) and hydrogenase (Mfh2)) mediates
electrogenic H+-translocation during formate oxidation. The
putative cation/proton antiporter may be involved in the
transformation of the proton gradient to a sodium gradient,
which is utilized for ATP synthesis. An understanding of the
mechanism involved in the coupling of formate oxidation to
the energy conservation will have to await the determination
of the roles of the components in the gene cluster17-19.
In summary, this work presents the first evidence for the
ability of a single microorganism alone to grow on formate
along with H2 evolution and ATP generation via a formate
dehydrogenase and an energy-conserving hydrogenase. As
such, it represents one of the simplest anaerobic respirations
described so far.
[Figure 6] Proposed mechanism of coupling of formate oxidation to CO2 and H2 with
the synthesis of ATP in T. onnurineus NA1.
[Figure 2] Growth of T. onnurineus NA1 on formate. a,
T. onnurineus NA1 was inoculated into minimal medium containing 1 g/l of yeast
extract in the presence (closed symbols) or absence (open symbols) of 10 g/l
formate. Changes in cell mass (squares), formate (circles), H2 (diamonds) and CO2
(triangles) were determined at the times indicated (mean ± s.d.; n=2). b, Actual
Gibbs energy values for formate degradation to H2 and bicarbonate at 80°C.
[Figure 3] ATP synthesis from cell suspensions. ATP content (squares), formate
(circles), H2 (diamonds) and CO2 (triangles) were analyzed by the addition of 150
mM sodium formate using cell suspensions (1 mg protein) at the times indicated
mean ± s.d.; n=3).
[Figure 4] Gene expression analysis in T. onnurineus NA1.
Transcript levels of the fdh1-mfh1-mnh1, fdh2-mfh2-mnh2 and fdh3-sulfI gene
clusters in cells cultured in formate-containing medium were compared with those
from cells cultured in sulfur-containing medium. The colors of genes represent the
fold-change in expression. Asterisks indicate the target genes for RT-PCR and gene
disruption (see Fig. 5).
[Figure 5] Quantitative RT-PCR analysis and gene disruption in T. onnurineus NA1.
a, Quantitative RT-PCR analysis of the large subunits of the mfh1 (TON_0276), mfh2
(TON_1569) and sulfI (TON_0534) hydrogenases in sulfur- (1) and formate-
containing (2) medium. cha, a chaperonin-encoding gene from T. onnurineus NA1,
was used as a control to normalize expression levels. b, Growth and H2 production
of wild-type and mutant strains on formate-containing medium (mean ± s.d.; n=2).
Wild-type (squares), Δƒmfh1 (circles), Δƒmfh2 (diamonds) and ΔƒsulfI (triangles).
References
1. Dolfing, J., Jiang, B., Henstra, A. M., Stams, A. J. M. & Plugge, C.
M. Appl. Environ. Microbiol. 74, 6126-6131 (2008).
2. Stams, A. J. M. & Plugge, C. M. Nat. Rev. Microbiol. 7, 568-577
(2009).
3. Andrews, S. C., Berks, B. C., McClay, J., Ambler, A., Quail, M. A.,
Golby, P. & Guest, J. R. Microbiology 143, 3633?3647 (1997).
4. Bohm, R., Sauter, M. & Bock, A. Mol. Microbiol. 4, 231-243
(1990).
5. Sauter, M., Bohm, R. & Bock, A. Mol. Microbiol. 6, 1523-1532
(1992).
Trchounian, A. FEBS Lett. 516, 172-178 (2002).
7. Takacs, M., Toth, A., Bogos, B., Varga, A., Rakhely, G. & Kovacs,
K. L. BMC Microbiol. 8, 88 (2008).
8. Schauer, N. L. & Ferry, J. G. J. Bacteriol. 142, 800-807 (1980).
9. Baron, S. F. & Ferry, J. G. J. Bacteriol. 171, 3854-3859 (1989).
Methods Summary T. onnurineus NA1 was cultured in the modified
medium 120 including 35 g/l NaCl, 0.5 or 1.0 g/l yeast extract and 10 g/l sodium formate or 10 g/l sulfur at 80°C under anaerobic condition. Cell suspensions were prepared by washing cells with an anaerobic buffer containing 20 mM imidazole, 600 mM NaCl, 30 mM MgCl2, 10 mM KCl, 5 mM dithiothreitol, pH 6.9 and resuspending them in the same buffer at cell densities of 1 mg protein/2.5 ml. Gases in the headspace of serum bottles were measured with gas chromatography and formate was detected with liquid chromatography. The amount of bicarbonates in the liquid was determined by measuring CO2 formed by acidifying the cell suspensions. The ATP content of the cells was measured using the luciferin/luciferase assay kit. Thermodynamic calculations were done using the Nernst equation to correct Gibbs energy values (G) for the actual temperature and the actual concentrations of reactants and products. The
standard Gibbs energy value (G o) was corrected to a temperature of 80oC (G o= -2.6 kJ/mol at 80oC) by linear interpolation from tabulated values for 70 and 85oC21. Activities rather than concentrations of reactants and products were considered using the Debye-Huckel equation and they gave a negligible effect on Gibbs energy values (less than 0.27 kJ/mol).
A custom microarray was manufactured by Roche Nimblegen (Madison, WI). Arrays were scanned using a GenePix 4000B scanner (Molecular Devices, Union City, CA), and the data were extracted using NimbleScan 2.4 software (Roche NimbleGen, Madison, WI). For quantitative RT-PCR, cDNAs were synthesized from 350 ng of total RNA using SuperScript II reverse transcriptase and PCR reactions were performed with gene-specific primers using rTaq DNA polymerase (Takara, Otsu, Japan). Gene disruption was performed according to the methods applied to a hyperthermophilic archaeon Thermococcus kodakaraensis KOD122.
10. Wood, G. E., Haydock, A. K. & Leigh, J. A. J. Bacteriol. 185, 2548-
2554 (2003).
11. Lupa, B., Hendrickson, E. L., Leigh, J. A. & Whitman, W. B. Appl. Environ. Microbiol. 74, 6584-6590 (2008).
12. Lee, H. S., Kang, S. G., Bae, S. S., Lim, J. K., Cho, Y., Kim, Y. J.,
Jeon, J. H., Cha, S.-S., Kwon, K. K., Kim, H.-T., Park, C.-J., Lee,
H.-W., Kim, S. I., Chun, J., Colwell, R. R., Kim, S.-J. & Lee, J.-H.
J. Bacteriol. 190, 7491-7499 (2008).
13. Thauer, R. K. & Morris, J. G. in Prokaryotes and Eukaryotes, The Microbe, Part II (eds Kelly, D. P. & Carr, N. G.) 123-168
(Cambridge University Press, Cambridge, 1984).
14. Schink, B. Microbiol. Mol. Biol. Rev. 61, 262-280 (1997).
15. Moller, S., Croning, M. D. R. & Apweiler, R. Bioinformatics 17,
646-653 (2001).
16. Gardy, J. L., Laird, M. R., Chen, F., Rey, S., Walsh, C. J., Ester, M.
& Brinkman, F. S. L. Bioinformatics 21, 617-623 (2005).
17. Sapra, R., Verhagen, M. F. & Adams, M. W. Bacteriol. 182, 3423-
3428 (2000).
18. Hedderich, R. & Forzi, L. J. Mol. Microbiol. Biotechnol. 10, 92-
104 (2005).
19. Jenney, F. E. Jr. & Adams, M. W. Ann. N. Y. Acad. Sci. 1125, 252-
266 (2008).
20. Sokolova, T. G., Jeanthon, C., Kostrikina, N. A., Chernyh, N. A.,
Lebedinsky, A. V., Stackebrandt, E., & Bonch-Osmolovskaya, E.
A. Extremophiles 8, 317-323 (2004).
21. Amend, J. P. & Shock, E. L. FEMS Microbiol. Rev. 25, 175-243
(2001).
22. Matsumi, R., Manabe, K., Fukui, T., Atomi, H. & Imanaka, T. J. Bacteriol. 189, 2683-2691 (2007).
References
1. Dolfing, J., Jiang, B., Henstra, A. M., Stams, A. J. M. & Plugge, C.
M. Appl. Environ. Microbiol. 74, 6126-6131 (2008).
2. Stams, A. J. M. & Plugge, C. M. Nat. Rev. Microbiol. 7, 568-577
(2009).
3. Andrews, S. C., Berks, B. C., McClay, J., Ambler, A., Quail, M. A.,
Golby, P. & Guest, J. R. Microbiology 143, 3633?3647 (1997).
4. Bohm, R., Sauter, M. & Bock, A. Mol. Microbiol. 4, 231-243
(1990).
5. Sauter, M., Bohm, R. & Bock, A. Mol. Microbiol. 6, 1523-1532
(1992).
Trchounian, A. FEBS Lett. 516, 172-178 (2002).
7. Takacs, M., Toth, A., Bogos, B., Varga, A., Rakhely, G. & Kovacs,
K. L. BMC Microbiol. 8, 88 (2008).
8. Schauer, N. L. & Ferry, J. G. J. Bacteriol. 142, 800-807 (1980).
9. Baron, S. F. & Ferry, J. G. J. Bacteriol. 171, 3854-3859 (1989).
Methods Summary T. onnurineus NA1 was cultured in the modified
medium 120 including 35 g/l NaCl, 0.5 or 1.0 g/l yeast extract and 10 g/l sodium formate or 10 g/l sulfur at 80°C under anaerobic condition. Cell suspensions were prepared by washing cells with an anaerobic buffer containing 20 mM imidazole, 600 mM NaCl, 30 mM MgCl2, 10 mM KCl, 5 mM dithiothreitol, pH 6.9 and resuspending them in the same buffer at cell densities of 1 mg protein/2.5 ml. Gases in the headspace of serum bottles were measured with gas chromatography and formate was detected with liquid chromatography. The amount of bicarbonates in the liquid was determined by measuring CO2 formed by acidifying the cell suspensions. The ATP content of the cells was measured using the luciferin/luciferase assay kit. Thermodynamic calculations were done using the Nernst equation to correct Gibbs energy values (G) for the actual temperature and the actual concentrations of reactants and products. The
standard Gibbs energy value (G o) was corrected to a temperature of 80oC (G o= -2.6 kJ/mol at 80oC) by linear interpolation from tabulated values for 70 and 85oC21. Activities rather than concentrations of reactants and products were considered using the Debye-Huckel equation and they gave a negligible effect on Gibbs energy values (less than 0.27 kJ/mol).
A custom microarray was manufactured by Roche Nimblegen (Madison, WI). Arrays were scanned using a GenePix 4000B scanner (Molecular Devices, Union City, CA), and the data were extracted using NimbleScan 2.4 software (Roche NimbleGen, Madison, WI). For quantitative RT-PCR, cDNAs were synthesized from 350 ng of total RNA using SuperScript II reverse transcriptase and PCR reactions were performed with gene-specific primers using rTaq DNA polymerase (Takara, Otsu, Japan). Gene disruption was performed according to the methods applied to a hyperthermophilic archaeon Thermococcus kodakaraensis KOD122.
10. Wood, G. E., Haydock, A. K. & Leigh, J. A. J. Bacteriol. 185, 2548-
2554 (2003).
11. Lupa, B., Hendrickson, E. L., Leigh, J. A. & Whitman, W. B. Appl. Environ. Microbiol. 74, 6584-6590 (2008).
12. Lee, H. S., Kang, S. G., Bae, S. S., Lim, J. K., Cho, Y., Kim, Y. J.,
Jeon, J. H., Cha, S.-S., Kwon, K. K., Kim, H.-T., Park, C.-J., Lee,
H.-W., Kim, S. I., Chun, J., Colwell, R. R., Kim, S.-J. & Lee, J.-H.
J. Bacteriol. 190, 7491-7499 (2008).
13. Thauer, R. K. & Morris, J. G. in Prokaryotes and Eukaryotes, The Microbe, Part II (eds Kelly, D. P. & Carr, N. G.) 123-168
(Cambridge University Press, Cambridge, 1984).
14. Schink, B. Microbiol. Mol. Biol. Rev. 61, 262-280 (1997).
15. Moller, S., Croning, M. D. R. & Apweiler, R. Bioinformatics 17,
646-653 (2001).
16. Gardy, J. L., Laird, M. R., Chen, F., Rey, S., Walsh, C. J., Ester, M.
& Brinkman, F. S. L. Bioinformatics 21, 617-623 (2005).
17. Sapra, R., Verhagen, M. F. & Adams, M. W. Bacteriol. 182, 3423-
3428 (2000).
18. Hedderich, R. & Forzi, L. J. Mol. Microbiol. Biotechnol. 10, 92-
104 (2005).
19. Jenney, F. E. Jr. & Adams, M. W. Ann. N. Y. Acad. Sci. 1125, 252-
266 (2008).
20. Sokolova, T. G., Jeanthon, C., Kostrikina, N. A., Chernyh, N. A.,
Lebedinsky, A. V., Stackebrandt, E., & Bonch-Osmolovskaya, E.
A. Extremophiles 8, 317-323 (2004).
21. Amend, J. P. & Shock, E. L. FEMS Microbiol. Rev. 25, 175-243
(2001).
22. Matsumi, R., Manabe, K., Fukui, T., Atomi, H. & Imanaka, T. J. Bacteriol. 189, 2683-2691 (2007).
Kinetic resolution of GPH / Sung Gyun Kang
Synoptic eddy feedback and Polar climate changes / Jong Seong Kug
Snapping shrimp sound / Bong-Chae Kim
A simple two-way coupling method / Sang Ho Kim
Analysis of unstable vortical structure / Bu-Geun Paik
Estimation of soil weathering degree / Myoung Hak Oh
Ration Size Restriction on Compensatory Growth / Sung-Yong Oh
Intertidal sediment characteristics / Joo-Hyung Ryu
Infrasonic Noise Measurements / Seongwook Lee
Synthetic analogs of indole-containing natural produests / Yeon Ju Lee
Novel [NiFe]-Hydrogenases / Hyun Sook Lee
Crystal structure of Lon protease / Sun-Shin Cha
Protective effect against oxidative stress / Soo-Jin Heo
Temporal trend, spatial distribution / Sang Hee Hong
Articles
Synoptic eddy feedback and Polar climate changes / Jong Seong Kug
Snapping shrimp sound / Bong-Chae Kim
A simple two-way coupling method / Sang Ho Kim
Analysis of unstable vortical structure / Bu-Geun Paik
Estimation of soil weathering degree / Myoung Hak Oh
Ration Size Restriction on Compensatory Growth / Sung-Yong Oh
Intertidal sediment characteristics / Joo-Hyung Ryu
Infrasonic Noise Measurements / Seongwook Lee
Synthetic analogs of indole-containing natural produests / Yeon Ju Lee
Novel [NiFe]-Hydrogenases / Hyun Sook Lee
Crystal structure of Lon protease / Sun-Shin Cha
Protective effect against oxidative stress / Soo-Jin Heo
Temporal trend, spatial distribution / Sang Hee Hong
Articles
As a continuous effort of developing highly enantioselective epoxide hydrolase from marine
microorganisms, it was found that Rhodobacterales bacterium HTCC2654 was highly enantioselective
toward racemic Glycidyl Phenyl Ether (GPE). An Open Reading Frame (ORF) encoding a putative Epoxide
Hydrolase (EHase) was cloned from the genome of R. bacterium HTCC2654, followed by expression and
purification in Escherichiacoli. The purified EHase (REH) hydrolyzed (S)-GPE preferentially over (R)-GPE.
Enantiopure (R)-GPE from kinetic resolution of 29.2 mM racemic GPE using the purified REH could be
obtained with enantiopurity of more than 99.9% enantiomeric excess (ee) and 38.4% yield (theoretical, 50%)
within 20 min (enantiomeric ratio (E-value): 38.4). The enantioselective activity of REH toward GPE was also
confirmed by the analysis of the vicinal diol, 3-phenoxy-1,2-propanediol. To our knowledge, this study
demonstrates the highest enantioselective resolution of racemic GPE using a purified biocatalyst among the
known native EHases.
12 | KORDI S&T
iocatalytic resolution of glycidyl phenyl ether using a novel epoxide hydrolase from a marine bacterium, Maritimibacter alkaliphilus KCCM 42376
Articles
[email protected]
Amplified polar warming and moistening under global warming are critical issues for the climate
changes. The authors find that a poleward shift of the westerly jet stream and associated synoptic eddy
feedback play a critical role in enhancing polar warming and moistening. Namely, the mean circulation
changes due to anthropogenic forcing lead to the changes in storm feedbacks, which reinforce again
climate responses, particularly the polar responses such as the enhanced polar warming and moistening. It
is demonstrated here that the storm feedback can be explained by a simple rule based on the mean
circulation change. This rule can be used for understanding other regional climate responses to the
anthropogenic forcing.
ole of synoptic eddy feedback on polar climate responses to the anthropogenic forcing
Jong Seong Kug Climate Change & Coastal Disaster Research Department
[email protected]
Articles
[Figure 1] The schematic representation of enantioselective hydrolysis of racemic GPE.
[Figure 2] Kinetic resolution of racemic GPE by the purified REH. The changes of (A) racemic GPE and (B) 3-phenoxy-1,2- propanediol.
[Table 1] The comparison of kinetic resolution of EHases and the purified REH toward GPE.
a Wet cell weight b No information. a Dry cell weight. b Calculated with an ee of 99.99%.
B R
NATURE | VOL. 467 | 16 September 2010 GEOPHYSICAL RESEARCH LETTERS, VOL. 37, 2010
Aspergillus niger
Agrobacterium radiobacter
(mM) Temp.
As a continuous effort of developing highly enantioselective epoxide hydrolase from marine
microorganisms, it was found that Rhodobacterales bacterium HTCC2654 was highly enantioselective
toward racemic Glycidyl Phenyl Ether (GPE). An Open Reading Frame (ORF) encoding a putative Epoxide
Hydrolase (EHase) was cloned from the genome of R. bacterium HTCC2654, followed by expression and
purification in Escherichiacoli. The purified EHase (REH) hydrolyzed (S)-GPE preferentially over (R)-GPE.
Enantiopure (R)-GPE from kinetic resolution of 29.2 mM racemic GPE using the purified REH could be
obtained with enantiopurity of more than 99.9% enantiomeric excess (ee) and 38.4% yield (theoretical, 50%)
within 20 min (enantiomeric ratio (E-value): 38.4). The enantioselective activity of REH toward GPE was also
confirmed by the analysis of the vicinal diol, 3-phenoxy-1,2-propanediol. To our knowledge, this study
demonstrates the highest enantioselective resolution of racemic GPE using a purified biocatalyst among the
known native EHases.
12 | KORDI S&T
iocatalytic resolution of glycidyl phenyl ether using a novel epoxide hydrolase from a marine bacterium, Maritimibacter alkaliphilus KCCM 42376
Articles
[email protected]
Amplified polar warming and moistening under global warming are critical issues for the climate
changes. The authors find that a poleward shift of the westerly jet stream and associated synoptic eddy
feedback play a critical role in enhancing polar warming and moistening. Namely, the mean circulation
changes due to anthropogenic forcing lead to the changes in storm feedbacks, which reinforce again
climate responses, particularly the polar responses such as the enhanced polar warming and moistening. It
is demonstrated here that the storm feedback can be explained by a simple rule based on the mean
circulation change. This rule can be used for understanding other regional climate responses to the
anthropogenic forcing.
ole of synoptic eddy feedback on polar climate responses to the anthropogenic forcing
Jong Seong Kug Climate Change & Coastal Disaster Research Department
[email protected]
Articles
[Figure 1] The schematic representation of enantioselective hydrolysis of racemic GPE.
[Figure 2] Kinetic resolution of racemic GPE by the purified REH. The changes of (A) racemic GPE and (B) 3-phenoxy-1,2- propanediol.
[Table 1] The comparison of kinetic resolution of EHases and the purified REH toward GPE.
a Wet cell weight b No information. a Dry cell weight. b Calculated with an ee of 99.99%.
B R
NATURE | VOL. 467 | 16 September 2010 GEOPHYSICAL RESEARCH LETTERS, VOL. 37, 2010
Aspergillus niger
Agrobacterium radiobacter
(mM) Temp.
14 | KORDI S&T No. 3 March 2011 | 15
[Figure 1] Typical temporal waveforms of snapping shrimp sounds produced by the three species of snapping shrimp.
[Figure 2] Normalized spectra of sounds produced by the three species of snapping shrimp.
[Figure 3] Normalized spectra of sounds produced by the species A. lobidens with different claw lengths.
The typical temporal waveforms and spectra of the sounds produced by the three species of snapping
shrimp with different claw shapes and almost the same claw lengths were investigated under laboratory
conditions. The sound spectra generated by one species of snapping shrimp were also investigated for
various claw lengths. For the three species of snapping shrimp, their typical temporal waveforms were
similar, but their sound spectra and pulse durations differed. This difference was related to the size of the
single cavitation bubble, which was generated by the high-speed water jet emitted from the snapping
shrimp claw. The range of difference in the times between the snapping shrimp claw closure and the
collapse of the single cavitation bubble for the three species of snapping shrimp seemed to be determined
by the difference in the claw shape. The collapse time, the equilibrium radius, and the maximal radius of the
cavitation bubble for each species were estimated from the first peak frequency component in the snapping
shrimp sound spectrum. For one species of snapping shrimp, the peak frequency components in the sound
spectra were observed for various claw lengths and their superposition could be considered as the cause
that the broad peak frequency components were variously observed in the averaged snapping shrimp sound
spectra, which were measured in many shallow water areas.
napping shrimp sound measured under laboratory conditions
Bong-Chae Kim East Sea Environment Research Department
[email protected]
A numerical method, which combines the Boundary Element Method (BEM) and the Volume Of the
Fluid method (VOF method), has been presented to solve wave-structure interactions; the intense wave
motion at the proximity of the structure is modeled by the VOF method and the rest of the fluid region is
modeled by the BEM. The combined method can considerably reduce the time-consuming VOF domain, and
thus practically makes it possible to apply the VOF method for random wave calculations, in which long
time computations are usually required to obtain statistically meaningful results, and therefore the use of
the single-VOF model often becomes prohibitive in terms of computational time and storage memories. A
VOF model CADMAS-SURF, which is based on SMAC scheme and had been constructed by a number of VOF
researchers in coastal engineering in Japan, is used in the combined BEM-VOF model. The two-way
coupling treatment, which enables us to deal with bidirectional wave propagations, which was originally
given for the SOLA-VOF model by Yan et al. (2003a) and later improved by Kim et al. (2007), was modified for
the SMAC scheme. The coupling treatments are described in detail in the paper. The validity of the
combined BEM-VOF model was investigated by comparing the numerical results with the theoretical
results for the propagations of Stokes 5th order waves and random waves.
simple two-way coupling method of BEM and VOF model for random wave calculations
Sang Ho Kim Marine Structure & Plant Research Department
[email protected]
Articles Articles
S A
Jpn. J. Appl. Phys. 49 (2010) 07HG04 Coastal Engineering 57 (2010) 1018-1028
14 | KORDI S&T No. 3 March 2011 | 15
[Figure 1] Typical temporal waveforms of snapping shrimp sounds produced by the three species of snapping shrimp.
[Figure 2] Normalized spectra of sounds produced by the three species of snapping shrimp.
[Figure 3] Normalized spectra of sounds produced by the species A. lobidens with different claw lengths.
The typical temporal waveforms and spectra of the sounds produced by the three species of snapping
shrimp with different claw shapes and almost the same claw lengths were investigated under laboratory
conditions. The sound spectra generated by one species of snapping shrimp were also investigated for
various claw lengths. For the three species of snapping shrimp, their typical temporal waveforms were
similar, but their sound spectra and pulse durations differed. This difference was related to the size of the
single cavitation bubble, which was generated by the high-speed water jet emitted from the snapping
shrimp claw. The range of difference in the times between the snapping shrimp claw closure and the
collapse of the single cavitation bubble for the three species of snapping shrimp seemed to be determined
by the difference in the claw shape. The collapse time, the equilibrium radius, and the maximal radius of the
cavitation bubble for each species were estimated from the first peak frequency component in the snapping
shrimp sound spectrum. For one species of snapping shrimp, the peak frequency components in the sound
spectra were observed for various claw lengths and their superposition could be considered as the cause
that the broad peak frequency components were variously observed in the averaged snapping shrimp sound
spectra, which were measured in many shallow water areas.
napping shrimp sound measured under laboratory conditions
Bong-Chae Kim East Sea Environment Research Department
[email protected]
A numerical method, which combines the Boundary Element Method (BEM) and the Volume Of the
Fluid method (VOF method), has been presented to solve wave-structure interactions; the intense wave
motion at the proximity of the structure is modeled by the VOF method and the rest of the fluid region is
modeled by the BEM. The combined method can considerably reduce the time-consuming VOF domain, and
thus practically makes it possible to apply the VOF method for random wave calculations, in which long
time computations are usually required to obtain statistically meaningful results, and therefore the use of
the single-VOF model often becomes prohibitive in terms of computational time and storage memories. A
VOF model CADMAS-SURF, which is based on SMAC scheme and had been constructed by a number of VOF
researchers in coastal engineering in Japan, is used in the combined BEM-VOF model. The two-way
coupling treatment, which enables us to deal with bidirectional wave propagations, which was originally
given for the SOLA-VOF model by Yan et al. (2003a) and later improved by Kim et al. (2007), was modified for
the SMAC scheme. The coupling treatments are described in detail in the paper. The validity of the
combined BEM-VOF model was investigated by comparing the numerical results with the theoretical
results for the propagations of Stokes 5th order waves and random waves.
simple two-way coupling method of BEM and VOF model for random wave calculations
Sang Ho Kim Marine Structure & Plant Research Department
[email protected]
Articles Articles
S A
Jpn. J. Appl. Phys. 49 (2010) 07HG04 Coastal Engineering 57 (2010) 1018-1028
16 | KORDI S&T No. 3 March 2011 | 17
A two-frame Particle Image Velocimetry (PIV) technique was used to investigate the flow
characteristics of a complicated propeller wake influenced by a hull wake. As the propeller is significantly
affected by the hull wake of a marine vessel, measurements of the propeller wake under the hull wake are
certainly needed for more reliable validation of numerical predictions. Velocity field measurements were
conducted in a cavitation tunnel with a simulated hull wake. Generally, the hull wake generated by the hull
of a marine ship may cause different loading distributions on the propeller blade in both the upper and the
lower propeller planes. The unstable propeller wake caused by the ship’s hull was interpreted in terms of
Turbulent Kinetic Energy (TKE) to obtain useful information for flow modeling. The unstable or unsteady
phenomenon in the upper propeller wake was identified by using the Proper Orthogonal Decomposition
(POD) method to characterize the coherent flow structure with turbulent kinetic energy. Strong
unsteadiness appeared in the second and higher modes, largely affecting the downstream flow
characteristics. The first eigenmode can be used to appropriately identify the tip vortex positions even in the
unstable downstream region, which are helpful for establishing reliable wake modeling.
nalysis of unstable vortical structure in a propeller wake affected by a simulated hull wake
Bu-Geun Paik Marine Transportation Research Department
[email protected]
The electrical resistivity of soil having different Chemical Weathering Index(CWI) was measured, and
the correlation between CWI and the electrical resistivity was estimated. The electrical resistivity of soil
varies with CWI of soil. The difference in the electrical resistivities of soils having different weathering
degrees is clear at lower water contents. At the volumetric water contents estimated in this study, CWI
could be described by a linear equation of electrical resistivity with the constants related to the volumetric
water content. The findings in this study suggest that the electrical resistivity could be used as an effective
alternative for estimating the weathering degree of soil.
stimation of soil weathering degree using electrical resistivity
Myoung Hak Oh Coastal Engineering & Ocean Energy Research Department
[email protected]
Relationship between chemical weathering index and
electrical resistivity
A E
Exp Fluids (2010) 48:1121-1133 Environ Earth Sci (2010) 59;1319-1326
[Table 1] Uncertainties of displacement vectors measured by the PIV system used in this study
RMS Min. Max.
[Figure 1] Schematic diagram of the experimental setup
[Figure 2] Simulated hull wake and wake screen used in the
cavitation tunnel. a Simulated hull wake (axial velocity); b typical
wake screen
16 | KORDI S&T No. 3 March 2011 | 17
A two-frame Particle Image Velocimetry (PIV) technique was used to investigate the flow
characteristics of a complicated propeller wake influenced by a hull wake. As the propeller is significantly
affected by the hull wake of a marine vessel, measurements of the propeller wake under the hull wake are
certainly needed for more reliable validation of numerical predictions. Velocity field measurements were
conducted in a cavitation tunnel with a simulated hull wake. Generally, the hull wake generated by the hull
of a marine ship may cause different loading distributions on the propeller blade in both the upper and the
lower propeller planes. The unstable propeller wake caused by the ship’s hull was interpreted in terms of
Turbulent Kinetic Energy (TKE) to obtain useful information for flow modeling. The unstable or unsteady
phenomenon in the upper propeller wake was identified by using the Proper Orthogonal Decomposition
(POD) method to characterize the coherent flow structure with turbulent kinetic energy. Strong
unsteadiness appeared in the second and higher modes, largely affecting the downstream flow
characteristics. The first eigenmode can be used to appropriately identify the tip vortex positions even in the
unstable downstream region, which are helpful for establishing reliable wake modeling.
nalysis of unstable vortical structure in a propeller wake affected by a simulated hull wake
Bu-Geun Paik Marine Transportation Research Department
[email protected]
The electrical resistivity of soil having different Chemical Weathering Index(CWI) was measured, and
the correlation between CWI and the electrical resistivity was estimated. The electrical resistivity of soil
varies with CWI of soil. The difference in the electrical resistivities of soils having different weathering
degrees is clear at lower water contents. At the volumetric water contents estimated in this study, CWI
could be described by a linear equation of electrical resistivity with the constants related to the volumetric
water content. The findings in this study suggest that the electrical resistivity could be used as an effective
alternative for estimating the weathering degree of soil.
stimation of soil weathering degree using electrical resistivity
Myoung Hak Oh Coastal Engineering & Ocean Energy Research Department
[email protected]
Relationship between chemical weathering index and
electrical resistivity
A E
Exp Fluids (2010) 48:1121-1133 Environ Earth Sci (2010) 59;1319-1326
[Table 1] Uncertainties of displacement vectors measured by the PIV system used in this study
RMS Min. Max.
[Figure 1] Schematic diagram of the experimental setup
[Figure 2] Simulated hull wake and wake screen used in the
cavitation tunnel. a Simulated hull wake (axial velocity); b typical
wake screen
Compensatory growth and proximate composition of dark-banded rockfish(mean weight: 13.6 g) were
examined after fish had experienced five different prefeeding regimes over a 7-week period. Fish were fed
at 0% (R0), 25% (R25), 50% (R50), 75% (R75) and 100% (R100, control) satiation for 2 weeks before satiation
feeding for 5 weeks. Fish of R50 and R75 achieved the same body weight as the control fish after satiation
feeding for 5 and 2 weeks, respectively. Although the specific growth rate and feed efficiency of R0 and R25
fish were higher than those of the control fish during the first 3 weeks of satiation feeding, fish in these
tanks did not catch-up with the body weight of the control fish at the end of the 5 week. At Week 2 and Week
7, the lipid ratios to the body mass of R0, R25 and R50 fish were significantly lower than those of the control
fish, but there was no difference between the control and R75 fish. This result suggests that the fish
subjected to a prerestricted feeding regime of 50-75% satiation feeding for 2 weeks result in complete
compensatory growth, while the fish experiencing more severe feed restriction (0-25% satiation) only show
partial compensatory growth capacity.
ffect of Ration Size Restriction on Compensatory Growth and Proximate Composition of Dark-banded Rockfish, Sebastes inermis
Sung-Yong Oh Tongyeong Marine Living Resources Research & Conservation Center
[email protected]
[Figure 1] Changes in body weight (g/fish) of dark-banded rockfish
subjected to five feeding treatments during the 7-week feeding trial:
R100, control, fish fed to satiation continuously throughout the
experiment; R75, fish fed at 75% satiation; R50, fish fed at 50%
satiation; R25, fish fed at 25% satiation; R0, fish fed at 0% satiation. All
ration size of feed restriction lasted 2 weeks before satiation feeding
started at week 3. Means with different letters in the same week are
significantly different (P < 0.05). Error bars represent mean ±SD.
Articles Articles
[Figure 2] Changes in specific growth rate (SGR) of dark-banded
rockfish in five feeding treatments during the satiation feeding
period from Week 3 to Week 7. Feeding treatment abbreviations are
shown in Figure 1. Means with different letters in the same week
are significantly different (P < 0.05). Error bars represent mean ±
SD.
[Figure 3] Changes in feed intake (FI) of dark-banded rockfish in
five feeding treatments during the satiation feeding period from
Week 3 to Week 7. Feeding treatment abbreviations are shown in
Figure. 1. Means with different letters in the same week are
significantly different (P < 0.05). Error bars represent mean ± SD.
[Figure 4] Changes in feed efficiency (FE) of dark-banded rockfish
in five feeding treatments during the satiation feeding period from
Fig. 1. Means with different letters in the same week are
significantly different(P < 0.05). Error bars represent mean ± SD.
R100
16.87a
10.84a
8.42a
0.50a
4.81c
66.40c
16.30a
13.46a
9.00a
0.64a
4.81a
65.33a
Date Chemical attribute Treatments
[Table 1] Proximate composition (%, wet weight basis)and energy content (kJ/g) of dark-banded rockfish at Week 2 (n=2) and Week 7 (n=3) in five feeding treatments1
1Values with different letters in the same row are significantly different (P < 0.05). 2Lipid/LBM is the ratio of lipid to sum of protein and ash. R100, control, fish fed to satiation continuously throughout the experiment; R75, fish fed at 75% satiation for 2 weeks and then fed to satiation; R50, fish fed at 50% satiation for 2 weeks and then fed to satiation; R25, fish fed at 25% satiation for 2 weeks and then fed to satiation; R0, fish fed at 0% satiation for 2 weeks and then fed to satiation.
18 | KORDI S&T No. 3 March 2011 | 19
Compensatory growth and proximate composition of dark-banded rockfish(mean weight: 13.6 g) were
examined after fish had experienced five different prefeeding regimes over a 7-week period. Fish were fed
at 0% (R0), 25% (R25), 50% (R50), 75% (R75) and 100% (R100, control) satiation for 2 weeks before satiation
feeding for 5 weeks. Fish of R50 and R75 achieved the same body weight as the control fish after satiation
feeding for 5 and 2 weeks, respectively. Although the specific growth rate and feed efficiency of R0 and R25
fish were higher than those of the control fish during the first 3 weeks of satiation feeding, fish in these
tanks did not catch-up with the body weight of the control fish at the end of the 5 week. At Week 2 and Week
7, the lipid ratios to the body mass of R0, R25 and R50 fish were significantly lower than those of the control
fish, but there was no difference between the control and R75 fish. This result suggests that the fish
subjected to a prerestricted feeding regime of 50-75% satiation feeding for 2 weeks result in complete
compensatory growth, while the fish experiencing more severe feed restriction (0-25% satiation) only show
partial compensatory growth capacity.
ffect of Ration Size Restriction on Compensatory Growth and Proximate Composition of Dark-banded Rockfish, Sebastes inermis
Sung-Yong Oh Tongyeong Marine Living Resources Research & Conservation Center
[email protected]
[Figure 1] Changes in body weight (g/fish) of dark-banded rockfish
subjected to five feeding treatments during the 7-week feeding trial:
R100, control, fish fed to satiation continuously throughout the
experiment; R75, fish fed at 75% satiation; R50, fish fed at 50%
satiation; R25, fish fed at 25% satiation; R0, fish fed at 0% satiation. All
ration size of feed restriction lasted 2 weeks before satiation feeding
started at week 3. Means with different letters in the same week are
significantly different (P < 0.05). Error bars represent mean ±SD.
Articles Articles
[Figure 2] Changes in specific growth rate (SGR) of dark-banded
rockfish in five feeding treatments during the satiation feeding
period from Week 3 to Week 7. Feeding treatment abbreviations are
shown in Figure 1. Means with different letters in the same week
are significantly different (P < 0.05). Error bars represent mean ±
SD.
[Figure 3] Changes in feed intake (FI) of dark-banded rockfish in
five feeding treatments during the satiation feeding period from
Figure. 1. Means with different letters in the same week are
significantly different (P < 0.05). Error bars represent mean ± SD.
[Figure 4] Changes in feed efficiency (FE) of dark-banded rockfish
in five feeding treatments during the satiation feeding period from
Fig. 1. Means with different letters in the same week are
significantly different(P < 0.05). Error bars represent mean ± SD.
R100
16.87a
10.84a
8.42a
0.50a
4.81c
66.40c
16.30a
13.46a
9.00a
0.64a
4.81a
65.33a
Date Chemical attribute Treatments
[Table 1] Proximate composition (%, wet weight basis)and energy content (kJ/g) of dark-banded rockfish at Week 2 (n=2) and Week 7 (n=3) in five feeding treatments1
1Values with different letters in the same row are significantly different (P < 0.05). 2Lipid/LBM is the ratio of lipid to sum of protein and ash. R100, control, fish fed to satiation continuously throughout the experiment; R75, fish fed at 75% satiation for 2 weeks and then fed to satiation; R50, fish fed at 50% satiation for 2 weeks and then fed to satiation; R25, fish fed at 25% satiation for 2 weeks and then fed to satiation; R0, fish fed at 0% satiation for 2 weeks and then fed to satiation.
20 | KORDI S&T
High spatial resolution satellite data (IKONOS) combined with in situ data was used to quantitatively
estimate the spatial distribution of tidal flat surface sedimentary facies for the Hwangdo tidal flat, Cheonsu
Bay, Korea. The classification result was accurate in terms of a comparison with the in situ data, and the
overall accuracy was 90.7%, which confirmed the validity of the classification. GIS analysis based on a
probabilistic model was applied to a quantitative estimation of the relationship between each surface
sedimentary facies and the spectral reflectance. Mud flat facies showed a high positive correlation (R2 =
0.91), and sand flat facies showed a high negative correlation (R2 = 1.00), which was a good reflection of the
sedimentary characteristics of Hwangdo tidal flat. Relationships between each sedimentary facies and DEM
also showed good agreement with the topographic characteristics in the study area. The study revealed that
tidal flat surface sediment classification using high resolution remote sensing imagery and in situ data
successfully shows spectral and topographic characteristics of the study area. It was noted that spectral
reflectance was affected by a combination of environmental factors, including grain size, topography, and
remnant surface water. It is possible to determine the type of tidal flat through quantitative estimates of the
spatial distribution of surface sediments according to their spectral reflectance.
uantitative estimation of intertidal sediment characteristics using remote sensing and GIS
Joo-Hyung Ryu Korea Ocean Satellite Center
[email protected]
Articles Articles
Estuarine, Coastal and Shelf Science 88(2010) 125-134
[Figure 1] (a) The Landsat ETM+ image of the Cheonsu Bay and Hwangdo tidal flat acquired on Februray 14, 2002. The red line represents the line of echo sounding measurements. (b) The IKONOS RGB (432 bands) composite image of the Hwangdo tidal flat acquired on February 26, 2001 overlaid with 43 sampling positions for grain size analysis acquired in early March, 2004. The blue points are grab sample positions and the yellow points are field sample positions.
[Figure 2] Characteristics of sedimentary environments of the Hwangdo tidal flat from (a) grain size analysis at the ebb tide sampling points, and (b) topographic heights of line A calculated by echo-sounder.
[Figure 3] (a) The distribution map of surface sedimentary facies derived from the IKONOS image, and (b) its 3-D visualization overlaid on the DEM.
[Figure 4] Spatial relationships between the IKONOS digital number and each of four classes of surface sedimentary facies in the study area.
20 | KORDI S&T
High spatial resolution satellite data (IKONOS) combined with in situ data was used to quantitatively
estimate the spatial distribution of tidal flat surface sedimentary facies for the Hwangdo tidal flat, Cheonsu
Bay, Korea. The classification result was accurate in terms of a comparison with the in situ data, and the
overall accuracy was 90.7%, which confirmed the validity of the classification. GIS analysis based on a
probabilistic model was applied to a quantitative estimation of the relationship between each surface
sedimentary facies and the spectral reflectance. Mud flat facies showed a high positive correlation (R2 =
0.91), and sand flat facies showed a high negative correlation (R2 = 1.00), which was a good reflection of the
sedimentary characteristics of Hwangdo tidal flat. Relationships between each sedimentary facies and DEM
also showed good agreement with the topographic characteristics in the study area. The study revealed that
tidal flat surface sediment classification using high resolution remote sensing imagery and in situ data
successfully shows spectral and topographic characteristics of the study area. It was noted that spectral
reflectance was affected by a combination of environmental factors, including grain size, topography, and
remnant surface water. It is possible to determine the type of tidal flat through quantitative estimates of the
spatial distribution of surface sediments according to their spectral reflectance.
uantitative estimation of intertidal sediment characteristics using remote sensing and GIS
Joo-Hyung Ryu Korea Ocean Satellite Center
[email protected]
Articles Articles
Estuarine, Coastal and Shelf Science 88(2010) 125-134
[Figure 1] (a) The Landsat ETM+ image of the Cheonsu Bay and Hwangdo tidal flat acquired on Februray 14, 2002. The red line represents the line of echo sounding measurements. (b) The IKONOS RGB (432 bands) composite image of the Hwangdo tidal flat acquired on February 26, 2001 overlaid with 43 sampling positions for grain size analysis acquired in early March, 2004. The blue points are grab sample positions and the yellow points are field sample positions.
[Figure 2] Characteristics of sedimentary environments of the Hwangdo tidal flat from (a) grain size analysis at the ebb tide sampling points, and (b) topographic heights of line A calculated by echo-sounder.
[Figure 3] (a) The distribution map of surface sedimentary facies derived from the IKONOS image, and (b) its 3-D visualization overlaid on the DEM.
[Figure 4] Spatial relationships between the IKONOS digital number and each of four classes of surface sedimentary facies in the study area.
22 | KORDI S&T
Effects of screening a hydrophone with open-cell foams are determined to reduce the level of
infrasonic background noise, which is the self-noise probably induced by the presence of flow around the
hydrophone, in shallow and deep seas. The result obtained in shallow sea with bottommounted geometry
shows that the level of background noise could be reduced by more than 20 dB below 10 Hz if the
hydrophone is screened. Also, the result of ship noise measurement conducted in deep sea with drifting
geometry shows that a maximum background noise reduction of 15 dB could be achieved in the infrasonic
band without affecting the true acoustic signals.
nfrasonic Noise Measurements in Ocean Using Screened Hydrophones
Seongwook Lee Ocean Satellite Remote Sensing & Observation Technology Research Department
[email protected]
[Figure 1] Schematic of test of screened hydrophone in shallow sea.
[Figure 2] Spectrum level of ambient noise measured in shallow sea.
[Figure 3] Schematic of test of screened hydrophone in deep sea.
[Figure 4] Spectrum level of ship noise measured in deep sea.
ynthetic analogs of indole-containing natural products as inhibitors of sortase A and isocitrate lyase
Yeon Ju Lee Marine Biotechnology Research Center
[email protected]
Guided by the inhibitory activities of indole-containing natural products against isocitrate lyase (ICL)
from Candida albicans and sortase A (Srt A) from Staphylococcus aureus, a series of compounds
structurally analogous to natural products were synthesized. Eight Srt A inhibitors and an ICL inhibitor
having higher activities than the natural products were discovered by screening the enzyme inhibitory
activities of synthesized compounds. Among the Srt A inhibitors discovered, six exhibited higher activities
than p-hydroxymercuribenzoic acid, which suggests that these compounds have great potential as
alternative antibacterial agents.
Japanese Journal of Applied Physics 49 (2010) 07HG06 Bioorg. Med. Chem. Lett. 20 (2010) 6882-6885
22 | KORDI S&T
Effects of screening a hydrophone with open-cell foams are determined to reduce the level of
infrasonic background noise, which is the self-noise probably induced by the presence of flow around the
hydrophone, in shallow and deep seas. The result obtained in shallow sea with bottommounted geometry
shows that the level of background noise could be reduced by more than 20 dB below 10 Hz if the
hydrophone is screened. Also, the result of ship noise measurement conducted in deep sea with drifting
geometry shows that a maximum background noise reduction of 15 dB could be achieved in the infrasonic
band without affecting the true acoustic signals.
nfrasonic Noise Measurements in Ocean Using Screened Hydrophones
Seongwook Lee Ocean Satellite Remote Sensing & Observation Technology Research Department
[email protected]
[Figure 1] Schematic of test of screened hydrophone in shallow sea.
[Figure 2] Spectrum level of ambient noise measured in shallow sea.
[Figure 3] Schematic of test of screened hydrophone in deep sea.
[Figure 4] Spectrum level of ship noise measured in deep sea.
ynthetic analogs of indole-containing natural products as inhibitors of sortase A and isocitrate lyase
Yeon Ju Lee Marine Biotechnology Research Center
[email protected]
Guided by the inhibitory activities of indole-containing natural products against isocitrate lyase (ICL)
from Candida albicans and sortase A (Srt A) from Staphylococcus aureus, a series of compounds
structurally analogous to natural products were synthesized. Eight Srt A inhibitors and an ICL inhibitor
having higher activities than the natural products were discovered by screening the enzyme inhibitory
activities of synthesized compounds. Among the Srt A inhibitors discovered, six exhibited higher activities
than p-hydroxymercuribenzoic acid, which suggests that these compounds have great potential as
alternative antibacterial agents.
Japanese Journal of Applied Physics 49 (2010) 07HG06 Bioorg. Med. Chem. Lett. 20 (2010) 6882-6885
24 | KORDI S&T
Hydrogenases are the key enzymes involved in the metabolism of H2, catalyzing the chemical reaction
2H+ + 2e- H2. Three genes encoding Group 4 [NiFe]-hydrogenases from Thermococcus onnurineus NA1
were found to be organized into three separate gene clusters: fdh1-mfh1-mnh1, fdh2-mfh2-mnh2 and
codh-mch-mnh3 (Figure 1). The open reading frames in the clusters can be divided into three-modules of
dehydrogenase-hydrogenase-cation/proton antiporter subunits. Phylogenetic analysis of the large subunits
of all the target hydrogenases revealed that the target hydrogenases grouped together in a separate cluster
4b in Group 4 (Figure 2). By sequence alignment of subgroup 4b hydrogenases, a pair of highly conserved
motifs (L1 and L2) were revealed, which represent two regions surrounding the two pairs of cysteine ligands
of the NiFe center of the large subunits of hydrogenases (Figure 3). Biochemical and physiological
experiments could assess the roles of the novel hydrogenases and other components of the tripartite
clusters.
dentification of a Novel Class of Membrane-Bound [NiFe]-Hydrogenases in Thermococcus onnurineus NA1 by In Silico Analysis
Hyun Sook Lee Marine Biotechnology Research Center
[email protected]
[Figure 1] Gene organization of fdh1-mfh1-mnh1, fdh2- mfh2-mnh2 (A) and codh-mch-mnh3 clusters (B).
[Figure 3] Sequence logo representations of L1 (up) and L2 (down) motif patterns of Group 4b hydrogenases.
[Figure 2] Phylogenetic tree of the large subunits of Group 4 hydrogenases.
rystal structure of Lon protease: Molecular architecture of gated entry to a sequestered degradation chamber
Sun-Shin Cha Marine Biotechnology Research Center
[email protected]
No. 3 March 2011 | 25
Lon proteases are distributed in all kingdoms of life and are required for survival of cells under stress.
Lon is a tandem fusion of an AAA+ molecular chaperone and a protease with a serine-lysine catalytic dyad.
We report the 2.0- resolution crystal structure of Thermococcus onnurineus NA1 Lon (TonLon). The
structure is a three-tiered hexagonal cylinder with a large sequestered chamber accessible via an axial
channel. Conserved loops extending from the AAA+ domain combine with an insertion domain containing
the membrane anchor to form an apical domain that serves as a gate governing substrate access to an
internal unfolding and degradation chamber. Alternating AAA+ domains are in tight- and weak-binding
nucleotide states with different domain orientations and intersubunit contacts, reflecting intramolecular
dynamics during ATP-driven protein unfolding and translocation. The bowl-shaped proteolytic chamber is
contiguous with the chaperone chamber allowing internalized proteins direct access to the proteolytic sites
without further gating restrictions.
APPL. ENVIRON. MICROBIOL. 76(18) (2010) 6286-6289 The EMBO Journal (2010) 29, 3520-3530
24 | KORDI S&T
Hydrogenases are the key enzymes involved in the metabolism of H2, catalyzing the chemical reaction
2H+ + 2e- H2. Three genes encoding Group 4 [NiFe]-hydrogenases from Thermococcus onnurineus NA1
were found to be organized into three separate gene clusters: fdh1-mfh1-mnh1, fdh2-mfh2-mnh2 and
codh-mch-mnh3 (Figure 1). The open reading frames in the clusters can be divided into three-modules of
dehydrogenase-hydrogenase-cation/proton antiporter subunits. Phylogenetic analysis of the large subunits
of all the target hydrogenases revealed that the target hydrogenases grouped together in a separate cluster
4b in Group 4 (Figure 2). By sequence alignment of subgroup 4b hydrogenases, a pair of highly conserved
motifs (L1 and L2) were revealed, which represent two regions surrounding the two pairs of cysteine ligands
of the NiFe center of the large subunits of hydrogenases (Figure 3). Biochemical and physiological
experiments could assess the roles of the novel hydrogenases and other components of the tripartite
clusters.
dentification of a Novel Class of Membrane-Bound [NiFe]-Hydrogenases in Thermococcus onnurineus NA1 by In Silico Analysis
Hyun Sook Lee Marine Biotechnology Research Center
[email protected]
[Figure 1] Gene organization of fdh1-mfh1-mnh1, fdh2- mfh2-mnh2 (A) and codh-mch-mnh3 clusters (B).
[Figure 3] Sequence logo representations of L1 (up) and L2 (down) motif patterns of Group 4b hydrogenases.
[Figure 2] Phylogenetic tree of the large subunits of Group 4 hydrogenases.
rystal structure of Lon protease: Molecular architecture of gated entry to a sequestered degradation chamber
Sun-Shin Cha Marine Biotechnology Research Center
[email protected]
No. 3 March 2011 | 25
Lon proteases are distributed in all kingdoms of life and are required for survival of cells under stress.
Lon is a tandem fusion of an AAA+ molecular chaperone and a protease with a serine-lysine catalytic dyad.
We report the 2.0- resolution crystal structure of Thermococcus onnurineus NA1 Lon (TonLon). The
structure is a three-tiered hexagonal cylinder with a large sequestered chamber accessible via an axial
channel. Conserved loops extending from the AAA+ domain combine with an insertion domain containing
the membrane anchor to form an apical domain that serves as a gate governing substrate access to an
internal unfolding and degradation chamber. Alternating AAA+ domains are in tight- and weak-binding
nucleotide states with different domain orientations and intersubunit contacts, reflecting intramolecular
dynamics during ATP-driven protein unfolding and translocation. The bowl-shaped proteolytic chamber is
contiguous with the chaperone chamber allowing internalized proteins direct access to the proteolytic sites
without further gating restrictions.
APPL. ENVIRON. MICROBIOL. 76(18) (2010) 6286-6289 The EMBO Journal (2010) 29, 3520-3530
26 | KORDI S&T
In the present study, the protective effect of diphlorethohydroxycarmalol (DPHC) isolated from Ishige
okamurae, a brown algae, on high glucose-induced-oxidative stress was investigated using human
umbilical vein endothelial cells (HUVECs). High concentration of glucose (30 mM) treatment induced
cytotoxicity whereas DPHC prevented cells from high glucose-induced damage; restoring cell viability was
significantly increased. In addition, the lipid peroxidation, intracellular Reactive Oxygen Species (ROS), and
Nitric Oxide (NO) levels induced by high glucose treatment were effectively inhibited by addition of DPHC in
a dose-dependent manner. DPHC also suppressed the over-expressions of Inducible Nitric Oxide Synthase
(iNOS) and cyclooxygenase-2 (COX-2) proteins as well as nuclear factor-kappa B (NF-KB) activation induced
by high glucose in HUVECs. These finding indicate that DPHC might be used as potential pharmaceutical
agent which will reduce the damage caused by high glucose-induced-oxidative stress associated with
diabetes.
Soo-Jin Heo Marine Living Resources Research Department
[email protected]
[Figure 1] Effect of DPHC on high glucose-induced intracellular ROS of HUVECs.
[Figure 3] Effect of DPHC on high glucose-induced NF-kB activation of HUVECs. (A) NF-kB protein expression, (B) p65 DNA-binding activity.
NF- KB
β- actin
[Figure 2] Effect of DPHC on high glucose-induced iNOS and COX-2 expression of HUVECs.
emporal trend, spatial distribution, and terrestrial sources of PBDEs and PCBs in Masan Bay, Korea
Sang Hee Hong South Sea Environment Research Department
[email protected]
Polybrominateddiphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) are potentially toxic and
persistent anthropogenic chemicals. PBDEs are a class of brominated flame-retardants that are used in
the plastics, electronic circuitry, television sets, building materials and textiles. PCBs has been widely used
for industrial applications such as dielectric fluids in capacitors and transformers, print inks, paints,
pesticidesdue to their chemical and physical stability. Stockholm Convention recognized them as priority
persistent organic compounds for cautious regulation in the world. In this study, congener specific
determination of PBDEs and PCBs was carried out in 24 surface sediment samples and a sediment core
from Masan Bay, Korea. Among the 40 PBDE congeners targeted only 29 were detectable. PBDE congener
profile within sediments was dominated by BDE-209 followed by BDEs-99, -47, -153 and -183, sequentially,
which reflects well the dominant usage of Deca-BDE commercial mixture in Korea. In surface sediments,
the average PBDEs levels approached that of average PCBs values. However, trends observed in the
sediment core suggest that this pattern will alter over time and result in higher surface sediment PBDE
concentrations than PCBs in the future. Various diffuse and point sources were identified for PBDEs and
PCBs in this location. Shipping and other industrial activities were associated with PCB contamination while
domestic and industrial waste discharges corresponded with PBDE contamination. The average
concentration for PBDEs and PCBs in surface sediments were 5.7, 7.2 ng/g dry weight, respectively.
Food and Chemical Toxicology 48 (2010) 1448-1454 Marine Pollution Bulletin 60 (2010) 1836-1841
[Figure 1] Sampling locations in Masan Bay with concentrations (ng/g dry weight) of target chemicals in surface sediments (station 1-21, ). Core sample was taken at station 6 ( ).
[Figure 3] Isomeric profile of PCBs and PBDEs in surface sediment in Masan Bay.
[Figure 2] Vertical profile of PBDEs and PCBs in Masan Bay sediment core. Simultaneous measurement of 210Pb in the same fractions determine the age of the fraction.
26 | KORDI S&T
In the present study, the protective effect of diphlorethohydroxycarmalol (DPHC) isolated from Ishige
okamurae, a brown algae, on high glucose-induced-oxidative stress was investigated using human
umbilical vein endothelial cells (HUVECs). High concentration of glucose (30 mM) treatment induced
cytotoxicity whereas DPHC prevented cells from high glucose-induced damage; restoring cell viability was
significantly increased. In addition, the lipid peroxidation, intracellular Reactive Oxygen Species (ROS), and
Nitric Oxide (NO) levels induced by high glucose treatment were effectively inhibited by addition of DPHC in
a dose-dependent manner. DPHC also suppressed the over-expressions of Inducible Nitric Oxide Synthase
(iNOS) and cyclooxygenase-2 (COX-2) proteins as well as nuclear factor-kappa B (NF-KB) activation induced
by high glucose in HUVECs. These finding indicate that DPHC might be used as potential pharmaceutical
agent which will reduce the damage caused by high glucose-induced-oxidative stress associated with
diabetes.
Soo-Jin Heo Marine Living Resources Research Department
[email protected]
[Figure 1] Effect of DPHC on high glucose-induced intracellular ROS of HUVECs.
[Figure 3] Effect of DPHC on high glucose-induced NF-kB activation of HUVECs. (A) NF-kB protein expression, (B) p65 DNA-binding activity.
NF- KB
&bet

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