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Ansan P.O.Box 29, Seoul 425-600, Korea TEL : +82-31-400-6000 FAX
: +82-31-408-5820
www.kordi.re.kr
KORDI S&T ● 발행인: 강정극 ● 기획·편집: 성과확산팀 ● 디자인: 모모새 비지니스 ● 발행일:
2011. 3 ● 발행처: 한국해양연구원
KORDI, in quest of the world’s best oceanscience 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 productionYun Jae Kim I
Hyun Sook Lee I Jung-Hyun Lee I Sung Gyun Kang
[ NATURE I VOL.467/16 September 2010 ]
-
ContentsArticles
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
Constant velocint for an vane shear strength measuring
device
Vibration Apparatus
12
13
14
15
16
17
18
20
22
23
24
25
26
27
30
30
31
31
32
32
33
33
34
34
35
35
36
36
37
37
-
ContentsArticles
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
Constant velocint for an vane shear strength measuring
device
Vibration Apparatus
12
13
14
15
16
17
18
20
22
23
24
25
26
27
30
30
31
31
32
32
33
33
34
34
35
35
36
36
37
37
-
Formate-drivengrowth coupledwith H2 production
Yun Jae Kim Marine Biotechnology Research Center●
[email protected]
Although a common reaction in anaerobicenvironments, the
conversion of formate tobicarbonate 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. *Theseauthors contributed
equally to this work.
Formate-dependent H2 production is dependent uponformate
hydrogen lyase systems composed of theformate dehydrogenase and
membrane-associated
hydrogenase3. In Escherichia coli and Thermococcus
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
cation/proton antiporters while the small gene cluster
(fdh3-
sulfI) lacks one subcluster and the hydrogenase genes code
for a cytoplasmic hydrogenase.
To investigate the growth potential of T. onnurineus NA1
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
Hyun Sook Lee Marine Biotechnology Research Center●
[email protected]
Jung-Hyun Lee Marine Biotechnology Research Center●
[email protected]
Sung Gyun KangMarine Biotechnology Research Center●
[email protected]
[Figure 1] Gene organization of formate dehydrogenase gene
clusters from
T. onnurineus NA1.
-
Formate-drivengrowth coupledwith H2 production
Yun Jae Kim Marine Biotechnology Research Center●
[email protected]
Although a common reaction in anaerobicenvironments, the
conversion of formate tobicarbonate 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. *Theseauthors contributed
equally to this work.
Formate-dependent H2 production is dependent uponformate
hydrogen lyase systems composed of theformate dehydrogenase and
membrane-associated
hydrogenase3. In Escherichia coli and Thermococcus
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
cation/proton antiporters while the small gene cluster
(fdh3-
sulfI) lacks one subcluster and the hydrogenase genes code
for a cytoplasmic hydrogenase.
To investigate the growth potential of T. onnurineus NA1
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
Hyun Sook Lee Marine Biotechnology Research Center●
[email protected]
Jung-Hyun Lee Marine Biotechnology Research Center●
[email protected]
Sung Gyun KangMarine Biotechnology Research Center●
[email protected]
[Figure 1] Gene organization of formate dehydrogenase gene
clusters from
T. onnurineus NA1.
-
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.
Depending on the subcellular localization of formate
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.
The relative importance of the fdh2-mfh2-mnh2 gene
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.
KORDI S&T No. 3 March 2011
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.
ⓒ2010 Macmillan Publishers Limited. All rights reserved ⓒ2010
Macmillan Publishers Limited. All rights reserved
[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.
Depending on the subcellular localization of formate
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.
The relative importance of the fdh2-mfh2-mnh2 gene
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.
KORDI S&T No. 3 March 2011
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.
ⓒ2010 Macmillan Publishers Limited. All rights reserved ⓒ2010
Macmillan Publishers Limited. All rights reserved
[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).
-
KORDI S&T No. 3 March 2011
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).
6. Bagramyan, K., Mnatsakanyan, N., Poladian, A., Vassilian, A.
&
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).
NatureNATURE | VOL. 467 | 16 September 2010NATURE | VOL. 467 |
16 September 2010Nature
ⓒ2010 Macmillan Publishers Limited. All rights reserved ⓒ2010
Macmillan Publishers Limited. All rights reserved
Methods SummaryT. onnurineus NA1 was cultured in the
modified
medium 120 including 35 g/l NaCl, 0.5 or 1.0 g/l yeastextract
and 10 g/l sodium formate or 10 g/l sulfur at80°C under anaerobic
condition. Cell suspensionswere prepared by washing cells with an
anaerobicbuffer containing 20 mM imidazole, 600 mM NaCl, 30mM
MgCl2, 10 mM KCl, 5 mM dithiothreitol, pH 6.9 andresuspending them
in the same buffer at celldensities of 1 mg protein/2.5 ml. Gases
in theheadspace of serum bottles were measured with
gaschromatography and formate was detected with
liquidchromatography. The amount of bicarbonates in theliquid was
determined by measuring CO2 formed byacidifying the cell
suspensions. The ATP content of thecells was measured using the
luciferin/luciferaseassay kit. Thermodynamic calculations were
doneusing the Nernst equation to correct Gibbs energyvalues (△G)
for the actual temperature and the actualconcentrations of
reactants and products. The
standard Gibbs energy value (△G o) was corrected toa temperature
of 80oC (△G o= -2.6 kJ/mol at 80oC) bylinear interpolation from
tabulated values for 70 and85oC21. Activities rather than
concentrations ofreactants and products were considered using
theDebye-Huckel equation and they gave a negligibleeffect on Gibbs
energy values (less than 0.27 kJ/mol).
A custom microarray was manufactured byRoche Nimblegen (Madison,
WI). Arrays werescanned using a GenePix 4000B scanner
(MolecularDevices, Union City, CA), and the data were
extractedusing NimbleScan 2.4 software (Roche NimbleGen,Madison,
WI). For quantitative RT-PCR, cDNAs weresynthesized from 350 ng of
total RNA usingSuperScript II reverse transcriptase and
PCRreactions were performed with gene-specificprimers using rTaq
DNA polymerase (Takara, Otsu,Japan). Gene disruption was performed
according tothe methods applied to a hyperthermophilicarchaeon
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).
-
KORDI S&T No. 3 March 2011
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).
6. Bagramyan, K., Mnatsakanyan, N., Poladian, A., Vassilian, A.
&
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).
NatureNATURE | VOL. 467 | 16 September 2010NATURE | VOL. 467 |
16 September 2010Nature
ⓒ2010 Macmillan Publishers Limited. All rights reserved ⓒ2010
Macmillan Publishers Limited. All rights reserved
Methods SummaryT. onnurineus NA1 was cultured in the
modified
medium 120 including 35 g/l NaCl, 0.5 or 1.0 g/l yeastextract
and 10 g/l sodium formate or 10 g/l sulfur at80°C under anaerobic
condition. Cell suspensionswere prepared by washing cells with an
anaerobicbuffer containing 20 mM imidazole, 600 mM NaCl, 30mM
MgCl2, 10 mM KCl, 5 mM dithiothreitol, pH 6.9 andresuspending them
in the same buffer at celldensities of 1 mg protein/2.5 ml. Gases
in theheadspace of serum bottles were measured with
gaschromatography and formate was detected with
liquidchromatography. The amount of bicarbonates in theliquid was
determined by measuring CO2 formed byacidifying the cell
suspensions. The ATP content of thecells was measured using the
luciferin/luciferaseassay kit. Thermodynamic calculations were
doneusing the Nernst equation to correct Gibbs energyvalues (△G)
for the actual temperature and the actualconcentrations of
reactants and products. The
standard Gibbs energy value (△G o) was corrected toa temperature
of 80oC (△G o= -2.6 kJ/mol at 80oC) bylinear interpolation from
tabulated values for 70 and85oC21. Activities rather than
concentrations ofreactants and products were considered using
theDebye-Huckel equation and they gave a negligibleeffect on Gibbs
energy values (less than 0.27 kJ/mol).
A custom microarray was manufactured byRoche Nimblegen (Madison,
WI). Arrays werescanned using a GenePix 4000B scanner
(MolecularDevices, Union City, CA), and the data were
extractedusing NimbleScan 2.4 software (Roche NimbleGen,Madison,
WI). For quantitative RT-PCR, cDNAs weresynthesized from 350 ng of
total RNA usingSuperScript II reverse transcriptase and
PCRreactions were performed with gene-specificprimers using rTaq
DNA polymerase (Takara, Otsu,Japan). Gene disruption was performed
according tothe methods applied to a hyperthermophilicarchaeon
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
-
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
-
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 usinga novel
epoxide hydrolase from a marine bacterium,Maritimibacter
alkaliphilus KCCM 42376
Articles
Sung Gyun KangMarine BiotechnologyResearch Center●
[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 climateresponses to the
anthropogenic forcing
Jong Seong KugClimate Change &Coastal DisasterResearch
Department●
[email protected]
No. 3 March 2011 | 13
Articles
[Figure 1] The schematic representation of enantioselective
hydrolysis ofracemic GPE.
[Figure 2] Kinetic resolution of racemicGPE 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
purifiedREH toward GPE.
a Wet cell weightb 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
Bacillus megaterium ECU1001
B. megaterium ECU1001
Trichosporon loubierii
R. bacterium HTCC2654
Cells
Enzyme
Cells
Cells
Cells
Enzyme (REH)
20
1
60
75
67
29.2
27
30
35
30
30
25
7.5
9.0
7.5
8.0
8.0
8.0
240
n.i.
1800
1440
270
20
100/(R)
>99/(R)
100/(S)
100/(S)
>99/(R)
100/(S)
26
28
25.6
n.i.
35
38.4
n.i.b
12
47.8
39
20
38.4d
(37)
(22)
(38)
(8)
(39)
This stu
75a
0.025-0.125
9.1 c
7c
50 a
0.02
Epoxide hydrolaseCat. Form GPE conc.
(mM)Temp.
(oC)pH Time
(min)ee (%)/abs.
conf.Yield(%)
E Ref.Cat. conc.(g/L)
-
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 usinga novel
epoxide hydrolase from a marine bacterium,Maritimibacter
alkaliphilus KCCM 42376
Articles
Sung Gyun KangMarine BiotechnologyResearch Center●
[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 climateresponses to the
anthropogenic forcing
Jong Seong KugClimate Change &Coastal DisasterResearch
Department●
[email protected]
No. 3 March 2011 | 13
Articles
[Figure 1] The schematic representation of enantioselective
hydrolysis ofracemic GPE.
[Figure 2] Kinetic resolution of racemicGPE 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
purifiedREH toward GPE.
a Wet cell weightb 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
Bacillus megaterium ECU1001
B. megaterium ECU1001
Trichosporon loubierii
R. bacterium HTCC2654
Cells
Enzyme
Cells
Cells
Cells
Enzyme (REH)
20
1
60
75
67
29.2
27
30
35
30
30
25
7.5
9.0
7.5
8.0
8.0
8.0
240
n.i.
1800
1440
270
20
100/(R)
>99/(R)
100/(S)
100/(S)
>99/(R)
100/(S)
26
28
25.6
n.i.
35
38.4
n.i.b
12
47.8
39
20
38.4d
(37)
(22)
(38)
(8)
(39)
This stu
75a
0.025-0.125
9.1 c
7c
50 a
0.02
Epoxide hydrolaseCat. Form GPE conc.
(mM)Temp.
(oC)pH Time
(min)ee (%)/abs.
conf.Yield(%)
E Ref.Cat. conc.(g/L)
-
14 | KORDI S&T No. 3 March 2011 | 15
[Figure 1] Typical temporalwaveforms of snapping shrimpsounds
produced by the threespecies of snapping shrimp.
[Figure 2] Normalized spectra ofsounds produced by the
threespecies of snapping shrimp.
[Figure 3] Normalized spectra ofsounds produced by the speciesA.
lobidens with different clawlengths.
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 laboratoryconditions
Bong-Chae KimEast Sea EnvironmentResearch 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 VOFmodel for random
wave calculations
Sang Ho Kim Marine Structure &Plant ResearchDepartment●
[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 temporalwaveforms of snapping shrimpsounds
produced by the threespecies of snapping shrimp.
[Figure 2] Normalized spectra ofsounds produced by the
threespecies of snapping shrimp.
[Figure 3] Normalized spectra ofsounds produced by the speciesA.
lobidens with different clawlengths.
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 laboratoryconditions
Bong-Chae KimEast Sea EnvironmentResearch 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 VOFmodel for random
wave calculations
Sang Ho Kim Marine Structure &Plant ResearchDepartment●
[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 flowcharacteristics 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
wakeaffected by a simulated hull wake
Bu-Geun Paik Marine TransportationResearch 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 usingelectrical
resistivity
Myoung Hak OhCoastal Engineering &Ocean Energy
ResearchDepartment●
[email protected]
Articles Articles
Relationship between electrical resistivity and
volumetric water content of soil
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 measuredby the
PIV system used in this study
RMS Min. Max.
Fluctuations (μm)
0.050
0.082
σΔх
σΔу
6.367
8.4562
-6.317
-8.052
[Figure 1] Schematic diagram of the experimental setup
[Figure 2] Simulated hull wake and wake screen used in
thecavitation 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 flowcharacteristics 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
wakeaffected by a simulated hull wake
Bu-Geun Paik Marine TransportationResearch 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 usingelectrical
resistivity
Myoung Hak OhCoastal Engineering &Ocean Energy
ResearchDepartment●
[email protected]
Articles Articles
Relationship between electrical resistivity and
volumetric water content of soil
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 measuredby the
PIV system used in this study
RMS Min. Max.
Fluctuations (μm)
0.050
0.082
σΔх
σΔу
6.367
8.4562
-6.317
-8.052
[Figure 1] Schematic diagram of the experimental setup
[Figure 2] Simulated hull wake and wake screen used in
thecavitation tunnel. a Simulated hull wake (axial velocity); b
typical
wake screen
-
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 Growthand
Proximate Composition of Dark-banded Rockfish,Sebastes inermis
Sung-Yong OhTongyeong MarineLiving ResourcesResearch
&Conservation Center●
[email protected]
[Figure 1] Changes in body weight (g/fish) of dark-banded
rockfishsubjected 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
E
JOURNAL OF THE WORLD AQUACULTURE SOCIETY 41(6) 2010
[Figure 2] Changes in specific growth rate (SGR) of
dark-bandedrockfish 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
infive 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
rockfishin five feeding treatments during the satiation feeding
period from
Week 3 to Week 7. Feeding treatment abbreviations are shown
in
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
Week 2
(n = 2)
Week 7
(n = 3)
Protein
Lipid
Energy
Lipid/LBM2
Ash
Moisture
Protein
Lipid
Energy
Lipid/LBM
Ash
Moisture
R75
16.29b
10.15b
8.10b
0.48ab
4.98b
68.41b
16.86a
13.67a
8.85a
0.63a
4.95a
65.72a
R50
16.13b
9.59b
7.97b
0.45b
5.09b
68.44b
16.02a
12.45b
8.90a
0.58b
5.02a
67.28a
R25
15.23c
9.07c
7.37c
0.45b
5.09b
69.41ab
16.17a
11.21b
8.84a
0.53b
4.85a
67.78a
R0
14.68d
8.84c
7.31c
0.43b
5.80a
70.09a
15.97a
10.63b
8.74a
0.51b
4.73a
67.92a
Pooled SEM
0.031
0.039
0.026
0.003
0.02
0.124
0.107
0.105
0.065
0.004
0.036
0.221
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 andthen fed to satiation; R50, fish fed at 50% satiation for
2 weeks and then fed to satiation; R25, fish fed at 25% satiation
for2 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 Growthand
Proximate Composition of Dark-banded Rockfish,Sebastes inermis
Sung-Yong OhTongyeong MarineLiving ResourcesResearch
&Conservation Center●
[email protected]
[Figure 1] Changes in body weight (g/fish) of dark-banded
rockfishsubjected 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
E
JOURNAL OF THE WORLD AQUACULTURE SOCIETY 41(6) 2010
[Figure 2] Changes in specific growth rate (SGR) of
dark-bandedrockfish 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
infive 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
rockfishin five feeding treatments during the satiation feeding
period from
Week 3 to Week 7. Feeding treatment abbreviations are shown
in
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
Week 2
(n = 2)
Week 7
(n = 3)
Protein
Lipid
Energy
Lipid/LBM2
Ash
Moisture
Protein
Lipid
Energy
Lipid/LBM
Ash
Moisture
R75
16.29b
10.15b
8.10b
0.48ab
4.98b
68.41b
16.86a
13.67a
8.85a
0.63a
4.95a
65.72a
R50
16.13b
9.59b
7.97b
0.45b
5.09b
68.44b
16.02a
12.45b
8.90a
0.58b
5.02a
67.28a
R25
15.23c
9.07c
7.37c
0.45b
5.09b
69.41ab
16.17a
11.21b
8.84a
0.53b
4.85a
67.78a
R0
14.68d
8.84c
7.31c
0.43b
5.80a
70.09a
15.97a
10.63b
8.74a
0.51b
4.73a
67.92a
Pooled SEM
0.031
0.039
0.026
0.003
0.02
0.124
0.107
0.105
0.065
0.004
0.036
0.221
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 andthen fed to satiation; R50, fish fed at 50% satiation for
2 weeks and then fed to satiation; R25, fish fed at 25% satiation
for2 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 sedimentcharacteristics
using remote sensing and GIS
Joo-Hyung RyuKorea Ocean SatelliteCenter●
[email protected]
No. 3 March 2011 | 21
Articles Articles
Q
Estuarine, Coastal and Shelf Science 88(2010) 125-134
[Figure 1] (a) The Landsat ETM+ image ofthe Cheonsu Bay and
Hwangdo tidal flatacquired on Februray 14, 2002. The red
linerepresents the line of echo soundingmeasurements. (b) The
IKONOS RGB (432bands) composite image of the Hwangdotidal flat
acquired on February 26, 2001overlaid with 43 sampling positions
for grainsize analysis acquired in early March, 2004.The blue
points are grab sample positionsand the yellow points are field
samplepositions.
[Figure 2] Characteristics of sedimentary environments ofthe
Hwangdo tidal flat from (a) grain size analysis at the ebbtide
sampling points, and (b) topographic heights of line Acalculated by
echo-sounder.
[Figure 3] (a) The distribution map of surface sedimentary
faciesderived from the IKONOS image, and (b) its 3-D
visualizationoverlaid on the DEM.
[Figure 4] Spatial relationships between the IKONOS
digitalnumber and each of four classes of surface sedimentaryfacies
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 sedimentcharacteristics
using remote sensing and GIS
Joo-Hyung RyuKorea Ocean SatelliteCenter●
[email protected]
No. 3 March 2011 | 21
Articles Articles
Q
Estuarine, Coastal and Shelf Science 88(2010) 125-134
[Figure 1] (a) The Landsat ETM+ image ofthe Cheonsu Bay and
Hwangdo tidal flatacquired on Februray 14, 2002. The red
linerepresents the line of echo soundingmeasurements. (b) The
IKONOS RGB (432bands) composite image of the Hwangdotidal flat
acquired on February 26, 2001overlaid with 43 sampling positions
for grainsize analysis acquired in early March, 2004.The blue
points are grab sample positionsand the yellow points are field
samplepositions.
[Figure 2] Characteristics of sedimentary environments ofthe
Hwangdo tidal flat from (a) grain size analysis at the ebbtide
sampling points, and (b) topographic heights of line Acalculated by
echo-sounder.
[Figure 3] (a) The distribution map of surface sedimentary
faciesderived from the IKONOS image, and (b) its 3-D
visualizationoverlaid on the DEM.
[Figure 4] Spatial relationships between the IKONOS
digitalnumber and each of four classes of surface sedimentaryfacies
in the study area.
-
22 | KORDI S&T
Effects of screening a hydrophone with open-cell foams are
determined to reduce the level ofinfrasonic 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 UsingScreened
Hydrophones
Seongwook LeeOcean Satellite RemoteSensing &
ObservationTechnology ResearchDepartment●
[email protected]
[Figure 1] Schematic of test of screened hydrophone inshallow
sea.
[Figure 2] Spectrum level of ambient noise measuredin shallow
sea.
[Figure 3] Schematic of test of screened hydrophone indeep
sea.
[Figure 4] Spectrum level of ship noise measured indeep sea.
ynthetic analogs of indole-containing naturalproducts as
inhibitors of sortase A and isocitratelyase
Yeon Ju LeeMarine BiotechnologyResearch Center●
[email protected]
Articles Articles
I S
No. 3 March 2011 | 23
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 ofinfrasonic 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 UsingScreened
Hydrophones
Seongwook LeeOcean Satellite RemoteSensing &
ObservationTechnology ResearchDepartment●
[email protected]
[Figure 1] Schematic of test of screened hydrophone inshallow
sea.
[Figure 2] Spectrum level of ambient noise measuredin shallow
sea.
[Figure 3] Schematic of test of screened hydrophone indeep
sea.
[Figure 4] Spectrum level of ship noise measured indeep sea.
ynthetic analogs of indole-containing naturalproducts as
inhibitors of sortase A and isocitratelyase
Yeon Ju LeeMarine BiotechnologyResearch Center●
[email protected]
Articles Articles
I S
No. 3 March 2011 | 23
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 reaction2H+ + 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 onnurineusNA1 by
In Silico Analysis
Hyun Sook LeeMarine BiotechnologyResearch 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 Group4
hydrogenases.
rystal structure of Lon protease: Moleculararchitecture of gated
entry to a sequestereddegradation chamber
Sun-Shin ChaMarine BiotechnologyResearch Center●
[email protected]
Articles Articles
I C
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-Å 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
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24 | KORDI S&T
Hydrogenases are the key enzymes involved in the metabolism of
H2, catalyzing the chemical reaction2H+ + 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-
