bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of mechanical stretch‐induced activation activity of back and leg muscle satellite cells in vitro
Authors: TATSUMI Ryuichi , MITSUHASHI Kei , ASHIDA Ken , HARUNO Atsushi , HATTORI Akihito , IKEUCHI Yoshihide , ALLEN Ronald E. 
Published: July 2004

ABSTRACTIt has previously been shown that mechanical stretch induces activation of cultured quiescent satellite cells by rapid release of hepatocyte growth factor (HGF) from its extracellular association with satellite cells and its subsequent presentation to the c‐met receptor. The present study provides evidence that the stretch activation activity varies according to the origin of satellite cells from back and leg skeletal muscles in vitro. Satellite cells were isolated from three muscle groups, back (BK), upper hind limb (UL) and lower hind limb (LL) muscles, of adult male rats and stretch activation activities were compared. In response to stretch, lower hind limb satellite cells showed significantly greater response than upper hind limb and back muscles (LL > UL > BK). Immunoblots of stretched culture media revealed a higher HGF‐releasing capacity of lower hind limb satellite cells than back muscle satellite cells. In addition, lower hind limb satellite cells exhibited a greater activation activity in response to exogenous HGF added to culture media than compared to satellite cells from back and upper hind limb (LL > UL > BK). The increased ability to release HGF and the increased cellular responsiveness might account for higher stretch activation activities of lower hind limb satellite cells. Electrophoretic analysis of myosin heavy chain isoforms verified a higher content of slow muscle fibers in lower limb muscles (LL > UL > BK), suggesting a difference in stretch‐induced activation activity between satellite cells associated with fast and slow muscle fibers.
Myofibrillar proteolysis in chick muscle cell cultures during heat stress
Authors: NAKASHIMA Kazuki , NONAKA Itoko , MASAKI Shigehiko , YAMAZAKI Makoto , ABE Hiroyuki 
Published: July 2004

ABSTRACTThe effect of heat stress on protein oxidation and myofibrillar proteolysis in chick myotubes was investigated. Myotubes were incubated at 37 or 41°C for 6 and 24 h. Protein carbonyl content, as an index of protein oxidation, increased more at 41°C than at 37°C for 6 and 24 h incubations. Nτ‐methylhistidine release as an index of myofibrillar proteolysis also increased more at 41°C than at 37°C for 6 and 24 h incubations. Proteasome activity also increased more under those same conditions. Calpain and cathepsin D but not B + L activities showed a greater increase at 41°C than at 37°C for 24 but not the 6 h incubation. These results indicate that heat stress increases protein oxidation and proteasome activity, resulting in an increase in myofibrillar proteolysis for short‐term incubation and, for long‐term incubation, it increases calpain, proteasome and cathepsin D activities, finally accelerating myofibrillar proteolysis in chick myotubes.
Effects of slaughter age on the levels of free amino acids and dipeptides in fattening cattle
Authors: WATANABE Akira , UEDA Yasuko , HIGUCHI Mikito 
Published: July 2004

ABSTRACTThe effects of slaughter age, breed type and postmortem period were studied on the concentrations of free amino acids (FAA) and dipeptides (carnosine and anserine) in Longissimus dorsi muscle of beef. Slaughter age affected the levels of most FAA and dipeptides, and the concentrations of these compounds were significantly lower at 35 months of age than either 15 or 25 months of age. Slight increases were observed at 25 months compared with 15 months, but the differences were not significant except for a few FAA. These tendencies still remained when the concentrations were recalculated on the basis of protein. A significant breed effect was observed for taurine, carnosine and anserine. Almost all FAA were significantly increased during postmortem conditioning, but the level of each FAA fluctuated, and the fluctuations could not be explained statistically by slaughter age or breed differences.
Questionnaire‐based study on consumer requirements for beef quality in Japan
Authors: SASAKI Keisuke , MITSUMOTO Mitsuru 
Published: July 2004

ABSTRACTA questionnaire study examining Japanese consumers’ requirements for beef quality was carried out in April 2002 in Tsukuba, Ibaraki, Japan. Answers from 532 participants were used for the statistical analysis. Twenty questions about sensory properties, appearance, safety and freshness, production area, price, and other properties were prepared. The answers were applied to principal component analysis. Five principal components were obtained and defined, and the principle component scores were used to classify participants. The panels were classified into four groups profiled as ‘specific quality orientated’, ‘Wagyu (Japanese beef) orientated’, ‘safety and freshness orientated’ and ‘overall high quality orientated’. In addition, gender and age characteristics were different among the groups. Sensory properties did not affect the classification of respondents.
Development of immune assay system for both CpG and non‐CpG DNA from lactic acid bacteria using a transfectant of swine Toll‐like receptor 9
Authors: SHIMOSATO Takeshi , KITAZAWA Haruki , TOHNO Masanori , KATOH Shinichiro , KAWAI Yasushi , SAITO Tadao 
Published: July 2004

ABSTRACTBacterial DNA is expected to be a potent immune stimulating agent to Toll‐like receptor (TLR) 9 expressed cells such as macrophages, monocytes, B lymphocytes, NK cells and dendritic cells. In the present study, we constructed a transfectant of swine TLR9 with mammalian cells. We demonstrated that the transfectant, recognizing both CpG and non‐CpG oligonucleotides from lactic acid bacteria, induced NF‐κB activation by gene reporter assay. These findings indicate that the swine TLR9 transfectant will be highly useful for the screening of immunostimulatory DNA from lactic acid bacteria.
The Sodium-Driven Flagellar Motor Controls Exopolysaccharide Expression in
Vibrio cholerae
Authors: Lauriano Crystal M. , Ghosh Chandradipa , Correa Nidia E. , Klose Karl E. 
Published: July 2004

ABSTRACT

Vibrio cholerae
causes the life-threatening diarrheal disease cholera. This organism persists in aquatic environments in areas of endemicity, and it is believed that the ability of the bacteria to form biofilms in the environment contributes to their persistence. Expression of an exopolysaccharide (EPS), encoded by two
vps
gene clusters, is essential for biofilm formation and causes a rugose colonial phenotype. We previously reported that the lack of a flagellum induces
V. cholerae
EPS expression. To uncover the signaling pathway that links the lack of a flagellum to EPS expression, we introduced into a rugose
flaA
strain second-site mutations that would cause reversion back to the smooth phenotype. Interestingly, mutation of the genes encoding the sodium-driven motor (
mot
) in a nonflagellated strain reduces EPS expression, biofilm formation, and
vps
gene transcription, as does the addition of phenamil, which specifically inhibits the sodium-driven motor. Mutation of
vpsR
, which encodes a response regulator, also reduces EPS expression, biofilm formation, and
vps
gene transcription in nonflagellated cells. Complementation of a
vpsR
strain with a constitutive
vpsR
allele likely to mimic the phosphorylated state (D59E) restores EPS expression and biofilm formation, while complementation with an allele predicted to remain unphosphorylated (D59A) does not. Our results demonstrate the involvement of the sodium-driven motor and suggest the involvement of phospho-VpsR in the signaling cascade that induces EPS expression. A nonflagellated strain expressing EPS is defective for intestinal colonization in the suckling mouse model of cholera and expresses reduced amounts of cholera toxin and toxin-coregulated pili in vitro. Wild-type levels of virulence factor expression and colonization could be restored by a second mutation within the
vps
gene cluster that eliminated EPS biosynthesis. These results demonstrate a complex relationship between the flagellum-dependent EPS signaling cascade and virulence.
Three Different Systems Participate in
l
-Cystine Uptake in
Bacillus subtilis
Authors: Burguière Pierre , Auger Sandrine , Hullo Marie-Françoise , Danchin Antoine , Martin-Verstraete Isabelle 
Published: July 2004

ABSTRACT

The symporter YhcL and two ATP binding cassette transporters, YtmJKLMN and YckKJI, were shown to mediate
l
-cystine uptake in
Bacillus subtilis
. A triple Δ
yhcL
Δ
ytmJKLMN
Δ
yckK
mutant was unable to grow in the presence of
l
-cystine and to take up
l
-cystine. We propose that
yhcL
,
ytmJKLMN
, and
yckKJI
should be renamed
tcyP
,
tcyJKLMN
, and
tcyABC
, respectively. The
l
-cystine uptake by YhcL (

K
m

= 0.6 μM) was strongly inhibited by seleno-
dl
-cystine, while the transport due to the YtmJKLMN system (

K
m

= 2.5 μM) also drastically decreased in the presence of
dl
-cystathionine,
l
-djenkolic acid, or
S
-methyl-
l
-cysteine. Accordingly, a Δ
ytmJKLMN
mutant did not grow in the presence of 100 μM
dl
-cystathionine, 100 μM
l
-djenkolic acid, or 100 μM
S
-methyl-
l
-cysteine. The expression of the
ytmI
operon and the
yhcL
gene was regulated in response to sulfur availability, while the level of expression of the
yckK
gene remained low under all the conditions tested.
Molecular Cloning and Characterization of
Bifidobacterium bifidum
1,2-α-
l
-Fucosidase (AfcA), a Novel Inverting Glycosidase (Glycoside Hydrolase Family 95)
Authors: Katayama Takane , Sakuma Akiko , Kimura Takatoshi , Makimura Yutaka , Hiratake Jun , Sakata Kanzo , Yamanoi Takashi , Kumagai Hidehiko , Yamamoto Kenji 
Published: July 2004

ABSTRACT

A genomic library of
Bifidobacterium bifidum
constructed in
Escherichia coli
was screened for the ability to hydrolyze the α-(1→2) linkage of 2′-fucosyllactose, and a gene encoding 1,2-α-
l
-fucosidase (AfcA) was isolated. The
afcA
gene was found to comprise 1,959 amino acid residues with a predicted molecular mass of 205 kDa and containing a signal peptide and a membrane anchor at the N and C termini, respectively. A domain responsible for fucosidase activity (the Fuc domain; amino acid residues 577 to 1474) was localized by deletion analysis and then purified as a hexahistidine-tagged protein. The recombinant Fuc domain specifically hydrolyzed the terminal α-(1→2)-fucosidic linkages of various oligosaccharides and a sugar chain of a glycoprotein. The stereochemical course of the hydrolysis of 2′-fucosyllactose was determined to be inversion by using
1
H nuclear magnetic resonance. The primary structure of the Fuc domain exhibited no similarity to those of any glycoside hydrolases (GHs) but showed high similarity to those of several hypothetical proteins in a database. Thus, it was revealed that the AfcA protein constitutes a novel inverting GH family (GH family 95).
A Novel
p
-Nitrophenol Degradation Gene Cluster from a Gram-Positive Bacterium,
Rhodococcus opacus
SAO101
Authors: Kitagawa Wataru , Kimura Nobutada , Kamagata Yoichi 
Published: July 2004

ABSTRACT

p
-Nitrophenol (4-NP) is recognized as an environmental contaminant; it is used primarily for manufacturing medicines and pesticides. To date, several 4-NP-degrading bacteria have been isolated; however, the genetic information remains very limited. In this study, a novel 4-NP degradation gene cluster from a gram-positive bacterium,
Rhodococcus opacus
SAO101, was identified and characterized. The deduced amino acid sequences of
npcB
,
npcA
, and
npcC
showed identity with phenol 2-hydroxylase component B (reductase, PheA2) of
Geobacillus thermoglucosidasius
A7 (32%), with 2,4,6-trichlorophenol monooxygenase (TcpA) of
Ralstonia eutropha
JMP134 (44%), and with hydroxyquinol 1,2-dioxygenase (ORF2) of
Arthrobacter
sp. strain BA-5-17 (76%), respectively. The
npcB
,
npcA
, and
npcC
genes were cloned into pET-17b to construct the respective expression vectors pETnpcB, pETnpcA, and pETnpcC. Conversion of 4-NP was observed when a mixture of crude cell extracts of
Escherichia coli
containing pETnpcB and pETnpcA was used in the experiment. The mixture converted 4-NP to hydroxyquinol and also converted 4-nitrocatechol (4-NCA) to hydroxyquinol. Furthermore, the crude cell extract of
E. coli
containing pETnpcC converted hydroxyquinol to maleylacetate. These results suggested that
npcB
and
npcA
encode the two-component 4-NP/4-NCA monooxygenase and that
npcC
encodes hydroxyquinol 1,2-dioxygenase. The
npcA
and
npcC
mutant strains, SDA1 and SDC1, completely lost the ability to grow on 4-NP as the sole carbon source. These results clearly indicated that the cloned
npc
genes play an essential role in 4-NP mineralization in
R. opacus
SAO101.
Ribosomal Protein S1 Specifically Binds to the 5′ Untranslated Region of the
Pseudomonas aeruginosa
Stationary-Phase Sigma Factor
rpoS
mRNA in the Logarithmic Phase of Growth
Authors: Ševo Milica , Buratti Emanuele , Venturi Vittorio 
Published: July 2004

ABSTRACT

The
rpoS
gene encodes the stationary-phase sigma factor (RpoS or σ
s
), which was identified in several gram-negative bacteria as a central regulator controlling the expression of genes involved in cell survival in response to cessation of growth (stationary phase) and providing cross-protection against various stresses. In
Pseudomonas aeruginosa
, the levels of σ
s
increase dramatically at the onset of the stationary phase and are regulated at the transcriptional and posttranscriptional levels. The
P. aeruginosa rpoS
gene is transcribed as a monocistronic
rpoS
mRNA transcript comprised of an unusually long 373-bp 5′ untranslated region (5′ UTR). In this study, the 5′ UTR and total protein extracts from
P. aeruginosa
logarithmic and stationary phases of growth were used in order to investigate the protein-RNA interactions that may modulate the translational process. It was observed that a 69-kDa protein, which corresponded to ribosomal protein S1, preferentially binds the 5′ UTR of the
rpoS
mRNA in the logarithmic phase and not in the stationary phase. This is the first report of a protein-
rpoS
mRNA 5′ UTR interaction in
P. aeruginosa
, and the possible involvement of protein S1 in translation regulation of
rpoS
is discussed.
PspG, a New Member of theYersinia enterocoliticaPhage Shock Protein Regulon
Authors: Green Rebecca C. , Darwin Andrew J. 
Published: July 2004

ABSTRACTTheYersinia enterocoliticaphage shock protein (Psp) system is induced when the Ysc type III secretion system is produced or when only the YscC secretin component is synthesized. Somepspnull mutants have a growth defect when YscC is produced and a severe virulence defect in animals. TheY. enterocolitica psplocus is made up of two divergently transcribed cistrons,pspFandpspABCDycjXF. pspAoperon expression is dependent on RpoN (σ54) and the enhancer-binding protein PspF. Previous data indicated that PspF also controls at least one gene that is not part of thepsplocus. In this study we describe the identification ofpspG, a new member of the PspF regulon. Predicted RpoN-binding sites upstream of thepspAgenes from different bacteria have a common divergence from the consensus sequence, which may be a signature of PspF-dependent promoters. TheY. enterocolitica pspGgene was identified because its promoter also has this signature. Like thepspAoperon,pspGis positively regulated by PspF, negatively regulated by PspA, and induced in response to the production of secretins. Purified His6-PspF protein specifically interacts with thepspAandpspGcontrol regions. ApspAoperon deletion mutant has a growth defect when the YscC secretin is produced and a virulence defect in a mouse model of infection. These phenotypes were exacerbated by apspGnull mutation. Therefore, PspG is the missing component of theY. enterocoliticaPsp regulon that was previously predicted to exist.
Systematic Mutagenesis of the
Escherichia coli
Genome
Authors: Kang Yisheng , Durfee Tim , Glasner Jeremy D. , Qiu Yu , Frisch David , Winterberg Kelly M. , Blattner Frederick R. 
Published: July 2004

ABSTRACT

A high-throughput method has been developed for the systematic mutagenesis of the
Escherichia coli
genome. The system is based on in vitro transposition of a modified Tn
5
element, the Sce-poson, into linear fragments of each open reading frame. The transposon introduces both positive (kanamycin resistance) and negative (I-SceI recognition site) selectable markers for isolation of mutants and subsequent allele replacement, respectively. Reaction products are then introduced into the genome by homologous recombination via the λRed proteins. The method has yielded insertion alleles for 1976 genes during a first pass through the genome including, unexpectedly, a number of known and putative essential genes. Sce-poson insertions can be easily replaced by markerless mutations by using the I-SceI homing endonuclease to select against retention of the transposon as demonstrated by the substitution of amber and/or in-frame deletions in six different genes. This allows a Sce-poson-containing gene to be specifically targeted for either designed or random modifications, as well as permitting the stepwise engineering of strains with multiple mutations. The promiscuous nature of Tn
5
transposition also enables a targeted gene to be dissected by using randomly inserted Sce-posons as shown by a
lacZ
allelic series. Finally, assessment of the insertion sites by an iterative weighted matrix algorithm reveals that these hyperactive Tn
5
complexes generally recognize a highly degenerate asymmetric motif on one end of the target site helping to explain the randomness of Tn
5
transposition.
Fibronectin Binding to theSalmonella entericaSerotype Typhimurium ShdA Autotransporter Protein Is Inhibited by a Monoclonal Antibody Recognizing the A3 Repeat
Authors: Kingsley Robert A. , Abi Ghanem Daad , Puebla-Osorio Nahum , Keestra A. Marijke , Berghman Luc , Bäumler Andreas J. 
Published: July 2004

ABSTRACTShdA is a large outer membrane protein of the autotransporter family whose passenger domain binds the extracellular matrix proteins fibronectin and collagen I, possibly by mimicking the host ligand heparin. The ShdA passenger domain consists of ∼1,500 amino acid residues that can be divided into two regions based on features of the primary amino acid sequence: an N-terminal nonrepeat region followed by a repeat region composed of two types of imperfect direct amino acid repeats, called type A and type B. The repeat region bound bovine fibronectin with an affinity similar to that for the complete ShdA passenger domain, while the nonrepeat region exhibited comparatively low fibronectin-binding activity. A number of fusion proteins containing truncated fragments of the repeat region did not bind bovine fibronectin. However, binding of the passenger domain to fibronectin was inhibited in the presence of immune serum raised to one truncated fragment of the repeat region that contained repeats A2, B8, A3, and B9. Furthermore, a monoclonal antibody that specifically recognized an epitope in a recombinant protein containing the A3 repeat inhibited binding of ShdA to fibronectin.
Two Biosynthetic Pathways for Aromatic Amino Acids in the Archaeon
Methanococcus maripaludis
Authors: Porat Iris , Waters Brian W. , Teng Quincy , Whitman William B. 
Published: July 2004

ABSTRACT

Methanococcus maripaludis
is a strictly anaerobic, methane-producing archaeon. Aromatic amino acids (AroAAs) are biosynthesized in this autotroph either by the de novo pathway, with chorismate as an intermediate, or by the incorporation of exogenous aryl acids via indolepyruvate oxidoreductase (IOR). In order to evaluate the roles of these pathways, the gene that encodes the third step in the de novo pathway, 3-dehydroquinate dehydratase (DHQ), was deleted. This mutant required all three AroAAs for growth, and no DHQ activity was detectible in cell extracts, compared to 6.0 ± 0.2 mU mg
−1
in the wild-type extract. The growth requirement for the AroAAs could be fulfilled by the corresponding aryl acids phenylacetate, indoleacetate, and
p
-hydroxyphenylacetate. The specific incorporation of phenylacetate into phenylalanine by the IOR pathway was demonstrated in vivo by labeling with [1-
13
C]phenylacetate.
M. maripaludis
has two IOR homologs. A deletion mutant for one of these homologs contained 76, 74, and 42% lower activity for phenylpyruvate,
p
-hydoxyphenylpyruvate, and indolepyruvate oxidation, respectively, than the wild type. Growth of this mutant in minimal medium was inhibited by the aryl acids, but the AroAAs partially restored growth. Genetic complementation of the IOR mutant also restored much of the wild-type phenotype. Thus, aryl acids appear to regulate the expression or activity of the de novo pathway. The aryl acids did not significantly inhibit the activity of the biosynthetic enzymes chorismate mutase, prephenate dehydratase, and prephenate dehydrogenase in cell extracts, so the inhibition of growth was probably not due to an effect on these enzymes.
Characterization of the 3-
O
-Methylgallate Dioxygenase Gene and Evidence of Multiple 3-
O
-Methylgallate Catabolic Pathways in
Sphingomonas paucimobilis
SYK-6
Authors: Kasai Daisuke , Masai Eiji , Miyauchi Keisuke , Katayama Yoshihiro , Fukuda Masao 
Published: July 2004

ABSTRACT

Sphingomonas paucimobilis
SYK-6 is able to grow on various lignin-derived biaryls as the sole source of carbon and energy. These compounds are degraded to vanillate and syringate by the unique and specific enzymes in this strain. Vanillate and syringate are converted to protocatechuate (PCA) and 3-
O
-methylgallate (3MGA), respectively, by the tetrahydrofolate-dependent
O
-demethylases. Previous studies have suggested that these compounds are further degraded via the PCA 4,5-cleavage pathway. However, our subsequent analysis of the
ligB
insertion mutant, which encodes the β subunit of PCA 4,5-dioxygenase, suggested that at least one alternative route is involved in 3MGA degradation. In the present study, we isolated the
desZ
gene, which confers 3MGA degradation activity on
Escherichia coli
. The deduced amino acid sequence of
desZ
showed ca. 20 to 43% identity with the type II extradiol dioxygenases. Gas chromatography-mass spectrometry analysis suggested that DesZ catalyzes the 3,4-cleavage of 3MGA. Disruption of both
desZ
and
ligB
in SYK-6 resulted in loss of the dioxygen-dependent 3MGA transformation activity, but the resulting mutant retained the ability to grow on syringate. We found that the cell extract of the
desZ ligB
double mutant was able to convert 3MGA to gallate when tetrahydrofolate was added to the reaction mixture, and the cell extract of this mutant degraded gallate to the same degree as the wild type did. All these results suggest that syringate is degraded through multiple 3MGA degradation pathways in which
ligAB
,
desZ
, 3MGA
O
-demethylase, and gallate dioxygenase are participants.