bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Cysteine Desulfurase IscS Is Required for Synthesis of All Five Thiolated Nucleosides Present in tRNA from
Salmonella enterica
Serovar Typhimurium
Authors: Nilsson Kristina , Lundgren Hans K. , Hagervall Tord G. , Björk Glenn R. 
Published: November 2002

ABSTRACT

Deficiency of a modified nucleoside in tRNA often mediates suppression of +1 frameshift mutations. In
Salmonella enterica
serovar Typhimurium strain TR970 (
hisC3737
), which requires histidine for growth, a potential +1 frameshifting site, CCC-CAA-UAA, exists within the frameshifting window created by insertion of a C in the
hisC
gene. This site may be suppressed by peptidyl-tRNA
Procmo5UGG
(cmo
5
U is uridine-5-oxyacetic acid), making a frameshift when decoding the near-cognate codon CCC, provided that a pause occurs by, e.g., a slow entry of the tRNA
Glnmnm5s2UUG
(mnm
5
s
2
U is 5-methylaminomethyl-2-thiouridine) to the CAA codon located in the A site. We selected mutants of strain TR970 that were able to grow without histidine, and one such mutant (
iscS51
) was shown to have an amino acid substitution in the
l
-cysteine desulfurase IscS. Moreover, the levels of all five thiolated nucleosides 2-thiocytidine, mnm
5
s
2
U, 5-carboxymethylaminomethyl-2-thiouridine, 4-thiouridine, and
N
-6-(4-hydroxyisopentenyl)-2-methylthioadenosine present in the tRNA of
S. enterica
were reduced in the
iscS51
mutant. In logarithmically growing cells of
Escherichia coli
, a deletion of the
iscS
gene resulted in nondetectable levels of all thiolated nucleosides in tRNA except
N
-6-(4-hydroxyisopentenyl)-2-methylthioadenosine, which was present at only 1.6% of the wild-type level. After prolonged incubation of cells in stationary phase, a 20% level of 2-thiocytidine and a 2% level of
N
-6-(4-hydroxyisopentenyl)-2-methylthioadenosine was observed, whereas no 4-thiouridine, 5-carboxymethylaminomethyl-2-thiouridine, or mnm
5
s
2
U was found. We attribute the frameshifting ability mediated by the
iscS51
mutation to a slow decoding of CAA by the tRNA
Glnmnm5s2UUG
due to mnm
5
s
2
U deficiency. Since the growth rate of the
iscS
deletion mutant in rich medium was similar to that of a mutant (
mnmA
) lacking only mnm
5
s
2
U, we suggest that the major cause for the reduced growth rate of the
iscS
deletion mutant is the lack of mnm
5
s
2
U and 5-carboxymethylaminomethyl-2-thiouridine and not the lack of any of the other three thiolated nucleosides that are also absent in the
iscS
deletion mutant.
Bacteriophage HP2 of
Haemophilus influenzae
Authors: Williams Bryan J. , Golomb Miriam , Phillips Thomas , Brownlee Joshua , Olson Maynard V. , Smith Arnold L. 
Published: November 2002

ABSTRACT

Temperate bacteriophages effect chromosomal evolution of their bacterial hosts, mediating rearrangements and the acquisition of novel genes from other taxa. Although the
Haemophilus influenzae
genome shows evidence of past phage-mediated lateral transfer, the phages presumed responsible have not been identified. To date, six different
H. influenzae
phages are known; of these, only the HP1/S2 group, which lyosogenizes exclusively Rd strains (which were originally encapsulated serotype d), is well characterized. Phages in this group are genetically very similar, with a highly conserved set of genes. Because the majority of
H. influenzae
strains are nonencapsulated (nontypeable), it is important to characterize phages infecting this larger, genetically more diverse group of respiratory pathogens. We have identified and sequenced HP2, a bacteriophage of nontypeable
H. influenzae
. Although related to the fully sequenced HP1 (and even more so to the partially sequenced S2) and similar in genetic organization, HP2 has a few novel genes and differs in host range; HP2 will not infect or lysogenize Rd strains. Genomic comparisons between HP1/S2 and HP2 suggest recent divergence, with new genes completely replacing old ones at certain loci. Sequence comparisons suggest that
H. influenzae
phages evolve by recombinational exchange of genes with each other, with cryptic prophages, and with the host chromosome.
Characterization of a Fourth Tungsten-Containing Enzyme from the Hyperthermophilic Archaeon
Pyrococcus furiosus
Authors: Roy Roopali , Adams Michael W. W. 
Published: November 2002

ABSTRACT

Pyrococcus furiosus
grows optimally near 100°C using peptides and carbohydrates as carbon sources, and it reduces elemental sulfur (S
0
), if present, to H
2
S. Tungsten (W), an element rarely used in biology, is required for optimal growth, and three different tungsten-containing enzymes have been previously purified from this organism. They all oxidize aldehydes of various types and are thought to play primary roles in the catabolism of sugars or amino acids. Here, the purification of a fourth tungsten-containing enzyme, termed WOR 4, from cell extracts of
P. furiosus
grown with S
0
is described. This was achieved by monitoring through multiple chromatography steps the W that is not associated with the three characterized tungstoenzymes. The N-terminal sequence of WOR 4 and the approximate molecular weight of its subunit determined electrophoretically (69,000) correspond to the product of an ORF (PF1961,
wor4
) present in the complete genome sequence of
P. furiosus
. WOR 4 is a homodimer and contains approximately one W, three Fe, three or four acid-labile sulfide, and one Ca atom per subunit. The visible and electron paramagnetic resonance spectra of the oxidized and reduced enzyme indicate the presence of an unusual iron-sulfur chromophore. WOR 4 does not oxidize aliphatic or aromatic aldehydes or hydroxy acids, nor does it reduce keto acids. Consistent with prior microarray data, the protein could not be purified from
P. furiosus
cells grown in the absence of S
0
, suggesting that it may have a role in S
0
metabolism.
Repression of Glutamate Dehydrogenase Formation in
Klebsiella aerogenes
Requires Two Binding Sites for the Nitrogen Assimilation Control Protein, NAC
Authors: Goss Thomas J. , Janes Brian K. , Bender Robert A. 
Published: November 2002

ABSTRACT

In
Klebsiella aerogenes
, the
gdhA
gene codes for glutamate dehydrogenase, one of the enzymes responsible for assimilating ammonia into glutamate. Expression of a
gdhAp-lacZ
transcriptional fusion was strongly repressed by the nitrogen assimilation control protein, NAC. This strong repression (>50-fold under conditions of severe nitrogen limitation) required the presence of two separate NAC binding sites centered at −89 and +57 relative to the start of
gdhA
transcription. Mutants lacking either or both of these sites lost the strong repression. The distance between the two sites was less important than the face of the helix on which they lay. Insertion or deletion of 10 bp between the sites had little effect on the strong repression, but insertion of 5 bp or deletion of either 5 or 15 bp decreased the repression significantly. We propose that the strong repression of
gdhAp-lacZ
expression requires an interaction between the NAC molecules bound at the two sites. A weaker repression of
gdhAp-lacZ
expression (about threefold) required only the NAC site centered at −89. This weaker repression appears to result from NAC's ability to prevent the action of a positive effector the target of which overlaps the NAC binding site centered at −89. Point mutations and deletions of this region result in the same threefold reduction in
gdhAp-lacZ
expression as the presence of NAC at this site.
The
Escherichia coli gabDTPC
Operon: Specific γ-Aminobutyrate Catabolism and Nonspecific Induction
Authors: Schneider Barbara L. , Ruback Stephen , Kiupakis Alexandros K. , Kasbarian Hillary , Pybus Christine , Reitzer Larry 
Published: November 2002

ABSTRACT

Nitrogen limitation induces the nitrogen-regulated (Ntr) response, which includes proteins that assimilate ammonia and scavenge nitrogen. Nitrogen limitation also induces catabolic pathways that degrade four metabolically related compounds: putrescine, arginine, ornithine, and γ-aminobutyrate (GABA). We analyzed the structure, function, and regulation of the
gab
operon, whose products degrade GABA, a proposed intermediate in putrescine catabolism. We showed that the
gabDTPC
gene cluster constitutes an operon based partially on coregulation of GabT and GabD activities and the polarity of an insertion in
gabT
on
gabC
. A Δ
gabDT
mutant grew normally on all of the nitrogen sources tested except GABA. The unexpected growth with putrescine resulted from specific induction of
gab
-independent enzymes. Nac was required for
gab
transcription in vivo and in vitro. Ntr induction did not require GABA, but various nitrogen sources did not induce enzyme activity equally. A
gabC
(formerly
ygaE
) mutant grew faster with GABA and had elevated levels of
gab
operon products, which suggests that GabC is a repressor. GabC is proposed to reduce nitrogen source-specific modulation of expression. Unlike a wild-type strain, a
gabC
mutant utilized GABA as a carbon source and such growth required σ
S
. Previous studies showing σ
S
-dependent
gab
expression in stationary phase involved
gabC
mutants, which suggests that such expression does not occur in wild-type strains. The seemingly narrow catabolic function of the
gab
operon is contrasted with the nonspecific (nitrogen source-independent) induction. We propose that the
gab
operon and the Ntr response itself contribute to putrescine and polyamine homeostasis.
Identification and Localization of the Gene Cluster Encoding Biosynthesis of the Antitumor Macrolactam Leinamycin in
Streptomyces atroolivaceus
S-140
Authors: Cheng Yi-Qiang , Tang Gong-Li , Shen Ben 
Published: November 2002

ABSTRACT

Leinamycin (LNM), produced by
Streptomyces atroolivaceus
, is a thiazole-containing hybrid peptide-polyketide natural product structurally characterized with an unprecedented 1,3-dioxo-1,2-dithiolane moiety that is spiro-fused to a 18-member macrolactam ring. LNM exhibits a broad spectrum of antimicrobial and antitumor activities, most significantly against tumors that are resistant to clinically important anticancer drugs, resulting from its DNA cleavage activity in the presence of a reducing agent. Using a PCR approach to clone a thiazole-forming nonribosomal peptide synthetase (NRPS) as a probe, we localized a 172-kb DNA region from
S. atroolivaceus
S-140 that harbors the
lnm
biosynthetic gene cluster. Sequence analysis of 11-kb DNA revealed three genes,
lnmG
,
lnmH
, and
lnmI
, and the deduced product of
lnmI
is characterized by domains characteristic to both NRPS and polyketide synthase (PKS). The involvement of the cloned gene cluster in LNM biosynthesis was confirmed by disrupting the
lnmI
gene to generate non-LNM-producing mutants and by characterizing LnmI as a hybrid NRPS-PKS megasynthetase, the NRPS module of which specifies for
l
-Cys and catalyzes thiazole formation. These results have now set the stage for full investigations of LNM biosynthesis and for generation of novel LNM analogs by combinatorial biosynthesis.
Alcaligin Siderophore Production by
Bordetella bronchiseptica
Strain RB50 Is Not Repressed by the BvgAS Virulence Control System
Authors: Brickman Timothy J. , Armstrong Sandra K. 
Published: November 2002

ABSTRACT

A previous study found that alcaligin siderophore production by
Bordetella bronchiseptica
strain RB50 is Bvg repressed. In contrast, we report that alcaligin production by RB50 does not require Bvg phenotypic phase modulation and that isogenic Bvg(Con) and Bvg
−
phase-locked mutants both produce alcaligin in response to iron starvation.
Preparation and photoconducting property of C60Cln‐m‐bonded poly(N‐vinylcarbazole) with C60Cln/CuCl/Bpy catalyst system
Authors: Hua Jing , Chen Dianbao , Jing Xiongke , Xu Ling , Yu Yongliong , Zhang Yifeng 
Published: November 2002

AbstractC60Cln‐m bonded poly(N‐vinylcarbazole) (C60‐PVK) has been synthesized by C60Cln (the average value of n is 20)/CuCl/ Bpy (2,2′‐bipyridine) catalyst system and its structure was analyzed by UV‐Vis and proton NMR. The polymerization mechanism was proposed proceeding via a atom transfer radical polymerization (ATRP). The block copolymer of poly N‐vinylcarbazole‐block‐polystyrene can also be compounded by adding styrene after N‐vinylcarbazole polymerized completely in this polymerization system. The photoconducting properties of C60Cln‐m‐bonded poly(N‐vinylcarbazole) was better than poly(N‐vinylcarbazole) initiated by AIBN. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 87: 606–609, 2003
Discrimination of various poly(propylene) copolymers and prediction of their ethylene content by near‐infrared and Raman spectroscopy in combination with chemometric methods
Authors: Furukawa Tsuyoshi , Watari Masahiro , Siesler Heinz W. , Ozaki Yukihiro 
Published: November 2002

AbstractNear‐infrared (NIR) diffuse reflectance (DR) spectra and Fourier‐transform (FT) Raman spectra were measured for 12 kinds of block and random poly(propylene) (PP) copolymers with different ethylene content in pellets and powder states to propose calibration models that predict the ethylene content in PP and to deepen the understanding of the NIR and Raman spectra of PP. Band assignments were proposed based calculation of the second derivatives of the original spectra, analysis of loadings and regression coefficient plots of principal component analysis (PCA) and principal component regression (PCR) (predicting the ethylene content) models, and comparison of the NIR and Raman spectra of PP with those of linear low‐density polyethylene (LLDPE) with short branches. PCR and partial least squares (PLS) regression were applied to the second derivatives of the NIR spectra and the NIR spectra after multiplicative scatter correction (MSC) to develop the calibration models. After MSC treatment, the original spectra yield slightly better results for the standard error of prediction (SEP) than the second derivatives. A plot of regression coefficients for the PCR model shows peaks due to the CH2 groups pointing upwards and those arising from the CH3 groups pointing downwards, clearly separating the bands due to CH3 and CH2 groups. For the Raman data, MSC and normalization were applied to the original spectra, and then PCR and PLS regression were carried out to build the models. The PLS regression for the normalized spectra yields the best results for the correlation coefficient and the SEP. Raman bands at 1438, 1296, and 1164 cm−1 play key roles in the prediction of the ethylene content in PP. The NIR chemometric evaluation of the data gave better results than those derived from the Raman spectra and chemometric analysis. Possible reasons for this observation are discussed. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 87: 616–625, 2003
Modulation of uptake of organic cationic drugs in cultured human colon adenocarcinoma Caco‐2 cells by an ecto‐alkaline phosphatase activity
Authors: Calhau C. , Martel F. , Hipólito‐Reis C. , Azevedo I. 
Published: November 2002

AbstractAlkaline phosphatase (ALP) refers to a group of nonspecific phosphomonoesterases located primarily in cell plasma membrane. It has been described in different cell lines that ecto‐ALP is directly or indirectly involved in the modulation of organic cation transport. We aimed to investigate, in Caco‐2 cells, a putative modulation of 1‐methyl‐4‐phenylpyridinium (MPP+) apical uptake by an ecto‐ALP activity. Ecto‐ALP activity and 3H‐MPP+ uptake were evaluated in intact Caco‐2 cells (human colon adenocarcinoma cell line), in the absence and presence of a series of drugs. The activity of membrane‐bound ecto‐ALP expressed on the apical surface of Caco‐2 cells was studied at physiological pH using p‐nitrophenylphosphate as substrate. The results showed that Caco‐2 cells express ALP activity, characterized by an ecto‐oriented active site functional at physiological pH. Genistein (250 µM), 3‐isobutyl‐1‐methylxanthine (1 mM), verapamil (100 µM), and ascorbic acid (1 mM) significantly increased ecto‐ALP activity and decreased 3H‐MPP+ apical transport in this cell line. Orthovanadate (100 µM) showed no effect on 3H‐MPP+ transport and on ecto‐ALP activity. On the other hand, okadaic acid (310 nM) and all trans‐retinoic acid (1 µM) significantly increased 3H‐MPP+ uptake and inhibited ecto‐ALP activity. There is a negative correlation between the effect of drugs upon ecto‐ALP activity and 3H‐MPP+ apical transport (r = −0.9; P = 0.0014). We suggest that apical uptake of organic cations in Caco‐2 cells is affected by phosphorylation/dephosphorylation mechanisms, and that ecto‐ALP activity may be involved in this process. J. Cell. Biochem. 87: 408–416, 2002. © 2002 Wiley‐Liss, Inc.
CCL9/MIP‐1γ and its receptor CCR1 are the major chemokine ligand/receptor species expressed by osteoclasts
Authors: Lean Jenny M. , Murphy Chiho , Fuller Karen , Chambers Timothy J. 
Published: November 2002

AbstractAlthough much has been learned recently of the mechanisms by which the differentiation of osteoclasts is induced, less is known of the factors that regulate their migration and localization, and their interactions with other bone cells. In related cell types, chemokines play a major role in these processes. We therefore systematically tested the expression of RNA for chemokines and their receptors by osteoclasts. Because bone is the natural substrate for osteoclasts and may influence osteoclast behavior, we also tested expression on bone slices. Quantitative RT‐PCR using real‐time analysis with SYBR Green was therefore performed on RNA isolated from bone marrow cells after incubation with macrophage‐colony stimulating factor (M‐CSF) with/without receptor‐activator of NFκB ligand (RANKL), on plastic or bone. We found that RANKL induced expression of CCL9/MIP‐1γ to levels comparable to that of tartrate‐resistant acid phosphatase (TRAP), a major specialized product of osteoclasts. CCL22/MDC, CXCL13/BLC/BCA‐1, and CCL25/TECK were also induced. The dominant chemokine receptor expressed by osteoclasts was CCR1, followed by CCR3 and CX3CR1. Several receptors expressed on macrophages and associated with inflammatory responses, including CCR2 and CCR5, were down‐regulated by RANKL. CCL9, which acts through CCR1, stimulated cytoplasmic motility and polarization in osteoclasts, identical to that previously observed in response to CCL3/MIP‐1α, which also acts through CCR1 and is chemotactic for osteoclasts. These results identify CCL9 and its receptor CCR1 as the major chemokine and receptor species expressed by osteoclasts, and suggest a crucial role for CCL9 in the regulation of bone resorption. J. Cell. Biochem. 87: 386–393, 2002. © 2002 Wiley‐Liss, Inc.
Wideband disc‐ring dielectric resonator antenna
Authors: Ong Swee Huat , Kishk Ahmed A. , Glisson Allen W. 
Published: November 2002

AbstractA dielectric resonator excited by a coaxial probe and designed for an omni‐directional pattern is considered. Combining two dielectric resonators of different dielectric material with each other enhances bandwidth. The effect of antenna parameters such as dielectric constant and probe length are investigated. The analysis is performed numerically, using the method of moments and verified by the FDTD method. The agreement between the two methods is excellent. A 45% bandwidth is achieved with this structure. © 2002 Wiley Periodicals, Inc. Microwave Opt Technol Lett 35: 425–428, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10628
Stability of narrow zigzag carbon nanotubes
Authors: Cabria I. , Mintmire J. W. , White C. T. 
Published: November 2002

AbstractFirst principles calculations of the electronic structure and total energy of narrow zigzag carbon nanotubes and their corresponding flat graphene strips have been carried out to assess the relative stability of the tube form. The results indicate that the smallest energetically stable carbon nanotube has a radius of about 0.2 nm. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2003
Grids and Grid technologies for wide‐area distributed computing
Authors: Baker Mark , Buyya Rajkumar , Laforenza Domenico 
Published: November 2002

AbstractThe last decade has seen a substantial increase in commodity computer and network performance, mainly as a result of faster hardware and more sophisticated software. Nevertheless, there are still problems, in the fields of science, engineering, and business, which cannot be effectively dealt with using the current generation of supercomputers. In fact, due to their size and complexity, these problems are often very numerically and/or data intensive and consequently require a variety ofheterogeneous resources that are not available on a single machine. A number of teams have conducted experimental studies on the cooperative use of geographically distributed resources unified to act as a single powerful computer. This new approach is known by several names, such as metacomputing, scalable computing, global computing, Internet computing, and more recently peer‐to‐peer or Grid computing. The early efforts in Grid computing started as a project to link supercomputing sites, but have now grown far beyond their original intent. In fact, many applications can benefit from the Grid infrastructure, including collaborative engineering, data exploration, high‐throughput computing, and of course distributed supercomputing. Moreover, due to the rapid growth of the Internet and Web, there has been a rising interest in Web‐based distributed computing, and many projects have been started and aim to exploit the Web as an infrastructure for running coarse‐grained distributed and parallel applications. In this context, the Web has the capability to be a platform for parallel and collaborative work as well as a key technology to create a pervasive and ubiquitous Grid‐based infrastructure. This paper aims to present the state‐of‐the‐art of Grid computing and attempts to survey the major international efforts in developing this emerging technology. Copyright © 2002 John Wiley & Sons, Ltd.
The DnaK Chaperone Is Necessary for α-Complementation of β-Galactosidase in
Escherichia coli
Authors: Lopes Ferreira Nicolas , Alix Jean-Hervé 
Published: November 2002

ABSTRACT

We show here the involvement of the molecular chaperone DnaK from
Escherichia coli
in the in vivo α-complementation of the β-galactosidase. In the
dnaK756
(Ts) mutant, α-complementation occurs when the organisms are grown at 30°C but not at 37 or 40°C, although these temperatures are permissive for bacterial growth. Plasmid-driven expression of wild-type
dnaK
restores the α-complementation in the mutant but also stimulates it in a
dnaK
+
strain. In a mutant which contains a disrupted
dnaK
gene (
ΔdnaK52
::Cm
r
), α-complementation is also impaired, even at 30°C. This observation provides an easy and original phenotype to detect subtle functional changes in a protein such as the DnaK756 chaperone, within the physiologically relevant temperature.