bluuebunny/crossref_metadata_2025_split huggingface dataset:
Micronucleus evaluation in mitogen‐stimulated lymphocytes of narrow‐band (311 nm TL01) UVB‐treated patients
Authors: Ferahbas Ayten , Donmez‐Altuntas Hamiyet , Hamurcu Zuhal , Aktas Ekrem , Utas Serap 
Published: March 2004

Background: Narrow‐band UVB (311 nm) lamps (TL01) are being increasingly used for phototherapy of psoriasis and other dermatoses, for their excellent effect compared with broad‐band UVB sources and photochemotherapy. It is acknowledged that the TL01 lamp is probably two to three times more carcinogenic per minimum erythema dose than broad‐band UVB, but the cumulative dose is considerably less than broadband UVB sources. Micronucleus (MN) test is used to detect both clastogenic (breaking) and aneugenic (abnormal segregation) effect of physical/chemical agents on chromosomes. The aim of this study is to evaluate MN frequencies in mitogen‐stimulated lymphocytes of narrow‐band UVB‐treated patients.Methods: Frequency of micronuclei in 72 h cultivated/mitogen‐stimulated lymphocytes of 36 patients (age 7–73 years, mean±SD: 25.33±18.54) have been evaluated at pretreatment and after 20, 40, 60 sessions of narrowband UVB treatment.Results: While the beginning MN frequency ±SD (%) was 1.07±0.63, it increased to 1.47±0.92, 1.47± 0.77, 1.41±0.31 corresponding, respectively, to 20, 40, 60 sessions. These sessions reciprocally correspond to 0.85±0.23, 2.97±0.72, 5.68±1.46 J/cm2 doses of narrow‐band UVB. Difference of MN frequency was statistically significant (P=0.002). Significant differences have been observed between the initial MN frequency and after that of 20, 40, 60 sessions (P=0.001, 0.004, 0.002, respectively).Conclusion: The results of this study show that narrow‐band UVB treatment causes a detectable chromosome damaging effect.
Nonlinear Elasticity
for Modeling Fracture of Isotropic Brittle Solids
Authors: Volokh K. Y. 
Published: March 2004

Abstract
A softening hyperelastic continuum model is proposed for analysis of brittle fracture. Isotropic material is characterized by two standard parameters—shear and bulk modulus—and an additional parameter of the volumetric separation work. The model can be considered as a volumetric generalization of the concept of the cohesive surface. The meaning of the proposed constitutive equations is clarified by the examples of simple shear and hydrostatic pressure. It is emphasized that the proposed constitutive model includes only smooth functions and the necessary computational techniques are those of nonlinear elasticity.
Complete Genomic Sequence of the Virulent
Salmonella
Bacteriophage SP6
Authors: Dobbins Aleisha T. , George Matthew , Basham Daryl A. , Ford Michael E. , Houtz Jennifer M. , Pedulla Marisa L. , Lawrence Jeffrey G. , Hatfull Graham F. , Hendrix Roger W. 
Published: March 2004

ABSTRACT

We report the complete genome sequence of enterobacteriophage SP6, which infects
Salmonella enterica
serovar Typhimurium. The genome contains 43,769 bp, including a 174-bp direct terminal repeat. The gene content and organization clearly place SP6 in the coliphage T7 group of phages, but there is ∼5 kb at the right end of the genome that is not present in other members of the group, and the homologues of T7 genes
1.3
through
3
appear to have undergone an unusual reorganization. Sequence analysis identified 10 putative promoters for the SP6-encoded RNA polymerase and seven putative rho-independent terminators. The terminator following the gene encoding the major capsid subunit has a termination efficiency of about 50% with the SP6-encoded RNA polymerase. Phylogenetic analysis of phages related to SP6 provided clear evidence for horizontal exchange of sequences in the ancestry of these phages and clearly demarcated exchange boundaries; one of the recombination joints lies within the coding region for a phage exonuclease. Bioinformatic analysis of the SP6 sequence strongly suggested that DNA replication occurs in large part through a bidirectional mechanism, possibly with circular intermediates.
Transcriptional Analysis of Butanol Stress and Tolerance in
Clostridium acetobutylicum
Authors: Tomas Christopher A. , Beamish Jeffrey , Papoutsakis Eleftherios T. 
Published: March 2004

ABSTRACT

The effects of challenges with low (0.25%, vol/vol) and high (0.75%) concentrations of butanol on the growth, glucose metabolism, product formation, and transcriptional program of the solvent-tolerant
Clostridium acetobutylicum
strain 824(pGROE1) and the plasmid control strain 824(pSOS95del) were used to study solvent tolerance and stress response. Strain 824(pGROE1) was generated by
groESL
overexpression. The growth of 824(pGROE1) was less inhibited than that of 824(pSOS95del), and 824(pGROE1) was able to metabolize glucose over the entire course of the culture (60 h postchallenge) while glucose metabolism in 824(pSOS95del) lasted 24 h. A comparison of their respective DNA array-based transcriptional profiles identified genes with similar expression patterns (these genes are likely to be part of a general butanol stress response) and genes with opposite expression patterns (these genes are likely to be associated with increased tolerance to butanol). Both strains exhibited a butanol dose-dependent increase in expression of all major stress protein genes, including
groES
,
dnaKJ
,
hsp18
, and
hsp90
; all major solvent formation genes, including
aad
,
ctfA
and -
B
,
adc
, and
bdhA
and -
B
(an unexpected and counterintuitive finding); the butyrate formation genes (
ptb
and
buk
); the butyryl coenzyme A biosynthesis operon genes; fructose bisphosphate aldolase; and a gene with homology to
Bacillus subtilis kinA
. A dose-dependent decrease in expression was observed for the genes of the major fatty acid synthesis operon (also an unexpected and counterintuitive finding), several glycolytic genes, and a few sporulation genes. Genes with opposite expression kinetics included
rlpA
,
artP
, and a gene encoding a hemin permease. Taken together, these data suggest that stress, even when it derives from the solvent product itself, triggers the induction of the solvent formation genes.
DNA Sequence Duplication in
Rhodobacter sphaeroides
2.4.1: Evidence of an Ancient Partnership between Chromosomes I and II
Authors: Choudhary Madhusudan , Fu Yun-Xin , Mackenzie Chris , Kaplan Samuel 
Published: March 2004

ABSTRACT

The complex genome of
Rhodobacter sphaeroides
2.4.1, composed of chromosomes I (CI) and II (CII), has been sequenced and assembled. We present data demonstrating that the
R. sphaeroides
genome possesses an extensive amount of exact DNA sequence duplication, 111 kb or ∼2.7% of the total chromosomal DNA. The chromosomal DNA sequence duplications were aligned to each other by using MUMmer. Frequency and size distribution analyses of the exact DNA duplications revealed that the interchromosomal duplications occurred prior to the intrachromosomal duplications. Most of the DNA sequence duplications in the
R. sphaeroides
genome occurred early in species history, whereas more recent sequence duplications are rarely found. To uncover the history of gene duplications in the
R. sphaeroides
genome, 44 gene duplications were sampled and then analyzed for DNA sequence similarity against orthologous DNA sequences. Phylogenetic analysis revealed that ∼80% of the total gene duplications examined displayed type A phylogenetic relationships; i.e., one copy of each member of a duplicate pair was more similar to its orthologue, found in a species closely related to
R. sphaeroides
, than to its duplicate, counterpart allele. The data reported here demonstrate that a massive level of gene duplications occurred prior to the origin of the
R. sphaeroides
2.4.1 lineage. These findings lead to the conclusion that there is an ancient partnership between CI and CII of
R. sphaeroides
2.4.1.
Transcriptional Activation byBacillus subtilisResD: Tandem Binding to Target Elements and Phosphorylation-Dependent and -Independent Transcriptional Activation
Authors: Geng Hao , Nakano Shunji , Nakano Michiko M. 
Published: March 2004

ABSTRACTThe expression of genes involved in nitrate respiration inBacillus subtilisis regulated by the ResD-ResE two-component signal transduction system. The membrane-bound ResE sensor kinase perceives a redox-related signal(s) and phosphorylates the cognate response regulator ResD, which enables interaction of ResD with ResD-dependent promoters to activate transcription. Hydroxyl radical footprinting analysis revealed that ResD tandemly binds to the −41 to −83 region ofhmpand the −46 to −92 region ofnasD. In vitro runoff transcription experiments showed that ResD is necessary and sufficient to activate transcription of the ResDE regulon. Although phosphorylation of ResD by ResE kinase greatly stimulated transcription, unphosphorylated ResD, as well as ResD with a phosphorylation site (Asp57) mutation, was able to activate transcription at a low level. The D57A mutant was shown to retain the activity in vivo to induce transcription of the ResDE regulon in response to oxygen limitation, suggesting that ResD itself, in addition to its activation through phosphorylation-mediated conformation change, senses oxygen limitation via an unknown mechanism leading to anaerobic gene activation.
Agrobacterium-Mediated Transformation ofAspergillus awamoriin the Absence of Full-Length VirD2, VirC2, or VirE2 Leads to Insertion of Aberrant T-DNA Structures
Authors: Michielse Caroline B. , Ram Arthur F. J. , Hooykaas Paul J. J. , van den Hondel Cees A. M. J. J. 
Published: March 2004

ABSTRACTReductions to 2, 5, and 42% of the wild-type transformation efficiency were found whenAgrobacteriummutants carrying transposon insertions invirD2,virC2, andvirE2, respectively, were used to transformAspergillus awamori. The structures of the T-DNAs integrated into the host genome by these mutants were analyzed by Southern and sequence analyses. The T-DNAs of transformants obtained with thevirE2mutant had left-border truncations, whereas those obtained with thevirD2mutant had truncated right ends. From this analysis, it was concluded that the virulence proteins VirD2 and VirE2 are required for full-length T-DNA integration and that these proteins play a role in protecting the right and left T-DNA borders, respectively. Multicopy and truncated T-DNA structures were detected in the majority of the transformants obtained with thevirC2mutant, indicating that VirC2 plays a role in correct T-DNA processing and is required for single-copy T-DNA integration.
The
fixABCX
Genes in
Rhodospirillum rubrum
Encode a Putative Membrane Complex Participating in Electron Transfer to Nitrogenase
Authors: Edgren Tomas , Nordlund Stefan 
Published: March 2004

ABSTRACT

In our efforts to identify the components participating in electron transport to nitrogenase in
Rhodospirillum rubrum
, we used mini-Tn
5
mutagenesis followed by metronidazole selection. One of the mutants isolated, SNT-1, exhibited a decreased growth rate and about 25% of the in vivo nitrogenase activity compared to the wild-type values. The in vitro nitrogenase activity was essentially wild type, indicating that the mutation affects electron transport to nitrogenase. Sequencing showed that the Tn
5
insertion is located in a region with a high level of similarity to
fixC
, and extended sequencing revealed additional putative
fix
genes, in the order
fixABCX
. Complementation of SNT-1 with the whole
fix
gene cluster in
trans
restored wild-type nitrogenase activity and growth. Using Western blotting, we demonstrated that expression of
fixA
and
fixB
occurs only under conditions under which nitrogenase also is expressed. SNT-1 was further shown to produce larger amounts of both ribulose 1,5-bisphosphate carboxylase/oxgenase and polyhydroxy alkanoates than the wild type, indicating that the redox status is affected in this mutant. Using Western blotting, we found that FixA and FixB are soluble proteins, whereas FixC most likely is a transmembrane protein. We propose that the
fixABCX
genes encode a membrane protein complex that plays a central role in electron transfer to nitrogenase in
R. rubrum
. Furthermore, we suggest that FixC is the link between nitrogen fixation and the proton motive force generated in the photosynthetic reactions.
Biochemical Characterization of a Dihydromethanopterin Reductase Involved in Tetrahydromethanopterin Biosynthesis in
Methylobacterium extorquens
AM1
Authors: Caccamo Marco A. , Malone Courtney S. , Rasche Madeline E. 
Published: March 2004

ABSTRACT

During growth on one-carbon (C
1
) compounds, the aerobic α-proteobacterium
Methylobacterium extorquens
AM1 synthesizes the tetrahydromethanopterin (H
4
MPT) derivative dephospho-H
4
MPT as a C
1
carrier in addition to tetrahydrofolate. The enzymes involved in dephospho-H
4
MPT biosynthesis have not been identified in bacteria. In archaea, the final step in the proposed pathway of H
4
MPT biosynthesis is the reduction of dihydromethanopterin (H
2
MPT) to H
4
MPT, a reaction analogous to the reaction of the bacterial dihydrofolate reductase. A gene encoding a dihydrofolate reductase homolog has previously been reported for
M. extorquens
and assigned as the putative H
2
MPT reductase gene (
dmrA
). In the present work, we describe the biochemical characterization of H
2
MPT reductase (DmrA), which is encoded by
dmrA
. The gene was expressed with a six-histidine tag in
Escherichia coli
, and the recombinant protein was purified by nickel affinity chromatography and gel filtration. Purified DmrA catalyzed the NAD(P)H-dependent reduction of H
2
MPT with a specific activity of 2.8 μmol of NADPH oxidized per min per mg of protein at 30°C and pH 5.3. Dihydrofolate was not a substrate for DmrA at the physiological pH of 6.8. While the existence of an H
2
MPT reductase has been proposed previously, this is the first biochemical evidence for such an enzyme in any organism, including archaea. Curiously, no DmrA homologs have been identified in the genomes of known methanogenic archaea, suggesting that bacteria and archaea produce two evolutionarily distinct forms of dihydromethanopterin reductase. This may be a consequence of different electron donors, NAD(P)H versus reduced F
420
, used, respectively, in bacteria and methanogenic archaea.
Pleiotropic Effects of Inactivating a Carboxyl-Terminal Protease, CtpA, in
Borrelia burgdorferi
Authors: Östberg Yngve , Carroll James A. , Pinne Marija , Krum Jonathan G. , Rosa Patricia , Bergström Sven 
Published: March 2004

ABSTRACT

A gene encoding a putative carboxyl-terminal protease (CtpA), an unusual type of protease, is present in the
Borrelia burgdorferi
B31 genome. The
B. burgdorferi
CtpA amino acid sequence exhibits similarities to the sequences of the CtpA enzymes of the cyanobacterium
Synechocystis
sp. strain PCC 6803 and higher plants and also exhibits similarities to the sequences of putative CtpA proteins in other bacterial species. Here, we studied the effect of
ctpA
gene inactivation on the
B. burgdorferi
protein expression profile. Total
B. burgdorferi
proteins were separated by two-dimensional gel electrophoresis, and the results revealed that six proteins of the wild type were not detected in the
ctpA
mutant and that nine proteins observed in the
ctpA
mutant were undetectable in the wild type. Immunoblot analysis showed that the integral outer membrane protein P13 was larger and had a more acidic pI in the
ctpA
mutant, which is consistent with the theoretical change in pI for P13 not processed at the carboxyl terminus. Matrix-assisted laser desorption ionization—time of flight data indicated that in addition to P13, the BB0323 protein may serve as a substrate for carboxyl-terminal processing by CtpA. Complementation analysis of the
ctpA
mutant provided strong evidence that the observed effect on proteins depended on inactivation of the
ctpA
gene alone. We show that CtpA in
B. burgdorferi
is involved in the processing of proteins such as P13 and BB0323 and that inactivation of
ctpA
has a pleiotropic effect on borrelial protein synthesis. To our knowledge, this is the first analysis of both a CtpA protease and different substrate proteins in a pathogenic bacterium.
Plasmid Evolution and Interaction between the Plasmid Addiction Stability Systems of Two Related Broad-Host-Range IncQ-Like Plasmids
Authors: Deane Shelly M. , Rawlings Douglas E. 
Published: March 2004

ABSTRACTPlasmid pTC-F14 contains a plasmid stability system calledpas(plasmid addiction system), which consists of two proteins, a PasA antitoxin and a PasB toxin. This system is closely related to thepasof plasmid pTF-FC2 (81 and 72% amino acid identity for PasA and PasB, respectively) except that thepasof pTF-FC2 contains a third protein, PasC. As both pTC-F14 and pTF-FC2 are highly promiscuous broad-host-range plasmids isolated from bacteria that share a similar ecological niche, the plasmids are likely to encounter each other. We investigated the relative efficiencies of the two stability systems and whether they had evolved apart sufficiently for eachpasto stabilize a plasmid in the presence of the other. The three-component pTF-FC2paswas more efficient at stabilization of a heterologous tester plasmid than the two componentpasof pTC-F14 inEscherichia colihost cells (±92% and ±60% after 100 generations, respectively). The PasA antidote of eachpaswas unable to neutralize the PasB toxin of the other plasmid. Thepasproteins of each plasmid autoregulated their own expression as well as that of thepasof the other plasmid. Thepasof pTF-FC2 was more effective at repressing thepasoperon of pTC-F14 than thepasof pTC-F14 was able to repress itself or thepasof pTF-FC2. This increased efficiency was not due to the PasC of pTF-FC2. The effect of this stronger repression was that pTF-FC2 displaced pTC-F14 when the two plasmids were coresident in the sameE. colihost cell. Plasmid curing resulted in the arrest of cell growth but did not cause cell death, and plasmid stability was not influenced by theE. coli mazEFgenes.
Characterization of Transcriptional Regulatory Genes for Biphenyl Degradation in
Rhodococcus
sp. Strain RHA1
Authors: Takeda Hisashi , Yamada Akihiro , Miyauchi Keisuke , Masai Eiji , Fukuda Masao 
Published: March 2004

ABSTRACT

Transcription of the
bphA1A2A3A4C1B
genes, which are responsible for the conversion of biphenyl and polychlorinated biphenyl to the
meta
-cleavage products in
Rhodococcus
sp. strain RHA1, was examined. The
bphA1
promoter (P

bphA1

) was identified and was shown to promote transcription induction by biphenyl and ethylbenzene. An 8.8-kb HindIII fragment that promotes transcription induction of P

bphA1

in
Rhodococcus erythropolis
IAM1399 was isolated from the region downstream of
bphB
by using a reporter plasmid containing P

bphA1

. Analysis of the nucleotide sequence of this fragment revealed a set of putative two-component regulatory system genes, which were designated
bphS
and
bphT
. Deletion analysis of the 8.8-kb HindIII fragment indicated that
bphT
is responsible for the basal activation of P

bphA1

and that both
bphS
and
bphT
are required for the elevated basal activation of and transcriptional induction by biphenyl of P

bphA1

. These results support the notion that
bphS
and
bphT
encode a sensor kinase and a response regulator, respectively, of a two-component regulatory system. The
bphS
and
bphT
genes promote transcriptional induction by a variety of aromatic compounds, including biphenyl, benzene, alkylbenzenes, and chlorinated benzenes. A promoter activity assay and reverse transcription (RT)-PCR analysis revealed a weak constitutive promoter in the adjacent region upstream of
bphS
. RT-PCR analysis indicated that there is induced transcription of
bphA1
through
bphT
, in which P

bphA1

is thought to take part. An insertionally inactivated
bphS
mutant, SDR1, did not grow on biphenyl. Growth was restored by introduction of an intact
bphS
gene into SDR1. These results indicate that at least
bphS
is indispensably responsible for the growth of RHA1 on biphenyl.
Selenocysteine-Containing Proteins in Anaerobic Benzoate Metabolism of
Desulfococcus multivorans
Authors: Peters Franziska , Rother Michael , Boll Matthias 
Published: March 2004

ABSTRACT

The sulfate-reducing bacterium
Desulfococcus multivorans
uses various aromatic compounds as sources of cell carbon and energy. In this work, we studied the initial steps in the aromatic metabolism of this strictly anaerobic model organism. An ATP-dependent benzoate coenzyme A (CoA) ligase (AMP plus PP
i
forming) composed of a single 59-kDa subunit was purified from extracts of cells grown on benzoate. Specific activity was highest with benzoate and some benzoate derivatives, whereas aliphatic carboxylic acids were virtually unconverted. The N-terminal amino acid sequence showed high similarities with benzoate CoA ligases from
Thauera aromatica
and
Azoarcus evansii
. When cultivated on benzoate, cells strictly required selenium and molybdenum, whereas growth on nonaromatic compounds, such as cyclohexanecarboxylate or lactate, did not depend on the presence of the two trace elements. The growth rate on benzoate was half maximal with 1 nM selenite present in the growth medium. In molybdenum- and/or selenium-depleted cultures, growth on benzoate could be induced by addition of the missing trace elements. In extracts of cells grown on benzoate in the presence of [
75
Se]selenite, three radioactively labeled proteins with molecular masses of ∼100, 30, and 27 kDa were detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. The 100- and 30-kDa selenoproteins were 5- to 10-fold induced in cells grown on benzoate compared to cells grown on lactate. These results suggest that the dearomatization process in
D. multivorans
is not catalyzed by the ATP-dependent Fe-S enzyme benzoyl-CoA reductase as in facultative anaerobes but rather involves unknown molybdenum- and selenocysteine-containing proteins.
Multiple Formaldehyde Oxidation/Detoxification Pathways in
Burkholderia fungorum
LB400
Authors: Marx Christopher J. , Miller Jonathan A. , Chistoserdova Ludmila , Lidstrom Mary E. 
Published: March 2004

ABSTRACT

Burkholderia
species are free-living bacteria with a versatile metabolic lifestyle. The genome of
B. fungorum
LB400 is predicted to encode three different pathways for formaldehyde oxidation: an NAD-linked, glutathione (GSH)-independent formaldehyde dehydrogenase; an NAD-linked, GSH-dependent formaldehyde oxidation system; and a tetrahydromethanopterin-methanofuran-dependent formaldehyde oxidation system. The other
Burkholderia
species for which genome sequences are available,
B. mallei
,
B. pseudomallei
, and
B. cepacia
, are predicted to contain only the first two of these pathways. The roles of the three putative formaldehyde oxidation pathways in
B. fungorum
LB400 have been assessed via knockout mutations in each of these pathways, as well as in all combinations of knockouts. The resulting mutants have the expected loss of enzyme activities and exhibit defects of varying degrees of severity during growth on choline, a formaldehyde-producing substrate. Our data suggest that all three pathways are involved in formaldehyde detoxification and are functionally redundant under the tested conditions.
Evidence for Multiple Levels of Regulation ofOenococcus oeni clpP-clpLLocus Expression in Response to Stress
Authors: Beltramo Charlotte , Grandvalet Cosette , Pierre Fabrice , Guzzo Jean 
Published: March 2004

ABSTRACTA locus containing theclpPandclpLgenes in the lactic acid bacteriumOenococcus oeniwas studied. Real-time reverse transcription-PCR analysis revealed different induction factors involved in expression of these genes during stress. According to the conditions, clpPandclpLgenes could be transcripted as two distinct transcripts or cotranscripted. TheclpPpromoter depended on the CtsR regulator, but surprisingly theclpLpromoter did not. The amount of theclpLtranscript depended on mRNA stability. ThisclpATPase gene is at least controlled at the posttranscriptional level.