bluuebunny/crossref_metadata_2025_split huggingface dataset:
The fibroblast growth factor‐2 is not essential for melanoma formation in a transgenic mouse model
Authors: Ackermann Julien , Beermann Friedrich 
Published: July 2005

SummaryFibroblast growth factor 2 (FGF2) has been assigned a role in melanocyte proliferation and in development of human cutaneous melanoma. We have used a transgenic mouse melanoma model in combination with mice lacking mouse FGF2 to analyse the possible implication of FGF2 in melanomagenesis. Tyr::N‐rasQ61K transgenic mice which are deficient for FGF2 and the tumor suppressors p16INK4a and p19ARF are hyperpigmented and develop cutaneous metastasizing melanoma, with no difference to mice wildtype for FGF2. We conclude from our data, that FGF2 is not essential for melanoma progression and metastasis.
Melanocyte‐specific, cytotoxic T cell responses in vitiligo: the effective variant of melanoma immunity?
Authors: Garbelli Silvia , Mantovani Stefania , Palermo Belinda , Giachino Claudia 
Published: July 2005

SummaryVitiligo is a relatively common progressive depigmentary condition that is believed to be due to the autoimmune‐mediated loss of epidermal melanocytes. An interesting aspect of vitiligo is its relation to melanoma: cytotoxic T lymphocytes directed to self‐antigens shared by normal melanocytes and melanoma cells are found in both conditions and might prove important in melanocyte destruction, yet the resulting immune reactions are completely different. From this standpoint, the selective destruction of pigment cells that occurs in cases of vitiligo is the therapeutic goal sought in melanoma research. In the present article, we will address these issues by reviewing current literature on the subject as well as by posing some speculations.
Changes in responses of UVB irradiated skin of brownish guinea pigs with aging
Authors: Tobiishi Megumi , Haratake Akinori , Kaminaga Hiroko , Nakahara Michio , Komiya Aya , Koishikawa Hisa , Uchiwa Hideyo , Kawa Yoko , Mizoguchi Masako 
Published: July 2005

SummaryIt is known that skin often shows irregular pigmentation during aging, which is frequently associated with hyperpigmentation. Many studies have utilized brownish A1 guinea pigs to investigate the pathogenesis of ultraviolet B (UVB)‐induced skin pigmentation, however, responses associated with aging following UVB irradiation have not been elucidated. To characterize those responses, dorsal skin of A1 guinea pigs from 14‐weeks to 5‐yr old were investigated. The minimal erythema dose was found to increase with aging. Further, in pigmentation induced by UVB radiation, skin brightness (ΔL*‐value) decreased equally in both the 14‐week old (young) group and in the 3‐yr old (old) group of guinea pigs. The ΔL*‐value recovered in the young group from 21 d after UVB irradiation, whereas no such recovery was seen in the old group. In addition, the amount of melanin and the number of melanocytes returned near pre‐irradiation levels in the young group, while they remained high in the old group. Our results therefore demonstrate for the first time that skin responses following UVB irradiation change with aging in A1 guinea pigs.
Convergence Behaviors of Reduced-Order Models For Frictional
Contacts
Authors: Deshmukh D. V. , Berger E. J. , Mackin T. J. , Inglis H. 
Published: July 2005

Abstract
Numerical models to simulate interface behavior of friction connections under cyclic loading are investigated. The question of validity of lower-order models in successfully capturing response of friction joints under cyclic loading is addressed. Single-element macroslip models are not capable of capturing localized interface behavior prior to gross interfacial slip. This paper focuses on the convergence behavior of a multipoint contact microslip model comprised of Iwan-type elements for different physical parameters such as system response amplitude and kinematic state of the friction joint. System dynamics play a significant role in determining the convergence of structural behavior, especially for tuned damper sets in the nonzero damper mass case. This behavior is explored using simple linearized models that explain the response sensitivity in terms of the overall modal density near the forcing frequency. Convergence of the interface response kinematics is also considered, with a focus on the number of damping elements operating in the stick, stick-slip, and slip regimes at steady state. Energy dissipation scaling under light forcing is also examined, with the class of models considered here yielding scaling exponents consistent with experimental observations and analytical predictions from the literature. We show that the interface kinematic behavior converges at a slower rate than the structural response and therefore requires a higher-order interface model. These results suggest that extremely low-order models (i.e., &lt;5 damping elements) provide predictions that are model order dependent, while higher-order models (i.e., &gt;50 damping elements) are not. This result impacts model development and calibration approaches, as well as providing clues for appropriate model reduction strategies.
Salicylate Biosynthesis: Overexpression, Purification, and Characterization of Irp9, a Bifunctional Salicylate Synthase fromYersinia enterocolitica
Authors: Kerbarh Olivier , Ciulli Alessio , Howard Nigel I. , Abell Chris 
Published: July 2005

ABSTRACTIn some bacteria, salicylate is synthesized using the enzymes isochorismate synthase and isochorismate pyruvate lyase. In contrast, gene inactivation and complementation experiments withYersinia enterocoliticasuggest the synthesis of salicylate in the biosynthesis of the siderophore yersiniabactin involves a single protein, Irp9, which converts chorismate directly into salicylate. In the present study, Irp9 was for the first time heterologously expressed inEscherichia colias a hexahistidine fusion protein, purified to near homogeneity, and characterized biochemically. The recombinant protein was found to be a dimer, each subunit of which has a molecular mass of 50 kDa. Enzyme assays, reverse-phase high-pressure liquid chromatography and1H nuclear magnetic resonance (NMR) spectroscopic analyses confirmed that Irp9 is a salicylate synthase and converts chorismate to salicylate with aKmfor chorismate of 4.2 μM and akcatof 8 min−1. The reaction was shown to proceed through the intermediate isochorismate, which was detected directly using1H NMR spectroscopy.
Characterization of the Gallate Dioxygenase Gene: Three Distinct Ring Cleavage Dioxygenases Are Involved in Syringate Degradation by
Sphingomonas paucimobilis
SYK-6
Authors: Kasai Daisuke , Masai Eiji , Miyauchi Keisuke , Katayama Yoshihiro , Fukuda Masao 
Published: July 2005

ABSTRACT

Sphingomonas paucimobilis
SYK-6 converts vanillate and syringate to protocatechuate (PCA) and 3-
O
-methylgallate (3MGA) in reactions with the tetrahydrofolate-dependent
O
-demethylases LigM and DesA, respectively. PCA is further degraded via the PCA 4,5-cleavage pathway, whereas 3MGA is metabolized via three distinct pathways in which PCA 4,5-dioxygenase (LigAB), 3MGA 3,4-dioxygenase (DesZ), and 3MGA
O
-demethylase (LigM) are involved. In the 3MGA O-demethylation pathway, LigM converts 3MGA to gallate, and the resulting gallate appears to be degraded by a dioxygenase other than LigAB or DesZ. Here, we isolated the gallate dioxygenase gene,
desB
, which encodes a 418-amino-acid protein with a molecular mass of 46,843 Da. The amino acid sequences of the N-terminal region (residues 1 to 285) and the C-terminal region (residues 286 to 418) of DesB exhibited ca. 40% and 27% identity with the sequences of the PCA 4,5-dioxygenase β and α subunits, respectively. DesB produced in
Escherichia coli
was purified and was estimated to be a homodimer (86 kDa). DesB specifically attacked gallate to generate 4-oxalomesaconate as the reaction product. The

K
m

for gallate and the
V
max
were determined to be 66.9 ± 9.3 μM and 42.7 ± 2.4 U/mg, respectively. On the basis of the analysis of various SYK-6 mutants lacking the genes involved in syringate degradation, we concluded that (i) all of the three-ring cleavage dioxygenases are involved in syringate catabolism, (ii) the pathway involving LigM and DesB plays an especially important role in the growth of SYK-6 on syringate, and (iii) DesB and LigAB are involved in gallate degradation.
The Stringent Response Is Required for Amino Acid and Nitrate Utilization, Nod Factor Regulation, Nodulation, and Nitrogen Fixation in
Rhizobium etli
Authors: Calderón-Flores Arturo , Du Pont Gisela , Huerta-Saquero Alejandro , Merchant-Larios Horacio , Servín-González Luis , Durán Socorro 
Published: July 2005

ABSTRACT

A
Rhizobium etli
Tn
5
insertion mutant, LM01, was selected for its inability to use glutamine as the sole carbon and nitrogen source. The Tn
5
insertion in LM01 was localized to the
rsh
gene, which encodes a member of the RelA/SpoT family of proteins. The LM01 mutant was affected in the ability to use amino acids and nitrate as nitrogen sources and was unable to accumulate (p)ppGpp when grown under carbon and nitrogen starvation, as opposed to the wild-type strain, which accumulated (p)ppGpp under these conditions. The
R. etli rsh
gene was found to restore (p)ppGpp accumulation to a Δ
relA
Δ
spoT
mutant of
Escherichia coli
. The
R. etli
Rsh protein consists of 744 amino acids, and the Tn
5
insertion in LM01 results in the synthesis of a truncated protein of 329 amino acids; complementation experiments indicate that this truncated protein is still capable of (p)ppGpp hydrolysis. A second
rsh
mutant of
R. etli
, strain AC1, was constructed by inserting an Ω element at the beginning of the
rsh
gene, resulting in a null allele. Both AC1 and LM01 were affected in Nod factor production, which was constitutive in both strains, and in nodulation; nodules produced by the
rsh
mutants in
Phaseolus vulgaris
were smaller than those produced by the wild-type strain and did not fix nitrogen. In addition, electron microscopy revealed that the mutant bacteroids lacked poly-β-hydroxybutyrate granules. These results indicate a central role for the stringent response in symbiosis.
Identification, Characterization, and Classification of Genes Encoding Perchlorate Reductase
Authors: Bender Kelly S. , Shang Ching , Chakraborty Romy , Belchik Sara M. , Coates John D. , Achenbach Laurie A. 
Published: July 2005

ABSTRACT

The reduction of perchlorate to chlorite, the first enzymatic step in the bacterial reduction of perchlorate, is catalyzed by perchlorate reductase. The genes encoding perchlorate reductase (
pcrABCD
) in two
Dechloromonas
species were characterized. Sequence analysis of the
pcrAB
gene products revealed similarity to α- and β-subunits of microbial nitrate reductase, selenate reductase, dimethyl sulfide dehydrogenase, ethylbenzene dehydrogenase, and chlorate reductase, all of which are type II members of the microbial dimethyl sulfoxide (DMSO) reductase family. The
pcrC
gene product was similar to a
c
-type cytochrome, while the
pcrD
gene product exhibited similarity to molybdenum chaperone proteins of the DMSO reductase family members mentioned above. Expression analysis of the
pcrA
gene from
Dechloromonas agitata
indicated that transcription occurred only under anaerobic (per)chlorate-reducing conditions. The presence of oxygen completely inhibited
pcrA
expression regardless of the presence of perchlorate, chlorate, or nitrate. Deletion of the
pcrA
gene in
Dechloromonas aromatica
abolished growth in both perchlorate and chlorate but not growth in nitrate, indicating that the
pcrABCD
genes play a functional role in perchlorate reduction separate from nitrate reduction. Phylogenetic analysis of PcrA and other α-subunits of the DMSO reductase family indicated that perchlorate reductase forms a monophyletic group separate from chlorate reductase of
Ideonella dechloratans
. The separation of perchlorate reductase as an activity distinct from chlorate reductase was further supported by DNA hybridization analysis of (per)chlorate- and chlorate-reducing strains using the
pcrA
gene as a probe.
Involvement of AlgQ in Transcriptional Regulation of Pyoverdine Genes in
Pseudomonas aeruginosa
PAO1
Authors: Ambrosi Cecilia , Tiburzi Federica , Imperi Francesco , Putignani Lorenza , Visca Paolo 
Published: July 2005

ABSTRACT

In response to iron limitation,
Pseudomonas aeruginosa
produces the fluorescent siderophore pyoverdine. Transcription of pyoverdine biosynthetic (
pvd
) genes is driven by the iron starvation sigma factor PvdS, which is negatively regulated by the Fur-Fe(II) holorepressor. We studied the effect of AlgQ, the
Escherichia coli
Rsd orthologue, on pyoverdine production by
P. aeruginosa
PAO1. AlgQ is a global regulatory protein which activates alginate, ppGpp, and inorganic polyphosphate synthesis through a cascade involving nucleoside diphosphate kinase (Ndk). AlgQ is also capable of interacting with region 4 of RpoD. In a reconstituted
E. coli
system, PvdS-dependent transcription from the
pvdA
promoter was doubled by the multicopy
algQ
gene. The
P. aeruginosa
Δ
algQ
mutant exhibited a moderate but reproducible reduction in pyoverdine production compared with wild-type PAO1, as a result of a decline in transcription of
pvd
genes. PvdS expression was not affected by the
algQ
mutation. Single-copy
algQ
fully restored pyoverdine production and expression of
pvd
genes in the Δ
algQ
mutant, while
ndk
did not. An increased intracellular concentration of RpoD mimicked the Δ
algQ
phenotype, whereas PvdS overexpression suppressed the
algQ
mutation.
E. coli rsd
could partially substitute for
algQ
in transcriptional modulation of
pvd
genes. We propose that AlgQ acts as an anti-sigma factor for RpoD, eliciting core RNA polymerase recruitment by PvdS and transcription initiation at
pvd
promoters. AlgQ provides a link between the pyoverdine and alginate regulatory networks. These systems have similarities in responsiveness and physiological function: both depend on alternative sigma factors, respond to nutrient starvation, and act as virulence determinants for
P. aeruginosa
.
Transcriptional Analysis of the
Bacillus anthracis
Capsule Regulators
Authors: Drysdale Melissa , Bourgogne Agathe , Koehler Theresa M. 
Published: July 2005

ABSTRACT

The poly-
d
-glutamic acid capsule of
Bacillus anthracis
is essential for virulence. Control of capsule synthesis occurs at the level of transcription and involves positive regulation of the capsule biosynthetic operon
capBCAD
by a CO
2
/bicarbonate signal and three plasmid-borne regulators:
atxA
,
acpA
, and
acpB
. Although the molecular mechanism for control of
cap
transcription is unknown,
atxA
affects
cap
expression via positive control of
acpA
and
acpB
, two genes with partial functional similarity. Transcriptional analyses of a genetically complete strain indicate that
capB
expression is several hundred-fold higher during growth in 5% CO
2
compared to growth in air.
atxA
was expressed appreciably during growth in air and induced only 2.5-fold by CO
2
. In contrast, expression of
acpA
and
acpB
was induced up to 23-fold and 59-fold, respectively, by CO
2
. The 5′-end mapping of gene transcripts revealed
atxA
-regulated and
atxA
-independent apparent transcription start sites for
capB
,
acpA
, and
acpB
. Transcripts mapping to all
atxA
-regulated start sites were increased during growth in elevated CO
2
. The
acpA
gene has one
atxA
-regulated and one
atxA
-independent start site.
acpB
lies downstream of
capBCAD
. A single
atxA
-independent start site maps immediately upstream of
acpB. atxA
-mediated control of
acpB
appears to occur via transcriptional read-through from
atxA
-dependent start sites 5′ of
capB
. One
atxA
-independent and two
atxA
-regulated start sites map upstream of
capB
. Transcription from the
atxA-
regulated start sites of
capBCAD
was reduced significantly in an
acpA acpB
double mutant but unaffected in mutants with deletion of only
acpA
or
acpB
, in agreement with the current model for epistatic relationships between the regulators.
Distribution, Expression, and Motif Variability of Ankyrin Domain Genes inWolbachia pipientis
Authors: Iturbe-Ormaetxe Iñaki , Burke Gaelen R. , Riegler Markus , O'Neill Scott L. 
Published: July 2005

ABSTRACTThe endosymbiotic bacteriumWolbachia pipientisinfects a wide range of arthropods, in which it induces a variety of reproductive phenotypes, including cytoplasmic incompatibility (CI), parthenogenesis, male killing, and reversal of genetic sex determination. The recent sequencing and annotation of the firstWolbachiagenome revealed an unusually high number of genes encoding ankyrin domain (ANK) repeats. These ANK genes are likely to be important in mediating theWolbachia-host interaction. In this work we determined the distribution and expression of the different ANK genes found in the sequencedWolbachia wMel genome in nineWolbachiastrains that induce different phenotypic effects in their hosts. A comparison of the ANK genes ofwMel and the non-CI-inducingwAuWolbachiastrain revealed significant differences between the strains. This was reflected in sequence variability in shared genes that could result in alterations in the encoded proteins, such as motif deletions, amino acid insertions, and in some cases disruptions due to insertion of transposable elements and premature stops. In addition, onewMel ANK gene, which is part of an operon, was absent in thewAu genome. These variations are likely to affect the affinity, function, and cellular location of the predicted proteins encoded by these genes.
Bacillus subtilisPhosphorylated PhoP: Direct Activation of the EσA- and Repression of the EσE-ResponsivephoB-PS+VPromoters during Pho Response
Authors: Abdel-Fattah Wael R. , Chen Yinghua , Eldakak Amr , Hulett F. Marion 
Published: July 2005

ABSTRACTThephoBgene ofBacillus subtilisencodes an alkaline phosphatase (PhoB, formerly alkaline phosphatase III) that is expressed from separate promoters during phosphate deprivation in a PhoP-PhoR-dependent manner and at stage two of sporulation under phosphate-sufficient conditions independent of PhoP-PhoR. Isogenic strains containing either the completephoBpromoter or individualphoBpromoter fusions were used to assess expression from each promoter under both induction conditions. ThephoBpromoter responsible for expression during sporulation,phoB-PS, was expressed in a wild-type strain during phosphate deprivation, but induction occurred >3 h later than induction of Pho regulon genes and the levels were approximately 50-fold lower than that observed for the PhoPR-dependent promoter,phoB-PV. EσEwas necessary and sufficient for PSexpression in vitro. PSexpression in aphoPRmutant strain was delayed 2 to 3 h compared to the expression in a wild-type strain, suggesting that expression or activation of σEis delayed in aphoPRmutant under phosphate-deficient conditions, an observation consistent with a role for PhoPR in spore development under these conditions. Phosphorylated PhoP (PhoP∼P) repressed PSin vitro via direct binding to the promoter, the first example of an EσE-responsive promoter that is repressed by PhoP∼P. Whereas either PhoP or PhoP∼P in the presence of EσAwas sufficient to stimulate transcription from thephoB-PVpromoter in vitro, roughly 10- and 17-fold-higher concentrations of PhoP than of PhoP∼P were required for PVpromoter activation and maximal promoter activity, respectively. The promoter for a second gene in the Pho regulon,ykoL, was also activated by elevated concentrations of unphosphorylated PhoP in vitro. However, because no Pho regulon gene expression was observed in vivo during Pi-replete growth and PhoP concentrations increased only threefold in vivo duringphoPRautoinduction, a role for unphosphorylated PhoP in Pho regulon activation in vivo is not likely.
Transcriptional Analysis of a Gene Cluster Involved in Glucose Tolerance in
Zymomonas mobilis
: Evidence for an Osmoregulated Promoter
Authors: Christogianni Anastasia , Douka Eugenia , Koukkou Anna I. , Hatziloukas Efstathios , Drainas Constantin 
Published: July 2005

ABSTRACT

Exponentially growing cells of
Zymomonas mobilis
normally exhibit a lag period of up to 3 h when they are transferred from a liquid medium containing 2% glucose to a liquid medium containing 10% glucose. A mutant of
Z. mobilis
(CU1) exhibited a lag period of more than 20 h when it was grown under the same conditions, whereas it failed to grow on a solid medium containing 10% glucose. The glucose-defective phenotype of mutant CU1 was due to a spontaneous insertion in a putative gene (ORF4) identified as part of an operon (
glc
) which includes three additional putative genes (ORF1, ORF2, and ORF3) with no obvious involvement in the glucose tolerance mechanism. The common promoter controlling
glc
operon transcription, designated P

glc

, was found to be osmoregulated and stimulated by the putative product of ORF4 in an autoregulated fashion, as indicated by expression of the
gfp
reporter gene. Additionally, reverse transcriptase PCR analysis showed that the gene cluster produces a single mRNA, which verified the operon organization of this transcription unit. Further transcriptional analysis demonstrated that
glc
operon expression is regulated by the concentration of glucose, which supported the hypothesis that this operon is directly involved in the uncharacterized glucose tolerance mechanism of
Z. mobilis
.
Functional Characterization of a Na
+
-Coupled Dicarboxylate Carrier Protein from
Staphylococcus aureus
Authors: Hall Jason A. , Pajor Ana M. 
Published: July 2005

ABSTRACT

We have cloned and functionally characterized a Na
+
-coupled dicarboxylate transporter, SdcS, from
Staphylococcus aureus
. This carrier protein is a member of the divalent anion/Na
+
symporter (DASS) family and shares significant sequence homology with the mammalian Na
+
/dicarboxylate cotransporters NaDC-1 and NaDC-3. Analysis of SdcS function indicates transport properties consistent with those of its eukaryotic counterparts. Thus, SdcS facilitates the transport of the dicarboxylates fumarate, malate, and succinate across the cytoplasmic membrane in a Na
+
-dependent manner. Furthermore, kinetic work predicts an ordered reaction sequence with Na
+
(
K
0.5
of 2.7 mM) binding before dicarboxylate (

K
m

of 4.5 μM). Because this transporter and its mammalian homologs are functionally similar, we suggest that SdcS may serve as a useful model for DASS family structural analysis.
Resistance ofNeisseria meningitidisto the Toxic Effects of Heme Iron and Other Hydrophobic Agents Requires Expression ofght
Authors: Rasmussen Andrew W. , Alexander Heather L. , Perkins-Balding Donna , Shafer William M. , Stojiljkovic Igor 
Published: July 2005

ABSTRACTSeveral genetic systems that allow the use of iron-protoporphyrin IX (heme) have been described for the pathogenic bacteriumNeisseria meningitidis. However, many questions about the process of heme acquisition and utilization remain to be answered. To isolate and analyze unidentified genes that play a role in heme iron uptake and utilization, aHimar1transposon mutant library was screened inN. meningitidisserogroup A strain IR4162. One locus identified by transposon mutagenesis conferred protection against heme toxicity. A mutant with a deletion in a gene termedght(gene of hydrophobic agent tolerance) within this locus was susceptible to heme and other hydrophobic agents compared to the parental strain. Transcriptional analysis indicated thatghtis cotranscribed with an upstream open reading frame NMA2149. Uncharacterized orthologues ofghtwere identified in many other gram-negative bacteria. We present genetic evidence for the importance ofghtin resistance to hydrophobic agents and its potential role in interaction with other hydrophobic agent resistance mechanisms withinN. meningitidis.