bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical and immunohistochemical assessment of the effect of cyclosporin in keratinocytes and dermal dendrocytes in psoriasis
Authors: Lago Eduardo , Carneiro Sueli , Cuzzi Tullia , Magalhães Geraldo , Cássia Flavia , Pessanha Fátima , Ramos‐e‐Silva Marcia
Published: September 2006

Background:  Cyclosporine is a potent immunosupressor, which induces cytokeratin expression pattern changes and dermal dendrocytes number increase.

Objectives:  To evaluate its clinical effect in psoriasis, on keratinocytic proliferation and differentiation, and on dermal dendrocytes proliferation.

Methods:  Thirty patients with psoriasis were treated and evaluated for 8 weeks. Clinical improvement was evaluated by Psoriasis Area and Severity Index (PASI). Biopsies were performed initially and after 8 weeks. Immunohistochemistry [CK markers 10, 14, and 16, and factor XIIIa+ (FXIIIa+)] was performed.

Results:  Mean PASI before treatment was 26.32 and 3.71 after. Mean initial and final PASI difference was 22.61 (p < 0.001). Two patients had serum creatinine and six uric acid increase. Before and after treatment, mean numbers per field of dermal dendrocytes were 7.07 and 3.68, respectively. Mean difference was 3.39, with p < 0.001. CK10 immunohistochemical pattern demonstrated recovery of normal expression pattern in 26 patients, while CK14 pattern demonstrated improvement in 21 patients.

Conclusions:  Cyclosporine was effective and safe for psoriasis in low doses, with significant decrease of PASI and dermal dendrocytes number after 8 weeks of therapy. CK10 and 14 pattern changed and, less prominently, CK16 expression. These modifications occur later than the PASI and dermal dendrocytes variation.
Implications of Shift Work for Parent‐Adolescent Relationships in Dual‐Earner Families
Authors: Davis Kelly D. , Crouter Ann C. , McHale Susan M.
Published: September 2006

Abstract: This investigation examined the implications of shift work for parent‐adolescent relationship quality—intimacy, conflict, parental knowledge, and involvement—in a sample of 376 dual‐earner families. The findings suggested that mothers’ relationships with their adolescents were not negatively impacted by their working nonstandard schedules but fathers’ relationships were. Adolescents with shift working mothers reported more relationship intimacy than adolescents with daytime working mothers. In contrast, fathers with nonstandard shifts knew significantly less about their teens’ daily activities than did fathers with daytime shifts. The combination of fathers having nonstandard schedules and a marriage with high conflict predicted less intimacy with adolescents. Our findings suggest the need for policy that assists nonstandard workers with staying knowledgeable about their adolescents’ daily activities.
Covering Adoption: General Depictions in Broadcast News
Authors: Kline Susan L. , Karel Amanda I. , Chatterjee Karishma
Published: September 2006

Abstract: Using theories of stigma (Goffman, 1963) and media frames (Iyengar, 1991), 292 news stories pertaining to adoption that appeared on major broadcast networks between 2001 and 2004 were analyzed. Media coverage of adoptees contained more problematic than positive depictions. Although birth parents were not always depicted, adoptive parent and adoptive family depictions were more positive than problematic. Fourteen percent of the news stories contained stigmatizing claims without refuting these claims. Stories that contained stigmatizing claims were more likely to use human interest, conflict, and morality frames. News coverage of reunions, open adoptions, and adoption recommendations is beginning to show a more forward view of adoption. Recommended programs for adoption education are included.
Comparison of two hydroxyethyl starch 200/0.5 formulations with regard to hemorheology, coagulation and elimination kinetics
Authors: GOPINATH RAMACHANDRAN , KAUL SUBHASH
Published: September 2006

Objective:  To compare the elimination kinetics and the effects on coagulation of two hydroxyethyl starch (HES) preparations with identical labeling.

Methods:  Two formulations of 6% HES 200/0.5 [HAES‐steril™, Fresenius Kabi, India (group A) and HESTAR‐200™, Claris Lifesciences, India (group B)] were compared in a randomized, double‐blind, prospective study in 22 stroke patients receiving HES for therapeutic hemodilution over 10 days.

Results:  Mean in vivo molecular weight (Mw) of HES on day 6 was 98,036 ± 5631 Da in group A and 157,254 ± 5200 Da in group B (P < 0.0001). On day 11 these values were 102,727 ± 4440 Da and 146,856 ± 9006 Da in group A and group B, respectively (P = 0.0002). From day 2 to day 11, plasma HES concentrations were significantly higher in group B than in group A (P < 0.05). Group A showed less thromboelastographic abnormalities.

Conclusion:  Two HES formulations with similar Mw and degree of substitution should not be considered equivalent based on label claims only.
Platelet biology – an overview
Authors: KICKLER THOMAS S.
Published: September 2006

Understanding the biology of platelet is important for one to treat patients with acquired or inherited platelet disorders. Platelets provide primary hemostasis by performing five primary functions: adhesion, aggregation, secretion, and providing procoagulant surface and clot retraction. The elucidation of the molecular mechanisms carrying out these functions has led to a better understanding of the pathophysiology of bleeding and the development of new approaches in treating patients with qualitative and quantitative platelet disorders. The purpose of this review is to provide a foundation for understanding the other papers in this publication on the treatment of platelet disorders.
Humanization of Yeast to Produce Complex Terminally Sialylated Glycoproteins
Authors: Hamilton Stephen R. , Davidson Robert C. , Sethuraman Natarajan , Nett Juergen H. , Jiang Youwei , Rios Sandra , Bobrowicz Piotr , Stadheim Terrance A. , Li Huijuan , Choi Byung-Kwon , Hopkins Daniel , Wischnewski Harry , Roser Jessica , Mitchell Teresa , Strawbridge Rendall R. , Hoopes Jack , Wildt Stefan , Gerngross Tillman U.
Published: September 2006

Yeast is a widely used recombinant protein expression system. We expanded its utility by engineering the yeast
Pichia pastoris
to secrete human glycoproteins with fully complex terminally sialylated N-glycans. After the knockout of four genes to eliminate yeast-specific glycosylation, we introduced 14 heterologous genes, allowing us to replicate the sequential steps of human glycosylation. The reported cell lines produce complex glycoproteins with greater than 90% terminal sialylation. Finally, to demonstrate the utility of these yeast strains, functional recombinant erythropoietin was produced.
Temporal and Spatial Enumeration Processes in the Primate Parietal Cortex
Authors: Nieder Andreas , Diester Ilka , Tudusciuc Oana
Published: September 2006

Humans and animals can nonverbally enumerate visual items across time in a sequence or rapidly estimate the set size of spatial dot patterns at a single glance. We found that temporal and spatial enumeration processes engaged different populations of neurons in the intraparietal sulcus of behaving monkeys. Once the enumeration process was completed, however, another neuronal population represented the cardinality of a set irrespective of whether it had been cued in a spatial layout or across time. These data suggest distinct neural processing stages for different numerical formats, but also a final convergence of the segregated information to form most abstract quantity representations.
An Antigen Produced by Splicing of Noncontiguous Peptides in the Reverse Order
Authors: Warren Edus H. , Vigneron Nathalie J. , Gavin Marc A. , Coulie Pierre G. , Stroobant Vincent , Dalet Alexandre , Tykodi Scott S. , Xuereb Suzanne M. , Mito Jeffrey K. , Riddell Stanley R. , Van den Eynde Benoît J.
Published: September 2006

CD8-positive T lymphocytes recognize peptides that are usually derived from the degradation of cellular proteins and are presented by class I molecules of the major histocompatibility complex. Here we describe a human minor histocompatibility antigen created by a polymorphism in the
SP110
nuclear phosphoprotein gene. The antigenic peptide comprises two noncontiguous SP110 peptide segments spliced together in reverse order to that in which they occur in the predicted SP110 protein. The antigenic peptide could be produced in vitro by incubation of precursor peptides with highly purified 20
S
proteasomes. Cutting and splicing probably occur within the proteasome by transpeptidation.
Immunoglobulin G, A, and M Responses to BK Virus in Renal Transplantation
Authors: Randhawa Parmjeet S. , Gupta Gaurav , Vats Abhay , Shapiro Ron , Viscidi Raphael P.
Published: September 2006

Immunoglobulin G (IgG), IgA, and IgM antibodies were measured in serum samples from 71 organ donors, 81 kidney transplant recipients at transplantation, and 67 patients during the posttransplant period by using a virus-like particle-based enzyme-linked immunosorbent assay (ELISA). BK virus (BKV) and JC virus DNA were detected in urine and plasma by real-time PCR. IgG antibodies to BKV were demonstrated in the majority (80.3 to 100%) of patients irrespective of clinical category, but titers were highest in patients with active viral replication. IgA antibodies were present with greater frequency (72.7 to 81.3% versus 0 to 23.6%;
P
< 0.001) and higher titer (mean optical density, 0.11 to 0.15 versus 0.05 to 0.08;
P
< 0.001) in patients who were BKV DNA positive than those who were BKV DNA negative. IgM antibodies showed a similar pattern of reactivity but lower frequency in the setting of active viral replication (9.1 to 43.7% versus 0 to 1.4%;
P
< 0.001). A rise in IgG level of >0.577 optical density (OD) units or a rise in IgA or IgM level of >0.041 OD units was strongly associated with active viral replication. Urine viral load showed a positive correlation with IgM titer (
r
= 0.22) but a negative correlation with IgG titer (
r
= −0.28) and IgA titer (
r
= −0.1). Chronic dialysis patients typically did not have serologic or virologic evidence of active BKV infection. Anti-BKV titers did not rise in patients with JC viruria. In conclusion, measurement of anti-BKV antibody titer and class response can be used to detect the onset of viral replication. ELISAs can be quite specific despite considerable sequence homology between BK virus and JC virus.
Functional Characterization of IS
1999
, an IS
4
Family Element Involved in Mobilization and Expression of β-Lactam Resistance Genes
Authors: Aubert Daniel , Naas Thierry , Héritier Claire , Poirel Laurent , Nordmann Patrice
Published: September 2006

IS
1999
and a point mutant derivative, IS
1999.2
, have been described inserted upstream of emerging antibiotic resistance genes
bla
VEB-1
and
bla
OXA-48
. 5′ Rapid amplification of cDNA ends experiments revealed that expression of these β-lactamase genes was driven by the outward-directed promoter, P
out
, located in the IS
1999
elements. These findings led us to study IS
1999
-mediated gene mobilization. Thus, the transposition properties of IS
1999
and of IS
1999
-based composite transposons, made of two copies of IS
1999
in different orientations, were investigated. IS
1999
or IS
1999
-based composite transposons were capable of transposing onto the conjugative plasmid pOX38-Gen. Sequence analysis of the insertion sites revealed that IS
1999
inserted preferentially into DNA targets containing the consensus sequence NGCNNNGCN. Transposition was more efficient when at least one left inverted repeat end was located at an outside end of the transposon. The transposition frequency of IS
1999.2
was 10-fold lower than that of IS
1999
, and transposition frequencies of the putative natural transposon, Tn
1999
, were below detection limits of our transposition assay. This reduced transposition frequency of IS
1999.2
-based elements may result from a lower transcription of the transposase gene, as revealed by reverse transcription-PCR analyses.
Hypoxanthine Incorporation Is Nonmutagenic in
Escherichia coli
Authors: Budke Brian , Kuzminov Andrei
Published: September 2006

Endonuclease V, encoded by the
nfi
gene, initiates removal of the base analogs hypoxanthine and xanthine from DNA, acting to prevent mutagenesis from purine base deamination within the DNA. On the other hand, the RdgB nucleotide hydrolase in
Escherichia coli
is proposed to prevent hypoxanthine and xanthine incorporation into DNA by intercepting the noncanonical DNA precursors dITP and dXTP. Because many base analogs are mutagenic when incorporated into DNA, it is intuitive to think of RdgB as acting to prevent similar mutagenesis from deaminated purines in the DNA precursor pools. To test this idea, we used a set of Claire Cupples' strains to detect changes in spontaneous mutagenesis spectra, as well as in nitrous acid-induced mutagenesis spectra, in wild-type cells and in
rdgB
single,
nfi
single, and
rdgB nfi
double mutants. We found neither a significant increase in spontaneous mutagenesis in
rdgB
and
nfi
single mutants or the double mutant nor any changes in nitrous acid-induced mutagenesis for
rdgB
mutant strains. We conclude that incorporation of deaminated purines into DNA is nonmutagenic.
Characterization of Stg Fimbriae from an Avian Pathogenic
Escherichia coli
O78:K80 Strain and Assessment of Their Contribution to Colonization of the Chicken Respiratory Tract
Authors: Lymberopoulos Maria H. , Houle Sébastien , Daigle France , Léveillé Simon , Brée Annie , Moulin-Schouleur Maryvonne , Johnson James R. , Dozois Charles M.
Published: September 2006

In a previous study,
ecs-3
, a sequence from avian pathogenic
Escherichia coli
(APEC) O78:K80 strain χ7122, was found to be expressed in vivo in infected chicken tissues. The region encompassing
ecs-3
carries a fimbrial gene cluster that is a putative ortholog of the
stg
fimbrial gene cluster of
Salmonella enterica
serovar Typhi. This APEC fimbrial gene cluster, which we have termed
stg
, is a member of a distinct group of related fimbriae that are located in the
glmS
-
pstS
intergenic region of certain
E. coli
and
S. enterica
strains. Under the control of the pBAD promoter, the production of Stg fimbriae was demonstrated by Western blotting and immunogold electron microscopy with
E. coli
K-12. Transcriptional fusions suggest that
stg
expression is influenced by the carbohydrate source and decreased by the addition of iron and that Fur plays a role in the regulation of
stg
expression.
stg
sequences were associated with APEC O78 isolates, and
stg
was phylogenetically distributed among
E. coli
reference strains and clinical isolates from human urinary tract infections. Stg fimbriae contributed to the adherence of a nonfimbriated
E. coli
K-12 strain to avian lung sections and human epithelial cells in vitro. Coinfection experiments with APEC strain χ7122 and an isogenic Δ
stg
mutant demonstrated that compared to the wild-type parent, the Δ
stg
mutant was less able to colonize air sacs, equally able to colonize lungs, and able to more effectively colonize tracheas of infected chickens. Stg fimbriae, together with other adhesins, may therefore contribute to the colonization of avian respiratory tissues by certain APEC strains.
Identification of a Novel Galactosyl Transferase Involved in Biosynthesis of the Mycobacterial Cell Wall
Authors: Mikušová Katarína , Beláňová Martina , Korduláková Jana , Honda Kristine , McNeil Michael R. , Mahapatra Sebabrata , Crick Dean C. , Brennan Patrick J.
Published: September 2006

The possibility of the Rv3782 protein of
Mycobacterium tuberculosis
being a putative galactosyl transferase (GalTr) implicated in galactan synthesis arose from its similarity to the known GalTr Rv3808c, its classification as a nucleotide sugar-requiring inverting glycosyltransferase (GT-2 family), and its location within the “possible arabinogalactan biosynthetic gene cluster” of
M. tuberculosis.
In order to study the function of the enzyme, active membrane and cell wall fractions from
Mycobacterium smegmatis
containing the overexpressed Rv3782 protein were incubated with endogenous decaprenyldiphosphoryl-
N
-acetylglucosaminyl-rhamnose (C
50
-P-P-GlcNAc-Rha) as the primary substrate for galactan synthesis and UDP-[
14
C]galactopyranose as the immediate precursor of UDP-[
14
C]galactofuranose, the ultimate source of all of the galactofuranose (Gal
f
) units of galactan. Obvious increased and selective synthesis of C
50
-P-P-GlcNAc-Rha-Gal
f-
Gal
f
, the earliest product in the pathway leading to the fully polymerized galactan, was observed, suggesting that Rv3782 encodes a GalTr involved in the first stages of galactan synthesis. Time course experiments pointed to a possible bifunctional enzyme responsible for the initial synthesis of C
50
-P-P-GlcNAc-Rha-Gal
f
, followed by immediate conversion to C
50
-P-P-GlcNAc-Rha-Gal
f-
Gal
f
. Thus, Rv3782 appears to be the initiator of galactan synthesis, while Rv3808c continues with the subsequent polymerization events.
Localized Induction of the
ntcA
Regulatory Gene in Developing Heterocysts of
Anabaena
sp. Strain PCC 7120
Authors: Olmedo-Verd Elvira , Muro-Pastor Alicia M. , Flores Enrique , Herrero Antonia
Published: September 2006

The
ntcA
gene encodes an N-control transcriptional regulator in cyanobacteria. In the N
2
-fixing, heterocyst-forming cyanobacterium
Anabaena
sp. strain PCC 7120,
ntcA
is an autoregulatory gene that is transcribed from a complex promoter region that includes a constitutive promoter (P
2
) and promoters that are induced upon N step-down (P
1
and P
3
). Expression of
ntcA
was investigated with the use of an
ntcA-gfp
translational fusion, which was introduced both in the natural
ntcA
locus and in a heterologous genomic place. Induction of
ntcA-gfp
took place after N step-down in all the cells of the filament, but at especially high levels in developing heterocysts. Localized induction could be driven independently by P
3
and P
1
.
Both Subunits of ATP-Citrate Lyase fromChlorobium tepidumContribute to Catalytic Activity
Authors: Kim Wonduck , Tabita F. Robert
Published: September 2006

ATP-citrate lyase (ACL) is an essential enzyme of the reductive tricarboxylic acid (RTCA) pathway of CO2assimilation. The RTCA pathway occurs in several groups of autotrophic prokaryotes, including the green sulfur bacteria. ACL catalyzes the coenzyme A (CoA)-dependent and MgATP-dependent cleavage of citrate into oxaloacetate and acetyl-CoA, representing a key step in the RTCA pathway. To characterize this enzyme from the green sulfur bacteriumChlorobium tepidumand determine the role of its two distinct polypeptide chains, recombinant holo-ACL as well as its two individual subunit polypeptides were synthesized inEscherichia coli. The recombinant holoenzyme, prepared from coexpressed large and small ACL genes, and the individual large and small subunit polypeptides, prepared from singly expressed genes, were all purified to homogeneity to high yield. Purified recombinant holo-ACL was isolated at high specific activity, and itskcatwas comparable to that of previously prepared nativeC. tepidumACL. Moreover, the purified recombinant large and small subunit polypeptides were able to reconstitute the holo-ACL in vitro, with activity levels approaching that of recombinant holo-ACL prepared from coexpressed genes. Stoichiometric amounts of each subunit protein were required to maximize the activity and form the most stable structure of reconstituted holo-ACL. These results suggested that this reconstitution system could be used to discern the catalytic role of specific amino acid residues on each subunit. Reconstitution and mutagenesis studies together indicated that residues of each subunit contributed to different aspects of the catalytic mechanism, suggesting that both subunit proteins contribute to the active site ofC. tepidumACL.
Tungsten Transport Protein A (WtpA) inPyrococcus furiosus: the First Member of a New Class of Tungstate and Molybdate Transporters
Authors: Bevers Loes E. , Hagedoorn Peter-Leon , Krijger Gerard C. , Hagen Wilfred R.
Published: September 2006

A novel tungstate and molybdate binding protein has been discovered from the hyperthermophilic archaeonPyrococcus furiosus. This tungstate transport protein A (WtpA) is part of a new ABC transporter system selective for tungstate and molybdate. WtpA has very low sequence similarity with the earlier-characterized transport proteins ModA for molybdate and TupA for tungstate. Its structural gene is present in the genome of numerous archaea and some bacteria. The identification of this new tungstate and molybdate binding protein clarifies the mechanism of tungstate and molybdate transport in organisms that lack the known uptake systems associated with the ModA and TupA proteins, like many archaea. The periplasmic protein of this ABC transporter, WtpA (PF0080), was cloned and expressed inEscherichia coli. Using isothermal titration calorimetry, WtpA was observed to bind tungstate (dissociation constant [KD] of 17 ± 7 pM) and molybdate (KDof 11 ± 5 nM) with a stoichiometry of 1.0 mol oxoanion per mole of protein. These lowKDvalues indicate that WtpA has a higher affinity for tungstate than do ModA and TupA and an affinity for molybdate similar to that of ModA. A displacement titration of molybdate-saturated WtpA with tungstate showed that the tungstate effectively replaced the molybdate in the binding site of the protein.
Hundreds of Flagellar Basal Bodies Cover the Cell Surface of the Endosymbiotic Bacterium
Buchnera aphidicola
sp. Strain APS
Authors: Maezawa Kazuki , Shigenobu Shuji , Taniguchi Hisaaki , Kubo Takeo , Aizawa Shin-ichi , Morioka Mizue
Published: September 2006

Buchnera aphidicola
is the endosymbiotic bacterium of the pea aphid. Due to its small genome size,
Buchnera
lacks many essential genes for autogenous life but obtains nutrients from the host. Although the
Buchnera
cell is nonmotile, it retains clusters of flagellar genes that lack the late genes necessary for motility, including the flagellin gene. In this study, we show that the flagellar genes are actually transcribed and translated and that the
Buchnera
cell surface is covered with hundreds of hook-basal-body (HBB) complexes. The abundance of HBB complexes suggests a role other than motility. We discuss the possibility that the HBB complex may serve as a protein transporter not only for the flagellar proteins but also for other proteins to maintain the symbiotic system.
Identification and Characterization of the Chemotactic Transducer in
Pseudomonas aeruginosa
PAO1 for Positive Chemotaxis to Trichloroethylene
Authors: Kim Hye-Eun , Shitashiro Maiko , Kuroda Akio , Takiguchi Noboru , Ohtake Hisao , Kato Junichi
Published: September 2006

Pseudomonas aeruginosa
PAO1 is repelled by trichloroethylene (TCE), and the methyl-accepting chemotaxis proteins PctA, PctB, and PctC serve as the major chemoreceptors for negative chemotaxis to TCE. In this study, we found that the
pctABC
triple mutant of
P. aeruginosa
PAO1 was attracted by TCE. Chemotaxis assays of a set of mutants containing deletions in 26 potential
mcp
genes revealed that
mcpA
(PA0180) is the chemoreceptor for positive chemotaxis to TCE. McpA also detects tetrachloroethylene and dichloroethylene isomers as attractants.
Expression of the Primary Carbohydrate Component of the
Bordetella bronchiseptica
Biofilm Matrix Is Dependent on Growth Phase but Independent of Bvg Regulation
Authors: Irie Yasuhiko , Preston Andrew , Yuk Ming H.
Published: September 2006

We previously showed that the Bvg virulence control system regulates biofilm formation in
Bordetella bronchiseptica
(Y. Irie, S. Mattoo, and M. H. Yuk, J. Bacteriol.
186:
5692-5698, 2004). Analyses of the extracellular components of
B. bronchiseptica
biofilm matrix revealed that the major sugar component in the matrix was xylose, and linkage analysis indicated a majority of it to be in a 4-linked polymeric form. The production of xylose was independent of Bvg regulation but instead was dependent on bacterial growth phase. In addition,
N
-acetyl-glucosamine in the matrix was found to be important for the initial development of the biofilm. These results suggest that
B. bronchiseptica
biofilm formation is growth phase dependent in addition to being regulated by the Bvg virulence system.
Characterization of Ferric and Ferrous Iron Transport Systems inVibrio cholerae
Authors: Wyckoff Elizabeth E. , Mey Alexandra R. , Leimbach Andreas , Fisher Carolyn F. , Payne Shelley M.
Published: September 2006

Vibrio choleraehas multiple iron acquisition systems, including TonB-dependent transport of heme and of the catechol siderophore vibriobactin. Strains defective in both of these systems grow well in laboratory media and in the infant mouse intestine, indicating the presence of additional iron acquisition systems. Previously uncharacterized potential iron transport systems, including a homologue of the ferrous transporter Feo and a periplasmic binding protein-dependent ATP binding cassette (ABC) transport system, termed Fbp, were identified in theV. choleraegenome sequence. Clones encoding either the Feo or the Fbp system exhibited characteristics of iron transporters: both repressed the expression oflacZcloned under the control of a Fur-regulated promoter inEscherichia coliand also conferred growth on aShigella flexnerimutant that has a severe defect in iron transport. Two other ABC transporters were also evaluated but were negative by these assays. Transport of radioactive iron by the Feo system into theS. flexneriiron transport mutant was stimulated by the reducing agent ascorbate, consistent with Feo functioning as a ferrous transporter. Conversely, ascorbate inhibited transport by the Fbp system, suggesting that it transports ferric iron. The growth ofV. choleraestrains carrying mutations in one or more of the potential iron transport genes indicated that both Feo and Fbp contribute to iron acquisition. However, a mutant defective in the vibriobactin, Fbp, and Feo systems was not attenuated in a suckling mouse model, suggesting that at least one other iron transport system can be used in vivo.
DsdX Is the Second
d
-Serine Transporter in Uropathogenic
Escherichia coli
Clinical Isolate CFT073
Authors: Anfora Andrew T. , Welch Rodney A.
Published: September 2006

d
-Serine is an amino acid present in mammalian urine that is inhibitory to
Escherichia coli
strains lacking a functional
dsdA
gene. Counterintuitively, a
dsdA
strain of
E. coli
clinical isolate CFT073 hypercolonizes the bladder and kidneys of mice relative to wild type during a coinfection in the murine model of urinary tract infection. We are interested in the mechanisms for uptake of
d
-serine in CFT073.
d
-Serine enters
E. coli
K-12 via CycA, the
d
-alanine transporter and
d
-cycloserine sensitivity locus. CFT073
cycA
can grow on minimal medium with
d
-serine as a sole carbon source. The
dsdX
gene of the
dsdCXA
locus is a likely candidate for an additional
d
-serine transporter based on its predicted amino acid sequence similarity to gluconate transporters. In minimal medium, CFT073
dsdX
can grow on
d
-serine as a sole carbon source; however, CFT073
dsdX cycA
cannot. Additionally, CFT073
dsdXA cycA
is not sensitive to inhibitory concentrations of
d
-serine during growth on glycerol and
d
-serine minimal medium.
d
-[
14
C]serine uptake experiments with CFT073
dsdX cycA
harboring
dsdX
or
cycA
recombinant plasmids confirm that
d
-serine is able to enter
E. coli
cells via CycA or DsdX. In whole-cell
d
-[
14
C]serine uptake experiments, DsdX has an apparent

K
m

of 58.75 μM and a
V
max
of 75.96 nmol/min/mg, and CycA has an apparent

K
m

of 82.40 μM and a

V
max

of 58.90 nmol/min/mg. Only
d
-threonine marginally inhibits DsdX-mediated
d
-serine transport, whereas
d
-alanine, glycine, and
d
-cycloserine inhibit CycA-mediated
d
-serine transport. DsdX or CycA is sufficient to transport physiological quantities of
d
-serine, but DsdX is a
d
-serine-specific permease.
The AlgT-Dependent Transcriptional Regulator AmrZ (AlgZ) Inhibits Flagellum Biosynthesis in Mucoid, Nonmotile
Pseudomonas aeruginosa
Cystic Fibrosis Isolates
Authors: Tart Anne H. , Blanks Michael J. , Wozniak Daniel J.
Published: September 2006

Pseudomonas aeruginosa
is a microorganism associated with the disease cystic fibrosis. While environmental
P. aeruginosa
strains are generally nonmucoid and motile, isolates recovered from the cystic fibrosis lung frequently display a mucoid, nonmotile phenotype. This phenotypic conversion is mediated by the alternative sigma factor AlgT. Previous work has shown that repression of
fleQ
by AlgT accounts for the loss of flagellum biosynthesis in these strains. Here, we elucidate the mechanism involved in the AlgT-mediated control of
fleQ.
Electrophoretic mobility shift assays using purified AlgT and extracts derived from isogenic AlgT
+
and AlgT
−
strains revealed that AlgT inhibits
fleQ
indirectly. We observed that the AlgT-dependent transcriptional regulator AmrZ interacts directly with the
fleQ
promoter. To determine whether AmrZ functions as a repressor of
fleQ
, we mutated
amrZ
in the mucoid, nonmotile
P. aeruginosa
strain FRD1. Unlike the parental strain, the
amrZ
mutant was nonmucoid and motile. Complementation of the mutant with
amrZ
restored the mucoid, nonmotile phenotype. Thus, our data show that AlgT inhibits flagellum biosynthesis in mucoid, nonmotile
P. aeruginosa
cystic fibrosis isolates by promoting expression of AmrZ, which subsequently represses
fleQ
. Since
fleQ
directly or indirectly controls the expression of almost all flagellar genes, its repression ultimately leads to the loss of flagellum biosynthesis.
Thiamine Is Synthesized by a Salvage Pathway in
Rhizobium leguminosarum
bv. viciae Strain 3841
Authors: Karunakaran R. , Ebert K. , Harvey S. , Leonard M. E. , Ramachandran V. , Poole P. S.
Published: September 2006

In the absence of added thiamine,
Rhizobium leguminosarum
bv. viciae strain 3841 does not grow in liquid medium and forms only “pin” colonies on agar plates, which contrasts with the good growth of
Sinorhizobium meliloti
1021,
Mesorhizobium loti
303099, and
Rhizobium etli
CFN42. These last three organisms have
thiCOGE
genes, which are essential for de novo thiamine synthesis. While
R. leguminosarum
bv. viciae 3841 lacks
thiCOGE
, it does have
thiMED
. Mutation of
thiM
prevented formation of pin colonies on agar plates lacking added thiamine, suggesting thiamine intermediates are normally present. The putative functions of ThiM, ThiE, and ThiD are 4-methyl-5-(β-hydroxyethyl) thiazole (THZ) kinase, thiamine phosphate pyrophosphorylase, and 4-amino-5-hydroxymethyl-2-methyl pyrimidine (HMP) kinase, respectively. This suggests that a salvage pathway operates in
R. leguminosarum
, and addition of HMP and THZ enabled growth at the same rate as that enabled by thiamine in strain 3841 but elicited no growth in the
thiM
mutant (RU2459). There is a putative
thi
box sequence immediately upstream of the
thiM
, and a
gfp-mut3.1
fusion to it revealed the presence of a promoter that is strongly repressed by thiamine. Using fluorescent microscopy and quantitative reverse transcription-PCR, it was shown that
thiM
is expressed in the rhizosphere of vetch and pea plants, indicating limitation for thiamine. Pea plants infected by RU2459 were not impaired in nodulation or nitrogen fixation. However, colonization of the pea rhizosphere by the
thiM
mutant was impaired relative to that of the wild type. Overall, the results show that a thiamine salvage pathway operates to enable growth of
Rhizobium leguminosarum
in the rhizosphere, allowing its survival when thiamine is limiting.
Sequence Analysis of the Lactococcal Plasmid pNP40: a Mobile Replicon for Coping with Environmental Hazards
Authors: O'Driscoll Jonathan , Glynn Frances , Fitzgerald Gerald F. , Sinderen Douwe van
Published: September 2006

The conjugative lactococcal plasmid pNP40, identified in
Lactococcus lactis
subsp.
diacetylactis
DRC3, possesses a potent complement of bacteriophage resistance systems, which has stimulated its application as a fitness-improving, food-grade genetic element for industrial starter cultures. The complete sequence of this plasmid allowed the mapping of previously known functions including replication, conjugation, bacteriocin resistance, heavy metal tolerance, and bacteriophage resistance. In addition, functions for cold shock adaptation and DNA damage repair were identified, further confirming pNP40's contribution to environmental stress protection. A plasmid cointegration event appears to have been part of the evolution of pNP40, resulting in a “stockpiling” of bacteriophage resistance systems.
Transcriptional Response ofEscherichia colito TPEN
Authors: Sigdel Tara K. , Easton J. Allen , Crowder Michael W.
Published: September 2006

DNA microarrays were used to probe the transcriptional response ofEscherichia colitoN,N,N′,N′-tetrakis(2-pyridylmethyl)ethylenediamine (TPEN). Fifty-five transcripts were significantly up-regulated, including all of the genes that are regulated by Zur and many that are regulated by Fur. In the same TPEN-treated cells, 46 transcripts were significantly down-regulated.
Mlc of
Thermus thermophilus
: a Glucose-Specific Regulator for a Glucose/Mannose ABC Transporter in the Absence of the Phosphotransferase System
Authors: Chevance Fabienne F. V. , Erhardt Marc , Lengsfeld Christina , Lee Sung-Jae , Boos Winfried
Published: September 2006

We report the presence of Mlc in a thermophilic bacterium. Mlc is known as a global regulator of sugar metabolism in gram-negative enteric bacteria that is controlled by sequestration to a glucose-transporting EII
Glc
of the phosphotransferase system (PTS). Since thermophilic bacteria do not possess PTS, Mlc in
Thermus thermophilus
must be differently controlled. DNA sequence alignments between Mlc from
T. thermophilus
(Mlc
Tth
) and Mlc from
E. coli
(Mlc
Eco
) revealed that Mlc
Tth
conserved five residues of the glucose-binding motif of glucokinases. Here we show that Mlc
Tth
is not a glucokinase but is indeed able to bind glucose (

K
D

= 20 μM), unlike Mlc
Eco
. We found that
mlc
of
T. thermophilus
is the first gene within an operon encoding an ABC transporter for glucose and mannose, including a glucose/mannose-binding protein and two permeases.
malK1
, encoding the cognate ATP-hydrolyzing subunit, is located elsewhere on the chromosome. The system transports glucose at 70°C with a

K
m

of 0.15 μM and a
V
max
of 4.22 nmol per min per ml at an optical density (OD) of 1. Mlc
Tth
negatively regulates itself and the entire glucose/mannose ABC transport system operon but not
malK1
, with glucose acting as an inducer. MalK1 is shared with the ABC transporter for trehalose, maltose, sucrose, and palatinose (TMSP). Mutants lacking
malK1
do not transport either glucose or maltose. The TMSP transporter is also able to transport glucose with a

K
m

of 1.4 μM and a
V
max
of 7.6 nmol per min per ml at an OD of 1, but it does not transport mannose.
ThehmuQandhmuDGenes fromBradyrhizobium japonicumEncode Heme-Degrading Enzymes
Authors: Puri Sumant , O'Brian Mark R.
Published: September 2006

Utilization of heme by bacteria as a nutritional iron source involves the transport of exogenous heme, followed by cleavage of the heme macrocycle to release iron.Bradyrhizobium japonicumcan use heme as an iron source, but no heme-degrading oxygenase has been described. Here, bioinformatics analyses of theB. japonicumgenome identified two paralogous genes renamedhmuQ(bll7075) andhmuD(bll7423) that encode proteins with weak similarity to the heme-degrading monooxygenase IsdG fromStaphylococcus aureus. ThehmuQgene is clustered with known heme transport genes in the genome. Recombinant HmuQ bound heme with aKdvalue of 0.8 μM and showed spectral properties consistent with a heme oxygenase. In the presence of a reductant, HmuQ catalyzed the degradation of heme and the formation of biliverdin. ThehmuQandhmuDgenes complemented aCorynebacterium ulceransheme oxygenase mutant intransfor utilization of heme as the sole iron source for growth. Furthermore, homologs ofhmuQandhmuDwere identified in many bacterial genera, and the recombinant homolog fromBrucella melitensisbound heme and catalyzed its degradation. The findings show thathmuQandhmuDencode heme oxygenases and indicate that the IsdG family of heme-degrading monooxygenases is not restricted to gram-positive pathogenic bacteria.
Gliding Motility of
Mycoplasma mobile
Can Occur by Repeated Binding to
N
-Acetylneuraminyllactose (Sialyllactose) Fixed on Solid Surfaces
Authors: Nagai Ryoichiro , Miyata Makoto
Published: September 2006

Mycoplasma mobile
relies on an unknown mechanism to glide across solid surfaces including glass, animal cells, and plastics. To identify the direct binding target, we examined the factors that affect the binding of
Mycoplasma pneumoniae
to solid surfaces and concluded that
N
-acetylneuraminyllactose (sialyllactose) attached to a protein can mediate glass binding on the basis of the following four lines of evidence: (i) glass binding was inhibited by
N
-acetylneuraminidase, (ii) glass binding was inhibited by
N
-acetylneuraminyllactose in a structure-dependent manner, (iii) binding occurred on glass pretreated with bovine serum albumin attached to
N
-acetylneuraminyllactose, and (iv) gliding speed depended on the density of
N
-acetylneuraminyllactose on glass.
Characteristic Features in the Structure and Collagen-Binding Ability of a Thermophilic Collagenolytic Protease from the Thermophile
Geobacillus collagenovorans
MO-1
Authors: Itoi Yuichi , Horinaka Mano , Tsujimoto Yoshiyuki , Matsui Hiroshi , Watanabe Kunihiko
Published: September 2006

A collagen-degrading thermophile,
Geobacillus collagenovorans
MO-1, extracellularly produces a collagenolytic protease with a large molecular mass. Complete nucleotide sequencing of this gene after gene cloning revealed that the collagenolytic protease is a member of the subtilisin family of serine proteases and consists of a signal sequence for secretion, a prosequence for maturation, a catalytic region, 14 direct repeats of 20 amino acids at the C terminus, and a region with unknown function intervening between the catalytic region and the numerous repeats. Since the unusual repeats are most likely to be cleaved in the secreted form of the enzyme, the intervening region was investigated to determine whether it participates in collagen binding to facilitate collagen degradation. It was found that the mature collagenolytic protease containing the intervening region at the C terminus bound collagen but not the other insoluble proteins, elastin and keratin. Furthermore, the intervening region fused with glutathione
S
-transferase showed a collagen-binding ability comparable to that of the mature collagenolytic protease. The collagen-binding ability was finally attributed to two-thirds of the intervening region which is rich in β-strands and is approximately 35 kDa in molecular mass. In the collagenolytic protease from strain MO-1, hydrogen bonds most likely predominate over the hydrophobic interaction for collagen binding, since a higher concentration of NaCl released collagen from the enzyme surface but a nonionic detergent could not. To the best of our knowledge, this is the first report of a thermophilic collagenolytic protease containing the collagen-binding segment.
Identification of an Essential Gene ofListeria monocytogenesInvolved in Teichoic Acid Biogenesis
Authors: Dubail Iharilalao , Bigot Armelle , Lazarevic Vladimir , Soldo Blazenka , Euphrasie Daniel , Dupuis Marion , Charbit Alain
Published: September 2006

Listeria monocytogenesis a facultative intracellular gram-positive bacterium responsible for severe opportunistic infections in humans and animals. We had previously identified a gene encoding a putative UDP-N-acetylglucosamine 2-epimerase, a precursor of the teichoic acid linkage unit, in the genome ofL monocytogenesstrain EGD-e. This gene, now designated lmo2537, encodes a protein that shares 62% identity with the cognate epimerase MnaA ofBacillus subtilisand 55% identity with Cap5P ofStaphylococcus aureus. Here, we addressed the role of lmo2537 inL. monocytogenespathogenesis by constructing a conditional knockout mutant. The data presented here demonstrate that lmo2537 is an essential gene ofL. monocytogenesthat is involved in teichoic acid biogenesis. In vivo, the conditional mutant is very rapidly eliminated from the target organs of infected mice and thus is totally avirulent.
3-Hydroxy-3-Methylglutaryl-Coenzyme A (CoA) Synthase Is Involved in Biosynthesis of Isovaleryl-CoA in the Myxobacterium
Myxococcus xanthus
during Fruiting Body Formation
Authors: Bode Helge B. , Ring Michael W. , Schwär Gertrud , Kroppenstedt Reiner M. , Kaiser Dale , Müller Rolf
Published: September 2006

Isovaleryl-coenzyme A (IV-CoA) is the starting unit for some secondary metabolites and iso-odd fatty acids in several bacteria. According to textbook biochemistry, IV-CoA is derived from leucine degradation, but recently an alternative pathway that branches from the well-known mevalonate-dependent isoprenoid biosynthesis has been described for myxobacteria. A double mutant was constructed in
Myxococcus xanthus
by deletion of genes involved in leucine degradation and disruption of
mvaS
encoding the 3-hydroxy-3-methylglutaryl-coenzyme A synthase. A dramatic decrease of IV-CoA-derived iso-odd fatty acids was observed for the mutant, confirming
mvaS
to be involved in the alternative pathway. Additional quantitative real-time reverse transcription-PCR experiments indicated that
mvaS
is transcriptionally regulated by isovalerate. Furthermore, feeding studies employing an intermediate specific for the alternative pathway revealed that this pathway is induced during fruiting body formation, which presumably increases the amount of IV-CoA available when leucine is limited.
AN ANALYTICAL SOLUTION FOR THE STOCHASTIC MODEL OF A TURBULENT CASCADE
Authors: MASOUDI A. A. , ANARAKI P. AZIMI
Published: September 2006

In this paper we are going to derive the Fokker–Planck equation (FPE) which is based on the Langevin equation for the stochastic model of a turbulent cascade and then we exactly solve the FPE for a certain case and find an explicit form of the probability distribution function (PDF) by the operator method. Finally, by using this PDF, we calculate the velocity moments for this system.
STUDY OF THERMAL TRANSPORT PARAMETERS IN PbI2 SINGLE CRYSTAL USING A PHOTOACOUSTIC TECHNIQUE
Authors: AHLAWAT D. S. , MOHAN D. , GHOSHAL S. K. , SINGH R. D. , SHARMA MEENAKSHI
Published: September 2006

The present work discusses the study of the transport properties of the PbI 2 single crystal using an indigenously developed photoacoutistic spectrometer. The amplitude photoacoustic signal, being a function of the modulation frequency of the incident optical beam, has been measured by using the front-side detection configuration. The characteristic frequency (fc) of the single crystal has been found to be 55 Hz. The values of thermal diffusivity, thermal conductivity and thermal effusivity in the case of PbI 2 have been derived experimentally. Their values have been compared with the values reported in a case which studied other materials in the literature. Thermal diffusion lengths have also been calculated at different chopping frequencies from 15 Hz to 90 Hz.
A NEW EXPANDING INTEGRABLE HIERARCHY OF KAUP–NEWELL HIERARCHY
Authors: DONG HUANHE
Published: September 2006

A higher loop algebra is constructed which is devoted to establish an isospectral Lax pair. Integrable coupling of the well-known Kaup–Newell hierarchy is obtained by using a relation of direct sum between two sub-algebras. As in the reduction case, an integrable coupling of a generalized MKdV equation is presented. The approach presented in the paper can be used generally.
THE CWKB PARTICLE PRODUCTION AND CLASSICAL CONDENSATE IN DE SITTER SPACE–TIME
Authors: BISWAS S. , CHOWDHURY I.
Published: September 2006

The complex time WKB approximation is an effective tool in studying particle production in curved space–time. We use it in this work to understand the formation of classical condensate in expanding de Sitter space–time. The CWKB leads to the emergence of thermal spectrum that depends crucially on horizons (as in de Sitter space–time) or observer dependent horizons (as in Rindler space–time). A connection is sought between the horizon and the formation of classical condensate. We concentrate on de Sitter space–time and study the cosmological perturbation of k = 0 mode with various values of m/H0. We find that, for a minimally coupled free scalar field for [Formula: see text], the one-mode occupation number grows more than unity soon after the physical wavelength of the mode crosses the Hubble radius and soon after that, diverges as [Formula: see text], where [Formula: see text]. The results substantiate the previous works in this direction. We also find the correct oscillation and behavior of N(z) at small z from a single expression using CWKB approximation for various values of m/H0. We also discuss decoherence in relation to the formation of classical condensate. We further find that the squeezed state formalism and CWKB method give identical results.
ON THE SUPERSTRING HAMILTONIAN IN THE FRIEDMANN SPACE–TIME
Authors: POLLOCK M. D.
Published: September 2006

The ten-dimensional effective Lagrangian [Formula: see text] for the gravitational sector of the heterotic superstring theory is known up to quartic higher-derivative order [Formula: see text]. In cosmology, the reduced, four-dimensional line element assumes the Friedmann form ds2 = dt2 - a(t)2dx2, where t is comoving time and a(t) ≡ a0eα(t) is the radius function of the three-space dx2, whose curvature is k = 0, ± 1. The four-Lagrangian can then be expressed as the power-series [Formula: see text], where ˙ ≡ d/dt, from which the field equation can be derived by the method of Ostrogradsky. Here, we determine the coefficients Λ0, An, Bn, Cn, and Kn, which are all non-vanishing in general. We recover the previously obtained, high-curvature, anti-de Sitter vacuum state [Formula: see text] with effective cosmological constant Λ = {18/[175ζ(3) - 1/2]}1/3A r κ-2, whose existence makes it possible to envisage a singularity-free and horizon-free cosmological solution, stable to linear perturbations. It is interesting that all the coefficients of quartic origin arise from the near-cancellation of sums of opposite sign but magnitude f ≈ (28.6–369) times larger than the answer. They thus exhibit a slight asymmetry with regard to positive and negative energies, the anti-de Sitter vacuum being characterized by positive Nordström energy, and therefore only accessible at high curvatures. This vacuum state is a Bose–Einstein condensate of non-interacting gravitons at zero temperature, which, referred to comoving time, can only be formulated after the Wick rotation t → ±iτ, resulting in an imaginary horizon.
EFFECTIVE COSMOLOGICAL CONSTANT IN BRANE COSMOLOGY
Authors: HU SEN , WANG JING-RONG
Published: September 2006

We consider a brane-world of co-dimension one without reflection symmetry. Through it, we give a possible explanation of the great discrepancy between the vacuum energy and the observed cosmological constant without contradiction to the knowledge we have about our Universe. We also show the gravity observed will be standard four-dimensional gravity as long as the discrepancy of the bulk cosmological constant at different sides of the brane is small enough.
ELECTROMAGNETIC MASS IN (n + 2)-DIMENSIONAL SPACE–TIMES
Authors: RAY SAIBAL
Published: September 2006

Einstein–Maxwell field equations corresponding to a higher-dimensional description of static spherically symmetric space–time are solved under two specific sets of conditions: (i) ρ ≠ 0, ν′ = 0 and (ii) ρ = 0, ν′ ≠ 0, where ρ and ν represent the mass density and metric potential. The solution sets thus obtained satisfy the criteria of being an electromagnetic mass model such that the gravitational mass vanishes for the vanishing charge density σ and also the space–time becomes flat. Physical features related to other parameters are also discussed.
STOCHASTIC ATTRACTORS FOR NON-ERGODIC MARKOV PROCESSES: SOME EXAMPLES
Authors: DAI PRA PAOLO , MINELLI IDA
Published: September 2006

We discuss the notion of stochastic attractor for Markov processes. We exhibit some nontrivial examples of Markov processes possessing more than one stationary distributions, for which the stochastic attractor can be explicitly determined.