bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhanced Exopolymer Production and Chromium Stabilization inPseudomonas putidaUnsaturated Biofilms
Authors: Priester John H. , Olson Scott G. , Webb Samuel M. , Neu Mary P. , Hersman Larry E. , Holden Patricia A.
Published: March 2006

Chromium-contaminated soils threaten surface and groundwater quality at many industrial sites. In vadose zones, indigenous bacteria can reduce Cr(VI) to Cr(III), but the subsequent fate of Cr(III) and the roles of bacterial biofilms are relatively unknown. To investigate, we culturedPseudomonas putida, a model organism for vadose zone bioremediation, as unsaturated biofilms on membranes overlaying iron-deficient solid media either containing molecular dichromate from potassium dichromate (Cr-only treatment) or with deposits of solid, dichromate-coated hematite (Fe+Cr treatment) to simulate vadose zone conditions. Controls included iron-deficient solid medium and an Fe-only treatment using solid hematite deposits. Under iron-deficient conditions, chromium exposure resulted in lower cell yield and lower amounts of cellular protein and carbohydrate, but providing iron in the form of hematite overcame these toxic effects of Cr. For the Cr and Fe+Cr treatments, Cr(VI) was completely reduced to Cr(III) that accumulated on biofilm cells and extracellular polymeric substances (EPSs). Chromium exposure resulted in elevated extracellular carbohydrates, protein, DNA, and EPS sugars that were relatively enriched inN-acetyl-glucosamine, rhamnose, glucose, and mannose. The proportions of EPS protein and carbohydrate relative to intracellular pools suggested Cr toxicity-mediated cell lysis as the origin. However, DNA accumulated extracellularly in amounts far greater than expected from cell lysis, and Cr was liberated when extracted EPS was treated with DNase. These results demonstrate that Cr accumulation in unsaturated biofilms occurs with enzymatic reduction of Cr(VI), cellular lysis, cellular association, and extracellular DNA binding of Cr(III), which altogether can facilitate localized biotic stabilization of Cr in contaminated vadose zones.
Gene Expression Regulation by the Curli Activator CsgD Protein: Modulation of Cellulose Biosynthesis and Control of Negative Determinants for Microbial Adhesion
Authors: Brombacher Eva , Baratto Andrea , Dorel Corinne , Landini Paolo
Published: March 2006

Curli fibers, encoded by thecsgBACgenes, promote biofilm formation inEscherichia coliand other enterobacteria. Curli production is dependent on the CsgD transcription activator, which also promotes cellulose biosynthesis. In this study, we investigated the effects of CsgD expression from a weak constitutive promoter in the biofilm formation-deficient PHL565 strain ofE. coli. We found that despite its function as a transcription activator, the CsgD protein is localized in the cytoplasmic membrane. Constitutive CsgD expression promotes biofilm formation by PHL565 and activates transcription from thecsgBACpromoter; however,csgBACexpression remains dependent on temperature and the growth medium. Constitutive expression of the CsgD protein results in altered transcription patterns for at least 24 novel genes, in addition to the previously identified CsgD-dependent genes. ThecspAandfecRgenes, encoding regulatory proteins responding to cold shock and to iron, respectively, andyoaD, encoding a putative negative regulator of cellulose biosynthesis, were found to be some of the novel CsgD-regulated genes. Consistent with the predicted functional role, increased expression of theyoaDgene negatively affects cell aggregation, whileyoaDinactivation results in stimulation of cell aggregation and leads to increased cellulose production. Inactivation offecRresults in significant increases in both cell aggregation and biofilm formation, while the effects ofcspAare not as strong in the conditions tested. Our results indicate that CsgD can modulate cellulose biosynthesis through activation of theyoaDgene. In addition, the positive effect of CsgD on biofilm formation might be enhanced by repression of thefecRgene.
A Complete Lipopolysaccharide Inner Core Oligosaccharide Is Required for Resistance of
Burkholderia cenocepacia
to Antimicrobial Peptides and Bacterial Survival In Vivo
Authors: Loutet Slade A. , Flannagan Ronald S. , Kooi Cora , Sokol Pamela A. , Valvano Miguel A.
Published: March 2006

Burkholderia cenocepacia
is an important opportunistic pathogen of patients with cystic fibrosis. This bacterium is inherently resistant to a wide range of antimicrobial agents, including high concentrations of antimicrobial peptides. We hypothesized that the lipopolysaccharide (LPS) of
B. cenocepacia
is important for both virulence and resistance to antimicrobial peptides. We identified
hldA
and
hldD
genes in
B. cenocepacia
strain K56-2. These two genes encode enzymes involved in the modification of heptose sugars prior to their incorporation into the LPS core oligosaccharide. We constructed a mutant, SAL1, which was defective in expression of both
hldA
and
hldD
, and by performing complementation studies we confirmed that the functions encoded by both of these
B. cenocepacia
genes were needed for synthesis of a complete LPS core oligosaccharide. The LPS produced by SAL1 consisted of a short lipid A-core oligosaccharide and was devoid of O antigen. SAL1 was sensitive to the antimicrobial peptides polymyxin B, melittin, and human neutrophil peptide 1. In contrast, another
B. cenocepacia
mutant strain that produced complete lipid A-core oligosaccharide but lacked polymeric O antigen was not sensitive to polymyxin B or melittin. As determined by the rat agar bead model of lung infection, the SAL1 mutant had a survival defect in vivo since it could not be recovered from the lungs of infected rats 14 days postinfection. Together, these data show that the
B. cenocepacia
LPS inner core oligosaccharide is needed for in vitro resistance to three structurally unrelated antimicrobial peptides and for in vivo survival in a rat model of chronic lung infection.
Common and Variable Contributions of Fis Residues to High-Affinity Binding at Different DNA Sequences
Authors: Feldman-Cohen Leah S. , Shao Yongping , Meinhold Derrick , Miller Charmi , Colón Wilfredo , Osuna Robert
Published: March 2006

Fis is a nucleoid-associated protein that interacts with poorly related DNA sequences with a high degree of specificity. A difference of more than 3 orders of magnitude in apparent

K
d

values was observed between specific (

K
d

, ∼1 to 4 nM) and nonspecific (

K
d

, ∼4 μM) DNA binding. To examine the contributions of Fis residues to the high-affinity binding at different DNA sequences, 13 alanine substitutions were generated in or near the Fis helix-turn-helix DNA binding motif, and the resulting proteins were purified. In vitro binding assays at three different Fis sites (
fis
P II,
hin
distal, and λ
attR
) revealed that R85, T87, R89, K90, and K91 played major roles in high-affinity DNA binding and that R85, T87, and K90 were consistently vital for binding to all three sites. Other residues made variable contributions to binding, depending on the binding site. N84 was required only for binding to the λ
attR
Fis site, and the role of R89 was dramatically altered by the λ
attR
DNA flanking sequence. The effects of Fis mutations on
fis
P II or
hin
distal site binding in vitro generally correlated with their abilities to mediate
fis
P repression or DNA inversion in vivo, demonstrating that the in vitro DNA-binding effects are relevant in vivo. The results suggest that while Fis is able to recognize a minimal common set of DNA sequence determinants at different binding sites, it is also equipped with a number of residues that contribute to the binding strength, some of which play variable roles.
The Tra Domain of the Lactococcal CluA Surface Protein Is a Unique Domain That Contributes to Sex Factor DNA Transfer
Authors: Stentz Régis , Gasson Mike , Shearman Claire
Published: March 2006

CluA is a cell surface-presented protein that causes cell aggregation and is essential for a high-efficiency conjugation process in
Lactococcus lactis
. We know from previous work that in addition to promoting cell-to-cell contact, CluA is involved in sex factor DNA transfer. To define the CluA domains involved in aggregation and in transfer, we first performed random mutagenesis of the
cluA
gene using a modified mini-Tn
7
element which generated five amino acid insertions located throughout the encoded protein. Thirty independent
cluA
insertion mutants expressing modified CluA proteins at the cell surface were isolated and characterized further. The level of aggregation of each mutant was determined. The cell binding capacity of CluA was affected strongly when the protein had a mutation in its N-terminal region, which defined an aggregation domain extending from amino acid 153 to amino acid 483. Of the
cluA
mutants that still exhibited aggregation, eight showed an attenuated ability to conjugate, and six mutations were located in a 300-amino-acid C-terminal region of the protein defining a transfer domain (Tra). This result was confirmed by a phenotypic analysis of an additional five mutants obtained using site-directed mutagenesis in which charged amino acids of the Tra domain were replaced by alanine residues. Two distinct functional domains of the CluA protein were defined in this work; the first domain is involved in cell binding specificity, and the Tra domain is probably involved in the formation of the DNA transport machinery. This is the first report of a protein involved in conjugation that actively contributes to DNA transfer and mediates contact between donor and recipient strains.
Function of the N-Terminal Cap of the PAS Domain in Signaling by the Aerotaxis Receptor Aer
Authors: Watts Kylie J. , Sommer Kirsten , Fry Sheena L. , Johnson Mark S. , Taylor Barry L.
Published: March 2006

Aer, the
Escherichia coli
receptor for behavioral responses to oxygen (aerotaxis), energy, and redox potential, contains a PAS sensory-input domain. Within the PAS superfamily, the N-terminal segment (N-cap) is poorly conserved and its role is not well understood. We investigated the role of the N-cap (residues 1 to 19) in the Aer PAS domain by missense and truncation mutagenesis. Aer-PAS N-cap truncations and an Aer-M21P substitution resulted in low cellular levels of the mutant proteins, suggesting that the N-terminal region was important for stabilizing the structure of the PAS domain. The junction of the N-cap and PAS core was critical for signaling in Aer. Mutations and truncations in the sequence encoding residues 15 to 21 introduced a range of phenotypes, including defects in FAD binding, constant tumbling motility, and an inverse response in which
E. coli
cells migrated away from oxygen concentrations to which they are normally attracted. The proximity of two N-cap regions in an Aer dimer was assessed in vivo by oxidatively cross-linking serial cysteine substitutions. Cross-linking of several cysteine replacements at 23°C was attenuated at 10°C, indicating contact was not at a stable dimer interface but required lateral mobility. We observed large multimers of Aer when we combined cross-linking of N-cap residues with a cysteine replacement that cross-links exclusively at the Aer dimer interface. This suggests that the PAS N-cap faces outwards in a dimer and that PAS-PAS contacts can occur between adjacent dimers.
Functional Studies of [FeFe] Hydrogenase Maturation in an
Escherichia coli
Biosynthetic System
Authors: King Paul W. , Posewitz Matthew C. , Ghirardi Maria L. , Seibert Michael
Published: March 2006

Maturation of [FeFe] hydrogenases requires the biosynthesis and insertion of the catalytic iron-sulfur cluster, the H cluster. Two radical
S
-adenosylmethionine (SAM) proteins proposed to function in H cluster biosynthesis, HydEF and HydG, were recently identified in the
hydEF-1
mutant of the green alga
Chlamydomonas reinhardtii
(M. C. Posewitz, P. W. King, S. L. Smolinski, L. Zhang, M. Seibert, and M. L. Ghirardi, J. Biol. Chem. 279:25711-25720, 2004). Previous efforts to study [FeFe] hydrogenase maturation in
Escherichia coli
by coexpression of
C. reinhardtii
HydEF and HydG and the HydA1 [FeFe] hydrogenase were hindered by instability of the
hydEF
and
hydG
expression clones. A more stable [FeFe] hydrogenase expression system has been achieved in
E. coli
by cloning and coexpression of
hydE
,
hydF
, and
hydG
from the bacterium
Clostridium acetobutylicum
. Coexpression of the
C. acetobutylicum
maturation proteins with various algal and bacterial [FeFe] hydrogenases in
E. coli
resulted in purified enzymes with specific activities that were similar to those of the enzymes purified from native sources. In the case of structurally complex [FeFe] hydrogenases, maturation of the catalytic sites could occur in the absence of an accessory iron-sulfur cluster domain. Initial investigations of the structure and function of the maturation proteins HydE, HydF, and HydG showed that the highly conserved radical-SAM domains of both HydE and HydG and the GTPase domain of HydF were essential for achieving biosynthesis of active [FeFe] hydrogenases. Together, these results demonstrate that the catalytic domain and a functionally complete set of Hyd maturation proteins are fundamental to achieving biosynthesis of catalytic [FeFe] hydrogenases.
Global Control of Cysteine Metabolism by CymR inBacillus subtilis
Authors: Even Sergine , Burguière Pierre , Auger Sandrine , Soutourina Olga , Danchin Antoine , Martin-Verstraete Isabelle
Published: March 2006

YrzC has previously been identified as a repressor controllingytmIexpression via its regulation of YtlI activator synthesis inBacillus subtilis.We identified YrzC as a master regulator of sulfur metabolism. Gene expression profiles ofB. subtilisΔyrzCmutant and wild-type strains grown in minimal medium with sulfate as the sole sulfur source were compared. In the mutant, increased expression was observed for 24 genes previously identified as repressed in the presence of sulfate. Since several genes involved in the pathways leading to cysteine formation were found, we propose to rename YrzC CymR, for “cysteine metabolism repressor.” A CymR-dependent binding to the promoter region of theytlI,ssuB,tcyP,yrrT,yxeK,cysK, orydbMgene was demonstrated using gel shift experiments. A potential CymR target site, TAAWNCN2ANTWNAN3ATMGGAATTW, was found in the promoter region of these genes. In a DNase footprint experiment, the protected region in theytlIpromoter region contained this consensus sequence. Partial deletion or introduction of point mutations in this sequence confirmed its involvement inytlI,yrrT, andyxeKregulation. The addition ofO-acetylserine in gel shift experiments prevented CymR-dependent binding to DNA for all of the targets characterized. Transcriptome analysis of a ΔcymRmutant and the wild-type strain also brought out significant changes in the expression level of a large set of genes related to stress response or to transition toward anaerobiosis.
The Mechanism of the Tyrosine Transporter TyrP Supports a Proton Motive Tyrosine Decarboxylation Pathway in
Lactobacillus brevis
Authors: Wolken Wout A. M. , Lucas Patrick M. , Lonvaud-Funel Aline , Lolkema Juke S.
Published: March 2006

The tyrosine decarboxylase operon of
Lactobacillus brevis
IOEB9809 contains, adjacent to the tyrosine decarboxylase gene, a gene for TyrP, a putative tyrosine transporter. The two genes potentially form a proton motive tyrosine decarboxylation pathway. The putative tyrosine transporter gene of
L. brevis
was expressed in
Lactococcus lactis
and functionally characterized using right-side-out membranes. The transporter very efficiently catalyzes homologous tyrosine-tyrosine exchange and heterologous exchange between tyrosine and its decarboxylation product tyramine. Tyrosine-tyramine exchange was shown to be electrogenic. In addition to the exchange mode, the transporter catalyzes tyrosine uniport but at a much lower rate. Analysis of the substrate specificity of the transporter by use of a set of 19 different tyrosine substrate analogues showed that the main interactions between the protein and the substrates involve the amino group and the phenyl ring with the
para
hydroxyl group. The carboxylate group that is removed in the decarboxylation reaction does not seem to contribute to the affinity of the protein for the substrates significantly. The properties of the TyrP protein are those typical for precursor-product exchangers that operate in proton motive decarboxylation pathways. It is proposed that tyrosine decarboxylation in
L. brevis
results in proton motive force generation by an indirect proton pumping mechanism.
The Integrase of the Conjugative Transposon Tn916Directs Strand- and Sequence-Specific Cleavage of the Origin of Conjugal Transfer,oriT, by the Endonuclease Orf20
Authors: Rocco Jennifer M. , Churchward Gordon
Published: March 2006

Orf20 of the conjugative transposon Tn916was purified as a chimeric protein fused to maltose binding protein (MBP-Orf20). The chimeric protein possessed endonucleolytic activity, cleaving both strands of the Tn916origin of conjugal transfer (oriT) at several distinct sites and favoring GT dinucleotides. Incubation of theoriTDNA with purified Tn916integrase (Int) and MBP-Orf20 resulted in strand- and sequence-specific cleavage oforiTat a TGGT motif in the transferred strand. This motif lies immediately adjacent to a sequence inoriTpreviously shown to be protected from DNase I cleavage by Int. The endonucleolytic cleavages produced by Orf20 generated a 3′ OH group that could be radiolabeled by dideoxy ATP and terminal transferase. The production of a 3′ OH group distinguished these Orf20-dependent cleavage events from those catalyzed by Int at the ends of Tn916. Thus, Orf20 functions as the relaxase of Tn916, nickingoriTas the first step in conjugal DNA transfer. Remarkably for a tyrosine recombinase, Tn916Int acts as a specificity factor in the reaction, conferring both strand and sequence specificities on the endonucleolytic cleavage activity of Orf20.
Cyclo(Phe-Pro) Modulates the Expression ofompUinVibriospp
Authors: Park Dae-Kyun , Lee Ko-Eun , Baek Chang-Ho , Kim In Hwang , Kwon Ji-Hyoun , Lee Won Koo , Lee Kyu-Ho , Kim Byung-Soo , Choi Sang-Ho , Kim Kun-Soo
Published: March 2006

Vibrio vulnificuswas found to produce a chemical that induced the expression ofVibrio fischeri luxgenes. Electron spray ionization-mass spectrometry and1H nuclear magnetic resonance analyses indicated that the compound was cyclo(l-Phe-l-Pro) (cFP). The compound was produced at a maximal level when cell cultures reached the onset of stationary phase. Sodium dodecyl sulfate-polyacrylamide gel analysis of the total proteins ofV. vulnificusindicated that expression of OmpU was enhanced by exogenously added synthetic or purified cFP. AtoxR-null mutant failed to expressompUdespite the addition of cFP. The relatedVibriospp.V. cholerae,V. parahaemolyticus, andV. harveyialso produced cFP, which induced the expression of their ownompUgenes. cFP also enhanced the expression inV. choleraeof thectxgenes, which are known to be regulated by ToxR. Our results suggest that cFP is a signal molecule controlling the expression of genes important for the pathogenicity ofVibriospp.
Identification of New Flagellar Genes ofSalmonella entericaSerovar Typhimurium
Authors: Frye Jonathan , Karlinsey Joyce E. , Felise Heather R. , Marzolf Bruz , Dowidar Naeem , McClelland Michael , Hughes Kelly T.
Published: March 2006

RNA levels of flagellar genes in eight different genetic backgrounds were compared to that of the wild type by DNA microarray analysis. Cluster analysis identified new, potential flagellar genes, three putative methyl-accepting chemotaxis proteins, STM3138 (McpA), STM3152 (McpB), and STM3216(McpC), and a CheV homolog, STM2314, inSalmonella, that are not found inEscherichia coli. Isolation and characterization of Mud-lacinsertions incheV,mcpB,mcpC, and the previously uncharacterizedaerlocus ofS. entericaserovar Typhimurium revealed them to be controlled by σ28-dependent flagellar class 3 promoters. In addition, thesrfABCoperon previously isolated as an SsrB-regulated operon clustered with the flagellar class 2 operon and was determined to be under FlhDC control. The previously unclassifiedfliBgene, encoding flagellin methylase, clustered as a class 2 gene, which was verified using reporter fusions, and thefliBtranscriptional start site was identified by primer extension analysis. RNA levels of all flagellar genes were elevated inflgMorfliTnull strains. RNA levels of class 3 flagellar genes were elevated in afliSnull strain, while deletion of thefliY,fliZ, orflkgene did not affect flagellar RNA levels relative to those of the wild type. ThecafA(RNase G) andyhjHgenes clustered with flagellar class 3 transcribed genes. Null alleles incheV,mcpA,mcpB,mcpC, andsrfBdid not affect motility, while deletion ofyhjHdid result in reduced motility compared to that of the wild type.
Coordination between Chromosome Replication, Segregation, and Cell Division inCaulobacter crescentus
Authors: Jensen Rasmus B.
Published: March 2006

Progression through theCaulobacter crescentuscell cycle is coupled to a cellular differentiation program. The swarmer cell is replicationally quiescent, and DNA replication initiates at the swarmer-to-stalked cell transition. There is a very short delay between initiation of DNA replication and movement of one of the newly replicated origins to the opposite pole of the cell, indicating the absence of cohesion between the newly replicated origin-proximal parts of theCaulobacterchromosome. The terminus region of the chromosome becomes located at the invaginating septum in predivisional cells, and the completely replicated terminus regions stay associated with each other after chromosome replication is completed, disassociating very late in the cell cycle shortly before the final cell division event. Invagination of the cytoplasmic membrane occurs earlier than separation of the replicated terminus regions and formation of separate nucleoids, which results in trapping of a chromosome on either side of the cell division septum, indicating that there is not a nucleoid exclusion phenotype.
Complete Genome Sequence of the Dehalorespiring Bacterium
Desulfitobacterium hafniense
Y51 and Comparison with
Dehalococcoides ethenogenes
195
Authors: Nonaka Hiroshi , Keresztes Gabor , Shinoda Yoshifumi , Ikenaga Yuko , Abe Miyuki , Naito Kae , Inatomi Kenichi , Furukawa Kensuke , Inui Masayuki , Yukawa Hideaki
Published: March 2006

Desulfitobacterium
strains have the ability to dechlorinate halogenated compounds under
anaerobic conditions by dehalorespiration. The complete genome of the
tetrachloroethene (PCE)-dechlorinating strain
Desulfitobacterium hafniense
Y51 is a 5,727,534-bp
circular chromosome harboring 5,060 predicted protein coding sequences.
This genome contains only two reductive dehalogenase genes, a lower
number than reported in most other dehalorespiring strains. More than
50 members of the dimethyl sulfoxide reductase superfamily and 30
paralogs of the flavoprotein subunit of the fumarate reductase are
encoded as well. A remarkable feature of the genome is the large number
of
O
-demethylase paralogs, which allow utilization of
lignin-derived phenyl methyl ethers as electron donors. The large
genome reveals a more versatile microorganism that can utilize a larger
set of specialized electron donors and acceptors than previously
thought. This is in sharp contrast to the PCE-dechlorinating strain
Dehalococcoides ethenogenes
195, which has a relatively small
genome with a narrow metabolic repertoire. A genomic comparison of
these two very different strains allowed us to narrow down the
potential candidates implicated in the dechlorination process. Our
results provide further impetus to the use of desulfitobacteria as
tools for
bioremediation.
Global Gene Expression Analysis of Iron-Inducible Genes in
Magnetospirillum magneticum
AMB-1
Authors: Suzuki Takeyuki , Okamura Yoshiko , Calugay Ronie J. , Takeyama Haruko , Matsunaga Tadashi
Published: March 2006

Iron uptake systems were identified by global expression profiling of
Magnetospirillum magneticum
AMB-1.
feo
,
tpd
, and
ftr
, which encode ferrous iron transporters, were up-regulated under iron-rich conditions. The concomitant rapid iron uptake and magnetite formation suggest that these uptake systems serve as iron supply lines for magnetosome synthesis.
Harpin Mediates Cell Aggregation in
Erwinia chrysanthemi
3937
Authors: Mee-Ngan Yap , Rojas Clemencia M. , Yang Ching-Hong , Charkowski Amy O.
Published: March 2006

The hypersensitive response elicitor harpin (HrpN) of soft rot pathogen
Erwinia chrysanthemi
strains 3937 and EC16 is secreted via the type III secretion system and remains cell surface bound. Strain 3937 HrpN is essential for cell aggregation, but the C-terminal one-third of the protein is not required for aggregative activity.
Simplified Phenotypic Scheme Evaluated by 16S rRNA Sequencing for Differentiation between
Yersinia enterocolitica
and
Y. enterocolitica
-Like species
Authors: Hallanvuo Saija , Peltola Joanna , Heiskanen Tarja , Siitonen Anja
Published: March 2006

Many clinical laboratories are familiar with a sizeable group of “unserotypeable
Yersinia enterocolitica
” strains. Due to identification problems, this group may hide
Y. bercovieri
,
Y. mollaretii
, and
Y. rohdei
strains. We present a simple scheme to distinguish between pathogenic
Y. enterocolitica
and potentially nonpathogenic
Y. enterocolitica-
like strains.
Molecular Characterization of Wild-Type Polioviruses Isolated in Greece during the 1996 Outbreak in Albania
Authors: Kyriakopoulou Zaharoula , Kottaridi Christine , Dedepsidis Evaggelos , Bolanaki Eugenia , Levidiotou-Stefanou Stamatina , Markoulatos Panayotis
Published: March 2006

During the present study three type 1 poliovirus strains isolated in Greece during the 1996 poliomyelitis outbreak in Albania were retrospectively investigated and determination of their relationship with other epidemic strains isolated in Albania or elsewhere during previous epidemics was attempted. SimPlot analysis revealed that the three Greek strains are the result of a recombination event in the VP2 coding region.
Ulocladium atrum
Keratitis
Authors: Badenoch P. R. , Halliday C. L. , Ellis D. H. , Billing K. J. , Mills R. A. D.
Published: March 2006

We report a case of
Ulocladium atrum
keratitis in a 43-year-old man. No predisposing event was known. He received natamycin and fluconazole drops and the infection resolved. The isolate was identified by morphological and rRNA gene sequence analyses.
U. atrum
is a dematiaceous hyphomycete not hitherto reported to infect humans.
Rapid Screening of Fluoroquinolone Resistance Determinants in
Streptococcus pneumoniae
by PCR-Restriction Fragment Length Polymorphism and Single-Strand Conformational Polymorphism
Authors: Ip Margaret , Chau Shirley S. L. , Chi Fang , Qi Amy , Lai Raymond W. M.
Published: March 2006

A rapid method, using PCR-restriction fragment length and single-strand conformation polymorphism (SSCP), was applied to screen for mutations of the fluoroquinolone resistance determinants in
Streptococcus pneumoniae
. One hundred nonduplicate
Streptococcus pneumoniae
isolates with ciprofloxacin MICs of ≥4.0 μg/ml from the Prince of Wales Hospital, Hong Kong, years 2000 to 2003, were examined. For each isolate, PCR amplicons of quinolone resistance-determining regions (QRDRs) of
gyrA
,
gyrB
,
parC
, and
parE
genes were digested with AluI, HinfI, Sau3AI, and MspI, respectively, and analyzed by SSCP. Each SSCP pattern was given a number, and each isolate obtained a four-digit code, e.g., 1111, that represented the SSCP profile. The SSCP patterns were correlated to mutations characterized from sequence analyses of PCR amplicons. The most common SSCP profile obtained was no. 5232 (40%), which included strains with two amino acid substitutions in the ParC (Lys-137-Asn) and ParE (Ile-460-Val) genes, followed by the SSCP profile 5223 (17%), which included strains with amino acid substitutions in the ParE (Ile-460-Val) gene only. Ten isolates (10%) with amino acid substitutions at GyrA and ParE (±ParC) genes were resistant to levofloxacin with a MIC of ≥16 μg/ml. Other SSCP profiles were unique in distinguishing the common amino acid substitutions in GyrA (Ser-81-Phe) and ParC (Lys-137-Asn, Ser-79-Phe plus Lys-137-Asn, Asp-83-Asn plus Lys-137-Asn, Ser-79-Phe, and Glu-96-Asp). SSCP analysis of restricted fragments generated patterns that were highly discriminative for mutations present in the QRDRs of
gyrA
,
gyrB
,
parC
, and
parE
. This method provides a database of high resolution profiles on these mutations and allows rapid screening for new mutations of the fluoroquinolone resistance genes.
Pre- and Postvaccination Clonal Compositions of Invasive Pneumococcal Serotypes for Isolates Collected in the United States in 1999, 2001, and 2002
Authors: Beall Bernard , McEllistrem M. Catherine , Gertz Robert E. , Wedel Stephanie , Boxrud David J. , Gonzalez Antonio L. , Medina Marie-Jo , Pai Rekha , Thompson Terry A. , Harrison Lee H. , McGee Lesley , Whitney Cynthia G. ,   the Active Bacterial Core Surveillance Team
Published: March 2006

Monitoring of serotypes and their clonal associations is critical as pneumococci adapt to the selective pressures exerted by the pneumococcal seven-valent conjugate vaccine (PCV7). We genotyped 1,476 invasive isolates from the Active Bacterial Core surveillance (705 [89.8%] of the isolates were obtained from children <5 years of age, and 771 [18.4%] of the isolates were obtained from individuals >5 years of age) in 2001 and 2002 (after the introduction of PCV7). The data were compared to the results for 1,168 invasive isolates (855 [83.9%] of the isolates were from children <5 years of age) collected in 1999. Among children <5 years of age, the incidence of invasive disease due to non-PCV7 serogroups together with serogroup 19A increased (P< 0.001). Eighty-three clonal sets, representing 177 multilocus sequence types (STs), were compiled from the 3-year isolate set. Among the non-PCV7 serogroups, newly emerging clones were uncommon; and a significant expansion of already established clones occurred for serotypes 3 (ST180), 7F (ST191), 15BCF (ST199), 19A (ST199), 22F (ST433), 33F (ST662), and 38 (ST393). However, additional minor clonal types within serotypes 1, 6A, 6B, 7C, 9N, 10A, 12F, 14, 15B/C, 17F, 19A, 19F, 20, 22F, and 33F that were absent in 1999 were found during 2001 and 2002. Although 23 clonal sets exhibited multiple serotypes, for most serotypes there were either no changes or modest changes in clonal compositions since the introduction of PCV7. The only example of an identical ST shared between non-PCV7 and PCV7 or PCV7-related serotypes was ST199; however, ST199 was prevalent within serotypes 15B/C and 19A before and after PCV7 introduction. Continued genotypic surveillance is warranted, since certain clones not targeted by PCV7 are expanding, and their emergence as significant pathogens could occur with maintained vaccine pressure.
Ethnic differences in control of cardiovascular risk factors in patients with type 2 diabetes attending an Inner London diabetes clinic
Authors: Chowdhury T A , Lasker S S , Mahfuz R
Published: March 2006

Background

South Asians have higher risk of diabetic complications compared with white Europeans. The aim of this study was to compare management of cardiovascular risk factors between Bangladeshis and white Europeans.

Methods

A retrospective survey of all diabetic patients attending an Inner London hospital diabetic clinic over one year was undertaken. Data were obtained from the hospital diabetes database: presence of macrovascular (myocardial infarction, angina, stroke, transient ischaemic attack, cardiac intervention) and microvascular disease (neuropathy, retinopathy, and nephropathy), glycated haemoglobin, blood pressure, lipids, smoking, and body mass index (BMI) were all determined.

Results

A total of 1162 white European and 912 Bangladeshi patients with full data available were included in the analyses. The groups were equivalent in age, sex, duration of diabetes. Compared with white Europeans, Bangladeshis had more macrovascular disease (19.5% v 11.9% p<0.01), sight threatening retinopathy (7.2% v 3.8%, p<0.01), and nephropathy (15.3% v 9.1%, p<0.01). In addition, Bangladeshis had significantly more male smokers (28.1% v 22.1%, p<0.01), poorer glycaemic control (mean HbA1c 8.6% v 8.1%, p = 0.039), greater proportion with uncontrolled hypercholesterolaemia (total cholesterol >5.0 mmol/l, 31.6% v 26% p = 0.05), and poorer control of blood pressure (proportion with BP >140/80 mm Hg, 43.2% v 32.1%, p<0.01).

Conclusions

South Asians with type 2 diabetes have poorer glycaemic, blood pressure, and lipid control than white Europeans. The reasons for this are probably multifactorial.
Ventilator associated pneumonia
Authors: Hunter J D
Published: March 2006

Hospital acquired or nosocomial infections continue to be an important cause of morbidity and mortality. The critically ill patient is at particular risk of developing intensive care unit acquired infection, with the lungs being especially vulnerable. Nosocomial bacterial pneumonia occurring after two days of mechanical ventilation is referred to as ventilator associated pneumonia, and is the most common nosocomial infection seen in the intensive care unit. Intubation of the trachea and mechanical ventilation is associated with a 7-fold to 21-fold increase in the incidence of pneumonia and up to 28% of patients receiving mechanical ventilation will develop this complication. Its development is associated with an attributable increase in morbidity and mortality. The establishment of an accurate diagnosis of ventilator associated pneumonia remains problematic and as yet there is still no accepted “gold standard” for diagnosis. The responsible pathogens vary according to case mix, local resistance patterns, and methodology of sampling. However, there is general agreement that rapid initiation of appropriate antimicrobial therapy improves outcome.
Utility of N terminal pro brain natriuretic peptide in elderly patients
Authors: Sivakumar R , Wellsted D , Parker K , Lynch M , Ghosh P , Khan S A
Published: March 2006

Objective

To evaluate the utility of N terminal pro brain natriuretic peptide (NT-proBNP) as a diagnostic marker for diastolic dysfunction or failure, systolic dysfunction, and significant valve disorders in patients over 75 years.

Design

Cohort study.

Setting

Outpatient echocardiography service in a district general hospital.

Participants

100 consecutive patients.

Main outcome measures

Sensitivity, specificity, positive predictive values, negative predictive values, and area under receiver operating characteristic curve for NT-proBNP assay in the diagnosis of left ventricular diastolic dysfunction or failure, systolic dysfunction, and significant valve disorders.

Results

For diagnosis of systolic dysfunction NT-proBNP level of 424 pg/ml had a sensitivity of 96%, specificity of 45%, positive predictive value of 36%, and negative predictive value of 96%. The area under the curve was 0.71 (95% confidence intervals: 0.69 to 0.89). In valve heart disease, level of 227 pg/ml had sensitivity of 91%, specificity of 43%, positive predictive value of 40%, and negative predictive value of 92%. Patients with diastolic dysfunction/failure had lower plasma concentrations.

Conclusions

This study showed that NT-proBNP had excellent negative predictive value for systolic dysfunction and significant valve disorders in very elderly patients. It increased significantly in systolic dysfunction, valve heart disease, and atrial fibrillation. NT-proBNP is not useful in the diagnosis of diastolic dysfunction or diastolic heart failure using standard echocardiography criteria.
DYNAMICAL DARK ENERGY OR VARIABLE COSMOLOGICAL PARAMETERS?
Authors: SOLÀ JOAN , ŠTEFANČIĆ HRVOJE
Published: March 2006

One of the main aims in the next generation of precision cosmology experiments will be an accurate determination of the equation of state (EOS) for the dark energy (DE). If the latter is dynamical, the resulting barotropic index ω should exhibit a nontrivial evolution with the redshift. This is usually interpreted as a sign that the mechanism responsible for the DE is related to some dynamical scalar field, and in some cases this field may behave non-canonically (phantom field). Present observations seem to favor an evolving DE with a potential phantom phase near our time. In the literature, there is a plethora of dynamical models trying to describe this behavior. Here we show that the simplest option, namely a model with a variable cosmological term, Λ = Λ(t), leads in general to a nontrivial effective EOS, with index ωe, which may naturally account for these data features. We prove that in this case there is always a "crossing" of the ωe = -1 barrier near our time. We also show how this effect is modulated (or even completely controlled) by a variable Newton's gravitational coupling G = G(t).
DARK MATTER PAIR-PRODUCTION IN b → s TRANSITIONS
Authors: BIRD C. , KOWALEWSKI R. , POSPELOV M.
Published: March 2006

The flavor-changing neutral current transition b → s can serve as a sensitive probe of WIMP dark matter models, if the WIMP mass is under 2 GeV. In this work we extend our earlier analysis to a generic class of models where the interaction between the dark matter sector and the Standard Model matter sector is mediated by the Higgs boson(s). We show that experimental limits on the decays of B-mesons to K(K*) and missing energy provide stringent constraints on the parameter space of such models, but do not rule out sub-GeV WIMPs in a model-independent way. We find that in the context of the NMSSM with light pseudoscalar Higgs, the WIMP masses under a few hundred MeV are generically excluded with the exception of few highly tuned points in the parameter space.
ON THE CONSTRUCTION OF CORRELATION FUNCTIONS FOR THE INTEGRABLE SUPERSYMMETRIC FERMION MODELS
Authors: ZHAO SHAO-YOU , YANG WEN-LI , ZHANG YAO-ZHONG
Published: March 2006

We review the recent progress on the construction of the determinant representations of the correlation functions for the integrable supersymmetric fermion models. The factorizing F-matrices (or the so-called F-basis) play an important role in the construction. In the F-basis, the creation (and the annihilation) operators and the Bethe states of the integrable models are given in completely symmetric forms. This leads to the determinant representations of the scalar products of the Bethe states for the models. Based on the scalar products, the determinant representations of the correlation functions may be obtained. As an example, in this review, we give the determinant representations of the two-point correlation function for the Uq(gl(2|1)) (i.e. q-deformed) supersymmetric t-J model. The determinant representations are useful for analyzing physical properties of the integrable models in the thermodynamical limit.
A CHAOS-BASED CRYPTOGRAPHIC HASH FUNCTION FOR MESSAGE AUTHENTICATION
Authors: KWOK H. S. , TANG WALLACE K. S.
Published: March 2006

In this paper, a chaos-based cryptographic hash function is proposed for message authentication where a fixed length message digest can be generated from any messages with arbitrary length. The compression function in-use is developed according to the diffusion and confusion properties of a novel high-dimensional discrete chaotic map. A symmetric key structure can also be easily embedded based on the high sensitivity to initial conditions and system parameters of the map. As demonstrated in experiments, the throughput of the proposed scheme is about 1.5 times of that with MD5, and the hash value appears randomly without any correlation with the message or the key.
A WAVE-BASED CNN GENERATOR FOR THE CONTROL AND ACTUATION OF A LAMPREY-LIKE ROBOT
Authors: ARENA PAOLO , FORTUNA LUIGI , FRASCA MATTIA , VAGLIASINDI GUIDO
Published: March 2006

In this work a project which aims at the construction of LampBot II, an autonomous biologically-inspired swimming robot, is presented. LampBot II is capable of mimicking the undulatory swimming of a sea lamprey. The system used to generate locomotion is based on the paradigm of the Central Pattern Generator (CPG) and is implemented on a chip based on a Cellular Nonlinear Network (CNN). Two prototype structures have been developed in order to evaluate the feasibility of the actuation by means of Shape Memory Alloy (SMA) wires or servo motors.
LINEAR AND NONLINEAR PROPERTIES OF PRESTIMULUS VENTRAL CORD SIGNALS DISTINGUISH SWIMMING RESPONSE OF THE LEECH TO INTRACELLULAR STIMULATION
Authors: ALBANO A. M. , BRODFUEHRER P. D. , TAPYRIK L. , SUNDER S.
Published: March 2006

Stimulation of a trigger interneuron of an isolated nerve cord preparation of the medicinal leech, Hirudo medicinalis, sometimes leads to swimming; sometimes it does not. The known synaptic interactions in the swim-initiating pathway do not adequately explain the observed behavioral variability. We investigate signals propagating in the ventral cord and show that, (i) prior to stimulation, the standard deviation of the signals that precede swimming (TS) is greater than that of the signals that do not (NS), (ii) linear correlations of NS signals are indistinguishable from those of TS signals, (iii) nonlinear correlations measured by mutual information of time-delayed epochs of TS signals are greater than those of NS signals, and (iv) for small time differences, the mutual information of time-delayed epochs of NS and TS signals are different from surrogates that have the same cross-correlations but are otherwise random.
IMPULSIVE SYNCHRONIZATION OF CHAOTIC SYSTEMS VIA LINEAR MATRIX INEQUALITIES
Authors: JI Y. , WEN C. Y. , LI Z. G.
Published: March 2006

Impulsive synchronization of chaotic systems is studied in this paper. By exploring the structural knowledge of the systems and using linear matrix inequalities, some less conservative conditions than existing results are derived. With the new conditions, the bound of intervals for transmitting impulses can be increased and this results in higher bandwidth efficiency. Our results are thus able to improve the efficiencies of the existing technologies on chaotic secure communications and chaotic spread communications.
ANALYTICAL SOLUTION FOR THE STEADY-STATE CHRONOAMPEROMETRIC CURRENT FOR AN EC′ REACTION AT SPHEROIDAL ULTRAMICROELECTRODES
Authors: RAJENDRAN L.
Published: March 2006

The steady-state chronoamperometric current for an EC′ reactions at spheroidal ultramicroelectrodes is derived from the non-steady-state diffusion limited current. The polynomial expressions pertaining to two extreme limits of reaction rates are combined for all reaction rates. Starting with the result for spheroidal electrode, equations are obtained for the steady-state currents at disc, oblate, hemisphere and prolate electrodes. Tabular compilation of dimensionless current for disc electrodes are reported. A good agreement with previously available simulation results is noticed.
THEORETICAL STUDY ON THE INTERNAL ROTATION OF NITROTYL OF BENZALDOXIMES
Authors: LI GUOPING , XU WEIREN , ZHANG CHAOJUN , WANG JIANWU , LIU CHENGBU
Published: March 2006

The internal rotations of nitrotyl around the bond C–C in Z- and E-benzaldoximes and their various substituted species have been investigated theoretically by the method of density functional theory (DFT) at the B3LYP/6-31G* level. The corresponding rotation transition states have been optimized. The potential barriers and the rates of the internal rotations of various species have been calculated. The rotation barrier of Z-benzaldoxime is lower than that of E-isomer. The para-substitution has only a small influence on the rotation barriers. The conjugations are consolidated in the acidic and basic species of both Z- and E-isomers. The experimental NMR spectrums of Z- and E-benzaldoxime are explained based on the calculation results.
State-of-Art of Knowledge Storage and Access in Indian Industry
Authors: Pillania Rajesh K.
Published: March 2006

We are in an era of knowledge revolution where knowledge occupies the centre stage. Its continuous generation, sharing and implementation have become crucial for firms and countries. This revolution is supported by the revolution in information technologies. This present research is an attempt to find out the state of knowledge storage and access in Indian industry. To have a macro view of the situation, industry and academia experts and policy makers were consulted regarding knowledge storage and access in Indian industry. To have the micro view, five firms were selected from both the software and pharmaceutical industries, and four firms from the petroleum marketing sector, thus covering both private and public sectors. The findings were mixed. Whereas access to knowledge is good, in general there is a lack of continuous update of stored knowledge.
Localized PtdIns 3,5-P2 synthesis to regulate early endosome dynamics and fusion
Authors: Ikonomov Ognian C. , Sbrissa Diego , Shisheva Assia
Published: March 2006

Perturbations in the intracellular PtdIns 3,5-P2 pool or the downstream transmission of PtdIns 3,5-P2 signals often result in a gradual development of gross morphological changes in the pleiomorphic multivesicular endosomes, culminating with the appearance of cytoplasmic vacuoles. To identify the onset of PtdIns 3,5-P2 functional requirements along the endocytic system, in this study we characterized the morphological changes associated with early expression of the dominant-negative kinase-deficient form (K1831E) of the PtdIns 3,5-P2-producing kinase PIKfyve, before the formation of cytoplasmic vacuoles in transfected COS cells. Enlarged PIKfyveK1831E-positive vesicles co-localizing with dilated EEA1- and Rab5aWT-positive perinuclear endosomes were observed (WT, wild type). This was dependent on the presence of active forms of Rab5 and the generation of PtdIns 3-P-enriched platforms on early endosomess. Because PIKfyveWT did not substantially colocalize with EEA1- or Rab5-positive endosomes in COS cells, the dynamic PIKfyve-catalyzed PtdIns 3-to-PtdIns 3,5-P2 switch was suggested to drive away PIKfyveWT from early endosomes toward later compartments. Late endosomes/lysosomes marked by LAMP1 or Rab7 were dislocated from their typical perinuclear position upon PIKfyveK1831E early expression. Cytosols derived from cells stably expressing PIKfyveK1831E stimulated endosome fusion in vitro, whereas PIKfyveWT-enriched cytosols had the opposite effect, consistent with PtdIns 3,5-P2 production negatively regulating the endosome fusion. Together, our data indicate that PtdIns 3,5-P2 defines specific endosome platforms at the onset of the degradation pathway to regulate the complex process of membrane remodeling and dynamics.