bluuebunny/crossref_metadata_2025 huggingface dataset:
Phototrophic Fe(II) Oxidation Promotes Organic Carbon Acquisition by
Rhodobacter capsulatus
SB1003
Authors: Caiazza Nicky C. , Lies Douglas P. , Newman Dianne K.
Published: August 2007

Anoxygenic phototrophic Fe(II) oxidation is usually considered to be a lithoautotrophic metabolism that contributes to primary production in Fe-based ecosystems. In this study, we employed
Rhodobacter capsulatus
SB1003 as a model organism to test the hypothesis that phototrophic Fe(II) oxidation can be coupled to organic carbon acquisition.
R. capsulatus
SB1003 oxidized Fe(II) under anoxic conditions in a light-dependent manner, but it failed to grow lithoautotrophically on soluble Fe(II). When the strain was provided with Fe(II)-citrate, however, growth was observed that was dependent upon microbially catalyzed Fe(II) oxidation, resulting in the formation of Fe(III)-citrate. Subsequent photochemical breakdown of Fe(III)-citrate yielded acetoacetic acid that supported growth in the light but not the dark. The deletion of genes (RRC00247 and RRC00248) that encode homologs of
atoA
and
atoD
, required for acetoacetic acid utilization, severely impaired the ability of
R. capsulatus
SB1003 to grow on Fe(II)-citrate. The growth yield achieved by
R. capsulatus
SB1003 in the presence of citrate cannot be explained by lithoautotrophic growth on Fe(II) enabled by indirect effects of the ligand [such as altering the thermodynamics of Fe(II) oxidation or preventing cell encrustation]. Together, these results demonstrate that
R. capsulatus
SB1003 grows photoheterotrophically on Fe(II)-citrate. Nitrilotriacetic acid also supported light-dependent growth on Fe(II), suggesting that Fe(II) oxidation may be a general mechanism whereby some Fe(II)-oxidizing bacteria mine otherwise inaccessible organic carbon sources.
Internal and Surface-Localized Major Surface Proteases ofLeishmaniaspp. and Their Differential Release from Promastigotes
Authors: Yao Chaoqun , Donelson John E. , Wilson Mary E.
Published: August 2007

Major surface protease (MSP), also called GP63, is a virulence factor ofLeishmaniaspp. protozoa. There are three pools of MSP, located either internally within the parasite, anchored to the surface membrane, or released into the extracellular environment. The regulation and biological functions of these MSP pools are unknown. We investigated here the trafficking and extrusion of surface versus internal MSPs. VirulentLeishmania chagasiundergo a growth-associated lengthening in thet1/2of surface-localized MSP, but this did not occur in the attenuated L5 strain. The release of surface-localized MSP was enhanced in a dose-dependent manner by MβCD, which chelates membrane cholesterol-ergosterol. Furthermore, incubation of promastigotes at 37°C with Matrigel matrix, a soluble basement membrane extract of Engelbreth-Holm-Swarm tumor cells, stimulated the release of internal MSP but not of surface-located MSP. Taken together, these data indicate that MSP subpopulations in distinct cellular locations are released from the parasite under different environmental conditions. We hypothesize that the internal MSP with its lengthyt1/2does not serve as a pool for promastigote surface MSP in the sand fly vector but that it instead functions as an MSP pool ready for quick release upon inoculation of metacyclic promastigotes into mammals. We present a model in which these different MSP pools are released under distinct life cycle-specific conditions.
Ku Heterodimer-Independent End Joining inTrypanosoma bruceiCell Extracts Relies upon Sequence Microhomology
Authors: Burton Peter , McBride David J. , Wilkes Jonathan M. , Barry J. David , McCulloch Richard
Published: August 2007

DNA double-strand breaks (DSBs) are repaired primarily by two distinct pathways: homologous recombination and nonhomologous end joining (NHEJ). NHEJ has been found in all eukaryotes examined to date and has been described recently for some bacterial species, illustrating its ancestry.Trypanosoma bruceiis a divergent eukaryotic protist that evades host immunity by antigenic variation, a process in which homologous recombination plays a crucial function. While homologous recombination has been examined in some detail inT. brucei, little work has been done to examine what other DSB repair pathways the parasite utilizes. Here we show thatT. bruceicell extracts support the end joining of linear DNA molecules. These reactions are independent of the Ku heterodimer, indicating that they are distinct from NHEJ, and are guided by sequence microhomology. We also demonstrate bioinformatically thatT. brucei, in common with other kinetoplastids, does not encode recognizable homologues of DNA ligase IV or XRCC4, suggesting that NHEJ is either absent or mechanistically diverged in these pathogens.
Site-Directed Mutagenesis Studies of Tn
5
Transposase Residues Involved in Synaptic Complex Formation
Authors: Vaezeslami Soheila , Sterling Rachel , Reznikoff William S.
Published: August 2007

Transposition (the movement of discrete segments of DNA, resulting in rearrangement of genomic DNA) initiates when transposase forms a dimeric DNA-protein synaptic complex with transposon DNA end sequences. The synaptic complex is a prerequisite for catalytic reactions that occur during the transposition process. The transposase-DNA interactions involved in the synaptic complex have been of great interest. Here we undertook a study to verify the protein-DNA interactions that lead to synapsis in the Tn
5
system. Specifically, we studied (i) Arg342, Glu344, and Asn348 and (ii) Ser438, Lys439, and Ser445, which, based on the previously published cocrystal structure of Tn
5
transposase bound to a precleaved transposon end sequence, make
cis
and
trans
contacts with transposon end sequence DNA, respectively. By using genetic and biochemical assays, we showed that in all cases except one, each of these residues plays an important role in synaptic complex formation, as predicted by the cocrystal structure.
Sequence Analysis of the
Staphylococcus aureus srrAB
Loci Reveals that Truncation of
srrA
Affects Growth and Virulence Factor Expression
Authors: Pragman Alexa A. , Herron-Olson Lisa , Case Laura C. , Vetter Sara M. , Henke Evan E. , Kapur Vivek , Schlievert Patrick M.
Published: August 2007

The SrrAB system regulates metabolism and virulence factors in
Staphylococcus aureus
. We sequenced the
srrAB
loci of 21 isolates and performed a phylogenetic analysis. Vaginal and bovine isolates clustered together, while skin isolates were genetically diverse. Few nucleotide polymorphisms were observed, and most were synonymous. Two strains (N2 and N19) with N-terminal truncations in SrrA displayed defects in growth and abnormally upregulated virulence factor expression under low-oxygen conditions.
Characterization of Riboflavin (Vitamin B2) Transport Proteins fromBacillus subtilisandCorynebacterium glutamicum
Authors: Vogl Christian , Grill Simon , Schilling Oliver , Stülke Jörg , Mack Matthias , Stolz Jürgen
Published: August 2007

Riboflavin (vitamin B2) is the direct precursor of the flavin cofactors flavin mononucleotide and flavin adenine dinucleotide, essential components of cellular biochemistry. In this work we investigated the unrelated proteins YpaA fromBacillus subtilisand PnuX fromCorynebacterium glutamicumfor a role in riboflavin uptake. Based on the regulation of the corresponding genes by a riboswitch mechanism, both proteins have been predicted to be involved in flavin metabolism. Moreover, their primary structures suggested that these proteins integrate into the cytoplasmic membrane. We provide experimental evidence that YpaA is a plasma membrane protein with five transmembrane domains and a cytoplasmic C terminus. InB. subtilis, riboflavin uptake was increased whenypaAwas overexpressed and abolished whenypaAwas deleted. Riboflavin uptake activity and the abundance of the YpaA protein were also increased when riboflavin auxotrophic mutants were grown in limiting amounts of riboflavin. YpaA-mediated riboflavin uptake was sensitive to protonophors and reduced in the absence of glucose, demonstrating that the protein requires metabolic energy for substrate translocation. In addition, we demonstrate that PnuX fromC. glutamicumalso is a riboflavin transporter. Transport by PnuX was not energy dependent and had high apparent affinity for riboflavin (Km11 μM). Roseoflavin, a toxic riboflavin analog, appears to be a substrate of PnuX and YpaA. We propose to designate the gene namesribUforypaAandribMforpnuXto reflect that the encoded proteins function in riboflavin uptake and that the genes have different phylogenetic origins.
Biochemical and Genetic Investigation of Initial Reactions in Aerobic Degradation of the Bile Acid Cholate in
Pseudomonas
sp. Strain Chol1
Authors: Birkenmaier Antoinette , Holert Johannes , Erdbrink Henrike , Moeller Heiko M. , Friemel Anke , Schoenenberger René , Suter Marc J.-F. , Klebensberger Janosch , Philipp Bodo
Published: August 2007

Bile acids are surface-active steroid compounds with toxic effects for bacteria. Recently, the isolation and characterization of a bacterium,
Pseudomonas
sp. strain Chol1, growing with bile acids as the carbon and energy source was reported. In this study, initial reactions of the aerobic degradation pathway for the bile acid cholate were investigated on the biochemical and genetic level in strain Chol1. These reactions comprised A-ring oxidation, activation with coenzyme A (CoA), and β-oxidation of the acyl side chain with the C
19
-steroid dihydroxyandrostadienedione as the end product. A-ring oxidizing enzyme activities leading to Δ
1,4
-3-ketocholyl-CoA were detected in cell extracts and confirmed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Cholate activation with CoA was demonstrated in cell extracts and confirmed with a chemically synthesized standard by LC-MS/MS. A transposon mutant with a block in oxidation of the acyl side chain accumulated a steroid compound in culture supernatants which was identified as 7α,12α-dihydroxy-3-oxopregna-1,4-diene-20-carboxylate (DHOPDC) by nuclear magnetic resonance spectroscopy. The interrupted gene was identified as encoding a putative acyl-CoA-dehydrogenase (ACAD). DHOPDC activation with CoA in cell extracts of strain Chol1 was detected by LC-MS/MS. The growth defect of the transposon mutant could be complemented by the wild-type ACAD gene located on the plasmid pBBR1MCS-5. Based on these results, the initiating reactions of the cholate degradation pathway leading from cholate to dihydroxyandrostadienedione could be reconstructed. In addition, the first bacterial gene encoding an enzyme for a specific reaction step in side chain degradation of steroid compounds was identified, and it showed a high degree of similarity to genes in other steroid-degrading bacteria.
Characterization of an Acid-Dependent Arginine Decarboxylase Enzyme from
Chlamydophila pneumoniae
Authors: Giles Teresa N. , Graham David E.
Published: August 2007

Genome sequences from members of the
Chlamydiales
encode diverged homologs of a pyruvoyl-dependent arginine decarboxylase enzyme that nonpathogenic euryarchaea use in polyamine biosynthesis. The
Chlamydiales
lack subsequent genes required for polyamine biosynthesis and probably obtain polyamines from their host cells. To identify the function of this protein, the CPn1032 homolog from the respiratory pathogen
Chlamydophila pneumoniae
was heterologously expressed and purified. This protein self-cleaved to form a reactive pyruvoyl group, and the subunits assembled into a thermostable (αβ)
3
complex. The mature enzyme specifically catalyzed the decarboxylation of
l
-arginine, with an unusually low pH optimum of 3.4. The CPn1032 gene complemented a mutation in the
Escherichia coli adiA
gene, which encodes a pyridoxal 5′-phosphate-dependent arginine decarboxylase, restoring arginine-dependent acid resistance. Acting together with a putative arginine-agmatine antiporter, the CPn1032 homologs may have evolved convergently to form an arginine-dependent acid resistance system. These genes are the first evidence that obligately intracellular chlamydiae may encounter acidic conditions. Alternatively, this system could reduce the host cell arginine concentration and produce inhibitors of nitric oxide synthase.
The Alcohol Dehydrogenase Gene
adhA
in
Corynebacterium glutamicum
Is Subject to Carbon Catabolite Repression
Authors: Arndt Annette , Eikmanns Bernhard J.
Published: August 2007

Corynebacterium glutamicum
has recently been shown to grow on ethanol as a carbon and energy source and to possess high alcohol dehydrogenase (ADH) activity when growing on this substrate and low ADH activity when growing on ethanol plus glucose or glucose alone. Here we identify the
C. glutamicum
ADH gene (
adhA
), analyze its transcriptional organization, and investigate the relevance of the transcriptional regulators of acetate metabolism RamA and RamB for
adhA
expression. Sequence analysis of
adhA
predicts a polypeptide of 345 amino acids showing up to 57% identity with zinc-dependent ADH enzymes of group I. Inactivation of the chromosomal
adhA
gene led to the inability to grow on ethanol and to the absence of ADH activity, indicating that only a single ethanol-oxidizing ADH enzyme is present in
C. glutamicum
. Transcriptional analysis revealed that the
C. glutamicum adhA
gene is monocistronic and that its expression is repressed in the presence of glucose and of acetate in the growth medium, i.e., that
adhA
expression is subject to catabolite repression. Further analyses revealed that RamA and RamB directly bind to the
adhA
promoter region, that RamA is essential for the expression of
adhA
, and that RamB exerts a negative control on
adhA
expression in the presence of glucose or acetate in the growth medium. However, since the glucose- and acetate-dependent down-regulation of
adhA
expression was only partially released in a RamB-deficient mutant, there might be an additional regulator involved in the catabolite repression of
adhA
.
Recombining Population Structure of
Plesiomonas shigelloides
(
Enterobacteriaceae
) Revealed by Multilocus Sequence Typing
Authors: Salerno Anna , Delétoile Alexis , Lefevre Martine , Ciznar Ivan , Krovacek Karel , Grimont Patrick , Brisse Sylvain
Published: August 2007

Plesiomonas shigelloides
is an emerging pathogen that is widespread in the aquatic environment and is responsible for intestinal diseases and extraintestinal infections in humans and other animals. Virtually nothing is known about its genetic diversity, population structure, and evolution, which severely limits epidemiological control. We addressed these questions by developing a multilocus sequence typing (MLST) system based on five genes (
fusA
,
leuS
,
pyrG
,
recG
, and
rpoB
) and analyzing 77 epidemiologically unrelated strains from several countries and several ecological sources. The phylogenetic position of
P. shigelloides
within family
Enterobacteriaceae
was precisely defined by phylogenetic analysis of the same gene portions in other family members. Within
P. shigelloides
, high levels of nucleotide diversity (average percentage of nucleotide differences between strains, 1.49%) and genotypic diversity (64 distinct sequence types; Simpson's index, 99.7%) were found, with no salient internal phylogenetic structure. We estimated that homologous recombination in housekeeping genes affects
P. shigelloides
alleles and nucleotides 7 and 77 times more frequently than mutation, respectively. These ratios are similar to those observed in the naturally transformable species
Streptococcus pneumoniae
with a high rate of recombination. In contrast, recombination within
Salmonella enterica
,
Escherichia coli
, and
Yersinia enterocolitica
was much less frequent.
P. shigelloides
thus stands out among members of the
Enterobacteriaceae
. Its high rate of recombination results in a lack of association between genomic background and O and H antigenic factors, as observed for the 51 serotypes found in our sample. Given its robustness and discriminatory power, we recommend MLST as a reference method for population biology studies and epidemiological tracking of
P. shigelloides
strains.
Genome Analysis of Phage JS98 Defines a Fourth Major Subgroup of T4-Like Phages in
Escherichia coli
Authors: Zuber Sophie , Ngom-Bru Catherine , Barretto Caroline , Bruttin Anne , Brüssow Harald , Denou Emmanuel
Published: August 2007

Numerous T4-like
Escherichia coli
phages were isolated from human stool and environmental wastewater samples in Bangladesh and Switzerland. The sequences of the major head gene (
g23
) revealed that these coliphages could be placed into four subgroups, represented by the phages T4, RB69, RB49, and JS98. Thus, JS98 defines a new major subgroup of
E. coli
T4-like phages. We conducted an analysis of the 169-kb JS98 genome sequence. Overall, 198 of the 266 JS98 open reading frames (ORFs) shared amino acid sequence identity with the reference T4 phage, 41 shared identity with other T4-like phages, and 27 ORFs lacked any database matches. Genes on the plus strand encoded virion proteins, which showed moderate to high sequence identity with T4 proteins. The right genome half of JS98 showed a higher degree of sequence conservation with T4 and RB69, even for the nonstructural genes, than did the left genome half, containing exclusively nonstructural genes. Most of the JS98-specific genes were found in the left genome half. Two came as a hypervariability cluster, but most represented isolated genes, suggesting that they were acquired separately in multiple acquisition events. No evidence for DNA exchange between JS98 phage and the
E. coli
host genome or coliphages other than T4 was observed. No undesired genes which could compromise its medical use were detected in the JS98 genome sequence.
Synergistic Interaction of
Clostridium cellulovorans
Cellulosomal Cellulases and HbpA
Authors: Matsuoka Satoshi , Yukawa Hideaki , Inui Masayuki , Doi Roy H.
Published: August 2007

Clostridium cellulovorans
, an anaerobic bacterium, produces a small nonenzymatic protein called HbpA, which has a surface layer homology domain and a type I cohesin domain similar to those found in the cellulosomal scaffolding protein CbpA. In this study, we demonstrated that HbpA could bind to cell wall fragments from
C. cellulovorans
and insoluble polysaccharides and form a complex with cellulosomal cellulases endoglucanase B (EngB) and endoglucanase L (EngL). Synergistic degradative action of the cellulosomal cellulase and HbpA complexes was demonstrated on acid-swollen cellulose, Avicel, and corn fiber. We propose that HbpA functions to bind dockerin-containing cellulosomal enzymes to the cell surface and complements the activity of cellulosomes.
Identification of the Origin of Transfer (
oriT
) and DNA Relaxase Required for Conjugation of the Integrative and Conjugative Element ICE
Bs1
of
Bacillus subtilis
Authors: Lee Catherine A. , Grossman Alan D.
Published: August 2007

Integrative and conjugative elements (ICEs), also known as conjugative transposons, are mobile genetic elements that can transfer from one bacterial cell to another by conjugation. ICE
Bs1
is integrated into the
trnS-leu2
gene of
Bacillus subtilis
and is regulated by the SOS response and the RapI-PhrI cell-cell peptide signaling system. When
B. subtilis
senses DNA damage or high concentrations of potential mating partners that lack the element, ICE
Bs1
excises from the chromosome and can transfer to recipients. Bacterial conjugation usually requires a DNA relaxase that nicks an origin of transfer (
oriT
) on the conjugative element and initiates the 5′-to-3′ transfer of one strand of the element into recipient cells. The ICE
Bs1 ydcR
(
nicK
) gene product is homologous to the pT181 family of plasmid DNA relaxases. We found that transfer of ICE
Bs1
requires
nicK
and identified a
cis
-acting
oriT
that is also required for transfer. Expression of
nicK
leads to nicking of ICE
Bs1
between a GC-rich inverted repeat in
oriT
, and NicK was the only ICE
Bs1
gene product needed for nicking. NicK likely mediates conjugation of ICE
Bs1
by nicking at
oriT
and facilitating the translocation of a single strand of ICE
Bs1
DNA through a transmembrane conjugation pore.
Cell Surface Filaments of the Gliding Bacterium
Flavobacterium johnsoniae
Revealed by Cryo-Electron Tomography
Authors: Liu Jun , McBride Mark J. , Subramaniam Sriram
Published: August 2007

Flavobacterium johnsoniae
cells glide rapidly over surfaces by an as-yet-unknown mechanism. Using cryo-electron tomography, we show that wild-type cells display tufts of ∼5-nm-wide cell surface filaments that appear to be anchored to the inner surface of the outer membrane. These filaments are absent in cells of a nonmotile
gldF
mutant but are restored upon expression of plasmid-encoded GldF, a component of a putative ATP-binding cassette transporter.
Quorum-Sensing Regulation of the Production of Blp Bacteriocins in
Streptococcus thermophilus
Authors: Fontaine Laetitia , Boutry Céline , Guédon Eric , Guillot Alain , Ibrahim Mariam , Grossiord Benoît , Hols Pascal
Published: August 2007

The
blp
gene cluster identified in the genome sequences of
Streptococcus thermophilus
(
blp
St
) LMG18311, CNRZ1066, and LMD-9 displays all the characteristics of a class II bacteriocin locus. In the present study, we showed that the
blp
St
locus is only fully functional in strain LMD-9 and regulates the production of antimicrobial peptides that inhibit strains LMG18311 and CNRZ1066. The
blp
St
cluster of LMD-9 contains 23 genes that are transcriptionally organized in six operons:
blpABC
St
(peptide transporter genes and pheromone gene);
blpRH
St
(two-component regulatory system genes);
blpD
St
-
orf1, blpU
St
-
orf3
, and
blpE-F
St
(bacteriocin precursors and immunity genes); and
blpG-X
St
(unknown function). All the operons, except the regulatory unit
blpRH
St
, were shown to be coregulated at the transcriptional level by a quorum-sensing mechanism involving the mature
S. thermophilus
pheromone BlpC* (BlpC*
St
), which was extracellularly detected as two active forms (30 and 19 amino acids). These operons are differentially transcribed depending on growth phase and pheromone concentration. They all contain a motif with two imperfect direct repeats in their mapped promoter regions that could serve as binding sites of the response regulator BlpR
St
. Through the construction of deletion mutants, the
blp
St
locus of strain LMD-9 was shown to encode all the essential functions associated with bacteriocin production, quorum-sensing regulation, and immunity.
Complex Formation by the
mrpABCDEFG
Gene Products, Which Constitute a Principal Na
+
/H
+
Antiporter in
Bacillus subtilis
Authors: Kajiyama Yusuke , Otagiri Masato , Sekiguchi Junichi , Kosono Saori , Kudo Toshiaki
Published: August 2007

The
Bacillus subtilis
Mrp (also referred to as Sha) is a particularly unusual Na
+
/H
+
antiporter encoded by
mrpABCDEFG
. Using His tagging of Mrp proteins, we showed complex formation by the
mrpABCDEFG
gene products by pull-down and blue native polyacrylamide gel electrophoresis analyses. This is the first molecular evidence that the Mrp is a multicomponent antiporter in the cation-proton antiporter 3 family.
PhoPQ-Mediated Regulation Produces a More Robust Permeability Barrier in the Outer Membrane ofSalmonella entericaSerovar Typhimurium
Authors: Murata Takeshi , Tseng Will , Guina Tina , Miller Samuel I. , Nikaido Hiroshi
Published: August 2007

The PhoPQ two-component system ofSalmonella entericaserovar Typhimurium produces a remodeling of the lipid A domain of the lipopolysaccharide, including the PagP-catalyzed addition of palmitoyl residue, the PmrAB-regulated addition of the cationic sugar 4-aminoarabinose and phosphoethanolamine, and the LpxO-catalyzed addition of a 2-OH group onto one of the fatty acids. By using the diffusion rates of the dyes ethidium, Nile red, and eosin Y across the outer membrane, as well as the susceptibility of cells to large, lipophilic agents, we evaluated the function of this membrane as a permeability barrier. We found that the remodeling process in PhoP-constitutive strains produces an outer membrane that serves as a very effective permeability barrier in an environment that is poor in divalent cations or that contains cationic peptides, whereas its absence inphoPnull mutants produces an outer membrane severely compromised in its barrier function under these conditions. Removing combinations of the lipid A-remodeling functions from a PhoP-constitutive strain showed that the known modification reactions explain a major part of the PhoPQ-regulated changes in permeability. We believe that the increased barrier property of the remodeled bilayer is important in making the pathogen more resistant to the stresses that it encounters in the host, including attack by the cationic antimicrobial peptides. On the other hand, drug-induced killing assays suggest that the outer membrane containing unmodified lipid A may serve as a better barrier in the presence of high concentrations (e.g., 5 mM) of Mg2+.
Osmolality, Temperature, and Membrane Lipid Composition Modulate the Activity of Betaine Transporter BetP in
Corynebacterium glutamicum
Authors: Özcan Nuran , Ejsing Christer S. , Shevchenko Andrej , Lipski Andrej , Morbach Susanne , Krämer Reinhard
Published: August 2007

The gram-positive soil bacterium
Corynebacterium glutamicum
, a major amino acid-producing microorganism in biotechnology, is equipped with several osmoregulated uptake systems for compatible solutes, which is relevant for the physiological response to osmotic stress. The most significant carrier, BetP, is instantly activated in response to an increasing cytoplasmic K
+
concentration. Importantly, it is also activated by chill stress independent of osmotic stress. We show that the activation of BetP by both osmotic stress and chill stress is altered in
C. glutamicum
cells grown at and adapted to low temperatures. BetP from cold-adapted cells is less sensitive to osmotic stress. In order to become susceptible for chill activation, cold-adapted cells in addition needed a certain amount of osmotic stimulation, indicating that there is cross talk of these two types of stimuli at the level of BetP activity. We further correlated the change in BetP regulation properties in cells grown at different temperatures to changes in the lipid composition of the plasma membrane. For this purpose, the glycerophospholipidome of
C. glutamicum
grown at different temperatures was analyzed by mass spectrometry using quantitative multiple precursor ion scanning. The molecular composition of glycerophospholipids was strongly affected by the growth temperature. The modulating influence of membrane lipid composition on BetP function was further corroborated by studying the influence of artificial modulation of membrane dynamics by local anesthetics and the lack of a possible influence of internally accumulated betaine on BetP activity.
Cj0011c, a Periplasmic Single- and Double-Stranded DNA-Binding Protein, Contributes to Natural Transformation in
Campylobacter jejuni
Authors: Jeon Byeonghwa , Zhang Qijing
Published: August 2007

Campylobacter jejuni
is an important bacterial pathogen causing gastroenteritis in humans.
C. jejuni
is capable of natural transformation, which is considered a major mechanism mediating horizontal gene transfer and generating genetic diversity. Despite recent efforts to elucidate the transformation mechanisms of
C. jejuni
, the process of DNA binding and uptake in this organism is still not well understood. In this study, we report a previously unrecognized DNA-binding protein (Cj0011c) in
C. jejuni
that contributes to natural transformation. Cj0011c is a small protein (79 amino acids) with a partial sequence homology to the C-terminal region of ComEA in
Bacillus subtilis
. Cj0011c bound to both single- and double-stranded DNA. The DNA-binding activity of Cj0011c was demonstrated with a variety of DNAs prepared from
C. jejuni
or
Escherichia coli
, suggesting that the DNA binding of Cj0011c is not sequence dependent. Deletion of the cj0011c gene from
C. jejuni
resulted in 10- to 50-fold reductions in the natural transformation frequency. Different from the
B. subtilis
ComEA, which is an integral membrane protein, Cj0011c is localized in the periplasmic space of
C. jejuni
. These results indicate that Cj0011c functions as a periplasmic DNA receptor contributing to the natural transformation of
C. jejuni
.
Frequent nuclear expression of β-catenin protein but rareβ-cateninmutation in pulmonary sclerosing haemangioma
Authors: Chiang P-M , Yuan R-H , Hsu H-C , Mao T-L , Hu R-H , Lai P-L , Jeng Y-M
Published: August 2007

Background:

Pulmonary sclerosing haemangioma (PSH) is an uncommon tumour that is composed of glandular/papillary lining cells and polygonal cells. The biological behaviour of this tumour has been investigated; however, the molecular pathogenesis of PSH remains unknown.

Aims:

To characterise the role of the Wnt/β-catenin pathway in the genesis of PSH.

Methods:

37 PSH samples were investigated immunohistochemically for detection of the β-catenin protein and direct sequencing of exon 3 of theβ-cateningene.

Results:

Nuclear expression of β-catenin was found in the lining component of 23 tumours (62%) and in the polygonal component of 11 tumours (30%). The expression of β-catenin was stronger in the lining component, but weaker in the polygonal component. Interestingly, all the tumours with expression of β-catenin in the polygonal component also expressed β-catenin in the lining component. However, mutation of exon 3 of theβ-cateningene was detected in only one tumour that expressed nuclear β-catenin in lining and polygonal components.

Conclusions:

The Wnt/β-catenin pathway is involved in the genesis of PSH, but mutation of exon 3 of theβ-cateningene rarely contributes to the activation of the Wnt/β-catenin pathway in PSH.
Value of multicolour fluorescence in situ hybridisation (UroVysion) in the differential diagnosis of flat urothelial lesions
Authors: Schwarz S , Rechenmacher M , Filbeck T , Knuechel R , Blaszyk H , Hartmann A , Brockhoff G
Published: August 2007

Aims:

During the past 10 years, multitarget fluorescence in situ hybridisation has been established as a valuable adjunct in the cytological diagnosis of precancerous and malignant lesions of the urinary tract. The aim of the present study was to define its value in detecting chromosomal imbalances in patients with various flat urothelial lesions in routine paraffin-embedded bladder biopsy samples. In addition, the HER2 gene amplification and HER2 expression pattern were examined, since alterations of the HER2 expression patterns have been demonstrated in invasive bladder cancer.

Methods:

29 samples of normal urothelium and 86 flat urothelial lesions (hyperplasia, reactive atypia, dysplasia and carcinoma in situ (CIS)) from 73 patients were analysed patients using tissue microarrays and centromeric probes for chromosomes 3, 7 and 17, and gene-specific probes for 9p21/P16 and HER2 (UroVysion, PathVysion). The expression of HER2 was studied by immunohistochemistry.

Results:

Polysomy of at least one of the chromosomes was found in about half of the dysplastic cells, and in more than 90% of cells in CIS or cells in invasive bladder tumours. Polysomic cells were found in only 17% of urothelial hyperplasia, reactive atypia and normal urothelium of healthy patients, whereas about 30% of non-neoplastic lesions in patients with concomitant urothelial carcinoma showed polysomy of at least one chromosome. These alterations indicate a field effect and are associated with synchronous development of dysplastic lesions of a higher grade. Deletion of the P16 locus was most frequently observed in aneuploid lesions, whereas overexpression of HER2 was found in 10–20% of invasive urothelial carcinomas, and only occasionally in CIS (5%). An altered HER2 expression pattern was present in non-neoplastic lesions (25%).

Conclusions:

UroVysion fluorescence in situ hybridisation is a valuable tool for the detection of genetically unstable flat urothelial lesions, and can help to resolve difficult cases, particularly the differential diagnosis of reactive atypia and dysplasia.
Small bowel gastric metaplasia: a report of three cases in children
Authors: Drut R , Altamirano E
Published: August 2007

Aims:

To report three children displaying gastric metaplasia antral pyloric type of the small bowel mucosa.

Methods:

Analysis of clinical, histopathological and immunohistochemical data.

Results:

The first patient was a 14-year-old girl with history of chronic intestinal pseudo-obstruction and chronic jejunitis; the second patient was a 6-year-old girl with a long-lasting jejunostomy; and the third patient was a 5-year-old girl with ileal–rectal anastomosis. The foci of gastric metaplasia were obvious with H&E-stained sections. The cells at the gastric metaplasia mucosa proved to be MUC-1 and sialyl-Tn positive by immunohistochemistry and they were in a pattern that was different from that of the adjacent mucosa; the cells were autofluorescent in H&E-stained sections.

Conclusions:

Gastric metaplasia of the small bowel mucosa in these cases seems to have resulted from chronic inflammation and persistent regenerative activity. This has rarely been reported outside Crohn disease, and if ever in children.
A MODEL OF GRID CELLS BASED ON A TWISTED TORUS TOPOLOGY
Authors: GUANELLA ALEXIS , KIPER DANIEL , VERSCHURE PAUL
Published: August 2007

The grid cells of the rat medial entorhinal cortex (MEC) show an increased firing frequency when the position of the animal correlates with multiple regions of the environment that are arranged in regular triangular grids. Here, we describe an artificial neural network based on a twisted torus topology, which allows for the generation of regular triangular grids. The association of the activity of pre-defined hippocampal place cells with entorhinal grid cells allows for a highly robust-to-noise calibration mechanism, suggesting a role for the hippocampal back-projections to the entorhinal cortex.
RECURRENT NEURAL NETWORKS ARE UNIVERSAL APPROXIMATORS
Authors: SCHÄFER ANTON MAXIMILIAN , ZIMMERMANN HANS-GEORG
Published: August 2007

Recurrent Neural Networks (RNN) have been developed for a better understanding and analysis of open dynamical systems. Still the question often arises if RNN are able to map every open dynamical system, which would be desirable for a broad spectrum of applications. In this article we give a proof for the universal approximation ability of RNN in state space model form and even extend it to Error Correction and Normalized Recurrent Neural Networks.
ON THE RELATION BETWEEN MINIMIZERS OF A Γ-LIMIT ENERGY AND OPTIMAL LIFTING IN BV-SPACE
Authors: IGNAT RADU , POLIAKOVSKY ARKADY
Published: August 2007

We study the minimizers of an energy functional which is obtained as the Γ-limit of a family of functionals depending on a small parameter ε > 0, associated with a function u ∈ BV(Ω, S1) and a positive parameter p. We find necessary and sufficient conditions on p and the dimension under which these minimizers coincide with the optimal liftings of u, for everyu ∈ BV(Ω, S1).
THE PARTICLE SWARM AS COLLABORATIVE SAMPLING OF THE SEARCH SPACE
Authors: KENNEDY JAMES
Published: August 2007

The particle swarm algorithm uses principles derived from social psychology to find optimal points in a search space. The present paper decomposes and reinterprets the particle swarm in order to discover new ways of implementing the algorithm. Some essential characteristics of the method are illuminated, and some inessential features are discarded. Various new forms are tested and found to perform well on a suite of test functions. In particular, it is shown that the traditional trajectory formulas can be replaced with random number generators sampling from various symmetrical probability distributions. The excellent performance of these new versions demonstrates that the strength of the algorithm is in the interactions of the particles, rather than in their behavior as individuals.
CELLULAR AUTOMATA AND CLUSTER COMPUTING: AN APPLICATION TO THE SIMULATION OF LASER DYNAMICS
Authors: GUISADO J. L. , JIMÉNEZ-MORALES F. , FERNÁNDEZ DE VEGA F.
Published: August 2007

Firstly, the application of a cellular automata (CA) model to simulate the dynamics of lasers is reviewed. With this kind of model, the macroscopic properties of the laser system emerge as a cooperative phenomenon from elementary components locally interacting under simple rules. Secondly, a parallel implementation of this kind of model for distributed-memory parallel computers is presented. Performance and scalability of this parallel implementation running on a computer cluster are analyzed, giving very satisfactory results. This confirms the feasibility of running large 3D simulations — unaffordable on an individual machine — on computer clusters, in order to simulate specific real laser systems.
Adenine nucleotide translocator promotes oxidative phosphorylation and mild uncoupling in mitochondria after dexamethasone treatment
Authors: Arvier Matthieu , Lagoutte Laëtitia , Johnson Gyasi , Dumas Jean-François , Sion Benoit , Grizard Genevieve , Malthièry Yves , Simard Gilles , Ritz Patrick
Published: August 2007

The composition of the mitochondrial inner membrane and uncoupling protein [such as adenine nucleotide translocator (ANT)] contents are the main factors involved in the energy-wasting proton leak. This leak is increased by glucocorticoid treatment under nonphosphorylating conditions. The aim of this study was to investigate mechanisms involved in glucocorticoid-induced proton leak and to evaluate the consequences in more physiological conditions (between states 4 and 3). Isolated liver mitochondria, obtained from dexamethasone-treated rats (1.5 mg·kg−1·day−1), were studied by polarography, Western blotting, and high-performance thin-layer chromatography. We confirmed that dexamethasone treatment in rats induces a proton leak in state 4 that is associated with an increased ANT content, although without any change in membrane surface or lipid composition. Between states 4 and 3, dexamethasone stimulates ATP synthesis by increasing both the mitochondrial ANT and F1-F0 ATP synthase content. In conclusion, dexamethasone increases mitochondrial capacity to generate ATP by modifying ANT and ATP synthase. The side effect is an increased leak in nonphosphorylating conditions.
Insulin at physiological concentrations increases microvascular perfusion in human myocardium
Authors: Liu Zhenqi
Published: August 2007

Vascular endothelium regulates vascular tone and tissue perfusion in response to various physiological and pathological stimuli. Insulin and meal feeding increase microvascular perfusion and thus oxygen, nutrient, and hormone delivery to human skeletal muscle. Meal feeding also increases cardiac microvascular perfusion in healthy humans. To examine whether insulin at physiological concentrations increases microvascular perfusion in human myocardium, we studied 13 healthy, overnight-fasted, lean, young human volunteers by using myocardial contrast echocardiography (MCE) and insulin-clamp techniques. We measured cardiac microvascular blood volume (MBV), microvascular flow velocity (MFV), and microvascular blood flow (MBF) at baseline, 60 min, and 120 min after initiating insulin infusion at 1 mU·kg−1·min−1. MBF is the product of MBV and MFV and represents microvascular perfusion. Insulin increased myocardial MBV by 23% at 60 min ( P < 0.01) and by 41% at 120 min ( P = 0.001) without changing MFV. As a result, insulin-mediated myocardial MBF increased significantly at both 60 min ( P < 0.01) and 120 min ( P < 0.0005). Insulin also significantly increased brachial artery diameter, flow velocity, and total blood flow at 60 and 120 min ( P < 0.05 for all). The changes in cardiac MBV correlated positively with quantitative insulin sensitivity check index (QUICKI) and negatively with body mass index but not with the steady-state glucose-infusion rates or the changes in brachial artery parameters. We conclude that insulin, at physiologically relevant concentrations, increases microvascular perfusion in human heart muscle by increasing cardiac MBV in healthy, insulin-sensitive adults. This insulin-mediated cardiac microvascular perfusion may play an important role in normal human myocardial oxygen and substrate physiology.
The history of the capillary wall: doctors, discoveries, and debates
Authors: Hwa Charlotte , Aird William C.
Published: August 2007

In 1628, William Harvey provided definitive evidence that blood circulates. The notion that blood travels around the body in a circle raised the important question of how nutrients pass between blood and underlying tissue. Perhaps, Harvey posited, arterial blood pours into the flesh as into a sponge, only then to find its way into the veins. Far from solving this problem, Marcello Malpighi's discovery of the capillaries in 1661 only added to the dilemma: surely, some argued, these entities are little more than channels drilled into tissues around them. As we discuss in this review, it would take over 200 years to arrive at a consensus on the basic structure and function of the capillary wall. A consideration of the history of this period provides interesting insights into not only the central importance of the capillary as a focus of investigation, but also the enormous challenges associated with studying these elusive structures.
Endothelin-1-mediated vasoconstriction at rest and during dynamic exercise in healthy humans
Authors: Wray D. Walter , Nishiyama Steven K. , Donato Anthony J. , Sander Mikael , Wagner Peter D. , Richardson Russell S.
Published: August 2007

It is now generally accepted that α-adrenoreceptor-mediated vasoconstriction is attenuated during exercise, but the efficacy of nonadrenergic vasoconstrictor pathways during exercise remains unclear. Thus, in eight young (23 ± 1 yr), healthy volunteers, we contrasted changes in leg blood flow (ultrasound Doppler) before and during intra-arterial infusion of the α1-adrenoreceptor agonist phenylephrine (PE) with that of the nonadrenergic endothelin A (ETA)/ETBreceptor agonist ET-1. Heart rate, arterial blood pressure, common femoral artery diameter, and mean blood velocity were measured at rest and during knee-extensor exercise at 20%, 40%, and 60% of maximal work rate (WRmax). Drug infusion rates were adjusted for blood flow to maintain comparable doses across all subjects and conditions. At rest, PE infusion (8 ng·ml−1·min−1) provoked a rapid and significant decrease in leg blood flow (−51 ± 3%) within 2.5 min. Resting ET-1 infusion (40 pg·ml−1·min−1) significantly decreased leg blood flow within 5 min, reaching a maximal vasoconstriction (−34 ± 3%) after 25–30 min of continuous infusion. Compared with rest, an exercise intensity-dependent attenuation to PE-mediated vasoconstriction was observed (−18 ± 5%, −7 ± 2%, and −1 ± 3% change in leg blood flow at 20%, 40%, and 60% of WRmax, respectively). Vasoconstriction in response to ET-1 was also blunted in an exercise intensity-dependent manner (−13 ± 3%, −7 ± 4%, and 2 ± 3% change in leg blood flow at 20%, 40%, and 60% of WRmax, respectively). These findings support a significant contribution of ET-1 and α-adrenergic receptors in the regulation of skeletal muscle blood flow in the human leg at rest and suggest a similar, intensity-dependent “lysis” of peripheral ET and α-adrenergic vasoconstriction during dynamic exercise.
Paving the road for lung stem cell biology: bronchioalveolar stem cells and other putative distal lung stem cells
Authors: Kim Carla F.
Published: August 2007

New discoveries in stem cell biology are making the biology of solid tissues increasingly complex. Important seminal studies demonstrating the presence of damage-resistant cell populations together with new isolation and characterization techniques suggest that stem cells exist in the adult lung. More detailed in vivo molecular and cellular characterization of bronchioalveolar stem cells (BASCs), other putative lung stem and progenitor cells, and differentiated cells is needed to determine the lineage relationships in adult lung. Lung diseases such as cystic fibrosis or chronic obstructive pulmonary disease, as well as the most common form of lung cancer in the United States, all involve apparent bronchiolar and alveolar cell defects. It is likely that the delicate balance of stem, progenitor, and differentiated cell functions in the lung is critically affected in patients with these devastating diseases. Thus the discovery of BASCs and other putative lung stem cells will lay the foundation for new inroads to understanding lung biology related to lung disease.
Neonatal lung side population cells demonstrate endothelial potential and are altered in response to hyperoxia-induced lung simplification
Authors: Irwin D. , Helm K. , Campbell N. , Imamura M. , Fagan K. , Harral J. , Carr M. , Young K. A. , Klemm D. , Gebb S. , Dempsey E. C. , West J. , Majka S.
Published: August 2007

Lung side population (SP) cells are resident lung precursor cells with both epithelial and mesenchymal potential that are believed to play a role in normal lung development and repair. Neonatal hyperoxic exposure impairs lung development leading to a long-term decrease in gas exchange surfaces. The hypothesis that lung SP cells are altered during impaired lung development has not been studied. To address this issue, we characterized the endothelial potential of neonatal lung SP and subsets of lung SP from neonatal mice following hyperoxic exposure during room air recovery. Lung SP cells were isolated and sorted on the basis of their capacity to efflux Hoechst 33342. The lung SP was further sorted based on expression of Flk-1 and CD45. In vitro, both CD45pos/Flk-1posand CD45neg/Flk-1posbind isolectin B4 and incorporate LDL and form networks in matrigel, indicating that these populations have endothelial cell characteristics. Hyperoxic exposure of neonatal mice resulted in subtle changes in vascular and alveolar density on P13, which persisted with room air recovery to P41. During room air recovery, a decrease in lung SP cells was detected in the hyperoxic-exposed group on postnatal day 13 followed by an increase on day 41. Within this group, the lung SP subpopulation of cells expressing CD45 increased on day 21, 41, and 55. Here, we show that lung SP cells demonstrate endothelial potential and that the population distribution changes in number as well as composition following hyperoxic exposure. The hyperoxia-induced changes in lung SP cells may limit their ability to effectively contribute to tissue morphogenesis during room air recovery.
Regulation of vascular endothelial cell barrier function and cytoskeleton structure by protein phosphatases of the PPP family
Authors: Csortos Csilla , Kolosova Irina , Verin Alexander D.
Published: August 2007

Reversible phosphorylation of cytoskeletal and cytoskeleton-associated proteins is a significant element of endothelial barrier function regulation. Therefore, understanding the mechanisms of phosphorylation/dephosphorylation of endothelial cell cytoskeletal proteins is vital to the treatment of severe lung disorders such as high permeability pulmonary edema. In vivo, there is a controlled balance between the activities of protein kinases and phosphatases. Due to various external or internal signals, this balance may be shifted. The actual balances at a given time alter the phosphorylation level of certain proteins with appropriate physiological consequences. The latest information about the structure and regulation of different types of Ser/Thr protein phosphatases participating in the regulation of endothelial cytoskeletal organization and barrier function will be reviewed here.