bluuebunny/crossref_metadata_2025 huggingface dataset:
The Human Heart: A Self‐Renewing Organ
Authors: Kajstura Jan , Hosoda Toru , Bearzi Claudia , Rota Marcello , Maestroni Silvia , Urbanek Konrad , Leri Annarosa , Anversa Piero
Published: May 2008

The dogma that the heart is a static organ which contains an irreplaceable population of cardiomyocytes prevailed in the cardiovascular field for the last several decades. However, the recent identification of progenitor cells that give rise to differentiated myocytes has prompted a re‐interpretation of cardiac biology. The heart cannot be viewed any longer as a postmitotic organ characterized by a predetermined number of myocytes that is defined at birth and is preserved throughout life. The myocardium constitutes a dynamic entity in which new young parenchymal cells are formed to substitute old damaged dying myocytes. The regenerative ability of the heart was initially documented with a classic morphometric approach and more recently with the demonstration that DNA synthesis, mitosis, and cytokinesis take place in the newly formed myocytes of the normal and pathologic heart. Importantly, replicating myocytes correspond to the differentiated progeny of cardiac stem cells. These findings point to the possibility of novel therapeutic strategies for the diseased heart.
Schematic homotopy types and non-abelian Hodge theory
Authors: Katzarkov L. , Pantev T. , Toën B.
Published: May 2008

We use Hodge theoretic methods to study homotopy types of complex projective manifolds with arbitrary fundamental groups. The main tool we use is the schematization functor$X \mapsto (X\otimes \mathbb {C})^{\mathrm {sch}}$, introduced by the third author as a substitute for the rationalization functor in homotopy theory in the case of non-simply connected spaces. Our main result is the construction of a Hodge decomposition on $(X\otimes \mathbb {C})^{\mathrm {sch}}$. This Hodge decomposition is encoded in an action of the discrete group $\mathbb {C}^{\times \delta }$ on the object $(X\otimes \mathbb {C})^{\mathrm {sch}}$ and is shown to recover the usual Hodge decomposition on cohomology, the Hodge filtration on the pro-algebraic fundamental group, and, in the simply connected case, the Hodge decomposition on the complexified homotopy groups. We show that our Hodge decomposition satisfies a purity property with respect to a weight filtration, generalizing the fact that the higher homotopy groups of a simply connected projective manifold have natural mixed Hodge structures. As applications we construct new examples of homotopy types which are not realizable as complex projective manifolds and we prove a formality theorem for the schematization of a complex projective manifold.
Nonlinear Buckling of Compressed FRP Cylindrical Shells and Their Imperfection Sensitivity
Authors: Yamada Seishi , Croll James G. A. , Yamamoto Nobuhisa
Published: May 2008

An elastic, nonlinear, Ritz analysis has been developed to allow investigation of the imperfect behavior of axially compressed orthotropic fiber reinforced polymer cylindrical shells. In a particular mode, buckling loads are shown to be strongly influenced by the constitutive material coefficients and are sensitive to initial geometric imperfections. Just as for the previously analyzed isotropic cylindrical shells, the reduced stiffness criteria are shown to provide close lower bounds to the imperfection sensitive elastic buckling loads. The potential benefits in the use of the reduced stiffness theoretical results to allow specification of the optimal designs are illustrated.
Almost Sure Stability of a Moving Elastic Band
Authors: Pavlović Ratko , Rajković Predrag , Pavlović Ivan
Published: May 2008

In this paper, the stochastic stability problem of a moving elastic band subjected to action in-plane acting forces is investigated. Each force consists of a constant part and a time-dependent zero mean stochastic function. By using the direct Liapunov functional method, almost sure asymptotic stability conditions are obtained as the function of stochastic process variance, damping coefficient, and geometric and physical parameters of the band. Numerical calculations are performed for infinite mode and compared with known results. Almost sure stability regions are shown for infinite and first mode the two-dimensional density probability function, and for higher modes when the edge load Gaussian or harmonic process is known.
A Numerical and Analytical Study of Thermally Driven Combustion Oscillations in a Perfectly Stirred Reactor
Authors: Petrova Maria V. , McGarry Matthew , Wang Hai
Published: May 2008

The oscillatory behaviors of methane and hydrogen oxidation in a perfectly stirred reactor (PSR) are examined. The work explores the parameter spaces in which oscillatory combustion and ignition take place using heat transfer coefficient, mean residence time, and reactor wall temperatures as variables. An analytic model was developed using an eigenvalue analysis to determine the nature and stability of these oscillations. Both numerical and analytical studies suggest that combustion oscillations occur at the extinction turning point of the hysteresis curve or the boundary of combustion extinction. These oscillations are found to be driven by the coupling of the heat released from the reaction and the heat dissipation through the reactor wall, and these are unstable, which perhaps explains why they were never or rarely observed experimentally. In the case of hydrogen oxidation, we demonstrate the existence of two additional types of oscillations, namely, hybrid oscillation and oscillatory ignition, both of which occur at or near the turning point of ignition. These oscillations are stable and driven by detailed reaction kinetics. The numerical results for hydrogen oxidation were compared with previous experiments and found to be within 5K of the observed wall temperature where oscillations were observed.
A Numerical Study of Flow and Heat Transfer Between Two Rotating Spheres With Time-Dependent Angular Velocities
Authors: Moghadam Ali Jabari , Rahimi Asghar Baradaran
Published: May 2008

The transient motion and the heat transfer of a viscous incompressible fluid contained between two vertically eccentric spheres maintained at different temperatures and rotating about a common axis with different angular velocities are numerically considered when the angular velocities are arbitrary functions of time. The resulting flow pattern, temperature distribution, and heat transfer characteristics are presented for the various cases including exponential and sinusoidal angular velocities. Long delays in heat transfer of large portions of the fluid in the annulus are observed because of the angular velocities of the corresponding spheres. As the eccentricity increases and the gap between the spheres decreases, the Coriolis forces and convection heat transfer effect in the narrower portion increase. Special results for concentric spheres are obtained by letting eccentricity tends to zero.
Two-Phase Convective Heat Transfer in Miniature Pipes Under Normal and Microgravity Conditions
Authors: Narayanan Chidambaram , Lakehal Djamel
Published: May 2008

Detailed numerical simulations have been performed to study the effect of flow orientation with respect to gravity on two-phase flow heat transfer (without phase change) in small diameter pipes. The Nusselt number distribution shows that the bubbly, slug, and slug-train regimes transport as much as three to four times more heat from the tube wall to the bulk flow than pure water flow. The flow blockage effect of the inclusions results in a circulating liquid flow superimposed on the mean flow. For upflow, the breakup into bubbles/slugs occurs earlier and at a higher frequency. The average Nusselt numbers are not significantly affected by the flow orientation with respect to gravity. A mechanistic heat transfer model based on frequency and length scale of inclusions is also presented.
Effect of Specimen Size on the Dissipated Energy Density in Compression
Authors: Ferro Giuseppe , Carpinteri Alberto
Published: May 2008

The size effects in compression on drilled cylindrical concrete specimens obtained from a unique concrete block over a large scale range (1:19) are analyzed. The experimental results show scale effects on dissipated energy density rather than on the compressive strength. A theoretical explanation for such a phenomenon is presented, assuming a noninteger physical dimension of the subdomain where dissipation occurs. A comparison between experimental and theoretical values is discussed and a renormalization procedure to obtain a scale-independent constitutive law is presented.
Analytical Solutions for the Modeled k Equation
Authors: Absi Rafik
Published: May 2008

The semitheoretical function of Nezu and Nakagawa (1993, Turbulence in Open-Channel Flows, A. A. Balkema, ed., Rotterdam, The Netherlands) for the turbulent kinetic energy k is valid only where local equilibrium is a good approximation. From an estimation of the difference between the energy production and its dissipation G−ϵ, we present in this study an analytical solution for the modeled k equation. Comparisons with direct numerical simulation data of turbulent channel flows show good agreement. A universal function for k+ is deducted for y+<20.
The Dynamic Compressive Response of Open-Cell Foam Impregnated With a Newtonian Fluid
Authors: Dawson M. A. , McKinley G. H. , Gibson L. J.
Published: May 2008

This analysis considers the flow of a highly viscous Newtonian fluid in a reticulated, elastomeric foam undergoing dynamic compression. A comprehensive model for the additional contribution of viscous Newtonian flow to the dynamic response of a reticulated, fluid-filled, elastomeric foam under dynamic loading is developed. For highly viscous Newtonian fluids, the flow in the reticulated foam is assumed to be dominated by viscous forces for nearly all achievable strain rates; Darcy’s law is assumed to govern the flow. The model is applicable for strains up to the densified strain for all grades of low-density, open-cell, elastomeric foam. Low-density, reticulated foam is known to deform linear elastically and uniformly up to the elastic buckling strain. For strains greater than the elastic buckling strain but less than the densified strain, the foam exhibits bimodal behavior with both linear-elastic and densified regimes. The model presented in this analysis is applicable for all strains up to the densified strain. In the bimodal regime, the model is developed by formulating a boundary value problem for the appropriate Laplace problem that is obtained directly from Darcy’s law. The resulting analytical model is more tractable than previous models. The model is compared with experimental results for the stress-strain response of low-density polyurethane foam filled with glycerol under dynamic compression. The model describes the data for foam grades varying from 70ppito90ppi and strain rates varying from 2.5×10−3to101s−1 well. The full model can also be well approximated by a simpler model, based on the lubrication approximation, which is applicable to analyses where the dimension of the foam in the direction of fluid flow (radial) is much greater than the dimension of the foam in the direction of loading (axial). The boundary value model is found to rapidly converge to the lubrication model in the limit of increasing aspect ratio given by the ratio of the radius R, to the height h, of the foam specimen with negligible error for aspect ratios greater than R∕h∼4.
Stationary Response of MDOF Dissipated Hamiltonian Systems to Poisson White Noises
Authors: Wu Y. , Zhu W. Q.
Published: May 2008

The stationary response of multi-degree-of-freedom dissipated Hamiltonian systems to random pulse trains is studied. The random pulse trains are modeled as Poisson white noises. The approximate stationary probability density function and mean-square value for the response of MDOF dissipated Hamiltonian systems to Poisson white noises are obtained by solving the fourth-order generalized Fokker–Planck–Kolmogorov equation using perturbation approach. As examples, two nonlinear stiffness coupled oscillators under external and parametric Poisson white noise excitations, respectively, are investigated. The validity of the proposed approach is confirmed by using the results obtained from Monte Carlo simulation. It is shown that the non-Gaussian behavior depends on the product of the mean arrival rate of the impulses and the relaxation time of the oscillator.
Highly Sensitive and Specific PCR Assay for Reliable Detection of
Cyclospora cayetanensis
Oocysts
Authors: Lalonde Laura F. , Gajadhar Alvin A.
Published: May 2008

Multiple outbreaks of food-borne gastroenteritis caused by the coccidian parasite
Cyclospora cayetanensis
have been reported annually in North America since 1995. Detection of
C. cayetanensis
contamination typically relies on laborious and subjective microscopic examination of produce washes. Molecular detection methods based on nested PCR, restriction fragment length polymorphism, or multiplex PCR have been developed for
C. cayetanensis
; however, they have not been adequately validated for use on food products. Further challenges include reliably extracting DNA from coccidian oocysts since their tough outer wall is resistant to lysis and overcoming PCR inhibitors in sample matrices. We describe preliminary validation of a reliable DNA extraction method for
C. cayetanensis
oocysts and a sensitive and specific novel PCR assay. The sensitivity and repeatability of the developed methods were evaluated by multiple DNA extractions and PCR amplifications using 1,000-, 100-, 10-, or 1-ooycst aliquots of
C. cayetanensis
oocysts in water or basil wash sediment. Successful PCR amplification was achieved on 15 and 5 replicates extracted from aliquots containing 1,000 oocysts in water and basil wash, respectively. All 45 replicates of the 100-oocyst aliquots in water and 5 in basil wash were amplified successfully, as were 43/45 and 41/45 of the 10- and 1-oocyst aliquots in water and 9/15 and 2/15 in basil wash, respectively. The developed primers showed no cross-reactivity when tested against bacteria, nematodes, and protozoans, including
Eimeria
,
Giardia
, and
Cryptosporidium
. Our results indicate that these methods are specific, can reliably detect a single oocyst, and overcome many of the limitations of microscopic diagnosis.
Genomic and Functional Characterization of the Modular Broad-Host-Range RA3 Plasmid, the Archetype of the IncU Group
Authors: Kulinska Anna , Czeredys Magdalena , Hayes Finbarr , Jagura-Burdzy Grazyna
Published: May 2008

IncU plasmids are a distinctive group of mobile elements with highly conserved backbone functions and variable antibiotic resistance gene cassettes. The IncU archetype is conjugative plasmid RA3, whose sequence (45,909 bp) shows it to be a mosaic, modular replicon with a class I integron different from that of other IncU replicons. Functional analysis demonstrated that RA3 possesses a broad host range and can efficiently self-transfer, replicate, and be maintained stably in alpha-, beta-, and gammaproteobacteria. RA3 contains 50 open reading frames clustered in distinct functional modules. The replication module encompasses the
repA
and
repB
genes embedded in long repetitive sequences. RepA, which is homologous to antitoxin proteins from alpha- and gammaproteobacteria, contains a Cro/cI-type DNA-binding domain present in the XRE family of transcriptional regulators. The
repA
promoter is repressed by RepA and RepB. The minireplicon encompasses
repB
and the downstream repetitive sequence r1/r2. RepB shows up to 80% similarity to putative replication initiation proteins from environmental plasmids of beta- and gammaproteobacteria, as well as similarity to replication proteins from alphaproteobacteria and
Firmicutes
. Stable maintenance functions of RA3 are most like those of IncP-1 broad-host-range plasmids and comprise the active partitioning apparatus formed by IncC (ParA) and KorB (ParB), the antirestriction protein KlcA, and accessory stability components KfrA and KfrC. The RA3 origin of transfer was localized experimentally between the maintenance and conjugative-transfer operons. The putative conjugative-transfer module is highly similar in organization and in its products to transfer regions of certain broad-host-range environmental plasmids.
Spontaneous Deletion of a 209-Kilobase-Pair Fragment from the
Escherichia coli
Genome Occurs with Acquisition of Resistance to an Assortment of Infectious Phages
Authors: Tanji Yasunori , Hattori Kenji , Suzuki Kohichi , Miyanaga Kazuhiko
Published: May 2008

To breed resistance to an assortment of infectious phages, continuous cultures of
Escherichia coli
JM109 grown in a chemostat were exposed to phage mixtures prepared from sewage influent. Four sequential chemostat-grown cultures were each infected with a different phage mixture. At the end of a chemostat run, one phage-resistant colony was isolated and used to inoculate the subsequent culture. This process was repeated, and increased phage resistance of the input bacterial strain resulted from the successive challenges with different phage cocktails. Multiple mutations apparently accumulated progressively. A mutant isolated at the end of the four runs, designated D198, showed resistance to 38 of 40 phages that infect the parent strain, JM109. D198 produced less outer membrane protein C (OmpC) than JM109. However, restoration of the OmpC protein by plasmid-mediated complementation did not completely restore the susceptibility of D198 to the 38 phages. Therefore, alterations beyond the level of OmpC protein production contribute to the phage resistance of D198. PCR-based genetic analysis revealed that D198 has a genome that is 209 kbp (about 200 genes) smaller than JM109. The deletion includes the chromosomal section from
ompC
to
wbbL
that encodes the rhamnosyl transferase involved in lipopolysaccharide biosynthesis. Strains D198 and JM109 were comparable in their growth characteristics and their abilities to express a recombinant protein.
Analysis of Vaginal Lactobacilli from Healthy and Infected Brazilian Women
Authors: Martinez Rafael C. R. , Franceschini Sílvio A. , Patta Maristela C. , Quintana Silvana M. , Nunes Álvaro C. , Moreira João L. S. , Anukam Kingsley C. , Reid Gregor , De Martinis Elaine C. P.
Published: May 2008

Culture-dependent PCR-amplified rRNA gene restriction analysis and culture-independent (PCR-denaturing gradient gel electrophoresis) methodologies were used to examine vaginal lactobacilli from Brazilian women who were healthy or had been diagnosed with vulvovaginal candidiasis (VVC) or bacterial vaginosis. Only
Lactobacillus crispatus
was detected accordingly by both methods, and H
2
O
2
-producing lactobacilli were not associated with protection against VVC.
Agrobacterium
-Mediated Disruption of a Nonribosomal Peptide Synthetase Gene in the Invertebrate Pathogen
Metarhizium anisopliae
Reveals a Peptide Spore Factor
Authors: Moon Yong-Sun , Donzelli Bruno G. G. , Krasnoff Stuart B. , McLane Heather , Griggs Mike H. , Cooke Peter , Vandenberg John D. , Gibson Donna M. , Churchill Alice C. L.
Published: May 2008

Numerous secondary metabolites have been isolated from the insect pathogenic fungus
Metarhizium anisopliae
, but the roles of these compounds as virulence factors in disease development are poorly understood. We targeted for disruption by
Agrobacterium tumefaciens
-mediated transformation a putative nonribosomal peptide synthetase (NPS) gene, Ma
NPS1
. Four of six gene disruption mutants identified were examined further. Chemical analyses showed the presence of serinocyclins, cyclic heptapeptides, in the extracts of conidia of control strains, whereas the compounds were undetectable in ΔMa
nps1
mutants treated identically or in other developmental stages, suggesting that Ma
NPS1
encodes a serinocyclin synthetase. Production of the cyclic depsipeptide destruxins,
M. anisopliae
metabolites also predicted to be synthesized by an NPS, was similar in ΔMa
nps1
mutant and control strains, indicating that Ma
NPS1
does not contribute to destruxin biosynthesis. Surprisingly, a Ma
NPS1
fragment detected DNA polymorphisms that correlated with relative destruxin levels produced in vitro, and Ma
NPS1
was expressed concurrently with in vitro destruxin production. ΔMa
nps1
mutants exhibited in vitro development and responses to external stresses comparable to control strains. No detectable differences in pathogenicity of the ΔMa
nps1
mutants were observed in bioassays against beet armyworm and Colorado potato beetle in comparison to control strains. This is the first report of targeted disruption of a secondary metabolite gene in
M. anisopliae
, which revealed a novel cyclic peptide spore factor.
Potential Prebiotic Properties of Almond (Amygdalus communisL.) Seeds
Authors: Mandalari G. , Nueno-Palop C. , Bisignano G. , Wickham M. S. J. , Narbad A.
Published: May 2008

Almonds are known to have a number of nutritional benefits, including cholesterol-lowering effects and protection against diabetes. They are also a good source of minerals and vitamin E, associated with promoting health and reducing the risk for chronic disease. For this study we investigated the potential prebiotic effect of almond seeds in vitro by using mixed fecal bacterial cultures. Two almond products, finely ground almonds (FG) and defatted finely ground almonds (DG), were subjected to a combined model of the gastrointestinal tract which included in vitro gastric and duodenal digestion, and the resulting fractions were subsequently used as substrates for the colonic model to assess their influence on the composition and metabolic activity of gut bacteria populations. FG significantly increased the populations of bifidobacteria andEubacterium rectale, resulting in a higher prebiotic index (4.43) than was found for the commercial prebiotic fructooligosaccharides (4.08) at 24 h of incubation. No significant differences in the proportions of gut bacteria groups were detected in response to DG. The increase in the numbers ofEubacterium rectaleduring fermentation of FG correlated with increased butyrate production. In conclusion, we have shown that the addition of FG altered the composition of gut bacteria by stimulating the growth of bifidobacteria andEubacterium rectale.
Retail Survey of Brazilian Milk and Minas Frescal Cheese and a Contaminated Dairy Plant To Establish Prevalence, Relatedness, and Sources of
Listeria monocytogenes
Isolates
Authors: Brito J. Renaldi F. , Santos Emilia M. P. , Arcuri Edna F. , Lange Carla C. , Brito Maria A. V. P. , Souza Guilherme N. , Cerqueira Mônica M. P. O. , Beltran J. Marcela Soto , Call Jeffrey E. , Liu Yanhong , Porto-Fett Anna C. S. , Luchansky John B.
Published: May 2008

A study was designed to recover
Listeria monocytogenes
from pasteurized milk and Minas frescal cheese (MFC) sampled at retail establishments (REs) and to identify the contamination source(s) of these products in the corresponding dairy processing plant. Fifty milk samples (9 brands) and 55 MFC samples (10 brands) were tested from REs located in Juiz de Fora, Minas Gerais, Brazil. All milk samples and 45 samples from 9 of 10 MFC brands tested negative for
L. monocytogenes
; however, “brand F” of MFC obtained from REs 119 and 159 tested positive. Thus, the farm/plant that produced brand F MFC was sampled; all samples from the milking parlor tested negative for
L. monocytogenes
, whereas several sites within the processing plant and the MFC samples tested positive. All 344 isolates recovered from retail MFC, plant F MFC, and plant F environmental samples were serotype 1/2a and displayed the same AscI or ApaI fingerprints. Since these results established that the storage coolers served as the contamination source of the MFC, plant F was closed so that corrective renovations could be made. Following renovation, samples from sites that previously tested positive for the pathogen were collected from the processing environment and from MFC on multiple visits; all tested negative for
L. monocytogenes
. In addition, on subsequent visits to REs 159 and 119, all MFC samples tested negative for the pathogen. Studies are ongoing to quantify the prevalence, levels, and types of
L. monocytogenes
in MFC and associated processing plants to lessen the likelihood of listeriosis in Brazil.
Role of the White Collar 1 Photoreceptor in Carotenogenesis, UV Resistance, Hydrophobicity, and Virulence of
Fusarium oxysporum
Authors: Ruiz-Roldán M. Carmen , Garre Victoriano , Guarro Josep , Mariné Marçal , Roncero M. Isabel G.
Published: May 2008

Knockout mutants of
Fusarium oxysporum
lacking the putative photoreceptor Wc1 were impaired in aerial hyphae, surface hydrophobicity, light-induced carotenogenesis, photoreactivation after UV treatment, and upregulation of photolyase gene transcription. Infection experiments with tomato plants and immunodepressed mice revealed that Wc1 is dispensable for pathogenicity on plants but required for full virulence on mammals.
Candida albicans
Ferric Reductases Are Differentially Regulated in Response to Distinct Forms of Iron Limitation by the Rim101 and CBF Transcription Factors
Authors: Baek Yong-Un , Li Mingchun , Davis Dana A.
Published: May 2008

Iron is an essential nutrient that is severely limited in the mammalian host.
Candida albicans
encodes a family of 15 putative ferric reductases, which are required for iron acquisition and utilization. Despite the central role of ferric reductases in iron acquisition and mobilization, relatively little is known about the regulatory networks that govern ferric reductase gene expression in
C. albicans
. Here we have demonstrated the differential regulation of two ferric reductases,
FRE2
and
FRP1
, in response to distinct iron-limited environments.
FRE2
and
FRP1
are both induced in alkaline-pH environments directly by the Rim101 transcription factor. However,
FRP1
but not
FRE2
is also induced by iron chelation. We have identified a CCAAT motif as the critical regulatory sequence for chelator-mediated induction and have found that the CCAAT binding factor (CBF) is essential for
FRP1
expression in iron-limited environments. We found that a
hap5
Δ/
hap5
Δ mutant, which disrupts the core DNA binding activity of CBF, is unable to grow under iron-limited conditions.
C. albicans
encodes three CBF-dependent transcription factors, and we identified the Hap43 protein as the CBF-dependent transcription factor required for iron-limited responses. These studies provide key insights into the regulation of ferric reductase gene expression in the fungal pathogen
C. albicans
.
Pet191 Is a Cytochrome
c
Oxidase Assembly Factor in
Saccharomyces cerevisiae
Authors: Khalimonchuk Oleh , Rigby Kevin , Bestwick Megan , Pierrel Fabien , Cobine Paul A. , Winge Dennis R.
Published: May 2008

The twin-Cx
9
C motif protein Pet191 is essential for cytochrome
c
oxidase maturation. The motif Cys residues are functionally important and appear to be present in disulfide linkages within a large oligomeric complex associated with the mitochondrial inner membrane. The import of Pet191 differs from that of other twin-Cx
9
C motif class of proteins in being independent of the Mia40 pathway.
A Class 1 Integron Present in a Human Commensal Has a Hybrid Transposition Module Compared to Tn
402
: Evidence of Interaction with Mobile DNA from Natural Environments
Authors: Labbate M. , Chowdhury P. Roy , Stokes H. W.
Published: May 2008

In a survey of class 1 integrons from human stools, an unusual class 1 integron from a strain of
Enterobacter cloacae
was isolated and characterized in detail. Sequence analysis of a fosmid containing the class 1 integron revealed a complex set of transposons which included two Tn
402
-like transposons. One of these transposons, Tn
6007
, included a class 1 integron with two non-antibiotic-resistance-type gene cassettes and a complete transposition module. This
tni
module is a hybrid with a boundary within the
res
site compared to Tn
402
, implying that a site-specific recombination event generated either Tn
6007
or Tn
402
. The second Tn
402
-like transposon, Tn
6008
, possesses neither a
mer
operon nor an integron, and most of its
tni
module has been deleted. Tn
6007
, Tn
6008
, and the 2,478 bases between them, collectively designated Tn
6006
, have transposed into a Tn
5036
/Tn
3926
-like transposon as a single unit. Tn
6006
, Tn
6007
, and Tn
6008
could all transpose as discrete entities. Database analysis also revealed that a version of Tn
6008
was present in the genome of
Xanthomonas campestris
pv. vesicatoria. Overall, the
E. cloacae
isolate further demonstrated that functional class 1 integrons/transposons are probably common in bacterial communities and have the potential to add substantially to the problem of multidrug-resistant nosocomial infections.
Type II Secretory Pathway for Surface Secretion of DraD Invasin from the Uropathogenic
Escherichia coli
Dr
+
Strain
Authors: Zalewska-Piątek Beata , Bury Katarzyna , Piątek Rafał , Bruździak Piotr , Kur Józef
Published: May 2008

The virulence of the uropathogenic
Escherichia coli
Dr
+
IH11128 strain is associated with the presence of Dr fimbrial structures and a DraD invasin which can act as a fimbrial capping domain at the bacterial cell surface. However, a recent study suggests that the DraD protein is surface exposed in two forms: fimbria associated and fimbria nonassociated (prone to interaction with the N-terminal extension of the DraE protein located on the fimbrial tip). The actual mechanism of DraD surface secretion is presently unknown. We identified a previously unrecognized type II secretory pathway (secreton) in the uropathogenic
E. coli
Dr
+
strain which is well conserved among gram-negative bacteria and used mainly for secretion of virulence determinants. An active secreton is composed of 12 to 15 different proteins, among which GspD functions as an outer-membrane channel to permit extrusion of proteins in a folded state. Therefore, we inactivated the pathway by inserting the group II intron into a
gspD
gene of the type II secretion machinery by site-specific recombination. DraD secretion by the
E. coli
Dr
+
and
gspD
mutant strains was determined by immunofluorescence microscopy (with antibodies raised against DraD) and an assay of cell binding between bacteria and HeLa cells. The specificity of DraD-mediated bacterial binding for the integrin receptor was confirmed by examination of the adhesion of DraD-coated beads to HeLa cells in the presence and absence of α
5
β
1
monoclonal antibodies. The investigations that we performed showed that type II secretion in
E. coli
Dr
+
strains leads to DraD translocation at the bacterial cell surfaces.
Cell Cycle Characteristics of
Crenarchaeota
: Unity among Diversity
Authors: Lundgren Magnus , Malandrin Laurence , Eriksson Stefan , Huber Harald , Bernander Rolf
Published: May 2008

The hyperthermophilic archaea
Acidianus hospitalis
,
Aeropyrum pernix
,
Pyrobaculum aerophilum
,
Pyrobaculum calidifontis
, and
Sulfolobus tokodaii
representing three different orders in the phylum
Crenarchaeota
were analyzed by flow cytometry and combined phase-contrast and epifluorescence microscopy. The overall organization of the cell cycle was found to be similar in all species, with a short prereplicative period and a dominant postreplicative period that accounted for 64 to 77% of the generation time. Thus, in all
Crenarchaeota
analyzed to date, cell division and initiation of chromosome replication occur in close succession, and a long time interval separates termination of replication from cell division. In
Pyrobaculum
, chromosome segregation overlapped with or closely followed DNA replication, and further genome separation appeared to occur concomitant with cellular growth. Cell division in
P. aerophilum
took place without visible constriction.
The Production In Vivo of Microcin E492 with Antibacterial Activity Depends on Salmochelin and EntF
Authors: Mercado Gabriela , Tello Mario , Marín Macarena , Monasterio Octavio , Lagos Rosalba
Published: May 2008

Microcin E492 is a channel-forming bacteriocin that is found in two forms, namely, a posttranslationally modified form obtained by the covalent linkage of salmochelin-like molecules to serine 84 and an unmodified form. The production of modified microcin E492 requires the synthesis of enterochelin, which is subsequently glycosylated by MceC and converted into salmochelin.mceCmutants produced inactive microcin E492, and this phenotype was reversed either by complementation withiroBfromSalmonella entericaor by the addition of exogenous salmochelin. Cyclic salmochelin uptake byEscherichia colioccurred mainly through the outer membrane catecholate siderophore receptor Fiu. The production of inactive microcin E492 by mutants inentBandentCwas reverted by the addition of the end product of the respective mutated pathway (2,3-dihydroxybenzoic acid and enterochelin/salmochelin, respectively), while mutants inentFdid not produce active microcin E492 in the presence of enterochelin or salmochelin. The EntF adenylation domain was the only domain required for this microcin E492 maturation step. Inactivation of the enzymatic activity of this domain by site-directed mutagenesis did not prevent the synthesis of active microcin E492 in the presence of salmochelin, indicating that the adenylation activity is not essential for the function of EntF at this stage of microcin E492 maturation.
Xenorhabdus nematophila lrhAIs Necessary for Motility, Lipase Activity, Toxin Expression, and Virulence inManduca sextaInsects
Authors: Richards Gregory R. , Herbert Erin E. , Park Youngjin , Goodrich-Blair Heidi
Published: May 2008

The gram-negative insect pathogenXenorhabdus nematophilapossesses potential virulence factors including an assortment of toxins, degradative enzymes, and regulators of these compounds. Here, we describe thelysR-likehomologA(lrhA) gene, a gene required byX. nematophilafor full virulence inManduca sextainsects. In several other gram-negative bacteria, LrhA homologs are transcriptional regulators involved in the expression (typically repression) of virulence factors. Based on phenotypic and genetic evidence, we report thatX. nematophilaLrhA has a positive effect on transcription and expression of certain potential virulence factors, including a toxin subunit-encoding gene,xptD1. Furthermore, anlrhAmutant lacks in vitro lipase activity and has reduced swimming motility compared to its wild-type parent. Quantitative PCR revealed that transcript levels of flagellar genes, a lipase gene, andxptD1were significantly lower in thelrhAmutant than in the wild type. In addition,lrhAitself is positively regulated by the global regulator Lrp. This work establishes a role for LrhA as a vital component of a regulatory hierarchy necessary forX. nematophilapathogenesis and expression of surface-localized and secreted factors. Future research is aimed at identifying and characterizing virulence factors within the LrhA regulon.
A Staphylococcal GGDEF Domain Protein Regulates Biofilm Formation Independently of Cyclic Dimeric GMP
Authors: Holland Linda M. , O'Donnell Sinéad T. , Ryjenkov Dmitri A. , Gomelsky Larissa , Slater Shawn R. , Fey Paul D. , Gomelsky Mark , O'Gara James P.
Published: May 2008

Cyclic dimeric GMP (c-di-GMP) is an important biofilm regulator that allosterically activates enzymes of exopolysaccharide biosynthesis. Proteobacterial genomes usually encode multiple GGDEF domain-containing diguanylate cyclases responsible for c-di-GMP synthesis. In contrast, only one conserved GGDEF domain protein, GdpS (forGGDEFdomainprotein fromStaphylococcus), and a second protein with a highly modified GGDEF domain, GdpP, are present in the sequenced staphylococcal genomes. Here, we investigated the role of GdpS in biofilm formation inStaphylococcus epidermidis. Inactivation ofgdpSimpaired biofilm formation in medium supplemented with NaCl under static and flow-cell conditions, whereasgdpSoverexpression complemented the mutation and enhanced wild-type biofilm development. GdpS increased production of theicaADBC-encoded exopolysaccharide, poly-N-acetyl-glucosamine, by elevatingicaADBCmRNA levels. Unexpectedly, c-di-GMP synthesis was found to be irrelevant for the ability of GdpS to elevateicaADBCexpression. Mutagenesis of the GGEEF motif essential for diguanylate cyclase activity did not impair GdpS, and the N-terminal fragment of GdpS lacking the GGDEF domain partially complemented thegdpSmutation. Furthermore, heterologous diguanylate cyclases expressed intransfailed to complement thegdpSmutation, and the purified GGDEF domain from GdpS possessed no diguanylate cyclase activity in vitro. ThegdpSgene fromStaphylococcus aureusexhibited similar characteristics to itsS. epidermidisortholog, suggesting that the GdpS-mediated signal transduction is conserved in staphylococci. Therefore, GdpS affects biofilm formation through a novel c-di-GMP-independent mechanism involving increasedicaADBCmRNA levels and exopolysaccharide biosynthesis. Our data raise the possibility that staphylococci cannot synthesize c-di-GMP and have only remnants of a c-di-GMP signaling pathway.
A Specialized Citric Acid Cycle Requiring Succinyl-Coenzyme A (CoA):Acetate CoA-Transferase (AarC) Confers Acetic Acid Resistance on the Acidophile
Acetobacter aceti
Authors: Mullins Elwood A. , Francois Julie A. , Kappock T. Joseph
Published: May 2008

Microbes tailor macromolecules and metabolism to overcome specific environmental challenges. Acetic acid bacteria perform the aerobic oxidation of ethanol to acetic acid and are generally resistant to high levels of these two membrane-permeable poisons. The citric acid cycle (CAC) is linked to acetic acid resistance in
Acetobacter aceti
by several observations, among them the oxidation of acetate to CO
2
by highly resistant acetic acid bacteria and the previously unexplained role of
A. aceti
citrate synthase (AarA) in
a
cetic
a
cid
r
esistance at a low pH. Here we assign specific biochemical roles to the other components of the
A. aceti
strain 1023
aarABC
region. AarC is succinyl-coenzyme A (CoA):acetate CoA-transferase, which replaces succinyl-CoA synthetase in a variant CAC. This new bypass appears to reduce metabolic demand for free CoA, reliance upon nucleotide pools, and the likely effect of variable cytoplasmic pH upon CAC flux. The putative
aarB
gene is reassigned to SixA, a known activator of CAC flux. Carbon overflow pathways are triggered in many bacteria during metabolic limitation, which typically leads to the production and diffusive loss of acetate. Since acetate overflow is not feasible for
A. aceti
, a CO
2
loss strategy that allows acetic acid removal without substrate-level (de)phosphorylation may instead be employed. All three
aar
genes, therefore, support flux through a complete but unorthodox CAC that is needed to lower cytoplasmic acetate levels.
Lysine Represses Transcription of the
Escherichia coli dapB
Gene by Preventing Its Activation by the ArgP Activator
Authors: Bouvier Jean , Stragier Patrick , Morales Violette , Rémy Elisabeth , Gutierrez Claude
Published: May 2008

The
Escherichia coli dapB
gene encodes one of the enzymes of the biosynthetic pathway leading to lysine and its immediate precursor, diaminopimelate. Expression of
dapB
is repressed by lysine, but no
trans
-acting regulator has been identified so far. Our analysis of the
dapB
regulatory region shows that sequences located in the −81/−118 interval upstream of the transcription start site are essential for full expression of
dapB
, as well as for lysine repression. Screening a genomic library for a gene that could alleviate lysine repression when present in multicopy led to the recovery of
argP
, a gene encoding an activating protein of the LysR-type family, known to use lysine as an effector. An
argP
null mutation strongly decreases
dapB
transcription that becomes insensitive to lysine. Purified His
6
-tagged ArgP protein binds with an apparent
K

d

of 35 nM to the
dapB
promoter in a gel retardation assay, provided that sequences up to −103 are present. In the presence of
l
-lysine and
l
-arginine, the binding of ArgP to
dapB
is partly relieved. These results fit with a model in which ArgP contributes to enhanced transcription of
dapB
when lysine becomes limiting.
Elucidation of the 4-Hydroxyacetophenone Catabolic Pathway in
Pseudomonas fluorescens
ACB
Authors: Moonen Mariëlle J. H. , Kamerbeek Nanne M. , Westphal Adrie H. , Boeren Sjef A. , Janssen Dick B. , Fraaije Marco W. , van Berkel Willem J. H.
Published: May 2008

The catabolism of 4-hydroxyacetophenone in
Pseudomonas fluorescens
ACB is known to proceed through the intermediate formation of hydroquinone. Here, we provide evidence that hydroquinone is further degraded through 4-hydroxymuconic semialdehyde and maleylacetate to β-ketoadipate. The
P. fluorescens
ACB genes involved in 4-hydroxyacetophenone utilization were cloned and characterized. Sequence analysis of a 15-kb DNA fragment showed the presence of 14 open reading frames containing a gene cluster (
hapCDEFGHIBA
) of which at least four encoded enzymes are involved in 4-hydroxyacetophenone degradation: 4-hydroxyacetophenone monooxygenase (
hapA
), 4-hydroxyphenyl acetate hydrolase (
hapB
), 4-hydroxymuconic semialdehyde dehydrogenase (
hapE
), and maleylacetate reductase (
hapF
). In between
hapF
and
hapB
, three genes encoding a putative intradiol dioxygenase (
hapG
), a protein of the Yci1 family (
hapH
), and a [2Fe-2S] ferredoxin (
hapI
) were found. Downstream of the
hap
genes, five open reading frames are situated encoding three putative regulatory proteins (
orf10, orf12
, and
orf13
) and two proteins possibly involved in a membrane efflux pump (
orf11
and
orf14
). Upstream of
hapE
, two genes (
hapC
and
hapD
) were present that showed weak similarity with several iron(II)-dependent extradiol dioxygenases. Based on these findings and additional biochemical evidence, it is proposed that the
hapC
and
hapD
gene products are involved in the ring cleavage of hydroquinone.
Additional taxonomic studies on Avena fatuoids: some morphological attributes seen using the scanning electron microscope
Authors: Baum Bernard R.
Published: May 2008

This paper describes and evaluates the results of a scanning electron microscopic study of the sculpture of the surfaces of caryopses, glumes, lemmas, awn columns, and awn subules of Avena fatua, normal cultivated oats (A. sativa), fatuoids, and F1 hybrids A. fatua × sativa. Only qualitative differences were sought, and none were detected in the glumes and on the caryopses. The prickles on the lemmas, on the awn columns, and on the awn subules all appear in two character states. In the case of the lemmas one state is found in the normal cultivated oats, fatuoids, and F1 hybrids, and the other in A. fatua. On the other hand in the awn subules one state is found in the normal cultivated oats and the other in fatuoids, F1 hybrids, and A. fatua, while in the awn columns one state occurs in cultivated oats and the other in A. fatua, but in the F1 hybrids and fatuoids both states occur. These findings provide taxonomic evidence additional to that described earlier based on lodicules coupled with traditional characters.
The roles of disturbance and succession in upland forest at Candle Lake, Saskatchewan
Authors: Dix R. L. , Swan J. M. A.
Published: May 2008

Eighty-nine upland forest stands were selected to cover the ranges of tree species composition, stand ages, understory composition, and site in the area. The role of each tree species as a pioneer, transient, or self-maintaining component of the forest was determined from the number of stems, their vigor, and distribution in tree, sapling, and seedling strata among all stands and from growth increment cores of trees and saplings in 39 stands. Conclusions are drawn regarding the species likely to dominate different sites following severe fire and the kinds of vegetational change likely to occur on them between disturbances. Changing patterns in the non-arboreal vascular flora, moss, and lichen cover were related to changes in tree species composition with site and time. The forest and its environment are linked in an irregular "pulse" strategy of alternating disturbance and regrowth that repeatedly rejuvenates the growing stock.
Increase of indoleacetic acid oxidase isoenzymes by gibberellic acid in tobacco callus cultures
Authors: Lee T. T.
Published: May 2008

Indoleacetic acid (IAA) oxidase in tobacco callus tissues (Nicotiana tabacum L., cultivar White Gold) grown on a medium supplemented with gibberellic acid (GA3), IAA, and kinetin was resolved into seven isoenzymes by polyacrylamide gel electrophoresis. Gibberellic acid promoted the development of three fast-migrating IAA oxidase isoenzymes which were 7- to 10-fold more active than those of the control. Gibberellic acid was effective at 2 × 10−9 M and its activity increased with increasing concentration up to 2 × 10−7 M. Actinomycin D and cycloheximide inhibited the development of these isoenzymes, suggesting a requirement for both RNA and protein synthesis. The GA3-promoted IAA oxidase isoenzymes increased with time and were positively associated with the GA3-induced characteristic type of growth.The expression of the GA3 effect on IAA oxidase isoenzymes and growth was dependent on IAA and kinetin. In the presence of appropriate concentrations of kinetin, the combined effect of GA3 and IAA was more than additive. A possible interpretation of the GA3–IAA interaction is discussed.
The effect of CCC and gibberellins A3 and A7 on the cold hardiness of Kharkov 22 MC winter wheat
Authors: Roberts D. W. A.
Published: May 2008

Continuously feeding a suitable concentration (3 × 10−5 or 3 × 10−4 M) of chlorocholine chloride (CCC) through the roots of Kharkov 22 MC winter wheat grown at both hardening (4 to 6 °C) and non-hardening (21°) temperatures induced small increases in its cold hardiness. In plants grown at 21 °C supplying 3 × 10−3 M CCC reduced cold hardiness. Under hardening conditions gibberellins A3 and A7 and under non-hardening conditions gibberellin A3 reduced the cold hardiness of Kharkov 22 MC. CCC produced morphological changes in plants grown at 21 °C that partially duplicated those induced by growing the plants at 6 °C. In plants grown at 6 °C gibberellins A3 and A7 produced morphological changes that caused the plants to partially resemble those grown at 21 °C. These results are discussed in relation to the hypothesis that one of the changes accompanying cold hardening in winter wheat is a reduction of the content of endogenous gibberellins. The conclusion is reached that if a reduction in gibberellin levels occurs it can only account for a part of the change in cold hardiness produced by natural hardening temperatures.
Opaline silica bodies in the range grasses of southern Alberta
Authors: Blackman Elizabeth
Published: May 2008

The types and distribution of silica bodies (opaline phytoliths) of 26 species of native and introduced grasses of the range grasslands of southern Alberta are described. The genera examined are Bromus, Festuca, Poa, Koeleria, Deschampsia, Calamagrostis, Phleum, Agropyron, Elymus, Stipa, Danthonia, and Bouteloua. Scale drawings of representative silica bodies for each genus are provided.The observations are discussed in relation to grass taxonomy, and to the overall role of silica in grasses.