bluuebunny/crossref_metadata_2025 huggingface dataset:
Lifetime of Imidazolium Salts at Elevated
Temperatures
Authors: Blake Daniel M. , Moens Luc , Rudnicki Daniel , Pilath Heidi
Published: January 2006

This report summarizes progress to date on the thermal stability of imidazolium salts being considered for application as heat transfer and thermal storage fluids in solar parabolic trough power systems. Imidazolium salts are a subset of the general class of molten salts. They are termed ionic liquids because many have freezing points at or below room temperature. This class of salts was selected for initial study because there were many examples that were reported to be stable at high temperatures. These reports were usually based on the results of standard thermal gravimetric analysis (TGA) methods. Work by our subcontractor at the University of Alabama and at NREL showed that slow heating rates or when the temperature is held constant for long times resulted in decomposition temperatures that are much lower than those found with the usual TGA methods. We have used a TGA technique that allows calculation of the rates of thermal decomposition as a function of temperature. The results lead us to the conclusion that the imidazolium salts known to be the most thermally stable would not have useful lifetimes above about 200°C. At present this determination is based on the rough approximation that the fluid in a solar trough system experiences a constant, high temperature. Better estimates of the useful lifetime will require a system model that takes into account the time at temperature distribution of a fluid moving through the different components in a solar plant.
Experimental Study on a Hybrid Desiccant Dehumidification and Air Conditioning System
Authors: Yong Li , Sumathy K. , Dai Y. J. , Zhong J. H. , Wang R. Z.
Published: January 2006

This paper presents the experimental tests on hybrid desiccant dehumidification and air conditioning systems. Experimental tests are carried out with LiCl desiccant at typical operative ranges for air conditioning applications, particularly for high humid regions like Hong Kong. Results are reported in terms of coefficient of performance (COP) based on primary energy usage and electrical energy usage, respectively. Experiments have demonstrated consistent reduction in humidity ratio satisfying the sensible as well as latent load through a respective subsystem and thereby resulting in a higher COP based on primary energy usage. Also, results show that the regeneration temperature as well as process air flow rate have a significant role on the system performance. It is found that the hybrid system can achieve a higher part load performance, and hence can assure of its effective operation all year around in hot humid regions.
Modeling and Optimizing the Size of the Power Conditioning Unit for Photovoltaic Systems
Authors: Abd El-Aal Abou El-Maaty M. , Schmid Jürgen , Bard Jochen , Caselitz Peter
Published: January 2006

Photovoltaic (PV) systems, grid-connected or stand-alone, use the power conditioning unit (PCU) to optimize the energy transfer from the PV generator to the user load by using the maximum power point tracker, and also to invert, regulate, and wave shape the power between the components of the system. To study and optimize this system, different PCU models are applied. In this work different empirical models of the PCU have been set up. The purpose of this investigation is to verify the possibility of the PCU application to this system and study the different mathematical energy efficiency models. All these models have been simulated and compared with a typical real system to show which one is better. The second part of the paper includes the optimal size of the PCU with the PV system and also an application comparison between two possible locations for varied geographical latitudes, in Kassel/Germany (middle Europe) and Cairo/Egypt (North Africa).
An Independent-Flow-Field Model for a SDOF Nonlinear Structural System–Part I: Identification and Comparisons
Authors: Yim Solomon C. S. , Lin Huan
Published: January 2006

An independent-flow-field (IFF) model selected in this study to investigate the nonlinear response behavior of a medium-scale, experimental, submerged, moored structure is validated via parametric studies. Bifurcations in experimental responses are frequently observed, and the associated nonlinear primary and secondary resonances are identified in frequency response diagrams. Distinct from previous investigations, this study intends to identify a set of “best-fit” constant coefficients for predictions and comparisons over the entire wave frequencies examined. It is concluded that the small-body, IFF model predicts, reasonably well, the nonlinear, moored, and submerged structural response subjected to regular waves.
Extreme Events in Nonlinear Random Seas
Authors: Fedele Francesco
Published: January 2006

In this paper, the occurrence of extreme events due to the four-wave resonance interaction in weakly nonlinear water waves is investigated. The starting point is the Zakharov equation, which governs the dynamics of the spectral components of the surface displacement. It is proven that the optimal spectral components giving an extreme crest are solutions of a well-defined constrained optimization problem. A new analytical expression for the probability of exceedance of the wave crest is then proposed for the prediction of freak wave events.
Fatigue Analysis of Load-Carrying Fillet Welds
Authors: Sørensen John Dalsgaard , Tychsen Jesper , Andersen Jens Ulfkjær , Brandstrup Ronnie D.
Published: January 2006

The fatigue strength of load-carrying fillet welds is, in most codes of practice, performed neglecting the influence of bending in the weld throat section. However, some commonly applied structural details give rise to significant bending in the weld throat section. An example of such a detail is a doubler plate connection, which is often applied in connection with modifications of offshore structures. As a part of the present work, fatigue tests have been performed with test specimens fabricated by the current industry standard for welded offshore steel structures. The fatigue tests show that the degree of bending (DOB) has an influence on the fatigue lifetime. The fatigue lifetime decreases significantly when increasing the bending stress. In order to take into account the effect of the bending, a new fatigue stress definition applicable for fillet welds failing through the weld is presented. Using the test results, it is shown that the new definition of fatigue stress can be used for a wide range of DOB with a low standard deviation of the resulting SN curve.
A Simple Lab Exercise to Determine the Coefficient of Static Friction
Authors: Kinsler Mark , Kinzel Evelyn
Published: January 2006

This paper describes a quick, simple, and reliable physics lab exercise for determining the coefficient of static friction between common materials. Only a meter stick, a protractor, and samples of the materials are needed. A mathematical derivation is given to show why the method works. The mathematical skill level needed to understand the experiment is suitable for advanced high school or beginning college students.
Quantitative Investigation of Thermal Expansion Using Single-Slit Diffraction
Authors: Fakhruddin Hasan
Published: January 2006

There are a number of interesting articles1 that have discussed qualitative, quantitative, and other aspects of thermal expansion. A method to determine linear coefficient of thermal expansion using readily available materials is presented here. The design of the apparatus for this method allows for the width of a single slit to increase by the same amount as the thermal expansion of a length of a strip or a rod of a material. A laser is used to obtain a diffraction pattern for the single slit. The increase in the slit width, hence the linear expansion, can be measured by analyzing the diffraction pattern. The value of the linear coefficient of thermal expansion of the material can then be calculated.
Sine Waves in the Snow
Authors: Bartlett Albert A.
Published: January 2006

Last summer our neighbors put up a new, high board fence whose horizontal top board was approximately 10 cm wide. This top board quickly became a superhighway for squirrels. Figure 1 shows the top of the fence after the winter's first snowfall. One squirrel running in the snow on top of the fence has left the snow neatly sculptured into a good approximation of a sine wave. If the top of the fence is designated y = 0 and x is measured horizontally along the top of the fence, the equation for the approximate sine wave would be: y = a + A[1 + (2πx/ λ + φ)].
An Alternative Approach to Explaining Beats
Authors: Newburgh Ronald
Published: January 2006

This note examines the phenomenon of beats by noting that two sine functions of different frequency come into phase when the difference between their arguments is 2π. By using this analysis one can emphasize the physical meaning of trigonometric functions and the interpretation of phase.
Hanging by a Thread
Authors: Partensky Peretz D. , Partensky Michael B.
Published: January 2006

A popular problem1 asks for the equilibrium separation between two mutually repelling charges. The charges are suspended on strings of equal length fastened to a common point [Fig. 1(a)]. Students are typically asked to find the equilibrium separation s between the charges or a related quantity such as the deflection angle. In this paper, we modify this problem slightly by considering two opposite and therefore attracting charges [Fig. 1(b)]. Now, in order to generate an equilibrium state at finite distance s, we suspend the charges at a finite initial separation s0. One might expect that this problem is just a routine extension of the original one. It turns out, however, that this is not the case. The discussion leading to the solutions introduces some very interesting physics, including “catastrophic” behavior.
Phase-Space Orbits and the Ping-Pong Ball Impact Oscillator
Authors: Millet Peter , Schreve James , Coxeter Peter
Published: January 2006

Notions of chaotic behavior burst into the popular consciousness two decades ago.1 Since then a number of tabletop experiments2 have been devised for the classroom and teaching laboratory. In that vein we describe a readily assembled impact oscillator and present the use of phase-space plots in its study. It can be shown as a chaos demonstration or incorporated into a laboratory exercise. Its behavior is rich enough that it can also be studied as an open-ended project.3
Accelerating Around an Unbanked Curve
Authors: Mungan Carl E.
Published: January 2006

The December 2004 issue of TPT presented a problem concerning how a car should accelerate around an unbanked curve of constant radius r starting from rest if it is to avoid skidding.1 Interestingly enough, two solutions were proffered by readers.2 The purpose of this note is to compare and contrast the two approaches. Further experimental investigation of various turning strategies using a remote-controlled car and overhead video analysis could make for an interesting student project.
The Learning Cycle: A Reintroduction
Authors: Maier Steven J. , Marek Edmund A.
Published: January 2006

The learning cycle is an inquiry approach to instruction that continues to demonstrate significant effectiveness in the classroom.1–3 Rooted in Piaget's theory of intellectual development, learning cycles provide a structured means for students to construct concepts from direct experiences with science phenomena. Learning cycles have been the subject of numerous articles in science practitioner periodicals as well as the focus of much research in science education journals.4 This paper reintroduces the learning cycle by giving a brief description, followed by an example suitable for a range of physics classrooms.
Convert Your Common Physical Balance into a Microbalance
Authors: Inbanathan S. S. R. , Balasubramanian G.
Published: January 2006

The common physical balance consists of a beam supported at the center by a knife edge made of steel or agate. This knife edge rests on a plate of hard material fixed to the top of the pillar. At the two ends of the beam and at equal distances from the central knife edge, there are two knife edges pointing upward. From these are hung two stirrups that carry scale pans of equal masses. A pointer is attached to the middle of the beam perpendicular to it and this moves over an ivory scale fixed at the bottom of the pillar. This is the simple description of the common physical balance. By fixing a reflector and mirror, this can be converted into a very sensible balance and can even be used as a microbalance.
Assign a Writing Task to Improve Student Engagement at Public Lectures
Authors: Slater Timothy F.
Published: January 2006

Did you see the news? A famous scientist is going to be visiting a museum nearby and is giving a public lecture. You'll probably think to yourself, “Wow, this is a unique opportunity I want my students to experience!” But, as a new teacher, you might be totally surprised just how little students sometimes seem to gain from attending even the most entertaining public lecture. It seems to me that if we are knowledgeable about the processes of effective teaching and learning, we might be able to improve the chances that students will have a positive and perhaps life-guiding experience.
The Ste5 Scaffold Allosterically Modulates Signaling Output of the Yeast Mating Pathway
Authors: Bhattacharyya Roby P. , Reményi Attila , Good Matthew C. , Bashor Caleb J. , Falick Arnold M. , Lim Wendell A.
Published: January 2006

Scaffold proteins organize signaling proteins into pathways and are often viewed as passive assembly platforms. We found that the Ste5 scaffold has a more active role in the yeast mating pathway: A fragment of Ste5 allosterically activated autophosphorylation of the mitogen-activated protein kinase Fus3. The resulting form of Fus3 is partially active—it is phosphorylated on only one of two key residues in the activation loop. Unexpectedly, at a systems level, autoactivated Fus3 appears to have a negative regulatory role, promoting Ste5 phosphorylation and a decrease in pathway transcriptional output. Thus, scaffolds not only direct basic pathway connectivity but can precisely tune quantitative pathway input-output properties.
Characterization of the Biosynthetic Pathway of Glucosylglycerate in the Archaeon
Methanococcoides burtonii
Authors: Costa Joana , Empadinhas Nuno , Gonçalves Luís , Lamosa Pedro , Santos Helena , da Costa Milton S.
Published: January 2006

The pathway for the synthesis of the organic solute glucosylglycerate (GG) is proposed based on the activities of the recombinant glucosyl-3-phosphoglycerate synthase (GpgS) and glucosyl-3-phosphoglycerate phosphatase (GpgP) from
Methanococcoides burtonii
. A mannosyl-3-phosphoglycerate phosphatase gene homologue (
mpgP
) was found in the genome of
M. burtonii
(
http://www.jgi.doe.gov
), but an
mpgS
gene coding for mannosyl-3-phosphoglycerate synthase (MpgS) was absent. The gene upstream of the
mpgP
homologue encoded a putative glucosyltransferase that was expressed in
Escherichia coli
. The recombinant product had GpgS activity, catalyzing the synthesis of glucosyl-3-phosphoglycerate (GPG) from GDP-glucose and
d
-3-phosphoglycerate, with a high substrate specificity. The recombinant MpgP protein dephosphorylated GPG to GG and was also able to dephosphorylate mannosyl-3-phosphoglycerate (MPG) but no other substrate tested. Similar flexibilities in substrate specificity were confirmed in vitro for the MpgPs from
Thermus thermophilus
,
Pyrococcus horikoshii
, and “
Dehalococcoides ethenogenes
.” GpgS had maximal activity at 50°C. The maximal activity of GpgP was at 50°C with GPG as the substrate and at 60°C with MPG. Despite the similarity of the sugar donors GDP-glucose and GDP-mannose, the enzymes for the synthesis of GPG or MPG share no amino acid sequence identity, save for short motifs. However, the hydrolysis of GPG and MPG is carried out by phosphatases encoded by homologous genes and capable of using both substrates. To our knowledge, this is the first report of the elucidation of a biosynthetic pathway for glucosylglycerate.
Complex Regulation of Arsenite Oxidation in
Agrobacterium tumefaciens
Authors: Kashyap Des R. , Botero Lina M. , Franck William L. , Hassett Daniel J. , McDermott Timothy R.
Published: January 2006

Seminal regulatory controls of microbial arsenite [As(III)] oxidation are described in this study. Transposon mutagenesis of
Agrobacterium tumefaciens
identified genes essential for As(III) oxidation, including those coding for a two-component signal transduction pair. The transposon interrupted a response regulator gene (referred to as
aoxR
), which encodes an
ntrC
-like protein and is immediately downstream of a gene (
aoxS
) encoding a protein with primary structural features found in sensor histidine kinases. The structural genes for As(III) oxidase (
aoxAB
), a
c
-type cytochrome (
cytc
2
), and molybdopterin biosynthesis (
chlE
) were downstream of
aoxR
. The mutant could not be complemented by
aoxSR
in
trans
but was complemented by a clone containing
aoxS
-
aoxR
-
aoxA
-
aoxB
-
cytc
2
and consistent with reverse transcriptase (RT) PCR experiments, which demonstrated these genes are cotranscribed as an operon. Expression of
aoxAB
was monitored by RT-PCR and found to be up-regulated by the addition of As(III) to cell cultures. Expression of
aoxAB
was also controlled in a fashion consistent with quorum sensing in that (i) expression of
aoxAB
was absent in As(III)-unexposed early-log-phase cells but was observed in As(III)-unexposed, late-log-phase cells and (ii) treating As(III)-unexposed, early-log-phase cells with ethyl acetate extracts of As(III)-unexposed, late-log-phase culture supernatants also resulted in
aoxAB
induction. Under inducing conditions,
aoxS
expression was readily observed in the wild-type strain but significantly reduced in the mutant, indicating that AoxR is autoregulatory and at least partially controls the expression of the
aox
operon. In summary, regulation of
A. tumefaciens
As(III) oxidation is complex, apparently being controlled by As(III) exposure, a two-component signal transduction system, and quorum sensing.
The Fnr Regulon of
Bacillus subtilis
Authors: Reents Heike , Münch Richard , Dammeyer Thorben , Jahn Dieter , Härtig Elisabeth
Published: January 2006

The
Bacillus subtilis
transcriptional regulator Fnr is an integral part of the regulatory cascade required for the adaptation of the bacterium to low oxygen tension. The
B. subtilis
Fnr regulon was defined via transcriptomic analysis in combination with bioinformatic-based binding site prediction. Four distinct groups of Fnr-dependent genes were observed. Group 1 genes (
narKfnr
,
narGHJI
, and
arfM
) are generally induced by Fnr under anaerobic conditions. All corresponding promoters contain an essential Fnr-binding site centered −41.5/−40.5 bp upstream of the transcriptional start point, suggesting their induction by direct Fnr interaction. Group 2 genes (
alsSD
,
ldh lctP
,
ywcJ
, and
cydABCD
) are characterized by anaerobic repression in the presence of nitrate. Mutational analysis of the Fnr-binding sites found in three of the corresponding promoters excluded their function in Fnr-mediated repression. Genetic evidence showing that group 2 genes are anaerobically repressed by nitrate reductase formation was accumulated. A possible role of the redox regulator YdiH in the regulation of group 2 genes was initially investigated. Group 3 genes are characterized by their Fnr-dependent activation in the presence of nitrate and the lack of an Fnr-binding site in their promoters. The analysis of Group 3 gene transcription (
ykuNOP
and
ydbN
) indicated that Fnr induces nitrate reductase production, which leads to the formation of the regulatory compound nitrite from nitrate. Finally, the group 4 operon
acoABCL
, lacking an Fnr-binding site, requires Fnr-dependent nitrate reductase formation for its general anaerobic induction. A regulatory model for the observed complex Fnr-mediated gene expression was deduced.
Serotype Differences and Lack of Biofilm Formation Characterize
Yersinia pseudotuberculosis
Infection of the
Xenopsylla cheopis
Flea Vector of
Yersinia pestis
Authors: Erickson David L. , Jarrett Clayton O. , Wren Brendan W. , Hinnebusch B. Joseph
Published: January 2006

Yersinia pestis
, the agent of plague, is usually transmitted by fleas. To produce a transmissible infection,
Y. pestis
colonizes the flea midgut and forms a biofilm in the proventricular valve, which blocks normal blood feeding. The enteropathogen
Yersinia pseudotuberculosis
, from which
Y. pestis
recently evolved, is not transmitted by fleas. However, both
Y. pestis
and
Y. pseudotuberculosis
form biofilms that adhere to the external mouthparts and block feeding of
Caenorhabditis elegans
nematodes, which has been proposed as a model of
Y. pestis
-flea interactions. We compared the ability of
Y. pestis
and
Y. pseudotuberculosis
to infect the rat flea
Xenopsylla cheopis
and to produce biofilms in the flea and in vitro. Five of 18
Y. pseudotuberculosis
strains, encompassing seven serotypes, including all three serotype O3 strains tested, were unable to stably colonize the flea midgut. The other strains persisted in the flea midgut for 4 weeks but did not increase in numbers, and none of the 18 strains colonized the proventriculus or produced a biofilm in the flea.
Y. pseudotuberculosis
strains also varied greatly in their ability to produce biofilms in vitro, but there was no correlation between biofilm phenotype in vitro or on the surface of
C. elegans
and the ability to colonize or block fleas. Our results support a model in which a genetic change in the
Y. pseudotuberculosis
progenitor of
Y. pestis
extended its pre-existing ex vivo biofilm-forming ability to the flea gut environment, thus enabling proventricular blockage and efficient flea-borne transmission.
Horizontal Gene Transfer and the Evolution of Microvirid Coliphage Genomes
Authors: Rokyta D. R. , Burch C. L. , Caudle S. B. , Wichman H. A.
Published: January 2006

Bacteriophage genomic evolution has been largely characterized by rampant, promiscuous horizontal gene transfer involving both homologous and nonhomologous source DNA. This pattern has emerged through study of the tailed double-stranded DNA (dsDNA) phages and is based upon a sparse sampling of the enormous diversity of these phages. The single-stranded DNA phages of the family
Microviridae
, including φX174, appear to evolve through qualitatively different mechanisms, possibly as result of their strictly lytic lifestyle and small genome size. However, this apparent difference could reflect merely a dearth of relevant data. We sought to characterize the forces that contributed to the molecular evolution of the
Microviridae
and to examine the genetic structure of this single family of bacteriophage by sequencing the genomes of microvirid phage isolated on a single bacterial host. Microvirids comprised 3.5% of the detectable phage in our environmental samples, and sequencing yielded 42 new microvirid genomes. Phylogenetic analysis of the genes contained in these and five previously described microvirid phages identified three distinct clades and revealed at least two horizontal transfer events between clades. All members of one clade have a block of five putative genes that are not present in any member of the other two clades. Our data indicate that horizontal transfer does contribute to the evolution of the microvirids but is both quantitatively and qualitatively different from what has been observed for the dsDNA phages.
Structural and Functional Studies Suggest a Catalytic Mechanism for the Phosphotransacetylase from
Methanosarcina thermophila
Authors: Lawrence Sarah H. , Luther Kelvin B. , Schindelin Hermann , Ferry James G.
Published: January 2006

Phosphotransacetylase (EC 2.3.1.8) catalyzes reversible transfer of the acetyl group from acetyl phosphate to coenzyme A (CoA), forming acetyl-CoA and inorganic phosphate. Two crystal structures of phosphotransacetylase from the methanogenic archaeon
Methanosarcina thermophila
in complex with the substrate CoA revealed one CoA (CoA
1
) bound in the proposed active site cleft and an additional CoA (CoA
2
) bound at the periphery of the cleft. The results of isothermal titration calorimetry experiments are described, and they support the hypothesis that there are distinct high-affinity (equilibrium dissociation constant [

K
D

], 20 μM) and low-affinity (

K
D

, 2 mM) CoA binding sites. The crystal structures indicated that binding of CoA
1
is mediated by a series of hydrogen bonds and extensive van der Waals interactions with the enzyme and that there are fewer of these interactions between CoA
2
and the enzyme. Different conformations of the protein observed in the crystal structures suggest that domain movements which alter the geometry of the active site cleft may contribute to catalysis. Kinetic and calorimetric analyses of site-specific replacement variants indicated that there are catalytic roles for Ser
309
and Arg
310
, which are proximal to the reactive sulfhydryl of CoA
1
. The reaction is hypothesized to proceed through base-catalyzed abstraction of the thiol proton of CoA by the adjacent and invariant residue Asp
316
, followed by nucleophilic attack of the thiolate anion of CoA on the carbonyl carbon of acetyl phosphate. We propose that Arg
310
binds acetyl phosphate and orients it for optimal nucleophilic attack. The hypothesized mechanism proceeds through a negatively charged transition state stabilized by hydrogen bond donation from Ser
309
.
Suppression of Engulfment Defects inBacillus subtilisby Elevated Expression of the Motility Regulon
Authors: Perez Ana R. , Abanes-De Mello Angelica , Pogliano Kit
Published: January 2006

DuringBacillus subtilissporulation, the transient engulfment defect ofspoIIBstrains is enhanced byspoVGnull mutations and suppressed byspoVSnull mutations. These mutations have opposite effects on expression of the motility regulon, as thespoVGmutation reduces and thespoVSmutation increases σD-directed gene expression, cell separation, and autolysis. Elevating σDactivity by eliminating the anti-σ factor FlgM also suppressesspoIIB spoVG, and bothflgMandspoVSmutations cause continued expression of the σDregulon during sporulation. We propose that peptidoglycan hydrolases induced during motility can substitute for sporulation-specific hydrolases during engulfment. We find that sporulating cells are heterogeneous in their expression of the motility regulon, which could result in phenotypic variation between individual sporulating cells.
A
Bacteroides
Conjugative Transposon, CTnERL, Can Transfer a Portion of Itself by Conjugation without Excising from the Chromosome
Authors: Whittle Gabrielle , Hamburger Nathan , Shoemaker Nadja B. , Salyers Abigail A.
Published: January 2006

CTnERL, a
Bacteroides
conjugative transposon, transferred DNA by an Hfr-type mechanism during conjugation when it was excision deficient due to an insertion in the integrase gene. Rescue of the conjugative transposon sequences required the recipient to be RecA proficient and to contain an integrated CTnERL. The transfer efficiency was only 10- to 30-fold lower than the normal element transfer efficiency, and the direction of transfer from the
oriT
gene showed that the integrase end was transferred first and that the transfer genes were transferred last.
Salmonella enterica
Strains Lacking the Frataxin Homolog CyaY Show Defects in Fe-S Cluster Metabolism In Vivo
Authors: Vivas E. , Skovran E. , Downs D. M.
Published: January 2006

In
Salmonella enterica
, the
isc
operon contains genes necessary for the synthesis of Fe-S clusters and strains lacking this operon have severe defects in a variety of cellular processes. Other cellular loci that impact Fe-S cluster synthesis to a lesser extent have been described. The
cyaY
locus encodes a frataxin homolog, and it is shown here that lesions in this locus affect Fe-S cluster metabolism. When present in combination with other lesions, mutations in
cyaY
can result in a strain with more severe defects than those lacking the
isc
locus.
A
pmrA
Constitutive Mutant Sensitizes
Escherichia coli
to Deoxycholic Acid
Authors: Froelich Jamie M. , Tran Khoa , Wall Daniel
Published: January 2006

An
Escherichia coli
mutant was isolated and shown to be polymyxin B resistant. Mapping and sequence analysis revealed a missense mutation at codon 53 within the
pmrA
(
basR
) gene that results in a G-to-V substitution. Fusions of promoters from the
pmrC
,
yibD
, and
pmrH
genes with the
lacZ
reporter showed that they were constitutively expressed in
pmrA53
cells. In
pmrA
+
strains, these promoters were induced by iron and zinc, while a Δ
pmrA
mutation blocked induction. The PmrA regulon regulates genes whose products remodel the composition and charge of lipid A and hence the barrier properties of the outer membrane. Along these lines, the
pmrA53
mutant was also found to be hypersensitive to the anionic bile detergent deoxycholic acid.
Topologically Fixed SecG Is Fully Functional
Authors: van der Sluis Eli O. , van der Vries Erhard , Berrelkamp Greetje , Nouwen Nico , Driessen Arnold J. M.
Published: January 2006

It has been proposed that the bitopic membrane protein SecG undergoes topology inversion during translocation of (pre)proteins via SecYEG. Here we show that SecG covalently cross-linked to SecY cannot invert its topology while remaining fully functional in protein translocation. Our results strongly disfavor topology inversion of SecG during protein translocation.
Transcriptional Slippage in
mxiE
Controls Transcription and Translation of the Downstream
mxiD
Gene, Which Encodes a Component of the
Shigella flexneri
Type III Secretion Apparatus
Authors: Penno Christophe , Parsot Claude
Published: January 2006

The
Shigella flexneri
transcription activator MxiE is produced by transcriptional slippage from two overlapping open reading frames. By using plasmids encoding a
mxiD-lacZ
translational fusion, we showed that transcriptional slippage in
mxiE
influences both transcription and translation of the downstream
mxiD
gene encoding an essential component of the type III secretion apparatus.
Transcriptome Analysis Applied to Survival of
Shewanella oneidensis
MR-1 Exposed to Ionizing Radiation
Authors: Qiu Xiaoyun , Daly Michael J. , Vasilenko Alexander , Omelchenko Marina V. , Gaidamakova Elena K. , Wu Liyou , Zhou Jizhong , Sundin George W. , Tiedje James M.
Published: January 2006

The ionizing radiation (IR) dose that yields 20% survival (D
20
) of
Shewanella oneidensis
MR-1 is lower by factors of 20 and 200 than those for
Escherichia coli
and
Deinococcus radiodurans
, respectively. Transcriptome analysis was used to identify the genes of MR-1 responding to 40 Gy (D
20
). We observed the induction of 170 genes and repression of 87 genes in MR-1 during a 1-h recovery period after irradiation. The genomic response of MR-1 to IR is very similar to its response to UV radiation (254 nm), which included induction of systems involved in DNA repair and prophage synthesis and the absence of differential regulation of tricarboxylic acid cycle activity, which occurs in IR-irradiated
D. radiodurans
. Furthermore, strong induction of genes encoding antioxidant enzymes in MR-1 was observed. DNA damage may not be the principal cause of high sensitivity to IR, considering that MR-1 carries genes encoding a complex set of DNA repair systems and 40 Gy IR induces less than one double-strand break in its genome. Instead, a combination of oxidative stress, protein damage, and prophage-mediated cell lysis during irradiation and recovery might underlie this organism's great sensitivity to IR.
Analysis of the Lateral Flagellar Gene System ofAeromonas hydrophilaAH-3
Authors: Canals Rocío , Altarriba Maria , Vilches Silvia , Horsburgh Gavin , Shaw Jonathan G. , Tomás Juan M. , Merino Susana
Published: January 2006

MesophilicAeromonasstrains express a polar flagellum in all culture conditions, and certain strains produce lateral flagella on semisolid media or on surfaces. AlthoughAeromonaslateral flagella have been described as a colonization factor, little is known about their organization and expression. Here we characterized the complete lateral flagellar gene cluster ofAeromonas hydrophilaAH-3 containing 38 genes, 9 of which (lafA-U) have been reported previously. Among theflgLLandlafAstructural genes we found a modification accessory factor gene (maf-5) that is involved in formation of lateral flagella; this is the first time that such a gene has been described for lateral flagellar gene systems. AllAeromonaslateral flagellar genes were located in a unique chromosomal region, in contrast toVibrio parahaemolyticus, in which the analogous genes are distributed in two different chromosomal regions. InA. hydrophilamutations inflhAL,lafK,fliJL,flgNL,flgEL, andmaf-5resulted in a loss of lateral flagella and reductions in adherence and biofilm formation, but they did not affect polar flagellum synthesis. Furthermore, we also cloned and sequenced theA. hydrophilaAH-3 alternative sigma factor σ54(rpoN); mutation of this factor suggested that it is involved in expression of both types of flagella.
Topology and Boundaries of the Aerotaxis Receptor Aer in the Membrane ofEscherichia coli
Authors: Amin Divya N. , Taylor Barry L. , Johnson Mark S.
Published: January 2006

Escherichia colichemoreceptors are type I membrane receptors that have a periplasmic sensing domain, a cytosolic signaling domain, and two transmembrane segments. The aerotaxis receptor, Aer, is different in that both its sensing and signaling regions are proposed to be cytosolic. This receptor has a 38-residue hydrophobic segment that is thought to form a membrane anchor. Most transmembrane prediction programs predict a single transmembrane-spanning segment, but such a topology is inconsistent with recent studies indicating that there is direct communication between the membrane flanking PAS and HAMP domains. We studied the overall topology and membrane boundaries of the Aer membrane anchor by a cysteine-scanning approach. The proximity of 48 cognate cysteine replacements in Aer dimers was determined in vivo by measuring the rate and extent of disulfide cross-linking after adding the oxidant copper phenanthroline, both at room temperature and to decrease lateral diffusion in the membrane, at 4°C. Membrane boundaries were identified in membrane vesicles using 5-iodoacetamidofluorescein and methoxy polyethylene glycol 5000 (mPEG). To map periplasmic residues, accessible cysteines were blocked in whole cells by pretreatment with 4-acetamido-4′-maleimidylstilbene-2, 2′ disulfonic acid before the cells were lysed in the presence of mPEG. The data were consistent with two membrane-spanning segments, separated by a short periplasmic loop. Although the membrane anchor contains a central proline residue that reaches the periplasm, its position was permissive to several amino acid and peptide replacements.
Peptidoglycan O Acetylation and Autolysin Profile ofEnterococcus faecalisin the Viable but Nonculturable State
Authors: Pfeffer John M. , Strating Hendrik , Weadge Joel T. , Clarke Anthony J.
Published: January 2006

The O acetylation of peptidoglycan occurs specifically at the C-6 hydroxyl group of muramoyl residues. Using a combination of high-performance liquid chromatography-based organic acid analysis and carbohydrate analysis by high-pH anion-exchange chromatography, we determined that strains ofEntercoccus durans,E. faecalis,E. faecium, andE. hiraeproduce O-acetylated peptidoglycan. The levels of O acetylation ranged from 19% to 72% relative to the muramic acid content, and they were found to vary with the growth phase of the culture. Increases of 10 to 40% in O acetylation were observed with cultures entering the stationary phase. Cells ofE. faecalisin the viable but nonculturable (VBNC) state had the highest levels of peptidoglycan O acetylation. The presence of this modification to peptidoglycan was shown to inhibit the action of hen egg white lysozyme in a concentration-dependent manner. Zymography using sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels containing either O-acetylated or chemically de-O-acetylated peptidoglycan was used to monitor the production of specific autolysins inE. faecalis. Differences in the expression of specific autolysins were observed with the age of the culture, and VBNCE. faecalisproduced the highest levels of these enzymes. This technique also permitted classification of the enterococcal autolysins into enzymes that preferentially hydrolyze either O-acetylated or non-O-acetylated peptidoglycan and enzymes that show no apparent preference for either substrate type.
Function and Evolution of Plasmid-Borne Genes for Pyrimidine Biosynthesis inBorreliaspp
Authors: Zhong Jianmin , Skouloubris Stephane , Dai Qiyuan , Myllykallio Hannu , Barbour Alan G.
Published: January 2006

ThethyXgene for thymidylate synthase of the Lyme borreliosis (LB) agentBorrelia burgdorferiis located in a 54-kb linear plasmid. In the present study, we identified an orthologous thymidylate synthase gene in the relapsing fever (RF) agentBorrelia hermsii, located it in a 180-kb linear plasmid, and demonstrated its expression. The functions of theB. hermsiiandB. burgdorferi thyXgene products were evaluated both in vivo, by complementation of a thymidylate synthase-deficientEscherichia colimutant, and in vitro, by testing their activities after purification. TheB. hermsii thyXgene complemented thethyAmutation inE. coli, and purifiedB. hermsiiThyX protein catalyzed the conversion of dTMP from dUMP. In contrast, theB. burgdorferiThyX protein had only weakly detectable activity in vitro, and theB. burgdorferi thyXgene did not provide complementation in vivo. The lack of activity ofB. burgdorferi's ThyX protein was associated with the substitution of a cysteine for a highly conserved arginine at position 91. TheB. hermsii thyXlocus was further distinguished by the downstream presence in the plasmid of orthologues ofnrdI,nrdE, andnrdF, which encode the subunits of ribonucleoside diphosphate reductase and which are not present in the LB agentsB. burgdorferiandBorrelia garinii. Phylogenetic analysis suggested that thenrdIEFcluster ofB. hermsiiwas acquired by horizontal gene transfer. These findings indicate thatBorreliaspp. causing RF have a greater capability for de novo pyrimidine synthesis than those causing LB, thus providing a basis for some of the biological differences between the two groups of pathogens.
Arginine-Dependent Gene Regulation via the ArgR Repressor Is Species Specific inChlamydia
Authors: Schaumburg Chris S. , Tan Ming
Published: January 2006

Some, but not all,Chlamydiaspp. are predicted to encode a homolog of ArgR, a master regulatory molecule that modulates arginine biosynthesis and catabolism in bacteria in response to intracellular arginine levels. While genes for arginine biosynthesis are apparently missing inChlamydia, a putative arginine transport system encoded byglnP,glnQ, andartJis present. We found that recombinantChlamydia pneumoniaeArgR functions as an arginine-dependent aporepressor that bound specifically to operator sequences upstream of theglnPQoperon. ArgR was able to repress transcription in a promoter-specific manner that was dependent on the concentration of the corepressorl-arginine. We were able to locate ArgR operators upstream ofglnPQinC. pneumoniaeandChlamydophila caviaebut notChlamydia trachomatis, which corresponded to the predicted presence or absence of ArgR in these chlamydial species. Our findings indicate that only some members of the familyChlamydiaceaehave an arginine-responsive mechanism of gene regulation that is predicted to control arginine uptake from the host cell. This is the first study to directly demonstrate a species-specific mechanism of transcriptional regulation inChlamydia.
Two DNA Invertases Contribute to Flagellar Phase Variation in
Salmonella enterica
Serovar Typhimurium Strain LT2
Authors: Kutsukake Kazuhiro , Nakashima Hisashi , Tominaga Akira , Abo Tatsuhiko
Published: January 2006

Salmonella enterica
serovar Typhimurium strain LT2 possesses two nonallelic structural genes,
fliC
and
fljB
, for flagellin, the component protein of flagellar filaments. Flagellar phase variation occurs by alternative expression of these two genes. This is controlled by the inversion of a DNA segment, called the H segment, containing the
fljB
promoter. H inversion occurs by site-specific recombination between inverted repetitious sequences flanking the H segment. This recombination has been shown in vivo and in vitro to be mediated by a DNA invertase, Hin, whose gene is located within the H segment. However, a search of the complete genomic sequence revealed that LT2 possesses another DNA invertase gene that is located adjacent to another invertible DNA segment within a resident prophage, Fels-2. Here, we named this gene
fin
. We constructed
hin
and
fin
disruption mutants from LT2 and examined their phase variation abilities. The
hin
disruption mutant could still undergo flagellar phase variation, indicating that Hin is not the sole DNA invertase responsible for phase variation. Although the
fin
disruption mutant could undergo phase variation,
fin hin
double mutants could not. These results clearly indicate that both Hin and Fin contribute to flagellar phase variation in LT2. We further showed that a phase-stable serovar, serovar Abortusequi, which is known to possess a naturally occurring
hin
mutation, lacks Fels-2, which ensures the phase stability in this serovar.
FljA-Mediated Posttranscriptional Control of Phase 1 Flagellin Expression in Flagellar Phase Variation of
Salmonella enterica
Serovar Typhimurium
Authors: Yamamoto Shouji , Kutsukake Kazuhiro
Published: January 2006

Flagellar phase variation of
Salmonella
is a phenomenon where two flagellin genes,
fliC
(phase 1) and
fljB
(phase 2), are expressed alternately. This is controlled by the inversion of a DNA segment containing the promoter for the
fljB
gene. The
fljB
gene constitutes an operon with the
fljA
gene, which encodes a negative regulator for
fliC
expression. Previous biochemical analysis suggested that phase variation might depend on alternative synthesis of phase-specific flagellin mRNA (H. Suzuki and T. Iino, J. Mol. Biol.
81:
57-70, 1973). However, recently reported results suggested that FljA-dependent inhibition might be mediated by a posttranscriptional control mechanism (H. R. Bonifield and K. T. Hughes, J. Bacteriol.
185:
3567-3574, 2003). In this study, we reexamined the mechanism of FljA-mediated inhibition of
fliC
expression more carefully. Northern blotting analysis revealed that no
fliC
mRNA was detected in phase 2 cells. However, only a moderate decrease in β-galactosidase activity was observed from the
fliC-lacZ
transcriptional fusion gene in phase 2 cells compared with that in phase 1 cells. In contrast, the expression of the
fliC-lacZ
translational fusion gene was severely impaired in phase 2 cells. The half-life of
fliC
mRNA was shown to be much shorter in phase 2 cells than in phase 1 cells. Purified His-tagged FljA protein was shown to bind specifically to
fliC
mRNA and inhibit the translation from
fliC
mRNA in vitro. On the basis of these results, we propose that in phase 2 cells, FljA binds to
fliC
mRNA and inhibits its translation, which in turn facilitates its degradation.
GTPase Activity, Structure, and Mechanical Properties of Filaments Assembled from Bacterial Cytoskeleton Protein MreB
Authors: Esue Osigwe , Wirtz Denis , Tseng Yiider
Published: January 2006

MreB, a major component of the recently discovered bacterial cytoskeleton, displays a structure homologous to its eukaryotic counterpart actin. Here, we study the assembly and mechanical properties of
Thermotoga maritima
MreB in the presence of different nucleotides in vitro. We found that GTP, not ADP or GDP, can mediate MreB assembly into filamentous structures as effectively as ATP. Upon MreB assembly, both GTP and ATP release the gamma phosphate at similar rates. Therefore, MreB is an equally effective ATPase and GTPase. Electron microscopy and quantitative rheology suggest that the morphologies and micromechanical properties of filamentous ATP-MreB and GTP-MreB are similar. In contrast, mammalian actin assembly is favored in the presence of ATP over GTP. These results indicate that, despite high structural homology of their monomers,
T. maritima
MreB and actin filaments display different assembly, morphology, micromechanics, and nucleotide-binding specificity. Furthermore, the biophysical properties of
T. maritima
MreB filaments, including high rigidity and propensity to form bundles, suggest a mechanism by which MreB helical structure may be involved in imposing a cylindrical architecture on rod-shaped bacterial cells.
A
selC
-Associated Genomic Island of the Extraintestinal Avian Pathogenic
Escherichia coli
Strain BEN2908 Is Involved in Carbohydrate Uptake and Virulence
Authors: Chouikha Iman , Germon Pierre , Brée Annie , Gilot Philippe , Moulin-Schouleur Maryvonne , Schouler Catherine
Published: January 2006

The complete nucleotide sequence and genetic organization of a new genomic island (AGI-3) isolated from the extraintestinal avian pathogenic
Escherichia coli
strain BEN2908 is reported. This 49,600-bp island is inserted at the
selC
locus and contains putative mobile genetic elements such as a phage-related integrase gene, transposase genes, and direct repeats. AGI-3 shows a mosaic structure of five modules. Some of these modules are present in other
E. coli
strains and in other pathogenic bacterial species. The gene cluster
aec-35
to
aec-37
of module 1 encodes proteins associated with carbohydrates assimilation such as a major facilitator superfamily transporter (Aec-36), a glycosidase (Aec-37), and a putative transcriptional regulator of the LacI family (Aec-35). The
aec-35
to
aec-37
cluster was found in 11.6% of the tested pathogenic and nonpathogenic
E. coli
strains. When present, the
aec-35
to
aec-37
cluster is strongly associated with the
selC
locus (97%). Deletion of the
aec-35-aec-37
region affects the assimilation of seven carbohydrates, decreases the growth rate of the strain in minimal medium containing galacturonate or trehalose, and attenuates the virulence of
E. coli
BEN2908 for chickens.
Regulation of the Glucosyltransferase (
gtfBC
) Operon by CovR in
Streptococcus mutans
Authors: Biswas Saswati , Biswas Indranil
Published: January 2006

Streptococcus mutans
is an important etiological agent of dental caries in humans. The extracellular polysaccharides synthesized by cell-associated glucosyltransferases (encoded by
gtfBC
) from sucrose have been recognized as one of the important virulence factors that promote cell aggregation and adherence to teeth, leading to dental plaque formation. In this study, we have characterized the effect of CovR, a global response regulator, on glucosyltransferase expression. Inactivation of
covR
in strain UA159 resulted in a marked increase in the GtfB and GtfC proteins, as analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. With the use of a transcriptional reporter system of a single chromosomal copy of the P
gtfB
-
gusA
and P
gtfC
-
gusA
fusions, we confirmed the transcriptional regulation of these promoters by CovR. By in vitro electrophoretic mobility shift assays with purified CovR protein, we showed that CovR regulates these promoters directly. DNase I footprinting analyses suggest that CovR binds to large regions on these promoters near the transcription start sites. Taken together, our results indicate that CovR negatively regulates the expression of the
gtfB
and
gtfC
genes by directly binding to the promoter region.
GENERICITY AND LARGE CARDINALS
Authors: FRIEDMAN Sy. D.
Published: January 2006

We lift Jensen's coding method into the context of Woodin cardinals. By a theorem of Woodin, any real which preserves a "strong witness" to Woodinness is set-generic. We show however that there are class-generic reals which are not set-generic but preserve Woodinness, using "weak witnesses".