bluuebunny/crossref_metadata_2025 huggingface dataset:
ASSOCIATION OF MHC CLASS I WITH SPONDYLOARTHROPATHIES IN KUWAIT
Authors: Alharbi S.A. , Mahmoud F.F. , AwAdi A. Al , Jumma R.A. Al , Khodakhast F. , Alsulaiman S.M.
Published: April 2007

This study is the first to assess the prevalence of HLA B27 in Kuwaiti patients with ankylosing spondylitis (AS) or related spondyloarthropathies compared to healthy controls. Positive HLA B27 was found in nine (25.7%) of 35 patients, but only in 22 (4%) of 544 controls (P = 0.000). A significant difference in Cw2 and Cw6 between patients and controls was also found (P < 0.01 and 0.000, respectively), suggesting a linkage disequilibrium between B27 and Cw2 (P < 0.000) in the Kuwaiti population. These findings suggest that B27‐positive Kuwaitis are at high risk of developing AS and spondyloarthropathies, especially if they carry Cw2 and Cw6. The importance of HLA Cw loci is becoming increasingly apparent in disease association studies.
INVESTIGATION OF THE ASSOCIATION OF MAJOR HISTOCOMPATIBILITY COMPLEX GENES, INCLUDING HLA CLASS I, CLASS II and TAP GENES, WITH CLINICAL FORMS OF CROHN'S DISEASE
Authors: Hesresbach D. , Alizadeh M. , Bretagne J.F. , Gautier A. , Quillivic F. , Lemarchand B. , Gosselin M. , Genetet B. , Semana G.
Published: April 2007

The aim of this study was to determine immunogenetic markers of susceptibility in Crohn's disease (CD), taking the different features of the clinical course of the disease into account. HLA class I, HLA class II and TAP transporter gene polymorphisms were studied using DNA typing methods. Gene and antigen frequencies were analysed and compared in a group of 102 CD patients and 200 unrelated healthy controls from the same area. Analysis of the whole CD patient population revealed no definite association with either HLA or TAP gene alleles, with the exception of an association with DRB1*1302 (Pc < 0.05). However, when clinical subgroups of patients were considered, specific associations with some genetic markers were found. The most definitive results involved a genetic association in the group of patients who did not respond to glucocorticoid therapy. This group was characterized by a high frequency of HLA‐DRB1*04 (P < 0.05). Conversely, a positive association with the TAP2‐A allele was found in cortico‐responder patients (Pc < 0.03). Furthermore, analysis of the distribution of HLA class II alleles in relation to the presence of extra‐intestinal manifestations revealed an association with the DQB 1*0501 or *0503 suballele of DQ5 (P < 0.05). Finally, patients with lesions in the small bowel were more frequently HLA DRB1 *07 (P < 0.05). The present study supports the concept of clinical heterogeneity in Crohn's disease associated with a background of genetic heterogeneity.
Sociodemographic Differences in Depressed Mood: Results From a Nationally Representative Sample of High School Adolescents
Authors: Paxton Raheem J. , Valois Robert F. , Watkins Ken W. , Huebner E. Scott , Drane J. Wanzer
Published: April 2007

Background:  Research on adolescent mental health suggests that prevalence rates for depressed mood are not uniformly distributed across all populations. This study examined demographic difference in depressed mood among a nationally representative sample of high school adolescents.

Methods:  The 2003 National Youth Risk Behavior Survey was utilized to examine the association between depressed mood and demographic variables. To examine demographic associations, chi‐square and follow‐up logistic regression models were created for the sample of high school adolescents (N = 15,214).

Results:  Caucasians and African Americans were significantly less likely to report depressed mood when compared to Hispanics and Others. Women were also more likely than men to report depressed mood. No significant differences were observed among levels of urbanicity and age.

Conclusions:  An understanding of the difference in the prevalence and correlates of depressed mood among adolescents of various ethnic/racial and gender groups deserves increased attention. Given the fact that challenges with depressed mood in adolescents can be substantial and relatively unrecognized, there is an increased need to identify these adolescents early and intervene with culturally appropriate interventions.
Modeling comodulation masking release using an equalization-cancellation mechanism
Authors: Piechowiak Tobias , Ewert Stephan D. , Dau Torsten
Published: April 2007

This study presents an auditory processing model that accounts for the perceptual phenomenon of comodulation masking release (CMR). The model includes an equalization-cancellation (EC) stage for the processing of activity across the audio-frequency axis. The EC process across frequency takes place at the output of a modulation filterbank assumed for each audio-frequency channel. The model was evaluated in three experimental conditions: (i) CMR with four widely spaced flanking bands in order to study pure across-channel processing, (ii) CMR with one flanking band varying in frequency in order to study the transition between conditions dominated by within-channel processing and those dominated by across-channel processing, and (iii) CMR obtained in the “classical” band-widening paradigm in order to study the role of across-channel processing in a condition which always includes within-channel processing. The simulations support the hypothesis that within-channel contributions to CMR can be as large as 15dB. The across-channel process is robust but small (about 2–4dB) and only observable at small masker bandwidths. Overall, the proposed model might provide an interesting framework for the analysis of fluctuating sounds in the auditory system.
Measurement and prediction of speech and noise levels and the Lombard effect in eating establishments
Authors: Hodgson Murray , Steininger Gavin , Razavi Zohreh
Published: April 2007

Measurements made of the acoustical characteristics of, and occupied noise levels in, ten eating establishments are described. Levels to which diners and employees were exposed varied from 45 to 82dB(A). From these levels and diner questionnaire responses, the number of customers present and average noise levels to which individual diners were exposed during their visits were estimated. These data, assumptions about the number of talkers per customer, and classical room-acoustical theory were used to deduce talker voice output levels. These varied from slightly above “casual” to “loud.” An iterative model for predicting speech and noise levels in eating establishments, including the Lombard effect as described by a new, proposed model, was developed. With the measured noise levels as the target for prediction, optimization techniques were used to find best estimates of unknown prediction parameters—such as those defining the Lombard effect, the number of talkers per customer, and the average absorption per customer—with highly credible results. The prediction algorithm and optimal parameters constitute a novel model for predicting speech and noise levels—and thus speech intelligibility—in eating establishments, as a function of the number of customers, including a proven, realistic model of the Lombard effect.
Comparison of level discrimination, increment detection, and comodulation masking release in the audio- and envelope-frequency domains
Authors: Nelson Paul C. , Ewert Stephan D. , Carney Laurel H. , Dau Torsten
Published: April 2007

In general, the temporal structure of stimuli must be considered to account for certain observations made in detection and masking experiments in the audio-frequency domain. Two such phenomena are (1) a heightened sensitivity to amplitude increments with a temporal fringe compared to gated level discrimination performance and (2) lower tone-in-noise detection thresholds using a modulated masker compared to those using an unmodulated masker. In the current study, translations of these two experiments were carried out to test the hypothesis that analogous cues might be used in the envelope-frequency domain. Pure-tone carrier amplitude-modulation (AM) depth-discrimination thresholds were found to be similar using both traditional gated stimuli and using a temporally modulated fringe for a fixed standard depth (ms=0.25) and a range of AM frequencies (4–64Hz). In a second experiment, masked sinusoidal AM detection thresholds were compared in conditions with and without slow and regular fluctuations imposed on the instantaneous masker AM depth. Release from masking was obtained only for very slow masker fluctuations (less than 2Hz). A physiologically motivated model that effectively acts as a first-order envelope change detector accounted for several, but not all, of the key aspects of the data.
The time required to focus on a cued signal frequency
Authors: Scharf Bertram , Reeves Adam , Suciu John
Published: April 2007

How quickly can a listener focus on a single tonal cue that indicates the frequency of an upcoming signal? Initial measurements were made with frequency uncertainty (signal frequency varies randomly from trial to trial) and with certainty (same frequency on all trials). Measured by a yes–no procedure, thresholds for 40- and 20-ms signals presented in continuous broadband noise at 50dB SPL were higher in uncertainty than in certainty; the difference decreased monotonically from 5dB at frequencies below 500Hz to under 3dB above about 2500Hz. This decrease in the detrimental effect from uncertainty, which comes about with increasing signal frequency, may result from preferential attention to higher frequencies. In a second experiment, frequency again varied randomly, but each trial now began with a cue at the signal frequency. The critical variable was the delay from cue onset to signal onset. A delay of 352ms eliminated the detrimental effect of frequency uncertainty at all frequencies. At the shortest delays of 52 and 82ms the detrimental effect was reduced primarily at lower frequencies. Our analysis suggests that shifting focus to a cued frequency region, under optimal stimulus conditions, requires less than 52ms.
Bi-static sonar applications of intensity processing
Authors: Naluai Nathan K. , Lauchle Gerald C. , Gabrielson Thomas B. , Joseph John H.
Published: April 2007

Acoustic intensity processing of signals from directional sonobuoy acoustic subsystems is used to enhance the detection of submerged bodies in bi-static sonar applications. In some directions, the scattered signals may be completely dominated by the incident blast from the source, depending upon the geometry, making the object undetectable by traditional pressure measurements. Previous theoretical derivations suggest that acoustic vector intensity sensors, and the associated intensity processing, are a potential solution to this problem. Deep water experiments conducted at Lake Pend Oreille in northern Idaho are described. A large, hollow cylindrical body is located between a source and a number of SSQ-53D sonobuoys positioned from 5 to 30 body lengths away from the scattering body. Measurements show changes in the acoustic pressure of less than 0.5dB when the scattering body is inserted in the field. However, the phase of the acoustic intensity component formed between the acoustic pressure and particle velocity component orthogonal to the direction of incident wave propagation varies by as much as 55°. This metric is shown to be a repeatable and strong indicator of the presence of the scattering body.
Nonlinear surface waves in soft, weakly compressible elastic media
Authors: Zabolotskaya Evgenia A. , Ilinskii Yurii A. , Hamilton Mark F.
Published: April 2007

Nonlinear surface waves in soft, weakly compressible elastic media are investigated theoretically, with a focus on propagation in tissue-like media. The model is obtained as a limiting case of the theory developed by Zabolotskaya [J. Acoust. Soc. Am. 91, 2569–2575 (1992)] for nonlinear surface waves in arbitrary isotropic elastic media, and it is consistent with the results obtained by Fu and Devenish [Q. J. Mech. Appl. Math. 49, 65–80 (1996)] for incompressible isotropic elastic media. In particular, the quadratic nonlinearity is found to be independent of the third-order elastic constants of the medium, and it is inversely proportional to the shear modulus. The Gol’dberg number characterizing the degree of waveform distortion due to quadratic nonlinearity is proportional to the square root of the shear modulus and inversely proportional to the shear viscosity. Simulations are presented for propagation in tissue-like media.
Acoustic diffraction effects at the Hellenistic amphitheater of Epidaurus: Seat rows responsible for the marvelous acoustics
Authors: Declercq Nico F. , Dekeyser Cindy S. A.
Published: April 2007

The Hellenistic theater of Epidaurus, on the Peloponnese in Greece, attracts thousands of visitors every year who are all amazed by the fact that sound coming from the middle of the theater reaches the outer seats, apparently without too much loss of intensity. The theater, renowned for its extraordinary acoustics, is one of the best conserved of its kind in the world. It was used for musical and poetical contests and theatrical performances. The presented numerical study reveals that the seat rows of the theater, unexpectedly play an essential role in the acoustics—at least when the theater is not fully filled with spectators. The seats, which constitute a corrugated surface, serve as an acoustic filter that passes sound coming from the stage at the expense of surrounding acoustic noise. Whether a coincidence or not, the theater of Epidaurus was built with optimized shape and dimensions. Understanding and application of corrugated surfaces as filters rather than merely as diffuse scatterers of sound, may become imperative in the future design of modern theaters.
Silent research vessels are not quiet
Authors: Ona Egil , Godø Olav Rune , Handegard Nils Olav , Hjellvik Vidar , Patel Ruben , Pedersen Geir
Published: April 2007

Behavior of herring (Clupea harengus) is stimulated by two ocean-going research vessels; respectively designed with and without regard to radiated-noise-standards. Both vessels generate a reaction pattern, but, contrary to expectations, the reaction initiated by the silent vessel is stronger and more prolonged than the one initiated by the conventional vessel. The recommendations from the scientific community on noise-reduced designs were motivated by the expectation of minimizing bias on survey results caused by vessel-induced fish behavior. In conclusion, the candidate stimuli for vessel avoidance remain obscure. Noise reduction might be necessary but is insufficient to obtain stealth vessel assets during surveys.
Sex differences in the length of the organ of Corti in humans
Authors: Miller James D.
Published: April 2007

Sato et al. [Acta. Otolaryngol. 111 (6), 1037–1040 (1991)] reported that the human cochlea is, on average, 15% longer for males than females. This corresponds to 4.7mm in length and to 2.78 standard deviations (SD). Anatomical measurements of the lengths of cochleas from 148 heads (194 cochleas) from eleven sources are reviewed and summarized. A sex difference of 3.36% is observed. This corresponds to 1.11mm in length and to 0.49SD. The mean lengths of the male and female cochleas are approximately 34 and 33mm, respectively, and the population SD is 2.28mm. The statistical significance of the observed difference is questionable.
Phased array focusing with guided waves in a viscoelastic coated hollow cylinder
Authors: Luo Wei , Rose Joseph L.
Published: April 2007

Guided wave phased array focusing has shown many advantages in long-range pipeline inspection, such as, longer inspection distance, greater wave penetration power and higher detection resolution. Viscoelastic coatings applied to a large percentage of pipes for protection purposes created some challenges in terms of focusing feasibility and inspection ability. Previous studies were all based on bare pipe models. In this work, guided wave phased array focusing in viscoelastic coated pipes is studied for the first time. Work was carried out with both numerical and experimental methods. A three-dimensional finite element model was developed for quantitatively and systematically modeling guided waves in pipes with different viscoelastic materials. A method of transforming measured coating properties to finite element method inputs was created in order to create a physically based model of guided waves in coated pipes. Guided wave focusing possibilities in viscoelastic coated pipes and the effects from coatings were comprehensively studied afterwards. A comparison of focusing and nonfocusing inspections was also studied quantitatively in coated pipe showing that focusing increased the wave energy and consequently the inspection ability tremendously. This study provides an important base line and guidance for guided wave propagation and focusing in a real field pipeline under various coating and environmental conditions.
Coccoid Form of
Helicobacter pylori
as a Morphological Manifestation of Cell Adaptation to the Environment
Authors: Azevedo N. F. , Almeida C. , Cerqueira L. , Dias S. , Keevil C. W. , Vieira M. J.
Published: March 2007

After characterization of preferred conditions for
Helicobacter pylori
survival in the sessile state, it was observed that the bacterium transforms from spiral to coccoid under mild circumstances, whereas under extreme ones it is unable to undergo shape modification. This strongly supports the view that transformation into the coccoid form is an active, biologically led process, switched on by the bacterium as a protection mechanism.
Monochloramine Inactivation of Bacterial Select Agents
Authors: Rose Laura J. , Rice Eugene W. , Hodges Lisa , Peterson Alicia , Arduino Matthew J.
Published: March 2007

Seven species of bacterial select agents were tested for susceptibility to monochloramine. Under test conditions, the monochloramine routinely maintained in potable water would reduce six of the species by 2 orders of magnitude within 4.2 h.
Bacillus anthracis
spores would require up to 3.5 days for the same inactivation with monochloramine.
Identification of Novel Genes Involved in Long-Chain
n
-Alkane Degradation by
Acinetobacter
sp. Strain DSM 17874
Authors: Throne-Holst Mimmi , Wentzel Alexander , Ellingsen Trond E. , Kotlar Hans-Kristian , Zotchev Sergey B.
Published: March 2007

Acinetobacter
sp. strain DSM 17874 is capable of utilizing
n
-alkanes with chain lengths ranging from that of decane (C
10
H
22
) to that of tetracontane (C
40
H
82
) as a sole carbon source. Two genes encoding AlkB-type alkane hydroxylase homologues, designated
alkMa
and
alkMb
, have been shown to be involved in the degradation of
n
-alkanes with chain lengths of from 10 to 20 C atoms in this strain. Here, we describe a novel high-throughput screening method and the screening of a transposon mutant library to identify genes involved in the degradation of
n
-alkanes with C chain lengths longer than 20, which are solid at 30°C, the optimal growth temperature for
Acinetobacter
sp. strain DSM 17874. A library consisting of approximately 6,800
Acinetobacter
sp. strain DSM 17874 transposon mutants was constructed and screened for mutants unable to grow on dotriacontane (C
32
H
66
) while simultaneously showing wild-type growth characteristics on shorter-chain
n
-alkanes. For 23 such mutants isolated, the genes inactivated by transposon insertion were identified. Targeted inactivation and complementation studies of one of these genes, designated
almA
and encoding a putative flavin-binding monooxygenase, confirmed its involvement in the strain's metabolism of long-chain
n
-alkanes. To our knowledge,
almA
represents the first cloned gene shown to be involved in the bacterial degradation of long-chain
n
-alkanes of 32 C's and longer. Genes encoding AlmA homologues were also identified in other long-chain
n
-alkane-degrading
Acinetobacter
strains.
Genome Sequence of the Cellulolytic Gliding Bacterium
Cytophaga hutchinsonii
Authors: Xie Gary , Bruce David C. , Challacombe Jean F. , Chertkov Olga , Detter John C. , Gilna Paul , Han Cliff S. , Lucas Susan , Misra Monica , Myers Gerald L. , Richardson Paul , Tapia Roxanne , Thayer Nina , Thompson Linda S. , Brettin Thomas S. , Henrissat Bernard , Wilson David B. , McBride Mark J.
Published: March 2007

The complete DNA sequence of the aerobic cellulolytic soil bacterium
Cytophaga hutchinsonii
, which belongs to the phylum
Bacteroidetes
, is presented. The genome consists of a single, circular, 4.43-Mb chromosome containing 3,790 open reading frames, 1,986 of which have been assigned a tentative function. Two of the most striking characteristics of
C. hutchinsonii
are its rapid gliding motility over surfaces and its contact-dependent digestion of crystalline cellulose. The mechanism of
C. hutchinsonii
motility is not known, but its genome contains homologs for each of the
gld
genes that are required for gliding of the distantly related bacteroidete
Flavobacterium johnsoniae. Cytophaga-Flavobacterium
gliding appears to be novel and does not involve well-studied motility organelles such as flagella or type IV pili. Many genes thought to encode proteins involved in cellulose utilization were identified. These include candidate endo-β-1,4-glucanases and β-glucosidases. Surprisingly, obvious homologs of known cellobiohydrolases were not detected. Since such enzymes are needed for efficient cellulose digestion by well-studied cellulolytic bacteria,
C. hutchinsonii
either has novel cellobiohydrolases or has an unusual method of cellulose utilization. Genes encoding proteins with cohesin domains, which are characteristic of cellulosomes, were absent, but many proteins predicted to be involved in polysaccharide utilization had putative D5 domains, which are thought to be involved in anchoring proteins to the cell surface.
Characterization of a Gene Cluster Responsible for the Biosynthesis of Anticancer Agent FK228 in
Chromobacterium violaceum
No. 968
Authors: Cheng Yi-Qiang , Yang Min , Matter Andrea M.
Published: March 2007

A gene cluster responsible for the biosynthesis of anticancer agent FK228 has been identified, cloned, and partially characterized in
Chromobacterium violaceum
no. 968. First, a genome-scanning approach was applied to identify three distinctive
C. violaceum
no. 968 genomic DNA clones that code for portions of nonribosomal peptide synthetase and polyketide synthase. Next, a gene replacement system developed originally for
Pseudomonas aeruginosa
was adapted to inactivate the genomic DNA-associated candidate natural product biosynthetic genes in vivo with high efficiency. Inactivation of a nonribosomal peptide synthetase-encoding gene completely abolished FK228 production in mutant strains. Subsequently, the entire FK228 biosynthetic gene cluster was cloned and sequenced. This gene cluster is predicted to encompass a 36.4-kb DNA region that includes 14 genes. The products of nine biosynthetic genes are proposed to constitute an unusual hybrid nonribosomal peptide synthetase-polyketide synthase-nonribosomal peptide synthetase assembly line including accessory activities for the biosynthesis of FK228. In particular, a putative flavin adenine dinucleotide-dependent pyridine nucleotide-disulfide oxidoreductase is proposed to catalyze disulfide bond formation between two sulfhydryl groups of cysteine residues as the final step in FK228 biosynthesis. Acquisition of the FK228 biosynthetic gene cluster and acclimation of an efficient genetic system should enable genetic engineering of the FK228 biosynthetic pathway in
C. violaceum
no. 968 for the generation of structural analogs as anticancer drug candidates.
Geographical Distribution and Diversity of Bacteria Associated with Natural Populations of
Drosophila melanogaster
Authors: Corby-Harris Vanessa , Pontaroli Ana Clara , Shimkets Lawrence J. , Bennetzen Jeffrey L. , Habel Kristin E. , Promislow Daniel E. L.
Published: March 2007

Drosophila melanogaster
is one of the most widely used model systems in biology. However, little is known about its associated bacterial community. As a first step towards understanding these communities, we compared bacterial 16S rRNA gene sequence libraries recovered from 11 natural populations of adult
D. melanogaster
. Bacteria from these sequence libraries were grouped into 74 distinct taxa, spanning the phyla
Proteobacteria
,
Bacteroidetes
, and
Firmicutes
, which were unevenly spread across host populations. Summed across populations, the distribution of abundance of genera was closely fit by a power law. We observed differences among host population locations both in bacterial community richness and in composition. Despite this significant spatial variation, no relationship was observed between species richness and a variety of abiotic factors, such as temperature and latitude. Overall, bacterial communities associated with adult
D. melanogaster
hosts are diverse and differ across host populations.
Diversification of Lupine
Bradyrhizobium
Strains: Evidence from Nodulation Gene Trees
Authors: Stępkowski Tomasz , Hughes Colin E. , Law Ian J. , Markiewicz Łukasz , Gurda Dorota , Chlebicka Agnieszka , Moulin Lionel
Published: March 2007

Bradyrhizobium
strains isolated in Europe from Genisteae and serradella legumes form a distinct lineage, designated clade II, on nodulation gene trees. Clade II bradyrhizobia appear to prevail also in the soils of Western Australia and South Africa following probably accidental introduction with seeds of their lupine and serradella hosts. Given this potential for dispersal, we investigated
Bradyrhizobium
isolates originating from a range of native New World lupines, based on phylogenetic analyses of nodulation (
nodA
,
nodZ
,
noeI
) and housekeeping (
atpD
,
dnaK
,
glnII
,
recA
) genes. The housekeeping gene trees revealed considerable diversity among lupine bradyrhizobia, with most isolates placed in the
Bradyrhizobium japonicum
lineage, while some European strains were closely related to
Bradyrhizobium canariense
. The
nodA
gene tree resolved seven strongly supported groups (clades I to VII) that correlated with strain geographical origins and to some extent with major
Lupinus
clades. All European strains were placed in clade II, whereas only a minority of New World strains was placed in this clade. This work, as well as our previous studies, suggests that clade II diversified predominately in the Old World, possibly in the Mediterranean. Most New World isolates formed subclade III.2, nested in a large “pantropical” clade III, which appears to be New World in origin, although it also includes strains originating from nonlupine legumes. Trees generated using
nodZ
and
noeI
gene sequences accorded well with the
nodA
tree, but evidence is presented that the
noeI
gene may not be required for nodulation of lupine and that loss of this gene is occurring.
A Marine
Mesorhizobium
sp. Produces Structurally Novel Long-Chain
N
-Acyl-
l
-Homoserine Lactones
Authors: Krick Anja , Kehraus Stefan , Eberl Leo , Riedel Kathrin , Anke Heidrun , Kaesler Ines , Graeber Ingeborg , Szewzyk Ulrich , König Gabriele M.
Published: March 2007

Our study focused on a
Mesorhizobium
sp. that is phylogenetically affiliated by 16S rRNA gene sequence to other marine and saline bacteria of this genus. Liquid chromatography-mass spectrometry investigations of the extract obtained from solid-phase extraction of cultures of this bacterium indicated the presence of several
N
-acyl homoserine lactones (AHLs), with chain lengths of C
10
to C
16
. Chromatographic separation of the active bacterial extract yielded extraordinarily large amounts of two unprecedented acylated homoserine lactones, 5-
cis
-3-oxo-C
12
-homoserine lactone (5-
cis
-3-oxo-C
12
-HSL) (compound 1) and 5-
cis
-C
12
-HSL (compound 2). Quorum-sensing activity of compounds 1 and 2 was shown in two different biosensor systems [
Escherichia coli
MT102(pSB403) and
Pseudomonas putida
F117(pKR-C12)]. Furthermore, it was shown that both compounds can restore protease and pyoverdin production of an AHL-deficient
Pseudomonas aeruginosa
PAO1
lasI rhlI
double mutant, suggesting that these signal molecules maybe used for intergenus signaling. In conclusion, these data indicate that the quorum-sensing activity of compounds 1 and 2 is modulated by the chain length and functional groups of the acyl moiety. Additionally, compound 1 showed antibacterial and cytotoxic activities.
Variable-Number Tandem Repeats as Molecular Markers for Biotypes of
Pasteuria ramosa
in
Daphnia
spp
Authors: Mouton Laurence , Nong Guang , Preston James F. , Ebert Dieter
Published: March 2007

Variable-number tandem repeats (VNTRs) have been identified in populations of
Pasteuria ramosa
, a castrating endobacterium of
Daphnia
species. The allelic polymorphisms at 14 loci in laboratory and geographically diverse soil samples showed that VNTRs may serve as biomarkers for the genetic characterization of
P. ramosa
isolates.
PsrA, the
Pseudomonas
Sigma Regulator, Controls Regulators of Epiphytic Fitness, Quorum-Sensing Signals, and Plant Interactions in
Pseudomonas syringae
pv. tomato Strain DC3000
Authors: Chatterjee Asita , Cui Yaya , Hasegawa Hiroaki , Chatterjee Arun K.
Published: March 2007

Pseudomonas syringae
pv. tomato strain DC3000, a pathogen of tomato and
Arabidopsis
, occurs as an epiphyte. It produces
N
-acyl homoserine lactones (AHLs) which apparently function as quorum-sensing signals. A Tn
5
insertion mutant of DC3000, designated PsrA
−
(Psr is for
Pseudomonas
sigma regulator), overexpresses
psyR
(a LuxR-type regulator of
psyI
) and
psyI
(the gene for AHL synthase), and it produces a ca. 8-fold-higher level of AHL than does DC3000. The mutant is impaired in its ability to elicit the hypersensitive reaction and is attenuated in its virulence in tomato. These phenotypes correlate with reduced expression of
hrpL
, the gene for an alternate sigma factor, as well as several
hrp
and
hop
genes during early stages of incubation in a Hrp-inducing medium. PsrA also positively controls
rpoS
, the gene for an alternate sigma factor known to control various stress responses. By contrast, PsrA negatively regulates
rsmA1
, an RNA-binding protein gene known to function as negative regulator, and
aefR
, a
tetR
-like gene known to control AHL production and epiphytic fitness in
P. syringae
pv. syringae. Gel mobility shift assays and other lines of evidence demonstrate a direct interaction of PsrA protein with
rpoS
promoter DNA and
aefR
operator DNA. In addition, PsrA negatively autoregulates and binds the
psrA
operator. In an AefR
−
mutant, the expression of
psyR
and
psyI
and AHL production are lower than those in DC3000, the AefR
+
parent. In an RpoS
−
mutant, on the other hand, the levels of AHL and transcripts of
psyR
and
psyI
are much higher than those in the RpoS
+
parent, DC3000. We present evidence, albeit indirect, that the RpoS effect occurs via
psyR
. Thus, AefR positively regulates AHL production, whereas RpoS has a strong negative effect. We show that AefR and RpoS do not regulate PsrA and that the PsrA effect on AHL production is exerted via its cumulative, but independent, effects on both AefR and RpoS.
Seasonal Variations in the Contributions of Different Bacterial Groups to the Uptake of Low-Molecular-Weight Compounds in Northwestern Mediterranean Coastal Waters
Authors: Alonso-Sáez Laura , Gasol Josep M.
Published: March 2007

We analyzed the contributions of different heterotrophic bacterial groups to the uptake of several low-molecular weight compounds during a seasonal cycle on the northwestern Mediterranean coast (Blanes Bay Microbial Observatory). The bacterial assemblage structure had been shown to change substantially year-round for this site, but whether changes in the activities of the different bacterial groups also occurred on the seasonal scale was unknown. Microautoradiography combined with catalyzed reporter deposition fluorescence in situ hybridization was used to analyze the patterns of glucose, amino acid, and ATP uptake by different bacterial groups.GammaproteobacteriaandBacteroideteswere not very active in the uptake of glucose at any time of the year (<10% of cells were active) compared toAlphaproteobacteria(generally >20% of cells were active). Dissolved free amino acids were taken up considerably byAlphaproteobacteriaandGammaproteobacteriabut not byBacteroidetes. Relatively high percentages of cells of the three broad phylogenetic groups actively took up ATP, which could be related to the important phosphorous limitation of bacterial production during most of the year in Blanes Bay. The contribution of SAR11 to the uptake of the monomers was variable year-round, generally with fewer than 30% of the cells being active. By contrast,Roseobacterwere highly overrepresented in the uptake of all the substrates throughout all the year, with more than 50% of cells being active in all the samples and for all substrates. Our results suggest that substantial changes in the activity of some phylogenetic groups of bacteria occur throughout the year.
Use of PCR-Targeted Mutagenesis To Disrupt Production of Fusaricidin-Type Antifungal Antibiotics in
Paenibacillus polymyxa
Authors: Li Jingru , Beatty Perrin K. , Shah Saleh , Jensen Susan E.
Published: March 2007

Paenibacillus polymyxa
(formerly
Bacillus polymyxa
) PKB1 has been identified as a potential agent for biocontrol of blackleg disease of canola, caused by the pathogenic fungus
Leptosphaeria maculans
. The factors presumed to contribute to disease suppression by strain PKB1 include the production of fusaricidin-type antifungal metabolites that appear around the onset of bacterial sporulation. The fusaricidins are a family of lipopeptide antibiotics consisting of a β-hydroxy fatty acid linked to a cyclic hexapeptide. Using a reverse genetic approach based on conserved motifs of nonribosomal peptide synthetases, a DNA fragment that appears to encode the first two modules of the putative fusaricidin synthetase (
fusA
) was isolated from PKB1. To confirm the involvement of
fusA
in production of fusaricidins, a modified PCR targeting mutagenesis protocol was developed to create a
fusA
mutation in PKB1. A DNA fragment internal to
fusA
was replaced by a gene disruption cassette containing two antibiotic resistance genes for independent selection of apramycin resistance in
Escherichia coli
and chloramphenicol resistance in
P. polymyxa
. Inclusion of an
oriT
site in the disruption cassette allowed efficient transfer of the inactivated
fusA
allele to
P. polymyxa
by intergeneric conjugation. Targeted disruption of
fusA
led to the complete loss of antifungal activity against
L. maculans
, suggesting that
fusA
plays an essential role in the nonribosomal synthesis of fusaricidins.
Identification of Unconventional Intestinal Pathogenic
Escherichia coli
Isolates Expressing Intermediate Virulence Factor Profiles by Using a Novel Single-Step Multiplex PCR
Authors: Müller Daniel , Greune Lilo , Heusipp Gerhard , Karch Helge , Fruth Angelika , Tschäpe Helmut , Schmidt M. Alexander
Published: March 2007

Intestinal pathogenic
Escherichia coli
represents a global health problem for mammals, including humans. At present, diarrheagenic
E. coli
bacteria are grouped into seven major pathotypes that differ in their virulence factor profiles, severity of clinical manifestations, and prognosis. In this study, we developed and evaluated a one-step multiplex PCR (MPCR) for the straightforward differential identification of intestinal pathotypes of
E. coli
. The specificity of this novel MPCR was validated by using a subset of reference strains and further confirmed by PCR-independent pheno- and genotypic characterization. Moreover, we tested 246 clinical
E. coli
isolates derived from diarrhea patients from several distinct geographic regions. Interestingly, besides strains belonging to the defined and well-described pathotypes, we identified five unconventional strains expressing intermediate virulence factor profiles. These strains have been further characterized and appear to represent intermediate strains carrying genes and expressing factors associated with enteropathogenic
E. coli
, Shiga toxin-producing
E. coli
, enterotoxigenic
E. coli
, and enteroaggregative
E. coli
alike. These strains represent further examples of the extraordinary plasticity of the
E. coli
genome. Moreover, this implies that the important identification of specific pathotypes has to be based on a broad matrix of indicator genes. In addition, the presence of intermediate strains needs to be accounted for.
Shiga Toxin Gene Loss and Transfer In Vitro and In Vivo during Enterohemorrhagic
Escherichia coli
O26 Infection in Humans
Authors: Bielaszewska Martina , Prager Rita , Köck Robin , Mellmann Alexander , Zhang Wenlan , Tschäpe Helmut , Tarr Phillip I. , Karch Helge
Published: March 2007

Escherichia coli
serogroup O26 consists of enterohemorrhagic
E. coli
(EHEC) and atypical enteropathogenic
E. coli
(aEPEC). The former produces Shiga toxins (Stx), major determinants of EHEC pathogenicity, encoded by bacteriophages; the latter is Stx negative. We have isolated EHEC O26 from patient stools early in illness and aEPEC O26 from stools later in illness, and vice versa. Intrapatient EHEC and aEPEC isolates had quite similar pulsed-field gel electrophoresis (PFGE) patterns, suggesting that they might have arisen by conversion between the EHEC and aEPEC pathotypes during infection. To test this hypothesis, we asked whether EHEC O26 can lose
stx
genes and whether aEPEC O26 can be lysogenized with Stx-encoding phages from EHEC O26 in vitro. The
stx
2
loss associated with the loss of Stx2-encoding phages occurred in 10% to 14% of colonies tested. Conversely, Stx2- and, to a lesser extent, Stx1-encoding bacteriophages from EHEC O26 lysogenized aEPEC O26 isolates, converting them to EHEC strains. In the lysogens and EHEC O26 donors, Stx2-converting bacteriophages integrated in
yecE
or
wrbA
. The loss and gain of Stx-converting bacteriophages diversifies PFGE patterns; this parallels findings of similar but not identical PFGE patterns in the intrapatient EHEC and aEPEC O26 isolates. EHEC O26 and aEPEC O26 thus exist as a dynamic system whose members undergo ephemeral interconversions via loss and gain of Stx-encoding phages to yield different pathotypes. The suggested occurrence of this process in the human intestine has diagnostic, clinical, epidemiological, and evolutionary implications.
Chitosan, the Deacetylated Form of Chitin, Is Necessary for Cell Wall Integrity in
Cryptococcus neoformans
Authors: Baker Lorina G. , Specht Charles A. , Donlin Maureen J. , Lodge Jennifer K.
Published: March 2007

Cryptococcus neoformans
is an opportunistic fungal pathogen that causes cryptococcal meningoencephalitis, particularly in immunocompromised patients. The fungal cell wall is an excellent target for antifungal therapies as it is an essential organelle that provides cell structure and integrity, it is needed for the localization or attachment of known virulence factors, including the polysaccharide capsule, melanin, and phospholipase, and it is critical for host-pathogen interactions. In
C. neoformans
, chitosan produced by the enzymatic removal of acetyl groups from nascent chitin polymers has been implicated as an important component of the vegetative cell wall. In this study, we identify four putative chitin/polysaccharide deacetylases in
C. neoformans
. We have demonstrated that three of these deacetylases, Cda1, Cda2, and Cda3, can account for all of the chitosan produced during vegetative growth in culture, but the function for one, Fpd1, remains undetermined. The data suggest a model for chitosan production in vegetatively growing
C. neoformans
where the three chitin deacetylases convert chitin generated by the chitin synthase Chs3 into chitosan. Utilizing a collection of chitin/polysaccharide deacetylase deletion strains, we determined that during vegetative growth, chitosan helps to maintain cell integrity and aids in bud separation. Additionally, chitosan is necessary for maintaining normal capsule width and the lack of chitosan results in a “leaky melanin” phenotype. Our analysis indicates that chitin deacetylases and the chitosan made by them may prove to be excellent antifungal targets.
Insights into the Autotrophic CO
2
Fixation Pathway of the Archaeon
Ignicoccus hospitalis
: Comprehensive Analysis of the Central Carbon Metabolism
Authors: Jahn Ulrike , Huber Harald , Eisenreich Wolfgang , Hügler Michael , Fuchs Georg
Published: March 2007

Ignicoccus hospitalis
is an autotrophic hyperthermophilic archaeon that serves as a host for another parasitic/symbiotic archaeon,
Nanoarchaeum equitans
. In this study, the biosynthetic pathways of
I. hospitalis
were investigated by in vitro enzymatic analyses, in vivo
13
C-labeling experiments, and genomic analyses. Our results suggest the operation of a so far unknown pathway of autotrophic CO
2
fixation that starts from acetyl-coenzyme A (CoA). The cyclic regeneration of acetyl-CoA, the primary CO
2
acceptor molecule, has not been clarified yet. In essence, acetyl-CoA is converted into pyruvate via reductive carboxylation by pyruvate-ferredoxin oxidoreductase. Pyruvate-water dikinase converts pyruvate into phosphoenolpyruvate (PEP), which is carboxylated to oxaloacetate by PEP carboxylase. An incomplete citric acid cycle is operating: citrate is synthesized from oxaloacetate and acetyl-CoA by a (re)-specific citrate synthase, whereas a 2-oxoglutarate-oxidizing enzyme is lacking. Further investigations revealed that several special biosynthetic pathways that have recently been described for various archaea are operating. Isoleucine is synthesized via the uncommon citramalate pathway and lysine via the α-aminoadipate pathway. Gluconeogenesis is achieved via a reverse Embden-Meyerhof pathway using a novel type of fructose 1,6-bisphosphate aldolase. Pentosephosphates are formed from hexosephosphates via the suggested ribulose-monophosphate pathway, whereby formaldehyde is released from C-1 of hexose. The organism may not contain any sugar-metabolizing pathway. This comprehensive analysis of the central carbon metabolism of
I. hospitalis
revealed further evidence for the unexpected and unexplored diversity of metabolic pathways within the (hyperthermophilic) archaea.
Growth Rate Toxicity Phenotypes and Homeostatic Supercoil Control Differentiate
Escherichia coli
from
Salmonella enterica
Serovar Typhimurium
Authors: Champion Keith , Higgins N. Patrick
Published: March 2007

Escherichia coli
and
Salmonella enterica
serovar Typhimurium share high degrees of DNA and amino acid identity for 65% of the homologous genes shared by the two genomes. Yet, there are different phenotypes for null mutants in several genes that contribute to DNA condensation and nucleoid formation. The mutant R436-S form of the GyrB protein has a temperature-sensitive phenotype in
Salmonella
, showing disruption of supercoiling near the terminus and replicon failure at 42°C. But this mutation in
E. coli
is lethal at the permissive temperature. A unifying hypothesis for why the same mutation in highly conserved homologous genes of different species leads to different physiologies focuses on homeotic supercoil control. During rapid growth in mid-log phase,
E. coli
generates 15% more negative supercoils in pBR322 DNA than
Salmonella
. Differences in compaction and torsional strain on chromosomal DNA explain a complex set of single-gene phenotypes and provide insight into how supercoiling may modulate epigenetic effects on chromosome structure and function and on prophage behavior in vivo.
SpontaneoustrpYMutants and Mutational Analysis of the TrpY Archaeal Transcription Regulator
Authors: Čuboňová L'ubomíra , Sandman Kathleen , Karr Elizabeth A. , Cochran Andrew J. , Reeve John N.
Published: March 2007

Over 90% ofMethanothermobacter thermautotrophicusmutants isolated as spontaneously resistant to 5-methyl tryptophan had mutations intrpY. Most were single-base-pair substitutions that identified separate DNA- and tryptophan-binding regions in TrpY. In vivo and in vitro studies revealed that DNA binding was sufficient for TrpY repression oftrpYtranscription but that TrpY must bind DNA and tryptophan to assemble a complex that repressestrpEGCFBAD.
Microcin J25 Has Dual and Independent Mechanisms of Action inEscherichia coli: RNA Polymerase Inhibition and Increased Superoxide Production
Authors: Bellomio Augusto , Vincent Paula A. , de Arcuri Beatriz F. , Farías Ricardo N. , Morero Roberto D.
Published: March 2007

Microcin J25 (MccJ25) uptake byEscherichia colirequires the outer membrane receptor FhuA and the inner membrane proteins TonB, ExbD, ExbB, and SbmA. MccJ25 appears to have two intracellular targets: (i) RNA polymerase (RNAP), which has been described inE. coliandSalmonella entericaserovars, and (ii) the respiratory chain, reported only inS. entericaserovars. In the current study, it is shown that the observed difference between the actions of microcin on the respiratory chain inE. coliandS. entericais due to the relatively low microcin uptake via the chromosomally encoded FhuA. Higher expression by a plasmid-encoded FhuA allowed greater uptake of MccJ25 byE. colistrains and the consequent inhibition of oxygen consumption. The two mechanisms, inhibition of RNAP and oxygen consumption, are independent of each other. Further analysis revealed for the first time that MccJ25 stimulates the production of reactive oxygen species (O2·−) in bacterial cells, which could be the main reason for the damage produced on the membrane respiratory chain.
The Anaerobic Regulatory Network Required for
Pseudomonas aeruginosa
Nitrate Respiration
Authors: Schreiber Kerstin , Krieger Robert , Benkert Beatrice , Eschbach Martin , Arai Hiroyuki , Schobert Max , Jahn Dieter
Published: March 2007

In
Pseudomonas aeruginosa
, the
narK
1
K
2
GHJI
operon encodes two nitrate/nitrite transporters and the dissimilatory nitrate reductase. The
narK
1
promoter is anaerobically induced in the presence of nitrate by the dual activity of the oxygen regulator Anr and the N-oxide regulator Dnr in cooperation with the nitrate-responsive two-component regulatory system NarXL. The DNA bending protein IHF is essential for this process. Similarly,
narXL
gene transcription is enhanced under anaerobic conditions by Anr and Dnr. Furthermore, Anr and NarXL induce expression of the N-oxide regulator gene
dnr
. Finally, NarXL in cooperation with Dnr is required for anaerobic nitrite reductase regulatory gene
nirQ
transcription. A cascade regulatory model for the fine-tuned genetic response of
P. aeruginosa
to anaerobic growth conditions in the presence of nitrate was deduced.
Analysis of LuxR Regulon Gene Expression during Quorum Sensing inVibrio fischeri
Authors: Qin Nan , Callahan Sean M. , Dunlap Paul V. , Stevens Ann M.
Published: March 2007

The regulation of theluxoperon (luxICDABEG) ofVibrio fischerihas been intensively studied as a model for quorum sensing in proteobacteria. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis previously identified several non-Lux proteins inV. fischeriMJ-100 whose expression was dependent on LuxR and 3-oxo-hexanoyl-l-homoserine lactone (3-oxo-C6-HSL). To determine if the LuxR-dependent regulation of the genes encoding these proteins was due to direct transcriptional control by LuxR and 3-oxo-C6-HSL or instead was due to indirect control via an unidentified regulatory element, promoters of interest were cloned into alacZreporter and tested for their LuxR and 3-oxo-C6-HSL dependence in recombinantEscherichia coli. The promoters forqsrP,acfA, andribBwere found to be directly activated via LuxR-3-oxo-C6-HSL. The sites of transcription initiation were established via primer extension analysis. Based on this information and the position of theluxbox-binding site near position −40, all three promoters appear to have a class II-type promoter structure. In order to more fully characterize the LuxR regulon inV. fischeriMJ-100, real-time reverse transcription-PCR was used to study the temporal expression ofqsrP,acfA, andribBduring the exponential and stationary phases of growth, and electrophoretic mobility shift assays were used to compare the binding affinities of LuxR to the promoters under investigation. Taken together, the results demonstrate that regulation of the production of QsrP, RibB, and AcfA is controlled directly by LuxR at the level of transcription, thereby establishing that there is a LuxR regulon inV. fischeriMJ-100 whose genes are coordinately expressed during mid-exponential growth.