bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlinear and diffraction effects in propagation of N-waves in randomly inhomogeneous moving media
Authors: Averiyanov Mikhail , Blanc-Benon Philippe , Cleveland Robin O. , Khokhlova Vera
Published: April 2011

Finite amplitude acoustic wave propagation through atmospheric turbulence is modeled using a Khokhlov–Zabolotskaya–Kuznetsov (KZK)-type equation. The equation accounts for the combined effects of nonlinearity, diffraction, absorption, and vectorial inhomogeneities of the medium. A numerical algorithm is developed which uses a shock capturing scheme to reduce the number of temporal grid points. The inhomogeneous medium is modeled using random Fourier modes technique. Propagation of N-waves through the medium produces regions of focusing and defocusing that is consistent with geometrical ray theory. However, differences up to ten wavelengths are observed in the locations of fist foci. Nonlinear effects are shown to enhance local focusing, increase the maximum peak pressure (up to 60%), and decrease the shock rise time (about 30 times). Although the peak pressure increases and the rise time decreases in focal regions, statistical analysis across the entire wavefront at a distance 120 wavelengths from the source indicates that turbulence: decreases the mean time-of-flight by 15% of a pulse duration, decreases the mean peak pressure by 6%, and increases the mean rise time by almost 100%. The peak pressure and the arrival time are primarily governed by large scale inhomogeneities, while the rise time is also sensitive to small scales.
Identification of geometric parameters influencing the flow-induced vibration of a two-layer self-oscillating computational vocal fold model
Authors: Pickup Brian A. , Thomson Scott L.
Published: April 2011

Simplified models have been used to simulate and study the flow-induced vibrations of the human vocal folds. While it is clear that the models’ responses are sensitive to geometry, it is not clear how and to what extent specific geometric features influence model motion. In this study geometric features that played significant roles in governing the motion of a two-layer (body-cover), two-dimensional, finite element vocal fold model were identified. The model was defined using a flow solver based on the viscous, unsteady, Navier–Stokes equations and a solid solver that allowed for large strain and deformation. A screening-type design-of-experiments approach was used to identify the relative importance of 13 geometric parameters. Five output measures were analyzed to assess the magnitude of each geometric parameter’s effect on the model’s motion. The measures related to frequency, glottal width, flow rate, intraglottal angle, and intraglottal phase delay. The most significant geometric parameters were those associated with the cover—primarily the pre-phonatory intraglottal angle—as well as the body inferior angle. Some models exhibited evidence of improved model motion, including mucosal wave-like motion and alternating convergent-divergent glottal profiles, although further improvements are still needed to more closely mimic human vocal fold motion.
Shallow water narrowband coherence measurements in the Florida Strait
Authors: Heaney Kevin D.
Published: April 2011

A set of measures of coherence are defined and applied to the CALOPS experiment, conducted off the coast of Florida in the summer of 2007. A set of narrowband CW tones were transmitted from a towed source received on a 118-element bottom mounted horizontal line array (206 m aperture) with broadside oriented along the 250 m isobath. Two coherence measures are based upon the eigenvalue spread: the power factor and the eigenvalue ratio. This approach is not sensitive to array element error or model mismatch. Two measures are based upon phase residuals; these include the rms-phase error and the coherence function. Three measures are based upon power responses: beam width, array signal gain degradation, and array gain. These approaches have varying sensitivity to array location errors, model mismatch, signal-to-noise ratio, and the structure of the noise field. A Gaussian noise model is used to infer a coherence length from most of the coherence measures. The primary result is that coherence lengths increase with frequency and are on the order of 200 m, the length of the array. The frequency increased coherence length with frequency goes against conventional wisdom, which is to define the coherence length as a fixed number of wavelengths.
Effect of broadband-noise masking on the behavioral response of a harbor porpoise (Phocoena phocoena) to 1-s duration 6–7 kHz sonar up-sweeps
Authors: Kastelein Ronald A. , Steen Nele , de Jong Christ , Wensveen Paul J. , Verboom Willem C.
Published: April 2011

Naval sonar systems produce signals which may affect the behavior of harbor porpoises, though their effect may be reduced by ambient noise. To show how natural ambient noise influences the effect of sonar sweeps on porpoises, a porpoise in a pool was exposed to 1-s duration up-sweeps, similar in frequency range (6–7 kHz) to those of existing naval sonar systems. The sweep signals had randomly generated sweep intervals of 3–7 s (duty cycle: 19%). Behavioral parameters during exposure to signals were compared to those during baseline periods. The sessions were conducted under five background noise conditions: the local normal ambient noise and four conditions mimicking the spectra for wind-generated noise at Sea States 2–8. In all conditions, the sweeps caused the porpoise to swim further away from the transducer, surface more often, swim faster, and breathe more forcefully than during the baseline periods. However, the higher the background noise level, the smaller the effects of the sweeps on the surfacing behavior of the porpoise. Therefore, the effects of naval sonar systems on harbor porpoises are determined not only by the received level of the signals and the hearing sensitivity of the animals but also by the background noise.
The modal projector
Authors: Butler John L. , Butler Alexander L. , Butler Stephen C.
Published: April 2011

The superposition of acoustical modes radiated from a transducer can provide directionality from a compact projector. This paper presents the foundation, as well as examples, of piezoelectric ceramic, piezoelectric single crystal, and magnetostrictive versions of this “modal projector.” Measured and analytical, as well as finite element analysis modeled, results show good agreement and establish this transducer as a viable source of intensity with the advantages of an improved directivity index, reducing the power needed from a compact source.
Acoustic radiation torque and the conservation of angular momentum (L)
Authors: Zhang Likun , Marston Philip L.
Published: April 2011

This note concerns the evaluation of the static acoustic radiation torque exerted by an acoustic field on a scatterer immersed in a nonviscous fluid based on far-field scattering. The radiation torque is expressed as the integral of the time-averaged flux of angular momentum over a spherical surface far removed from the scattering object with its center at the centroid of the object. That result was given previously [G. Maidanik, J. Acoust. Soc. Am. 30, 620–623 (1956)]. Another expression given recently [Z. W. Fan et al., J. Acoust. Soc. Am. 124, 2727–2732 (2008)] is simplified to this formula. Comments are made on obtaining it directly from the general theorem of angular momentum conservation in the integral form.
Measurement of material nonlinearity using surface acoustic wave parametric interaction and laser ultrasonics
Authors: Stratoudaki Theodosia , Ellwood Robert , Sharples Steve , Clark Matthew , Somekh Michael G. , Collison Ian J.
Published: April 2011

A dual frequency mixing technique has been developed for measuring velocity changes caused by material nonlinearity. The technique is based on the parametric interaction between two surface acoustic waves (SAWs): The low frequency pump SAW generated by a transducer and the high frequency probe SAW generated and detected using laser ultrasonics. The pump SAW stresses the material under the probe SAW. The stress (typically <5 MPa) is controlled by varying the timing between the pump and probe waves. The nonlinear interaction is measured as a phase modulation of the probe SAW and equated to a velocity change. The velocity–stress relationship is used as a measure of material nonlinearity. Experiments were conducted to observe the pump–probe interaction by changing the pump frequency and compare the nonlinear response of aluminum and fused silica. Experiments showed these two materials had opposite nonlinear responses, consistent with previously published data. The technique could be applied to life-time predictions of engineered components by measuring changes in nonlinear response caused by fatigue.
Exploring the additivity of binaural and monaural masking release
Authors: Hall Joseph W. , Buss Emily , Grose John H.
Published: April 2011

Experiment 1 examined comodulation masking release (CMR) for a 700-Hz tonal signal under conditions of NoSo (noise and signal interaurally in phase) and NoSπ (noise in phase, signal out of phase) stimulation. The baseline stimulus for CMR was either a single 24-Hz wide narrowband noise centered on the signal frequency [on-signal band (OSB)] or the OSB plus, a set of flanking noise bands having random envelopes. Masking noise was either gated or continuous. The CMR, defined with respect to either the OSB or the random noise baseline, was smaller for NoSπ than NoSo stimulation, particularly when the masker was continuous. Experiment 2 examined whether the same pattern of results would be obtained for a 2000-Hz signal frequency; the number of flanking bands was also manipulated (two versus eight). Results again showed smaller CMR for NoSπ than NoSo stimulation for both continuous and gated masking noise. The CMR was larger with eight than with two flanking bands, and this difference was greater for NoSo than NoSπ. The results of this study are compatible with serial mechanisms of binaural and monaural masking release, but they indicate that the combined masking release (binaural masking-level difference and CMR) falls short of being additive.
HIV Transmission: Time for Translational Studies to Bridge the Gap
Authors: Anton Peter , Herold Betsy C.
Published: April 2011

A large clinical trial reveals that HIV-1 RNA loads predict the risk of heterosexual transmission and identifies new directions for translational research.
Impact of Recently Emerged Sterol 14α-Demethylase (CYP51) Variants of Mycosphaerella graminicola on Azole Fungicide Sensitivity
Authors: Cools Hans J. , Mullins Jonathan G. L. , Fraaije Bart A. , Parker Josie E. , Kelly Diane E. , Lucas John A. , Kelly Steven L.
Published: April 2011

The progressive decline in the effectiveness of some azole fungicides in controlling
Mycosphaerella graminicola
, causal agent of the damaging
Septoria
leaf blotch disease of wheat, has been correlated with the selection and spread in the pathogen population of specific mutations in the
M. graminicola CYP51
(
MgCYP51
) gene encoding the azole target sterol 14α-demethylase. Recent studies have suggested that the emergence of novel MgCYP51 variants, often harboring substitution S524T, has contributed to a decrease in the efficacy of prothioconazole and epoxiconazole, the two currently most effective azole fungicides against
M. graminicola
. In this study, we establish which amino acid alterations in novel MgCYP51 variants have the greatest impact on azole sensitivity and protein function. We introduced individual and combinations of identified alterations by site-directed mutagenesis and functionally determined their impact on azole sensitivity by expression in a
Saccharomyces cerevisiae
mutant YUG37::
erg11
carrying a regulatable promoter controlling native
CYP51
expression. We demonstrate that substitution S524T confers decreased sensitivity to all azoles when introduced alone or in combination with Y461S. In addition, S524T restores the function in
S. cerevisiae
of MgCYP51 variants carrying the otherwise lethal alterations Y137F and V136A. Sensitivity tests of
S. cerevisiae
transformants expressing recently emerged MgCYP51 variants carrying combinations of alterations D134G, V136A, Y461S, and S524T reveal a substantial impact on sensitivity to the currently most widely used azoles, including epoxiconazole and prothioconazole. Finally, we exploit a recently developed model of the MgCYP51 protein to predict that the substantial structural changes caused by these novel combinations reduce azole interactions with critical residues in the binding cavity, thereby causing resistance.
Competing Formate- and Carbon Dioxide-Utilizing Prokaryotes in an Anoxic Methane-Emitting Fen Soil
Authors: Hunger Sindy , Schmidt Oliver , Hilgarth Maik , Horn Marcus A. , Kolb Steffen , Conrad Ralf , Drake Harold L.
Published: April 2011

Methanogenesis in wetlands is dependent on intermediary substrates derived from the degradation of biopolymers. Formate is one such substrate and is stimulatory to methanogenesis and acetogenesis in anoxic microcosms of soil from the fen Schlöppnerbrunnen. Formate dissimilation also yields CO
2
as a potential secondary substrate. The objective of this study was to resolve potential differences between anaerobic formate- and CO
2
-utilizing prokaryotes of this fen by stable isotope probing. Anoxic soil microcosms were pulsed daily with low concentrations of [
13
C]formate or
13
CO
2
(i.e., [
13
C]bicarbonate). Taxa were evaluated by assessment of 16S rRNA genes,
mcrA
(encoding the alpha-subunit of methyl-coenzyme M reductase), and
fhs
(encoding formyltetrahydrofolate synthetase). Methanogens, acetogens, and formate-hydrogen lyase-containing taxa appeared to compete for formate. Genes affiliated with
Methanocellaceae
,
Methanobacteriaceae
,
Acetobacteraceae
, and
Rhodospirillaceae
were
13
C enriched (i.e., labeled) in [
13
C]formate treatments, whereas genes affiliated with
Methanosarcinaceae
,
Conexibacteraceae
, and
Solirubrobacteraceae
were labeled in
13
CO
2
treatments. [
13
C]acetate was enriched in [
13
C]formate treatments, but labeling of known acetogenic taxa was not detected. However, several phylotypes were affiliated with acetogen-containing taxa (e.g.,
Sporomusa
).
Methanosaetaceae
-affiliated methanogens appeared to participate in the consumption of acetate. Twelve and 58 family-level archaeal and bacterial 16S rRNA phylotypes, respectively, were detected, approximately half of which had no isolated representatives.
Crenarchaeota
constituted half of the detected archaeal 16S rRNA phylotypes. The results highlight the unresolved microbial diversity of the fen Schlöppnerbrunnen, suggest that differing taxa competed for the same substrate, and indicate that
Methanocellaceae
,
Methanobacteriaceae
,
Methanosarcinaceae
, and
Methanosaetaceae
were linked to the production of methane, but they do not clearly resolve the taxa responsible for the apparent conversion of formate to acetate.
Cryptic Aspergillus nidulans Antimicrobials
Authors: Giles Steve S. , Soukup Alexandra A. , Lauer Carrie , Shaaban Mona , Lin Alexander , Oakley Berl R. , Wang Clay C. C. , Keller Nancy P.
Published: April 2011

Secondary metabolite (SM) production by fungi is hypothesized to provide some fitness attribute for the producing organisms. However, most SM clusters are “silent” when fungi are grown in traditional laboratory settings, and it is difficult to ascertain any function or activity of these SM cluster products. Recently, the creation of a chromatin remodeling mutant in
Aspergillus nidulans
induced activation of several cryptic SM gene clusters. Systematic testing of nine purified metabolites from this mutant identified an emodin derivate with efficacy against both human fungal pathogens (inhibiting both spore germination and hyphal growth) and several bacteria. The ability of catalase to diminish this antimicrobial activity implicates reactive oxygen species generation, specifically, the generation of hydrogen peroxide, as the mechanism of emodin hydroxyl activity.
Phosphotransferase System-Independent Glucose Utilization in Corynebacterium glutamicum by Inositol Permeases and Glucokinases
Authors: Lindner Steffen N. , Seibold Gerd M. , Henrich Alexander , Krämer Reinhard , Wendisch Volker F.
Published: April 2011

Phosphoenolpyruvate-dependent glucose phosphorylation via the phosphotransferase system (PTS) is the major path of glucose uptake in
Corynebacterium glutamicum
, but some growth from glucose is retained in the absence of the PTS. The growth defect of a deletion mutant lacking the general PTS component HPr in glucose medium could be overcome by suppressor mutations leading to the high expression of inositol utilization genes or by the addition of inositol to the growth medium if a glucokinase is overproduced simultaneously. PTS-independent glucose uptake was shown to require at least one of the inositol transporters IolT1 and IolT2 as a mutant lacking IolT1, IolT2, and the PTS component HPr could not grow with glucose as the sole carbon source. Efficient glucose utilization in the absence of the PTS necessitated the overexpression of a glucokinase gene in addition to either
iolT1
or
iolT2
. IolT1 and IolT2 are low-affinity glucose permeases with

K
s

values of 2.8 and 1.9 mM, respectively. As glucose uptake and phosphorylation via the PTS differs from glucose uptake via IolT1 or IolT2 and phosphorylation via glucokinase by the requirement for phosphoenolpyruvate, the roles of the two pathways for
l
-lysine production were tested. The
l
-lysine yield by
C. glutamicum
DM1729, a rationally engineered
l
-lysine-producing strain, was lower than that by its PTS-deficient derivate DM1729Δ
hpr
, which, however, showed low production rates. The combined overexpression of
iolT1
or
iolT2
with
ppgK
, the gene for PolyP/ATP-dependent glucokinase, in DM1729Δ
hpr
enabled
l
-lysine production as fast as that by the parent strain DM1729 but with 10 to 20% higher
l
-lysine yield.
Life in the Cold: a Proteomic Study of Cold-Repressed Proteins in the Antarctic Bacterium Pseudoalteromonas haloplanktis TAC125
Authors: Piette Florence , D'Amico Salvino , Mazzucchelli Gabriel , Danchin Antoine , Leprince Pierre , Feller Georges
Published: April 2011

The proteomes expressed at 4°C and 18°C by the psychrophilic Antarctic bacterium
Pseudoalteromonas haloplanktis
were compared using two-dimensional differential in-gel electrophoresis with special reference to proteins repressed by low temperatures. Remarkably, the major cold-repressed proteins, almost undetectable at 4°C, were heat shock proteins involved in folding assistance.
Isolation from Animal Tissue and Genetic Transformation of Coxiella burnetii Are Facilitated by an Improved Axenic Growth Medium
Authors: Omsland Anders , Beare Paul A. , Hill Joshua , Cockrell Diane C. , Howe Dale , Hansen Bryan , Samuel James E. , Heinzen Robert A.
Published: April 2011

We recently described acidified citrate cysteine medium (ACCM), which supports host cell-free (axenic) growth of
Coxiella burnetii
. After 6 days of incubation, greater than 3 logs of growth was achieved with the avirulent Nine Mile phase II (NMII) strain. Here, we describe modified ACCM and culture conditions that support improved growth of
C. burnetii
and their use in genetic transformation and pathogen isolation from tissue samples. ACCM was modified by replacing fetal bovine serum with methyl-β-cyclodextrin to generate ACCM-2. Cultivation of NMII in ACCM-2 with moderate shaking and in 2.5% oxygen yielded 4 to 5 logs of growth over 7 days. Similar growth was achieved with the virulent Nine Mile phase I and G isolates of
C. burnetii
. Colonies that developed after 6 days of growth in ACCM-2 agarose were approximately 0.5 mm in diameter, roughly 5-fold larger than those formed in ACCM agarose. By electron microscopy, colonies consisted primarily of the
C. burnetii
small cell variant morphological form. NMII was successfully cultured in ACCM-2 when medium was inoculated with as little as 10 genome equivalents contained in tissue homogenates from infected SCID mice. A completely axenic
C. burnetii
genetic transformation system was developed using ACCM-2 that allowed isolation of transformants in about 2 1/2 weeks. Transformation experiments demonstrated clonal populations in colonies and a transformation frequency of approximately 5 × 10
−5
. Cultivation in ACCM-2 will accelerate development of
C. burnetii
genetic tools and provide a sensitive means of primary isolation of the pathogen from Q fever patients.
Immediate Reduction of Salmonella enterica Serotype Typhimurium Viability via Membrane Destabilization following Exposure to Multiple-Hurdle Treatments with Heated, Acidified Organic Acid Salt Solutions
Authors: Milillo S. R. , Martin E. , Muthaiyan A. , Ricke S. C.
Published: April 2011

The antimicrobial activity of organic acids in combination with nonchemical treatments was evaluated for inactivation of
Salmonella enterica
serotype Typhimurium within 1 min. It was observed that the effectiveness of the multiple-hurdle treatments was temperature (
P
≤ 0.05) and pH (
P
≤ 0.05) dependent and corresponded to the degree of organic acid lipophilicity (sodium acetate being least effective and sodium propionate being the most effective). This led to the hypothesis that the loss in viability was due at least in part to cell membrane disruption. Evaluation of osmotic response, potassium ion leakage, and transmission electron micrographs confirmed treatment effects on the cell membrane. Interestingly, all treatments, even those with no effect on viability, such as with sodium acetate, resulted in measurable cellular stress. Microarray experiments explored the specific response of
S
. Typhimurium to sodium acetate and sodium propionate, the most similar of the tested treatments in terms of pK
a
and ionic strength, and found little difference in the changes in gene expression following exposure to either, despite their very different effects on viability. Taken together, the results reported support our hypothesis that treatment with heated, acidified, organic acid salt solutions for 1 min causes loss of
S
. Typhimurium viability at least in part by membrane damage and that the degree of effectiveness can be correlated with lipophilicity of the organic acid. Overall, the data presented here indicate that a combined thermal, acidified sodium propionate treatment can provide an effective antimicrobial treatment against
Salmonella
.
Hpa2 Required by HrpF To Translocate Xanthomonas oryzae Transcriptional Activator-Like Effectors into Rice for Pathogenicity
Authors: Li Yu-Rong , Che Yi-Zhou , Zou Hua-Song , Cui Yi-Ping , Guo Wei , Zou Li-Fang , Biddle Eulandria M. , Yang Ching-Hong , Chen Gong-You
Published: April 2011

Xanthomonas oryzae
pv. oryzicola, the causative agent of bacterial leaf streak, injects a plethora of effectors through the type III secretion system (T3SS) into rice cells to cause disease. The T3SS, encoded by the
hrp
genes, is essential for the pathogen to elicit the hypersensitive response (HR) in nonhost tobacco and for pathogenicity in host rice. Whether or not a putative lytic transglycosylase, Hpa2, interacts with a translocon protein, HrpF, to facilitate bacterial pathogenicity remains unknown. Here we demonstrated that both the
hpa2
and
hrpF
genes are required for the pathogenicity of
X. oryzae
pv. oryzicola strain RS105 in rice but not for HR induction in tobacco. The expression of
hpa2
was positively regulated by HrpG and HrpD6 but not by HrpX.
In vivo
secretion and subcellular localization analyses confirmed that Hpa2 secretion is dependent on HpaB (a T3SS exit protein) and that Hpa2 binds to the host cell membrane. Protein-protein assays demonstrated that Hpa2 interacts with HrpF.
In planta
translocation of AvrXa10 indicated that the mutation in
hpa2
and
hrpF
inhibits the injection of the HpaB-dependent transcriptional activator-like (TAL) effector into rice. These findings suggest that Hpa2 and HrpF form a complex to translocate T3S effectors into plant cells for pathogenesis in host rice.
Cocirculation of Two Transmission Lineages of Echovirus 6 in Jinan, China, as Revealed by Environmental Surveillance and Sequence Analysis
Authors: Tao Zexin , Wang Haiyan , Li Yan , Xu Aiqiang , Zhang Yong , Song Lizhi , Yoshida Hiromu , Xu Qing , Yang Jing , Zhang Yan , Liu Yao , Feng Lei , Xu Wenbo
Published: April 2011

Enterovirus environmental surveillance on sewage from the city of Jinan, Shandong Province, China, was initiated in 2008. Thirty echovirus 6 (E6) strains—1 in 2008 and 29 in 2010—were isolated and identified. Most E6 isolates (
n
= 21) came from the sewage collected on August 2010, revealing high local E6 activity at that time. Interestingly, the VP1 sequences of most isolates, even from the same sewage, were not identical. Phylogenetic analysis of VP1 sequences revealed two lineages for these isolates, with 78.0 to 80.0% nucleotide identities with one another, 94.8 to 100.0% identity within the major lineage, and 92.7 to 98.5% identity within the minor one. The VP1 sequences of environmental isolates, clinical isolates from 1998 to 2010, and global E6 were subjected to evolutionary analysis using Bayesian phylodynamic methods. The inferred E6 VP1 ancestral sequence dated back to 1901 (range, 1873 to 1928) and evolved with 7.047 × 10
−3
substitutions per site per year. Shandong E6 segregated into three clusters, and the two environmental lineages belonged to clusters A and C, which originated in 2003 and 1992, respectively. The antigenicity analysis via neutralization assay confirmed great antigenic differences between Shandong isolates and a prototype strain. These findings underscore the value of continuous environmental surveillance and genetic analysis to monitor circulating enteroviruses in the population and give further insight into E6 evolution.
The F-Box Protein Fbp1 Regulates Sexual Reproduction and Virulence in Cryptococcus neoformans
Authors: Liu Tong-Bao , Wang Yina , Stukes Sabriya , Chen Qing , Casadevall Arturo , Xue Chaoyang
Published: April 2011

Cryptococcus neoformansis the leading cause of fungal meningitis in immunocomprised populations. Although extensive studies have been conducted on signal transduction pathways important for fungal sexual reproduction and virulence, how fungal virulence is regulated during infection is still not understood. In this study, we identified the F-box protein Fbp1, which contains a putative F-box domain and 12 leucine-rich repeats (LRR). Althoughfbp1mutants showed normal growth and produced normal major virulence factors, such as melanin and capsule, Fbp1 was found to be essential for fungal virulence, asfbp1mutants were avirulent in a murine systemic-infection model. Fbp1 is also important for fungal sexual reproduction. Basidiospore production was blocked in bilateral mating betweenfbp1mutants, even though normal dikaryotic hyphae were observed during mating.In vitroassays of stress responses revealed thatfbp1mutants are hypersensitive to SDS, but not calcofluor white (CFW) or Congo red, indicating that Fbp1 may regulate cell membrane integrity. Fbp1 physically interacts with Skp1 homologues in bothSaccharomyces cerevisiaeandC. neoformansvia its F-box domain, suggesting it may function as part of an SCF (Skp1, Cullins, F-box proteins) E3 ligase. Overall, our study revealed that the F-box protein Fbp1 is essential for fungal sporulation and virulence inC. neoformans, which likely represents a conserved novel virulence control mechanism that involves the SCF E3 ubiquitin ligase-mediated proteolysis pathway.
Targeted Gene Deletion and
In Vivo
Analysis of Putative Virulence Gene Function in the Pathogenic Dermatophyte Arthroderma benhamiae
Authors: Grumbt Maria , Defaweux Valérie , Mignon Bernard , Monod Michel , Burmester Anke , Wöstemeyer Johannes , Staib Peter
Published: April 2011

Dermatophytes cause the majority of superficial mycoses in humans and animals. However, little is known about the pathogenicity of this specialized group of filamentous fungi, for which molecular research has been limited thus far. During experimental infection of guinea pigs by the human pathogenic dermatophyte
Arthroderma benhamiae
, we recently detected the activation of the fungal gene encoding malate synthase AcuE, a key enzyme of the glyoxylate cycle. By the establishment of the first genetic system for
A. benhamiae
, specific Δ
acuE
mutants were constructed in a wild-type strain and, in addition, in a derivative in which we inactivated the nonhomologous end-joining pathway by deletion of the
A. benhamiae KU70
gene. The absence of Aben
KU70
resulted in an increased frequency of the targeted insertion of linear DNA by homologous recombination, without notably altering the monitored
in vitro
growth abilities of the fungus or its virulence in a guinea pig infection model. Phenotypic analyses of Δ
acuE
mutants and complemented strains depicted that malate synthase is required for the growth of
A. benhamiae
on lipids, major constituents of the skin. However, mutant analysis did not reveal a pathogenic role of the
A. benhamiae
enzyme in guinea pig dermatophytosis or during epidermal invasion of the fungus in an
in vitro
model of reconstituted human epidermis. The presented efficient system for targeted genetic manipulation in
A. benhamiae
, paired with the analyzed infection models, will advance the functional characterization of putative virulence determinants in medically important dermatophytes.
The Putative Saccharomyces cerevisiae Hydrolase Ldh1p Is Localized to Lipid Droplets
Authors: Thoms Sven , Debelyy Mykhaylo O. , Connerth Melanie , Daum Günther , Erdmann Ralf
Published: April 2011

Here, we report the identification of a novel hydrolase in
Saccharomyces cerevisiae
. Ldh1p (systematic name, Ybr204cp) comprises the typical GXSXG-type lipase motif of members of the α/β-hydrolase family and shares some features with the peroxisomal lipase Lpx1p. Both proteins carry a putative peroxisomal targeting signal type1 (PTS1) and can be aligned with two regions of homology. While Lpx1p is known as a peroxisomal enzyme, subcellular localization studies revealed that Ldh1p is predominantly localized to lipid droplets, the storage compartment of nonpolar lipids. Ldh1p is not required for the function and biogenesis of peroxisomes, and targeting of Ldh1p to lipid droplets occurs independently of the PTS1 receptor Pex5p.
Involvement of the Saccharomyces cerevisiae Hydrolase Ldh1p in Lipid Homeostasis
Authors: Debelyy Mykhaylo O. , Thoms Sven , Connerth Melanie , Daum Günther , Erdmann Ralf
Published: April 2011

Here, we report the functional characterization of the newly identified lipid droplet hydrolase Ldh1p. Recombinant Ldh1p exhibits esterase and triacylglycerol lipase activities. Mutation of the serine in the hydrolase/lipase motif GXSXG completely abolished esterase activity. Ldh1p is required for the maintenance of a steady-state level of the nonpolar and polar lipids of lipid droplets. A characteristic feature of the
Saccharomyces cerevisiae
Δ
ldh1
strain is the appearance of giant lipid droplets and an excessive accumulation of nonpolar lipids and phospholipids upon growth on medium containing oleic acid as a sole carbon source. Ldh1p is thought to play a role in maintaining the lipid homeostasis in yeast by regulating both phospholipid and nonpolar lipid levels.
Biological Systems Discovery In Silico: Radical
S
-Adenosylmethionine Protein Families and Their Target Peptides for Posttranslational Modification
Authors: Haft Daniel H. , Basu Malay Kumar
Published: April 2011

Data mining methods in bioinformatics and comparative genomics commonly rely on working definitions of protein families from prior computation. Partial phylogenetic profiling (PPP), by contrast, optimizes family sizes during its searches for the cooccurring protein families that serve different roles in the same biological system. In a large-scale investigation of the incredibly diverse radical
S
-adenosylmethionine (SAM) enzyme superfamily, PPP aided in building a collection of 68 TIGRFAMs hidden Markov models (HMMs) that define nonoverlapping and functionally distinct subfamilies. Many identify radical SAM enzymes as molecular markers for multicomponent biological systems; HMMs defining their partner proteins also were constructed. Newly found systems include five groupings of protein families in which at least one marker is a radical SAM enzyme while another, encoded by an adjacent gene, is a short peptide predicted to be its substrate for posttranslational modification. The most prevalent, in over 125 genomes, featuring a peptide that we designate SCIFF (
s
ix
c
ysteines
i
n
f
orty-
f
ive residues), is conserved throughout the class
Clostridia
, a distribution inconsistent with putative bacteriocin activity. A second novel system features a tandem pair of putative peptide-modifying radical SAM enzymes associated with a highly divergent family of peptides in which the only clearly conserved feature is a run of His-Xaa-Ser repeats. A third system pairs a radical SAM domain peptide maturase with selenocysteine-containing targets, suggesting a new biological role for selenium. These and several additional novel maturases that cooccur with predicted target peptides share a C-terminal additional 4Fe4S-binding domain with PqqE, the subtilosin A maturase AlbA, and the predicted mycofactocin and Nif11-class peptide maturases as well as with activators of anaerobic sulfatases and quinohemoprotein amine dehydrogenases. Radical SAM enzymes with this additional domain, as detected by TIGR04085, significantly outnumber lantibiotic synthases and cyclodehydratases combined in reference genomes while being highly enriched for members whose apparent targets are small peptides. Interpretation of comparative genomics evidence suggests unexpected (nonbacteriocin) roles for natural products from several of these systems.
ATP Requirement for Acidic Resistance in Escherichia coli
Authors: Sun Yirong , Fukamachi Toshihiko , Saito Hiromi , Kobayashi Hiroshi
Published: April 2011

ATP participates in many cellular metabolic processes as a major substrate to supply energy. Many systems for acidic resistance (AR) under extremely acidic conditions have been reported, but the role of ATP has not been examined. To clarify whether or not ATP is necessary for the AR in
Escherichia coli
, the AR of mutants deficient in genes for ATP biosynthesis was investigated in this study. The deletion of
purA
or
purB
, each of which encodes enzymes to produce AMP from inosinate (IMP), markedly decreased the AR. The content of ATP in these mutants decreased rapidly at pH 2.5 compared to that of the wild type. The AR was again decreased significantly by the mutation of
adk
, which encoded an enzyme to produce ADP from AMP. The DNA damage in the
purA
and
purB
mutants was higher than that in the wild type. These results demonstrated that metabolic processes that require ATP participate in survival under extremely acidic conditions, and that one such system is the ATP-dependent DNA repair system.
Genome Sequences of Salmonella enterica Serovar Typhimurium, Choleraesuis, Dublin, and Gallinarum Strains of Well- Defined Virulence in Food-Producing Animals
Authors: Richardson Emily J. , Limaye Bhakti , Inamdar Harshal , Datta Avik , Manjari K. Sunitha , Pullinger Gillian D. , Thomson Nicholas R. , Joshi Rajendra R. , Watson Michael , Stevens Mark P.
Published: April 2011

Salmonella enterica
is an animal and zoonotic pathogen of worldwide importance and may be classified into serovars differing in virulence and host range. We sequenced and annotated the genomes of serovar Typhimurium, Choleraesuis, Dublin, and Gallinarum strains of defined virulence in each of three food-producing animal hosts. This provides valuable measures of intraserovar diversity and opportunities to formally link genotypes to phenotypes in target animals.
Complete Genome Sequence of the Thermoacidophilic Crenarchaeon Thermoproteus uzoniensis 768-20
Authors: Mardanov Andrey V. , Gumerov Vadim M. , Beletsky Alexey V. , Prokofeva Maria I. , Bonch-Osmolovskaya Elizaveta A. , Ravin Nikolai V. , Skryabin Konstantin G.
Published: April 2011

Thermoproteus uzoniensis
768-20 is a thermoacidophilic anaerobic crenarchaeon isolated from a solfataric field in Kamchatka, Russia. The complete genome sequence reveals genes for protein and carbohydrate-active enzymes, beta-oxidation of fatty acids, the Embden-Meyerhof and Entner-Doudoroff pathways for glucose metabolism, the tricarboxylic acid cycle, the dicarboxylate/4-hydroxybutyrate cycle, hydrogenase, and sulfur reductase.
Genome Sequence of Lactobacillus amylovorus GRL1118, Isolated from Pig Ileum
Authors: Kant Ravi , Paulin Lars , Alatalo Edward , de Vos Willem M. , Palva Airi
Published: April 2011

Lactobacillus amylovorusis a common member of the beneficial microbiota present in the pig gastrointestinal tract. Here, we report the genome sequence of the surface layer (S-layer) protein-carrying and potentially probiotic strainL. amylovorusGRL1118, which was isolated from porcine ileum and which shows strong adherence to pig intestinal epithelial cells.
The Genome of Erysipelothrix rhusiopathiae, the Causative Agent of Swine Erysipelas, Reveals New Insights into the Evolution of Firmicutes and the Organism's Intracellular Adaptations
Authors: Ogawa Yohsuke , Ooka Tadasuke , Shi Fang , Ogura Yoshitoshi , Nakayama Keisuke , Hayashi Tetsuya , Shimoji Yoshihiro
Published: April 2011

Erysipelothrix rhusiopathiaeis a Gram-positive bacterium that represents a new class,Erysipelotrichia, in the phylumFirmicutes. The organism is a facultative intracellular pathogen that causes swine erysipelas, as well as a variety of diseases in many animals. Here, we report the first complete genome sequence analysis of a member of the classErysipelotrichia. TheE. rhusiopathiaegenome (1,787,941 bp) is one of the smallest genomes in the phylumFirmicutes. Phylogenetic analyses based on the 16S rRNA gene and 31 universal protein families suggest thatE. rhusiopathiaeis phylogenetically close toMollicutes, which comprisesMycoplasmaspecies. Genome analyses show that the overall features of theE. rhusiopathiaegenome are similar to those of other Gram-positive bacteria; it possesses a complete set of peptidoglycan biosynthesis genes, two-component regulatory systems, and various cell wall-associated virulence factors, including a capsule and adhesins. However, it lacks many orthologous genes for the biosynthesis of wall teichoic acids (WTA) and lipoteichoic acids (LTA) and thedltABCDoperon, which is responsible ford-alanine incorporation into WTA and LTA, suggesting that the organism has an atypical cell wall. In addition, likeMollicutes, its genome shows a complete loss of fatty acid biosynthesis pathways and lacks the genes for the biosynthesis of many amino acids, cofactors, and vitamins, indicating reductive genome evolution. The genome encodes nine antioxidant factors and nine phospholipases, which facilitate intracellular survival in phagocytes. Thus, theE. rhusiopathiaegenome represents evolutionary traits of bothFirmicutesandMollicutesand provides new insights into its evolutionary adaptations for intracellular survival.
First Case of Fulminant Sepsis Due to Wohlfahrtiimonas chitiniclastica
Authors: Almuzara Marisa N. , Palombarani Susana , Tuduri Alicia , Figueroa Silvia , Gianecini Ariel , Sabater Laura , Ramirez Maria S. , Vay Carlos A.
Published: April 2011

We report the first case of fulminant sepsis due to
Wohlfahrtiimonas chitiniclastica
. This case is also the first one reported in South America. We emphasize the importance of recognizing bacteria that live in the larvae of a parasitic fly as the causative agent of severe infections in homeless patients.
Application of TaqMan Low-Density Arrays for Simultaneous Detection of Multiple Respiratory Pathogens
Authors: Kodani Maja , Yang Genyan , Conklin Laura M. , Travis Tatiana C. , Whitney Cynthia G. , Anderson Larry J. , Schrag Stephanie J. , Taylor Thomas H. , Beall Bernard W. , Breiman Robert F. , Feikin Daniel R. , Njenga M. Kariuki , Mayer Leonard W. , Oberste M. Steven , Tondella Maria Lucia C. , Winchell Jonas M. , Lindstrom Stephen L. , Erdman Dean D. , Fields Barry S.
Published: April 2011

The large and growing number of viral and bacterial pathogens responsible for respiratory infections poses a challenge for laboratories seeking to provide rapid and comprehensive pathogen identification. We evaluated a novel application of the TaqMan low-density array (TLDA) cards for real-time PCR detection of 21 respiratory-pathogen targets. The performance of the TLDA was compared to that of individual real-time PCR (IRTP) assays with the same primers and probes using (i) nucleic acids extracted from the 21 pathogen strains and 66 closely related viruses and bacteria and (ii) 292 clinical respiratory specimens. With spiked samples, TLDA cards were about 10-fold less sensitive than IRTP assays. By using 292 clinical specimens to generate 2,238 paired individual assays, the TLDA card exhibited 89% sensitivity (95% confidence interval [CI], 86 to 92%; range per target, 47 to 100%) and 98% specificity (95% CI, 97 to 99%; range per target, 85 to 100%) overall compared to IRTP assays as the gold standard with a threshold cycle (

C
T

) cutoff of 43. The TLDA card approach offers promise for rapid and simultaneous identification of multiple respiratory pathogens for outbreak investigations and disease surveillance.
Laboratory and Clinical Evaluation of Screening Agar Plates for Detection of Carbapenem-Resistant Enterobacteriaceae from Surveillance Rectal Swabs
Authors: Adler Amos , Navon-Venezia Shiri , Moran-Gilad Jacob , Marcos Evgeniya , Schwartz David , Carmeli Yehuda
Published: April 2011

The increased worldwide spread of carbapenem-resistant
Enterobacteriaceae
(CRE) emphasizes the need for a sensitive screening procedure to identify these microorganisms. Gastrointestinal carriers may serve as the reservoir for cross-transmission in the health care setting, and thus active surveillance is a key part in preventing the spread of such strains. Three agar-based methods for direct CRE detection from rectal swabs were compared: CHROMagar-KPC (Chrom); MacConkey agar with imipenem at 1 μg/ml (MacI); and MacConkey plates with imipenem, meropenem, and ertapenem disks (MacD). First, we compared the levels of detection (LODs) of 10 molecularly characterized carbapenemase-producing
Enterobacteriaceae
strains by the three methods. Second, we compared their performance in a surveillance study using rectal swabs (
n
= 139). The LODs of carbapenemase-producing
Enterobacteriaceae
strains were influenced by their MICs to carbapenems and were best for MacI, followed by Chrom. The MacD method was able to detect only the strains exhibiting MICs of ≥32 μg/ml to at least ertapenem. In the surveillance study, both Chrom and MacI had greater sensitivity (85%) than MacD (76%). However, MacI was the most specific method. In conclusion, MacI appears to be most appropriate medium for the detection of CRE in settings in which multiclonal CRE strains with various MICs to carbapenems are circulating.
Intercompartmental Recombination of HIV-1 Contributes toenvIntrahost Diversity and Modulates Viral Tropism and Sensitivity to Entry Inhibitors
Authors: Brown Richard J. P. , Peters Paul J. , Caron Catherine , Gonzalez-Perez Maria Paz , Stones Leanne , Ankghuambom Chiambah , Pondei Kemebradikumo , McClure C. Patrick , Alemnji George , Taylor Stephen , Sharp Paul M. , Clapham Paul R. , Ball Jonathan K.
Published: April 2011

HIV-1 circulates within an infected host as a genetically heterogeneous viral population. Viral intrahost diversity is shaped by substitutional evolution and recombination. Although many studies have speculated that recombination could have a significant impact on viral phenotype, this has never been definitively demonstrated. We report here phylogenetic and subsequent phenotypic analyses of envelope genes obtained from HIV-1 populations present in different anatomical compartments. Assessment ofenvcompartmentalization from immunologically discrete tissues was assessed utilizing a single genome amplification approach, minimizingin vitro-generated artifacts. Genetic compartmentalization of variants was frequently observed. In addition, multiple incidences of intercompartment recombination, presumably facilitated by low-level migration of virus or infected cells between different anatomic sites and coinfection of susceptible cells by genetically divergent strains, were identified. These analyses demonstrate that intercompartment recombination is a fundamental evolutionary mechanism that helps to shape HIV-1envintrahost diversity in natural infection. Analysis of the phenotypic consequences of these recombination events showed that genetic compartmentalization often correlates with phenotypic compartmentalization and that intercompartment recombination results in phenotype modulation. This represents definitive proof that recombination can generate novel combinations of phenotypic traits which differ subtly from those of parental strains, an important phenomenon that may have an impact on antiviral therapy and contribute to HIV-1 persistencein vivo.
Temporal Profiling of the Coding and Noncoding Murine Cytomegalovirus Transcriptomes
Authors: Lacaze Paul , Forster Thorsten , Ross Alan , Kerr Lorraine E. , Salvo-Chirnside Eliane , Lisnic Vanda Juranic , López-Campos Guillermo H. , García-Ramírez José J. , Messerle Martin , Trgovcich Joanne , Angulo Ana , Ghazal Peter
Published: April 2011

The global transcriptional program of murine cytomegalovirus (MCMV), involving coding, noncoding, and antisense transcription, remains unknown. Here we report an oligonucleotide custom microarray platform capable of measuring both coding and noncoding transcription on a genome-wide scale. By profiling MCMV wild-type and immediate-early mutant strains in fibroblasts, we found rapid activation of the transcriptome by 6.5 h postinfection, with absolute dependency on
ie3
, but not
ie1
or
ie2
, for genomic programming of viral gene expression. Evidence is also presented to show, for the first time, genome-wide noncoding and bidirectional transcription at late stages of MCMV infection.
Prevention of sport injury II: a systematic review of clinical science research
Authors: McBain Kellen , Shrier Ian , Shultz Rebecca , Meeuwisse Willem H , Klügl Martin , Garza Daniel , Matheson Gordon O
Published: April 2011

Objective

To characterise the nature of the sport injury prevention literature by reviewing published articles that evaluate specific clinical interventions designed to reduce sport injury risks.

Data sources

PubMed, Cinahl, Web of Science and Embase.

Main results

Only 139 of 2525 articles retrieved met the inclusion criteria. Almost 40% were randomised controlled trials and 30.2% were cohort studies. The focus of the study was protective equipment in 41%, training in 32.4%, education in 7.9%, rules and regulations in 4.3%, and 13.3% involved a combination of the above. Equipment research studied stability devices (42.1%), head and face protectors (33.3%), attenuating devices (17.5%) as well as other devices (7%). Training studies often used a combination of interventions (eg, balance and stretching); most included balance and coordination (63.3%), with strength and power (36.7%) and stretching (22.5%) being less common. Almost 70% of the studies examined lower extremity injuries, and a majority of these were joint (non-bone)-ligament injuries. Contact sports were most frequently studied (41.5%), followed by collision (39.8%) and non-contact (20.3%).

Conclusion

The authors found only 139 publications in the existing literature that examined interventions designed to prevent sports injury. Of these, the majority investigated equipment or training interventions whereas only 4% focused on changes to the rules and regulations that govern sport. The focus of intervention research is on acute injuries in collision and contact sports whereas only 20% of the studies focused on non-contact sports.