bluuebunny/crossref_metadata_2025 huggingface dataset:
Ventricular Septal Aneurysm: A Complication of Myocardial Infarction
Authors: Dixon Simon R. , Legget Malcolm E. , Wong Selwyn P.
Published: December 2007

We report the case of a ventricular septal aneurysm in a patient with a previous inferior myocardial infarction. Two‐dimensional echocardiography demonstrated a cystic cavity in the muscular septum with a small communication into the left ventricle. No evidence of left‐to‐right shunt was detected with Doppler echocardiography or during left ventriculography.
Design of an Ultrasound Contrast Agent for Myocardial Perfusion
Authors: Schneider Michel
Published: December 2007

Myocardial contrast echography (MCE) has been a major research objective in cardiovascular ultrasound for almost two decades. The design of a contrast agent fulfilling the needs of MCE requires taking into consideration a number of points: a basic decision has to be made whether a deposit agent or a free‐flowing agent would be more appropriate and whether an agent active at low/medium mechanical index (MI) is preferable to an agent active only at high MI; only a small percentage of the cardiac output enters the coronary microcirculation, which means that highly sensitive bubble detection methods, such as harmonic imaging or pulse inversion, are needed; the low velocity of blood in the microcirculation that leads to extensive bubble destruction during imaging means that intermittent imaging and/or an agent active at low MI is (are) required; the duration of the contrast effect must be sufficient to allow a complete examination and is affected by the rate of contrast administration; the performance of the contrast agent should not be equipment‐dependent. The ultimate goal in MCE is to be able to quantify blood flow in the various segments to determine if adequate oxygenation is achieved. Ultrasound‐mediated bubble destruction followed by the measurement of bubble replenishment kinetics opens new perspectives for quantification. SonoVue is a free‐flowing ultrasound contrast agent made of sulphur hexafluoride microbubbles stabilized by a highly elastic phospholipid monolayer. SonoVue is able to produce myocardial opacification at a wide range of acoustic pressures and in particular at Mis as low as 0.1. Its performance is not equipment‐dependent. Good results for myocardial opacification have been observed in all animal species tested (dogs, minipigs, rabbits), using continuous as well as intermittent imaging. Trials are in progress to demonstrate the clinical utility of SonoVue for rest and stress perfusion studies, in particular for the diagnosis of CAD, the detection of myocardial infarction, the assessment of the success of interventions and myocardial viability, and the detection of hibernating myocardium.
Clinical Experience with SonoVue in Myocardial Perfusion Imaging
Authors: Rovai Daniele , Morales Maria‐Aurora , Amyot Robert , Abbate Antonio '
Published: December 2007

Ultrasound‐enhancing agents have the potential to evaluate myocardial perfusion, adding a new dimension to echocardiography. This article summarizes the clinical studies involving SonoVue, a new intravenous ultrasound contrast agent, in assessing myocardial perfusion. Safe and well tolerated, SonoVue coupled with echocardiography has the capability to identify perfusion abnormalities, as confirmed by scintigraphic imaging. While the optimal modalities for ultrasound perfusion assessment are not yet determined, numerous technical advances have been introduced: continuous infusion or slow intravenous administration of the agent, harmonic intermittent imaging, pulse inversion, background subtraction, color coding, and others. SonoVue is a promising new agent in the booming field of myocardial contrast echocardiography.
Identification of β-Lactamase in Antibiotic-Resistant
Bacillus cereus
Spores
Authors: Fenselau Catherine , Havey Crystal , Teerakulkittipong Nuttinee , Swatkoski Stephen , Laine Olli , Edwards Nathan
Published: December 2007

β-Lactamase type I is reported for the first time to occur in the sporulated form in a penicillin-resistant
Bacillus
species. The enzyme was readily characterized from the
B. cereus
5/B line (ATCC 13061) by mass spectrometry and two-dimensional gel electrophoresis.
Molecular Detection and Characterization of Gastroenteritis Viruses Occurring Naturally in the Stream Waters of Manaus, Central Amazônia, Brazil
Authors: Miagostovich Marize P. , Ferreira Fabiana F. M. , Guimarães Flávia R. , Fumian Túlio M. , Diniz-Mendes Leonardo , Luz Sérgio Luiz B. , Silva Luciete A. , Leite José Paulo G.
Published: December 2007

To assess the presence of the four main viruses responsible for human acute gastroenteritis in a hydrographic network impacted by a disordered urbanization process, a 1-year study was performed involving water sample collection from streams in the hydrographic basin surrounding the city of Manaus, Amazonas, Brazil. Thirteen surface water sample collection sites, including different areas of human settlement characterized as urban, rural, and primary forest, located in the Tarumã-Açu, São Raimundo, Educandos, and Puraquequara microbasins, were defined with a global positioning system. At least one virus was detected in 59.6% (31/52) of the water samples analyzed, and rotavirus was the most frequent (44.2%), followed by human adenovirus (30.8%), human astrovirus (15.4%), and norovirus (5.8%). The viral contamination observed mainly in the urban streams reflected the presence of a local high-density population and indicated the gastroenteritis burden from pathogenic viruses in the water, principally due to recreational activities such as bathing. The presence of viral genomes in areas where fecal contamination was not demonstrated by bacterial indicators suggests prolonged virus persistence in aquatic environments and emphasizes the enteric virus group as the most reliable for environmental monitoring.
Root Infection and Systemic Colonization of Maize byColletotrichum graminicola
Authors: Sukno Serenella A. , García Verónica M. , Shaw Brian D. , Thon Michael R.
Published: December 2007

Colletotrichum graminicolais a filamentous ascomycete that causes anthracnose disease of maize. While the fungus can cause devastating foliar leaf blight and stalk rot diseases, little is known about its ability to infect roots. Previously published reports suggest thatC. graminicolamay infect maize roots and that root infections may contribute to the colonization of aboveground plant tissues, leading to disease. To determine whetherC. graminicolacan infect maize roots and whether root infections can result in the colonization of aboveground plant tissues, we developed a green fluorescent protein-tagged strain and used it to study the plant root colonization and infection process in vivo. We observed structures produced by other root pathogenic fungi, including runner hyphae, hyphopodia, and microsclerotia. A mosaic pattern of infection resulted from specific epidermal and cortical cells becoming infected by intercellular hyphae while surrounding cells were uninfected, a pattern that is distinctly different from that described for leaves. Interestingly, falcate conidia, normally restricted to acervuli, were also found filling epidermal cells and root hairs. Twenty-eight percent of plants challenged with soilborne inoculum became infected in aboveground plant parts (stem and/or leaves), indicating that root infection can lead to asymptomatic systemic colonization of the plants. Many of the traits observed forC. graminicolahave been previously reported for other root-pathogenic fungi, suggesting that these traits are evolutionally conserved in multiple fungal lineages. These observations suggest that root infection may be an important component of the maize anthracnose disease cycle.
Secretion of Flavins byShewanellaSpecies and Their Role in Extracellular Electron Transfer
Authors: von Canstein Harald , Ogawa Jun , Shimizu Sakayu , Lloyd Jonathan R.
Published: December 2007

Fe(III)-respiring bacteria such asShewanellaspecies play an important role in the global cycle of iron, manganese, and trace metals and are useful for many biotechnological applications, including microbial fuel cells and the bioremediation of waters and sediments contaminated with organics, metals, and radionuclides. Several alternative electron transfer pathways have been postulated for the reduction of insoluble extracellular subsurface minerals, such as Fe(III) oxides, byShewanellaspecies. One such potential mechanism involves the secretion of an electron shuttle. Here we identify for the first time flavin mononucleotide (FMN) and riboflavin as the extracellular electron shuttles produced by a range ofShewanellaspecies. FMN secretion was strongly correlated with growth and exceeded riboflavin secretion, which was not exclusively growth associated but was maximal in the stationary phase of batch cultures. Flavin adenine dinucleotide was the predominant intracellular flavin but was not released by live cells. The flavin yields were similar under both aerobic and anaerobic conditions, with total flavin concentrations of 2.9 and 2.1 μmol per gram of cellular protein, respectively, after 24 h and were similar under dissimilatory Fe(III)-reducing conditions and when fumarate was supplied as the sole electron acceptor. The flavins were shown to act as electron shuttles and to promote anoxic growth coupled to the accelerated reduction of poorly crystalline Fe(III) oxides. The implications of flavin secretion byShewanellacells living at redox boundaries, where these mineral phases can be significant electron acceptors for growth, are discussed.
Low Temperature Decreases the Phylogenetic Diversity of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofiltration Systems
Authors: Urakawa Hidetoshi , Tajima Yoshiyuki , Numata Yoshiyuki , Tsuneda Satoshi
Published: December 2007

The phylogenetic diversity and species richness of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were examined with aquarium biofiltration systems. Species richness, deduced from rarefaction analysis, and diversity indices indicated that the phylogenetic diversity and species richness of AOA are greater than those of AOB; the diversity of AOA and of AOB is minimized in cold-water aquaria. This finding implies that temperature is a key factor influencing the population structure and diversity of AOA and AOB in aquarium biofiltration systems.
Determination of the Shear Force at the Balance between Bacterial Attachment and Detachment in Weak-Adherence Systems, Using a Flow Displacement Chamber
Authors: Nejadnik M. Reza , van der Mei Henny C. , Busscher Henk J. , Norde Willem
Published: December 2007

We introduce a procedure for determining shear forces at the balance between attachment and detachment of bacteria under flow. This procedure can be applied to derive adhesion forces in weak-adherence systems, such as polymer brush coatings, which are currently at the center of attention for their control of bacterial adhesion and biofilm formation.
Role of
galK
and
galM
in Galactose Metabolism by
Streptococcus thermophilus
Authors: Vaillancourt Katy , Bédard Nathalie , Bart Christian , Tessier Mélanie , Robitaille Gilles , Turgeon Nathalie , Frenette Michel , Moineau Sylvain , Vadeboncoeur Christian
Published: December 2007

Streptococcus thermophilus
is unable to metabolize the galactose moiety of lactose. In this paper, we show that a transformant of
S. thermophilus
SMQ-301 expressing
Streptococcus salivarius galK
and
galM
was able to grow on galactose and expelled at least twofold less galactose into the medium during growth on lactose.
Aerosolization of Particulate (1→3)-β-
d
-Glucan from Moldy Materials
Authors: Seo Sung-Chul , Reponen Tiina , Levin Linda , Borchelt Tiffany , Grinshpun Sergey A.
Published: December 2007

Mold-damaged building materials may contain biologically active agents, such as (1→3)-β-
d
-glucan, allergens, and mycotoxins, which have been associated with adverse health effects. The release of these components from contaminated surfaces into the air is not well understood. The purpose of this study was to characterize the release of particulate (1→3)-β-
d
-glucan from the surface of artificially mold-contaminated materials.
Aspergillus versicolor
and
Stachybotrys chartarum
were grown on malt extract agar (MEA), white ceiling tiles, and a wall-papered gypsum board for 1 and 6 months. The (1→3)-β-
d
-glucan on the surfaces of moldy materials and in air samples collected from these materials was analyzed by the
Limulus
amebocyte lysate assay. The aerosolization ratio was defined as the amount of (1→3)-β-
d
-glucan in the air divided by the amount on the surface. The results showed that the aerosolization of particulate (1→3)-β-
d
-glucan was influenced mainly by the type of material and the fungal species. For
A. versicolor
, the aerosolization ratios of particulate (1→3)-β-
d
-glucan released from the three types of material were not significantly different. However, the ratios for
S. chartarum
released from ceiling tiles and gypsum board were significantly higher than the ratios for this organism released from MEA (
P
< 0.001) and were comparable to those for
A. versicolor
. These findings indicate that the use of MEA in aerosolization experiments is likely to underestimate the release of
S. chartarum
particles from building materials. These results provide important background information for design of future laboratory or animal experiments, as well as for interpretation of field measurement data.
Characterization of the Gene Cluster Responsible for Cylindrospermopsin Biosynthesis
Authors: Mihali Troco Kaan , Kellmann Ralf , Muenchhoff Julia , Barrow Kevin D. , Neilan Brett A.
Published: December 2007

Toxic cyanobacterial blooms cause economic losses and pose significant public health threats on a global scale. Characterization of the gene cluster for the biosynthesis of the cyanobacterial toxin cylindrospermopsin (cyr) inCylindrospermopsis raciborskiiAWT205 is described, and the complete biosynthetic pathway is proposed. Thecyrgene cluster spans 43 kb and is comprised of 15 open reading frames containing genes required for the biosynthesis, regulation, and export of the toxin. Biosynthesis is initiated via an amidinotransfer onto glycine followed by five polyketide extensions and subsequent reductions, and rings are formed via Michael additions in a stepwise manner. The uracil ring is formed by a novel pyrimidine biosynthesis mechanism and tailoring reactions, including sulfation and hydroxylation that complete biosynthesis. These findings enable the design of toxic strain-specific probes and allow the future study of the regulation and biological role of cylindrospermopsin.
Bacteriophage Prevalence in the Genus
Azospirillum
and Analysis of the First Genome Sequence of an
Azospirillum brasilense
Integrative Phage
Authors: Boyer Mickaël , Haurat Jacqueline , Samain Sylvie , Segurens Béatrice , Gavory Frédérick , González Víctor , Mavingui Patrick , Rohr René , Bally René , Wisniewski-Dyé Florence
Published: December 2007

The prevalence of bacteriophages was investigated in 24 strains of four species of plant growth-promoting rhizobacteria belonging to the genus
Azospirillum
. Upon induction by mitomycin C, the release of phage particles was observed in 11 strains from three species. Transmission electron microscopy revealed two distinct sizes of particles, depending on the identity of the
Azospirillum
species, typical of the
Siphoviridae
family. Pulsed-field gel electrophoresis and hybridization experiments carried out on phage-encapsidated DNAs revealed that all phages isolated from
A. lipoferum
and
A. doebereinerae
strains had a size of about 10 kb whereas all phages isolated from
A. brasilense
strains displayed genome sizes ranging from 62 to 65 kb. Strong DNA hybridizing signals were shown for most phages hosted by the same species whereas no homology was found between phages harbored by different species. Moreover, the complete sequence of the
A. brasilense
Cd bacteriophage (ΦAb-Cd) genome was determined as a double-stranded DNA circular molecule of 62,337 pb that encodes 95 predicted proteins. Only 14 of the predicted proteins could be assigned functions, some of which were involved in DNA processing, phage morphogenesis, and bacterial lysis. In addition, the ΦAb-Cd complete genome was mapped as a prophage on a 570-kb replicon of strain
A. brasilense
Cd, and a region of 27.3 kb of ΦAb-Cd was found to be duplicated on the 130-kb pRhico plasmid previously sequenced from
A. brasilense
Sp7, the parental strain of
A. brasilense
Cd.
RNA Silencing Gene Truncation in the Filamentous Fungus
Aspergillus nidulans
Authors: Hammond T. M. , Bok J. W. , Andrewski M. D. , Reyes-Domínguez Y. , Scazzocchio C. , Keller N. P.
Published: December 2007

The genus
Aspergillus
is ideally suited for the investigation of RNA silencing evolution because it includes species that have experienced a variety of RNA silencing gene changes. Our work on this subject begins here with the model species
Aspergillus nidulans
. Filamentous ascomycete fungi generally each encode two of the core RNA silencing proteins, Dicer and Argonaute, but
A. nidulans
appears to have lost one of each to gene truncation events. Although a role in growth, development, or RNA silencing was not detected for the truncated genes, they do produce spliced and poly(A)-tailed transcripts, suggesting that they may have an undetermined biological function. Population analysis demonstrates that the truncated genes are fixed at the species level and that their full-length orthologs in a closely related species are also unstable. With these gene truncation events,
A. nidulans
encodes only a single intact Dicer and Argonaute. Their deletion results in morphologically and reproductively normal strains that are incapable of experimental RNA silencing. Thus, our results suggest that the remaining
A. nidulans
RNA silencing genes have a “nonhousekeeping” function, such as defense against viruses and transposons.
Fission Yeast Mitogen-Activated Protein Kinase Sty1 Interacts with Translation Factors
Authors: Asp Eva , Nilsson Daniel , Sunnerhagen Per
Published: December 2007

Signaling by stress-activated mitogen-activated protein kinase (MAPK) pathways influences translation efficiency in mammalian cells and budding yeast. We have investigated the stress-activated MAPK from fission yeast, Sty1, and its downstream protein kinase, Mkp1/Srk1, for physically associated proteins using tandem affinity purification tagging. We find Sty1, but not Mkp1, to bind to the translation elongation factor eukaryotic elongation factor 2 (eEF2) and the translation initiation factor eukaryotic initiation factor 3a (eIF3a). The Sty1-eIF3a interaction is weakened under oxidative or hyperosmotic stress, whereas the Sty1-eEF2 interaction is stable. Nitrogen deprivation causes a transient strengthening of both the Sty1-eEF2 and the Sty1-Mkp1 interactions, overlapping with the time of maximal Sty1 activation. Analysis of polysome profiles from cells under oxidative stress, or after hyperosmotic shock or nitrogen deprivation, shows that translation in
sty1
mutant cells recovers considerably less efficiently than that in the wild type. Cells lacking the Sty1-regulated transcription factor Atf1 are deficient in maintaining and recovering translational activity after hyperosmotic shock but not during oxidative stress or nitrogen starvation. In cells lacking Sty1, eIF3a levels are decreased, and phosphorylation of eIF3a is reduced. Taken together, our data point to a central role in translational adaptation for the stress-activated MAPK pathway in fission yeast similar to that in other investigated eukaryotes, with the exception that fission yeast MAPK-activated protein kinases seem not to be directly involved in this process.
PhoP-PhoP Interaction at Adjacent PhoP Binding Sites Is Influenced by Protein Phosphorylation
Authors: Sinha Akesh , Gupta Sankalp , Bhutani Shweta , Pathak Anuj , Sarkar Dibyendu
Published: December 2007

Mycobacterium tuberculosis
PhoP regulates the expression of unknown virulence determinants and the biosynthesis of complex lipids. PhoP, like other members of the OmpR family, comprises a phosphorylation domain at the amino-terminal half and a DNA-binding domain at the carboxy-terminal half of the protein. To explore structural effect of protein phosphorylation and to examine effect of phosphorylation on DNA binding, purified PhoP was phosphorylated by acetyl phosphate in a reaction that was dependent on Mg
2+
and Asp-71. Protein phosphorylation was not required for DNA binding; however, phosphorylation enhanced in vitro DNA binding through protein-protein interaction(s). Evidence is presented here that the protein-protein interface is different in the unphosphorylated and phosphorylated forms of PhoP and that specific DNA binding plays a critical role in changing the nature of the protein-protein interface. We show that phosphorylation switches the transactivation domain to a different conformation, which specifies additional protein-protein contacts between PhoP protomers bound to adjacent cognate sites. Together, our observations raise the possibility that PhoP, in the unphosphorylated and phosphorylated forms, may be capable of adopting different orientations as it binds to a vast array of genes to activate or repress transcription.
A Transposase-Independent Mechanism Gives Rise to Precise Excision of IS256from Insertion Sites inStaphylococcus epidermidis
Authors: Hennig Susanne , Ziebuhr Wilma
Published: December 2007

The mobile element IS256causes phase variation of biofilm formation inStaphylococcus epidermidisby insertion and precise excision from theicaADBCoperon. Precise excision, i.e., removal of the target site duplications (TSDs) and restoration of the original DNA sequence, occurs rarely but independently of functional transposase. Instead, the integrity of the TSDs is crucial for precise excision. Excision increased significantly when the TSDs were brought into closer spatial proximity, suggesting that excision is a host-driven process that might involve most likely illegitimate recombination.
Phage Response to CRISPR-Encoded Resistance in
Streptococcus thermophilus
Authors: Deveau Hélène , Barrangou Rodolphe , Garneau Josiane E. , Labonté Jessica , Fremaux Christophe , Boyaval Patrick , Romero Dennis A. , Horvath Philippe , Moineau Sylvain
Published: December 2007

Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated genes are linked to a mechanism of acquired resistance against bacteriophages. Bacteria can integrate short stretches of phage-derived sequences (spacers) within CRISPR loci to become phage resistant. In this study, we further characterized the efficiency of CRISPR1 as a phage resistance mechanism in
Streptococcus thermophilus
. First, we show that CRISPR1 is distinct from previously known phage defense systems and is effective against the two main groups of
S. thermophilus
phages. Analyses of 30 bacteriophage-insensitive mutants of
S. thermophilus
indicate that the addition of one new spacer in CRISPR1 is the most frequent outcome of a phage challenge and that the iterative addition of spacers increases the overall phage resistance of the host. The added new spacers have a size of between 29 to 31 nucleotides, with 30 being by far the most frequent. Comparative analysis of 39 newly acquired spacers with the complete genomic sequences of the wild-type phages 2972, 858, and DT1 demonstrated that the newly added spacer must be identical to a region (named proto-spacer) in the phage genome to confer a phage resistance phenotype. Moreover, we found a CRISPR1-specific sequence (NNAGAAW) located downstream of the proto-spacer region that is important for the phage resistance phenotype. Finally, we show through the analyses of 20 mutant phages that virulent phages are rapidly evolving through single nucleotide mutations as well as deletions, in response to CRISPR1.
Diversity, Activity, and Evolution of CRISPR Loci in
Streptococcus thermophilus
Authors: Horvath Philippe , Romero Dennis A. , Coûté-Monvoisin Anne-Claire , Richards Melissa , Deveau Hélène , Moineau Sylvain , Boyaval Patrick , Fremaux Christophe , Barrangou Rodolphe
Published: December 2007

Clustered regularly interspaced short palindromic repeats (CRISPR) are hypervariable loci widely distributed in prokaryotes that provide acquired immunity against foreign genetic elements. Here, we characterize a novel
Streptococcus thermophilus
locus, CRISPR3, and experimentally demonstrate its ability to integrate novel spacers in response to bacteriophage. Also, we analyze CRISPR diversity and activity across three distinct CRISPR loci in several
S. thermophilus
strains. We show that both CRISPR repeats and
cas
genes are locus specific and functionally coupled. A total of 124 strains were studied, and 109 unique spacer arrangements were observed across the three CRISPR loci. Overall, 3,626 spacers were analyzed, including 2,829 for CRISPR1 (782 unique), 173 for CRISPR2 (16 unique), and 624 for CRISPR3 (154 unique). Sequence analysis of the spacers revealed homology and identity to phage sequences (77%), plasmid sequences (16%), and
S. thermophilus
chromosomal sequences (7%). Polymorphisms were observed for the CRISPR repeats, CRISPR spacers,
cas
genes, CRISPR motif, locus architecture, and specific sequence content. Interestingly, CRISPR loci evolved both via polarized addition of novel spacers after exposure to foreign genetic elements and via internal deletion of spacers. We hypothesize that the level of diversity is correlated with relative CRISPR activity and propose that the activity is highest for CRISPR1, followed by CRISPR3, while CRISPR2 may be degenerate. Globally, the dynamic nature of CRISPR loci might prove valuable for typing and comparative analyses of strains and microbial populations. Also, CRISPRs provide critical insights into the relationships between prokaryotes and their environments, notably the coevolution of host and viral genomes.
CotC-CotU Heterodimerization during Assembly of the
Bacillus subtilis
Spore Coat
Authors: Isticato Rachele , Pelosi Assunta , Zilhão Rita , Baccigalupi Loredana , Henriques Adriano O. , De Felice Maurilio , Ricca Ezio
Published: December 2007

We report evidence that CotC and CotU, two previously identified components of the
Bacillus subtilis
spore coat, are produced concurrently in the mother cell chamber of the sporulating cell under the control of σ
K
and GerE and immediately assembled around the forming spore. In the coat, the two proteins interact to form a coat component of 23 kDa. The CotU-CotC interaction was not detected in two heterologous hosts, suggesting that it occurs only in
B. subtilis
. Monomeric forms of both CotU and CotC failed to be assembled at the surface of the developing spore and accumulated in the mother cell compartment of cells mutant for
cotE
. In contrast, neither CotU nor CotC accumulated in the mother cell compartment of cells mutant for
cotH
. These results suggest that CotH is required to protect both CotU and CotC in the mother cell compartment of the sporangium and that CotE is needed to allow their assembly and subsequent interaction at the spore surface.
The Genome and Structural Proteome of YuA, a New
Pseudomonas aeruginosa
Phage Resembling M6
Authors: Ceyssens Pieter-Jan , Mesyanzhinov Vadim , Sykilinda Nina , Briers Yves , Roucourt Bart , Lavigne Rob , Robben Johan , Domashin Artem , Miroshnikov Konstantin , Volckaert Guido , Hertveldt Kirsten
Published: December 2007

Pseudomonas aeruginosa
phage YuA (
Siphoviridae
) was isolated from a pond near Moscow, Russia. It has an elongated head, encapsulating a circularly permuted genome of 58,663 bp, and a flexible, noncontractile tail, which is terminally and subterminally decorated with short fibers. The YuA genome is neither Mu- nor λ-like and encodes 78 gene products that cluster in three major regions involved in (i) DNA metabolism and replication, (ii) host interaction, and (iii) phage particle formation and host lysis. At the protein level, YuA displays significant homology with phages M6, φJL001, 73, B3, DMS3, and D3112. Eighteen YuA proteins were identified as part of the phage particle by mass spectrometry analysis. Five different bacterial promoters were experimentally identified using a promoter trap assay, three of which have a σ
54
-specific binding site and regulate transcription in the genome region involved in phage particle formation and host lysis. The dependency of these promoters on the host σ
54
factor was confirmed by analysis of an
rpoN
mutant strain of
P. aeruginosa
PAO1. At the DNA level, YuA is 91% identical to the recently (July 2007) annotated phage M6 of the Lindberg typing set. Despite this level of DNA homology throughout the genome, both phages combined have 15 unique genes that do not occur in the other phage. The genome organization of both phages differs substantially from those of the other known
Pseudomonas
-infecting
Siphoviridae
, delineating them as a distinct genus within this family.
A Point Mutation in the Two-Component Regulator PhoP-PhoR Accounts for the Absence of Polyketide-Derived Acyltrehaloses but Not That of Phthiocerol Dimycocerosates in
Mycobacterium tuberculosis
H37Ra
Authors: Chesne-Seck Marie-Laure , Barilone Nathalie , Boudou Frédéric , Asensio Jesús Gonzalo , Kolattukudy Pappachan E. , Martín Carlos , Cole Stewart T. , Gicquel Brigitte , Gopaul Deshmukh N. , Jackson Mary
Published: December 2007

Similarities between
Mycobacterium tuberculosis phoP-phoR
mutants and the attenuated laboratory strain
M. tuberculosis
H37Ra in terms of morphological and cytochemical properties, lipid content, gene expression and virulence attenuation prompted us to analyze the functionality of this two-component regulator in the latter strain. Sequence analysis revealed a base substitution resulting in a one-amino-acid change in the likely DNA-binding region of PhoP in H37Ra relative to H37Rv. Using gel-shift assays, we show that this mutation abrogates the ability of the H37Ra PhoP protein to bind to a 40-bp segment of its own promoter. Consistent with this result, the
phoP
gene from H37Rv but not that from H37Ra was able to restore the synthesis of sulfolipids, diacyltrehaloses and polyacyltrehaloses in an isogenic
phoP-phoR
knock-out mutant of
M. tuberculosis
Moreover, complementation of H37Ra with
phoP
from H37Rv fully restored sulfolipid, diacyltrehalose and polyacyltrehalose synthesis, clearly indicating that the lack of production of these lipids in H37Ra is solely due to the point mutation in
phoP
. Using a
pks2-3/4
knock-out mutant of
M. tuberculosis
H37Rv, evidence is further provided that the above-mentioned polyketide-derived acyltrehaloses do not significantly contribute to the virulence of the tubercle bacillus in a mouse model of infection. Reasons for the attenuation of H37Ra thus most likely stand in other virulence factors, many of which are expected to belong to the PhoP regulon and another of which, unrelated to PhoP, appears to be the lack of production of phthiocerol dimycocerosates in this strain.
Interplay of Different Transporters in the Mediation of Divalent Heavy Metal Resistance in
Pseudomonas putida
KT2440
Authors: Leedjärv Anu , Ivask Angela , Virta Marko
Published: December 2007

According to in silico analysis, the genome of
Pseudomonas putida
KT2440 encodes at least four Zn/Cd/Pb efflux transporters—two P-type ATPases (CadA1 and CadA2) and two
czc
chemiosmotic transporters (CzcCBA1 and CzcCBA2). In this study we showed that all these transporters are functional, but under laboratory conditions only two of them were involved in the mediation of heavy metal resistance in
P. putida
KT2440. CadA2 conferred Cd
2+
and Pb
2+
resistance, whereas CzcCBA1 was involved in export of Zn
2+
, Cd
2+
, and possibly Pb
2+
. CadA1, although nonfunctional in
P. putida
, improved Zn
2+
resistance and slightly improved Cd
2+
resistance when it was expressed in
Escherichia coli
. CzcCBA2 contributed to Zn resistance of a
czcA1
-defective
P. putida
strain or when the CzcA2 subunit was overexpressed in a transporter-deficient strain. It seemed that CzcA2 could complex with CzcC1 and CzcB1 subunits and therefore complement the loss of CzcA1. The CzcCBA2 transporter itself, however, did not function. Expression of
cadA1
,
cadA2
, and
czcCBA1
was induced by heavy metals, and the expression levels were dependent on the growth medium and growth phase. Expression of
cadA2
and
czcCBA1
was nonspecific; both genes were induced by Zn
2+
, Cd
2+
, Pb
2+
, Ni
2+
, Co
2+
, and Hg
2+
. On the other hand, remarkably, expression of
cadA1
was induced only by Zn
2+
. Possible roles of distinct but simultaneously functioning transporters are discussed.
Influence of thespxBGene on Competence inStreptococcus pneumoniae
Authors: Bättig Patrick , Mühlemann Kathrin
Published: December 2007

InStreptococcus pneumoniaeexpression of pyruvate oxidase (SpxB) peaks during the early growth phase, coincident with the time of natural competence. This study investigated whether SpxB influences parameters of competence, such as spontaneous transformation frequency, expression of competence genes, and DNA release. Knockout of thespxBgene in strain D39 abolished spontaneous transformation (compared to a frequency of 6.3 × 10−6in the parent strain [P< 0.01]). It also reduced expression levels ofcomCandrecAas well as DNA release from bacterial cells significantly during the early growth phase, coincident with the time of spontaneous competence in the parent strain. In thespxBmutant, supplementation with competence-stimulating peptide 1 (CSP-1) restored transformation (rate, 1.8 × 10−2). This speaks against the role of SpxB as a necessary source of energy for competence. Neither supplementation with CSP-1 nor supplementation with the SpxB products H2O2and acetate altered DNA release. Supplementation of the parent strain with catalase did not reduce DNA release significantly. In conclusion, the pneumococcalspxBgene influences competence; however, the mechanism remains elusive.
Ma-LMM01 Infecting Toxic
Microcystis aeruginosa
Illuminates Diverse Cyanophage Genome Strategies
Authors: Yoshida Takashi , Nagasaki Keizo , Takashima Yukari , Shirai Yoko , Tomaru Yuji , Takao Yoshitake , Sakamoto Shigetaka , Hiroishi Shingo , Ogata Hiroyuki
Published: December 2007

Cyanobacteria and their phages are significant microbial components of the freshwater and marine environments. We identified a lytic phage, Ma-LMM01, infecting
Microcystis aeruginosa
, a cyanobacterium that forms toxic blooms on the surfaces of freshwater lakes. Here, we describe the first sequenced freshwater cyanomyovirus genome of Ma-LMM01. The linear, circularly permuted, and terminally redundant genome has 162,109 bp and contains 184 predicted protein-coding genes and two tRNA genes. The genome exhibits no colinearity with previously sequenced genomes of cyanomyoviruses or other
Myoviridae
. The majority of the predicted genes have no detectable homologues in the databases. These findings indicate that Ma-LMM01 is a member of a new lineage of the
Myoviridae
family. The genome lacks homologues for the photosynthetic genes that are prevalent in marine cyanophages. However, it has a homologue of
nblA
, which is essential for the degradation of the major cyanobacteria light-harvesting complex, the phycobilisomes. The genome codes for a site-specific recombinase and two prophage antirepressors, suggesting that it has the capacity to integrate into the host genome. Ma-LMM01 possesses six genes, including three coding for transposases, that are highly similar to homologues found in cyanobacteria, suggesting that recent gene transfers have occurred between Ma-LMM01 and its host. We propose that the Ma-LMM01 NblA homologue possibly reduces the absorption of excess light energy and confers benefits to the phage living in surface waters. This phage genome study suggests that light is central in the phage-cyanobacterium relationships where the viruses use diverse genetic strategies to control their host's photosynthesis.
Structure of [NiFe] Hydrogenase Maturation Protein HypE from
Escherichia coli
and Its Interaction with HypF
Authors: Rangarajan Erumbi S. , Asinas Abdalin , Proteau Ariane , Munger Christine , Baardsnes Jason , Iannuzzi Pietro , Matte Allan , Cygler Miroslaw
Published: December 2007

Hydrogenases are enzymes involved in hydrogen metabolism, utilizing H
2
as an electron source. [NiFe] hydrogenases are heterodimeric Fe-S proteins, with a large subunit containing the reaction center involving Fe and Ni metal ions and a small subunit containing one or more Fe-S clusters. Maturation of the [NiFe] hydrogenase involves assembly of nonproteinaceous ligands on the large subunit by accessory proteins encoded by the
hyp
operon. HypE is an essential accessory protein and participates in the synthesis of two cyano groups found in the large subunit. We report the crystal structure of
Escherichia coli
HypE at 2.0-Å resolution. HypE exhibits a fold similar to that of PurM and ThiL and forms dimers. The C-terminal catalytically essential Cys336 is internalized at the dimer interface between the N- and C-terminal domains. A mechanism for dehydration of the thiocarbamate to the thiocyanate is proposed, involving Asp83 and Glu272. The interactions of HypE and HypF were characterized in detail by surface plasmon resonance and isothermal titration calorimetry, revealing a

K
d

(dissociation constant) of ∼400 nM. The stoichiometry and molecular weights of the complex were verified by size exclusion chromatography and gel scanning densitometry. These experiments reveal that HypE and HypF associate to form a stoichiometric, hetero-oligomeric complex predominantly consisting of a [EF]
2
heterotetramer which exists in a dynamic equilibrium with the EF heterodimer. The surface plasmon resonance results indicate that a conformational change occurs upon heterodimerization which facilitates formation of a productive complex as part of the carbamate transfer reaction.
Pseudomonas aeruginosa
Exhibits Sliding Motility in the Absence of Type IV Pili and Flagella
Authors: Murray Thomas S. , Kazmierczak Barbara I.
Published: December 2007

Pseudomonas aeruginosa
exhibits swarming motility on 0.5 to 1% agar plates in the presence of specific carbon and nitrogen sources. We have found that PAO1 double mutants expressing neither flagella nor type IV pili (
fliC pilA
) display sliding motility under the same conditions. Sliding motility was inhibited when type IV pilus expression was restored; like swarming motility, it also decreased in the absence of rhamnolipid surfactant production. Transposon insertions in
gacA
and
gacS
increased sliding motility and restored tendril formation to spreading colonies, while transposon insertions in
retS
abolished motility. These changes in motility were not accompanied by detectable changes in rhamnolipid surfactant production or by the appearance of bacterial surface structures that might power sliding motility. We propose that
P. aeruginosa
requires flagella during swarming to overcome adhesive interactions mediated by type IV pili. The apparent dependence of sliding motility on environmental cues and regulatory pathways that also affect swarming motility suggests that both forms of motility are influenced by similar cohesive factors that restrict translocation, as well as by dispersive factors that facilitate spreading. Studies of sliding motility may be particularly well-suited for identifying factors other than pili and flagella that affect community behaviors of
P. aeruginosa
.
Mesaconyl-Coenzyme A Hydratase, a New Enzyme of Two Central Carbon Metabolic Pathways in Bacteria
Authors: Zarzycki Jan , Schlichting Ansgar , Strychalsky Nina , Müller Michael , Alber Birgit E. , Fuchs Georg
Published: December 2007

The coenzyme A (CoA)-activated C
5
-dicarboxylic acids mesaconyl-CoA and β-methylmalyl-CoA play roles in two as yet not completely resolved central carbon metabolic pathways in bacteria. First, these compounds are intermediates in the 3-hydroxypropionate cycle for autotrophic CO
2
fixation in
Chloroflexus aurantiacus
, a phototrophic green nonsulfur bacterium. Second, mesaconyl-CoA and β-methylmalyl-CoA are intermediates in the ethylmalonyl-CoA pathway for acetate assimilation in various bacteria, e.g., in
Rhodobacter sphaeroides
,
Methylobacterium extorquens
, and
Streptomyces
species. In both cases, mesaconyl-CoA hydratase was postulated to catalyze the interconversion of mesaconyl-CoA and β-methylmalyl-CoA. The putative genes coding for this enzyme in
C. aurantiacus
and
R. sphaeroides
were cloned and heterologously expressed in
Escherichia coli
, and the proteins were purified and studied. The recombinant homodimeric 80-kDa proteins catalyzed the reversible dehydration of
erythro
-β-methylmalyl-CoA to mesaconyl-CoA with rates of 1,300 μmol min
−1
mg protein
−1
. Genes coding for similar enzymes with two (
R
)-enoyl-CoA hydratase domains are present in the genomes of
Roseiflexus
,
Methylobacterium
,
Hyphomonas
,
Rhodospirillum
,
Xanthobacter
,
Caulobacter
,
Magnetospirillum
,
Jannaschia
,
Sagittula
,
Parvibaculum
,
Stappia
,
Oceanicola
,
Loktanella
,
Silicibacter
,
Roseobacter
,
Roseovarius
,
Dinoroseobacter
,
Sulfitobacter
,
Paracoccus
, and
Ralstonia
species. A similar yet distinct class of enzymes containing only one hydratase domain was found in various other bacteria, such as
Streptomyces
species. The role of this widely distributed new enzyme is discussed.
Role of the Clp System in Stress Tolerance, Biofilm Formation, and Intracellular Invasion inPorphyromonas gingivalis
Authors: Capestany Cindy A. , Tribble Gena D. , Maeda Kazuhiko , Demuth Donald R. , Lamont Richard J.
Published: December 2007

Clp proteases and chaperones are ubiquitous among prokaryotes and eukaryotes, and in many pathogenic bacteria the Clp stress response system is also involved in regulation of virulence properties. In this study, the roles of ClpB, ClpC, and ClpXP in stress resistance, homotypic and heterotypic biofilm formation, and intracellular invasion in the oral opportunistic pathogenPorphyromonas gingivaliswere investigated. Absence of ClpC and ClpXP, but not ClpB, resulted in diminished tolerance to high temperatures. Response to oxidative stress was not affected by the loss of any of the Clp proteins. TheclpCandclpXPmutants demonstrated elevated monospecies biofilm formation, and the absence of ClpXP also enhanced heterotypicP. gingivalis-Streptococcus gordoniibiofilm formation. Allclpmutants adhered to gingival epithelial cells to the same level as the wild type; however, ClpC and ClpXP were found to be necessary for entry into host epithelial cells. ClpB did not play a role in entry but was required for intracellular replication and survival. ClpXP negatively regulated the surface exposure of the minor fimbrial (Mfa) protein subunit ofP. gingivalis, which stimulates biofilm formation but interferes with epithelial cell entry. Collectively, these results show that the Clp protease complex and chaperones control several processes that are important for the colonization and survival ofP. gingivalisin the oral cavity.
The Complete Genome Sequence of
Actinobacillus pleuropneumoniae
L20 (Serotype 5b)
Authors: Foote Simon J. , Bossé Janine T. , Bouevitch Anne B. , Langford Paul R. , Young N. Martin , Nash John H. E.
Published: December 2007

There are 16 capsule-based serotypes of
Actinobacillus pleuropneumoniae
, all of which are capable of causing disease in pigs. Here we report the finished and annotated genome sequence of the reference serotype 5b strain L20. This strain has a rough appearance and readily forms biofilms, as is typical for most field isolates (6).
The epidemiology of rock-climbing injuries
Authors: Jones G , Asghar A , Llewellyn D J
Published: December 2007

Objectives:

To determine the prevalence and nature of rock-climbing injuries, and the factors associated with these injuries.

Design:

A retrospective cross-sectional study.

Setting:

Rock climbers were recruited at five outdoor and six indoor climbing venues in the UK.

Participants:

201 active rock climbers (163 male, 38 female climbers) aged 16–62 years.

Assessment of risk factors:

Rock climbing behaviours and key demographics.

Main outcome measures:

Injuries requiring medical attention or withdrawal from participation for ⩾1 day.

Results:

Around 50% of climbers had sustained ⩾1 injury in the past 12 months, causing a total of 275 distinct anatomical injuries. 21 climbers (10%) had sustained acute climbing injuries as a result of a fall, 67 (33%) had chronic overuse injuries, and 57 (28%) had acute injuries caused by strenuous climbing moves. Dedicated climbers participating in different forms of rock climbing more often and at a higher level of technical difficulty may be more prone to injury, particularly overuse injuries of the finger and shoulder. The principal sources of treatment or advice sought by climbers were physiotherapists (18%), other climbers (14%) and doctors (11%).

Conclusions:

Climbing frequency and technical difficulty are associated with climbing injuries occurring at both indoor and outdoor venues, particularly cumulative trauma to the upper extremities.
A prospective cohort study of the incidence of injuries among junior Australian football players: evidence for an effect of playing-age level
Authors: Romiti M , Finch C F , Gabbe B
Published: December 2007

Objective:

To determine the rate of injury in junior Australian football, and to describe the patterns and severity of these injuries across nine levels of play (U9 to U18).

Design:

Prospective cohort study.

Setting:

Junior Australian football games and training sessions were observed for 54 teams from New South Wales and Victoria over the 2004 playing season.

Participants:

Six teams from each level of play were invited to participate in the study. Overall, data were collected for 51 teams over 40 208 hours of player exposure.

Independent variables:

Participation and injury data were collected prospectively.

Main outcome measures:

Injury was defined as “any trauma that causes some disability or pain”. Injury severity was identified by the action of players immediately after the injury event.

Results:

The overall injury rate was 18.0 (95% CI 16.6 to 19.3) injuries per 1000 player hours. The main cause of injury was body contact (67.3%). There was an increased frequency of sprains and strains, and injury severity with increasing level of play. The rates of injury for players who stayed off the field (6.4 injuries per 1000 hours, 95% CI 5.6 to 7.2) or were advised to seek off-field medical advice (5.0 injuries per 1000 hours, 95% CI 4.3 to 5.7) were low.

Conclusion:

Compared with the adult game, junior Australian football is relatively safe. However, injury rates increase as children progress across age-determined levels of play towards the more adult form of the game.
Workload demands in professional multi-stage cycling races of varying duration
Authors: Rodríguez-Marroyo J A , García-López J , Juneau C-É , Villa J G
Published: December 2007

Objetive:

To analyse and compare the workload exerted by professional cyclists in 5-day, 8-day and 21-day stage races (5-SR, 8-SR, 21-SR).

Methods:

The study subjects were 30 professional cyclists competing in 10 5-SR, 5 8-SR and 5 21-SR. Heart rate (HR) was measured during the races and categorised into three intensity zones: Z1 (below the ventilatory threshold (VT)), Z2 (between VT and the respiratory compensation threshold (RCT)) and Z3 (above RCT). The training impulse (TRIMP) was calculated by multiplying the sum of the time spent in each zone by 1, 2 and 3, respectively. Monotony (average TRIMP/SD) and strain (total TRIMP×monotony) were also calculated for each race type.

Results:

The average time spent in Z3 during each stage was significantly (p<0.05) higher for 5-SR (∼31 min) and 8-SR (∼28 min) than for 21-SR (∼14 min). Daily TRIMP values in 5-SR (∼400) and 8-SR (∼395) were also higher than in 21-SR (∼370). Monotony was similar across races (∼3) but strain was about three times higher for 21-SR than for 5-SR and 8-SR.

Conclusions:

The cyclists’ effort by stage was less for 21-SR than for 5-SR and 8-SR. Competition strain and monotony accumulated during longer races influence the choice of strategies adopted by cyclists. It is likely that the intensity of each stage is modulated by total race duration, with longer races averaging the lowest daily workload.