bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsatellite variability of sulfonylurea‐resistant and susceptible populations of Schoenoplectus juncoides (Cyperaceae) in Kinki, Japan
Authors: Yamada Y , Tominaga T , Ohsako T 
Published: October 2013

SummarySchoenoplectus juncoides is one of the most harmful weeds found in East Asian paddy fields. Recent emergence of biotypes that are resistant to the herbicide sulfonylurea (SU) has made weed control difficult. To examine the effect of the evolution of this herbicide resistance on genetic diversity within local populations, we investigated microsatellite variability within and among paddy field populations of S. juncoides in Kinki, Japan. In vivo assay of acetolactate synthase activity and root elongation assay in the presence of SU revealed that of 21 populations, five were sulfonylurea‐susceptible (SU‐S) and eight were completely sulfonylurea‐resistant (SU‐R). The remaining eight populations were a mixture of SU‐S and SU‐R individuals. The average gene diversity for SU‐R populations (HS = 0.168) was lower than those for SU‐S (HS = 0.256) and mixed (HS = 0.209) populations, but the difference was not significant. This indicates that positive selection for SU‐R phenotype did not cause a genome‐wide reduction in genetic diversity. Genetic differentiation among S. juncoides populations was higher than that observed for most weed species studied previously. Although populations in neighbouring paddy fields showed a high level of differentiation, Bayesian clustering analyses suggested that some level of gene flow occurs among them and that the genetic exchange or colonisation between neighbouring populations could contribute to the geographical expansion of the resistant allele.
Prevalence and Molecular Characteristics of Methicillin‐Resistant Staphylococcus aureus (MRSA) in Organic Pig Herds in The Netherlands
Authors: van de Vijver L. P. L. , Tulinski P. , Bondt N. , Mevius D. , Verwer C. 
Published: October 2013

SummaryThe prevalence of the methicillin‐resistant Staphylococcus aureus (MRSA) among conventional pig herds in the Netherlands is high (around 71%). Nevertheless, information about the prevalence of MRSA among organic pig herds is lacking. Here, we report a study on 24 of the 49 organic pig herds in the Netherlands. The prevalence of MRSA positive herds showed to be 21%. The genetic characteristics of the MRSA isolates were similar to MRSA CC398 described in conventional pigs except one exceptional HA‐MRSA CC30 found in one herd, which was presumably caused by human to animal transmission. This resulted in a prevalence of MRSA CC398 in the organic herds of 16.7%.
Clonal Spread of Salmonella enterica Serovar Infantis in Serbia: Acquisition of Mutations in the Topoisomerase Genes gyrA and parC Leads to Increased Resistance to Fluoroquinolones
Authors: Velhner M. , Kozoderović G. , Grego E. , Galić N. , Stojanov I. , Jelesić Z. , Kehrenberg C. 
Published: October 2013

SummaryQuinolone‐resistant Salmonella Infantis (n = 64) isolated from human stool samples, food and poultry during the years 2006–2011 were analysed for their resistance phenotypes, macrorestriction patterns and molecular mechanisms of decreased susceptibility to fluoroquinolones. Minimum inhibitory concentrations (MICs) of nalidixic acid (NAL) and ciprofloxacin (CIP) were determined by the agar dilution procedure, and the susceptibility to additional antimicrobial agents was determined by the disc diffusion method. To assess the influence of enhanced efflux activity, MICs were determined in the presence and absence of the inhibitor PAβN. The results of pulsed‐field gel electrophoresis (PFGE) typing revealed that quinolone‐resistant S. Infantis in Serbia had similar or indistinguishable PFGE profiles, suggesting a clonal spread. All S. Infantis showed combined resistance to NAL and tetracycline, whereas multiple drug resistance to three or more antibiotic classes was rare (2 isolates of human origin). The MICs ranged between 512 and 1024 μg/mL for NAL and 0.125–2 μg/mL for CIP. A single‐point mutation in the gene gyrA leading to a Ser83→Tyr exchange was detected in all isolates, and a second exchange (Ser80→Arg) in the gene parC was only present in eight S. Infantis isolates exhibiting slightly higher MICs of CIP (2 μg/mL). The inhibitor PAβN decreased the MIC values of CIP by two dilution steps and of NAL by at minimum 3–6 dilution steps, indicating that enhanced efflux plays an important role in quinolone resistance in these isolates. The plasmid‐mediated genes qnr, aac(6′)‐lb‐cr and qepA were not detected by PCR assays.
The importance of the smooth muscle cytoskeleton to preterm labour
Authors: Morgan Kathleen G. 
Published: October 2013

New Findings
What is the topic of this review?
This report discusses current work on the cytoskeletal dynamics in myometrial smooth muscle and its possible connection to the function of the myometrium in the setting of normal and preterm labour.
What advances does it highlight?
The report highlights findings from my research group on changes in focal adhesion dynamics and extracellular signal‐regulated kinase signalling in both rodent and human pregnancy that appear to be a contributing cause of the onset of labour.
Multiple mechanisms have been shown to regulate the onset of labour in a co‐operative and complex manner. One factor, myometrial stretch and associated increases in wall tension, has been implicated clinically in the initiation of labour and especially the aetiology of preterm labour. Recent work on the mechanisms involved has led to the finding that the intracellular Ca2+ requirement for activation of the myometrial contractile filaments increases during gestation. The decreased Ca2+ sensitivity correlates with an increase in the expression of caldesmon, an actin‐binding protein and inhibitor of myosin activation, during pregnancy. In late pregnancy, an increase in extracellular signal‐regulated kinase‐mediated caldesmon phosphorylation occurs, which appears to reverse the inhibitory action of caldesmon during labour. Force generated by the myometrial contractile filaments is communicated across the plasmalemma to the uterine wall through focal adhesions. Phospho‐tyrosine screening and mass spectrometry of stretched myometrial samples identified several stretch‐activated focal adhesion proteins. This Src‐mediated focal adhesion signalling appears to provide a tunable, i.e. regulated, tension sensor and force transmitter in the myometrial cell. In other parallel studies, biophysical measurements of smooth muscle compliance at both the cellular and tissue levels suggest that decreases in cellular compliance due to changing interactions of the actin cytoskeleton with the focal adhesions may also promote increases in uterine wall tension. These results, taken together, suggest that focal adhesion proteins and their interaction with the cytoskeleton may present a new mode of regulation of uterine contractility.
Cortical control of the autonomic nervous system
Authors: Cechetto David F. 
Published: October 2013

New FindingsWhat is the topic of this review?The pathways in the brain by which visceral information, in particular cardiopulmonary afferents, ascend to the cerebral cortex have been delineated in animal models. Studies using functional magnetic resonance imaging in humans have confirmed what was known from the animal studies and established the critical sites in the cerebral cortex of humans for autonomic control and the significance of these sites for cognitive emotional function.What advances does it highlight?Stimulation of cardiopulmonary afferents in humans has consistently resulted in activation in the insular cortex and the anterior cingulate cortex. It has been shown that individuals who are characterized as cardiovascular responders to mental stress have a different pattern of activity in the cortex related to the cardiac changes.A number of animal studies in the rat and cat have been particularly useful for determining the pathways and the sites in the forebrain and cortex that are responsible for autonomic control. For example, these experiments have demonstrated that there is a viscerotopically organized pathway, with the first site of termination in the nucleus of the solitary tract and with subsequent relays in the parabrachial nucleus and the ventroposterior parvocellular nucleus of the thalamus before final visceral afferent inputs in the insular cortex. Several neuroimaging studies in humans, using cardiopulmonary manipulations, have confirmed the importance of the insular cortex as a site of for visceral afferent inputs. The anterior cingulate cortex has also been implicated in cardiopulmonary control. Both the insular cortex and the infralimbic cortex have been shown to be involved in descending control of the cardiovascular system. Neuroimaging with functional magnetic resonance imaging has demonstrated that the cortical autonomic control pathways are different in individuals who are characterized as cardiovascular reactors to mental stress. There is evidence that this alteration in pathways in the cortex may be due to past experiences, including childhood trauma.
Confidence intervals for the parameters estimated from simulated O2 uptake kinetics: effects of different data treatments
Authors: Francescato M. P. , Cettolo V. , Bellio R. 
Published: October 2013

New Findings
What is the central question of this study?Is the accuracy and/or precision of the O2 uptake kinetics parameters, estimated by non‐linear regression, affected by different data treatments applied to reduce the noise of breath fluctuations?
What is the main finding and its importance?Simulations showed that, even after the averaging of more repetitions, the width of the asymptotic confidence intervals was narrower than the real ones, in particular when the O2 uptake responses were resampled at time intervals shorter than the average breath duration (e.g. 1 s). The reasons for this discrepancy were investigated, allowing us to identify simple methods to obtain the correct confidence interval of the O2 uptake kinetics parameters.
The behaviour of pulmonary O2 uptake following a moderate‐intensity step exercise increment is usually described by a first brief increase, followed by a second exponential time course reaching the new steady state (phase II). The parameters describing the phase II kinetics are investigated by applying different data treatments to the acquired O2 uptake data to reduce the effects of their noise before running a non‐linear regression procedure. The effects of different data treatments (nothing, resampling at various time intervals or averaging of more repetitions) on the precision and/or accuracy of the kinetics parameters estimated by non‐linear regression with a simple mono‐exponential model were investigated by artificially generating 105 simulated responses with average breath duration of 3.5 s. The simulations showed that, whatever the explored data treatment, the average estimated parameters were close to the theoretical ones. Nevertheless, in all the explored conditions, the non‐linear regression provided narrower asymptotic confidence intervals than the real ones. In particular, when the responses were resampled at 1 s time intervals, the width of the asymptotic confidence interval for the time constant was 50% of the real one, even after the averaging of more repetitions. The reasons for this discrepancy were investigated further, allowing us to identify some methods to obtain the correct confidence interval of the O2 uptake kinetics parameters. The simplest method to obtain an asymptotic confidence interval close to the real one is to average more responses resampled to a time interval slightly longer than the average breath duration.
Fully 3D iterative CT reconstruction using polar coordinates
Authors: Thibaudeau Christian , Leroux Jean‐Daniel , Fontaine Réjean , Lecomte Roger 
Published: October 2013

Purpose:This paper demonstrates the feasibility of fully 3D iterative computed tomography reconstruction of highly resolved fields of view using polar coordinates.Methods:System matrix is computed using a ray‐tracing approach in cylindrical or spherical coordinates. By using polar symmetries inherent to the acquisition geometry, the system matrix size can be reduced by a factor corresponding to the number of acquired projections. Such an important decrease in size allows the system matrix to be precomputed, and loaded all at once into memory prior to reconstruction. By carefully ordering the field of view voxels and the sinogram data, reconstruction speed is also enhanced by a cache‐oblivious computer implementation. The reconstruction algorithm is also compatible with the ordered‐subsets acceleration method. A final polar‐to‐Cartesian transformation is applied to the reconstructed image in order to allow proper visualization.Results:The ray‐tracing and reconstruction algorithms were implemented in polar representation. Large 3D system matrices were calculated in cylindrical and spherical coordinates, and the performance assessed against Cartesian ray‐tracers in terms of speed and memory requirements. Images of analytical phantoms were successfully reconstructed in both cylindrical and spherical coordinates. Fully 3D images of phantoms and small animals were acquired with a Gamma Medica Triumph X‐O small animal CT scanner and reconstructed using the manufacturerˈs software and the proposed polar approach to demonstrate the accuracy and robustness of the later. The noise was found to be reduced while preserving the same level of spatial resolution, without noticeable polar artifacts.Conclusions:Under a reasonable set of assumptions, the memory size of the system matrix can be reduced by a factor corresponding to the number of projections. Using this strategy, iterative reconstruction from high resolution clinical and preclinical systems can be more easily performed using general‐purpose personal computers.
The impact of leaf width and plan complexity on DMLC tracking of prostate intensity modulated arc therapy
Authors: Pommer Tobias , Falk Marianne , Poulsen Per Rugaard , Keall Paul J. , O’Brien Ricky T. , Munck af Rosenschöld Per 
Published: October 2013

Purpose:Intensity modulated arc therapy (IMAT) is commonly used to treat prostate cancer. The purpose of this study was to evaluate the impact of leaf width and plan complexity on dynamic multileaf collimator (DMLC) tracking for prostate motion management during IMAT treatments.Methods:Prostate IMAT plans were delivered with either a high‐definition MLC (HDMLC) or a Millennium MLC (M‐MLC) (0.25 and 0.50 cm central leaf width, respectively), with and without DMLC tracking, to a dosimetric phantom that reproduced four prostate motion traces. The plan complexity was varied by applying leaf position constraints during plan optimization. A subset of the M‐MLC plans was converted for delivery with the HDMLC, isolating the effect of the different leaf widths. The gamma index was used for evaluation. Tracking errors caused by target localization, leaf fitting, and leaf adjustment were analyzed.Results:The gamma pass rate was significantly improved with DMLC tracking compared to no tracking (p < 0.001). With DMLC tracking, the average gamma index pass rate was 98.6% (range 94.8%–100%) with the HDMLC and 98.1% (range 95.4%–99.7%) with the M‐MLC, using 3%, 3 mm criteria and the planned dose as reference. The corresponding pass rates without tracking were 87.6% (range 76.2%–94.7%) and 91.1% (range 81.4%–97.6%), respectively. Decreased plan complexity improved the pass rate when static target measurements were used as reference, but not with the planned dose as reference. The main cause of tracking errors was leaf fitting errors, which were decreased by 42% by halving the leaf width.Conclusions:DMLC tracking successfully compensated for the prostate motion. The finer leaf width of the HDMLC improved the tracking accuracy compared to the M‐MLC. The tracking improvement with limited plan complexity was small and not discernible when using the planned dose as reference.
Preparation of Sticky Escherichia coli through Surface Display of an Adhesive Catecholamine Moiety
Authors: Park Joseph P. , Choi Min-Jung , Kim Se Hun , Lee Seung Hwan , Lee Haeshin 
Published: October 2013

ABSTRACT

Mussels attach to virtually all types of inorganic and organic surfaces in aqueous environments, and catecholamines composed of 3,4-dihydroxy-
l
-phenylalanine (DOPA), lysine, and histidine in mussel adhesive proteins play a key role in the robust adhesion. DOPA is an unusual catecholic amino acid, and its side chain is called catechol. In this study, we displayed the adhesive moiety of DOPA-histidine on
Escherichia coli
surfaces using outer membrane protein W as an anchoring motif for the first time. Localization of catecholamines on the cell surface was confirmed by Western blot and immunofluorescence microscopy. Furthermore, cell-to-cell cohesion (i.e., cellular aggregation) induced by the displayed catecholamine and synthesis of gold nanoparticles on the cell surface support functional display of adhesive catecholamines. The engineered
E. coli
exhibited significant adhesion onto various material surfaces, including silica and glass microparticles, gold, titanium, silicon, poly(ethylene terephthalate), poly(urethane), and poly(dimethylsiloxane). The uniqueness of this approach utilizing the engineered sticky
E. coli
is that no chemistry for cell attachment are necessary, and the ability of spontaneous
E. coli
attachment allows one to immobilize the cells on challenging material surfaces such as synthetic polymers. Therefore, we envision that mussel-inspired catecholamine yielded sticky
E. coli
that can be used as a new type of engineered microbe for various emerging fields, such as whole living cell attachment on versatile material surfaces, cell-to-cell communication systems, and many others.
Bacteriophage Orphan DNA Methyltransferases: Insights from Their Bacterial Origin, Function, and Occurrence
Authors: Murphy James , Mahony Jennifer , Ainsworth Stuart , Nauta Arjen , van Sinderen Douwe 
Published: October 2013

ABSTRACT

Type II DNA methyltransferases (MTases) are enzymes found ubiquitously in the prokaryotic world, where they play important roles in several cellular processes, such as host protection and epigenetic regulation. Three classes of type II MTases have been identified thus far in bacteria which function in transferring a methyl group from
S
-adenosyl-
l
-methionine (SAM) to a target nucleotide base, forming N-6-methyladenine (class I), N-4-methylcytosine (class II), or C-5-methylcytosine (class III). Often, these MTases are associated with a cognate restriction endonuclease (REase) to form a restriction-modification (R-M) system protecting bacterial cells from invasion by foreign DNA. When MTases exist alone, which are then termed orphan MTases, they are believed to be mainly involved in regulatory activities in the bacterial cell. Genomes of various lytic and lysogenic phages have been shown to encode multi- and mono-specific orphan MTases that have the ability to confer protection from restriction endonucleases of their bacterial host(s). The ability of a phage to overcome R-M and other phage-targeting resistance systems can be detrimental to particular biotechnological processes such as dairy fermentations. Conversely, as phages may also be beneficial in certain areas such as phage therapy, phages with additional resistance to host defenses may prolong the effectiveness of the therapy. This minireview will focus on bacteriophage-encoded MTases, their prevalence and diversity, as well as their potential origin and function.
Novel Psychropiezophilic Oceanospirillales Species Profundimonas piezophila gen. nov., sp. nov., Isolated from the Deep-Sea Environment of the Puerto Rico Trench
Authors: Cao Yi , Chastain Roger A. , Eloe Emiley A. , Nogi Yuichi , Kato Chiaki , Bartlett Douglas H. 
Published: October 2013

ABSTRACT

The diversity of deep-sea high-pressure-adapted (piezophilic) microbes in isolated monoculture remains low. In this study, a novel obligately psychropiezophilic bacterium was isolated from seawater collected from the Puerto Rico Trench at a depth of ∼6,000 m. This isolate, designated YC-1, grew best in a nutrient-rich marine medium, with an optimal growth hydrostatic pressure of 50 MPa (range, 20 to 70 MPa) at 8°C. Under these conditions, the maximum growth rate was extremely slow, 0.017 h
−1
, and the maximum yield was 3.51 × 10
7
cells ml
−1
. Cell size and shape changed with pressure, shifting from 4.0 to 5.0 μm in length and 0.5 to 0.8 μm in width at 60 MPa to 0.8- to 1.0-μm diameter coccoid cells under 20 MPa, the minimal pressure required for growth. YC-1 is a Gram-negative, facultatively anaerobic heterotroph. Its predominant cellular fatty acids are the monounsaturated fatty acids (MUFAs) C
16:1
and C
18:1
. Unlike many other psychropiezophiles, YC-1 does not synthesize any polyunsaturated fatty acids (PUFAs). Phylogenetic analysis placed YC-1 within the family of
Oceanospirillaceae
, closely related to the uncultured symbiont of the deep-sea whale bone-eating worms of the genus
Osedax
. In common with some other members of the
Oceanospirillales
, including those enriched during the Deepwater Horizon oil spill, YC-1 is capable of hydrocarbon utilization. On the basis of its characteristics, YC-1 appears to represent both a new genus and a new species, which we name
Profundimonas piezophila
gen. nov., sp. nov.
A New Synthetic Route to
N
-Benzyl Carboxamides through the Reverse Reaction of
N
-Substituted Formamide Deformylase
Authors: Hashimoto Yoshiteru , Sakashita Toshihide , Fukatsu Hiroshi , Sato Hiroyoshi , Kobayashi Michihiko 
Published: October 2013

ABSTRACT

Previously, we isolated a new enzyme,
N
-substituted formamide deformylase, that catalyzes the hydrolysis of
N
-substituted formamide to the corresponding amine and formate (H. Fukatsu, Y. Hashimoto, M. Goda, H. Higashibata, and M. Kobayashi, Proc. Natl. Acad. Sci. U. S. A. 101:13726–13731, 2004,
doi:10.1073/pnas.0405082101
). Here, we discovered that this enzyme catalyzed the reverse reaction, synthesizing
N
-benzylformamide (NBFA) from benzylamine and formate. The reverse reaction proceeded only in the presence of high substrate concentrations. The effects of pH and inhibitors on the reverse reaction were almost the same as those on the forward reaction, suggesting that the forward and reverse reactions are both catalyzed at the same catalytic site. Bisubstrate kinetic analysis using formate and benzylamine and dead-end inhibition studies using a benzylamine analogue, aniline, revealed that the reverse reaction of this enzyme proceeds via an ordered two-substrate, two-product (bi-bi) mechanism in which formate binds first to the enzyme active site, followed by benzylamine binding and the subsequent release of NBFA. To our knowledge, this is the first report of the reverse reaction of an amine-forming deformylase. Surprisingly, analysis of the substrate specificity for acids demonstrated that not only formate, but also acetate and propionate (namely, acids with numbers of carbon atoms ranging from C
1
to C
3
), were active as acid substrates for the reverse reaction. Through this reaction,
N
-substituted carboxamides, such as NBFA,
N
-benzylacetamide, and
N
-benzylpropionamide, were synthesized from benzylamine and the corresponding acid substrates.