bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional group richness: implications of biodiversity for light use and lipid yield in microalgae
Authors: Stockenreiter Maria , Haupt Florian , Graber Anne‐Kathrin , Seppälä Jukka , Spilling Kristian , Tamminen Timo , Stibor Herwig
Published: June 2013

Currently, very few studies address the relationship between diversity and biomass/lipid production in primary producer communities for biofuel production. Basic studies on the growth of microalgal communities, however, provide evidence of a positive relationship between diversity and biomass production. Recent studies have also shown that positive diversity–productivity relationships are related to an increase in the efficiency of light use by diverse microalgal communities. Here, we hypothesize that there is a relationship between diversity, light use, and microalgal lipid production in phytoplankton communities. Microalgae from all major freshwater algal groups were cultivated in treatments that differed in species richness and functional group richness. Polycultures with high functional group richness showed more efficient light use and higher algal lipid content with increasing species richness. There was a clear correlation between light use and lipid production in functionally diverse communities. Hence, a powerful and cost‐effective way to improve biofuel production might be accomplished by incorporating diversity related, resource‐use‐dynamics into algal biomass production.
OPTIMAL SELLING RULES FOR MONETARY INVARIANT CRITERIA: TRACKING THE MAXIMUM OF A PORTFOLIO WITH NEGATIVE DRIFT
Authors: Elie Romuald , Espinosa Gilles‐Edouard
Published: June 2013

Considering a positive portfolio diffusion X with negative drift, we investigate optimal stopping problems of the form

urn:x-wiley:09601627:media:mafi12036:mafi12036-math-0001where f is a nonincreasing function, τ is the next random time where the portfolio X crosses zero and θ is any stopping time smaller than τ. Hereby, our motivation is the obtention of an optimal selling strategy minimizing the relative distance between the liquidation value of the portfolio and its highest possible value before it reaches zero. This paper unifies optimal selling rules observed for the quadratic absolute distance criteria in this stationary framework with bang–bang type ones observed for monetary invariant criteria but in finite horizon. More precisely, we provide a verification result for the general stopping problem of interest and derive the exact solution for two classical criteria f of the literature. For the power utility criterion with , instantaneous selling is always optimal, which is consistent with previous observations for the Black‐Scholes model in finite observation. On the contrary, for a relative quadratic error criterion, , selling is optimal as soon as the process X crosses a specified function φ of its running maximum . These results reinforce the idea that optimal stopping problems of similar type lead easily to selling rules of very different nature. Nevertheless, our numerical experiments suggest that the practical optimal selling rule for the relative quadratic error criterion is in fact very close to immediate selling.
The Episure Autodetect syringe, a loss‐of‐resistance technique for locating the epidural space, used in pediatric patients
Authors: Tielens Luc K. P. , Bruhn Jörgen , Vogt Mark , van Geffen Geert‐Jan , Scheffer Gert Jan
Published: June 2013

Introduction

The Episure Autodetect syringe, a spring‐loaded syringe, is a loss‐of‐resistance syringe with an internal compression that applies constant pressure on the plunger. As the principle of loss‐of‐resistance is the same for adult and for pediatric patients, the Episure Autodetect syringe should be able to identify correctly the epidural space also in pediatric patients.

Methods

A retrospective review was carried out for all pediatric patients, in which the Episure Autodetect syringe was used for locating the epidural space between 2007 and 2011 in our department.

Results

In 17 pediatric patients (9 months–14 years, 7.5–43 kg weight), the Episure syringe was used. In all 17 patients, the epidural space was correctly identified using the spring‐loaded syringe as evidenced by satisfactory analgesia. No accidental dural punctures or false loss‐of‐resistances were observed.

Conclusion

The spring‐loaded Episure Autodetect syringe might be a potentially useful loss‐of‐resistance syringe for identification of the epidural space in pediatric patients.
Controlled rapid sequence induction and intubation – an analysis of 1001 children
Authors: Neuhaus Diego , Schmitz Achim , Gerber Andreas , Weiss Markus
Published: June 2013

Background

Classic rapid sequence induction puts pediatric patients at risk of cardiorespiratory deterioration and traumatic intubation due to their reduced apnea tolerance and related shortened intubation time. A ‘controlled’ rapid sequence induction and intubation technique (cRSII) with gentle facemask ventilation prior to intubation may be a safer and more appropriate approach in pediatric patients. The aim of this study was to analyze the benefits and complications of cRSII in a large cohort.

Methods

Retrospective cohort analysis of all patients undergoing cRSII according to a standardized institutional protocol between 2007 and 2011 in a tertiary pediatric hospital. By means of an electronic patient data management system, vital sign data were reviewed for cardiorespiratory parameters, intubation conditions, general adverse respiratory events, and general anesthesia parameters.

Results

A total of 1001 patients with cRSII were analyzed. Moderate hypoxemia (SpO2 80–89%) during cRSII occurred in 0.5% (n = 5) and severe hypoxemia (SpO2 <80%) in 0.3% of patients (n = 3). None of these patients developed bradycardia or hypotension. Overall, one single gastric regurgitation was observed (0.1%), but no pulmonary aspiration could be detected. Intubation was documented as ‘difficult’ in two patients with expected (0.2%) and in three patients with unexpected difficult intubation (0.3%). The further course of anesthesia as well as respiratory conditions after extubation did not reveal evidence of ‘silent aspiration’ during cRSII.

Conclusion

Controlled RSII with gentle facemask ventilation prior to intubation supports stable cardiorespiratory conditions for securing the airway in children with an expected or suspected full stomach. Pulmonary aspiration does not seem to be significantly increased.
Assessing minimum contrast parameter estimation for spatial and spatiotemporal log‐Gaussian Cox processes
Authors: Davies Tilman M. , Hazelton Martin L.
Published: June 2013

The univariate log‐Gaussian Cox process (LGCP) has shown considerable potential for the flexible modelling of the spatial, and more recently, spatiotemporal, intensity functions of planar point patterns within a restricted region in space. Its flexibility and mathematical tractability are partly offset by the need to acquire sensible estimates of the parameters controlling the dependence structure of the Gaussian field given the observed data. The method of minimum contrast, which compares theoretical descriptors of the process with their non‐parametric counterparts in order to obtain the required estimates, is arguably the most popular in practice to date. This article provides a comprehensive set of simulation studies focused on gauging the performance and impact of minimum contrast methods for parameter estimation of these processes. Results indicate that concerns over arbitrariness of implementation of minimum contrast give way to satisfactory practical performance.
Identification and characterization of the major histocompatibility complex class IIDQB (MhcMath‐DQB1) alleles in Tibetan macaques (Macaca thibetana)
Authors: Yao Y.‐F. , Zhao J.‐J. , Dai Q.‐X. , Li J.‐Y. , Zhou L. , Wang Y.‐t. , Ni Q.‐Y. , Zhang M.‐w. , Xu H.‐L.
Published: June 2013

Tibetan macaque (Macaca thibetana), an endangered primate species endemic to China, have been used as experimental animal model for various human diseases. Major histocompatibility complex (MHC) genes play a crucial role in the susceptibility and/or resistance to many human diseases, but little is known about Tibetan macaques. To gain an insight into the MHC background and to facilitate the experimental use of Tibetan macaques, the second exon of Mhc‐DQB1 gene was sequenced in a cohort of wild Tibetan macaques living in the Sichuan province of China. A total of 23 MhcMath‐DQB1 alleles were identified for the first time, illustrating a marked allelic polymorphism at the DQB1 locus for these macaques. Most of the sequences (74%) observed in this study belong to DQB1*06 (9 alleles) and DQB1*18 (8 alleles) lineages, and the rest (26%) belong to DQB1*15 (3 alleles) and DQB1*17 (3 alleles) lineages. The most frequent alleles detected among these macaques were MhcMath‐DQB1*15:02:02 (17.9%), followed by Math‐DQB1*06:06, 17:03 and 18:01, which were detected in 9 (16.1%) of the monkeys, respectively. Non‐synonymous substitutions occurred at a significantly higher frequency than synonymous substitutions in the peptide‐binding region, suggesting balancing selection for maintaining polymorphisms at the MHC class II DQB1 locus. Phylogenetic analyses confirms the trans‐species model of evolution of the Mhc‐DQB1 genes in non‐human primates, and in particular, the extensive allele sharing is observed between Tibetan and other macaque species.
VALIDATION OF NEW BITE BLOCK‐TYPE HEAD‐IMMOBILIZATION DEVICES FOR RADIOTHERAPY IN DOGS
Authors: Maruo Takuya , Nakamura Shiori , Fukuyama Yasuhiro , Kawarai Shinpei
Published: June 2013

An ideal head‐immobilization method provides a high level of accuracy and reproducibility in the immobilization. Various head‐immobilization methods for radiotherapy have been published and are excellent in terms of accuracy; however, these methods are complicated to use, and labor intensive. The present study describes two new bite block‐type head‐immobilization devices designed for higher stability and lower vertical variation. The device designed in our previous study (the bite block‐type head‐immobilization device; Device A) was modified by making a groove on the top the horizontal plate (Device B) for a stable ventral‐dorsal position, or beneath the horizontal plate (Device C) for a stable dorsal‐ventral position. The three devices were objectively compared with respect to setup time, and accuracy of the computed tomography scan images by two authors independently. Five male healthy beagles were used in this study. For each device, the setup time and the variation in the coordinates were measured five times for each dog. The mean setup times for Devices A, B, and C were 3.3, 1.5, and 2.4 min, respectively, showing the groove modifications were able to reduce the setup time (in device B, by at least 50%). Moreover, three‐dimensional analysis of the computed tomography images revealed that the measurement variability of Device A (1.6 ± 1.0 mm) was significantly higher than that of Device C (0.7 ± 0.4 mm; P < 0.001). Collectively, our results show that use of a bite block‐type head‐immobilization device with a groove improves the setup time and head‐immobilization accuracy.
Numerical Analysis of the Fluid Flow in the First Stage of a Two-Stage Centrifugal Pump With a Vaned Diffuser
Authors: Stel H. , Amaral G. D. L. , Negrão C. O. R. , Chiva S. , Estevam V. , Morales R. E. M.
Published: June 2013

This work presents a numerical investigation of the fluid flow in the first stage of a two-stage centrifugal pump with a vaned diffuser. A computational fluid dynamics (CFD) analysis is performed by using the ANSYS-CFX software for a wide range of volumetric flow rates and also for different rotor speeds. The numerical results are validated against measured values of pressure rise through the impeller and diffuser of the first stage with an overall good agreement. Nevertheless, not only the best efficiency point evaluated numerically is overestimated in comparison with the measured two-stage pump values but also the computed hydraulic efficiency of the first stage. Investigation of the flow pattern for different flow rates reveals that the flow becomes badly oriented for part-load conditions. In such cases, significant levels of turbulence and blade orientation effects are observed, mainly in the diffuser. In spite of different flow rates or rotor speeds, the flow pattern is quite similar if the flow dimensionless coefficient is kept constant, showing that classical similarity rules can be applied in this case. By using such rules, it was also possible to derive a single equation for the pump head to represent the whole operational range of the pump.
Fuel Cell Systems as Power Sources for Sensor Applications
Authors: Thampan Tony M. , Govoni Mark A. , Clark John T.
Published: June 2013

The increasing use of unattended sensors by the Information, Surveillance, and Reconnaissance community requires the development of higher power and energy density sources to provide increased capabilities and operation time while minimizing size and weight. Among the emerging power sources, fuel cell (FC) systems potentially offer an improved alternative to existing solutions. The Communications and Electronics Research and Development and Engineering Center/Command, Power & Integration Directorate/Army Power Division's Power Sources branch has been evaluating fuel cells to meet tactical power military applications. Testing of methanol based FC systems indicates 50% weight savings over a secondary Li-ion rechargeable system at 200 W h, and 30% weight savings over a primary Li battery at 600 W h. However, significant technical barriers to fuel cell based power sources for sensor deployment exist, including requirements for additional size and weight reduction to meet portable sensor design requirements. Additionally, testing of FC systems demonstrate the importance of appropriate battery hybridization to maintain load following as well as increasing system power density. A comparison of a Reformed Methanol FC system and a Direct Methanol FC system was also completed, and results for the system size, weight, and fuel consumption are similar for both technologies. To examine the benefits of larger power fuel cells appropriate for stationary unattended sensor use, a comparison of power and weight available from a solar/battery hybrid system versus a solar/battery/RMFC hybrid system was also completed. Although the solar/battery hybrid system's size and weight are larger than the hybrid system with an FC unit, 14 kg versus 8 kg, respectively, there is significant logistic burden when utilizing a FC system due to its methanol refueling requirement.
Electronic surface and dielectric interface states on GaN and AlGaN
Authors: Eller Brianna S. , Yang Jialing , Nemanich Robert J.
Published: June 2013

GaN and AlGaN have shown great potential in next-generation high-power electronic devices; however, they are plagued by a high density of interface states that affect device reliability and performance, resulting in large leakage current and current collapse. In this review, the authors summarize the current understanding of the gate leakage current and current collapse mechanisms, where awareness of the surface defects is the key to controlling and improving device performance. With this in mind, they present the current research on surface states on GaN and AlGaN and interface states on GaN and AlGaN-based heterostructures. Since GaNand AlGaN are polar materials, both are characterized by a large bound polarization charge on the order of 1013charges/cm2 that requires compensation. The key is therefore to control the compensation charge such that the electronic states do not serve as electron traps or affect device performance and reliability. Band alignment modeling and measurement can help to determine the electronic state configuration. In particular, band bending can determine how the polarization bound charge is compensated;however, the band bending is extremely sensitive to the specific processing steps such as cleaning, dielectric or metal deposition, postdeposition or postmetallization treatments, which affect oxygen coverage, carbon contamination,structural defects, bonding configurations, defect states, absorbates, and Fermi pinning states. In many cases, the specific effects of these treatments on the surface and interface states are not entirely clear as the nature of the electronic states has been obscured in complexity and subtlety. Consequently, a more systematic and methodical approach may be required.
Investigation of structure, magnetic, and transport properties of Mn-doped SiC films
Authors: Sun Xianke , Guo Ruisong , An Yukai , Liu Jiwen
Published: June 2013

Mn-doped SiC films were fabricated by radio frequency magnetron sputtering technique. The structure, composition, and magnetic and transport properties of the films were investigated. The results show the films have the 3C-SiC crystal structure and the doped Mn atoms in the form of Mn2+ ions substitute for C sites in SiC lattice. All the films are ferromagnetic at 300 K, and the ferromagnetism in films arises from the doped Mn atoms and some extended defects. In addition, the saturation magnetization increases with the Mn-doped concentration increasing. The Mn doping does not change the semiconductor characteristics of the SiC films.
InGaN light-emitting diodes: Efficiency-limiting processes at high injection
Authors: Avrutin Vitaliy , Hafiz Shopan din Ahmad , Zhang Fan , Özgür Ümit , Morkoç Hadis , Matulionis Arvidas
Published: June 2013

The authors discuss a relatively comprehensive theoretical and experimental study aimed on unveiling the dominant efficiency loss mechanism at high injection levels in InGaN light-emitting diodes(LEDs), which still limits their application for general lighting despite the breathtaking performance demonstration. A large body of theoretical and experimental data ascribes the observed efficiency loss to overflow of hot electrons aggravated by nonuniform distribution of carriers in the active region as the primary origin of the efficiency droop-phenomenon, but Auger recombination has also been invoked as the genesis of the efficiency loss. The electron overflowand the associated efficiency loss can be reduced substantially by inserting, in the n-side of the InGaN active region, an InGaN stair-case electron injector (SEI) with a step-like increased indium composition to operate as an “electron cooler.” In contrast to electron-blocking layer usually employed to prevent the electron leakage from the active region, the SEI does not impede hole injection due to the absence of valence band offset with p-GaN. Moreover, SEI does not generate piezoelectric polarizationfield in addition to differential spontaneous polarization field that pulls down the conduction band at the AlGaN/GaN interface aggravating the electron rollover. In terms of the active region design, owing to their high three-dimensional density of states, it is argued that double heterostructures (DHs) are more attractive for general-lighting LEDs than necessarily quantum wells. The authors demonstrate that DH-based LED active regions,particularly wide ones and those composed of multiple DHs separated by thin (3 nm)In0.06Ga0.94N barriers of reduced barrier height, meant to allow efficient hole transport across the active regions, naturally act as an electron cooler, thus considerably reducing the electron overflow at high injection. However, a wide separation of electron and hole distribution functions in DHs wider than 6 nm substantially reduces the radiative recombination efficiency at injection current densities below∼200 A/cm2. Consequently, the LEDs with dual 6 nm and quad (4×) 3 nm DHs separated by 3-nm In0.06Ga0.94N barriers exhibit the highest external quantum efficiency with substantially reduced efficiency degradation at injection current densities of special interest for low-voltage general-lighting applications. The authors conclude that, for achieving the highest possible LED efficiency, it is imperative that optimum the SEI and the active region should be designed to operate in unison.
Results from a multicenter prostate IMRT dosimetry intercomparison for an OCOG‐TROG clinical trial
Authors: Healy B. , Frantzis J. , Murry R. , Martin J. , Plank A. , Middleton M. , Catton C. , Kron T.
Published: June 2013

Purpose:

A multi‐institution dosimetry intercomparison has been undertaken of prostate intensity modulated radiation therapy (IMRT) delivery. The dosimetry intercomparison was incorporated into the quality assurance for site credentialing for the Trans‐Tasman Radiation Oncology Group Prostate Fractionated Irradiation Trial 08.01 clinical trial.

Methods:

An anthropomorphic pelvic phantom with realistic anatomy was used along with multiplanar dosimetry tools for the assessment. Nineteen centers across Australia and New Zealand participated in the study.

Results:

In comparing planned versus measured dose to the target at the isocenter within the phantom, all centers were able to achieve a total delivered dose within 3% of planned dose. In multiplanar analysis with radiochromic film using the gamma analysis method to compare delivered and planned dose, pass rates for a 5%/3 mm criterion were better than 90% for a coronal slice through the isocenter. Pass rates for an off‐axis coronal slice were also better than 90% except for one instance with 84% pass rate.

Conclusions:

Strengths of the dosimetry assessment procedure included the true anthropomorphic nature of the phantom used, the involvement of an expert from the reference center in carrying out the assessment at every site, and the ability of the assessment to detect and resolve dosimetry discrepancies.
Disambiguating durational cues for speech segmentation
Authors: Monaghan Padraic , White Laurence , Merkx Marjolein M.
Published: June 2013

Vowels are lengthened in lexically stressed syllables and also in word-final syllables. Both stress and final-syllable lengthening can assist in word segmentation from continuous speech, but in languages like English, with a preponderance of stress-initial words, lengthening cues may conflict for indicating word boundaries. An analysis of a large corpus of English speech demonstrated that speakers provide distributional information sufficient to potentially allow listeners to determine whether vowel lengthening is associated with lexical stress or word finality without relying on a congruence of multiple suprasegmental cues to make the distinction.
The roles of fundamental frequency contours and sentence context in Mandarin Chinese speech intelligibility
Authors: Wang Jiuju , Shu Hua , Zhang Linjun , Liu Zhaoxing , Zhang Yang
Published: June 2013

Flattening the fundamental frequency (F0) contours of Mandarin Chinese sentences reduces their intelligibility in noise but not in quiet. It is unclear, however, how the absence of primary acoustic cue for lexical tones might be compensated with the top-down information of sentence context. In this study, speech intelligibility was evaluated when participants listened to sentences and word lists with or without F0 variations in quiet and noise. The results showed that sentence context partially explained the unchanged intelligibility of monotonous Chinese sentences in quiet and further indicate that F0 variations and sentence context act in concert during speech comprehension.
Dispersal and Survival of Flavobacterium psychrophilum PhagesIn Vivoin Rainbow Trout andIn Vitrounder Laboratory Conditions: Implications for Their Use in Phage Therapy
Authors: Madsen Lone , Bertelsen Sif K. , Dalsgaard Inger , Middelboe Mathias
Published: June 2013

Attention has been drawn to phage therapy as an alternative approach for controlling pathogenic bacteria such asFlavobacterium psychrophilumin salmonid aquaculture, which can give rise to high mortalities, especially in rainbow trout fry. Recently, phages have been isolated with a broad host range and a strong lytic potential against pathogenicF. psychrophilumunder experimental conditions. However, little is known about the fate of phages at environmental conditions. Here, we quantified the dispersal and fate ofF. psychrophilumphages and hosts in rainbow trout fry after intraperitoneal injection. Both phages and bacteria were isolated from the fish organs for up to 10 days after injection, and coinjection with both bacteria and phages resulted in a longer persistence of the phage in the fish organs, than when the fish had been injected with the phages only. The occurrence of both phage and bacterium was most prevalent in the kidney and spleen, with only minor occurrence in the brain. The experiment showed that injected phages were rapidly spread in the internal organs of the fish, also in the absence of bacteria. Parallel examination of the regulation of bacteriophage infectivity in controlled laboratory experiments at various environmental conditions showed that pH had only minor effects on long-term (3 months) phage infectivity within a pH range of 4.5 to 7.5, whereas phage infectivity was immediately lost at pH 3. In the absence of host cells, phage infectivity decreased by a factor of 10,000 over 55 days in untreated pond water, while the sterilization and removal of particles caused a 100-fold increase in phage survival relative to the control. In addition,F. psychrophilum-specific phages maintained their infectivity for ∼2 months in glycerol at −80°C, whereas infectivity decreased by a factor 10 when kept in a buffer at 20°C. Only a very small degradation in infectivity was seen when bacteriophages were added and dried on fish feed pellets. Together, these results indicate that application of bacteriophages represents a promising approach for the control ofF. psychrophiluminfections in trout and suggest fish feed as a potential delivery method.
Activating Phosphoenolpyruvate Carboxylase and Phosphoenolpyruvate Carboxykinase in Combination for Improvement of Succinate Production
Authors: Tan Zaigao , Zhu Xinna , Chen Jing , Li Qingyan , Zhang Xueli
Published: June 2013

Phosphoenolpyruvate (PEP) carboxylation is an important step in the production of succinate by
Escherichia coli
. Two enzymes, PEP carboxylase (PPC) and PEP carboxykinase (PCK), are responsible for PEP carboxylation. PPC has high substrate affinity and catalytic velocity but wastes the high energy of PEP. PCK has low substrate affinity and catalytic velocity but can conserve the high energy of PEP for ATP formation. In this work, the expression of both the
ppc
and
pck
genes was modulated, with multiple regulatory parts of different strengths, in order to investigate the relationship between PPC or PCK activity and succinate production. There was a positive correlation between PCK activity and succinate production. In contrast, there was a positive correlation between PPC activity and succinate production only when PPC activity was within a certain range; excessive PPC activity decreased the rates of both cell growth and succinate formation. These two enzymes were also activated in combination in order to recruit the advantages of each for the improvement of succinate production. It was demonstrated that PPC and PCK had a synergistic effect in improving succinate production.
Longitudinal Monitoring of Extended-Spectrum-Beta-Lactamase/AmpC-Producing Escherichia coli at German Broiler Chicken Fattening Farms
Authors: Laube H. , Friese A. , von Salviati C. , Guerra B. , Käsbohrer A. , Kreienbrock L. , Roesler U.
Published: June 2013

Antimicrobial resistance of
Escherichia coli
to modern beta-lactam antibiotics due to the production of extended-spectrum beta-lactamases (ESBL) and/or plasmid-mediated AmpC beta-lactamases (AmpC) represents an emerging and increasing resistance problem that dramatically limits therapeutic options in both human and veterinary medicine. The presence of ESBL/AmpC genes in commensal
E. coli
from food-producing animals like broilers may pose a human health hazard. However, there are no data available concerning the prevalence of ESBL/AmpC-producing
E. coli
in German broiler flocks using selective methods. In this longitudinal study, samples were taken from seven conventional broiler fattening farms at three different times within one fattening period. Various samples originating from the animals as well as from their direct environment in the barn were investigated for the occurrence of ESBL/AmpC-producing
E. coli
. Average detection levels of 51, 75, and 76% in animal samples collected during the three samplings in the course of the fattening period demonstrate a colonization of even 1-day-old chicks, as well as a continuous significant (
P
< 0.001) increase in prevalence thereafter. The detection frequencies in housing environmental samples were relatively high, with an increase over time, and ranged between 54.2 and 100%. A total of 359
E. coli
isolates were characterized by PCR and partly via the disc diffusion method. This study shows that prevalence of ESBL/AmpC-producing
E. coli
increases during the fattening period of the broiler flocks examined. Both colonized day-old chicks and contaminated farm environments could represent significant sources of ESBL/AmpC-producing
E. coli
in German broiler fattening farms.
PCR Characterization Suggests that an Unusual Range of Bartonella Species Infect the Striped Field Mouse (Apodemus agrarius) in Central Europe
Authors: Hildebrand Joanna , Paziewska-Harris Anna , Zaleśny Grzegorz , Harris Philip D.
Published: June 2013

Blood samples from
Apodemus agrarius
from Poland yielded PCR amplicons of
Bartonella
species. These included
B. grahamii
,
B. taylorii
, and
B. birtlesii
, as is typical of European
Apodemus
, as well as
B. elizabethae
-like forms and a recombinant strain of
B. taylorii
, most closely related to an American isolate from
Tamiasciurus hudsonicus
.
Strain/Species-Specific Probe Design for Microbial Identification Microarrays
Authors: Tu Qichao , He Zhili , Deng Ye , Zhou Jizhong
Published: June 2013

Specific identification of microorganisms in the environment is important but challenging, especially at the species/strain level. Here, we have developed a novel
k
-mer-based approach to select strain/species-specific probes for microbial identification with diagnostic microarrays. Application of this approach to human microbiome genomes showed that multiple (≥10 probes per strain) strain-specific 50-mer oligonucleotide probes could be designed for 2,012 of 3,421 bacterial strains of the human microbiome, and species-specific probes could be designed for most of the other strains. The method can also be used to select strain/species-specific probes for sequenced genomes in any environments, such as soil and water.
Shiga Toxin 2-Encoding Bacteriophages in Human Fecal Samples from Healthy Individuals
Authors: Martinez-Castillo Alexandre , Quirós Pablo , Navarro Ferran , Miró Elisenda , Muniesa Maite
Published: June 2013

Shiga toxin-converting bacteriophages (Stx phages) carry thestxgene and convert nonpathogenic bacterial strains into Shiga toxin-producing bacteria. Previous studies have shown that high densities of free and infectious Stx phages are found in environments polluted with feces and also in food samples. Taken together, these two findings suggest that Stx phages could be excreted through feces, but this has not been tested to date. In this study, we purified Stx phages from 100 fecal samples from 100 healthy individuals showing no enteric symptoms. The phages retrieved from each sample were then quantified by quantitative PCR (qPCR). In total, 62% of the samples carried Stx phages, with an average value of 2.6 × 104Stx phages/g. This result confirms the excretion of free Stx phages by healthy humans. Moreover, the Stx phages from feces were able to propagate in enrichment cultures ofstx-negativeEscherichia coli(strains C600 and O157:H7) and inShigella sonnei, indicating that at least a fraction of the Stx phages present were infective. Plaque blot hybridization revealed lysis by Stx phages from feces. Our results confirm the presence of infectious free Stx phages in feces from healthy persons, possibly explaining the environmental prevalence observed in previous studies. It cannot be ruled out, therefore, that some positivestxresults obtained during the molecular diagnosis of Shiga toxin-producingEscherichia coli(STEC)-related diseases using stool samples are due to the presence of Stx phages.
Induction of Biofilm Formation in the Betaproteobacterium Burkholderia unamae CK43B Exposed to Exogenous Indole and Gallic Acid
Authors: Kim Dongyeop , Sitepu Irnayuli R. , Hashidoko Yasuyuki
Published: June 2013

Burkholderia unamae
CK43B, a member of the
Betaproteobacteria
that was isolated from the rhizosphere of a
Shorea balangeran
sapling in a tropical peat swamp forest, produces neither indole nor extracellular polymeric substances associated with biofilm formation. When cultured in a modified Winogradsky's medium supplemented with up to 1.7 mM indole,
B. unamae
CK43B maintains its planktonic state by cell swelling and effectively degrades exogenous indole. However, in medium supplemented with 1.7 mM exogenous indole and 1.0 mM gallic acid,
B. unamae
CK43B produced extracellular polymeric substances and formed a biofilm. The concentration indicated above of gallic acid alone had no effect on either the growth or the differentiation of
B. unamae
CK43B cells above a certain concentration threshold, whereas it inhibited indole degradation by
B. unamae
CK43B to 3-hydroxyindoxyl. In addition, coculture of
B. unamae
CK43B with indole-producing
Escherichia coli
in nutrient-rich Luria-Bertani medium supplemented with 1.0 mM gallic acid led to the formation of mixed cell aggregates. The viability and active growth of
B. unamae
CK43B cells in a coculture system with
Escherichia coli
were evidenced by fluorescence
in situ
hybridization. Our data thus suggest that indole facilitates intergenus communication between indole-producing gammaproteobacteria and some indole-degrading bacteria, particularly in gallic acid-rich environments.
The Microcosm Mediates the Persistence of Shiga Toxin-Producing Escherichia coli in Freshwater Ecosystems
Authors: Mauro Steven A. , Opalko Hannah , Lindsay Kyle , Colon Michael P. , Koudelka Gerald B.
Published: June 2013

Water is a major route for infection of humans by exotoxin-producing bacteria, including Shiga toxin-producing
Escherichia coli
(STEC). While STEC has the potential to be present in nearly every type of water source, its distribution is sporadic, and an understanding of factors that govern its emergence and persistence within water is lacking. In this study, we examined the influence of microbe content on STEC persistence in freshwater. We found that depletion of microbes in the water leads to a considerable increase in the persistence of STEC, an effect that can be mitigated by adding grazing protists to the water. STEC strains appear to be more resistant to the impact of grazing protists than
E. coli
strains that lack the Shiga toxin (
stx
) gene. Our results demonstrate that the microcosm can dramatically influence the persistence of STEC in aquatic ecosystems and that the overall impact by microbes on STEC strains is fundamentally different from that of non-STEC strains of bacteria. Overall, these results provide insight into why STEC and possibly other exotoxin-producing bacterial pathogens display such variability in abundance, distribution, and persistence in aquatic ecosystems.
Draft Genome Sequences of Mycoplasma auris and Mycoplasma yeatsii, Two Species of the Ear Canal of
Caprinae
Authors: Dordet-Frisoni Emilie , Baranowski Eric , Barré Aurélien , Blanchard Alain , Breton Marc , Couture Carole , Dupuy Virginie , Gaurivaud Patrice , Jacob Daniel , Lemaitre Claire , Manso-Silván Lucía , Nikolski Macha , Nouvel Laurent-Xavier , Poumarat François , Sirand-Pugnet Pascal , Thébault Patricia , Theil Sébastien , Thiaucourt François , Citti Christine , Tardy Florence
Published: June 2013

We report here the draft genome sequences of
Mycoplasma auris
and
Mycoplasma yeatsii
, two species commonly isolated from the external ear canal of
Caprinae
.
Has the Bacterial Biphenyl Catabolic Pathway Evolved Primarily To Degrade Biphenyl? The Diphenylmethane Case
Authors: Pham Thi Thanh My , Sylvestre Michel
Published: June 2013

In this work, we have compared the ability of
Pandoraea pnomenusa
B356 and of
Burkholderia xenovorans
LB400 to metabolize diphenylmethane and benzophenone, two biphenyl analogs in which the phenyl rings are bonded to a single carbon. Both chemicals are of environmental concern.
P. pnomenusa
B356 grew well on diphenylmethane. On the basis of growth kinetics analyses, diphenylmethane and biphenyl were shown to induce the same catabolic pathway. The profile of metabolites produced during growth of strain B356 on diphenylmethane was the same as the one produced by isolated enzymes of the biphenyl catabolic pathway acting individually or in coupled reactions. The biphenyl dioxygenase oxidizes diphenylmethane to 3-benzylcyclohexa-3,5-diene-1,2-diol very efficiently, and ultimately this metabolite is transformed to phenylacetic acid, which is further metabolized by a lower pathway. Strain B356 was also able to cometabolize benzophenone through its biphenyl pathway, although in this case, this substrate was unable to induce the biphenyl catabolic pathway and the degradation was incomplete, with accumulation of 2-hydroxy-6,7-dioxo-7-phenylheptanoic acid. Unlike strain B356,
B. xenovorans
LB400 did not grow on diphenylmethane. Its biphenyl pathway enzymes metabolized diphenylmethane, but they poorly metabolize benzophenone. The fact that the biphenyl catabolic pathway of strain B356 metabolized diphenylmethane and benzophenone more efficiently than that of strain LB400 brings us to postulate that in strain B356, this pathway evolved divergently to serve other functions not related to biphenyl degradation.
Length Control of the Flagellar Hook in a Temperature-Sensitive
flgE
Mutant of Salmonella enterica Serovar Typhimurium
Authors: Uchida Kaoru , Dono Kohei , Aizawa Shin-Ichi
Published: June 2013

The flagellar hook is a short, curved, extracellular structure located between the basal body and the filament. The hook is composed of the FlgE protein. In this study, we analyzed flagellum assembly in a temperature-sensitive
flgE
mutant of
Salmonella enterica
serovar Typhimurium. When the mutant cells were grown at 30°C, they produced flagella of a normal length (71% of the population) and short hooks without filaments (26%). At 37°C, 70% of the basal bodies lacked hooks, and intact flagella made up only 6% of the population. Mutant cells secreted monomeric FlgE in abundance at 37°C, suggesting that the mutant FlgE protein might be defective in polymerization at higher temperatures. The average length of the hooks in intact filaments was 55 nm, whereas after acid treatment, it was 45 nm. SDS-PAGE analysis of the hook-basal body showed that HAP1 was missing in the mutant but not in the wild type. We concluded that hook length in the mutant is controlled in the same way as in the wild type, but the hook appeared short after acid treatment due to the lack of HAP1. We also learned that the true length of the hook is possibly 45 nm, not 55 nm, as has been believed.
The Escherichia coli CydX Protein Is a Member of the CydAB Cytochrome
bd
Oxidase Complex and Is Required for Cytochrome
bd
Oxidase Activity
Authors: VanOrsdel Caitlin E. , Bhatt Shantanu , Allen Rondine J. , Brenner Evan P. , Hobson Jessica J. , Jamil Aqsa , Haynes Brittany M. , Genson Allyson M. , Hemm Matthew R.
Published: June 2013

Cytochrome
bd
oxidase operons from more than 50 species of bacteria contain a short gene encoding a small protein that ranges from ∼30 to 50 amino acids and is predicted to localize to the cell membrane. Although cytochrome
bd
oxidases have been studied for more than 70 years, little is known about the role of this small protein, denoted CydX, in oxidase activity. Here we report that
Escherichia coli
mutants lacking CydX exhibit phenotypes associated with reduced oxidase activity. In addition, cell membrane extracts from Δ
cydX
mutant strains have reduced oxidase activity
in vitro
. Consistent with data showing that CydX is required for cytochrome
bd
oxidase activity, copurification experiments indicate that CydX interacts with the CydAB cytochrome
bd
oxidase complex. Together, these data support the hypothesis that CydX is a subunit of the CydAB cytochrome
bd
oxidase complex that is required for complex activity. The results of mutation analysis of CydX suggest that few individual amino acids in the small protein are essential for function, at least in the context of protein overexpression. In addition, the results of analysis of the paralogous small transmembrane protein AppX show that the two proteins could have some overlapping functionality in the cell and that both have the potential to interact with the CydAB complex.
Numbers of Individual Nutrient Germinant Receptors and Other Germination Proteins in Spores of Bacillus subtilis
Authors: Stewart Kerry-Ann V. , Setlow Peter
Published: June 2013

Germination of dormant
Bacillus subtilis
spores with specific nutrient germinants is dependent on a number of inner membrane (IM) proteins, including (i) the GerA, GerB, and GerK germinant receptors (GRs) that respond to nutrient germinants; (ii) the GerD protein, essential for optimal GR function; and (iii) SpoVA proteins, essential for the release of the spore-specific molecule dipicolinic acid (DPA) during spore germination. Levels of GR A and C subunit proteins, GerD, and SpoVAD in wild-type spores were determined by Western blot analysis of spore fractions or total disrupted spores by comparison with known amounts of purified proteins. Surprisingly, after disruption of decoated
B. subtilis
spores with lysozyme and fractionation, ∼90% of IM fatty acids and GR subunits remained with the spores' insoluble integument fraction, indicating that yields of purified IM are low. The total lysate from disrupted wild-type spores contained ∼2,500 total GRs/spore: GerAA and GerAC subunits each at ∼1,100 molecules/spore and GerBC and GerKA subunits each at ∼700 molecules/spore. Levels of the GerBA subunit determined previously were also predicted to be ∼700 molecules/spore. These results indicate that the A/C subunit stoichiometry in GRs is most likely 1:1, with GerA being the most abundant GR. GerD and SpoVAD levels were ∼3,500 and ∼6,500 molecules/spore, respectively. These values will be helpful in formulating mathematic models of spore germination kinetics as well as setting lower limits on the size of the GR-GerD complex in the spores' IM, termed the germinosome.
Regulation of the
ald
Gene Encoding Alanine Dehydrogenase by AldR in Mycobacterium smegmatis
Authors: Jeong Ji-A , Baek Eun-Young , Kim Si Wouk , Choi Jong-Soon , Oh Jeong-Il
Published: June 2013

The regulatory gene
aldR
was identified 95 bp upstream of the
ald
gene encoding
l
-alanine dehydrogenase in
Mycobacterium smegmatis
. The AldR protein shows sequence similarity to the regulatory proteins of the Lrp/AsnC family. Using an
aldR
deletion mutant, we demonstrated that AldR serves as both activator and repressor for the regulation of
ald
gene expression, depending on the presence or absence of
l
-alanine. The purified AldR protein exists as a homodimer in the absence of
l
-alanine, while it adopts the quaternary structure of a homohexamer in the presence of
l
-alanine. The binding affinity of AldR for the
ald
control region was shown to be increased significantly by
l
-alanine. Two AldR binding sites (O1 and O2) with the consensus sequence GA-N
2
-ATC-N
2
-TC and one putative AldR binding site with the sequence GA-N
2
-GTT-N
2
-TC were identified upstream of the
ald
gene. Alanine and cysteine were demonstrated to be the effector molecules directly involved in the induction of
ald
expression. The cellular level of
l
-alanine was shown to be increased in
M. smegmatis
cells grown under hypoxic conditions, and the hypoxic induction of
ald
expression appears to be mediated by AldR, which senses the intracellular level of alanine.
Phage-Encoded Inhibitor of Staphylococcus aureus Transcription Exerts Context-Dependent Effects on Promoter Function in a Modified Escherichia coli-Based Transcription System
Authors: Montero-Diez Cristina , Deighan Padraig , Osmundson Joseph , Darst Seth A. , Hochschild Ann
Published: June 2013

Promoter recognition in bacteria is mediated primarily by the σ subunit of RNA polymerase (RNAP), which makes sequence-specific contacts with the promoter −10 and −35 elements in the context of the RNAP holoenzyme. However, the RNAP α subunit can also contribute to promoter recognition by making sequence-specific contacts with upstream (UP) elements that are associated with a subset of promoters, including the rRNA promoters. In
Escherichia coli
, these interactions between the RNAP α subunit (its C-terminal domain [CTD], in particular) and UP element DNA result in significant stimulation of rRNA transcription. Among the many cellular and bacteriophage-encoded regulators of transcription initiation that have been functionally dissected, most exert their effects via a direct interaction with either the σ or the α subunit. An unusual example is provided by a phage-encoded inhibitor of RNA synthesis in
Staphylococcus aureus
. This protein, phage G1 gp67, which binds tightly to σ in the context of the
S. aureus
RNAP holoenzyme, has recently been shown to exert selective effects on transcription by inhibiting the function of the α subunit CTD (αCTD). Here we report the development of a gp67-responsive
E. coli
-based transcription system. We examine transcription
in vitro
from promoters that do or do not carry the UP element associated with a well-characterized
E. coli
rRNA promoter. Our findings indicate that the αCTD can increase promoter activity significantly even in the absence of an UP element. We also find that gp67 can exert αCTD-dependent or αCTD-independent effects on transcription depending on the particular promoter, indicating that the mechanism of gp67 action is context dependent.
Quorum Sensing Regulatory Cascades Control Vibrio fluvialis Pathogenesis
Authors: Wang Yunduan , Wang Hui , Liang Weili , Hay Amanda J. , Zhong Zengtao , Kan Biao , Zhu Jun
Published: June 2013

Quorum sensing (QS) is a process by which individual bacteria are able to communicate with one another, thereby enabling the population as a whole to coordinate gene regulation and subsequent phenotypic outcomes. Communication is accomplished through production and detection of small molecules in the extracellular milieu. In many bacteria, particularly
Vibrio
species, multiple QS systems result in multiple signals, as well as cross talk between systems. In this study, we identify two QS systems in the halophilic enteric pathogen
Vibrio fluvialis
: one acyl-homoserine lactone (AHL) based and one CAI-1/AI-2 based. We show that a LuxI homolog, VfqI, primarily produces 3-oxo-C10-HSL, which is sensed by a LuxR homolog, VfqR. VfqR-AHL is required to activate
vfqI
expression and autorepress
vfqR
expression. In addition, we have shown that similar to that in
V. cholerae
and
V. harveyi
,
V. fluvialis
produces CAI-1 and AI-2 signal molecules to activate the expression of a
V. cholerae
HapR homolog through LuxO. Although VfqR-AHL does not regulate
hapR
expression, HapR can repress
vfqR
transcription. Furthermore, we found that QS in
V. fluvialis
positively regulates production of two potential virulence factors, an extracellular protease and hemolysin. QS also affects cytotoxic activity against epithelial tissue cultures. These data suggest that
V. fluvialis
integrates QS regulatory pathways to play important physiological roles in pathogenesis.
Lithobezoar, a rare cause of acute oesophageal obstruction: surgery after failure of endoscopic removal
Authors: Chaudhry Ikram , Asban Ammar , Kazoun Rabih , Khurshid Imtiaz
Published: June 2013

Oesophageal lithobezoar is a very rare clinical entity, especially presenting as a case of acute dysphagia. A 54-year-old man, with long-standing psychiatric illness, presented with a recent episode of vomiting and chest pain followed by dysphagia. Chest x-ray revealed a radio opaque shadow in the posterior mediastinum. Endoscopy showed a calcified foreign body in the lower oesophagus. Endoscopic attempts to remove or fragment the foreign body were unsuccessful. Foreign body was removed successfully through oesophagotomy using left posterolateral thoracotomy. Pathology revealed oesophageal lithobezoar.