bluuebunny/crossref_metadata_2025 huggingface dataset:
TEM Characterization of Single‐ and Multilayer Triol‐Based Sol–Gel PZT (53/47) Thin Films
Authors: Zhou Zhaoxia , Reaney Ian M. , Wang Peiyi , Hind David , Khemprasit Jinda , Milne Steven J.
Published: November 2006

Integrated lead zirconate titanate thin films deposited on Pt/Ti/SiO2/Si substrates using a novel triol‐based route were characterized using X‐ray diffraction and transmission electron microscopy. Crack‐free single‐layer PZT films of up to 200 nm thick were prepared by triol‐based sol–gel processing onto Pt/Ti/SiO2/Si substrates. Films ∼75 nm thick exhibited a microstructure free of pores and second phase. As film thickness increased, film texture changed from {100} to {111} perovskite. Essentially, single‐phase multilayer films could be prepared by the deposition and pyrolysis of several 75 nm layers, followed by a single crystallization step. The influence of heat‐treatment schedule on the microstructure and orientation of the multilayer films is discussed. Comparison has been made between multilayer films prepared using the triol‐based sol and an inverted mixing order/acetic acid‐based sol.
Influence of Cu2O on Interface Behavior of Copper/SiCp Composite Prepared by Spark Plasma Sintering
Authors: Zhang Rui , Gao Lian , Guo Jingkun
Published: November 2006

Copper/SiCp composites were prepared by spark plasma sintering. X‐ray photoelectron spectroscopy, X‐ray diffraction, transmission electron microscopy, and energy dispersive spectroscopy techniques were used to characterize the sintered samples. Cu2O was found to facilitate the physical wetting at the interface through the formation of an amorphous intergranular phase. The reaction between SiC and copper was detected in the samples containing little Cu2O. It led to the degradation of SiC reinforcements and the decrease in hardness of copper/SiCp composites.
Training of disaster managers at a masters degree level: From emergency care to managerial control
Authors: MacFarlane Campbell , Joffe Anthony Lyle , Naidoo Shan
Published: November 2006

The world has faced huge disasters over the last few decades and concerns have been expressed by nearly all international agencies involved that there is a scarcity of managerial skills to deal with the mitigation and management of disasters. Disaster risks are also on the increase throughout Africa and Southern Africa because of changes in the development process, settlement patterns and conflicts in the region. Emergency physicians are but one important resource in dealing with disasters. The need for a comprehensive multisectoral approach to disasters and more importantly to deal with its mitigation is becoming increasingly evident, especially in developing countries. Hence, the need for specially trained professionals in disaster management. In an effort to improve national, regional and continental capacity, and in support of the South African Disaster Management Act, the University of the Witwatersrand, Johannesburg, South Africa, has developed a Master of Public Health degree in Disaster Management. The MPH is aimed at preparing professionals from health and allied fields to play leadership roles in the management, improvement and evaluation of health and the health‐care system. Emergency physicians have an important role to play in the development of disaster medicine and disaster management programmes and it is important that they engage in this activity, collaborating with colleagues of various other disciplines as appropriate. The following paper outlines the background to the programme and the current programme.
Psychiatric Illness Presenting with a Sexual Complaint and Management by Psychotropic Medications: A Case Report
Authors: Krychman Michael , Carter Jeanne , Amsterdam Alison
Published: November 2006

Introduction

Sexual medicine healthcare professionals, who do not normally examine men and women with psychiatric disorders, need to be aware that those with psychiatric disorders can and do present with sexual medicine problems. In particular, psychiatric individuals may present with a variety of delusions including those that have sexual content or sexual implications. The rare disorder of reverse delusional misidentification syndrome may be encountered in schizophrenic patients and may be best managed by the combined team effort of a sexual medicine specialist and psychiatrist.

Aim

To report a case study that reiterates the assessment and sexual medicine management of a female with sexual dysfunction who believed she was transforming into a male.

Methods

Case report of a woman who attended an outpatient clinic in an academic medical center.

Results

A 60-year-old woman with a history of paranoid schizophrenia presented to a gynecologist for ovarian cancer screening. Evaluation revealed complaints that the patient’s ovaries were testes that produced sperm and her clitoris was a penis capable of erection and ejaculation. Gynecological examination revealed only atrophic vaginitis. The patient was treated with local minimally absorbed vaginal estrogens and referred for psychological assessment and counseling. Psychotropic medication compliance was encouraged, weekly psychotherapy was continued, and delusional symptoms were minimized.

Conclusion

Sexual medicine healthcare providers should be prepared to manage sex health concerns of men and women with psychiatric disorders, including delusional misidentification syndrome, in conjunction with a psychiatrist.
Sexual Outcomes and Satisfaction with Hysterectomy: Influence of Patient Education
Authors: Bradford Andrea , Meston Cindy
Published: November 2006

Introduction

Many women experience improved sexual function after hysterectomy. However, a sizeable minority of women report worsened sexual function after the surgery, and concerns about the effect of surgery on sexual function are common among women planning to undergo hysterectomy.

Aim

The present study examined the role of education about the potential sexual consequences of hysterectomy in predicting self-reported outcomes and satisfaction with the procedure.

Methods

We conducted a cross-sectional survey of 204 women who had undergone simple hysterectomy in the preceding 3–12 months. Participants volunteered in response to a Web-based advertisement.

Main Outcome Measures

Participants indicated their current sexual function using the Female Sexual Function Index (FSFI), and reported positive and negative sexual outcomes experienced after hysterectomy using a checklist. Participants also completed questionnaire items regarding satisfaction with hysterectomy and education from their physicians about sexual risks and benefits prior to surgery.

Results

Current sexual function scores were related to self-reports of positive and negative sexual outcomes following hysterectomy and overall satisfaction with hysterectomy. Education from a physician about possible adverse sexual outcomes was largely unrelated to self-reports of having experienced those outcomes. However, education about possible negative sexual outcomes predicted overall satisfaction with hysterectomy when controlling for self-reports of positive and negative sexual outcomes.

Conclusion

Education about potential negative sexual outcomes after surgery may enhance satisfaction with hysterectomy, independent of whether negative sexual outcomes were experienced. Including a discussion of potential sexual changes after surgery may enhance the benefits of presurgical counseling prior to hysterectomy.
Erectile Dysfunctions in Patient–Physician Communication: Optimized Strategies for Addressing Sexual Issues and the Benefit of Using a Patient Questionnaire
Authors: Hartmann Uwe , Burkart Martin
Published: November 2006

Introduction

Erectile dysfunctions are prevalent but underdiagnosed and undertreated health problems. Communication barriers between patients and physicians are one of the main reasons for this and responsible for a low report rate of sexual dysfunction.

Aim

The main aim of the study was to investigate which phrasing and communication strategies gained the highest acceptance from physicians and their patients and were considered the most effective.

Main Outcome Measures

A documentation form on which each consultation was rated by the participating physicians.

Methods

A large group of physicians was asked to hand out a short patient questionnaire to all male patients over 30 years. The physician was instructed to discuss the questionnaire with the patient and to ask him about sexual problems. A total of 1,191 physicians took part in the study that documented a total of 10,622 consultations with an average duration of 15 minutes.

Results

The main results were: (i) the patient questionnaire found a high level of acceptance and 54% of discussions of sexual health were prompted by it; (ii) the patients’ reaction to physicians addressing sexual health was positive in more than two-thirds of the sample and characterized by openness, willingness to communicate, and relief that their sexual problems had been addressed; (iii) from the physicians’ perspective, the most favored communication strategies were a clear signaling of a willingness to talk, and addressing treatment possibilities or signaling that help was available; and (iv) the resulting discussion led to further diagnostic measures in 25% of patients and to further therapeutic measures in 60% of patients.

Conclusion

There are good grounds for concluding that: (i) addressing a patient’s sexual health as part of a physician’s everyday routine is feasible in terms of duration and content; and (ii) a short patient questionnaire is an excellent aid for patients and physicians for initiating communication on the topic.
Optimization of HDR brachytherapy dose distributions using linear programming with penalty costs
Authors: Alterovitz Ron , Lessard Etienne , Pouliot Jean , Hsu I‐Chow Joe , O'Brien James F. , Goldberg Ken
Published: November 2006

Prostate cancer is increasingly treated with high‐dose‐rate (HDR) brachytherapy, a type of radiotherapy in which a radioactive source is guided through catheters temporarily implanted in the prostate. Clinicians must set dwell times for the source inside the catheters so the resulting dose distribution minimizes deviation from dose prescriptions that conform to patient‐specific anatomy. The primary contribution of this paper is to take the well‐established dwell times optimization problem defined by Inverse Planning by Simulated Annealing (IPSA) developed at UCSF and exactly formulate it as a linear programming (LP) problem. Because LP problems can be solved exactly and deterministically, this formulation provides strong performance guarantees: one can rapidly find the dwell times solution that globally minimizes IPSA's objective function for any patient case and clinical criteria parameters. For a sample of 20 prostates with volume ranging from , the new LP method optimized dwell times in less than per case on a standard PC. The dwell times solutions currently being obtained clinically using simulated annealing (SA), a probabilistic method, were quantitatively compared to the mathematically optimal solutions obtained using the LP method. The LP method resulted in significantly improved objective function values compared to SA , but none of the dosimetric indices indicated a statistically significant difference . The results indicate that solutions generated by the current version of IPSA are clinically equivalent to the mathematically optimal solutions.
X‐ray spectrum optimization of full‐field digital mammography: Simulation and phantom study
Authors: Bernhardt Philipp , Mertelmeier Thomas , Hoheisel Martin
Published: November 2006

In contrast to conventional analog screen‐film mammography new flat detectors have a high dynamic range and a linear characteristic curve. Hence, the radiographic technique can be optimized independently of the receptor exposure. It can be exclusively focused on the improvement of the image quality and the reduction of the patient dose. In this paper we measure the image quality by a physical quantity, the signal difference‐to‐noise ratio (SDNR), and the patient risk by the average glandular dose (AGD). Using these quantities, we compare the following different setups through simulations and phantom studies regarding the detection of microcalcifications and tumors for different breast thicknesses and breast compositions: Monochromatic radiation, three different anode/filter combinations: Molybdenum/molybdenum , molybdenum/rhodium , and tungsten/rhodium , different filter thicknesses, use of anti‐scatter grids, and different tube voltages. For a digital mammography system based on an amorphous selenium detector it turned out that, first, the combination is the best choice for all detection tasks studied. Second, monochromatic radiation can further reduce the AGD by a factor of up to 2.3, maintaining the image quality in comparison with a real polychromatic spectrum of an x‐ray tube. And, third, the use of an anti‐scatter grid is only advantageous for breast thicknesses larger than approximately .
A novel method of radiochromic film dosimetry using a color scanner
Authors: Hupe Oliver , Brunzendorf Jens
Published: November 2006

A procedure that allows the improved extraction of the dose information based on the multicolor scanning of the radiochromic film is presented. The basic principle is the determination of the dose values from each color channel of the digital film image in RGB format by applying a nonlinear calibration function. The best estimate of the dose is then a weighted mean of the dose values derived from each color channel. The weighting factors are determined in such a way that the noise in the two‐dimensional dose profile is at the minimum. The calculation of the weighting factors is presented; they are chosen to be proportional to the signal‐to‐noise ratio, , in all three color channels, =red, green, or blue. The data reduction can be fully computerized, including the “cleaning” of the digital image from dust and scratches. It is highly reproducible, which is important for quality assurance, and easy to use. Our novel evaluation procedure combines the good response in the low dose range of the red color with the extended dose range of the blue and green color channels (response up to ), making use of one single, steady evaluation function. Therefore, a smooth evaluation is possible in a wide dose range. For the interpretation of measurements with the radiochromic films the spatial inhomogeneity of the film's response to ionizing radiation is very important. Investigations on both film types, HS and MD55‐2, as well as on the new EBT film have been carried out.
Characterization of difference of Gaussian filters in the detection of mammographic regions
Authors: Catarious David M. , Baydush Alan H. , Floyd Carey E.
Published: November 2006

In this article, we present a characterization of the effect of difference of Gaussians (DoG) filters in the detection of mammographic regions. DoG filters have been used previously in mammographic mass computer‐aided detection (CAD) systems. As DoG filters are constructed from the subtraction of two bivariate Gaussian distributions, they require the specification of three parameters: the size of the filter template and the standard deviations of the constituent Gaussians. The influence of these three parameters in the detection of mammographic masses has not been characterized. In this work, we aim to determine how the parameters affect (1) the physical descriptors of the detected regions, (2) the true and false positive rates, and (3) the classification performance of the individual descriptors. To this end, 30 DoG filters are created from the combination of three template sizes and four values for each of the Gaussians’ standard deviations. The filters are used to detect regions in a study database of 181 craniocaudal‐view mammograms extracted from the Digital Database for Screening Mammography. To describe the physical characteristics of the identified regions, morphological and textural features are extracted from each of the detected regions. Differences in the mean values of the features caused by altering the DoG parameters are examined through statistical and empirical comparisons. The parameters’ effects on the true and false positive rate are determined by examining the mean malignant sensitivities and false positives per image (FPpI). Finally, the effect on the classification performance is described by examining the variation in FPpI at the point where 81% of the malignant masses in the study database are detected. Overall, the findings of the study indicate that increasing the standard deviations of the Gaussians used to construct a DoG filter results in a dramatic decrease in the number of regions identified at the expense of missing a small number of malignancies. The sharp reduction in the number of identified regions allowed the identification of textural differences between large and small mammographic regions. We find that the classification performances of the features that achieve the lowest average FPpI are influenced by all three of the parameters.
Feasibility of calibrating elongated brachytherapy sources using a well‐type ionization chamber
Authors: Meigooni Ali S. , Awan Shahid B. , Dou Kai
Published: November 2006

Recently, elongated brachytherapy sources (active length ) have become commercially available for interstitial prostate implants. These sources were introduced to improve the quality of brachytherapy procedures by eliminating the migration and seed bunching associated with loose seed‐type implants. However, the inability to calibrate elongated brachytherapy sources with the Wide‐Angle Free‐Air Chamber (WAFAC) used by the National Institute of Standards and Technology (NIST) hinders the experimental determination of dosimetric parameters of these source types. In order to resolve this shortcoming, an interim solution has been introduced for calibration of elongated brachytherapy sources using a commercially available well‐type ionization chamber. The feasibility of this procedure was examined by calibrating sources with active lengths ranging from 1 to .
Identification of Genomic Species in
Agrobacterium
Biovar 1 by AFLP Genomic Markers
Authors: Portier Perrine , Fischer-Le Saux Marion , Mougel Christophe , Lerondelle Catherine , Chapulliot David , Thioulouse Jean , Nesme Xavier
Published: November 2006

Biovar 1 of the genus
Agrobacterium
consists of at least nine genomic species that have not yet received accepted species names. However, rapid identification of these organisms in various biotopes is needed to elucidate crown gall epidemiology, as well as
Agrobacterium
ecology. For this purpose, the AFLP methodology provides rapid and unambiguous determination of the genomic species status of agrobacteria, as confirmed by additional DNA-DNA hybridizations. The AFLP method has been proven to be reliable and to eliminate the need for DNA-DNA hybridization. In addition, AFLP fragments common to all members of the three major genomic species of agrobacteria, genomic species G1 (reference strain, strain TT111), G4 (reference strain, strain B6, the type strain of
Agrobacterium tumefaciens
), and G8 (reference strain, strain C58), have been identified, and these fragments facilitate analysis and show the applicability of the method. The maximal infraspecies current genome mispairing (CGM) value found for the biovar 1 taxon is 10.8%, while the smallest CGM value found for pairs of genomic species is 15.2%. This emphasizes the gap in the distribution of genome divergence values upon which the genomic species definition is based. The three main genomic species of agrobacteria in biovar 1 displayed high infraspecies current genome mispairing values (9 to 9.7%). The common fragments of a genomic species are thus likely “species-specific” markers tagging the core genomes of the species.
Culture Isolation and Culture-Independent Clone Libraries Reveal New MarineSynechococcusEcotypes with Distinctive Light and N Physiologies
Authors: Ahlgren Nathan A. , Rocap Gabrielle
Published: November 2006

Marine microbial communities often contain multiple closely related phylogenetic clades, but in many cases, it is still unclear what physiological traits differentiate these putative ecotypes. The numerically abundant marine cyanobacteriumSynechococcuscan be divided into at least 14 clades. In order to better understand ecotype differentiation in this genus, we assessed the diversity of aSynechococcuscommunity from a well-mixed water column in the Sargasso Sea during March 2002, a time of year when this genus typically reaches its annual peak in abundance. Diversity was estimated from water sampled at three depths (approximately 5, 70, and 170 m) using both culture isolation and construction of cyanobacterial 16S-23S rRNA internal transcribed sequence clone libraries. Clonal isolates were obtained by enrichment with ammonium, nitrite, or nitrate as the sole N source, followed by pour plating. Each method sampled the in situ diversity differently. The combined methods revealed a total of sevenSynechococcusphylotypes including two new putative ecotypes, labeled XV and XVI. Although most other isolates grow on nitrate, clade XV exhibited a reduced efficiency in nitrate utilization, and both clade XV and XVI are capable of chromatic adaptation, demonstrating that this trait is more widely distributed amongSynechococcusstrains than previously known. Thus, as in its sister genusProchlorococcus, light and nitrogen utilization are important factors in ecotype differentiation in the marineSynechococcuslineage.
Cell Surface Expression of Bacterial Esterase A by
Saccharomyces cerevisiae
and Its Enhancement by Constitutive Activation of the Cellular Unfolded Protein Response
Authors: Breinig Frank , Diehl Björn , Rau Sabrina , Zimmer Christian , Schwab Helmut , Schmitt Manfred J.
Published: November 2006

Yeast cell surface display is a powerful tool for expression and immobilization of biocatalytically active proteins on a unicellular eukaryote. Here bacterial carboxylesterase EstA from
Burkholderia gladioli
was covalently anchored into the cell wall of
Saccharomyces cerevisiae
by in-frame fusion to the endogenous yeast proteins Kre1p, Cwp2p, and Flo1p. When
p
-nitrophenyl acetate was used as a substrate, the esterase specific activities of yeast expressing the protein fusions were 103 mU mg
−1
protein for Kre1/EstA/Cwp2p and 72 mU mg
−1
protein for Kre1/EstA/Flo1p. In vivo cell wall targeting was confirmed by esterase solubilization after laminarinase treatment and immunofluorescence microscopy. EstA expression resulted in cell wall-associated esterase activities of 2.72 U mg
−1
protein for Kre1/EstA/Cwp2p and 1.27 U mg
−1
protein for Kre1/EstA/Flo1p. Furthermore, esterase display on the yeast cell surface enabled the cells to effectively grow on the esterase-dependent carbon source glycerol triacetate (Triacetin). In the case of Kre1/EstA/Flo1p, in vivo maturation within the yeast secretory pathway and final incorporation into the wall were further enhanced when there was constitutive activation of the unfolded protein response pathway. Our results demonstrate that esterase cell surface display in yeast, which, as shown here, is remarkably more effective than EstA surface display in
Escherichia coli
, can be further optimized by activating the protein folding machinery in the eukaryotic secretion pathway.
Use of Multiplex Terminal Restriction Fragment Length Polymorphism for Rapid and Simultaneous Analysis of Different Components of the Soil Microbial Community
▿
Authors: Singh Brajesh K. , Nazaries Loic , Munro Stacey , Anderson Ian C. , Campbell Colin D.
Published: November 2006

A multiplex terminal restriction fragment length polymorphism (M-TRFLP) fingerprinting method was developed and validated for simultaneous analysis of the diversity and community structure of two or more microbial taxa (up to four taxa). The reproducibility and robustness of the method were examined using soil samples collected from different habitats. DNA was PCR amplified separately from soil samples using individual taxon-specific primers for bacteria, archaea, and fungi. The same samples were also subjected to a multiplex PCR with the primers for all three taxa. The terminal restriction fragment length polymorphism profiles generated for the two sets of PCR products were almost identical not only in terms of the presence of peaks but also in terms of the relative peak intensity. The M-TRFLP method was then used to investigate rhizosphere bacterial, fungal, and rhizobial/agrobacterial communities associated with the dwarf shrub
Calluna vulgaris
growing in either open moorland, a mature pine forest, or a transition zone between these two habitats containing naturally regenerating pine trees. Rhizosphere microbial communities associated with
Vaccinium myrtillus
collected from the native pine forest were also investigated. In this study, individual PCR products from the three taxa were also pooled before restriction digestion and fragment size analysis. The terminal restriction fragment length polymorphism profiles obtained with PCR products amplified individually and with multiplexed and pooled PCR products were found to be consistent with each other in terms of the number, position, and relative intensity of peaks. The results presented here confirm that M-TRFLP analysis is a highly reproducible and robust molecular tool for simultaneous investigation of multiple taxa, which allows more complete and higher resolution of microbial communities to be obtained more rapidly and economically.
Phylogenetic Comparisons of Bacterial Communities from Serpentine and Nonserpentine Soils
Authors: Oline David K.
Published: November 2006

I present the results of a culture-independent survey of soil bacterial communities from serpentine soils and adjacent nonserpentine comparator soils using a variety of newly developed phylogenetically based statistical tools. The study design included site-based replication of the serpentine-to-nonserpentine community comparison over a regional scale (∼100 km) in Northern California and Southern Oregon by producing 16S rRNA clone libraries from pairs of samples taken on either side of the serepentine-nonserpentine edaphic boundary at three geographical sites. At the division level, the serpentine and nonserpentine communities were similar to each other and to previous data from forest soils. Comparisons of both richness and Shannon diversity produced no significant differences between any of the libraries, but the vast majority of phylogenetically based tests were significant, even with only 50 sequences per library. These results suggest that most samples were distinct, consisting of a collection of lineages generally not found in other samples. The pattern of results showed that serpentine communities tended to be more similar to each other than they were to nonserpentine communities, and these differences were at a lower taxonomic scale. Comparisons of two nonserpentine communities generally showed differences, and some results suggest that the geographical site may control community composition as well. These results show the power of phylogenetic tests to discern differences between 16S rRNA libraries compared to tests that discard DNA data to bin sequences into operational taxonomic units, and they stress the importance of replication at larger scales for inferences regarding microbial biogeography.
Advantage of Using Inosine at the 3′ Termini of 16S rRNA Gene Universal Primers for the Study of Microbial Diversity
Authors: Ben-Dov Eitan , Shapiro Orr H. , Siboni Nachshon , Kushmaro Ariel
Published: November 2006

To overcome the shortcomings of universal 16S rRNA gene primers 8F and 907R when studying the diversity of complex microbial communities, the 3′ termini of both primers were replaced with inosine. A comparison of the clone libraries derived using both primer sets showed seven bacterial phyla amplified by the altered primer set (8F-I/907R-I) whereas the original set amplified sequences belonging almost exclusively toProteobacteria(95.8%). Sequences belonging toFirmicutes(42.6%) andThermotogae(9.3%) were more abundant in a library obtained by using 8F-I/907R-I at a PCR annealing temperature of 54°C, whileProteobacteriasequences were more frequent (62.7%) in a library obtained at 50°C, somewhat resembling the result obtained using the original primer set. The increased diversity revealed by using primers 8F-I/907R-I confirms the usefulness of primers with inosine at the 3′ termini in studying the microbial diversity of environmental samples.
An Anaerobic Methane-Oxidizing Community of ANME-1b Archaea in Hypersaline Gulf of Mexico Sediments
Authors: Lloyd Karen G. , Lapham Laura , Teske Andreas
Published: November 2006

Sediments overlying a brine pool methane seep in the Gulf of Mexico (Green Canyon 205) were analyzed using molecular and geochemical approaches to identify geochemical controls on microbial community composition and stratification. 16S rRNA gene and rRNA clone libraries, as well as
mcrA
gene clone libraries, showed that the archaeal community consists predominantly of ANME-1b methane oxidizers; no archaea of other ANME subgroups were found with general and group-specific PCR primers. The ANME-1b community was found in the sulfate-methane interface, where undersaturated methane concentrations of ca. 100 to 250 μM coexist with sulfate concentrations around 10 mM. Clone libraries of
dsrAB
genes and bacterial 16S rRNA genes show diversified sulfate-reducing communities within and above the sulfate-methane interface. Their phylogenetic profiles and occurrence patterns are not linked to ANME-1b populations, indicating that electron donors other than methane, perhaps petroleum-derived hydrocarbons, drive sulfate reduction. The archaeal component of anaerobic oxidation of methane is comprised of an active population of mainly ANME-1b in this hypersaline sediment.
Spatiometabolic Stratification of
Shewanella oneidensis
Biofilms
Authors: Teal Tracy K. , Lies Douglas P. , Wold Barbara J. , Newman Dianne K.
Published: November 2006

Biofilms, or surface-attached microbial communities, are both ubiquitous and resilient in the environment. Although much is known about how biofilms form, develop, and detach, very little is understood about how these events are related to metabolism and its dynamics. It is commonly thought that large subpopulations of cells within biofilms are not actively producing proteins or generating energy and are therefore dead. An alternative hypothesis is that within the growth-inactive domains of biofilms, significant populations of living cells persist and retain the capacity to dynamically regulate their metabolism. To test this, we employed unstable fluorescent reporters to measure growth activity and protein synthesis in vivo over the course of biofilm development and created a quantitative routine to compare domains of activity in independently grown biofilms. Here we report that
Shewanella oneidensis
biofilm structures reproducibly stratify with respect to growth activity and metabolism as a function of size. Within domains of growth-inactive cells, genes typically upregulated under anaerobic conditions are expressed well after growth has ceased. These findings reveal that, far from being dead, the majority of cells in mature
S. oneidensis
biofilms have actively turned-on metabolic programs appropriate to their local microenvironment and developmental stage.
The Mosaic Nature of Intergenic 16S-23S rRNA Spacer Regions Suggests rRNA Operon Copy Number Variation in
Clostridium difficile
Strains
Authors: Sadeghifard Nourkhoda , Gürtler Volker , Beer Michael , Seviour Robert J.
Published: November 2006

Clostridium difficile
is a major spore-forming environmental pathogen that causes serious health problems in patients undergoing antibiotic therapy. Consequently, reliable and sensitive methods for typing individual strains are required for epidemiological and environmental studies. Ribotyping is generally considered the best method, but it fails to account for sequence diversity which might exist in intergenic 16S-23S rRNA spacer regions (ISRs) within and among strains of this organism. Therefore, this study was undertaken to compare the sequence of each individual ISR in five strains of
C. difficile
to explore the extent of this diversity and see whether such information might provide the basis for more sensitive and discriminatory strain typing methods. After targeted PCR amplification, cloning, and sequencing, the diversity of the ISRs was used as a measure of rRNA operon copy number. In
C. difficile
strains 630, ATCC 43593, A, and B, 11, 11, 7, and 8 ISR length variants, respectively, were found (containing different combinations of sequence groups [i to xiii]), suggesting 11, 11, 7, and 8
rrn c
opies in the respective strains. Many ISRs of the same length differed markedly in their sequences, and some of these were restricted in occurrence to a single strain. Most of these ISRs did not contain any tRNA genes, and only single copies of the tRNA
Ala
gene were found in those that did. The presence of ISR sequence groups (i to xiii) varied between strains, with some found in one, two, three, four, or all five strains. We conclude that the intergenic 16S-23S rRNA spacer regions showed a high degree of diversity, not only among the
rrn
operons in different strains and different
rrn
copies in a single strain but also among ISRs of the same length. It appears that
C. difficile
ISRs vary more at the inter- and intragenic levels than those of other species as determined by empirical comparison of sequences. The precise characterization of these sequences has demonstrated a high level of mosaic sequence block rearrangements that are present or absent in multiple strain-variable
rrn
copies within and between five different strains of
C. difficile
.
Effects of Mutations in the Substrate-Binding Domain of Poly[(
R
)-3-Hydroxybutyrate] (PHB) Depolymerase from
Ralstonia pickettii
T1 on PHB Degradation
Authors: Hiraishi Tomohiro , Hirahara Yoko , Doi Yoshiharu , Maeda Mizuo , Taguchi Seiichi
Published: November 2006

Poly[(
R
)-3-hydroxybutyrate] (PHB) depolymerase from
Ralstonia pickettii
T1 (PhaZ
RpiT1
) adsorbs to denatured PHB (dPHB) via its substrate-binding domain (SBD) to enhance dPHB degradation. To evaluate the amino acid residues participating in dPHB adsorption, PhaZ
RpiT1
was subjected to a high-throughput screening system consisting of PCR-mediated random mutagenesis targeted to the SBD gene and a plate assay to estimate the effects of mutations in the SBD on dPHB degradation by PhaZ
RpiT1
. Genetic analysis of the isolated mutants with lowered activity showed that Ser, Tyr, Val, Ala, and Leu residues in the SBD were replaced by other residues at high frequency. Some of the mutant enzymes, which contained the residues replaced at high frequency, were applied to assays of dPHB degradation and adsorption, revealing that those residues are essential for full activity of both dPHB degradation and adsorption. These results suggested that PhaZ
RpiT1
adsorbs on the surface of dPHB not only via hydrogen bonds between hydroxyl groups of Ser in the enzyme and carbonyl groups in the PHB polymer but also via hydrophobic interaction between hydrophobic residues in the enzyme and methyl groups in the PHB polymer. The L441H enzyme, which displayed lower dPHB degradation and adsorption abilities, was purified and applied to a dPHB degradation assay to compare it with the wild-type enzyme. The kinetic analysis of the dPHB degradation suggested that lowering the affinity of the SBD towards dPHB causes a decrease in the dPHB degradation rate without the loss of its hydrolytic activity for the polymer chain.
Engineering of Primary Carbohydrate Metabolism for Increased Production of Actinorhodin in
Streptomyces coelicolor
Authors: Ryu Yong-Gu , Butler Michael J. , Chater Keith F. , Lee Kye Joon
Published: November 2006

The objectives of the current studies were to determine the roles of key enzymes in central carbon metabolism in the context of increased production of antibiotics in
Streptomyces coelicolor
. Genes for glucose-6-phosphate dehydrogenase and phosphoglucomutase (Pgm) were deleted and those for the acetyl coenzyme A carboxylase (ACCase) were overexpressed. Under the conditions tested, glucose-6-phosphate dehydrogenase encoded by
zwf2
plays a more important role than that encoded by
zwf1
in determining the carbon flux to actinorhodin (Act), while the function of Pgm encoded by SCO7443 is not clearly understood. The
pgm
-deleted mutant unexpectedly produced abundant glycogen but was impaired in Act production, the exact reverse of what had been anticipated. Overexpression of the ACCase resulted in more rapid utilization of glucose and sharply increased the efficiency of its conversion to Act. From the current experiments, it is concluded that carbon storage metabolism plays a significant role in precursor supply for Act production and that manipulation of central carbohydrate metabolism can lead to an increased production of Act in
S. coelicolor
.
Identification of Potentially Human-Pathogenic
Enterocytozoon bieneusi
Genotypes in Various Birds
Authors: Lobo Maria Luísa , Xiao Lihua , Cama Vitaliano , Magalhães Nuno , Antunes Francisco , Matos Olga
Published: November 2006

Enterocytozoon bieneusi
was detected in 24 of 83 samples from birds of the orders Columbiformes, Passeriformes, and Psittaciformes. It was identical to or closely related to the Peru6 genotype, which was previously found in humans in Peru. Thus, various birds can be a significant source of environmental contamination by potentially human-pathogenic
E. bieneusi
.
Mechanism of Augmentation of Organotin Decomposition by Ferripyochelin: Formation of Hydroxyl Radical and Organotin-Pyochelin-Iron Ternary Complex
Authors: Sun Guo-Xin , Zhong Jian-Jiang
Published: November 2006

Pyochelin (PCH), a kind of siderophore secreted by
Pseudomonas aeruginosa
, was recently found to have triphenyltin (TPT)-decomposing capacity. In this work, significant augmentation of TPT decomposition by ferripyochelin (FePCH), the chelating compound of PCH with iron, was demonstrated in Tris-HCl buffer (pH 8.0). The generation of hydroxyl radical (HO·) in the presence of FePCH was observed. Inhibition of HO· generation by adding catalase and HO· scavengers (methanol and dimethyl sulfoxide) decreased TPT decomposition, while an increase in HO· formation in the presence of H
2
O
2
enhanced its decomposition. Our findings indicated that HO· generated in the reaction system was responsible for the enhanced TPT decomposition by FePCH versus PCH. The existence of the TPT-pyochelin-iron ternary complex was demonstrated by electron spray ionization-mass spectrometry, tandem mass spectrometry, and
1
H nuclear magnetic resonance. On the basis of the above results, HO· produced in the presence of FePCH was deduced to be in close proximity to TPT and has more opportunity to attack the Sn-C bond, which resulted in the enhanced organotin decomposition. The information obtained may have considerable environmental significance.
Genetic Characterization of the Resorcinol Catabolic Pathway in
Corynebacterium glutamicum
Authors: Huang Yan , Zhao Ke-Xin , Shen Xi-Hui , Chaudhry Muhammad Tausif , Jiang Cheng-Ying , Liu Shuang-Jiang
Published: November 2006

Corynebacterium glutamicum
grew on resorcinol as a sole source of carbon and energy. By genome-wide data mining, two gene clusters, designated NCgl1110-NCgl1113 and NCgl2950-NCgl2953, were proposed to encode putative proteins involved in resorcinol catabolism. Deletion of the NCgl2950-NCgl2953 gene cluster did not result in any observable phenotype changes. Disruption and complementation of each gene at NCgl1110-NCgl1113, NCgl2951, and NCgl2952 indicated that these genes were involved in resorcinol degradation. Expression of NCgl1112, NCgl1113, and NCgl2951 in
Escherichia coli
revealed that NCgl1113 and NCgl2951 both coded for hydroxyquinol 1,2-dioxygenases and NCgl1112 coded for maleylacetate reductases. NCgl1111 encoded a putative monooxygenase, but this putative hydroxylase was very different from previously functionally identified hydroxylases. Cloning and expression of NCgl1111 in
E. coli
revealed that NCgl1111 encoded a resorcinol hydroxylase that needs NADPH as a cofactor.
E. coli
cells containing Ncgl1111 and Ncgl1113 sequentially converted resorcinol into maleylacetate. NCgl1110 and NCgl2950 both encoded putative TetR family repressors, but only NCgl1110 was transcribed and functional. NCgl2953 encoded a putative transporter, but disruption of this gene did not affect resorcinol degradation by
C. glutamicum
. The function of NCgl2953 remains unclear.
Functional Analysis of the Twin-Arginine Translocation Pathway in
Corynebacterium glutamicum
ATCC 13869
Authors: Kikuchi Yoshimi , Date Masayo , Itaya Hiroshi , Matsui Kazuhiko , Wu Long-Fei
Published: November 2006

Compared to those of other gram-positive bacteria, the genetic structure of the
Corynebacterium glutamicum
Tat system is unique in that it contains the
tatE
gene in addition to
tatA
,
tatB
, and
tatC
. The
tatE
homologue has been detected only in the genomes of gram-negative enterobacteria. To assess the function of the
C. glutamicum
Tat pathway, we cloned the
tatA
,
tatB
,
tatC
, and
tatE
genes from
C. glutamicum
ATCC 13869 and constructed mutants carrying deletions of each
tat
gene or of both the
tatA
and
tatE
genes. Using green fluorescent protein (GFP) fused with the twin-arginine signal peptide of the
Escherichia coli
TorA protein, we demonstrated that the minimal functional Tat system required TatA and TatC. TatA and TatE provide overlapping function. Unlike the TatB proteins from gram-negative bacteria,
C. glutamicum
TatB was dispensable for Tat function, although it was required for maximal efficiency of secretion. The signal peptide sequence of the isomaltodextranase (IMD) of
Arthrobacter globiformis
contains a twin-arginine motif. We showed that both IMD and GFP fused with the signal peptide of IMD were secreted via the
C. glutamicum
Tat pathway. These observations indicate that IMD is a bona fide Tat substrate and imply great potential of the
C. glutamicum
Tat system for industrial production of heterologous folded proteins.
Construction of a Reporter Vector for the Analysis of
Bifidobacterium longum
Promoters
Authors: Klijn A. , Moine D. , Delley M. , Mercenier A. , Arigoni F. , Pridmore R. D.
Published: November 2006

In order to initiate studies on promoter activities in
Bifidobacterium longum
and to independently confirm transcriptional data generated by microarray experiments, we have constructed a versatile reporter plasmid based on a
B. longum
cryptic plasmid and the
Escherichia coli gusA
gene. The resulting plasmid, pMDY23, has been tested using three
B. longum
promoters.
Application of Multilocus Variable-Number Tandem-Repeat Analysis for Molecular Typing of the Agent of Leptospirosis
Authors: Salaün Laurence , Mérien Fabrice , Gurianova Svetlana , Baranton Guy , Picardeau Mathieu
Published: November 2006

Leptospirosis is a worldwide-distributed zoonosis, endemic in tropical areas. Epidemiologic investigations of leptospirosis still rely on tedious serological identification tests. Recently, molecular typing systems based on variable-number tandem-repeat (VNTR) analysis have been described and have been used to identify
Leptospira interrogans
strains. Although
L. interrogans
is the most common
Leptospira
species encountered in human infections around the world, other pathogenic species, such as
Leptospira kirschneri
and
Leptospira borgpetersenii
, are also frequently associated with human leptospirosis. In this study, we aimed to extend multilocus VNTR analysis (MLVA) identification of strains to species other than
L. interrogans
. We designed primers for VNTR loci found in
L. interrogans
,
L. kirschneri
, and
L. borgpetersenii
. The discriminatory power of the redefined primers was evaluated on collection strains and then on clinical strains. We also carried out a retrospective study on 156 strains isolated from patients and animals from New Caledonia, an area of high endemicity in the South Pacific. Our results show that this simple PCR-based MLVA typing technique is a powerful methodology for the epidemiology of leptospirosis.
Susceptibilities of
Propionibacterium acnes
Ophthalmic Isolates to Ertapenem, Meropenem, and Cefepime
Authors: Shames Robert , Satti Farhana , Vellozzi Ernestine M. , Smith Miriam A.
Published: November 2006

We investigated the in vitro susceptibilities of 23
Propionibacterium acnes
ophthalmic isolates to ertapenem, meropenem, and cefepime by utilizing the Etest. The MICs ranged from 0.094 μg/ml to 0.75 μg/ml, 0.094 μg/ml to 1.5 μg/ml, and 1 μg/ml to 12 μg/ml for ertapenem, meropenem, and cefepime, respectively. Based on our excellent in vitro carbapenem susceptibility results, in vivo studies using ertapenem and meropenem in a rabbit model of
P. acnes
endophthalmitis are warranted.
Measurement of Serum
d
-Arabinitol/Creatinine Ratios for Initial Diagnosis and for Predicting Outcome in an Unselected, Population-Based Sample of Patients with
Candida
Fungemia
Authors: Yeo Siew Fah , Huie Sharon , Sofair Andre N. , Campbell Sheldon , Durante Amanda , Wong Brian
Published: November 2006

d
-Arabinitol (DA) is a useful diagnostic marker for candidiasis in patients with neutropenia and other high-risk groups, but its use in unselected patients with a broad range of underlying diseases and conditions has not been studied. We used an automated enzymatic fluorometric assay to measure serum DA/creatinine ratios (DA/cr's) in 30 healthy adults, 100 hospitalized controls without
Candida
fungemia, and 83 patients from a study of all
Candida
fungemias in Connecticut between October 1998 and September 1999. Sixty-three of 83 (76%) fungemic patients and 11 of 100 (11%) nonfungemic controls had serum DA/cr's ≥3.9 μM/mg/dl (mean + 3 standard deviations for 30 healthy adults). High serum DA/cr's were less frequent in patients with cancer or fungemia caused by the DA nonproducer
Candida glabrata
than in patients with cancer or fungemia caused by a DA producer,
C. albicans
,
C. tropicalis
, or
C. parapsilosis
. The serum DA/cr was first ≥3.9 μM/mg/dl before, on the same day as, or after the first positive blood culture was drawn for 30 (36%), 22 (27%), and 11 (13%) fungemia patients, respectively. Mortality did not differ significantly among the patients with high or normal initial or peak serum DA/cr's, but mortality was higher if any serum DA/cr value was ≥3.9 μM/mg/dl 3 or more days after the onset of fungemia (18/27 versus 4/24 patients, respectively;
P
< 0.001). We conclude that serum DA/cr's are useful both for the initial diagnosis of
Candida
fungemia and for prognostic purposes for unselected patients with a broad range of underlying diseases and conditions.
Report of Two Cases of Aseptic Meningitis with Persistence of Pneumococcal Cell Wall Components in Cerebrospinal Fluid after Pneumococcal Meningitis
Authors: Angoulvant François , Lachenaud Julie , Mariani-Kurkdjian Patricia , Aubertin Guillaume , Houdouin Véronique , Lorrot Mathie , de Los Angeles Laure , Bingen Edouard , Bourrillon Antoine , Faye Albert
Published: November 2006

We describe two cases of aseptic meningitis occurring some time after pneumococcal meningitis. Both cases may have resulted from an inflammatory response to persistent pneumococcal cell membrane components, as the cerebrospinal fluid samples were positive by the Binax NOW
Streptococcus pneumoniae
antigen test. Potential mechanisms and diagnostic impact are discussed.