bluuebunny/crossref_metadata_2025 huggingface dataset:
Solution structure of the bb′ domains of human protein disulfide isomerase
Authors: Denisov Alexey Y. , Määttänen Pekka , Dabrowski Christian , Kozlov Guennadi , Thomas David Y. , Gehring Kalle
Published: January 2009

Protein disulfide isomerase is the most abundant and best studied of the disulfide isomerases that catalyze disulfide bond formation in the endoplasmic reticulum, yet the specifics of how it binds substrate have been elusive. Protein disulfide isomerase is composed of four thioredoxin‐like domains (abb′a′). Cross‐linking studies with radiolabeled peptides and unfolded proteins have shown that it binds incompletely folded proteins primarily via its third domain, b′. Here, we determined the solution structure of the second and third domains of human protein disulfide isomerase (b and b′, respectively) by triple‐resonance NMR spectroscopy and molecular modeling. NMR titrations identified a large hydrophobic surface within the b′ domain that binds unfolded ribonuclease A and the peptides mastoparan and somatostatin. Protein disulfide isomerase‐catalyzed refolding of reduced ribonuclease A in vitro was inhibited by these peptides at concentrations equal to their affinity to the bb′ fragment. Our findings provide a structural basis for previous kinetic and cross‐linking studies which have shown that protein disulfide isomerase exhibits a saturable, substrate‐binding site.
Erectile Dysfunction in Type 2 Diabetic Men: Relationship to Exercise Fitness and Cardiovascular Risk Factors in the Look AHEAD Trial
Authors: Rosen Raymond C. , Wing Rena R. , Schneider Stephen , Wadden Thomas A. , Foster Gary D. , West Delia Smith , Kitabchi Abbas E. , Brancati Frederick L. , Maschak-Carey Barbara J. , Bahnson Judy L. , Lewis Cora E. , Gendrano Isaias N.
Published: January 2009

Introduction

Determinants of erectile dysfunction in diabetic men have not been adequately investigated as potential mediators of change.

Aim

To determine the prevalence and correlates of erectile dysfunction (ED) in overweight men with type 2 diabetes in the multicenter, Look AHEAD trial (Action for Health in Diabetes).

Main Outcome Measures

International Index of Erectile Function (IIEF), self-reported use of phosphodiesterase type 5 inhibitors, laboratory measures of adiposity, cardiometabolic parameters, and exercise fitness.

Methods

Male participants aged 45–75 in the Look AHEAD trial in a committed relationship were recruited for an ongoing study of sexual function and diabetes. Eligible participants completed the IIEF questionnaire and provided updated information on use of medical treatments for sexual dysfunction. Baseline sexual function results for participants in the male ancillary study are reported here; intervention data and results for female participants are presented elsewhere.

Results

A total of 373 eligible male participants completed all sexual function questionnaires, of whom 263 (68.7%) were sexually active at the time of the study. Almost half (49.8%) of the men reported mild or moderate degrees of ED, and 24.8% had complete ED. Among sexually active participants, 42.6% had sought medical help for their problem, and 39.7% reported use of ED medications. ED was significantly associated with age (odds ratio [OR] = 1.05; confidence interval [CI]: 1.01–1.10) baseline HbA1c (OR = 1.31; CI: 1.05–1.63), hypertension history (OR = 2.41; CI: 1.34–4.36), and metabolic syndrome (OR = 3.05, CI: 1.31–7.11). Of note, cardiorespiratory fitness was found to be protective of ED in a multivariable analysis (OR = 0.61; P < 0.001).

Conclusions

ED is prevalent in this sample of obese, type 2 diabetic men in the Look AHEAD study. Cardiovascular risk factors were highly associated with ED in this population, and cardiorespiratory fitness was protective in this analysis.
Microstructure, Thermophysical, and Ablative Performances of a 3D Needled C/C–SiC Composite
Authors: Nie Jingjiang , Xu Yongdong , Zhang Litong , Fan Shangwu , Xu Fang , Cheng Laifei , Ma Junqiang , Yin Xiaowei
Published: January 2009

The microstructure, thermophysical, and ablative properties of a 3D needled C/C–SiC composite fabricated by chemical vapor infiltration combined with the liquid silicon infiltration process were investigated. The composite was composed of 64 wt% C, 20 wt% SiC, and 16 wt% Si. The thermal diffusivity in the plane direction was much higher than that in the through‐the‐thickness direction, while it was reversed for the coefficients of thermal expansion, and the differences reduced with increasing temperature. The linear and mass ablation rates in the oxyacetylene flame were 0.0039 mm/s and 0.0016 g/s on average, respectively. Various ablation processes including sublimation, thermochemical denudation, and oxidations occurred in different sections.
The Model for Oxidation Kinetics of Titanium Nitride Coatings
Authors: Hou Xinmei , Chou Kuo‐Chih , Zhang Mei
Published: January 2009

The oxidation kinetics of titanium nitride (TiN) film has been studied based on the experimental data summarized in the literature. The analysis shows that the diffusion process is the rate‐controlling step. Based on the experimental data, a new model for predicting the oxidation process is used. In this paper, the effects of factors, such as temperature and heating rate, on the oxidation behavior are discussed not only qualitatively but also quantitatively. The results obtained show that our new model can fit the oxidation data very well. Compared with the previous oxidation studies of TiN coatings, the new model can provide a clear physical meaning of all parameters and therefore it will be useful for a theoretical discussion. The new model can also perform a simple calculation. Most importantly, the new model will lead to a more accurate calculation result; therefore, it can be used to predict the oxidation behavior of TiN materials based on limited experimental information.
Leaching and Solubility Analysis of Porcelain‐Recycled Tile Residues in Clay Bricks
Authors: Da Silva Paula Marcos Marques , De Lorenzi Vicente , Da Silva Luciano , Fiori Márcio Antônio , Bernardin Adriano Michael
Published: January 2009

In this study, a porcelain tile residue was used to produce clay bricks. The residue was characterized (XRF, PSD, dilatometry, solubility, and leaching analyses) and was added to a brick paste, forming compositions that were extruded, dried, and fired at 1000°C. The fired specimens were tested [compressive strength, shrinkage, apparent density, water absorption, phase analysis (XRD), microstructure (SEM), leaching, and solubility]. The results showed that the porcelain residue was a noninert material. When added to the brick paste, the residue shows an improvement of some properties due to its alkaline content acting as a flux in the clay paste and causing the vitrification of the structure.
Faraday Glasses with a Large Size and High Performance
Authors: Li Weinan , Zou Kuaisheng , Lu Min , Peng Bo , Zhao Wei
Published: January 2009

A kind of Faraday glass with a size of Φ40 mm × 14 mm and Φ100–300 mm × 25 mm, respectively, was prepared by the melting and casting process, which had neither a Pt particulate nor a bubble or striation. The measurement results showed that the surface homogeneity of the samples was up to ± 1 × 10−6, the laser threshold reached 10 J/cm2(1ω, 3 ns), and the Verdet constants of the glasses were −0.273 min/Oe/cm at 632.8 nm and −0.076 min/Oe/cm at 1064 nm, respectively.
Particle‐Filled PHPS Silazane‐Based Coatings on Steel
Authors: Günthner Martin , Kraus Tobias , Krenkel Walter , Motz Günter , Dierdorf Andreas , Decker Daniel
Published: January 2009

Precursor‐based composite coatings were developed as barrier coatings on steel against oxidation and corrosion using a silazane in the system SiN as a polymer material and BN particles as a passive filler. After thermal treatment in air up to 800°C, dense and very well adhered ceramic composite SiNO/BN coatings with a thickness of 12 μm were achieved. These were investigated by means of scanning electron microscopy, energy‐dispersive spectrum, glow discharge optical emission spectroscopy, and adhesion measurements. Static oxidation tests on coated mild steel substrates up to 700°C displayed parabolic oxidation kinetics and a reduced weight gain by two orders in magnitude compared with uncoated substrates.
Interaction between a Dark Septate Endophytic Isolate from Dendrobium sp. and Roots of D. nobile Seedlings
Authors: Hou Xiao‐Qiang , Guo Shun‐Xing
Published: January 2009

Interactions between an isolate of dark septate endophytes (DSE) and roots of Dendrobium nobile Lindl. seedlings are reported in this paper. The isolate was obtained from orchid mycorrhizas on Dendrobium sp. in subtropical forest. The fungus formed typical orchid mycorrhiza in aseptic co‐culture with D. nobile seedlings on modified Murashige‐Skoog (MMS) medium. Anatomic observations of the infected roots showed that the DSE hyphae invaded the velamen layer, passed through passage cells in exodermis, entered the cortex cells, and then formed fungal pelotons of orchid mycorrhiza. D. nobile seedlings' plant height, stem diameter, new roots number and biomass were greatly enhanced by inoculating the fungus to seedlings. The fungus was identified as Leptodontidium by sequencing the polymerase chain reaction‐amplified rDNA ITS1‐5.8S‐ITS2 (internal transcribed spacer (ITS)) regions and comparison with similar taxa.
The popularity of foodservice systems in Australian hospitals
Authors: Assaf A.
Published: February 2009

Research in the area of foodservice systems is limited. This paper provides details of the current prevalence, characteristics and popularity of different foodservice systems in Australian hospitals. The results from 90 hospitals show that the traditional cook‐fresh system is still popular in Australian hospitals, with cook‐chill and hybrid systems to a lesser extent. The trend of shifting away from in‐house production and using external suppliers is also growing.
Will the EU ban on bird imports mean the demise of bird populations in EAZA collections?
Authors: WALTER O. , ELLIS J. A. , BINGAMAN LACKEY L.
Published: January 2009

It is felt, among zoo bird curators, that the European Union (EU) Regulation banning bird imports may have a hugely detrimental effect on European Association of Zoos and Aquaria (EAZA) bird populations. This paper discusses the possible effects of the legislation despite a derogation that allows some birds to be brought into the EU for zoos. The ban would only affect EAZA populations if reliant on large‐scale commercial importers either directly or indirectly through affecting private collections or non‐EAZA zoos. Data from the International Species Information System (ISIS) and EAZA Taxon Advisory Group (TAG) surveys were used to determine the sustainability and the main source of recruitment for these populations. The feeling that the ban will cause the demise of EAZA bird populations is not upheld by the data used, with the exception of white‐eyes (Zosteropidae). However, this conclusion must be taken in context of the data available. The reality of commercial importers in underpinning EAZA populations through intermediates is possibly being masked by the way data have been entered by ISIS‐member zoos. A positive outcome of discussions within EAZA Bird TAGs was to identify several other issues that need to be addressed which may be hindering population survival in EAZA collections.
Rule and Meaning in the Teaching of Grammar
Authors: Davis Joseph
Published: February 2009

While the construct of rule as a manipulation of purely formal properties of language has been widely abandoned in both formal and functional linguistics, it persists, though with diminished importance, in the field of second language acquisition. This is true even in form‐focused instruction, including focus‐on‐form, which emphasizes meaning as both classroom focus and element of language structure. This paper illustrates the meaningfulness of grammar, even where treatment has often appealed to such rules; identifies areas of overlap between what is identified by the term rule and what is identified by the terms meaning (semantics) and form (morphology); and points out the lack of descriptive adequacy of some familiar rules. The author offers research‐ and practice‐based recommendations for pursuing a fully meaning‐based communicative approach to teaching grammar even while suitable and comprehensive resource materials for such methods in language education are lacking.
Climatology at Urban Long‐Term Ecological Research Sites: Baltimore Ecosystem Study and Central Arizona–Phoenix
Authors: Brazel Anthony J. , Heisler Gordon M.
Published: January 2009

The Baltimore Ecosystem Study (BES) and Central Arizona–Phoenix (CAP) Long‐Term Ecological Research (LTER) programs, established in 1997, are part of an international National Science Foundation long‐term ecology monitoring and research network. The study sites are excellent laboratories to integrate ideas on climate of urban areas and how climate change and local variability of climate relate to social, political, economic, and ecological processes over a long time period. A large variety of research data are available online from individual LTER Web sites and a combined database called CLIMDB/HYDRODB is available for climate and ecology researchers and others, to investigate climate and hydrology in LTER study regions including those of BES and CAP. The basic program, climate aspects of these two areas, selected past research, and current ongoing work is briefly reviewed. A large benefit of this National Science Foundation program is the maintenance of support over a very long period of time. With the advent of a National Ecological Observatory Network, continuing collection of climate and environmental information over the coming decades at the local and regional scales, and maintenance of protocols of measurement, it is hoped that a more meaningfully integrated urban climatology with urban ecology will emerge. This will better prepare scientists to gage the impending rapid global warming expected not only of natural environments, but also of burgeoning urban places around the world.
Should Economic Geographers Count?
Authors: Essletzbichler Jurgen
Published: January 2009

With the rise of political economy and humanistic approaches in geography in the 1970s, quantitative geography was criticized for its positivist epistemology, its search for generalizations rather than local differentiation, its claim to objective research and the removal of the researcher from the research process, its reactionary political outlook and the inability to excite students. These criticisms have been echoed by ‘cultural turn’ economic geographers. This article argues that many of the criticisms are misdirected and unfounded in the light of recent advances in quantitative methodologies that stress the local, computational and visual and that explicitly incorporate the subjective beliefs of the researcher. Moreover, while serving the interests of proponents and opponents of quantitative economic geography, the artificial separation between quantitative and qualitative economic geography does little for a pluralist discipline founded on critical engagement among economic geographers striving to build an emancipatory, critical and policy‐relevant economic geography.
Factors Associated With Low Levels of Subclinical Vascular Disease in Older Adults: Multi‐Ethnic Study of Atherosclerosis
Authors: Michos Erin D. , Rice Kenneth M. , Szklo Moyses , Burke Gregory L. , Siscovick David S. , Tracy Russell P. , Graham Barr R. , Nettleton Jennifer A. , Greenland Philip , Jacobs Jr David R. , Post Wendy
Published: January 2009

Coronary artery calcium (CAC), carotid intima‐media thickness (CIMT), and reduced ankle brachial indices (ABI) are markers of subclinical vascular disease strongly associated with aging. The authors identified factors associated with low levels of subclinical vascular disease in 1824 participants 70 years and older in the Multi‐Ethnic Study of Atherosclerosis. A total of 452 had low CAC (<25th percentile), 441 had low CIMT (<25th percentile), 1636 had normal ABI (>0.9), and 165 had a combination index indicating favorable values for all 3 parameters. This combination index was independently associated with younger age (odds ratio [OR] 2.5 per 1 SD [95% confidence interval (CI), 1.8–3.6]), female sex (OR 3.0 [95% CI, 1.9–4.8]), lower body mass index (OR 1.6 per 1 SD [95% CI, 1.2–2.0]), absence of hypertension (OR 1.8 [95% CI, 1.2–2.6]), absence of dyslipidemia (OR 1.6 [95% CI, 1.04–2.4]), and never‐smoking (OR 1.7 [95% CI, 1.1–2.6]). No significant associations were observed for C‐reactive protein, education, diet, or physical activity. Favorable levels of multiple traditional risk factors, but not several novel risk factors, were associated with subclinical markers of successful cardiovascular aging.
Molecular evidence for the identity of the Magenta petrel
Authors: LAWRENCE HAYLEY A. , MILLAR CRAIG D. , IMBER MICHAEL J. , CROCKETT DAVID E. , ROBINS JUDITH H. , SCOFIELD R. PAUL. , TAYLOR GRAEME A. , LAMBERT DAVID M.
Published: January 2009

A lone petrel was shot from the decks of an Italian warship (the ‘Magenta’) while it was sailing the South Pacific Ocean in 1867, far from land. The species, unknown to science, was named the ‘Magenta petrel’ (Procellariiformes, Procellariidae, Pterodroma magentae). No other specimens of this bird were collected and the species it represented remained a complete enigma for over 100 years. We compared DNA sequence of the mitochondrial cytochrome b gene from the Magenta petrel to that of other petrels using phylogenetic methods and ancient DNA techniques. Our results strongly suggest that the Magenta petrel specimen is a Chatham Island taiko. Furthermore, given the collection location of the Magenta petrel, our finding indicates that the Chatham Island taiko forages far into the Pacific Ocean (near South America). This has implications for the conservation of the taiko, one of the world's rarest seabirds.
Isolation and characterization of nuclear microsatellite loci from Ceratopetalum apetalum (Cunoniaceae)
Authors: HESLEWOOD MARGARET M. , PORTER CAROLYN , AVINO MARIANO , ROSSETTO MAURIZIO
Published: January 2009

We identified 16 polymorphic nuclear microsatellite loci from an AG‐enriched library of Ceratopetalum apetalum. These loci were tested across two populations of C. apetalum, a single population of C. gummiferum and representatives of four other congeneric taxa. Fourteen loci were identified as polymorphic in at least one other species. These microsatellites will be used to look at population dynamics of species with varying distributions and presumed low dispersal capabilities within the genus Ceratopetalum.
Selecting barcoding loci for plants: evaluation of seven candidate loci with species‐level sampling in three divergent groups of land plants
Authors: HOLLINGSWORTH MICHELLE L. , ANDRA CLARK ALEX , FORREST LAURA L. , RICHARDSON JAMES , PENNINGTON R. TOBY , LONG DAVID G. , COWAN ROBYN , CHASE MARK W. , GAUDEUL MYRIAM , HOLLINGSWORTH PETER M.
Published: January 2009

There has been considerable debate, but little consensus regarding locus choice for DNA barcoding land plants. This is partly attributable to a shortage of comparable data from all proposed candidate loci on a common set of samples. In this study, we evaluated the seven main candidate plastid regions (rpoC1, rpoB, rbcL, matK, trnH‐psbA, atpF‐atpH, psbK‐psbI) in three divergent groups of land plants [Inga (angiosperm); Araucaria (gymnosperm); Asterella s.l. (liverwort)]. Across these groups, no single locus showed high levels of universality and resolvability. Interspecific sharing of sequences from individual loci was common. However, when multiple loci were combined, fewer barcodes were shared among species. Evaluation of the performance of previously published suggestions of particular multilocus barcode combinations showed broadly equivalent performance. Minor improvements on these were obtained by various new three‐locus combinations involving rpoC1, rbcL, matK and trnH‐psbA, but no single combination clearly outperformed all others. In terms of absolute discriminatory power, promising results occurred in liverworts (e.g. c. 90% species discrimination based on rbcL alone). However, Inga (rapid radiation) and Araucaria (slow rates of substitution) represent challenging groups for DNA barcoding, and their corresponding levels of species discrimination reflect this (upper estimate of species discrimination = 69% in Inga and only 32% in Araucaria; mean = 60% averaging all three groups).
Isolation and characterization of microsatellite loci in Merluccius australis and cross‐species amplification
Authors: MACHADO‐SCHIAFFINO G. , GARCIA‐VAZQUEZ E.
Published: January 2009

Eight novel and two heterologous microsatellite pairs of primers are presented for the Austral hake (Merluccius australis), representing the first microsatellite markers available for this species. Loci were characterized for 50 individuals from two populations in South America (Argentinean and Chilean coasts). All loci were polymorphic within M. australis (5 to 30 alleles per locus; observed heterozygosity between 0.320 and 0.840), and therefore useful for population genetic studies within the species. Cross‐species transferability was tested for 100 individuals from four additional species within the Merluccius genus (M. albidus, M. bilinearis, M. gayi and M. hubbsi), and results indicate that most of these primers pairs will likely be useful for population genetic studies on Merluccius species.
Development of simple sequence repeat markers for Japanese isolates of Magnaporthe grisea
Authors: SUZUKI F. , SUGA H. , TOMIMURA K. , FUJI S. , ARAI M. , KOBA A. , NAKAJIMA T.
Published: January 2009

We developed nine simple sequence repeat (SSR) markers useful for differentiating Japanese isolates of Magnaporthe grisea through a bioinformatic approach. Repeat sequences in the genome of M. grisea were identified by a Tandem Repeat Finding program. Length polymorphisms at 28 loci were examined, nine of which were selected on the basis of detected polymorphisms. These nine SSR markers showed a Nei's gene diversity ranging from 0.23 to 0.91 among 48 field isolates of two natural populations. These SSR markers are well suited for M. grisea epidemiology and population genetics.
Isolation and characterization of microsatellite markers from the great hornbill, Buceros bicornis
Authors: CHAMUTPONG SIRIPHATR , SAITO DAICHI S. , VISESHAKUL NAREERAT , NISHIUMI ISAO , POONSWAD PILAI , PONGLIKITMONGKOL MATHUROSE
Published: January 2009

Thirteen polymorphic microsatellite markers were isolated and characterized from the great hornbill, Buceros bicornis. In analyses of 20 individuals, the numbers of alleles per locus varied from two to 11. The expected and observed heterozygosities ranged from 0.22 to 0.88 and from 0.20 to 1.00, respectively. The mean polymorphic information content was 0.62. Among these, three loci deviated from the Hardy–Weinberg equilibrium. However, no significant genotypic disequilibrium was detected between any pair of loci. These microsatellite markers are useful for the population genetic study of the great hornbill.
Isolation and characterization of microsatellite markers in tree lizards (Urosaurus ornatus)
Authors: HAENEL GREGORY J.
Published: January 2009

Tree lizards (Urosaurus ornatus) are a highly accessible species useful in testing theories of life‐history evolution and behavioural ecology. A polymerase chain reaction‐based method was used to isolate nine polymorphic tetranucleotide microsatellite loci from the genome of these lizards. The isolated loci displayed 5 to 9 alleles in the populations screened. Observed heterozygosity ranged from 0.333 to 0.900. Results indicate these loci now provide a basis to study mate choice, parentage, and population genetic structure within this species.
Novel microsatellite loci in the grass snake (Natrix natrix) and cross‐amplification in the dice snake (Natrix tessellata)
Authors: MEISTER B. , ARMBRUSTER G. F. J. , FRAUENFELDER N. , BAUR B.
Published: January 2009

Six novel polymorphic microsatellite loci are presented for the grass snake (Natrix natrix), a species with declining populations in many regions. The number of alleles per locus ranged from two to seven. Four dice snake (Natrix tessellata) microsatellites were polymorphic in the grass snake with three to four alleles. At two loci, the expected heterozygosity differed significantly from observed heterozygosity. Cross‐amplification of the grass snake markers in the dice snake showed two polymorphic microsatellites with two and four alleles.
Microsatellite markers for the endemic New Zealand long‐tailed bat (Chalinolobus tuberculatus)
Authors: DEKROUT ANDREA , CURSONS RAYMOND T. , WILKINS RICHARD J.
Published: January 2009

The New Zealand long‐tailed bat (Chalinolobus tuberculatus) is an endangered species which is now absent from many habitats where they were previously observed. However, population genetics studies have been hampered by the lack of reliable genetic markers. We have developed 13 microsatellite markers, and at least eight of these are suitable for population studies. Nine of these markers also cross‐react with the closely related Australian species C. gouldii. These markers may prove of general utility in the genus Chalinolobus.
Microsatellite loci for Ponto‐Caspian gobies: markers for assessing exotic invasions
Authors: FELDHEIM KEVIN A. , WILLINK PHILLIP , BROWN JOSHUA E. , MURPHY DOUGLAS J. , NEILSON MATTHEW E. , STEPIEN CAROL A.
Published: January 2009

We developed and tested eight polymorphic microsatellite loci for Ponto‐Caspian ‘neogobiin’ gobies, many of which are invasive in Eurasia and North America, whose study will aid understanding of the population genetics underlying their success. We tested samples from one to two locations from 12 taxa in the recently revised genera Babka, Benthophilus, Mesogobius, Neogobius = Apollonia, Ponticola and Proterorhinus; including the bighead, Caspian, knout, monkey, racer, round, tadpole and tubenose gobies; and taxa from introduced vs. native populations, those diverging between fresh and marine waters, and those differentiated between the Black and Caspian Seas. Populations conformed to Hardy–Weinberg equilibrium expectations, averaging five to 15 alleles per locus and 0.11 to 0.67 mean heterozygosity. Allelic variation significantly differentiated among all taxa and populations.
Effect of bromfenac ophthalmic solution on ocular inflammation following cataract surgery
Authors: Miyanaga Masaru , Miyai Takashi , Nejima Ryohei , Maruyama Yoko , Miyata Kazunori , Kato Satoshi
Published: January 2009

Purpose:  This study compared the post‐cataract surgery anti‐inflammatory effects of topical treatment with 0.1% bromfenac, 0.1% betamethasone or both on postoperative anterior chamber inflammation and corneal swelling.

Methods:  Seventy‐two patients with no eye disease other than cataract were enrolled in a prospective, randomized study to undergo phacoemulsification combined with intraocular lens implantation. After cataract surgery, patients were randomized to treatment with bromfenac, betamethasone or both agents. Twenty‐five eyes were assigned to bromfenac, 23 to betamethasone and 24 to the combined treatment group. Inflammatory reactions in the anterior chamber were measured with laser flare photometry preoperatively and at 1 and 3 days, 1 and 2 weeks, and 1 and 2 months postoperatively. Intraocular pressure (IOP) and corneal thickness were measured at the same time‐points. Best corrected visual acuity (BCVA) was measured preoperatively and at 2 days, 1 and 2 weeks, and 1 and 2 months postoperatively. Specular microscope endothelial photography of the central region of the cornea was performed preoperatively and at 3 months after surgery.

Results:  There were no significant differences among the bromfenac, betamethasone and combined treatment groups in BCVA, IOP, aqueous flare or corneal thickness. Cystoid macular oedema was present in one eye treated with betamethasone.

Conclusions:  There were no significant differences in anti‐inflammatory effects among the three treatments. These findings suggest that bromfenac is as effective as betamethasone in minimizing inflammatory reactions after cataract surgery.
Autosomal dominant pericentral retinal dystrophy caused by a novel missense mutation in the TOPORS gene
Authors: Selmer Kaja Kristine , Grøndahl Jan , Riise Ruth , Brandal Kristin , Braaten Øivind , Bragadottir Ragnheidur , Undlien Dag Erik
Published: January 2009

Purpose:  This study aimed to identify the genetic cause of autosomal dominant pericentral retinal dystrophy (adPRD) in a large Norwegian family with 35 affected members.

Methods:  The family was characterized by clinical ophthalmological examination along with fundus photography, dark adaptometry and electroretinography. We performed a genome‐wide linkage analysis followed by sequencing of a candidate gene to identify the mutation causing the disease.

Results:  The ophthalmological examinations revealed an atypical form of retinitis pigmentosa (RP), which we prefer to call adPRD. Compared with classical RP, this phenotype has a favourable prognosis. Linkage analysis showed a linkage peak covering the most recently reported adRP gene TOPORS. This gene was sequenced in 19 family members and a novel missense mutation, c.1205a>c, resulting in an amino acid substitution p.Q402P, was detected in all affected members. The mutation showed complete co‐segregation with the disease in this family, with a LOD score of 7.3. It is located in a highly conserved region and alignment with the appropriate DNA sequence from other species shows complete conservation of this amino acid. The mutation was not detected in 207 healthy, unrelated controls of Norwegian origin.

Conclusions:  We present a novel mutation in the TOPORS gene co‐segregating with a distinct phenotype of adPRD in a large Norwegian family.
A local shift‐variant Fourier model and experimental validation of circular cone‐beam computed tomography artifacts
Authors: Bartolac Steven , Clackdoyle Rolf , Noo Frederic , Siewerdsen Jeff , Moseley Douglas , Jaffray David
Published: February 2009

Large field of view cone‐beam computed tomography (CBCT) is being achieved using circular source and detector trajectories. These circular trajectories are known to collect insufficient data for accurate image reconstruction. Although various descriptions of the missing information exist, the manifestation of this lack of data in reconstructed images is generally nonintuitive. One model predicts that the missing information corresponds to a shift‐variant cone of missing frequency components. This description implies that artifacts depend on the imaging geometry, as well as the frequency content of the imaged object. In particular, objects with a large proportion of energy distributed over frequency bands that coincide with the missing cone will be most compromised. These predictions were experimentally verified by imaging small, localized objects (acrylic spheres, stacked disks) at varying positions in the object space and observing the frequency spectrums of the reconstructions. Measurements of the internal angle of the missing cone agreed well with theory, indicating a right circular cone for points on the rotation axis, and an oblique, circular cone elsewhere. In the former case, the largest internal angle with respect to the vertical axis corresponds to the (half) cone angle of the CBCT system (typically in IGRT). Object recovery was also found to be strongly dependent on the distribution of the object's frequency spectrum relative to the missing cone, as expected. The observed artifacts were also reproducible via removal of local frequency components, further supporting the theoretical model. Larger objects with differing internal structures (cellular polyurethane, solid acrylic) were also imaged and interpreted with respect to the previous results. Finally, small animal data obtained using a clinical CBCT scanner were observed for evidence of the missing cone. This study provides insight into the influence of incomplete data collection on the appearance of objects imaged in large field of view CBCT.
Dynamics of Polyphosphate-Accumulating Bacteria in Wastewater Treatment Plant Microbial Communities Detected via DAPI (4′,6′-Diamidino-2-Phenylindole) and Tetracycline Labeling
Authors: Günther S. , Trutnau M. , Kleinsteuber S. , Hause G. , Bley T. , Röske I. , Harms H. , Müller S.
Published: January 2009

Wastewater treatment plants with enhanced biological phosphorus removal represent a state-of-the-art technology. Nevertheless, the process of phosphate removal is prone to occasional failure. One reason is the lack of knowledge about the structure and function of the bacterial communities involved. Most of the bacteria are still not cultivable, and their functions during the wastewater treatment process are therefore unknown or subject of speculation. Here, flow cytometry was used to identify bacteria capable of polyphosphate accumulation within highly diverse communities. A novel fluorescent staining technique for the quantitative detection of polyphosphate granules on the cellular level was developed. It uses the bright green fluorescence of the antibiotic tetracycline when it complexes the divalent cations acting as a countercharge in polyphosphate granules. The dynamics of cellular DNA contents and cell sizes as growth indicators were determined in parallel to detect the most active polyphosphate-accumulating individuals/subcommunities and to determine their phylogenetic affiliation upon cell sorting. Phylotypes known as polyphosphate-accumulating organisms, such as a “
Candidatus
Accumulibacter”-like phylotype, were found, as well as members of the genera
Pseudomonas
and
Tetrasphaera
. The new method allows fast and convenient monitoring of the growth and polyphosphate accumulation dynamics of not-yet-cultivated bacteria in wastewater bacterial communities.
Improved Fermentation Performance of a Lager Yeast after Repair of Its
AGT1
Maltose and Maltotriose Transporter Genes
Authors: Vidgren Virve , Huuskonen Anne , Virtanen Hannele , Ruohonen Laura , Londesborough John
Published: January 2009

The use of more concentrated, so-called high-gravity and very-high-gravity (VHG) brewer's worts for the manufacture of beer has economic and environmental advantages. However, many current strains of brewer's yeasts ferment VHG worts slowly and incompletely, leaving undesirably large amounts of maltose and especially maltotriose in the final beers. α-Glucosides are transported into
Saccharomyces
yeasts by several transporters, including Agt1, which is a good carrier of both maltose and maltotriose. The
AGT1
genes of brewer's ale yeast strains encode functional transporters, but the
AGT1
genes of the lager strains studied contain a premature stop codon and do not encode functional transporters. In the present work, one or more copies of the
AGT1
gene of a lager strain were repaired with DNA sequence from an ale strain and put under the control of a constitutive promoter. Compared to the untransformed strain, the transformants with repaired
AGT1
had higher maltose transport activity, especially after growth on glucose (which represses endogenous α-glucoside transporter genes) and higher ratios of maltotriose transport activity to maltose transport activity. They fermented VHG (24° Plato) wort faster and more completely, producing beers containing more ethanol and less residual maltose and maltotriose. The growth and sedimentation behaviors of the transformants were similar to those of the untransformed strain, as were the profiles of yeast-derived volatile aroma compounds in the beers.
Stress- and Growth Rate-Related Differences between Plate Count and Real-Time PCR Data during Growth of
Listeria monocytogenes
Authors: Reichert-Schwillinsky Franziska , Pin Carmen , Dzieciol Monika , Wagner Martin , Hein Ingeborg
Published: January 2009

To assess the overestimation of bacterial cell counts in real-time PCR in relation to stress and growth phase, four different strains of
L. monocytogenes
were exposed to combinations of osmotic stress (0.5 to 8% [vol/vol] NaCl) and acid stress (pH 5 to 7) in a culture model at a growth temperature of 10°C or were grown under optimal conditions. Growth curves obtained from real-time PCR, optical density, and viable count data were compared. As expected, optical density data revealed entirely different growth curves. Good to moderate growth conditions yielded good correlation of real-time PCR data and plate count data (
r
2
= 0.96 and 0.99) with similar cell counts. When growth conditions became worse, the numbers of CFU decreased during the stationary phase, whereas real-time-PCR-derived bacterial cell equivalents differed in this regard; the correlation worsened (
r
2
= 0.84). However, fitted growth curves revealed that maximum growth rates calculated from real-time PCR data were not significantly different from those derived from plate count data. The overestimation of bacterial cell counts by real-time PCR observed in the stationary phase under higher-stress conditions might be explained by the accumulation of viable but nonculturable bacteria or dead bacteria and extracellular DNA. Considering these results, real-time PCR data collected from naturally contaminated samples should be viewed with caution.
Construction of Disarmed Ti Plasmids Transferable between
Escherichia coli
and
Agrobacterium
Species
Authors: Kiyokawa Kazuya , Yamamoto Shinji , Sakuma Kei , Tanaka Katsuyuki , Moriguchi Kazuki , Suzuki Katsunori
Published: January 2009

Agrobacterium
-mediated plant transformation has been used widely, but there are plants that are recalcitrant to this type of transformation. This transformation method uses bacterial strains harboring a modified tumor-inducing (Ti) plasmid that lacks the transfer DNA (T-DNA) region (disarmed Ti plasmid). It is desirable to develop strains that can broaden the host range. A large number of
Agrobacterium
strains have not been tested yet to determine whether they can be used in transformation. In order to improve the disarming method and to obtain strains disarmed and ready for the plant transformation test, we developed a simple scheme to make certain Ti plasmids disarmed and simultaneously maintainable in
Escherichia coli
and mobilizable between
E. coli
and
Agrobacterium
. To establish the scheme in nopaline-type Ti plasmids, a neighboring segment to the left of the left border sequence, a neighboring segment to the right of the right border sequence of pTi-SAKURA, a cassette harboring the pSC101 replication gene between these two segments, the broad-host-range IncP-type
oriT
, and the gentamicin resistance gene were inserted into a suicide-type
sacB
-containing vector. Replacement of T-DNA with the cassette in pTiC58 and pTi-SAKURA occurred at a high frequency and with high accuracy when the tool plasmid was used. We confirmed that there was stable maintenance of the modified Ti plasmids in
E. coli
strain S17-1λpir and conjugal transfer from
E. coli
to Ti-less
Agrobacterium
strains and that the reconstituted
Agrobacterium
strains were competent to transfer DNA into plant cells. As the modified plasmid delivery system was simple and efficient, conversion of strains to the disarmed type was easy and should be applicable in studies to screen for useful strains.
Evolutionary History of the
phl
Gene Cluster in the Plant-Associated Bacterium
Pseudomonas fluorescens
Authors: Moynihan Jennifer A. , Morrissey John P. , Coppoolse Eric R. , Stiekema Willem J. , O'Gara Fergal , Boyd E. Fidelma
Published: January 2009

Pseudomonas fluorescens
is of agricultural and economic importance as a biological control agent largely because of its plant association and production of secondary metabolites, in particular 2,4-diacetylphloroglucinol (2,4-DAPG). This polyketide, which is encoded by the eight-gene
phl
cluster, has antimicrobial effects on phytopathogens, promotes amino acid exudation from plant roots, and induces systemic resistance in plants. Despite its importance, 2,4-DAPG production is limited to a subset of
P. fluorescens
strains. Determination of the evolution of the
phl
cluster and understanding the selective pressures promoting its retention or loss in lineages of
P. fluorescens
will help in the development of
P. fluorescens
as a viable and effective inoculant for application in agriculture. In this study, genomic and sequence-based approaches were integrated to reconstruct the phylogeny of
P. fluorescens
and the
phl
cluster. It was determined that 2,4-DAPG production is an ancestral trait in the species
P. fluorescens
but that most lineages have lost this capacity through evolution. Furthermore, intragenomic recombination has relocated the
phl
cluster within the
P. fluorescens
genome at least three times, but the integrity of the cluster has always been maintained. The possible evolutionary and functional implications for retention of the
phl
cluster and 2,4-DAPG production in some lineages of
P. fluorescens
are discussed.
Codon-Optimized Fluorescent Proteins Designed for Expression in Low-GC Gram-Positive Bacteria
Authors: Sastalla Inka , Chim Kannie , Cheung Gordon Y. C. , Pomerantsev Andrei P. , Leppla Stephen H.
Published: January 2009

Fluorescent proteins have wide applications in biology. However, not all of these proteins are properly expressed in bacteria, especially if the codon usage and genomic GC content of the host organism are not ideal for high expression. In this study, we analyzed the DNA sequences of multiple fluorescent protein genes with respect to codons and GC content and compared them to a low-GC gram-positive bacterium,
Bacillus anthracis
. We found high discrepancies for cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), and the photoactivatable green fluorescent protein (PAGFP), but not GFP, with regard to GC content and codon usage. Concomitantly, when the proteins were expressed in
B. anthracis
, CFP- and YFP-derived fluorescence was undetectable microscopically, a phenomenon caused not by lack of gene transcription or degradation of the proteins but by lack of protein expression. To improve expression in bacteria with low genomic GC contents, we synthesized a codon-optimized
gfp
and constructed optimized photoactivatable
pagfp
,
cfp
, and
yfp
, which were in contrast to nonoptimized genes highly expressed in
B. anthracis
and in another low-GC gram-positive bacterium,
Staphylococcus aureus.
Using optimized GFP as a reporter, we were able to monitor the activity of the protective antigen promoter of
B. anthracis
and confirm its dependence on bicarbonate and regulators present on virulence plasmid pXO1.
Inc A/C Plasmids Are Prevalent in Multidrug-Resistant
Salmonella enterica
Isolates
Authors: Lindsey Rebecca L. , Fedorka-Cray Paula J. , Frye Jonathan G. , Meinersmann Richard J.
Published: January 2009

Bacterial plasmids are fragments of extrachromosomal double-stranded DNA that can contain a variety of genes that are beneficial to the host organism, like those responsible for antimicrobial resistance. The objective of this study was to characterize a collection of 437
Salmonella enterica
isolates from different animal sources for their antimicrobial resistance phenotypes and plasmid replicon types and, in some cases, by pulsed-field gel electrophoresis (PFGE) in an effort to learn more about the distribution of multidrug resistance in relation to replicon types. A PCR-based replicon typing assay consisting of three multiplex PCRs was used to detect 18 of the 26 known plasmid types in the
Enterobacteriaceae
based on their incompatibility (Inc) replicon types. Linkage analysis was completed with antibiograms, replicon types, serovars, and Inc A/C. Inc A/C plasmids were prevalent in multidrug-resistant isolates with the notable exception of
Salmonella enterica
serovar Typhimurium. Cluster analysis based on PFGE of a subset of 216 isolates showed 155 unique types, suggesting a variable population, but distinct clusters of isolates with Inc A/C plasmids were apparent. Significant linkage of serovar was also seen with Inc replicon types B/O, I1, Frep, and HI1. The present study showed that the combination of
Salmonella
, the Inc A/C plasmids, and multiple-drug-resistant genes is very old. Our results suggest that some strains, notably serovar Typhimurium and closely related types, may have once carried the plasmid but that the resistance genes were transferred to the chromosome with the subsequent loss of the plasmid.
Insights into Structure-Activity Relationships in the C-Terminal Region of Divercin V41, a Class IIa Bacteriocin with High-Level Antilisterial Activity
Authors: Rihakova Jitka , Petit Vanessa W. , Demnerova Katerina , Prévost Hervé , Rebuffat Sylvie , Drider Djamel
Published: January 2009

Divercin V41 (DvnV41) is a class IIa bacteriocin with potent antilisterial activity isolated from
Carnobacterium divergens
V41. Previously, we expressed from a synthetic gene, in
Escherichia coli
Origami, a recombinant DvnV41 designated DvnRV41, which possesses four additional amino acids (AMDP) in the N-terminal region that result from enzymatic cleavage and retains the initial DvnV41 activity. To unravel the relationship between the structure of DvnRV41 and its particularly elevated activity, we produced by site-directed mutagenesis eight variants in which a single amino acid replacement was specifically introduced into the sequence. The point mutations were designed to change either conserved residues in class IIa bacteriocins or residues specific to DvnV41 located mainly in the C-terminal region. The fusion proteins were purified from the cytosoluble fractions by immobilized affinity chromatography. DvnRV41 and its variants were released from the fusion proteins by enzymatic cleavage, using enterokinase. The purity of DvnRV41 and of the variants was checked by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, high-performance liquid chromatography, and mass spectrometry. The antibacterial activity of DvnRV41 and its variants was assessed using different indicator strains, including
Listeria monocytogenes
EGDe and
Enterococcus faecalis
JH2-2. The activity of all of the variants appeared to be less than the activity of DvnRV41. The decrease in activity did not appear to be related to a global conformational change, as determined by circular dichroism. Overall, the variants of DvnRV41 produced in the present study provide interesting insights into structure-activity relationships of class IIa bacteriocins.
Complete Genome of the Broad-Host-Range
Erwinia amylovora
Phage ΦEa21-4 and Its Relationship to
Salmonella
Phage Felix O1
Authors: Lehman Susan M. , Kropinski Andrew M. , Castle Alan J. , Svircev Antonet M.
Published: January 2009

The first complete genome sequence for a myoviridal bacteriophage, ΦEa21-4, infecting
Erwinia amylovora, Erwinia pyrifoliae
, and
Pantoea agglomerans
strains has been determined. The unique sequence of this terminally redundant, circularly permuted genome is 84,576 bp. The ΦEa21-4 genome has a GC content of 43.8% and contains 117 putative protein-coding genes and 26 tRNA genes. ΦEa21-4 is the first phage in which a precisely conserved rho-independent terminator has been found dispersed throughout the genome, with 24 copies in all. Also notable in the ΦEa21-4 genome are the presence of tRNAs with six- and nine-base anticodon loops, the absence of a small packaging terminase subunit, and the presence of
nadV
, a principle component of the NAD
+
salvage pathway, which has been found in only a few phage genomes to date. ΦEa21-4 is the first reported Felix O1-like phage genome; 56% of the predicted ΦEa21-4 proteins share homology with those of the
Salmonella
phage. Apart from this similarity to Felix O1, the ΦEa21-4 genome appears to be substantially different, both globally and locally, from previously reported sequences. A total of 43 of the 117 genes are unique to ΦEa21-4, and 32 of the Felix O1-like genes do not appear in any phage genome sequences other than ΦEa21-4 and Felix O1. N-terminal sequencing and matrix-assisted laser desorption ionization-time of flight analysis resulted in the identification of five ΦEa21-4 genes coding for virion structural proteins, including the major capsid protein.