bluuebunny/crossref_metadata_2025 huggingface dataset:
A new multiplex PCR-based reverse line-blot hybridization (mPCR/RLB) assay for rapid staphylococcal cassette chromosome mec (SCCmec) typing
Authors: Cai Lin , Kong Fanrong , Wang Qinning , Wang Huiping , Xiao Meng , Sintchenko Vitali , Gilbert Gwendolyn L.
Published: July 2009

The aim of this study was to develop a new discriminatory method for MRSA SCCmec typing based on multiplex PCR-based reverse line-blot hybridization (mPCR/RLB) assay to enable rapid identification and classification of MRSA SCCmec types in a clinical laboratory. Forty-five primer sets and 49 probes were designed and tested in uniplex PCR (uPCR) and mPCR/RLB. Probes were compared in silico to 14 whole-genome sequences and 18 partial SCCmec gene sequences of Staphylococcus aureus and complete genome and partial SCCmec genes of seven non-MRSA strains, including meticillin-susceptible S. aureus and meticillin-resistant coagulase-negative staphylococci. The method was tested on a set of 42 well-characterized reference MRSA strains. It identified all five epidemiologically relevant SCCmec types and 26 subtypes, including established and new subtypes of SCCmec III, IV (eight subtypes each) and V (three subtypes). The discriminatory power of mPCR/RLB SCCmec typing was similar to that of MLST and spa typing (Simpson indices of diversity of 0.916, 0.926 and 0.882, respectively; differences not statistically significant). The application of mPCR/RLB hybridization assay to MRSA SCCmec typing can improve the specificity, discriminatory power and throughput of the typing procedure. The detection of up to 43 mPCR products in a single hybridization assay transforms MRSA SCCmec typing from passive epidemiological library typing into a potential tool for near-real-time infection control surveillance and tracking of MRSA transmission in hospitals.
Antifungal activity of thymol against clinical isolates of fluconazole-sensitive and -resistant Candida albicans
Authors: Guo Na , Liu Jingbo , Wu Xiuping , Bi Xingming , Meng Rizeng , Wang Xuelin , Xiang Hua , Deng Xuming , Yu Lu
Published: July 2009

Thymol (THY) was found to havein vitroantifungal activity against 24 fluconazole (FLC)-resistant and 12 FLC-susceptible clinical isolates ofCandida albicans, standard strain ATCC 10231 and one experimentally induced FLC-resistantC. albicansS-1. In addition, synergism was observed for clinical isolates ofC. albicanswith combinations of THY–FLC and THY–amphotericin B (AMB) evaluated by the chequerboard microdilution method. The interaction intensity was determined by spectrophotometry for the chequerboard assay, and the nature of the interactions was assessed using two non-parametric approaches [fractional inhibitory concentration index (FICI) and ΔE models]. The interaction between THY–FLC or THY–AMB in FLC-resistant and -susceptible strains ofC. albicansshowed a high percentage of synergism by the FICI method and the ΔEmethod. The ΔE model gave results consistent with FICI, and no antagonistic action was observed in the strains tested.
Colonization of the tip of a thoracic catheter by Enterococcus faecalis resistant to vancomycin and linezolid
Authors: Cian Franca , Luzzati Roberto , Deiana Maria Luisa , Ferrantelli Nicoletta , Tonin Enrico , Lagatolla Cristina , Dolzani Lucilla
Published: July 2009

We report the isolation ofEnterococcus faecalisresistant to vancomycin and linezolid from the tip of a thoracic drainage catheter in an elderly patient. He was treated with vancomycin for a pleural empyema due to a meticillin-resistantStaphylococcus aureusbut never received linezolid. A surveillance rectal swab yielded both linezolid-susceptible and -resistant strains, and the two isolates were not genotypically related. Careful monitoring for linezolid-resistance is critical to avoid potential therapy failure and transmission of resistantE. faecalis.
Triclosan resistance in clinical isolates of Acinetobacter baumannii
Authors: Chen Yagang , Pi Borui , Zhou Hua , Yu Yunsong , Li Lanjuan
Published: July 2009

The susceptibility to triclosan of 732 clinical Acinetobacter baumannii isolates obtained from 25 hospitals in 16 cities in China from December 2004 to December 2005 was screened by using an agar dilution method. Triclosan MICs ranged between 0.015 and 16 mg l−1, and the MIC90 was 0.5 mg l−1, lower than the actual in-use concentration of triclosan. Twenty triclosan-resistant isolates (MICs ≥1 mg l−1) were characterized by antibiotic susceptibility, clonal relatedness, fabI mutation, fabI expression, and efflux pump phenotype and expression to elucidate the resistance mechanism of A. baumannii to triclosan. The resistance rates of triclosan-resistant isolates to imipenem, levofloxacin, amikacin and tetracycline were higher than those of triclosan-sensitive isolates. Triclosan resistance was artificially classified as low level (MICs 1–2 mg l−1) or high level (MICs ≥4 mg l−1). High-level triclosan resistance could be explained by a Gly95Ser mutation of FabI, whilst wild-type fabI was observed to be overexpressed in low-level resistant isolates. Active efflux did not appear to be a major reason for acquired triclosan resistance, but acquisition of resistance appeared to be dependent on a background of intrinsic triclosan efflux.
Lactobacillus salivarius modulates cytokine induction and virulence factor gene expression in Helicobacter pylori
Authors: Ryan Kieran A. , O'Hara Ann M. , van Pijkeren Jan-Peter , Douillard François P. , O'Toole Paul W.
Published: July 2009

Human infection by the gastric pathogenHelicobacter pyloriis characterized by a robust immune response which rarely prevents persistentH. pyloricolonization. Emerging evidence suggests that lactobacilli may reduceH. pyloriinfection rates and associated inflammation. In this study, we measured the ability of two model strains ofLactobacillus salivarius(UCC118 and UCC119) to modulate gastric epithelial cell chemokine responses toH. pyloriinfection. Pre-treatment of AGS cells with eitherL. salivariusstrain significantly decreased interleukin-8 (IL-8) production upon exposure toH. pylori, but not in cells stimulated with TNF-α. The production of the chemokines CCL20 and IP-10 by AGS cells infected withH. pyloriwas also altered following pre-treatment with UCC118 and UCC119. We showed that a greater reduction in IL-8 production with UCC119 was due to the production of more acid by this strain. Furthermore, UV-killed cells of both lactobacillus strains were still able to reduceH. pylori-induced IL-8 in the absence of acid production, indicating the action of a second anti-inflammatory mechanism. This immunomodulatory activity was not dependent on adhesion to epithelial cells or bacteriocin production. Real-time RT-PCR analysis showed that expression of eight of twelve Cag pathogenicity island genes tested was downregulated by exposure toL. salivarius, but not by cells of four other lactobacillus species. CagA accumulated inH. pyloricells following exposure toL. salivariuspresumably as a result of loss of functionality of the Cag secretion system. These data identified a new mechanism whereby some probiotic bacteria have a positive effect onH. pylori-associated inflammation without clearing the infection.
Distribution of Escherichia coli F4 adhesion phenotypes in pigs of 15 Chinese and Western breeds and a White Duroc×Erhualian intercross
Authors: Yan Xueming , Huang Xiang , Ren Jun , Zou Zhengzhi , Yang Shujin , Ouyang Jing , Zeng Weihong , Yang Bin , Xiao Shijun , Huang Lusheng
Published: July 2009

Diarrhoea in newborn and weaned piglets is mainly caused by enterotoxigenicEscherichia coli(ETEC) with fimbriae F4. To investigate the prevalence of resistance to three fimbrial strains, F4ab, F4ac and F4ad, among Chinese indigenous pigs and Western commercial pigs introduced into China, we determined the ETEC F4 adhesion phenotypes in 292 pure-bred piglets from three Western commercial breeds and 12 Chinese indigenous breeds, and a total of 1093 adult pigs in a White Duroc×Erhualian intercross, by anin vitromicroscopic adhesion assay. All the Tibet and Lantang pigs and a majority of the Erhualian and Rongchang pigs were resistant (nonadherent) to ETEC F4 whereas all the Laiwu pigs and most of the Jiangquhai and Tongcheng pigs were susceptible (adhesive) to at least one of the F4 strains. Yushan Black pigs were uniformly resistant to F4ab, and Jinhua pigs were predominantly resistant to F4ac. Susceptible and resistant animals were observed in the other breeds, indicating that diarrhoea caused by ETEC F4 could be prevalent in these breeds. This study confirmed the existence of eight previously reported F4 adhesion patterns, and supported the assumption that the three F4 receptors are encoded by distinct loci. Expression of the weakly adherent phenotype was observed in six pure-bred piglets and 90 adult F2/F3animals, and the inheritance of this phenotype and its correlation with susceptibility to disease are still not known.
Role of PCR in the diagnosis of pertussis infection in infants: 5 years' experience of provision of a same-day real-time PCR service in England and Wales from 2002 to 2007
Authors: Fry Norman K. , Duncan John , Wagner Karen , Tzivra Oceanis , Doshi Nita , Litt David J. , Crowcroft Natasha , Miller Elizabeth , George Robert C. , Harrison Timothy G.
Published: July 2009

As part of an enhanced surveillance programme for pertussis in England and Wales, a real-time PCR service for the detection ofBordetella pertussiswas introduced for infants aged ≤6 months admitted to a paediatric intensive care unit or paediatric ward with a respiratory illness compatible with pertussis. Two real-time fluorescent resonance energy transfer hybridization probe LightCycler (Roche Diagnostics) PCR assays were used. One (designed in-house) targeted the pertussis toxin S1 promoter (ptxA-pr), and included an internal process control to test for sample inhibition and reagent performance. The other (already published) targeted the insertion element IS481. The analytical sensitivities of the assays were 100 and 10 fg per reaction for theptxA-pr and IS481PCRs, respectively. TheptxA-pr assay was specific forB. pertussis, whilst the IS481PCR also showed some cross-reactivity withBordetella holmesiiand the type strain ofBordetella parapertussis. From April 2002 to March 2007, 848 samples were received from 774 patients and DNA was extracted. Of 824 samples that were suitable for testing, 183 (22.2 %) had evidence ofBordetellainfection (18.9 %ptxA-pr and IS481; 3.3 % IS481only), 621 (75.4 %) were negative and 20 (2.4 %) were inhibitory for the PCR. Within the targeted age group of ≤6 months, most patients (130/138) with evidence ofBordetellaspp. by PCR were ≤3 months old. The overall percentage increase in laboratory-confirmed cases due to PCR compared with culture for the 5 year period described ranged from 9 to 26 % per year (mean 19 %). Real-time PCR is an invaluable tool both for enhanced epidemiological surveillance and for the provision of a rapid diagnosis of pertussis where results can affect patient and contact management.
Bacteroides fragilis signals through Toll-like receptor (TLR) 2 and not through TLR4
Authors: Alhawi Mohammad , Stewart John , Erridge Clett , Patrick Sheila , Poxton Ian R.
Published: July 2009

Although it is desirable to identify the interactions between endotoxin/LPS and the innate immune mechanism, it is often not possible to isolate these interactions from other cell wall-related structures of protein or polysaccharide origin. There is no universally accepted method to extract different LPSs from different bacteria, and their natural state will be influenced by their interactions with the associated molecules in the bacterial outer membrane. It is now believed that Toll-like receptor (TLR) 4 is the main signal transducer of classical LPS (i.e.Escherichia coliLPS), while TLR2 is used by certain non-classical LPSs. There are contradictory reports as to whetherBacteroides fragilisLPS, a non-classical LPS, signals primarily through TLR2 or TLR4. This study was designed to address this problem. Different non-purified and purifiedB. fragilisLPSs extracted by different methods together with different heat-killed, whole-cell populations ofB. fragiliswere used to elucidate the TLR specificity. All of theseB. fragilispreparations showed a significant signalling specificity for TLR2 but not for TLR4. This indicates that changing the extraction methods, with or without applying a repurification procedure, and varying the cell populations do not alter the TLR specificity ofB. fragilisLPS.
Relevance of resistance levels to carbapenems and integron-borne bla IMP-1, bla IMP-7, bla IMP-10 and bla VIM-2 in clinical isolates of Pseudomonas aeruginosa
Authors: Zhao Wei-Hua , Chen Gelin , Ito Ribu , Hu Zhi-Qing
Published: July 2009

Molecular detection and surveillance of the resistance genes harboured byPseudomonas aeruginosaare becoming increasingly important in assessing and controlling spread and colonization in hospitals, and in guiding the treatment of infections. This study analysed the resistance mechanisms of carbapenem-resistant clinical isolates ofP. aeruginosaand identified the associated integron-borne metallo-β-lactamase (MBL)-encoding genes. Twenty-seven imipenem (IPM)-resistant clinical isolates ofP. aeruginosawere divided into three groups according to their resistance levels to carbapenems. Strains bearingblaIMP-10showed extremely high-level resistance to IPM, with MICs of 512–2048 μg ml−1. By comparison, strains bearingblaIMP-1,blaIMP-7andblaVIM-2showed an intermediate level of resistance, with MICs of 32–256 μg ml−1. The non-MBL-producing strains showed a low level of resistance, with MICs of 8–32 μg ml−1. The same trend in resistance levels was also observed when resistance to other carbapenems, such as meropenem and panipenem, was determined. DNA sequencing showed that the MBL-encoding gene cassettes were carried by class 1 integrons. TheblaIMP-1,blaIMP-7andblaIMP-10gene cassettes were preceded by a hybridPantpromoter, TGGACA-N17-TAAACT, and theblaVIM-2gene cassette was preceded by a weak promoter, TGGACA-N17-TAAGCT. Most of the MBL-encoding genes were linked to one or two resistance genes encoding aminoglycoside-modifying enzymes, such asaac(6′)Iae,aac(6′)II,aacA7,aacC4,aadA1,aadA2andaadA6, highlighting the multidrug-resistant properties of these clinical isolates.
Distribution of espM and espT among enteropathogenic and enterohaemorrhagic Escherichia coli
Authors: Arbeloa Ana , Blanco Miguel , Moreira Fabiana C. , Bulgin Richard , López Cecilia , Dahbi Ghizlane , Blanco Jesús E. , Mora Azucena , Alonso María Pilar , Mamani Rosalia Ceferina , Gomes Tânia A. T. , Blanco Jorge , Frankel Gad
Published: July 2009

EnterohaemorrhagicEscherichia coli(EHEC) and enteropathogenicE. coli(EPEC) translocate dozens of type III secretion system effectors, including the WxxxE effectors Map, EspM and EspT that activate Rho GTPases. Whilemap, which is carried on the LEE pathogenicity island, is absolutely conserved among EPEC and EHEC strains, the prevalence ofespMandespTis not known. Here we report the results of a large screen aimed at determining the prevalence ofespMandespTamong clinical EPEC and EHEC isolates. The results suggest thatespM, detected in 51 % of the tested strains, is more commonly found in EPEC and EHEC serogroups that are linked to severe human infections. In contrast,espTwas absent from all the EHEC isolates and was found in only 1.8 % of the tested EPEC strains. Further characterization of the virulence gene repertoire of theespT-positive strains led to the identification of a newζ2 intimin variant. All theespT-positive strains but two contained thetccPgene.espTwas first found inCitrobacter rodentiumand laterin silicoin EPEC E110019, which is of particular interest as this strain was responsible for a particularly severe diarrhoeal outbreak in Finland in 1987 that affected 650 individuals in a school complex and an additional 137 associated household members. Comparing the protein sequences of EspT to that of E110019 showed a high level of conservation, with only three strains encoding EspT that differed in 6 amino acids. At present, it is not clear whyespTis so rare, and what impact EspM and EspT have on EPEC and EHEC infection.
Loss of Halophytism by Interference with SOS1 Expression
Authors: Oh Dong-Ha , Leidi Eduardo , Zhang Quan , Hwang Sung-Min , Li Youzhi , Quintero Francisco J. , Jiang Xingyu , D'Urzo Matilde Paino , Lee Sang Yeol , Zhao Yanxiu , Bahk Jeong Dong , Bressan Ray A. , Yun Dae-Jin , Pardo José M. , Bohnert Hans J.
Published: July 2009

The contribution of SOS1 (for Salt Overly Sensitive 1), encoding a sodium/proton antiporter, to plant salinity tolerance was analyzed in wild-type and RNA interference (RNAi) lines of the halophytic Arabidopsis (Arabidopsis thaliana)-relative Thellungiella salsuginea. Under all conditions, SOS1 mRNA abundance was higher in Thellungiella than in Arabidopsis. Ectopic expression of the Thellungiella homolog ThSOS1 suppressed the salt-sensitive phenotype of a Saccharomyces cerevisiae strain lacking sodium ion (Na+) efflux transporters and increased salt tolerance of wild-type Arabidopsis. thsos1-RNAi lines of Thellungiella were highly salt sensitive. A representative line, thsos1-4, showed faster Na+ accumulation, more severe water loss in shoots under salt stress, and slower removal of Na+ from the root after removal of stress compared with the wild type. thsos1-4 showed drastically higher sodium-specific fluorescence visualized by CoroNa-Green, a sodium-specific fluorophore, than the wild type, inhibition of endocytosis in root tip cells, and cell death in the adjacent elongation zone. After prolonged stress, Na+ accumulated inside the pericycle in thsos1-4, while sodium was confined in vacuoles of epidermis and cortex cells in the wild type. RNAi-based interference of SOS1 caused cell death in the root elongation zone, accompanied by fragmentation of vacuoles, inhibition of endocytosis, and apoplastic sodium influx into the stele and hence the shoot. Reduction in SOS1 expression changed Thellungiella that normally can grow in seawater-strength sodium chloride solutions into a plant as sensitive to Na+ as Arabidopsis.
Abscisic Acid Has a Key Role in Modulating Diverse Plant-Pathogen Interactions
Authors: Fan Jun , Hill Lionel , Crooks Casey , Doerner Peter , Lamb Chris
Published: July 2009

We isolated an activation-tagged Arabidopsis (Arabidopsis thaliana) line, constitutive disease susceptibility2-1D (cds2-1D), that showed enhanced bacterial growth when challenged with various Pseudomonas syringae strains. Systemic acquired resistance and systemic PATHOGENESIS-RELATED GENE1 induction were also compromised in cds2-1D. The T-DNA insertion adjacent to NINE-CIS-EPOXYCAROTENOID DIOXYGENASE5 (NCED5), one of six genes encoding the abscisic acid (ABA) biosynthetic enzyme NCED, caused a massive increase in transcript level and enhanced ABA levels >2-fold. Overexpression of NCED genes recreated the enhanced disease susceptibility phenotype. NCED2, NCED3, and NCED5 were induced, and ABA accumulated strongly following compatible P. syringae infection. The ABA biosynthetic mutant aba3-1 showed reduced susceptibility to virulent P. syringae, and ABA, whether through exogenous application or endogenous accumulation in response to mild water stress, resulted in increased bacterial growth following challenge with virulent P. syringae, indicating that ABA suppresses resistance to P. syringae. Likewise ABA accumulation also compromised resistance to the biotrophic oomycete Hyaloperonospora  arabidopsis, whereas resistance to the fungus Alternaria brassicicola was enhanced in cds2-1D plants and compromised in aba3-1 plants, indicating that ABA promotes resistance to this necrotroph. Comparison of the accumulation of salicylic acid and jasmonic acid in the wild type, cds2-1D, and aba3-1 plants challenged with P. syringae showed that ABA promotes jasmonic acid accumulation and exhibits a complex antagonistic relationship with salicylic acid. Our findings provide genetic evidence that the abiotic stress signal ABA also has profound roles in modulating diverse plant-pathogen interactions mediated at least in part by cross talk with the jasmonic acid and salicylic acid biotic stress signal pathways.
Arabidopsis Methionineγ-Lyase Is Regulated According to Isoleucine Biosynthesis Needs But Plays a Subordinate Role to Threonine Deaminase
Authors: Joshi Vijay , Jander Georg
Published: July 2009

The canonical pathway for isoleucine biosynthesis in plants begins with the conversion of threonine to 2-ketobutyrate by threonine deaminase (OMR1). However, demonstration of methionine γ-lyase (MGL) activity in Arabidopsis (Arabidopsis thaliana) suggested that production of 2-ketobutyrate from methionine can also lead to isoleucine biosynthesis. Rescue of the isoleucine deficit in a threonine deaminase mutant by MGL overexpression, as well as decreased transcription of endogenous Arabidopsis MGL in a feedback-insensitive threonine deaminase mutant background, shows that these two enzymes have overlapping functions in amino acid biosynthesis. In mgl mutant flowers and seeds, methionine levels are significantly increased and incorporation of [13C]Met into isoleucine is decreased, but isoleucine levels are unaffected. Accumulation of free isoleucine and other branched-chain amino acids is greatly elevated in response to drought stress in Arabidopsis. Gene expression analyses, amino acid phenotypes, and labeled precursor feeding experiments demonstrate that MGL activity is up-regulated by osmotic stress but likely plays a less prominent role in isoleucine biosynthesis than threonine deaminase. The observation that MGL makes a significant contribution to methionine degradation, particularly in reproductive tissue, suggests practical applications for silencing the expression of MGL in crop plants and thereby increasing the abundance of methionine, a limiting essential amino acid.
Comparative Large-Scale Analysis of Interactions between Several Crop Species and the Effector Repertoires from Multiple Pathovars of Pseudomonas and Ralstonia
Authors: Wroblewski Tadeusz , Caldwell Katherine S. , Piskurewicz Urszula , Cavanaugh Keri A. , Xu Huaqin , Kozik Alexander , Ochoa Oswaldo , McHale Leah K. , Lahre Kirsten , Jelenska Joanna , Castillo Jose A. , Blumenthal Daniel , Vinatzer Boris A. , Greenberg Jean T. , Michelmore Richard W.
Published: July 2009

Bacterial plant pathogens manipulate their hosts by injection of numerous effector proteins into host cells via type III secretion systems. Recognition of these effectors by the host plant leads to the induction of a defense reaction that often culminates in a hypersensitive response manifested as cell death. Genes encoding effector proteins can be exchanged between different strains of bacteria via horizontal transfer, and often individual strains are capable of infecting multiple hosts. Host plant species express diverse repertoires of resistance proteins that mediate direct or indirect recognition of bacterial effectors. As a result, plants and their bacterial pathogens should be considered as two extensive coevolving groups rather than as individual host species coevolving with single pathovars. To dissect the complexity of this coevolution, we cloned 171 effector-encoding genes from several pathovars of Pseudomonas and Ralstonia. We used Agrobacterium tumefaciens-mediated transient assays to test the ability of each effector to induce a necrotic phenotype on 59 plant genotypes belonging to four plant families, including numerous diverse accessions of lettuce (Lactuca sativa) and tomato (Solanum lycopersicum). Known defense-inducing effectors (avirulence factors) and their homologs commonly induced extensive necrosis in many different plant species. Nonhost species reacted to multiple effector proteins from an individual pathovar more frequently and more intensely than host species. Both homologous and sequence-unrelated effectors could elicit necrosis in a similar spectrum of plants, suggesting common effector targets or targeting of the same pathways in the plant cell.
Defining Core Metabolic and Transcriptomic Responses to Oxygen Availability in Rice Embryos and Young Seedlings
Authors: Narsai Reena , Howell Katharine A. , Carroll Adam , Ivanova Aneta , Millar A. Harvey , Whelan James
Published: July 2009

Analysis reveals that there is limited overlap in the sets of transcripts that show significant changes in abundance during anaerobiosis in different plant species. This may be due to the fact that a combination of primary effects, changes due to the presence or absence of oxygen, and secondary effects, responses to primary changes or tissue and developmental responses, are measured together and not differentiated from each other. In order to dissect out these responses, the effect of the presence or absence of oxygen was investigated using three different experimental designs using rice (Oryza sativa) as a model system. A total of 110 metabolites and 9,596 transcripts were found to change significantly in response to oxygen availability in at least one experiment. However, only one-quarter of these showed complementary responses to oxygen in all three experiments, allowing the core response to oxygen availability to be defined. A total of 10 metabolites and 1,136 genes could be defined as aerobic responders (up-regulated in the presence of oxygen and down-regulated in its absence), and 13 metabolites and 730 genes could be defined as anaerobic responders (up-regulated in the absence of oxygen and down-regulated in its presence). Defining core sets of transcripts that were sensitive to oxygen provided insights into alterations in metabolism, specifically carbohydrate and lipid metabolism and the putative regulatory mechanisms that allow rice to grow under anaerobic conditions. Transcript abundance of a specific set of transcription factors was sensitive to oxygen availability during all of the different experiments conducted, putatively identifying primary regulators of gene expression under anaerobic conditions. Combined with the possibility of selective transcript degradation, these transcriptional processes are involved in the core response of rice to anaerobiosis.
BOBBER1Is a Noncanonical Arabidopsis Small Heat Shock Protein Required for Both Development and Thermotolerance
Authors: Perez Dahlia E. , Hoyer J. Steen , Johnson Ayanna I. , Moody Zachary R. , Lopez Joseph , Kaplinsky Nicholas J.
Published: July 2009

Plants have evolved a range of cellular responses to maintain developmental homeostasis and to survive over a range of temperatures. Here, we describe the in vivo and in vitro functions of BOBBER1 (BOB1), a NudC domain containing Arabidopsis (Arabidopsisthaliana) small heat shock protein. BOB1 is an essential gene required for the normal partitioning and patterning of the apical domain of the Arabidopsis embryo. Because BOB1 loss-of-function mutants are embryo lethal, we used a partial loss-of-function allele (bob1-3) to demonstrate that BOB1 is required for organismal thermotolerance and postembryonic development. Recombinant BOB1 protein functions as a molecular chaperone and prevents the aggregation of a model protein substrate in vitro. In plants, BOB1 is cytoplasmic at basal temperatures, but forms heat shock granules containing canonical small heat shock proteins at high temperatures. In addition to thermotolerance defects, bob1-3 exhibits pleiotropic development defects during all phases of development. bob1-3 phenotypes include decreased rates of shoot and root growth as well as patterning defects in leaves, flowers, and inflorescence meristems. Most eukaryotic chaperones play important roles in protein folding either during protein synthesis or during cellular responses to denaturing stress. Our results provide, to our knowledge, the first evidence of a plant small heat shock protein that has both developmental and thermotolerance functions and may play a role in both of these folding networks.
Finite Mixture Models with Concomitant Information: Assessing Diagnostic Criteria for Diabetes
Authors: Thompson Theodore J. , Smith Philip J. , Boyle James P.
Published: July 2009

The World Health Organization (WHO) diagnostic criteria for diabetes mellitus were determined in part by evidence that in some populations the plasma glucose level 2 h after an oral glucose load is a mixture of two distinct distributions. We present a finite mixture model that allows the two component densities to be generalized linear models and the mixture probability to be a logistic regression model. The model allows us to estimate the prevalence of diabetes and sensitivity and specificity of the diagnostic criteria as a function of covariates and to estimate them in the absence of an external standard. Sensitivity is the probability that a test indicates disease conditionally on disease being present. Specificity is the probability that a test indicates no disease conditionally on no disease being present. We obtained maximum likelihood estimates via the EM algorithm and derived the standard errors from the information matrix and by the bootstrap. In the application to data from the diabetes in Egypt project a two-component mixture model fits well and the two components are interpreted as normal and diabetes. The means and variances are similar to results found in other populations. The minimum misclassification cutpoints decrease with age, are lower in urban areas and are higher in rural areas than the 200 mg dl-1 cutpoint recommended by the WHO. These differences are modest and our results generally support the WHO criterion. Our methods allow the direct inclusion of concomitant data whereas past analyses were based on partitioning the data.
Species and kinds: a critique of Rieppel’s “one of a kind” account of species
Authors: Reydon Thomas A.C.
Published: July 2009

A major issue in philosophical debates on the species problem concerns the opposition between two seemingly incompatible views of the metaphysics of species: the view that species are individuals and the view that species are natural kinds. In two recent papers in this journal, Olivier Rieppel suggested that this opposition is much less deep than it seems at first sight. Rieppel used a recently developed philosophical account of natural kindhood, namely Richard Boyd’s “homeostatic property cluster” theory, to argue that every species taxon can be conceived of as an individual that constitutes the single member of its own specific natural kind. In this paper I criticize Rieppel’s approach and argue that it does not deliver what it is supposed to, namely an account of species as kinds about which generalized statements can be made.
Long‐term results of patients with malignant carcinoid syndrome receiving octreotide LAR
Authors: TOUMPANAKIS C. , GARLAND J. , MARELLI L. , SRIRAJASKANTHAN R. , SOH J. , DAVIES P. , BUSCOMBE J. , CAPLIN M. E.
Published: July 2009

Background  Octreotide LAR is an established treatment for malignant carcinoid syndrome. However, studies with large number of patients and long follow‐up are lacking.

Aim  To present long‐terms results with octreotide LAR, assessing duration of clinical and objective response and treatment tolerance, in a large, homogeneous cohort of patients with malignant carcinoid syndrome.

Methods  A total of 108 patients with metastatic midgut neuroendocrine tumours were included in this 8‐year study. Clinical evaluation was based on a symptom score. Radiological assessment was based on RECIST (Response Evaluation Criteria In Solid Tumours) criteria.

Results  Of the 108 patients, 24% had a sustained symptomatic response. In the remaining patients, loss of symptomatic response with the initial dose was noted within 3‐60 months. In 17% of them, symptoms were controlled by just an increase of octreotide LAR dose, whilst the other patients required additional treatment. Overall, in 45.3% of patients, symptoms were well controlled during the study period with only octreotide LAR, and no additional treatment was required. No significant adverse effects were noted.

Conclusions  Octreotide LAR treatment provides a sustained symptomatic response in about half of the patients with malignant carcinoid syndrome and contributes to disease stabilization for a longer period than previously described.
Diagnostic yield of oesophagogastroduodenoscopy in children with abdominal pain
Authors: THAKKAR K. , CHEN L. , TATEVIAN N. , SHULMAN R. J. , MCDUFFIE A. , TSOU M. , GILGER M. A. , EL‐SERAG H. B.
Published: July 2009

Background  Abdominal pain is the most common indication for oesophagogastroduodenoscopy (OGD) in children. However, existing studies examining the diagnostic outcomes of OGD in children with abdominal pain are limited.

Aim  To examine the diagnostic yield of OGD with biopsy in the evaluation of abdominal pain and to describe the endoscopic and histological findings in patients undergoing OGD for abdominal pain of unclear aetiology.

Methods  We performed a retrospective cross‐sectional cohort study in children under 18 years of age who had OGD for the primary indication of abdominal pain, at Texas Children’s Hospital and Children’s Hospital of The King’s Daughters from 1 January 2002 to 30 June 2005.

Results  Overall, OGD was diagnostic in 454 (38.1%) of the 1191 procedures, including reflux oesophagitis (23%, n = 271), Helicobacter pylori infections (5%, n = 55), peptic ulcers (3%, n = 32), eosinophilic oesophagitis (2%, n = 25), celiac disease (1%, n = 9) and Crohn’s disease (0.5%, n = 7). Male gender, older age, elevated C‐reactive protein and vomiting were associated with increased diagnostic yield.

Conclusions  Our findings suggest that OGD is valuable for the evaluation of chronic abdominal pain in children, with a diagnostic yield of 38%. The majority of alarm symptoms and routine laboratory tests are not significantly associated with diagnostic yield.
Allergenicity and cross‐reactivity of pine pollen
Authors: Gastaminza G. , Lombardero M. , Bernaola G. , Antepara I. , Muñoz D. , Gamboa P. M. , Audicana M. T. , Marcos C. , Ansotegui I. J.
Published: July 2009

Background
Pine pollen has long been considered a non‐allergenic pollen. The large size of the grain and its low levels of proteins are the main reasons invoked to explain this low allergenicity. The aim of this study was to describe the main allergenic bands of Pinus radiata (PR) and its cross‐reactivity with other pine species, other conifers and grass pollen.

Methods
Sixty‐five pine‐pollen‐allergic patients (51% also sensitized to grass pollen) were studied. Skin prick tests (SPT) to a battery of allergens including PR, Pinus pinea, Pinus sylvestris, Pinus nigra and Cupressus sempervirens pollens and specific IgE determination to PR and Pinus strobus were performed. IgE‐immunoblotting to a PR extract and other pine pollens was also carried out. UniCAP inhibition and immunoblotting inhibition studies were performed to assess the cross‐reactivity between different pollens.

Results
The SPTs were positive with all the pine pollen extracts tested in 69% of the patients. Specific IgE was positive to PR or P. strobus in 77% of the patients, and to Lolium perenne in 51%. Nine different allergenic bands were detected. The two main allergens were a 42 kDa band recognized by 85% of the patients and a band of approximately 6–8 kDa recognized by 40%. A high degree of cross‐reactivity was observed between different pine pollen species, but not between pines and C. sempervirens pollen. A partial cross‐reactivity could be seen between pine and grass pollens only in patients also sensitized to L. perenne.

Conclusions
Pine pollen should be considered as a potential allergenic pollen especially where this pollen is abundant. The detection of a high number of patients that were monosensitized to pine pollen suggests the possibility of treating these patients with specific immunotherapy.
Improvement of fractional flow reserve and collateral flow by treatment with external counterpulsation (Art.Net.‐2 Trial)
Authors: Buschmann E. E. , Utz W. , Pagonas N. , Schulz‐Menger J. , Busjahn A. , Monti J. , Maerz W. , Le Noble F. , Thierfelder L. , Dietz R. , Klauss V. , Gross M. , Buschmann I.R. ,   On behalf of the Arteriogenesis Network (Art. Net.)
Published: July 2009

Background  Arteriogenesis (collateral artery growth) is nature’s most efficient rescue mechanism to overcome the fatal consequences of arterial occlusion or stenosis. The goal of this trial was to investigate the effect of external counterpulsation (ECP) on coronary collateral artery growth.

Materials and methods  A total of 23 patients (age 61 ± 2·5 years) with stable coronary artery disease and at least one haemodynamic significant stenosis eligible for percutaneous coronary intervention were prospectively recruited into the two study groups in a 2 : 1 manner (ECP : control). One group (ECP group, n = 16) underwent 35 1‐h sessions of ECP in 7 weeks. In the control group (n = 7), the natural course of collateral circulation over 7 weeks was evaluated. All patients underwent a cardiac catheterization at baseline and after 7 weeks, with invasive measurements of the pressure‐derived collateral flow index (CFIp, primary endpoint) and fractional flow reserve (FFR).

Results  In the ECP group, the CFIp (from 0·08 ± 0·01 to 0·15 ± 0·02; P < 0·001) and FFR (from 0·68 ± 0·03 to 0·79 ± 0·03; P = 0·001) improved significantly, while in the control group no change was observed. Only the ECP group showed a reduction of the Canadian Cardiovascular Society (CCS, P = 0·008) and New York Heart Association (NYHA, P < 0·001) classification.

Conclusion  In this study, we provide direct functional evidence for the stimulation of coronary arteriogenesis via ECP in patients with stable coronary artery disease. These data might open a novel noninvasive and preventive treatment avenue for patients with non‐acute vascular stenotic disease.
Soil hydraulic properties in relation to local rapid soil changes induced by field drainage: a case study
Authors: Frison A. , Cousin I. , Montagne D. , Cornu S.
Published: July 2009

The impact of human activities on soil changes is poorly recognized and quantified. We performed an experiment to estimate the impact of 20 years, subsurface drainage on water retention in an Albeluvisol. The studied soil comprises heterogeneous horizons that exhibit a complex juxtaposition of two elementary pedological volumes (EPVs) with a silty white and a clayey ochre EPV. The water retention characteristics of each EPV were determined at four distances from the drain in the E&Bt heterogeneous horizon. The water retention property of the whole horizon was calculated by using an additive equation in order to obtain the available water content of the horizon, and thus to estimate the soil functioning. Whatever the distance to the drain, the silty white EPVs retained more water for water potentials between saturation and approximately −300 cm than the clayey ochre EPVs, and less for water potentials lower than approximately −300 cm. The available water content of the white EPVs and the whole horizon increased near the drain. These changes in water retention properties were interpreted in terms of effects on the horizon structure, which were enhanced by the horizontal fluxes enhanced by the installation of the drains. The present work demonstrates the great influence of agricultural drainage on rapid soil change and on soil spatial variability.

Modification des propriétés hydrodynamiques des sols en relation avec les évolutions pédogénétiques rapides liées au drainage: une étude de cas

Les conséquences des activités anthropiques sur l’évolution des sols sont actuellement très peu reconnues. Nous avons mis en place une expérience afin d’estimer l’impact d’un drainage agricole installé depuis 20 ans sur les propriétés hydriques d’un Albeluvisol. Le sol étudié comprend des horizons hétérogènes composés d’une juxtaposition complexe de Volumes Pédologiques Elémentaires (VPE): des VPE clairs limoneux et des VPE ocre plus argileux. Les propriétés de rétention en eau de chaque VPE de l’horizon E&Bt ont été déterminées en fonction de la distance au drain. Nous avons calculé la courbe de rétention effective pour l’ensemble de l’horizon en utilisant l’équation d’additivité. Nous avons ainsi estimé la réserve en eau de l’horizon afin de discuter du fonctionnement hydrique du sol. Quelle que soit la distance au drain, les VPE clairs retiennent (i) plus d’eau pour des potentiels matriciels compris entre la saturation et ∼−300 cm que les VPE ocre, et (ii) moins d’eau pour des potentiels matriciels inférieurs à∼−300 cm. Les réserves en eau utiles des VPE clairs et de l’ensemble de l’horizon augmentent lorsque l’on se rapproche du drain. Ces évolutions des propriétés de rétention en eau ont été interprétées en terme de changements de structure de l’horizon, lesquels sont la résultante des flux horizontaux accrus par l’installation du réseau de drainage. Ce travail contribue à démontrer l’importante influence du drainage agricole sur l’évolution rapide des sols.
Measurement of aggregate bond energy using ultrasonic dispersion
Authors: Zhu Z. L. , Minasny B. , Field D. J.
Published: July 2009

Numerous protocols have been developed to assess soil stability, such as wet sieving, end‐over‐end shaking and rainfall simulation, but a major limitation of these procedures is that they apply an arbitrary application of mechanical energy that is not quantified, resulting in a stability assessment that can only be related to the context in which it is being used. To address this, previous authors demonstrated that the energy (L) responsible for dispersing soil could be determined when using ultrasonic agitation. Changes in ultrasonic equipment, with the inclusion of a feedback system to adjust the output energy, Ep, of the ultrasonic probe, preclude the assumption that Epis the same in pure water and in dispersed and undispersed soil–water systems, which may explain why previous approaches have not been routinely adopted. Our paper presents a new theory for estimating the components of the energy balance in an ultrasonic system fitted with a power‐adjusting feedback mechanism facilitating the estimate of L. Using Vertisol and Ferrasol soil samples, the components of the ultrasonic energy balance were successfully estimated and the estimate of L was greater than that reported in earlier work. When used to calculate the soil dispersion characteristic curve, it was found that the critical dispersive energy (Ld) was in the range of 100–600 J g−1, which appears to be much larger compared with previously published values, and the Ldconstituted 3–20% of the total energy applied to the soil–water system.
The trophic ecology of castes in harvester ant colonies
Authors: Smith Chris R. , Suarez Andrew V.
Published: July 2009

1.The castes of social insects can vary dramatically in physiology, morphology and behaviour, and are a model of phenotypic plasticity. Dietary variation has been implicated in the evolution of castes and is involved in developmental differentiation. This study uses the elemental and isotopic composition of castes to infer the diets they consumed during larval development, when caste was determined.

2.We analysed the elemental (C : N) and isotopic (δ13C and δ15N) composition of individuals of all castes in colonies ofPogonomyrmex badius, the Florida seed harvester ant, at each of two sites. Sampled herbivores and insectivores were used to calibrate measures of colony trophic position. The proportions of insects and seeds foraged by colonies correlated with inferred trophic position, strengthening the inference of diet from isotopic composition.

3.Pupae of each of the four castes (male, reproductive female or gyne, major worker and minor worker) are distinguishable based on their composition and inferred diet during the larval phase.

4.Within colonies, larval diet inferred from δ15N suggests that the largest individuals assimilated more insect/protein relative to seeds. This result was consistent across colonies despite high variation in a colony’s relative trophic position.

5.Carbon to nitrogen ratio (C : N) of each caste was also different, and differences were consistent across colonies and sites. While females increase in N content with increasing size, the pattern is reversed in males. This result may reflect basic life history differences (e.g. life span) between males and females. Since female reproductive potential correlates with female size in this species, the decrease in N content with increasing female caste size supports that reproductive development is N‐limited, and that workers are trophically castrated due to N deprivation during larval development.
Carbon‐nitrogen interactions in fertility island soil from a tropical semi‐arid ecosystem
Authors: Perroni‐Ventura Yareni , Montaña Carlos , García‐Oliva Felipe
Published: July 2009

1. Biological nitrogen (N) fixation by symbiotic and free‐living organisms is considered the main pathway for N soil enrichment in desert and semi‐desert ecosystems. This fact is more noticeable in tropical ecosystems where legume species have a high relative abundance. However, this biological fixation pathway does not guarantee the maintenance of soil N pools, and N conservation pathways are important in understanding controls over soil N cycling.

2. In dryland ecosystems, desert plants can form a ‘fertility island’ (FI) as soils beneath plants show higher concentrations of N and organic matter.

3. Here we assess how carbon (C) and N may interact to conserve soil N within the FI soil of two legume species (Prosopis laevigata and Parkinsonia praecox), one a known N‐fixer and the other believed not to fix N, as well as within adjacent bare ground soil. In a semi‐arid tropical ecosystem in central Mexico, we examined spatial patterns in C and N pools and transformation rates, and we investigated seasonal variations in these relationships.

4. Results show that FI soil C and N could be linked to total N storage through net C and N immobilization in microbial biomass and heterotrophic microbial activity. Soil under P. laevigata canopy had greater total N as well as N accumulated in microbial biomass than soil under P. praecox and bare ground soil. Nevertheless, inorganic N and potential net N mineralization rates were similar under soils of both species, although we expected higher inorganic N and N‐mineralization values in N‐fixer species to explain the greater total N. Higher total N concentrations under P. laevigata probably result from greater inputs of organic C and a higher potential net C mineralization rate in comparison to P. praecox and bare ground soil.

5. Even though N input and output values were not measured, the results highlight the importance of assessing the role of organic C, heterotrophic microbial activity, and N storage in microbial biomass in order to understand controls over N retention in soil N cycling. Thus, soil C‐N interactions could be a control factor of N soil conservation in this tropical semi‐arid ecosystem.
Isolation of a novel strain of Bacillus pumilus from penaeid shrimp that is inhibitory against marine pathogens.
Authors: Hill J E , Baiano J C F , Barnes A C
Published: July 2009

A bacterium was isolated from the mid‐gut of healthy black tiger shrimp, Penaeus monodon, based on a large zone of inhibition in mixed culture on solid medium. The isolate was a Gram‐positive, motile spore former, with an optimum pH range for growth in tryptone soya broth containing 2% NaCl of between pH 6 and 9. The bacterium was highly salt tolerant with concentrations between 0% and 8% having no detrimental effect on growth. The isolate was identified as Bacillus pumilus based on physiological capabilities using the API50CHB and Biolog systems. Amplification and sequencing of the 16S rRNA gene followed by phylogenetic analysis confirmed its identity. The Bacillus pumilus isolate was strongly inhibitory against the marine bacterial pathogens Vibrio alginolyticus, V. mimicus and V. harveyi, and weakly inhibitory against V. parahaemolyticus in cross‐streaking assays on solid medium. The organism was marginally self‐inhibitory, and inhibited B. licheniformis and B. subtilis. The suitability of the B. pumilus isolate for use as a probiotic in farmed shrimp was further supported by the absence of any of the known B. cereus enterotoxin genes. Based on these in vitro results, in vivo safety and efficacy trials are underway to determine suitability of the novel strain as a commercial probiotic.