bluuebunny/crossref_metadata_2025 huggingface dataset:
Tracking single coccolith dissolution with picogram resolution and implications for CO
2
sequestration and ocean acidification
Authors: Hassenkam T. , Johnsson A. , Bechgaard K. , Stipp S. L. S.
Published: May 2011

Coccoliths are micrometer scale shields made from 20 to 60 individual calcite (CaCO
3
) crystals that are produced by some species of algae. Currently, coccoliths serve as an important sink in the global carbon cycle, but decreasing ocean pH challenges their stability. Chalk deposits, the fossil remains of ancient algae, have remained remarkably unchanged by diagenesis, the process that converts sediment to rock. Even after 60 million years, the fossil coccolith crystals are still tiny (< 1 
μm
), compared with inorganically produced calcite, where one day old crystals can be 10 times larger, which raises the question if the biogenic nature of coccolith calcite gives it different properties than inorganic calcite? And if so, can these properties protect coccoliths in CO
2
challenged oceans? Here we describe a new method for tracking dissolution of individual specimens, at picogram (10
-12
 g) resolution. The results show that the behavior of modern and fossil coccoliths is similar and both are more stable than inorganic calcite. Organic material associated with the biogenic calcite provides the explanation. However, ancient and modern coccoliths, that resist dissolution in Ca-free artificial seawater at pH > 8, all dissolve when pH is 7.8 or lower. Ocean pH is predicted to fall below 7.8 by the year 2100, in response to rising CO
2
levels. Our results imply that at these conditions the advantages offered by the biogenic nature of calcite will disappear putting coccoliths on algae and in the calcareous bottom sediments at risk.
Focal adhesion kinase protein regulatesWnt3agene expression to control cell fate specification in the developing neural plate
Authors: Fonar Yuri , Gutkovich Yoni E. , Root Heather , Malyarova Anastasia , Aamar Emil , Golubovskaya Vita M. , Elias Sarah , Elkouby Yaniv M. , Frank Dale
Published: May 2011

Focal adhesion kinase (FAK) is a cytoplasmic tyrosine kinase protein localized to regions called focal adhesions, which are contact points between cells and the extracellular matrix. FAK protein acts as a scaffold to transfer adhesion-dependent and growth factor signals into the cell. Increased FAK expression is linked to aggressive metastatic and invasive tumors. However, little is known about its normal embryonic function. FAK protein knockdown during early Xenopus laevis development anteriorizes the embryo. Morphant embryos express increased levels of anterior neural markers, with reciprocally reduced posterior neural marker expression. Posterior neural plate folding and convergence-extension is also inhibited. This anteriorized phenotype resembles that of embryos knocked down zygotically for canonical Wnt signaling. FAK and Wnt3a genes are both expressed in the neural plate, and Wnt3a expression is FAK dependent. Ectopic Wnt expression rescues this FAK morphant anteriorized phenotype. Wnt3a thus acts downstream of FAK to balance anterior–posterior cell fate specification in the developing neural plate. Wnt3a gene expression is also FAK dependent in human breast cancer cells, suggesting that this FAK–Wnt linkage is highly conserved. This unique observation connects the FAK- and Wnt-signaling pathways, both of which act to promote cancer when aberrantly activated in mammalian cells.
The LRRK2-related Roco kinase Roco2 is regulated by Rab1A and controls the actin cytoskeleton
Authors: Kicka Sebastian , Shen Zhouxin , Annesley Sarah J. , Fisher Paul R. , Lee Susan , Briggs Steven , Firtel Richard A.
Published: May 2011

We identify a new pathway that is required for proper pseudopod formation. We show that Roco2, a leucine-rich repeat kinase 2 (LRRK2)-related Roco kinase, is activated in response to chemoattractant stimulation and helps mediate cell polarization and chemotaxis by regulating cortical F-actin polymerization and pseudopod extension in a pathway that requires Rab1A. We found that Roco2 binds the small GTPase Rab1A as well as the F-actin cross-linking protein filamin (actin-binding protein 120, abp120) in vivo. We show that active Rab1A (Rab1A-GTP) is required for and regulates Roco2 kinase activity in vivo and that filamin lies downstream from Roco2 and controls pseudopod extension during chemotaxis and random cell motility. Therefore our study uncovered a new signaling pathway that involves Rab1A and controls the actin cytoskeleton and pseudopod extension, and thereby, cell polarity and motility. These findings also may have implications in the regulation of other Roco kinases, including possibly LRRK2, in metazoans.
Sequential assembly of translesion DNA polymerases at UV-induced DNA damage sites
Authors: Andersen Parker L. , Xu Fang , Ziola Barry , McGregor W. Glen , Xiao Wei
Published: May 2011

In response to DNA damage such as from UV irradiation, mammalian Y-family translesion synthesis (TLS) polymerases Polη and Rev1 colocalize with proliferating cell nuclear antigen at nuclear foci, presumably representing stalled replication sites. However, it is unclear whether the localization of one polymerase is dependent on another. Furthermore, there is no report on the in vivo characterization of the Rev3 catalytic subunit of the B-family TLS polymerase Polζ. Here we describe the detection of endogenous human Polη, Rev1, and Rev3 by immunocytochemistry using existing or newly created antibodies, as well as various means of inhibiting their expression, which allows us to examine the dynamics of endogenous TLS polymerases in response to UV irradiation. It is found that Rev1 and Polη are independently recruited to the nuclear foci, whereas the Rev3 nuclear focus formation requires Rev1 but not Polη. In contrast, neither Rev1 nor Polη recruitment requires Rev3. To further support these conclusions, we find that simultaneous suppression of Polη and Rev3 results in an additive cellular sensitivity to UV irradiation. These observations suggest a cooperative and sequential assembly of TLS polymerases in response to DNA damage. They also support and extend the current polymerase switch model.
ReMark: an automatic program for clustering orthologs flexibly combining a Recursive and a Markov
clustering algorithms
Authors: Kim Kangseok , Kim Wonil , Kim Sunshin
Published: May 2011

Summary: ReMark is a fully automatic tool for clustering orthologs by combining a Recursive and a Markov clustering (MCL) algorithms. The ReMark detects and recursively clusters ortholog pairs through reciprocal BLAST best hits between multiple genomes running software program (RecursiveClustering.java) in the first step. Then, it employs MCL algorithm to compute the clusters (score matrices generated from the previous step) and refines the clusters by adjusting an inflation factor running software program (MarkovClustering.java). This method has two key features. One utilizes, to get more reliable results, the diagonal scores in the matrix of the initial ortholog clusters. Another clusters orthologs flexibly through being controlled naturally by MCL with a selected inflation factor. Users can therefore select the fitting state of orthologous protein clusters by regulating the inflation factor according to their research interests.

Availability and Implementation: Source code for the orthologous protein clustering software is freely available for non-commercial use at http://dasan.sejong.ac.kr/~wikim/notice.html, implemented in Java 1.6 and supported on Windows and Linux.

Contact:  wikim@sejong.ac.kr; sskim04@hotmail.com
Multiple-rule bias in the comparison of classification rules
Authors: Yousefi Mohammadmahdi R. , Hua Jianping , Dougherty Edward R.
Published: May 2011

Motivation: There is growing discussion in the bioinformatics community concerning overoptimism of reported results. Two approaches contributing to overoptimism in classification are (i) the reporting of results on datasets for which a proposed classification rule performs well and (ii) the comparison of multiple classification rules on a single dataset that purports to show the advantage of a certain rule.

Results: This article provides a careful probabilistic analysis of the second issue and the ‘multiple-rule bias’, resulting from choosing a classification rule having minimum estimated error on the dataset. It quantifies this bias corresponding to estimating the expected true error of the classification rule possessing minimum estimated error and it characterizes the bias from estimating the true comparative advantage of the chosen classification rule relative to the others by the estimated comparative advantage on the dataset. The analysis is applied to both synthetic and real data using a number of classification rules and error estimators.

Availability: We have implemented in C code the synthetic data distribution model, classification rules, feature selection routines and error estimation methods. The code for multiple-rule analysis is implemented in MATLAB. The source code is available at http://gsp.tamu.edu/Publications/supplementary/yousefi11a/. Supplementary simulation results are also included.

Contact:  edward@ece.tamu.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq
Authors: Li Yang , Chien Jeremy , Smith David I. , Ma Jian
Published: May 2011

Motivation: Fusion transcripts can be created as a result of genome rearrangement in cancer. Some of them play important roles in carcinogenesis, and can serve as diagnostic and therapeutic targets. With more and more cancer genomes being sequenced by next-generation sequencing technologies, we believe an efficient tool for reliably identifying fusion transcripts will be desirable for many groups.

Results: We designed and implemented an open-source software tool, called FusionHunter, which reliably identifies fusion transcripts from transcriptional analysis of paired-end RNA-seq. We show that FusionHunter can accurately detect fusions that were previously confirmed by RT-PCR in a publicly available dataset. The purpose of FusionHunter is to identify potential fusions with high sensitivity and specificity and to guide further functional validation in the laboratory.

Availability:  http://bioen-compbio.bioen.illinois.edu/FusionHunter/.

Contact:  jianma@illinois.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Mixture models for analysis of the taxonomic composition of metagenomes
Authors: Meinicke Peter , Aßhauer Kathrin Petra , Lingner Thomas
Published: May 2011

Motivation: Inferring the taxonomic profile of a microbial community from a large collection of anonymous DNA sequencing reads is a challenging task in metagenomics. Because existing methods for taxonomic profiling of metagenomes are all based on the assignment of fragmentary sequences to phylogenetic categories, the accuracy of results largely depends on fragment length. This dependence complicates comparative analysis of data originating from different sequencing platforms or resulting from different preprocessing pipelines.

Results: We here introduce a new method for taxonomic profiling based on mixture modeling of the overall oligonucleotide distribution of a sample. Our results indicate that the mixture-based profiles compare well with taxonomic profiles obtained with other methods. However, in contrast to the existing methods, our approach shows a nearly constant profiling accuracy across all kinds of read lengths and it operates at an unrivaled speed.

Availability: A platform-independent implementation of the mixture modeling approach is available in terms of a MATLAB/Octave toolbox at http://gobics.de/peter/taxy. In addition, a prototypical implementation within an easy-to-use interactive tool for Windows can be downloaded.

Contact:  pmeinic@gwdg.de; thomas@gobics.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Pathway analysis of high-throughput biological data within a Bayesian network framework
Authors: Isci Senol , Ozturk Cengizhan , Jones Jon , Otu Hasan H.
Published: May 2011

Motivation: Most current approaches to high-throughput biological data (HTBD) analysis either perform individual gene/protein analysis or, gene/protein set enrichment analysis for a list of biologically relevant molecules. Bayesian Networks (BNs) capture linear and non-linear interactions, handle stochastic events accounting for noise, and focus on local interactions, which can be related to causal inference. Here, we describe for the first time an algorithm that models biological pathways as BNs and identifies pathways that best explain given HTBD by scoring fitness of each network.

Results: Proposed method takes into account the connectivity and relatedness between nodes of the pathway through factoring pathway topology in its model. Our simulations using synthetic data demonstrated robustness of our approach. We tested proposed method, Bayesian Pathway Analysis (BPA), on human microarray data regarding renal cell carcinoma (RCC) and compared our results with gene set enrichment analysis. BPA was able to find broader and more specific pathways related to RCC.

Availability: Accompanying BPA software (BPAS) package is freely available for academic use at http://bumil.boun.edu.tr/bpa.

Contact:  hotu@bidmc.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
BINOCh: binding inference from nucleosome occupancy changes
Authors: Meyer Clifford A. , He Housheng H. , Brown Myles , Liu X. Shirley
Published: May 2011

Summary: Transcription factor binding events are frequently associated with a pattern of nucleosome occupancy changes in which nucleosomes flanking the binding site increase in occupancy, while those in the vicinity of the binding site itself are displaced. Genome-wide information on enhancer proximal nucleosome occupancy can be readily acquired using ChIP-seq targeting enhancer-related histone modifications such as H3K4me2. Here, we present a software package, BINOCh that allows biologists to use such data to infer the identity of key transcription factors that regulate the response of a cell to a stimulus or determine a program of differentiation.

Availability: The BINOCh open source Python package is freely available at http://liulab.dfci.harvard.edu/BINOCh under the FreeBSD license.

Contact:  cliff@jimmy.harvard.edu; xsliu@jimmy.harvard.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Renal Colic
Authors: Cruickshank Ross , Coulter Suzanne
Published: May 2011

Renal colic is a common condition, which will often be seen by GPs throughout their careers. Making up 1% of all emergency admissions to hospital, specialist review and care may be frequently required; however, the responsibilities of initial prompt diagnosis and treatment, followed by patient education and secondary prevention will often lie with the primary care physician. This article aims to provide an overview of renal tract calculi and provide trainees with a general understanding of its aetiology, presentation and acute and long-term treatment.
Independent Predictors and Outcomes of Unanticipated Early Postoperative Tracheal Intubation after Nonemergent, Noncardiac Surgery
Authors: Ramachandran Satya Krishna , Nafiu Olubukola O. , Ghaferi Amir , Tremper Kevin K. , Shanks Amy , Kheterpal Sachin
Published: May 2011

Background

Although the risk of hypoxemia is greatest during the first 72 h after surgery, little is known of the incidence of respiratory failure during this period. The authors studied the incidence and predictors of unanticipated early postoperative intubation (within 3 days) and its role in mortality.

Methods

A total of 222,094 adult patients undergoing nonemergent, noncardiac surgery in the American College of Surgeons-National Surgical Quality Improvement Program database were studied to determine the incidence and independent predictors of unanticipated early postoperative intubation. A risk-class model was developed and subsequently validated in 109,636 patients.

Results

Overall, 2,828 of 5,725 (49.4%) unanticipated tracheal intubations in a period of 30 days occurred within the first 3 days after surgery. The incidence of unanticipated early postoperative intubation was 0.83-0.9% in the derivation and validation cohorts. Independent predictors of unanticipated early postoperative intubation included current ethanol use, current smoker, dyspnea, chronic obstructive pulmonary disease, diabetes mellitus needing insulin therapy, active congestive heart failure, hypertension requiring medication, abnormal liver function, cancer, prolonged hospitalization, recent weight loss, body mass index less than 18.5 or ≥ 40 kg/m, medium-risk surgery, high-risk surgery, very-high-risk surgery, and sepsis. Unanticipated early postoperative intubation was an independent predictor of 30-day mortality, with an adjusted odds ratio of 9.2. Higher risk classes were associated with increasing incidence of unanticipated early postoperative intubation and death.

Conclusions

One half of unanticipated tracheal intubations in a period of 30 days occurred within the first 3 days after nonemergent, noncardiac surgery and were independently associated with a 9-fold increase in mortality. The authors present a validated perioperative risk class index for determining risk of unanticipated early postoperative intubation.
Evidence‐based Guidelines From ESPGHAN and NASPGHAN for Helicobacter pylori Infection in Children
Authors: Koletzko Sibylle , Jones Nicola L. , Goodman Karen J. , Gold Benjamin , Rowland Marion , Cadranel Samy , Chong Sonny , Colletti Richard B. , Casswall Thomas , Elitsur Yoram , Guarner Jeannette , Kalach Nicolas , Madrazo Armando , Megraud Francis , Oderda Giuseppina ,   H pylori Working Groups of ESPGHAN and NASPGHAN
Published: May 2011

Objective:

As the clinical implications of Helicobacter pylori infection in children and adolescents continue to evolve, ESPGHAN and NASPGHAN jointly renewed clinical guidelines using a standardized evidence‐based approach to develop updated recommendations for children and adolescents in North America and Europe.

Methods:

An international panel of 11 pediatric gastroenterologists, 2 epidemiologists, 1 microbiologist, and 1 pathologist was selected by societies that developed evidence‐based guidelines based on the Delphi process with anonymous voting in a final face‐to‐face meeting. A systematic literature search was performed on 8 databases of relevance including publications from January 2000 to December 2009. After excluding nonrelevant publications, tables of evidence were constructed for different focus areas according to the Oxford classification. Statements and recommendations were formulated in the following areas: whom to test, how to test, whom to treat, and how to treat. Grades of evidence were assigned to each recommendation based on the GRADE system.

Results:

A total of 2290 publications were identified, from which 738 were finally reviewed. A total of 21 recommendations were generated, and an algorithm was proposed by the joint committee providing evidence‐based guidelines on the diagnostic workup and treatment of children with H pylori infection.

Conclusions:

These clinical practice guidelines represent updated, best‐available evidence and are meant for children and adolescents living in Europe and North America, but they may not apply to those living on other continents, particularly in developing countries with a high H pylori infection rate and limited health care resources.
Hasllibacter halocynthiae gen. nov., sp. nov., a nutriacholic acid-producing bacterium isolated from the marine ascidian Halocynthia roretzi
Authors: Kim Sung Hun , Yang Hyun Ok , Shin Yun Kyung , Kwon Hak Cheol
Published: May 2011

A Gram-negative, aerobic, ovoid to rod-shaped bacterial strain, KME 002Twas isolated from a marine ascidian,Halocynthia roretzi, off the coast of Gangneung, Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that this strain belonged to the familyRhodobacteraceaein the classAlphaproteobacteriaand was closely related to the type strains ofDinoroseobacter shibae,Roseovarius crassostreaeandPseudoruegeria aquimariswith 95.0, 94.7 and 94.5 % 16S rRNA gene sequence similarities, respectively. KME 002Twas an obligately halophilic bacterium requiring 1 to 5 % (w/v) NaCl, with an absolute requirement for magnesium chloride for growth. Cells were motile by means of a single polar flagellum and showed budding fission. The predominant cellular fatty acid of the isolate was C18 : 1ω7cand Q-10 was the major ubiquinone. The DNA G+C content of the strain was 71.6 mol%. The major secondary metabolites from cultures in liquid medium were cholic acid derivatives, including 3α,12α-hydroxy-3-keto-glycocholanic acid, 12-hydroxy-3-keto-glycocholanic acid, nutriacholic acid and deoxycholic acid. These characteristics determined in this polyphasic study suggest that strain KME 002Trepresents a novel species in a new genus of the familyRhodobacteraceae. The nameHasllibacter halocynthiaegen. nov., sp. nov. is proposed for this isolate, and the type strain is KME 002T( = JCM 16214T = KCCM 90082T).
Algoriphagus aquaeductus sp. nov., isolated from a freshwater pipe
Authors: Rau Jan Erik , Blotevogel Karl-Heinz , Fischer Ulrich
Published: May 2011

A Gram-staining-negative, aerobic to microaerophilic, rod-shaped, red-coloured bacterium, strain T4T, was isolated from a freshwater pipe on Tenerife island. A polyphasic taxonomic study was performed in order to characterize the strain in detail. The isolate is surrounded by a slime capsule, occurs singly, in the form of short chains, or in aggregates, and exhibits catalase and oxidase activities. Growth was observed at 15–42 °C. Optimum growth occurred at pH 8 with mono- and disaccharides, followed by polysaccharides and deoxysaccharides, but the bacterium utilized only a restricted spectrum of alcohols, alditols, amides, amines, carboxylic acids and amino acids. Strain T4T tolerated concentrations of 0–4 % (w/v) NaCl and contained MK-7 as predominant isoprenoid quinone as well as carotenoids, but lacked pigments of the flexirubin type. The predominant fatty acids were iso-C15 : 0 (32.2 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 22.5 %), and iso-C17 : 0 3-OH (7.9 %). Major polar lipids were phosphatidylethanolamine, phospholipids, aminophospholipids and other lipids of unknown character. The DNA G+C content was approximately 41.8 mol%. The sequence of the 16S-rRNA gene assigned strain T4T to the CFB group, forming a coherent cluster with species of the genus Algoriphagus with the highest similarity of 98.8 % to Algoriphagus aquatilis A8-7T. DNA–DNA hybridization revealed 37.5 % relatedness to strain A8-7T. Based on morphological, physiological and molecular properties as well as on phylogenetic distinctiveness, strain T4T should be placed into the genus Algoriphagus as a novel species, for which the name Algoriphagus aquaeductus sp. nov. (type strain T4T  = DSM 19759T  = LMG 24398T  = NCIMB 14399T) is proposed.
Bryocella elongata gen. nov., sp. nov., a member of subdivision 1 of the Acidobacteria isolated from a methanotrophic enrichment culture, and emended description of Edaphobacter aggregans Koch et al. 2008
Authors: Dedysh Svetlana N. , Kulichevskaya Irina S. , Serkebaeva Yulia M. , Mityaeva Maria A. , Sorokin Vladimir V. , Suzina Natalia E. , Rijpstra W. Irene C. , Sinninghe Damsté Jaap S.
Published: May 2011

An aerobic, pink-pigmented, chemo-organotrophic bacterium, designated strain SN10T, was isolated from a methanotrophic enrichment culture obtained from an acidic Sphagnum peat. This isolate was represented by Gram-negative, non-motile rods that multiply by normal cell division and form rosettes. Strain SN10T is an obligately acidophilic, mesophilic bacterium capable of growth at pH 3.2–6.6 (with an optimum at pH 4.7–5.2) and at 6–32 °C (with an optimum at 20–24 °C). The preferred growth substrates are sugars and several heteropolysaccharides of plant and microbial origin, such as pectin, lichenan, fucoidan and gellan gum. While not being capable of growth on C1 compounds, strain SN10T can develop in co-culture with exopolysaccharide-producing methanotrophs by utilization of their capsular material. The major fatty acids determined in strain SN10T using the conventional lipid extraction procedure are iso-C15 : 0 and C16 : 1ω7c. Upon hydrolysis of total cell material, substantial amounts of the uncommon membrane-spanning lipid 13,16-dimethyl octacosanedioic acid (isodiabolic acid) were also detected. The polar lipids are two phosphohexoses, phosphatidylethanolamine, phosphatidylglycerol and several phospholipids of unknown structure. The major quinone is MK-8. Pigments are carotenoids. The G+C content of the DNA is 60.7 mol%. Strain SN10T forms a separate lineage within subdivision 1 of the phylum Acidobacteria and displays 94.0–95.4 % 16S rRNA gene sequence similarity to members of the genera Edaphobacter and Granulicella, 93.0–93.7 % similarity to members of the genus Terriglobus and 92.2–92.3 % similarity to the type strains of Telmatobacter bradus and Acidobacterium capsulatum. Therefore, strain SN10T is classified within a novel genus and species, for which the name Bryocella elongata gen. nov., sp. nov. is proposed. Strain SN10T ( = LMG 25276T  = DSM 22489T) is the type strain of Bryocella elongata. An emended description of Edaphobacter aggregans Koch et al. 2008 is also given.
Sphingobacterium wenxiniae sp. nov., a cypermethrin-degrading species from activated sludge
Authors: Zhang Jun , Zheng Jin-Wei , Cho Byung Cheol , Hwang Chung Yeon , Fang Chengxiang , He Jian , Li Shun-Peng
Published: May 2011

A Gram-negative, non-motile, non-spore-forming, non-flagellated rod capable of degrading cypermethrin, designated LQY-18T, was isolated from activated sludge of a wastewater treatment plant in China. Strain LQY-18T grew at 8–40 °C (optimum 30 °C), at pH 5.0–10.0 (optimum pH 7.0) and with 0–5 % (w/v) NaCl (optimum 1 %). The predominant menaquinone was MK-7 (97 %) and the major fatty acids were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH. The DNA G+C content was 40.3 mol%. Phylogenetic analysis revealed that the isolate belonged to the genus Sphingobacterium of the phylum Bacteroidetes and showed low 16S rRNA gene sequence similarity with recognized members of the genus Sphingobacterium. The closest neighbour was Sphingobacterium mizutaii ATCC 33299T (92.9 % 16S rRNA gene sequence similarity). On the basis of phenotypic, genetic and phylogenetic data, strain LQY-18T ( = ACCC 05410T = CCTCC AB 2010005T = KCTC 23009T) should be classified as a representative of a novel species of the genus Sphingobacterium, for which the name Sphingobacterium wenxiniae sp. nov. is proposed.
FvbA is required for vibriobactin utilization in Pseudomonas aeruginosa
Authors: Elias Sivan , Degtyar Elena , Banin Ehud
Published: May 2011

Bacteria acquire iron through a highly specific mechanism involving iron-chelating molecules termed siderophores. The Gram-negative bacteriumPseudomonas aeruginosacan utilize siderophores produced by other micro-organisms to facilitate iron uptake. Here we show that aP. aeruginosastrain deficient in siderophore production can use theVibrio choleraesiderophore vibriobactin as an iron source. In addition, we identified aP. aeruginosagene, PA4156 (fvbA), encoding a protein highly homologous to theV. choleraevibriobactin receptor (ViuA). AP. aeruginosamutant in the two endogenous siderophores (pyoverdine and pyochelin) and infvbAwas unable to utilize vibriobactin as an iron source. Additionally, preliminary analyses revealed the involvement of vibriobactin, Fur protein and an IclR-type regulator, FvbR (PA4157), infvbAregulation.
Stenotrophomonas maltophilia strains replicate and persist in the murine lung, but to significantly different degrees
Authors: Rouf Ruella , Karaba Sara M. , Dao Jenny , Cianciotto Nicholas P.
Published: May 2011

The environmental bacterium Stenotrophomonas maltophilia is increasingly described as a multidrug-resistant pathogen of humans, being associated with pneumonia, among other diseases. But the degree to which S. maltophilia is capable of replicating in a mammalian host has been an issue of controversy. Using a model of intranasal inoculation into adult A/J mice, we now document that S. maltophilia strain K279a, the clinical isolate of S. maltophilia whose complete genome sequence was recently determined, is in fact capable of replicating in lungs, displaying as much as a 10-fold increase in c.f.u. in the first 8 h of infection. Importantly, as few as 104 c.f.u. deposited into the A/J lung was sufficient to promote bacterial outgrowth. Bacterial replication in the lungs of the A/J mice was followed by elevations in pro-inflammatory cytokines and also promoted resistance to subsequent challenge. We also found that DBA/2 mice were permissive for S. maltophilia K279a replication, although the level of growth and persistence in these animals was less than it was in the A/J mice. In contrast, the BALB/c and C57BL/6 mouse strains were non-permissive for S. maltophilia K279a growth. Interestingly, when five additional clinical isolates were introduced into the A/J lung, marked differences in survival were observed, with some strains being much less infective than K279a and others being appreciably more infective. These data suggest that the presence of major virulence determinants is variable among clinical isolates. Overall, this study confirms the infectivity of S. maltophilia for the mammalian host, and illustrates how both host and bacterial factors affect the outcome of Stenotrophomonas infection.
Carboxypeptidase activity common to viridans group streptococci cleaves angiotensin I to angiotensin II: an activity homologous to angiotensin-converting enzyme (ACE)
Authors: Harty Derek W. S. , Hunter Neil
Published: May 2011

We have found that Streptococcus gordonii FSS2, an infective endocarditis (IE) isolate, expresses a dipeptidyl-carboxypeptidase with activity homologous to angiotensin-converting enzyme (ACE). The carboxypeptidase activity was purified to homogeneity as a complex/aggregate from a bacterial surface extract and was also active as a 165 kDa monomer. The specific activity for the carboxypeptidase activity was eightfold higher than that for recombinant human ACE. Selected ACE inhibitors, captopril, lisinopril and enalapril, did not inhibit the ACE activity. The carboxypeptidase also hydrolysed the Aα and Bβ-chains of human fibrinogen, which resulted in impaired fibrin formation by thrombin. The gene encoding ACE carboxypeptidase activity was sequenced and the inferred polypeptide product showed 99 % amino acid homology to SGO_0566, sgc, ‘challisin’ of S. gordonii CL1 Challis, and had no significant amino acid sequence homology to human ACE. Homologues of challisin ACE activity were commonly detected among the viridans group streptococci most often associated with IE.
The flavanone naringenin reduces the production of quorum sensing-controlled virulence factors in Pseudomonas aeruginosa PAO1
Authors: Vandeputte Olivier M. , Kiendrebeogo Martin , Rasamiravaka Tsiry , Stévigny Caroline , Duez Pierre , Rajaonson Sanda , Diallo Billo , Mol Adeline , Baucher Marie , El Jaziri Mondher
Published: May 2011

Preliminary screening of the Malagasy plantCombretum albiflorumfor compounds attenuating the production of quorum sensing (QS)-controlled virulence factors in bacteria led to the identification of active fractions containing flavonoids. In the present study, several flavonoids belonging to the flavone, flavanone, flavonol and chalcone structural groups were screened for their capacity to reduce the production of QS-controlled factors in the opportunistic pathogenPseudomonas aeruginosa(strain PAO1). Flavanones (i.e. naringenin, eriodictyol and taxifolin) significantly reduced the production of pyocyanin and elastase inP. aeruginosawithout affecting bacterial growth. Consistently, naringenin and taxifolin reduced the expression of several QS-controlled genes (i.e.lasI,lasR,rhlI,rhlR,lasA,lasB,phzA1andrhlA) inP. aeruginosaPAO1. Naringenin also dramatically reduced the production of the acylhomoserine lactonesN-(3-oxododecanoyl)-l-homoserine lactone (3-oxo-C12-HSL) andN-butanoyl-l-homoserine lactone (C4-HSL), which is driven by thelasIandrhlIgene products, respectively. In addition, using mutant strains deficient for autoinduction (ΔlasIand ΔrhlI) and LasR- and RhlR-based biosensors, it was shown that QS inhibition by naringenin not only is the consequence of a reduced production of autoinduction compounds but also results from a defect in the proper functioning of the RlhR–C4-HSL complex. Widely distributed in the plant kingdom, flavonoids are known for their numerous and determinant roles in plant physiology, plant development and in the success of plant–rhizobia interactions, but, as shown here, some of them also have a role as inhibitors of the virulence of pathogenic bacteria by interfering with QS mechanisms.
Extended telephone‐based continuing care for alcohol dependence: 24‐month outcomes and subgroup analyses
Authors: McKay James R. , Van Horn Deborah , Oslin David W. , Ivey Megan , Drapkin Michelle L. , Coviello Donna M. , Yu Qin , Lynch Kevin G.
Published: May 2011

Aims  To determine whether 18 months of telephone continuing care improves 24‐month outcomes for patients with alcohol dependence. Subgroup analyses were performed to identify patients who would benefit most from continuing care.

Design  Comparative effectiveness trial of continuing care that consisted of monitoring and feedback only (TM) or monitoring and feedback plus counseling (TMC). Patients were randomized to treatment as usual (TAU), TAU plus TM or TAU plus TMC, and followed quarterly for 24 months.

Setting  Publicly funded intensive out‐patient programs (IOP).

Participants  A total of 252 alcohol‐dependent patients (49% with current cocaine dependence) who completed 3 weeks of IOP.

Measurements  Percentage of days drinking, any heavy drinking and a composite good clinical outcome.

Findings  In the intent‐to‐treat sample, group differences in alcohol outcomes out to 18 months favoring TMC over TAU were no longer present in months 19–24. There was also a non‐significant trend for TMC to perform better than usual care on the good clinical outcome measure (60% vs. 46% good clinical outcome in months 19–24). Overall significant effects favoring TMC and TM over TAU were seen for women; and TMC was also superior to TAU for participants with social support for drinking, low readiness to change and prior alcohol treatments. Most of these effects were obtained on at least two of three outcomes. However, no effects remained significant at 24 months.

Conclusions  The benefits of an extended telephone‐based continuing care programme to treat alcohol dependence did not persist after the end of the intervention. A post‐hoc analysis suggested that women and individuals with social support for drinking, low readiness to change or prior alcohol treatments may benefit from the intervention.
Adoptive parents' suspicion of preadoption abuse of their adopted children and the use of support services
Authors: Ward B. W.
Published: May 2011

Background  Adopted children have a higher risk of developmental, mental, behavioural and social problems compared with non‐adopted children, and their use of postadoption support services is of interest. Little attention has been given to the impact of preadoption abuse on the use of these services, and therefore this study examines whether or not adoptive parents' suspicion of preadoption abuse has a significant impact on the use of support services by adopted children.

Methods  Data from the National Survey of Adoptive Parents, a US nationally representative survey of adopted children, were used to examine parents' suspicion of preadoption abuse and its effects on the use of postadoption support services by children aged 6–17 years (n= 1411). Statistical analyses were used to examine the relationship between suspected abuse and the use of support services while controlling for characteristics of the adopted child and adoptive parents/household.

Results  Seven out of 10 adopted children have used some form of support service, and a larger percentage of 6‐ to 12‐year‐old children suspected of experiencing preadoption abuse used a support service compared with children not suspected of experiencing abuse. Significant relationships existed between various types of suspected preadoption abuse and the use of different types of postadoption support services. These relationships may go unaccounted for when only examining if any preadoption abuse occurred, or if any support service was used.

Conclusions  The type of preadoption abuse suspected appears to play a modest role in predicting the type of postadoption support services used by an adopted child. Giving further attention to understanding the relationship between different types of preadoption abuse and types of postadoption support services may help better understand the problems and difficulties experienced by adopted children.
Exploring nursing staff’s attitudes and use of music for older people with dementia in long‐term care facilities
Authors: Sung Huei‐Chuan , Lee Wen‐Li , Chang Shu‐Min , Smith Graeme D
Published: May 2011

Aims.  This study aimed to explore nursing staff’s attitudes and use of music for older people with dementia in long‐term care facilities.

Background.  Music has shown positive outcomes in managing behavioural symptoms of older people with dementia. Older people living in long‐term care facilities often do not have access to trained music therapists. Nursing staff provide the majority of direct care for institutionalised older people with dementia, therefore, will be the most appropriate personnel to learn and implement music therapy for those with dementia. To date, no studies have explored nursing staff’s attitudes and use of music for those with dementia.

Design.  A cross‐sectional research design was used.

Methods.  A convenience sample of 285 nursing staff caring for those with dementia in long‐term care facilities in Taiwan were recruited. Participants received a self‐administered questionnaire consisted of items exploring nursing staff’s attitude and use of music for those with dementia. A total of 214 participants completed the questionnaires, giving a response rate of 75·1%.

Results.  Most nursing staff held positive attitudes towards use of music for older people with dementia (mean = 84·89, range 23–115), but only 30·6% (n = 66) had used music for those with dementia in practice. The majority perceived that they had limited knowledge and skills about use of music (72·9%). Over half of the participants reported that they lacked resources and time to implement music therapy in practice.

Conclusions.  Nursing staff need more formal training to use music for those with dementia. Nursing staff can be the suitable personnel to learn easily and implement music therapy as a part of routine activity programmes for those with dementia.

Relevance to clinical practice.  Appropriately trained nursing staff in long‐term care facilities who use music therapy may help improve the mental health of older people with dementia.
Factors influencing iron nutrition among one‐year‐old healthy children in Sweden
Authors: Bramhagen Ann‐Cathrine , Svahn Johan , Hallström Inger , Axelsson Irene
Published: May 2011

Aims and objectives. To describe possible social, nutritional and biological factors influencing iron intake and iron status among healthy one‐year‐old children in southern Sweden.

Background. Iron deficiency is one of the most important nutritional disorders and increases the risk of delayed mental and motor development. Children are at risk because of rapid growth, which entails relatively high requirements of iron.

Design. A prospective study using survey methods.

Method. Randomly selected one‐year‐old children (n = 90) and their parents participated. Parents answered a questionnaire enquiring about demographic data and the child’s feeding and health during the first year. The child’s total food intake and blood samples (haemoglobin, mean corpuscular volume, S‐ferritin and transferring receptor) were obtained.

Results. Twenty‐seven per cent of the children had an iron intake below the Nordic Nutrition Recommendations of 8 mg/day (NNR 2004). Follow‐on formula and iron‐fortified porridge contributed to 64% of the child’s total iron intake. Partial breastfeeding and low maternal education correlated negatively with iron intake from complementary food. In total, 10·3% (n = 9) of the children were found to be iron‐depleted (S‐ferritin ≤12 μg/l), and 2·3% (n = 2) had iron deficiency with or without anaemia (Hb ≤100 g/l).

Conclusions. One‐year‐old children in Sweden may be at risk of developing iron deficiency, but information about iron‐rich food can improve iron status.

Relevance to clinical practice. Knowledge about factors influencing children’s iron intake and iron status may improve the nutritional advice and education from the Child Health Services to prevent or detect iron deficiency.
PIPKs are essential for rhizoid elongation and caulonemal cell development in the moss Physcomitrella patens
Authors: Saavedra Laura , Balbi Virginia , Lerche Jennifer , Mikami Koji , Heilmann Ingo , Sommarin Marianne
Published: May 2011

PtdIns‐4,5‐bisphosphate is a lipid messenger of eukaryotic cells that plays a critical role in processes such as cytoskeleton organization, intracellular vesicular trafficking, secretion, cell motility, regulation of ion channels and nuclear signalling pathways. The enzymes responsible for the synthesis of PtdIns(4,5)P2 are phosphatidylinositol phosphate kinases (PIPKs). The moss Physcomitrella patens contains two PIPKs, PpPIPK1 and PpPIPK2. To study their physiological role, both genes were disrupted by targeted homologous recombination and as a result mutant plants with lower PtdIns(4,5)P2 levels were obtained. A strong phenotype for pipk1, but not for pipk2 single knockout lines, was obtained. The pipk1 knockout lines were impaired in rhizoid and caulonemal cell elongation, whereas pipk1‐2 double knockout lines showed dramatic defects in protonemal and gametophore morphology manifested by the absence of rapidly elongating caulonemal cells in the protonemal tissue, leafy gametophores with very short rhizoids, and loss of sporophyte production. pipk1 complemented by overexpression of PpPIPK1 fully restored the wild‐type phenotype whereas overexpression of the inactive PpPIPK1E885A did not. Overexpression of PpPIPK2 in the pipk1‐2 double knockout did not restore the wild‐type phenotype demonstrating that PpPIPK1 and PpPIPK2 are not functionally redundant. In vivo imaging of the cytoskeleton network revealed that the shortened caulonemal cells in the pipk1 mutants was the result of the absence of the apicobasal gradient of cortical F‐actin cables normally observed in wild‐type caulonemal cells. Our data indicate that both PpPIPKs play a crucial role in the development of the moss P. patens, and particularly in the regulation of tip growth.
Phylogenetic variation in glycosidases and glycanases acting on plant cell wall polysaccharides, and the detection of transglycosidase and trans‐β‐xylanase activities
Authors: Franková Lenka , Fry Stephen C.
Published: May 2011

Wall polysaccharide chemistry varies phylogenetically, suggesting a need for variation in wall enzymes. Although plants possess the genes for numerous putative enzymes acting on wall carbohydrates, the activities of the encoded proteins often remain conjectural. To explore phylogenetic differences in demonstrable enzyme activities, we extracted proteins from 57 rapidly growing plant organs with three extractants, and assayed their ability to act on six oligosaccharides ‘modelling’ selected cell‐wall polysaccharides. Based on reaction products, we successfully distinguished exo‐ and endo‐hydrolases and found high taxonomic variation in all hydrolases screened: β‐d‐xylosidase, endo‐(1→4)‐β‐d‐xylanase, β‐d‐mannosidase, endo‐(1→4)‐β‐d‐mannanase, α‐d‐xylosidase, β‐d‐galactosidase, α‐l‐arabinosidase and α‐l‐fucosidase. The results, as GHATAbase, a searchable compendium in Excel format, also provide a compilation for selecting rich sources of enzymes acting on wall carbohydrates. Four of the hydrolases were accompanied, sometimes exceeded, by transglycosylase activities, generating products larger than the substrate. For example, during β‐xylosidase assays on (1→4)‐β‐d‐xylohexaose (Xyl6), Marchantia, Selaginella and Equisetum extracts gave negligible free xylose but approximately equimolar Xyl5 and Xyl7, indicating trans‐β‐xylosidase activity, also found in onion, cereals, legumes and rape. The yield of Xyl9 often exceeded that of Xyl7–8, indicating that β‐xylanase was accompanied by an endotransglycosylase activity, here called trans‐β‐xylanase, catalysing the reaction 2Xyl6→ Xyl3 + Xyl9. Similar evidence also revealed trans‐α‐xylosidase, trans‐α‐arabinosidase and trans‐α‐arabinanase activities acting on xyloglucan oligosaccharides and (1→5)‐α‐l‐arabino‐oligosaccharides. In conclusion, diverse plants differ dramatically in extractable enzymes acting on wall carbohydrate, reflecting differences in wall polysaccharide composition. Besides glycosidase and glycanase activities, five new transglycosylase activities were detected. We propose that such activities function in the assembly and re‐structuring of the wall matrix.
Large‐scale detection of rare variants via pooled multiplexed next‐generation sequencing: towards next‐generation Ecotilling
Authors: Marroni Fabio , Pinosio Sara , Di Centa Eleonora , Jurman Irena , Boerjan Wout , Felice Nicoletta , Cattonaro Federica , Morgante Michele
Published: May 2011

Common variants, such as those identified by genome‐wide association scans, explain only a small proportion of trait variation. Growing evidence suggests that rare functional variants, which are usually missed by genome‐wide association scans, play an important role in determining the phenotype. We used pooled multiplexed next‐generation sequencing and a customized analysis workflow to detect mutations in five candidate genes for lignin biosynthesis in 768 pooled Populus nigra accessions. We identified a total of 36 non‐synonymous single nucleotide polymorphisms, one of which causes a premature stop codon. The most common variant was estimated to be present in 672 of the 1536 tested chromosomes, while the rarest was estimated to occur only once in 1536 chromosomes. Comparison with individual Sanger sequencing in a selected sub‐sample confirmed that variants are identified with high sensitivity and specificity, and that the variant frequency was estimated accurately. This proposed method for identification of rare polymorphisms allows accurate detection of variation in many individuals, and is cost‐effective compared to individual sequencing.
Additive inheritance of histone modifications in Arabidopsis thaliana intra‐specific hybrids
Authors: Moghaddam Ali M. Banaei , Roudier Francois , Seifert Michael , Bérard Caroline , Magniette Marie‐Laure M. , Ashtiyani Raheleh Karimi , Houben Andreas , Colot Vincent , Mette Michael F.
Published: May 2011

Plant genomes are earmarked with defined patterns of chromatin marks. Little is known about the stability of these epigenomes when related, but distinct genomes are brought together by intra‐species hybridization. Arabidopsis thaliana accessions and their reciprocal hybrids were used as a model system to investigate the dynamics of histone modification patterns. The genome‐wide distribution of histone modifications H3K4me2 and H3K27me3 in the inbred parental accessions Col‐0, C24 and Cvi and their hybrid offspring was compared by chromatin immunoprecipitation in combination with genome tiling array hybridization. The analysis revealed that, in addition to DNA sequence polymorphisms, chromatin modification variations exist among accessions of A. thaliana. The range of these variations was higher for H3K27me3 (typically a repressive mark) than for H3K4me2 (typically an active mark). H3K4me2 and H3K27me3 were rather stable in response to intra‐species hybridization, with mainly additive inheritance in hybrid offspring. In conclusion, intra‐species hybridization does not result in gross changes to chromatin modifications.