bluuebunny/crossref_metadata_2025 huggingface dataset:
A role for microRNAs in the Drosophila circadian clock
Authors: Kadener Sebastian , Menet Jerome S. , Sugino Ken , Horwich Michael D. , Weissbein Uri , Nawathean Pipat , Vagin Vasia V. , Zamore Phillip D. , Nelson Sacha B. , Rosbash Michael
Published: August 2009

Little is known about the contribution of translational control to circadian rhythms. To address this issue and in particular translational control by microRNAs (miRNAs), we knocked down the miRNA biogenesis pathway in Drosophila circadian tissues. In combination with an increase in circadian-mediated transcription, this severely affected Drosophila behavioral rhythms, indicating that miRNAs function in circadian timekeeping. To identify miRNA–mRNA pairs important for this regulation, immunoprecipitation of AGO1 followed by microarray analysis identified mRNAs under miRNA-mediated control. They included three core clock mRNAs—clock (clk), vrille (vri), and clockworkorange (cwo). To identify miRNAs involved in circadian timekeeping, we exploited circadian cell-specific inhibition of the miRNA biogenesis pathway followed by tiling array analysis. This approach identified miRNAs expressed in fly head circadian tissue. Behavioral and molecular experiments show that one of these miRNAs, the developmental regulator bantam, has a role in the core circadian pacemaker. S2 cell biochemical experiments indicate that bantam regulates the translation of clk through an association with three target sites located within the clk 3′ untranslated region (UTR). Moreover, clk transgenes harboring mutated bantam sites in their 3′ UTRs rescue rhythms of clk mutant flies much less well than wild-type CLK transgenes.
Singapore Genome Variation Project: A haplotype map of three Southeast Asian populations
Authors: Teo Yik-Ying , Sim Xueling , Ong Rick T.H. , Tan Adrian K.S. , Chen Jieming , Tantoso Erwin , Small Kerrin S. , Ku Chee-Seng , Lee Edmund J.D. , Seielstad Mark , Chia Kee-Seng
Published: August 2009

The Singapore Genome Variation Project (SGVP) provides a publicly available resource of 1.6 million single nucleotide polymorphisms (SNPs) genotyped in 268 individuals from the Chinese, Malay, and Indian population groups in Southeast Asia. This online database catalogs information and summaries on genotype and phased haplotype data, including allele frequencies, assessment of linkage disequilibrium (LD), and recombination rates in a format similar to the International HapMap Project. Here, we introduce this resource and describe the analysis of human genomic variation upon agglomerating data from the HapMap and the Human Genome Diversity Project, providing useful insights into the population structure of the three major population groups in Asia. In addition, this resource also surveyed across the genome for variation in regional patterns of LD between the HapMap and SGVP populations, and for signatures of positive natural selection using two well-established metrics: iHS and XP-EHH. The raw and processed genetic data, together with all population genetic summaries, are publicly available for download and browsing through a web browser modeled with the Generic Genome Browser.
Extracellular DNA Is Required for Root Tip Resistance to Fungal Infection
Authors: Wen Fushi , White Gerard J. , VanEtten Hans D. , Xiong Zhongguo , Hawes Martha C.
Published: August 2009

Plant defense involves a complex array of biochemical interactions, many of which occur in the extracellular environment. The apical 1- to 2-mm root tip housing apical and root cap meristems is resistant to infection by most pathogens, so growth and gravity sensing often proceed normally even when other sites on the root are invaded. The mechanism of this resistance is unknown but appears to involve a mucilaginous matrix or “slime” composed of proteins, polysaccharides, and detached living cells called “border cells.” Here, we report that extracellular DNA (exDNA) is a component of root cap slime and that exDNA degradation during inoculation by a fungal pathogen results in loss of root tip resistance to infection. Most root tips (>95%) escape infection even when immersed in inoculum from the root-rotting pathogen Nectria haematococca. By contrast, 100% of inoculated root tips treated with DNase I developed necrosis. Treatment with BAL31, an exonuclease that digests DNA more slowly than DNase I, also resulted in increased root tip infection, but the onset of infection was delayed. Control root tips or fungal spores treated with nuclease alone exhibited normal morphology and growth. Pea (Pisum sativum) root tips incubated with [32P]dCTP during a 1-h period when no cell death occurs yielded root cap slime containing 32P-labeled exDNA. Our results suggest that exDNA is a previously unrecognized component of plant defense, an observation that is in accordance with the recent discovery that exDNA from white blood cells plays a key role in the vertebrate immune response against microbial pathogens.
SAUR39, a Small Auxin-Up RNA Gene, Acts as a Negative Regulator of Auxin Synthesis and Transport in Rice
Authors: Kant Surya , Bi Yong-Mei , Zhu Tong , Rothstein Steven J.
Published: August 2009

The phytohormone auxin plays a critical role for plant growth by regulating the expression of a set of genes. One large auxin-responsive gene family of this type is the small auxin-up RNA (SAUR) genes, although their function is largely unknown. The expression of the rice (Oryza sativa) SAUR39 gene showed rapid induction by transient change in different environmental factors, including auxin, nitrogen, salinity, cytokinin, and anoxia. Transgenic rice plants overexpressing the SAUR39 gene resulted in lower shoot and root growth, altered shoot morphology, smaller vascular tissue, and lower yield compared with wild-type plants. The SAUR39 gene was expressed at higher levels in older leaves, unlike auxin biosynthesis, which occurs largely in the meristematic region. The transgenic plants had a lower auxin level and a reduced polar auxin transport as well as the down-regulation of some putative auxin biosynthesis and transporter genes. Biochemical analysis also revealed that transgenic plants had lower chlorophyll content, higher levels of anthocyanin, abscisic acid, sugar, and starch, and faster leaf senescence compared with wild-type plants at the vegetative stage. Most of these phenomena have been shown to be negatively correlated with auxin level and transport. Transcript profiling revealed that metabolic perturbations in overexpresser plants were largely due to transcriptional changes of genes involved in photosynthesis, senescence, chlorophyll production, anthocyanin accumulation, sugar synthesis, and transport. The lower growth and yield of overexpresser plants was largely recovered by exogenous auxin application. Taken together, the results suggest that SAUR39 acts as a negative regulator for auxin synthesis and transport.
At4g24160, a Soluble Acyl-Coenzyme A-Dependent Lysophosphatidic Acid Acyltransferase
Authors: Ghosh Ananda K. , Chauhan Neha , Rajakumari Sona , Daum Guenther , Rajasekharan Ram
Published: August 2009

Human CGI-58 (for comparative gene identification-58) and YLR099c, encoding Ict1p in Saccharomyces cerevisiae, have recently been identified as acyl-CoA-dependent lysophosphatidic acid acyltransferases. Sequence database searches for CGI-58 like proteins in Arabidopsis (Arabidopsis thaliana) revealed 24 proteins with At4g24160, a member of the α/β-hydrolase family of proteins being the closest homolog. At4g24160 contains three motifs that are conserved across the plant species: a GXSXG lipase motif, a HX4D acyltransferase motif, and V(X)3HGF, a probable lipid binding motif. Dendrogram analysis of yeast ICT1, CGI-58, and At4g24160 placed these three polypeptides in the same group. Here, we describe and characterize At4g24160 as, to our knowledge, the first soluble lysophosphatidic acid acyltransferase in plants. A lipidomics approach revealed that At4g24160 has additional triacylglycerol lipase and phosphatidylcholine hydrolyzing enzymatic activities. These data establish At4g24160, a protein with a previously unknown function, as an enzyme that might play a pivotal role in maintaining the lipid homeostasis in plants by regulating both phospholipid and neutral lipid levels.
Hydrogen Production in Chlamydomonas: Photosystem II-Dependent and -Independent Pathways Differ in Their Requirement for Starch Metabolism
Authors: Chochois Vincent , Dauvillée David , Beyly Audrey , Tolleter Dimitri , Cuiné Stéphan , Timpano Hélène , Ball Steven , Cournac Laurent , Peltier Gilles
Published: August 2009

Under sulfur deprivation conditions, the green alga Chlamydomonas reinhardtii produces hydrogen in the light in a sustainable manner thanks to the contribution of two pathways, direct and indirect. In the direct pathway, photosystem II (PSII) supplies electrons to hydrogenase through the photosynthetic electron transport chain, while in the indirect pathway, hydrogen is produced in the absence of PSII through a photosystem I-dependent process. Starch metabolism has been proposed to contribute to both pathways by feeding respiration and maintaining anoxia during the direct pathway and by supplying reductants to the plastoquinone pool during the indirect pathway. At variance with this scheme, we report that a mutant lacking starch (defective for sta6) produces similar hydrogen amounts as the parental strain in conditions of sulfur deprivation. However, when PSII is inhibited by 3-(3,4-dichlorophenyl)-1,1-dimethylurea, conditions where hydrogen is produced by the indirect pathway, hydrogen production is strongly reduced in the starch-deficient mutant. We conclude that starch breakdown contributes to the indirect pathway by feeding electrons to the plastoquinone pool but is dispensable for operation of the direct pathway that prevails in the absence of DCMU. While hydrogenase induction was strongly impaired in the starch-deficient mutant under dark anaerobic conditions, wild-type-like induction was observed in the light. Because this light-driven hydrogenase induction is DCMU insensitive and strongly inhibited by carbonyl cyanide-p-trifluoromethoxyphenylhydrazone or 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone, we conclude that this process is regulated by the proton gradient generated by cyclic electron flow around PSI.
A Pair of Allelic WRKY Genes Play Opposite Roles in Rice-Bacteria Interactions
Authors: Tao Zeng , Liu Hongbo , Qiu Deyun , Zhou Yan , Li Xianghua , Xu Caiguo , Wang Shiping
Published: August 2009

Although allelic diversity of genes has been reported to play important roles in different physiological processes, information on allelic diversity of defense-responsive genes in host-pathogen interactions is limited. Here, we report that a pair of allelic genes, OsWRKY45-1 and OsWRKY45-2, which encode proteins with a 10-amino acid difference, play opposite roles in rice (Oryza sativa) resistance against bacterial pathogens. Bacterial blight caused by Xanthomonas  oryzae pv oryzae (Xoo), bacterial streak caused by Xanthomonas oryzae pv oryzicola (Xoc), and fungal blast caused by Magnaporthe grisea are devastating diseases of rice worldwide. OsWRKY45-1-overexpressing plants showed increased susceptibility and OsWRKY45-1-knockout plants showed enhanced resistance to Xoo and Xoc. In contrast, OsWRKY45-2-overexpressing plants showed enhanced resistance and OsWRKY45-2-suppressing plants showed increased susceptibility to Xoo and Xoc. Interestingly, both OsWRKY45-1- and OsWRKY45-2-overexpressing plants showed enhanced resistance to M. grisea. OsWRKY45-1-regulated Xoo resistance was accompanied by increased accumulation of salicylic acid and jasmonic acid and induced expression of a subset of defense-responsive genes, while OsWRKY45-2-regulated Xoo resistance was accompanied by increased accumulation of jasmonic acid but not salicylic acid and induced expression of another subset of defense-responsive genes. These results suggest that both OsWRKY45-1 and OsWRKY45-2 are positive regulators in rice resistance against M. grisea, but the former is a negative regulator and the latter is a positive regulator in rice resistance against Xoo and Xoc. The opposite roles of the two allelic genes in rice-Xoo interaction appear to be due to their mediation of different defense signaling pathways.
Biochemical and Structural Studies of the Large Ycf4-Photosystem I Assembly Complex of the Green AlgaChlamydomonas reinhardtii
Authors: Ozawa Shin-ichiro , Nield Jon , Terao Akihiro , Stauber Einar J. , Hippler Michael , Koike Hiroyuki , Rochaix Jean-David , Takahashi Yuichiro
Published: August 2009

Ycf4 is a thylakoid protein essential for the accumulation of photosystem I (PSI) in Chlamydomonas reinhardtii. Here, a tandem affinity purification tagged Ycf4 was used to purify a stable Ycf4-containing complex of >1500 kD. This complex also contained the opsin-related COP2 and the PSI subunits PsaA, PsaB, PsaC, PsaD, PsaE, and PsaF, as identified by mass spectrometry (liquid chromatography–tandem mass spectrometry) and immunoblotting. Almost all Ycf4 and COP2 in wild-type cells copurified by sucrose gradient ultracentrifugation and subsequent ion exchange column chromatography, indicating the intimate and exclusive association of Ycf4 and COP2. Electron microscopy revealed that the largest structures in the purified preparation measure 285 × 185 Å; these particles may represent several large oligomeric states. Pulse-chase protein labeling revealed that the PSI polypeptides associated with the Ycf4-containing complex are newly synthesized and partially assembled as a pigment-containing subcomplex. These results indicate that the Ycf4 complex may act as a scaffold for PSI assembly. A decrease in COP2 to 10% of wild-type levels by RNA interference increased the salt sensitivity of the Ycf4 complex stability but did not affect the accumulation of PSI, suggesting that COP2 is not essential for PSI assembly.
Control of Nuclear and Nucleolar Localization of Nuclear Inclusion Protein a of Picorna-LikePotato virus AinNicotianaSpecies
Authors: Rajamäki Minna-Liisa , Valkonen Jari P.T.
Published: August 2009

The multifunctional nuclear inclusion protein a (NIa) of potyviruses (genus Potyvirus; Potyviridae) accumulates in the nucleus of virus-infected cells for unknown reasons. In this study, two regions in the viral genome-linked protein (VPg) domain of NIa in Potato virus A (PVA) were found to constitute nuclear and nucleolar localization signals (NLS) in plant cells (Nicotiana spp). Amino acid substitutions in both NLS I (residues 4 to 9) and NLS II (residues 41 to 50) prevented nuclear localization, whereas mutations in either single NLS did not. Mutations in either NLS, however, prevented nucleolar localization and prevented or diminished virus replication in protoplasts, accumulation in infected plant tissues, and/or systemic movement in plants. One NLS mutant was partially complemented by the wild-type VPg expressed in transgenic plants. Furthermore, NLS I controlled NIa accumulation in Cajal bodies. The VPg domain interacted with fibrillarin, a nucleolar protein, and depletion of fibrillarin reduced PVA accumulation. Overexpression of VPg in leaf tissues interfered with cosuppression of gene expression (i.e., RNA silencing), whereas NLS I and NLS II mutants, which exhibited reduced nuclear and nucleolar localization, showed no such activity. These results demonstrate that some of the most essential viral functions required for completion of the infection cycle are tightly linked to regulation of the NIa nuclear and nucleolar localization.
Nuclear Pore Complex Component MOS7/Nup88 Is Required for Innate Immunity and Nuclear Accumulation of Defense Regulators inArabidopsis
Authors: Cheng Yu Ti , Germain Hugo , Wiermer Marcel , Bi Dongling , Xu Fang , García Ana V. , Wirthmueller Lennart , Després Charles , Parker Jane E. , Zhang Yuelin , Li Xin
Published: August 2009

Plant immune responses depend on dynamic signaling events across the nuclear envelope through nuclear pores. Nuclear accumulation of certain resistance (R) proteins and downstream signal transducers are critical for their functions, but it is not understood how these processes are controlled. Here, we report the identification, cloning, and analysis of Arabidopsis thaliana  modifier of snc1,7 (mos7-1), a partial loss-of-function mutation that suppresses immune responses conditioned by the autoactivated R protein snc1 (for suppressor of npr1-1, constitutive 1). mos7-1 single mutant plants exhibit defects in basal and R protein–mediated immunity and in systemic acquired resistance but do not display obvious pleiotropic defects in development, salt tolerance, or plant hormone responses. MOS7 is homologous to human and Drosophila melanogaster nucleoporin Nup88 and resides at the nuclear envelope. In animals, Nup88 attenuates nuclear export of activated NF-κB transcription factors, resulting in nuclear accumulation of NF-κB. Our analysis shows that nuclear accumulation of snc1 and the defense signaling components Enhanced Disease Susceptibility 1 and Nonexpresser of PR genes 1 is significantly reduced in mos7-1 plants, while nuclear retention of other tested proteins is unaffected. The data suggest that specifically modulating the nuclear concentrations of certain defense proteins regulates defense outputs.
Optimal Energy R&D Portfolio Investments in Response to a Carbon Tax
Authors: Shittu Ekundayo , Baker Erin
Published: August 2009

In this paper, we deal with a very timely issue-R&D strategies needed for compliance with a climate policy in an economically optimal way. We provide interesting insights into the composition of R&D portfolios across the main mitigation options for decision makers and policy makers. We address the optimal R&D investment response of a decision maker or an engineering manager-at the firm level with a portfolio of alternative technologies-to a rising carbon tax. Understanding the optimal allocation of investments in these technologies is crucial because like most economic resources, there is a limitation on the investment capabilities of a firm to undertake these innovative efforts. In addition, environmental R&D spending is irreversible and investment decisions made today have multiperiod consequences on the energy technologies landscape. Thus, we explore the reaction of a firm's optimal investment in an energy R&D portfolio comprising four different technologies to increases in a future carbon tax. We find that investment allocation depends on the elasticity of substitution between fossil and nonfossil energy inputs, and the relative costs and efficacy of the R&D programs; and that overall investment tends to decrease in risk depending on firm flexibility and specifications.
On Bandwidth Tiered Service
Authors: Rouskas George N. , Baradwaj Nikhil
Published: August 2009

Many network operators offer some type of tiered service, in which users may select only from a small set of service levels (tiers). Such a service has the potential to simplify a wide range of core network functions, allowing the providers to scale their operations efficiently. In this work, we study a number of problem variants related to service tier selection. Our contributions include: (1) a faster algorithm for obtaining optimal service tiers; (2) a new formulation and optimal algorithm to optimize jointly the number and magnitude of each service tier; and (3) the concept of ??TDM emulation?? in which all service tiers are multiples of the same (software-configurable) bandwidth unit, and a suite of algorithms to select jointly the basic unit and service tiers. Our work provides a systematic framework for reasoning about and tackling algorithmically the general problem of service tier selection, and has applications to a number of networking contexts, including access networks (e.g., determining the tiers for ADSL, cable modem networks or PONs) and core networks (e.g., LSP sizing for MPLS networks).
The phylogeny of the Pantropical genus Arrhipis Bonvouloir (Coleoptera, Eucnemidae)
Authors: Brüstle Lena , Alaruikka Diane , Muona Jyrki , Teräväinen Marianna
Published: August 2009

The phylogeny of the genus Arrhipis Bonvouloir (Coleoptera, Eucnemidae) is clarified with a cladistic analysis based on five molecular markers and morphology. Sixteen species from Africa, America, Asia, and Australia are included in the analysis. Two separate Asian clades are recovered, one of them being the sister group to a clade with the American and African species. With the exception of the continental south‐east Asian species, all Gondwanan regions have monophyletic faunas. According to the present data, the continental south‐east Asian fauna comprises two monophyletic groups, one of which is the sister group to African and American species. Vicariance seems to be the logical explanation for the distribution of these lignicolous beetles.

© The Willi Hennig Society 2009.
Risk factors of scabies in psychiatric and long‐term care hospitals: A nationwide mail‐in survey in Japan
Authors: MAKIGAMI Kuniko , OHTAKI Noriko , ISHII Norihisa , YASUMURA Seiji
Published: August 2009

Despite the commonness of scabies in Japanese institutional settings, the nationwide prevalence of scabies has not been elucidated. This study was conducted to assess the prevalence of scabies and control measures in Japanese hospitals. A questionnaire on scabies epidemiology (e.g. number of patients and onsets of outbreak) and preventive measures were sent to psychiatric hospitals and long‐term care hospitals nationwide (n = 1795) in January 2005. Seven hundred and forty‐one hospitals responded (41.3%). Three hundred and thirty‐three (44.9%) respondent hospitals had one or more scabies cases in 2004. Among 159 hospitals that had experienced scabies outbreak, only 32 of them reported cases of crusted scabies. Multivariate regression analysis showed that hospitals had a greater number of beds, and that acute‐ and long‐term care wards were more likely to experience scabies onsets. Hospitals that compiled their infection control manuals on scabies, treated suspicious patients with scabicides without confirmed diagnosis, and performed skin checkup of inpatients were more likely to experience scabies cases. Infection control personnel should be aware that unrecognized crusted scabies can cause outbreaks. Higher patient turnover is a risk factor for scabies introduction into a hospital. Preventive measures against scabies, such as patient screening at admission and treating all suspicious patients without confirmed diagnosis, were not effective to avoid scabies introduction.
Enhanced immune response to pneumococcal infection in malnourished mice nasally treated with heat‐killed Lactobacillus casei
Authors: Villena Julio , Barbieri Natalia , Salva Susana , Herrera Matías , Alvarez Susana
Published: August 2009

The present study analyzed whether nasal administration of viable and non‐viable Lactobacillus casei CRL 431 to immunocompromised mice was capable of increasing resistance against Streptococcus pneumoniae. Weaned mice were malnourished after consuming a PFD for 21 days. Malnourished mice were fed a BCD for 7 days or BCD for 7 days with viable or non‐viable L. casei nasal treatments on day 6 and day 7 (BCD+LcV and BCD+LcN, respectively). The MNC group received PFD whereas the WNC mice consumed BCD. MNC mice showed greater lung colonization, more severe lung injuries, impaired leukocyte recruitment and reduced antibodies and cytokine production when compared with WNC mice. Administration of L. casei increased the resistance of malnourished mice to the infection. Both BCD+LcV and BCD+LcN treatments prevented the dissemination of the pathogen to the blood and induced its lung clearance. BCD+LcV or BCD+LcN groups showed improved production of TNF‐α and activity of phagocytes in the respiratory tract, an effect that was not observed in the BCD control group. In addition, IL‐4 and IL‐10 were significantly increased in BCD+LcV and BCD+LcN groups, which correlated with the increase in the levels of specific respiratory IgA. The nasal treatments with L. casei were also effective at stimulating the production of specific IgG at both the systemic and the respiratory levels. The comparative study between the viable and the non‐viable bacteria demonstrated that viability would be an important factor to achieve maximum protective effects. However, the results from this study suggest that heat‐killed lactic acid bacteria are also effective in the immunomodulation of the systemic and respiratory immune system.
Serum antibody responses to Wolbachia surface protein in patients with human lymphatic filariasis
Authors: Shiny Chandanapurath , Krushna Nagampalli S.A. , Archana Bairavasundaram , Farzana Begum , Narayanan Rangarajan B.
Published: August 2009

Wolbachia surface protein (WSP), which is the most abundantly expressed protein of Wolbachia from the human filarial parasite Brugia malayi, was chosen for the present study. B‐cell epitope prediction of the WSP protein sequence indicates a high antigenicity, surface probability and hydrophilicity by DNA STAR software analysis. ProPred analysis suggests the presence of HLA class II binding regions in the WSP protein that contribute to T‐cell responses and isotype reactivity. In order to validate these findings, the gene coding for endosymbiont WSP was PCR‐amplified from the genomic DNA of the human filarial parasite Brugia malayi and cloned in T‐7 expression vector pRSET‐A. Western blot and ELISA at the total IgG level with recombiant WSP indicated a significantly elevated reactivity in CP compared to MF, EN and NEN individuals. Isotype ELISA also suggested an elevated reactivity in CP patients at the IgG1 level. In contrast, WSP‐specific IgG4 levels were found to be elevated in MF patients compared to CP and EN. Besides this, WSP‐specific IgE levels indicated an elevated reactivity in CP and MF patients compared to normals. Observations from ELISA supported the in silico predictions that indicate the presence of B‐ and T‐cell epitopes. Hence, a combinatorial approach of in silico predictions and wet‐lab studies provides interesting insights into the role of Wolbachia proteins in filarial pathogenesis.
A single dose of intravenous esomeprazole decreases gastric secretion in healthy volunteers
Authors: NICHITA C. , ABDOU A. E.‐W. , MAERTEN P. , HERRANZ M. , MOURET N. , THALMANN C. , MICHETTI P. F. , DORTA G.
Published: August 2009

Background  Data suggest that esomeprazole decreases gastric secretion.

Aims  To assess the effect of a single i.v. esomeprazole dose on gastric secretion volume 3 h after drug administration, as a primary endpoint, and to evaluate, as secondary endpoints, the reduction 1 and 5 h after dosing; time when the gastric pH was <2.5 and esomeprazole’s safety.

Methods  In all, 23 healthy Helicobacter pylori‐negative volunteers (10 men, 13 women, mean age 28.2 ± 6) participated in this single‐centre, randomized, double‐blind, placebo‐controlled, 2‐way, single‐dose cross‐over study. In different sessions, volunteers received i.v. either esomeprazole 40 mg or placebo. An inserted double‐lumen nasogastric tube perfused and aspirated gastric liquid. Mechanical fractioned aspiration measured secretion volume; aliquot spectrophotometry assessed gastric secretion volume lost to the duodenum.

Results  Three hours post‐i.v. esomeprazole, average gastric secretion decreased by 77.6% (vs. baseline) compared to placebo. Values 1 and 5 h after dosing were 73.5% and 74.5%. Five hours after esomeprazole, the gastric pH was <2.5 3.9% of the time and 73.3% after placebo (P < 0.002). Esomeprazole was well‐tolerated. No serious adverse events occurred.

Conclusions  Intravenous esomeprazole decreases gastric secretions. The potential clinical impact in averting bronchoaspiration during anaesthesia induction and in intensive care patients should be investigated in further studies.
Long‐term process evaluation of a school‐based programme for overweight prevention
Authors: Muckelbauer R. , Libuda L. , Clausen K. , Kersting M.
Published: August 2009

Background  The epidemic increase in childhood overweight demands effective and also feasible prevention programmes. A school‐based environmental and educational intervention focusing on the promotion of water consumption was found to be effective for overweight prevention in children. Process evaluation and long‐term surveillance are necessary to evaluate the feasibility and sustainability of the intervention programme in a school setting.

Methods  Process evaluation was conducted during the intervention period (one school year) and a 19‐month follow‐up after the intervention trial on the prevention of overweight in 17 elementary schools. Data were collected through measuring the water flow of water fountains installed in schools, and questionnaires and interviews were administered to teachers and headmasters of intervention schools. Main outcomes were implementation of the intervention components, behavioural modification of the children concerning water consumption, and teacher and headmaster attitudes towards the intervention.

Results  Eleven out of 17 intervention schools maintained the water fountains until 19‐month follow‐up. The mean water flow of the fountains decreased initially, but remained stable after the during the follow‐up period. The implementation rate of the educational units by teachers varied between the units from 13% to 84%. Teachers graded the overall concept of the intervention as good, continuously during the intervention and follow‐up period. The majority of teachers organized the water supply of the fountains on the class level during the intervention period but not during the follow‐up.

Conclusions  The long‐term process evaluation showed that the combined educational and environmental intervention has potential for sustained modifications in the beverage consumption habits of children. It also identified barriers and promoting factors of a sustainable and feasible implementation of the preventive programme in a school setting.
A framework of children's hand skills for assessment and intervention
Authors: Chien C‐W. , Brown T. , McDonald R.
Published: August 2009

Background  Hand skill development or mastery has a huge influence on children's early development and participation in everyday activities. Assessment of difficulties with children's hand skills typically involves a systematic process considering all potential factors that may impact on hand skills. This helps identify key hand skill difficulties and select specific interventions that are relevant to the individual child. This paper describes the development of the Children's Hand Skills Framework (CHSF) that can be used as a conceptual guide to analyse and describe children's hand skills in the assessment and intervention process.

Methods  A comprehensive literature review of the existing hand skill models and instruments was conducted to develop the CHSF content, and experts' reviews via an evaluation feedback questionnaire were used as a means to validate the CHSF.

Results  The literature review revealed that the functional repertoire of children's hand skills can be divided into six distinct categories. Manual gesture and body contact hand skills are two categories, in which the hands do not make contact with any object. Arm–hand use, adaptive skilled hand use and bimanual use are object‐related hand skill categories where the hands do contact objects. The final category is related to the general quality of children's hand skills. Each of the six hand skill categories can be further broken down into three to seven subcategories. The feedback from the experts further demonstrated high levels of agreement for the inclusion of the CHSF subcategories.

Conclusions  The CHSF offers a helpful guide to comprehensively describe the complexity of children's hand skills in the assessment process and has the potential to enhance and promote communication about functional use of children's hand skills among professionals. The CHSF is also conceptually compatible with the International Classification of Functioning, Disability, and Health, providing a holistic consideration of both children's hand skills and relevant International Classification of Functioning, Disability, and Health factors for further assessment and intervention planning.
Course of behaviour problems of children with cerebral palsy: the role of parental stress and support
Authors: Sipal R. F. , Schuengel C. , Voorman J. M. , Van Eck M. , Becher J. G.
Published: August 2009

Background Cerebral palsy (CP) is a well‐recognized neurodevelopmental condition persisting through the lifespan. In many individuals with CP, motor disorders are accompanied by other disturbances, including emotional and behavioural problems. Little is known on the course of such problems, also in relation to possible exacerbating or mitigating factors. Aims of this study were to test whether parental stress and support, apart from the severity of CP of the child, played a significant role in the course of behaviour problems.

Method The participants aged 9, 11 and 13 were assessed (baseline) and followed up after 1, 2 and 3 years. Situational and relational sources of support and stress for the primary caregiver were rated with a questionnaire: (CBCL), behaviour problems with the Child Behaviour Checklist. Physicians rated motor ability using the Gross Motor Function Classification System.

Results Behaviour problems of children with CP started significantly higher than in the general population, but diminished over the 3‐year period. Older children showed less problems overall, and girls showed less externalizing problems than boys. Children with the most severe CP had more externalizing problems; effects on internalizing problems were not significant. Across time, an excess of stress vs. support related to parents' socio‐economic and living situation and to parents' social relationships was positively related to total behaviour problems, internalizing and externalizing behaviours of children.

Conclusions Levels of behaviour problems are elevated but diminish during adolescence for children with CP. Severity of CP plays a role as well as the family context in terms of the stress and support that caregivers experience.
Fibrotest or Fibroscan for evaluation of liver fibrosis in haemophilia patients infected with hepatitis C
Authors: MAOR Y. , HALFON P. , BASHARI D. , PÉNARANDA G. , MORALI G. , KLAR R. , BAR‐MEIR S. , MARTINOWITZ U. , OREN R.
Published: August 2009

Summary.  Non‐invasive modalities to estimate fibrosis stage are desirable in hepatitis C‐infected haemophilia patients. Previous studies found a high rate of significant fibrosis both by Fibrotest (FT) and Fibroscan (FS) in these patients. To estimate liver fibrosis and to assess the concordance between FT and FS in hepatitis C‐infected haemophilia patients. FT and FS were performed at different laboratories and were unaware of the results of the alternative test. Three successive liver stiffness measurements (LSM) were performed at different sites on the liver. Two‐validated algorithms were used to improve evaluation of fibrosis by non‐invasive methods. Fifty‐seven hepatitis C‐infected haemophilia patients were evaluated by FT and FS. Acquisition of LSMs was not feasible in two patients: obesity – one, surgical scars – one. Fibrosis stage ≥F2, ≥F3 or =F4 were estimated in about a half, about a third and in 15–20% of the evaluated patients by FS and FT respectively. The corresponding concordance rates and κ score for fibrosis stage ≥F2, ≥F3 or =F4 between FT and FS were 62%, 69%, 85% and 0.24, 0.32, 0.44 respectively. Using the two aforementioned algorithms, additional 14 patients could be reliably estimated for fibrosis stage ≥F2. High proportion hepatitis C‐infected haemophilia patients were estimated with significant or advanced stages of liver fibrosis using both tests. Nevertheless, the agreement between modalities was only fair and improved with more advanced stages of fibrosis. Practical algorithms for the accuracy of FT and FS may improve reliable evaluation of fibrosis in this population.
Challenge studies of European stocks of redfin perch, Perca fluviatilis L., and rainbow trout, Oncorhynchus mykiss (Walbaum), with epizootic haematopoietic necrosis virus
Authors: Ariel E , Jensen B Bang
Published: August 2009

A challenge model for comparison of the virulence of epizootic haematopoietic necrosis virus (EHNV) to European stocks of redfin perch, Perca fluviatilis L., and rainbow trout, Oncorhynchus mykiss (Walbaum), was tested. The model investigated intraperitoneal (IP), bath and cohabitation routes at 10, 15 and 20 °C for 5–6 g fish and 15 °C for 20 g perch. In the IP challenges of perch, significant mortality occurred at 15 °C and 20 °C. In challenge trials for rainbow trout, significant mortalities were observed in IP and bath challenges at 20 °C. The mortality observed in IP challenged 20 g perch was not significantly different from that recorded for 6 g fish challenged IP. No significant mortality was observed in any other treatment groups. Re‐isolation of ranavirus was confirmed by IFAT and was consistently associated with dead or moribund fish in the trial groups challenged with EHNV. The findings indicate that EHNV does not pose a high risk for wild perch and trout populations in Europe by natural exposure. Mortality appears to be primarily a function of environmental factors, with temperature playing an important role, and not just the presence of the virus in the fish.
Antigenic differences of the scuticociliate Miamiensis avidus from Japan
Authors: Song J‐Y , Sasaki K , Okada T , Sakashita M , Kawakami H , Matsuoka S , Kang H‐S , Nakayama K , Jung S‐J , Oh M‐J , Kitamura S‐I
Published: August 2009

In Japan and Korea, outbreaks of scuticociliatosis have frequently occurred in Japanese flounder, Paralichthys olivaceus. Morphological observations and small subunit rRNA gene sequences have shown that the causative agent of scuticociliatosis in the flounder is Miamiensis avidus (syn. Philasterides dicentrarchi). In this study, we elucidated the antigenic differences between six Japanese M. avidus isolates as an initial step toward developing an effective vaccine against the disease. Four Japanese flounder isolates (IyoI, Nakajima, JF05To and Mie0301 isolates), one spotted knifejaw, Oplegnathus punctatus, isolate (SK05Kyo), and one ridged‐eye flounder, Pleuronichthys cornutus, isolate (RF05To) were subjected to serological analysis. Antisera against IyoI, SK05Kyo, Nakajima and Mie0301 isolates were raised in rabbits and used for immobilization assays and Western blotting. Immobilization assays showed that the six isolates could be divided into three groups, tentatively designated serotype I for IyoI, JF05To, RF05To, SK05Kyo, serotype II for Nakajima and serotype III for Mie0301. Western blotting results supported these three serotypes, with marked similarities in the banding profiles of IyoI, JF05To, RF05To and SK05Kyo isolates, which were distinct from the Nakajima and Mie0301 isolates. Three isolates, IyoI, Nakajima and Mie0301 that were selected as representatives of each serotype, were highly pathogenic to Japanese flounder by experimental infection. Based on these findings, we propose that there are at least three M. avidus serotypes in Japan.
Photooxidation technology for correlated light and electron microscopy
Authors: MEIßLITZER‐RUPPITSCH C. , RÖHRL C. , NEUMÜLLER J. , PAVELKA M. , ELLINGER A.
Published: August 2009

The combination of the capabilities of light microscopical techniques with the power of resolution of electron microscopy along with technical advances has led to a gradual decline of the gap between classical light and electron microscopy. Among the correlative techniques using the synergistic opportunities, photooxidation methods have been established as valuable tools for visualizing cell structures at both light and electron microscopic level. Fluorescent dyes are used to oxidize the substrate diaminobenzidine, which in its oxidized state forms fine granular precipitates. Stained with osmium, the diaminobenzidine precipitates are well discernible in the electron microscope, thus labelling and defining the cellular structures, which at light microscopy level are recorded by fluorescent probes. The underlying photooxidation reaction is based on the excitation of free oxygen radicals that form upon illumination of fluorochromes; this is a central step in the procedure, which mainly influences the success of the method. This article summarizes basic steps of the technology and progresses, shows efforts and elaborated pathways, and focuses on methodical solutions as to the applicability of different fluorochromes, as well as conditions for fine structural localizations of the reaction products.
Focused ion beam‐scanning electron microscope: exploring large volumes of atherosclerotic tissue
Authors: HEKKING L.H.P. , LEBBINK M.N. , DE WINTER D.A.M. , SCHNEIJDENBERG C.T.W.M. , BRAND C.M. , HUMBEL B.M. , VERKLEIJ A.J. , POST J.A.
Published: August 2009

Atherogenesis is a pathological condition in which changes in the ultrastructure and in the localization of proteins occur within the vasculature during all stages of the disease. To gain insight in those changes, high‐resolution imaging is necessary. Some of these changes will only be present in a small number of cells, positioned in a ‘sea’ of non‐affected cells. To localize this relatively small number of cells, there is a need to first navigate through a large area of the sample and subsequently zoom in onto the area of interest. This approach enables the study of specific cells within their in vivo environment and enables the study of (possible) interactions of these cells with their surrounding cells/environment. The study of a sample in a correlative way using light and electron microscopy is a promising approach to achieve this; however, it is very laborious and additional ultrastructural techniques might be very valuable to find the places of interest.

In this report we show that the focused ion beam‐scanning electron microscope is a powerful tool to study biological specimens in a correlative way. With this microscope one can scan for the area of interest at low magnification, in this case the atherosclerotic plaque, and subsequently zoom in, for further analysis on an ultrastructural level, rendering valuable and detailed two‐ and three‐dimensional information of, in this case, the endothelial cells and the vessel wall. Moreover, in combination with pre‐embedment labelling of surface exposed antigens, the method allows insight into the 3D distribution of these markers.
Marginal bone loss around three different implant systems: radiographic evaluation after 1 year
Authors: PIAO C. M. , LEE J. E. , KOAK J. Y. , KIM S. K. , RHYU I. C. , HAN C. H. , HERR Y. , HEO S. J.
Published: August 2009

Summary  This study was designed to radiographically evaluate the effect of surface macro‐and microstructures within the coronal portion of the external hex implant at the marginal bone change after loading. The fifty‐four patients included in the study were randomly assigned to treatment groups with rough‐surface implants (TiUnite, n = 45), a hybrid of smooth and rough surface implants (Restore, n = 45) or rough‐surface with microthreads implants (Hexplant, n = 45). Clinical and radiographic examinations were conducted at the time of implant loading (baseline) and at 1‐year post‐loading. A three‐level mixed‐effect ancova was used to test the significance of the mean marginal bone change of the three implant groups from baseline to 1‐year follow‐up. At 1‐year, significant differences were noted in marginal bone loss recorded for the three groups (P < 0·0001). The rough surface with microthread implants had a mean crestal bone loss of 0·42 ± 0·27 mm; the rough surface implants, 0·81 ± 0·27 mm; and the hybrid surface implants, 0·89 ± 0·41 mm. Within the limitations of this study, a rough surface with microthreads at the coronal part of implant maintained the marginal bone level against functional loading better than implants without these two features.
Comparative analysis of complete orthologous centromeres from two subspecies of rice reveals rapid variation of centromere organization and structure
Authors: Wu Jianzhong , Fujisawa Masaki , Tian Zhixi , Yamagata Harumi , Kamiya Kozue , Shibata Michie , Hosokawa Satomi , Ito Yukiyo , Hamada Masao , Katagiri Satoshi , Kurita Kanako , Yamamoto Mayu , Kikuta Ari , Machita Kayo , Karasawa Wataru , Kanamori Hiroyuki , Namiki Nobukazu , Mizuno Hiroshi , Ma Jianxin , Sasaki Takuji , Matsumoto Takashi
Published: August 2009

Centromeres are sites for assembly of the chromosomal structures that mediate faithful segregation at mitosis and meiosis. This function is conserved across species, but the DNA components that are involved in kinetochore formation differ greatly, even between closely related species. To shed light on the nature, evolutionary timing and evolutionary dynamics of rice centromeres, we decoded a 2.25‐Mb DNA sequence covering the centromeric region of chromosome 8 of an indica rice variety, ‘Kasalath’ (Kas‐Cen8). Analysis of repetitive sequences in Kas‐Cen8 led to the identification of 222 long terminal repeat (LTR)‐retrotransposon elements and 584 CentO satellite monomers, which account for 59.2% of the region. A comparison of the Kas‐Cen8 sequence with that of japonica rice ‘Nipponbare’ (Nip‐Cen8) revealed that about 66.8% of the Kas‐Cen8 sequence was collinear with that of Nip‐Cen8. Although the 27 putative genes are conserved between the two subspecies, only 55.4% of the total LTR‐retrotransposon elements in ‘Kasalath’ had orthologs in ‘Nipponbare’, thus reflecting recent proliferation of a considerable number of LTR‐retrotransposons since the divergence of two rice subspecies of indica and japonica within Oryza sativa. Comparative analysis of the subfamilies, time of insertion, and organization patterns of inserted LTR‐retrotransposons between the two Cen8 regions revealed variations between ‘Kasalath’ and ‘Nipponbare’ in the preferential accumulation of CRR elements, and the expansion of CentO satellite repeats within the core domain of Cen8. Together, the results provide insights into the recent proliferation of LTR‐retrotransposons, and the rapid expansion of CentO satellite repeats, underlying the dynamic variation and plasticity of plant centromeres.
A hairpin RNA construct residing in an intron efficiently triggered RNA‐directed DNA methylation in tobacco
Authors: Dalakouras Athanasios , Moser Mirko , Zwiebel Michèle , Krczal Gabi , Hell Rüdiger , Wassenegger Michael
Published: August 2009

So far, conventional hairpin RNA (hpRNA) constructs consisting of an inverted repeat (IR) of target promoters directly introduced into an expression cassette have been used to mediate de novo DNA methylation. Transcripts of such constructs resemble mRNA molecules, and are likely to be exported to the cytoplasm. The presence of hpRNAs in the cytoplasm and the nucleus may account for the simultaneous activation of post‐transcriptional gene silencing (PTGS) and RNA‐directed DNA methylation (RdDM). We hypothesized that by retaining hpRNAs in the nucleus, efficient induction of only RdDM may be achieved. Thus, we introduced into tobacco a transgene containing an intron into which an IR of a target promoter was inserted. The intronic hpRNA initiated highly specific cis‐ and trans‐methylation, but did not induce PTGS. No spreading of methylation into sequences flanking the region of homology between the hpRNA and the target DNA was detectable. The efficient methylation‐directing activity of the intronic hpRNA may indicate a previously unrecognized role of introns, potentially regulating gene expression at the transcriptional level.