bluuebunny/crossref_metadata_2025 huggingface dataset:
Lensless high-resolution on-chip optofluidic microscopes for
Caenorhabditis elegans
and cell imaging
Authors: Cui Xiquan , Lee Lap Man , Heng Xin , Zhong Weiwei , Sternberg Paul W. , Psaltis Demetri , Yang Changhuei
Published: July 2008

Low-cost and high-resolution on-chip microscopes are vital for reducing cost and improving efficiency for modern biomedicine and bioscience. Despite the needs, the conventional microscope design has proven difficult to miniaturize. Here, we report the implementation and application of two high-resolution (≈0.9 μm for the first and ≈0.8 μm for the second), lensless, and fully on-chip microscopes based on the optofluidic microscopy (OFM) method. These systems abandon the conventional microscope design, which requires expensive lenses and large space to magnify images, and instead utilizes microfluidic flow to deliver specimens across array(s) of micrometer-size apertures defined on a metal-coated CMOS sensor to generate direct projection images. The first system utilizes a gravity-driven microfluidic flow for sample scanning and is suited for imaging elongate objects, such as
Caenorhabditis elegans
; and the second system employs an electrokinetic drive for flow control and is suited for imaging cells and other spherical/ellipsoidal objects. As a demonstration of the OFM for bioscience research, we show that the prototypes can be used to perform automated phenotype characterization of different
Caenorhabditis elegans
mutant strains, and to image spores and single cellular entities. The optofluidic microscope design, readily fabricable with existing semiconductor and microfluidic technologies, offers low-cost and highly compact imaging solutions. More functionalities, such as on-chip phase and fluorescence imaging, can also be readily adapted into OFM systems. We anticipate that the OFM can significantly address a range of biomedical and bioscience needs, and engender new microscope applications.
Poly(A) leader of eukaryotic mRNA bypasses the dependence of translation on initiation factors
Authors: Shirokikh Nikolay E. , Spirin Alexander S.
Published: July 2008

Eukaryotic mRNAs in which a poly(A) sequence precedes the initiation codon are known to exhibit a significantly enhanced cap-independent translation, both
in vivo
and in cell-free translation systems. Consistent with high expression levels of poxviral mRNAs, they contain poly(A) sequences at their 5′ ends, immediately before the initiation AUG codon. Here we show that poly(A) as a leader sequence in mRNA constructs promotes the recruitment of the 40S ribosomal subunits and the efficient formation of initiation complexes at cognate AUG initiation codons in the absence of two essential translation initiation factors, eIF3 and eIF4F. These factors are known to be indispensable for the cap-dependent (and ATP-dependent) mechanism of translation initiation but are shown here to be not required if an mRNA contains a 5′-proximal poly(A). Thus, the presence of a pre-AUG poly(A) sequence results in an alternative mechanism of translation initiation. It involves the binding of initiating 40S ribosomal subunits within the 5′ UTR and their phaseless, ATP-independent, diffusional movement (“phaseless wandering”) along the leader sequence, with subsequent recognition of the initiation (AUG) codon.
Post‐graduation reflections on the value of a degree
Authors: Brooks Rachel , Everett Glyn
Published: July 2008

This article investigates the impact of a changing higher education system on young adults' priorities and motivations. A considerable number of studies have explored the impact of recent changes on patterns of participation within higher education. However, there has been less emphasis on how such changes have been played out in the experiences of graduates and, more specifically, in the interface between higher education and lifelong learning. To redress this gap, this article explores the changes to graduates' experiences brought about by the ‘massification’ of the higher education system. Research conducted amongst young people in Australia has suggested that as result of the normalisation of post‐compulsory education and the encouragement of high aspirations, young people have come to assume a one‐to‐one relationship between being qualified and having a lasting professional career. It has been argued that as a result of these assumptions, young adults are often disappointed when they do eventually enter the labour market, and experience uncertainties previously associated with the end of compulsory schooling. If young adults do indeed feel misled about the rewards of a higher education, it is possible that this may have a significant bearing on their perceptions of the value of engaging in further education and training in the future. Drawing on 90 life history interviews with graduates in their mid‐twenties, this article explores the prevalence of such attitudes in the UK and their impact on young adults' attitudes to lifelong learning.
Sensor Fusion in Integrated Circuit Fault Diagnosis Using a Belief Function Model
Authors: Zhu Daqi , Gu Wei
Published: July 2008

In this paper, a multi-senor information fusion method based on the D-S (Dempster-Shafer) evidence theory is presented for fault diagnosis in an integrated circuit. By measuring the temperature and voltages of circuit components, the fault belief function assignment of two sensors to circuit components is calculated, and the fusion fault belief function assignment is obtained by using the D-S evidence theory. Then the actual fault component is precisely found according to the fusion data. Comparing the diagnosis results based on separate original data with the ones based on D-S theory fusion method, it is shown that the D-S information fusion fault diagnosis method is more accurate. Finally, two fault diagnosis examples of the simple signal magnification circuit and the integrated circuit of industrial case are given.
Sensor Queries: Algebraic Optimization for Time and Energy
Authors: Zadorozhny Vladimir I. , Chrysanthis Panos K. , Sharma Divyasheel
Published: July 2008

Sensor networks naturally apply to a broad range of applications that involve system monitoring and information tracking (e.g., airport security infrastructure, monitoring of children in metropolitan areas, product transition in warehouse networks, fine-grained weather/environmental measurements, etc.). Meanwhile, there are considerable performance deficiencies in applying existing sensornets in the applications that have stringent requirements for efficient mechanisms for querying sensor data and delivering the query result. The amount of data collected from all relevant sensors may be quite large and will require high data transmission rates to satisfy time constraints. It implies that excessive packet collisions can lead to packet losses and retransmissions resulting in significant energy costs and latency. In this paper we provide a formal consideration of a Data Transmission Algebra (DTA) that supports application-driven data interrogation patterns and optimization across multiple network layers. We use a logical framework to specify DTA semantics and to prove its soundness and completeness. Further, we prove that DTA query execution schedules have the key property of being collision-free. Finally, we describe and evaluate an algebraic query optimizer performing collision-aware query scheduling that both improve the response time and reduce the energy consumption.
Transcriptional role of p53 in interferon-mediated antiviral immunity
Authors: Muñoz-Fontela César , Macip Salvador , Martínez-Sobrido Luis , Brown Lauren , Ashour Joseph , García-Sastre Adolfo , Lee Sam W. , Aaronson Stuart A.
Published: July 2008

Tumor suppressor p53 is activated by several stimuli, including DNA damage and oncogenic stress. Previous studies (Takaoka, A., S. Hayakawa, H. Yanai, D. Stoiber, H. Negishi, H. Kikuchi, S. Sasaki, K. Imai, T. Shibue, K. Honda, and T. Taniguchi. 2003. Nature. 424:516–523) have shown that p53 is also induced in response to viral infections as a downstream transcriptional target of type I interferon (IFN) signaling. Moreover, many viruses, including SV40, human papillomavirus, Kaposi's sarcoma herpesvirus, adenoviruses, and even RNA viruses such as polioviruses, have evolved mechanisms designated to abrogate p53 responses. We describe a novel p53 function in the activation of the IFN pathway. We observed that infected mouse and human cells with functional p53 exhibited markedly decreased viral replication early after infection. This early inhibition of viral replication was mediated both in vitro and in vivo by a p53-dependent enhancement of IFN signaling, specifically the induction of genes containing IFN-stimulated response elements. Of note, p53 also contributed to an increase in IFN release from infected cells. We established that this p53-dependent enhancement of IFN signaling is dependent to a great extent on the ability of p53 to activate the transcription of IFN regulatory factor 9, a central component of the IFN-stimulated gene factor 3 complex. Our results demonstrate that p53 contributes to innate immunity by enhancing IFN-dependent antiviral activity independent of its functions as a proapoptotic and tumor suppressor gene.
Prospective Randomized Trial of 3 Antiseptic Solutions for Prevention of Catheter Colonization in an Intensive Care Unit for Adult Patients
Authors: Vallés J. , Fernández I. , Alcaraz D. , Chacón E. , Cazorla A. , Canals M. , Mariscal D. , Fontanals D. , Morón A.
Published: July 2008

Objective.

To compare the effectiveness for prevention of central venous and arterial catheter colonization of 3 skin antisepsis with 1 of 3 antiseptic solutions: 10% aqueous povidone iodine (aqueous PI), 2% aqueous chlorhexidine gluconate (aqueous CG), and 0.5% alcoholic chlorhexidine gluconate (alcoholic CG).

Design.

Prospective, randomized controlled trial.

Setting.

Intensive care unit in a teaching hospital.

Methods.

Patients were randomly assigned to 1 of the 3 skin antisepsis groups. The distal tips of catheters were semiquantitatively cultured when the catheters were no longer necessary or if there was a suspicion of catheter-related infection. Rates of catheter colonization, catheter-related sepsis, and catheter-related bacteremia were compared among the 3 groups.

Results.

A total of 631 catheters were included in the study (194 from the aqueous PI group, 211 from the aqueous CG group, and 226 from the alcoholic CG group). The incidence of catheter colonization was significantly lower in the alcoholic CG than in the aqueous PI group (14.2% vs 24.7%; relative risk, 0.5 [95% confidence interval, 0.3-0.8; P < .01]); it was also significantly lower in the aqueous CG group than in the aqueous PI group (16.1 % vs 24.7%; relative risk, 0.6 [95% confidence interval, 0.4-0.9; P = .03]). There were no significant differences between the aqueous CG and the alcoholic CG groups. Incidences of catheter-related bacteremia were similar for all 3 groups. The aqueous and alcoholic CG solutions were superior to the aqueous PI solution in preventing catheter colonization due to gram-positive bacteria.

Conclusions.

The aqueous and alcoholic CG solutions for cutaneous antisepsis were similarly effective in preventing colonization of central venous catheters and arterial catheters. Both had significantly lower incidences of colonization than did the aqueous PI solution; this effect seems to be related to the CG solutions' more efficacious prevention of colonization with gram-positive bacteria.
Centers of degenerate cyclotomic Hecke algebras and parabolic category 𝒪
Authors: Brundan Jonathan
Published: July 2008

We prove that the center of each degenerate cyclotomic Hecke algebra associated to the complex reflection group of typeBd(l)B_d(l)consists of symmetric polynomials in its commuting generators. The classification of the blocks of the degenerate cyclotomic Hecke algebras is an easy consequence. We then apply Schur-Weyl duality for higher levels to deduce analogous results for parabolic categoryO\mathcal Ofor the Lie algebragln(C)\mathfrak {gl}_n(\mathbb {C}).
ExactFDR: exact computation of false discovery rate estimate in case-control association studies
Authors: Wojcik Jérôme , Forner Karl
Published: July 2008

Summary: Genome-wide association studies require accurate and fast statistical methods to identify relevant signals from the background noise generated by a huge number of simultaneously tested hypotheses. It is now commonly accepted that exact computations of association probability value (P-value) are preferred to χ2 and permutation-based approximations. Following the same principle, the ExactFDR software package improves speed and accuracy of the permutation-based false discovery rate (FDR) estimation method by replacing the permutation-based estimation of the null distribution by the generalization of the algorithm used for computing individual exact P-values. It provides a quick and accurate non-conservative estimator of the proportion of false positives in a given selection of markers, and is therefore an efficient and pragmatic tool for the analysis of genome-wide association studies.

Availability: A Java 1.6 (1.5-compatible) version is available on SourceForge: http://sourceforge.net/projects/exactfdr.

Contact:  Jerome.wojcik@merckserono.net

Supplementary information:  Supplementary data are available at Bioinformatics online.
dbNEI2.0: building multilayer network for drug–NEI–disease
Authors: Zhang Jing , Ma Tao , Li Yanda , Li Shao
Published: July 2008

Summary: The neuro-endocrine-immune (NEI) system plays a critical regulatory role in modulating host homeostasis and optimizing health. We created the dbNEI 2 years ago to collect NEI molecules and interactions. For transferring the conceptual NEI to the systematic NEI network and uncovering the NEI's medical function, we updated the dbNEI 2.0 in three ways: (i) extended NEI molecules to 2242 genes and 7657 chemical compounds by using gene ontology-based (GO-based) data mining strategy, (ii) added multilayer interactions of NEI molecules including KEGG signal transduction and metabolic pathways, HPRD protein–protein interactions (PPI), transcription factor and microRNA regulations and (iii) connected 611 drugs and 823 diseases through multilayer NEI interactions. The reconstructed drug–NEI–disease network will facilitate the systematic study of NEI system.

Availability:  http://bioinfo.au.tsinghua.edu.cn/dbNEIweb/

Contact:  shaoli@mail.tsinghua.edu.cn
DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks
Authors: Xiong Bing , Liu Ke , Wu Jie , Burk David L. , Jiang Hualiang , Shen Jingkang
Published: July 2008

Summary: DrugViz is a Cytoscape plugin that is designed to visualize and analyze small molecules within the framework of the interactome. DrugViz can import drug–target network information in an extended SIF file format to Cytoscape and display the two-dimensional (2D) structures of small molecule nodes in a unified visualization environment. It also can identify small molecule nodes by means of three different 2D structure searching methods, namely isomorphism, substructure and fingerprint-based similarity searches. After selections, users can furthermore conduct a two-side clustering analysis on drugs and targets, which allows for a detailed analysis of the active compounds in the network, and elucidate relationships between these drugs and targets. DrugViz represents a new tool for the analysis of data from chemogenomics, metabolomics and systems biology.

Availability: DrugViz and data set used in Application are freely available for download at http://202.127.30.184:8080/software.html

Contact:  jkshen@mail.shcnc.ac.cn
The CellML Model Repository
Authors: Lloyd Catherine M. , Lawson James R. , Hunter Peter J. , Nielsen Poul F.
Published: July 2008

Summary: The CellML Model Repository provides free access to over 330 biological models. The vast majority of these models are derived from published, peer-reviewed papers. Model curation is an important and ongoing process to ensure the CellML model is able to accurately reproduce the published results. As the CellML community grows, and more people add their models to the repository, model annotation will become increasingly important to facilitate data searches and information retrieval.

Availability: The CellML Model Repository is publicly accessible at http://www.cellml.org/models

Contact:  c.lloyd@auckland.ac.nz
End-joining long nucleic acid polymers
Authors: van den Hout M. , Hage S. , Dekker C. , Dekker N. H.
Published: July 2008

Many experiments involving nucleic acids require the hybridization and ligation of multiple DNA or RNA molecules to form a compound molecule. When one of the constituents is single stranded, however, the efficiency of ligation can be very low and requires significant individually tailored optimization. Also, when the molecules involved are very long (>10 kb), the reaction efficiency typically reduces dramatically. Here, we present a simple procedure to efficiently and specifically end-join two different nucleic acids using the well-known biotin-streptavidin linkage. We introduce a two-step approach, in which we initially bind only one molecule to streptavidin (STV). The second molecule is added only after complete removal of the unbound STV. This primarily forms heterodimers and nearly completely suppresses formation of unwanted homodimers. We demonstrate that the joining efficiency is 50 ± 25% and is insensitive to molecule length (up to at least 20 kb). Furthermore, our method eliminates the requirement for specific complementary overhangs and can therefore be applied to both DNA and RNA. Demonstrated examples of the method include the efficient end-joining of DNA to single-stranded and double-stranded RNA, and the joining of two double-stranded RNA molecules. End-joining of long nucleic acids using this procedure may find applications in bionanotechnology and in single-molecule experiments.
Biomaterials in orthopaedics
Authors: Navarro M , Michiardi A , Castaño O , Planell J.A
Published: July 2008

At present, strong requirements in orthopaedics are still to be met, both in bone and joint substitution and in the repair and regeneration of bone defects. In this framework, tremendous advances in the biomaterials field have been made in the last 50 years where materials intended for biomedical purposes have evolved through three different generations, namely first generation (bioinert materials), second generation (bioactive and biodegradable materials) and third generation (materials designed to stimulate specific responses at the molecular level). In this review, the evolution of different metals, ceramics and polymers most commonly used in orthopaedic applications is discussed, as well as the different approaches used to fulfil the challenges faced by this medical field.
Dual gratings interspersed on a single butterfly scale
Authors: Ingram Abigail L , Lousse Virginie , Parker Andrew R , Vigneron Jean Pol
Published: July 2008

Iridescent butterfly wing colours result from the interaction of light with sub-micrometre structures in the scales. Typically, one scale contains one such photonic structure that produces a single iridescent signal. Here, however, we show how the dorsal wings of male
Lamprolenis nitida
emit two independent signals from two separate photonic structures in the same scale. Multiple independent signals from separate photonic structures within the same sub-micrometre device are currently unknown in animals. However, they would serve to increase the complexity and specificity of the optical signature, enhancing the information conveyed. This could be important during intrasexual encounters, in which iridescent male wing colours are employed as threat displays. Blazed diffraction gratings, like those found in
L. nitida
, are asymmetric photonic structures and drive most of the incident light into one diffraction order. Similar gratings are used in spectrometers, limiting the spectral range over which the spectrometer functions. By incorporating two interchangeable gratings onto a single structure, as they are in
L. nitida
, the functional range of spectrometers could be extended.
Geographic profiling applied to testing models of bumble-bee foraging
Authors: Raine Nigel E , Rossmo D. Kim , Le Comber Steven C
Published: July 2008

Geographic profiling (GP) was originally developed as a statistical tool to help police forces prioritize lists of suspects in investigations of serial crimes. GP uses the location of related crime sites to make inferences about where the offender is most likely to live, and has been extremely successful in criminology. Here, we show how GP is applicable to experimental studies of animal foraging, using the bumble-bee
Bombus terrestris
. GP techniques enable us to simplify complex patterns of spatial data down to a small number of parameters (2–3) for rigorous hypothesis testing. Combining computer model simulations and experimental observation of foraging bumble-bees, we demonstrate that GP can be used to discriminate between foraging patterns resulting from (i) different hypothetical foraging algorithms and (ii) different food item (flower) densities. We also demonstrate that combining experimental and simulated data can be used to elucidate animal foraging strategies: specifically that the foraging patterns of real bumble-bees can be reliably discriminated from three out of nine hypothetical foraging algorithms. We suggest that experimental systems, like foraging bees, could be used to test and refine GP model predictions, and that GP offers a useful technique to analyse spatial animal behaviour data in both the laboratory and field.
The changing face of kuru: a personal perspective
Authors: Mathews John D
Published: July 2008

The epidemic of kuru is now known to have been transmitted among the Fore by ritual consumption of infected organs from deceased relatives. As cannibalism was suppressed by government patrol officers during the 1950s, most transmission had ceased by 1957, when the kuru research programme first commenced. As predicted in the 1960s, the epidemic has waned, with progressive ageing of kuru-affected cohorts over the years to 2007. The few cases seen in the twenty-first century, with the longest incubation periods, were almost certainly exposed as children prior to 1960. Although the research programme had almost no role in bringing the kuru epidemic to an end, it did provide important knowledge that was to help the wider world in controlling the later epidemics of iatrogenic and variant Creutzfeldt–Jakob disease and bovine spongiform encephalopathy.
Mechanisms to suppress multipolar divisions in cancer cells with extra centrosomes
Authors: Kwon Mijung , Godinho Susana A. , Chandhok Namrata S. , Ganem Neil J. , Azioune Ammar , Thery Manuel , Pellman David
Published: July 2008

Multiple centrosomes in tumor cells create the potential for multipolar divisions that can lead to aneuploidy and cell death. Nevertheless, many cancer cells successfully divide because of mechanisms that suppress multipolar mitoses. A genome-wide RNAi screen in Drosophila S2 cells and a secondary analysis in cancer cells defined mechanisms that suppress multipolar mitoses. In addition to proteins that organize microtubules at the spindle poles, we identified novel roles for the spindle assembly checkpoint, cortical actin cytoskeleton, and cell adhesion. Using live cell imaging and fibronectin micropatterns, we found that interphase cell shape and adhesion pattern can determine the success of the subsequent mitosis in cells with extra centrosomes. These findings may identify cancer-selective therapeutic targets: HSET, a normally nonessential kinesin motor, was essential for the viability of certain extra centrosome-containing cancer cells. Thus, morphological features of cancer cells can be linked to unique genetic requirements for survival.
In Planta Analysis of the Cell Cycle-Dependent Localization of AtCDC48A and Its Critical Roles in Cell Division, Expansion, and Differentiation
Authors: Park Sookhee , Rancour David Michael , Bednarek Sebastian York
Published: July 2008

CDC48/p97 is a conserved homohexameric AAA-ATPase chaperone required for a variety of cellular processes but whose role in the development of a multicellular model system has not been examined. Here, we have used reverse genetics, visualization of a functional Arabidopsis (Arabidopsis thaliana) CDC48 fluorescent fusion protein, and morphological analysis to examine the subcellular distribution and requirements for AtCDC48A in planta. Homozygous Atcdc48A T-DNA insertion mutants arrest during seedling development, exhibiting decreased cell expansion and displaying pleiotropic defects in pollen and embryo development. Atcdc48A insertion alleles show significantly reduced male transmission efficiency due to defects in pollen tube growth. Yellow fluorescent protein-AtCDC48A, a fusion protein that functionally complements the insertion mutant defects, localizes in the nucleus and cytoplasm and is recruited to the division mid-zone during cytokinesis. The pattern of nuclear localization differs according to the stage of the cell cycle and differentiation state. Inducible expression of an Atcdc48A Walker A ATPase mutant in planta results in cytokinesis abnormalities, aberrant cell divisions, and root trichoblast differentiation defects apparent in excessive root hair emergence. At the biochemical level, our data suggest that the endogenous steady-state protein level of AtCDC48A is dependent upon the presence of ATPase-active AtCDC48A. These results demonstrate that CDC48A/p97 is critical for cytokinesis, cell expansion, and differentiation in plants.
The EPIP Peptide of INFLORESCENCE DEFICIENT IN ABSCISSION Is Sufficient to Induce Abscission inArabidopsisthrough the Receptor-Like Kinases HAESA and HAESA-LIKE2
Authors: Stenvik Grethe-Elisabeth , Tandstad Nora M. , Guo Yongfeng , Shi Chun-Lin , Kristiansen Wenche , Holmgren Asbjørn , Clark Steven E. , Aalen Reidunn B. , Butenko Melinka A.
Published: July 2008

In Arabidopsis thaliana, the final step of floral organ abscission is regulated by INFLORESCENCE DEFICIENT IN ABSCISSION (IDA): ida mutants fail to abscise floral organs, and plants overexpressing IDA display earlier abscission. We show that five IDA-LIKE (IDL) genes are expressed in different tissues, but plants overexpressing these genes have phenotypes similar to IDA-overexpressing plants, suggesting functional redundancy. IDA/IDL proteins have N-terminal signal peptides and a C-terminal conserved motif (extended PIP [EPIP]) at the C terminus (EPIP-C). IDA can, similar to CLAVATA3, be processed by an activity from cauliflower meristems. The EPIP-C of IDA and IDL1 replaced IDA function in vivo, when the signal peptide was present. In addition, synthetic IDA and IDL1 EPIP peptides rescued ida and induced early floral abscission in wild-type flowers. The EPIP-C of the other IDL proteins could partially substitute for IDA function. Similarly to ida, a double mutant between the receptor-like kinases (RLKs) HAESA (HAE) and HAESA-LIKE2 (HSL2) displays nonabscising flowers. Neither overexpression of IDA nor synthetic EPIP or EPIP-C peptides could rescue the hae hsl2 abscission deficiency. We propose that IDA and the IDL proteins constitute a family of putative ligands that act through RLKs to regulate different events during plant development.
TheCladosporium fulvumVirulence Protein Avr2 Inhibits Host Proteases Required for Basal Defense
Authors: van Esse H. Peter , van't Klooster John W. , Bolton Melvin D. , Yadeta Koste A. , van Baarlen Peter , Boeren Sjef , Vervoort Jacques , de Wit Pierre J.G.M. , Thomma Bart P.H.J.
Published: July 2008

Cladosporium fulvum (syn. Passalora fulva) is a biotrophic fungal pathogen that causes leaf mold of tomato (Solanum lycopersicum). During growth in the apoplast, the fungus establishes disease by secreting effector proteins, 10 of which have been characterized. We have previously shown that the Avr2 effector interacts with the apoplastic tomato Cys protease Rcr3, which is required for Cf-2–mediated immunity. We now show that Avr2 is a genuine virulence factor of C. fulvum. Heterologous expression of Avr2 in Arabidopsis thaliana causes enhanced susceptibility toward extracellular fungal pathogens, including Botrytis cinerea and Verticillium dahliae, and microarray analysis showed that Avr2 expression triggers a global transcriptome reflecting pathogen challenge. Cys protease activity profiling showed that Avr2 inhibits multiple extracellular Arabidopsis Cys proteases. In tomato, Avr2 expression caused enhanced susceptibility toward Avr2-defective C. fulvum strains and also toward B. cinerea and V. dahliae. Cys protease activity profiling in tomato revealed that, in this plant also, Avr2 inhibits multiple extracellular Cys proteases, including Rcr3 and its close relative Pip1. Finally, silencing of Avr2 significantly compromised C. fulvum virulence on tomato. We conclude that Avr2 is a genuine virulence factor of C. fulvum that inhibits several Cys proteases required for plant basal defense.
Detection of serum anti‐Neoparamoeba spp. antibodies in amoebic gill disease‐affected Atlantic salmon Salmo salar
Authors: Vincent B. N. , Nowak B. F. , Morrison R. N.
Published: July 2008

Amoebic gill disease (AGD)‐affected Atlantic salmon Salmo salar sometimes developed a serum‐antibody response to wild‐type Neoparamoeba spp. Five of 103 AGD‐affected S. salar sampled possessed detectable antibodies that bound wild‐type Neoparamoeba spp. western blotting revealed two distinctly different binding profiles.
Twenty‐three novel microsatellite markers developed from Atlantic cod Gadus morhua L. expressed sequence tags
Authors: Delghandi M. , Wesmajervi M. S. , Tafese T. , Nilsen F.
Published: July 2008

Twenty‐three novel polymorphic microsatellite markers were developed from c. 2000 expressed sequence tags of Atlantic cod Gadus morhua L. Gene identity was determined at 12 loci, confirming the associated microsatellites as type I markers. These microsatellite markers provide useful tools for studies of population genetics and reproductive ecology and for constructing linkage maps of G. morhua.
Shark jaws and teeth: an unexploited resource for population genetic studies
Authors: Ahonen H. , Stow A. J.
Published: July 2008

Declines in shark populations worldwide are of particular concern to fishery managers and conservation biologists. Molecular‐based technologies provide an efficient means to collect basic life‐history information and estimates of dispersal that are critical to management. A novel method for obtaining high quality mtDNA from shark jaws and teeth for shark population genetic studies is described.
Flow cytometry for the evaluation of chromosomal damage in turbot Psetta maxima (L.) exposed to the dissolved fraction of heavy fuel oil in sea water: a comparison with classical biomarkers
Authors: Goanvec C. , Theron M. , Lacoue‐Labarthe T. , Poirier E. , Guyomarch J. , Le‐Floch S. , Laroche J. , Nonnotte L. , Nonnotte G.
Published: July 2008

Turbot Psetta maxima were exposed 5 days to the dissolved fraction of fuel oil number 2, then decontaminated over 30 days in clean sea water. Biliary metabolites and ethoxyresorufin‐O‐deethylase (EROD) activity were evaluated during and after the contamination. These results were compared with chromosomal damage measured by flow cytometry (FCM). Erythrocyte nuclear abnormality, micronuclei and immaturity were also evaluated over the exposure period. Biliary metabolites and EROD analyses showed a clear and early response: biliary metabolites were detected from the first day of contamination to the 14th day of depuration, EROD activity increased during the contamination period reached a maximum 3 days after the beginning of the decontamination and decreased to the control value after 1 month of depuration. FCM showed a bimodal response: a first increase of coefficient of variation of blood cell DNA content was observed during the contamination and a second one started after 14 days of depuration and was maintained for at least 2 weeks. Erythrocyte morphology analysis showed a strong increase in nuclear abnormality during the contamination period. These results confirm previous work and show that in the context of marine accidental pollution by heavy fuel oil, the measurements of chromosomal damage by FCM allow the detection of a genotoxic response in fishes.
Heteromorphic sex chromosomes in the ninespine stickleback Pungitius pungitius
Authors: Ocalewicz K. , Fopp‐Bayat D. , Woznicki P. , Jankun M.
Published: July 2008

Specimens from two freshwater populations of the ninespine stickleback Pungitius pungitius in Poland showed morphologically differentiated sex chromosomes. A heteromorphic pair of chromosomes appeared only in male diploid cells. The Y chromosome was the largest chromosome in the P. pungitius karyotype.
Phytoplankton response to light and internal phosphorus loading from sediment release
Authors: CYMBOLA JENNIFER , OGDAHL MARY , STEINMAN ALAN D.
Published: July 2008

1. A 2 × 2 factorial design was employed to look at the influence of two levels of phosphorus (P; high and low) and two levels of light (high and low) and their interactions, on phytoplankton abundance, elemental tissue composition and community structure in two seasons (April and June) of 2005.

2. A novel feature of the experiment was the creation of high and low P levels by manipulating sediment core conditions in the laboratory. Sediment cores were incubated with their associated overlaying water column from four different sites in Mona Lake, Michigan, under anaerobic or aerobic conditions, respectively.

3. After 24 days, the water overlaying the sediment cores was collected and used as growth media for phytoplankton collected from Mona Lake. Phytoplankton communities were grown in the laboratory in the high or low P water, and subjected to high (250 μmol m−2 s−1) or low (10 μmol m−2 s−1) light for 9 (April) or 14 (June) days.

4. In the April experiment, high P treatments resulted in significantly higher chlorophyll‐a concentrations, significantly lower C : P ratios from two of the four sites, and greater dominance by Scenedesmus at all sites relative to low P treatments. High light generally led to higher chlorophyll‐a concentrations, higher C : P ratios and greater Scenedesmus and Fragilaria biovolume at all sites. A significant interaction was measured between P and light for chlorophyll‐a and Scenedesmus biovolume, suggesting the influence of P was more apparent at high light than at low light levels.

5. In the June experiment, high P increased ash‐free dry mass (AFDM), lowered C : P ratios and resulted in increased Pediastrum biovolume. High light levels led to greater chlorophyll‐a concentrations, AFDM and C : P ratios, as well as increased biovolumes of Scendesmus, Pediastrum and Fragilaria. A significant interaction was found between P and light for all three taxa, as the positive influence of P was more pronounced at high light levels.

6. The results of our study demonstrate that sediment‐derived P stimulates phytoplankton growth, but that its effect on phytoplankton dynamics is modulated by other factors, such as light.
Reflection across plant cell boundaries in confocal laser scanning microscopy
Authors: LIU D.Y.T. , KUHLMEY B.T. , SMITH P.M.C. , DAY D.A. , FAULKNER C.R. , OVERALL R.L.
Published: July 2008

The fluorescence patterns of proteins tagged with the green fluorescent protein (GFP) and its derivatives are routinely used in conjunction with confocal laser scanning microscopy to identify their sub‐cellular localization in plant cells. GFP‐tagged proteins localized to plasmodesmata, the intercellular junctions of plants, are often identified by single or paired punctate labelling across the cell wall. The observation of paired puncta, or ‘doublets’, across cell boundaries in tissues that have been transformed through biolistic bombardment is unexpected if there is no intercellular movement of the GFP‐tagged protein, since bombardment usually leads to the transformation of single, isolated cells. We expressed a putative plasmodesmal protein tagged with GFP by bombarding Allium porrum epidermal cells and assessed the nature of the doublets observed at the cell boundaries. Doublets were formed when fluorescent spots were abutting a cell boundary and were only observable at certain focal planes. Fluorescence emitted from the half of a doublet lying outside the transformed cells was polarized. Optical simulations performed using finite‐difference time‐domain computations showed a dramatic distortion of the confocal microscope's point spread function when imaging voxels close to the plant cell wall due to refractive index differences between the wall and the cytosol. Consequently, axially and radially out‐of‐focus light could be detected. A model of this phenomenon suggests how a doublet may form when imaging only a single real fluorescent body in the vicinity of a plant cell wall using confocal microscopy. We suggest, therefore, that the appearance of doublets across cell boundaries is insufficient evidence for plasmodesmal localization due to the effects of the cell wall on the reflection and scattering of light.
The Thyroid‐Brain Interaction in Thyroid Disorders and Mood Disorders
Authors: Bauer M. , Goetz T. , Glenn T. , Whybrow P. C.
Published: July 2008

Thyroid hormones play a critical role in the metabolic activity of the adult brain, and neuropsychiatric manifestations of thyroid disease have long been recognised. However, it is only recently that methodology such as functional neuroimaging has been available to facilitate investigation of thyroid hormone metabolism. Although the role of thyroid hormones in the adult brain is not yet specified, it is clear that without optimal thyroid function, mood disturbance, cognitive impairment and other psychiatric symptoms can emerge. Additionally, laboratory measurements of peripheral thyroid function may not adequately characterise central thyroid metabolism. Here, we review the relationship between thyroid hormone and neuropsychiatric symptoms in patients with primary thyroid disease and primary mood disorders.
Developing more positive attitudes towards mental health nursing in undergraduate students: part 2‐the impact of theory and clinical experience
Authors: HAPPELL B. , ROBINS A. , GOUGH K.
Published: July 2008

Previous research examining the impact of education on nursing students' attitudes towards mental health nursing as a career has highlighted clinical experience as the primary influencing factor and generally has not considered the impact of theory. The current study compared a cohort of second‐year and a cohort of third‐year nursing students from the same university. Second‐year students had received more theory and clinical experience than their counterparts. Questionnaires were distributed to the total population of students before commencement of, and after completion of clinical placement. This paper examines students' perceived preparedness for and satisfaction with clinical experience, attitudes towards people with mental illness, and attitudes towards mental health nursing as a career option following the completion of differing amounts of theory and clinical experience. The results demonstrate some statistically significant differences with increased amounts of theory and clinical experience in the second‐year cohort being positively influential. The findings suggest that an increased component of theoretical and clinical experience in psychiatric/mental health nursing is likely to produce more positive attitudes towards people with mental illness and psychiatric/mental health nursing. However, little difference in perceived preparedness for and satisfaction with clinical experience was noted between the two cohorts.
Developing and testing an intervention to prevent homelessness among individuals discharged from psychiatric wards to shelters and ‘No Fixed Address’
Authors: FORCHUK C. , MACCLURE S. K. , VAN BEERS M. , SMITH C. , CSIERNIK R. , HOCH J. , JENSEN E.
Published: July 2008

Shelter data in a recent study revealed discharges from psychiatric facilities to shelters or the street occurred at least 194 times in 2002 in London, Ontario, Canada. This problem must be addressed to reduce the disastrous effects of such discharge, including re‐hospitalization and prolonged homelessness. An intervention was developed and tested to prevent homelessness associated with discharge directly to no fixed address. A total of 14 participants at‐risk of being discharged without housing were enrolled, with half randomized into the intervention group. The intervention group was provided with immediate assistance in accessing housing and assistance in paying their first and last month's rent. The control group received usual care. Data was collected from participants prior to discharge, at 31 and 6‐months post‐discharge. All the individuals in the intervention group maintained housing after 3 and 6 months. All but one individual in the control group remained homeless after 3 and 6 months. The exception joined the sex trade to avoid homelessness. The results of this pilot were so dramatic that randomizing to the control group was discontinued. Discussions are underway to routinely implement the intervention. Systemic improvements can prevent homelessness for individuals being discharged from psychiatric wards.
Transcriptional activation by MarA, SoxS and Rob of two tolC promoters using one binding site: a complex promoter configuration for tolC in Escherichia coli
Authors: Zhang Aixia , Rosner Judah L. , Martin Robert G.
Published: July 2008

The Escherichia coli tolC encodes a major outer membrane protein with multiple functions in export (e.g. diverse xenobiotics, haemolysin) and as an attachment site for phage and colicins. tolC is regulated in part by MarA, SoxS and Rob, three paralogous transcriptional activators which bind a sequence called the marbox and which activate multiple antibiotic and superoxide resistance functions. Two previously identified tolC promoters, p1 and p2, are not regulated by MarA, SoxS or Rob but p2 is activated by EvgAS and PhoPQ which also regulate other functions. Using transcriptional fusions and primer extension assays, we show here that tolC has two additional strong overlapping promoters, p3 and p4, which are downstream of p1, p2 and the marbox and are activated by MarA, SoxS and Rob. p3 and p4 are configured so that a single marbox suffices to activate transcription from both promoters. At the p3 promoter, the marbox is separated by 20 bp from the −10 hexamer for RNA polymerase but at the p4 promoter, the same marbox is separated by 30 bp from the −10 hexamer. The multiple tolC promoters may allow the cell to respond to diverse environments by co‐ordinating tolC transcription with other appropriate functions.
An international collaborative study to establish a replacement World Health Organization International Standard for human immunodeficiency virus 1 RNA nucleic acid assays
Authors: Davis C. , Berry N. , Heath A. , Holmes H.
Published: July 2008

Background and Objectives An international collaborative study was undertaken to identify a replacement for the World Health Organization (WHO) 1st International Standard for human immunodeficiency virus 1 (HIV‐1) RNA for use in nucleic acid‐based techniques (NAT) (code 97/656). In the original study to establish the 1st International Standard, a second candidate material (code 97/650) had been shown to perform well and this was re‐evaluated to establish whether it would be a suitable replacement.

Materials and Methods Eight laboratories from six different countries participated in the collaborative study to evaluate the candidate replacement standard. A total of eight different NATs were used, five in a quantitative format and three qualitative, of which five were commercially available.

Results The results showed that the estimates of RNA copies in the current study were generally in line with those of the original study and there was no evidence of any drift in overall levels expressed in International Units (IU) for the candidate standard between the two studies. Furthermore, it was shown to be stable over long‐term storage at –20°C.

Conclusions The candidate material code 97/650 was established by the WHO as the 2nd International Standard for HIV‐1 RNA for use in NAT and assigned a unitage of 5·56 log10(363 078) IU/vial.
Trans‐sialidase inhibition assay for the detection of Trypanosoma cruzi infection in blood donor samples from Argentina
Authors: Blejer J. L. , Sartor P. A. , Bottasso O. , Salamone H. J. , Leguizamón M. S.
Published: July 2008

Background and Objectives  Conventional serology tests for Trypanosoma cruzi blood banks screening are neither sensitive nor specific enough, and currently no gold standard assay is available. Trans‐sialidase inhibition assay (TIA) detects neutralizing antibodies against T. cruzi trans‐sialidase. Conventional serology inconclusive, positive and negative blood donor samples were evaluated by employing TIA as a supplementary test.

Materials and Methods  Three hundred and twenty‐one blood donor samples were tested using a combination of assays. Based on the results of testing, these were divided into a number of groups. All samples were tested by TIA.

Results  In conventional serology inconclusive samples 48·1% were TIA‐positive, 1/54 conventional serology positive samples was TIA‐negative. All negative samples from donors without epidemiological risks were TIA‐negative; 1/48 was positive in those with epidemiological risk.

Conclusion  Trans‐sialidase inhibition assay application in blood banks may be useful to resolve inconclusive samples, and thus improves donor counseling and allows individual re‐entry. The use of TIA in samples from negative conventional test donors but positive epidemiological antecedents may contribute to decrease transfusional risk.
Validation of the Chinese version of the Mood Disorder Questionnaire in a psychiatric population in Hong Kong
Authors: Chung Ka‐Fai , Tso Kwok‐Chu , Cheung Erik , Wong Michael
Published: July 2008

Aims:  The aim of the present study was to determine the validity of a Chinese version of the Mood Disorder Questionnaire (MDQ) as a screening instrument for bipolar disorder in a psychiatric outpatient population in Hong Kong.

Methods:  A total of 185 patients primarily being treated for mood disorders were asked to fill in the Chinese MDQ and supply other personal data during their scheduled clinic visit. The mean age was 43.0 years and 65.9% were female. A subsample of 102 randomly selected subjects, stratified by the MDQ symptom score, received a telephone‐based Structured Clinical Interview for DSM‐IV (SCID). Sixty‐two patients (60.8%) were suffering from bipolar disorder (bipolar I, n = 48; bipolar II, n = 9; bipolar disorder not otherwise specified, n = 5), 35 (34.3%) from depressive disorder, and one (1.0%) from substance dependence, while four (3.9%) were unaffected by either mood or alcohol/substance use disorder. The internal consistency, factor structure and operating characteristics of the Chinese MDQ were analyzed.

Results:  The internal consistency of the Chinese MDQ, evaluated using Cronbach alpha, was 0.82. Principal component analysis with varimax rotation indicated an ‘energized‐activity’ factor and an ‘irritability‐racing thoughts’ factor, which explained 47.2% of the rotated variance. The optimal cut‐off was seven or more manic symptoms occurring within the same time period, which yielded a sensitivity of 0.73 and a specificity of 0.88 for detecting bipolar disorder. An additional criterion that the symptoms cause impairment resulted in significant loss of sensitivity.

Conclusion:  The Chinese MDQ is a valid screening instrument for bipolar disorder in a psychiatric outpatient population.