bluuebunny/crossref_metadata_2025 huggingface dataset:
Psychotherapie von Patienten mit Depression und Abhängigkeitserkrankung
Authors: Loeber Sabine , Dinter Christina , Mann Karl
Published: October 2011

Fragestellung: Im Verlauf einer Suchterkrankung kommt es häufig zum Auftreten depressiver Störungen. Depressive Symptome, die auch nach Abschluss der Entzugsphase persistieren, erweisen sich als ein zentraler Prädiktor für einen Rückfall und sollten im Rahmen von Diagnostik und Therapie berücksichtigt werden. Methodik: In der vorliegenden Arbeit wurde eine systematische Literaturrecherche durchgeführt, um sowohl randomisierte Therapievergleichsstudien als auch weitere klinische Studien zu identifizieren, die die Effektivität einer integrativen Behandlung von Abhängigkeitserkrankungen und Depression untersuchen. Ergebnisse: Die Ergebnisse der wenigen identifizierten Untersuchungen zeigen, dass durch ein integratives Behandlungskonzept, bei dem sowohl die Suchterkrankung als auch depressive Störungen behandelt werden, eine Reduktion depressiver Symptome und eine Steigerung der Abstinenzquote erzielt wird. Schlussfolgerungen: Methodische Mängel der vorliegenden Untersuchungen bzw. die noch ausstehende Replikation von Befunden schränken jedoch gegenwärtig die vorliegenden positiven Ergebnisse zur integrierten Behandlung ein. Ferner gestaltet sich die Etablierung integrierter Behandlungsansätze aufgrund der nach wie vor zu beobachtenden Trennung zwischen Einrichtungen der Suchtkrankenhilfe und allgemein-psychiatrischen Einrichtungen schwierig.
Molecular mechanisms of endolysosomal Ca2+ signalling in health and disease
Authors: Morgan Anthony J. , Platt Frances M. , Lloyd-Evans Emyr , Galione Antony
Published: October 2011

Endosomes, lysosomes and lysosome-related organelles are emerging as important Ca2+ storage cellular compartments with a central role in intracellular Ca2+ signalling. Endocytosis at the plasma membrane forms endosomal vesicles which mature to late endosomes and culminate in lysosomal biogenesis. During this process, acquisition of different ion channels and transporters progressively changes the endolysosomal luminal ionic environment (e.g. pH and Ca2+) to regulate enzyme activities, membrane fusion/fission and organellar ion fluxes, and defects in these can result in disease. In the present review we focus on the physiology of the inter-related transport mechanisms of Ca2+ and H+ across endolysosomal membranes. In particular, we discuss the role of the Ca2+-mobilizing messenger NAADP (nicotinic acid adenine dinucleotide phosphate) as a major regulator of Ca2+ release from endolysosomes, and the recent discovery of an endolysosomal channel family, the TPCs (two-pore channels), as its principal intracellular targets. Recent molecular studies of endolysosomal Ca2+ physiology and its regulation by NAADP-gated TPCs are providing exciting new insights into the mechanisms of Ca2+-signal initiation that control a wide range of cellular processes and play a role in disease. These developments underscore a new central role for the endolysosomal system in cellular Ca2+ regulation and signalling.
Domain assembly of NAADP-gated two-pore channels
Authors: Churamani Dev , Hooper Robert , Brailoiu Eugen , Patel Sandip
Published: October 2011

TPCs (two-pore channels) have recently been identified as targets for the Ca2+-mobilizing messenger NAADP (nicotinic acid–adenine dinucleotide phosphate). TPCs have a unique structure consisting of cytosolic termini, two hydrophobic domains (I and II) each comprising six transmembrane regions and a pore, and a connecting cytosolic loop; however, little is known concerning how these channels are assembled. In the present paper, we report that both domain I and II of human TPCs are capable of independent insertion into membranes, whereas the loop linking the domains fails to insert. Pairs of transmembrane regions within domain I of TPC1 are also capable of insertion, consistent with sequential translational integration of hydrophobic regions. Insertion of the first two transmembrane regions, however, was inefficient, indicating possible interaction between transmembrane regions during translation. Both domains, and each pair of transmembrane regions within domain I, were capable of forming oligomers, highlighting marked redundancy in the molecular determinants driving oligomer formation. Each hydrophobic domain formed dimers upon cross-linking. The first four transmembrane regions of TPC1 also formed dimers, whereas transmembrane regions 5 and 6, encompassing the pore loop, formed both dimers and tetramers. TPCs thus probably assemble as dimers through differential interactions between transmembrane regions. The present study provides new molecular insight into the membrane insertion and oligomerization of TPCs.
Who's who and Where's Where: Constructing Feminist Literary Studies
Authors: Eagleton Mary
Published: October 2011

This article is concerned with the construction of feminist literary studies in the last twenty years and points out how we have created a literary history which is both selective and schematic. It suggests that we should be more critically aware of what we are constructing, how we are constructing it and of the political consequences of those constructs. It stresses three critical modes which might help us to complicate our history: a greater awareness of institutional contexts, a concern with empirical detail, and an ongoing analysis of the cultural and political significance of feminist literary practice. This article briefly applies these critical modes in a survey of eleven introductions to feminist literary studies – introductions which feature frequently and influentially in the teaching situation. The final section focuses on the key problem of inclusion and exclusion. Considering arguments from Third World feminism and postmodernist feminism, the study concludes that white, academic feminists should confront the privilege of their own inclusion as a necessary spur to political action.
Galaxies on Sub-Galactic Scales
Authors: Jerjen Helmut
Published: October 2011

The Sloan Digital Sky Survey has been immensely successful in detecting new Milky Way satellite galaxies over the past seven years. It was instrumental in finding examples of the least luminous galaxies we know in the Universe, uncovering apparent inconsistencies between cold dark matter theory and dwarf galaxy properties, providing first evidence for a possible lower mass limit for dark matter halos in visible galaxies, and reopening the discussion about the building block scenario for the Milky Way halo. Nonetheless, these results are still drawn only from a relatively small number of galaxies distributed over an area covering about 29% of the sky, which leaves us currently with more questions than answers. The study of these extreme stellar systems is a multi-parameter problem: ages, metallicities, star formation histories, dark matter contents, population fractions and spatial distributions must be determined. Progress in the field is discussed and attention drawn to some of the limitations that currently hamper our ability to fully understand the phenomenon of the ‘ultra-faint dwarf galaxy’. In this context, the Stromlo Milky Way Satellite Survey represents a new initiative to systematically search and scrutinize optically elusive Milky Way satellite galaxies in the Southern hemisphere. In doing so, the program aims at investigating some of the challenging questions in stellar evolution, galaxy formation and near-field cosmology.
Modelling lead(II) sorption to ferrihydrite and soil organic matter
Authors: Gustafsson Jon Petter , Tiberg Charlotta , Edkymish Abubaker , Kleja Dan Berggren
Published: October 2011

Environmental contextLead(II) is a toxic metal pollutant with many anthropogenic sources. We show that lead(II) is bound more strongly to soil surfaces than previously understood. This knowledge may lead to better models for lead(II) dissolution from the soils, which will improve risk assessments for this metal.
AbstractLead(II) adsorption to soil organic matter and iron (hydr)oxides is strong, and may control the geochemical behaviour of this metal. Here, we report the adsorption of Pb2+ (i) to 2-line ferrihydrite, and (ii) to a mor layer. The results showed that ferrihydrite has heterogeneous Pb2+ binding. Use of a surface complexation model indicated that ~1 % of the surface sites adsorbed Pb2+ more strongly than the remaining 99 %. Although only one surface complexation reaction was used (a bidentate complex of the composition (≡FeOH)2Pb+), three classes of sites with different affinity for Pb2+ were needed to simulate Pb2+ binding correctly over all Pb/Fe ratios analysed. For the mor layer, Pb2+ sorption was much stronger than current models for organic complexation suggest. The results could be described by the Stockholm Humic Model when the binding heterogeneity was increased, and when it was assumed that 0.2 % of the binding sites were specific for Pb. Use of revised model parameters for nine Vietnamese soils suggest that lead(II) binding was more correctly simulated than before. Thus, underestimation of lead(II) sorption to both (hydr)oxide surfaces and organic matter may explain the failure of previous geochemical modelling attempts for lead(II).
Divergence of the growth characteristics and longevity of coexisting Platycephalidae (Pisces)
Authors: Barnes L. M. , Gray C. A. , Williamson J. E.
Published: October 2011

Divergent age and growth characteristics can reduce deleterious competitive interactions between taxonomically related species facilitating coexistence. Five platycephalid fish species, Platycephalus caeruleopunctatus, Platycephalus longispinis, Platycephalus richardsoni, Ambiserrula jugosa and Ratabulus diversidens, inhabit inner continental shelf habitats along the east coast of Australia. We tested the hypothesis that the age and growth characteristics of these five species are unique. The age of each species was estimated by counting the number of opaque zones in sectioned otoliths. The maximum observed age ranged from 4 years for A. jugosa to 16 years for P. longispinis. von Bertalanffy growth functions were fitted to length-at-age data for each combination of species, sex and location and compared using likelihood ratio tests. The age and growth characteristics of each species were unique and each species displayed sexually dimorphic growth, with females growing larger than males. The unique species-specific growth characteristics may assist length-based partitioning of resources, reducing competitive interactions and facilitate coexistence between these platycephalid species.
Quantum state and process tomography of energy transfer systems via ultrafast spectroscopy
Authors: Yuen-Zhou Joel , Krich Jacob J. , Mohseni Masoud , Aspuru-Guzik Alán
Published: October 2011

The description of excited state dynamics in energy transfer systems constitutes a theoretical and experimental challenge in modern chemical physics. A spectroscopic protocol that systematically characterizes both coherent and dissipative processes of the probed chromophores is desired. Here, we show that a set of two-color photon-echo experiments performs quantum state tomography (QST) of the one-exciton manifold of a dimer by reconstructing its density matrix in real time. This possibility in turn allows for a complete description of excited state dynamics via quantum process tomography (QPT). Simulations of a noisy QPT experiment for an inhomogeneously broadened ensemble of model excitonic dimers show that the protocol distills rich information about dissipative excitonic dynamics, which appears nontrivially hidden in the signal monitored in single realizations of four-wave mixing experiments.
Numerical study of the plasma chemistry in inductively coupled SF6 and SF6/Ar plasmas used for deep silicon etching applications
Authors: Mao M , Wang YN , Bogaerts A
Published: October 2011

A hybrid model, called the hybrid plasma equipment model, was used to study inductively coupled SF6 plasmas used for Si etching applications. The plasma properties such as number densities of electrons, positive and negative ions, and neutrals are calculated under typical etching conditions. The electron kinetics is analysed by means of the electron energy probability function. The plasma chemistry taking place in pure SF6 and in an Ar/SF6 mixture is also discussed, and finally the effect of the argon fraction on the plasma properties is investigated.
Variation of leakage mechanism and potential barrier in La and Ru co-doped BiFeO3 thin films
Authors: Yan Feng , Lai Man-On , Lu Li , Zhu Tie-Jun
Published: October 2011

Epitaxial c-axis-oriented La and Ru co-doped BiFeO3 (BLFRO) films are deposited on (0 0 1)-orientated Nb–SrTiO3 substrates by pulsed laser deposition. The phase and domain structures, ferroelectric and dielectric properties are characterized. The leakage current mechanisms of the BLFRO film are investigated at various temperatures. Poole–Frenkel (PF) and space-charge-limited current (SCLC) mechanisms are found to be dominant at high and low electric fields, respectively. PF emission is the dominant mechanism at high temperatures, whereas SCLC is dominant at low temperatures. The potential barriers at the electrode interfaces are estimated to be approximately 0.8 eV for the BLFRO film.
Structural and ferroelectric behaviours in blends of vinylidene fluoride oligomer and poly(vinylidene fluoride-trifluoroethylene) copolymer thin film
Authors: Zhang XiuLi , Dong Wenbin , Liu Yunfeiyue , Xu Guoqiang , Xu HaiSheng
Published: October 2011

The structure and ferroelectric properties of ultrathin blend films fabricated by the spin-coating process at room temperature from the mixed solution of vinylidene fluoride oligomers (OVDF) (n = 18) and poly(vinylidene fluoride-trifluoroethylene) copolymers (PVDF-TrFE) are investigated in detail. When OVDF content in mixture is between 40% and 60%, the remanent polarization and fatigue behaviour of the P(VDF-TrFE)/OVDF blend films are all improved. The ferroelectric thin film capacitor with poly(styrenesulfonate) (PSSH) interlayer exhibits a prominent performance with a remanent polarization of 120 mC m−2 even as the thickness of the blend film is 80 nm. Meanwhile, we demonstrate that the increase in the OVDF content from 0% to 100% cannot affect the molecular chain orientation of the P(VDF-TrFE)/OVDF blend films and the molecular chains are in parallel with the substrate.
The group of automorphisms of the spectral ball
Authors: Kosiński Łukasz
Published: October 2011

It is shown that the conjecture on the description of the group of automorphisms of the spectral ball posed by Ransford and White is false.
N-Glycosylation instead of cholesterol mediates oligomerization and apical sorting of GPI-APs in FRT cells
Authors: Imjeti Naga Salaija , Lebreton Stéphanie , Paladino Simona , de la Fuente Erwin , Gonzalez Alfonso , Zurzolo Chiara
Published: October 2011

Sorting of glycosylphosphatidyl-inositol–anchored proteins (GPI-APs) in polarized epithelial cells is not fully understood. Oligomerization in the Golgi complex has emerged as the crucial event driving apical segregation of GPI-APs in two different kind of epithelial cells, Madin–Darby canine kidney (MDCK) and Fisher rat thyroid (FRT) cells, but whether the mechanism is conserved is unknown. In MDCK cells cholesterol promotes GPI-AP oligomerization, as well as apical sorting of GPI-APs. Here we show that FRT cells lack this cholesterol-driven oligomerization as apical sorting mechanism. In these cells both apical and basolateral GPI-APs display restricted diffusion in the Golgi likely due to a cholesterol-enriched membrane environment. It is striking that N-glycosylation is the critical event for oligomerization and apical sorting of GPI-APs in FRT cells but not in MDCK cells. Our data indicate that at least two mechanisms exist to determine oligomerization in the Golgi leading to apical sorting of GPI-APs. One depends on cholesterol, and the other depends on N-glycosylation and is insensitive to cholesterol addition or depletion.
Exposure of bipartite hydrophobic signal triggers nuclear quality control of Ndc10 at the endoplasmic reticulum/nuclear envelope
Authors: Furth Noa , Gertman Or , Shiber Ayala , Alfassy Omri S. , Cohen Itamar , Rosenberg Masha M. , Doron Nurit Kleinberger , Friedler Assaf , Ravid Tommer
Published: October 2011

Proper functioning of the protein-folding quality control network depends on the network's ability to discern diverse structural perturbations to the native states of its protein substrates. Despite the centrality of the detection of misfolded states to cell home­ostasis, very little is known about the exact sequence and structural features that mark a protein as being misfolded. To investigate these features, we studied the requirements for the degradation of the yeast kinetochore protein Ndc10p. Mutant Ndc10p is a substrate of a protein-folding quality control pathway mediated by the E3 ubiquitin (Ub) ligase Doa10p at the endoplasmic reticulum (ER)/nuclear envelope membrane. Analysis of Ndc10p mutant derivatives, employing a reverse genetics approach, identified an autonomous quality control–associated degradation motif near the C-terminus of the protein. This motif is composed of two indispensable hydrophobic elements: a hydrophobic surface of an amphipathic helix and a loosely structured hydrophobic C-terminal tail. Site-specific point mutations expose these elements, triggering ubiquitin-mediated and HSP70 chaperone–dependent degradation of Ndc10p. These findings substantiate the ability of the ER quality control system to recognize subtle perturbation(s) in the native structure of a nuclear protein.
The schizophrenia susceptibility factor dysbindin and its associated complex sort cargoes from cell bodies to the synapse
Authors: Larimore Jennifer , Tornieri Karine , Ryder Pearl V. , Gokhale Avanti , Zlatic Stephanie A. , Craige Branch , Lee Joshua D. , Talbot Konrad , Pare Jean-Francois , Smith Yoland , Faundez Victor
Published: October 2011

Dysbindin assembles into the biogenesis of lysosome-related organelles complex 1 (BLOC-1), which interacts with the adaptor protein complex 3 (AP-3), mediating a common endosome-trafficking route. Deficiencies in AP-3 and BLOC-1 affect synaptic vesicle composition. However, whether AP-3-BLOC-1–dependent sorting events that control synapse membrane protein content take place in cell bodies upstream of nerve terminals remains unknown. We tested this hypothesis by analyzing the targeting of phosphatidylinositol-4-kinase type II α (PI4KIIα), a membrane protein present in presynaptic and postsynaptic compartments. PI4KIIα copurified with BLOC-1 and AP-3 in neuronal cells. These interactions translated into a decreased PI4KIIα content in the dentate gyrus of dysbindin-null BLOC-1 deficiency and AP-3–null mice. Reduction of PI4KIIα in the dentate reflects a failure to traffic from the cell body. PI4KIIα was targeted to processes in wild-type primary cultured cortical neurons and PC12 cells but failed to reach neurites in cells lacking either AP-3 or BLOC-1. Similarly, disruption of an AP-3–sorting motif in PI4KIIα impaired its sorting into processes of PC12 and primary cultured cortical neuronal cells. Our findings indicate a novel vesicle transport mechanism requiring BLOC-1 and AP-3 complexes for cargo sorting from neuronal cell bodies to neurites and nerve terminals.
Differential interactions of the formins INF2, mDia1, and mDia2 with microtubules
Authors: Gaillard Jeremie , Ramabhadran Vinay , Neumanne Emmanuelle , Gurel Pinar , Blanchoin Laurent , Vantard Marylin , Higgs Henry N.
Published: October 2011

A number of cellular processes use both microtubules and actin filaments, but the molecular machinery linking these two cytoskeletal elements remains to be elucidated in detail. Formins are actin-binding proteins that have multiple effects on actin dynamics, and one formin, mDia2, has been shown to bind and stabilize microtubules through its formin homology 2 (FH2) domain. Here we show that three formins, INF2, mDia1, and mDia2, display important differences in their interactions with microtubules and actin. Constructs containing FH1, FH2, and C-terminal domains of all three formins bind microtubules with high affinity (Kd< 100 nM). However, only mDia2 binds microtubules at 1:1 stoichiometry, with INF2 and mDia1 showing saturating binding at approximately 1:3 (formin dimer:tubulin dimer). INF2-FH1FH2C is a potent microtubule-bundling protein, an effect that results in a large reduction in catastrophe rate. In contrast, neither mDia1 nor mDia2 is a potent microtubule bundler. The C-termini of mDia2 and INF2 have different functions in microtubule interaction, with mDia2's C-terminus required for high-affinity binding and INF2's C-terminus required for bundling. mDia2's C-terminus directly binds microtubules with submicromolar affinity. These formins also differ in their abilities to bind actin and microtubules simultaneously. Microtubules strongly inhibit actin polymerization by mDia2, whereas they moderately inhibit mDia1 and have no effect on INF2. Conversely, actin monomers inhibit microtubule binding/bundling by INF2 but do not affect mDia1 or mDia2. These differences in interactions with microtubules and actin suggest differential function in cellular processes requiring both cytoskeletal elements.
The design of optimal therapeutic small interfering RNA molecules targeting diverse strains of influenza A virus
Authors: ElHefnawi Mahmoud , Hassan Nafisa , Kamar Mona , Siam Rania , Remoli Anna Lisa , El-Azab Iman , AlAidy Osama , Marsili Giulia , Sgarbanti Marco
Published: October 2011

Motivation: There is an urgent need for new medications to combat influenza pandemics.

Methods: Using the genome analysis of the influenza A virus performed previously, we designed and performed a combinatorial exhaustive systematic methodology for optimal design of universal therapeutic small interfering RNA molecules (siRNAs) targeting all diverse influenza A viral strains. The rationale was to integrate the factors for highly efficient design in a pipeline of analysis performed on possible influenza-targeting siRNAs. This analysis selects specific siRNAs that has the ability to target highly conserved, accessible and biologically significant regions. This would require minimal dosage and side effects.

Results and Discussion: First, >6000 possible siRNAs were designed. Successive filtration followed where a novel method for siRNA scoring filtration layers was implemented. This method excluded siRNAs below the 90% experimental inhibition mapped scores using the intersection of 12 different scoring algorithms. Further filtration of siRNAs is done by eliminating those with off-targets in the human genome and those with undesirable properties and selecting siRNA targeting highly probable single-stranded regions. Finally, the optimal properties of the siRNA were ensured through selection of those targeting 100% conserved, biologically functional short motifs. Validation of a predicted active (sh114) and a predicted inactive (sh113) (that was filtered out in Stage 8) silencer of the NS1 gene showed significant inhibition of the NS1 gene for sh114, with negligible decrease for sh113 which failed target accessibility. This demonstrated the fertility of this methodology.

Contact:  mahef@aucegypt.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data
Authors: Zhang Jin , Wu Yufeng
Published: October 2011

Motivation: Structural variation (SV), such as deletion, is an important type of genetic variation and may be associated with diseases. While there are many existing methods for detecting SVs, finding deletions is still challenging with low-coverage short sequence reads. Existing deletion finding methods for sequence reads either use the so-called split reads mapping for detecting deletions with exact breakpoints, or rely on discordant insert sizes to estimate approximate positions of deletions. Neither is completely satisfactory with low-coverage sequence reads.

Results: We present SVseq, an efficient two-stage approach, which combines the split reads mapping and discordant insert size analysis. The first stage is split reads mapping based on the Burrows–Wheeler transform (BWT), which finds candidate deletions. Our split reads mapping method allows mismatches and small indels, thus deletions near other small variations can be discovered and reads with sequencing errors can be utilized. The second stage filters the false positives by analyzing discordant insert sizes. SVseq is more accurate than an alternative approach when applying on simulated data and empirical data, and is also much faster.

Availability: The program SVseq can be downloaded at http://www.engr.uconn.edu/~jiz08001/

Contact:  jinzhang@engr.uconn.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
BioTextQuest: a web-based biomedical text mining suite for concept discovery
Authors: Papanikolaou Nikolas , Pafilis Evangelos , Nikolaou Stavros , Ouzounis Christos A. , Iliopoulos Ioannis , Promponas Vasilis J.
Published: October 2011

Summary: BioTextQuest combines automated discovery of significant terms in article clusters with structured knowledge annotation, via Named Entity Recognition services, offering interactive user-friendly visualization. A tag-cloud-based illustration of terms labeling each document cluster are semantically annotated according to the biological entity, and a list of document titles enable users to simultaneously compare terms and documents of each cluster, facilitating concept association and hypothesis generation. BioTextQuest allows customization of analysis parameters, e.g. clustering/stemming algorithms, exclusion of documents/significant terms, to better match the biological question addressed.

Availability:  http://biotextquest.biol.ucy.ac.cy

Contact:  vprobon@ucy.ac.cy; iliopj@med.uoc.gr

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Pico-inplace-inversions between human and chimpanzee
Authors: Hou Minmei , Yao Ping , Antonou Angela , Johns Mitrick A.
Published: October 2011

Motivation: There have been several studies on the micro-inversions between human and chimpanzee, but there are large discrepancies among their results. Furthermore, all of them rely on alignment procedures or existing alignment results to identify inversions. However, the core alignment procedures do not take very small inversions into consideration. Therefore, their analyses cannot find inversions that are too small to be detected by a classic aligner. We call such inversions pico-inversions.

Results: We re-analyzed human–chimpanzee alignment from the UCSC Genome Browser for micro-inplace-inversions and screened for pico-inplace-inversions using a likelihood ratio test. We report that the quantity of inplace-inversions between human and chimpanzee is substantially greater than what had previously been discovered. We also present the software tool PicoInversionMiner to detect pico-inplace-inversions between closely related species.

Availability: Software tools, scripts and result data are available at http://faculty.cs.niu.edu/~hou/PicoInversion.html.

Contact:  mhou@cs.niu.edu
FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis
Authors: Kumar Sudhir , Konikoff Charlotte , Van Emden Bernard , Busick Christopher , Davis Kailah T. , Ji Shuiwang , Wu Lin-Wei , Ramos Hector , Brody Thomas , Panchanathan Sethuraman , Ye Jieping , Karr Timothy L. , Gerold Kristyn , McCutchan Michael , Newfeld Stuart J.
Published: October 2011

Summary: Images containing spatial expression patterns illuminate the roles of different genes during embryogenesis. In order to generate initial clues to regulatory interactions, biologists frequently need to know the set of genes expressed at the same time at specific locations in a developing embryo, as well as related research publications. However, text-based mining of image annotations and research articles cannot produce all relevant results, because the primary data are images that exist as graphical objects. We have developed a unique knowledge base (FlyExpress) to facilitate visual mining of images from Drosophila melanogaster embryogenesis. By clicking on specific locations in pictures of fly embryos from different stages of development and different visual projections, users can produce a list of genes and publications instantly. In FlyExpress, each queryable embryo picture is a heat-map that captures the expression patterns of more than 4500 genes and more than 2600 published articles. In addition, one can view spatial patterns for particular genes over time as well as find other genes with similar expression patterns at a given developmental stage. Therefore, FlyExpress is a unique tool for mining spatiotemporal expression patterns in a format readily accessible to the scientific community.

Availability:  http://www.flyexpress.net

Contact:  s.kumar@asu.edu
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data
Authors: Althammer Sonja , González-Vallinas Juan , Ballaré Cecilia , Beato Miguel , Eyras Eduardo
Published: October 2011

Motivation: High-throughput sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein–DNA and protein–RNA binding, as well as for measuring RNA expression. With increasing variety and sequencing depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing.

Results: We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. We prove the effectiveness of Pyicos to select for significant signals and show that its accuracy is comparable and sometimes superior to that of methods specifically designed for each particular type of experiment. Pyicos facilitates the analysis of a variety of HTS datatypes through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics.

Availability: Open-source software, with tutorials and protocol files, is available at http://regulatorygenomics.upf.edu/pyicos or as a Galaxy server at http://regulatorygenomics.upf.edu/galaxy

Contact:  eduardo.eyras@upf.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology
Authors: Blakes Jonathan , Twycross Jamie , Romero−Campero Francisco Jose , Krasnogor Natalio
Published: October 2011

Summary: The Infobiotics Workbench is an integrated software suite incorporating model specification, simulation, parameter optimization and model checking for Systems and Synthetic Biology. A modular model specification allows for straightforward creation of large-scale models containing many compartments and reactions. Models are simulated either using stochastic simulation or numerical integration, and visualized in time and space. Model parameters and structure can be optimized with evolutionary algorithms, and model properties calculated using probabilistic model checking.

Availability: Source code and binaries for Linux, Mac and Windows are available at http://www.infobiotics.org/infobiotics-workbench/; released under the GNU General Public License (GPL) version 3.

Contact:  Natalio.Krasnogor@nottingham.ac.uk
Automatic generation of protein structure cartoons with Pro-origami
Authors: Stivala Alex , Wybrow Michael , Wirth Anthony , Whisstock James C. , Stuckey Peter J.
Published: October 2011

Summary: Protein topology diagrams are 2D representations of protein structure that are particularly useful in understanding and analysing complex protein folds. Generating such diagrams presents a major problem in graph drawing, with automatic approaches often resulting in errors or uninterpretable results. Here we apply a breakthrough in diagram layout to protein topology cartoons, providing clear, accurate, interactive and editable diagrams, which are also an interface to a structural search method.

Availability: Pro-origami is available via a web server at http://munk.csse.unimelb.edu.au/pro-origami

Contact:  a.stivala@pgrad.unimelb.edu.au; pjs@csse.unimelb.edu.au
The Type III Effector HsvG of the Gall-Forming Pantoea agglomerans Mediates Expression of the Host Gene HSVGT
Authors: Nissan Gal , Manulis-Sasson Shulamit , Chalupowicz Laura , Teper Doron , Yeheskel Adva , Pasmanik-Chor Metsada , Sessa Guido , Barash Isaac
Published: October 2011

The type III effector HsvG of the gall-forming Pantoea agglomerans pv. gypsophilae is a DNA-binding protein that is imported to the host nucleus and involved in host specificity. The DNA-binding region of HsvG was delineated to 266 amino acids located within a secondary structure region near the N-terminus of the protein but did not display any homology to canonical DNA-binding motifs. A binding site selection procedure was used to isolate a target gene of HsvG, named HSVGT, in Gypsophila paniculata. HSVGT is a predicted acidic protein of the DnaJ family with 244 amino acids. It harbors characteristic conserved motifs of a eukaryotic transcription factor, including a bipartite nuclear localization signal, zinc finger, and leucine zipper DNA-binding motifs. Quantitative real-time polymerase chain reaction analysis demonstrated that HSVGT transcription is specifically induced in planta within 2 h after inoculation with the wild-type P. agglomerans pv. gypsophilae compared with the hsvG mutant. Induction of HSVGT reached a peak of sixfold at 4 h after inoculation and progressively declined thereafter. Gel-shift assay demonstrated that HsvG binds to the HSVGT promoter, indicating that HSVGT is a direct target of HsvG. Our results support the hypothesis that HsvG functions as a transcription factor in gypsophila.
A Plant Arabinogalactan-Like Glycoprotein Promotes a Novel Type of Polar Surface Attachment by Rhizobium leguminosarum
Authors: Xie Fang , Williams Alan , Edwards Anne , Downie J. Allan
Published: October 2011

Rhizobium leguminosarum bv. viciae can attach to the roots of legume and non-legume plants. We wanted to determine whether root exudates could affect in vitro surface attachment in a confocal microscopy assay. Root exudate from pea, other legumes, wheat, and Arabidopsis induced R. leguminosarum bv. viciae to attach end-on (in a polar manner) to glass in hexagonal close-packed arrays, rather than attaching along their long axis. This did not involve a reorientation but was probably due to altered growth. The polar attachment involves a novel bacterial component because it occurred in mutants lacking a symbiosis plasmid (and hence nodulation genes) and polar glucomannan. The major surface (acidic) exopolysaccharide was required, and mutations affecting exported proteins and flagella delayed but did not block polar attachment. The polar attachment activity was purified as a high molecular weight fraction from pea root exudate and is an arabinogalactan protein (AGP) based on its carbohydrate content, reactivity with AGP-specific monoclonal antibodies and Yariv reagent, and sensitivity to enzymes that degrade proteins and carbohydrates. We propose that this novel mode of AGP-induced attachment may be important for growth of these bacteria on the roots of both legumes and non-legumes.
First Report of Gray Mold Caused by Botrytis cinerea on Yellow Cosmos (Bidens sulphurea) in Brazil
Authors: Guatimosim E. , Fuga C. A. G. , Pinto H. J. , Barreto R. W.
Published: October 2011

Bidens sulphurea (synonym Cosmos sulphureus) (Asteraceae), commonly known as yellow cosmos, is a native herbaceous species from Mexico that is widely used as an ornamental. It has been introduced in Brazil and has escaped from gardens, becoming a minor weed in ruderal, crop and pasture areas (2). In June 2010, groups of B. sulphurea individuals were found in a garden at the locality of Piúna, municipality of Viçosa (state of Minas Gerais, Brazil), that were severely attacked by gray mold. The disease led to flower rot with dieback of infected peduncles and stems. Plant tissues became brown to grayish brown and were covered by extensive fungal sporulation; in addition, seeds were colonized and destroyed by the fungus. A hyphomycete was regularly found associated with the diseased flowers, which was readily recognized as having a morphology typical of Botrytis cinerea: conidiophores solitary, cylindrical, terminally branched, 15 to 20 μm wide, grayish to olivaceous gray, and smooth; conidiogenous cells polyblastic, subcylindrical to ampulliform, and 120 to 230 × (13-) 14 to 16 (-19) μm; conidia ellipsoid to obovoid, 8 to 12 × 6.5 to 8 (-9) μm, with a discrete hilum at the base, 1 to 2 μm, aseptate, and hyaline. The fungus was isolated in pure culture and inoculation of one isolate on healthy B. suphurea individuals was carried out with a 2.14 × 106 conidia/ml suspension, which was sprayed to runoff onto three plants bearing four to six inflorescences. All plants were left in a moist chamber for 48 h and later transferred to a bench in a greenhouse at 21 ± 3°C. Gray mold symptoms appeared after 10 days that led to rapid and complete necrosis of flowers and peduncles. Infection first appeared on the flowers but progressed downward, leading to top dieback and finally plant death (not seen in the field). Only Botrytis cinerea was obtained in isolations from diseased flowers, demonstrating the pathogenicity of the fungus. A representative sample was deposited in the UFV herbarium (VIC 31602). The only other record of Botrytis cinerea causing gray mold of B. sulphurea is from China (1,3). To our knowledge, this is the first record of Botrytis cinerea causing gray mold on B. sulphurea in Brazil.

References: (1) D. F. Farr and A. Y. Rossman. Fungal Databases. Systematic Botany and Mycology Laboratory, ARS, UDSA. Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , 2011. (2) H. Lorenzi and H. M. Souza. Plantas Ornamentais no Brasil. Plantarum, Nova Odessa, Brazil. 1995. (3) Z. Zhang. Flora Fungorum Sinicorum. Vol. 26. Botrytis, Ramularia. Science Press, Beijing, China. 2006.
Production of baculovirus defective interfering particles during serial passage is delayed by removing transposon target sites in fp25k
Authors: Giri Lopamudra , Feiss Michael G. , Bonning Bryony C. , Murhammer David W.
Published: October 2011

Accumulation of baculovirus defective interfering particle (DIP) and few polyhedra (FP) mutants is a major limitation to continuous large-scale baculovirus production in insect-cell culture. Although overcoming these mutations would result in a cheaper platform for producing baculovirus biopesticides, little is known regarding the mechanism of FP and DIP formation. This issue was addressed by comparing DIP production of wild-type (WT) Autographa californica multiple nucleopolyhedrovirus (AcMNPV) with that of a recombinant AcMNPV (denoted Ac-FPm) containing a modified fp25k gene with altered transposon insertion sites that prevented transposon-mediated production of the FP phenotype. In addition to a reduction in the incidence of the FP phenotype, DIP formation was delayed on passaging of Ac-FPm compared with WT AcMNPV. Specifically, the yield of DIP DNA in Ac-FPm was significantly lower than in WT AcMNPV up to passage 16, thereby demonstrating that modifying the transposon insertion sites increases the genomic stability of AcMNPV. A critical component of this investigation was the optimization of a systematic method based on the use of pulsed-field gel electrophoresis (PFGE) to characterize extracellular virus DNA. Specifically, PFGE was used to detect defective genomes, determine defective genome sizes and quantify the amount of defective genome within a heterogeneous genome population of passaged virus.
A matter of life or death: How microsatellites emerge in and vanish from the human genome
Authors: Kelkar Yogeshwar D. , Eckert Kristin A. , Chiaromonte Francesca , Makova Kateryna D.
Published: October 2011

Microsatellites—tandem repeats of short DNA motifs—are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypothesized to follow a life cycle, wherein they are born and expand into adulthood, until their degradation and death. Here we identified microsatellite births/deaths in human, chimpanzee, and orangutan genomes, using macaque and marmoset as outgroups. We inferred mutations causing births/deaths based on parsimony, and investigated local genomic environments affecting them. We also studied birth/death patterns within transposable elements (Alus and L1s), coding regions, and disease-associated loci. We observed that substitutions were the predominant cause for births of short microsatellites, while insertions and deletions were important for births of longer microsatellites. Substitutions were the cause for deaths of microsatellites of virtually all lengths. AT-rich L1 sequences exhibited elevated frequency of births/deaths over their entire length, while GC-richAlus only in their 3′ poly(A) tails and middle A-stretches, with differences depending on transposable element integration timing. Births/deaths were strongly selected against in coding regions. Births/deaths occurred in genomic regions with high substitution rates, protomicrosatellite content, and L1 density, but low GC content andAludensity. The majority of the 17 disease-associated microsatellites examined are evolutionarily ancient (were acquired by the common ancestor of simians). Our genome-wide investigation of microsatellite life cycle has fundamental applications for predicting the susceptibility of birth/death of microsatellites, including many disease-causing loci.
A Critical Role of STAYGREEN/Mendel’s I Locus in Controlling Disease Symptom Development during Pseudomonas syringae pv tomato Infection of Arabidopsis
Authors: Mecey Christy , Hauck Paula , Trapp Marisa , Pumplin Nathan , Plovanich Anne , Yao Jian , He Sheng Yang
Published: October 2011

Production of disease symptoms represents the final phase of infectious diseases and is a main cause of crop loss and/or marketability. However, little is known about the molecular basis of disease symptom development. In this study, a genetic screening was conducted to identify Arabidopsis (Arabidopsis thaliana) mutants that are impaired specifically in the development of disease symptoms (leaf chlorosis and/or necrosis) after infection with the bacterial pathogen Pseudomonas syringae pv tomato (Pst) DC3000. An ethyl methanesulfonate-induced Arabidopsis mutant (no chlorosis1 [noc1]) was identified. In wild-type plants, the abundance of chlorophylls decreased markedly after Pst DC3000 infection, whereas the total amount of chlorophylls remained relatively unchanged in the noc1 mutant. Interestingly, noc1 mutant plants also exhibited reduced disease symptoms in response to the fungal pathogen Alternaria brassicicola. Genetic and molecular analyses showed that the nuclear gene STAYGREEN (SGR; or Mendel’s I locus) is mutated (resulting in the aspartic acid to tyrosine substitution at amino acid position 88) in noc1 plants. Transforming wild-type SGR cDNA into the noc1 mutant rescued the chlorosis phenotype in response to Pst DC3000 infection. The SGR transcript was highly induced by Pst DC3000, A. brassicicola, or coronatine (COR), a bacterial phytotoxin that promotes chlorosis. The induction of SGR expression by COR is dependent on COI1, a principal component of the jasmonate receptor complex. These results suggest that pathogen/COR-induced expression of SGR is a critical step underlying the development of plant disease chlorosis.
Size influences the spatial distribution and fish‐aggregating device use of five Mediterranean fish species
Authors: SINOPOLI M. , BADALAMENTI F. , D’ANNA G. , GRISTINA M. , ANDALORO F.
Published: October 2011

Abstract Fish‐aggregating devices are floating objects used worldwide to improve pelagic fishery yield. Fish‐aggregating devices use the natural attraction exerted by floating objects on juveniles and adults of both pelagic and demersal fish. In this study, it was hypothesised that fish change their degree and type of interaction with moored floating objects depending on size. This is because fishes in early life stage remain close to floating objects, using them as a shelter, but as they grow they move further away from floating objects spending their time swimming to seek food. To test this hypothesis, the spatial distribution and habitat use of five Mediterranean fish species were quantified. The results enabled the hypothesis to be accepted for all species, exceptBalistes carolinensisGmelin. For this species, a shelter from predator model was applicable, but for the other species, the generalised meeting point model was more adaptable.
Movement, home range and habitat selection of stocked juvenile muskellunge, Esox masquinongy, in Forbes Lake, Illinois: exploring the effects of latitudinal origin
Authors: WAGNER C. P. , WAHL D. H.
Published: October 2011

Abstract  Intraspecific, seasonal and diel variation in movement behaviours of three stocks of juvenile (age‐2; 399–610 mm total length) muskellunge, Esox masquinongy Mitchill, were assessed using radio telemetry in Forbes Lake (225 ha), IL, USA. Experimental populations included muskellunge from the Upper Mississippi (Leech Lake, MN, USA) and Ohio (Cave Run Lake, KY, USA) river drainages, as well as progeny from North Spring Lake, IL, a mixed‐origin stock. No differences in hourly movement rates or home ranges were detected among stocks. Movement rates were greatest during spring (mean ± SE = 42 ± 4 m h−1), lowest during summer (16 ± 3 m h−1) and intermediate in autumn (28 ± 5 m h−1). Additionally, movement rates during the summer were greater at night than crepuscular periods. Home range sizes were similar during spring and autumn (mean ± SE = 17–18 ± 3–4 ha) and decreased during summer (5 ± 3 ha). Although habitat selection characteristics were generally similar among stocks, fish from the Upper Mississippi River drainage occupied deeper water more frequently and selected the pelagic zone more strongly during the spring than those from the Ohio River and mixed‐origin stocks. Within the littoral zone, muskellunge selected coarse woody habitat and aquatic macrophytes. Collectively, these findings suggest little behavioural differentiation among genetically divergent stocks when evaluated in a common reservoir environment.
Modelling the migratory behaviour of salmonids in relation to environmental and physiological parameters using telemetry data
Authors: BENDALL B. , MOORE A. , MAXWELL D. , DAVISON P. , EDMONDS N. , ARCHER D. , SOLOMON D. , GREEST V. , WYATT R. , BROAD K.
Published: October 2011

Abstract  Advances in the field of telemetry techniques during the last few decades have greatly expanded our knowledge on migratory behaviour and provided the opportunity to obtain practically useful data for the conservation and management of salmonid populations. However, applying this information to the development of much needed population‐based migration models has been limited. Furthermore, this research has generally been restricted to assessing the role of river flow on fish movement. Models derived from a 6‐year telemetry study on the movements of Atlantic salmon, Salmo salar L., and sea trout, Salmo trutta L., in the River Tyne are presented together with an assessment of counter data from the same river to highlight the importance of additional environmental and physiological parameters in regulating fish movement. The data are discussed in relation to the advantages of telemetry data, the need to develop predictive models, the statistical methods used and the potential direction of future work in this area.