bluuebunny/crossref_metadata_2025 huggingface dataset:
Arabidopsis mutant deficient in 3 abscisic acid-activated protein kinases reveals critical roles in growth, reproduction, and stress
Authors: Fujii Hiroaki , Zhu Jian-Kang
Published: May 2009

Abscisic acid (ABA) is an important phytohormone regulating seed dormancy, germination, seedling growth, and plant transpiration. We report here an Arabidopsis triple mutant that is disrupted in 3 SNF1-related protein kinase subfamily 2 (SnRK2s) and nearly completely insensitive to ABA. These SnRK2s, SnRK2.2, SnRK2.3, and SnRK2.6 (also known as OST1), are activated by ABA and can phosphorylate the ABA-responsive element binding factor family of b-ZIP transcription factors, which are important for the activation of ABA-responsive genes. Although stomatal regulation of
snrk2.6
and seed germination and seedling growth of the
snrk2.2
/
2.3
double mutant are insensitive to ABA, ABA responses are still present in these mutants, and the growth and reproduction of these mutants are not very different from those of the WT. In contrast, the
snrk2.2
/
2.3
/
2.6
triple mutant grows poorly and produces few seeds. The triple mutant plants lose water extremely fast when ambient humidity is not high. Even on 50 μM ABA, the triple mutant can germinate and grow, whereas the most insensitive known mutants cannot develop on 10 μM ABA. In-gel kinase assays showed that all ABA-activated protein kinase activities are eliminated in the triple mutant. Also, the expression of ABA-induced genes examined is completely blocked in the triple mutant. These results demonstrate that the protein kinases SnRK2.2, SnRK2.3, and SnRK2.6 have redundant functions, and suggest that ABA signaling is critical for plant growth and reproduction.
Facilitated diffusion with DNA coiling
Authors: Lomholt Michael A. , van den Broek Bram , Kalisch Svenja-Marei J. , Wuite Gijs J. L. , Metzler Ralf
Published: May 2009

When DNA-binding proteins search for their specific binding site on a DNA molecule they alternate between linear 1-dimensional diffusion along the DNA molecule, mediated by nonspecific binding, and 3-dimensional volume excursion events between successive dissociation from and rebinding to DNA. If the DNA molecule is kept in a straight configuration, for instance, by optical tweezers, these 3-dimensional excursions may be divided into long volume excursions and short hops along the DNA. These short hops correspond to immediate rebindings after dissociation such that a rebinding event to the DNA occurs at a site that is close to the site of the preceding dissociation. When the DNA molecule is allowed to coil up, immediate rebinding may also lead to so-called intersegmental jumps, i.e., immediate rebindings to a DNA segment that is far away from the unbinding site when measured in the chemical distance along the DNA, but close by in the embedding 3-dimensional space. This effect is made possible by DNA looping. The significance of intersegmental jumps was recently demonstrated in a single DNA optical tweezers setup. Here we present a theoretical approach in which we explicitly take the effect of DNA coiling into account. By including the spatial correlations of the short hops we demonstrate how the facilitated diffusion model can be extended to account for intersegmental jumping at varying DNA densities. It is also shown that our approach provides a quantitative interpretation of the experimentally measured enhancement of the target location by DNA-binding proteins.
What makes teachers tick? Sustaining events in new teachers’ lives
Authors: Morgan Mark , Ludlow Larry , Kitching Karl , O'Leary Michael , Clarke Aleisha
Published: May 2009

To investigate what keeps teachers motivated on a day‐to‐day basis, we traced the importance of routinely encounteredaffective episodes. Significant research on emotions already highlights the relative importance of positive versus negative episodes, the importance of perceived origins of events and the need to differentiate between the frequency and affective intensity of episodes. Survey reports from 749 recently qualified primary teachers in Ireland strongly suggest theabsenceof positive experiences undermines commitment and efficacy rather than theoccurrenceof negative events. Furthermore, while remote structural factors may heavily influence teaching, it is the perception of events at micro‐level that impinge most strongly on motivation. Finally, the importance of particular experiences was, crucially, more related to their frequency than intensity. A major implication for teachers’ job satisfaction is the suggestion that while adverse episodes may be inevitably experienced, positive events (that occur independently of negative ones) fortify motivation and resilience.
A comparative study of peer and teacher feedback and of various peer feedback forms in a secondary school writing curriculum
Authors: Gielen Sarah , Tops Lies , Dochy Filip , Onghena Patrick , Smeets Stijn
Published: May 2009

This study examines whether peer feedback can be a substitute for teacher feedback and which measures can be taken to improve its effectiveness. A pre‐test post‐test control group design examined the long‐term learning effects of individual peer feedback and of collective teacher feedback on writing assignments in secondary education. Moreover, it examined the added value of a priori question forms and a posteriori reply forms aimed at supporting the assessee's response to peer feedback. The study supports the ‘non‐inferiority’ hypothesis of there being no significant difference in students’ progress after plain substitutional peer feedback or teacher feedback. Both groups (plain peer feedback and teacher feedback), however, improved significantly less than the groups that worked with question or reply forms, confirming the added‐value of these forms. Almost half of the students found the received peer feedback helpful, but less than a quarter considered giving feedback an aid in their own learning process.
Integration of perceptual information in word access
Authors: Richter Tobias , Zwaan Rolf A.
Published: May 2009

According to experiential theories of language comprehension, perceptual information plays an essential role when word meanings are accessed. We conducted four experiments to investigate how different types of perceptual information such as colour and shape are combined during word access. One possibility is that the colour and shape of a word's referent are activated independently from one another and are combined in an additive manner. Alternatively, words might activate perceptual representations via a multiplicative integration of colour and shape. Experiment 1 established that participants follow a multiplicative similarity rule when they judge the similarity of schematic pictures to actual fruits and vegetables. In Experiments 2 to 4, participants performed a classification task, a lexical decision task, or a word-naming task on names of fruits and vegetables that were superimposed on a background picture. Responses were facilitated only when both colour and shape of the picture matched the word's referents. Response times were associated negatively with mean similarity ratings and the consistency of these ratings obtained in the first experiment. These results suggest a multiplicative integration of different types of perceptual information during word access.
Short article: The processing of subject and object relative clauses in Spanish: An eye-tracking study
Authors: Betancort Moisés , Carreiras Manuel , Sturt Patrick
Published: May 2009

A normative study and an eye-tracking experiment investigated the influence of animacy on the processing of subject and object relative clauses in Spanish. The results showed that object relative clauses caused more difficulty than subject relative clauses, but that animacy modulated this preference. The overall pattern was similar to findings in other languages. However, because of the syntactic characteristics of Spanish relative clauses, the results give novel insights into the processing mechanisms that underlie relative clause processing.
Neutronics R&D efforts in support of the European breeder blanket development programme
Authors: Fischer U. , Batistoni P. , Klix A. , Kodeli I. , Leichtle D. , Perel R.L.
Published: May 2009

The recent progress in the R&D neutronics efforts spent in the EU to support the development of the HCLL and HCPB breeder blankets is presented. These efforts include neutronic design activities performed in the framework of the European DEMO reactor study, validation efforts by means of neutronics mock-up experiments using 14 MeV neutron generators and the development of dedicated computational tools such as the conversion software McCad for the automatic generation of a Monte Carlo geometry model from available CAD data, and the MCSEN code for Monte Carlo based calculations of sensitivities and uncertainties by using the track length estimator. The supporting validation effort is devoted to the capability of the neutronics tools and data to predict the tritium production and other nuclear responses of interest in neutronics mock-up experiments. Such an experiment has been conducted on a HCPB mock-up while another on a HCLL mock-up is in progress.
The Cytoplasmic Tail of GM3 Synthase Defines Its Subcellular Localization, Stability, and In Vivo Activity
Authors: Uemura Satoshi , Yoshida Sayaka , Shishido Fumi , Inokuchi Jin-ichi
Published: May 2009

GM3 synthase (SAT-I) is the primary glycosyltransferase responsible for the biosynthesis of ganglio-series gangliosides. In this study, we identify three isoforms of mouse SAT-I proteins, named M1-SAT-I, M2-SAT-I, and M3-SAT-I, which possess distinct lengths in their NH2-terminal cytoplasmic tails. These isoforms are produced by leaky scanning from mRNA variants of mSAT-Ia and mSAT-Ib. M2-SAT-I and M3-SAT-I were found to be localized in the Golgi apparatus, as expected, whereas M1-SAT-I was exclusively found in the endoplasmic reticulum (ER). Specific multiple arginines (R) arranged in an R-based motif, RRXXXXR necessary for ER targeting, were found in the cytoplasmic tail of M1-SAT-I, and in vivo GM3 biosynthesis by M1-SAT-I was very low because of restricted transport to the Golgi apparatus. In addition, M1-SAT-I and M3-SAT-I had a long half-life relative to M2-SAT-I. This is the first report demonstrating the presence of an ER-targeting R-based motif in the cytoplasmic tail of a protein in the mammalian glycosyltransferase family of enzymes. The system, which produces SAT-I isoforms having distinct characteristics, is likely to be of critical importance for the regulation of GM3 biosynthesis under various pathological and physiological conditions.
Cortical F-Actin, the Exocytic Mode, and Neuropeptide Release in Mouse Chromaffin Cells Is Regulated by Myristoylated Alanine-rich C-Kinase Substrate and Myosin II
Authors: Doreian Bryan W. , Fulop Tiberiu G. , Meklemburg Robert L. , Smith Corey B.
Published: May 2009

Adrenal medullary chromaffin cells are innervated by the sympathetic splanchnic nerve and translate graded sympathetic firing into a differential hormonal exocytosis. Basal sympathetic firing elicits a transient kiss-and-run mode of exocytosis and modest catecholamine release, whereas elevated firing under the sympathetic stress response results in full granule collapse to release catecholamine and peptide transmitters into the circulation. Previous studies have shown that rearrangement of the cell actin cortex regulates the mode of exocytosis. An intact cortex favors kiss-and-run exocytosis, whereas disrupting the cortex favors the full granule collapse mode. Here, we investigate the specific roles of two actin-associated proteins, myosin II and myristoylated alanine-rich C-kinase substrate (MARCKS) in this process. Our data demonstrate that MARCKS phosphorylation under elevated cell firing is required for cortical actin disruption but is not sufficient to elicit peptide transmitter exocytosis. Our data also demonstrate that myosin II is phospho-activated under high stimulation conditions. Inhibiting myosin II activity prevented disruption of the actin cortex, full granule collapse, and peptide transmitter release. These results suggest that phosphorylation of both MARCKS and myosin II lead to disruption of the actin cortex. However, myosin II, but not MARCKS, is required for the activity-dependent exocytosis of the peptide transmitters.
IC97 Is a Novel Intermediate Chain of I1 Dynein That Interacts with Tubulin and Regulates Interdoublet Sliding
Authors: Wirschell Maureen , Yang Chun , Yang Pinfen , Fox Laura , Yanagisawa Haru-aki , Kamiya Ritsu , Witman George B. , Porter Mary E. , Sale Winfield S.
Published: May 2009

Our goal is to understand the assembly and regulation of flagellar dyneins, particularly the Chlamydomonas inner arm dynein called I1 dynein. Here, we focus on the uncharacterized I1-dynein IC IC97. The IC97 gene encodes a novel IC without notable structural domains. IC97 shares homology with the murine lung adenoma susceptibility 1 (Las1) protein—a candidate tumor suppressor gene implicated in lung tumorigenesis. Multiple, independent biochemical assays determined that IC97 interacts with both α- and β-tubulin subunits within the axoneme. I1-dynein assembly mutants suggest that IC97 interacts with both the IC138 and IC140 subunits within the I1-dynein motor complex and that IC97 is part of a regulatory complex that contains IC138. Microtubule sliding assays, using axonemes containing I1 dynein but devoid of IC97, show reduced microtubule sliding velocities that are not rescued by kinase inhibitors, revealing a critical role for IC97 in I1-dynein function and control of dynein-driven motility.
IC138 Defines a Subdomain at the Base of the I1 Dynein That Regulates Microtubule Sliding and Flagellar Motility
Authors: Bower Raqual , VanderWaal Kristyn , O'Toole Eileen , Fox Laura , Perrone Catherine , Mueller Joshua , Wirschell Maureen , Kamiya R. , Sale Winfield S. , Porter Mary E.
Published: May 2009

To understand the mechanisms that regulate the assembly and activity of flagellar dyneins, we focused on the I1 inner arm dynein (dynein f) and a null allele, bop5-2, defective in the gene encoding the IC138 phosphoprotein subunit. I1 dynein assembles in bop5-2 axonemes but lacks at least four subunits: IC138, IC97, LC7b, and flagellar-associated protein (FAP) 120—defining a new I1 subcomplex. Electron microscopy and image averaging revealed a defect at the base of the I1 dynein, in between radial spoke 1 and the outer dynein arms. Microtubule sliding velocities also are reduced. Transformation with wild-type IC138 restores assembly of the IC138 subcomplex and rescues microtubule sliding. These observations suggest that the IC138 subcomplex is required to coordinate I1 motor activity. To further test this hypothesis, we analyzed microtubule sliding in radial spoke and double mutant strains. The results reveal an essential role for the IC138 subcomplex in the regulation of I1 activity by the radial spoke/phosphorylation pathway.
CycSim—an online tool for exploring and experimenting with genome-scale metabolic models
Authors: Le Fèvre F. , Smidtas S. , Combe C. , Durot M. , d'Alché-Buc Florence , Schachter V.
Published: May 2009

Summary:  CycSim is a web application dedicated to in silico experiments with genome-scale metabolic models coupled to the exploration of knowledge from BioCyc and KEGG. Specifically, CycSim supports the design of knockout experiments: simulation of growth phenotypes of single or multiple gene deletions mutants on specified media, comparison of these predictions with experimental phenotypes and direct visualization of both on metabolic maps. The web interface is designed for simplicity, putting constraint-based modelling techniques within easier reach of biologists. CycSim also functions as an online repository of genome-scale metabolic models.

Availability:  http://www.genoscope.cns.fr/cycsim

Contact:  cycsim@genoscope.cns.fr
Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency
Authors: Klingelhoefer Jochen W. , Moutsianas Loukas , Holmes Chris
Published: May 2009

Motivation: Short interfering RNA (siRNA)-induced RNA interference is an endogenous pathway in sequence-specific gene silencing. The potency of different siRNAs to inhibit a common target varies greatly and features affecting inhibition are of high current interest. The limited success in predicting siRNA potency being reported so far could originate in the small number and the heterogeneity of available datasets in addition to the knowledge-driven, empirical basis on which features thought to be affecting siRNA potency are often chosen. We attempt to overcome these problems by first constructing a meta-dataset of 6483 publicly available siRNAs (targeting mammalian mRNA), the largest to date, and then applying a Bayesian analysis which accommodates feature set uncertainty. A stochastic logistic regression-based algorithm is designed to explore a vast model space of 497 compositional, structural and thermodynamic features, identifying associations with siRNA potency.

Results: Our algorithm reveals a number of features associated with siRNA potency that are, to the best of our knowledge, either under reported in literature, such as anti-sense 5′ −3′ motif ‘UCU’, or not reported at all, such as the anti-sense 5′ -3′ motif ‘ACGA’. These findings should aid in improving future siRNA potency predictions and might offer further insights into the working of the RNA-induced silencing complex (RISC).

Contact:  cholmes@stats.ox.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa
Authors: Dupierris Véronique , Masselon Christophe , Court Magali , Kieffer-Jaquinod Sylvie , Bruley Christophe
Published: May 2009

Summary: The IRMa toolbox provides an interactive application to assist in the validation of Mascot® search results. It allows automatic filtering of Mascot® identification results as well as manual confirmation or rejection of individual PSM (a match between a fragmentation mass spectrum and a peptide). Dynamic grouping and coherence of information are maintained by the software in real time. Validated results can be exported under various forms, including an identification database (MSIdb). This allows biologists to compile search results from a whole study in a unique repository in order to provide a summarized view of their project. IRMa also features a fully automated version that can be used in a high-throughput pipeline. Given filter parameters, it can delete hits with no significant PSM, regroup hits identified by the same peptide(s) and export the result to the specified format without user intervention.

Availability:  http://biodev.extra.cea.fr/docs/irma (java 1.5 or higher needed)

Contact:  christophe.bruley@cea.fr
RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions
Authors: Rueda Oscar M. , Diaz-Uriarte Ramon
Published: May 2009

Summary: Several methods have been proposed to detect copy number changes and recurrent regions of copy number variation from aCGH, but few methods return probabilities of alteration explicitly, which are the direct answer to the question ‘is this probe/region altered?’ RJaCGH fits a Non-Homogeneous Hidden Markov model to the aCGH data using Markov Chain Monte Carlo with Reversible Jump, and returns the probability that each probe is gained or lost. Using these probabilites, recurrent regions (over sets of individuals) of copy number alteration can be found.

Availability: RJaCGH is available as an R package from CRAN repositories (e.g. http://cran.r-project.org/web/packages).

Contact:  rueda.om@gmail.com; rueda.om@gmail.com
Planar dynamics of a rigid body system with frictional impacts. II. Qualitative analysis and numerical simulations
Authors: Zhao Zhen , Liu Caishan , Brogliato Bernard
Published: May 2009

The objective of this paper is to implement and test the theory presented in a companion paper for the non-smooth dynamics exhibited in a bouncing dimer. Our approach revolves around the use of rigid body dynamics theory combined with constraint equations from the Coulomb's frictional law and the complementarity condition to identify the contact status of each contacting point. A set of impulsive differential equations based on Darboux–Keller shock dynamics is established that can deal with the complex behaviours involved in multiple collisions, such as the frictional effects, the local dissipation of energy at each contact point, and the dispersion of energy among various contact points. The paper will revisit the experimental phenomena found in Dorbolo
et al
. (

Dorbolo
et al
. 2005

Phys. Rev. Lett.
95
, 044101), and then present a qualitative analysis based on the theory proposed in part I. The value of the static coefficient of friction between the plate and the dimer is successfully estimated, and found to be responsible for the formation of the drift motion of the bouncing dimer. Plenty of numerical simulations are carried out, and precise agreements are obtained by the comparisons with the experimental results.
The elastochrone: the descent time of a sphere on a flexible beam
Authors: Aristoff Jeffrey M. , Clanet Christophe , Bush John W.M.
Published: May 2009

We present the results of a combined experimental and theoretical investigation of the motion of a sphere on an inclined flexible beam. A theoretical model based on Euler–Bernoulli beam theory is developed to describe the dynamics, and in the limit where the beam reacts instantaneously to the loading, we obtain exact solutions for the load trajectory and descent time. For the case of an initially horizontal beam, we calculate the period of the resulting oscillations. Theoretical predictions compare favourably with our experimental observations in this quasi-static regime. The time taken for descent along an elastic beam, the elastochrone, is shown to exceed the classical brachistochrone, the shortest time between two points in a gravitational field.
Fatal attraction: adaptations to prey on native frogs imperil snakes after invasion of toxic toads
Authors: Hagman Mattias , Phillips Benjamin L. , Shine Richard
Published: May 2009

Adaptations that enhance fitness in one situation can become liabilities if circumstances change. In tropical Australia, native snake species are vulnerable to the invasion of toxic cane toads. Death adders (
Acanthophis praelongus
) are ambush foragers that (i) attract vertebrate prey by caudal luring and (ii) handle anuran prey by killing the frog then waiting until the frog's chemical defences degrade before ingesting it. These tactics render death adders vulnerable to toxic cane toads (
Bufo marinus
), because toads elicit caudal luring more effectively than do native frogs, and are more readily attracted to the lure. Moreover, the strategy of delaying ingestion of a toad after the strike does not prevent fatal poisoning, because toad toxins (unlike those of native frogs) do not degrade shortly after the prey dies. In our laboratory and field trials, half of the death adders died after ingesting a toad, showing that the specialized predatory behaviours death adders use to capture and process prey render them vulnerable to this novel prey type. The toads' strong response to caudal luring also renders them less fit than native anurans (which largely ignored the lure): all toads bitten by adders died. Together, these results illustrate the dissonance in behavioural adaptations that can arise following the arrival of invasive species, and reveal the strong selection that occurs when mutually naive species first interact.
Sea lice and salmon population dynamics: effects of exposure time for migratory fish
Authors: Krkošek Martin , Morton Alexandra , Volpe John P. , Lewis Mark A.
Published: May 2009

The ecological impact of parasite transmission from fish farms is probably mediated by the migration of wild fishes, which determines the period of exposure to parasites. For Pacific salmon and the parasitic sea louse,
Lepeophtheirus salmonis
, analysis of the exposure period may resolve conflicting observations of epizootic mortality in field studies and parasite rejection in experiments. This is because exposure periods can differ by 2–3 orders of magnitude, ranging from months in the field to hours in experiments. We developed a mathematical model of salmon–louse population dynamics, parametrized by a study that monitored naturally infected juvenile salmon held in ocean enclosures. Analysis of replicated trials indicates that lice suffer high mortality, particularly during pre-adult stages. The model suggests louse populations rapidly decline following brief exposure of juvenile salmon, similar to laboratory study designs and data. However, when the exposure period lasts for several weeks, as occurs when juvenile salmon migrate past salmon farms, the model predicts that lice accumulate to abundances that can elevate salmon mortality and depress salmon populations. The duration of parasite exposure is probably critical to salmon–louse population dynamics, and should therefore be accommodated in coastal planning and management where fish farms are situated on wild fish migration routes.
Incipient allochronic speciation by climatic disruption of the reproductive period
Authors: Yamamoto Satoshi , Sota Teiji
Published: May 2009

Disruptive selection of life-cycle timing may cause temporal isolation directly and, ultimately, allochronic speciation. Despite the fact that segregation of the reproductive period among related species has been broadly observed across taxa, it remains controversial whether temporal isolation can function as the primary process of speciation. In the Japanese winter geometrid mothInurois punctigera, allochronic divergence has resulted from climatic disruption of the reproductive period. In habitats with severe midwinter, two sympatric groups of moth reproduce allochronically in early and late winter. These groups are genetically diverging sister lineages and now co-occur allochronically throughout Japan. By contrast, in habitats with milder midwinter these lineages form a continuous adult period and gene flow has been facilitated between the lineages. These results, together with the fact that there is no difference in larval host use, indicate that temporal isolation has been the sole mechanism for allochronic isolation in colder habitats and that allochrony is not a by-product of other adaptations. Thus, the allochronic divergence of sympatricI. punctigerapopulations represents an incipient speciation process driven by midwinter disruption of the reproductive period.
‘Heritability’ of dispersal propensity in a patchy population
Authors: Doligez Blandine , Gustafsson Lars , Pärt Tomas
Published: May 2009

Although dispersal is often considered to be a plastic, condition-dependent trait with low heritability, growing evidence supports medium to high levels of dispersal heritability. Obtaining unbiased estimates of dispersal heritability in natural populations nevertheless remains crucial to understand the evolution of dispersal strategies and their population consequences. Here we show that dispersal propensity (i.e. the probability of dispersal between habitat patches) displays a significant heritability in the collared flycatcherFicedula albicollis, as estimated by within-family resemblance when accounting for environmental factors. Offspring of dispersing mothers or fathers had a higher propensity to disperse to a new habitat patch themselves. The effect of parental dispersal status was additional to that of local habitat quality, as measured by local breeding population size and success, confirming previous results about condition-dependent dispersal in this population. The estimated levels of heritability varied between 0.30±0.07 and 0.47±0.10, depending on parent–offspring comparisons made and correcting for a significant assortative mating with respect to dispersal status. Siblings also displayed a significant resemblance in dispersal propensity. These results suggest that variation in between-patch natal dispersal in the collared flycatcher is partly genetically determined, and we discuss ways to quantify this genetic basis and its implications.
Flexible responses to visual and olfactory stimuli by foragingManduca sexta: larval nutrition affects adult behaviour
Authors: Goyret Joaquín , Kelber Almut , Pfaff Michael , Raguso Robert A.
Published: May 2009

Here, we show that the consequences of deficient micronutrient (β-carotene) intake during larval stages ofManduca sextaare carried across metamorphosis, affecting adult behaviour. Our manipulation of larval diet allowed us to examine how developmental plasticity impacts the interplay between visual and olfactory inputs on adult foraging behaviour. Larvae ofM. sextawere reared on natural (Nicotiana tabacum) and artificial laboratory diets containing different concentrations of β-carotene (standard diet, low β-carotene, high β-carotene and cornmeal). This vitamin-A precursor has been shown to be crucial for photoreception sensitivity in the retina ofM. sexta. After completing development, post-metamorphosis, starved adults were presented with artificial feeders that could be either scented or unscented. Regardless of their larval diet, adult moths fed with relatively high probabilities on scented feeders. When feeders were unscented, moths reared on tobacco were more responsive than moths reared on β-carotene-deficient artificial diets. Strikingly, moths reared on artificial diets supplemented with increasing amounts of β-carotene (low β and high β) showed increasing probabilities of response to scentless feeders. We discuss these results in relationship to the use of complex, multi-modal sensory information by foraging animals.
Experimental evidence for group hunting via eavesdropping in echolocating bats
Authors: Dechmann Dina K.N. , Heucke Silke L. , Giuggioli Luca , Safi Kamran , Voigt Christian C. , Wikelski Martin
Published: May 2009

Group foraging has been suggested as an important factor for the evolution of sociality. However, visual cues are predominantly used to gain information about group members' foraging success in diurnally foraging animals such as birds, where group foraging has been studied most intensively. By contrast, nocturnal animals, such as bats, would have to rely on other cues or signals to coordinate foraging. We investigated the role of echolocation calls as inadvertently produced cues for social foraging in the insectivorous batNoctilio albiventris. Females of this species live in small groups, forage over water bodies for swarming insects and have an extremely short daily activity period. We predicted and confirmed that (i) free-ranging bats are attracted by playbacks of echolocation calls produced during prey capture, and that (ii) bats of the same social unit forage together to benefit from passive information transfer via the change in group members' echolocation calls upon finding prey. Network analysis of high-resolution automated radio telemetry confirmed that group members flew within the predicted maximum hearing distance 94±6 per cent of the time. Thus, echolocation calls also serve as intraspecific communication cues. Sociality appears to allow for more effective group foraging strategies via eavesdropping on acoustical cues of group members in nocturnal mammals.
High-throughput genotyping by whole-genome resequencing
Authors: Huang Xuehui , Feng Qi , Qian Qian , Zhao Qiang , Wang Lu , Wang Ahong , Guan Jianping , Fan Danlin , Weng Qijun , Huang Tao , Dong Guojun , Sang Tao , Han Bin
Published: May 2009

The next-generation sequencing technology coupled with the growing number of genome sequences opens the opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis. We have developed a high-throughput method for genotyping recombinant populations utilizing whole-genome resequencing data generated by the Illumina Genome Analyzer. A sliding window approach is designed to collectively examine genome-wide single nucleotide polymorphisms for genotype calling and recombination breakpoint determination. Using this method, we constructed a genetic map for 150 rice recombinant inbred lines with an expected genotype calling accuracy of 99.94% and a resolution of recombination breakpoints within an average of 40 kb. In comparison to the genetic map constructed with 287 PCR-based markers for the rice population, the sequencing-based method was ∼20× faster in data collection and 35× more precise in recombination breakpoint determination. Using the sequencing-based genetic map, we located a quantitative trait locus of large effect on plant height in a 100-kb region containing the rice “green revolution” gene. Through computer simulation, we demonstrate that the method is robust for different types of mapping populations derived from organisms with variable quality of genome sequences and is feasible for organisms with large genome sizes and low polymorphisms. With continuous advances in sequencing technologies, this genome-based method may replace the conventional marker-based genotyping approach to provide a powerful tool for large-scale gene discovery and for addressing a wide range of biological questions.
TGF β‐like regulation of matrix metalloproteinases by anti‐transforming growth factor‐β, and anti‐transforming growth factor‐β1 antibodies in dermal fibroblasts: Implications for wound healing
Authors: Philips Neena , Keller Thomas , Gonzalez Salvador
Published: May 2009

Transforming growth factor beta (TGF‐β) stimulates collagen and matrix metalloproteinase‐2 expression and inhibits MMP‐1 expression in dermal fibroblasts. Anti‐TGF‐β antibodies have been proposed in the prevention of wound scars. The goal of this research was to investigate the regulation of matrix metalloproteinases‐1 and ‐2 expression at the protein, mRNA, and transcriptional levels using an anti‐TGF‐β antibody to TGF‐β 1, 2, 3, and 5 (all isoforms), and specifically by an anti‐TGF‐β1 antibody. Both antibodies, though at doses lower than the recommended neutralization dose, stimulated the expression of TGF‐β, and exhibited TGF‐β–like regulation of the matrix metalloproteinases. The antibodies inhibited matrix metalloproteinase‐1 protein, mRNA, and promoter activity. The protein levels of matrix metalloproteinase‐2 were up‐regulated to a greater extent than the matrix metalloproteinase‐2 mRNA level by both antibodies. These effects of anti‐TGF‐β and anti‐TGF‐β1 antibodies on matrix metalloproteinase regulation were mimicked by exogenous TGF‐β1 but not rabbit or chicken IgG. We infer that the anti‐TGF‐β1 isoform that forms part of the composition of the anti‐TGF‐β antibody to all isoforms may be responsible for the feedback stimulation of TGF‐β and the resultant alterations in the expression of the matrix metalloproteinases by the anti‐TGF‐β antibodies.
The JCR:LA‐cp rat: A novel model for impaired wound healing
Authors: Bauer barbara S. , Ghahary Aziz , Scott Paul G. , Iwashina Takashi , Demare Jack , Russell James C. , Tredget Edward E.
Published: May 2009

JCR:LA‐cp/cp obese rats and their lean controls were evaluated as a type 2 diabetic wound healing model and the healing quality was characterized. This model of insulin resistance has been used extensively to study atherosclerosis but has not previously been used to study wound healing. Six circular excisional wounds were made on the dorsum of each rat and followed to day 21.Tracings of the wounds were made and used to assess the rate of wound closure. Planimetry showed a significantly diminished contraction of wounds in obese rats, but no significant difference in reepithelialization was observed. Collagen content was determined from the hydroxyproline content in wounded and unwounded skin. There were significantly lower levels of hydroxyproline in the wounds of obese compared to lean animals at day 21. Histology showed adipose tissue in place of dermal tissue in the JCR:LA‐cp/cp rat in both unwounded tissue and in the wound at day 21. Active transforming growth factor‐β1 (TGF‐β1) was measured in the serum using the plasminogen activator inhibitor‐1/luciferase assay and serum total TGF‐β was measured using an enzyme‐linked immunosorbent assay. Active TGF‐β was significantly higher in the serum of obese animals compared with lean animals, while total TGF‐β1 was not significantly different between the groups. Both active and total TGF‐β was measured in tissue sections using the plasminogen activator inhibitor‐1/luciferase assay. There was no significant difference in active TGF‐β between genotypes, while obese rats had significantly higher levels of total TGF‐β at day 21. These results indicate a deficiency in wound healing in obese animals characterized by decreased wound contraction, decreased collagen production, and changes in histology. The JCR:LA‐cp rat develops insulin resistance, atherosclerosis and early type 2 diabetes and may be a good model for impairment of wound healing in humans with metabolic syndrome.
Dkk‐3 expression in the tumor endothelium: A novel prognostic marker of pancreatic adenocarcinomas
Authors: Fong Dominic , Hermann Martin , Untergasser Gerold , Pirkebner Daniela , Draxl Anna , Heitz Martin , Moser Patrizia , Margreiter Raimund , Hengster Paul , Amberger Albert
Published: May 2009

Dkk‐3 is proposed to be a new specific marker for tumor endothelial cells. Here we analyzed the clinical relevance of Dkk‐3 expression in pancreas adenocarcinomas and determined its role on endothelial cell growth in vitro. Microvessel density in tumor samples was immunohistochemically determined using Dkk‐3 and CD31 as endothelial cell markers, respectively. Based on the median microvessel density as a cut‐off point, patients were categorized into high and low microvessel density groups and a correlation with survival and clinical parameters was assessed. Moreover, the role of Dkk‐3 expression on chemosensitivity of endothelial cells was analyzed. In contrast to CD31 staining, Dkk‐3‐positive vessels were found only in tumor tissue and Dkk‐3 microvessel density significantly correlated negative with tumor grading. In survival analysis the median survival time was 7 months for patients with Dkk‐3 low, and 15 months for Dkk‐3 high microvessel density (P = 0.0013). Subset analysis of patients receiving gemcitabine therapy showed that overall survival was significantly decreased in Dkk‐3 low tumors than in high tumors (P = 0.009). In Cox regression Dkk‐3 emerged as a significant independent parameter (P = 0.024). Dkk‐3 overexpression in endothelial cells resulted in significantly enhanced growth inhibition after 5‐fluorouracil or gemcitabine treatment compared to control endothelial cells and cancer cell lines. Dkk‐3 low microvessel density was associated with tumor progression and worse clinical outcome. Overexpression of Dkk‐3 enhanced endothelial cell growth inhibition to chemotherapeutic drugs. Therefore, we suggest that Dkk‐3 high microvessel density may help to select patients who may benefit from chemotherapy. (Cancer Sci 2009)
Bone marrow cells from patients with Shwachman‐Diamond syndrome abnormally express genes involved in ribosome biogenesis and RNA processing
Authors: Rujkijyanont Piya , Adams Sally‐Lin , Beyene Joseph , Dror Yigal
Published: May 2009

Shwachman‐Diamond Syndrome (SDS) is a multi‐system genetic disorder with bone marrow failure. SBDS, the gene associated with SDS, has been postulated to play a role in ribosome biogenesis and RNA processing, but its functions are still unknown. To study whether these pathways are interrupted when Sbds protein is lost, we studied the expression of related genes in patient SBDS−/− cells by an oligonucleotide microarray. We first analysed ribosomal protein (RP) genes, which are normally co‐regulated. In SDS, 27 of the 85 RP genes were downregulated. Among the downregulated RP genes, seven are known to be associated with the inhibition of apoptosis. RPS27L, which mediates p53‐dependent induction of apoptosis, was the only upregulated RP gene. Interestingly, several genes involved in RP mRNA transcription were downregulated without affecting the expression of genes involved in mRNA degradation, suggesting that the downregulation of the RP gene expression might be at the transcriptional level. Importantly we also found dysregulation of multiple genes involved in rRNA transcription and pre‐rRNA processing. We conclude that SDS marrow cells exhibit major dysregulation of RP, RNA processing and RNA transcription genes.
Concurrent occurrence of medullary thyroid carcinoma and papillary thyroid carcinoma in the same thyroid should be considered as coincidental
Authors: Kim Won Gu , Gong Gyungyub , Kim Eui Young , Kim Tae Yong , Hong Suck Joon , Kim Won Bae , Shong Young Kee
Published: May 2009

Objectives  The simultaneous occurrence of medullary thyroid carcinoma (MTC) and papillary thyroid carcinoma (PTC) in the same thyroid gland is documented. In this study, we evaluated the prevalence and characteristics of patients with concurrent MTC and PTC.

Design  Retrospective analysis of patients with MTC in a single centre and review of the literature.

Patients and measurements  Patients with MTC who underwent initial surgical treatment between 1996 and 2006 at Asan Medical Centre, Seoul, Korea were enrolled. We additionally reviewed the medical records of patients who initially underwent surgery for Graves’ disease (GD) or follicular thyroid carcinoma (FTC) during the same period. The concurrent occurrence rate of PTC in MTC patients was compared with that in GD and FTC patients.

Results  Ten of 53 (19%) MTC patients displayed the concomitant PTC. In all 10 cases, the MTC and PTC components were separated by normal thyroid tissue, with the maximal diameters of PTC being less than 1·0 cm in the majority of patients. The rates of concurrent PTC in patients with MTC, GD and FTC were 19%, 15% and 19%, respectively, which were not significantly different.

Conclusions  Our results suggest that the occurrence of concurrent MTC/PTC is generally a simple reflection of incidental papillary microcarcinoma.
Relationships between structure and function in streams contrasting in temperature
Authors: FRIBERG NIKOLAI , DYBKJÆR JOHN B. , OLAFSSON JON S. , GISLASON GISLI MAR , LARSEN SØREN E. , LAURIDSEN TORBEN L.
Published: May 2009

1. We studied 10 first‐order Icelandic streams differing in geothermal influence in separate catchments. Summer temperature (August–September) ranged between 6 and 23 °C.

2. Macroinvertebrate evenness and species overlap decreased significantly with temperature whereas taxon richness showed no response. In total, 35 macroinvertebrate species were found with Chironomidae the dominant taxonomic group. Macroinvertebrate density increased significantly with temperature. Dominant species in the warm streams wereLymnaea peregraandSimulium vittatum. Algal biomass, macrophyte cover and richness were unrelated to temperature. Densities of trout (Salmo trutta), the only fish species present, reflected habitat conditions and to a lesser degree temperature.

3. Density of filter‐feeders increased significantly with temperature whereas scraper density, the other dominant functional feeding group, was unrelated to temperature. Stable isotope analysis revealed a positive relationship between δ15N and temperature across several trophic levels. No pattern was found with regard to δ13C and temperature.

4. Leaf litter decomposition in both fine and coarse mesh leaf bags were significantly correlated to temperature. In coarse mesh leaf packs breakdown rates were almost doubled compared with fine mesh, ranging between 0.5 and 1.3 g DW 28 days−1. Nutrient diffusion substrates showed that the streams were primarily nitrogen limited across the temperature gradient while a significant additional effect of phosphorous was found with increasing temperature.

5. Structural and functional attributes gave complementary information which all indicated a change with temperature similar to what is found in moderately polluted streams. Our results therefore suggest that lotic ecosystems could be degraded by global warming.
Differences in winter‐hardening between phenotypes of Lolium perenne with contrasting water‐soluble carbohydrate concentrations
Authors: Hanslin H. M. , Höglind M.
Published: May 2009

Carbohydrates are essential for the winter‐hardening of temperate grasses, affecting both rate of hardening and level of frost hardiness. The rate and extent of winter‐hardening of contrasting phenotypes of two Lolium perenne cultivars targeted for differences in water‐soluble carbohydrates concentration were quantified under controlled hardening conditions and standardized freeze testing. The phenotype with the lowest water‐soluble carbohydrates concentration had a lower rate of hardening and tolerated less frost than the other phenotypes but the effect of water‐soluble carbohydrate concentrations on the hardening processes levelled off at increasing water‐soluble carbohydrate concentrations, indicating a threshold. Contrasting responses to freezing were found for survival and for potential for tillering and regrowth. Mortality was little affected by the higher test temperatures, while tillering was negatively affected, even at −5°C. Compensatory regrowth of tillers surviving the lower test temperatures partially compensated for the effects of loss of tillers on regrowth. The hardiest phenotypes had a rapid lowering of LT50 during the first 3 d (−1·65°C d−1), acquiring LT50 values at −15°C or below in 10 d. The hypothesis that rate and maximum level of hardening increase with water‐soluble carbohydrates concentrations in stubble is supported by the results.
Influence of herbage species, cultivar and cutting date on fatty acid composition of herbage and lipid metabolism during ensiling
Authors: Van Ranst G. , Fievez V. , Vandewalle M. , De Riek J. , Van Bockstaele E.
Published: May 2009

The fatty acid (FA) concentration of herbage and lipid metabolism in silage, mainly oxidation and lipolysis, of different species (perennial ryegrass, red clover and white clover) and three cultivars of white and red clover at three cutting dates in the growing season (April, July and October) were studied. FA concentration and composition was strongly affected by species and cutting date. Perennial ryegrass had lower concentrations of C16:1, C18:0, C18:1 and C18:2 than red and white clover. Within red and white clover, the effect of cultivar was small. Oxidation of C18:3 during wilting was different between species and cutting date despite similar wilting conditions. Lipolysis in silage was also influenced by cutting date, species and to some extent by cultivar. Furthermore, in some cuts silages of red and white clover displayed a lower lipolysis than silage of perennial ryegrass. On average, over the three cutting dates proportionately 0·903, 0·864 and 0·857 of the membrane lipids in perennial ryegrass, red clover and white clover were hydrolysed during ensiling. In red clover this could be due to the lipid‐protecting properties of polyphenol oxidase (PPO) activity. This was not observed in perennial ryegrass or white clover. Nevertheless, differences in lipolysis in silage between cultivars of red clover were not correlated with PPO activity.