bluuebunny/crossref_metadata_2025 huggingface dataset:
Alternative Requirements for Vestigial, Scalloped, and Dmef2 during Muscle Differentiation inDrosophila melanogaster
Authors: Deng Hua , Hughes Sarah C. , Bell John B. , Simmonds Andrew J.
Published: November 2008

Vertebrate development requires the activity of the myocyte enhancer factor 2 (mef2) gene family for muscle cell specification and subsequent differentiation. Additionally, several muscle-specific functions of MEF2 family proteins require binding additional cofactors including members of the Transcription Enhancing Factor-1 (TEF-1) and Vestigial-like protein families. In Drosophila there is a single mef2 (Dmef2) gene as well single homologues of TEF-1 and vestigial-like, scalloped (sd), and vestigial (vg), respectively. To clarify the role(s) of these factors, we examined the requirements for Vg and Sd during Drosophila muscle specification. We found that both are required for muscle differentiation as loss of sd or vg leads to a reproducible loss of a subset of either cardiac or somatic muscle cells in developing embryos. This muscle requirement for Sd or Vg is cell specific, as ubiquitous overexpression of either or both of these proteins in muscle cells has a deleterious effect on muscle differentiation. Finally, using both in vitro and in vivo binding assays, we determined that Sd, Vg, and Dmef2 can interact directly. Thus, the muscle-specific phenotypes we have associated with Vg or Sd may be a consequence of alternative binding of Vg and/or Sd to Dmef2 forming alternative protein complexes that modify Dmef2 activity.
Distinct Apical and Basolateral Membrane Requirements for Stretch-induced Membrane Traffic at the Apical Surface of Bladder Umbrella Cells
Authors: Yu Weiqun , Khandelwal Puneet , Apodaca Gerard
Published: November 2008

Epithelial cells respond to mechanical stimuli by increasing exocytosis, endocytosis, and ion transport, but how these processes are initiated and coordinated and the mechanotransduction pathways involved are not well understood. We observed that in response to a dynamic mechanical environment, increased apical membrane tension, but not pressure, stimulated apical membrane exocytosis and ion transport in bladder umbrella cells. The exocytic response was independent of temperature but required the cytoskeleton and the activity of a nonselective cation channel and the epithelial sodium channel. The subsequent increase in basolateral membrane tension had the opposite effect and triggered the compensatory endocytosis of added apical membrane, which was modulated by opening of basolateral K+channels. Our results indicate that during the dynamic processes of bladder filling and voiding apical membrane dynamics depend on sequential and coordinated mechanotransduction events at both membrane domains of the umbrella cell.
Recql5 Plays an Important Role in DNA Replication and Cell Survival after Camptothecin Treatment
Authors: Hu Yiduo , Lu Xincheng , Zhou Guangjin , Barnes Ellen L. , Luo Guangbin
Published: November 2008

Disruption of replication can lead to loss of genome integrity and increase of cancer susceptibility in mammals. Thus, a replication impediment constitutes a formidable challenge to these organisms. Recent studies indicate that homologous recombination (HR) plays an important role in suppressing genome instability and promoting cell survival after exposure to various replication inhibitors, including a topoisomerase I inhibitor, camptothecin (CPT). Here, we report that the deletion of RecQ helicase Recql5 in mouse ES cells and embryonic fibroblast (MEF) cells resulted in a significant increase in CPT sensitivity and a profound reduction in DNA replication after the treatment with CPT, but not other DNA-damaging agents. This CPT-induced cell death is replication dependent and occurs primarily after the cells had exited the first cell cycle after CPT treatment. Furthermore, we show that Recql5 functions nonredundantly with Rad51, a key factor for HR to protect mouse ES cells from CPT-induced cytotoxicity. These new findings strongly suggest that Recql5 plays an important role in maintaining active DNA replication to prevent the collapse of replication forks and the accumulation of DSBs in order to preserve genome integrity and to prevent cell death after replication stress as a result of topoisomerase I poisoning.
Specific Biarsenical Labeling of Cell Surface Proteins Allows Fluorescent- and Biotin-tagging of Amyloid Precursor Protein and Prion Proteins
Authors: Taguchi Yuzuru , Shi Zhen-Dan , Ruddy Brian , Dorward David W. , Greene Lois , Baron Gerald S.
Published: November 2008

Fluorescent tagging is a powerful tool for imaging proteins in living cells. However, the steric effects imposed by fluorescent tags impair the behavior of many proteins. Here, we report a novel technique, Instant with DTT, EDT, And Low temperature (IDEAL)-labeling, for rapid and specific FlAsH-labeling of tetracysteine-tagged cell surface proteins by using prion protein (PrP) and amyloid precursor protein (APP) as models. In prion-infected cells, FlAsH-labeled tetracysteine-tagged PrP converted from the normal isoform (PrPsen) to the disease-associated isoform (PrPres), suggesting minimal steric effects of the tag. Pulse-chase analysis of PrP and APP by fluorescent gel imaging demonstrated the utility of IDEAL labeling in investigating protein metabolism by identifying an as-yet-unrecognized C-terminal fragment (C3) of PrPsen and by characterizing the kinetics of PrPres and APP metabolism. C3 generation and N-terminal truncation of PrPres were inhibited by the anti-prion compound E64, a cysteine protease inhibitor. Surprisingly, E64 did not inhibit the synthesis of new PrPres, providing insight into the mechanism by which E64 reduces steady-state PrPres levels in prion-infected cells. To expand the versatility of tetracysteine tagging, we created new Alexa Fluor- and biotin-conjugated tetracysteine-binding molecules that were applied to imaging PrP endocytosis and ultrastructural localization. IDEAL-labeling extends the use of biarsenical derivatives to extracellular proteins and beyond microscopic imaging.
LIM Kinase 1 and Cofilin Regulate Actin Filament Population Required for Dynamin-dependent Apical Carrier Fission from theTrans-Golgi Network
Authors: Salvarezza Susana B. , Deborde Sylvie , Schreiner Ryan , Campagne Fabien , Kessels Michael M. , Qualmann Britta , Caceres Alfredo , Kreitzer Geri , Rodriguez-Boulan Enrique
Published: November 2008

The functions of the actin cytoskeleton in post-Golgi trafficking are still poorly understood. Here, we report the role of LIM Kinase 1 (LIMK1) and its substrate cofilin in the trafficking of apical and basolateral proteins in Madin-Darby canine kidney cells. Our data indicate that LIMK1 and cofilin organize a specialized population of actin filaments at the Golgi complex that is selectively required for the emergence of an apical cargo route to the plasma membrane (PM). Quantitative pulse-chase live imaging experiments showed that overexpression of kinase-dead LIMK1 (LIMK1-KD), or of LIMK1 small interfering RNA, or of an activated cofilin mutant (cofilin S3A), selectively slowed down the exit from the trans-Golgi network (TGN) of the apical PM marker p75-green fluorescent protein (GFP) but did not interfere with the apical PM marker glycosyl phosphatidylinositol-YFP or the basolateral PM marker neural cell adhesion molecule-GFP. High-resolution live imaging experiments of carrier formation and release by the TGN and analysis of peri-Golgi actin dynamics using photoactivatable GFP suggest a scenario in which TGN-localized LIMK1-cofilin regulate a population of actin filaments required for dynamin-syndapin-cortactin–dependent generation and/or fission of precursors to p75 transporters.
Spatial variability of seabird distribution associated with environmental factors: a case study of marine Important Bird Areas in the Azores
Authors: Amorim Patrícia , Figueiredo Miguel , Machete Miguel , Morato Telmo , Martins Ana , Serrão Santos Ricardo
Published: November 2008

Amorim, P., Figueiredo, M., Machete, M., Morato, T., Martins, A., and Serrão Santos, R. 2009. Spatial variability of seabird distribution associated with environmental factors: a case study of marine Important Bird Areas in the Azores. – ICES Journal of Marine Science, 66: 29–40. The spatial structure and distribution at sea of Cory's shearwaters (Calonectris diomedea borealis), common terns (Sterna hirundo), and roseate terns (Sterna dougallii) were analysed in the Azores for various environmental factors: sea surface temperature, chlorophyll a concentration, distance to fronts, wind, distance to island shore or tern colonies, distance to seamounts, seabed slope, and depth. Data on seabird sightings were collected by observers on board fishing vessels, 2002–2006. Generalized linear modelling (GLM) explained 43 and 11% of the abundance variability for terns (both species pooled) and Cory's shearwaters, respectively. Variability in seabird abundance was mainly explained by month, wind, distance to shore and/or tern colonies, and distance to seamounts. Variogram modelling indicated that species distribution presented a small-scale spatial structure (i.e. low autocorrelation). Cory's shearwater predictive distribution maps showed widespread distribution patterns of abundance, despite occurring at a greater intensity around the islands and around some seamounts, which are areas of fishery interest. Conversely, terns were essentially concentrated near the shore. The establishment of marine important bird areas should be encouraged close to seabird colonies and around some seamount areas.
Lr34-Mediated Leaf Rust Resistance in Wheat: Transcript Profiling Reveals a High Energetic Demand Supported by Transient Recruitment of Multiple Metabolic Pathways
Authors: Bolton Melvin D. , Kolmer James A. , Xu Wayne W. , Garvin David F.
Published: November 2008

The wheat gene Lr34 confers partial resistance to all races of Puccinia triticina, the causal agent of wheat leaf rust. However, the biological basis for the exceptional durability of Lr34 is unclear. We used the Affymetrix GeneChip Wheat Genome Array to compare transcriptional changes of near-isogenic lines of Thatcher wheat in a compatible interaction, an incompatible interaction conferred by the resistance gene Lr1, and the race-nonspecific response conditioned by Lr34 3 and 7 days postinoculation (dpi) with P. triticina. No differentially expressed genes were detected in Lr1 plants at either timepoint whereas, in the compatible Thatcher interaction, differentially expressed genes were detected only at 7 dpi. In contrast, differentially expressed genes were identified at both timepoints in P. triticina-inoculated Lr34 plants. At 3 dpi, upregulated genes associated with Lr34-mediated resistance encoded various defense and stress-related proteins, secondary metabolism enzymes, and transcriptional regulation and cellular-signaling proteins. Further, coordinated upregulation of key genes in several metabolic pathways that can contribute to increased carbon flux through the tricarboxylic cycle was detected. This indicates that Lr34-mediated resistance imposes a high energetic demand that leads to the induction of multiple metabolic responses to support cellular energy requirements. These metabolic responses were not sustained through 7 dpi, and may explain why Lr34 fails to inhibit the pathogen fully but does increase the latent period.
Infiltration with Agrobacterium tumefaciens Induces Host Defense and Development-Dependent Responses in the Infiltrated Zone
Authors: Pruss Gail J. , Nester Eugene W. , Vance Vicki
Published: November 2008

Despite the widespread use of Agrobacterium tumefaciens to transfer genes into plant systems, host responses to this plant pathogen are not well understood. The present study shows that disarmed strains of Agrobacterium induce distinct host responses when infiltrated into leaves of Nicotiana tabacum. The responses are limited to the infiltrated zone and consist of i) induction of pathogenesis-related (PR) gene PR-1 expression and resistance to subsequent infection with tobacco mosaic virus, ii) chlorosis and loss of chloroplast rRNAs, and iii) inhibition of leaf expansion. Induction of the latter two sets of responses depends on the age of the leaf and is most apparent in young leaves. Strains with or without binary vectors induce all the responses, showing that DNA transfer is neither required nor inhibitory. A. tumefaciens cured of the tumor-inducing (Ti) plasmid is slightly defective for induction of the three responses, showing that Ti plasmid-encoded factors produced by the disarmed strains contribute only slightly. However, T-DNA-encoded factors alter at least one of the host responses, because infiltration with the oncogenic strain C58 induced more pronounced chlorosis than the disarmed control. Auxin is one of the T-DNA products responsible for disease induction by oncogenic A. tumefaciens. We found that C58-infiltrated zones—but not those infiltrated with the disarmed control—have increased levels of miR393, a microRNA that represses auxin signaling and contributes to antibacterial resistance.
Niche-Specificity and the Variable Fraction of the Pectobacterium Pan-Genome
Authors: Glasner J. D. , Marquez-Villavicencio M. , Kim H.-S. , Jahn C. E. , Ma B. , Biehl B. S. , Rissman A. I. , Mole B. , Yi X. , Yang C.-H. , Dangl J. L. , Grant S. R. , Perna N. T. , Charkowski A. O.
Published: November 2008

We compare genome sequences of three closely related soft-rot pathogens that vary in host range and geographical distribution to identify genetic differences that could account for lifestyle differences. The isolates compared, Pectobacterium atrosepticum SCRI1043, P. carotovorum WPP14, and P. brasiliensis 1692, represent diverse lineages of the genus. P. carotovorum and P. brasiliensis genome contigs, generated by 454 pyrosequencing ordered by reference to the previously published complete circular chromosome of P. atrosepticum genome and each other, account for 96% of the predicted genome size. Orthologous proteins encoded by P. carotovorum and P. brasiliensis are approximately 95% identical to each other and 92% identical to P. atrosepticum. Multiple alignment using Mauve identified a core genome of 3.9 Mb conserved among these Pectobacterium spp. Each core genome is interrupted at many points by species-specific insertions or deletions (indels) that account for approximately 0.9 to 1.1 Mb. We demonstrate that the presence of a hrpK-like type III secretion system-dependent effector protein in P. carotovorum and P. brasiliensis and its absence from P. atrosepticum is insufficient to explain variability in their response to infection in a plant. Additional genes that vary among these species include those encoding peptide toxin production, enzyme production, secretion proteins, and antibiotic production, as well as differences in more general aspects of gene regulation and metabolism that may be relevant to pathogenicity.
Suppression of Reactive Oxygen Species and Enhanced Stress Tolerance in Rubia cordifolia Cells Expressing the rolC Oncogene
Authors: Bulgakov Victor P. , Aminin Dmitry L. , Shkryl Yuri N. , Gorpenchenko Tatiana Y. , Veremeichik Galina N. , Dmitrenok Pavel S. , Zhuravlev Yuri N.
Published: November 2008

It is known that expression of the Agrobacterium rhizogenes rolC gene in transformed plant cells causes defense-like reactions, such as increased phytoalexin production and expression of pathogenesis-related proteins. In the present study, we examined whether this phenomenon is associated with increased production of reactive oxygen species (ROS). Single-cell assays based on confocal microscopy and fluorogenic dyes (2,7-dichlorofluorescein diacetate and dihydrorhodamine 123) showed reduced steady-state levels of ROS in rolC-expressing Rubia cordifolia cells as compared with normal cells. Paraquat, a ROS inducer, caused significant ROS elevation in normal cells but had little effect on rolC-transformed cells. Likewise, ROS elevation triggered by a light stress was suppressed in transformed cells. Our results indicate that the rolC gene acts as a ROS suppressor in unstressed cells and its expression prevents stress-induced ROS elevations. We detected a two- to threefold increase in tolerance of rolC-transformed cells to salt, heat, and cold treatments. Simultaneously, rolC-transformed cells maintained permanently active defensive status, as found by measuring isochorismate synthase gene expression and anthraquinone production. Thus, the oncogene provoked multiple effects in which ROS production and phytoalexin production were clearly dissociated.
A Tannic Acid–Inducible and Hypoviral-Regulated Laccase3 Contributes to the Virulence of the Chestnut Blight FungusCryphonectria parasitica
Authors: Chung Hea-Jong , Kwon Bo-Ra , Kim Jung-Mi , Park Seung-Moon , Park Jong-Kun , Cha Byeong-Jin , Yang Moon-Sik , Kim Dae-Hyuk
Published: November 2008

A new laccase gene (lac3) from the chestnut blight fungus Cryphonectria parasitica was induced by the presence of tannic acid, which is abundant in the bark of chestnut trees and is assumed to be one of the major barriers against pathogen infection. However, other commonly known laccase inducers, including ferulic acid, 2,5-xylidine, catechol, and pH, did not induce lac3 transcription. Moreover, the hypovirus modulated the induction of lac3 transcription, abolishing the transcriptional induction of the lac3 gene by tannic acid. A functional analysis of lac3 using a lac3-null mutant indicated that fungal growth and other morphological characteristics, including pigmentation and sporulation, were not affected. However, a virulence assay indicated that the loss of function of a tannic acid–inducible and hypoviral-regulated laccase resulted in reduced virulence without detectable changes in the morphological features. The constitutive expression of lac3 resulted in no significant differences in the necrotic lesions from those caused by the wild type, but its expression in the presence of the hypovirus led to larger lesions than those caused by the hypovirulent strain. These results suggest that the lac3 gene product may not be the only determinant of fungal virulence in chestnut trees but is an important factor.
The Pea Sym37 Receptor Kinase Gene Controls Infection-Thread Initiation and Nodule Development
Authors: Zhukov Vladimir , Radutoiu Simona , Madsen Lene H. , Rychagova Tamara , Ovchinnikova Evgenia , Borisov Alex , Tikhonovich Igor , Stougaard Jens
Published: November 2008

Phenotypic characterization of pea symbiotic mutants has provided a detailed description of the symbiosis with Rhizobium leguminosarum bv. viciae strains. We show here that two allelic non-nodulating pea mutants, RisNod4 and K24, are affected in the PsSym37 gene, encoding a LysM receptor kinase similar to Lotus japonicus NFR1 and Medicago truncatula LYK3. Phenotypic analysis of RisNod4 and K24 suggests a role for the SYM37 in regulation of infection-thread initiation and nodule development from cortical-cell division foci. We show that RisNod4 plants carrying an L to F substitution in the LysM1 domain display a restrictive symbiotic phenotype comparable to the PsSym2A lines that distinguish ‘European’ and ‘Middle East’ Rhizobium leguminosarum bv. viciae strains. RisNod4 mutants develop nodules only in the presence of a ‘Middle East’ Rhizobium strain producing O-acetylated Nod factors indicating the SYM37 involvement in Nod-factor recognition. Along with the PsSym37, a homologous LysM receptor kinase gene, PsK1, was isolated and characterized. We show that PsK1 and PsSym37 are genetically linked to each other and to the PsSym2 locus. Allelic complementation analyses and sequencing of the extracellular regions of PsSym37 and PsK1 in several ‘European’ and ‘Afghan’ pea cultivars point towards PsK1 as possible candidate for the elusive PsSym2 gene.
Galactinol Is a Signaling Component of the Induced Systemic Resistance Caused by Pseudomonas chlororaphis O6 Root Colonization
Authors: Kim Mi Seong , Cho Song Mi , Kang Eun Young , Im Yang Ju , Hwangbo Hoon , Kim Young Cheol , Ryu Choong-Min , Yang Kwang Yeol , Chung Gap Chae , Cho Baik Ho
Published: November 2008

Root colonization by Pseudomonas chlororaphis O6 in cucumber elicited an induced systemic resistance (ISR) against Corynespora cassiicola. In order to gain insight into O6-mediated ISR, a suppressive subtractive hybridization technique was applied and resulted in the isolation of a cucumber galactinol synthase (CsGolS1) gene. The transcriptional level of CsGolS1 and the resultant galactinol content showed an increase several hours earlier under O6 treatment than in the water control plants following C. cassiicola challenge, whereas no difference was detected in the plants without a pathogen challenge. The CsGolS1-overexpressing transgenic tobacco plants demonstrated constitutive resistance against the pathogens Botrytis cinerea and Erwinia carotovora, and they also showed an increased accumulation in galactinol content. Pharmaceutical application of galactinol enhanced the resistance against pathogen infection and stimulated the accumulation of defense-related gene transcripts such as PR1a, PR1b, and NtACS1 in wild-type tobacco plants. Both the CsGolS1-overexpressing transgenic plants and the galactinol-treated wild-type tobacco plants also demonstrated an increased tolerance to drought and high salinity stresses.
The mathematical structure of multiphase thermal models of flow in porous media
Authors: van Odyck Daniel E.A , Bell John B , Monmont Franck , Nikiforakis Nikolaos
Published: November 2008

This paper is concerned with the formulation and numerical solution of equations for modelling multicomponent, two-phase, thermal fluid flow in porous media. The fluid model consists of individual chemical component (species) conservation equations, Darcy's law for volumetric flow rates and an energy equation in terms of enthalpy. The model is closed with an equation of state and phase equilibrium conditions that determine the distribution of the chemical components into phases. It is shown that, in the absence of diffusive forces, the flow equations can be split into a system of hyperbolic conservation laws for the species and enthalpy and a parabolic equation for pressure. This decomposition forms the basis of a sequential formulation where the pressure equation is solved implicitly and then the component and enthalpy conservation laws are solved explicitly. A numerical method based on this sequential formulation is presented and used to demonstrate some typical flow behaviour that occurs during fluid injection into a reservoir.
On a certain stability of the Hermite–Hadamard inequality
Authors: Házy Attila , Páles Zsolt
Published: November 2008

The classical Hermite–Hadamard inequality, under some regularity assumptions, characterizes convexity of real functions. The aim of this paper is to establish connections between the stability forms of the functional inequalities related to Jensen convexity, convexity and the Hermite–Hadamard inequality.
Insects had it first: surfactants as a defence against predators
Authors: Rostás Michael , Blassmann Katrin
Published: November 2008

Insects have evolved an astonishing array of defences to ward off enemies. Well known and widespread is the regurgitation of oral secretion (OS), fluid that repels attacking predators. In herbivores, the effectiveness of OS has been ascribed so far to the presence of deterrent secondary metabolites sequestered from the host plant. This notion implies, however, that generalists experience less protection on plants with low amounts of secondary metabolites or with compounds ineffective against potential enemies. Resolving the dilemma, we describe a novel defence mechanism that is independent of deterrents as it relies on the intrinsic detergent properties of the OS. The OS ofSpodoptera exigua(and other species) was found to be highly amphiphilic and well capable of wetting the hydrophobic cuticle of predatory ants. As a result, affected ants stopped attacking and engaged in extensive cleansing. The presence of surfactants was sufficient to explain the defensive character of herbivore OS. We hypothesize that detergency is a common but unrecognized mode of defence, which provides a base level of protection that may or may not be further enhanced by plant-derived deterrents. Our study also proves that insects ‘invented’ the use of defensive surfactants long before modern agriculture had started applying them as insecticides.
A new theory of MHC evolution: beyond selection on the immune genes
Authors: van Oosterhout Cock
Published: November 2008

The major histocompatibility complex (MHC) is a dense region of immune genes with high levels of polymorphism, which are arranged in haplotype blocks. Traditional models of balancing selection (i.e. overdominance and negative frequency dependence) were developed to study the population genetics of single genes. However, the MHC is a multigene family surrounded by linked (non-neutral) polymorphisms, and not all of its features are well explained by these models. For example, (i) the high levels of polymorphism in small populations, (ii) the unexpectedly large genetic differentiation between populations, (iii) the shape of the allelic genealogy associated with trans-species evolution, and (iv) the close associations between particular MHC (human leucocyte antigen, HLA) haplotypes and the approximately 100 pathologies in humans. Here, I propose a new model of MHC evolution named Associative Balancing Complex evolution that can explain these phenomena. The model proposes that recessive deleterious mutations accumulate as a ‘sheltered load’ nearby MHC genes. These mutations can accumulate because (i) they are rarely expressed as homozygotes given the high MHC gene diversity and (ii) purifying selection is inefficient with low recombination rates (cf. Muller's ratchet). Once fixed, these mutations add to balancing selection and further reinforce linkage through epistatic selection against recombinants.
A 2000 km genetic wake yields evidence for northern glacial refugia and hybrid zone movement in a pair of songbirds
Authors: Krosby Meade , Rohwer Sievert
Published: November 2008

Hybrid zones are natural experiments that expose the forces maintaining species differences. But for cases where a trait of one of the hybridizing pair appears shifted into the range of the other, the underlying mechanism can be difficult to infer. For example, hybridization between hermit warbler (Dendroica occidentalis) and Townsend's warbler (Dendroica townsendi) is restricted to narrow hybrid zones in Washington and Oregon, yet hermit mtDNA can be found in phenotypically pure Townsend's populations up to 2000 km north along the Pacific coast. This could reflect introgression of selectively favoured hermit mitochondria north across the hybrid zones, or a neutral genetic wake left behind following southern zone movement. Hermit mitochondrial haplotypes in populations of coastal Townsend's exhibit relatively high genetic diversity and significant divergence from those found in populations of hermit warblers. This contradicts the predictions of selective introgression, but is consistent with a northern population of hermits diverging in a glacial refugium before being replaced by Townsend's via aggressive hybridization. Previous field studies showing Townsend's males to be competitively superior to hermit males support this scenario, and suggest that the extreme hybrid zone movement evidenced by the hermit mitochondrial wake represents an extinction in progress.
The ocean is not deep enough: pressure tolerances during early ontogeny of the blue musselMytilus edulis
Authors: Mestre Nélia C , Thatje Sven , Tyler Paul A
Published: November 2008

Early ontogenetic adaptations reflect the evolutionary history of a species. To understand the evolution of the deep-sea fauna and its adaptation to high pressure, it is important to know the effects of pressure on their shallow-water relatives. In this study we analyse the temperature and pressure tolerances of early life-history stages of the shallow-water speciesMytilus edulis. This species expresses a close phylogenetic relationship with hydrothermal-vent mussels of the subfamily Bathymodiolinae. Tolerances to pressure and temperature are defined in terms of fertilization success and embryo developmental rates in laboratory-based experiments. InM. edulis, successful fertilization under pressure is possible up to 500 atm (50.66 MPa), at 10, 15 and 20°C. A slower embryonic development is observed with decreasing temperature and with increasing pressure; principally, pressure narrows the physiological tolerance window in different ontogenetic stages ofM. edulis, and slows down metabolism. This study provides important clues on possible evolutionary pathways of hydrothermal vent and cold-seep bivalve species and their shallow-water relatives. Evolution and speciation patterns of species derive mostly from their ability to adapt to variable environmental conditions, within environmental constraints, which promote morphological and genetic variability, often differently for each life-history stage. The present results support the view that a direct colonization of deep-water hydrothermal vent environments by a cold eurythermal shallow-water ancestor is indeed a possible scenario for the Mytilinae, challenging previous hypothesis of a wood/bone to seep/vent colonization pathway.
Reverse hierarchies and sensory learning
Authors: Ahissar Merav , Nahum Mor , Nelken Israel , Hochstein Shaul
Published: November 2008

Revealing the relationships between perceptual representations in the brain and mechanisms of adult perceptual learning is of great importance, potentially leading to significantly improved training techniques both for improving skills in the general population and for ameliorating deficits in special populations. In this review, we summarize the essentials of reverse hierarchy theory for perceptual learning in the visual and auditory modalities and describe the theory's implications for designing improved training procedures, for a variety of goals and populations.
GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses
Authors: Yilmaz Alper , Nishiyama Milton Y. , Fuentes Bernardo Garcia , Souza Glaucia Mendes , Janies Daniel , Gray John , Grotewold Erich
Published: November 2008

Transcription factors (TFs) are major players in gene regulatory networks and interactions between TFs and their target genes furnish spatiotemporal patterns of gene expression. Establishing the architecture of regulatory networks requires gathering information on TFs, their targets in the genome, and the corresponding binding sites. We have developed GRASSIUS (Grass Regulatory Information Services) as a knowledge-based Web resource that integrates information on TFs and gene promoters across the grasses. In its initial implementation, GRASSIUS consists of two separate, yet linked, databases. GrassTFDB holds information on TFs from maize (Zea mays), sorghum (Sorghum bicolor), sugarcane (Saccharum spp.), and rice (Oryza sativa). TFs are classified into families and phylogenetic relationships begin to uncover orthologous relationships among the participating species. This database also provides a centralized clearinghouse for TF synonyms in the grasses. GrassTFDB is linked to the grass TFome collection, which provides clones in recombination-based vectors corresponding to full-length open reading frames for a growing number of grass TFs. GrassPROMDB contains promoter and cis-regulatory element information for those grass species and genes for which enough data are available. The integration of GrassTFDB and GrassPROMDB will be accomplished through GrassRegNet as a first step in representing the architecture of grass regulatory networks. GRASSIUS can be accessed from www.grassius.org.
The Role of Plasma Membrane Intrinsic Protein Aquaporins in Water Transport through Roots: Diurnal and Drought Stress Responses Reveal Different Strategies between Isohydric and Anisohydric Cultivars of Grapevine
Authors: Vandeleur Rebecca K. , Mayo Gwenda , Shelden Megan C. , Gilliham Matthew , Kaiser Brent N. , Tyerman Stephen D.
Published: November 2008

We report physiological and anatomical characteristics of water transport across roots grown in soil of two cultivars of grapevine (Vitis vinifera) differing in response to water stress (Grenache, isohydric; Chardonnay, anisohydric). Both cultivars have similar root hydraulic conductances (L  o; normalized to root dry weight) that change diurnally. There is a positive correlation between L  o and transpiration. Under water stress, both cultivars have reduced minimum daily L  o (predawn) attributed to the development of apoplastic barriers. Water-stressed and well-watered Chardonnay had the same diurnal change in amplitude of L  o, while water-stressed Grenache showed a reduction in daily amplitude compared with well-watered plants. Hydraulic conductivity of root cortex cells (L  pcell) doubles in Chardonnay but remains unchanged in Grenache. Of the two most highly expressed plasma membrane intrinsic protein (PIP) aquaporins in roots (VvPIP1;1 and VvPIP2;2), only VvPIP2;2 functions as a water channel in Xenopus laevis oocytes. VvPIP1;1 interacts with VvPIP2;2 to induce 3-fold higher water permeability. These two aquaporins are colocated in the root from in situ hybridization and immunolocalization of VvPIP1 and VvPIP2 subfamily members. They occur in root tip, exodermis, root cortex (detected up to 30 mm), and stele. VvPIP2;2 mRNA does not change diurnally or with water stress, in contrast to VvPIP1;1, in which expression reflects the differences in L  o and L  pcell between cultivars in their responses to water stress and rewatering. VvPIP1;1 may regulate water transport across roots such that transpirational demand is matched by root water transport capacity. This occurs on a diurnal basis and in response to water stress that corresponds to the difference in drought tolerance between the cultivars.
Flux Balance Analysis of Barley Seeds: A Computational Approach to Study Systemic Properties of Central Metabolism
Authors: Grafahrend-Belau Eva , Schreiber Falk , Koschützki Dirk , Junker Björn H.
Published: November 2008

The accumulation of storage compounds is an important aspect of cereal seed metabolism. Due to the agronomical importance of the storage reserves of starch, protein, and oil, the understanding of storage metabolism is of scientific interest, with practical applications in agronomy and plant breeding. To get insight into storage patterning in developing cereal seed in response to environmental and genetic perturbation, a computational analysis of seed metabolism was performed. A metabolic network of primary metabolism in the developing endosperm of barley (Hordeum vulgare), a model plant for temperate cereals, was constructed that includes 257 biochemical and transport reactions across four different compartments. The model was subjected to flux balance analysis to study grain yield and metabolic flux distributions in response to oxygen depletion and enzyme deletion. In general, the simulation results were found to be in good agreement with the main biochemical properties of barley seed storage metabolism. The predicted growth rate and the active metabolic pathway patterns under anoxic, hypoxic, and aerobic conditions predicted by the model were in accordance with published experimental results. In addition, the model predictions gave insight into the potential role of inorganic pyrophosphate metabolism to maintain seed metabolism under oxygen deprivation.
The Arabidopsis A4 Subfamily of Lectin Receptor Kinases Negatively Regulates Abscisic Acid Response in Seed Germination
Authors: Xin Zeyu , Wang Anyou , Yang Guohua , Gao Peng , Zheng Zhi-Liang
Published: November 2008

Abscisic acid (ABA) is an important plant hormone for a wide array of growth and developmental processes and stress responses, but the mechanism of ABA signal perception on the plasma membrane remains to be dissected. A previous GeneChip analysis revealed that a member of the A4 subfamily of lectin receptor kinases (LecRKs) of Arabidopsis (Arabidopsis thaliana), At5g01540 (designated LecRKA4.1), is up-regulated in response to a low dose of ABA in the rop10-1 background. Here, we present functional evidence to support its role in ABA response. LecRKA4.1 is expressed in seeds and leaves but not in roots, and the protein is localized to the plasma membrane. A T-DNA knockout mutant, lecrka4.1-1, slightly enhanced ABA inhibition of seed germination. Interestingly, LecRKA4.1 is adjacent to two other members of the A4 subfamily of LecRK genes, At5g01550 (LecRKA4.2) and At5g01560 (LecRKA4.3). We found that loss-of-function mutants of LecRKA4.2 and LecRKA4.3 exhibited similarly weak enhancement of ABA response in seed germination inhibition. Furthermore, LecRKA4.2 suppression by RNA interference in lecrka4.1-1 showed stronger ABA inhibition of seed germination than lecrka4.1-1, while the response to gibberellic acid was not affected in lecrka4.1-1 and lecrka4.1-1; LecRKA4.2 (RNAi) lines. Expression studies, together with network-based analysis, suggest that LecRKA4.1 and LecRKA4.2 regulate some of the ABA-responsive genes. Taken together, our results demonstrate that the A4 subfamily of LecRKs has a redundant function in the negative regulation of ABA response in seed germination.
AucsiaGene Silencing Causes Parthenocarpic Fruit Development in Tomato
Authors: Molesini Barbara , Pandolfini Tiziana , Rotino Giuseppe Leonardo , Dani Valeria , Spena Angelo
Published: November 2008

In angiosperms, auxin phytohormones play a crucial regulatory role in fruit initiation. The expression of auxin biosynthesis genes in ovules and placenta results in uncoupling of tomato (Solanum lycopersicum) fruit development from fertilization with production of parthenocarpic fruits. We have identified two newly described genes, named Aucsia genes, which are differentially expressed in auxin-synthesis (DefH9-iaaM) parthenocarpic tomato flower buds. The two tomato Aucsia genes encode 53-amino-acid-long peptides. We show, by RNA interference-mediated gene suppression, that Aucsia genes are involved in both reproductive and vegetative plant development. Aucsia-silenced tomato plants exhibited auxin-related phenotypes such as parthenocarpic fruit development, leaf fusions, and reflexed leaves. Auxin-induced rhizogenesis in cotyledon explants and polar auxin transport in roots were reduced in Aucsia-silenced plants compared with wild-type plants. In addition, Aucsia-silenced plants showed an increased sensitivity to 1-naphthylphthalamic acid, an inhibitor of polar auxin transport. We further prove that total indole-3-acetic acid content was increased in preanthesis Aucsia-silenced flower buds. Thus, the data presented demonstrate that Aucsia genes encode a novel family of plant peptides that control fruit initiation and affect other auxin-related biological processes in tomato. Aucsia homologous genes are present in both chlorophytes and streptophytes, and the encoded peptides are distinguished by a 16-amino-acid-long (PYSGXSTLALVARXSA) AUCSIA motif, a lysine-rich carboxyl-terminal region, and a conserved tyrosine-based endocytic sorting motif.
Multi‐gene phylogeny of the pantropical subfamily Chrysophylloideae (Sapotaceae): evidence of generic polyphyly and extensive morphological homoplasy
Authors: Swenson Ulf , Richardson James E. , Bartish Igor V.
Published: November 2008

We present a molecular phylogeny of 26 out of the 28 currently accepted genera in the subfamily Chrysophylloideae (Sapotaceae) using parsimony, parsimony jackknifing, and Bayesian inference. A data matrix of 8984 characters was obtained from DNA sequences of seven chloroplast loci, two nuclear loci, indels coded as binary characters, and morphology. Our phylogenetic reconstruction suggests that Chrysophyllum, Pouteria, and Pradosia, as well as some sections within Chrysophyllum and Pouteria, are all polyphyletic. These taxa were previously described largely on the basis of unique combinations of states for a set of morphological characters. Mapping some of these characters onto one of the most parsimonious trees indicates that the symplesiomorphic flower in the subfamily was probably 5‐merous, had stamens inserted in the tube orifice, staminodes, seeds with foliaceous cotyledons, exserted radicle, and endosperm. These characters have subsequently been lost multiple times and cannot be used as synapomorphies to support broad generic concepts. Despite the high degree of homoplasy some well‐defined clades can be described on the basis of alternative character state combinations. Also, many of these well‐supported clades appear to be restricted to particular geographical areas (e.g. all taxa in Australasia form a monophyletic group). Hence, we suggest that the segregate genera Aningeria, Malacantha, and Martiusella may ultimately be resurrected, and probably also Donella and Gambeya, but their circumscriptions are still unclear. One species, Chrysophyllum cuneifolium, may have originated from a hybridization event between continents where the maternal genome (cpDNA) comes from South America and the nuclear genome comes from Africa.

© The Willi Hennig Society 2008.
A randomized trial of short psychotherapy versus sustained‐release bupropion for smoking cessation
Authors: Zernig Gerald , Wallner Reinhild , Grohs Ursula , Kriechbaum Norbert , Kemmler Georg , Saria Alois
Published: November 2008

Aims To compare the efficacy and safety of a novel psychological intervention for smoking cessation called psychodynamic model (PDM) training to an active control condition of sustained‐release bupropion.

Design Randomized controlled clinical trial with allocation concealment.

Setting Private psychiatric practice.

Participants Seven hundred and seventy‐nine adult smokers recruited by advertising.

Interventions PDM training (n = 366 participants) consisted of a very brief (1.5 days) psychoeducation and a supervised training in autosuggestion techniques (guided imageries) aimed at enhancing self‐management, decidedness, assertiveness, security and competence in relationships, natural functions of organs and awareness of bodily functions. Bupropion SR (n = 413) was increased to 150 mg twice daily over 1 week and given over a 8‐week period.

Measurements Twelve‐month continuous abstinence confirmed by exhaled carbon monoxide (CO) of 9 parts per million (p.p.m.) or less at all interviews conducted at 3, 6 and 12 months.

Findings Intention‐to‐treat analysis revealed Russell standard 12‐month continuous abstinence rates of 39.1% in the psychotherapy group versus 12.3% in the bupropion SR group (P < 0.001) with a relative benefit (RB) of 3.16 (2.38–4.26). Completer analysis revealed 12‐month continuous abstinence rates of 39.9% in the psychotherapy group versus 22.5% in the bupropion group [P < 0.001; RB 1.78 (1.35–2.34)]. Of note, bupropion abstinence rates were comparable to previous medications/placebo‐only comparisons in geographically different samples.

Conclusions The 1.5‐day psychotherapy exceeded bupropion's efficacy, presenting an alternative to pharmacological smoking cessation aids, especially for smokers who reject drugs to treat their substance dependence, at a similar cost (€350) as the bupropion treatment (€355).
Recollective experience in alcohol dependence: a laboratory study
Authors: Thoma Patrizia , Johann Katharina , Wähner Alfred , Juckel Georg , Daum Irene
Published: November 2008

Aims  Alcohol dependence has been linked to dysfunction of fronto‐temporo‐striatal circuits which mediate memory and executive function. The present study aimed to explore the specificity of recognition memory changes in alcohol dependence.

Design, setting and participants  Twenty hospitalized alcohol‐dependent detoxified patients and 20 healthy control subjects completed a verbal list discrimination task.

Measurements  Hits and false alarm rates were analysed. Additionally, both the dual process signal detection model (DPSD) and the process dissociation procedure (PDP) were used to derive estimates of the contribution of recollection and familiarity processes to the recognition memory performance in patients and controls.

Findings  Alcohol‐dependent patients showed intact hit rates, but increased false alarm rates and an impaired ability to remember the learning context. Both the DPSD model and PDP estimates yielded significantly reduced recollection estimates in the alcohol‐dependent compared to control subjects. Whether or not familiarity was impaired, depended upon the sensitivity of the estimation procedure.

Conclusion  Taken together, the result pattern suggests a significant impairment in recollection and mild familiarity changes in recently detoxified, predominantly male, alcohol‐dependent subjects.
Ciprofloxacin‐induced torsades de pointes in a methadone‐dependent patient
Authors: Nair Murali K. , Patel Krunal , Starer Perry J.
Published: November 2008

Background Methadone has been associated with QT prolongation and Torsades de pointes. Ciprofloxacin may prolong QT interval and induce Torsades de pointes when other risk factors are present.

Case description A case is described in which a patient receiving methadone treatment developed Torsades de pointes following the addition of ciprofloxacin.

Conclusion Ciprofloxacin should be used with caution in patients receiving methadone.
A large kindred with X‐linked neutropenia with an I294T mutation of the Wiskott‐Aldrich syndrome gene
Authors: Beel Karolien , Cotter Melanie M. , Blatny Jan , Bond Jonathan , Lucas Geoff , Green Frances , Vanduppen Vik , Leung Daisy W. , Rooney Sean , Smith Owen P. , Rosen Michael K. , Vandenberghe Peter
Published: November 2008

X‐linked neutropenia (XLN, OMIM #300299) is a rare form of severe congenital neutropenia. It was originally described in a three‐generation family with five affected members that had an L270P mutation in the GTP‐ase binding domain (GBD) of the Wiskott‐Aldrich syndrome protein (WASP) [Devriendt et al (2001) Nature Genetics, Vol. 27, 313–317]. Here, we report and describe a large three‐generation family with XLN, with 10 affected males and eight female carriers. A c.882T>C mutation was identified in the WAS gene, resulting in an I294T mutation. The infectious course is variable and mild in view of the profound neutropenia. In addition to the original description, low‐normal IgA levels, low to low‐normal platelet counts and reduced natural killer (NK)‐cell counts also appear as consistent XLN features. However, inverted CD4/CD8 ratios were not found in this family, nor were cases identified with myelodysplastic syndrome or acute myeloid leukaemia. Female carriers exhibited a variable attenuated phenotype. Like L270P WASP, I294T WASP is constitutively active towards actin polymerization. In conclusion, this largest XLN kindred identified to date provides new independent genetic evidence that mutations disrupting the auto‐inhibitory GBD of WASP are the cause of XLN. Reduced NK cells, low to low normal platelet counts and low to low‐normal IgA levels are also features of XLN.
Cytogenetics of paediatric and adolescent acute lymphoblastic leukaemia
Authors: Harrison Christine J.
Published: November 2008

Cytogenetics has determined the incidence and prognostic significance of chromosomal abnormalities in acute lymphoblastic leukaemia (ALL). The development of fluorescence in situ hybridization (FISH) and array technologies has led to the discovery of novel aberrations. Five ‘hot topics’ are presented in which cytogenetics and related techniques have been instrumental in understanding the role of genetics in leukaemogenesis: (i) genetic changes are integral to the biology of T‐cell ALL; (ii) intrachromosomal amplification of chromosome 21 is a new recurrent abnormality in precursor‐B ALL (BCP‐ALL); (iii) the immunoglobulin heavy chain gene (IGH@) is significant in BCP‐ALL; (iv) alterations in genes involved in B‐cell development and cell cycle control contribute to the pathogenesis of BCP‐ALL; (v) age‐related cytogenetic profiles define ALL in children and adolescents as distinct biological entities. In this molecular era, cytogenetics continues to be integral to our understanding of the genetics of this disease.