bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing Lévy walks as models of animal foraging
Authors: James Alex , Plank Michael J. , Edwards Andrew M.
Published: June 2011

The hypothesis that the optimal search strategy is a Lévy walk (LW) or Lévy flight, originally suggested in 1995, has generated an explosion of interest and controversy. Long-standing empirical evidence supporting the LW hypothesis has been overturned, while new models and data are constantly being published. Statistical methods have been criticized and new methods put forward. In parallel with the empirical studies, theoretical search models have been developed. Some theories have been disproved while others remain. Here, we gather together the current state of the art on the role of LWs in optimal foraging theory. We examine the body of theory underpinning the subject. Then we present new results showing that deviations from the idealized one-dimensional search model greatly reduce or remove the advantage of LWs. The search strategy of an LW with exponentμ= 2 is therefore not as robust as is widely thought. We also review the available techniques, and their potential pitfalls, for analysing field data. It is becoming increasingly recognized that there is a wide range of mechanisms that can lead to the apparent observation of power-law patterns. The consequence of this is that the detection of such patterns in field data implies neither that the foragers in question are performing an LW, nor that they have evolved to do so. We conclude that LWs are neither a universal optimal search strategy, nor are they as widespread in nature as was once thought.
The early education of a Nobel laureate: Henry Dale's schooldays
Authors: Tansey E. M.
Published: June 2011

This paper examines the early schooling, in London and in Cambridge, of the later Nobel laureate and President of the Royal Society, the physiologist Sir Henry Dale (1875–1968). The influence of key teachers who directed the boy's interest towards science, and the impact of his schooling on his university education and later scientific career, are examined in particular. The significance of the zoologist Edward Butler of Tollington Park College, who taught Dale in his early teenage years, is highlighted.
Strategic female reproductive investment in response to male attractiveness in birds
Authors: Horváthová Terézia , Nakagawa Shinichi , Uller Tobias
Published: June 2011

Life-history theory predicts that individuals should adjust their reproductive effort according to the expected fitness returns on investment. Because sexually selected male traits should provide honest information about male genetic or phenotypic quality, females may invest more when paired with attractive males. However, there is substantial disagreement in the literature whether such differential allocation is a general pattern. Using a comparative meta-regression approach, we show that female birds generally invest more into reproduction when paired with attractive males, both in terms of egg size and number as well as food provisioning. However, whereas females of species with bi-parental care tend to primarily increase the number of eggs when paired with attractive males, females of species with female-only care produce larger, but not more, eggs. These patterns may reflect adaptive differences in female allocation strategies arising from variation in the signal content of sexually selected male traits between systems of parental care. In contrast to reproductive effort, female allocation of immune-stimulants, anti-oxidants and androgens to the egg yolk was not consistently increased when mated to attractive males, which probably reflects the context-dependent costs and benefits of those yolk compounds to females and offspring.
Latitude, elevational climatic zonation and speciation in New World vertebrates
Authors: Cadena Carlos Daniel , Kozak Kenneth H. , Gómez Juan Pablo , Parra Juan Luis , McCain Christy M. , Bowie Rauri C. K. , Carnaval Ana C. , Moritz Craig , Rahbek Carsten , Roberts Trina E. , Sanders Nathan J. , Schneider Christopher J. , VanDerWal Jeremy , Zamudio Kelly R. , Graham Catherine H.
Published: June 2011

Many biodiversity hotspots are located in montane regions, especially in the tropics. A possible explanation for this pattern is that the narrow thermal tolerances of tropical species and greater climatic stratification of tropical mountains create more opportunities for climate-associated parapatric or allopatric speciation in the tropics relative to the temperate zone. However, it is unclear whether a general relationship exists among latitude, climatic zonation and the ecology of speciation. Recent taxon-specific studies obtained different results regarding the role of climate in speciation in tropical versus temperate areas. Here, we quantify overlap in the climatic distributions of 93 pairs of sister species of mammals, birds, amphibians and reptiles restricted to either the New World tropics or to the Northern temperate zone. We show that elevational ranges of tropical- and temperate-zone species do not differ from one another, yet the temperature range experienced by species in the temperate zone is greater than for those in the tropics. Moreover, tropical sister species tend to exhibit greater similarity in their climatic distributions than temperate sister species. This pattern suggests that evolutionary conservatism in the thermal niches of tropical taxa, coupled with the greater thermal zonation of tropical mountains, may result in increased opportunities for allopatric isolation, speciation and the accumulation of species in tropical montane regions. Our study exemplifies the power of combining phylogenetic and spatial datasets of global climatic variation to explore evolutionary (rather than purely ecological) explanations for the high biodiversity of tropical montane regions.
The presence of an embryonic opercular flap in amniotes
Authors: Richardson Jo , Shono Takanori , Okabe Masataka , Graham Anthony
Published: June 2011

The operculum is a large flap consisting of several flat bones found on the side of the head of bony fish. During development, the opercular bones form within the second pharyngeal arch, which expands posteriorly and comes to cover the gill-bearing arches. With the evolution of the tetrapods and the assumption of a terrestrial lifestyle, it was believed that the operculum was lost. Here, we demonstrate that an embryonic operculum persists in amniotes and that its early development is homologous with that of teleosts. As in zebrafish, the second pharyngeal arch of the chick embryo grows disproportionately and comes to cover the posterior arches. We show that the developing second pharyngeal arch in both chick and zebrafish embryos express orthologous genes and require shh signalling for caudal expansion. In amniotes, however, the caudal edge of the expanded second arch fuses to the surface of the neck. We have detailed how this process occurs and also demonstrated a requirement for thyroid signalling here. Our results thus demonstrate the persistence of an embryonic opercular flap in amniotes, that its fusion mirrors aspects of amphibian metamorphosis and gives insights into the origin of branchial cleft anomalies in humans.
Phylogenetic differences of mammalian basal metabolic rate are not explained by mitochondrial basal proton leak
Authors: Polymeropoulos E. T. , Heldmaier G. , Frappell P. B. , McAllan B. M. , Withers K. W. , Klingenspor M. , White C. R. , Jastroch M.
Published: June 2011

Metabolic rates of mammals presumably increased during the evolution of endothermy, but molecular and cellular mechanisms underlying basal metabolic rate (BMR) are still not understood. It has been established that mitochondrial basal proton leak contributes significantly to BMR. Comparative studies among a diversity of eutherian mammals showed that BMR correlates with body mass and proton leak. Here, we studied BMR and mitochondrial basal proton leak in liver of various marsupial species. Surprisingly, we found that the mitochondrial proton leak was greater in marsupials than in eutherians, although marsupials have lower BMRs. To verify our finding, we kept similar-sized individuals of a marsupial opossum (Monodelphis domestica) and a eutherian rodent (Mesocricetus auratus) species under identical conditions, and directly compared BMR and basal proton leak. We confirmed an approximately 40 per cent lower mass specific BMR in the opossum although its proton leak was significantly higher (approx. 60%). We demonstrate that the increase in BMR during eutherian evolution is not based on a general increase in the mitochondrial proton leak, although there is a similar allometric relationship of proton leak and BMR within mammalian groups. The difference in proton leak between endothermic groups may assist in elucidating distinct metabolic and habitat requirements that have evolved during mammalian divergence.
Different types of oscillations in Notch and Fgf signaling regulate the spatiotemporal periodicity of somitogenesis
Authors: Niwa Yasutaka , Shimojo Hiromi , Isomura Akihiro , González Aitor , Miyachi Hitoshi , Kageyama Ryoichiro
Published: June 2011

Somitogenesis is controlled by cyclic genes such as Notch effectors and by the wave front established by morphogens such as Fgf8, but the precise mechanism of how these factors are coordinated remains to be determined. Here, we show that effectors of Notch and Fgf pathways oscillate in different dynamics and that oscillations in Notch signaling generate alternating phase shift, thereby periodically segregating a group of synchronized cells, whereas oscillations in Fgf signaling released these synchronized cells for somitogenesis at the same time. These results suggest that Notch oscillators define the prospective somite region, while Fgf oscillators regulate the pace of segmentation.
The yeast rapid tRNA decay pathway primarily monitors the structural integrity of the acceptor and T-stems of mature tRNA
Authors: Whipple Joseph M. , Lane Elizabeth A. , Chernyakov Irina , D'Silva Sonia , Phizicky Eric M.
Published: June 2011

tRNAs, like other RNAs, are subject to quality control steps during and after biosynthesis. We previously described a rapid tRNA degradation (RTD) pathway in which the 5′–3′ exonucleases Rat1 and Xrn1 degrade mature tRNAVal(AAC) in yeast mutants lacking m7G and m5C, and mature tRNASer(CGA) in mutants lacking Um and ac4C. To understand how the RTD pathway selects substrate tRNAs among different tRNAs lacking the same modifications, we used a genetic screen to examine tRNASer(CGA) variants. Our results suggest that RTD substrate recognition in vivo depends primarily on the stability of the acceptor and T-stems, and not the anti-codon stem, and does not necessarily depend on modifications, since fully modified tRNAs are subject to RTD if appropriately destabilized. We found that weaker predicted stability of the acceptor and T-stems of tRNAs is strongly correlated with RTD sensitivity, increased RNase T2 sensitivity of this region of the tRNA in vitro, and increased exposure of the 5′ end to phosphatase. We also found that purified Xrn1 selectively degrades RTD substrate tRNAs in vitro under conditions in which nonsubstrates are immune. These results suggest that tRNAs have evolved not only for accurate translation, but for resistance to attack by RTD.
Regulation of the Dbp5 ATPase cycle in mRNP remodeling at the nuclear pore: a lively new paradigm for DEAD-box proteins
Authors: Ledoux Sarah , Guthrie Christine
Published: June 2011

It is commonly assumed that all DEAD-box ATPases function via a shared mechanism, since this is the case for the few proteins characterized thus far. Hodge and colleagues (pp. 1052–1064) and Noble and colleagues (pp. 1065–1077) now describe a novel model for Dbp5's ATPase cycle in mRNA (messenger RNA)/protein complex (mRNP) remodeling during nuclear export. Notably, unlike other DEAD-box proteins, Dbp5 uses a conformational change distinct from ATP hydrolysis for its activity and requires an ADP release factor to reset its ATPase cycle.
Methylation specifies distinct estrogen-induced binding site repertoires of CBP to chromatin
Authors: Ceschin Danilo Guillermo , Walia Mannu , Wenk Sandra Simone , Duboé Carine , Gaudon Claudine , Xiao Yu , Fauquier Lucas , Sankar Martial , Vandel Laurence , Gronemeyer Hinrich
Published: June 2011

Multiple signaling pathways ultimately modulate the epigenetic information embedded in the chromatin of gene promoters by recruiting epigenetic enzymes. We found that, in estrogen-regulated gene programming, the acetyltransferase CREB-binding protein (CBP) is specifically and exclusively methylated by the coactivator-associated arginine methyltransferase (CARM1) in vivo. CARM1-dependent CBP methylation and p160 coactivators were required for estrogen-induced recruitment to chromatin targets. Notably, methylation increased the histone acetyltransferase (HAT) activity of CBP and stimulated its autoacetylation. Comparative genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) studies revealed a variety of patterns by which p160, CBP, and methyl-CBP (meCBP) are recruited (or not) by estrogen to chromatin targets. Moreover, significant target gene-specific variation in the recruitment of (1) the p160 RAC3 protein, (2) the fraction of a given meCBP species within the total CBP, and (3) the relative recruitment of different meCBP species suggests the existence of a target gene-specific “fingerprint” for coregulator recruitment. Crossing ChIP-seq and transcriptomics profiles revealed the existence of meCBP “hubs” within the network of estrogen-regulated genes. Together, our data provide evidence for an unprecedented mechanism by which CARM1-dependent CBP methylation results in gene-selective association of estrogen-recruited meCBP species with different HAT activities and specifies distinct target gene hubs, thus diversifying estrogen receptor programming.
Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex
Authors: Vandiedonck Claire , Taylor Martin S. , Lockstone Helen E. , Plant Katharine , Taylor Jennifer M. , Durrant Caroline , Broxholme John , Fairfax Benjamin P. , Knight Julian C.
Published: June 2011

The human major histocompatibility complex (MHC) on chromosome 6p21 is a paradigm for genomics, showing remarkable polymorphism and striking association with immune and non-immune diseases. The complex genomic landscape of the MHC, notably strong linkage disequilibrium, has made resolving causal variants very challenging. A promising approach is to investigate gene expression levels considered as tractable intermediate phenotypes in mapping complex diseases. However, how transcription varies across the MHC, notably relative to specific haplotypes, remains unknown. Here, using an original hybrid tiling and splice junction microarray that includes alternate allele probes, we draw the first high-resolution strand-specific transcription map for three common MHC haplotypes (HLA-A1-B8-Cw7-DR3, HLA-A3-B7-Cw7-DR15, and HLA-A26-B18-Cw5-DR3-DQ2) strongly associated with autoimmune diseases including type 1 diabetes, systemic lupus erythematosus, and multiple sclerosis. We find that haplotype-specific differences in gene expression are common across the MHC, affecting 96 genes (46.4%), most significantly the zing finger protein gene ZFP57. Differentially expressed probes are correlated with polymorphisms between haplotypes, consistent with cis effects that we directly demonstrate for ZFP57 in a cohort of healthy volunteers (P = 1.2 × 10−14). We establish that alternative splicing is significantly more frequent in the MHC than genome-wide (72.5% vs. 62.1% of genes, P ≤ 1 × 10−4) and shows marked haplotypic differences. We also unmask novel and abundant intergenic transcription involving 31% of transcribed blocks identified. Our study reveals that the renowned MHC polymorphism also manifests as transcript diversity, and our novel haplotype-based approach marks a new step toward identification of regulatory variants involved in the control of MHC-associated phenotypes and diseases.
From IMGT-ONTOLOGY DESCRIPTION Axiom to IMGT Standardized Labels: For Immunoglobulin (IG) and T Cell Receptor (TR) Sequences and Structures
Authors: Lefranc Marie-Paule
Published: June 2011

INTRODUCTION

More than 560 IMGT standardized labels have been defined for the description of immunoglobulin (IG) and T cell receptor (TR) sequences and structures. These labels, as detailed here, are based on the concepts of description (generated from the DESCRIPTION axiom) of IMGT-ONTOLOGY, the global reference in immunogenetics and immunoinformatics, built by IMGT, the international ImMunoGeneTics information system. IMGT labels for nucleotide sequences correspond to the “Molecule_EntityPrototype” concept with its leafconcepts (a leafconcept is the finest level of granularity), its associated concepts of description, and its prototypes or graphical representations. These labels have been essential for the IG and TR description in the IMGT sequence and gene databases (IMGT/LIGM-DB, IMGT/GENE-DB) and tools (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/HighV-QUEST, IMGT/LIGMotif). IMGT labels for amino acid sequences and structures correspond to the “RECEPTOR,” “CHAIN,” and “DOMAIN” concepts. These labels have been crucial for the IG and TR description in the IMGT two-dimensional (2D) and three-dimensional (3D) databases (IMGT/2Dstructure-DB, IMGT/3Dstructure-DB) and tools (IMGT/DomainDisplay, IMGT/DomainGapAlign). As all leafconcepts of description are directly translated into IMGT standardized labels for use in the IMGT databases and tools, IMGT-ONTOLOGY concepts of description contribute to data coherence and consistency and facilitate the interoperability between the different components of IMGT, bridging the description of sequences and structures.
IMGT Collier de Perles for the Variable (V), Constant (C), and Groove (G) Domains of IG, TR, MH, IgSF, and MhSF
Authors: Lefranc Marie-Paule
Published: June 2011

INTRODUCTION

The “IMGT Collier de Perles” (or “IMGT_Collier_de_Perles”) concept is a major concept of numerotation (generated from the NUMEROTATION axiom) of IMGT-ONTOLOGY, the global reference in immunogenetics and immunoinformatics, built by IMGT, the international ImMunoGeneTics information system. The “IMGT Collier de Perles” concept, described here, allows standardized two-dimensional (2D) graphical representations of the domains, based on the IMGT unique numbering. Three leafconcepts (a leafconcept is a concept that corresponds to the finest level of granularity) have been defined: for the variable (V) domain and constant (C) domain of the immunoglobulin superfamily (IgSF) and for the groove (G) domain of the major histocompatibility (MH) superfamily (MhSF). IMGT Colliers de Perles are obtained, starting from V, C, or G domain amino acid sequences, using IMGT/DomainGapAlign and IMGT/Collier de Perles tools. In IMGT/3Dstructure-DB, IMGT Colliers de Perles of V and C domains are provided with hydrogen bonds and those of G domains with IMGT pMH contact analysis. IMGT Colliers de Perles allows one to bridge the gap between sequences and three-dimensional (3D) structures, whatever the species, the IgSF or MhSF protein, or the chain type. They are particularly useful for antibody engineering, sequence-structure analysis, visualization and comparison of positions for mutations, polymorphisms and contact analysis of immunoglobulins (IG), T cell receptors (TR), MH, and related proteins of the immune system (RPI) belonging to the IgSF and MhSF.
Dissection and Staining of Drosophila Optic Lobes at Different Stages of Development
Authors: Morante Javier , Desplan Claude
Published: June 2011

INTRODUCTION

The Drosophila visual system is composed of the retina and the optic lobes, which are the ganglia where photoreceptors project and initial processing of visual inputs occur. This protocol outlines procedures for dissecting the optic lobes from Drosophila larvae, pupae, and adults. It also describes methods for visualizing the anatomy of brain neural circuits by staining with fluorescent secondary antibodies and primary antibodies specific for various neuronal populations and architectural features.
IMGT/JunctionAnalysis: IMGT Standardized Analysis of the V-J and V-D-J Junctions of the Rearranged Immunoglobulins (IG) and T Cell Receptors (TR)
Authors: Giudicelli Véronique , Lefranc Marie-Paule
Published: June 2011

INTRODUCTION

IMGT/JunctionAnalysis is the online IMGT tool for the detailed and standardized analysis of the junctions between the variable (V), diversity (D), and joining (J) genes (V-J and V-D-J junctions) of the rearranged immunoglobulin (IG) or antibody and T cell receptor (TR) variable domains. The V-(D)-J junctions comprise the rearranged CDR3-IMGT and its anchors 2nd-CYS 104 and J-PHE or J-TRP 118. The diversity of the junctions that determines the antigen receptor specificity results from complex molecular mechanisms that occur at the DNA level during the IG and TR synthesis and create combinatorial diversity, N-diversity and, for IG, somatic hypermutations. The annotation of V-J or V-D-J junctions in rearranged IG and TR sequences represents a huge challenge due to its uniqueness and complexity. IMGT/JunctionAnalysis has been a major breakthrough by providing, for the first time, a very detailed and accurate analysis of the junctions. The tool, whose use is described here, identifies the D genes in the IGH, TRB, and TRD junctions, the trimmed nucleotides (nt) at the end of the genes which recombine, and the palindromic P regions in the absence of gene trimming. It delimits the N regions that result from the N-diversity, calculates the ratio of G+C nucleotides in the N regions, and evaluates the number of somatic hypermutations for each gene within the junction.
IMGT/Collier de Perles: IMGT Standardized Representation of Domains (IG, TR, and IgSF Variable and Constant Domains, MH and MhSF Groove Domains)
Authors: Ehrenmann François , Giudicelli Véronique , Duroux Patrice , Lefranc Marie-Paule
Published: June 2011

INTRODUCTION

IMGT/Collier de Perles is the IMGT online tool that allows one to draw standardized IMGT two-dimensional (2D) graphical representations of protein domains, or IMGT Colliers de Perles, starting from the user’s own domain amino acid (AA) sequences. The use of this tool is described here. IMGT Colliers de Perles can be drawn for three domain types: the variable (V) domain and constant (C) domain of the immunoglobulin (IG) and T cell receptor (TR) and other members of the immunoglobulin superfamily (IgSF), and the groove (G) domain of the major histocompatibility (MH) and other members of the MH superfamily (MhSF). Sequences have to be gapped according to the IMGT unique numbering, using, for example, IMGT/DomainGapAlign. Resulting IMGT Colliers de Perles allow one to quickly visualize amino acids, which are important for the three-dimensional (3D) structural configuration, and to delimit the standardized framework regions (FR-IMGT) and complementarity determining regions (CDR-IMGT) of the IG and TR V-DOMAIN. The length of the strands, loops, and turns and, for the G type, the length of the helix represented in IMGT Colliers de Perles become crucial information in the domain characterization.
IMGT/DomainGapAlign: IMGT Standardized Analysis of Amino Acid Sequences of Variable, Constant, and Groove Domains (IG, TR, MH, IgSF, MhSF)
Authors: Ehrenmann François , Lefranc Marie-Paule
Published: June 2011

INTRODUCTION

IMGT/DomainGapAlign is the IMGT online tool for the analysis of amino acid (AA) sequences and two-dimensional (2D) structures of domains. The use of this tool is described here. Three domain types can be analyzed: the variable (V) and constant (C) domains of the immunoglobulins (IG) and T cell receptors (TR) and other immunoglobulin superfamily (IgSF) proteins, and the groove (G) domain of major histocompatibility (MH) and other MH superfamily (MhSF) proteins. IMGT/DomainGapAlign creates gaps in the user amino acid sequences and delimits, for the V and C domains, the framework regions (FR-IMGT) and complementarity determining regions (CDR-IMGT), and, for the G domains, the strands and helix, according to the IMGT unique numbering. The tool provides alignments with the closest sequences from the IMGT domain directory of IMGT/DomainDisplay. For the IG and TR V domains that result from V-(D)-J rearrangement, the tool provides alignments with the translation of the IMGT/GENE-DB germline V and joining (J) genes. IMGT/DomainGapAlign displays the amino acid changes, highlights them in IMGT Colliers de Perles, and provides tables with their detailed description, according to the IMGT rules. Several amino acid sequences can be analyzed simultaneously, provided that they belong to the same domain type.
IMGT/3Dstructure-DB: Querying the IMGT Database for 3D Structures in Immunology and Immunoinformatics (IG or Antibodies, TR, MH, RPI, and FPIA)
Authors: Ehrenmann François , Lefranc Marie-Paule
Published: June 2011

INTRODUCTION

IMGT/3Dstructure-DB is the three-dimensional (3D) structure database of IMGT, the international ImMunoGenetics information system that is acknowledged as the global reference in immunogenetics and immunoinformatics. IMGT/3Dstructure-DB contains 3D structures of (1) antigen receptors that comprise immunoglobulins (IG) or antibodies and T cell receptors (TR), (2) major histocompatibility (MH) proteins of class I (MH1) and class II (MH2), (3) peptide/MH (pMH) complexes (pMH1, pMH2), (4) antigen receptor/antigen complexes (IG/Ag, TR/pMH), and (5) related proteins of the immune system (RPI) belonging to the immunoglobulin and MH superfamilies (IgSF and MhSF, respectively) and found in complexes with IG, TR, or MH. IMGT/3Dstructure-DB data are annotated according to the IMGT criteria, using IMGT/DomainGapAlign, and based on the IMGT-ONTOLOGY axioms and concepts. The use of IMGT/3Dstructure-DB is described here. It provides IMGT gene and allele identification (CLASSIFICATION), region and domain delimitations (DESCRIPTION), and amino acid (AA) positions according to the IMGT unique numbering (NUMEROTATION). IMGT/3Dstructure-DB provides the closest genes and alleles that are expressed in the AA sequences of the 3D structures, by aligning these sequences with the IMGT domain reference directory.
Engineering Light-Regulated Ion Channels: Figure 1.
Authors: Fortin Doris L. , Dunn Timothy W. , Kramer Richard H.
Published: June 2011

INTRODUCTION

Optical regulation provides unrivaled spatial and temporal precision for the control of protein function. We describe a strategy to engineer photosensitivity onto ion channels based on small photoisomerizable molecules. Photosensitivity is targeted to the ion channel of interest by combining the photoisomerizable moiety with a specific agonist or antagonist. Inclusion of a cysteine-reactive maleimide group enables covalent attachment of the photoswitch to a genetically engineered cysteine on the surface of the ion channel. Exposure to different wavelengths of light triggers changes in the properties of the photoswitch that enable control of protein function.
Optical Projection Tomography of Vertebrate Embryo Development
Authors: Quintana Laura , Sharpe James
Published: June 2011

INTRODUCTION

This article includes a brief introduction to optical projection tomography (OPT) as a method for imaging whole vertebrate embryos. To place OPT in its proper context within the field of three-dimensional (3D) embryo imaging, the article starts with a brief overview of the previously existing techniques, both destructive and nondestructive. Next is a description of how OPT works and its advantages over other approaches. Two practical sections are then presented that consider the applications of OPT and how to get the best results from OPT in terms of specimen preparation and imaging modes.
Perturbation of spermine synthase Gene Expression and Transcript Profiling Provide New Insights on the Role of the Tetraamine Spermine in Arabidopsis Defense against Pseudomonas viridiflava
Authors: Gonzalez María Elisa , Marco Francisco , Minguet Eugenio Gómez , Carrasco-Sorli Pedro , Blázquez Miguel Angel , Carbonell Juan , Ruiz Oscar Adolfo , Pieckenstain Fernando Luis
Published: June 2011

The role of the tetraamine spermine in plant defense against pathogens was investigated by using the Arabidopsis (Arabidopsis thaliana)-Pseudomonas viridiflava pathosystem. The effects of perturbations of plant spermine levels on susceptibility to bacterial infection were evaluated in transgenic plants (35S::spermine synthase [SPMS]) that overexpressed the SPMS gene and accumulated spermine, as well as in spms mutants with low spermine levels. The former exhibited higher resistance to P. viridiflava than wild-type plants, while the latter were more susceptible. Exogenous supply of spermine to wild-type plants also increased disease resistance. Increased resistance provided by spermine was partly counteracted by the polyamine oxidase inhibitor SL-11061, demonstrating that the protective effect of spermine partly depends on its oxidation. In addition, global changes in gene expression resulting from perturbations of spermine levels were analyzed by transcript profiling 35S::SPMS-9 and spms-2 plants. Overexpression of 602 genes was detected in 35S::SPMS-9 plants, while 312 genes were down-regulated, as compared to the wild type. In the spms-2 line, 211 and 158 genes were up- and down-regulated, respectively. Analysis of gene ontology term enrichment demonstrated that many genes overexpressed only in 35S::SPMS-9 participate in pathogen perception and defense responses. Notably, several families of disease resistance genes, transcription factors, kinases, and nucleotide- and DNA/RNA-binding proteins were overexpressed in this line. Thus, a number of spermine-responsive genes potentially involved in resistance to P. viridiflava were identified. The obtained results support the idea that spermine contributes to plant resistance to P. viridiflava.
Novel alternative splicing by exon skipping in KIT associated with whole‐body roan in an intercrossed population of Landrace and Korean Native pigs
Authors: Lim H. T. , Zhong T. , Cho I. C. , Seo B. Y. , Kim J. H. , Lee S. S. , Ko M. S. , Park H. B. , Kim B. W. , Lee J. H. , Jeon J. T.
Published: June 2011

The KIT locus has been suggested to be a strong candidate region linked with whole‐body roan in the F2 population produced by intercrosses between Landrace and Korean Native pigs. In this manuscript, we report the finding of a novel alternative splicing event in the porcine KIT gene that results in the skipping of exon 5 in the IRn allele. KIT mRNAs that lack exon 5 were identified in the large intestine and skin, suggesting that the mechanism responsible for the skipping of exon 5 may be tissue specific. A U26 repeat in intron 5 showed complete linkage (LOD = 11.8) with the roan phenotype and absolute association with the black phenotype of the Korean Native pig (KNP) population samples, inferring that the repeat pattern may alter the complementary base‐pairing‐mediated looping‐out of introns 4 and 5, which may mediate the exon 5‐skipping event. Although the sample size in our study was relatively small, we speculate that the R3 allele containing the U26 repeat is a causative element for the roan phenotype via alternative control of the exon skipping in our roan pedigree.
An international collaborative study comparing Swedish and Japanese nurses’ reactions to elder abuse
Authors: Erlingsson Christen , Ono Mitsu , Sasaki Akiko , Saveman Britt‐Inger
Published: June 2011

erlingsson c., ono m., sasaki a. & saveman b.‐I. (2012) An international collaborative study comparing Swedish and Japanese nurses’ reactions to elder abuse. Journal of Advanced Nursing68(1), 56–68.

Aim.  This paper reports an analysis of aggregated data from two national studies on Swedish community‐based nurses’ and Japanese Public Health Nurses’ responses to hypothetical elder abuse cases.

Background.  Elder abuse is an under‐researched area despite being globally recognized as a serious and escalating problem. Yet research, adding needed socio‐cultural perspectives to current knowledge has been limited.

Methods.  Eighty‐one community‐based nurses in Sweden and 124 Public Health Nurses in Japan responded to a questionnaire based on three hypothetical elder abuse cases. Swedish and Japanese results (data collection 2006–2007) were combined and the aggregated data were analysed using manifest and qualitative content analyses.

Results.  Nurses’ response patterns in the aggregated data were similar across all three hypothetical cases and within themes Awareness, Assessment and Intervention. However, there were also noteworthy differences between Swedish and Japanese responses, e.g. Swedish responses were generally practical, action oriented and involved increased levels of suspicion and personal intervention to achieve increased control; whereas Japanese responses concerned better understanding that involved the family members and their situation, focusing on interventions grounded in collaboration.

Conclusion.  Despite cultural differences, responses of Swedish and Japanese nurses were very similar which points to a global ‘humanness’ of the problem of, and nurses’ responses to, elder abuse. Results endorse the value of international collaborations that give information and inspiration to nursing colleagues across cultural boundaries. Results also give hope that global tools for elder abuse assessment and intervention can be developed.
The impact of a pathogenic bacterium on a social carnivore population
Authors: Höner Oliver P. , Wachter Bettina , Goller Katja V. , Hofer Heribert , Runyoro Victor , Thierer Dagmar , Fyumagwa Robert D. , Müller Thomas , East Marion L.
Published: June 2011

1. The long‐term ecological impact of pathogens on group‐living, large mammal populations is largely unknown. We evaluated the impact of a pathogenic bacterium,Streptococcus equi ruminatorum, and other key ecological factors on the dynamics of the spotted hyenaCrocuta crocutapopulation in the Ngorongoro Crater, Tanzania.

2. We compared key demographic parameters during two years when external signs of bacterial infection were prevalent (‘outbreak’) and periods of five years before and after the outbreak when such signs were absent or rare. We also tested for density dependence and calculated the basic reproductive rateR0of the bacterium.

3. During the five pre‐outbreak years, the mean annual hyena mortality rate was 0·088, and annual population growth was relatively high (13·6%). During the outbreak, mortality increased by 78% to a rate of 0·156, resulting in an annual population decline of 4·3%. After the outbreak, population size increased moderately (5·1%) during the first three post‐outbreak years before resuming a growth similar to pre‐outbreak levels (13·9%). We found no evidence that these demographic changes were driven by density dependence or other ecological factors.

4. Most hyenas showed signs of infection when prey abundance in their territory was low. During the outbreak, mortality increased among adult males and yearlings, but not among adult females – the socially dominant group members. These results suggest that infection and mortality were modulated by factors linked to low social status and poor nutrition. During the outbreak, we estimatedR0for the bacterium to be 2·7, indicating relatively fast transmission.

5. Our results suggest that the short‐term ‘top–down’ impact ofS. equi ruminatorumduring the outbreak was driven by ‘bottom–up’ effects on nutritionally disadvantaged age–sex classes, whereas the longer‐term post‐outbreak reduction in population growth was caused by poor survival of juveniles during the outbreak and subsequent poor recruitment of breeding females. These results suggest synergistic effects of ‘bottom–up’ and ‘top–down’ processes on host population dynamics.
Exploring risk factors for depression among older men residing in Macau
Authors: Chan Moon Fai , Zeng Wen
Published: June 2011

Aim.  To determine the prevalence of depression level of older men in Macau and identify factors that predict depression.

Background.  Studies have revealed the contribution of psychosocial factors such as stress, dissatisfaction at work and stressful life events to older men and the mental health burdens pose a grave threat to their quality of life.

Design.  A descriptive survey.

Method.  The study was conducted from July–August 2004 in six parishes in Macau; 839 older men aged 60+ completed a structured questionnaire.

Outcome measures.  Predisposing characteristics, social and daily activities, health history and need/behaviours and depression level were collected. Multiple logistic regression models were used to identify factors to predict older men who will have depression.

Results.  The prevalence rate of depression of older men was 8·6%. It showed that a history of stroke (p = 0·039), insomnia (p < 0·001), palpitations (p = 0·014), poor social network (p = 0·005) and self‐perceived health status (p = 0·001) and perceived low ability to meet living costs (p < 0·001) were significant risk factors for depression.

Conclusion.  We should focus on older men by reducing their burden to meet living costs, improving their sleep quality and helping them to expand their social network. These should help in both prevention and recognition of the onset of depression. Those with the low social network scores could be targeted for more intensive support from the beginning.

Relevance to clinical practice.  It is important to screen regularly for depression status among older men in the community. Attention to poor perceived health and not enough on the ability to meet living costs were needed and important to follow up.
The emotional sequelae of whistleblowing: findings from a qualitative study
Authors: Peters Kath , Luck Lauretta , Hutchinson Marie , Wilkes Lesley , Andrew Sharon , Jackson Debra
Published: June 2011

Aims and objectives.  To highlight and illuminate the emotional sequelae of whistleblowing from whistleblowers and subjects of whistleblowing complaints.

Background.  Whistleblowing has the potential to have a negative impact on individuals’ physical and emotional well‐being. However, few empirical studies have been conducted using qualitative methods to provide an in‐depth exploration of the emotional consequences for those involved in whistleblowing incidents.

Design.  Qualitative narrative inquiry design.

Method.  Purposive sampling was used to recruit participants who had been involved in whistleblowing incidents. During interviews participants’ accounts were digitally recorded and then transcribed verbatim. Data were then analysed by two researchers until consensus was reached.

Results.  Findings revealed that participants’ emotional health was considerably compromised as a result of the whistleblowing incident. Analysis of the data revealed the following dominant themes: ‘I felt sad and depressed’: overwhelming and persistent distress; ‘I was having panic attacks and hyperventilating’: acute anxiety; and, ‘I had all this playing on my mind’: nightmares, flashbacks and intrusive thoughts.

Conclusions.  While it has been previously acknowledged that whistleblowing has the potential to have a negative impact on all aspects of an individual’s life, this study notably highlights the intensity of emotional symptoms suffered by participants as well as the extended duration of time these symptoms were apparent.

Relevance to clinical practice.  As professionals, nurses, as well as organisations, have a responsibility to identify those who may be suffering the emotional trauma of whistleblowing and ensure they have access to appropriate resources.
Attitude and practice of the health care professionals towards the clinical practice guidelines in King Khalid University Hospital in Saudi Arabia
Authors: Wahabi Hayfaa A. , Alzeidan Rasmieh A. , Fayed Amel A. , Esmaeil Samia A. , Al Aseri Zohair A.
Published: June 2011

Rationale, aims and objectives  To explore the opinion and practice of the health care providers in King Khalid University Hospital (KKUH) towards clinical practice guidelines (CPGs).

Methods  A cross‐sectional self‐reported anonymous survey was distributed to 2225 health care professionals working in KKUH clinical departments.

Results  The response rate was 56.5%. The respondents had a positive attitude towards CPGs; 90% thought that CPG unify patients' care and 96% agreed that CPGs improve the quality of services provided. The respondents' practice in using CPGs concurred with their attitude and opinion. A total of 86.3% agreed that CPGs changed the way they manage their patients and 71.8% agreed with the statement that they have already used CPGs in the management of the patients. Compared to nurses, physicians were significantly less likely to use CPGs in practice (P < 0.05); moreover, the practice of using guidelines differs significantly according to the years of experience, with 71% of respondents with experience of 15 years or more using CPGs in the management of their patients, compared to 60% among respondents with less years of experience (P < 0.05).

Conclusion  The health care providers at KKUH have positive practice and attitude towards CPGs in general, which could positively influence the future introduction and implementation of evidence‐based CPGs.
EIN2 regulates salt stress response and interacts with a MA3 domain‐containing protein ECIP1 in Arabidopsis
Authors: LEI GANG , SHEN MING , LI ZHI‐GANG , ZHANG BO , DUAN KAI‐XUAN , WANG NING , CAO YANG‐RONG , ZHANG WAN‐KE , MA BIAO , LING HONG‐QING , CHEN SHOU‐YI , ZHANG JIN‐SONG
Published: June 2011

Ethylene signalling regulates plant growth and development. However, its roles in salt stress response are less known. Here we studied functions of EIN2, a central membrane protein of ethylene signalling, and its interacting protein ECIP1 in salt stress responses. Mutation of EIN2 led to extreme salt sensitivity as revealed by phenotypic and physiological changes, and overexpression of C‐terminus of EIN2 suppressed salt sensitivity in ein2‐5, indicating that EIN2 is required for salt tolerance. Downstream components EIN3 and EIL1 are also essential for salt tolerance because ein3‐1eil1‐1 double mutant showed extreme salt‐sensitive phenotype. A MA3 domain‐containing protein ECIP1 was further identified to interact with EIN2 in yeast two‐hybrid assay and GST pull‐down assay. Loss‐of‐function of ECIP1 resulted in enhanced ethylene response but altered salt response during seed germination and plant growth. Double mutant analysis revealed that ein2‐1 was epistatic to ecip1, and ecip1 mutation partially suppressed ethylene‐insensitivity of etr2‐1 and ein4‐1. These studies strengthen that interactions between ECIP1 and EIN2 or ethylene receptors regulate ethylene response and stress response.
Carbonic anhydrase and the molecular evolution of C4 photosynthesis
Authors: LUDWIG MARTHA
Published: June 2011

C4 photosynthesis, a biochemical CO2‐concentrating mechanism (CCM), evolved more than 60 times within the angiosperms from C3 ancestors. The genus Flaveria, which contains species demonstrating C3, C3–C4, C4‐like or C4 photosynthesis, is a model for examining the molecular evolution of the C4 pathway. Work with carbonic anhydrase (CA), and C3 and C4Flaveria congeners has added significantly to the understanding of this process. The C4 form of CA3, a β‐CA, which catalyses the first reaction in the C4 pathway by hydrating atmospheric CO2 to bicarbonate in the cytosol of mesophyll cells (mcs), evolved from a chloroplastic C3 ancestor. The molecular modifications to the ancestral CA3 gene included the loss of the sequence encoding the chloroplast transit peptide, and mutations in regulatory regions that resulted in high levels of expression in the C4 mesophyll. Analyses of the CA3 proteins and regulatory elements from Flaveria photosynthetic intermediates indicated C4 biochemistry very likely evolved in a specific, stepwise manner in this genus. The details of the mechanisms involved in the molecular evolution of other C4 plant β‐CAs are unknown; however, comparative genetics indicate gene duplication and neofunctionalization played significant roles as they did in Flaveria.
Identification of a homolog of Arabidopsis DSP4 (SEX4) in chestnut: its induction and accumulation in stem amyloplasts during winter or in response to the cold
Authors: BERROCAL‐LOBO MARTA , IBAÑEZ CRISTIAN , ACEBO PALOMA , RAMOS ALBERTO , PEREZ‐SOLIS ESTEFANIA , COLLADA CARMEN , CASADO ROSA , ARAGONCILLO CIPRIANO , ALLONA ISABEL
Published: June 2011

Oligosaccharide synthesis is an important cryoprotection strategy used by woody plants during winter dormancy. At the onset of autumn, starch stored in the stem and buds is broken down in response to the shorter days and lower temperatures resulting in the buildup of oligosaccharides. Given that the enzyme DSP4 is necessary for diurnal starch degradation in Arabidopsis leaves, this study was designed to address the role of DSP4 in this seasonal process in Castanea sativa Mill. The expression pattern of the CsDSP4 gene in cells of the chestnut stem was found to parallel starch catabolism. In this organ, DSP4 protein levels started to rise at the start of autumn and elevated levels persisted until the onset of spring. In addition, exposure of chestnut plantlets to 4 °C induced the expression of the CsDSP4 gene. In dormant trees or cold‐stressed plantlets, the CsDSP4 protein was immunolocalized both in the amyloplast stroma and nucleus of stem cells, whereas in the conditions of vegetative growth, immunofluorescence was only detected in the nucleus. The studies indicate a potential role for DSP4 in starch degradation and cold acclimation following low temperature exposure during activity–dormancy transition.
Role of peroxidases in the compensation of cytosolic ascorbate peroxidase knockdown in rice plants under abiotic stress
Authors: BONIFACIO AURENIVIA , MARTINS MARCIO O. , RIBEIRO CAROLINA W. , FONTENELE ADILTON V. , CARVALHO FABRICIO E. L. , MARGIS‐PINHEIRO MÁRCIA , SILVEIRA JOAQUIM A. G.
Published: June 2011

Current studies, particularly in Arabidopsis, have demonstrated that mutants deficient in cytosolic ascorbate peroxidases (APXs) are susceptible to the oxidative damage induced by abiotic stress. In contrast, we demonstrate here that rice mutants double silenced for cytosolic APXs (APx1/2s) up‐regulated other peroxidases, making the mutants able to cope with abiotic stress, such as salt, heat, high light and methyl viologen, similar to non‐transformed (NT) plants. The APx1/2s mutants exhibited an altered redox homeostasis, as indicated by increased levels of H2O2 and ascorbate and glutathione redox states. Both mutant and NT plants exhibited similar photosynthesis (CO2 assimilation and photochemical efficiency) under both normal and stress conditions. Overall, the antioxidative compensatory mechanism displayed by the mutants was associated with increased expression of OsGpx genes, which resulted in higher glutathione peroxidase (GPX) activity in the cytosolic and chloroplastic fractions. The transcript levels of OsCatA and OsCatB and the activities of catalase (CAT) and guaiacol peroxidase (GPOD; type III peroxidases) were also up‐regulated. None of the six studied isoforms of OsApx were up‐regulated under normal growth conditions. Therefore, the deficiency in cytosolic APXs was effectively compensated for by up‐regulation of other peroxidases. We propose that signalling mechanisms triggered in rice mutants could be distinct from those proposed for Arabidopsis.