bluuebunny/crossref_metadata_2025_split huggingface dataset:
Behavioural activity levels and expression of stress proteins under predation risk in two damselfly species
Authors: SLOS STEFANIE , MEESTER LUC D. , STOKS ROBBY 
Published: February 2009

Abstract1. It has become apparent that predators may strongly decrease prey fitness without direct contact with the prey, as they induce the development of defence systems that limit the availability of energy for growth and reproduction. Recent studies suggest that stress proteins may help prey organisms deal with this stress. The pattern is not general, however, and little is known about species differences in physiological traits in coping with predator stress, and covariation of physiological with other antipredator traits.2. To explore these issues, we quantified levels of constitutive and fish‐induced stress proteins (Hsp60 and Hsp70) and anti‐predator behaviours in larvae of two damselfly species that differ in lifestyle. Both stress proteins were fixed at higher levels inErythromma najas, which has a slow lifestyle, than inLestes sponsa, which has a fast lifestyle. Similarly, anti‐predator behaviours were fixed at safer levels inE. najasthan inL. sponsa.3. These results suggest that stress proteins may be part of anti‐predator syndromes of damselfly larvae, and there may be trait co‐specialisation between stress proteins and behavioural anti‐predator traits. Studies formally testing these hypotheses in more species may prove rewarding in advancing our understanding of the functional integration of physiological anti‐predator traits in relation to the prey’s lifestyle.
Predator richness has no effect in a diverse marine food web
Authors: O’Connor Mary I. , Bruno John F. 
Published: February 2009

SummaryIn many ecosystems, predator abundance, composition and diversity vary naturally among seasons and habitats. In addition, predator assemblages are changing due to overharvesting, habitat destruction and species invasions.Predator species composition and richness can influence prey community structure and these effects can cascade to influence plant abundance and composition.To test the effects of predator presence, composition and species richness on prey abundance, species richness and composition, we conducted three experiments in a subtidal marine food web. Experimental food webs were drawn from species pools of 5–7 predator species, 19–52 prey species, benthic micro‐algae and 5 macro‐algae.Predators reduced prey abundance in the mesocosm experiment, but this effect was diminished or absent in field experiments. Predator species differed in their effects on prey, but we found no effect of predator richness (via complementarity or selection) on any aspect of prey community structure.The absence of a predator richness effect could be due to several factors including potentially opposing effects of individual predator species, intraguild predation, or greater importance of colonization relative to competition in structuring prey assemblages. Although predators can have strong top‐down effects in this system, selection or resource‐use complementarity among predators do not affect prey community structure.
No experimental evidence for local competition in the nestling phase as a driving force for density‐dependent avian clutch size
Authors: Nicolaus Marion , Both Christiaan , Ubels Richard , Edelaar Pim , Tinbergen Joost M. 
Published: February 2009

SummaryIn birds, local competition for food between pairs during the nestling phase may affect nestling growth and survival. A decrease in clutch size with an increase in breeding density could be an adaptive response to this competition. To investigate whether breeding density causally affected the clutch size of great tits (Parus major), we manipulated breeding density in three out of eight study plots by increasing nest‐box densities. We expected clutch size in these plots to be reduced compared to that in control plots.We analysed both the effects of variation in annual mean density (between‐year comparisons) and experimental density (within‐year comparison between plots) on clutch size variation, the occurrence of second broods and nestling growth. We examined within‐female variation in clutch size to determine whether individual responses explain the variation over years.Over the 11 years, population breeding density increased (from 0·33 to 0·50 pairs ha−1) while clutch size and the occurrence of second broods decreased (respectively from 10·0 to 8·5 eggs and from 0·39 to 0·05), consistent with a negative density‐dependent effect for the whole population. Nestling growth showed a declining but nonsignificant trend over years.The decline in population clutch size over years was primarily explained by changes occurring within individuals rather than selective disappearance of individuals laying large clutches.Within years, breeding density differed significantly between manipulated plots (0·16 pairs ha−1vs. 0·77 pairs ha−1) but clutch size, occurrence of second broods and nestling growth were not affected by the experimental treatment, resulting in a discrepancy between the effects of experimental and annual variation in density on reproduction.We discuss two hypotheses that could explain this discrepancy: (i) the decline in breeding performance over time was not due to density, but resulted from other, unknown factors. (ii) Density did cause the decline in breeding performance, but this was not due to local competition in the nestling phase. Instead, we suggest that competition acting in a different phase (e.g. before egg laying or after fledgling) was responsible for the density effect on clutch size among years.
A geographical pattern of Antirrhinum (Scrophulariaceae) speciation since the Pliocene based on plastid and nuclear DNA polymorphisms
Authors: Vargas Pablo , Carrió Elena , Guzmán Beatriz , Amat Elena , Güemes Jaime 
Published: February 2009

AbstractAim  To infer phylogenetic relationships among Antirrhinum species and to reconstruct the historical distribution of observed sequence polymorphism through estimates of haplotype clades and lineage divergence.Location  Antirrhinum is distributed primarily throughout the western Mediterranean, with 22 of 25 species in the Iberian Peninsula.Methods  Plastid (83 trnS‐trnG and 83 trnK‐matK) and nuclear (87 ITS) sequences were obtained from 96 individuals representing 24 of the 25 Antirrhinum species. Sequences were analysed using maximum parsimony, Bayesian inference and statistical parsimony networking. Molecular clock estimates were obtained for plastid trnK‐matK sequences using the penalized likelihood approach.Results  Phylogenetic results gave limited support for monophyletic groups within Antirrhinum. Fifty‐one plastid haplotypes were detected and 27 missing haplotypes inferred, which were all connected in a single, star‐like network. A significant number of species shared both the same haplotypes and the same geographical areas, primarily in eastern Iberia. Furthermore, many species harboured populations with unrelated haplotypes from divergent haplotype clades. Plastid haplotype distribution, together with nucleotide additivity in 59 of the 86 nuclear ribosomal ITS sequences, is interpreted as evidence of extensive hybridization. Lineage divergence estimates indicated that differentiation within Antirrhinum post‐dates the Miocene, when the Mediterranean climate was established.Main conclusions  Incongruence between plastid sequences, nuclear sequences and taxonomic delimitation is interpreted as strong evidence of limited cladogenetic processes in Antirrhinum. Rather, extensive nucleotide additivities in ITS sequences in conjunction with haplotype and haplotype‐clade distributions related to geographical areas support both recent and ancient hybridization. This geographical pattern of Antirrhinum speciation, particularly in eastern Iberia, is congruent with isolation–contact–isolation processes in the Pleistocene.
Macrophages and Abnormal BCL‐6 or c‐MYC Gene Expression Affect the Resistance of Peritoneal B Cells to Induction of Hyporesponsiveness
Authors: Liou L.‐B. , Wu M.‐W. , Chao W.‐J. 
Published: February 2009

AbstractOur earlier results indicate that peritoneal B cells (PEB cells) were not hyporesponsive to in vitro crosslinking of the immunoglobulin (Ig) with a secondary anti‐IgG reagent. In this study, the response of PEB cells was reduced by the same treatment given i.p. PEB cells were only sensitive to anti‐IgM hyper‐crosslinking in the presence of peritoneal macrophages. This sensitivity was partially reversed by anti‐interferon‐β antibody. Elevated BCL‐6 with c‐MYC gene expression in NZB/W F1 splenic B cells after anti‐IgM treatment correlated well with reduction of IgM secretion. On the contrary, PEB cells not sensitive to induction of hyporesponsiveness cause abnormal BCL‐6/c‐MYC gene expression after challenges. A bigger change of increased BCL‐6 gene expression after anti‐IgM treatment was seen in PEB cells than in splenic B cells. Higher BCL‐2 gene expression in NZB/W splenic B cells than those in NZB/W PEB cells do not prevent hyporesponsiveness in the former. In conclusion, the relationship between BCL‐6/c‐MYC gene expression and IgM secretion in NZB/W F1 splenic B cells is similar to that of conventional B2 cells. Although PEB cells from wild type strain can be rendered hyporesponsive in vivo in the presence of macrophages, the resistance to hyporesponsiveness of challenged autoimmune NZB/W PEB cells in vivo is probably related to abnormal BCL‐6/c‐MYC gene expression. These combined findings suggest that autoimmune B1 cells violate the accepted paradigm for expression of differentiation‐associated transcription factors in B2 cells.
Genome‐wide Gene Expression Profiling of SCID Mice with T‐cell‐mediated Colitis
Authors: Brudzewsky D. , Pedersen A. E. , Claesson M. H. , Gad M. , Kristensen N. N. , Lage K. , Jensen T. , Tommerup N. , Larsen L. A. , Knudsen S. , Tümer Z. 
Published: February 2009

AbstractInflammatory bowel disease (IBD) is a multifactorial disorder with an unknown aetiology. The aim of this study is to employ a murine model of IBD to identify pathways and genes, which may play a key role in the pathogenesis of IBD and could be important for discovery of new disease markers in human disease. Here, we have investigated severe combined immunodeficient (SCID) mice, which upon adoptive transfer with concanavalin A‐activated CD4+ T cells develop inflammation of the colon with predominance in rectum. Mice with increasing level of inflammation was studied. RNA from rectum of transplanted and non‐transplanted SCID mice was investigated by a genome‐wide gene expression analysis using the Affymetrix mouse expression array 430A (MOE430A) including 22,626 probe sets. A significant change in gene expression (P = 0.00001) is observed in 152 of the genes between the non‐transplanted control mice and colitis mice, and among these genes there is an overrepresentation of genes involved in inflammatory processes. Some of the most significant genes showing higher expression encode S100A proteins and chemokines involved in trafficking of leucocytes in inflammatory areas. Classification by gene clustering based on the genes with the significantly altered gene expression corresponds to two different levels of inflammation as established by the histological scoring of the inflamed rectum. These data demonstrate that this SCID T‐cell transfer model is a useful animal model for human IBD and can be used for suggesting candidate genes involved in the pathogenesis and for identifying new molecular markers of chronic inflammation in human IBD.
Particle Size Determines Activation of the Innate Immune System in the Lung
Authors: Samuelsen M. , Nygaard U. C. , Løvik M. 
Published: February 2009

AbstractOur knowledge about particle size in relation to activation of the innate immune system is limited. Therefore, the acute effect of particle exposure on the innate immune system was studied in a lung model using the intracellular bacterium Listeria monocytogenes. Female Balb/cA mice were instilled intratracheally with polystyrene particles (PSP) of different diameters (0.064, 0.202, 1.053 and 4.646 μm) simultaneously with or 1 day prior to inoculation of 105 bacteria. Mice were sacrificed 1 day after Listeria challenge, and the numbers of viable bacteria in the lungs and the spleen were determined as a measure of cellular activation. In separate experiments, bronchoalveolar lavage (BAL) fluid was collected. Only mice exposed to the smallest PSP (0.064 and 0.202 μm) had significantly reduced bacterial numbers in the lung after particles and Listeria were given simultaneously. When particles were given 1 day prior to Listeria challenge also the largest 4.646 μm PSP, but not the medium size 1.053 μm PSP, reduced bacterial numbers. The number of neutrophils in BAL fluid was increased for all PSP‐exposed groups after 24 h, and tended to be highest in the group exposed to 4.646 μm PSP. TNF‐α, IL‐1β and MIP‐2 were significantly increased in BAL fluid after exposure to the largest compared with the smallest PSP. In conclusion, activation of the innate immune system by chemical‐free particles was size‐dependent. Ultrafine and coarse particles appeared to activate cells by different mechanisms, which implies qualitative differences between the health effects of ambient air particulate matter size fractions.
Identification of a novel E3 ubiquitin ligase that is required for suppression of premature senescence in Arabidopsis
Authors: Raab Sabine , Drechsel Gabriele , Zarepour Maryam , Hartung Wolfram , Koshiba Tomokazu , Bittner Florian , Hoth Stefan 
Published: February 2009

SummaryDuring leaf senescence, resources are recycled by redistribution to younger leaves and reproductive organs. Candidate pathways for the regulation of onset and progression of leaf senescence include ubiquitin‐dependent turnover of key proteins. Here, we identified a novel plant U‐box E3 ubiquitin ligase that prevents premature senescence in Arabidopsis plants, and named it SENESCENCE‐ASSOCIATED E3 UBIQUITIN LIGASE 1 (SAUL1). Using in vitro ubiquitination assays, we show that SAUL1 has E3 ubiquitin ligase activity. We isolated two alleles of saul1 mutants that show premature senescence under low light conditions. The visible yellowing of leaves is accompanied by reduced chlorophyll content, decreased photochemical efficiency of photosystem II and increased expression of senescence genes. In addition, saul1 mutants exhibit enhanced abscisic acid (ABA) biosynthesis. We show that application of ABA to Arabidopsis is sufficient to trigger leaf senescence, and that this response is abolished in the ABA‐insensitive mutants abi1‐1 and abi2‐1, but enhanced in the ABA‐hypersensitive mutant era1‐3. We found that increased ABA levels coincide with enhanced activity of Arabidopsis aldehyde oxidase 3 (AAO3) and accumulation of AAO3 protein in saul1 mutants. Using label transfer experiments, we showed that interactions between SAUL1 and AAO3 occur. This suggests that SAUL1 participates in targeting AAO3 for ubiquitin‐dependent degradation via the 26S proteasome to prevent premature senescence.
Asymmetric allele‐specific expression in relation to developmental variation and drought stress in barley hybrids
Authors: Von Korff Maria , Radovic Slobodanka , Choumane Wafaa , Stamati Konstantina , Udupa Sripada M. , Grando Stefania , Ceccarelli Salvatore , Mackay Ian , Powell Wayne , Baum Michael , Morgante Michele 
Published: February 2009

SummaryIn the present study, we analysed allele‐specific expression (ASE) in the selfing species barley to assess the frequency of cis‐acting regulatory variation and the effects of genetic background, developmental differences and drought stress on allelic expression levels. We measured ASE ratios in 30 genes putatively involved in stress responses in five hybrids and their reciprocals, namely Hordeum spontaneum 41‐1/Alexis (HAl), Hordeum spontaneum 41‐1/Arta (HAr), Sloop/WI3408 (SW), Tadmor/Sloop (TS) and Tadmor/WI3408 (TW). In order to detect cis‐acting variation related to drought and developmental changes, the barley hybrids were grown under control and water‐limited conditions, and leaf tissue was harvested at two developmental stages. The analysis demonstrated that more than half of the genes measured (63%) showed allelic differences in expression of up to 19‐fold due to cis‐regulatory variation in at least one cross by treatment/stage combination. Drought stress induced changes in allelic expression ratios, indicating differences between drought responsive cis‐elements. In addition, ASE differences between developmental stages suggested the presence of cis‐acting elements interacting with developmental cues. We were also able to demonstrate that the levels and frequency of allelic imbalance and hence differences in cis‐regulatory elements are correlated with the genetic divergence between the parental lines, but may also arise as an adaptation to diverse habitats. Our findings suggest that cis‐regulatory variation is a common phenomenon in barley, and may provide a molecular basis of transgression. Differential expression of near‐isogenic members of the same gene family could potentially result in hybrid lines out performing their parents in terms of expression level, timing and response to developmental and environmental cues. Identification and targeted manipulation of cis‐regulatory elements will assist in breeding improved crops with a better adaptation to changing environments.
Transient expression in Nicotiana benthamiana fluorescent marker lines provides enhanced definition of protein localization, movement and interactions in planta
Authors: Martin Kathleen , Kopperud Kristin , Chakrabarty Romit , Banerjee Rituparna , Brooks Robert , Goodin Michael M. 
Published: February 2009

SummaryHere, we report on the construction of a novel series of Gateway‐compatible plant transformation vectors containing genes encoding autofluorescent proteins, including Cerulean, Dendra2, DRONPA, TagRFP and Venus, for the expression of protein fusions in plant cells. To assist users in the selection of vectors, we have determined the relative in planta photostability and brightness of nine autofluorescent proteins (AFPs), and have compared the use of DRONPA and Dendra2 in photoactivation and photoconversion experiments. Additionally, we have generated transgenic Nicotiana benthamiana lines that express fluorescent protein markers targeted to nuclei, endoplasmic reticulum or actin filaments. We show that conducting bimolecular fluorescence complementation assays in plants that constitutively express cyan fluorescent protein fused to histone 2B provides enhanced data quality and content over assays conducted without the benefit of a subcellular marker. In addition to testing protein interactions, we demonstrate that our transgenic lines that express red fluorescent protein markers offer exceptional support in experiments aimed at defining nuclear or endomembrane localization. Taken together, the new combination of pSITE‐BiFC and pSITEII vectors for studying intracellular protein interaction, localization and movement, in conjunction with our transgenic marker lines, constitute powerful tools for the plant biology community.
Rapid, combinatorial analysis of membrane compartments in intact plants with a multicolor marker set
Authors: Geldner Niko , Dénervaud‐Tendon Valérie , Hyman Derek L. , Mayer Ulrike , Stierhof York‐Dieter , Chory Joanne 
Published: February 2009

SummaryPlant membrane compartments and trafficking pathways are highly complex, and are often distinct from those of animals and fungi. Progress has been made in defining trafficking in plants using transient expression systems. However, many processes require a precise understanding of plant membrane trafficking in a developmental context, and in diverse, specialized cell types. These include defense responses to pathogens, regulation of transporter accumulation in plant nutrition or polar auxin transport in development. In all of these cases a central role is played by the endosomal membrane system, which, however, is the most divergent and ill‐defined aspect of plant cell compartmentation. We have designed a new vector series, and have generated a large number of stably transformed plants expressing membrane protein fusions to spectrally distinct, fluorescent tags. We selected lines with distinct subcellular localization patterns, and stable, non‐toxic expression. We demonstrate the power of this multicolor ‘Wave’ marker set for rapid, combinatorial analysis of plant cell membrane compartments, both in live‐imaging and immunoelectron microscopy. Among other findings, our systematic co‐localization analysis revealed that a class of plant Rab1‐homologs has a much more extended localization than was previously assumed, and also localizes to trans‐Golgi/endosomal compartments. Constructs that can be transformed into any genetic background or species, as well as seeds from transgenic Arabidopsis plants, will be freely available, and will promote rapid progress in diverse areas of plant cell biology.
The ZIM domain mediates homo‐ and heteromeric interactions between Arabidopsis JAZ proteins
Authors: Chini Andrea , Fonseca Sandra , Chico Jose M. , Fernández‐Calvo Patricia , Solano Roberto 
Published: February 2009

SummaryDiscovery of the jasmonate ZIM‐domain (JAZ) repressors defined the core jasmonate (JA) signalling module as COI1–JAZ–MYC2, and allowed a full view of the JA signalling pathway from hormone perception to transcriptional reprogramming. JAZ proteins are repressors of MYC2 and targets of SCFCOI1, which is the likely jasmonate receptor. Upon hormone perception, JAZ repressors are degraded by the proteasome releasing MYC2 and allowing the activation of JA responses. All members of the JAZ family share two conserved domains, the Jas motif, required for JAZ interactions with MYC2 and COI1, and the ZIM domain, the function of which is so far unknown. Here, we show that the ZIM domain acts as a protein–protein interaction domain mediating homo‐ and heteromeric interactions between JAZ proteins. These JAZ–JAZ interactions are independent of the presence of the hormone. The observation that only a few members of the JAZ family form homo‐ and heteromers may suggest the relevance of these proteins in the regulation of JA signalling. Interestingly, the JAZ3ΔJas protein interacts with several JAZ proteins, providing new clues to understanding the dominant JA insensitivity promoted by truncated JAZΔJas proteins. We also provide evidence that the Jas motif mediates the hormone‐dependent interaction between Arabidopsis JAZ3 and COI1, and further confirm that the Jas motif is required and sufficient for Arabidopsis JAZ3–MYC2 interaction. Finally, we show that interaction with MYC2 is a common feature of the JAZ family, as most JAZ proteins can bind MYC2 in pull‐down and yeast two‐hybrid assays.