bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suppression of inflammation in rat autoimmune myocarditis by S100A8/A9 through modulation of the proinflammatory cytokine network
Authors: Otsuka Kaoru , Terasaki Fumio , Ikemoto Masaki , Fujita Shuichi , Tsukada Bin , Katashima Takashi , Kanzaki Yumiko , Sohmiya Koichi , Kono Tatsuji , Toko Haruhiro , Fujita Masatoshi , Kitaura Yasushi 
Published: January 2009

AimsS100A8/A9 is expressed in activated monocytes/macrophages and assumed to be heavily involved in the pathogenesis of acute inflammation. Although several studies have asserted that S100A8/A9 has a proinflammatory function, the exact biological function of S100A8/A9 is yet to be described. We examined the anti‐inflammatory effects of S100A8/A9 on experimental autoimmune myocarditis (EAM) in rats.Methods and resultsExperimental autoimmune myocarditis was induced in Lewis rats by immunization with porcine cardiac myosin. The recombinant (R‐) S100A8/A9 was injected intraperitoneally into EAM rats. R‐S100A8/A9 attenuated the severity of myocarditis, as evidenced by echocardiographic and histological findings. In addition, we found that not only the mRNA expression of proinflammatory cytokines [interleukin (IL)‐1β, IL‐6, and tumour necrosis factor (TNF)‐α] in the myocardium, but also their serum concentrations were suppressed in EAM rats treated with R‐S100A8/A9. Nuclear factor‐kappa B expression in inflammatory cells was also suppressed in the treated rats. To elucidate the mechanistic function of S100A8/A9 on proinflammatory cytokines in vivo, we used an ELISA on the supernatant of homogenized heart tissue treated with R‐S100A8/A9. The findings revealed high‐affinity binding of R‐S100A8/A9 with IL‐1β, IL‐6, and TNF‐α in the myocardium, suggesting the trapping of proinflammatory cytokines by R‐S100A8/A9.ConclusionS100A8/A9 attenuates EAM through modulation of the proinflammatory cytokine network.
The advantage of explicitly incorporating predation mortality into age-structured stock assessment models: an application for Atlantic mackerel
Authors: Moustahfid H. , Link J. S. , Overholtz W. J. , Tyrrell M. C. 
Published: January 2009

AbstractMoustahfid, H., Link, J. S., Overholtz, W. J., and Tyrrell, M. C. 2009. The advantage of explicitly incorporating predation mortality into age-structured stock assessment models: an application for Atlantic mackerel. – ICES Journal of Marine Science, 66: 445–454. An age-structured assessment programme (ASAP) that explicitly incorporates predation mortality was applied to Atlantic mackerel (Scomber scombrus) in the Northwest Atlantic. Predatory removals were modelled in the same manner as fishing mortality, with a comparable set of time-series, to produce estimates of predation mortality at age and for each year. Results from the analysis showed that incorporating predation into a mackerel stock assessment model notably altered model outputs. When excluding explicitly modelled rates of predation, the model underestimated the magnitude and uncertainty in spawning-stock biomass (SSB) and recruitment. Further, the rates of predation mortality varied across time and were higher for younger fish. Predation mortality was higher than fishing mortality for fish aged 1 year, approximately equal for 2-year-olds, and lower for older fish (3 years and older). Biological reference points for Atlantic mackerel differed considerably when predation mortality was included. For example, SSBMSY was more than twice as high in the model where predation was incorporated than in the fisheries-only model. Although there are several caveats to the predation model outputs, chief of which is that the estimates are conservative because some mackerel predators were excluded, the results demonstrate the feasibility of executing such an approach with an extant tool. The approach presented here ultimately has the advantage of detecting, and upon detection parsing out, the impact of predators relative to fisheries and has the potential to provide useful information to those interested in small pelagic fish and their associated fisheries.
A simple genetic identification method for Northeast Atlantic smoothhound sharks (Mustelus spp.)
Authors: Farrell Edward D. , Clarke Maurice W. , Mariani Stefano 
Published: January 2009

Abstract
Farrell, E. D., Clarke, M. W., and Mariani, S. 2009. A simple genetic identification method for Northeast Atlantic smoothhound sharks (Mustelus spp.). – ICES Journal of Marine Science, 66: 561–565. Considerable ambiguity exists in the identification of the commercially valuable smoothhound sharks (Mustelus spp.) in the Northeast (NE) Atlantic. The lack of a clear and accurate method of identification prevents the collation of reliable species-specific landings and survey data for these fish and hinders the accurate delineation of the distribution ranges of species and stock boundaries, making it impossible to apply sound species-specific conservation and management strategies. This paper reports on the development of a multiplex PCR reaction that utilizes a set of mtDNA primers for the identification of Mustelus asterias, Mustelus mustelus, and Galeorhinus galeus. The high throughput method allows for the rapid and cost-effective identification of large numbers of samples; its application to 431 fish collected between 2006 and 2008 also raises important questions regarding the biogeography of the genus Mustelus in the NE Atlantic.
Seasonal and interannual variability of primary and export production in the South China Sea: a three-dimensional physical–biogeochemical model study
Authors: Liu Guimei , Chai Fei 
Published: January 2009

Abstract
Liu, G., and Chai, F. 2009. Seasonal and interannual variability of primary and export production in the South China Sea: a three-dimensional physical–biogeochemical model study. – ICES Journal of Marine Science, 66: 420–431. To investigate the seasonal and interannual variations in biological productivity in the South China Sea (SCS), a Pacific basin-wide physical–biogeochemical model has been developed and used to estimate the biological productivity and export flux in the SCS. The Pacific circulation model, based on the Regional Ocean Model Systems (ROMS), is forced with daily air–sea fluxes derived from the NCEP (National Centers for Environmental Prediction) reanalysis between 1990 and 2004. The biogeochemical processes are simulated with a carbon, Si(OH)4, and nitrogen ecosystem (CoSiNE) model consisting of silicate, nitrate, ammonium, two phytoplankton groups (small phytoplankton and large phytoplankton), two zooplankton grazers (small micrograzers and large mesozooplankton), and two detritus pools. The ROMS–CoSiNE model favourably reproduces many of the observed features, such as Chl a, nutrients, and primary production (PP) in the SCS. The modelled depth-integrated PP over the euphotic zone (0–125 m) varies seasonally, with the highest value of 386 mg C m−2 d−1 during winter and the lowest value of 156 mg C m−2 d−1 during early summer. The annual mean value is 196 mg C m−2 d−1. The model-integrated annual mean new production (uptake of nitrate), in carbon units, is 64.4 mg C m−2 d−1, which yields an f-ratio of 0.33 for the entire SCS. The modelled export ratio (e-ratio: the ratio of export to PP) is 0.24 for the basin-wide SCS. The year-to-year variation of biological productivity in the SCS is weaker than the seasonal variation. The large phytoplankton group tends to dominate over the smaller phytoplankton group, and likely plays an important role in determining the interannual variability of primary and new production.
Lack of spatial genetic variation in the edible crab (Cancer pagurus) in the Kattegat–Skagerrak area
Authors: Ungfors Anette , McKeown Niall J. , Shaw Paul W. , André Carl 
Published: January 2009

Abstract
Ungfors, A., McKeown, N. J., Shaw, P. W., and André, C. 2009. Lack of spatial genetic variation in the edible crab (Cancer pagurus) in the Kattegat–Skagerrak area. – ICES Journal of Marine Science, 66: 462–469. The stock structure of the edible crab (Cancer pagurus L.) in the Kattegat and Skagerrak was investigated using eight microsatellite DNA loci. Replicate samples, collected 4–6 years apart, were derived from the Kattegat (Grove Bank, 57°N) and the Skagerrak (Lunneviken, 59°N), plus a geographical outgroup sample from the Norwegian Sea (Midsund, 62°N). Genetic differentiation among samples, estimated as global FST = 0.002, was significant (p = 0.03) when the statistical test was based on allele frequencies, but not when based on genotype frequencies. Moreover, all single- and multilocus pairwise tests between samples were non-significant. An analysis of molecular variance, AMOVA, did not reveal significant differentiation between spatial (Kattegat vs. Skagerrak) or temporal (2001/2002 vs. 2006/2007) groups of samples. Power analysis suggested that the loci and sample sizes employed conferred a power of >90% of detecting even low (true FST = 0.002) levels of population structure. Low spatial and temporal genetic structure might be explained by either or both of (i) high levels of contemporary gene flow in the area attributable to adult migration or larval dispersal or both factors taken together, and (ii) patterns of historical gene flow persisting among recently founded large populations.
Induced Postharvest Yellowing in Southern U.S. Rice Cultivars
Authors: Belefant‐Miller Helen 
Published: January 2009

ABSTRACTRice can yellow during storage if moisture levels and temperatures are allowed to increase. This postharvest yellowed (PHY), or stackburn, rice is reduced in value but no study has investigated the inherent potential within rice germplasm for limiting PHY. To screen a large number of cultivars for propensity to PHY, a laboratory method for PHY using a small amount of rice was used. Ninety‐eight popular southern U.S. rice cultivars were yellowed under laboratory conditions. Additional samples of the low‐yellowing and high‐yellowing cultivars were retested after two and three years of storage as rough rice using higher amounts and larger containers. All cultivars showed greater color change with the higher amounts of rice and when yellowed as milled rather than as rough rice. Length of time of storage and storage temperature did not affect the degree of PHY. The low‐ and high‐yellowing groups remained distinguishable but the overall high level of coloring in southern U.S. rice cultivars indicates that a more diverse germplasm should be investigated to increase the likelihood of identifying low‐PHY cultivars.
Autophagy Is Enhanced and Floral Development Is Impaired in AtHVA22d RNA Interference Arabidopsis
Authors: Chen Ching-Nen Nathan , Chen Hau-Ren , Yeh Su-Ying , Vittore Gina , Ho Tuan-Hua David 
Published: January 2009

Abstract
Autophagy is an intracellular process in which a portion of cytoplasm is transported into vacuoles for recycling. Physiological roles of autophagy in plants include recycling nutrients during senescence, sustaining life during starvation, and the formation of central digestive vacuoles. The regulation of autophagy and the formation of autophagosomes, spherical double membrane structures containing cytoplasm moving toward vacuoles, are poorly understood. HVA22 is a gene originally cloned from barley (Hordeum vulgare), which is highly induced by abscisic acid and environmental stress. Homologs of HVA22 include Yop1 in yeast, TB2/DP1 in human, and AtHVA22a to -e in Arabidopsis (Arabidopsis thaliana). Reverse genetics followed by a cell biology approach were employed to study the function of HVA22 homologs. The AtHVA22d RNA interference (RNAi) Arabidopsis plants produced small siliques with reduced seed yield. This phenotype cosegregated with the RNAi transgene. Causes of the reduced seed yield include short filaments, defective carpels, and dysfunctional pollen grains. Enhanced autophagy was observed in the filament cells. The number of autophagosomes in root tips of RNAi plants was also increased dramatically. The yop1 deletion mutant of Saccharomyces cerevisiae was used to verify our hypothesis that HVA22 homologs are suppressors of autophagy. Autophagy activity of this mutant during nitrogen starvation increased in 5 min and reached a plateau after 2 h, with about 80% of cells showing autophagy, while the wild-type cells exhibited low levels of autophagy following 8 h of nitrogen starvation. We conclude that HVA22 homologs function as suppressors of autophagy in both plants and yeast. Potential mechanisms of this suppression and the roles of abscisic acid-induced HVA22 expression in vegetative and reproductive tissues are discussed.
Biotic and Abiotic Stimulation of Root Epidermal Cells Reveals Common and Specific Responses to Arbuscular Mycorrhizal Fungi
Authors: Genre Andrea , Ortu Giuseppe , Bertoldo Chiara , Martino Elena , Bonfante Paola 
Published: January 2009

Abstract
During arbuscular mycorrhizal (AM) colonization, a focal accumulation of organelles occurs in root epidermal cells, prior to fungal penetration, beneath adhering hyphopodia. This is followed by the appearance of the prepenetration apparatus (PPA), a transcellular column of cytoplasm connected to the nucleus and rich in cytoskeleton and secretory endomembranes. This apparatus appears to be responsible for the construction of an apoplastic compartment that confines the fungus within the cell lumen. To identify AM-specific elements within the PPA response, we challenged root cultures of Medicago truncatula, expressing a green fluorescent protein tag for the endoplasmic reticulum, with an AM symbiont, a necrotrophic pathogen, a hemibiotrophic pathogen, a noncompatible endomycorrhizal fungus, or abiotic physical stimuli. Parallel experiments were made on a M. truncatula nonsymbiotic mutant (doesn't make infections, dmi3-1). The results have highlighted a correlation between physical stimulation of the cell surface and nuclear repositioning. Cytoplasmic aggregation was only induced by contact with compatible fungi, whereas PPA appearance was specifically triggered by the AM fungus. The dmi3-1 mutant did not develop cytoplasmic aggregation or PPA and underwent cell death upon physical stimulation. The up-regulation of an expansin-like gene, already identified as an early marker of AM fungal contact, was triggered in wild-type roots by all the fungi tested. Such observations identify responses that are specific to mycorrhizal interactions and extend the role of the DMI3 protein, a calcium/calmodulin-dependent kinase, from symbiotic to pathogenic interactions.
Chloroplast NADPH-Thioredoxin Reductase Interacts with Photoperiodic Development in Arabidopsis
Authors: Lepistö Anna , Kangasjärvi Saijaliisa , Luomala Eeva-Maria , Brader Günter , Sipari Nina , Keränen Mika , Keinänen Markku , Rintamäki Eevi 
Published: January 2009

AbstractChloroplast NADPH-thioredoxin reductase (NTRC) belongs to the thioredoxin systems that control crucial metabolic and regulatory pathways in plants. Here, by characterization of T-DNA insertion lines of NTRC gene, we uncover a novel connection between chloroplast thiol redox regulation and the control of photoperiodic growth in Arabidopsis (Arabidopsis thaliana). Transcript and metabolite profiling revealed severe developmental and metabolic defects in ntrc plants grown under a short 8-h light period. Besides reduced chlorophyll and anthocyanin contents, ntrc plants showed alterations in the levels of amino acids and auxin. Furthermore, a low carbon assimilation rate of ntrc leaves was associated with enhanced transpiration and photorespiration. All of these characteristics of ntrc were less severe when plants were grown under a long 16-h photoperiod. Transcript profiling revealed that the mutant phenotypes of ntrc were accompanied by differential expression of genes involved in stomatal development, chlorophyll biosynthesis, chloroplast biogenesis, and circadian clock-linked light perception systems in ntrc plants. We propose that NTRC regulates several key processes, including chlorophyll biosynthesis and the shikimate pathway, in chloroplasts. In the absence of NTRC, imbalanced metabolic activities presumably modulate the chloroplast retrograde signals, leading to altered expression of nuclear genes and, ultimately, to the formation of the pleiotrophic phenotypes in ntrc mutant plants.
Substrates Related to Chromatin and to RNA-Dependent Processes Are Modified by Arabidopsis SUMO Isoforms That Differ in a Conserved Residue with Influence on Desumoylation
Authors: Budhiraja Ruchika , Hermkes Rebecca , Müller Stefan , Schmidt Jürgen , Colby Thomas , Panigrahi Kishore , Coupland George , Bachmair Andreas 
Published: January 2009

AbstractThe higher plant Arabidopsis (Arabidopsis thaliana) has eight genes potentially coding for small ubiquitin-related modifier (SUMO) proteins. However, two well-expressed isoforms differ from fungal and animal consensus in a conserved glutamine (Gln) residue situated four residues from the carboxyl terminus. We tested deviations in this position in the background of SUMO1, the isoform with the highest expression level, and found that changes do not prevent conjugation to substrate proteins in vivo. Replacement of this conserved Gln by alanine resulted in a protein that was less readily removed from a substrate by SUMO protease EARLY IN SHORT DAYS4 in an in vitro reaction and apparently led to higher levels of SUMO conjugates when expressed in vivo. We used the SUMO1 variant with the Gln-to-alanine substitution, as well as SUMO3 and SUMO5 (which carry methionine and leucine, respectively, at this position), to enrich in vivo substrates. Identification of the most abundant proteins contained in these fractions indicated that they are involved in DNA-related, or in RNA-dependent, processes, such as regulation of chromatin structure, splicing, or translation. The majority of the identified bona fide substrates contain predicted sumoylation sites. A subset of the proteins was expressed in Escherichia coli and could be sumoylated in vitro.
Multiple Repeats of a Promoter Segment Causes Transcription Factor Autoregulation in Red Apples
Authors: Espley Richard V. , Brendolise Cyril , Chagné David , Kutty-Amma Sumathi , Green Sol , Volz Richard , Putterill Jo , Schouten Henk J. , Gardiner Susan E. , Hellens Roger P. , Allan Andrew C. 
Published: January 2009

AbstractMutations in the genes encoding for either the biosynthetic or transcriptional regulation of the anthocyanin pathway have been linked to color phenotypes. Generally, this is a loss of function resulting in a reduction or a change in the distribution of anthocyanin. Here, we describe a rearrangement in the upstream regulatory region of the gene encoding an apple (Malus × domestica) anthocyanin-regulating transcription factor, MYB10. We show that this modification is responsible for increasing the level of anthocyanin throughout the plant to produce a striking phenotype that includes red foliage and red fruit flesh. This rearrangement is a series of multiple repeats, forming a minisatellite-like structure that comprises five direct tandem repeats of a 23-bp sequence. This MYB10 rearrangement is present in all the red foliage apple varieties and species tested but in none of the white fleshed varieties. Transient assays demonstrated that the 23-bp sequence motif is a target of the MYB10 protein itself, and the number of repeat units correlates with an increase in transactivation by MYB10 protein. We show that the repeat motif is capable of binding MYB10 protein in electrophoretic mobility shift assays. Taken together, these results indicate that an allelic rearrangement in the promoter of MYB10 has generated an autoregulatory locus, and this autoregulation is sufficient to account for the increase in MYB10 transcript levels and subsequent ectopic accumulation of anthocyanins throughout the plant.
ENDOSPERM DEFECTIVE1 Is a Novel Microtubule-Associated Protein Essential for Seed Development inArabidopsis
Authors: Pignocchi Cristina , Minns Gregory E. , Nesi Nathalie , Koumproglou Rachil , Kitsios Georgios , Benning Christoph , Lloyd Clive W. , Doonan John H. , Hills Matthew J 
Published: January 2009

AbstractEarly endosperm development involves a series of rapid nuclear divisions in the absence of cytokinesis; thus, many endosperm mutants reveal genes whose functions are essential for mitosis. This work finds that the endosperm of Arabidopsis thaliana endosperm-defective1 (ede1) mutants never cellularizes, contains a reduced number of enlarged polyploid nuclei, and features an aberrant microtubule cytoskeleton, where the specialized radial microtubule systems and cytokinetic phragmoplasts are absent. Early embryo development is substantially normal, although occasional cytokinesis defects are observed. The EDE1 gene was cloned using a map-based approach and represents the pioneer member of a conserved plant-specific family of genes of previously unknown function. EDE1 is expressed in the endosperm and embryo of developing seeds, and its expression is tightly regulated during cell cycle progression. EDE1 protein accumulates in nuclear caps in premitotic cells, colocalizes along microtubules of the spindle and phragmoplast, and binds microtubules in vitro. We conclude that EDE1 is a novel plant-specific microtubule-associated protein essential for microtubule function during the mitotic and cytokinetic stages that generate the Arabidopsis endosperm and embryo.
A Critical Role for the TIFY Motif in Repression of Jasmonate Signaling by a Stabilized Splice Variant of the JASMONATE ZIM-Domain Protein JAZ10 inArabidopsis
Authors: Chung Hoo Sun , Howe Gregg A. 
Published: January 2009

AbstractJASMONATE ZIM-domain (JAZ) proteins act as repressors of jasmonate (JA) signaling. Perception of bioactive JAs by the F-box protein CORONATINE INSENSITIVE1 (COI1) causes degradation of JAZs via the ubiquitin-proteasome pathway, which in turn activates the expression of genes involved in plant growth, development, and defense. JAZ proteins contain two highly conserved sequence regions: the Jas domain that interacts with COI1 to destabilize the repressor and the ZIM domain of unknown function. Here, we show that the conserved TIFY motif (TIFF/YXG) within the ZIM domain mediates homo- and heteromeric interactions between most Arabidopsis thaliana JAZs. We have also identified an alternatively spliced form (JAZ10.4) of JAZ10 that lacks the Jas domain and, as a consequence, is highly resistant to JA-induced degradation. Strong JA-insensitive phenotypes conferred by overexpression of JAZ10.4 were suppressed by mutations in the TIFY motif that block JAZ10.4–JAZ interactions. We conclude that JAZ10.4 functions to attenuate signal output in the presence of JA and further suggest that the dominant-negative action of this splice variant involves protein–protein interaction through the ZIM/TIFY domain. The ability of JAZ10.4 to interact with MYC2 is consistent with a model in which a JAZ10.4-containing protein complex directly represses the activity of transcription factors that promote expression of JA response genes.