bluuebunny/crossref_metadata_2025 huggingface dataset:
Hysteretic effects of dry friction: modelling and experimental studies
Authors: Wojewoda Jerzy , Stefański Andrzej , Wiercigroch Marian , Kapitaniak Tomasz
Published: October 2007

In this paper, the phenomena of hysteretic behaviour of friction force observed during experiments are discussed. On the basis of experimental and theoretical analyses, we argue that such behaviour can be considered as a representation of the system dynamics. According to this approach, a classification of friction models, with respect to their sensitivity on the system motion characteristic, is introduced. General friction modelling of the phenomena accompanying dry friction and a simple yet effective approach to capture the hysteretic effect are proposed. Finally, the experimental results are compared with the numerical simulations for the proposed friction model.
OsMADS51 Is a Short-Day Flowering Promoter That Functions Upstream of Ehd1, OsMADS14, and Hd3a
Authors: Kim Song Lim , Lee Shinyoung , Kim Hyo Jung , Nam Hong Gil , An Gynheung
Published: October 2007

Although flowering regulatory mechanisms have been extensively studied in Arabidopsis (Arabidopsis thaliana), those in other species have not been well elucidated. Here, we investigated the role of OsMADS51, a type I MADS-box gene in the short-day (SD) promotion pathway in rice (Oryza sativa). In SDs OsMADS51 null mutants flowered 2 weeks later than normal, whereas in long days loss of OsMADS51 had little effect on flowering. Transcript levels of three flowering regulators—Ehd1, OsMADS14, and Hd3a—were decreased in these mutants, whereas those of OsGI and Hd1 were unchanged. Ectopic expression of OsMADS51 caused flowering to occur about 7 d earlier only in SDs. In ectopic expression lines, transcript levels of Ehd1, OsMADS14, and Hd3a were increased, but those of OsGI and Hd1 remained the same. These results indicate that OsMADS51 is a flowering promoter, particularly in SDs, and that this gene functions upstream of Ehd1, OsMADS14, and Hd3a. To further investigate the relationship with other flowering promoters, we generated transgenic plants in which expression of Ehd1 or OsGI was suppressed. In Ehd1 RNA interference plants, OsMADS51 expression was not affected, supporting our conclusion that the MADS-box gene functions upstream of Ehd1. However, in OsGI antisense plants, the OsMADS51 transcript level was reduced. In addition, the circadian expression pattern for this MADS-box gene was similar to that for OsGI. These results demonstrate that OsMADS51 functions downstream of OsGI. In summary, OsMADS51 is a novel flowering promoter that transmits a SD promotion signal from OsGI to Ehd1.
Identification and Characterization of Lineage-Specific Genes within the Poaceae
Authors: Campbell Matthew A. , Zhu Wei , Jiang Ning , Lin Haining , Ouyang Shu , Childs Kevin L. , Haas Brian J. , Hamilton John P. , Buell C. Robin
Published: October 2007

Using the rice (Oryza sativa) sp. japonica genome annotation, along with genomic sequence and clustered transcript assemblies from 184 species in the plant kingdom, we have identified a set of 861 rice genes that are evolutionarily conserved among six diverse species within the Poaceae yet lack significant sequence similarity with plant species outside the Poaceae. This set of evolutionarily conserved and lineage-specific rice genes is termed conserved Poaceae-specific genes (CPSGs) to reflect the presence of significant sequence similarity across three separate Poaceae subfamilies. The vast majority of rice CPSGs (86.6%) encode proteins with no putative function or functionally characterized protein domain. For the remaining CPSGs, 8.8% encode an F-box domain-containing protein and 4.5% encode a protein with a putative function. On average, the CPSGs have fewer exons, shorter total gene length, and elevated GC content when compared with genes annotated as either transposable elements (TEs) or those genes having significant sequence similarity in a species outside the Poaceae. Multiple sequence alignments of the CPSGs with sequences from other Poaceae species show conservation across a putative domain, a novel domain, or the entire coding length of the protein. At the genome level, syntenic alignments between sorghum (Sorghum bicolor) and 103 of the 861 rice CPSGs (12.0%) could be made, demonstrating an additional level of conservation for this set of genes within the Poaceae. The extensive sequence similarity in evolutionarily distinct species within the Poaceae family and an additional screen for TE-related structural characteristics and sequence discounts these CPSGs as being misannotated TEs. Collectively, these data confirm that we have identified a specific set of genes that are highly conserved within, as well as specific to, the Poaceae.
Oxo-Phytodienoic Acid-Containing Galactolipids in Arabidopsis: Jasmonate Signaling Dependence
Authors: Kourtchenko Olga , Andersson Mats X. , Hamberg Mats , Brunnström Åsa , Göbel Cornelia , McPhail Kerry L. , Gerwick William H. , Feussner Ivo , Ellerström Mats
Published: October 2007

The jasmonate family of phytohormones, as represented by 12-oxo-phytodienoic acid (OPDA), dinor-phytodienoic acid (dn-OPDA), and jasmonic acid in Arabidopsis (Arabidopsis thaliana), has been implicated in a vast array of different developmental processes and stress responses. Recent reports indicate that OPDA and dn-OPDA occur not only as free acids in Arabidopsis, but also as esters with complex lipids, so-called arabidopsides. Recently, we showed that recognition of the two bacterial effector proteins AvrRpm1 and AvrRpt2 induced high levels of a molecule consisting of two OPDAs and one dn-OPDA esterified to a monogalactosyl diacylglycerol moiety, named arabidopside E. In this study, we demonstrate that the synthesis of arabidopsides is mainly independent of the prokaryotic lipid biosynthesis pathway in the chloroplast, and, in addition to what previously has been reported, arabidopside E as well as an all-OPDA analog, arabidopside G, described here accumulated during the hypersensitive response and in response to wounding. We also show that different signaling pathways lead to the formation of arabidopsides during the hypersensitive response and the wounding response, respectively. However, the formation of arabidopsides during both responses is dependent on an intact jasmonate signaling pathway. Additionally, we report inhibition of growth of the fungal necrotrophic pathogen Botrytis cinerea and in planta release of free jasmonates in a time frame that overlaps with the observed reduction of arabidopside levels. Thus, arabidopsides may have a dual function: as antipathogenic substances and as storage compounds that allow the slow release of free jasmonates.
Genomic Organization and Evolutionary Conservation of Plant D-Type Cyclins
Authors: Menges Margit , Pavesi Giulio , Morandini Piero , Bögre Laszlo , Murray James A.H.
Published: October 2007

Plants contain more genes encoding core cell cycle regulators than other organisms but it is unclear whether these represent distinct functions. D-type cyclins (CYCD) play key roles in the G1-to-S-phase transition, and Arabidopsis (Arabidopsis thaliana) contains 10 CYCD genes in seven defined subgroups, six of which are conserved in rice (Oryza sativa). Here, we identify 22 CYCD genes in the poplar (Populus trichocarpa) genome and confirm that these six CYCD subgroups are conserved across higher plants, suggesting subgroup-specific functions. Different subgroups show gene number increases, with CYCD3 having three members in Arabidopsis, six in poplar, and a single representative in rice. All three species contain a single CYCD7 gene. Despite low overall sequence homology, we find remarkable conservation of intron/exon boundaries, because in most CYCD genes of plants and mammals, the first exon ends in the conserved cyclin signature. Only CYCD3 genes contain the complete cyclin box in a single exon, and this structure is conserved across angiosperms, again suggesting an early origin for the subgroup. The single CYCD gene of moss has a gene structure closely related to those of higher plants, sharing an identical exon/intron structure with several higher plant subgroups. However, green algae have CYCD genes structurally unrelated to higher plants. Conservation is also observed in the location of potential cyclin-dependent kinase phosphorylation sites within CYCD proteins. Subgroup structure is supported by conserved regulatory elements, particularly in the eudicot species, including conserved E2F regulatory sites within CYCD3 promoters. Global expression correlation analysis further supports distinct expression patterns for CYCD subgroups.
Differential Expression of the TFIIIA Regulatory Pathway in Response to Salt Stress between Medicago truncatula Genotypes
Authors: de Lorenzo Laura , Merchan Francisco , Blanchet Sandrine , Megías Manuel , Frugier Florian , Crespi Martin , Sousa Carolina
Published: October 2007

Soil salinity is one of the most significant abiotic stresses for crop plants, including legumes. These plants can establish root symbioses with nitrogen-fixing soil bacteria and are able to grow in nitrogen-poor soils. Medicago truncatula varieties show diverse adaptive responses to environmental conditions, such as saline soils. We have compared the differential root growth of two genotypes of M. truncatula (108-R and Jemalong A17) in response to salt stress. Jemalong A17 is more tolerant to salt stress than 108-R, regarding both root and nodulation responses independently of the nitrogen status of the media. A dedicated macroarray containing 384 genes linked to stress responses was used to compare root gene expression during salt stress in these genotypes. Several genes potentially associated with the contrasting cellular responses of these plants to salt stress were identified as expressed in the more tolerant genotype even in the absence of stress. Among them, a homolog of the abiotic stress-related COLD-REGULATEDA1 gene and a TFIIIA-related transcription factor (TF), MtZpt2-1, known to regulate the former gene. Two MtZpt2 TFs (MtZpt2-1 and MtZpt2-2) were found in Jemalong A17 plants and showed increased expression in roots when compared to 108-R. Overexpression of these TFs in the sensitive genotype 108-R, but not in Jemalong A17, led to increased root growth under salt stress, suggesting a role for this pathway in the adaptive response to salt stress of these M. truncatula genotypes.
Antisense Repression of the Medicago truncatula Nodule-Enhanced Sucrose Synthase Leads to a Handicapped Nitrogen Fixation Mirrored by Specific Alterations in the Symbiotic Transcriptome and Metabolome
Authors: Baier Markus C. , Barsch Aiko , Küster Helge , Hohnjec Natalija
Published: October 2007

We analyzed the role of the sucrose (Suc) synthase MtSucS1 during nodulation of the model legume Medicago truncatula, integrating data for the developmental, transcriptional, and metabolic processes affected downstream of an impaired Suc cleavage in root nodules. To reduce carbohydrate supply to nodule tissues, transgenic plants expressing a p35S-driven MtSucS1-antisense fusion were constructed. These plants displayed an up to 90% reduction of MtSucS1 proteins in roots and nodules. Phenotypic studies of two independent MtSucS1-reduced lines demonstrated that only under conditions depending on nodulation, these plants appeared to be impaired in above-ground growth. Specifically plant height, shoot weight, leaf development, flowering, as well as seed maturation were reduced, and the efficiency of photosynthesis was affected. Concomitantly, a significantly enhanced root to shoot ratio with a marked increase in root tip numbers was observed. Root nodule formation was found retarded and the impaired nodulation was accompanied by a less efficient nitrogen (N) acquisition. The decreased total N content of MtSucS1-antisense lines and an enhanced carbon to N ratio in roots, nodules, and shoots correlated with the extent of MtSucS1 knockdown. On the level of transcription, effects of an MtSucS1 reduction were evident for genes representing important nodes of the nodule carbon and N metabolism, while metabolite profiling revealed significantly lower levels of amino acids and their derivatives particularly in strongly MtSucS1-reduced nodules. Our results support the model that nodule-enhanced Suc synthase 1 of the model legume M. truncatula is required for the establishment and maintenance of an efficient N-fixing symbiosis.
Mutation in Nicotianamine Aminotransferase Stimulated the Fe(II) Acquisition System and Led to Iron Accumulation in Rice
Authors: Cheng Longjun , Wang Fang , Shou Huixia , Huang Fangliang , Zheng Luqing , He Fei , Li Jinhui , Zhao Fang-Jie , Ueno Daisei , Ma Jian Feng , Wu Ping
Published: October 2007

Higher plants acquire iron (Fe) from the rhizosphere through two strategies. Strategy II, employed by graminaceous plants, involves secretion of phytosiderophores (e.g. deoxymugineic acid in rice [Oryza sativa]) by roots to solubilize Fe(III) in soil. In addition to taking up Fe in the form of Fe(III)-phytosiderophore, rice also possesses the strategy I-like system that may absorb Fe(II) directly. Through mutant screening, we isolated a rice mutant that could not grow with Fe(III)-citrate as the sole Fe source, but was able to grow when Fe(II)-EDTA was supplied. Surprisingly, the mutant accumulated more Fe and other divalent metals in roots and shoots than the wild type when both were supplied with EDTA-Fe(II) or grown under water-logged field conditions. Furthermore, the mutant had a significantly higher concentration of Fe in both unpolished and polished grains than the wild type. Using the map-based cloning method, we identified a point mutation in a gene encoding nicotianamine aminotransferase (NAAT1), which was responsible for the mutant phenotype. Because of the loss of function of NAAT1, the mutant failed to produce deoxymugineic acid and could not absorb Fe(III) efficiently. In contrast, nicotianamine, the substrate for NAAT1, accumulated markedly in roots and shoots of the mutant. Microarray analysis showed that the expression of a number of the genes involved in Fe(II) acquisition was greatly stimulated in the naat1 mutant. Our results demonstrate that disruption of deoxymugineic acid biosynthesis can stimulate Fe(II) acquisition and increase iron accumulation in rice.
Two DEAD-Box Proteins May Be Part of RNA-Dependent High-Molecular-Mass Protein Complexes in Arabidopsis Mitochondria
Authors: Matthes Annemarie , Schmidt-Gattung Stephanie , Köhler Daniela , Forner Joachim , Wildum Steffen , Raabe Monika , Urlaub Henning , Binder Stefan
Published: October 2007

Posttranscriptional processes are important for regulation of gene expression in plant mitochondria. DEAD-box proteins, which form a huge protein family with members from all kingdoms, are fundamental components in virtually all types of processes in RNA metabolism. Two members of this protein family, designated PMH1 and PMH2 (for PUTATIVE MITOCHONDRIAL RNA HELICASE), were analyzed and characterized in mitochondria of Arabidopsis (Arabidopsis thaliana). Green fluorescent protein tagging with N-terminal PMH1 and PMH2 sequences supports the mitochondrial localization of these proteins. Northern experiments, as well as histochemical β-glucuronidase staining of transgenic plants carrying respective promoter:β-glucuronidase fusion constructs, revealed differing transcription patterns for the two genes. In response to cold, however, transcript levels of both genes increased. Immunodetection analyses of mitochondrial protein complexes after two-dimensional blue native/urea SDS-PAGE and after fractionation on sucrose gradients strongly suggest that one or both proteins are part of RNA-dependent complexes. Cold treatment of cell cultures or solubilization of mitochondria in the presence of MgCl2 favored the detection of high-molecular-mass complexes. This study paves the way for detailed analysis of high-molecular-mass complexes in mitochondria of higher plants.
Alternative Splicing and mRNA Levels of the Disease Resistance Gene RPS4 Are Induced during Defense Responses
Authors: Zhang Xue-Cheng , Gassmann Walter
Published: October 2007

The Arabidopsis (Arabidopsis thaliana) disease resistance protein RESISTANCE TO PSEUDOMONAS SYRINGAE4 (RPS4) activates defenses in response to bacterial pathogens expressing avrRps4 in a gene-for-gene specific manner. The RPS4 gene produces multiple transcripts via alternative splicing of two regular introns flanking exon 3 and a cryptic intron within exon 3. We showed previously that RPS4-mediated resistance requires the combined presence of transcripts encoding both full-length and truncated open reading frames. Here, we demonstrate that alternative splicing of RPS4 undergoes dynamic changes specifically during the resistance response. Furthermore, RPS4 expression was induced by the presence of AvrRps4 in an EDS1-dependent manner. Interestingly, inducible alternative splicing was not limited to the avrRps4-RPS4 interaction, indicating that regulation of alternative splicing may be a general response to prime the plant stress response system. Intron-deficient transgenes lacking only one intron were previously shown to be nonfunctional. Here, we establish quantitatively that the absence of one intron had no effect on the splicing frequency of remaining introns. Given the lack of functionality of single intron-deficient transgenes, this suggests that the products of individual transcripts have distinct functions during RPS4-triggered resistance. Transient expression of truncated RPS4 proteins in Nicotiana benthamiana induced hypersensitive response-like cell death in the absence of AvrRps4. Interestingly, different truncated proteins had markedly differing stability. In summary, RPS4 function is regulated at multiple levels, including gene expression, alternative splicing, and protein stability, presumably to fine-tune activity and limit damage inflicted by activated RPS4 protein.
Nitrite Acts as a Transcriptome Signal at Micromolar Concentrations in Arabidopsis Roots
Authors: Wang Rongchen , Xing Xiujuan , Crawford Nigel
Published: October 2007

Nitrate serves as a potent signal to control gene expression in plants and algae, but little is known about the signaling role of nitrite, the direct product of nitrate reduction. Analysis of several nitrate-induced genes showed that nitrite increases mRNA levels as rapidly as nitrate in nitrogen-starved Arabidopsis (Arabidopsis thaliana) roots. Both nitrite and nitrate induction are apparent at concentrations as low as 100 nm. The response at low nitrite concentrations was not due to contaminating nitrate, which was present at <1% of the nitrite concentration. High levels of ammonium (20 mm) in the growth medium suppressed induction of several genes by nitrate, but had varied effects on the nitrite response. Transcriptome analysis using 250 or 5 μ  m nitrate or nitrite showed that over one-half of the nitrate-induced genes, which included genes involved in nitrate and ammonium assimilation, energy production, and carbon and nitrogen metabolism responded equivalently to nitrite; however, the nitrite response was more robust and there were many genes that responded specifically to nitrite. Thus, nitrite can serve as a signal as well as if not better than nitrate.
Evolution of Cinnamate/p-Coumarate Carboxyl Methyltransferases and Their Role in the Biosynthesis of Methylcinnamate
Authors: Kapteyn Jeremy , Qualley Anthony V. , Xie Zhengzhi , Fridman Eyal , Dudareva Natalia , Gang David R.
Published: October 2007

Methylcinnamate, which is widely distributed throughout the plant kingdom, is a significant component of many floral scents and an important signaling molecule between plants and insects. Comparison of an EST database obtained from the glandular trichomes of a basil (Ocimum basilicum) variety that produces high levels of methylcinnamate (line MC) with other varieties producing little or no methylcinnamate identified several very closely related genes belonging to the SABATH family of carboxyl methyltransferases that are highly and almost exclusively expressed in line MC. Biochemical characterization of the corresponding recombinant proteins showed that cinnamate and p-coumarate are their best substrates for methylation, thus designating these enzymes as cinnamate/p-coumarate carboxyl methyltransferases (CCMTs). Gene expression, enzyme activity, protein profiling, and metabolite content analyses demonstrated that CCMTs are responsible for the formation of methylcinnamate in sweet basil. A phylogenetic analysis of the entire SABATH family placed these CCMTs into a clade that includes indole-3-acetic acid carboxyl methyltransferases and a large number of uncharacterized carboxyl methyltransferase–like proteins from monocots and lower plants. Structural modeling and ligand docking suggested active site residues that appear to contribute to the substrate preference of CCMTs relative to other members of the SABATH family. Site-directed mutagenesis of specific residues confirmed these findings.
MIDGETUnravels Functions of theArabidopsisTopoisomerase VI Complex in DNA Endoreduplication, Chromatin Condensation, and Transcriptional Silencing
Authors: Kirik Viktor , Schrader Andrea , Uhrig Joachim F. , Hulskamp Martin
Published: October 2007

The plant homologs of the archaeal DNA topoisomerase VI complex are required for the progression of endoreduplication cycles. Here, we describe the identification of MIDGET (MID) as a novel component of topoisomerase VI. We show that mid mutants show the same phenotype as rhl1, rhl2, and top6B mutants and that MID protein physically interacts with RHL1. The phenotypic analysis revealed new phenotypes, indicating that topoisomerase VI is involved in chromatin organization and transcriptional silencing. In addition, genetic evidence is provided suggesting that the ATR-dependent DNA damage repair checkpoint is activated in mid mutants, and CYCB1;1 is ectopically activated. Finally, we demonstrate that overexpression of CYCB1;2 can rescue the endoreduplication defects in mid mutants, suggesting that in mid mutants, a specific checkpoint is activated preventing further progression of endoreduplication cycles.
Rituximab and 17‐allylamino‐17‐demethoxygeldanamycin induce synergistic apoptosis in B‐cell chronic lymphocytic leukaemia
Authors: Johnson Amy J. , Wagner Amy J. , Cheney Carolyn M. , Smith Lisa L. , Lucas David M. , Guster Sara K. , Grever Michael R. , Lin Thomas S. , Byrd John C.
Published: October 2007

Treatment options for chronic lymphocytic leukaemia (CLL) are limited and eventually fail because of the development of toxicities or drug resistance. Thus, identification of new therapeutic strategies and targets is a high priority. The semisynthetic geldanamycin derivative 17‐allylamino‐17‐demethoxygeldanamycin (17‐AAG) inhibits heat shock protein 90 (Hsp90) binding to client proteins, thereby leading to their degradation. We demonstrate that at biologically active and clinically attainable levels (1 μmol/l), 17‐AAG treatment of CLL B cells in vitro causes modest apoptosis as well as decreased AKT protein levels. Given the potential activation of AKT following antibody therapy in CLL, we evaluated the combination of 17‐AAG and rituximab. These agents produced synergistic cytotoxicity of CLL cells in vitro. However, rituximab‐mediated antibody‐dependent cellular cytotoxicity was modestly reduced with 17‐AAG, and complement‐dependent cytotoxicity was not altered. We conclude that the combination of Hsp90 inhibitors with therapeutic antibodies, such as rituximab may represent a novel strategy to enhance therapeutic response in CLL. Furthermore, our data indicates that AKT and Hsp70 protein levels are relevant pharmacodynamic endpoints to monitor the in vivo effect of 17‐AAG therapy.
The influence of environment and spawning distribution on the survival of anchovy (Engraulis encrasicolus) larvae in the Bay of Biscay (NE Atlantic) investigated by biophysical simulations
Authors: ALLAIN GWENHAEL , PETITGAS PIERRE , LAZURE PASCAL
Published: October 2007

A growth and survival model of the early life stages was run along virtual drift trajectories tracked in a hydrodynamic model to simulate the annual recruitment process of anchovy (Engraulis encrasicolus) in the Bay of Biscay (NE Atlantic). These biophysical simulations concerning three different years were analysed in order to investigate the influence of environment and spawning dynamics on the survival of larvae and juveniles. The location of space–time survival windows suggested major environmental mechanisms involved in simulated recruitment variability at the different scales – retention of larvae and juveniles in favourable habitats over the shelf margins and turbulence effects. These small‐scale and meso‐scale mechanisms were related to the variations in wind direction and intensity during spring and summer. Survival was also variable according to the origin of the drift trajectories, that is spawning distribution in space and time. The observed spawning distribution (according to field surveys) was compared with the spawning distribution that would maximize survival (according to the biophysical model) on a seasonal scale, which revealed factors not considered in the biophysical model (e.g. spawning behaviour of the different age classes). The variation of simulated survival according to spawning distribution was examined on a multi‐annual scale and showed a coherent pattern with past and present stock structures. The interaction processes between the population (influence on spawning) and its environment (influence on survival) and its implications on recruitment and stock dynamics are discussed.
Biophysical modelling of larval drift, growth and survival for the prediction of anchovy (Engraulis encrasicolus) recruitment in the Bay of Biscay (NE Atlantic)
Authors: ALLAIN GWENHAEL , PETITGAS PIERRE , LAZURE PASCAL , GRELLIER PATRICK
Published: October 2007

Fish recruitment is the result of the integration of small‐scale processes affecting larval survival over a season and large oceanic areas. A hydrodynamic model was used to explore and model these physical–biological interaction mechanisms and then to perform the integration from individual to population scales in order to provide recruitment predictions for fisheries management. This method was applied to the case of anchovy (Engraulis encrasicolus) in the Bay of Biscay (NE Atlantic). The main data available to investigate survival mechanisms were past growth (otolith) records of larvae and juveniles sampled at sea. The drift history of these individuals was reconstructed by a backtracking procedure using hydrodynamic simulations. The relationships between (real) growth variation and variations in physical parameters (estimated by hydrodynamic simulations) were explored along the individual trajectories obtained. These relationships were then used to build and adjust individual‐based growth and survival models. Thousands of virtual buoys were released in the hydrodynamic model in order to reproduce the space–time spawning dynamics. Along the buoy trajectories (representative of sub‐cohorts), the biophysical model was run to simulate growth and survival as a function of the environment encountered. The survival rate after 3 months of drift was estimated for each sub‐cohort. The sum of all these survival rates over the season constituted an annual recruitment index. This index was validated over a series of recruitment estimations. The modelling choices, model results and the potential use of the recruitment index for fisheries management are discussed.
Oceanographic investigation of the American Samoa albacore (Thunnus alalunga) habitat and longline fishing grounds
Authors: DOMOKOS RÉKA , SEKI MICHAEL P. , POLOVINA JEFFREY J. , HAWN DONALD R.
Published: October 2007

The American Samoa fishing ground is a dynamic region with strong mesoscale eddy activity and temporal variability on scales of <1 week. Seasonal and interannual variability in eddy activity, induced by baroclinic instability that is fueled by horizontal shear between the eastward‐flowing South Equatorial Counter Current (SECC) and the westward‐flowing South Equatorial Current (SEC), seems to play an important role in the performance of the longline fishery for albacore. Mesoscale eddy variability in the American Samoa Exclusive Economic Zone (EEZ) peaks from March to April, when the kinetic energy of the SECC is at its strongest. Longline albacore catch tends to be highest at the eddy edges, while albacore catch per effort (CPUE) shows intra‐annual variability with high CPUE that lags the periods of peak eddy activity by about 2 months. When CPUE is highest, the values are distributed toward the northern half of the EEZ, the region affected most by the SECC. Further indication of the possible importance of the SECC for longline performance is the significant drop in eddy variability in 2004 when compared with that observed in 2003 – resulting from a weak SECC – which was accompanied by a substantial drop in albacore CPUE rates and a lack of northward intensification of CPUE. From an ecosystem perspective, evidence to support higher micronekton biomass in the upper 200 m at eddy boundaries is inconclusive. Albacore's vertical distribution seems to be governed by the presence of prey. Albacore spend most of their time between 150 and 250 m, away from the deep daytime and shallow nighttime sonic scattering layers, at depths coinciding with those of small local maxima in micronekton biomass whose backscattering properties are consistent with those of albacore's preferred prey. Settling depths of longline sets during periods of decreased eddy activity correspond to those most occupied by albacore, possibly contributing to the lower CPUE by reducing catchability through rendering bait less attractive to albacore in the presence of prey.
Temperature‐dependent stock‐recruitment model for walleye pollock (Theragra chalcogramma) around northern Japan
Authors: FUNAMOTO TETSUICHIRO
Published: October 2007

Changes in fish year‐class strength have been attributed to year‐to‐year variability in environmental conditions and spawning stock biomass (SSB). In particular, sea temperature has been shown to be linked to fish recruitment. In the present study, I examined the relationship between sea surface temperature (SST), SSB and recruitment for two stocks of walleye pollock (Theragra chalcogramma) around northern Japan [Japanese Pacific stock (JPS) and northern Japan Sea stock (JSS)] using a temperature‐dependent stock‐recruitment model (TDSRM). The recruitment fluctuation of JPS was successfully reproduced by the TDSRM with February and April SSTs, and February SST was a better environmental predictor than April SST. In addition, the JPS recruitment was positively related to February SST and negatively to April SST. The JSS recruitment modeled by the TDSRM incorporating February SST was also consistent with the observation, whereas the relationship between recruitment and February SST was negative, that is the opposite trend to JPS. These findings suggest that SST in February is important as a predictor of recruitment for both stocks, and that higher and lower SSTs in February act favorably on the recruitment of JPS and JSS respectively. Furthermore, Ricker‐type TDSRM was not selected for either of the stocks, suggesting that the strong density‐dependent effect as in the Ricker model does not exist for JPS and JSS. I formulate hypotheses to explain the links between SST and recruitment, and note that these relationships should be considered in any future attempts to understand the recruitment dynamics of JPS and JSS.
Diving behaviour of a Baird’s beaked whale, Berardius bairdii, in the slope water region of the western North Pacific: first dive records using a data logger
Authors: MINAMIKAWA SHINGO , IWASAKI TOSHIHIDE , KISHIRO TOSHIYA
Published: October 2007

A depth and temperature data logger was deployed by air gun on an individual Baird’s beaked whale (Berardius bairdii) off the Pacific coast of Japan. The retrieved data logger recorded 81 dives over approximately 29 h. The maximum recorded depth and the longest dive duration were 1777 m and 64.4 min, respectively. All dives were classified into three categories by depth: deep dives (>1000 m), intermediate dives (100–1000 m), and shallow dives (<100 m). Several intermediate dives generally followed a deep dive, and sequential shallow dives followed several intermediate dives in the record of the Baird’s beaked whale.
Multiple G‐protein‐coupling specificity of β‐adrenoceptor in macrophages
Authors: Magocsi Maria , Vizi E. Sylvester , Selmeczy Zsolt , Brózik Anna , Szelenyi Judith
Published: October 2007

Adrenergic signalling of the immune system is one of the important modulator pathways of the inflammatory immune response realized via G protein‐mediated pathways. The resulted signal depends on the type of the receptor‐coupled G‐protein (GPCR) that, according to the classical paradigm in the case of β‐adrenergic receptor (β‐AR), is Gs‐type. Recently, alternate and/or multiple G protein coupling specificity of GPCRs have been demonstrated including a switch from Gs to Gi binding. The possibility of a Gs/Gi switch and its role in the immune response of macrophages has not been investigated yet. In this study, we demonstrate that β‐adrenergic stimulation itself is able to induce a transient mitogen‐activated protein kinase phosphorylation in murine peritoneal macrophages in a pertussis toxin‐sensitive manner, suggesting that the Gs/Gi switch also occurs in the immune system. Although this process is very rapid, it can influence different signalling pathways and can reprogramme effector functions suggesting that sympathetic modulation of the defence mechanism of the innate immune system has an additional, Gs/Gi switch‐dependent component.
Antigen processing and CD24 expression determine antigen presentation by splenic CD4+ and CD8+ dendritic cells
Authors: Askew David , Harding Clifford V.
Published: October 2007

To examine heterogeneity in dendritic cell (DC) antigen presentation function, murine splenic DCs were separated into CD4+ and CD8+ populations and assessed for the ability to process and present particulate antigen to CD4+ and CD8+ T cells. CD4+ and CD8+ DCs both processed exogenous particulate antigen, but CD8+ DCs were much more efficient than CD4+ DCs for both major histocompatibility complex (MHC) class II antigen presentation and MHC class I cross‐presentation. While antigen processing efficiency contributed to the superior antigen presentation function of CD8+ DCs, our studies also revealed an important contribution of CD24. CD8+ DCs were also more efficient than CD4+ DCs in inducing naïve T cells to acquire certain effector T‐cell functions, for example generation of cytotoxic CD8+ T cells and interferon (IFN)‐γ‐producing CD4+ T cells. In summary, CD8+ DCs are particularly potent antigen‐presenting cells that express critical costimulators and efficiently process exogenous antigen for presentation by both MHC class I and II molecules.
Different types of in vitro generated human monocyte‐derived dendritic cells release exosomes with distinct phenotypes
Authors: Johansson Sara M. , Admyre Charlotte , Scheynius Annika , Gabrielsson Susanne
Published: October 2007

Human in vitro generated dendritic cells and the exosomes they release are potential tools for the modulation of immune responses. Here, we characterized differently generated monocyte‐derived dendritic cells (MDDCs) and their exosomes. Culturing of peripheral CD14+ cells from the same individuals with either interleukin (IL)‐4 and granulocyte–macrophage colony‐stimulating factor (GM‐CSF) (conventional MDDCs) or alternatively with IL‐4 and IL‐3 generated immature MDDCs in 7 days. Fluorescence‐activated cell sorting (FACS) analysis showed that the IL‐4/IL‐3‐generated MDDCs had significantly lower percentages of CD1a+, CD40+ and CD80+ cells and a higher percentage of CD86+ cells as compared with conventional MDDCs. In addition, IL‐4/IL‐3‐generated MDDCs had significantly higher densities of major histocompatibility complex (MHC) class I [human leucocyte antigen (HLA)‐ABC], MHC class II (HLA‐DR), CD11c and the tetraspanin CD81 as compared with conventional MDDCs. In a comparison of their ability to stimulate CD8+ T cells, we found that the IL‐4/IL‐3 MDDCs were slightly more efficient than the conventional MDDCs at inducing interferon (IFN)‐γ release in response to viral peptides. Exosome morphology was confirmed by electron microscopy and exosome phenotypes were analysed by flow cytometry and western blot. In comparison to exosomes from conventional MDDCs, exosomes from IL‐4/IL‐3‐generated MDDCs showed significantly stronger signals for HLA‐ABC, HLA‐DR, CD11c, CD63 and CD81. Thus, phenotypically the exosomes largely reflected their MDDCs of origin. When exosomes were loaded with viral peptides, both types of exosomes induced IFN‐γ release from CD8+ T cells. Our findings might have significance for the development of DC‐ and exosome‐based therapies.
Comparison of MMP‐2 and MMP‐9 secretion from T helper 0, 1 and 2 lymphocytes alone and in coculture with macrophages
Authors: Oviedo‐Orta Ernesto , Bermudez‐Fajardo Alexandra , Karanam Sharada , Benbow Ulrike , Newby Andrew C.
Published: October 2007

Metalloproteinases (MMPs) participate in extracellular matrix remodelling and regulatory signalling during chronic inflammatory states such as atherosclerosis formation. However, the sources and mediators of MMP upregulation need clarification. We investigated whether proinflammatory mouse T helper type 1 (Th1) lymphocytes are more active in MMP secretion than naïve Th0 or anti‐inflammatory Th2 phenotypes, in the absence of specific antigenic stimulation, under baseline conditions and after contact with irradiated macrophages. We also compared the effect of Th0, Th1 or Th2 lymphocyte‐conditioned medium and irradiated lymphocytes on MMP production from macrophages. Finally, we investigated whether CD40–CD40 ligand (CD40L) interactions were involved in T‐cell‐stimulated MMP secretion from macrophages. Under baseline conditions, MMP‐2 messenger RNA (mRNA) and protein levels were greater in Th1 than Th0 or Th2 lymphocytes; MMP‐9 mRNA, but not protein, was also upregulated. In the presence of irradiated macrophages MMP‐2 and MMP‐9 production from Th1 and Th2 was greater than from Th0 lymphocytes. Conditioned media from Th1 but not Th0 or Th2 cells increased MMP‐9 secretion from macrophages. Irradiated Th1 lymphocytes stimulated both MMP‐2 and MMP‐9 secretion from macrophages more than irradiated Th2 or Th0 cells; this activation was independent of CD40–CD40L interaction. These findings demonstrate for the first time greater MMP secretion by Th1 than Th2 or Th0 lymphocytes and their greater ability to upregulate macrophage MMP secretion in the absence of specific antigenic stimulation. These mechanisms could promote matrix turnover in inflammatory states and, for example, promote atherosclerotic plaque rupture.
Comparison of open and double‐blind placebo‐controlled food challenges in diagnosis of food hypersensitivity amongst children
Authors: Venter C. , Pereira B. , Voigt K. , Grundy J. , Clayton C. B. , Gant C. , Higgins B. , Dean T.
Published: October 2007

Background  Correct diagnosis of food hypersensitivity (FHS) is important to ensure appropriate patient care and to accurately establish the population prevalence and incidence. Food challenges play a very important role in the diagnosis of FHS, but it is unclear when open food challenges (OFCs) opposed to double‐blind placebo‐controlled food challenges (DBPCFCs) should be used. This study investigated the use of OFCs and DBPCFCs when diagnosing FHS.

Methods  Children with a reported history of FHS or with sensitization to a food without known previous consumption were invited to undergo food challenges. Children of consenting parents underwent an OFC and those with a positive OFC were approached to undergo a DBPCFC. Food challenges were either performed as 1‐day or 1‐week challenges depending on sensitization status and clinical history.

Results  Forty‐one children underwent both OFCs and DBPCFCs. The positive predictive values for 1‐day and 1‐week OFCs were 73% (8/11; 95% CI: 39–94%) and 57% (20/35; 95% CI: 39–74%) respectively. There was no evidence to indicate that the younger children were more likely to have a positive OFC confirmed by a DBPCFC compared to older children (Fisher’s exact P = 0.53). In the 1‐day challenges parents indicated a preference for OFC rather than DBPCFC. By contrast, in the 1‐week challenge parents indicated a preference for DBPCFC (P = 0.0192).

Conclusion  Open food challenge may be suitable for diagnosing immediate objective symptoms, whereas DBPCFC may be needed for the diagnosis of delayed and mainly subjective symptoms, irrespective of the child’s age.
Characterization of HMW‐PBPs from the rod‐shaped actinomycete Corynebacterium glutamicum: peptidoglycan synthesis in cells lacking actin‐like cytoskeletal structures
Authors: Valbuena Noelia , Letek Michal , Ordóñez Efrén , Ayala Juan , Daniel Richard A. , Gil José A. , Mateos Luis M.
Published: October 2007

Analysis of the complete genome sequence of Corynebacterium glutamicum indicated that, in addition to ftsI, there are eight proteins with sequence motifs that are strongly conserved in penicillin binding proteins (PBPs): four genes that code for high‐molecular‐weight (HMW)‐PBPs (PBP1a, PBP1b, PBP2a and PBP2b), two genes encoding low‐molecular‐weight PBPs (PBP4 and PBP4b) and two probable β‐lactamases (PBP5 and PBP6). Here, the function of the four HMW‐PBPs in C. glutamicum was investigated using a combination of genetic knockouts, enhanced green fluorescent protein 2 (EGFP2) fusions and penicillin staining of membrane preparations. The four HMW‐PBPs were expressed in a growing culture of C. glutamicum, but none of four pbp genes was individually essential for the growth of the bacterium, and only the simultaneous disruption of both pbp1b and pbp2b was lethal. The fused EGFP2–PBP proteins were functional in vivo, which allowed correct determination of their cellular localization. EGFP2 fusions to PBP1a, PBP1b and PBP2b localized at the poles and at the septum, whereas EGFP2–PBP2a was predominantly found at the septum. Cefsulodin treatment specifically delocalized PBP1a and PBP1b (class A HMW‐PBPs), whereas mecillinam caused the specific delocalization of PBP2b and PBP2a (class B HMW‐PBPs). The results provide new insight into the mechanisms involved in the synthesis of the cell wall in this bacterial species, which lacks a known actin‐like cytoskeletal structure.
Carrier Potential Properties of Bacillus thuringiensis Cry1A Toxins for a Diphtheria Toxin Epitope
Authors: Guerrero G. G. , Moreno‐Fierros L.
Published: October 2007

The N‐terminal half or toxic fragment of Bacillus thuringiensis Cry proteins is comprised of three structural domains. In a previous paper, we showed that this region plays an important role in the immunogenicity of the B. thuringiensis Cry proteins. Due to this ability and along with their stability it is worthy of investigating whether this region has carrier potential. To approach this, an eight amino acid hydrophobic motif in α‐helix 7 of wild‐type (WT) Cry1A toxins was exchanged for a diphtheria toxin epitope (DTB). The resultant recombinant toxins were tested for their ability to induce specific anti‐Cry and anti‐diphtheria toxin antibodies in mice after intraperitoneal and nasal immunization. We found that recombinant Cry1A toxins retained their ability to induce serum and mucosal anti‐Cry Ab as well as IgG subclasses, although with a varied magnitude. By the systemic route, the effect of the amino acid substitution in the ratio of the IgG1/IgG2a Ab, leading in some sites toward IgG1 or IgG2a is more evident. Interestingly, mice produced specific anti‐DTB IgG, and IgA after intranasal immunization. Together, our results support and show the immunogenic properties of the WT Cry1A toxins as well as its carrier potential for a DTB.
Lactate Dehydrogenase‐elevating Virus Infection at the Sensitization and Challenge Phases Reduces the Development of Delayed Eosinophilic Allergic Rhinitis in BALB/c Mice
Authors: Sasaki Y. , Hayashi T. , Hasegawa K.
Published: October 2007

The present study was conducted to determine whether lactate dehydrogenase‐elevating virus (LDV) infection at the sensitization and challenge phases affect the development of delayed allergic eosinophilic rhinitis induced by ovalbumin (OVA) in BALB/c mice (DAR group). Compared to the DAR group, LDV infection at the priming (DAR/LDVs group) and immunizing (DAR/LDVc group) phases reduced the induction of eosinophils in the bone marrow (BM) and/or blood. However, the number of eosinophils in the BM was not affected in the DAR/LDVc group. In addition, total blood IgE values were reduced in the DAR/LDVs but not the DAR/LDVc groups. Compared to the production of cytokines from splenic cells and blood IgE values in the DAR group, OVA‐specific IL‐4 and IFN‐γ productions and IgE values were reduced in the DAR/LDVs, whereas OVA‐specific IFN‐γ and IL‐4 productions were increased and decreased, respectively in the DAR/LDVc,but not the DAR/LDVs groups. Both DAR/LDVs and DAR/LDVc groups reduced the development of eosinophilic rhinitis associated with reduced VCAM‐1 expression on endothelium in blood vessels and ICAM‐1 expression on nasal respiratory epithelium at inflamed areas. The present study suggests that LDV infection at the sensitization phase may reduce the development of T helper (Th) 1 and Th2 responses, whereas LDV infection at the challenge phase may inhibit the development of Th2 response by shifting to Th1 response. These may be responsible for the reduction of the development of DAR by LDV infection.
Lung Tissue and Tumour‐infiltrating T Lymphocytes in Patients with Non‐small Cell Lung Carcinoma and Chronic Obstructive Pulmonary Disease (COPD): Moderate/Severe Versus Mild Stage of COPD1
Authors: Marc M. M. , Korosec P. , Kern I. , Sok M. , Ihan A. , Kosnik M.
Published: October 2007

Cytotoxic CD8+ T cells have been suggested to be key players in the pathogenesis of chronic obstructive pulmonary disease (COPD). We wanted to investigate the phenotype of lung tissue T lymphocytes (LTL) and tumour‐infiltrating T lymphocytes (TIL) in smokers with peripheral non‐small cell lung carcinoma (NSCLC) with moderate/severe versus mild COPD. Lung tissue and tumour samples were obtained from patients with moderate/severe stage of COPD (n = 10) and from patients with mild stage of COPD (n = 7) at lung resection for a solitary peripheral NSCLC, processed and analysed by flow cytometry. The flow‐cytometric results showed that lung tissue T cells, regardless of the severity of COPD, were mostly of the activated phenotype, expressed the CXCR3 chemokine receptor characteristic of type 1 T cells, and did neither significantly differ in the expression of activation markers (CD69, CD25 and HLA‐DR), differentiation markers (CD27 and CD28) and chemokine receptors (CXCR3 and CCR4) between the selected groups, nor showed any significant correlation with lung function measured as forced expiratory volume in 1 s (FEV1) or TLCO. Compared with LTL, a significantly greater proportion of TIL expressed the activation markers CD69 and CD25, but a lower proportion showed a fully differentiated CD27−28− phenotype. We conclude that lung LTL patterns are similar in NSCLC patients with moderate/severe or mild stages of COPD, and are not significantly related to lung function. LTL and TIL possess different phenotype characteristics. The majority of tumour tissue T cells are activated, but it seems that their process of differentiation is incomplete.