bluuebunny/crossref_metadata_2025_split huggingface dataset:
The transcription of bradyzoite genes in Toxoplasma gondii is controlled by autonomous promoter elements
Authors: Behnke Michael S. , Radke Josh B. , Smith Aaron T. , Sullivan Jr William J. , White Michael W. 
Published: April 2008

SummaryExperimental evidence suggests that apicomplexan parasites possess bipartite promoters with basal and regulated cis‐elements similar to other eukaryotes. Using a dual luciferase model adapted for recombinational cloning and use in Toxoplasma gondii, we show that genomic regions flanking 16 parasite genes, which encompass examples of constitutive and tachyzoite‐ and bradyzoite‐specific genes, are able to reproduce the appropriate developmental stage expression in a transient luciferase assay. Mapping of cis‐acting elements in several bradyzoite promoters led to the identification of short sequence spans that are involved in control of bradyzoite gene expression in multiple strains and under different bradyzoite induction conditions. Promoters that regulate the heat shock protein BAG1 and a novel bradyzoite‐specific NTPase during bradyzoite development were fine mapped to a 6–8 bp resolution and these minimal cis‐elements were capable of converting a constitutive promoter to one that is induced by bradyzoite conditions. Gel‐shift experiments show that mapped cis‐elements are bound by parasite protein factors with the appropriate functional sequence specificity. These studies are the first to identify the minimal sequence elements that are required and sufficient for bradyzoite gene expression and to show that bradyzoite promoters are maintained in a ‘poised’ chromatin state throughout the intermediate host life cycle in low passage strains. Together, these data demonstrate that conventional eukaryotic promoter mechanisms work with epigenetic processes to regulate developmental gene expression during tissue cyst formation.
The identity of the transcription +1 position is crucial for changes in gene expression in response to amino acid starvation in Bacillus subtilis
Authors: Krásný Libor , Tišerová Hana , Jonák Jiří , Rejman Dominik , Šanderová Hana 
Published: April 2008

SummaryWe identify here a pattern in the transcription start sites (+1A or +1G) of σA‐dependent promoters of genes that are up‐/downregulated in response to amino acid starvation (stringent response) in Bacillus subtilis. Upregulated promoters initiate mostly with ATP and downregulated promoters with GTP. These promoters appear to be sensitive to changes in initiating nucleoside triphosphate concentrations. During the stringent response in B. subtilis, when ATP and GTP levels change reciprocally, the identity of the +1 position (A or G) of these promoters is a factor important in their regulation. Mutations that change the identity of position +1 (A for G and vice versa) change the response of the promoter to amino acid starvation.
Silencing the crowd: high‐throughput functional genomics inMagnaporthe oryzae
Authors: Caracuel‐Rios Zaira , Talbot Nicholas J. 
Published: April 2008

SummaryA new high‐throughput RNA‐silencing system has been developed for use in the rice blast fungusMagnaporthe oryzae, allowing rapid generation of transformants in which individual genes have been silenced. Development of this system will allow large‐scale functional analysis of genes in the fungus to define the cellular processes required for plant infection and disease symptoms. Functional analysis of 37 genes predicted to be involved in calcium signalling was carried out by RNA silencing to validate the new strategy and has provided new insight into the role of calcium‐mediated signal transduction in plant pathogenic fungi.
Demonstration of strain‐specific CD8 T cell responses to Theileria annulata
Authors: MACHUGH N. D. , BURRELLS A. C. , MORRISON W. I. 
Published: April 2008

SUMMARY The present study set out to examine the nature and specificity of the bovine CD8 T cell response at the clonal level in a group of eight animals immunized with a cloned population of Theileria annulata. The results demonstrated that immunized animals generated parasite‐specific CD8 T cells that produced IFNγ in response to parasite stimulation but had highly variable levels of cytotoxicity for parasitized cells. The study also demonstrated that these parasite‐specific CD8 T cells could be propagated and cloned in vitro from the memory T cell pool of cattle immunized with live T. annulata parasites. Within the small group of animals studied, there was evidence that responses were preferentially directed to antigens presented by an A10+ class I major histocompatibility complex (MHC) haplotype, suggesting that responses restricted by products of this haplotype may be dominant. The A10‐restricted responses showed differential recognition of different parasite isolates and clones. By using a cloned population of parasites both for immunization of the animals and for in vitro analyses of the responses, we obtained unambiguous evidence that at least a proportion of CD8 T cells restricted by one MHC haplotype were parasite strain restricted.
Selenium supplementation enhances the protective response to Toxocara canis larvae in mice
Authors: PILARCZYK B. , DOLIGALSKA M. J. , DONSKOW‐SCHMELTER K. , BALICKA‐RAMISZ A. , RAMISZ A. 
Published: April 2008

SUMMARY The effect of oral and intraperitoneal supply of sodium selenite on the immune response to, and the course of T. canis larvae infection in mice were determined. The number of worms in the host tissue was reduced but the migratory route of larvae was not affected. Selenite (Se) supplementation influences Se retention in the liver, enhanced IL‐5 and eosinophil responses and evoked IL‐6 production in mice infected with T. canis. The enhanced protection in mice given Se intraperitoneally was associated with high levels of parasite‐specific IgE, and enhanced concentration of Th1‐related cytokines such IL‐12p70, TNF‐α and IFN‐γ. In mice given Se orally, the predominant cytokines produced were IL‐10, MCP‐1 and IL‐6 and these mice had lower protection. In conclusion, Se supplementation increases production of specific cytokines in mice infected with T. canis and increases protection against infection.
Elevated CO2 increases photosynthesis, biomass and productivity, and modifies gene expression in sugarcane
Authors: DE SOUZA AMANDA PEREIRA , GASPAR MARILIA , DA SILVA EMERSON ALVES , ULIAN EUGÊNIO CÉSAR , WACLAWOVSKY ALESSANDRO JAQUIEL , NISHIYAMA JR. MILTON YUTAKA , DOS SANTOS RENATO VICENTINI , TEIXEIRA MARCELO MENOSSI , SOUZA GLAUCIA MENDES , BUCKERIDGE MARCOS SILVEIRA 
Published: April 2008

ABSTRACTBecause of the economical relevance of sugarcane and its high potential as a source of biofuel, it is important to understand how this crop will respond to the foreseen increase in atmospheric [CO2]. The effects of increased [CO2] on photosynthesis, development and carbohydrate metabolism were studied in sugarcane (Saccharum ssp.). Plants were grown at ambient (∼370 ppm) and elevated (∼720 ppm) [CO2] during 50 weeks in open‐top chambers. The plants grown under elevated CO2 showed, at the end of such period, an increase of about 30% in photosynthesis and 17% in height, and accumulated 40% more biomass in comparison with the plants grown at ambient [CO2]. These plants also had lower stomatal conductance and transpiration rates (−37 and −32%, respectively), and higher water‐use efficiency (c.a. 62%). cDNA microarray analyses revealed a differential expression of 35 genes on the leaves (14 repressed and 22 induced) by elevated CO2. The latter are mainly related to photosynthesis and development. Industrial productivity analysis showed an increase of about 29% in sucrose content. These data suggest that sugarcane crops increase productivity in higher [CO2], and that this might be related, as previously observed for maize and sorghum, to transient drought stress.
Towards global understanding of plant defence against aphids – timing and dynamics of early Arabidopsis defence responses to cabbage aphid (Brevicoryne brassicae) attack
Authors: KUŚNIERCZYK ANNA , WINGE PER , JØRSTAD TOMMY S. , TROCZYŃSKA JOANNA , ROSSITER JOHN T. , BONES ATLE M. 
Published: April 2008

ABSTRACTInsect feeding on plants causes a complex series of coordinated defence responses. Little is known, however, about the time‐dependent aspect of induced changes. Here we present a time series‐based investigation of Arabidopsis thaliana Ler subjected to attack by a specialist pest of Brassicaceae species, Brevicoryne brassicae. Transcriptome and metabolome changes were studied at 6, 12, 24 and 48 h after infestation to monitor the progress of early induced responses. The use of full‐genome oligonucleotide microarrays revealed the initiation of extensive gene expression changes already during the first 6 h of infestation. Data indicated the involvement of reactive oxygen species (ROS) and calcium in early signalling, and salicylic acid (SA) and jasmonic acid (JA) in the regulation of defence responses. Transcripts related to senescence, biosynthesis of anti‐insect proteins, indolyl glucosinolates (GS) and camalexin, as well as several uncharacterized to date WRKY transcription factors, were induced. Follow‐up studies of defence‐involved secondary metabolites revealed depositions of callose at the insects’ feeding sites, a decrease in the total level of aliphatic GS, particularly 3‐hydroxypropyl glucosinolate, and accumulation of 4‐methoxyindol‐3‐ylmethyl glucosinolate 48 h after the attack. The novel role of camalexin, induced as a part of defence against aphids, was verified in fitness experiments. Fecundity of B. brassicae was reduced on camalexin‐accumulating wild‐type (WT) plants as compared with camalexin‐deficient pad3‐1 mutants. Based on experimental data, a model of plant–aphid interactions at the early phase of infestation was proposed.
Tomato fruit ascorbic acid content is linked with monodehydroascorbate reductase activity and tolerance to chilling stress
Authors: STEVENS R. , PAGE D. , GOUBLE B. , GARCHERY C. , ZAMIR D. , CAUSSE M. 
Published: April 2008

ABSTRACTQuantitative trait loci (QTL) mapping is a step towards the identification of factors regulating traits such as fruit ascorbic acid content. A previously identified QTL controlling variations in tomato fruit ascorbic acid has been fine mapped and reveals that the QTL has a polygenic and epistatic architecture. A monodehydroascorbate reductase (MDHAR) allele is a candidate for a proportion of the increase in fruit ascorbic acid content. The MDHAR enzyme is active in different stages of fruit ripening, shows increased activity in the introgression lines containing the wild‐type (Solanum pennellii) allele, and responds to chilling injury in tomato along with the reduced/oxidized ascorbate ratio. Low temperature storage of different tomato introgression lines with all or part of the QTL for ascorbic acid and with or without the wild MDHAR allele shows that enzyme activity explains 84% of the variation in the reduced ascorbic acid levels of tomato fruit following storage at 4 °C, compared with 38% at harvest under non‐stress conditions. A role is indicated for MDHAR in the maintenance of ascorbate levels in fruit under stress conditions. Furthermore, an increased fruit MDHAR activity and a lower oxidation level of the fruit ascorbate pool are correlated with decreased loss of firmness because of chilling injury.
Polymorphisms of the TAP 1 and 2 Gene May Influence Clinical Outcome of Primary Dengue Viral Infection
Authors: Soundravally R. , Hoti S. L. 
Published: April 2008

AbstractAntigen peptides are actively transported across the endoplasmic reticulum by the transporters associated with antigen presentation (TAP). TAP genes polymorphism could influence the selection process that determines which antigen peptides play a role in the pathogenesis of dengue infection. The aim of this study was to investigate the association of TAP genes polymorphism in diverse pathogenesis of dengue infection. This study included 197 dengue‐infected patients who were further categorized into 64, 23 and 11 primary dengue fever (DF), dengue hemorrhagic fever (DHF), dengue shock syndrome (DSS) cases, respectively and 26, 52, and 21 secondary DF, DHF and DSS cases, respectively as per WHO grading system. TAP1 and 2 gene polymorphisms were performed by the amplification refractory mutation system‐polymerase chain reaction (ARMS‐PCR). Analysis of TAP1 gene polymorphism demonstrated decreased frequency of Ile/Ile genotype at TAP1333 in primary DHF cases (39.1%) when compared with primary DF (64.1%, P < 0.034, OR = 0.611).The genotype frequency of Val/Val at TAP2379 locus was significantly decreased among primary DHF (43.5%) in comparison to primary DF (71.9%, P = 0.015, OR = 0.605). Significant low proportion of primary DSS were found to have TAP1637 Asp/Asp genotypes (54.5%) when compared with primary DF (70.3%, P = 0.043). Asp/Asp genotype at TAP1637 was found to reduce the risk by 0.643 times for primary DSS. There was no significant difference in the genotypes studied between primary and secondary infection and also within secondary dengue infection in all three clinical groups. This report on TAP gene polymorphisms in dengue suggested that among the primary‐infected individuals, homozygous patterns for Ile at TAP1333 Val at TAP2379 loci and Asp at TAP1637 were found to be a protective factor against development of DHF and DSS, respectively.
Molecular and genomic basis of volatile‐mediated indirect defense against insects in rice
Authors: Yuan Joshua S. , Köllner Tobias G. , Wiggins Greg , Grant Jerome , Degenhardt Jörg , Chen Feng 
Published: April 2008

SummaryRice plants fed on by fall armyworm (Spodoptera frugiperda, FAW) caterpillars emit a blend of volatiles dominated by terpenoids. These volatiles were highly attractive to females of the parasitoid Cotesia marginiventris. Microarray analysis identified 196 rice genes whose expression was significantly upregulated by FAW feeding, 18 of which encode metabolic enzymes potentially involved in volatile biosynthesis. Significant induction of expression of seven of the 11 terpene synthase (TPS) genes identified through the microarray experiments was confirmd using real‐time RT‐PCR. Enzymes encoded by three TPS genes, Os02g02930, Os08g07100 and Os08g04500, were biochemically characterized. Os02g02930 was found to encode a monoterpene synthase producing the single product S‐linalool, which is the most abundant volatile emitted from FAW‐damaged rice plants. Both Os08g07100 and Os08g04500 were found to encode sesquiterpene synthases, each producing multiple products. These three enzymes are responsible for production of the majority of the terpenes released from FAW‐damaged rice plants. In addition to TPS genes, several key genes in the upstream terpenoid pathways were also found to be upregulated by FAW feeding. This paper provides a comprehensive analysis of FAW‐induced volatiles and the corresponding volatile biosynthetic genes potentially involved in indirect defense in rice. Evolution of the genetic basis governing volatile terpenoid biosynthesis for indirect defense is discussed.
NRPD1a and NRPD1b are required to maintain post‐transcriptional RNA silencing and RNA‐directed DNA methylation in Arabidopsis
Authors: Eamens Andrew , Vaistij Fabián E. , Jones Louise 
Published: April 2008

SummaryIn plants, both transcriptional (TGS) and post‐transcriptional gene silencing (PTGS) can be self‐reinforcing, and this allows maintenance of silencing once the initiator has been removed or suppressed. For TGS, this can be accomplished by the generation of small interfering RNAs (siRNAs) from methylated DNA templates by RNA polymerase IV (PolIV), RNA‐dependent RNA polymerase 2 (RDR2), DICER‐LIKE 3 (DCL3), and the RNA‐directed DNA methylation (RdDM) machinery. Maintenance of PTGS requires RNA‐dependent RNA polymerase 6 (RDR6), and may be associated with DNA methylation and transitive production of secondary siRNAs. In this work, mutants defective for the NRPD1a and NRPD1b alternative largest subunits of PolIV were tested for their ability to undergo RdDM, transitive RNA silencing and maintenance of PTGS. PTGS could be initiated in both nrpd1a and nrpd1b mutants, and this was associated with production of secondary siRNAs; silencing was not maintained however. nrpd1a mutants could support RdDM although this was lost upon reversal of silencing, as was methylation in rdr6 mutants. We conclude that components of the machinery that maintain TGS are required for maintenance of PTGS, and that RDR6 uses distinct templates in the initiation and maintenance phases of RNA silencing.
Wheat FT protein regulates VRN1 transcription through interactions with FDL2
Authors: Li Chengxia , Dubcovsky Jorge 
Published: April 2008

SummaryA precise regulation of flowering time is central to plant species survival. Therefore, mechanisms have evolved in plants to integrate various environmental cues to optimize flowering time. In this study, we show that the product of the wheat gene TaFT, which integrates photoperiod and vernalization signals promoting flowering, interacts with bZIP proteins TaFDL2 and TaFDL6. We also show that TaFDL2 can interact in vitro with five ACGT elements in the promoter of the meristem identity gene VRN1, suggesting that TaFDL2 is a functional homologue of Arabidopsis FD. No direct interactions between the TaFT protein and the VRN1 promoter were detected. Transgenic wheat plants over‐expressing TaFT showed parallel increases in VRN1 transcripts, suggesting that TaFT provides transcriptional activation of VRN1, possibly through interactions with the TaFDL2 protein. The same transgenic plants also showed increased transcript levels of TaFT2 (a TaFT paralogue), indicating that TaFT2 acts downstream of TaFT. The fact that TaFT2 interacts with another bZIP protein TaFDL13, which lacks the ability to interact with the VRN1 promoter, suggests that TaFT and TaFT2 have different gene targets. This observation agrees with the functional divergence observed for the TaFT and TaFT2 orthologous genes in rice. The temperate cereals analyzed so far show VRN1 transcripts in the leaves, a characteristic not observed in Arabidopsis or rice. The high levels of TaFDL2 transcripts observed in wheat leaves provide a simple explanation for this difference. We present a hypothesis to explain the conservation of VRN1 expression in the leaves of temperate cereals.
CUL1 regulates TOC1 protein stability in the Arabidopsis circadian clock
Authors: Harmon Frank , Imaizumi Takato , Gray William M. 
Published: April 2008

SummaryThe circadian clock is the endogenous timer that coordinates physiological processes with daily and seasonal environmental changes. In Arabidopsis thaliana, establishment of the circadian period relies on targeted degradation of TIMING OF CAB EXPRESSION 1 (TOC1) by the 26S proteasome. ZEITLUPE (ZTL) is the F‐box protein that associates with the SCF (Skp/Cullin/F‐box) E3 ubiquitin ligase that is responsible for marking TOC1 for turnover. CULLIN1 (CUL1) is a core component of SCF complexes and is involved in multiple signaling pathways. To assess the contribution of CUL1‐containing SCF complexes to signaling within the plant oscillator, circadian rhythms were examined in the recessive, temperature‐sensitive CUL1 allele axr6‐3. The activity of CUL1 in this mutant declines progressively with increasing ambient temperature, resulting in more severe defects in CUL1‐dependent activities at elevated temperature. Examination of circadian rhythms in axr6‐3 revealed circadian phenotypes comparable to those observed in ztl null mutants; namely, lengthened circadian period, altered expression of core oscillator genes, and limited degradation of TOC1. In addition, treatment of seedlings with exogenous auxin did not alter TOC1 stability. These results demonstrate that CUL1 is required for TOC1 degradation and further suggest that this protein is the functional cullin for the SCFZTL complex.
Effect of Compaction and Tillage on the Yield and Percolation Loss of Rice in Lateritic Sandy Loam Soil
Authors: Bhadoria P. B. S. 
Published: April 2008

AbstractThere is a large area of acid lateritic soils (Acrorthox) around Kharagpur in the state of West Bengal, India, where the top thin layer of soil mostly of detrital material, is underlain by a deep and highly porous lateritic crust (burried). Management of these soils poses a problem for their exceedingly high permeable nature. With the objective of increasing the production of rice in lateritic tract by way of reducing deep percolation, artificially compaction with the help of roller (800 kg) at the surface and subsurface levels were introduced under field conditions. Results indicate that the 6 passes of roller reduced the percolation by more than 3 folds over control. The increase in percolation rate with tillage depth was associated with the change in pore geometry obtained by tillage. The percentage increase in grain yield over the control was about 37 per cent at 4 passes of compaction, the increase was attributed to the reduction of deep percolation losses. The decrease in yield at high level (6 passes) compaction may be attributed to increased mechanical impedence and reduced condition (low Eh) in the compacted soil. Yield of rice has increased significantly with tillage depths at high level (6 passes) compaction probably due to increased root penetration.
A Multivariate Analysis of Soybean Genotypes Grown Under Different Cropping Systems
Authors: Sharma S. K. , Mehta H. , Rana N. D. 
Published: April 2008

AbstractNature and magnitude of genetic diversity was assessed using Mahalanobis's D2 statistics and canonical analysis in 50 genotypes of soybean grown in monoculture and in association with maize. All the genotypes were grouped in 10 clusters in case of monoculture, while 8 clusters were formed for intercropping. Monoculture was more suitable environment for expressing the genetic diversity than intercrop. Some genotypes had consistently the similar clustering pattern in both the cropping systems, while others were affected by the cropping system in expressing the genetic diversity. This was confirmed by the canonical analysis. Days to flowering and maturity, seed yield/plant, plant height and 100‐seed weight were mainly responsible for genetic diversity in monoculture. Besides phenological traits, pod length and width, and seed yield/plant exerted marked influence on the genetic diversity of soybean genotypes grown in association with maize. Geographical distribution was not necessarily reflected by the genetic divergence, though some degree of relationship between geographic diversity and genetic diversity was evident under both the cropping systems. The performance of some genotypes varied from cropping system to another, while that of others remained unaffected. Breeding programmes to develop varieties suitable for sole crop, intercrop and both the cropping systems have been suggested.
Drought Tolerance Aspects in Pearl Millet
Authors: Ibrahim Y. M. , Marcarian V. , Dobrenz A. K. 
Published: April 2008

AbstractDifferent indices for selection of lines grown under low and high water levels were examined from both theoretical and practical standpoints. Pearl millet (Pennisetum americanum (L.) K. Schum) was planted under a sprinkler irrigation gradient in 1983 and 1984. Equations were developed for drought tolerance for both yield and forage production. Correlation coefficients were developed for yield and yield components.The equations showed that drought will generally result in decreased productivity of both grain and forage. Grain yield was found to be positively correlated with seed weight and with the number of seeds in the main head, and negatively correlated with plant height under low water level. Dry matter was positively correlated with tiller number.