bluuebunny/crossref_metadata_2025 huggingface dataset:
Limits of Performance for Alternate Fuel Energy to Mechanical Work Conversion Systems
Authors: Adebiyi George A.
Published: August 2006

The major alternatives for producing work from fuel energy include combustion systems and fuel cells. Combustion systems are subject to several performance-limiting constraints. Key amongst these is the fact that combustion is an uncontrolled chemical reaction and is typically highly irreversible. The requirement to operate below the metallurgical limit adds to the irreversibility of practical combustion systems. Furthermore, the use of heat exchangers, which must have finite temperature differences between fluid streams, compounds the exergy consumption. The fuel cell conversion system is a major alternative to combustion systems. It operates as a direct conversion device and is often cited as having a potential for 100% second-law efficiency. Realistically, however, the chemical reactions involved are not reversible. More importantly, the available fuel resources must be reformed to make the chemical energy of the fuel convertible to work. The significant exergy input required must be factored into the determination of the overall exergy conversion efficiency attainable. This paper gives a simplified first- and second-law analysis for the limits of efficiency of these alternate systems for the conversion of fuel exergy to mechanical work, thus providing a more realistic comparison of the potential of both systems.
Cross Talk between PML and p53 during Poliovirus Infection: Implications for Antiviral Defense
Authors: Pampin Mathieu , Simonin Yannick , Blondel Bruno , Percherancier Yann , Chelbi-Alix Mounira K.
Published: August 2006

PML nuclear bodies (NBs) are dynamic intranuclear structures harboring numerous transiently or permanently localized proteins. PML, the NBs' organizer, is directly induced by interferon, and its expression is critical for antiviral host defense. We describe herein the molecular events following poliovirus infection that lead to PML-dependent p53 activation and protection against virus infection. Poliovirus infection induces PML phosphorylation through the extracellular signal-regulated kinase pathway, increases PML SUMOylation, and induces its transfer from the nucleoplasm to the nuclear matrix. These events result in the recruitment of p53 to PML NBs, p53 phosphorylation on Ser15, and activation of p53 target genes leading to the induction of apoptosis. Moreover, the knock-down of p53 by small interfering RNA results in higher poliovirus replication, suggesting that p53 participates in antiviral defense. This effect, which requires the presence of PML, is transient since poliovirus targets p53 by inducing its degradation in a proteasome- and MDM2-dependent manner. Our results provide evidence of how poliovirus counteracts p53 antiviral activity by regulating PML and NBs, thus leading to p53 degradation.
The E6 Protein of the Cutaneous Human Papillomavirus Type 8 Can Stimulate the Viral Early and Late Promoters by Distinct Mechanisms
Authors: Müller-Schiffmann Andreas , Beckmann Julia , Steger Gertrud
Published: August 2006

The expression of the proteins encoded by human papillomaviruses (HPVs) is tightly linked to the differentiation program of the infected keratinocytes. The late promoter, expressing the structural proteins, becomes activated in the differentiated keratinocytes, while the early promoter is also active in the basal layers. We have shown previously that the viral transcriptional regulator E2 and the cellular coactivator p300 cooperate in activation of gene expression of HPV8, which infects the skin and is associated with epidermodysplasia verruciformis. Here we demonstrate that this activation is further stimulated after overexpression of the E6 oncoprotein of HPV8 (8E6). RNase protection experiments revealed that 8E6 efficiently cooperates with 8E2 and p300 in activation of the late promoter. In addition, the early promoter, which did not respond to 8E2 and/or p300, was stimulated more than fourfold by 8E6. Our data suggest that both promoters are activated via distinct mechanisms, since the activation of the early promoter was achieved by the N-terminal moiety of 8E6; in contrast, its C-terminal half was sufficient for late promoter activation. This was markedly reduced by the deletion of amino acids 132 to 136 of 8E6, which also abolished the binding to p300, indicating that a direct interaction between 8E6 and p300 is involved. Moreover, a 45-amino-acid segment within the C/H3 region of p300 is required for 8E6 to stimulate the coactivator function of p300. Our results demonstrate for the first time that an E6 oncoprotein of HPV directly contributes to the regulation of HPV gene expression.
Mutational Pathways, Resistance Profile, and Side Effects of Cyanovirin Relative to Human Immunodeficiency Virus Type 1 Strains with N-Glycan Deletions in Their gp120 Envelopes
Authors: Balzarini Jan , Van Laethem Kristel , Peumans Willy J. , Van Damme Els J. M. , Bolmstedt Anders , Gago Federico , Schols Dominique
Published: August 2006

Limited data are available on the genotypic and phenotypic resistance profile of the α-(1-2)mannose oligomer-specific prokaryotic lectin cyanovirin (CV-N). Therefore, a more systematic investigation was carried out to obtain a better view of the interaction between CV-N and human immunodeficiency virus type 1 (HIV-1) gp120. When HIV-1-infected CEM cell cultures were exposed to CV-N in a dose-escalating manner, a total of eight different amino acid mutations exclusively located at N-glycosylation sites in the envelope surface gp120 were observed. Six of the eight mutations resulted in the deletion of high-mannose type N-glycans (i.e., at amino acid positions 230, 332, 339, 386, 392, and 448). Two mutations (i.e., at position 136 and 160) deleted a complex type N-glycan in the variable V1/V2 domain of gp120. The level of phenotypic resistance of the mutated virus strains against CV-N generally correlated with the number of glycan deletions in gp120, although deletion of the glycans at N-230, N-392, and N-448 generally afforded a more pronounced CV-N resistance than other N-glycan deletions. However, the extent of the decrease of antiviral activity of CV-N against the mutated virus strains was markedly less pronounced than observed for α(1-3)- and α(1-6)-mannose-specific plant lectins
Hippeastrum
hybrid agglutinin (HHA) and
Galanthus nivalis
agglutinin (GNA), which points to the existence of a higher genetic barrier for CV-N. This is in agreement with a more consistent suppression of a wider variety of HIV-1 clades by CV-N than by HHA and GNA. Whereas the antiviral and in vitro antiproliferative activity of CV-N can be efficiently reversed by mannan, the pronounced mitogenic activity of CV-N on peripheral blood mononuclear cells was unaffected by mannan, indicating that some of the observed side effects of CV-N are unrelated to its carbohydrate specificity/activity.
Rational Design of Genetically Stable, Live-Attenuated Poliovirus Vaccines of All Three Serotypes: Relevance to Poliomyelitis Eradication
Authors: Macadam Andrew J. , Ferguson Geraldine , Stone David M. , Meredith Janet , Knowlson Sarah , Auda Ghazi , Almond Jeffrey W. , Minor Philip D.
Published: August 2006

The global eradication of poliomyelitis caused by wild-type virus is likely to be completed within the next few years, despite immense logistic and political difficulties, and may ultimately be followed by the cessation of vaccination. However, the existing live-attenuated vaccines have the potential to revert to virulence, causing occasional disease, and viruses can be shed by immunocompromised individuals for prolonged periods of time. Moreover, several outbreaks of poliomyelitis have been shown to be caused by viruses derived from the Sabin vaccine strains. The appearance of such strains depends on the prevailing circumstances but poses a severe obstacle to strategies for stopping vaccination. Vaccine strains that are incapable of reversion at a measurable rate would provide a possible solution. Here, we describe the constructions of strains of type 3 poliovirus that are stabilized by the introduction of four mutations in the 5′ noncoding region compared to the present vaccine. The strains are genetically and phenotypically stable under conditions where the present vaccine loses the attenuating mutation in the 5′ noncoding region completely. Type 1 and type 2 strains in which the entire 5′ noncoding regions of Sabin 1 and Sabin 2 were replaced exactly with that of one of the type 3 strains were also constructed. The genetic stability of 5′ noncoding regions of these viruses matched that of the type 3 strains, but significant phenotypic reversion occurred, illustrating the potential limitations of a rational approach to the genetic stabilization of live RNA virus vaccines.
Abrogation of Viral Interleukin-6 (vIL-6)-Induced Signaling by Intracellular Retention and Neutralization of vIL-6 with an Anti-vIL-6 Single-Chain Antibody Selected by Phage Display
Authors: Kovaleva Marina , Bussmeyer Ingo , Rabe Björn , Grötzinger Joachim , Sudarman Enge , Eichler Jutta , Conrad Udo , Rose-John Stefan , Scheller Jürgen
Published: August 2006

Human herpesvirus 8 (HHV-8) encodes several putative oncogenes, which are homologues to cellular host genes known to function in cell cycle regulation, control of apoptosis, and cytokine signaling. Viral interleukin (vIL-6) is believed to play an important role in the pathogenesis of Kaposi's sarcoma as well as primary effusion lymphoma and multicentric Castleman's disease. Therefore, vIL-6 is a promising target for novel therapies directed against HHV-8-associated diseases. By phage display screening of human synthetic antibody libraries, we have selected a specific recombinant antibody, called monoclonal anti-vIL-6 (MAV), binding to vIL-6. The epitope recognized by MAV was localized on the top of the D helix of the vIL-6 protein, which is a part of receptor binding site III. Consequently, MAV specifically inhibits vIL-6-mediated growth of the primary effusion lymphoma-derived cell line BCBL-1 and blocks STAT3 phosphorylation in the human hepatoma cell line HepG2. Since it was previously found that vIL-6 can also induce signals from within the cell, presumably within the endoplasmic reticulum, we fused the recombinant antibody MAV with the endoplasmic retention sequence KDEL (MAV-KDEL). As a result, COS-7 cells expressing MAV-KDEL and synthesizing vIL-6 ceased to secrete the cytokine. Moreover, we observed that vIL-6 that was bound to MAV-KDEL and retained in the endoplasmic reticulum did not induce STAT3 phosphorylation in HepG2 cells. We conclude that the activity of the intracellularly retained vIL-6 protein is neutralized by MAV-KDEL. Our results might represent a novel therapeutic strategy to neutralize virally encoded growth factors or oncogenes.
All Three Variable Regions of the TRIM5α B30.2 Domain Can Contribute to the Specificity of Retrovirus Restriction
Authors: Ohkura Sadayuki , Yap Melvyn W. , Sheldon Tom , Stoye Jonathan P.
Published: August 2006

Recent studies have revealed the contribution of TRIM5α to retrovirus restriction in cells from a variety of primate species. TRIM5α consists of a tripartite motif (the RBCC domain) followed by a B30.2 domain. The B30.2 domain is thought to be involved in determination of restriction specificity and contains three variable regions. To investigate the relationship between the phylogeny of primate TRIM5α and retrovirus restriction specificity, a series of chimeric TRIM5α consisting of the human RBCC domain followed by the B30.2 domain from various primates was constructed. These constructs showed restriction profiles largely consistent with the origin of the B30.2 domain. Restriction specificity was further investigated with a variety of TRIM5αs containing mixed or mutated B30.2 domains. This study revealed the importance of all three variable regions for determining restriction specificity. Based on the molecular structures of other PRYSPRY domains solved recently, a model for the molecular structure of the B30.2 domain of TRIM5α was developed. The model revealed that the variable regions of the B30.2 domain are present as loops located on one side of the B30.2 core structure. It is hypothesized that these three loops form a binding surface for virus and that evolutionary changes in any one of the loops can alter restriction specificity.
Murine Polyomavirus Requires the Endoplasmic Reticulum Protein Derlin-2 To Initiate Infection
Authors: Lilley Brendan N. , Gilbert Joanna M. , Ploegh Hidde L. , Benjamin Thomas L.
Published: August 2006

The pathways by which viruses enter cells are diverse, but in all cases, infection necessitates the transfer of the viral genome across a cellular membrane. Polyomavirus (Py) particles, after binding to glycolipid and glycoprotein receptors at the cell surface, are delivered to the lumen of the endoplasmic reticulum (ER). The nature and extent of virus disassembly in the ER, how the viral genome is transported to the cytosol and subsequently to the nucleus, and whether any cellular proteins are involved are not known. Here, we identify an ER-resident protein, Derlin-2, a factor implicated in the removal of misfolded proteins from the ER for cytosolic degradation, as a component of the machinery required for mouse Py to establish an infection. Inhibition of Derlin-2 function by expression of either a dominant-negative form of Derlin-2 or a short hairpin RNA that reduces Derlin-2 levels blocks Py infection by 50 to 75%. The block imposed by Derlin-2 inhibition occurs after the virus reaches the ER and can be bypassed by the introduction of Py DNA into the cytosol. These findings suggest a mode of Py entry that involves cytosolic access via the quality control machinery in the ER.
Endoplasmic Reticulum Stress and Neurodegeneration in Rats Neonatally Infected with Borna Disease Virus
Authors: Williams B. L. , Lipkin W. I.
Published: August 2006

Borna disease virus infection of neonatal rats results in a characteristic behavioral syndrome and apoptosis of subsets of neurons in the hippocampus and cerebellum (neonatal Borna disease [NBD]). The cellular mechanisms leading to neurodevelopmental damage in NBD have not been fully elucidated. Insights into this model may have general implications for understanding the pathogenesis of virus-associated neurodevelopmental damage. Here we report the presence of endoplasmic reticulum (ER) stress markers and activation of the unfolded protein response in the NBD hippocampus and cerebellum. Specific findings included enhanced PERK-mediated phosphorylation of eif2α and concomitant regulation of ATF4 translation; IRE1-mediated splicing of XBP1 mRNA; and cleavage of the ATF6 protein in NBD rat brains. We found evidence for regional and cell type-specific divergence in the expression of ER stress-induced proapoptotic and quality control signals. Our results demonstrate that ER stress induction in death-susceptible Purkinje neurons in NBD is associated with the expression of the proapoptotic molecule CHOP in the absence of compensatory expression of the ER quality control molecules Bip and protein disulfide isomerase. In contrast, ER stress in death-resistant astrocytes is associated with complementary expression of CHOP and ER quality control signals. These results implicate an imbalance between ER stress-mediated apoptosis and survival signaling as a critical determinant of neural cell fate in NBD.
Antibody Responses Elicited in Macaques Immunized with Human Immunodeficiency Virus Type 1 (HIV-1) SF162-Derived gp140 Envelope Immunogens: Comparison with Those Elicited during Homologous Simian/Human Immunodeficiency Virus SHIVSF162P4and Heterologous HIV-1 Infection
Authors: Derby Nina R. , Kraft Zane , Kan Elaine , Crooks Emma T. , Barnett Susan W. , Srivastava Indresh K. , Binley James M. , Stamatatos Leonidas
Published: August 2006

The antibody responses elicited in rhesus macaques immunized with soluble human immunodeficiency virus (HIV) Env gp140 proteins derived from the R5-tropic HIV-1 SF162 virus were analyzed and compared to the broadly reactive neutralizing antibody responses elicited during chronic infection of a macaque with a simian/human immunodeficiency virus (SHIV) expressing the HIV-1 SF162 Env, SHIVSF162P4, and humans infected with heterologous HIV-1 isolates. Four gp140 immunogens were evaluated: SF162gp140, ΔV2gp140 (lacking the crown of the V2 loop), ΔV3gp140 (lacking the crown of the V3 loop), and ΔV2ΔV3gp140 (lacking both the V2 and V3 loop crowns). SF162gp140 and ΔV2gp140 have been previously evaluated by our group in a pilot study, but here, a more comprehensive analysis of their immunogenic properties was performed. All four gp140 immunogens elicited stronger anti-gp120 than anti-gp41 antibodies and potent homologous neutralizing antibodies (NAbs) that primarily targeted the first hypervariable region (V1 loop) of gp120, although SF162gp140 also elicited anti-V3 NAbs. Heterologous NAbs were elicited by SF162gp140 and ΔV2gp140 but were weak in potency and narrow in specificity. No heterologous NAbs were elicited by ΔV3gp140 or ΔV2ΔV3gp140. In contrast, the SHIVSF162P4-infected macaque and HIV-infected humans generated similar titers of anti-gp120 and anti-gp41 antibodies and NAbs of significant breadth against primary HIV-1 isolates, which did not target the V1 loop. The difference in V1 loop immunogenicity between soluble gp140 and virion-associated gp160 Env proteins derived from SF162 may be the basis for the observed difference in the breadth of neutralization in sera from the immunized and infected animals studied here.
Development and characterization of EST-SSR markers for the crown rust pathogen of ryegrass (Puccinia coronataf.sp.lolii)
Authors: Dracatos Peter M , Dumsday Jeremy L , Olle Rhiannon S , Cogan Noel O.I , Dobrowolski Mark P , Fujimori Masahiro , Roderick Hywel , Stewart Alan V , Smith Kevin F , Forster John W
Published: August 2006

The causative organism of crown rust in ryegrasses (Puccinia coronata f.sp. lolii) is an obligate biotroph that causes significant economic losses within the temperate grazing industries of dairy, meat, and wool production. This study reports on the development, transferability, and utility of gene-associated simple sequence repeat (SSR) molecular markers for crown rust. Analysis of 1100 expressed sequence tag (EST) sequences from a urediniospore-derived cDNA library detected 55 SSR loci. The majority of EST-SSR arrays contained perfect trinucleotide repeats with consistently low repeat numbers, and the motifs (ACC)nand (CAT)nwere most commonly represented. DNA extraction from single pustules, in conjunction with multiple displacement amplification, provided the basis for PCR-based screening to evaluate genetic marker performance. An example of the identification of intraspecific genetic diversity was obtained from the analysis of 16 P. coronata isolates originating from the United Kingdom, Australia, New Zealand, and Japan. A subset of 12 robust EST-SSR markers was informative for determination of pathogen diversity within and between these localities. It was also demonstrated that crown rust EST-SSR markers were capable of cross-amplification in closely related fungal taxa (Puccinia spp.) and filamentous fungi within the Ascomycota.Key words: Puccinia coronata, simple sequence repeat, expressed sequence tags, urediniospore, genetic diversity, pathogen.
Karyotyping ofNeurospora crassausing synaptonemal complex spreads of translocation quadrivalents
Authors: Lu Benjamin C
Published: August 2006

The purposes of the present research are (i) to establish the karyotype of Neursopora crassa using visualization of kinetochores in the synaptonemal complex (SC) spreads, (ii) to assign each chromosome to a linkage group, and (iii) to examine chromosome pairing and recombination nodules in quadrivalents. Two strains containing reciprocal translocations were used: T(I;II)4637, which involves linkage groups I and II, and alcoy, which contains 3 independent translocations involving I and II, IV and V, and III and VI. Visualization of kinetochores in the spreads requires the use of freshly prepared fixatives. Kinetochore locations and arm ratios were documented in all 7 N. crassa chromosomes. This new information, based on kinetochore position, arm ratios, chromosome length, and quadrivalent analyses, enabled unequivocal confirmation of chromosome assignments to genetic linkage groups. Chromosome pairing in a translocation quadrivalent starts at the 4 terminal regions, and proceeds right up to the translocation break point. Recombination nodules are found in all 4 arms of quadrivalents. The ability to identify a specific chromosome to a genetic linkage group together with the ability to visualize recombination nodules and their locations will allow future cytological analysis of recombination events.Key words: Neurospora, synaptonemal complex, translocation, karyotype, kinetochore, linkage groups, recombination nodules.
LegumeDB1bioinformatics resource: comparative genomic analysis and novel cross-genera marker identification in lupin and pasture legume species
Authors: Moolhuijzen P , Cakir M , Hunter A , Schibeci D , Macgregor A , Smith C , Francki M , Jones M G.K , Appels R , Bellgard M
Published: August 2006

The identification of markers in legume pasture crops, which can be associated with traits such as protein and lipid production, disease resistance, and reduced pod shattering, is generally accepted as an important strategy for improving the agronomic performance of these crops. It has been demonstrated that many quantitative trait loci (QTLs) identified in one species can be found in other plant species. Detailed legume comparative genomic analyses can characterize the genome organization between model legume species (e.g., Medicago truncatula, Lotus japonicus) and economically important crops such as soybean (Glycine max), pea (Pisum sativum), chickpea (Cicer arietinum), and lupin (Lupinus angustifolius), thereby identifying candidate gene markers that can be used to track QTLs in lupin and pasture legume breeding. LegumeDB is a Web-based bioinformatics resource for legume researchers. LegumeDB analysis of Medicago truncatula expressed sequence tags (ESTs) has identified novel simple sequence repeat (SSR) markers (16 tested), some of which have been putatively linked to symbiosome membrane proteins in root nodules and cell-wall proteins important in plant-pathogen defence mechanisms. These novel markers by preliminary PCR assays have been detected in Medicago truncatula and detected in at least one other legume species, Lotus japonicus, Glycine max, Cicer arietinum, and (or) Lupinus angustifolius (15/16 tested). Ongoing research has validated some of these markers to map them in a range of legume species that can then be used to compile composite genetic and physical maps. In this paper, we outline the features and capabilities of LegumeDB as an interactive application that provides legume genetic and physical comparative maps, and the efficient feature identification and annotation of the vast tracks of model legume sequences for convenient data integration and visualization. LegumeDB has been used to identify potential novel cross-genera polymorphic legume markers that map to agronomic traits, supporting the accelerated identification of molecular genetic factors underpinning important agronomic attributes in lupin.Key words: legumes, comparative genomics, bioinformatics, expressed sequence tags (ESTs), simple sequence repeats (SSRs).
Karyotypes, constitutive heterochromatin, and genomic DNA values in the blowfly generaChrysomya,Lucilia, andProtophormia(Diptera: Calliphoridae)
Authors: Ullerich Fritz-Helmut , Schöttke Michael
Published: August 2006

The karyotypes and C-banding patterns of Chrysomya species C. marginalis, C. phaonis, C. pinguis, C. saffranea, C. megacephala (New Guinean strain), Lucilia sericata, and Protophormia terraenovae are described. All species are amphogenic and have similar chromosome complements (2n = 12), including an XY–XX sex-chromosome pair varying in size and morphology between species. Additionally, the C-banding pattern of the monogenic species Chrysomya albiceps is presented. The DNA contents of these and of further species Chrysomya rufifacies, Chrysomya varipes, and Chrysomya putoria were assessed on mitotic metaphases by Feulgen cytophotometry. The average 2C DNA value of the male genomes ranged from 1.04 pg in C. varipes to 2.31 pg in C. pinguis. The DNA content of metaphase X chromosomes varied from 0.013 pg (= 1.23% of the total genome) in C. varipes to 0.277 pg (12.20%) in L. sericata; that of Y chromosomes ranged from 0.003 pg (0.27%) in C. varipes to 0.104 pg (5.59%) in L. sericata. In most species, the corresponding 5 large chromosome pairs showed similar relative DNA contents. The data suggest that the interspecific DNA differences in most species are mainly due to quantitative variation of (repetitive) sequences lying outside the centromeric heterochromatin blocks of the large chromosomes. The results are also discussed with regard to phylogenetic relationships of some species.Key words: DNA content, C value, C banding, sex determination, genome evolution.
Evaluation of amplified fragment length polymorphism and simple sequence repeats for tomato germplasm fingerprinting: utility for grouping closely related traditional cultivars
Authors: García-Martínez Santiago , Andreani Lorella , Garcia-Gusano Marta , Geuna Filippo , Ruiz Juan J
Published: August 2006

Cultivated tomato (Solanum lycopersicum L.) germplasm shows limited genetic variation. Many DNA marker systems have been used for genetic diversity studies in wild and cultivated tomatoes, but their usefulness for characterizing phenotypic differences among very closely related cultivars remains uncertain. We have used 19 selected simple sequence repeat (SSR) markers and 7 amplified fragment length polymorphism (AFLP) primer combinations to characterize 48 cultivars of tomato, mainly traditional cultivars from the south-east of Spain. The main types were Solanum lycopersicum L. 'Muchamiel', 'De la pera', and 'Moruno'. The robustness of the dendrograms and the discrimination power reached with each marker type were similar. Unique fingerprinting even of the most closely related tomato cultivars could be obtained using a combination of some SSR and AFLP markers. A better grouping of the 'Muchamiel' cultivars was observed with SSR markers, whereas the grouping of cultivars of 'De la pera' type was best achieved with AFLPs. However, both types of markers adequately grouped cultivars of the main types, confirming the utility of SSR and AFLP markers for the identification of traditional cultivars of tomato.Key words: genetic variability, molecular markers, Solanum lycopersicum.
DNA typing and genetic relations among European hazelnut (Corylus avellanaL.) cultivars using microsatellite markers
Authors: Boccacci P , Akkak A , Botta R
Published: August 2006

In this work, 78 hazelnut (Corylus avellana L.) cultivars from various germplasm repositories were studied at 16 simple sequence repeat (SSR) loci in order to identify the genotypes and investigate their genetic relations. Polymorphism at SSR loci was evaluated on the basis of number of alleles (mean: 9.4), expected heterozygosity (mean: 0.78), and power of discrimination (mean: 0.91). Several synonyms reported in the literature were confirmed, and new cases of synonymy were identified. The parentage of North American cultivars 'Butler', 'Ennis', and 'Royal', the French selection 'Fercoril-Corabel', and 'Impératrice Eugenie' was investigated on the basis of the alleles present at 16 loci and analysis at 8 additional loci. A dendrogram generated from cluster analysis using the unweighted pair group method with arithmetic mean grouped cultivars according to their pedigrees or geographical origins. There was an evident differentiation of the northern European cultivars from the southern European ones and from the Turkish cultivars. The latter clustered close to but separate from the Italian and Spanish clusters. It is very likely that exchanges of cultivars occurred between the central and western Mediterranean basin as a result of human migration and trade. A database containing the SSR profiles of the most important hazelnut cultivars will be useful for identification of cultivars and synonyms, legal protection, and parentage analysis.Key words: fingerprinting, germplasm characterization, filbert, SSR.
RAPD analysis of jasmine rice-specific genomic structure
Authors: Wu Y J , Chen Y , Wang J , Zhu C X , Xu B L
Published: August 2006

Total genomic DNA was extracted from 29 samples of rice seed, including jasmine rice Oryza sativa L. subsp indica 'KDML105', 'KDML105'-derived varieties, nonaromatic Thailand rice, and japonica rice. Polymorphism in RAPD profiles was analyzed to explore the genomic structure specific to jasmine rice. The degree of band sharing was used to evaluate genetic distance between varieties and to construct a phylogenetic tree. RD15, CNTLR85033, and CNT87040 were found to be closest to 'KDML105', which was consistent with the true relation among them. Four RAPD fragments that cooperatively distinguished jasmine rice from others were cloned and sequenced. PCR amplification using pairs of primers designed specifically further confirmed the credibility of the RAPD result. Comparison through Genbank revealed that a 454 bp RAPD band was similar to the first intron of a putative Cf2/Cf5 disease resistance gene and a 1107 bp RAPD band similar to a wall-associated kinase (wak) gene sequence.Key words: Jasmine rice, RAPD, specific sequence.
Characterization of a maize isochromosome 8S·8S
Authors: Yu Weichang , Han Fangpu , Kato Akio , Birchler James A
Published: August 2006

An isochromosome was found in the maize HiII Parent B line during somatic karyotyping with a multiprobe fluorescence in situ hybridization (FISH) system. Cytological analyses showed that it pairs with the short arm of chromosome 8 during the pachytene stage of meiosis. The chromosome 8 short arm origin of this isochromosome was also confirmed by FISH at mitotic metaphase. Knob heterochromatin signals were present at the short arms of chromosome 8 when subjected to prolonged exposure and also observed at both ends of the isochromosome. This isochromosome can be a univalent or a trivalent by pairing with the normal chromosome 8 short arms during meiosis. At anaphase and telophase, the isochromosome lagged behind other chromosomes. It had a transmission rate of 17%–20% from both male and female gametes. One plant homozygous for the isochromosome contained 2 isochromosomes that differed in the quantity of their CentC centromere repeat sequence. Both variations of the isochromosome were transmitted to the next generation. Because the 2 isochromosomes should be identical by descent, these observations document a radical change in copy number of the centromere repeat array within 1 generation. Plants with 1 isochromosome were not normal as compared with the original HiII Parent B plants. Those that contained a pair of this isochromosome (6 total copies of 8S) were even more abnormal and had reduced fertility. The results indicate the ability of the somatic karyotyping system to recognize and characterize chromosomal aberrations.Key words: maize, isochromosome, FISH, karyotyping, chromosomal aberration.
Distribution, structure, organ-specific expression, and phylogenic analysis of the pathogenesis-related protein-3 chitinase gene family in rice (Oryza sativaL.)
Authors: Nakazaki T , Tsukiyama T , Okumoto Y , Kageyama D , Naito K , Inouye K , Tanisaka T
Published: August 2006

Rice (Oryza sativa L.) pathogenesis-related (PR)-3 chitinases, like other PR proteins, are each coded by one of the genes of a multigene family in the plant genome. We assembled the database information about rice PR-3 chitinase sequences. A total of 12 PR-3 chitinase loci (Cht1 to Cht12) were found deployed in the rice genome. Some of the loci were occupied by 2 or more alleles. For all the loci expect Cht4, Cht5, Cht6, and Cht11, the amino acid sequence was polymorphic between japonica and indica varieties of rice, but glutamic acid acting as a catalytic residue was completely conserved in all the loci expect Cht7. All the genes except Cht7, which was not tested in this study, were transcripted in some organs (leaf, sheath, root, and meristem) of rice plants. These results suggest that chitinase proteins encoded by the genes at these loci have important biological effects, at least antifungal activities, on rice plants. We also proposed a new classification of rice PR-3 chitinases based on their domain structures. This classification was consistent with the results of phylogenetic analysis of rice chitinases.Key words: allelic relationship, classification, organ-specific expression, PR-3 chitinase, rice (Oryza sativa L.).
Chromatin diminution in the copepod Mesocyclops edax: diminution of tandemly repeated DNA families from somatic cells
Authors: Drouin Guy
Published: August 2006

Chromatin diminution, i.e., the loss of selected chromosomal regions during the differentiation of early embryonic cells into somatic cells, has been described in taxa as varied as ciliates, copepods, insects, nematodes, and hagfish. The nature of the eliminated DNA has been extensively studied in ciliate, nematode, and hagfish species. However, the small size of copepods, which makes it difficult to obtain enough DNA from early embryonic cells for cloning and sequencing, has limited such studies. Here, to identify the sequences eliminated from the somatic cells of a copepod species that undergoes chromatin diminution, we randomly amplified DNA fragments from germ line and somatic line cells of Mesocyclops edax, a freshwater cyclopoid copepod. Of 47 randomly amplified germ line clones, 45 (96%) contained short, tandemly repeated sequences composed of either 2 bp CA-repeats, 8 bp CAAATAGA-repeats, or 9 bp CAAATTAAA-repeats. In contrast, of 83 randomly amplified somatic line clones, only 47 (57%) contained such short, tandemly repeated sequences. As previously observed in some nematode species, our results therefore show that there is partial elimination of chromosomal regions containing (CAAATAGA and CAAATTAAA) repeated sequences during the chromatin diminution observed in the somatic cells of M. edax. We speculate that chromatin diminution might have evolved repeatedly by recruitment of RNAi-related mechanisms to eliminate nonfunctional tandemly repeated DNA sequences from the somatic genome of some species.Key words: chromatin diminution, Mesocyclops edax, copepod, satellite DNA, hetorochromatin.
Hand-preference training in the mouse reveals key elements of its learning and memory process and resolves the phenotypic complexity in the behaviour
Authors: Biddle Fred G , Eales Brenda A
Published: August 2006

Handedness in the mouse comprises 2 different behaviours. Some strains have a conditional behaviour, in that the mice learn a direction of hand preference in response to reaching for food, whereas other strains have an innate or constitutive behaviour, and prior experience has no measurable effect on their hand preference. However, hybrids from different strains have revealed both recessive and dominant forms of constitutive hand preference. We proposed that kinetic parameters of the learning process would resolve this genetic heterogeneity as well as the phenotypic complexity in the behaviour. We conducted and report here a detailed kinetic analysis of hand-preference training in the C57BL/6J strain. It revealed elements of the fundamental process of learning and long-term memory that underlies the behaviour by documenting consolidation of memory, blocking of this consolidation by an inhibitor of protein synthesis, retention of memory, and speed of learning in response to training reaches. Furthermore, speed of learning is clearly described by 2 parameters that we call "capacity" (or maximum amount of learned preference) and "ability" (or number of training reaches to achieve half the capacity). These 2 kinetic parameters can vary independently among genetically different strains that learn a preference, and we used them to demonstrate that the respective recessive and dominant forms of constitutive hand-preference may be the consequence of a true null or loss of function and a gain of function, possibly a memory regulator, in the learning process. The quantitative measures provide a sensitive and selective method to establish the fundamental learning process underlying mouse hand preference and to demonstrate empirically how genes and contextual environment shape its phenotypic complexity.Key words: mouse, hand-preference, behavioural genetics, learning, memory, complexity, kinetics, capacity, ability, memory regulator gene.
Reproductive mode of grape phylloxera (Daktulosphaira vitifoliae, Homoptera: Phylloxeridae) in Europe: molecular evidence for predominantly asexual populations and a lack of gene flow between them
Authors: Vorwerk Sonja , Forneck Astrid
Published: August 2006

The genetic structure of European grape phylloxera populations, Daktulosphaira vitifoliae (Homoptera: Phylloxeridae), was analyzed using 6 polymorphic microsatellite markers. Genetic diversity data of 6 populations originating from northern and southern European viticultural regions was assessed for geographic differences, and the structure of 2 additional populations was examined in more detail, focusing on specific host plant and habitat charac ter istics. To test for "signatures" of clonal reproduction, different population genetic measures were applied to the data obtained from these populations. A total of 195 multilocus genotypes were detected in 360 individuals tested. Significant deviations from Hardy–Weinberg equilibrium, negative FISvalues (from –0.148 to –0.658 per population), and the presence of multicopy genotypes revealed that the current major reproductive mode at each of the locations tested was asexual. The high genotypic diversity detected within and among populations, however, together with the occurrence of unique D. vitifoliae genotypes, indicates sexual recombination events took place, probably prior to the multiple introductions into Europe. The absence of overlapping genotypes between the sampling sites suggests low migration rates among the populations studied and implies that the main mode of insect dispersal is through infested plant material carried by human agency. The specific features of European D. vitifoliae habitats are illustrated to discuss the role of habitat and life cycle in the genetic structure of this globally important pest aphid species.Key words: Daktulosphaira vitifoliae, microsatellites, genetic structure, asexual reproduction, parthenogenesis.
Genetic and molecular basis of grain size and grain number and its relevance to grain productivity in higher plants
Authors: Gupta Pushpendra K , Rustgi Sachin , Kumar Neeraj
Published: August 2006

Grain size and grain number constitute 2 important components of grain yield. In particular, the grain size also influences the end-use quality (e.g., flour yield and protein content) and attracts consumer preference. These 2 traits are also the components of the domestication syndrome of crop plants. A number of important studies have recently been conducted to understand the genetic and molecular basis of these 2 important yield-contributing traits. Information generated from these studies was collected and synthesized for the benefit of plant biologists, particularly plant breeders. In the present article, this information is briefly reviewed and the prospects of using this information for improvement of grain productivity in crop plants are discussed.Key words: grain size, grain number, grain productivity, genetics, domestication.
Geographic information system based roadway construction planning
Authors: Seo Jongwon , Kang Sanghyeok
Published: August 2006

The planning process for roadway construction involves a large amount of information on design, construction methods, quantities, unit costs, production rates, and site conditions. Therefore, it is very important to acquire, manage, and process the necessary information efficiently to produce a rigorous construction plan. The geographic information system (GIS) is a very effective tool for integrating and managing various types of information, including spatial and nonspatial data, required for roadway construction planning. This paper proposes a GIS-based system for improving roadway construction planning with its "interactive space scheduling" and "operation level planning" functions, which are supported by the integration of various data required for planning. The proposed system can assist construction planners in a unique way by integrating design and construction information and creating modularized design elements for space scheduling in real time using its interactive space scheduling function. In addition, operation level planning on earthwork can be conducted via the ability of the system to analyze haul routes in three dimensions and selecting the best equipment combination. It is expected that the proposed system could improve the efficiency of roadway construction planning.Key words: geographic information system (GIS), roadway construction planning, information integration, space scheduling.
Analytical solutions using the equivalent strut tie method of infilled steel frames and experimental verification
Authors: Kaltakcı M Y , Köken A , Korkmaz H H
Published: August 2006

Frame systems are commonly used in structural design. Beams and columns are essential in the design and analysis of these types of structures. Since no practical and generally recognized method has yet been developed to determine the failure loads of these systems, nonstructural components such as architectural walls are not usually taken into consideration in the analyses. In this study, the experimental failure loads and failure types of 30 partially or fully infilled steel frame systems were determined after testing these systems under reversed cyclic horizontal loading. After the analytical study was carried out, the failure loads and failure modes of the samples were obtained analytically using the equivalent strut tie method, and experimental and analytical results were compared.Key words: infilled steel frames, partially infilled frames, lateral load-carrying capacity, equivalent strut tie method.
Development of the 2004 Canadian Standards Association (CSA) A23.3 shear provisions for reinforced concrete
Authors: Bentz Evan C , Collins Michael P
Published: August 2006

This paper describes the development of the 2004 Canadian Standards Association (CSA) A23.3 shear design provisions for reinforced and prestressed concrete structures. These methods are similar to the 1994 standard in providing a simplified and general shear design method. They differ from previous standards by providing a direct link between these two methods and simple equations for the calculation of β and θ used in the general method rather than providing these values in a table. The paper explains the basic assumptions behind the new shear provisions, provides a derivation of the new equations, and compares designs made with the new equations to designs obtained from previous standards. In general, the new shear provisions require slightly less shear reinforcement than that required by the previous standard. The new general method is significantly easier to use, particularly with spreadsheets.Key words: shear, building codes, reinforced concrete, size effect, structural design.
Optimal lined channel design
Authors: Aksoy Bülent , Altan-Sakarya A Burcu
Published: August 2006

The optimum values of the section variables (side slope, bottom width, flow depth, and radius) for triangular, rectangular, trapezoidal, and circular channels are computed by minimizing the cost of the channel section. Manning's uniform flow formula is treated as the constraint of the optimization model. The cost function is arranged to include the cost of lining, the cost of earthwork, and the increment in the cost of earthwork with depth below the ground surface. The optimum values of section variables are expressed as explicit functions of unit cost terms. Unique values of optimum section variables are obtained for the case of minimum area or minimum wetted perimeter problems. Key words: open channel design, optimization, minimum cost, best hydraulic section.
Impacts of some parameters affecting the hydraulic performance of U-shaped side spillways
Authors: Montazar A , Neyshabori S A. Salehi
Published: August 2006

Side channel spillways are one type of outlet works at dams with wide applications in irrigation and drainage systems and in water and wastewater facilities. When the flow enters the side channel through the end and two side weirs of the spillway, it is called a three-sided spillway. Based on the results of laboratory experiments, the present study investigates the impacts of variation in end-sill elevation and location and the bed slope of the side channel for different inflow rates into a spillway. In these evaluations, variation in flow regime is taken as a qualitative index and the flow turbulence index is taken as a quantitative index. The values for the latter index were calculated from readings of momentary pressures using a datalogger system. The results showed that the sill elevation had the greatest effect on pressure fluctuations and on the hydraulic performance of the side channel in these spillways. Increasing the sill height decreased the quantitative value of the water turbulence index in the side channel. According to the findings of the present study, the location of the sill in relation to the side channel does not have a considerable effect on pressure fluctuations. It was also found that increasing the channel bed slope reduces pressure fluctuations by about 3%. Greater increases in the bed slope cause increased flow turbulence. Increasing the channel bed slope in the reverse (negative) direction had considerable effects on reducing the channel flow turbulence.Key words: hydraulic performance, pressure fluctuations, spatially varied flow, three-sided channel spillway, U-shaped spillway.
Determining a reasonable concession period for private sector provision of public works and service
Authors: Zhang Xueqing , AbouRizk Simaan M
Published: August 2006

The concession period is one of the most important issues to be addressed in private sector provision of public works and services through concession arrangements as it, to some extent, demarcates the rights and responsibilities between public and private sectors in a project's life cycle, and it is also critical to the project's sustainable development. This paper proposes a methodology for the determination of an appropriate length of the concession based on a win–win principle for parties involved and exercises simulation techniques in measuring and evaluating construction and economic uncertainties and risks. A case study of a hypothetical infrastructure project is provided to demonstrate the application of the proposed methodology, mathematical model, and simulation techniques.Key words: build–own–transfer, concession, critical path method, financial management, infrastructure, Monte Carlo simulation, partnerships, procurement, risk analysis.