bluuebunny/crossref_metadata_2025 huggingface dataset:
Some factors influencing landholder opinion of the native grass Microlaena stipoides
Authors: Allan Catherine , Whalley R. D. B.
Published: March 2005

Microlaena stipoides is widespread in the higher rainfall areas of Australia. It is consistently reported in the literature as providing high quality forage, yet anecdotal evidence suggests a wide range of opinions about the value of M. stipoides among graziers who manage areas with abundant M. stipoides. This paper addresses three questions relating to this divergence of opinion. Are landholders responding to inherent variability within M. stipoides? Is M. stipoides responding to different site and management conditions, prompting landholders to value it preferentially where site or management suit? Or are the landholders' judgments of M. stipoides influenced less by the actual performance of the grass on their properties than by social factors?
Data collected from ten properties in the Victorian Upper Murray included a morphological assessment of M. stipoides samples, quantitative site and pasture information and qualitative data from interviews with property managers. Ecotypic variation and responses to site and management variables were found, but there were no apparent relationships between these parameters and the value judgments made by the landholders. The only physical factor which appeared to have any influence on landholder opinion was the annual rainfall for their property, although this was not through direct impact on other site attributes. It seems that social rather than physical factors may need to be explored in order to understand the factors influencing landholder opinion of M. stipoides.
Problems of population structure exemplified by the invasive tropical shrub Parkinsonia aculeata l. in northern Australia
Authors: Grice A. C. , Campbell S. D. , McKenzie J. R. , Whiteman L. V. , Pattison M. , Headricks K. , Andrew M. H.
Published: March 2005

Age-class frequency distributions are valuable means of describing plant populations because they can be used to infer population history. Variables other than age are also often used to describe plant populations, either because they more accurately reflect an attribute of interest, or because it is difficult to determine age. However, interpretation of frequency distributions based on variables other than age can be problematic. We discuss these problems and illustrate them using data from six populations of the invasive rangeland shrub Parkinsonia aculeata L. We used three different measures of plant size: height, canopy diameter and stem cross-sectional area. Structures based on these measures were compared with structures based on three different estimates of above-ground biomass derived from them. For each variable, structures differed greatly between populations, and for each population, they were strongly dependent on the variable used to describe it. Population structures based on three-dimensional variables (above-ground biomass) tend to be more strongly positively skewed than those based on two-dimensional (area) measures of plant size. These in turn are more strongly positively skewed than those based on one-dimensional (height, diameter) measures. The statistical basis of this general phenomenon is discussed. The results highlight the difficulties of deriving histories and projecting futures of populations from size-class frequency distributions without accompanying knowledge of the temporal patterns of change in size variables as plants grow.
Enhanced T cell-mediated protection against malaria in human challenges by using the recombinant poxviruses FP9 and modified vaccinia virus Ankara
Authors: Webster Daniel P. , Dunachie Susanna , Vuola Jenni M. , Berthoud Tamara , Keating Sheila , Laidlaw Stephen M. , McConkey Samuel J. , Poulton Ian , Andrews Laura , Andersen Rikke F. , Bejon Philip , Butcher Geoff , Sinden Robert , Skinner Michael A. , Gilbert Sarah C. , Hill Adrian V. S.
Published: March 2005

Malaria is a major global health problem for which an effective vaccine is required urgently. Prime-boost vaccination regimes involving plasmid DNA and recombinant modified vaccinia virus Ankara-encoding liver-stage malaria antigens have been shown to be powerfully immunogenic for T cells and capable of inducing partial protection against experimental malaria challenge in humans, manifested as a delay in time to patent parasitemia. Here, we report that substitution of plasmid DNA as the priming vector with a specific attenuated recombinant fowlpox virus, FP9, vaccine in such prime-boost regimes can elicit complete sterile protection that can last for 20 months. Protection at 20 months was associated with persisting memory but not effector T cell responses. The protective efficacy of various immunization regimes correlated with the magnitude of induced immune responses, supporting the strategy of maximizing durable T cell immunogenicity to develop more effective liver-stage vaccines againstPlasmodium falciparummalaria.
Molecular crowding enhances native state stability and refolding rates of globular proteins
Authors: Cheung Margaret S. , Klimov Dmitri , Thirumalai D.
Published: March 2005

The presence of macromolecules in cells geometrically restricts the available space for poplypeptide chains. To study the effects of macromolecular crowding on folding thermodynamics and kinetics, we used an off-lattice model of the all-β-sheet WW domain in the presence of large spherical particles whose interaction with the polypeptide chain is purely repulsive. At all volume fractions, ϕ
c
, of the crowding agents the stability of the native state is enhanced. Remarkably, the refolding rates, which are larger than the value at ϕ
c
= 0, increase nonmonotonically as ϕ
c
increases, reaching a maximum at

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\begin{equation*}{\varphi}_{{\mathrm{c}}}={\varphi}_{{\mathrm{c}}}^{*}\end{equation*}\end{document}

. At high values of ϕ
c
, the depletion-induced intramolecular attraction produces compact structures with considerable structure in the denatured state. Changes in native state stability and folding kinetics at ϕ
c
can be quantitatively mapped onto confinement in a volume-fraction-dependent spherical pore with radius
R
s
≈ (4π/3ϕ
c
)
1/3
R
c
(
R
c
is the radius of the crowding particles) as long as

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\begin{equation*}{\varphi}_{{\mathrm{c}}}{\leq}{\varphi}_{{\mathrm{c}}}^{*}\end{equation*}\end{document}

. We show that the extent of native state stabilization at finite ϕ
c
is comparable with that in a spherical pore. In both situations, rate enhancement is due to destabilization of the denatured states with respect to ϕ
c
= 0.
Proteins of the S100 family regulate the oligomerization of p53 tumor suppressor
Authors: Fernandez-Fernandez Maria Rosario , Veprintsev Dmitry B. , Fersht Alan R.
Published: March 2005

S100B protein is elevated in the brains of patients with early stages of Alzheimer's disease and Down's syndrome. S100A4 is correlated with the development of metastasis. Both proteins bind to p53 tumor suppressor. We found that both S100B and S100A4 bind to the tetramerization domain of p53 (residues 325-355) only when exposed in lower oligomerization states and so they disrupt the tetramerization of p53. In addition, S100B binds to the negative regulatory and nuclear localization domains, which results in a very tight binding to p53 protein sequences that exposed the tetramerization domain in their C terminus. Because the trafficking of p53 depends on its oligomerization state, we suggest that S100B and S100A4 could regulate the subcellular localization of p53. But, the differences in the way these proteins bind to p53 could result in S100B and S1004 having different effects on p53 function in cell-cycle control.
Associations between concentrations of α- and γ-tocopherol and concentrations of glucose, glycosylated haemoglobin, insulin and C-peptide among US adults
Authors: Ford E. S. , Mokdad A. H. , Ajani U. A. , Liu S.
Published: March 2005

Our objective was to study the cross-sectional associations between concentrations of α- and γ-tocopherol and concentrations of glucose, glycosylated haemoglobin, insulin and C-peptide among US adults. We used data for 1289 participants without self-reported diabetes who were aged ≥20 years in the National Health and Nutrition Examination Survey 1999–2000. α-Tocopherol concentration was inversely associated with glucose concentration (β per mmol/l=−0·01064, se 0·00356, P=0·004) after adjusting for age, sex, race or ethnicity, education, smoking status, concentrations of total cholesterol and triacylglycerols, systolic blood pressure, waist circumference, alcohol use, physical activity, time watching television or videos or using a computer, and use of vitamin/mineral/dietary supplements. Among 659 participants who did not report using supplements, this association was no longer significant whereas the concentration of α-tocopherol was inversely associated with concentration of C-peptide (β per mmol/l=−0·01121, se 0·00497, P=0·024). γ-Tocopherol concentration was positively associated with concentration of glucose (β per mmol/l=0·09169, se 0·02711, P=0·001) and glycosylated haemoglobin (β per mmol/l=0·04954, se 0·01284, P<0·001), but not insulin or C-peptide. The relationships between physiologic concentrations of the various forms of vitamin E and measures of glucose intolerance deserve additional investigation.
Physical dormancy in seeds of six genera of Australian Rhamnaceae
Authors: Turner S.R. , Merritt D.J. , Baskin C.C. , Dixon K.W. , Baskin J.M.
Published: March 2005

Physical dormancy (PY) was identified in six genera representative of Australian Rhamnaceae and subsequently was broken, based on identification of key seed dormancy characteristics: (1) isolation and classification of embryo features; (2) imbibition experiments to determine the rate and amount of water uptake in seeds; and (3) determination of optimum temperature regimes for germination. All six species had relatively large spatulate embryos. Imbibition studies showed all species possessed PY (i.e. a water-impervious seed coat) that was broken by a hot-water treatment. Alleviation of PY resulted in high germination (<70%) at 7/18°C, temperatures similar to winter in south-west Western Australia. Germination was suppressed at higher temperatures and in the presence of light. The study adds information to our knowledge of seed dormancy in Australian Rhamnaceae, and highlights the benefits of understanding dormancy states in seeds prior to evaluating dormancy-release mechanisms on wild species used in restoration ecology and horticulture.
TGF-β1 activates two distinct type I receptors in neurons
Authors: König Hans-Georg , Kögel Donat , Rami Abdelhaq , Prehn Jochen H.M.
Published: March 2005

Transforming growth factor-βs (TGF-βs) are pleiotropic cytokines involved in development and maintenance of the nervous system. In several neural lesion paradigms, TGF-β1 exerts potent neuroprotective effects. Neurons treated with TGF-β1 activated the canonical TGF-β receptor I/activin-like kinase receptor 5 (ALK5) pathway. The transcription factor nuclear factor-κB (NF-κB) plays a fundamental role in neuroprotection. Treatment with TGF-β1 enhanced NF-κB activity in gelshift and reporter gene analyses. However, ectopic expression of a constitutively active ALK5 failed to mimic these effects. ALK1 has been described as an alternative TGF-β receptor in endothelial cells. Interestingly, we detected significant basal expression of ALK1 and its injury-induced up-regulation in neurons. Treatment with TGF-β1 also induced a pronounced increase in downstream Smad1 phosphorylation. Overexpression of a constitutively active ALK1 mimicked the effect of TGF-β1 on NF-κB activation and neuroprotection. Our data suggest that TGF-β1 simultaneously activates two distinct receptor pathways in neurons and that the ALK1 pathway mediates TGF-β1–induced NF-κB survival signaling.
Hrp59, an hnRNP M protein in Chironomus and Drosophila, binds to exonic splicing enhancers and is required for expression of a subset of mRNAs
Authors: Kiesler Eva , Hase Manuela E. , Brodin David , Visa Neus
Published: March 2005

Here, we study an insect hnRNP M protein, referred to as Hrp59. Hrp59 is relatively abundant, has a modular domain organization containing three RNA-binding domains, is dynamically recruited to transcribed genes, and binds to premRNA cotranscriptionally. Using the Balbiani ring system of Chironomus, we show that Hrp59 accompanies the mRNA from the gene to the nuclear envelope, and is released from the mRNA at the nuclear pore. The association of Hrp59 with transcribed genes is not proportional to the amount of synthesized RNA, and in vivo Hrp59 binds preferentially to a subset of mRNAs, including its own mRNA. By coimmunoprecipitation of Hrp59–RNA complexes and microarray hybridization against Drosophila whole-genome arrays, we identify the preferred mRNA targets of Hrp59 in vivo and show that Hrp59 is required for the expression of these target mRNAs. We also show that Hrp59 binds preferentially to exonic splicing enhancers and our results provide new insights into the role of hnRNP M in splicing regulation.
The nucleocytoplasmic shuttling protein CIZ reduces adult bone mass by inhibiting bone morphogenetic protein–induced bone formation
Authors: Morinobu Mikihiko , Nakamoto Tetsuya , Hino Kazunori , Tsuji Kunikazu , Shen Zhong-Jian , Nakashima Kazuhisa , Nifuji Akira , Yamamoto Haruyasu , Hirai Hisamaru , Noda Masaki
Published: March 2005

Osteoporosis is a major health problem; however, the mechanisms regulating adult bone mass are poorly understood. Cas-interacting zinc finger protein (CIZ) is a nucleocytoplasmic shuttling protein that localizes at cell adhesion plaques that form where osteoblasts attach to substrate. To investigate the potential role of CIZ in regulating adult bone mass, we examined the bones in CIZ-deficient mice. Bone volume was increased and the rates of bone formation were increased in CIZ-deficient mice, whereas bone resorption was not altered. CIZ deficiency enhanced the levels of mRNA expression of genes encoding proteins related to osteoblastic phenotypes, such as alkaline phosphatase (ALP) as well as osterix mRNA expression in whole long bones. Bone marrow cells obtained from the femora of CIZ-deficient mice revealed higher ALP activity in culture and formed more mineralized nodules than wild-type cells. CIZ deficiency enhanced bone morphogenetic protein (BMP)–induced osteoblastic differentiation in bone marrow cells in cultures, indicating that BMP is the target of CIZ action. CIZ deficiency increased newly formed bone mass after femoral bone marrow ablation in vivo. Finally, BMP-2–induced bone formation on adult mouse calvariae in vivo was enhanced by CIZ deficiency. These results establish that CIZ suppresses the levels of adult bone mass through inhibition of BMP-induced activation of osteoblasts.
Inhibition of platelet-derived growth factor signaling attenuates pulmonary fibrosis
Authors: Abdollahi Amir , Li Minglun , Ping Gong , Plathow Christian , Domhan Sophie , Kiessling Fabian , Lee Leslie B. , McMahon Gerald , Gröne Hermann-Josef , Lipson Kenneth E. , Huber Peter E.
Published: March 2005

Pulmonary fibrosis is the consequence of a variety of diseases with no satisfying treatment option. Therapy-induced fibrosis also limits the efficacy of chemotherapy and radiotherapy in numerous cancers. Here, we studied the potential of platelet-derived growth factor (PDGF) receptor tyrosine kinase inhibitors (RTKIs) to attenuate radiation-induced pulmonary fibrosis. Thoraces of C57BL/6 mice were irradiated (20 Gy), and mice were treated with three distinct PDGF RTKIs (SU9518, SU11657, or Imatinib). Irradiation was found to induce severe lung fibrosis resulting in dramatically reduced mouse survival. Treatment with PDGF RTKIs markedly attenuated the development of pulmonary fibrosis in excellent correlation with clinical, histological, and computed tomography results. Importantly, RTKIs also prolonged the life span of irradiated mice. We found that radiation up-regulated expression of PDGF (A–D) isoforms leading to phosphorylation of PDGF receptor, which was strongly inhibited by RTKIs. Our findings suggest a pivotal role of PDGF signaling in the pathogenesis of pulmonary fibrosis and indicate that inhibition of fibrogenesis, rather than inflammation, is critical to antifibrotic treatment. This study points the way to a potential new approach for treating idiopathic or therapy-related forms of lung fibrosis.
Asthmatic bronchial epithelial cells have a deficient innate immune response to infection with rhinovirus
Authors: Wark Peter A.B. , Johnston Sebastian L. , Bucchieri Fabio , Powell Robert , Puddicombe Sarah , Laza-Stanca Vasile , Holgate Stephen T. , Davies Donna E.
Published: March 2005

Rhinoviruses are the major trigger of acute asthma exacerbations and asthmatic subjects are more susceptible to these infections. To investigate the underlying mechanisms of this increased susceptibility, we examined virus replication and innate responses to rhinovirus (RV)-16 infection of primary bronchial epithelial cells from asthmatic and healthy control subjects.

Viral RNA expression and late virus release into supernatant was increased 50- and 7-fold, respectively in asthmatic cells compared with healthy controls. Virus infection induced late cell lysis in asthmatic cells but not in normal cells. Examination of the early cellular response to infection revealed impairment of virus induced caspase 3/7 activity and of apoptotic responses in the asthmatic cultures. Inhibition of apoptosis in normal cultures resulted in enhanced viral yield, comparable to that seen in infected asthmatic cultures. Examination of early innate immune responses revealed profound impairment of virus-induced interferon-β mRNA expression in asthmatic cultures and they produced >2.5 times less interferon-β protein. In infected asthmatic cells, exogenous interferon-β induced apoptosis and reduced virus replication, demonstrating a causal link between deficient interferon-β, impaired apoptosis and increased virus replication. These data suggest a novel use for type I interferons in the treatment or prevention of virus-induced asthma exacerbations.
Immunization with a bovine herpesvirus 1 glycoprotein B DNA vaccine induces cytotoxic T-lymphocyte responses in mice and cattle
Authors: Huang Y. , Babiuk L. A. , van Drunen Littel-van den Hurk S.
Published: March 2005

Virus-specific cytotoxic T lymphocytes (CTLs) are considered to be important in protection against and recovery from viral infections. In this study, several approaches to induce cytotoxicity against bovine herpesvirus 1 (BHV-1) were evaluated. Vaccination of C57BL/6 mice with BHV-1 induced a strong humoral, but no CTL, response, which may be due to downregulation of major histocompatibility complex class I molecules. In contrast, vaccinia virus expressing glycoprotein B (gB) elicited a weaker antibody response, but strong cytotoxicity, in mice. As an approach to inducing both strong humoral and cellular immune responses, a plasmid vector was then used to express gB. Both antibody and CTL responses were induced by the plasmid encoding gB in C57BL/6 and C3H mice, regardless of the type of vector backbone. This demonstrated that DNA immunization induces a broad-based immune response to BHV-1 gB. Interestingly, removal of the membrane anchor, which resulted in secretion of gB from transfected cells, did not result in reduced cytotoxicity. Here, it is shown that, compared with the cell-associated counterpart, plasmid-encoded secreted protein may induce enhanced immune responses in cattle. Therefore, calves were immunized intradermally with pMASIAtgB, a plasmid encoding the secreted form of gB (tgB), using a needle-free injection system. This demonstrated that pMASIAtgB elicited both humoral responses and activated gamma interferon-secreting CD8+CTLs, suggesting that a DNA vaccine expressing tgB induces a CTL response in the natural host of BHV-1.
Structural organization of an encephalitic human isolate of Banna virus (genus Seadornavirus, family Reoviridae)
Authors: Jaafar Fauziah Mohd , Attoui Houssam , Mertens Peter P. C. , de Micco Philippe , de Lamballerie Xavier
Published: March 2005

Banna virus (BAV) is the type species of the genus Seadornavirus within the family Reoviridae. The Chinese BAV isolate (BAV-Ch), which causes encephalitis in humans, was shown to have a structural organization and particle morphology reminiscent of that of rotaviruses, with fibre proteins projecting from the surface of the particle. Intact BAV-Ch virus particles contain seven structural proteins, two of which (VP4 and VP9) form the outer coat. The inner (core) particles contain five additional proteins (VP1, VP2, VP3, VP8 and VP10) and are ‘non-turreted’, with a relatively smooth surface appearance. VP2 is the ‘T=2’ protein that forms the innermost ‘subcore’ layer, whilst VP8 is the ‘T=13’ protein forming the core-surface layer. Sequence comparisons indicate that BAV VP9 and VP10 are equivalent to the VP8* and VP5* domains, respectively, of rotavirus outer-coat protein VP4 (GenBank accession no. P12976). VP9 has also been shown to be responsible for virus attachment to the host-cell surface and may be involved in internalization. These similarities reveal a previously unreported genetic link between the genera Rotavirus and Seadornavirus, although the expression of BAV VP9 and VP10 from two separate genome segments, rather than by the proteolytic cleavage of a single gene product (as seen in rotavirus VP4), suggests a significant evolutionary jump between the members of these two genera.
Heterologous gene expression by infectious and replicon vectors derived from tick-borne encephalitis virus and direct comparison of this flavivirus system with an alphavirus replicon
Authors: Gehrke Rainer , Heinz Franz X. , Davis Nancy L. , Mandl Christian W.
Published: March 2005

The flavivirus tick-borne encephaltis virus (TBEV) was established as a vector system for heterologous gene expression. The variable region of the genomic 3′ non-coding region was replaced by an expression cassette consisting of the reporter gene enhanced green fluorescent protein (EGFP) under the translational control of an internal ribosomal entry site element, both in the context of an infectious virus genome and of a replicon lacking the genes of the surface proteins prM/M and E. The expression level and the stability of expression were measured by fluorescence-activated cell-sorting analysis and compared to an established alphavirus replicon vector derived from Venezuelan equine encephaltis virus (VEEV), expressing EGFP under the control of its natural subgenomic promoter. On the first day, the alphavirus replicon exhibited an approximately 180-fold higher expression level than the flavivirus replicon, but this difference decreased to about 20- and 10-fold on days 2 and 3, respectively. Four to six days post-transfection, foreign gene expression by the VEEV replicon vanished almost completely, due to extensive cell killing. In contrast, in the case of the TBEV replicon, the percentage of positive cells and the amount of EGFP expression exhibited only a moderate decline over a time period of almost 4 weeks. The infectious TBEV vector expressed less EGFP than the TBEV replicon at all times. Significant expression from the infectious vector was maintained for four cell-culture passages. The results indicate that the VEEV vector is superior with respect to achieving high expression levels, but the TBEV system may be advantageous for applications that require a moderate, but more enduring, gene expression.
In vitro demonstration of neural transmission of avian influenza A virus
Authors: Matsuda Kazuya , Shibata Takuma , Sakoda Yoshihiro , Kida Hiroshi , Kimura Takashi , Ochiai Kenji , Umemura Takashi
Published: March 2005

Neural involvement following infections of influenza viruses can be serious. The neural transport of influenza viruses from the periphery to the central nervous system has been indicated by using mouse models. However, no direct evidence for neuronal infection has been obtainedin vitroand the mechanisms of neural transmission of influenza viruses have not been reported. In this study, the transneural transmission of a neurotropic influenza A virus was examined using compartmentalized cultures of neurons from mouse dorsal root ganglia, and the results were compared with those obtained using the pseudorabies virus, a virus with well-established neurotransmission. Both viruses reached the cell bodies of the neurons via the axons. This is the first report on axonal transport of influenza A virusin vitro. In addition, the role of the cytoskeleton (microtubules, microfilaments and intermediate filaments) in the neural transmission of influenza virus was investigated by conducting cytoskeletal perturbation experiments. The results indicated that the transport of avian influenza A virus in the neurons was independent of microtubule integrity but was dependent on the integrity of intermediate filaments, whereas pseudorabies virus needed both for neural spread.
Development of bovine herpesvirus 4 as an expression vector using bacterial artificial chromosome cloning
Authors: Gillet L. , Daix V. , Donofrio G. , Wagner M. , Koszinowski U. H. , China B. , Ackermann M. , Markine-Goriaynoff N. , Vanderplasschen A.
Published: March 2005

Several features make bovine herpesvirus 4 (BoHV-4) attractive as a backbone for use as a viral expression vector and/or as a model to study gammaherpesvirus biology. However, these developments have been impeded by the difficulty in manipulating its large genome using classical homologous recombination in eukaryotic cells. In the present study, the feasibility of exploiting bacterial artificial chromosome (BAC) cloning and prokaryotic recombination technology for production of BoHV-4 recombinants was explored. Firstly, the BoHV-4 genome was BAC cloned using two potential insertion sites. Both sites of insertion gave rise to BoHV-4 BAC clones stably maintained in bacteria and able to regenerate virions when transfected into permissive cells. Reconstituted virus replicated comparably to wild-type parental virus and theloxP-flanked BAC cassette was excised by growing them on permissive cells stably expressing Cre recombinase. Secondly, BoHV-4 recombinants expressingIxodes ricinusanti-complement protein I or II (IRAC I/II) were produced using a two-step mutagenesis procedure inEscherichia coli. Both recombinants induced expression of high levels of functional IRAC molecules in the supernatant of infected cells. This study demonstrates that BAC cloning and prokaryotic recombination technology are powerful tools for the development of BoHV-4 as an expression vector and for further fundamental studies of this gammaherpesvirus.
Further studies on hepatitis C virus NS5A–SH3 domain interactions: identification of residues critical for binding and implications for viral RNA replication and modulation of cell signalling
Authors: Macdonald Andrew , Mazaleyrat Sabine , McCormick Christopher , Street Andrew , Burgoyne Nicholas J. , Jackson Richard M. , Cazeaux Virginie , Shelton Holly , Saksela Kalle , Harris Mark
Published: March 2005

The NS5A protein of hepatitis C virus has been shown to interact with a subset of Src homology 3 (SH3) domain-containing proteins. The molecular mechanisms underlying these observations have not been fully characterized, therefore a previous analysis of NS5A–SH3 domain interactions was extended. By using a semi-quantitative ELISA assay, a hierarchy of binding between various SH3 domains for NS5A was demonstrated. Molecular modelling of a polyproline motif within NS5A (termed PP2.2) bound to the FynSH3 domain predicted that the specificity-determining RT-loop region within the SH3 domain did not interact directly with the PP2.2 motif. However, it was demonstrated that the RT loop did contribute to the specificity of binding, implicating the involvement of other intermolecular contacts between NS5A and SH3 domains. The modelling analysis also predicted a critical role for a conserved arginine located at the C terminus of the PP2.2 motif; this was confirmed experimentally. Finally, it was demonstrated that, in comparison with wild-type replicon cells, inhibition of the transcription factor AP-1, a function previously assigned to NS5A, was not observed in cells harbouring a subgenomic replicon containing a mutation within the PP2.2 motif. However, the ability of the mutated replicon to establish itself within Huh-7 cells was unaffected. The highly conserved nature of the PP2.2 motif within NS5A suggests that functions involving this motif are of importance, but are unlikely to play a role in replication of the viral RNA genome. It is more likely that they play a role in altering the cellular environment to favour viral persistence.
Cucumber mosaic virus 2a polymerase and 3a movement proteins independently affect both virus movement and the timing of symptom development in zucchini squash
Authors: Choi Seung Kook , Palukaitis Peter , Min Byoung Eun , Lee Mi Yeon , Choi Jang Kyung , Ryu Ki Hyun
Published: March 2005

The basis for differences in the timing of systemic symptom elicitation in zucchini squash between a pepper strain of Cucumber mosaic virus (Pf-CMV) and a cucurbit strain (Fny-CMV) was analysed. The difference in timing of appearance of systemic symptoms was shown to map to both RNA 2 and RNA 3 of Pf-CMV, with pseudorecombinant viruses containing either RNA 2 or RNA 3 from Pf-CMV showing an intermediate rate of systemic symptom development compared with those containing both or neither Pf-CMV RNAs. Symptom phenotype was shown to map to two single-nucleotide changes, both in codons for Ile at aa 267 and 168 (in Fny-CMV RNAs 2 and 3, respectively) to Thr (in Pf-CMV RNAs 2 and 3). The differential rate of symptom development was shown to be due to differences in the rates of cell-to-cell movement in the inoculated cotyledons, as well as differences in the rate of egress of the virus from the inoculated leaves. These data indicate that both the CMV 3a movement protein and the CMV 2a polymerase protein affect the rate of movement of CMV in zucchini squash and that these two proteins function independently of each other in their interactions with the host, facilitating virus movement.
A role for virus promoters in determining the pathogenesis of Rinderpest virus in cattle
Authors: Banyard Ashley C. , Baron Michael D. , Barrett Thomas
Published: March 2005

Rinderpest virus (RPV) is a morbillivirus that causes cattle plague, a disease of large ruminants. The viral genome is flanked at the 3′ and 5′ genome termini by the genome promoter (GP) and antigenome promoter (AGP), respectively. These promoters play essential roles in directing replication and transcription as well as RNA encapsidation and packaging. It has previously been shown that individual changes to the GP of RPV greatly affect promoter activity in a minigenome assay and it was therefore proposed that individual nucleotide changes in the GP and AGP might also have significant effects on the ability of the virus to replicate and cause disease in cattle. The Plowright vaccine strain of RPV has been derived by tissue-culture passage from the virulent Kabete ‘O’ isolate (KO) and is highly attenuated for all ruminant species in which it has been used. Here, it was shown that swapping the GP and the first 76 nt of the AGP between virulent and avirulent strains affected disease progression. In particular, it was shown that flanking the virulent strain with the vaccine GP and AGP sequences, while not appreciably affecting virus growth in vitro, led to attenuation in vivo. The reverse was not true, since the KO promoters did not alter the vaccine's attenuated nature. The GP/AGP therefore play a role in attenuation, but are not the only determinants of attenuation in this vaccine.
Discovery of Epstein–Barr virus (EBV)-encoded RNA signal and EBV nuclear antigen leader protein DNA sequence in pet dogs
Authors: Chiou Shiow-Her , Chow Kuan-Chih , Yang Chih-Huan , Chiang Shu-Fen , Lin Chun-Hao
Published: March 2005

The aim of this study was to investigate Epstein–Barr virus (EBV)-related virus infection in pet dogs. The presence of antibodies to EBV antigens and EBV-related DNA was determined by Western blot analysis and PCR, respectively. Among 36 pet dogs examined for serum antibodies, 32 (88·9 %) were positive for EBV-specific thymidine kinase, 15 (41·7 %) for EBV-encoded DNA-binding protein and 10 (27·8 %) for EBV-specific DNA polymerase. A BamHI W fragment sequence encoding part of the EBV nuclear antigen leader protein was detected by PCR in corresponding leukocyte DNA samples. Among 21 dogs tested, 15 (71·4 %) were positive for the BamHI W fragment sequence. The specificity of the amplified DNA fragments was confirmed by DNA sequencing. Within the amplified region of the BamHI W fragment (241 bp), DNA sequences detected in 10 dogs had 99·2 % (two nucleotide variations), 99·6 % (one nucleotide variation) or 100 % identity to that of EBV. Furthermore, an EBV-encoded RNA signal was detected by in situ hybridization in dog lymphocytes, as well as in bone-marrow sections, indicating a latent infection with EBV or an EBV-like virus. In conclusion, although the sample size was small, these results showed that a widespread EBV-related gammaherpesvirus could be detected in the peripheral blood and bone marrow of pet dogs. Although no evident zoonotic transmission was detected, further studies are imperative for disclosing the biological significance of this canine EBV-like virus, which may correlate with human disorders.
Cloning, characterization and analysis by RNA interference of various genes of the Chelonus inanitus polydnavirus
Authors: Bonvin Marianne , Marti Dorothee , Wyder Stefan , Kojic Dejan , Annaheim Marc , Lanzrein Beatrice
Published: March 2005

Successful parasitism of some endoparasitic wasps depends on an obligately symbiotic association with polydnaviruses. These unique viruses have a segmented genome consisting of circles of double-stranded (ds) DNA and do not replicate in the parasitized host. They are produced in the wasp's ovary and injected into the host along with the egg. Chelonus inanitus is an egg–larval parasitoid; its polydnavirus (CiV) has been shown to protect the parasitoid larva from the host's immune system and to induce developmental arrest in the prepupal stage. The genome of CiV consists of at least 10–12 segments and five have been sequenced up to now. Here, the complete (CiV12g2) or partial (CiV12g1, CiV16.8g1) cloning of three new CiV genes is reported. All three occur only on one viral segment and have no similarity to other known polydnavirus genes, with the exception of a high similarity of CiV12g1 to CiV14g1 and CiV12g2 to CiV14g2. Furthermore, the first attempt of in vivo application of RNA interference to study the function of polydnavirus genes is shown. Injection of dsRNA of two late- and one early- and late-expressed CiV genes into CiV/venom-containing host eggs partially rescued last-instar larvae from developmental arrest. Injection of the same dsRNAs into parasitized eggs partially reduced parasitoid survival, mainly by preventing the successful emergence of the parasitoid from the host. These viral genes thus seem to be involved in inducing developmental arrest and in keeping the cuticle soft, which appears to be necessary for parasitoid emergence and host feeding.
The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern
Authors: De La Vega Francisco M. , Isaac Hadar , Collins Andrew , Scafe Charles R. , Halldórsson Bjarni V. , Su Xiaoping , Lippert Ross A. , Wang Yu , Laig-Webster Marion , Koehler Ryan T. , Ziegle Janet S. , Wogan Lewis T. , Stevens Junko F. , Leinen Kyle M. , Olson Sheri J. , Guegler Karl J. , You Xiaoqing , Xu Lily H. , Hemken Heinz G. , Kalush Francis , Itakura Mitsuo , Zheng Yi , de Thé Guy , O'Brien Stephen J. , Clark Andrew G. , Istrail Sorin , Hunkapiller Michael W. , Spier Eugene G. , Gilbert Dennis A.
Published: March 2005

The extent and patterns of linkage disequilibrium (LD) determine the feasibility of association studies to map genes that underlie complex traits. Here we present a comparison of the patterns of LD across four major human populations (African-American, Caucasian, Chinese, and Japanese) with a high-resolution single-nucleotide polymorphism (SNP) map covering almost the entire length of chromosomes 6, 21, and 22. We constructed metric LD maps formulated such that the units measure the extent of useful LD for association mapping. LD reaches almost twice as far in chromosome 6 as in chromosomes 21 or 22, in agreement with their differences in recombination rates. By all measures used, out-of-Africa populations showed over a third more LD than African-Americans, highlighting the role of the population's demography in shaping the patterns of LD. Despite those differences, the long-range contour of the LD maps is remarkably similar across the four populations, presumably reflecting common localization of recombination hot spots. Our results have practical implications for the rational design and selection of SNPs for disease association studies.
Chromosome triplication found across the tribe Brassiceae
Authors: Lysak Martin A. , Koch Marcus A. , Pecinka Ales , Schubert Ingo
Published: March 2005

We have used an ∼8.7-Mb BAC contig of Arabidopsis thaliana Chromosome 4 to trace homeologous chromosome regions in 21 species of the family Brassicaceae. Homeologs of this segment could be identified in all tested species. Painting of pachytene chromosomes of Calepina, Conringia, and Sisymbrium species (2n = 14, 16), traditionally placed in tribe Brassiceae, showed one homeologous copy of the Arabidopsis contig, while the remaining taxa of the tribe (2n = 14–30) revealed three, and three Brassica species (2n = 34, 36, and 38) and Erucastrum gallicum (2n = 30) had six copies corresponding to the 8.7-Mb segment. The multiple homeologous copies corresponded structurally to the Arabidopsis segment or were rearranged by inversions and translocations within the diploidized genomes. These chromosome rearrangements accompanied by chromosome fusions/fissions led to the present-day chromosome number variation within the Brassiceae. Phylogenetic relationships based on the chloroplast 5′-trnL (UAA)–trnF(GAA) region and estimated divergence times based on sequence data of the chalcone synthase gene are congruent with comparative painting data and place Calepina, Conringia, and Sisymbrium outside the clade of Brassiceae species with triplicated genomes. Most likely, species containing three or six copy pairs descended from a common hexaploid ancestor with basic genomes similar to that of Arabidopsis. The presumed hexaploidization event occurred after the Arabidopsis–Brassiceae split, between 7.9 and 14.6 Mya.
Corrosion behaviour of carbon steel in polyvinyl alcohol
Authors: Rajendran S. , Sridevi S.P. , Anthony N. , Amalraj A. John , Sundaravadivelu M.
Published: March 2005

Purpose

To evaluate the inhibition efficiency (IE) of polyvinyl alcohol (PVA) in controlling the corrosion of carbon steel immersed in neutral aqueous solutions containing 60 ppm of Cl−, in the absence and presence of Zn2+. To investigate the influence of sodium sulphite (Na2SO3), sodium dodecyl sulphate (SDS), pH and duration of immersion on the IE of PVA‐Zn2+ system. To analyse the protective film formed on the metal surface.

Design/methodology/approach

The IE has been evaluated by weight loss method. The protective film was analysed by FTIR and fluorescence spectra.

Findings

A formulation consisting of 100 ppm of PVA and 75 ppm of Zn2+ offered 81 per cent IE to carbon steel immersed in a solution containing 60 ppm of Cl−. A synergistic effect on inhibition of a combination of PVA and Zn2+ was observed during the tests. The protective film consisted of the Fe2+‐PVA complex and Zn(OH)2. It was found to be UV‐fluorescent. When SDS was added to the PVA‐Zn2+ system, the mixture showed maximum IE at the critical micelle concentration (200 ppm) of SDS (an anionic surfactant). The oxygen‐scavenging effect of Na2SO3 increased as the concentration of Na2SO3 was increased. At lower concentrations of Na2SO3, the transport of the inhibitors played a more major role than did the removal of dissolved oxygen. As the pH value was increased, the IE of the PVA‐Zn2+ system decreased. As the duration of immersion was increased, the IE was observed to decrease.

Research limitations/implications

Electrochemical studies such as polarization and AC impedance spectra will enlighten more on the mechanistic aspects of corrosion inhibition.

Practical implications

If this study is carried out at high temperature under simulated conditions, the findings may find applications in cooling water systems.

Originality/value

The role of transport of inhibitors towards the metal surface from the bulk of the solution, formation of micelles by surfactants, removal of dissolved oxygen by oxygen scavenger, competition between formation of insoluble iron‐inhibitor complex on metal surface and formation of soluble iron chloride in influencing the inhibitive property has been investigated. The protective film was analysed by FTIR spectra and fluorescence spectra.
Ortho‐, meta‐, and para‐aminophenol‐N‐salicylidenes as corrosion inhibitors of zinc in sulfuric acid
Authors: Talati J.D. , Desai M.N. , Shah N.K.
Published: March 2005

Purpose

The evaluation of Schiff bases derived from o‐, m‐ and p‐aminophenols and salicylaldehyde as corrosion inhibitors of zinc in sulfuric acid and to study their action mechanism.

Design/methodology/approach

The effect of various parameters on the behaviour of these inhibitors has been studied using the weight loss and polarization measurements.

Findings

In general, the ortho isomer was highly effective as a corrosion inhibitor because it formed a chelate with a six‐membered ring and moreover the ortho isomer possessed pronounced electromeric effect. These inhibitors obey the Langmuir adsorption isotherm. The almost constant performance with temperature in the case of ortho and para isomers in 0.5 M sulfuric acid suggested strong adsorption bonds. The thermodynamic parameters suggested that this strong interaction of the inhibitor molecules with the metal surface resulted in spontaneous adsorption. It may be concluded that a good inhibitor is characterised by a relatively greater decrease in free energy of adsorption, lower entropy of adsorption and higher heat of adsorption. Polarization data indicated that all these isomers were predominantly cathodic inhibitors. The conjoint effect of external cathodic current and these inhibitors was either synergistic or additive.

Research limitations/implications

Even more powerful Schiff bases need to be synthesised and evaluated as corrosion inhibitors with a number of metals and alloys in diverse media, which may be effective at low concentrations.

Originality/value

Very few inhibitors exhibit such excellent inhibitive effect on zinc in aggressive corrosive media. Rarely do we find such detailed studies.
Scholarly journal usage: the results of deep log analysis
Authors: Nicholas David , Huntington Paul , Watkinson Anthony
Published: March 2005

Purpose

To present the latest results of research conducted at University College London as part of the Virtual Scholar Research Programme, investigating the impact of the digital roll‐out of information services to academics and researchers. This is the second study to look at the information seeking behaviour of academics and researchers in regard to digital journal libraries, and concentrates on the users and usage of Blackwell Synergy.

Design/methodology/approach

Nearly a million users making ten million item requests were investigated employing deep log methods, developed by the authors to provide robust and big picture analyses of digital information consumers and their behaviour.

Findings

Usage data has been embellished with user data (for 500,000 people), so enabling comparisons to be made between the information seeking behaviour, for instance, of students and staff, academics and practitioners, scientists and social scientists. We believe this is the first time this type of analysis has been attempted with logs. Of particular note is the “repeat visitor” evaluation and the analysis of one and a quarter million search sessions which categorised sessions in terms of how “busy” they were for a whole range of user groups.

Research limitations/implications

Demonstrates a powerful and new method, deep log analysis, for mapping and evaluating information seeking behaviour.

Practical implications

Important data for publishers to enable them to target their services more effectively

Originality/value

Probably the first analysis of its type, hence showing an aspect of information seeking not previously seen.
BMW first to adopt data matrix for engine “track and trace”
Authors: Mortimer John
Published: March 2005

Purpose

Describes how BMW is implementing data matrix technology to trace and track major engine components.

Design/methodology/approach

Describes the major production line hardware components of a new system that is being installed at the company's Hams Hall, UK engine plant that will be used in conjunction with Tecnomatix's XFactory intelligent software to provide a comprehensive database both for the purposes of production control as well as for use in service.

Findings

The basic hardware elements of the data matrix system have already been proven out at Hams Hall using RVSI's HawkEye 1510 cutting‐edge cameras and data matrix marking machines supplied by Technifor Ltd of Leamington Spa. Technifor, also supplied the 2D data matrix readers and verifiers from RVSI in Nashua, New Hampshire, USA. The XFactory software was installed in the last month of 2004.

Research limitations/implications

Engineers at BMW plan to expand the technology to enable them to use it for selective machining of cylinder heads for various types of engine. Also, as component suppliers to BMW also adopt the technology, data matrix tracking will be used for a large variety of engine components for use in assembly. It also has implications during CMM inspection to quickly identify which machining operations might be faulty.

Practical implications

Data matrix technology offers a low‐cost approach to the tracking and tracing of complex major engine components during both machining and assembly.

Originality/value

BMW claims it is the first automotive engine supplier in the UK to use data matrix technology to track and trace components.
Solution framework proposal: taking effective control over the project delivery chain with automatic identification and agent‐based solutions
Authors: Ilie Zudor E. , Holmstrom J.
Published: March 2005

Purpose

The objective of this paper is to propose a solution framework for better project delivery control.

Design/methodology/approach

Three emerging technologies that may offer practical solutions are reviewed. These are: automatic product identification, merge‐in‐transit (MIT), and agent based control systems.

Findings

Combining project site level and shipment specific control makes it possible to implement MIT in the project delivery chain. This basic functionality of merging deliveries is needed to react to project delays, and improve rescheduling project resources.

Research limitations/implications

Systems design and trials are needed for further development of the proposed solution framework.

Practical implications

Organizations responsible for coordinating project deliveries need to think about the incentives and costs for logistics service providers, and other business partners to participate in MIT solutions.

Originality/value

The proposed framework is based on an open identification scheme. This makes it possible for new project delivery partners and service providers to locate and start using the controlling software applications without prior notification and arrangement.