bluuebunny/crossref_metadata_2025 huggingface dataset:
Unlocking Public Sector Information
Authors: Tullo Carol
Published: December 2007

Carol Tullo, Director of the Office of Public Sector Information, explains what comprises public sector information and how her office is planning to promote the re-use of such information, to the benefit of the citizens of this country via sophisticated web technologies.
The Status of (Secondary) Community Law in the French Internal Order
Authors: Charpy Chloé
Published: December 2007

Conseil constitutionnel and Conseil d'Etat now both hold that Article 88-1 of the French Constitution contains the duty to implement Community law – The Conseil constitutionnel tests whether acts of parliament manifestly contravene unconditional and precisely phrased provisions of Community law – Duty to implement Community law limited by France's constitutional identity for the Conseil constitutionnel, by the absence of equivalent protection on the Community level for the Conseil d'Etat – Supremacy of the Constitution not affected
Yunying Jia v Migrationsverket – Court of Justice of the European Communities
Authors: Olivier Ben , Reestman Jan Herman
Published: December 2007

What governs the first entrance to the territory of a member state by a third country national who is a family-member of a European citizen who has migrated to that member state: (secondary) Community law or national law? This question, of the utmost constitutional importance as it regards the power to decide on the entrance of foreigners on national territory, one of the pearls in the crown of traditional national sovereignty, was facing the Court of Justice of the European Communities in the case of Yunying Jia v. Migrationsverket. Earlier the Court had sent out different signals. Now, in the long-awaited and remarkably short full Court decision of 9 January 2007, the Court carefully manoeuvred between Scylla (the member states are in full control) and Charybdis (Community law decides all): a member state is not required to make the grant of a residence permit to a third country national subject to the condition of lawful residence in a member state – but it apparently may do so. It is quite unlikely that this judgment once and for all settles the question.
An evaluation of the thermal properties and albedo of a macrotidal flat
Authors: Kim Tae‐Wan , Cho Yang‐Ki , Dever Edward P.
Published: December 2007

The thermal properties of sediment and the albedo are critical in calculating the heat flux of a tidal flat. However, they are not well known because of the difficulties of sampling and observing tidal flats. We use extensive field observations of a macrotidal flat on the western coast of Korea to determine its sediment heat capacity and albedo. The estimated heat capacity of the upper 0.1 m is 3.65 × 106 J m−3 K−1 with a water content of 70%. Heat capacity decreases with depth to 2.96 × 106 J m−3 K−1 at 0.4 m depth. Estimated thermal diffusivities are 0.47–0.63 × 10−6 m2 s−1 and 0.38–0.64 × 10−6 m2 s−1 in spring and summer, respectively. The calculated albedo is a strong function of the solar altitude and the atmospheric transmittance. Atmospheric transmittance is especially important to the albedo when the solar altitude is low. Seasonal mean albedos are 0.13 and 0.15 in spring and summer, respectively. The heat capacity and albedo values obtained above were verified by using them to make independent heat flux estimates at other stations. Estimates based on heat capacity were correlated to albedo‐based heat flux estimates with an r2 greater than 0.7.
Patterns of precursory rockfall prior to slope failure
Authors: Rosser Nick , Lim Michael , Petley David , Dunning Stuart , Allison Robert
Published: December 2007

In this paper we examine data generated using high‐resolution three‐dimensional laser scanning monitoring of coastal rock cliffs. These data are used to identify spatial and temporal patterns in rockfall activity behavior prior to slope failure. Analysis of the data suggests that given sufficient measurement precision precursory behavior, here manifest as the rate of rockfall activity prior to failure, can be detected, measured, and monitored. Environmental conditions appear to have a diminishing influence on the occurrence of increasingly large slope failures. The monitoring data implies a time‐dependent sequence in the occurrence of smaller rockfalls in the period leading to the largest failures recorded. This behavior is attributed to the mechanisms of strain accumulation in the rock mass resulting from brittle failure of the slope. The implication is that combining these data with models of failure mechanisms may allow failure time to be forecast from wide‐area monitoring of precursory behavior. These findings have implications for the management of potentially unstable slopes, the understanding of slope failure mechanisms, and the generation of a new type of slope failure warning systems.
Signal strength and climate calibration of a European tree‐ring isotope network
Authors: Treydte K. , Frank D. , Esper J. , Andreu L. , Bednarz Z. , Berninger F. , Boettger T. , D'Alessandro C. M. , Etien N. , Filot M. , Grabner M. , Guillemin M. T. , Gutierrez E. , Haupt M. , Helle G. , Hilasvuori E. , Jungner H. , Kalela‐Brundin M. , Krapiec M. , Leuenberger M. , Loader N. J. , Masson‐Delmotte V. , Pazdur A. , Pawelczyk S. , Pierre M. , Planells O. , Pukiene R. , Reynolds‐Henne C. E. , Rinne K. T. , Saracino A. , Saurer M. , Sonninen E. , Stievenard M. , Switsur V. R. , Szczepanek M. , Szychowska‐Krapiec E. , Todaro L. , Waterhouse J. S. , Weigl M. , Schleser G. H.
Published: December 2007

We present the first European network of tree ring δ13C and δ18O, containing 23 sites from Finland to Morocco. Common climate signals are found over broad climatic‐ecological ranges. In temperate regions we find positive correlations with summer maximum temperatures and negative correlations with summer precipitation and Palmer Drought Severity Indices (PDSI) with no obvious species‐specific differences. Regional δ13C and δ18O chronologies share high common variance in year‐to‐year variations. Long‐term variations, however, exhibit differences that may reflect spatial variability in environmental forcings, age trends and/or plant physiological responses to increasing atmospheric CO2 concentration. Rotated principal component analysis (RPCA) and climate field correlations enable the identification of four sub‐regions in the δ18O network ‐ northern and eastern Central Europe, Scandinavia and the western Mediterranean. Regional patterns in the δ13C network are less clear and are timescale dependent. Our results indicate that future reconstruction efforts should concentrate on δ18O data in the identified European regions.
Analytical solution for flow of gelling solutions in porous media
Authors: Bolisetti Tirupati , Reitsma Stanley , Balachandar Ram
Published: December 2007

Chemical grouts are polymer solutions that form gel when reacted with cross‐linkers. These gelling liquids are injected into porous media for geotechnical applications such as soil improvement; geoenvironmental (environmental containment) applications and secondary petroleum recovery applications. The polymer solutions and cross‐linkers when injected into porous media react at a predefined time to form gels, usually referred to as gel time. The formation of gels modifies the porous media hydraulic conductivity. In the present study, an analytical solution is developed to obtain the pressures required to inject a gelling solution. While considering the effect of advection, it is assumed that the dispersion does not affect gelation and hence the grout injection. The analytical solution has applications in analyzing the problems, such as effects of gelation time, ratio of gelation time to injection time and verifying the numerical models that simulate flow and transport of solutions with time varying viscosity.
A trajectory‐based estimate of the tropospheric ozone column using the residual method
Authors: Schoeberl M. R. , Ziemke J. R. , Bojkov B. , Livesey N. , Duncan B. , Strahan S. , Froidevaux L. , Kulawik S. , Bhartia P. K. , Chandra S. , Levelt P. F. , Witte J. C. , Thompson A. M. , Cuevas E. , Redondas A. , Tarasick D. W. , Davies J. , Bodeker G. , Hansen G. , Johnson B. J. , Oltmans S. J. , Vömel H. , Allaart M. , Kelder H. , Newchurch M. , Godin‐Beekmann S. , Ancellet G. , Claude H. , Andersen S. B. , Kyrö E. , Parrondos M. , Yela M. , Zablocki G. , Moore D. , Dier H. , von der Gathen P. , Viatte P. , Stübi R. , Calpini B. , Skrivankova P. , Dorokhov V. , de Backer H. , Schmidlin F. J. , Coetzee G. , Fujiwara M. , Thouret V. , Posny F. , Morris G. , Merrill J. , Leong C. P. , Koenig‐Langlo G. , Joseph E.
Published: December 2007

We estimate the tropospheric column ozone using a forward trajectory model to increase the horizontal resolution of the Aura Microwave Limb Sounder (MLS) derived stratospheric column ozone. Subtracting the MLS stratospheric column from Ozone Monitoring Instrument total column measurements gives the trajectory enhanced tropospheric ozone residual (TTOR). Because of different tropopause definitions, we validate the basic residual technique by computing the 200‐hPa‐to‐surface column and comparing it to the same product from ozonesondes and Tropospheric Emission Spectrometer measurements. Comparisons show good agreement in the tropics and reasonable agreement at middle latitudes, but there is a persistent low bias in the TTOR that may be due to a slight high bias in MLS stratospheric column. With the improved stratospheric column resolution, we note a strong correlation of extratropical tropospheric ozone column anomalies with probable troposphere‐stratosphere exchange events or folds. The folds can be identified by their colocation with strong horizontal tropopause gradients. TTOR anomalies due to folds may be mistaken for pollution events since folds often occur in the Atlantic and Pacific pollution corridors. We also compare the 200‐hPa‐to‐surface column with Global Modeling Initiative chemical model estimates of the same quantity. While the tropical comparisons are good, we note that chemical model variations in 200‐hPa‐to‐surface column at middle latitudes are much smaller than seen in the TTOR.
A stratigraphically controlled multiproxy chronostratigraphy for the eastern Mediterranean
Authors: Casford J. S. L. , Abu‐Zied R. , Rohling E. J. , Cooke S. , Fontanier C. , Leng M. , Millard A. , Thomson J.
Published: December 2007

An Accelerator Mass Spectrometry (AMS) 14C dated multiparameter event stratigraphy is developed for the Aegean Sea on the basis of highly resolved (centimeter to subcentimeter) multiproxy data collected from four late glacial to Holocene sediment cores. We quantify the degree of proportionality and synchroneity of sediment accumulation in these cores and use this framework to optimize the confidence levels in regional marine, radiocarbon‐based chronostratigraphies. The applicability of the framework to published, lower‐resolution records from the Aegean Sea is assessed. Next this is extended into the wider eastern Mediterranean, using new and previously published high‐resolution data from the northern Levantine and Adriatic cores. We determine that the magnitude of uncertainties in the intercore comparison of AMS 14C datings based on planktonic foraminifera in the eastern Mediterranean is of the order of ±240 years (2 SE). These uncertainties are attributed to synsedimentary and postsedimentary processes that affect the materials dated. This study also offers a background age control that allows for vital refinements to radiocarbon‐based chronostratigraphy in the eastern Mediterranean, with the potential for similar frameworks to be developed for any other well‐studied region.
Traveling waves on two‐ and three‐dimensional periodic arrays of lossless scatterers
Authors: Shore Robert A. , Yaghjian Arthur D.
Published: December 2007

The kd–βd (dispersion) equations are found for traveling waves on two‐ and three‐dimensional infinite periodic arrays of small lossless acoustic monopoles, electric or magnetic dipoles, and magnetodielectric spheres. Using Floquet mode expansions and then expressions for the rapid summation of Schlömilch series, prohibitively slowly convergent summations are converted to forms that can be used for the efficient calculation of the kd–βd equations. Computer programs have been written to obtain the kd–βd diagrams for all the arrays treated, and representative numerical results are presented and discussed. Expressions, more accurate than the Clausius‐Mossotti relations, are obtained for the effective or bulk permittivity and permeability of the arrays utilizing quantities readily available from the solutions of the kd–βd equations. Exact computable expressions for the fields of three‐dimensional lossless or lossy magnetodielectric sphere arrays that are finite in the direction of the array axis, illuminated by a plane wave parallel to the array axis, are obtained from the analyses performed to obtain the kd–βd curves for the infinite arrays.
Soluble expression of human DRR1 (down‐regulated in renal cell carcinoma 1) in Escherichia coli and preparation of its polyclonal antibodies
Authors: Zhao Xin‐Yu , Li Hong‐Xia , Liang Shu‐Fang , Yuan Zhu , Yan Fei , Ruan Xu‐Zhi , You Jia , Xiong Shao‐Quan , Tang Ming‐Hai , Wei Yu‐Quan
Published: December 2007

Human DRR1 (down‐regulated in renal cell carcinoma 1) is widely expressed in normal tissues but dramatically reduced or even undetectable in a number of different cancer cell lines and primary tumour types. DRR1 from Homo sapiens was cloned into the pQE30 vector for fusion‐protein expression with six histidine residues in Escherichia coli BL21(DE3). A soluble protein with a molecular mass of approx. 19 kDa on SDS/PAGE that matches the expected rDRR1 (recombinant DRR1) molecular mass (18.7 kDa) was obtained. The soluble and insoluble expression of recombinant protein DRR1 (rDRR1) was temperature‐dependent. The expression rDRR1 was in soluble and insoluble forms at 37 °C, and approx. 80% of total rDRR1 was soluble at 37 °C, while rDRR1 was almost exclusively expressing in soluble form at 20 °C. The expressed rDRR1 at 20 °C was affinity‐purified on Ni2+‐charged resin under native conditions. The purified protein was further identified by ESI–MS (electrospray ionization MS). The purified recombinant protein rDRR1 was further used to raise anti‐(human DRR1) polyclonal antibodies, which were suitable for detecting both the recombinant exogenous DRR1 and the endogenous DRR1 from tissues and cells by immunoblotting and immunohistochemistry. The purified rDRR1 and our prepared anti‐(human DRR1) polyclonal antibodies may provide useful tools for future biological function studies on DRR1.
An Integrated Evaluation Method of Accessibility, Quality of Life, and Social Interaction
Authors: Doi Kenji , Kii Masanobu , Nakanishi Hitomi
Published: December 2007

Since accessibility is an essential factor in land-use and transport planning, several methods have been developed to evaluate it. Nevertheless, it has seldom been an essential part of performance measures for policy evaluation from the viewpoint of individuals' quality of life (QoL). The objective of this study is to develop an integrated evaluation method of accessibility, QoL, and social interaction which contributes to the evaluation of land-use and transport policies for livable and sustainable urban development. In this paper, based on quantification of the weights of multielements of QoL, we develop a QoL-based accessibility measure and a QoL performance measure to address appropriate policies of land-use transport coordination and integration by disentangling the mismatch between real urban structures and people's demand for QoL. Furthermore, we explore embryonic ideas for the development of a generalised framework of QoL evaluation, incorporating social interactions and institutional design which link the QoL concept with quality of space and quality of procedure.
Children's Travel to School: Discrete Choice Modeling of Correlated Motorized and Nonmotorized Transportation Modes Using Covariance Heterogeneity
Authors: Ulfarsson Gudmundur F , Shankar Venkataraman N
Published: December 2007

Children's school travel mode is changing, especially away from walking and bicycling and towards private automobiles. Simultaneously we see warning signs from a public health standpoint as children are becoming less active. It has been suggested that walking and bicycling to or from school could help shift this trend, moving it towards greater activity, and researchers are therefore exploring choices of school-trip mode in relation to the pedestrian friendliness of the built environment. Mode-choice models are generally framed as multinomial logit (MNL) models. However, the limitations of MNL models can cause unrealistic effects when walking and bicycling are included with motorized modes. In this paper the focus is on accounting for individual-specific heterogeneity, since different children or families may have very different tastes or tolerances, such as travel time, when it comes to choosing between driving a private automobile, taking the school bus, bicycling, or walking to or from school. The results show that such heterogeneity exists, and that it is more important for nonmotorized modes than for the motorized modes. The results show that accounting for correlation across modes leads to more realistic marginal rates of substitution (cross-elasticities) across modes—in particular, an increase in the walking distance negatively affects the probability both of walking and of bicycling.
Systematics of the Apteropanorpidae (Insecta : Mecoptera) based on morphological and molecular evidence
Authors: Palmer Christopher M. , Trueman John W. H. , Yeates David K.
Published: December 2007

Apteropanorpa Carpenter, 1941 is a genus of scorpionflies endemic to Tasmania. The genus comprised two described species before the current study. However, many anecdotal reports suggested that Apteropanorpa was more widespread in Tasmania than had previously been thought, and that more species awaited discovery and description. Intensive field surveys for the Apteropanorpidae were conducted from 2001 to 2003 in a range of altitudes and habitats all over Tasmania. These surveys yielded a large number of adult specimens, collected at many new localities and at a range of elevations. Cladistic analyses of COI molecular and morphological data were congruent in their inferred species composition of the family. Phylogenetic analyses with evaluation of species concepts provided evidence for two new species: Apteropanorpa warra, sp. nov. and A. hartzi, sp. nov. The distribution of the Apteropanorpidae is much more extensive than was previously thought; many populations discovered as part of this research represent extensions of the known ranges of A. evansi Byers & Yeates and A. tasmanica Carpenter. A key to species is presented. The altitudinal range of each species is closely associated with the local climatic treeline. Hypotheses concerning the biogeography of the family are consistent with the glacial history of Tasmania.
Nanosecond electron tunneling between the hemes in cytochrome
bo
3
Authors: Jasaitis Audrius , Johansson Mikael P. , Wikström Mårten , Vos Marten H. , Verkhovsky Michael I.
Published: December 2007

Biological electron transfer (eT) between redox-active cofactors is thought to occur by quantum-mechanical tunneling. However, in many cases the observed rate is limited by other reactions coupled to eT, such as proton transfer, conformational changes, or catalytic chemistry at an active site. A prominent example of this phenomenon is the eT between the heme groups of mitochondrial cytochrome
c
oxidase, which has been reported to take place in several different time domains. The question of whether pure eT tunneling in the nanosecond regime between the heme groups can be observed has been the subject of some experimental controversy. Here, we report direct observations of eT between the heme groups of the quinol oxidase cytochrome
bo
3
from
Escherichia coli
, where the reaction is initiated by photolysis of carbon monoxide from heme
o
3
. eT from CO-dissociated ferrous heme
o
3
to the low-spin ferric heme
b
takes place at a rate of (1.2 ns)
−1
at 20°C as determined by optical spectroscopy. These results establish heme–heme electron tunneling in the
bo
3
enzyme, a bacterial relative to the mitochondrial cytochrome
c
oxidase. The properties of eT between the closely lying heme groups in the heme–copper oxidases are discussed in terms of the reorganization energy for the process, and two methods for assessing the rate of electron tunneling are presented.
Construction and application of chimeric virus-like particles of tick-borne encephalitis virus and mosquito-borne Japanese encephalitis virus
Authors: Yoshii Kentaro , Goto Akiko , Kawakami Kazue , Kariwa Hiroaki , Takashima Ikuo
Published: December 2007

We have previously reported a system for packaging tick-borne encephalitis (TBE) virus subgenomic replicon RNAs into single-round infectious virus-like particles (VLPs) by using in
trans expression of viral C/prM/E structural proteins. In this study, the trans-packaging system was applied to the generation of chimeric VLPs with mosquito-borne Japanese encephalitis (JE) virus. Although trans-expression of TBE virus C and JE virus prM/E proteins resulted in the secretion of VLPs, the expression of JE virus C/prM/E proteins did not lead to the secretion of VLPs, suggesting that homologous interaction between C and non-structural proteins or the genomic RNA is important for efficient assembly of infectious particles. Neutralization testing showed that the antigenic characteristics of the VLPs were similar to those of the native virus. Furthermore, the infectivities of the TBE virus- and JE virus-enveloped VLPs for the ISE6 tick cell line and C6/36 mosquito cell line were investigated. The VLPs were able to enter only those cells that were derived from the natural vectors for the respective viruses. TBE virus replicon RNA packaged in VLPs produced TBE virus non-structural proteins in tick cells, but could neither replicate nor produce viral proteins in mosquito cells. These findings indicate the importance of specific cellular factors for virus entry and replication during flavivirus infection of arthropods. These results demonstrate that chimeric VLPs are useful tools for the study of viral genome packaging and cellular factors involved in vector specificity, with the additional safety aspect that these chimeric VLPs can be used instead of full-length chimeric viruses.
Seven nucleotide changes characteristic of the hepatitis C virus genotype 3 5′ untranslated region: correlation with reduced in vitro replication
Authors: Masante Cyril , Mahias Kathleen , Lourenço Sofia , Dumas Estelle , Cahour Annie , Trimoulet Pascale , Fleury Hervé , Astier-Gin Thérèse , Ventura Michel
Published: December 2007

Computer analysis of 158 hepatitis C virus (HCV) 5′ untranslated region (5′ UTR) sequences from the six genotypes showed that the 5′ UTR from genotype 3 displays seven specific non-contiguous nucleotide changes, at positions 8, 13, 14, 70, 97, 203 and 224. The purpose of this study was to investigate the impact of these changes on translation and replication activities. Indeed, these modifications could alter both the internal ribosome entry site (IRES) present in the 5′ UTR of the plus-strand RNA and the 3′ end of the minus strand involved in the initiation of plus-strand RNA synthesis. We found that the genotype 3-specific nucleotide changes do not modify the in vitro or ex vivo translation activity of the corresponding IRES, in comparison with that of genotype 1. In contrast, in vitro replication from the minus-strand RNA is eight times less efficient for genotype 3 than for genotype 1 RNA, suggesting the involvement of some nucleotide changes in the reduction of RNA synthesis. Nucleotides 13, 14 and 224 were found to be responsible for this effect. Moreover, a reduced replicative activity was confirmed ex vivo for genotype 3, but to a lesser extent than that observed in vitro, using an RNA minigenome.
Isolation and characterization of the full coding sequence of a novel densovirus from the mosquito Culex pipiens pallens
Authors: Zhai You-gang , Lv Xin-jun , Sun Xiao-hong , Fu Shi-hong , Gong Zheng-da , Fen Yun , Tong Su-xiang , Wang Zhao-xiao , Tang Qing , Attoui Houssam , Liang Guo-dong
Published: December 2007

During an investigation of arboviruses in China, a novel densovirus (DNV) was isolated from the adult female Culex pipiens pallens. The virus, designated Culex pipiens pallens densovirus (CppDNV), caused cytopathic effect in C6/36 cells. The virus particles were icosahedral, non-enveloped and had a mean diameter of 24 nm. The complete coding region of CppDNV was found to be 3335 nt and it contained three open reading frames (ORFs). CppDNV shares 82–93 % identical nucleotides with isolates of the Aedes albopictus densovirus [isolates AalDNV-1, AalDNV-2 (C6/36 DNV) and AalDNV-3], Aedes aegypti densovirus (AaeDNV) and Haemagogus equines densovirus (HeDNV). The nucleotide sequence identity among CppDNV isolates exceeds 98 %. Phylogenetic trees based on non-structural (NS1 and NS2) and capsid (VP) genes show that CppDNV clustered with the species AaeDNV and represents a novel variant of this species within the genus Brevidensovirus.
Functional analysis of human cytomegalovirus pUS28 mutants in infected cells
Authors: Stropes Melissa P. M. , Miller William E.
Published: December 2007

The human cytomegalovirus (HCMV)-encoded viral G protein-coupled receptor pUS28 contributes to an array of biological effects, including cell migration and proliferation. Using FIX-BAC (bacterial artificial chromosome, derived from the HCMV clinical isolate VR1814) and lambda red recombination techniques, we generated HCMV recombinants expressing amino-terminally FLAG-tagged versions of wild-type pUS28 (FLAG–US28/WT), G-protein coupling deficient pUS28 (FLAG–US28/R129A) and chemokine-binding domain deficient pUS28 (FLAG–US28/ΔN). Infection with the FLAG–US28/R129A virus failed to induce inositol phosphate accumulation, indicating that G-protein coupling is essential for pUS28 signalling to phospholipase C-β(PLC-β) during HCMV infection. The FLAG–US28/ΔN virus induced about 80 % of the level of PLC-βsignalling induced by the FLAG–US28/WT virus, demonstrating that the N-terminal chemokine-binding domain is not required for pUS28-induced PLC-βsignalling in infected cells. The data presented here are the first to describe the functional analyses of several key pUS28 mutants in HCMV-infected cells. Elucidating the mechanisms by which pUS28 signals during infection will provide important insights into HCMV pathogenesis.
Molecular characterization of begomoviruses and DNA satellites from Vietnam: additional evidence that the New World geminiviruses were present in the Old World prior to continental separation
Authors: Ha Cuong , Coombs Steven , Revill Peter , Harding Rob , Vu Man , Dale James
Published: December 2007

Sixteen viruses, belonging to 16 species of begomovirus, that infect crops and weeds in Vietnam were identified. Sequence analysis of the complete genomes showed that nine of the viruses (six monopartite and three bipartite) belong to novel species and five of them were identified in Vietnam for the first time. Additionally, eight DNA-βand three nanovirus-like DNA-1 molecules were also found associated with some of the monopartite viruses. Five of the DNA-βmolecules were novel. Importantly, a second bipartite begomovirus,Corchorusgolden mosaic virus, shared several features with the previously characterized virusCorchorusyellow vein virus and with other bipartite begomoviruses from the New World, supporting the hypothesis that New World-like viruses were present in the Old World. This, together with a high degree of virus diversity that included putative recombinant viruses, satellite molecules and viruses with previously undescribed variability in the putative stem–loop sequences, suggested that South-East Asia, and Vietnam in particular, is one of the origins of begomovirus diversity.
Differences in the expression of the hepatitis C virus core+1 open reading frame between a nuclear and a cytoplasmic expression system
Authors: Vassilaki Niki , Kalliampakou Katerina I. , Mavromara Penelope
Published: December 2007

The hepatitis C virus (HCV) genome possesses an open reading frame (ORF) overlapping the core gene at +1 nucleotide (core+1 ORF). Initialin vitrostudies suggested that the core+1 ORF is translated by a ribosomal −2/+1 frameshift mechanism during elongation of the viral polyprotein. Recent studies, however, based on transfection of mammalian cells with reporter constructs have shown that translation of the core+1 ORF is mediated from internal core+1 codons. To resolve the apparent discrepancies associated with the mechanism of core+1 translation, we examined the expression of the HCV-1 and HCV-1a (H) core+1 ORF in a cytoplasmic transcription system based on Huh-7/T7 cells that constitutively synthesize the T7 RNA polymerase in comparison to that in Huh-7 cells. We showed that the efficiency of both the −2/+1 and −1/+2 frameshift events operating at the HCV-1 core codons 8–11 is significantly enhanced in the Huh-7/T7 cytoplasmic transcription system and is dependent on the presence of the consecutive adenine (A) residues within core codons 8–11. In contrast, internal translation initiation at core+1 codons 85/87 occurs in both the nuclear and cytoplasmic transcription systems and is not repressed by the ribosomal frameshifting event. Finally, although core+1 codons 85/87 is the most efficient site for internal initiation of core+1 translation, it may not be unique, as additional internal core+1 codon(s) appear to drive translation at low levels.
Antigenic differences among porcine circovirus type 2 strains, as demonstrated by the use of monoclonal antibodies
Authors: Lefebvre D. J. , Costers S. , Van Doorsselaere J. , Misinzo G. , Delputte P. L. , Nauwynck H. J.
Published: December 2007

This study examined whether antigenic differences among porcine circovirus type 2 (PCV-2) strains could be detected using monoclonal antibodies (mAbs). A subtractive immunization protocol was used for the genotype 2 post-weaning multisystemic wasting syndrome (PMWS)-associated PCV-2 strain Stoon-1010. Sixteen stable hybridomas that produced mAbs with an immunoperoxidase monolayer assay (IPMA) titre of 1000 or more to Stoon-1010 were obtained. Staining of recombinant PCV-2 virus-like particles demonstrated that all mAbs were directed against the PCV-2 capsid protein. Cross-reactivity of mAbs was tested by IPMA and neutralization assay for genotype 1 strains 48285, 1206, VC2002 and 1147, and genotype 2 strains 1121 and 1103. Eleven mAbs (9C3, 16G12, 21C12, 38C1, 43E10, 55B1, 63H3, 70A7, 94H8, 103H7 and 114C8) recognized all strains in the IPMA and demonstrated neutralization of Stoon-1010, 48285, 1206 and 1103, but not VC2002, 1147 and 1121. mAbs 31D5, 48B5, 59C6 and 108E8 did not react with genotype 1 strains or had a reduced affinity compared with genotype 2 strains in the IPMA and neutralization assay. mAb 13H4 reacted in the IPMA with PMWS-associated strains Stoon-1010, 48285, 1206 and VC2002, and the porcine dermatitis and nephropathy syndrome-associated strain 1147, but not with reproductive failure-associated strains 1121 and 1103. mAb 13H4 did not neutralize any of the tested strains. It was concluded that, despite the high amino acid identity of the capsid protein (≥91 %), antigenic differences at the capsid protein level are present among PCV-2 strains with a different genetic and clinical background.
Molecular characterization of the first polyomavirus from a New World primate: squirrel monkey polyomavirus
Authors: Verschoor Ernst J. , Groenewoud Marlous J. , Fagrouch Zahra , Kewalapat Aruna , van Gessel Sabine , Kik Marja J. L. , Heeney Jonathan L.
Published: December 2007

DNA samples from a variety of New World monkeys were screened by using a broad-spectrum PCR targeting the VP1 gene of polyomaviruses. This resulted in the characterization of the first polyomavirus from a New World primate. This virus naturally infects squirrel monkeys (Saimiri sp.) and is provisionally named squirrel monkey polyomavirus (SquiPyV). The complete genome of SquiPyV is 5075 bp in length, and encodes the small T and large T antigens and the three structural proteins VP1, VP2 and VP3. Interestingly, the late region also encodes a putative agnoprotein, a feature that it shares with other polyomaviruses from humans, baboons and African green monkeys. Comparison with other polyomaviruses revealed limited sequence similarity to any other polyomavirus, and phylogenetic analysis of the VP1 gene confirmed its uniqueness.
Putative receptor-binding sites of hepatitis E virus
Authors: He Shuizhen , Miao Ji , Zheng Zizheng , Wu Ting , Xie Minghui , Tang Ming , Zhang Jun , Ng Mun-Hon , Xia Ningshao
Published: December 2007

A truncated structural protein of hepatitis E virus (HEV), p239, occurs as 23 nm particles consisting of partial homodimers. As the latter resemble the HEV capsomere structurally and antigenically, it was postulated that the recombinant protein may serve as a probe for the HEV receptor. This hypothesis was supported by findings that purified p239 bound and penetrated different cell lines that are susceptible to HEV, and inhibited HEV infection of these cells. The binding was blocked by four of six monoclonal antibodies (mAbs) reactive against the dimeric domain of p239, and by two of three mAbs reactive against its monomeric domain, suggesting that binding may involve a portion of each domain. Mutation affecting the monomeric domain had no effect on binding or capacity to block HEV infection, whereas that affecting the dimeric domain diminished binding of the mutant peptide markedly and abrogated its capacity to block HEV infection. These results suggest that HEV infection might involve distinct receptor-binding sites.
Novel reassortant of swine influenza H1N2 virus in Germany
Authors: Zell Roland , Motzke Susann , Krumbholz Andi , Wutzler Peter , Herwig Volker , Dürrwald Ralf
Published: December 2007

European porcine H1N2 influenza viruses arose after multiple reassortment steps involving a porcine influenza virus with avian-influenza-like internal segments and human H1N1 and H3N2 viruses in 1994. In Germany, H1N2 swine influenza viruses first appeared in 2000. Two German H1N2 swine influenza virus strains isolated from pigs with clinical symptoms of influenza are described. They were characterized by the neutralization test, haemagglutination inhibition (HI) test and complete sequencing of the viral genomes. The data demonstrate that these viruses represent a novel H1N2 reassortant. The viruses showed limited neutralization by sera raised against heterologous A/sw/Bakum/1832/00-like H1N2 viruses. Sera pools from recovered pigs showed a considerably lower HI reaction, indicative of diagnostic difficulties in using the HI test to detect these viruses with A/sw/Bakum/1832/00-like H1N2 antigens. Genome sequencing revealed the novel combination of the human-like HAH1 gene of European porcine H1N2 influenza viruses and the NAN2 gene of European porcine H3N2 viruses.
Interferons and viruses: an interplay between induction, signalling, antiviral responses and virus countermeasures
Authors: Randall Richard E. , Goodbourn Stephen
Published: December 2007

The interferon (IFN) system is an extremely powerful antiviral response that is capable of controlling most, if not all, virus infections in the absence of adaptive immunity. However, viruses can still replicate and cause diseasein vivo, because they have some strategy for at least partially circumventing the IFN response. We reviewed this topic in 2000 [Goodbourn, S., Didcock, L. & Randall, R. E. (2000).J Gen Virol81, 2341–2364] but, since then, a great deal has been discovered about the molecular mechanisms of the IFN response and how different viruses circumvent it. This information is of fundamental interest, but may also have practical application in the design and manufacture of attenuated virus vaccines and the development of novel antiviral drugs. In the first part of this review, we describe how viruses activate the IFN system, how IFNs induce transcription of their target genes and the mechanism of action of IFN-induced proteins with antiviral action. In the second part, we describe how viruses circumvent the IFN response. Here, we reflect upon possible consequences for both the virus and host of the different strategies that viruses have evolved and discuss whether certain viruses have exploited the IFN response to modulate their life cycle (e.g. to establish and maintain persistent/latent infections), whether perturbation of the IFN response by persistent infections can lead to chronic disease, and the importance of the IFN system as a species barrier to virus infections. Lastly, we briefly describe applied aspects that arise from an increase in our knowledge in this area, including vaccine design and manufacture, the development of novel antiviral drugs and the use of IFN-sensitive oncolytic viruses in the treatment of cancer.
N-Myristoyltransferase isozymes exhibit differential specificity for human immunodeficiency virus type 1 Gag and Nef
Authors: Seaton Kelly E. , Smith Charles D.
Published: December 2007

Myristoylation of the human immunodeficiency virus type 1 (HIV-1) proteins Gag and Nef byN-myristoyltransferase (NMT) is a key process in retroviral replication and virulence, yet remains incompletely characterized. Therefore, the roles of the two isozymes, NMT1 and NMT2, in myristoylating Gag and Nef were examined using biochemical and molecular approaches. Fluorescently labelled peptides corresponding to the N terminus of HIV-1 Gag or Nef were myristoylated by recombinant human NMT1 and NMT2. Kinetic analyses indicated that NMT1 and NMT2 had 30- and 130-fold lowerKmvalues for Nef than Gag, respectively. Values forKcatindicated that, once Gag or Nef binds to the enzyme, myristoylation by NMT1 and NMT2 proceeds at comparable rates. Furthermore, the catalytic efficiencies for the processing of Gag by NMT1 and NMT2 were equivalent. In contrast, NMT2 had approximately 5-fold higher catalytic efficiency for the myristoylation of Nef than NMT1. Competition experiments confirmed that the Nef peptide acts as a competitive inhibitor for the myristoylation of Gag. Experiments using full-length recombinant Nef protein also indicated a lowerKmfor Nef myristoylation by NMT2 than NMT1. Small interfering RNAs were used to selectively deplete NMT1 and/or NMT2 from HEK293T cells expressing a recombinant Nef–sgGFP fusion protein. Depletion of NMT1 had minimal effect on the intracellular distribution of Nef–sgGFP, whereas depletion of NMT2 altered distribution to a diffuse, widespread pattern, mimicking that of a myristoylation-deficient mutant of Nef–sgGFP. Together, these findings indicate that Nef is preferentially myristoylated by NMT2, suggesting that selective inhibition of NMT2 may provide a novel means of blocking HIV virulence.
β-Catenin is a Nek2 substrate involved in centrosome separation
Authors: Bahmanyar Shirin , Kaplan Daniel D. , DeLuca Jennifer G. , Giddings Thomas H. , O’Toole Eileen T. , Winey Mark , Salmon Edward D. , Casey Patrick J. , Nelson W. James , Barth Angela I.M.
Published: December 2007

β-Catenin plays important roles in cell adhesion and gene transcription, and has been shown recently to be essential for the establishment of a bipolar mitotic spindle. Here we show that β-catenin is a component of interphase centrosomes and that stabilization of β-catenin, mimicking mutations found in cancers, induces centrosome splitting. Centrosomes are held together by a dynamic linker regulated by Nek2 kinase and its substrates C-Nap1 (centrosomal Nek2-associated protein 1) and Rootletin. We show that β-catenin binds to and is phosphorylated by Nek2, and is in a complex with Rootletin. In interphase, β-catenin colocalizes with Rootletin between C-Nap1 puncta at the proximal end of centrioles, and this localization is dependent on C-Nap1 and Rootletin. In mitosis, when Nek2 activity increases, β-catenin localizes to centrosomes at spindle poles independent of Rootletin. Increased Nek2 activity disrupts the interaction of Rootletin with centrosomes and results in binding of β-catenin to Rootletin-independent sites on centrosomes, an event that is required for centrosome separation. These results identify β-catenin as a component of the intercentrosomal linker and define a new function for β-catenin as a key regulator of mitotic centrosome separation.
The Mitochondrion Is a Site of Trypanocidal Action of the Aromatic Diamidine DB75 in Bloodstream Forms of
Trypanosoma brucei
Authors: Lanteri Charlotte A. , Tidwell Richard R. , Meshnick Steven R.
Published: December 2007

Human African trypanosomiasis (HAT) is a fatal tropical disease caused by infection with protozoans of the species
Trypanosoma brucei gambiense
and
T. b. rhodesiense
. An oral prodrug, DB289, is a promising new therapy undergoing phase III clinical trials for early-stage HAT. DB289 is metabolically converted to the active trypanocidal diamidine DB75 [2,5-bis(4-amidinophenyl)furan]. We previously determined that DB75 inhibits yeast mitochondrial function (C. A. Lanteri, B. L. Trumpower, R. R. Tidwell, and S. R. Meshnick, Antimicrob. Agent Chemother. 48:3968-3974, 2004). The purpose of this study was to investigate if DB75 targets the mitochondrion of
T. b. brucei
bloodstream forms. DB75 rapidly accumulates within the mitochondria of living trypanosomes, as indicated by the fluorescent colocalization of DB75 with a mitochondrion-specific dye. Fluorescence-activated cell sorting analysis of rhodamine 123-stained living trypanosomes shows that DB75 and other trypanocidal diamidines (pentamidine and diminazene) collapse the mitochondrial membrane potential. DB75 inhibits ATP hydrolysis within
T. brucei
mitochondria and appears to inhibit the oligomycin-sensitive F
1
F
0
-ATPase and perhaps other ATPases. DB75 is most likely not an inhibitor of electron transport within trypanosome mitochondria, since DB75 fails to inhibit mitochondrial respiration when glycerol-3-phosphate is used as the respiratory substrate. However, DB75 inhibits whole-cell respiration (50% inhibitory concentration, 20 μM) at drug concentrations and incubation durations that also result in the dissipation of the mitochondrial membrane potential. Taken together, these findings suggest that the mitochondrion is a target of the trypanocidal action of DB75.
Antimycobacterial Activity and Mechanism of Action of NAS-91
Authors: Gratraud Paul , Surolia Namita , Besra Gurdyal S. , Surolia Avadhesha , Kremer Laurent
Published: December 2007

The antimalarial agents NAS-91 and NAS-21 were found to express potent antimycobacterial activity, NAS-91 being more active than NAS-21. They partially inhibited mycolic acid biosynthesis and profoundly altered oleic acid production. The development of a cell-free assay for Δ9-desaturase activity allowed direct demonstration of the inhibition of oleic acid biosynthesis by these compounds.
Lincomycin Resistance Gene
lnu
(D) in
Streptococcus uberis
Authors: Petinaki Efthymia , Guérin-Faublée Véronique , Pichereau Vianney , Villers Corinne , Achard Adeline , Malbruny Brigitte , Leclercq Roland
Published: December 2007

Streptococcus uberis
UCN 42, isolated from a case of bovine mastitis, was intermediately resistant to lincomycin (MIC = 2 μg/ml) while remaining susceptible to clindamycin (MIC = 0.06 μg/ml) and erythromycin. A 1.1-kb SacI fragment was cloned from
S. uberis
UCN 42 total DNA on plasmid pUC 18 and introduced into
Escherichia coli
AG100A, where it conferred resistance to both clindamycin and lincomycin. The sequence analysis of the fragment showed the presence of a new gene, named
lnu
(D), that encoded a 164-amino-acid protein with 53% identity with Lnu(C) previously reported to occur in
Streptococcus agalactiae
. Crude lysates of
E. coli
AG100A containing the cloned
lnu
(D) gene inactivated lincomycin and clindamycin in the presence of ATP and MgCl
2
. Mass spectrometry experiments demonstrated that the
lnu
(D) enzyme catalyzed adenylylation of clindamycin. A domain conserved in deduced sequences of lincosamide
O
-nucleotidyltransferases Lnu(A), Lnu(C), LinA
N2
, and Lin(D) and in the aminoglycoside nucleotidyltransferase ANT(2′′) was identified.
Resistance of
Porphyromonas gingivalis
ATCC 33277 to Direct Killing by Antimicrobial Peptides Is Protease Independent
Authors: Bachrach Gilad , Altman Hamutal , Kolenbrander Paul E. , Chalmers Natalia I. , Gabai-Gutner Michal , Mor Amram , Friedman Michael , Steinberg Doron
Published: December 2007

Antimicrobial peptides are short, positively charged, amphipathic peptides that possess a wide spectrum of antimicrobial activity and have an important role in the host's innate immunity. Lack of, or dysfunctions in, antimicrobial peptides have been correlated with infectious diseases, including periodontitis.
Porphyromonas gingivalis
, a gram-negative anaerobe and a major pathogen associated with periodontal diseases, is resistant to antimicrobial peptides of human and nonhuman origin, a feature that likely contributes to its virulence. Expressing a robust proteolytic activity,
P. gingivalis
hydrolyzes antimicrobial peptides. In this study,
P. gingivalis
inactivated three antimicrobial peptides, while a
d
-enantiomer was resistant to degradation.
P. gingivalis
was resistant to the protease-resistant
d
-enantiomer peptide, and importantly, a protease-deficient
P. gingivalis
mutant was also resistant to the antimicrobial peptide. Finally, the binding of a fluorescently labeled antimicrobial peptide to protease-deficient
P. gingivalis
was much weaker than the binding of susceptible
Escherichia coli
. Our results suggest that the resistance of
P. gingivalis
ATCC 33277 to direct killing by antimicrobial peptides is protease independent and results (at least partially) from the low affinity of antimicrobial peptides to
P. gingivalis
.
Increases in
SLT2
Expression and Chitin Content Are Associated with Incomplete Killing of
Candida glabrata
by Caspofungin
Authors: Cota Jason M. , Grabinski Jodi L. , Talbert Robert L. , Burgess David S. , Rogers P. David , Edlind Thomas D. , Wiederhold Nathan P.
Published: December 2007

Incomplete killing was observed for caspofungin against
Candida glabrata
, which was associated with increased
SLT2
expression and elevated chitin content. In contrast, fungicidal activity and no chitin increase were observed in an isogenic Δ
slt2
strain, suggesting a role for
SLT2
and chitin production in the response of
C. glabrata
to caspofungin.