bluuebunny/crossref_metadata_2025 huggingface dataset:
Design of a femtosecond laser assisted tomographic atom probe
Authors: Gault B. , Vurpillot F. , Vella A. , Gilbert M. , Menand A. , Blavette D. , Deconihout B.
Published: April 2006

A tomographic atom probe (TAP) in which the atoms are field evaporated by means of femtosecond laser pulses has been designed. It is shown that the field evaporation is assisted by the laser field enhanced by the subwavelength dimensions of the specimen without any significant heating of the specimen. In addition, as compared with the conventional TAP, due to the very short duration of laser pulses, no spread in the energy of emitted ions is observed, leading to a very high mass resolution in a straight TAP in a wide angle configuration. At last, laser pulses can be used to bring the intense electric field required for the field evaporation on poor conductive materials such as intrinsic Si at low temperature. In this article, the performance of the laser TAP is described and illustrated through the investigation of metals, oxides, and silicon materials.
Impact of oxygen supply during growth on the electrical properties of crystalline Gd2O3 thin films on Si(001)
Authors: Czernohorsky M. , Bugiel E. , Osten H. J. , Fissel A. , Kirfel O.
Published: April 2006

We investigated the influence of additional oxygen supply and temperature during the growth of thin Gd2O3 layers on Si(001) with molecular beam epitaxy. Additional oxygen supply during growth improves the dielectric properties significantly; however, too high oxygen partial pressures lead to an increase in the lower permittivity interfacial layer thickness. The growth temperature mainly influences the dielectric gate stack properties due to changes of the Gd2O3∕Si interface structure. Optimized conditions (600°C and pO2=5×10−7mbar) were found to achieve equivalent oxide thickness values below 1nm accompanied by leakage current densities below 1mA∕cm2 at 1V.
Pulsed versus dc I-V characteristics of resistive manganites
Authors: Fisher B. , Genossar J. , Chashka K. B. , Patlagan L. , Reisner G. M.
Published: April 2006

We report on pulsed and dc I-V characteristics of polycrystalline samples of three charge-ordered manganites, Pr2∕3Ca1∕3MnO3, Pr1∕2Ca1∕2MnO3, and Bi1∕2Sr1∕2MnO3, and of a double perovskite, Sr2MnReO6, in a temperature range where their Ohmic resistivity obeys the Efros-Shklovskii variable range hopping relation [J. Phys. C 8, L49 (1975)]. For all samples, the dc I(V) exhibits at high currents negative differential resistance and hysteresis, which mask a perfectly Ohmic or a moderately non-Ohmic conductivity obtained by pulsed measurements. This demonstrates that the widely used dc I-V measurements are usually misleading.
Soft x-ray imaging system for picosecond time-resolved absorption spectroscopy using a femtosecond-laser-plasma source
Authors: Okano Yasuaki , Oguri Katsuya , Nishikawa Tadashi , Nakano Hidetoshi
Published: April 2006

We have developed an imaging system for time-resolved soft x-ray absorption spectroscopy. The system consists of a femtosecond-laser-plasma x-ray source for time-resolved measurements and an x-ray microscope with critical illumination for imaging. The temporal and spatial resolutions were 23ps and better than 12.5μm, respectively. We applied this system to the measurement of an aluminum ablation plume induced by irradiation with a 120fs laser pulse. The shift of the L-shell photoabsorption edge in the expanding plume was observed in the spatiotemporally resolved absorbance spectrum. The space- and time-resolved x-ray absorption spectrum of an expanding laser ablation plume was clearly obtained using the developed system.
Performances of homoepitaxial single crystal diamond in diagnostic x-ray dosimetry
Authors: Garino Y. , Lo Giudice A. , Manfredotti C. , Marinelli Marco , Milani E. , Tucciarone A. , Verona-Rinati G.
Published: April 2006

Pulsed x-ray dose measurements have been carried at maximum x-ray energies from 40to120KeV out by using a single crystal epitaxial diamond sample grown by chemical vapor deposition (CVD). Delivered doses were between 0.1 and 10mGy and pulse duration times between 0.01 and 0.5s. Values of dose linearity index very close to 1 (between 1.02 and 1.07) at increasing x-ray energies and pulse decay times between 15 and 20ms were obtained. The reproducibility was very good with no memory effects. CVD homoepitaxial diamond results to be very promising for x-ray diagnostic applications.
Nicotine inhibits apoptosis induced by chemotherapeutic drugs by up-regulating XIAP and survivin
Authors: Dasgupta Piyali , Kinkade Rebecca , Joshi Bharat , DeCook Christina , Haura Eric , Chellappan Srikumar
Published: April 2006

Non-small cell lung cancer (NSCLC) demonstrates a strong etiologic association with smoking. Although nicotine is not carcinogenic, it can induce cell proliferation and angiogenesis and suppress apoptosis induced by certain agents. Here we show that nicotine inhibits apoptosis induced by the drugs gemcitabine, cisplatin, and taxol, which are used to treat NSCLCs. This protection correlated with the induction of XIAP and survivin by nicotine in a panel of human NSCLC cell lines, and depletion of XIAP and survivin ablated the protective effects of nicotine. The antiapoptotic effects of nicotine were mediated by dihydro β-erythroidine-sensitive α3-containing nicotinic acetylcholine receptors and required the Akt pathway. Chromatin immunoprecipitation assays demonstrated that nicotine stimulation caused an increased recruitment of E2F1 and concomitant dissociation of retinoblastoma tumor suppressor protein (Rb) from survivin promoter in A549 cells. Moreover, ablation of E2F1 levels caused abrogation of the protective effects of nicotine against cisplatin-induced apoptosis in A549 cells whereas ablation of signal transducer and activator of transcription 3 levels had no effect. These studies suggest that exposure to nicotine might negatively impact the apoptotic potential of chemotherapeutic drugs and that survivin and XIAP play a key role in the antiapoptotic activity of nicotine.
Antarctic birds breed later in response to climate change
Authors: Barbraud Christophe , Weimerskirch Henri
Published: April 2006

In the northern hemisphere, there is compelling evidence for climate-related advances of spring events, but no such long-term biological time series exist for the southern hemisphere. We have studied a unique data set of dates of first arrival and laying of first eggs over a 55-year period for the entire community of Antarctic seabirds in East Antarctica. The records over this long period show a general unexpected tendency toward later arrival and laying, an inverse trend to those observed in the northern hemisphere. Overall, species now arrive at their colonies 9.1 days later, on average, and lay eggs an average of 2.1 days later than in the early 1950s. Furthermore, these delays are linked to a decrease in sea ice extent that has occurred in eastern Antarctica, which underlies the contrasted effects of global climate change on species in Antarctica.
Transmissibility of cholera:
In vivo
-formed biofilms and their relationship to infectivity and persistence in the environment
Authors: Faruque Shah M. , Biswas Kuntal , Udden S. M. Nashir , Ahmad Qazi Shafi , Sack David A. , Nair G. Balakrish , Mekalanos John J.
Published: April 2006

The factors that enhance the waterborne spread of bacterial epidemics and sustain the epidemic strain in nature are unclear. Although the epidemic diarrheal disease cholera is known to be transmitted by water contaminated with pathogenic
Vibrio cholerae
, routine isolation of pathogenic strains from aquatic environments is challenging. Here, we show that conditionally viable environmental cells (CVEC) of pathogenic
V. cholerae
that resist cultivation by conventional techniques exist in surface water as aggregates (biofilms) of partially dormant cells. Such CVEC can be recovered as fully virulent bacteria by inoculating the water into rabbit intestines. Furthermore, when
V. cholerae
shed in stools of cholera patients are inoculated in environmental water samples in the laboratory, the cells exhibit characteristics similar to CVEC, suggesting that CVEC are the infectious form of
V. cholerae
in water and that CVEC in nature may have been derived from human cholera stools. We also observed that stools from cholera patients contain a heterogenous mixture of biofilm-like aggregates and free-swimming planktonic cells of
V. cholerae
. Estimation of the relative infectivity of these different forms of
V. cholerae
cells suggested that the enhanced infectivity of
V. cholerae
shed in human stools is largely due to the presence of clumps of cells that disperse
in vivo
, providing a high dose of the pathogen. The results of this study support a model of cholera transmission in which
in vivo
-formed biofilms contribute to enhanced infectivity and environmental persistence of pathogenic
V. cholerae
.
Chaperone-mediated assembly of centromeric chromatinin vitro
Authors: Furuyama Takehito , Dalal Yamini , Henikoff Steven
Published: April 2006

Every eukaryotic chromosome requires a centromere for attachment to spindle microtubules for chromosome segregation. Although centromeric DNA sequences vary greatly among species, centromeres are universally marked by the presence of a centromeric histone variant, centromeric histone 3 (CenH3), which replaces canonical histone H3 in centromeric nucleosomes. Conventional chromatin is maintained in part by histone chaperone complexes, which deposit the S phase-limited (H3) and constitutive (H3.3) forms of histone 3. However, the mechanism that deposits CenH3 specifically at centromeres and faithfully maintains its chromosome location through mitosis and meiosis is unknown. To address this problem, we have biochemically purified a soluble assembly complex that targets tagged CenH3 to centromeres inDrosophilacells. Two different affinity procedures led to purification of the same complex, which consists of CenH3, histone H4, and a single protein chaperone, RbAp48, a highly abundant component of various chromatin assembly, remodeling, and modification complexes. The corresponding CenH3 assembly complex reconstitutedin vitrois sufficient for chromatin assembly activity, without requiring additional components. The simple CenH3 assembly complex is in contrast to the multisubunit complexes previously described for H3 and H3.3, suggesting that centromeres are maintained by a passive mechanism that involves exclusion of the complexes that deposit canonical H3s during replication and transcription.
Sparse time-frequency representations
Authors: Gardner Timothy J. , Magnasco Marcelo O.
Published: April 2006

Auditory neurons preserve exquisite temporal information about sound features, but we do not know how the brain uses this information to process the rapidly changing sounds of the natural world. Simple arguments for effective use of temporal information led us to consider the reassignment class of time-frequency representations as a model of auditory processing. Reassigned time-frequency representations can track isolated simple signals with accuracy unlimited by the time-frequency uncertainty principle, but lack of a general theory has hampered their application to complex sounds. We describe the reassigned representations for white noise and show that even spectrally dense signals produce sparse

reassignments: the representation collapses onto a thin set of lines arranged in a froth-like pattern. Preserving phase information allows reconstruction of the original signal. We define a notion of “consensus,” based on stability of reassignment to time-scale changes, which produces sharp spectral estimates for a wide class of complex mixed signals. As the only currently known class of time-frequency representations that is always “in focus” this methodology has general utility in signal analysis. It may also help explain the remarkable acuity of auditory perception. Many details of complex sounds that are virtually undetectable in standard sonograms are readily perceptible and visible in reassignment.
Vta1p and Vps46p regulate the membrane association and ATPase activity of Vps4p at the yeast multivesicular body
Authors: Lottridge Jillian M. , Flannery Andrew R. , Vincelli Jennifer L. , Stevens Tom H.
Published: April 2006

Previous two-hybrid analysis of the 17 soluble class E Vps yeast proteins revealed that Vps46p/Did2p interacts with Vta1p and the AAA (ATPase associated with a variety of cellular activities) ATPase Vps4p. Here we report that the binding of Vps46p to Vps4p and Vta1p is direct and not mediated by additional proteins, and the binding of Vps46p to Vps4p is ATP independent. Vps46p regulates the membrane association of Vps4p and is required for the interaction of Vta1p with Vps32p/Snf7p of the ESCRT-III complex. Vta1p is a potent activator of Vps4p, stimulating the ATPase activity by 6- to 8-fold. These results reveal functional roles for the Vps46p and Vta1p proteins in regulating the ESCRT complex assembly/disassembly cycle in protein sorting at the yeast late endosome.
Antibodies Against β2‐Glycoprotein I Complexed With an Oxidised Lipoprotein Relate to Intima Thickening of Carotid Arteries in Primary Antiphospholipid Syndrome
Authors: Ames P. R. J. , Alves J. Delgado , Lopez L. R. , Gentile F. , Margarita A. , Pizzella L. , Batuca J. , Scenna G. , Brancaccio V. , Matsuura E.
Published: April 2006

To explore whether antibodies against β2‐glycoprotein I (β2GPI) complexed to 7‐ketocholesteryl‐9‐carboxynonanoate (oxLig‐1) and to oxidised low‐density lipoproteins (oxLDL) relate to paraoxonase activity (PONa) and/or intima media thickness (IMT) of carotid arteries in primary antiphospholipid syndrome (PAPS). As many as 29 thrombotic patients with PAPS, 10 subjects with idiopathic antiphospholipid antibodies (aPL) without thrombosis, 17 thrombotic patients with inherited thrombophilia and 23 healthy controls were investigated. The following were measured in all participants: β2GPI−oxLDL complexes, IgG anti‐β2GPI−oxLig‐1, IgG anti‐β2GPI−oxLDL antibodies (ELISA), PONa, (para‐nitrophenol method), IMT of common carotid (CC) artery, carotid bifurcation (B), internal carotid (IC) by high resolution sonography. β2GPI−oxLDL complex was highest in the control group (p < 0.01), whereas, IgG anti‐β2GPI−oxLig1 and IgG anti‐β2GPI−oxLDL were highest in PAPS (p < 0.0001). In healthy controls, β2GPI−oxLDL complexes positively correlated to IMT of the IC (p = 0.007) and negatively to PONa after correction for age (p < 0.03). PONa inversely correlated with age (p = 0.008). In PAPS, IgG anti‐2GPI−oxLig‐1 independently predicted PONa (p = 0.02) and IMT of B (p = 0.003), CC, (p = 0.03) and of IC (p = 0.04). In PAPS, PONa inversely correlated to the IMT of B, CC and IC (p = 0.01, 0.02 and 0.003, respectively). IgG anti‐2GPI−oxLig‐1 may be involved in PAPS related atherogenesis via decreased PON activity.
Serum Islet Cell Autoantibodies During Interferon α Treatment in Patients With HCV‐Genotype 4 Chronic Hepatitis
Authors: Badra Gamal , Waked Imam , Selmi Carlo , Saleh Saleh M. , El-Shaarawy Ahmed , Lotfy Mahmoud
Published: April 2006

Chronic hepatitis C virus (HCV) infection is a leading cause of end‐stage liver disease worldwide and HCV genotype 4 (HCV4) is predominant in African and Middle Eastern countries. It is well established that interferon‐α (IFNa) treatment for HCV may trigger serum autoantibodies against pancreatic islet cells (ICA) in a subgroup of patients. Available data on the incidence of ICA during IFNa therapy for chronic HCV4 infection are not conclusive. We investigated the appearance of ICA in 40 naïve Egyptian patients (38 males, 32 ± 6 years) with histologically defined chronic HCV4 infection undergoing IFNa treatment at a dose of 9‐million U/week for 24 weeks. Serum samples were collected at baseline and following IFNa therapy and ICA were detected using indirect immunofluorescence. Baseline evaluation indicated that 2/40 (5%) patients had detectable serum ICA. After the completion of the treatment scheme, 12/38 (32%) previously ICA negative patients became ICA positive; however, no patient developed impaired glucose tolerance (IGT) or diabetes during follow‐up. In conclusion, we submit that IFNa treatment for chronic hepatitis C (CHC) may induce serum ICA in one‐third of Egyptian patients with HCV4. These autoantibodies, however, do not lead to alterations in glucose metabolism.
Postulated Vasoactive Neuropeptide Autoimmunity in Fatigue‐Related Conditions: A Brief Review and Hypothesis
Authors: Staines Donald R.
Published: April 2006

Disorders such as chronic fatigue syndrome (CFS) and gulf war syndrome (GWS) are characterised by prolonged fatigue and a range of debilitating symptoms of pain, intellectual and emotional impairment, chemical sensitivities and immunological dysfunction. Sudden infant death syndrome (SIDS) surprisingly may have certain features in common with these conditions. Post‐infection sequelae may be possible contributing factors although ongoing infection is unproven. Immunological aberration may prove to be associated with certain vasoactive neuropeptides (VN) in the context of molecular mimicry, inappropriate immunological memory and autoimmunity.

Adenylate cyclase‐activating VNs including pituitary adenylate cyclase‐activating polypeptide (PACAP), vasoactive intestinal peptide (VIP) and calcitonin gene‐related peptide (CGRP) act as hormones, neurotransmitters, neuroregulators, immune modulators and neurotrophic substances. They and their receptors are potentially immunogenic. VNs are widely distributed in the body particularly in the central and peripheral nervous systems and have been identified in the gut, adrenal gland, blood cells, reproductive system, lung, heart and other tissues. They have a vital role in maintaining cardio‐respiratory function, thermoregulation, memory, concentration and executive functions such as emotional responses including social cues and appropriate behaviour. They are co‐transmitters for a number of neurotransmitters including acetylcholine and gaseous transmitters, are potent immune regulators with primarily anti‐inflammatory activity, and have a significant role in protection of the nervous system against toxic assault as well as being important in the maintenance of homeostasis.

This paper describes a biologically plausible mechanism for the development of certain fatigue‐related syndromes based on loss of immunological tolerance to these VNs or their receptors following infection, other events or de novo resulting in significant pathophysiology possibly mediated via CpG fragments and heat shock (stress) proteins. These conditions extend the public health context of autoimmunity and VN dysregulation and have implications for military medicine where radiological, biological and chemical agents may have a role in pathogenesis. Possible treatment and prevention options are considered.
Antigenic Complementarity in the Origins of Autoimmunity: A General Theory Illustrated With a Case Study of Idiopathic Thrombocytopenia Purpura
Authors: Root-Bernstein Robert , Couturier Jacob
Published: April 2006

We describe a novel, testable theory of autoimmunity, outline novel predictions made by the theory, and illustrate its application to unravelling the possible causes of idiopathic thrombocytopenia purpura (ITP). Pairs of stereochemically complementary antigens induce complementary immune responses (antibody or T‐cell) that create loss of regulation and civil war within the immune system itself. Antibodies attack antibodies creating circulating immune complexes; T‐cells attack T‐cells creating perivascular cuffing. This immunological civil war abrogates the self‐nonself distinction. If at least one of the complementary antigens mimics a self antigen, then this unregulated immune response will target host tissues as well. Data demonstrating that complementary antigens are found in some animal models of autoimmunity and may be present in various human diseases, especially ITP, are reviewed. Specific mechanisms for preventing autoimmunity or suppressing existing autoimmunity are derived from the theory, and critical tests proposed. Finally, we argue that Koch′s postulates are inadequate for establishing disease causation for multiple‐antigen diseases and discuss the possibility that current research has failed to elucidate the causes of human autoimmune diseases because we are using the wrong criteria.
Analysing the ability to retain sidechain hydrogen-bonds in mutant proteins
Authors: Cuff Alison L. , Janes Robert W. , Martin Andrew C.R.
Published: April 2006

Motivation: Hydrogen bonds are one of the most important inter-atomic interactions in biology. Previous experimental, theoretical and bioinformatics analyses have shown that the hydrogen bonding potential of amino acids is generally satisfied and that buried unsatisfied hydrogen-bond-capable residues are destabilizing. When studying mutant proteins, or introducing mutations to residues involved in hydrogen bonding, one needs to know whether a hydrogen bond can be maintained. Our aim, therefore, was to develop a rapid method to evaluate whether a sidechain can form a hydrogen-bond.

Results: A novel knowledge-based approach was developed in which the conformations accessible to the residues involved are taken into account. Residues involved in hydrogen bonds in a set of high resolution crystal structures were analyzed and this analysis is then applied to a given protein. The program was applied to assess mutations in the tumour-suppressor protein, p53. This raised the number of distinct mutations identified as disrupting sidechain–sidechain hydrogen bonding from 181 in our previous analysis to 202 in this analysis.

Availability:  

Contact:  andrew@bioinf.org.uk
SNAP: Combine and Map modules for multilocus population genetic analysis
Authors: Aylor David L. , Price Eric W. , Carbone Ignazio
Published: April 2006

Summary: We have added two software tools to our Suite of Nucleotide Analysis Programs (SNAP) for working with DNA sequences sampled from populations. SNAP Map collapses DNA sequence data into unique haplotypes, extracts variable sites and manipulates output into multiple formats for input into existing software packages for evolutionary analyses. Map collapses DNA sequence data into unique haplotypes, extracts variable sites and manipulates output into multiple formats for input into existing software packages for evolutionary analyses. Map includes novel features such as recoding insertions or deletions, including or excluding variable sites that violate an infinite-sites model and the option of collapsing sequences with corresponding phenotypic information, important in testing for significant haplotype–phenotype associations. SNAP Combine merges multiple DNA sequence alignments into a single multiple alignment file. The resulting file can be the union or intersection of the input files. SNAP Combine currently reads from and writes to several sequence alignment file formats including both sequential and interleaved formats. Combine also keeps track of the start and end positions of each separate alignment file allowing the user to exclude variable sites or taxa, important in creating input files for multilocus analyses.

Availability: SNAP Combine and Map are freely available at . These programs can be downloaded separately for Mac, Windows and Unix operating systems or bundled in SNAP Workbench. Each program includes online documentation and a sample dataset.

Contact:  ignazio_carbone@ncsu.edu

Supplementary information: A description of system requirements and installation instructions can be found at
Adaptive significance of death feigning posture as a specialized inducible defence against gape-limited predators
Authors: Honma Atsushi , Oku Shintaro , Nishida Takayoshi
Published: April 2006

Death feigning is fairly common in a number of taxa, but the adaptive significance of this behaviour is still unclear and has seldom been tested. To date, all proposed hypotheses have assumed that prey manage to escape predation by sending a death-mimicking signal, although death-feigning postures are markedly different from those of dead animals. Moreover, the efficacy of this technique may largely depend on the foraging mode of the predator; death feigning seldom works with sit-and-wait predators that make the decision to attack and consume prey within a very brief time. We examined whether death feigning in the pygmy grasshopper
Criotettix japonicus
Haan was an inducible defence behaviour against the frog
Rana nigromaculata
, a sit-and-wait, gape-limited predator. The characteristic posture assumed by the grasshopper during death feigning enlarges its functional body size by stretching each of three body parts (pronotum, hind legs and lateral spines) in three different directions, thereby making it difficult for the predator to swallow the prey. Our result is the first consistent explanation for why death-mimicking animals do not always mimic the posture of dead animals.
Facultative adjustment of pre-fledging mass loss by nestling swifts preparing for flight
Authors: Wright Jonathan , Markman Shai , Denney Shaun M
Published: April 2006

Nestling birds often maintain nutritional reserves to ensure continual growth during interruptions in parental provisioning. However, mass-dependent flight costs require the loss of excess mass before fledging. Here we test whether individual variable mass loss prior to fledging is controlled through facultative adjustments by nestlings, or whether it reflects physiologically inflexible developmental schedules. We show that in the face of natural and experimental variation in nestling body mass and wing length, swifts always achieve very similar wing loadings (body mass per wing area) prior to fledging, presumably because this represents the optimum for flight. Experimental weights (approx. 5% body mass) temporarily attached to nestlings caused additional reductions in mass, such that final wing loadings still matched those of control siblings. Experimental reductions in nestling wing length (approx. 5% trimmed from feather tips) resulted in similar additional mass reductions, allowing wing loadings at fledging to approach control levels. We suggest that nestlings may assess their body mass relative to wing area via wing flapping and special ‘push-ups’ (on the tips of extended wings) performed in the nest. Thus, by facultatively adjusting body mass, but not wing growth, nestling swifts are always able to fledge with aerodynamically appropriate wing loadings.
Rapid dissemination of a pathogenic simian/human immunodeficiency virus to systemic organs and active replication in lymphoid tissues following intrarectal infection
Authors: Miyake Ariko , Ibuki Kentaro , Enose Yoshimi , Suzuki Hajime , Horiuchi Reii , Motohara Makiko , Saito Naoki , Nakasone Tadashi , Honda Mitsuo , Watanabe Toshiki , Miura Tomoyuki , Hayami Masanori
Published: April 2006

A better understanding of virological events during the early phase of human immunodeficiency virus 1 (HIV-1) infection is important for development of effective antiviral vaccines. In this study, by using quantitative PCR and an infectious plaque assay, virus distribution and replication were examined in various internal organs of rhesus macaques for almost 1 month after intrarectal inoculation of a pathogenic simian immunodeficiency virus/HIV chimeric virus (SHIV-C2/1-KS661c). At 3 days post-inoculation (p.i.), proviral DNA was detected in the rectum, thymus and axillary lymph node. In lymphoid tissues, infectious virus was first detected at 6 days p.i. and a high level of proviral DNA and infectious virus were both detected at 13 days p.i. By 27 days p.i., levels of infectious virus decreased dramatically, although proviral DNA load remained unaltered. In the intestinal tract, levels of infectious virus detected were much lower than in lymphoid tissues, whereas proviral DNA was detected at the same level as in lymphoid tissues throughout the infection. In the thymus and jejunum, CD4CD8 double-positive T cells were depleted earlier than CD4 single-positive cells. These results show that the virus spread quickly to systemic tissues after mucosal transmission. Thereafter, infectious virus was actively produced in the lymphoid tissues, but levels decreased significantly after the peak of viraemia. In contrast, in the intestinal tract, infectious virus was produced at low levels from the beginning of infection. Moreover, virus pathogenesis differed in CD4 single-positive and CD4CD8 double-positive T cells.
Genome-wide mapping of foamy virus vector integrations into a human cell line
Authors: Nowrouzi Ali , Dittrich Marcus , Klanke Chuck , Heinkelein Martin , Rammling Matthias , Dandekar Thomas , von Kalle Christof , Rethwilm Axel
Published: April 2006

Integration-site selection by retroviruses and retroviral vectors has gained increased scientific interest. Foamy viruses (FVs) constitute a unique subfamily (Spumavirinae) of the familyRetroviridae, for which the integration pattern into the human genome has not yet been determined. To accomplish this, 293 cells were transduced with FV vectors and the integration sites into the cellular genome were determined by a high-throughput method based on inverse PCR. For comparison, a limited number of murine leukemia virus (MLV) and human immunodeficiency virus (HIV) integration sites were analysed in parallel. Altogether, 628 FV, 87 HIV and 141 MLV distinct integration sites were mapped to the human genome. The sequences were analysed for RefSeq genes, promoter regions, CpG islands and insertions into cellular oncogenes. Compared with the integration-site preferences of HIV, which strongly favours active genes, and MLV, which favours integration near transcription-start regions, our results indicate that FV integration has neither of these preferences. However, once integration has occurred into a transcribed region of the genome, FVs tend to target promoter-close regions, albeit with less preference than MLV. Furthermore, our study revealed a palindromic consensus sequence for integration, which was centred on the virus-specific, four-base-duplicated target site. In summary, it is shown that the integration pattern of FVs appears to be unique compared with those of other retroviral genera.
Intradermal immune response after infection with Vaccinia virus
Authors: Jacobs Nathalie , Chen Ron A.-J. , Gubser Caroline , Najarro Pilar , Smith Geoffrey L.
Published: April 2006

Although Vaccinia virus (VACV) was used to eradicate smallpox by dermal vaccination, there is little information available about the immune response induced at the vaccination site. Previously, an intradermal murine model that mimics smallpox vaccination was established. Here, this model was used to investigate which leukocytes are recruited to the infected lesion and what are the kinetics of recruitment. Data presented show that VACV infection induced the infiltration of macrophages, followed by granulocytes and lymphocytes. Up to 4 days post-infection, the major lymphocyte population was TCRγδ T cells, but thereafter, there was a large recruitment of CD4+ and CD8+ T cells. Interestingly, the majority of T cells expressed the natural killer-cell marker DX5. This report is the first to characterize the local immune response sequence to VACV infection and represents a benchmark against which the responses induced by genetically modified VACVs may be compared.
Genome of a novel circovirus of starlings, amplified by multiply primed rolling-circle amplification
Authors: Johne Reimar , Fernández-de-Luco Daniel , Höfle Ursula , Müller Hermann
Published: April 2006

The genusCircoviruscomprises small non-enveloped viruses with a circular single-stranded DNA genome. By using PCR with degenerate primers, a novel circovirus (starling circovirus, StCV) was detected in spleen samples of wild starlings (Sturnus vulgarisandSturnus unicolor) found dead during an epidemic outbreak of septicaemic salmonellosis in northeastern Spain. Using a specific PCR, StCV was also detected in apparently healthy birds from the same population. The genome was amplified using multiply primed rolling-circle amplification and cloned. Open reading frames (ORFs) with similarities to the replication-associated protein and the capsid protein of circoviruses as well as an additional ORF encoding a protein of 106 aa were evident from the sequence. Phylogenetic analysis of circovirus genomes revealed the highest degree of similarity (67·1 %) between StCV and canary circovirus. A similar analysis of the evolutionarily conserved cytochromebgene of the circovirus host species revealed a strict co-evolution of circoviruses with their hosts; however, the circoviruses showed about a threefold higher genetic divergence than their hosts.
Role of the cellular protein hDaxx in human cytomegalovirus immediate-early gene expression
Authors: Preston Chris M. , Nicholl Mary Jane
Published: April 2006

Human cytomegalovirus (HCMV) immediate-early (IE) transcription is stimulated by virion phosphoprotein pp71, the product of gene UL82. It has previously been shown that pp71 interacts with the cellular protein hDaxx and, in the studies presented here, the significance of this interaction was investigated for HCMV IE gene expression. In co-transfection experiments, the presence of hDaxx increased the transcriptional response of the HCMV major IE promoter (MIEP) to pp71, but it was not possible to determine whether the effect was due to an interaction between the two proteins or to stimulation of hDaxx synthesis by pp71. The use of small interfering RNA (siRNA) in long- and short-term transfection approaches reduced intracellular hDaxx levels to no more than 3 % of normal. Infection of hDaxx-depleted cells with herpes simplex virus recombinants containing the HCMV MIEP revealed significantly greater promoter activity when hDaxx levels were minimal. Similarly, reducing intracellular hDaxx amounts resulted in greater IE gene expression during infection with an HCMV mutant lacking pp71, but had no effect on IE transcription during infection with wild-type HCMV. The results suggest that hDaxx is not important as a positive-acting factor for the stimulation of HCMV IE transcription by pp71. Instead, it appears that hDaxx acts as a repressor of IE gene expression, and it is proposed here that the interaction of pp71 with hDaxx is important to relieve repression and permit efficient initiation of productive replication.
Rotavirus spike protein VP5* binds α2β1 integrin on the cell surface and competes with virus for cell binding and infectivity
Authors: Graham Kate L. , Takada Yoshikazu , Coulson Barbara S.
Published: April 2006

Rotaviruses recognize several cell-surface molecules, including the α2β1 integrin, and the processes of rotavirus cell attachment and entry appear to be multifactorial. The VP5* subunit of the rotavirus spike protein VP4 contains the α2β1 ligand sequence Asp–Gly–Glu at residues 308–310. Binding to α2β1 and infectivity of monkey rotavirus strain RRV and human rotavirus strain Wa, but not porcine rotavirus strain CRW-8, are inhibited by peptides containing Asp–Gly–Glu. Asp308 and Gly309 are necessary for the binding of RRV VP5* (aa 248–474) to expressed I domain of the α2 integrin subunit. Here, the ability of RRV VP5* to bind cells and affect rotavirus–integrin interactions was determined. Interestingly, VP5* bound to cells at 4 and 37 °C, both via α2β1 and independently of this integrin. Prior VP5* binding at 37 °C eliminated RRV binding to cellular α2β1 and reduced RRV and Wa infectivity in MA104 cells by 38–46 %. VP5* binding did not affect the infectivity of CRW-8. VP5* binding at 4 °C did not affect permissive-cell infection by RRV, indicating an energy requirement for VP5* competition with virus for infectivity. Mutagenesis of VP5* Asp308 and Gly309 eliminated VP5* binding to α2β1 and the VP5* inhibition of rotavirus cell binding and infection, but not α2β1-independent cell binding by VP5*. These studies show for the first time that expressed VP5* binds cell-surface α2β1 using Asp308 and Gly309 and inhibits the infection of homologous and heterologous rotaviruses that use α2β1 as a receptor.
Epstein–Barr virus origin of lytic replication mediates association of replicating episomes with promyelocytic leukaemia protein nuclear bodies and replication compartments
Authors: Amon Wolfgang , White Robert E. , Farrell Paul J.
Published: April 2006

Epstein–Barr virus (EBV) establishes a latent persistence from which it can be reactivated to undergo lytic replication. Late lytic-cycle gene expression is linked to lytic DNA replication, as it is sensitive to the same inhibitors that block lytic replication, and it has recently been shown that the viral origin of lytic replication (ori lyt) is required in cis for late-gene expression. During the lytic cycle, the viral genome forms replication compartments, which are usually adjacent to promyelocytic leukaemia protein (PML) nuclear bodies. A tetracycline repressor DNA-binding domain–enhanced green fluorescent protein fusion was used to visualize replicating plasmids carrying a tetracycline operator sequence array. ori lyt mediated the production of plasmid replication compartments that were associated with PML nuclear bodies. Plasmids carrying ori lyt and EBV itself were visualized in the same cells and replicated in similar regions of the nucleus, further supporting the validity of the plasmids for studying late-gene regulation.
Trypsin increases pseudorabies virus production through activation of the ERK signalling pathway
Authors: Riteau Béatrice , de Vaureix Christiane , Lefèvre François
Published: April 2006

Extracellular proteases that are expressed in primary and secondary foci of viral infection are potentially important mediators of infectious inflammatory processes. For some viruses, such as influenza virus and rotaviruses, proteases such as trypsin enhance infectivity by a direct proteolytic effect on some virion proteins. By using an in vitro model of herpesvirus infection, the possibility that proteases modulate the viral cycle through signalling delivered to the infected cell was investigated. It is reported that exposure of pseudorabies virus-infected cells to trypsin increased virus production. Moreover, this treatment induced synergistic and sustained activation of the extracellular signal-regulated kinase (ERK) 1/2 signalling pathway, which appeared to be necessary for this increased viral production. These results suggest that herpesviruses could take advantage of the inflammatory context and particularly of the presence of proteases to increase their replication. Thus, these data point to a potentially important role of extracellular proteases in herpesvirus infection.
Double-stranded RNA-binding protein E3 controls translation of viral intermediate RNA, marking an essential step in the life cycle of modified vaccinia virus Ankara
Authors: Ludwig Holger , Suezer Yasemin , Waibler Zoe , Kalinke Ulrich , Schnierle Barbara S. , Sutter Gerd
Published: April 2006

Infection of human cells with modified vaccinia virus Ankara (MVA) activates the typical cascade-like pattern of viral early-, intermediate- and late-gene expression. In contrast, infection of human HeLa cells with MVA deleted of the E3L gene (MVA-ΔE3L) results in high-level synthesis of intermediate RNA, but lacks viral late transcription. The viral E3 protein is thought to bind double-stranded RNA (dsRNA) and to act as an inhibitor of dsRNA-activated 2′-5′-oligoadenylate synthetase (2′-5′OA synthetase)/RNase L and protein kinase (PKR). Here, it is demonstrated that viral intermediate RNA can form RNase A/T1-resistant dsRNA, suggestive of activating both the 2′-5′OA synthetase/RNase L pathway and PKR in various human cell lines. Western blot analysis revealed that failure of late transcription in the absence of E3L function resulted from the deficiency to produce essential viral intermediate proteins, as demonstrated for vaccinia late transcription factor 2 (VLTF 2). Substantial host cell-specific differences were found in the level of activation of either RNase L or PKR. However, both rRNA degradation and phosphorylation of eukaryotic translation initiation factor-2α(eIF2α) inhibited the synthesis of VLTF 2 in human cells. Moreover, intermediate VLTF 2 and late-protein production were restored in MVA-ΔE3L-infected mouse embryonic fibroblasts fromPkr0/0mice. Thus, both host-response pathways may be involved, but activity of PKR is sufficient to block the MVA molecular life cycle. These data imply that an essential function of vaccinia virus E3L is to secure translation of intermediate RNA and, thereby, expression of other viral genes.
Hepatitis C virus entry: potential receptors and their biological functions
Authors: Cocquerel Laurence , Voisset Cécile , Dubuisson Jean
Published: April 2006

Several cellular molecules have been identified as putative receptors forHepatitis C virus(HCV): CD81 tetraspanin, scavenger receptor class B type I (SR-BI), mannose-binding lectins DC-SIGN and L-SIGN, low-density lipoprotein receptor, heparan sulphate proteoglycans and the asialoglycoprotein receptor. Due to difficulties in propagating HCV in cell culture, most of these molecules have been identified by analysing their interaction with a soluble, truncated form of HCV glycoprotein E2. A recent major step in investigating HCV entry was the development of pseudoparticles (HCVpp), consisting of unmodified HCV envelope glycoproteins assembled onto retroviral core particles. This system has allowed the investigation of the role of candidate receptors in the early steps of the HCV life cycle and the data obtained can now be confirmed with the help of a newly developed cell-culture system that allows efficient amplification of HCV (HCVcc). Interestingly, CD81 and SR-BI have been shown to play direct roles in HCVpp and/or HCVcc entry. However, co-expression of CD81 and SR-BI in non-hepatic cell lines does not lead to HCVpp entry, indicating that other molecule(s), expressed only in hepatic cells, are necessary for HCV entry. In this review, the molecules that have been proposed as potential HCV receptors are described and the experimental data indicating that CD81 and SR-BI are potentially involved in HCV entry are presented.
Analysis of mutations in the E6/E7 oncogenes and L1 gene of human papillomavirus 16 cervical cancer isolates from China
Authors: Wu Yuping , Chen Yulong , Li Longyu , Yu Guifang , He Ying , Zhang Yanling
Published: April 2006

Human papillomavirus type 16 (HPV16) has a number of intratypic variants; each has a different geographical distribution and some are associated with enhanced oncogenic potential. Cervical samples were collected from 223 cervical cancer patients and from 196 age-matched control subjects in China. DNA samples were amplified by using primers specific for the E6, E7 and partial L1 regions. Products were sequenced and analysed. It was found by using a PCR–sequence-based typing method that HPV infection rates in China were 92·8 % in cervical cancer patients and 15·8 % in healthy controls. HPV16 was detected in 70·4 % of cervical cancer patients and in 6·1 % of controls. In HPV16-positive cervical cancers, 23·6 % belonged to the prototype, 65·5 % were of the Asian variant, 5·5 % were of African type 1 and 3·6 % were European variants, whilst only one was a new variant that differed from any variant published so far. Prevalences of HPV16 E6 D25E and E113D variants were 67·3 and 9 %, respectively. In addition to D25E and E113D, the following E6 variations were found in this study: R129K, E89Q, S138C, H78Y, L83V and F69L. The results also showed that the prevalences of three hot spots of E7 nucleotide variation, N29S, S63F and a silent variation, nt T846C, were 70·2 % (33/47), 51·1 % (24/47) and 61·7 % (29/47), respectively. The following L1 variations were found in this study: S377A, K387E, E378D, K382E and T379P. It was also found that the average age of Asian variant-positive cervical cancer patients (42·98±10·43 years) was 7·56 years lower than that of prototype-positive patients (50·54±10·91). It is suggested that the high frequency of HPV16 Asian variants might contribute to the high incidence of cervical cancer in China.
Protection of mice against Human respiratory syncytial virus by wild-type and aglycosyl mouse–human chimaeric IgG antibodies to subgroup-conserved epitopes on the G glycoprotein
Authors: Mekseepralard C. , Toms G. L. , Routledge E. G.
Published: April 2006

Monoclonal antibodies (mAbs) to conserved epitopes on the G glycoprotein of human respiratory syncytial virus (HRSV) subgroup A fail to neutralize the virus in cell culture in the absence of complement, but are protective in rodent models of infection. They may have potential as prophylactic agents in human infants. In order to investigate the role of Fc-dependent pathways in protection by one such antibody, 1C2, the VHand VLgenes were isolated by RT-PCR and assembled with humanκlight-chain and humanγ1 heavy-chain constant-region genes to form two mouse–human chimaeras, which were expressed in NS0 cells. One of the chimaeras carried a wild-typeγ1 chain, whilst the other had an aglycosyl mutation in the CH2 domain rendering the antibody defective in complement activation and FcγR binding. Whilst both chimaeric antibodies exhibited similar avidity for HRSV in ELISA, only the fully glycosylated wild type was capable of neutralizing the virus in the presence of complement. In mice passively immunized with either murine or wild-typeγ1 chimaeric antibody, no virus could be recovered from the lungs 4 days after intranasal inoculation of HRSV. In mice immunized with the aglycosylγ1 chimaera, however, virus was present in the lungs following challenge, although virus titres were significantly reduced compared with controls (P<0·005). These results indicate that the protective effect of this antibody is mediated by both Fc-dependent and Fc-independent pathways.
In vivo antiviral activity: defective interfering virus protects better against virulent Influenza A
virus than avirulent virus
Authors: Dimmock Nigel J. , Marriott Anthony C.
Published: April 2006

A defective interfering (DI) virus differs from the infectious virus from which it originated in having at least one major deletion in its genome. Such DI genomes are replicated only in cells infected in trans with homologous infectious virus and, as their name implies, they interfere with infectious virus replication and reduce the yield of progeny virus. This potent antiviral activity has been abundantly demonstrated in cell culture with many different DI animal viruses, but few in vivo examples have been reported, with the notable exception of DI Influenza A
virus. A clue to this general lack of success arose recently when an anomaly was discovered in which DI Influenza A virus solidly protected mice from lethal disease caused by A/PR/8/34 (H1N1) and A/WSN/40 (H1N1) viruses, but protected only marginally from disease caused by A/Japan/305/57 (A/Jap, H2N2). The problem was not any incompatibility between the DI and infectious genomes, as A/Jap replicated the DI RNA in vivo. However, A/Jap required 300-fold more mouse infectious units to cause clinical disease than A/PR8 and it was hypothesized that it was this excess of infectivity that abrogated the protective activity of the DI virus. This conclusion was verified by varying the proportions of DI and challenge virus and showing that increasing the DI virus : infectious virus ratio in infected mice resulted in interference. Thus, counter-intuitively, DI virus is most effective against viruses that cause disease with low numbers of particles, i.e. virulent viruses.
Does Drinking Promote Risky Sexual Behavior?
Authors: Cooper M. Lynne
Published: April 2006

The present review argues that, popular lore notwithstanding, the well-documented association between usual patterns of alcohol use and risky sex reflects multiple underlying processes that are both causal and noncausal (spurious) in nature. It is further argued that even alcohol's acute causal effects on sexual behavior are more variable than they are commonly assumed to be. Drinking can promote, inhibit, or have no effect on behavior, depending on the interplay of factors governing behavior in a particular situation and the content of individually held beliefs about alcohol's effects.