bluuebunny/crossref_metadata_2025 huggingface dataset:
Behavioural manipulation in a grasshopper harbouring hairworm: a proteomics approach
Authors: Biron D.G , Marché L , Ponton F , Loxdale H.D , Galéotti N , Renault L , Joly C , Thomas F
Published: September 2005

The parasitic Nematomorph hairworm,Spinochordodes tellinii(Camerano) develops inside the terrestrial grasshopper,Meconema thalassinum(De Geer) (Orthoptera: Tettigoniidae), changing the insect's responses to water. The resulting aberrant behaviour makes infected insects more likely to jump into an aquatic environment where the adult parasite reproduces. We used proteomics tools (i.e. two-dimensional gel electrophoresis (2-DE), computer assisted comparative analysis of host and parasite protein spots and MALDI-TOF mass spectrometry) to identify these proteins and to explore the mechanisms underlying this subtle behavioural modification. We characterized simultaneously the host (brain) and the parasite proteomes at three stages of the manipulative process, i.e. before, during and after manipulation. For the host, there was a differential proteomic expression in relation to different effects such as the circadian cycle, the parasitic status, the manipulative period itself, and worm emergence. For the parasite, a differential proteomics expression allowed characterization of the parasitic and the free-living stages, the manipulative period and the emergence of the worm from the host. The findings suggest that the adult worm alters the normal functions of the grasshopper's central nervous system (CNS) by producing certain ‘effective’ molecules. In addition, in the brain of manipulated insects, there was found to be a differential expression of proteins specifically linked to neurotransmitter activities. The evidence obtained also suggested that the parasite produces molecules from the family Wnt acting directly on the development of the CNS. These proteins show important similarities with those known in other insects, suggesting a case of molecular mimicry. Finally, we found many proteins in the host's CNS as well as in the parasite for which the function(s) are still unknown in the published literature (www) protein databases. These results support the hypothesis that host behavioural changes are mediated by a mix of direct and indirect chemical manipulation.
Seasonal matching of habitat quality and fitness in a migratory bird
Authors: Gunnarsson Tómas Grétar , Gill Jennifer A , Newton Jason , Potts Peter M , Sutherland William J
Published: September 2005

When species occupy habitats that vary in quality, choice of habitat can be critical in determining individual fitness. In most migratory species, juveniles migrate independently of their parents and must therefore choose both breeding and winter habitats. Using a unique dataset of marked black-tailed godwits (
Limosa limosa islandica
) tracked throughout their migratory range, combined with analyses of stable carbon isotope ratios, we show that those individuals that occupy higher quality breeding sites also use higher quality winter sites. This seasonal matching can severely inflate inequalities in individual fitness. This population has expanded over the last century into poorer quality breeding and winter habitats and, across the whole population; individual birds tend to occupy either novel or traditional sites in both seasons. Winter and breeding season habitat selection are thus strongly linked throughout this population; these links have profound implications for a wide range of population and evolutionary processes. As adult godwits are highly philopatric, the initial choice of winter habitat by juveniles will be critical in determining future survival, timing of migration and breeding success.
Population size and molecular evolution on islands
Authors: Woolfit Megan , Bromham Lindell
Published: September 2005

The nearly neutral theory predicts that the rate and pattern of molecular evolution will be influenced by effective population size (Ne), because in small populations more slightly deleterious mutations are expected to drift to fixation. This important prediction has not been widely empirically tested, largely because of the difficulty of comparing rates of molecular evolution in sufficient numbers of independent lineages which differ only inNe. Island endemic species provide an ideal test of the effect ofNeon molecular evolution because species restricted to islands frequently have smallerNethan closely related mainland species, and island endemics have arisen from mainland lineages many times in a wide range of taxa. We collated a dataset of 70 phylogenetically independent comparisons between island and mainland taxa, including vertebrates, invertebrates and plants, from 19 different island groups. The rate of molecular evolution in these lineages was estimated by maximum likelihood using two measures: overall substitution rate and the ratio of non-synonymous to synonymous substitution rates. We show that island lineages have significantly higher ratios of non-synonymous to synonymous substitution rates than mainland lineages, as predicted by the nearly neutral theory, although overall substitution rates do not differ significantly.
Importance of climatological downscaling and plant phenology for red deer in heterogeneous landscapes
Authors: Pettorelli Nathalie , Mysterud Atle , Yoccoz Nigel G , Langvatn Rolf , Stenseth Nils Chr
Published: September 2005

Understanding how climate influences ecosystems represents a challenge in ecology and natural resource management. Although we know that climate affects plant phenology and herbivore performances at any single site, no study has directly coupled the topography–climate interaction (i.e. the climatological downscaling process) with large-scale vegetation dynamics and animal performances. Here we show how climatic variability (measured by the North Atlantic oscillation ‘NAO’) interacts with local topography in determining the vegetative greenness (as measured by the normalized difference vegetation index ‘NDVI’) and the body masses and seasonal movements of red deer (
Cervus elaphus
) in Norway. Warm springs induced an earlier onset of vegetation, resulting in earlier migration and higher body masses. Increasing values of the winter-NAO corresponded to less snow at low altitude (warmer, more precipitation results in more rain), but more snow at high altitude (colder, more precipitation corresponds to more snow) relative to winters with low winter-NAO. An increasing NAO thus results in a spatially more variable phenology, offering migrating deer an extended period with access to high-quality forage leading to increased body mass. Our results emphasize the importance of incorporating spring as well as the interaction between winter climate and topography when aiming at understanding how plant and animal respond to climate change.
Females use self-referent cues to avoid mating with previous mates
Authors: Ivy Tracie M , Weddle Carie B , Sakaluk Scott K
Published: September 2005

Females of many species mate repeatedly throughout their lives, often with many different males (polyandry). Females can secure genetic benefits by maximizing their diversity of mating partners, and might be expected, therefore, to forego matings with previous partners in favour of novel males. Indeed, a female preference for novel mating partners has been shown in several taxa, but the mechanism by which females distinguish between novel males and previous mates remains unknown. We show that female crickets (
Gryllodes sigillatus
) mark males with their own unique chemical signatures during mating, enabling females to recognize prior mates in subsequent encounters and to avoid remating with them. Because self-referent chemosensory cues provide females with a simple, but reliable mechanism of identifying individuals with whom they have mated without requiring any special cognitive ability, they may be a widespread means by which females across a broad range of animal mating systems maximize the genetic benefits of polyandry.
Energetics of the smallest: do bacteria breathe at the same rate as whales?
Authors: Makarieva Anastassia M , Gorshkov Victor G , Li Bai-Lian
Published: September 2005

Power laws describing the dependence of metabolic rate on body mass have been established for many taxa, but not for prokaryotes, despite the ecological dominance of the smallest living beings. Our analysis of 80 prokaryote species with cell volumes ranging more than 1 000 000-fold revealed no significant relationship between mass-specific metabolic rateqand cell mass. By absolute values, mean endogenous mass-specific metabolic rates of non-growing bacteria are similar to basal rates of eukaryote unicells, terrestrial arthropods and mammals. Maximum mass-specific metabolic rates displayed by growing bacteria are close to the record tissue-specific metabolic rates of insects, amphibia, birds and mammals. Minimum mass-specific metabolic rates of prokaryotes coincide with those of larger organisms in various energy-saving regimes: sit-and-wait strategists in arthropods, poikilotherms surviving anoxia, hibernating mammals. These observations suggest a size-independent value around which the mass-specific metabolic rates vary bounded by universal upper and lower limits in all body size intervals.
Müllerian mimicry: an examination of Fisher's theory of gradual evolutionary change
Authors: Balogh Alexandra C.V , Leimar Olof
Published: September 2005

In 1927, Fisher suggested that Müllerian mimicry evolution could be gradual and driven by predator generalization. A competing possibility is the so-called two-step hypothesis, entailing that Müllerian mimicry evolves through major mutational leaps of a less-protected species towards a better-protected, which sets the stage for coevolutionary fine-tuning of mimicry. At present, this hypothesis seems to be more widely accepted than Fisher's suggestion. We conducted individual-based simulations of communities with predators and two prey types to assess the possibility of Fisher's process leading to a common prey appearance. We found that Fisher's process worked for initially relatively similar appearances. Moreover, by introducing a predator spectrum consisting of several predator types with different ranges of generalization, we found that gradual evolution towards mimicry occurred also for large initial differences in prey appearance. We suggest that Fisher's process together with a predator spectrum is a realistic alternative to the two-step hypothesis and, furthermore, it has fewer problems with purifying selection. We also examined the factors influencing gradual evolution towards mimicry and found that not only the relative benefits from mimicry but also the mutational schemes of the prey types matter.
Modelling information exchange in worker–queen conflict over sex allocation
Authors: Pen Ido , Taylor Peter D
Published: September 2005

We investigate the conflict between queen and worker over sex allocation, specifically the allocation of the queen's eggs between workers and reproductives and the allocation of the reproductive eggs between male and female. In contrast to previous models, we allow workers to observe and use information about the strategy of the queen. We consider three conflict models: simultaneous (no information exchange), sequential (a one-way information exchange) and negotiated (an iterated two-way information exchange). We find that the first model produces sex ratios intermediate between the classic queen (1 : 1) and worker (1 : 3) optima. The second model, in which the worker has information about the queen's decisions, produces a different result and one that is somewhat counter-intuitive in that the sex ratios are less female-biased than for the other two models, and in fact are often male-biased. The third model predicts sex ratios intermediate between the first two models. We discuss how these findings may shed new light on observed sex allocation patterns in social insects and we suggest some experimental tests.
A ratio model of perceived speed in the human visual system
Authors: Hammett Stephen T , Champion Rebecca A , Morland Antony B , Thompson Peter G
Published: September 2005

The perceived speed of moving images changes over time. Prolonged viewing of a pattern (adaptation) leads to an exponential decrease in its perceived speed. Similarly, responses of neurones tuned to motion reduce exponentially over time. It is tempting to link these phenomena. However, under certain conditions, perceived speed increases after adaptation and the time course of these perceptual effects varies widely. We propose a model that comprises two temporally tuned mechanisms whose sensitivities reduce exponentially over time. Perceived speed is taken as the ratio of these filters' outputs. The model captures increases and decreases in perceived speed following adaptation and describes our data well with just four free parameters. Whilst the model captures perceptual time courses that vary widely, parameter estimates for the time constants of the underlying filters are in good agreement with estimates of the time course of adaptation of direction selective neurones in the mammalian visual system.
Conflict between parasites with different transmission strategies infecting an amphipod host
Authors: Haine Eleanor R , Boucansaud Karelle , Rigaud Thierry
Published: September 2005

Competition between parasites within a host can influence the evolution of parasite virulence and host resistance, but few studies examine the effects of unrelated parasites with conflicting transmission strategies infecting the same host. Vertically transmitted (VT) parasites, transmitted from mother to offspring, are in conflict with virulent, horizontally transmitted (HT) parasites, because healthy hosts are necessary to maximize VT parasite fitness. Resolution of the conflict between these parasites should lead to the evolution of one of two strategies: avoidance, or sabotage of HT parasite virulence by the VT parasite. We investigated two co-infecting parasites in the amphipod host,Gammarus roeseli: VT microsporidia have little effect on host fitness, but acanthocephala modify host behaviour, increasing the probability that the amphipod is predated by the acanthocephalan's definitive host. We found evidence for sabotage: the behavioural manipulation induced by the AcanthocephalaPolymorphus minutuswas weaker in hosts also infected by the microsporidiaDictyocoelasp. (roeselum) compared to hosts infected byP. minutusalone. Such conflicts may explain a significant portion of the variation generally observed in behavioural measures, and since VT parasites are ubiquitous in invertebrates, often passing undetected, conflict via transmission may be of great importance in the study of host–parasite relationships.
Brain size and resource specialization predict long-term population trends in British birds
Authors: Shultz Susanne , B. Bradbury Richard , L. Evans Karl , D. Gregory Richard , M. Blackburn Tim
Published: September 2005

Large-scale population declines have been documented across many faunal assemblages. However, there is much variation in population trends for individual species, and few indications of which specific ecological and behavioural characteristics are associated with such trends. We used the British Common Birds Census (1968–1995) to identify specific traits associated with long-term abundance trends in UK farmland birds. Two factors, resource specialization and relative brain size, were significantly associated with population trend, such that species using atypical resources and with relatively small brains were most likely to have experienced overall declines. Further analyses of specific brain components indicated that the relative size of the telencephalon, the part of the brain associated with problem solving and complex behaviours, and the brain stem might be better predictors of population trend than overall brain size. These results suggest that flexibility in resource use and behaviour are the most important characteristics for determining a species' ability to cope with large-scale habitat changes.
Molecular evolution of the sheep prion protein gene
Authors: Slate Jon
Published: September 2005

Transmissible spongiform encephalopathies (TSEs) are infectious, fatal neurodegenerative diseases characterized by aggregates of modified forms of the prion protein (PrP) in the central nervous system. Well known examples include variant Creutzfeldt-Jakob Disease (vCJD) in humans, BSE in cattle, chronic wasting disease in deer and scrapie in sheep and goats. In humans, sheep and deer, disease susceptibility is determined by host genotype at the prion protein gene (PRNP). Here I examine the molecular evolution ofPRNPin ruminants and show that variation in sheep appears to have been maintained by balancing selection, a profoundly different process from that seen in other ruminants. Scrapie eradication programs such as those recently implemented in the UK, USA and elsewhere are based on the assumption thatPRNPis under positive selection in response to scrapie. If, as these data suggest, that assumption is wrong, eradication programs will disrupt this balancing selection, and may have a negative impact on the fitness or scrapie resistance of national flocks.
Does Bertrand's rule apply to macronutrients?
Authors: Raubenheimer D , Lee K.P , Simpson S.J
Published: September 2005

It has been known for over a century that the dose–response curve for many micronutrients is non-monotonic, having an initial stage of increasing benefits with increased intake, followed by increasing costs as excesses become toxic. This phenomenon, termed Bertrand's rule, is widely assumed not to apply to caloric macronutrients. To date this assumption has been safe, owing to the considerable methodological challenges involved in coaxing animals to over-ingest macronutrients in a way that enables the effects of specific food components to be isolated. Here we report an experiment which overcomes these difficulties, to test whether the second phase (incurring costs with excessive intake) applies to carbohydrate intake by the generalist-feeding caterpillar
Spodoptera littoralis
. The results showed that excess carbohydrate intake caused increased mortality, thus extending Bertrand's rule to macronutrients.
Long-term ecological dynamics: reciprocal insights from natural and anthropogenic gradients
Authors: Fukami Tadashi , Wardle David A
Published: September 2005

Many ecological dynamics occur over time-scales that are well beyond the duration of conventional experiments or observations. One useful approach to overcome this problem is extrapolation of temporal dynamics from spatial variation. We review two complementary variants of this approach that have been of late increasingly employed: the use of natural gradients to infer anthropogenic effects and the use of anthropogenic gradients to infer natural dynamics. Recent studies have considered a variety of naturally occurring gradients associated with climate, CO
2
, disturbance and biodiversity gradients, as well as anthropogenic gradients such as those created by biological invasions, habitat fragmentation and land abandonment. These studies show that natural gradients are useful in predicting long-term consequences of human-induced environmental changes, whereas anthropogenic gradients are helpful in inferring the mechanisms behind natural dynamics because covarying factors are often more clearly understood in anthropogenic gradients than in natural gradients. We classify these studies into several categories, each with different strengths and weaknesses, and outline how the limitations can be overcome by combining the gradient-based approach with other approaches. Overall, studies reviewed here demonstrate that the development of basic ecological concepts and the application of these concepts to environmental problems can be more effective when conducted complementarily than when pursued separately.
Host–parasitoid spatial ecology: a plea for a landscape-level synthesis
Authors: Cronin James T , Reeve John D
Published: September 2005

A growing body of literature points to a large-scale research approach as essential for understanding population and community ecology. Many of our advances regarding the spatial ecology of predators and prey can be attributed to research with insect parasitoids and their hosts. In this review, we focus on the progress that has been made in the study of the movement and population dynamics of hosts and their parasitoids in heterogeneous landscapes, and how this research approach may be beneficial to pest management programs. To date, few studies have quantified prey and predator rates and ranges of dispersal and population dynamics at the patch level—the minimum of information needed to characterize population structure. From host–parasitoid studies with sufficient data, it is clear that the spatial scale of dispersal can differ significantly between a prey and its predators, local prey extinctions can be attributed to predators and predator extinction risk at the patch level often exceeds that of the prey. It is also evident that populations can be organized as a single, highly connected (patchy) population or as semi-independent extinction-prone local populations that collectively form a persistent metapopulation. A prey and its predators can also differ in population structure. At the landscape level, agricultural studies indicate that predator effects on its prey often spill over between the crop and surrounding area (matrix) and can depend strongly on landscape structure (e.g. the proportion of suitable habitat) at scales extending well beyond the crop margins. In light of existing empirical data, predator–prey models are typically spatially unrealistic, lacking important details on boundary responses and movement behaviour within and among patches. The tools exist for conducting empirical and theoretical research at the landscape level and we hope that this review calls attention to fertile areas for future exploration.
Pluralism in mathematics
Authors: Davies E.B
Published: September 2005

We defend pluralism in mathematics, and in particular Errett Bishop's constructive approach to mathematics, on pragmatic grounds, avoiding the philosophical issues which have dissuaded many mathematicians from taking it seriously. We also explain the computational value of interval arithmetic.
The problems and promise of DNA barcodes for species diagnosis of primate biomaterials
Authors: Lorenz Joseph G , Jackson Whitney E , Beck Jeanne C , Hanner Robert
Published: September 2005

The Integrated Primate Biomaterials and Information Resource (
www.IPBIR.org
) provides essential research reagents to the scientific community by establishing, verifying, maintaining, and distributing DNA and RNA derived from primate cell cultures. The IPBIR uses mitochondrial cytochrome
c
oxidase subunit I sequences to verify the identity of samples for quality control purposes in the accession, cell culture, DNA extraction processes and prior to shipping to end users. As a result, IPBIR is accumulating a database of ‘DNA barcodes’ for many species of primates. However, this quality control process is complicated by taxon specific patterns of ‘universal primer’ failure, as well as the amplification or co-amplification of nuclear pseudogenes of mitochondrial origins. To overcome these difficulties, taxon specific primers have been developed, and reverse transcriptase PCR is utilized to exclude these extraneous sequences from amplification. DNA barcoding of primates has applications to conservation and law enforcement. Depositing barcode sequences in a public database, along with primer sequences, trace files and associated quality scores, makes this species identification technique widely accessible. Reference DNA barcode sequences should be derived from, and linked to, specimens of known provenance in web-accessible collections in order to validate this system of molecular diagnostics.
Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications
Authors: Saunders Gary W
Published: September 2005

Marine macroalgae, especially the Rhodophyta, can be notoriously difficult to identify owing to their relatively simple morphology and anatomy, convergence, rampant phenotypic plasticity, and alternation of heteromorphic generations. It is thus not surprising that algal systematists have come to rely heavily on genetic tools for molecular assisted alpha taxonomy. Unfortunately the number of suitable marker systems in the three available genomes is enormous and, although most workers have settled on one of three or four models, the lack of an accepted standard hinders the comparison of results between laboratories. The advantages of a standard system are obvious for practical purposes of species discovery and identification; as well, compliance with a universal marker, such as
cox1
being developed under the label ‘DNA barcode’, would allow algal systematists to benefit from the rapidly emerging technologies. Novel primers were developed for red algae to PCR amplify and sequence the 5′
cox1
‘barcode’ region and were used to assess three known species-complex questions: (i)
Mazzaella
species in the Northeast Pacific; (ii) species of the genera
Dilsea
and
Neodilsea
in the Northeast Pacific; and (iii)
Asteromenia peltata
from three oceans. These models were selected because they have all caused confusion with regards to species number, distribution, and identification in the field, and because they have all been studied with molecular tools. In all cases the DNA barcode resolved accurately and unequivocally species identities and, with the enhanced sampling here, turned up a variety of novel observations in need of further taxonomic investigation.
Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences
Authors: Markmann Melanie , Tautz Diethard
Published: September 2005

Organisms living in or on the sediment layer of water bodies constitute the benthos fauna, which is known to harbour a large number of species of diverse taxonomic groups. The benthos plays a significant role in the nutrient cycle and it is, therefore, of high ecological relevance. Here, we have explored a DNA-taxonomic approach to access the meiobenthic organismic diversity, by focusing on obtaining signature sequences from a part of the large ribosomal subunit rRNA (28S), the D3–D5 region. To obtain a broad representation of taxa, benthos samples were taken from 12 lakes in Germany, representing different ecological conditions. In a first approach, we have extracted whole DNA from these samples, amplified the respective fragment by PCR, cloned the fragments and sequenced individual clones. However, we found a relatively large number of recombinant clones that must be considered PCR artefacts. In a second approach we have, therefore, directly sequenced PCR fragments that were obtained from DNA extracts of randomly picked individual organisms. In total, we have obtained 264 new unique sequences, which can be readily placed into taxon groups, based on phylogenetic comparison with currently available database sequences. The group with the highest taxon abundance were nematodes and protozoa, followed by chironomids. However, we find also that we have by far not exhausted the diversity of organisms in the samples. Still, our data provide a framework within which a meiobenthos DNA signature sequence database can be constructed, that will allow to develop the necessary techniques for studying taxon diversity in the context of ecological analysis. Since many taxa in our analysis are initially only identified via their signature sequences, but not yet their morphology, we propose to call this approach ‘reverse taxonomy’.
TaxI: a software tool for DNA barcoding using distance methods
Authors: Steinke Dirk , Vences Miguel , Salzburger Walter , Meyer Axel
Published: September 2005

DNA barcoding is a promising approach to the diagnosis of biological diversity in which DNA sequences serve as the primary key for information retrieval. Most existing software for evolutionary analysis of DNA sequences was designed for phylogenetic analyses and, hence, those algorithms do not offer appropriate solutions for the rapid, but precise analyses needed for DNA barcoding, and are also unable to process the often large comparative datasets. We developed a flexible software tool for DNA taxonomy, named TaxI. This program calculates sequence divergences between a query sequence (taxon to be barcoded) and each sequence of a dataset of reference sequences defined by the user. Because the analysis is based on separate pairwise alignments this software is also able to work with sequences characterized by multiple insertions and deletions that are difficult to align in large sequence sets (i.e. thousands of sequences) by multiple alignment algorithms because of computational restrictions. Here, we demonstrate the utility of this approach with two datasets of fish larvae and juveniles from Lake Constance and juvenile land snails under different models of sequence evolution. Sets of ribosomal 16S rRNA sequences, characterized by multiple indels, performed as good as or better than
cox1
sequence sets in assigning sequences to species, demonstrating the suitability of rRNA genes for DNA barcoding.
Towards writing the encyclopaedia of life: an introduction to DNA barcoding
Authors: Savolainen Vincent , Cowan Robyn S , Vogler Alfried P , Roderick George K , Lane Richard
Published: September 2005

An international consortium of major natural history museums, herbaria and other organizations has launched an ambitious project, the ‘Barcode of Life Initiative’, to promote a process enabling the rapid and inexpensive identification of the estimated 10 million species on Earth. DNA barcoding is a diagnostic technique in which short DNA sequence(s) can be used for species identification. The first international scientific conference on Barcoding of Life was held at the Natural History Museum in London in February 2005, and here we review the scientific challenges discussed during this conference and in previous publications. Although still controversial, the scientific benefits of DNA barcoding include: (i) enabling species identification, including any life stage or fragment, (ii) facilitating species discoveries based on cluster analyses of gene sequences (e.g.
cox1
=
CO1
, in animals), (iii) promoting development of handheld DNA sequencing technology that can be applied in the field for biodiversity inventories and (iv) providing insight into the diversity of life.
Transcriptomal analysis of varicella-zoster virus infection using long oligonucleotide-based microarrays
Authors: Kennedy Peter G. E. , Grinfeld Esther , Craigon Marie , Vierlinger Klemens , Roy Douglas , Forster Thorsten , Ghazal Peter
Published: September 2005

Varicella-zoster virus (VZV) is a human herpes virus that causes varicella as a primary infection and herpes zoster following reactivation of the virus from a latent state in trigeminal and spinal ganglia. In order to study the global pattern of VZV gene transcription, VZV microarrays using 75-base oligomers to 71 VZV open reading frames (ORFs) were designed and validated. The long-oligonucleotide approach maximizes the stringency of detection and polarity of gene expression. To optimize sensitivity, microarrays were hybridized to target RNA and the extent of hybridization measured using resonance light scattering. Microarray data were normalized to a subset of invariant ranked host-encoded positive-control genes and the data subjected to robust formal statistical analysis. The programme of viral gene expression was determined for VZV (Dumas strain)-infected MeWo cells and SVG cells (an immortalized human astrocyte cell line) 72 h post-infection. Marked quantitative and qualitative differences in the viral transcriptome were observed between the two different cell types using the Dumas laboratory-adapted strain. Oligonucleotide-based VZV arrays have considerable promise as a valuable tool in the analysis of viral gene transcription during both lytic and latent infections, and the observed heterogeneity in the global pattern of viral gene transcription may also have diagnostic potential.
Sequence analysis of the 5′ untranslated region of swine vesicular disease virus reveals block deletions between the end of the internal ribosomal entry site and the initiation codon
Authors: Shaw Andrew E. , Reid Scott M. , Knowles Nick J. , Hutchings Geoffrey H. , Wilsden Ginette , Brocchi Emiliana , Paton David , King Donald P.
Published: September 2005

Swine vesicular disease virus (SVDV) is a picornavirus closely related to the human pathogen coxsackievirus B5. In common with other picornaviruses, the 5′ untranslated region (5′ UTR) of SVDV contains an internal ribosomal entry site (IRES) that plays an important role in cap-independent translation. The aim of this study was to use RT-PCR and sequencing to characterize a fragment of the 5′ UTR encompassing the entire IRES. Sequence analysis demonstrated high nucleotide identities within the IRES between 33 representative SVDV isolates. These data support the choice of this region as a diagnostic target and provide information for the improvement of laboratory-based molecular assays to detect SVDV. In contrast to the relative conservation of the IRES element, there was considerable nucleotide variability in the spacer region located between the cryptic AUG at the 3′ end of the IRES and the initiation codon of the polyprotein. Interestingly, 11 SVDV isolates had block deletions of between 6 and 125 nt in this region. Nine of these isolates were of recent European origin and were phylogenetically closely related. In vitro growth studies showed that selected isolates with these deletions had a significantly reduced plaque diameter and grew to a significantly lower titre relative to an isolate with a full-length 5′ UTR. Further work is required to define the significance of these deletions and to assess whether they impact on the pathogenesis of SVD.
Variants of human papillomaviruses 16 and 18 and their natural history in human immunodeficiency virus-positive women
Authors: Schlecht Nicolas F. , Burk Robert D. , Palefsky Joel M. , Minkoff Howard , Xue Xiaonan , Massad L. Stewart , Bacon Melanie , Levine Alexandra M. , Anastos Kathryn , Gange Stephen J. , Watts D. Heather , Costa Maria M. Da , Chen Zigui , Bang Ji Yon , Fazzari Melissa , Hall Charles , Strickler Howard D.
Published: September 2005

Highly oncogenic human papillomavirus (HPV) 16 and 18 variants might be expected to be particularly aggressive in HIV-positive women. The association of HPV16 and 18 variant lineages with race, human immunodeficiency virus (HIV) coinfection, CD4+ T-cell count, HIV-RNA level, time-to-clearance of HPV infection and presence of squamous intraepithelial lesions (SIL) among women in the Women's Interagency HIV Study was studied. Subjects were followed semi-annually with Pap smear and cervicovaginal lavage (CVL). HPV DNA was detected in CVLs using MY09/11 L1 PCR assay. Specimens positive for HPV16/18 underwent E6 PCR and sequencing to determine the variant present. Specimens from 195 HPV16- and 162 HPV18-positive women were classified into variant lineages based on sequencing results. African variants of HPV16 and HPV18 were significantly more prevalent among African-Americans than among Caucasians [42 versus 14 % (P=0·001) and 60 versus 13 % (P<0·001), respectively]. However, it was not possible to detect associations between the HPV16 or 18 variant lineages and other factors studied. African variants of HPV16/18 were more common in women of African descent living outside Africa, which could reflect mixing behaviours and/or immunogenetic factors. However, in a large population of HIV-infected women, the variant of HPV16 or 18 was unrelated to persistence of infection or presence of SIL. If non-European variants are more oncogenic, the effect may involve a late stage in cervical tumorigenesis.
Intra-host evolutionary dynamics of hepatitis C virus E2 in treated patients
Authors: Alfonso Victoria , Mbayed Viviana Andrea , Sookoian Silvia , Campos Rodolfo Héctor
Published: September 2005

Hepatitis C virus (HCV) displays high genetic diversity. Inter-host sequence variability may mainly reflect a neutral drift evolution. In contrast, intra-host evolution may be driven by an adaptive selection to host responses to infection. Here, HCV E2 intra-host evolution in two patients during the course and follow-up of successive treatments with IFN-α and IFN-α/ribavirin was investigated. Phylogenetic analyses suggested that adaptive pressures prompt a continuous selection of viral variants derived from the previous ones (intra-lineage evolution) and/or a swapping of viral lineages during the course of the infection (inter-lineage evolution). Selection would act not only on the phenotypic features of hypervariable region 1 (HVR1) but also on those of the flanking regions. The pressures operate mainly at the amino acid level, but they also appeared to act on nucleotide sequences. Moreover, HVR1 heterogeneity seemed to be strongly constrained. This work contributes to the knowledge of HCV intra-host evolution during chronicity.
Ectromelia virus: the causative agent of mousepox
Authors: Esteban David J. , Buller R. Mark L.
Published: September 2005

Ectromelia virus(ECTV) is an orthopoxvirus whose natural host is the mouse; it is related closely toVariola virus, the causative agent of smallpox, andMonkeypox virus, the cause of an emerging zoonosis. The recent sequencing of its genome, along with an effective animal model, makes ECTV an attractive model for the study of poxvirus pathogenesis, antiviral and vaccine testing and viral immune and inflammatory responses. This review discusses the pathogenesis of mousepox, modulation of the immune response by the virus and the cytokine and cellular components of the skin and systemic immune system that are critical to recovery from infection.
High-level expression of biologically active bovine alpha interferon by Bovine herpesvirus 1 interferes only marginally with recombinant virus replication in vitro
Authors: Höhle Constanze , Karger Axel , König Patricia , Giesow Katrin , Keil Günther M.
Published: September 2005

An artificial open reading frame (ORF) for bovine alpha interferon (boIFN-α) with the codon preference of Bovine herpesvirus 1 (BHV-1) glycoprotein B was constructed to assess the effect of expression of boIFN-α by BHV-1 from an expression cassette. Transient expression of the ORF revealed that transfected cells secreted substantial amounts of biologically active boIFN-α, which moderately inhibited replication of BHV-1 after stimulation of bovine cells with 104 U ml−1. The boIFN-α-encoding expression cassette was recombined into the glycoprotein E locus of the glycoprotein E-negative BHV-1 vaccine strain GKD. Cells infected with the resulting recombinant BHV-1/boIFN-α secreted up to 107 U boIFN-α per ml cell culture supernatant, which is about 40- to more than 100-fold the activity reached with other virus expression systems. Bioassays demonstrated that the BHV-1-expressed interferon induced a rapid and sustained antiviral state in stimulated bovine cells. Analysis of the in vitro growth properties of the recombinant revealed, depending on the cell line used, no or only slight inhibition in direct spreading from cell to cell and a modest delay in virus egress from infected cells. Final titres, however, were comparable to those reached by the parent strain. Penetration into cells was not affected. The results from this study demonstrate that BHV-1/boIFN-α expresses high levels of boIFN-α, grows to high titres in cell culture and thus represents a potential alternative means to deliver endogenously produced boIFN-α
in situ for a period of time.
The bovine herpesvirus 1 gene encoding infected cell protein 0 (bICP0) can inhibit interferon-dependent transcription in the absence of other viral genes
Authors: Henderson Gail , Zhang Yange , Jones Clinton
Published: September 2005

The infected cell protein 0 (bICP0) encoded byBovine herpesvirus 1(BHV-1) stimulates viral gene expression and productive infection. As bICP0 is expressed constitutively during productive infection, it is considered to be the major viral regulatory protein. Like other alphaherpesvirus ICP0 homologues, bICP0 contains a zinc RING finger near its N terminus that activates transcription and regulates subcellular localization. In this study, evidence is provided that bICP0 represses the human beta interferon (IFN-β) promoter and a simple promoter with consensus IFN-stimulated response elements following stimulation with double-stranded RNA (polyinosinic–polycytidylic acid), IFN regulatory factor 3 (IRF3) or IRF7. bICP0 also inhibits the ability of two protein kinases (TBK1 and IKKε) to activate IFN-βpromoter activity. The zinc RING finger is necessary for inhibiting IFN-dependent transcription in certain cell types. Collectively, these studies suggest that bICP0 activates productive infection by stimulating viral gene expression and inhibiting IFN-dependent transcription.
Interferon resistance of hepatitis C virus replicon-harbouring cells is caused by functional disruption of type I interferon receptors
Authors: Naka Kazuhito , Takemoto Kazunori , Abe Ken-ichi , Dansako Hiromichi , Ikeda Masanori , Shimotohno Kunitada , Kato Nobuyuki
Published: September 2005

Hepatitis C virus (HCV) replicon-harbouring cell lines possessing interferon (IFN)-resistant phenotypes have recently been established. These were divided into two classes: partially IFN resistant and highly IFN resistant. Here, the viral and cellular factors contributing to the IFN resistance of HCV replicon-harbouring cells were evaluated. The results revealed that cellular factors rather than viral factors contributed to a highly IFN-resistant phenotype. The possibility of genetic abnormality of the factors involved in IFN signalling was investigated. As a result, nonsense mutations and deletions in type I IFN receptor genes (IFNAR1 and IFNAR2c) were found in replicon-harbouring cells showing a highly IFN-resistant phenotype, but rarely appeared in cells showing a partially IFN-resistant phenotype. Furthermore, similar genetic alterations were also found in IFN-resistant phenotype, replicon-harbouring cell lines obtained additionally by IFN-β treatment. Moreover, it was shown that ectopic expression of wild-type IFNAR1 in IFN-resistant phenotype, replicon-harbouring cells possessing the IFNAR1 mutant restored type I IFN signalling.
Phylogenetic relationships among rhabdoviruses inferred using the L polymerase gene
Authors: Bourhy H. , Cowley J. A. , Larrous F. , Holmes E. C. , Walker P. J.
Published: September 2005

RNA viruses of the familyRhabdoviridaeinclude arthropod-borne agents that infect plants, fish and mammals, and also include a variety of non-vector-borne mammalian viruses. Herein is presented a molecular phylogenetic analysis, the largest undertaken to date, of 56 rhabdoviruses, including 20 viruses which are currently unassigned or assigned as tentative species within theRhabdoviridae. Degenerate primers targeting a region of block III of the L polymerase gene were defined and used for RT-PCR amplification and sequencing. A maximum-likelihood phylogenetic analysis of a 158-residue L polymerase amino acid sequence produced an evolutionary tree containing the six recognized genera of theRhabdoviridaeand also enabled us to identify four more monophyletic groups of currently unclassified rhabdoviruses that we refer to as the ‘Hart Park’, ‘Almpiwar’, ‘Le Dantec’ and ‘Tibrogargan’ groups. The broad phylogenetic relationships among these groups and genera also indicate that the evolutionary history of rhabdoviruses was strongly influenced by mode of transmission, host species (plant, fish or mammal) and vector (orthopteran, homopteran or dipteran).
Linkage map of protein–protein interactions of Porcine teschovirus
Authors: Zell Roland , Seitz Simone , Henke Andreas , Munder Thomas , Wutzler Peter
Published: September 2005

A yeast two-hybrid study was conducted to catalogue the protein–protein interactions of the Porcine teschovirus non-structural proteins. Five homodimer, three reciprocal heterodimer and four unidirectional heterodimer interactions were observed. While several interactions are similar to those described in previous studies using enteroviruses, such as homo- and heterodimeric interactions of the 2B, 3CD and 3D proteins, several were not found previously. Among these is the binding of the leader protein L to the proteinases 3C and 3CD. Unlike the poliovirus 3C, the teschovirus 3C proteinase dimerizes and interacts with 2BC, 3CD and 3D. The strongest interactions were observed for L–3C, L–3CD and 3C–3CD.
Quantification of vertical transmission of Murine polyoma virus by real-time quantitative PCR
Authors: Zhang Shaojie , McNees Adrienne L. , Butel Janet S.
Published: September 2005

Pathogenesis studies of viral infectionsin vivorequire sensitive assay methods. A sensitive and specific real-time quantitative PCR (RQ-PCR) assay was developed to detectMurine polyoma virus(MuPyV) DNA sequences. A quantitative assay to measure the single-copy murine wild-type p53 gene was developed to normalize viral gene copies to cell numbers. Both assays were sensitive over a seven-log dynamic range, with a reproducible detection limit of 10 copies per reaction. To determine viral loads and tissue distribution following vertical transmission of MuPyV, pregnant BALB/c mice were inoculated intraperitoneally with virus in late pregnancy. Progeny animals born to infected mothers were followed for 21 days. Viral loads in four tissues (salivary gland, kidney, liver and spleen) were highest at 7 days after birth and dropped to low levels by 14 and 21 days of age, with loads ranging from 5 to 2 million MuPyV copies per 103cells. Significant animal-to-animal variation occurred. Fourteen of 21 (67 %) progeny were virus-positive in one or more tissue samples. Transplacental transmission was observed in 6/7 (86 %) litters. Infected fetuses per positive litter ranged from 1/7 (14 %) to 5/6 (83 %) with viral loads ranging from 5 to 25 417 MuPyV copies per 1000 fetal cells. Maternal tissues and blood were frequently highly positive 2 days after inoculation, but viral loads were low by day 14. This study demonstrated the vertical transmission, including transplacental transmission, of MuPyV following acute infection of pregnant mice. It should be considered that there is a possibility that other polyomaviruses, including those in humans, may be vertically transmitted.
The αvβ6 integrin receptor for Foot-and-mouth disease virus is expressed constitutively on the epithelial cells targeted in cattle
Authors: Monaghan Paul , Gold Sarah , Simpson Jennifer , Zhang Zhidong , Weinreb Paul H. , Violette Shelia M. , Alexandersen Soren , Jackson Terry
Published: September 2005

Field strains ofFoot-and-mouth disease virus(FMDV) use a number ofαv-integrins as receptors to initiate infection on cultured cells, and integrins are believed to be the receptors used to target epithelial cells in animals. In this study, immunofluorescence confocal microscopy and real-time RT-PCR were used to investigate expression of two of the integrin receptors of FMDV,αvβ6 andαvβ3, within various epithelia targeted by this virus in cattle. These studies show thatαvβ6 is expressed constitutively on the surfaces of epithelial cells at sites where infectious lesions occur during a natural infection, but not at sites where lesions are not normally formed. Expression ofαvβ6 protein at these sites showed a good correlation with the relative abundance ofβ6 mRNA. In contrast,αvβ3 protein was only detected at low levels on the vasculature and not on the epithelial cells of any of the tissues investigated. Together, these data suggest that in cattle,αvβ6, rather thanαvβ3, serves as the major receptor that determines the tropism of FMDV for the epithelia normally targeted by this virus.