bluuebunny/crossref_metadata_2025 huggingface dataset:
Lessons from agri-environmental policies in other countries for dealing with salinity in Australia
Authors: Weersink A. , Wossink A.
Published: December 2005

Approaches to environmental policy for the agricultural sector have involved education programs, direct regulations, and market mechanisms. The effectiveness of these policies has varied depending on the characteristics of the environmental issue and incentives facing producers. This paper reviews, and provides examples of, agri-environmental policy options and points out the scenarios under which the instrument would be most effective. The paper concludes with recommendations on determining the policy solutions to the problem of salinity in Australia.
Social persistence of plant-based management of dryland salinity
Authors: Barr N. , Wilkinson R.
Published: December 2005

Rural areas of Australia are undergoing rapid social and economic transformations, creating a divergence between those rural landscapes that are depopulating and those that are repopulating. In the depopulating landscape of the cropping zones at risk to salinity, the new paradigm of salinity management based on the development of new plant production systems may be the best strategy available. We suspect this strategy will be less suited to the repopulating rural areas, where amenity is a major factor in population growth. In these landscapes, investment in recharge control based upon commercial pasture production or plantation forest industries is unlikely to be socially compatible with the aspirations of future residents. Strategies aimed at low-cost re-establishment of native vegetation may be more appropriate, but will still be limited in their application. Any discussion of the sustainability of plant-based management systems for dryland salinity needs to include not only biological or agronomic persistence, but also social persistence.
Microarray-based detection of genetic heterogeneity, antimicrobial resistance, and the viable but nonculturable state in human pathogenic
Vibrio spp.
Authors: Vora Gary J. , Meador Carolyn E. , Bird Michele M. , Bopp Cheryl A. , Andreadis Joanne D. , Stenger David A.
Published: December 2005

The morbidity and mortality associated with
Vibrio
-mediated waterborne diseases necessitates the development of sensitive detection technologies that are able to elucidate the identity, potential pathogenicity, susceptibility, and viability of contaminating bacteria in a timely manner. For this purpose, we have designed a single multiplex PCR assay to simultaneously amplify 95 diagnostic regions (encompassing species/serogroup-specific, antimicrobial resistance, and known toxin markers) and combined it with a long oligonucleotide microarray to create a platform capable of rapidly detecting and discriminating the major human pathogenic species from the genus
Vibrio
:
V. cholerae, V. parahaemolyticus, V. vulnificus
, and
V. mimicus
. We were able to validate this strategy by testing 100 geographically and temporally distributed isolates and observed an excellent concordance between species- and serotype-level microarray-based identification and traditional typing methods. In addition to accurate identification, the microarray simultaneously provided evidence of antibiotic resistance genes and mobile genetic elements, such as sulfamethoxazole-trimethoprim constins and class I integrons, and common toxin (
ctxAB, rtxA, hap, hlyA, tl, tdh, trh, vvhA, vlly
, and
vmhA
) and pathogenicity (
tcpA
, type III secretion system) genes that are associated with pathogenic
Vibrio
. The versatility of this method was further underscored by its ability to detect the expression of known toxin and virulence genes from potentially harmful viable but nonculturable organisms. The results suggest that this molecular identification method provides rapid and definitive information that would be of value in epidemiological, environmental, and health risk assessment surveillance.
TGF-β regulates the mechanical properties and composition of bone matrix
Authors: Balooch Guive , Balooch Mehdi , Nalla Ravi K. , Schilling Stephen , Filvaroff Ellen H. , Marshall Grayson W. , Marshall Sally J. , Ritchie Robert O. , Derynck Rik , Alliston Tamara
Published: December 2005

The characteristic toughness and strength of bone result from the nature of bone matrix, the mineralized extracellular matrix produced by osteoblasts. The mechanical properties and composition of bone matrix, along with bone mass and architecture, are critical determinants of a bone's ability to resist fracture. Several regulators of bone mass and architecture have been identified, but factors that regulate the mechanical properties and composition of bone matrix are largely unknown. We used a combination of high-resolution approaches, including atomic-force microscopy, x-ray tomography, and Raman microspectroscopy, to assess the properties of bone matrix independently of bone mass and architecture. Properties were evaluated in genetically modified mice with differing levels of TGF-β signaling. Bone matrix properties correlated with the level of TGF-β signaling. Smad3+/– mice had increased bone mass and matrix properties, suggesting that the osteopenic Smad3–/– phenotype may be, in part, secondary to systemic effects of Smad3 deletion. Thus, a reduction in TGF-β signaling, through its effector Smad3, enhanced the mechanical properties and mineral concentration of the bone matrix, as well as the bone mass, enabling the bone to better resist fracture. Our results provide evidence that bone matrix properties are controlled by growth factor signaling.
Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
Authors: Tobi Dror , Bahar Ivet
Published: December 2005

Protein–protein binding usually involves structural changes that may extend beyond the rearrangements on a local scale, and cannot be explained by a classical lock-and-key mechanism. Several models have been advanced to explain the flexible binding of proteins such as the induced fit mechanism where the ligand is postulated to induce a conformational change at the interaction site upon binding, or the preexisting equilibrium hypothesis that assumes that protein samples an ensemble of conformations at equilibrium conditions and that the ligand binds selectively to an active conformation. We explored the equilibrium motions of proteins that exhibit relatively large (nonlocal) conformational changes upon protein binding using the Gaussian network model and the anisotropic network model of protein dynamics. For four complexes, LIR-1/HLA-A2, Actin/DNase I, CDK2/cyclin, and CDK6/p16
INK4a
, the motions calculated for the monomer exhibiting the largest conformational change, in its unbound (free) form, correlate with the experimentally observed structural changes upon binding. This study emphasizes the preexisting equilibrium/conformational selection as a mechanism for protein–protein interaction and lends support the concept that proteins, in their native conformation, are predisposed to undergo conformational fluctuations that are relevant to, or even required for, their biological functions.
Jasmonate-inducible plant enzymes degrade essential amino acids in the herbivore midgut
Authors: Chen Hui , Wilkerson Curtis G. , Kuchar Jason A. , Phinney Brett S. , Howe Gregg A.
Published: December 2005

The plant hormone jasmonic acid (JA) activates host defense responses against a broad spectrum of herbivores. Although it is well established that JA controls the expression of a large set of target genes in response to tissue damage, very few gene products have been shown to play a direct role in reducing herbivore performance. To test the hypothesis that JA-inducible proteins (JIPs) thwart attack by disrupting digestive processes in the insect gut, we used a MS-based approach to identify host proteins that accumulate in the midgut of
Manduca sexta
larvae reared on tomato (
Solanum lycopersicum
) plants. We show that two JIPs, arginase and threonine deaminase (TD), act in the
M. sexta
midgut to catabolize the essential amino acids Arg and Thr, respectively. Transgenic plants that overexpress arginase were more resistant to
M. sexta
larvae, and this effect was correlated with reduced levels of midgut Arg. We present evidence indicating that the ability of TD to degrade Thr in the midgut is enhanced by herbivore-induced proteolytic removal of the enzyme's C-terminal regulatory domain, which confers negative feedback regulation by isoleucine
in planta
. Our results demonstrate that the JA signaling pathway strongly influences the midgut protein content of phytophagous insects and support the hypothesis that catabolism of amino acids in the insect digestive tract by host enzymes plays a role in plant protection against herbivores.
A 10-aa-long sequence in SLP-76 upstream of the Gads binding site is essential for T cell development and function
Authors: Kumar Lalit , Feske Stefan , Rao Anjana , Geha Raif S.
Published: December 2005

The adapter SLP-76 is essential for T cell development and function. SLP-76 binds to the src homology 3 domain of Lckin vitro. This interaction depends on amino acids 185–194 of SLP-76. To examine the role of the Lck-binding region of SLP-76 in T cell development and function, SLP-76-/-mice were reconstituted with an SLP-76 mutant that lacks amino acids 185–194. Double and single positive thymocytes from reconstituted mice were severely reduced in numbers and exhibited impaired positive selection and increased apoptosis. Peripheral T cells were also reduced in numbers, exhibited impaired phospholipase C-γ1 and Erk phosphorylation, and failed to flux calcium, secrete IL-2, and proliferate in response to T cell antigen receptor ligation. Delayed cutaneous hypersensitivity responses and Ab responses to T cell-dependent antigen were severely impaired. These results indicate that the Lck binding region of SLP-76 is essential for T cell antigen receptor signaling and normal T cell development and function.
Grammatical Subjects in home sign: Abstract linguistic structure in adult primary gesture systems without linguistic input
Authors: Coppola Marie , Newport Elissa L.
Published: December 2005

Language ordinarily emerges in young children as a consequence of both linguistic experience (for example, exposure to a spoken or signed language) and innate abilities (for example, the ability to acquire certain types of language patterns). One way to discern which aspects of language acquisition are controlled by experience and which arise from innate factors is to remove or manipulate linguistic input. However, experimental manipulations that involve depriving a child of language input are impossible. The present work examines the communication systems resulting from natural situations of language deprivation and thus explores the inherent tendency of humans to build communication systems of particular kinds, without any conventional linguistic input. We examined the gesture systems that three isolated deaf Nicaraguans (ages 14-23 years) have developed for use with their hearing families. These deaf individuals have had no contact with any conventional language, spoken or signed. To communicate with their families, they have each developed a gestural communication system within the home called “home sign.” Our analysis focused on whether these systems show evidence of the grammatical category of Subject. Subjects are widely considered to be universal to human languages. Using specially designed elicitation tasks, we show that home signers also demonstrate the universal characteristics of Subjects in their gesture productions, despite the fact that their communicative systems have developed without exposure to a conventional language. These findings indicate that abstract linguistic structure, particularly the grammatical category of Subject, can emerge in the gestural modality without linguistic input.
Endocannabinoids regulate interneuron migration and morphogenesis by transactivating the TrkB receptor
Authors: Berghuis Paul , Dobszay Marton B. , Wang Xinyu , Spano Sabrina , Ledda Fernanda , Sousa Kyle M. , Schulte Gunnar , Ernfors Patrik , Mackie Ken , Paratcha Gustavo , Hurd Yasmin L. , Harkany Tibor
Published: December 2005

In utero
exposure to Δ
9
-tetrahydrocannabinol (Δ
9
-THC), the active component from marijuana, induces cognitive deficits enduring into adulthood. Although changes in synaptic structure and plasticity may underlie Δ
9
-THC-induced cognitive impairments, the neuronal basis of Δ
9
-THC-related developmental deficits remains unknown. Using a Boyden chamber assay, we show that agonist stimulation of the CB
1
cannabinoid receptor (CB
1
R) on cholecystokinin-expressing interneurons induces chemotaxis that is additive with brain-derived neurotrophic factor (BDNF)-induced interneuron migration. We find that Src kinase-dependent TrkB receptor transactivation mediates endocannabinoid (eCB)-induced chemotaxis in the absence of BDNF. Simultaneously, eCBs suppress the BDNF-dependent morphogenesis of interneurons, and this suppression is abolished by Src kinase inhibition
in vitro
. Because sustained prenatal Δ
9
-THC stimulation of CB
1
Rs selectively increases the density of cholecystokinin-expressing interneurons in the hippocampus
in vivo
, we conclude that prenatal CB
1
R activity governs proper interneuron placement and integration during corticogenesis. Moreover, eCBs use TrkB receptor-dependent signaling pathways to regulate subtype-selective interneuron migration and specification.
A selection for mutants that interfere with folding of
Escherichia coli
thioredoxin-1
in vivo
Authors: Huber Damon , Cha Myoung-il , Debarbieux Laurent , Planson Anne-Gaëlle , Cruz Nelly , López Gary , Tasayco María Luisa , Chaffotte Alain , Beckwith Jon
Published: December 2005

Escherichia coli
thioredoxin is normally a cytoplasmic protein involved in the reduction of disulfide bonds. However, thioredoxin can be translocated to the periplasm when it is attached to a cotranslational signal sequence. When exported to the periplasm, it can partially replace the activity of DsbA in promoting the formation of disulfide bonds. In contrast, when thioredoxin is fused to a posttranslational signal sequence, very little of it appears in the periplasm. We propose that this absence of posttranslational export is due to the rapid folding of thioredoxin in the cytoplasm. We sought mutants of thioredoxin that retarded its folding in the cytoplasm, which we accomplished by fusing thioredoxin to a posttranslational signal sequence and selecting for mutants in which thioredoxin was exported to the periplasm, where it could replace DsbA. The collection of mutants obtained represents a limited number of amino acid changes in the protein.
In vitro
studies on purified mutant proteins show that all but one are defective in the kinetics and thermodynamics of protein folding. We propose that the slower folding of the thioredoxin mutant proteins in the cytoplasm allows their export by a posttranslational pathway. We discuss some implications of this class of mutants for aspects of the folding pathway of thioredoxin and for its mechanism of export. In particular, the finding that a folding mutant that allows protein translocation alters an amino acid at the C terminus of the protein suggests that the degree to which thioredoxin folds during its translation must be severely restricted.
eQTL Explorer: integrated mining of combined genetic linkage and expression experiments
Authors: Mueller Michael , Goel Anuj , Thimma Manjula , Dickens Nicholas J , Aitman Timothy J. , Mangion Jonathan
Published: December 2005

Summary: The development of computational resources to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. eQTL Explorer stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer provides a new and powerful tool to interrogate these very large and complex datasets.

Availability: The application is freely available for non-commercial research.

Contact:  jon.mangion@csc.mrc.ac.uk

Supplementary Information: Documentation, source code and a demonstration version are available at
Mass-dependent predation risk as a mechanism for house sparrow declines?
Authors: MacLeod Ross , Barnett Phil , Clark Jacquie , Cresswell Will
Published: December 2005

House sparrow (
Passer domesticus
) numbers have declined rapidly in both rural and urban habitats across Western Europe over the last 30 years, leading to their inclusion on the UK conservation red list. The decline in farmland has been linked to a reduction in winter survival caused by reduced food supply. This reduction in food supply is associated with agricultural intensification that has led to the loss of seed-rich winter stubble and access to spilt grain. However, urban house sparrows have also declined, suggesting that reduced food supply in farmland is not the sole reason for the decline. Here, we show that changes in house sparrow mass and thus fat reserves are not regulated to minimize starvation risk, as would be expected if limited winter food were the only cause of population decline. Instead, the species appears to be responding to mass-dependent predation risk, with starvation risk and predation risk traded-off such that house sparrows may be particularly vulnerable to environmental change that reduces the predictability of the food supply.
Sinking velocities of phytoplankton measured on a stable density gradient by laser scanning
Authors: Walsby Anthony E , Holland Daryl P
Published: December 2005

Two particular difficulties in measuring the sinking velocities of phytoplankton cells are preventing convection within the sedimenting medium and determining the changing depth of the cells. These problems are overcome by using a density-stabilized sedimentation column scanned by a laser. For freshwater species, a suspension of phytoplankton is layered over a vertical density gradient of Percoll solution; as the cells sink down the column their relative concentration is measured by the forward scattering of light from a laser beam that repeatedly scans up and down the column. The Percoll gradient stabilizes the column, preventing vertical mixing by convection, radiation or perturbation of density by the descending cells. Measurements were made on suspensions of 15 μm polystyrene microspheres with a density of 1050 kg m
−3
; the mean velocity was 6.28 μm s
−1
, within 1.5% of that calculated by the Stokes equation, 6.36 μm s
−1
. Measurements made on the filamentous cyanobacterium
Planktothrix rubescens
gave mean velocities within the theoretical range of values based on the range of size, shape, orientation and density of the particles in a modified Stokes equation. Measurements on marine phytoplankton may require density gradients prepared with other substances.
Dry stiction of micro structures—theory and experiment
Authors: Meinhart Mark , Miller Norman , Saif M. Taher A
Published: December 2005

It is well known that compliant freestanding microstructures often stick to the underlying substrate due to capillary pull during wet processing. Hence, it is generally believed that dry processing, which involves only gases, avoids stiction. Contrary to this expectation, here we show experimentally that stiction may also occur during dry processing. We investigate both experimentally and theoretically possible origins of the force that brings the microstructures into contact leading to stiction in a dry environment. The study suggests that aerodynamic drag is the primary force that is responsible for dry stiction. It comes into play during venting or purging with nitrogen the vacuum chambers (reactive ion etcher (RIE)) with compliant microstructures. During the venting process, gases rush into the chamber through an inlet setting up local flows inside the chamber, and subjecting the freestanding microstructures to aerodynamic drag. If the structures are close to one another, such as two parallel structural beams anchored at the ends (studied in detail in this paper), the beam facing the flow shields the downstream beam from the flow. Thus, the upstream beam experiences a larger drag compared to the shielded one, and the gap between them reduces. Smaller is the gap, higher is the shielding effect. The upstream beam may contact the downstream one, and depending on the surface properties of the beams (such as pure aluminium surface prior to oxidation), they may stick to one another through a zipping action. Dry stiction may thus be avoided by slowing down the venting or purging process of RIE chambers with compliant microstructures.
Monochromatic surface waves at the interface between poroelastic and fluid halfspaces
Authors: Albers Bettina
Published: December 2005

The topic of the previous work of Albers and Wilmanski was the study of monochromatic surface waves at the boundary between a porous medium and a vacuum. This article is an extension of this research to the propagation of surface waves on the interface between a porous halfspace and a fluid halfspace. Results for phase and group velocities and attenuations are shown in dependence on both the frequency and the surface permeability. In contrast to classical papers on surface waves where only the limits of the frequencyω→0,ω→∞ and the limits of the surface permeability (fully sealed and fully open boundary) were studied, we investigate the problem in the full range of both parameters. For the analysis we use the ‘simple mixture model’ which is a simplification of the classical Biot model for poroelastic media. The construction of a solution is shown and the dispersion relation solved numerically. There exist three surface waves for this boundary: a leaky Rayleigh wave and both a true and a leaky Stoneley wave. The true Stoneley wave exists only in a limited range of the surface permeability.
No simple answers for ecological immunology: relationships among immune indices at the individual level break down at the species level in waterfowl
Authors: Matson Kevin D , Cohen Alan A , Klasing Kirk C , Ricklefs Robert E , Scheuerlein Alexander
Published: December 2005

Understanding immune function in the context of other life-history traits is crucial to understand the evolution of life histories, at both the individual and species levels. As the interest in assessing immune function for these comparative purposes grows, an important question remains unanswered: can immune function be broadly characterized using one or two simple measures? Often, interpretation of individual assays is ambiguous and relationships among different measures of immune function remain poorly understood. Thus, we employed five protocols to measure 13 variables of immune function in ten species of waterfowl (Anseriformes). All assays were based on a single blood sample subdivided into leukocyte (blood smear) and plasma (frozen until analysis) components. All assays were run using samples from every individual, and a nested analysis was used to partition variation/covariation at the levels of species and individuals within species. We detected positive correlations between functionally related measures of immunity within species, but these were absent from comparisons between species. A canonical correlation analysis revealed no significant relationships between the plasma and leukocyte assays at the levels of both individual and species, suggesting that these measures of immunity are neither competitive nor synergistic. We conclude that one measure of each assay type may be required to maximally characterize immune function in studies of a single species, while the same is not true in studies among species.
Dynamics of multiple symbiont density regulation during host development: tsetse fly and its microbial flora
Authors: Rio Rita V.M , Wu Yi-neng , Filardo Giovanni , Aksoy Serap
Published: December 2005

Symbiotic associations often enhance hosts' physiological capabilities, allowing them to expand into restricted terrains, thus leading to biological diversification. Stable maintenance of partners is essential for the overall biological system to succeed. The viviparous tsetse fly (Diptera: Glossinidae) offers an exceptional system to examine factors that influence the maintenance of multiple symbiotic organisms within a single eukaryotic host. This insect harbours three different symbionts representing diverse associations, coevolutionary histories and transmission modes. The enterics, obligate mutualistWigglesworthiaand beneficialSodalis, are maternally transmitted to the intrauterine larvae, while parasiticWolbachiainfects the developing oocyte. In this study, the population dynamics of these three symbionts were examined through host development and during potentially disruptive events, including host immune challenge, the presence of third parties (such as African trypanosomes) and environmental perturbations (such as fluctuating humidity levels). While mutualistic partners exhibited well-regulated density profiles over different host developmental stages, parasiticWolbachiainfections varied in individual hosts. Host immune status and the presence of trypanosome infections did not impact the steady-state density levels observed for mutualistic microbes in either sex, while these factors resulted in an increase inWolbachiadensity in males. Interestingly, perturbation of the maternal environment resulted in the deposition of progeny harbouring greater overall symbiont loads. The regulation of symbiont density, arising from coadaptive processes, may be an important mechanism driving inter-specific relations to ensure their competitive survival and to promote specialization of beneficial associations.
Inference of cowpox virus transmission rates between wild rodent host classes using space–time interaction
Authors: Carslake David , Bennett Malcolm , Hazel Sarah , Telfer Sandra , Begon Michael
Published: December 2005

There have been virtually no studies of ‘who acquires infection from whom’ in wildlife populations, but patterns of transmission within and between different classes of host are likely to be reflected in the spatiotemporal distribution of infection among those host classes. Here, we use a modified form ofK-function analysis to test for space–time interaction among bank voles and wood mice infectious with cowpox virus. There was no evidence for transmission between the two host species, supporting previous evidence that they act as separate reservoirs for cowpox. Among wood mice, results suggested that transmission took place primarily between individuals of the opposite sex, raising the possibility that cowpox is sexually transmitted in this species. Results for bank voles indicated that infected females might be a more important source of infection to either sex than are males. The suggestion of different modes of transmission in the two species is itself consistent with the apparent absence of transmission between species.
CCAAT/enhancer-binding protein β represses human papillomavirus 11 upstream regulatory region expression through a promoter-proximal YY1-binding site
Authors: Ralph Walter M. , Liu Kai , Auborn Karen J.
Published: December 2005

CCAAT/enhancer-binding protein β (C/EBPβ) can function as a repressor or as an activator of human papillomavirus (HPV) gene expression, depending on which cell type the experiments are conducted. In this report, it was shown that within primary human foreskin keratinocyte cells (HFK) the activity of C/EBPβ can be switched from that of a repressor of HPV11 expression to an activator by mutating a single promoter-proximal consensus YY1-binding site within the HPV11 upstream regulatory region (URR). It was shown that in HFK cells, exogenous expression of C/EBPβ significantly activates the expression of mutant HPV11 URR reporter plasmids that contain deletions which overlap a 127 bp region (−269 to −142). Inclusive in this region are binding sites for multiple transcription factors, including AP1, YY1 and C/EBPα. Only mutation of the YY1 site resulted in the switch in phenotype, indicating that C/EBPβ represses HPV11 expression in these cells via YY1 binding. The level of YY1 activity was also measured in HFK cells transfected with a C/EBPβ expression plasmid and a significant increase in YY1 activity as compared with mock-transfected cells was found. C33A cells, which exhibit activation of wild-type HPV11 gene expression with exogenous C/EBPβ co-expression, failed to demonstrate C/EBPβ-induced YY1 activation. It was concluded that in HFK cells, exogenous C/EBPβ induces the activity of YY1, which, in turn, can repress HPV11 URR expression through the promoter-proximal YY1-binding site.
Selective transmission of hepatitis C virus genotypes and quasispecies in humans and experimentally infected chimpanzees
Authors: Nainan Omana V. , Lu Ling , Gao Feng-Xiang , Meeks Emory , Robertson Betty H. , Margolis Harold S.
Published: December 2005

This study determined whether selective transmission of hepatitis C virus (HCV) species occurred among human and chimpanzee recipients of contaminated blood products or plasma containing multiple genotypes, subgenotypes and quasispecies. Commercially prepared factor VIII concentrate (lot DO56), produced prior to HCV testing and inactivation, was subsequently found by direct cloning to contain the following subgenotypes: 1a and 1b (73 % of clones), 2a (13 % of clones), 2b (11 % of clones) and 3a (4 % of clones). A patient transfused with factor VIII concentrate DO56 was diagnosed with clinical non-A, non-B hepatitis and subsequently found to be infected with HCV subgenotype 1b. Among five chimpanzees inoculated experimentally with the same factor VIII concentrate, two were infected only with HCV subgenotype 1a and three were infected with approximately equivalent clonal proportions of subgenotypes 1a and 1b. HCV hypervariable region 1 (HVR1) quasispecies analysis of the DO56 factor VIII concentrate and a serum specimen from the single chimpanzee that developed a chronic HCV infection following inoculation with DO56 showed 0–56 % nucleotide variation. However, specimens from chimpanzees infected in the second to fourth passages of the DO56 inoculum had 0–8 % HVR1 quasispecies nucleotide variation. The high HVR1 quasispecies variation in the factor VIII concentrate and its first passage in chimpanzees indicates the presence of multiple HCV isolates, whereas the low variation in the second to fourth chimpanzee passages suggests transmission of a single HCV isolate. These findings strongly suggest selective transmission of HCV isolates during experimental chimpanzee infection and among humans exposed to multiple HCV species.
Pathological prion protein in muscles of hamsters and mice infected with rodent-adapted BSE or vCJD
Authors: Thomzig Achim , Cardone Franco , Krüger Dominique , Pocchiari Maurizio , Brown Paul , Beekes Michael
Published: December 2005

Recently, pathological prion protein (PrPTSE) was detected in muscle from sheep infected with scrapie, the archetype of transmissible spongiform encephalopathies (TSEs). This finding has highlighted the question of whether mammalian muscle may potentially also provide a reservoir for TSE agents related to bovine spongiform encephalopathy (BSE) and variant Creutzfeldt–Jakob Disease (vCJD). Here, results are reported from studies in hamsters and mice that provide direct experimental evidence, for the first time, of BSE- and vCJD-associated PrPTSE deposition in muscles. Our findings emphasize the need for further assessment of possible public-health risks from TSE involvement of skeletal muscle.
Liao ning virus, a new Chinese seadornavirus that replicates in transformed and embryonic mammalian cells
Authors: Attoui Houssam , Jaafar Fauziah Mohd , Belhouchet Mourad , Tao Sanju , Chen Boquan , Liang Guodong , Tesh Robert B. , de Micco Philippe , de Lamballerie Xavier
Published: December 2005

Seadornaviruses are emerging arboviral pathogens from the south-east of Asia. The genus Seadornavirus contains two distinct species, Banna virus (BAV) isolated from humans with encephalitis and Kadipiro virus. BAV replicates within insect cells and mice but not in cultured mammalian cells. Here, the discovery of Liao ning virus (LNV), a new seadornavirus from the Aedes dorsalis mosquito, which was completely sequenced and was found to be related to BAV and Kadipiro virus, is reported. Two serotypes of LNV could be distinguished by a serum neutralization assay. According to amino acid identity with other seadornaviruses, and to criteria set by the ICTV for species delineation, LNV was identified as a member of a new species of virus. Its morphology was characterized by electron microscopy and found to be similar to that of BAV. LNV is the first reported seadornavirus that replicates in mammalian cells, leading to massive cytopathic effect in all transformed or embryonic cell lines tested. LNV- and BAV-infected mice producing a viraemia lasting for 5 days was followed by viral clearance. Mice infection generated virus quasi-species for LNV (the first reported observation for quasi-species in the family Reoviridae) but not for BAV. Challenge with BAV in mice immunized against BAV did not lead to productive infection. However, challenge with LNV in mice immunized against LNV was lethal with a new phase of viraemia and massive haemorrhage.
Expression of hepatitis C virus-derived core or NS3 antigens in human dendritic cells leads to induction of pro-inflammatory cytokines and normal T-cell stimulation capabilities
Authors: Li Wen , Li Jie , Tyrrell D. Lorne J. , Agrawal Babita
Published: December 2005

The majority of hepatitis C virus (HCV)-infected individuals become chronically infected, which can result in liver cirrhosis and hepatocellular carcinoma. Patients with chronic HCV are unable to prime and maintain vigorous T-cell responses, which are required to rid the body of the viral infection. Dendritic cells (DCs) are the professional antigen-presenting cells that probably play a dominant role in priming and maintaining vigorous T-cell responses in HCV infection. Furthermore, inefficient DC function may play an important role in HCV chronicity. In order to determine the effect of HCV NS3 and core proteins on phenotype and function of human DCs, recombinant adenoviral vectors containing NS3 or core genes were used to infect human DCs. HCV NS3- or core-protein expression in DCs was confirmed by Western blotting and immunofluorescence staining. The DCs expressing HCV NS3 or core proteins expressed several inflammatory cytokine mRNAs, had a normal phenotype and effectively stimulated allogeneic T cells, as well as T cells specific for another foreign antigen (tetanus toxoid). These findings are important for rational design of cellular-vaccine approaches for the immunotherapy of chronic HCV.
Identification of B-cell epitopes in the capsid protein of avian hepatitis E virus (avian HEV) that are common to human and swine HEVs or unique to avian HEV
Authors: Guo H. , Zhou E.-M. , Sun Z. F. , Meng X.-J. , Halbur P. G.
Published: December 2005

Avian hepatitis E virus (avian HEV) was recently discovered in chickens from the USA that had hepatitis–splenomegaly (HS) syndrome. The complete genomic sequence of avian HEV shares about 50 % nucleotide sequence identity with those of human and swine HEVs. The open reading frame 2 (ORF2) protein of avian HEV has been shown to cross-react with human and swine HEV ORF2 proteins, but the B-cell epitopes in the avian HEV ORF2 protein have not been identified. Nine synthetic peptides from the predicted four antigenic domains of the avian HEV ORF2 protein were synthesized and corresponding rabbit anti-peptide antisera were generated. Using recombinant ORF2 proteins, convalescent pig and chicken antisera, peptides and anti-peptide rabbit sera, at least one epitope at the C terminus of domain II (possibly between aa 477–492) that is unique to avian HEV, one epitope in domain I (aa 389–410) that is common to avian, human and swine HEVs, and one or more epitopes in domain IV (aa 583–600) that are shared between avian and human HEVs were identified. Despite the sequence difference in ORF2 proteins between avian and mammalian HEVs and similar ORF2 sequence between human and swine HEV ORF2 proteins, rabbit antiserum against peptide 6 (aa 389–399) recognized only human HEV ORF2 protein, suggesting complexity of the ORF2 antigenicity. The identification of these B-cell epitopes in avian HEV ORF2 protein may be useful for vaccine design and may lead to future development of immunoassays for differential diagnosis of avian, swine and human HEV infections.
Structural analysis of the human respiratory syncytial virus phosphoprotein: characterization of an α-helical domain involved in oligomerization
Authors: Llorente María T. , García-Barreno Blanca , Calero Miguel , Camafeita Emilio , López Juan A. , Longhi Sonia , Ferrón François , Varela Paloma F. , Melero José A.
Published: December 2005

Human respiratory syncytial virus (HRSV) phosphoprotein (P), an essential cofactor of the viral polymerase, is much shorter (241 aa) than and has no sequence similarity to P of other paramyxoviruses. Nevertheless, bioinformatic analysis of HRSV P sequence revealed a modular organization, reminiscent of other paramyxovirus Ps, with a central structured domain (aa 100–200), flanked by two intrinsically disordered regions (1–99 and 201–241). To test the predicted structure experimentally, HRSV P was purified from cell extracts infected with recombinant vaccinia virus or HRSV. The estimated molecular mass of P by gel filtration (∼500 kDa) greatly exceeded the theoretical mass of a homotetramer, proposed as the oligomeric form of native P. Nevertheless, the profile of cross-linked products obtained with purified P resembled that reported by others with P purified from bacteria or mammalian cells. Thus, the shape of HRSV P probably influences its elution from the gel filtration column, as reported for other paramyxovirus Ps. Digestion of purified HRSV P with different proteases identified a trypsin-resistant fragment (X) that reacted with a previously characterized monoclonal antibody (021/2P). N-terminal sequencing and mass spectrometry analysis placed the X fragment boundaries (Glu-104 and Arg-163) within the predicted structured domain of P. Cross-linking and circular dichroism analyses indicated that fragment X was oligomeric, with a high α-helical content, properties resembling those of the multimerization domain of Sendai and rinderpest virus P. These results denote structural features shared by HRSV and other paramyxovirus Ps and should assist in elucidation of the HRSV P structure.
Broad cellular immunity with robust memory responses to simian immunodeficiency virus following serial vaccination with adenovirus 5- and 35-based vectors
Authors: Barratt-Boyes Simon M. , Soloff Adam C. , Gao Wentao , Nwanegbo Edward , Liu Xiangdong , Rajakumar Premeela A. , Brown Kevin N. , Robbins Paul D. , Murphey-Corb Michael , Day Richard D. , Gambotto Andrea
Published: December 2005

Adenovirus serotype 35 (Ad35) is a promising vaccine platform for human immunodeficiency virus (HIV) infection and emerging infectious diseases as it is uncommon in humans worldwide and is distinct from Ad5, the major vaccine serotype for which many individuals have pre-existing immunity. The immunogenicity of a first-generation, replication-competent Ad35-based vaccine was tested in the simian immunodeficiency virus (SIV) rhesus macaque model by evaluating its capacity to boost immunity generated by Ad5-based vectors. A series of four immunizations with replication-defective Ad5 vectors expressing SIVmac239gaginduced high-frequency responses mediated by both CD8+and CD4+T cells directed against several epitopes. Ad5-specific neutralizing antibody responses that did not neutralize Ad35 were rapidly induced but waned over time. Subsequent immunization with Ad5-based vectors was minimally effective, whereas immunization with Ad35-based vectors generated a strong increase in the frequency of Gag-specific T cells with specificities that were unchanged. While this boosting response was relatively transient, challenge with the distinct pathogenic isolate SIV/DeltaB670 generated robust and selective recall responses to Gag with similar specificities as induced by vaccination that were elevated for 25 weeks relative to controls. Vaccination had measurable albeit minor effects on virus load. Unexpectedly, regional hypervariability within the Gag sequence of SIV/DeltaB670 was associated with mutation of the conserved CD8+T-cell epitope CM9 without concurrent flanking mutations and in the absence of immune pressure. These findings support the further development of Ad35 as a vaccine vector, and promote vaccine regimens that utilize serial administration of heterologous adenoviruses.
Isolation and characterization of a chimpanzee alphaherpesvirus
Authors: Luebcke Emily , Dubovi Edward , Black Darla , Ohsawa Kazutaka , Eberle Richard
Published: December 2005

Although both beta- and gammaherpesviruses indigenous to great-ape species have been isolated, to date all alphaherpesviruses isolated from apes have proven to be human viruses [herpes simplex virus types 1 (HSV1) and 2 (HSV2) or varicella-zoster virus]. If the alphaherpesviruses have co-evolved with their host species, some if not all ape species should harbour their own alphaherpesviruses. Here, the isolation and characterization of an alphaherpesvirus from a chimpanzee (ChHV) are described. Sequencing of a number of genes throughout the ChHV genome indicates that it is collinear with that of HSV. Phylogenetic analyses place ChHV in a clade with HSV1 and HSV2, the alphaherpesviruses of Old World monkeys comprising a separate clade. Analysis of reactivity patterns of HSV2-immune human sera and ChHV-immune chimpanzee sera by competition ELISA support this relationship. Phylogenetic analyses also place ChHV rather than HSV1 as the closest relative of HSV2.
Tectonic, a novel regulator of the Hedgehog pathway required for both activation and inhibition
Authors: Reiter Jeremy F. , Skarnes William C.
Published: December 2005

We report the identification of a novel protein that participates in Hedgehog-mediated patterning of the neural tube. This protein, named Tectonic, is the founding member of a previously undescribed family of evolutionarily conserved secreted and transmembrane proteins. During neural tube development, mouse Tectonic is required for formation of the most ventral cell types and for full Hedgehog (Hh) pathway activation. Epistasis analyses reveal that Tectonic modulates Hh signal transduction downstream of Smoothened (Smo) and Rab23. Interestingly, characterization of Tectonic Shh and Tectonic Smo double mutants indicates that Tectonic plays an additional role in repressing Hh pathway activity.
The Rad50S allele promotes ATM-dependent DNA damage responses and suppresses ATM deficiency: implications for the Mre11 complex as a DNA damage sensor
Authors: Morales Monica , Theunissen Jan-Willem F. , Kim Carla F. Bender , Kitagawa Risa , Kastan Michael B. , Petrini John H.J.
Published: December 2005

Genetic and cytologic data from Saccharomyces cerevisiae and mammals implicate the Mre11 complex, consisting of Mre11, Rad50, and Nbs1, as a sensor of DNA damage, and indicate that the complex influences the activity of ataxia-telangiectasia mutated (ATM) in the DNA damage response. Rad50S/S mice exhibit precipitous apoptotic attrition of hematopoietic cells. We generated ATM- and Chk2-deficient Rad50S/S mice and found that Rad50S/S cellular attrition was strongly ATM and Chk2 dependent. The hypomorphic Mre11ATLD1 and Nbs1ΔB alleles conferred similar rescue of Rad50S/S-dependent hematopoietic failure. These data indicate that the Mre11 complex activates an ATM–Chk2-dependent apoptotic pathway. We find that apoptosis and cell cycle checkpoint activation are parallel outcomes of the Mre11 complex–ATM pathway. Conversely, the Rad50S mutation mitigated several phenotypic features of ATM deficiency. We propose that the Rad50S allele is hypermorphic for DNA damage signaling, and that the resulting constitutive low-level activation of the DNA damage response accounts for the partial suppression of ATM deficiency in Rad50S/S Atm-/- mice.
Mixed effects of habitat fragmentation on species richness and community structure in a microarthropod microecosystem
Authors: Hoyle Martin , Harborne Alastair R.
Published: December 2005

Abstract. 1. Theory is unclear about the optimal degree of isolation of habitat fragments where the aim is to maximise species richness. In a field‐based microecosystem of Collembola and predatory and non‐predatory mites, moss patches of the same total area were fragmented to varying degrees. The habitat was left for several months to allow the communities to approach a new state of equilibrium.

2. The species richness (in particular of predatory mites) of a given area of habitat was greater when it was part of a large mainland area than part of an island, in agreement with theory.

3. Conversely, species richness and abundance were largely unaffected by fragmentation of a fixed area of island habitat. In this case, it is suggested here that the advantages of several small patches (e.g. reduced impact of environmental stochasticity, wider range of habitats overall) were equally balanced by the advantages of a single large patch (e.g. reduced effect of demographic stochasticity, wider range of habitats within a single patch, reduced edge effect), or that both effects were small.

4. The shapes of rank–abundance curves were similar among the levels of fragmentation of a fixed area of island habitat, implying that fragmentation had little impact on community structure. Conversely, the species composition of non‐predatory mites varied weakly, but significantly, by fragmentation.
Profitable self‐superparasitism in an infanticidal parasitoid when conspecifics are present: self‐superparasitism deters later attackers from probing for infanticide
Authors: Ito Emi , Yamada Yoshihiro Y.
Published: December 2005

Abstract.  1. To reveal the profitability of self‐superparasitism when conspecifics are present, the total combined fitness returns from the first and second ovipositions under triple parasitism were compared with fitness returns from the first oviposition under double parasitism, using the small brown hopper Laodelphax striatellus and its semi‐solitary infanticidal parasitoid Echthrodelphax fairchildii.

2. The total combined survival rate of the first and second comers under triple parasitism with oviposition intervals of 1/24 h (where 1 and 24 h represent the first‐to‐second and second‐to‐third oviposition intervals respectively) was nearly double the survival rate of the first comer under double parasitism with a 25‐h oviposition interval, although there was no difference between these triple and double parasitisms in terms of head width and developmental time. Under the conditions of other oviposition intervals, self‐superparasitism produced null (1/1‐ and 24/24‐h intervals) or negative fitness returns (24/1‐h intervals). This suggests that self‐superparasitism on hosts that were self‐parasitised 1 h previously is profitable when conspecifics are present.

3. When the female parasitoid laid an egg on a host harbouring the earlier comer(s) on the non‐oviposition side, she often probed the non‐oviposition side for infanticide, i.e. killing the first offspring. When the first and second comers were on different sides, the probing frequency at the third oviposition in triple parasitism with 1/24‐h oviposition intervals was lower than that at the second oviposition in double parasitism with a 25‐h oviposition interval. This difference was responsible for the above difference in survival rate between the triple and double parasitisms.
537. Impatiens Namchabarwensis
Authors: Morgan Raymond J. , Yong‐Ming Yuan , Xue‐Jun Ge
Published: December 2005

Summary.  Impatiens namchabarwensis, a new species of Impatiens found in Tibet, is described together with its taxonomy, distribution, ecology and notes on cultivation.
540. Betula Insignis
Authors: McAllister Hugh
Published: December 2005

Summary.  Betula insignis Franch. from central and western China is described and illustrated. Its similarity to the fossil species, B. leopoldii McGintie, described from the Eocene in British Columbia is noted.