bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and Evaluation of an Online, Inquiry‐Based Food Safety Education Program for Secondary Teachers and Their Students
Authors: Beffa‐Negrini Patricia A. , Cohen Nancy L. , Laus Mary Jane , McLandsborough Lynne A.
Published: September 2007

ABSTRACT:  Secondary science teachers who integrate food safety (FS) into curricula can provide FS knowledge and skills to youth while reinforcing science skills and concepts. National science education standards and the Biological Science Curriculum Study 5E Inquiry‐based Learning Model were used to design an online training, Food Safety FIRST. The training has 3 modules, each with 15 h of web‐based instruction, interactive discussion, and tools to conduct experiments or critical evaluation projects. A CD‐ROM, web site (http://foodsafetyfirst.org), and lab kit were developed to accompany module activities. Seventy‐one teachers registered for the program; 38 matched pretest/posttest evaluations were analyzed. When asked their intention to teach FS in the next year, enrollees responded “definitely” (60.5%) or “possibly” (34.2%), reaching potentially 3570 students. Participants found the training very valuable (71.1%) and were significantly more comfortable teaching FS at posttest (3.6 ± 0.5 on a 4‐point Likert scale) than at pretest (2.8 ± 1.0; P < 0.0001, n= 35). Self‐reported FS practices also improved from pretest (24.8 ± 5.7 out of a possible 35) to posttest (27.7 ± 4.8; P < 0.001, n= 32). On 4‐point Likert scales, teachers were confident answering FS questions (3.4); confident that if they did a good job teaching this topic, students would be interested in FS (3.4); and confident FS concepts taught would meet national science standards (3.4). They found the program satisfactory for demonstrating inquiry‐based learning (3.8). Most agreed that they would change FS habits (3.2). Using 5‐point scales, participants agreed that they felt more able to critically evaluate FS information on the Internet (4.2) and that the training was enjoyable in an online format (4.3).
Biomorphic Silicon Nitride Ceramics with Fibrous Morphology Prepared by Sol Infiltration and Reduction–Nitridation
Authors: Luo Min , Gao Ji‐Qiang , Yang Jian‐Feng , Fang Jun‐Zhuo , Wang Zheng
Published: September 2007

Biomorphic silicon nitride (Si3N4) ceramics with fibrous morphology were fabricated by combining sol–gel infiltration with carbothermal reduction nitridation from wood precursor. Y2O3‐incorporated silica sol was used as the infiltrated solution to promote the formation of fibrous Si3N4 grain at 1600°C under high nitrogen pressure (0.6 MPa). The influence of sintering conditions (additive and temperature) on the phase composition and microstructure of sintering bodies was analyzed, and the reaction mechanism is discussed.
Structural Aspects of SBA‐1 Cubic Mesoporous Silica Synthesized via a Sol–Gel Process Using a Silatrane Precursor
Authors: Tanglumlert Walairat , Imae Toyoko , White Timothy J. , Wongkasemjit Sujitra
Published: September 2007

Silatrane prepared from fumed silica and triethanolamine was used as a precursor for SBA‐1 synthesis at room temperature using cationic surfactants, derived from alkyltrimethylammonium bromides, CnTMAB (n=14, 16, and 18), as templates in dilute solutions. The influence of acidity, alkyl chain length of the surfactant, and synthesis temperature was studied. The shape of the SBA‐1 crystals was dependent on the alkyl chain length of the surfactant. At a high surfactant concentration and an elevated reaction temperature (50°C), three‐dimensionally ordered mesopores were invariably produced. Both X‐ray diffraction and transmission electron microscopic results showed characteristics of the three‐dimensional cubic structure. Scanning electron microscopic images of SBA‐1 indicated the crystalline‐like appearance of an octadecahedron (18‐hedron) consistent with six square {100} and 12 hexagonal {110} planes with a cubic symmetry. The surface area of the product was as high as 1000–1500 m2/g with an adsorption volume of 0.6–1.0 cm3/g.
Netrin‐G2 and netrin‐G2 ligand are both required for normal auditory responsiveness
Authors: Zhang W. , Rajan I. , Savelieva K. V. , Wang C.‐Y. , Vogel P. , Kelly M. , Xu N. , Hasson B. , Jarman W. , Lanthorn T. H.
Published: September 2007

Mice in which netrin‐G2 has been genetically inhibited do not startle to an acoustic stimulus, but otherwise perform normally through a behavioral test battery. Light microscopic examination of the inner ear showed no obvious structural abnormalities. Brainstem responses to acoustic stimuli (auditory brainstem responses, ABR) were also present, confirming the lack of any overarching defects in the inner ear or auditory nerve. Genetic inhibition of netrin‐G2 ligand produced a nearly identical phenotype, that is, no startle with ABR present, and otherwise normal. This similarity confirms that these two proteins act in the same biological pathway. We have also determined that the affinity between the two proteins is strong, around 2.5 nm, similar to that observed between netrin‐G1 and netrin‐G1 ligand – 2.3 nm in our hands. The combination of equivalent phenotypes when genetically inhibited coupled with evidence of a strong biochemical interaction supports the notion of a receptor–ligand interaction between these two proteins in vivo. This interaction is critical for auditory synaptic responsiveness in the brain.
Lesions in the central nervous system associated with perinatal lamb mortality
Authors: DUTRA F , QUINTANS G , BANCHERO G
Published: September 2007

Objective  To identify and describe the occurrence of neurological lesions that could have an effect on lamb mortality.

Procedure  The central nervous system was investigated macroscopically (n = 92) and microscopically (n = 72) in lambs dying in the perinatal period during 3 years in flocks of adult Corriedale ewes. The central nervous system was removed intact and samples of cerebral cortex, basal ganglia, thalamus, hippocampus, mesencephalon, cerebellar cortex, medulla oblongata, and cervical spinal cord were scored microscopically for the severity of neuronal dead, cytotoxic and perivascular oedema, and haemorrhage.

Results  Neurologic findings between birth and 6 days included haemorrhages in meninges, brain congestion and oedema, neuronal ischemic necrosis, intraparenchymal haemorrhages in medulla oblongata and cervical spinal cord, parasagittal cerebral necrosis, and periventricular leukomalacia. No significant lesions were found in anteparturient deaths or in those aged between 7 and 16 days. Oedema was more severe in the brain than in other regions of the central nervous system. Ischaemic neurons first appeared 24 hours post partum, increased linearly in number between 48 hours and 5 days post partum, and had a laminar distribution in the cerebral cortex, indicating a hypoxic‐ischemic encephalopathy. Haemorrhages were most severe in the gray matter of medulla oblongata and cervical spinal cord, suggesting trauma due to instability of atlantoaxialis joint.

Conclusion  Lesions in the central nervous system can explain most deaths at birth and within 6 days of birth. The lesions were hypoxic‐ischemic and appeared to be related to birth injury.
Genetic analysis of canine parvovirus from dogs in Australia
Authors: MEERS J , KYAW‐TANNER M , BENSINK Z , ZWIJNENBERG R
Published: September 2007

Objective To determine the genetic variants of canine parvovirus‐2 (CPV) present in domestic dogs in Australia and to investigate 26 cases of apparent vaccine failure.

Design Thirty‐three samples of faeces or intestinal tissues and 16 cell culture virus isolates collected over a period from 1980 to 2005 from five Australian states were analysed.

Procedure DNA was extracted from the samples and a 1975 bp fragment of the VP1/2 gene of CPV was amplified by polymerase chain reaction (PCR) and sequenced. Sequences were compared to published strains of CPV‐2, CPV‐2a, CPV‐2b and CPV‐2c.

Results Forty‐one of 43 PCR‐positive samples contained CPV‐2a viruses. One sample collected in 2002 from a pup in northern NSW contained a CPV‐2b virus. One sample that had been included in the study as a CPV‐antigen negative control sample contained a CPV‐2 virus.

Conclusion CPV‐2a remains the predominant genetic variant of CPV in dogs in Australia and has not been replaced by CPV‐2b or CPV‐2c as in many other countries. The vaccine failures investigated in the study were likely caused not by genetic variation of field viruses but by maternal antibody interference in the response of pups to vaccination.
The Shift from Dating to Hooking up in College: What Scholars Have Missed
Authors: Bogle Kathleen A.
Published: September 2007

In recent years, research has been building that suggests dating has been replaced by hooking up as the dominant way for heterosexual students to get together on college campuses. Although recent studies have documented the phenomenon of hooking up, there is evidence that this behavior was likely in place long before it was recognized in the literature. Yet, for the past several decades, scholars have continued to examine ‘dating’ among college students. This calls into question whether scholars missed a fundamental shift in how heterosexual men and women form sexual and romantic relationships on campus. In this paper, I will (i) review the major findings on hooking up, (ii) explain the differences between traditional dating and hooking up, (iii) explore when traditional dating declined and hooking up emerged on the college campus, and (iv) discuss the effect of this shift on the literature.
Sociology of Terrorism and Counterterrorism: A Social Science Understanding of Terrorist Threat
Authors: Tosini Domenico
Published: September 2007

The purpose of this article is to outline a social science understanding of terrorist threat, with special reference to political violence of new terrorist groups, fundamentalist movements and extremist organisations such as Al‐Qaeda. Four main terrorism topics will be examined: (i)Definition of terrorism. We will make explicit the political and moral implications of the word ‘terrorism’ by tracing a brief history of terrorism; at the same time, a definition of terrorism will be proposed based on an overview of terrorism studies. (ii)Typology of terrorism. The topic to be addressed here concerns the classification of terrorist groups, paying special attention to contemporary fundamentalist movements and extremist organisations (particularly after World War II). (iii)Explanation of terrorism.Criticism will be made of psychological explanations of terrorism that try to trace political violence back to specific personal traits or psychopathological profiles of terrorists. We will offer an alternative explanation, focusing on specific social, cultural and religious factors to be considered the root causes of terrorism. Suicide terrorism will be used as a case study. (iv) Counterterrorism policy. Here, we will discuss some of the limitations and counterproductive effects of the counterterrorism measures adopted by governments after 9/11, including new antiterrorism legislation, the case of special detention at Guantanamo Bay, and the Iraq invasion. Most of such limitations are due to a misunderstanding of the political culture and ideology of Islamic extremism and fundamentalism (Islamism). Some concluding remarks will summarise the findings of the article and underline the most important suggestions for a future research agenda in the sociology of terrorism and counterterrorism.
Temporal environmental variation and phenotypic plasticity: a mechanism underlying priority effects
Authors: T. Hoverman Jason , A. Relyea Rick
Published: September 2007

Understanding the role of history in the formation of communities has been a major challenge in community ecology. Here, we explore the role of phenotypic plasticity and its associated trait‐mediated indirect interactions as a mechanism behind priority effects. Using organisms with inducible defenses as a model system, we examine how aquatic communities initially containing different predator environments are affected at the individual and community level by the colonization of a second predator. Snails and tadpoles were established in four different caged‐predator environments (no predator, fish, crayfish or water bugs). These four communities were then crossed with three predator colonization treatments (no colonization, early colonization, or late colonization) using lethal water bugs as the predator. The snails responded to the caged predator environments with predator‐specific behavioral and morphological defenses. In the colonization treatments, snails possessing the wrong phenotype attempted to induce phenotypic changes to defend themselves against the new risk. However, snails initially induced by a different predator environment often suffered high predation rates. Hence, temporal variation in predation risk not only challenged the snail prey to try to track this environmental variation through time by adjusting their defensive phenotypes, but also caused trait‐mediated interactions between snails and the colonizing predator. For tadpoles within these communities, there was little evidence that the morphological responses of snails indirectly effected tadpole predation rates by colonizing water bugs. Unexpectedly, predation rates on tadpoles by colonizing water bugs were generally higher in the three caged‐predator treatments, suggesting that water bugs elevated their foraging activity in response to potentially competing predators. In summary, we demonstrate an important priority effect in which the initial occurrence of one species of predator can facilitate predation by a second predator that colonizes at a later date (i.e. a TMII) suggesting that phenotypic plasticity can be an important driver behind priority effects (i.e. historical exposure to predators).
The influence of bite size on foraging at larger spatial and temporal scales by mammalian herbivores
Authors: Shipley Lisa A.
Published: September 2007

Organisms respond to their heterogeneous environment in complex ways at many temporal and spatial scales. Here, I examine how the smallest scale process in foraging by mammalian herbivores, taking a bite, influences plants and herbivores over larger scales. First, because cropping bites competes with chewing them, bite size influences short‐term intake rate of herbivores within plant patches. On the other hand, herbivores can chew bites while searching for new ones, thus influencing the time spent vigilant and intake rate as animals move among food patches. Therefore, bite size affects how much time herbivores must spend foraging each day. Because acquiring energy is necessary for fitness, herbivores recognize the importance of bite size and select bites, patches and diets based on tradeoffs between harvesting rates, digestion, and sheering forces. In turn, induced structural defenses of plants, such as thorns, allow plants to respond immediately to herbivory by reducing bite size and thus tissue loss. Over evolutionary time, herbivores have adapted mouth morphology that allows them to maximize bite size on their primary forage plant, whereas plants faced with large mammalian herbivores have adapted structures such as divarication that minimize bite size and protect themselves from herbivory. Finally, bite size available among plant communities can drive habitat segregation and migration of larger herbivores across landscapes.
Tree species richness affects litter production and decomposition rates in a tropical biodiversity experiment
Authors: Scherer‐Lorenzen Michael , Luis Bonilla José , Potvin Catherine
Published: September 2007

We report data on leaf litter production and decomposition from a manipulative biodiversity experiment with trees in tropical Panama, which has been designed to explore the relationship between tree diversity and ecosystem functioning. A total of 24 plots (2025 m2) were established in 2001 using six native tree species, with 1‐, 3‐, and 6‐species mixtures. We estimated litter production during the dry season 2005 with litter traps; decomposition was assessed with a litter bag approach during the following wet season.

Litter production during the course of the dry season was highly variable among the tree species. Tree diversity significantly affected litter production, and the majority of the intermediate diverse mixtures had higher litter yields than expected based on yields in monoculture. In contrast, high diverse mixtures did not show such overyielding in litter production. Litter decomposition rates were also highly species‐specific, and were related to various measures of litter quality (C/N, lignin/N, fibre content). We found no overall effect of litter diversity if the entire litter mixtures were analyzed, i.e. mixing species resulted in pure additive effects and observed decomposition rates were not different from expected rates. However, the individual species changed their decomposition pattern depending on the diversity of the litter mixture, i.e. there were species‐specific responses to mixing litter. The analysis of temporal C and N dynamics within litter mixtures gave only limited evidence for nutrient transfer among litters of different quality.

At this early stage of our tree diversity experiment, there are no coherent and general effects of tree species richness on both litter production and decomposition. Within the scope of the biodiversity‐ecosystem functioning relationship, our results therefore highlight the process‐specific effects diversity may have. Additionally, species‐specific effects on ecosystem processes and their temporal dynamics are important, but such effects may change along the gradient of tree diversity.
Abundance variability of benthic intertidal species: effects of changing scale on patterns perception
Authors: Pech Daniel , Ardisson Pedro‐Luis , Bourget Edwin , Condal Alfonso R.
Published: September 2007

For the last years scale issues have contributed to the understanding of the complex organization of communities. In practice however the choice of observational scales remains one of the major issues of discussion among ecologists. Case studies showing the implications of tuning up the observational scales are still needed to illustrate the crucial role played by sampling designs on the perception of population and community variability. On the ground of simulations on real data sets, this paper presents empirical evidence showing how the abundance patterns of benthic intertidal species change according to the scale (grain size and extent) of observation. A field experimental study was carried out in which abundance of rocky shore intertidal benthic species and physical factors associated to the substratum were recorded in contiguous quadrats (5×10 cm) along three 100‐m transect lines. Subsampling routines were developed to generate different scale scenarios by monotonically increasing the grain size and extent of the data. Results showed that: 1) changes in the observational grain size and extent convey different information about the spatial patterning of the recorded factors, and 2) the strength of the relationship between species abundance and physical factors tends to decrease as extent increase. Under the continuous simulations of scale scenarios along transects, variance estimation was the criterion adopted to make explicit the degree of precision in patterns description obtained by each scale scenario. The experimental variogram demonstrated to be a useful statistic for estimating the variance associated with discrete levels along the continuous varying function of scale.
Late Archean Biospheric Oxygenation and Atmospheric Evolution
Authors: Kaufman Alan J. , Johnston David T. , Farquhar James , Masterson Andrew L. , Lyons Timothy W. , Bates Steve , Anbar Ariel D. , Arnold Gail L. , Garvin Jessica , Buick Roger
Published: September 2007

High-resolution geochemical analyses of organic-rich shale and carbonate through the 2500 million-year-old Mount McRae Shale in the Hamersley Basin of northwestern Australia record changes in both the oxidation state of the surface ocean and the atmospheric composition. The Mount McRae record of sulfur isotopes captures the widespread and possibly permanent activation of the oxidative sulfur cycle for perhaps the first time in Earth's history. The correlation of the time-series sulfur isotope signals in northwestern Australia with equivalent strata from South Africa suggests that changes in the exogenic sulfur cycle recorded in marine sediments were global in scope and were linked to atmospheric evolution. The data suggest that oxygenation of the surface ocean preceded pervasive and persistent atmospheric oxygenation by 50 million years or more.
Comment on "A Semi-Empirical Approach to Projecting Future Sea-Level Rise"
Authors: Schmith Torben , Johansen Søren , Thejll Peter
Published: September 2007

Rahmstorf (Reports, 19 January 2007, p. 368) used the observed relation between rates of change of global surface temperature and sea level to predict future sea-level rise. We revisit the application of the statistical methods used and show that estimation of the regression coefficient is not robust. Methods commonly used within econometrics may be more appropriate for the problem of projected sea-level rise.
Structures of the CCR5 N Terminus and of a Tyrosine-Sulfated Antibody with HIV-1 gp120 and CD4
Authors: Huang Chih-chin , Lam Son N. , Acharya Priyamvada , Tang Min , Xiang Shi-Hua , Hussan Syed Shahzad-ul , Stanfield Robyn L. , Robinson James , Sodroski Joseph , Wilson Ian A. , Wyatt Richard , Bewley Carole A. , Kwong Peter D.
Published: September 2007

The CCR5 co-receptor binds to the HIV-1 gp120 envelope glycoprotein and facilitates HIV-1 entry into cells. Its N terminus is tyrosine-sulfated, as are many antibodies that react with the co-receptor binding site on gp120. We applied nuclear magnetic resonance and crystallographic techniques to analyze the structure of the CCR5 N terminus and that of the tyrosine-sulfated antibody 412d in complex with gp120 and CD4. The conformations of tyrosine-sulfated regions of CCR5 (α-helix) and 412d (extended loop) are surprisingly different. Nonetheless, a critical sulfotyrosine on CCR5 and on 412d induces similar structural rearrangements in gp120. These results now provide a framework for understanding HIV-1 interactions with the CCR5 N terminus during viral entry and define a conserved site on gp120, whose recognition of sulfotyrosine engenders posttranslational mimicry by the immune system.
The Disaster Business
Authors: Ash Caroline
Published: September 2007

Scénario Catastrophe
.
Christian Delécraz, Laurie Durussel, and Alessia Fondrini, curators
. Musée d'Ethnographie, Genève, Switzerland, through 6 January 2008.
www.ville-ge.ch/musinfo/ethg/expo06_uk.php

Scénario Catastrophe
.
Christian Delécraz and Laurie Durussel, Eds.
. Infolio, Gollion, Switzerland, 2007. 352 pp, Paper. CHF 16, €11. ISBN 9780521858915.

The curators draw on a huge variety of objects, videos, and recordings to illuminate how human cultures deal with catastrophes such as hurricanes, genocide, and epidemics.
Genetic Rearrangements of Tn
1546
-Like Elements in Vancomycin-Resistant
Enterococcus faecium
Isolates Collected from Hospitalized Patients over a Seven-Year Period
Authors: Park Il Joong , Lee Wee Gyo , Lim Young Ae , Cho Sung Ran
Published: September 2007

The heterogeneity of Tn
1546
results from point mutations, deletions, and the integration of insertion sequence (IS) elements. Among these variations, the presence of IS elements accounts for much of the heterogeneity. Such a rearrangement could play a key role in the evolution of the
vanA
gene cluster, and hence, it may modify its transferability. In this study, we characterized the consequence of Tn
1546
in
vanA
-containing
Enterococcus faecium
isolates collected from patients over time. From 1998 to 2004, 57
vanA
-containing
E. faecium
isolates were collected from hospitalized patients at Ajou University Hospital in Korea. PCR amplification of internal regions of Tn
1546
was performed, and both DNA strands were directly sequenced by the dideoxy termination method. All isolates were divided into three main types, including the prototype, according to the distribution of IS elements integrated into Tn
1546
elements. Type I was characterized by an IS
1542
insertion in the
orf2-vanR
intergenic region and an IS
1216V
insertion in the
vanX-vanY
intergenic region. Type II was represented by the presence of two copies of IS
1216V
at the 3′ end of IS
1542
and in the
vanX-vanY
intergenic region, as well as IS
1542
in the
orf2-vanR
intergenic region. Seventeen strains isolated from 1998 to 2000 represented type I, and 38 strains isolated from 2000 to 2004 represented type II. The remaining two isolates were the prototype. The tendency for the rearrangement of Tn
1546
was that the sequences were shortened as time passed, especially at the left or the right end, and hence, this could gradually modulate their transferability.
Identification of an APOBEC3G Binding Site in Human Immunodeficiency Virus Type 1 Vif and Inhibitors of Vif-APOBEC3G Binding
Authors: Mehle Andrew , Wilson Heather , Zhang Chengsheng , Brazier Andrew Jay , McPike Mark , Pery Erez , Gabuzda Dana
Published: September 2007

The APOBEC3 cytidine deaminases are potent antiviral factors that restrict replication of human immunodeficiency virus type 1 (HIV-1). HIV-1 Vif binds APOBEC3G and APOBEC3F and targets these proteins for ubiquitination by forming an E3 ubiquitin ligase with cullin 5 and elongins B and C. The N-terminal region of Vif is required for APOBEC3G binding, but the binding site(s) is unknown. To identify the APOBEC3G binding site in Vif, we established a scalable binding assay in a format compatible with development of high-throughput screens. In vitro binding assays using recombinant proteins identified Vif peptides and monoclonal antibodies that inhibit Vif-APOBEC3G binding and suggested involvement of Vif residues 33 to 83 in APOBEC3G binding. Cell-based binding assays confirmed these results and demonstrated that residues 40 to 71 in the N terminus of Vif contain a nonlinear binding site for APOBEC3G. Mutation of the highly conserved residues His42/43 but not other charged residues in this region inhibited Vif-APOBEC3G binding, Vif-mediated degradation of APOBEC3G, and viral infectivity. In contrast, mutation of these residues had no significant effect on Vif binding and degradation of APOBEC3F, suggesting a differential requirement for His42/43 in Vif binding to APOBEC3G and APOBEC3F. These results identify a nonlinear APOBEC3 binding site in the N terminus of Vif and demonstrate that peptides or antibodies directed against this region can inhibit Vif-APOBEC3G binding, validating the Vif-APOBEC3 interface as a potential drug target.
CD4+CCR5+T-Cell Dynamics during Simian Immunodeficiency Virus Infection of Chinese Rhesus Macaques
Authors: Monceaux V. , Viollet L. , Petit F. , Cumont M. C. , Kaufmann G. R. , Aubertin A. M. , Hurtrel B. , Silvestri G. , Estaquier J.
Published: September 2007

Simian immunodeficiency virus (SIV) infection of rhesus macaques (RMs) provides a reliable model to study the relationship between lentivirus replication, cellular immune responses, and CD4+T-cell dynamics. Here we investigated, using SIVmac251-infected RMs of a Chinese genetic background (which experience a slower disease progression than Indian RMs), the dynamics of CD4+CCR5+T cells, as this subset of memory/activated CD4+T cells is both a preferential target of virus replication and a marker of immune activation. As expected, we observed that the number of circulating CD4+CCR5+T cells decreases transiently at the time of peak viremia. However, at 60 days postinfection, i.e., when set-point viremia is established, the level of CD4+CCR5+T cells was increased compared to the baseline level. Interestingly, this increase correlated with faster disease progression, higher plasma viremia, and early loss of CD4+T-cell function, as measured by CD4+T-cell count, the fraction of memory CD4+T cells, and the recall response to purified protein derivative. Taken together, these data show a key difference between the dynamics of the CD4+CCR5+T-cell pool (and its relationship with disease progression) in Chinese RMs and those described in previous reports for Indian SIVmac251-infected RMs. As the SIV-associated changes in the CD4+CCR5+T-cell pool reflect the opposing forces of SIV replication (which reduces this cellular pool) and immune activation (which increases it), our data suggest that in SIV-infected Chinese RMs the impact of immune activation is more prominent than that of virus replication in determining the size of the pool of CD4+CCR5+T cells in the periphery. As progression of HIV infection in humans also is associated with a relative expansion of the level of CD4+CCR5+T cells, we propose that SIV infection of Chinese RMs is a very valuable and important animal model for understanding the pathogenesis of human immunodeficiency virus infection.
HC-Pro Protein of
Potato Virus Y
Can Interact with Three
Arabidopsis
20S Proteasome Subunits In Planta
Authors: Jin Yongsheng , Ma Dongyuan , Dong Jiangli , Jin Jingchen , Li Daofeng , Deng Changwang , Wang Tao
Published: September 2007

The multifunctional protein helper component proteinase (HC-Pro) is thought to interfere with the activity of the 20S proteasome; however, no sites of interaction have been identified for either protein. Here, we first show that the
Potato virus Y
(PVY) HC-Pro protein can interact with three
Arabidopsis
20S proteasome subunits (PAA, PBB, and PBE), using a yeast two-hybrid system and the bimolecular fluorescence complement assay. In addition, yeast two-hybrid analysis of the interaction between several mutant subunits of the 20S proteasome and PVY HC-Pro confirmed that residues 81 to 140 of PAA, 1 to 80 of PBB, and 160 to 274 of PBE are necessary for binding PAA, PBB, and PBE to PVY HC-Pro, respectively. Deletion mutant analysis of PVY HC-Pro showed that the N terminus (residues 1 to 97) is necessary for its interaction with three
Arabidopsis
20S proteasome subunits. The ability of HC-Pro to interact and interfere with the activity of the 20S proteasome may help explain the molecular basis of its multifunctional character.
Activation of the Human T-Cell Leukemia Virus Type 1 Long Terminal Repeat by the Ternary Complex Factor Elk-1
Authors: Winter Heather Y. , Dayaram Tajhal , Marriott Susan J.
Published: September 2007

Serum response factor (SRF) was recently shown to bind and activate the human T-cell leukemia virus type 1 (HTLV-1) promoter at bases −116 to −125 relative to the transcription start site. In addition to the SRF binding site (CArG box), serum response elements (SRE) also typically contain a binding site for a member of the ternary complex factor (TCF) family. Here we demonstrate the presence of two TCF binding sites upstream of the viral CArG box. Binding of the TCF family member Elk-1 to these sites was shown to activate transcription of the promoter. Based on these results, the position of the previously described viral SRE (vSRE) within the HTLV-1 promoter can be extended from −116 to −157 to include the two newly identified TCF sites. Purified Elk-1 bound to a probe containing the vSRE, and this complex formed a ternary complex with SRF. In addition, the complex formed by nuclear extract on this probe contained Elk-1, as shown by electrophoretic mobility shift assay supershift. Both of the predicted TCF sites independently bound Elk-1. Elk-1 activated transcription of the HTLV-1 long terminal repeat (LTR), and mutations within either of the TCF sites or the CArG box reduced responsiveness of the LTR to Elk-1. Chromatin immunoprecipitation demonstrated that Elk-1 associates with the HTLV-1 LTR in vivo. These results identify a functional SRE within the HTLV-1 LTR and suggest that both Elk-1 and SRF play important roles in regulating basal HTLV-1 gene expression.
Virp1 Is a Host Protein with a Major Role in
Potato Spindle Tuber Viroid
Infection in
Nicotiana
Plants
Authors: Kalantidis K. , Denti M. A. , Tzortzakaki S. , Marinou E. , Tabler M. , Tsagris M.
Published: September 2007

Viroids are small, circular, single-stranded RNA molecules that, while not coding for any protein, cause several plant diseases. Viroids rely for their infectious cycle on host proteins, most of which are likely to be involved in endogenous RNA-mediated phenomena. Therefore, characterization of host factors interacting with the viroid may contribute to the elucidation of RNA-related pathways of the hosts.
Potato spindle tuber viroid
(PSTVd) infects several members of the
Solanaceae
family. In an RNA ligand screening we have previously isolated the tomato protein Virp1 by its ability to specifically interact with PSTVd positive-strand RNA. Virp1 is a bromodomain-containing protein with an atypical RNA binding domain and a nuclear localization signal. Here we investigate the role of Virp1 in the viroid infection cycle by the use of transgenic lines of
Nicotiana tabacum
and
Nicotiana benthamiana
that either overexpress the tomato
Virp1
RNA or suppress the orthologous
Nicotiana
genes through RNA silencing. Plants of the
Virp1
-suppressed lines were not infected by PSTVd or
Citrus exocortis viroid
through mechanical inoculation, indicating a major role of Virp1 in viroid infection. On the other hand, overexpression of tomato Virp1 in
N. tabacum
and
N. benthamiana
plants did not affect PSTVd KF 440-2 infectivity or symptomatology in these species. Transfection experiments with isolated protoplasts revealed that
Virp1
-suppressed cells were unable to sustain viroid replication, suggesting that resistance to viroid infection in
Virp1
-suppressed plants is likely the result of cell-autonomous events.
The Conserved FRNK Box in HC-Pro, a Plant Viral Suppressor of Gene Silencing, Is Required for Small RNA Binding and Mediates Symptom Development
Authors: Shiboleth Yoel Moshe , Haronsky Elina , Leibman Diana , Arazi Tzahi , Wassenegger Michael , Whitham Steven A. , Gaba Victor , Gal-On Amit
Published: September 2007

The helper component-proteinase (HC-Pro) protein of potyviruses is a suppressor of gene silencing and has been shown to elicit plant developmental-defect-like symptoms. In
Zucchini yellow mosaic virus
(ZYMV), a mutation in the highly conserved FR
180
NK box of HC-Pro to FI
180
NK causes attenuation of these symptoms. At 5 days postinoculation and before symptoms appear, virus accumulation, HC-Pro protein levels, and viral short interfering RNA (siRNA) levels are similar for the severe (FRNK) and attenuated (FINK) strains. At this stage, ZYMV
FRNK
caused greater accumulation of most microRNAs (miRNAs), and especially of their complementary miRNA “passenger” strands (miRNA*s), in systemically infected leaves than the attenuated ZYMV
FINK
did. HC-Pro
FRNK
specifically bound artificial siRNA and miRNA/miRNA* duplexes with a much higher affinity than the mutated HC-Pro
FINK
. Further analysis of the mutant and wild-type HC-Pro proteins revealed that suppressor activity of the ZYMV HC
FINK
mutant was not diminished. However, the FINK mutation caused a loss of HC-Pro suppressor function in other potyviruses. Replacement of the second positively charged amino acid in the ZYMV FRNK box to result in FRNA also caused symptom attenuation and reduced small RNA duplex-binding affinity without loss of suppressor activity. Our data suggest that the highly conserved FRNK box in the HC-Pro of potyviruses is a probable point of contact with siRNA and miRNA duplexes. The interaction of the FRNK box with populations of miRNAs directly influences their accumulation levels and regulatory functions, resulting in symptom development.
Plasma Cell-Specific Transcription Factor XBP-1s Binds to and Transactivates the Epstein-Barr Virus BZLF1 Promoter
Authors: Sun Chia Chi , Thorley-Lawson David A.
Published: September 2007

Epstein-Barr virus (EBV) in vivo is known to establish persistent infection in resting, circulating memory B cells and to productively replicate in plasma cells. Until now, the molecular mechanism of how EBV switches from latency to lytic replication in vivo was not known. Here, we report that the plasma cell differentiation factor, XBP-1s, activates the expression of the master regulator of EBV lytic activation, BZLF1. Using reporter assays, we observed that XBP-1s was able to transactivate the BZLF1 promoter, Zp, in a plasma cell line and other lymphoid cell lines but, interestingly, not in epithelial cell lines. We have identified an XBP-1s binding site on the ZID/ZII region of Zp, which when abolished by site-directed mutagenesis led to abrogation of XBP-1s binding and promoter activation. Using the chromatin immunoprecipitation assay, we observed direct binding of XBP-1s to endogenous Zp in an EBV-infected plasma cell line. Finally, in the same cell line, we observed that overexpression of XBP-1s resulted in increased expression of BZLF1, while knockdown of XBP-1s with short hairpin RNA drastically reduces BZLF1 expression. We suggest that EBV harnesses the B-cell terminal differentiation pathway via XBP-1s as a physiological signal to reactivate and begin viral replication. We are currently investigating other signals, such as the endoplasmic reticulum stress response proteins, which act upstream of XBP-1s, to identify other interacting factors that initiate and/or amplify the lytic switch.
The Human Papillomavirus Type 16 E7 Oncoprotein Activates the Fanconi Anemia (FA) Pathway and Causes Accelerated Chromosomal Instability in FA Cells
Authors: Spardy Nicole , Duensing Anette , Charles Domonique , Haines Nathan , Nakahara Tomomi , Lambert Paul F. , Duensing Stefan
Published: September 2007

Fanconi anemia (FA) patients have an increased risk for squamous cell carcinomas (SCCs) at sites of predilection for infection with high-risk human papillomavirus (HPV) types, including the oral cavity and the anogenital tract. We show here that activation of the FA pathway is a frequent event in cervical SCCs. We found that FA pathway activation is triggered mainly by the HPV type 16 (HPV-16) E7 oncoprotein and is associated with an enhanced formation of large FANCD2 foci and recruitment of FANCD2 as well as FANCD1/BRCA2 to chromatin. Episomal expression of HPV-16 oncoproteins was sufficient to activate the FA pathway. Importantly, the expression of HPV-16 E7 in FA-deficient cells led to accelerated chromosomal instability. Taken together, our findings establish the FA pathway as an early host cell response to high-risk HPV infection and may help to explain the greatly enhanced susceptibility of FA patients to squamous cell carcinogenesis at anatomic sites that are frequently infected by high-risk HPVs.
Identification of Five Major and Two Minor Genotypes of Varicella-Zoster Virus Strains: a Practical Two-Amplicon Approach Used To Genotype Clinical Isolates in Australia and New Zealand
Authors: Loparev Vladimir N. , Rubtcova Elena N. , Bostik Vanda , Govil Dhwani , Birch Christopher J. , Druce Julian D. , Schmid D. Scott , Croxson Margaret C.
Published: September 2007

Whole genome phylogenetic analysis in this study resolved a total of five major genotypes among the 22 varicella-zoster virus (VZV) strains or isolates for which complete genomic sequences are available. Consistent with earlier publications we have designated these genotypes European 1 (E1), European 2 (E2), Japanese (J), mosaic 1 (M1), and mosaic 2 (M2). Single nucleotide polymorphism (SNP) analysis performed in a whole-genome alignment revealed that VZV isolates of all five genotypes can be accurately genotyped using SNPs from two amplicons: open reading frame 22 (ORF22) and either ORF21 or ORF50. This modified approach identifies all of the genotypes observed using any of the published genotyping protocols. Of 165 clinical varicella and zoster isolates from Australia and New Zealand typed using this approach, 67 of 127 eastern Australian isolates were E1, 30 were E2, 16 were J, 10 were M1, and 4 were M2; 25 of 38 New Zealand isolates were E1, 8 were E2, and 5 were M1. VZV strain diversity in eastern Australia is thus broader than has been described for any other region, including Europe, Africa, and North America. J strains were far more prevalent than previously observed in countries other than Japan. Two-amplicon typing was in complete accord with genotypes derived using SNP in multiple ORFs (ORFs 1, 21, 22, 38, 50, 54, and 62). Two additional minor genotypes, M3 and M4, could also be resolved using two-amplicon typing.
FoxP3+CD25+CD8+T-Cell Induction during Primary Simian Immunodeficiency Virus Infection in Cynomolgus Macaques Correlates with Low CD4+T-Cell Activation and High Viral Load
Authors: Karlsson Ingrid , Malleret Benoît , Brochard Patricia , Delache Benoît , Calvo Julien , Le Grand Roger , Vaslin Bruno
Published: September 2007

The early immune response fails to prevent the establishment of chronic human immunodeficiency virus (HIV) infection but may influence viremia during primary infection, thereby possibly affecting long-term disease progression. CD25+FoxP3+regulatory T cells may contribute to HIV/simian immunodeficiency virus (SIV) pathogenesis by suppressing efficient antiviral responses during primary infection, favoring high levels of viral replication and the establishment of chronic infection. In contrast, they may decrease immune activation during chronic infection. CD4+regulatory T cells have been studied in the most detail, but CD8+CD25+FoxP3+T cells also have regulatory properties. We monitored the dynamics of CD25+FoxP3+T cells during primary and chronic SIVmac251 infection in cynomolgus macaques. The number of peripheral CD4+CD25+FoxP3+T cells paralleled that of memory CD4+T cells, with a rapid decline during primary infection followed by a rebound to levels just below baseline and gradual depletion during the course of infection. No change in the proportion of CD25+FoxP3+T cells was observed in peripheral lymph nodes. A small number of CD4+CD25+FoxP3+T cells at set point was associated with a high plasma viral load. In contrast, peripheral CD8+CD25+FoxP3+T cells were induced a few days after peak plasma viral load during primary infection. The number of these cells was positively correlated with viral load and negatively correlated with CD4+T-cell activation, SIV antigen-specific proliferative responses during primary infection, and plasma viral load at set point, with large numbers of CD8+CD25+FoxP3+T cells being indicative of a poor prognosis.
Entry of Hepatitis Delta Virus Requires the Conserved Cysteine Residues of the Hepatitis B Virus Envelope Protein Antigenic Loop and Is Blocked by Inhibitors of Thiol-Disulfide Exchange
Authors: Abou-Jaoudé Georges , Sureau Camille
Published: September 2007

Hepatitis delta virus (HDV) particles are coated with the envelope proteins (large, middle, and small) of the hepatitis B virus (HBV). The large protein bears an infectivity determinant in its pre-S1 domain, whereas a second determinant has been proposed to map to the cysteine-rich antigenic loop (AGL) within the S domain of all three envelope proteins (G. Abou Jaoudé and C. Sureau, J. Virol. 79:10460-10466, 2006). In this study, the AGL cysteines were substituted by serine or alanine, and the mutants were evaluated for their function at viral entry using HDV particles and susceptible HepaRG cells. Mutations of cysteines 121 to 149 were tolerant of the production of HDV virions. The mutations altered the structure and antigenicity of the conserved “a” determinant of the AGL, as measured by conformation-sensitive antibodies, and they created a block to infectivity. Substitution of Cys-90 or Cys-221, located outside of the AGL, had no impact on the “a” determinant or viral entry. Furthermore, infectivity was maintained when the AGL CxxC motif at position 121 to 124 was modified by single-amino-acid deletion or insertion, suggesting that cysteines 121 and 124 are not catalyzers of thiol/disulfide exchange. However, membrane-impermeable inhibitors of thiol/disulfide isomerazation demonstrated a dose-dependent inhibition of infection in an in vitro assay when applied to the virus prior to inoculation or during the virus-cell interaction period. Overall, the results demonstrate the essential role of the AGL cysteines at viral entry, and they establish a correlation between the cysteine disulfide network, the conformation of the “a” determinant, and infectivity.
A High Viral Burden Predicts the Loss of CD8 T-Cell Responses Specific for Subdominant Gag Epitopes during Chronic Human Immunodeficiency Virus Infection
Authors: Geldmacher Christof , Gray Clive , Nason Martha , Currier Jeffrey R. , Haule Antelmo , Njovu Lilian , Geis Steffen , Hoffmann Oliver , Maboko Leonard , Meyerhans Andreas , Cox Josephine , Hoelscher Michael
Published: September 2007

Human immunodeficiency virus (HIV)-specific CD8 T-cell responses targeting products encoded within the Gag open reading frame have frequently been associated with better viral control and disease outcome during the chronic phase of HIV infection. To further clarify this relationship, we have studied the dynamics of Gag-specific CD8 T-cell responses in relation to plasma viral load and time since infection in 33 chronically infected subjects over a 9-month period. High baseline viral loads were associated with a net loss of breadth (P< 0.001) and a decrease in the total magnitude of the Gag-specific T-cell response in general (P= 0.03). Most importantly, the baseline viral load predicted the subsequent change in the breadth of Gag recognition over time (P< 0.0001,r2= 0.41). Compared to maintained responses, lost responses were low in magnitude (P< 0.0001) and subdominant in the hierarchy of Gag-specific responses. The present study indicates that chronic exposure of the human immune system to high levels of HIV viremia is a determinant of virus-specific CD8 T-cell loss.
Replication Initiator Protein NS1 of the Parvovirus Minute Virus of Mice Binds to Modular Divergent Sites Distributed throughout Duplex Viral DNA
Authors: Cotmore Susan F. , Gottlieb Robert L. , Tattersall Peter
Published: September 2007

To initiate DNA synthesis, the NS1 protein of minute virus of mice (MVM) first binds to a simple cognate recognition sequence in the viral origins, comprising two to three tandem copies of the tetranucleotide TGGT. However, this motif is also widely dispersed throughout the viral genome. Using an immunoselection procedure, we show that NS1 specifically binds to many internal sites, so that all viral fragments of more than ∼170 nucleotides effectively compete for NS1, often binding with higher affinity to these internal sites than to sites in the origins. We explore the diversity of the internal sites using competitive binding and DNase I protection assays and show that they vary between two extreme forms. Simple sites with three somewhat degenerate, tandem TGGT reiterations bind effectively but are minimally responsive to ATP, while complex sites, containing multiple variably spaced TGGT elements arranged as opposing clusters, bind NS1 with an affinity that can be enhanced ∼10-fold by ATP. Using immuno-selection procedures with randomized sequences embedded within specific regions of the genome, we explore possible binding configurations in these two types of site. We conclude that binding is modular, combinatorial, and highly flexible. NS1 recognizes two to six variably spaced, more-or-less degenerate forms of the 5′-TGGT-3′ motif, so that it binds efficiently to a wide variety of sequences. Thus, despite complex coding constraints, binding sites are configured at frequent intervals throughout duplex forms of viral DNA, suggesting that NS1 may serve as a form of chromatin to protect and tailor the environment of replicating genomes.