bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving Access to Research
Authors: Courant Paul N. , O'Donnell James J. , Okerson Ann , Taylor Crispin B.
Published: January 2010

Unless you sit on your Institution's Library Advisory Committee, a professional society's publications committee, or a journal editorial board, you may have paid only passing attention to the debate over public access to scientific research, which has been swirling through these communities ever since science journals started publishing online 15 years ago. That is about to change. Last week, the U.S. House Science and Technology Committee's Roundtable on Scholarly Publishing (on which we served along with 10 others) released a report
*
arguing that journal articles derived from federal research funding should be made publicly available as quickly as practicable—generally in a year or less after publication—and in ways that will improve scholarship by maximizing the scope for interoperability across articles, among disciplines, and internationally. Currently, there is no consistency regarding which version of an article is freely available. In contrast, the roundtable's report recommends that access policies aim toward making the “Version of Record” (the final version of an article in its published form) publicly available. And the report also asserts that any successful scheme for public access must provide methods for permanent public access.
Foreshadowing Haiti's Catastrophe
Authors: Kerr Richard A.
Published: January 2010

Tens of thousands likely perished in what may be the Western Hemisphere's worst disaster in a century. But the devastation of last week's earthquake in Haiti was more the result of lack of infrastructure than the strength of the quake itself, which barely qualified as major.
Models Foresee More-Intense Hurricanes in the Greenhouse
Authors: Kerr Richard A.
Published: January 2010

Fewer but fiercer and more-destructive hurricanes will sweep the Atlantic Basin in the 21st century as climate change continues, a new modeling study by U.S. government researchers, reported on page
454
of this week's issue of
Science
, suggests.
Killing of Professor Sparks Fight Over His Science and His Politics
Authors: Bhattacharjee Yudhijit
Published: January 2010

Last week, Iranian physicist Masoud Alimohammadi was assassinated by a remote-controlled motorcycle bomb outside of his apartment. Iranian authorities characterized the killing as an attempt by U.S. and Israeli intelligence agencies to rein in Iran's nuclear program. But colleagues and others believe that the government may actually be the culprit.
Google Plots Exit Strategy As China Shores Up 'Great Firewall'
Authors: Stone Richard , Xin Hao
Published: January 2010

Google's declaration last week that it will no longer play ball with Chinese censors has inflamed tensions between backers of the free flow of information and advocates of China's increasingly assertive efforts to cleanse the Internet of offensive material.
Under Fire From Pharma, Institute May Lose Its Director
Authors: Vogel Gretchen
Published: January 2010

A long-running feud between pharmaceutical companies and the German institute that evaluates the effectiveness of medical treatments could cost the institute director his job.
Flows on Mars But No Water
Authors: Kerr Richard A.
Published: January 2010

Researchers operating the next-generation camera orbiting Mars have found eight more of the steep gullies where it looks as if water recently gushed downhill. But the timing and geographic distribution of the flows point not to liquid water but to bone-dry flows of debris somehow facilitated by a ground frosting of frozen carbon dioxide, they announced at the fall meeting of the American Geophysical Union.
Antarctic Glacier Off Its Leash
Authors: Kerr Richard A.
Published: January 2010

An unmanned autonomous submarine has discovered a sea-floor ridge that may have been the last hope for stopping the now-accelerating retreat of the Pine Island Glacier, a crumbling keystone of the West Antarctic Ice Sheet, researchers announced at the fall meeting of the American Geophysical Union.
Inexpensive Designer Antigen for Anti-HIV Antibody Detection with High Sensitivity and Specificity
Authors: Talha Sheikh M. , Salminen Teppo , Chugh Deepti A. , Swaminathan Sathyamangalam , Soukka Tero , Pettersson Kim , Khanna Navin
Published: January 2010

A novel recombinant multiepitope protein (MEP) has been designed that consists of four linear, immunodominant, and phylogenetically conserved epitopes, taken from human immunodeficiency virus (HIV)-encoded antigens that are used in many third-generation immunoassay kits. This HIV-MEP has been evaluated for its diagnostic potential in the detection of anti-HIV antibodies in human sera. A synthetic MEP gene encoding these epitopes, joined by flexible peptide linkers in a single open reading frame, was designed and overexpressed in
Escherichia coli
. The recombinant HIV-MEP was purified using a single affinity step, yielding >20 mg pure protein/liter culture, and used as the coating antigen in an in-house immunoassay. Bound anti-HIV antibodies were detected by highly sensitive time-resolved fluorometry, using europium(III) chelate-labeled anti-human antibody. The sensitivity and specificity of the HIV-MEP were evaluated using Boston Biomedica worldwide HIV performance, HIV seroconversion, and viral coinfection panels and were found to be comparable with those of commercially available anti-HIV enzyme immunoassay (EIA) kits. The careful choice of epitopes, high epitope density, and an
E. coli-
based expression system, coupled with a simple purification protocol and the use of europium(III) chelate-labeled tracer, provide the capability for the development of an inexpensive diagnostic test with high degrees of sensitivity and specificity.
Immunization of Mice with Single PspA Fragments Induces Antibodies Capable of Mediating Complement Deposition on Different Pneumococcal Strains and Cross-Protection
Authors: Moreno Adriana T. , Oliveira Maria Leonor S. , Ferreira Daniela M. , Ho Paulo L. , Darrieux Michelle , Leite Luciana C. C. , Ferreira Jorge M. C. , Pimenta Fabiana C. , Andrade Ana Lúcia S. S. , Miyaji Eliane N.
Published: January 2010

PspA is an important candidate for a vaccine with serotype-independent immunity against pneumococcal infections. Based on sequence relatedness, PspA has been classified into three families comprising six clades. We have previously addressed the cross-reactivity of antibodies against PspA fragments containing the N-terminal and proline-rich regions of PspA from clades 1 to 5 (PspA1, PspA2, PspA3, PspA4, and PspA5) by Western blot analysis and reported that anti-PspA4 and anti-PspA5 were able to recognize pneumococci expressing PspA proteins from all of the clades analyzed. We have now analyzed the functional capacity of these antibodies to bind and to mediate complement deposition on intact bacteria
in vitro
. Our results show that both PspA4 and PspA5 elicit antibodies that are able to bind and to mediate complement deposition efficiently on pneumococcal strains bearing PspA proteins from clades 1 to 5. Moreover, mice immunized with PspA4 and PspA5 were protected against an intranasal lethal challenge with strains expressing PspA proteins from the two major families. PspA4 and PspA5 are thus able to induce antibodies with a high degree of cross-reactivity
in vitro
, which is reflected in cross-protection of mice. We have also analyzed the contribution of the nonproline (NonPro) block within the conserved proline-rich region to the reactivity of anti-PspA antibodies, and the results indicate that N-terminal α-helical region, the blocks of proline repeats, and the NonPro region can influence the degree of cross-reactivity of antibodies to PspA.
Subtilase Cytotoxin-Encoding
subAB
Operon Found Exclusively among Shiga Toxin-Producing
Escherichia coli
Strains
Authors: Irino Kinue , Vieira Mônica A. Midolli , Gomes Tânia A. Tardelli , Guth Beatriz E. Cabilio , Naves Zita V. Furtado , Oliveira Murilo Gomes , dos Santos Luis Fernando , Guirro Mirian , Timm Claudio D. , Pigatto Caroline P. , Farah Sonia M. S. S. , Vaz Tânia M. I.
Published: January 2010

The presence of
subAB
was investigated for 3,453
Escherichia coli
strains of various pathogenic categories. The occurrence of other virulence genes in
subAB
-positive strains was investigated. The
subAB
operon was detected among some Shiga toxin-producing
E. coli
(STEC) serotypes devoid of
eae
and carrying
ehx
A. Most
subAB
-positive strains also harbored
stx
2
,
iha
,
saa
, and
lpfA
O113
.
Predominance and Emergence of Clones of Hospital-Acquired Methicillin-Resistant
Staphylococcus aureus
in Malaysia
Authors: Ghaznavi-Rad Ehsanollah , Shamsudin Mariana Nor , Sekawi Zamberi , Khoon Liew Yun , Aziz Mohammad Nazri , Hamat Rukman Awang , Othman Norlijah , Chong Pei Pei , van Belkum Alex , Ghasemzadeh-Moghaddam Hamed , Neela Vasanthakumari
Published: January 2010

We define the epidemiology of predominant and sporadic methicillin-resistant
Staphylococcus aureus
(MRSA) strains in a central teaching and referral hospital in Kuala Lumpur, Malaysia. This is done on the basis of
spa
sequencing, multilocus sequence typing (MLST), staphylococcal cassette chromosome
mec
(SCC
mec
) typing, and virulence gene profiling. During the period of study, the MRSA prevalence was 44.1%, and 389 MRSA strains were included. The prevalence of MRSA was found to be significantly higher in the patients of Indian ethnicity (
P
< 0.001). The majority (92.5%) of the isolates belonged to ST-239,
spa
type t037, and possessed the type III or IIIA SCC
mec
. The arginine catabolic mobile element (ACME)
arcA
gene was detected in three (1.05%) ST-239 isolates. We report the first identification of ACME
arcA
gene-positive ST-239. Apart from this predominant clone, six (1.5%) isolates of ST-22, with two related
spa
types (t032 and t4184) and a singleton (t3213), carrying type IVh SCC
mec
, were detected for the first time in Asia. A limited number of community-acquired (CA) MRSA strains were also detected. These included ST-188/t189 (2.1%), ST-1/t127 (2.3%), and ST-7/t091 (1%). Panton-Valentin leukocidin (PVL) was detected in all ST-1 and ST-188 strains and in 0.7% of the ST-239 isolates. The majority of the isolates carried
agr
I, except that ST-1 strains were
agr
III positive. Virulence genes
seg
and
sei
were seen only among ST-22 isolates. In conclusion, current results revealed the predominance of ST-239-SCC
mec
III/IIIA and the penetration of ST-22 with different virulence gene profiles. The emergence in Malaysia of novel clones of known epidemic and pathogenic potential should be taken seriously.
Molecular Changes Associated with Altered Patterns of Norovirus Outbreak Epidemics in Victoria, Australia, in 2006 to 2007
Authors: Bruggink Leesa D. , Marshall John A.
Published: January 2010

Noroviruses (NoVs) are now considered the most common cause of outbreaks of nonbacterial gastroenteritis, but the factors which control the incidence of NoVs are poorly understood. In 2006, the pattern of NoV outbreak epidemics in Victoria, Australia, changed compared to the pattern for 2002 to 2005 and 2007. This study examined molecular correlates of the changed NoV periodicity. For the period of 2002 to 2007, 8,507 fecal specimens from 1,495 gastroenteritis outbreaks were tested for NoV by reverse transcription-PCR, and 1,018 NoV outbreaks were identified. Nucleotide sequence analysis was used to define genotypes and GII.4 variants. For 2002 to 2007, GII.4 was the predominant genotype. For the period of 2002 to 2005 and 2007, a single NoV outbreak epidemic occurred in warmer months of each year, but in 2006 two epidemics occurred in 1 year, one in colder months and one in warmer months of the year. For 2002 to 2007, four major GII.4 variants, “2002 Oxford/Farmington Hills,” “2004 Hunter,” “2006a,” and “2006b,” were identified. Each NoV outbreak epidemic was linked principally to one of these four variants, and there was a time link, a delay of 2 to 6 months, between the first detection of a GII.4 variant and the first outbreak epidemic in which it was the principal variant. The unusual 2006 pattern of outbreak epidemics can then be correlated with the appearance of two GII.4 variants within a short space of time, resulting in two outbreak epidemics in a short space of time, i.e., in the 1 year. This study provides a potentially greater ability to predict the characteristics of NoV epidemics.
Human Papillomavirus DNA Detection in Menstrual Blood from Patients with Cervical Intraepithelial Neoplasia and Condyloma Acuminatum
Authors: Wong Sze Chuen Cesar , Au Thomas Chi Chuen , Chan Sammy Chung Sum , Chan Charles Ming Lok , Lam Money Yan Yee , Zee Benny Chung Ying , Pong Wei Mei , Chan Anthony Tak Cheung
Published: January 2010

The Papanicolaou test generates pain and embarrassment, and cytology screening has limited sensitivity for detection of cervical neoplasia. These factors urge the use of another screening test that can overcome these limitations. We explore a completely noninvasive method using detection of human papillomavirus (HPV) DNA in women's menstrual blood (MB). The participants were divided into 3 cohorts: (i) 235 patients with cervical intraepithelial neoplasia 3 (CIN 3) (
n
= 48), CIN 2 (
n
= 60), CIN 1 (
n
= 58), or condyloma acuminatum (CAC) (
n
= 69) before treatment or remission; (ii) from the first cohort of patients, 108 CIN 3 or CIN 2 patients after treatment and 62 CIN 1 or CAC patients after remission; and (iii) 323 apparently normal subjects (ANS) without any cervical disease. The HPV genotypes of the infected patients were confirmed by direct sequencing. Quantitative real-time PCR (QRT-PCR) was used to measure the MB HPV16 load for 15 infected patients. Results showed that the sensitivity, specificity, and positive and negative predictive values for detection of MB HPV DNA in samples from patients with CIN or CAC were 82.8%, 93.1%, 90.0%, and 87.9%, respectively. Moreover, MB HPV DNA was found in samples from 22.2% of CIN 3 or CIN 2 patients after treatment, 0.0% of CIN 1 or CAC patients after remission, and 8.1% of ANS, 4 of whom were found to have CIN 1 or CAC. Furthermore, QRT-PCR showed that the normalized MB HPV16 DNA copy numbers in samples from patients with CIN 1 to CIN 3 were significantly increased. These preliminary results suggested that MB HPV DNA is a potential noninvasive marker for these premalignant cervical diseases.
Influenza Virus Inactivation for Studies of Antigenicity and Phenotypic Neuraminidase Inhibitor Resistance Profiling
Authors: Jonges Marcel , Liu Wai Ming , van der Vries Erhard , Jacobi Ronald , Pronk Inge , Boog Claire , Koopmans Marion , Meijer Adam , Soethout Ernst
Published: January 2010

Introduction of a new influenza virus in humans urges quick analysis of its virological and immunological characteristics to determine the impact on public health and to develop protective measures for the human population. At present, however, the necessity of executing pandemic influenza virus research under biosafety level 3 (BSL-3) high-containment conditions severely hampers timely characterization of such viruses. We tested heat, formalin, Triton X-100, and β-propiolactone treatments for their potencies in inactivating human influenza A(H3N2) and avian A(H7N3) viruses, as well as seasonal and pandemic A(H1N1) virus isolates, while allowing the specimens to retain their virological and immunological properties. Successful heat inactivation coincided with the loss of hemagglutinin (HA) and neuraminidase (NA) characteristics, and β-propiolactone inactivation reduced the hemagglutination titer and NA activity of the human influenza virus 10-fold or more. Although Triton X-100 treatment resulted in inconsistent HA activity, the NA activities in culture supernatants were enhanced consistently. Nonetheless, formalin treatment permitted the best retention of HA and NA properties. Triton X-100 treatment proved to be the easiest-to-use influenza virus inactivation protocol for application in combination with phenotypic NA inhibitor susceptibility assays, while formalin treatment preserved B-cell and T-cell epitope antigenicity, allowing the detection of both humoral and cellular immune responses. In conclusion, we demonstrated successful influenza virus characterization using formalin- and Triton X-100-inactivated virus samples. Application of these inactivation protocols limits work under BSL-3 conditions to virus culture, thus enabling more timely determination of public health impact and development of protective measures when a new influenza virus, e.g., pandemic A(H1N1)v virus, is introduced in humans.
Novel Screening Agar for Detection of Vancomycin-Nonsusceptible
Staphylococcus aureus
Authors: Carey-Ann Burnham D. , Weber Carol J. , Dunne W. Michael
Published: January 2010

In January 2006, the Clinical and Laboratory Standards Institute (CLSI) updated breakpoints for vancomycin susceptibility testing for
Staphylococcus aureus
such that an MIC greater than 2 mg/liter was considered to represent nonsusceptibility to vancomycin. Previously, an MIC of 4 mg/liter had been considered to represent susceptibility. Additionally, in 2009, the CLSI altered the guidelines for staphylococci such that disk diffusion was no longer an acceptable means for testing vancomycin susceptibility in these organisms. To accommodate the change in breakpoints and methodological updates, we designed a medium consisting of brain heart infusion agar with 3 mg/liter vancomycin (BHI-V3) to screen for isolates of
S. aureus
with reduced susceptibility to vancomycin. We challenged this medium using a previously characterized collection of 100 isolates of
S. aureus
, including 55 vancomycin-susceptible isolates and 45 isolates representing vancomycin-intermediate strains of
S. aureus
(VISA) (with vancomycin MICs of 4 mg/liter or greater). All of the VISA isolates grew on the agar, for 100% sensitivity. Nineteen vancomycin-susceptible isolates also grew on the agar, for 65% specificity. We then incorporated BHI-V3 into clinical practice. In the first 60 days postimplementation, we identified 17 potential VISA isolates out of 421
S. aureus
isolates tested. Thirteen out of the 17 were confirmed to represent VISA isolates. In light of the excellent sensitivity of this medium, we recommend that clinical laboratories incorporate BHI-V3 to screen for vancomycin-nonsusceptible isolates of
S. aureus
.
Toll-Like Receptor Agonists Synergistically Increase Proliferation and Activation of B Cells by Epstein-Barr Virus
Authors: Iskra Stefanie , Kalla Markus , Delecluse Henri-Jacques , Hammerschmidt Wolfgang , Moosmann Andreas
Published: January 2010

Epstein-Barr virus (EBV) efficiently drives proliferation of human primary B cellsin vitro, a process relevant for human diseases such as infectious mononucleosis and posttransplant lymphoproliferative disease. Human B-cell proliferation is also driven by ligands of Toll-like receptors (TLRs), notably viral or bacterial DNA containing unmethylated CpG dinucleotides, which triggers TLR9. Here we quantitatively investigated how TLR stimuli influence EBV-driven B-cell proliferation and expression of effector molecules. CpG DNA synergistically increased EBV-driven proliferation and transformation, T-cell costimulatory molecules, and early production of interleukin-6. CpG DNA alone activated only memory B cells, but CpG DNA enhanced EBV-mediated transformation of both memory and naive B cells. Ligands for TLR2 or TLR7/8 or whole bacteria had a weaker but still superadditive effect on B-cell transformation. Additionally, CpG DNA facilitated the release of transforming virus by established EBV-infected lymphoblastoid cell lines. These results suggest that the proliferation of EBV-infected B cells and their capability to interact with immune effector cells may be directly influenced by components of bacteria or other microbes present at the site of infection.
New, Closely Related Haloarchaeal Viral Elements with Different Nucleic Acid Types
Authors: Roine Elina , Kukkaro Petra , Paulin Lars , Laurinavičius Simonas , Domanska Aušra , Somerharju Pentti , Bamford Dennis H.
Published: January 2010

During the search for haloarchaeal viruses, we isolated and characterized a new pleomorphic lipid-containing virus,
Haloarcula hispanica
pleomorphic virus 1 (HHPV-1), that infects the halophilic archaeon
Haloarcula hispanica
. The virus contains a circular double-stranded DNA genome of 8,082 bp in size. The organization of the genome shows remarkable synteny and amino acid sequence similarity to the genome and predicted proteins of the halovirus HRPV-1, a pleomorphic single-stranded DNA virus that infects a halophilic archaeon
Halorubrum
sp. Analysis of the two halovirus sequences, as well as the entire nucleotide sequence of the 10.8-kb pHK2-plasmid and a 12.6-kb chromosomal region in
Haloferax volcanii
, allows us to suggest a new group of closely related viruses with genomes of either single-stranded or double-stranded DNA. Currently, closely related viruses are considered to have the same genome type. Our observation clearly contradicts this categorization and indicates that we should reconsider the way we classify viruses. Our results also provide a new example of related viruses where the viral structural proteins have not diverged as much as the proteins associated with genome replication. This result further strengthens the proposal for higher-order classification to be based on virion architecture rather than on genome type or replication mechanism.
Virus Shedding and Potential for Interspecies Waterborne Transmission of Highly Pathogenic H5N1 Influenza Virus in Sparrows and Chickens
Authors: Forrest Heather L. , Kim Jeong-Ki , Webster Robert G.
Published: January 2010

To elucidate the role of sparrows as intermediate hosts of highly pathogenic avian influenza H5N1 viruses, we assessed shedding and interspecies waterborne transmission of A/duck/Laos/25/06 in sparrows and chickens. Inoculated birds shed virus at high titers from the oropharynx and cloaca, and infection was fatal. Waterborne transmission from inoculated sparrows to contact chickens was absent, while 25% of sparrows were infected via waterborne transmission from chickens. The viral shedding and susceptibility to infection we observed in sparrows, coupled with their presence in poultry houses, could facilitate virus spread among poultry and wild birds in the face of an H5N1 influenza virus outbreak.
Extralymphoid CD8
+
T Cells Resident in Tissue from Simian Immunodeficiency Virus SIVmac239Δnef-Vaccinated Macaques Suppress SIVmac239 Replication
Ex Vivo
Authors: Greene Justin M. , Lhost Jennifer J. , Burwitz Benjamin J. , Budde Melisa L. , Macnair Caitlin E. , Weiker Madelyn K. , Gostick Emma , Friedrich Thomas C. , Broman Karl W. , Price David A. , O'Connor Shelby L. , O'Connor David H.
Published: January 2010

Live-attenuated vaccination with simian immunodeficiency virus (SIV) SIVmac239Δnef is the most successful vaccine product tested to date in macaques. However, the mechanisms that explain the efficacy of this vaccine remain largely unknown. We utilized an
ex vivo
viral suppression assay to assess the quality of the immune response in SIVmac239Δnef-immunized animals. Using major histocompatibility complex-matched Mauritian cynomolgus macaques, we did not detect SIV-specific functional immune responses in the blood by gamma interferon (IFN-γ) enzyme-linked immunospot assay at select time points; however, we found that lung CD8
+
T cells, unlike blood CD8
+
T cells, effectively suppress virus replication by up to 80%. These results suggest that SIVmac239Δnef may be an effective vaccine because it elicits functional immunity at mucosal sites. Moreover, these results underscore the limitations of relying on immunological measurements from peripheral blood lymphocytes in studies of protective immunity to HIV/SIV.
E1A Interacts with Two Opposing Transcriptional Pathways To Induce Quiescent Cells into S Phase
Authors: Sha Jingfeng , Ghosh Mrinal K. , Zhang Keman , Harter Marian L.
Published: January 2010

Despite data suggesting that the adenovirus E1A protein of 243 amino acids creates an S-phase environment in quiescent cells by overcoming the nucleosomal repression of E2F-regulated genes, the precise mechanisms underlying E1A's ability in this process have not yet been defined at the biochemical level. In this study, we show by kinetic analysis that E1A, as opposed to an E1A mutant failing to bind p130, can temporally eliminate corepressor complexes consisting of p130-E2F4 and HDAC1/2-mSin3B from the promoters of E2F-regulated genes in quiescent cells. Once the complexes are removed, the di-methylation of H3K9 at these promoters becomes dramatically diminished, and this in turn allows for the acetylation of H3K9/14 and the recruitment of activating E2F family members, which is then followed by the transcriptional activity of the E2F-regulated genes. Remarkably, although an E1A mutant that can no longer bind to a histone acetyltransferase (PCAF) is as capable as wild-type E1A in eliminating corepressor complexes and methyl groups from the promoters of these genes, it cannot mediate the acetylation of H3K9/14 or induce their transcription. These findings suggest that corepressors as well as coactivators are acted upon by E1A to derepress E2F-regulated genes in quiescent cells. Thus, our results highlight for the first time a functional relationship between E1A and two transcriptional pathways of differing functions for transitioning cells out of quiescence and into S phase.
Directional Spread of Surface-Associated Retroviruses Regulated by Differential Virus-Cell Interactions
Authors: Sherer Nathan M. , Jin Jing , Mothes Walther
Published: January 2010

The spread of viral infections involves the directional progression of virus particles from infected cells to uninfected target cells. Prior to entry, the binding of virus particles to specific cell surface receptors can trigger virus surfing, an actin-dependent lateral transport of viruses toward the cell body (M. J. Lehmann et al., J. Cell Biol. 170:317-325, 2005; M. Schelhaas, et al., PLoS Pathog. 4:e1000148, 2008; J. L. Smith, D. S. Lidke, and M. A. Ozbun, Virology 381:16-21, 2008). Here, we have used live-cell imaging to demonstrate that for cells chronically infected with the gammaretrovirus murine leukemia virus in which receptor has been downregulated, a significant portion of completely assembled virus particles are not immediately released into the supernatant but retain long-term association with the cell surface. Retention can be attributed, at least in part, to nonspecific particle attachment to cell surface glycosylaminoglycans. In contrast to virus surfing, viruses retained at the surface of infected cells undergo a lateral motility that is random and actin independent. This diffusive motility can be abruptly halted and converted into inward surfing after treatment with Polybrene, a soluble cation that increases virus-cell adsorption. In the absence of Polybrene, particle diffusion allows for an outward flow of viruses to the infected cell periphery. Peripheral particles are readily captured by and transmitted to neighboring uninfected target cells in a directional fashion. These data demonstrate a surface-based mechanism for the directional spread of viruses regulated by differential virus-cell interactions.
Distinct Hepatitis B Virus Dynamics in the Immunotolerant and Early Immunoclearance Phases
Authors: Wang Hurng-Yi , Chien Ming-Hung , Huang Hsiang-Po , Chang Hsiao-Chi , Wu Chung-Che , Chen Pei-Jer , Chang Mei-Hwei , Chen Ding-Shinn
Published: January 2010

Little is known about hepatitis B virus (HBV) diversity changes within a host during the immunotolerant phase of chronic HBV infection. Such knowledge, nevertheless, may help in understanding how host immunity and HBV interact at the early stage of infection. In this study, serial serum samples were collected from a long-term (>17 years) follow-up cohort of seven patients, and multiple copies of the full-length viral genome from serially sampled sera were recovered and analyzed. Viral genetic diversity was positively correlated with host immunity, represented by levels of alanine aminotransferase (ALT), but was negatively correlated with the viral copy number. During the immunotolerant phase, when the host immunity was feeble (ALT < 20 U/liter), viral nucleotide diversity decreased while copy numbers increased. Rates of evolutionary change derived for different patients were in a very narrow range (1.6 × 10−5to 5.4 × 10−5/site/year). As the disease progressed toward the immunoclearance phase (ALT > 20 U/liter), viral diversity increased but copy numbers decreased. Evolutionary rates varied among patients in accordance with their levels of ALT, ranging from 9.6 × 10−6to 3.2 × 10−4/site/year. More than half (19/32 sites) of positively selected sites resided in immune epitopes, suggesting their possible role in host immunity. Our results demonstrate that host immunity is a dominant factor in HBV evolution. Different selective forces, including immune-mediated positive selection and virus-mediated negative selection, operate in tandem in shaping viral population dynamics within a host.
Recombinant Yellow Fever Vaccine Virus 17D Expressing Simian Immunodeficiency Virus SIVmac239 Gag Induces SIV-Specific CD8
+
T-Cell Responses in Rhesus Macaques
Authors: Bonaldo Myrna C. , Martins Mauricio A. , Rudersdorf Richard , Mudd Philip A. , Sacha Jonah B. , Piaskowski Shari M. , Costa Neves Patrícia C. , Veloso de Santana Marlon G. , Vojnov Lara , Capuano Saverio , Rakasz Eva G. , Wilson Nancy A. , Fulkerson John , Sadoff Jerald C. , Watkins David I. , Galler Ricardo
Published: January 2010

Here we describe a novel vaccine vector for expressing human immunodeficiency virus (HIV) antigens. We show that recombinant attenuated yellow fever vaccine virus 17D expressing simian immunodeficiency virus SIVmac239 Gag sequences can be used as a vector to generate SIV-specific CD8
+
T-cell responses in the rhesus macaque. Priming with recombinant BCG expressing SIV antigens increased the frequency of these SIV-specific CD8
+
T-cell responses after recombinant YF17D boosting. These recombinant YF17D-induced SIV-specific CD8
+
T cells secreted several cytokines, were largely effector memory T cells, and suppressed viral replication in CD4
+
T cells.
Host Range, Prevalence, and Genetic Diversity of Adenoviruses in Bats
Authors: Li Yan , Ge Xingyi , Zhang Huajun , Zhou Peng , Zhu Yan , Zhang Yunzhi , Yuan Junfa , Wang Lin-Fa , Shi Zhengli
Published: January 2010

Bats are the second largest group of mammals on earth and act as reservoirs of many emerging viruses. In this study, a novel bat adenovirus (AdV) (BtAdV-TJM) was isolated from bat fecal samples by using a bat primary kidney cell line. Infection studies indicated that most animal and human cell lines are susceptible to BtAdV-TJM, suggesting a possible wide host range. Genome analysis revealed 30 putative genes encoding proteins homologous to their counterparts in most known AdVs. Phylogenetic analysis placed BtAdV-TJM within the genus
Mastadenovirus
, most closely related to tree shrew and canine AdVs. PCR analysis of 350 bat fecal samples, collected from 19 species in five Chinese provinces during 2007 and 2008, indicated that 28 (or 8%) samples were positive for AdVs. The samples were from five bat species,
Hipposideros armiger
,
Myotis horsfieldii
,
M. ricketti
,
M
yotis
spp., and
Scotophilus kuhlii
. The prevalence ranged from 6.25% (
H. armiger
in 2007) to 40% (
M. ricketti
in 2007). Comparison studies based on available partial sequences of the
pol
gene demonstrated a great genetic diversity among bat AdVs infecting different bat species as well as those infecting the same bat species. This is the first report of a genetically diverse group of DNA viruses in bats. Our results support the notion, derived from previous studies based on RNA viruses (especially coronaviruses and astroviruses), that bats seem to have the unusual ability to harbor a large number of genetically diverse viruses within a geographic location and/or within a taxonomic group.
Hepatitis B Virus (HBV) Surface Antigen Interacts with and Promotes Cyclophilin A Secretion: Possible Link to Pathogenesis of HBV Infection
Authors: Tian Xiaochen , Zhao Chao , Zhu Hongguang , She Weimin , Zhang Jiming , Liu Jing , Li Lanjuan , Zheng Shusen , Wen Yu-Mei , Xie Youhua
Published: January 2010

Cyclophilin A (CypA), predominantly located intracellularly, is a multifunctional protein. We previously reported decreased CypA levels in hepatocytes of transgenic mice expressing hepatitis B virus (HBV) surface antigen (HBsAg). In this study, we found that expression of HBV small surface protein (SHBs) in human hepatoma cell lines specifically triggered CypA secretion, whereas SHBs added extracellularly to culture medium did not. Moreover, CypA secretion was not promoted by the expression of a secretion deficient SHBs mutant, suggesting a close association between secretion of CypA and SHBs. Interaction between CypA and SHBs was observed by using coimmunoprecipitation and glutathione
S
-transferase pull-down assays. Hydrodynamic injection of the SHBs expression construct into C57BL/6J mice resulted in increased serum CypA levels and ALT/AST levels, as well as the infiltration of inflammatory cells surrounding SHBs-positive hepatocytes. The inflammatory response and serum ALT/AST level were reduced when the chemotactic effect of CypA was inhibited by cyclosporine and anti-CD147 antibody. Furthermore, higher serum CypA levels were detected in chronic hepatitis B patients than in healthy individuals. In HBV patients who had received liver transplantation, serum CypA levels declined dramatically after the loss of HBsAg as a consequence of liver transplantation. Taken together, these results indicate that expression and secretion of SHBs can promote CypA secretion, which may contribute to the pathogenesis of HBV infection.
HIV-1 Vpr Induces the K48-Linked Polyubiquitination and Proteasomal Degradation of Target Cellular Proteins To Activate ATR and Promote G
2
Arrest
Authors: Belzile Jean-Philippe , Richard Jonathan , Rougeau Nicole , Xiao Yong , Cohen Éric A.
Published: January 2010

HIV-1 viral protein R (Vpr) induces cell cycle arrest at the G
2
/M phase by a mechanism involving the activation of the DNA damage sensor ATR. We and others recently showed that Vpr performs this function by subverting the activity of the DDB1-CUL4A (VPRBP) E3 ubiquitin ligase. Vpr could thus act as a connector between the E3 ligase and an unknown cellular factor whose ubiquitination would induce G
2
arrest. While attractive, this model is based solely on the indirect observation that some mutants of Vpr retain their interaction with the E3 ligase but fail to induce G
2
arrest. Using a tandem affinity purification approach, we observed that Vpr interacts with ubiquitinated cellular proteins and that this association requires the recruitment of an active E3 ligase given that the depletion of VPRBP by RNA interference or the overexpression of a dominant negative mutant of CUL4A decreased this association. Importantly, G
2
-arrest-defective mutants of Vpr in the C-terminal putative substrate-interacting domain displayed a decreased association with ubiquitinated proteins. We also found that the inhibition of proteasomal activity increased this association and that the ubiquitin chains were at least in part constituted of classical K48 linkages. Interestingly, the inhibition of K48 polyubiquitination specifically impaired the Vpr-induced phosphorylation of H2AX, an early target of ATR, but did not affect UV-induced H2AX phosphorylation. Overall, our results provide direct evidence that the association of Vpr with the DDB1-CUL4A (VPRBP) E3 ubiquitin ligase induces the K48-linked polyubiquitination of as-yet-unknown cellular proteins, resulting in their proteasomal degradation and ultimately leading to the activation of ATR and G
2
arrest.
Virological Synapse-Mediated Spread of Human Immunodeficiency Virus Type 1 between T Cells Is Sensitive to Entry Inhibition
Authors: Martin Nicola , Welsch Sonja , Jolly Clare , Briggs John A. G. , Vaux David , Sattentau Quentin J.
Published: January 2010

Human immunodeficiency virus type 1 (HIV-1) can disseminate between CD4
+
T cells via diffusion-limited cell-free viral spread or by directed cell-cell transfer using virally induced structures termed virological synapses. Although T-cell virological synapses have been well characterized, it is unclear whether this mode of viral spread is susceptible to inhibition by neutralizing antibodies and entry inhibitors. We show here that both cell-cell and cell-free viral spread are equivalently sensitive to entry inhibition. Fluorescence imaging analysis measuring virological synapse lifetimes and inhibitor time-of-addition studies implied that inhibitors can access preformed virological synapses and interfere with HIV-1 cell-cell infection. This concept was supported by electron tomography that revealed the T-cell virological synapse to be a relatively permeable structure. Virological synapse-mediated HIV-1 spread is thus efficient but is not an immune or entry inhibitor evasion mechanism, a result that is encouraging for vaccine and drug design.
Reducing shear strength uncertainties in clays by multivariate correlations
Authors: Ching Jianye , Phoon Kok-Kwang , Chen Yi-Chu
Published: January 2010

Quantifications of uncertainties in soil shear strengths, including undrained shear strength of clay, are essential for geotechnical reliability-based design. In particular, how to reduce the uncertainties in undrained shear strengths based on all available information by correlation is a practical research subject, given the considerable cost of a typical site investigation. Although it is simple to reduce the uncertainties by correlation when the information is one dimensional (or univariate), it is quite challenging to reduce the uncertainties by using multivariate information through multiple correlations. This study proposes a systematic way of achieving multivariate correlations on undrained shear strengths. A set of simplified equations are obtained through Bayesian analysis for the purpose of reducing uncertainties: the inputs to the equations are the results of in situ or laboratory tests and the outputs are the updated mean values and coefficients of variation (c.o.v.s) of the undrained shear strengths. Two case studies are used to demonstrate the consistency of the proposed simplified equations. Results show that uncertainties in undrained shear strengths can be effectively reduced by incorporating multivariate information. Given that reliability-based design can justify more economical design with reduced uncertainties, the proposed equations essentially link the value of more and better tests directly to final design savings.
New mixed boundary, true triaxial loading device for testing three-dimensional stress–strain–strength behaviour of geomaterials
Authors: Yin Jian-Hua , Cheng Chun-Man , Kumruzzaman Md. , Zhou Wan-Huan
Published: January 2010

This paper presents a brief review of true triaxial apparatuses (TTAs) developed in the past and their advantages and limitations. Considering the limitations of previous designs, a new true triaxial loading device that provides mixed boundary conditions for a true triaxial apparatus (TTA) is introduced. This loading device consists of four sliding rigid plates and two flexible loading faces. The setup of the loading device together with the whole true triaxial system is described. Frictions between sliding plates and the soil membrane surfaces in the new loading device are examined. A three-dimensional finite element (FE) modelling study is carried out on the stress and strain distribution of a soil specimen subjected to loading from two different loading devices. It is found that stresses and strains of a soil specimen subjected to loading from the new sliding plates are far more uniform than those subjected to loading from nonsliding plates with preset gaps. Finally, the paper presents the applications of the present TTA with the new loading device for testing studies of a completely decomposed granite soil and a geofoam. Typical results are presented and discussed. It is found that the present mixed boundary loading device is very suitable for true triaxial testing on both soils and geofoam, especially under large strains or compression without corner contact problems.
Resistance of simple plant root systems to uplift loads
Authors: Mickovski S. B. , Bransby M. F. , Bengough A. G. , Davies M. C.R. , Hallett P. D.
Published: January 2010

Plant root systems frequently permeate both natural and engineered soil slopes, influencing slope stability via mechanical reinforcement and soil drying. These root systems are often loaded by external forces during slope movements and when plant stems are subject to animal foraging or wind gusts. A series of physical model tests were conducted to examine how root geometries, root properties, and soil effective stress states affect the pullout capacity of simple unbranched model roots. Lengths of wood, rubber, and real roots were pulled from dry and partially saturated sand. The tests revealed the importance of the root to soil stiffness ratio during progressive failure, the mechanical properties of soil (and interfaces) at low effective stresses, the root diameter, and the tortuosity of the root material. Scaling issues due to shear banding are more important, and effective stresses under wet conditions are smaller than in conventional geotechnical practice because roots have a relatively small diameter (typically 10−4–10−1 m) and are at shallow depth (typically 0–2 m). After careful consideration of these effects, predictions were made for the pullout capacity of small root sections based on material data for willow roots (Salix viminalis) in sand.
Heat transport simulations in a heterogeneous aquifer used for aquifer thermal energy storage (ATES)
Authors: Bridger D. W. , Allen D. M.
Published: January 2010

A modelling study was carried out to evaluate the influence of aquifer heterogeneity, as represented by geologic layering, on heat transport and storage in an aquifer used for aquifer thermal energy storage (ATES). An existing ATES system in Agassiz, British Columbia, Canada, was used as a case study. The system consists of four production wells completed in an unconfined heterogeneous aquifer consisting of interbedded sands and gravels. An additional dump well was installed to provide for heat dissipation during the peak cooling periods. Three monitoring wells and the production wells were logged for temperature periodically within the first 1.5 years of operation. A three-dimensional groundwater flow and heat transport model was developed using FEFLOW. Simulation results indicate that heat and (or) cold energy moved preferentially in discrete zones within the aquifer or at least entered the wells over discrete intervals. Monitoring data support model results, but show that thermal storage was successfully achieved despite a significant cooling operation during the first year.
Photosynthate allocation in loblolly pine (Pinustaedd) seedlings as affected by moisture stress
Authors: Kuhns M. R. , Gjerstad D. H.
Published: January 2010

The effects of recent water stress on distribution of 14C-labelled photosynthate in loblolly pine (Pinustaeda L.) seedlings were examined. Leaves on a lateral branch were allowed to photosynthetically fix 14C, and 14C levels in seven biochemical fractions in the source leaves and in each of five other plant parts were determined 72 h later. Regardless of stress level, about 95% of the 14C originally presented was taken up and 60% was respired during the 72 h translocation period. Most 14C was found in exposed or source leaves and in the roots, with very little occurring above the level of the exposed branch. The bud and nonexposed leaves contained 1.2% or less of the seedling's 14C. As preexposure stress level increased, translocation to roots and other sinks decreased. Sugars contained most of the 14C in parts other than the bud and nonexposed leaves. The proportion of 14C in sugars in these parts increased as stress increased. Structural compounds contained less 14C as stress increased, indicating a lasting effect of stress on growth. In all cases, organic acids and amino acids contained very little 14C. Mild stress resulted in increased starch production in the source leaves relative to no stress, while severe stress reduced starch production.
Growth and acclimation of planted white pine and white spruce seedlings in response to environmental conditions
Authors: Brand David G. , Janas Peter S.
Published: January 2010

A factorial experiment was used to examine the effects of soil temperature, brush competition, and fertility on the postplanting growth and development of white spruce (Piceaglauca (Moench) Voss) and white pine (Pinusstrobus L.) on a clear-cut forest site at the Petawawa National Forestry Institute. Environmental monitoring was used to confirm that soil temperature treatments were effective and that the brush competition treatments caused significant (α = 0.0001) differences in photosynthetically active radiation at tree level. On the basis of foliar analysis, both fertilization and brush control improved nutrient availability to the planted trees. Owing to adequate, well-distributed precipitation, soil moisture tension was not greater than 0.6 bars (1 bar = 100 kPa) in any treatment during the growing season. Growth response by both species was dominantly controlled by the soil temperature factor. Fertility produced secondary benefits to white pine, and brush control had secondary benefits to white spruce. Examination of a developmental sequence of height growth, leaf length growth, basal area growth, and terminal bud mass indicated that soil temperature treatments were beneficial throughout the growing season, that brush control was important only in late season, and that fertilization had slight negative effects in early season but a positive effect by late season. Developmental features also indicated that soil temperature effects were manifested by reduced shoot and needle extension in the trees, competition effects by reduced availability of light, nutrients, and moisture, and fertilizer effects by increased foliar element concentrations.
A logit analysis of private woodlot owner's harvesting decisions in New Brunswick
Authors: Jamnick M. S. , Beckett D. R.
Published: January 2010

A maximum likelihood logit model of New Brunswick's private woodlot owner's harvesting decisions indicates that these decisions are related to owner and ownership characteristics. The model was able to correctly classify 75.2% of the observations from the data used to construct the model and 75.7% of the observations from an independent data set. Examples of how the model can be used to develop policies to encourage or discourage harvesting or as a screening tool for forest extension personnel are discussed.