bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification of dust‐borne transmission of highly pathogenic avian influenza virus between chickens
Authors: Spekreijse Dieuwertje , Bouma Annemarie , Koch Guus , Stegeman Arjan 
Published: April 2012

Please cite this paper as: Spekreijse et al. (2013) Quantification of dust‐borne transmission of highly pathogenic avian influenza virus between chickens. Influenza and Other Respiratory Viruses 7(2) 132–138.Background  Understanding the transmission of highly pathogenic avian influenza virus (HPAIv) between poultry flocks is essential to prevent and control epidemics. Dust, produced in infected chicken flocks, has been hypothesized to be an important mechanical vector for between‐flock transmission of HPAIv.Objectives  The aim of our study was to quantify the amount of virus shed by infected birds and its relation to deposition of virus in the environment and the rate of dust‐borne transmission between groups of chickens.Methods  Four replicate experiments were performed, each replicate with two groups of 14 chickens housed in two separate rooms. In one group, chickens were inoculated with HPAIv. Ventilation forced the air from that room to the second (recipient) group through a tube. Deceased birds in the inoculated group were replaced with new susceptible birds up to day 10 p.i. Dust samples were collected daily. Trachea and cloaca swabs were collected daily to determine virus shedding and virus spread to the recipient group.Results  The amount of virus detected in dust samples in the recipient room was, on average, 103·7 EID50/m3. Virus transmission from the inoculated to the recipient group occurred in two experiments. The transmission rate parameter for dust‐borne transmission was estimated at 0·08 new infections/infectious chicken/day.Conclusions  The results of this study are a first step to elucidate the importance of dust‐borne transmission of HPAIv between flocks and help interpret environmental samples.
Serological evidence of swine influenza in Brazil
Authors: Rajão Daniela S. , Alves Fabiana , Del Puerto Helen L. , Braz Gissandra F. , Oliveira Fernanda G. , Ciacci‐Zanella Janice R. , Schaefer Rejane , dos Reis Jenner K. P. , Guedes Roberto M. C. , Lobato Zélia I. P. , Leite Rômulo C. 
Published: April 2012

Please cite this paper as: Rajão et al. (2013). Serological evidence of swine influenza in Brazil. Influenza and Other Respiratory Viruses 7(2), 109–112.The aim of this work was to detect serum antibodies specific to influenza viruses in swine in Brazil. Serum samples of 355 pigs from 17 herds in Minas Gerais state were tested by hemagglutination inhibition (HI) for antibodies against H1N1 swine (SIV) and human influenza viruses, and H3N2 SIV. HI revealed that 158 animals (44·5%) and 11 herds (64·7%) were positive for H1N1 SIV, 36 animals (10·1%) and four herds (23·5%) were positive for H3N2 SIV, and 136 animals (38·3%) and 10 herds (58·8%) were positive for H1N1 human. This study indicates that swine influenza is disseminated throughout Minas Gerais state, Brazil.
Estimating Potential E. coli Sources in a Watershed Using Spatially Explicit Modeling Techniques1
Authors: Riebschleager K.J. , Karthikeyan R. , Srinivasan R. , McKee K. 
Published: April 2012

Riebschleager, K.J., R. Karthikeyan, R. Srinivasan, and K. McKee, 2012. Estimating Potential E. coli Sources in a Watershed Using Spatially Explicit Modeling Techniques. Journal of the American Water Resources Association (JAWRA) 48(4): 745‐761. DOI: 10.1111/j.1752‐1688.2012.00649.xAbstract:  The Spatially Explicit Load Enrichment Calculation Tool (SELECT) was automated to characterize waste and the associated pathogens from various sources within a mixed land use watershed. Potential Escherichia coli loads in Lake Granbury watershed were estimated using spatially variable governing factors, such as land use, soil condition, and distance to streams. A new approach for characterizing E. coli loads resulting from malfunctioning on‐site wastewater treatment systems (OWTSs) was incorporated into SELECT along with the Pollutant Connectivity Factor (PCF) module. The PCF component was applied to identify areas contributing E. coli loads during runoff events by incorporating the influence of potential E. coli loading, runoff potential, and travel distance to waterbodies. Simulation results indicated livestock and wildlife are potential E. coli contributing sources in the watershed. The areas in which these sources are potentially contributing are not currently monitored for E. coli. The bacterial water quality violations seen around Lake Granbury are most likely the result of malfunctioning OWTSs and pet wastes. SELECT results demonstrate the need to evaluate each contributing source separately to effectively allocate site specific best management practices (BMPs) utilizing stakeholder inputs. It also serves as a powerful screening tool for determining areas where detailed investigation is merited.
Sustaining conservation values in selectively logged tropical forests: the attained and the attainable
Authors: Putz Francis E. , Zuidema Pieter A. , Synnott Timothy , Peña‐Claros Marielos , Pinard Michelle A. , Sheil Douglas , Vanclay Jerome K. , Sist Plinio , Gourlet‐Fleury Sylvie , Griscom Bronson , Palmer John , Zagt Roderick 
Published: April 2012

AbstractMost tropical forests outside protected areas have been or will be selectively logged so it is essential to maximize the conservation values of partially harvested areas. Here we examine the extent to which these forests sustain timber production, retain species, and conserve carbon stocks. We then describe some improvements in tropical forestry and how their implementation can be promoted. A simple meta‐analysis based on >100 publications revealed substantial variability but that: timber yields decline by about 46% after the first harvest but are subsequently sustained at that level; 76% of carbon is retained in once‐logged forests; and, 85–100% of species of mammals, birds, invertebrates, and plants remain after logging. Timber stocks will not regain primary‐forest levels within current harvest cycles, but yields increase if collateral damage is reduced and silvicultural treatments are applied. Given that selectively logged forests retain substantial biodiversity, carbon, and timber stocks, this “middle way” between deforestation and total protection deserves more attention from researchers, conservation organizations, and policy‐makers. Improvements in forest management are now likely if synergies are enhanced among initiatives to retain forest carbon stocks (REDD+), assure the legality of forest products, certify responsible management, and devolve control over forests to empowered local communities.
The Removal of RNA Primers from DNA Synthesized by the Reverse Transcriptase of the Retrotransposon Tf
1
Is Stimulated by Tf
1
Integrase
Authors: Herzig Eytan , Voronin Nickolay , Hizi Amnon 
Published: April 2012

ABSTRACT

The Tf
1
retrotransposon represents a group of long terminal repeat retroelements that use an RNA self-primer for initiating reverse transcription while synthesizing the minus-sense DNA strand. Tf
1
reverse transcriptase (RT) was found earlier to generate the self-primer
in vitro
. Here, we show that this RT can remove from the synthesized cDNA the entire self-primer as well as the complete polypurine tract (PPT) sequence (serving as a second primer for cDNA synthesis). However, these primer removals, mediated by the RNase H activity of Tf
1
RT, are quite inefficient. Interestingly, the integrase of Tf
1
stimulated the specific Tf
1
RT-directed cleavage of both the self-primer and PPT, although there was no general enhancement of the RT's RNase H activity (and the integrase by itself is devoid of any primer cleavage). The RTs of two prototype retroviruses, murine leukemia virus and human immunodeficiency virus, showed only a partial and nonspecific cleavage of both Tf
1
-associated primers with no stimulation by Tf
1
integrase. Mutagenesis of Tf
1
integrase revealed that the complete Tf
1
integrase protein (excluding its chromodomain) is required for stimulating the Tf
1
RT primer removal activity. Nonetheless, a double mutant integrase that has lost its integration functions can still stimulate the RT's activity, though heat-inactivated integrase cannot enhance primer removals. These findings suggest that the enzymatic activity of Tf
1
integrase is not essential for stimulating the RT-mediated primer removal, while the proper folding of this protein is obligatory for this function. These results highlight possible new functions of Tf
1
integrase in the retrotransposon's reverse transcription process.
Functions of the Epstein-Barr Virus EBNA1 Protein in Viral Reactivation and Lytic Infection
Authors: Sivachandran Nirojini , Wang Xueqi , Frappier Lori 
Published: April 2012

ABSTRACT
EBNA1 is the only nuclear Epstein-Barr virus (EBV) protein expressed in both latent and lytic modes of infection. While EBNA1 is known to play several important roles in latent infection, the reason for its continued expression in lytic infection is unknown. Here we identified two roles for EBNA1 in the reactivation of latent EBV to the lytic cycle in epithelial cells. First, EBNA1 depletion in latently infected cells was shown to positively contribute to spontaneous EBV reactivation, showing that EBNA1 has a role in suppressing reactivation. Second, when the lytic cycle was induced, EBNA1 depletion decreased lytic gene expression and DNA amplification, showing that it positively contributed to lytic infection. Since we have previously shown that EBNA1 disrupts promyelocytic leukemia (PML) nuclear bodies, we investigated whether this function could account for the effects of EBNA1 on lytic infection by repeating the experiments with cells lacking PML proteins. In the absence of PML, EBNA1 did not promote lytic infection, indicating that the EBNA1-mediated PML disruption is responsible for promoting lytic infection. In keeping with this conclusion, PML silencing was found to be sufficient to induce the EBV lytic cycle. Finally, by generating cells with single PML isoforms, we showed that individual PML isoforms were sufficient to suppress EBV lytic reactivation, although PML isoform IV (PML IV) was ineffective because it was most efficiently degraded by EBNA1. Our results provide the first function for EBNA1 in lytic infection and show that EBNA1 interactions with PML IV lead to a loss of PML nuclear bodies (NBs) that promotes lytic infection.
Residues within the C-Terminal Arm of the Herpes Simplex Virus 1 Glycoprotein B Ectodomain Contribute to Its Refolding during the Fusion Step of Virus Entry
Authors: Connolly Sarah A. , Longnecker Richard 
Published: April 2012

ABSTRACT
Herpesvirus entry into cells requires coordinated interactions among several viral glycoproteins. The final membrane fusion step of entry is executed by glycoprotein B (gB), a class III viral fusion protein that is conserved across all herpesviruses. Fusion proteins are metastable proteins that mediate fusion by inserting into a target membrane and refolding from a prefusion to postfusion conformation to bring the viral and cell membranes together. Although the structure of gB has been solved in a conformation that likely represents its postfusion form, its prefusion structure and the details of how it refolds to execute fusion are unknown. The postfusion gB structure contains a trimeric coiled-coil at its core and a long C-terminal arm within the ectodomain packs against this coil in an antiparallel manner. This coil-arm complex is reminiscent of the six-helix bundle that provides the energy for fusion in class I fusogens. To determine the role of the coil-arm complex, we individually mutated residues in the herpes simplex virus 1 gB coil-arm complex to alanine and assessed the contribution of each residue to cell-cell and virus-cell fusion. Several coil mutations resulted in a loss of cell surface expression, indicating that the coil residues are important for proper processing of gB. Three mutations in the arm region (I671A, H681A, and F683A) reduced fusion without affecting expression. Combining these three arm mutations drastically reduced the ability of gB to execute fusion; however, fusion function could be restored by adding known hyperfusogenic mutations to the arm mutant. We propose that the formation of the coil-arm complex drives the gB transition to a postfusion conformation and the coil-arm complex performs a function similar to that of the six-helix bundle in class I fusion. Furthermore, we suggest that these specific mutations in the arm may energetically favor the prefusion state of gB.
Integrated Clinical, Pathologic, Virologic, and Transcriptomic Analysis of H5N1 Influenza Virus-Induced Viral Pneumonia in the Rhesus Macaque
Authors: Shinya Kyoko , Gao Yuwei , Cilloniz Cristian , Suzuki Yasuhiro , Fujie Masahiro , Deng Guohua , Zhu Qiyun , Fan Shufang , Makino Akiko , Muramoto Yukiko , Fukuyama Satoshi , Tamura Daisuke , Noda Takeshi , Eisfeld Amie J. , Katze Michael G. , Chen Hualan , Kawaoka Yoshihiro 
Published: April 2012

ABSTRACTViral pneumonia has been frequently reported during early stages of influenza virus pandemics and in many human cases of highly pathogenic avian influenza (HPAI) H5N1 virus infection. To better understand the pathogenesis of this disease, we produced nonlethal viral pneumonia in rhesus macaques by using an HPAI H5N1 virus (A/Anhui/2/2005; referred to as Anhui/2). Infected macaques were monitored for 14 days, and tissue samples were collected at 6 time points for virologic, histopathologic, and transcriptomic analyses. Anhui/2 efficiently replicated in the lung from 12 h to 3 days postinfection (p.i.) and caused temporal but severe pneumonia that began to resolve by day 14. Lung transcriptional changes were first observed at 6 h, and increased expression of vascular permeability regulators and neutrophil chemoattractants correlated with increased serum leakage and neutrophil infiltrationin situ. Additional inflammatory, antiviral, and apoptotic genes were upregulated from 12 h, concurrent with viral antigen detection and increasing immune cell populations. A shift toward upregulation of acquired immunity was apparent after day 6. Expression levels of established immune cell molecular markers revealed remarkable similarity with pathological findings, indicating early and robust neutrophil infiltration, a slight delay in macrophage accumulation, and abundant late populations of T lymphocytes. We also characterized the putative mechanisms regulating a unique, pneumonia-associated biphasic fever pattern. Thus, this study is the first to use a comprehensive and integrative approach to delineate specific molecular mechanisms regulating influenza virus-induced pneumonia in nonhuman primates, an important first step toward better management of human influenza virus disease.
Characterization of the Viral
O
-Glycopeptidome: a Novel Tool of Relevance for Vaccine Design and Serodiagnosis
Authors: Cló Emiliano , Kračun Stjepan K. , Nudelman Aaron S. , Jensen Knud J. , Liljeqvist Jan-Åke , Olofsson Sigvard , Bergström Tomas , Blixt Ola 
Published: April 2012

ABSTRACT

Viral envelope proteins mediate interactions with host cells, leading to internalization and intracellular propagation. Envelope proteins are glycosylated and are known to serve important functions in masking host immunity to viral glycoproteins. However, the viral infectious cycle in cells may also lead to aberrant glycosylation that may elicit immunity. Our knowledge of immunity to aberrant viral glycans and glycoproteins is limited, potentially due to technical limitations in identifying immunogenic glycans and glycopeptide epitopes. This work describes three different complementary methods for high-throughput screening and identification of potential immunodominant
O
-glycopeptide epitopes on viral envelope glycoproteins: (i) on-chip enzymatic glycosylation of scan peptides, (ii) chemical glycopeptide microarray synthesis, and (iii) a one-bead-one-compound random glycopeptide library. We used herpes simplex virus type 2 (HSV-2) as a model system and identified a simple
O
-glycopeptide pan-epitope,
501
PPA(GalNAc)TAPG
507
, on the mature gG-2 glycoprotein that was broadly recognized by IgG antibodies in HSV-2-infected individuals but not in HSV-1-infected or noninfected individuals. Serum reactivity to the extended sialyl-T glycoform was tolerated, suggesting that self glycans can participate in immune responses. The methods presented provide new insight into viral immunity and new targets for immunodiagnostic and therapeutic measures.
A 3-
O
-Sulfated Heparan Sulfate Binding Peptide Preferentially Targets Herpes Simplex Virus 2-Infected Cells
Authors: Ali Mohamed M. , Karasneh Ghadah A. , Jarding Min Jung , Tiwari Vaibhav , Shukla Deepak 
Published: April 2012

ABSTRACT

Herpes simplex virus 2 (HSV-2) is the primary cause of genital herpes, which is one of the most common sexually transmitted viral infections worldwide and a major cofactor for human immunodeficiency virus infection. The lack of an effective vaccine or treatment and the emergence of drug-resistant strains highlight the need for developing new antivirals for HSV-2. Here, we demonstrate that a low-molecular-weight peptide isolated against 3-
O
-sulfated heparan sulfate (3-OS HS) can efficiently block HSV-2 infection. Treatment with the peptide inhibited viral entry and cell-to-cell spread both
in vitro
and
in vivo
using a mouse model of genital HSV-2 infection. Quite interestingly, the peptide showed a preferential binding to HSV-2-infected cells, with more than 200% increased binding compared to uninfected cells. Our additional results show that heparan sulfate expression is upregulated by 25% upon HSV-2 infection, which is a significant new finding that could be exploited for designing new diagnostic tests and treatment strategies against HSV-2-infected cells. In addition, our results also raise the possibility that 3-OS HS modifications within HS may be upregulated even more to accommodate for a significantly higher increase in the peptide binding to the infected cells.
A Pan-H1 Anti-Hemagglutinin Monoclonal Antibody with Potent Broad-Spectrum EfficacyIn Vivo
Authors: Tan Gene S. , Krammer Florian , Eggink Dirk , Kongchanagul Alita , Moran Thomas M. , Palese Peter 
Published: April 2012

ABSTRACTSeasonal epidemics caused by antigenic variations in influenza A virus remain a public health concern and an economic burden. The isolation and characterization of broadly neutralizing anti-hemagglutinin monoclonal antibodies (MAb) have highlighted the presence of highly conserved epitopes in divergent influenza A viruses. Here, we describe the generation and characterization of a mouse monoclonal antibody designed to target the conserved regions of the hemagglutinin of influenza A H1 viruses, a subtype that has caused pandemics in the human population in both the 20th and 21st centuries. By sequentially immunizing mice with plasmid DNA encoding the hemagglutinin of antigenically different H1 influenza A viruses (A/South Carolina/1/1918, A/USSR/92/1977, and A/California/4/2009), we isolated and identified MAb 6F12. Similar to other broadly neutralizing MAb previously described, MAb 6F12 has no hemagglutination inhibition activity against influenza A viruses and targets the stalk region of hemagglutinins. As designed, it has neutralizing activity against a divergent panel of H1 virusesin vitro, representing 79 years of antigenic drift. Most notably, MAb 6F12 prevented gross weight loss against divergent H1 viruses in passive transfer experiments in mice, both in pre- and postexposure prophylaxis regimens. The broad but specific activity of MAb 6F12 highlights the potent efficacy of monoclonal antibodies directed against a single subtype of influenza A virus.
Patterns of Acute Rhesus Cytomegalovirus (RhCMV) Infection Predict Long-Term RhCMV Infection
Authors: Assaf Basel T. , Mansfield Keith G. , Westmoreland Susan V. , Kaur Amitinder , Oxford Kristie L. , Diamond Don J. , Barry Peter A. 
Published: April 2012

ABSTRACT
We previously reported that long-term rhesus cytomegalovirus (RhCMV) excretion in infected macaques was related to UL/b′ coding content. Acute biopsy specimens of the inoculation sites from the previous study have now been analyzed to determine whether there were acute phenotypic predictors of long-term RhCMV infection. Only in animals displaying acute endothelial tropism and neutrophilic inflammation was RhCMV excretion detected. The results imply that vaccinating against these early viral determinants would significantly impede long-term RhCMV infection.
Determinants in the Maturation of Rubella Virus P200 Replicase Polyprotein Precursor
Authors: Matthews Jason D. , Tzeng Wen-Pin , Frey Teryl K. 
Published: April 2012

ABSTRACT

Rubella virus (RUBV), a positive-strand RNA virus, replicates its RNA within membrane-associated replication complexes (RCs) in the cytoplasm of infected cells. RNA synthesis is mediated by the nonstructural proteins (NSPs) P200 and its cleavage products, P150 and P90 (N and C terminal within P200, respectively), which are processed by a protease residing at the C terminus of P150. In this study of NSP maturation, we found that early NSP localization into foci appeared to target the membranes of the endoplasmic reticulum. During maturation, P150 and P90 likely interact within the context of P200 and remain in a complex after cleavage. We found that P150-P90 interactions were blocked by mutational disruption of an alpha helix at the N terminus (amino acids [aa] 36 to 49) of P200 and that these mutations also had an effect on NSP targeting, processing, and membrane association. While the P150-P90 interaction also required residues 1700 to 1900 within P90, focus formation required the entire RNA-dependent RNA polymerase (aa 1700 to 2116). Surprisingly, the RUBV capsid protein (CP) rescued RNA synthesis by several alanine-scanning mutations in the N-terminal alpha helix, and packaged replicon assays showed that rescue could be mediated by CP in the virus particle. We hypothesize that CP rescues these mutations as well as internal deletions of the Q domain within P150 and mutations in the 5′ and 3′
cis
-acting elements in the genomic RNA by chaperoning the maturation of P200. CP's ability to properly target the otherwise aggregated plasmid-expressed P200 provides support for this hypothesis.
Foamy Virus Pol Protein Expressed as a Gag-Pol Fusion Retains Enzymatic Activities, Allowing for Infectious Virus Production
Authors: Lee Eun-Gyung , Sinicrope Amber , Jackson Dana L. , Yu Shuyuarn F. , Linial Maxine L. 
Published: April 2012

ABSTRACT

Foamy viruses (FV) synthesize Pol from a spliced
pol
mRNA independently of Gag, unlike orthoretroviruses, which synthesize Pol as a Gag-Pol protein that coassembles with Gag. We found that prototype FV (PFV) mutants expressing Gag and Pol only as a Gag-Pol protein without the spliced Pol contain protease activity equivalent to that of wild-type (WT) Pol. Regardless of the presence or absence of the spliced Pol, the PFV Gag-Pol proteins can assemble into virus-like particles (VLPs), in contrast to the orthoretroviral Gag-Pol proteins, which cannot form VLPs. However, the PFV Gag-Pol VLPs have aberrant morphologies and are not infectious. In the absence of the spliced Pol, coexpression of a PFV Gag-Pol protein with Gag can produce infectious virions. Our results suggest that enzymes encoded by PFV
pol
(protease, reverse transcriptase, and integrase) are enzymatically active if they are synthesized as part of a Gag-Pol protein.