bluuebunny/crossref_metadata_2025 huggingface dataset:
Poly(vinyl sulfate) Potassium Salt XPS Reference Core Level and Energy Loss Spectra
Authors: Louette Pierre , Bodino Frederic , Pireaux Jean-Jacques
Published: March 2007

XPS measurements of poly(vinyl sulfate) potassium salt recorded with a SSX-100 spectrometer in standardized experimental conditions are presented: survey scan, high resolution core level spectra as well as the energy loss regions of carbon, sulphur, potassium and oxygen peaks are analyzed. This is part of a contract work aiming to record spectra in the very same conditions of some 40 different polymers.
Poly(methyl hydrogen siloxane) (PMHS) XPS Reference Core Level and Energy Loss Spectra
Authors: Louette Pierre , Bodino Frederic , Pireaux Jean-Jacques
Published: March 2007

XPS measurements of poly(methyl hydrogen siloxane) recorded with a SSX-100 spectrometer in standardized experimental conditions are presented: survey scan, high resolution core level spectra as well as the energy loss regions of carbon and oxygen peaks are analyzed. This is part of a contract work aiming to record spectra in the very same conditions of some 40 different polymers.
Poly(ether ether ketone) (PEEK) XPS Reference Core Level and Energy Loss Spectra
Authors: Louette Pierre , Bodino Frederic , Pireaux Jean-Jacques
Published: March 2007

XPS measurements of poly(ether ether ketone) recorded with a SSX-100 spectrometer in standardized experimental conditions are presented: survey scan, high resolution core level spectra as well as the energy loss regions of carbon and oxygen peaks are analyzed. This is part of a contract work aiming to record spectra in the very same conditions of some 40 different polymers.
Poly(acroleine) XPS Reference Core Level and Energy Loss Spectra
Authors: Louette Pierre , Bodino Frederic , Pireaux Jean-Jacques
Published: March 2007

XPS measurements of poly(acroleine) recorded with a SSX-100 spectrometer in standardized experimental conditions are presented: survey scan, high resolution core level spectra as well as the energy loss regions of carbon and oxygen peaks are analyzed. This is part of a contract work aiming to record spectra in the very same conditions of some 40 different polymers.
Poly(vinyl butyral) XPS Reference Core Level and Energy Loss Spectra
Authors: Louette Pierre , Köhler Laurent , Bodino Frederic , Pireaux Jean-Jacques
Published: March 2007

XPS measurements of poly(vinyl butyral) recorded with a SSX-100 spectrometer in standardized experimental conditions are presented: survey scan, high resolution core level spectra as well as the energy loss regions of carbon and oxygen peaks are analyzed. This is part of a contract work aiming to record spectra in the very same conditions of some 40 different polymers.
Poly(vinyl formal) XPS Reference Core Level and Energy Loss Spectra
Authors: Louette Pierre , Köhler Laurent , Bodino Frederic , Pireaux Jean-Jacques
Published: March 2007

XPS measurements of poly(vinyl formal) recorded with a SSX-100 spectrometer in standardized experimental conditions are presented: survey scan, high resolution core level spectra as well as the energy loss regions of carbon and oxygen peaks are analyzed. This is part of a contract work aiming to record spectra in the very same conditions of some 40 different polymers
The Latitudinal Gradient in Recent Speciation and Extinction Rates of Birds and Mammals
Authors: Weir Jason T. , Schluter Dolph
Published: March 2007

Although the tropics harbor greater numbers of species than do temperate zones, it is not known whether the rates of speciation and extinction also follow a latitudinal gradient. By sampling birds and mammals, we found that the distribution of the evolutionary ages of sister species—pairs of species in which each is the other's closest relative—adheres to a latitudinal gradient. The time to divergence for sister species is shorter at high latitudes and longer in the tropics. Birth-death models fitting these data estimate that the highest recent speciation and extinction rates occur at high latitudes and decline toward the tropics. These results conflict with the prevailing view that links high tropical diversity to elevated tropical speciation rates. Instead, our findings suggest that faster turnover at high latitudes contributes to the latitudinal diversity gradient.
The Structural Basis of Ribozyme-Catalyzed RNA Assembly
Authors: Robertson Michael P. , Scott William G.
Published: March 2007

Life originated, according to the RNA World hypothesis, from self-replicating ribozymes that catalyzed ligation of RNA fragments. We have solved the 2.6 angstrom crystal structure of a ligase ribozyme that catalyzes regiospecific formation of a 5′ to 3′ phosphodiester bond between the 5′-triphosphate and the 3′-hydroxyl termini of two RNA fragments. Invariant residues form tertiary contacts that stabilize a flexible stem of the ribozyme at the ligation site, where an essential magnesium ion coordinates three phosphates. The structure of the active site permits us to suggest how transition-state stabilization and a general base may catalyze the ligation reaction required for prebiotic RNA assembly.
From Gombe to the World
Authors: Small Meredith F.
Published: March 2007

Jane Goodall
. The Woman Who Redefined Man.
By Dale Peterson
. Houghton Mifflin, Boston, 2006. 768 pp. $35, C$45.95. ISBN 9780395854051.

In this authorized biography, Peterson offers an absorbing portrait of the life, fieldwork, and activism of the pioneering primatologist.
Recent Sea-Level Contributions of the Antarctic and Greenland Ice Sheets
Authors: Shepherd Andrew , Wingham Duncan
Published: March 2007

After a century of polar exploration, the past decade of satellite measurements has painted an altogether new picture of how Earth's ice sheets are changing. As global temperatures have risen, so have rates of snowfall, ice melting, and glacier flow. Although the balance between these opposing processes has varied considerably on a regional scale, data show that Antarctica and Greenland are each losing mass overall. Our best estimate of their combined imbalance is about 125 gigatons per year of ice, enough to raise sea level by 0.35 millimeters per year. This is only a modest contribution to the present rate of sea-level rise of 3.0 millimeters per year. However, much of the loss from Antarctica and Greenland is the result of the flow of ice to the ocean from ice streams and glaciers, which has accelerated over the past decade. In both continents, there are suspected triggers for the accelerated ice discharge—surface and ocean warming, respectively—and, over the course of the 21st century, these processes could rapidly counteract the snowfall gains predicted by present coupled climate models.
Our Branch in the Tree of Life
Authors: Winters R. Scott
Published: March 2007

Hall of Human Origins
.
Ian Tattersall and Rob DeSalle, curators
. American Museum of Natural History, New York.
www.amnh.org/exhibitions/permanent/humanorigins/

This new exhibit blends findings from genomics and recent fossil discoveries to present the evolutionary story of humankind from the earliest hominids to
Homo sapiens
.
Anti-p19 Antibody Treatment Exacerbates Lyme Arthritis and Enhances Borreliacidal Activity
Authors: Peterson Sara Heil , Nardelli Dean T. , Warner Thomas F. , Callister Steven M. , Torrealba Jose R. , Schell Ronald F.
Published: March 2007

Considerable effort has been made to elucidate the mechanism of Lyme arthritis. We focused on p19, a cell cycle-regulating molecule, because it is known to inhibit cell cycle division of T lymphocytes which may be responsible for the induction of arthritis. We show that anti-p19 antibody treatment enhances the inflammatory response normally detected at the tibiotarsal joints ofBorrelia burgdorferi-vaccinated andBorrelia bissettii-challenged mice. Specifically, anti-p19 antibody treatment augmented the severity of inflammation within the synovial and subsynovial tissue. Moreover, treatment with anti-p19 antibody caused severe erosion of cartilage and bone with ankle joint destruction. In addition, anti-p19 antibody treatment ofBorrelia-vaccinated and -challenged mice enhanced the borreliacidal antibody response, especially against the vaccine isolate. The novel activities of anti-p19 antibody show that p19 may be an important therapeutic site for the treatment of Lyme arthritis.
Use of Serological Assays for Diagnosis of Hepatitis E Virus Genotype 1 and 3 Infections in a Setting of Low Endemicity
Authors: Herremans M. , Bakker J. , Duizer E. , Vennema H. , Koopmans M. P. G.
Published: March 2007

Because of the occurrence of genotype 3 hepatitis E virus (HEV) in regions of low endemicity, it is important to validate the currently used serological assays for diagnosing infections with viruses belonging to this lineage, since these assays only use antigens derived from genotype 1 and 2 viruses. We evaluated the Genelabs enzyme-linked immunosorbent assay (ELISA) and the RecomBlot from Mikrogen for the detection of HEV-specific immunoglobulin M (IgM) and IgG under conditions of low endemicity. We compared test results of 16 patients with locally acquired genotype 3 HEV, 8 genotype 1 patients, 167 healthy controls from the general population, and 101 cases with hepatitis due to other viral causes. The measured specificities of the ELISA (98%) and the RecomBlot (97%) were comparable to those given by the manufacturer for IgM but were significantly lower for IgG (93% by ELISA and 66% by immunoblotting, versus reported values of 98% for ELISA and 95% for blotting). Antibody levels detected following infections with genotype 3 were lower than those following genotype 1 infections except for those measured in the IgM ELISA. Reactivity to the four antigens used in the immunoblot assay were analyzed and showed differences in the IgM immunoblot reactions between genotype 1 patients and genotype 3 patients. The ORF3 antigen was the most specific antigen. The specificity could be improved by a combined testing regimen with confirmation by immunoblotting of all positive ELISA results and by raising the cutoff of the IgG immunoblot assay without loss of sensitivity. We conclude that a combination of ELISA and immunoblotting is needed for acceptable specificity and sensitivity of HEV assays under conditions of low endemicity.
Galactoxylomannan Does Not Exhibit Cross-Reactivity in the PlateliaAspergillusEnzyme Immunoassay
Authors: De Jesus Magdia , Hackett Emily , Durkin Michelle , Connolly Patricia , Casadevall Arturo , Petraitiene Ruta , Walsh Thomas J. , Wheat L. Joseph
Published: March 2007

Given the recent report of a false-positive result in the PlateliaAspergillusenzyme immunoassay in a patient with cryptococcosis and in yeast extracts and purified galactoxylomannan ofCryptococcus neoformans, we evaluated culture extracts, purified polysaccharides, clinical specimens, and specimens from animals following experimental infection. Our results revealed no cross-reactions.
OspC Phylogenetic Analyses Support the Feasibility of a Broadly Protective Polyvalent Chimeric Lyme Disease Vaccine
Authors: Earnhart Christopher G. , Marconi Richard T.
Published: March 2007

Using available
Borrelia
outer surface protein C (OspC) sequences, a phylogenetic analysis was undertaken to delineate the number of antigenic domains required for inclusion in a broadly protective, chimeric, OspC-based Lyme disease vaccine. The data indicate that approximately 34 would be required and that an OspC-based vaccinogen is feasible.
Reevaluation of Clinical and Laboratory Standards Institute Disk Diffusion Breakpoints for Tetracyclines for Testing
Enterobacteriaceae
Authors: Sader Helio S. , Ferraro Mary J. , Reller L. Barth , Schreckenberger Paul C. , Swenson Jana M. , Jones Ronald N.
Published: March 2007

We reevaluated
Enterobacteriaceae
disk diffusion breakpoints for the tetracyclines published in the Clinical and Laboratory Standards Institute (CLSI) document M100-S16, which were (susceptible/resistant) ≥19 mm/≤14 mm for tetracycline, ≥16 mm/≤12 mm for doxycycline, and ≥19 mm/≤14 mm for minocycline. A collection of 504 recent clinical isolates of
Enterobacteriaceae
were tested against these tetracycline compounds by disk diffusion and broth microdilution methods according to CLSI guidelines. Regression line and scattergram plot analyses determined intermethod accuracy for current disk diffusion breakpoints and showed excellent
r
values of 0.91 to 0.95. However, error rates (minor/major [false-resistant]/very major [false-susceptible]) were 14.9/0.8/0.0% for tetracycline, 11.5/0.4/0.0% for doxycycline, and 30.6/0.7/0.0% for minocycline and only 4.4/0.0/0.0% for tetracycline, 5.6/0.0/0.2% for doxycycline, and 8.3/0.0/0.3% for minocycline when proposed breakpoints were modified to (susceptible/resistant) ≥15 mm/≤11 mm for tetracycline, ≥14 mm/≤10 mm for doxycycline, and ≥16 mm/≤12 mm for minocycline. Listed modifications were recently approved by the CLSI (M100-S17).
Design and Validation of an H5 TaqMan Real-Time One-Step Reverse Transcription-PCR and Confirmatory Assays for Diagnosis and Verification of Influenza A Virus H5 Infections in Humans
Authors: Ellis Joanna S. , Smith Joanne W. , Braham Sharleen , Lock Matthew , Barlow Katrina , Zambon Maria C.
Published: March 2007

Increasing diversity among influenza H5N1 viruses has resulted in the need for sensitive and specific diagnostic assays, fully validated for the detection of H5 viruses belonging to all hemagglutinin (HA) clades, particularly the recently circulating H5N1 viruses of clade 2. In this report, the development and validation of a real-time, one-step TaqMan reverse transcription-PCR (RT-PCR) assay specific for the detection of influenza A H5 viruses from clades 1, 1′, 2, and 3 is described. The real-time assay for H5 virus was shown to be highly sensitive, detecting H5 virus levels of <1 PFU from each of the HA clades. Specificity of the H5 RT-PCR for influenza A H5 viruses was demonstrated by using influenza A viruses of different subtypes, clinical samples containing influenza A viruses H1N1, H3N2, and H5N1, influenza B viruses, and other respiratory viruses. The usefulness of the inclusion of a distinguishable assay positive control and of confirmatory assays for the laboratory diagnosis and verification of H5 virus infections was demonstrated. A real-time RT-PCR pyrosequencing assay, a restriction enzyme digestion assay, and direct sequencing of the H5 real-time RT-PCR amplicon were validated for the confirmation of H5 detection by the diagnostic real-time assay. The H5 real-time assay was applied to diagnostic testing for suspected cases of influenza A virus H5 infection in the United Kingdom. Influenza A H5 viruses were not detected in the cases analyzed; however, influenza A H3N2 virus was detected in 57% of the suspected cases of H5. The H5 TaqMan real-time RT-PCR and confirmatory assays will be useful tools for the laboratory surveillance and rapid diagnosis of H5 infections in humans.
A Recently Evolved Sublineage of the
Mycobacterium tuberculosis
Beijing Strain Family Is Associated with an Increased Ability to Spread and Cause Disease
Authors: Hanekom M. , van der Spuy G. D. , Streicher E. , Ndabambi S. L. , McEvoy C. R. E. , Kidd M. , Beyers N. , Victor T. C. , van Helden P. D. , Warren R. M.
Published: March 2007

This study aimed to reconstruct the evolutionary history of Beijing strains of
Mycobacterium tuberculosis
and to test the hypothesis that evolution has influenced the ability of the Beijing strains within the different Beijing sublineages to spread and cause disease. A PCR-based method was used to analyze the genome structure of 40 different loci in 325 Beijing isolates collected from new and retreatment tuberculosis patients from an urban setting and 270 Beijing isolates collected from high-risk tuberculosis patients from a rural setting in the Western Cape, South Africa. The resulting data were subjected to phylogenetic analysis using the neighbor joining algorithm. Phylogenetic reconstructions were highly congruent with the “gold standard” phylogenetic tree based on synonymous single-nucleotide polymorphisms, thereby allowing a prediction of the order in which the evolutionary events had occurred. A total of seven independently evolving Beijing sublineages were identified. Analysis of epidemiological data in relation to the Beijing sublineage suggested an association between recent evolutionary change and frequency of occurrence in an urban population (
P
< 0.001) as well as in the rural population (
P
< 0.001). This concept was further supported by an association between more recently evolved Beijing strains and an increased ability to transmit and to cause disease (odds ratio, 5.82; 95% confidence interval, 3.13 to 10.82 [
P
< 0.001]). An association between Beijing sublineage and demographic and clinical parameters and drug resistance could not be demonstrated. From these data, we suggest that the pathogenic characteristics of Beijing strains are not conserved but rather that strains within individual lineages have evolved unique pathogenic characteristics.
Etiological Role of Viruses in Outbreaks of Acute Gastroenteritis in The Netherlands from 1994 through 2005
Authors: Svraka Sanela , Duizer Erwin , Vennema Harry , de Bruin Erwin , van der Veer Bas , Dorresteijn Bram , Koopmans Marion
Published: March 2007

Acute gastroenteritis is one of the most common diseases worldwide. In developed countries, viruses, particularly noroviruses, are recognized as the leading cause. In The Netherlands, the surveillance of gastroenteritis outbreaks with suspected viral etiologies (as determined by Kaplan criteria) was established by the National Institute for Public Health and the Environment in 1994. This paper presents an overview of viral gastroenteritis outbreaks reported from 1994 through 2005. A minimum epidemiological data set consisting of the associated setting(s), the probable transmission mode, the date of the first illness and the date of sampling, the number of persons affected, and the number of hospitalizations was requested for each reported outbreak. Stool samples were tested for the presence of norovirus, sapovirus, rotavirus, astrovirus, adenovirus, and Aichi virus by electron microscopy, enzyme-linked immunosorbent assay, and/or reverse transcription-PCR. A total of 6,707 stool samples from 941 gastroenteritis outbreaks were investigated. Noroviruses were detected as the causative agent in 735 (78.1%) of the outbreaks, and rotaviruses, adenoviruses, and astroviruses were found to be responsible for 46 (4.9%), 9 (1.0%), and 5 (0.5%) outbreaks, respectively. Among the gastroenteritis outbreaks in which a mode of transmission was identified, most outbreaks (38.1%) were associated with person-to-person transmission, and the majority (54.9%) of the outbreaks investigated were reported by residential institutions. Since 2002, the total number of outbreaks reported and the number of unexplained outbreaks have increased. Furthermore, the number of rotavirus-associated outbreaks has increased, especially in nursing homes. Despite thorough testing, 115 (12.2%) outbreaks suspected of having viral etiologies remain unexplained. Increases in numbers of reported outbreaks may indicate undefined changes in the criteria for reporting or the emergence of new pathogens.
Genetic Polymorphisms Influence
Plasmodium ovale
PCR Detection Accuracy
Authors: Calderaro A. , Piccolo G. , Perandin F. , Gorrini C. , Peruzzi S. , Zuelli C. , Ricci L. , Manca N. , Dettori G. , Chezzi C. , Snounou G.
Published: March 2007

Detection of
Plasmodium ovale
by use of a nested PCR assay with a novel
Plasmodium ovale
primer set was superior to detection of
Plasmodium ovale
by real-time PCR assays. Nested PCR was also better at detecting
P. malariae
. The detection of
P. ovale
in many patients first admitted >2 months following their return to Italy indicated that
P. ovale
relapses are common.
Leptospira
Immunoglobulin-Like Proteins as a Serodiagnostic Marker for Acute Leptospirosis
Authors: Croda Julio , Ramos João G. R. , Matsunaga James , Queiroz Adriano , Homma Akira , Riley Lee W. , Haake David A. , Reis Mitermayer G. , Ko Albert I.
Published: March 2007

There is an urgent need for improved diagnosis of leptospirosis, an emerging infectious disease which imparts a large disease burden in developing countries. We evaluated the use of
Leptospira
immunoglobulin (Ig)-like (Lig) proteins as a serodiagnostic marker for leptospirosis. Lig proteins have bacterial immunoglobulin-like (Big) tandem repeat domains, a moiety found in virulence factors in other pathogens. Sera from patients identified during urban outbreaks in Brazil reacted strongly with immunoblots of a recombinant fragment comprised of the second to sixth Big domains of LigB from
L. interrogans
serovar Copenhageni, the principal agent for transmission in this setting. Furthermore, the sera recognized an analogous LigB fragment derived from
L. kirschneri
serovar Grippotyphosa, a pathogenic serovar which is not endemic to the study area. The immunoblot assay detected anti-LigB IgM antibodies in sera from 92% (95% confidence interval, 85 to 96%) of patients during acute-phase leptospirosis. The assay had a sensitivity of 81% for sera from patients with less than 7 days of illness. Anti-LigB antibodies were found in sera from 57% of the patients who did not have detectable anti-whole-
Leptospira
responses as detected by IgM enzyme-linked immunosorbent assay and microagglutination test. The specificities of the assay were 93 to 100% and 90 to 97% among sera from healthy individuals and patients with diseases that have clinical presentations that overlap with those of leptospirosis, respectively. These findings indicate that the antibody response to this putative virulence determinant is a sensitive and specific marker for acute infection. The use of this marker may aid the prompt and timely diagnosis required to reduce the high mortality associated with severe forms of the disease.
Human Influenza A Virus (H5N1) Detection by a Novel Multiplex PCR Typing Method
Authors: Zou Shumei , Han Jian , Wen Leying , Liu Yan , Cronin Kassi , Lum Shanjuan H. , Gao Lu , Dong Jie , Zhang Ye , Guo Yuanji , Shu Yuelong
Published: March 2007

We report the use of ResPlex III for genotyping influenza A viruses. The performance characteristics of the assay with regard to H5N1 are further evaluated. The ResPlex system incorporates a novel multiplex PCR technology, target-enriched multiplex PCR, to simultaneously amplify multiple molecular targets in one reaction. The ResPlex III assay targets the H1, H2, H3, H5, H7, H9, N1, and N2 genes from the influenza A virus as well as the NS genes from influenza A (NSA) and B (NSB) viruses, providing detection and genotyping of influenza A and B viruses. The analytical sensitivities for detecting the H5, N1, and NSA genes were 1, 10
−1
, and 10 50% tissue culture infectious doses/200 μl/reaction, respectively. A total of 217 sequential clinical samples including 14 samples with human H5N1 infections were tested by the ResPlex III assay, and the results were compared to a reference standard combined with results of viral culture and conventional reverse transcriptase and real-time PCR. The clinical sensitivity and specificity for detecting H5N1 were 93.3% and 100%, respectively, indicating that different subtypes of influenza A virus can be quickly and correctly identified using the ResPlex III genotyping approach.
Sodium Butyrate: a Chemical Inducer of In Vivo Reactivation of Herpes Simplex Virus Type 1 in the Ocular Mouse Model
Authors: Neumann Donna M. , Bhattacharjee Partha S. , Hill James M.
Published: March 2007

Recent studies have explored the chromatin structures associated with the herpes simplex virus type 1 (HSV-1) genome during latency, particularly with regard to specific histone tail modifications such as acetylation and dimethylation. The objective of our present study was to develop a rapid systemic method of in vivo HSV-1 reactivation to further explore the changes that occur in the chromatin structures associated with HSV-1 at early time points after the initiation of HSV reactivation. We present a uniform, rapid, and reliable method of in vivo HSV-1 reactivation in mice that yields high reactivation frequencies (75 to 100%) by using sodium butyrate, a histone deacetylase inhibitor, and demonstrate that the reactivating virus can be detected at the original site of infection.
Unique Mutational Patterns in the Envelope α2 Amphipathic Helix and Acquisition of Length in gp120 Hypervariable Domains Are Associated with Resistance to Autologous Neutralization of Subtype C Human Immunodeficiency Virus Type 1
Authors: Rong Rong , Gnanakaran S. , Decker Julie M. , Bibollet-Ruche Frederic , Taylor Jesse , Sfakianos Jeffrey N. , Mokili John L. , Muldoon Mark , Mulenga Joseph , Allen Susan , Hahn Beatrice H. , Shaw George M. , Blackwell Jerry L. , Korber Bette T. , Hunter Eric , Derdeyn Cynthia A.
Published: March 2007

Autologous neutralizing antibodies (NAb) against human immunodeficiency virus type 1 generate viral escape variants; however, the mechanisms of escape are not clearly defined. In a previous study, we determined the susceptibilities of 48 donor and 25 recipient envelope (Env) glycoproteins from five subtype C heterosexual transmission pairs to NAb in donor plasma by using a virus pseudotyping assay, thereby providing an ideal setting to probe the determinants of susceptibility to neutralization. In the present study, acquisition of length in the Env gp120 hypervariable domains was shown to correlate with resistance to NAb in donor plasma (
P
= 0.01; Kendall's tau test) but not in heterologous plasma. Sequence divergence in the gp120 V1-to-V4 region also correlated with resistance to donor (
P
= 0.0002) and heterologous (
P
= 0.001) NAb. A mutual information analysis suggested possible associations of nine amino acid positions in V1 to V4 with NAb resistance to the donor's antibodies, and five of these were located within an 18-residue amphipathic helix (α2) located on the gp120 outer domain. High nonsynonymous-to-synonymous substitution (dN/dS) ratios, indicative of positive selection, were also found at these five positions in subtype C sequences in the database. Nevertheless, exchange of the entire α2 helix between resistant donor Envs and sensitive recipient Envs did not alter the NAb phenotype. The combined mutual information and dN/dS analyses suggest that unique mutational patterns in α2 and insertions in the V1-to-V4 region are associated with NAb resistance during subtype C infection but that the selected positions within the α2 helix must be linked to still other changes in Env to confer antibody escape. These findings suggest that subtype C viruses utilize mutations in the α2 helix for efficient viral replication and immune avoidance.
Entry of Duck Hepatitis B Virus into Primary Duck Liver and Kidney Cells after Discovery of a Fusogenic Region within the Large Surface Protein
Authors: Maenz Claudia , Chang Shau-Feng , Iwanski Alicja , Bruns Michael
Published: March 2007

Hepatitis B viruses exhibit a narrow host range specificity that is believed to be mediated by a domain of the large surface protein, designated L. For duck hepatitis B virus, it has been shown that the pre-S domain of L binds to carboxypeptidase D, a cellular receptor present in many species on a wide variety of cell types. Nonetheless, only hepatocytes become infected. It has remained vague which viral features determine host range specificity and organotropicity. By using chymotrypsin to treat duck hepatitis B virus, we addressed the question of whether a putative fusogenic region within the amino-terminal end of the small surface protein may participate in viral entry and possibly constitute one of the determinants of the host range of the virus. Addition of the enzyme to virions resulted in increased infectivity. Remarkably, even remnants of enzyme-treated subviral particles proved to be inhibitory to infection. A noninfectious deletion mutant devoid of the binding region for carboxypeptidase D could be rendered infectious for primary duck hepatocytes by treatment with chymotrypsin. Although because of the protease treatment mutant and wild-type viruses may have become infectious in an unspecific and receptor-independent manner, their host range specificity was not affected, as shown by the inability of the virus to replicate in different hepatoma cell lines, as well as primary chicken hepatocytes. Instead, the organotropicity of the virus could be reduced, which was demonstrated by infection of primary duck kidney cells.
Allelic Variation in the Hepatitis C Virus NS4B Protein Dramatically Influences RNA Replication
Authors: Blight Keril J.
Published: March 2007

In the Huh-7.5 hepatoma cell line, replication of the genotype 1a H77 strain of hepatitis C virus (HCV) is attenuated compared to that of the genotype 1b Con1 strain. This study identifies the poorly characterized integral membrane protein, NS4B, as a major determinant for this replication difference. Chimeric H77 subgenomic replicons containing the entire NS4B gene from Con1 in place of the H77 NS4B sequence replicated approximately 10-fold better than the H77 parent and to levels similar to that of the adapted Con1 replicon. An intermediate level of replication enhancement was conferred by H77 chimeras containing the poorly conserved N-terminal 47 residues or the remaining less-divergent C terminus of Con1 NS4B. The replication-enhancing activity within the N terminus of NS4B was further mapped to two Con1-specific amino acids. Experiments to elucidate the mechanism of enhanced H77 replication revealed that Con1 NS4B primarily increased H77 RNA synthesis on a per cell basis, as indicated by the similar capacities of chimeric and parental replicons to establish replication in Huh-7.5 cells and the higher levels of both positive- and negative-strand RNAs for the chimeras than for the H77 parent. Additionally, enhanced H77 replication was not the result of Con1 NS4B-mediated effects on HCV translation efficiency or alterations in polyprotein processing. Expression of Con1 NS4B in
trans
did not improve the replication of the H77 parental replicon, suggesting a
cis
-dominant role for NS4B in HCV replication. These results provide the first evidence that allelic variation in the NS4B sequence between closely related isolates significantly impacts HCV replication in cell culture.
Old World and Clade C New World Arenaviruses Mimic the Molecular Mechanism of Receptor Recognition Used by α-Dystroglycan's Host-Derived Ligands
Authors: Rojek Jillian M. , Spiropoulou Christina F. , Campbell Kevin P. , Kunz Stefan
Published: March 2007

α-Dystroglycan (DG) is an important cellular receptor for extracellular matrix (ECM) proteins and also serves as the receptor for Old World arenaviruses Lassa fever virus (LFV) and lymphocytic choriomeningitis virus (LCMV) and clade C New World arenaviruses. In the host cell, α-DG is subject to a remarkably complex pattern of O glycosylation that is crucial for its interactions with ECM proteins. Two of these unusual sugar modifications, protein O mannosylation and glycan modifications involving the putative glycosyltransferase LARGE, have recently been implicated in arenavirus binding. Considering the complexity of α-DG O glycosylation, our present study was aimed at the identification of the specific O-linked glycans on α-DG that are recognized by arenaviruses. As previously shown for LCMV, we found that protein O mannosylation of α-DG is crucial for the binding of arenaviruses of distinct phylogenetic origins, including LFV, Mobala virus, and clade C New World arenaviruses. In contrast to the highly conserved requirement for O mannosylation, more generic O glycans present on α-DG are dispensable for arenavirus binding. Despite the critical role ofO-mannosyl glycans for arenavirus binding under normal conditions, the overexpression of LARGE in cells deficient in O mannosylation resulted in highly glycosylated α-DG that was functional as a receptor for arenaviruses. Thus, modifications by LARGE but notO-mannosyl glycans themselves are most likely the crucial structures recognized by arenaviruses. Together, the data demonstrate that arenaviruses recognize the same highly conserved O-glycan structures on α-DG involved in ECM protein binding, indicating a strikingly similar mechanism of receptor recognition by pathogen- and host-derived ligands.
Hepatitis B Virus Splice-Generated Protein Induces T-Cell Responses in HLA-Transgenic Mice and Hepatitis B Virus-Infected Patients
Authors: Mancini-Bourgine Maryline , Bayard Florence , Soussan Patrick , Deng Qiang , Lone Yu-Chun , Kremsdorf Dina , Michel Marie-Louise
Published: March 2007

Hepatitis B virus splice-generated protein (HBSP), encoded by a spliced hepatitis B virus RNA, was recently identified in liver biopsy specimens from patients with chronic active hepatitis B. We investigated the possible generation of immunogenic peptides by the processing of this protein in vivo. We identified a panel of potential epitopes in HBSP by using predictive computational algorithms for peptide binding to HLA molecules. We used transgenic mice devoid of murine major histocompatibility complex (MHC) class I molecules and positive for human MHC class I molecules to characterize immune responses specific for HBSP. Two HLA-A2-restricted peptides and one immunodominant HLA-B7-restricted epitope were identified following the immunization of mice with DNA vectors encoding HBSP. Most importantly, a set of overlapping peptides covering the HBSP sequence induced significant HBSP-specific T-cell responses in peripheral blood mononuclear cells from patients with chronic hepatitis B. The response was multispecific, as several epitopes were recognized by CD8+and CD4+human T cells. This study provides the first evidence that this protein generated in vivo from an alternative reading frame of the hepatitis B virus genome activates T-cell responses in hepatitis B virus-infected patients. Given that hepatitis B is an immune response-mediated disease, the detection of T-cell responses directed against HBSP in patients with chronic hepatitis B suggests a potential role for this protein in liver disease progression.
Physical and Functional Interactions of Human Endogenous Retrovirus Proteins Np9 and Rec with the Promyelocytic Leukemia Zinc Finger Protein
Authors: Denne Miriam , Sauter Marlies , Armbruester Vivienne , Licht Jonathan D. , Roemer Klaus , Mueller-Lantzsch Nikolaus
Published: March 2007

Only few of the human endogenous retrovirus (HERV) sequences in the human genome can produce proteins. We have previously reported that (i) patients with germ cell tumors often make antibodies against proteins encoded by HERV-K elements, (ii) expression of the HERV-K
rec
gene in transgenic mice can interfere with germ cell development and induce carcinoma in situ, and (iii) HERV-K
np9
transcript is overproduced in many tumors including breast cancers. Here we document that both Np9 and Rec physically and functionally interact with the promyelocytic leukemia zinc finger (PLZF) tumor suppressor, a transcriptional repressor and chromatin remodeler implicated in cancer and the self-renewal of spermatogonial stem cells. Interaction is mediated via two different central and C-terminal domains of Np9 and Rec and the C-terminal zinc fingers of PLZF. One major target of PLZF is the c-
myc
proto-oncogene. Coexpression of Np9 and Rec with PLZF abrogates the transcriptional repression of the c-
myc
gene promoter by PLZF and results in c-Myc overproduction, altered expression of c-Myc-regulated genes, and corresponding effects on cell proliferation and survival. Thus, the human endogenous retrovirus proteins Np9 and Rec may act oncogenically by derepressing c-
myc
through the inhibition of PLZF.
The Genome of
Gryllus bimaculatus
Nudivirus Indicates an Ancient Diversification of Baculovirus-Related Nonoccluded Nudiviruses of Insects
Authors: Wang Yongjie , Kleespies Regina G. , Huger Alois M. , Jehle Johannes A.
Published: March 2007

The
Gryllus bimaculatus
nudivirus (GbNV) infects nymphs and adults of the cricket
Gryllus bimaculatus
(Orthoptera: Gryllidae). GbNV and other nudiviruses such as
Heliothis zea
nudivirus 1 (HzNV-1) and
Oryctes rhinoceros
nudivirus (OrNV) were previously called “nonoccluded baculoviruses” as they share some similar structural, genomic, and replication aspects with members of the family
Baculoviridae
. Their relationships to each other and to baculoviruses are elucidated by the sequence of the complete genome of GbNV, which is 96,944 bp, has an AT content of 72%, and potentially contains 98 predicted protein-coding open reading frames (ORFs). Forty-one ORFs of GbNV share sequence similarities with ORFs found in OrNV, HzNV-1, baculoviruses, and bacteria. Most notably, 15 GbNV ORFs are homologous to the baculovirus core genes, which are associated with transcription (
lef
-
8
,
lef
-
9
,
lef
-
4
,
vlf
-
1
, and
lef-5
), replication (
dnapol
), structural proteins (
p74
,
pif
-
1
,
pif
-
2
,
pif
-
3
,
vp91
, and
odv-e56
), and proteins of unknown function (
38K
,
ac81
, and
19kda
). Homologues to these baculovirus core genes have been predicted in HzNV-1 as well. Six GbNV ORFs are homologous to nonconserved baculovirus genes
dnaligase
,
helicase 2
,
rr1
,
rr2
,
iap
-
3
, and
desmoplakin
. However, the remaining 57 ORFs revealed no homology or poor similarities to the current gene databases. No homologous repeat (
hr
) sequences but fourteen short direct repeat (
dr
) regions were detected in the GbNV genome. Gene content and sequence similarity suggest that the nudiviruses GbNV, HzNV-1, and OrNV form a monophyletic group of nonoccluded double-stranded DNA viruses, which separated from the baculovirus lineage before this radiated into dipteran-, hymenopteran-, and lepidopteran-specific clades of occluded nucleopolyhedroviruses and granuloviruses. The accumulated information on the GbNV genome suggests that nudiviruses form a highly diverse and phylogenetically ancient sister group of the baculoviruses, which have evolved in a variety of highly divergent host orders.
A new erinaceid (Mammalia, Insectivora) from the Late Paleocene of western Canada
Authors: Scott Craig S
Published: March 2007

A new genus and species of erinaceid lipotyphlan (Mammalia, Insectivora) from the late Paleocene of western Canada is described. Oncocherus krishtalkai gen. et sp. nov. is known from three late Tiffanian localities in central Alberta and southeastern Saskatchewan and is but one of several erinaceomorph and soricomorph taxa known from the Late Paleocene of western Canada. Oncocherus possesses apomorphies that link it to other primitive erinaceids (e.g., enlarged upper and lower fourth premolars, lower molars markedly decreasing in size from m1-m3, talonid basins V-shaped), yet its affinity with any of the recognized erinaceid subfamilies is uncertain. Although Oncocherus is phenetically, and probably phylogenetically, closest to Litolestes Jepsen, the genus is clearly distinguished from Litolestes and other erinaceid taxa by its proportionately larger and more inflated premolars and lower crowned molars, features that were likely adaptations for durophagy. Oncocherus joins a number of endemic mammalian taxa that were apparently confined to more northerly latitudes of the Western Interior of North America during the Late Paleocene.
New material ofProcolophon(Parareptilia: Procolophonoidea) from the Lower Triassic of Brazil, with remarks on the ages of the Sanga do Cabral and Buena Vista formations of South America
Authors: Dias-da-Silva Sérgio , Modesto Sean Patrick , Schultz Cesar Leandro
Published: March 2007

We describe a large, fragmentary procolophonid skull and three large vertebrae from the Sanga do Cabral Formation, Paraná Basin, Lower Triassic of Brazil. Cranial and dental morphology allow us to refer the skull to the genus Procolophon; the fragmentary nature of the specimen, however, does not permit identification to species. The vertebrae are tentatively assigned to Procolophon. They are of a size expected for an individual represented by the skull, although the cranial and postcranial elements were not directly associated. The vertebrae are unusual for a procolophonid in exhibiting neural arches that are twice as broad as they are long, a dimension seen elsewhere among parareptiles only in pareiasaurs. A comparison of the manner of tetrapod preservation between the Sanga do Cabral and Katberg formations reveals that tetrapods in the former occur within conglomerates, whereas in the latter they are recovered mainly from mudstones. This taphonomic disparity may account for the absence in South America of the nearly cosmopolitan synapsid Lystrosaurus. The recent recognition of Permian tetrapods from the Buena Vista Formation of Uruguay, regarded widely to be a lateral equivalent of the Sanga do Cabral Formation, is assessed. We conclude that there is no compelling evidence of Permian tetrapods from the Buena Vista Formation and that the available information is suggestive of an Early Triassic age for that formation.
Nass River on the move: radar facies analysis of glaciofluvial sedimentation and its response to sea-level change in northwestern British Columbia
Authors: McCuaig S J , Roberts M C
Published: March 2007

The Nass Valley of northwestern British Columbia is a glacial fiord containing extensive glaciomarine and glaciofluvial sediments. Two parallel braidplains, separated by a bedrock ridge, were deposited within the fiord. Mapping of these deposits led to the hypothesis that the braidplains must have terminated at deltas. However, a lack of surface exposures meant that ground-penetrating radar was needed to investigate these deposits. Radar facies analysis aided in the identification of braidplain, braid delta and glaciomarine depositional environments, as well as underlying bedrock. Several deltas graded to different sea levels were discovered, allowing inferences to be made about the relationship of falling sea level to sediment architecture. The upper section of the western braidplain is graded to a sea level of 185 m above sea level (asl), indicating that the proto-Nass River flowed on the western side of the bedrock ridge when the sea was at that level. However, the river moved to the east side of the ridge as sea level fell, depositing the extensive Aiyansh Braidplain – Braid Delta, which is graded to a 152 m sea-level stand. Several other deltas also formed at this sea-level stand. Avulsion occurred and the river flowed on the west side of the ridge again when sea level fell to 134 m asl. The river remained in this position throughout late glacial time and eventually evolved into the modern Nass River. The coarse-grained deposits are indicative of forced regression, with both stepped-top attached and detached stratal architecture present.
Geochemical and metallogenic relations in volcanic rocks of the southern Slave Province: implications for late Neoarchean tectonics
Authors: Goodwin A M , Lambert M B , Ujike O
Published: March 2007

Late Neoarchean volcanic belts in the southern Slave Province include (1) in the east, the Cameron River – Beaulieu River belts, which are characterized by stratigraphically thin, flow-rich, classic calc-alkaline, arc-type sequences with accompanying syngenetic volcanogenic massive sulphide deposits; and (2) in the west, the Yellowknife belt, which is characterized by stratigraphically thick, structurally complex, pyroclastic-rich, adakitic, back-arc basin-type sequences, with accompanying epigenetic lode-gold deposits. The volcanic belt association bears persuasive chemical evidence of subduction-initiated magma generation. However, the greenstone belts, together with coeval matching patterned belts in Superior Province of the southern Canadian Shield, bear equally persuasive evidence of prevailing autochthonous–parautochthonous relations with respect to component stratigraphic parts and to older gneissic basement. The eastern and western volcanic belts in question are petrogenetically ascribed to a "westerly inclined" (present geography) subduction zone(s) that produced shallower (east) to deeper (west), slab-initiated, mantle wedge-generated, parent magmas. This early stage microplate tectonic process involved modest mantle subduction depths, small tectonic plates, and small sialic cratons. In the larger context of Earth's progressively cooling, hence subduction-deepening mantle, this late Neoarchean greenstone belt development (2.73–2.66 Ga) merged with the massive end-Archean tonalite–trondhjemite–granodiorite–granite (TTGG) "bloom" (2.65–2.55 Ga), resulting in greatly enhanced craton stability. Successive subduction-deepening, plate-craton-enlarging stages, with appropriate metallotectonic response across succeeding Proterozoic time and beyond, led to modern-mode plate tectonics.
Determination of alteration facies using the normative mineral alteration index: Selbaie Cu–Zn deposit, northern Abitibi greenstone belt, Canada
Authors: Piché Mathieu , Jébrak Michel
Published: March 2007

The Selbaie Cu–Zn deposit is located in the northeastern portion of the northern Archean Abitibi volcanic belt. It is one of the most important base metal deposits in Canada. It includes stratiform pyrite levels in the volcanites and shallow-water sediments, stockworks in a rhyodacitic breccia, and a copper-rich vein, in a caldera context. The study of the regional alteration distribution is based on a database of more than 2300 chemical sample analyses using the NORMAT normative mineral alteration index. This method allows independent analysis of the numerous lithologic variations in the Selbaie district. Five facies are distinguished in a vast sodium-depleted zone, from the core to the periphery of the hydrothermal system: chlorite–pyrophyllite in the mineralized zones, chlorite–sericite, sericite, sericite–orthoclase and orthoclase at the periphery. The carbonates also show zoning, with ankerite–dolomite at the periphery and siderite–magnesite at the core. With NORMAT, it is possible to highlight overprinted alterations. The zoning observed at Selbaie corresponds to the overprinting of a system showing sulphide ore and acid-type epithermal deposit characteristics, with abundant pyrophyllite, very likely related to a deeper porphyritic system
Sox9-dependent transcriptional regulation of the proprotein convertase furin
Authors: Guimont Philippe , Grondin Francine , Dubois Claire M.
Published: March 2007

The proprotein convertase furin participates in the maturation/bioactivation of a variety of proproteins involved in chondrogenesis events. These include parathyroid hormone-related peptide (PTHrP), an autocrine/paracrine factor that is crucial to both normal cartilage development and cartilage-related pathological processes. Despite the known importance of furin activity in the bioactivation of the polypeptides, the mechanisms that control furin regulation in chondrogenesis remain unknown. To gain insight into the molecular regulation of furin, we used the mouse prechondrogenic ATDC5 cell line, an established in vitro model of cartilage differentiation. Peak expression of both furin mRNA and furin PTHrP maturation was observed during chondrocyte nodule formation stage, an event that correlated with increased mRNA levels of Sox9, a potent high-mobility-group (HMG) box-containing transcription factor required for cartilage formation. Inhibition of furin activity led to a diminution in maturation of PTHrP, suggesting a relationship between Sox9-induced regulation of furin and chondrogenesis events. Transient transfection of Sox9 in nonchondrogenic cells resulted in a marked increase in furin mRNA and in the transactivation of the furin P1A promoter. Direct Sox9 action on the P1A promoter was narrowed down to a critical paired site with Sox9 binding capability in vitro and in vivo. Sox9 transactivation effect was inhibited by L-Sox5 and Sox-6, two Sox9 homologs also expressed in ATDC5 cells. Sox6 inhibitory effect was reduced when using Sox6-HMG-box mutants, indicating a repressive effect through direct HMG-box/DNA binding. Our work suggests a mechanism by which furin is regulated during chondrogenesis. It also adds to the complexity of Sox molecule interaction during gene regulation.