bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Epidemiology of Human Coronavirus OC43 Reveals Evolution of Different Genotypes over Time and Recent Emergence of a Novel Genotype due to Natural Recombination
Authors: Lau Susanna K. P. , Lee Paul , Tsang Alan K. L. , Yip Cyril C. Y. , Tse Herman , Lee Rodney A. , So Lok-Yee , Lau Yu-Lung , Chan Kwok-Hung , Woo Patrick C. Y. , Yuen Kwok-Yung 
Published: August 2011

ABSTRACT
Although human coronavirus OC43-OC43 (HCoV-OC43) is the coronavirus most commonly associated with human infections, little is known about its molecular epidemiology and evolution. We conducted a molecular epidemiology study to investigate different genotypes and potential recombination in HCoV-OC43. Twenty-nine HCoV-OC43 strains from nasopharyngeal aspirates, collected from 2004 to 2011, were subjected to RNA-dependent RNA polymerase (RdRp), spike, and nucleocapsid gene analysis. Phylogenetic analysis showed at least three distinct clusters of HCoV-OC43, although 10 unusual strains displayed incongruent phylogenetic positions between RdRp and spike genes. This suggested the presence of four HCoV-OC43 genotypes (A to D), with genotype D most likely arising from recombination. The complete genome sequencing of two genotype C and D strains and bootscan analysis showed recombination events between genotypes B and C in the generation of genotype D. Of the 29 strains, none belonged to the more ancient genotype A, 5 from 2004 belonged to genotype B, 15 from 2004 to 2006 belonged to genotype C, and 1 from 2004 and all 8 from 2008 to 2011 belonged to the recombinant genotype D. Molecular clock analysis using spike and nucleocapsid genes dated the most recent common ancestor of all genotypes to the 1950s, genotype B and C to the 1980s, genotype B to the 1990s, and genotype C to the late 1990s to early 2000s, while the recombinant genotype D strains were detected as early as 2004. This represents the first study to describe natural recombination in HCoV-OC43 and the evolution of different genotypes over time, leading to the emergence of novel genotype D, which is associated with pneumonia in our elderly population.
Upregulation of BST-2/Tetherin by HIV Infection
In Vivo
Authors: Homann Stefanie , Smith Davey , Little Susan , Richman Douglas , Guatelli John 
Published: August 2011

ABSTRACT

The interferon-inducible antiviral factor BST-2 prevents several enveloped viruses, including HIV, from escaping infected cells. The HIV protein Vpu antagonizes this host defense. Little is known about the expression of BST-2 during HIV infection
in vivo
and whether it can be modulated to the host's advantage. We studied the expression of BST-2 on blood cells from HIV-infected patients during the acute and chronic phases of disease as well as after antiretroviral treatment (ART). The expression of BST-2 was increased on mononuclear leukocytes, including CD4-positive T lymphocytes from HIV-positive patients, compared to that on cells of uninfected controls. The expression of BST-2 was highest during acute infection and decreased to levels similar to those of uninfected individuals after ART. Treatment of primary blood mononuclear cells
in vitro
with alpha interferon or with Toll-like receptor (TLR) agonists increased the expression of BST-2 to levels similar to those found during infection
in vivo
. The interferon-induced levels were sufficient to overcome the Vpu protein
in vitro
, reducing the release of wild-type HIV. These data show that BST-2 is upregulated during HIV infection, consistent with its role as an interferon-stimulated gene. The data further suggest that this upregulation is sufficient to saturate the activity of Vpu and inhibit wild-type HIV.
A Panel of IgG1 b12 Variants with Selectively Diminished or Enhanced Affinity for Fcγ Receptors To Define the Role of Effector Functions in Protection against HIV
Authors: Moldt Brian , Schultz Niccole , Dunlop D. Cameron , Alpert Michael D. , Harvey Jackson D. , Evans David T. , Poignard Pascal , Hessell Ann J. , Burton Dennis R. 
Published: August 2011

ABSTRACT
Passive transfer of neutralizing antibodies is effective in protecting rhesus macaques against simian/human immunodeficiency virus (SHIV) challenge. In addition to neutralization, effector functions of the crystallizable fragment (Fc) of antibodies are involved in antibody-mediated protection against a number of viruses. We recently showed that interaction between the Fc fragment of the broadly neutralizing antibody IgG1 b12 and cellular Fcγ receptors (FcγRs) plays an important role in protection against SHIV infection in rhesus macaques. The specific nature of this Fc-dependent protection is largely unknown. To investigate, we generated a panel of 11 IgG1 b12 antibody variants with selectively diminished or enhanced affinity for the two main activating FcγRs, FcγRIIa and FcγRIIIa. All 11 antibody variants bind gp120 and neutralize virus as effectively as does wild-type b12. Binding studies using monomeric (enzyme-linked immunosorbent assay [ELISA] and surface plasmon resonance [SPR]) and cellularly expressed Fcγ receptors show decreased (up to 5-fold) and increased (up to 90-fold) binding to FcγRIIa and FcγRIIIa with this newly generated panel of antibodies. In addition, there was generally a good correlation between b12 variant affinity for Fcγ receptor and variant function in antibody-dependent cell-mediated virus inhibition (ADCVI), phagocytosis, NK cell activation assays, and antibody-dependent cellular cytotoxicity (ADCC) assays. In future studies, these b12 variants will enable the investigation of the protective role of individual FcγRs in HIV infection.
Norovirus RNA-Dependent RNA Polymerase Is Phosphorylated by an Important Survival Kinase, Akt
Authors: Eden John-Sebastian , Sharpe Laura J. , White Peter A. , Brown Andrew J. 
Published: August 2011

ABSTRACTViruses commonly use host cell survival mechanisms to their own advantage. We show that Akt, an important signaling kinase involved in cell survival, phosphorylates the RNA-dependent RNA polymerase (RdRp) from norovirus, the major cause of gastroenteritis outbreaks worldwide. The Akt phosphorylation of RdRp appears to be a feature unique to the more prevalent norovirus genotypes such as GII.4 and GII.b. This phosphorylation event occurs at a residue (Thr33) located at the interface where the RdRp finger and thumb domains interact and decreasesde novoactivity of the polymerase. This finding provides fresh insights into virus-host cell interactions.
Compensation by the E138K Mutation in HIV-1 Reverse Transcriptase for Deficits in Viral Replication Capacity and Enzyme Processivity Associated with the M184I/V Mutations
Authors: Xu Hong-Tao , Asahchop Eugene L. , Oliveira Maureen , Quashie Peter K. , Quan Yudong , Brenner Bluma G. , Wainberg Mark A. 
Published: August 2011

ABSTRACTRecently, several phase 3 clinical trials (ECHO and THRIVE) showed that E138K and M184I were the most frequent mutations to emerge in patients who failed therapy with rilpivirine (RPV) together with two nucleos(t)ide reverse transcriptase inhibitors, emtricitabine (FTC) and tenofovir (TDF). To investigate the basis for the copresence of E138K and M184I, we generated recombinant mutated and wild-type (WT) reverse transcriptase (RT) enzymes and HIV-1NL4-3infectious clones. Drug susceptibilities were determined in cord blood mononuclear cells (CBMCs). Structural modeling was performed to analyze any impact on deoxynucleoside triphosphate (dNTP) binding. The results of phenotyping showed that viruses containing both the E138K and M184V mutations were more resistant to each of FTC, 3TC, and ETR than viruses containing E138K and M184I. Viruses with E138K displayed only modest resistance to ETR, little resistance to efavirenz (EFV), and no resistance to either FTC or 3TC. E138K restored viral replication capacity (RC) in the presence of M184I/V, and this was confirmed in cell-free RT processivity assays. RT enzymes containing E138K, E138K/184I, or E138K/184V exhibited higher processivity than WT RT at low dNTP concentrations. Steady-state kinetic analysis demonstrated that the E138K mutation resulted in decreasedKms for dNTPs. In contrast, M184I/V resulted in an increasedKmfor dNTPs compared to those for WT RT. These results indicate that the E138K mutation compensates for both the deficit in dNTP usage and impairment in replication capacity by M184I/V. Structural modeling shows that the addition of E138K to M184I/V promotes tighter dNTP binding.
Effects of job strain on fatigue: cross-sectional and prospective views of the job content questionnaire and effort–reward imbalance in the GAZEL cohort
Authors: Sembajwe Grace , Wahrendorf Morten , Siegrist Johannes , Sitta Remi , Zins Marie , Goldberg Marcel , Berkman Lisa 
Published: August 2011

ObjectivesThe objectives this study were (1) to investigate correlations between measures of psychosocial workplace stress as measured in separate years by the Job Content Questionnaire (JCQ) and Effort–Reward Imbalance (ERI) scales; (2) to establish a valid measure of psychosocial job stress with its components (by identifying the individual and interactive associations of job stress components) and (3) to use the component measures to assess the risk of psychosocial strain at work on fatigue.MethodsThe JCQ and ERI from the annual survey of the GAZEL cohort established in 1989 initially with 20 624 respondents were used to investigate the associations of workplace stress on mental and physical fatigue in two separate years (1998 and 2006). First, the JCQ measures from separate years (1997 and 1999) were combined to create a measure for the same year as ERI (1998). The new measure was validated for internal and external consistency. Using logistic regression, the subcomponents of stress (upper tertiles of psychological demands, physical demands, decision latitude, social support, effort, reward, ERI and overcommitment) were tested for associations with the highest reporting of mental and physical fatigue.ResultsBy combining JCQ responses from 1997 to 1999, we were able to increase the amount of information available on psychosocial factors in 1998. Psychometric properties of the workplace stress scales also showed expected factor loadings. Workplace psychosocial factors had greater associations with fatigue among men than women. Although psychosocial factors became less predictive of fatigue at 8 years of follow-up, associations between fatigue and psychosocial components (overcommitment, social support and rewards) remained significant.ConclusionsThese analyses continue to validate the various subcomponents scales of workplace stress as measured by the JCQ and effort–reward imbalance model in GAZEL. They also highlight the importance of psychosocial work factors in the experience of overall fatigue even after an 8-year follow-up.
NMR and MS study of the formation of β-d-glucopyranosylamine uronic acid in aqueous solution
Authors: Ghadban Ali , Albertin Luca , Condamine Eric , Mounguengui Rédéo W. Moussavou , Heyraud Alain 
Published: August 2011

The products of the reaction of d-glucuronic acid with various combinations of ammonia and volatile ammonium salts in water were studied by NMR and MS spectroscopy. For long reaction times (~24 h), the expected products β-d-glucopyranosylamine uronic acid and ammonium N-(β-d-glucopyranosyluronic acid)carbamate were obtained in good-to-high yield, whereas seven intermediate species were identified in samples taken at earlier reaction times. 1H–1H homonuclear and 1H–13C heteronuclear correlation experiments enabled a complete assignment of the 1H and 13C NMR spectra of the starting and final compounds, and a partial assignment of the peaks of intermediate species. Based on these results, a 1H NMR protocol for the quantification of the different compounds taking part in the reaction was developed, which was used to monitor the evolution of the composition of an early reaction sample redissolved in D2O. It was thus established that two of the observed intermediate species are actually the α anomer of the main products, whereas the others are precursors to the formation of α/β-d-glucopyranosylamine uronic acid and ammonium N-(α/β-d-glucopyranosyluronic acid)carbamate. The correct assignments for the 1H and 13C spectra of d-glucuronic acid in D2O are also reported.
Preparation and photocatalytic activity of TiO2 nanocomposites coated with monolayer-protected gold clusters
Authors: Amaratunga Piyadarsha , Lee Myeongsoon , Kim Junhyung , Lee Dongil 
Published: August 2011

We report the preparation and photocatalytic activity of TiO2 nanocomposites modified with monolayer-protected gold clusters (MPCs). Highly monodisperse tiopronin-coated MPCs with core diameters of 2.2 ± 0.2 nm were pre-prepared and then anchored onto a TiO2 surface using the bifunctional tiopronin linker. In this method, the gold core size was preserved after calcination at 260 °C as well as the anchoring process, and the gold loading on TiO2 could be precisely controlled by the experimental condition. The photocatalytic degradation of Rhodamine 590 (Rh-590) was carried out with thus prepared MPC–TiO2 composites. Mechanistic study of the photocatalytic reactions revealed that the degradation of Rh-590 occurs via the oxidative pathway by photogenerated holes. The photocatalytic activity of the MPC–TiO2 composites was found to increase significantly upon calcination at 260 °C, whereas the size of gold particles remained at their initial size. The photocatalytic activity of the composites, however, drastically decreased when the composites were calcined at 400 °C. X-ray photoelectron spectroscopy analysis of the calcined composites was conducted to understand the vastly different calcination results. A significant amount of oxidized sulfur remained in the composites after calcination at 400 °C, which appears to be responsible for the drastic decrease in the photocatalytic activity.
Feasibility of using red pigment producing fungi to stain wood for decorative applications
Authors: Robinson Sara C. , Tudor Daniela , Cooper Paul A. 
Published: August 2011

This research investigated the use of red pigment producing fungi in controlled inoculation into woody substrates for decorative applications. Two Fusarium species isolated from red-stained wood and two strains of Arthrographis cuboidea capable of producing red stain in culture were inoculated onto sugar maple ( Acer saccharum Marsh.), incubated for 6–14 weeks, and evaluated for their ability to produce a high-saturation, penetrating stain. Both Fusarium species failed to produce significant pigmentation either externally or internally. Both strains of A. cuboidea produced high amounts of surface and penetrating red stain within a moderate incubation period (over 80% of the wood samples stained by 10 weeks of incubation) but were capable of doing so only under sterile or semisterile conditions. Production of red stain did not differ between A. cuboidea isolates except at 6 and 8 weeks where isolate ELS-1 had significantly higher internal red stain. It was also found that an increase in incubation time for A. cuboidea past 8 weeks led to increasing amounts of blue pigment on external wood surfaces. The findings indicate that A. cuboidea is suitable for production of red pigmentation on decorative wood applications only if utilized under sterile or semisterile conditions and incubation is halted before blue pigment begins to form.
Gap dynamics in aspen stands of the Clay Belt of northwestern Quebec following a forest tent caterpillar outbreak
Authors: Moulinier Julien , Lorenzetti François , Bergeron Yves 
Published: August 2011

Forest tent caterpillar (FTC; Malacosoma disstria Hübner) outbreaks represent an important natural disturbance in broadleaf-dominated stands; however, their effects on forest gap dynamics are not well understood. To describe such effects on canopy gaps and tree recruitment patterns, we investigated 20 trembling aspen (Populus tremuloides Michx.) dominated stands defoliated severely over 0 to 3 years during the last outbreak (1998–2003) in the northwestern Clay Belt of Quebec. Results show that canopy opening more than tripled (12.3%–43.7%) from 0 to 3 years of severe defoliation, and mean gap size was more than 12 times greater (7.2–87.5 m2) over the same gradient. Regeneration patterns suggest that aspen recruitment is not sufficient to completely restore closed canopies in stands defoliated 0, 1, and 2 years, whereas it should be sufficient in stands defoliated 3 years, where large gaps allow trembling aspen establishment. Our results clearly indicate that FTC outbreaks represent an important factor of gap formation in trembling aspen stands. At the stand level, gaps create uneven stand structures, and at the landscape level, FTC defoliation duration creates a large range of even to uneven stand structures.
Adaptations to nitrogen form: comparing inorganic nitrogen and amino acid availability and uptake by four temperate forest plants
Authors: Metcalfe R.J. , Nault J. , Hawkins B.J. 
Published: August 2011

There are few examinations of the relative availability and plant uptake of inorganic N and amino acid N in temperate forest regions. We determined the availability of amino acid N and inorganic N in soils under two shrub species ( Vaccinium ovalifolium Sm. versus Rubus spectabilis Pursh) on three sites near Jordan River, British Columbia, over a growing season. We compared biomass production of the two shrubs and two conifers ( Picea sitchensis (Bong.) Carr. and Pseudotsuga menziesii (Mirb.) Franco var. menziesii) when given inorganic N (20:80 or 80:20 NH4+–NO3–) or organic N (glycine and glutamic acid) and assessed short-term uptake (24 h) of 15N-labelled NH4+, NO3–, glycine, or glutamic acid by the four species. Water-extracted soil concentrations of NH4+ were up to 1.5 times greater than NO3– averaged across sites. Concentrations of amino acid N and inorganic N were similar on soils under Rubus , but the amino acid N to inorganic N ratio was up to 2.4:1 in soils under Vaccinium . Soils dominated by Rubus had up to twice the NO3–-N and two thirds the amino acid N concentrations of soils dominated by Vaccinium, averaged across sites and Rubus had relatively high short-term 15NO3– uptake. The dry biomass of conifers was approximately four times greater when supplied mainly with NH4+ compared with NO3–, but biomass of the two shrub species was similar in both inorganic N treatments. All plants had comparable rates of short-term 15N uptake from amino acids and inorganic N, suggesting that amino acids could contribute to the N nutrition of these temperate species; however, dry biomass of all four species grown with amino acids was less than one half that of plants grown with inorganic N.
Late Aptian to Turonian stratigraphy of the eastern Arabian Plate – depositional sequences and lithostratigraphic nomenclature
Authors: van Buchem F. S. P. , Simmons M. D. , Droste H. J. , Davies R. B. 
Published: August 2011

ABSTRACT
This stratigraphic article summarizes a number of observations on the mid-Cretaceous stratigraphy of Arabia made during the 2nd Arabian Plate Geology Workshop held in Abu Dhabi in January 2010. These observations pertain to the lithostratigraphic nomenclature applied on the eastern Arabian Plate and its relationship to mid-Cretaceous (Late Aptian–Turonian) depositional systems and sequences recognized plate-wide. It appears that several of the commonly applied lithostratigraphic terms are diachronous as a result of (i) plate-wide migration of carbonate and siliciclastic facies belts; (ii) the occurrence of intra-shelf basins at different times and locations; (iii) differential preservation beneath erosional unconformities; and (iv) simple differences in usage across political boundaries. A plate-wide sequence stratigraphic scheme is thus a powerful tool for regional correlation and mapping, and for reconciling lithostratigraphic differences.
The studied interval can be subdivided into two primary sedimentary systems that differ in lithology, depositional geometries and dominant faunal assemblages. First, latest Aptian- and Albian-aged systems, which are characterized by volumetrically significant Arabian Shield-derived siliciclastics (both sandstones and claystones) that alternate with carbonate beds. The carbonate beds thicken up-section and have generally very low-angle, muddy ramp depositional geometries. Organic-rich basinal facies are found only in the Kazhdumi Basin in SW Iran at this time. The faunal composition of the carbonates is dominated by benthic foraminifera (notably orbitolinids). Within this succession three third-order depositional sequences are distinguished (MFS K90, K100 and K110). Secondly, Cenomanian–early Turonian-aged sedimentary systems are characterized by a marked reduction in siliciclastic influx, the development of carbonate platform to intra-shelf basin topography and deposition of basinal source rocks. Rudists are the dominant component of grainy, high-energy platform margin/barrier facies, and are also present in the platform top sediments. Within this succession three Cenomanian sequences can be correlated clearly at the scale of the plate (MFS K120, K130 and K140), whereas the number of sequences in the Turonian interval is less well known owing to significant local erosion and/or non-deposition during a period of tectonic instability.
Applying this robust sequence stratigraphic framework in combination with a synthesis of biostratigraphic age calibration demonstrates the diachronous character of the Mauddud, Safaniya, Ahmadi and Mishrif formations and equivalents from the southern to the northern part of the Arabian Plate.
Epithelial Protein-Tyrosine Phosphatase 1B Contributes to the Induction of Mammary Tumors by HER2/Neu but Is Not Essential for Tumor Maintenance
Authors: Balavenkatraman Kamal K. , Aceto Nicola , Britschgi Adrian , Mueller Urs , Bence Kendra K. , Neel Benjamin G. , Bentires-Alj Mohamed 
Published: August 2011

Abstract
Protein-tyrosine phosphatase 1B (PTP1B), a well-established metabolic regulator, plays an important role in breast cancer. Using whole-body PTP1B knockout mice, recent studies have shown that PTP1B ablation delays HER2/Neu-induced mammary cancer. Whether PTP1B plays a cell-autonomous or a noncell-autonomous role in HER2/Neu-evoked tumorigenesis and whether it is involved in tumor maintenance was unknown. We generated mice expressing HER2/Neu and lacking PTP1B specifically in the mammary epithelium. We found that mammary-specific deletion of PTP1B delays the onset of HER2/Neu-evoked mammary tumors, establishing a cell autonomous role for PTP1B in such neoplasms. We also deleted PTP1B in established mouse mammary tumors or depleted PTP1B in human breast cancer cell lines grown as xenografts. PTP1B inhibition did not affect tumor growth in either model showing that neither epithelial nor stromal PTP1B is necessary for tumor maintenance. Taken together, our data show that despite the PTP1B contribution to tumor onset, it is not essential for tumor maintenance. This suggests that PTP1B inhibition could be effective in breast tumor prevention. Mol Cancer Res; 9(10); 1377–84. ©2011 AACR.