bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and Assay of RNA Transcripts of Enterovirus Species A to D, Rhinovirus Species A to C, and Human Parechovirus: Assessment of Assay Sensitivity and Specificity of Real-Time Screening and Typing Methods
Authors: McLeish Nigel J. , Witteveldt Jeroen , Clasper Lucy , McIntyre Chloe , McWilliam Leitch E. Carol , Hardie Alison , Bennett Susan , Gunson Rory , Carman William F. , Feeney Susan A. , Coyle Peter V. , Vipond Barry , Muir Peter , Benschop Kimberley , Wolthers Katja , Waris Matti , Osterback Riikka , Johannessen Ingo , Templeton Kate , Harvala Heli , Simmonds Peter 
Published: June 2012

ABSTRACT
Nucleic acid amplification methods such as the PCR have had a major impact on the diagnosis of viral infections, often achieving greater sensitivities and shorter turnaround times than conventional assays and an ability to detect viruses refractory to conventional isolation methods. Their effectiveness is, however, significantly influenced by assay target sequence variability due to natural diversity and rapid sequence changes in viruses that prevent effective binding of primers and probes. This was investigated for a diverse range of enteroviruses (EVs; species A to D), human rhinoviruses (HRVs; species A to C), and human parechovirus (HPeV) in a multicenter assay evaluation using a series of full-length prequantified RNA transcripts. RNA concentrations were quantified by absorption (NanoDrop) and fluorescence methods (RiboGreen) prior to dilution in buffer supplemented with RNase inhibitors and carrier RNA. RNA transcripts were extremely stable, showing minimal degradation after prolonged storage at temperatures between ambient and −20°C and after multiple freeze-thaw cycles. Transcript dilutions distributed to six referral laboratories were screened by real-time reverse transcriptase PCR assays using different primers and probes. All of the laboratories reported high assay sensitivities for EV and HPeV transcripts approaching single copies and similar amplification kinetics for all four EV species. HRV detection sensitivities were more variable, often with substantially impaired detection of HRV species C. This could be accounted for in part by the placement of primers and probes to genetically variable target regions. Transcripts developed in this study provide reagents for the ongoing development of effective diagnostics that accommodate increasing knowledge of genetic heterogeneity of diagnostic targets.
Distinct Roles for Extracellular Signal-Regulated Kinase 1 (ERK1) and ERK2 in the Structure and Production of a Primate Gammaherpesvirus
Authors: Woodson Evonne N. , Kedes Dean H. 
Published: June 2012

ABSTRACT
During their progression from intranuclear capsids to mature trilaminar virions, herpesviruses incorporate an extensive array of viral as well as a smaller subset of cellular proteins. Our laboratory previously reported that rhesus monkey rhadinovirus (RRV), a close homolog of the human pathogen Kaposi's sarcoma-associated herpesvirus (KSHV), is comprised of at least 33 different virally encoded proteins. In the current study, we found that RRV infection activated the extracellular signal-regulated kinase (ERK) pathway and nascent virions preferentially incorporated the activated form of ERK2 (pERK2) into the tegument. This was evident even in the face of greatly diminished stores of intracellular ERK2, suggesting a clear bias toward the incorporation of pERK2 into the RRV particle. Similar to earlier findings with KSHV, activation of ERK was essential for the production of lytic viral proteins and virions. Knockdown of intracellular ERK, however, failed to inhibit virus production, likely due to maintenance of residual pools of intracellular pERK2. Paradoxically, selective knockdown of ERK1 enhanced virion production nearly 5-fold and viral titers more than 10-fold. These data are the first to implicate ERK1 as a negative regulator of lytic replication in a herpesvirus and the first to demonstrate the incorporation of an activated signaling molecule within a herpesvirus. Together, the results further our understanding of how herpesviruses interact with host cells during infection and demonstrate how this family of viruses can exploit cellular signal transduction pathways to modulate their own replication.
Key Molecular Factors in Hemagglutinin and PB2 Contribute to Efficient Transmission of the 2009 H1N1 Pandemic Influenza Virus
Authors: Zhang Ying , Zhang Qianyi , Gao Yuwei , He Xijun , Kong Huihui , Jiang Yongping , Guan Yuntao , Xia Xianzhu , Shu Yuelong , Kawaoka Yoshihiro , Bu Zhigao , Chen Hualan 
Published: June 2012

ABSTRACT
Animal influenza viruses pose a clear threat to public health. Transmissibility among humans is a prerequisite for a novel influenza virus to cause a human pandemic. A novel reassortant swine influenza virus acquired sustained human-to-human transmissibility and caused the 2009 influenza pandemic. However, the molecular aspects of influenza virus transmission remain poorly understood. Here, we show that an amino acid in hemagglutinin (HA) is important for the 2009 H1N1 influenza pandemic virus (2009/H1N1) to bind to human virus receptors and confer respiratory droplet transmissibility in mammals. We found that the change from glutamine (Q) to arginine (R) at position 226 of HA, which causes a switch in receptor-binding preference from human α-2,6 to avian α-2,3 sialic acid, resulted in a virus incapable of respiratory droplet transmission in guinea pigs and reduced the virus's ability to replicate in the lungs of ferrets. The change from alanine (A) to threonine (T) at position 271 of PB2 also abolished the virus's respiratory droplet transmission in guinea pigs, and this mutation, together with the HA Q226R mutation, abolished the virus's respiratory droplet transmission in ferrets. Furthermore, we found that amino acid 271A of PB2 plays a key role in virus acquisition of the mutation at position 226 of HA that confers human receptor recognition. Our results highlight the importance of both the PB2 and HA genes on the adaptation and transmission of influenza viruses in humans and provide important insights for monitoring and evaluating the pandemic potential of field influenza viruses.
Negative Elongation Factor-Mediated Suppression of RNA Polymerase II Elongation of Kaposi's Sarcoma-Associated Herpesvirus Lytic Gene Expression
Authors: Toth Zsolt , Brulois Kevin F. , Wong Lai-Yee , Lee Hye-Ra , Chung Brian , Jung Jae U. 
Published: June 2012

ABSTRACT
Genome-wide chromatin immunoprecipitation assays indicate that the promoter-proximal pausing of RNA polymerase II (RNAPII) is an important postinitiation step for gene regulation. During latent infection, the majority of Kaposi's sarcoma-associated herpesvirus (KSHV) genes is silenced via repressive histone marks on their promoters. Despite the absence of their expression during latency, however, several lytic promoters are enriched with activating histone marks, suggesting that mechanisms other than heterochromatin-mediated suppression contribute to preventing lytic gene expression. Here, we show that the RNAPII-mediated transcription of the KSHV OriLytL, K5, K6, and K7 (OriLytL-K7) lytic genes is paused at the elongation step during latency. Specifically, the RNAPII-mediated transcription is stalled by the host's negative elongation factor (NELF) at the promoter regions of OriLytL-K7 lytic genes during latency, leading to the hyperphosphorylation of the serine 5 residue and the hypophosphorylation of the serine 2 of the C-terminal domain of the RNAPII large subunit, a hallmark of stalled RNAPII. Consequently, depletion of NELF expression induced transition of stalled RNAPII into a productive transcription elongation at the promoter-proximal regions of OriLytL-K7 lytic genes, leading to their RTA-independent expression. Using an RTA-deficient recombinant KSHV, we also showed that expression of the K5, K6, and K7 lytic genes was highly inducible upon external stimuli compared to other lytic genes that lack RNAPII on their promoters during latency. These results indicate that the transcription elongation of KSHV OriLytL-K7 lytic genes is inhibited by NELF during latency, but can also be promptly reactivated in an RTA-independent manner upon external stimuli.
Noninvasive Follow-Up of Simian Immunodeficiency Virus Infection in Wild-Living Nonhabituated Western Lowland Gorillas in Cameroon
Authors: Etienne Lucie , Locatelli Sabrina , Ayouba Ahidjo , Esteban Amandine , Butel Christelle , Liegeois Florian , Aghokeng Avelin , Delaporte Eric , Mpoudi Ngole Eitel , Peeters Martine 
Published: June 2012

ABSTRACT

Simian immunodeficiency viruses infecting western lowland gorillas (SIVgor) are closely related to HIV-1 and are most likely the ancestors of HIV-1 groups O and P. At present, limited data are available on genetic diversity, transmission, viral evolution, and pathogenicity of SIVgor in its natural host. Between 2004 and 2011, 961 putative gorilla fecal samples were collected at the Campo Ma'an National Park, Cameroon. Among them, 16% cross-reacted with HIV-1 antibodies, corresponding to at least 34 infected gorillas. Combining host genotyping and field data, we identified four social groups composed of 7 to 15 individuals each, with SIV rates ranging from 13% to 29%. Eleven SIVgor-infected gorillas were sampled multiple times; two most likely seroconverted during the study period, showing that SIVgor continues to spread. Phylogenetic analysis of partial
env
and
pol
sequences revealed cocirculation of closely related and divergent strains among gorillas from the same social group, indicating SIVgor transmissions within and between groups. Parental links could be inferred for some gorillas infected with closely related strains, suggesting vertical transmission, but horizontal transmission by sexual or aggressive behavior was also suspected. Intrahost molecular evolution in one gorilla over a 5-year period showed viral adaptations characteristic of escape mutants, i.e., V1V2 loop elongation and an increased number of glycosylation sites. Here we show for the first time the feasibility of noninvasive monitoring of nonhabituated gorillas to study SIVgor infection over time at both the individual and population levels. This approach can also be applied more generally to study other pathogens in wildlife.
The C11R Gene, Which Encodes the Vaccinia Virus Growth Factor, Is Partially Responsible for MVA-Induced NF-κB and ERK2 Activation
Authors: Martin Stefani , Harris Daniel T. , Shisler Joanna 
Published: June 2012

ABSTRACT
MVA is an attenuated strain of vaccinia virus (VACV) that is a popular vaccine vector. MVA infection activates NF-κB. For 293T cells, it is known that MVA early gene expression activates extracellular signal-regulated kinase 2 (ERK2), resulting in NF-κB activation. However, other viral and cellular mechanisms responsible for this event are ill defined. The data presented here show that the epidermal growth factor receptor (EGFR) is at least one apical trigger in this pathway: ERK2 and NF-κB activation was diminished when MVA infections occurred in cells devoid of the EGFR (CHO K1 cells) or in the presence of a drug that inhibits EGFR activation (AG1478) in 293T cells. The expression of dominant negative Ras or Raf proteins still permitted NF-κB activation, suggesting that a nonclassical EGFR-based signal transduction pathway triggered ERK2–NF-κB activation. C11R is an early gene present in MVA and other orthopoxviruses. It encodes the soluble, secreted vaccinia virus growth factor (VGF), a protein that binds to and stimulates the EGFR. Here it was observed that NF-κB was activated in 293T cells transfected with a plasmid encoding the C11R gene. Silencing by small interfering RNA (siRNA) or deletion of the C11R gene (MVAΔC11R) reduced both MVA-induced ERK2 and NF-κB activation in 293T cells or the keratinocyte line Hacat, suggesting that this mechanism of MVA-induced NF-κB activation may be common for several cell types.
Sex-ratio variation versus interplant distances in the regulation of pollen deposition and seed production in dioecious Cirsium arvense (Asteraceae)1This article is part of a Special Issue entitled “Pollination biology research in Canada: Perspectives on a mutualism at different scales”.
Authors: Van Drunen Wendy E. , Dorken Marcel E. 
Published: June 2012

Pollination success in dioecious plants is expected to be regulated by the ratio of female:male plants and the distances between plants of each sex. These factors have received considerable attention in studies of dioecious and other gender dimorphic plants, yet their effects have rarely been jointly considered. We documented sex ratios in 26 populations of Cirsium arvense (L.) Scop. (creeping thistle), a widely distributed clonal dioecious plant, and show that population sex ratios are generally female biased (∼60% of shoots were female, and 15 of 26 populations were female biased). We found clear evidence for a negative association between pollen loads and distances between females and males within populations. In contrast, and in spite of broad variation in sex ratios among populations (range: 0.11–0.99 female), we found no relationship between sex ratios and pollen receipt by females. However, both sex ratios and interplant distances were associated with female seed production: seed production declined with distances between females and males and increased with the proportion of male shoots. Our data suggest that female plants of C. arvense might often be pollen limited and that distances between individual females and males drive pollen limitation more strongly than the overall frequency of males within sites.
Histological and anatomical responses in avocado, Persea americana, induced by the vascular wilt pathogen, Raffaelea lauricola
Authors: Inch Sharon , Ploetz Randy , Held Benjamin , Blanchette Robert 
Published: June 2012

Raffaelea lauricola causes laurel wilt of avocado, Persea americana. Host × pathogen interactions were examined with light and scanning electron microscopy. The susceptible avocado cultivar ‘Simmonds’ was inoculated and examined 5 cm above the inoculation site 3, 7, 14, 21, and 42 days after inoculation (dai). No external symptoms were observed at 3 and 7 dai, and there were no anatomical differences when compared with the mock-inoculated plants. By 14 dai, external symptoms were present and dark discoloration had developed in sapwood. Tylose development increased significantly by 14 dai, and was positivity correlated with disease severity (P < 0.05). By 14 dai, gels formed in xylem vessels, fibers, and adjacent parenchyma cells; they were associated with xylem blockage and composed of phenols, pectin, and lipids, as suggested by, respectively, toluidine blue O, ruthenium red, and Sudan III stains. With a chitin-specific stain, fluorescein-conjugated wheat germ agglutinin, infrequent mycelia, and conidia of R. lauricola were visualized within xylem lumena and fibers, regardless of sample date. Understanding how avocado responds to the presence of this pathogen could assist the development of laurel wilt-resistant avocado genotypes and inform efforts to manage this disease with other measures.
Sex-ratio variation and the function of staminodes inAralia nudicaulis1This article is part of a Special Issue entitled “Pollination biology research in Canada: Perspectives on a mutualism at different scales”.
Authors: Nicholls Emony I.E. , Dorken Marcel E. 
Published: June 2012

Aralia nudicaulis L. is a clonal dioecious herb common to forested ecosystems in eastern North America. Across 15 sites, the frequency of female ramets ranged between 5% and 95%. This variation was used to examine hypotheses involving the life history and pollination biology of A. nudicaulis. Because female reproductive function is thought to incur greater resource costs than male function, we predicted that female ramets should (i) be more common where resources (and light in particular) are more abundant and (ii) have lower rates of survival than male ramets. However, there was (i) no significant association between light availability (measured as canopy closure) and female frequencies across sites and (ii) ramet ages were skewed towards older ages for females, not males. Female A. nudicaulis produce staminodes that render female inflorescences visually similar to male inflorescences. We experimentally manipulated the presence–absence of staminodes and found that pollen receipt by females without staminodes was substantially lower than for plants with intact staminodes. Finally, pollinators tend to prefer visiting male over female flowers. We were interested in evaluating whether such preferences might scale up to the population level, with higher pollinator abundances at male-dominated sites. However, we instead found a strong positive association between pollinator abundances and female frequencies. Although there is unlikely to be a causal relationship between them, the identification of a common variable underlying variation in female frequencies and pollinator abundances might reveal key insights into the factors regulating the life history and pollination of forest understory plants.
Pollen diversity collected by honey bees in the vicinity of Vaccinium spp. crops and its importance for colony development1This article is part of a Special Issue entitled “Pollination biology research in Canada: Perspectives on a mutualism at different scales”.
Authors: Girard Mélissa , Chagnon Madeleine , Fournier Valérie 
Published: June 2012

Access to a rich diversity of flowering plants is very important for the development of honey bee colonies introduced in crops for pollination. The aim of this observational study was to determine the impact of surrounding pollen diversity on the health of honey bee colonies introduced in lowbush blueberries ( Vaccinium angustifolium Ait.) in June and cranberries ( Vaccinium macrocarpon Ait.) in July. The results suggest that monocultures of lowbush blueberries are not suitable for optimal brood rearing. In the blueberry environments we studied, the dominant pollen collected by honey bees were Alnus Mill. spp. and Taraxacum officinale F.H. Wigg., which are deficient in some essential amino acids. Significant reduction of brood rearing during honey bees’ stay in blueberry monocultures in June may, therefore, be explained by nutritional deficiencies. In July, the polliniferous flora in the vicinity of cranberry monocultures was poorer but of better nutritional quality. Pollen analysis allowed the identification of Brassicaceae, Trifolium L. spp., and V. macrocarpon as the three dominant taxa collected by honey bees during this period. The complete lists of plant taxa foraged by honey bees for pollen during the pollination of lowbush blueberries and cranberries are provided.
Pollen-ovule ratios in seven species ofVaccinium(Ericaceae) and stamen structure inVaccinium myrtilloidesandVaccinium vitis-idaea1This article is part of a Special Issue entitled “Pollination biology research in Canada: Perspectives on a mutualism at different scales”.
Authors: Stephens Danielle T. , Levesque Danielle E. , Davis Arthur R. 
Published: June 2012

Pollen-ovule (P/O) ratios were determined for five Vaccinium species (Ericaceae) native to eastern Canada (Nova Scotia: V. angustifolium, V. boreale, V. caespitosum, V. corymbosum, V. uliginosum), one in western Canada (Saskatchewan: V. myrtilloides), and one (V. vitis-idaea) from both provinces. Pollen, released at maturity as tetrads, was converted to total pollen grains per flower to yield P/O ratios ranging from 238 (V. caespitosum) to 2008 (V. vitis-idaea), but 736 for the latter in Saskatchewan. These P/O ratios are indicative of facultative autogamy to facultative xenogamy. Additionally, the structure of mature stamens and pollen tetrads was studied in V. myrtilloides and V. vitis-idaea. Each anther was functionally bilocular; had a single-cell thickness (i.e., epidermis) with regularly occurring papillae; lacked an endothecium; and possessed two distal, hollow tubules each terminating in a pore. Overall pollen grain viability was 76%–97% (V. myrtilloides) and 51%–93% (V. vitis-idaea), with about 20% of tetrads having only 1–3 grains viable, and 12% and 27% of tetrads entirely nonviable in V. myrtilloides and V. vitis-idaea, respectively. Pollen tetrads occasionally were connected by a sticky substance resembling pollenkitt, but viscin threads were absent. One instance of precocious (in situ) germination of tetrads was recorded within anthers of V. myrtilloides.
Discussion of “New zircon shock phenomena and their use for dating and reconstruction of large impact structures revealed by electron nanobeam (EBSD, CL, EDS) and isotopic U–Pb and (U–Th)/He analysis of the Vredefort dome”1Appears in Canadian Journal of Earth Sciences, 2011, 48(2): 117–139 [doi: dx.doi.org/10.1139/e11-011].
Authors: Rajesh H.M. , Knoper M.W. 
Published: June 2012

Spodumene pegmatites occur in the southeastern sector of the 2.02 Ga Vredefort impact structure in South Africa. Moser et al. (published in 2011) presented an isotope dilution – thermal ionization mass spectrometry (ID–TIMS) age of 1136 ± 47 Ma for these spodumene pegmatites. This discussion questions the reliability of this age. Field relations indicate that the spodumene pegmatites are not affected by the structural fabric that affected the host amphibolites. The crosscutting impact-related veins of pseudotachylitic breccia clearly argues a preimpact age for the spodumene pegmatites. The high-uranium content of one of the two zircons used by Moser et al. to obtain the age is correlated to the ∼1.1 Ga Pb-loss event, widely observed in different rocks within the Vredefort impact structure.
40Ar–39Ar ages for detrital white mica in Meguma terrane, Nova Scotia, Canada: implications for provenance of the Goldenville and Halifax groups
Authors: Reynolds P.H. , White C.E. , Barr S.M. , Muir C.M. 
Published: June 2012

Single-grain 40Ar/39Ar ages are reported for detrital white mica, along with conventional step-heating data for whole rocks, from low-grade metasandstone samples from the Goldenville, Halifax, and Rockville Notch groups in the Meguma terrane of southern Nova Scotia. The majority (166) of single grains from 11 samples yielded ages between ca. 615 and 350 Ma, and the remaining 12 grains yielded ages between ca. 1900 and 870 Ma. The late Neoproterozoic–Paleozoic age distributions are consistent with derivation of sediments from the rapidly uplifted flanks of an active rift, where partial to complete resetting of white mica ages occurred at ca. 520–500 Ma, preceding sediment deposition. The ca. 615 Ma ages may be relics of the original detrital white mica that existed in the source rocks prior to the rifting event. Ages from the Upper Silurian White Rock Formation appear to reflect this same ca. 520–500 Ma event, suggesting that sediments in the White Rock Formation were recycled from the Goldenville and Halifax groups. The older Precambrian ages are inferred to represent white mica in the source region, likely Amazonia. The whole-rock age spectra are discordant, with pronounced age gradients and no well-defined age plateaus. Initial gas released from five of the samples at low laboratory extraction temperatures (ca. 450–500 °C) yielded ages of ca. 260–300 Ma, not seen in the single-grain data, whereas gas released at the highest extraction temperatures yielded ages in the range ca. 510–530 Ma, possibly reflecting the principal result obtained from the single-grain data.