bluuebunny/crossref_metadata_2025 huggingface dataset:
A hydrothermal after-ripening time model for seed dormancy loss in Bromus tectorum L.
Authors: Bair Necia B. , Meyer Susan E. , Allen Phil S.
Published: February 2006

After-ripening, the loss of dormancy under dry conditions, is associated with a decrease in mean base water potential for germination ofBromus tectorumL. seeds. After-ripening rate is a linear function of temperature above a base temperature, so that dormancy loss can be quantified using a thermal after-ripening time (TAR) model. To incorporate storage water potential into TAR, we created a hydrothermal after-ripening time (HTAR) model. Seeds from twoB. tectorumpopulations were stored under controlled temperatures (20 or 30 °C) and water potentials (−400 to −40 MPa). Subsamples were periodically removed from each storage treatment and incubated at 15 or 25 °C to determine germination time courses. Dormancy status (mean base water potential) was calculated from each time course using hydrothermal time equations developed for each seed collection. Seeds stored at −400 MPa did not after-ripen. At water potentials from −400 to −150 MPa, the rate of after-ripening increased approximately linearly with increasing water potential. Between −150 and −80 MPa, there was no further increase in after-ripening rate, while at −40 MPa seeds did not after-ripen and showed loss of vigour. These results suggest that the concept of critical water potential thresholds, previously shown to be associated with metabolic activity and desiccation damage in partially hydrated seeds, is also relevant to the process of after-ripening. The HTAR model generally improved field predictions of dormancy loss when the soil was very dry. Reduced after-ripening rate under such conditions provides an ecologically relevant explanation of how seeds prolong dormancy at high summer soil temperatures.
Mdm38 interacts with ribosomes and is a component of the mitochondrial protein export machinery
Authors: Frazier Ann E. , Taylor Rebecca D. , Mick David U. , Warscheid Bettina , Stoepel Nadine , Meyer Helmut E. , Ryan Michael T. , Guiard Bernard , Rehling Peter
Published: February 2006

Saccharomyces cerevisiae Mdm38 and Ylh47 are homologues of human Letm1, a protein implicated in Wolf-Hirschhorn syndrome. We analyzed the function of Mdm38 and Ylh47 in yeast mitochondria to gain insight into the role of Letm1. We find that mdm38Δ mitochondria have reduced amounts of certain mitochondrially encoded proteins and low levels of complex III and IV and accumulate unassembled Atp6 of complex V of the respiratory chain. Mdm38 is especially required for efficient transport of Atp6 and cytochrome b across the inner membrane, whereas Ylh47 plays a minor role in this process. Both Mdm38 and Ylh47 form stable complexes with mitochondrial ribosomes, similar to what has been reported for Oxa1, a central component of the mitochondrial export machinery. Our results indicate that Mdm38 functions as a component of an Oxa1-independent insertion machinery in the inner membrane and that Mdm38 plays a critical role in the biogenesis of the respiratory chain by coupling ribosome function to protein transport across the inner membrane.
The tumor suppressor DAPK inhibits cell motility by blocking the integrin-mediated polarity pathway
Authors: Kuo Jean-Cheng , Wang Won-Jing , Yao Chung-Chen , Wu Pei-Rung , Chen Ruey-Hwa
Published: February 2006

Death-associated protein kinase (DAPK) is a calmodulin-regulated serine/threonine kinase and possesses apoptotic and tumor-suppressive functions. However, it is unclear whether DAPK elicits apoptosis-independent activity to suppress tumor progression. We show that DAPK inhibits random migration by reducing directional persistence and directed migration by blocking cell polarization. These effects are mainly mediated by an inhibitory role of DAPK in talin head domain association with integrin, thereby suppressing the integrin–Cdc42 polarity pathway. We present evidence indicating that the antimigratory effect of DAPK represents a mechanism through which DAPK suppresses tumors. First, DAPK can block migration and invasion in certain tumor cells that are resistant to DAPK-induced apoptosis. Second, using an adenocarcinoma cell line and its highly invasive derivative, we demonstrate DAPK level as a determining factor in tumor invasiveness. Collectively, our study identifies a novel function of DAPK in regulating cell polarity during migration, which may act together with its apoptotic function to suppress tumor progression.
Early aging–associated phenotypes in Bub3/Rae1 haploinsufficient mice
Authors: Baker Darren J. , Jeganathan Karthik B. , Malureanu Liviu , Perez-Terzic Carmen , Terzic Andre , van Deursen Jan M.A.
Published: February 2006

Aging is a highly complex biological process that is believed to involve multiple mechanisms. Mice that have small amounts of the mitotic checkpoint protein BubR1 age much faster than normal mice, but whether other mitotic checkpoint genes function to prevent the early onset of aging is unknown. In this study, we show that several aging-associated phenotypes appear early in mice that are double haploinsufficient for the mitotic checkpoint genes Bub3 and Rae1 but not in mice that are single haploinsufficient for these genes. Mouse embryonic fibroblasts (MEFs) from Bub3/Rae1 haploinsufficient mice undergo premature senescence and accumulate high levels of p19, p53, p21, and p16, whereas MEFs from single haploinsufficient mice do not. Furthermore, although BubR1 hypomorphic mice have less aneuploidy than Bub3/Rae1 haploinsufficient mice, they age much faster. Our findings suggest that early onset of aging-associated phenotypes in mice with mitotic checkpoint gene defects is linked to cellular senescence and activation of the p53 and p16 pathways rather than to aneuploidy.
Huntingtin–HAP40 complex is a novel Rab5 effector that regulates early endosome motility and is up-regulated in Huntington's disease
Authors: Pal Arun , Severin Fedor , Lommer Barbara , Shevchenko Anna , Zerial Marino
Published: February 2006

The molecular mechanisms underlying the targeting of Huntingtin (Htt) to endosomes and its multifaceted role in endocytosis are poorly understood. In this study, we have identified Htt-associated protein 40 (HAP40) as a novel effector of the small guanosine triphosphatase Rab5, a key regulator of endocytosis. HAP40 mediates the recruitment of Htt by Rab5 onto early endosomes. HAP40 overexpression caused a drastic reduction of early endosomal motility through their displacement from microtubules and preferential association with actin filaments. Remarkably, endogenous HAP40 was up-regulated in fibroblasts and brain tissue from human patients affected by Huntington's disease (HD) as well as in STHdhQ111 striatal cells established from a HD mouse model. These cells consistently displayed altered endosome motility and endocytic activity, which was restored by the ablation of HAP40. In revealing an unexpected link between Rab5, HAP40, and Htt, we uncovered a new mechanism regulating cytoskeleton-dependent endosome dynamics and its dysfunction under pathological conditions.
A repeated IMP-binding motif controls oskar mRNA translation and anchoring independently of Drosophila melanogaster IMP
Authors: Munro Trent P. , Kwon Sunjong , Schnapp Bruce J. , St Johnston Daniel
Published: February 2006

Zip code–binding protein 1 (ZBP-1) and its Xenopus laevis homologue, Vg1 RNA and endoplasmic reticulum–associated protein (VERA)/Vg1 RNA-binding protein (RBP), bind repeated motifs in the 3′ untranslated regions (UTRs) of localized mRNAs. Although these motifs are required for RNA localization, the necessity of ZBP-1/VERA remains unresolved. We address the role of ZBP-1/VERA through analysis of the Drosophila melanogaster homologue insulin growth factor II mRNA–binding protein (IMP). Using systematic evolution of ligands by exponential enrichment, we identified the IMP-binding element (IBE) UUUAY, a motif that occurs 13 times in the oskar 3′UTR. IMP colocalizes with oskar mRNA at the oocyte posterior, and this depends on the IBEs. Furthermore, mutation of all, or subsets of, the IBEs prevents oskar mRNA translation and anchoring at the posterior. However, oocytes lacking IMP localize and translate oskar mRNA normally, illustrating that one cannot necessarily infer the function of an RBP from mutations in its binding sites. Thus, the translational activation of oskar mRNA must depend on the binding of another factor to the IBEs, and IMP may serve a different purpose, such as masking IBEs in RNAs where they occur by chance. Our findings establish a parallel requirement for IBEs in the regulation of localized maternal mRNAs in D. melanogaster and X. laevis.
Pseudo-Outbreak ofMycobacterium chelonaeandMethtlobactertum mesophilicumCaused by Contamination of an Automated Endoscopy Washer
Authors: Kressel Amy Beth , Kidd Francine
Published: February 2006

Objective:

To evaluate an unusual number of rapidly growing acid-fast bacilli, later identified asMycobacterium chelonae,and pink bacteria, later identified asMethylo-bacterium mesophilicum,from fungal cultures obtained by bronchoscopy.

Design:

Outbreak investigation.

Setting:

An academic medical center performing approximately 500 bronchoscopies and 4,000 gastrointestinal endoscopies in 1998.

Patients:

Patients undergoing bronchoscopy July 21 to October 2, 1998.

Methods:

The infection control department reviewed patient charts and bronchoscopy logs; obtained cultures of source water, faucets, washers, unopened glutaraldehyde, glutaraldehyde from the washers, and endoscopes; observed endoscope and bronchoscope cleaning and disinfecting procedures; reviewed glutaraldehyde monitoring records; and sentM chelonaeisolates for DNA fingerprinting.

Results:

M chelonae, M mesophilicum,gram-negative bacteria, and various molds grew from endoscopes, automated washers, and glutaraldehyde from the washers but not from unopened glutaraldehyde. The endoscopy unit regularly monitored the pH of glutaraldehyde, and the logs contained no deficiencies. The above sources remained positive for the same organisms after a glutaraldehyde cleaning cycle of the automated washers. DNA fingerprinting of theM chelonaerevealed that they were clonally related.

Conclusions:

The automated washers were contaminated with a biofilm that rendered them resistant to decontamination. The washers then contaminated the endoscopes and bronchoscopes they were used to disinfect. Our institution purchased new endoscopes and a new paracetic acid sterilization system.
Role of myristoylation and N-terminal basic residues in membrane association of the human immunodeficiency virus type 1 Nef protein
Authors: Bentham Matthew , Mazaleyrat Sabine , Harris Mark
Published: February 2006

Human immunodeficiency virus type 1 Nef protein is N-terminally myristoylated, a modification reported to be required for the association of Nef with cytoplasmic membranes. As myristate alone is not sufficient to anchor a protein stably into a membrane, it has been suggested that N-terminal basic residues contribute to Nef membrane association via electrostatic interactions with acidic phospholipids. Here, data are presented pertaining to the role of the myristate and basic residues in Nef membrane association, subcellular localization and function. Firstly, by using a biochemical assay for membrane association it was shown that, whereas myristoylation of Nef was not essential, mutation of a cluster of four arginines between residues 17 and 22 reduced membrane association dramatically. Mutation of two lysines at residues 4 and 7 had negligible effect alone, but when combined with the arginine substitutions, abrogated membrane association completely. By using indirect immunofluorescence, it was demonstrated that mutation of either of the two basic clusters altered the subcellular distribution of Nef dramatically. Thirdly, the requirement of the arginine and lysine clusters for Nef-mediated CD4 downmodulation was shown to correlate precisely with membrane association. These data suggest that membrane localization and subcellular targeting of Nef are controlled by a complex interplay of signals at the N terminus of the protein.
Genetic diversity of small-ruminant lentiviruses: characterization of Norwegian isolates of Caprine arthritis encephalitis virus
Authors: Gjerset Britt , Storset Anne K. , Rimstad Espen
Published: February 2006

Small-ruminant lentiviruses (SRLVs), includingCaprine arthritis encephalitis virus(CAEV) in goats and maedi-visna virus (MVV) in sheep, are lentiviruses that, despite overall similarities, show considerable genetic variation in regions of the SRLV genome. To gain further knowledge about the genetic diversity and phylogenetic relationships among field isolates of SRLVs occurring in geographically distinct areas, the full-length genomic sequence of a CAEV isolate (CAEV-1GA) and partialenvsequences obtained from Norwegian CAEV-infected goats were determined. The genome of CAEV-1GA consisted of 8919 bp. Alignment studies indicated significant diversity from published SRLV sequences. Deletions and hypervariability in the 5′ part of theenvgene have implications for the size of the proposed CAEV-1GA Rev protein and the encoded surface glycoprotein (SU). The variable regions in the C-terminal part of SU obtained from Norwegian CAEV isolates demonstrate higher sequence divergence than has been described previously for SRLVs. Phylogenetic analysis based onSUsequences gives further support for a unique group designation. The results described here reveal a distant genetic relationship between Norwegian CAEV and other SRLVs and demonstrate that there is more geographical heterogeneity among SRLVs than reported previously.
Complete nucleotide sequence and genome organization of a single-stranded RNA virus infecting the marine fungoid protist Schizochytrium sp.
Authors: Takao Yoshitake , Mise Kazuyuki , Nagasaki Keizo , Okuno Tetsuro , Honda Daiske
Published: February 2006

The complete nucleotide sequence of the genomic RNA of a marine fungoid protist-infecting virus (Schizochytrium single-stranded RNA virus; SssRNAV) has been determined. The viral RNA is single-stranded with a positive sense and is 9018 nt in length [excluding the 3′ poly(A) tail]. It contains two long open reading frames (ORFs), which are separated by an intergenic region of 92 nt. The 5′ ORF (ORF1) is preceded by an untranslated leader sequence of 554 nt. The 3′ large ORF (ORF2) and an additional ORF (ORF3) overlap ORF2 by 431 nt and are followed by an untranslated region of 70 nt [excluding the 3′ poly(A) tail]. The deduced amino acid sequences of ORF1 and ORF2 products show similarity to non-structural and structural proteins of dicistroviruses, respectively. However, Northern blot analysis suggests that SssRNAV synthesizes subgenomic RNAs to translate ORF2 and ORF3, showing that the translation mechanism of downstream ORFs is distinct from that of dicistroviruses. Furthermore, although considerable similarities were detected by using a blast genome database search, phylogenetic analysis based on both the nucleotide and amino acid sequences of the putative RNA-dependent RNA polymerase (RdRp) and the RNA helicase suggests that SssRNAV is phylogenetically distinct from other virus families. Therefore, it is concluded that SssRNAV is not a member of any currently defined virus family and belongs to a novel, unrecognized virus group.
Dual mutations in the Autographa californica nucleopolyhedrovirus FP-25 and p35 genes result in plasma-membrane blebbing in Trichoplusia ni cells
Authors: Kelly Barbara J. , King Linda A. , Possee Robert D. , Chapple Susan D. J.
Published: February 2006

Spodoptera frugiperda cells infected with Autographa californica nucleopolyhedrovirus (AcMNPV) lacking a functional anti-apoptotic p35 protein undergo apoptosis. However, such mutants replicate normally in Trichoplusia ni (TN-368) cells. An AcMNPV plaque isolate (AcdefrT) was identified during propagation of a virus deficient in p35 in TN-368 cells. This virus exhibited enhanced budded-particle formation in TN-368 cells, but was partially defective for polyhedra production in the same cells. Virus replication in AcdefrT-infected TN-368 cells was accompanied by extensive plasma-membrane blebbing and caspase activation late in infection, both features of apoptosis. Rescue of the p35 locus of AcdefrT continued to result in a reduction in polyhedra and increase in budded virus production in TN-368 cells, but no plasma-membrane blebbing was observed. The mutation was mapped to the FP-25 gene locus. This gene mutation combined with the non-functional p35 was found to be responsible for the cell-blebbing effect observed in AcdefrT-infected TN-368 cells.
Cytological analysis of Saccharomyces cerevisiae cells supporting cymbidium ringspot virus defective interfering RNA replication
Authors: Navarro Beatriz , Russo Marcello , Pantaleo Vitantonio , Rubino Luisa
Published: February 2006

The replicase proteins p33 and p92 of Cymbidium ringspot virus (CymRSV) were found to support the replication of defective interfering (DI) RNA in Saccharomyces cerevisiae cells. Two yeast strains were used, differing in the biogenesis of peroxisomes, the organelles supplying the membranous vesicular environment in which CymRSV RNA replication takes place in infected plant cells. Double-labelled immunofluorescence showed that both p33 and p92 replicase proteins localized to peroxisomes, independently of one another and of the presence of the replication template. It is suggested that these proteins are sorted initially from the cytosol to the endoplasmic reticulum and then to peroxisomes. However, only the expression of p33, but not p92, increased the number of peroxisomes and induced membrane proliferation. DI RNA replication occurred in yeast cells, as demonstrated by the presence of monomers and dimers of positive and negative polarities. Labelling with BrUTP showed that peroxisomes were the sites of nascent viral synthesis, whereas in situ hybridization indicated that DI RNA progeny were diffused throughout the cytoplasm. DI RNA replication also took place in yeast cells devoid of peroxisomes. It is suggested that replication in these cells was targeted to the endoplasmic reticulum.
Transcribing paramyxovirus RNA polymerase engages the template at its 3′ extremity
Authors: Cordey Samuel , Roux Laurent
Published: February 2006

For the non-segmented, negative-stranded RNA viruses, the mechanism controlling transcription or replication is still a matter of debate. To gain information about this mechanism and about the nature of the RNA polymerase involved, the length of an intervening sequence separating the 3′ end of Sendai virus minigenomes and a downstream transcription-initiation signal was increased progressively. It was found that transcription, as measured by green fluorescent protein (GFP) expression, decreased progressively in proportion to the increase in length of the intervening sequence. GFP expression correlated well with the levels of GFP mRNA in the cells, as measured by quantitative primer extension and by RNase protection. Thus, mRNA transcription was inversely proportional to the length of the inserted sequence. These data are evidence that the RNA polymerase initiating transcription at the downstream transcription signal somehow sees the distance separating this signal and the template 3′ extremity. Implication of this observation for the nature of the Sendai virus RNA polymerase and for the mechanism by which it synthesizes mRNAs or replication products is presented.
Efficient cleavage by signal peptide peptidase requires residues within the signal peptide between the core and E1 proteins of hepatitis C virus strain J1
Authors: Hope R. Graham , McElwee Marion J. , McLauchlan John
Published: February 2006

Maturation of hepatitis C virus (HCV) core protein requires cleavage by signal peptidase (SP) and signal peptide peptidase (SPP) at a signal peptide between core and the E1 glycoprotein. For HCV strain Glasgow, amino acids Ala180, Ser183 and Cys184 within the signal peptide have previously been shown to be essential for efficient SPP cleavage. By contrast, these residues apparently did not contribute to core maturation in HCV strain J1. In the present study, the source of this discrepancy has been analysed and it is concluded that interpretation of the strain J1 data was incorrect, due to the inability to separate wild-type and mutant forms of core on gels by using standard buffer systems.
Hepatitis C virus complete genome sequences identified from China representing subtypes 6k and 6n and a novel, as yet unassigned subtype within genotype 6
Authors: Lu Ling , Nakano Tatsunori , Li Chunhua , Fu Yongshui , Miller Steve , Kuiken Carla , Robertson Betty H. , Hagedorn Curt H.
Published: February 2006

Here, the complete genome sequences for three hepatitis C virus (HCV) variants identified from China and belonging to genotype 6 are reported: km41, km42 and gz52557. Their entire genome lengths were 9430, 9441 and 9448 nt, respectively; the 5′ untranslated regions (UTRs) contained 341, 342 and 339 nt, followed by single open reading frames of 9045, 9045 and 9057 nt, respectively; the 3′ UTRs, up to the poly(U) tracts, were 41, 51 and 52 nt, respectively. Phylogenetic analyses showed that km41 is classified into subtype 6k and km42 into subtype 6n. Although gz52557 clustered distantly with subtype 6g, it appeared to belong to a distinct subtype. Analysis with 53 and 105 partial core and NS5B region sequences, respectively, representing 17 subtypes from 6a to 6q and three unassigned isolates of genotype 6 in co-analyses demonstrated that gz52557 was equidistant from all of these isolates, indicating that it belongs to a novel subtype. However, based on a recent consensus that three or more examples are required for a new HCV subtype designation, it is suggested that gz52557 remains unassigned to any subtype.
Comparative studies on mucosal and intravenous transmission of simian immunodeficiency virus (SIVsm): evolution of coreceptor use varies with pathogenic outcome
Authors: Laurén Anna , Vödrös Dalma , Thorstensson Rigmor , Fenyö Eva Maria
Published: February 2006

Coreceptor usage of isolates from 30 cynomolgus macaques infected intrarectally (n=22) or intravenously (n=8) with simian immunodeficiency virus of sooty mangabey origin (SIVsm) was evaluated in U87.CD4 and GHOST(3) cell lines. Based on progression rate, the animals were divided into progressors (18 animals), slow progressors (five animals) and long-term non-progressors (seven animals). There was no difference in how many or which coreceptors were used according to route of infection. All isolates but one used CCR5 for cell entry, and CCR5 was also the major coreceptor in 70 out of 105 isolates tested. In general, early isolates were multitropic, using CCR5, CXCR6 and/or gpr15. Interestingly, CXCR4-using viruses could be isolated on human peripheral blood mononuclear cells (PBMCs), but not on cynomolgus macaque PBMCs, suggesting that human PBMCs select for variants with CXCR4 use. Even though CXCR4-using SIV isolates have been reported rarely, we could recover CXCR4-using viruses from 13 monkeys. CXCR4 use either appeared early during the acute phase of infection and disappeared later or only appeared late in infection during immunodeficiency. Surprisingly, one late isolate from a progressor monkey did not use CCR5 at all and used the CXCR4 receptor with high efficiency. The ability to use many different receptors decreased over time in long-term non-progressor monkeys, whilst the majority of progressor monkeys showed broadening of coreceptor use, stable coreceptor use or fluctuation between the different coreceptor-usage patterns. The results indicate that, in the infected host, evolution of SIV coreceptor usage occurs, involving changes in the mode of coreceptor use.
Comparative studies on mucosal and intravenous transmission of simian immunodeficiency virus (SIVsm): the kinetics of evolution to neutralization resistance are related to progression rate of disease
Authors: Laurén Anna , Thorstensson Rigmor , Fenyö Eva Maria
Published: February 2006

The kinetics of appearance of autologous neutralizing antibodies were studied in cynomolgus macaques infected with simian immunodeficiency virus (SIVsm) by the intravenous (IV) route (six monkeys) or the intrarectal (IR) route (ten monkeys). The SIVsm inoculum virus and reisolates obtained at 2 weeks, 3 or 4 months and later than 1 year were tested in a GHOST(3) cell line-based plaque-reduction assay with autologous sera collected at the same sampling times. All monkeys developed a neutralizing-antibody response to the inoculum virus, those infected by the IV route earlier than monkeys infected by the IR route. Animals were divided into progressor (P), slow-progressor (SP) and long-term non-progressor (LTNP) monkeys, based on progression rate. In P monkeys, neutralization escape could be demonstrated by 3 months post-infection. Neutralization-resistant variants also emerged in SP and LTNP monkeys, but were much delayed compared with P monkeys. Evolution of neutralization resistance was also demonstrated by a positive-control serum in the heterologous reaction. Pooled sera from four LTNP monkeys showed a broad neutralizing capacity, including neutralization of escape variants. These results from a large group of infected monkeys showed that SIV evolves to neutralization resistance in the infected host and that the kinetics of this evolution are related to the route of transmission and the progression rate of SIV disease. The results suggest an important role for neutralizing antibodies in controlling viraemia. Although this control is transient in the infected host, neutralization resistance is relative and variant viruses may be neutralized by a broadly cross-neutralizing serum pool.
Role of non-raft cholesterol in lymphocytic choriomeningitis virus infection via α-dystroglycan
Authors: Shah Waris A. , Peng Huashan , Carbonetto Salvatore
Published: February 2006

Dystroglycan (DG) is an extracellular matrix receptor necessary for the development of metazoans from flies to humans and is also an entry route for various pathogens.Lymphocytic choriomeningitis virus(LCMV), a member of the familyArenaviridae, infects by binding toα-DG. Here, the role of cholesterol lipid rafts in infection by LCMV viaα-DG was investigated. The cholesterol-sequestering drugs methyl-β-cyclodextrin (MβCD), filipin and nystatin inhibited the infectivity of LCMV selectively, but did not affect infection by vesicular stomatitis virus. Cholesterol loading after depletion with MβCD restored infectivity to control levels. DG was not found in lipid rafts identified with the raft marker ganglioside GM1. Treatment with MβCD, however, enhanced the solubility of DG. This may reflect the association of DG with cholesterol outside lipid rafts and suggests that association of DG with non-raft cholesterol is critical for infection by LCMV throughα-DG.
A new promoter-binding site in the PB1 subunit of the influenza A virus polymerase
Authors: Jung Tanis E. , Brownlee George G.
Published: February 2006

The influenza A virus RNA-dependent RNA polymerase consists of three subunits PB1, PB2 and PA. The 5′ and 3′ terminal sequences of the viral RNA (vRNA) form the viral promoter and are bound by the PB1 subunit. The putative promoter-binding sites of the PB1 subunit have been mapped in previous studies but with contradictory results. The aim of the current study was to investigate the function of two evolutionary conserved regions in PB1 – from aa 233 to 249 and 269 to 281, which lie immediately N- and C-terminal, respectively, of a previously proposed binding site for the 3′ end of the vRNA promoter. The previously proposed binding site extended from aa 249 to 256 and centred on two phenylalanine residues (F251 and F254). However, the fact that F251 is required for polymerase activity was not confirmed here. Instead, it was proposed that the 233–249 region contains a new 5′ vRNA promoter-binding site, and arginine residues crucial for this activity were characterized. However, residues 269–281 were unlikely to be directly involved in promoter binding. These results are discussed in relation to the previous studies and a new model for vRNA promoter binding to the influenza RNA polymerase is presented.
Cloning of the genome of Alcelaphine herpesvirus 1 as an infectious and pathogenic bacterial artificial chromosome
Authors: Dewals B. , Boudry C. , Gillet L. , Markine-Goriaynoff N. , de Leval L. , Haig D. M. , Vanderplasschen A.
Published: February 2006

Alcelaphine herpesvirus 1 (AlHV-1), carried asymptomatically by wildebeest, causes malignant catarrhal fever (MCF) following cross-species transmission to a variety of susceptible species of the order Artiodactyla. The study of MCF pathogenesis has been impeded by an inability to produce recombinant virus, mainly due to the fact that AlHV-1 becomes attenuated during passage in culture. In this study, these difficulties were overcome by cloning the entire AlHV-1 genome as a stable, infectious and pathogenic bacterial artificial chromosome (BAC). A modified loxP-flanked BAC cassette was inserted in one of the two large non-coding regions of the AlHV-1 genome. This insertion allowed the production of an AlHV-1 BAC clone stably maintained in bacteria and able to regenerate virions when transfected into permissive cells. The loxP-flanked BAC cassette was excised from the genome of reconstituted virions by growing them in permissive cells stably expressing Cre recombinase. Importantly, BAC-derived AlHV-1 virions replicated comparably to the virulent (low-passage) AlHV-1 parental strain and induced MCF in rabbits that was indistinguishable from that of the virulent parental strain. The availability of the AlHV-1 BAC is an important advance for the study of MCF that will allow the identification of viral genes involved in MCF pathogenesis, as well as the production of attenuated recombinant candidate vaccines.
Essential role of the Box II cis element and cognate host factors in regulating the promoter of Rice tungro bacilliform virus
Authors: Dai Shunhong , Zhang Zhihong , Bick Jennifer , Beachy Roger N.
Published: February 2006

Rice tungro bacilliform virus (RTBV) is a double-stranded DNA virus with a single, tissue-specific promoter that is expressed primarily in phloem tissues. Rice transcription factors RF2a and RF2b bind to Box II, a cis element adjacent to the TATA box, and control gene expression from the promoter. Mutations were made in the promoter to delete or mutate Box II and the mutated promoters were fused to a reporter gene; the chimeric genes were expressed in transient BY-2 protoplast assays and in transgenic Arabidopsis plants. The results of these studies showed that Box II is essential to the activity of the RTBV promoter. A chimeric β-glucuronidase (GUS) reporter gene containing the Box II sequence and a minimal promoter derived from the Cauliflower mosaic virus 35S promoter were co-transfected into protoplasts with gene constructs that encoded RF2a or RF2b. The reporter gene produced threefold higher GUS activity when co-transfected with RF2a, and 11-fold higher activity when co-transfected with RF2b, than in the absence of added transcription factors. Moreover, chimeric reporter genes were activated by approximately threefold following induction of expression of the RF2a gene in transgenic Arabidopsis plants. The work presented here and earlier findings show that Box II and its interactions with cognate rice transcription factors, including RF2a and RF2b, are essential to the activity of the RTBV promoter and are probably involved in expression of the RTBV genome during virus replication.
An RNA aptamer that distinguishes between closely related human influenza viruses and inhibits haemagglutinin-mediated membrane fusion
Authors: Gopinath Subash C. B. , Misono Tomoko S. , Kawasaki Kazunori , Mizuno Takafumi , Imai Masaki , Odagiri Takato , Kumar Penmetcha K. R.
Published: February 2006

Aptamers selected against various kinds of targets have shown remarkable specificity and affinity, similar to those displayed by antibodies to their antigens. To employ aptamers as genotyping reagents for the identification of pathogens and their strains, in vitro selections were carried out to find aptamers that specifically bind and distinguish the closely related human influenza A virus subtype H3N2. The selected aptamer, P30-10-16, binds specifically to the haemagglutinin (HA) region of the target strain A/Panama/2007/1999(H3N2) and failed to recognize other human influenza viruses, including another strain with the same subtype, H3N2. The aptamer displayed over 15-fold-higher affinity to the HA compared with the monoclonal antibody, and efficiently inhibited HA-mediated membrane fusion. These studies delineate the application of aptamers in the genotyping of viruses.
Putative neutralization epitopes and broad cross-genotype neutralization of Hepatitis E virus confirmed by a quantitative cell-culture assay
Authors: Emerson Suzanne U. , Clemente-Casares Pilar , Moiduddin Nasser , Arankalle Vidya A. , Torian Udana , Purcell Robert H.
Published: February 2006

Monolayers of Hep G2/C3A cells were inoculated with genotype 1 Hepatitis E virus (HEV) mixed with either anti-HEV or an appropriate control. After 5 or 6 days, cell monolayers were stained with anti-HEV and infected cells were identified by immunofluorescence microscopy and counted. Anti-HEV from vaccinated or infected rhesus monkeys neutralized the virus, as did mAbs that recognized epitopes on the C terminus of a recombinant vaccine protein. Antibodies were broadly cross-reactive, since convalescent serum from animals infected with any one of the four mammalian genotypes all neutralized the genotype 1 virus.
Structural and functional integrity of the coxsackievirus B3 oriR: spacing between coaxial RNA helices
Authors: van Ooij Mark J. M. , Glaudemans Dirk H. R. F. , Heus Hans A. , van Kuppeveld Frank J. M. , Melchers Willem J. G.
Published: February 2006

The enterovirusoriR is composed of two helices, X and Y, anchored by a kissing (K) interaction. For properoriR function, certain areas of these helices should be specifically oriented towards each other. It was hypothesized that the single-stranded nucleotides bridging the coaxial helices (Y–X and K–Y linkers) are important to determine this orientation. Spatial changes were introduced by altering the linker length between the helices of the coxsackievirus B3oriR. Changing the linker lengths resulted in defective RNA replication, probably because of an alteredoriR geometry. The identity of the linker residues also played a role, possibly because of sequence-specific ligand recognition. Although each point mutation altering the primary sequence of the Y–X spacer resulted in defective growth at 36 °C, the mutations had a wild-type phenotype at 39 °C, indicating a cold-sensitive phenotype. The results show that the intrinsic connection betweenoriR structure and function is fine-tuned by the spacing between the coaxial RNA helices.
Identifying cellular genes crucial for the reactivation of Kaposi's sarcoma-associated herpesvirus latency
Authors: Bryan Benjaman A. , Dyson Ossie F. , Akula Shaw M.
Published: February 2006

Kaposi's sarcoma-associated herpesvirus (KSHV) is the latest addition to the long list of human herpesviruses. Reactivation of latent herpesvirus infections is still a mystery. It was demonstrated recently that the phorbol ester TPA was efficient in inducing a reactivation of KSHV infection in the S phase of the cell cycle. In the present study, flow cytometry-sorted, TPA-induced, KSHV-infected haematopoietic cells (BCBL-1) were used to analyse the expression profiles of cancer-related cellular genes in the S phase of the cell cycle compared with the G0/1 phase by using microarrays. Overall, the S phase of the cell cycle seems to provide KSHV with an apt environment for a productive lytic cycle of infection. The apt conditions include cellular signalling that promotes survivability, DNA replication and lipid metabolism, while blocking cell-cycle progression to M phase. Some of the important genes that were overexpressed during the S phase of the cell cycle compared with the G0/1 phase of TPA-induced BCBL-1 cells arev-mybmyeloblastosis (MYBL2), protein kinase-membrane associated tyrosine/threonine 1 (PKMYT1), ribonucleotide reductase M1 polypeptide (RRM1) and peroxisome proliferator-activated receptors delta (PPARD). Inhibition of PKMYT1 expression by the use of specific short interfering RNAs significantly lowered the TPA-induced KSHV lytic cycle of infection. The significance of these and other genes in the reactivation of KSHV is discussed in the following report. Taken together, a flow cytometry–microarray-based method to study the cellular conditions critical for the reactivation of KSHV infection is reported here for the first time.
How Lutherans Read the Bible: A North American and Global Conversation
Authors: Olson Dennis T.
Published: February 2006

Abstract:  Recent debates and conflicts over the interpretation of the Bible among Lutherans both in the U.S. and in other parts of the world impel us to consider our history in a Lutheran tradition, our present challenges, and an agenda for future directions. This introductory essay briefly introduces some of the distinctive Lutheran emphases in the use of Scripture, provides an overview of the other essays in this issue of Dialog which are largely focused on the North American context, and then offers a sample of what two Lutheran scholars in places other than the U.S. are thinking about their experiences as Lutherans using the Bible in places like Malaysia and Argentina.
Reading the Bible in the Lutheran Tradition
Authors: Reisz H. Frederick
Published: February 2006

Abstract:  In theological and ethical discussions, Lutherans appeal to a “Lutheran hermeneutic.” The content of this hermeneutic often is assumed more than defined. When defined, often a theological short‐hand is employed: the Word of God, law and gospel, grace through faith alone, and the like. This article suggests a more complex context for Lutherans reading the Bible and engaging in hermeneutics. There are “orientational dimensions” which create an environment for this biblical exegesis, interpretation, and proclamation. Noticing these orientational dimensions can deepen our understanding of the Lutheran tradition and also its ecumenical rootage.
The Canonical Sense of Scripture: Trinitarian or Christocentric?
Authors: Padgett Alan G.
Published: February 2006

Abstract:  In this essay I develop a threefold sense for Scripture today: conventional, canonical, and contemporary. This is my “grammar” for evangelical theological hermeneutics. I explore in particular the canonical sense: the level of meaning of the biblical passage read in the light of the whole of Scripture, with Christ as the center and key. In dialogue with the Orthodox, I argue that such a christocentric approach must also be, finally, a Trinitarian one.
The “Strange Acts of God:” The Hermeneutics of Concealment and Revelation in Luther and Shakespeare
Authors: Fabiny Tibor
Published: February 2006

Abstract:  Martin Luther called himself “God's court‐jester”. He saw history as one of the “masks of God,” and he understood God as hiding Godself often behind the mask of the Devil. Luther developed a paradoxical theology, a theology of the cross, that is surprisingly compatible in certain respects with the paradoxical artistic vision of Shakespeare, especially in Hamlet, King Lear and Measure for Measure. Crucial motifs of Luther's theology—the hidden God, indirect revelation, revelation by concealment, revelation under the opposite, the “strange acts of God,” God's “rearward parts”(posteriora), and suffering (Anfechtungen and melancholy)—resonate with certain latent, even if at times blasphemeous, theological motifs and themes in Shakespeare. They also resonate with the experience of the Lutheran church in Hungary both in its past under communism and today in post‐communist Hungary.
Forgiveness, the Gift, and Ecclesiology
Authors: Saarinen Risto
Published: February 2006

Abstract:  This article responds to the work of George Lindbeck and John Milbank while putting forth a new position on the theology of gift and forgiveness. Saarinen constructs a rudimentary theological anthropology, focusing on God and human beings as givers. As an example of applying this “giver‐oriented perspective” he outlines a fourfold typology of forgiveness as (1) negative giving, forgetting; (2) negative and positive giving, forgetting; (3) negative giving, forgetting and remembering; (4) negative and positive giving, forgetting and remembering.
Styles of Sociological Thought: Sociologies, Epistemologies, and the Mexican and U.S. Quests for Truth
Authors: Abend Gabriel
Published: February 2006

Both U.S. and Mexican sociologies allege that they are in the business of making true scientific knowledge claims about the social world. Conventional conceptions of science notwithstanding, I demonstrate that their claims to truth and scientificity are based on alternative epistemological grounds. Drawing a random sample of nonquantitative articles from four leading journals, I show that, first, they assign a different role to theories, and indeed they have dissimilar understandings of what a theory should consist of. Second, whereas U.S. sociology actively struggles against subjectivity, Mexican sociology maximizes the potentials of subjective viewpoints. Third, U.S. sociologists tend to regard highly and Mexican sociologists to eagerly disregard the principle of ethical neutrality. These consistent and systematic differences raise two theoretical issues. First, I argue that Mexican and U.S. sociologies are epistemologically, semantically, and perceptually incommensurable. I contend that this problem is crucial for sociology's interest in the social conditioning of scientific knowledge's content. Second, I suggest four lines of thought that can help us explain the epistemological differences I find. Finally, I argue that sociologists would greatly profit from studying epistemologies in the same fashion they have studied other kinds of scientific and nonscientific beliefs.
The Return of the Native: A Cultural and Social-Psychological Critique of Durkheim's Suicide Based on the Guarani-Kaiowá of Southwestern Brazil
Authors: Hamlin Cynthia Lins , Brym Robert J.
Published: February 2006

This article argues that Durkheim's theory of suicide is deficient because of its monocausal reasoning, its conception of suicide as an action without subjects, and its characterization of preliterate societies as harmonious, self-contained, and morphologically static. It shows that these deficiencies can be overcome by including cultural and social-psychological considerations in the analysis of suicide—specifically by including culture as a causal force in its own right and drawing links between social circumstances, cultural beliefs and values, and individual dispositions. The authors make their case by analyzing ethnographic and quantitative data on the preliterate Guarani-Kaiowá of southwestern Brazil, one of the most suicide-prone groups in the world.
Macro-Micro Relationships in Durkheim's Analysis of Egoistic Suicide
Authors: Berk Bernard B.
Published: February 2006

Contemporary theory is increasingly concerned with macro-micro integration. An attempt is made to integrate these levels of analysis in Durkheim's theory of egoistic suicide. Does Durkheim's theory, which is a social system analysis designed to explain differences in suicide rates between groups, have micro implications for specifying which particular individuals within the group will take their lives? In attempting to answer this question by exploring the causal linkages between integration and suicide, Durkheim's theory of egoistic suicide was revealed not to be a singular theory but rather contained several different explanations. The numerous interpretations have resulted from his incompletely specified, inconsistent, unsystematized, and inadequately tested theory. These ambiguities also account for the historically inconsistent research findings that have limited sociologists' ability to advance beyond Durkheim's century-old formulations. Further areas for new research and illustrative hypothesis are suggested.
Breaching the Theoretical Divide: Reassessing the Ordinary and Everyday in Habermas and Garfinkel
Authors: Beemer Jeffrey K.
Published: February 2006

This article argues that Habermas and Garfinkel present complementary perspectives on the dynamics of ordinary language and the ways in which communication is configured and prefigured in interactive settings. Together they provide a basis for thinking about action and its environments not simply in terms of the in situ or formal conditions in isolation from one another, but as extensions of an integrated dependency between the local (indexical) contexts in which interactions occur and the rational (pretheoretical) presuppositions that make such interactions possible. The conditions on which actors are identified as rational agents or as being bound by the structured environments in which they move are not differentiated in the course of everyday life. Communication consists of produced events that admit both rational presuppositions and practical accomplishments. Taken concomitantly, these properties constitute the necessary and sufficient conditions for creating the intersubjective links that individuals rely on when interacting.
The Determinants of Debt Maturity Structure: Evidence from France, Germany and the UK
Authors: Antoniou Antonios , Guney Yilmaz , Paudyal Krishna
Published: February 2006

We examine the determinants of the debt maturity structure of French, German and British firms. These countries represent different financial and legal traditions that may have implications on corporate debt maturity structure. Our model incorporates the factors representing three major theories (tax considerations, liquidity and signalling, and contracting costs) of debt maturity. It also controls for capital market conditions. The results confirm the applicability of most theories of debt maturity structure for the UK firms. However, the evidence from France and Germany are mixed. Overall the findings suggest that the debt maturity structure of a firm is determined by firm‐specific factors and the country's financial systems and institutional traditions in which it operates.
European Foreign Exchange Risk Exposure
Authors: Muller Aline , Verschoor Willem F. C.
Published: February 2006

We find that about 13% of our sample of 817 European multinational firms experienced economically significant exposure effects to the Japanese yen, 14% to the US dollar and 22% to the UK pound. Our evidence differs substantially from the US experience and is robust across sub‐sample periods, suggesting that a depreciating (appreciating) euro against foreign currencies has a net negative (positive) impact on European stock returns. Short‐term exposure seems to be relatively well hedged, where considerable evidence of long‐term exposure is found. Firms with weak liquidity positions tend to have smaller exposures. Foreign exposure is found to increase with firm size.
Corporate Performance, Corporate Governance and Top Executive Turnover in Finland
Authors: Maury Benjamin
Published: February 2006

This paper empirically investigates how corporate governance forces and firm performance affect top executive turnover in Finnish listed companies. I document an increase in CEO, top management, and board turnover in response to poor stock price performance and operating losses. The sensitivity of the relation between stock price performance and CEO turnover is significantly higher in firms with a two‐tier board structure (when the CEO is not the chairman), but significantly lower when the CEO or a board member is the controlling shareholder. These results suggest that both the ownership structure and the board design have implications for the disciplining of managers.