bluuebunny/crossref_metadata_2025 huggingface dataset:
Aspergillus fumigatus germ tube growth and not conidia ingestion induces expression of inflammatory mediator genes in the human lung epithelial cell line A549
Authors: Bellanger Anne-Pauline , Millon Laurence , Khoufache Khaled , Rivollet Danièle , Bièche Ivan , Laurendeau Ingrid , Vidaud Michel , Botterel Françoise , Bretagne Stéphane
Published: January 2009

Inhalation of conidia is the main cause of invasive pulmonary aspergillosis (IPA) and the respiratory epithelium is the first line of defence. To explore the triggering factor for the inflammatory response toAspergillus fumigatus, the species mainly responsible for IPA, this study analysed the differential expression of three inflammatory genes in A549 cells after challenge with live and killed conidia. The influence of steroids, one of the main risk factors for developing IPA, was also investigated. Quantification of mRNAs of the inflammatory mediator genes encoding interleukin (IL)-8, tumour necrosis factor (TNF)-αand granulocyte–monocyte colony-stimulating factor (GM-CSF) was carried out using real-time PCR. Ingestion rates were studied for the conidia ofA. fumigatusandPenicillium chrysogenumusing a fluorescence brightener. Similar results were obtained for both species, with ingestion rates ranging from 35 to 40 %. Exposure of A549 cells to liveA. fumigatusconidia only induced a four- to fivefold increase in the mRNA levels of the three genes, starting 8 h after the initial contact. Both inactivation of liveA. fumigatusconidia and treatment by dexamethasone (10−7 M) prevented the overexpression of TNF-α, IL-8 and GM-CSF. Fungal growth, rather than conidia ingestion, appears to be the main stimulus for the production of inflammatory mediators by epithelial cells, and this production is inhibited by steroid therapy. These results underline the role that the epithelium plays in the innate response against IPA.
Fusion of a viral antigen to invariant chain leads to augmented T-cell immunity and improved protection in gene-gun DNA-vaccinated mice
Authors: Grujic Mirjana , Holst Peter J. , Christensen Jan P. , Thomsen Allan R.
Published: January 2009

It has recently been demonstrated that a recombinant replication-deficient human adenovirus 5 (Ad5) vector expressing lymphocytic choriomeningitis virus (LCMV) glycoprotein (GP) fused to the p31 invariant (Ii) chain confers broad, long-lasting T-cell immunity that completely protects C57BL/6 mice against lethal peripheral challenge. The current study questioned whether the same strategy, i.e. linkage of GP to an Ii chain, could be applied to a naked DNA vaccine. Following gene-gun immunization with the linked construct (DNA–IiGP), GP-specific CD4+T cells could not be detected by flow cytometry. However, inclusion of the Ii chain augmented the priming of GP-specific CD8+T cells directed towards both immunodominant (GP33–41) and subdominant (GP276–286and GP92–101) epitopes, and vaccination with DNA–IiGP conferred significantly improved protection against systemic LCMV infection compared with the unlinked construct. In contrast, substantial protection against peripheral challenge was not observed. Additional experiments with T-cell subset-depleted or perforin-deficient mice revealed that virus control in vaccinated mice depends critically on cytotoxic CD8+T cells. Finally, priming with the naked DNA vaccine was shown to augment the immune response raised by subsequent immunization with the Ad5 vector. In conclusion, this study showed that the immunoenhancing effect of Ii chain linkage is not limited to the Ad5 vector, but is also relevant with a DNA platform. Furthermore, given the fact that the Ii chain enhances the presentation of more than one epitope, this suggests that Ii-chain-based DNA vaccines may be promising candidates for various heterologous prime–boost regimes.
T-cell intrinsic expression of MyD88 is required for sustained expansion of the virus-specific CD8+ T-cell population in LCMV-infected mice
Authors: Bartholdy Christina , Christensen Jeanette E. , Grujic Mirjana , Christensen Jan P. , Thomsen Allan R.
Published: January 2009

Acute infection with lymphocytic choriomeningitis virus (LCMV) normally results in robust clonal expansion of virus-specific CD8+T cells, which in turn control the primary infection. However, similar infection of myeloid differentiation factor 88 (MyD88)-deficient mice leads to a markedly impaired T-cell response and chronic infection. It has been found previously that impairment of the innate immune response is not sufficient to explain this profound change in outcome. Using adoptive transfer of CD8+T cells, this study demonstrated unequivocally that T-cell expression of MyD88 is critical for a normal T-cell response to LCMV. In addition, it was found that expression of MyD88 is superfluous during early activation and proliferation of the antigen-activated CD8+T cells, but plays a critical role in the sustained expansion of the antigen-specific CD8+T-cell population during the primary T-cell response. Interestingly, a critical role for MyD88 was evident only under conditions of systemic infection with virus capable of causing prolonged infection, suggesting that MyD88 expression may function as an internal regulator of the threshold for antigen-driven, exhaustive differentiation.
Quasispecies dynamics and molecular evolution of human norovirus capsid P region during chronic infection
Authors: Carlsson Beatrice , Lindberg A. Michael , Rodriguez-Díaz Jesús , Hedlund Kjell-Olof , Persson Bengt , Svensson Lennart
Published: January 2009

In this novel study, we have for the first time identified evolutionarily conserved capsid residues in an individual chronically infected with norovirus (GGII.3). From 2000 to 2003, a total of 147 P1-1 and P2 capsid sequences were sequenced and investigated for evolutionarily conserved and functionally important residues by the evolutionary trace (ET) algorithm. The ET algorithm revealed more absolutely conserved residues (ACR) in the P1-1 domain (47/53, 88 %) as compared with the P2 domain (86/133, 64 %). The capsid P1-1 and P2 domains evolved in time-dependent manner, with a distinct break point observed between autumn/winter of year 2000 (isolates P1, P3 and P5) and spring to autumn of year 2001 (isolates P11, P13 and P15), which presumably coincided with a change of clinical symptoms. Furthermore, the ET analysis revealed a similar receptor-binding pattern as reported for Norwalk and VA387 strains, with the CS-4 and CS-5 patch (Norwalk strain) including residues 329 and 377 and residues 306 and 310, respectively, all being ACR in all partitions. Most interesting was that residues 343, 344, 345, 374, 390 and 391 of the proposed receptor A and B trisaccharide binding site (VA387 strain) within the P2 domain remained ACR in all partitions, presumably because there was no selective advantage to alter the histo blood group antigens (HBGA) receptor binding specificity. In conclusion, this study provides novel insights to the evolutionary process of norovirus during chronic infection.
A haemocyte tropism for an arbovirus
Authors: Parikh Grishma R. , Oliver Jonathan D. , Bartholomay Lyric C.
Published: January 2009

Horizontally transmitted mosquito-borne viruses enter the midgut with a blood meal then disseminate to infect the salivary glands. En route to the salivary glands, these viruses encounter the plasma (haemolymph) and blood cells (haemocytes). Haemocytes respond to a variety of micro-organisms, but their role in virus replication and dissemination has not been described. To look for a potential haemocyte tropism for an arbovirus, a Sindbis virus was injected intrathoracically into four species of mosquito. Virus infects haemocytes as early as 6 h post injection (p.i.) and infection was evident in these cells for as long as 4 days p.i. More than 90 % of haemocytes were infected, most often the phagocytic granulocytes. Virus titres in the haemolymph increased from 24 h p.i. through 60 h p.i. Similar results were found when Aedes aegypti mosquitoes were injected with orally infectious Sindbis. These data prove that an arbovirus infects, and replicates in, haemocytes.
Co-localization of constituents of the dengue virus translation and replication machinery with amphisomes
Authors: Panyasrivanit Mingkwan , Khakpoor Atefeh , Wikan Nitwara , Smith Duncan R.
Published: January 2009

Infections with dengue virus (DENV) are a significant public health concern in tropical and subtropical regions. However, little detail is known about how DENV interacts with the host-cell machinery to facilitate its translation and replication. In DENV-infected HepG2 cells, an increase in the level of LC3-II (microtubule-associated protein 1 light chain 3 form II), the autophagosomal membrane-bound form of LC3, was observed, and LC3 was found to co-localize with dsRNA and DENV NS1 protein, as well as ribosomal protein L28, indicating the presence of at least some of the DENV translation/replication machinery on autophagic vacuoles. Inhibition of fusion of autophagic vacuoles with lysosomes resulted in an increase in both intracellular and extracellular virus, and co-localization observed between mannose-6-phosphate receptor (MPR) and dsRNA and between MPR and LC3 identified the autophagic vacuoles as amphisomes. Amphisomes are formed as a result of fusion between endosomal and autophagic vacuoles, and as such provide a direct link between virus entry and subsequent replication and translation.
Reverse genetics-generated elastase-dependent swine influenza viruses are attenuated in pigs
Authors: Masic Aleksandar , Babiuk Lorne A. , Zhou Yan
Published: January 2009

Influenza A virus causes significant morbidity in swine, resulting in a substantial economic burden. Swine influenza virus (SIV) infection also poses important human public health concerns. It has been shown that conversion of the haemagglutinin (HA) cleavage site from a trypsin-sensitive motif to an elastase-sensitive motif resulted in attenuated viruses in mouse models. However, application of this attenuation approach in a natural host has not been achieved yet. Here, we report that using reverse genetics, we generated two mutant SIVs derived from strain A/SW/SK/18789/02 (H1N1). Mutant A/SW/SK-R345V carries a mutation from arginine to valine at aa 345 of HA. Similarly, mutant A/SW/SK-R345A encodes alanine instead of arginine at aa 345 of HA. Our data showed that both mutants are solely dependent on neutrophil elastase cleavage in tissue culture. These tissue culture-grown mutant SIVs showed similar growth properties in terms of plaque size and growth kinetics to the wild-type virus. In addition, SIV mutants were able to maintain their genetic information after multiple passaging on MDCK cells. Furthermore, mutant SIVs were highly attenuated in pigs. Thus, these mutants may have the potential to serve as live attenuated vaccines.
Deformed wing virus: replication and viral load in mites (Varroa destructor)
Authors: Gisder Sebastian , Aumeier Pia , Genersch Elke
Published: January 2009

Deformed wing virus (DWV) normally causes covert infections but can have devastating effects on bees by inducing morphological deformity or even death when transmitted by the ectoparasitic mite Varroa destructor. In order to determine the role of V. destructor in the development of crippled wings, we analysed individual mites for the presence and replication of DWV. The results supported the correlation between viral replication in mites and morphologically deformed bees. Quantification of viral genome equivalents revealed that mites capable of inducing an overt DWV infection contained 1010–1012 genome equivalents per mite. In contrast, mites which could not induce crippled wings contained a maximum of only 108 viral genome equivalents per mite. We conclude that the development of crippled wings not only depends on DWV transmission by V. destructor but also on viral replication in V. destructor and on the DWV titre in the parasitizing mites.
Adeno-associated virus type 5 exploits two different entry pathways in human embryo fibroblasts
Authors: Bantel-Schaal Ursula , Braspenning-Wesch Ilona , Kartenbeck Juergen
Published: January 2009

The helper-dependent adeno-associated viruses (AAVs) have attracted great interest as vectors for gene therapy. Uptake and intracellular trafficking pathways of AAV are of importance, since they are often rate-limiting steps in infection. Here, we have investigated the entry of AAV type 5 (AAV5) in primary human embryo fibroblasts. At low binding temperatures, numerous virions are concentrated between cells, at contact points between cells and cellular protrusions, and at filopodia. When the temperature is raised to 37 °C, uptake of AAV5 takes place but up to 80 % of the bound virions dissociate from the cells. Uptake is achieved by cellular structures that are part of at least two different entry pathways. In addition to the common clathrin-dependent route, caveolar endocytosis and caveosome-like organelles are involved in a second pathway not yet described for parvoviruses. Both pathways can be used in parallel to enter an individual cell.
The active form of the norovirus RNA-dependent RNA polymerase is a homodimer with cooperative activity
Authors: Högbom Martin , Jäger Katrin , Robel Ivonne , Unge Torsten , Rohayem Jacques
Published: January 2009

Norovirus (NV) is a leading cause of gastroenteritis worldwide and a major public health concern. So far, the replication strategy of NV remains poorly understood, mainly because of the lack of a cell system to cultivate the virus. In this study, the function and the structure of a key viral enzyme of replication, the RNA-dependent RNA polymerase (RdRp, NS7), was examined. The overall structure of the NV NS7 RdRp was determined by X-ray crystallography to a 2.3 Å (0.23 nm) resolution (PDB ID 2B43), displaying a right-hand fold typical of the template-dependent polynucleotide polymerases. Biochemical analysis evidenced that NV NS7 RdRp is active as a homodimer, with an apparent K
d of 0.649 μM and a positive cooperativity (Hill coefficient nH=1.86). Crystals of the NV NS7 homodimer displayed lattices containing dimeric arrangements with high shape complementarity statistics. This experimental data on the structure and function of the NV RdRp may set the cornerstone for the development of polymerase inhibitors to control the infection with NV, a medically relevant pathogen.
Mutagenesis of the nucleocapsid protein of Nipah virus involved in capsid assembly
Authors: Ong Swee Tin , Yusoff Khatijah , Kho Chiew Ling , Abdullah Janna Ong , Tan Wen Siang
Published: January 2009

The nucleocapsid protein of Nipah virus produced in Escherichia coli assembled into herringbone-like particles. The amino- and carboxy-termini of the N protein were shortened progressively to define the minimum contiguous sequence involved in capsid assembly. The first 29 aa residues of the N protein are dispensable for capsid formation. The 128 carboxy-terminal residues do not play a role in the assembly of the herringbone-like particles. A region with amino acid residues 30–32 plays a crucial role in the formation of the capsid particle. Deletion of any of the four conserved hydrophobic regions in the N protein impaired capsid formation. Replacement of the central conserved regions with the respective sequences from the Newcastle disease virus restored capsid formation.
Influenza B mutant viruses with truncated NS1 proteins grow efficiently in Vero cells and are immunogenic in mice
Authors: Wressnigg Nina , Shurygina Anna Polina , Wolff Thorsten , Redlberger-Fritz Monika , Popow-Kraupp Therese , Muster Thomas , Egorov Andrej , Kittel Christian
Published: January 2009

Contemporary influenza B virus strains were generated encoding C-terminally truncated NS1 proteins. Viable viruses containing the N-terminal 14, 38, 57 or 80 aa of the NS1 protein were rescued in Vero cells. The influenza B virus NS1-truncated mutants were impaired in their ability to counteract interferon (IFN) production, induce antiviral pro-inflammatory cytokines early after infection and show attenuated or restricted growth in IFN-competent hosts. In Vero cells, all of the mutant viruses replicated to high titres comparable to the wild-type influenza B virus. Mice that received a single, intranasal immunization of the NS1-truncated mutants elicited an antibody response and protection against wild-type virus challenge. Therefore, these NS1-truncated mutants should prove useful as potential candidates for live-attenuated influenza virus vaccines.
Epstein–Barr virus BART gene expression
Authors: Al-Mozaini Maha , Bodelon Gustavo , Karstegl Claudio Elgueta , Jin Boquan , Al-Ahdal Mohammed , Farrell Paul J.
Published: January 2009

Introns from the Epstein–Barr virus (EBV) BART RNAs produce up to 20 micro RNAs (miRNAs) but the spliced exons of the BART RNAs have also been investigated as possible mRNAs, with the potential to express the RPMS1 and A73 proteins. Recombinant RPMS1 and A73 proteins were expressed in Escherichia coli and used to make new monoclonal antibodies that reacted specifically with artificially expressed RPMS1 and A73. These antibodies did not detect endogenous expression of A73 and RPMS1 proteins in a panel of EBV-infected cell lines representing the different known types of EBV infection. BART RNA could not be detected on Northern blots of cytoplasmic poly(A)+ RNA from the C666.1 NPC cell line and BART RNA was found to be mainly in the nucleus of C666.1 cells, arguing against an mRNA role for BART RNAs. In contrast, some early lytic cycle EBV mRNAs were found to be expressed in C666.1 cells. Artificially expressed A73 protein was known to be able to bind to the cellular RACK1 protein and has now also been shown to be able to regulate calcium flux, presumably via RACK1. Overall, the results support the conclusion that the miRNAs are functionally important products of BART transcription in the cell lines studied because the A73 and RPMS1 proteins could not be detected in natural EBV infections. However, the possibility remains that A73 and RPMS1 might be expressed in some situations because of the clear potential relevance of their biochemical functions.
Two viruses that cause salivary gland hypertrophy in Glossina pallidipes and Musca domestica are related and form a distinct phylogenetic clade
Authors: Garcia-Maruniak Alejandra , Abd-Alla Adly M. M. , Salem Tamer Z. , Parker Andrew G. , Lietze Verena-Ulrike , van Oers Monique M. , Maruniak James E. , Kim Woojin , Burand John P. , Cousserans François , Robinson Alan S. , Vlak Just M. , Bergoin Max , Boucias Drion G.
Published: January 2009

Glossina pallidipes and Musca domestica salivary gland hypertrophy viruses (GpSGHV and MdSGHV) replicate in the nucleus of salivary gland cells causing distinct tissue hypertrophy and reduction of host fertility. They share general characteristics with the non-occluded insect nudiviruses, such as being insect-pathogenic, having enveloped, rod-shaped virions, and large circular double-stranded DNA genomes. MdSGHV measures 65×550 nm and contains a 124 279 bp genome (∼44 mol% G+C content) that codes for 108 putative open reading frames (ORFs). GpSGHV, measuring 50×1000 nm, contains a 190 032 bp genome (28 mol% G+C content) with 160 putative ORFs. Comparative genomic analysis demonstrates that 37 MdSGHV ORFs have homology to 42 GpSGHV ORFs, as some MdSGHV ORFs have homology to two different GpSGHV ORFs. Nine genes with known functions (dnapol, ts, pif-1, pif-2, pif-3, mmp, p74, odv-e66 and helicase-2), a homologue of the conserved baculovirus gene Ac81 and at least 13 virion proteins are present in both SGHVs. The amino acid identity ranged from 19 to 39 % among ORFs. An (A/T/G)TAAG motif, similar to the baculovirus late promoter motif, was enriched 100 bp upstream of the ORF transcription initiation sites of both viruses. Six and seven putative microRNA sequences were found in MdSGHV and GpSGHV genomes, respectively. There was genome. Collinearity between the two SGHVs, but not between the SGHVs and the nudiviruses. Phylogenetic analysis of conserved genes clustered both SGHVs in a single clade separated from the nudiviruses and baculoviruses. Although MdSGHV and GpSGHV are different viruses, their pathology, host range and genome composition indicate that they are related.
Histopathology and growth kinetics of influenza viruses (H1N1 and H3N2) in the upper and lower airways of guinea pigs
Authors: Tang Xuehui , Chong Kong T.
Published: January 2009

Recent investigations have shown that guinea pigs are important for the study of influenza A virus (IAV) transmission. However, very little is known about IAV replication and histopathology in the guinea pig respiratory tract. Here, we describe viral growth kinetics, target cells and histopathology in the nasosinus, trachea and lungs of IAV-infected guinea pigs. We found that guinea pigs infected with either A/Puerto Rico/8/34 (H1N1) or A/Hong Kong/8/68 (H3N2) developed a predominantly upper airway infection with high nasal viral titres. IAV grew to moderate titres in the lungs but induced marked inflammatory responses, resulting in severe bronchopneumonia and alveolitis. Although non-lethal at the high dose of 2×106 p.f.u., infections with these IAV strains were associated with reduced weight gain. IAV infection in guinea pigs is characterized by extensive viral replication in the ciliated nasal epithelial cells followed by heavy nasal mucus secretion.
Determination of the henipavirus phosphoprotein gene mRNA editing frequencies and detection of the C, V and W proteins of Nipah virus in virus-infected cells
Authors: Lo Michael K. , Harcourt Brian H. , Mungall Bruce A. , Tamin Azaibi , Peeples Mark E. , Bellini William J. , Rota Paul A.
Published: January 2009

The henipaviruses, Nipah virus (NiV) and Hendra virus (HeV), are highly pathogenic zoonotic paramyxoviruses. Like many other paramyxoviruses, henipaviruses employ a process of co-transcriptional mRNA editing during transcription of the phosphoprotein (P) gene to generate additional mRNAs encoding the V and W proteins. The C protein is translated from the P mRNA, but in an alternate reading frame. Sequence analysis of multiple, cloned mRNAs showed that the mRNA editing frequencies of the P genes of the henipaviruses are higher than those reported for other paramyxoviruses. Antisera to synthetic peptides from the P, V, W and C proteins of NiV were generated to study their expression in infected cells. All proteins were detected in both infected cells and purified virions. In infected cells, the W protein was detected in the nucleus while P, V and C were found in the cytoplasm.
Analysis of the entire genomes of torque teno midi virus variants in chimpanzees: infrequent cross-species infection between humans and chimpanzees
Authors: Ninomiya Masashi , Takahashi Masaharu , Hoshino Yu , Ichiyama Koji , Simmonds Peter , Okamoto Hiroaki
Published: January 2009

Humans are frequently infected with three anelloviruses which have circular DNA genomes of 3.6–3.9 kb [Torque teno virus (TTV)], 2.8–2.9 kb [Torque teno mini virus (TTMV)] and 3.2 kb [a recently discovered anellovirus named Torque teno midi virus (TTMDV)]. Unexpectedly, human TTMDV DNA was not detectable in any of 74 chimpanzees tested, although all but one tested positive for both human TTV and TTMV DNA. Using universal primers for anelloviruses, novel variants of TTMDV that are phylogenetically clearly separate from human TTMDV were identified from chimpanzees, and over the entire genome, three chimpanzee TTMDV variants differed by 17.9–20.3 % from each other and by 40.4–43.6 % from all 18 reported human TTMDVs. A newly developed PCR assay that uses chimpanzee TTMDV-specific primers revealed the high prevalence of chimpanzee TTMDV in chimpanzees (63/74, 85 %) but low prevalence in humans (1/100). While variants of TTV and TTMV from chimpanzees and humans were phylogenetically interspersed, those of TTMDV were monophyletic for each species, with sequence diversity of <33 and <20 % within the 18 human and three chimpanzee TTMDV variants, respectively. Maximum within-group divergence values for TTV and TTMV were 51 and 57 %, respectively; both of these values were substantially greater than the maximum divergence among TTMDV variants (44 %), consistent with a later evolutionary emergence of TTMDV. However, substantiation of this hypothesis will require further analysis of genetic diversity using an expanded dataset of TTMDV variants in humans and chimpanzees. Similarly, the underlying mechanism of observed infrequent cross-species infection of TTMDV between humans and chimpanzees deserves further analysis.
The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)
Authors: Miller Webb , Drautz Daniela I. , Janecka Jan E. , Lesk Arthur M. , Ratan Aakrosh , Tomsho Lynn P. , Packard Mike , Zhang Yeting , McClellan Lindsay R. , Qi Ji , Zhao Fangqing , Gilbert M. Thomas P. , Dalén Love , Arsuaga Juan Luis , Ericson Per G.P. , Huson Daniel H. , Helgen Kristofer M. , Murphy William J. , Götherström Anders , Schuster Stephan C.
Published: January 2009

We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%–15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples’ heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes.
Chicken ovalbumin upstream promoter transcription factor II in human breast carcinoma: Possible regulator of lymphangiogenesis via vascular endothelial growth factor‐C expression
Authors: Nagasaki Shuji , Suzuki Takashi , Miki Yasuhiro , Akahira Jun‐ichi , Shibata Hirotaka , Ishida Takanori , Ohuchi Noriaki , Sasano Hironobu
Published: January 2009

Chicken ovalbumin upstream promoter transcription factors (COUP‐TF) are orphan members of the nuclear receptor superfamily and consist of COUP‐TFI and COUP‐TFII. COUP‐TFI was reported to be overexpressed in human breast cancer and to promote estrogen‐independent transcriptional activity of estrogen receptor α. COUP‐TFII, however, has not been examined in the breast. Therefore, we carried out immunohistochemical analysis of COUP‐TFII in human breast cancer in order to clarify its biological and clinical significance. We immunolocalized COUP‐TFII in 119 human breast cancers and correlated the findings with various clinicopathological parameters. Fifty‐nine percent of the cases were immunohistochemically positive for COUP‐TFII. COUP‐TFII positivity was correlated with poor clinical outcome, and a statistically significant correlation was detected between COUP‐TFII and the following clinicopathological parameters: clinical stage, lymph node status, histological grade, and estrogen receptor α status. In addition, short interfering RNA‐mediated knockdown of COUP‐TFII in the breast carcinoma cell line MCF‐7 decreased the level of vascular endothelial growth factor‐C mRNA expression, which is a known inducer of lymphangiogenesis and lymph node metastasis. These results suggest that COUP‐TFII is involved in the development of advanced human breast cancer. (Cancer Sci 2009; 100: 639–645)
PVYNTN elicits a diverse gene expression response in different potato genotypes in the first 12 h after inoculation
Authors: BAEBLER ŠPELA , KREČIČ‐STRES HANA , ROTTER ANA , KOGOVŠEK POLONA , CANKAR KATARINA , KOK ESTHER J. , GRUDEN KRISTINA , KOVAČ MAJA , ŽEL JANA , POMPE‐NOVAK MARUŠA , RAVNIKAR MAJA
Published: January 2009

Host gene expression changes in the early response to potato virus YNTN interaction were compared in two differently sensitive potato cultivars: the resistant cultivar Santé and the sensitive cultivar Igor. Hybridization of potato TIGR cDNA microarrays allowed us to monitor the expression of approximately 10 000 genes simultaneously at 0.5 and 12 h post‐inoculation (hpi). Microarray data, analysed by statistics and data mining, were complemented by subtraction library construction and sequence analysis to validate the findings. The expression profiles of the two cultivars were similar and faint at 0.5 hpi, but they differed substantially at 12 hpi. Although, at 0.5 hpi, cv. Santé responded by the differential expression of a greater number of genes, at 12 hpi the number was higher in cv. Igor. The majority of genes in this cultivar were down‐regulated at 12 hpi, indicating a host gene shut‐off. Suites of genes that exhibited altered transcript abundance in response to the virus were identified, and included genes involved in the processes of photosynthesis, perception, signalling and defence responses. The expression of the considerable number of genes associated with photosynthesis was surprisingly up‐regulated as early as 0.5 hpi and down‐regulated at 12 hpi in both cultivars. The expression of genes involved in perception and signalling was increased in the sensitive cultivar at 12 hpi. By contrast, a simultaneous strong defence response at the transcriptional level was evident in the resistant cultivar, as shown by the up‐regulation of genes involved in brassinosteroid, polyamine and secondary metabolite biosynthesis, and of genes coding for pathogenesis‐related proteins.
The Rcs phosphorelay system is essential for pathogenicity in Erwinia amylovora
Authors: WANG DONGPING , KORBAN SCHUYLER S. , ZHAO YOUFU
Published: January 2009

The Rcs phosphorelay system is a modified two‐component signal transduction system found exclusively in Enterobacteriaceae. In this study, we characterized the roles of the Rcs system in Erwinia amylovora, a highly virulent and necrogenic enterobacterium causing fire blight disease on rosaceous plants. Our results showed that rcsB, rcsC, rcsD and rcsBD mutants were non‐pathogenic on immature pear fruit. The bacterial growth of these mutants was also greatly reduced compared with that of the wild‐type strain in immature pear fruit. In an in vitro amylovoran assay, rcsB and rcsD mutants were deficient in amylovoran production, whereas the rcsC mutant exhibited higher amylovoran production than that of the wild‐type. Consistent with amylovoran production, expression of the amylovoran biosynthetic gene amsG, using green fluorescent protein as a reporter, was not detectable in rcsB, rcsD and rcsBD mutants both in vitro and in vivo. The expression of amsG in vitro was higher in the rcsC mutant than in the wild‐type, whereas its expression in vivo was higher in the wild‐type than in the rcsC mutant. In addition, rcs mutants were more susceptible to polymyxin B treatment than the wild‐type, suggesting that the Rcs system conferred some level of resistance to polymyxin B. Furthermore, rcs mutants showed irregular and slightly reduced motility on swarming plates. Together, these results indicate that the Rcs system plays a major role in virulence and survival of E. amylovora in immature pear fruit.
Infliximab dependency in children with Crohn’s disease
Authors: DURICOVA D. , PEDERSEN N. , LENICEK M. , HRADSKY O. , BRONSKY J. , ADAMCOVA M. , ELKJAER M. , ANDERSEN P. S. , VITEK L. , LARSEN K. , LUKAS M. , NEVORAL J. , WEWER V. , MUNKHOLM P.
Published: January 2009

Background  Recently, infliximab dependency has been described.

Aim  To assess frequency of ID in 82 consecutive Crohn’s disease children treated with infliximab 2000–2006 and to describe clinical and genetic predictors of long‐term infliximab response.

Methods  A phenotype model of infliximab dependency was used to assess treatment response: ‘immediate outcome’ (30 days after infliximab start) – complete/partial/no response. ‘Long‐term outcome’: (i) prolonged response: maintenance of complete/partial response; (ii) infliximab dependency: relapse ≤90 days after intended infliximab cessation requiring repeated infusions to regain complete/partial response or need of infliximab >12 months to sustain response. Polymorphisms TNF‐308 A>G, TNF‐857 C>T, Casp9 93 C>T, FasL‐844 C>T, LTA 252 C>T and CARD15 (R702W, G908R, 1007fs) were analysed.

Results  Ninety‐four per cent of children obtained complete/partial response. In long‐term outcome, 22% maintained prolonged response, 12% had no response, while 66% became infliximab dependent. Perianal disease and no previous surgery were associated with infliximab dependency (OR 5.34, 95% CI: 1.24–22.55; OR 6.7, 95% CI: 1.67–26.61). No association was found with studied polymorphisms. The cumulative probability of surgery 50 months after starting infliximab was 10% in infliximab dependency, 30% in prolonged responders and 70% in nonresponders (P = 0.0002).

Conclusions  Sixty‐six per cent of children became infliximab dependent. Perianal disease and no surgery prior to infliximab were associated with infliximab dependency phenotype.
Time trends in peptic ulcer, erosive reflux oesophagitis, gastric and oesophageal cancers in a multiracial Asian population
Authors: GOH K.‐L. , WONG H.‐ T. , LIM C.‐H. , ROSAIDA M. S.
Published: January 2009

Background  Dramatic changes in the prevalence and pattern of gastrointestinal disease has taken place in Asia in recent years.

Aim  To compare the prevalence of duodenal (DU) and gastric ulcers (GU), erosive oesophagitis (EO), gastric cancer (GCA) and oesophageal cancer (OCA) and Helicobacter pylori infection over a 10‐year interval of time in a multiracial South‐East Asian population.

Methods  Endoscopy records of first time gastroscopy in the University of Malaya Medical Centre, Kuala Lumpur, Malaysia were reviewed for 1989/1990 and 1999/2000.

Results  In the period of 1989–1990, 3252 records and in 1999–2000, 4615 records were analysed. Both DU (21.1–9.5%) and GU (11.9–9.4%) had decreased significantly (P < 0.001). EO had increased significantly from 2.0% to 8.4% (P < 0.001). Both GCA and OCA had declined in the 10‐year interval. Helicobacter pylori prevalence had decreased from 51.7% to 30.3% (P < 0.001).The decrease in DU and GU was seen in all racial groups. The increase in EO was most marked in Indians and the decrease in GCA in Chinese. The proportion of H. pylori‐associated DU and GU had also decreased with time.

Conclusions  Peptic ulcers and H. pylori infection had declined over a 10‐year period of time and showed an opposing time trend with EO, which had increased dramatically. Both GCA and OCA had declined in prevalence.
Clinical trials: healing of erosive oesophagitis with dexlansoprazole MR, a proton pump inhibitor with a novel dual delayed‐release formulation – results from two randomized controlled studies
Authors: SHARMA P. , SHAHEEN N. J. , PEREZ M. C. , PILMER B. L. , LEE M. , ATKINSON S. N. , PEURA D.
Published: January 2009

Background  Dexlansoprazole MR employs a dual delayed‐release delivery system that extends drug exposure and prolongs pH control compared with lansoprazole.

Aim  To assess the efficacy and safety of dexlansoprazole MR in healing erosive oesophagitis (EO).

Methods  Patients in two identical double‐blind, randomized controlled trials (n = 4092) received dexlansoprazole MR 60 or 90 mg or lansoprazole 30 mg once daily. Week 8 healing was assessed using a closed testing procedure – first for non‐inferiority, then superiority, vs. lansoprazole. Secondary endpoints included week 4 healing and week 8 healing in patients with moderate‐to‐severe disease (Los Angeles Classification grades C and D). Life‐table and crude rate analyses were performed. Symptoms and tolerability were assessed.

Results  Dexlansoprazole MR achieved non‐inferiority to lansoprazole, allowing testing for superiority. Using life‐table analysis, dexlansoprazole MR healed 92–95% of patients in individual studies vs. 86–92% for lansoprazole; the differences were not statistically significant (P > 0.025). Using crude rate analysis, dexlansoprazole MR 90 mg was superior to lansoprazole in both studies and 60 mg was superior in one study. Week 4 healing was >64% with all treatments in both studies. In an integrated analysis of 8‐week healing in patients with moderate‐to‐severe EO, dexlansoprazole MR 90 mg was superior to lansoprazole. All treatments effectively relieved symptoms and were well tolerated.

Conclusion  Dexlansoprazole MR is highly effective in healing EO and offers benefits over lansoprazole, particularly in moderate‐to‐severe disease.
Meta‐analysis: efficacy of bovine lactoferrin in Helicobacter pylori eradication
Authors: SACHDEVA A. , NAGPAL J.
Published: January 2009

Background  Several randomized‐controlled trials (RCTs) have sought to determine the efficacy of bovine lactoferrin in Helicobacter pylori eradication with equivocal results.

Aim  To evaluate the effect of bovine lactoferrin supplementation in H. pylori eradication.

Methods  Electronic databases, reviews, bibliographies, abstracts and conference proceedings were searched. Included trials had to be randomized or quasi‐randomized and controlled, using bovine lactoferrin in the intervention group, treating Helicobacter‐infected subjects and evaluating eradication of H. pylori as an outcome.

Results  The search identified five eligible RCTs (of 169). Data were available for 682 subjects (bovine lactoferrin group‐n = 316; control group‐n = 366). The pooled odds ratio (five studies) for eradication by intention‐to‐treat analysis was 2.22 (95% CI 1.44–3.44; P = 0.0003) using the fixed effects model (FEM) and 2.24 (95% CI 1.15–4.35; P = 0.0003) using the random effects model (REM) (Cochran’s Q = 6.83; P = 0.145). The pooled risk difference was 0.11 (95% CI 0.05–0.16; P = 0.0001) by FEM (Cochran’s Q = 6.67; P = 0.154) and 0.10 (95% CI 0.04–0.17; P = 0.0023) by REM. There was no significant difference in incidence of adverse effects.

Conclusion  Bovine lactoferrin potentially improves H. pylori eradication rates without any impact on adverse effects, but available evidence is limited and further research is necessary to confirm the findings.
Seismic analysis of clinoform depositional sequences and shelf‐margin trajectories in Lower Cretaceous (Albian) strata, Alaska North Slope
Authors: Houseknecht David W. , Bird Kenneth J. , Schenk Christopher J.
Published: January 2009

Lower Cretaceous strata beneath the Alaska North Slope include clinoform depositional sequences that filled the western Colville foreland basin and overstepped the Beaufort rift shoulder. Analysis of Albian clinoform sequences with two‐dimensional (2D) seismic data resulted in the recognition of seismic facies inferred to represent lowstand, transgressive and highstand systems tracts. These are stacked to produce shelf‐margin trajectories that appear in low‐resolution seismic data to alternate between aggradational and progradational. Higher‐resolution seismic data reveal shelf‐margin trajectories that are more complex, particularly in net‐aggradational areas, where three patterns commonly are observed: (1) a negative (downward) step across the sequence boundary followed by mostly aggradation in the lowstand systems tract (LST), (2) a positive (upward) step across the sequence boundary followed by mostly progradation in the LST and (3) an upward backstep across a mass‐failure décollement. These different shelf‐margin trajectories are interpreted as (1) fall of relative sea level below the shelf edge, (2) fall of relative sea level to above the shelf edge and (3) mass‐failure removal of shelf‐margin sediment. Lowstand shelf margins mapped using these criteria are oriented north–south in the foreland basin, indicating longitudinal filling from west to east. The shelf margins turn westward in the north, where the clinoform depositional system overstepped the rift shoulder, and turn eastward in the south, suggesting progradation of depositional systems from the ancestral Brooks Range into the foredeep. Lowstand shelf‐margin orientations are consistently perpendicular to clinoform‐foreset‐dip directions. Although the Albian clinoform sequences of the Alaska North Slope are generally similar in stratal geometry to clinoform sequences elsewhere, they are significantly thicker. Clinoform‐sequence thickness ranges from 600–1000 m in the north to 1700–2000 m in the south, reflecting increased accommodation from the rift shoulder into the foredeep. The unusually thick clinoform sequences suggest significant subsidence followed by rapid sediment influx.
Interactions to the fifth trophic level: secondary and tertiary parasitoid wasps show extraordinary efficiency in utilizing host resources
Authors: Harvey Jeffrey A. , Wagenaar Roel , Bezemer T. Martijn
Published: January 2009

Parasitoid wasps are highly efficient organisms at utilizing and assimilating limited resources from their hosts. This study explores interactions over three trophic levels, from the third (primary parasitoid) to the fourth (secondary parasitoid) and terminating in the fifth (tertiary parasitoid).

Host utilization and adult body mass of the secondary and tertiary parasitoid Gelis agilis was determined when developing on pre‐pupae of its primary parasitoid host, Cotesia glomerata, and from pre‐pupae of another secondary parasitoid, Lysibia nana that had developed initially on pre‐pupae of C. glomerata.

In both C. glomerata and G. agilis, the body mass of emerging adult parasitoids was strongly positively correlated with initial cocoon mass. For a given cocoon mass at parasitism, emerging adult G. agilis wasps were almost 90% as large as C. glomerata adults developing in healthy cocoons of comparable mass. Furthermore, G. agilis adults were still 75% as large as C. glomerata adults even when developing on L. nana that in turn had developed on C. glomerata. Otherwise, in terms of adult body mass per unit of host resources, there was no apparent difference in the quality of C. glomerata or L. nana hosts for the development of G. agilis.

Analyses of carbon and nitrogen in body tissues of the parasitoids over the third to the fifth trophic level revealed that percentage nitrogen was higher and carbon lower in G. agilis and L. nana than in C. glomerata. Furthermore, percentage carbon was lower in adult G. agilis wasps that had developed from L. nana than from C. glomerata.

We argue that the remarkable efficiency which characterizes the development of secondary and tertiary parasitoids is based on the very high nutritional quality of resources that increase in quality up the food chain and rigid selection optimizing allocation of limited host resources. Consequently, food webs involving secondary and tertiary parasitoids can go to levels hitherto unexplored thus far in empirical studies. The use of molecular markers in future studies may reveal just how long food chains involving these insects may extend.
Body size and predatory performance in wolves: is bigger better?
Authors: MacNulty Daniel R. , Smith Douglas W. , Mech L. David , Eberly Lynn E.
Published: January 2009

Large body size hinders locomotor performance in ways that may lead to trade‐offs in predator foraging ability that limit the net predatory benefit of larger size. For example, size‐related improvements in handling prey may come at the expense of pursuing prey and thus negate any enhancement in overall predatory performance due to increasing size.

This hypothesis was tested with longitudinal data from repeated observations of 94 individually known wolves (Canis lupus) hunting elk (Cervus elaphus) in Yellowstone National Park, USA. Wolf size was estimated from an individually based sex‐specific growth model derived from body mass measurements of 304 wolves.

Larger size granted individual wolves a net predatory advantage despite substantial variation in its effect on the performance of different predatory tasks; larger size improved performance of a strength‐related task (grappling and subduing elk) but failed to improve performance of a locomotor‐related task (selecting an elk from a group) for wolves > 39 kg.

Sexual dimorphism in wolf size also explained why males outperformed females in each of the three tasks considered (attacking, selecting, and killing).

These findings support the generalization that bigger predators are overall better hunters, but they also indicate that increasing size ultimately limits elements of predatory behaviour that require superior locomotor performance. We argue that this could potentially narrow the dietary niche of larger carnivores as well as limit the evolution of larger size if prey are substantially more difficult to pursue than to handle.
Food web topology and parasites in the pelagic zone of a subarctic lake
Authors: Amundsen Per‐Arne , Lafferty Kevin D. , Knudsen Rune , Primicerio Raul , Klemetsen Anders , Kuris Armand M.
Published: January 2009

Parasites permeate trophic webs with their often complex life cycles, but few studies have included parasitism in food web analyses. Here we provide a highly resolved food web from the pelagic zone of a subarctic lake and explore how the incorporation of parasites alters the topology of the web.

Parasites used hosts at all trophic levels and increased both food‐chain lengths and the total number of trophic levels. Their inclusion in the network analyses more than doubled the number of links and resulted in an increase in important food‐web characteristics such as linkage density and connectance.

More than half of the parasite taxa were trophically transmitted, exploiting hosts at multiple trophic levels and thus increasing the degree of omnivory in the trophic web.

For trophically transmitted parasites, the number of parasite–host links exhibited a positive correlation with the linkage density of the host species, whereas no such relationship was seen for nontrophically transmitted parasites. Our findings suggest that the linkage density of free‐living species affects their exposure to trophically transmitted parasites, which may be more likely to adopt highly connected species as hosts during the evolution of complex life cycles.

The study supports a prominent role for parasites in ecological networks and demonstrates that their incorporation may substantially alter considerations of food‐web structure and functioning.