bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Changes in the Polymerase Genes (PA and PB1) Associated with High Pathogenicity of H5N1 Influenza Virus in Mallard Ducks
Authors: Hulse-Post D. J. , Franks J. , Boyd K. , Salomon R. , Hoffmann E. , Yen H. L. , Webby R. J. , Walker D. , Nguyen T. D. , Webster R. G. 
Published: June 2007

ABSTRACT
The highly pathogenic (HP) influenza viruses H5 and H7 are usually nonpathogenic in mallard ducks. However, the currently circulating HP H5N1 viruses acquired a different phenotype and are able to cause mortality in mallards. To establish the molecular basis of this phenotype, we cloned the human A/Vietnam/1203/04 (H5N1) influenza virus isolate that is highly pathogenic in ferrets, mice, and mallards and found it to be a heterogeneous mixture. Large-plaque isolates were highly pathogenic to ducks, mice, and ferrets, whereas small-plaque isolates were nonpathogenic in these species. Sequence analysis of the entire genome revealed that the small-plaque and the large-plaque isolates differed in the coding of five amino acids. There were two differences in the hemagglutinin (HA) gene (K52T and A544V), one in the PA gene (T515A), and two in the PB1 gene (K207R and Y436H). We inserted the amino acid changes into the wild-type reverse genetic virus construct to assess their effects on pathogenicity in vivo. The HA gene mutations and the PB1 gene K207R mutation did not alter the HP phenotype of the large-plaque virus, whereas constructs with the PA (T515A) and PB1 (Y436H) gene mutations were nonpathogenic in orally inoculated ducks. The PB1 (Y436H) construct was not efficiently transmitted in ducks, whereas the PA (T515A) construct replicated as well as the wild-type virus did and was transmitted efficiently. These results show that the PA and PB1 genes of HP H5N1 influenza viruses are associated with lethality in ducks. The mechanisms of lethality and the perpetuation of this lethal phenotype in ducks in nature remain to be determined.
Recombination Confounds the Early Evolutionary History of Human Immunodeficiency Virus Type 1: Subtype G Is a Circulating Recombinant Form
Authors: Abecasis Ana B. , Lemey Philippe , Vidal Nicole , de Oliveira Túlio , Peeters Martine , Camacho Ricardo , Shapiro Beth , Rambaut Andrew , Vandamme Anne-Mieke 
Published: June 2007

ABSTRACT
Human immunodeficiency virus type 1 (HIV-1) is classified in nine subtypes (A to D, F, G, H, J, and K), a number of subsubtypes, and several circulating recombinant forms (CRFs). Due to the high level of genetic diversity within HIV-1 and to its worldwide distribution, this classification system is widely used in fields as diverse as vaccine development, evolution, epidemiology, viral fitness, and drug resistance. Here, we demonstrate how the high recombination rates of HIV-1 may confound the study of its evolutionary history and classification. Our data show that subtype G, currently classified as a pure subtype, has in fact a recombinant history, having evolved following recombination between subtypes A and J and a putative subtype G parent. In addition, we find no evidence for recombination within one of the lineages currently classified as a CRF, CRF02_AG. Our analysis indicates that CRF02_AG was the parent of the recombinant subtype G, rather than the two having the opposite evolutionary relationship, as is currently proposed. Our results imply that the current classification of HIV-1 subtypes and CRFs is an artifact of sampling history, rather than reflecting the evolutionary history of the virus. We suggest a reanalysis of all pure subtypes and CRFs in order to better understand how high rates of recombination have influenced HIV-1 evolutionary history.
Hydrophobic Residues That Form Putative Fusion Loops of Epstein-Barr Virus Glycoprotein B Are Critical for Fusion Activity
Authors: Backovic Marija , Jardetzky Theodore S. , Longnecker Richard 
Published: June 2007

ABSTRACT

To test the importance of the hydrophobic residues within the putative Epstein-Barr virus (EBV) glycoprotein B (gB) fusion loops in membrane fusion, WY
112-113
and WLIW
193-196
were mutated into alanine, glutamic acid, or the analogous residues from herpes simplex virus type 1 (HSV-1) gB (HR and RVEA). All gB variants exhibited cell surface expression, demonstrating that the substitutions did not perturb gB trafficking. None of six gB variants was, however, capable of mediating fusion with either epithelial or B cells. These data demonstrate that the bulky and hydrophobic EBV loop residues, which differ from the more hydrophilic HSV-1 residues and appear more compatible with membrane insertion, are essential for EBV gB-dependent fusion.
Evolutionary Processes among Sylvatic Dengue Type 2 Viruses
Authors: Vasilakis Nikos , Holmes Edward C. , Fokam Eric B. , Faye Ousmane , Diallo Mawlouth , Sall Amadou A. , Weaver Scott C. 
Published: June 2007

ABSTRACT

Sylvatic dengue viruses (DENV) are transmitted in an enzootic cycle between nonhuman primates and arboreal
Aedes
mosquitoes in Southeast Asia and West Africa. Although previous analyses have revealed the evolutionary processes among endemic (human) DENV, little is known about viral evolution in the sylvatic cycle. Through an analysis of 14 complete coding regions of sylvatic Dengue type 2 virus sampled over a 33-year period, we show that both the rate of evolutionary change and the pattern of natural selection are similar among endemic and sylvatic DENV, although the latter have a uniquely high frequency of positive selection in the NS4B protein gene. Our findings support a recent cross-species transmission event and suggest the possibility of future DENV reemergence from the sylvatic cycle.
Cellular PVC-U: Current Technology and Future Challenges
Authors: Thomas N.L. 
Published: June 2007

This study discusses the formulation technology involved in the production of rigid PVC foams, and typical formulations for rigid foam sheet and profile are presented. Particular reference is given to acrylic processing aids and their effect on melt extensibility and strength. Measurements carried out using an elongational rheometer have confirmed that melt extensibility and rupture stress are increased with increasing addition level and/or molecular weight of the processing aid used. The challenges faced by the PVC foam industry are also addressed. These include environmental issues, such as the need to develop formulations with sustainable additives and to increase recycling of PVC products. Future developments include the use of organic-based stabilizers (OBS) and the use of nanofillers.
Comparison of Tibial Graft Fixation between Simulated Arthroscopic and Open Inlay Techniques for Posterior Cruciate Ligament Reconstruction
Authors: Campbell R. Brick , Torrie Alec , Hecker Aaron , Sekiya Jon K. 
Published: June 2007

Background Techniques for reconstruction of the posterior cruciate ligament continue to evolve to improve clinical results. Recent arthroscopic reconstruction methods using tibial inlay grafts require suture fixation to avoid a posterior approach to the knee. Hypothesis Early strength of the tibial fixation of posterior cruciate ligament inlay grafts, designed for an arthroscopic approach and using suture fixation, is not significantly different than that of open technique grafts using screw fixation. Study Design Controlled laboratory study. Methods Six paired human tibias were randomized to a reconstruction using an open inlay technique with two 4.0-mm cancellous lag screws or an instrumented technique suitable for an all-arthroscopic approach using 2 No. 5 Ethibond sutures tied over a button on the anterior tibial cortex. Cyclic testing of each construct was done before loading to failure. Results The loads for each group at 3-mm displacement and at 5-mm displacement were not found to be significantly different. Ultimate load for the screw group was 762 N and for the suture group was 582 N (P = .31). Stiffness was 89.8 N/mm for the screw inlays and 85.1 N/mm for the suture inlays (P = .68). Cyclic testing demonstrated no advantages of screw fixation over sutures. No suture failure was noted. Conclusion The suture fixation technique for tibial inlay posterior cruciate ligament reconstruction appears to approximate the early strength of screw fixation. Clinical Relevance Arthroscopic techniques for tibial inlay reconstruction of the posterior cruciate ligament requiring suture fixation may offer similar initial biomechanical fixation as current open inlay techniques without the need for an open posterior knee approach.
Point mutations involved in red cell stomatocytosis convert the electroneutral anion exchanger 1 to a nonselective cation conductance
Authors: Guizouarn Hélène , Martial Sonia , Gabillat Nicole , Borgese Franck 
Published: June 2007

AbstractThe anion exchanger 1 (AE1) is encoded by the SLC4A1 gene and catalyzes the electroneutral anion exchange across cell plasma membrane. It is the most abundant transmembrane protein expressed in red cell where it is involved in CO2 transport. Recently, 4 new point mutations of SLC4A1 gene have been described leading to missense mutations in the protein sequence (L687P, D705Y, S731P, or H734R). These point mutations were associated with hemolytic anemia, and it was shown that they confer a cation transport feature to the human AE1. Facing this unexpected property for an electroneutral anion exchanger, we have studied the transport features of mutated hAE1 by expression in xenopus oocytes. Our results show that the point mutations of hAE1 convert the electroneutral anion exchanger to a cation conductance: the exchangers are no longer able to exchange Cl− and HCO3−, whereas they transport Na+ and K+ through a conductive mechanism. These data shed new light on transport mechanisms showing the tiny difference, in terms of primary sequence, between an electroneutral exchange and a conductive pathway.
Replacement of the essential Dictyostelium Arp2 gene by its Entamoeba homologue using parasexual genetics
Authors: Zaki Mehreen , King Jason , Fütterer Klaus , Insall Robert H 
Published: June 2007

AbstractBackgroundCell motility is an essential feature of the pathogenesis and morbidity of amoebiasis caused byEntamoeba histolytica. As motility depends on cytoskeletal organisation and regulation, a study of the molecular components involved is key to a better understanding of amoebic pathogenesis. However, little is known about the physiological roles, interactions and regulation of the proteins of theEntamoebacytoskeleton.ResultsWe have established a genetic strategy that uses parasexual genetics to allow essentialDictyostelium discoideumgenes to be manipulated and replaced with modified or tagged homologues. Our results show that actin related protein 2 (Arp2) is essential for survival, but that theDictyosteliumprotein can be complemented byE. histolyticaArp2, despite the presence of an insertion of 16 amino acids in an otherwise highly conserved protein. Replacement of endogenous Arp2 withmyc-taggedEntamoebaorDictyosteliumArp2 has no obvious effects on growth and the protein incorporates effectively into the Arp2/3 complex.ConclusionWe have established an effective two-step method for replacing genes that are required for survival. Our protocol will allow such genes to be studied far more easily, and also allows an unambiguous demonstration that particular genes are truly essential. In addition, cells in which theDictyosteliumArp2 has been replaced by theEntamoebaprotein are potential targets for drug screens.
Sensitive and robust gene expression changes in fish exposed to estrogen – a microarray approach
Authors: Gunnarsson Lina , Kristiansson Erik , Förlin Lars , Nerman Olle , Larsson D G Joakim 
Published: June 2007

Abstract

Background
Vitellogenin is a well established biomarker for estrogenic exposure in fish. However, effects on gonadal differentiation at concentrations of estrogen not sufficient to give rise to a measurable vitellogenin response suggest that more sensitive biomarkers would be useful. Induction of zona pellucida genes may be more sensitive but their specificities are not as clear. The objective of this study was to find additional sensitive and robust candidate biomarkers of estrogenic exposure.

Results
Hepatic mRNA expression profiles were characterized in juvenile rainbow trout exposed to a measured concentration of 0.87 and 10 ng ethinylestradiol/L using a salmonid cDNA microarray. The higher concentration was used to guide the subsequent identification of generally more subtle responses at the low concentration not sufficient to induce vitellogenin. A meta-analysis was performed with data from the present study and three similar microarray studies using different fish species and platforms. Within the generated list of presumably robust responses, several well-known estrogen-regulated genes were identified. Two genes, confirmed by quantitative RT-PCR (qPCR), fulfilled both the criteria of high sensitivity and robustness; the induction of the genes encoding zona pellucida protein 3 and a nucleoside diphosphate kinase (nm23).

Conclusion
The cross-species, cross-platform meta-analysis correctly identified several robust responses. This adds confidence to our approach used for identifying candidate biomarkers. Specifically, we propose that analyses of an nm23 gene together with zona pellucida genes may increase the possibilities to detect an exposure to low levels of estrogenic compounds in fish.
Cytokine responses of CD4+ T cells during a Plasmodium chabaudi chabaudi (ER) blood-stage infection in mice initiated by the natural route of infection
Authors: Fonseca Luis , Seixas Elsa , Butcher Geoffrey , Langhorne Jean 
Published: June 2007

AbstractBackgroundInvestigation of host responses to blood stages of Plasmodium spp, and the immunopathology associated with this phase of the life cycle are often performed on mice infected directly with infected red blood cells. Thus, the effects of mosquito bites and the pre-erythrocytic stages of the parasite, which would be present in natural infection, are ignored In this paper,Plasmodium chabaudi chabaudiinfections of mice injected directly with infected red blood cells were compared with those of mice infected by the bites of infected mosquitoes, in order to determine whether the courses of primary infection and splenic CD4 T cell responses are similar.MethodsC57Bl/6 mice were injected with red blood cells infected withP. chabaudi(ER) or infected via the bite ofAnopheles stephensimosquitoes. Parasitaemia were monitored by Giemsa-stained thin blood films. Total spleen cells, CD4+ T cells, and cytokine production (IFN-γ, IL-2, IL-4, IL-10) were analysed by flow cytometry. In some experiments, mice were subjected to bites of uninfected mosquitoes prior to infectious bites in order to determine whether mosquito bitesper secould affect a subsequentP. chabaudiinfection.ResultsP. chabaudi(ER) infections initiated by mosquito bite were characterized by lower parasitaemia of shorter duration than those observed after direct blood challenge. However, splenomegaly was comparable suggesting that parasitaemia alone does not account for the increase in spleen size. Total numbers of CD4 T cells and those producing IFN-γ, IL-10 and IL-2 were reduced in comparison to direct blood challenge. By contrast, the reduction in IL-4 producing cells was less marked suggesting that there is a proportionally lower Th1-like response in mice infected via infectious mosquitoes. Strikingly, pre-exposure to bites of uninfected mosquitoes reduced the magnitude and duration of the subsequent mosquito-transmitted infection still further, but enhanced the response of CD4 T cells producing IFN-γ and IL-4.ConclusionThe data in this paper suggest that studying early host responses in blood stage malaria infections measured after direct blood challenge of mice may not completely reflect the natural situation, and more detailed investigations of blood-stage immunity after mosquito transmission in experimental models should be considered.
Identification of novel androgen receptor target genes in prostate cancer
Authors: Jariwala Unnati , Prescott Jennifer , Jia Li , Barski Artem , Pregizer Steve , Cogan Jon P , Arasheben Armin , Tilley Wayne D , Scher Howard I , Gerald William L , Buchanan Grant , Coetzee Gerhard A , Frenkel Baruch 
Published: June 2007

Abstract

Background
The androgen receptor (AR) plays critical roles in both androgen-dependent and castrate-resistant prostate cancer (PCa). However, little is known about AR target genes that mediate the receptor's roles in disease progression.

Results
Using Chromatin Immunoprecipitation (ChIP) Display, we discovered 19 novel loci occupied by the AR in castrate resistant C4-2B PCa cells. Only four of the 19 AR-occupied regions were within 10-kb 5'-flanking regulatory sequences. Three were located up to 4-kb 3' of the nearest gene, eight were intragenic and four were in gene deserts. Whereas the AR occupied the same loci in C4-2B (castrate resistant) and LNCaP (androgen-dependent) PCa cells, differences between the two cell lines were observed in the response of nearby genes to androgens. Among the genes strongly stimulated by DHT in C4-2B cells – D-dopachrome tautomerase (DDT), Protein kinase C delta (PRKCD), Glutathione S- transferase theta 2 (GSTT2), Transient receptor potential cation channel subfamily V member 3 (TRPV3), and Pyrroline-5-carboxylate reductase 1 (PYCR1) – most were less strongly or hardly stimulated in LNCaP cells. Another AR target gene, ornithine aminotransferase (OAT), was AR-stimulated in a ligand-independent manner, since it was repressed by AR siRNA knockdown, but not stimulated by DHT. We also present evidence for in vivo AR-mediated regulation of several genes identified by ChIP Display. For example, PRKCD and PYCR1, which may contribute to PCa cell growth and survival, are expressed in PCa biopsies from primary tumors before and after ablation and in metastatic lesions in a manner consistent with AR-mediated stimulation.

Conclusion
AR genomic occupancy is similar between LNCaP and C4-2B cells and is not biased towards 5' gene flanking sequences. The AR transcriptionally regulates less than half the genes nearby AR-occupied regions, usually but not always, in a ligand-dependent manner. Most are stimulated and a few are repressed. In general, response is stronger in C4-2B compared to LNCaP cells. Some of the genes near AR-occupied regions appear to be regulated by the AR in vivo as evidenced by their expression levels in prostate cancer tumors of various stages. Several AR target genes discovered in the present study, for example PRKCD and PYCR1, may open avenues in PCa research and aid the development of new approaches for disease management.
Molecular response to aromatase inhibitor treatment in primary breast cancer
Authors: Mackay Alan , Urruticoechea Ander , Dixon J Michael , Dexter Tim , Fenwick Kerry , Ashworth Alan , Drury Suzanne , Larionov Alexey , Young Oliver , White Sharon , Miller William R , Evans Dean B , Dowsett Mitch 
Published: June 2007

Abstract
Background
Aromatase inhibitors such as anastrozole and letrozole are highly effective suppressants of estrogen synthesis in postmenopausal women and are the most effective endocrine treatments for hormone receptor positive breast cancer in such women. Little is known of the molecular effects of these agents on human breast carcinomas in vivo.

Methods
We randomly assigned primary estrogen receptor positive breast cancer patients to treatment with anastrozole or letrozole for 2 weeks before surgery. Expression profiling using cDNA arrays was conducted on pretreatment and post-treatment biopsies. Sample pairs from 34 patients provided sufficient RNA for analysis.

Results
Profound changes in gene expression were seen with both aromatase inhibitors, including many classical estrogen-dependent genes such as TFF1, CCND1, PDZK1 and AGR2, but also many other genes that are likely to represent secondary responses; decrease in the expression of proliferation-related genes were particularly prominent. Many upregulated genes are involved in extracellular matrix remodelling, including collagens and members of the small leucine-rich proteoglycan family (LUM, DCN, and ASPN). No significant differences were seen between letrozole and anastrozole in terms of molecular effects. The gene changes were integrated into a Global Index of Dependence on Estrogen (GIDE), which enumerates the genes changing by at least twofold with therapy. The GIDE varied markedly between tumours and related significantly to pretreatment levels of HER2 and changes in immunohistochemically detected Ki67.

Conclusion
Our findings identify the transcriptional signatures associated with aromatase inhibitor treatment of primary breast tumours. Larger datasets using this approach should enable identification of estrogen-dependent molecular changes, which are the determinants of benefit or resistance to endocrine therapy.
RAD marker microarrays enable rapid mapping of zebrafish mutations
Authors: Miller Michael R , Atwood Tressa S , Eames B Frank , Eberhart Johann K , Yan Yi-Lin , Postlethwait John H , Johnson Eric A 
Published: June 2007

AbstractWe constructed a restriction site associated DNA (RAD) marker microarray to facilitate rapid genetic mapping of zebrafish mutations. Using these microarrays with a bulk segregant approach, we localized previously unmapped mutations to genomic regions just a few centiMorgans in length. Furthermore, we developed an approach to assay individual RAD markers in pooled populations and refined one region. The RAD approach is highly effective for genetic mapping in zebrafish and is an attractive option for mapping in other organisms.
'Normalization' of germfree mice with anaerobically cultured caecal flora of 'normal' mice
Authors: Koopman J. P. , Kennis Henriëtte M. , Mullink J. W. M. A. , Prins R. A. , Stadhouders A. M. , De Boer H. , Hectors Magda P. 
Published: June 2007

Germfree (GF) mice were inoculated with a cultured flora from 10-1, 10-3, 10-5, and 10-7 dilutions of caecal contents from a 'normal' mouse. GF mice associated with a flora of a 'normal' mouse served as controls. The following intestinal parameters were determined: Colonization resistance (CR), Relative caecal weight (RCW), villus:crypt ratio (jejunum and ileum), IgA-producing cells (jejunum and ileum), ß-aspartyl glycine (faeces), volatile and non-volatile fatty acids (caecum) and bile acids (faeces). Only the 10-1 culture was able to induce similar changes in the GF mice to a 'normal' flora. The GF + 10-5 and GF + 10-7 groups deviated markedly from the controls while the GF + 10-3 group showed in general intermediate values between GF + SPF and GF + 10-1 on the one hand and GF + 10-5 and GF + 10-7 on the other hand. ß-aspartyl glycine was present only in the GF + 10-7 group. Scanning electron microscopy (SEM) of ileal contents revealed segmented filamentous organisms in the ileum of controls and the GF + 10-1 group. The faecal flora consisted mainly of fusiform organisms. In the faeces of the 10-5 and 10-7 groups increasing amounts of non-bacterial matter were found, while in the faeces of the other groups virtually only bacteria were seen.
Induction of pregnancy-associated murine protein-1 in dwarf mice by human growth hormone
Authors: Hau J. , Poulsen O. M. , Hansen N. F. Dagnæs , Worm K. R. 
Published: June 2007

Pregnancy-associated murine protein-1 (PAMP-1) could not be detected in peripheral blood of female dwarf mice (genotype dw/dw of the DW strain). By contrast the normal size females of the DW strain (genotypes +/+ and +/dw) had PAMP-1 serum levels of 18·9 AU ± 15·7 AU/ml. Following administration of biosynthetic human growth hormone (hGH) every 2h for 52 h PAMP-1 was detected in all dwarf females at concentrations of 16·0 AU ± 3·3 AU/ml. The albumin levels in the circulation of DW females of normal size were significantly higher ( P<0·05) than those of DW dwarfs, and the hGH administration did not change the serum albumin levels. The present experiment adds weight to the suggestion that the PAMP-1 serum level is regulated by GH.