bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Papillomavirus Type 31 Uses a Caveolin 1- and Dynamin 2-Mediated Entry Pathway for Infection of Human Keratinocytes
Authors: Smith Jessica L. , Campos Samuel K. , Ozbun Michelle A. 
Published: July 2007

ABSTRACT
Papillomaviruses are species-specific and epitheliotropic DNA viruses that cause tumors in their natural hosts. Certain infections with genital human papillomavirus (HPV) types are causally related to cervical cancer development. Most papillomaviruses are thought to infect cells via a clathrin-dependent pathway, yet no studies have determined the entry route in permissive host epithelial cells. Employing fluorescently labeled and native virions, we tested the effects of dominant-negative and biochemical inhibitors of cellular endocytosis pathways. Infections of human keratinocytes, a natural host cell type for HPVs, were assessed visually and by infectious entry assays. We found that HPV type 31 (HPV31) entry and initiation of early infection events require both caveolin 1 and dynamin 2 and occur independently of clathrin-mediated endocytosis. Treatment with chlorpromazine and filipin had opposing effects on HPV31 and HPV16 infection. HPV31 entry was remarkably slow, with a half-time of ≈14 h, whereas the entry half-time of HPV16 was 4 h. Consistent with a caveola-mediated entry pathway for HPV31, the virions associated with detergent-resistant lipid rafts. During a 16-h microscopic tracking of HPV31 and HPV16 virions, no colocalization of the two viral types was observed. These data suggest that HPV31 and HPV16 virions use distinct routes for host epithelial cell entry.
Recruitment of Human Cytomegalovirus Immediate-Early 2 Protein onto Parental Viral Genomes in Association with ND10 in Live-Infected Cells
Authors: Sourvinos George , Tavalai Nina , Berndt Anja , Spandidos Demetrios A. , Stamminger Thomas 
Published: July 2007

ABSTRACT
The human cytomegalovirus (HCMV) immediate-early 2 (IE2) transactivator has previously been shown to form intranuclear, dot-like accumulations in association with subnuclear structures known as promyelocytic leukemia protein (PML) nuclear bodies or ND10. We recently observed that IE2 can form dot-like structures even after infection of PML knockdown cells, which lack genuine ND10. To further analyze the determinants of IE2 subnuclear localization, a recombinant HCMV expressing IE2 fused to the enhanced green fluorescent protein was constructed. We infected primary human fibroblasts expressing Sp100 fused to the autofluorescent protein mCherry while performing live-cell imaging experiments. These experiments revealed a very dynamic association of IE2 dots with ND10 structures during the first hours postinfection: juxtaposed structures rapidly fused to precise colocalizations, followed by segregation, and finally, the dispersal of ND10 accumulations. Furthermore, by infecting PML knockdown cells we determined that the number of IE2 accumulations was dependent on the multiplicity of infection. Since time-lapse microscopy in live-infected cells revealed that IE2 foci developed into viral replication compartments, we hypothesized that viral DNA could act as a determinant of IE2 accumulations. Direct evidence that IE2 molecules are associated with viral DNA early after HCMV infection was obtained using fluorescence in situ hybridization. Finally, a DNA-binding-deficient IE2 mutant could no longer be recruited into viral replication centers, suggesting that the association of IE2 with viral DNA is mediated by a direct DNA contact. Thus, we identified viral DNA as an important determinant of IE2 subnuclear localization, which suggests that the formation of a virus-induced nucleoprotein complex and its spatial organization is likely to be critical at the early stages of a lytic infection.
DDB1 and Cul4A Are Required for Human Immunodeficiency Virus Type 1 Vpr-Induced G
2
Arrest
Authors: Tan Lindi , Ehrlich Elana , Yu Xiao-Fang 
Published: July 2007

ABSTRACT

Vpr-mediated induction of G
2
cell cycle arrest has been postulated to be important for human immunodeficiency virus type 1 (HIV-1) replication, but the precise role of Vpr in this cell cycle arrest is unclear. In the present study, we have shown that HIV-1 Vpr interacts with damaged DNA binding protein 1 (DDB1) but not its partner DDB2. The interaction of Vpr with DDB1 was inhibited when DCAF1 (VprBP) expression was reduced by short interfering RNA (siRNA) treatment. The Vpr mutant (Q65R) that was defective for DCAF1 interaction also had a defect in DDB1 binding. However, Vpr binding to DDB1 was not sufficient to induce G
2
arrest. A reduction in DDB1 or DDB2 expression in the absence of Vpr also did not induce G
2
arrest. On the other hand, Vpr-induced G
2
arrest was impaired when the intracellular level of DDB1 or Cullin 4A was reduced by siRNA treatment. Furthermore, Vpr-induced G
2
arrest was largely abolished by a proteasome inhibitor. These data suggest that Vpr assembles with DDB1 through interaction with DCAF1 to form an E3 ubiquitin ligase that targets cellular substrates for proteasome-mediated degradation and G
2
arrest.
Epstein-Barr Virus BHRF1 Micro- and Stable RNAs during Latency III and after Induction of Replication
Authors: Xing Li , Kieff Elliott 
Published: July 2007

ABSTRACT

Epstein-Barr virus (EBV) microRNAs miR-BHRF1-1, -2, and -3 have been detected in latency III-infected lymphoblasts, where they are encoded within EBNA transcripts (X. Cai, A. Schafer, S. Lu, J. P. Bilello, R. C. Desrosiers, R. Edwards, N. Raab-Traub, and B. R. Cullen, PLoS Pathog.
2:
e23, 2006). In latency III-infected lymphoblasts, we have also identified a stable 1.3-kb RNA, which begins 3′ to miR-BHRF1-1, includes the BHRF1 open reading frame, and ends near miR-BHRF1-2. This 1.3-kb RNA is the residue of Drosha cleavage of the BHRF1 microRNAs from EBNA transcripts. Early after induction of EBV replication in latency I-infected Akata lymphoblasts, BHRF1 spliced 1.4-kb mRNA accumulated along with low levels of miR-BHRF1-2 and -3 and a 0.9-kb Drosha or miR-BHRF1-2 cleavage product of BHRF1 mRNA. The turning on of latency III infection at 48 to 72 h after induction of EBV replication was associated with higher miR-BHRF1-1, -2, and -3 levels; accumulation of the 1.3-kb RNA residue in the nucleus; abundant BHRF1 spliced 1.4-kb mRNA in the cytoplasm; and more abundant 0.9-kb mRNA cleavage product in the cytoplasm. These findings implicate miR-BHRF1-2 in 3′ cleavage of BHRF1 mRNA in the cytoplasm and Drosha in cleavage of latency III EBNA and EBV replication-associated BHRF1 transcripts in the nucleus.
The effect of sandstorms and air pollution on cause-specific hospital admissions in Taipei, Taiwan
Authors: Bell M L , Levy J K , Lin Z 
Published: July 2007

Objective:Relatively little research exists focusing on the impact of air pollution on hospital admissions in Asia compared to the extensive work conducted in the USA and Europe. The issue is of particular importance because of the frequency, intensity and health effects of Asian sandstorms. This work investigates the relation between cause-specific hospital admissions and sandstorms and air pollution in Taipei, Taiwan’s capital.Methods:Time-series analyses of asthma, pneumonia, ischaemic heart disease and cerebrovascular disease hospital admissions were performed for Taipei. An eight-year time period (1995–2002) was considered for various indicators of sandstorms and the pollutants NO2, CO, ozone, SO2, PM10, and PM2.5. Pollution effects based on single-day lags of 0, 1, 2 and 3 days were explored, along with the average of the same day and previous three days (L03).Results:The risk of ischaemic heart disease admissions was associated with several sandstorm metrics, including indicators of high PM10levels in the Taipei area, indicators of high PM10at a monitor designed to measure background pollution, the PM coarse fraction, and the ratio of PM10to PM2.5. However, the lag structure of effect was not consistent across sandstorm indicators. Hospital admissions for this disease were 16–21% higher on sandstorm days compared to other days. This cause was also associated with transportation-related pollutants, NO2, CO and PM2.5. Asthma admissions rose 4.48% (95% CI 0.71% to 8.38%) per 28 μg/m3increase in L03 PM10levels and 7.60% (95% CI 2.87% to 12.54%) per 10 ppb increase in L03 ozone. Cerebrovascular disease admissions were associated with PM10and CO, both at lag 3 days. SO2exhibited no relation with admissions.Conclusions:Risk of hospital admissions in Taipei may be increased by air pollution and sandstorms. Additional research is needed to clarify the lag structure and magnitude of such effects.
Low organisational justice and heavy drinking: a prospective cohort study
Authors: Kouvonen Anne , Kivimäki Mika , Elovainio Marko , Väänänen Ari , De Vogli Roberto , Heponiemi Tarja , Linna Anne , Pentti Jaana , Vahtera Jussi 
Published: July 2007

Objectives:To investigate whether low perceived organisational injustice predicts heavy drinking among employees.Methods:Data from a prospective occupational cohort study, the 10-Town Study, on 15 290 Finnish public sector local government employees nested in 2432 work units, were used. Non-drinkers were excluded. Procedural, interactional and total organisational justice, heavy drinking (⩾210 g of absolute alcohol per week) and other psychosocial factors were determined by means of questionnaire in 2000–2001 (phase 1) and 2004 (phase 2). Multilevel logistic regression analyses taking into account the hierarchical structure of the data were conducted and adjustments were made for sex, age, socio-economic status, marital status, baseline heavy drinking, psychological distress and other psychosocial risk factors such as job strain and effort/reward imbalance.Results:After adjustments, participants who reported low procedural justice at phase 1 were approximately 1.2 times more likely to be heavy drinkers at phase 2 compared with their counterparts reporting high justice. Low perceived justice in interpersonal treatment and low perceived total organisational justice were associated with increased prevalence of heavy drinking only in the model adjusted for sociodemographics.Conclusions:This is the first longitudinal study to show that low procedural justice is weakly associated with an increased likelihood of heavy drinking.
Judicial Reform and the Possibility of Democratic Rule in Jordan: A Policy Perspective on Judicial Independence
Authors: Burgis Michelle 
Published: July 2007

AbstractStudying the independence of Jordan's judiciary provides an opportunity for appreciating current structural impediments to democratic governance and economic reform. In this article, judicial independence is critically explored through an examination of Jordan's legal system, its political culture as well as regional and international policy initiatives. A number of suggestions are advanced in a bid to encourage ongoing dialogue about the central role an independent judiciary must play in advancing the interests of all stakeholders in future reform efforts whether in Jordan or the wider Arab region.
Airway dendritic cell phenotypes in inflammatory diseases of the human lung
Authors: Lommatzsch M. , Bratke K. , Bier A. , Julius P. , Kuepper M. , Luttmann W. , Virchow J. C. 
Published: July 2007

Airway dendritic cells (DCs) are key regulators of pulmonary immune responses. However, information is limited regarding the characteristics of airway DCs in human lung diseases.Plasmacytoid DCs (pDCs) and myeloid DCs (mDCs) were analysed using four-colour flow cytometry in bronchoalveolar lavage fluid (BALF) from nonsmoking controls and patients with sarcoidosis, idiopathic pulmonary fibrosis (IPF) and pneumonia (in the presence or absence of immunosuppression).Compared with controls, immunocompetent patients with pneumonia displayed strongly enhanced pDC counts in BALF. In contrast, pDC counts in BALF from immunocompromised patients with pneumonia were even lower than in controls. This discrepancy was not explained by a different chemotactic milieu in the airways; all patients with pneumonia were characterised by strongly increased concentrations of the pDC-attracting chemokine, CXC chemokine ligand 10, in BALF. Patients with IPF were characterised by normal percentages of DC subtypes. However, the mDCs of patients with IPF were not as mature (CD83-positive) as those of controls. Patients with sarcoidosis displayed a unique increase in CD1a-negative mDCs in the airways. In addition, there was altered expression of costimulatory molecules (increased CD80 and decreased CD86 expression) on mDCs in patients with sarcoidosis.These data suggest that inflammatory diseases of the human lung are associated with a differential phenotype and recruitment of airway dendritic cells.
HoxPred: automated classification of Hox proteins using combinations of generalised profiles
Authors: Thomas-Chollier Morgane , Leyns Luc , Ledent Valérie 
Published: July 2007

Abstract

Background
Correct identification of individual Hox proteins is an essential basis for their study in diverse research fields. Common methods to classify Hox proteins focus on the homeodomain that characterise homeobox transcription factors. Classification is hampered by the high conservation of this short domain. Phylogenetic tree reconstruction is a widely used but time-consuming classification method.

Results
We have developed an automated procedure, HoxPred, that classifies Hox proteins in their groups of homology. The method relies on a discriminant analysis that classifies Hox proteins according to their scores for a combination of protein generalised profiles. 54 generalised profiles dedicated to each Hox homology group were produced de novo from a curated dataset of vertebrate Hox proteins. Several classification methods were investigated to select the most accurate discriminant functions. These functions were then incorporated into the HoxPred program.

Conclusion
HoxPred shows a mean accuracy of 97%. Predictions on the recently-sequenced stickleback fish proteome identified 44 Hox proteins, including HoxC1a only found so far in zebrafish. Using the Uniprot databank, we demonstrate that HoxPred can efficiently contribute to large-scale automatic annotation of Hox proteins into their paralogous groups. As orthologous group predictions show a higher risk of misclassification, they should be corroborated by additional supporting evidence. HoxPred is accessible via SOAP and Web interface http://cege.vub.ac.be/hoxpred/. Complete datasets, results and source code are available at the same site.
Down-regulation of SFRP1 as a putative tumor suppressor gene can contribute to human hepatocellular carcinoma
Authors: Huang Jian , Zhang Yun-Li , Teng Xiao-Mei , Lin Yun , Zheng Da-Li , Yang Peng-Yuan , Han Ze-Guang 
Published: July 2007

Abstract

Background
Hepatocellular carcinoma (HCC) is one of the most common cancers in the world. SFRP1 (the secreted frizzled-related protein 1), a putative tumor suppressor gene mapped onto chromosome 8p12-p11.1, the frequent loss of heterozygosity (LOH) region in human HCC, encodes a Wingless-type (Wnt) signaling antagonist and is frequently inactivated by promoter methylation in many human cancers. However, whether the down-regulation of SFRP1 can contribute to hepatocarcinogenesis still remains unclear.

Methods
We investigated the expression of SFRP1 through real time RT-PCR and immunohistochemistry staining. The cell growth and colony formation were observed as the overexpression and knockdown of SFRP1. The DNA methylation status within SFRP1 promoter was analyzed through methylation-specific PCR or bisulphate-treated DNA sequencing assays. Loss of heterozygosity was here detected with microsatellite markers.

Results
SFRP1 was significantly down-regulated in 76.1% (35/46) HCC specimens at mRNA level and in 30% (30/100) HCCs indicated by immunohistochemistry staining, as compared to adjacent non-cancerous livers. The overexpression of SFRP1 can significantly inhibit the cell growth and colony formation of YY-8103, SMMC7721, and Hep3B cells. The RNA interference against the constitutional SFRP1 in the offspring SMMC7721 cells, which were stably transfected by ectopic SFRP1, can markedly promote cell growth of these cells. LOH of both microsatellite markers D8S532 and D8SAC016868 flanking the gene locus was found in 13% (6 of 46 HCCs) and 6.5% (3 of 46 HCCs) of the informative cases, respectively, where 5 of 8 HCC specimens with LOH showed the down-regulation of SFRP1. DNA hypermethylation within SFRP1 promoter was identified in two of three HCC specimens without SFRP1 expression. Moreover, the DNA methylation of SFRP1 promoter was significantly reduced, along with the re-expression of the gene, in those HCC cell lines, Bel7404, QGY7701, and MHCC-H, as treated by DAC.

Conclusion
Our data suggested that the down-regulation of SFRP1 as a candidate tumor suppressor gene, triggered by the epigenetic and/or genetic events, could contribute to the oncogenesis of HCC.
Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties
Authors: Byun Jung-Sue , Rhee Jin-Kyu , Kim Nam Doo , Yoon JeongHyeok , Kim Dong-Uk , Koh Eunhee , Oh Jong-Won , Cho Hyun-Soo 
Published: July 2007

Abstract

Background
EstE1 is a hyperthermophilic esterase belonging to the hormone-sensitive lipase family and was originally isolated by functional screening of a metagenomic library constructed from a thermal environmental sample. Dimers and oligomers may have been evolutionally selected in thermophiles because intersubunit interactions can confer thermostability on the proteins. The molecular mechanisms of thermostabilization of this extremely thermostable esterase are not well understood due to the lack of structural information.

Results
Here we report for the first time the 2.1-Å resolution crystal structure of EstE1. The three-dimensional structure of EstE1 exhibits a classic α/β hydrolase fold with a central parallel-stranded beta sheet surrounded by alpha helices on both sides. The residues Ser154, Asp251, and His281 form the catalytic triad motif commonly found in other α/β hydrolases. EstE1 exists as a dimer that is formed by hydrophobic interactions and salt bridges. Circular dichroism spectroscopy and heat inactivation kinetic analysis of EstE1 mutants, which were generated by structure-based site-directed mutagenesis of amino acid residues participating in EstE1 dimerization, revealed that hydrophobic interactions through Val274 and Phe276 on the β8 strand of each monomer play a major role in the dimerization of EstE1. In contrast, the intermolecular salt bridges contribute less significantly to the dimerization and thermostability of EstE1.

Conclusion
Our results suggest that intermolecular hydrophobic interactions are essential for the hyperthermostability of EstE1. The molecular mechanism that allows EstE1 to endure high temperature will provide guideline for rational design of a thermostable esterase/lipase using the lipolytic enzymes showing structural similarity to EstE1.
Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily
Authors: Ibryashkina Elena M , Zakharova Marina V , Baskunov Vladimir B , Bogdanova Ekaterina S , Nagornykh Maxim O , Den'mukhamedov Marat M , Melnik Bogdan S , Kolinski Andrzej , Gront Dominik , Feder Marcin , Solonin Alexander S , Bujnicki Janusz M 
Published: July 2007

Abstract

Background
The majority of experimentally determined crystal structures of Type II restriction endonucleases (REases) exhibit a common PD-(D/E)XK fold. Crystal structures have been also determined for single representatives of two other folds: PLD (R.BfiI) and half-pipe (R.PabI), and bioinformatics analyses supported by mutagenesis suggested that some REases belong to the HNH fold. Our previous bioinformatic analysis suggested that REase R.Eco29kI shares sequence similarities with one more unrelated nuclease superfamily, GIY-YIG, however so far no experimental data were available to support this prediction. The determination of a crystal structure of the GIY-YIG domain of homing endonuclease I-TevI provided a template for modeling of R.Eco29kI and prompted us to validate the model experimentally.

Results
Using protein fold-recognition methods we generated a new alignment between R.Eco29kI and I-TevI, which suggested a reassignment of one of the putative catalytic residues. A theoretical model of R.Eco29kI was constructed to illustrate its predicted three-dimensional fold and organization of the active site, comprising amino acid residues Y49, Y76, R104, H108, E142, and N154. A series of mutants was constructed to generate amino acid substitutions of selected residues (Y49A, R104A, H108F, E142A and N154L) and the mutant proteins were examined for their ability to bind the DNA containing the Eco29kI site 5'-CCGCGG-3' and to catalyze the cleavage reaction. Experimental data reveal that residues Y49, R104, E142, H108, and N154 are important for the nuclease activity of R.Eco29kI, while H108 and N154 are also important for specific DNA binding by this enzyme.

Conclusion
Substitutions of residues Y49, R104, H108, E142 and N154 predicted by the model to be a part of the active site lead to mutant proteins with strong defects in the REase activity. These results are in very good agreement with the structural model presented in this work and with our prediction that R.Eco29kI belongs to the GIY-YIG superfamily of nucleases. Our study provides the first experimental evidence for a Type IIP REase that does not belong to the PD-(D/E)XK or HNH superfamilies of nucleases, and is instead a member of the unrelated GIY-YIG superfamily.
Does a referral from home to hospital affect satisfaction with childbirth? A cross-national comparison
Authors: Christiaens Wendy , Gouwy Anneleen , Bracke Piet 
Published: July 2007

AbstractBackgroundThe Belgian and Dutch societies present many similarities but differ with regard to the organisation of maternity care. The Dutch way of giving birth is well known for its high percentage of home births and its low medical intervention rate. In contrast, home births in Belgium are uncommon and the medical model is taken for granted. Dutch and Belgian maternity care systems are compared with regard to the influence of being referred to specialist care during pregnancy or intrapartum while planning for a home birth. We expect that a referral will result in lower satisfaction with childbirth, especially in Belgium.MethodsTwo questionnaires were filled out by 605 women, one at 30 weeks of pregnancy and one within the first two weeks after childbirth, either at home or in a hospital. Of these, 563 questionnaires were usable for analysis. Women were invited to participate in the study by independent midwives and obstetricians during antenatal visits in 2004–2005. Satisfaction with childbirth was measured by the Mackey Satisfaction with Childbirth Rating Scale, which takes into account the multidimensional nature of the concept.ResultsBelgian women are more satisfied than Dutch women and home births are more satisfying than hospital births. Women who are referred to the hospital while planning for a home birth are less satisfied than women who planned to give birth in hospital and did. A referral has a greater negative impact on satisfaction for Dutch women.ConclusionThere is no reason to believe Dutch women receive hospital care of lesser quality than Belgian women in case of a referral. Belgian and Dutch attach different meaning to being referred, resulting in a different evaluation of childbirth. In the Dutch maternity care system home births lead to higher satisfaction, but once a referral to the hospital is necessary satisfaction drops and ends up lower than satisfaction with hospital births that were planned in advance. We need to understand more about referral processes and how women experience them.