bluuebunny/crossref_metadata_2025_split huggingface dataset:
Encapsidation Determinants Located Downstream of the Major Splice Donor in the Maedi-Visna Virus Leader Region
Authors: Bjarnadottir Helga , Gudmundsson Bjarki , Gudnason Janus , Jonsson Jon J. 
Published: November 2006

ABSTRACT

We investigated the role of the 5′-untranslated region between the primer binding site and the
gag
initiation codon in ovine lentivirus maedi-visna virus (MVV) genomic RNA encapsidation. We identified five computer-predicted stem-loops, three of which were highly conserved in primary sequence and structure. One stable 83-nucleotide (nt) stem-loop (SL4) was not conserved in the primary sequence, but phylogenetic analysis revealed several base pair covariations. The deletion of individual stem-loops did not markedly affect the relative encapsidation efficiency (REE). Only one mutant, carrying a disruption of a 31-nt stem-loop (SL5), had 58% REE in fetal ovine synovial (FOS) cells. A 168-nt deletion (Δ3MSD) downstream of the major splice donor (MSD) which removed three stem-loops, including SL5, resulted in 24% and 20% REE in FOS and 293T cells, respectively. A 100-nt deletion (Δ5MSD) upstream of the MSD resulted in 15-fold lower cellular genomic RNA levels than the wild-type levels in 293T cells. The Δ5MSD mutant and a double mutant (DM) (Δ5MSD and Δ3MSD) did not express detectable levels of virion proteins in 293T cells. In contrast, the region deleted in Δ5MSD was dispensable in FOS cells, and the DM had the same REE as the Δ3MSD virus. Thus, the region upstream of the MSD contains sequences critical for RNA and protein expression in a cell type-specific fashion. Our results indicate that MVV encapsidation determinants are located downstream of the MSD. These results provide comparative insight into lentiviral encapsidation and can be utilized in the design of MVV-based gene transfer vectors.
Replication of Murine Hepatitis Virus Is Regulated by Papain-Like Proteinase 1 Processing of Nonstructural Proteins 1, 2, and 3
Authors: Graham Rachel L. , Denison Mark R. 
Published: November 2006

ABSTRACTCoronaviruses are positive-strand RNA viruses that translate their genome RNA into polyproteins that are co- and posttranslationally processed into intermediate and mature replicase nonstructural proteins (nsps). In murine hepatitis virus (MHV), nsps 1, 2, and 3 are processed by two papain-like proteinase activities within nsp3 (PLP1 and PLP2) to yield nsp1, an nsp2-3 intermediate, and mature nsp2 and nsp3. To determine the role in replication of processing between nsp2 and nsp3 at cleavage site 2 (CS2) and PLP1 proteinase activity, mutations were engineered into the MHV genome at CS2, at CS1 and CS2, and at the PLP1 catalytic site, alone and in combination. Mutant viruses with abolished cleavage at CS2 were delayed in growth and RNA synthesis but grew to wild-type titers of >107PFU/ml. Mutant viruses with deletion of both CS1 and CS2 exhibited both a delay in growth and a decrease in peak viral titer to ∼104PFU/ml. Inactivation of PLP1 catalytic residues resulted in a mutant virus that did not process at either CS1 or CS2 and was severely debilitated in growth, achieving only 102PFU/ml. However, when both CS1 and CS2 were deleted in the presence of inactivated PLP1, the growth of the resulting mutant virus was partially compensated, comparable to that of the CS1 and CS2 deletion mutant. These results demonstrate that interactions of PLP1 with CS1 and CS2 are critical for protein processing and suggest that the interactions play specific roles in regulation of the functions of nsp1, 2, and 3 in viral RNA synthesis.
Cryoelectron Microscopy of Protein IX-Modified Adenoviruses Suggests a New Position for the C Terminus of Protein IX
Authors: Marsh Michael P. , Campos Samuel K. , Baker Matthew L. , Chen Christopher Y. , Chiu Wah , Barry Michael A. 
Published: November 2006

ABSTRACT
Recombinant human adenovirus is a useful gene delivery vector for clinical gene therapy. Minor capsid protein IX of adenovirus has been of recent interest since multiple studies have shown that modifications can be made to its C terminus to alter viral tropism or add molecular tags and/or reporter proteins. We examined the structure of an engineered adenovirus displaying the enhanced green fluorescent protein (EGFP) fused to the C terminus of protein IX. Cryoelectron microscopy and reconstruction localized the C-terminal EGFP fusion between the H2 hexon and the H4 hexon, positioned between adjacent facets, directly above the density previously assigned as protein IIIa. The original assignment of IIIa was based largely on indirect evidence, and the data presented herein support the reassignment of the IIIa density as protein IX.
Structurally Mapping the Diverse Phenotype of Adeno-Associated Virus Serotype 4
Authors: Govindasamy Lakshmanan , Padron Eric , McKenna Robert , Muzyczka Nicholas , Kaludov Nikola , Chiorini John A. , Agbandje-McKenna Mavis 
Published: November 2006

ABSTRACT
The adeno-associated viruses (AAVs) can package and deliver foreign DNA into cells for corrective gene delivery applications. The AAV serotypes have distinct cell binding, transduction, and antigenic characteristics that have been shown to be dictated by the capsid viral protein (VP) sequence. To understand the contribution of capsid structure to these properties, we have determined the crystal structure of AAV serotype 4 (AAV4), one of the most diverse serotypes with respect to capsid protein sequence and antigenic reactivity. Structural comparison of AAV4 to AAV2 shows conservation of the core β strands (βB to βI) and helical (αA) secondary structure elements, which also exist in all other known parvovirus structures. However, surface loop variations (I to IX), some containing compensating structural insertions and deletions in adjacent regions, result in local topological differences on the capsid surface. These include AAV4 having a deeper twofold depression, wider and rounder protrusions surrounding the threefold axes, and a different topology at the top of the fivefold channel from that of AAV2. Also, the previously observed “valleys” between the threefold protrusions, containing AAV2's heparin binding residues, are narrower in AAV4. The observed differences in loop topologies at subunit interfaces are consistent with the inability of AAV2 and AAV4 VPs to combine for mosaic capsid formation in efforts to engineer novel tropisms. Significantly, all of the surface loop variations are associated with amino acids reported to affect receptor recognition, transduction, and anticapsid antibody reactivity for AAV2. This observation suggests that these capsid regions may also play similar roles in the other AAV serotypes.
Live Attenuated Influenza Virus Expressing Human Interleukin-2 Reveals Increased Immunogenic Potential in Young and Aged Hosts
Authors: Ferko Boris , Kittel Christian , Romanova Julia , Sereinig Sabine , Katinger Hermann , Egorov Andrej 
Published: November 2006

ABSTRACTDespite the reported efficacy of commercially available influenza virus vaccines, a considerable proportion of the human population does not respond well to vaccination. In an attempt to improve the immunogenicity of live influenza vaccines, an attenuated, cold-adapted (ca) influenza A virus expressing human interleukin-2 (IL-2) from the NS gene was generated. Intranasal immunization of young adult and aged mice with the IL-2-expressing virus resulted in markedly enhanced mucosal and cellular immune responses compared to those of mice immunized with the nonrecombinantcaparent strain. Interestingly, the mucosal immunoglobulin A (IgA) and CD8+T-cell responses in the respiratory compartment could be restored in aged mice primed with the IL-2-expressing virus to magnitudes similar to those in young adult mice. The immunomodulating effect of locally expressed IL-2 also gave rise to a systemic CD8+T-cell and distant urogenital IgA response in young adult mice, but this effect was less distinct in aged mice. Importantly, only mice immunized with the recombinant IL-2 virus were completely protected from a pathogenic wild-type virus challenge and revealed a stronger onset of virus-specific CD8+T-cell recall response. Our findings emphasize the potential of reverse genetics to improve the efficacy of live influenza vaccines, thus rendering them more suitable for high-risk age groups.
Hepatitis C Virus Entry Requires a Critical Postinternalization Step and Delivery to Early Endosomes via Clathrin-Coated Vesicles
Authors: Meertens Laurent , Bertaux Claire , Dragic Tatjana 
Published: November 2006

ABSTRACT
Hepatitis C virus (HCV) is a major human pathogen associated with life-threatening liver disease. Entry into hepatocytes requires CD81 and a putative second receptor. In this study, we elucidated the postreceptor attachment stages of HCV entry using HCV pseudoparticles (HCVpp) as a model system. By means of dominant-negative mutants and short interfering RNAs of various cellular proteins, we showed that HCVpp enter via clathrin-coated vesicles and require delivery to early but not to late endosomes. However, the kinetics of HCV envelope glycoprotein-mediated fusion are delayed compared to those of other viruses that enter in early endosomes. Entry of HCVpp can be efficiently blocked by bafilomycin A1, which neutralizes the pH in early endosomes and impairs progression of endocytosis beyond this stage. However, low-pH exposure of bafilomycin A1-treated target cells does not induce entry of HCVpp at the plasma membrane or in the early stages of endocytosis. These observations indicate that, subsequent to internalization, HCVpp entry necessitates additional, low-pH-dependent interactions, modifications, or trafficking, and that these events are irreversibly disrupted by bafilomycin A1 treatment.
Genetic and Neutralization Properties of Subtype C Human Immunodeficiency Virus Type 1 Molecular
env
Clones from Acute and Early Heterosexually Acquired Infections in Southern Africa
Authors: Li Ming , Salazar-Gonzalez Jesus F. , Derdeyn Cynthia A. , Morris Lynn , Williamson Carolyn , Robinson James E. , Decker Julie M. , Li Yingying , Salazar Maria G. , Polonis Victoria R. , Mlisana Koleka , Karim Salim Abdool , Hong Kunxue , Greene Kelli M. , Bilska Miroslawa , Zhou Jintao , Allen Susan , Chomba Elwyn , Mulenga Joseph , Vwalika Cheswa , Gao Feng , Zhang Ming , Korber Bette T. M. , Hunter Eric , Hahn Beatrice H. , Montefiori David C. 
Published: November 2006

ABSTRACT
A standard panel of subtype C human immunodeficiency virus type 1 (HIV-1) Env-pseudotyped viruses was created by cloning, sequencing, and characterizing functional gp160 genes from 18 acute and early heterosexually acquired infections in South Africa and Zambia. In general, the gp120 region of these clones was shorter (most evident in V1 and V4) and less glycosylated compared to newly transmitted subtype B viruses, and it was underglycosylated but no different in length compared to chronic subtype C viruses. The gp120s also exhibited low amino acid sequence variability (12%) in V3 and high variability (39%) immediately downstream of V3, a feature shared with newly transmitted subtype B viruses and chronic viruses of both subtypes. When tested as Env-pseudotyped viruses in a luciferase reporter gene assay, all clones possessed an R5 phenotype and resembled primary isolates in their sensitivity to neutralization by HIV-1-positive plasmas. Results obtained with a multisubtype plasma panel suggested partial subtype preference in the neutralizing antibody response to infection. The clones were typical of subtype C in that all were resistant to 2G12 (associated with loss of N-glycosylation at position 295) and most were resistant to 2F5, but all were sensitive to 4E10 and many were sensitive to immunoglobulin G1b12. Finally, conserved neutralization epitopes in the CD4-induced coreceptor binding domain of gp120 were poorly accessible and were difficult to induce and stabilize with soluble CD4 on Env-pseudotyped viruses. These results illustrate key genetic and antigenic properties of subtype C HIV-1 that might impact the design and testing of candidate vaccines. A subset of these gp160 clones are suitable for use as reference reagents to facilitate standardized assessments of vaccine-elicited neutralizing antibody responses.
Characterization of
White Bream Virus
Reveals a Novel Genetic Cluster of Nidoviruses
Authors: Schütze Heike , Ulferts Rachel , Schelle Barbara , Bayer Sonja , Granzow Harald , Hoffmann Bernd , Mettenleiter Thomas C. , Ziebuhr John 
Published: November 2006

ABSTRACT

The order
Nidovirales
comprises viruses from the families
Coronaviridae
(genera
Coronavirus
and
Torovirus
),
Roniviridae
(genus
Okavirus
), and
Arteriviridae
(genus
Arterivirus
). In this study, we characterized
White bream virus
(WBV), a bacilliform plus-strand RNA virus isolated from fish. Analysis of the nucleotide sequence, organization, and expression of the 26.6-kb genome provided conclusive evidence for a phylogenetic relationship between WBV and nidoviruses. The polycistronic genome of WBV contains five open reading frames (ORFs), called ORF1a, -1b, -2, -3, and -4. In WBV-infected cells, three subgenomic RNAs expressing the structural proteins S, M, and N were identified. The subgenomic RNAs were revealed to share a 42-nucleotide, 5′ leader sequence that is identical to the 5′-terminal genome sequence. The data suggest that a conserved nonanucleotide sequence, CA(G/A)CACUAC, located downstream of the leader and upstream of the structural protein genes acts as the core transcription-regulating sequence element in WBV. Like other nidoviruses with large genomes (>26 kb), WBV encodes in its ORF1b an extensive set of enzymes, including putative polymerase, helicase, ribose methyltransferase, exoribonuclease, and endoribonuclease activities. ORF1a encodes several membrane domains, a putative ADP-ribose 1"-phosphatase, and a chymotrypsin-like serine protease whose activity was established in this study. Comparative sequence analysis revealed that WBV represents a separate cluster of nidoviruses that significantly diverged from toroviruses and, even more, from coronaviruses, roniviruses, and arteriviruses. The study adds to the amazing diversity of nidoviruses and appeals for a more extensive characterization of nonmammalian nidoviruses to better understand the evolution of these largest known RNA viruses.
Identification of Carboxypeptidase of Glutamate Like-B as a Candidate Suppressor in Cell Growth and Metastasis in Human Hepatocellular Carcinoma
Authors: Zhang Pingping , Chan David Wai , Zhu YiYi , Li Jin Jun , Ng Irene Oi-Lin , Wan Dafang , Gu Jianren 
Published: November 2006

Abstract
Purpose: We have previously done large-scale cDNA transfection screening on human hepatocellular carcinoma (HCC) cells and have identified 3,806 cDNA genes that possess the ability of either stimulating or inhibiting cell growth. In this study, we characterized one of these growth suppressor genes, carboxypeptidase of glutamate like-B (CPGL-B), in HCC.
Experimental Design: Semiquantitative reverse-transcription PCR was used to examine the expression levels of CPGL-B. The cellular localization and functions of CPGL-B were investigated by enforced expression of CPGL-B in HCC cells.
Results: From our previous cDNA transfection screening, we identified a gene named CPGL and its isoform, CPGL-B. With computational analysis, CPGL was located at chromosome 18q22.3 and was a homologue of peptidase family M20. CPGL was expressed in all adult and fetal tissues, whereas its isoform, CPGL-B, lacking exons 3 and 4, was expressed in all fetal tissues but only in liver and placenta of adult tissues. In HCC, CPGL-B was frequently underexpressed (35 of 90, 38.9%) in tumorous tissues compared with the corresponding nontumorous livers. Intriguingly, the underexpression was significantly associated with the presence of venous invasion (P = 0.018) and tumor microsatellite formation (P = 0.004). Stable transfection of CPGL-B in SMMC7721 HCC cells showed significant inhibition in cell viability, colony formation, cell invasion, and tumor formation in nude mice. CPGL-B also down-regulated CXCR3, matrix metalloproteinase 11, and CD44s, which are involved in cell growth and cell migration.
Conclusions: These findings suggest that the frequent underexpression of CPGL-B may be associated with cell growth and metastasis of HCC.
Activation of mammalian target of rapamycin and the p70 S6 kinase by arsenic trioxide in BCR-ABL–expressing cells
Authors: Yoon Patrick , Giafis Nick , Smith Jessica , Mears Heather , Katsoulidis Efstratios , Sassano Antonella , Altman Jessica , Redig Amanda J. , Tallman Martin S. , Platanias Leonidas C. 
Published: November 2006

Abstract
Arsenic trioxide (As2O3) exhibits important antitumor activities in vitro and in vivo, but the precise mechanisms by which it induces its effects are not known. We provide evidence that during treatment of BCR-ABL–expressing cells with As2O3, there is activation of a cellular pathway involving the p70 S6 kinase (p70S6K). Our data show that p70S6K is rapidly phosphorylated on Thr421 and Ser424 and is activated in an As2O3-inducible manner. The mammalian target of rapamycin (mTOR) is also phosphorylated/activated in an As2O3-inducible manner, and its activity is required for downstream engagement of p70S6K. p70S6K subsequently phosphorylates the S6 ribosomal protein on Ser235/Ser236 and Ser240/Ser244 to promote initiation of mRNA translation. Treatment of chronic myelogenous leukemia–derived cell lines with As2O3 also results in phosphorylation of the 4E-BP1 repressor of mRNA translation on Thr37/Thr46 and Thr70, sites required for its deactivation and its dissociation from the eukaryotic initiation factor 4E complex to allow cap-dependent mRNA translation. In studies to determine the functional relevance of this pathway, we found that inhibition of mTOR and downstream cascades enhances induction of apoptosis by As2O3. Consistent with this, the mTOR inhibitor rapamycin strongly potentiated As2O3-mediated suppression of primitive leukemic progenitors from the bone marrow of chronic myelogenous leukemia patients. Altogether, our data show that the mTOR/p70S6K pathway is activated in a negative feedback regulatory manner in response to As2O3 in BCR-ABL–transformed cells and plays a key regulatory role in the induction of anti-leukemic responses. [Mol Cancer Ther 2006;5(11):2815–23]
The Environmental Resonance of Daoist Moving Meditations
Authors: Nixon Denver Vale 
Published: November 2006

AbstractRather than focus solely on traditional philosophical categories, as has often been the case in the discourse on Daoism and ecology, this paper explores the connections between a Daoist theory of practice, moving meditations of Daoist origin, and environmental resonance. Major themes explored include internalized action tradeoffs, preventative and integrated health awareness, alternative epistemologies, and an extemporaneous ethic sensitive to ecological change. It is suggested that collectively, Daoist cultivational practices may contribute toward social behaviour that is at least neutral, if not benevolent, toward the non-human world. Autoethnographic journal entries vivify the arguments presented. It is hoped that this practice oriented approach will not only reveal some overlooked connections between Daoism and ecology worthy of further study, but also appreciate the religious heritage of the Daoism to which such practices owe their naissance.
Perception of Unmet Basic Needs as a Predictor of Physical Functioning Among Community-Dwelling Older Adults
Authors: Sachs-Ericsson Natalie , Schatschneider Chris , Blazer Dan G. 
Published: November 2006

Objectives: The present study examined the influence of participant’s perception that their basic needs were not being met on their physical functioning problems. The association between lower social economic status (SES), typically indexed by income and education, and physical disability has been clearly established. Although income and education are not easily modifiable among older adults, perceptions of resource deficits may be more easily influenced through interventions. Method: Among community-dwelling older adults ( N = 4,162), the authors examined the influence of participants’ perception that their basic needs were not being met on physical functioning problems during a 10-year period using growth curve analyses. Results: Baseline problems meeting basic needs influenced the growth in physical functioning problems, even after controlling for more objective indices of SES and for health problems and behaviors. Discussion: Interventions focused on providing older adults with resources for meeting basic needs may substantially reduce the subsequent level of disability.
The Role of Medication Use and Health on the Decision to Quit Drinking Among Older Adults
Authors: Pringle Kristine E. , Heller Debra A. , Ahern Frank M. , Gold Carol H. , Brown Theresa V. 
Published: November 2006

Objectives: To determine the extent to which changes in medication use and health influence the decision to quit drinking among older adults. Method: The sample consisted of 8,883 elderly enrolled in Pennsylvania's Pharmaceutical Assistance Contract for the Elderly (PA-PACE) program who completed surveys in 2000 and 2002. Survey data were linked with prescription claims to examine medication and health factors associated with drinking cessation between baseline and follow-up. Results: Overall, 3.9% of those using alcohol at baseline quit drinking during the study period. Logistic regression results showed that individuals who initiated antipsychotic (OR = 2.92) and antineoplastic therapies (OR = 2.67) were the most likely to quit drinking. Discussion: These findings support the hypothesis that elderly quit drinking in response to ill health. Results have implications for alcohol interventions in older adults and underscore the importance of separating former drinkers from lifetime abstainers in the study of alcohol-health relationships.
‘Mind in general’ by Sir Alexander Crichton
Authors: Berrios G. E. 
Published: November 2006

The history of the ‘philosophies of psychiatry’ can be defined as the contextualized study of past theoretical views on the nature, understanding and management of madness and related notions. The application of an hermeneutic apparatus to past psychiatric narratives gives rise to the history of psychiatry; its application to current narrative gives origin to the philosophy of psychiatry. If the latter employs off-the-shelf, ready-made, external philosophies, it follows a centripetal approach; if it starts from the inside of psychiatry and generates its own tools and meta-language, it follows a centrifugal approach.Psychiatry is burdened by intrinsic and extrinsic philosophical problems. The former result from its hybrid nature, i.e., from the fact that psychiatry unsteadily straddles the natural and human sciences. The latter are borrowed from the conceptual frames into which psychiatry has been inscribed since the 19th century.The philosophy of psychiatry may anticipate or follow empirical research. The ante rem mode is based on the idea that empirical research requires conceptual supervision, audit and guidance, for it is always ideology-and theory-laden. The post rem mode is based on the view that science is the only way to ‘truth’ and hence all that the philosophy of psychiatry can (or should) do is facilitate, interpret, justify, defend or glorify empirical findings.The Classic Text that follows was written by Sir Alexander Crichton at the end of the 18th century, and is a good example of the centripetal mode of philosophy-making.