bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biological Significance of a Human Enterovirus B-Specific RNA Element in the 3′ Nontranslated Region
Authors: Merkle Ingrid , van Ooij Mark J. M. , van Kuppeveld Frank J. M. , Glaudemans Dirk H. R. F. , Galama Jochem M. D. , Henke Andreas , Zell Roland , Melchers Willem J. G. 
Published: September 2002

ABSTRACT
The secondary structures predicted for the enteroviral 3′ nontranslated region (3′NTR) all seem to indicate a conformation consisting of two (X and Y) hairpin structures. The higher-order RNA structure of the 3′NTR appears to exist as an intramolecular kissing interaction between the loops of these two hairpin structures. The enterovirus B-like subgroup possesses an additional stem-loop structure, domain Z, which is not present in the poliovirus-like enteroviruses. It has been suggested that the Z domain originated from a burst of short sequence repetitions (E. V. Pilipenko, S. V. Maslova, A. N. Sinyakov, and V. I. Agol, Nucleic Acids Res. 20:1739-1745, 1992). However, no functional features have yet been ascribed to this enterovirus B-like-specific RNA element in the 3′NTR. In this study, we tested the functional characteristics and biological significance of domain Z. A mutant of the cardiovirulent coxsackievirus group B3 strain Nancy which completely lacked the Z domain and which therefore acquired enterovirus C-like secondary structures exhibited a wild-type growth phenotype, as determined by single-cycle growth analysis with BGM cells. This result proves that the Z domain is virtually dispensable for viral growth in tissue cultures. Partial distortion of the Z domain structure resulted in a disabled virus with reduced growth kinetics, probably due to alternative conformations of the overall structure of the domain. Infection of mice showed that the recombinant coxsackievirus group B3 mutant which completely lacked the Z domain was less virulent. Pancreatic tissues from mice infected with wild-type virus and recombinant virus were equally affected. However, the heart tissue from mice infected with the recombinant virus showed only slight signs of myocarditis. These results suggest that the enterovirus B-like-specific Z domain plays a role in coxsackievirus-induced pathogenesis.
Large Hepatitis Delta Antigen Is Not a Suppressor of Hepatitis Delta Virus RNA Synthesis once RNA Replication Is Established
Authors: Macnaughton Thomas B. , Lai Michael M. C. 
Published: September 2002

ABSTRACT
Moderation of hepatitis delta virus (HDV) replication is a likely prerequisite in the establishment of chronic infections and is thought to be mediated by the intracellular accumulation of large hepatitis delta antigen (L-HDAg). The regulatory role of this protein was suggested from several studies showing that cotransfection of plasmid cDNAs expressing both L-HDAg and HDV RNA results in a potent inhibition of HDV RNA replication. However, since this approach differs significantly from natural HDV infections, where HDV RNA replication is initiated from an RNA template, and L-HDAg appears only late in the replication cycle, it remains unclear whether L-HDAg can modulate HDV RNA replication in the natural HDV replication cycle. In this study, we investigated the effect of L-HDAg, produced as a result of the natural HDV RNA editing event, on HDV RNA replication. The results showed that following cDNA-free HDV RNA transfection, a steady-state level of RNA was established at 3 to 4 days posttransfection. The same level of HDV RNA was reached when a mutant HDV genome unable to make L-HDAg was used, suggesting that L-HDAg did not play a role. The rates of HDV RNA synthesis, as measured by metabolic labeling experiments, were identical at 4 and 8 days posttransfection and in the wild type and the L-HDAg-deficient mutant. We further examined the effect of overexpression of L-HDAg at various stages of the HDV replication cycle, showing that HDV RNA synthesis was resistant to L-HDAg when it was overexpressed 3 days after HDV RNA replication had initiated. Finally, we showed that, contrary to conventional thinking, L-HDAg alone, at a certain molar ratio with HDV RNA, can initiate HDV RNA replication. Thus, L-HDAg does not inherently inhibit HDV RNA synthesis. Taken together, these results indicated that L-HDAg affects neither the rate of HDV RNA synthesis nor the final steady-state level of HDV RNA and that L-HDAg is unlikely to act as an inhibitor of HDV RNA replication in the natural HDV replication cycle.
Strategy for Nonenveloped Virus Entry: a Hydrophobic Conformer of the Reovirus Membrane Penetration Protein μ1 Mediates Membrane Disruption
Authors: Chandran Kartik , Farsetta Diane L. , Nibert Max L. 
Published: September 2002

ABSTRACT
The mechanisms employed by nonenveloped animal viruses to penetrate the membranes of their host cells remain enigmatic. Membrane penetration by the nonenveloped mammalian reoviruses is believed to deliver a partially uncoated, but still large (∼70-nm), particle with active transcriptases for viral mRNA synthesis directly into the cytoplasm. This process is likely initiated by a particle form that resembles infectious subvirion particles (ISVPs), disassembly intermediates produced from virions by proteolytic uncoating. Consistent with that idea, ISVPs, but not virions, can induce disruption of membranes in vitro. Both activities ascribed to ISVP-like particles, membrane disruption in vitro and membrane penetration within cells, are linked to N-myristoylated outer-capsid protein μ1, present in 600 copies at the surfaces of ISVPs. To understand how μ1 fulfills its role as the reovirus penetration protein, we monitored changes in ISVPs during the permeabilization of red blood cells induced by these particles. Hemolysis was preceded by a major structural transition in ISVPs, characterized by conformational change in μ1 and elution of fibrous attachment protein σ1. The altered conformer of μ1 was required for hemolysis and was markedly hydrophobic. The structural transition in ISVPs was further accompanied by derepression of genome-dependent mRNA synthesis by the particle-associated transcriptases. We propose a model for reovirus entry in which (i) primed and triggered conformational changes, analogous to those in enveloped-virus fusion proteins, generate a hydrophobic μ1 conformer capable of inserting into and disrupting cell membranes and (ii) activation of the viral particles for membrane interaction and mRNA synthesis are concurrent events. Reoviruses provide an opportune system for defining the molecular details of membrane penetration by a large nonenveloped animal virus.
Inhibitory Activity of Synthetic Peptide Antibiotics on Feline Immunodeficiency Virus Infectivity In Vitro
Authors: Ma Jia , Kennedy-Stoskopf Suzanne , Jaynes Jesse M. , Thurmond Linda M. , Tompkins Wayne A. 
Published: September 2002

ABSTRACTNatural peptide antibiotics are part of host innate immunity against a wide range of microbes, including some viruses. Synthetic peptides modeled after natural peptide antibiotics interfere with microbial membranes and are termed peptidyl membrane-interactive molecules (peptidyl-MIM [Demegen Inc, Pittsburgh, Pa.]). Sixteen peptidyl-MIM candidates were tested for activity against feline immunodeficiency virus (FIV) on infected CrFK cells. Three of them (D4E1, DC1, and D1D6) showed potent anti-FIV activity in chronically infected CrFK cells as measured by decreased reverse transcriptase (RT) activity, having 50% inhibitory concentrations of 0.46, 0.75, and 0.94 μM, respectively, which were approximately 10 times lower than their direct cytotoxic concentrations. Treatment of chronically infected CrFK cells with 2 μM D4E1 for 3 days completely reversed virus-induced cytopathic effect. Immunofluorescence revealed reduced p26 staining in these cells. Treatment of chronically infected CrFK cells with 2 μM D4E1 suppressed virus production (∼50%) for up to 7 days, The virions from the D4E1-treated culture had impaired infectivity, as measured by the 50% tissue culture infectious dose and nested PCR analysis of proviral DNA. However, these noninfectious virions were able to bind and internalize, suggesting a defect at some postentry step. After chronically infected CrFK cells were treated with D4E1 for 24 h, increased cell-associated mature p26 Gag and decreased extracellular virus-associated p26 Gag were observed by Western blot analysis, suggesting that virus assembly and/or release may be blocked by D4E1 treatment, whereas virus binding, penetration, RNA synthesis, and protein synthesis appear to be unaffected. Synthetic peptide antibiotics may be useful tools in the search for antiviral drugs having a wide therapeutic window for host cells.
Intact Microtubules Support Adenovirus and Herpes Simplex Virus Infections
Authors: Mabit Hélène , Nakano Michel Y. , Prank Ute , Saam Bianca , Döhner Katinka , Sodeik Beate , Greber Urs F. 
Published: September 2002

ABSTRACT
Capsids and the enclosed DNA of adenoviruses, including the species C viruses adenovirus type 2 (Ad2) and Ad5, and herpesviruses, such as herpes simplex virus type 1 (HSV-1), are targeted to the nuclei of epithelial, endothelial, fibroblastic, and neuronal cells. Cytoplasmic transport of fluorophore-tagged Ad2 and immunologically detected HSV-1 capsids required intact microtubules and the microtubule-dependent minus-end-directed motor complex dynein-dynactin. A recent study with epithelial cells suggested that Ad5 was transported to the nucleus and expressed its genes independently of a microtubule network. To clarify the mechanisms by which Ad2 and, as an independent control, HSV-1 were targeted to the nucleus, we treated epithelial cells with nocodazole (NOC) to depolymerize microtubules and measured viral gene expression at different times and multiplicities of infections. Our results indicate that in NOC-treated cells, viral transgene expression was significantly reduced at up to 48 h postinfection (p.i.). A quantitative analysis of subcellular capsid localization indicated that NOC blocked the nuclear targeting of Ad2 and also HSV-1 by more than 90% at up to 7 h p.i. About 10% of the incoming Texas Red-coupled Ad2 (Ad2-TR) was enriched at the nucleus in microtubule-depleted cells at 5 h p.i. This result is consistent with earlier observations that Ad2-TR capsids move randomly in NOC-treated cells at less than 0.1 μm/s and over distances of less than 5 μm, characteristic of Brownian motion. We conclude that fluorophore-tagged Ad2 and HSV-1 particles are infectious and that microtubules play a prominent role in efficient nuclear targeting during entry and gene expression of species C Ads and HSV-1.
Large-Scale, pH-Dependent, Quaternary Structure Changes in an RNA Virus Capsid Are Reversible in the Absence of Subunit Autoproteolysis
Authors: Taylor Derek J. , Krishna Neel K. , Canady Mary A. , Schneemann Anette , Johnson John E. 
Published: September 2002

ABSTRACT

The assembly and maturation of the coat protein of a T=4, nonenveloped, single-stranded RNA virus,
Nudaurelia capensis
ω
virus
(NωV), was examined by using a recombinant baculovirus expression system. At pH 7.6, the coat protein assembles into a stable particle called the procapsid, which is 450 Å in diameter and porous. Lowering the pH to 5.0 leads to a concerted reorganization of the subunits into a 410-Å-diameter particle called the capsid, which has no obvious pores. This conformational change is rapid but reversible until slow, autoproteolytic cleavage occurs in at least 15% of the subunits at the lower pH. In this report, we show that expression of subunits with replacement of Asn-570, which is at the cleavage site, with Thr results in assembly of particles with expected morphology but that are cleavage defective. The conformational change from procapsid to capsid is reversible in N570T mutant virus-like particles, in contrast to wild-type particles, which are locked into the capsid conformation after cleavage of the coat protein. The reexpanded procapsids display slightly different properties than the original procapsid, suggesting hysteretic effects. Because of the stability of the procapsid under near-neutral conditions and the reversible properties of the cleavage-defective mutant, NωV provides an excellent model for the study of pH-induced conformational changes in macromolecular assemblies. Here, we identify the relationship between cleavage and the conformational change and propose a pH-dependent helix-coil transition that may be responsible for the structural rearrangement in NωV.
Decreased Levels of Recent Thymic Emigrants in Peripheral Blood of Simian Immunodeficiency Virus-Infected Macaques Correlate with Alterations within the Thymus
Authors: Sodora Donald L. , Milush Jeffrey M. , Ware Felecia , Wozniakowski Aneta , Montgomery Lisa , McClure Harold M. , Lackner Andrew A. , Marthas Marta , Hirsch Vanessa , Johnson R. Paul , Douek Daniel C. , Koup Richard A. 
Published: September 2002

ABSTRACTThe thymus is responsible for de novo production of CD4+and CD8+T cells and therefore is essential for T-cell renewal. The goal of this study was to assess the impact of simian immunodeficiency virus (SIV) infection on the production of T cells by the thymus. Levels of recent thymic emigrants within the peripheral blood were assessed through quantification of macaque T-cell receptor excision circles (TREC). Comparison of SIV-infected macaques (n= 15) to uninfected macaques (n= 23) revealed stable or increased TREC levels at 20 to 34 weeks postinfection. Further assessment of SIV-infected macaques (n= 4) determined that TREC levels decreased between 24 and 48 weeks postinfection. Through the assessment of longitudinal time points in three additional SIVmac239-infected macaques, the SIV infection was divided into two distinct phases. During phase 1 (16 to 30 weeks), TREC levels remained stable or increased within both the CD4 and CD8 T-cell populations. During phase 2 (after 16 to 30 weeks), TREC levels declined in both T-cell populations. As has been described for human immunodeficiency virus (HIV)-infected patients, this decline in TREC levels did at times correlate with an increased level of T-cell proliferation (Ki67+cells). However, not all TREC decreases could be attributed to increased T-cell proliferation. Further evidence for thymic dysfunction was observed directly in a SIVmac239-infected macaque that succumbed to simian AIDS at 65 weeks postinfection. The thymus of this macaque contained an increased number of memory/effector CD8+T cells and an increased level of apoptotic cells. In summary, reduced levels of TREC can be observed beginning at 16 to 30 weeks post-SIV infection and correlate with changes indicative of dysfunction within the thymic tissue. SIV infection of macaques will be a useful model system to elucidate the mechanisms responsible for the thymic dysfunction observed in HIV-infected patients.
The African Swine Fever Virus Protein j4R Binds to the Alpha Chain of Nascent Polypeptide-Associated Complex
Authors: Goatley Lynnette C. , Twigg Steve R. F. , Miskin James E. , Monaghan Paul , St-Arnaud René , Smith Geoffrey L. , Dixon Linda K. 
Published: September 2002

ABSTRACT
The African swine fever virus (ASFV) j4R protein is expressed late during the virus replication cycle and is present in both the nucleus and the cytoplasm of infected cells. By using the yeast two-hybrid system, direct binding, and coprecipitation from cells, we showed that the j4R protein binds to the alpha chain of nascent polypeptide-associated complex (αNAC). Confocal microscopy indicated that a proportion of j4R and αNAC interact in areas close to the plasma membrane, as well as through the cytoplasm in cells. In vitro binding studies suggested that binding of j4R to αNAC did not interfere with the binding of α- and βNAC subunits (the BTF3 transcription factor).
UBIQUITOUS INFORMATION AGENTS
Authors: BERGENTI FEDERICO , POGGI AGOSTINO 
Published: September 2002

Ubiquity is one of the most important keyword of the next generation software systems. We want our systems to follow users wherever they go, and we want our systems to extend their reach to the telephony world and to its base of several hundred million users. The ever-increasing diffusion of handy appliances, e.g. palmtops and cellular phones, is familiarizing people with the use of computers for their everyday job and, more impressively, for their everyday life. This suggests that the market of software systems for mobile applications will increase dramatically in the near future.
PROBLEM-SOLVING METHODS AND COOPERATIVE INFORMATION AGENTS
Authors: GOMEZ MARIO , PLAZA ENRIC , ABASOLO CHEMA 
Published: September 2002

Cooperative Information Agents and modern information systems in general have to access large amounts of information distributed across multiple heterogeneous sources. A great challenge of such systems is to evolve by adding new information sources or adapting the existing components for different domain knowledge. We propose the [Formula: see text] framework as a methodology to build Information Agents by reusing a library of problem-solving components that are defined in a domain-independent manner. Moreover, the [Formula: see text] language is used as an Agent Capability Description Language (ACDL) suitable to configure an agent-based application. From this approach, a new application is built by linking the components of the library with a particular domain and a collection of heterogeneous information sources. Adaptability and dynamic configuration of such a system is achieved by reasoning about the [Formula: see text] specification of the agent capabilities. Independence of the domain and semantic interoperability are achieved by using ontologies and bridges (mappings between ontologies), while independence from the information sources is based again in the use of ontologies to overcome semantic heterogeneity and wrappers to achieve syntactic interoperability.
COOPERATIVE INFORMATION AGENTS: BEST PAPERS OF CIA 2001 GUEST EDITORS' INTRODUCTION
Authors: KLUSCH MATTHIAS , ZAMBONELLI FRANCO 
Published: September 2002

This special issues contains a selection of the best papers presented at the Fifth International Workshop on Cooperative Information Agents, held in Modena, Italy, September 6–8, 2001. Information agent technology has become one of the major key technologies for the Internet and the World Wide Web.2,5 It mainly emerged as a response to the challenges of cyberspace from both the technological and human user perspective. Development of information agents requires expertise from different research disciplines such as Artificial Intelligence (AI), advanced databases and knowledge base systems, distributed information systems, information retrieval, and Human Computer Interaction (HCI). The Fifth International Workshop on Cooperative Information Agents (CIA) continued the tradition by capturing the intrinsic interdisciplinary nature of the above research area by calling for contributions from different research communities, and by promoting open and informative discussions on all related topics. In keeping with tradition, the workshop featured a sequence of regular and invited talks of excellence given by leading experts in the field. As a novelty, the CIA 2001 workshop issued two awards for best paper and best system innovation to acknowledge particularly significant advances in research and development respectively, in the area of information agents. An extended version of the awarded best paper authored by Onn Shehory is included in this special issue.
Psychiatric trainees' experiences of, and reactions to, patient suicide
Authors: Dewar Ian , Eagles John , Klein Susan , Gray Nicola , Alexander David 
Published: September 2002

Aims and MethodThis survey is the first UK study of trainee psychiatrists' experiences of patient suicide. One hundred and three senior and specialist registrars in psychiatry working in Scotland completed the questionnaire, representing an 81% response rate.ResultsAlmost half (47%) had experienced suicide of a patient in their care or otherwise known to them (e.g. through on-call experiences). Although only 28% recalled previous training on issues to consider following a suicide, all of these doctors found this to be of value. Many reported that patient suicide had a deleterious impact on their personal and professional lives. The most valuable supports were informal, and the trainees' consultants appeared particularly well placed to offer support and advice.Clinical ImplicationsMany trainee psychiatrists experience the suicide of a patient. Such experiences have potential for adverse effects on doctors' professional practice and personal life. Greater availability of training in this area would allow trainees to be better prepared for such an event. Trainees' consultants have a pivotal role to play in providing appropriate advice and support after a patient suicide.
Size does matter
Authors: Carson Alan J. , Shah Prem 
Published: September 2002

Aims and MethodsTo examine antidepressant prescribing in a general medical hospital in the UK. The data used were extracted from a prescription database prospectively maintained by the hospital pharmacy. All prescriptions of antidepressants over a five-year period, both new and continuation, were recorded.ResultsDuring the study period there were 2037 prescriptions of tricyclic antidepressants. Only 18% of these prescriptions were at conventional therapeutic doses. This compared with 773 prescriptions of selective serotonin reuptake inhibitors, 70% of which were at conventional therapeutic doses. It is shown that antidepressants were prescribed at a dose in accordance with the smallest tablet size available.Clinical ImplicationsWe suggest that reformulation of tablets to allow one tablet daily prescribing may lead to improved antidepressant prescribing.
What trainees and trainers think about supervision
Authors: Sembhi Sati , Livingston Gill 
Published: September 2002

Aims and MethodA confidential questionnaire was mailed to all trainers and trainees on the UCL/North London rotation (n=127), asking about the content and ways of improving supervision.ResultsSeventy-six per cent of trainees received regular, timetabled supervision. Ninety-four per cent of trainees felt it was a good idea, but identified improvements, including more planning, setting an agenda and flexibility. There were differences between reports from trainers and trainees regarding the content of supervision. Respondents' comments are included.Clinical ImplicationsAlthough supervision is popular and widely practised, this survey suggests that it is still not universally practised despite College stipulations. The content of supervision could be broadened to include more non-clinical matters such as teaching and careers guidance.
Towards the development of a reciprocal liaison service
Authors: Davies Mark 
Published: September 2002

Aims and MethodThe aim of this survey was to determine attitudes among consultants in different specialities towards the development of a reciprocal liaison service providing access for psychiatric patients to medical and surgical liaison services equal to the access of medical and surgical patients to psychiatric liaison services. All medical, surgical and psychiatric consultants in a district health service were surveyed, with a total response rate of 48%.ResultsThe mean number of medical and surgical patients requiring a psychiatric liaison service was 6%. The mean number of psychiatric patients requiring medical and surgical liaison services was 11%. Ratings overall for various components of the two types of liaison service were generally similar, with acute assessments and follow-up being given a high priority for both types.Clinical ImplicationsAs liaison services are developed, the notion of equity of access for all patients is paramount. Commissioning of such services should thereby specify the reciprocal nature of development. This survey shows that generally there is a positive attitude to the development of such a service.