bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cloning of idiotype immunoglobulin genes in B cell lymphomas by anchored PCR and production of individual recombinant idiotype vaccines in Escherichia coli
Authors: Bertinetti Cristina , Simon Frederic , Zirlik Katja , Heining‐Mikesch Kristina , Pfeifer Dietmar , Osterroth Frank , Rosenthal Felicia M. , Veelken Hendrik 
Published: July 2006

Abstract:  Objectives: Individual immunoglobulins expressed by B‐cell lymphomas represent tumor‐specific antigens (‘idiotypes’). Immunization with idiotype in follicular lymphoma patients may induce specific immune responses, sustained progression‐free survival, and disappearance of minimal residual disease. Manufacturing of idiotype vaccines has mostly relied on heterohybridomas established from viable lymphoma cells. This paper describes the feasibility of production of GMP‐grade idiotype vaccines as recombinant Fab fragments in Escherichia coli. Methods: IgH and IgL transcripts were analyzed by anchored PCR from 106 lymphoma and nine control biopsies. Lymphoma‐derived V segments were inserted into prokaryotic expression plasmids. Recombinant idiotype Fab fragments were expressed in E. coli in a fermentation system. Results: Idiotype IgH and IgL transcripts were identified in 95% of 106 lymphoma biopsies according to stringent clonality criteria. Large‐scale idiotype expression was successful in 69 of 78 cases (89%) and yielded a median of 17 mg (range: 1.2–250 mg) recombinant Fab protein. After affinity chromatography, median vaccine purity was 99% heterodimeric Fab protein (range: 72–100%). Bacterial protein contamination was detectable in one vaccine only. Fab proteins with IgL lambda chains had a tendency for inferior yield and lesser purity than κ‐type Fabs. Among other structural idiotype features (isotype, V family usage, somatic hypermutation pattern, novel glycosylation sites, CDR III net charge), no consistent influences on Fab yield or purity were detected. Conclusions: Anchored PCR cloning and subsequent protein expression in E. coli provides a reliable technological basis for clinical idiotype vaccination trials.
Dynamics of compact object clusters: a post-Newtonian study
Authors: Kupi Gábor , Amaro-Seoane Pau , Spurzem Rainer 
Published: July 2006

Abstract
Compact object clusters are likely to exist in the centres of some galaxies because of mass segregation. The high densities and velocities reached in them need a better understanding. The formation of binaries and their subsequent merging by gravitational radiation emission are important to the evolution of such clusters. We address the evolution of such a system in a relativistic regime. The recurrent mergers at high velocities create an object with a mass much larger than the average. For this purpose we modified the direct Nbody6++ code to include post-Newtonian effects on the force during two-body encounters. We adjusted the equations of motion to include for the first time the effects of both periastron shift and energy loss by emission of gravitational waves, and so to study the eventual decay and merger of radiating binaries. The method employed allows us to give here an accurate post-Newtonian description of the formation of a runaway compact object by successive mergers with surrounding particles, as well as the distribution of characteristic eccentricities in the events. This study should be envisaged as a first step towards a detailed, accurate study of possible gravitational wave sources, thanks to the combination of the direct Nbody numerical tool with the implementation of post-Newtonian terms.
EMERGENT SCENARIOS, SYNERGIES AND SUPPRESSIONS UNCOVERED WITHIN CONJOINT ANALYSIS*
Authors: GOFMAN ALEX 
Published: July 2006

ABSTRACT The article introduces two approaches to identify the direction and magnitude of interaction between concept elements in a conjoint analysis task. Both approaches use main effects experimental designs, permuted to create hundreds of new designs isomorphic to the original design structure. In the first approach, the scenario analysis creates a distinct mutually exclusive and exhaustive set of subgroups from concepts with specific elements, runs a dummy variable regression within each subgroup and identifies the effect of one element on the utilities of the others. In the second approach, the interaction analysis of complete set of raw data forces in the linear terms for the single elements, and then allows significant pair‐wise combinations to enter if they contribute significant additional predictability to the model. The two approaches identify the existence of and then measure the impact of one element on the performance of others (scenario), and the unexpected effect of mixing two concept elements (interaction analysis). The approach is illustrated by two case histories: communicating the sensory and refreshment benefits of an orange beverage, and identifying the features of a cookie.
OLFACTORY DECREMENTS AS A FUNCTION OF TWO NIGHTS OF SLEEP DEPRIVATION
Authors: MCBRIDE SHARON A. , BALKIN THOMAS J. , KAMIMORI GARY H. , KILLGORE WILLIAM D.S. 
Published: July 2006

ABSTRACT We recently reported that odor identification accuracy declined significantly following 24 h of continuous wakefulness. In the present study, we attempted to extend these findings by testing odor identification accuracy when the duration of wakefulness was more than doubled to over 52 h. The accuracy of odor identification decreased significantly following this period of extended wakefulness, although performance decrements were similar in magnitude to those previously reported following 24 h without sleep. These findings suggest that sleep loss impairs the ability to correctly identify common odors, but this effect does not appear to be exacerbated by additional sleep loss beyond the first 24 h.
Ixodes frontalis and avian tick‐related syndrome in the United Kingdom
Authors: Monks D. , Fisher M. , Forbes N. A. 
Published: July 2006

Objectives: This study aimed to characterise tick species responsible for avian tick infestations in the UK, to analyse various risk factors for tick‐related syndrome in tick‐infested birds and to test samples for the presence of certain tick‐transmitted pathogens. Methods: Ticks, blood, splenic tissue and tick attachment site tissue from birds with attached ticks were requested from veterinarians and wildlife sanctuaries around the UK. Ticks were identified according to standard keys, and samples were analysed via DNA PCR test for Borrelia burgdorferi sensu lato, Babesia species, Bartonella species and Ehrlichia species. Results:
Ixodes frontalis was the most commonly identified tick, and an association of adult female I frontalis with tick‐related syndrome in birds was demonstrated. Tick infestation was markedly seasonal. I frontalis was found on 32 species of birds. DNA PCR testing was uniformly negative. Of the birds known to have been treated, 75 per cent (nine of 12) survived. Clinical Significance: Tick‐related syndrome is a poorly understood syndrome, with sporadic distribution, both geographically and seasonally. This study confirms I frontalis as the most common cause of this syndrome in the UK and identifies some features of the tick life cycle in this country. The benefit of treatment in affected birds is highlighted. Risk factors for tick‐related syndrome are examined and preventive strategies discussed.
Feline osteoarthritis: a prospective study of 28 cases
Authors: Clarke S. P. , Bennett D. 
Published: July 2006

Objectives:To identify a cohort of cats with clinical osteoarthritis and to report on the clinical signs, the frequency of joints affected and the possible aetiopathogenesis within this population.Methods:Inclusion criteria for this prospective study were presence of historical evidence and/or clinical signs of osteoarthritis, together with radiographic evidence of osteoarthritis. Patients showed clinical improvement within four weeks of analgesic administration and were free from other disease processes, which might explain the clinical signs and/or their response to analgesia.Results:Twenty‐eight cases were included in the cohort. The elbow (45 per cent) and the hip (38 per cent) were the most frequently affected joints. Seventy‐one per cent of cases had primary/idiopathic aetiology. Alterations in both the ability to jump (71 per cent) and the height (67 per cent) of jump (lifestyle changes) were the most frequent signs of disease. Sixty‐one per cent of owners felt that their pet had made a marked improvement following administration of an analgesic/anti‐inflammatory drug. There were statistically significant improvements in the ability to jump (P<0·001), the height of jump (P<0·001), lameness (P=0·03), stiff gait (P=0·04) and the activity level (P=0·02) when compared with the start and the end of the study period.ClinicalSignificance:Osteoarthritis is a clinical problem in cats, but overt lameness is not the most common clinical feature.
A Conserved Gly436-Trp-Leu-Ala-Gly-Leu-Phe-Tyr Motif in Hepatitis C Virus Glycoprotein E2 Is a Determinant of CD81 Binding and Viral Entry
Authors: Drummer Heidi E. , Boo Irene , Maerz Anne L. , Poumbourios Pantelis 
Published: July 2006

ABSTRACTThe hepatitis C virus (HCV) glycoproteins E1 and E2 form a heterodimer that mediates CD81 receptor binding and viral entry. In this study, we used site-directed mutagenesis to examine the functional role of a conserved G436WLAGLFY motif of E2. The mutants could be placed into two groups based on the ability of mature virion-incorporated E1E2 to bind the large extracellular loop (LEL) of CD81 versus the ability to mediate cellular entry of pseudotyped retroviral particles. Group 1 comprised E2 mutants where LEL binding ability largely correlated with viral entry ability, with conservative and nonconservative substitutions (W437 L/A, L438A, L441V/F, and F442A) inhibiting both functions. These data suggest that Trp-437, Leu-438, Leu-441, and Phe-442 directly interact with the LEL. Group 2 comprised E2 glycoproteins with more conservative substitutions that lacked LEL binding but retained between 20% and 60% of wild-type viral entry competence. The viral entry competence displayed by group 2 mutants was explained by residual binding by the E2 receptor binding domain to cellular full-length CD81. A subset of mutants maintained LEL binding ability in the context of intracellular E1E2 forms, but this function was largely lost in virion-incorporated glycoproteins. These data suggest that the CD81 binding site undergoes a conformational transition during glycoprotein maturation through the secretory pathway. The G436P mutant was an outlier, retaining near-wild-type levels of CD81 binding but lacking significant viral entry ability. These findings indicate that the G436WLAGLFY motif of E2 functions in CD81 binding and in pre- or post-CD81-dependent stages of viral entry.
Compensatory Substitutions Restore Normal Core Assembly in Simian Immunodeficiency Virus Isolates with Gag Epitope Cytotoxic T-Lymphocyte Escape Mutations
Authors: Yeh Wendy W. , Cale Evan M. , Jaru-Ampornpan Pimkwan , Lord Carol I. , Peyerl Fred W. , Letvin Norman L. 
Published: July 2006

ABSTRACTThe evolution of human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) as they replicate in infected individuals reflects a balance between the pressure on the virus to mutate away from recognition by dominant epitope-specific cytotoxic T lymphocytes (CTL) and the structural constraints on the virus' ability to mutate. To gain a further understanding of the strategies employed by these viruses to maintain replication competency in the face of the intense selection pressure exerted by CTL, we have examined the replication fitness and morphological ramifications of a dominant epitope mutation and associated flanking amino acid substitutions on the capsid protein (CA) of SIV/simian-human immunodeficiency virus (SHIV). We show that a residue 2 mutation in the immunodominant p11C, C-M epitope (T47I) of SIV/SHIV not only decreased CA protein expression and viral replication, but it also blocked CA assembly in vitro and virion core condensation in vivo. However, these defects were restored by the introduction of upstream I26V and/or downstream I71V substitutions in CA. These findings demonstrate how flanking compensatory amino acid substitutions can facilitate viral escape from a dominant epitope-specific CTL response through the effects of these associated mutations on the structural integrity of SIV/SHIV.
Psittacid Herpesvirus 1 and Infectious Laryngotracheitis Virus: Comparative Genome Sequence Analysis of Two Avian Alphaherpesviruses
Authors: Thureen Dean R. , Keeler Calvin L. 
Published: July 2006

ABSTRACT

Psittacid herpesvirus 1 (PsHV-1) is the causative agent of Pacheco's disease, an acute, highly contagious, and potentially lethal respiratory herpesvirus infection in psittacine birds, while infectious laryngotracheitis virus (ILTV) is a highly contagious and economically significant avian herpesvirus which is responsible for an acute respiratory disease limited to galliform birds. The complete genome sequence of PsHV-1 has been determined and compared to the ILTV sequence, assembled from published data. The PsHV-1 and ILTV genomes exhibit similar structural characteristics and are 163,025 bp and 148,665 bp in length, respectively. The PsHV-1 genome contains 73 predicted open reading frames (ORFs), while the ILTV genome contains 77 predicted ORFs. Both genomes contain an inversion in the unique long region similar to that observed in pseudorabies virus. PsHV-1 is closely related to ILTV, and it is proposed that it be assigned to the
Iltovirus
genus. These two avian herpesviruses represent a phylogenetically unique clade of alphaherpesviruses that are distinct from the Marek's disease-like viruses (
Mardivirus
). The determination of the complete genomic nucleotide sequences of PsHV-1 and ILTV provides a tool for further comparative and functional analysis of this unique class of avian alphaherpesviruses.
A 38-Amino-Acid Sequence Encompassing the Arm Domain of the
Cucumber Necrosis Virus
Coat Protein Functions as a Chloroplast Transit Peptide in Infected Plants
Authors: Xiang Yu , Kakani Kishore , Reade Ron , Hui Elizabeth , Rochon D'Ann 
Published: July 2006

ABSTRACT

Experiments to determine the subcellular location of the coat protein (CP) of the tombusvirus
Cucumber necrosis virus
(CNV) have been conducted. By confocal microscopy, it was found that an agroinfiltrated CNV CP-green fluorescent protein (GFP) fusion targets chloroplasts in
Nicotiana benthamiana
leaves and that a 38-amino-acid (aa) region that includes the complete CP arm region plus the first 4 amino acids of the shell domain are sufficient for targeting. Western blot analyses of purified and fractionated chloroplasts showed that the 38-aa region directs import to the chloroplast stroma, suggesting that the CNV arm can function as a chloroplast transit peptide (TP) in plants. Several features of the 38-aa region are similar to features typical of chloroplast TPs, including (i) the presence of an alanine-rich uncharged region near the N terminus, followed by a short region rich in basic amino acids; (ii) a conserved chloroplast TP phosphorylation motif; (iii) the requirement that the CNV 38-aa sequence be present at the amino terminus of the imported protein; and (iv) specific proteolytic cleavage upon import into the chloroplast stroma. In addition, a region just downstream of the 38-aa sequence contains a 14-3-3 binding motif, suggesting that chloroplast targeting requires 14-3-3 binding, as has been suggested for cellular proteins that are targeted to chloroplasts. Chloroplasts of CNV-infected plants were found to contain CNV CP, but only the shell and protruding domain regions were present, indicating that CNV CP enters chloroplasts during infection and that proteolytic cleavage occurs as predicted from agroinfiltration studies. We also found that particles of a CNV CP mutant deficient in externalization of the arm region have a reduced ability to establish infection. The potential biological significance of these findings is discussed.
Oncogenic Activity of Epstein-Barr Virus Latent Membrane Protein 1 (LMP-1) Is Down-Regulated by Lytic LMP-1
Authors: Pandya Jyotsna , Walling Dennis M. 
Published: July 2006

ABSTRACT
The Epstein-Barr virus (EBV) is an oncogenic human herpesvirus. EBV latent membrane protein 1 (LMP-1) is a viral oncogene that manifests its oncogenic phenotype through activation of cellular signaling pathways involved in cell growth, survival, differentiation, and transformation. Lytic LMP-1 (lyLMP-1) is a related EBV gene without oncogenic properties. The lyLMP-1 gene is found in 60% of the EBV strains circulating in nature, but it is not found in EBV strains associated with nasopharyngeal carcinoma. We recently demonstrated that lyLMP-1 down-regulates the half-life of LMP-1 in epithelial cells. Therefore in this study, we tested the hypothesis that lyLMP-1 concomitantly down-regulates LMP-1 oncogenic activity. The results demonstrated that lyLMP-1 inhibits LMP-1-mediated intracellular signaling activation, epithelial cell growth and survival, and fibroblast cell transformation in a dose-dependent manner. Lytic LMP-1 manifested this effect through the promotion of LMP-1 degradation and a reduction in the expressed quantity of LMP-1. Thus, lyLMP-1 functions as a posttranslational negative regulator of LMP-1 oncogenesis. These results support a model of EBV-associated epithelial oncogenesis in which lyLMP-1 may act in vivo to reduce the risk of LMP-1-mediated transformation and is therefore subjected to negative selection in nasopharyngeal carcinoma pathogenesis.
Contribution of Vpu, Env, and Nef to CD4 Down-Modulation and Resistance of Human Immunodeficiency Virus Type 1-Infected T Cells to Superinfection
Authors: Wildum Steffen , Schindler Michael , Münch Jan , Kirchhoff Frank 
Published: July 2006

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) utilizes Vpu, Env, and Nef to down-modulate its primary CD4 receptor from the cell surface, and this function seems to be critical for the pathogenesis of AIDS. The physiological relevance of CD4 down-modulation, however, is currently not well understood. In the present study, we analyzed the kinetics of CD4 down-modulation and the susceptibility of HIV-1-infected T cells to superinfection using proviral HIV-1 constructs containing individual and combined defects in
vpu
,
env
, and
nef
and expressing red or green fluorescent proteins. T cells infected with HIV-1 mutants containing functional
nef
genes expressed low surface levels of CD4 from the first moment that viral gene expression became detectable. In comparison, Vpu and Env had only minor to moderate effects on CD4 during later stages of infection. Consistent with these quantitative differences, Nef inhibited superinfection more efficiently than Vpu and Env. Notably,
nef
alleles from AIDS patients were more effective in preventing superinfection than those derived from a nonprogressor of HIV-1 infection. Our data suggest that protection against X4-tropic HIV-1 superinfection involves both CD4-independent and CD4-dependent mechanisms of HIV-1 Nef. X4 was effectively down-regulated by simian immunodeficiency virus and HIV-2 but not by HIV-1 Nef proteins. Thus, maximal protection seems to involve an as-yet-unknown mechanism that is independent of CD4 or coreceptor down-modulation. Finally, we demonstrate that superinfected primary T cells show enhanced levels of apoptosis. Accordingly, one reason that HIV-1 inhibits CD4 surface expression and superinfection is to prevent premature cell death in order to expand the period of effective virus production.
Epstein-Barr Virus Nuclear Antigen 2
trans
-Activates the Cellular Antiapoptotic
bfl-1
Gene by a CBF1/RBPJκ-Dependent Pathway
Authors: Pegman Pamela M. , Smith Sinéad M. , D'Souza Brendan N. , Loughran Sinéad T. , Maier Sabine , Kempkes Bettina , Cahill Paul A. , Simmons Matthew J. , Gélinas Céline , Walls Dermot 
Published: July 2006

ABSTRACT

The human herpesvirus Epstein-Barr virus (EBV) establishes latency and
promotes the long-term survival of its host B cell by targeting the
molecular machinery controlling cell fate decisions. The cellular
antiapoptotic
bfl-1
gene confers protection from apoptosis
under conditions of growth factor deprivation when expressed
ectopically in an EBV-negative Burkitt's lymphoma-derived cell line (B.
D'Souza, M. Rowe, and D. Walls, J. Virol.
74:6652-6658, 2000), and the EBV latent membrane protein 1
(LMP1) and its cellular functional homologue CD40 can both drive
bfl-1
via an NF-κB-dependent enhancer element in the
bfl-1
promoter (B. N. D'Souza, L. C.
Edelstein, P. M. Pegman, S. M. Smith, S.
T. Loughran, A. Clarke, A. Mehl, M. Rowe, C. Gélinas, and D.
Walls, J. Virol. 78:1800-1816, 2004). Here we show
that the EBV nuclear antigen 2 (EBNA2) also upregulates
bfl-1
.
EBNA2
trans
-activation of
bfl-1
requires CBF1 (or
RBP-Jκ), a nuclear component of the Notch signaling pathway,
and there is an essential role for a core consensus CBF1-binding site
on the
bfl-1
promoter.
trans
-activation is dependent
on the EBNA2-CBF1 interaction, is modulated by other EBV gene products
known to interact with the CBF1 corepressor complex, and does not
involve activation of NF-κB.
bfl-1
expression is
induced and maintained at high levels by the EBV growth program in a
lymphoblastoid cell line, and withdrawal of either EBNA2 or LMP1 does
not lead to a reduction in
bfl-1
mRNA levels in this context,
whereas the simultaneous loss of both EBV proteins results in a major
decrease in
bfl-1
expression. These findings are relevant to
our understanding of EBV persistence, its role in malignant disease,
and the B-cell developmental
process.
Isolation and Characterization of Monoclonal Antibodies Which Neutralize Human Metapneumovirus In Vitro and In Vivo
Authors: Ulbrandt Nancy D. , Ji Hong , Patel Nita K. , Riggs Jeffrey M. , Brewah Yambasu A. , Ready Shannon , Donacki Nanci E. , Folliot Karyn , Barnes Arnita S. , Senthil Kannaki , Wilson Susan , Chen Mingzhong , Clarke Lori , MacPhail Mia , Li Jia , Woods Robert M. , Coelingh Kathy , Reed Jennifer L. , McCarthy Michael P. , Pfarr David S. , Osterhaus Albert D. M. E. , Fouchier Ron A. M. , Kiener Peter A. , Suzich JoAnn A. 
Published: July 2006

ABSTRACT

Human metapneumovirus (hMPV) is a recently described member of the
Paramyxoviridae
family/
Pneumovirinae
subfamily and
shares many common features with respiratory syncytial virus (RSV),
another member of the same subfamily. hMPV causes respiratory tract
illnesses that, similar to human RSV, occur predominantly during the
winter months and have symptoms that range from mild to severe cough,
bronchiolitis, and pneumonia. Like RSV, the hMPV virus can be
subdivided into two genetic subgroups, A and B. With RSV, a single
monoclonal antibody directed at the fusion (F) protein can prevent
severe lower respiratory tract RSV infection. Because of the high level
of sequence conservation of the F protein across all the hMPV
subgroups, this protein is likely to be the preferred antigenic target
for the generation of cross-subgroup neutralizing antibodies. Here we
describe the generation of a panel of neutralizing monoclonal
antibodies that bind to the hMPV F protein. A subset of these
antibodies has the ability to neutralize prototypic strains of both the
A and B hMPV subgroups in vitro. Two of these antibodies exhibited
high-affinity binding to the F protein and were shown to protect
hamsters against infection with hMPV. The data suggest that a
monoclonal antibody could be used prophylactically to prevent lower
respiratory tract disease caused by
hMPV.