bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recognition patterns ofNeospora caninumtachyzoite antigens by bovine IgG at different IFAT titres
Authors: Okeoma C. M. , Williamson N. B. , Pomroy W. E. , Stowell K. M. 
Published: September 2004

SUMMARYThis study describes qualitative and quantitative antibody response in cows naturally infected withNeospora caninum.The study was carried out with 269 serum samples obtained from 24 cows over a period of 15 weeks. Prior to sample collection, the cows were tested with ELISA. The 269 samples were screened with IFAT and categorized into seven IFAT titre groups (< 1 : 80, 1 : 80, 1 : 200, 1 : 600, 1 : 1000, 1 : 2000, > 1 : 2000). The samples were finally analysed by Western blotting. Seven immunodominant antigens (∼18‐, ∼25‐, ∼33‐, ∼35–36‐, ∼45–46‐, ∼47‐, ∼60–62 kDa) and five minor antigens (∼25, ∼51, ∼64, ∼77, ∼116 kDa) were recognized by cow sera. The recognition of ∼46 kDa antigen by cow sera was common to samples with IFAT titre 1 : 80 and above. Another common antigen was the ∼18 kDa antigen, which was recognized by samples with IFAT titre 1 : 200 and above. The most remarkable observation was the presence of the 45–46 kDa, the 77 kDa, and absence of the 18 kDa antigenic bands in samples with IFAT titre 1 : 80. This observation was consistent even in the face of fluctuating antibody titre where serum antibody titres from an animal exceeded then failed to reach 1 : 80. Antibody fluctuation was observed across all cows (pregnant and aborted) with no discernible fluctuation pattern. However, the fluctuation in antibody titre observed appeared to be most remarkable in initially ELISA‐negative pregnant cows, and to a lesser extent in ELISA‐positive pregnant cows, and ELISA‐positive aborted cows. Although there was fluctuation in antibody titre, the banding patterns ofN. caninumtachyzoite antigens by cows within the same IFAT titre group remained similar.
Dental caries and salivary immunoglobulin A in Down syndrome children
Authors: Lee SR , Kwon HK , Song KB , Choi YH 
Published: September 2004

Objectives:  This study investigated the relationship between dental caries and the salivary Streptococcus mutans specific antibodies in Down syndrome children.Methods:  Nineteen children with Down syndrome and 41 normal children aged 8−17 years were selected. The oral health status (dental caries experience, pit and fissure depth, dental arch space, and Simplified Oral Hygiene Index) was examined and unstimulated saliva was collected. The total salivary immunoglobulin A (IgA) and S. mutans specific salivary IgA concentrations were measured using ELISA.Results:  The decayed and filled surface index of the deciduous teeth, and the decayed, missing, and filled surfaces index of the permanent teeth in Down syndrome children were significantly lower compared to those in normal children. The salivary S. mutans (serotype g and c) specific IgA concentrations were significantly higher in Down syndrome children than in the normal children. There was no significant difference in the tooth characteristics and oral hygiene between the two groups.Conclusions:  The low caries prevalence in Down syndrome children appears to be due to immune protection caused by the elevated salivary S. mutans specific IgA concentrations.
Beauty: soul or surface?
Authors: Fatović‐Ferenčić S , Dürrigl M‐A , Holubar K 
Published: September 2004

SummaryIt is proposed that beauty can be external or internal or both. External or physical beauty is immediately visible. Internal or inner beauty is not always immediately visible. Ideally both types of beauty are connected and spring from one another.The opposite situation, in which only one exists while the other is suppressed, is exemplified in this paper, using a tale from 19th century Croatian literature as a model. The main character is Tena. Initially physically beautiful, she is later disfigured by smallpox. Consequently her psyche metamorphoses through illness, distress and destitution, and she discovers an inner self that allows her full personality to develop. The story of Tena illustrates how love based only on outer appearance may end in unhappiness. Perhaps true love depends more on soul than surface.Endless quests for external beauty are part of medical practice today more then ever before. Skin is the paradigm of this. The dermatologist needs many clinical skills, including an understanding of psychology, when addressing skin‐related problems – appearance‐related problems in particular. Sometimes the humanities (e.g. literature, poetry, etc.), may help broaden our perspective of such a complex phenomenon as beauty.
Synthesis and Characterization of a Native, Oligomeric Form of Recombinant Severe Acute Respiratory Syndrome Coronavirus Spike Glycoprotein
Authors: Song Hyun Chul , Seo Mi-Young , Stadler Konrad , Yoo Byoung J. , Choo Qui-Lim , Coates Stephen R. , Uematsu Yasushi , Harada Takashi , Greer Catherine E. , Polo John M. , Pileri Piero , Eickmann Markus , Rappuoli Rino , Abrignani Sergio , Houghton Michael , Han Jang H. 
Published: September 2004

ABSTRACT

We have expressed and characterized the severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein in cDNA-transfected mammalian cells. The full-length spike protein (S) was newly synthesized as an endoglycosidase H (endo H)-sensitive glycoprotein (gp170) that is further modified into an endo H-resistant glycoprotein (gp180) in the Golgi apparatus. No substantial proteolytic cleavage of S was observed, suggesting that S is not processed into head (S1) and stalk (S2) domains as observed for certain other coronaviruses. While the expressed full-length S glycoprotein was exclusively cell associated, a truncation of S by excluding the C-terminal transmembrane and cytoplasmic tail domains resulted in the expression of an endoplasmic reticulum-localized glycoprotein (gp160) as well as a Golgi-specific form (gp170) which was ultimately secreted into the cell culture medium. Chemical cross-linking, thermal denaturation, and size fractionation analyses suggested that the full-length S glycoprotein of SARS-CoV forms a higher order structure of ∼500 kDa, which is consistent with it being an S homotrimer. The latter was also observed in purified virions. The intracellular form of the C-terminally truncated S protein (but not the secreted form) also forms trimers, but with much less efficiency than full-length S. Deglycosylation of the full-length homotrimer with peptide
N-
glycosidase-F under native conditions abolished recognition of the protein by virus-neutralizing antisera raised against purified virions, suggesting the importance of the carbohydrate in the correct folding of the S protein. These data should aid in the design of recombinant vaccine antigens to prevent the spread of this emerging pathogen.
Human T-Cell Leukemia Virus Type 1 (HTLV-1) and HTLV-2 Tax Oncoproteins Modulate Cell Cycle Progression and Apoptosis
Authors: Sieburg Michelle , Tripp Adam , Ma Jung-Woo , Feuer Gerold 
Published: September 2004

ABSTRACTHuman T-cell leukemia virus type 1 (HTLV-1) is the etiologic agent of adult T-cell leukemia and lymphoma, an aggressive clonal malignancy of human CD4-bearing T lymphocytes. HTLV-2, although highly related to HTLV-1 at the molecular level, has not been conclusively linked to development of lymphoproliferative disorders. Differences between the biological activities of the respectivetaxgene products (Tax1 and Tax2) may be one factor which accounts for the differential pathogenicities associated with infection. To develop an in vitro model to investigate and compare the effects of constitutive expression of Tax1 and Tax2, Jurkat T-cell lines were infected with lentivirus vectors encoding Tax1 and Tax2 in conjunction with green fluorescent protein, and stably transduced clonal cell lines were generated by serial dilution in the absence of drug selection. Jurkat cells that constitutively express Tax1 and Tax2 (Tax1/Jurkat and Tax2/Jurkat, respectively) showed notably reduced kinetics of cellular replication, and Tax1 inhibited cellular replication to a higher degree in comparison to Tax2. Tax1 markedly activated transcription from the cdk inhibitor p21cip1/waf1promoter in comparison to Tax2, suggesting that upregulation of p21cip1/waf1may account for the differential inhibition of cellular replication kinetics displayed by Tax1/Jurkat and Tax2/Jurkat cells. The presence of binucleated and multinucleated cells, reminiscent of large lymphocytes with cleaved or cerebriform nuclei often seen in HTLV-1- and -2-seropositive patients, was noted in cultures expressing Tax1 and Tax2. Although Tax1 and Tax2 expression mediated elevated resistance to apoptosis in Jurkat cells after serum deprivation, Tax1 was unique in protection from apoptosis after exposure to camptothecin and etoposide, inhibitors of topoisomerase I and II, respectively. Characterization of the unique phenotypes displayed by Tax1 and Tax2 in vitro will provide information as to the relative roles of these oncoproteins and their contribution to HTLV-1 and -2 pathogenesis in vivo.
Human Macrophages, but Not Dendritic Cells, Are Activated and Produce Alpha/Beta Interferons in Response to Mopeia Virus Infection
Authors: Pannetier Delphine , Faure Caroline , Georges-Courbot Marie-Claude , Deubel Vincent , Baize Sylvain 
Published: September 2004

ABSTRACT

Lassa virus
(LV) and
Mopeia virus
(MV) are closely related members of the
Arenavirus
genus, sharing 75% amino acid sequence identity. However, LV causes hemorrhagic fever in humans and nonhuman primates, whereas MV cannot induce disease. We have previously shown that antigen-presenting cells (APC)—macrophages (MP) and dendritic cells (DC)—sustain high replication rates of LV but are not activated, suggesting that they play a role in the immunosuppression observed in severe cases of Lassa fever. Here, we infected human APC with MV and analyzed the cellular responses induced. MV infection was productive in MP and even more so in DC. Apoptosis was not induced in either cell type. Moreover, unlike DC, MP were early and strongly activated in response to MV, as shown by the increased surface expression of CD86, CD80, CD54, CD40, and HLA-abc and by the production of mRNA encoding alpha interferon (IFN-α), IFN-β, tumor necrosis factor alpha and interleukin-6. In addition, MV-infected MP produced less of the virus than DC, which was related to the fact that these cells secreted IFN-α. Thus, the strong activation of MP is probably a major event in the control of MV infection and may be involved in the induction of an adaptive immune response in infected hosts. These results may explain the difference in pathogenicity between LV and MV.
Assessing the Roles of Endogenous Retrovirus EAV-HP in Avian Leukosis Virus Subgroup J Emergence and Tolerance
Authors: Sacco Melanie A. , Howes Ken , Smith Lorraine P. , Nair Venugopal K. 
Published: September 2004

ABSTRACT

Avian leukosis virus (ALV) subgroup J is thought to have emerged through a recombination event between an unknown exogenous ALV and the endogenous retrovirus elements designated EAV-HP. All EAV-HP elements identified to date in the chicken genome show large deletions, including that of the entire
pol
gene. Here we report the identification of four segregating chicken EAV-HP proviruses with complete
pol
genes, one of which shows exceptionally high sequence identity and a close phylogenetic relationship with ALV-J with respect to the
env
gene. Embryonic expression of EAV-HP
env
has been suggested as a factor associated with immunological tolerance induction in a proportion of ALV-J-infected meat-type chickens. In support of this,
env
gene transcripts expressed from two of the four newly identified EAV-HP proviruses were demonstrated in chicken embryos. However, when ALV-J-infected outbred meat-type chickens were assessed, the presence of intact EAV-HP proviruses failed to directly correlate with ALV-J tolerance. This association was further examined using F
2
progeny of two inbred lines of layer chicken that differed in EAV-HP status and immunological responses to ALV-J. Immunological tolerance developed in a small proportion of F
2
progeny birds, reflecting the expected phenotypic ratio for inheritance of a double-recessive genotype; however, the status of tolerance did not show any direct correlation with the presence of the intact EAV-HP sequence. Nevertheless, identification of an intact chicken EAV-HP locus showing a uniquely close relationship to the ALV-J prototype clone HPRS-103 in the
env
region provides the strongest evidence of its contribution to the emergence of ALV-J by recombination.
Dynamics of Intermittent Viremia during Highly Active Antiretroviral Therapy in Patients Who Initiate Therapy during Chronic versus Acute and Early Human Immunodeficiency Virus Type 1 Infection
Authors: Di Mascio Michele , Markowitz Martin , Louie Michael , Hurley Arlene , Hogan Christine , Simon Viviana , Follmann Dean , Ho David D. , Perelson Alan S. 
Published: September 2004

ABSTRACT

The meaning of viral blips in human immunodeficiency virus type 1 (HIV-1)-infected patients treated with seemingly effective highly active antiretroviral therapy (HAART) is still controversial and under investigation. Blips might represent low-level ongoing viral replication in the presence of drug or simply release of virions from the latent reservoir. Patients treated early during HIV-1 infection are more likely to have a lower total body viral burden, a homogenous viral population, and preserved HIV-1-specific immune responses. Consequently, viral blips may be less frequent in them than in patients treated during chronic infection. To test this hypothesis, we compared the occurrence of viral blips in 76 acutely infected patients (primary HIV infection [PHI] group) who started therapy within 6 months of the onset of symptoms with that in 47 patients who started HAART therapy during chronic infection (chronic HIV infection [CHI] group). Viral blip frequency was approximately twofold higher in CHI patients (0.122 ± 0.12/viral load [VL] sample, mean ± standard deviation) than in PHI patients (0.066 ± 0.09/VL sample). However, in both groups, viral blip frequency did not increase with longer periods of observation. Also, no difference in viral blip frequency was observed between treatment subgroups, and the occurrence of a blip was not associated with a recent change in CD4
+
T-cell count. Finally, in PHI patients the VL set point was a significant predictor of blip frequency during treatment.
Genetic Bottlenecks Reduce Population Variation in an Experimental RNA Virus Population
Authors: Li Hongye , Roossinck Marilyn J. 
Published: September 2004

ABSTRACT

Genetic bottlenecks are stochastic events that limit genetic variation in a population and result in founding populations that can lead to genetic drift. Evidence of past genetic bottlenecks in numerous biological systems, from mammals to viruses, has been described. In this study, we used an artificial population of
Cucumber mosaic virus
consisting of 12 restriction enzyme marker-bearing mutants. This population was inoculated onto young leaves of tobacco plants and monitored throughout the course of systemic infection. We show here that the genetic variation in a defined population of an RNA virus is significantly, stochastically, and reproducibly reduced during the systemic infection process, providing clear evidence of a genetic bottleneck.
Tête à Tête of Tomato Yellow Leaf Curl Virus and Tomato Yellow Leaf Curl Sardinia Virus in Single Nuclei
Authors: Morilla Gabriel , Krenz Björn , Jeske Holger , Bejarano Eduardo R. , Wege Christina 
Published: September 2004

ABSTRACT

Since 1997 two distinct geminivirus species,
Tomato yellow leaf curl Sardinia virus
(TYLCSV) and
Tomato yellow leaf curl virus
(TYLCV), have caused a similar yellow leaf curl disease in tomato, coexisted in the fields of southern Spain, and very frequently doubly infected single plants. Tomatoes as well as experimental test plants (e.g.,
Nicotiana benthamiana
) showed enhanced symptoms upon mixed infections under greenhouse conditions. Viral DNA accumulated to a similar extent in singly and doubly infected plants. In situ tissue hybridization showed TYLCSV and TYLCV DNAs to be confined to the phloem in both hosts, irrespective of whether they were inoculated individually or in combination. The number of infected nuclei in singly or doubly infected plants was determined by in situ hybridization of purified nuclei. The percentage of nuclei containing viral DNA (i.e., 1.4% in tomato or 6% in
N. benthamiana
) was the same in plants infected with either TYLCSV, TYLCV, or both. In situ hybridization of doubly infected plants, with probes that discriminate between both DNAs, revealed that at least one-fifth of infected nuclei harbored DNAs from both virus species. Such a high number of coinfected nuclei may explain why recombination between different geminivirus DNAs occurs frequently. The impact of these findings for epidemiology and for resistance breeding concerning tomato yellow leaf curl diseases is discussed.
Temporal Modulation of an Autoprotease Is Crucial for Replication and Pathogenicity of an RNA Virus
Authors: Lackner T. , Müller A. , Pankraz A. , Becher P. , Thiel H.-J. , Gorbalenya A. E. , Tautz N. 
Published: September 2004

ABSTRACTPestiviruses belong to the familyFlaviviridae, and their genome is a single-stranded RNA of positive polarity encoding one large polyprotein which is further processed into mature proteins. Noncytopathogenic (noncp) strains of the pestivirus bovine viral diarrhea virus (BVDV) can establish persistent infection. In persistently infected animals, noncp BVDVs occasionally acquire mutations in viral nonstructural protein 2 (NS2) that give rise to cytopathogenic (cp) BVDV variants, and, eventually, lead to the onset of lethal disease. A molecular marker of cp BVDV infection is a high-level expression of the replicative NS3 protease/helicase that together with NS2 is derived from NS2-3. Here, we present evidence for NS2-3 autoprocessing by a newly identified cysteine protease in NS2 that is distantly related to the NS2-3 autoprotease of hepatitis C and GB viruses. The vital role of this autoprotease in BVDV infection was established, implying an essential function for NS3 in pestiviral RNA replication which cannot be supplied by its NS2-3 precursor. Accordingly, and contrary to a current paradigm, we detected almost complete cleavage of NS2-3 in noncp BVDV at early hours of infection. At 6 to 9 h postinfection, NS2-3 autoprocessing diminished to barely detectable levels for noncp BVDV but decreased only moderately for cp BVDV. Viral RNA synthesis rates strictly correlated with different NS3 levels in noncp and cp BVDV-infected cells, implicating the NS2 autoprotease in RNA replication control. The biotype-specific modulation of NS2-3 autoprocessing indicates a crucial role of the NS2 autoprotease in the pathogenicity of BVDV.
GASP: Gapped Ancestral Sequence Prediction for proteins
Authors: Edwards Richard J , Shields Denis C 
Published: September 2004

Abstract
Background
The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate alignments and phylogenies. Several algorithms exist based on Maximum Parsimony or Maximum Likelihood methods but many current implementations are unable to process residues with gaps, which may represent insertion/deletion (indel) events or sequence fragments.

Results
Here we present a new algorithm, GASP (Gapped Ancestral Sequence Prediction), for predicting ancestral sequences from phylogenetic trees and the corresponding multiple sequence alignments. Alignments may be of any size and contain gaps. GASP first assigns the positions of gaps in the phylogeny before using a likelihood-based approach centred on amino acid substitution matrices to assign ancestral amino acids. Important outgroup information is used by first working down from the tips of the tree to the root, using descendant data only to assign probabilities, and then working back up from the root to the tips using descendant and outgroup data to make predictions. GASP was tested on a number of simulated datasets based on real phylogenies. Prediction accuracy for ungapped data was similar to three alternative algorithms tested, with GASP performing better in some cases and worse in others. Adding simple insertions and deletions to the simulated data did not have a detrimental effect on GASP accuracy.

Conclusions
GASP (Gapped Ancestral Sequence Prediction) will predict ancestral sequences from multiple protein alignments of any size. Although not as accurate in all cases as some of the more sophisticated maximum likelihood approaches, it can process a wide range of input phylogenies and will predict ancestral sequences for gapped and ungapped residues alike.
GDR (G enome D atabase for R osaceae): integrated web resources for Rosaceae genomics and genetics research
Authors: Jung Sook , Jesudurai Christopher , Staton Margaret , Du Zhidian , Ficklin Stephen , Cho Ilhyung , Abbott Albert , Tomkins Jeffrey , Main Dorrie 
Published: September 2004

Abstract
Background
Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools.

Description
The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity.

Conclusions
The GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at http://www.genome.clemson.edu/gdr/.