bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional Changes Induced by Bovine Papillomavirus Type 1 in Equine Fibroblasts
Authors: Yuan Z. Q. , Nicolson L. , Marchetti B. , Gault E. A. , Campo M. S. , Nasir L. 
Published: April 2008

ABSTRACT

Bovine papillomavirus type 1 (BPV-1) and, less commonly, BPV-2 are associated with the pathogenesis of common equine skin tumors termed sarcoids. In an attempt to understand the mechanisms by which BPV-1 induces sarcoids, we used gene expression profiling as a screening tool to identify candidate genes implicated in disease pathogenesis. Gene expression profiles of equine fibroblasts transformed by BPV-1 experimentally or from explanted tumors were compared with those of control equine fibroblasts to identify genes associated with expression of BPV-1. Analysis of the microarray data identified 81 probe sets that were significantly (
P
< 0.01) differentially expressed between the BPV-1-transformed and control cell lines. Expression of several deregulated genes, including
MMP-1, CXCL5, FRA-1, NKG7, TLR4
, and the gene encoding the major histocompatibility complex class I (MHC-I) protein, was confirmed using other BPV-1-transformed cell lines. Furthermore, expression of these genes was examined using a panel of 10 sarcoids. Increased expression of
MMP-1, CXCL5, FRA-1
, and
NKG7
was detected in a subset of tumors, and
TLR4
and
MHC I
showed robust down-regulation in all tumors. Deregulated expression was confirmed at the protein level for MMP-1 and MHC-I. The present report identifies genes modulated by BPV-1 transformation and will help identify the molecular mechanisms involved in disease pathogenesis.
Nuclear Marginalization of Host Cell Chromatin Associated with Expansion of Two Discrete Virus-Induced Subnuclear Compartments during Baculovirus Infection
Authors: Nagamine Toshihiro , Kawasaki Yu , Abe Atsushi , Matsumoto Shogo 
Published: April 2008

ABSTRACT

Chromatin structure is strictly regulated during the cell cycle. DNA viruses occasionally disturb the spatial organization of the host cell chromatin due to formation of the viral DNA replication compartment. To examine chromatin behavior in baculovirus-infected cells, we constructed recombinant plasmids expressing fluorescent protein-tagged histone H4 molecules and visualized the intracellular localization of chromatin by their transient expression in live infected cells. Similar to other DNA viruses, the baculovirus
Bombyx mori
nucleopolyhedrovirus induced marginal relocation of chromatin within the nuclei of BmN cells, simultaneously with expansion of the viral DNA replication compartment, the virogenic stroma (VS). In the late stage of infection, however, the peristromal region (PR), another virus-induced subnuclear compartment, was also excluded from the chromatin-localizing area. Provided that late-gene products such as PR proteins (e.g., envelope proteins of the occlusion-derived virus) were expressed, blockage of viral DNA synthesis failed to inhibit chromatin relocation, despite abrogation of VS expansion. Instead, chromatin became marginalized concomitantly with PR expansion, suggesting that the PR contributes directly to chromatin replacement. In addition, chromatin was excluded from relatively large subnuclear structures that were induced in uninfected cells by cotransfection with four baculovirus genes,
ie1
,
lef3
,
p143
, and
hr
. Omission of any of the four genes, however, failed to result in formation of the large structures or chromatin exclusion. This correlation between compartmentalization and chromatin exclusion suggests the possibility that a chromatin-exclusive property of viral molecules, at least in part, supports nuclear compartmentalization of virus-infected cells.
Generation of Recombinant Rotavirus with an Antigenic Mosaic of Cross-Reactive Neutralization Epitopes on VP4
Authors: Komoto Satoshi , Kugita Masanori , Sasaki Jun , Taniguchi Koki 
Published: April 2008

ABSTRACT
Recombinant rotavirus (RV) with cDNA-derived chimeric VP4 was generated using recently developed reverse genetics for RV. The rescued virus, KU//rVP4(SA11)-II(DS-1), contains SA11 (simian RV strain, G3P[2])-based VP4, in which a cross-reactive neutralization epitope (amino acids 381 to 401) on VP5* is replaced by the corresponding sequence of a different P-type DS-1 (human RV strain, G2P[4]). Serological analyses with a panel of anti-VP4- and -VP7-neutralizing monoclonal antibodies revealed that the rescued virus carries a novel antigenic mosaic of cross-reactive neutralization epitopes on its VP4 surface. This is the first report of the generation of a recombinant RV with artificial amino acid substitutions.
Autocrine and Paracrine Promotion of Cell Survival and Virus Replication by Human Herpesvirus 8 Chemokines
Authors: Choi Young Bong , Nicholas John 
Published: April 2008

ABSTRACT
Human herpesvirus 8 (HHV-8), which is associated with the endothelial tumor Kaposi's sarcoma, encodes three CC/β-chemokines. These are expressed early during productive (lytic) infection and are believed to be involved in immune evasion, in addition to viral pathogenesis via induction of angiogenic cytokines. Here we report that two of the HHV-8 chemokines, CCR8 agonists vCCL-1 and vCCL-2, have direct effects on endothelial survival and virus replication. The v-chemokines stimulated virus replication when added to infected cultures exogenously, and CCR8 knockdown absent v-chemokine supplementation inhibited virus production, indicative of autocrine effects of endogenously produced vCCLs. This was verified and proreplication functions of each chemokine were demonstrated via shRNA-mediated vCCL depletion. The v-chemokines inhibited expression of lytic cycle-induced proapoptotic protein Bim, RNA interference-mediated suppression of which mimicked v-chemokine proreplication functions. Our data show for the first time that the v-chemokines have direct effects on virus biology, independently of their postulated immune evasion functions, and suggest that in vivo the v-chemokines might play direct roles in Kaposi's sarcomagenesis via paracrine prosurvival signaling.
Human vs. machine: identification of bat species from their echolocation calls by humans and by artificial neural networks
Authors: Jennings N. , Parsons S. , Pocock M. J.O. 
Published: April 2008

Automated remote ultrasound detectors allow large amounts of data on bat presence and activity to be collected. Processing of such data involves identifying bat species from their echolocation calls. Automated species identification has the potential to provide more consistent, predictable, and potentially higher levels of accuracy than identification by humans. In contrast, identification by humans permits flexibility and intelligence in identification, as well as the incorporation of features and patterns that may be difficult to quantify. We compared humans with artificial neural networks (ANNs) in their ability to classify short recordings of bat echolocation calls of variable signal to noise ratios; these sequences are typical of those obtained from remote automated recording systems that are often used in large-scale ecological studies. We presented 45 recordings (1–4 calls) produced by known species of bats to ANNs and to 26 human participants with 1 month to 23 years of experience in acoustic identification of bats. Humans correctly classified 86% of recordings to genus and 56% to species; ANNs correctly identified 92% and 62%, respectively. There was no significant difference between the performance of ANNs and that of humans, but ANNs performed better than about 75% of humans. There was little relationship between the experience of the human participants and their classification rate. However, humans with <1 year of experience performed worse than others. Currently, identification of bat echolocation calls by humans is suitable for ecological research, after careful consideration of biases. However, improvements to ANNs and the data that they are trained on may in future increase their performance to beyond those demonstrated by humans.
Factors affecting the relationship between seed removal and seed mortality
Authors: Moore J. E. , Swihart R. K. 
Published: April 2008

S.B. Vander Wall et al. (Ecology, 86: 801–806 (2005)) criticized seed dispersal studies that use seed removal as a proxy for seed predation, because secondary dispersal processes following removal are important to seed fates for many plants. We compared seed removal rates with direct estimates of seed mortality and another mortality index, based on a 3-year experiment that included five temperate deciduous tree species and four exclosure treatments designed to identify effects of different seed consumer groups. Patterns of seed removal rates generally did not match patterns of mortality. Removal and mortality rates were both highest in seed-poor years, indicative of response to food limitation, but annual food abundance interacted with seed type differently for removal rates than for mortality rates. The effect of exclosure type (access by different consumers) on removal rates was opposite its effect on mortality rates; seeds were removed fastest from exclosures that allowed access to tree squirrels (genus Sciurus L., 1758), but these seeds had the lowest mortality because Sciurus is an important seed disperser. We discuss types of studies in which seed removal may be a reasonable index of seed mortality, and we stress the importance of justifying assumptions concerning links between removal and predation.
On Krasnoselskii's Cone Fixed Point Theorem
Authors: Kwong Man Kam 
Published: April 2008

AbstractIn recent years, the Krasnoselskii fixed point theorem for cone maps and its many generalizations have been successfully applied to establish the existence of multiple solutions in the study of boundary value problems of various types. In the first part of this paper, we revisit the Krasnoselskii theorem, in a more topological perspective, and show that it can be deduced in an elementary way from the classical Brouwer-Schauder theorem. This viewpoint also leads to a topology-theoretic generalization of the theorem. In the second part of the paper, we extend the cone theorem in a different direction using the notion of retraction and show that a stronger form of the often cited Leggett-Williams theorem is a special case of this extension.
The Book of Daniel in Recent Research (Part 1)
Authors: Valeta David M. 
Published: April 2008

This is the first of two articles exploring recent research on the book of Daniel. The focus of Part 1 is the court tale narratives of Daniel 1—6, with particular attention to genre identification, sociological and ideological viewpoints, and textual and language issues. Other topics of interest are represented in the bibliography, which identifies important publications since 1993. Foundational works published prior to 1993 are also included. Historical-critical analysis of Daniel 1—6 has furthered understanding of important topics such as the nature of court tale literature and the context of conquest, exile and empire in the ancient Near East, and how those constructs affect the biblical writings. New explorations of Daniel 1—6 that focus on literary, multi-critical and interdisciplinary approaches to the study of this book suggest interesting answers to perennial debates over issues such as the language, genre and ideology of these court tales, and are a main focus of this survey article. Part 2 will explore the apocalyptic material of Daniel 7—12, including discussion of topics such as the Son of Man and the nature of vision material in the Hebrew Bible.
Macrophage mannose receptor on lymphatics controls cell trafficking
Authors: Marttila-Ichihara Fumiko , Turja Raisa , Miiluniemi Mari , Karikoski Marika , Maksimow Mikael , Niemelä Jussi , Martinez-Pomares Luisa , Salmi Marko , Jalkanen Sirpa 
Published: April 2008

Abstract
Macrophage mannose receptor (MR) participates in pathogen recognition, clearance of endogenous serum glycoproteins, and antigen presentation. MR is also present on lymphatic vessels, where its function is unknown. Here we show that migration of lymphocytes from the skin into the draining lymph nodes through the afferent lymphatics is reduced in MR-deficient mice, while the structure of lymphatic vasculature remains normal in these animals. Moreover, in a tumor model the primary tumors grow significantly bigger in MR−/− mice than in the wild-type (WT) controls, whereas the regional lymph node metastases are markedly smaller. Adhesion of both normal lymphocytes and tumor cells to lymphatic vessels is significantly decreased in MR-deficient mice. The ability of macrophages to present tumor antigens is indistinguishable between the 2 genotypes. Thus, MR on lymphatic endothelial cells is involved in leukocyte trafficking and contributes to the metastatic behavior of cancer cells. Blocking of MR may provide a new approach to controlling inflammation and cancer metastasis by targeting the lymphatic vasculature.
SAGE analysis demonstrates increased expression of TOSO contributing to Fas-mediated resistance in CLL
Authors: Proto-Siqueira Rodrigo , Panepucci Rodrigo A. , Careta Francisco P. , Lee Abigail , Clear Andrew , Morris Kelly , Owen Carolyn , Rizzatti Edgar G. , Silva Wilson A. , Falcão Roberto P. , Zago Marco A. , Gribben John G. 
Published: April 2008

Abstract
To identify novel genes involved in the molecular pathogenesis of chronic lymphocytic leukemia (CLL) we performed a serial analysis of gene expression (SAGE) in CLL cells, and compared this with healthy B cells (nCD19+). We found a high level of similarity among CLL subtypes, but a comparison of CLL versus nCD19+ libraries revealed 55 genes that were over-represented and 49 genes that were down-regulated in CLL. A gene ontology analysis revealed that TOSO, which plays a functional role upstream of Fas extrinsic apoptosis pathway, was over-expressed in CLL cells. This finding was confirmed by real-time reverse transcription–polymerase chain reaction in 78 CLL and 12 nCD19+ cases (P < .001). We validated expression using flow cytometry and tissue microarray and demonstrated a 5.6-fold increase of TOSO protein in circulating CLL cells (P = .013) and lymph nodes (P = .006). Our SAGE results have demonstrated that TOSO is a novel over-expressed antiapoptotic gene in CLL.
Losing helena: The extinction of a drosophila line-like element
Authors: Rebollo Rita , Lerat Emmanuelle , Kleine Liliana Lopez , Biémont Christian , Vieira Cristina 
Published: April 2008

AbstractBackgroundTransposable elements (TEs) are major players in evolution. We know that they play an essential role in genome size determination, but we still have an incomplete understanding of the processes involved in their amplification and elimination from genomes and populations. Taking advantage of differences in the amount and distribution of the Long Interspersed Nuclear Element (LINE),helenainDrosophila melanogasterand D.simulans, we analyzed the DNA sequences of copies of this element in samples of various natural populations of these two species.ResultsIn situhybridization experiments revealed thathelenais absent from the chromosome arms ofD. melanogaster, while it is present in the chromosome arms ofD. simulans, which is an unusual feature for a TE in these species. Molecular analyses showed that thehelenasequences detected inD. melanogasterwere all deleted copies, which diverged from the canonical element. Natural populations ofD. simulanshave several copies, a few of them full-length, but most of them internally deleted.ConclusionOverall, our data suggest that a mechanism that induces internal deletions in thehelenasequences is active in theD. simulansgenome.
Cell division in Escherichia colicultures monitored at single cell resolution
Authors: Roostalu Johanna , Jõers Arvi , Luidalepp Hannes , Kaldalu Niilo , Tenson Tanel 
Published: April 2008

Abstract

Background
A fundamental characteristic of cells is the ability to divide. To date, most parameters of bacterial cultures, including cell division, have been measured as cell population averages, assuming that all bacteria divide at a uniform rate.

Results
We monitored the division of individual cells in Escherichia coli cultures during different growth phases. Our experiments are based on the dilution of green fluorescent protein (GFP) upon cell division, monitored by flow cytometry. The results show that the vast majority of E. coli cells in exponentially growing cultures divided uniformly. In cultures that had been in stationary phase up to four days, no cell division was observed. However, upon dilution of stationary phase culture into fresh medium, two subpopulations of cells emerged: one that started dividing and another that did not. These populations were detectable by GFP dilution and displayed different side scatter parameters in flow cytometry. Further analysis showed that bacteria in the non-growing subpopulation were not dead, neither was the difference in growth capacity reducible to differences in stationary phase-specific gene expression since we observed uniform expression of several stress-related promoters. The presence of non-growing persisters, temporarily dormant bacteria that are tolerant to antibiotics, has previously been described within growing bacterial populations. Using the GFP dilution method combined with cell sorting, we showed that ampicillin lyses growing bacteria while non-growing bacteria retain viability and that some of them restart growth after the ampicillin is removed. Thus, our method enables persisters to be monitored even in liquid cultures of wild type strains in which persister formation has low frequency.

Conclusion
In principle, the approaches developed here could be used to detect differences in cell division in response to different environmental conditions and in cultures of unicellular organisms other than E. coli.
An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana
Authors: Ehlting Jürgen , Sauveplane Vincent , Olry Alexandre , Ginglinger Jean-François , Provart Nicholas J , Werck-Reichhart Danièle 
Published: April 2008

Abstract

Background
Sequencing of the first plant genomes has revealed that cytochromes P450 have evolved to become the largest family of enzymes in secondary metabolism. The proportion of P450 enzymes with characterized biochemical function(s) is however very small. If P450 diversification mirrors evolution of chemical diversity, this points to an unexpectedly poor understanding of plant metabolism. We assumed that extensive analysis of gene expression might guide towards the function of P450 enzymes, and highlight overlooked aspects of plant metabolism.

Results
We have created a comprehensive database, 'CYPedia', describing P450 gene expression in four data sets: organs and tissues, stress response, hormone response, and mutants of Arabidopsis thaliana, based on public Affymetrix ATH1 microarray expression data. P450 expression was then combined with the expression of 4,130 re-annotated genes, predicted to act in plant metabolism, for co-expression analyses. Based on the annotation of co-expressed genes from diverse pathway annotation databases, co-expressed pathways were identified. Predictions were validated for most P450s with known functions. As examples, co-expression results for P450s related to plastidial functions/photosynthesis, and to phenylpropanoid, triterpenoid and jasmonate metabolism are highlighted here.

Conclusion
The large scale hypothesis generation tools presented here provide leads to new pathways, unexpected functions, and regulatory networks for many P450s in plant metabolism. These can now be exploited by the community to validate the proposed functions experimentally using reverse genetics, biochemistry, and metabolic profiling.
N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study
Authors: Juhanson Peeter , Kepp Katrin , Org Elin , Veldre Gudrun , Kelgo Piret , Rosenberg Mai , Viigimaa Margus , Laan Maris 
Published: April 2008

Abstract

Background
Kidneys have an important function in blood pressure (BP) regulation and elevated BP may lead to kidney failure. Chr2p12-p13 region linked to BP traits in multiple studies harbours a potential candidate for BP and renal function, N-acetyltransferase 8 (NAT8) expressed in embryonic and adult kidney and associated with nephrotoxicity response.

Methods/Results
We report the first study exploring NAT8 as a potential candidate gene for blood pressure and kidney function. The resequencing (n = 42, random Estonian samples) identified 15 NAT8 polymorphisms, including 6 novel variants. The diversity of NAT8 5' upstream region (π/bp = 0.00320) exceeded up to 10 times the variation in the NAT8 genic region (π/bp = 0.00037) as well as the average variation (π/bp = 0.00040) for the promoters of 29 reference genes associated with hypertension. We suggest that a potential source for such high variation could be an active gene conversion process from NAT8B duplicate gene to NAT8. Similarly to NAT8, several reference genes with the most variable upstream regions have also duplicate copies. The NAT8 promoter SNPs were targeted with pilot quantitative association studies for blood pressure (n = 137, healthy unrelated individuals) and for the index of kidney function – estimated glomerular filtration rate (eGFR; n = 157 hypertensives with and without nephropathy). Minor alleles of these polymorphisms revealed a significant protective effect against elevated systolic BP as well as kidney failure in hypertension patients (p < 0.05; linear regression model, addictive effect).

Conclusion
The full resequencing and pilot association study of a novel positional candidate gene for blood pressure and renal function, human N-acetyltransferase 8, suggested a contribution of highly variable NAT8 promoter polymorphisms in determination of systolic blood pressure and eGFR. Based on in silico analysis, we raise the hypothesis that the alternative SNP alleles of the NAT8 upstream region may have differential effect on gene expression.