bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular evolution of the reactive oxygen-generating NADPH oxidase (Nox/Duox) family of enzymes
Authors: Kawahara Tsukasa , Quinn Mark T , Lambeth J David 
Published: July 2007

AbstractBackgroundNADPH-oxidases (Nox) and the related Dual oxidases (Duox) play varied biological and pathological roles via regulated generation of reactive oxygen species (ROS). Members of the Nox/Duox family have been identified in a wide variety of organisms, including mammals, nematodes, fruit fly, green plants, fungi, and slime molds; however, little is known about the molecular evolutionary history of these enzymes.ResultsWe assembled and analyzed the deduced amino acid sequences of 101 Nox/Duox orthologs from 25 species, including vertebrates, urochordates, echinoderms, insects, nematodes, fungi, slime mold amoeba, alga and plants. In contrast to ROS defense enzymes, such as superoxide dismutase and catalase that are present in prokaryotes, ROS-generating Nox/Duox orthologs only appeared later in evolution. Molecular taxonomy revealed seven distinct subfamilies of Noxes and Duoxes. The calcium-regulated orthologs representing 4 subfamilies diverged early and are the most widely distributed in biology. Subunit-regulated Noxes represent a second major subdivision, and appeared first in fungi and amoeba. Nox5 was lost in rodents, and Nox3, which functions in the inner ear in gravity perception, emerged the most recently, corresponding to full-time adaptation of vertebrates to land. The sea urchinStrongylocentrotus purpuratuspossesses the earliest Nox2 co-ortholog of vertebrate Nox1, 2, and 3, while Nox4 first appeared somewhat later in urochordates. Comparison of evolutionary substitution rates demonstrates that Nox2, the regulatory subunits p47phoxand p67phox, and Duox are more stringently conserved in vertebrates than other Noxes and Nox regulatory subunits. Amino acid sequence comparisons identified key catalytic or regulatory regions, as 68 residues were highly conserved among all Nox/Duox orthologs, and 14 of these were identical with those mutated in Nox2 in variants of X-linked chronic granulomatous disease. In addition to canonical motifs, the B-loop, TM6-FAD, VXGPFG-motif, and extreme C-terminal regions were identified as important for Nox activity, as verified by mutational analysis. The presence of these non-canonical, but highly conserved regions suggests that all Nox/Duox may possess a common biological function remained in a long history of Nox/Duox evolution.ConclusionThis report provides the first comprehensive analysis of the evolution and conserved functions of Nox and Duox family members, including identification of conserved amino acid residues. These results provide a guide for future structure-function studies and for understanding the evolution of biological functions of these enzymes.
Trichostatin A effects on gene expression in the protozoan parasite Entamoeba histolytica
Authors: Ehrenkaufer Gretchen M , Eichinger Daniel J , Singh Upinder 
Published: July 2007

AbstractBackgroundHistone modification regulates chromatin structure and influences gene expression associated with diverse biological functions including cellular differentiation, cancer, maintenance of genome architecture, and pathogen virulence. InEntamoeba, a deep-branching eukaryote, short chain fatty acids (SCFA) affect histone acetylation and parasite development. Additionally, a number of active histone modifying enzymes have been identified in the parasite genome. However, the overall extent of gene regulation tied to histone acetylation is not known.ResultsIn order to identify the genome-wide effects of histone acetylation in regulatingE. histolyticagene expression, we used whole-genome expression profiling of parasites treated with SCFA and Trichostatin A (TSA). Despite significant changes in histone acetylation patterns, exposure of parasites to SCFA resulted in minimal transcriptional changes (11 out of 9,435 genes transcriptionally regulated). In contrast, exposure to TSA, a more specific inhibitor of histone deacetylases, significantly affected transcription of 163 genes (122 genes upregulated and 41 genes downregulated). Genes modulated by TSA were not regulated by treatment with 5-Azacytidine, an inhibitor of DNA-methyltransferase, indicating that inE. histolyticathe crosstalk between DNA methylation and histone modification is not substantial. However, the set of genes regulated by TSA overlapped substantially with genes regulated during parasite development: 73/122 genes upregulated by TSA exposure were upregulated inE. histolyticacysts (p-value = 6 × 10-53) and 15/41 genes downregulated by TSA exposure were downregulated inE. histolyticacysts (p-value = 3 × 10-7).ConclusionThis work represents the first genome-wide analysis of histone acetylation and its effects on gene expression inE. histolytica. The data indicate that SCFAs, despite their ability to influence histone acetylation, have minimal effects on gene transcription in cultured parasites. In contrast, the effect of TSA onE. histolyticagene expression is more substantial and includes genes involved in the encystation pathway. These observations will allow further dissection of the effects of histone acetylation and the genetic pathways regulating stage conversion in this pathogenic parasite.
Sialyl Lewis x expression in canine malignant mammary tumours: correlation with clinicopathological features and E-Cadherin expression
Authors: Pinho Salomé S , Matos Augusto JF , Lopes Célia , Marcos Nuno T , Carvalheira Júlio , Reis Celso A , Gärtner Fátima 
Published: July 2007

Abstract

Background
Sialyl Lewis x (sLex) antigen is a carbohydrate antigen that is considered not only a marker for cancer but also implicated functionally in the malignant behaviour of cancer cells. Overexpression of sLex is associated with enhanced progression and metastases of many types of cancer including those of the mammary gland. Canine mammary tumours can invade and give rise to metastases via either lymphatic or blood vessels.
E-Cadherin is specifically involved in epithelial cell-to-cell adhesion. In cancer, E-Cadherin underexpression is one of the alterations that characterizes the invasive phenotype and is considered an invasion/tumour suppressor gene. Partial or complete loss of E-Cadherin expression correlates with poor prognosis in canine malignant mammary cancer.
The aim of this study was to analyse the sLex expression in canine malignant mammary tumours and to evaluate if the presence of sLex correlates with the expression of E-Cadherin and with clinicopathological features.

Methods
Fifty-three cases of canine mammary carcinomas were analysed immunohistochemically using monoclonal antibodies against sLex (IgM) and E-Cadherin (IgG). The clinicopathological data were then assessed to determine whether there was a correlation with sLex tumour expression. Double labelled immunofluorescence staining was performed to analyse the combined expression of sLex and E-Cadherin.

Results
sLex expression was consistently demonstrated in all cases of canine mammary carcinomas with different levels of expression. We found a significant relationship between the levels of sLex expression and the presence of lymph node metastases. We also demonstrated that when E-Cadherin expression was increased sLex was reduced and vice-versa. The combined analysis of both adhesion molecules revealed an inverse relationship.

Conclusion
In the present study we demonstrate the importance of sLex in the malignant phenotype of canine malignant mammary tumours. Our results support the use of sLex as a prognostic tumour marker in canine mammary carcinomas. Furthermore, we showed that sLex and E-Cadherin expression were inversely correlated. Future studies are warranted to clarify the molecular mechanism underlying the relation between sLex and E-Cadherin in canine mammary carcinoma cells which represents an important comparative model to woman breast cancer.
Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches
Authors: Knizewski Lukasz , Kinch Lisa N , Grishin Nick V , Rychlewski Leszek , Ginalski Krzysztof 
Published: July 2007

AbstractBackgroundPD-(D/E)XK nucleases constitute a large and highly diverse superfamily of enzymes that display little sequence similarity despite retaining a common core fold and a few critical active site residues. This makes identification of new PD-(D/E)XK nuclease families a challenging task as they usually escape detection with standard sequence-based methods. We developed a modified transitive meta profile search approach and to consider the structural diversity of PD-(D/E)XK nuclease fold more thoroughly we analyzed also lower than threshold Meta-BASIC hits to select potentially correct predictions placed among unreliable or incorrect ones.ResultsApplication of a modified transitive Meta-BASIC searches on updated PFAM families and PDB structures resulted in detection of five new PD-(D/E)XK nuclease families encompassing hundreds of so far uncharacterized and poorly annotated proteins. These include four families catalogued in PFAM database as domains of unknown function (DUF506, DUF524, DUF1626 and DUF1703) and YhgA-like family of putative transposases. Three of these families represent extremely distant homologs (DUF506, DUF524, and YhgA-like), while two are newly defined in updated database (DUF1626 and DUF1703). In addition, we also confidently identified an extended AAA-ATPase domain in the N-terminal region of DUF1703 family proteins.ConclusionObtained results suggest that detailed analysis of below threshold Meta-BASIC hits may push limits further for distant homology detection in the 'midnight zone' of homology. All identified families conserve the core evolutionary fold, secondary structure and hydrophobic patterns common to existing PD-(D/E)XK nucleases and maintain critical active site motifs that contribute to nucleic acid cleavage. Further experimental investigations should address the predicted activity and clarify potential substrates providing further insight into detailed biological role of these newly detected nucleases.
Expression and function of junctional adhesion molecule-C in human and experimental arthritis
Authors: Palmer Gaby , Busso Nathalie , Aurrand-Lions Michel , Talabot-Ayer Dominique , Chobaz-Péclat Véronique , Zimmerli Claudia , Hammel Philippe , Imhof Beat A , Gabay Cem 
Published: July 2007

AbstractJunctional adhesion molecule-C (JAM-C) is an adhesion molecule involved in transendothelial migration of leukocytes. In this study, we examined JAM-C expression in the synovium and investigated the role of this molecule in two experimental mouse models of arthritis. JAM-C expression was investigated by reverse transcriptase-polymerase chain reaction and immunohistochemistry. The effects of a monoclonal anti-JAM-C antibody were assessed in antigen-induced arthritis (AIA) and K/BxN serum transfer-induced arthritis. JAM-C was expressed by synovial fibroblasts in the lining layer and associated with vessels in the sublining layer in human and mouse arthritic synovial tissue. In human tissue, JAM-C expression was increased in rheumatoid arthritis (RA) as compared to osteoarthritis synovial samples (12.7 ± 1.3 arbitrary units in RA versus 3.3 ± 1.1 in OA; p < 0.05). Treatment of mice with a monoclonal anti-JAM-C antibody decreased the severity of AIA. Neutrophil infiltration into inflamed joints was selectively reduced as compared to T-lymphocyte and macrophage infiltration (0.8 ± 0.3 arbitrary units in anti-JAM-C-treated versus 2.3 ± 0.6 in isotype-matched control antibody-treated mice; p < 0.05). Circulating levels of the acute-phase protein serum amyloid A as well as antigen-specific and concanavalin A-induced spleen T-cell responses were significantly decreased in anti-JAM-C antibody-treated mice. In the serum transfer-induced arthritis model, treatment with the anti-JAM-C antibody delayed the onset of arthritis. JAM-C is highly expressed by synovial fibroblasts in RA. Treatment of mice with an anti-JAM-C antibody significantly reduced the severity of AIA and delayed the onset of serum transfer-induced arthritis, suggesting a role for JAM-C in the pathogenesis of arthritis.
Whole-genome analysis of mRNA decay in Plasmodium falciparumreveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle
Authors: Shock Jennifer L , Fischer Kael F , DeRisi Joseph L 
Published: July 2007

Abstract
Background:
The rate of mRNA decay is an essential element of post-transcriptional regulation in all organisms. Previously, studies in several organisms found that the specific half-life of each mRNA is precisely related to its physiologic role, and plays an important role in determining levels of gene expression.

Results:
We used a genome-wide approach to characterize mRNA decay in Plasmodium falciparum. We found that, globally, rates of mRNA decay increase dramatically during the asexual intra-erythrocytic developmental cycle. During the ring stage of the cycle, the average mRNA half-life was 9.5 min, but this was extended to an average of 65 min during the late schizont stage of development. Thus, a major determinant of mRNA decay rate appears to be linked to the stage of intra-erythrocytic development. Furthermore, we found specific variations in decay patterns superimposed upon the dominant trend of progressive half-life lengthening. These variations in decay pattern were frequently enriched for genes with specific cellular functions or processes.

Conclusion:
Elucidation of Plasmodium mRNA decay rates provides a key element for deciphering mechanisms of genetic control in this parasite, by complementing and extending previous mRNA abundance studies. Our results indicate that progressive stage-dependent decreases in mRNA decay rate function are a major determinant of mRNA accumulation during the schizont stage of intra-erythrocytic development. This type of genome-wide change in mRNA decay rate has not been observed in any other organism to date, and indicates that post-transcriptional regulation may be the dominant mechanism of gene regulation in P. falciparum.
Polyclonal B cell activation in infections: infectious agents’ devilry or defense mechanism of the host?
Authors: Montes Carolina L , Acosta-Rodríguez Eva V , Merino Maria Cecilia , Bermejo Daniela A , Gruppi Adriana 
Published: July 2007

AbstractPolyclonal B cell activation is not a peculiar characteristic to a particular infection, as many viruses, bacteria, and parasites induce a strong polyclonal B cell response resulting in hyper-γ-globulinemia. Here, we discuss the different roles proposed for polyclonal B cell activation, which can be crucial for early host defense against rapidly dividing microorganisms by contributing antibodies specific for a spectrum of conserved structures present in the pathogens. In addition, polyclonal B cell activation can be responsible for maintenance of memory B cell responses because of the continuous, unrestricted stimulation of memory B cells whose antibody production may be sustained in the absence of the antigens binding-specific BCR. Conversely, polyclonal activation can be triggered by microorganisms to avoid the host-specific, immune response by activating B cell clones, which produce nonmicroorganism-specific antibodies. Finally, some reports suggest a deleterious role for polyclonal activation, arguing that it could potentially turn on anti-self-responses and lead to autoimmune manifestations during chronic infections.
Transfer of a Human Chromosomal Vector from a Hamster Cell Line to a Mouse Embryonic Stem Cell Line
Authors: Paulis Marianna , Bensi Mirella , Orioli Donata , Mondello Chiara , Mazzini Giuliano , D'Incalci Maurizio , Falcioni Cristiano , Radaelli Enrico , Erba Eugenio , Raimondi Elena , De Carli Luigi 
Published: July 2007

Abstract
Two transchromosomic mouse embryonic stem (ES) sublines (ESMClox1.5 and ESMClox2.1) containing a human minichromosome (MC) were established from a sample of hybrid colonies isolated in fusion experiments between a normal diploid mouse ES line and a Chinese hamster ovary line carrying the MC. DNA cytometric and chromosome analyses of ESMClox1.5 and ESMClox2.1 indicated a mouse chromosome complement with a heteroploid constitution in a subtetraploid range; the karyotypes showed various degrees of polysomy for different chromosomes. A single copy of the MC was found in the majority of cells in all the isolated hybrid colonies and was stably maintained in the established sublines for more than 100 cell generations either with or without the selective agent. No significant differences from the ES parental cells were observed in growth characteristics of the transchromosomic ES sublines. ESMClox1.5 cells were unable to grow in soft agar; when cultured in hanging drops, they formed embryoid bodies, and when inoculated in nude mice, they produced teratomas. They were able to express the early development markers Oct4 and Nanog, as demonstrated by reverse transcription-polymerase chain reaction assay. All these features are in common with the ES parental line. Further research using the transchromosomic ES sublines described here may allow gene expression studies on transferred human minichromosomes and could shed light on the relationships among ploidy, pluripotency, cell transformation, and tumorigenesis.
Disclosure of potential conflicts of interest is found at the end of this article.
Mesenchymal Stem Cells Enhance Wound Healing Through Differentiation and Angiogenesis
Authors: Wu Yaojiong , Chen Liwen , Scott Paul G. , Tredget Edward E. 
Published: July 2007

Abstract
Although chronic wounds are common, treatment for these disabling conditions remains limited and largely ineffective. In this study, we examined the benefit of bone marrow-derived mesenchymal stem cells (BM-MSCs) in wound healing. Using an excisional wound splinting model, we showed that injection around the wound and application to the wound bed of green fluorescence protein (GFP)+ allogeneic BM-MSCs significantly enhanced wound healing in normal and diabetic mice compared with that of allogeneic neonatal dermal fibroblasts or vehicle control medium. Fluorescence-activated cell sorting analysis of cells derived from the wound for GFP-expressing BM-MSCs indicated engraftments of 27% at 7 days, 7.6% at 14 days, and 2.5% at 28 days of total BM-MSCs administered. BM-MSC-treated wounds exhibited significantly accelerated wound closure, with increased re-epithelialization, cellularity, and angiogenesis. Notably, BM-MSCs, but not CD34+ bone marrow cells in the wound, expressed the keratinocyte-specific protein keratin and formed glandular structures, suggesting a direct contribution of BM-MSCs to cutaneous regeneration. Moreover, BM-MSC-conditioned medium promoted endothelial cell tube formation. Real-time polymerase chain reaction and Western blot analysis revealed high levels of vascular endothelial growth factor and angiopoietin-1 in BM-MSCs and significantly greater amounts of the proteins in BM-MSC-treated wounds. Thus, our data suggest that BM-MSCs promote wound healing through differentiation and release of proangiogenic factors.
Disclosure of potential conflicts of interest is found at the end of this article.
Limitations of Green Fluorescent Protein as a Cell Lineage Marker
Authors: Swenson E. Scott , Price Joanna G. , Brazelton Timothy , Krause Diane S. 
Published: July 2007

Abstract
The enhanced green fluorescent protein (GFP) reporter has been widely adopted for tracking cell lineage. Here, we compare three transgenic mouse strains in which GFP is considered “ubiquitously expressed,” with the GFP transgene under control of the chicken β-actin (CBA) or human ubiquitin C (UBC) promoter. We compared the expression of GFP using flow cytometry, direct tissue fluorescence, and immunostaining with multiple commercially available anti-GFP antibodies. Mice of CBA-GFP strain 1Osb have strong but variegated expression of GFP in adult liver, kidney, small intestine, and blood. Mice of CBA-GFP strain Y01 have the highest proportion of GFP-positive peripheral blood cells yet limited GFP expression in liver, intestine, and kidney. UBC-GFP mice express GFP only weakly in solid organs and variably in blood. Direct fluorescent detection of GFP in formalin-fixed, paraffin-embedded tissue sections was the simplest approach, but it was useful only in high-expressing strains and potentially subject to artifact because of tissue autofluorescence. Immunofluorescence using either primary goat or primary rabbit antibodies was much more sensitive and allowed better discrimination of authentic signal from autofluorescence. Immunohistochemical staining was less sensitive than direct fluorescence or immunofluorescence and was subject to false-positive signal in the small intestine. In conclusion, there is considerable variability of expression within and between GFP transgenic strains. None of the tested strains gave truly ubiquitous GFP expression. A detailed analysis of GFP expression in one's tissues of interest must guide the choice of reporter mouse strain when GFP is used as a marker of cell lineage or donor origin.
Disclosure of potential conflicts of interest is found at the end of this article.
The Pollution Haven Paradox: Can an Effluent Tax Improve both Profits and Welfare?
Authors: Driskill Robert , Horowitz Andrew W. 
Published: July 2007

Abstract
Stringent environmental taxes in high-income countries are assumed to drive dirty industries to low-income countries, but the empirical evidence for ``pollution havens" is surprisingly weak. We demonstrate that a government trying to prevent flight by a ``dirty" durable good monopolist can impose an effluent tax that is offset by a lump-sum subsidy so that both firm profits and host-country welfare are increased. The scheme exploits the Coase Conjecture insight: a durable goods monopolist has a time-consistency dilemma that limits its ability to restrict future output. In this environment the effluent tax provides a credible commitment that restricts future supply. We assert that the use of lump-sum subsidies in strategic location competition is consistent with this mechanism, and this paradigm may be an important piece of the ``pollution haven paradox."
Human Capital and Welfare Dynamics in Canada
Authors: Hansen Jorgen 
Published: July 2007

Abstract
This paper analyzes the effects of human capital on welfare dynamics in Canada using data from the Self-Sufficiency Project (SSP). SSP offered a time-limited earnings supplement to a randomly assigned group of new welfare applicants who remained on welfare for one year and, in the subsequent year, left welfare for full-time employment. The results suggest that high school completion has no significant impact on the exit rate from welfare or on the re-entry rate. Moreover, full-time work experience is found to reduce the risk of returning to welfare but not for respondents who were assigned to the treatment group. This finding suggests that the provision of an earnings subsidy encourages welfare recipients to accept low-wage jobs with little gains from work experience. Thus, the rationale for such a policy that work today will raise experience and consequently future wages is not supported by the results in this paper.