bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunogenicity of
Anaplasma marginale
Type IV Secretion System Proteins in a Protective Outer Membrane Vaccine
Authors: Lopez Job E. , Palmer Guy H. , Brayton Kelly A. , Dark Michael J. , Leach Stephanie E. , Brown Wendy C. 
Published: March 2007

ABSTRACT

Rickettsial pathogens in the genera
Anaplasma
and
Ehrlichia
cause acute infection in immunologically naive hosts and are major causes of tick-borne disease in animals and humans. Immunization with purified outer membranes induces protection against acute
Anaplasma marginale
infection and disease, and a proteomic and genomic approach recently identified 21 proteins within the outer membrane immunogen in addition to the well-characterized major surface proteins MSP1 to MSP5. Among the newly described proteins were the type IV secretion system (TFSS) proteins VirB9, VirB10, and conjugal transfer protein (CTP). In other gram-negative bacteria, TFSS proteins form channels, facilitate secretion of molecules, and are required for intracellular survival. However, TFSS proteins have not been explored as vaccine antigens. In this study we demonstrate that in
Anaplasma marginale
outer membrane-vaccinated cattle, VirB9, VirB10, and CTP are recognized by serum immunoglobulin G2 (IgG2) and stimulate memory T-lymphocyte proliferation and gamma interferon secretion. VirB9 induced the greatest proliferation in CD4
+
T-cell lines, and VirB9-specific CD4
+
T-cell clones responded to three
A. marginale
strains, confirming the VirB9-specific T-cell responses are directed against epitopes in the native protein. The three TFSS proteins are highly conserved with orthologous proteins in
Anaplasma phagocytophilum
,
Ehrlichia chaffeensis
, and
Ehrlichia canis
. Recognition of TFSS antigens by CD4
+
T cells and by IgG2 from cattle immunized with the protective outer membrane fraction provides a rationale for including these proteins in development of vaccines against
A. marginale
and related pathogens.
CpG Oligodeoxynucleotide Treatment Enhances Innate Resistance and Acquired Immunity to African Trypanosomes
Authors: Harris Tajie H. , Mansfield John M. , Paulnock Donna M. 
Published: March 2007

ABSTRACTRelative resistance to African trypanosomiasis is based on the development of a type I cytokine response, which is partially dependent on innate immune responses generated through MyD88 and Toll-like receptor 9 (TLR9). Therefore, we asked whether enhancement of the immune response by artificial stimulation with CpG oligodeoxynucleotide (ODN), a TLR9 agonist, would result in enhanced protection against trypanosomes. In susceptible BALB/c mice, relative resistance to infection was significantly enhanced by CpG ODN treatment and was associated with decreased parasite burden, increased cytokine production, and elevated parasite-specific B- and T-cell responses. In relatively resistant C57BL/6 mice, survival was not enhanced but early parasitemia levels were reduced 100-fold and the majority of the parasites were nondividing, short stumpy (SS) forms. CpG ODN treatment of lymphocyte-deficient C57BL/6-scidand BALB/cByJ-scidmice also enhanced survival and reduced parasitemia, indicating that innate resistance to trypanosome infection can be enhanced. In C57BL/6-scidand BALB/cByJ-scidmice, the parasites were also predominantly SS forms during the outgrowth of parasitemia. However, the effect of CpG ODN treatment on parasite morphology was not as marked in gamma interferon (IFN-γ)-knockout mice, suggesting that downstream effects of IFN-γ production may play a discrete role in parasite cell differentiation. Overall, these studies provide the first evidence that enhancement of resistance to African trypanosomes can be induced in susceptible animals in a TLR9-dependent manner and that CpG ODN treatment may influence the developmental life cycle of the parasites.
Niche-Specific Activation of the Oxidative Stress Response by the Pathogenic FungusCandida albicans
Authors: Enjalbert Brice , MacCallum Donna M. , Odds Frank C. , Brown Alistair J. P. 
Published: March 2007

ABSTRACTCandida albicansis a major opportunistic pathogen of humans. The pathogenicity of this fungus depends upon its ability to deal effectively with the host defenses and, in particular, the oxidative burst of phagocytic cells. We have explored the activation of the oxidative stress response inC. albicansin ex vivo infection models and during systemic infection of a mammalian host. We have generatedC. albicansstrains that contain specific green fluorescent protein (GFP) promoter fusions and hence act as biosensors of environmental oxidative stress at the single-cell level. Having confirmed thatCTA1-,TRX1-, andTTR1/GRX2-GFPreporters respond specifically to oxidative stress, and not to heat shock, nitrosative, or osmotic stresses, we used these reporters to show that individualC. albicanscells activate an oxidative stress response following phagocytosis by neutrophils, but not by macrophages. Significantly, only a small proportion ofC. albicanscells (about 4%) activated an oxidative stress response during systemic infection of the mouse kidney. The response of these cells was generally equivalent to exposure to 0.4 mM hydrogen peroxide in vitro. We conclude that mostC. albicanscells are exposed to an oxidative stress when they come into contact with neutrophils in the bloodstream of the host but that oxidative killing is no longer a significant threat once an infection has been established in the kidney.
Immunomodulatory Effects of theLutzomyia longipalpisSalivary Gland Protein Maxadilan on Mouse Macrophages
Authors: Brodie Tess M. , Smith Matthew C. , Morris Robin V. , Titus Richard G. 
Published: March 2007

ABSTRACTInfection withLeishmania majoris enhanced when the sand flyLutzomyia longipalpissalivary peptide maxadilan (MAX) is injected along with the parasite. Here we determined the effect that MAX has on the secretion of cytokines and nitric oxide (NO) and on parasite survival in macrophages (MΦs). The cytokines produced by MΦs can enhance a type 1 response, which will increase NO and the killing of intracellular pathogens such asL. major, or a type 2 response, leading to antibody production that is ineffective against intracellular pathogens such asL. major. A mouse macrophage cell line (RAW 264.7) was stimulated with various concentrations of MAX and lipopolysaccharide (LPS), and the supernatants were collected after 1, 2, and 3 days. Supernatants were assayed for interleukin-12p70 (IL-12p70), IL-10, IL-6, transforming growth factor β (TGF-β), NO, and tumor necrosis factor alpha (TNF-α). Our results indicate that the addition of MAX upregulates the cytokines associated with a type 2 response (IL-10, IL-6, and TGF-β) but downregulates type 1 cytokines (IL-12p70 and TNF-α) and NO. MAX was also added toL. major-infected mouse peritoneal exudate cells (PECs), and the parasite load increased significantly. The enhanced parasite load correlated with decreased NO production by PECs that were stimulated with LPS and gamma interferon in the presence of MAX. The ability of MAX to foster a type 2 response, to enhance parasite survival, and to decrease NO argues that MAX may be crucial for the early survival ofLeishmaniain the vertebrate host, and therefore, MAX holds considerable promise as an antigenic component for a vaccine againstLeishmania.
QseA Directly Activates Transcription of
LEE1
in Enterohemorrhagic
Escherichia coli
Authors: Sharp Faith C. , Sperandio Vanessa 
Published: March 2007

ABSTRACT

Quorum sensing (QS) in enterohemorrhagic
Escherichia coli
(EHEC) regulates the expression of the locus of enterocyte effacement (LEE). The LEE contains five major operons named
LEE1
through
LEE5
. QseA was previously shown to be activated through QS and to activate the transcription of
LEE1
. The
LEE1
operon encodes Ler, the transcription activator of all other LEE genes, and has two promoters: a distal promoter (P1) and a proximal promoter (P2). We have previously reported that QseA acts on P1 and not P2. To identify the minimal region of
LEE1
that is necessary for QseA-mediated activation, a series of nested-deletion constructs of the
LEE1
promoter fused to a
lacZ
reporter were constructed in both the EHEC and
E. coli
K-12 backgrounds. In an EHEC background, QseA-dependent activation of
LEE1
can be observed for the entire regulatory region (beginning at nucleotide −393 and ending at nucleotide −123). In contrast to what occurred in EHEC, in K-12 there was no QseA-dependent activation of
LEE1
transcription between base pairs −393 and −343. These data indicate that a QseA-dependent EHEC-specific regulator is required for the activation of transcription in this region. We also observed QseA-dependent
LEE1
activation from nucleotides −218 to −123 in K-12, similar to results of the nested-deletion analysis performed with EHEC. Electrophoretic mobility shift assays established that QseA directly binds to the region of
LEE1
from bp −173 to −42 and not to the region from bp −393 to −343. These studies suggest that QseA activates the transcription of
LEE1
by directly binding upstream of its P1 promoter region.
Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray study
Authors: Shankavaram Uma T. , Reinhold William C. , Nishizuka Satoshi , Major Sylvia , Morita Daisaku , Chary Krishna K. , Reimers Mark A. , Scherf Uwe , Kahn Ari , Dolginow Douglas , Cossman Jeffrey , Kaldjian Eric P. , Scudiero Dominic A. , Petricoin Emanuel , Liotta Lance , Lee Jae K. , Weinstein John N. 
Published: March 2007

Abstract
To evaluate the utility of transcript profiling for prediction of protein expression levels, we compared profiles across the NCI-60 cancer cell panel, which represents nine tissues of origin. For that analysis, we present here two new NCI-60 transcript profile data sets (A based on Affymetrix HG-U95 and HG-U133A chips; Affymetrix, Santa Clara, CA) and one new protein profile data set (based on reverse-phase protein lysate arrays). The data sets are available online at http://discover.nci.nih.gov in the CellMiner program package. Using the new transcript data in combination with our previously published cDNA array and Affymetrix HU6800 data sets, we first developed a “consensus set” of transcript profiles based on the four different microarray platforms. Using that set, we found that 65% of the genes showed statistically significant transcript-protein correlation, and the correlations were generally higher than those reported previously for panels of mammalian cells. Using the predictive analysis of microarray nearest shrunken centroid algorithm for functional prediction of tissue of origin, we then found that (a) the consensus mRNA set did better than did data from any of the individual mRNA platforms and (b) the protein data seemed to do somewhat better (P = 0.027) on a gene-for-gene basis in this particular study than did the consensus mRNA data, but both did well. Analysis based on the Gene Ontology showed protein levels of structure-related genes to be well predicted by mRNA levels (mean r = 0.71). Because the transcript-based technologies are more mature and are currently able to assess larger numbers of genes at one time, they continue to be useful, even when the ultimate aim is information about proteins. [Mol Cancer Ther 2007;6(3):820–32]
Atmospheric Teleconnections of Tropical Atlantic Variability: Interhemispheric, Tropical–Extratropical, and Cross-Basin Interactions
Authors: Wu Lixin , He Feng , Liu Zhengyu , Li Chun 
Published: March 2007

Abstract
In this paper, the atmospheric teleconnections of the tropical Atlantic SST variability are investigated in a series of coupled ocean–atmosphere modeling experiments. It is found that the tropical Atlantic climate not only displays an apparent interhemispheric link, but also significantly influences the North Atlantic Oscillation (NAO) and the El Niño–Southern Oscillation (ENSO). In spring, the tropical Atlantic SST exhibits an interhemispheric seesaw controlled by the wind–evaporation–SST (WES) feedback that subsequently decays through the mediation of the seasonal migration of the ITCZ. Over the North Atlantic, the tropical Atlantic SST can force a significant coupled NAO–dipole SST response in spring that changes to a coupled wave train–horseshoe SST response in the following summer and fall, and a recurrence of the NAO in the next winter. The seasonal changes of the atmospheric response as well as the recurrence of the next winter’s NAO are driven predominantly by the tropical Atlantic SST itself, while the resulting extratropical SST can enhance the atmospheric response, but it is not a necessary bridge of the winter-to-winter NAO persistency. Over the Pacific, the model demonstrates that the north tropical Atlantic (NTA) SST can also organize an interhemispheric SST seesaw in spring in the eastern equatorial Pacific that subsequently evolves into an ENSO-like pattern in the tropical Pacific through mediation of the ITCZ and equatorial coupled ocean–atmosphere feedback.
The Crisis in Religious Socialization: An Analytical Proposal
Authors: Sabe Jordi Collet 
Published: March 2007

English The deep crisis of the traditional socializing institutions (school, family and churches) has its counterpart in the crisis of the way socialization processes have been working up till now. The author proposes an analytical framework to reconsider the changes in the recent processes of religious socialization. This analytical proposal, using four ideal types, shows the new ways of religious socialization, which could be called “complex”. At the same time, the analytical framework suggests that the affective and relational elements are quite influential in the undlerstanding of its development and outcome. French La crise profond des institutions socialisatrices traditionnelles (école, famille et églises) va de pair avec la crise liée à la maniere clont les processus de socialisation religieuse se sont développesjusqu' à présent. L'auteur propose un cadre analytique permettant de reconsidérer les changements recents dle processus de socialisation religieuse. Ce cadre d'analyse, basé sur quatre types-ideaux, met à jour de nouveaux procédé s de socialisation religieuse qui pourraient être qualifiés de "complexes". Dans le même temps, ce cadlre per-met d'entrevoir l'influence d'éléments qffectifs et relationnels dans la compréhension dlu développement et des résultats de cette socialisation religieuse.
Visualization of three-way comparisons of omics data
Authors: Baran Richard , Robert Martin , Suematsu Makoto , Soga Tomoyoshi , Tomita Masaru 
Published: March 2007

Abstract

Background
Density plot visualizations (also referred to as heat maps or color maps) are widely used in different fields including large-scale omics studies in biological sciences. However, the current color-codings limit the visualizations to single datasets or pairwise comparisons.

Results
We propose a color-coding approach for the representation of three-way comparisons. The approach is based on the HSB (hue, saturation, brightness) color model. The three compared values are assigned specific hue values from the circular hue range (e.g. red, green, and blue). The hue value representing the three-way comparison is calculated according to the distribution of three compared values. If two of the values are identical and one is different, the resulting hue is set to the characteristic hue of the differing value. If all three compared values are different, the resulting hue is selected from a color gradient running between the hues of the two most distant values (as measured by the absolute value of their difference) according to the relative position of the third value between the two. The saturation of the color representing the three-way comparison reflects the amplitude (or extent) of the numerical difference between the two most distant values according to a scale of interest. The brightness is set to a maximum value by default but can be used to encode additional information about the three-way comparison.

Conclusion
We propose a novel color-coding approach for intuitive visualization of three-way comparisons of omics data.
New probes used for IS1245 and IS1311 restriction fragment length polymorphism of Mycobacterium avium subsp. avium and Mycobacterium avium subsp. hominissuis isolates of human and animal origin in Norway
Authors: Johansen Tone Bjordal , Olsen Ingrid , Jensen Merete Rusås , Dahle Ulf R , Holstad Gudmund , Djønne Berit 
Published: March 2007

Abstract

Background

Mycobacterium avium is an environmental mycobacterium that can be divided into the subspecies avium, hominissuis, paratuberculosis and silvaticum. Some M. avium subspecies are opportunistic pathogens for animals and humans. They are ubiquitous in nature and can be isolated from natural sources of water, soil, plants and bedding material. Isolates of M. avium originating from humans (n = 37), pigs (n = 51) and wild birds (n = 10) in Norway were examined by IS1245 and IS1311 RFLP using new and specific probes and for the presence of IS901 and ISMpa1 by PCR. Analysis and generation of a dendrogram were performed with the software BioNumerics.

Results
IS1311 RFLP provided clear results that were easy to interpret, while IS1245 RFLP generated more complex patterns with a higher discriminatory power. The combination of the two methods gave additional discrimination between isolates. All avian isolates except one were M. avium subsp. avium with two copies of IS1311 and one copy of IS1245, while the isolates of human and porcine origin belonged to M. avium subsp.hominissuis. The isolates from human patients were distributed randomly among the clusters of porcine isolates. There were few identical isolates. However, one isolate from a human patient was identical to a porcine isolate. Regional differences were detected among the porcine isolates, while there was no clustering of human isolates according to type of clinical symptoms or geographical location of the patient's home addresses.

Conclusion
The results demonstrate that a wide range of M. avium subsp.hominissuis are present in pigs and humans in Norway, and that some of these isolates are very similar. It remains to be determined whether humans are infected from pigs or if they are infected from common environmental sources.
Identification and characterization of bovine regulator of telomere length elongation helicase gene (RTEL): molecular cloning, expression distribution, splice variants and DNA methylation profile
Authors: Du Zhuo , Zhao DingSheng , Zhao YongHui , Wang ShaoHua , Gao Yu , Li Ning 
Published: March 2007

Abstract

Background
The genetic basis of telomere length heterogeneity among mammalian species is still not well understood. Recently, a gene named regulator of telomere length elongation helicase (RTEL) was identified and predicted to be an essential participant in species-specific telomere length regulation in two murine species. To obtain broader insights into its structure and biological functions and to ascertain whether RTEL is also a candidate gene in the regulation of telomere length diversity in other mammalian species, data from other mammals may be helpful.

Results
Here we report the cDNA cloning, genomic structure, chromosomal location, alternative splicing pattern, expression distribution and DNA methylation profile of the bovine homolog of RTEL. The longest transcript of bovine RTEL is 4440 nt, encompassing 24.8 kb of genomic sequence that was mapped to chromosome 13q2.2. It encodes a conserved helicase-like protein containing seven characterized helicase motifs in the first 750 aa and a PIP box in the C-terminus. Four splice variants were identified within the transcripts in both the coding and 5'-untranslated regions; Western blot revealed that the most abundant splice variant SV-1 was translated to a truncated isoform of RTEL. The different 5'UTRs imply alternative transcription start sites in the promoter; Bovine RTEL was transcribed at the blastocyst stage, and expression levels were highest in adult testis, liver and ovary. DNA methylation analysis of tissues that differed significantly in expression level indicated that relatively low DNA methylation is associated with higher expression.

Conclusion
In this study, we have identified and characterized a bovine RTEL homolog and obtained basic information about it, including gene structure, expression distribution, splice variants and profile of DNA methylation around two putative transcription start sites. These data may be helpful for further comparative and functional analysis of RTEL in mammals.
A new molecular breast cancer subclass defined from a large scale real-time quantitative RT-PCR study
Authors: Chanrion Maïa , Fontaine Hélène , Rodriguez Carmen , Negre Vincent , Bibeau Frédéric , Theillet Charles , Hénaut Alain , Darbon Jean-Marie 
Published: March 2007

AbstractBackgroundCurrent histo-pathological prognostic factors are not very helpful in predicting the clinical outcome of breast cancer due to the disease's heterogeneity. Molecular profiling using a large panel of genes could help to classify breast tumours and to define signatures which are predictive of their clinical behaviour.MethodsTo this aim, quantitative RT-PCR amplification was used to study the RNA expression levels of 47 genes in 199 primary breast tumours and 6 normal breast tissues. Genes were selected on the basis of their potential implication in hormonal sensitivity of breast tumours. Normalized RT-PCR data were analysed in an unsupervised manner by pairwise hierarchical clustering, and the statistical relevance of the defined subclasses was assessed by Chi2 analysis. The robustness of the selected subgroups was evaluated by classifying an external and independent set of tumours using these Chi2-defined molecular signatures.ResultsHierarchical clustering of gene expression data allowed us to define a series of tumour subgroups that were either reminiscent of previously reported classifications, or represented putative new subtypes. The Chi2 analysis of these subgroups allowed us to define specific molecular signatures for some of them whose reliability was further demonstrated by using the validation data set. A new breast cancer subclass, called subgroup 7, that we defined in that way, was particularly interesting as it gathered tumours with specific bioclinical features including a low rate of recurrence during a 5 year follow-up.ConclusionThe analysis of the expression of 47 genes in 199 primary breast tumours allowed classifying them into a series of molecular subgroups. The subgroup 7, which has been highlighted by our study, was remarkable as it gathered tumours with specific bioclinical features including a low rate of recurrence. Although this finding should be confirmed by using a larger tumour cohort, it suggests that gene expression profiling using a minimal set of genes may allow the discovery of new subclasses of breast cancer that are characterized by specific molecular signatures and exhibit specific bioclinical features.