bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of a Novel ADAM Protease Expressed byPneumocystis carinii
Authors: Kennedy Cassie C. , Kottom Theodore J. , Limper Andrew H. 
Published: May 2009

ABSTRACTPneumocystisspecies are opportunistic fungal pathogens that cause severe pneumonia in immunocompromised hosts. Recent evidence has suggested that unidentified proteases are involved inPneumocystislife cycle regulation. Proteolytically active ADAM (named for “a disintegrin and metalloprotease”) family molecules have been identified in some fungal organisms, such asAspergillus fumigatusandSchizosaccharomyces pombe, and some have been shown to participate in life cycle regulation. Accordingly, we sought to characterize ADAM-like molecules in the fungal opportunistic pathogen,Pneumocystis carinii(PcADAM). After an in silico search of theP. cariniigenomic sequencing project identified a 329-bp partial sequence with homology to known ADAM proteins, the full-length PcADAMsequence was obtained by PCR extension cloning, yielding a final coding sequence of 1,650 bp. Sequence analysis detected the presence of a typical ADAM catalytic active site (HEXXHXXGXXHD). Expression of PcADAMover thePneumocystislife cycle was analyzed by Northern blot. Southern and contour-clamped homogenous electronic field blot analysis demonstrated its presence in theP. cariniigenome. Expression of PcADAMwas observed to be increased inPneumocystiscysts compared to trophic forms. The full-length gene was subsequently cloned and heterologously expressed inSaccharomyces cerevisiae. Purified PcADAMp protein was proteolytically active in casein zymography, requiring divalent zinc. Furthermore, native PcADAMp extracted directly from freshly isolatedPneumocystisorganisms also exhibited protease activity. This is the first report of protease activity attributable to a specific, characterized protein in the clinically important opportunistic fungal pathogenPneumocystis.
CovS Simultaneously Activates and Inhibits the CovR-Mediated Repression of Distinct Subsets of Group A
Streptococcus
Virulence Factor-Encoding Genes
Authors: Treviño Jeanette , Perez Nataly , Ramirez-Peña Esmeralda , Liu Zhuyun , Shelburne Samuel A. , Musser James M. , Sumby Paul 
Published: May 2009

ABSTRACT

To colonize and cause disease at distinct anatomical sites, bacterial pathogens must tailor gene expression in a microenvironment-specific manner. The molecular mechanisms that control the ability of the human bacterial pathogen group A
Streptococcus
(GAS) to transition between infection sites have yet to be fully elucidated. A key regulator of GAS virulence gene expression is the CovR-CovS two-component regulatory system (also known as CsrR-CsrS).
covR
and
covS
mutant strains arise spontaneously during invasive infections and, in in vivo models of infection, rapidly become dominant. Here, we compared wild-type GAS with
covR
,
covS
, and
covRS
isogenic mutant strains to investigate the heterogeneity in the types of natural mutations that occur in
covR
and
covS
and the phenotypic consequences of
covR
or
covS
mutation. We found that the response regulator CovR retains some regulatory function in the absence of CovS and that CovS modulates CovR to significantly enhance repression of one group of genes (e.g., the
speA
,
hasA
, and
ska
genes) while it reduces repression of a second group of genes (e.g., the
speB
,
grab
, and
spd3
genes). We also found that different in vivo-induced
covR
mutations can lead to strikingly different transcriptomes. While
covS
mutant strains show increased virulence in several invasive models of infection, we determined that these mutants are significantly outcompeted by wild-type GAS during growth in human saliva, an ex vivo model of upper respiratory tract infection. We propose that CovS-mediated regulation of CovR activity plays an important role in the ability of GAS to cycle between pharyngeal and invasive infections.
Natural Antibody to Conserved Targets ofHaemophilus influenzaeLimits Colonization of the Murine Nasopharynx
Authors: Zola Tracey A. , Lysenko Elena S. , Weiser Jeffrey N. 
Published: May 2009

ABSTRACTNasopharyngeal colonization represents the initial interaction betweenHaemophilus influenzaeand its human host. Factors that influence bacterial carriage likely affect transmission and incidence of infection. Therefore, we investigated host factors involved in limitingH. influenzaecolonization in BALB/c mice, as colonization can be established in this genetic background. Unlike what is observed in the C57BL/6 background, initial colonization of BALB/c mice was mainly limited by adaptive immune components. This effect on colonization did not require either CD4- or CD8-positive T cells. Instead, initial colonization by genetically diverse strains was limited by preexisting natural antibody with a lesser contribution of complement activity and the presence of neutrophils. Natural serum immunoglobulin from mice was able to bind to the bacterial surface and exhibited complement-dependent bactericidal activity against these genetically diverseH. influenzaestrains. Moreover, natural immunoglobulin G (IgG) recognizing these strains was detected at the nasopharyngeal mucosal surface. This antibody-mediated effect required exposure to the normal mouse microbial flora, since mice raised under germfree (GF) conditions showed increased levels ofH. influenzaecolonization that were not limited by adaptive immunity. In addition, serum IgG from GF mice exhibited less surface binding toH. influenzae, suggesting that natural antibody, induced through prior exposure to the microbial flora, mediated the observed reduction in initial colonization. The broad effect of natural IgG against genetically diverse isolates suggests the presence of conserved species-wide protective targets of antibody.
Analysis of DNA Binding by a Eubacterial Zinc Finger Transcription Factor
Authors: McAlister Victor J. , Christie Gail E. 
Published: May 2009

ABSTRACT

The
Serratia marcescens
NucC protein is structurally and functionally homologous to the P2 Ogr family of eubacterial zinc finger transcription factors required for late gene expression in P2- and P4-related bacteriophages. These activators exhibit site-specific binding to a conserved DNA sequence, TGT-N
3
-R-N
4
-Y-N
3
-aCA, that is located upstream of NucC-dependent
S. marcescens
promoters and the late promoters of P2-related phages. In this report we describe the interactions of NucC with the P2
FETUD
late operon promoter P

F

. NucC is shown to bind P

F

as a tetramer and to make 12 symmetrical contacts to the DNA phosphodiester backbone. The backbone contacts are centered on the TGT-N
3
-R-N
4
-Y-N
3
-aCA motif. Major groove base contacts can be seen at most positions within the ∼24-bp binding site. Minor groove contacts map to adjacent positions in the downstream half of the binding site, which corresponds to the area in which the DNA also appears to be bent by NucC binding. NucC binding provides a new example of protein-DNA interaction that is strikingly different from the DNA binding demonstrated for eukaryotic zinc-finger transcription factors.
Quantitative health impact assessment of transport policies: two simulations related to speed limit reduction and traffic re-allocation in the Netherlands
Authors: Schram-Bijkerk D , van Kempen E , Knol A B , Kruize H , Staatsen B , van Kamp I 
Published: May 2009

Background:Few quantitative health impact assessments (HIAs) of transport policies have been published so far and there is a lack of a common methodology for such assessments.Objective:To evaluate the usability of existing HIA methodology to quantify health effects of transport policies at the local level.Methods:Health impact of two simulated but realistic transport interventions — speed limit reduction and traffic re-allocation — was quantified by selecting traffic-related exposures and health endpoints, modelling of population exposure, selecting exposure-effect relations and estimating the number of local traffic-related cases and disease burden, expressed in disability-adjusted life-years (DALYs), before and after the intervention.Results:Exposure information was difficult to retrieve because of the local scale of the interventions, and exposure-effect relations for subgroups and combined effects were missing. Given uncertainty in the outcomes originating from this kind of missing information, simulated changes in population health by two local traffic interventions were estimated to be small (<5%), except for the estimated reduction in DALYs by less traffic accidents (60%) due to speed limit reduction.Conclusions:Quantitative HIA of transport policies at a local scale is possible, provided that data on exposures, the exposed population and their baseline health status are available. The interpretation of the HIA information should be carried out in the context of the quality of input data and assumptions and uncertainties of the analysis.
PRINCIPALIZATION OF IDEALS IN ABELIAN EXTENSIONS OF NUMBER FIELDS
Authors: BOSCA SÉBASTIEN 
Published: May 2009

We give a self-contained proof of a general conjecture of Gras on principalization of ideals in Abelian extensions of a given field L, which was solved by Kurihara in the case of totally real extensions L of the rational field ℚ. More precisely, for any given extension L/K of number fields, in which at least one infinite place of K totally splits, and for any ideal class cL of L, we construct a finite Abelian extension F/K, in which all infinite places totally split, such that cL become principal in the compositum M = LF.
Test-driven design for introductory OO programming
Authors: Proulx Viera K. 
Published: May 2009

Test-Driven Design (TDD) has been shown to increase the productivity of programming teams and improve the quality of the code they produce. However, most of the introductory curricula provide no introduction to test design, no support for defining the tests, and do not insist on a comprehensive test coverage that is the driving force of the TDD.
This paper presents a curriculum, pedagogy, and the software support for introductory object-oriented program design that uses the TDD consistently from the very beginning. The testing software does not increase the program complexity and is designed to work with the simplest programs. It has been used by hundreds of students at several colleges and is freely available on the web.
Our experiences show that besides improving the quality of code students produce, TDD combined with the novice-appropriate test libraries reinforces students' understanding of the object oriented program design.
Dereferee
Authors: Allevato Anthony , Edwards Stephen H. , Pérez-Quiñones Manuel A. 
Published: May 2009

Dynamic memory management and the use of pointers are critical topics in teaching the C++ language. They are also some of the most difficult for students to grasp properly. The responsibility of ensuring that students understand these concepts does not end with the instructor's lectures---a library enhanced with diagnostics beyond those provided by the language's run-time system itself is a useful tool for giving students more detailed information when their code fails.
We have designed such a toolkit, Dereferee, which students can incorporate into their code with minimal intrusion into the learning process. To demonstrate its effectiveness, we examine C++ code from students in a course that relied solely on the built-in memory management behavior of the language, without any significant additional diagnostic or debugging facilities. We instrument this code with Dereferee in order to explore the causes of errors that result in program crashes and to expose hidden faults that previously lay undetected. Dereferee provided enhanced diagnostics for bugs in 63% of student submissions, and pinpointed the source of 83% of abnormal program terminations. 95% of the students would have received extra diagnostic help from using Dereferee.
Erlotinib and Bevacizumab Have Synergistic Activity against Melanoma
Authors: Schicher Nikolaus , Paulitschke Verena , Swoboda Alexander , Kunstfeld Rainer , Loewe Robert , Pilarski Peter , Pehamberger Hubert , Hoeller Christoph 
Published: May 2009

AbstractPurpose: Melanoma is one of the most aggressive types of cancer with currently no chance of cure once the disease has spread to distant sites. Therapeutic options for advanced stage III and IV are very limited, mainly palliative, and show response in only ∼20% of all cases. The presented preclinical study was done to investigate the influence of a combined treatment of the epidermal growth factor receptor inhibitor erlotinib and the vascular endothelial growth factor monoclonal antibody bevacizumab in melanoma.Experimental Design and Results: The epidermal growth factor receptor was expressed in all cell lines tested, and treatment with erlotinib did inhibit the activation of the MEK/extracellular signal-regulated kinase and AKT signaling pathways. Whereas in vitro no influence on tumor cell proliferation was seen with erlotinib or bevacizumab monotherapy, a decreased invasive potential on erlotinib treatment in a three-dimensional Matrigel assay was observed. Furthermore, both drugs inhibited proliferation and sprouting of endothelial cells. In vivo, in a severe combined immunodeficient mouse xenotransplantation model, reduction in tumor volume under combined treatment with erlotinib and bevacizumab was superior to the additive effect of both single agents. This was associated with reduced cell proliferation, increased apoptosis, and a reduction in tumor angiogenesis compared with control or single treatment groups. Likewise, the reduction in the extent of lymph node and lung metastasis was most pronounced in animals treated with both drugs.Conclusion: The presented data strongly support the use of a combination of erlotinib and bevacizumab as a novel treatment regimen for metastatic melanoma.
A Structured Educational Program Improves Metabolic Control in Patients With Type 2 Diabetes
Authors: Scain Suzana Fiore , Friedman Rogério , Gross Jorge Luiz 
Published: May 2009

Purpose To evaluate the effectiveness of a structured education group program in metabolic control in patients with type 2 diabetes. Methods A randomized controlled trial was conducted in a public teaching hospital and tertiary care center. Participants were 104 patients with type 2 diabetes not using insulin (aged 59 ± 9.5 years, diabetes duration of 10.5 ± 6.70 years, 53% women) randomized to attend an 8-hour structured group education program (delivered in 4 sessions, for 4 weeks, by a trained nurse educator) or to usual care. A pretest and posttest assessed the patients' knowledge before and after the course. The main outcome measures were A1C, weight, blood pressure, and lipids at 4-month intervals, up to 12 months. Results A1C levels decreased significantly in the intervention group after the 4th month and remained lower than in the control group until the 12th month (multivariate analysis of covariance, with baseline A1C as a covariate). Weight, blood pressure levels, total cholesterol, and high-density lipoprotein levels improved significantly, and similarly, in both groups. Conclusions A structured education group program centered in self-management improves the glycemic control in patients with type 2 diabetes, reaching the peak effect at 4 months, and lasting for up to 12 months.
The mitochondrial genome structure of Xenoturbella bocki(phylum Xenoturbellida) is ancestral within the deuterostomes
Authors: Bourlat Sarah J , Rota-Stabelli Omar , Lanfear Robert , Telford Maximilian J 
Published: May 2009

AbstractBackgroundMitochondrial genome comparisons contribute in multiple ways when inferring animal relationships. As well as primary sequence data, rare genomic changes such as gene order, shared gene boundaries and genetic code changes, which are unlikely to have arisen through convergent evolution, are useful tools in resolving deep phylogenies.Xenoturbella bockiis a morphologically simple benthic marine worm recently found to belong among the deuterostomes. Here we present analyses comparing theXenoturbella bockimitochondrial gene order, genetic code and control region to those of other metazoan groups.ResultsThe complete mitochondrial genome sequence ofXenoturbella bockiwas determined. The gene order is most similar to that of the chordates and the hemichordates, indicating that this conserved mitochondrial gene order might be ancestral to the deuterostome clade. Using data from all phyla of deuterostomes, we infer the ancestral mitochondrial gene order for this clade. Using inversion and breakpoint analyses of metazoan mitochondrial genomes, we test conflicting hypotheses for the phylogenetic placement ofXenoturbellaand find a closer affinity to the hemichordates than to other metazoan groups. Comparative analyses of the control region reveal similarities in the transcription initiation and termination sites and origin of replication ofXenoturbellawith those of the vertebrates. Phylogenetic analyses of the mitochondrial sequence indicate a weakly supported placement as a basal deuterostome, a result that may be the effect of compositional bias.ConclusionThe mitochondrial genome ofXenoturbella bockihas a very conserved gene arrangement in the deuterostome group, strikingly similar to that of the hemichordates and the chordates, and thus to the ancestral deuterostome gene order. Similarity to the hemichordates in particular is suggested by inversion and breakpoint analysis. Finally, while phylogenetic analyses of the mitochondrial sequences support a basal deuterostome placement, support for this decreases with the use of more sophisticated models of sequence evolution.
Activation of p53-regulated pro-apoptotic signaling pathways in PrP-mediated myopathy
Authors: Liang Jingjing , Parchaliuk Debra , Medina Sarah , Sorensen Garrett , Landry Laura , Huang Shenghai , Wang Meiling , Kong Qingzhong , Booth Stephanie A 
Published: May 2009

AbstractBackgroundWe have reported that doxycycline-induced over-expression of wild type prion protein (PrP) in skeletal muscles of Tg(HQK) mice is sufficient to cause a primary myopathy with no signs of peripheral neuropathy. The preferential accumulation of the truncated PrP C1 fragment was closely correlated with these myopathic changes. In this study we use gene expression profiling to explore the temporal program of molecular changes underlying the PrP-mediated myopathy.ResultsWe used DNA microarrays, and confirmatory real-time PCR and Western blot analysis to demonstrate deregulation of a large number of genes in the course of the progressive myopathy in the skeletal muscles of doxycycline-treated Tg(HQK) mice. These include the down-regulation of genes coding for the myofibrillar proteins and transcription factor MEF2c, and up-regulation of genes for lysosomal proteins that is concomitant with increased lysosomal activity in the skeletal muscles. Significantly, there was prominent up-regulation of p53 and p53-regulated genes involved in cell cycle arrest and promotion of apoptosis that paralleled the initiation and progression of the muscle pathology.ConclusionThe data provides the firstin vivoevidence that directly links p53 to a wild type PrP-mediated disease. It is evident that several mechanistic features contribute to the myopathy observed in PrP over-expressing mice and that p53-related apoptotic pathways appear to play a major role.
Gene organization and sequence analyses of transfer RNA genes in Trypanosomatid parasites
Authors: Padilla-Mejía Norma E , Florencio-Martínez Luis E , Figueroa-Angulo Elisa E , Manning-Cela Rebeca G , Hernández-Rivas Rosaura , Myler Peter J , Martínez-Calvillo Santiago 
Published: May 2009

Abstract

Background
The protozoan pathogens Leishmania major, Trypanosoma brucei and Trypanosoma cruzi (the Tritryps) are parasites that produce devastating human diseases. These organisms show very unusual mechanisms of gene expression, such as polycistronic transcription. We are interested in the study of tRNA genes, which are transcribed by RNA polymerase III (Pol III). To analyze the sequences and genomic organization of tRNA genes and other Pol III-transcribed genes, we have performed an in silico analysis of the Tritryps genome sequences.

Results
Our analysis indicated the presence of 83, 66 and 120 genes in L. major, T. brucei and T. cruzi, respectively. These numbers include several previously unannotated selenocysteine (Sec) tRNA genes. Most tRNA genes are organized into clusters of 2 to 10 genes that may contain other Pol III-transcribed genes. The distribution of genes in the L. major genome does not seem to be totally random, like in most organisms. While the majority of the tRNA clusters do not show synteny (conservation of gene order) between the Tritryps, a cluster of 13 Pol III genes that is highly syntenic was identified. We have determined consensus sequences for the putative promoter regions (Boxes A and B) of the Tritryps tRNA genes, and specific changes were found in tRNA-Sec genes. Analysis of transcription termination signals of the tRNAs (clusters of Ts) showed differences between T. cruzi and the other two species. We have also identified several tRNA isodecoder genes (having the same anticodon, but different sequences elsewhere in the tRNA body) in the Tritryps.

Conclusion
A low number of tRNA genes is present in Tritryps. The overall weak synteny that they show indicates a reduced importance of genome location of Pol III genes compared to protein-coding genes. The fact that some of the differences between isodecoder genes occur in the internal promoter elements suggests that differential control of the expression of some isoacceptor tRNA genes in Tritryps is possible. The special characteristics found in Boxes A and B from tRNA-Sec genes from Tritryps indicate that the mechanisms that regulate their transcription might be different from those of other tRNA genes.
Generation of Phaseolus vulgaris ESTs and investigation of their regulation upon Uromyces appendiculatus infection
Authors: Thibivilliers Sandra , Joshi Trupti , Campbell Kimberly B , Scheffler Brian , Xu Dong , Cooper Bret , Nguyen Henry T , Stacey Gary 
Published: May 2009

Abstract

Background

Phaseolus vulgaris (common bean) is the second most important legume crop in the world after soybean. Consequently, yield losses due to fungal infection, like Uromyces appendiculatus (bean rust), have strong consequences. Several resistant genes were identified that confer resistance to bean rust infection. However, the downstream genes and mechanisms involved in bean resistance to infection are poorly characterized.

Results
A subtractive bean cDNA library composed of 10,581 unisequences was constructed and enriched in sequences regulated by either bean rust race 41, a virulent strain, or race 49, an avirulent strain on cultivar Early Gallatin carrying the resistance gene Ur-4. The construction of this library allowed the identification of 6,202 new bean ESTs, significantly adding to the available sequences for this plant. Regulation of selected bean genes in response to bean rust infection was confirmed by qRT-PCR. Plant gene expression was similar for both race 41 and 49 during the first 48 hours of the infection process but varied significantly at the later time points (72–96 hours after inoculation) mainly due to the presence of the Avr4 gene in the race 49 leading to a hypersensitive response in the bean plants. A biphasic pattern of gene expression was observed for several genes regulated in response to fungal infection.

Conclusion
The enrichment of the public database with over 6,000 bean ESTs significantly adds to the genomic resources available for this important crop plant. The analysis of these genes in response to bean rust infection provides a foundation for further studies of the mechanism of fungal disease resistance. The expression pattern of 90 bean genes upon rust infection shares several features with other legumes infected by biotrophic fungi. This finding suggests that the P. vulgaris-U. appendiculatus pathosystem could serve as a model to explore legume-rust interaction.