bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular taxonomy of Brazilian tyrant‐flycatchers (Passeriformes: Tyrannidae)
Authors: CHAVES A. V. , CLOZATO C. L. , LACERDA D. R. , SARI E. H. R. , SANTOS F. R. 
Published: September 2008

AbstractThe tyrannids are one of the most diverse groups of birds in the world, and the most numerous suboscine family in the Neotropics. Reflecting such diversity, many taxonomic issues arise in this group, mainly due to morphological similarities, even among phylogenetically distant species. Other issues appear at higher taxonomic levels, mostly brought up by genetic studies, making systematics a rather inconclusive issue. This study looks into the use of DNA barcodes method to discriminate and identify Tyrannidae species occurring in the Atlantic Forest and Cerrado biomes of Brazil. We analysed 266 individuals of 71 tyrant‐flycatcher species from different geographical locations by sequencing 542 bp of the mtDNA COI gene. The great majority of the analysed species showed exclusive haplotypes, usually displaying low intraspecific diversity and high interspecific divergence. Only Casiornis fuscus and Casiornis rufus, suggested in some studies to belong to a single species, could not be phylogenetically separated. High intraspecific diversity was observed among Elaenia obscura individuals, which can suggest the existence of cryptic species in this taxon. The same was also observed for Suiriri suiriri, considered by some authors to comprise at least two species, and by others to be divided into three subspecies. Additionally, the use of sequences from voucher specimens allowed us to correct four misidentifications that had happened in the field. Our findings suggest a great power of the COI barcodes to discriminate species of the Tyrannidae family that are found in Brazil.
Characterization of eight single nucleotide polymorphism markers in Aedes aegypti
Authors: PADUAN KS , RIBOLLA PEM 
Published: September 2008

AbstractSequencing of part of seven genes from Aedes aegypti collected in 16 Brazilian cities revealed the existence of 53 single nucleotide polymorphisms (SNPs), representing one SNP every 52 base pairs. From these 53 SNPs, we selected eight that are independent and highly polymorphic. We describe the use of these markers for differentiation of Brazilian populations of A. aegypti. These are the first SNPs developed for delineating population structure in A. aegypti, and will be a useful complement to epidemiological studies.
Isolation and characterization of microsatellite markers for Pinellia ternata and cross‐species amplification
Authors: CHEN FANGJIAN , ZHANG LIXIN , ZHAO CHANGMING 
Published: September 2008

AbstractIn this study, we isolated and characterized 12 microsatellite loci for Pinellia ternata. Polymorphism of these 12 loci was assessed in 46 individuals collected from two wild populations. All the loci were polymorphic with four to 13 alleles per locus and the observed and expected heterozygosities ranged from 0.312 to 0.680 and from 0.506 to 0.734, respectively. None of the loci showed significant deviation from Hardy–Weinberg equilibrium (P < 0.05). No significant linkage disequilibrium was observed between pairs of studied loci. In addition, most markers amplified successfully in three closely related taxa that are Pinellia cordata, P. peltata and P. pedatisecta. These microsatellite markers could provide a useful tool for genetic structure studies of the Pinellia species.
DNA barcoding of eight North American coregonine species
Authors: SCHLEI ORA L. , CRÊTE‐LAFRENIÈRE ALEXIS , WHITELEY ANDREW R. , BROWN RANDY J. , OLSEN JEFFREY B. , BERNATCHEZ LOUIS , WENBURG JOHN K. 
Published: September 2008

AbstractCoregonine fishes have a circumpolar distribution in the Arctic and sub‐Arctic Northern Hemisphere. This subfamily of Salmonidae consists of three genera: Prosopium, Stenodus and Coregonus, including over 30 species. Many species overlap spatially and are difficult to distinguish based on morphological characteristics, especially as larvae or juveniles. Here we present a method for rapid and cost‐effective species identification for representatives of the three genera based on sequence variation at the mitochondrial cytochrome c oxidase subunit I gene (COI). We examined eight species common to North America with distributional overlap in Alaska. Mean pairwise sequence divergence for all eight species was 7.04% and ranged from 0.46% to 14.23%. This sequence variation was used to develop a genetic assay based on restriction fragment length polymorphism. In a blind test, this assay provided correct species assignment for 48 of 49 individuals representing all eight species. The single incorrect assignment may reflect hybridization between two closely related species. This DNA barcode‐based assay promises to aid fishery managers and researchers by providing a cost‐effective alternative to large‐scale sequence analysis for identification of North American coregonine fishes.
Cellulose acetate electrophoresis of canine plasma after fibrinogen precipitation by ethanol
Authors: Rossi Silvia , Bertazzolo Walter , Paltrinieri Saverio , Giordano Alessia 
Published: September 2008

Background: In routine canine medicine, anticoagulated blood is often the only sample sent to laboratories for diagnostic purposes. This hampers the interpretation of protein electrophoretic tracings because plasma contains fibrinogen, which migrates in the β–γ region. In human medicine, fibrinogen can be precipitated from plasma using ethanol.Objectives: The purpose of this study was to assess ethanol precipitation as a method for removing fibrinogen from canine plasma so as to facilitate the interpretation of electorphoresis results.Methods: Blood samples collected from 40 dogs were divided into plain tubes and tubes containing EDTA (n=20) or lithium–heparin (n=20). An aliquot of plasma from each sample was incubated with ethanol at a final concentration of 100 mL/L. Cellulose acetate electrophoresis was then performed on serum, plasma, and plasma treated with ethanol. To verify the efficiency of ethanol treatment, fibrinogen was added to 5 canine serum samples at final concentrations of 2.5, 5.0, and 10.0 g/L, and electrophoresis was performed before and after ethanol treatment.Results: Visual analysis of electrophoretograms from ethanol‐treated samples confirmed the disappearance of the fibrinogen peak from the β2‐globulin region. Treatment with ethanol caused a significant decrease in the percentage of β2‐globulins and a significant increase in the percentage of α2‐globulins. Absolute values of most electrophoretic fractions were significantly decreased in ethanol‐treated plasma compared with serum.Conclusions: Ethanol treatment successfully removed fibrinogen from canine plasma and normalized electrophoretic profiles, but probably also precipitated proteins other than fibrinogen. Ethanol treatment is recommended to facilitate visual identification of abnormal monoclonal peaks, but not for determining absolute protein concentrations in electrophoretic fractions.
Pyrosequencing To Detect Mutations in
FKS1
That Confer Reduced Echinocandin Susceptibility in
Candida albicans
Authors: Wiederhold Nathan P. , Grabinski Jodi L. , Garcia-Effron Guillermo , Perlin David S. , Lee Samuel A. 
Published: September 2008

ABSTRACT

Pyrosequencing was compared to Sanger dideoxy sequencing to detect mutations in
FKS1
responsible for reduced echinocandin susceptibility in
Candida albicans
. These methods were in complete agreement for 10 of 12 clinical isolates with elevated echinocandin MICs, supporting the potential feasibility of pyrosequencing to detect mutations within diploid fungi.
Enhanced Susceptibility to Antifungal Oligopeptides in Yeast Strains Overexpressing ABC Multidrug Efflux Pumps
Authors: Wakieć Roland , Gabriel Iwona , Prasad Rajendra , Becker Jeffrey M. , Payne John W. , Milewski Sławomir 
Published: September 2008

ABSTRACT

The susceptibility to several oligopeptide and amino acid antifungals of a
Saccharomyces cerevisiae
strain carrying multiple deletions in yeast multidrug resistance genes was compared to transformants containing the
CDR1
,
CDR2
, or
MDR1
genes that encode the major
Candida albicans
drug efflux pumps. Recombinant yeast strains overexpressing Cdr1p and Cdr2p showed enhanced susceptibilities to all tested oligopeptide antifungals. The enhanced susceptibilities of multidrug-resistant yeast strains to oligopeptide antifungals corresponded to higher rates of oligopeptide uptake. Yeast cells overexpressing Cdr1p or Cdr2p effluxed protons at higher rates than the reference cells lacking these ABC transporters. An increased plasma membrane electrochemical gradient caused by the functional overexpression of Cdr1p or Cdr2p appeared to increase cellular susceptibility to oligopeptide antifungals by stimulating their uptake via oligopeptide permeases.
Mutation of Two
Mycoplasma arthritidis
Surface Lipoproteins with Divergent Functions in Cytadherence
Authors: Bird Daniel W. , Graber Kelly , Knutson Allison , Washburn Leigh R. 
Published: September 2008

ABSTRACT

Mycoplasma arthritidis
is a natural pathogen of rats, causing an acute polyarthritis. Previous studies identified two membrane-bound lipoproteins, Maa1 and Maa2, thought to be associated with cytadherence of
M. arthritidis
strain 158p10p9. We have since confirmed that Maa1 is a major adhesin, although the role of Maa2 has proven more elusive. Both proteins were capable of eliciting protective immunity in rats against challenge with the virulent strain 158p10p9, suggesting that they may be important in pathogenesis. The purpose of this study was to better understand the roles of Maa1 and Maa2 in cytadherence in vitro. Insertion mutants were created for both genes by transposon mutagenesis. In vitro adherence of the Maa1 mutant KOMaa1 to rat L2 lung cells was reduced to the level previously reported for a spontaneous low-adherence mutant of 158p10p9 in which Maa1 is truncated and nonfunctional. Surprisingly, adherence of the Maa2 mutant KOMaa2 was approximately fivefold greater than that of the wild type. Complementation of KOMaa1 and KOMaa2 with wild-type alleles of
maa1
and
maa2
, respectively, returned adherence to wild-type levels. This work confirms our earlier observation that Maa1 is a major adhesin for
M. arthritidis
strain 158p10p9. Maa2, on the other hand, may play a suppressive or modulatory role, possibly serving to release organisms from microcolonies at certain stages of infection.
Meningococcal Outer Membrane Protein NhhA Is Essential for Colonization and Disease by Preventing Phagocytosis and Complement Attack
Authors: Sjölinder Hong , Eriksson Jens , Maudsdotter Lisa , Aro Helena , Jonsson Ann-Beth 
Published: September 2008

ABSTRACT

Neisseria meningitidis
is a leading cause of meningitis and septicemia worldwide, with a rapid onset of disease and a high morbidity and mortality. NhhA is a meningococcal outer membrane protein included in the family of trimeric autotransporter adhesins. The protein binds to the extracellular matrix proteins heparan sulfate and laminin and facilitates attachment to host epithelial cells. In this study, we show that NhhA is essential for bacterial colonization of the nasopharyngeal mucosa in a murine model of meningococcal disease. Successful colonization depends on bacterial attachment but also to the capacity to overcome innate host immune responses. We found that NhhA protected bacteria from phagocytosis, which is important for the mucosal survival of bacteria. In addition, NhhA mediated extensive serum resistance that increased bacterial survival in blood and promoted lethal sepsis. The presence of NhhA protected bacteria from complement-mediated killing by preventing the deposition of the membrane attack complex. Taken together, the results of this work reveal that NhhA inhibits phagocytosis and protects bacteria against complement-mediated killing, which enhances both nasal colonization and the development of sepsis in vivo.
Important Role for Toll-Like Receptor 9 in Host Defense against Meningococcal Sepsis
Authors: Sjölinder Hong , Mogensen Trine H. , Kilian Mogens , Jonsson Ann-Beth , Paludan Søren R. 
Published: September 2008

ABSTRACT

Neisseria meningitidis
is a leading cause of meningitis and sepsis. The pathogenesis of meningococcal disease is determined by both bacterial virulence factors and the host inflammatory response. Toll-like receptors (TLRs) are prominent activators of the inflammatory response, and TLR2, -4, and -9 have been reported to be involved in the host response to
N. meningitidis
. While TLR4 has been suggested to play an important role in early containment of infection, the roles of TLR2 and TLR9 in meningococcal disease are not well described. Using a model for meningococcal sepsis, we report that TLR9
−/−
mice displayed reduced survival and elevated levels of bacteremia compared to wild-type mice. In contrast, TLR2
−/−
mice controlled the infection in a manner comparable to that of wild-type mice. TLR9 deficiency was also associated with reduced bactericidal activity in vitro, which was accompanied by reduced production of nitric oxide by TLR9-deficient macrophages. Interestingly, TLR9
−/−
mice recruited more macrophages to the bloodstream than wild-type mice and produced elevated levels of cytokines at late time points during infection. At the cellular level, activation of signal transduction and induction of cytokine gene expression were independent of TLR2 or TLR9 in macrophages and conventional dendritic cells. In contrast, plasmacytoid dendritic cells relied entirely on TLR9 to induce these activities. Thus, our data demonstrate an important role for TLR9 in host defense against
N. meningitidis
.
Recombination-Based In Vivo Expression Technology IdentifiesHelicobacter pyloriGenes Important for Host Colonization
Authors: Castillo Andrea R. , Woodruff Andrew J. , Connolly Lynn E. , Sause William E. , Ottemann Karen M. 
Published: September 2008

ABSTRACTHere we undertook to identify colonization and gastric disease-promoting factors of the human gastric pathogenHelicobacter pylorias genes that were induced in response to the stomach environment. Using recombination-based in vivo expression technology (RIVET), we identified six promoters induced in the host compared to laboratory conditions. Three of these promoters, designated Pivi10, Pivi66, and Pivi77, regulate genes thatH. pylorimay use to interact with other microbes or the host. Pivi10likely regulates themobA,mobB, andmobDgenes, which have potential roles in horizontal gene transfer through plasmid mobilization. Pivi66occurs in the cytotoxin-associated gene pathogenicity island, a genomic region known to be associated with more severe disease outcomes, and likely regulatescagZ,virB11, andvirD4. Pivi77likely regulates HP0289, an uncharacterized paralogue of thevacAcytotoxin gene. We assessed the roles of a subset of these genes in colonization by creating deletion mutants and analyzing them in single-strain and coinfection experiments. We found that amobABDmutant was defective for murine host colonization and that acagZmutant outcompeted the wild-type strain in a coinfection analysis. Our work supports the conclusion that RIVET is a valuable tool for identifyingH. pylorifactors with roles in host colonization.
CadA Negatively Regulates
Escherichia coli
O157:H7 Adherence and Intestinal Colonization
Authors: Vazquez-Juarez Roberto C. , Kuriakose Jeeba A. , Rasko David A. , Ritchie Jennifer M. , Kendall Melissa M. , Slater Terry M. , Sinha Mala , Luxon Bruce A. , Popov Vsevolod L. , Waldor Matthew K. , Sperandio Vanessa , Torres Alfredo G. 
Published: September 2008

ABSTRACT

Adherence of pathogenic
Escherichia coli
strains to intestinal epithelia is essential for infection. For enterohemorrhagic
E. coli
(EHEC) serotype O157:H7, we have previously demonstrated that multiple factors govern this pathogen's adherence to HeLa cells (A. G. Torres and J. B. Kaper, Infect. Immun. 71:4985-4995, 2003). One of these factors is CadA, a lysine decarboxylase, and this protein has been proposed to negatively regulate virulence in several enteric pathogens. In the case of EHEC strains, CadA modulates expression of the intimin, an outer membrane adhesin involved in pathogenesis. Here, we inactivated
cadA
in O157:H7 strain 86-24 to investigate the role of this gene in EHEC adhesion to tissue-cultured monolayers, global gene expression patterns, and colonization of the infant rabbit intestine. The
cadA
mutant did not possess lysine decarboxylation activity and was hyperadherent to tissue-cultured cells. Adherence of the
cadA
mutant was nearly twofold greater than that of the wild type, and the adherence phenotype was independent of pH, lysine, or cadaverine in the media. Additionally, complementation of the
cadA
defect reduced adherence back to wild-type levels, and it was found that the mutation affected the expression of the intimin protein. Disruption of the
eae
gene (intimin-encoding gene) in the
cadA
mutant significantly reduced its adherence to tissue-cultured cells. However, adherence of the
cadA eae
double mutant was greater than that of an 86-24
eae
mutant, suggesting that the enhanced adherence of the
cadA
mutant is not entirely attributable to enhanced expression of intimin in this background. Gene array analysis revealed that the
cadA
mutation significantly altered EHEC gene expression patterns; expression of 1,332 genes was downregulated and that of 132 genes was upregulated in the mutant compared to the wild-type strain. Interestingly, the gene expression variation shows an EHEC-biased gene alteration including intergenic regions. Two putative adhesins, flagella and F9 fimbria, were upregulated in the
cadA
mutant, suggestive of their association with adherence in the absence of the Cad regulatory mechanism. In the infant rabbit model, the
cadA
mutant outcompeted the wild-type strain in the ileum but not in the cecum or mid-colon, raising the possibility that CadA negatively regulates EHEC pathogenicity in a tissue-specific fashion.
Immunization with Recombinant V10 Protects Cynomolgus Macaques from Lethal Pneumonic Plague
Authors: Cornelius Claire A. , Quenee Lauriane E. , Overheim Katie A. , Koster Frederick , Brasel Trevor L. , Elli Derek , Ciletti Nancy A. , Schneewind Olaf 
Published: September 2008

ABSTRACTVaccine and therapeutic strategies that prevent infections withYersinia pestishave been sought for over a century. Immunization with live attenuated (nonpigmented) strains and immunization with subunit vaccines containing recombinant low-calcium-response V antigen (rLcrV) and recombinant F1 (rF1) antigens are considered effective in animal models. Current antiplague subunit vaccines in development for utilization in humans contain both antigens, either as equal concentrations of the two components (rF1 plus rLcrV) or as a fusion protein (rF1-rLcrV). Here, we show that immunization with either purified rLcrV (a protein at the tip of type III needles) or a variant of this protein, recombinant V10 (rV10) (lacking amino acid residues 271 to 300), alone or in combination with rF1, prevented pneumonic lesions and disease pathogenesis. In addition, passive immunization studies showed that specific antibodies of macaques immunized with rLcrV, rV10, or rF1, either alone or in combination, conferred protection against bubonic plague challenge in mice. Finally, we found that when we compared the reactivities of anti-rLcrV and anti-rV10 immune sera from cynomolgus macaques, BALB/c mice, and brown Norway rats with LcrV-derived peptides, rV10, but not rLcrV immune sera, lacked antibodies recognizing linear LcrV oligopeptides.
In-transit lymph node metastases in breast cancer: a possible source of local recurrence after Sentinel Node procedure
Authors: van Deurzen C H M , Borgstein P J , van Diest P J 
Published: September 2008

Aims:In-transit lymph node metastases are a common phenomenon in melanoma patients and have been increasingly recognised since the introduction of the Sentinel Node (SN) procedure. To which extent this also occurs in patients with breast cancer has not been studied yet. The aim of this study was therefore to explore the occurrence of in-transit lymph node metastases in patients with breast cancer.Methods:Afferent lymph vessels to the SN identified by blue dye were removed from 17 patients with breast cancer during a regular SN procedure.Results:Three out of 17 patients showed a lymph node associated with the afferent lymph vessel. One of these lymph nodes showed a breast cancer macrometastasis, to be regarded as an in-transit metastasis. This metastasis would normally have been left in situ.Conclusions:In-transit lymph nodes associated with the afferent SN lymph vessels seem to occur in a significant proportion of patients with breast cancer. These lymph nodes may contain metastases, which are a potential source of local recurrence when left in situ. This finding generates the hypothesis that there may be an indication to remove these lymph vessels during the SN procedure.
METADATA RANKING AND PRUNING FOR FAILURE DETECTION IN GRIDS
Authors: ZEINALIPOUR-YAZTI DEMETRIOS , PAPADAKIS HARRIS , GEORGIOU CHRYSSIS , DIKAIAKOS MARIOS D. 
Published: September 2008

The objective of Grid computing is to make processing power as accessible and easy to use as electricity and water. The last decade has seen an unprecedented growth in Grid infrastructures which nowadays enables large-scale deployment of applications in the scientific computation domain. One of the main challenges in realizing the full potential of Grids is making these systems dependable. In this paper we present FailRank, a novel framework for integrating and ranking information sources that characterize failures in a grid system. After the failing sites have been ranked, these can be eliminated from the job scheduling resource pool yielding in that way a more predictable, dependable and adaptive infrastructure. We also present the tools we developed towards evaluating the FailRank framework. In particular, we present the FailBase Repository which is a 38GB corpus of state information that characterizes the EGEE Grid for one month in 2007. Such a corpus paves the way for the community to systematically uncover new, previously unknown patterns and rules between the multitudes of parameters that can contribute to failures in a Grid environment. Additionally, we present an experimental evaluation study of the FailRank system over 30 days which shows that our framework identifies failures in 93% of the cases and can achieve this by only fetching 65% of the available information sources. We believe that our work constitutes another important step towards realizing adaptive Grid computing systems.
The Translational Research Working Group Developmental Pathway for Image-Based Assessment Modalities
Authors: Dorfman Gary S. , Sullivan Daniel C. , Schnall Mitchell D. , Matrisian Lynn M. ,   for the Translational Research Working Group
Published: September 2008

Abstract
The Image-based assessment modality (IM) pathway refers to one of six Translational Research Working Group (TRWG) pathways that, together, describe the core domains of early translational cancer research. This pathway focuses on approaches that are based on the interaction of energy and living organisms to analyze tissue noninvasively so as to reveal properties relevant to the detection, diagnosis, or prognosis of cancer and precancer; or the response of the cancer to therapy. Examples include, but are not limited to, magnetic resonance imaging and positron emission tomography, as well as contemporary contrast agents designed to probe specific molecular constituents of tumors. The IM pathway is presented as a general outline of the steps required for the effective development, optimization, testing, and validation of image-based modalities. The distinctive features of the IM pathway and issues encountered that represent obstacles to effective and efficient progress through the pathway are discussed. The IM pathway also forms a framework to identify opportunities to address current barriers and is expected to adapt and evolve as the field advances.