bluuebunny/crossref_metadata_2025 huggingface dataset:
‘Everyone has a story to tell’
Authors: Thumim Nancy
Published: October 2009

This article addresses a global phenomenon: mediated selfrepresentations by ‘ordinary people’, and focuses on public cultural institutions. In order to address how processes of mediation shape institutionally mediated self-representations, the article explores two UK projects, the Museum of London’s London’s Voices and BBC Wales’ Capture Wales. It is suggested that processes of institutional mediation are constituted through tensions in four key areas: the purposes of the projects; the construct of the ‘ordinary person’; the construct of ‘community’; and defining and achieving quality. I argue that critical analysis of the production processes shaping self-representations is crucial to examining the challenge to the power of media institutions implied by their inviting ‘ordinary people’ to represent themselves. The article concludes that, while institutional power is not fundamentally altered in the projects discussed, nevertheless empowerment of participants does have the potential to effect shifts in the role of public cultural institutions; and this is important at a time when that role is questioned, worldwide, as a result of technological, social and political developments. Finally, I suggest that the notion of mediation processes as constituted through tensions, provides analytic tools with which to critically examine the self-representation landscape.
Selling Alberta at the Mall
Authors: Gauthier Jennifer L.
Published: October 2009

This article examines the representation of the Canadian province of Alberta at the 2006 Smithsonian Folklife Festival. Through a close analysis of the site layout of the festival, the author points to a conflict between the anthropological goals of the Smithsonian Institution and the political/industrial goals of the province. The article draws upon scholarship from the fields of anthropology, museum studies and cultural studies, using Gramsci’s notion of folklore and a comparison between the Folklife Festival and World’s Fairs.
Understanding homeschooling
Authors: Kunzman Robert
Published: October 2009

Drawing from six years of qualitative research, this article analyzes the broad range of proposed and existing homeschool regulations throughout the United States. It argues that current homeschool regulations — and most proposals for how to improve them — misjudge the complexity of such an endeavor; state resources are misused and the basic interests of children are not protected. Theoretical arguments about the relative interests of parents, children and the state are important to consider, but our policies must also recognize the limits of what we can and should demand of this unique form of nonpublic schooling. A more modest approach to regulation that focuses on basic skills testing would ultimately be more effective at helping the students who need it most.
Leadership as the Hybrid Production of Presence(s)
Authors: Fairhurst Gail T. , Cooren François
Published: October 2009

Leadership scholars and lay actors often attribute a certain presence to great leaders in describing a commanding style or a charismatic personality. However, leadership presence and its mirror concept, absence, have been difficult concepts for researchers to study. This article proposes to redress this short coming using actor-network theory (ANT). In ANT, the focus is on human and nonhuman agents, their hybrid forms, networked socialaction, and macro acting, the latter of which enables leaders or followers to speak on behalf of their organizations. Together with ANT’s emphasis on the role of narrative, this approach directs analysts to the situated construction of actor networks in which leadership presence or absence is attributed. An emphasis on discourse also shows how various actants are imbued with meaning, enabling analysts to unravel networks andflows of power associated with leadership presence/absence. Leadership discourses involving charismatic/transformational leadership are considered as well as the disaster management networking associated with two US Governors, Arnold Schwarzenegger and Kathleen Blanco, for their respective handling of the California wildfires and hurricane Katrina.
Effect of nitrogen content on nanostructure and mechanical properties of TiCxNy thin films
Authors: Wang J P , Lu Y H , Shen Y G
Published: October 2009

A series of TiCxNy thin films were deposited at 500°C on Si (100) substrates by way of incorporation of different amounts of nitrogen into TiC0·45 using reactive unbalanced dc magnetron sputtering method. Their phase configurations, microstructures and mechanical behaviours were subsequently investigated by X-ray diffraction, X-ray photoelectron spectroscopy and microindentation methods. The result indicated that TiC0·45 showed a fcc-like B-NaCl polycrystallite, and a solid solution nanocrystalline (nc-) TiCxNy with the same structure was formed by way of dissolution of nitrogen into TiC0·45 lattice when the atomic ratio of (C+N)/Ti was less than one unit. Both hardness and residual compressive stress values were increased with increasing N content. Their maximums were believed to be obtained at nc-Ti(C,N) solid solution with an atomic ratio of one unit. Enhancement of both of them was attributed to solid solution.
Pneumolysin induces release of matrix metalloproteinase-8 and -9 from human neutrophils
Authors: Cockeran R. , Mitchell T. J. , Feldman C. , Anderson R.
Published: October 2009

The research question addressed in the current study was: does the pneumococcal pore-forming toxin, pneumolysin, mobilise matrix metalloproteinase (MMP) -8 and -9 from isolated human blood neutrophils at sublytic concentrations of 5, 10 and 20 ng·mL−1?

MMPs were measured in the supernatants of unstimulated neutrophils and of cells exposed to pneumolysin and the chemoattractantN-formyl-l-methionyl-l-leucyl-l-phenylalanine (f-MLP; 0.1 μM), individually and in combination, using ELISA procedures, and alterations in cytosolic Ca2+concentrations were monitored using a fura-2 acetoxymethyl ester (fura-2/AM)-based spectrofluorimetric method.

Treatment of neutrophils with pneumolysin alone caused dose-related release of both MMPs, whereas f-MLP caused modest increases; the combination of both activators was, however, most effective. Pneumolysin/f-MLP-activated release of the MMPs from the cells was paralleled by increases in cytosolic Ca2+.

Exposure of human neutrophils to pneumolysin is accompanied by mobilisation of MMPs, which is potentiated by f-MLP. If operativein vivo, pneumolysin-mediated release of MMPs from neutrophils and other cell types may contribute to the pathogenesis of severe pneumococcal disease.
Migrant tuberculosis screening in the EU/EEA: yield, coverage and limitations
Authors: Klinkenberg E. , Manissero D. , Semenza J. C. , Verver S.
Published: October 2009

A systematic literature review was performed with the objective of assessing the effectiveness of tuberculosis (TB) screening methods and strategies in migrants in European Union/European Economic Area (including Switzerland) countries.

Extracted data on yield and coverage were used as indicators of effectiveness. Reported yields varied considerably between studies and countries. Considering only the 14 studies representative of national screening programmes, a median yield of TB disease of 0.18% (interquartile range 0.10–0.35%) was reported.

The data did not indicate differences in effectiveness between the three main strategies: 1) screening at port of entry; 2) screening just after arrival in reception/holding centres; and 3) screening in the community following arrival in European Union countries. The variation seen probably reflects variation in risk factors for TB, in particular the composition of the migrants entering the country.

Recommendations include the need for improved data for guiding the optimal frequency and duration of screening; assessment and improvement of cost-effectiveness; access to healthcare for migrants, including illegal migrants; ensuring a continuum of care for those screened; and consideration of screening for latent TB infection with caution. Finally, screening should be a component of a wider approach, rather than a stand-alone intervention.
Quantitative trait loci for resistance to trichostrongylid infection in Spanish Churra sheep
Authors: Gutiérrez-Gil Beatriz , Pérez Jorge , Álvarez Lorena , Martínez-Valladares Maria , de la Fuente Luis-Fernando , Bayón Yolanda , Meana Aranzazu , Primitivo Fermin San , Rojo-Vázquez Francisco-Antonio , Arranz Juan-José
Published: October 2009

Background

For ruminants reared on grazing systems, gastrointestinal nematode (GIN) parasite infections represent the class of diseases with the greatest impact on animal health and productivity. Among the many possible strategies for controlling GIN infection, the enhancement of host resistance through the selection of resistant animals has been suggested by many authors. Because of the difficulty of routinely collecting phenotypic indicators of parasite resistance, information derived from molecular markers may be used to improve the efficiency of classical genetic breeding.

Methods

A total of 181 microsatellite markers evenly distributed along the 26 sheep autosomes were used in a genome scan analysis performed in a commercial population of Spanish Churra sheep to detect chromosomal regions associated with parasite resistance. Following a daughter design, we analysed 322 ewes distributed in eight half-sib families. The phenotypes studied included two faecal egg counts (LFEC0 and LFEC1), anti-Teladorsagia circumcincta LIV IgA levels (IgA) and serum pepsinogen levels (Peps).

Results

The regression analysis revealed one QTL at the 5% genome-wise significance level on chromosome 6 for LFEC1 within the marker interval BM4621-CSN3. This QTL was found to be segregating in three out of the eight families analysed. Four other QTL were identified at the 5% chromosome-wise level on chromosomes 1, 10 and 14. Three of these QTL influenced faecal egg count, and the other one had an effect on IgA levels.

Conclusion

This study has successfully identified segregating QTL for parasite resistance traits in a commercial population. For some of the QTL detected, we have identified interesting coincidences with QTL previously reported in sheep, although most of those studies have been focused on young animals. Some of these coincidences might indicate that some common underlying loci affect parasite resistance traits in different sheep breeds. The identification of new QTL may suggest the existence of complex host-parasite relationships that have unique features depending on the host-parasite combination, perhaps due to the different mechanisms underlying resistance in adult sheep (hypersensitivity reactions) and lambs (immunity). The most significant QTL identified on chromosome 6 for LFEC
1 may be the target for future fine-mapping research efforts.
A novel R-package graphic user interface for the analysis of metabonomic profiles
Authors: Izquierdo-García Jose L , Rodríguez Ignacio , Kyriazis Angelos , Villa Palmira , Barreiro Pilar , Desco Manuel , Ruiz-Cabello Jesús
Published: October 2009

Background

Analysis of the plethora of metabolites found in the NMR spectra of biological fluids or tissues requires data complexity to be simplified. We present a graphical user interface (GUI) for NMR-based metabonomic analysis. The "Metabonomic Package" has been developed for metabonomics research as open-source software and uses the R statistical libraries.

Results

The package offers the following options:

Raw 1-dimensional spectra processing: phase, baseline correction and normalization.

Importing processed spectra.

Including/excluding spectral ranges, optional binning and bucketing, detection and alignment of peaks.

Sorting of metabolites based on their ability to discriminate, metabolite selection, and outlier identification.

Multivariate unsupervised analysis: principal components analysis (PCA).

Multivariate supervised analysis: partial least squares (PLS), linear discriminant analysis (LDA), k-nearest neighbor classification.

Neural networks.

Visualization and overlapping of spectra.

Plot values of the chemical shift position for different samples.

Furthermore, the "Metabonomic" GUI includes a console to enable other kinds of analyses and to take advantage of all R statistical tools.

Conclusion

We made complex multivariate analysis user-friendly for both experienced and novice users, which could help to expand the use of NMR-based metabonomics.
multiplierz: an extensible API based desktop environment for proteomics data analysis
Authors: Parikh Jignesh R , Askenazi Manor , Ficarro Scott B , Cashorali Tanya , Webber James T , Blank Nathaniel C , Zhang Yi , Marto Jarrod A
Published: October 2009

Background

Efficient analysis of results from mass spectrometry-based proteomics experiments requires access to disparate data types, including native mass spectrometry files, output from algorithms that assign peptide sequence to MS/MS spectra, and annotation for proteins and pathways from various database sources. Moreover, proteomics technologies and experimental methods are not yet standardized; hence a high degree of flexibility is necessary for efficient support of high- and low-throughput data analytic tasks. Development of a desktop environment that is sufficiently robust for deployment in data analytic pipelines, and simultaneously supports customization for programmers and non-programmers alike, has proven to be a significant challenge.

Results

We describe multiplierz, a flexible and open-source desktop environment for comprehensive proteomics data analysis. We use this framework to expose a prototype version of our recently proposed common API (mzAPI) designed for direct access to proprietary mass spectrometry files. In addition to routine data analytic tasks, multiplierz supports generation of information rich, portable spreadsheet-based reports. Moreover, multiplierz is designed around a "zero infrastructure" philosophy, meaning that it can be deployed by end users with little or no system administration support. Finally, access to multiplierz functionality is provided via high-level Python scripts, resulting in a fully extensible data analytic environment for rapid development of custom algorithms and deployment of high-throughput data pipelines.

Conclusion

Collectively, mzAPI and multiplierz facilitate a wide range of data analysis tasks, spanning technology development to biological annotation, for mass spectrometry-based proteomics research.
Annotation, phylogenetics, and expression of the nuclear receptors in Daphnia pulex
Authors: Thomson Susanne A , Baldwin William S , Wang Ying H , Kwon Gwijun , LeBlanc Gerald A
Published: October 2009

Background

The nuclear receptor superfamily currently consists of seven gene subfamilies that encompass over 80 distinct receptor proteins. These transcription factors typically share a common five-domain structure with a highly conserved DNA-binding domain. Some nuclear receptors are ubiquitous among the metazoans, while others are unique to specific phylogenetic groups. Crustaceans represent the second largest group of arthropods with insects being the largest. However, relative to insects, little is known about the nuclear receptors of crustaceans. The aim of this study was to identify putative nuclear receptors from the first assembled genome of a crustaceanDaphnia pulexhttp://wFleaBase.org. Nuclear receptor expression was evaluated and receptors were subjected to phylogenetic analyses to gain insight into evolution and function.

Results

Twenty-five putative nuclear receptors were identified inD. pulexbased on the presence of a conserved DNA-binding domain. All of the nuclear receptor protein sequences contain a highly homologous DNA-binding domain and a less conserved ligand-binding domain with the exception of the NR0A group. These receptors lack a ligand-binding domain. Phylogenetic analysis revealed the presence of all seven receptor subfamilies. TheD. pulexgenome contains several nuclear receptors that have vertebrate orthologs. However, several nuclear receptor members that are represented in vertebrates are absent fromD. pulex. Notable absences include receptors of the 1C group (peroxisome proliferators-activated receptors), the 3A group (estrogen receptor), and the 3C group (androgen, progestogen, mineralcorticoid, and glucocorticoid receptors). TheD. pulexgenome also contains nuclear receptor orthologs that are present in insects and nematodes but not vertebrates, including putative nuclear receptors within the NR0A group. A novel group of receptors, designated HR97, was identified inD. pulexthat groups with the HR96/CeNHR8/48/DAF12 clade, but forms its own sub-clade. Gene products were detected in adult femaleD. pulexfor 21 of the 25 receptors.

Conclusion

Nuclear receptors are ancient proteins with highly conserved DNA-binding domains. The DNA-binding domains of the nuclear receptors ofD. pulexcontain the same degree of conservation that is typically found within nuclear receptors of other species. Most of the receptors identified inD. pulexhave orthologs within the vertebrate and invertebrate lineages examined with the exception of the novel HR97 group and the Dappu-HR10 and potentially the Dappu-HR11 receptors found inD. pulex. These groups of receptors may harbour functions that are intrinsic to crustacean physiology.
Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar)
Authors: Andreassen Rune , Lunner Sigbjørn , Høyheim Bjørn
Published: October 2009

Background

Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs) are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. FLIcs will therefore be an extremely useful resource for the Atlantic salmon sequencing project. In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. In contrast to the large number of ESTs available, including the ESTs from 23 developmental and tissue specific cDNA libraries contributed by the Salmon Genome Project (SGP), the number of sequences where the full-length of the cDNA insert has been determined has been small.

Results

High quality full-length insert sequences from 560 pre-smolt white muscle tissue specific cDNAs were generated, accession numbers [GenBank: BT043497 - BT044056]. Five hundred and ten (91%) of the transcripts were annotated using Gene Ontology (GO) terms and 440 of the FLIcs are likely to contain a complete coding sequence (cCDS). The sequence information was used to identify putative paralogs, characterize salmon Kozak motifs, polyadenylation signal variation and to identify motifs likely to be involved in the regulation of particular genes. Finally, conserved 7-mers in the 3'UTRs were identified, of which some were identical to miRNA target sequences.

Conclusion

This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We have demonstrated that many FLIcs contained a complete coding sequence (cCDS). This suggests that the remaining cDNA libraries generated by SGP represent a valuable cCDS FLIc source. The conservation of 7-mers in 3'UTRs indicates that these motifs are functionally important. Identity between some of these 7-mers and miRNA target sequences suggests that they are miRNA targets in Salmo salar transcripts as well.
EST and microarray analysis of horn development in Onthophagus beetles
Authors: Kijimoto Teiya , Costello James , Tang Zuojian , Moczek Armin P , Andrews Justen
Published: October 2009

Background

The origin of novel traits and their subsequent diversification represent central themes in evo-devo and evolutionary ecology. Here we explore the genetic and genomic basis of a class of traits that is both novel and highly diverse, in a group of organisms that is ecologically complex and experimentally tractable: horned beetles.

Results

We developed two high quality, normalized cDNA libraries for larval and pupal Onthophagus taurus and sequenced 3,488 ESTs that assembled into 451 contigs and 2,330 singletons. We present the annotation and a comparative analysis of the conservation of the sequences. Microarrays developed from the combined libraries were then used to contrast the transcriptome of developing primordia of head horns, prothoracic horns, and legs. Our experiments identify a first comprehensive list of candidate genes for the evolution and diversification of beetle horns. We find that developing horns and legs show many similarities as well as important differences in their transcription profiles, suggesting that the origin of horns was mediated partly, but not entirely, by the recruitment of genes involved in the formation of more traditional appendages such as legs. Furthermore, we find that horns developing from the head and prothorax differ in their transcription profiles to a degree that suggests that head and prothoracic horns are not serial homologs, but instead may have evolved independently from each other.

Conclusion

We have laid the foundation for a systematic analysis of the genetic basis of horned beetle development and diversification with the potential to contribute significantly to several major frontiers in evolutionary developmental biology.
Selenoproteins regulate macrophage invasiveness and extracellular matrix-related gene expression
Authors: Carlson Bradley A , Yoo Min-Hyuk , Sano Yasuyo , Sengupta Aniruddha , Kim Jin Young , Irons Robert , Gladyshev Vadim N , Hatfield Dolph L , Park Jin Mo
Published: October 2009

Background

Selenium, a micronutrient whose deficiency in diet causes immune dysfunction and inflammatory disorders, is thought to exert its physiological effects mostly in the form of selenium-containing proteins (selenoproteins). Incorporation of selenium into the amino acid selenocysteine (Sec), and subsequently into selenoproteins is mediated by Sec tRNA[Ser]Sec.

Results

To define macrophage-specific selenoprotein functions, we generated mice with the Sec tRNA[Ser]Sec gene specifically deleted in myeloid cells. These mutant mice were devoid of the "selenoproteome" in macrophages, yet exhibited largely normal inflammatory responses. However, selenoprotein deficiency led to aberrant expression of extracellular matrix-related genes, and diminished migration of macrophages in a protein gel matrix.

Conclusion

Selenium status may affect immune defense and tissue homeostasis through its effect on selenoprotein expression and the trafficking of tissue macrophages.
Response of Bacillus cereus ATCC 14579 to challenges with sublethal concentrations of enterocin AS-48
Authors: Grande Burgos María J , Kovács Ákos T , Mirończuk Aleksandra M , Abriouel Hikmate , Gálvez Antonio , Kuipers Oscar P
Published: October 2009

Background

Enterocin AS-48 is produced by Enterococcus faecalis S48 to compete with other bacteria in their environment. Due to its activity against various Gram positive and some Gram negative bacteria it has clear potential for use as a food preservative. Here, we studied the effect of enterocin AS-48 challenges on vegetative cells of Bacillus cereus ATCC 14579 by use of transcriptome analysis.

Results

Of the 5200 genes analysed, expression of 24 genes was found to change significantly after a 30 min treatment with a subinhibitory bacteriocin concentration of 0.5 μg/ml. Most of up-regulated genes encode membrane-associated or secreted proteins with putative transmembrane segments or signal sequences, respectively. One operon involved in arginine metabolism was significantly downregulated. The BC4206-BC4207 operon was found to be the most upregulated target in our experiments. BC4206 codes for a PadR type transcriptional regulator, while BC4207 codes for a hypothetical membrane protein. The operon structure and genes are conserved in B. cereus and B. thuringiensis species, but are not present in B. anthracis and B. subtilis. Using real-time qPCR, we show that these genes are upregulated when we treated the cells with AS-48, but not upon nisin treatment. Upon overexpression of BC4207 in B. cereus, we observed an increased resistance against AS-48. Expression of BC4207 in B. subtilis 168, which lacks this operon also showed increased resistance against AS-48.

Conclusion

BC4207 membrane protein is involved in the resistance mechanism of B. cereus cells against AS-48.
Influences of naturally occurring agents in combination with fluoride on gene expression and structural organization of Streptococcus mutans in biofilms
Authors: Jeon Jae-Gyu , Klein Marlise I , Xiao Jin , Gregoire Stacy , Rosalen Pedro L , Koo Hyun
Published: October 2009

Background

The association of specific bioactive flavonoids and terpenoids with fluoride can modulate the development of cariogenic biofilms by simultaneously affecting the synthesis of exopolysaccharides (EPS) and acid production by Streptococcus mutans, which enhanced the cariostatic effectiveness of fluoride in vivo. In the present study, we further investigated whether the biological actions of combinations of myricetin (flavonoid), tt-farnesol (terpenoid) and fluoride can influence the expression of specific genes of S. mutans within biofilms and their structural organization using real-time PCR and confocal fluorescence microscopy.

Results

Twice-daily treatment (one-minute exposure) during biofilm formation affected the gene expression by S. mutans both at early (49-h) and later (97-h) stages of biofilm development. Biofilms treated with combination of agents displayed lower mRNA levels for gtfB and gtfD (associated with exopolysaccharides synthesis) and aguD (associated with S. mutans acid tolerance) than those treated with vehicle-control (p < 0.05). Furthermore, treatment with combination of agents markedly affected the structure-architecture of S. mutans biofilms by reducing the biovolume (biomass) and proportions of both EPS and bacterial cells across the biofilm depth, especially in the middle and outer layers (vs. vehicle-control, p < 0.05). The biofilms treated with combination of agents were also less acidogenic, and had reduced amounts of extracellular insoluble glucans and intracellular polysaccharides than vehicle-treated biofilms (p < 0.05).

Conclusion

The data show that the combination of naturally-occurring agents with fluoride effectively disrupted the expression of specific virulence genes, structural organization and accumulation of S. mutans biofilms, which may explain the enhanced cariostatic effect of our chemotherapeutic approach.
Evolutionary relationships among salivarius streptococci as inferred from multilocus phylogenies based on 16S rRNA-encoding, recA, secA, and secY gene sequences
Authors: Pombert Jean-François , Sistek Viridiana , Boissinot Maurice , Frenette Michel
Published: October 2009

Background

Streptococci are divided into six phylogenetic groups,i.e, anginosus, bovis, mitis, mutans, pyogenic, and salivarius, with the salivarius group consisting of only three distinct species. Two of these species,Streptococcus salivariusandStreptococcus vestibularis, are members of the normal human oral microflora whereas the third,Streptococcus thermophilus, is found in bovine milk. Given thatS. salivariusandS. vestibularisshare several physiological characteristics, in addition to inhabiting the same ecosystem, one would assume that they would be more closely related to each other than toS. thermophilus. However, the few phylogenetic trees published so far suggest thatS. vestibularisis more closely related toS. thermophilus. To determine whether this phylogenetic relationship is genuine, we performed phylogenetic inferences derived fromsecAandsecY, the general secretion housekeeping genes,recA, a gene from a separate genetic locus that encodes a major component of the homologous recombinational apparatus, and 16S rRNA-encoding gene sequences using other streptococcal species as outgroups.

Results

The maximum likelihood (ML) and maximum parsimony (MP) phylogenetic inferences derived from thesecAandrecAgene sequences provided strong support for theS. vestibularis/S. thermophilussister-relationship, whereas 16S rRNA-encoding andsecY-based analyses could not discriminate between alternate topologies. Phylogenetic analyses derived from the concatenation of these sequences unambiguously supported the close affiliation ofS. vestibularisandS. thermophilus.

Conclusion

Our results corroborated the sister-relationship betweenS. vestibularisandS. thermophilusand the concomitant early divergence ofS. salivariusat the base of the salivarius lineage.
Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae
Authors: Teste Marie-Ange , Duquenne Manon , François Jean M , Parrou Jean-Luc
Published: October 2009

Background

Real-time RT-PCR is the recommended method for quantitative gene expression analysis. A compulsory step is the selection of good reference genes for normalization. A few genes often referred to as HouseKeeping Genes (HSK), such as ACT1, RDN18 or PDA1 are among the most commonly used, as their expression is assumed to remain unchanged over a wide range of conditions. Since this assumption is very unlikely, a geometric averaging of multiple, carefully selected internal control genes is now strongly recommended for normalization to avoid this problem of expression variation of single reference genes. The aim of this work was to search for a set of reference genes for reliable gene expression analysis in Saccharomyces cerevisiae.

Results

From public microarray datasets, we selected potential reference genes whose expression remained apparently invariable during long-term growth on glucose. Using the algorithm geNorm, ALG9, TAF10, TFC1 and UBC6 turned out to be genes whose expression remained stable, independent of the growth conditions and the strain backgrounds tested in this study. We then showed that the geometric averaging of any subset of three genes among the six most stable genes resulted in very similar normalized data, which contrasted with inconsistent results among various biological samples when the normalization was performed with ACT1. Normalization with multiple selected genes was therefore applied to transcriptional analysis of genes involved in glycogen metabolism. We determined an induction ratio of 100-fold for GPH1 and 20-fold for GSY2 between the exponential phase and the diauxic shift on glucose. There was no induction of these two genes at this transition phase on galactose, although in both cases, the kinetics of glycogen accumulation was similar. In contrast, SGA1 expression was independent of the carbon source and increased by 3-fold in stationary phase.

Conclusion

In this work, we provided a set of genes that are suitable reference genes for quantitative gene expression analysis by real-time RT-PCR in yeast biological samples covering a large panel of physiological states. In contrast, we invalidated and discourage the use of ACT1 as well as other commonly used reference genes (PDA1, TDH3, RDN18, etc) as internal controls for quantitative gene expression analysis in yeast.
Clinical trial participant characteristics and saliva and DNA metrics
Authors: Nishita Denise M , Jack Lisa M , McElroy Mary , McClure Jennifer B , Richards Julie , Swan Gary E , Bergen Andrew W
Published: October 2009

Background

Clinical trial and epidemiological studies need high quality biospecimens from a representative sample of participants to investigate genetic influences on treatment response and disease. Obtaining blood biospecimens presents logistical and financial challenges. As a result, saliva biospecimen collection is becoming more frequent because of the ease of collection and lower cost. This article describes an assessment of saliva biospecimen samples collected through the mail, trial participant demographic and behavioral characteristics, and their association with saliva and DNA quantity and quality.

Methods

Saliva biospecimens were collected using the Oragene® DNA Self-Collection Kits from participants in a National Cancer Institute funded smoking cessation trial. Saliva biospecimens from 565 individuals were visually inspected for clarity prior to and after DNA extraction. DNA samples were then quantified by UV absorbance, PicoGreen®, and qPCR. Genotyping was performed on 11 SNPs using TaqMan® SNP assays and two VNTR assays. Univariate, correlation, and analysis of variance analyses were conducted to observe the relationship between saliva sample and participant characteristics.

Results

The biospecimen kit return rate was 58.5% among those invited to participate (n = 967) and 47.1% among all possible COMPASS participants (n = 1202). Significant gender differences were observed with males providing larger saliva volume (4.7 vs. 4.5 ml, p = 0.019), samples that were more likely to be judged as cloudy (39.5% vs. 24.9%, p < 0.001), and samples with greater DNA yield as measured by UV (190.0 vs. 138.5, p = 0.002), but reduced % human DNA content (73.2 vs. 77.6 p = 0.005) than females. Other participant characteristics (age, self-identified ethnicity, baseline cigarettes per day) were associated with saliva clarity. Saliva volume and saliva and DNA clarity were positively correlated with total DNA yield by all three quantification measurements (all r > 0.21, P < 0.001), but negatively correlated with % human DNA content (saliva volume r = -0.148 and all P < 0.010). Genotyping completion rate was not influenced by saliva or DNA clarity.

Conclusion

Findings from this study show that demographic and behavioral characteristics of smoking cessation trial participants have significant associations with saliva and DNA metrics, but not with the performance of TaqMan® SNP or VNTR genotyping assays.

Trial registration

COMPASS; registered as NCT00301145 at clinicaltrials.gov.
Candidate genetic analysis of plasma high-density lipoprotein-cholesterol and severity of coronary atherosclerosis
Authors: Chen Suet Nee , Cilingiroglu Mehmet , Todd Josh , Lombardi Raffaella , Willerson James T , Gotto Antonio M , Ballantyne Christie M , Marian AJ
Published: October 2009

Background

Plasma level of high-density lipoprotein-cholesterol (HDL-C), a heritable trait, is an important determinant of susceptibility to atherosclerosis. Non-synonymous and regulatory single nucleotide polymorphisms (SNPs) in genes implicated in HDL-C synthesis and metabolism are likely to influence plasma HDL-C, apolipoprotein A-I (apo A-I) levels and severity of coronary atherosclerosis.

Methods

We genotyped 784 unrelated Caucasian individuals from two sets of populations (Lipoprotein and Coronary Atherosclerosis Study- LCAS, N = 333 and TexGen, N = 451) for 94 SNPs in 42 candidate genes by 5' nuclease assays. We tested the distribution of the phenotypes by the Shapiro-Wilk normality test. We used Box-Cox regression to analyze associations of the non-normally distributed phenotypes (plasma HDL-C and apo A-I levels) with the genotypes. We included sex, age, body mass index (BMI), diabetes mellitus (DM), and cigarette smoking as covariates. We calculated the q values as indicators of the false positive discovery rate (FDR).

Results

Plasma HDL-C levels were associated with sex (higher in females), BMI (inversely), smoking (lower in smokers), DM (lower in those with DM) and SNPs in APOA5, APOC2, CETP, LPL and LIPC (each q ≤0.01). Likewise, plasma apo A-I levels, available in the LCAS subset, were associated with SNPs in CETP, APOA5, and APOC2 as well as with BMI, sex and age (all q values ≤0.03). The APOA5 variant S19W was also associated with minimal lumen diameter (MLD) of coronary atherosclerotic lesions, a quantitative index of severity of coronary atherosclerosis (q = 0.018); mean number of coronary artery occlusions (p = 0.034) at the baseline and progression of coronary atherosclerosis, as indicated by the loss of MLD.

Conclusion

Putatively functional variants of APOA2, APOA5, APOC2, CETP, LPL, LIPC and SOAT2 are independent genetic determinants of plasma HDL-C levels. The non-synonymous S19W SNP in APOA5 is also an independent determinant of plasma apo A-I level, severity of coronary atherosclerosis and its progression.
Stimulation of glioma cell motility by expression, proteolysis, and release of the L1 neural cell recognition molecule
Authors: Yang Muhua , Adla Shalini , Temburni Murali K , Patel Vivek P , Lagow Errin L , Brady Owen A , Tian Jing , Boulos Magdy I , Galileo Deni S
Published: October 2009

Background

Malignant glioma cells are particularly motile and can travel diffusely through the brain parenchyma, apparently without following anatomical structures to guide their migration. The neural adhesion/recognition protein L1 (L1CAM; CD171) has been implicated in contributing to stimulation of motility and metastasis of several non-neural cancer types. We explored the expression and function of L1 protein as a stimulator of glioma cell motility using human high-grade glioma surgical specimens and established rat and human glioma cell lines.

Results

L1 protein expression was found in 17 out of 18 human high-grade glioma surgical specimens by western blotting. L1 mRNA was found to be present in human U-87/LacZ and rat C6 and 9L glioma cell lines. The glioma cell lines were negative for surface full length L1 by flow cytometry and high resolution immunocytochemistry of live cells. However, fixed and permeablized cells exhibited positive staining as numerous intracellular puncta. Western blots of cell line extracts revealed L1 proteolysis into a large soluble ectodomain (~180 kDa) and a smaller transmembrane proteolytic fragment (~32 kDa). Exosomal vesicles released by the glioma cell lines were purified and contained both full-length L1 and the proteolyzed transmembrane fragment. Glioma cell lines expressed L1-binding αvβ5 integrin cell surface receptors. Quantitative time-lapse analyses showed that motility was reduced significantly in glioma cell lines by 1) infection with an antisense-L1 retroviral vector and 2) L1 ectodomain-binding antibodies.

Conclusion

Our novel results support a model of autocrine/paracrine stimulation of cell motility in glioma cells by a cleaved L1 ectodomain and/or released exosomal vesicles containing L1. This mechanism could explain the diffuse migratory behavior of high-grade glioma cancer cells within the brain.
Expression of nodal signalling components in cycling human endometrium and in endometrial cancer
Authors: Papageorgiou Irene , Nicholls Peter K , Wang Fang , Lackmann Martin , Makanji Yogeshwar , Salamonsen Lois A , Robertson David M , Harrison Craig A
Published: October 2009

Background

The human endometrium is unique in its capacity to remodel constantly throughout adult reproductive life. Although the processes of tissue damage and breakdown in the endometrium have been well studied, little is known of how endometrial regeneration is achieved after menstruation. Nodal, a member of the transforming growth factor-beta superfamily, regulates the processes of pattern formation and differentiation that occur during early embryo development.

Methods

In this study, the expression of Nodal, Cripto (co-receptor) and Lefty A (antagonist) was examined by RT-PCR and immunohistochemistry across the menstrual cycle and in endometrial carcinomas.

Results

Nodal and Cripto were found to be expressed at high levels in both stromal and epithelial cells during the proliferative phase of the menstrual cycle. Although immunoreactivity for both proteins in surface and glandular epithelium was maintained at relatively steady-state levels across the cycle, their expression was significantly decreased within the stromal compartment by the mid-secretory phase. Lefty expression, as has previously been reported, was primarily restricted to glandular epithelium and surrounding stroma during the late secretory and menstrual phases. In line with recent studies that have shown that Nodal pathway activity is upregulated in many human cancers, we found that Nodal and Cripto immunoreactivity increased dramatically in the transition from histologic Grade 1 to histologic Grades 2 and 3 endometrial carcinomas. Strikingly, Lefty expression was low or absent in all cancer tissues.

Conclusion

The expression of Nodal in normal and malignant endometrial cells that lack Lefty strongly supports an important role for this embryonic morphogen in the tissue remodelling events that occur across the menstrual cycle and in tumourogenesis.
In Vivo Evidence that Truncated Trkb.T1 Participates in Nociception
Authors: Renn Cynthia L , Leitch Carmen C , Dorsey Susan G
Published: October 2009

Brain-Derived Neurotrophic Factor (BDNF) is a central nervous system modulator of nociception. In animal models of chronic pain, BDNF exerts its effects on nociceptive processing by binding to the full-length receptor tropomyosin-related kinase B (trkB.FL) and transducing intracellular signaling to produce nocifensive behaviors. In addition to trkB.FL, the trkB locus also produces a widely-expressed alternatively-spliced truncated isoform, trkB.T1. TrkB.T1 binds BDNF with high affinity; however the unique 11 amino acid intracellular cytoplasmic tail lacks the kinase domain of trkB.FL. Recently, trkB.T1 was shown to be specifically up-regulated in a model of HIV-associated neuropathic pain, potentially implicating trkB.T1 as a modulator of nociception. Here, we report that trkB.T1 mRNA and protein is up-regulated in the spinal dorsal horn at times following antiretroviral drug treatment and hind paw inflammation in which nocifensive behaviors develop. While genetic depletion of trkB.T1 did not affect baseline mechanical and thermal thresholds, the absence of trkB.T1 resulted in significant attenuation of inflammation- and antiretroviral-induced nocifensive behaviors. Our results suggest that trkB.T1 up-regulation following antiretroviral treatment and tissue inflammation participates in the development and maintenance of nocifensive behavior and may represent a novel therapeutic target for pain treatment.
iTriplet, a rule-based nucleic acid sequence motif finder
Authors: Ho Eric S , Jakubowski Christopher D , Gunderson Samuel I
Published: October 2009

Background

With the advent of high throughput sequencing techniques, large amounts of sequencing data are readily available for analysis. Natural biological signals are intrinsically highly variable making their complete identification a computationally challenging problem. Many attempts in using statistical or combinatorial approaches have been made with great success in the past. However, identifying highly degenerate and long (>20 nucleotides) motifs still remains an unmet challenge as high degeneracy will diminish statistical significance of biological signals and increasing motif size will cause combinatorial explosion. In this report, we present a novel rule-based method that is focused on finding degenerate and long motifs. Our proposed method, named iTriplet, avoids costly enumeration present in existing combinatorial methods and is amenable to parallel processing.

Results

We have conducted a comprehensive assessment on the performance and sensitivity-specificity of iTriplet in analyzing artificial and real biological sequences in various genomic regions. The results show that iTriplet is able to solve challenging cases. Furthermore we have confirmed the utility of iTriplet by showing it accurately predicts polyA-site-related motifs using a dual Luciferase reporter assay.

Conclusion

iTriplet is a novel rule-based combinatorial or enumerative motif finding method that is able to process highly degenerate and long motifs that have resisted analysis by other methods. In addition, iTriplet is distinguished from other methods of the same family by its parallelizability, which allows it to leverage the power of today's readily available high-performance computing systems.
The relationship between disease activity, sleep, psychiatric distress and pain sensitivity in rheumatoid arthritis: a cross-sectional study
Authors: Lee Yvonne C , Chibnik Lori B , Lu Bing , Wasan Ajay D , Edwards Robert R , Fossel Anne H , Helfgott Simon M , Solomon Daniel H , Clauw Daniel J , Karlson Elizabeth W
Published: October 2009

Introduction

Despite recent advances in anti-inflammatory therapy, rheumatoid arthritis (RA) patients continue to rate pain as a priority. The etiology of RA pain is likely multifactorial, including both inflammatory and non-inflammatory components. In this study, we examine the association between disease activity, sleep, psychiatric distress and pain sensitivity in RA.

Methods

Fifty-nine female RA patients completed questionnaires and underwent pressure pain threshold testing to assess hyperalgesia/allodynia at joint and non-joint sites. Blood samples were taken to measure C-reactive protein (CRP). The association between disease activity, sleep problems, psychiatric distress and pain threshold was assessed using Pearson/Spearman correlations and multivariable linear regression. Disease activity levels, sleep problems and psychiatric distress were compared between RA patients with fibromyalgia and RA patients without fibromyalgia.

Results

In unadjusted analyses, CRP was not correlated with pain threshold, but tender joint count was inversely correlated with pain threshold at all sites (P ≤ 0.004). Sleep problems were associated with low pain threshold at all sites (P ≤ 0.0008). Psychiatric distress was associated with low pain threshold at the wrist and thumbnail (P ≤ 0.006). In multivariable linear regression models, CRP was inversely associated with wrist pain threshold (P = 0.003). Sleep problems were inversely associated with pain threshold at all sites (P ≤ 0.01), but psychiatric distress was not. Despite differences in pain threshold, CRP levels and sleep problems between RA patients with fibromyalgia and those without fibromyalgia, associations between these variables did not change when patients with fibromyalgia were excluded.

Conclusions

Multivariable models are essential in analyses of pain. Among RA patients, inflammation is associated with heightened pain sensitivity at joints. In contrast, poor sleep is associated with diffuse pain sensitivity, as noted in central pain conditions such as fibromyalgia. Future studies examining pain sensitivity at joint and non-joint sites may identify patients with different underlying pain mechanisms and suggest alternative approaches to treating RA pain.
Clinical significance of neurological abnormalities in psychosis
Authors: Picchioni Marco M. , Dazzan Paola
Published: October 2009

The neurological deficits in sensory and motor function in schizophrenia have been described using a confusing variety of terms, reflecting their uncertain relevance and significance to psychosis. In this article we explore the nature of neurological abnormalities in psychosis, describe their assessment and suggest their potential relevance for clinician and patient. We propose that the assessment of neurological abnormalities and extrapyramidal side-effects should figure in the assessment of any patient with psychosis, particularly at illness onset. Furthermore, we suggest that neurological abnormalities can inform prognostic predictions and help to identify patients with more complex future care needs.