bluuebunny/crossref_metadata_2025 huggingface dataset:
Suppressing type IV failure via modification of heat affected zone microstructures using high boron content in 9Cr heat resistant steel welded joints
Authors: Kondo M. , Tabuchi M. , Tsukamoto S. , Yin F. , Abe F.
Published: April 2006

Creep rupture strength at 923 K and microstructural evolution of welded joints have been investigated for high boron–low nitrogen–9Cr heat resistant steels developed at the National Institute for Materials Science (Japan). Welded joints were prepared from plates containing 47–180 ppm boron using gas tungsten arc welding and Inconel type filler metal, and showed superior creep properties to those of welded joints of conventional high chromium steels such as P92 and P122. No type IV failure was observed in the boron steel welded joints. A large grained microstructure was observed in the heat affected zone heated to Ac 3 ( Ac 3 HAZ) during welding, whereas the grains are refined at the same location in conventional steel welded joints. The simulated Ac 3 HAZ structures of the boron steels have a creep life almost equal to that of the base metal. Large grained HAZ microstructures and stabilisation of M23C6 precipitates are probable reasons for suppression of type IV failure and improved creep resistance of the boron steel welded joints.
IL-4 induced MUC4 enhancement in respiratory epithelial cells in vitro is mediated through JAK-3 selective signaling
Authors: Damera Gautam , Xia Baoyun , Sachdev Goverdhan P
Published: April 2006

Background

Recent studies have identified MUC4 mucin as a ligand for activation of ErbB2, a receptor tyrosine kinase that modulates epithelial cell proliferation following epithelial damage in airways of asthmatics. In this study, we investigated the potential role of IL-4, one of the Th2 inflammatory cytokines persistent in asthmatic airways, in regulating MUC4 expression using a cell line NCI-H650.

Methods

Real time PCR analysis was performed to determine concentration and time dependent effects of IL-4 uponMUC4expression. Nuclear run on experiments were carried out to explore potential transcriptional modulation. Western blotting experiments using a monoclonal antibody specific to ASGP-2 domain of MUC4 were performed to analyze MUC4 glycoprotein levels in plasma membrane fractions. To analyze potential signal transduction cascades, IL-4 treated confluent cultures were co-incubated, separately with a pan-JAK inhibitor, a JAK-3 selective inhibitor or a MEK-1, 2 (MAPK) inhibitor at various concentrations beforeMUC4transcript analysis. Corresponding transcription factor activation was tested by western blotting using a monoclonal p-STAT-6 antibody.

Results

MUC4levels increased in a concentration and time specific fashion reaching peak expression at 2.5 ng/ml and 8 h. Nuclear run on experiments revealed transcriptional enhancement. Corresponding increases in MUC4 glycoprotein levels were observed in plasma membrane fractions. Pan-JAK inhibitor revealed marked reduction in IL-4 stimulatedMUC4levels and JAK3 selective inhibitor down-regulated MUC4 mRNA expression in a concentration-dependent fashion. In accordance with the above observations, STAT-6 activation was detected within 5 minutes of IL-4 stimulus. No effect inMUC4levels was observed on using a MAPK inhibitor.

Conclusion

These observations signify a potential role for IL-4 in MUC4 up-regulation in airway epithelia.
Neonatal immune responses to TLR2 stimulation: Influence of maternal atopy on Foxp3 and IL-10 expression
Authors: Schaub Bianca , Campo Monica , He Hongzhen , Perkins David , Gillman Matthew W , Gold Diane R , Weiss Scott , Lieberman Ellice , Finn Patricia W
Published: April 2006

Background

Maternal atopic background and stimulation of the adaptive immune system with allergen interact in the development of allergic disease. Stimulation of the innate immune system through microbial exposure, such as activation of the innate Toll-like-receptor 2 (TLR2), may reduce the development of allergy in childhood. However, little is known about the immunological effects of microbial stimulation on early immune responses and in association with maternal atopy.

Methods

We analyzed immune responses of cord blood mononuclear cells (CBMC) from 50 healthy neonates (31 non-atopic and 19 atopic mothers). Cells were stimulated with the TLR2 agonist peptidoglycan (Ppg) or the allergen house dust mite Dermatophagoides farinae (Derf1), and results compared to unstimulated cells. We analyzed lymphocyte proliferation and cytokine secretion of CBMC. In addition, we assessed gene expression associated with T regulatory cells including the transcription factor Foxp3, the glucocorticoid-induced TNF receptor (GITR), and the cytotoxic lymphocyte antigen 4 (CTLA4). Lymphocyte proliferation was measured by3H-Thymidine uptake, cytokine concentrations determined by ELISA, mRNA expression of T cell markers by real-time RT-PCR.

Results

Ppg stimulation induced primarily IL-10 cytokine production, in addition to IFN-γ, IL-13 and TNF-α secretion. GITR was increased following Ppg stimulation (p = 0.07). Ppg-induced IL-10 production and induction of Foxp3 were higher in CBMC without, than with maternal atopy (p = 0.04, p = 0.049). IL-10 production was highly correlated with increased expression of Foxp3 (r = 0.53, p = 0.001), GITR (r = 0.47, p = 0.004) and CTLA4 (r = 0.49, p = 0.003), independent of maternal atopy.

Conclusion

TLR2 stimulation with Ppg induces IL-10 and genes associated with T regulatory cells, influenced by maternal atopy. Increased IL-10 and Foxp3 induction in CBMC of non-atopic compared to atopic mothers, may indicate an increased capacity to respond to microbial stimuli.
The Directly Observed Therapy Short-Course (DOTS) strategy in Samara Oblast, Russian Federation
Authors: Balabanova Y , Drobniewski F , Fedorin I , Zakharova S , Nikolayevskyy V , Atun R , Coker R
Published: April 2006

Background

The World Health Organisation (WHO) defines Russia as one of the 22 highest-burden countries for tuberculosis (TB). The WHO Directly Observed Treatment Short Course (DOTS) strategy employing a standardised treatment for 6 months produces the highest cure rates for drug sensitive TB. The Russian TB service traditionally employed individualised treatment.

The purpose of this study was to implement a DOTS programme in the civilian and prison sectors of Samara Region of Russia, describe the clinical features and outcomes of recruited patients, determine the proportion of individuals in the cohorts who were infected with drug resistant TB, the degree to which resistance was attributed to the Beijing TB strain family and establish risk factors for drug resistance.

Methods

prospective study

Results

2,099 patients were recruited overall. Treatment outcomes were analysed for patients recruited up to the third quarter of 2003 (n = 920). 75.3% of patients were successfully treated. Unsuccessful outcomes occurred in 7.3% of cases; 3.6% of patients died during treatment, with a significantly higher proportion of smear-positive cases dying compared to smear-negative cases. 14.0% were lost and transferred out. A high proportion of new cases (948 sequential culture-proven TB cases) had tuberculosis that was resistant to first-line drugs; (24.9% isoniazid resistant; 20.3% rifampicin resistant; 17.3% multidrug resistant tuberculosis). Molecular epidemiological analysis demonstrated that half of all isolated strains (50.7%; 375/740) belonged to the Beijing family. Drug resistance including MDR TB was strongly associated with infection with the Beijing strain (for MDR TB, 35.2% in Beijing strains versus 9.5% in non-Beijing strains, OR-5.2. Risk factors for multidrug resistant tuberculosis were: being a prisoner (OR 4.4), having a relapse of tuberculosis (OR 3.5), being infected with a Beijing family TB strain (OR 6.5) and having an unsuccessful outcome from treatment (OR 5.0).

Conclusion

The implementation of DOTS in Samara, Russia, was feasible and successful. Drug resistant tuberculosis rates in new cases were high and challenge successful outcomes from a conventional DOTS programme alone.
Can HRCT be used as a marker of airway remodelling in children with difficult asthma?
Authors: Saglani S , Papaioannou G , Khoo L , Ujita M , Jeffery PK , Owens C , Hansell DM , Payne DN , Bush A
Published: April 2006

Background

Whole airway wall thickening on high resolution computed tomography (HRCT) is reported to parallel thickening of the bronchial epithelial reticular basement membrane (RBM) in adult asthmatics. A similar relationship in children with difficult asthma (DA), in whom RBM thickening is a known feature, may allow the use of HRCT as a non-invasive marker of airway remodelling. We evaluated this relationship in children with DA.

Methods

27 children (median age 10.5 [range 4.1–16.7] years) with DA, underwent endobronchial biopsy from the right lower lobe and HRCT less than 4 months apart. HRCTs were assessed for bronchial wall thickening (BWT) of the right lower lobe using semi-quantitative and quantitative scoring techniques. The semi-quantitative score (grade 0–4) was an overall assessment of BWT of all clearly identifiable airways in HRCT scans. The quantitative score (BWT %; defined as [airway outer diameter – airway lumen diameter]/airway outer diameter ×100) was the average score of all airways visible and calculated using electronic endpoint callipers. RBM thickness in endobronchial biopsies was measured using image analysis. 23/27 subjects performed spirometry and the relationships between RBM thickness and BWT with airflow obstruction evaluated.

Results

Median RBM thickness in endobronchial biopsies was 6.7(range 4.6 – 10.0) μm. Median qualitative score for BWT of the right lower lobe was 1(range 0 – 1.5) and quantitative score was 54.3 (range 48.2 – 65.6)%. There was no relationship between RBM thickness and BWT in the right lower lobe using either scoring technique. No relationship was found between FEV1 and BWT or RBM thickness.

Conclusion

Although a relationship between RBM thickness and BWT on HRCT has been found in adults with asthma, this relationship does not appear to hold true in children with DA.
Prenatal and postnatal tobacco smoke exposure and respiratory health in Russian children
Authors: Jaakkola Jouni JK , Kosheleva Anna A , Katsnelson Boris A , Kuzmin Sergey V , Privalova Larissa I , Spengler John D
Published: April 2006

Background

Only few studies have assessed the relative impact of prenatal and postnatal exposure to tobacco smoke on the child's later asthma or chronic respiratory symptoms and to our knowledge no studies have elaborated respiratory infections and allergies in this context.

Objective

To assess the effects of prenatal and postnatal exposure to tobacco smoke on respiratory health of Russian school children.

Methods

We studied a population of 5951 children (8 to12 years old) from 9 Russian cities, whose parents answered a questionnaire on their children's respiratory health, home environment, and housing characteristics. The main health outcomes were asthma, allergies, chronic respiratory symptoms, chronic bronchitis, and upper respiratory infections. We used adjusted odds ratios (ORs) from logistic regression analyses as measures of effect.

Results

Prenatal exposure due to maternal smoking had the strongest effects on asthma (adjusted OR 2.46, 95% CI 1.19–5.08), chronic bronchitis (adjusted OR 1.45, 95% CI 1.08–1.96) and respiratory symptoms, such as wheezing (adjusted OR 1.30, 95% CI 0.90–1.89). The associations were weaker for exposure during early-life (adjusted ORs 1.38/1.27/1.15 respectively) and after 2 years of age (adjusted ORs 1.45/1.34/1.18) compared to prenatal exposure and the weakest or non-existent for current exposure (adjusted ORs 1.05/1.09/1.06). Upper respiratory infections were associated more strongly with early-life exposure (adjusted OR 1.25, 95% CI 1.09–1.42) than with prenatal (adjusted OR 0.74, 95% CI 0.54–1.01) or current exposure (adjusted OR1.05, 95% CI 0.92–1.20). The risk of allergies was also related to early life exposure to tobacco smoke (adjusted OR 1.26, 95% CI 1.13–1.42).

Conclusion

Adverse effects of tobacco smoke on asthma, chronic bronchitis, and chronic respiratory symptoms are strongest when smoking takes place during pregnancy. The relations are weaker for exposure during early-life and after 2 years of age and weakest or non-existent for current exposure.
Tissue fibrocytes in patients with mild asthma: A possible link to thickness of reticular basement membrane?
Authors: Nihlberg Kristian , Larsen Kristoffer , Hultgårdh-Nilsson Anna , Malmström Anders , Bjermer Leif , Westergren-Thorsson Gunilla
Published: April 2006

Background

Myofibroblasts, proposed as being derived from circulating fibrocytes, are considered to be important cells in thickening of the basement membrane in patients with asthma. We have studied the correlation of tissue fibrocyte levels to basement membrane thickness and the presence of fibrocytes in bronchoalveolar lavage fluid (BALF) in steroid-naive patients with mild asthma and controls.

Methods

Patients with mild asthma (n = 9) were recruited and divided into two categories based on whether or not fibroblast-like cells could be established from BALF. Non-asthmatic healthy subjects (n = 5) were used as controls. Colocalization of the fibrocyte markers CD34, CD45RO, procollagen I, and α-smooth muscle actin (α-SMA) were identified in bronchial biopsies from patients and controls by confocal microscopy. Kruskall-Wallis method was used to calculate statistical significance and Spearman coefficient of rank correlation was used to assess the degree of association.

Results

In patients with BALF fibroblasts, a 14-fold increase of tissue cells expressing CD34/CD45RO/α-SMA and a 16-fold increase of tissue cells expressing CD34/procollagen I was observed when compared to controls (p < 0.05). In contrast, patients without BALF fibroblasts displayed a 2-fold increase when compared to controls (p < 0.05). Fibrocytes were localized close to the basement membrane which was significantly thicker in patients with BALF fibroblasts when compared to the other two groups of subjects. Furthermore, basement membrane thickness could be correlated to the number of fibrocytes in tissue (r = 0.711). Fibroblasts-like cells were cultured from BALF where 17.6% of these cells expressed CD34, CD45RO and α-SMA.

Conclusion

These findings indicate a correlation between recruited fibrocytes in tissue and thickness of basement membrane. Fibroblast progenitor cells may therefore be important in airway remodeling in steroid-naive patients with mild asthma.
EAAC1 is expressed in rat and human prostate epithelial cells; functions as a high-affinity L-aspartate transporter; and is regulated by prolactin and testosterone
Authors: Franklin Renty B , Zou Jing , Yu Ziqiang , Costello Les C
Published: April 2006

Background

Prostate epithelial cells accumulate a high level of aspartate that is utilized as a substrate for their unique function of production and secretion of enormously high levels of citrate. In most mammalian cells aspartate is synthesized; and, therefore is a non-essential amino acid. In contrast, in citrate-producing prostate cells, aspartate is an essential amino acid that must be derived from circulation. The prostate intracellular/extracellular conditions present a 40:1 concentration gradient. Therefore, these cells must possess a plasma membrane-associated aspartate uptake transport process to achieve their functional activity. In earlier kinetic studies we identified the existence of a unique Na+-dependent high-affinity L-aspartate transport process in rat prostate secretory epithelial cells. The present report is concerned with the identification of this putative L-aspartate transporter in rat and human prostate cells.

Results

The studies show for the first time that EAAC1 is expressed in normal rat prostate epithelial cells, in normal and hyperplastic human prostate glands, and in human malignant prostate cell lines. EAAC1 expression and high-affinity L-aspartate transport are correspondingly down-regulated by EAAC1 siRNA knock down. Exposure of prostate cells to physiological levels of prolactin or testosterone results in an up-regulation of EAAC1 expression and a corresponding increase in the high-affinity transport of L-aspartate into the cells.

Conclusion

This study shows that EAAC1 functions as the high-affinity L-aspartate transporter that is responsible for the uptake and accumulation of aspartate in prostate cells. In other cells (predominantly excitable tissue cells), EAAC1 has been reported to function as a glutamate transporter rather than as an aspartate transporter. The regulation of EAAC1 expression and L-aspartate transport by testosterone and prolactin is consistent with their regulation of citrate production in prostate cells. The identification of EAAC1 as the high-affinity L-aspartate transporter now permits studies to elucidate the mechanism of hormonal regulation of EAAC1 gene expression, and to investigate the mechanism by which the cellular environment effects the functioning of EAAC1 as an aspartate transporter or as a glutamate transporter.
Choosing the best heuristic for seeded alignment of DNA sequences
Authors: Sun Yanni , Buhler Jeremy
Published: April 2006

Background

Seeded alignment is an important component of algorithms for fast, large-scale DNA similarity search. A good seed matching heuristic can reduce the execution time of genomic-scale sequence comparison without degrading sensitivity. Recently, many types of seed have been proposed to improve on the performance of traditional contiguous seeds as used in, e.g., NCBI BLASTN. Choosing among these seed types, particularly those that use information besides the presence or absence of matching residue pairs, requires practical guidance based on a rigorous comparison, including assessment of sensitivity, specificity, and computational efficiency. This work performs such a comparison, focusing on alignments in DNA outside widely studied coding regions.

Results

We compare seeds of several types, including those allowing transition mutations rather than matches at fixed positions, those allowing transitions at arbitrary positions ("BLASTZ" seeds), and those using a more general scoring matrix. For each seed type, we use an extended version of our Mandala seed design software to choose seeds with optimized sensitivity for various levels of specificity. Our results show that, on a test set biased toward alignments of noncoding DNA, transition information significantly improves seed performance, while finer distinctions between different types of mismatches do not. BLASTZ seeds perform especially well. These results depend on properties of our test set that are not shared by EST-based test sets with a strong bias toward coding DNA.

Conclusion

Practical seed design requires careful attention to the properties of the alignments being sought. For noncoding DNA sequences, seeds that use transition information, especially BLASTZ-style seeds, are particularly useful. The Mandala seed design software can be found at http://www.cse.wustl.edu/~yanni/mandala/.
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat
Authors: Chen Feng-Chi , Chen Chuang-Jong , Ho Jar-Yi , Chuang Trees-Juen
Published: April 2006

Background

Alternative splicing (AS) is important for evolution and major biological functions in complex organisms. However, the extent of AS in mammals other than human and mouse is largely unknown, making it difficult to study AS evolution in mammals and its biomedical implications.

Results

Here we describe a cross-species EST-to-genome comparison algorithm (ENACE) that can identify novel exons for EST-scanty species and distinguish conserved and lineage-specific exons. The identified exons represent not only novel exons but also evolutionarily meaningful AS events that are not previously annotated. A genome-wide AS analysis in human, mouse and rat using ENACE reveals a total of 758 novel cassette-on exons and 167 novel retained introns that have no EST evidence from the same species. RT-PCR-sequencing experiments validated ~50 ~80% of the tested exons, indicating high presence of exons predicted by ENACE. ENACE is particularly powerful when applied to closely related species. In addition, our analysis shows that the ENACE-identified AS exons tend not to pass the nonsynonymous-to-synonymous substitution ratio test and not to contain protein domain, implying that such exons may be under positive selection or relaxed negative selection. These AS exons may contribute to considerable inter-species functional divergence. Our analysis further indicates that a large number of exons may have been gained or lost during mammalian evolution. Moreover, a functional analysis shows that inter-species divergence of AS events may be substantial in protein carriers and receptor proteins in mammals. These exons may be of interest to studies of AS evolution. The ENACE programs and sequences of the ENACE-identified AS events are available for download.

Conclusion

ENACE can identify potential novel cassette exons and retained introns between closely related species using a comparative approach. It can also provide information regarding lineage- or species-specificity in transcript isoforms, which are important for evolutionary and functional studies.
A joint model for nonparametric functional mapping of longitudinal trajectory and time-to-event
Authors: Lin Min , Wu Rongling
Published: April 2006

Background

The characterization of the relationship between a longitudinal response process and a time-to-event has been a pressing challenge in biostatistical research. This has emerged as an important issue in genetic studies when one attempts to detect the common genes or quantitative trait loci (QTL) that govern both a longitudinal trajectory and developmental event.

Results

We present a joint statistical model for functional mapping of dynamic traits in which the event times and longitudinal traits are taken to depend on a common set of genetic mechanisms. By fitting the Legendre polynomial of orthogonal properties for the time-dependent mean vector, our model does not rely on any curve, which is different from earlier parametric models of functional mapping. This newly developed nonparametric model is demonstrated and validated by an example for a forest tree in which stemwood growth and the time to first flower are jointly modelled.

Conclusion

Our model allows for the detection of specific QTL that govern both longitudinal traits and developmental processes through either pleiotropic effects or close linkage, or both. This model will have great implications for integrating longitudinal and event data to gain better insights into comprehensive biology and biomedicine.
A computational approach to discovering the functions of bacterial phytochromes by analysis of homolog distributions
Authors: Lamparter Tilman
Published: April 2006

Background

Phytochromes are photoreceptors, discovered in plants, that control a wide variety of developmental processes. They have also been found in bacteria and fungi, but for many species their biological role remains obscure. This work concentrates on the phytochrome system of Agrobacterium tumefaciens, a non-photosynthetic soil bacterium with two phytochromes. To identify proteins that might share common functions with phytochromes, a co-distribution analysis was performed on the basis of protein sequences from 138 bacteria.

Results

A database of protein sequences from 138 bacteria was generated. Each sequence was BLASTed against the entire database. The homolog distribution of each query protein was then compared with the homolog distribution of every other protein (target protein) of the same species, and the target proteins were sorted according to their probability of co-distribution under random conditions. As query proteins, phytochromes from Agrobacterium tumefaciens, Pseudomonas aeruginosa, Deinococcus radiodurans and Synechocystis PCC 6803 were chosen along with several phytochrome-related proteins from A. tumefaciens. The Synechocystis photosynthesis protein D1 was selected as a control. In the D1 analyses, the ratio between photosynthesis-related proteins and those not related to photosynthesis among the top 150 in the co-distribution tables was > 3:1, showing that the method is appropriate for finding partner proteins with common functions. The co-distribution of phytochromes with other histidine kinases was remarkably high, although most co-distributed histidine kinases were not direct BLAST homologs of the query protein. This finding implies that phytochromes and other histidine kinases share common functions as parts of signalling networks. All phytochromes tested, with one exception, also revealed a remarkably high co-distribution with glutamate synthase and methionine synthase. This result implies a general role of bacterial phytochromes in ammonium assimilation and amino acid metabolism.

Conclusion

It was possible to identify several proteins that might share common functions with bacterial phytochromes by the co-distribution approach. This computational approach might also be helpful in other cases.
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models
Authors: Waack Stephan , Keller Oliver , Asper Roman , Brodag Thomas , Damm Carsten , Fricke Wolfgang Florian , Surovcik Katharina , Meinicke Peter , Merkl Rainer
Published: April 2006

Background

Horizontal gene transfer (HGT) is considered a strong evolutionary force shaping the content of microbial genomes in a substantial manner. It is the difference in speed enabling the rapid adaptation to changing environmental demands that distinguishes HGT from gene genesis, duplications or mutations. For a precise characterization, algorithms are needed that identify transfer events with high reliability. Frequently, the transferred pieces of DNA have a considerable length, comprise several genes and are called genomic islands (GIs) or more specifically pathogenicity or symbiotic islands.

Results

We have implemented the program SIGI-HMM that predicts GIs and the putative donor of each individual alien gene. It is based on the analysis of codon usage (CU) of each individual gene of a genome under study. CU of each gene is compared against a carefully selected set of CU tables representing microbial donors or highly expressed genes. Multiple tests are used to identify putatively alien genes, to predict putative donors and to mask putatively highly expressed genes. Thus, we determine the states and emission probabilities of an inhomogeneous hidden Markov model working on gene level. For the transition probabilities, we draw upon classical test theory with the intention of integrating a sensitivity controller in a consistent manner. SIGI-HMM was written in JAVA and is publicly available. It accepts as input any file created according to the EMBL-format.

It generates output in the common GFF format readable for genome browsers. Benchmark tests showed that the output of SIGI-HMM is in agreement with known findings. Its predictions were both consistent with annotated GIs and with predictions generated by different methods.

Conclusion

SIGI-HMM is a sensitive tool for the identification of GIs in microbial genomes. It allows to interactively analyze genomes in detail and to generate or to test hypotheses about the origin of acquired genes.
INTEGRATOR: interactive graphical search of large protein interactomes over the Web
Authors: Chang Aaron N , McDermott Jason , Frazier Zachary , Guerquin Michal , Samudrala Ram
Published: April 2006

Background

The rapid growth of protein interactome data has elevated the necessity and importance of network analysis tools. However, unlike pure text data, network search spaces are of exponential complexity. This poses special challenges for storing, searching, and navigating this data efficiently. Moreover, development of effective web interfaces has been difficult.

Results

We present Integrator, a web-integrated graphical search tool for protein-protein interaction networks across 50+ genomes.

Conclusion

Integrator provides single and multiple protein searches of the Bioverse database containing experimentally-derived and predicted protein-protein interactions. The interface provides animated local network views, rapid subgraph manipulation, and cross-referencing of functional annotations. Integrator is available at http://bioverse.compbio.washington.edu/integrator.
Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features
Authors: Semeiks JR , Rizki A , Bissell MJ , Mian IS
Published: April 2006

Background

Ensemble attribute profile clustering is a novel, text-based strategy for analyzing a user-defined list of genes and/or proteins. The strategy exploits annotation data present in gene-centered corpora and utilizes ideas from statistical information retrieval to discover and characterize properties shared by subsets of the list. The practical utility of this method is demonstrated by employing it in a retrospective study of two non-overlapping sets of genes defined by a published investigation as markers for normal human breast luminal epithelial cells and myoepithelial cells.

Results

Each genetic locus was characterized using a finite set of biological properties and represented as a vector of features indicating attributes associated with the locus (a gene attribute profile). In this study, the vector space models for a pre-defined list of genes were constructed from the Gene Ontology (GO) terms and the Conserved Domain Database (CDD) protein domain terms assigned to the loci by the gene-centered corpus LocusLink. This data set of GO- and CDD-based gene attribute profiles, vectors of binary random variables, was used to estimate multiple finite mixture models and each ensuing model utilized to partition the profiles into clusters. The resultant partitionings were combined using a unanimous voting scheme to produce consensus clusters, sets of profiles that co-occured consistently in the same cluster. Attributes that were important in defining the genes assigned to a consensus cluster were identified. The clusters and their attributes were inspected to ascertain the GO and CDD terms most associated with subsets of genes and in conjunction with external knowledge such as chromosomal location, used to gain functional insights into human breast biology. The 52 luminal epithelial cell markers and 89 myoepithelial cell markers are disjoint sets of genes. Ensemble attribute profile clustering-based analysis indicated that both lists contained groups of genes with the functional properties of membrane receptor biology/signal transduction and nucleic acid binding/transcription. A subset of the luminal markers was associated with metabolic and oxidoreductase activities, whereas a subset of myoepithelial markers was associated with protein hydrolase activity.

Conclusion

Given a set of genes and/or proteins associated with a phenomenon, process or system of interest, ensemble attribute profile clustering provides a simple method for collating and sythesizing the annotation data pertaining to them that are present in text-based, gene-centered corpora. The results provide information about properties common and unique to subsets of the list and hence insights into the biology of the problem under investigation.
CARMA: A platform for analyzing microarray datasets that incorporate replicate measures
Authors: Greer Kevin A , McReynolds Matthew R , Brooks Heddwen L , Hoying James B
Published: April 2006

Background

The incorporation of statistical models that account for experimental variability provides a necessary framework for the interpretation of microarray data. A robust experimental design coupled with an analysis of variance (ANOVA) incorporating a model that accounts for known sources of experimental variability can significantly improve the determination of differences in gene expression and estimations of their significance.

Results

To realize the full benefits of performing analysis of variance on microarray data we have developed CARMA, a microarray analysis platform that reads data files generated by most microarray image processing software packages, performs ANOVA using a user-defined linear model, and produces easily interpretable graphical and numeric results. No pre-processing of the data is required and user-specified parameters control most aspects of the analysis including statistical significance criterion. The software also performs location and intensity dependent lowess normalization, automatic outlier detection and removal, and accommodates missing data.

Conclusion

CARMA provides a clear quantitative and statistical characterization of each measured gene that can be used to assess marginally acceptable measures and improve confidence in the interpretation of microarray results. Overall, applying CARMA to microarray datasets incorporating repeated measures effectively reduces the number of gene incorrectly identified as differentially expressed and results in a more robust and reliable analysis.
GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions
Authors: Doherty Jason M , Carmichael Lynn K , Mills Jason C
Published: April 2006

Background

The ever-expanding population of gene expression profiles (EPs) from specified cells and tissues under a variety of experimental conditions is an important but difficult resource for investigators to utilize effectively. Software tools have been recently developed to use the distribution of gene ontology (GO) terms associated with the genes in an EP to identify specific biological functions or processes that are over- or under-represented in that EP relative to other EPs. Additionally, it is possible to use the distribution of GO terms inherent to each EP to relate that EP as a whole to other EPs. Because GO term annotation is organized in a tree-like cascade of variable granularity, this approach allows the user to relate (e.g., by hierarchical clustering) EPs of varying length and from different platforms (e.g., GeneChip, SAGE, EST library).

Results

Here we present GOurmet, a software package that calculates the distribution of GO terms represented by the genes in an individual expression profile (EP), clusters multiple EPs based on these integrated GO term distributions, and provides users several tools to visualize and compare EPs. GOurmet is particularly useful in meta-analysis to examine EPs of specified cell types (e.g., tissue-specific stem cells) that are obtained through different experimental procedures. GOurmet also introduces a new tool, the Targetoid plot, which allows users to dynamically render the multi-dimensional relationships among individual elements in any clustering analysis. The Targetoid plotting tool allows users to select any element as the center of the plot, and the program will then represent all other elements in the cluster as a function of similarity to the selected central element.

Conclusion

GOurmet is a user-friendly, GUI-based software package that greatly facilitates analysis of results generated by multiple EPs. The clustering analysis features a dynamic targetoid plot that is generalizable for use with any clustering application.
Domain-based small molecule binding site annotation
Authors: Snyder Kevin A , Feldman Howard J , Dumontier Michel , Salama John J , Hogue Christopher WV
Published: April 2006

Background

Accurate small molecule binding site information for a protein can facilitate studies in drug docking, drug discovery and function prediction, but small molecule binding site protein sequence annotation is sparse. The Small Molecule Interaction Database (SMID), a database of protein domain-small molecule interactions, was created using structural data from the Protein Data Bank (PDB). More importantly it provides a means to predict small molecule binding sites on proteins with a known or unknown structure and unlike prior approaches, removes large numbers of false positive hits arising from transitive alignment errors, non-biologically significant small molecules and crystallographic conditions that overpredict ion binding sites.

Description

Using a set of co-crystallized protein-small molecule structures as a starting point, SMID interactions were generated by identifying protein domains that bind to small molecules, using NCBI's Reverse Position Specific BLAST (RPS-BLAST) algorithm. SMID records are available for viewing at http://smid.blueprint.org. The SMID-BLAST tool provides accurate transitive annotation of small-molecule binding sites for proteins not found in the PDB. Given a protein sequence, SMID-BLAST identifies domains using RPS-BLAST and then lists potential small molecule ligands based on SMID records, as well as their aligned binding sites. A heuristic ligand score is calculated based on E-value, ligand residue identity and domain entropy to assign a level of confidence to hits found. SMID-BLAST predictions were validated against a set of 793 experimental small molecule interactions from the PDB, of which 472 (60%) of predicted interactions identically matched the experimental small molecule and of these, 344 had greater than 80% of the binding site residues correctly identified. Further, we estimate that 45% of predictions which were not observed in the PDB validation set may be true positives.

Conclusion

By focusing on protein domain-small molecule interactions, SMID is able to cluster similar interactions and detect subtle binding patterns that would not otherwise be obvious. Using SMID-BLAST, small molecule targets can be predicted for any protein sequence, with the only limitation being that the small molecule must exist in the PDB. Validation results and specific examples within illustrate that SMID-BLAST has a high degree of accuracy in terms of predicting both the small molecule ligand and binding site residue positions for a query protein.
DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions
Authors: Arner Erik , Tammi Martti T , Tran Anh-Nhi , Kindlund Ellen , Andersson Bjorn
Published: April 2006

Background

Many genome projects are left unfinished due to complex, repeated regions. Finishing is the most time consuming step in sequencing and current finishing tools are not designed with particular attention to the repeat problem.

Results

We have developed DNPTrapper, a shotgun sequence finishing tool, specifically designed to address the problems posed by the presence of repeated regions in the target sequence. The program detects and visualizes single base differences between nearly identical repeat copies, and offers the overview and flexibility needed to rapidly resolve complex regions within a working session. The use of a database allows large amounts of data to be stored and handled, and allows viewing of mammalian size genomes. The program is available under an Open Source license.

Conclusion

With DNPTrapper, it is possible to separate repeated regions that previously were considered impossible to resolve, and finishing tasks that previously took days or weeks can be resolved within hours or even minutes.
Modeling Sage data with a truncated gamma-Poisson model
Authors: Thygesen Helene H , Zwinderman Aeilko H
Published: April 2006

Background

Serial Analysis of Gene Expressions (SAGE) produces gene expression measurements on a discrete scale, due to the finite number of molecules in the sample. This means that part of the variance in SAGE data should be understood as the sampling error in a binomial or Poisson distribution, whereas other variance sources, in particular biological variance, should be modeled using a continuous distribution function, i.e. a prior on the intensity of the Poisson distribution. One challenge is that such a model predicts a large number of genes with zero counts, which cannot be observed.

Results

We present a hierarchical Poisson model with a gamma prior and three different algorithms for estimating the parameters in the model. It turns out that the rate parameter in the gamma distribution can be estimated on the basis of a single SAGE library, whereas the estimate of the shape parameter becomes unstable. This means that the number of zero counts cannot be estimated reliably. When a bivariate model is applied to two SAGE libraries, however, the number of predicted zero counts becomes more stable and in approximate agreement with the number of transcripts observed across a large number of experiments. In all the libraries we analyzed there was a small population of very highly expressed tags, typically 1% of the tags, that could not be accounted for by the model. To handle those tags we chose to augment our model with a non-parametric component. We also show some results based on a log-normal distribution instead of the gamma distribution.

Conclusion

By modeling SAGE data with a hierarchical Poisson model it is possible to separate the sampling variance from the variance in gene expression. If expression levels are reported at the gene level rather than at the tag level, genes mapped to multiple tags must be kept separate, since their expression levels show a different statistical behavior. A log-normal prior provided a better fit to our data than the gamma prior, but except for a small subpopulation of tags with very high counts, the two priors are similar.
Amplification of the Gene Ontology annotation of Affymetrix probe sets
Authors: Muro Enrique M , Perez-Iratxeta Carolina , Andrade-Navarro Miguel A
Published: April 2006

Background

The annotations of Affymetrix DNA microarray probe sets with Gene Ontology terms are carefully selected for correctness. This results in very accurate but incomplete annotations which is not always desirable for microarray experiment evaluation.

Results

Here we present a protocol to amplify the set of Gene Ontology annotations associated to Affymetrix DNA microarray probe sets using information from related databases.

Conclusion

Predicted novel annotations and the evidence producing them can be accessed at Probe2GO: http://www.ogic.ca/p2g. Scripts are available on demand.
An application of statistics to comparative metagenomics
Authors: Rodriguez-Brito Beltran , Rohwer Forest , Edwards Robert A
Published: April 2006

Background

Metagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the potential to identify significantly different metabolic potential in different environments.

Results

Here we use a statistical method to compare curated subsystems, to predict the physiology, metabolism, and ecology from metagenomes. This approach can be used to identify those subsystems that are significantly different between metagenome sequences. Subsystems that were overrepresented in the Sargasso Sea and Acid Mine Drainage metagenome when compared to non-redundant databases were identified.

Conclusion

The methodology described herein applies statistics to the comparisons of metabolic potential in metagenomes. This analysis reveals those subsystems that are more, or less, represented in the different environments that are compared. These differences in metabolic potential lead to several testable hypotheses about physiology and metabolism of microbes from these ecosystems.
Optic cup and facial patterning defects in ocular ectoderm β-catenin gain-of-function mice
Authors: Miller Leigh-Anne D , Smith April N , Taketo M Mark , Lang Richard A
Published: April 2006

Background

The canonical Wnt signaling pathway has a number of critical functions during embryonic development and, when activated aberrantly, in the genesis of cancer. Current evidence suggests that during eye development, regulation of Wnt signaling is critical for patterning the surface ectoderm that will contribute to multiple components of the eye. Wnt signaling loss-of-function experiments show that a region of periocular ectoderm will form ectopic lentoid bodies unless the Wnt pathway modifies its fate towards other structures. Consistent with this, Wnt signaling gain of function in the ocular region ectoderm results in a suppression of lens fate.

Results

Here we demonstrate that ectoderm-specific Wnt signaling gain-of-function embryos exhibit additional defects besides those noted in the lens. There are profound facial defects including a foreshortened snout, malformation of the nasal region, and clefting of the epidermis along the ocular-nasal axis. Furthermore, despite the restriction of Wnt pathway gain-of-function to the surface ectoderm, the optic cup is inappropriately patterned and ultimately forms a highly convoluted, disorganized array of epithelium with the characteristics of retina and retinal pigmented epithelium.

Conclusion

We suggest that activation of the Wnt pathway in surface ectoderm may disrupt the normal exchange of signals between the presumptive lens and retina that coordinate development of a functional eye.
Long-term maintenance of in vitro cultured honeybee (Apis mellifera) embryonic cells
Authors: Bergem Monica , Norberg Kari , Aamodt Randi M
Published: April 2006

Background

In vitrocultivation of cells allows novel investigation ofin vivo-mechanisms and is a helpful tool in developmental biology, biochemistry and functional genomics. Numerous cell lines of insect species, e.g., silkworm and mosquito, have been reported. However, this is not the case for successful long-term cultivation of cells in honeybees.

Results

Methods for cultivation of honeybee embryonic cells are discussed here. Pre-gastrula stage embryos were used to initiate cultures, and cells were reared on 96-wells microplates with Grace insect medium, supplemented with Fetal Bovine Serum. Cells proliferated in clusters, and maintained viable and mitotic for more than three months.

Conclusion

We report here, for the first time, long-term cultivation of honeybee cells. Results represent a highly usefulin vitro-system for studying a model organism of increasing importance in areas such as aging, sociality and neurobiology.
Expression profiles of cIRF6, cLHX6 and cLHX7in the facial primordia suggest specific roles during primary palatogenesis
Authors: Washbourne Belinda J , Cox Timothy C
Published: April 2006

Background

The LIM-homeodomain transcription factors LHX7 and LHX6 have been implicated in palatogenesis in mice and thus may also contribute to the incidence of isolated palatal clefts and/or clefts of the lip and primary palate (CL/P) in humans. Causative mutations in the transcription factor IRF6 have also been identified in two allelic CL/P syndromes and common polymorphisms in the same gene are significantly associated with non-syndromal CL/P in different populations.

Results

Here we report the isolation of chick orthologues of LHX7, LHX6 and IRF6 and the first characterisation of their profiles of expression during morphogenesis of the midface with emphasis on the period around formation of the primary palate. LHX7 and LHX6 expression was restricted to the ectomesenchyme immediately underlying the ectoderm of the maxillary and mandibular primordia as well as to the lateral globular projections of the medial nasal process, again underlying the pre-fusion primary palatal epithelia. In contrast, IRF6 expression was restricted to surface epithelia, with elevated levels around the frontonasal process, the maxillary primordia, and the nasal pits. Elsewhere, high expression was also evident in the egg tooth primordium and in the apical ectodermal ridge of the developing limbs.

Conclusion

The restricted expression of both LHX genes and IRF6 in the facial primordia suggests roles for these gene products in promoting directed outgrowth and fusion of the primary palate. The manipulability, minimal cost and susceptibility of chicks to CL/P will enable more detailed investigations into how perturbations of IRF6, LHX6 and LHX7 contribute to common orofacial clefts.