bluuebunny/crossref_metadata_2025 huggingface dataset:
Frogs and toads in the food of the Great Grey Shrike (Lanius excubitor): larders and skinning as two ways to consume dangerous prey
Authors: Antczak Marcin , Hromada Martin , Tryjanowski Piotr
Published: July 2005

In this note we present several previously unpublished cases of Great Grey Shrike, Lanius excubitor, predation in western Poland on adult amphibians, including poisonous toads, and a novel special behaviour — skinning toads. We briefly discuss the potential implications of these observations for understanding shrike foraging behaviour and gaps in our current knowledge on bird-toad interactions.
Assessment of the movement behaviour of the bullhead (Cottus gobio), an endangered European freshwater fish
Authors: Knaepkens  , Baekelandt  , Eens
Published: July 2005

Despite the increasing recognition that in-stream movement probably represents an important aspect of the ecology of many stream fish populations, there is still limited and often conflicting information on the movement behaviour of a wide range of fish, especially species that are threatened and/or with no economic interest. In this study, movement behaviour of the endangered bullhead (Cottus gobio), a small, bottom-dwelling European freshwater fish, was assessed by mark-recapture in a Flemish (northern part of Belgium) lowland river between September 2002 and May 2003. The majority (61-72%) of tagged bullheads recaptured during the different sampling occasions were found at or near (< 10 m) their initial tagging site. The other re-sighted specimens however had covered distances between 20 and 270 m. There were no significant indications of seasonal differences in bullhead movement behaviour. In general, our results strongly suggest that bullhead populations not only consist of stationary individuals but also of relatively mobile fish. Consequently, to effectively conserve this endangered species, fisheries managers should (i) consider sufficiently large areas of habitat as critical to bullhead populations, and (ii) minimise the impact of physical barriers on bullhead movement.
Morphological divergence among populations of Testudo graeca from west-central Morocco
Authors: Carretero Miguel , Znari Mohammed , Harris D. James , Macé Jean
Published: July 2005

Morphometric analyses were carried out on Testudo graeca from west-central Morocco, and compared to previously published mitochondrial DNA sequence variation. We measured 41 characters on 244 tortoises from three localities, including one population of T. g. soussensis from Souss Valley. All three populations could be statistically differentiated in a multivariate space using these characters. The population from the Jbilet mountains was the most differentiated (no overlap), those from Essaouira on the coast and from Admine showed limited overlap (5%). Sexual size dimorphism (males < females) remained constant between sites. Sexual shape dimorphism was prominent in all populations, but the degree of dimorphism differed for some characters when corrected for size. Tortoises from Jbilet living under harsher conditions (low precipitation, high thermal amplitude, low plant cover) were smaller, lighter, more flattened and less dimorphic in shape than the others. Although the Admine population (currently assigned to T. g. soussensis) was morphologically distinct, its distinctiveness was less supported than in the case of Jbilet; several other qualitative traits previously considered as defining this subspecies were also questionable. Moreover, this morphological variation contrasted with the available genetic evidence (12S rRNA mtDNA) which did not reveal significant variation between any of the populations. This implies that morphological differences have either arisen very recently or can be attributed to phenotypic plasticity. This should be taken into account when using morphological traits for taxonomic considerations and conservation management.
Human CTLA4 knock-in mice unravel the quantitative link between tumor immunity and autoimmunity induced by anti–CTLA-4 antibodies
Authors: Lute Kenneth D. , May Kenneth F. , Lu Ping , Zhang Huiming , Kocak Ergun , Mosinger Bedrick , Wolford Christopher , Phillips Gary , Caligiuri Michael A. , Zheng Pan , Liu Yang
Published: July 2005

Although results from preclinical studies in animal models have proven the concept for use of anti–cytotoxic T-lymphocyte antigen 4 (CTLA-4) antibodies in cancer immunotherapy, 2 major obstacles have hindered their successful application for human cancer therapy. First, the lack of in vitro correlates of the antitumor effect of the antibodies makes it difficult to screen for the most efficacious antibody by in vitro analysis. Second, significant autoimmune side effects have been observed in a recent clinical trial. In order to address these 2 issues, we have generated human CTLA4 gene knock-in mice and used them to compare a panel of anti–human CTLA-4 antibodies for their ability to induce tumor rejection and autoimmunity. Surprisingly, while all antibodies induced protection against cancer and demonstrated some autoimmune side effects, the antibody that induced the strongest protection also induced the least autoimmune side effects. These results demonstrate that autoimmune disease does not quantitatively correlate with cancer immunity. Our approach may be generally applicable to the development of human therapeutic antibodies.
Airway cellularity, lipid laden macrophages and microbiology of gastric juice and airways in children with reflux oesophagitis
Authors: Chang AB , Cox NC , Purcell J , Marchant JM , Lewindon PJ , Cleghorn GJ , Ee LC , Withers GD , Patrick MK , Faoagali J
Published: July 2005

Background

Gastroesophageal reflux disease (GORD) can cause respiratory disease in children from recurrent aspiration of gastric contents. GORD can be defined in several ways and one of the most common method is presence of reflux oesophagitis. In children with GORD and respiratory disease, airway neutrophilia has been described. However, there are no prospective studies that have examined airway cellularity in children with GORD but without respiratory disease. The aims of the study were to compare (1) BAL cellularity and lipid laden macrophage index (LLMI) and, (2) microbiology of BAL and gastric juices of children with GORD (G+) to those without (G-).

Methods

In 150 children aged <14-years, gastric aspirates and bronchoscopic airway lavage (BAL) were obtained during elective flexible upper endoscopy. GORD was defined as presence of reflux oesophagitis on distal oesophageal biopsies.

Results

BAL neutrophil% in G- group (n = 63) was marginally but significantly higher than that in the G+ group (n = 77), (median of 7.5 and 5 respectively, p = 0.002). Lipid laden macrophage index (LLMI), BAL percentages of lymphocyte, eosinophil and macrophage were similar between groups. Viral studies were negative in all, bacterial cultures positive in 20.7% of BALs and in 5.3% of gastric aspirates. BAL cultures did not reflect gastric aspirate cultures in all but one child.

Conclusion

In children without respiratory disease, GORD defined by presence of reflux oesophagitis, is not associated with BAL cellular profile or LLMI abnormality. Abnormal microbiology of the airways, when present, is not related to reflux oesophagitis and does not reflect that of gastric juices.
Proceedings of the Second Annual Conference of the MidSouth Computational Biology and Bioinformatics Society
Authors: Wren Jonathan D , Slikker William
Published: July 2005

The MCBIOS 2004 conference brought together regional researchers and students in biology, computer science and bioinformatics on October 7th-9th 2004 to present their latest work. This editorial describes the conference itself and introduces the twelve peer-reviewed manuscripts accepted for publication in the Proceedings of the MCBIOS 2004 Conference. These manuscripts included new methods for analysis of high-throughput gene expression experiments, EST clustering, analysis of mass spectrometry data and genomic analysis
Reproducible Clusters from Microarray Research: Whither?
Authors: Garge Nikhil R , Page Grier P , Sprague Alan P , Gorman Bernard S , Allison David B
Published: July 2005

Motivation

In cluster analysis, the validity of specific solutions, algorithms, and procedures present significant challenges because there is no null hypothesis to test and no 'right answer'. It has been noted that a replicable classification is not necessarily a useful one, but a useful one that characterizes some aspect of the population must be replicable. By replicable we mean reproducible across multiple samplings from the same population. Methodologists have suggested that the validity of clustering methods should be based on classifications that yield reproducible findings beyond chance levels. We used this approach to determine the performance of commonly used clustering algorithms and the degree of replicability achieved using several microarray datasets.

Methods

We considered four commonly used iterative partitioning algorithms (Self Organizing Maps (SOM), K-means, Clutsering LARge Applications (CLARA), and Fuzzy C-means) and evaluated their performances on 37 microarray datasets, with sample sizes ranging from 12 to 172. We assessed reproducibility of the clustering algorithm by measuring the strength of relationship between clustering outputs of subsamples of 37 datasets. Cluster stability was quantified using Cramer's v

2
from a kXk table. Cramer's v

2
is equivalent to the squared canonical correlation coefficient between two sets of nominal variables. Potential scores range from 0 to 1, with 1 denoting perfect reproducibility.

Results

All four clustering routines show increased stability with larger sample sizes. K-means and SOM showed a gradual increase in stability with increasing sample size. CLARA and Fuzzy C-means, however, yielded low stability scores until sample sizes approached 30 and then gradually increased thereafter. Average stability never exceeded 0.55 for the four clustering routines, even at a sample size of 50. These findings suggest several plausible scenarios: (1) microarray datasets lack natural clustering structure thereby producing low stability scores on all four methods; (2) the algorithms studied do not produce reliable results and/or (3) sample sizes typically used in microarray research may be too small to support derivation of reliable clustering results. Further research should be directed towards evaluating stability performances of more clustering algorithms on more datasets specially having larger sample sizes with larger numbers of clusters considered.
Microarray scanner calibration curves: characteristics and implications
Authors: Shi Leming , Tong Weida , Su Zhenqiang , Han Tao , Han Jing , Puri Raj K , Fang Hong , Frueh Felix W , Goodsaid Federico M , Guo Lei , Branham William S , Chen James J , Xu Z Alex , Harris Stephen C , Hong Huixiao , Xie Qian , Perkins Roger G , Fuscoe James C
Published: July 2005

Background

Microarray-based measurement of mRNA abundance assumes a linear relationship between the fluorescence intensity and the dye concentration. In reality, however, the calibration curve can be nonlinear.

Results

By scanning a microarray scanner calibration slide containing known concentrations of fluorescent dyes under 18 PMT gains, we were able to evaluate the differences in calibration characteristics of Cy5 and Cy3. First, the calibration curve for the same dye under the same PMT gain is nonlinear at both the high and low intensity ends. Second, the degree of nonlinearity of the calibration curve depends on the PMT gain. Third, the two PMTs (for Cy5 and Cy3) behave differently even under the same gain. Fourth, the background intensity for the Cy3 channel is higher than that for the Cy5 channel. The impact of such characteristics on the accuracy and reproducibility of measured mRNA abundance and the calculated ratios was demonstrated. Combined with simulation results, we provided explanations to the existence of ratio underestimation, intensity-dependence of ratio bias, and anti-correlation of ratios in dye-swap replicates. We further demonstrated that although Lowess normalization effectively eliminates the intensity-dependence of ratio bias, the systematic deviation from true ratios largely remained. A method of calculating ratios based on concentrations estimated from the calibration curves was proposed for correcting ratio bias.

Conclusion

It is preferable to scan microarray slides at fixed, optimal gain settings under which the linearity between concentration and intensity is maximized. Although normalization methods improve reproducibility of microarray measurements, they appear less effective in improving accuracy.
Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential
Authors: Shi Leming , Tong Weida , Fang Hong , Scherf Uwe , Han Jing , Puri Raj K , Frueh Felix W , Goodsaid Federico M , Guo Lei , Su Zhenqiang , Han Tao , Fuscoe James C , Xu Z aAlex , Patterson Tucker A , Hong Huixiao , Xie Qian , Perkins Roger G , Chen James J , Casciano Daniel A
Published: July 2005

Background

The acceptance of microarray technology in regulatory decision-making is being challenged by the existence of various platforms and data analysis methods. A recent report (E. Marshall, Science, 306, 630–631, 2004), by extensively citing the study of Tan et al. (Nucleic Acids Res., 31, 5676–5684, 2003), portrays a disturbingly negative picture of the cross-platform comparability, and, hence, the reliability of microarray technology.

Results

We reanalyzed Tan's dataset and found that the intra-platform consistency was low, indicating a problem in experimental procedures from which the dataset was generated. Furthermore, by using three gene selection methods (i.e., p-value ranking, fold-change ranking, and Significance Analysis of Microarrays (SAM)) on the same dataset we found that p-value ranking (the method emphasized by Tan et al.) results in much lower cross-platform concordance compared to fold-change ranking or SAM. Therefore, the low cross-platform concordance reported in Tan's study appears to be mainly due to a combination of low intra-platform consistency and a poor choice of data analysis procedures, instead of inherent technical differences among different platforms, as suggested by Tan et al. and Marshall.

Conclusion

Our results illustrate the importance of establishing calibrated RNA samples and reference datasets to objectively assess the performance of different microarray platforms and the proficiency of individual laboratories as well as the merits of various data analysis procedures. Thus, we are progressively coordinating the MAQC project, a community-wide effort for microarray quality control.
Genome-wide estimation of gender differences in the gene expression of human livers: Statistical design and analysis
Authors: Delongchamp Robert R , Velasco Cruz , Dial Stacey , Harris Angela J
Published: July 2005

Background

Gender differences in gene expression were estimated in liver samples from 9 males and 9 females. The study tested 31,110 genes for a gender difference using a design that adjusted for sources of variation associated with cDNA arrays, normalization, hybridizations and processing conditions.

Results

The genes were split into 2,800 that were clearly expressed (expressed genes) and 28,310 that had expression levels in the background range (not expressed genes). The distribution of p-values from the 'not expressed' group was consistent with no gender differences. The distribution of p-values from the 'expressed' group suggested that 8 % of these genes differed by gender, but the estimated fold-changes (expression in males / expression in females) were small. The largest observed fold-change was 1.55. The 95 % confidence bounds on the estimated fold-changes were less than 1.4 fold for 79.3 %, and few (1.1%) exceed 2-fold.

Conclusion

Observed gender differences in gene expression were small. When selecting genes with gender differences based upon their p-values, false discovery rates exceed 80 % for any set of genes, essentially making it impossible to identify any specific genes with a gender difference.
Automating Genomic Data Mining via a Sequence-based Matrix Format and Associative Rule Set
Authors: Wren Jonathan D , Johnson David , Gruenwald Le
Published: July 2005

There is an enormous amount of information encoded in each genome – enough to create living, responsive and adaptive organisms. Raw sequence data alone is not enough to understand function, mechanisms or interactions. Changes in a single base pair can lead to disease, such as sickle-cell anemia, while some large megabase deletions have no apparent phenotypic effect. Genomic features are varied in their data types and annotation of these features is spread across multiple databases. Herein, we develop a method to automate exploration of genomes by iteratively exploring sequence data for correlations and building upon them. First, to integrate and compare different annotation sources, a sequence matrix (SM) is developed to contain position-dependant information. Second, a classification tree is developed for matrix row types, specifying how each data type is to be treated with respect to other data types for analysis purposes. Third, correlative analyses are developed to analyze features of each matrix row in terms of the other rows, guided by the classification tree as to which analyses are appropriate. A prototype was developed and successful in detecting coinciding genomic features among genes, exons, repetitive elements and CpG islands.
CLU: A new algorithm for EST clustering
Authors: Ptitsyn Andrey , Hide Winston
Published: July 2005

Background

The continuous flow of EST data remains one of the richest sources for discoveries in modern biology. The first step in EST data mining is usually associated with EST clustering, the process of grouping of original fragments according to their annotation, similarity to known genomic DNA or each other. Clustered EST data, accumulated in databases such as UniGene, STACK and TIGR Gene Indices have proven to be crucial in research areas from gene discovery to regulation of gene expression.

Results

We have developed a new nucleotide sequence matching algorithm and its implementation for clustering EST sequences. The program is based on the original CLU match detection algorithm, which has improved performance over the widely used d2_cluster. The CLU algorithm automatically ignores low-complexity regions like poly-tracts and short tandem repeats.

Conclusion

CLU represents a new generation of EST clustering algorithm with improved performance over current approaches. An early implementation can be applied in small and medium-size projects. The CLU program is available on an open source basis free of charge. It can be downloaded from http://compbio.pbrc.edu/pti
Decision Forest Analysis of 61 Single Nucleotide Polymorphisms in a Case-Control Study of Esophageal Cancer; a novel method
Authors: Xie Qian , Ratnasinghe Luke D , Hong Huixiao , Perkins Roger , Tang Ze-Zhong , Hu Nan , Taylor Philip R , Tong Weida
Published: July 2005

Background

Systematic evaluation and study of single nucleotide polymorphisms (SNPs) made possible by high throughput genotyping technologies and bioinformatics promises to provide breakthroughs in the understanding of complex diseases. Understanding how the millions of SNPs in the human genome are involved in conferring susceptibility or resistance to disease, or in rendering a drug efficacious or toxic in the individual is a major goal of the relatively new fields of pharmacogenomics. Esophageal squamous cell carcinoma is a high-mortality cancer with complex etiology and progression involving both genetic and environmental factors. We examined the association between esophageal cancer risk and patterns of 61 SNPs in a case-control study for a population from Shanxi Province in North Central China that has among the highest rates of esophageal squamous cell carcinoma in the world.

Methods

High-throughput Masscode mass spectrometry genotyping was done on genomic DNA from 574 individuals (394 cases and 180 age-frequency matched controls). SNPs were chosen from among genes involving DNA repair enzymes, and Phase I and Phase II enzymes.

We developed a novel adaptation of the Decision Forest pattern recognition method named Decision Forest for SNPs (DF-SNPs). The method was designated to analyze the SNP data.

Results

The classifier in separating the cases from the controls developed with DF-SNPs gave concordance, sensitivity and specificity, of 94.7%, 99.0% and 85.1%, respectively; suggesting its usefulness for hypothesizing what SNPs or combinations of SNPs could be involved in susceptibility to esophageal cancer. Importantly, the DF-SNPs algorithm incorporated a randomization test for assessing the relevance (or importance) of individual SNPs, SNP types (Homozygous common, heterozygous and homozygous variant) and patterns of SNP types (SNP patterns) that differentiate cases from controls. For example, we found that the different genotypes of SNP GADD45B E1122 are all associated with cancer risk.

Conclusion

The DF-SNPs method can be used to differentiate esophageal squamous cell carcinoma cases from controls based on individual SNPs, SNP types and SNP patterns. The method could be useful to identify potential biomarkers from the SNP data and complement existing methods for genotype analyses.
Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS)
Authors: Hong Huixiao , Dragan Yvonne , Epstein Joshua , Teitel Candee , Chen Bangzheng , Xie Qian , Fang Hong , Shi Leming , Perkins Roger , Tong Weida
Published: July 2005

Background

Proteomic profiling of complex biological mixtures by the ProteinChip technology of surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS) is one of the most promising approaches in toxicological, biological, and clinic research. The reliable identification of protein expression patterns and associated protein biomarkers that differentiate disease from health or that distinguish different stages of a disease depends on developing methods for assessing the quality of SELDI-TOF mass spectra. The use of SELDI data for biomarker identification requires application of rigorous procedures to detect and discard low quality spectra prior to data analysis.

Results

The systematic variability from plates, chips, and spot positions in SELDI experiments was evaluated using biological and technical replicates. Systematic biases on plates, chips, and spots were not found. The reproducibility of SELDI experiments was demonstrated by examining the resulting low coefficient of variances of five peaks presented in all 144 spectra from quality control samples that were loaded randomly on different spots in the chips of six bioprocessor plates. We developed a method to detect and discard low quality spectra prior to proteomic profiling data analysis, which uses a correlation matrix to measure the similarities among SELDI mass spectra obtained from similar biological samples. Application of the correlation matrix to our SELDI data for liver cancer and liver toxicity study and myeloma-associated lytic bone disease study confirmed this approach as an efficient and reliable method for detecting low quality spectra.

Conclusion

This report provides evidence that systematic variability between plates, chips, and spots on which the samples were assayed using SELDI based proteomic procedures did not exist. The reproducibility of experiments in our studies was demonstrated to be acceptable and the profiling data for subsequent data analysis are reliable. Correlation matrix was developed as a quality control tool to detect and discard low quality spectra prior to data analysis. It proved to be a reliable method to measure the similarities among SELDI mass spectra and can be used for quality control to decrease noise in proteomic profiling data prior to data analysis.
Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling
Authors: Fang H , Tong W , Perkins R , Shi L , Hong H , Cao X , Xie Q , Yim SH , Ward JM , Pitot HC , Dragan YP
Published: July 2005

Background

The completion of the sequencing of human, mouse and rat genomes and knowledge of cross-species gene homologies enables studies of differential gene expression in animal models. These types of studies have the potential to greatly enhance our understanding of diseases such as liver cancer in humans. Genes co-expressed across multiple species are most likely to have conserved functions. We have used various bioinformatics approaches to examine microarray expression profiles from liver neoplasms that arise in albumin-SV40 transgenic rats to elucidate genes, chromosome aberrations and pathways that might be associated with human liver cancer.

Results

In this study, we first identified 2223 differentially expressed genes by comparing gene expression profiles for two control, two adenoma and two carcinoma samples using an F-test. These genes were subsequently mapped to the rat chromosomes using a novel visualization tool, the Chromosome Plot. Using the same plot, we further mapped the significant genes to orthologous chromosomal locations in human and mouse. Many genes expressed in rat 1q that are amplified in rat liver cancer map to the human chromosomes 10, 11 and 19 and to the mouse chromosomes 7, 17 and 19, which have been implicated in studies of human and mouse liver cancer. Using Comparative Genomics Microarray Analysis (CGMA), we identified regions of potential aberrations in human. Lastly, a pathway analysis was conducted to predict altered human pathways based on statistical analysis and extrapolation from the rat data. All of the identified pathways have been known to be important in the etiology of human liver cancer, including cell cycle control, cell growth and differentiation, apoptosis, transcriptional regulation, and protein metabolism.

Conclusion

The study demonstrates that the hepatic gene expression profiles from the albumin-SV40 transgenic rat model revealed genes, pathways and chromosome alterations consistent with experimental and clinical research in human liver cancer. The bioinformatics tools presented in this paper are essential for cross species extrapolation and mapping of microarray data, its analysis and interpretation.
Evaluation of Glycine max mRNA clusters
Authors: Frank Ronald L , Ercal Fikret
Published: July 2005

Background

Clustering the ESTs from a large dataset representing a single species is a convenient starting point for a number of investigations into gene discovery, genome evolution, expression patterns, and alternatively spliced transcripts. Several methods have been developed to accomplish this, the most widely available being UniGene, a public domain collection of gene-oriented clusters for over 45 different species created and maintained by NCBI. The goal is for each cluster to represent a unique gene, but currently it is not known how closely the overall results represent that reality. UniGene's build procedure begins with initial mRNA clusters before joining ESTs. UniGene's results for soybean indicate a significant amount of redundancy among some sequences reported to be unique mRNAs. To establish a valid non-redundant known gene set forGlycine maxwe applied our algorithm to the clustering of only mRNA sequences. The mRNA dataset was run through the algorithm using two different matching stringencies. The resulting cluster compositions were compared to each other and to UniGene. Clusters exhibiting differences among the three methods were analyzed by 1) nucleotide and amino acid alignment and 2) submitting authors conclusions to determine whether members of a single cluster represented the same gene or not.

Results

Of the 12 clusters that were examined closely most contained examples of sequences that did not belong in the same cluster. However, neither the two stringencies of PECT nor UniGene had a significantly greater record of accuracy in placing paralogs into separate clusters.

Conclusion

Our results reveal that, although each method produces some errors, using multiple stringencies for matching or a sequential hierarchical method of increasing stringencies can provide more reliable results and therefore allow greater confidence in the vast majority of clusters that contain only ESTs and no mRNA sequences.
A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools
Authors: Xu Zengjun , Patterson Tucker A , Wren Jonathan D , Han Tao , Shi Leming , Duhart Helen , Ali Syed F , Slikker William
Published: July 2005

Background

This paper describes a microarray study including data quality control, data analysis and the analysis of the mechanism of toxicity (MOT) induced by 1-methyl-4-phenylpyridinium (MPP+) in a rat adrenal pheochromocytoma cell line (PC12 cells) using bioinformatics tools. MPP+depletes dopamine content and elicits cell death in PC12 cells. However, the mechanism of MPP+-induced neurotoxicity is still unclear.

Results

In this study, Agilent rat oligo 22K microarrays were used to examine alterations in gene expression of PC12 cells after 500 μM MPP+treatment. Relative gene expression of control and treated cells represented by spot intensities on the array chips was analyzed using bioinformatics tools. Raw data from each array were input into the NCTR ArrayTrack database, and normalized using a Lowess normalization method. Data quality was monitored in ArrayTrack. The means of the averaged log ratio of the paired samples were used to identify the fold changes of gene expression in PC12 cells after MPP+treatment. Our data showed that 106 genes and ESTs (Expressed Sequence Tags) were changed 2-fold and above with MPP+treatment; among these, 75 genes had gene symbols and 59 genes had known functions according to the Agilent gene Refguide and ArrayTrack-linked gene library. The mechanism of MPP+-induced toxicity in PC12 cells was analyzed based on their genes functions, biological process, pathways and previous published literatures.

Conclusion

Multiple pathways were suggested to be involved in the mechanism of MPP+-induced toxicity, including oxidative stress, DNA and protein damage, cell cycling arrest, and apoptosis.
CLPM: A Cross-Linked Peptide Mapping Algorithm for Mass Spectrometric Analysis
Authors: Tang Yong , Chen Yingfeng , Lichti Cheryl F , Hall Roger A , Raney Kevin D , Jennings Steven F
Published: July 2005

Background

Protein-protein, protein-DNA and protein-RNA interactions are of central importance in biological systems. Quadrapole Time-of-flight (Q-TOF) mass spectrometry is a sensitive, promising tool for studying these interactions. Combining this technique with chemical crosslinking, it is possible to identify the sites of interactions within these complexes. Due to the complexities of the mass spectrometric data of crosslinked proteins, new software is required to analyze the resulting products of these studies.

Result

We designed a Cross-Linked Peptide Mapping (CLPM) algorithm which takes advantage of all of the information available in the experiment including the amino acid sequence from each protein, the identity of the crosslinker, the identity of the digesting enzyme, the level of missed cleavage, and possible chemical modifications. The algorithm does in silico digestion and crosslinking, calculates all possible mass values and matches the theoretical data to the actual experimental data provided by the mass spectrometry analysis to identify the crosslinked peptides.

Conclusion

Identifying peptides by their masses can be an efficient starting point for direct sequence confirmation. The CLPM algorithm provides a powerful tool in identifying these potential interaction sites in combination with chemical crosslinking and mass spectrometry. Through this cost-effective approach, subsequent efforts can quickly focus attention on investigating these specific interaction sites.
Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis
Authors: Metpally Raghu Prasad Rao , Sowdhamini Ramanathan
Published: July 2005

Background

The G-protein-coupled receptors (GPCRs) constitute one of the largest and most ancient superfamilies of membrane proteins. They play a central role in physiological processes affecting almost all aspects of the life cycle of an organism. Availability of the complete sets of putative members of a family from diverse species provides the basis for cross genome comparative studies.

Results

We have defined the repertoire of GPCR superfamily of Tetraodon complement with the availability of complete sequence of the freshwater puffer fish Tetraodon nigroviridis. Almost all 466 Tetraodon GPCRs (Tnig-GPCRs) identified had a clear human homologue. 189 putative human and Tetraodon GPCR orthologous pairs could be identified. Tetraodon GPCRs are classified into five GRAFS families, by phylogenetic analysis, concurrent with human GPCR classification.

Conclusion

Direct comparison of GPCRs in Tetraodon and human genomes displays a high level of orthology and supports large-scale gene duplications in Tetraodon. Examples of lineage specific gene expansions were also observed in opsin and odorant receptors. The human and Tetraodon GPCR sequences are analogous in terms of GPCR subfamilies but display disproportionate numbers of receptors at the subfamily level. The teleost genome with its expanded set of GPCRs provides additional and interesting comparators to study both evolution and function of these receptors.
Sirolimus increases tissue factor expression but not activity in cultured human vascular smooth muscle cells
Authors: Zhu Shengsi , Viswambharan Hema , Gajanayake Thusitha , Ming Xiu-Fen , Yang Zhihong
Published: July 2005

Background

Sirolimus-eluting stents (CYPHER stents) demonstrated remarkable efficacy in reducing restenosis rates in patients with coronary artery disease. There is a concern of sub-acute and late stent thrombosis. Tissue factor (TF) is critical in thrombosis. This study investigated the effect of sirolimus on TF expression and activity in cultured human vascular smooth muscle cells (SMCs).

Methods

SMCs were cultured from human saphenous veins and aortas. Quiescent cells were stimulated with sirolimus (0.1 – 20 ng/ml) over 24 hours. Cellular TF expression and activity released into culture medium were measured. The effect of sirolimus on activation of
m
ammalian
t
arget
o
f rapamycin (mTOR) was measured by phosphorylation of the substrate p70s6k at T389, and activation of RhoA was measured by pull-down assay.

Results

Sirolimus increased TF protein level in cultured human SMCs in a concentration and time-dependent manner (about 2-fold, p < 0.01) reaching maximal effect at 5 ng/ml. The stimulation of TF expression by sirolimus was associated with inhibition of basal activity of mTOR. No effects of sirolimus on RhoA or p38mapk activation that are positive regulators of TF in vascular wall cells were observed. The stimulation of TF expression by sirolimus (20 ng/ml) was prevented by the HMG-CoA reductase inhibitor fluvastatin (1 μmol/L). However, no increase in TF activity released from SMC into culture medium was observed after sirolimus treatment.

Conclusion

Although sirolimus stimulates TF protein expression in human SMC associated with inhibition of mTOR, it does not enhance TF activity released from the cells, suggesting a relatively safe profile of CYPHER stents. The inhibition of TF expression by fluvastatin favors clinical use of statins in patients undergoing coronary stenting.
Bacteriophage- based tests for the detection of Mycobacterium tuberculosis in clinical specimens: a systematic review and meta- analysis
Authors: Kalantri Shriprakash , Pai Madhukar , Pascopella Lisa , Riley Lee , Reingold Arthur
Published: July 2005

Background

Sputum microscopy, the most important conventional test for tuberculosis, is specific in settings with high burden of tuberculosis and low prevalence of non tuberculous mycobacteria. However, the test lacks sensitivity. Although bacteriophage-based tests for tuberculosis have shown promising results, their overall accuracy has not been systematically evaluated.

Methods

We did a systematic review and meta-analysis of published studies to evaluate the accuracy of phage-based tests for the direct detection ofM. tuberculosisin clinical specimens. To identify studies, we searched Medline, EMBASE, Web of science and BIOSIS, and contacted authors, experts and test manufacturers. Thirteen studies, all based on phage amplification method, met our inclusion criteria. Overall accuracy was evaluated using forest plots, summary receiver operating (SROC) curves, and subgroup analyses.

Results

The data suggest that phage-based assays have high specificity (range 0.83 to 1.00), but modest and variable sensitivity (range 0.21 to 0.88). The sensitivity ranged between 0.29 and 0.87 among smear-positive, and 0.13 to 0.78 among smear-negative specimens. The specificity ranged between 0.60 and 0.88 among smear-positive and 0.89 to 0.99 among smear-negative specimens. SROC analyses suggest that overall accuracy of phage-based assays is slightly higher than smear microscopy in direct head-to-head comparisons.

Conclusion

Phage-based assays have high specificity but lower and variable sensitivity. Their performance characteristics are similar to sputum microscopy. Phage assays cannot replace conventional diagnostic tests such as microscopy and culture at this time. Further research is required to identify methods that can enhance the sensitivity of phage-based assays without compromising the high specificity.
Recovery of NIS expression in thyroid cancer cells by overexpression of Pax8 gene
Authors: Presta Ivan , Arturi Franco , Ferretti Elisabetta , Mattei Tiziana , Scarpelli Daniela , Tosi Emanuele , Scipioni Angela , Celano Marilena , Gulino Alberto , Filetti Sebastiano , Russo Diego
Published: July 2005

Background

Recovery of iodide uptake in thyroid cancer cells by means of obtaining the functional expression of the sodium/iodide symporter (NIS) represents an innovative strategy for the treatment of poorly differentiated thyroid cancer. However, the NIS gene expression alone is not always sufficient to restore radioiodine concentration ability in these tumour cells.

Methods

In this study, the anaplastic thyroid carcinoma ARO cells were stably transfected with a Pax8 gene expression vector. A quantitative RT-PCR was performed to assess the thyroid specific gene expression in selected clones. The presence of NIS protein was detected by Western blot and localized by immunofluorescence. A iodide uptake assay was also performed to verify the functional effect of NIS induction and differentiation switch.

Results

The clones overexpressing Pax8 showed the re-activation of several thyroid specific genes including NIS, Pendrin, Thyroglobulin, TPO and TTF1. In ARO-Pax8 clones NIS protein was also localized both in cell cytoplasm and membrane. Thus, the ability to uptake the radioiodine was partially restored, associated to a high rate of efflux. In addition, ARO cells expressing Pax8 presented a lower rate of cell growth.

Conclusion

These finding demonstrate that induction of Pax8 expression may determine a re-differentiation of thyroid cancer cells, including a partial recovery of iodide uptake, fundamental requisite for a radioiodine-based therapeutic approach for thyroid tumours.
Otitis media in young Aboriginal children from remote communities in Northern and Central Australia: a cross-sectional survey
Authors: Morris Peter S , Leach Amanda J , Silberberg Peter , Mellon Gabrielle , Wilson Cate , Hamilton Elizabeth , Beissbarth Jemima
Published: July 2005

Background

Middle ear disease (otitis media) is common and frequently severe in Australian Aboriginal children. There have not been any recent large-scale surveys using clear definitions and a standardised middle ear assessment. The aim of the study was to determine the prevalence of middle ear disease (otitis media) in a high-risk population of young Aboriginal children from remote communities in Northern and Central Australia.

Methods

709 Aboriginal children aged 6–30 months living in 29 communities from 4 health regions participated in the study between May and November 2001. Otitis media (OM) and perforation of the tympanic membrane (TM) were diagnosed by tympanometry, pneumatic otoscopy, and video-otoscopy. We used otoscopic criteria (bulging TM or recent perforation) to diagnose acute otitis media.

Results

914 children were eligible to participate in the study and 709 were assessed (78%). Otitis media affected nearly all children (91%, 95%CI 88, 94). Overall prevalence estimates adjusted for clustering by community were: 10% (95%CI 8, 12) for unilateral otitis media with effusion (OME); 31% (95%CI 27, 34) for bilateral OME; 26% (95%CI 23, 30) for acute otitis media without perforation (AOM/woP); 7% (95%CI 4, 9) for AOM with perforation (AOM/wiP); 2% (95%CI 1, 3) for dry perforation; and 15% (95%CI 11, 19) for chronic suppurative otitis media (CSOM). The perforation prevalence ranged from 0–60% between communities and from 19–33% between regions. Perforations of the tympanic membrane affected 40% of children in their first 18 months of life. These were not always persistent.

Conclusion

Overall, 1 in every 2 children examined had otoscopic signs consistent with suppurative ear disease and 1 in 4 children had a perforated tympanic membrane. Some of the children with intact tympanic membranes had experienced a perforation that healed before the survey. In this high-risk population, high rates of tympanic perforation were associated with high rates of bulging of the tympanic membrane.
Mass ivermectin treatment for Onchocerciasis: Lack of evidence for collateral impact on transmission of Wuchereria bancroftiin areas of co-endemicity
Authors: Richards FO , Eigege A , Pam D , Kal A , Lenhart A , Oneyka JOA , Jinadu MY , Miri ES
Published: July 2005

There has long been interest in determining if mass ivermectin administration for onchocerciasis has 'unknowingly' interrupted lymphatic filariasis (LF) transmission where the endemicity of the two diseases' overlaps. We studied 11 communities in central Nigeria entomologically for LF by performing mosquito dissections on Anopheline LF vectors. Six of the communities studied were located within an onchocerciasis treatment zone, and five were located outside of that zone. Communities inside the treatment zone had been offered ivermectin treatment for two-five years, with a mean coverage of 81% of the eligible population (range 58–95%). We found 4.9% of mosquitoes were infected with any larval stage of W. bancrofti in the head or thorax in 362 dissections in the untreated villages compared to 4.7% infected in 549 dissections in the ivermectin treated villages (Mantel-Haenszel ChiSquare 0.02, P = 0.9). We concluded that ivermectin annual therapy for onchocerciasis has not interrupted transmission of Wuchereria bancrofti (the causative agent of LF in Nigeria).
Telomerase inhibition by siRNA causes senescence and apoptosis in Barrett's adenocarcinoma cells: mechanism and therapeutic potential
Authors: Shammas Masood A , Koley Hemanta , Batchu Ramesh B , Bertheau Robert C , Protopopov Alexei , Munshi Nikhil C , Goyal Raj K
Published: July 2005

Background

In cancer cells, telomerase induction helps maintain telomere length and thereby bypasses senescence and provides enhanced replicative potential. Chemical inhibitors of telomerase have been shown to reactivate telomere shortening and cause replicative senescence and apoptotic cell death of tumor cells while having little or no effect on normal diploid cells.

Results

We designed siRNAs against two different regions of telomerase gene and evaluated their effect on telomere length, proliferative potential, and gene expression in Barrett's adenocarcinoma SEG-1 cells. The mixture of siRNAs in nanomolar concentrations caused a loss of telomerase activity that appeared as early as day 1 and was essentially complete at day 3. Inhibition of telomerase activity was associated with marked reduction in median telomere length and complete loss of detectable telomeres in more than 50% of the treated cells. Telomere loss caused senescence in 40% and apoptosis in 86% of the treated cells. These responses appeared to be associated with activation of DNA sensor HR23B and subsequent activation of p53 homolog p73 and p63 and E2F1. Changes in these gene regulators were probably the source of observed up-regulation of cell cycle inhibitors, p16 and GADD45. Elevated transcript levels of FasL, Fas and caspase 8 that activate death receptors and CARD 9 that interacts with Bcl10 and NFKB to enhance mitochondrial translocation and activation of caspase 9 were also observed.

Conclusion

These studies show that telomerase siRNAs can cause effective suppression of telomerase and telomere shortening leading to both cell cycle arrest and apoptosis via mechanisms that include up-regulation of several genes involved in cell cycle arrest and apoptosis. Telomerase siRNAs may therefore be strong candidates for highly selective therapy for chemoprevention and treatment of Barrett's adenocarcinoma.
Validation of a patient-administered questionnaire to measure the activity impairment experienced by women with uncomplicated urinary tract infection: the Activity Impairment Assessment (AIA)
Authors: Wild Diane J , Clayson Darren J , Keating Karen , Gondek Kathleen
Published: July 2005

Background

To validate a questionnaire to assess the activity impairment associated with uncomplicated urinary tract infection (uUTI).

Methods

The Activity Impairment Assessment (AIA) assesses the amount of time an individual's work or regular activities have been impaired as a result of their UTI. The measure was completed by 276 women with uUTI who had participated in a prospective, open-label, non-comparative multi-centre clinical trial of CIPRO® XR (extended-release ciprofloxacin). Baseline scores on the King's Health Questionnaire (KHQ) and clinical symptom evaluations were collected for validation purposes.

Results

An exploratory factor analysis showed that all items loaded >0.84 on a single component. This uni-dimensional structure was supported by Rasch analysis. The AIA was found to have excellent levels of internal consistency (Cronbach's alpha = 0.93), convergent validity (all rs >.70) and divergent validity (rs = .078). The AIA displayed excellent discriminant validity in relation to clinical evaluations, and was found to be responsive to change across all clinical evaluations.

Conclusion

The unidimensional AIA shows high levels of internal reliability, convergent and divergent validity, discriminant validity and responsiveness. It is an excellent tool for measuring activity impairment in UTI.