bluuebunny/crossref_metadata_2025 huggingface dataset:
Recycling of Raft-associated Prohormone Sorting Receptor Carboxypeptidase E Requires Interaction with ARF6
Authors: Arnaoutova Irina , Jackson Catherine L. , Al-Awar Omayma S. , Donaldson Julie G. , Loh Y. Peng
Published: September 2003

Little is known about the molecular mechanism of recycling of intracellular receptors and lipid raft-associated proteins. Here, we have investigated the recycling pathway and internalization mechanism of a transmembrane, lipid raft-associated intracellular prohormone sorting receptor, carboxypeptidase E (CPE). CPE is found in the trans-Golgi network (TGN) and secretory granules of (neuro)endocrine cells. An extracellular domain of the IL2 receptor α-subunit (Tac) fused to the transmembrane domain and cytoplasmic tail of CPE (Tac-CPE25) was used as a marker to track recycling of CPE. We show in (neuro)endocrine cells, that upon stimulated secretory granule exocytosis, raft-associated Tac-CPE25was rapidly internalized from the plasma membrane in a clathrin-independent manner into early endosomes and then transported through the endocytic recycling compartment to the TGN. A yeast two-hybrid screen and in vitro binding assay identified the CPE cytoplasmic tail sequence S472ETLNF477as an interactor with active small GTPase ADP-ribosylation factor (ARF) 6, but not ARF1. Expression of a dominant negative, inactive ARF6 mutant blocked this recycling. Mutation of residues S472or E473to A in the cytoplasmic tail of CPE obliterated its binding to ARF6, and internalization from the plasma membrane of Tac-CPE25mutated at S472or E473was significantly reduced. Thus, CPE recycles back to the TGN by a novel mechanism requiring ARF6 interaction and activity.
Intersectin Regulates Fission and Internalization of Caveolae in Endothelial Cells
Authors: Predescu Sanda A. , Predescu Dan N. , Timblin Barbara K. , Stan Radu V. , Malik Asrar B.
Published: September 2003

Intersectin, a multiple Eps15 homology and Src homology 3 (SH3) domain–containing protein, is a component of the endocytic machinery in neurons and nonneuronal cells. However, its role in endocytosis via caveolae in endothelial cells (ECs) is unclear. We demonstrate herein by coimmunoprecipitation, velocity sedimentation on glycerol gradients, and cross-linking that intersectin is present in ECs in a membrane-associated protein complex containing dynamin and SNAP-23. Electron microscopy (EM) immunogold labeling studies indicated that intersectin associated preferentially with the caveolar necks, and it remained associated with caveolae after their fission from the plasmalemma. A cell-free system depleted of intersectin failed to support caveolae fission from the plasma membrane. A biotin assay used to quantify caveolae internalization and extensive EM morphological analysis of ECs overexpressing wt-intersectin indicated a wide range of morphological changes (i.e., large caveolae clusters marginated at cell periphery and pleiomorphic caveolar necks) as well as impaired caveolae internalization. Biochemical evaluation of caveolae-mediated uptake by ELISA showed a 68.4% inhibition by reference to control. We also showed that intersectin interaction with dynamin was important in regulating the fission and internalization of caveolae. Taken together, the results indicate the crucial role of intersectin in the mechanism of caveolae fission in endothelial cells.
Glom Is a Novel Mitochondrial DNA Packaging Protein inPhysarum polycephalumand Causes Intense Chromatin Condensation without Suppressing DNA Functions
Authors: Sasaki Narie , Kuroiwa Haruko , Nishitani Chikako , Takano Hiroyoshi , Higashiyama Tetsuya , Kobayashi Tamaki , Shirai Yuki , Sakai Atsushi , Kawano Shigeyuki , Murakami-Murofushi Kimiko , Kuroiwa Tsuneyoshi
Published: September 2003

Mitochondrial DNA (mtDNA) is packed into highly organized structures called mitochondrial nucleoids (mt-nucleoids). To understand the organization of mtDNA and the overall regulation of its genetic activity within the mt-nucleoids, we identified and characterized a novel mtDNA packaging protein, termed Glom (a protein inducing agglomeration of mitochondrial chromosome), from highly condensed mt-nucleoids of the true slime mold, Physarum polycephalum. This protein could bind to the entire mtDNA and package mtDNA into a highly condensed state in vitro. Immunostaining analysis showed that Glom specifically localized throughout the mt-nucleoid. Deduced amino acid sequence revealed that Glom has a lysine-rich region with proline-rich domain in the N-terminal half and two HMG boxes in C-terminal half. Deletion analysis of Glom revealed that the lysine-rich region was sufficient for the intense mtDNA condensation in vitro. When the recombinant Glom proteins containing the lysine-rich region were expressed in Escherichia coli, the condensed nucleoid structures were observed in E. coli. Such in vivo condensation did not interfere with transcription or replication of E. coli chromosome and the proline-rich domain was essential to keep those genetic activities. The expression of Glom also complemented the E. coli mutant lacking the bacterial histone-like protein HU and the HMG-boxes region of Glom was important for the complementation. Our results suggest that Glom is a new mitochondrial histone-like protein having a property to cause intense DNA condensation without suppressing DNA functions.
Myosin IIA Drives Neurite Retraction
Authors: Wylie Steven R. , Chantler Peter D.
Published: September 2003

Neuritic extension is the resultant of two vectorial processes: outgrowth and retraction. Whereas myosin IIB is required for neurite outgrowth, retraction is driven by a motor whose identity has remained unknown until now. Preformed neurites in mouse Neuro-2A neuroblastoma cells undergo immediate retraction when exposed to isoform-specific antisense oligonucleotides that suppress myosin IIB expression, ruling out myosin IIB as the retraction motor. When cells were preincubated with antisense oligonucleotides targeting myosin IIA, simultaneous or subsequent addition of myosin IIB antisense oligonucleotides did not elicit neurite retraction, both outgrowth and retraction being curtailed. Even during simultaneous application of antisense oligonucleotides against both myosin isoforms, lamellipodial spreading continued despite the complete inhibition of neurite extension, indicating an uncoupling of lamellipodial dynamics from movement of the neurite. Significantly, lysophosphatidate- or thrombin-induced neurite retraction was blocked not only by the Rho-kinase inhibitor Y27632 but also by antisense oligonucleotides targeting myosin IIA. Control oligonucleotides or antisense oligonucleotides targeting myosin IIB had no effect. In contrast, Y27632 did not inhibit outgrowth, a myosin IIB-dependent process. We conclude that the conventional myosin motor, myosin IIA, drives neurite retraction.
Asymmetric Distribution of Myosin IIB in Migrating Endothelial Cells Is Regulated by a rho-dependent Kinase and Contributes to Tail Retraction
Authors: Kolega John
Published: September 2003

All vertebrates contain two nonmuscle myosin II heavy chains, A and B, which differ in tissue expression and subcellular distributions. To understand how these distinct distributions are controlled and what role they play in cell migration, myosin IIA and IIB were examined during wound healing by bovine aortic endothelial cells. Immunofluorescence showed that myosin IIA skewed toward the front of migrating cells, coincident with actin assembly at the leading edge, whereas myosin IIB accumulated in the rear 15–30 min later. Inhibition of myosin light-chain kinase, protein kinases A, C, and G, tyrosine kinase, MAP kinase, and PIP3kinase did not affect this asymmetric redistribution of myosin isoforms. However, posterior accumulation of myosin IIB, but not anterior distribution of myosin IIA, was inhibited by dominant-negative rhoA and by the rho-kinase inhibitor, Y-27632, which also inhibited myosin light-chain phosphorylation. This inhibition was overcome by transfecting cells with constitutively active myosin light-chain kinase. These observations indicate that asymmetry of myosin IIB, but not IIA, is regulated by light-chain phosphorylation mediated by rho-dependent kinase. Blocking this pathway inhibited tail constriction and retraction, but did not affect protrusion, suggesting that myosin IIB functions in pulling the rear of the cell forward.
Sec3p Is Needed for the Spatial Regulation of Secretion and for the Inheritance of the Cortical Endoplasmic Reticulum
Authors: Wiederkehr Andreas , Du Yunrui , Pypaert Marc , Ferro-Novick Susan , Novick Peter
Published: September 2003

Sec3p is a component of the exocyst complex that tethers secretory vesicles to the plasma membrane at exocytic sites in preparation for fusion. Unlike all other exocyst structural genes, SEC3 is not essential for growth. Cells lacking Sec3p grow and secrete surprisingly well at 25°C; however, late markers of secretion, such as the vesicle marker Sec4p and the exocyst subunit Sec8p, localize more diffusely within the bud. Furthermore, sec3Δ cells are strikingly round relative to wild-type cells and are unable to form pointed mating projections in response to α factor. These phenotypes support the proposed role of Sec3p as a spatial landmark for secretion. We also find that cells lacking Sec3p exhibit a dramatic defect in the inheritance of cortical ER into the bud, whereas the inheritance of mitochondria and Golgi is unaffected. Overexpression of Sec3p results in a prominent patch of the endoplasmic reticulum (ER) marker Sec61p-GFP at the bud tip. Cortical ER inheritance in yeast has been suggested to involve the capture of ER tubules at the bud tip. Sec3p may act in this process as a spatial landmark for cortical ER inheritance.
The Simultaneous Production of Phosphatidic Acid and Diacylglycerol Is Essential for the Translocation of Protein Kinase Cϵ to the Plasma Membrane in RBL-2H3 Cells
Authors: Jose Lopez-Andreo Maria , Gomez-Fernandez Juan C. , Corbalan-Garcia Senena
Published: September 2003

To evaluate the role of the C2 domain in protein kinase Cϵ (PKCϵ) localization and activation after stimulation of the IgE receptor in RBL-2H3 cells, we used a series of mutants located in the phospholipid binding region of the enzyme. The results obtained suggest that the interaction of the C2 domain with the phospholipids in the plasma membrane is essential for anchoring the enzyme in this cellular compartment. Furthermore, the use of specific inhibitors of the different pathways that generate both diacylglycerol and phosphatidic acid has shown that the phosphatidic acid generated via phospholipase D (PLD)-dependent pathway, in addition to the diacylglycerol generated via phosphoinosite-phospholipase C (PLC), are involved in the localization of PKCϵ in the plasma membrane. Direct stimulation of RBL-2H3 cells with very low concentrations of permeable phosphatidic acid and diacylglycerol exerted a synergistic effect on the plasma membrane localization of PKCϵ. Moreover, the in vitro kinase assays showed that both phosphatidic acid and diacylglycerol are essential for enzyme activation. Together, these results demonstrate that phosphatidic acid is an important and essential activator of PKCϵ through the C2 domain and locate this isoenzyme in a new scenario where it acts as a downstream target of PLD.
Integration of Cell Attachment, Cytoskeletal Localization, and Signaling by Integrin-linked Kinase (ILK), CH-ILKBP, and the Tumor Suppressor PTEN
Authors: Attwell Sarah , Mills Julia , Troussard Armelle , Wu Chuanyue , Dedhar Shoukat
Published: September 2003

Cell attachment and the assembly of cytoskeletal and signaling complexes downstream of integrins are intimately linked and coordinated. Although many intracellular proteins have been implicated in these processes, a new paradigm is emerging from biochemical and genetic studies that implicates integrin-linked kinase (ILK) and its interacting proteins, such as CH-ILKBP (α-parvin), paxillin, and PINCH in coupling integrins to the actin cytoskeleton and signaling complexes. Genetic studies in Drosophila, Caenorhabditis elegans, and mice point to an essential role of ILK as an adaptor protein in mediating integrin-dependent cell attachment and cytoskeletal organization. Here we demonstrate, using several different approaches, that inhibiting ILK kinase activity, or expression, results in the inhibition of cell attachment, cell migration, F-actin organization, and the specific cytoskeletal localization of CH-ILKBP and paxillin in human cells. We also demonstrate that the kinase activity of ILK is elevated in the cytoskeletal fraction and that the interaction of CH-ILKBP with ILK within the cytoskeleton stimulates ILK activity and downstream signaling to PKB/Akt and GSK-3. Interestingly, the interaction of CH-ILKBP with ILK is regulated by the Pi3 kinase pathway, because inhibition of Pi3 kinase activity by pharmacological inhibitors, or by the tumor suppressor PTEN, inhibits this interaction as well as cell attachment and signaling. These data demonstrate that the kinase and adaptor properties of ILK function together, in a Pi3 kinase–dependent manner, to regulate integrin-mediated cell attachment and signal transduction.
The Angiotensin II Type I Receptor-associated Protein, ATRAP, Is a Transmembrane Protein and a Modulator of Angiotensin II Signaling
Authors: Lopez-Ilasaca Marco , Liu Xiushi , Tamura Koichi , Dzau Victor J.
Published: September 2003

Our group identified angiotensin II type 1 (AT1) receptor-associated protein (ATRAP) in a yeast two-hybrid screen for proteins that bind to the carboxyl-terminal cytoplasmic domain of the AT1. In this work, we characterize ATRAP as a transmembrane protein localized in intracellular trafficking vesicles and plasma membrane that functions as a modulator of angiotensin II-induced signal transduction. ATRAP contains three hydrophobic domains at the amino-terminal end of the protein, encompassing the amino acid residues 14–36, 55–77, and 88–108 and a hydrophilic cytoplasmic carboxyl-terminal tail from residues 109–161. Endogenous and transfected ATRAP cDNA shows a particulate distribution; electron microscopy reveals the presence of ATRAP in prominent perinuclear vesicular membranes; and colocalization analysis by immunofluorescence shows that ATRAP colocalizes in an intracellular vesicular compartment corresponding to endoplasmic reticulum, Golgi, and endocytic vesicles. Real-time tracking of ATRAP vesicles shows constitutive translocation toward the plasma membrane. Using epitope-tagged forms of ATRAP at either the amino or carboxyl end of the molecule, we determined the orientation of the amino end as being outside the cell. Mutant forms of ATRAP lacking the carboxyl end are unable to bind to the AT1 receptor, leading to the formation of prominent perinuclear vesicle clusters. Functional analysis of the effects of ATRAP on angiotensin II-induced AT1 receptor signaling reveals a moderate decrease in the generation of inositol lipids, a marked decrease in the angiotensin II-stimulated transcriptional activity of the c-fos promoter luciferase reporter gene, and a decrease in cell proliferation.
Genetic and Biochemical Evaluation of the Importance of Cdc6 in Regulating Mitotic Exit
Authors: Archambault Vincent , Li Caihong X. , Tackett Alan J. , Wäsch Ralph , Chait Brian T. , Rout Michael P. , Cross Frederick R.
Published: September 2003

We evaluated the hypothesis that the N-terminal region of the replication control protein Cdc6 acts as an inhibitor of cyclin-dependent kinase (Cdk) activity, promoting mitotic exit. Cdc6 accumulation is restricted to the period from mid-cell cycle until the succeeding G1, due to proteolytic control that requires the Cdc6 N-terminal region. During late mitosis, Cdc6 is present at levels comparable with Sic1 and binds specifically to the mitotic cyclin Clb2. Moderate overexpression of Cdc6 promotes viability of CLB2Δdb strains, which otherwise arrest at mitotic exit, and rescue is dependent on the N-terminal putative Cdk-inhibitory domain. These observations support the potential for Cdc6 to inhibit Clb2-Cdk, thus promoting mitotic exit. Consistent with this idea, we observed a cytokinesis defect in cdh1Δ sic1Δ cdc6Δ2–49 triple mutants. However, we were able to construct viable strains, in three different backgrounds, containing neither SIC1 nor the Cdc6 Cdk-inhibitory domain, in contradiction to previous work. We conclude, therefore, that although both Cdc6 and Sic1 have the potential to facilitate mitotic exit by inhibiting Clb2-Cdk, mitotic exit nevertheless does not require any identified stoichiometric inhibitor of Cdk activity.
Diffusion-based Transport of Nascent Ribosomes in the Nucleus
Authors: Ritland Politz Joan C. , Tuft Richard A. , Pederson Thoru
Published: September 2003

Although the complex process of ribosome assembly in the nucleolus is beginning to be understood, little is known about how the ribosomal subunits move from the nucleolus to the nuclear membrane for transport to the cytoplasm. We show here that large ribosomal subunits move out from the nucleolus and into the nucleoplasm in all directions, with no evidence of concentrated movement along directed paths. Mobility was slowed compared with that expected in aqueous solution in a manner consistent with anomalous diffusion. Once nucleoplasmic, the subunits moved in the same random manner and also sometimes visited another nucleolus before leaving the nucleus.
PRECIS: Protein reports engineered from concise information in SWISS-PROT
Authors: Mitchell A.L. , Reich J.R. , Attwood T.K.
Published: September 2003

Motivation: There have been several endeavours to address the problem of annotating sequence data computationally, but the task is non-trivial and few tools have emerged that gather useful information on a given sequence, or set of sequences, in a simple and convenient manner. As more genome projects bear fruit, the mass of uncharacterized sequence data accumulating in public repositories grows ever larger. There is thus a pressing need for tools to support the process of automatic analysis and annotation of newly determined sequences. With this in mind, we have developed PRECIS, which automatically creates protein reports from sets of SWISS-PROT entries, collating results into structured reports, detailing known biological and medical information, literature and database cross-references, and relevant keywords.

Availability: The software is accessible online at: http://www.bioinf.man.ac.uk/cgi-bin/dbbrowser/precis/blast_precis.cgi
ESTAP—an automated system for the analysis of EST data
Authors: Mao Chunhong , Cushman John C. , May Gregory D. , Weller Jennifer W.
Published: September 2003

Summary: The EST Analysis Pipeline (ESTAP) is a set of analytical procedures that automatically verify, cleanse, store and analyze ESTs generated on high-throughput platforms. It uses a relational database to store sequence data and analysis results, which facilitates both the search for specific information and statistical analysis. ESTAP provides for easy viewing of the original and cleansed data, as well as the analysis results via a Web browser. It also allows the data owner to submit selected sequences to dbEST in a semi-automated fashion.

Availablity:  http://www.vbi.vt.edu/~estap
Statistical significance analysis of longitudinal gene expression data
Authors: Guo Xu , Qi Huilin , Verfaillie Catherine M. , Pan Wei
Published: September 2003

Motivation: Time-course microarray experiments are designed to study biological processes in a temporal fashion. Longitudinal gene expression data arise when biological samples taken from the same subject at different time points are used to measure the gene expression levels. It has been observed that the gene expression patterns of samples of a given tumor measured at different time points are likely to be much more similar to each other than are the expression patterns of tumor samples of the same type taken from different subjects. In statistics, this phenomenon is called the within-subject correlation of repeated measurements on the same subject, and the resulting data are called longitudinal data. It is well known in other applications that valid statistical analyses have to appropriately take account of the possible within-subject correlation in longitudinal data.

Results: We apply estimating equation techniques to construct a robust statistic, which is a variant of the robust Wald statistic and accounts for the potential within-subject correlation of longitudinal gene expression data, to detect genes with temporal changes in expression. We associate significance levels to the proposed statistic by either incorporating the idea of the significance analysis of microarrays method or using the mixture model method to identify significant genes. The utility of the statistic is demonstrated by applying it to an important study of osteoblast lineage-specific differentiation. Using simulated data, we also show pitfalls in drawing statistical inference when the within-subject correlation in longitudinal gene expression data is ignored.
MedScan, a natural language processing engine for MEDLINE abstracts
Authors: Novichkova Svetlana , Egorov Sergei , Daraselia Nikolai
Published: September 2003

Motivation: The importance of extracting biomedical information from scientific publications is well recognized. A number of information extraction systems for the biomedical domain have been reported, but none of them have become widely used in practical applications. Most proposals to date make rather simplistic assumptions about the syntactic aspect of natural language. There is an urgent need for a system that has broad coverage and performs well in real-text applications.

Results: We present a general biomedical domain-oriented NLP engine called MedScan that efficiently processes sentences from MEDLINE abstracts and produces a set of regularized logical structures representing the meaning of each sentence. The engine utilizes a specially developed context-free grammar and lexicon. Preliminary evaluation of the system's performance, accuracy, and coverage exhibited encouraging results. Further approaches for increasing the coverage and reducing parsing ambiguity of the engine, as well as its application for information extraction are discussed.

Availability: MedScan is available for commercial licensing from Ariadne Genomics, Inc.
SignalViewer: analyzing microarray images
Authors: Laws R.J. , Bergemann T.L. , Quiaoit F. , Zhao L.P.
Published: September 2003

Summary: Microarray technology is now routinely used to monitor genome-wide expression profiles. However, current microarray imaging and analysis packages typically require manual intervention and assumptions on alignments. Unfortunately, limitations and assumptions are typically undisclosed and methods are not published. To facilitate exploration of image data, we developed SignalViewer. This paper presents a description of the application.

Availability: SignalViewer is available at http://qge.fhcrc.org/signalviewer/

Supplementary information: Screenshots are available at the above location, along with downloads for Windows 2000 and Linux (Redhat 7.2).
Diametrical clustering for identifying anti-correlated gene clusters
Authors: Dhillon Inderjit S. , Marcotte Edward M. , Roshan Usman
Published: September 2003

Motivation: Clustering genes based upon their expression patterns allows us to predict gene function. Most existing clustering algorithms cluster genes together when their expression patterns show high positive correlation. However, it has been observed that genes whose expression patterns are strongly anti-correlated can also be functionally similar. Biologically, this is not unintuitive—genes responding to the same stimuli, regardless of the nature of the response, are more likely to operate in the same pathways.

Results: We present a new diametrical clustering algorithm that explicitly identifies anti-correlated clusters of genes. Our algorithm proceeds by iteratively (i) re-partitioning the genes and (ii) computing the dominant singular vector of each gene cluster; each singular vector serving as the prototype of a 'diametric' cluster. We empirically show the effectiveness of the algorithm in identifying diametrical or anti-correlated clusters. Testing the algorithm on yeast cell cycle data, fibroblast gene expression data, and DNA microarray data from yeast mutants reveals that opposed cellular pathways can be discovered with this method. We present systems whose mRNA expression patterns, and likely their functions, oppose the yeast ribosome and proteosome, along with evidence for the inverse transcriptional regulation of a number of cellular systems.

Availability: See http://bioinformatics.icmb.utexas.edu for the experimental results. Software is available on request.
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data
Authors: Wu Baolin , Abbott Tom , Fishman David , McMurray Walter , Mor Gil , Stone Kathryn , Ward David , Williams Kenneth , Zhao Hongyu
Published: September 2003

Motivation: Novel methods, both molecular and statistical, are urgently needed to take advantage of recent advances in biotechnology and the human genome project for disease diagnosis and prognosis. Mass spectrometry (MS) holds great promise for biomarker identification and genome-wide protein profiling. It has been demonstrated in the literature that biomarkers can be identified to distinguish normal individuals from cancer patients using MS data. Such progress is especially exciting for the detection of early-stage ovarian cancer patients. Although various statistical methods have been utilized to identify biomarkers from MS data, there has been no systematic comparison among these approaches in their relative ability to analyze MS data.

Results: We compare the performance of several classes of statistical methods for the classification of cancer based on MS spectra. These methods include: linear discriminant analysis, quadratic discriminant analysis, k-nearest neighbor classifier, bagging and boosting classification trees, support vector machine, and random forest (RF). The methods are applied to ovarian cancer and control serum samples from the National Ovarian Cancer Early Detection Program clinic at Northwestern University Hospital. We found that RF outperforms other methods in the analysis of MS data.

Supplementary information:  http://bioinformatics.med.yale.edu/proteomics/BioSupp1.html
Consensus alignment for reliable framework prediction in homology modeling
Authors: Prasad J.C. , Comeau S.R. , Vajda S. , Camacho C.J.
Published: September 2003

Motivation: Even the best sequence alignment methods frequently fail to correctly identify the framework regions for which backbones can be copied from the template into the target structure. Since the underprediction and, more significantly, the overprediction of these regions reduces the quality of the final model, it is of prime importance to attain as much as possible of the true structural alignment between target and template.

Results: We have developed an algorithm called Consensus that consistently provides a high quality alignment for comparative modeling. The method follows from a benchmark analysis of the 3D models generated by ten alignment techniques for a set of 79 homologous protein structure pairs. For 20-to-40% of the targets, these methods yield models with at least 6 Å root mean square deviation (RMSD) from the native structure. We have selected the top five performing methods, and developed a consensus algorithm to generate an improved alignment. By building on the individual strength of each method, a set of criteria was implemented to remove the alignment segments that are likely to correspond to structurally dissimilar regions. The automated algorithm was validated on a different set of 48 protein pairs, resulting in 2.2 Å average RMSD for the predicted models, and only four cases in which the RMSD exceeded 3 Å. The average length of the alignments was about 75% of that found by standard structural superposition methods. The performance of Consensus was consistent from 2 to 32% target–template sequence identity, and hence it can be used for accurate prediction of framework regions in homology modeling.

Availability: The algorithm is available as a server at http://structure.bu.edu/cgi-bin/consensus/consensus.cgi
Comparison of sequence masking algorithms and the detection of biased protein sequence regions
Authors: Kreil David P. , Ouzounis Christos A.
Published: September 2003

Motivation: Separation of protein sequence regions according to their local information complexity and subsequent masking of low complexity regions has greatly enhanced the reliability of function prediction by sequence similarity. Comparisons with alternative methods that focus on compositional sequence bias rather than information complexity measures have shown that removal of compositional bias yields at least as sensitive and much more specific results. Besides the application of sequence masking algorithms to sequence similarity searches, the study of the masked regions themselves is of great interest. Traditionally, however, these have been neglected despite evidence of their functional relevance.

Results: Here we demonstrate that compositional bias seems to be a more effective measure for the detection of biologically meaningful signals. Typical results on proteins are compared to results for sequences that have been randomized in various ways, conserving composition and local correlations for individual proteins or the entire set. It is remarkable that low-complexity regions have the same form of distribution in proteins as in randomized sequences, and that the signal from randomized sequences with conserved local correlations and amino acid composition almost matches the signal from proteins. This is not the case for sequence bias, which hence seems to be a genuinely biological phenomenon in contrast to patches of low complexity.

Availability: Software in executable form is available on request from the authors.

Supplementary information: There is an online supplement with additional supporting figures. (http://www.inference.phy.cam.ac.uk/dpk20/sup/)
Detecting putative orthologs
Authors: Wall D. P. , Fraser H. B. , Hirsh A. E.
Published: September 2003

Summary: We developed an algorithm that improves upon the common procedure of taking reciprocal best blast hits (rbh) in the identification of orthologs. The method—reciprocal smallest distance algorithm (rsd)—relies on global sequence alignment and maximum likelihood estimation of evolutionary distances to detect orthologs between two genomes. rsd finds many putative orthologs missed by rbh because it is less likely than rbh to be misled by the presence of a close paralog.

Availability: A Python program and ReadMe file are freely available from: http://charles.stanford.edu/~dennis/research.html
GFPE: gene-finding program evaluation
Authors: Wang Jian , Kraemer Eileen
Published: September 2003

Summary: Gene-finding program evaluation (GFPE) is a set of Java classes for evaluating gene-finding programs. A command-line interface is also provided. Inputs to the program include the sequence data (in FASTA format), annotations of 'actual' sequence features, and annotations of 'predicted' sequence features. Annotation files are in the General Feature Format promoted by the Sanger center. GFPE calculates a number of metrics of accuracy of predictions at three levels: the coding level, the exon level, and the protein level.

Availability: The program is freely available at: ftp://anonymous@iubio.bio.indiana.edu/molbio/genefind/
PathMiner: predicting metabolic pathways by heuristic search
Authors: McShan D.C. , Rao S. , Shah I.
Published: September 2003

Motivation: Automated methods for biochemical pathway inference are becoming increasingly important for understanding biological processes in living and synthetic systems. With the availability of data on complete genomes and increasing information about enzyme-catalyzed biochemistry it is becoming feasible to approach this problem computationally. In this paper we present PathMiner, a system for automatic metabolic pathway inference. PathMiner predicts metabolic routes by reasoning over transformations using chemical and biological information.

Results: We build a biochemical state-space using data from known enzyme-catalyzed transformations in Ligand, including, 2917 unique transformations between 3890 different compounds. To predict metabolic pathways we explore this state-space by developing an informed search algorithm. For this purpose we develop a chemically motivated heuristic to guide the search. Since the algorithm does not depend on predefined pathways, it can efficiently identify plausible routes using known biochemical transformations.

Availability: The system is available for testing at http://pathminer.uchsc.edu
FindGDPs: identification of primers for labeling microbial transcriptomes for DNA microarray analysis
Authors: Blick Robert J. , Revel Andrew T. , Hansen Eric J.
Published: September 2003

Summary: FindGDPs is a program that uses a greedy algorithm to quickly identify a set of genome-directed primers that specifically anneal to all of the open reading frames in a genome and that do not exhibit full-length complementarity to the members of another user-supplied set of nucleotide sequences.

Availability: The program code is distributed under the GNU General Public License at http://www3.utsouthwestern.edu/microbiology/pages/faculty/hansen.html
A comparative analysis of HGSC and Celera human genome assemblies and gene sets
Authors: Li Shuyu , Cutler Gene , Liu Jane Jijun , Hoey Timothy , Chen Liangbiao , Schultz Peter G. , Liao Jiayu , Ling Xuefeng Bruce
Published: September 2003

Motivation: Since the simultaneous publication of the human genome assembly by the International Human Genome Sequencing Consortium (HGSC) and Celera Genomics, several comparisons have been made of various aspects of these two assemblies. In this work, we set out to provide a more comprehensive comparative analysis of the two assemblies and their associated gene sets.

Results: The local sequence content for both draft genome assemblies has been similar since the early releases, however it took a year for the quality of the Celera assembly to approach that of HGSC, suggesting an advantage of HGSC's hierarchical shotgun (HS) sequencing strategy over Celera's whole genome shotgun (WGS) approach. While similar numbers of ab initio predicted genes can be derived from both assemblies, Celera's Otto approach consistently generated larger, more varied gene sets than the Ensembl gene build system. The presence of a non-overlapping gene set has persisted with successive data releases from both groups. Since most of the unique genes from either genome assembly could be mapped back to the other assembly, we conclude that the gene set discrepancies do not reflect differences in local sequence content but rather in the assemblies and especially the different gene-prediction methodologies.
ProSAT: functional annotation of protein 3D structures
Authors: Gabdoulline Razif R. , Hoffmann René , Leitner Florian , Wade Rebecca C.
Published: September 2003

Summary: ProSAT (for Protein Structure Annotation Tool) is a tool to facilitate interactive visualization of non-structure-based functional annotations in protein 3D structures. It performs automated mapping of the functional annotations onto the protein structure and allows functional sites to be readily identified upon visualization. The current version of ProSAT can be applied to large datasets of protein structures for fast visual identification of active and other functional sites derived from the SwissProt and Prosite databases.

Availability:  http://projects.villa-bosch.de/mcm/database/prosat/
E-Cell 2: Multi-platform E-Cell simulation system
Authors: Takahashi K. , Ishikawa N. , Sadamoto Y. , Sasamoto H. , Ohta S. , Shiozawa A. , Miyoshi F. , Naito Y. , Nakayama Y. , Tomita M.
Published: September 2003

Summary: A new version of the E-Cell simulation system, which runs on Windows as well as Linux, has been released as free software under the terms of the GNU General Public License.

Availability: Downloadable from http://www.E-Cell.org
Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs
Authors: Park Keun-Joon , Kanehisa Minoru
Published: September 2003

Motivation: The subcellular location of a protein is closely correlated to its function. Thus, computational prediction of subcellular locations from the amino acid sequence information would help annotation and functional prediction of protein coding genes in complete genomes. We have developed a method based on support vector machines (SVMs).

Results: We considered 12 subcellular locations in eukaryotic cells: chloroplast, cytoplasm, cytoskeleton, endoplasmic reticulum, extracellular medium, Golgi apparatus, lysosome, mitochondrion, nucleus, peroxisome, plasma membrane, and vacuole. We constructed a data set of proteins with known locations from the SWISS-PROT database. A set of SVMs was trained to predict the subcellular location of a given protein based on its amino acid, amino acid pair, and gapped amino acid pair compositions. The predictors based on these different compositions were then combined using a voting scheme. Results obtained through 5-fold cross-validation tests showed an improvement in prediction accuracy over the algorithm based on the amino acid composition only. This prediction method is available via the Internet.

Availability:  http://www.genome.ad.jp/SIT/ploc.html

Supplementary information:  http://web.kuicr.kyoto-u.ac.jp/~park/Seqdata/
Secondary structure prediction with support vector machines
Authors: Ward J. J. , McGuffin L. J. , Buxton B. F. , Jones D. T.
Published: September 2003

Motivation: A new method that uses support vector machines (SVMs) to predict protein secondary structure is described and evaluated. The study is designed to develop a reliable prediction method using an alternative technique and to investigate the applicability of SVMs to this type of bioinformatics problem.

Methods: Binary SVMs are trained to discriminate between two structural classes. The binary classifiers are combined in several ways to predict multi-class secondary structure.

Results: The average three-state prediction accuracy per protein (Q3) is estimated by cross-validation to be 77.07 ± 0.26% with a segment overlap (Sov) score of 73.32 ± 0.39%. The SVM performs similarly to the 'state-of-the-art' PSIPRED prediction method on a non-homologous test set of 121 proteins despite being trained on substantially fewer examples. A simple consensus of the SVM, PSIPRED and PROFsec achieves significantly higher prediction accuracy than the individual methods.

Availability: The SVM classifier is available from the authors. Work is in progress to make the method available on-line and to integrate the SVM predictions into the PSIPRED server.
CRANN: detecting adaptive evolution in protein-coding DNA sequences
Authors: Creevey C.J. , McInerney J.O.
Published: September 2003

Summary: A software program CRANN has been developed in order to detect adaptive evolution in protein-coding DNA sequences.

Availability: CRANN is available from http://bioinf.may.ie/crann/

Supplementary Information: CRANN has been written in the C programming language. Source code is available on request.
An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis
Authors: Barker Jonathan A. , Thornton Janet M.
Published: September 2003

Motivation: Structural templates consisting of a few atoms in a specific geometric conformation provide a powerful tool for studying the relationship between protein structure and function. Current methods for template searching constrain template syntax and semantics by their design. Hence there is a need for a more flexible core algorithm upon which to build more sophisticated tools. Statistical analysis of structural similarity is still in its infancy when compared with its analogue in sequence alignment. In the context of template matching, there is an urgent need for normalization of scores so that results from templates with differing sensitivity may be compared directly.

Results: We introduce Jess, a fast and flexible algorithm for searching protein structures for small groups of atoms under arbitrary constraints on geometry and chemistry. We apply the algorithm to a set of manually derived enzyme active site templates, and derive an empirical measure for estimating the relative significance of hits encountered using differing templates.

Availability: Jess will be available in the near future under a restricted open source licence.
The effect of replication on gene expression microarray experiments
Authors: Pavlidis Paul , Li Qinghong , Noble William Stafford
Published: September 2003

Motivation: We examine the effect of replication on the detection of apparently differentially expressed genes in gene expression microarray experiments. Our analysis is based on a random sampling approach using real data sets from 16 published studies. We consider both the ability to find genes that meet particular statistical criteria as well as the stability of the results in the face of changing levels of replication.

Results: While dependent on the data source, our findings suggest that stable results are typically not obtained until at least five biological replicates have been used. Conversely, for most studies, 10–15 replicates yield results that are quite stable, and there is less improvement in stability as the number of replicates is further increased. Our methods will be of use in evaluating existing data sets and in helping to design new studies.

Supplementary information:  http://microarray.cpmc.columbia.edu/pavlidis/pub/gxrep
ddbRNA: detection of conserved secondary structures in multiple alignments
Authors: di Bernardo Diego , Down Thomas , Hubbard Tim
Published: September 2003

Motivation: Structured non-coding RNAs (ncRNAs) have a very important functional role in the cell. No distinctive general features common to all ncRNA have yet been discovered. This makes it difficult to design computational tools able to detect novel ncRNAs in the genomic sequence.

Results: We devised an algorithm able to detect conserved secondary structures in both pairwise and multiple DNA sequence alignments with computational time proportional to the square of the sequence length. We implemented the algorithm for the case of pairwise and three-way alignments and tested it on ncRNAs obtained from public databases. On the test sets, the pairwise algorithm has a specificity greater than 97% with a sensitivity varying from 22.26% for Blast alignments to 56.35% for structural alignments. The three-way algorithm behaves similarly. Our algorithm is able to efficiently detect a conserved secondary structure in multiple alignments.

Availability: The executable file, the code and a PDF file containing the instructions, as well as the test data sets can be requested free of charge from the authors (dibernardo@tigem.it) or from the website http://www.tigem.it/research/dibernardo/default.htm
CGH-Plotter: MATLAB toolbox for CGH-data analysis
Authors: Autio Reija , Hautaniemi Sampsa , Kauraniemi Päivikki , Yli-Harja Olli , Astola Jaakko , Wolf Maija , Kallioniemi Anne
Published: September 2003

Summary: CGH-Plotter is a MATLAB toolbox with a graphical user interface for the analysis of comparative genomic hybridization (CGH) microarray data. CGH-Plotter provides a tool for rapid visualization of CGH-data according to the locations of the genes along the genome. In addition, the CGH-Plotter identifies regions of amplifications and deletions, using k-means clustering and dynamic programming. The application offers a convenient way to analyze CGH-data and can also be applied for the analysis of cDNA microarray expression data. CGH-Plotter toolbox is platform independent and requires MATLAB 6.1 or higher to operate.

Availability:  http://sigwww.cs.tut.fi/TICSP/CGH-Plotter
Web-based exchange of biochemical information
Authors: Güler Sinan , Eberhart Andreas , Rojas Isabel
Published: September 2003

Summary: In this paper we present a web-based system for the semantic integration of biological data using a database model and an XML exchange format. The prototype developed integrates data related to enzymes.

Availability:  http://projects.eml.org/sdbv/wbe/
Intergenic sequence inspector: searching and identifying bacterial RNAs
Authors: Pichon Christophe , Felden Brice
Published: September 2003

Summary:Intergenic Sequence Inspector (ISI) is a program that helps in identifying bacterial ribonucleic acids (RNAs). It automatically extracts, selects and visualizes candidate intergenic regions (IGRs) that bear conservations between phylogenetically related species, displaying sequence and structural signatures of RNA genes encompassing putative promoters, terminators, RNA secondary structure predictions and the G + C percent of the selected sequences. ISI is intentionally modular to analyze various bacterial genomes according to their intrinsic specificities and to the available data. ISI provides a sum of information to the user who can evaluate whether or not an IGR is susceptible to express RNAs.

Availability: The program can be downloaded at http://www.biochpharma.univ-rennes1.fr/ under the subsection 'Software'.
Are Life Insurance Holdings Related to Financial Vulnerabilities?
Authors: Bernheim B. Douglas , Carman Katherine Grace , Gokhale Jagadeesh , Kotlikoff Laurence J.
Published: September 2003

Using the 1995 Survey of Consumer Finances and an elaborate life‐cycle model, we quantify the potential financial impact of each individual's death on his or her survivors and measure the degree to which life insurance moderates these consequences. Life insurance is essentially uncorrelated with financial vulnerability at every stage of the life cycle. As a result, the impact of insurance among at‐risk households is modest, and substantial uninsured vulnerabilities are widespread, particularly among younger couples. We also identify a systematic gender bias: For any given level of financial vulnerability, couples provide significantly more protection for wives than for husbands. (JEL D10, G22)
Determinants of Scholarly Productivity among Male and Female Economists
Authors: Maske Kellie L. , Durden Garey C. , Gaynor Patricia E.
Published: September 2003

A model of the determinants of articles produced by male and female economists is estimated using data from a survey of members of the American Economics Association. Years of experience, coauthorship rates, gender, research‐teaching orientation of the respondent's institution, and teaching loads are shown to be important estimators. Coauthorship appears to increase the overall production of articles and may help explain why collaboration among economists has increased in recent years. Males produce, on average, about seven more articles than females, with approximately 59% of gender‐specific differentials left unexplained by the variables included in the model. (JEL JØ)
Time‐Series Evidence on the Nonlinearity Hypothesis for Public Spending
Authors: Mittnik Stefan , Neumann Thorsten
Published: September 2003

Barro‐type endogenous growth models propose a nonmonotonic relationship between productive public spending and growth. Under this so‐called nonlinearity hypothesis the size and direction of growth effects due to an increase in public spending depend on the share of public spending in GDP. Employing German time‐series data we examine the validity of the nonlinearity hypothesis. We estimate growth effects by using models whose coefficients are allowed to vary with the share of public spending in GDP. Our results support the hypothesis for public consumption but not for public investment data. (JEL H54, E62, C22)