bluuebunny/crossref_metadata_2025 huggingface dataset:
Cytoplasmic Processing Is a Prerequisite for Presentation of an Endogenous Antigen by Major Histocompatibility Complex Class II Proteins
Authors: Lich John D. , Elliott John F. , Blum Janice S.
Published: July 2002

Biochemical and functional studies have demonstrated major histocompatibility complex (MHC) class II–restricted presentation of select epitopes derived from cytoplasmic antigens, with few insights into the processing reactions necessary for this alternate pathway. Efficient presentation of an immunodominant epitope derived from glutamate decarboxylase (GAD) was observed regardless of whether this antigen was delivered exogenously or via a cytoplasmic route into human histocompatibility leukocyte antigen class II–DR4+ antigen-presenting cells. Presentation of exogenous as well as cytoplasmic GAD required the intersection of GAD peptides and newly synthesized class II proteins. By contrast, proteolytic processing of this antigen was highly dependent upon the route of antigen delivery. Exogenous GAD followed the classical pathway for antigen processing, with an absolute requirement for endosomal/lysosomal acidification as well as cysteine and aspartyl proteases resident within these organelles. Presentation of endogenous GAD was dependent upon the action of cytoplasmic proteases, including the proteasome and calpain. Thus, translocation of processed antigen from the cytoplasm into membrane organelles is necessary for class II–restricted presentation via this alternate pathway. Further trimming of these peptides after translocation was mediated by acidic proteases within endosomes/lysosomes, possibly after or before class II antigen binding. These studies suggest that processing of exogenous and cytoplasmic proteins occurs through divergent but overlapping pathways. Furthermore, two cytoplasmic proteases, the proteasome and calpain, appear to play important roles in MHC class II–restricted antigen presentation.
Immune Cell Activation by Bacterial Cpg-DNA through Myeloid Differentiation Marker 88 and Tumor Necrosis Factor Receptor–Associated Factor (Traf)6
Authors: Häcker Hans , Vabulas Ramunas M. , Takeuchi Osamu , Hoshino Katsuaki , Akira Shizuo , Wagner Hermann
Published: July 2002

Transition of immature antigen presenting cells (APCs) to the state of professional APCs is essential for initiation of cell-mediated immune responses to pathogens. Signal transduction via molecules of the Toll-like receptor (TLR)/interleukin 1 receptor (IL-1R) pathway is critical for activation of APCs either by pathogen-derived pattern ligands like lipopolysaccharides (LPS) or by CD40 ligation through T helper cells. The capacity of bacterial DNA (CpG-DNA) to induce APCs to differentiate into professional APCs represents an interesting discovery. However, the signaling pathways involved are poorly understood. Here we show that CpG-DNA activates the TLR/IL-1R signaling pathway via the molecules myeloid differentiation marker 88 (MyD88) and tumor necrosis factor receptor–associated factor 6 (TRAF6), leading to activation of kinases of the IκB kinase complex and the c-jun NH2-terminal kinases. Moreover, cells of TLR2- and TLR4-deficient mice are activated by CpG-DNA, whereas cells of MyD88-deficient mice do not respond. The data suggest that CpG-DNA initiates signaling via the TLR/IL-1R pathway in APCs in a manner similar to LPS and to T helper cell–mediated CD40 ligation. Activation of the TLR/IL-1R signaling pathway by foreign bacterial DNA may be one way to initiate innate defense mechanisms against infectious pathogens in vivo.
T Cells Compete for Access to Antigen-Bearing Antigen-Presenting Cells
Authors: Kedl Ross M. , Rees William A. , Hildeman David A. , Schaefer Brian , Mitchell Tom , Kappler John , Marrack Philippa
Published: July 2002

These studies tested whether antigenic competition between T cells occurs. We generated CD8+ T cell responses in H-2b mice against the dominant ovalbumin epitope SIINFEKL (ova8) and subdominant epitope KRVVFDKL, using either vaccinia virus expressing ovalbumin (VV-ova) or peptide-pulsed dendritic cells. CD8+ T cell responses were visualized by major histocompatibility complex class I–peptide tetrameric molecules. Transfer of transgenic T cells with high affinity for ova8 (OT1 T cells) completely inhibited the response of host antigen-specific T cells to either antigen, demonstrating that T cells can directly compete with each other for response to antigen. OT1 cells also inhibited CD8+ T cell responses to an unrelated peptide, SIYRYGGL, providing it was presented on the same dendritic cells as ova8. These inhibitions were not due to a more rapid clearance of virus or antigen-presenting cells (APCs) by the OT1 cells. Rather, the inhibition was caused by competition for antigen and antigen-bearing cells, since it could be overcome by the injection of large numbers of antigen-pulsed dendritic cells. These results imply that common properties of T cell responses, such as epitope dominance and secondary response affinity maturation, are the result of competitive interactions between antigen-bearing APC and T cell subsets.
A Dendritic Cell–Specific Intercellular Adhesion Molecule 3–Grabbing Nonintegrin (Dc-Sign)–Related Protein Is Highly Expressed on Human Liver Sinusoidal Endothelial Cells and Promotes HIV-1 Infection
Authors: Bashirova Arman A. , Geijtenbeek Teunis B.H. , van Duijnhoven Gerard C.F. , van Vliet Sandra J. , Eilering Jeroen B.G. , Martin Maureen P. , Wu Li , Martin Thomas D. , Viebig Nicola , Knolle Percy A. , KewalRamani Vineet N. , van Kooyk Yvette , Carrington Mary
Published: July 2002

The discovery of dendritic cell (DC)-specific intercellular adhesion molecule (ICAM)-3–grabbing nonintegrin (DC-SIGN) as a DC-specific ICAM-3 binding receptor that enhances HIV-1 infection of T cells in trans has indicated a potentially important role for adhesion molecules in AIDS pathogenesis. A related molecule called DC-SIGNR exhibits 77% amino acid sequence identity with DC-SIGN. The DC-SIGN and DC-SIGNR genes map within a 30-kb region on chromosome 19p13.2-3. Their strong homology and close physical location indicate a recent duplication of the original gene. Messenger RNA and protein expression patterns demonstrate that the DC-SIGN–related molecule is highly expressed on liver sinusoidal cells and in the lymph node but not on DCs, in contrast to DC-SIGN. Therefore, we suggest that a more appropriate name for the DC-SIGN–related molecule is L-SIGN, liver/lymph node–specific ICAM-3–grabbing nonintegrin. We show that in the liver, L-SIGN is expressed by sinusoidal endothelial cells. Functional studies indicate that L-SIGN behaves similarly to DC-SIGN in that it has a high affinity for ICAM-3, captures HIV-1 through gp120 binding, and enhances HIV-1 infection of T cells in trans. We propose that L-SIGN may play an important role in the interaction between liver sinusoidal endothelium and trafficking lymphocytes, as well as function in the pathogenesis of HIV-1.
Increased Turnover of T Lymphocytes in HIV-1 Infection and Its Reduction by Antiretroviral Therapy
Authors: Mohri Hiroshi , Perelson Alan S. , Tung Keith , Ribeiro Ruy M. , Ramratnam Bharat , Markowitz Martin , Kost Rhonda , Hurley  , Weinberger Leor , Cesar Denise , Hellerstein Marc K. , Ho David D.
Published: July 2002

The mechanism of CD4+ T cell depletion in human immunodeficiency virus (HIV)-1 infection remains controversial. Using deuterated glucose to label the DNA of proliferating cells in vivo, we studied T cell dynamics in four normal subjects and seven HIV-1–infected patients naive to antiretroviral drugs. The results were analyzed using a newly developed mathematical model to determine fractional rates of lymphocyte proliferation and death. In CD4+ T cells, mean proliferation and death rates were elevated by 6.3- and 2.9-fold, respectively, in infected patients compared with normal controls. In CD8+ T cells, the mean proliferation rate was 7.7-fold higher in HIV-1 infection, but the mean death rate was not significantly increased. Five of the infected patients underwent subsequent deuterated glucose labeling studies after initiating antiretroviral therapy. The lymphocyte proliferation and death rates in both CD4+ and CD8+ cell populations were substantially reduced by 5–11 weeks and nearly normal by one year. Taken together, these new findings strongly indicate that CD4+ lymphocyte depletion seen in AIDS is primarily a consequence of increased cellular destruction, not decreased cellular production.
Correlation between Charge Movement and Ionic Current during Slow Inactivation in Shaker K+ Channels
Authors: Olcese Riccardo , Latorre Ramón , Toro Ligia , Bezanilla Francisco , Stefani Enrico
Published: July 2002

Prolonged depolarization induces a slow inactivation process in some K+ channels. We have studied ionic and gating currents during long depolarizations in the mutant Shaker H4-Δ(6–46) K+ channel and in the nonconducting mutant (Shaker H4-Δ(6–46)-W434F). These channels lack the amino terminus that confers the fast (N-type) inactivation (Hoshi, T., W.N. Zagotta, and R.W. Aldrich. 1991. Neuron. 7:547–556). Channels were expressed in oocytes and currents were measured with the cut-open-oocyte and patch-clamp techniques. In both clones, the curves describing the voltage dependence of the charge movement were shifted toward more negative potentials when the holding potential was maintained at depolarized potentials. The evidences that this new voltage dependence of the charge movement in the depolarized condition is associated with the process of slow inactivation are the following: (a) the installation of both the slow inactivation of the ionic current and the inactivation of the charge in response to a sustained 1-min depolarization to 0 mV followed the same time course; and (b) the recovery from inactivation of both ionic and gating currents (induced by repolarizations to −90 mV after a 1-min inactivating pulse at 0 mV) also followed a similar time course. Although prolonged depolarizations induce inactivation of the majority of the channels, a small fraction remains non–slow inactivated. The voltage dependence of this fraction of channels remained unaltered, suggesting that their activation pathway was unmodified by prolonged depolarization. The data could be fitted to a sequential model for Shaker K+ channels (Bezanilla, F., E. Perozo, and E. Stefani. 1994. Biophys. J. 66:1011–1021), with the addition of a series of parallel nonconducting (inactivated) states that become populated during prolonged depolarization. The data suggest that prolonged depolarization modifies the conformation of the voltage sensor and that this change can be associated with the process of slow inactivation.
Timing of Ca2+ Release from Intracellular Stores and the Electrical Response of Limulus Ventral Photoreceptors to Dim Flashes
Authors: Payne Richard , Demas James
Published: July 2002

Light-induced release of Ca2+ from stores in Limulus ventral photoreceptors was studied using confocal fluorescence microscopy and the Ca2+ indicator dyes, Oregon green-5N and fluo-4. Fluorescence was collected from a spot within 4 μm of the microvillar membrane. A dual-flash protocol was used to reconstruct transient elevations of intracellular free calcium ion concentration (Cai) after flashes delivering between 10 and 5 × 105 effective photons. Peak Cai increased with flash intensity to 138 ± 76 μM after flashes delivering ∼104 effective photons, while the latent period of the elevation of Cai fell from ∼140 to 21 ms. The onset of the light-induced elevation of Cai was always highly correlated with that of the receptor potential. The time for Cai to exceed 2 μM was approximately equal to that for the receptor potential to exceed 8 mV (mean difference; 2.2 ± 6.4 ms). Cai was also measured during steps of light delivering ∼105 effective photons/s to photoreceptors that had been bleached with hydroxylamine so as to reduce their quantum efficiency. Elevations of Cai were detected at the earliest times of the electrical response to the steps of light, when a significant receptor potential had yet to develop. Successive responses exhibited stochastic variation in their latency of up to 20 ms, but the elevation of Cai and the receptor potential still rose at approximately the same time, indicating a shared process generating the latent period. Light-induced elevations of Cai resulted from Ca2+ release from intracellular stores, being abolished by cyclopiazonic acid (CPA), an inhibitor of endoplasmic reticulum Ca2+ pumps, but not by removal of extracellular Ca2+ ions. CPA also greatly diminished and slowed the receptor potential elicited by dim flashes. The results demonstrate a rapid release of Ca2+ ions that appears necessary for a highly amplified electrical response to dim flashes.
Functional Triads Consisting of Ryanodine Receptors, Ca2+ Channels, and Ca2+-Activated K+ Channels in Bullfrog Sympathetic Neurons
Authors: Akita Tenpei , Kuba Kenji
Published: July 2002

Fluorescent ryanodine revealed the distribution of ryanodine receptors in the submembrane cytoplasm (less than a few micrometers) of cultured bullfrog sympathetic ganglion cells. Rises in cytosolic Ca2+ ([Ca2+]i) elicited by single or repetitive action potentials (APs) propagated at a high speed (150 μm/s) in constant amplitude and rate of rise in the cytoplasm bearing ryanodine receptors, and then in the slower, waning manner in the deeper region. Ryanodine (10 μM), a ryanodine receptor blocker (and/or a half opener), or thapsigargin (1–2 μM), a Ca2+-pump blocker, or ω-conotoxin GVIA (ω-CgTx, 1 μM), a N-type Ca2+ channel blocker, blocked the fast propagation, but did not affect the slower spread. Ca2+ entry thus triggered the regenerative activation of Ca2+-induced Ca2+ release (CICR) in the submembrane region, followed by buffered Ca2+ diffusion in the deeper cytoplasm. Computer simulation assuming Ca2+ release in the submembrane region reproduced the Ca2+ dynamics. Ryanodine or thapsigargin decreased the rate of spike repolarization of an AP to 80%, but not in the presence of iberiotoxin (IbTx, 100 nM), a BK-type Ca2+-activated K+ channel blocker, or ω-CgTx, both of which decreased the rate to 50%. The spike repolarization rate and the amplitude of a single AP-induced rise in [Ca2+]i gradually decreased to a plateau during repetition of APs at 50 Hz, but reduced less in the presence of ryanodine or thapsigargin. The amplitude of each of the [Ca2+]i rise correlated well with the reduction in the IbTx-sensitive component of spike repolarization. The apamin-sensitive SK-type Ca2+-activated K+ current, underlying the afterhyperpolarization of APs, increased during repetitive APs, decayed faster than the accompanying rise in [Ca2+]i, and was suppressed by CICR blockers. Thus, ryanodine receptors form a functional triad with N-type Ca2+ channels and BK channels, and a loose coupling with SK channels in bullfrog sympathetic neurons, plastically modulating AP.
Effects of Dantrolene on Steps of Excitation-Contraction Coupling in Mammalian Skeletal Muscle Fibers
Authors: Szentesi Péter , Collet Claude , Sárközi Sándor , Szegedi Csaba , Jona István , Jacquemond Vincent , Kovács László , Csernoch László
Published: July 2002

The effects of the muscle relaxant dantrolene on steps of excitation-contraction coupling were studied on fast twitch muscles of rodents. To identify the site of action of the drug, single fibers for voltage-clamp measurements, heavy SR vesicles for calcium efflux studies and solubilized SR calcium release channels/RYRs for lipid bilayer studies were isolated. Using the double Vaseline-gap or the silicone-clamp technique, dantrolene was found to suppress the depolarization-induced elevation in intracellular calcium concentration ([Ca2+]i) by inhibiting the release of calcium from the SR. The suppression of [Ca2+]i was dose-dependent, with no effect at or below 1 μM and a 53 ± 8% (mean ± SEM, n = 9, cut fibers) attenuation at 0 mV with 25 μM of extracellularly applied dantrolene. The drug was not found to be more effective if injected than if applied extracellularly. Calculating the SR calcium release revealed an equal suppression of the steady (53 ± 8%) and of the early peak component (46 ± 6%). The drug did not interfere with the activation of the voltage sensor in as much as the voltage dependence of both intramembrane charge movements and the L-type calcium currents (ICa) were left, essentially, unaltered. However, the inactivation of ICa was slowed fourfold, and the conductance was reduced from 200 ± 16 to 143 ± 8 SF−1 (n = 10). Dantrolene was found to inhibit thymol-stimulated calcium efflux from heavy SR vesicles by 44 ± 10% (n = 3) at 12 μM. On the other hand, dantrolene failed to affect the isolated RYR incorporated into lipid bilayers. The channel displayed a constant open probability for as long as 30–50 min after the application of the drug. These data locate the binding site for dantrolene to be on the SR membrane, but be distinct from the purified RYR itself.
Novel Role for CFTR in Fluid Absorption from the Distal Airspaces of the Lung
Authors: Fang X. , Fukuda N. , Barbry P. , Sartori C. , Verkman A.S. , Matthay M.A.
Published: July 2002

The active absorption of fluid from the airspaces of the lung is important for the resolution of clinical pulmonary edema. Although ENaC channels provide a major route for Na+ absorption, the route of Cl− transport has been unclear. We applied a series of complementary approaches to define the role of Cl− transport in fluid clearance in the distal airspaces of the intact mouse lung, using wild-type and cystic fibrosis ΔF508 mice. Initial studies in wild-type mice showed marked inhibition of fluid clearance by Cl− channel inhibitors and Cl− ion substitution, providing evidence for a transcellular route for Cl− transport. In response to cAMP stimulation by isoproterenol, clearance was inhibited by the CFTR inhibitor glibenclamide in both wild-type mice and the normal human lung. Although isoproterenol markedly increased fluid absorption in wild-type mice, there was no effect in ΔF508 mice. Radioisotopic clearance studies done at 23°C (to block active fluid absorption) showed ∼20% clearance of 22Na in 30 min both without and with isoproterenol. However, the clearance of 36Cl was increased by 47% by isoproterenol in wild-type mice but was not changed in ΔF508 mice, providing independent evidence for involvement of CFTR in cAMP-stimulated Cl− transport. Further, CFTR played a major role in fluid clearance in a mouse model of acute volume-overload pulmonary edema. After infusion of saline (40% body weight), the lung wet-to-dry weight ratio increased by 28% in wild-type versus 64% in ΔF508 mice. These results provide direct evidence for a functionally important role for CFTR in the distal airspaces of the lung.
On restarting the Arnoldi method for large nonsymmetric eigenvalue problems
Authors: Morgan Ronald
Published: July 2002

The Arnoldi method computes eigenvalues of large nonsymmetric matrices. Restarting is generally needed to reduce storage requirements and orthogonalization costs. However, restarting slows down the convergence and makes the choice of the new starting vector difficult if several eigenvalues are desired. We analyze several approaches to restarting and show why Sorensen’s implicit QR approach is generally far superior to the others. Ritz vectors are combined in precisely the right way for an effective new starting vector. Also, a new method for restarting Arnoldi is presented. It is mathematically equivalent to the Sorensen approach but has additional uses.
Fully explicit quasiconvexification of the mean-square deviation of the gradient of the state in optimal design
Authors: Pedregal Pablo
Published: July 2002

We explicitly compute the quasiconvexification of the resulting integrand associated with the mean-square deviation of the gradient of the state with respect to a given target field, when the underlying optimal design problem in conductivity is reformulated as a purely variational problem. What is remarkable, more than the formula itself, is the fact that it can be shown to be the full quasiconvexification.
A genetic algorithm for designing gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor protein superfamily.
Authors: Kel A , Ptitsyn A , Babenko V , Meier-Ewert S , Lehrach H
Published: July 2002

MOTIVATION: Massive oligonucleotide hybridization is one of the most promising technologies of functional genome analysis. The critical point is to design appropriate sets of oligonucleotides that can be used effectively in identification by hybridization. RESULTS: Using a genetic algorithm approach, we have attempted to design sets of oligo probes capable of identifying new genes belonging to a defined gene family within a cDNA or genomic library. It is not limited by oligonucleotide length and admits the letter 'N' in the structure of the oligonucleotides selected. One of the major advantages of this approach is the low homology required to identify functional families of sequences with little homology. We have designed the oligonucleotide sets that are most selective for the cDNA clones of transmembrane G protein-coupled receptors (GPCRs), a large family of proteins that form part of a modular system of extracellular signal transduction to the intracellular second messenger pathways. The accuracy of identification has been checked on the EST library containing 713 870 cDNA sequences. A set of 15 oligos between 7 and 14 bases in length has correctly identified 70% of the GPCR cDNA collection sequences with 0.02% false positives. AVAILABILITY: The developed software is available by ftp://ftp.bionet.nsc. ru/pub/biology/ and on the Web page http://www.bionet.nsc. ru/SRCG/Oligoselector/. CONTACT: kel@.bionet.nsc.ru; sebastian. meier-ewert@gpc-ag.com
DIALIGN: finding local similarities by multiple sequence alignment.
Authors: Morgenstern B , Frech K , Dress A , Werner T
Published: July 2002

MOTIVATION: DIALIGN is a new method for pairwise as well as multiple alignment of nucleic acid and protein sequences. While standard alignment programs rely on comparing single residues and imposing gap penalties, DIALIGN constructs alignments by comparing whole segments of the sequences. No gap penalty is employed. This point of view is especially adequate if sequences are not globally related, but share only local similarities, as is the case in genomic DNA sequences and in many protein families. RESULTS: Using four different data sets, we show that DIALIGN is able correctly to align conserved motifs in protein sequences. Alignments produced by DIALIGN are compared systematically to the results of five other alignment programs. AVAILABILITY: DIALIGN is available to the scientific community free of charge for non-commercial use. Executables for various UNIX platforms including LINUX can be downloaded at http://www.gsf.de/biodv/dialign.html Contact: werner, morgenstern@gsf.de
ModBase: A database of comparative protein structure models
Authors: Sánchez Roberto , S̆ali Andrej
Published: July 2002

Summary: ModBase is a database of evaluated and annotated comparative protein structure models. The database also includes fold assignments and alignments on which the models were based.

Availability: ModBase is accessible on the Web at http://guitar.rockefeller.edu/modbase. Models for yeast proteins are also accessible through links from the Sacch3D database at http://genome-www.stanford.edu/Sacch3D.

Contact: sali@rockefeller.edu; http//guitar.rockefeller.edu/
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history.
Authors: Knudsen B , Hein J
Published: July 2002

MOTIVATION: Many computerized methods for RNA secondary structure prediction have been developed. Few of these methods, however, employ an evolutionary model, thus relevant information is often left out from the structure determination. This paper introduces a method which incorporates evolutionary history into RNA secondary structure prediction. The method reported here is based on stochastic context-free grammars (SCFGs) to give a prior probability distribution of structures. RESULTS: The phylogenetic tree relating the sequences can be found by maximum likelihood (ML) estimation from the model introduced here. The tree is shown to reveal information about the structure, due to mutation patterns. The inclusion of a prior distribution of RNA structures ensures good structure predictions even for a small number of related sequences. Prediction is carried out using maximum a posteriori estimation (MAP) estimation in a Bayesian approach. For small sequence sets, the method performs very well compared to current automated methods.
BIND—a data specification for storing and describing
biomolecular interactions, molecular complexes and pathways
Authors: Bader Gary D. , Hogue Christopher W. V.
Published: July 2002

* To whom correspondence should be addressed.

Motivation: Proteomics is gearing up towards high-throughput methods for identifying and characterizing all of the proteins, protein domains and protein interactions in a cell and will eventually create more recorded biological information than the Human Genome Project. Each protein expressed in a cell can interact with various other proteins and molecules in the course of its function. A standard data specification is required that can describe and store this information in all its detail and allow efficient cross-platform transfer of data. A complete specification must be the basis for any database or tool for managing and analysing this information.

Results: We have defined a complete data specification in ASN.1 that can describe information about biomolecular interactions, complexes and pathways. Our group is using this data specification in our database, the Biomolecular Interaction Network Database (BIND). An interaction record is based on the interaction between two objects. An object can be a protein, DNA, RNA, ligand, molecular complex or an interaction. Interaction description encompasses cellular location, experimental conditions used to observe the interaction, conserved sequence, molecular location, chemical action, kinetics, thermodynamics, and chemical state. Molecular complexes are defined as collections of more than two interactions that form a complex, with extra descriptive information such as complex topology. Pathways are defined as collections of more than two interactions that form a pathway, with additional descriptive information such as cell cycle stage. A request for proposal of a human readable flat-file format that mirrors the BIND data specification is also tendered for interested parties.

Availability: The ASN.1 data specification for biomolecular interaction, molecular complex and pathway data is available at ftp://bioinfo.mshri.on.ca/pub/BIND/Spec/bind.asn. An interactive browser for this document is available through our homepage at http://bioinfo.mshri.on.ca/BIND/asn-browser/.

Contact: hogue@mshri.on.ca
Phylogenetically enhanced statistical tools for RNA structure
prediction
Authors: Akmaev Viatcheslav R. , Kelley Scott T. , Stormo Gary D.
Published: July 2002

Motivation: Methods that predict the structure of molecules by looking for statistical correlation have been quite effective. Unfortunately, these methods often disregard phylogenetic information in the sequences they analyze. Here, we present a number of statistics for RNA molecular-structure prediction. Besides common pair-wise comparisons, we consider a few reasonable statistics for base-triple predictions, and present an elaborate analysis of these methods. All these statistics incorporate phylogenetic relationships of the sequences in the analysis to varying degrees, and the different nature of these tests gives a wide choice of statistical tools for RNA structure prediction.

Results: Starting from statistics that incorporate phylogenetic information only as independent sequence evolution models for each position of a multiple alignment, and extending this idea to a joint evolution model of two positions, we enhance the usual purely statistical methods (e.g. methods based on the Mutual Information statistic) with the use of phylogenetic information available in the sequences. In particular, we present a joint model based on the HKY evolution model, and consequently a \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \({\chi}^{2}\) \end{document}test of independence for two positions. A significant part of this work is devoted to some mathematical analysis of these methods. We tested these statistics on regions of 16S and 23S rRNA, and tRNA.

Availability: The programs are available upon request.

Contact: slava@colorado.edu
Visualizing large hierarchical clusters in hyperbolic space
Authors: Bingham Jonathan , Sudarsanam Sucha
Published: July 2002

Summary: HyperTree is an application to visualize and navigate large trees in hyperbolic space. It includes color-coding, search mechanisms and navigational aids, as well as focus+context viewing, allowing enormous trees to fit within the fixed space of a computer screen or printed page.

Availability: A demo is available online at http://www.kinase.com/tools/HyperTree.html

Contact: sucha-sudarsanam@sugen.com
Nucleosome formation potential of eukaryotic DNA: calculation
and promoters analysis
Authors: Levitsky Victor G. , Podkolodnaya Olga A. , Kolchanov Nikolay A. , Podkolodny Nikolay L.
Published: July 2002

Motivation: A rapid growth in the number of genes with known sequences calls for developing automated tools for their classification and analysis. It became clear that nucleosome packaging of eukaryotic DNA is very important for gene functioning. Automated computer tools for characterization of nucleosome packaging density could be useful for studying of gene regulation and genome annotation.

Results: A program for constructing nucleosome formation potential profiles of eukaryotic DNA sequences was developed. Nucleosome packaging density was analyzed for different functional types of human promoters. It was found that in promoters of tissue-specific genes, the nucleosome formation potential was essentially higher than in genes expressed in many tissues, or housekeeping genes. Hence, capability of nucleosome positioning in the promoter region may serve as a factor regulating gene expression.

Availability: The program for nucleosome sites recognition is included into the GeneExpress system; section ‘DNA Nucleosomal Organization’, http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/.

Contact: levitsky@bionet.nsc.ru

* To whom correspondence should be addressed.
A probabilistic method for identifying start codons in
bacterial genomes
Authors: Suzek Baris E. , Ermolaeva Maria D. , Schreiber Mark , Salzberg Steven L.
Published: July 2002

As the pace of genome sequencing has accelerated, the need for highly accurate gene prediction systems has grown. Computational systems for identifying genes in prokaryotic genomes have sensitivities of 98–99% or higher (Delcher et al. , Nucleic Acids Res. , 27, 4636–4641, 1999). These accuracy figures are calculated by comparing the locations of verified stop codons to the predictions. Determining the accuracy of start codon prediction is more problematic, however, due to the relatively small number of start sites that have been confirmed by independent, non-computational methods. Nonetheless, the accuracy of gene finders at predicting the exact gene boundaries at both the 5′ and 3′ ends of genes is of critical importance for microbial genome annotation, especially in light of the important signaling information that is sometimes found on the 5′ end of a protein coding region. In this paper we propose a probabilistic method to improve the accuracy of gene identification systems at finding precise translation start sites. The new system, RBSfinder, is tested on a validated set of genes from Escherichia coli , for which it improves the accuracy of start site locations predicted by computational gene finding systems from the range 67–77% to 90% correct.

* To whom correspondence should be addressed.
Conformational model for binding site recognition by the
E.coli MetJ transcription factor
Authors: Liu Rongxiang , Blackwell Thomas W. , States David J.
Published: July 2002

Motivation: Current methods for identifying sequence specific binding sites in DNA sequence using position specific weight matrices are limited in both sensitivity and specificity. Double strand DNA helix exhibits sequence dependent variations in conformation. Interactions between macromolecules result from complementarity of the two tertiary structures. We hypothesize that this conformational variation plays a role in transcription factor binding site recognition, and that the use of this structure information will improve the predictive power of transcription factor binding site models.

Results: Conformation models for the sequence dependence of DNA helix distortion have been developed. Using our conformational models, we defined a tertiary structure template for the met operon repressor MetJ binding site. Both naturally occurring sites and precursor binding sites identified through in vitro selection were used as the basis for template definition. The conformational model appears to recognize features of protein binding sites that are distinct from the features recognized by primary sequence based profiles. Combining the conformational model and primary sequence profile yields a hybrid model with improved discriminatory power compared with either the conformational model or sequence profile alone. Using our hybrid model, we searched the E.coli genome. We are able to identify the documented MetJ sites in the promoter regions of metA, metB, metC, metR and metF. In addition, we find several novel loci with characteristics suggesting that they are functional MetJ repressor binding sites. Novel MetJ binding sites are found upstream of the metK gene, as well as upstream of a gene, abc, a gene that encodes for a component of a multifunction transporter which may transport amino acids across the membrane. The false positive rate is significantly lower than the sequence profile method.

Availability: The programs of implementation of this algorithm are available upon request. The list of crystal structures used for compiling the mean base step parameters of DNA is available by anonymous ftp at http://stateslab.wustl.edu/pub/helix/StructureList.

Contact: states@ccb.wustl.edu

* To whom correspondence should be addressed.
PAL: an object-oriented programming library for molecular
evolution and phylogenetics
Authors: Drummond Alexei , Strimmer Korbinian
Published: July 2002

Summary: Phylogenetic Analysis Library (PAL) is a collection of Java classes for use in molecular evolution and phylogenetics. PAL provides a modular environment for the rapid construction of both special-purpose and general analysis programs. PAL version 1.1 consists of 145 public classes or interfaces in 13 packages, including classes for models of character evolution, maximum-likelihood estimation, and the coalescent, with a total of more than 27000 lines of code. The PAL project is set up as a collaborative project to facilitate contributions from other researchers.

Availability: The program is free and is available at http://www.pal-project.org. It requires Java 1.1 or later. PAL is licensed under the GNU General Public License.

Contact: a.drummond@auckland.ac.nz; korbinian.strimmer@zoo.ox.ac.uk

Supplementary information: An online description of the Application Programming Interface (API) of all public classes in PAL is available at http://www.pal-project.org/api/.

* To whom correspondence should be addressed.
Evaluation of protein multiple alignments by SAM-T99 using the
BAliBASE multiple alignment test set
Authors: Karplus Kevin , Hu Birong
Published: July 2002

Motivation: SAM-T99 is an iterative hidden Markov model-based method for finding proteins similar to a single target sequence and aligning them. One of its main uses is to produce multiple alignments of homologs of the target sequence. Previous tests of SAM-T99 and its predecessors have concentrated on the quality of the searches performed, not on the quality of the multiple alignment. In this paper we report on tests of multiple alignment quality, comparing SAM-T99 to the standard multiple aligner, CLUSTALW.

Results: The paper evaluates the multiple-alignment aspect of the SAM-T99 protocol, using the BAliBASE benchmark alignment database. On these benchmarks, SAM-T99 is comparable in accuracy with ClustalW.

Availability: The SAM-T99 protocol can be run on the web at http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-query.html and the alignment tune-up option described here can be run at http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-tuneup.html. The protocol is also part of the standard SAM suite of tools. http://www.cse.ucsc.edu/research/compbio/sam/
The Bioinformatics Template Library—generic components
for biocomputing
Authors: Pitt W. R. , Williams M. A. , Steven M. , Sweeney B. , Bleasby A. J. , Moss D. S.
Published: July 2002

Motivation: The efficiency of bioinformatics programmers can be greatly increased through the provision of ready-made software components that can be rapidly combined, with additional bespoke components where necessary, to create finished programs. The new standard for C++ includes an efficient and easy to use library of generic algorithms and data-structures, designed to facilitate low-level component programming. The extension of this library to include functionality that is specifically useful in compute-intensive tasks in bioinformatics and molecular modelling could provide an effective standard for the design of reusable software components within the biocomputing community.

Results: A novel application of generic programming techniques in the form of a library of C++ components called the Bioinformatics Template Library (BTL) is presented. This library will facilitate the rapid development of efficient programs by providing efficient code for many algorithms and data-structures that are commonly used in biocomputing, in a generic form that allows them to be flexibly combined with application specific object-oriented class libraries.

Availability: The BTL is available free of charge from our web site http://www.cryst.bbk.ac.uk/~classlib/ and the EMBL file server http://www.embl-ebi.ac.uk/FTP/index.html

Contact: d.moss@mail.cryst.bbk.ac.uk; m.williams@biochemistry.ucl.ac.uk

* To whom correspondence should be addressed.

3 Present address: Celltech Chiroscience, Granta Park, Great Abingdon, Cambridge CB1 6GS, UK.

4 Present address: Department of Biochemistry & Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
Preclinical safety evaluation of moxifloxacin, a novel fluoroquinolone
Authors: von Keutz Eckhard , Schlüter Gerhard
Published: July 2002

The toxicity of moxifloxacin (BAY 12-8039), a novel fluoroquinolone with a broad spectrum of antibacterial activity, was evaluated in a comprehensive programme of toxicological studies that included single and multiple dose toxicity studies in rats, mice, dogs and monkeys, reproductive system toxicity studies in rats and monkeys and in-vitro and in-vivo mutagenicity assays. Although moxifloxacin is not intended for long-term clinical use, an accelerated bioassay in target organs to assess carcinogenesis was performed in rats. In addition to the routine toxicological programme required for the development of a drug intended for short-term administration, a major part of the preclinical programme for moxifloxacin comprised studies designed specifically to address the safety issues known to be features of fluoroquinolones, i.e. adverse effects on the central nervous and cardiovascular systems, phototoxicity, arthrotoxicity and oculotoxicity. The results of the toxicological investigations confirmed that the safety profile of moxifloxacin is comparable to those of other fluoroquinolones.
Population biology of human onchocerciasis
Authors: Basáñez María-Gloria , Boussinesq Michel
Published: July 2002

Human onchocerciasis (river blindness) is the filarial infection caused byOnchocerca volvulusand transmitted among people through the bites of theSimuliumvector. Some 86 million people around the world are at risk of acquiring the nematode, with 18 million people infected and 600 000 visually impaired, half of them partially or totally blind. 99% of cases occur in tropical Africa; scattered foci exist in Latin America. Until recently control programmes, in operation since 1975, have consisted of antivectorial measures. With the introduction of ivermectin in 1988, safe and effective chemotherapy is now available. With the original Onchocerciasis Control Programme of West Africa coming to an end, both the new African Programme for Onchocerciasis Control and the Onchocerciasis Elimination Programme for the Americas, rely heavily on ivermectin self–sustained mass delivery. In consequence, the need for understanding the processes regulating parasite abundance in human and simuliid populations is of utmost importance. We present a simple mathematical framework built around recent analyses of exposure– and density–dependent processes operating, respectively, within the human and vector hosts. An expression for the basic reproductive ratio,R0, is derived and related to the minimum vector density required for parasite persistence in localities of West Africa in general and northern Cameroon in particular. Model outputs suggest that constraints acting against parasite establishment in both humans and vectors are necessary to reproduce field observations, but those in humans may not fully protect against reinfection. Analyses of host age–profiles of infection prevalence, intensity, and aggregation for increasing levels of endemicity and intensity of transmission in the Vina valley of northern Cameroon are in agreement with these results and discussed in light of novel work on onchocerciasis immunology.
Emerging infectious pathogens of wildlife
Authors: Dobson A. , Foufopoulos J.
Published: July 2002

The first part of this paper surveys emerging pathogens of wildlife recorded on the ProMED Web site for a 2–year period between 1998 and 2000. The majority of pathogens recorded as causing disease outbreaks in wildlife were viral in origin. Anthropogenic activities caused the outbreaks in a significant majority of cases. The second part of the paper develops some matrix models for quantifying the basic reproductive number,R0, for a variety of potential types of emergent pathogen that cause outbreaks in wildlife. These analyses emphasize the sensitivity ofR0to heterogeneities created by either the spatial structure of the host population, or the ability of the pathogens to utilize multiple host species. At each stage we illustrate how the approach provides insight into the initial dynamics of emergent pathogens such as canine parvovirus, Lyme disease, and West Nile virus in the United States.
A homeobox gene, PRESSED FLOWER, regulates lateral axis-dependent development of Arabidopsis flowers
Authors: Matsumoto Noritaka , Okada Kiyotaka
Published: July 2002

It is postulated that the symmetric organization of plant lateral organs is based on two crossed axes, the abaxial–adaxial and the lateral axes. The PRESSED FLOWER (PRS) gene, the expression and function of which are dependent on the lateral axis, is reported in this study. In the prs mutant, growth of the lateral sepals is repressed, and although the size and shape of the abaxial and adaxial sepals are normal, the cell files at the lateral margins are missing. Double-mutant analyses showed that the PRSgene functions independently of the determinations of both floral organ identity and floral meristem size. The PRS gene, encoding a putative transcriptional factor with a homeodomain, was shown to be required for cell proliferation. PRS gene expression is spatially and temporally unique and is expressed in a restricted number of L1 cells at the lateral regions of flower primordia, floral organ primordia, and young leaf primordia. Our study strongly suggests that the PRS gene is involved in the molecular mechanism of lateral axis-dependent development of lateral organs in Arabidopsis.
Multi‐slice helical CT: Scan and reconstruction
Authors: Hu Hui
Published: July 2002

The multi‐slice CT scanner refers to a special CT system equipped with a multiple‐row detector array to simultaneously collect data at different slice locations. The multi‐slice CT scanner has the capability of rapidly scanning large longitudinal (z) volume with high z‐axis resolution. It also presents new challenges and new characteristics. In this paper, we study the scan and reconstruction principles of the multi‐slice helical CT in general and the 4‐slice helical CT in particular. The multi‐slice helical computed tomography consists of the following three key components: the preferred helical pitches for efficient z sampling in data collection and better artifact control; the new helical interpolation algorithms to correct for fast simultaneous patient translation; and the z‐filtering reconstruction for providing multiple tradeoffs of the slice thickness, image noise and artifacts to suit for different application requirements. The concept of the preferred helical pitch is discussed with a newly proposed z sampling analysis. New helical reconstruction algorithms and z‐filtering reconstruction are developed for multi‐slice CT in general. Furthermore, the theoretical models of slice profile and image noise are established for multi‐slice helical CT. For 4‐slice helical CT in particular, preferred helical pitches are discussed. Special reconstruction algorithms are developed. Slice profiles, image noises, and artifacts of 4‐slice helical CT are studied and compared with single slice helical CT. The results show that the slice profile, image artifacts, and noise exhibit performance peaks or valleys at certain helical pitches in the multi‐slice CT, whereas in the single‐slice CT the image noise remains unchanged and the slice profile and image artifacts steadily deteriorate with helical pitch. The study indicates that the 4‐slice helical CT can provide equivalent image quality at 2 to 3 times the volume coverage speed of the single slice helical CT.
The finite element model for the propagation of light in scattering media: A direct method for domains with nonscattering regions
Authors: Arridge Simon R. , Dehghani Hamid , Schweiger Martin , Okada Eiji
Published: July 2002

We present a method for handling nonscattering regions within diffusing domains. The method develops from an iterative radiosity‐diffusion approach using Green's functions that was computationally slow. Here we present an improved implementation using a finite element method (FEM) that is direct. The fundamental idea is to introduce extra equations into the standard diffusion FEM to represent nondiffusive light propagation across a nonscattering region. By appropriate mesh node ordering the computational time is not much greater than for diffusion alone. We compare results from this method with those from a discrete ordinate transport code, and with Monte Carlo calculations. The agreement is very good, and, in addition, our scheme allows us to easily model time‐dependent and frequency domain problems.
An experiment to study a “nondiffracting” light beam
Authors: McQueen C. A. , Arlt J. , Dholakia K.
Published: July 2002

We present a simple experiment by which a student can generate and study a zeroth-order Bessel beam. Such beams are often termed nondiffracting (propagation invariant) as they have a central maximum that can propagate for extended distances without experiencing appreciable spreading.