bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of known bacterial protein vaccine antigens reveals biased physical properties and amino acid composition
Authors: Mayers Carl , Duffield Melanie , Rowe Sonya , Miller Julie , Lingard Bryan , Hayward Sarah , Titball Richard W. 
Published: October 2003

AbstractMany vaccines have been developed from live attenuated forms of bacterial pathogens or from killed bacterial cells. However, an increased awareness of the potential for transient side‐effects following vaccination has prompted an increased emphasis on the use of sub‐unit vaccines, rather than those based on whole bacterial cells. The identification of vaccine sub‐units is often a lengthy process and bioinformatics approaches have recently been used to identify candidate protein vaccine antigens. Such methods ultimately offer the promise of a more rapid advance towards pre‐clinical studies with vaccines. We have compared the properties of known bacterial vaccine antigens against randomly selected proteins and identified differences in the make‐up of these two groups. A computer algorithm that exploits these differences allows the identification of potential vaccine antigen candidates from pathogenic bacteria on the basis of their amino acid composition, a property inherently associated with sub‐cellular location. Copyright © 2003 John Wiley & Sons, Ltd.
Quantitative proteomics of lymphocytes
Authors: Lefkovits Ivan 
Published: October 2003

AbstractLymphocytes are the best‐studied higher eukaryote cells. In this report, quantitative relationships of the protein components in resting cell, blast cell and plasma cell types are evaluated. The comparison of these cell types leads to the conclusion that resting cells synthesize about one‐twentieth of the protein species as compared to blast cells. Blast cells seem to be metabolically the most robust lymphocyte type. Plasma cells are geared towards synthesis of one main product (antibody in B plasma cells), while most of the synthesis of other protein species (including those for housekeeping and repair) decreases as the messages decay. Although the data presented in this communication allow a meaningful comparison of three cell populations, they are far from providing a full picture. Both silver staining and radiofluorography depict only proteins of high or intermediate abundance. Silver staining misses most proteins present at <10 000 copies/cell, while radiofluorography misses all those proteins with slow turnover (and those with no methionine residue in their sequence). The detection of 1100 spots in the blast cell‐related radiofluorograph includes visualization of some 97–99% of protein mass, but some 3900 polypeptide species in the remaining 1–3% of protein mass will pass undetected. This protein mass (0.7–2 pg) reflects some 2500–7500 copies of each of those 3900 polypeptide species that are present in the cell below the detection limit. The work emphasizes that full understanding of cellular function can be achieved only if quantitative aspects of cell inventory are considered. Copyright © 2003 John Wiley & Sons, Ltd.
Proposal for a standard representation of two‐dimensional gel electrophoresis data
Authors: Jones Andrew , Wastling Jonathan , Hunt Ela 
Published: October 2003

AbstractThe global analysis of proteins is now feasible due to improvements in techniques such as two‐dimensional gel electrophoresis (2‐DE), mass spectrometry, yeast two‐hybrid systems and the development of bioinformatics applications. The experiments form the basis of proteomics, and present significant challenges in data analysis, storage and querying. We argue that a standard format for proteome data is required to enable the storage, exchange and subsequent re‐analysis of large datasets. We describe the criteria that must be met for the development of a standard for proteomics. We have developed a model to represent data from 2‐DE experiments, including difference gel electrophoresis along with image analysis and statistical analysis across multiple gels. This part of proteomics analysis is not represented in current proposals for proteomics standards. We are working with the Proteomics Standards Initiative to develop a model encompassing biological sample origin, experimental protocols, a number of separation techniques and mass spectrometry. The standard format will facilitate the development of central repositories of data, enabling results to be verified or re‐analysed, and the correlation of results produced by different research groups using a variety of laboratory techniques. Copyright © 2003 John Wiley & Sons, Ltd.
The journey to smORFland
Authors: Davids Wagied , Fuxelius Hans‐Henrik , Andersson Siv G. E. 
Published: October 2003

AbstractThe genome sequences completed so far contain more than 20 000 genes with unknown function and no similarity to genes in other genomes. The origin and evolution of the orphan genes is an enigma. Here, we discuss the suggestion that some orphan genes may represent pseudogenes or short fragments of genes that were functional in the genome of a common ancestor. These may be the remains of unsuccessful duplication or horizontal gene transfer events, in which the acquired sequences have entered the fragmentation process and thereby lost their similarity to genes in other species. This scenario is supported by a recent case study of orphan genes in several closely related species of Rickettsia, where full‐length ancestral genes were reconstructed from sets of short, overlapping orphan genes. One of these was found to display similarity to genes encoding proteins with ankyrin‐repeat domains. Copyright © 2003 John Wiley & Sons, Ltd.
Padlock and proximity probes for in situ and array‐based analyses: tools for the post‐genomic era
Authors: Landegren Ulf , Dahl Fredrik , Nilsson Mats , Fredriksson Simon , Banér Johan , Gullberg Mats , Jarvius Jonas , Gustafsdottir Sigrun , Söderberg Ola , Ericsson Olle , Stenberg Johan , Schallmeiner Edith 
Published: October 2003

AbstractHighly specific high‐throughput assays will be required to take full advantage of the accumulating information about the macromolecular composition of cells and tissues, in order to characterize biological systems in health and disease. We discuss the general problem of detection specificity and present the approach our group has taken, involving the reformatting of analogue biological information to digital reporter segments of genetic information via a series of DNA ligation assays. The assays enable extensive, coordinated analyses of the numbers and locations of genes, transcripts and protein. Copyright © 2003 John Wiley & Sons, Ltd.
Fishing with (Proto)Net—a principled approach to protein target selection
Authors: Linial Michal 
Published: October 2003

AbstractStructural genomics strives to represent the entire protein space. The first step towards achieving this goal is by rationally selecting proteins whose structures have not been determined, but that represent an as yet unknown structural superfamily or fold. Once such a structure is solved, it can be used as a template for modelling homologous proteins. This will aid in unveiling the structural diversity of the protein space. Currently, no reliable method for accurate 3D structural prediction is available when a sequence or a structure homologue is not available. Here we present a systematic methodology for selecting target proteins whose structure is likely to adopt a new, as yet unknown superfamily or fold. Our method takes advantage of a global classification of the sequence space as presented by ProtoNet‐3D, which is a hierarchical agglomerative clustering of the proteins of interest (the proteins in Swiss‐Prot) along with all solved structures (taken from the PDB). By navigating in the scaffold of ProtoNet‐3D, we yield a prioritized list of proteins that are not yet structurally solved, along with the probability of each of the proteins belonging to a new superfamily or fold. The sorted list has been self‐validated against real structural data that was not available when the predictions were made. The practical application of using our computational–statistical method to determine novel superfamilies for structural genomics projects is also discussed. Copyright © 2003 John Wiley & Sons, Ltd.
Meeting Report: ESF Programme on Functional Genomics 1st European Conference: Functional Genomics and Disease 2003
Authors: Wixon Jo , Marsh Joan 
Published: October 2003

AbstractIn this report from the 1st European Conference of the European Science Foundation Programme on Functional Genomics, we provide coverage of the high‐profile plenary talks and a cross‐section of the many presentations in the disease analysis symposia and functional genomics technologies workshops. Copyright © 2003 John Wiley & Sons, Ltd.
Theoretical and numerical analyses of convective instability in porous media with temperature‐dependent viscosity
Authors: Lin Ge , Zhao Chongbin , Hobbs B. E. , Ord A. , Mühlhaus H. B. 
Published: October 2003

AbstractExact analytical solutions of the critical Rayleigh numbers have been obtained for a hydrothermal system consisting of a horizontal porous layer with temperature‐dependent viscosity. The boundary conditions considered are constant temperature and zero vertical Darcy velocity at both the top and bottom of the layer. Not only can the derived analytical solutions be readily used to examine the effect of the temperature‐dependent viscosity on the temperature‐gradient driven convective flow, but also they can be used to validate the numerical methods such as the finite‐element method and finite‐difference method for dealing with the same kind of problem. The related analytical and numerical results demonstrated that the temperature‐dependent viscosity destabilizes the temperature‐gradient driven convective flow and therefore, may affect the ore body formation and mineralization in the upper crust of the Earth. Copyright © 2003 John Wiley & Sons, Ltd.
An efficient and accurate algorithm for generating spatially‐correlated random fields
Authors: Fang Jiannong , Tacher Laurent 
Published: October 2003

AbstractThis paper presents a new computer algorithm for generating spatially‐correlated random fields. Such fields are often encountered in hydrology and hydrogeology and in the earth sciences and used as inputs for Monte Carlo simulations. The algorithm is designed by using a multilevel grid strategy and combining the matrix decomposition (MD) method and the screening sequential simulation (SSS) method. The idea originates from the facts: (i) the MD method accounts for all possible nodal correlation values and hence the accuracy of the method is high, but it can be extremely computationally intensive for fine meshes with large number of nodes, and (ii) the SSS method is more efficient because a small search neighbourhood for conditioning can be used due to the screening effect of measurements, however, for large separation distances, correlation values from the SSS method is significantly inferior to the values obtained by the MD method. Numerical examples are presented to demonstrate the new method. It is shown that the presented method is much more efficient than the MD method and more accurate than the SSS method. The new algorithm is also versatile: it can directly simulate fields of irregular geometry without additional efforts. Copyright © 2003 John Wiley & Sons, Ltd.
Mixed variational methods for finite element analysis of geometrically non‐linear, inelastic Bernoulli–Euler beams
Authors: Hjelmstad K. D. , Taciroglu E. 
Published: October 2003

AbstractBernoulli–Euler beam theory has long been the standard for the analysis of reticulated structures. The need to accurately compute the non‐linear (material and geometric) response of structures has renewed interest in the application of mixed variational approaches to this venerable beam theory. Recent contributions in the literature on mixed methods and the so‐called (but quite related) non‐linear flexibility methods have left open the question of what is the best approach to the analysis of beams. In this paper we present a consistent computational approach to one‐, two‐, and three‐field variational formulations of non‐linear Bernoulli–Euler beam theory, including the effects of non‐linear geometry and inelasticity. We examine the question of superiority of methods through a set of benchmark problems with features typical of those encountered in the structural analysis of frames. We conclude that there is no clear winner among the various approaches, even though each has predictable computational strengths. Copyright © 2003 John Wiley & Sons, Ltd.
Optimizing operating system performance for CC‐NUMA architectures
Authors: Chang Moon Seok 
Published: October 2003

AbstractThe CC‐NUMA (cache‐coherent non‐uniform memory access) architecture is an attractive solution to scalable servers. The performance of a CC‐NUMA system heavily depends on the number of accesses to remote memory through an interconnection network. To reduce the number of remote accesses, an operating system needs to exploit the potential locality of the architecture. This paper describes the design and implementation of a UNIX‐based operating system supporting the CC‐NUMA architecture. The operating system implements various enhancements by revising kernel algorithms and data structures. This paper also analyzes the performance of the enhanced operating system by running commercial benchmarks on a real CC‐NUMA system. The performance analysis shows that the operating system can achieve improved performance and scalability for CC‐NUMA by implementing kernel data striping, localization and load balancing. Copyright © 2003 John Wiley & Sons, Ltd.
Genetic and genomic tools for zebrafish research: The NIH zebrafish initiative
Authors: Rasooly Rebekah S. , Henken Deborah , Freeman Nancy , Tompkins Laurie , Badman David , Briggs Josephine , Hewitt A. Tyl 
Published: October 2003

AbstractThe National Institutes of Health (NIH) has been a leading advocate of the zebrafish as a model organism for the study of vertebrate development, physiology, and disease. Genomic tools, developed with the support of NIH funding, have made zebrafish even more attractive as a genetic system and have stimulated research using this model. The NIH continues to provide support for new and existing community resources, such as the Zebrafish International Resource Center and the Zebrafish Information Network, research tool development and mutant screens, and a wide array of investigator‐initiated studies that are using zebrafish to elucidate many aspects of vertebrate biology. Developmental Dynamics, 2003. Published 2003 Wiley‐Liss, Inc.
Expression of zebrafish Lc3 synthase gene in embryonic lens requires hedgehog signaling
Authors: Cao Ying , Zhao Jue , Wang Ying , Meng Anming 
Published: October 2003

AbstractGlycosyltransferases are involved in synthesis of various glycolipids and glycoproteins that play important roles in many biological processes. We have identified a zebrafish gene encoding a member of β1,3‐N‐acetylglucosaminyltransferase family, the Lc3 synthase/bGn‐T5. Whole‐mount in situ hybridization reveals that the Lc3 synthase gene is expressed in two distinct phases during the zebrafish embryogenesis. The early phase extends from late blastulation to the completion of epiboly, during which the expression occurs in the superficial layer of the embryos. The second phase of expression starts during mid‐segmentation and persists until day 3, during which the expression occurs prominently in the developing lens. The expression of the Lc3 synthase gene in the lens is inhibited in you‐too (yot) mutant embryos that are defective in Hedgehog signaling. The expression in the lens also decreases in cyclops (cyc) and one‐eyed‐pinhead (oep) mutant embryos and lefty1‐injected embryos, which are deficient in Nodal signaling and lack Hedgehog activity in the ventral brain. These results suggest that Hedgehog signaling is required for the Lc3 synthase expression in embryonic lens. Developmental Dynamics, 2003. © 2003 Wiley‐Liss, Inc.
Expression and phylogenetic analyses of three zebrafish FoxI class genes
Authors: Solomon Keely S. , Logsdon John M. , Fritz Andreas 
Published: October 2003

AbstractWe have identified three novel members of the zebrafish forkhead class I gene family, which we have named foxi2, foxi3a, and foxi3b. We have reported previously the identification of zebrafish foxi1, which is required for otic placode and jaw development. Expression analysis shows that foxi2 is expressed within the chordamesoderm during early somitogenesis and the retina and pharyngeal arches during later stages. The foxi3a and foxi3b genes likely represent a recently duplicated pair, and they are similarly expressed in epidermal mucous cells throughout embryogenesis and early larval stages. None of these newly identified FoxI genes are expressed in otic precursor cells and, therefore, are unlikely to share functional overlap with foxi1 in the development of the inner ear. In addition to these zebrafish FoxI paralogs, we have identified 16 new FoxI sequences in species ranging from Ciona intestinalis to Homo sapiens. We present an extensive phylogenetic analysis of the FoxI class that includes these new sequences together with those previously reported. This analysis supports the existence of three subfamilies within the FoxI class, each containing at least one zebrafish member. Developmental Dynamics, 2003. © 2003 Wiley‐Liss, Inc.
Insertional mutagenesis in zebrafish
Authors: Amsterdam Adam 
Published: October 2003

AbstractInsertional mutagenesis is a method for identifying genes essential for a given biological process by using the integration of DNA as the mutagen, thereby facilitating the cloning of the mutated gene. The use of retrovirus‐mediated insertional mutagenesis in zebrafish has led to the mutation and rapid identification of hundreds of genes required for embryonic development and cell viability and growth, revealing the diversity of gene products required for the development of this vertebrate. Here, I will review the methodology of this approach and the results to date, as well as other potential ways to use insertional mutagenesis for genetic screens. Developmental Dynamics, 2003. © 2003 Wiley‐Liss, Inc.
Integrity of the midbrain region is required to maintain the diencephalic–mesencephalic boundary in zebrafishno isthmus/pax2.1mutants
Authors: Scholpp Steffen , Brand Michael 
Published: October 2003

AbstractInitial anterior–posterior patterning of the neural tube into forebrain, midbrain, and hindbrain primordia occurs already during gastrulation, in response to signals patterning the gastrula embryo. After the initial establishment, further development within each brain part is thought to proceed largely independently of the others. However, mechanisms should exist that ensure proper delineation of brain subdivisions also at later stages; such mechanisms are, however, poorly understood. In zebrafishno isthmusmutant embryos, inactivation of thepax2.1gene leads to a failure of the midbrain and isthmus primordium to develop normally from the gastrula stage onward (Lun and Brand [1998] Development 125:3049–3062). Here, we report that, after the initially correct establishment during gastrulation stages, the neighbouring forebrain primordium and, partially, the hindbrain primordium expand into the misspecified midbrain territory inno isthmusmutant embryos. The expansion is particularly evident for the posterior part of the diencephalon and less so for the first rhombomeric segment, the territories immediately abutting the midbrain/isthmus primordium. The nucleus of the posterior commissure is expanded in size, and marker genes of the forebrain and rhombomere 1 expand progressively into the misspecified midbrain primordium, eventually resulting in respecification of the midbrain primordium. We therefore suggest that the genetic program controlled by Pax2.1 is not only involved in initiating but also in maintaining the identity of midbrain and isthmus cells to prevent them from assuming a forebrain or hindbrain fate. Developmental Dynamics, 2003. © 2003 Wiley‐Liss, Inc.
Postembryonic development of the cranial lateral line canals and neuromasts in zebrafish
Authors: Webb Jacqueline F. , Shirey Jonathan E. 
Published: October 2003

AbstractThe development of the cranial lateral line canals and neuromast organs are described in postembryonic zebrafish (0–80 days postfertilization). Cranial canal development commences several weeks after hatch, is initiated in the vicinity of individual neuromasts, and occurs in four discrete stages that are described histologically. Neuromasts remain in open canal grooves for several weeks during which they dramatically change shape and increase in size by adding hair cells at a rate one‐tenth that in the zebrafish inner ear. Scanning electron microscopy demonstrates that neuromasts elongate perpendicular to the canal axis and the axis of hair cell polarization and that they lack a prominent nonsensory cell population surrounding the hair cells—features that make zebrafish neuromasts unusual among fishes. These results demand a reassessment of neuromast and lateral line canal diversity among fishes and highlight the utility of the lateral line system of postembryonic zebrafish for experimental and genetic studies of the development and growth of hair cell epithelia. Developmental Dynamics, 2003. © 2003 Wiley‐Liss, Inc.
Two divergent slit1 genes in zebrafish
Authors: Hutson Lara D. , Jurynec Michael J. , Yeo Sang‐Yeob , Okamoto Hitoshi , Chien Chi‐Bin 
Published: October 2003

AbstractMembers of the Slit family regulate axon guidance and cell migration. To date, three vertebrate slit1 genes have been identified in mammals and orthologs of two, slit2 and slit3, have been identified in zebrafish. Here, we describe the cloning of full‐length cDNAs for two zebrafish slit orthologs, slit1a and slit1b. Both predicted proteins contain the conserved motifs that characterize other vertebrate Slits. slit1a and slit1b are both expressed in the midline, hypochord, telencephalon, and hindbrain. Apart from these shared expression domains, however, their expression patterns largely differ. Whereas slit1a is expressed broadly in the central nervous system (CNS) and in the somites, pectoral fin buds, tail bud, and caudal fin folds, slit1b is expressed in the olfactory system throughout embryonic and larval development, and in the retina during larval stages. Their expression patterns, particularly that of slit1a, suggest that Slit proteins may have roles in tissue morphogenesis in addition to their established roles in axon guidance and cell migration. Developmental Dynamics, 2003. © 2003 Wiley‐Liss, Inc.
Developmental morphology of the axial skeleton of the zebrafish,Danio rerio(Ostariophysi: Cyprinidae)
Authors: Bird Nathan C. , Mabee Paula M. 
Published: October 2003

AbstractBefore our rapidly increasing knowledge of gene interactions can be connected with the morphologic defects in mutant zebrafish, the normal course of skeletal development must be understood. Here, we describe the developmental morphology of the axial skeleton of zebrafish and review it in relation to the morphology of related species. The relative sequence of ossification in the skeleton is described. Two separate centers of development were found in the axial skeleton (Weberian apparatus and caudal fin) in contrast to tetrapods, which have a single anterior center. Slight variation was found in the overall relative timing of development. The extensive ichthyological literature on teleost anatomy and recent genetic data form the basis for our review and interpretation of homologies of various elements of the axial skeleton. Because homology forms the basis for all evolutionary comparisons, these data are critical for integration in evo–devo studies. Developmental Dynamics, 2003. © 2003 Wiley‐Liss, Inc.