bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequencing templates – shotgun clone isolation versus amplification approaches
Authors: Deadman Rebecca , Fuller Carl W. 
Published: April 2005

AbstractPreparation of good‐quality DNA is essential for obtaining high‐quality DNA sequence data. Alkaline lysis remains the most popular method for isolating small and large DNA constructs, but new techniques including solid‐phase immobilization and rolling circle amplification offer alternatives to the traditional approaches. Quality, quantity, and consistency of isolated DNA vary from method to method, and the choice of DNA isolation method should be carefully considered, particularly when a variety of vectors or host strains will be used.
The technology tour de force of theHumanGenomeProject
Authors: Mardis Elaine R. 
Published: April 2005

AbstractThe monumental task that entailed the sequencing of the human genome required rapid improvements to the technology that underlies large‐scale DNA sequencing. As such, the efforts of many groups of biochemists, molecular biologists, engineers, and bioinformaticians, working both in academia and industry, were required. This article provides a brief overview of some of the key developments in technology that helped to fuel the increased scale of this critical scientific endeavor.
Overlapping genes in the human genome
Authors: Makalowska Izabela 
Published: April 2005

Abstract
Overlapping genes in mammalian genomes are unexpected phenomena. Over 700 pairs of protein‐coding overlapping genes have been reported so far. Overlapping genes can be divided into those that share the same locus but the overlaps are only between exonic region in one gene and intronic area in another and genes that share not only locus but also exonic sequences. Depending on which parts of two genes share the genomic region, we can also categorize these overlaps as head to head when they overlap in the 5′ regions, and tail to tail when overlap involves the 3′ ends. Special types are embedded genes, a case where one gene lies completely in the area of another one. The biologic functions of natural antisense transcripts, their involvement in physiological processes and gene regulation in living organisms are not fully understood. Similarly, evolution of such genes is not known, existing hypotheses can explain only selected cases of mammalian gene overlaps.
Human
micro
RNAs
Authors: Griffiths‐Jones Sam 
Published: April 2005

Abstract
MicroRNAs (miRNAs) are a diverse class of 20–22 nucleotide small RNAs that regulate translation of a wide range of genes by complementary binding to untranslated regions of mRNA targets. Over 1300 miRNA sequences have been identified from animals and plants, with over 200 genes in the human genome. miRNAs appear to be expressed from a variety of genomic contexts including from autonomous promoters, as polycistronic transcripts, and processed from introns of protein‐coding genes.
Reverse vaccinology: a critical analysis
Authors: Grandi Guido 
Published: April 2005

AbstractReverse vaccinology is a relatively new approach aimed at facilitating and accelerating the discovery of vaccine candidates. It basically consists of the exploitation of genome sequences to predict, among all available genes, those ones encoding proteins likely to represent the targets of protective immune responses (surface‐associated proteins, virulence factors, toxins, etc.). Once predictions are made, selected proteins are recombinantly expressed, purified, and finally tested in correlate‐of‐protection assays to ultimately identify the protective antigens. Since its first published successful application (Pizzaet al.,), reverse vaccinology has been applied to several bacterial pathogens with promising results. The scope of this review is to describe a few examples of this technology, highlighting the main achievements. In addition, the review also examines the critical aspects of the technology and attempts to draw a series of guidelines for future improvements.
Genome‐wide analysis of groupAStreptococcus
Authors: Green Nicole M. , Musser James M. 
Published: April 2005

AbstractThe human pathogenic bacterium group AStreptococcus(GAS) is a major cause of morbidity and mortality worldwide. The genomes of seven GAS strains commonly causing pharyngitis and invasive disease have been sequenced recently. These genome sequences have yielded extensive new information important for GAS pathogenesis research, and have provided new insight into the extent of strain variation within and between serotypes. Importantly, these studies have revealed that bacteriophages are the primary source of variation in gene content between strains. Genome‐wide studies also have provided important new data bearing on the molecular mechanisms underlying changes in GAS epidemic behavior. Expression microarray analyses have identified genes and gene networks used by GAS to respond and survive in various environments, including exposure to human polymorphonuclear leukocytes and whole blood. Taken together, genome‐wide study of GAS is an area of intensive research that has greatly enhanced our understanding of this pathogen.
Technologies for systematic analysis of eukaryotic transcriptomes
Authors: Strausberg Robert L. 
Published: April 2005

AbstractComprehensive high‐throughput analysis of the eukaryotic transcriptome provides unprecedented opportunity to understand gene structure and gene expression, and to use that knowledge to gain perspective of biological function. During the past decade, several new technologies based on DNA sequencing and hybridization approaches have been developed and applied to transcriptome analysis. In this overview, applications of these current technologies are discussed, as is the need for continued technology development.
Tandem mass spectrometry database searching
Authors: Eng Jimmy K. , Martin Daniel B. , Aebersold Ruedi 
Published: April 2005

AbstractAssociated with the emergence of mass spectrometry–based proteomics analysis, a host of novel algorithms for tandem mass spectrometry database searching have been published. These tools apply a breadth of computational and statistical approaches to solving the problem of identifying peptides based on interpreting tandem mass spectra with the constraint of sequences present in publicly available protein, transcript, and genomic sequence database repositories. With increasing data volumes due to continuous advances in instrumentation, the need for tools that perform automated peptide identifications and validation of those identifications will be magnified. An overview of database search and postsearch validation tools is summarized.
Time‐of‐flight mass spectrometry
Authors: Cotter Robert J. 
Published: April 2005

AbstractTime‐of‐flight (TOF) mass spectrometers have become the instruments of choice where high molecular masses must be measured. Pulsed extraction, orthogonal extraction, and reflectron designs have greatly improved mass resolution. In addition, hybrid and tandem instruments, such as quadrupole/TOF, ion trap/TOF, and TOF/TOF mass spectrometers now provide the opportunity for obtaining tandem mass spectra. Time‐of‐flight instruments are used in proteomics for determining the molecular weights of intact proteins, for accurate mass measurements of tryptic peptides (mass fingerprinting), for amino acid sequencing (sequence tags) and for determining the locations and structures of posttranslational modifications.
Tutorial on tandem mass spectrometry database searching
Authors: Eng Jimmy K. 
Published: April 2005

AbstractIdentifying peptides, and ultimately proteins, by searching sequence databases with tandem mass spectra of peptides is one of the most widely used proteomics techniques. The steps by which a user actually performs a search are fairly straightforward and are described in this article. Although this article goes through the identification process of searching a single tandem mass spectrum to identify a single peptide, most users will not usually selective search only one spectrum but would query the full set of tandem mass spectra acquired in an entire LC‐MS/MS run. The underlying steps and analysis considerations outlined here are relevant in either scenario.
Improvement of sequence coverage in peptide mass fingerprinting
Authors: Hjernø Karin , Roepstorff Peter 
Published: April 2005

Abstract

In order to fully characterize and understand the biological significance of a protein (in a proteomics study), it needs to be characterized with respect to the presence of splice variants, isoforms, and posttranslational processing/modification. This requires full coverage of the protein sequence including that of minor variants of the protein. However, protein identification is often based on sequence coverages as low as 10–20%, and search for the remaining peptides is frequently like the search for
the needle in the haystack
. Here we present some approaches, which may be helpful for increasing the sequence coverage in proteomics studies.
Handling membrane proteins
Authors: Goode Robert J. A. , Simpson Richard J. 
Published: April 2005

Abstract
Membrane proteins fulfill several vital roles, including cell adhesion, solute transport, and receptor functions. Despite these important biological functions, very little is known about the structure and expression of these proteins at the protein level due to their low abundance, inherent hydrophobicity, and variable posttranslational modifications. In order to overcome these obstacles, classical proteomic techniques have been adapted and several techniques have been developed, allowing characterization of elusive membrane proteins.
ICAT
and other labeling strategies for semiquantitative
LC
‐based expression profiling
Authors: Byrne Connie , Cagney Gerard 
Published: April 2005

Abstract
Comprehensive proteome analysis requires efficient, robust, and practical methods for the identification and quantification of all proteins in complex biological samples. Mass spectrometry is a well‐established protein identification tool and semiquantitative proteomics has traditionally been performed using two‐dimensional gel electrophoresis (2‐DE) coupled with mass spectrometry. However, other separation strategies based on liquid chromatography now complement 2‐DE as a central method for analysis of proteins in complex biological systems. In this review, we discuss the most promising methodological developments in this area with particular attention to their merits and limitations.
Image analysis
Authors: Dowsey Andrew W. , Dunn Michael J. , Yang Guang‐Zhong 
Published: April 2005

Abstract

Owing to the volume of data and its experimental geometric and expression uncertainties, quantitative analysis of 2D gel electrophoresis data with image processing and modeling is an actively pursued research topic. The results of this analysis include accurate protein quantification, p
I
and
M
r
estimation, and the extraction of differential expression between control and sample gels. Systematic errors such as current leakage and background inhomogeneities need to be corrected for, followed by the segmentation, modeling, and quantification of each protein spot. To establish spot correspondences between multiple gels, a number of image registration and spot matching techniques for correcting geometric distortion have been proposed. They have facilitated the detection and quantification of differential expression through the statistical analysis of outliers and bias field. For large‐scale analysis, classification and clustering techniques can be employed to uncover intrinsic trends and relationships in the protein spot patterns. This section provides a short review of the computational techniques used in the analysis of 2‐DE gels and examines the pitfalls of existing methods. Some of the key areas that need to be developed in the coming years are highlighted, especially those related to statistical expression analysis (SEA) based on multiple gel runs, and image mining techniques through the use of high‐throughput processing based on the Grid technology.
Detecting protein posttranslational modifications using small molecule probes and multiwavelength imaging devices
Authors: Patton Wayne F. 
Published: April 2005

Abstract
Though there are alternatives to polyacrylamide gel electrophoresis, such as solution‐phase capillary electrophoresis, multidimensional chromatography, and microfluidic separations, the simplicity, reliability, and ready accessibility of the polyacrylamide gel ensures that it will remain a vital tool in proteomics endeavors for the foreseeable future. Two‐dimensional gel electrophoresis (2‐DE) remains the single most powerful analytical tool in the proteomics arsenal for global analysis of protein posttranslational modifications. Recently, the capabilities of 2‐DE have been dramatically enhanced through the introduction of fluorescence‐ and chemiluminescence‐based detection technologies, as well as complementary advanced imaging instrumentation, that permit routine detection of protein modifications such as phosphorylation, glycosylation, and S‐nitrosylation. These detection reagents are also applicable to the analysis of subproteomes on simple one‐dimensional SDS‐polyacrylamide gels, permitting rapid, higher throughput screening of fractionated proteins for the identification of potentially interesting samples that may subsequently be evaluated in greater detail by 2‐DE. Small‐molecule probes and multiwavelength imaging devices together greatly extend the capacity of gel electrophoresis with respect to the investigation of proteome‐wide changes in protein posttranslational modification levels without resorting to the use of radiolabeling.
Real‐time measurements of protein dynamics
Authors: Concannon Caoimhín G. , Duessmann Heiko , Prehn Jochen H. M. 
Published: April 2005

Abstract
Undoubtedly, the advent of green fluorescent protein (GFP) technology has made great advancements into our understanding of how key cellular functions unfold. The ability to fluorescently tag a protein without perturbing its functioning is central to this and has allowed us to perform quantitative bioimaging of protein movements and concentrations within living cells. The challenge for the future is to further expand this technology with more sophisticated imaging equipment and improved fluorescent proteins with increased spectral variation, thus improving our current understanding of protein dynamics.
Arraying proteins and antibodies
Authors: Wilson David S. , Nock Steffen 
Published: April 2005

Abstract

Protein arrays (
see
Protein microarrays as an emerging tool for proteomics
and
Protein arrays
) enable investigators to characterize multiple proteins in parallel while expending minimal amounts of precious biological samples. The individual features of arrays can be either arranged in a two‐dimensional grid on a planar surface, or they can be constructed from optically encoded particles suspended in a solution. A variety of substrates, chemistries, and arraying methods have been described. The choice among these methods should be made according to the nature of the application and the types and numbers of proteins that need to be arrayed.
Investigating protein–protein interactions in multisubunit proteins: the case of eukaryotic
RNA
polymerases
Authors: Guglielmi Benjamin , Zaros Cécile , Thuriaux Pierre , Werner Michel 
Published: April 2005

Abstract
The physiological functions executed by eukaryotic cells are often catalyzed by large multiprotein complexes. Very few complexes have been analyzed at a detailed structural level, and one therefore strongly relies on generic but indirect methods to establish protein–protein interaction maps between the polypeptide subunits of these complexes, and to delineate the relevant interacting domains. Currently, the two more popular approaches are based on protein “pull‐down” assays, where the ability of two partner polypeptides is measured by fast copurification tests, and by two‐hybrid interaction mapping, where interacting proteins reconstitute a functional heterodimeric transcriptional activator in vivo. If carefully implemented, both provide important insight into the organization of multiprotein complexes. The predictive power of these approaches will be assessed at the light of our current knowledge of eukaryotic DNA‐dependent RNA polymerases.
Functional classification of proteins based on protein interaction data
Authors: Brun Christine , Baudot Anaïs , Jacq Bernard 
Published: April 2005

Abstract
Deciphering gene/protein function for a better understanding of cell functioning and organism development is one of the main goals in biology. For this purpose, approaches have been designed following both methodological progress and thinking advancement. In this respect, computational methods played a constant role over time, evolving with the way biologists were apprehending gene/protein function. After a brief review of the more prominent bioinformatics methods and their implication in understanding gene/protein function, this article aims at explaining the importance of analyzing the protein–protein network with regard to the new vision of the cell functioning that it provides. In this respect, PRODISTIN, a computational method permitting the functional classification of proteins based on the analysis of the interaction network is presented along with the main conclusions it allowed us to reach.
FRET
‐based reporters for intracellular enzyme activity
Authors: Sato Moritoshi , Umezawa Yoshio 
Published: April 2005

Abstract
Fluorescence imaging is the most powerful technique available for observing spatial and temporal dynamics of ions and molecules in the single living cells. However, almost all the molecular events, including those involving second messengers and protein phosphorylation, are analyzed by conventional destructive methods, such as radio immunoassay and immunoblotting of cell lysates prepared from millions of cells. Here, we describe fluorescent reporters for protein phosphorylation and lipid second messengers that we recently developed, and show how their spatial and temporal dynamics can be monitored in single living cells. The present fluorescent reporters should be an indispensable tool not only for understanding the complex mechanism of the signal transduction in single cells and organisms but also for high‐throughput screening of pharmaceutical candidates that regulate the cellular extent of protein phosphorylation and lipid second messengers.
siRNAapproaches in cell biology
Authors: Gampel Alexandra , Mellor Harry 
Published: April 2005

AbstractThe success of the genome sequencing projects has given us access to the genetic identities of a wide range of organisms. Clearly, the greatest challenge now is to make use of this wealth of information and, specifically, to associate genes with physiological functions. In one of the bizarre coincidences that litter the history of scientific research, this challenge has emerged at the same time as a powerful new technique that seems ideally suited to the job in hand.
Quantitative image analysis and the Open Microscopy Environment
Authors: Swedlow Jason R. , Allan Chris , Falconi Andrea , Burel Jean‐Marie 
Published: April 2005

Abstract

Many advances have been made in instrumentation and image analysis algorithms for light microscope, yet computational cell biology remains out of reach for many investigators. The use of proprietary file formats by commercial software complicates the storage, analysis, and querying of image data. Integration of new algorithms into proprietary packages is difficult at best, and there are inadequate standards for sharing image data and results with colleagues. We have developed an open‐source software framework to address these limitations called the Open Microscopy Environment (
http://openmicroscopy.org
). The foundation of our system is a data model that is specifically designed for five‐dimensional microscope images (X, Y, Z, wavelengths, and time). This model is instantiated as an XML file that serves as a convenient data migration format for biological imaging. In addition, the OME Data Model is used to build an OME database and associated interfaces that serve as an integrated data storage, management, and analysis tool. The database stores all information regarding acquisition and all subsequent results from processing, analysis, and measurement. Using standard software interfaces, this design removes barriers of communication between different proprietary software packages. The Data Model, and by extension, the OME XML File and the OME database can be adapted to the requirements of local facilities. Finally, the system provides Web‐based and stand‐alone clients applications for visualizing image data and analytic results. OME is an open‐source software project, and OME code is licensed under the Less GNU General Public License. The latest documentation for OME and software releases are at
http://openmicroscopy.org
.
Structure/function of

N

‐glycans
Authors: Dwek Miriam V. , Brooks Susan 
Published: April 2005

Abstract
The posttranslational modification of proteins with N‐linked glycans is a topic of intense research as the N‐linked glycans attached to proteins have been found to have a profound effect on both structure and function of many glycoproteins. This article describes the biosynthesis and function of a range of proteins that are glycosylated with N‐linked oligosaccharides.
O‐linkedN‐acetylglucosamine (O‐GlcNAc)
Authors: Whelan Stephen A. , Hart Gerald W. 
Published: April 2005

AbstractO‐linked β‐N‐acetylglucosamine (O‐GlcNAc) is an abundant and dynamic posttranslational modification that occurs on serine and threonine residues in functionally diverse nucleocytoplasmic proteins in all metazoans.O‐GlcNAc has been characterized to have functional roles in a number of disease states, as a nutrient sensor, in protein–protein interactions, and protein degradation. The regulation of these cellular functions, as well as many other potential functions, is studied through the use and development of proteomic techniques. IdentifyingO‐GlcNAc sites, in conjunction with other posttranslational modifications, will continue to play an essential role toward elucidating the complex regulation of proteins and the control on the cellular state.
Posttranslational cleavage of cell‐surface receptors
Authors: Stacey Martin , Davies John , Gordon Siamon , Lin Hsi‐Hsien 
Published: April 2005

Abstract
Nascent polypeptides generated by eukaryotes rarely represent the true form of mature proteins. Instead, many newly synthesized proteins undergo posttranslational modifications that may mediate either subtle or profound effects on the function of the protein. In this review, we focus on proteolytic cleavage as a type of irreversible posttranslational modification. We describe the different proteolytic mechanisms of three disparate families of cell‐surface receptors; Notch receptors, protease‐activated receptors (PARs) and G‐protein receptor proteolytic site (GPS) containing receptors. All of these exemplify how posttranslational modification by proteolysis can greatly affect receptor function through a variety of intriguing mechanisms.
Metalloproteins
Authors: Degtyarenko Kirill 
Published: April 2005

Abstract
Blood is red in vertebrates and blue in molluscs thanks to protein–metal complexes. Metalloproteins are involved in all fundamental biochemical processes including respiration, oxygenic photosynthesis, regulation of transcription and translation, nitrogen fixation, and metabolism of xenobiotics. Metalloenzymes were the first biological catalysts on Earth. Later, when the composition of the Earth's atmosphere changed dramatically due to photosynthesis, the metalloproteins evolved to counter the toxic effects of oxygen and harness it for new physiological functions. Currently, over one‐half of all proteins are estimated to bind metals. This article introduces but a small number of metalloprotein families, with emphasis on oxidoreductases, electron‐transfer proteins, and photosynthetic complexes.