bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinetoplastid genomics
Authors: Peacock Chris , Hertz‐Fowler Christiane 
Published: April 2005

AbstractThe last decade has seen a significant development in the volume and quality of genomic data generated for many of the kinetoplastid organisms, in particular, those of medical and veterinary importance. The most advanced projects are for the three annotated and almost complete genomes of the important human and animal pathogensLeishmania major,Trypanosoma brucei, andTrypanosoma cruzi. This short review describes some of the current areas of genomic research on the Kinetoplastida and provides a list of the publicly available genome and post‐genomic data resources.
Environmental shotgun sequencing
Authors: Tyson Gene W. , Hugenholtz Philip 
Published: April 2005

Abstract
Shotgun sequencing of microbial communities is a promising means for delving into community function and interactions, population structure and dynamics, and bypassing the cultivation bottleneck in microbiology. However, this approach is mostly blind to low‐abundance species as it effectively samples only the dominant populations in a community. It also faces a number of technical challenges such as the assembly and separation of individual genomes from a mixture of genomic fragments compounded by sampling unevenness and data scalability. Despite these limitations, environmental shotgun sequencing should rapidly advance the fields of microbial ecology and evolution.
The neisserial genomes: what they reveal about the diversity and behavior of these species
Authors: Saunders Nigel J. , Snyder Lori A. S. 
Published: April 2005

AbstractConsidered singly and together, the neisserial genomes provide global perspectives of the great genetic and functional flexibility of these species. They provide a useful model for the behaviors and diversifying strategies that are common to many of the naturally transformable, relatively panmictic, bacterial species. Comparisons of gene complements suggest that the very different pathogenic potentials of these species are associated with a relatively limited number of key genes. Differences between the strains and species can be used to address their behavior, but to be informative this has to include assessments of several different types of diversity. These species have differences not only in gene complements, but also in phase‐variable genes, genes containing repeats altering protein structures, and in genome organization, all of which have the potential to affect function and behavior. These studies have to be extended to functional comparisons based upon expression analysis at both transcript and protein levels, and for each such investigation the genome sequences and annotations are an essential platform.
Yersinia
Authors: Thomson Nicholas R. 
Published: April 2005

AbstractTheYersiniahave generated much attention both recently and historically. Part of the reason for this is the fact that an infection by one of the pathogenic yersiniae can result in sequelae ranging from self‐limiting gastroenteritis to bubonic plague. Media attention, focused on bioterrorism, has also been significant. Scientific research has focused on the plasmid encoded virulence determinants and in particular on using the yersiniae as model organisms for the genetic dissection of type III secretion systems. However, it is clear that the genomes themselves also hold clues that can help us understand how these pathogens have evolved and are able to cause such a diversity of disease.
Mapping by admixture linkage disequilibrium (MALD)
Authors: Smith Michael William 
Published: April 2005

AbstractA novel opportunity to discover the variants of genes underlying human phenotypes (particularly those relating to disease) exists because of the mixing of peoples during the last few centuries. Termed mapping by admixture linkage disequilibrium (MALD), the approach fundamentally utilizes those infrequent genetic variants that largely differentiate the racial/ethnic groups and the segmental nature of genomic material in individuals of mixed group ancestry. The methodology requires both genetic markers that differentiate groups – culled from the limited set of genetic differences between groups – and powerful analysis methodologies. Such markers are now available for MALD analysis of admixed African‐Americans, and are being developed for Hispanics and other admixed groups. Together, the differentiating markers and analytic approaches allow the application of MALD to many diseases whose incidence differs between the founding groups of African‐Americans and Hispanics along with other modern day populations of recently melded origins. Of course, the proof of MALD as a valid gene discovery approach rests on its successful application to disease gene discovery.
Disease gene candidacy and
ESTs
Authors: McCarthy Mark I. 
Published: April 2005

Abstract
The effort to identify and characterize the genetic variants that underlie susceptibility to common multifactorial traits represents one of the main challenges in biomedical research today. Key to this research is the capacity to assess the biological candidacy of potential susceptibility genes by matching their characteristics to known features of the disease. Tissue expression patterns provide one of the most obvious and useful parameters in this respect. There is a growing body of available data on the expression state of human genes, including information inherent in the tissue origins of the expressed sequence tags (ESTs) that can be associated with a chosen transcript. This short review discusses the value of transcript sequence data in the mapping of human disease genes.
Using
Uni
Gene
,
STACK
, and
TIGR
indices
Authors: Christoffels Alan G. 
Published: April 2005

Abstract
Expressed sequence tags (ESTs) are fragmented, single‐pass reads that are processed into nonredundant gene loci to produce gene indices that are useful for genome sequence annotation. Three gene‐indexing projects, namely, UniGene, STACK, and TIGR gene index have been developed independently in order to meet specific research goals. The utility of these indices have been enhanced by the availability of visualization tools for exploratory data analysis. In addition, the clustering tools for the generation of STACK and TIGR gene indices are made available to the research community.
Interpreting tandem mass spectra of peptides
Authors: Johnson Richard S. 
Published: April 2005

AbstractA brief tutorial is presented for manually determining peptide sequences from low energy collision induced dissociation tandem mass spectra. Peptide fragmentations are described, including a discussion of the influence of “mobile protons” in the production of fragment ions. Ambiguities inherent in deriving peptide sequences from mass spectra are described, and two examples are presented.
Sample preparation for proteomics
Authors: Rabilloud Thierry 
Published: April 2005

Abstract
Various types of sample preparation for downstream proteomics analysis are outlined. The rationales for native or denaturing extractions are discussed, together with the constraints brought by the protein or peptide separation methods, that is, one‐ or two‐dimensional denaturing protein electrophoresis, native protein electrophoresis, or peptide chromatography. The constraints discussed in this chapter also include the removal of nonprotein substances interfering with the proteomics analysis.
Nano‐
MALDI
and Nano‐
ESI MS
Authors: Marko‐Varga Gyorgy , Nilsson Johan , Laurell Thomas 
Published: April 2005

Abstract
Chip‐based techniques are impacting bioanalytical methodology at an increasing rate. The major reason for this is found in the benefits that may be gained by the scaling laws that govern the physics and chemistry, determining the performance of these systems. Mass spectrometry as an analytical tool has dramatically impacted and is still revolutionizing the way that bioanalytical research is executed. It can therefore be anticipated that the oncoming decade will demonstrate remarkable performance improvements in the area. Microscaled technologies have already proved to be an important route in advancing throughput, reducing sample volume requirements, and increasing readout sensitivity in mass spectrometry. In this respect, the current chapter overviews some of the strategies pursued to gain system performance as the dimensions were reduced when processing and delivering biological sample for MS readout.
Multidimensional liquid chromatography tandem mass spectrometry for biological discovery
Authors: Delahunty Claire M. , Yates John R. 
Published: April 2005

Abstract
Biological systems organize physiological functions and communications into collections of proteins. Multidimensional liquid chromatography (MudPIT) in combination with tandem mass spectrometry can be used to identify proteins in such structures. This data reveals potential roles for proteins in the context of the structures.
Techniques for ion dissociation (fragmentation) and scanning in MS/MS
Authors: Watson Jack Throck , Sparkman O. David 
Published: April 2005

Abstract

A determination of the mass of an ion, although important, may be insufficient for identification (
see
Mass spectrometry
,
FT‐ICR
,
Quadrupole MS
, and
Quadrupole Ion Traps and a New Era of Evolution
). Often, the manner in which and/or the degree to which an ion can be made to dissociate provides a wealth of characteristic and structural information. There are different instrumental approaches to promote and conduct ion dissociation, and there are several different “scanning” modes to obtain and utilize the ion dissociation information.
MS‐based methods for identification of 2‐DE‐resolved proteins
Authors: Treumann Achim , Gerner Christopher 
Published: April 2005

AbstractSeparation of proteins by two‐dimensional gel electrophoresis followed by mass spectrometric protein identification is one of the main procedural workflows in proteomics. Peptide mass fingerprinting and peptide fragmentation are the two most frequently used applications of mass spectrometry for this purpose. We present an introductory overview and a short discussion of the respective merits of both approaches.
Protein interactions in cellular signaling
Authors: Pawson Tony 
Published: April 2005

Abstract
Protein–protein interactions provide a fundamental mechanism through which cellular regulatory systems are organized, and specificity is imposed during signal transduction. Furthermore, the association of proteins into larger complexes supports the formation of more extended biochemical pathways and interaction networks that link and integrate different aspects of cellular behavior. The molecular principles that underlie protein–protein interactions also explain the ability of proteins to recognize specific phospholipids, nucleic acids, and second messengers, and, therefore, define a general theme in proteomics and cell biology.
Inferring gene function and biochemical networks from protein interactions
Authors: Michnick Stephen W. 
Published: April 2005

Abstract
Systematic studies of the organization of biochemical networks that make up the living cell can be defined by studying the organization and dynamics of protein–protein interaction. Here, I describe experimental strategies that can achieve this aim and how perturbations of interactions can be used to define the organization of biochemical networks. Resulting perturbation profiles and subcellular locations of interactions allow us to “place” each gene product at its relevant point in a network. I discuss how network mapping by PCA could work with or be used in conjunction with other genome‐wide analyses of protein interactions and gene transcription to determine the dynamics of information flow through biochemical networks in the living cell. It is through such dynamic studies that the intricate networks that make up their chemical machinery of the cell may begin to be elucidated.
Using photoactivatable
GFPs
to study protein dynamics and function
Authors: Chudakov Dmitry M. , Lukyanov Konstantin A. 
Published: April 2005

Abstract

Green fluorescent protein (GFP) from jellyfish

Aequorea victoria

, its mutants, and homologs from other organisms have become an integral part of modern methodology in cell and molecular biology. GFP‐like proteins represent the only genetically encoded fluorescent tags that can be widely used to label organisms, cells, organelles, and proteins. This review is focused on photoactivatable GFP‐like proteins, that is, proteins capable of manyfold increase of fluorescence intensity at certain excitation‐emission wavelengths in response to irradiation with specific light. Photoactivatable tags make it possible to “switch‐on” fluorescent signal by a beam of light in precisely chosen part of organism or cell in order to track the movement of the labeled objects. The spectral properties and mechanisms of the photoactivation for the most experimentally useful photoconvertible proteins are described in detail. In particular, we discuss GFP and its mutant PA‐GFP, green‐to‐red convertible protein Kaede from a stony coral

Trachyphyllia geoffroyi

, and kindling fluorescent protein (KFP) from a sea anemone

Anemonia sulcata

. Considerable progress is still required to enrich the palette of monomeric photoactivatable GFP‐like proteins, which would extend the field of possible applications.
Elucidating protein dynamics and function using fluorescence correlation spectroscopy (
FCS
)
Authors: Schwille Petra 
Published: April 2005

Abstract
The principles and most prominent recent applications of fluorescence correlation spectroscopy (FCS) are outlined, with special focus on intracellular studies, particularly protein dynamics and interactions in situ. FCS is a very valuable alternative to other fluorescence‐based techniques such as FRET, due to its extreme sensitivity that can readily reach the single‐molecule level, and due to its high temporal resolution that allows us to study molecular dynamics on millisecond to microsecond scales.
High content screening
Authors: Taylor D. Lansing , Giuliano Kenneth A. 
Published: April 2005

Abstract
High Content Screening (HCS) has emerged as a powerful platform technology that is being used to “industrialize” cell biology; especially in academic research and drug discovery. Information on the distribution, in time and space, as well as the activity of cellular constituents is helping to define the functions of proteins and other critical cellular components. The ability of these methods to be automated and run at high throughput will revolutionize the analysis of protein function using cell biology.
Posttranslational modification of proteins
Authors: Larsen Martin R. , Jensen Ole N. 
Published: April 2005

Abstract
The elucidation of posttranslational modification of proteins is a prerequisite for understanding the molecular details of living organisms, from bacteria to plants and mammals. Protein phosphorylation plays a key role in cell signaling during cellular development, growth, and differentiation. Protein processing is required for the maturation of proteins and for activation and turnover. The ability to detect and monitor posttranslational modifications and processing of proteins by mass spectrometry and other analytical methods is already providing exciting insights into key regulatory events in cells and organisms, in health, and in disease.
Protein phosphorylation analysis by mass spectrometry
Authors: Steen Hanno , Jebanathirajah Judith A. 
Published: April 2005

AbstractPhosphorylation is arguably the most important posttranslational protein modification, being heavily involved in the dynamic regulation of protein function during signaling, proliferation, and differentiation. Localizing and quantitating the sites of phosphorylation on proteins is of paramount importance toward understanding the regulation of proteins by phosphorylation. Although biochemical methods in combination with methods based on the detection of the radioactive phosphorus isotopes32P and33P are still used, radioactive‐free methods utilizing mass spectrometry are becoming widespread because of its speed, sensitivity, and the ability to handle complex protein and peptide mixtures. This review summarizes recent and established methods used for the selective enrichment, derivatization, and selective mass spectrometric detection of phosphorylated species, which have proven to be extremely useful in numerous studies. In addition, the latest trends in the field of mass spectrometric analysis of protein phosphorylation are introduced.
Glycosylation in bacteria: that, what, how, why, now what?
Authors: Appelmelk Ben J. , Vandenbroucke‐Grauls Christina M. J. E. , Bitter Wilbert 
Published: April 2005

Abstract
Once considered mavericks, many bacterial species produce glycoproteins. Bacterial polypeptide glycans vary from mono‐ to polysaccharides, are O‐ or N‐linked, may or may not have a eukaryotic signature, and require an apparatus sometimes organized in glycosylation islands. Recent work shows that also in prokaryotes, glycan chains serve as information carriers, and are often involved in interactions between prokaryotes and their environment, including host–pathogen interaction in human and nonhuman hosts.
O

‐glycan processing
Authors: Corfield Anthony P. 
Published: April 2005

Abstract

The Ser (Thr)‐GalNAc class of
O
‐glycan chains found in glycoproteins are formed through a series of sequential transfer reactions without participation of lipid intermediates. The products of these pathways generate predictable structures found on a wide variety of proteins. The formation of truncated, incomplete glycans arises through regulation of the expression of the transferases on these pathways or through the action of glycosidases and other catabolic enzymes. Examples of
O
‐glycan involvement with the processing of glycoproteins is described for protein synthesis and expression, proteolytic processing, subcellular localization of proteins, developmental expression of proteins, and immune cell expression and response.
S
‐nitrosylation and thiolation
Authors: Huang Yunfei , Snyder Solomon H. 
Published: April 2005

Abstract
Cysteine, one of the most reactive residues, is indispensable to the biological functions of many proteins. It constitutes the reactive centers of crucial enzymes and maintains protein confirmation of key cellular regulators. The posttranslational modifications of reactive cysteine residues, S‐nitrosylation and thiolation, have now emerged as evolutionally conserved fundamental cell signals in all species.
Protein phosphorylation analysis – a primer
Authors: Jebanathirajah Judith A. , Steen Hanno 
Published: April 2005

AbstractProtein phosphorylation is possibly the most common intracellular protein modification affecting several different amino acid residues. Its dynamic nature makes it extremely important in cellular regulation mechanisms warranting the need for reliable, fast, sensitive methods for the detection of this modification. The primer gives a brief synopsis on the method that is most commonly used in today's biological laboratories with references to the original literature for more detailed reading.
Mass spectrometry
Authors: Harvey David J. 
Published: April 2005

AbstractMass spectrometry is one of the most sensitive and specific techniques for the identification of organic compounds. It has been used for the structural analysis of proteins, glycoproteins, and nucleic acids since the introduction in the late 1980s of the techniques of matrix‐assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) that have allowed these large biopolymers to be ionized. The article describes these techniques and the types of mass spectrometer that are used to mass‐analyze the resulting ions. Methods for obtaining fragment ions from carbohydrates are described, and the use of mass spectrometry for the structural determination of glycoproteins and carbohydrates is briefly discussed.
Analysis of N‐ and O‐linked glycans of glycoproteins
Authors: Merry Tony H. , Royle Louise , Radcliffe Catherine M. , Astrautsova Sviatlana A. , Dwek Raymond A. , Rudd Pauline M. 
Published: April 2005

AbstractAnalysis of glycosylation is an important aspect of the characterization of glycoproteins, which is often overlooked. Over 75% of proteins including the majority of secreted and cell surface proteins that are important in cellular signaling events are potentially glycosylated. The molecular structures and the mechanism of the interactions of glycoproteins cannot be fully appreciated without knowledge of the structure and distribution of the associated glycans. Although glycan analysis still requires some specialized expertise and understanding of glycobiology, the strategies based on HPLC, gel and capillary electrophoresis, and mass spectrometry that are now available allow the analysis to be performed by many laboratories with protein chemistry expertise.
Transporter protein families
Authors: Ren Qinghu , Paulsen Ian T. 
Published: April 2005

AbstractMembrane transporters play important roles in many fundamental processes and cellular functions of both prokaryotes and eukaryotes. System approaches have been adopted to the classification of transporter families (TCDB) based on mode of transport and energy‐coupling mechanism, molecular phylogeny, and substrate specificity, as well as the whole‐genome transporter analyses (TransportDB). The advantage of the incorporation of phylogeny into the classification system and the importance of a phylogenetic approach are underlined by the fact that phylogeny provides reliable guide to the structure, function, and mechanism of transporter proteins, as shown in the example of the phylogenetic study of human ABC transporter.
The
PRINTS
protein fingerprint database: functional and evolutionary applications
Authors: Attwood Teresa K. , Bradley Paul M. , Gaulton Anna , Maudling Neil , Mitchell Alexander L. , Moulton Georgina 
Published: April 2005

Abstract
The PRINTS database is a compendium of protein fingerprints used to assign uncharacterized sequences to known families and hence to infer tentative functions. Fingerprints are groups of conserved sequence motifs that together provide diagnostic family signatures – the diagnostic potency of fingerprints derives largely from the mutual context afforded by matching motif neighbors, a feature that cannot be exploited by single‐motif approaches. In addition to its use as a signature resource, and the development of an automatic supplement, prePRINTS, we describe here other features that distinguish PRINTS from, and render it complementary to, related protein family databases. We also outline its application to investigations of the evolutionary relationships between model organisms, its use in predicting functional sites in complex gene families, and in annotating publicly available single nucleotide polymorphism data.
Pfam: the protein families database
Authors: Finn Robert D. 
Published: April 2005

Abstract

Systematic analysis has shown that the majority of proteins can be grouped into approximately 1000 sequence families. These sequence families are often representative of domains. Pfam is a protein families database. The basic contents and availability of the Pfam database are described. Genome sequencing projects, including the human and fly, have used Pfam extensively for large‐scale functional annotation of genomic data, while smaller research groups, devoted to a single protein or biochemical pathway, frequently use Pfam for their analyses. Typically, Pfam matches between 55 and 90% of proteins from complete proteome sets. Pfam also allows the domain distributions to be compared for completed genomes. In addition to sequence domain annotation, Pfam also contains information on domain–domain interactions. The new resource that describes domain–domain interactions at the molecular level is called
i
Pfam. The contents of
i
Pfam are briefly outlined.