bluuebunny/crossref_metadata_2025 huggingface dataset:
Pseudogenes
Authors: Torrents David
Published: April 2005

Pseudogenes are nonfunctional genomic regions that arise mostly from the duplication of functional genes. Two types of pseudogenes are generally formed by independent mechanisms that are believed to have different implications in gene evolution.Nonprocessedpseudogenes arise after partial or complete segmental duplication of genes and subsequent loss of function by mutations.Processedpseudogenes, in contrast, are formed through the reverse transcription of mature RNAs and their integration back in the genome (retrotransposition). As pseudogenes share many sequence characteristic with functional genes, the identification and differentiation of pseudogenes is often difficult and prone to controversy. Nevertheless, a few sequence features that suggest the absence of functionality have been exploited to obtain pseudogene collections from different available genomes. In human and rodents, nearly 20 000 pseudogenes have been identified, most of which were found to have a retrotranspositional origin. In contrast, a much lower number of pseudogenes could be identified in other organisms, such as chicken and nonvertebrates. Despite the recent identification of large collections of pseudogenes, improvements in the distinction between functional and pseudogenic regions are still required in order to determine what the actual impact of these regions is in the evolution of the genomes.
Endogenous retroviruses
Authors: Mayer Jens
Published: April 2005

Endogenous retroviruses (ERVs) are an integral part of vertebrate genomes. ERVs became inherited genomic components by formation of proviruses of exogenous retroviruses in germ cell genomes. Repeated endogenization of diverse exogenous retroviruses and subsequent increase of provirus numbers resulted in a considerable retroviral load in host genomes. For instance, the human and the mouse genome hold 8 and 10%, respectively, of sequences of retroviral origin. Most ERV sequences accumulated numerous nonsense mutations over time, rendering them defective. Nevertheless, ERVs can affect the host genome in various ways. Long terminal repeats influence transcription of nearby cellular genes. ERV proteins protect from exogenous retrovirus infection. Human ERV sequences may be involved in placenta development and in the formation of germ cell tumors. ERVs are therefore important genome components that contributed significantly to the evolution of host genomes.
Mouse models
Authors: Goldsworthy Michelle E. , Cox Roger D.
Published: April 2005

The mouse has a proven track record as a model organism that has made a significant contribution to the understanding of disease and biology relevant to the human. It is not the only model organism by any means but for the study of human disease it is perhaps one of the most widely used. We have tried to illustrate in this review the multiple approaches that have been utilized using as examples the study of type 2 diabetes and obesity in the mouse. Spontaneous mutations and knockouts have given insight into the relative contributions of differing genes in the regulation of glucose homeostasis, insulin resistance, β‐cell function, and adiposity. Tissue‐specific knockouts have gone some way in dissecting the relative contributions of multiple tissues and organs to disease progression. Combinations of different mutants, which individually would not produce disease, have provided polygenic models of type 2 diabetes. Sensitized ENU mutagenesis screens may yield additional novel diabetes genes. The mouse has only been one of the approaches available to us to investigate human disease but together with studies in human populations, other model organisms, and in vitro systems, it has opened unprecedented opportunities in this new century to tackle the problem of common human disease.
Mouse mutagenesis and gene function
Authors: Kühn Ralf , Wurst Wolfgang
Published: April 2005

With the completion of the mouse and human genome sequences, a major challenge is the functional characterization of every gene within the mammalian genome. The mouse offers many advantages for the use of genetics to the study of human biology and disease. A variety of mouse mutagenesis technologies, either gene‐ or phenotype‐driven, are used as systematic approaches. The availability of the mouse genome supports gene‐driven approaches such as gene‐trap and targeted mutagenesis in embryonic stem (ES) cells, allowing an efficiency and precision of gene disruption unmatched among other mammals. Furthermore, chemical and transposon mutagenesis of the mouse genome allows to perform phenotype‐driven screens for the unbiased identification of phenotype–genotype correlations. These technologies already resulted in a collection of several thousand mutants. In this article on mouse mutagenesis and gene function, we present a comprehensive review of gene‐ and phenotype‐driven mouse mutagenesis strategies. Besides a summary of the basic principles of each approach, we emphasize on the latest and future developments of mouse mutagenesis.
Functional genomics in

S
accharomyces cerevisiae
Authors: Dolinski Kara , Troyanskaya Olga
Published: April 2005

The availability of the
Saccharomyces cerevisiae
genome has fueled an explosion of high‐throughput methods aimed at the functional characterization of all proteins in yeast. These diverse methods include expression and protein microarray experiments, protein–protein and protein–DNA interaction studies, proteomics data, and phenotype analyses. Integrated bioinformatics analysis is necessary to utilize the full potential of these data. Such analysis can be facilitated by public distribution of these data sets in standardized form and by development of accurate and efficient analysis algorithms. In this chapter, we outline available data sources and their distribution, data sharing standards, and data integration methods.
The

D
rosophila

genome(s)
Authors: Russell Steven , Bergman Casey M.
Published: April 2005

Since its introduction as a research tool in the early twentieth century,

Drosophila melanogaster

has occupied center stage in genetics as an experimentally tractable model for understanding the structure of genomes. It was used to prove the chromosomal theory of heredity (Bridges,

) and to first localize particular genes to cytologically defined regions of the chromosome (Bridges,

). With the virtual completion of the genome sequence, the fly continues to hold sway. We briefly assess the status of the current sequence, describe how other
Drosophila
sequences are being used to provide an evolutionary perspective to the genome and highlight how the sequence is enabling large‐scale functional analysis of conserved aspects of eukaryotic biology. Finally, we consider how the polytene chromosomes may provide a system to move from the linear DNA sequence to the challenging area of chromatin organization and chromosome structure.
Genomics of the

M
ycobacterium tuberculosis

complex and

M
ycobacterium leprae
Authors: Gordon Stephen V. , Brosch Roland
Published: April 2005

Diseases caused by mycobacteria continue to exact a terrible burden across the globe, with an urgent need for new treatments and control strategies. Elucidation of the genome sequences of these pathogens therefore offers a cost‐effective approach to catalyze research and accelerates our understanding of them. The genome sequence of the hallmark strain,
Mycobacterium tuberculosis
H37Rv, has been available since 1997 and this serves as the lynchpin for comparative genomics across the complex. Our review will use comparative genomics to explore the wealth of sequence data available for the pathogenic mycobacteria and highlight similarities and parallels that impact upon important biological characteristics. Such analyses are providing novel insights into how pathogenic mycobacteria exploit the in vivo niche, and in so doing expose targets for drug development and diagnostic reagents.
Genomics of enterobacteriaceae
Authors: Glasner Jeremy D. , Perna Nicole T.
Published: April 2005

Enterobacteria were among the earliest targets for genome sequencing and are still the most densely sampled clade of bacteria in the genomics arena. Twenty complete genome sequences are available for members of the family as of September 2004, and the NCBI list of genomes in progress includes another 20 enterobacteria. This is undoubtedly an underestimate of the sequences that will be available for enterobacteria in the coming two years. Among the complete genomes are representatives of nine genera, including
Escherichia
,
Shigella
,
Salmonella
,
Yersinia
,
Erwinia
,
Buchnera
,
Photorhabdus
,
Wigglesworthia,
and
Candidatus Blochmannia
. Genomes in progress will add additional strains and species of these, as well as additional genera such as
Klebsiella
,
Proteus
,
Citrobacter
,
Enterobacter
,
Dickeya
, and
Pantoea
. Among these are standard laboratory research strains, human pathogens, livestock pathogens, plant pathogens, and insect endosymbionts. Each genome sequence aids in understanding the biology of the individual organism, but some of the greatest insights come from comparisons between the genomes. For many of these genera, sequences are available for multiple species or strains, providing unique perspectives on genome‐wide polymorphism. Enterobacteria are also very experimentally tractable, and we are beginning to see a boom in downstream research making use of the sequences.
The organelles of apicomplexan parasites
Authors: Ajioka James W. , Brooke‐Powell Elizabeth T. , Wan Kiew‐Lian
Published: April 2005

The apicomplexa are a highly diverse phylum of parasitic protists that are descended from a secondary endosymbiosis of a photosynthetic algae and single eukaryotic cell. Throughout the evolution of the phylum, most species have maintained a single mitochondrion and a plastid‐like organelle called the apicoplast. The genomes associated with these organelles are vastly reduced compared to counterparts in other eukaryotic lineages and this probably reflects a concomitant reduction in function.
Kinetoplastid genomics
Authors: Peacock Chris , Hertz‐Fowler Christiane
Published: April 2005

The 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

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

Considered 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

TheYersiniahave 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

A 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

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

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

A 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

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

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

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

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

Separation 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

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

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.
Protein interaction databases
Authors: Hermjakob Henning , Apweiler Rolf
Published: April 2005

Protein interactions are a key element of cellular processes, from regulation to metabolic processes and structural properties. The biological importance of protein interactions and the advent of technologies producing protein interaction data on a large scale have led to the creation of a significant number of protein interaction databases, with a broad spectrum of contents and features.
Using photoactivatable
GFPs
to study protein dynamics and function
Authors: Chudakov Dmitry M. , Lukyanov Konstantin A.
Published: April 2005

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

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

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

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

Phosphorylation 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

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

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

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

Protein 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

Mass 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

Analysis 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

Membrane 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

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

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.
COGs
: an evolutionary classification of genes and proteins from sequenced genomes
Authors: Koonin Eugene V.
Published: April 2005

A comprehensive classification of genes from sequenced genomes, based on evolutionary principles, is a must for the success of comparative and functional genomics. One such classification system is the database of Clusters of Orthologous Groups of proteins (COGs), which was constructed by clustering the results of an all‐against‐all comparison of the protein sequences encoded in prokaryotic and eukaryotic genomes. Each COG includes genes or sets of genes from three or more genomes, which are orthologous to each other, that is, evolved from a single ancestral gene in the common ancestor of the analyzed organisms. Between 50 and 85% of the genes from the sequenced genomes belong to COGs, indicating notable evolutionary conservation. The COG system is a natural framework for comparative genomics and has the potential of facilitating both functional annotation of genomes and large‐scale evolutionary studies.
Functionally and structurally relevant residues in PROSITE motif descriptors
Authors: Sigrist Christian J. A. , De Castro Edouard , Langendijk‐Genevaux Petra S. , Saux Virginie Le , Bairoch Amos , Hulo Nicolas
Published: April 2005

PROSITE is an annotated collection of motif descriptors, which are either patterns (regular expressions) or generalized profiles (weight matrices). Whereas patterns perform well for the identification of short well‐conserved regions such as active sites, profiles usually cover the full length of the protein or domain and can accept a mismatch at a highly conserved position if the rest of the sequence shows a sufficiently high level of similarity. Hence, a profile can match a structural domain even if the active site is mutated and thus is no longer functional. To distinguish these cases and make functional predictions more accurate, biologically meaningful residues of a profile can be tagged and the corresponding residues in the sequence retrieved and checked for their biological properties.
Classification of proteins by clustering techniques
Authors: Kriventseva Evgenia V.
Published: April 2005

In the past few years, the technology of sequencing has developed to the stage at which the sequencing of a complete genome can be contemplated as a practical and routine possibility. To cope with the exponentially growing data, methodologies for computational classification of biological sequences are required. Recently, several approaches for automatic functional classification of proteins were developed. This review describes the most widely applied clustering algorithms in Bioinformatics and resources developed for protein classification.
New approaches to bridging the timescale gap in the computer simulation of biomolecular processes
Authors: Caves Leo S. D. , Verma Chandra S.
Published: April 2005

Current state‐of‐the‐art computer simulations of biomolecules probe timescales that are generally very short compared to those that characterize most interesting biochemical and biological processes. New developments in simulation methods extend the reach of simulation in a trend that reflects the increasing time resolution of experimental spectroscopic techniques. We propose that the tools of dynamical systems analysis offer a potentially powerful approach to reconciling the view of biomolecular dynamics emerging from both simulation and experiment.
Constraint‐based modeling of metabolomic systems
Authors: Beard Daniel A. , Qian Hong
Published: April 2005

Constraint‐based analysis of large‐scale metabolic systems is the computational exploration of metabolic fluxes and concentrations constrained by the physical chemical laws of mass conservation and thermodynamics. This chapter reviews the mathematical formulation of the constraints on reaction fluxes and reactant concentrations that arise as a consequence of the stoichiometry of a specified network of biochemical reactions. Linear algebraic constraints arising from steady state mass balance form the basis of the related computational technologies metabolic flux analysis (MFA) and flux‐balance analysis (FBA). Thermodynamic laws, while introducing inherent nonlinearities into the mathematical description of the feasible space, facilitate the introduction of reactant concentrations to the constraint‐based framework. Together, the mass‐balance and thermodynamic constraints form the basis of an approach to modeling and analysis of biochemical systems that is alternate and complementary to detailed chemical kinetics.
A complex systems approach to understand how cells control their shape and make cell fate decisions
Authors: Ingber Donald E. , Huang Sui
Published: April 2005

In this chapter, we analyze the mechanisms by which mammalian cells maintain their physical shape and make cell fate decisions whether to grow, move, differentiate, or die in response to chemical and physical signals during tissue development. We address how these robust and mutually exclusive, system‐level behavioral programs emerge from the dynamics of molecular networks that establish both the hardware (structure) and the software (information processing) of the cell. Molecular filaments within the cytoskeleton self‐organize using tensegrity architectural principles in which prestress and force balances between different filaments play key stabilizing roles. In this manner, the filaments form a physical network structure that stabilizes the shape of the cell while providing it with the flexibility necessary for movement. As for cellular information processing, genome‐wide regulatory networks impose constraints on the collective dynamics of signaling molecules, so that the biochemical activity of genes and proteins exhibits large‐scale coherent patterns that correspond to stable, high‐dimensional attractor states. These attractors define distinct cell fates that are stable, yet can undergo regulated all‐or‐none transitions between distinct stable cell phenotypes. Because of the robustness of these attractors, physical cues devoid of molecular specificity, such as mechanical stress and cell shape distortion, can produce similar effects on cell behavior as highly specific growth factors. This coordination between structural networks and information networks is critical for the formation and homeostasis of complex tissue structures in multicellular organisms. Taken together, this work conveys the importance of complementing existing “bottom‐up” approaches in systems biology that emphasize comprehensive characterization of molecular processes, with “top‐down” approaches that place these molecular activities within the context of actual system‐level properties at the level of the whole living cell.
Systems biology of the heart
Authors: Noble Denis
Published: April 2005

Models of the heart have been developed since 1960, starting with the discovery and modeling of potassium channels. The first models of calcium balance were made in the 1980s and have now reached a high degree of physiological detail. During the 1990s, these cell models have been incorporated into anatomically detailed tissue and organ models. Systems biology of the heart is now well developed and is proving increasingly useful in unraveling complicated physiological functions and in understanding disease states.
Integrative modeling of the pancreatic β‐cell
Authors: Sherman Arthur , Bertram Richard
Published: April 2005

Pancreatic β‐cells secrete insulin, which regulates the concentration of plasma glucose. Dysfunction of this system is a necessary contributing factor to Type II diabetes, and may be sufficient. Insulin secretion is controlled by oscillations of membrane potential, calledbursting oscillations, which drive oscillations of cytosolic calcium. We describe the development of mathematical models for this mechanism, beginning with the Chay–Keizer model.
EGFRnetwork
Authors: Shvartsman Stanislav Y.
Published: April 2005

The epidermal growth factor receptor (EGFR) network is an evolutionarily conserved regulator of epithelial tissues. At this time, we have a relatively good understanding of the mechanisms by which the EGFR network can control the physiology of a single cell. The current challenge, however, is to understand how this network operates in multicellular systems and tissues. To accomplish this, it will be necessary to integrate information from genetic, biochemical, and cellular studies into predictive, quantitative models.
Contig mapping and analysis
Authors: Siddiqui Asim , Jones Steven
Published: April 2005

Physical mapping and the creation of contig maps remains a valuable tool for genomics research. This section describes the methods and techniques used to create contig maps from restriction fragment fingerprint information. It mentions some of the bioinformatics challenges associated with building a high‐quality map and points to ongoing research that is attempting to address this problem. This section also illustrates how tiling path clones are chosen from a redundant set of clones.
Comparative analysis for mapping and sequence assembly
Authors: Milosavljevic Aleksandar
Published: April 2005

The increasing number of assembled reference sequences produced by ongoing genome sequencing projects provides information that is useful for the mapping and assembly of related genomes. Comparative information has the potential to both decrease the cost and accelerate mapping and sequencing projects by reducing experimental effort. Anchoring of contigs from one species onto an assembled genome of the other related species provides hypothetical order, orientation, and distance information. Mapping cloned genomic fragments, such as Bacterial Artificial Chromosomes (BACs), of one species onto an already assembled genome of another may be either used to select clones for targeted comparative sequencing or to infer the hypothetical order and orientation of BACs. Assembled genomic sequence of one species can be used as a template to guide the assembly of another, related species.
Information theory as a model of genomic sequences
Authors: Bi Chengpeng , Rogan Peter K.
Published: April 2005

Shannon information theory can be used to quantify overall sequence conservation among sets of related sequences. Variation in nucleic acid sequences recognized by proteins can be comprehensively modeled with information weight matrices that permit each member sequence to be rank‐ordered according to its respective individual information contents. These rankings can be used to compute the affinities of recognition sites by proteins and to predict the effects of nucleotide substitutions in the sequences of these sites. The distribution of information across a set of protein‐binding sites in DNA is related to the pattern of intermolecular contacts that stabilize the protein‐nucleic acid complex (i.e., the corresponding helical structure of double‐stranded DNA).
Gene structure prediction by genomic sequence alignment
Authors: Morgenstern Burkhard
Published: April 2005

Traditional gene‐finding programs are based on stochastical approaches such as hidden Markov models (HMM) describing the statistical composition of coding and noncoding regions for a given organism. Comparative gene prediction, by contrast, is based on the
phylogenetic footprinting
principle. During evolution, functionally important sites in the genome tend to be more conserved than nonfunctional regions. Thus, local sequence conservation usually indicates biological functionality. Comparative gene‐finding approaches start with an
alignment
of evolutionary related genomic sequences and try to identify splice signals in areas of local sequence conservation. This way, putative exons are identified that are used to construct gene models. In this chapter, the comparative genefinder AGenDA is described. Its performance is compared to more traditional approaches, and possible future developments are discussed.
Reconstructing vertebrate phylogenetic trees
Authors: Kumar Sudhir , Filipski Alan
Published: April 2005

Within the last three decades, the methodology underlying vertebrate phylogenetic analysis, including the dating of speciation events, has grown from the use of morphological characters in living organisms and fossils to an increased emphasis on molecular phylogenetics. Here, we use a selected set of examples to give a brief survey of how these approaches have been used together to resolve some interesting and difficult questions regarding both lower‐ and higher‐level relationships of vertebrate species.
Mapping mutations on phylogenies
Authors: Nielsen Rasmus
Published: April 2005

This chapter provides a short review of recent methodologies developed for mapping mutations on phylogenies. Mapping of mutations, or character changes in general, using the maximum parsimony principle has been one of the most powerful tools in phylogenetics, and it has been used in a variety of different applications, for example, in the detection of correlated evolution and to identify selection acting on DNA sequences. However, many uses of parsimony mappings have been criticized because they focus on only one of many possible mappings and/or because they do not incorporate statistical uncertainty in the mapping. Recently developed probabilistic methods can incorporate statistical uncertainty in the character mappings. In these methods, focus is on a probability distribution of mutational mappings instead of a single estimate of the mutational mapping.