bluuebunny/crossref_metadata_2025_split huggingface dataset:
Restriction fragment fingerprinting software
Authors: Soderlund Carol A. 
Published: January 2005

Abstract
A physical map is an ordering of clones and markers. Whole‐genome physical maps may be constructed using restriction fragment fingerprinting. With this approach, two clones are considered overlapping if they contain a similar set of fragments. The FPC (FingerPrinted Contig) software is described, which assembles fingerprinted clones into contigs. Markers can also be used to aid the assembly and results in a partial ordering of the markers. Genetic or radiation hybrid markers are used to anchor the contigs to the chromosomes. A minimal tiling path of clones may be selected for sequencing. FPC may be used with the two salient types of fingerprinting, which are agarose based and HICF (High Information Content Fingerprinting).
The mouse genome sequence
Authors: Jackson Ian J. 
Published: January 2005

Abstract
The mouse is the leading mammalian model organism for the study of genetics. Its genome consists of about 2500 Mb of DNA and contains about 30 000 genes, virtually all of which have close homologs in the human genome. Comparison of the mouse with other mammalian genomes indicates that it is not only the coding sequences of genes that have been maintained in evolution; putative conserved control elements can be identified by aligning multiple genomes. The DNA of the mouse (and rat) is accumulating changes at a much more rapid rate than the human genome. Base substitutions in neutral sequences have accumulated about twice as fast in the mouse when compared to humans, since their last common ancestor 75 million years ago. Furthermore, transposable elements have been more active in the rodent lineage, and there have been more chromosomal rearrangements that alter long‐range relationships between genes.
Eukaryotic parasite genome projects
Authors: Hall Neil 
Published: January 2005

Abstract

Genome sequence data is transforming the field of parasitology, and is proving to be a leading technology in the hunt for new drugs and vaccines for some of the most serious diseases affecting mankind. In this chapter, I will describe some of the key scientific contributions made by the genome projects and draw on some specific examples in protist parasites such as genetics in

Trypanosome brucei

, the discovery of polycistronic transcription

Leishmania major

, and the evolution of the apicoplast in

Plasmodium falciparum

.
Chlamydiae
Authors: Read Timothy D. 
Published: January 2005

Abstract
The chlamydiae are a group of obligate intracellular pathogens with a unique biphasic life cycle. The six genomes sequenced are approximately 1.05–1.2 Mb and show no signs of pathogenicity islands or other recent horizontal transfer events. There are about 750 genes conserved across all genomes, encoding core functions. Potential virulence determinants include type III secretion systems, toxins, variable surface proteins, and tryptophan biosynthesis proteins.
Comparative genomics of the ɛ‐proteobacterial human pathogens

H
elicobacter pylori

and

C
ampylobacter jejuni
Authors: Dorrell Nick , Brendan Wren 
Published: January 2005

Abstract

Helicobacter pylori

and

Campylobacter jejuni

are among the most common bacterial pathogens encountered by humans, but despite the prevalence and importance of the diseases caused by these organisms, they have only been recognized as human pathogens within the last 25 years. However, they are now among the most comprehensively studied organisms, due in no small part to the availability of complete genome sequences for both bacteria. Subsequent genomic studies have started to explain the genetic, ecological, and pathogenic similarities and differences between these two major human pathogens. Understanding the dynamic and complex interplay between these pathogens and the host will place the emphasis on converting this knowledge into appropriate intervention strategies to reduce the burden on human health.
FT‐ICR
Authors: Barrow Mark P. , Burkitt William I. , Derrick Peter J. 
Published: January 2005

AbstractFourier transform ion cyclotron resonance (FT‐ICR) mass spectrometry has become an increasingly significant technique within recent years. The inherently ultrahigh resolution and mass accuracy allow unequivocal assignments of elemental composition to be made for biomolecules. Structural elucidation can be conducted through tandem mass spectrometry experiments. With the advent of electrospray ionization (ESI), FT‐ICR mass spectrometry has become a powerful tool for the investigation of biological macromolecules, including aspects of noncovalent interactions.
Laser‐based microdissection approaches and applications
Authors: Banks Rosamonde E. 
Published: January 2005

AbstractThe analysis and interpretation of either physiological or pathological protein changes in tissue is difficult due to the cellular heterogeneity, with multiple cell types being present. In disease, the situation may be even more complex due to diseased cells being adjacent to normal cells, the presence of distinct microenvironments such as hypoxic areas, and additional infiltrating cells such as lymphocytes. Attempting to understand the biology or pathology of particular cells against such a heterogeneous background is therefore a challenge. Laser‐assisted microdissection systems have now been developed, which allow the enrichment of specific cell types for subsequent analysis. These systems have been reviewed, together with a consideration of some of the technical issues and examples of downstream proteomic applications.
Hybrid
MS
Authors: Bateman R. H. , Langridge J. I. 
Published: January 2005

Abstract
Tandem mass spectrometry, or MS/MS, is the preferred technology for many applications in which mass spectrometry plays a part. Tandem mass spectrometry allows selection and isolation of specific components in the presence of complex matrices and their subsequent identification and/or quantification. Hybrid MS instruments consist of two mass analyzers in series and a means for fragmenting ions. That means is most commonly that of promoting collision‐induced decomposition (CID) by subjecting ions to energetic collisions with gas molecules. In most hybrid MS instrumentation, the processes of mass selection, fragmentation, and product ion mass analysis take place sequentially in space. In some instances, fragmentation can take place in one of the mass analyzers wherein one or other of the processes take place sequentially in time. Different combinations of mass analyzers have different characteristics that make them more or less suited for certain applications. It is possible to combine most types of mass analyzer in almost any sequence, and numerous combinations have been constructed. A brief description is provided of those hybrid instruments that are most commonly used for studies in the life sciences; namely, the triple quadrupole, the quadrupole–ion trap (Q‐Trap), the ion trap–time‐of‐flight (Trap‐TOF), the time‐of‐flight–time‐of‐flight (TOF‐TOF), the quadrupole–orthogonal time‐of‐flight (Q‐TOF), the ion trap–orthogonal time‐of‐flight (Trap‐TOF), the quadrupole‐FTMS and, the ion trap–FTMS. For each instrument type, the principle applications are discussed.
Making nanocolumns and tips
Authors: Delahunty Claire , Yates John R. 
Published: January 2005

Abstract
This tutorial describes the construction of fritless nanocolumns and tips from 100‐µm microcapillary tubing. Protocols are given for pulling the tips using a commercial laser puller as well as for packing a single‐phase or multidimensional column. The nanocolumns described are for use in in‐line µLC separations and are typically coupled to an ESI source.
Probing protein function in cells usingCALI
Authors: Diefenbach Thomas J. , Jay Daniel G. 
Published: January 2005

AbstractChromophore‐assisted laser inactivation (CALI) is a method utilizing dye‐labeled antibodies combined with light of specific wavelengths for acute knockdown of protein function at the cellular and tissue level with high spatial and temporal resolution. In recent years, the techniques of CALI have evolved, although the goal of direct knockdown of the protein function remains the same. This article will examine the utility, applications, and derivations of CALI as a tool to probe in vitro and in vivo protein function.
Immunofluorescent labeling and fluorescent dyes
Authors: Watson Peter , Palmer Krysten J. , Stephens David J. 
Published: January 2005

AbstractThis article sets out to cover some of the key points to consider when processing living cells and tissues for immunofluorescence. We discuss approaches to fix and image cells following immunolabeling, including using high‐throughput screening technologies. We review the production and relative merits of different antibodies and compare different fluorophores, including recently developed reagents such as quantum dots. We also consider the use of recombinant antibody technology and the correlation of images obtained first by immunofluorescence microscopy at low resolution (e.g., confocal), and higher resolution ultrastructural analyses by electron microscopy.
Glycosylphosphatidylinositol anchors – a structural perspective
Authors: Mehlert Angela 
Published: January 2005

AbstractGPI anchors are found attached to many proteins in eukaryotes. The structural characterization of a GPI is challenging owing to the complex nature of the molecule. Certain techniques that take advantage of the unique nature of certain moieties within the GPIs have been used to analyze their structures. Techniques for labeling GPIs with either a radioactive or fluorescent tracer are described, along with a recent “proteomics” style of detecting GPI‐anchored proteins from Western blots.
Classification of proteins into families
Authors: Mulder Nicola J. , Apweiler Rolf 
Published: January 2005

AbstractFunctional annotation of proteins is vital for a thorough understanding of genomic systems, diseases, and pathogenesis. With the genome era in full swing, thousands of new sequences from genome sequencing projects are available, but they cannot be manually annotated. Reliable methods for automatic functional classification of proteins are being developed. The most useful tools use various methods for identifying motifs or domains found in previously characterized protein families. Protein families can be classified using two main approaches: sequence clustering and protein signatures. Once members of a protein family are discovered, inference of functional annotation to all members is possible. This chapter reviews the existing methods using these approaches and the major databases in the public domain that implement the methods.
Equivalog protein families in the
TIGRFAMs
database
Authors: Selengut Jeremy D. , Haft Daniel H. 
Published: January 2005

Abstract
An equivalog is a family of proteins conserved in function since their last common ancestor. This term differs from the term ortholog, which is not limited to groups with conserved function but is strictly limited to speciation events (and excludes horizontal gene transfers). Hidden Markov Models (HMMs) are mathematical constructs representing multiple sequence alignments. The TIGRFAMs database includes a large number of HMMs that represent equivalog families. The great utility of these models is that a sequence scoring higher than a threshold value versus an equivalog has a very high likelihood of being a member of the family and sharing the same function. Equivalog HMMs are useful in automatic genome annotation. The information that is manually attached to a gene by an annotator is instead attached to the equivalog HMM. This is then used to transfer the information automatically to the appropriate genes. Furthermore, groups of equivalog HMMs can be linked together to create computable objects representing proteins that act together in a biological process (such as a metabolic pathway). Such compound objects can be used in metabolic reconstruction and applied to genomic sequence data even prior to annotation.
Fundamentals of protein structure and function
Authors: Bradford James R. , Siepen Jennifer A. , Westhead David R. 
Published: January 2005

Abstract
This chapter describes the steps involved in the formation of three‐dimensional structure from amino acid sequence. Proteins have adapted their three‐dimensional structures to carry out metabolic and regulatory processes such as enzyme catalysis, molecular transport, signaling, the immune response, and gene expression. To understand the relationship between a protein's structure and function fully, knowledge of that protein's evolutionary history and its interactions is essential. Therefore, we describe the mechanisms by which proteins have evolved. We also describe how molecular recognition drives protein interactions and the types of interaction that take place.
X
‐ray crystallography
Authors: Firbank Susan 
Published: January 2005

Abstract
Since the late 1950s, X‐ray crystallography has been used to determine the structure of proteins with known functions. With the dawn of proteomics, protein‐structure determination is now being carried out in order to shed light upon proteins of unknown function, with the hope that knowledge of the structure itself will allow, or at least assist in, the identification of possible protein action. This article describes the stages of protein‐structure determination by X‐ray crystallography, the basic requirements and considerations at each step, and how crystallography can be applied and is being adapted to benefit the structural‐genomics community.
Spliced alignment
Authors: Huang Xiaoqiu 
Published: January 2005

AbstractWe first describe a dynamic programming algorithm for computing an optimal spliced alignment of a genomic sequence and a cDNA sequence. Then, we present a fast method for dealing with a large set of genomic sequences and a set of cDNA sequences. We also describe methods used in existing spliced alignment programs. We conclude with a discussion of future developments in this area.
Protein repeats
Authors: Perez‐Iratxeta Carolina , Andrade Miguel A. 
Published: January 2005

Abstract
More than 10% of all protein sequences contain a protein domain composed of units of similar structure, often of similar sequence, therefore arising by a process of duplication from an ancestral gene fragment. Structural and evolutionary constraints limit the length and structure of these repeats to a small number of categories. These domains composed of repeats are used mainly for protein binding and are more frequent in metazoan organisms than elsewhere. Low constraints in sequence allow high rates of sequence divergence between repeats, making their detection by sequence similarity difficult.
Sequence complexity of proteins and its significance in annotation
Authors: Eisenhaber Birgit , Eisenhaber Frank 
Published: January 2005

Abstract
If protein sequences are viewed as a string of letters representing amino acid types, the complexity of the text message can be evaluated by analyzing residue composition and repetitive occurrence of short motifs and also by applying entropy‐ or information‐like measures. Low complexity segments represent more than a quarter of the total length of proteins in databases and their relative amount tends to increase with the sequencing of eukaryote genomes. In contrast, only about 0.5% of the residues in structures of known globular domains are located in usually short stretches with strong compositional bias. Low complexity segments with bias toward hydrophobic residues or with a repetitive hydrophobic pattern are typically involved in fibrillar or membrane‐embedded protein structures. In contrast, the structure forming potential and the molecular function of low complexity regions with primarily polar residues remains insufficiently understood, although, for some of them, their mutational variation has already been implicated in pathological processes.
The
P
rotein
D
ata
B
ank (
PDB
) and the
W
orldwide
PDB
http://www.wwpdb.org
Authors: Berman Helen , Nakamura Haruki , Henrick Kim 
Published: January 2005

Abstract

The Protein Data Bank is the primary source of information on the 3D structure of biological macromolecules. The PDB is a rich source of structural information that holds significant promise for the pharmaceutical and biotechnology industries in the search for new drugs, and the efforts to understand the mechanism of disease. The PDB is managed by the wwPDB (
http://www.wwpdb.org
), and the wwPDB members enable science worldwide by providing resources to improve our understanding of structure‐function relationships in biological systems.
TAMBIS
: transparent access to multiple bioinformatics services
Authors: Stevens Robert , Paton Norman W. , Bechhofer Sean , Ng Gary , Peim Martin , Baker Patricia , Goble Carole , Brass Andy 
Published: January 2005

Abstract
Transparent Access to Multiple Bioinformatics Information Sources (TAMBIS) addresses the perennial problem of heterogeneity and distribution of bioinformatics resources in performing bioinformatics analyses. Asking questions of these resources usually requires multiple resources to be used and data transferred between those resources. A biologist using these resources needs much knowledge of which resources to use, where they are to be found, in which order they should be used, and how to overcome the heterogeneity between those resources. TAMBIS seeks to make this knowledge burden transparent by cap turing knowledge about molecular biology and bioinformatics tasks in an ontology. The TAMBIS ontology acts as a global schema over diverse resources and drives a query formulation interface offering a common language over those resources. High‐level, conceptual, source‐independent queries are rewritten to concrete query plans. As a result of its transparency, TAMBIS frees a biologist from needing informatics knowledge to concentrate upon the biological question.
Automatic concept identification in biomedical literature
Authors: Majoros William H. 
Published: January 2005

Abstract

While the potential benefits of automatically extracting useful knowledge from biomedical literature are seemingly many and great, nearly all of the techniques that have been considered for doing this rely on a central, nontrivial problem: that of unambiguously identifying the named entities that occur in a particular text. This problem has two parts: (1) identifying the precise boundaries of phrases in a text which refer to biomedical entities and (2) resolving those entity names to known concepts in a knowledge base such as an ontology. These two tasks represent the
syntactic
and
semantic
aspects of the problem of concept identification, and both are described in this article along with the currently known methods and their limitations.
Detecting protein homology usingNCBItools
Authors: Matten Wayne T. , McGinnis Scott D. 
Published: January 2005

AbstractThe National Center for Biotechnology Information (NCBI) processes more than 100 000 sequence similarity searches a day using the computer program, BLAST®– Basic Local Alignment Search Tool. A common use of BLAST is to locate sequences in the NCBI databases that are related to the query sequence. Various “flavors” of BLAST can also detect known conserved domains in the query sequence, find related sequences that contain a supplied pattern, and perform sensitive searches using automated construction of position‐specific scoring matrices. The results of precomputed BLAST searches are available for nearly all protein sequences housed at the NCBI. Similarly, solved protein structures are compared to identify structurally related proteins using the Vector Alignment Search Tool (VAST).
HiddenMarkov models and neural networks
Authors: Kremer Stefan C. , Baldi Pierre 
Published: January 2005

AbstractIn this contribution, we discuss the application of machine learning methods, particularly hidden Markov models and artificial neural networks, to bioinformatics tasks. We begin with a brief summary of the two paradigms as computational and learning systems and describe the nature of the problems to which these two approaches can be applied. Then, we give some examples of their application to bioinformatics, briefly discuss the strengths and weaknesses of these two approaches, and provide some avenues for further reading.
The
MATLAB
bioinformatics toolbox
Authors: Henson Robert , Cetto Lucio 
Published: January 2005

Abstract

MATLAB
®
(The MathWorks, Inc.) is a general‐purpose technical computing language and development environment that is widely used in scientific and engineering applications. The Bioinformatics Toolbox for MATLAB is a library of functions that adds bioinformatics capabilities to the MATLAB environment. This article describes the functions in the Bioinformatics Toolbox and gives an example of how these can be used for phylogenetic analysis of Human Immunodeficiency Virus (HIV) and Simian Immunodeficiency Virus (SIV) sequence data.
Inside Front Cover: An Ultraviolet Organic Thin‐Film Solid‐State Laser for Biomarker Applications (Adv. Mater. 1/2005)
Authors: Schneider D. , Rabe T. , Riedl T. , Dobbertin T. , Kröger M. , Becker E. , Johannes H.‐H. , Kowalsky W. , Weimann T. , Wang J. , Hinze P. , Gerhard A. , Stössel P. , Vestweber H. 
Published: January 2005

AbstractThin‐film organic solid‐state lasers operating in the ultraviolet wavelength region are fabricated using a novel spiro‐linked material as active organic layer in an optically pumped distributed feedback (DFB) structure in work reported by Riedl and co‐workers on p. 31. The laser wavelength is tunable between 377.7 nm and 395 nm, the shortest laser wavelength reported so far for thin‐film organic solid‐state lasers. The lasers' suitability for spectroscopic applications was tested by use as an excitation source for solutions containing the common fluorescent dyes Coumarin 6, Coumarin 152, and Rhodamine 6G.
Transition to pulsing flow in trickle‐bed reactors studied using MRI
Authors: Sederman A. J. , Gladden L. F. 
Published: January 2005

AbstractUltrafast magnetic resonance imaging (MRI) is used to provide two‐dimensional (2‐D) images of gas‐liquid distribution within trickle‐bed reactors with data acquisition times of 20 and 40 ms. Gas‐water, cocurrent downflow through a fixed bed of cylindrical porous pellets of length and dia. 3 mm, packed within a 43 mm internal dia. column, was studied in both the trickle‐ and pulsing‐flow regimes. Superficial gas velocities in the range 50–345 mm s−1 (0.06–0.42 kg m−2 s−1), and superficial liquid velocities in the range 0.4–13.3 mm s−1 (0.4–13.3 kg m−2 s−1) were used. MRI is used to investigate the stability of the gas‐liquid distribution in the trickle‐ and pulsing‐flow regimes. At the onset of the transition to pulsing flow, local pulsing, at the length‐scale of the size of the packing elements is observed within the bed. Increasing liquid velocity causes an increase in the number of these local pulses until a velocity is reached at which the system transforms to the rapidly‐changing gas‐liquid distribution typical of pulsing flow. © 2005 American Institute of Chemical Engineers AIChE J, 51: 615–621, 2005