bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two‐dimensional gel electrophoresis (2‐DE)
Authors: McGregor Emma , Dunn Michael J. 
Published: January 2005

AbstractTwo‐dimensional gel electrophoresis (2‐DE) with immobilized pH gradients (IPGs) combined with protein identification by mass spectrometry (MS) is currently the method of choice in the majority of proteomic projects. In spite of the development of novel gel‐free technologies, 2‐DE remains the only technique that can be routinely applied to parallel quantitative expression profiling of large sets of complex protein mixtures such as whole‐cell lysates. 2‐DE involves the separation of solubilized proteins in the first dimension according to their charge properties (isoelectric point, pI) by isoelectric focusing (IEF) under denaturing conditions, followed by their separation in the second dimension by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS‐PAGE), according to their relative molecular mass (Mr). As the charge and mass properties of proteins are essentially independent parameters, this orthogonal combination of charge (pI) and size (Mr) separations results in the sample proteins being distributed across the two‐dimensional gel profile. 2‐DE can resolve more than 5000 proteins simultaneously (∼2000 proteins routinely), and can detect <1 ng of protein per spot. Furthermore, it delivers a map of intact proteins, which reflects changes in protein expression level, isoforms, or posttranslational modifications. In this article, we outline the various steps in the 2‐DE proteomics workflow, namely, sample preparation, solubilization, first‐dimension IEF with IPGs, second‐dimension SDS‐PAGE, protein detection and visualization, and protein identification by mass spectrometry. The various parameters that must be considered and optimized for successful 2‐DE separations of various types of sample are discussed.
Membrane‐anchored protein complexes
Authors: Stagljar Igor 
Published: January 2005

AbstractProteins associated with membranes total approximately one‐third of all proteins in a typical eukaryotic cell. Owing to their pivotal role in many cellular processes, their direct link to human disease, and their often extracellular accessibility toward drugs, an understanding of membrane protein function is desirable. However, the hydrophobic nature of membrane proteins often results in insoluble proteins, which makes protein isolation difficult and therefore hinders the determination of protein complex composition and protein function. This article provides a brief overview of the available yeast‐based interactive proteomic technologies for detecting protein interactions among membrane proteins.
Structure/function ofO‐glycans
Authors: Corfield Anthony P. 
Published: January 2005

AbstractO‐glycans linked to protein through anO‐glycosidic linkage betweenN‐acetylgalactosamine and serine or threonine form a large group of oligosaccharides present in a variety of proteins. This article describes the structural characteristics ofO‐glycans, prediction of their occurrence, and location in proteins. The biosynthetic pathways leading to their formation are presented, with examples for selected structures. Examples of the variety of biological functions associated withO‐glycans cover several major areas. These include their influence on protein conformation and stability; their roles in recognition phenomena, including cell proliferation and growth, glycoprotein trafficking and clearance, immunological recognition, selectin ligands, multivalent binding patterns in signal transduction, fertilization; and finally, their roles in the activity of signaling molecules.
O

‐Mannosylation
Authors: Endo Tamao 
Published: January 2005

Abstract

Mammalian cells produce many glycoproteins, that is, proteins with covalently attached sugar chains. The major glycans of glycoproteins can be classified into two groups,
N
‐glycan and
O
‐glycan, according to their glycan‐peptide linkage regions. Developments in glycobiology have revealed a new type of glycosidic linkage to the peptide portion, the
O
‐mannosyl linkage. This linkage used to be considered specific to yeast but has recently been found in mammals. Recently,
O
‐mannosylation has been shown to be important in muscle and brain development. This chapter describes the structure, biosynthesis, and biology of
O
‐mannosylation.
Target selection for structural genomics
Authors: Frishman Dmitrij 
Published: January 2005

Abstract
Bioinformatics analyses provide invaluable guidance in finding the shortest path to the ultimate goal of structural genomics – full understanding of structure–function relationships in proteins and exhaustive exploration of the sequence‐structure space. Advanced computational tools allow for predicting currently intractable target proteins and those that already have a known fold, grouping sequences into families, and propagating available structural information to a large number of protein sequences by means of homology modeling. Rational target selection is also a major cost‐saving factor because it prevents the international structural genomics consortia from duplicating effort and helps to identify the most economical set of target proteins. The main strategies in target selection include the systematic determination of protein structures from completely sequenced genomes of selected model organisms, elucidation of all fold types existing in nature, and exhaustive covering of the entire sequence space with structural information.
Integrative approaches to biology in the twenty‐first century
Authors: Cassman Marvin 
Published: January 2005

Abstract
Systems or integrative biology has become wildly popular in just the past few years. (The two terms will be used interchangeably to refer to the quantitative analysis of biological networks, at whatever level of organization.) The reason is clear – the volume of experimental data generated by genomics and other high‐throughput techniques pose both a problem and an opportunity. The problem is that the mass of data overwhelms the ability to intuitively understand it. The opportunity is that the data may be able to be manipulated in a manner that allows for an unprecedented understanding of the integrated behavior of biological systems. The mechanistic studies that have generated an amazing ability to decipher the molecular workings of individual biological molecules can now be linked to computational approaches, which will illuminate the functions of tightly coupled and highly regulated biological systems. At the end, the processes underlying health and disease will be understood in greater depth than has previously been possible. This article will discuss some of the questions currently facing investigators attempting to move this discipline forward, with a particular emphasis on the concepts of modularity and robustness.
Functional networks in mammalian cells
Authors: Xiong Yuguang , Iyengar Ravi 
Published: January 2005

AbstractThe basic functional unit of multicellular organism is the cell. Cells are complex systems that perform many required fundamental functions such as environmental adaptation, energy utilization, proliferation, and differentiation in a regulated manner. Even cell death is often a controlled process. Cellular functions involve numerous components participating in a variety of processes. A critical aspect for normal cell functionality is the rigorous control of all cellular processes that may take place at different cellular locations at different rates and at different times. Such regulation is achieved by a central intracellular signaling network that receives and processes signals from both extracellular and intracellular sources. The processed signals are then used to regulate the different cellular machines such that they can function co‐operatively to evoke complex physiological responses. In order to achieve reliable functionality, the cell has developed multiple redundant systems that can regulate the cellular machines. Additionally, the systems are arranged in a modular fashion such that disturbances do not substantially propagate between modules. This architecture leads to a complex system where both robustness and fragility are dynamically balanced.
Algorithmic challenges in mammalian whole‐genome assembly
Authors: Batzoglou Serafim 
Published: January 2005

AbstractSequencing of the human, mouse, and rat genomes was accomplished more quickly than had seemed feasible a mere eight years ago. The accelerating pace of sequencing has been made possible by the development of large‐scale laboratory operations, assembly algorithms, and less so by changes in the underlying sequencing technologies. This short review summarizes the computational challenges of whole‐genome assembly and the algorithms and software systems that enabled the recent advances in sequencing of mammalian genomes.
Genome signals and assembly
Authors: Kimmel Marek 
Published: January 2005

AbstractQuality of genome assembly depends to a large extent on the structure of genomic sequences, notably signals such as repeats, polymorphisms, and nucleotide asymmetry as well as structural motifs (seeStatistical signals) such as protein motifs (seeComputational motif discovery), gene promoters, enhancers and suppressors (seePromoter predictionandExon splicing enhancers), transcription factor binding sites, exon/intron splice junctions, regions of homology between sequences (seeIMPALA/RPS‐BLAST/PSI‐BLAST in protein sequence analysis), and protein docking sites. We address probabilistic and statistical issues, departing from modeling the genome assembly as a binomial/Poisson process and considerations of contig size. We then consider estimation of genome size, when repeats are involved, and estimation of the total gap length and of the stringency ratio. Then we consider bubble smoothing in the context of polymorphisms and empirical estimates of the impact of low GC contents on stringency. Finally, we refer to some special issues and examples.
Operon finding in bacteria
Authors: Ermolaeva Maria D. 
Published: January 2005

Abstract
A number of different strategies can be used to find operons and transcriptional units in bacterial and archaeal genomes. Some of these methods are purely computational: they rely only on the whole‐genome sequence and gene predictions and do not require additional experimental data. Two such methods are discussed in this article: one relies on the fact that the distances between genes are shorter within transcriptional units than between them, while the second one takes advantage of the observation that operons tend to be conserved between genomes. Before discussing these operon‐finding algorithms, we first present a purely computational approach for estimating the number of transcriptional units in the genome.
Computational motif discovery
Authors: Tompa Martin 
Published: January 2005

Abstract
The goal of computational motif discovery is to predict short subsequences of biological sequences that are good candidates to serve some biological function. This article focuses on the computational prediction of protein binding sites in nucleotide sequences. Three types of motif model are described: consensus, IUPAC, and weight matrix. Two types of application are described, statistical overrepresentation (in which the input sequences come from a single genome and are believed to contain instances of a single motif) and phylogenetic footprinting (in which the input sequences are homologous, typically one from each of multiple related genomes). Programs of each of these types are briefly described, with references to fuller descriptions and web sites where the programs are available.
DNA
/protein modeling
Authors: Lavery Richard 
Published: January 2005

Abstract
Considerable progress has been made in modeling both DNA and protein‐DNA complexes. The results help explain how specific base sequences can modify the properties of the double helix, influencing its structure and mechanical properties. These changes are important for the understanding of DNA recognition and packing. In the case of protein‐DNA complexes, modeling can help in identifying protein‐binding sites and in understanding the consequences of mutations in either of the interacting partners. Modeling can also be used to obtain structural and dynamic information from a variety of experimental data and will also contribute to extending the nanotechnological applications of the double helix.
Merging and comparing ontologies
Authors: Noy Natalya F. 
Published: January 2005

Abstract

The use of formal systems to define biomedical concepts and to represent and store biomedical knowledge has never been more important to the informatics community. In the past few years, ontologies have become the cornerstone of the information‐systems research. With the wider use of ontologies, the problem of
ontology management
began to arise: ontology developers and users must be able to find and compare existing ontologies or their parts, merge and align ontologies, compare different versions, and translate ontologies from one formalism to another. We describe various approaches to the ontology‐management tasks and the recent developments in defining a general ontology‐management framework.
Description logics:
OWL
and
DAML
+
OIL
Authors: Lord Phillip , Stevens Robert D. , Goble Carole A. , Horrocks Ian 
Published: January 2005

Abstract

In this chapter, we introduce Description Logics. These logics have achieved mainstream credibility as ontology languages by forming the basis of the W3C Web Ontology Language OWL, and its predecessor,
DAML
+
OIL
. From a case study, we explain how the rich expressivity of OWL can be used to model the complexities of biology and bioinformatics. We discuss automated reasoning technologies and the roles that they can play in supporting the process of building ontologies.
Support vector machine software
Authors: Noble William Stafford 
Published: January 2005

Abstract
The support vector machine has been used successfully to perform pattern recognition on many different types of biological data. However, applying the algorithm to a new problem domain is often nontrivial, because the algorithm offers many tunable parameters. Most important among these are the choice of the kernel function and the strength of the soft margin. This chapter describes the SVM algorithm and gives some practical advice for applying the algorithm to real biological data.
Cover Picture: Photolithographic Route to the Fabrication of Micro/Nanowires of III–V Semiconductors (Adv. Funct. Mater. 1/2005)
Authors: Sun Y. , Khang D.‐Y. , Hua F. , Hurley K. , Nuzzo R. G. , Rogers J. A. 
Published: January 2005

AbstractThe cover shows a patterned assembly of GaAs nanowires with their ends tethered to a bulk single‐crystal wafer as described on p. 30 by Rogers and co‐workers. These wires, which have triangular cross‐sections, were fabricated via a top–down process that combines photolithography and anisotropic chemical etching.Nano/microwires of semiconducting materials (e.g., GaAs and InP) with triangular cross‐sections can be fabricated by “top–down” approaches that combine lithography of high‐quality bulk wafers (using either traditional photolithography or phase‐shift optical lithography) with anisotropic chemical etching. This method gives good control over the lateral dimensions, lengths, and morphologies of free‐standing wires. The behaviors of many different resist layers and etching chemistries are presented. It is shown how wire arrays with highly ordered alignments can be transfer printed onto plastic substrates. This “top–down” approach provides a simple, effective, and versatile way of generating high‐quality single‐crystalline wires of various compound semiconductors. The resultant wires and wire arrays have potential applications in electronics, optics, optoelectronics, and sensing.
Cover Picture: Nanostructured Electrodes and the Low‐Temperature Performance of Li‐Ion Batteries (Adv. Mater. 1/2005)
Authors: Sides C. R. , Martin C. R. 
Published: January 2005

AbstractThe cover image shows a scanning electron micrograph of a commercially available track‐etch polycarbonate filter. This porous membrane serves as the host for the template‐synthesis of V2O5 nanowires of various diameters. Nanowires that are 70 nm in diameter are shown in the inset. Because V2O5 reversibly intercalates Li‐ions, it has potential for use as a cathode material in Li‐ion batteries. On p. 125, Sides and Martin report the use of these V2O5 nanowires as tools to investigate the poor low‐temperature performance of Li‐ion batteries.
Effect of thermohydraulic conditions on fouling of calcium oxalate and silica
Authors: Yu Hong , Sheikholeslami Roya , Doherty William O. S. 
Published: January 2005

AbstractCalcium oxalate (CaOx) and amorphous silica (SiO2) have been identified as the most intractable components of scale formed in sugar mill evaporators. Effects of thermohydraulic conditions such as surface superheat (5–15 K), fluid velocity (0.8–1.8 m/s), and bulk subcooling (20–30 K) on the composite fouling process of CaOx and SiO2 and deposit characteristics were investigated in a dynamic system that contained a fouling loop under subcooled nucleate flow boiling. The rate of composite fouling was found to increase with increasing superheat as a result of enhanced bubble activities at the boiling surface and increase in deposit strength. For a constant surface superheat, the fouling rate reached a maximum value at a subcooling of 25 K, but remained constant over a range of fluid velocity (≥1.1 m/s). This was attributed to the counterbalancing effects of deposit consolidation and hydrodynamic lift forces at the fouled tube wall. Scanning electron microscopy (SEM) analysis of composite deposits demonstrated the presence of two layers arising from deposit consolidation by CaOx in SiO2 matrix through microlayer evaporation during nucleate boiling. Chemical microanalysis by energy dispersive X‐ray spectroscopy (EDS) also indicated that the degree of deposit consolidation increased with surface superheat, fluid velocity, and bulk subcooling because of an increase in heat flux. © 2005 American Institute of Chemical Engineers AIChE J, 51: 641–648, 2005
Katalysatoren machen's möglich: Selektive C‐C‐Kupplungen mit nichtaktivierten Alkylhalogeniden
Authors: Frisch Anja C. , Beller Matthias 
Published: January 2005

AbstractIn den vergangenen Jahren hat das Interesse an metallkatalysierten Kreuzkupplungen mit Alkylhalogeniden stetig zugenommen, obwohl diese Reaktionen inhärent problematisch sind. Detaillierte mechanistische Untersuchungen brachten eine Reihe neuer Protokolle für die selektive Verknüpfung nichtaktivierter Alkylhalogenide mit β‐Wasserstoffatomen hervor. Unter milden Reaktionsbedingungen gelingen Kupplungen mit verschiedenen Organometallnucleophilen. In diesem Kurzaufsatz werden ausgewählte Beispiele vorgestellt, die dazu anregen sollen, das Potenzial dieser wichtigen metallkatalysierten Kupplungsmethoden in der organischen Synthese zu nutzen.
Modellierung der Lebensdauer und Abbaubarkeit organischer Verbindungen in Luft, Boden und Wasser
Authors: Schüürmann Gerrit 
Published: January 2005

AbstractDie Abbaubarkeit organischer Verbindungen in Luft, Boden und Wasser ist der wichtigste Faktor zur Beurteilung des Umweltschicksals chemischer Verbindungen und ihrer möglichen Schadenswirkung auf Mensch und Umwelt.
Neben dieser Priorisierung der Exposition und der für das Umweltschicksal wesentlichen Abbauparameter im Rahmen der Risikobewertung bei Chemikalien sind als alternative Sichtweisen die Betonung des Schadwirkungspotenzials der Verbindungen sowie die Betrachtung von Exposition und Wirkung als gleichrangige Komponenten für die Risikobewertung bei Umweltchemikalien vorhanden. Das Risiko ist hierbei durch eine (mathematische) Verknüpfung von Schadensausmaß (Schadwirkungspotenzial oder Gefahrenpotenzial) und zugehöriger Eintrittswahrscheinlichkeit (Exposition) definiert.
In der Troposphäre erfolgt der Abbau chemischer Verbindungen vor allen durch Reaktion mit OH‐Radikalen, in den Kompartimenten Boden und Wasser hingegen durch Bioabbau. Die Ziele dieses Berichts sind: 1) eine Übersicht über publizierte Modelle und ihre Evaluierung zu geben, 2) eine eigene Bewertung der allgemeinen Modelle zur Abschätzung des Abbaus organischer Chemikalien in der Troposphäre und ihres Bioabbaus durchzuführen und 3) Empfehlungen für zuverlässige Verfahren zur Abschätzung des Abbaubarkeit chemischer Verbindungen in der Umwelt zu geben. Ergebnis der umfangreichen Evaluierung ist, dass die Gruppenbeitragsmethode von Atkinson das genaueste Verfahren zur Abschätzung des Abbaus organischer Verbindungen in der Troposphäre ist. Obwohl dieses Verfahren einigen Beschränkungen unterliegt, scheint es die Methode der Wahl zu sein. Eine zukunftsträchtige Alternative ist die direkte Berechnung der Geschwindigkeitskonstanten der Reaktionen mit OH‐Radikalen, was heute schon beinahe routinemäßig möglich ist, und zwar mit einem Verfahren, das mithilfe semiempirischer Energiehyperflächen die Geschwindigkeitskonstanten mit einer maximalen Abweichung von ihren experimentellen Werten um den Faktor 2 liefert. Für die Abschätzung des vollständigen Bioabbaus organischer Verbindungen haben sich als beste Verfahren ein PLS‐Modell (PLS=partial least squares, partielle Regression) und ein Satz von sieben Bioabbau‐Regeln erwiesen. Allerdings wird empfohlen, zur Abschätzung des Bioabbaus alle vier untersuchten Modelle parallel einzusetzen. Sofern deren Vorhersagen übereinstimmen, kann die entsprechende Prognose als recht zuverlässig angesehen werden.
Im englischen Original wird die Prognose bei Übereinstimmung aller vier Modelle als “very reliable” beschrieben.
Dithiol Proteins as Guardians of the Intracellular Redox Milieu in Parasites: Old and New Drug Targets in Trypanosomes and Malaria‐Causing Plasmodia
Authors: Krauth‐Siegel R. Luise , Bauer Holger , Schirmer R. Heiner 
Published: January 2005

AbstractParasitic diseases such as sleeping sickness, Chagas' heart disease, and malaria are major health problems in poverty‐stricken areas. Antiparasitic drugs that are not only active but also affordable and readily available are urgently required. One approach to finding new drugs and rediscovering old ones is based on enzyme inhibitors that paralyze antioxidant systems in the pathogens. These antioxidant ensembles are essential to the parasites as they are attacked in the human host by strong oxidants such as peroxynitrite, hypochlorite, and H2O2. The pathogen‐protecting system consists of some 20 thiol and dithiol proteins, which buffer the intraparasitic redox milieu at a potential of −250 mV. In trypanosomes and leishmania the network is centered around the unique dithiol trypanothione (N1,N8‐bis(glutathionyl)spermidine). In contrast, malaria parasites have a more conservative dual antioxidative system based on glutathione and thioredoxin. Inhibitors of antioxidant enzymes such as trypanothione reductase are, indeed, parasiticidal but they can also delay or prevent resistance against a number of other antiparasitic drugs.
Catalysts for Cross‐Coupling Reactions with Non‐activated Alkyl Halides
Authors: Frisch Anja C. , Beller Matthias 
Published: January 2005

AbstractDespite the problems inherent to metal‐catalyzed cross‐coupling reactions with alkyl halides, these reactions have become increasingly important during the last few years. Detailed mechanistic investigations have led to a variety of novel procedures for the selective cross‐coupling of non‐activated alkyl halides bearing β hydrogen atoms with a variety of organometallic nucleophiles under mild reaction conditions. This Minireview highlights selected examples of metal‐catalyzed coupling methods and is intended to encourage chemists to exploit the potential of these approaches in organic synthesis.