bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amino Acid Substitutions: Effects on Protein Stability
Authors: Weng Zhiping , DeLisi Charles 
Published: September 2006

Abstract
The ability of a protein to function in its biochemical role(s) is determined by its geometry, which in turn is determined by the amino acid sequence and the environment. Amino acid mutations affect the thermodynamics of folding and their effects can be investigated experimentally by such techniques as site‐specific mutation, random point mutations and shuffling.
Protein Folding: Overview of Pathways
Authors: Wedemeyer William J , Scheraga Harold A 
Published: September 2006

AbstractMost proteins can function only if they are folded – i.e. if they have adopted a specific, stable tertiary structure. The ‘protein folding problem’ is to determine how and why the initially unstructured protein converges to this native structure. A typical sequence of structural changes during the folding of a protein molecule is referred to as a folding pathway.
Chaperonins
Authors: Consalvi Valerio , Chiaraluce Roberta 
Published: September 2006

AbstractThe protein folding problem is the production of the native, active conformation from the primary sequence information.In vivo, in the cytosolic environment, acquisition of the native conformation is on competition with proteolytic degradation and/or intracellular precipitation. Chaperone proteins are responsible for assistance during the process of finding the native fold, and these key components of the cellular machinery occur ubiquitously through archaea, bacteria and eukarya.
Genome, Proteome, and the Quest for a Full Structure–Function Description of an Organism
Authors: Hung Li‐Wei , Kim Sung‐Hou 
Published: September 2006

Abstract
Using sequencing techniques developed in the 1990s, the genome projects have now successfully identified all the genes in several organisms encrypted in a four‐letter alphabet. The gene products – proteins and RNAs coded by the genes – are the actual nuts and bolts of a living organism and the elucidation of their function and how they interact to sustain life remains one of the biggest challenges of the twenty‐first century.
Protein Structure Classification
Authors: Pearl Frances MG , Orengo Christine A , Thornton Janet M 
Published: September 2006

Abstract
To understand and map the universe of protein structures, it is necessary to collate, annotate and classify these structures in a rational scheme. The different approaches that have been taken to tackle this problem include the identification of protein domains, phylogenetic and phenetic classification, and hierarchical and nearest‐neighbour clustering. Powerful new sequence searching methods enable structural assignments to be allocated to genomic data.
Circular Dichroism: Studies of Proteins
Authors: Price Nicholas C 
Published: September 2006

Abstract
Circular dichroism is the differential absorption of the left‐ and right‐circularly polarized components of plane‐polarized electromagnetic radiation. It can provide structural and dynamic information about biological macromolecules, particularly proteins; although it cannot provide the high‐resolution structural data available from X‐ray crystallography or nuclear magnetic resonance, its speed and convenience make it the technique of choice in many applications.
Low‐angle Scattering of Neutrons and X‐rays
Authors: Trewhella Jill 
Published: September 2006

Abstract
Low‐angle scattering of X‐rays and neutrons provides information about the structures of proteins and DNA in solution, domain interactions within proteins, and protein–protein and protein–DNA interactions within their functional complexes. Recent advances in synchrotron sources and instrumentation have made possible low‐angle scattering studies of time‐dependent changes in protein structure.
ATP‐binding Motifs
Authors: Matte Allan , Delbaere Louis TJ 
Published: September 2006

Abstract
Proteins bind ATP with the use of a variety of motifs, the most common being the P loop that interacts with phosphoryl groups. There are a few sequence specific motifs that recognize adenine/adenosine but there is no single fingerprint motif because main‐chain protein contacts are usually more important here than side‐chain contacts.
Immunoglobulin Fold: Structures of Proteins in the Immunoglobulin Superfamily
Authors: Gelfand Israel M , Chothia Cyrus , Kister Alexander E 
Published: September 2006

Abstract
Proteins of the immunoglobulin fold are built of homologous domains of approximately 100 residues and with a structure formed by two β sheets packed face to face. Functions of the proteins are mainly in the immune system, cell–cell recognition or in the structural organization and regulation of muscle.
EF–hand Calcium‐binding Proteins
Authors: Nelson Melanie R , Chazin Walter J 
Published: September 2006

AbstractCalcium and the proteins that bind to it play important roles in normal physiological processes and have been implicated in a variety of disease states. The importance of Ca2+is due mainly to its role as a second messenger in signal transduction. The Ca2+signal is mediated and controlled by many proteins in the cell, the majority of which belong to the EF‐hand superfamily of calcium‐binding proteins.
Chlorarachniophytes
Authors: McFadden Geoffrey I 
Published: September 2006

Abstract
Chlorarachniophytes are unicellular marine algae with green chloroplasts surrounded by four membranes. Chloroplasts were acquired by secondary endosymbiosis of a green alga. The green algal endosymbiont is drastically reduced. The endosymbiont nucleus (nucleomorph) is the smallest known eukaryotic nucleus and is estimated to contain only 300 genes.
History of Plant Sciences
Authors: Browne Janet 
Published: September 2006

Abstract
The study of plants has played a significant, if sometimes undervalued, role in history. Plants have been important in science, medicine and economic affairs since Antiquity. The herbal tradition dominated investigations until the Renaissance after which it ran alongside developing areas of expertise in classification and physiology. In the eighteenth century, plant sciences became significant in geographical exploration and in general culture. Nineteenth‐century botanists used plants for investigating cell theory and early genetics as well as in evolutionary biology.
History of Classical Genetics
Authors: Harman Oren S 
Published: September 2006

Abstract
Classical genetics has its origin in the 1850s and 1860s, when the Moravian monk Gregor Mendel attempted to formalize the rules of inheritance governing plant hybridization. When Mendel's laws were rediscovered in 1900, breeding experiments were wedded to cytological observation of chromosomes in the nucleus of organisms – most notably in the fruit fly – and classical genetics was born, culminating towards mid‐century in models of what genes do, and what they are made of.
Nuclear Magnetic Resonance (
NMR
) Spectroscopy in the Study of Whole‐animal Metabolism
Authors: Gillies Robert J , Raghunand Natarajan 
Published: September 2006

Abstract
NMR‐active isotopes are present in living systems and, because the radiofrequency of nuclear magnetic resonance experiments is non‐ionizing, NMR signals can be obtained noninvasively and nondestructively from whole living organisms.
Mass Spectrometry: Analysis of Two‐dimensional Protein Gels
Authors: Lim Hanjo , Yates John R 
Published: September 2006

Abstract
Matrix‐assisted laser desorption/ionization mass spectrometry and electrospray tandem mass spectrometry, coupled with liquid chromatography, enable high‐throughput protein identification and further characterization, such as post‐translational modification, of proteins, after initial separation by two‐dimensional gel electrophoresis.
p
H
and Buffers
Authors: Segel Irwin H , Segel Leigh D 
Published: September 2006

Abstract
Many biomolecules possess weakly acidic or weakly basic groups whose ionization state can affect both biological function and stability, and many biological processes, such as oxidation–reduction reactions, produce or consume hydrogen ions. The extents of the reactions and the rates at which they proceed depend on the acidity of the reaction environment. Buffers are used to maintain a constant hydrogen ion activity.
Protein Quaternary Structure: Subunit–Subunit Interactions
Authors: Jones Susan , Thornton Janet M 
Published: September 2006

Abstract
The quaternary structure of proteins is the highest level of structural organization observed in these macromolecules. The multimeric proteins that result from quaternary structure formation involve the association of protein subunits through hydrophobic and electrostatic interactions. Protein quaternary structure has important implications for protein folding and function.
Watson–Crick Base Pairs
Authors: Marky Luis A , Garcia Angel 
Published: September 2006

Abstract
Watson–Crick base pairs are crucial in the formation of double helical DNA and in the storage of genetic information. They comprise two of the most common geometries involving the pairing of dA with dT and dG with dC through the formation of two and three hydrogen bonds, respectively. The complementarity of the anti‐parallel strands forming a double helix is crucial in DNA replication since the complementary strand is synthesized by adding the Watson–Crick complementary bases of the parent strand. The hybridization of DNA or DNA–RNA strands is widely used in biotechnology and molecular biology for multiple purposes.
Base Pairing inDNA: Unusual Patterns
Authors: Gmeiner William H , Walberer Bernhard J 
Published: September 2006

AbstractWatson–Crick base pairs comprise just two of 44 reasonable base pairing geometries involving the four common deoxyribonucleotides (dA, dC, dG, dT) in either their neutral or protonated forms. Most of the 42 non‐Watson–Crick base pairs have been observed experimentally in DNA. Although these unusual base pairs are difficult to detectin vivo, unusual base pairing may be significant for the biological functions of DNA.
RNA Structure: Pseudoknots
Authors: Gultyaev Alexander P , Pleij Cornelis WA , Westhof Eric 
Published: September 2006

Abstract
An RNA pseudoknot results from Watson–Crick base pairing interactions of a single‐stranded segment, occurring between two paired sequence fragments, with a complementary sequence that is not located between the paired fragments. RNA pseudoknots adopt different folding topologies and are an essential part of various functional RNA molecules.
Protein–Nucleic Acid Interaction: Major Groove Recognition Determinants
Authors: Xiong Yong , Sundaralingam Muttaiya 
Published: September 2006

Abstract
Protein–nucleic acid interactions play a crucial role in central biological processes. It is known that the most common binding element of proteins is an α helix and the primary binding site on DNA is in the major groove. Some general rules of the α helix binding to the DNA major groove have been derived, but there is no general code (one‐to‐one correspondence) for recognition.
Nucleic Acids: Subtractive Hybridization
Authors: Byers Richard J , Hoyland Judith A , Freemont Anthony J 
Published: September 2006

Abstract
Cells can be characterized phenotypically by demonstrating expressed proteins or messenger RNA. ‘Subtracting’ the gene expression profile of one cell from that of a different cell eliminates the signal from common shared ‘housekeeping’ genes and allows the functional gene expression profile of one cell to be defined. Subtractive hybridization is one of the major methods for achieving this.
Polymerase Chain Reaction (PCR): Specialized Reactions
Authors: Tsirka Stella E , Frohman Michael A 
Published: September 2006

AbstractThe polymerase chain reaction is a technique that rapidly amplifies selected subsets of DNA or complementary DNA from initially complex biological mixtures. The efficiency of amplification or the sequence of the amplified material can then be examined for any of many purposes, including genotyping or the characterization of new genes, gene expression patterns, mutations or polymorphisms.
Stream and River Community Structure
Authors: Alexander Laurie C , Palmer Margaret A 
Published: September 2006

Abstract
Streams and rivers are inhabited by diverse communities of fish, insects, crustaceans and other organisms that have adapted to the physical and chemical conditions found in running water environments. The assemblage of species found in any particular stream is not random: it is determined by many current and historical factors, including regional environmental conditions, species interactions, evolutionary processes and human activities. All of these factors interact in complex ways to create the observed species diversity, abundance and composition in stream and river communities.
Tropical Forests
Authors: Thomas Sean C , Baltzer Jennifer L 
Published: September 2006

AbstractTropical forests, while occupying only one‐tenth of the world's land area, are disproportionately important in terms of global biogeochemical cycles and as home to more than half of the world's species. Research on these most complex of ecological systems has focused on mechanisms for the maintenance of high diversity, and forest responses to fragmentation, logging, and other human impacts.
Mediterranean Ecosystems
Authors: Joffre Richard , Rambal Serge 
Published: September 2006

AbstractMediterranean regions are defined by their unique climate, which is characterized by a hot drought period in summer and cool wet period in winter. They partly cover the Mediterranean Basin, California, southwestern and southern Australia, central Chile and southern Africa. Mediterranean‐type ecosystems present strong similarities concerning vegetation types and functioning, as well as land‐use patterns and general appearance of the landscape.
Photosynthesis: Ecology
Authors: Johnson Giles 
Published: September 2006

Abstract
While most plants depend directly on photosynthesis for energy, their ability to capture light energy and grow will be affected by many other environmental factors, including water supply, nutrients and temperature. Various adaptations of photosynthesis exist that allow plants to tolerate extreme environmental conditions. Ultimately, the overall net photosynthetic rate of ecosystems has a major impact on the global carbon budget.
Biogeographical Regions
Authors: Huggett Richard 
Published: September 2006

Abstract
Species are not uniformly distributed over the land surface. Fauna and flora display regional differences. The largest regions of animals and plants are biogeographical regions, each bearing a distinctive fauna and flora. Some families and even some orders of animals are endemic to particular biogeographical regions. Other families are shared by two or more regions. A few families are cosmopolitan, being found in all biogeographical regions.
Agricultural Systems: Ecology
Authors: Edwards Clive A 
Published: September 2006

Abstract
Agricultural systems have four main inputs, cultivations, nutrients, crops and pest management, all of which are interlinked and influenced by each other. They are affected by land and water and energy availability and soil erosion. To achieve long‐term agricultural sustainability, the need for fossil‐fuel‐based inputs should be minimized and the biological and ecological inputs maximized.
Theoretical Ecology
Authors: Lundberg Per 
Published: September 2006

AbstractTheoretical ecology is the study of the fundamental forces and processes determining the course of evolution and how ecological systems are assembled and maintained. Theoretical ecology therefore typically encompasses almost all levels of biological organization (from genes to ecosystems). Theoretical ecology progresses under the common scientific attitude that we indeed are able to reveal generalities and law‐like behaviours of nature despite the overwhelming diversity of life on Earth.
Satellite Remote Sensing of the Environment
Authors: Bamber Jonathan L 
Published: September 2006

Abstract
Remote sensing (RS) is the derivation of information about an object that is not in direct contact with the observer. It is achieved by detecting changes in the energy field caused by the object. This could be a perturbation to the electromagnetic (EM), acoustic (seismology), gravity or magnetic field. In general, when related to satellite observations of the Earth, it involves the use of EM radiation.
Cellulose: Biogenesis and Degradation
Authors: Stone Bruce 
Published: September 2006

Abstract
Cellulose is synthesized by plasma membrane‐bound cellulose synthase complexes found in bacteria, slime moulds, algae and embryophytes. Cellulases produced by many bacteria, protistans and fungi break down cellulose to soluble saccharides for use in growth and energy production. Plant pathogens use cellulases to gain access to the contents of plant cells by digesting their walls, and in embryophytes cellulases have a role in cell wall development and differentiation.
Sperm–Egg Interactions: Sperm–Egg Binding in Invertebrates
Authors: Carroll David J 
Published: September 2006

Abstract
During fertilization, spermatozoa undergo a series of responses (including chemoattraction and the acrosome reaction) to egg‐derived factors before they contact the egg proper. Specific cell surface proteins direct the interactions between the sperm and the egg that lead to fusion and egg activation.
Chromatin Remodelling and Histone Modification in Transcription Regulation
Authors: Urnov Fyodor D , Wolffe Alan P 
Published: September 2006

Abstract
The eukaryotic genome is assembled into chromatin, localized alterations of which are a major feature of gene control pathways. A wide variety of dedicated enzymatic complexes are targeted by particular transcriptional regulators to specific loci in the genome and remodel the structure of chromatin via energy‐dependent disruption of histone–DNA contacts and covalent modification of histones, both with major regulatory consequences.
Lung Development
Authors: Malpel Sarah , Cardoso Wellington V 
Published: September 2006

AbstractLung morphogenesis and differentiation result from activation of a complex network of signalling molecules in epithelial and mesenchymal cells. Regional expression of these signals along the developing respiratory system determines the pattern of branching of the airways and the appearance of the distinct cell types that characterize the tracheobronchial tree and the alveoli.
Predation (Including Parasites and Disease) and Herbivory
Authors: Hartvigsen Gregg 
Published: September 2006

Abstract
Organisms generally fall into two broad categories: either they are enemies or they are victims. Predation, parasitism, diseases, and herbivory all constitute ecological interactions that involve both enemies and victims. Predation is the act of an animal (enemy) capturing, killing, and consuming prey (victim). Parasites and diseases (or the agents which cause some bodily degradation) vary in their effects on victims from hardly noticeable to causing death. Finally, herbivory is that act of an animal consuming a plant. The effect of herbivory, like the effect of parasites and diseases, may be relatively minor or result in the death of the plant.
Dinosaur Feeding
Authors: Norman David B 
Published: September 2006

Abstract

Most dinosaurs can be relatively easily divided into those that were ‘classic’ carnivores like
Tyrannosaurus rex
or those that were
Diplodocus–Stegosaurus–Triceratops
style herbivores. However, a number of dinosaurs cannot be so easily categorized and therefore challenge our understanding of their likely feeding behaviours; for these latter creatures a more deductive approach must be adopted.
Molecular Farming in Plants
Authors: Biemelt Sophia , Sonnewald Uwe 
Published: September 2006

Abstract
The commonly used term ‘molecular farming’ describes the large‐scale production of valuable proteins in transgenic plants, including antibodies, vaccines, other pharmaceuticals and industrial proteins. Compared to traditionally used systems such as microbial cultures, plants offer many advantages with respect to economy, quality and safety, although constraints concerning protein yield and public acceptance must be overcome before the plant's full potential can be exploited.
Mammalian Pheromones
Authors: Fadool Debra Ann 
Published: September 2006

AbstractPheromones are a vehicle for chemical communication in vertebrates and serve to relay information important for reproduction, mate selection, species and gender identification and social status. Activation of cellular signalling cascades in the vomeronasal organ combined with hormonal changes mediating reproduction are driven by pheromones that must be transduced from an external chemical message into an electrical signal read by the central nervous system.
Stem Cells and Treatment of Neurodegenerative Disorders
Authors: Limke Tobi L , Rao Mahendra S 
Published: September 2006

Abstract
Cell‐based therapy using neural stem and progenitor cells offers great hope for treating neurodegenerative diseases, including Parkinson and Huntington diseases. Therapeutic strategies include cell replacement through transplantation of exogenous cells, cell replacement through mobilization of endogenous cells and delivery of therapeutic agents through transplantation of genetically engineered cells.
Patch‐clamp Technique
Authors: Hamill Owen P 
Published: September 2006

Abstract
The patch‐clamp technique enables the measurement of single membrane ion channel currents that underlie a wide variety of electrical and ionic signalling mechanisms in living cells. Biophysically, it provides the unique opportunity to follow in real time the conformational transitions of single membrane channel proteins with microsecond resolution and can be used as a functional membrane protein assay that is far more sensitive than traditional methods.
Regeneration of Functional Neuronal Connections
Authors: Schwab Martin E , Buchli Anita 
Published: September 2006

Abstract
Major differences exist in the molecular processes of nerve fibre regeneration in peripheral nerves and the central nervous system (CNS: brain and spinal cord) of higher animals and humans that allow spontaneous functional recovery to occur only in the peripheral nervous system. Some of the mechanisms blocking fibre regeneration in the CNS can now be experimentally influenced in animal models leading to improved recovery after spinal cord injury or stroke.
National Institutes of Health (NIH)
Authors: Harden Victoria A , Hannaway Caroline 
Published: September 2006

Abstract
The National Institutes of Health (NIH), founded in 1887, is the United States federal government's principal agency for the support of medical research both at its campus in Bethesda, Maryland, and through grants and contracts awarded to biomedical research scientists at institutions across the United States, and, to a more limited extent, in other countries. Its mission is science in pursuit of fundamental knowledge about the nature and behaviour of living systems and the application of that knowledge to extend healthy life and reduce the burdens of illness and disability.
Laboratory of Molecular Biology (LMB)
Authors: Perutz Max F 
Published: September 2006

Abstract
The Laboratory opened in 1962 in Cambridge, UK. Its goal is to interpret biological phenomena at the molecular level by a wide range of studies on the structure of proteins, nucleic acids, membranes, organelles and viruses, and by research on the mechanisms and control of gene expression and the three‐dimensional organization of cells.
Rockefeller Foundation: Biomedical and Life Sciences Offshoots
Authors: Abir‐Am Pnina G 
Published: September 2006

Abstract
Established in 1913 in New York City, New York, USA, the Rockefeller Foundation was the most influential philanthropic foundation sponsoring the biomedical and life sciences in the first half of the twentieth century. It emerged as a key policy maker in steering the course of biological progress as part of a global strategy to promote social stability.