bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteome profile of the MCF7 cancer cell line: a mass spectrometric evaluation
Authors: Sarvaiya Hetal A. , Yoon Jung H. , Lazar Iulia M. 
Published: September 2006

AbstractThe development of novel proteomic technologies that will enable the discovery of disease specific biomarkers is essential in the clinical setting to facilitate early diagnosis and increase survivability rates. We are reporting a shotgun two‐dimensional (2D) strong cationic exchange/reversed‐phase liquid chromatography/electrospray ionization tandem mass spectrometry (SCX/RPLC/ESI‐MS/MS) protocol for the analysis of proteomic constituents in cancerous cells. The MCF7 breast cancer cell line was chosen as a model system. A series of optimization steps were performed to improve the LC/MS experimental setup, sample preparation, data acquisition and database search protocols, and a data filtering strategy was developed to enable confident identification of a large number of proteins and potential biomarkers. This research has resulted in the identification of >2000 proteins using multiple filtering and p‐value sorting. Approximately 1600–1900 proteins had p < 0.001, and, of these, ∼60% were matched by ≥2 unique peptides. Alternatively, >99% of the proteins identified by ≥2 unique peptides had p < 0.001. When searching the data against a reversed database of proteins, the rate of false positive identifications was 0.1% at the peptide level and 0.4% at the protein level. The typical reproducibility in detecting overlapping proteins across replicate runs exceeded 90% for proteins matched by ≥2 unique peptides. According to their biological function, approximately 200 proteins were involved in cancer‐relevant cellular processes, and over 25 proteins were previously described in the literature as putative cancer biomarkers, as they were found to be differentially expressed between normal and cancerous cell states. Among these, biomarkers such PCNA, cathepsin D, E‐cadherin, 14‐3‐3‐sigma, antigen Ki‐67, TP53RK, and calreticulin were identified. These data were generated by subjecting to MS analysis ∼42 µg of sample, analyzing 16 SCX peptide fractions, and interpreting ∼55 000 MS2 spectra. Total MS time required for analysis was 40 h. Copyright © 2006 John Wiley & Sons, Ltd.
Benzyl ions from 1,1‐(2,2′‐dimethoxyphenyl)‐substituted 2‐methylpropanes under electron ionization
Authors: Bongiorno David , Ceraulo Leopoldo , Filizzola Felice , Fontana Gianfranco , Natoli Maria Concetta 
Published: September 2006

AbstractThe electron ionization (EI)‐induced fragmentations of a series of 1,1‐(2,2′‐dimethoxyphenyl)‐substituted 2‐methylpropanes (1–20) in both 70 eV and mass‐analyzed ion kinetic energy (MIKE) spectra have been investigated. The EI‐MS spectra of these compounds are characterized by the presence of abundant benzyl ions. These ions result from competitive hydrogen migration from the 2‐ and 2′‐methoxy groups on the carbenium center of the diphenylmethyl cations formed by benzylic cleavage of the molecular ions. The relative abundances of the benzyl ions arising from such competitive processes are discussed and rationalized. The steric effect of the 3‐ or 3′‐substituents is the main discriminating factor between the two competitive processes. The structural information, arising either from the 70 eV or the MIKE spectra, is discussed. Copyright © 2006 John Wiley & Sons, Ltd.
Quantitative analyses of indoloquinazoline alkaloids in Fructus Evodiae by high‐performance liquid chromatography with atmospheric pressure chemical ionization tandem mass spectrometry
Authors: Zhou Yan , Li Sheng‐Hong , Jiang Ren‐Wang , Cai Min , Liu Xin , Ding Li‐Sheng , Xu Hong‐Xi , But Paul Pui‐Hay , Shaw Pang‐Chui 
Published: September 2006

AbstractFructus Evodiae (Wuzhuyu), the fruits of Evodia rutaecarpa and related varieties, is widely used in traditional Chinese medicine. The bioactive constituents include the indoloquinazoline alkaloids rutaecarpine, evodiamine and dehydroevodiamine. A new assay based on high‐performance liquid chromatography/atmospheric pressure chemical ionization tandem mass spectrometry (HPLC/UV/APCI‐MS/MS) was developed for the measurement of the indoloquinazoline alkaloids in commercial Fructus Evodiae products. Initially, the MS/MS fragmentation pathways of indoloquinazoline alkaloids were investigated to identify fragment ions that might be useful for the sensitive and selective detection of trace indoloquinazoline alkaloids during LC/MS/MS. Then, quantitative MS analysis of five indoloquinazoline alkaloids in 12 commercial Fructus Evodiae products from different geographical sources was performed. Analyte recovery was in the range of 97.5–105.3% for all with relative standard deviations (RSDs) below 6%, the intra‐assay and inter‐assay RSDs were less than 7%, and good linear relationships were shown with correlation coefficients for the analytes exceeding 0.999. Therefore, this LC/MS/MS assay facilitated the rapid quantitative analysis of rutaecarpine, evodiamine, evodiamide, 14‐formyldihydrorutaecarpine and dehydroevodiamine in 12 commercial Fructus Evodiae products with excellent recovery, repeatability, accuracy and sensitivity. This method is simple and specific and can be used for identification and quality control of this traditional Chinese remedy. Copyright © 2006 John Wiley & Sons, Ltd.
Highly efficient enrichment and subsequent digestion of proteins in the mesoporous molecular sieve silicate SBA‐15 for matrix‐assisted laser desorption/ionization mass spectrometry with time‐of‐flight/time‐of‐flight analyzer peptide mapping
Authors: Zuo Chao , Yu Wenjia , Zhou Xufeng , Zhao Dongyuan , Yang Pengyuan 
Published: September 2006

AbstractBased on a previous study of protein digestion inside the nanoreactor channels of the mesoporous molecular sieve silicate SBA‐15 (Chem. Eur. J. 2005, 11: 5391), we have developed a highly efficient enrichment and subsequent tryptic digestion of proteins in SBA‐15 for matrix‐assisted laser desorption/ionization mass spectrometry with time‐of‐flight/time‐of‐flight analyzer (MALDI‐TOF/TOF) peptide mapping. The performance of the method is exemplified with myoglobin and cytochrome c. First, protein adsorption isotherms for two standard proteins with a range of initial concentration of proteins were investigated at room temperature. The results revealed that the kinetic adsorption rate of a protein within SBA‐15 was independent of initial protein concentration, and a 15‐min protein enrichment within SBA‐15 could be enough for protein identification in biological samples. It was noticed that no washing steps were needed to avoid protein loss due to desorption from the mesochannels into solution. Second, protein digestion inside the channels of SBA‐15 was also optimized. After adsorption of proteins into SBA‐15 in 15 min, the trypsin solution (pH 8) was directly added to the SBA‐15 beads with immobilized proteins by centrifugation, and then the digestion was performed for 15 min at 37°C. It was observed that a higher peptide sequence covering of 98% for myoglobin was obtained by MALDI‐TOF/TOF analysis, compared to in‐solution digestion. So the protein digestion inside SBA‐15 was proved to be significantly faster and yielded a better sequence coverage. The new procedure allows for rapid protein enrichment and digestion inside SBA‐15, and has great potential for protein analysis. Copyright © 2006 John Wiley & Sons, Ltd.
Ionization energies of LinX (n = 2, 3; X = Cl, Br, I) molecules
Authors: Veličković Suzana , Djordjević Vesna , Cvetićanin Jelena , Djustebek Jasmina , Veljković Miomir , Nešković Olivera 
Published: September 2006

AbstractMolecules of LinX (n = 2, 3; X = Cl, Br, I) were examined with a magnetic sector mass spectrometer by surface ionization using a triple rhenium filament impregnated with fullerene (C60). The ionization energies obtained for Li2Cl, Li2Br and Li2I molecules are 3.8 ± 0.1, 3.9 ± 0.1 and 4.0 ± 0.1 eV, respectively. The first ionization energy of Li2Cl is documented, while there are no literature data for the ionization energies of Li2Br and Li2I. The molecules of Li3Cl, Li3Br and Li3I were detected experimentally for the first time with ionization energies of 4.0 ± 0.1, 4.1 ± 0.1 and 4.1 ± 0.1 eV, respectively. The ionization energies of LinX (n = 2, 3; X = Cl, Br, I) are in correlation with the theoretical prediction of their hyperlithiated configurations. Copyright © 2006 John Wiley & Sons, Ltd.
Acetylcholine
Authors: Salvaterra Paul M 
Published: September 2006

Abstract
Acetylcholine is a neurotransmitter found in the nervous systems of all animals. It is involved in the control of functions as diverse as locomotion, digestion, cardiac rate, ‘fight and flight’ responses, secretion, learning and memory. Cholinergic dysfunction is associated with neuromuscular diseases such as myasthenia gravis and neurodegenerative disorders such as Alzheimer disease.
Arachidonic Acid
Authors: Bazan Nicolas G 
Published: September 2006

Abstract
Bioactive lipids have significant neurobiological actions such
as in the function of ion channels, receptors, neurotransmitter release,
synaptic plasticity and programmes of neuronal gene expression. As a result,
there is rapid increase in the size of the brain's free fatty acid
pool, particularly of arachidonic acid. Arachidonic acid is converted into a
variety of biologically active derivatives through cyclooxygenation and
lipoxygenation.
Receptor Binding in Drug Discovery
Authors: Jarnagin Kurt 
Published: September 2006

Abstract
Receptors have formed one of the most successful classes of drug targets, with receptor‐binding analysis being a central component of drug discovery for such targets. Receptor assays are easily established in robust formats, and the advent of high‐throughput screening equipment using robotics and fast, reliable assay technology has made receptor binding one of the most reliable drug discovery technologies available.
Invertebrate Neuropeptides
Authors: Nässel Dick R 
Published: September 2006

Abstract
Invertebrate neuropeptides are found in neurosecretory cells, interneurons and motor neurons, as well as in endocrine cells of the intestine and in glandular cells of non‐nervous tissue. Neuropeptides can act as neurohormones released into the circulation and/or as local neurohormones released in a paracrine fashion within the nervous system or at muscles or glands.
Axonal Transport and the Neuronal Cytoskeleton
Authors: Baas PW , Ahmad FJ 
Published: September 2006

Abstract
The neuronal cytoskeleton is a system of highly organized
polymers that provide architectural support for axons and dendrites, and also
provide railways for the transport of various classes of cytoplasmic
constituents. Molecular motor proteins provide the energy for the transport of
organelles along the cytoskeletal polymers and for the transport of the
polymers themselves.
Repetitive Action Potential Firing
Authors: Canavier CC , Baxter DA , Byrne JH 
Published: September 2006

Abstract
The biophysical basis of repetitive action potential firing can be understood in terms of the opposing positive and negative feedback processes that generate the repetitive activity. The relative timescales of these processes, which can include ion channel activation and inactivation as well as ion accumulation within a cell, are a key factor in the generation of repetitive single‐spike firing, intrinsic burst firing, and network burst firing.
Cyclic Nucleotide‐gated Ion Channels
Authors: Kramer Richard H 
Published: September 2006

Abstract
Cyclic nucleotide‐gated (CNG) channels are activated by cAMP or cGMP, crucial intracellular messenger molecules that regulate physiological activities in a wide variety of cells. In photoreceptors and olfactory neurons, CNG channels play an essential role in transducing sensory stimuli into electrical and chemical responses.
G Protein‐coupled Receptors
Authors: Bockaert Joël 
Published: September 2006

Abstract
Among membrane‐bound receptors that recognize regulatory
messages (hormones, neurotransmitters, photon, odours, etc.) the seven
transmembrane receptors coupled to G proteins are the most numerous (1%
of the genome in vertebrates). They belong to six families that share no
sequence similarities and are targets for more than 50% of the drugs
used in therapy.
Serotonin
Authors: Azmitia Efrain CG 
Published: September 2006

Abstract
In humans, serotonin is found in all tissues and body fluids. Serotonin can modify a variety of biological and behavioural functions,
including sex, aggression, appetite, locomotor activity, learning and memory,
sleep and hormonal secretion, and it is implicated in a variety of human
illnesses, such as depression, Alzheimer disease, attention deficit disorder,
anorexia nervosa, bulimia, autism and schizophrenia.
Serotonin Receptors
Authors: Hoyer Daniel 
Published: September 2006

Abstract
Serotonin (5‐hydroxytryptamine, 5‐HT) receptors are found both in the central and peripheral nervous system as well as in a number of non‐neuronal tissues in the gut, cardiovascular system and blood cells. 5‐HT has been implicated in the aetiology of a number of diseases such as migraine, hypertension, depression, anxiety, schizophrenia, eating disorders and vomiting. Many of the current treatments for such disorders interact with the 5‐HT system.
Sodium Channels
Authors: Stühmer Walter 
Published: September 2006

Abstract
Biological cells are surrounded by an electrical insulating membrane and have a negative intracellular potential. The energy required to generate this potential difference is efficiently obtained through metabolic energy, which establishes a gradient of ions across membranes. Nature has developed miniature batteries that use this gradient to generate a membrane potential in the form of molecules called ion channels. Sodium channels use the sodium ion gradient to generate positive membrane potentials. Furthermore, generation and conduction of the nervous impulse is based on ionic gradients, as is the generation of electrical discharges used by electric fish to stun their prey while hunting.
Neural Information Processing
Authors: Gabbiani Fabrizio , Midtgaard Jens 
Published: September 2006

Abstract
The central nervous system (CNS) is specialized in processing
information originating from a variety of internal and external sources. Its
basic information processing units are called nerve cells, or neurons. Within
the CNS, these elementary building blocks are densely interconnected in
hierarchical and parallel pathways. Information originating from sensory
neurons in contact with the body periphery is gradually transformed along
these pathways to generate specific actions through signals relayed by motor
neurons to peripheral organs.
Limbic System
Authors: Isaacson Robert L 
Published: September 2006

Abstract
The limbic system is a set of neural structures lying underneath
the neocortex and gathered around the deep medial portions of the forebrain.
The nuclei and primitive cortical areas of the limbic system are critically
important for the satisfaction of the essential needs of the individual,
including those of sustenance, procreation, self‐protection and the protection
of offspring.
Synaptic Vesicle Traffic
Authors: Dunlap David , Valtorta Flavia , Fesce Riccardo 
Published: September 2006

Abstract
Signals travel along nerve cell membranes as electrical impulses but are transmitted from one neuron to other neurons and/or effector cells by the release of neurotransmitter across a small intervening space (synaptic cleft). Such neurotransmitter is contained within synaptic vesicles that fuse with the plasma membrane when it depolarizes, to release their contents. The
vesicles are then rapidly retrieved and refurbished to sustain further synaptic activity.
Touch
Authors: Gardner Esther P 
Published: September 2006

Abstract
Touch is defined as direct contact between two physical bodies. In neuroscience, touch describes the special sense by which contact with the body of an organism is perceived in the conscious mind. Some touch involves an active motor component – stroking, tapping or pressing – whereby a part of the body is moved against another surface. The sensory and motor components of touch are intimately connected anatomically in the brain, and are important functionally in guiding behaviour.
Visual Cascade
Authors: Baehr Wolfgang , Liebman Paul 
Published: September 2006

Abstract

Vision begins in the outer segments of rod and cone photoreceptor cells when visual pigments absorb light photons and become activated. Some 10
4
to 10
5
cyclic nucleotide molecules are affected by activation of one rhodopsin molecule, so that signal generation requires enormous amplification through numerous molecules and mechanisms in the visual cascade.
Visual System
Authors: Van Hooser Stephen D , Nelson Sacha B 
Published: September 2006

Abstract
Humans and many other animals obtain much of their information about the world through their eyes. Patterns of light are transformed into nerve impulses in the retina and visual information is processed by nerve cells in the primary visual cortex. In the human brain, about one‐half of the cerebral cortex is dedicated in some way to the processing of visual information.
GABA
B
Receptors
Authors: Kaupmann Klemens , Froestl Wolfgang , Bettler Bernhard 
Published: September 2006

Abstract

γ‐Aminobutyric acid (GABA), the principal inhibitory neurotransmitter in the brain, signals through ionotropic (GABA
A/C
) and metabotropic (GABA
B
) receptor systems. GABA
B
receptors modulate synaptic transmission and are structurally related to the metabotropic glutamate receptors. The properties of the recently cloned GABA
B
R1a and ‐b receptors are compared to brain GABA
B
receptors.
Glutamatergic Synapses: Molecular Organization
Authors: Sheng Morgan , Lin Jerry W 
Published: September 2006

Abstract
Glutamatergic synapses, which comprise the majority of excitatory synapses in the mammalian central nervous system, function by presynaptic release of glutamate onto postsynaptic glutamate receptors. At the postsynaptic site, the molecular interactions between glutamate receptors and various intracellular proteins suggest an intimate relationship between synaptic structure and function, and may provide insight into the mechanisms of synaptic plasticity that underlie learning and memory.
Nicotinic Acetylcholine Receptors in Muscle
Authors: Hucho Ferdinand 
Published: September 2006

Abstract
Acetylcholine is the neurotransmitter carrying the excitatory signal at the neuromuscular endplate from the presynaptic to the postsynaptic side across the synaptic cleft. Together with acetylcholinesterase, the nicotinic acetylecholine receptor regulates the intensity and duration of the signal at the muscle.
Nicotinic Acetylcholine Receptors
Authors: Lindstrom Jon 
Published: September 2006

AbstractNicotinic acetylcholine receptors are receptors for the neurotransmitter acetylcholine in which binding of acetylcholine triggers the opening of a transmembrane channel through the centre of the receptor protein. Nicotinic receptors are part of a gene superfamily of transmitter gated ion channels that includes receptors for glycine and gamma amino butyric acid. Nicotinic receptors are distinct from muscarinic acetylcholine receptors, which are part of a gene superfamily of metabotropic G‐protein linked receptors.
Parkinson Disease
Authors: Hornykiewicz Oleh 
Published: September 2006

Abstract

Parkinson disease is a common, chronic, relentlessly progressive neurodegenerative basal ganglia disorder of movement, consequent to incessant loss of the dopamine‐containing neurons of the substantia nigra. Correction with
l
‐dihydroxyphenylalanine (
l
‐DOPA) of the severe brain dopamine deficit characteristic for Parkinson disease represents the most efficacious treatment of this disorder.
Cellular Neuromodulation
Authors: Wilson Gisela F 
Published: September 2006

Abstract
Neuromodulation confers context‐sensitive flexibility to the
signalling properties of neurons. The neuron is the central point of
integration for an array of extracellular signals, and the output of the
neuron, namely electrical activity and neurotransmitter release, is a function
of the biochemical integration process. Remarkably, the choice between
behaviours in different environmental or physiological contexts can often be
ascribed to the biochemical processing that occurs at the level of a single
neuron.
Memory in Fruit Flies and Nematodes
Authors: Tanchuk Tracy L , Galloway Jennifer A , Peters Kevin R , Rankin Catharine H 
Published: September 2006

Abstract

A change in the behaviour of an organism that results from that individual's exposure to stimuli/events in the environment.
Drosophila melanogaster
and
Caenorhabditis elegans
have been the focus of much research in the areas of learning and memory.
Neurotransmitter Receptors in the Postsynaptic Neuron
Authors: Stephenson F Anne , Hawkins Lynda M 
Published: September 2006

Abstract
The neurotransmitter receptor proteins are integral components
in the communication between adjacent cells of the nervous system, spanning
the width of the postsynaptic membrane and protruding into the synaptic cleft
and cell cytoplasm. They mediate the effects of neurotransmitters between
adjacent neurons.
Algae: Phylogeny and Evolution
Authors: Moestrup Øjvind 
Published: September 2006

Abstract
Ideas on the phylogeny and evolution of the algae are presently based on a combination of ultrastructural and molecular data. Following the discovery that the chloroplasts of eukaryotic algae arose after one or more symbiotic events, the term algae is now used as a colloquial term for primitive plants, including both prokaryotic and eukaryotic species.
Phycology
Authors: Lewin Ralph A , Borowitzka Michael A 
Published: September 2006

Abstract
The study of algae is generally called ‘phycology’, from the Greek word phykos meaning ‘seaweed’. Just what algae are is difficult to define, because they belong to many different and unrelated classes including both prokaryotic and eukaryotic representatives. Broadly speaking, the algae comprise all, mainly aquatic, plants that can use light energy to fix carbon dioxide and evolve oxygen, but which are not specialized land plants like mosses, ferns, coniferous trees and flowering plants. This is a negative definition, but it serves its purpose.
Alkaliphiles
Authors: Horikoshi Koki 
Published: September 2006

Abstract
Alkaliphiles grow optimally or very well at pH values above 9, often between 10 and 12, but cannot grow, or grow only slowly, at more neutral pH values. The enzymology, physiology, ecology, molecular biology and genetics of alkaliphiles as well as industrial applications of these microorganisms have been investigated extensively and several enzymes have been put to use on an industrial scale.
Bacterial Taxis
Authors: Armitage Judith P 
Published: September 2006

Abstract
Bacteria swim by rotating semirigid helical flagella. They can swim at speeds of many body lengths per second. They can sense a wide range of environmental signals; chemical changes, light, oxygen levels, changes in temperature and even the earth's magnetic field. By temporally sampling their environment they bias their overall direction of swimming to an optimum environment for growth.
Biogeochemical Cycles
Authors: Ehrlich Henry L , Oremland Ronald S , Zehr Jonathan P 
Published: September 2006

Abstract
The biosphere harbours large quantities of the elements essential to life, but the largest portion is tied up as minerals and sediments. Dead biomass and some of the nutrients immobilized in rocks and sediments are made available to living organisms through recyling (biodegradation) by microbes.