X-ray detection by the olfactory system: ozone as a masking odorant.

The technique of masking was used to test the hypothesis that x-ray detection is mediated by an odorant produced in irradiated air. Rats conditioned to cease licking during exposure to x-ray (conditioned suppression) did not display this conditioned response in the presence of ozone and strong volatile oxidants.

Plant "primary perception": electrophysiological unresponsiveness to brine shrimp killing.

A test of the "primary perception" hypothesis proposed by Backster in 1968 was made by recording electrical activity from the leaves of Philodendra scandentia while randomly ejecting the contents of micropipettes filled with brine shrimp or distilled water into boiling water. Test conditions conformed to those published by Backster or communicated in personal exchanges. Data were analysed from five experiments, in each of which recordings were made from four plants in the presence of three brine shrimp killings and two control water ejections. Inspection of the data and analysis by two statistical methods revealed no relationship between brine shrimp killing and electrical "responsiveness" of philodendron.

High-throughput mass spectrometric discovery of protein post-translational modifications.

The availability of genome sequences, affordable mass spectrometers and high-resolution two-dimensional gels has made possible the identification of hundreds of proteins from many organisms by peptide mass fingerprinting. However, little attention has been paid to how information generated by these means can be utilised for detailed protein characterisation. Here we present an approach for the systematic characterisation of proteins using mass spectrometry and a software tool FindMod. This tool, available on the internet at http://www.expasy.ch/sprot/findmod.html , examines peptide mass fingerprinting data for mass differences between empirical and theoretical peptides. Where mass differences correspond to a post-translational modification, intelligent rules are applied to predict the amino acids in the peptide, if any, that might carry the modification. FindMod rules were constructed by examining 5153 incidences of post-translational modifications documented in the SWISS-PROT database, and for the 22 post-translational modifications currently considered (acetylation, amidation, biotinylation, C-mannosylation, deamidation, flavinylation, farnesylation, formylation, geranyl-geranylation, gamma-carboxyglutamic acids, hydroxylation, lipoylation, methylation, myristoylation, N -acyl diglyceride (tripalmitate), O-GlcNAc, palmitoylation, phosphorylation, pyridoxal phosphate, phospho-pantetheine, pyrrolidone carboxylic acid, sulphation) a total of 29 different rules were made. These consider which amino acids can carry a modification, whether the modification occurs on N-terminal, C-terminal or internal amino acids, and the type of organisms on which the modification can be found. We illustrate the utility of the approach with proteins from 2-D gels of Escherichia coli and sheep wool, where post-translational modifications predicted by FindMod were confirmed by MALDI post-source decay peptide fragmentation. As the approach is amenable to automation, it presents a potentially large-scale means of protein characterisation in proteome projects.

Protein identification with N and C-terminal sequence tags in proteome projects.

Genome sequences are available for increasing numbers of organisms. The proteomes (protein complement expressed by the genome) of many such organisms are being studied with two-dimensional (2D) gel electrophoresis. Here we have investigated the application of short N-terminal and C-terminal sequence tags to the identification of proteins separated on 2D gels. The theoretical N and C termini of 15, 519 proteins, representing all SWISS-PROT entries for the organisms Mycoplasma genitalium, Bacillus subtilis, Escherichia coli, Saccharomyces cerevisiae and human, were analysed. Sequence tags were found to be surprisingly specific, with N-terminal tags of four amino acid residues found to be unique for between 43% and 83% of proteins, and C-terminal tags of four amino acid residues unique for between 74% and 97% of proteins, depending on the species studied. Sequence tags of five amino acid residues were found to be even more specific. To utilise this specificity of sequence tags for protein identification, we created a world-wide web-accessible protein identification program, TagIdent (http://www.expasy.ch/www/tools.html), which matches sequence tags of up to six amino acid residues as well as estimated protein pI and mass against proteins in the SWISS-PROT database. We demonstrate the utility of this identification approach with sequence tags generated from 91 different E. coli proteins purified by 2D gel electrophoresis. Fifty-one proteins were unambiguously identified by virtue of their sequence tags and estimated pI and mass, and a further 11 proteins identified when sequence tags were combined with protein amino acid composition data. We conlcude that the TagIdent identification approach is best suited to the identification of proteins from prokaryotes whose complete genome sequences are available. The approach is less well suited to proteins from eukaryotes, as many eukaryotic proteins are not amenable to sequencing via Edman degradation, and tag protein identification cannot be unambiguous unless an organism's complete sequence is available.

Caudate unit activity and somal diameters in intact and nigral lesioned cats.

In a search for morphofunctional relationships in the head of the caudate nucleus (CN), we recorded extracellular unit activity in intact cats and in cats that had received bilateral injections of 6-OHDA into the substantia nigra (SN) 30 days previously. Only units firing spontaneously and continuously for 2 min were studied. In dorsal regions, potentials were small and iterative at almost constant intervals; the somal diameters were relatively small. In the ventrolateral region, potentials were bigger and appeared in bursts; somal diameters were significantly larger (p less than 0.05). For the centromedial region a histogram of numbers of neurons as a function of diameters revealed a Gaussian distribution extending from small to large neurons. Most dorsal neurons increased their firing rate to radial nerve, visual, SN, and/or nucleus centralis medialis (NCM) stimulation. Ventral neurons usually responded with excitation followed by long lasting inhibition, particularly to SN and NCM stimulation. A few neurons responded to all four inputs and some showed long-lasting potentiation in response to low frequency stimulation, suggesting a more general function. Greatest convergence (65%) was found for NCM and SN inputs. In lesioned cats, there was no SN driving, NCM's inhibitory actions almost disappeared, and the excitatory action of the other stimuli was reduced.

Multisystemic chromatolytic neuronal degeneration in Cairn terriers. A case with generalized cataplectic episodes.

Multisystemic chromatolytic neuronal degeneration, a newly recognized disease of Cairn Terriers, is described in a second affected North American puppy. In this puppy, the early onset of hind limb weakness at 11 weeks and rapid development of signs of diffuse CNS involvement were distinctive. Signs of cerebellar dysfunction were prominent, but bouts of cataplectic collapse in this puppy constituted the most distinguishing clinical feature. Although electroencephalograph (EEG) recordings lacked a true rapid eye movement (REM) pattern during cataplectic episodes, cervical electromyograph (EMG) potentials ceased or diminished, and imipramine injection was associated with arousal. Postmortem studies revealed that chromatolytic degeneration was very widespread, affecting many neuronal populations in the brain and spinal cord as well as neurons in sensory ganglia. Although the pattern of chromatolysis varied among affected perikarya, chromatolysis was consistently related to dispersion and loss of ribosomes. In this puppy, as opposed to six studied previously, thoracolumbar myelomalacia also occurred symmetrically in the dorsal horns and adjoining funicular white matter. The metabolic derangement underlying this chromatolytic neuronal degeneration and myelomalacia remains unknown.

Interictal afterdischarge in focal penicillin epilepsy: thalamocortical unit activity.

The involvement of thalamic versus cortical structures for the initiation and maintenance of brief interictal afterdischarge was evaluated by recording extracellularly units and field potentials from different subcortical and cortical sites. Afterdischarge oscillations at 16 to 22/s that followed interictal spikes with a delay of 170 to 220 ms usually appeared 10 to 30 min after the topical application of penicillin to the cat's precruciate cortex. Units in the ventrolateral nucleus of the thalamus fired in burst discharges during cortical afterdischarge and less reliably during the cortical interictal spike. In contrast, units recorded at the cortical penicillin focus and homologous contralateral site remained silent during afterdischarge but had a typical burst discharge during the interictal spike. Although these data support a thalamic basis for the rhythm, the lack of an afterdischarge-like oscillation in the thalamic field potential and the independent appearance of afterdischarge and cortical recruiting waves elicited by stimulation of the nucleus reticularis would favor its cortical origin. In accordance with its frequency characteristics and data gained from earlier cooling studies we suggest a cortical mechanism requiring thalamic triggering for the generation of afterdischarge.

SWISS-PROT: connecting biomolecular knowledge via a protein database.

With the explosive growth of biological data, the development of new means of data storage was needed. More and more often biological information is no longer published in the conventional way via a publication in a scientific journal, but only deposited into a database. In the last two decades these databases have become essential tools for researchers in biological sciences. Biological databases can be classified according to the type of information they contain. There are basically three types of sequence-related databases (nucleic acid sequences, protein sequences and protein tertiary structures) as well as various specialized data collections. It is important to provide the users of biomolecular databases with a degree of integration between these databases as by nature all of these databases are connected in a scientific sense and each one of them is an important piece to biological complexity. In this review we will highlight our effort in connecting biological information as demonstrated in the SWISS-PROT protein database.

LALNVIEW: a graphical viewer for pairwise sequence alignments.

LALNVIEW is a graphical program for visualising local alignments between two sequences (protein or nucleic acids). Sequences are represented by coloured rectangles to give an overall picture of their similarities. LALNVIEW can display sequence features (exon, intron, active site, domain, propeptide, etc.) along with the alignment. When using LALNVIEW through our Web servers, sequence features are automatically extracted from database annotations (SWISS-PROT, GenBank, EMBL or HOVERGEN) and displayed with the alignment. LALNVIEW is a useful tool for analysing pairwise sequence alignments and for making the link between sequence homology and what is known about the structure or function of sequences. LALNVIEW executables for UNIX, Macintosh and PC computers are freely available from our server (http:// expasy.hcuge.ch/sprot/lalnview.html).

A comprehensive web resource on RNA helicases from the baker's yeast Saccharomyces cerevisiae.

Members of the RNA helicase protein family are defined by several motifs that have been widely conserved during evolution. They are found in all organisms-from bacteria to humans-and many viruses. The minimum number of RNA helicases present within a eukaryotic cell can be predicted from the complete sequence of the Saccharomyces cerevisiae genome. Recent progress in the functional analysis of various family members has confirmed the significance of RNA helicases for most cellular RNA metabolic processes. We have assembled a web resource that focuses on RNA helicases from the budding yeast Saccharomyces cerevisiae. It includes descriptions of RNA helicases and their functions, links to sequence- and yeast-specific databases, an extensive list of references, and links to non-yeast helicase web resources.

Interictal afterdischarge in focal penicillin epilepsy: block by thalamic cooling.

Interictal spikes recorded from a penicillin focus in the precruciate cortex of urethane-anesthetized cats were followed by brief afterdischarge oscillations that occurred at a delay of 170 to 220 ms from the interictal spike and consisted of as many as five cycles at 16 to 22/s. The origin of this afterdischarge was investigated by cooling different subcortical sites and thus blocking them reversibly. At none of the sites did cooling result in a block of the interictal spike whereas cooling of the ventrolateral nucleus of the thalamus resulted in block of the afterdischarge. Other subcortical sites had either no or less reliable effects on it. We conclude that afterdischarge but not the interictal spike depends on thalamic input, either as a generator of the rhythm or as a trigger for a cortically maintained oscillation.

Annotation of glycoproteins in the SWISS-PROT database.

SWISS-PROT is a protein sequence database, which aims to be nonredundant, fully annotated and highly cross-referenced. Most eukaryotic gene products undergo co- and/or post-translational modifications, and these need to be included in the database in order to describe the mature protein. SWISS-PROT includes information on many types of different protein modifications. As glycosylation is the most common type of post-translational protein modification, we are currently placing an emphasis on annotation of protein glycosylation in SWISS-PROT. Information on the position of the sugar within the polypeptide chain, the reducing terminal linkage as well as additional information on biological function of the sugar is included in the database. In this paper we describe how we account for the different types of protein glycosylation, namely N-linked glycosylation, O-linked glycosylation, proteoglycans, C-linked glycosylation and the attachment of glycosyl-phosphatidylinosital anchors to proteins.

GlycoMod--a software tool for determining glycosylation compositions from mass spectrometric data.

GlycoMod (http://www.expasy.ch/tools/glycomod/) is a software tool designed to find all possible compositions of a glycan structure from its experimentally determined mass. The program can be used to predict the composition of any glycoprotein-derived oligosaccharide comprised of either underivatised, methylated or acetylated monosaccharides, or with a derivatised reducing terminus. The composition of a glycan attached to a peptide can be computed if the sequence or mass of the peptide is known. In addition, if the protein is known and is contained in the SWISS-PROT or TrEMBL databases, the program will match the experimentally determined masses against all the predicted protease-produced peptides (including any post-translational modifications annotated in these databases) which have the potential to be glycosylated with either N- or O-linked oligosaccharides. Since many possible glycan compositions can be generated from the same mass, the program can apply compositional constraints to the output if the user supplies either known or suspected monosaccharide constituents. Furthermore, known oligosaccharide structural constraints on monosaccharide composition are also incorporated into the program to limit the output.

Two-dimensional gel electrophoresis for proteome projects: the effects of protein hydrophobicity and copy number.

Two-dimensional (2-D) gel electrophoresis is often used in proteome projects to provide a global view of the proteins expressed in any cell or tissue type. Here we have investigated the effects of protein hydrophobicity and cellular protein copy number on a protein's presence or absence on a two-dimensional gel. The average hydropathy values of all known proteins from Bacillus subtilis, Escherichia coli and Saccharomyces cerevisiae were calculated, thus defining the range of protein hydrophobicity and hydrophilicity in these organisms. The average hydropathy values were then calculated for a total of 427 proteins from these species, which had been identified elsewhere on 2-D gels. Strikingly, it was seen that no highly hydrophobic proteins, as defined by average hydrophobicity values, have been found to date on 2-D gel separations of whole cell lysates. A clear hydrophobicity cutoff point was seen, above which current 2-D electrophoresis methods appear not to be useful for protein separation. The effect of cellular protein copy number on a protein's presence on a 2-D gel was investigated by means of a graphical model. This model showed how variations in protein loading and copy number per cell interact to determine the quantity of a protein that will be present on a 2-D gel. Considering the current maximum in 2-D gel loading capacity, it was found that 2-D probably can not visualize or produce analytical quantities of proteins present at less than 1000 copies per cell. We conclude that further developments of 2-D electrophoresis techniques are desirable to enable the visualization and analysis of all proteins expressed by a cell or tissue.