GlimmerM,Exonomy and Unveil: three ab initio eukaryotic genefinders

We present three programs for ab initio gene prediction in eukaryotes: Exonomy, Unveil and GlimmerM. Exonomy is a 23-state Generalized Hidden Markov Model (GHMM), Unveil is a 283-state standard Hidden Markov Model (HMM) and GlimmerM is a previously-described genefinder which utilizes decision trees and Interpolated Markov Models (IMMs). All three are readily re-trainable for new organisms and have been found to perform well compared to other genefinders. Results are presented for Arabidopsis thaliana. Cases have been found where each of the genefinders outperforms each of the others, demonstrating the collective value of this ensemble of genefinders. These programs are all accessible through webservers at http://www.tigr.org/software.     

Antimycobacterial evaluation of Peruvian plants

We present the results of an antimycobacterial screening of 270 Peruvian plant samples representing 216 species from 171 genera in 63 families. Dichloromethane extracts were tested at a concentration of 50 microg/ml for inhibition of Mycobacterium tuberculosis in radiometric culture. Slightly more than half of the samples tested showed inhibition of M. tuberculosis at this concentration.     

Digital morphonuclear analyses of sensitive versus resistant neoplastic cells to vinca-alkaloid, alkylating, and intercalating drugs

We tested 12 resistant cell lines in vitro in order to evaluate common morphonuclear characteristics induced by various cytotoxic drugs on cell lines of different origins. We used the MXT mouse mammary cancer and the neoplastic J82 and T24 human bladder cell lines, whose variants are either sensitive or resistant to a vinca alkaloid derivative (Navelbine, NVB), to an investigational alkylating agent (PE1001), and to Adriamycin (ADR). We tested cell population variants resistant to NVB + PE1001 + ADR. The level of chemoresistance was evaluated by a colorimetric assay assessing the 50% concentration-induced inhibition of cellular growth (IC50) brought about by each drug on the growth of each cell variant under study. We show that resistant neoplastic cell nuclei present common morphonuclear characteristics, independent of cell origin (neoplastic mouse mammary versus human bladder cells) and the drug used (vinca alkaloid, alkylating, and intercalating derivatives). Our results further indicate that the phenotype of resistant versus sensitive cells corresponds to cell nuclei populations with smaller nuclei and less nuclear DNA content and, as a consequence, a chromatin texture showing large pale areas with some hyperchromatic clumps.     

Chemical recognition of conspecifics in a neotropical lizard, <Emphasis Type="Italic">Liolaemus pacha</Emphasis> (Iguania: Liolaemidae): relation to visual displays,season and sex

Chemical cues play an important role in sexual recognition in several lizard species. Here, we investigated whether the neotropical lizard, Liolaemus pacha (Iguania: Liolaemidae) can discriminate between chemical information obtained from males or females. In addition, we also considered the effect of season (reproductive vs. post-reproductive) and the sex of the tested individual. We experimentally tested scent discrimination, using a terrarium previously occupied by a male, a female, and an untreated terrarium as control as sources of different chemical scents. We counted the number of tongue flicks, a measure of chemical exploratory behavior, and the visual displays triggered by these scents for 10 min. Males performed significantly more tongue flicks when female scent was present than when male and control scents were present, indicating sexual recognition. However, females did not show a significant difference in those same conditions, indicating a lack of sexual recognition. For visual displays, males showed significantly higher rates to female and male scents than to control, whereas females did not show any difference. During the reproductive season, the number of tongue flicks and visual displays were higher than during the post-reproductive season. Our results suggest that for male L. pacha, chemical cues play an important role in mate recognition. We discuss the apparent lack of recognition in females. We suggest that the observed seasonal behavioral differences might be associated with physiological changes related mainly to reproduction.     

Rate of gene sequence evolution and species diversification in flowering plants: a re-evaluation

Barraclough and co-workers (in a paper published in 1996) observed that there was a significant positive correlation between the rate of evolution of the rbcL chloroplast gene within families of flowering plants and the number of species in those families. We tested three additional data sets of our own (based on both plastid and nuclear genes) and used methods designed specifically for the comparison of sister families (based on random speciation and extinction). We show that, over all sister groups, the correlation between the rate of gene evolution and an increased diversity is not always present. Despite tending towards a positive association, the observation of individual probabilities presents a U-shaped distribution of association (i.e. it can be either significantly positive or negative). We discuss the influence of both phylogenetic sampling and applied taxonomies on the results.     

Distribution of a COOH-terminal amino acid extension of liver fructose-1,6-bisphosphatase among rodent species

We have recently established from sequence analysis that rat liver fructose-1,6-bisphosphatase contains a 24-26 residue extension beyond the COOH-terminal amino acid of other mammalian fructose-1,6-bisphosphatases that results in an increased subunit molecular weight (Rittenhouse et al. (1983) J. Biol. Chem. 258, 7648-7652). In the present work the distribution of the COOH-terminal extension of fructose-1,6-bisphosphatases was tested by subunit molecular weight analysis of the enzyme immunoprecipitated from liver extracts. Of all rodent species tested, including several Muridae other than Rattus; only the enzyme from animals of the genus Rattus was found to have the extension. Further studies on the distribution of the enzyme extension could provide a simple tool to study the phylogeny of the genus Rattus.     

Sexual dimorphism and gonadal control of ultrasonic vocalizations in adult pine voles, Microtus pinetorum

We investigated the vocalizations produced by adult pine voles during various social interactions by presenting an experimental animal with either an anesthetized or awake (unanesthetized) conspecific. Ultrasonic vocalizations (USVs) occurred frequently during tests in which an awake male was present, but were rarely detected in tests involving only awake females, or when a female was presented with an anesthetized conspecific. Higher rates of USVs were produced when males were tested with a familiar female than when tested with an unfamiliar male or female. Equivalent rates were produced when males were presented with either anesthetized or awake animals, but female-soiled bedding failed to elicit USVs from males. Sonic vocalizations (SVs) were produced by both sexes and were associated with aggressive behavior, but occurred only in tests between awake, unfamiliar animals. Castration greatly reduced and testosterone therapy restored USVs emitted by males in response to anesthetized conspecifics. Our results suggest that (i) USVs are emitted predominantly by males; (ii) familiarity enhances USV response; (iii) SVs are produced during aggressive interactions; and (iv) androgens regulate the production of USVs by males. Possible roles for pine vole vocalizations are discussed.     

A decomposition model to track gene expression signatures: preview on observer-independent classification of ovarian cancer

MOTIVATION: A number of algorithms and analytical models have been employed to reduce the multidimensional complexity of DNA array data and attempt to extract some meaningful interpretation of the results. These include clustering, principal components analysis, self-organizing maps, and support vector machine analysis. Each method assumes an implicit model for the data, many of which separate genes into distinct clusters defined by similar expression profiles in the samples tested. A point of concern is that many genes may be involved in a number of distinct behaviours, and should therefore be modelled to fit into as many separate clusters as detected in the multidimensional gene expression space. The analysis of gene expression data using a decomposition model that is independent of the observer involved would be highly beneficial to improve standard and reproducible classification of clinical and research samples. RESULTS: We present a variational independent component analysis (ICA) method for reducing high dimensional DNA array data to a smaller set of latent variables, each associated with a gene signature. We present the results of applying the method to data from an ovarian cancer study, revealing a number of tissue type-specific and tissue type-independent gene signatures present in varying amounts among the samples surveyed. The observer independent results of such molecular analysis of biological samples could help identify patients who would benefit from different treatment strategies. We further explore the application of the model to similar high-throughput studies.     

The destruction box of the cyclin Clb2 binds the anaphase-promoting complex/cyclosome subunit Cdc23

Properly regulated cyclin proteolysis is critical for normal cell cycle progression. A nine-amino acid peptide motif called the destruction box (D box) is present at the N terminus of the yeast mitotic cyclins. This short sequence is required for cyclin ubiquitination and subsequent proteolysis. The anaphase-promoting complex/cyclosome (APC/C) is a multisubunit E3 required for cyclin ubiquitination. We have tested the D box of five mitotic cyclins for interaction with six APC/C subunits. The APC/C subunit Cdc23, but not five other subunits tested, interacted by two-hybrid analysis with the N terminus of wild-type Clb2. None of these subunits interacted with the N termini of the cyclins Clb1, Clb3, or Clb5. Mutations in the D box sequences of Clb2 inhibited interaction with Cdc23 both in vivo and in vitro. Our results provide the first evidence for a direct interaction between an APC/C substrate (Clb2) and an APC/C subunit (Cdc23).     

A fruity note: crossmodal associations between odors and musical notes

Odors are notoriously difficult to describe, but they seem prone to a variety of crossmodal associations. In the present study, we generalize the previously-shown association between odors (from perfumery) and pitch (Belkin et al. 1997) to odors related to food and drink (in this case those associated with wine). We also demonstrate that, to a lesser extent (25% of the odor tested), participants preferentially match specific odors to certain types of instruments. The ratings of the odors along a number of dimensions are used in principal components analysis (PCA) to explore the psychological dimensions underlying the odor-pitch associations. The results demonstrate that both pleasantness and complexity, but not intensity, appear to play a role when choosing a pitch to match an odor. Our results suggest that these features of odor stimuli constitute psychological dimensions that can be consistently matched to auditory features.     

Genetic analysis of populations of threatened snake species using RAPD markers

Snakes are a particularly threatened vertebrate taxon, with distributions of many species and populations becoming increasingly fragmented. At present, little is known about the degree of genetic differentiation that exists between isolated populations even though such information may be critical to their survival and conservation. As an example of how recently developed RAPD genetic markers can be used in conservation genetics, we present preliminary results from a study which used these DNA-based markers to assess population divergence in two threatened Canadian snakes, the black rat snake ( Elaphe o. obsoleta ) and the eastern massasauga rattlesnake ( Sistrurus c. catenatus ). We present information on the levels of variation and reliability of amplification for fragments generated from five primers. We then use a recently developed analytical technique to estimate levels of nucleotide diversity within populations and sequence divergence between populations. Our results show that intrapopulation levels of divergence as estimated by the methods of Clark & Lanigan ( Molecular Biology and Evolution 1993, 10 , 1096–1111) approximate those found for mtDNA in vertebrates and that diversity between snake populations is small and non-significant when tested using randomization procedures. Thus, our study provides an example of how RAPDs can be applied to conservation genetic studies of vertebrates and suggest that the snake populations we examined have only recently become isolated and maybe considered genetically equivalent from a conservation perspective, although this conclusion needs to be confirmed with other DNA-based markers.     

Stimulatory effects of bioamines norepinephrine and dopamine on locomotion of Pyrrhocoris apterus (L.): is the adipokinetic hormone involved?

In the present paper we studied the effects of five biogenic amines - norepinephrine, dopamine, octopamine, serotonin and histamine - on the locomotory activity and mobilization of lipids in the adult females of the firebug, Pyrrhocoris apterus (L.). We tested the hypothesis (1) whether the stimulation of walking activity in the bugs injected with the bioamines is associated also with their hyperlipaemic effects, like in the case of adipokinetic hormones (AKHs), and (2) whether these effects are direct or mediated through a release of the AKHs into the hemolymph. The results demonstrated that all five tested biogenic amines mobilized the fat body lipids, but only norepinephrine and dopamine were capable to enhance the walking activity simultaneously with an elevation of the lipid level in the hemolymph. Those two amines had no effect on the level of AKHs in CNS, but modulated the AKHs level in hemolymph: norepinephrine increased it, while dopamine decreased it. The results indicate an apparent feedback between AKH characteristics and dopamine and norepinephrine actions occurring in this insect species. While the stimulatory effects of norepinephrine on lipid mobilization and walking activity could involve the release of bug's own AKHs, dopamine probably employs an independent stimulatory pathway.     

Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR

With an increased emphasis on genotyping of single nucleotide polymorphisms (SNPs) in disease association studies, the genotyping platform of choice is constantly evolving. In addition, the development of more specific SNP assays and appropriate genotype validation applications is becoming increasingly critical to elucidate ambiguous genotypes. In this study, we have used SNP specific Locked Nucleic Acid (LNA) hybridization probes on a real-time PCR platform to genotype an association cohort and propose three criteria to address ambiguous genotypes. Based on the kinetic properties of PCR amplification, the three criteria address PCR amplification efficiency, the net fluorescent difference between maximal and minimal fluorescent signals and the beginning of the exponential growth phase of the reaction. Initially observed SNP allelic discrimination curves were confirmed by DNA sequencing (n = 50) and application of our three genotype criteria corroborated both sequencing and observed real-time PCR results. In addition, the tested Caucasian association cohort was in Hardy-Weinberg equilibrium and observed allele frequencies were very similar to two independently tested Caucasian association cohorts for the same tested SNP. We present here a novel approach to effectively determine ambiguous genotypes generated from a real-time PCR platform. Application of our three novel criteria provides an easy to use semi-automated genotype confirmation protocol.     

Analysis of protein expression in cell microarrays: a tool for antibody-based proteomics.

Tissue microarray (TMA) technology provides a possibility to explore protein expression patterns in a multitude of normal and disease tissues in a high-throughput setting. Although TMAs have been used for analysis of tissue samples, robust methods for studying in vitro cultured cell lines and cell aspirates in a TMA format have been lacking. We have adopted a technique to homogeneously distribute cells in an agarose gel matrix, creating an artificial tissue. This enables simultaneous profiling of protein expression in suspension- and adherent-grown cell samples assembled in a microarray. In addition, the present study provides an optimized strategy for the basic laboratory steps to efficiently produce TMAs. Presented modifications resulted in an improved quality of specimens and a higher section yield compared with standard TMA production protocols. Sections from the generated cell TMAs were tested for immunohistochemical staining properties using 20 well-characterized antibodies. Comparison of immunoreactivity in cultured dispersed cells and corresponding cells in tissue samples showed congruent results for all tested antibodies. We conclude that a modified TMA technique, including cell samples, provides a valuable tool for high-throughput analysis of protein expression, and that this technique can be used for global approaches to explore the human proteome.     

Toward localization of the Werner syndrome gene by linkage disequilibrium and ancestral haplotyping: lessons learned from analysis of 35 chromosome 8p11.1-21.1 markers.

Werner syndrome (WS) is an autosomal recessive disorder characterized by premature onset of a number of age-related diseases. The gene for WS, WRN, has been mapped to the 8p 11.1-21.1 region with further localization through linkage disequilibrium mapping. Here we present the results of linkage disequilibrium and ancestral haplotype analyses of 35 markers to further refine the location of WRN. We identified an interval in this region in which 14 of 18 markers tested show significant evidence of linkage disequilibrium in at least one of the two populations tested. Analysis of extended and partial haplotypes covering 21 of the markers studied supports the existence of both obligate and probable ancestral recombinant events which localize WRN almost certainly to the interval between D8S2196 and D8S2186, and most likely to the narrower interval between D8S2168 and D8S2186. These haplotype analyses also suggest that there are multiple WRN mutations in each of the two populations under study. We also present a comparison of approaches to performing disequilibrium tests with multiallelic markers, and show that some commonly used approximations for such tests perform poorly in comparison to exact probability tests. Finally, we discuss some of the difficulties introduced by the high mutation rate at microsatellite markers which influence our ability to use ancestral haplotype analysis to localize disease genes.     

Guanidinoacetate Inhibits Glutamate Uptake in Rat Striatum of Rats at Different Ages

Glutamate plays a central role in the excitatory synaptic transmission and is important for brain development and functioning. Increased glutamate levels in the synaptic cleft are related to neuronal damage associated with excitotoxicity. Guanidinoacetate methyltransferase (GAMT) deficiency is an inherited neurometabolic disorder biochemically characterized by tissue accumulation of guanidinoacetate (GAA) and depletion of creatine. Affected patients present epilepsy and mental retardation whose pathogeny is unclear. In the present study we investigated the in vitro and in vivo (intrastriatal administration) effect of GAA on glutamate uptake by striatum slices of developing and adult rats. Results showed that GAA significantly inhibited in vitro glutamate uptake at 50 μM and 100 μM in all ages tested. We also tested the effect of taurine on the inhibition of glutamate uptake caused by GAA. Taurine significantly attenuated the inhibitory effect caused by 50 μM GAA, but did not alter that provoked by 100 μM GAA. Furthermore, intrastriatal administration of a solution of 30 μM GAA (0.06 nmol/striatum) significantly inhibited glutamate uptake by rat striatum slices. Our results suggest that the inhibition of striatal glutamate uptake caused by GAA might be involved in the neuropathology and especially in the acute neurological features present in patients with GAMT-deficiency.     

Preparation of a functional, highly selective polymer by molecular imprinting. A demonstration with L-p-aminophenylalanine anilide as a template molecule allowing multiple points of attachment

The technique of molecular imprinting was tested using various phenylalanine derivatives. It could be shown that polymers obtained by imprinting with L-p-aminophenylalanine anilide gave best recognition of the original L-form, with separation factors (alpha) above 8, on applying racemic mixtures to the polymer obtained and present in a HPLC column. We believe that these results are due to multiple points of attachment that are possible between print or template (guest) molecules and the formed polymer (host).     

Yucca: an efficient algorithm for small-molecule docking

In this paper, we present a new algorithm, which is based on an efficient heuristic for local search, for rigid protein-small-molecule docking. We tested our algorithm, called Yucca, on the recent 100-complex benchmark, using the conformer generator OMEGA to generate a set of low-energy conformers. The results showed that Yucca is competitive both in terms of algorithm efficiency and docking accuracy.