Temporal variation in the vocal behaviour of southern right whales in the Auckland Islands, New Zealand.

Autonomous recorders are frequently used for examining vocal behaviour of animals, and are particularly effective in remote habitats. Southern right whales are known to have an extensive acoustic repertoire. A recorder was moored at the isolated sub-Antarctic Auckland Islands for a year to examine whether the acoustic behaviour of southern right whales differed seasonally and throughout the day at their main calving ground in New Zealand. Recordings were made in each month except June, and vocalizations were audible in all months with recordings except January. A total of 35 487 calls were detected, of which upcalls were the most common (11 623). Call rate peaked in August (288 ± 5.9 [s.e.] calls/hour) and July (194 ± 8.3). Vocal behaviour varied diurnally with highest call rates detected at dusk and night, consistent with the concept that upcalls function primarily as contact calls. Zero-inflated model results confirmed that seasonal variation was the most important factor for explaining differences in vocal behaviour. An automated detector designed to expedite the analysis process for North Atlantic right whales correctly identified 80% of upcalls, although false detections were frequent, particularly when call rates were low. This study is the first to attempt year-round monitoring of southern right whale presence in New Zealand.

Analysis of high density expression microarrays with signed-rank call algorithms.

MOTIVATION: We consider the detection of expressed genes and the comparison of them in different experiments with the high-density oligonucleotide microarrays. The results are summarized as the detection calls and comparison calls, and they should be robust against data outliers over a wide target concentration range. It is also helpful to provide parameters that can be adjusted by the user to balance specificity and sensitivity under various experimental conditions. RESULTS: We present rank-based algorithms for making detection and comparison calls on expression microarrays. The detection call algorithm utilizes the discrimination scores. The comparison call algorithm utilizes intensity differences. Both algorithms are based on Wilcoxon's signed-rank test. Several parameters in the algorithms can be adjusted by the user to alter levels of specificity and sensitivity. The algorithms were developed and analyzed using spiked-in genes arrayed in a Latin square format. In the call process, p-values are calculated to give a confidence level for the pertinent hypotheses. For comparison calls made between two arrays, two primary normalization factors are defined. To overcome the difficulty that constant normalization factors do not fit all probe sets, we perturb these primary normalization factors and make increasing or decreasing calls only if all resulting p-values fall within a defined critical region. Our algorithms also automatically handle scanner saturation.

A shape-based machine learning tool for drug design.

Building predictive models for iterative drug design in the absence of a known target protein structure is an important challenge. We present a novel technique, Compass, that removes a major obstacle to accurate prediction by automatically selecting conformations and alignments of molecules without the benefit of a characterized active site. The technique combines explicit representation of molecular shape with neural network learning methods to produce highly predictive models, even across chemically distinct classes of molecules. We apply the method to predicting human perception of musk odor and show how the resulting models can provide graphical guidance for chemical modifications.

Pattern descriptors and the unidentified reading frame 6 human mtDNA dinucleotide-binding site.

In an effort to identify the structural elements essential to a given protein function a new pattern-directed inference system has been developed. It has been employed to identify a potential dinucleotide-binding domain within the human mitochondrial unidentified reading frame 6 product, thereby supporting an earlier study that this gene may encode a NADH dehydrogenase subunit.

Prediction of a common structural domain in aminoacyl-tRNA synthetases through use of a new pattern-directed inference system.

The aminoacyl-tRNA synthetases are united by a common function with little evidence of a common structural relationship. Outside of an 11 amino acid stretch called the "signature sequence", no global primary sequence similarity exists. The signature sequence matches 4-11 amino acids in several aminoacyl-tRNA synthetases. High-resolution X-ray data are available for two of these enzymes, revealing that their signature sequence regions are small segments of a common mononucleotide binding foldlike structure. A new methodology for the analysis of dissimilar primary sequences supports the expectation that all of the signature sequence regions form a common structure. In our analysis, two complex pattern descriptors were constructed to describe the synthetase mononucleotide binding fold. These were compared to primary sequences annotated with predicted secondary structures and hydropathy profiles. Regions in 8 out of 12 (67%) heterologous aminoacyl-tRNA synthetase groups (where each group is specific for the same amino acid) match the first descriptor, and 7 of these (58%) also match the second descriptor. In contrast, only 4 regions in a set of 54 control proteins (7.4%) match the first descriptor, and only 2 regions (3.7%) match both. Alignment of these 8 regions to the descriptor (1) positions all known signature sequence regions as the first loop of a mononucleotide binding foldlike structure, (2) extends the previous alignments by another 40-odd amino acids, and (3) identifies potential sites in 3 out of 6 heterologous aminoacyl-tRNA synthetases with no previous alignments. Potential sites are also proposed for two additional heterologous synthetases on the basis of matches to less specific descriptors.

Polyethylene glycol-induced heteroassociation of malate dehydrogenase and citrate synthase.

Studies by dynamic and total intensity light scattering, ultracentrifugation, electron microscopy, and chemical crosslinking on solutions of the pig heart mitochondrial enzymes, malate dehydrogenase and citrate synthase (separately and together) demonstrate that polyethylene glycol induces very large homoassociations of each enzyme, and still larger heteroenzyme complexes between these two enzymes in the solution phase. Specificity of this heteroassociation is indicated by the facts that heteroassociations with bovine serum albumin were not observed for either the mitochondrial dehydrogenase or the synthase or between cytosolic malate dehydrogenase and citrate synthase. The weight fraction of the enzymes in the mitochondrial dehydrogenase-synthase associated particles in the solution phase was less than 0.03% with the dilute conditions used in the dynamic light scattering measurements. Neither palmitoyl-CoA nor other solution conditions tested significantly increased this weight fraction of associated enzymes in the solution phase. Because of the extremely low solubility of the associated species, however, the majority of the enzymes can be precipitated as the heteroenzyme complex. This precipitation is a classical first-order transition in spite of the large particle sizes and broad size distribution. Ionic effects on the solubility of the heteroenzyme complex appear to be of general electrostatic nature. Polyethylene glycol was found to be more potent in precipitating this complex than dextrans, polyvinylpyrrolidones, ficoll, and beta-lactoglobulin.

Evidence for dispensable sequences inserted into a nucleotide fold.

Previous experimental results along with the structural modeling presented indicate that a nucleotide fold starts in the amino-terminal part of Escherichia coli isoleucyl-transfer RNA synthetase, a single chain polypeptide of 939 amino acids. Internal deletions were created in the region of the nucleotide fold. A set of deletions that collectively span 145 contiguous amino acids yielded active enzymes. Further extensions of the deletions yielded inactive or unstable proteins. The three-dimensional structure of an evidently homologous protein suggests that the active deletions lack portions of a segment that connects two parts of the nucleotide fold. Therefore, the results imply that removal of major sections of the polypeptide that connects these two parts of the fold does not result in major perturbation of the nucleotide binding site.

Now that we have pulse oximeters and capnographs, we don't need precordial and esophageal stethoscopes.

One clinician argues that precordial and esophageal stethoscopes are obsolete. Current technology, including pulse oximetry, electrocardiography, and capnography, is both easier to use and more accurate. Another clinician argues that these stethoscopes have an important place in safe patient management. They are an inexpensive but effective extension of the anesthesiologist's own senses.

Consensus topography in the ATP binding site of the simian virus 40 and polyomavirus large tumor antigens.

The location and sequence composition of a consensus element of the nucleotide binding site in both simian virus 40 (SV40) and polyomavirus (PyV) large tumor antigens (T antigens) can be predicted with the assistance of a computer-based pattern-matching system, ARIADNE. The latter was used to optimally align elements of T antigen primary sequence and predicted secondary structure with a "descriptor" for a mononucleotide binding fold. Additional consensus elements of the nucleotide binding site in these two proteins were derived from comparisons of T antigen primary and predicted secondary structures with x-ray structures of the nucleotide binding sites in four otherwise unrelated proteins. Each of these elements was predicted to be encompassed within a 110-residue segment that is highly conserved between the two T antigens residues 418-528 in SV40 T antigen and residues 565-675 in PyV). Results of biochemical and immunologic experiments on the nucleotide binding behavior of these proteins were found to be consistent with these predictions. Taken together, the latter have resulted in a topological model of the ATP binding site in these two oncogene products.

Primary structures of both subunits of Escherichia coli glycyl-tRNA synthetase.

Escherichia coli glycyl-tRNA synthetase is one of two aminoacyl-tRNA synthetases which is comprised of two different subunits (in an alpha 2 beta 2 structure). The two coding regions occur in tandem in the order alpha + beta and are synthesized from a single mRNA (Keng, T., Webster, T. A., Sauer, R. T., and Schimmel, P. R. (1982) J. Biol. Chem. 257, 12503-12508). Primary structures of both proteins were determined by DNA sequencing of each coding region and by analysis of tryptic fragments of the enzyme. The alpha-subunit is 303 codons and terminates with TAA; the beta-subunit is 689 codons followed by tandem TAA stops. S1 nuclease mapping of the 3'-end of the two-cistron glyS mRNA showed that it predominantly ends 33/34 bases beyond the tandem stops with an RNA polymerse terminator sequence. Altogether, 43% of the translated polypeptide sequences were confirmed by mass spectrometric analysis of peptide fragments including confirmation of the COOH-terminal end of the beta-chain. This involved determinations, by fast atom bombardment mass spectrometry, of the masses of numerous whole tryptic fragments (with an accuracy of better than 1 Da) and of fragments truncated by one to three cycles of Edman degradations. The primary structures of the two subunits show no homologies with each other and have no internal sequence repeats of significance. While there are no extensive homologies with five other sequenced, or partially sequenced, synthetases, the alpha-subunit has a short sequence which can be aligned with sequences found in functionally important areas of two other synthetases and in uncharacterized parts of a third and fourth synthetase.

Gene for Escherichia coli glycyl-tRNA synthetase has tandem subunit coding regions in the same reading frame.

Glycyl-tRNA synthetase is one of two Escherichia coli aminoacyl tRNA synthetases which has two different subunits. A 5.1-kilobase pair HindIII chromosomal DNA fragment was isolated, cloned into pBR322 (to give plasmid pTK201), and shown to direct synthesis in maxicells of both subunits (Mr = 35,000 (alpha) and Mr = 65,000 (beta) of glycyl-tRNA synthetase. Locations of alpha- and beta-subunit coding regions were established by introduction of Tn5 insertions into various positions within the 5.1-kilobase pair HindIII segment of pTK201 and by determining the effect of each Tn5 insertion on synthesis of alpha- and beta-subunits and on enzymatic activity. From the Tn5 insertion analysis, regions encoding the NH2 terminus of the alpha-subunit and of the beta-subunit were approximately defined and these regions were sequenced. To locate rigorously the respective NH2-terminal encoding sections in the DNA sequence, NH2-terminal amino acid sequences of alpha- and beta-subunits were established by standard Edman degradations and these sequences were aligned with the DNA sequence. This analysis established the following: 1) coding regions for the subunits are in tandem; 2) a single promoter is used for transcription of both coding sections and the order of transcription is from alpha to beta; 3) in the 500 nucleotides 5' to the start of the alpha-subunit coding section, there is no sequence arrangement like that found for regulatory regions of bacterial amino acid biosynthetic operons; 4) nine nucleotides serve as the spacer between the TAA stop of the alpha- and the ATG start of the beta-subunit coding regions, thus making both coding regions in the same reading frame; and 5) the TAA stop of the alpha-subunit and the next for nucleotides associated with the intersubunit region are complementary to the 3'-end of 16 S rRNA; this arrangement suggests ribosome re-initiation in the spacer region gives balanced synthesis of both subunits.