Evaluation of intra-muscular EMG signal decomposition algorithms.

We propose and test a tool to evaluate and compare EMG signal decomposition algorithms. A model for the generation of synthetic intra-muscular EMG signals, previously described, has been used to obtain reference decomposition results. In order to evaluate the performance of decomposition algorithms it is necessary to define indexes which give a compact but complete indication about the quality of the decomposition. The indexes given by traditional detection theory are in this paper adapted to the multi-class EMG problem. Moreover, indexes related to model parameters are also introduced. It is possible in this way to compare the sensitivity of an algorithm to different signal features. An example application of the technique is presented by comparing the results obtained from a set of synthetic signals decomposed by expert operators having no information about the signal features using two different algorithms. The technique seems to be appropriate for evaluating decomposition performance and constitutes a useful tool for EMG signal researchers to identify the algorithm most appropriate for their needs.     

Identification of a neuritogenic ligand of the neural cell adhesion molecule using a combinatorial library of synthetic peptides.

The neural cell adhesion molecule (NCAM) plays a key role in neural development, regeneration, and learning. In this study, we identified a synthetic peptide-ligand of the NCAM Ig1 module by combinatorial chemistry and showed it could modulate NCAM-mediated cell adhesion and signal transduction with high potency. In cultures of dissociated neurons, this peptide, termed C3, stimulated neurite outgrowth by activating a signaling pathway identical to that activated by homophilic NCAM binding. A similar effect was shown for the NCAM Ig2 module, the endogenous ligand of NCAM Ig1. By nuclear magnetic resonance spectroscopy, the C3 binding site in the NCAM Ig1 module was mapped and shown to be different from the binding site of the NCAM Ig2 module. The C3 peptide may prove useful as a lead in development of therapies for neurodegenerative disorders, and the C3 binding site of NCAM Ig1 may represent a target for discovery of nonpeptide drugs.     

IIb‐RAD‐sequencing coupled with random forest classification indicates regional population structuring and sex‐specific differentiation in salmon lice (Lepeophtheirus salmonis)

The aquaculture industry has been dealing with salmon lice problems forming serious threats to salmonid farming. Several treatment approaches have been used to control the parasite. Treatment effectiveness must be optimized, and the systematic genetic differences between subpopulations must be studied to monitor louse species and enhance targeted control measures. We have used IIb‐RAD sequencing in tandem with a random forest classification algorithm to detect the regional genetic structure of the Norwegian salmon lice and identify important markers for sex differentiation of this species. We identified 19,428 single nucleotide polymorphisms (SNPs) from 95 individuals of salmon lice. These SNPs, however, were not able to distinguish the differential structure of lice populations. Using the random forest algorithm, we selected 91 SNPs important for geographical classification and 14 SNPs important for sex classification. The geographically important SNP data substantially improved the genetic understanding of the population structure and classified regional demographic clusters along the Norwegian coast. We also uncovered SNP markers that could help determine the sex of the salmon louse. A large portion of the SNPs identified to be under directional selection was also ranked highly important by random forest. According to our findings, there is a regional population structure of salmon lice associated with the geographical location along the Norwegian coastline.     

Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria

Mitochondria are tailored to meet the metabolic and signaling needs of each cell. To explore its molecular composition, we performed a proteomic survey of mitochondria from mouse brain, heart, kidney, and liver and combined the results with existing gene annotations to produce a list of 591 mitochondrial proteins, including 163 proteins not previously associated with this organelle. The protein expression data were largely concordant with large-scale surveys of RNA abundance and both measures indicate tissue-specific differences in organelle composition. RNA expression profiles across tissues revealed networks of mitochondrial genes that share functional and regulatory mechanisms. We also determined a larger "neighborhood" of genes whose expression is closely correlated to the mitochondrial genes. The combined analysis identifies specific genes of biological interest, such as candidates for mtDNA repair enzymes, offers new insights into the biogenesis and ancestry of mammalian mitochondria, and provides a framework for understanding the organelle's contribution to human disease.     

Specific and selective biosensor for Salmonella and its detection in the environment

The specific and selective detection of Salmonella typhymurium based on the use of a polyclonal antibody immobilized by the Langmuir-Blodgett method on the surface of a quartz crystal acoustic wave device was demonstrated in liquid samples. These biosensors were selective to S. typhymurium in the presence of large concentrations of Escherichia coli O157:H7. They were also specific to S. typhymurium since bacteria preincubated with free antibody produced no signal. Dark-field and electron microscopy showed that two different antibodies, polyvalent somatic O and flagellar H7, were immobilized on the sensor surface producing two distinct attachments of bacteria at the liquid-solid interface. The somatic O antibody exhibits a rigid, binding, while the flagellar H7 antibody forms a flexible connection allowing a large degree of freedom. When the attachment of bacteria was rigid and strong, the responses of the acoustic wave sensors correlated with changes in the mass of bacteria present at the liquid-solid interface. In contrast, when attachment was flexible, the sensor signals were inversely proportional to the additional mass of bound bacteria. This difference is probably determined by the interfacial viscoelasticity and by acoustic and electromagnetic coupling. The signals of environmentally aged sensors with either predominantly rigid or flexible positioning of bacteria were correlated with changes in mass at the liquid-solid interface. Sensors with O or H type of binding could be used for analytical purposes.     

The RDP (Ribosomal Database Project) continues

The Ribosomal Database Project (RDP-II), previously described by Maidak et al., continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 7.1 (September 17, 1999) included more than 10 700 small subunit rRNA sequences. More than 850 type strain sequences were identified and added to the prokaryotic alignment, bringing the total number of type sequences to 3324 representing 2460 different species. Availability of an RDP-II mirror site in Japan is also near completion. RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/ ). Analysis services include rRNA probe checking, approx-i-mate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment length polymorphism (T-RFLP) experiments.     

Effects of crosslinking on the thermal stability of hemoglobin. I. The use of bis(3,5-dibromosalicyl) fumarate

The double-headed aspirin, bis(3,5-dibromosalicyl) fumarate, has been used to crosslink hemoglobin A between Lys 82 beta 1 and Lys 82 beta 2 (J. A. Walder et al. (1979) Biochemistry 18,4265). Denaturation experiments were used to compare the stability of this crosslinked protein to that of hemoglobin A. Thermal denaturations, done in 0.01 M 4-morpholine-propanesulfonic acid, pH 7, containing 0.9 M guanidine to prevent precipitation at high temperatures, were monitored by changes in absorbance between 190 and 650 nm using a diode array spectrophotometer. The sample was heated from 25 to 70 degrees C at 0.3 degrees C/min. The data were analyzed by using both a two-state model and a novel first derivative method. As expected, methemoglobin A had a single, broad transition with a midpoint of 40.7 degrees C. The crosslinked methemoglobin showed a transition at 57.1 degrees C. Two minor transitions, one of which was apparently due to residual unmodified hemoglobin, were also observed in the crosslinked sample. Thus, a single crosslink between only two of the four subunits can lead to a significantly more stable molecule. These results can be explained by Le Chatelier's principle, since crosslinking prevents dissociation of the beta-subunits and, thereby, holds the entire tetramer together.     

Vasoactive intestinal polypeptide and acetylcholine stimulate exocrine secretion of epidermal growth factor from the rat submandibular gland

The effect of vasoactive intestinal polypeptide (VIP) and acetylcholine on secretion of epidermal growth factor (EGF) from the rat salivary glands was investigated. VIP in doses of 3 X 10(-10) to 3 X 10(-8) mol/kg per h stimulated secretion of saliva and total output of EGF dose-dependently. Acetylcholine also stimulated salivation and output of EGF. VIP in a dose of 3 X 10(-11) to 3 X 10(-10) mol/kg per h enhanced the stimulatory effect of acetylcholine, but this effect disappeared when the dose of VIP was increased. Adrenalectomy decreased acetylcholine stimulated total output of EGF by approximately 50%, but only by 20% when acetylcholine plus VIP was administered. EGF was localized to the convoluted granular tubules in the submandibular gland, whereas EGF could not be detected in the remaining salivary glands. The results suggest that VIP and acetylcholine cooperate in the control of exocrine secretion from the rat salivary glands. The effect of acetylcholine, however, seems to be partly dependent on circulating catecholamines.