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PubMed2006

A confirmation of Rexed's laminar hypothesis using the Sholl linear method complemented by nonparametric statistics.

Images of Golgi-impregnated neurons from laminae I to VI in the dorsal horn of the cat spinal cord were subjected to the linear Sholl analysis of concentric circles to support Rexed's hypothesis on the laminar organization of spinal gray matter in mammals. Since Rexed's determination of the laminae is based upon size, location, and grouping of cell bodies, neglecting one of the principal morphologic attributes of the neuron-the dendritic tree, the purpose of the present study was to evaluate Rexed's hypothesis testing the structure of dendritic arborization patterns of neurons. The differences in the complexity of dendritic trees between the groups of neurons from different laminae were evaluated by nonparametric statistics. Data obtained using Sholl's method is not always subjected to complete statistical analysis. The problem becomes particularly apparent in the quantitative examination of dendritic structures. Our aim was also to perform a careful analysis of our data for normality, in order to choose the appropriate statistical method for data processing. In the linear Sholl analysis, it is important to properly represent and interpret the frequency functions. The objective of this study was also to investigate the problems of determining the frequency functions, plotting the corresponding lines of regression, and measuring the degree of fluctuation of experimental data points around these lines. The main result of our testing is a confirmation of Rexed's laminar scheme: we have proved that there are 6 out of 10 possible pairs of samples where one member significantly differs from the other, i.e. one lamina is significantly distinguishable from the other.

Algorithms↗
PubMed1998

Herd-level test performance based on uncertain estimates of individual test performance, individual true prevalence and herd true prevalence.

A generalized model was derived for understanding the performance of herd-testing protocols when there is uncertainty and variability in individual-level sensitivity, specificity, prevalence of infection within infected herds, and prevalence of infected herds in the population. The model uses Monte-Carlo techniques to provide estimates of test performance for a dichotomous classification of herd-disease status. Uncertainty and variability in input assumptions are described using empirical and parametric probability distributions. The model permits both cluster-correlated behavior of inputs and sampling of animals without replacement. Disease due to obligate parasites is modeled differently from that due to organisms that persist for long periods in the environment. Dependence among model outcomes is assessed using Spearman's rank correlation. Model output is suitable for inclusion in risk-assessment models requiring probabilistic estimates of herd-level test performance, such as those developed for food-safety decision making and import-export risk assessment. The model was demonstrated using an example scenario based on Shiga-like toxin (SLT) producing Escherichia coli O157 in Ontario beef-cattle herds. Inputs were derived from the literature and Statistics Canada agricultural census data. Where appropriate, these data were subjected to distribution-fitting techniques. Otherwise, subjective interpretation was used to select input distributions and their parameters. Simulation revealed that the distribution of herd-level sensitivity for detecting herds infected with SLT producing E. coli O157 has a large range (0.003-0.99) and a median of 0.19. Herd-level specificity also had a large range (0.58-1) and a median of 0.94. Distributions of herd-level positive and negative predictive values exhibited similar degrees of uncertainty. In combination with poor likelihood ratios for positive and negative herd tests, results indicate that the testing protocol investigated has limited ability to discriminate between herds infected and not infected with SLT producing E. coli O157.

Algorithms↗
PubMed2002

Complex patterns of colonization and refugia revealed for European grayling Thymallus thymallus, based on complete sequencing of the mitochondrial DNA control region.

The complete mitochondrial DNA (mtDNA) control region (1043 base pairs) and 162-bp of flanking transfer RNA genes were sequenced in 316 European grayling, Thymallus thymallus, from 44 populations throughout the Western European range of the species. A total of 58 haplotypes were revealed with pairwise divergence ranging from 0.001 to 0.038. An inferred intraspecific phylogenetic tree revealed two well-supported clades within the Danube basin, one highly divergent clade in the Adriatic basin, and one large, diverse group representing most other populations. A deeply divergent haplotype fixed in the Loire basin in central France, more groups of haplotypes from distinct Danubian tributaries, and a relatively ancestral haplotype fixed in former tributaries of the Elbe in Denmark all suggest a complex pattern of interglacial and postglacial expansions originating from disjunct refugia throughout central Europe. Despite some evidence of human-mediated stock transfers, parsimony-network-based nested-clade analysis (NCA) supported specific inferences relating to corridors of postglacial expansion such as the lower Rhine (Moselle) and Elbe systems (Danish populations) serving as sources for expansion into the Baltic to the north as well as the upper Rhine and Danube to the south; and specific Rhine populations (Doller, Orbe and Reuss) serving as sources for colonization of the Rhone. The multiple divergent clades representing populations in the upper Danube, as well as the deeply divergent haplotypes found in the Adriatic and Loire basins (> 5% divergence from Asian outgroups) support the theory that European grayling have had a long history in Western Europe, pre-dating Pleistocene glacial cycles. The patterns of mtDNA divergence shown here support a perspective of rich inter- and intrabasin genetic diversity that should be protected from current trends to translocate brood stocks for rearing and release in response to declining populations, especially in southern European basins.

Animals↗
PubMed2003

Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae.

The mRNA and protein expression in Saccharomyces cerevisiae cultured in rich or minimal media was analyzed by oligonucleotide arrays and quantitative multidimensional protein identification technology. The overall correlation between mRNA and protein expression was weakly positive with a Spearman rank correlation coefficient of 0.45 for 678 loci. To place the data sets in a proper biological context, a clustering approach based on protein pathways and protein complexes was implemented. Protein expression levels were transcriptionally controlled for not only single loci but for entire protein pathways (e.g., Met, Arg, and Leu biosynthetic pathways). In contrast, the protein expression of loci in several protein complexes (e.g., SPT, COPI, and ribosome) was posttranscriptionally controlled. The coupling of the methods described provided insight into the biology of S. cerevisiae and a clustering strategy by which future studies should be based.

Amino Acid Sequence↗
PubMed2006

Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment.

MOTIVATION: A quantitative study of molecular evolutionary events such as substitutions, insertions and deletions from closely related genomes requires (1) an accurate multiple sequence alignment program and (2) a method to annotate the insertions and deletions that explain the 'gaps' in the alignment. Although the former requirement has been extensively addressed, the latter problem has received little attention, especially in a comprehensive probabilistic framework. RESULTS: Here, we present Indelign, a program that uses a probabilistic evolutionary model to compute the most likely scenario of insertions and deletions consistent with an input multiple alignment. It is also capable of modifying the given alignment so as to obtain a better agreement with the evolutionary model. We find close to optimal performance and substantial improvement over alternative methods, in tests of Indelign on synthetic data. We use Indelign to analyze regulatory sequences in Drosophila, and find an excess of insertions over deletions, which is different from what has been reported for neutral sequences. AVAILABILITY: The Indelign program may be downloaded from the website http://veda.cs.uiuc.edu/indelign/ SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.

Algorithms↗
PubMed1999

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

In this paper we present SFCHECK, a stand-alone software package that features a unified set of procedures for evaluating the structure-factor data obtained from X-ray diffraction experiments and for assessing the agreement of the atomic coordinates with these data. The evaluation is performed completely automatically, and produces a concise PostScript pictorial output similar to that of PROCHECK [Laskowski, MacArthur, Moss & Thornton (1993). J. Appl. Cryst. 26, 283-291], greatly facilitating visual inspection of the results. The required inputs are the structure-factor amplitudes and the atomic coordinates. Having those, the program summarizes relevant information on the deposited structure factors and evaluates their quality using criteria such as data completeness, structure-factor uncertainty and the optical resolution computed from the Patterson origin peak. The dependence of various parameters on the nominal resolution (d spacing) is also given. To evaluate the global agreement of the atomic model with the experimental data, the program recomputes the R factor, the correlation coefficient between observed and calculated structure-factor amplitudes and Rfree (when appropriate). In addition, it gives several estimates of the average error in the atomic coordinates. The local agreement between the model and the electron-density map is evaluated on a per-residue basis, considering separately the macromolecule backbone and side-chain atoms, as well as solvent atoms and heterogroups. Among the criteria are the normalized average atomic displacement, the local density correlation coefficient and the polymer chain connectivity. The possibility of computing these criteria using the omit-map procedure is also provided. The described software should be a valuable tool in monitoring the refinement procedure and in assessing structures deposited in databases.

Amino Acid Sequence↗
PubMed1992

Translation initiation in Escherichia coli: sequences within the ribosome-binding site.

The translational roles of the Shine-Dalgarno sequence, the initiation codon, the space between them, and the second codon have been studied. The Shine-Dalgarno sequence UAAGGAGG initiated translation roughly four times more efficiently than did the shorter AAGGA sequence. Each Shine-Dalgarno sequence required a minimum distance to the initiation codon in order to drive translation; spacing, however, could be rather long. Initiation at AUG was more efficient than at GUG or UUG at each spacing examined; initiation at GUG was only slightly better than UUG. Translation was also affected by residues 3' to the initiation codon. The second codon can influence the rate of initiation, with the magnitude depending on the initiation codon. The data are consistent with a simple kinetic model in which a variety of rate constants contribute to the process of translation initiation.

Base Sequence↗
PubMed2006

CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks.

BACKGROUND: One-dimensional protein structures such as secondary structures or contact numbers are useful for three-dimensional structure prediction and helpful for intuitive understanding of the sequence-structure relationship. Accurate prediction methods will serve as a basis for these and other purposes. RESULTS: We implemented a program CRNPRED which predicts secondary structures, contact numbers and residue-wise contact orders. This program is based on a novel machine learning scheme called critical random networks. Unlike most conventional one-dimensional structure prediction methods which are based on local windows of an amino acid sequence, CRNPRED takes into account the whole sequence. CRNPRED achieves, on average per chain, Q3 = 81% for secondary structure prediction, and correlation coefficients of 0.75 and 0.61 for contact number and residue-wise contact order predictions, respectively. CONCLUSION: CRNPRED will be a useful tool for computational as well as experimental biologists who need accurate one-dimensional protein structure predictions.

Algorithms↗
PubMed1993

Analysis of four microsatellite markers on the long arm of chromosome 9 by meiotic recombination in flow-sorted single sperm.

Meiotic recombination in flow-sorted single sperm was used to analyze four highly polymorphic microsatellite markers on the long arm of chromosome 9. The microsatellites comprised three tightly linked markers: 9CMP1 (D9S109), 9CMP2 (D9S127), and D9S53, which map to 9q31, and a reference marker, ASS, which is located in 9q34.1. Haplotypes of single sperm were assessed by using PCR in a single-step multiplex reaction to amplify each locus. Recombinant haplotypes were identified by their relative infrequency and were analyzed using THREELOC, a maximum-likelihood-analysis program, and an adaptation of CRI-MAP. The most likely order of these markers was cen-D9S109-D9S127-D9S53-ASS-tel with D9S109, D9S127, and D9S53 being separated by a genetic distance of approximately 3%. The order of the latter three markers did not however achieve statistical significance using the THREELOC program.

Base Sequence↗