YAKUSA: a fast structural database scanning method

YAKUSA is a program designed for rapid scanning of a structural database with a query protein structure. It searches for the longest common substructures called SHSPs (structural high-scoring pairs) existing between a query structure and every structure in the structural database. It makes use of protein backbone internal coordinates (alpha angles) in order to describe protein structures as sequences of symbols. The structural similarities are established in 5 steps, the first 3 being analogous to those used in BLAST: (1) building up a deterministic finite automaton describing all patterns identical or similar to those in the query structure; (2) searching for all these patterns in every structure in the database; (3) extending the patterns to longer matching substructures (i.e., SHSPs); (4) selecting compatible SHSPs for each query-database structure pair; and (5) ranking the query-database structure pairs using 3 scores based on SHSP similarity, on SHSP probabilities, and on spatial compatibility of SHSPs. Structural fragment probabilities are estimated according to a mixture transition distribution model, which is an approximation of a high-order Markov chain model. With regard to sensitivity and selectivity of the structural matches, YAKUSA compares well to the best related programs, although it is by far faster: A typical database scan takes about 40 s CPU time on a desktop personal computer. It has also been implemented on a Web server for real-time searches.     

Laser scanning cytometry: a novel method for the detection of platelet--endothelial cell adhesion

BACKGROUND: Adherence of platelets to endothelial cells may be a significant event in the development of vascular thrombosis. Existing models, which examine platelet-endothelial cell interactions, compromise endothelial cell integrity or use radioactivity to identify platelets that adhere to endothelial cells. We report a novel method for in vitro detection of platelet-endothelial cell adhesion that allows endothelial cells to remain as an intact monolayer and for visualization of individual platelets. METHODS: Fluorescently labeled platelets were incubated with a confluent monolayer of endothelial cells. Laser scanning cytometry (LSC) identified platelets bound to endothelial cells based on their fluorescent signals. RESULTS: LSC detection of platelets reliably reproduced well-described findings of thrombin-induced platelet-endothelial cell adhesion. Results demonstrating reduced adhesion with a glycoprotein IIb-IIIa-specific blocking monoclonal antibody confirmed the specificity of the LSC detection of platelet-endothelial cell adhesion. CONCLUSIONS: LSC is a novel method for detecting platelet--endothelial cell adhesion. Its advantages over other methods are: (a) endothelial cells remain undisturbed and adherent throughout; (b) the ability to detect individual bound platelets and subpopulations; (c) the ability to store images and slides and then relocate, revisualize, and reanalyze individual cells or cell populations of interest; and (d) no radioactivity.     

Tree scanning: a method for using haplotype trees in phenotype/genotype association studies

We use evolutionary trees of haplotypes to study phenotypic associations by exhaustively examining all possible biallelic partitions of the tree, a technique we call tree scanning. If the first scan detects significant associations, additional rounds of tree scanning are used to partition the tree into three or more allelic classes. Two worked examples are presented. The first is a reanalysis of associations between haplotypes at the Alcohol Dehydrogenase locus in Drosophila melanogaster that was previously analyzed using a nested clade analysis, a more complicated technique for using haplotype trees to detect phenotypic associations. Tree scanning and the nested clade analysis yield the same inferences when permutation testing is used with both approaches. The second example is an analysis of associations between variation in various lipid traits and genetic variation at the Apolipoprotein E (APOE) gene in three human populations. Tree scanning successfully identified phenotypic associations expected from previous analyses. Tree scanning for the most part detected more associations and provided a better biological interpretative framework than single SNP analyses. We also show how prior information can be incorporated into the tree scan by starting with the traditional three electrophoretic alleles at APOE. Tree scanning detected genetically determined phenotypic heterogeneity within all three electrophoretic allelic classes. Overall, tree scanning is a simple, powerful, and flexible method for using haplotype trees to detect phenotype/genotype associations at candidate loci.     

Dideoxy polymorphism scanning,a gene-based method for marker development for genetic linkage mapping

One of the fastest growing areas of biotechnology research today is marker-assisted breeding of crops. As a prerequisite to marker assisted breeding, genetic linkage maps are currently being developed for many species. For many purposes gene-based markers are the marker type of choice. The biggest problem in genetic linkage mapping using gene-based markers is the identification of polymorphisms between the parents of the population. To improve the efficiency of marker generation, we have developed a simple, and reasonable-cost method of polymorphism detection termed dideoxy polymorphism scanning. Since most of the time required to develop a gene-based linkage map is spent in identification of useful polymorphisms, this method will significantly shorten the time required for map generation and therefore reduce the overall cost.     

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between ¹³C, ¹⁵N and ¹H chemical shifts and backbone torsion angles ϕ and ψ (Cornilescu et al. J Biomol NMR 13 289–302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly differ from those observed in the crystalline state, the accuracy of predicted ϕ and ψ angles, equals ±13°. Large discrepancies between predictions and crystal structures are primarily limited to loop regions, and for the few cases where multiple X-ray structures are available such residues are often found in different states in the different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the neural network component of the program also predicts secondary structure with good accuracy. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Development of a rapid and effective method for preparing delicate dinoflagellates for scanning electron microscopy

We developed a rapid and effective procedure for scanning electron microscopy of three delicate dinoflagellates, Karlodinium micrum, Akashiwo sanguinea, and Heterocapsa niei. Good results were obtained when the specimens were fixed with a modified Párducz’s fixative (2% osmium tetroxide:saturated mercuric chloride = 5:1 v/v) for 10 min, washed in 0.05 M sodium cacodylate trihydrate buffer for 2 min, dehydrated in tert-butanol for 10 min and dried with hexamethyldisilazane in air for 3 min in a fume hood because reagents are very toxic. This method could be completed in 25 min. Compared with other preparative techniques, the present protocol has significant advantages for SEM observation by limiting distortion of delicate specimens and reducing the preparation time.     

FIMO: scanning for occurrences of a given motif

A motif is a short DNA or protein sequence that contributes to the biological function of the sequence in which it resides. Over the past several decades, many computational methods have been described for identifying, characterizing and searching with sequence motifs. Critical to nearly any motif-based sequence analysis pipeline is the ability to scan a sequence database for occurrences of a given motif described by a position-specific frequency matrix. RESULTS: We describe Find Individual Motif Occurrences (FIMO), a software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices. The program computes a log-likelihood ratio score for each position in a given sequence database, uses established dynamic programming methods to convert this score to a P-value and then applies false discovery rate analysis to estimate a q-value for each position in the given sequence. FIMO provides output in a variety of formats, including HTML, XML and several Santa Cruz Genome Browser formats. The program is efficient, allowing for the scanning of DNA sequences at a rate of 3.5 Mb/s on a single CPU. Availability and Implementation: FIMO is part of the MEME Suite software toolkit. A web server and source code are available at http://meme.sdsc.edu.     

A new method for constructing linker scanning mutants.

A new procedure for the construction of linker scanning mutants is described. A plasmid containing the target DNA is randomly linearized and slightly shortened by a novel combination of established methods. After partial apurination with formic acid a specific nick or small gap is introduced at the apurinic site by exonuclease III, followed by nuclease S1 cleavage of the strand opposite the nick/gap. Synthetic linkers are ligated to the ends and plasmids having the linker inserted in the target DNA are enriched. Putative linker scanning mutants are identified by their topoisomer patterns after relaxation with topoisomerase I. This technique allows the distinction of plasmids differing in length by a single basepair. We have used this rapid and efficient strategy to generate a set of 32 linker scanning mutants covering the chicken lysozyme promoter from -208 to +15.     

Alternate method for endocardial pacemaker lead implantation: A hybrid mini-thoracotomy approach

Although the conventional methods for endo-cardial pacemaker lead implantation via subclavian or cephalic or axillary vein routes is common, but sometimes due to anatomical variations it is not feasible to access these veins Emergence of newer techniques are useful for lead implantation. This case report focuses on a hybrid approach of combined mini-thoracotomy for endocardial pacemaker lead implantation. This fluoroscopy guided minimal thoracotomy approach with endocardial MRI compatible lead placement had the benefits of simple procedural, minimal hospital stay, low early complication rates and economically viable to the patient.     

A hybrid symbolic-numerical method for determining model structure

In this article, we present a method for determining whether a model is at least locally identifiable and in the case of non-identifiable models whether any of the parameters are individually at least locally identifiable. This method combines symbolic and numeric methods to create an algorithm that is extremely accurate compared to other numeric methods and computationally inexpensive. A series of generic computational steps are developed to create a method that is ideal for practitioners to use. The algorithm is compared to symbolic methods for two capture-recapture models and a compartment model.     

A hybrid ligand method for androgen receptor measurement

Existing techniques for androgen receptor (AR) assay are complicated by cross-reactivity of ligand binding affinities that can lead to incorrect estimation of receptor concentration. Two most frequently used ligands are [3H]dihydrotestosterone [( 3H]DHT) and [3H]methyltrienolone [( 3H]R1881), which in addition to binding to AR also bind to sex hormone binding globulin (SHBG; Kd = 1.5 nM) and progesterone receptors (PgR; Human Kd = 1 nM, rat Kd = 6 nM) respectively. Triamcinolone acetonide (TMA) is commonly used to block binding of [3H]R1881 to PgR, however at high concentrations TMA itself will bind AR (Kd = 7 microM). We have developed a hybrid ligand method for the measurement of AR in the presence of SHBG and PgR. This method used [3H]R1881 as the high specific activity labelled tracer and DHT as the unlabelled competitor of specific AR binding. Using this assay, 20% of human colorectal carcinomas were found to contain AR.     

A simplified method for preparing rotifer trophi for scanning electron microscopy

A simple, quick technique for the preparation of rotifer trophi for scanning electron microscopy is described. The method permits visual monitoring of the extraction process and does not require critical point drying of the specimens. Micrographs showing fine, structural detail of the hard parts of the mastax of representatives of the following genera are presented:Asplanchna, Conochilus, Filinia, Hexarthra, Keratella, Proalides, Synchaeta, andTrichocerca.     

Confocal laser scanning microscopy of fluorescently stained wood cells: a new method for three-dimensional imaging of xylem elements

Summary Xylem cells were fluorescently stained with periodic acid — Schiff reaction or with Schiffs reagent alone and studied by confocal laser scanning microscopy. Single images with extremely low depth of focus, series of optical sections, computed stereo scopic images and shadow casting images as well as x-z images are obtained. In contrast to scanning electron microscopy, not only are the surfaces imaged, but elements concealed by other structures can be visualized by this system. Quantitative data on cell depth are provided and differences in lignification are detected.     

Sequence scanning chicken cosmids: a methodology for genome screening

The chicken genome is relatively poorly studied at the molecular level. The karyotype 2n=78 is divided into three main chromosomal sub-groups: the macrochromosomes (six pairs), the intermediate microchromosomes (four pairs) and the microchromosomes (29 pairs). Whilst the microchromosome group comprise only 25% of the DNA, increasing evidence is proving that this is disproportionate to their gene content. This paper demonstrates the utility of cosmid sequence scanning as a potential method for analysing the chicken genome, providing an economical method for the production of a molecular map. The GC content, gene density and repeat distribution are analysed relative to chromosomal origin. Results indicate that gene density is higher on the microchromosomes. During the scanning process an example of conserved linkage between chicken and human (12q34.2) has been demonstrated.