Single-step methods for genomic evaluation in pigs

Genetic evaluation based on information from phenotypes, pedigree and markers can be implemented using a recently developed single-step method. In this paper we compare accuracies of predicted breeding values for daily gain and feed conversion ratio (FCR) in Danish Duroc pigs obtained from different versions of single-step methods, the traditional pedigree-based method and the genomic BLUP (GBLUP) method. In particular, we present a single-step method with an adjustment of the genomic relationship matrix so that it is compatible to the pedigree-based relationship matrix. Comparisons are made for both genotyped and non-genotyped animals and univariate and bivariate models. The results show that the three methods with marker information (two single-step methods and GBLUP) produce more accurate predictions of genotyped animals than the pedigree-based method. In addition, single-step methods provide more accurate predictions for non-genotyped animals. The results also show that the single-step method with adjusted genomic relationship matrix produce more accurate predictions than the original single-step method. Finally, the results for the bivariate analyses show a somewhat improved accuracy and reduced inflation of predictions for FCR for the two single-step methods compared with the univariate analyses. The conclusions are: first, the methods with marker information improve prediction compared with the pedigree-based method; second, a single-step method, contrary to GBLUP, provides improved predictions for all animals compared to the pedigree-based method; and third, a single-step method should be used with an adjustment of the genomic relationship matrix.     

Optimization for peptide sample preparation for urine peptidomics

Analysis of native or endogenous peptides in biofluids can provide valuable insights into disease mechanisms. Furthermore, the detected peptides may also have utility as potential biomarkers for non-invasive monitoring of human diseases. The non-invasive nature of urine collection and the abundance of peptides in the urine makes analysis by high-throughput ‘peptidomics’ methods , an attractive approach for investigating the pathogenesis of renal disease. However, urine peptidomics methodologies can be problematic with regards to difficulties associated with sample preparation. The urine matrix can provide significant background interference in making the analytical measurements that it hampers both the identification of peptides and the depth of the peptidomics read when utilizing LC-MS based peptidome analysis. We report on a novel adaptation of the standard solid phase extraction (SPE) method to a modified SPE (mSPE) approach for improved peptide yield and analysis sensitivity with LC-MS based peptidomics in terms of time, cost, clogging of the LC-MS column, peptide yield, peptide quality, and number of peptides identified by each method. Expense and time requirements were comparable for both SPE and mSPE, but more interfering contaminants from the urine matrix were evident in the SPE preparations (e.g., clogging of the LC-MS columns, yellowish background coloration of prepared samples due to retained urobilin, lower peptide yields) when compared to the mSPE method. When we compared data from technical replicates of 4 runs, the mSPE method provided significantly improved efficiencies for the preparation of samples from urine (e.g., mSPE peptide identification 82% versus 18% with SPE; p = 8.92E-05). Additionally, peptide identifications, when applying the mSPE method, highlighted the biology of differential activation of urine peptidases during acute renal transplant rejection with distinct laddering of specific peptides, which was obscured for most proteins when utilizing the conventional SPE method. In conclusion, the mSPE method was found to be superior to the conventional, standard SPE method for urine peptide sample preparation when applying LC-MS peptidomics analysis due to the optimized sample clean up that provided improved experimental inference from the confidently identified peptides.     

Preparation of Antigen for the Counterimmunoelectrophoretic Test for Plasmacytosis in Mink*

Counterimmunoelectrophoresis as a test method for making the diagnosis of plasmacytosis in mink demands the specific virus antigen. The method for preparation of the antigen according to Cho & Ingram (1972 a, b) with minor modifications is described in details, and results obtained at 62 antigen preparations are presented. In addition an ultrafiltration method is outlined which may be useful as a replacement for ultracentrifugation procedures used in the technique described by Cho & Ingram (1974).     

Interval Estimation for Ratios in Bioequivalence Trials

The problem for assessment of equivalence in variability of bioavailability between two drug products is considered. An exact confidence region for the ratio between intrasubject variabilities is derived when the intersubject variance is known. When the intersubject variance is unknown, a large sample approximation is considered. The proposed method for assessing equivalence in variability of bioavailability appears to be asymptotically uncorrelated with the sample mean ratio for average bioavailabilty. As a result, the proposed method in conjunction with the sample mean ratio method can be utilized for assessing population bioequivalence. An example concerning a bioequivalence trial with 24 healthy volunteers is presented to illustrate the proposed method.     

An efficient method for explant sterilization for reduced contamination

An improved method for sterilization of explants was tested and found to be suitable for plants with elongated internodes, such as bamboos. Final cutting of the explants into single nodal segments for inoculation was done only after surface sterilization of multi-nodal explants in a stoppered glass measuring cylinder. This minimized penetration of the contaminants and the sterilizing agents into the exposed intercellular spaces and vascular cavities at the cut ends, thereby minimizing their harmful effects. The method was experimented upon three different plants, viz., bamboo, tea and rose. Through this method the number of cultures getting contaminated was substantially reduced as compared to the conventional means where single nodal explants were used, employing identical treatments. Moreover, in this method, the number of cultures showing bud-break also showed a marked increase thereby resulting in a tremendous increase in the percentage of successfully established proliferating cultures.     

A method for increasing the number of mitoses available for cytogenetic analysis in rainbow trout

A new method for the cytogenetic analysis of fishes with special interest for the rainbow trout (Salmo gairdneri Rich.) is described. This reliable method that includes treatment with a yeast solution provides high quality spreads of a great number of metaphases.     

A Rapid Method for Microbial Sample Preparation for the Scanning Electron Microscope

A synthetic aromatic polymer has been used for preparing replicas of different microorganisms. This method of preparing highly concentrated (9.6 k) microbiological samples for scanning electron microscopy was compared with a standard method. The micrographs of the replicated samples are satisfactory. This method is rapid, cost effective and produces good results, especially in the case of spore-forming mycelial microorganisms.     

Corneal endothelium: a modified method for cultivation

A modified method for establishing cultures of rabbit corneal cells is described. The new technique utilized a Lucite disc in combination with a Tygon ring for growth of pure cell cultures and was compared with an explant method for growing cells. Each method provided adequate cell cultures for biochemical or ultrastructure studies of rabbit corneal cells, but the ring and disc method described here allowed the isolation of specific cell types without the interference of stromal cell contamination.     

A novel tetrazolium method for peroxidase histochemistry and immunohistochemistry.

We developed a new method for the histochemical demonstration of peroxidase. This method, which has a novel reaction mechanism, is based on the oxidation of phenol by peroxidase and coupling of this reaction to the reduction of a tetrazolium salt, with the deposition of an insoluble formazan at sites of enzyme activity. This new method was compared with an established diaminobenzidine (DAB) technique for peroxidase histochemistry and immunohistochemistry. Although both methods identified peroxidase activity in myeloid cells of bone marrow biopsy specimens, there was no interference from red cell pseudoperoxidase activity with the phenol-tetrazolium method, in contrast to the diaminobenzidine method. The detection of cytokeratin using an indirect immunoperoxidase technique was compared with both methods for demonstrating peroxidase activity. The phenol-tetrazolium method gave results similar to that obtained with DAB and appeared to be at least as sensitive as DAB in detecting low amounts of antigen. In addition, the production of a formazan as the final reaction product means that the phenol-tetrazolium method is ideally suited for quantitative peroxidase histochemistry. Therefore, the phenol-tetrazolium method represents a useful alternative method to DAB and for certain applications offers significant advantages over DAB.     

Corneal endothelium: A modified method for cultivation

Summary A modified method for establishing cultures of rabbit corneal cells is described. The new technique utilized a Lucite disc in combination with a Tygon ring for growth of pure cell cultures and was compared with an explant method for growing cells. Each method provided adequate cell cultures for biochemical or ultrastructure studies of rabbit corneal cells, but the ring and disc method described here allowed the isolation of specific cell types without the interference of stromal cell contamination.     

A method for measuring support for synapomorphy using character state distributions on phylogenetic trees

Synapomorphies are fundamental to phylogenetic systematics as they offer empirical evidence of monophyletic groups. However, no method exists to directly measure synapomorphy. Here, we propose a method that quantifies synapomorphy using the pattern of character state distribution over a cladogram separately for each character and for each clade. We define a fully synapomorphic character state as one shared by all of a clade’s terminal taxa and at the same time completely absent from all terminal taxa outside that clade. The extent to which this condition is met corresponds to the support for the character state being synapomorphic or, in short, support for synapomorphy. It is calculated as the probability of randomly selecting, by multi‐stage sampling following the topology of the tree, two terminals from inside a clade sharing the same character state and one terminal from outside the clade bearing a different character state. The method is independent of tree inference and free of transformational assumptions, and so can be applied to any tree and used for any type of discrete character. By measuring synapomorphy, the method offers a potential tool for determining diagnostic character states for taxa on different hierarchical levels, for evaluating alternative systems of character coding, and for evaluating clade support. We show how the method differs from ancestral character state reconstruction methods and goodness‐of‐fit indices. We demonstrate the behaviour of our method with several hypothetical scenarios and its potential use with two real‐life examples.     

Experimental basis for using Soviet bentonite clays as immunosorbents for serological studies

The methodological principles of using Soviet bentonite clays as immunosorbents necessary for serological studies in bacterial infections were worked out. The method for the preparation of antigenic bentonite diagnostic reagents was experimentally substantiated. Bentonite diagnostic reagents were first used in a new method for the rapid indication of bacterial antigens in environmental objects with a view of solving epidemiological problems.     

A simplified and efficient method for in situ hybridization to whole Drosophila embryos, using electrophoresis for removing non-hybridized probes

We report a simplified and reliable method for non-radioactive in situ hybridization to whole Drosophila embryos. In the previous method (Tautz and Pfeifle, 1989) the post-hybridization wash, or the procedure for washing non-hybridized probe away from embryos depends simply on diffusion. We modified the method with application of electrophoresis to the wash. After hybridized with RNA probe, embryos were transferred to a small well where an electric charge was given to drive non-hybridized probe away from the embryos. This procedure enables us to acquire a much higher signal-to-noise ratio than that obtained from a conventional method. Furthermore, this is a time-saving method. We propose a term "electro-wash" for this procedure.     

A quick microwave histochemical stain for copper

A rapid microwave method is described for staining copper in liver. This procedure was compared with a conventional method for copper. To this end, liver sections obtained from patients affected by several liver diseases associated with copper overload, were stained both with the standard rubeanic acid method for copper and with our modification of the same method, incorporating microwave treatment. Liver sections from a normal human newborn were used as a positive control. In Wilson's disease in the cirrhotic stage, copper was detected by the conventional method solely in periportal cells; following the microwave treatment, we were able to demonstrate copper in the whole lobule. In alcoholic cirrhosis, rubeanic acid stained copper only in a few periportal cells, while, by our modified method, copper was detected in almost all periportal hepatocytes. In chronic biliary tract disease, and in the newborn liver, copper was demonstrated in a few periportal cells by both the two histochemical procedures. In conclusion, although copper was detected by both procedures, a different degree of positivity was sometimes observed by using microwaves. Moreover, the microwave-treated sections showed more contrast and less artifacts. From a practical point of view, for the simplicity of employment and, above all, for its quickness (10 min), we suggest the use of our method in all conditions where copper overload is suspected.     

Exact inference for matched case-control studies

In an epidemiological study with a small sample size or a sparse data structure, the use of an asymptotic method of analysis may not be appropriate. In this paper we present an alternative method of analyzing data for case-control studies with a matched design that does not rely on large-sample assumptions. A recursive algorithm to compute the exact distribution of the conditional sufficient statistics of the parameters of the logistic model for such a design is given. This distribution can be used to perform exact inference on model parameters, the methodology of which is outlined. To illustrate the exact method, and compare it with the conventional asymptotic method, analyses of data from two case-control studies are also presented.     

Evaluation of a cushioned method for centrifugation and processing for freezing boar semen

The purpose of this investigation was to evaluate the use of an iodixanol cushion during centrifugation on sperm recovery and yield after centrifugation (sperm recovery, sperm motility, viability, membrane lipid disorder, acrosome reaction and ROS generation); and to investigate how this procedure affects sperm function after freezing-thawing (sperm motility, membrane lipid disorder, acrosomal status and homologous in vitro penetration test). The sperm-rich fractions from fertile boars were centrifuged under two centrifugation régimes: 800xg for 10min (standard method) and 1000xg for 20min with an iodixanol (60% w/v) cushion at the bottom of the centrifuge tubes (Cushion method). The highest recovery was achieved using the cushion method (sperm loss for cushion method was 0.50%+/-0.18 versus 2.97%+/-0.43 for standard method, P<0.01) and sperm quality was not significantly affected by the centrifugation régime. The motion parameters (% progressive motility, % motility, VCL, VSL, VAP, ALH, BCF, P<0.05) of frozen-thawed samples showed higher values using the standard method. However, a higher number of viable spermatozoa with lower lipid disorders were found in spermatozoa processed with the cushion method. The in vitro penetration assay showed that the individual boar influenced the parameters studied but there were no differences between the two centrifugation régimes used. Our results support the hypothesis that the proportion of sperm loss in frozen-thawed semen was significantly influenced by the centrifugation régime. Therefore, the iodixanol cushion method is a suitable tool for cryopreservation of boar semen in order to reduce sperm loss without affecting sperm quality.     

A procedure for analysis of stopped-flow transients for protein-ligand association

A method for extracting kinetic and optical parameters from progress curves for protein-ligand association, obtained by stopped-flow experiments, is described. The method is limited to one-step and two-step association kinetics, but it allows concentration of protein and offset of the signals to be adjustable parameters during an interactive non-linear least-squares fitting procedure. The method is tested on simulated pseudo-experimental data and applied to progress curves obtained in a stopped-flow spectrofluorimeter, for association of the translation initiation factor eIF4E with 7-methyl-GDP, an analog of 5'-end of mRNA.     

A modified method for estimation of chemical oxygen demand for samples having high suspended solids

Determination of chemical oxygen demand (COD) of samples having high suspended solids concentration such as cattle dung slurry with open reflux method of APHA-AWWA-WPCF did not give consistent results. This study presents a modification of the open reflux method (APHA-AWWA-WPCF) to make it suitable for samples with high percentage of suspended solids. The new method is based on a different technique of sample preparation, modified quantities of reagents and higher reflux time as compared to the existing open reflux method. For samples having solids contents of 14.0 g/l or higher, the modified method was found to give higher value of COD with much higher consistency and accuracy as compared to the existing open reflux method.     

The distorted shell method for clustering for syndrome classification.

Syndrome classification may be described as the arrangement of individuals into groups on the basis of their phenotypic resemblance. This paper describes how phenotypic resemblance may be quantified and demonstrates a numerical method called distorted shell clustering, which isolates groups of phenotypically similar individuals representing syndromes. This new method takes into consideration apparent biological properties of syndromes. It allows for overlapping phenotypes between syndromes, and differing character association and variability within syndromes. This method is compared to four other clustering methods by using suspects for a syndrome of known etiology (Down syndrome). The numerical results based on the phenotype then can be compared with the actual diagnosis. Only the distorted shell method classifies patients, without error, into two major clusters: the Down and the non-Down, while maintaining a high level of efficiency.     

A method for easily customizable gradient gel electrophoresis

Gradient polyacrylamide gel electrophoresis is a powerful tool for the resolution of polypeptides by relative mobility. Here, we present a simplified method for generating polyacrylamide gradient gels for routine analysis without the need for specialized mixing equipment. The method allows for easily customizable gradients which can be optimized for specific polypeptide resolution requirements. Moreover, the method eliminates the possibility of buffer cross contamination in mixing equipment, and the time and resources saved with this method in place of traditional gradient mixing, or the purchase of pre-cast gels, are noteworthy given the frequency with which many labs use gradient gel SDS-PAGE.