Optimizing genomic prediction for Australian Red dairy cattle.

The reliability of genomic prediction is influenced by several factors, including the size of the reference population, which makes genomic prediction for breeds with a relatively small population size challenging, such as Australian Red dairy cattle. Including other breeds in the reference population may help to increase the size of the reference population, but the reliability of genomic prediction is also influenced by the relatedness between the reference and validation population. Our objective was to optimize the reference population for genomic prediction of Australian Red dairy cattle. A reference population comprising up to 3,248 Holstein bulls, 48,386 Holstein cows, 807 Jersey bulls, 8,734 Jersey cows, and 3,041 Australian Red cows and a validation population with between 208 and 224 Australian Red Bulls were used, with records for milk, fat, and protein yield, somatic cell count, fertility, and survival. Three different analyses were implemented: single-trait genomic best linear unbiased predictor (GBLUP), multi-trait GBLUP, and single-trait Bayes R, using 2 different medium-density SNP panels: the standard 50K chip and a custom array of variants that were expected to be enriched for causative mutations. Various reference populations were constructed containing the Australian Red cows and all Holstein and Jersey bulls and cows, all Holstein and Jersey bulls, all Holstein bulls and cows, all Holstein bulls, and a subset of the Holstein individuals varying the relatedness between Holsteins and Australian Reds and the number of Holsteins. Varying the relatedness between reference and validation populations only led to small changes in reliability. Whereas adding a limited number of closely related Holsteins increased reliabilities compared with within-breed prediction, increasing the number of Holsteins decreased the reliability. The multi-trait GBLUP, which considered the same trait in different breeds as correlated traits, yielded higher reliabilities than the single-trait GBLUP. Bayes R yielded lower reliabilities than multi-trait GBLUP and outperformed single-trait GBLUP for larger reference populations. Our results show that increasing the size of a multi-breed reference population may result in a reference population dominated by one breed and reduce the reliability to predict in other breeds.

Automatic poisson peak harvesting for high throughput protein identification.

High throughput identification of proteins by peptide mass fingerprinting requires an efficient means of picking peaks from mass spectra. Here, we report the development of a peak harvester to automatically pick monoisotopic peaks from spectra generated on matrix-assisted laser desorption/ionisation time of flight (MALDI-TOF) mass spectrometers. The peak harvester uses advanced mathematical morphology and watershed algorithms to first process spectra to stick representations. Subsequently, Poisson modelling is applied to determine which peak in an isotopically resolved group represents the monoisotopic mass of a peptide. We illustrate the features of the peak harvester with mass spectra of standard peptides, digests of gel-separated bovine serum albumin, and with Escherictia coli proteins prepared by two-dimensional polyacrylamide gel electrophoresis. In all cases, the peak harvester proved effective in its ability to pick similar monoisotopic peaks as an experienced human operator, and also proved effective in the identification of monoisotopic masses in cases where isotopic distributions of peptides were overlapping. The peak harvester can be operated in an interactive mode, or can be completely automated and linked through to peptide mass fingerprinting protein identification tools to achieve high throughput automated protein identification.

On the use of local statistical properties in focusing microscopy images.

Techniques to extract focus properties of microscopy images are many and varied. Many of them, however, rely on the summation of local statistical properties. Presented here is an examination of conventional focus determination algorithms, and a new method based on planar histograms of these local statistical properties. It is shown that this new method provides finer discernment of the focus properties of an image, and provides a means to extend the focus of an optical microscopy system.

Optical flow analysis of the ventral cellular layer of the migrating Dictyostelium discoideum slug.

A digital image analysis system for extracting motion information from time-varying digital light microscopy images is presented. This system is then used to map out the movement profile of the surface layer of cells in contact with the substratum through the extracellular matrix (ECM) of the migrating Dictyostelium discoideum slug. From digital high magnification light microscopy images, the morphology of moving cells within the tail region of a young migrating wild-type WS380B slug is described, and compared with the morphology of streaming D. discoideum cells. It is shown that: (i) when the migrating tip of the slug touches the agar substrate, cells in the anterior ventral surface layer of the tip region slow dramatically; (ii) overall cell movement in the ventral surface layer of the migrating D. discoideum slug is slower than the movement of the slug as a whole; and (iii) in less than 10% of cases a wave of movement (groups of cells synchronously slowing down and then accelerating forward) propagates down the slug axis at approx. 1.2 microns s-1. The time interval between waves may be related to the time interval between tip-to-substratum contact that is periodically re-established during normal WS380B slug migration after each aerial projection of the tip.

Length regulation in the Dictyostelium discoideum slug is a late event.

Time-lapse video light microscopy was used to study the emergence and maturation of the migratory slug from a D. discoideum aggregate. The anterior part, the tip of this simple multicellular organism, establishes migration prior to the definition of the rear, and hence the length of the slug. It was found that newly formed slugs of wild-type strain WS380B can reach lengths greater than 1 cm, yet mature slugs of this strain are rarely longer than 2-3 mumm. Often the tip extended out of the aggregation mound upon an arching pillar of cells. After the tip first touched the substratum, it commenced migration with a rapid succession of movement steps. Here we show that at the initiation of migration, a differential rate of cell movement along the developing slug axis results in a series of complicated changes, before the stable and mature shape of the slug is formed. Our results lead to new conclusions about D. discoideum slug formation and shape maintenance. Evidence is presented for regulation of slug length.

Dynamic arrays for fast, efficient, data manipulation during image analysis: a new software tool for exploratory data analysis.

Memory reallocation is used to construct a run-time data structure for fast/efficient storage of information during collection and analysis. The data structure presented uses dynamic memory but does not require the use of pointers to link nodes of information together. It allows for simple and efficient access to data via array indexing rather than through the use of lists or tree structures and it provides flexibility for competing storage requirements that are determined dynamically. The data structure is developed in the C programming language and a suite of ANSI standard C subroutines that make up a run-time data structure management system is provided.

Hash function performance on different biological databases.

Open hashing is used to demonstrate the effectiveness of several hashing functions for the uniform distribution of biological records. The three types of database tested include (1) genetic nomenclature, mutation sites and strain names, (2) surnames extracted from literature files and (3) a set of 1000 numeric ASCII strings. Several hash functions (hashpjw, hashcrc and hashquad) showed considerable versatility on all data sets examined while two hash functions, hashsum and hashsmc, performed poorly, on the same databases.

Movement of the Dictyostelium discoideum slug: models, musings, and images.

The last 5 years have resulted in many advances in knowledge of the cytoskeleton and motility of individual cells. Here the problem of multicellular movement is addressed. The Dictyostelium discoideum slug is examined, and models for how approximately 100,000 cells become coordinated to move are briefly reviewed. Experiments that contributed to model building as well as those used to test models are considered. Four levels of experimentation are considered: (1) the extracellular matrix (ECM) is examined as a component of the system; (2) information obtained by examining the organisation of slug cells through sectioning is presented; (3) time, the 4th dimension, is considered, and approaches to studying the dynamics of cell interactions from the point of view of movement are outlined, and (4) cell adhesion molecules are addressed.