Chicken globin gene number.

Using complementary DNA prepared from adult chicken globin messenger RNA, we show the existence of 2-3 non-cross-hybridising globin sequences in the chicken genome, each of which is present in only one copy per haploid genome. This was done by solution hybridization to total DNA under conditions of cDNA excess. The data agreses with results of RNA-driven hybridisation of globin complementary DNA, and with protein data.     

Phagocytosis of bacteria by polymorphonuclear leukocytes: a freeze-fracture, scanning electron microscope, and thin-section investigation of membrane structure

The changes in membrane structure of rabbit polymorphonuclear (PMN) leukocytes during bacterial phagocytosis was investigated with scanning electron microscope (SEM), thin-section, and freeze-fracture techniques. SEM observations of bacterial attachment sites showed the involvement of limited areas of PMN membrane surface (0.01-0.25μm(2)). Frequently, these areas of attachment were located on membrane extensions. The membrane extensions were present before, during, and after the engulfment of bacteria, but were diminished in size after bacterial engulfment. In general, the results obtained with SEM and thin-section techniques aided in the interpretation of the three-dimensional freeze-fracture replicas. Freeze-fracture results revealed the PMN leukocytes had two fracture faces as determined by the relative density of intramembranous particles (IMP). Membranous extensions of the plasma membrane, lysosomes, and phagocytic vacuoles contained IMP's with a distribution and density similar to those of the plasma membrane. During phagocytosis, IMPs within the plasma membrane did not undergo a massive aggregation. In fact, structural changes within the membranes were infrequent and localized to regions such as the attachment sites of bacteria, the fusion sites on the plasma membrane, and small scale changes in the phagocytic vacuole membrane during membrane fusion. During the formation of the phagocytic vacuole, the IMPs of the plasma membrane appeared to move in with the lipid bilayer while maintaining a distribution and density of IMPs similar to those of the plasma membranes. Occasionally, IMPs were aligned to linear arrays within phagocytic vacuole membranes. This alignment might be due to an interaction with linearly arranged motile structures on the side of the phagocytic vacuole membranes. IMP-free regions were observed after fusion of lysosomes with the phagocytic vacuoles or plasma membrane. These IMP-free areas probably represent sites where membrane fusion occurred between lysosomal membrane and phagocytic vacuole membrane or plasma membrane. Highly symmetrical patterns of IMPs were not observed during lysosomal membrane fusion.     

Isolation of a human anti-haemophilic factor IX cDNA clone using a unique 52-base synthetic oligonucleotide probe deduced from the amino acid sequence of bovine factor IX

A unique 52mer oligonucleotide deduced from the amino acid sequence of bovine Factor IX was synthesized and used as a probe to screen a human liver cDNA bank. The Factor IX clone isolated shows 5 differences in nucleotide and deduced amino acid sequence as compared to a previously isolated clone. In addition, precisely one codon has been deleted.     

Structural organization of a 17 KB segment of the alpha 2 collagen gene: evaluation by R loop mapping.

A recombinant phage, SpC3, containing a 17 kb genomic DNA insert representing approximately 60% of the 3' portion of the sheep collagen alpha 2 gene, was evaluated by electron microscopic R loop analysis. A minimum of 17 intervening sequences (introns) and 18 alpha 2 coding sequences (exons) were mapped. With the exception of the 850 base pair exon located at the extreme 3' end of the insert, all exons contained 250 base pairs or less. The total length of all the exons in SpC3 was 3,014 base pairs. The length distribution of the 17 introns ranged from 300 to 1600 base pairs; together, all of the introns comprised 14,070 base pairs of SpC3 DNA. Thus, the DNA region required for coding the interspersed 3 kb of alpha 2 collagen genetic information was 5.6 fold longer than the corresponding alpha 2 mRNA coding sequences.     

δβ-Thalassemia is due to a gene deletion

DNA has been prepared from peripheral blood or cultured skin fibroblasts obtained from three Sicilian and one Greek δβ-thalassemia homozygotes. Globin-gene analysis was carried out using a cDNA_β probe, and the results indicate that δβ-thalassemia has arisen from a deletion of the β-globin genes. A similar result was obtained using DNA prepared from cultured skin fibroblasts from an individual homozygous for the Negro form of hereditary persistence of fetal hemoglobin (HPFH). In both cases, the deletion has spared the ^Gγ and ^Aγ loci directing the γ chains of hemoglobin F, but it has not been possible to demonstrate any difference between the size of the deletion involved in the production of δβ-thalassemia and that which gave rise to HPFH. These experiments provide further direct evidence that deletions of critical areas of the γ-δ-β gene cluster result in persistent γ chain synthesis in adult life.     

Evaluation of recombinant DNA-directed E.coli produced alpha 1-antitrypsin as an anti-neutrophil elastase for potential use as replacement therapy of alpha 1-antitrypsin deficiency

alpha 1-antitrypsin (alpha 1AT) deficiency is an inherited disorder almost always associated with the development of panacinar emphysema in the fourth to fifth decades. One source of alpha 1AT for chronic replacement therapy of such individuals is that produced by E.coli directed by a cDNA coding for the human alpha 1AT molecule. Using TG1(E.coli), an alpha 1AT molecule produced by E.coli transformed with the plasmid-expressing vector pTG922, the present study shows that recombinant DNA-directed E.coli-produced alpha 1AT is as an effective inhibitor of neutrophil elastase as alpha 1AT purified from plasma. Importantly, TG1(E.coli) inhibited human neutrophil elastase with an association rate constant of 1.3 +/- 0.4X10(7) M-1 sec-1, similar to that of normal plasma alpha 1AT (1.1 +/- 0.1, p greater than 0.2). Furthermore, when TG1(E.coli) was added to alpha 1AT-deficient plasma obtained from homozygous alpha 1AT type Z individuals, the TG1(E.coli) remained functional and augmented the anti-neutrophil elastase activity of the serum proportional to the amount of TG1(E.coli) added. These observations suggest that if sufficient amounts of recombinant DNA methodology-produced alpha 1AT molecules could be safely delivered to the alveolar structures of alpha 1AT-deficient individuals, they would function to protect the alveolar walls from elastolytic attack.     

Effects of data structure on the estimation of covariance functions to describe genotype by environment interactions in a reaction norm model

Covariance functions have been proposed to predict breeding values and genetic (co)variances as a function of phenotypic within herd-year averages (environmental parameters) to include genotype by environment interaction. The objective of this paper was to investigate the influence of definition of environmental parameters and non-random use of sires on expected breeding values and estimated genetic variances across environments. Breeding values were simulated as a linear function of simulated herd effects. The definition of environmental parameters hardly influenced the results. In situations with random use of sires, estimated genetic correlations between the trait expressed in different environments were 0.93, 0.93 and 0.97 while simulated at 0.89 and estimated genetic variances deviated up to 30% from the simulated values. Non random use of sires, poor genetic connectedness and small herd size had a large impact on the estimated covariance functions, expected breeding values and calculated environmental parameters. Estimated genetic correlations between a trait expressed in different environments were biased upwards and breeding values were more biased when genetic connectedness became poorer and herd composition more diverse. The best possible solution at this stage is to use environmental parameters combining large numbers of animals per herd, while losing some information on genotype by environment interaction in the data.     

Right-hand-side updating for fast computing of genomic breeding values

Background

Since both the number of SNPs (single nucleotide polymorphisms) used in genomic prediction and the number of individuals used in training datasets are rapidly increasing, there is an increasing need to improve the efficiency of genomic prediction models in terms of computing time and memory (RAM) required.

Methods

In this paper, two alternative algorithms for genomic prediction are presented that replace the originally suggested residual updating algorithm, without affecting the estimates. The first alternative algorithm continues to use residual updating, but takes advantage of the characteristic that the predictor variables in the model (i.e. the SNP genotypes) take only three different values, and is therefore termed “improved residual updating”. The second alternative algorithm, here termed “right-hand-side updating” (RHS-updating), extends the idea of improved residual updating across multiple SNPs. The alternative algorithms can be implemented for a range of different genomic predictions models, including random regression BLUP (best linear unbiased prediction) and most Bayesian genomic prediction models. To test the required computing time and RAM, both alternative algorithms were implemented in a Bayesian stochastic search variable selection model.

Results

Compared to the original algorithm, the improved residual updating algorithm reduced CPU time by 35.3 to 43.3%, without changing memory requirements. The RHS-updating algorithm reduced CPU time by 74.5 to 93.0% and memory requirements by 13.1 to 66.4% compared to the original algorithm.

Conclusions

The presented RHS-updating algorithm provides an interesting alternative to reduce both computing time and memory requirements for a range of genomic prediction models.     

A comparison of principal component regression and genomic REML for genomic prediction across populations

Background

Genomic prediction faces two main statistical problems: multicollinearity and n ≪ p (many fewer observations than predictor variables). Principal component (PC) analysis is a multivariate statistical method that is often used to address these problems. The objective of this study was to compare the performance of PC regression (PCR) for genomic prediction with that of a commonly used REML model with a genomic relationship matrix (GREML) and to investigate the full potential of PCR for genomic prediction.

Methods

The PCR model used either a common or a semi-supervised approach, where PC were selected based either on their eigenvalues (i.e. proportion of variance explained by SNP (single nucleotide polymorphism) genotypes) or on their association with phenotypic variance in the reference population (i.e. the regression sum of squares contribution). Cross-validation within the reference population was used to select the optimum PCR model that minimizes mean squared error. Pre-corrected average daily milk, fat and protein yields of 1609 first lactation Holstein heifers, from Ireland, UK, the Netherlands and Sweden, which were genotyped with 50 k SNPs, were analysed. Each testing subset included animals from only one country, or from only one selection line for the UK.

Results

In general, accuracies of GREML and PCR were similar but GREML slightly outperformed PCR. Inclusion of genotyping information of validation animals into model training (semi-supervised PCR), did not result in more accurate genomic predictions. The highest achievable PCR accuracies were obtained across a wide range of numbers of PC fitted in the regression (from one to more than 1000), across test populations and traits. Using cross-validation within the reference population to derive the number of PC, yielded substantially lower accuracies than the highest achievable accuracies obtained across all possible numbers of PC.

Conclusions

On average, PCR performed only slightly less well than GREML. When the optimal number of PC was determined based on realized accuracy in the testing population, PCR showed a higher potential in terms of achievable accuracy that was not capitalized when PC selection was based on cross-validation. A standard approach for selecting the optimal set of PC in PCR remains a challenge.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-014-0060-x) contains supplementary material, which is available to authorized users.