Biomedical subjects

R E Hickson

Publications and source records attributed to R E Hickson.

7 recordsLinked to original sources

PubMed2006

Dystocia in beef heifers: a review of genetic and nutritional influences.

Breeding beef heifers for the first time at 15 months of age has potential to increase the efficiency of the beef breeding-cow herd. An increased incidence of dystocia in heifers calving at 2 years of age, compared to mature cows, is a major reason many farmers in New Zealand have not adopted the practice. The predominant type of dystocia affecting 2-year-old heifers is feto-maternal disproportion, a condition in which the fetus is too large relative to the size of the heifer's pelvis. Reducing birthweight of the calf is a means of reducing the incidence of dystocia. Birthweight and length of gestation are determined by genotype of the calf, maternal genetic effects and environmental effects. Bulls with low estimated breeding values for birthweight have been selected for mating heifers; however, the positive genetic correlation between birthweight and mature weight meant that the progeny of these bulls tended to be lighter at finishing, making them less desirable in the beef industry. The genotype of the dam also plays a role in determining the risk of dystocia; the maternal ability of the dam to nurture the fetus influences birthweight, and the dam's genetic potential for growth influences the size of her pelvic area. Heavy heifers tend to produce high birthweight calves, counteracting the reduction in the incidence of dystocia resulting from the larger pelvis in larger heifers. Manipulating feeding level during pregnancy offers an alternative method for manipulating the birthweight of calves. Little is known about the effects of nutrition in early gestation on placental development or birthweight of calves. No differences in the birthweight of calves have been observed in response to variation in feeding in mid-pregnancy, and variable responses in birthweight and the incidence of dystocia to feeding in the third trimester of pregnancy have been reported. Differences in birthweight have not always resulted in differences in the incidence of dystocia, primarily due to differences in liveweight of the heifer also induced by feeding regimens. Variability in the incidence of dystocia in response to feeding level in the third trimester of pregnancy makes it difficult to make recommendations for the feeding of heifers at this stage of gestation. More research is needed into the effects of nutrition in early gestation on fetal and placental development in cattle.

Animal Nutritional Physiological Phenomena↗

PubMed2006

Yields and persistency of lactation in Friesian and Jersey cows milked once daily.

Effects of milking cows once daily throughout lactation at high stocking rates (17% more cows/ha than for those milked twice daily) were studied in 2 Friesian and 2 Jersey herds during 3 lactations. Cows were allocated to 2 herds within breed and were milked either once or twice daily, based on age, genetic merit, and previous performance. Cows remained in their original herd and were milked at the same milking frequency during all lactations. Culled cows (20% per year) were replaced by 2-yr-old heifers. Yields of milk, lactose, protein, and fat were measured every 2 wk by commercial herd test. Cubic splines (5 knots) were used to approximate the lactation curve for each cow-yr to provide estimates of performance for each day of lactation. Yields of milk were greater for Friesian and Jersey cows milked twice daily (4,751 +/- 89 and 3,067 +/- 81 kg/cow) than for cows milked once daily (3,329 +/- 80 and 2,431 +/- 75 kg/cow), respectively. Cows milked once daily had lesser total and peak yields of milk, lactose, protein, and fat than cows milked twice daily. Friesians had greater total and peak yields than Jerseys. Peak production for all milk components occurred earlier in lactation for cows milked once daily than twice daily (d 24 to 39 vs. 32 to 44). Three measures of persistency of lactation were considered for each cow with 2 measures (Pers1 and Pers2) indicating that cows milked twice daily had better persistency than those milked once daily. Ranking of herds in persistency tended to match the ranking based on total yields. Measures of persistency (Pers1 and Pers2) were positively related to total yield in the Jerseys milked once daily and negatively related to peak yield in the Friesians. The third persistency measure (Pers3) ranked once-daily Jerseys first and twice-daily Friesians last, and was negatively correlated with total yield in the Friesian herds and negatively correlated with peak yield in all herds. For most performance measures, cows milked twice daily had better total yields and persistency than cows milked once daily.

Animals↗

PubMed2000

The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence.

The performances of five global multiple-sequence alignment programs (CLUSTAL W, Divide and Conquer, Malign, PileUp, and TreeAlign) were evaluated using part of the animal mitochondrial small subunit (12S) rRNA molecule. Conserved sequence motifs derived from an alignment based on secondary structural information were used to score how well each program aligned a data set of five vertebrate and five invertebrate taxa over a range of parameter values. All of the programs could align the motifs with reasonable accuracy for at least one set of parameter conditions, although if the whole sequence was considered, similarity to the structural alignment was only 25%-34%. Use of small gap costs generally gave more accurate results, although Malign and TreeAlign generated longer alignments when gap costs were low. The programs differed in the consistency of the alignments when gap cost was varied; CLUSTAL W, Divide and Conquer, and TreeAlign were the most accurate and robust, while PileUp performed poorly as gap cost values increased, and the accuracy of Malign fluctuated. Default settings for the programs did not give the best results, and attempting to select similar parameter values in different programs did not always result in more similar alignments. Poor alignment of even well-conserved motifs can occur if these are near sites with insertions or deletions. Since there is no a priori way to determine gap costs and because such costs can vary over the gene, alignment of rRNA sequences, particularly the less well conserved regions, should be treated carefully and aided by secondary structure and conserved motifs. Some motifs are single bases and so are often invisible to alignment programs. Our tests involved the most conserved regions of the 12S rRNA gene, and alignment of less well conserved regions will be more problematical. None of the alignments we examined produced a fully resolved phylogeny for the data set, indicating that this portion of 12S rRNA is insufficient for resolution of distant evolutionary relationships.

Algorithms↗

PubMed1997

Mhc allelic diversity and modern human origins.

Thirty complete coding sequences of human major histocompatibility complex (Mhc) class II DRB alleles, spanning 237 codons, were analyzed for phylogenetic information using distance, parsimony, and likelihood approaches. Allelic genealogies derived from different parts of the coding sequence (exon 2, the 5' and 3' ends of exon 2, respectively, and exons 3-6) were compared. Contrary to prior assertions, a rigorous analysis of allelic genealogies in this gene family cannot be used to justify the claim that the lineage leading to modern humans contained on average at least 100,000 individuals. Phylogenetic inferences based upon the exon 2 region of the DRB loci are complicated by selection and recombination, so this part of the gene does not provide a complete and accurate view of allelic relationships. Attempts to reconstruct human history from genetic data must use realistic models which consider the complicating factors of nonequilibrium populations, recombination, and different patterns of selection.

Alleles↗

PubMed1996

Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA.

Secondary structure models are an important step for aligning sequences, understanding probabilities of nucleotide substitutions, and evaluating the reliability of phylogenetic reconstructions. A set of conserved sequence motifs is derived from comparative sequence analysis of 184 invertebrate and vertebrate taxa (including many taxa from the same genera, families, and orders) with reference to a secondary structure model for domain III of animal mitochondrial small subunit (12S) ribosomal RNA. A template is presented to assist with secondary structure drawing. Our model is similar to previous models but is more specific to mitochondrial DNA, fitting both invertebrate and vertebrate groups, including taxa with markedly different nucleotide compositions. The second half of the domain III sequence can be difficult to align precisely, even when secondary structure information is considered. This is especially true for comparisons of anciently diverged taxa, but well-conserved motifs assist in determining biologically meaningful alignments. Patterns of conservation and variability in both paired and unpaired regions make differential phylogenetic weighting in terms of "stems" and "loops" unsatisfactory. We emphasize looking carefully at the sequence data before and during analyses, and advocate the use of conserved motifs and other secondary structure information for assessing sequencing fidelity.

Animals↗

PubMed1995

Use of spectral analysis to test hypotheses on the origin of pinnipeds.

The evolutionary origin of the pinnipeds (seals, sea lions, and walruses) is still uncertain. Most authors support a hypothesis of a monophyletic origin of the pinnipeds from a caniform carnivore. A minority view suggests a diphyletic origin with true seals being related to the mustelids (otters and ferrets). The phylogenetic relationships of the walrus to other pinniped and carnivore families are also still particularly problematic. Here we examined the relative support for mono- and diphyletic hypotheses using DNA sequence data from the mitochondrial small subunit (12S) rRNA and cytochrome b genes. We first analyzed a small group of taxa representing the three pinniped families (Phocidae, Otariidae, and Odobenidae) and caniform carnivore families thought to be related to them. We inferred phylogenetic reconstructions from DNA sequence data using standard parsimony and neighbor-joining algorithms for phylogenetic inference as well as a new method called spectral analysis (Hendy and Penny) in which phylogenetic information is displayed independently of any selected tree. We identified and compensated for potential sources of error known to lead to selection of incorrect phylogenetic trees. These include sampling error, unequal evolutionary rates on lineages, unequal nucleotide composition among lineages, unequal rates of change at different sites, and inappropriate tree selection criteria. To correct for these errors, we performed additional transformations of the observed substitution patterns in the sequence data, applied more stringent structural constraints to the analyses, and included several additional taxa to help resolve long, unbranched lineages in the tree. We find that there is strong support for a monophyletic origin of the pinnipeds from within the caniform carnivores, close to the bear/raccoon/panda radiation. Evidence for a diphyletic origin was very weak and can be partially attributed to unequal nucleotide compositions among the taxa analyzed. Subsequently, there is slightly more evidence for grouping the walrus with the eared seals versus the true seals. A more conservative interpretation, however, is that the walrus is an early, but not the first, independent divergence from the common pinniped ancestor.

Algorithms↗

PubMed1989

Self-splicing introns as a source for transposable genetic elements.

Previous theories have suggested that some introns with the ability to self-splice are derived from transposable elements. However, an interpretation is given here that suggests retrotransposons and retroviruses (transposable elements which move via RNA intermediates) have evolved from self-splicing introns. This is based on the involvement of RNA intermediates, the ancestral nature of the self-splicing reaction, and the assumed presence of introns in an RNA world. Conserved sequences within the introns, essential for splicing, and their wide phylogenetic distribution also make it unlikely that they are descended from transposable elements. Mitochondrial plasmids of Neurospora species containing features of both introns and retrotransposons have a central role in the resolution of the problem and are considered here to support the view that introns are, or have been, sources of mobile elements. The possibility of other transposable elements arising from introns is also considered.

Animals↗