Combined analysis of data from two granddaughter designs: A simple strategy for QTL confirmation and increasing experimental power in dairy cattle

A joint analysis of five paternal half-sib Holstein families that were part of two different granddaughter designs (ADR- or Inra-design) was carried out for five milk production traits and somatic cell score in order to conduct a QTL confirmation study and to increase the experimental power. Data were exchanged in a coded and standardised form. The combined data set (JOINT-design) consisted of on average 231 sires per grandsire. Genetic maps were calculated for 133 markers distributed over nine chromosomes. QTL analyses were performed separately for each design and each trait. The results revealed QTL for milk production on chromosome 14, for milk yield on chromosome 5, and for fat content on chromosome 19 in both the ADR- and the Inra-design (confirmed within this study). Some QTL could only be mapped in either the ADR- or in the Inra-design (not confirmed within this study). Additional QTL previously undetected in the single designs were mapped in the JOINT-design for fat yield (chromosome 19 and 26), protein yield (chromosome 26), protein content (chromosome 5), and somatic cell score (chromosome 2 and 19) with genomewide significance. This study demonstrated the potential benefits of a combined analysis of data from different granddaughter designs.     

Variability in responses to thermal stress in parasitoids

Abstract 1. To study phenotypic effects of stress, a stress is applied to cohorts of organisms with an increasing intensity. In the absence of mortality the response of traits will be a decreasing function of stress intensity because of increasing physiological costs. We call such decreasing functions type A responses. 2. However, when stress caused mortality, some studies have found that for high stress intensities, survivors performed as well as control individuals (type B responses). We proposed that type A responses are caused by the physiological cost of stress whereas type B responses are caused by a mixture of physiological costs and selection. 3. The present study exposed Aphidius picipes wasps to an increasing duration of cold storage (cold stress), and obtained variable responses as predicted when both physiological costs and selection of resistant individuals determine the outcome. 4. When cold storage of parasitoids for biological control is desirable, research should be carried out to find (i) the temperature regime and duration of storage and (ii) the least sensitive stage for storage to minimise losses from mortality and reduction of fitness of survivors. 5. Selection by cold stress as observed in the present study could result in rapid adaptation of populations exposed to such stress.     

腺嘌呤与氢化可的松大鼠肾阳虚模型造模方法比较

目的比较腺嘌呤诱导与氢化可的松诱导的SD大鼠肾阳虚模型的优劣,从而得到临床症状、生化指标更符合中医“肾阳虚”型的动物模型,以供科研、教学使用。方法雄性SD大鼠100只,随机分成正常组、腺嘌呤造模组及氢化可的松低剂量组、中剂量组、高剂量组各20只,造模成功后检测血肌酐（Scr）、尿素氮（BUN）、尿液中17-羟皮质类固醇（17-OH）和血浆中甲状腺激素（13、T4）、睾丸酮（T）、雌二醇（E2）及模型大鼠骨密度。结果无论从症状主证方面,还是客观指标方面（除骨密度外）,腺嘌呤诱导的SD大鼠肾阳虚型动物模型在生化指标研究方面均优于氢化可的松诱导组。结论腺嘌呤诱导的肾阳虚证SD大鼠模型在症状主证方面及其相关的生化研究方面优于氢化可的松组。     

A whole genome scan for differences in recombination rates among three Bos taurus breeds

Twenty paternal half-sib families of a granddaughter design were genotyped for 265 genetic markers, most of them microsatellites. These were 16 Holstein families, 3 Simmental families, and 1 Brown Swiss family. The number of sires per breed was 872, 170, and 32, respectively. Two-point recombination rates were estimated both jointly for all breeds and each single breed separately. Of 1168 marker intervals, 865 provided estimates for at least two breeds. Differences between breeds were tested by likelihood ratio tests. Four marker intervals, representing three genomic regions on BTA19, BTA24, and BTA27, show a significant impact of the breed at a false discovery rate of 0.23 and indicate a genetic component of observed heterogeneity of recombination. The variability of recombination rates between cattle breeds might not be a common feature of the whole genome, but rather might be restricted to certain chromosomal segments. Thus, attention should be paid to heterogeneities when pooling data of such regions from different breeds. Received: 14 March 2001 / Accepted: 8 May 2001     

Honeybee odometry: performance in varying natural terrain

Recent studies have shown that honeybees flying through short, narrow tunnels with visually textured walls perform waggle dances that indicate a much greater flight distance than that actually flown. These studies suggest that the bee's “odometer” is driven by the optic flow (image motion) that is experienced during flight. One might therefore expect that, when bees fly to a food source through a varying outdoor landscape, their waggle dances would depend upon the nature of the terrain experienced en route. We trained honeybees to visit feeders positioned along two routes, each 580 m long. One route was exclusively over land. The other was initially over land, then over water and, finally, again over land. Flight over water resulted in a significantly flatter slope of the waggle-duration versus distance regression, compared to flight over land. The mean visual contrast of the scenes was significantly greater over land than over water. The results reveal that, in outdoor flight, the honeybee's odometer does not run at a constant rate; rather, the rate depends upon the properties of the terrain. The bee's perception of distance flown is therefore not absolute, but scene-dependent. These findings raise important and interesting questions about how these animals navigate reliably.     

The ScPex13p SH3 domain exposes two distinct binding sites for Pex5p and Pex14p

Pex13p is an essential component of the peroxisomal protein import machinery and interacts via its C-terminal SH3 domain with the type II SH3-ligand Pex14p and the non-PXXP protein Pex5p. We report the solution structure of the SH3 domain of Pex13p from Saccharomyces cerevisiae and the identification of a novel-binding pocket, which binds a non-PXXP-peptide representing the binding site of Pex5p. Chemical shift assays revealed the binding sites for Pex5p and Pex14p ligand peptides to be distinct and spatially separated. Competition assays demonstrated that the two ligand peptides can bind simultaneously to the SH3 domain.     

The nature and identification of quantitative trait loci: a community's view

This white paper by eighty members of the Complex Trait Consortium presents a community's view on the approaches and statistical analyses that are needed for the identification of genetic loci that determine quantitative traits. Quantitative trait loci (QTLs) can be identified in several ways, but is there a definitive test of whether a candidate locus actually corresponds to a specific QTL?     

Protein evolution within and between species

Protein evolution can be seen as the successive replacement of amino acids by other amino acids. In general, it is a very slow process which is triggered by point mutations in the nucleotide sequence. These mutations can transform into single nucleotide polymorphisms (SNPs) within populations and diverging proteins between species. It is well known that in many cases amino acids can be replaced by others without impeding the functioning of the protein, even if these are of quite different physico-chemical character. In some cases, however, almost any replacement would result in a functionally deficient protein. Based upon comprehensive published SNP data and applying correlation analysis we quantified the two antagonist factors controlling the process of amino acid replacement and thus protein evolution: First, the degenerate structure of the genetic code which facilitates the exchange of certain amino acids and, second, the physico-chemical forces which limit the range of possible exchanges to maintain a functional protein. We found that the observed frequencies of amino acid exchanges within species are best explained by the genetic code and that the conservation of physico-chemical properties plays a subordinate role, but has nevertheless to be considered as a key factor. Between moderately diverged species genetic code and physico-chemical properties exert comparable influence on amino acid exchanges. We furthermore studied amino acid exchanges in more detail for six species (four mammals, one bird, and one insect) and found that the profiles are highly correlated across all examined species despite their large evolutionary divergence of up to 800 million years. The species specific exchange profiles are also correlated to the exchange profile observed between different species. The currently available huge body of SNP data allows to characterize the role of two major shaping forces of protein evolution more quantitatively than before.