基于等位基因的实数编码量子进化算法

为改善量子进化算法的早熟问题,提高算法搜索精度和收敛速度,提出了一种基于等位基因的实数编码量子进化算法。该算法以概率叠加的方式将实数变量按照等位基因进行编码,采用混合更新策略根据基因的"相对优良性"对等位基因进行变尺度变异,在全局搜索与局部搜索平衡的前提下提高搜索速度,之后引入Hε门更新等位基因对应的概率幅度。最后利用Markov链证明了其全局收敛性。数值算例将所提及算法与量子进化算法和基于双链编码的量子遗传算法进行比较,验证了算法的收敛速度和求解精度,并将该算法应用于纺织浆纱工艺参数的优化问题,获得了良好的优化效果。     

In vivo selectively infective phage as a tool to detect protein interactions: evaluation of a novel vector system with yeast Ste7p-Fus3p interacting proteins

The selectively infective phage (SIP) approach allows rapid identification of interacting proteins by linking protein-protein interaction to phage infectivity. Infection of E. coli by filamentous phage depends on viral g3p. This protein consists of three domains, N1, N2 and CT. Phages lacking the N1 domain are non-infective unless a bait (X)-prey (Y) interaction links it to phage anchored N2-CT domains. We have developed all the vectors required for an in vivo selectively infective phage strategy (SIP). This includes a bait vector, pG3N1, a prey vector, pHOS41, and a gene III deletion helper phage, HPd3. The bait vector pG3N1 allows expression of a bait protein (X) fused to the C-terminus of the N1 domain. The prey vector pHOS41 allows expression of prey (Y) proteins, fused to the N-terminus of the N2-CT domains. The gene III deletion helper phage delivers all phage proteins necessary for phage production, except g3p. Escherichia coli transformed with these three vectors produces non-infective phages unless a bait-prey interaction links the g3p domains. Fus3p and Ste7p, two proteins from the Saccharomyces cerevisiae pheromone-responsive pathway have been cloned to evaluate the SIP strategy. The presence of the interacting N1-Fus3p adapter increased the infectivity of Ste7p-N2-CT phages approximately 1400-fold, which makes SIP a promising technology for the detection and further investigation of interacting proteins.     

Chemical and sensory characterisation of pan-fried pork flavour: Interactions between raw meat quality, ageing and frying temperature

The effect of raw meat quality and cooking temperature on flavour generation in pork was investigated. The semimembranosus muscle was varied through genetics (carrier (HLY) and non-carrier (DLY) of the RN(-) allele) and ageing at 2°C (2, 15, and 22 days), whereas the pan-frying temperatures were 150°C and 250°C. HLY gave more pronounced 'fried' and 'burnt' notes than DLY after frying. This could partly be explained by a significantly higher concentration of glucose and glucose 6-phosphate in HLY after 22 days of ageing. HLY was generally perceived as more sour, which correlated well with the measured pH of HLY, but not to the l-lactate concentration. HLY was furthermore perceived as more tender and juicier than DLY, both attributes increased during ageing. Lipid-derived aroma volatiles dominated the samples fried at 150°C, while those from Maillard reactions mostly prevailed in the aroma profile at 250°C.     

Applications of high efficiency lithium acetate transformation of intact yeast cells using single-stranded nucleic acids as carrier

The highly efficient yeast lithium acetate transformation protocol of Schiestl and Gietz (1989) was tested for its applicability to some of the most important needs of current yeast molecular biology. The method allows efficient cloning of genes by direct transformation of gene libraries into yeast. When a random gene pool ligation reaction was transformed into yeast, the LEU2, HIS3, URA3, TRP1 and ARG4 genes were found among the primary transformants at a frequency of approximately 0.1%. The RAD4 gene, which is toxic to Escherichia coli, was also identified among the primary transformants of a ligation library at a frequency of 0.18%. Non-selective transformation using this transformation protocol was shown to increase the frequency of gene disruption three-fold. Co-transformation showed that 30-40% of the transformation-competent cells take up more than one DNA molecule which can be used to enrich for integration and deletion events 30- to 60-fold. Co-transformation was used in the construction of simultaneous double gene disruptions as well as disrupting both copies of one gene in a diploid which occurred at 2-5% the frequency of the single event.     

Using the unified relationship matrix adjusted by breed-wise allele frequencies in genomic evaluation of a multibreed population

The observed low accuracy of genomic selection in multibreed and admixed populations results from insufficient linkage disequilibrium between markers and trait loci. Failure to remove variation due to the population structure may also hamper the prediction accuracy. We verified if accounting for breed origin of alleles in the calculation of genomic relationships would improve the prediction accuracy in an admixed population. Individual breed proportions derived from the pedigree were used to estimate breed-wise allele frequencies (AF). Breed-wise and across-breed AF were estimated from the currently genotyped population and also in the base population. Genomic relationship matrices (G) were subsequently calculated using across-breed (G_AB) and breed-wise (G_BW) AF estimated in the currently genotyped and also in the base population. Unified relationship matrices were derived by combining different G with pedigree relationships in the evaluation of genomic estimated breeding values (GEBV) for genotyped and ungenotyped animals. The validation reliabilities and inflation of GEBV were assessed by a linear regression of deregressed breeding value (deregressed proofs) on GEBV, weighted by the reliability of deregressed proofs. The regression coefficients (b₁) from G_AB ranged from 0.76 for milk to 0.90 for protein. Corresponding b₁ terms from G_BW ranged from 0.72 to 0.88. The validation reliabilities across 4 evaluations with different G were generally 36, 40, and 46% for milk, protein, and fat, respectively. Unexpectedly, validation reliabilities were generally similar across different evaluations, irrespective of AF used to compute G. Thus, although accounting for the population structure in G_BW tends to simplify the blending of genomic- and pedigree-based relationships, it appeared to have little effect on the validation reliabilities.     

The DGAT1 K232A mutation is not solely responsible for the milk production quantitative trait locus on the bovine chromosome 14

The gene, acyl-CoA:diacylglycerol acyltransferase1 (DGAT1), was recently identified as the one underlying the quantitative trait locus (QTL) for milk production traits in the centromeric region of the bovine chromosome 14. Until now, 2 alleles, the lysine variant (increasing fat yield, fat and protein percentage) and the alanine variant (increasing protein and milk yield), were postulated at DGAT1. This study investigated whether the diallelic DGAT1 polymorphism is responsible for all the genetic variation at the centromeric region of this chromosome for milk, fat, and protein yield and fat and protein percentage. A statistical model was applied to a granddaughter design to analyze 16 German Holstein families. The model included the diallelic DGAT1 effect and the QTL transition probability estimated for each chromosomal position by a multiple marker approach. Because the regression coefficient of this probability was corrected for the diallelic DGAT1 polymorphism, it represented a putative conditional QTL effect. The effect of the DGAT1 gene was always highly significant. The conditional QTL effect was significant genomewise for fat percentage at the proximal end of the chromosome and for protein percentage at a more distal chromosomal region. Additional chromosomewise significance was found for fat and protein yield. Our results suggest an additional source of genetic variance on this chromosome for these traits; either one or more additional alleles segregating at DGAT1 that were not previously detected, a second quantitative trait locus affecting these traits, or both.     

Performance Evaluation of Lazy Deletion Methods in R-trees

Motivated by the way R-trees are implemented in commercial databases systems, in this paper we examine several deletion techniques for R-trees. In particular, in commercial systems R-tree entries are mapped onto relational tables, which implement their own concurrency protocols on top of existing table-level concurrency mechanisms. In analogy, the actual industrial implementations of B-trees do not apply the well-known merging procedure from textbooks in case of node underflows, but rather they apply the free-at-empty technique. This way, space is sacrificed for the benefit of faster deletions and less locking operations, whereas the search performance practically remains unaffected. In this context, we examine the efficiency of modifications to the original R-tree deletion algorithm, which relax certain constraints of this algorithm and perform a controlled reorganization procedure according to a specified criterion. We present the modified algorithms and experimental results about the impact of these modifications on the tree quality, the execution time for the deletion operation and the processing time of search queries, considering several parameters. The experimental results indicate that the modified algorithms improve the efficiency of the deletion operation, while they do not affect the quality of the R-tree and its performance with respect to search operations.     

Differential stability of human interleukin 1 beta fragments expressed in yeast

We have made deletions in a human interleukin 1 beta cDNA clonedin a yeast vector capable of directing the expression and secretionof foreign protein. Deletions at either the 5' or 3' end ofthe cDNA result in a dramatic drop in yield of protein. An investigationof some possible causes points to in stability of the truncatedpeptides as a major factor contributing to low yield. The resultssuggest that correct folding of mature interleukln 1 into aprotease resistant form requires almost the entire polypeptide.