Multi-objective engineering shape optimization using differential evolution interfaced to the Nimrod/O tool

This paper presents an enhancement of the Nimrod/O optimization tool by interfacing DEMO, an external multiobjective optimization algorithm. DEMO is a variant of differential evolution – an algorithm that has attained much popularity in the research community, and this work represents the first time that true multiobjective optimizations have been performed with Nimrod/O. A modification to the DEMO code enables multiple objectives to be evaluated concurrently. With Nimrod/O’s support for parallelism, this can reduce the wall-clock time significantly for compute intensive objective function evaluations. We describe the usage and implementation of the interface and present two optimizations. The first is a two objective mathematical function in which the Pareto front is successfully found after only 30 generations. The second test case is the three-objective shape optimization of a rib-reinforced wall bracket using the Finite Element software, Code_Aster. The interfacing of the already successful packages of Nimrod/O and DEMO yields a solution that we believe can benefit a wide community, both industrial and academic

Rapid Communication: Epidermal Growth Factor Maps to Pig Chromosome 8

Source and Description of Primers. Primers were designed from published sheep epidermal growth factor ( EGF) sequence (GenBank accession no. U36428) and were used to amplify across intron 3 of the EGF gene from porcine genomic DNA. Of sequences produced, 84 bp showed 82.1% identity to sheep EGF exon 3 and 81.0% to human EFG exon 3. For exon 4, the 75 bp showed 82.3% identity to sheep EGF exon 4 and 77.3% identity to human EGF exon 4. These sequences were further used to design pigspecific primers and have been submitted to GenBank (accession nos. AF079768 and AF079769)

Effect of farm system and milk urea phenotype on milk yield and milk composition of dairy cows in Canterbury

To investigate the effect of farm system, and cow selection for milk urea nitrogen (MUN), on milk yield and milk composition, a farmlet study was carried out between October 2018 and May 2019 in Lincoln, Canterbury. A farm system with a low stocking rate and low N fertiliser input (LSR, 2.9 cows/ha) sown with a conventional ryegrass clover and plantain diverse pastures was compared with a farm system with a moderate stocking rate and moderate N fertiliser (MSR, 3.9 cows/ha) using conventional ryegrass and white clover pastures and supplementing 3 kg DM/cow/d as crushed barley grain. Each farmlet had total herd size of 40 mixed-age HF x J spring-calving dairy cows which included six cows selected solely for a high MUN or a low MUN. There was no effect of farm system on milk fat, protein or lactose content but MUN was lower in LSR compared with MSR. Milk production was also lower for LSR (466 vs 429±12.4 kg MS/cow/ha, P<0.05), owing to poorer quality diet in mid lactation. Cows selected for low MUN tended to produce less milk compared with high MUN cows (4478 vs 3987±174 kg/cow, P<0.10) though this was partially offset by increased protein content in milk of low MUN cows. Farm system and animal selection for MUN have a greater impact on milk yield than on milk composition

Recent experimental probes of shear banding

Recent experimental techniques used to investigate shear banding are reviewed. After recalling the rheological signature of shear-banded flows, we summarize the various tools for measuring locally the microstructure and the velocity field under shear. Local velocity measurements using dynamic light scattering and ultrasound are emphasized. A few results are extracted from current works to illustrate open questions and directions for future research.Comment: Review paper, 23 pages, 11 figures, 204 reference

Stabilizing Salt-Bridge Enhances Protein Thermostability by Reducing the Heat Capacity Change of Unfolding

Most thermophilic proteins tend to have more salt bridges, and achieve higher thermostability by up-shifting and broadening their protein stability curves. While the stabilizing effect of salt-bridge has been extensively studied, experimental data on how salt-bridge influences protein stability curves are scarce. Here, we used double mutant cycles to determine the temperature-dependency of the pair-wise interaction energy and the contribution of salt-bridges to ΔCp in a thermophilic ribosomal protein L30e. Our results showed that the pair-wise interaction energies for the salt-bridges E6/R92 and E62/K46 were stabilizing and insensitive to temperature changes from 298 to 348 K. On the other hand, the pair-wise interaction energies between the control long-range ion-pair of E90/R92 were negligible. The ΔCp of all single and double mutants were determined by Gibbs-Helmholtz and Kirchhoff analyses. We showed that the two stabilizing salt-bridges contributed to a reduction of ΔCp by 0.8–1.0 kJ mol−1 K−1. Taken together, our results suggest that the extra salt-bridges found in thermophilic proteins enhance the thermostability of proteins by reducing ΔCp, leading to the up-shifting and broadening of the protein stability curves

Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged

We investigate changes in human c-type lysozyme flexibility upon mutation via a Distance Constraint Model, which gives a statistical mechanical treatment of network rigidity. Specifically, two dynamical metrics are tracked. Changes in flexibility index quantify differences within backbone flexibility, whereas changes in the cooperativity correlation quantify differences within pairwise mechanical couplings. Regardless of metric, the same general conclusions are drawn. That is, small structural perturbations introduced by single point mutations have a frequent and pronounced affect on lysozyme flexibility that can extend over long distances. Specifically, an appreciable change occurs in backbone flexibility for 48% of the residues, and a change in cooperativity occurs in 42% of residue pairs. The average distance from mutation to a site with a change in flexibility is 17–20 Å. Interestingly, the frequency and scale of the changes within single point mutant structures are generally larger than those observed in the hen egg white lysozyme (HEWL) ortholog, which shares 61% sequence identity with human lysozyme. For example, point mutations often lead to substantial flexibility increases within the β-subdomain, which is consistent with experimental results indicating that it is the nucleation site for amyloid formation. However, β-subdomain flexibility within the human and HEWL orthologs is more similar despite the lowered sequence identity. These results suggest compensating mutations in HEWL reestablish desired properties

Transcript profiling of candidate genes in testis of pigs exhibiting large differences in androstenone levels

<p>Abstract</p> <p>Background</p> <p>Boar taint is an unpleasant odor and flavor of the meat and occurs in a high proportion of uncastrated male pigs. Androstenone, a steroid produced in testis and acting as a sex pheromone regulating reproductive function in female pigs, is one of the main compounds responsible for boar taint. The primary goal of the present investigation was to determine the differential gene expression of selected candidate genes related to levels of androstenone in pigs.</p> <p>Results</p> <p>Altogether 2560 boars from the Norwegian Landrace and Duroc populations were included in this study. Testicle samples from the 192 boars with most extreme high or low levels of androstenone in fat were used for RNA extraction, and 15 candidate genes were selected and analyzed by real-competitive PCR analysis. The genes Cytochrome P450 c17 (<it>CYP17A1</it>), Steroidogenic acute regulatory protein (<it>STAR</it>), Aldo-keto reductase family 1 member C4 (<it>AKR1C4</it>), Short-chain dehydrogenase/reductase family member 4 (<it>DHRS4</it>), Ferritin light polypeptide (<it>FTL</it>), Sulfotransferase family 2A, dehydroepiandrosterone-preferring member 1 (<it>SULT2A1</it>), Cytochrome P450 subfamily XIA polypeptide 1 (<it>CYP11A1</it>), Cytochrome b5 (<it>CYB5A</it>), and 17-beta-Hydroxysteroid dehydrogenase IV (<it>HSD17B4</it>) were all found to be significantly (P < 0.05) up-regulated in high androstenone boars in both Duroc and Landrace. Furthermore, Cytochrome P450 c19A2 (<it>CYP19A2</it>) was down-regulated and progesterone receptor membrane component 1 (<it>PGRMC1</it>) was up-regulated in high-androstenone Duroc boars only, while <it>CYP21 </it>was significantly down-regulated (2.5) in high-androstenone Landrace only. The genes Nuclear Receptor co-activator 4 (<it>NCOA4</it>), Sphingomyrlin phosphodiesterase 1 (<it>SMPD1</it>) and 3β-hydroxysteroid dehydrogenase (<it>HSD3B</it>) were not significantly differentially expressed in any breeds. Additionally, association studies were performed for the genes with one or more detected SNPs. Association between SNP and androstenone level was observed in <it>CYB5A </it>only, suggesting cis-regulation of the differential transcription in this gene.</p> <p>Conclusion</p> <p>A large pig material of highly extreme androstenone levels is investigated. The current study contributes to the knowledge about which genes that is differentially expressed regard to the levels of androstenone in pigs. Results in this paper suggest that several genes are important in the regulation of androstenone level in boars and warrant further evaluation of the above mentioned candidate genes, including analyses in different breeds, identification of causal mutations and possible gene interactions.</p