Marker-assisted selection can reduce true as well as pedigree-estimated inbreeding

This study investigated whether selection using genotype information reduced the rate and level of true inbreeding, that is, identity by descent, at a selectively neutral locus as well as a locus under selection compared with traditional BLUP selection. In addition, the founder representation at these loci and the within-family selection at the nonneutral locus were studied. The study was carried out using stochastic simulation of a population resembling the breeding nucleus of a dairy cattle population for 25 yr. Each year, 10 proven bulls were selected across herds along with 100 dams from within each of 40 herds. Selection was performed using BLUP, marker-assisted, or gene-assisted selection for a trait with low heritability (h² = 0.04) only expressed in females, mimicking a health trait. The simulated genome consisted of 2 chromosomes. One biallelic quantitative trait loci (QTL) with an initial frequency of the favorable allele of 0.1, and initially explaining 25% of the genetic variance as well as 4 markers were simulated in linkage disequilibrium, all positioned at chromosome 1. Chromosome 2 was selectively neutral, and consisted of a single neutral locus. The results showed that in addition to reducing pedigree-estimated inbreeding, the incorporation of genotype information in the selection criteria also reduced the level and rate of true inbreeding. In general, true inbreeding in the QTL was greater than pedigree-estimated inbreeding with respect to both the level and rate of inbreeding, as expected. Also as expected, true and pedigree-estimated inbreeding in the neutral locus were the same. Furthermore, after 25 yr, or approximately 5 generations, the pedigree-estimated level of inbreeding was reduced by 11 and 24% compared with BLUP in gene- and marker-assisted selection, respectively, and the level of true inbreeding in the QTL was reduced by 22 and 13%, respectively. The difference between selection scenarios was found to be caused by a larger number of founders being represented at the QTL when using genotype information in the selection criteria. This in turn was caused by an increased selection of individuals sharing the favorable QTL allele rather than individuals sharing genes on average, which was shown by a higher Mendelian selection differential in the QTL. Hence, even though the selection pressure was increased at the QTL, more variation was retained. The results suggest that marker-assisted selection is a useful selection strategy.     

Optimization of ordered plasmid assembly by gap repair in Saccharomyces cerevisiae

Combinatorial genetic libraries are powerful tools for diversifying and optimizing biomolecules. The process of library assembly is a major limiting factor for library complexity and quality. Gap repair by homologous recombination in Saccharomyces cerevisiae can facilitate in vivo assembly of DNA fragments sharing short patches of sequence homology, thereby supporting generation of high‐complexity libraries without compromising fidelity. In this study, we have optimized the ordered assembly of three DNA fragments into a gapped vector by in vivo homologous recombination. Assembly is achieved by co‐transformation of the DNA fragments and the gapped vector, using a modified lithium acetate protocol. The optimal gap‐repair efficiency is found at a 1:80 molar ratio of gapped vector to each of the three fragments. We measured gap‐repair efficiency in different genetic backgrounds and observed increased efficiency in mutants carrying a deletion of the SGS1 helicase‐encoding gene. Using our experimental conditions, a gap‐repair efficiency of > 10⁶ plasmid‐harbouring colonies/µg gapped vector DNA is obtained in a single transformation, with a recombination fidelity > 90%. Copyright © 2012 John Wiley & Sons, Ltd.     

A quantitative approach towards a better understanding of the dynamics of Salmonella spp. in a pork slaughter-line

Pork contributes significantly to the public health disease burden caused by Salmonella infections. During the slaughter process pig carcasses can become contaminated with Salmonella. Contamination at the slaughter-line is initiated by pigs carrying Salmonella on their skin or in their faeces. Another contamination route could be resident flora present on the slaughter equipment. To unravel the contribution of these two potential sources of Salmonella a quantitative study was conducted. Process equipment (belly openers and carcass splitters), faeces and carcasses (skin and cutting surfaces) along the slaughter-line were sampled at 11 sampling days spanning a period of 4 months. Most samples taken directly after killing were positive for Salmonella. On 96.6% of the skin samples Salmonella was identified, whereas a lower number of animals tested positive in their rectum (62.5%). The prevalence of Salmonella clearly declined on the carcasses at the re-work station, either on the cut section or on the skin of the carcass or both (35.9%). Throughout the sampling period of the slaughter-line the total number of Salmonella per animal was almost 2 log lower at the re-work station in comparison to directly after slaughter. Seven different serovars were identified during the study with S. Derby (41%) and S. Typhimurium (29%) as the most prominent types. A recurring S. Rissen contamination of one of the carcass splitters indicated the presence of an endemic 'house flora' in the slaughterhouse studied. On many instances several serotypes per individual sample were found. The enumeration of Salmonella and the genotyping data gave unique insight in the dynamics of transmission of this pathogen in a slaughter-line. The data of the presented study support the hypothesis that resident flora on slaughter equipment was a relevant source for contamination of pork.     

Structural determination of ethylene‐propylene‐diene rubber (EPDM) containing high degree of controlled long‐chain branching

This work highlights an attempt to characterize the degree and nature of long‐chain branching (LCB) in an unknown sample of ethylene‐propylene‐diene rubber (EPDM). Two EPDM rubbers selected for this study were comparable in comonomer compositions but significantly different with respect to molar mass and the presence of LCB. Both rubbers contained 5‐ethylidene‐2‐norbornene (ENB) as diene. Solution cast films of pure EPDM samples were used for different characterization techniques. ¹H‐NMR, and ¹³C‐NMR were used for assessing the comonomer ratios and LCB. Size exclusion chromatography (SEC) equipped with triple detector system was used to determine the molar mass (both absolute and relative) and polydispersity index (PDI). Presence of branching was also detected using sec‐viscometry. Rheological analysis has also been used for characterizing LCB. Finally, on the basis of the experimental findings and the available theories, an attempt was made to identify the chemical nature and degree of LCB. This study reveals the possibility of detailed characterization of molecular architecture of EPDM containing LCB by comparing with an essentially linear EPDM in light of an existing theory. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009     

Nonlinear tracking in a diffusion process with a Bayesian filter and the finite element method

A new approach to nonlinear state estimation and object tracking from indirect observations of a continuous time process is examined. Stochastic differential equations (SDEs) are employed to model the dynamics of the unobservable state. Tracking problems in the plane subject to boundaries on the state-space do not in general provide analytical solutions. A widely used numerical approach is the sequential Monte Carlo (SMC) method which relies on stochastic simulations to approximate state densities. For off-line analysis, however, accurate smoothed state density and parameter estimation can become complicated using SMC because Monte Carlo randomness is introduced. The finite element (FE) method solves the Kolmogorov equations of the SDE numerically on a triangular unstructured mesh for which boundary conditions to the state-space are simple to incorporate. The FE approach to nonlinear state estimation is suited for off-line data analysis because the computed smoothed state densities, maximum a posteriori parameter estimates and state sequence are deterministic conditional on the finite element mesh and the observations. The proposed method is conceptually similar to existing point-mass filtering methods, but is computationally more advanced and generally applicable. The performance of the FE estimators in relation to SMC and to the resolution of the spatial discretization is examined empirically through simulation. A real-data case study involving fish tracking is also analysed.     

A novel high-power pulse PECVD method

A novel plasma enhanced CVD (PECVD) technique has been developed in order to combine energetic particle bombardment and high plasma densities found in ionized PVD with the advantages from PECVD such as a high deposition rate and the capability to coat complex and porous surfaces. In this PECVD method, an ionized plasma is generated above the substrate by means of a hollow cathode discharge. The hollow cathode is known to generate a highly ionized plasma and the discharge can be sustained in direct current (DC) mode, or in high-power pulsed (HiPP) mode using short pulses of a few tens of microsecond. The latter option is similar to the power scheme used in high power impulse magnetron sputtering (HiPIMS), which is known to generate a high degree of ionization of the sputtered material, and thus providing new and added means for the synthesis of tailor-made thin films. In this work amorphous carbon coatings containing copper, have been deposited using both HiPP and DC operating conditions. Investigations of the bulk plasma using optical emission spectroscopy verify the presence of Ar⁺, C⁺ as well as Cu⁺ when running in pulsed mode. Deposition rates in the range 30 μm/h have been obtained and the amorphous, copper containing carbon films have a low hydrogen content of 4–5 at%. Furthermore, the results presented here suggest that a more efficient PECVD process is obtained by using a superposition of HiPP and DC mode, compared to using only DC mode at the same average input power.     

Analytical model based on green criteria for optical backbone network interconnection

Key terms such as Global warming, Green House Gas emissions, or Energy efficiency are currently on the scope of scientific research. Regarding telecommunications networks, wireless applications, routing protocols, etc. are being designed following this new “Green” trend. This work contributes to the evaluation of the environmental impact of networks from physical interconnection point of view. Networks deployment, usage, and disposal are analyzed as contributing elements to ICT's (Information and Communications Technology) CO₂ emissions. This paper presents an analytical model for evaluating and quantifying the CO₂ emissions of optical backbone networks during their lifetime. The main goal of this work is to present the model and illustrate how to evaluate the physical interconnection of backbones from an environmental perspective. This model can be applied as a new type of decision support criteria for backbone's interconnection, since minimization of CO₂ emissions is becoming an important factor. In addition, two case studies are presented to illustrate the use and application of this model, and the need for de facto and international standards to reduce CO₂ emissions through good network planning.