Recent outbreaks of adenovirus (FAdV) infections in poultry flocks have been determined in many countries in Europe, Asia and Australia connected with economic consequences, and loses in poultry production. To better understand the evolution and transmission of FAdV viruses, de- tailed codon usage analysis was performed for 137 recently obtained FAdV strains. A high effec- tive number of codons, and an indication the presence of low codon usage were determined. The presence of mutations, and their influence on codon usage was confirmed by a correlation be- tween nucleotide compositions at the 3rd codon positions, HVRs1-4, and ENCs. This presence indicate some influence of natural selection, and antigenic properties of examined FAdV strains.
This paper presents the current stage of the development of EA-MOSGWA – a tool for identifying causal genes in Genome Wide Association Studies (GWAS). The main goal of GWAS is to identify chromosomal regions which are associated with a particular disease (e.g. diabetes, cancer) or with some quantitative trait (e.g height or blood pressure). To this end hundreds of thousands of Single Nucleotide Polymorphisms (SNP) are genotyped. One is then interested to identify as many SNPs as possible which are associated with the trait in question, while at the same time minimizing the number of false detections.
The software package MOSGWA allows to detect SNPs via variable selection using the criterion mBIC2, a modified version of the Schwarz Bayesian Information Criterion. MOSGWA tries to minimize mBIC2 using some stepwise selection methods, whereas EA-MOSGWA applies some advanced evolutionary algorithms to achieve the same goal. We present results from an extensive simulation study where we compare the performance of EA-MOSGWA when using different parameter settings. We also consider using a clustering procedure to relax the multiple testing correction in mBIC2. Finally we compare results from EA-MOSGWA with the original stepwise search from MOSGWA, and show that the newly proposed algorithm has good properties in terms of minimizing the mBIC2 criterion, as well as in minimizing the misclassification rate of detected SNPs.
Conservation of genetic resources by semen cryopreservation is essential for biodiversity conservation and storage of rare poultry breeds. Despite the widespread use of this method not all individuals presentia similar capacity for semen to be used after defrosting. The aim of the current study was to identify SNP markers and linked candidate genes potentially associated with rooster (Gallus gallus) sperm motility after cryopreservation. Genome-wide association studies were performed using 33 roosters from four breeds genotyped using Illumina Chicken 60K SNP BeadChip Calculations were performed using PLINK and EMMAX software. Significant SNP associations rs15557972 (p<1.36E-07) on chromosome 10 in the LOXL1 gene and rs15751385 (p<6.10E-06) on chromosome 6 in the intron of the ENSGALG00000052127 gene were identified. These findings associated with sperm motility SNPs will help to develop strategies for the selection of valuable individuals and the efficient conservation of the gene pool.
Animals as a source of organs and tissues for xenotransplantation could become a backup solution for the growing shortage of human donors. The presence of human xenoreactive anti- bodies directed against Galα1,3Gal antigens on the cell surface of a pig donor triggers the activa- tion of the complement leading to a hyperacute reaction. The development of genetic engineer- ing techniques has enabled the modification of genomes by knocking in and/or knocking out genes. In this paper, we report the generation of modified pigs with ZFN mediated disruption of the GGTA1 gene encoding the enzyme responsible for synthesis of Galα1,3Gal antigens. ZFN plasmids designed to target the exon 9 region of the pig GGTA1 gene encoding the catalytic domain were injected into the pronuclei of fertilized egg cells. Among 107 piglets of the F0 gene- ration analyzed, one female with 9-nt deletion in exon 9 of the GGTA1 gene was found. 13 of 33 piglets of the F1 generation represented the +/- GGTA1 genotype and 2 of 13 F2 piglets repre- sented the -/- GGTA1 genotype. No changes in the animals’ behavior, phenotype or karyotype were observed. Analysis confirmed heredity of the trait in all animals. A complex functional analysis of the modified animals, including flow cytometry, human serum cytotoxicity test and immunohistochemical detection, was performed to estimate the phenotype effect of genetic modification and this indicated an efficient GGTA1 knock-out in modified pigs.
Article published in Science, 2012 by Jennifer A. Doudna, Emmanuelle Charpentier and their team presented a novel tool named as CRISPR/Cas9. The original CRISPR/Cas9 tool and the whole system developed from it since then allow making precise changes in the nucleotide sequence in the defined locus of the genome. The article presents the already known as well the potential future applications of the system for improvement of cultivated plants. The separate section is devoted to present the background of the Court of Justice decision C-528/16. Discussed are the far reaching negative consequences of this, based not on the merit decision, for the future of European green biotechnology.