Template-Type: ReDIF-Article 1.0 Author-Name: Andrej Renčelj Author-Workplace-Name: Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia Author-Name: Martin Škrlep Author-Workplace-Name: Animal Production Department, Agricultural Institute of Slovenia, Ljubljana, Slovenia Author-Name: Meta Čandek-Potokar Author-Workplace-Name: Animal Production Department, Agricultural Institute of Slovenia, Ljubljana, Slovenia Author-Name: Peter Dovč Author-Workplace-Name: Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia Title: Tissue specific splicing of pre-mRNA porcine mitochondrial transcription factor A Abstract: Mitochondrial transcription factor A plays, due to its role in replication and transcription of the mitochondrial DNA, an important role in mitochondrial biogenesis and regulation of its activity. In different mammalian species, mitochondrial transcription factor A is present in two different splicing forms. The aim of the study was to verify the presence of both splicing forms and to estimate their ratio in different tissues. The expression levels of both splicing forms in two skeletal muscles (m. semispinalis capitis and m. semimembranosus), heart muscle, brain, spleen, and liver in commercial hybrids and in the autochthonous Krsko polje pig breed are reported. In all analyzed tissues the expression of the long form of the mitochondrial transcription factor A was about one order of magnitude higher compared to the short form, lacking almost the entire exon 4 region. Taking into account the expression ratio of both splicing forms and biological function of the mitochondrial transcription factor A, the possible explanation for the persistence of both forms in different mammalian species is provided. Keywords: pig, mitochondrion, mitochondrial biogenesis, splicing forms, expression Journal: Czech Journal of Animal Science Pages: 43-50 Volume: 63 Issue: 2 Year: 2018 DOI: 10.17221/29/2017-CJAS File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/29/2017-CJAS.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjs-201802-0001.txt Handle: RePEc:caa:jnlcjs:v:63:y:2018:i:2:id:29-2017-CJAS Template-Type: ReDIF-Article 1.0 Author-Name: Jana Vlčková Author-Workplace-Name: Institute of Animal Science, Prague-Uhříněves, Czech Republic Author-Workplace-Name: Czech University of Life Sciences Prague, Prague, Czech Republic Author-Name: Eva Tůmová Author-Workplace-Name: Czech University of Life Sciences Prague, Prague, Czech Republic Author-Name: Mohamed Ketta Author-Workplace-Name: Czech University of Life Sciences Prague, Prague, Czech Republic Author-Name: Michaela Englmaierová Author-Workplace-Name: Institute of Animal Science, Prague-Uhříněves, Czech Republic Author-Name: Darina Chodová Author-Workplace-Name: Czech University of Life Sciences Prague, Prague, Czech Republic Title: Effect of housing system and age of laying hens on eggshell quality, microbial contamination, and penetration of microorganisms into eggs Abstract: Hens of the laying hybrid ISA Brown were used in the study with the objective to evaluate eggshell quality, microbial contamination of eggshells, and penetration of microorganisms into the egg content in different housing systems (enriched cage: 60 hens, 10 hens per cage, 750 cm2 per hen vs free range: 60 hens, 9 hens per m2) and at different hen ages (26 vs 51 weeks) during storage time (0, 2, 7, 14, and 21 days). A significant interaction between the housing system and age was observed in egg weight and most of eggshell quality measurements. However, microbial contamination and penetration were affected mostly by the housing system and storage time. The numbers of Escherichia coli (P < 0.001, 4.51 vs 2.75 log cfu/eggshell) and Enterococcus (P < 0.001, 2.56 vs 1.11 log cfu/eggshell), and the total number of microorganisms (P < 0.001, 5.04 vs. 3.65 log cfu/eggshell) were higher in free range eggs compared to enriched cage eggs, respectively. The counts of Escherichia coli (P < 0.001, 4.23 vs 2.91 log cfu/eggshell) and Enterococcus (P < 0.001, 2.31 vs 1.27 log cfu/eggshell) decreased with storage time. A positive correlation between the total number of pores and penetration of Escherichia coli in both housing systems was observed in the albumen. It can be concluded that the housing system and age of laying hens significantly affected eggshell quality. Microbial contamination presumably affects the penetration of microorganisms. The correlation between the number of pores and penetration is assumed to be affected by the microbial species. Keywords: enriched cage, free range, egg safety, hen Journal: Czech Journal of Animal Science Pages: 51-60 Volume: 63 Issue: 2 Year: 2018 DOI: 10.17221/77/2017-CJAS File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/77/2017-CJAS.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjs-201802-0002.txt Handle: RePEc:caa:jnlcjs:v:63:y:2018:i:2:id:77-2017-CJAS Template-Type: ReDIF-Article 1.0 Author-Name: Mohamed Mahmoud Ibrahim Salem Author-Workplace-Name: Department of Animal and Fish Production, Faculty of Agriculture, University of Alexandria, Alexandria, Egypt Author-Name: Gertrude Thompson Author-Workplace-Name: Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Porto, Portugal Author-Name: Shanyuan Chen Author-Workplace-Name: Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Porto, Portugal Author-Name: Albano Beja-Pereira Author-Workplace-Name: Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Porto, Portugal Author-Workplace-Name: Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal Author-Name: Julio Carvalheira Author-Workplace-Name: Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Porto, Portugal Author-Workplace-Name: Abel Salazar Biomedical Sciences Institute, University of Porto, Porto, Portugal Title: Linkage disequilibrium and haplotype block structure in Portuguese Holstein cattle Abstract: The objectives of this study were to estimate linkage disequilibrium (LD), describe and scan a haplotype block for the presence of genes that may affect milk production traits in Portuguese Holstein cattle. Totally 526 animals were genotyped using the Illumina BovineSNP50 BeadChip, which contained a total of 52 890 single nucleotide polymorphisms (SNPs). The final set of markers remaining after considering quality control standards consisted of 37 031 SNPs located on 29 autosomes. The LD parameters historical recombinations through allelic association (D') and squared correlation coefficient between locus alleles frequencies ( r2) were estimated and haplotype block analyses were performed using the Haploview software. The averages of D' and r2 values were 0.628 and 0.122, respectively. The LD value decreased with increasing physical distance. The D' and r2 values decreased respectively from 0.815 and 0.283 at the distance of 0-30 kb to 0.578 and 0.090 at the distance of 401-500 kb. The identified total number of blocks was 969 and consisted of 4259 SNPs that covered 159.06 Mb (6.24% of the total genome) on 29 autosomes. Several genes inside the haplotype blocks were detected; CSN1S2 gene in haplotype block 51 on BTA 6, IL6 and B4GALT1 genes in haplotype blocks 6 and 33 on BTA 8, IL1B and ID2 genes in haplotype blocks 19 and 29 on BTA 11, and DGAT1 gene in haplotype block 1 on BTA 14. The extension of LD using BovineSNP50 BeadChip did not exceed 500 kb and its parameters r2 and D' were less than 0.2 and 0.70, respectively, after 70-100 kb. Consequently, the 50K BeadChip would have a poor power in genome wide association studies at distances between adjacent markers lower than 70 kb. Keywords: single nucleotide polymorphism, GWAS, dairy cattle Journal: Czech Journal of Animal Science Pages: 61-69 Volume: 63 Issue: 2 Year: 2018 DOI: 10.17221/56/2017-CJAS File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/56/2017-CJAS.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjs-201802-0003.txt Handle: RePEc:caa:jnlcjs:v:63:y:2018:i:2:id:56-2017-CJAS Template-Type: ReDIF-Article 1.0 Author-Name: Kemal Yazgan Title: RE-NUM-OR: Python-based renumbering and reordering software for pedigree files Abstract: RE-NUM-OR is a new, flexible, and user-friendly renumbering and reordering data arrangement software for unprocessed pedigree files used in genetic evaluation systems for personal computers. RE-NUM-OR was written using Python (Ver. 2.7.13) 64 byte programming language and compiled with PyInstaller-3.2.1 software which is a set of utilities for freezing Python scripts into executable. RE-NUM-OR not only runs on 32 or 64 byte MS Windows but also runs on 64 byte GNU/Linux. The program has new, practical, and simple interface and the user does not need to create a parameter file for running the program and .txt, .xlsx or .et extension files can be used as input files directly. Output files (.txt, .xlsx, .et, .dat) can be obtained. For animal, sire and dam IDs, it can read all standard characters (ASCII codes from 32 to 126) in input files. The program supports both dot (.) and comma (,) for numerical data. Pedigree lines for parents do not need to be arranged prior to their progeny. If pedigree lines for parents follow their progeny, the program can detect this and it can reorder the animals as pedigree lines placing parents prior to their progeny. Another feature of this software is that it has a pop-up window with error notification. Also, it supports repeated observations. RE-NUM-OR executable, its user manual, and sample input files are available from www.kemalyazgan.com.tr. Keywords: pedigree renumbering, pedigree reordering, data arrangement Journal: Czech Journal of Animal Science Pages: 70-77 Volume: 63 Issue: 2 Year: 2018 DOI: 10.17221/64/2017-CJAS File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/64/2017-CJAS.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjs-201802-0004.txt Handle: RePEc:caa:jnlcjs:v:63:y:2018:i:2:id:64-2017-CJAS Template-Type: ReDIF-Article 1.0 Author-Name: Anna Shaliutina-Kolešová Author-Workplace-Name: CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, P.R. China Author-Workplace-Name: Research Institute of Fish Culture and Hydrobiology, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Vodňany, Czech Republic Author-Name: Nian Rui Author-Workplace-Name: CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, P.R. China Author-Name: Saeed Ashtiani Author-Workplace-Name: CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, P.R. China Author-Name: Marek Rodina Author-Workplace-Name: Research Institute of Fish Culture and Hydrobiology, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Vodňany, Czech Republic Author-Name: Jacky Cosson Author-Workplace-Name: Research Institute of Fish Culture and Hydrobiology, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Vodňany, Czech Republic Author-Name: Otomar Linhart Author-Workplace-Name: Research Institute of Fish Culture and Hydrobiology, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Vodňany, Czech Republic Title: Oxidative stress and antioxidant enzyme defence system in seminal plasma of common carp (Cyprinus carpio) and rainbow trout (Oncorhynchus mykiss) during spawning season Abstract: Assessment of seminal oxidative stress indicators is emerging as a valuable prognostic tool in assisted reproductive technology. We investigated levels of oxidative stress caused by reactive oxygen species (ROS) and the antioxidant enzyme defence system comprising superoxide dismutase (SOD), glutathione reductase (GR), and glutathione peroxidase (GPx) in seminal plasma (SP) of common carp Cyprinus carpio and rainbow trout Oncorhynchus mykiss over the course of the spawning season. Oxidation was determined in lipids and proteins by assessing thiobarbituric acid reactive species (TBARS) and the 2,4-dinitrophenylhydrazine carbonyl groups, respectively. Levels of SOD were assessed by the autoxidation of pyrogallol. Determination of GR and GPx was based on the rate of NADPH oxidation. We observed clear alterations in lipids and proteins over the course of the spawning season in both species. The highest levels of TBARS and CP were recorded late in the season. SOD was not significantly altered in either species. The activity of GR was higher in carp SP late in spawning compared to other times (P < 0.05), while in rainbow trout, GR significantly increased (24.13 ± 2.8 mU/mg protein) in mid-season. A significantly lower GPx activity (9.18 ± 1.32 mU/mg protein) was found in rainbow trout SP early in the spawning season, but no significant differences in GPx were observed over the course of the season in carp. These results provide further understanding of the role of fish SP antioxidants and present new data on the oxidant and antioxidant balance in SP during the spawning season that may be of value in the development of methods for artificial reproduction of teleost species. Keywords: reproductive season, lipid peroxidation products, fish sperm, superoxide dismutase, glutathione reductase, glutathione peroxidase Journal: Czech Journal of Animal Science Pages: 78-84 Volume: 63 Issue: 2 Year: 2018 DOI: 10.17221/89/2017-CJAS File-URL: http://cjas.agriculturejournals.cz/doi/10.17221/89/2017-CJAS.html File-Format: text/html X-File-Ref: http://agriculturejournals.cz/RePEc/caa/references/cjs-201802-0005.txt Handle: RePEc:caa:jnlcjs:v:63:y:2018:i:2:id:89-2017-CJAS