Translational Research in Veterinary Science最新文献

{"title":"RNA-seq based SNP discovery in gluteus medius muscle of Polish Landrace pigs","authors":"M. Pierzchała, Magdalena Ogłuszka, E. Poławska, T. Blicharski, A. Roszczyk, A. Nawrocka, P. Urbański, Kamila Stepanow, Aleksandra Ciepłoch, D. Gołuch, Mateusz Sachajko, E. Juszczuk-Kubiak, Adrian Szczepański, M. Buszewska-Forajta, Joanna Szczepanek, C. Pareek","doi":"10.12775/trvs.2019.004","DOIUrl":"https://doi.org/10.12775/trvs.2019.004","url":null,"abstract":"","PeriodicalId":402923,"journal":{"name":"Translational Research in Veterinary Science","volume":"127 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132348905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Equine Back Disorders: A comparative study between palpation and radiographic findings","authors":"R. Henklewski","doi":"10.12775/trvs.2019.003","DOIUrl":"https://doi.org/10.12775/trvs.2019.003","url":null,"abstract":"The reason for performing this study was to investigate relationship between presence or absence of clinical signs of back problems with radiological findings and also to determine the prevalence of concurrent osseous pathology. Forty-four horses underwent clinical and radiological investigation of thoracolumbar spine. Results were recorded. Statistical analysis was performed to determine relationships between age, gender, work discipline, clinical and radiological features. The most common pathological finding was kissing spines syndrome. There was significant association between age, gender and work discipline and prevalence of pathological and radiological findings. X-rays revealed that horses with clinical signs of back problems were more likely to have osseous changes.","PeriodicalId":402923,"journal":{"name":"Translational Research in Veterinary Science","volume":"62 6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125937679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNA-seq based SNP discovery in liver transcriptome of Polish Landrace pigs","authors":"M. Pierzchała, Magdalena Ogłuszka, D. Gołuch, E. Poławska, T. Blicharski, A. Roszczyk, A. Nawrocka, P. Urbański, Kamila Stepanow, Aleksandra Ciepłoch, Mateusz Sachajko, M. Skowroński, Joanna Szczepanek, E. Juszczuk-Kubiak, Adrian Szczepański, M. Buszewska-Forajta, Xiangyang Miao, Vishnu Sharma, Sanjita Sharma, C. Pareek","doi":"10.12775/trvs.2019.005","DOIUrl":"https://doi.org/10.12775/trvs.2019.005","url":null,"abstract":"Background: RNA-seq technology is most commonly used in quantitative measurement of gene expression levels and identification of non-annotated transcripts. It is also used for the coding SNPs (cSNPs) discoveries in an efficient and cost-effective way. The aim of this study was to identify the putative genetic cSNPs variants in liver transcriptome of Polish Landrace pigs fed with high and low (normal) omega-6 and omega-3 polyunsaturated fatty acids (PUFAs) diets. Methods. RNA-seq based NGS experiment was performed on Polish Landrace pigs fed with high and low diets. Total RNA were isolated from liver tissues ofPUFAs dietary of Polish Landrace pigs. The RNA-seq libraries preparations were performed by mRNA enrichment, mRNA fragmentation, second strand cDNA synthesis, adaptor ligation, size selection and PCR amplification using the illumina TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego CA, USA), followed by NGS sequencing on MiSeq illumina platform. The quality control (QC) of raw RNA-seq data of liver transcriptome was performed using the Trimmomatic and FastQC tools. The paired-end mapping of the liver transcriptome RNA-seq data (n=12) was performed on the reference genome Sus scrofa v.10.2, followed by cSNPs discovery using GATK and SAMtools bioinformatics SNPs caller tools. Results: Two pooled paired-end libraries of 151bp liver transcriptome of Polish Landrace pigs were generated from MiSeq instrument and subsequent Fastq RNA-seq data were submitted to NCBI SRA database (https://www.ncbi.nlm.nih.gov/sra). Our study identified 25.3 million paired-end reads: representing 13,509,248 paired-end reads of high PUFAs dietary group and 11,815,696 paired-end reads of low PUFAs dietary group liver transcriptome. The SNP discovery results revealed identification of 25909 homozygous and 23290 heterozygous cSNPs in the liver transcriptome of both dietary groups of Polish Landrace pigs. With regards to same or alternative SNPs alleles encoding amino acids regions, a total of 27141 synonymous cSNP and 5989 non-synonymous cSNPs were identified in liver transcriptome representing high PUFAs dietary group. However, a total of 15128 synonymous cSNPs and 3900 non-synonymous cSNPs were identified in liver transcriptome representing low PUFAs dietary groups of Polish Landrace pigs. The identification of single nucleotide variations (SNVs) representing substitutions of all four possibilities (A,T,G,C) were ranged 2872 to 6868 SNVs (high PUFAs) and 2574 to 3654 SNVs (low PUFAs) in the homozygous cSNPs and 2452 to 2678 SNVs (high PUFAs) and 2094 to 2230 SNVs (low PUFAs) in the heterozygous cSNPs of liver transcriptomes of Polish Landrace pigs, respectively.","PeriodicalId":402923,"journal":{"name":"Translational Research in Veterinary Science","volume":"122 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125726647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quality control assessment of the RNA-Seq data generated from liver and pituitary transcriptome of Hereford bulls using StrandNGS software","authors":"C. Pareek, Mateusz Sachajko, Adrian Szczepański, M. Buszewska-Forajta, K. Żarczyńska, P. Sobiech, E. Juszczuk-Kubiak, Q. Shahzad, Yangqing Lu, Magdalena Ogłuszka, E. Poławska, M. Pierzchała","doi":"10.12775/TRVS.2019.001","DOIUrl":"https://doi.org/10.12775/TRVS.2019.001","url":null,"abstract":"Background : Quality control (QC) assessment is the most critical step in the high-throughput RNA-seq data analysis to characterize the in-depth understanding of genome and transcriptome assembling to a given reference genome. It provides not only a quick insight into the RNA-seq data quality to allow early identification of good or bad RNA-seq data samples, but also to verify the alignment QC checks for further essential high-throughput bioinformatics analysis such as, identification of novel genetic variants, differentially expressed genes (DEGs), gene network and metabolic pathways. Method : After isolation of total RNA from liver (n=15) and pituitary gland (n=15) tissues of young Hereford bulls, the pooled total RNA (n=30) were fragmented using GeneRead rRNA depletion kit (Qiagen, Hilden, Germany) and cDNA library preparation were preformed using ScriptSeq TM v2 RNA-Seq library preparation kit (Epicentre, illumina, USA), followed by high-throughput sequencing of combined liver and pituitary transcriptome using MiSeq reagent kit v2 (illumina, USA) to obtain high quality of paired-end RNA-seq reads of 251 base-pairs (bps). In this paper, the QC assessment of obtained RNA-seq raw data as well as post-alignment QC of processed RNA-seq data of combined liver and pituitary transcriptome (n=30) of Hereford bulls were performed using the strand NGS software v1.3 (Agilent; http://www.strand-ngs.com/ ) data analysis package. The reads were aligned with Bowtie using default settings against both Bull and Cow genome assembly. Results : Using two runs of MiSeq platform, a total of over 60 million paired-end RNA-seq reads were successfully obtained and submitted to NCBI SRA resources ( https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=312148 ). Library complexity plot results revealed 72.02% of duplicate reads with a low library complexity value of 0.28. The pre-alignment QC analysis of raw RNA-seq data revealed the sequence read lengths ranged from 35-251 bp size with more than 50% of all reads with length over 200bp and 10% of reads below 100bp. Conclusion : By testing the RNA-seq methodology on Illumina platform, two MiSeq sequencing runs yielded significantly high quality of 30 million sequencing reads per single MiSeq run. Our initial pre-alignment and post-alignment analysis of RNA-seq data analysis revealed that mapping of the Hereford liver and pituitary gland transcriptome to reference Bos taurus genome was successfully performed, however, more than 50% of all reads with length over 200bp were recovered. Therefore, obtained results concludes that liver and pituitary transcriptome sequencing with rRNA depletion method is less effective than mRNA RNA-seq method.","PeriodicalId":402923,"journal":{"name":"Translational Research in Veterinary Science","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134433208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Practical aspects of equine embryo transfer","authors":"M. Dordas-Perpinyà, J. Bruyas","doi":"10.12775/trvs.2019.002","DOIUrl":"https://doi.org/10.12775/trvs.2019.002","url":null,"abstract":"This article focuses on practical aspects and most specific points of equine embryo transfer (EET). Induction of polyovulations in donor mares is not possible. Only the repetition of embryo collections can increase the number of foals from the same mares. At each oestrus, follicular growth and artificial inseminations are conducted in the same way as for any brood mare. It is essential to know the number and timing of ovulations at least a 12-hours accuracy. Induction of ovulation is frequently required, GnRH agonists are used to do that. Embryos are flushed from the donor mare’s uterus, typically on day 7 or 8 after ovulation using a long (~1.5 m) and large (diameter 8 mm) Foley-type balloontipped catheter introduced by vaginal route just in front of the cervix. Some practical details are important to EET practitioners, firstly, the embryos are easily located under stereo-microscope after filtration of flushing medium, and secondly most equine embryos","PeriodicalId":402923,"journal":{"name":"Translational Research in Veterinary Science","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125850033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Legal aspects associated with the lack of possibilities of preventing the spread of toxocarosis and toxoplasmosis in Poland","authors":"M. Felsmann, M. Felsmann","doi":"10.12775/TRVS.2018.005","DOIUrl":"https://doi.org/10.12775/TRVS.2018.005","url":null,"abstract":"The aim of the study is to examine the impact of changes in Polish law the possibility of interrupting the roads spread toxoplasmosis and toxocarosis. The authors' assumption is to review the changes in Polish legal acts (acts and regulations) made in recent years in the context of combating toxocarosis and toxoplasmosis by the authorities of Polish government administration. An analysis was made of Polish laws regulating the control of zoonotic diseases (toxoplasmosis and toxocarosis), in particular acts which have been amended and changed in the last dozen or so years. The results of the analysis of changes in Polish law, relating to coping with toxocarosis and toxoplasmosis, clearly indicate the lack of legal grounds for effectively combating these diseases. The state public health services do not currently possess the legal means necessary to take effective action leading to the blocking of pathways along which these zoonoses spread. Currently the Polish law does not protect people against the possibility of contagion with toxoplasmosis and toxocarosis. The rights of animals, especially homeless cats, stand above the right of humans to protect themselves against parasites spread in public places by dogs and cats.","PeriodicalId":402923,"journal":{"name":"Translational Research in Veterinary Science","volume":"63 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134511554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of candidate genes for metabolic disorders expressed in liver and pituitary gland by comparing the RNA-seq data of Polish-HF and Polish-Red cattle","authors":"D. Wysocka, P. Sobiech, Magdalena Herudzińska, Mateusz Sachajko, C. Pareek","doi":"10.12775/TRVS.2018.004","DOIUrl":"https://doi.org/10.12775/TRVS.2018.004","url":null,"abstract":"Background: Metabolic disorder is a major health problem in dairy cattle, particularly to high milk producing dairy cattle. It is worthily emphasized that metabolic diseases have a very complex etiology and pathogenesis, and the impact of these diseases on hepatic and pituitary gland gene expression and organism oxidative balance is not fully described. The presented study was aimed to determine and predict the hepatic and pituitary gland expression of potential candidate genes in context to maintenance of oxidative balance, negative nitrogen balance, as well as ketosis in Polish HF and Polish Red cattle. Methods: Based on the RNA-seq experimental data, we investigated the candidate genes ( SOD1, SOD2, SOD3, GPx2, GPx3, GPx5, GPx6, GPx7, GPx8, BDH1, FN1, ACSL3 , HMGCL, HMGCS2, BDH2, ACSL6 , ACAT2, IDH3B, ACAT1, HMGCS1, ACSL4 , ACSL1 , PC, CPT1A, OXCT1 and ACSL5 respectively) expressions in liver and pituitary gland tissues of Polish HF and Polish Red cattle. The RNA-seq experimental design comprised of young bulls aged between 6 to 12 months were investigated. For each breed, six liver and six pituitary gland tissues were sequenced using Next-seq 500 illumina platform. The RNA-seq expression data were normalized by the reads per kilobase of exon per million reads mapped (RPKM) method. Results: By comparing the RNA-seq data of liver and pituitary gland tissues, the investigated candidate genes were highly expressed in the hepatic tissues than to pituitary gland in investigated cattle breeds. However, by comparing the Polish HF and Polish Red cattle breeds, results revealed a similar trend of gene expression profiling of all investigated candidate genes for both metabolic tissues. In case of hepatic gene expression profiling, the SOD1, FN1, HMGCL, HMGCS2, ACAT2, ACAT1, HMGCS1, ACSL1 and ACSL5 were highly expressed (FPKM values of >40), followed by SOD2, GPX3, IDH3B, PC and BDH2 as moderately expressed (FPKM values: >10 to 40), followed by SOD2, GPX8, IDH3B, ACAT1, ACSL4 and PC as moderately expressed (FPKM values: >10 to <40), and averagely expressed SOD3, GPX3,GPX5, GPX6, GPX7, GPX2, BDH1, BDH2, ACSL3 , ACSL6 , CPT1A, OXCT1, FN1, HMGCL, HMGCS2, ACAT2, ACAT1, HMGCS1, ACSL1 and ACSL5 respectively, in Polish HF and Polish Red breeds. Conclusions: Based on this presented results on hepatic and pituitary gland gene expression, a further research plan is an essential pre-requisite to validate the identified candidate genes. Study indicated the understanding the genetic factors that predispose metabolic disorders in cattle would benefit the dairy industry as a whole by providing producers, breeding services, and veterinarians a tool to forecast a cow’s susceptibility to metabolic disorders.","PeriodicalId":402923,"journal":{"name":"Translational Research in Veterinary Science","volume":"55 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128693114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influence of feto-pelvic disproportion on milk cows fertility","authors":"M. Gehrke, A. Sawa, J. Jaśkowski, B. Jaśkowski, Magdalena Herudzińska, Jakub Kulus","doi":"10.12775/trvs.2018.003","DOIUrl":"https://doi.org/10.12775/trvs.2018.003","url":null,"abstract":"The aim of the study was to evaluate relations between feto-pelvic proportion and further fertility of milk cows, select proportions and critical values of disproportion best predicting cows with lower fertility as a result of difficult calving as well as to evaluate fertility of cows selected on the basis of chosen criteria. The study was carried out on black-and-white and red-and-white Polish Holstein-Friesian cows in six farms diversified by the number of livestock (from 10 to 20 to over 180 cows) and milk yield (from 6.563 –","PeriodicalId":402923,"journal":{"name":"Translational Research in Veterinary Science","volume":"123 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132635754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influence of unilateral ovariectomy performed before ovulation on ovarian function, steroid hormone levels and development of porcine fetuses","authors":"K. Brüssow, J. Rátky, B. Kempisty, P. Antosik, Magdalena Herudzińska, J. Jaśkowski","doi":"10.12775/TRVS.2018.002","DOIUrl":"https://doi.org/10.12775/TRVS.2018.002","url":null,"abstract":"Corpus luteum (CL) activity is closely linked with initiation and maintenance of pregnancy and with fetal development. The present study was aimed to analyze the impact of unilateral ovarian removal on ovarian function, steroid hormone level and fetal distribution and development. Unilateral ovariectomy (uni-OVX) was performed in gilts one day before ovulation (group SHORT, n = 24), 20 days before subsequent ovulation (group LONG, n = 23) or ovaries remained intact (group INTACT, n = 22). Gilts were inseminated by single fixed-time laparoscopic intrauterine insemination (LIUI) after hormonal estrus synchronization. Two days before the end of a 15 day long altrenogest feeding, a part of gilts (n = 23) were surgically fitted with a jugular vein catheter and blood samples were collected to determine of estradiol (E2) and progesterone (P4) concentrations. All animals were slaughtered on day 30 of gestation and ovarian features as well as the number, weight and distribution of fetuses recorded. Altogether, 48 gilts (70%) were pregnant and pregnancy rates did not differ between groups. Short term uni-OVX affected CL number compared to intact and long term OVX gilts (9.9 ± 0.8 vs. 20.6 ± 1.9 and 17.5 ± 0.8; P < 0.05) and the number of fetuses (8.7 ± 0.5 vs. 15.0 ± 1.0 and 14.4 ± 1.1; P<0.05), respectively. Weights of individual CL were not influenced by treatment. Fetuses were differently distributed in the uterine horns after uni-OVX. A higher (P<0.05) proportion of fetuses was present always in the horn which bore the ovary. In all groups, weights of fetuses from uterine horns with an active ovary was similar; however, fetuses of the OVX horn of the SHORT group were lighter (P < 0.05). Steroid hormone profile was typical for pregnant gilts, but differences were observed between groups. Both, the preovulatory E2 concentrations and the early luteal phase P4 levels were higher (P < 0.05) in gilts of the INTACT and LONG groups. In summary, compared to intact gilts, only long term uni-OVX could compensate ovarian development. Short term uni-OVX affects (1) the total number of CL and fetuses, (2) the distribution and weight of fetuses in the uterine horns and (3) steroid hormone levels. Therefore, the time window, but not the uni-OXV per se, which alters the local supply of progesterone, has an impact on fetal development and survival.","PeriodicalId":402923,"journal":{"name":"Translational Research in Veterinary Science","volume":"37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125080695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of microRNAs in animal physiology and pathology","authors":"Joanna Szczepanek, C. S. Pareek, A. Tretyn","doi":"10.12775/TRVS.2018.001","DOIUrl":"https://doi.org/10.12775/TRVS.2018.001","url":null,"abstract":"MicroRNAs are a class of small, evolutionarily conserved, endogenous RNAs, capable of controlling gene expression. MicroRNAs are transcribed by RNA polymerases II and III, generating precursors that undergo a series of cleavage events to form mature microRNA. They play an important regulatory role in animals at the posttranscriptional levels by targeting mRNAs for direct cleavage of mRNAs or repression of mRNA translation. The main biological function of miRNA is the post-translation regulation of cells, like: proliferation and differentiation, cell death, fat metabolism, neuronal patterning and angiogenesis. These molecules are the main regulators of biological features of economic","PeriodicalId":402923,"journal":{"name":"Translational Research in Veterinary Science","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125157926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}