RNA-seq based SNP discovery in liver transcriptome of Polish Landrace pigs

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 PUFAs diets. Total RNA were isolated from liver tissues of low PUFAs (n=6) and high PUFAs dietary group (n=6) 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 of Polish Landrace pigs 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.Conclusions: Study concluded that identification of cSNPs dataset representing the liver transcriptome of Polish Landrace pigs fed with a control diet (low) and pigs fed with a PUFAs diet (high) may be helpful to develop a new set of genetic markers for trait-associated studies (viz., growth and metabolic traits) specific to Polish Landrace pig breed. Such cSNP markers eventually can be utilized in the genetic improvement of the pig production traits using the genome-wide association studies (GWAS) and to finally implement on marker assisted selection (MAS) and genomics selection (GS) program in active breeding population of Polish Landrace pigs in Poland

Impacts of Precipitation Sources on Simulated Total Amount of Nutrients in Surface Runoff for Silver Creek Watershed, IL, USA

In agricultural basin, multiple nutrients were carried from the agricultural land with runoff into the stream or creek. Silver-creek watershed, Madison county, Illinois covers the agricultural basin. Nutrient like Nitrogen and Phosphorous were observed in significant value due to surface runoff from agricultural land to the downstream. Comparison of simulated nutrients were carried out with different precipitation sources. Model calibration for hydrology was performed with CFSR and PRISM in SUFI-2 from January 1998 to December 2001 on daily basis. Similarly, model was validated daily from January 2002 to December 2004. Comparison of results for change in investigated amount of Nitrogen and Phosphorous in pour points (downstream at confluence point near Kaskaskia River) of watershed reveals that there is a high amount of nutrients in PRISM datasets. The model and analysis facilitates in the favor of using spatial distributed precipitation sources for the accurate analysis on hydrology

Coagulase gene polymorphism, enterotoxigenecity, biofilm production, and antibiotic resistance in Staphylococcus aureus isolated from bovine raw milk in North West India

Abstract Background Staphylococcus aureus is the predominant bacterium responsible for various diseases in animals and humans. Preventive strategies could be better implemented by understanding the prevalence, genetic patterns, and the presence of enterotoxin and biofilm-producing genes along with the antibiotic susceptibility of this organism. This study was conducted in Rajasthan, the northwestern state of India, holding the largest population of cattle that makes it the second largest milk producer in India and no such prior information is available on these aspects. Methods A total of 368 individual quarter bovine raw milk samples were collected from 13 districts of Rajasthan, and screened for the presence of S. aureus. Microbiological and molecular approaches were followed for bacterial identification. Genetic diversity was determined by polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) of coagulase gene (coa), whereas enterotoxin and biofilm-producing genes were studied by PCR analysis. Antibiotic strips were employed to study the antibiotic resistance among strains. Results In all, 73 S. aureus strains were obtained from 368 bovine raw milk samples out of that only 30 showed the presence of coa. Nine types of coa patterns ranging from 730 to 1130 bp were observed among these isolates. PCR–RFLP of coa distinguished the isolates into 15 genotypic patterns, of which patterns I, IV, V, and VI were predominant. Of the isolates, 30% were positive for sec, 10% for sea, and 3.3% for seb; these genes are responsible for enterotoxin production, whereas all isolates were found positive for icaAD and eno. The prevalence rates of other biofilm-producing genes fnbA, clfB, ebpS, sasG, fnbB, sasC, cna, bap, fib and, bbp were 97, 93, 90, 80, 80, 77, 53, 27, 10, and 6.6%, respectively. Twenty-seven (90%) strains were multidrug resistant, of which 15 were methicillin resistant. Maximum sensitivity was reported for kanamycin and it could be considered as a drug of choice for controlling S. aureus mediated cattle infections in the studied regions. Conclusions Overall, these strains could cause several diseases to humans, insisting the need for developing a stricter hygiene program for improving milking practices and animal health

A Study on Pattern of Retinal Detachment in Patients with Choroidal Coloboma and Its Outcome after Surgery at a Tertiary Eye Hospital in Nepal

Background. To review the pattern of retinal detachment (RD) in patients with choroidal coloboma and type of reattachment surgery performed and to study its outcome in terms of retinal reattachment, visual acuity, and postsurgical complications. Methods. Observational case series of a single tertiary eye institution of 13 eyes having choroidal coloboma with RD done from January 2015 to June 2017. Results. Mean age of presentation was 29.3 years (Range 14–60 years). Males were two times more affected than females (2.25 : 1). The overall rate of anatomic success achieved after RD repair and silicon oil removal at 6 months was 92.3% (12/13 eyes). Following surgery, visual acuity improved in 6 out of 11 eyes (54.54%), remained unchanged in 4 eyes (36.36%), and worsened in 1 eye (9.1%). The most common complication following surgery was secondary glaucoma in 30.7% (4/11 eyes). Conclusion. The overall anatomic success rate of retina reattachment surgery in colobomatous eye is good, and the visual outcome following surgery can improve in majority of the cases or may remain same in few cases. Hence, timely surgery is advocated. But careful follow-up is required as the risk of postoperative complications is also high

Prevalence and associated factors of diabetic retinopathy among people with diabetes screened using fundus photography at a community diabetic retinopathy screening program in Nepal

Abstract Background This study aimed to assess the prevalence and associated factors of diabetic retinopathy (DR) and vision threatening DR (VTDR) among people with diabetes screened using fundus photography in Nepal. Methods This is a retrospective study among people with diabetes presented for DR screening using fundus photography from 2013 to 2019. Detailed demographics, duration of diabetes, medical history, visual acuity, and grading of DR on fundus photography were analyzed. Fundus camera used in the study were;Topcon digital fundus camera 900 CXR and digital portable fundus cameras (Nidek-10 portable non-mydriatric fundus camera; Versacam & Trade & Alpha, France), and a Zeiss portable fundus camera (Zeiss Visucout 100). Macula centred and disc centred 45 degree two images were taken from each eye. Pupil were dilated in cases where there was media haze in un-dilated cases. DR was graded using early treatment diabetic retinopathy study criteria. The images were graded by fellowship trained retina specialist. DR prevalence included any DR changes in one or both eyes. Results Total of 25,196 patients with diabetes were enrolled. Mean age was 54.2 years with Standard Deviation (S.D):12.9 years, ranging from 6 years to 97 years. Type 1 and type 2 diabetes comprised of 451 people (1.79%) and 24,747 (98.21%) respectively. Overall, 1.8% of the images were un-gradable. DR prevalence was 19.3% (95% Confidence Interval (CI): 18.8 − 19.7%). DR prevalence in type 1 and type 2 diabetes was 15.5% (95% CI: 12.5 − 18.6%) and 19.3% (CI: 18.8 − 19.8%) respectively. Clinically significant macular edema (CSME) was found in 5.9% (95% CI: 5.6-6.2%) and VTDR in 7.9% (95% CI: 7.7-8.3%). In multivariate analysis, our study revealed strong evidence to suggest that there is meaningful association between DR and VTDR with duration of diabetes, diabetic foot, diabetic neuropathy, agriculture occupation, those under oral hypoglycaemic agents or insulin or both as compared to those under diet only, and presenting visual acuity > 0.3LogMAR. Conclusion Prevalence and associated factors for DR and VTDR were similar to other DR screening programs in the region. Emphasis on wider coverage of DR screening could help for timely detection and treatment of STDR to avoid irreversible blindness