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Öğe In silico discovery of epitopes of gag and env proteins for the development of a multi-epitope vaccine candidate against Maedi Visna Virus using reverse vaccinology approach(Academic Press Ltd- Elsevier Science Ltd, 2023) Kockaya, Ecem Su; Can, Hueseyin; Yaman, Yalcin; Uen, CemalMaedi Visna Virus (MVV) causes a chronic viral disease in sheep. Since there is no specific therapeutic drug that targets MVV, development of a vaccine against the MVV is inevitable. This study aimed to analyze the gag and env proteins as vaccine candidate proteins and to identify epitopes in these proteins. In addition, it was aimed to construct a multi-epitope vaccine candidate. According to the obtained results, the gag protein was detected to be more conserved and had a higher antigenicity value. Also, the number of alpha helix in the secondary structure was higher and transmembrane helices were not detected. Although many B cell and MHC-I/II epitopes were predicted, only 19 of them were detected to have the properties of antigenic, non-allergenic, non-toxic, soluble, and non-hemolytic. Of these epitopes, five were remarkable due to having the highest antigenicity value. However, the final multi-epitope vaccine was constructed with 19 epitopes. A strong affinity was shown between the final multi-epitope vaccine and TLR-2/4. In conclusion, the gag protein was a better antigen. However, both proteins had epitopes with high antigenicity value. Also, the final multi-epitope vaccine construct had a potential to be used as a peptide vaccine due to its immuno-informatics results.Öğe Molecular characterization of fecundity-related gene regions in some of Türkiye's native sheep breeds(Tubitak Scientific & Technological Research Council Turkey, 2024) Aymaz, Ramazan; Ozdil, Fulya; Yaman, YalcinIn this study, the BMP15 and GDF9 gene regions were examined through DNA sequencing in some native sheep breeds of Turkiye (Kivircik, Karacabey Merino, Chios, Gokceada, cine capari, Awassi, and Karakacan). In the BMP15 exon 2 region, two single nucleotide polymorphisms (SNPs) were identified: one synonymous SNP, P248P (proline/proline), and one nonsynonymous SNP, L251P (leucine/proline), resulting in a missense mutation. In the GDF9 exon 1 region, only a nonsynonymous SNP, R87H (histidine/ arginine), was found. In the GDF9 exon 2 region, four SNPs were identified: two nonsynonymous SNPs, E241K (glutamate/lysine) and V332I (valine/isoleucine), and two synonymous SNPs, L159L (leucine/leucine) and E326E (glutamate/glutamate). The identified haplotypes in the GDF9 gene region showed a high D' (linkage disequilibrium) value, indicating a strong association. Furthermore, a complete correlation was observed between the E326E and V332I variants in the studied breeds. The Chios breed exhibited significantly higher frequencies of heterozygosity for the E326E and V332I variants compared to the Kivircik and Karacabey Merino breeds. The heterozygosity frequencies for the E326E and V332I variants in the Kivircik, Karacabey Merino, and Chios breeds were determined to be 0.08, 0.13, and 0.46, respectively. The higher frequency of heterozygosity observed in E326E and V332I variants within the Chios breed suggests their association with the trait of multiple births.Öğe Newly developed peptide-ELISA successfully detected anti-IgG antibodies against Maedi-Visna virus in sheep(Elsevier, 2024) Kockaya, Ecem Su; Can, Huseyin; Yaman, Yalcin; Kandemir, Cagri; Taskin, Turgay; Karakavuk, Muhammet; Doskaya, Aysu DegirmenciMaedi Visna Virus (MVV) is a retrovirus that can infect sheep. There is still no effective therapy or vaccine against this virus and timely diagnosis is important to combat the complications of the disease. In this study, we aimed to develop an ELISA using peptides derived from gag protein as antigen. For this purpose, B cell epitopes of gag protein were predicted and a docking analysis with the B cell receptor was performed to select peptides to be used in ELISA. After three soluble epitopes with the highest antigenicity were produced as peptides, the immunogenicity of each peptide was determined by ELISA using sheep serum samples categorized as MVV positive (n=24) and negative (n=13). Subsequently, in house ELISA using above mentioned immunogenic peptides as antigen was used to investigate MVV seroprevalence in sheep (n=88). According to the results, among three peptides, two of them strongly reacted with MVV positive serum samples and the mean absorbance values detected among positive and negative serum samples were statistically significant, indicating that these peptides were immunogenic (P=0.016 and P=0.038). The third peptide also reacted with positive serum samples but the mean absorbance value was not statistically significant and this peptide was considered non-immunogenic (P=0.175). The immunogenic two peptides showed the same high sensitivity and specificity values of 91.60 and 92.80 according to the commercial kit. Moreover, MVV seroprevalence detected by peptide-ELISAs using CKQGSKE and CRPQGKAGHKG peptides as antigen was 3.40 % and 4.5 %, respectively. As a result, it was shown that these peptides can be successfully used for serological diagnosis of MVV.Öğe Ovine PAPPA2 gene coding variants are linked to decreased fecal egg shedding in native Turkish sheep naturally infected with gastrointestinal nematodes(Springer, 2023) Yaman, Yalcin; Bay, Veysel; Sevim, Semih; Aymaz, Ramazan; Keles, Murat; Onaldi, A. Taner; Ozuicli, MehmetIn this study, the association between PAPPA2 coding variants and gastrointestinal (GI) nematode fecal egg count (FEC) score in adult Turkish sheep was investigated. For this purpose, the FEC score was determined in adult sheep from six breeds: Karacabey Merino (n = 137), Kivircik (n = 116), Cine capari (n = 109), Karakacan (n = 102), Imroz (n = 73), and Chios (n = 50). Sheep were classified as shedders or non-shedders within breeds and flocks. The first group was the fecal egg shedders (> 50 per gram of feces), and the second group was the no fecal egg shedders (<= 50 per gram of feces). The exon 1, exon 2, exon 5, exon 7, and a part of 5 ' UTR of the ovine PAPPA2 gene were genotyped by Sanger sequencing of these two groups. Fourteen synonymous and three non-synonymous single-nucleotide polymorphisms (SNPs) were found. The non-synonymous SNPs, D109N, D391H, and L409R variants, are reported for the first time. Two haplotype blocks were constructed on exon 2 and exon 7. The specific haplotype, C(391)G(424)G(449)T(473)C(515)A(542) on the exon 2 that carries the 391H variant, was tested against four other common haplotypes. Our results indicate that C(391)G(424)G(449)T(473)C(515)A(542) haplotype was significantly associated with fecal egg shedding status in adult Turkish sheep (p-value, 0.044).Öğe Unveiling genetic signatures associated with resilience to neonatal diarrhea in lambs through two GWAS approaches(Nature Portfolio, 2024) Yaman, Yalcin; Kisi, Yigit Emir; Sengul, Serkan S.; Yildirim, Yasin; Bay, VeyselNeonatal diarrhea presents a significant global challenge due to its multifactorial etiology, resulting in high morbidity and mortality rates, and substantial economic losses. While molecular-level studies on genetic resilience/susceptibility to neonatal diarrhea in farm animals are scarce, prior observations indicate promising research directions. Thus, the present study utilizes two genome-wide association approaches, pKWmEB and MLM, to explore potential links between genetic variations in innate immunity and neonatal diarrhea in Karacabey Merino lambs. Analyzing 707 lambs, including 180 cases and 527 controls, revealed an overall prevalence rate of 25.5%. The pKWmEB analysis identified 13 significant SNPs exceeding the threshold of >= LOD 3. Moreover, MLM detected one SNP (s61781.1) in the SLC22A8 gene (p-value, 1.85eE-7), which was co-detected by both methods. A McNemar's test was conducted as the final assessment to identify whether there are any major effective markers among the detected SNPs. Results indicate that four markers-oar3_OAR1_122352257, OAR17_77709936.1, oar3_OAR18_17278638, and s61781.1-have a substantial impact on neonatal diarrhea prevalence (odds ratio: 2.03 to 3.10; statistical power: 0.88 to 0.99). Therefore, we propose the annotated genes harboring three of the associated markers, TIAM1, YDJC, and SLC22A8, as candidate major genes for selective breeding against neonatal diarrhea.
