Background: Classical scrapie susceptibility in sheep has been linked to three polymorphisms at c... more Background: Classical scrapie susceptibility in sheep has been linked to three polymorphisms at codon 136, 154, and 171 in the prion protein gene (PRNP) whereas atypical scrapie susceptibility is related to polymorphisms at position 141. Many other variants over the length of the PRNP have been reported. Some of the variants may play crucial roles in fighting against the emergence of a new form of scrapie disease. Scrapie surveillance, scrapie associated genotyping and PRNP characterization studies have been conducted across the globe. However, such in-depth studies have never addressed the African continent's sheep breeds. Therefore, genotyping native Ethiopian sheep breed's PRNP gene has socioeconomic and scientific merits. This study aimed to identify PRNP variants in three native Ethiopian sheep breeds and their potential effect on scrapie susceptibility. Results : Five novel variants were identified in the PRNP gene of three native Ethiopian sheep breeds. Four non-synonymous heterozygous substitutions i.e. H99Q (CAC-->CAA), H99L (CAC-->CTA), A116E (GCA-->GAA), A116T (GCA-->ACA), and one synonymous N103N (AAC-->AAT) were detected. In addition to the novel variants, polymorphisms at codon 126,127,138,142,146,231, and 237 were also identified. The haplotype ARR was observed in Menz and Afar breeds at frequencies of 0.02 and 0.05 respectively. Neither ARR/ARR nor VRQ/VRQ genotypes were identified in the population under study. : Two of the novel variants at codon 99 and 103 that are placed closer to the proteinase K cleavage site and the variant at codon 116 in the palindrome region along with variants at codon 127 in glycine repeat domain may influence the conformational flexibility of prion protein. The rarity of ARR haplotype and the abundance of 141L variant demonstrated that the present study population was less resistant to classical scrapie and less predisposed to genotype associated atypical scrapie. This study provides a valuable dataset that can be potentially integrated into selective breeding strategies during interbreeding, crossbreeding and help to take precautionary measures against scrapie.
With the increased number of space related studies, it has become a significant study field in bo... more With the increased number of space related studies, it has become a significant study field in both dependable and long term biology based life support systems for long term space flights. Plants have been the major focus of this research. The capability of cultivate plants in space can help to provide astronauts with essential nutrients as well as improve their psychological health. Simulating the space environment, detailed gene analysis, and detailed growth analyzes reveal the effects of the space environment on plants. From the first photosynthetic organisms in the sea to today's terrestrial higher plants, they have survived millions of years on the Earth with the power of adaptations and evolution. Therefore, compared to the Earth, in the space environment, plants will react differently to decreased gravity, increased radiation rate, lost light source, and they will have altered stress gene regulation. In this review, which is about the adaptation of plants to the space environment, how plants react when they encounter stressful conditions that cause changes in their structures in the space environment and the results are discussed with various experiments. As a result, with using different plant species, it looks like even though these tiny greens faced with the hard condition in space environment they have shown a resistance mechanism to all these tough environments.
To contain the pandemics caused by SARS-CoV-2, early detection approaches with high accuracy and ... more To contain the pandemics caused by SARS-CoV-2, early detection approaches with high accuracy and accessibility are critical. Generating an antigen-capture based detection system would be an ideal strategy complementing the current methods based on nucleic acids and antibody detection. The spike protein is found on the outside of virus particles and appropriate for antigen detection. In this study, we utilized bioinformatics approaches to explore the immunodominant fragments on spike protein of SARS-CoV-2. Results. The S1 subunit of spike protein was identified with higher sequence specificity. Three immunodominant fragments, Spike 56-94 , Spike 199-264 , and Spike 577-612 , located at the S1 subunit were finally selected via bioinformatics analysis. The glycosylation sites and high-frequency mutation sites on spike protein were circumvented in the antigen design. All the identified fragments present qualified antigenicity, hydrophilicity, and surface accessibility. A recombinant antigen with a length of 194 amino acids (aa) consisting of the selected immunodominant fragments as well as a universal Th epitope was finally constructed. The recombinant peptide encoded by the construct contains multiple immunodominant epitopes, which is expected to stimulate a strong immune response in mice and generate qualified antibodies for SARS-CoV-2 detection.
Özet: DNA analiziyle kimlik belirlenmesi temel olarak tıp alanında kullanılmak üzere geliştirilmi... more Özet: DNA analiziyle kimlik belirlenmesi temel olarak tıp alanında kullanılmak üzere geliştirilmiş ve zaman içerisinde hayvan yetiştiriciliği alanında da kullanılmaya başlanmıştır. DNA analizi hayvan yetiştiriciliğinde Yetiştirme, işleme ve pazarlama aşamalarında kaydedilen bilgilerin doğruluğunun araştırılmasında kullanılmaktadır. Bu çalışmada avrupa birliği tarafından çıkarılan ve 1.1.2000 tarihinden itibaren bütün üye ülkelerde yürürlüğe girecek olan (EG) Nr.820/97 sayılı yasanın gereklerinin yerine getirilebilmesi amacıyla değişik avrupa birliği ülkelerinde geliştirilen kontrol ve denetim sistemlerinin karşılaştırılması ve DNA analizlerinin bu amaçla kullanilabilirliği araştırılmıştır. Anahtar sözcükler: DNA analizleri, kimlik kontrolü, Avrupa birliği Anwendbarkeit der DNA-Analyse bei der Identitätskontrolle und neue Verordnung in der EU Zusammenfassung: Die Methode der Identitätskontrolle mit DNA analyze wurde zunächst beim Menschen entwickelt. Bald darauf gab es Bestrebungen, die neue Technik auf Haustiere zu übertragen.
A Deeper Insight into <i>COL4A3</i>, <i>COL4A4</i>, and <i>COL4A5 </i>Variants and Genotype-Phenotype Correlation of a Turkish Cohort with Alport Syndrome
Background Bartonella henselae is one of the most commonly identified Bartonella species associat... more Background Bartonella henselae is one of the most commonly identified Bartonella species associated with several human diseases. Although B. henselae was detected in humans and cats in Turkey, they have not been genotyped previously. Therefore, this study aimed to genotype B. henselae samples (n = 44) isolated from stray cats using the multi-locus sequence typing (MLST) method. For this aim, eight different housekeeping markers were amplified by nested PCR and then sequenced to reveal sequence types (STs) of B. henselae samples. Results Allelic profiles obtained from 40 B. henselae isolates (90.9%) were compatible with available allelic profiles in the MLST online database. However, allelic profiles obtained from the remaining 4 B. henselae isolates (9.1%) were incompatible with the database. Among B. henselae isolates with compatible allelic profiles, 5 different STs including ST1, ST5, ST9, ST35 and ST36 were identified according to the B. henselae MLST online database. ST35 was t...
Distribution of hemolysin genes in Turkish Vibrio anguillarum isolates
Bulletin of The European Association of Fish Pathologists, 2015
WOS: 000357701100001Vibrio anguillarum, is the cause of haemorrhagic septicemia in marine and fre... more WOS: 000357701100001Vibrio anguillarum, is the cause of haemorrhagic septicemia in marine and freshwater fish of various ages. Losses caused by this disease are among the most important problems in the Turkish aquaculture sector. This study characterised 51 V. anguillarum isolates obtained from sea bass, sea bream and alternative marine species cultivated in the Aegean region between 2006-2013. Isolates were identified with conventional bacteriological methods, confirmed with PCR and analysed for the presence of hemolysin genes (vah 1-5) using a multiplex PCR. Based on whole cell 0 antigen serotyping, a total of 42 isolates were serotype 01 and 9 serotype O2. The prevalence of hemolysin genes were found to be 72.54 % for vah 1, 100 % for vah 2, 86.27 % for vah 3, 82.35 % for vah 4 and 17.64 % for vah 5 respectively. Variation in serotype did not necessarily correlate with genotype. In particular, distribution of prevalence of vah genes appeared to somewhat independent of serotype, with differing numbers of hemolysin genes (vah 2,3 in 1 isolate; vah 3,4 in 1 isolate; vah 2, 4 in 3 isolates; vah 1,2,3,4 in 4 isolates) found in the 9 V. anguillarum (O 2) isolates. This data provides a useful indication of the phenotypic and genetic diversity of the V anguillarum isolates circulating in farmed marine fish reared in the Aegean region
SUMMARY: Ün C, Aydoğdu S.(GSF-National Research Center for Environment and Health, Institute of D... more SUMMARY: Ün C, Aydoğdu S.(GSF-National Research Center for Environment and Health, Institute of Developmental Genetics, Neuherberg. Germany and Department of Pediatrics, Ege University Faculty of Medicine, Izmir, Turkey). Molecular genetic fundaments of celiac ...
Detection of Bovine Spongiform Encephalopathy-Related Prion Protein Gene Promoter Polymorphisms in Local Turkish Cattle
Biochemical Genetics, Sep 18, 2008
Polymorphisms in open reading frames of the prion protein gene (PRNP) have been shown to be assoc... more Polymorphisms in open reading frames of the prion protein gene (PRNP) have been shown to be associated with prion disease susceptibility in humans, sheep, and mice. Studies in recent years have demonstrated a similar effect of PRNP promoter and intron-1 polymorphisms on bovine spongiform encephalopathy (BSE) susceptibility in cattle. In this study, the deletion/insertion (indel) polymorphisms of the bovine PRNP gene within the promoter sequence (23 bp) and intron 1 (12 bp) were analyzed in local Turkish cattle. For this, 150 animals belonging to three different local breeds--the South Anatolian red, the East Anatolian red, and the Turkish gray--were tested using DNA purification and polymerase chain reaction. The ins allele in the 12 bp indel, which is associated with low susceptibility to BSE, showed a high frequency in all three breeds. The low-susceptibility allele of the 23-bp indel was identified in Turkish gray cattle with a frequency of 0.80. Results of the study have shown that local Turkish cattle might have an important genetic value for selection against BSE.
Özet Araştırmanın amacı; İzmir ve Manisa illerinde bulunan kıl keçi sürülerinde scrapie hastalığı... more Özet Araştırmanın amacı; İzmir ve Manisa illerinde bulunan kıl keçi sürülerinde scrapie hastalığına ait risk faktörlerini belirlemektir. Bu çalışmada, sadece ankete dayalı olarak işletmelerde klinik olmayan ve sürü yönetimiyle ilgili risk faktörleri ele alınmıştır. Çalışma alanını; İzmir ve Manisa illerinde kıl keçi yetiştiriciliğinin yaygın olarak yapıldığı toplam 120 keçicilik işletmesi oluşturmaktadır. Anketler; kıl keçi sürüleri arasındaki dolaylı ekipman teması, kuru ot ve yoğun yem kullanımı, ilaç ve aşı uygulamaları ile kişisel bilgilere ait soruları içermektedir. Manisa ve İzmir illerinde ortalama işletmeci yaşı sırasıyla; 45.77 ve 51.84; eğitim düzeyi; 4.92 ve 5.42 yıl; hane halkı sayısı; 4.75 ve 5.62, toplam hayvan varlığı; 128.02 ve 248.34 baştır. İller arasında, incelenen özellikler bakımından saptanan fark, İzmir lehine önemli bulunmuştur (P<0.01). Keçilere süt yemi verenlerin oranı Manisa'da düşük (%32) İzmir'de ise daha yüksektir (%74). Bu özellik bakımından iller arasındaki ayrım önemlidir (P<0.01). Kıl keçi yetiştiren illerdeki işletmelerde doğum bölmesinin olmadığı ve ölen hayvanlara otopsi yapılmadığı saptanmıştır (P<0.01). Yetiştiricilerinin herhangi bir kayıt tutmadığı ve damızlık koyun-keçi birliğine üye olmadığı belirlenmiştir. Araştırmada, sağlık-koruma uygulamaları konusunda iller arasında önemli ayrımlar söz konusudur (P<0.05). Sonuç olarak, scrapie hastalığın bölge ya da işletmelerde yayılmasında rol oynayan en önemli risk faktörleri sırasıyla; kontrolsüz hayvan hareketleri, sürüler arasındaki doğrudan ya da dolaylı geçişler, ortak teke ve mera kullanımıdır. Doğrudan hayvanların kontrolü ile belirlenen etmenler, diğer scrapie risk faktörlerini oluşturmaktadır. Keçi yetiştiricisinin bilgi ve duyarlılık düzeyi, hastalıklı hayvanların en kısa sürede bir veterinere gösterilmesi gibi iyi sürü yönetimi uygulamaları, sürülerde scrapie risk faktörlerinin belirlenmesi ya da yayılmasını en aza indirecektir.
Prions are abnormal isoforms of the host-encoded cellular prion proteins which are misfolding in ... more Prions are abnormal isoforms of the host-encoded cellular prion proteins which are misfolding in its three-dimensional structure acquire pathogenicity. Prions cause transmissible spongiform encephalopathy (TSEs) in humans and some animal species including sheep, goats, cattle, cat, deer and elk. TSEs, also called "prion diseases," cause irreversible neurodegeneration in the central nervous system and are always fatal. Cellular prion proteins are encoded by prion protein gene (PRNP) in mammals; moreover, it is known that the variations in the PRNP gene have influence on the resistance and/or incubation period of the TSEs. It is well-documented that after exposure to the pathogenic prions, development of some TSEs depend on the host PRNP genotype, for example, scrapie in sheep, bovine spongiform encephalopathy (BSE) in cattle, Creutzfeldt-Jakob disease (CJD) and kuru in humans, as well. In this chapter, genetic resistance to prion diseases will be reviewed.
Introduction After a modification in its three-dimensional structure, a normal host-encoded prion... more Introduction After a modification in its three-dimensional structure, a normal host-encoded prion protein is converted into an abnormal isoform that is termed a prion. Prions cause transmissible spongiform encephalopathies (TSEs), which are fatal neurodegenerative disorders such as Gerstmann-Straussler-Scheinker (GSS) syndrome and Creutzfeldt-Jakob disease (CJD) in humans, bovine spongiform encephalopathy (BSE) in cattle, and scrapie in small ruminants (1). Scrapie is the oldest prion disease of sheep, known about for 250 years, and therefore regarded as the prototype of other TSEs (2). The disease is characterized by long incubation periods from months to years, progressive vacuolization, and amyloid plaque formation in the central nervous system (3). It is thought that the cattle prion disease BSE, which can be transmitted to humans and causes a new variant of CJD (4), originated from the use of the scrapie-contaminated products in cattle nutrition (5). It is well described that the prion protein gene (PrP) modulates susceptibility to classical scrapie. Polymorphisms at codons 136, 154, and 171 of the PrP have strong influence on the development of the disease in sheep (6). According to the PrP genotype, classical scrapie risk groups from R1 (at lowest risk) to R5 (at highest risk) were designated in the UK in 2001 (7), and several EU member states and the USA have adopted selective breeding programs aiming to increase genetic resistance to scrapie (8). In 1998, an atypical type of scrapie was diagnosed in Norway. Its histopathological features were different from those of classical scrapie and it was termed Nor98 (9). In the following years, many atypical cases were reported, especially in European states (10,11). Further studies have shown that some PrP variants are also related to atypical scrapie susceptibility (12,13). The Karacabey merino, one of the major breeds of the sheep industry in Turkey, was developed by crossbreeding German mutton-wool merino rams with native Kivircik ewes in the 1930s (14). The breed has adapted well, especially to the South and North Marmara as well as the West Anatolia regions of Turkey. Purebred Karacabey Abstract: Scrapie, the oldest prion disease of sheep, has two types: classical and atypical scrapie. It was determined that some nucleotide polymorphisms in the PrP coding gene have affected classical and atypical scrapie susceptibility. Consequently, EU member states have established breeding programs aiming to increase genetic resistance of their flocks to classical scrapie. These breeding programs have primarily been implemented in economically important breeds. Thus, we investigated classical and atypical scrapie related PrP genotypes of the Karacabey merino breed, which is of great economic importance in western regions of Turkey. In relation to classical scrapie, three alleles
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