Two N-terminal regions of the Sendai virus L RNA polymerase protein participate in oligomerization

AbstractThe RNA dependent RNA polymerase of Sendai virus consists of a complex of the large (L) and phosphoprotein (P) subunits where L is thought to be responsible for all the catalytic activities necessary for viral RNA synthesis. We previously showed that the L protein forms an oligomer [Smallwood, S., Cevik, B., Moyer, S.A., 2002. Intragenic complementation and oligomerization of the L subunit of the Sendai virus RNA polymerase. Virology 304, 235–245] and mapped the L oligomerization domain between amino acids 1 and 174 of the protein [Çevik, B., Smallwood, S., Moyer, S.A., 2003. The oligomerization domain resides at the very N-terminus of the Sendai virus L RNA polymerase protein. Virology 313, 525–536]. An internal deletion encompassing amino acids 20 to 178 of the L protein lost polymerase activity but still formed an L–L oligomer. The first 25 amino acids of paramyxovirus L proteins are highly conserved and site-directed mutagenesis within this region eliminated the biological activity of the L protein but did not have any effect on P–L or L–L interactions. Moreover deletion of amino acids 2–18 in L abolished biological activity, but again the L–L binding was normal demonstrating that the oligomerization domain of L protein resides in two N-terminal regions of the protein. Therefore, sequences between both aa 2–19 and aa 20–178 can independently mediate Sendai L oligomerization, however, both are required for the activity of the protein

Turunçgillerde Genetik Mühendisliği Uygulamaları

Diğer bitkilerde olduğu gibi turunçgillerde de genetik mühendisliği uygulamalarının yapılması ve yaygınlaşması, istenilen özellikleri sağlayacak genlerin bulunmasına ve bunları bitkiye aktaracak transformasyon yöntemlerinin geliştirilmesine bağlıdır. Bu iki temel koşulun sağlanmasıyla turunçgillere ıslah çalışmalarıyla kazandırılamayan bazı özellikler genetik mühendisliği yoluyla kazandırılabilir. Bu amaçla turunçgillerde son on yılda çok sayıda çalışma yapılmış olup farklı bitki materyali ve farklı gen aktarım yöntemleri kullanılarak transgenik bitkiler üretilmiştir. Başlangıçta transformasyon çalışmaları sadece raportör genler kullanılarak yapılmıştır. Daha sonra transformasyon yöntemlerinin optimizasyonu ve tarımsal açıdan önemli genlerin çeşitli kaynaklardan klonlanmasıyla turunçgillerde hastalık ve zararlılar yanında abiyotik streslere dayanıklılık ve meyve kalitesinin artırılmasına yönelik genetik mühendisliği uygulamaları da başlamıştır. Bu uygulamalar sonucunda birçok transgenik bitki üretilmiş olup halen bu transgenik bitkilerin moleküler ve biyolojik karakterizasyonları yapılmaktadır. Bu çalışmada dünyada turunçgillerde yapılan genetik transformasyon çalışmaları ve bunların sonuçları derlenerek yakın gelecekteki durumu ve ülkemiz açısından önemi tartışılmıştır. Anahtar sözcükler: Turunçgiller, genetik mühendisliği, genetik transformasyon, doku kültürü, Biyotik ve abiyotik streslere dayanıklılı

The Views of Field Experts in Determining the Mathematic Questions for Seventh Class Level Exam’s

Bu çalışmanın amacı, 2008 7. sınıf Seviye Belirleme Sınavı matematik sorularının üst düzey zihinsel becerileri ölçme düzeyine ve matematik kazanımları açısından üst düzey zihinsel becerilerin önem düzeyine ilişkin matematik eğitimi alan uzmanlarının görüşünü almaktır. Bu çalışmanın araştırma grubunu, Türkiye'nin çeşitli üniversitelerinde görev yapmakta olan 30 matematik eğitimi alan uzmanı oluşturmaktadır. Araştıma verileri, Çevik (2009) tarafından geliştirilen "Seviye Belirleme Sınavı 7. Sınıf Matematik Testi Üst Düzey Zihinsel Becerileri Belirleme Ölçeği" ile sağlanmıştır. Elde edilen verilerin yüzde ve frekansları hesaplanarak tablolaştırılmıştır. Araştırma sonunda yüzde ve frekans değerleri %50 ve üzerinde olan görüşler dikkate alındığında 2008 Seviye Belirleme Sınavı matematik sorularında üst düzey zihinsel becerileri ölçen soru bulunmadığı tespit edilmiştir. Ayrıca matematik eğitimi alan uzmanlarının ilgili üst düzey zihinsel becerilere matematik kazanımları açısından verdikleri önem düzeyi oldukça fazladır. Alan uzmanlarının görüşleri dikkate alınarak öğrenciler için hayati önem taşıyan sınavlarda yer alan 7. sınıf matematik soruların yapılandırılmasında üst düzey düşünmenin kapılarını açma ön plana alınmalıdır. Ülkemizde yapılan ulusal sınavlardaki testlerde yer alan soruların bilişsel alanın her düzeyini ölçer nitelikte olması gerekirThe purpose of this study was to determine the level achieved in measuring the higher order thinking skills in 2008 seventh grade mathematic questions and the level of importance given to these higher order thinking skills, according to the views of field experts. The research group for this study consisted of 30 mathematics education experts at various universities in Turkey. Research data was provided via the “SBS exam seventh grade Identifying Higher Order Thinking Skills of Mathematics Scale” developed by Çevik (2009). The data was obtained by calculating the percentage and frequency integrated table. As a result of this research, examined by taking the percentage and frequency values of opinions above 50% into consideration, it was found that the mathematic questions in the 2008 SBS exam do not contain questions that measure higher order thinking skills. Also, the level of importance given to higher order thinking skills by experts in terms of 7th grade math acqusitions is very high. In structuring the questions for exams, carrying vital importance for students, opening the door to higher order thinking must be brought into the foregroun

Genetic Diversity in the Coat Protein Genes of Prune dwarf virus Isolates from Sweet Cherry Growing in Turkey

Sweet cherry is an important fruit crop with increasing economical value in Turkey and the world. A number of viruses cause diseases and economical losses in sweet cherry. Prune dwarf virus (PDV), is one of the most common viruses of stone fruits including sweet cherry in the world. In this study, PDV was detected from 316 of 521 sweet cherry samples collected from 142 orchards in 10 districts of Isparta province of Turkey by double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA). The presence of PDV in ELISA positive samples was confirmed in 37 isolates by reverse transcription- polymerase chain reaction (RT-PCR) method. A genomic region of 862 bp containing the coat protein (CP) gene of PDV was re-amplified from 21 selected isolates by RT-PCR. Amplified DNA fragments of these isolates were purified and sequenced for molecular characterization and determining genetic diversity of PDV. Sequence comparisons showed 84–99% to 81–100% sequence identity at nucleotide and amino acid level, respectively, of the CP genes of PDV isolates from Isparta and other parts of the world. Phylogenetic analyses of the CP genes of PDV isolates from different geographical origins and diverse hosts revealed that PDV isolates formed different phylogenetic groups. While isolates were not grouped solely based on their geographical origins or hosts, some association between phylogenetic groups and geographical origins or hosts were observed

Genetic Diversity and Phylogenetic Analysis of Citrus tristeza virus Isolates from Turkey

The presence of Citrus tristeza virus (CTV) in Turkey has been known since the 1960s and the virus was detected in all citrus growing regions of the country. Even though serological and biological characteristics of CTV have been studied since the 1980s, molecular characteristics of CTV isolates have not been studied to date in Turkey. In this study, molecular characteristics of 15 CTV isolates collected from different citrus growing regions of Turkey were determined by amplification, cloning, and sequencing of their major coat protein (CP) genes. The sequence analysis showed that the CP genes were highly conserved among Turkish isolates. However, isolates from different regions showed more genetic variation than isolates from the same region. Turkish isolates were clustered into three phylogenetic groups showing no association with geographical origins, host, or symptoms induced in indicator plants. Phylogenetic analysis of Turkish isolates with isolates from different citrus growing regions of the world including well-characterized type isolates of previously established strain specific groups revealed that some Turkish isolates were closely related to severe quick decline or stem pitting isolates. The results demonstrated that although CTV isolates from Turkey are considered biologically mild, majority of them contain severe components potentially causing quick decline or stem pitting

Isparta ve Burdur İli Domates Üretim Alanlarında Tomato chlorosis virus'un Nested-RT-PCR Yöntemiyle Tanılanması

Bu çalışmada, Isparta ve Burdur illerin domates üretim alanlarında Tomato chlorosis virus (ToCV) varlığı araştırılmıştır. Bu amaçla bu illerin yoğun domates üretimi yapılan bazı bölgelerinde arazi çalışmaları yapılarak 24 farklı üretim alanından 85 adet domates örneği toplanmıştır. Elde edilen örneklerden öncelikle total nükleik asit izolasyonu yapılmış ve daha sonra tüm örneklere tersine transkripsiyon uygulanarak (reverse transcription, RT) cDNA sentezi sentezlenmiştir. Daha önce ToCV tanısında kullanılan ısı şoku protein homolog (heat shock protein homologue, hsp70h) genine spesifik primerler kullanılarak nested-RT-PCR yöntemiyle ToCV tanılaması yapılmıştır. Yapılan RT-PCR testleri sonucunda, 85 örnekten 6 tanesinin ToCV pozitif olduğu belirlenmiştir. Elde edilen sonuçlar Isparta ve Burdur illerinde ToCV varlığını ilk kez göstermiş, ancak enfeksiyon oranının düşük (Isparta % 5,71 ve Burdur % 8,00) olduğunu ortaya koymuştur. Burdur'dan elde edilen ToCV55 numaralı izolatının hsp70h geni yeniden çoğaltılarak DNA dizisi belirlenmiştir. Bu izolatın DNA dizisi dünyanın farklı domates üretim bölgelerinden elde edilen ToCV izolatların hsp70h genleriyle karşılaştırılmış ve filogenetik analizler yapılmıştır. Yapılan dizi analizleri sonucunda, Burdur 55 ToCV izolatının diğer ToCV izolatlarıyla %93-95 oranında benzerlik gösterdiği belirlenmiştir. Yapılan filogenetik analizler ToCV izolatlarının hsp70h genine göre iki ana gruba ayrıldığını, ancak Burdur 55 izolatının bu iki grubun dışında kalan farklı bir izolat olduğunu göstermiştir

The First Identified Citrus tristeza virus Isolate of Turkey Contains a Mixture of Mild and Severe Strains

The presence of Citrus tristeza virus (CTV) has previously been reported in citrus growing regions of Turkey. All serologically and biologically characterized isolates including Iğdır, which was the first identified CTV isolates from Turkey, were considered mild isolates. In this study, molecular characteristics of the Iğdır isolate were determined by different methods. Analysis of the Iğdır isolate by western blot and BD-RT-PCR assays showed the presence of MCA13 epitope, predominantly found in severe isolates, in the Iğdır isolate revealing that it contains a severe component. For further characterization, the coat protein (CP) and the RNA-dependent RNA polymerase (RdRp) genes representing the 3′ and 5′ half of CTV genome, respectively, were amplified from dsRNA by RT-PCR. Both genes were cloned separately and two clones for each gene were sequenced. Comparisons of nucleotide and deduced amino acid sequences showed that while two CP gene sequences were identical, two RdRp clones showed only 90% and 91% sequence identity in their nucleotide and amino acid sequences, respectively, suggesting a mixed infection with different strains. Phylogenetic analyses of the CP and RdRp genes of Iğdır isolate with previously characterized CTV isolates from different citrus growing regions showed that the CP gene was clustered with NZRB-TH30, a resistance breaking isolate from New Zealand, clearly showing the presence of severe component. Furthermore, two different clones of the RdRp gene were clustered separately with different CTV isolates with a diverse biological activity. While the RdRp-1 was clustered with T30 and T385, two well-characterized mild isolates from Florida and Spain, respectively, the RdRp-2 was most closely related to NZRB-G90 and NZRB-TH30, two well-characterized resistance breaking and stem pitting (SP) isolates from New Zealand confirming the mixed infection. These results clearly demonstrated that the Iğdır isolate, which was previously described as biologically a mild isolate, actually contains a mixture of mild and severe strains

Assessment of The Factors Affecting The Radiation Protection Levels of Radiology Department Personnel at A University Hospital

 Introduction: Hospitals are among organizations with the highest risk in terms of workplace safety. While almost all departments within hospitals are faced with various risks, radiology department employees, in particular, are more likely to be exposed to conditions that threaten their health due to exposure to radiation. This study aims to identify the factors that affect the radiation protection levels of radiology personnel.Materials and Methods: This study is cross-sectional quantitative research. The study was conducted on one of Turkey's most prestigious universities working in the radiology department of the hospital staff. A questionnaire consisting of 9 questions was used to determine the radiation protection level of the employees. The questionnaire was distributed to a total of 299 personnel, but there was a return from 155 employees (52%).Results: The results of the regression analysis showed that the variables of gender, occupation, and radiation protection training had significant impact on the level of measures taken by radiology personnel for radiation protection (p<0.05), whereas the variables of age, marital status, and work experience had a different pattern (p>0.05). R-squared value of the regression model indicates that 42.1% of the variation in the level of measures taken to protect the radiology staff against radiation has been explained by these variables (F=11.520; p<0.001).Conclusion: The results of the study suggest that training about radiation protection should be provided to the radiology personnel to prevent their health and safety.

Expression analysis of <i>WRKY</i> genes from <i>Poncirus trifoliata</i> in response to pathogen infection

<div><p>The majority of WRKY transcription factors (TFs) play a role in the regulation of defense response in plants. Three <i>WRKY</i> genes, <i>PtrWRKY1, PtrWRKY2 and PtrWRKY3</i>, were previously identified in <i>Poncirus</i> and their expressions were characterized in response to cold and drought in <i>Poncirus</i> and <i>Citrus</i>. In this study, expressions of these <i>WRKY</i> genes were studied in response to infection with two major pathogens of <i>Citrus</i>, <i>Citrus tristeza virus</i> (CTV) and <i>Phytophthora citrophthora</i>, in resistant <i>Poncirus</i> and susceptible pummelo (<i>Citrus grandis</i>) plants. Northern blot analysis showed that the expression of the <i>PtrWRKY1</i> gene was induced earlier and stronger in <i>Poncirus</i> than in pummelo in response to CTV infection. On the other hand, the expression of the <i>PtrWRKY1</i> gene was not altered in response to <i>P. citrophthora</i> infection neither in <i>Poncirus</i> nor in pummelo. When the expression of the <i>PtrWRKY2</i> gene was analyzed, it was repressed by CTV inoculation in <i>Poncirus</i> plants, whereas the expression was not changed in response to CTV infection in pummelo or in response to <i>P. citrophthora</i> inoculation in <i>Poncirus</i> or pummelo. Similarly, the expression of the <i>PtrWRKY3</i> gene was repressed in <i>Poncirus</i>, but not changed in pummelo by CTV inoculation; however, the expression of the <i>PtrWRKY3</i> gene was induced in <i>Poncirus</i>, but it was repressed in pummelo in response to <i>P. citrophthora</i> inoculation. The expression analysis of three different <i>WRKY</i> genes revealed that they are differentially expressed in response to CTV and <i>P. citrophthora</i> infection in resistant <i>Poncirus</i> and susceptible pummelo suggesting that they may play a role in disease resistance in <i>Poncirus</i>.</p></div