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Colorectal carcinogenesis involves environmental factors and genetic predispositions. Recent studies have suggested the associations between colorectal neoplasm and functional polymorphism of matrix metalloproteinases (MMPs) and cytokine genes. In this study, we analyzed polymorphisms of MMPs and tumor necrosis factor (TNF)-alpha genes, focusing on the susceptibility to colorectal neoplasm and the tumor progression. The subjects were 186 patients (95 men and 91 women) who underwent total colonoscopy, and were classified into cancer, adenoma and non-neoplasm (control) groups of 47, 72 and 67 patients, respectively. The polymorphisms at the MMP-2 ?1306C/T, MMP-3 ?1171 5A/6A, MMP-7 ?181A/G, MMP-9 ?1562C/T and TNF-alpha ?308G/A loci were analyzed. Regarding background factors, significant differences were found in the age, sex ratio and alcohol-drinking and cigarette-smoking histories in the adenoma and cancer groups, compared to those in the control group. On these factors-adjusted logistic regression analysis of polymorphisms and disease susceptibility, no significant difference was noted in the frequency of any polymorphism in the adenoma and cancer groups, compared to those in the control group. The analysis of the involvement of polymorphisms in tumor progression in the adenoma and cancer groups revealed that the odds ratio for the MMP-3 5A allele was significantly higher in the cancer group (2.74; 95% confidence interval = 1.11?6.74, P = 0.02). The polymorphisms of MMP genes and TNF-alpha genes were not associated with the susceptibility to colorectal neoplasm, but the involvement of the MMP-3 5A allele in the progression of adenoma to cancer was suggested.

Background Outbreaks of Marek’s disease (MD), caused by Marek’s disease virus (MDV), primarily occur in 10–12-week-old hens. Case presentation We report a case of MD in a breeding flock of 24–30-week-old vaccinated broilers in China. The clinical signs in the affected chickens appeared at 24 weeks, and the incidence of tumours peaked at 30 weeks. The morbidity and mortality of the hens were 5 % and 80 %, respectively. Hematoxylin–eosin staining of the tissues showed the typical characteristics of MD. MDV infection was confirmed in the hens with an agar gel diffusion precipitation assay for the MD antigen in the feather follicle epithelium. An MDV strain, designated AH1410, was isolated from the blood lymphocytes. Sequence analyses of the pp38, meq, and gB genes revealed that strain AH1410 had molecular features consistent with a virulent, previously identified MDV. Conclusion Our data provide evidence that not only is MDV becoming more virulent, but that the period of its onset in chickens is expanding. These findings provide the basis the molecular surveillance and further study of virulent MDV mutants and control strategies for MD in China.

International audience; In previous studies, the abundance and diversity of methanogenic archaea in the dental microbiota have been analysed by the detection of specific DNA sequences by PCR-based investigations and metagenomic studies. Few data issued regarding methanogens actually living in dental plaque. We collected dental plaque specimens in 15 control individuals and 65 periodontitis patients. Dental plaque specimens were cultured in an anoxic liquid medium for methanogens in the presence of negative control tubes. Dental plaque methanogens were cultured from 1/15 (6.67%) control and 36/65 (55.38%) periodontitis patient samples (p

Background The most common pediatric renal neoplasm is Wilms tumor, but clear cell sarcoma of the kidney or synovial sarcoma of the kidney are also sometimes encountered. Accurate pathological diagnosis is important, because adjuvant therapies including chemotherapy and radiotherapy differ according to the pathological type. Case presentation A 9-year-old boy presented with a headache, and ultrasonography, computed tomography, and magnetic resonance imaging revealed a heterogeneous enhancement of soft tissue originating from the upper pole of the left kidney, measuring approximately 11.0 × 10.0 × 8.0 cm. A left radical nephrectomy was performed using an intraperitoneal approach through an anterior subcostal incision. Pathological examination suggested clear cell sarcoma of the kidney or synovial sarcoma of the kidney based on morphological and immunohistological features. Using genetic analysis, a final diagnosis of spindle cell pattern clear cell sarcoma of the kidney was made based on the absence of the SYT-SSX fusion gene. After adjuvant chemo-radiotherapy was administered, no recurrence or metastasis has been identified as of 60 months postoperatively. Conclusion In this case, it was difficult to discriminate clear cell sarcoma of the kidney from synovial sarcoma of the kidney based on histopathological examination alone, and genetic analysis was required. Accurate pathological diagnosis of pediatric renal tumor is important for determining optimal treatment and preventing recurrence and metastasis.

Amaç: Bilinen bir hastalığı olmayan kişinin ölü bulunması veya kısa bir süre içinde nedeni anlaşılamadan ölmesi, bilinen bir hastalığı olan ancak bu hastalığı ölüme neden olacak bir klinik göstermeyen kişinin ölmesi genellikle yakınları tarafından beklenmedik ölüm olarak değerlendirilir. Bu tarz olgularda ölüm sebebinin anlaşılabilmesi için otopsi yapılması gereklidir. Otopside tüm incelemelerin yapılmasına rağmen bazı olgularda ölüm nedeni ortaya çıkarılamaz ve bu durumlar negatif otopsi olarak adlandırılır. Bu grup gelecek adli tıbbının çözüm bekleyen sorunlarının başında gelmektedir. Yapılacak moleküler otopsi uygulamaları da negatif otopsi oranlarını düşürmek adına yapılması gereken çalışmaların başında gelmektedir. Bu sebeple ani beklenmedik ölüm olgularında postmortem KCNQ1 genetik varyasyonu açısından değerlendirme yapılmıştır.Gereç ve Yöntem: T.C.Adalet Bakanlığı Adli Tıp Kurumu Adana Grup Başkanlığı Morg İhtisas Dairesi'nde otopsileri yapılan ve ölüm nedenleri ileri çalışmalara rağmen saptanamayan, ani beklenmedik ölüm kapsamındaki 0 – 50 yaş arası olgular çalışmamız kapsamına alınmıştır. Olgulardan alınan örneklerin patolojik incelemeleri yapılarak, tüm tıbbi ve adli geçmişi incelenmiş ve ayrıca EDTA'lı tüplere alınan kan örneklerinde Anabilim Dalı'mızda ''KCNQ1'' genetik varyasyonu açısından değerlendirme yapılmıştır.Bulgular: Çalışmamıza 42 ani-beklenmedik ölüm olgusu ve 5 kontrol grubu olmak üzere toplam 47 olgu dahil edildi. Ani-beklenmedik ölüm olgularından 0-50 yaş grubu olan olgular çalışmaya alındı. 42 olgudan 15'inin (% 35,7) 40 – 50 yaş aralığında olduğu ve olgu sayısının yaşla birlikte arttığı gözlendi. Olguların 29'u (% 69) erkek, 13'ü (% 31) kadın idi. Olguların Vücut-Kitle İndeksine göre değerlendirmeleri Dünya Sağlık Örgütü Vücut-Kitle İndeksi Sınıflamasına göre yapıldı. En fazla 21 olgu (% 50) ile normal kilolu olguya rastlandı. Olgularımızın tüm olgular içerisinden rastgele seçilmiş olmaması sebebiyle obezite-risk değerlendirilmesi yapılamadı. Olguların ölüm yerlerine göre dağılımları yapıldı. 17 olgunun (% 45,9) evde öldüğü görüldü. 5 olgunun ise ölüm yeri kayıtlarına ulaşılamadı. Tüm olguların patolojik değerlendirmeleri yapıldı. (Myokard-koroner arter ve kardiyak ileti sistemi) Patolojik çalışmalar sırasında Hematoksilen-Eosin boyama yöntemi kullanıldı. Özellikle ileti sistemine ait çalışmalarda SA nodda 9 olguda (% 21,4), AV nodda 13 olguda (% 30,9) fibrozis ve yağlı değişikliğe ait görünüm izlendi. Olgulara ait KCNQ1 genetik analizlerimiz sonucunda; ekzon 13 1638. nükleotitidinde ve ekzon 16 1986. nükleotid pozisyonunda sekans varyasyonları tespit edildi. Çalışmamızda tespit edilen sekans varyasyonları birçok çalışmada mutasyon olarak yorumlanmıştır. Ancak mutasyon hakkında gerçekçi yorum yapılabilmesi için daha geniş serilerde çalışılması ve daha zengin primerlerin kullanılması gerektiği kanısındayız. Sonuç: Özellikle ileti sistemi patolojisi tespit edilen ve KCNQ1 genetik analizi sonucunda sekans varyasyonları tespit edilen olgular, bize negatif otopsi oranlarını düşürmek için bu uygulamaların rutin uygulamalar arasına girmesi gerektiğini göstermektedir. Genetik analizler yapılmadan otopsinin sonlandırılmaması gerektiği Avrupa Kardiyovasküler Patoloji Birliği tarafından da önerilmektedir. Bu şekilde ölüm nedeni saptanamayan olguların azalacağı ve adaletin daha hızlı işlemesine katkıda bulunacağına ve genetik analizler doğrultusunda kişinin ailesinde gelişebilecek muhtemel bir ölüme karşı önlemler alınabileceğine inanılmaktadır. Aim: Deaths occuring without a known disease and/or a known cause, deaths with non-lethal diseases are interpretated as sudden-unexpected-suspected deaths. Autopsy should always required to evaluate the cause of death. Some of the cases can be termed as negative autopsy since the cause of death can not be determined. This is one of the main interests of the future forensics. Molecular autopsies are one of the main practices of to reduce the negative autopsy ratios. Thus, post-mortem KCNQ1 genetic variation tests are done in sudden unexpected death cases.Material and methods: In this study 0 – 50 years old sudden-unexpected-suspected deaths autopsy cases were handled from the Morgue Department of the Adana Branch of the Forensic Medicine Council of Turkey. Samples taken from cases were evaluated pathologically, all medical and forensic history was examined and also `KCNQ1` genetic variation tests were done with blood samples taken into EDTA vials in our Department.Results: This study included 47 cases of 42 sudden unexpected death cases and 5 control group. Cases of 0 – 50 age group were included in sudden-unexpected death cases. 15 of 42 cases were between 40 – 50 age group and number of cases were increasing with age. 29 of cases (% 69) were male while 13 (% 31) were female. Evaluation of body-mass index of cases were done with World Health Organization Body-Mass İndex Classification. Normal weighted cases were the most common with 21 cases (% 50). Obesity-risk evaluation couldn't be done because our cases were not chosen randomly among all cases. All cases were distributed according to death locations. 17 cases had died (% 45,9) at home. Death location records of 5 cases couldn't be found. Pathological examinations of all cases were done (Myocardium-Coronary Artery and Cardiac Conduction System). Hematoxylin eosin staining method used during pathological examinations. We had identified fibrosis and fatty change appearances in SA node of 9 cases (% 21,4) and AV node of 13 cases (% 30,9) especially in conduction tissue examinations. As the result of KCNQ1 genetic analysis of cases, we identified sequence variations in 1638th nucleotid of exon 13 and 1986th nucleotid of exon 16. Although sequence variations identified in our study was interpreted as mutations in several studies, we believe that studies should be made in larger series and more primers should be used for realistic interpretations.Conclusion: Cases with conduction system pathology and sequence variations of KCNQ1 genetic analysis shows that we are in need of these tests among routine practice to reduce negative autopsy ratios. European Cardiovascular Pathology Assosication recommends not to finalise an autopsy without genetic analysis. These new methods and use of molecular autopsy will sure reduce the negative results and will explain the cause of deaths to us. Genetic analysis will give us the opportunity to explain the cause of deaths and the precautions that has to be taken for both justice and the relief of the families. 82

Endüstriyel nanopartiküller, alışılmamış fizikokimyasal özelliklerinden dolayı canlılarda bulunan doku, organ, hücre, hücre içi yapılar, DNA ve protein düzeylerinde potansiyel olarak olumsuz etkiler oluşturabilmektedirler. Bugüne kadar yapılan çalışmalarda, ZnO nanopartiküllerin etkilerinin kısmen mi yoksa tamamen mi Zn+2 iyonlarından kaynaklandığı tam olarak anlaşılamamıştır. Bu çalışmada, ZnO nanopartikülünün ve uygun konsantrasyonlarda suda çözünebilen ZnCl2 kaynaklı Zn+2 iyonlarının larval zebra balıkları (Danio rerio, 72 saatlik) üzerine potansiyel toksik etkileri, stres gen (p53, rad51 ve mt2) ekspresyonlarındaki değişimler eş zamanlı kantitatif PZR (RT-qPCR) tekniği kullanılarak karşılaştırılmıştır. Ayrıca, ZnCl2 ve ZnO nanopartikülünün oluşturabileceği genotoksik etkiler belirlenmeye çalışılmıştır. Çalışma sonucunda, 0-60 mg/L aralığındaki konsantrasyonlarda ZnCl2 ve ZnO nanopartikülüne maruz bırakılan zebra balığı larvalarının % 50'sini öldüren letal konsantrasyonlar sırasıyla 4,66 ± 0,11 ve 21,37 ± 1,81 mg/L olarak hesaplanmıştır. Ayrıca, ZnCl2 ve ZnO nanopartikülüne 96 saat süreyle maruz bırakılan zebra balığı larvalarının kan hücrelerinde, konsantrasyona bağlı olarak DNA zincir kırıkları tespit edilmiştir. DNA hasarının ZnCl2'e (% 55,3) maruz bırakılan larvalarda, ZnO nanopartikülüne (% 25,4) maruz bırakılanlara oranla daha yüksek oranda olduğu tespit edilmiştir. Stres gen ekspresyon değişimlerinin ise direkt olarak konsantrasyona bağlı olmadığı tespit edilmesine rağmen ZnCl2 ve ZnO nanopartikülüne maruz bırakılan larvaların mt2 gen ekspresyonlarında kontrol grubuna oranla sırasıyla 20,5 ve 2,5 kat artış belirlenmiştir. Toksik etkilerin genel olarak benzerlik göstermesi, ZnO nanopartikülünün toksisitesinin iyonlaşma nedeniyle oluşan Zn+2 iyonlarından kaynaklandığını ortaya koymuştur. Engineered nanoparticles can potentially generate adverse effects on tissue, organ, cellular, subcellular, DNA, and protein levels due to their unique physico-chemical properties. To date it is not yet completely understood, whether effects of zinc oxide (ZnO) nanoparticles are solely or partly due to dissolved Zn2+. The present study compare potential effects of ZnO nanoparticles and corresponding concentrations of ion Zn2+ by water soluble ZnCl2 to larval (72 h post fertilization) zebrafish (Danio rerio) by analysing changes in expression levels of stress-related genes (p53, rad51, and mt2) by real-time quantitative PCR (RT-qPCR). Another objective was to assess genotoxicity of ZnO nanopartciles and ZnCl2. The lethal concentrations for 50% mortality (LC50) in larval zebrafish exposed (96 h) to 0-60 mg/L ZnO nanoparticles and ZnCl2 were 21.37 ± 1.81 and 4.66 ± 0.11 mg/L, respectively. A concentration-dependent increase in DNA strand breaks was detected in blood cells from larvae exposed (96 h) to ZnO nanoparticles and ZnCl2. DNA damage was higher in ZnCl2 (% 55.3) than ZnO nanoparticles (% 25.4) exposed larvae. Induction of stress-related genes in larvae was complex and not directly related to ZnO nanoparticles and ZnCl2 concentrations, although there was 20.5 and 2.5 fold increase in mt2 gene expression of larvae exposed to ZnCl2 and ZnO nanoparticles relative to control. The similarities of the effects lead to the coclusion that effects of ZnO nanoparticles are mainly related to the release of Zn2+ ions. 60

Here we describe a case of Neurofibromatosis type 1 (NF1) associated with an atypical histiocytic lesion and a new pathogenic mutation. The genetic analysis revealed an heterozygous mutation in the 5′ splice site of intron 32, 6,084 + 1G → T. Histopathological findings are compatible with juvenile xanthogranuloma. The new, not already described, splicing mutation, is possibly partly responsible of the association between NF1 and the histiocitic lesion.

Gen ifadesi deneylerinin bir aşamasında veriler manuel yöntemlerle elde edildiği için verilerin güvenilirliği düşüktür. Bu verilerin bir veri madenciliği algoritmasına ya da modele direkt girdi olması durumunda varılmak istenen sonuçların güvenilirliğinin olumsuz yönde etkilemesi kaçınılmazdır. Çalışmamızda, elde edilen verilerin belirsizliğini azaltmak için her verinin, örnek veri üretme teknikleriyle elde edilen veri kümeleriyle temsil edilmesini sağladık. Örnek veri yaklaşımı verilerin belirsizlik yüzdesini azaltırken işlem yapılan veri setinin örnek veri kümesi eleman sayısı oranında artmasına, dolayısıyla da ilgili veri işleme algoritmalarının sonuç üretme zamanının artmasına neden olmaktadır. Çalışmamızın ilk kısmında belirsiz verilerin hızlı bir biçimde kümelenebilmesi için çok çekirdekli sistemler üzerinde eş zamanlı çalışabilen M-FDBSCAN adını verdiğimiz bir `belirsiz veri kümeleme` algoritması geliştirdik. Algoritmada önerilen yöntemle yalnızca çok çekirdekli sistemlerde değil tek çekirdekli sistemlerde de veri işleme hızında büyük artışlar sağlandığı gösterdik. Çalışmamızın ikinci kısmında M-FDBSCAN algoritmasını, zaman serisi verilerinin hızlı ve etkin bir biçimde işlenebildiği, E-MFDBSCAN adı verilen bir `evrimsel kümeleme` algoritmasına dönüştürdük. Bu yeni algoritma global kümelerin oluşturulmasını sağlamaktadır. Çalışmamızın son aşamasında oluşturulan global kümelerin zaman bazlı evrimsel desenlerini kullanarak bir öngörü modeli geliştirdik. Bu öngörü modeliyle bir sonraki zaman noktasına ait bir global kümenin benzerlik ve desen bilgilerinin kestiriminin yapılabilmesini sağladık. Because of using manual methods in some parts of gene expression experiments, reliability of the data is low. If this data is directly utilized as input to a data mining algorithm or a model for evaluating gene expression data, then the adverse affects to the desired results will be inevitable. In order to eliminate aforementioned adverse affects and reduce the fuzziness, we represent the data with sample data sets that are generated by using uncertain data management techniques. Sample data approach not only reduces the percentage of fuzziness, but also it causes the output generation time to be increased due to an increase in the amount of processed data, which is directly proportional to the cardinality of the sample data set. In the first part of the study, we introduce an uncertain data clustering algorithm, named M-FDBSCAN, for enabling one to cluster uncertain data rapidly, which runs on multi-core systems in a concurrent fashion. We show that by using the proposed method, the algorithm yields considerable performance improvement on single core systems, as well. In the second part of the study, M-FDBSCAN algorithm is converted into an evolutionary clustering algorithm, named E-MFDBSCAN, by which time series data can be processed rapidly and efficiently. This new algorithm enables to generate global clusters. In the last part of the study, using time-based evolutionary patterns of global clusters a prediction model is constructed. The proposed prediction model enables us to predict the patterns and the similarities of a global cluster that will be generated at the next time point. 82

Ünal ZS. MK2 geninin hipoksik koşullarda mezenkimal ve nöral kök hücrelerin çoğalım ve farklılaşması üzerine etkisinin incelenmesi. İstanbul Üniversitesi Sağlık Bilimleri Enstitüsü, Cerrahpaşa Tıp Fakültesi. Tıbbi Biyoloji ABD. Doktora Tezi. İstanbul. 2014 Bu çalışma, İstanbul Üniversitesi Bilimsel Araştırma Projeleri Birimi tarafından desteklenmiştir. Proje No: 18843 Çalışmamızda %20 oksijen konsantrasyonu (normoksik) ve %3 oksijen konsantrasyonu (hipoksik) ile kültüre edilen, sıçan kemik iliği kaynaklı mezenkimal kök hücre(sKİ-MKH) ve nöral kök hücre(sNKH)'lerinde hücre bölünmesi, apoptoz, hücre farklılaşması ve inflamatuvar yanıt ile ilişkilendirilen p38MAPK yolağı substratlarından MK2 (Mitogen Activated Protein Kinase Activated Protein Kinase 2)'nin çoğalma ve farklılaşmadaki rolü araştırılmıştırMK2 proteini az oksijenli kültür koşullarında fosforile olup aktive olmaktaydı. Her iki kök hücre hattında MK2 geni lentiviral shRNA ile susturulmuş inaktif formda kalması sağlanmıştır. Gen susturma etkinliği Western blotlama ve gerçek-zamanlı PZR ile test edilmiştir. Normoksi ve hipokside kültüre edilen hücrelerde WST-1, annexin V-7ADD boyaması ve hücre siklüsü analizleri gerçekleştirilmiştir. Hücre hatları iki kültür koşulunda farklılaştırmaya alınmış değişimler immuno-histokimyasal ve gen düzeyinde karşılaştırılmıştır. MK2 susturulmuş sKİ-MKH'leri ve kontrollerin serum yoksunluğunda apoptoza dirençleri karşılaştırılmış ve hücre analiz cihazı (xCELLigence) ile hipokside hücrelerin çoğalma kapasiteleri incelenmiştir. MK2 geni susturulması sonrasında kök hücrelerin çoğalma kapasitesinin ve apoptoza dirençlerinin arttığı saptanmıştır. MK2 geninin susturulduğunda, farklılaşma öncesi ve sonrasında osteojenik belirteçlerin azaldığı ve bu etkilerin %3 oksijen konsantrasyonunda daha anlamlı bir düşüş gösterdiği tespit edilmiştir. Serum yoksunluğunda MK2 geni susturulan hücre grubunda apoptoza direncin daha fazla olduğu saptanmıştır. Sonuç olarak, çalışmamızda farklı oksijen konsantrasyonlarında MK2 geninin susturulmasının mezenkimal kök hücre ve nöral kök hücrelerin çoğalım ve farklılaşması üzerindeki etkilerinin tespit edilmesiyle, ilk kez bu gen ve ilişkili olduğu yolağın az oksijenli ve normal oksijenli kültür koşullarında olası yeni bir mekanizma olduğu ve gelecekte iskemik koşullara bağlı patolojik süreçlerin kök hücrelerle tedavisine oksijen kısıtlamasının da dahil edilebileceğine ilişkin önemli bulgulara ulaşılmıştır. Anahtar Kelimeler: Farklılaşma, gen susturma, hipoksi, kök hücreler, MK2. Ünal ZS. Effects of MK2 gene silencing on proliferation and differentiation of mesenchymal and neural stem cells under hypoxic culture conditions. İstanbul University, Institute of Health Science, Cerrahpaşa Medical Faculty. İstanbul. 2014The present work was supported by the Research Fund of Istanbul University. Project No. 18843 In our study,we analyze the effects of MK2(mitogen-activated protein kinase-activated protein kinase2),which belongs to MAP-kinase family member related with proliferation,cell cycle,apoptosis,differentiation and inflamatory response in long-term cultured rat bone marrow-derived mesenchymal stem cells(rBM-MSCs) and adult neural stem cells(rNSCs) both in 20%(normoxic) and 3%(hypoxic) oxygen levels.In both stem cell line MK2 gene silenced by lentiviral shRNA was expected to left MK2 in the inactive form.Gene silencing efficiency was analyzed with western blotting and RT-PCR. WST-1,AnnexinV-7AAD and cell cycle analysis were performed with cells cultured in normoxia and hypoxia.Immunohistochemical and RT-PCR analyzes were performed before and after differentiation.Resistance to apoptosis in MK2 silenced rBM-MSCs and controls were analysed with cell death detection ELISA and cell index was measured with xCELLigence cell-analyze device. After silencing the MK2 gene the cell proliferation capacity and anti-apoptotic effects were observed to be improved. Furthermore, the expression of osteogenic markers decreased in the silenced cells before and after osteogenic differentiation compared to normal cells, but the decline is more significant in 3%hypoxic oxygen concentration.Increased resistance to apoptosis was measured in MK2 silenced cells with serum starvation. By revealing the crucial role of MK2 gene in the proliferation and differentiation of silenced rBM-MSCs and rNSCs cultured under different oxygen concentrations,the importance of this gene and related pathways were demonstrated with their possible mechanisms.This study provides an evidence for the importance of hypoxic conditions in the cell cultures.In future aspects, possible new mechanisms,like as MK2 pathway, might be used in pathological processes for cell therapies in ischemic conditions.Key words: differentiation, gene silencing, hypoxia, MK2, stem cells. 169

We encountered a patient with variant of type 2B von Willebrand disease (vWD) who showed increased ristocetin-induced platelet aggregation, persistent thrombocytopenia, spontaneous platelet aggregation and normal vWF multimeric pattern in his plasma. However, we could not find any responsible mutations in or around the 505-695 disulfide loop (A1 loop) of the von Willebrand factor (vWF), at which all type 2B vWD candidate mutations have been reported to be clustered. This suggests that an unidentified vWF functional domain facilitating binding to platelet GPIb may exist at a site other than the A1 loop and the surrounding region.

Ｘ連鎖性劣性遺伝形式をとり、出生時より発症するＸ-linked myotubular myopathy（XLMTM）は、重度の筋緊張低下と筋力低下、呼吸障害により人工呼吸管理を必要とし、運動発達も遅延する予後不良の疾患である。myotubularin gene（MTM1遺伝子）により発現する蛋白質myotubularinは、ヒトの筋組織に散在し、tyrosin phosphataseと相同性を有するが、既知の蛋白質ではなく、その機能についても不明である。XLMTMの原因遺伝子（MTM1遺伝子）はX染色体長腕部（Xq28）に位置し、15個のエクソンから構成されることが解明されており、この領域の遺伝子変異がXLMTMの発症に関わることが近年報告された。今回我々は、臨床症状、筋組織学的所見、遺伝子解析によりXLMTMと診断された２症例を報告する。症例１はMTM1遺伝子のエクソン４において193から196の４塩基（AAAG）の欠失を認めた。このためフレームシフト変異を生じ、その後方25番目のアミノ酸がストップコドンとなっていた。母親はこの欠失遺伝子と正常遺伝子をヘテロ接合体として有する保因者と診断された。症例２はエクソン３の塩基163CがTに置換し、このためCGAがTGA（ストップコドン）となるナンセンス変異であった。この症例の母親と一卵性の姉は、同一の変異遺伝子と正常遺伝子をヘテロ接合体として有する保因者と診断された。これらの遺伝子異常によって、この遺伝子によりコードされているmyotubularinの酵素活性の低下が発症の原因である可能性を考察した。X-linked recessive myotubular myopathy （XLMTM） is a congenital myopathy characterized by severe hypotonia and muscle weakness, and respiratory insufficiency after birth. Surviving patients have prolong ventilator dependence and severely delayed motor milestones. Myotubularin, which is encoded by MTM1 gene, is a new family of putative tyrosine phosphatase and appears to be ubiquitously expressed, with a 3.9 kb transcript detected in all adult and fetal tissues studied. We present clinical, histological, and molecular analysis of two patients with XLMTM in which we identified mutations of the MTM1 gene. In one patient, an AAAG deletion was identified at the position of nucleotide 193 in coding exon 4. These 4 bp deletions caused a shift of the reading frame and created a stop codon （frameshift mutation）. His mother had both normal and mutant alleles heterozygously as a XLMTM carrier. In another patient, a C to T substitution of nucleotide 163, leading Arg 55 to stop codon （nonsense mutation） was identified. His mother who was an identical twin, had both normal and mutant alleles heterozygously as a XLMTM carrier. These mutations caused a development of an inactivation of the putative enzymatic activity of myotubularin.

The article presents evaluation of the application of Neo4j graph database to Gene Ontology graph analysis. Graph-based term similarity measures are calculated in order to assess the effectiveness of the system. Two types of common ancestor search are presented and evaluated, and parallel execution of the analysis is also evaluated., Studia Informatica, Vol 34, No 2A (2013)

Hypodermosise sebep olan türler Hypoderma bovis ve Hypoderma lineatum'dur. Mevsimsel olarak sonbahar, kış hatta ilkbahar döneminde görülen ve enfeste hayvanların dorsal ve lumbal bölgelerinde derialtı şişlikleriyle karakterize olan paraziter bir hastalıktır. Hypoderma türlerinin morfolojik teşhis yöntemleri literatürlerde sınırlı kalması, tanısının güç olması ve gelişen dünyamızda farklı teşhis yöntemlerinin ortaya çıkışı nedeniyle moleküler tekniklere gerek duyulmuştur. Bu çalışmada, Hypoderma türleri Van Belediye Mezbahasından kesim sonrası sığırların derialtı dokularından elde edildi ve Hypoderma larvaları için örneklenen PCR ürünleri COI (mt DNA) geni ve mt DNA kodsuz bölge başarıyla sekanslandı. Genomik DNA'lar ekstraksiyon kit kullanılarak elde edildi, agaroz jelde COI geni için 688bç'lik, mitokondrial noncoding bölgelede ? 1250-1320bç'lik ve nd1 geni için ? 321-1249bç'lik DNA ürünü veren mitokondrial DNA geninin polimeraz zincir reaksiyonuyla (PCR) amplifikasyonu sağlandı. PCR amplifikasyonu ve HinfI, RsaI ve TaqI restriksiyon enzimleri kullanılarak RFLP tekniği ile mitokondrial DNA gen bölgesi analiz edildi. Bu, Van şehrinde, Hypoderna türlerinin tanımlandığı ilk moleküler çalışmadır. The species, Hypoderma bovis and Hypoderma lineatum lead to Hypodermosise on cattle. Seasonally, it is seen in autumn, winter and even in spring and in the dorsal and lumbar regions of the infested animals is a parasitic disease which is characterized by subcutaneous protuberance. In the literature, morphological diagnostic methods of Hypoderma parts remain limited, its diagnosis is difficult and in the developing world doe to the emergence of different diagnostic methods, there is a need to molecular techniques. In this study, the types of Hypoderma were obtained from Van Local Slaughter House after the cutting of cattle subcutaneous of tissues and larvae of Hypoderma sampled for PCR products COI (mt DNA) gene and mt DNA noncoding region were successfully sequenced. DNAs were obtained using the extraction kit and Polymerase chain reaction (PCR) foe amplification of the mitochondrial DNA gene yielded for 688bp COI gene for ? 321-1249bp nd1 and ? 1250-1320bp mtDNA noncoding region on agarose gel. Using the PCR amplification and HinfI, RsAI and TaqI restriction enzymes, mitochondrial DNA gene regions were analyzed with the RFLP technique. This is the first molecular study of the Hypoderma types defined in Van 86

Böbrek kanseri ürolojik kanserlerin en ölümcül olanıdır ve yetişkin malignitelerin % 3? ünü oluşturur. Böbrek kanseri tek bir hastalık olmakla birlikte renal hücreli tümörler dahil olmak üzere farklı birçok türü bulunmaktadır. VHL geni RCC ile ilişkisi olduğu bilinen tümör baskılayıcı bir gendir. VHL, hipoksi indüklenebilir faktörlerin bir negatif düzenleyicisi olarak fonksiyon gösterir. Son zamanlarda yapılan dizi analizi çalışmalarında, ccRCC?de histon modifikasyonunda ve kromatin şekillenmesinde görev alan PBRM1 ve SETD2 gibi genlerde birçok yeni ve sık görülen mutasyonlar tanımlanmıştır. PBRM1 geni, tümör baskılayıcı olan VHL geninden sonra en çok mutasyon görülen ikinci gendir. Bu gen, belirli genlerin trankripsiyonel aktivasyonununda ve baskılanmasında görev alan BAF180 proteinini kodlamaktadır. SETD2 geni, histon H3?ün 36. pozisyondaki lizin amino asitinin trimetilasyonundan sorumlu bir histon metiltransferazı kodlamaktadır. Aynı zamnda tümör gelişiminde baskılayıcı bir rol alabilir. Bu çalışmada, böbrek kanseri çeşidine ve hastaların cinsiyet, ortalama yaş gibi klinik özelliklerine göre gruplanan 30 çift örnek, gen ifadesi, SSCP ve Sanger dizileme teknikleri ile analiz edilmiştir. VHL, PBRM1, SETD2 genlerinin aşağı yönlü düzenlendiği bulunmuştur. Ancak, Wilcoxon testi ile yapılan istatistiksel analizlerde anlamlı bir sonuca varılamamaıştır (p>0,05). Yapılan mutasyon taraması sonuçlarına göre farklı bir genotip saptanamamıştır. Sonuç olarak, taranan üç genin mRNA seviyesinde düşüş görülmüştür. RCC?nin patogenezinde görev alan moleküler mekanizmaların anlaşılması, böbrek kanseri moleküler hedefli ilaçların geliştirilmesi adına önem arz etmektedir.Anahtar Kelimeler: Böbrek kanseri, VHL, PBRM1, SETD2, Gen ifadesi analizleri, Mutasyon taraması Kidney cancer is the most lethal urological cancer and accounts for 3% of adult malignancies. Kidney cancer is not a single disease; it is made up of a number of different types including renal cell tumours as the most common type. VHL gene is a tumor suppressor, it is best known with RCC. The VHL functions as negative regulator of hypoxia inducible factors. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC including PBRM1 and SETD2. The PBRM1 gene is the second most common mutated gene after VHL, a tumor suppressor gene. It encodes the BAF180 protein, which involved in transcriptional activation and repression of selected genes.SETD2 encodes a histone methyltransferase, which is responsible for trimethylation of the lysine residue at position 36 of histone H3 and may play a role in suppressing tumor development. In this study, 30 paired tumor and normal samples that were grouped according to the types of kidney cancer and clinical characteristics of patients, including gender and average age were observed with gene expression analysis, SSCP and sequencing technique. Three of genes VHL, PBRM1 and SETD2 were relatively downregulated. However, statistically no significance found by Wilcoxon signed rank test (p>0,05). As a result of gene screening no mutation (no different genotype) was observed. In conclusion, the mRNA expression levels of three genes were insignificantly downregulated. Understanding the molecular mechanisms involved in the pathogenesis of RCC has aided the development of molecular-targeted drugs for kidney cancer. Keywords: Kidney cancer, VHL, PBRM1, SETD2, Expression analysis, Mutation screening 83

International audience; Background: This paper introduces a new constrained model and the corresponding algorithm, called unsupervised Bayesian linear unmixing (uBLU), to identify biological signatures from high dimensional assays like gene expression microarrays. The basis for uBLU is a Bayesian model for the data samples which are represented as an additive mixture of random positive gene signatures, called factors, with random positive mixing coefficients, called factor scores, that specify the relative contribution of each signature to a specific sample. The particularity of the proposed method is that uBLU constrains the factor loadings to be non-negative and the factor scores to be probability distributions over the factors. Furthermore, it also provides estimates of the number of factors. A Gibbs sampling strategy is adopted here to generate random samples according to the posterior distribution of the factors, factor scores, and number of factors. These samples are then used to estimate all the unknown parameters. Results: Firstly, the proposed uBLU method is applied to several simulated datasets with known ground truth and compared with previous factor decomposition methods, such as principal component analysis (PCA), non negative matrix factorization (NMF), Bayesian factor regression modeling (BFRM), and the gradient-based algorithm for general matrix factorization (GB-GMF). Secondly, we illustrate the application of uBLU on a real time-evolving gene expression dataset from a recent viral challenge study in which individuals have been inoculated with influenza A/H3N2/Wisconsin. We show that the uBLU method significantly outperforms the other methods on the simulated and real data sets considered here. Conclusions: The results obtained on synthetic and real data illustrate the accuracy of the proposed uBLU method when compared to other factor decomposition methods from the literature (PCA, NMF, BFRM, and GB-GMF). The uBLU method identifies an inflammatory component closely associated with clinical symptom scores collected during the study. Using a constrained model allows recovery of all the inflammatory genes in a single factor.

Adli bilimlerde DNA analizleri; kimliklendirme, babalık tayini, akrabalık ilişkilerinin belirlenmesinde ve olay yeri - suçlu arasında bağlantı kurulması için gereklidir. STR lokuslarının alel frekansları (sıklıkları) toplumdan topluma değişiklik göstermektedir.Bu tez çalışmasında, D10S1248, D14S1434, D22S1045, D4S2364, D2S441, D1S1677 mini STR lokuslarının Türkiye genelinde gen sıklıklarının saptanması ve kriminal laboratuvarlarda rutinde kullanılabilmesi amacıyla Türkiye genelinde 200 kişiden alınan kan örneklerinde 6 mini STR lokusu tiplendirildi. Bunun için; 6 lokusun PCR'ı 3'lü multipleks oluşturularak çalışıldı. Coble M. D. ve ark. 2005'te dizayn ettikleri primerler kullanılarak, 2011 yılında Ünsal T. ve ark. tarafından optimize edilmiş FAM, TET, HEX boyaları ile işaretlenmiş primerler kullanıldı. PCR için Top Taq Master Mix (Qiagen) kullanıldı. PCR ürünleri ABI 310 cihazında analiz edildi. 200 örnekte 6 mini STR lokusu için elde edilen alel tipleri Powerstat V1.2 (Promega) populasyon genetiği programı kullanılarak analiz edildi. Her bir lokusun Türkiye toplumundaki alel sıklıkları, homozigotluk ve heterozigotluk oranları, lokusların polimorfik bilgi içeriği, eşleşme olasılığı, ayırt etme gücü, dışlama gücü ve babalık indeksi oranları hesaplandı. Arlequin 3.11 programı ile her lokusun Hardy Weinberg Dengesine uyumu analiz edildi. Elde edilen veriler diğer popülasyonlar ile karşılaştırılması amacıyla Z değerleri hesaplandı.Bu tez çalışmasında D1S1677,D2S441, D4S2364, D10S1248, D14S1434, D22S1045 mini STR lokuslarının Türkiye'deki adli laboratuvarlarda olgu aydınlatılmada kullanılabilmesi için Türk toplumuna ait gen sıklıkları belirlendi. Elde edilen sonuçlar Türkiye popülasyonuna özgü olup, genel olarak babalık ve kimliklendirme çalışmalarında mutlaka kendi toplumumuza özgü gen sıklıklarının kullanılması gerekmektedir. In Forensic Sciences, DNA analysis is required for identifications, paternity test, understanding the relationships between people, and establishment of a connection between the creme scene and the quilty person. Frequencies of the STR loci varies between populations.The aim of the study is to determinate the alelle frequencies of D10S1248, D14S1434, D22S1045, D4S2364, D2S441, D1S1677 mini STR loci in Turkish population and to became a valuable tool for Turkish Criminal Laboratories. For this purpose 6 mini STR loci was identified blood samples, which were taken from 200 volunteer subjects. Therefore 6 STR loci were amplified by two different multiplex PCR reaction. Primer set which was designed by M.D. Coble on 2005 and optimized with FAM-HEX-TET dies by T. Unsal on 2011. Top TaqTM Master Mix (Qiagen ) was used for PCR reaction. PCR products were analysed on ABI 310 Genetic Analyser. Allele Frequencies were calculated with Powerstats V.1.2 ( Promega Cooperation) population genetics Excel workbook. As well as Allele Frequencies, Matching Probability, Polymorphism Information Content, Power of Discrimination, Power of Exculusion, Typical Paternity İndex , Number of Homozygotes and Heterozygotes were also calculated. Hardy Winberg Equlibrium was tested for each Loci with Arlequin 3.11 population istatistic program. Finally, In order to compare our data with other populations we calculate Z score for every allele.In this study, allele frequencies of 6 mini STR loci (D10S1248, D14S1434, D22S1045, D4S2364, D2S441, D1S1677) for Turkish population were statistically calculated and verified. The usage of 6 mini STR loci in Turkish Criminal Laboratories were establihed. The results obtained are specific to Turkey population. In general, it is necessary to use the frequency of specific in our own society for paternity and identification issues. 130

Amaç: Spontan veya tekrarlayan gebelik kayıplarında genetik etiyolojide sadece maternal değil, fetal ve paternal genetik faktörlerin de rolü olup olmadığının belirlenmesidir. Bu amaçla anne, baba ve düşük materyaline ait çeşitli polimorfizmlerin ve düşük materyalindeki sayısal kromozomal anomalilerin analizi hedeflenmiştir.Yöntem: Bu çalışmaya iki ya da daha fazla düşüğü olan 56 kadın ve bu kadınların eşleri, kontrol grubu olarak en az iki yaşayan çocuğu olan ve hiç spontan abortusu olmayan 43 kadın ve bu kadınların eşleri, ayrıca herhangi bir gebeliği spontan olarak sonlanan 22 anne ve bu annelere ait 23 düşük materyali dokusu dahil edilmiştir. Tüm gruplara ait toplam 243 örnekten genomik DNA izolasyonu sonrası, Faktör V Leiden (FVL), Protrombin G20210A, MTHFR C677T, MTHFR A1298C, PAI-1 5G/4G, ACE I/D, eNOS E298D, Apo E E2/E3/E4, VEGF A C936T, VEGF A C2578A, VEGF A C405G, VEGF A C460T polimorfizm analizleri için Real Time PCR yöntemi, düşük materyallerine ait analiz için QF-PCR yöntemi kullanılmıştır. Tüm habituel abortus çiftlerine (112 birey) sitogenetik analiz yapılmıştır.Bulgular: 23 düşük materyalinden 7 tanesinde sayısal kromozomal anomali (iki trizomi 21, iki trizomi 13, iki triploidi, bir monozomi X) saptanmıştır. Çalışılan polimorfizmlerden FVL, MTHFR C677T, MTHFR A1298C, PAI-1 5G/4G, ACE I/D, eNOS E298D, Apo E E2/E3/E4, VEGF A C405G, VEGF A C936T, VEGF A C460T polimorfizmleri ile spontan veya tekrarlayan gebelik kayıpları arasında ilişki olduğu (p

Odd-nosed monkeys represent one of the two major groups of Asian colobines. Our knowledge about this primate group is still limited as it is highlighted by the recent discovery of a new species in Northern Myanmar. Although a common origin of the group is now widely accepted, the phylogenetic relationships among its genera and species, and the biogeographic processes leading to their current distribution are largely unknown. To address these issues, we have analyzed complete mitochondrial genomes and 12 nuclear loci, including one X chromosomal, six Y chromosomal and five autosomal loci, from all ten odd-nosed monkey species. The gene tree topologies and divergence age estimates derived from different markers were highly similar, but differed in placing various species or haplogroups within the genera Rhinopithecus and Pygathrix. Based on our data, Rhinopithecus represent the most basal lineage, and Nasalis and Simias form closely related sister taxa, suggesting a Northern origin of odd-nosed monkeys and a later invasion into Indochina and Sundaland. According to our divergence age estimates, the lineages leading to the genera Rhinopithecus, Pygathrix and Nasalis+Simias originated in the late Miocene, while differentiation events within these genera and also the split between Nasalis and Simias occurred in the Pleistocene. Observed gene tree discordances between mitochondrial and nuclear datasets, and paraphylies in the mitochondrial dataset for some species of the genera Rhinopithecus and Pygathrix suggest secondary gene flow after the taxa initially diverged. Most likely such events were triggered by dramatic changes in geology and climate within the region. Overall, our study provides the most comprehensive view on odd-nosed monkey evolution and emphasizes that data from differentially inherited markers are crucial to better understand evolutionary relationships and to trace secondary gene flow. peerReviewed

ÖZET HELICOBACTER PYLORI cagA GENİNİN FİLOGENETİK ANALİZİ Helicobacter pylori cagA geni ile farklı mide patolojileri ve izolatların coğrafik dağılımı arasındaki olası bir ilişkiyle alakalı olarak literatürde çelişkili sonuçlar bulunmaktadır. Biz bu tezde Türkiye’deki izolatların cagA genlerinin moleküler düzeyde analizini yapmayı amaçladık. Çalışmamızdaki 170 hastadan (126 gastrit, 12 mide ülseri, 27 oniki parmak bağırsağı ülseri, 5 mide kanseri) 151 izolat elde ettik (1 mide ülseri ve bir oniki parmak bağırsağı ülseri hastasından 2’şer farklı izolat elde ettik). DNA izolasyonu, polimeraz zincir reaksiyonu, agaroz jel elektroforezi, DNA dizi analizi ve filogenetik analizler yaptık. Elde ettiğimiz 151 H. pylori izolatından (106 adet G, 13 adet MÜ, 27 adet DÜ ve 5 adet SA) 101 tanesinde (%66.9) cagA geni tespit ettik. 106 adet G izolatından 62’si (%58,5), 13 adet MÜ izolatından 12’si (%92,3), 27 adet DÜ izolatından 25’i (%92,6) ve 5 adet SA izolatından 2’si (%40) cagA pozitif olarak bulundu. 101 adet cagA pozitif suştan 16’sında (%15,8) sadece cagA 5’ uç bölgesi, 11’inde (%10,9) sadece cagA 3’ uç bölgesi 74’ünde (%73,3) ise hem cagA 5’ hem de cagA 3’ uç bölgesini aynı anda tespit ettik. İzolatlarımızın hem cagA 5’ hem de 3’ uç bölgelerine göre hpEurope grubuna ait olduğunu belirledik. “TCT TCC ATA AAG AGC TTT CAG AAA T” bazlarından oluşan ve tüm izolatlarımızın 5’ uç bölgelerinde bulunan korunmuş bir bölge tespit ettik. Bu korunmuş DNA bölgesi, Batı tipi & Doğu Asya tipi izolatların ayırt edilmesinde kullanılabilir. cagA geninin tespitinde hem 5’ hem de 3’ uç bölgelerinin farklı bir çok primerle çoğaltılarak analiz edilmesi daha güvenilir sonuçlar vermektedir. ABSTRACTPHYLOGENETIC ANALYSIS OF HELICOBACTER PYLORI cagA GENEThere are some discrepancies about the possible association of Helicobacter pylori cagA gene with the different gastric pathologies and the geographical distribution of H. pylori isolates in the literature. In this thesis we aimed to analyze cagA gene of Turkish isolates on molecular basis.We obtained 151 isolates from 170 patients (126 gastritis, 12 gastric ulcer, 27 duodenal ulcer and 5 gastric cancer patients). We could get 2 different isolates from one gastric ulcer patient and 2 different isolates from one duodenal ulcer patient. DNA isolation, polymerase chain reaction, agarose gel electrophoresis, DNA sequencing and phylogenetic analysis were applied. Among 151 isolates (106 gastritis, 13 gastric ulcer, 27 duodenal ulcer and 5 gastric cancer isolates) 101 (66,9%) were found to be cagA positive. 62 (58,5%) of 106 gastritis isolates, 12 (92,3%) of 13 gastric ulcer, 25 (92,6%) of 27 duodenal ulcer and 2 (40%) of 5 gastric cancer isolates were cagA positive. Our isolates were clustered in hpEurope population. We also detected a conserved region of “TCT TCC ATA AAG AGC TTT CAG AAA T” in the 5’ end region of cagA gene of our all isolates. The conserved region that we detected can be used to distinguish Western and East Asian isolates. We also state that using plenty of different primers for both 5’ and 3’ regions of cagA gives more reliable results for detection of cagA gene.

ÖZETFerhat Ege, Kalça Osteoartriti Olan Hastalarda Vitamin D Reseptör Gen Analizi, Bülent Ecevit Üniversitesi Tıp Fakültesi, Fiziksel Tıp ve Rehabilitasyon Tezi. Zonguldak, 2012.Osteoartrit (OA) en sık görülen eklem hastalığıdır. Eklem kıkırdağında erozyon, eklem kenarlarında kemik hipertrofisi, subkondral skleroz, synovial membran ve eklem kapsülünde birtakım biyokimyasal ve morfolojik değişiklikler ile karakterize dejeneratif bir eklem hastalığıdır. OA'da etkenler çok faktörlüdür ve risk faktörleri her eklem için farklılık gösterir. D vitamini gen polimorfizminin kalça osteoartrit riskinde belirleyici bir etken olup olmadığı tam olarak bilinmemektedir.Bu çalışmada Mart 2011 ve Mart 2012 tarihleri arasında Bülent Ecevit Üniversitesi Uygulama ve Araştırma Hastanesi Fizik Tedavi ve Rehabilitasyon Polikliniğine başvuran hastalar alınmıştır. Kalça OA tanısı alan 80 hasta (çalışma grubu) ve kalça ağrısı olmayan başka bir nedenle hastaneye başvuran aynı yaş grubunda 82 hasta (kontrol grubu) dâhil edilmiştir.Gruplara göre cinsiyet, yaş, vücut kitle indeksi (VKİ) ve vitamin D reseptör (VDR) gen polimorfizmi değerlendirildi.Kalça OA tanısı almış 80 hastanın 59'u kadın, 21'inin ise erkek olduğu tespit edildi. Kontrol grubuna alınan 82 hastanın 60'ı kadın, 22'si erkek olduğu saptandı. Çalışma grubunda ortalama yaş 62.75, kontrol grubunda ise ortalama yaş 61.87 yıl olarak tespit edildi. VDR gen analizi FokI ile çalışıldı. Hastalar VDR gen polimorfizmi açısından incelendiğinde çalışma grubunda 43 hastada FF genotipi, 35 hastada Ff genotipi ve 2 hastada ff genotipi varlığı gözlendi. Kontrol grubunda ise 40 hastada FF genotipi, 36 hastada ise Ff ve 6 hastada ff genotipi varlığı tespit edildi. Genotip dağılımları açısından incelendiğinde gruplar arasında istatistiksel açıdan anlamlı farklılık bulunmadı (p>0,05). Birçok genetik hastalıkta allel sıklığının hastalık etyopatogenezinde rol oynadığı göz önünde bulundurularak hasta ve kontrol gruplarındaki genetik yapı allel sıklığına göre de incelendi. Çalışma grubunda 39 hastada f allel, 121 hastada F allel saptandı. Kontrol grubunda 48 hastada f allel ve 116 hastada F allel varlığı tespit edildi. Allel sıklığı açısından hasta ve kontrol gruplarında yapılan istatistiksel incelemede anlamlı farklılık saptanmadı (p=0,320).Sonuç olarak çalışmamızda kalça OA ile VDR FokI gen polimorfizmi arasında istatistiksel olarak anlamlı bir ilişki olmadığını tespit ettik.Anahtar Kelimeler: Osteoartrit, vitamin D reseptör geni, polimorfizm, kalça osteoartriti ABSTRACTFerhat Ege, Vitamin D Receptor Gene Analysis of patients with osteoarthritis of the hip, Bülent Ecevit University School of Medicine, Physical Medicine and Rehabilitation Thesis. Zonguldak 2012.Osteoarthritis (OA) is the most common disease of the joint. Erosion of the articular cartilage is a degeneratif disorder that is characterized with bone hypertrophy on joint edges, subchondral sclerosis and biochemical and morphological changes in joint capsule. OA is a multifactorial disease which has different risk factors for each joint. It is not clear that Vitamin D receptor (VDR) gene polymorphism is a determining factor on hip OA.Patients who are admitted to Physical Medicine and Rehabilitation departmant of Bülent Ecevit University between March 2011 and March 2012 are included in this study. Eighty patients who have hip OA are included in the study group and 82 patients who are admitted hospital any reason out of hip pain are included in control group.Gender, age, body mass index (BMI), and VDR gene polymorphisms are evaluated according to groups.Fifty nine patients are female, 21 patients are male in the study group. 60 patients were female, 22 patients are male in the control group. The mean ages are 62.75 and 61.87 in the study group and control group respectively. VDR gene analysis is worked with Fokl. According to VDR gene polymorphism the genotypes are; FF genotype in 43 patients, Ff genotype in 35 patients, ff genotype in 2 patients in the study group. Genotypes in the control group are; FF genotype in 40 patients, Ff genotype in 36 patients and ff genotpe in 6 patients.There is no significant difference between two groups about genotypes (p>0.05).Allele frequency is also determined in genetic analysis because allele frequency has an effect on ethiology and pathogenesis of genetic disorders. There were 39 patients with f allele and 121 patients with F allele in the study group. There were 48 patients with f allel and 116 patients with F allele in the control group.There is no significant difference about allele frequency between study group and control group (p=0.320). As a result, in our study we assign that there is no significant relationship between hip osteoarthritis and Vitamin D receptor Fokl genotype.Keywords: Osteoarthritis, vitamin D receptor gene, polymorphisms, hip osteoarthritis 78

Pharmacogenomics is the study of how genetic variations influence the response to drugs, by correlating gene expression with the drug's efficacy and toxicity. This concept has recently been successfully applied in oncology. To test its applicability to PAH, we examined two experimental models of the disease: mice with deletion of the Vasoactive Intestinal Peptide gene (VIP(- /-)); and rats injected with monocrotaline (MCT). Since the two models express comparable phenotypic features, we analyzed their particular gene alterations, with special reference to genes related to pulmonary vasoconstriction, vascular remodeling, and inflammation. We then compared the phenotypic and genotypic responses in each model to treatment with the same drug, VIP. In untreated VIP(-/-) mice there was over-expression of almost all genes promoting vasoconstriction/ proliferation, as well as inflammation, and under-expression of all vasodilator/anti-proliferative genes. As expected, treatment with VIP fully corrected both the key PAH features, and all gene expression alterations. MCT-treated rats showed two distinct sets of alterations. One, similar to that in VIP(- /-) mice, i.e., tended to promote vascular remodeling and inflammation, e.g., up-regulation of myosin polypeptides, procollagen, and some inflammatory genes. The other was a set of opposite alterations that suggested an effort to modulate the PAH, e.g., up-regulation of the VIP and NOS3 genes. In this model, VIP treatment failed to correct many of the genotypic abnormalities, and, in parallel, incompletely corrected the phenotypic changes as well. This preliminary proof-of-concept study demonstrates the importance of genomic information in determining therapeutic outcome, and thus in selecting personalized therapy. Full validation of the merits of pharmacogenomics must await studies of lungs from patients with different forms of PAH.

Tezimin araştırma konusu, gen analizleri dolayısıyla kişilik haklarının ihlal edilmesi ve buna bağlı olarak ortaya çıkabilecek ihlallere karşı kişiliğin korunmasını amaçlayan hukuki temellerin belirlenmesidir. Gen analizleri sonucunda kişilik hakları zarara uğramakta ve buna bağlı olarak olumsuz sonuçlar meydana gelmektedir. Bu olumsuz sonuçlara karşı da kişiye sıkı sıkıya bağlı kişilik hakkı ihlali dolayısıyla kişinin tazminat istekleri ve dava hakkı gündeme gelmektedir. Bu çalışmada da önemi dolayısıyla kişilik haklarına geniş yer verilecektir. Türkiye'de tıp alanında gen tekniklerinin kullanıldığı bilinmektedir. Bu açıdan gen analizi konusu da çalışmamızda incelenip kapsamı tespit edilecektir.Tez çalışmam üç bölümden oluşmaktadır. Birinci bölümde, Gen Analizleri ile ilgili genel bilgiler, ikinci bölümde ise, Kişilik Hakları ile ilgili bilgiler verilmektedir. Yeri geldiğinde kişilik hakları konuları içerisinde gen analizleriyle bağlantılı olan kısımlarda açıklamalarda bulunulmaktadır. Üçüncü ve son bölümde ise gen analizleri ile kişilik hakları arasındaki bağlantı ve ihlallere değinilerek, korunmasına yönelik neler yapılabileceği belirtilmiştir.İnsanlar üzerindeki gen analizlerinin, hukuki açıdan onların çekirdek alanlarına (özel alanına, kişilik haklarına) bir tecavüz teşkil edebileceğine birçok defa işaret edilmiştir. Gen tekniği çalışmalarında elde edilen başarılı gelişmeler, kişilik haklarının daha fazla korunmasını da gerekli kılmaktadır. Türkiye açısından konuyu ele alacak olursak, tartışmaların etik boyuttan daha öteye gitmekte zorlandığını görmekteyiz. Bunun yanında yeterli düzenlemenin de ülkemiz açısından var olduğunu söyleyemeyiz. Çağın gereklerine uygun olarak bu alanda yeni düzenlemelerin yapılması kaçınılmaz gözükmektedir.Anahtar Kelimeler: Gen Analizleri, Kişilik, Kişilik Hakları The research subject of the thesis is gene analyses and so violation of personal rights and to state legal acts aiming protecting personal rights against violations that may be resulted from. Personal rights have been attacked because of gene analyses and thus there become negative results. These negative results give rise to violation of personal rights that are unduly attached to person and so claim for indemnification and right of action come up. Due to its importance, personal rights have a broad role in this study. It is known that in Turkey gene techniques are used in medical sciences. From this aspect, in this study, the subjects of gene analyses are investigated and the concept of it is determined.This study comprises of three sections. In the first chapter, general information about gene analyses is presented. In the second chapter, the literature about personal rights is given. When appropriate and necessary, the relations between gene analyses and personal rights are mentioned. In the third and last chapter, the relations and violations between gene analyses and personal rights are stated and the precautions to protect these are presented.It has been referred many times in the study that gene analyses on human beings may jurally be an infringement to their core area (private area, personal rights). The successful improvements in the studies of gene technology make protection of personal rights more necessary. It is clearly seen that from Turkey?s aspect, discussions are limited to ethics. Furthermore, it is difficult to mention that there are essential regulations in this aspect in Turkey. It is inevitable that new regulations are to be made regarding the necessities of this age.Keywords: Gene Analyses, Personality, Personal Rights 139

Objective: Case report of a patient with angioid streaks, peau d’orange, comet tail lesions, choroidal neovascularisation and presumed pseudoxanthoma elasticum (PXE). PXE was confirmed by gene analysis but not by skin biopsies. Methods: Case report of a patient with angioid streaks identified at age 21 and follow-up till age 43 with repeated fluorescein angiography (FA) and optical coherence tomography (OCT). Dermatologic examination, skin biopsies and genetical analysis performed to confirm suspected diagnosis of PXE. Results: At age 43, no specific skin lesions were identified and 3 biopsies could not confirm PXE. Genetic analysis showed a homozygous mutation in the ABCC6 gene and confirmed the diagnosis of PXE. Conclusions: This case illustrates that in patients with angioid streaks having strong ocular indicators of PXE, confirmation of PXE can be obtained not only with dermatologic examination and skin biopsies, but also with genetic analysis. PXE associated mutations can be detected occasionally in biopsy negative patients and for this reason are extremely helpful in confirming a suspected diagnosis., GMS Ophthalmology Cases; 1:Doc03; ISSN 2193-1496

Article, 信州医学雑誌 40(5): 407-421(1992)

The aim of the project was to identify biologically relevant novel gene clusters by using combined genomic data instead of using only gene expression data in isolation. The clustering algorithm based on self-organizing maps (Kasturi et al., 2005) was extended and implemented in order to use gene location data together with the gene expression and the motif occurrence data for gene clustering. A distance function was defined to be used with gene location data. The algorithm was also extended in order to use vector angle distance for gene expression data. Arabidopsis thaliana is chosen as a data source to evaluate the developed algorithm. A test data set was created by using 100 Arabidopsis genes that have gene expression data with seven different time points during cold stress condition, motif occurrence data which indicates the occurrence frequency of 614 different motifs and the chromosomal location data of each gene. Gene Ontology (http://www.geneontology.org) and TAIR (http://arabidopsis.org) databases were used to find the molecular function and biological process information of each gene in order to examine the biological accuracy of newly discovered clusters after using combined genomic data. The biological evaluation of the results showed that using combined genomic data to cluster genes resulted in new biologically relevant clusters.

The heart responds to stress signals by hypertrophic growth, which is the first step towards heart failure (HF). The genetic pattern underlying HF remains largely elusive. Although the transcription factor Myocyte Enhancer Factor-2 (MEF2) is known to be a common endpoint for several hypertrophic signaling pathways, its precise role in myocardial remodeling is unknown. To this end, we pursued comprehensive gain- and loss-of-function approaches for MEF2 transcriptional activity in heart muscle in vitro and in vivo. We generated transgenic mice overexpressing MEF2 in the heart, which resulted in HF. In line, adenoviral delivery of MEF2 to cultured cardiomyocytes induced myocyte elongation, myofibril degeneration, and redistribution of focal adhesions, as seen in failing hearts. We also generated mice expressing a dominant negative form of MEF2 and crossed these mice with calcineurin transgenic mice, a model for cardiac hypertrophy and heart failure. This did not prevent cardiac hypertrophy, but protected the mice from HF. To identify MEF2 target genes, we generated inducible stable cardiac cell lines, expressing the active form of MEF2, and performed microarray analysis. Functional clustering of MEF2 target genes revealed an overrepresentation of genes involved in cytoskeletal remodeling and cell-matrix adhesion. We describe myotonic dystrophy protein kinase (DMPK) as a direct transcriptional target for MEF2. By siRNA-mediated knockdown of DMPK expression, we demonstrate the involvement of this gene in the pathological aspects of MEF2 induced cardiomyocyte remodeling. Given the resemblance between MEF2 induced cardiac remodeling and the cardiac phenotype of mice lacking Muscle LIM Protein (MLP), an established mouse model for inherited dilated cardiomyopathy, we analyzed MEF2 transcription factor activity in MLP knockout mice by genetic crossbreeding with MEF2 reporter mice. Following confirmation that MEF2 activity was severely upregulated, we used conditional transgenesis to express a dominant-negative form of MEF2 (DNMEF2) in the murine MLP deficient heart and combined this with echocardiographic analysis to examine the effect on cardiac remodeling. Surprisingly, histological and functional analyses indicated that MEF2 inhibition in MLP knockout mice did not effect the genesis of dilated cardiomyopathy. Finally, the significance of MEF2 transcriptional activity was assessed in the setting of a more physiological model of biomechanical stress in the form of chronic murine pressure overload using conditional transgenesis to express a dominant-negative form of MEF2 (DNMEF2) in the postnatal heart. Surprisingly, echocardiography indicated that MEF2 inhibition did not improve end-diastolic and end-systolic ventricular dimensions and contractility as observed in calcineurin transgenic hearts with conditional MEF2 inhibition. In fact, cardiac function was significantly worsened in the setting of MEF2 inhibition, which could be correlated with specific defects in mitochondrial adaptation during pressure overload. Taken together, in this thesis we demonstrate that MEF2 activation in the heart does not evoke the classic hypertrophic response, yet promotes a gene program primarily involved in processes associated with dilated cardiomyopathy. Although MEF2 activation is required for maladaptive cardiac remodeling downstream of calcineurin signaling, its activity is not the sole trigger in certain forms of dilated cardiomyopathy, and is even necessary for the adaptive response of the heart during pressure overload.

The heart responds to stress signals by hypertrophic growth, which is the first step towards heart failure (HF). The genetic pattern underlying HF remains largely elusive. Although the transcription factor Myocyte Enhancer Factor-2 (MEF2) is known to be a common endpoint for several hypertrophic signaling pathways, its precise role in myocardial remodeling is unknown. To this end, we pursued comprehensive gain- and loss-of-function approaches for MEF2 transcriptional activity in heart muscle in vitro and in vivo. We generated transgenic mice overexpressing MEF2 in the heart, which resulted in HF. In line, adenoviral delivery of MEF2 to cultured cardiomyocytes induced myocyte elongation, myofibril degeneration, and redistribution of focal adhesions, as seen in failing hearts. We also generated mice expressing a dominant negative form of MEF2 and crossed these mice with calcineurin transgenic mice, a model for cardiac hypertrophy and heart failure. This did not prevent cardiac hypertrophy, but protected the mice from HF. To identify MEF2 target genes, we generated inducible stable cardiac cell lines, expressing the active form of MEF2, and performed microarray analysis. Functional clustering of MEF2 target genes revealed an overrepresentation of genes involved in cytoskeletal remodeling and cell-matrix adhesion. We describe myotonic dystrophy protein kinase (DMPK) as a direct transcriptional target for MEF2. By siRNA-mediated knockdown of DMPK expression, we demonstrate the involvement of this gene in the pathological aspects of MEF2 induced cardiomyocyte remodeling. Given the resemblance between MEF2 induced cardiac remodeling and the cardiac phenotype of mice lacking Muscle LIM Protein (MLP), an established mouse model for inherited dilated cardiomyopathy, we analyzed MEF2 transcription factor activity in MLP knockout mice by genetic crossbreeding with MEF2 reporter mice. Following confirmation that MEF2 activity was severely upregulated, we used conditional transgenesis to express a dominant-negative form of MEF2 (DNMEF2) in the murine MLP deficient heart and combined this with echocardiographic analysis to examine the effect on cardiac remodeling. Surprisingly, histological and functional analyses indicated that MEF2 inhibition in MLP knockout mice did not effect the genesis of dilated cardiomyopathy. Finally, the significance of MEF2 transcriptional activity was assessed in the setting of a more physiological model of biomechanical stress in the form of chronic murine pressure overload using conditional transgenesis to express a dominant-negative form of MEF2 (DNMEF2) in the postnatal heart. Surprisingly, echocardiography indicated that MEF2 inhibition did not improve end-diastolic and end-systolic ventricular dimensions and contractility as observed in calcineurin transgenic hearts with conditional MEF2 inhibition. In fact, cardiac function was significantly worsened in the setting of MEF2 inhibition, which could be correlated with specific defects in mitochondrial adaptation during pressure overload. Taken together, in this thesis we demonstrate that MEF2 activation in the heart does not evoke the classic hypertrophic response, yet promotes a gene program primarily involved in processes associated with dilated cardiomyopathy. Although MEF2 activation is required for maladaptive cardiac remodeling downstream of calcineurin signaling, its activity is not the sole trigger in certain forms of dilated cardiomyopathy, and is even necessary for the adaptive response of the heart during pressure overload.

This review will summarise the molecular approaches used to detect and analyse the genomes of Babesia bovis, B. bigemina and Anaplasma marginale which cause bovine babesiosis and anaplasmosis. These tick borne diseases are widely distributed in Africa, Asia, Australia, and Central and South America and for example, have been estimated to have an economic impact of US$15.9, $6.9, $6.2, $2.8, $22 million per annum in Australia, Kenya, Zimbabwe, Tanzania, and South Africa, respectively (McLeod and Kristjanson, 1999). The development and uptake of molecular tools to study these pathogens are reviewed to highlight potential directions for future research.African Journal of Biotechnology Vol. 4 (4), pp. 292-302, 2005

Cancer classification has traditionally been based on the morphological study of tumours. However, tumours with similar histological appearances can exhibit different responses to therapy, indicating differences in tumour characteristics on the molecular level. Thus, development of a novel, reliable and precise method for classification of tumours is essential for more successful diagnosis and treatment. The high-throughput gene expression data obtained using microarray technology are currently being investigated for diagnostic applications. However, these large datasets introduce a range of challenges, making data analysis a major part of every experiment for any application, including cancer classification and diagnosis. One of the major concerns in the application of microarrays to tumour diagnostics is the fact that the expression levels of many genes are not measurably affected by carcinogenic changes in the cells. Thus, a crucial step in the application of microarrays to cancer diagnostics is the selection of diagnostic marker genes from the gene expression profiles. These molecular markers give valuable additional information for tumour diagnosis, prognosis and therapy development.