In Memory of Dr. Ratip Kazancıgil

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Dynamics of transcription factor binding site evolution

Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ~10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of "pre-sites" or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genetics.Comment: 28 pages, 15 figure

A Spatial Estimation-based Handover Management For Challenging Femtocell Deployments

Tez (Yüksek Lisans) -- İstanbul Teknik Üniversitesi, Fen Bilimleri Enstitüsü, 2015Thesis (M.Sc.) -- İstanbul Technical University, Instıtute of Science and Technology, 2015Bu çalışmada, femtocell tabanlı ağlarda gereksiz aktarım sayısını düşürmeye yönelik, mobil kullanıcıların sinyal kaybı raporlarını kullanarak yeni bir aktarım yönetim mekanizması tasarlanmıştır. Tasarlanan mekanizmada sinyal kaybı değerlerini uzaysal olarak kestirebilmek için semivariogram analizi yapan Ordinary Kriging yöntemleri kullanmaktadır. Bu yöntem iki kısımdan oluşmaktadır. İlk olarak yeni tanımlanan sinyal kaybı değişkeni hesaplanır ve sonrasında bu değer önceden tanımlanan eşik değeri ile kıyaslanarak aktarım kararı alınır. Yeni tanımlanan sinyal kaybı değişkeni mobil kullanıcının gelecekte bulunacağı noktaların sinyal kaybı değişkenine dayanmaktadır. Sayısal veriler önerilen yöntemin geleneksel yönteme göre gereksiz aktarım sayısı ve ping-pong aktarım oranı anlamında daha iyi sonuçlar verdiği görülmüştür.In this study, a new path loss-based handover management mechanism is introduced in order to minimize the number of unnecessary handovers in femtocell-based networks by using path loss measurement reports from mobile stations. The proposed mechanism includes a spatial estimation of path loss step that depends on ordinary Kriging using Semivariogram Analysis. This method is composed of two parts. First calculate mobile station's newly defined path loss and then compare this value with the predefined threshold to make a handover decision. The newly defined path loss is calculated by considering the path loss of future locations which are the locations that the mobile station will most likely reach in the future. Numerical results demonstrate that the proposed handover scheme is superior to conventional handover scheme from the viewpoints of both unnecessary handover number and ping-pong handover rate.Yüksek LisansM.Sc

Investigation of metallo beta lactamases and oxacilinases in carbapenem resistant acinetobacter baumannii strains isolated from inpatients

Background: Resistance to beta-lactam antibiotics is widespread among Acinetobacter strains. Plasmid-mediated metallo beta lactamases (MBL) are responsible for carbapenem resistance, as are oxacillinases (OXA). In recent years, MBL producing carbapenem-resistant strains have been reported in the world and in Turkey in increasing rates. In our country, besides the OXA 51- like enzyme which is inherent in A. baumannii strains, OXA 58-like and OXA 23-like carbapenemases producing strains have also been widely detected. In addition, Verona Imipenemase (VIM) and (IMP)-type MBL have been reported in some centers. Aims: The aim of our study was to investigate the presence of carbapenemases in Acinetobacter strains isolated from hospitalized patients in Edirne. Study Design: Cross-sectional study. Methods: A total of 52 imipenem-resistant A. baumannii strains isolated between January and March 2013 were investigated. The presence of MBL was described phenotypically by the combined disk diffusion test (CDDT), double disk synergy test (DDST), MBL E- test (only performed in 28 strains) and modified Hodge test. blaIMP , blaVIM, blaGIM, blaSIM, blaSPM genes and blaOXA-23, blaOXA-51, blaOXA-40, blaOXA-58 genes were inves- tigated by multiplex polymerase chain reaction (PCR). The blaNDM-1 gene was determined by PCR. Results: By modified Hodge test, 50 strains (96%) were found to be MBL positive. Positivity of MBL was 21% by both CDDT (0.1 M EDTA) and DDST. Twen- ty-four of 28 strains (85.7%) were positive by MBL E-test. OXA 23-like and OXA 51-like carbapenemases were detected in all strains, but OXA 58-like and OXA 40-like carbapenemases-producing A. baumannii were not detected. Also, MBL genes were not detected by genotypic methods. Conclusion: Only OXA 23-like carbapenemase was responsible for carbapenem resistance in carbapenem- resistant Acinetobacter strains in Edirne. The MBL- producing Acinetobacter strain is not yet a problem in our hospital. MBL resistance was found by phenotyp- ing tests, which must be confirmed by genotypic meth- ods; multiplex PCR tests can be easily used for screen- ing MBL

The effect of salt stress on spinach leaf physiological characteristics

Tuz stresinin ıspanak yaprak fizyolojisinde oluşturduğu olumsuz etkilerin tespit edilmesi amacıyla bitkiler iklim odasında 22/18°C (gündüz/gece) sıcaklık, %70 nem, 10/14 saatlik (aydınlık/gece) fotoperiyodik düzende, 400 µmol m2s-1 ışık şiddetine sahip kontrollü koşullarda yetiştirilmiştir. Araştırmada materyal olarak Meridien F1 çeşidi ile San Moreno F1 çeşidi, hidroponik yetiştirme sisteminde ise Hoagland besin çözeltisi kullanılmıştır. Tuz uygulamaları bitkilerin 4-5 gerçek yapraklı olduğu dönemde yapılmaya başlanmış hasat dönemine kadar kaplardaki besin çözeltisinin tuzluluğu EC=2, 6, 8 ve 10 dSm-1 olacak şekilde NaCl ilave edilerek elde edilmiştir. Deneme tesadüf parselleri deneme desenine göre 3 tekerrürlü olarak kurulmuş ve her tekerrürde 2 çeşit (Meridyen F1 ve San Moreno F1) ve 4 tuz konstrasyonu (EC=kontrol, 6, 8 ve 10 dSm-1) uygulanmıştır. Tüm denemede toplam 24 parsel, her parselde 16 bitki ve tüm denemede toplam 384 bitki yetiştirilmiştir. Deneme süresince, yaprak su potansiyeli (MPa), yaprak oransal su içeriği (%), yaprak hücrelerinde membran zararlanması (%), yapraklarda bulunan toplam klorofil (SPAD değeri) miktarı ve yaprak stoma geçirgenliği (mmol m-2 s-1) belirlenmiştir. Elde edilen sonuçlara göre tuz stresine karşı Meridyen F1 toleranslı, San Moreno F1 çeşidi hassas olarak belirlenmiştir. Kontrol uygulamasına nazaran artan tuz ilavesine karşı; şafak öncesi ve gün ortası yaprak su potansiyelleri yaprak oransal su içerikleri, yapraklardaki toplam klorofil miktarı ile stoma geçirgenlikleri azalmış.In order to identify the adverse effects of salt stress on physiology of spinach leaves, plants were grown in a climate chamber with 22/18 °C (day/night) temperature, 70% humidity, 10/14 hours (light/night) photoperiod and 400 micromole m-2slight intensity conditions. In this research Meridian F1 and San Moreno F1 varieties and in hydroponic growing systems Hoagland nutrient solution were used. Salt applications have been started from the period which plants have 4-5 true leaves and continued to harvested time. The salinity of the nutrient solution in the containers has been set up as EC = 2, 6, 8 and 10 dSm-1. Trial coincidence plots were established with 3 replications and at each repetition including 2 varieties (Meridyen F1 and San Moreno F1) and 4 different salt concentration (EC = control, 6, 8 and 10 dSm-1) were applied. A total of 24 experimental plots in all, a total of 384 plants were grown in 16 plants in each plot and the entire trial. During the experiment, leaf water potential (MPa), leaf relative water content (%), membrane infestation in leaf cells (%), total chlorophyll amount contained in the leaves (SPAD value), and leaf stomata permeability (mmol m-2 s-1) were measured. According to obtained results, Meridian F1 variety has been identified as tolerant on the contrary San Moreno F1 variety has been identified as sensitive against salt stress. Increased salt concentration has shown that leaf water potentials measured before dawn and midday, leaf relative water content, the total amount of chlorophyll in leaves and stomata permeability are reducing, on the contrary the rate of harm produced in the leaf cell membrane is increasing

Proximal tibiofibular joint arthrodesis due to recurrent giant ganglion cyst causing peroneal nerve palsy

Ganglion cysts are masses that we encounter frequently in our daily practice, usually in the upper extremity, less frequently in the lower extremities, and rarely cause compression symptoms. We present a case of a massive ganglion cyst of the lower limb causing peroneal nerve compression, managed with excision and proximal tibiofibular joint arthrodesis to prevent recurrence.Examination and radiological imaging of a 45-year-old female patient who was admitted to our clinic showed new-onset weakness in right foot movements and numbness on the dorsum of the foot and lateral cruris, a mass consistent with a ganglion cyst expanding the muscle was detected in the peroneus longus muscle. In the first surgery, the cyst was carefully resected. After three months, the patient came with a repeated mass on the lateral side of the knee. After confirmation of the ganglion cyst with clinical examination and MRI, a second surgery was planned for the patient. In this stage, we performed a proximal tibiofibular arthrodesis for the patient. Her symptoms recovered during the early follow-up period and no recurrence occurred during the two years of the follow-up period.Although the treatment of ganglion cysts seems easy, it can sometimes be challenging. We think that arthrodesis may be a good treatment option in recurrent cases

Obez hastalarda proinflamatuvar sitokinler ile fibrinolitik sistem arasındaki ilişki

Amaç: Obez kişilerde proinflamatuar sitokinlerden TNF-? ve IL-6, fibrinolitik sistem parametrelerinden t-PA ve PAI-1 ve insülin direnci arasındaki ilişki araştırıldı. Hastalar ve Yöntemler: Çalışmaya obez (VKİ ?30 kg/m2) olarak değerlendirilen 54 kişi (41 kadın, 13 erkek; ort. yaş 33.5) ve obezite sorunu olmayan (VKİ <25 kg/m2) 30 kişi (19 kadın, 11 erkek; ort. yaş 22.3) alındı. Fibrinojen düzeyleri koagülometrik olarak ve TNF-?, IL-6, t-PA, PAI-1 düzeyleri ELISA yöntemiyle ölçüldü. Bulgular: Kontrol grubuyla karşılaştırıldığında, obez kişilerde fibrinojen (p<0.01), PAI-1 (p<0.001), TNF-? (p<0.01) ve IL-6 düzeyleri (p<0.001) anlamlı derecede yüksek, t-PA düzeyi (p<0.001) ve t-PA/PAI-1 oranı (p<0.001) anlamlı derecede düşük bulundu. Obezlerde TNF-? ile t-PA (p=0.007) ve t-PA/PAI-1 oranı (p=0.016) arasında ters ilişki saptandı. İnsülin direnci olan ve olmayan obez kişilerde parametreler arasında fark yoktu. Sonuç: Obezitede adipoz dokudan salgılanan özellikle TNF-? gibi inflamatuar sitokinlerin artması fibrinolizde azalmaya yol açar. Obez kişilerde görülen bu değişiklikler, insülin direncinden bağımsız olarak ateroskleroza neden olabilir.Objectives: The aim of this study was to investigate the relationship between proinflammatory cytokines (TNF-&amp;#945; and IL-6), and fibrinolytic system parameters (t-PA, and PAI-1) and insulin resistance in obese individuals. Patients and Methods: The study included 54 obese subjects (BMI &amp;#8805;30 kg/m2; 41 females, 13 males; mean age 33.5 years) and 30 non-obese healthy individuals (BMI &lt;25 kg/m2; 19 females, 11 males; mean age 22.3 years). Fibrinogen levels were measured by the coagulometric method and the measurements of TNF-&amp;#945;, IL-6, t-PA and PAI-1 were carried out by the ELISA method. Results: Compared with non-obese subjects, obese individuals had significantly higher fibrinogen (p&lt;0.01), PAI-1 (p&lt;0.001), TNF-&amp;#945; (p&lt;0.01), and IL-6 (p&lt;0.001) levels, and significantly lower t-PA level (p&lt;0.001) and t-PA/PAI-1 ratio (p&lt;0.001). We also found an inverse relationship between TNF-&amp;#945; and t-PA levels (p=0.007) and t-PA/PAI-1 ratio (p=0.016) in obese individuals. The presence or absence of insulin resistance did not affect proinflammatory cytokines and fibrinolytic system parameters in obese individuals. Conclusion: Our findings indicate increased inflammatory cytokine levels especially in TNF-&amp;#945; level, and decreased fibrinolysis in obese individuals. These changes may contribute to atherosclerotic process independent from insulin resistance in obesity

Relative importance of anxiety and motivational variables in predicting language achievement for college learners of Chinese

The growing worldwide enthusiasm in learning Chinese calls for more research on learner characteristics in Chinese classrooms to better inform teaching practice. Language anxiety, which falls under the umbrella of learner’s affect, is considered an important affective aspect that negatively influences language learning and acquisition. As research on language anxiety mainly focused on the learning of Western languages, this study constitutes an initial attempt to investigate anxiety in the learning of Chinese through the testing of a structural model. The purpose of the study was to examine the relative importance of language anxiety in predicting Chinese achievement when motivation, integrativeness, and attitudes toward the learning situation were controlled. The study took place in a Southwestern university in China. Adopting a correlational design, this study measured 14 variables from which five constructs were formed—anxiety, motivation, integrativeness, attitudes toward learning situation, and Chinese achievement. The anxiety measures were from the Chinese language learning anxiety scale. The motivational measures were adapted from the international attitude and motivation test battery. The achievement measures included a HSK listening test, a HSK reading test, and students’ final course grades. A total of 223 students from the International College participated in this study. Students completed a written survey containing all the anxiety and motivational measures. Then they took the HSK listening and reading test. Students’ course grades in the Comprehensive Chinese course were collected at the end of the spring semester. The findings of structural equation modeling suggested that language anxiety negatively predicted Chinese achievement when motivation and attitudes toward the learning situation were controlled. Students’ attitudes toward the learning situation predicted their motivation, but motivation did not predict Chinese achievement. The follow-up analysis showed that motivation predicted student’s course grades but not their performance on the HSK tests. It can be concluded that language anxiety had a negative effect on language achievement for international learners of Chinese. Teachers were recommended to have an awareness of the nervousness and discomfort experienced by their students in language classrooms and to take measures to create a low-anxiety learning environment

A Case of Mumps and Idiopathic Thrombocytopenic Purpura

Idiopatik trombositopenik purpura, çocuklarda görülen edinsel trombositopeninin en sık nedenidir. Çogunlukla akuttur ve spontan düzelir. Kabakulak enfeksiyonu sıklıkla çocukluk çagında görülen viral bir enfeksiyondur.Bu yazıda akut kabakulak enfeksiyonu sırasında saptanan semptomatik idiopatik trombositopenik purpura olgusu sunulmustur.Idiopathic thrombocytopenic purpura is the most common cause of acquired thrombocytopenia in children. It usually develops acutely and recovers spontaneously. Mumps is a viral infection which often appears in childhood. It rarely has severe complications. In this article, a symptomatic case of ITP occurred during acute mumps infection is presented