A novel approach for rapid screening of mitochondrial D310 polymorphism

BACKGROUND: Mutations in the mitochondrial DNA (mtDNA) have been reported in a wide variety of human neoplasms. A polynucleotide tract extending from 303 to 315 nucleotide positions (D310) within the non-coding region of mtDNA has been identified as a mutational hotspot of primary tumors. This region consists of two polycytosine stretches interrupted by a thymidine nucleotide. The number of cytosines at the first and second stretches are 7 and 5 respectively, according to the GeneBank sequence. The first stretch exhibits a polymorphic length variation (6-C to 9-C) among individuals and has been investigated in many cancer types. Large-scale studies are needed to clarify the relationship between cytosine number and cancer development/progression. However, time and money consuming methods such as radioactivity-based gel electrophoresis and sequencing, are not appropriate for the determination of this polymorphism for large case-control studies. In this study, we conducted a rapid RFLP analysis using a restriction enzyme, BsaXI, for the single step simple determination of 7-C carriers at the first stretch in D310 region. METHODS: 25 colorectal cancer patients, 25 breast cancer patients and 41 healthy individuals were enrolled into the study. PCR amplification followed by restriction enzyme digestion of D310 region was performed for RFLP analysis. Digestion products were analysed by agarose gel electrophoresis. Sequencing was also applied to samples in order to confirm the RFLP data. RESULTS: Samples containing 7-C at first stretch of D310 region were successfully determined by the BsaXI RFLP method. Heteroplasmy and homoplasmy for 7-C content was also determined as evidenced by direct sequencing. Forty-one percent of the studied samples were found to be BsaXI positive. Furthermore, BsaXI status of colorectal cancer samples were significantly different from that of healthy individuals. CONCLUSION: In conclusion, BsaXI RFLP analysis is a simple and rapid approach for the single step determination of D310 polymorphism of mitochondrial DNA. This method allows the evaluation of a significant proportion of samples without the need for sequencing- and/or radioactivity-based techniques

Bitki-su ilişkilerinin tıbbi adaçayı (Salvia officinalis L.)'nın verim, uçucu yağ üretimi ve kalitesi üzerine etkileri: Biyometrik ve fizyolojik incelemeler

In this research Salvia officinalis L. var. Extrakta was used as material in the Bornova ecological conditions in 2011, 2012 and 2013. We were investigated on effect of different nitrogen applications and water regimes in yield, qualty and biochemical parametres. In this context, it is established two different experiments, including pot and field trials. Field trials were arranged two-factor split-plot experimental design, with four replications. Experimental factors were water regimes of main plot: S1(irrigated when it's needed), S2( 20 days dry before harvesting) and S3(40 days dry before harvesting) and the sub-plot nitrogen applications (nitrogen free and 6 kg/da). It was determined that plant height (cm), gren herbage yield (kg/da), drug herbage ratio (%), drug herbage yield (kg/da), drug leaf ratio (%),drug leaf yield (kg/da), stem ratio(%), stem yield (kg/da), dry matter ratio (%), dry matter yield (kg/da), essential oil ratio (%), essential oil yield, essential oil content (%), antioxidant capacity (μmol FRAPgKM) and relative water content (gg-KM). Particularly, effects of different water applications (80%, 60%, 40% and 20% of field capacity) on biochemical characteristics were examined in pot experiments. In this research,water use efficieny (gg-KM), antioxidant capacity (μmol FRAPgKM), antiradical content (TROLOX/g), flavonoid content (mg RUTIN/g), chlorophyll a, b content (mg/ml) and carotenoids content (mgg-KM), fresh leaf-stem weight (g/plant), dry leaf-stem weight (g/plant), essential oil ratio (%), essential oil content (%) were determined. As the result of field and pot experiment, water deficit was reduced to yield parameters, chlorophyll and carotenoids content, while it was increased to essential oil ratio (%), water use efficiency and antioxidant capacity. The higest essential oil ratio was obtained as a mean 2.07% from S3 water doses. Both experiments as well as the principal main component was α+β thujone and it has been found to show a large variation. Considering all the water and nitrogen applications of field trials showed that nitrogen fertilization were distinguished, the data on plants where water applications S2.Tıbbi adaçayı (Salvia officinalis L.) bitkisine ait "Extrakta" çeşidinin materyal olarak kullanıldığı bu araştırma 2011, 2012 ve 2013 yıllarında Bornova ekolojik koşullarında yürütülmüştür. Çalışmada farklı azot ve su uygulamalarının bitkilerde bazı verim, kalite ve biyokimyasal özelliklere olan etkileri araştırılmıştır. Bu kapsamda tarla denemesi ve saksı denemesi olmak üzere iki ayrı deneme kurulmuştur. Tarla denemesi bölünmüş parseller deneme desenine göre iki faktörlü ve dört tekerrürlü olarak düzenlenmiştir. Ana parsellere su uygulamaları: S1(tarla tavında), S2 (hasat öncesi 20 gün susuz) ve S3 (hasat öncesi 40 gün susuz) dozları ; alt parsellere ise azot uygulamaları (0 kg/da azot ve 6 kg/da) yerleştirilmiştir. Araştırmada, bitki boyu (cm), yeşil herba verimi (kg/da), drog herba oranı (%), drog herba verimi (kg/da), drog yaprak oranı (%), drog yaprak verimi (kg/da), sap oranı (%), sap verimi (kg/da), kuru madde oranı (%), kuru madde verimi (kg/da), uçucu yağ oranı (%), uçucu yağ verimi (L/da), uçucu yağ bileşimi (%), antioksidan kapasitesi (μmol FRAPgKM) ve oransal su içerikleri (gg-KM) belirlenmiştir. Saksı denemesinde ise tıbbi adaçayının özellikle biyokimyasal özellikleri üzerine farklı su uygulamalarının (tarla kapasitesinin %80, %60, %40 ve %20'si) etkileri incelenmiştir. Araştırmada, su kullanım etkinliği (gg-KM), antioksidan içeriği (μmol FRAPgKM), antiradikal içeriği (TROLOX/g), flavonoit içeriği (mg RUTIN/g), klorofil a, b (mg/ml) ve karotenoit içeriği (mgg-KM), yaş yaprak-sap ağırlığı (g/bitki) ve kuru yaprak-sap ağırlığı (g/bitki), uçucu yağ oranı (%) ve uçucu yağ bileşimi (%) belirlenmiştir. Tarla ve saksı denemelarine ait sonuçlar genel olarak değerlendirildiğinde, su kısıtlamasının verime ilişkin değerler ile klorofil ve karatenoit içeriğini düşürdüğü, uçucu yağ oranı, su kullanım etkinliği ve antioksidan içeriğini yükselttiği saptanmıştır. Tarla denemesine ait üç yıllık sonuçlar incelendiğinde, en yüksek uçucu yağ oranının ortalama %2.07 ile S3 su uygulamasından elde edildiği saptanmıştır. Her iki denemede de başlıca ana bileşen olarak α+β Thujone belirlenmiştir. α+β Thujone oranlarının geniş bir varyasyon gösterdiği tespit edilmiştir. Tarla denemesine ait tüm su ve azot uygulamaları dikkate alındığında, azotlu gübrelemenin ve S2 su uygulamasının yapıldığı bitkilere ilişkin verilerin öne çıktığı görülmüştür

The Architect of Today on The Edge of Chaos; An Approach Through Chaos Theory

Today, in the frame of the transformation of the city and the social dynamics, there can be seen a congestion and repetition in the context of the city/citizen/architecture. It is possible to examine the spatial consequences of the social transformations that modern individuals experience, but only by comprehending the importance of the strong relationship between the space and the identity of individual. It seems difficult to produce ‘the new’ in architecture as long as the new ways of seeing not produced in this complex situation. Today, since the Chaos Theory gives us hope concerning the social sciences that include architecture and sociology, it can be used as a tool to investigate the current situation of architecture. Metropolitan cities can now be assumed as the most complex scene of architectural experience in the context of nonlinear natural atmosphere and linear orders created by society. There is a direct relationship between design process and the views of today's architect in the face of chaos and order. Through the Chaos Theory, this paper will discuss the views of the today’s individual on the line of complexity in daily life and the role of today’s architect on the edge of chaos. This role is evolving within the framework of the attitude and potential of the architect in today's metropolitan cities, in the face of complex problems. Therefore, this research focuses on which attitude of today’s architect can be an intervention tool to initiate the transformation of city/society