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Öğe Ancient DNA from 8400 Year-Old Catalhoyuk Wheat: Implications for the Origin of Neolithic Agriculture(PUBLIC LIBRARY SCIENCE, 2016) Bilgic, Hatice; Hakki, Erdogan E.; Pandey, Anamika; Khan, Mohd Kamran; Akkaya, Mahinur S.Human history was transformed with the advent of agriculture in the Fertile Crescent with wheat as one of the founding crops. Although the Fertile Crescent is renowned as the center of wheat domestication, archaeological studies have shown the crucial involvement of Catalhoyuk in this process. This site first gained attention during the 1961-65 excavations due to the recovery of primitive hexaploid wheat. However, despite the seeds being well preserved, a detailed archaeobotanical description of the samples is missing. In this article, we report on the DNA isolation, amplification and sequencing of ancient DNA of charred wheat grains from Catalhoyuk and other Turkish archaeological sites and the comparison of these wheat grains with contemporary wheat species including T. monococcum, T. dicoccum, T. dicoccoides, T. durum and T. aestivum at HMW glutenin protein loci. These ancient samples represent the oldest wheat sample sequenced to date and the first ancient wheat sample from the Middle East. Remarkably, the sequence analysis of the short DNA fragments preserved in seeds that are approximately 8400 years old showed that the Catalhoyuk wheat stock contained hexaploid wheat, which is similar to contemporary hexaploid wheat species including both naked (T. aestivum) and hulled (T. spelta) wheat. This suggests an early transitory state of hexaploid wheat agriculture from the Fertile Crescent towards Europe spanning present-day Turkey.Öğe Basic-fibroblast growth factor ve dexamethasone'un periodontal ligament hücrelerinin proliferasyonu, protein miktarı ve tip I kollajen mRNA ekspresyonu üzerine etkisi(2004) Hakkı, Sema S.; Hakkı, Erdoğan E.; Akkaya, Mahinur S.; Nohutcu, Rahime M.Amaç: Periodontal hastalıkların tedavisinde temel amaç, periodontal ataçmanın mineralize ve yumuşak doku bileşenlerinin rejenerasyonudur. Periodontal Ligamentin (PDL), ideal rejenerasyondan primer olarak sorumlu hücre grubunu içerdiği, yeni sement ve yeni kemik formasyonunu sağlayabilecek kapasitesi olduğu gösterilmiştir. PDL, sementoblast ve/veya osteoblasta farklılaşabilen, heterojen bir hücre popülasyonuna sahiptir. Son zamanlarda PDL'nin karak-terizasyonu ile ilgili çalışmalar, bu hücrelerin osteo-blast benzeri özelliklerinin belirlenmesi ve periodontal ligamentde osteoblastik hücre popülasyonunu uyarabilecek büyüme faktörlerinin tespit edilmesi yönünde yoğunlaşmıştır. Polipeptid büyüme ve farklılaşma faktörleri, yara iyileşmesi sürecinin düzenlenmesi ve uyarılmasında önemli rol oynayan biyolojik yönlendiricilerdir. Bu çalışmanın amacı, basic-Fibroblast Growth Factor (b-FGF) ve Dexamethasone (Dex) gibi biyolojik faktörlerin, PDL hücrelerinin fonksiyonlarına ve tip I kollajen mRNA ekspresyonlarına etkilerinin belirlenmesidir. Gereç ve Yöntemler: PDL hücreleri ortodontik nedenlerle çekilen premolar dişlerden elde edildi. İlk aşamada PDL hücrelerine farklı konsantrasyonlarda b-FGF ( 0.1, 1, 10 ve 50 ng/ml) uygulanarak etkin konsantrasyon saptandı. Takiben, PDL hücreleri, b-FGF (1 ng/ml), Dex (10-7 M) ve bu faktörlerin kombinasyonu ile muamele edildi. PDL hücrelerinin proliferas-yonu hemositometre ile ve total protein miktarı Lowry metodu ile 0, 3, 7, 10 ve 15. günlerde değerlendirildi. Hücrelerin mitotik aktivitelerinin tayini 3H thymi-dine kullanılarak 24. saatte gerçekleştirildi. Tüm gruplardan 0, 3 ve 7. günlerde total RNA izole edilerek, 'Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR)' tekniği ile tip I kollajen mRNA ekspresyonları belirlendi. Bulgular: PDL hücreleri için b-FGF'nin etkin konsantrasyonunun 1 ng/ml olduğu belirlendi. Üçüncü günde gruplar arasında anlamlı bir fark izlenmezken, b-FGF'nin, hücrelerin proliferasyonunu 10. ve 15. günlerde diğer gruplarla kıyaslandığında istatistiksel olarak anlamlı şekilde artırdığı gözlendi (p0.001). b-FGF'nin diğer gruplarla kıyaslandığında tüm zaman periyotlarında PDL hücrelerinin total protein miktarını artırdığı ancak bu artışın 3. ve 15. günlerde istatistiksel olarak anlamlı olduğu tespit edildi (p0.001). Dex'in tek başına hem proliferasyonu hem de protein miktarını anlamlı şekilde inhîbe ettiği gözlendi, b-FGF'nin PDL hücrelerinin mitotik aktivitesini 24. saatte diğer gruplarla kıyaslandığında anlamlı şekilde artırdığı saptandı. İnsan PDL hücrelerin, tip I kollajen mRNA ekspresyonunun, 3. günde b-FGF ve Dexb-FGF ile muamele edilen gruplarda, kontrol grubu ile kıyaslandığında azaldığı, 7. günde ise b-FGF'nin kontrol grubundakine benzer şekilde tip I kollajen mRNA ekspresyonu sergilediği tespit edildi. Tek başına Dex ile muamele edilen grupta ise kontrol grubu ile kıyaslandığında hem 3. günde, hem de 7. günde tip I kollajen mRNA ekspresyonunun çok az miktarda inhibe olduğu gözlendi. Sonuç: b-FGF ve/veya Dex'in PDL hücrelerinin aktivitesini farklı bir şekilde etkileyebildiğini ve b-FGF'nin periodontal rejenerasyon sürecinde hücrelerin biyolojik aktivitesini artırabileceğini düşündürmektedir. Ancak, bu faktörlerin PDL hücrelerine olan etki mekanizmasının açıklığa kavuşmasına yönelik daha fazla araştırma gerekmektedir.Öğe Dexamethasone and basic-fibroblast growth factor regulate markers of mineralization in cementoblasts in vitro(AMER ACAD PERIODONTOLOGY, 2005) Hakkı, Sema S.; Nohutçu, Rahime M.; Hakkı, Erdoğan E.; Berry, Janice E.; Akkaya, Mahinur S.; Somerman, Martha J.Background: The aim of this study was to determine the effects of basic-fibroblast growth factor (b-FGF) and/or dexamethasone (Dex) on cementoblasts in vitro. Methods: Murine cementoblasts were treated as follows: 1) 5% FBS (fetal bovine serum) + ascorbic acid (AA, 50 mu g/ml, control); 2) 5% FBS+Dex (10(-7)M)+AA; 3) 5% FBS+b-FGF (50 ng/ml)+AA; or 4) 5% FBS+Dex (10(-7) M)+b-FGF (50 ng/ml)+AA and then evaluated by Northern analysis for changes in specific genes and by von Kossa stain for changes in mineral nodule formation. Results: Mitotic activity: b-FGF stimulated DNA synthesis significantly versus negative control. Gene expression: osteocalcin (OCN): Dex or b-FGF or the combination resulted in a decrease in expression versus control. Bone sialoprotein (BSP): Dex increased expression of BSP mRNA levels, b-FGF decreased transcript for BSP at 6 and 24 hours. Long-term (8 days) Dex, b-FGF, or Dex plus b-FGF caused a decrease in BSP expression versus control; osteopontin (OPN): both Dex and b-FGF increased transcripts for OPN seen by 6 hours, with a greater increase noted with b-FGF versus Dex. No apparent additive effect of Dex with b-FGF was noted; matrix gamma-carboxyglutamic acid protein (MGP): b-FGF induced transcripts for MGP and addition of Dex increased this effect, while Dex alone had no effect on expression. Biomineralization: Dex increased cementoblast-mediated biornineralization, while b-FGF blocked this activity, and addition of Dex to b-FGF did not alter FGF associated inhibition. Conclusion: Dex and FGF alone and in combination alter cementoblast behavior, but additional studies are required to determine whether these factors have beneficial effects at the clinical level.Öğe Dna Fingerprinting of Cannabis Sativa L. Accessions Using Rapd and Aflp Markers(ELSEVIER SCI IRELAND LTD, 2003) Hakkı, Erdoğan Eşref; Uz, Elif; Sağ, A.; Atasoy, Sevil; Akkaya, Mahinur S.[Abstract not Available]Öğe From RFLP to DArT: molecular tools for wheat (Triticum spp.) diversity analysis(SPRINGER, 2014) Khan, Mohd Kamran; Pandey, Anamika; Choudhary, Saumya; Hakki, Erdogan E.; Akkaya, Mahinur S.; Thomas, GeorgeWheat (Triticum spp.) is a universally lucrative agricultural crop. An increase in wheat production has been shown through selection by the farmers which can increase the grain profitability. The determination of genetic associations among domestic cultivars is facilitated by molecular markers. Data on genetic polymorphism is valuable for the germplasm association and regarding the developing management strategies. The information would be supportive for potential genome mapping programs and for the relevance of intellectual property rights of wheat breeders. Present review is an effort for providing support information to wheat breeders to develop varieties with varied genetic environment to attain continuity in large-scale wheat production. In this review, we have tried to provide a collective depiction of relevant information about the usage of some commonly used markers in wheat. It may help researchers to find out the frequentness and application of different markers and compare their results. The manuscript may serve as a platform helping the intellectuals for the selection and modification of their marker system in wheat diversity analysis. The heart of this review is the emphasis on the performance of various molecular genetic markers in diversity studies in relation to definite approaches that are in practice since several years allied with the multifaceted wheat molecular breeding and its polyploid nature.Öğe Genetic diversity and population structure of wheat in India and Turkey(OXFORD UNIV PRESS, 2015) Khan, Mohd Kamran; Pandey, Anamika; Thomas, George; Akkaya, Mahinur S.; Kayis, Seyit Ali; Ozsensoy, Yusuf; Hamurcu, MehmetGenetic diversity among plant species offers prospects for improving the plant characteristics. Its assessment is necessary to help tackle the threats of environmental fluctuations and for the effective exploitation of genetic resources in breeding programmes. Although wheat is one of the most thoroughly studied crops in terms of genetic polymorphism studies, phylogenetic affinities of Indian and Turkish Triticum species have not been assessed to date. In this study, genetic association of 95 tetraploid and hexaploid wheat genotypes originating from India and Turkey was determined for the first time. Combined analysis of random amplified polymorphic DNA and inter-simple sequence repeat markers disclosed 177 polymorphic bands, and both the dendrogram and two-dimensional scatterplot showed similar groupings of the wheat genotypes. Turkish hexaploid varieties were basically divided into two clusters, one group showed its close association with Indian hexaploid varieties and the other with Indian tetraploid varieties. Analysis of molecular variance revealed high (77 %) genetic variation within Indian and Turkish populations. Population structure analysis elucidated distinct clustering of wheat genotypes on the basis of both geographical origin and ploidy. The results revealed in this study will support worldwide wheat breeding programmes and assist in achieving the target of sustainable wheat production.Öğe Genetic Relationship of Wild Einkorn Based on Geographical Distribution in Anatolia and Thrace using AFLP Markers(2009) Uz, Elif; Yıldırım Ersoy, Figen; Hakkı, Erdoğan E.; Akkaya, Mahinur S.Triticum monococcum L. ssp boeoticum Boiss., is the wild progenitor of domesticated einkorn. High throughput AFLP genetic analysis showed that the domestication of einkorn started in the northern part of the Fertile Crescent, near the Karacadag Mountains, Southeastern Turkey [1]. This study assesses the genetic distribution and the diversity of wild einkorn throughout Turkey, using total of 59 accessions from 22 locations in four different geographical regions. In our study, the four selective combinations of AFLP markers (E+ACC/M+ACT, E+ACC/M+ATA, E+ACT/M+ATA, and E+ATC/M+AAG) resulted in 161 AFLP marker loci. Phylogenetic trees for individual accessions and populations based on geographical regions were obtained using 'PopGen-32' population genetic analysis software. East and Southeast samples were genetically closest to each other among the samples from other regions. The samples from West, Northwest, and Central Anatolia were clustered together.Öğe WHEAT BIOFORTIFICATION - A POTENTIAL KEY TO HUMAN MALNUTRITION(POLISH SOCIETY MAGNESIUM RESEARCH, 2017) Khan, Mohd Kamran; Pandey, Anamika; Akkaya, Mahinur S.; Gezgin, Sait; Hamurcu, Mehmet; Hakki, Erdogan E.Wheat production is required to double by 2050 in order to facilitate the global food assurance. Along with the rise in wheat production, improvement of the nutrient value of wheat varieties is another crucial challenge faced by wheat breeders. It is well established that more than 40% people in the world are at a risk of malnutrition caused by the deficiency of Fe, Zn and protein in their food. Numerous strategies are adopted by scientists, breeders and food industries to combat the problem. In this context, biofortificaton has become a successful method for increasing, either genetically or agronomically, the micronutrient content in crop plants. Recently, substantial progress has been made in the use of molecular marker systems and quantitative trait loci (QTL) to augment the wheat iron, zinc and protein content. Determining the role of GPC-B1 gene in controlling the iron, zinc and protein content in wheat genotypes is a promising discoveries. Although the gene is found to be associated with an elevated micronutrient content, it is also responsible for a decrease in yield. In order to simultaneously achieve both high nutrient content and elevated yield, major efforts are required to reveal the genetic control of these traits. Moreover, identifying the wheat genomic resources with an elevated nutrient content can be crucial. Employment of the next generation sequencing methods and use of molecular markers in marker assisted selection appears to be a promising approach to attaining the objective of breeding nutrient rich varieties. Combining advanced molecular biology and plant breeding techniques for wheat development is a potential strategy in achieving a healthy, 'hidden hunger' free world.
