Browsing by Author "Kartal, E."

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Open Access
Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish light source "Turkish DeLight"
(TÜBİTAK, 2023-01-01) Atalay, N.; Akcan, E. K.; Gül, M.; Ayan, E.; Destan, E.; Ertem, F. B.; Tokay, N.; Çakılkaya, B.; Nergiz, Z.; Karakadıoğlu, G.; Kepçeoğlu, A.; Yapıcı, İ.; Tosun, B.; Baldır, N.; Yıldırım, G.; Johnson, J. A.; Güven, Ö.; Shafiei, A.; Arslan, N. E.; Yılmaz, M.; Kulakman, C.; Paydos, S. S.; Çinal, Zeynep Sena; Şabanoğlu, K.; Pazarçeviren, A.; Yılmaz, A.; Canbay, B.; Aşcı, B.; Kartal, E.; Tavlı, S.; Çalıseki, M.; Göç, G.; Mermer, A.; Yeşilay, G.; Altuntaş, S.; Tateishi, H.; Otsuka, M.; Fujita, M.; Tekin, Ş.; Çiftçi, H.; Durdağı, S.; Dinler Doğanay, G.; Karaca, E.; Kaplan Türköz, B.; Kabasakal, B. V.; Katı, A.; Demirci, H.
X-ray crystallography is a robust and powerful structural biology technique that provides high-resolution atomic structures of biomacromolecules. Scientists use this technique to unravel mechanistic and structural details of biological macromolecules (e.g., proteins, nucleic acids, protein complexes, protein-nucleic acid complexes, or large biological compartments). Since its inception, single-crystal cryocrystallography has never been performed in Türkiye due to the lack of a single-crystal X-ray diffractometer. The X-ray diffraction facility recently established at the University of Health Sciences, İstanbul, Türkiye will enable Turkish and international researchers to easily perform high-resolution structural analysis of biomacromolecules from single crystals. Here, we describe the technical and practical outlook of a state-of-the-art home-source X-ray, using lysozyme as a model protein. The methods and practice described in this article can be applied to any biological sample for structural studies. Therefore, this article will be a valuable practical guide from sample preparation to data analysis.
Open Access
Revisiting the complex architecture of ALS in Turkey: expanding genotypes, shared phenotypes, molecular networks, and a public variant database
(John Wiley and Sons, 2020) Tunca, C.; Şeker, T.; Akçimen, F.; Coşkun, C.; Bayraktar, E.; Palvadeau, R.; Zor, S.; Koçoğlu, C.; Kartal, E.; Şen, N. E.; Hamzeiy, H.; Özoğuz-Erimiş, A.; Norman, Utku; Karakahya, Oğuzhan; Olgun, Gülden; Akgün, T.; Durmuş, H.; Şahin, E.; Çakar, A.; Başar-Gürsoy, E.; Babacan-Yıldız, G.; İşak, B.; Uluç, K.; Hanağası, H.; Bilgiç, B.; Turgut, N.; Aysal, F.; Ertaş, M.; Boz, C.; Kotan, D.; İdrisoğlu, H.; Soysal, A.; Uzun-Adatepe, N.; Akalın, M. A.; Koç, F.; Tan, E.; Oflazer, P.; Deymeer, F.; Taştan, Ö.; Çiçek, A. Ercüment; Kavak, E.; Parman, Y.; Başak, A. N.
The last decade has proven that amyotrophic lateral sclerosis (ALS) is clinically and genetically heterogeneous, and that the genetic component in sporadic cases might be stronger than expected. This study investigates 1,200 patients to revisit ALS in the ethnically heterogeneous yet inbred Turkish population. Familial ALS (fALS) accounts for 20% of our cases. The rates of consanguinity are 30% in fALS and 23% in sporadic ALS (sALS). Major ALS genes explained the disease cause in only 35% of fALS, as compared with ~70% in Europe and North America. Whole exome sequencing resulted in a discovery rate of 42% (53/127). Whole genome analyses in 623 sALS cases and 142 population controls, sequenced within Project MinE, revealed well‐established fALS gene variants, solidifying the concept of incomplete penetrance in ALS. Genome‐wide association studies (GWAS) with whole genome sequencing data did not indicate a new risk locus. Coupling GWAS with a coexpression network of disease‐associated candidates, points to a significant enrichment for cell cycle‐ and division‐related genes. Within this network, literature text‐mining highlights DECR1, ATL1, HDAC2, GEMIN4, and HNRNPA3 as important genes. Finally, information on ALS‐related gene variants in the Turkish cohort sequenced within Project MinE was compiled in the GeNDAL variant browser (www.gendal.org).