Thermodynamic Characterization of Aminoglycoside-3′-Phosphotransferase IIIa

Aminoglycoside-3′-Phosphotransferase IIIa is a widespread, promiscuous member of the phosphotransferase family of aminoglycoside modifying enzymes. This study provides results of combined calorimetry/NMR experiments to characterize and dissect the global thermodynamic properties of aminoglycoside–APH(3′)-IIIa complexes. Aminoglycoside binding to APH(3′)-IIIa is enthalpically driven with strong entropic penalty. 2′- and 6′-amino groups have significant contributions to the observed binding parameters. Formation of APH(3′)-IIIa complexes with substrate aminoglycosides shows a complex dependence on pH and is linked to protonation and deprotonation of both ligand and enzyme groups. We report pKa upshifts of ~1 unit for N2′ and N2′′′ groups of enzyme-bound neomycin B while the pKa of N6′ changes by 0.3 unit and N6′′′ experiences no shift. Isotopic solvent and heat capacity change studies strongly suggest differential effects and reorganization of solvent in kanamycin and neomycin class complexes of the enzyme. We also determined unusually high binding ΔCp values in the range of -0.7 to -3.8 kcal/mol·deg which were not explained by changes in the solvent accessible surface area. A break at 30°C was observed in the ΔCp plot and temperaturedependent backbone amide proton chemical shifts of four residues surrounding the binding site of kanamycin-APH(3′)-IIIa complex. These results may indicate specific solvent reorganization sites away from the binding site of the enzyme

Culture, Socio-Economic Development, and Refugee Immigration: A Spatial Analysis of the 2017 Referendum in Turkey

The 2017 referendum on controversial constitutional amendments witnessed a fierce competition in Turkey. Despite the joint campaign of AK Party (current ruling party) and MHP (nationalist party), the electoral outcome yielded only a slight edge for accepting the amendments (Yes 51%, No 49%). Why was there such a narrow margin of victory? What explains the defection among MHP voters at the aggregate level? Our paper examines these questions through a unique dataset along with spatiallyautoregressive and multilevel modeling techniques. We collect the sub-provincial and provincial level electoral results since 2002, and match them with the 2004 socioeconomic development data from the Ministry of Development and the 2017 development data from the Ministry of Health. In addition, we add provincial level mosque information, and sub-provincial level official Syrian refugee numbers to the dataset. The advanced geospatial and multilevel models show strong empirical support for our hypotheses. Cultural indicators are as likely as socioeconomic features to explain the 2017 referendum results in Turkey after controlling for political factors. The number of Syrian refugees in provinces diminishes the level of support for “yes” whereas the number of mosques boosts its support. The refugee migration also explains the MHP voters who defected in the referendum: the higher the number of refugees in a sub-province, the more likely that the voters in that sub-province vote against the constitutional amendments. All models show that voting in Turkey has considerable levels of spatial dependency - the neighborhood matters

Predicting the Resilience of the Health Care System to New Arrivals: The Case of the Public Health System of Turkey

Purpose/Objectives: Since the start of the Syrian war, a significant population has moved out of the Syrian Republic into its neighborhood environs. Turkey has had a significant effect on its health system and society, as a significant new number has entered the Turkish society, increasingly using the Turkish healthcare system. Our aim is not only to numerically identify the size of the effect to the Turkish system, but to identify the domestic resources that allow the Turkish healthcare system and society to build up resilience against the significant health demand shock. The main objectives of this study is 1) To understand whether there is a complementarity between the earlier efforts in the Turkish health system and the current capabilities that is necessary to meet the Syrian Populations Health Needs. 2) To understand if the newly revamped Turkish Primary Healthcare System Provide a crucial buffer for the negative congestion effects that could have been caused by such a significant and relatively unhealthy refugee population being integrated into the health system, at a relatively rapid pace. Research method: The main two outcomes that the analysis plans to predict are the changing efficiency and the changing user satisfaction of the Turkish health system. Using multi-level regression models (MLO) we (i) Start by looking at the effect of the Syrian effect on the crucial Turkish health parameters, following this by (ii) Looking at the factors of family health program introduction, and family health system utilization to look at how the functionality of the health system, and the satisfaction that it brings to the Turkish population is being affected. We used fixed effect model to remove unobserved heterogeneity in each province (model specification in Appendix 1). We have controlled for health system variables (public primary physicians per 10,000; public hospital specialists per 10,000; public hospitals per 10,000; public PHC centres per 10,000; and the presence of a university hospital in the province) as well as population characteristics (rural population (%); population aged 65 and over (%); population aged 14 and under (%); and the province population). Because demographic data was available only for the years 2007-12, it was linearly extrapolated for the years 2002-6 and 13. The penetration of family medicine model in each province was measured by an indicator variable (0,1) for whether the MLO model was introduced, and the number of years since the introduction of the MLO model. The Syrian effect was measured through the proportion of Syrians under temporary protection status to the domestic province population. Main results: The health system status of the Turkish population is unaffected in the large period from 2011-2016. The significant effect in the initial period was significantly alleviated in the intervening years. The main sources of resilience were found to be the changing importance of the alternative primary health system that allowed Turks to receive a new option to the secondary part of the Turkish health system that was increasingly congested. Increasing use of the immunization for the same goal is also substantiated for the Turkish population. Recommendations: Turkey’s experience is instructive for a lot of the middle income countries, which can face similar refugee and migrant pressure in the next 50 years. The health systems priority to UHC and to (relative) open access that it offered to its citizen population and its outside populations alike, has served its efficacy in good stead. The health system must create enough elasticity to limit a drop in health system satisfaction and health system utilization in either of these critical populations

Kuantum Noktacığı Lüsiferaz BRET Çiftinin DNA Bağlanıcı Proteinler Kullanılarak DNA İskelesi Üzerinde Montajına Dayalı Bir Nanobiyosensör Platformunun Geliştirilmesi

TÜBİTAK MAG Proje01.04.2016Bir ışık proteiniyle floresan molekül arasında gerçekleşen enerji transferi olarak tanımlanan Biyolüminesans Rezonans Enerji Transferi (BRET)’e dayanan biyosensör platformları proteaz aktivitesi ölçümü, nükleik asit tayini, lenfatik görüntüleme ve fotodinamik terapi gibi amaçlar için başarıyla uygulanmıştır. Bu çalışmalarda donör-alıcı ikilisi olarak birbirine kovalent bağ ile bağlanmış lüsiferaz-kuantum noktacığı bileşenleri kullanılmıştır. DNA molekülü sahip olduğu yapısal ve fonksiyonel özellikleri açısından nanoteknolojik uygulamalar için ideal bir biyopolimer malzeme olarak ön plana çıkmaktadır. Bu proje kapsamında moleküler kendiliğinden düzenlenme prensibine dayalı olarak BRET donör-alıcı ikilisi olan lusiferaz-kuantum noktacığını, DNA bağlanıcı proteinler yoluyla bir DNA iskelesi üzerine monte etmek amaçlanmıştır. Alıcı molekül olarak streptavidin kaplı bir kuantum noktacığı kullanılarak, Nano-Tag peptidine bağlı bir DNA bağlanıcı protein yoluyla DNA iskelesi üzerinde konumlandırılmıştır. Proje, DNA bağlanıcı proteinler olan östrojen reseptör bileşeni CDC ve galaktoz metabolizmasından sorumlu Gal4 transkripsiyon faktörlerinin Renilla lusiferaz enzimi ve Nano-Tag peptidiyle hazırlanan füzyon proteinlerinin üretimiyle başlamış, fakat yeterli miktarda protein sağlanamaması üzerine platform in situ (hücre içi) kapsama taşınmıştır. Sensör bileşenlerini taşıyan MDA-MB-231 meme kanseri hucre hattında gerçekleştirilen çalışmalar sonucu ilke prensibi ispatına dayalı platformdan BRET sinyali elde edilmiştir. Elde edilen sinyal verimi (BRET oranı 0.2) bileşenlerin kovalent bağlı olduğu sistemlere oranla (0.3-0.6) daha düşüktür. Oluşturulan nanobiyosensör platformu rezonans enerji transfer veriminin iyileştirilmesidurumunda, özellikle DNA bağlanıcı ve modifiye edici moleküllerin (DBPler, Dnazlar, DNA metilazlar, vb.) aktivitelerini belirlemekte kullanılabilecek uygulama potansiyeline sahiptir

Klorotoksin Peptit Yapısına Dayalı Matriks Metalloproteinaz-2 İnhibitörlerinin Geliştirilmesi

TÜBİTAK KBAG Proje01.11.2017Bu projenin amacı, kanser gibi temel hastalıkların terapisinde önemli bir moleküler hedef olanMMP-2 enzimine spesifik, klorotoksin peptit yapısına dayalı, yüksek etkinlikte ve seçicilikteözgün bir inhibitör geliştirmektir.Geliştirilmeye çalışılan inhibitör, 36 amino asitten oluşan (4 kDa) ve akrep zehrinden izoleedilmiş seçici bir MMP-2 inhibitörü olan klorotoksin (CLTX) peptidinin yapısınadayanmaktadır. Proje stratejisi, ön çalışmalarımız sonucu CLTX yapısında belirlediğimiz dörtkritik pozisyonda (H10, K15, K23 ve K27) farklı karbon zinciri eklemeleriyle toplam 20 adettiyol ve azido alanin modifikasyonu gerçekleştirerek MMP-2 yapısındaki çinko elementinekoordinasyon sağlama prensibine dayanmaktadır.Proje süresinde lizin modifikasyonlarda sentezlerdeki sıkıntılardan dolayı strateji değiştirmeyegidilmesi gerekmiştir. Bu nedenle her bir lizinden 3 farklı modifikasyon sentezlenmiş ancakbunlardan da ikişer tanesinin katlanması başarı ile gerçekleşmiştir. Histidin modifikasyonumodel peptitte başarılı olunmasına rağmen esas peptitte click tepkimesinin başarısızlığınedeniyle gerçekleşememiştir. Elde edilen CLTX türevlerinin MMP-2 aktiviteleri ölçülmüşancak beklenen aksine inhibe etmek yerine aktive ettiği görülmüştür.Matrix metalloproteases (MMPs) are an enzyme class that functions in theremodeling of extracellular matrix. Matrix metalloprotease-2 (MMP-2) is a memberof gelatinase class of MMP family and it is an important drug target that is used inthe treatment of cancer and autoimmune diseases since it has high activity in thecancer of skin, prostate, bladder, breast, lung, and ovary.Compared to inhibitor design efforts for other enzymes, MMP inhibitor discoveryand development studies are considered to be not successful due to the specificityproblem. Previous studies are generally based on the zinc metal coordinationchemistry of small organic molecules or synthetic peptide molecules. Organicmolecules are not selective and inhibit various structurally similar members ofMMP family since they can enter the active site and coordinate to zinc easily.Synthetic peptides, on the other hand, are more target-specific but lack theinhibition potency of organic molecules.Objective of this project was to develop a novel, chlorotoxin (CTLX) peptidestructure-based, selective and highly potent inhibitor that targets MMP-2 which isan important molecular component in cancer therapy.Inhibitor design is based on the peptide CLTX which is a selective MMP-2 inhibitorwith 36 amino acids (4 kDa) originally isolated from the scorpion venom. Accordingto our preliminary work, the strategy for inhibitor design in this project is based onthe coordination of four critical positions (H10, K15, K23 ve K27) on CLTX to zincion in MMP-2 active site via 20 thiol and azido alanine modifications with differentcarbon chain lengths. Based on the different positions of the targeted amino acidswhich includes protein interaction loop regions, at least one of them is expected tobe near the active site for zinc coordination.Due to synthetic problems in the modififactions of lisine residues, an alternativemodification is developed and three different modified CLTX were synthesized foreach lysine residue and two out of three of these derivatives were successfullyfolded. Histidine modification could not be achieved since the click reaction wasfailed in the CLTX although it was succesfull in the model peptides. Activities of thefolded peptides were tested and surprisingly an increase in the MMP-2 activity wasobserved instead of decrease

SLC22A3 (Solute carrier family 22 member 3)

Review on SLC22A3, with data on DNA, on the protein encoded, and where the gene is implicated

PERP (PERP, TP53 apoptosis effector)

PERP is a p53/p63-regulated gene encoding a desmosomal protein that plays a critical role in stratified epithelial development, cell adhesion and tumor suppression

The Case of MRI Repetitions with Direct and Indirect Cost Implications: Evidence from Hacettepe University Hospitals

This study investigates the case of repeated MRIs using data from Hacettepe University Hospitals. Results indicate that almost 34% of MRI consultations have to be repeated within the same year due to suboptimal quality that hinders correct assessment and diagnosis. Suboptimal quality refers to; movement artefacts, use of wrong scan technique or sequence, inexperienced reader and/or shortened time intervals. In fact, almost 30% of those repetitions result in a change in diagnosis. Results suggest that the probability of repetition is higher among women and children

Nükleik asit tabanlı sandviç formatında mikroRNA dizi platformunun geliştirilmesi ve meme kanseri çalışmalarında kullanım potansiyelinin araştırılması

TÜBİTAK MAG01.09.201