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Aktif Bölge Mimarisinin Anlaşılması Temelinde, NAD + Bağımlı Mutant Candida methylica Format Dehidrogenaz Enziminin Spesifik Aktivitesinin Arttırılması
No full textFormat dehidrogenaz enzimi (FDH), endüstriyel biyokatalizörler arasında son yıllarda en çok
dikkat çeken enzimlerden biridir. Özellikle NAD(P)+ bağımlı FDH, gerçekleştirdiği
reaksiyonun düşük redoks potansiyeli nedeniyle biyoenerji üretimi ve saf kiral bileşiklerin
sentezi sırasında ihtiyaç duyulan sürekli NAD(P)H yenilenmesinin sağlanması için en çok
başvurulan enzimlerdendir. Endüstriyel biyoteknoloji için, NAD(P)+ bağımlı FDH’ın en büyük
dezavantajı mevcut FDH’ların (FDHs) düşük aktiviteye sahip olmasıdır. Bu nedenle özellikle
endüstriyel ölçekte biyokatalitik yöntemlerle değerli farmasötik saf kiral ara bileşiklerin sentezi
için gerekli olan sürekli NAD(P)H’nin yenilenmesinde FDH enziminin kullanılması oldukça
yüksek maliyetlidir.
Proje başvurusu öncesinde ön çalışma olarak literatürde rapor edilen ısıl kararlılığı arttırılmış
Candida methylica (Cm) mutant FDH’ın yapısı analiz edilmiştir. Bunun için, öncelikle Cm
FDH’ın homoloji yöntemi ile yapısı tahmin edilmiş ve elde edilen yapı moleküler dinamik ile
optimize edilmiştir. Sonra diğer kaynaklardan elde edilen FDH enzimlerin dizileri ve yapıları
ile karşılaştırılarak; Cm FDH için katalitik bölgeyi oluşturan, formik asit-NAD+ bağlanma
bölgesini oluşturan amino asit pozisyonları tahmin edilmiştir. Enzimin aktif bölgesini
oluşturduğu yada katalitik aktivitesinde etkili olabileceği tahmin edilen Thr67, Phe69, Gly92,
Val93, Gly94, Asp96, Arg258, Gln287, His311 dokuz (9) amino asit, ISM yönteminin CAST
tekniği için aday amino asit pozisyonları olarak belirlenmiştir.
Projenin kabulu sonrası ilk iş olarak, hesapsal yöntemler ve literatür bilgisi ile belirlenen
fonksiyonel amino asit pozisyonları için ISM/CAST ile mutant kütüphanesi oluşturulmuştur.
Petri platelerde oluşturulan her mutant kütüphanesi için 20-50 arasında koloni elde edilmiştir.
Oluşturulan mutant kütüphaneleri, substrat olarak NAD+ ve formik asite karşı yüksek spesifik
aktiviteye sahip mutant FDH’ı seçmek için taranmıştır. Tarama sonucu 13 tane mutant
koloninin aktif olduğu gözlemlenmiştir. Seçilen substratlara karşı doğal tip Cm FDH ile
karşılaştırıldığında spesifik aktivitesi yüksek olan mutant FDH’lar seçilerek, dizi ananlizi için
dizilemeye gönderilmiştir. Dizileme sonucu aktif olan 13 mutanttan sadece 3 tanesinde baz
değişimi olduğu görülmüştür. Bunlardan 2 tanesinde sessiz mutasyon, diğerinde ise N119R
değişimi tespit edilmiştir. TAGZyme sistemi ile saflaştırılmış ve yabanıl tip ve mutant enzimin
kinetik değerleri sırasıyla format ve NAD+’ye karşı KM 11,20 ve 0,95 mM, kcat 22,21 ve
54,56 s-1
olarak belirlenmiştir. Büyük yan zincirden kaynaklı substratlara ev sahipliği yapan
119. pozisyon için yerinin daha az su ile dolması ve substratlar ile daha çok etkileşmesi
seçilen substratlar için KM değerinde iyileşmeye neden olduğu tahmin edilmektedir. Ayrıca,
Arg119’a ait geniş hacimli yan zinciriyle His311’e hidrit transferinin kolaylaşması kcat’in
artmasına yol açtığı düşünülmektedir.
vii
Son olarak elde edilen mutant FDH enziminin substrat ile olan etkileşimleri, moleküler
dinamik simülasyonuyla elde edilen yapıda incelenmiştir. Modelleme çalışmaları sonuçları
göstermektedir ki; Arg119 mutasyonu iki monomerin birleşme noktasında olan Phe69
üzerinden yapısal değişikliklere yol açmaktadır. Bu mutasyonun, NAD+ ile bağlanmayı
güçlendiren etkilere sahip olduğu iyileşen kinetik değerlerden dolayı da tahmin edilmektedir.
Elde edilen yapı göstermektedir ki; arjinin sahip olduğu uzun yan zincir ile substratların doğru
yönde yönlendirilmesini, hidrit iyonunun formik asitten His311’e daha hızlı transfer olmasını
sağlamakta ve iyileşen KM ve kcat değerleri bu varsayımları desteklemektedir.
Proje sonunda; NAD+ ve formata karşı yaklaşık %10 katalitik aktivitesi arttırılmış, karakterize
edilmiş, ısıya dayanıklı mutant FDH enzimi tanımlanmıştır. 119. pozisyondaki Asn, Arg ile yer
değiştirmesi, substratların katalitik bölgeye daha iyi yönelmesini sağlamıştır. Arg, Asn gibi
karboksilat grubu üzerinden substratları koordine etmiştir. Yüksek katma değerli endüstriyel
biyokatalizör olarak aktivitesi yüksek olan mutant FDH enziminin patentlenmesi
planmaktadır
Analysis of Deep Learning Sequence Models for Short Term Load Forecasting
No full textShort Term Load Forecasting (STLF) is an essential part of generator scheduling in power plants. Better scheduling is crucial for both economic and environmental aspects. In this study, two different deep learning (DL) model architectures based on Long Short Term Memory (LSTM) and Convolutional Neural Networks (CNN) were tested and compared on load datasets from Spain and Turkey. In addition, a novel Long Short Term Memory (LSTM) model with embedding layer was proposed and compared with these two models. Optimum model design choices and practices were discussed for achieving reliable and robust results. It was showed that datasets with different characteristics require different model design choices. The simulations of the proposed DL method were carried out with Python and the performance parameters were also presented. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG
TECHNOLOGY, ARTIFICIAL INTELLIGENCE, AND ROBOTICS IN FUTURE WARS
No full textThis study aims to show the importance of initiating studies on the role of intelligence and its new uses in future wars without further delay and also to contribute to closing the current gap in this subject in the literature. This study aims to analyze the future post-modern wars through the reciprocal interoperability and multi-integration of technology and intelligence. This study, which adopts a qualitative research methodology, will primarily benefit from secondary data sources such as scientific books and articles in addition to scientific data analysis methods such as document and content analysis and interpretation. This study significantly contributes to the role of intelligence and the necessity to promote new scientific studies and to end the present gap in the data without delay. The ongoing developments taking place in technology will bring about the transformations clarified in this study. Ideas will be generated regarding the expected developments in technology and their roles on the battlefields of future wars. The scope of this study is the increasing importance and role of intelligence in developing network technologies as well as the potential areas where autonomous systems which can understand machinery can be used
In vitro, in silico and network pharmacological approaches
No full textThe present study aimed to evaluate the antioxidant and enzyme inhibition properties of aerial part of Verbascum cheiranthifolium Boiss. V. myriocarpum Boiss. & Heldr. and V. pyroliforme (Boiss. & Heldr.) Kuntze as well as their chemical profiles. Results showed that MeOH and hydromethanol recovered the highest total polyphenolic content with highest content obtained from V. cheiranthifolium (27.61and 27.69 mg GAE/g respectively) and V. myriocarpum (24.24 and 25.34 GAE/g respectively). The estimated content of verbascoside was quite higher in V. cheiranthifolium (987.05–6780.07 mg/100 g) and V. myriocarpum (1506.47–6433.73 mg/100 g) than V. pyroliforme (49.54–121.97 mg/100 g). All extracts of V. cheiranthifolium (274.17–713.79 mg/100 g) and polar ones of V. myriocarpum (185.67–304.51 mg/100 g) accumulated higher chlorogenic acid content than V. pyroliforme extracts (36.33–112.56 mg/100 g). The latter species was dominated by luteolin-7-O-glucoside and apigenin-7-O-glucoside with highest content recorded from the hydromethanolic extract (639.70 and 196.14 mg/100 g respectively). Extracts of V. cheiranthifolium (46.15–48.74 mg TE/g) and V. myriocarpum (46.05–48.50 mg TE/g) exerted significantly higher scavenging activity than those from V. pyroliforme (12.77–34.64 mg TE/g). Highest significant anti-acetylcholinesterase activity was obtained by MeOH extract of V. pyroliforme (2.65 mg GALAE/g) and V. myriocarpum (2.57 mg GALAE/g). In conclusion, extracts from the three investigated Verbascum spp. can be a potential source of bioactive metabolites with interesting antioxidant and enzyme inhibition properties. © 2023 Elsevier Lt
Evaluate student achievement by classifying brain structure and its functionality with novel hybrid method
No full textIn a labor market that demands a workforce well-trained in science, technology, engineering, and mathematics (STEM) subjects, it is required of children to successfully develop their mathematical skills in order to become highly productive adults. Recent developments in computer vision, artificial intelligence, machine learning, and medical imaging techniques give us new opportunities for building intelligent support tools to help us learn more about the neural underpinnings of how children learn math and how that knowledge relates to individual differences in skill. This study examines the brain activities of students during problem-solving by checking brain structure and its functionality. By using powerful techniques in the light of machine learning and image processing, the relationship between success and the background of a child was researched. The aim is to make a solid prediction of the possible future success of the children by observing their brain activities. The children we investigated were asked different questions to get information about their intelligence. In our study, we have tried to find how those questions and answers may affect the future success of a child. For this purpose, a novel hybrid classification model that utilizes cluster analysis, Random Forest, Logistic Regression, and ensemble learning is intended for classification tasks. Our study includes two main stages. Firstly, the image processing techniques were applied to create unique features of brain images. Then, machine learning tecnniques were used to select a set of features, and for getting prediction results our hybrid classification model was applied. In the end, we obtained useful results indicating that there is a complicated connection between the success rate and the history of a child. This novel approach to classification, which combines multiple methods by using a hybrid model, has the potential to be implemented in computational tools for strategic decision support systems
Security and Inclusion in the Education of Syrian Refugee Children in Istanbul
No full textAfter the Syrian crisis, the number of Syrian refugees in Turkey is estimated to be approximately four million. Currently, one of the most significant aspects of the integration process of refugees in Turkey is the education of refugee students. Investigating the process of the co-education of refugee and Turkish citizen students in public schools provides some insight into what the future might hold for these refugees and sheds light on the dynamics of living together with locals. The first aim of this research is to explore the reception of the refugee students by the teachers in order to understand inclusion and/or exclusion mechanisms in education. Second, this study examines the roles that ethno-religious and political identities play in relations between teachers and refugee students by focusing on ethno-religious identity and discrimination. Drawing on the debates on orientalism and securitization in migration, it explicates the ways in which teachers justify their judgments and impressions of the refugee students through orientalist codes. To achieve this, public school teachers from two districts of Istanbul were invited to take part in this ethnographic research which was conducted in 2018
Appraisals on the chemical characterization and biological potentials of Ranunculus constantinopolitanus extracts using chromatographic, computational, and molecular network approaches
No full textIn this context, phytochemicals were extracted from Ranunculus constantinopolitanus using ethyl acetate (EA), ethanol, ethanol/water (70%), and water solvent. The analysis encompassed quantification of total phenolic and flavonoid content using spectrophotometric assays, chemical profiling via high performance liquid chromatography-mass spectrometry/mass spectrometry (HPLC-MS/MS) for the extracts, and assessment of antioxidant activity via 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS), Cupric reducing antioxidant capacity (CUPRAC), ferric reducing antioxidant power (FRAP), metal chelating (MCA), and phosphomolybdenum (PBD) assays. Moreover, antimicrobial activity was assessed against four different bacterial strains, as well as various yeasts. Enzyme inhibitory activities were evaluated against five types of enzymes. Additionally, the extracts were examined for their anticancer and protective effects on several cancer cell lines and the human normal cell line. All of the extracts exhibited significant levels of ferulic acid, kaempferol, and caffeic acid. All tested extracts demonstrated antimicrobial activity, with Escherichia coli and Pseudomonas aeruginosa being most sensitive to EA and ethanol extracts. Molecular docking studies revealed that kaempferol-3-O-glucoside strong interactions with AChE, BChE and tyrosinase. In addition, network pharmacology showed an association between gastric cancer and kaempferol-3-O-glucoside. Based on the results, R. constantinopolitanus can be a potential reservoir of bioactive compounds for future bioproduct innovation and pharmaceutical industries. © 2023 Elsevier Lt
The Challenge of “Doing Business with Strangers”: Audit Reports as a “Signaling Instrument”
No full textThis paper discusses how firms in Turkiye have used audit reports of companies like Deloitte as a "costly signaling" instrument. The paper shows that the firms integrating into the global economy during 1990s were in intense competition to find global business partners. The need to do "business with strangers" created a new challenge for this firms: Broadcasting strong signals proving the capacity of being a reliable, long-standing business partner. When the partnerships were formed in smaller business circles, these signals were produced by face-to-face social interactions. But when the entrepreneurs cooperate/negotiate with firms from different national and cultural backgrounds, audit reports from prestigious companies became a universal signal about the firms' reliability. To illustrate the transformation in this "signaling" process, we conduct in-depth interviews with the managers of auditing firms, entrepreneurs and did an archival study on many resources of the period
Youth environmental citizenship formation: Struggled political subjectivities and everyday experiences of young people in Turkey
No full textThis ethnographic study reveals how young people become environmentally aware citizens. The study traces the lived worlds of early youth in Turkey by focusing on their environmental experiences and by problematising climate change and consumerism. Through online mapping activities and in-depth interviews, the applied geo-social methodology explores the social, spatial and political subjectivities of 21 young people from different parts of Turkey, elucidating their developing environmental agencies. This article further argues how these subjectivities are contextual to the intersectional aspects of environmental socialisation. The results provide youthful insights into today's authoritarian Turkey, which is facing an economic recession. © 2023 The Authors. Children & Society published by National Children's Bureau and John Wiley & Sons Ltd
In Vitro and Molecular Docking Evaluation of Larvicidal Effects of Essential Oils of Five Aromatic Plants on the Fall Armyworm Spodoptera frugiperda JE. Smith (Lepidoptera: Noctuidae) from Ivory Coast
No full textFaced with the serious consequences resulting from the abusive and repeated use of synthetic chemicals, today rethinking crop protection is more than necessary. It is in this context that the essential oils of the Lamiaceae Ocimum gratissimum and Ocimum canum, the Poaceae Cymbopogon citratus and nardus and a Rutaceae Citrus sp. of known chemical compositions were experimented. The evaluation of the larvicidal potential of the essential oils was done by the method of topical application of the test solutions, on the L1-L2 stage larvae from the first generation of S. frugiperda obtained after rearing in an air-conditioned room. Lethal concentrations (LC10, LC50 and LC90) were determined after 48 h. After assessing the larvicidal potential of essential oils, molecular docking was carried out to study protein-ligand interactions and their propensity to bind to insect enzyme sites (AChE). The essential oil of O. gratissimum was the most effective with the lowest lethal concentrations (LC10=0.91 %, LC50=1.91 % and LC90=3.92 %). The least toxic oil to larvae was Citrus sp. (LC10=5.44 %, LC50=20.50 % and LC90=77.41 %). Molecular docking revealed that p-cymene and thymol from O. gratissimum essential oil are structurally similar and bind to the AChE active site via predominantly hydrophobic interactions and a H-bond with Tyr374 in the case of thymol. The essential oil of O. gratissimum constitutes a potential candidate for the development of biological insecticides for the fight against insect pests and for the protection of the environment