Karakaya, Hüseyin Çağlar
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Karakaya, Çağlar H.
Karakaya, Hüseyin Ç.
Karakaya, Huseyin Caglar
Caglar Karakaya, H.
Karakaya, H. Çağlar
Karakaya, H. Caglar
Çağlar Karakaya, H.
Karakaya, H. Ç.
Karakaya, Huseyin C.
Karakaya, H. C.
Karakaya, Caglar H.
Karakaya, Hüseyin Ç.
Karakaya, Huseyin Caglar
Caglar Karakaya, H.
Karakaya, H. Çağlar
Karakaya, H. Caglar
Çağlar Karakaya, H.
Karakaya, H. Ç.
Karakaya, Huseyin C.
Karakaya, H. C.
Karakaya, Caglar H.
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caglarkarakaya@iyte.edu.tr
Main Affiliation
04.03. Department of Molecular Biology and Genetics
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Current Staff
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Sustainable Development Goals
1NO POVERTY
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2ZERO HUNGER
2
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3GOOD HEALTH AND WELL-BEING
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4QUALITY EDUCATION
1
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5GENDER EQUALITY
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6CLEAN WATER AND SANITATION
5
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7AFFORDABLE AND CLEAN ENERGY
3
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8DECENT WORK AND ECONOMIC GROWTH
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9INDUSTRY, INNOVATION AND INFRASTRUCTURE
6
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10REDUCED INEQUALITIES
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11SUSTAINABLE CITIES AND COMMUNITIES
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12RESPONSIBLE CONSUMPTION AND PRODUCTION
1
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13CLIMATE ACTION
4
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14LIFE BELOW WATER
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15LIFE ON LAND
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16PEACE, JUSTICE AND STRONG INSTITUTIONS
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17PARTNERSHIPS FOR THE GOALS
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Documents
19
Citations
718
h-index
11
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0
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0
Scholarly Output
28
Articles
15
Views / Downloads
56070/13147
Supervised MSc Theses
10
Supervised PhD Theses
2
WoS Citation Count
555
Scopus Citation Count
634
Patents
0
Projects
15
WoS Citations per Publication
19.82
Scopus Citations per Publication
22.64
Open Access Source
26
Supervised Theses
12
| Journal | Count |
|---|---|
| Doga, Turkish Journal of Botany | 2 |
| Journal of Trace Elements in Medicine and Biology | 2 |
| Gene | 2 |
| MicrobiologyOpen | 1 |
| Molecular and Cellular Biology | 1 |
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28 results
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Now showing 1 - 10 of 28
Master Thesis Molecular Cloning, Overexpression and Biochemical Characterization of Bacterial Amylase for Biotechnological Processes(Izmir Institute of Technology, 2012) Burhanoğlu, Tülin; Karakaya, Hüseyin Çağlar; Şanlı Mohamed, GülşahAmylases are the enzymes that act on glycosidic bond of starch and related polysaccarides. They comprise 25% of enzyme utilised in a variety of industry. It is used to obtain maltose, glucose and maltodextrins in various lenghts during industrial processes. Amylases are widely distributed enzymes in bacteria, fungi, higher plants and animals. Thermophilic enzymes are widely demanded in order to be stable at harsh process conditions. Isolating these enzymes from thermophilic microorganism is increasing trend because of ease of enzyme production. In this study α-amylase gene region from a thermophilic Bacillus sp. isolated from Balçova Geotermal region in İzmir was cloned to compotent E. coli BL 21 cells. Additionally protein expression was reinforced with pKJE7 chaperone plasmid. Cloned gene was sequenced and found as 1542 bp in length. Thermophilic amylase that has a 59.9 kD molecular weight was expressed and purified from this recombinant strain. Mass spectrometric analysis were performed and the enzyme was matched with α-amylase family protein of Geobacillus thermodenitrificans NG80-2 using NCBInr database. The aminoacid sequence of this enzyme was seen to be similar 92% with our obtained enzyme. According to the results of characterization studies, the amylase enzyme was seen to have highest activity at pH 8.0 and 60°C. The enzyme was also showed to have resonable activity between pH5 and 9. 85% of the enzyme activity was retained at 70°C. Furthermore, amylase activities at 65 and 85°C were observed to remain stable for 5 and 2 hours, respectively. It was also showed that the activity was stable and pH7 and 9 for 6 hours. The effects of some metal ions, chemical agents and organic solvents on enzyme activity were examined so, Co+2, Mg+2,Ca+2 was determined to be as inducer for the enzyme activity. Conversely the activity was inhibited by Cu+2. Furthermore methanol, DDT and Triton X-100 was found to have no effect on the enzyme activity.Master Thesis Identification and Characterization of Manganese Tolerance Genes in Beta Vulgaris Subsp. Maritima(Izmir Institute of Technology, 2011) Erbaşol, Işıl; Karakaya, Hüseyin ÇağlarManganese is an essential element for higher organisms however uptake of excess amount of manganese causes toxicity. Beta vulgaris subsp. maritima, the member of Chenopodiaceae family, is known to tolerate high concentration of sodium. Due to its living conditions, Beta vulgaris subsp. maritima adapted many different stress conditions. Therefore it is an ideal plant for studying plant tolerance mechanisms. In this study, we aimed to identify the genes which are responsible for manganese tolerance in Beta vulgaris subsp. maritima by screening its cDNA library in Saccharomyces cerevisiae cells. After initial screening in the presence of toxic manganese concentration; 2,7mM MnCl2, three resistant yeast colonies were selected. After the sequence and similarity analysis, two genes which might involve in manganese tolerance were identified and named as BmMn1 and BmMn2. The results of solid media tests with different yeast strains which transformed with the genes revealed that BmMn1 provides a remarkable manganese tolerance like BmMn2 and slightly nickel tolerance. They do not show tolerance to other metals such as zinc, cadmium, boron and cobalt. Identified manganese concentrations in pmr1 yeast strainstransformed with BmMn1, BmMn2 or empty vector pointed that BmMn1 and BmMn2 transport excess manganese out of the cell. In addition, GFP localization in the yeast cell proved that the BmMn1 and BmMn2 are located in Golgi apparatus. qRT-PCR analyses of Beta vulgaris subsp. maritima which was exposed to 2mM Mn2+ suggested a dynamic regulation for the expression of these two genes. The results indicate that BmMn1 and BmMn2 have a role in detoxification of excess amount of manganese in Beta vulgaris subsp. maritima.Master Thesis Alfa-Ketoglutaratın Maya (Saccharomyces Cerevisiae) Yaşlanması Üzerindeki Etkilerinin Proteomik Yaklaşımla Belirlenmesi(2025) Yayla, Dilay; Karakaya, Hüseyin Çağlar; Demir, Ayşe BanuAlfa-Ketoglutarat, hücre metabolizmasını, bazı amino asitlerin biyosentezini, kolajen sentezini, histon demetilasyonuyla epigenetik regülasyonu etkileyen bir metabolittir. AKG'nin yaşlanmayla ilişkisi üzerine farklı organizmalar kullanılarak araştırmalar, AKG'nin yaşlanmayı geciktirdiğini keşfetmiştir. Bu çalışmalar içinde genomik düzeydeki değişikliklere ya da AKG'ye bağlı spesifik proteinlerin seviyelerindeki değişikliklere yönelik çalışmalar olmasına rağmen tüm protein profili üzerine yapılmış kapsamlı bir proteomik çalışma bulunmamaktadır. Bu çalışmada, AKG uygulamasının maya hücrelerinin tüm protein profiline etkisini analiz ederek, hücresel düzeydeki etki mekanizmasının araştırılması amaçlanmıştır. Kontrol ve AKG uygulanmış maya hücrelerinin protein profilleri, LC-MS/MS analizi yapılarak incelenmiş, Proteome Discoverer LFQ modülüyle protein ifade farklılıkları analiz edilmiştir. Ham proteomik veriler filtrelenmiş ve 40 adet upregüle olmuş protein tespit edilmiştir. Bu proteinler moleküler fonksiyonlarına göre gruplandırıldığında, sürekli ekspresyon gösteren proteinlerin RNA bağlanması, transferaz, hidrolaz ve oksidoredüktaz fonksiyonları olduğu gözlemlenmiştir. Bu durum, AKG'nin metabolik aktiviteler, enerji üretimi, stres karşı direnç ve büyüme düzenlemesi üzerinde etkisi olduğunu düşündürmektedir. Alfa, alfa-trehaloz-fosfat sentazi, AP-1-benzeri transkripsiyon faktörü gibi yaşlanma ve stress direncini olumlu yönde etkileyen proteinler AKG uygulanmasının sonucunda upregüle olmuştur. Fakat, önceki Drosophila melanogaster, fare, ve insan üzerine yapılan genomik çalışmalarında otofaji ve mTOr gibi yaşlanma alakalı genler tespit edilmesine rağmen bizim proteomik çalışmamızda bu tür genlere rastlanmamıştır.Article Citation - WoS: 11Citation - Scopus: 14Proteomic Changes During Boron Tolerance in Barley (hordeum Vulgare) and the Role of Vacuolar Proton-Translocating Atpase Subunit E(Türkiye Klinikleri Journal of Medical Sciences, 2011) Atik, Ahmet Emin; Bozdağ, Gönensin Ozan; Akıncı, Ersin; Kaya, Alaattin; Koç, Ahmet; Yalçın, Talat; Karakaya, Hüseyin ÇağlarBoron is an essential micronutrient for plants and animals; however, it can be toxic when present at high concentrations. The purpose of this study was to understand the mechanisms of boron tolerance in the Turkish barley (Hordeum vulgare) Anadolu cultivar. For this purpose, 2-dimensional electrophoresis (2-DE) was used to screen differentially expressed proteins for both control and boron-stressed Anadolu barley genotypes. Seven proteins were revealed by 2-DE: 1) ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo large chain), 2) TLP5, a thaumatin-like protein, 3) PR5, a basic pathogenesis-related protein, 4) a RNase S-like protein, 5) a PSI type III chlorophyll a/b-binding protein, 6) a light-harvesting complex I LHC I, and 7) the vacuolar proton-translocating ATPase subunit E protein. These were found to be upregulated in response to boron treatment. Even though the protein encoded by the V-ATPase subunit E gene was overexpressed, its transcript level was downregulated by boron treatment. Heterologous expression of the barley V-ATPase subunit E gene in yeast provided boron resistance to yeast cells. These results indicated that the V-ATPase subunit E gene was functional and conferred tolerance to toxic boron levels in yeast and might play a role in the overall boron tolerance of barley. © TÜBITAK.Article Citation - WoS: 48Citation - Scopus: 52Boron Stress Activates the General Amino Acid Control Mechanism and Inhibits Protein Synthesis(Public Library of Science, 2011) Uluışık, İrem; Kaya, Alaattin; Fomenko, Dmitri E.; Karakaya, Hüseyin Çağlar; Carlson, Bradley A.; Gladyshev, Vadim N.; Koç, AhmetBoron is an essential micronutrient for plants, and it is beneficial for animals. However, at high concentrations boron is toxic to cells although the mechanism of this toxicity is not known. Atr1 has recently been identified as a boron efflux pump whose expression is upregulated in response to boron treatment. Here, we found that the expression of ATR1 is associated with expression of genes involved in amino acid biosynthesis. These mechanisms are strictly controlled by the transcription factor Gcn4 in response to boron treatment. Further analyses have shown that boron impaired protein synthesis by promoting phosphorylation of eIF2α in a Gcn2 kinase dependent manner. The uncharged tRNA binding domain (HisRS) of Gcn2 is necessary for the phosphorylation of eIF2α in the presence of boron. We postulate that boron exerts its toxic effect through activation of the general amino acid control system and inhibition of protein synthesis. Since the general amino acid control pathway is conserved among eukaryotes, this mechanism of boron toxicity may be of general importance.Article Evidence for the Presence of a Second Electron Donor for the Cytoplasmic Thioredoxins in the Yeast Saccharomyces Cerevisiae(TUBITAK, 2006) Koç, Ahmet; Karakaya, Hüseyin Çağlar; Ünlü, Ercan SelçukIn yeast, the cytoplasmic thioredoxin system is composed of NADPH, thioredoxin reductase-1 (TRR1) and 2 thioredoxin genes (TRX1, TRX2). In this study, using yeast knockout mutants for TRR1, TRX1 and TRX2 genes, the role of the thioredoxin system in methionine sulfoxide reduction was investigated. Cells lacking both TRX1 and TRX2 genes simultaneously were not able to reduce methionine sulfoxides to methionine; however, mutants missing the TRR1 gene were able to reduce methionine sulfoxides to methionine, which showed that electrons could be transferred from NADPH to thioredoxins in the absence of TRR1. Similar results were observed for 3-phosphoadenosine 5-phosphosulfate reduction in the inorganic sulfate assimilation pathway. Results from both assays suggested that yeast cells have additional cytoplasmic thioredoxin reductase activity that could compensate for methionine sulfoxide reduction and sulfate assimilation in the absence of TRR1. This report also constitutes the first evidence that thioredoxins are the in vivo electron donors for methionine sulfoxide reductases in yeast.Master Thesis Elucidation of Molecular Mechanisms Conferring Arsenic Tolerance To Yeast Cells(Izmir Institute of Technology, 2016) Işık, Esin; Karakaya, Hüseyin ÇağlarArsenic is a highly toxic metalloid available in the environment mainly as arsenite or arsenate. These compounds’ interference with many molecular mechanisms results in several diseases including cancer. Conversely, arsenic is used in therapeutic approaches, however, they are associated with drug resistance. Although some tolerance and toxicity mechanisms of arsenicals in yeast have been enlightened by previous studies, complete understanding, which is important for development of protection and therapy strategies, has not yet been achieved. Comprehensive genome-wide screening is a promising approach for the elucidation of novel genes involved in arsenic-associated mechanisms. The aim in this study was to screen a yeast genome library to characterize novel genes whose overexpression confers resistance to toxic concentrations of arsenate or arsenite in Saccharomyces cerevisiae. The plasmids from the colonies confirmed to be highly-resistant against arsenicals were sequenced to determine the genomic regions and seven genes were selected to clone into expression vectors. The overexpression of Pho86p and Vba3p provided yeast cells with the highest arsenate and arsenite resistance, respectively. Arsenate is a phosphate analogue and taken up by phosphate transporters. Pho86p is an ER-resident protein regulating ER-exit of the phosphate transporter. Therefore, it is reasonable that overexpression of Pho86p provides arsenate resistance. Vacuolar sequestration is a common route for the removal of toxic compounds from the cytosol and Vba3p is a vacuole-located transporter of basic amino acids with a likely role in arsenite resistance. Consequently, the screen in the current study revealed two genes with promising roles for tolerance mechanisms against arsenicals.Master Thesis Identification of Salt Stress Responsive Protyeins in Wild Sugar Beet (beta Maritima) Using 2d-Page With Maldi-tof/Tof System(Izmir Institute of Technology, 2012) Çakıroğlu, Çiğdem; Karakaya, Hüseyin ÇağlarHigh salinity is one of the abiotic stresses, which affects the homeostasis, growth and productivity of plants. In plants, uptake of the non-essential salt ions negatively affects the anatomy, physiology and metabolism, changes the osmotic balance in cells and causes abundant dehydration. In this case, higher plants develop salt tolerance mechanisms such as induction of related signaling pathways, effluxion of salt ions, accumulation of these toxic ions in their vacuoles, activation of their detoxification mechanisms and production of osmoprotectans. In this study, identification of salt responsive proteins in moderately halophyte wild type sugar beet Beta vulgaris ssp. maritima was aimed. In order to investigate the protein-based natural stress tolerating mechanisms, plants were exposed to 150 mM NaCl and total proteins were extracted. Differentially expressed proteins were identified by proteomic approaches including MALDI-TOF/TOF mass spectrometry combined two dimensional polyacrylamide gel electrophoresis. The results revealed that enzymatic antioxidants and secondary members of antioxidative pathways are responsive in salt stress. In conclusion, these detected proteins demonstrate that antioxidative system may be the major defense mechanism in halophytic plants.Article Citation - WoS: 1Citation - Scopus: 2Trna Wobble Base Modifications and Boric Acid Resistance in Yeast: Boron-Resistant Deletion Mutants Induce the General Amino Acid Control Mechanism and Activate Boron Efflux(Pleiades Publishing, 2020) Uluisik, I.; Karakaya, H.C.; Koc, A.Abstract: Boric acid is essential for plants and has many vital roles in animals and microorganisms. However, its high doses are toxic to all organisms. We previously screened yeast deletion collections to identify boric acid-resistant and susceptible mutants to identify genes that play a role in boron tolerance. Here, we analyzed boron resistant mutants (elp1∆, elp3∆, elp6∆, ncs2∆, ncs6∆ and kti12∆) for their abilities to modulate the general amino acid control system (GAAC) and to induce boron efflux pump ATR1. The mutants analyzed in this study lack the genes that play roles in tRNA Wobble base modifications. We found that all of the boron resistant mutants activated Gcn4-dependent reporter gene activity and increased the transcript level of the ATR1 gene. Additionally, boron resistant cells accumulated less boric acid in their cytoplasm compared to the wild type cells upon boron exposure. Thus, our findings suggested that loss of wobble base modifications in tRNA leads to GAAC activation and ATR1 induction, which in turn reduced intracellular boron levels and caused boron resistance. © 2020, Pleiades Publishing, Inc.Master Thesis Identification and Characterization of Boron Tolerant Genes in Hordeum Vulgare (barley) by Using Mrna Differential Display and Rt-Pcr Techniques(Izmir Institute of Technology, 2007) Akıncı, Ersin; Karakaya, Hüseyin ÇağlarBoron, is a microelement that plays a role in plant development. In contrast, excess amount of boron is toxic for plants. Turkey is the second country that has the largest boron reserve in the world, thus boron is one of the major problems in agriculture in Turkey. Barley (Hordeum vulgare) is the second widely produced cereal after wheat. Because barley is used in human diet, animal feeding and beer industry it is an economically valuable crop. There are ten different barley varieties in Turkey and these varieties show different genetic variations against boron toxicity. In this study, Hamidiye (boron sensitive) and Anadolu (boron tolerant) varieties were used to identify genes responsible for boron tolerance. RT-PCR and mRNA Differential Display techniques were used from root and leaf samples of Hamidiye and Anadolu varieties grown in laboratory with or without boron conditions. Eight differentially expressed genes identified by using mRNA Differential Display technique. Sequence of these genes gave homology to an eukaryotic translation initiation factor in Arabidopsis thaliana, a chlorophyll a/b binding protein precursor in Triticum aestivum, an elongation factor in Oryza sativa, short-chain dehydrogenase/reductase family protein in Arabidopsis thaliana, a thioredoxin h isoform in Triticum aestivum, a shaggy-like kinase protein in Triticum aestivum, chloroplast genome in Hordeum vulgare, a hypothetical protein in Arabidopsis thaliana. Expression level of six of forty three antiporter genes showed differences between Anadolu and Hamidiye cultivars in Real Time PCR.
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