Moleküler Biyoloji ve Genetik Bölümü / Department of Molecular Biology and Genetics
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Publication Aging-related diseases and autophagy(2016) Çoker Gürkan , Ajda; Palavan Unsal, Narcin; ARISAN, ELİF DAMLA; YERLİKAYA, PINAR OBAKANAutophagy is fundamental, evolutionary conserved physiological process at molecular level which targets long-lived cytosolic proteins and organelles to be recycled through lysosomal degradation. Diminished autophagic activity caused cellular stress in many organisms following aging, and inhibition of autophagy in model organisms causes degenerative changes and pathologic diseases observed with high incidence ratio generally in older ages. Consequently the delayed senescence or increased longevity in model organisms often stimulate autophagy, and autophagy inhibition compromises anti-aging effects. The cytoprotective function of autophagy is presented in various human diseases such as lung, liver, cardiovascular diseases, neurodegeneration, myopathies, cancer, stroke, infections and metabolic diseases which are found associated with autophagic targets. These pathologies are defined with their age-dependent characteristics, is not fully understood that how autophagy network regulates metabolism and may cause diseases in age-related manner. In this book chapter, we are going to discuss the autophagy and aging relationship in three different parts. In the first section autophagy and aging relationship is going to be presented through explaining responsible signalling network. The autophagy and age-related neurological disorders, genetic basis of age-dependent diseases and the functional role of autophagy is going to be discussed in the second and third part of the chapter.Publication Atiprimod induce apoptosis in pituitary adenoma: Endoplasmic reticulum stress and autophagy pathways(WILEY, 111 RIVER ST, HOBOKEN 07030-5774, NJ USA, 2019-12) Çoker Gürkan , Ajda; Keçeoğlu, Gizem; Palavan Unsal, Narcin; ARISAN, ELİF DAMLA; ŞAHİN, BURCU AYHAN; YERLİKAYA, PINAR OBAKANPituitary adenoma is the most common tumor with a high recurrence rate due to a hormone-dependent JAK/signal transducer and activator of transcriptions (STAT) signaling. Atiprimod, a novel compound belonging to the azaspirane class of cationic amphiphilic drugs, has antiproliferative, anticarcinogenic effects in multiple myeloma, breast, and hepatocellular carcinoma by blocking STAT3 activation. Therapeutic agents' efficiency depends on endoplasmic reticulum (ER) stress-autophagy regulation during drug-mediated apoptotic cell death decision. However, the molecular machinery of dose-dependent atiprimod treatment regarding ER stress-autophagy has not been investigated yet. Thus, our aim is to investigate the ER stress-autophagy axis in atiprimod-mediated apoptotic cell death in GH-secreting rat cell line (GH3) pituitary adenoma cells. Dose-dependent atiprimod treatment decreased GH3 cell viability, inhibited cell growth, and colony formation. Upregulation of Atg5, Atg12, Beclin-1 expressions, cleavage of LC-3II and formation of autophagy vacuoles were determined only after 1 mu M atiprimod exposure. In addition, atiprimod-triggered ER stress was evaluated by BiP, C/EBP-homologous protein (CHOP), p-PERK upregulation, and Ca+2 release after 1 mu M atiprimod exposure. Concomitantly, increasing concentration of atiprimod induced caspase-dependent apoptotic cell death via modulating Bcl(2) family members. Moreover, by N-acetyl cycteinc pretreatment, atiprimod triggered reactive oxygen species generation and prevented apoptotic induction. Concomitantly, dose-dependent atiprimod treatment decreased both GH and STAT3 expression in GH3 cells. In addition, overexpression of STAT3 increased atiprimod-mediated cell viability loss and apoptotic cell death through suppressing autophagy and ER stress key molecules expression profile. In conclusion, a low dose of atiprimod exposure triggers autophagy and mild-ER stress as a survival mechanism, but increased atiprimod dose induced caspase-dependent apoptotic cell death by targeting STAT3 in GH3 pituitary adenoma cells.Publication Genome organization changes in GM and non-GM soybean [Glycine max (L.) Merr.] under salinity stress by retro-transposition events(2020-04-09) Gözükırmızı, Nermin; Arı, Şule; Şahin, Olcay; Karlık, Elif; MERİÇ, SİNAN;Genetically modified (GM) crops are developed and cultivated worldwide, providing protection against insects and diseases, or tolerance to herbicides. However, despite the advantages that GM crops, they pose many concerns not only to human and animal health but also to the environment. In the present study, we perform inter-retrotransposon amplified polymorphism (IRAP)-PCR to reveal SIRE1, Bagy2 and Nikita transposition events in soybean [Glycine max (L.) Merr.] and GM soybean under increasing salt stress conditions (0 mM as control, 80 mm, 120 mM, 160 mM and 200 mM NaCl). Salinity dramatically affected soybean and GM soybean in a similar way that stem lengths, root lengths and leaf areas were reduced compared to control. According to IRAP-PCR results, polymorphism ratios of SIRE1, Bagy2 and Nikita retrotransposons among all samples were found to be 22–100%, 0–73% and 37–100%, respectively. These results are the first direct report to demonstrate the relationship between TEs polymorphisms and salinity stress in soybean and GM soybean. TEs, which may explain part of the new phenotypes, play essential roles in genome and gene evolution. Such information can be useful to understanding of genome organization differences derived from TEs between soybean and GM soybean.Publication GMO analysis methods for food: From today to tomorrow(2017) Çakır, Özgür; Arı, Şule; MERİÇ, SİNANIn the last decades, the dynamic face of biotechnology increased the number of M plants and abled the production of more precise genetically modified organisms. Since the introduction of recently developed new breeding techniques, there has been on-going debate on food safely and on the regulation concern of new biotech crops. The presently used one-by-one approach for CMOs which has been commercialized and developed by mainly transforming the usage of a transgenic insert so far, is reorganized for legislation needs of these new organisms. Furthermore, the growing number of complexities of G MOs in the commercialization pipeline and the possibility of the presence of unauthorized CMOs in the food chain has led to a demand for new technologies and stratagies to detect CMOs. In order to provide readers with current viewpoints on this topic, this chapter focuses on the key points at present. These are developing biotech plants, analysis methods for food and feed in the light of new breeding technologies, and the unintended effects of genetic transformation. It will summarize the DNA-based polymerase chain reaction (PCR) technique, the most widely accepted GMO detection method, which is classified into screening, gene-specific, construct specific, and transgenic event-specific methods according to the level of specificity. 'ubsequently, this chapter will elaborate the envisaged evolution of the GMO crops and the challenge for the detection methods of new biotech crops.Publication Identification of the antioxidant defense genes which may provide enhanced salt tolerance in Oryza sativa L.(2019-06) Çakır, Bilgin Candar; ATAK, ÇİMEN; ÇELİK, ÖZGEAntioxidative mechanisms are important to protect cells from the hazardous effects of reactive oxygen species (ROS). Salt stress is one of the environmental stress factors that leads to accumulation of ROS at toxic levels. In this study, we analyzed the responses of two rice (Oryza sativa L.) cultivars against NaCl stress at enzymatic and transcriptional levels. In 14day-old-seedlings, different antioxidant enzyme activities were observed. These findings were also supported by transcriptional analyses of the responsible genes. According to the results, Cyt-APX, CAT A, Cyt-GR1 and proline metabolism-related genes were differentially expressed between two rice varieties under different salt concentrations. Their regulational differences cause different salt sensitivities of the varieties. By this study, we provided an insight into understanding of the correlation between antioxidant defence genes and ROS enzymes under salt stress.Publication Investigation of PI3K-AKT and EMT-targeted miRNA profiles in palbociclib-treated Panc-1 and MiaPaCa-2 pancreatic cancer cells(2019-07) Çoker Gürkan, Ajda; YERLİKAYA, PINAR OBAKAN; RENCÜZOĞULLARI, ÖZGE; 222563; 156421; 125860The therapeutic strategies of pancreatic cancer (PC) are with the various combination treatment of anti-cancer drugs still in progress. However, the survival rate o f PC is still under 6%. because o f the limited therapeutics and no controllable prognosis. miRNAs have an important role in tire regulation of metabolic cascades which are critical in the differentiation of PC progression. In the current study, we aimed to investigate the role o f palbociclib (CDK4/6 inhibitor) on aberrantly activated pathways, PI3K/AKT, and EMT signaling axis through differently expressed miRNA profiles in Pane-1 and MiaPaCa-2 cells. The effect of palbociclib on cell viability was detennined by MTT cell viability test in time and dose-dependent maimer in PC cells. The expression profiles were analyzed by RT-PCR. We found that palbociclib effectively reduced cell viability and proliferation for following exposure of Panc-1 and MiaPaCa-2 cells for 24h. Additively, Panc-1 and MiaPaCa-2 cells were sensitive to palbociclib with the significant blockade in the G1 phase o f the cell cycle. Palbociclib decreased the expression o f PI3K and p-AKT in PC cells. Moreover, palbociclib downregulated the levels of B-catenin in Panc-1 cells, but not in MiaPaCa-2 cells. Palbociclib treatment led to increased levels of tumor suppressor miR- 506, miR-100, and miR-141 in MiaPaCa-2 cells, while the only detectable increase in tumor suppressor miRNA was detected formiR-100 levels in Panc-1 cells. Additionally, the oncomir miR-208 increased after palbociclib treatment in MiaPaCa-2 cells. In conclusion, palbociclib induced cell cycle arrest and reduced cell viability. However, palbociclib had a various effect on the regulation of PI3K/AKT and EMT signaling in each PC cell line. Investigating the effect of palbociclib on the tumor suppressor and oncomir miRNA profiles is a new therapeutic strategy to reduce cell viability and metastatic process of pancreatic cancer.Publication Investigation the Role of Palbociclib on Fatty Acid Synthase Metabolism through Regulation of miR-33a in Pancreatic Cancer Cells(2019-05-16) Telci, Dilek; ARISAN, ELİF DAMLA; RENCÜZOĞULLARI, ÖZGE; 222563; 34170; 113920Aberrant activation of fatty acid (FA) synthesis is associated with cancer development including pancreatic cancer (PC). SREBP is an important regulator of FA synthesis and modulated by growth factor signaling which is also targeted by miR-33a. We aim to determine the role of palbociclib, CDK4/6 inhibitor, on the regulation of FA synthase metabolism through targeting regulators of SREBP such as miR-33a in PC cells. The expression profiles of FA metabolism signaling axis were examined by immunoblotting. The levels of miRNA profiles were analyzed by RT-PCR. Oil red O staining determined the oil droplets in PC cells. Palbociclib exerted a controversial effect on the expression of FA synthesis signaling axis such as FASN, ACL in Panc-1 and MiaPaCa-2 cells. Palbociclib treatment increased the expression of FASN, p-ACL, and ACSL-1 in Panc-1 cells. However, the expression levels of mature SREBP2 were decreased by palbociclib treatment and overexpression of miR-33a resulted in a further decrease of precursor and mature SREBP protein levels in Panc-1 cells. Moreover, inhibition of miR-33a significantly upregulated the SREBP levels in palbociclib-treated Panc-1 cells. The content of lipid drops in Panc-1 cells was more reduced after co-treatment of miR33a with palbociclib. In conclusion, key regulatory factors of lipid metabolism such as FASN, SREBP are important targets to control PC cell proliferation. Overexpression of miR-33a decreased the level of SREBP2 which indicated the downregulation of FA metabolism. It was suggested that the effect of palbociclib on the downregulation of FA synthesis and cell viability was further increased by SREBP targeted-miR-33a.Publication Mechanistic Insights on Salicylic Acid Mediated Enhancement of Photosystem II Function in Oregano Seedlings Subjected to Moderate Drought Stress(MDPI, 2023) Moustakas, Michael; Sperdouli, Ilektra; Moustaka, Julietta; Şaş, Begüm; İŞGÖREN, SUMRUNAZ; Morales, FerminDramatic climate change has led to an increase in the intensity and frequency of drought episodes and, together with the high light conditions of the Mediterranean area, detrimentally influences crop production. Salicylic acid (SA) has been shown to supress phototoxicity, offering photosystem II (PSII) photoprotection. In the current study, we attempted to reveal the mechanism by which SA is improving PSII efficiency in oregano seedlings under moderate drought stress (MoDS). Foliar application of SA decreased chlorophyll content under normal growth conditions, but under MoDS increased chlorophyll content, compared to H2O-sprayed oregano seedlings. SA improved the PSII efficiency of oregano seedlings under normal growth conditions at high light (HL), and under MoDS, at both low light (LL) and HL. The mechanism by which, under normal growth conditions and HL, SA sprayed oregano seedlings compared to H2O-sprayed exhibited a more efficient PSII photochemistry, was the increased (17%) fraction of open PSII reaction centers (qp), and the increased (7%) efficiency of these open reaction centers (Fv '/Fm '), which resulted in an enhanced (24%) electron transport rate (ETR). SA application under MoDS, by modulating chlorophyll content, resulted in optimized antenna size and enhanced effective quantum yield of PSII photochemistry (phi(PSII)) under both LL (7%) and HL (25%), compared to non-SA-sprayed oregano seedlings. This increased effective quantum yield of PSII photochemistry (phi(PSII)) was due to the enhanced efficiency of the oxygen evolving complex (OEC), and the increased fraction of open PSII reaction centers (qp), which resulted in an increased electron transport rate (ETR) and a lower amount of singlet oxygen (O-1(2)) production with less excess excitation energy (EXC).Publication Molecular marker analyses of salt tolerant soybean mutants(2014-08) Çakır, Bilgin Candar; ATAK, ÇİMEN; ÇELİK, ÖZGEPublication Optimization of Tissue Culture Media Inducing Essential Oil Production of Levander (Lavandula angustifolia)(2019-09) Tuman, C.Büşra; Ayan, Alp; MERİÇ, SİNAN; ATAK, ÇİMEN; 219257Aim of this study is to induce in Vitro tissue cultures of levander which produces essential oils which have medical and aromatic properties. Media requirements were investigated for germination, shoot induction and development, rooting, callus initiation and suspenson culture induction. 1 mg/L BAP supplemented MS media presented the highest germination rate by 64.7 % and 2 mg/L BAP supplemented MS media initiated shoot propagation by 95.6 %. For rooting, MS media is supplemented with various NAA and IBA concentrations. The highest rooting rate was observed in 1.25 mg/L IBA supplemented MS media by 60 %. For callus induction MS media was supplemented with various concentrations of IAA, BAP and 2,4-D. The most efficient callus induction media for further suspension culteres was determined as 2 mg/L 2,4-D and 2 mg/L BAP supplemented MS media by 66 %. Characteristic blue pigmentation in suspension cultures were also evaluated spectroscopically. IAA supplemented MS media increased pigmentation significantly.Essential oil contents of suspension cultures were purified by steam destilation method and chacterized by fourier trasport infra red (FTIR) spectroscopy.Publication Palbociclib, a selective CDK4/6 inhibitor, restricts cell survival and epithelial-mesenchymal transition in Panc-1 and MiaPaCa-2 pancreatic cancer cells(2020-01-01) Telci, D.; ARISAN, ELİF DAMLA; YERLİKAYA, PINAR OBAKAN; RENCÜZOĞULLARI, ÖZGEThe mortality rate of pancreatic cancer has close parallels to its incidence rate because of limited therapeutics and lack of effective prognosis. Despite various novel chemotherapeutics combinations, the 5-year survival rate is still under 5%. In the current study, we aimed to modulate the aberrantly activated PI3K/AKT pathway and epithelial-mesenchymal transition (EMT) signaling with the treatment of CDK4/6 inhibitor PD-0332991 (palbociclib) in Panc-1 and MiaPaCa-2 pancreatic cancer cells. It was found that PD-0332991 effectively reduced cell viability and proliferation dose-dependently within 24 hours. In addition, PD-0332991 induced cell cycle arrest at the G1 phase by downregulation of aberrant expression of CDK4/6 through the dephosphorylation of Rb in each cell lines. Although PD-0332991 treatment increased epithelial markers and decreased mesenchymal markers, the nuclear translocation of β-catenin was not prevented by PD-0332991 treatment, especially in MiaPaCa-2 cells. Effects of PD-0332991 on the regulation of PI3K/AKT signaling and its downstream targets such as GSK-3 were cell type-dependent. Although the activity of AKT was inhibited in both cell lines, the phosphorylation of GSK-3β at Ser9 increased only in Panc-1. In conclusion, PD-0332991 induced cell cycle arrest and reduced the cell viability of Panc-1 and MiaPaCa-2 cells. However, PD-0332991 differentially affects the regulation of the PI3K/AKT pathway and EMT process in cells due to its distinct influence on Rb and GSK-3/β-catenin signaling. Understanding the effect of PD-0332991 on the aberrantly activated signaling axis may put forward a new therapeutic strategy to reduce the cell viability and metastatic process of pancreatic cancer. © 2019 Wiley Periodicals, Inc.Publication Policy into practice on sustainable development related teaching in higher education in Turkey(2018) Katayama, Junko; ÖRNEKTEKİN, SERMİN; DEMİR, SIDDIKA SEMAHATThis research explores the current status of implementing policy in sustainable development related teaching in higher education in Turkey. Turkish higher education policy has included increased commitment to sustainable development in recent years. However, there has not been much research conducted on its implementation. Hence, this study involves assessing the current status of sustainable development in teaching at higher education institutions (HEIs) in Turkey. Regarding the research design, a systematic review of accumulated sustainable development related teaching in all 193 HEIs in Turkey (as of the 2015-2016 academic year) was carried out. The accumulated programmes are categorised by occupation concerning sustainable development for the future of Turkey, and the courses are presented within those categories. Whilst many programmes and courses related to sustainable development were identified, the data also reveals the following features: the repetition of same courses; disciplinary partiality, particularly on environmental engineering; disciplinary conservatism and the lack of interdisciplinary practice in general; and last but not least, the differences between what sustainable development means in the European higher education political initiative and what the state of practice is in Turkish higher education.Publication Prognostic value of free/total PSA ratio in prediction of bone metastases in patient with prostate cancer(2018-08-30) Özdemir, Semra; Tan, Yusuf Ziya; Ersay, Ahmet Reşit; Koç Öztürk, Fulya; Özdemir, Beril SuPublication Raman spectroscopic and chemometric investigation of lipid-protein ratio contents of soybean mutants(2020) Yılmaz, Ayberk; Kabuk, Hayrunnisa Nur; Kaygısız, Ersin; Fausto, Rui; MERİÇ, SİNAN; AYAN, ALP; ATAK, ÇİMEN; ÇELİK, ÖZGE; ILDIZ, GÜLCE ÖĞRÜÇSeeds belonging to fourth generation mutants (M-4) of Ataem-7 cultivar (A7) variety and S04-05 (S) breeding line salt-tolerant soybeans were investigated by Raman spectroscopy, complemented by chemometrics methods, in order to evaluate changes induced by mutations in the relative lipid-protein contents, and to find fast, efficient strategies for discrimination of the mutants and the control groups based on their Raman spectra. It was concluded that gamma irradiation caused an increase in the lipid to protein ratio of the studied Ataem-7 variety mutants, while it led to a decrease of this ratio in the investigated S04-05 breeding line mutants. These results were found to be in agreement with data obtained by reflectance spectrum analysis of the seeds in the full ultraviolet to near-infrared spectral region and suggest the possibility of developing strategies where gamma irradiation can be used as a tool to improve mutant soybean plants targeted to different applications, either enriched in proteins or in lipids. Ward's clustering and principal component analysis showed a clear discrimination between mutants and controls and, in the case of the studied S-type species, discrimination between the different mutants. The grouping scheme is also found to be in agreement with the compositional information extracted from the analysis of the lipid-protein contents of the different samples.Publication RAPD Analysis of Salinity and Drought Tolerant Soybean (Glycine max (L.) Merr) Mutants Generated by Gamma Radiation(2019-09) AYAN, ALP; 185510Aim of this study is to evaluate genetic distances between M4 generation salinity and drought tolerant soybean mutants by using RAPD primers. AM1, SM1, SM2, SM3 and SM5 mutants were generated from present Ataem-07 and S04-05 soybean varieties by using Cs-137 gamma radiation source. All of the mutants are determined to be 90 mM NaCI and 5 days of drought tolerant comparing to their respected original varieties. Jaccard genetic similarity matrixes of mutants and their original varieties were generated according to the band profiles under untreated, drought and salt treated conditions. UPGMA dendograms were drawn based on the genetic similarity coefficients. In salt treated experimental groups, 22 random RAPD primers presented 61 polymorphic band among 191 total bands. Polymorphism ratio was calculated as 31.12 %. In drought treated experimental groups, 21 random RAPD primers were used and 68 in total of 203 bands were found to be polymorphic. Polymorphism ratio was calculated as 33.49%. Both salt and drought treated SM1 and SM3 mutants were found to be distant from their untreated controls.Publication Revealing The Functional Role of Bag-1 in MCF-7 Breast Cancer Cells Through CRISPR-Cas9-Mediated Gene Knockout(2019-07) Dinler Doğanay, Gizem; ARISAN, ELİF DAMLA; KILBAŞ, PELİN ÖZFİLİZ; 113920; 152975; 195744Bag-1 is a multifunctional protein target which has interactions with a number of cellular proteins. Therefore, Bag-1 participates in several significant biological processes such as cell proliferation, survival, and apoptosis. Elevated expression levels of Bag-1 arc associated with progression o f cancer and resistance mechanism against cancer. In our previous studies, we obtained results showing Bag-1 silencing enhancing the apoptotic potentials of cisplatin or paclitaxel through modulating PI3K/Akt/mT0R pathways in breast cancer cells, however, the function of Bag-1 knockout in these cells has not been fully explored. Here, we performed the CRISPR/Cas9 technique to knockout Bag-1 gene and successfully produced Bag-1 knockout cell line (Bag-1 KO). Sanger sequencing was used to confirm the gene knockout mediated insertions or deletions (indels) in MCF-7 cells. Correspondingly, the mRNA and protein expressions of Bag-1 were markedly reduced. We determined the effect o f Bag-1 KO on cell survival by M il and trypan blue dye exclusion assay. Alternations of total protein expression profiles between wild-type and Bag-1 KO cells were determined through pathscan analysis and immunoblotting assays. Our results showed that knockout of Bag-1 suppressed the proliferation and growth potential of MCF-7 cells by decreasing the number of colony formations. According to the immunoblotting results, knockout of Bag-1 significantly upregulated Akt phosphorylation and b-actin downregulation. We concluded that Bag-I inlluenced actin disorganization through stress-induced Akt activation and alternations on expression profiles o f focal adhesion kinases.Publication The molecular targets of diclofenac differs from ibuprofen to induce apoptosis and epithelial mesenchymal transition due to alternation on oxidative stress management p53 independently in PC3 prostate cancer cells(Elsevier INC., 2019-12) AKAR, REMZİ OKAN; Çoker Gürkan, Ajda; Akın, Beyza; Dener, Elif; Kayhan, Ecem; Palavan Ünsal, Narçın; YERLİKAYA, PINAR OBAKAN; ARISAN, ELİF DAMLA; RENCÜZOĞULLARI, ÖZGEBackground: Prostate cancer is the most common type of cancer among men. Studies showed that the regular use of nonsteroidal antiinflammatory drugs might reduce disease progression risk for prostate cancer patients with prostate cancer. We evaluated the effects of ectopic expression of p53 on the biological functions of ibuprofen and diclofenac. Materials and methods: For this purpose, We investigated cell death decision pathways related to survival and aggressive cellular phenotypes such as extrinsic/intrinsic apoptosis decision, Protein Kinase B/ Forkhead box O (AKT/FoxO) axis, mitogen-activated protein kinases (MAPKs), reactive oxygen species (ROS) generation, and EMT (epithelial mesenchymal transition) in wild type and p53 + PC3 prostate cancer cells. Results and Conclusions: Ibuprofen (1 mM) and diclofenac (250 mu M) effectively induced cell cycle arrest and led to apoptosis via modulating both extrinsic and intrinsic pathways. However, diclofenac was the only drug to generate ROS intermediates. Diclofenac triggered a typical EMT process with downregulated E-cadherin and upregulated N-cadherin, vimentin, and Snail in PC3 cells, regardless of p53 expression. In conclusion, although both drugs are effective on cell death mechanism, only diclofenac caused EMT because of increased ROS generation independent of p53. On the other hand, ibuprofen could inhibit metastasis via upregulating E-cadherin. The biological targets of both nonsteroidal antiinflammatory drugs are different to highlight their role in cell survival and death axis. (c) 2019 Asian Pacific Prostate Society, Published by Elsevier Korea LLC. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).Publication Tissue-specific transcriptional regulation of seven heavy metal stress-responsive miRNAs and their putative targets in nickel indicator castor bean (R. communis L.) plants(ACADEMIC PRESS INC ELSEVIER SCIENCE, 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA, 2019-04-15) Akdaş, Enes Yağız; ÇELİK, ÖZGER.communis L. has high capability to accumulate nickel which is a trace nutrient for higher plants and also an environmental contaminant causes toxicity related symptoms at higher concentrations. MicroRNAs (miRNAs) are known to be important modulators of responses against heavy metal stress for detoxification of the metal. In this study, we experimentally measured and validated the transcript levels of the seven heavy metal stress response-related miRNAs and the expression levels of target genes in both leaf and root tissues of R. communis L. subjected to three different concentrations of nickel stress via qRT-PCR quantification. The results demonstrated differential regulations of heavy metal stress-responsive miRNAs and their putative targets in both tissues in same stress treatments. This dynamic regulation suggest that regulatory processes differ between the tissues under nickel stress. Our data suggest that, miR838 was the most responsive to the Ni2+ stress. miR398 target gene Cu-Zn/SOD was found to be up-regulated in both root and leaf tissues. The relations between TCP and expression levels of miR159 and miR319 were also found statistically significant exclusive to leaf tissues. In leaf tissue, changes in miR395 level and its putative target genes, sulphate transporter and sulphate adenyltransferase gene were found in relation whereas, only expression level of sulphate transporter represented a statistically significant relation in root tissue. The sharp decrease in transcript levels of 2r3 myb gene at lower nickel dose suggest to investigate the role of r2r3 myb and the all MYB family members in primary and secondary metabolisms against nickel stress.Publication Triptolide overcome autocrine Growth Hormone (GH) Mediated Resistance in a Dose-Dependent Manner in MDA-MB-453 Breast Cancer Cells Via Acting on EMT Pathway(2019-07-06) Malcanlı, S; Ozkurt, E.; Palavan Unsal, N.; Coker Gürkan, A.; ŞAHİN, BURCU AYHAN; YERLİKAYA, PINAR OBAKAN; ARISAN, ELİF DAMLA; 30985Breast cancer is one o f the most common cancer types among women. Beyond environmental and genetic risk factors such as age and genetic background, many growth factors (e.g. VEGF) and hormones (estrogen) are known to affect the development o f breast cancer. Recently, autocrine growth hormone (GH), an essential hormone affecting post-natal growth, has been shown to trigger cell proliferation, invasion, metastasis, and also lead to drag resistance. Upregulation of GH and its receptor (GHR) expression was determined in mammary carcinoma cells. Forced GH expression induced drag resistance against tamoxifen, doxorubicin, mitomycin and curcumin in MCF-7, T47D and BT^I74 breast cancer cells. Triptolide is a diterpenoid triepoxide which have been demonstrated to have multiple biological activities and also triggers apoptotic cell death in breast cancer cells. In this study, our aim was to investigate the role of epithelial-mesenchymal transition (EMT) signalling during triptolide-induccd apoptotic cell death in MDA-MB-453 wt and GH+ breast cancer cells. Triptolide decreased cell viability in a dose-dependent manner, mitochondrial membrane potential loss and nuclear fragmentation were observed. 20 nM triptolide decreased cell viability by 25% and 15% in MDA-MB-453 wt and GH+ cells, respectively. Although autocrine GH expression triggered cell proliferation and colony formation in MDA-MB-453 cells, triptolide (20 nM) treatment suppressed forced GH-mediated invasion and metastasis. Furthermore, autocrine GH mediated aggressive profile was prevented by triprolide treatment through Slug, N-cadherin, Vimentin downregulation within 24 h. Triptolid induced caspase-dependent apoptotic cell death via modulating Bcl-2 family member's expression profile in MDA-MB-453. In consequence, autocrine GH overexpression increased aggressive phenotype of MDA-MD-453 breast cancer cells, however triptolide treatment overcame this resistance mechanism and induced apoptotic cell death.Publication Wnt-11 expression promotes invasiveness and correlates with survival in human pancreatic ductal adeno carcinoma(2019-11-11) Dart DA; Owen S.; Hao C.; Jiang WG; Uysal Onganer; ARISAN, ELİF DAMLAPancreatic ductal adenocarcinoma (PDAC) is one of the deadliest forms of cancer, proving difficult to manage clinically. Wnt-11, a developmentally regulated gene producing a secreted protein, has been associated with various carcinomas but has not previously been studied in PDAC. The present study aimed to elucidate these aspects first in vitro and then in a clinical setting in vivo. Molecular analyses of Wnt-11 expression as well as other biomarkers involved qRT-PCR, RNA-seq and siRNA. Proliferation was measured by MTT; invasiveness was quantified by Boyden chamber (Matrigel) assay. Wnt-11 mRNA was present in three different human PDAC cell lines. Wnt-11 loss affected epithelial-mesenchymal transition and expression of neuronal and stemness biomarkers associated with metastasis. Indeed, silencing Wnt-11 in Panc-1 cells significantly inhibited their Matrigel invasiveness without affecting their proliferative activity. Consistently with the in vitro data, human biopsies of PDAC showed significantly higher Wnt-11 mRNA levels compared with matched adjacent tissues. Expression was significantly upregulated during PDAC progression (TNM stage I to II) and maintained (TNM stages III and IV). Wnt-11 is expressed in PDAC in vitro and in vivo and plays a significant role in the pathophysiology of the disease; this evidence leads to the conclusion that Wnt-11 could serve as a novel, functional biomarker PDAC.