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Öğe A Review on Biomaterials for Organoid Modeling and Tumor Spheroids(Niyazi BULUT, 2022) Berk, ŞeydaOrganoids are miniature forms of organs to demonstrate spatio-temporal cellular structure and tissue function. The organoids creation revolutionized developmental biology and provided the opportunity to study and modify human development and disease in laboratory setting. Recently, new biomaterial-guided culture systems have represented the versatility for designing and producing of organoids in a constant and reproducible manner. Since 2D cell culture models often lack in vivo tissue architecture, recent detailed research has allowed many 3D culture models development demonstrating the characteristics of in vivo organ structure and function. Organoid models are able to create 3D structures complex that maintain multiple cell types and also hide the relevant organ functions in vivo, and therefore, the development of organoids in particular has revolutionized developmental biology, disease modeling, and drug discovery. The new biomaterials production has been important for development of in vitro 3D models. Further work with biomaterials has been on the creation of hybrid polymers that combine the advantages of both synthetic and natural polymers to take place of communal materials such as Matrigel and polydimethylsiloxane (PDMS). The creation of 3D culture systems has also revolutionized in vitro drug testing. Furthermore, recreating the three-dimensional environment of tumors and the functional arrangement of cancer cells has been a major motivation for developing new tumor models. Under defined culture conditions, cancer cells can form three-dimensional structures known as spheroids and advances in development of embryonic to self-organize into three-dimensional cultures known as organoids. These newly designed biomaterials using for tumor modeling will make an important contribution to understand the main mechanisms of cancer.Öğe Aloe vera Gel Extract Prolongs Lifespan in Caenorhabditis elegans(2024) Berk, ŞeydaCaenorhabditis elegans (C. elegans), with its superiority and physiological aging properties, has become a widely recognized model system in research on aging, longevity mechanisms, age-related diseases, and drug screening. Lifespan-extending mutations in C. elegans are known to slow the aging process by interfering with a number of signaling pathways such as the AMP-activated protein kinase (AMPK), mechanistic target of rapamycin (mTOR) and insulin/IGF-1 signaling (IIS) pathways. We aimed to see how Aloe vera (A. vera) gel affects the fertilization and lifespan of C. elegans. In the presence of all A. vera gel concentrations (0.312 - 5 mg/mL), the fertilization capacity of N2 worms increased and extended their lifespan as well as increased their body size. We found that in N2 worms cultured with 2.5 mg/ml A. vera gel, sgk-1, age-1, and let-363 mRNA expression was significantly increased, while rsks-1 mRNA expression was significantly decreased. We therefore conclude that it may extend lifespan through a mechanism specifically dependent on mTOR signaling. All these observations will provide a new perspective on mammalian life extension through the model organism C. elegans.Öğe DNA Barcoding of Commercial Cockroaches in Turkey(Sivas Cumhuriyet Üniversitesi, 2023) Berk, Şeyda; Pektaş, Ayşe NurAccurate species identification has become a precondition for accomplished biodiversity administration and further genetic research. Species acquaintance technics require molecular tools such as DNA barcoding as well as morphological identification for accurate identification. Particularly, the application of subunit I of the mitochondrial cytochrome c oxidase (COI) gene for DNA barcoding for insects has approved to be very useful in species acquaintance. The main aim of this study is to generate the first reference library of DNA barcode for cockroaches in Turkey using previously published data. As a result of the literature research, it has been observed that no study has been carried out on the DNA barcode of Turkish cockroaches. Therefore, in this study, we evaluated the advantage of DNA barcoding applied to two cockroach samples from Turkey for the first time. Our working samples implicated 10 DNA barcodes grounded on sequences created from our present study and 109 other DNA barcodes from BOLD. Various molecular analyzes including genetic distance-origin assessment (NeighborJoining and Maximum Likelihood trees) has been applied to accurately identify and describe species. In addition, Blaptica dubia (B. dubia) (Serville, 1838) and Nauphoeta cinerea (N. cinerea) (Olivier, 1789) have been reported as the first country records. It has been observed that reference libraries like BOLD are not yet sufficiently populated with COI sequences of Turkish cockroach species. In order for Turkish cockroach bio-assessment and biodiversity studies to benefit from the advantages of DNA barcoding, it is of great importance that cockroach inventories and taxonomic studies include DNA barcodes.Öğe Identification and Validation of Reference Genes for RT-qPCR Normalization in Nauphoeta cinerea (Olivier, 1789) (Blattodea, Blaberidae)(Kutbilge Akademisyenler Derneği, 2022) Özcan, Kübra; Pektaş, Ayşe Nur; Berk, ŞeydaQuantitative RT-PCR (q-RT-PCR) is a powerful tool that allows large-scale analysis of very small changes in gene expression. For the calculation of gene expression, such as the delta-delta Ct method, different PCR primer efficiencies (E) may affect the result, as PCR primer yields are assumed to be comparable for the gene of interest and housekeeping gene. Therefore, identification of a suitable reference gene for data normalization is an important step in the development of qPCR assays. Furthermore, accurate and reliable results depend on the use of stable reference genes for normalization. The aim of the current study is the identification and validation of a set of six housekeeping genes (GADPH, RPS18, α-TUB, EF1α, ArgK, and ACTB) in cockroach species Nauphoeta cinerea adults using five different algorithms (ΔCt method, Bestkeeper, geNorm, Normfinder and RefFinder) to evaluate the stability of selected reference genes expression. Our results show that α-Tub use provides accurate normalization of gene expression levels in N. cinerea adults. In addition, since the GADPH is selected as the second most stable reference gene, GADPH can be also used for transcript analysis N. cinerea adults. Our study also showed that ACTB (β-actin) should not be used for normalizing transcript levels when examining N. cinerea adults. Additionally, validation studies for reference genes in cockroaches are very few (only one) in the literature. Therefore, the results highlight the need for validation of reference genes under biotic and abiotic conditions in q-RT-PCR studies in cockroaches.Öğe Interplay between glucose and insulin/insulin-like growth factors in colorectal cancer (STEM) cells(Cumhuriyet Üniversitesi, 2017) Berk, Şeyda; Değerli, Naci; Özcan, ServetKolorektal kanser ve tip 2 diabetes mellitus tüm dünyada morbidite ve mortalitenin başlıca nedenlerindendir. Bu nedenle, kolon kanserini başlatan hücrelerin izolasyonu ve karakterizasyonu, yeni tanı ve tedavi yöntemleri geliştirmeye ve kanserin şeker hastalığı gibi diğer hastalıklarla olan ilişkisini aydınlatmada önemli katkılar sağlayabileceği ön görülmektedir. Bu çalışmada, kanserin dört farklı aşamasından köken almış dört faklı hücre hattı değerlendirilmiştir ve glukoz, insülin ve insülin benzeri büyüme faktörlerinin bu hücrelerin çoğalması, göç, hücre döngüsü ilerlemesindeki etkileri araştırılmıştır ve ayrıca yüksek ve düşük glukoz varlığında gen ifadesi düzeyinde faklılıklarının olup olmadığı araştırılmıştır. Elde edilen bulgulara göre, kolorektal kanserin erken aşamasındaki hücrelerin kanserin geç aşamasındaki hücrelere gore daha fazla glikoza bağımlı olarak çoğaldıkları gözlemlenmiştir. Diğer yandan insülinin ve insülin-benzeri büyüme faktörlerinin kolorektal kanser hücre çoğalması üzerindeki uyarıcı etkileri normal ve yüksek glukoz koşullarında ayrı ayrı değerlendirilmiş ve bu büyüme faktörlerinin kolorektal kanserin geç evresindeki hücrelerin çoğalmasını daha fazla uyardığı ortaya konmuştur. Hücrelerin normal ve yüksek glukoz varlığında gen ifadesindeki faklılıklar değerlendirildiğinde ise IGF-I ve IGF-II mRNA ifadesi kanserin erken safhasındaki hücrelerde daha yüksek iken; insülin ve insülin-benzeri büyüme faktör reseptör mRNA ifadesi ise kanserin geç aşamasındaki hücrelerde daha yüksek olduğu gözlemlenmiştir. Bu çalışmada ayrıca kolorektal kanserini başlatan hücrelerin özelliklerini ortaya koymak için MACS yöntemi ile kök hücreler izole edilmiş ve CD133 ve CD44 ekspresyonunun kolorektal kanser ilerlemesi üzerindeki rolünü araştırmak için küre oluşturma testi kullanılarak saflaştırılan bu hücreler karakterize edilmiştir. Elde edilen sonuçlara göre, SW620 ve COLO205 hücrelerinden saflaştırılan negatif ve pozitif klonal hücrelerin küre oluşturma kapasiteleri, pozitif ve negatif klonal SW1116 ve SW480 hücrelerine kıyasla daha yüsek olduğu saptanmıştır. SW1116 alt popülasyonları en düşük küre oluşturma kapasitesine sahipken; SW620 ve COLO205 alt popülasyonları en yüksek küre oluşturma kapasitesine sahip oldukları bulunmuştur. Verilerimiz CD133 ve CD44 hücre yüzey belirteçlerin, çalışmamızda değerlendirilen kolon kanser hücre hatlarında kök hücre belirteçleri olabileceğini öne sürmektedir. Bu çalışmada ayrıca kolorektal kanser hücre hatlarından elde edilen positif ve negative klonal hücrelerde IGF sistem bileşenlerinin mRNA ifade düzeyi değerlendirilmiştir. Elde edilen sonuçlara gore positif hücrelerdeki IGF-sistem bileşenlerinin mRNA ifade düzeyi negatif hücrelere kıyasla daha yüksek olduğu bulunmuştur. Daha ileri çalışmalarla potansiyel bir terapötik hedef olarak varsayılan kolorektal kanser hücre hatlarından elde edilen bu kanser kök hücrelerin rolünün açıklığa kavuşturması amaçlanmaktadır.Öğe Modifying Effects of Glucose and Insulin/Insulin-Like Growth Factors on Colon Cancer Cells(05.07.2021) Berk, Şeyda; Janssen, Joseph A. M. J. L.; Koetsveld, Peter M. van; Dogan, Fadime; Değerli, Naci; Özcan, Servet; Kelestimur, Fahrettin; Hofland, Leo J.There are only a few experimental studies which have investigated effects of glucose alone, and glucose in combination with insulin/insulin-like growth factors (IGF) on the growth of colon cancer. In the present study, we studied in vitro in human colorectal cancer cells originating from four Dukes’ stages of colorectal cancer the effects of glucose, insulin and IGFs on proliferation, migration, cell cycle progression and gene expression of the IGF system. Growth of colon cancer cells originating from a Dukes’ stage A was glucose-dependent, whereas growth of cancer cells from Dukes’ stage B, C and D was glucose-independent. Stimulatory effects of insulin and IGFs on cell growth were observed only in colon cancer cells originating from Dukes’ stage C and D. IGF-II stimulated migration in Dukes’ stage B cells only. The growth stimulatory effects in Dukes’ stage C and D colorectal cancer cells were accompanied by G2/M arrest and associated with an increased IGF-IR/IGF-II receptor ratio. In conclusion, our in vitro data suggest that the stimulating effects of glucose, IGFs and insulin on proliferation differ between colorectal cancer cells from early and late Dukes’ stages. Stimulatory effects of glucose on proliferation appear predominantly present in stage Dukes’ stage A colorectal cancer cells, while in contrast growth factor-mediated stimulation of cell proliferation is more pronounced in Dukes’ late stage (metastasized) colorectal cancer cells. Moreover, our study suggests that a stringent glucose control may be important to control tumor growth in early stages of colorectal cancer, while inhibition of the endocrine actions of the IGFs and insulin become more important in the late (metastasized) stages of colorectal cancer to restrain growth of colon cancer cells.Öğe Myrtus communis, Pistacia vera, Arum maculatum, Ceterach officinarum, Inula oculus-christi türlerinin antioksidan, anti-mikrobiyal ve DNA koruyucu aktivitelerinin araştırılması(Cumhuriyet Üniversitesi, 2012) Berk, Şeyda; Tepe, BektaşBu çalışmada Myrtus communis, Pistacia vera, Ceterach officinarum, Arum maculatum ve Inula oculus-christi türlerinden elde edilen polar özütlerin in vitro antioksidan, antimikrobiyal ve DNA koruyucu aktiviteleri araştırılmıştır. Çalışmanın ilk aşamasında polar özütlerin antioksidan aktiviteleri; ß-karoten / linoleik asit, DPPH, indirgeme gücü kapasitesi, metal şelatlama etkisi ve fosfomolibdenyum metotları olmak üzere 5 farklı test sistemiyle belirlenmiştir. M.communis'den elde edilen polar özütün tüm antioksidan test sistemlerinde oldukça yüksek aktiviteye sahip olduğu belirlenmiştir. Ayrıca özütlerin toplam fenolik ve flavonoid bileşik miktarları da ölçülmüştür. ß-karoten / linoleik asit test sisteminde M. communis, P. vera ve C. officinarum özütleri sentetik antioksidanlardan (BHA ve BHT) daha yüksek aktivite göstermişlerdir. DPPH serbest radikal giderim testi ve indirgeme gücü kapasitelerine bakıldığında, en yüksek aktivitenin M. communis ve P. vera tarafından sergilendiği görülmektedir. Şelatlama testinde ise bitki türlerinin hiçbirisinin EDTA kadar yüksek etkinliğe ulaşamadığı tespit edilmiştir. Ancak yine de çalışılan bitkiler arasında en yüksek aktiviteye sahip olan M. communis olmuştur. Fosfomolibdenyum yönteminin sonuçları diğer aktivite test sonuçlarıyla paralel çıkmış ve en yüksek aktiviteyi M. communis göstermiştir. Özütlerin toplam fenolik ve flavonoid bileşik miktarlarını kıyasladığımızda yine en yüksek içeriğin M. communis'e ait olduğu görülmektedir. Tüm antioksidan aktivite sonuçları bir arada değerlendirildiğinde, özütlerin toplam fenolik bileşik içeriği ile antioksidan aktiviteleri arasında paralellik olduğu görülmektedir. A. maculatum haricinde diğer 4 bitki türünün UV ve H2O2 varlığında scDNA'yı koruduğu görülmektedir. Dolayısıyla çalışma kapsamında değerlendirilen söz konusu 4 bitki türünün yüksek DNA koruyucu aktiviteye sahip olduklarını söylemek mümkündür. Özütlerin antimikrobiyal aktivite sonuçlarına baktığımızda en kuvvetli antimikrobiyal aktivite gösteren bitki P. vera'dır. Bu bitkiyi M. communis ve I. oculus-christi izlemektedir.Anahtar Kelimeler: Myrtus communis, Pistacia vera, Ceterach officinarum, Arum maculatum, Inula oculus-christi, Antioksidan aktivite, Antimikrobiyal aktivite, DNA koruyucu aktiviteÖğe Selection and Validation of Potential Reference Genes for Quantitative Real-Time PCR Analysis in Blaptica Dubia (Serville, 1838) (Blattidae, Blaberidae)(2022) Karakaş, Emin Ufuk; Pektaş, Ayşe Nur; Berk, ŞeydaReverse transcription-quantitative polymerase chain reaction (RT-qPCR) is an effective, reproducible, and dependable method for evaluating and targeting expression of genes. It is very important to normalize according to stably expressed housekeeping genes in order to facilitating gene expression studies and to acquire exact and meaningful results. The purpose of this study was to identify and validate six housekeeping genes (GADPH, RPS18, ?-TUB, EF1?, ArgK and ACTB) in adults of cockroach species Blaptica dubia employing five different algorithms (geNorm, Bestkeeper, Normfinder, ?Ct method and RefFinder) to assess putative housekeeping gene expression stability. Our study also showed that the geNorm, Normfinder ?Ct method and RefFinder algorithms identified GADPH as the most stable housekeeping gene in B. dubia adults. Additioanlly, RPS18 was suggested as the most stable gene by GeNorm and BestKeeeper. ACTB has been shown to be by far the least stable of all algorithms. In addition, since there are few validation studies for reference genes in cockroaches in the literature, it is considered that it would be beneficial to increase the number of studies related with RT-qPCR on the reference genes validation under biotic and abiotic conditions in cockroaches.Öğe Selection and Validation of Potential Reference Genes for Quantitative Real-Time PCR Analysis in Blaptica Dubia (Serville, 1838) (Blattidae, Blaberidae)(Sivas Cumhuriyet University, 2022) Karakaş, Emin Ufuk; Pektaş, Ayşe Nur; Berk, ŞeydaReverse transcription-quantitative polymerase chain reaction (RT-qPCR) is an effective, reproducible, and dependable method for evaluating and targeting expression of genes. It is very important to normalize according to stably expressed housekeeping genes in order to facilitating gene expression studies and to acquire exact and meaningful results. The purpose of this study was to identify and validate six housekeeping genes (GADPH, RPS18, α-TUB, EF1α, ArgK and ACTB) in adults of cockroach species Blaptica dubia employing five different algorithms (geNorm, Bestkeeper, Normfinder, ΔCt method and RefFinder) to assess putative housekeeping gene expression stability. Our study also showed that the geNorm, Normfinder ΔCt method and RefFinder algorithms identified GADPH as the most stable housekeeping gene in B. dubia adults. Additioanlly, RPS18 was suggested as the most stable gene by GeNorm and BestKeeeper. ACTB has been shown to be by far the least stable of all algorithms. In addition, since there are few validation studies for reference genes in cockroaches in the literature, it is considered that it would be beneficial to increase the number of studies related with RT-qPCR on the reference genes validation under biotic and abiotic conditions in cockroaches.Öğe Visualization of scientific production in Caenorhabditis elegans: a bibliometric analysis (1980–2023)(BioMed Central Ltd, 2024) Berk, Şeyda; Özdemir, Serkan; Pektaş, Ayşe NurCaenorhabditis elegans (C. elegans) is a nematode and model organism whose entire genome has been mapped, which allows for easy observation of the organism’s development due to its transparent structure, and which is appealing due to its ease of crossover, ease of culture, and low cost. Despite being separated by nearly a billion years of evolution, C. elegans homologs have been identified for the vast majority of human genes and are associated with C. elegans for many biological processes such as apoptosis, cell signaling, cell cycle, cell polarity, metabolism, and aging. A detailed bibliometric study is performed here to examine publication trends in this field. Data were taken from the Web of Science database and analyzed using the bibliometric application Biblioshiny (RStudio). In terms of publication, the results indicated a gradual increase each year between 1980 and 2023. A total of 20,322 records were issued in 96 countries, the majority of which were in the USA, China, and Japan. The most prolific writers, the journals most engaged in the area, the nations, institutions, and keywords used by authors were all determined using the Web of Science database and bibliometric rules. The number of papers in the C. elegans research field is increasing exponentially, and Genetics is the journal with the highest number of articles. This study presents how research patterns have evolved throughout time. As a result, worldwide cooperation and a potential field can be developed. © The Author(s) 2024.
