SEYDA BERK | Sivas Cumhuriyet üniversitesi (original) (raw)
Papers by SEYDA BERK
Nucleosides, Nucleotides & Nucleic Acids, 2024
Bilge International Journal of Science and Technology Research, 2022
Quantitative RT-PCR (q-RT-PCR) is a powerful tool that allows large-scale analysis of very small ... more Quantitative 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.
Phytomedicine, Apr 1, 2022
BACKGROUND It is well-known that flavonoids, which can be easily obtained from many fruits and ve... more BACKGROUND It is well-known that flavonoids, which can be easily obtained from many fruits and vegetables are widely preferred in the treatment of some important diseases. Some researchers noted that these chemical compounds exhibit high inhibition effect against various cancer types. Many experimental studies proving this ability of the flavonoids with high antioxidant activity are available in the literature. PUROPOSE The main aim of this review is to summarize comprehensively anticancer properties of flavonoids against the lung cancer in the light of experimental studies and well-known theory and electronic structure principles. In this review article, more detailed and current information about the using of flavonoids in the treatment of lung cancer is presented considering theoretical and experimental approaches. STUDY DESIGN In addition to experimental studies including the anticancer effects of flavonoids, we emphasized the requirement of the well-known electronic structure principle in the development of anticancer drugs. For this aim, Conceptual Density Functional Theory should be considered as a powerful tool. Searching the databases including ScienceDirect, PubMed and Web of Science, the suitable reference papers for this project were selected. METHODS Theoretical tools like DFT and Molecular Docking provides important clues about anticancer behavior and drug properties of molecular systems. Conceptual Density Functional Theory and CDFT based electronic structure principles and rules like Hard and Soft Acid-Base Principle (HSAB), Maximum Hardness Principle, Minimum Polarizability, Minimum Electrophilicity Principles and Maximum Composite Hardness Rule introduced by one of the authors of this review are so useful to predict the mechanisms and powers of chemical systems. Especially, it cannot be ignored the success of HSAB Principle in the explanations and highlighting of biochemical interactions. RESULTS Both theoretical analysis and experimental studies confirmed that flavonoids have higher inhibition effect against lung cancer. In addition to many superior properties like anticancer activity, antimicrobial activity, antioxidant activity, antidiabetic effect of flavonoids, their toxicities are also explained with the help of published popular papers. Action modes of the mentioned compounds are given in detail. CONCLUSION The review includes detailed information about the mentioned electronic structure principles and rules and their applications in the cancer research. In addition, the epidemiology and types of lung cancer anticancer activity of flavonoids in lung cancer are explained in details.
Journal of physical chemistry and functional materials, Dec 12, 2022
Organoids are miniature forms of organs to demonstrate spatio-temporal cellular structure and tis... more Organoids 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 constructions complex that maintain various cell types and also hide the relevant organ functions in vivo, and therefore, the development of organoids in particular has reformed drug discovery, disease modeling, and developmental biology. The new biomaterials production has been important for improving of in vitro 3D patterns. Future work with biomaterials has been about the creation of hybrid polymers combining the benefits of both synthetic and natural polymers to take place of communal supplies including Matrigel and polydimethylsiloxane (PDMS). The creation of 3D culture systems has also revolutionized in vitro drug testing. Furthermore, recreating the three-dimensional tumors microenvironment and the proper regulation of cancer cells have been encouraging to develop new tumor models. Under known culture conditions, cancer cells are able to form threedimensional structures known as spheroids and self-organize to further study advances in embryonic development in 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. This review aimed to focus on studies examining advances in 3D culture systems in disease pathology modeling and new drug discovery studies, focusing on the active roles of biomaterials.
Frontiers in Oncology, 2021
There are only a few experimental studies which have investigated effects of glucose alone, and g... more 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...
Cumhuriyet Science Journal, 2023
Accurate species identification has become a precondition for accomplished biodiversity administr... more Accurate 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 b...
RECORDS OF NATURAL PRODUCTS, 2011
This study was designed to examine the in vitro antimicrobial and antioxidant activities of the e... more This study was designed to examine the in vitro antimicrobial and antioxidant activities of the essential oil of T. boveii and T. hyemalis. According to the results of GC-EIMS analysis, essential oils were found rich in phenols and hydrocarbons. p-cymene, thymol and carvacrol were mainly found as the major compounds for the essential oils. Both plant species showed remarkable antioxidant activity in all test systems except chelating effect. In the case of antimicrobial activity, the oils showed remarkable growth inhibition against the tested microorganism except K. pneumoniae, P. aeruginosa, L. monocytogenes, P. fluorescens.
Experimental Parasitology, May 1, 2012
In some patients, complete treatment of amoebic keratitis is difficult because of the resistance ... more In some patients, complete treatment of amoebic keratitis is difficult because of the resistance of cysts to therapeutic agents. The aim of this study was to evaluate the in vitro amoebicidal activity of methanolic extracts of Origanum syriacum and Origanum laevigatum. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellanii trophozoites and cysts were decreased. Both extracts showed a time and dose dependent amoebicidal action on the trophozoites and cysts. Of the extracts tested, O. syriacum showed the stronger amoebicidal effect on the trophozoites and cysts. In the presence of 32 mg/ml extract, no viable trophozoites were observed within third hour. The extract was also found effective against the cysts within 24th hour. In the case of O. laevigatum, no viable trophozoites were observed within 72nd hour at the concentrations of 16 and 32 mg/ml. As expected, cysts were found more resistant to the extracts than the trophozoites.
Parasitology Research, Jan 4, 2012
Amebiasis is a severe illness caused by Entamoebachistolytica. The aim of this study is to evalua... more Amebiasis is a severe illness caused by Entamoebachistolytica. The aim of this study is to evaluate the in vitro amebicidal activity of the rhizomes and aerial parts of Allium sivasicum, an endemic plant species from the flora of Turkey. Both extracts showed a time-and dose-dependent amebicidal action on the trophozoites. Among the extracts tested, rhizomes of A. sivasicum showed the strongest amebicidal effect on the trophozoites. In the presence of the rhizome extract at 2.0 mg/ml concentration, all of the trophozoites available in media have completely been killed within the 72nd hour. At 4.0 mg/ml extract concentration, all of the trophozoites available in media have completely been killed by the rhizome extract from the time of 24th hour. At 32.0 mg/ml extract concentration, 73.7% of the trophozoites were successfully killed by the extract within the first experimental hour. Aerial part extract at 4.0 mg/ml concentration completely killed the trophozoited within the 48th hour of the experimental procedure. At 8.0 mg/ml extract concentration, all of the trophozoites available in media have completely been killed by the aerial part extract from the time of 24th hour. At 32.0 mg/ml extract concentration, 67.7% of the trophozoites were successfully killed by the extract within the first experimental hour. These results suggest that the plant species evaluated here is a potential therapeutic drug for the treatment of Entamoeba infections, but it still needs to be evaluated quantitatively for determining the active phytochemicals.
Parasitology Research, Jul 7, 2011
The aim of this study is to evaluate the in vitro amoebicidal activity of the aqueous extracts of... more The aim of this study is to evaluate the in vitro amoebicidal activity of the aqueous extracts of Pastinaca armenea and Inula oculus-christi from Turkey. In the presence of aqueous extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellanii trophozoites and cysts were decreased during the experimental process. Both extracts showed a time- and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, I. oculus showed the strongest amoebicidal effect on the trophozoites and cysts. In the presence of 32.00 mg/ml extract solution in the media, no viable trophozoites were determined from the time of 24 h. Moreover, in the presence of 16.00 mg/ml I. oculus-christi extract, no viable trophozoites were detected in 72 h of the experiment. Effectiveness of I. oculus-christi extract was found moderate against the cysts. In the presence of 32.00 mg/ml extract, only 25.3% of the total cysts were killed effectively. In the case of P. armenea, 40.3% and 23.0% of the trophozoites and cysts were killed in the presence of 32.00 mg/ml extract at the end of the experimental process (72 h), respectively.
Parasitology Research, Oct 26, 2011
Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts,... more Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts, which are less susceptible than trophozoites to the usual treatments. The aim of this study is to evaluate the in vitro amoebicidal activity of the methanolic extracts of Teucrium polium and Teucrium chamaedrys. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellani trophozoites and cysts were decreased during the experimental process. Both extracts showed time-and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, T. chamaedrys showed the strongest amoebicidal effect on the trophozoites. In the presence of 16 mg/ml or above extract concentrations, no viable trophozoites were observed within 48 h. In the case of T. polium, no viable trophozoites were observed within 48 h at 32 mg/ml concentration. As expected, cysts were found more resistant to the extracts than the trophozoites.
Parasitology Research, Dec 9, 2011
Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts,... more Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts, which are less susceptible than trophozoites to the usual treatments. The aim of this study is to evaluate the in vitro amoebicidal activity of the methanolic extracts of Satureja cuneifolia and Melissa officinalis. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoe castellanii trophozoites and cysts were decreased during the experimental process. Both extracts showed a time-and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, S. cuneifolia showed the strongest amoebicidal effect on the trophozoites and cysts. In the presence of 32 mg/ml extract, no viable trophozoites were observed within 24 h. At the same concentration value, the extract was found effective against the cysts at a rate of 46.3% within 72 h of the experimental process. At 16 mg/ml extract concentration, no viable trophozoites were also observed in the 24th hour of the experiment. At the end of the experimental process, 34.7% of the cysts were killed by the extract. M. officinalis showed moderate amoebicidal effect. At the concentration of 32 mg/ml, 44.3% and 30.0% of the trophozoites and cysts were killed by the extract, respectively. Results obtained from these concentration values were found statistically different in terms of their actions both on trophozoites and cysts (p<0.05).
Parasitology Research, May 28, 2011
Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts,... more Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts, which is less susceptible than trophozoites to the usual treatments. The aim of this study is to evaluate the in vitro amoebicidal activity of the methanolic extracts of Peucedanum caucasicum, Peucedanum palimbioides, Peucedanum chryseum, and Peucedanum longibracteolatum, which are endemic in Turkish flora except P. caucasicum. Extracts were evaluated for their amoebicidal activities using an inverted light microscope. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellani trophozoites and cysts were determined during the experimental process (72nd hour). All of the extracts showed a time and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, P. longibracteolatum showed the strongest amoebicidal effect on the trophozoites and cysts. In the case of 32 mg/ml concentration of extract, no viable trophozoites or cysts were determined between 24th and 72nd hour. Similar results were obtained from the extract at 16.0 mg/ml concentration against trophozoites. At this concentration value, number of viable cysts was determined as 10.6 ± 2.1 in the 24th hour. In the presence of 8.0 mg/ml extract solution, no viable trophozoites were determined in the 48th hour. At the same concentration, 51% of the cysts were killed by the extract in the 72nd hour. As expected, cysts were found more resistant to the extracts than the trophozoites.
Parasitology Research, 2012
Amebiasis is a severe illness caused by Entamoebachistolytica. The aim of this study is to evalua... more Amebiasis is a severe illness caused by Entamoebachistolytica. The aim of this study is to evaluate the in vitro amebicidal activity of the rhizomes and aerial parts of Allium sivasicum, an endemic plant species from the flora of Turkey. Both extracts showed a time-and dose-dependent amebicidal action on the trophozoites. Among the extracts tested, rhizomes of A. sivasicum showed the strongest amebicidal effect on the trophozoites. In the presence of the rhizome extract at 2.0 mg/ml concentration, all of the trophozoites available in media have completely been killed within the 72nd hour. At 4.0 mg/ml extract concentration, all of the trophozoites available in media have completely been killed by the rhizome extract from the time of 24th hour. At 32.0 mg/ml extract concentration, 73.7% of the trophozoites were successfully killed by the extract within the first experimental hour. Aerial part extract at 4.0 mg/ml concentration completely killed the trophozoited within the 48th hour of the experimental procedure. At 8.0 mg/ml extract concentration, all of the trophozoites available in media have completely been killed by the aerial part extract from the time of 24th hour. At 32.0 mg/ml extract concentration, 67.7% of the trophozoites were successfully killed by the extract within the first experimental hour. These results suggest that the plant species evaluated here is a potential therapeutic drug for the treatment of Entamoeba infections, but it still needs to be evaluated quantitatively for determining the active phytochemicals.
Parasitology Research, 2011
Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts,... more Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts, which are less susceptible than trophozoites to the usual treatments. The aim of this study is to evaluate the in vitro amoebicidal activity of the methanolic extracts of Satureja cuneifolia and Melissa officinalis. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoe castellanii trophozoites and cysts were decreased during the experimental process. Both extracts showed a time-and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, S. cuneifolia showed the strongest amoebicidal effect on the trophozoites and cysts. In the presence of 32 mg/ml extract, no viable trophozoites were observed within 24 h. At the same concentration value, the extract was found effective against the cysts at a rate of 46.3% within 72 h of the experimental process. At 16 mg/ml extract concentration, no viable trophozoites were also observed in the 24th hour of the experiment. At the end of the experimental process, 34.7% of the cysts were killed by the extract. M. officinalis showed moderate amoebicidal effect. At the concentration of 32 mg/ml, 44.3% and 30.0% of the trophozoites and cysts were killed by the extract, respectively. Results obtained from these concentration values were found statistically different in terms of their actions both on trophozoites and cysts (p<0.05).
Parasitology Research, 2011
The aim of this study is to evaluate the in vitro amoebicidal activity of the aqueous extracts of... more The aim of this study is to evaluate the in vitro amoebicidal activity of the aqueous extracts of Pastinaca armenea and Inula oculus-christi from Turkey. In the presence of aqueous extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellanii trophozoites and cysts were decreased during the experimental process. Both extracts showed a time- and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, I. oculus showed the strongest amoebicidal effect on the trophozoites and cysts. In the presence of 32.00 mg/ml extract solution in the media, no viable trophozoites were determined from the time of 24 h. Moreover, in the presence of 16.00 mg/ml I. oculus-christi extract, no viable trophozoites were detected in 72 h of the experiment. Effectiveness of I. oculus-christi extract was found moderate against the cysts. In the presence of 32.00 mg/ml extract, only 25.3% of the total cysts were killed effectively. In the case of P. armenea, 40.3% and 23.0% of the trophozoites and cysts were killed in the presence of 32.00 mg/ml extract at the end of the experimental process (72 h), respectively.
Parasitology Research, 2011
Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts,... more Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts, which are less susceptible than trophozoites to the usual treatments. The aim of this study is to evaluate the in vitro amoebicidal activity of the methanolic extracts of Teucrium polium and Teucrium chamaedrys. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellani trophozoites and cysts were decreased during the experimental process. Both extracts showed time-and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, T. chamaedrys showed the strongest amoebicidal effect on the trophozoites. In the presence of 16 mg/ml or above extract concentrations, no viable trophozoites were observed within 48 h. In the case of T. polium, no viable trophozoites were observed within 48 h at 32 mg/ml concentration. As expected, cysts were found more resistant to the extracts than the trophozoites.
Experimental Parasitology, 2012
In some patients, complete treatment of amoebic keratitis is difficult because of the resistance ... more In some patients, complete treatment of amoebic keratitis is difficult because of the resistance of cysts to therapeutic agents. The aim of this study was to evaluate the in vitro amoebicidal activity of methanolic extracts of Origanum syriacum and Origanum laevigatum. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellanii trophozoites and cysts were decreased. Both extracts showed a time and dose dependent amoebicidal action on the trophozoites and cysts. Of the extracts tested, O. syriacum showed the stronger amoebicidal effect on the trophozoites and cysts. In the presence of 32 mg/ml extract, no viable trophozoites were observed within third hour. The extract was also found effective against the cysts within 24th hour. In the case of O. laevigatum, no viable trophozoites were observed within 72nd hour at the concentrations of 16 and 32 mg/ml. As expected, cysts were found more resistant to the extracts than the trophozoites.
Cumhuriyet Science Journal, 2022
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is an effective, reproduci... more Reverse 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...
Nucleosides, Nucleotides & Nucleic Acids, 2024
Bilge International Journal of Science and Technology Research, 2022
Quantitative RT-PCR (q-RT-PCR) is a powerful tool that allows large-scale analysis of very small ... more Quantitative 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.
Phytomedicine, Apr 1, 2022
BACKGROUND It is well-known that flavonoids, which can be easily obtained from many fruits and ve... more BACKGROUND It is well-known that flavonoids, which can be easily obtained from many fruits and vegetables are widely preferred in the treatment of some important diseases. Some researchers noted that these chemical compounds exhibit high inhibition effect against various cancer types. Many experimental studies proving this ability of the flavonoids with high antioxidant activity are available in the literature. PUROPOSE The main aim of this review is to summarize comprehensively anticancer properties of flavonoids against the lung cancer in the light of experimental studies and well-known theory and electronic structure principles. In this review article, more detailed and current information about the using of flavonoids in the treatment of lung cancer is presented considering theoretical and experimental approaches. STUDY DESIGN In addition to experimental studies including the anticancer effects of flavonoids, we emphasized the requirement of the well-known electronic structure principle in the development of anticancer drugs. For this aim, Conceptual Density Functional Theory should be considered as a powerful tool. Searching the databases including ScienceDirect, PubMed and Web of Science, the suitable reference papers for this project were selected. METHODS Theoretical tools like DFT and Molecular Docking provides important clues about anticancer behavior and drug properties of molecular systems. Conceptual Density Functional Theory and CDFT based electronic structure principles and rules like Hard and Soft Acid-Base Principle (HSAB), Maximum Hardness Principle, Minimum Polarizability, Minimum Electrophilicity Principles and Maximum Composite Hardness Rule introduced by one of the authors of this review are so useful to predict the mechanisms and powers of chemical systems. Especially, it cannot be ignored the success of HSAB Principle in the explanations and highlighting of biochemical interactions. RESULTS Both theoretical analysis and experimental studies confirmed that flavonoids have higher inhibition effect against lung cancer. In addition to many superior properties like anticancer activity, antimicrobial activity, antioxidant activity, antidiabetic effect of flavonoids, their toxicities are also explained with the help of published popular papers. Action modes of the mentioned compounds are given in detail. CONCLUSION The review includes detailed information about the mentioned electronic structure principles and rules and their applications in the cancer research. In addition, the epidemiology and types of lung cancer anticancer activity of flavonoids in lung cancer are explained in details.
Journal of physical chemistry and functional materials, Dec 12, 2022
Organoids are miniature forms of organs to demonstrate spatio-temporal cellular structure and tis... more Organoids 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 constructions complex that maintain various cell types and also hide the relevant organ functions in vivo, and therefore, the development of organoids in particular has reformed drug discovery, disease modeling, and developmental biology. The new biomaterials production has been important for improving of in vitro 3D patterns. Future work with biomaterials has been about the creation of hybrid polymers combining the benefits of both synthetic and natural polymers to take place of communal supplies including Matrigel and polydimethylsiloxane (PDMS). The creation of 3D culture systems has also revolutionized in vitro drug testing. Furthermore, recreating the three-dimensional tumors microenvironment and the proper regulation of cancer cells have been encouraging to develop new tumor models. Under known culture conditions, cancer cells are able to form threedimensional structures known as spheroids and self-organize to further study advances in embryonic development in 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. This review aimed to focus on studies examining advances in 3D culture systems in disease pathology modeling and new drug discovery studies, focusing on the active roles of biomaterials.
Frontiers in Oncology, 2021
There are only a few experimental studies which have investigated effects of glucose alone, and g... more 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...
Cumhuriyet Science Journal, 2023
Accurate species identification has become a precondition for accomplished biodiversity administr... more Accurate 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 b...
RECORDS OF NATURAL PRODUCTS, 2011
This study was designed to examine the in vitro antimicrobial and antioxidant activities of the e... more This study was designed to examine the in vitro antimicrobial and antioxidant activities of the essential oil of T. boveii and T. hyemalis. According to the results of GC-EIMS analysis, essential oils were found rich in phenols and hydrocarbons. p-cymene, thymol and carvacrol were mainly found as the major compounds for the essential oils. Both plant species showed remarkable antioxidant activity in all test systems except chelating effect. In the case of antimicrobial activity, the oils showed remarkable growth inhibition against the tested microorganism except K. pneumoniae, P. aeruginosa, L. monocytogenes, P. fluorescens.
Experimental Parasitology, May 1, 2012
In some patients, complete treatment of amoebic keratitis is difficult because of the resistance ... more In some patients, complete treatment of amoebic keratitis is difficult because of the resistance of cysts to therapeutic agents. The aim of this study was to evaluate the in vitro amoebicidal activity of methanolic extracts of Origanum syriacum and Origanum laevigatum. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellanii trophozoites and cysts were decreased. Both extracts showed a time and dose dependent amoebicidal action on the trophozoites and cysts. Of the extracts tested, O. syriacum showed the stronger amoebicidal effect on the trophozoites and cysts. In the presence of 32 mg/ml extract, no viable trophozoites were observed within third hour. The extract was also found effective against the cysts within 24th hour. In the case of O. laevigatum, no viable trophozoites were observed within 72nd hour at the concentrations of 16 and 32 mg/ml. As expected, cysts were found more resistant to the extracts than the trophozoites.
Parasitology Research, Jan 4, 2012
Amebiasis is a severe illness caused by Entamoebachistolytica. The aim of this study is to evalua... more Amebiasis is a severe illness caused by Entamoebachistolytica. The aim of this study is to evaluate the in vitro amebicidal activity of the rhizomes and aerial parts of Allium sivasicum, an endemic plant species from the flora of Turkey. Both extracts showed a time-and dose-dependent amebicidal action on the trophozoites. Among the extracts tested, rhizomes of A. sivasicum showed the strongest amebicidal effect on the trophozoites. In the presence of the rhizome extract at 2.0 mg/ml concentration, all of the trophozoites available in media have completely been killed within the 72nd hour. At 4.0 mg/ml extract concentration, all of the trophozoites available in media have completely been killed by the rhizome extract from the time of 24th hour. At 32.0 mg/ml extract concentration, 73.7% of the trophozoites were successfully killed by the extract within the first experimental hour. Aerial part extract at 4.0 mg/ml concentration completely killed the trophozoited within the 48th hour of the experimental procedure. At 8.0 mg/ml extract concentration, all of the trophozoites available in media have completely been killed by the aerial part extract from the time of 24th hour. At 32.0 mg/ml extract concentration, 67.7% of the trophozoites were successfully killed by the extract within the first experimental hour. These results suggest that the plant species evaluated here is a potential therapeutic drug for the treatment of Entamoeba infections, but it still needs to be evaluated quantitatively for determining the active phytochemicals.
Parasitology Research, Jul 7, 2011
The aim of this study is to evaluate the in vitro amoebicidal activity of the aqueous extracts of... more The aim of this study is to evaluate the in vitro amoebicidal activity of the aqueous extracts of Pastinaca armenea and Inula oculus-christi from Turkey. In the presence of aqueous extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellanii trophozoites and cysts were decreased during the experimental process. Both extracts showed a time- and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, I. oculus showed the strongest amoebicidal effect on the trophozoites and cysts. In the presence of 32.00 mg/ml extract solution in the media, no viable trophozoites were determined from the time of 24 h. Moreover, in the presence of 16.00 mg/ml I. oculus-christi extract, no viable trophozoites were detected in 72 h of the experiment. Effectiveness of I. oculus-christi extract was found moderate against the cysts. In the presence of 32.00 mg/ml extract, only 25.3% of the total cysts were killed effectively. In the case of P. armenea, 40.3% and 23.0% of the trophozoites and cysts were killed in the presence of 32.00 mg/ml extract at the end of the experimental process (72 h), respectively.
Parasitology Research, Oct 26, 2011
Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts,... more Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts, which are less susceptible than trophozoites to the usual treatments. The aim of this study is to evaluate the in vitro amoebicidal activity of the methanolic extracts of Teucrium polium and Teucrium chamaedrys. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellani trophozoites and cysts were decreased during the experimental process. Both extracts showed time-and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, T. chamaedrys showed the strongest amoebicidal effect on the trophozoites. In the presence of 16 mg/ml or above extract concentrations, no viable trophozoites were observed within 48 h. In the case of T. polium, no viable trophozoites were observed within 48 h at 32 mg/ml concentration. As expected, cysts were found more resistant to the extracts than the trophozoites.
Parasitology Research, Dec 9, 2011
Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts,... more Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts, which are less susceptible than trophozoites to the usual treatments. The aim of this study is to evaluate the in vitro amoebicidal activity of the methanolic extracts of Satureja cuneifolia and Melissa officinalis. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoe castellanii trophozoites and cysts were decreased during the experimental process. Both extracts showed a time-and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, S. cuneifolia showed the strongest amoebicidal effect on the trophozoites and cysts. In the presence of 32 mg/ml extract, no viable trophozoites were observed within 24 h. At the same concentration value, the extract was found effective against the cysts at a rate of 46.3% within 72 h of the experimental process. At 16 mg/ml extract concentration, no viable trophozoites were also observed in the 24th hour of the experiment. At the end of the experimental process, 34.7% of the cysts were killed by the extract. M. officinalis showed moderate amoebicidal effect. At the concentration of 32 mg/ml, 44.3% and 30.0% of the trophozoites and cysts were killed by the extract, respectively. Results obtained from these concentration values were found statistically different in terms of their actions both on trophozoites and cysts (p<0.05).
Parasitology Research, May 28, 2011
Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts,... more Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts, which is less susceptible than trophozoites to the usual treatments. The aim of this study is to evaluate the in vitro amoebicidal activity of the methanolic extracts of Peucedanum caucasicum, Peucedanum palimbioides, Peucedanum chryseum, and Peucedanum longibracteolatum, which are endemic in Turkish flora except P. caucasicum. Extracts were evaluated for their amoebicidal activities using an inverted light microscope. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellani trophozoites and cysts were determined during the experimental process (72nd hour). All of the extracts showed a time and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, P. longibracteolatum showed the strongest amoebicidal effect on the trophozoites and cysts. In the case of 32 mg/ml concentration of extract, no viable trophozoites or cysts were determined between 24th and 72nd hour. Similar results were obtained from the extract at 16.0 mg/ml concentration against trophozoites. At this concentration value, number of viable cysts was determined as 10.6 ± 2.1 in the 24th hour. In the presence of 8.0 mg/ml extract solution, no viable trophozoites were determined in the 48th hour. At the same concentration, 51% of the cysts were killed by the extract in the 72nd hour. As expected, cysts were found more resistant to the extracts than the trophozoites.
Parasitology Research, 2012
Amebiasis is a severe illness caused by Entamoebachistolytica. The aim of this study is to evalua... more Amebiasis is a severe illness caused by Entamoebachistolytica. The aim of this study is to evaluate the in vitro amebicidal activity of the rhizomes and aerial parts of Allium sivasicum, an endemic plant species from the flora of Turkey. Both extracts showed a time-and dose-dependent amebicidal action on the trophozoites. Among the extracts tested, rhizomes of A. sivasicum showed the strongest amebicidal effect on the trophozoites. In the presence of the rhizome extract at 2.0 mg/ml concentration, all of the trophozoites available in media have completely been killed within the 72nd hour. At 4.0 mg/ml extract concentration, all of the trophozoites available in media have completely been killed by the rhizome extract from the time of 24th hour. At 32.0 mg/ml extract concentration, 73.7% of the trophozoites were successfully killed by the extract within the first experimental hour. Aerial part extract at 4.0 mg/ml concentration completely killed the trophozoited within the 48th hour of the experimental procedure. At 8.0 mg/ml extract concentration, all of the trophozoites available in media have completely been killed by the aerial part extract from the time of 24th hour. At 32.0 mg/ml extract concentration, 67.7% of the trophozoites were successfully killed by the extract within the first experimental hour. These results suggest that the plant species evaluated here is a potential therapeutic drug for the treatment of Entamoeba infections, but it still needs to be evaluated quantitatively for determining the active phytochemicals.
Parasitology Research, 2011
Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts,... more Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts, which are less susceptible than trophozoites to the usual treatments. The aim of this study is to evaluate the in vitro amoebicidal activity of the methanolic extracts of Satureja cuneifolia and Melissa officinalis. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoe castellanii trophozoites and cysts were decreased during the experimental process. Both extracts showed a time-and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, S. cuneifolia showed the strongest amoebicidal effect on the trophozoites and cysts. In the presence of 32 mg/ml extract, no viable trophozoites were observed within 24 h. At the same concentration value, the extract was found effective against the cysts at a rate of 46.3% within 72 h of the experimental process. At 16 mg/ml extract concentration, no viable trophozoites were also observed in the 24th hour of the experiment. At the end of the experimental process, 34.7% of the cysts were killed by the extract. M. officinalis showed moderate amoebicidal effect. At the concentration of 32 mg/ml, 44.3% and 30.0% of the trophozoites and cysts were killed by the extract, respectively. Results obtained from these concentration values were found statistically different in terms of their actions both on trophozoites and cysts (p<0.05).
Parasitology Research, 2011
The aim of this study is to evaluate the in vitro amoebicidal activity of the aqueous extracts of... more The aim of this study is to evaluate the in vitro amoebicidal activity of the aqueous extracts of Pastinaca armenea and Inula oculus-christi from Turkey. In the presence of aqueous extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellanii trophozoites and cysts were decreased during the experimental process. Both extracts showed a time- and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, I. oculus showed the strongest amoebicidal effect on the trophozoites and cysts. In the presence of 32.00 mg/ml extract solution in the media, no viable trophozoites were determined from the time of 24 h. Moreover, in the presence of 16.00 mg/ml I. oculus-christi extract, no viable trophozoites were detected in 72 h of the experiment. Effectiveness of I. oculus-christi extract was found moderate against the cysts. In the presence of 32.00 mg/ml extract, only 25.3% of the total cysts were killed effectively. In the case of P. armenea, 40.3% and 23.0% of the trophozoites and cysts were killed in the presence of 32.00 mg/ml extract at the end of the experimental process (72 h), respectively.
Parasitology Research, 2011
Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts,... more Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts, which are less susceptible than trophozoites to the usual treatments. The aim of this study is to evaluate the in vitro amoebicidal activity of the methanolic extracts of Teucrium polium and Teucrium chamaedrys. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellani trophozoites and cysts were decreased during the experimental process. Both extracts showed time-and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, T. chamaedrys showed the strongest amoebicidal effect on the trophozoites. In the presence of 16 mg/ml or above extract concentrations, no viable trophozoites were observed within 48 h. In the case of T. polium, no viable trophozoites were observed within 48 h at 32 mg/ml concentration. As expected, cysts were found more resistant to the extracts than the trophozoites.
Experimental Parasitology, 2012
In some patients, complete treatment of amoebic keratitis is difficult because of the resistance ... more In some patients, complete treatment of amoebic keratitis is difficult because of the resistance of cysts to therapeutic agents. The aim of this study was to evaluate the in vitro amoebicidal activity of methanolic extracts of Origanum syriacum and Origanum laevigatum. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoeba castellanii trophozoites and cysts were decreased. Both extracts showed a time and dose dependent amoebicidal action on the trophozoites and cysts. Of the extracts tested, O. syriacum showed the stronger amoebicidal effect on the trophozoites and cysts. In the presence of 32 mg/ml extract, no viable trophozoites were observed within third hour. The extract was also found effective against the cysts within 24th hour. In the case of O. laevigatum, no viable trophozoites were observed within 72nd hour at the concentrations of 16 and 32 mg/ml. As expected, cysts were found more resistant to the extracts than the trophozoites.
Cumhuriyet Science Journal, 2022
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is an effective, reproduci... more Reverse 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...