Haydar Bağiş - Academia.edu (original) (raw)

Papers by Haydar Bağiş

Research paper thumbnail of Differential expression of long non-coding RNAs during genotoxic stress-induced apoptosis in HeLa and MCF-7 cells

Clinical and Experimental Medicine, 2012

Long non-coding RNAs (lncRNAs) are emerging as new players in cancer as they are implicated in di... more Long non-coding RNAs (lncRNAs) are emerging as new players in cancer as they are implicated in diverse biological processes and aberrantly expressed in a variety of human cancers. No data are available on their function under genotoxic stress-induced apoptosis. In this work, we assessed the behavior of some candidate lncRNAs (HOTAIR, MALAT1, TUG1, lincRNA-p21, GAS5, MEG3, PANDA, UCA1, ANRIL, and CCND1) during DNA damage-induced cell death in HeLa and caspase-3-deficient MCF-7 cells using bleomycin (BLM) and γ-radiation to induce DNA damage. Cells were incubated in the presence of BLM for 24 h or irradiated. Apoptosis was analyzed by measurement of oligonucleosomal fragmentation of nuclear DNA. Our results reveal that basal RNA expression levels as well as the changes in the lncRNA expression rates during genotoxic stress-induced apoptosis were cell-type and/or DNA-damaging agent-specific. Generally, we found that some of the RNA molecules (HOTAIR and MALAT1) are down-regulated while many of them (lincRNA-p21, GAS5, MEG3, ANRIL, and ncRNA-CCND1) are up-regulated and some others (TUG1, UCA1, and PANDA) not affected. The decline in the expression of HOTAIR (approx. twofold, p < 0.01) and MALAT1 (approx 1.6-fold, p < 0.01) was clearly evident in BLM-treated HeLa and MCF cells (only HOTAIR, fivefold, p < 0.01). For lincRNA-p21, ncRNA-CCND1, and MEG3, a similar up-regulation pattern was obvious in both cell lines where the increase was generally more pronounced in BLM-treated cells. Interestingly, the induction of ANRIL and GAS5 was mainly restricted to irradiated cells. In conclusion, our findings reveal a differential regulation of individual lncRNAs during genotoxic stress-induced apoptosis.

Research paper thumbnail of Cryogenic effect of antifreeze protein on transgenic mouse ovaries and the production of live offspring by orthotopic transplantation of cryopreserved mouse ovaries

Molecular Reproduction and Development, 2008

The purpose of the present study was to evaluate the cryogenic effect of antifreeze protein (AFP)... more The purpose of the present study was to evaluate the cryogenic effect of antifreeze protein (AFP) on transgenic mouse ovaries which is expressed AFP type III from Ocean pout and the production of live offspring by orthotopic transplantation of cryopreserved mouse ovaries. In this study, whole transgenic and nontransgenic mouse ovaries were vitrified with 20% DMSO and 20% EG in M2 medium supplemented with 0.5 M sucrose. All vitrified and toxicity control and fresh ovaries were transplanted orthotopically into ovariectomized recipients bilaterally. For fresh ovaries transplantation, 5 mice delivered litters of 18 and 19 live pups in first and second matings, respectively. For toxicity control of chemicals, 6 mice delivered litters of 22 and 23 live pups. For nontransgenic mouse ovaries (vitrified) transplantation, 7 mice delivered litters of 22 and 23 live pups. For transgenic mouse ovaries (vitrified) transplantation, 10 mice delivered litters of 35 and 37 live pups. Litter sizes from pups of freshly transplanted ovaries were not significantly different from AFP-transplanted transgenic ovaries but those from nontransgenic-transplanted ovaries were significantly different from the AFP-transplanted transgenic ovaries group (P < 0.05). In this study, for the first time, it was shown that the ovarian tissue of AFP transgenic mice was protected from cryopreservation by vitrification. These results demonstrate that a normal reproductive lifespan can be restored by orthotopic transplantation of AFP transgenic-vitrified ovary. Mol. Reprod. Dev. 75: 608-613,

Research paper thumbnail of Investigation of antifreeze protein (AFP) expression in oocytes and embryos of transgenic mice with carrying AFP gene by immunohistochemical staining

Research paper thumbnail of Cryogenic effect of fish antifreeze protein (AFP) on one-cell stage transgenic mouse embryos by vitrification

Research paper thumbnail of 177 Gene Expression Profiles of in Vitro- and in Vivo-Derived Bovine Embryos

Reproduction, Fertility and Development, 2011

Microarray technology is one of the most powerful tools for gene expression profiling in animal s... more Microarray technology is one of the most powerful tools for gene expression profiling in animal sciences. The objectives of this study were to determine the effect of vitrification on gene expression in in vitro- and in vivo-derived bovine embryos, and to identify differential mRNA expression patterns between embryos produced by in vivo v. in vitro conditions. Three pools of in vivo- and in vitro-derived blastocyst-stage embryos were used for microarray analysis. Total RNA was isolated using the PicoPure RNA Isolation Kit (Arcturus Bioscience, Mountain View, CA). Bovine ovarian tissue total RNA was used as the reference. Total RNA samples were amplified using an Ovation® Pico WTA System (NuGEN Technologies, San Carlos, CA). The bovine 16 846-member microarrays spotted with 70-mer oligonucleotides were purchased from the Bovine Genomics Laboratory, University of Missouri. Amplified cDNA samples were labeled with Alexa Fluor 647 and 546 dyes (Molecular Probes, Eugene, OR), respectively. Combined, labeled samples were dried and resuspended in hybridization buffer containing 50% formamide (vol/vol), 5× SSC, and 0.1% sodium dodecyl sulfate (wt/vol). After denaturation and cooling, cDNA was applied onto a microarray slide. Microarrays were hybridized overnight at 42°C. Following hybridization, the slides were washed with different stringency buffers and water. After drying by centrifugation, the arrays were scanned on a GenePix 4000B scanner (Axon Instruments, Union City, CA). GenePix Pro4.1 software was used for griding and analysis of spot intensities. Good-quality spots were analyzed using the GeneSpring 7.3 software (Agilent Technologies, Inc., CA, Santa Clara, CA). The data were normalized per spot and per array by Lowess normalization. When comparing two treatments, the Welch t-test with Benjamini and Hochberg multiple testing correction was performed to determine the differentially expressed genes between embryo groups. Microarray experiments were performed in 3 biological and 2 technical replicates for all embryo samples. Differentially expressed genes between all embryo groups were identified. The DAVID Functional Annotation Tool was used to analyze the genes that were differentially expressed. The DAVID Functional Annotation Tool determined the co-occurrence probability and provided gene-GO term enrichment analysis to highlight the most relevant GO terms associated with a given gene list. Differentially expressed Kyoto Encyclopedia of Genes and Genomes pathways are as follows: Ribosome, oxidative phosphorylation, spliceosome, and oocyte meiosis were significantly upregulated in the fresh embryos, whereas sphingolipid and purine metabolism was the upregulated in the vitrified in vitro-derived embryos. Gene expression was very similar between fresh and vitrified in vivo-derived, as opposed to in vitro-derived, embryos. This study was funded by the TUBITAK (Project no. KAMAG107G027) and startup funds to Yuksel Agca at the University of Missouri.

Research paper thumbnail of İki farklı genin Güçlendirilmiş Yeşil Floresan protein geni İnsan gamma interferon geni ayrı ayrı veya birlikte mikroenjeksiyonunun transgenik fare eldesi üzerine etkilerinin araştırılması

Sunulan çalışmada hIFN-γ ve EGFP gen konstraktlarının farklı konsantrasyonları birlikte ve ayrı a... more Sunulan çalışmada hIFN-γ ve EGFP gen konstraktlarının farklı konsantrasyonları birlikte ve ayrı ayrı pronüklear safhadaki fare embriyolarına mikroenjekte edilmiştir. Mikroenjeksiyon deneyleri aktarılan gen konstraktlarının yalnız ve/veya birlikte aktarımlarına göre üç farklı deney grubu çalışılmıştır. I.Deney Grubunda hIFN-γ ve EGFP genleri birlikte mikroenjekte edilmiş, aktarımlar sonucunda toplam 39 yavru doğmuştur. Yapılan moleküler analizlerde toplam üç yavrunun transgenik olduğu belirlenmiştir. Üç transgenik yavrudan iki'si EGFP transgenik, bir tanesi ise hIFN-γ transgeniktir. II. Deney Grubunda yalnız hIFN-γ geni mikroenjekte edilmiş, aktarımlar sonucunda toplam 21 yavru doğmuştur. Yapılan moleküler analizlerde toplam iki yavrunun hIFN-γ transgenik olduğu belirlenmiştir. III.Deney Grubunda yalnız EGFP geni mikroenjekte edilmiş, aktarımlar sonucunda toplam beş yavru doğmuştur. Bu yavrulardan elde edilen DNA'lar ile yapılan moleküler analizlerde transgenik yavruya rastlanmamıştır. Sunulan çalışma da elde edilen sonuçlar ile iki farklı genin birlikte mikroenjeksiyonu sonunda doğan yavruların transgenik olma yüzdelerinin yüksek olduğu ortaya konmuştur. Sunulan çalışmada geliştirilen protokolün transgenik fare üretim çalışmalarında uygulanması durumunda; iki farklı geni ayrı ayrı veya birlikte taşıyan transgenik fare hatları elde edilebilecek, böylece ekonomi ve zaman açısından tasarruf sağlanabilecektir.

Research paper thumbnail of The Effect of Solid Surface Vitrification (SSV) Versus Classic Vitrification Technique on Survive Rate of in vitro Produced Bovine Blastocysts

Research paper thumbnail of Optimal Method of Mouse Blastomere Biopsy: In vitro Developmental Potential of the Biopsied Embryo to Blastocyst Stage after Aspirated Eight-Cell Mouse Embryos

Journal of Animal and Veterinary Advances, 2011

Research paper thumbnail of Clinical and molecular evaluation of MEFV gene variants in the Turkish population: a study by the National Genetics Consortium

Functional & Integrative Genomics, 2022

Familial Mediterranean fever (FMF) is a monogenic autoinflammatory disorder with recurrent fever,... more Familial Mediterranean fever (FMF) is a monogenic autoinflammatory disorder with recurrent fever, abdominal pain, serositis, articular manifestations, erysipelas-like erythema, and renal complications as its main features. Caused by the mutations in the MEditerranean FeVer (MEFV) gene, it mainly affects people of Mediterranean descent with a higher incidence in the Turkish, Jewish, Arabic, and Armenian populations. As our understanding of FMF improves, it becomes clearer that we are facing with a more complex picture of FMF with respect to its pathogenesis, penetrance, variant type (gain-of-function vs. loss-of-function), and inheritance. In this study, MEFV gene analysis results and clinical findings of 27,504 patients from 35 universities and institutions in Turkey and Northern Cyprus are combined in an effort to provide a better insight into the genotype-phenotype correlation and how a specific variant contributes to certain clinical findings in FMF patients. Our results may help better understand this complex disease and how the genotype may sometimes contribute to phenotype. Unlike many studies in the literature, our study investigated a broader symptomatic spectrum and the relationship between the genotype and phenotype data. In this sense, we aimed to guide all clinicians and academicians who work in this field to better establish a comprehensive data set for the patients. One of the biggest messages of our study is that lack of uniformity in some clinical and demographic data of participants may become an obstacle in approaching FMF patients and understanding this complex disease.

Research paper thumbnail of 28 Cloned Embryos Can Be Produced Using Donor Cells Obtained from a 72-HOUR Cooled Carcass

Reproduction, Fertility and Development, 2005

There are few reports on the use of cells from a dead mammal for nuclear transfer (NT). So far, m... more There are few reports on the use of cells from a dead mammal for nuclear transfer (NT). So far, most calves have been cloned from live adult cows or fresh fetal samples. The ability to produce cloned animals using postmortem tissue can provide an additional application to the field of NT. This study was conducted to investigate whether viable cells could be obtained from tissues chilled for 72 h and whether these cells could be used for NT. Bovine oocytes isolated from slaughterhouse ovaries were matured in TCM199 supplemented with 10% fetal calf serum (FBS), 50 μg/mL sodium pyruvate, 1% v:v penicillin-streptomycin (10,000 U/mL penicillin G, 10,000 μg/mL streptomycin), 10 ng/mL EGF, 0.5 μg/mL FSH, and 5 μg/mL LH. A cell line (MC) was established from leg muscle of a cow carcass stored at 0°C for 72 h. Tissues from muscle were cut into small pieces. Tissue explants were cultured in DMEM-F12 supplemented with 10% FBS at 37°C in 5% CO2 in air. Bovine granulosa cells (GC) were isolated ...

Research paper thumbnail of 150 in Vitro and in Vivo Development of Embryo Following Biopsy with Different Techniques in Mouse Embryos

Reproduction, Fertility and Development, 2013

In vitro development ratios, quality evaluation, in vivo implantation, and fetal development rati... more In vitro development ratios, quality evaluation, in vivo implantation, and fetal development ratios were investigated following aspiration biopsy in 8-cell mouse embryos and trophectoderm biopsy in blastocyst developed from 8-cell stage embryos in vitro. Superovulated CB6F1 hybrid female mice (5–6 weeks) were sacrificed 68 to 72 hours after hCG administration. Eight-cell embryos were flushed from oviducts of the sacrificed mouse with HTF medium supplemented with HEPES and 3 mg mL–1 BSA. Embryos were randomly divided into two groups. In the first group, embryos at 8-cell stage were used for a single cell blastomer aspiration; in the second group, embryos were cultured in vitro until blastocyst stage. Trophectoderm cells (15% of trophoblastic cells) were biopsied from developing blastocysts. There were also control groups for both groups. Biopsy procedures for both groups were applied in 50 µL drops of Ca2+/Mg2+ free HTF medium containing HEPES+3 mg mL–1 BSA+5 µg mL–1 cytochalasine B....

Research paper thumbnail of Vitrification of pronuclear‐stage mouse embryos on solid surface (SSV) versus in cryotube: Comparison of the effect of equilibration time and different sugars in the vitrification solution

Molecular Reproduction and Development, 2003

The cryopreservation of pronuclear‐stage embryos has particular importance in transgenic technolo... more The cryopreservation of pronuclear‐stage embryos has particular importance in transgenic technology and human assisted reproductive technology (ART). The objective of this study was to improve the efficiency of cryopreservation of pronuclear‐stage mouse embryos. Two vitrification methods (solid surface vitrification (SSV) vs. vitrification in cryotube) have been compared with special emphasis on the effect of the exposure of the embryos to the solutions for various times and the sugar content (trehalose, sucrose, or raffinose) of the vitrification solutions. Pronuclear‐stage embryos were either exposed to 1 M dimethyl sulfoxide (DMSO) + 1 M propylene‐glycol (PG) solution for 2, 5, 10, or 15 min or not exposed to this “equilibration” solution. The vitrification solutions consisted of 2.75 M DMSO and 2.75 M PG in M2 medium supplemented with 1 M trehalose (DPT), 1 M sucrose (DPS), or 1 M raffinose (DPR). In the cryotube method, groups of 15–25 embryos were transferred into a 1.8 ml cry...

Research paper thumbnail of The effect of equilibration time on survival and development rates of mouse pronuclear-stage embryos vitrified in solid surface (SSV) and convential straws: In vitro and In vivo evaluations

Molecular Reproduction and Development, 2005

The objective of this study was to improve the efficiency of cryopreservation of pronuclear-stage... more The objective of this study was to improve the efficiency of cryopreservation of pronuclear-stage (PN) mouse embryos. A novel vitrification technique (solid surface vitrification, SSV) was compared with a convential one in straws both for cryosurvival and obtaining progeny from cryopreserved PN mouse embryos. In the SSV method, 15-20 PN embryos were exposed to vitrification solutions for approximately 20 sec after equilibration, and then they were dropped in 2 microl drops onto a pre-cooled (-150 to -180 degrees C) metal surface. In the straws method, groups of 5-10 PN embryos were loaded in a single straw after equilibration. In experiment I, it was compared the effect of the vitrification solutions alone, without vitrification. No reduction was detected in survival, cleavage and blastocysts rates and the lowest development rate was obtained from hatched blastocyst for 20 min equilibration (24.5%). In experiment II, SSV method resulted in significantly higher survival and cleavage rates than that of in-straw vitrified 15-20 min group (87% vs. 60%, 83% vs. 67%, respectively; P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.05). There were no statistical differences among any of the blastocyts groups. However, there was a statistical difference in hatched blastocysts between 15 to 5, 10, and 20 min (P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.05). In experiment III, it was found no major effect among equilibration time periods in toxicity groups according to the mean cell number of blastocysts developed from PN embryos. But, there was a significant differences between 15 min SSV and 10 min in straw vitrified according to the mean cell number of blastocysts developed from PN embryos following vitrification (P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.05). The good results were obtained from 15 min equilibration group for SSV and 10 min equilibration group for straw vitrification. In the last experiment, embryo transfer after vitrification and toxicity was investigated. There were significant differences between SSV and straw just on the rate of pups born (30% and 20.5% respectively; P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.05). In conclusion, vitrification of PN mouse embryos by SSV can result in high rates of in vitro development to expanded and hatched blastocyst stage and in vivo development to live pups.

Research paper thumbnail of Exposure to warmer postoperative temperatures reduces hypothermia caused by anaesthesia and significantly increases the implantation rate of transferred embryos in the mouse

Laboratory Animals, 2004

Embryo transfer (ET) is among the key factors determining the overall efficiency of transgenic te... more Embryo transfer (ET) is among the key factors determining the overall efficiency of transgenic technology in the mouse. A successful ET depends among other factors on the quality of the transferred embryos, foster mothers and anaesthetic reagents and on the transfer techniques. Anaesthesia-caused deaths and suboptimal ET procedures are factors which reduce the success of transgenic experiments and mouse colony maintenance. Here we compared the effects of two anaesthetic reagents—a ketamine/xylazine combination, and tribromoethanol (Avertin)—on the rates of implantation and development to term of mouse zygotes transferred into the oviducts of CD-1 foster mothers, and evaluated whether hypothermia caused by anaesthetics after the ET operation could be overcome by postoperative incubation of the foster mothers. We established two experimental groups of fosters, one of which was kept at room temperature (RT, 21°C) with the other in an incubator (33°C) overnight after ET. Rates of implan...

Research paper thumbnail of The Effect of Linear Versus Circular Vector on Enhanced Green Fluorescent Protein (EGFP) Expression in Transgenic Zebrafish (Danio rerio)

Journal of Animal and Veterinary Advances, 2010

Research paper thumbnail of Production of recombinant therapeutic proteins in the milk of transgenic animals

Current Opinion in Biotechnology, 2011

Over the past 20 years the demand for recombinant proteins has increased significantly. Mammalian... more Over the past 20 years the demand for recombinant proteins has increased significantly. Mammalian cell lines have been extensively used to produce recombinant proteins. This expression system offers several advantages over microbial systems, mammalian cells have the cellular machinery to promote the secretion of the recombinant product and the posttranslational modifications, like glycosylation that is present in many of recombinant therapeutic proteins in the market. Human cell lines have emerged as a new and powerful alternative for production of such products. These cells are able to produce recombinant proteins with posttranslational modifications more similar to their natural counterparts, producing proteins with human-like glycosylation pattern avoiding immunogenic reactions against epitopes nonhumans. This review presents the available human cell lines that can be used in pharmaceutical industry, the advantages of this expression system and the main efforts made in this field.

Research paper thumbnail of High microsatellite and mitochondrial diversity in Anatolian native horse breeds shows Anatolia as a genetic conduit between Europe and Asia

Animal Genetics, 2011

SummaryThe horse has been a food source, but more importantly, it has been a means for transport.... more SummaryThe horse has been a food source, but more importantly, it has been a means for transport. Its domestication was one of the crucial steps in the history of human civilization. Despite the archaeological and molecular studies carried out on the history of horse domestication, which would contribute to conservation of the breeds, the details of the domestication of horses still remain to be resolved. We employed 21 microsatellite loci and mitochondrial control region partial sequences to analyse genetic variability within and among four Anatolian native horse breeds, Ayvacık Pony, Malakan Horse, Hınıs Horse and Canik Horse, as well as samples from indigenous horses of unknown breed ancestry. The aims of the study were twofold: first, to produce data from the prehistorically and historically important land bridge, Anatolia, in order to assess its role in horse domestication and second, to analyse the data from a conservation perspective to help the ministry improve conservation ...

Research paper thumbnail of Characterization of genetic resources and biodiversity conservation in domestic horse breeds

Research paper thumbnail of A gershoni-baruch syndrome variant or a new association

Journal of clinical neonatology, 2021

A pregnant woman with no previous routine pregnancy follow-up referred to our obstetrics clinic. ... more A pregnant woman with no previous routine pregnancy follow-up referred to our obstetrics clinic. Ultrasonography revealed the presence of a fetal heartbeat 26 weeks and 4 days old. Polyhydramnios, omphalocele, a diaphragmatic hernia, left ventricular hypoplasia, an occipital bone defect, a fetal head in severe retroflexion, and exaggerated cervicothoracic lordosis were detected in the fetus. After obtaining parental consent, the board decided to terminate the pregnancy. An examination performed after the termination revealed that the fetus was female and weighed 780 g. The first phalanx of the left thumb was hypoplastic. An X-ray examination showed coat hanger–shaped costal fusions and cranial structures consistent with iniencephaly. Fetus karyotyping revealed a normal 46, XX female karyotype. We speculate that this case represents a variant of Gershoni-Baruch syndrome.

Research paper thumbnail of Expressão do gene do receptor da vitamina D e de seus polimorfismos (BsmI, FokI e TaqI) em pacientes com pterígio

Research paper thumbnail of Differential expression of long non-coding RNAs during genotoxic stress-induced apoptosis in HeLa and MCF-7 cells

Clinical and Experimental Medicine, 2012

Long non-coding RNAs (lncRNAs) are emerging as new players in cancer as they are implicated in di... more Long non-coding RNAs (lncRNAs) are emerging as new players in cancer as they are implicated in diverse biological processes and aberrantly expressed in a variety of human cancers. No data are available on their function under genotoxic stress-induced apoptosis. In this work, we assessed the behavior of some candidate lncRNAs (HOTAIR, MALAT1, TUG1, lincRNA-p21, GAS5, MEG3, PANDA, UCA1, ANRIL, and CCND1) during DNA damage-induced cell death in HeLa and caspase-3-deficient MCF-7 cells using bleomycin (BLM) and γ-radiation to induce DNA damage. Cells were incubated in the presence of BLM for 24 h or irradiated. Apoptosis was analyzed by measurement of oligonucleosomal fragmentation of nuclear DNA. Our results reveal that basal RNA expression levels as well as the changes in the lncRNA expression rates during genotoxic stress-induced apoptosis were cell-type and/or DNA-damaging agent-specific. Generally, we found that some of the RNA molecules (HOTAIR and MALAT1) are down-regulated while many of them (lincRNA-p21, GAS5, MEG3, ANRIL, and ncRNA-CCND1) are up-regulated and some others (TUG1, UCA1, and PANDA) not affected. The decline in the expression of HOTAIR (approx. twofold, p &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.01) and MALAT1 (approx 1.6-fold, p &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.01) was clearly evident in BLM-treated HeLa and MCF cells (only HOTAIR, fivefold, p &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.01). For lincRNA-p21, ncRNA-CCND1, and MEG3, a similar up-regulation pattern was obvious in both cell lines where the increase was generally more pronounced in BLM-treated cells. Interestingly, the induction of ANRIL and GAS5 was mainly restricted to irradiated cells. In conclusion, our findings reveal a differential regulation of individual lncRNAs during genotoxic stress-induced apoptosis.

Research paper thumbnail of Cryogenic effect of antifreeze protein on transgenic mouse ovaries and the production of live offspring by orthotopic transplantation of cryopreserved mouse ovaries

Molecular Reproduction and Development, 2008

The purpose of the present study was to evaluate the cryogenic effect of antifreeze protein (AFP)... more The purpose of the present study was to evaluate the cryogenic effect of antifreeze protein (AFP) on transgenic mouse ovaries which is expressed AFP type III from Ocean pout and the production of live offspring by orthotopic transplantation of cryopreserved mouse ovaries. In this study, whole transgenic and nontransgenic mouse ovaries were vitrified with 20% DMSO and 20% EG in M2 medium supplemented with 0.5 M sucrose. All vitrified and toxicity control and fresh ovaries were transplanted orthotopically into ovariectomized recipients bilaterally. For fresh ovaries transplantation, 5 mice delivered litters of 18 and 19 live pups in first and second matings, respectively. For toxicity control of chemicals, 6 mice delivered litters of 22 and 23 live pups. For nontransgenic mouse ovaries (vitrified) transplantation, 7 mice delivered litters of 22 and 23 live pups. For transgenic mouse ovaries (vitrified) transplantation, 10 mice delivered litters of 35 and 37 live pups. Litter sizes from pups of freshly transplanted ovaries were not significantly different from AFP-transplanted transgenic ovaries but those from nontransgenic-transplanted ovaries were significantly different from the AFP-transplanted transgenic ovaries group (P < 0.05). In this study, for the first time, it was shown that the ovarian tissue of AFP transgenic mice was protected from cryopreservation by vitrification. These results demonstrate that a normal reproductive lifespan can be restored by orthotopic transplantation of AFP transgenic-vitrified ovary. Mol. Reprod. Dev. 75: 608-613,

Research paper thumbnail of Investigation of antifreeze protein (AFP) expression in oocytes and embryos of transgenic mice with carrying AFP gene by immunohistochemical staining

Research paper thumbnail of Cryogenic effect of fish antifreeze protein (AFP) on one-cell stage transgenic mouse embryos by vitrification

Research paper thumbnail of 177 Gene Expression Profiles of in Vitro- and in Vivo-Derived Bovine Embryos

Reproduction, Fertility and Development, 2011

Microarray technology is one of the most powerful tools for gene expression profiling in animal s... more Microarray technology is one of the most powerful tools for gene expression profiling in animal sciences. The objectives of this study were to determine the effect of vitrification on gene expression in in vitro- and in vivo-derived bovine embryos, and to identify differential mRNA expression patterns between embryos produced by in vivo v. in vitro conditions. Three pools of in vivo- and in vitro-derived blastocyst-stage embryos were used for microarray analysis. Total RNA was isolated using the PicoPure RNA Isolation Kit (Arcturus Bioscience, Mountain View, CA). Bovine ovarian tissue total RNA was used as the reference. Total RNA samples were amplified using an Ovation® Pico WTA System (NuGEN Technologies, San Carlos, CA). The bovine 16 846-member microarrays spotted with 70-mer oligonucleotides were purchased from the Bovine Genomics Laboratory, University of Missouri. Amplified cDNA samples were labeled with Alexa Fluor 647 and 546 dyes (Molecular Probes, Eugene, OR), respectively. Combined, labeled samples were dried and resuspended in hybridization buffer containing 50% formamide (vol/vol), 5× SSC, and 0.1% sodium dodecyl sulfate (wt/vol). After denaturation and cooling, cDNA was applied onto a microarray slide. Microarrays were hybridized overnight at 42°C. Following hybridization, the slides were washed with different stringency buffers and water. After drying by centrifugation, the arrays were scanned on a GenePix 4000B scanner (Axon Instruments, Union City, CA). GenePix Pro4.1 software was used for griding and analysis of spot intensities. Good-quality spots were analyzed using the GeneSpring 7.3 software (Agilent Technologies, Inc., CA, Santa Clara, CA). The data were normalized per spot and per array by Lowess normalization. When comparing two treatments, the Welch t-test with Benjamini and Hochberg multiple testing correction was performed to determine the differentially expressed genes between embryo groups. Microarray experiments were performed in 3 biological and 2 technical replicates for all embryo samples. Differentially expressed genes between all embryo groups were identified. The DAVID Functional Annotation Tool was used to analyze the genes that were differentially expressed. The DAVID Functional Annotation Tool determined the co-occurrence probability and provided gene-GO term enrichment analysis to highlight the most relevant GO terms associated with a given gene list. Differentially expressed Kyoto Encyclopedia of Genes and Genomes pathways are as follows: Ribosome, oxidative phosphorylation, spliceosome, and oocyte meiosis were significantly upregulated in the fresh embryos, whereas sphingolipid and purine metabolism was the upregulated in the vitrified in vitro-derived embryos. Gene expression was very similar between fresh and vitrified in vivo-derived, as opposed to in vitro-derived, embryos. This study was funded by the TUBITAK (Project no. KAMAG107G027) and startup funds to Yuksel Agca at the University of Missouri.

Research paper thumbnail of İki farklı genin Güçlendirilmiş Yeşil Floresan protein geni İnsan gamma interferon geni ayrı ayrı veya birlikte mikroenjeksiyonunun transgenik fare eldesi üzerine etkilerinin araştırılması

Sunulan çalışmada hIFN-γ ve EGFP gen konstraktlarının farklı konsantrasyonları birlikte ve ayrı a... more Sunulan çalışmada hIFN-γ ve EGFP gen konstraktlarının farklı konsantrasyonları birlikte ve ayrı ayrı pronüklear safhadaki fare embriyolarına mikroenjekte edilmiştir. Mikroenjeksiyon deneyleri aktarılan gen konstraktlarının yalnız ve/veya birlikte aktarımlarına göre üç farklı deney grubu çalışılmıştır. I.Deney Grubunda hIFN-γ ve EGFP genleri birlikte mikroenjekte edilmiş, aktarımlar sonucunda toplam 39 yavru doğmuştur. Yapılan moleküler analizlerde toplam üç yavrunun transgenik olduğu belirlenmiştir. Üç transgenik yavrudan iki'si EGFP transgenik, bir tanesi ise hIFN-γ transgeniktir. II. Deney Grubunda yalnız hIFN-γ geni mikroenjekte edilmiş, aktarımlar sonucunda toplam 21 yavru doğmuştur. Yapılan moleküler analizlerde toplam iki yavrunun hIFN-γ transgenik olduğu belirlenmiştir. III.Deney Grubunda yalnız EGFP geni mikroenjekte edilmiş, aktarımlar sonucunda toplam beş yavru doğmuştur. Bu yavrulardan elde edilen DNA'lar ile yapılan moleküler analizlerde transgenik yavruya rastlanmamıştır. Sunulan çalışma da elde edilen sonuçlar ile iki farklı genin birlikte mikroenjeksiyonu sonunda doğan yavruların transgenik olma yüzdelerinin yüksek olduğu ortaya konmuştur. Sunulan çalışmada geliştirilen protokolün transgenik fare üretim çalışmalarında uygulanması durumunda; iki farklı geni ayrı ayrı veya birlikte taşıyan transgenik fare hatları elde edilebilecek, böylece ekonomi ve zaman açısından tasarruf sağlanabilecektir.

Research paper thumbnail of The Effect of Solid Surface Vitrification (SSV) Versus Classic Vitrification Technique on Survive Rate of in vitro Produced Bovine Blastocysts

Research paper thumbnail of Optimal Method of Mouse Blastomere Biopsy: In vitro Developmental Potential of the Biopsied Embryo to Blastocyst Stage after Aspirated Eight-Cell Mouse Embryos

Journal of Animal and Veterinary Advances, 2011

Research paper thumbnail of Clinical and molecular evaluation of MEFV gene variants in the Turkish population: a study by the National Genetics Consortium

Functional & Integrative Genomics, 2022

Familial Mediterranean fever (FMF) is a monogenic autoinflammatory disorder with recurrent fever,... more Familial Mediterranean fever (FMF) is a monogenic autoinflammatory disorder with recurrent fever, abdominal pain, serositis, articular manifestations, erysipelas-like erythema, and renal complications as its main features. Caused by the mutations in the MEditerranean FeVer (MEFV) gene, it mainly affects people of Mediterranean descent with a higher incidence in the Turkish, Jewish, Arabic, and Armenian populations. As our understanding of FMF improves, it becomes clearer that we are facing with a more complex picture of FMF with respect to its pathogenesis, penetrance, variant type (gain-of-function vs. loss-of-function), and inheritance. In this study, MEFV gene analysis results and clinical findings of 27,504 patients from 35 universities and institutions in Turkey and Northern Cyprus are combined in an effort to provide a better insight into the genotype-phenotype correlation and how a specific variant contributes to certain clinical findings in FMF patients. Our results may help better understand this complex disease and how the genotype may sometimes contribute to phenotype. Unlike many studies in the literature, our study investigated a broader symptomatic spectrum and the relationship between the genotype and phenotype data. In this sense, we aimed to guide all clinicians and academicians who work in this field to better establish a comprehensive data set for the patients. One of the biggest messages of our study is that lack of uniformity in some clinical and demographic data of participants may become an obstacle in approaching FMF patients and understanding this complex disease.

Research paper thumbnail of 28 Cloned Embryos Can Be Produced Using Donor Cells Obtained from a 72-HOUR Cooled Carcass

Reproduction, Fertility and Development, 2005

There are few reports on the use of cells from a dead mammal for nuclear transfer (NT). So far, m... more There are few reports on the use of cells from a dead mammal for nuclear transfer (NT). So far, most calves have been cloned from live adult cows or fresh fetal samples. The ability to produce cloned animals using postmortem tissue can provide an additional application to the field of NT. This study was conducted to investigate whether viable cells could be obtained from tissues chilled for 72 h and whether these cells could be used for NT. Bovine oocytes isolated from slaughterhouse ovaries were matured in TCM199 supplemented with 10% fetal calf serum (FBS), 50 μg/mL sodium pyruvate, 1% v:v penicillin-streptomycin (10,000 U/mL penicillin G, 10,000 μg/mL streptomycin), 10 ng/mL EGF, 0.5 μg/mL FSH, and 5 μg/mL LH. A cell line (MC) was established from leg muscle of a cow carcass stored at 0°C for 72 h. Tissues from muscle were cut into small pieces. Tissue explants were cultured in DMEM-F12 supplemented with 10% FBS at 37°C in 5% CO2 in air. Bovine granulosa cells (GC) were isolated ...

Research paper thumbnail of 150 in Vitro and in Vivo Development of Embryo Following Biopsy with Different Techniques in Mouse Embryos

Reproduction, Fertility and Development, 2013

In vitro development ratios, quality evaluation, in vivo implantation, and fetal development rati... more In vitro development ratios, quality evaluation, in vivo implantation, and fetal development ratios were investigated following aspiration biopsy in 8-cell mouse embryos and trophectoderm biopsy in blastocyst developed from 8-cell stage embryos in vitro. Superovulated CB6F1 hybrid female mice (5–6 weeks) were sacrificed 68 to 72 hours after hCG administration. Eight-cell embryos were flushed from oviducts of the sacrificed mouse with HTF medium supplemented with HEPES and 3 mg mL–1 BSA. Embryos were randomly divided into two groups. In the first group, embryos at 8-cell stage were used for a single cell blastomer aspiration; in the second group, embryos were cultured in vitro until blastocyst stage. Trophectoderm cells (15% of trophoblastic cells) were biopsied from developing blastocysts. There were also control groups for both groups. Biopsy procedures for both groups were applied in 50 µL drops of Ca2+/Mg2+ free HTF medium containing HEPES+3 mg mL–1 BSA+5 µg mL–1 cytochalasine B....

Research paper thumbnail of Vitrification of pronuclear‐stage mouse embryos on solid surface (SSV) versus in cryotube: Comparison of the effect of equilibration time and different sugars in the vitrification solution

Molecular Reproduction and Development, 2003

The cryopreservation of pronuclear‐stage embryos has particular importance in transgenic technolo... more The cryopreservation of pronuclear‐stage embryos has particular importance in transgenic technology and human assisted reproductive technology (ART). The objective of this study was to improve the efficiency of cryopreservation of pronuclear‐stage mouse embryos. Two vitrification methods (solid surface vitrification (SSV) vs. vitrification in cryotube) have been compared with special emphasis on the effect of the exposure of the embryos to the solutions for various times and the sugar content (trehalose, sucrose, or raffinose) of the vitrification solutions. Pronuclear‐stage embryos were either exposed to 1 M dimethyl sulfoxide (DMSO) + 1 M propylene‐glycol (PG) solution for 2, 5, 10, or 15 min or not exposed to this “equilibration” solution. The vitrification solutions consisted of 2.75 M DMSO and 2.75 M PG in M2 medium supplemented with 1 M trehalose (DPT), 1 M sucrose (DPS), or 1 M raffinose (DPR). In the cryotube method, groups of 15–25 embryos were transferred into a 1.8 ml cry...

Research paper thumbnail of The effect of equilibration time on survival and development rates of mouse pronuclear-stage embryos vitrified in solid surface (SSV) and convential straws: In vitro and In vivo evaluations

Molecular Reproduction and Development, 2005

The objective of this study was to improve the efficiency of cryopreservation of pronuclear-stage... more The objective of this study was to improve the efficiency of cryopreservation of pronuclear-stage (PN) mouse embryos. A novel vitrification technique (solid surface vitrification, SSV) was compared with a convential one in straws both for cryosurvival and obtaining progeny from cryopreserved PN mouse embryos. In the SSV method, 15-20 PN embryos were exposed to vitrification solutions for approximately 20 sec after equilibration, and then they were dropped in 2 microl drops onto a pre-cooled (-150 to -180 degrees C) metal surface. In the straws method, groups of 5-10 PN embryos were loaded in a single straw after equilibration. In experiment I, it was compared the effect of the vitrification solutions alone, without vitrification. No reduction was detected in survival, cleavage and blastocysts rates and the lowest development rate was obtained from hatched blastocyst for 20 min equilibration (24.5%). In experiment II, SSV method resulted in significantly higher survival and cleavage rates than that of in-straw vitrified 15-20 min group (87% vs. 60%, 83% vs. 67%, respectively; P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.05). There were no statistical differences among any of the blastocyts groups. However, there was a statistical difference in hatched blastocysts between 15 to 5, 10, and 20 min (P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.05). In experiment III, it was found no major effect among equilibration time periods in toxicity groups according to the mean cell number of blastocysts developed from PN embryos. But, there was a significant differences between 15 min SSV and 10 min in straw vitrified according to the mean cell number of blastocysts developed from PN embryos following vitrification (P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.05). The good results were obtained from 15 min equilibration group for SSV and 10 min equilibration group for straw vitrification. In the last experiment, embryo transfer after vitrification and toxicity was investigated. There were significant differences between SSV and straw just on the rate of pups born (30% and 20.5% respectively; P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.05). In conclusion, vitrification of PN mouse embryos by SSV can result in high rates of in vitro development to expanded and hatched blastocyst stage and in vivo development to live pups.

Research paper thumbnail of Exposure to warmer postoperative temperatures reduces hypothermia caused by anaesthesia and significantly increases the implantation rate of transferred embryos in the mouse

Laboratory Animals, 2004

Embryo transfer (ET) is among the key factors determining the overall efficiency of transgenic te... more Embryo transfer (ET) is among the key factors determining the overall efficiency of transgenic technology in the mouse. A successful ET depends among other factors on the quality of the transferred embryos, foster mothers and anaesthetic reagents and on the transfer techniques. Anaesthesia-caused deaths and suboptimal ET procedures are factors which reduce the success of transgenic experiments and mouse colony maintenance. Here we compared the effects of two anaesthetic reagents—a ketamine/xylazine combination, and tribromoethanol (Avertin)—on the rates of implantation and development to term of mouse zygotes transferred into the oviducts of CD-1 foster mothers, and evaluated whether hypothermia caused by anaesthetics after the ET operation could be overcome by postoperative incubation of the foster mothers. We established two experimental groups of fosters, one of which was kept at room temperature (RT, 21°C) with the other in an incubator (33°C) overnight after ET. Rates of implan...

Research paper thumbnail of The Effect of Linear Versus Circular Vector on Enhanced Green Fluorescent Protein (EGFP) Expression in Transgenic Zebrafish (Danio rerio)

Journal of Animal and Veterinary Advances, 2010

Research paper thumbnail of Production of recombinant therapeutic proteins in the milk of transgenic animals

Current Opinion in Biotechnology, 2011

Over the past 20 years the demand for recombinant proteins has increased significantly. Mammalian... more Over the past 20 years the demand for recombinant proteins has increased significantly. Mammalian cell lines have been extensively used to produce recombinant proteins. This expression system offers several advantages over microbial systems, mammalian cells have the cellular machinery to promote the secretion of the recombinant product and the posttranslational modifications, like glycosylation that is present in many of recombinant therapeutic proteins in the market. Human cell lines have emerged as a new and powerful alternative for production of such products. These cells are able to produce recombinant proteins with posttranslational modifications more similar to their natural counterparts, producing proteins with human-like glycosylation pattern avoiding immunogenic reactions against epitopes nonhumans. This review presents the available human cell lines that can be used in pharmaceutical industry, the advantages of this expression system and the main efforts made in this field.

Research paper thumbnail of High microsatellite and mitochondrial diversity in Anatolian native horse breeds shows Anatolia as a genetic conduit between Europe and Asia

Animal Genetics, 2011

SummaryThe horse has been a food source, but more importantly, it has been a means for transport.... more SummaryThe horse has been a food source, but more importantly, it has been a means for transport. Its domestication was one of the crucial steps in the history of human civilization. Despite the archaeological and molecular studies carried out on the history of horse domestication, which would contribute to conservation of the breeds, the details of the domestication of horses still remain to be resolved. We employed 21 microsatellite loci and mitochondrial control region partial sequences to analyse genetic variability within and among four Anatolian native horse breeds, Ayvacık Pony, Malakan Horse, Hınıs Horse and Canik Horse, as well as samples from indigenous horses of unknown breed ancestry. The aims of the study were twofold: first, to produce data from the prehistorically and historically important land bridge, Anatolia, in order to assess its role in horse domestication and second, to analyse the data from a conservation perspective to help the ministry improve conservation ...

Research paper thumbnail of Characterization of genetic resources and biodiversity conservation in domestic horse breeds

Research paper thumbnail of A gershoni-baruch syndrome variant or a new association

Journal of clinical neonatology, 2021

A pregnant woman with no previous routine pregnancy follow-up referred to our obstetrics clinic. ... more A pregnant woman with no previous routine pregnancy follow-up referred to our obstetrics clinic. Ultrasonography revealed the presence of a fetal heartbeat 26 weeks and 4 days old. Polyhydramnios, omphalocele, a diaphragmatic hernia, left ventricular hypoplasia, an occipital bone defect, a fetal head in severe retroflexion, and exaggerated cervicothoracic lordosis were detected in the fetus. After obtaining parental consent, the board decided to terminate the pregnancy. An examination performed after the termination revealed that the fetus was female and weighed 780 g. The first phalanx of the left thumb was hypoplastic. An X-ray examination showed coat hanger–shaped costal fusions and cranial structures consistent with iniencephaly. Fetus karyotyping revealed a normal 46, XX female karyotype. We speculate that this case represents a variant of Gershoni-Baruch syndrome.

Research paper thumbnail of Expressão do gene do receptor da vitamina D e de seus polimorfismos (BsmI, FokI e TaqI) em pacientes com pterígio