Moleküler Biyoloji ve Genetik Bölümü Makale Koleksiyonu
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Öğe A novel, conserved and possibly functional motif “WHWGHTW” in mitochondrial transcription across Bilateria(2023) Aydemir, Merve Nur; Aydemir, Habeş Bilal; Budak, Mahir; Kızıltepe, Birsel; Çelebi, Melissa; Korkmaz, Ertan Mahir; Başıbüyük, Hasan HüseyinThe animal mitogenomes which undergone a reductive evolution has an obvious loss of coding capacity compared to their known closest relatives, but it has not yet been fully investigated why and how the intergenic regions do not encode protein and have no known functions, are stably maintained, replicated, and transmitted by the genome. These relatively small intergenic regions may not be under neutral evolution and they may have functional and/or regulatory roles that have yet to be identified. Here, the distribution pattern, sequence content and location of a novel sequence motif of ‘WWWGHTW’ were bioinformatically investigated and characterised by constructing a sampling mitogenome dataset of 1889 species from 14 phyla representing the clade of Bilateria. This motif is reverse complementary of the previously described DmTTF binding sequence and found in the nd4L- (X) -trnT gene cluster. This cluster commonly exhibits a strand displacement region and an intergenic region among the bilaterian superphylums, particularly in Ecdysozoa. This motif may be accepted as a substrate providing binding sites for the specific interaction with transcription factors because of (i) its reverse complementarity of previously described DmTTF binding sequence, and (ii) the possession of G and T nucleotides in the fourth and sixth positions, (iii) the bias on T and G nucleotides instead of C and A in the degenerated positions. This suggestion is also supported by the presence of a strand displacement region in the nd4L- (X) -trnT gene cluster, particularly in Ecdysozoa consisting of the most rearranged mitogenomes among the bilaterian superphylums.Öğe Differential sense and antisense expression profiles of Syrista parreyssi (Hymenoptera: Cephidae) mitochondrial transcripts(Mayıs 2023) Aydemir, Habeş Bilal; Aydemir, Merve Nur; Korkmaz, Ertan MahirThe transcription of the mitogenome shows a unique pattern that is both similar to and different from the nuclear and bacterial patterns. Mitochondrial transcription generates five polycistronic units from three promoters in Drosophila melanogaster, and different expression levels of genes were observed in both different and, interestingly, the same polycistronic units in D. melanogaster. This study was conducted to test this phenomenon in the mitogenome of Syrista parreyssi (Hymenoptera: Cephidae). RNA isolation and DNase digestion were performed using only one whole individual, and real-time polymerase chain reaction analyses were performed with complementary DNAs of 11 gene regions using gene-specific primers. It was found that the expression level of each gene exhibited differences from each other, and some genes (e.g., cox genes, and rrnS) were interestingly expressed at significant levels in the corresponding antisense chain. Additionally, the mitogenome of S. parreyssi was found to have the capacity to encode 169 additional peptides from 13 known protein-coding genes, most of which were encoded in antisense transcript units. One of the unique findings was a potential open reading frame sequence that was potentially encoded in the antisense rrnL gene and included a conserved cox3 domainÖğe Trichoderma atroviride suppresses Fusarium graminearum by altering primary and secondary metabolite biosynthesis profiling(Mayıs 2023) Özkale, Evrim; Yörük, Emre; Budak, Mahir; Korkmaz, Ertan MahirThe use of Trichoderma spp. offers an ecologically friendly tool for the struggle with mycotoxigenic Fusarium spp. Here, the alterations in transcriptome level were investigated in 6-day- old Fusarium graminearum cultures treated with Trichoderma atroviride and nontreated with T. atroviride (FGc), using whole transcriptome sequencing to better understand the associated biological processes. Transcriptome analysis indicated a total of 55 up-regulated genes and 728 down-regulated genes with padj < 0.05. Enrichment analysis revealed that the up-regulated genes were related to fatty acid biosynthesis, AMP-dependent biosynthesis, amino acid recognition/activation processes and secondary metabolite production, whereas down-regulated genes were involved in amino acid synthesis, oxidation–reduction processes, metal ion-binding and metabolic/ catalytic activities. Among the down-regulated genes, the expression of pigmentation-related genes such as aurO, gip1 and aurR2 was remarkable. Similarly, the expression levels of key enzyme-coding genes involved in deoxynivalenol mycotoxin production were significantly decreased in the range of −1.77 and −2.94. For up-regulated genes, nonribosomal peptide synthetase and polyketide synthase genes were notably distinguished from the remaining down-regulated genes as these genes can be involved in biosynthesis of common secondary metabolites. The results clearly emphasize that T. atroviride repressed the biosynthesis of primary metabolites in F. graminearum while simultaneously up-regulating the expression of genes involved in the synthesis of secondary metabolites. This is the first report showing how T. atroviride leads to transcriptome alterations and the findings suggest that T. atroviride could serve as an effective fungus by employing a wide variety of strategies against phytopathogenic fungi.Öğe Identification and characterization of globin gene from Bombus terrestris (Hymenoptera: Apocrita: Apidae)(Mart 2023) Aydemir, Habeş Bilal; Korkmaz, Ertan MahirHemoglobins are mainly functional in the transport and storage of O2, and are present in aerobic, lung respiratory metazoans. Based on recent studies, it has been determined that globin-like proteins are also found in invertebrate groups which have tracheal respiratory systems. Thus, it has been claimed that the globin molecules may have housekeeping functions beyond their known functions. In this study, the presence of a hemoglobin gene was investigated in a natural pollinator, Bombus terrestris. Bombus terrestris (Hymenoptera: Apidae: Bombinae) is an ecologically and economically important species, it has a wide distribution in high and low altitude habitats, can live in different localities in terms of altitude and temperature. The expression of globin gene was determined using real time qPCR and RACE system, and confirmed by SRA data. The potential globin ORF sequence was 516 bp nucleotide and 171 bp amino acid long. This data was deposited in the GenBank database under accession number OP312897. On the other hand, expression profiles were investigated in different hypoxic conditions at different developmental stages (larva, pupae and adult) and in different tissue types (abdomen, thorax, head and legs). It was determined that the globin gene is transcribed in all developmental stages, but only in abdomen; and that globin expression decreases with decreasing amount of oxygen.Öğe Mitochondrial genome of Poecilimon cretensis (Orthoptera: Tettigoniidae: Phaneropterinae): Strong phylogenetic signals in gene overlapping regions.(2023) Karakaç, Müşerref Y; Yahyaoğlu, Özgül; Uluar, Onur; Budak, Mahir; Ciplak, BattalWe report the complete mitochondrial genome of the Cretan bush cricket Poecilimon cretensis. The mitogenome consists of 13 protein-coding regions, 22 tRNAs, two rRNAs, and one control region. The length of mitogenome in P. cretensis varies between15477 and 15631 bp, mainly due to variability in control region. The start and stop codons of protein coding genes exhibit the general pattern in Phaneropterinae. Phylogenetic tree constructed with the mitogenome obtained during this study and 12 mitogenomes of Phaneropterinae downloaded from GenBank, placed P. cretensis in Barbitistini as sister group to Poecilimon luschani. Data indicate that the gene overlapping pattern exhibit strong phylogenetic signals.Öğe The complete mitochondrial genome sequence of Pachycephus smyrnensis Stein, 1876 (Hymenoptera: Cephidae) with phylogenetic analysis(Taylor \& Francis, 2023) Liu, Mengmeng; Xu, Min; Zejian, Li; Budak, Mahir; Wei, Meicai; Liu, LinThe complete mitochondrial genome of Pachycephus smyrnensis Stein, 1876 collected from Sivas, Turkey, is described. The circled genome is 20,393 bp in length and contains a typical set of 37 genes. The missing control regions, trnQ and trnI in previously reported P. smyrnensis (KX907846) were obtained in this precise assembly based on a considerable amount of raw data. A denser sampled phylogenetic analysis shows that the two P. smyrnensis constitute a branch sister to P. cruentatus (Eversmann, Citation1847). Pachycephus is a sister group of Phylloecus within Hartigiinae and remote from Characopygus, a genus within Cephinae. The monophyly of Pachycephini has been rejected.Öğe Identification of odorant receptor protein genes in two Cephid stem borers (Hymenoptera: Cephidae) by high-throughput sequencing(2023) Budak, MahirInsects are well adapted organisms to the terrestrial life on Earth. The evolution of the odorant receptor family is one of the causes underpinning this remarkable adaptation. Odorant receptors (ORs) sense aromas in the environment and cause the insect to respond. The ability of phytophagous insects to detect odor signals from their hosts is crucial for mating, oviposition, and feeding. The family of odorant receptor genes in Cephidae, pest on some economically important plants, is little understood. Bioinformatic tools were used to analyze the genomic data of the two pest species, Syrista parreyssii (Spinola, 1843) (Hymenoptera: Cephidae) (a rose pest) and Pachycephus smyrnensis J.P.E.F. Stein, 1876 (Hymenoptera: Cephidae), (a poppy pest), to determine their odorant receptors. The whole genome sequencing of P. smyrnensis collected in Sivas in 2020 was performed by next generation sequencing and short reads of S. parreyssii genome were obtained from previous studies. Following bioinformatic analyses, 67 and 82 putative odorant receptor genes were identified and annotated for P. smyrnensis and S. parreyssii, respectively. The ORs of these two species were found to be organized as repetitive genes in five separate clusters. No species-specific OR genes were identified in any of the investigated species. As a result, it was hypothesized that host specificity was acquired through the combined effect of multiple ORs.Öğe Biosorption of Rhodamine B dye from aqueous solution by Rhus coriaria L. plant: Equilibrium, kinetic, thermodynamic and DFT calculations(Elsevier, 2023) Çelik, Muhammed Safa; Akkuş Çetinus, Şenay; Yenidünya, Ali Fazıl; Çetinkaya, Serap; Tüzün, BurakWater-soluble basic rhodamine B (RhB) was adsorbed onto fruit powders of Rhus coriaria L. (Anacar- diaceae), sumac in batch reactions. Adsorption was optimized by employing concentration, pH, and time parameters. Experimental data were in accordance with the Freundlich isotherm, adsorption obeyed the pseudo-second-order kinetics, and thermodynamic parameters indicated that adsorption was exothermic, spontaneous, and chemical. Results were also evaluated by theoretical means: lowest Unoccupied Molec- ular Orbitals (LUMO), and the Highest Occupied Molecular Orbitals (HOMO). The HOMO energy values of the rhodamine B molecule had the highest activity with -3.3729 at the B3LYP level, -6.0361 at the HF level, and -4.3299 at the M062X level. In the calculations made, it was seen that the rhodamine B molecule has more electron density on the oxygen molecules. Taken together, the findings suggested that the dried fruit of the Rhus coriaria L. could be a useful biosorbent for the removal of dyes from aqueous media.Öğe Biosorption of lead ions (Pb2+) from water samples using dried Lemna minor biomass: experimental and density functional theory studies(Springer, 24.02.2023) Kaya,Savaş; Çetinkaya, Serap; Jalbani, Nida Shams; Yenidünya, Ali Fazıl; Kütük, Nurşah; Kasaka, Ergün; Maslov, Mikhail M.Lemna minor biomass, a novel source of biosorbent, was found to exhibit high adsorption potential over a wide range of concentrations of Pb2+. The biosorbent was characterized by Fourier transform infrared (FTIR) spectrophotometry, scanning electron microscopy (SEM), energy-dispersive X-ray (EDX) analysis, X-ray powder diffraction (XRD), and thermogravimetric analysis (TGA). Biosorption experiments were carried out under the optimized parameters such as solution pH, biosorbent amount, equilibrium time, and temperature. During the sorption, it has been observed that the above 85% removal of Pb2+ ions was achieved at acidic pH (4.5–5.1). Moreover, the maximum sorption was achieved using the 150 mg L−1 biosorbent. Equilibrium experiments were validated by the Langmuir, Freundlich, and Dubinin–Radushkevich isotherm models. From the results, it has been noticed that the experimental data was best fitted to the Langmuir model (R2, 0.986 and 969.18 mmol g−1). Standard enthalpy (∆H°), free energy (∆G°), and entropy (∆S°) changes were calculated. Results showed that biosorption of Pb2+ was spontaneous and endothermic. The biosorption mechanism was analyzed through pseudo-first-order and pseudo- second-order kinetic models. The results demonstrated that the biosorption of Pb2+ followed the pseudo-second-order kinetic model. Adsorbate-adsorbent interactions were scrutinized by density functional theory (DFT).Öğe Removal of Erythrosine B dye from wastewater by Penicillium italicum: experimental, DFT, and molecular docking studies(Taylor Francis, 8.03.2023) Çetinkaya, Serap; Eyupoglu, Volkan; Çetintaş, Halil İbrahim; Yenidünya, Ali Fazıl; Kebabcı, Özgür; Tüzün, BurakThe study involved the adsorption of Erythrosine B onto the dead, dry, and unmodified Penicillium italicum cells and the analytical, visual, theoretical assessment of the adsorbent-adsorbate interactions. It also included desorption studies and reiterative usability of the adsorbent. The fungus was a local isolate and it was identified by partial proteomic experiment in a MALDI-TOFF mass spectrometer. Chemical features of the adsorbent surface were analysed by FT-IR and EDX. Surface topology was visualized by SEM. Isotherm parameters of the adsorption were determined by using three most frequently used models. Erythrosine B appeared to form a monolayer onto the biosorbent and some of the dye molecules could have also penetrated into the adsorbent particles. Kinetic results suggested a spontaneous and exothermic reaction taken place between the dye molecules and the biomaterial. Theoretical approach involved the determination of some of the quantum parameters as well as the toxic or drug potentials of the some of the components of the biomaterial.Öğe Removal of safranin O from wastewater using Streptomyces griseobrunneus dead biomass and in silico calculations(Springer, 2.07.2023) Çelik, Muhammed Safa; Kütük, Nurşah; Yenidünya, Ali Fazıl; Çetinkaya, Serap; Tüzün, BurakEnvironmental pollution with the dye produced by the textile industry causes a serious problem worldwide. The aim of the study is to use the environmentally friendly and low-cost Streptomyces griseobrunneus (S. griseus S15) dead cells for the adsorption of safranin O from aqueous milieu. Optimum retention was achieved with 200 mg/L safranin O and 25 g/L adsorbent at pH 9. Biosorption was found to better fit the Langmuir isotherm and PSO kinetics. The maximum biosorption (qmax) was 188.67 mg/g. The reaction between S. griseus S15 and safranin O was chemical, exothermic, and spontaneous. S. griseus S15 biomass was reusable. Molecules supposed to be involved in the process were investigated by using a Gauss- ian software program, calculations B3LYP, HF, and M06-2X, 6-31G, 6-31++G, and 6-31++G**. For molecular docking calculations, the affinity of safranin O molecule to various proteins was investigated. Finally, ADME/T was applied to gain an insight into the possible effects of safranin O on human health.Öğe Equilibrium and DFT modeling studies for the biosorption of Safranin O dye from water samples using Bacillus subtilis biosorbent(Elsevier, 2023) Çetinkaya, Serap; Kaya,Savaş; Aksu, Aysun; Çetintaş, Halil İbrahim; Jalbani, Nida Shams; Erkan Sultan; Marzouki, RiadhCurrent study deals with the biosorption of Safranin O dye from water by using high potential Bacil- lus subtilis biosorbent material. The presence of functional groups and surface morphology of biosor- bent was analyzed by using sophisticated analytical techniques such as FT-IR (Fouirer Transform Infrared Spectrophotometer), SEM (Scanning Electron Microscopy), EDX (Energy Dispersive X-Ray Analysis), and TGA (Thermogravimetric Analysis). To check the dye removal potential of Bacillus subtilis sorbent, batch adsorption experiments were performed under the optimized conditions. The biosorption experiments showed that the Bacillus subtilis sorbents remove 80% of safranin O dye from water. The biosorption mechanism is depends upon the solution pH thus the maximum biosorption was observed at (5.5–6.5). Moreover, the biosorbent dose has been optimized and it has observed that the maximum concentra- tion of safranin O dye has been removed using the 50 mg.L −1 of Bacillus subtilis . The biosorption equi- librium data were well fitted by the Langmuir adsorption isotherm due to good regression coefficient value ( R 2 = 0.98) and better Langmuir capacity (0.383 mmol.g −1 ), while the kinetic studies indicated that the biosorption followed the pseudo-second-order model. The thermodynamic parameters values showed that the biosorption is process is endothermic and spontaneous nature. In addition, molecular docking was also performed to examine the interaction between the safranin O dye molecule and the Bacillus subtilis bacterial cell line.Öğe Molecular docking to investigate the inhibitory activity and the role of nitric oxide in anticonvulsant effects of vitamin D on pentylenetetrazole?induced epileptic seizures in rats(Journal of Molecular Structure, 2023) Akkaya, Recep; Akkaya, Birnur; Bello, R. O.© 2022 Elsevier B.V.Despite the great breakthroughs in the field of epilepsy studies, the present drugs are ineffective in one-third of the patients, as well as without providing a definite treatment. There is accumulating evidence suggesting the role of vitamin D in epilepsy. The aim of this study was to investigate the effect of vitamin D on seizure formation, post-seizure cognitive functions, and the possible role of nitric oxide and oxidative stress in this effect, in the PTZ-induced seizure rat model. Sixty male Wistar albino rats were used in this study. The rats were randomly divided into 11 groups each containing 6 animals: Group 1: Control; Group 2: Saline+PTZ (45 mg/kg); Group 3: Vitamin D (1.5 mg/kg)+PTZ; Group 4: L-Arginine (500 mg/kg)+PTZ; Group 5: L-NAME (60 mg/kg)+PTZ; Group 6: 7-Nitroindazole (40 mg/kg); Group 7: Aminoguanidine (100 mg/kg)+PTZ; Group 8: Vitamin D+L- Arginine+PTZ; Group 9: Vitamin D+L-NAME+PTZ; Group 10: Vitamin D+7-Nitroindazole+PTZ; Group 11: Vitamin D+Aminoguanidine+PTZ. Animal behavior was evaluated with open field and passive avoidance tests. Nitric oxide (NO), total oxidative status (TOS), and total antioxidant status (TAS) levels in the cortex and hippocampus brain regions were determined by ELISA method. The treatment of vitamin D in combination with NO inhibitors has a positive effect on the PTZ-induced seizures and ameliorate post-seizure learning deficits. Moreover, the combination of vitamin D with NO inhibitors reduced oxidative stress and NO levels after seizures in the cortex and hippocampus. Also, we employed molecular docking and density functional theory analysis to investigate the inhibitory activity, reactivity, and stability of Vitamin D with other NO inhibitors. Vitamin D supplementation could be effective as a supportive treatment drug in epileptic patients, according to the findings.Öğe Doxorubucin loaded pH-responsive chitosan-poly(acrylamide-maleic acid) composite hydrogel for anticancer targeting(Journal of Molecular Structure, 2023) Akkaya, Birnur; Akkaya, Recep; Çelikkaya, Sümeyye İdil; sarıaydın, Nurgül; Raheem, K.Y.© 2022 Elsevier B.V.A pH responsive superadsorbent composite hydrogel, chitosan-poly(acrylamide-maleic acid)(Ch-p(Ac-Ma)), were synthesized, characterized and loaded by Doxorubucin (Dox), anti-cancer drug. Chitosan solution was modified by blending biocompatible chitosan and poly(acrylamide-co-maleic acid) in the polymerization medium. This new composite hydrogel had a high loading capacity for Dox (∼90%). Some chemical characteristics of the prepared composite hydrogel were investigated by swelling test, SEM, FTIR, XRD. The drug release study confirmed the pH-responsive delivery of doxorubucin. The composite hydrogel was loaded by high efficiency and the release experiments exhibited that Dox is released more at pH 4.5 compared with pH 7.4 at 37 °C. The biocompatibility of the prepared composite hydrogel was demonstrated via XTT assay in MCF-7 cells. The Dox loaded composite showed a controlled release, especially at acidic region. The Ch-p(Ac-Ma) exhibited a good biocompatibility against breast cancer cells (MCF 7) and dose dependent drug delivery behavior. Also, we employed molecular docking and density functional theory analysis to investigate the inhibitory activity, reactivity, and stability of Doxorubucin and target protein HER2 ((Pdb ID: 7JXH). The interaction between Doxorubucin and target protein HER2 ((Pdb ID: 7JXH) was investigated in the light of Molecular Docking calculations.Öğe Chitosan-poly(acrylamide-co-maleic acid) composite synthesis, characterization, and investigation of protein adsorption behavior(POLYMER BULLETIN, 2023) Akkaya, Recep; Akkaya, Birnur; Taşkın Çakıcı GülşenA new environmentally friendly superabsorbent chitosan-poly(acrylamide-co-maleic acid) (chitosan/PAA-MA) was prepared by blending biocompatible chitosan and poly(acrylamide-co-maleic acid) in the polymerization medium. Poly(acrylamide-co-maleic acid) was obtained by direct polymerization of the acrylamide and the maleic acid. The prepared chitosan/PAA-MA superabsorbent composite was characterized by swelling ratio, Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), and scanning electron microscopy (SEM). The lysozyme was separated using superabsorbent composite. Lysozyme adsorption optimum conditions (such as pH, lysozyme concentration, temperature, and ionic strengths) were determined. The highest lysozyme adsorption was obtained at pH 9 with a maximum adsorption capacity of 220 mg g(-1). The desorption of lysozyme and the reusability of the chitosan/PAA-MA composite were also tested. As a result, this biodegradable polymer-based superabsorbent material will become an alternative for the adsorption of various proteins.Öğe Antimicrobially effective protein-loaded metal chelated chitosan composite(Journal of Polymer Engineering, 2023) Akkaya, Birnur; Akkaya, Recep; Taşkın Kafa Ayşe HümeyraThe immobilization of lysozyme onto a novel synthetic metal chelator composite based on chitosan/PAA-PMA (chitosan/acrylamide-maleic acid) and its effect on antimicrobial activity were the aim of the current study. The plain composite and the lysozyme immobilized composite were characterized according to scanning electron microscopy (SEM), Ultraviolet spectroscopy (UV), Fourier transform infrared (FT-IR), and X-ray diffraction (XRD) analysis. Furthermore, the activities of lysozyme and immobilized lysozyme were investigated, as well as their antimicrobial activity against Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterococcus faecalis, and Staphylococcus aureus, as well as their cytotoxic effects, which were both approximately greater than those of free lysozyme. The last step was cytotoxic studies on lysozyme, chitosan composite, and lysozyme-immobilized chitosan composite, which showed no cytotoxic effect. Several investigations have shown that metal chelators improve lysozyme’s antibacterial action. Two carboxylic acids containing maleic acid were used as a metal chelator in this study. Lysozyme was immobilized from a side other than carboxylic acids, so that carboxylic acid groups, which are metal chelating groups, do not prevent synergy by competing with metal binding at neutral pH. This enhanced antimicrobial activity.Öğe Magnetic chitosan oligomer-sulfonate-stearic acid triple combination as cisplatin carrier for site-specific targeted on MCF-7 cancer cells: Preparation, characterization and in vitro experiments(Chemical Biology and Drug Design, 2023) Akkaya, Birnur; Akkaya, Recep; Nazlım, ArifeIn this study, a new amphiphilic target-specific adsorbent, chitosan oligomer-sulfonate-stearic acid triple combination (S-Cho-SA), and magnetic chitosan oligomer-sulfonate-stearic acid triple combination (M-S-Cho-SA) by oleic acid (OA)-modified Fe3O4 via hydrophobic interaction are fabricated. By modifying the nanoparticle surfaces and having the ability to magnetically allow the target region, these particles attract attention as important particles used in targeting mechanisms in cancer therapy. With magnetic nanoparticles and an external magnetic field, it is possible to transport therapeutic agents to the target site and keep them in the desired effect zone for a longer period of time. These new adsorbents are characterized by scanning electron microscopy (SEM), attenuated total reflection Fourier transform infrared (ATR FT-IR) spectroscopy, nuclear magnetic resonance (NMR), X-ray diffraction (XRD), vibrating sample magnetometer (VSM), and thermogravimetric analysis (TG/DTA). After chemical characterization, it is complexed with cisplatin (CDDP). The magnetic adsorbents were loaded with high efficiency (>50%), and the release experiments exhibited that cisplatin is released more at pH 4.5 compared with pH 7.4 at 37°C. It showed better drug release results under a magnetic field for magnetic adsorbents (36% for pH 4.5 and 3.6% for pH 7.4). The biocompatibility of the prepared adsorbents was demonstrated via the XTT assay in MCF-7 cell lines. The results also exhibited that S-Cho-SA and M-S-Cho-SA were biocompatible, and free cisplatin and cisplatin-complexed adsorbents showed an antiproliferative effect. The results showed that these new cisplatin-loaded (M-S-Cho-SA) nanoparticles are good candidates for thermotherapy in cancer treatment in the future, as they can provide selectivity by site-specific targeting and hold onto an alternative magnetic field due to the magnetic nature of the nanoparticles.Öğe Preparation and characterization of lysozyme loaded cryogel for heavy metal removal(International Journal of Biological Macromolecules, 2023) Akkaya, BirnurIn the present study, monolithic poly(N-isopropylacrylamide-acrylamide)-acrilic acid (poly(npam-aam)-aac) cryogels were made. Swelling tests, SEM, XRD, and ATR-FTIR analyses revealed distinct cryogel and lysozyme-loaded cryogel properties. The equilibrium swelling degree was 6.2 g H2O/g cryogel. The created poly(npam-aam)-aac with pores of 10–100 μm was obviously seen in SEM images. Lysozyme adsorption capacity on poly(npam-aam)-aac was found to be 260 mg/g at pH 7.4 and 40 °C. After that, we used lysozyme adsorbed cryogel for the removal of the model heavy metal ion (cadmium). A series of pH, duration, and ionic strengths were used to conduct Cd2+ adsorption experiments. The results showed that the new adsorbent had a considerable chemical affinity for Cd2+ ions in its ability to bind them under eye ocular conditions (pH 7.4, 32–36 °C, 0,15 M NaCl). The traditional Langmuir adsorption model was the most suitable, achieving maximum uptake of ∼185 mg/g. Chemical adsorption was found to be the rate-controlling step, and the process was also compatible with the pseudo-second-order model. For the treatment of ocular pathologies, the most effective enzyme, lysozyme, must show its function. That is why there is a need for using lysozyme, and lysozyme is selected as a lignad to adsorb heavy metal ions because of its high heavy metal binding affinity. This material could be used for the treatment of ocular pathologies in the future.Öğe The complete mitochondrial genome of Talpa martinorum (Mammalia: Talpidae), a mole species endemic to Thrace: genome content and phylogenetic considerations(Springer, 2022) Demirtaş, Sadık; Budak, Mahir; Korkmaz, Ertan M.; Searle, Jeremy B.; Bilton, David T.; Gündüz, İslamThe complete mitogenome sequence of Talpa martinorum, a recently described Balkan endemic mole, was assembled from next generation sequence data. The mitogenome is similar to that of the three other Talpa species sequenced to date, being 16,835 bp in length, and containing 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, an origin of L-strand replication, and a control region or D-loop. Compared to other Talpa mitogenomes sequenced to date, that of T. martinorum differs in the length of D-loop and stop codon usage. TAG and T-- are the stop codons for the ND1 and ATP8 genes, respectively, in T. martinorum, whilst TAA acts as a stop codon for both ND1 and ATP8 in the other three Talpa species sequenced. Phylogeny reconstructions based on Maximum Likelihood and Bayesian inference analyses yielded phylogenies with similar topologies, demonstrating that T. martinorum nests within the western lineage of the genus, being closely related to T. aquitania and T. occidentalis.Öğe Phylogeography of Pholidopterini: Revising molecular clock calibration by Mid-Aegean Trench(14/06/2022) Korkmaz, Ertan MahirThe present study examines the phylogeography of Pholidopterini (Orthoptera, Tettigoniidae), a lineage distributed in the East Mediterranean and estimated substitution rates for the three mitochondrial and two nuclear gene segments. The last common ancestor of Pholidopterini was dated to 18 myr ago, in Early Miocene. Phylogeography of the lineage was marked with three waves of radiations, first during the Middle Miocene Climatic Optimum, the second during the Serravallian, and third during the ending of Messinian. The substitution rate estimations were 0.0187/0.018/0.0141/0.0010207 s/s/myr for COI/ND2/12S-tRNAval-6S/ITS1-5.8S rRNA-ITS2. The following main conclusions were drawn; (i) Radiation of Pholidopterini directed by the climatic shifts, (ii) signs of vicariant speciation were poor, contrary to the active tectonic history, (iii) the ultimate generic ancestors were dated to the Langhian and Serravallian, and (vi) the Tortonian transgression of Mid-Aegean Trench appears to be a reliable geographic calibration point for lineage splitting between Crete and Anatolia.
