Yazdıç, Ferit Can; Kar, Bülent; Karaman, Altuğ

In this study, phylogenetic relationships and genetic diversity of Salmo spp. populations in different water bodies in Türkiye were investigated, focusing on morphologically similar specimens to Salmo macrostigma. Significant genetic variability and evolutionary differentiation within these populations have been identified using mitochondrial regions sequences (12S rDNA, 16S rDNA, and Cyt-b), morphological observations, and cytogenetic analysis. Samples collected from eight river basins revealed three main phylogenetic clades and local adaptations influenced by ecological pressures. Cytogenetic findings showed that they have chromosome numbers ranging from 78 to 80 (2n), consistent with known Salmo species. For this purpose, three mitochondrial DNA fragments encoding 12S rDNA, 16S rDNA, and Cyt-b regions were amplified by PCR, sequenced, and then used for phylogenetic analysis of the studied species. The study revealed the need for comprehensive integrative taxonomic approaches to clarify the classification of Salmo spp. with critical implications for conservation strategies in Türkiye biodiversity hotspots. In conclusion, this study not only advances our knowledge of Salmo macrostigma or similar Salmo spp., but also suggests innovative approaches for future Salmonid phylogenetics and cytogenetics studies. The findings have important implications for understanding the evolution, taxonomy, and conservation of these economically and ecologically important fish.

İncele

Yazdıç, Ferit Can; Kar, Bülent; Karaman, Altuğ; Yücel, Halit; Araka, Özlem

Bu çalışmada, Türkiye Tunceli'deki tarım topraklarından izole edilen Bacillus licheniformis suşlarının antimikrobiyal potansiyelleri araştırılmıştır. Toprak örnekleri minimal olarak bozulmuş alanlardan toplanmış ve bakteri suşları morfolojik, biyokimyasal ve moleküler tanımlama yöntemleri kullanılarak izole edilmiştir. İzolatlar, 16S rDNA dizilemesi ve filogenetik analiz yoluyla Bacillus licheniformis oldukları başarılı bir şekilde doğrulanmıştır. Antimikrobiyal sekonder metabolitlerin üretimi, izolatların farklı karbon kaynaklarıyla (sükroz, glikoz ve fruktoz) kültürlenmesi ve disk difüzyon yöntemi kullanılarak Escherichia coli (ATCC 25922) ve Staphylococcus aureus'a (ATCC 25923) karşı aktivitelerinin test edilmesiyle değerlendirilmiştir. Sonuçlar, özellikle Escherichia coli'ye karşı antimikrobiyal aktiviteyi artırmak için en etkili karbon kaynağının sükroz olduğu belirlenmiştir. Antibakteriyel aktivite genellikle daha uzun inkübasyon süreleriyle artmıştır. Bu araştırma, Bacillus licheniformis'in antibakteriyel madde kaynağı olarak potansiyelini vurgulamaktadır. Patojenlerin biyolojik kontrolü için tarımdaki uygulamalarda kullanılması için çevre dostu bir alternatif sunmaktadır. Sonuç olarak, bu çalışmanın bulguları Bacillus licheniformis'in antimikrobiyal özellikleri hakkında bilgilere katkıda bulunmaktadır. Karbon kaynağındaki kullanılabilirliği ve metabolit üretimini etkileyen faktörleri anlamak, Bacillus licheniformis'in antimikrobiyal potansiyelinden yararlanmak için önemlidir.

İncele

Aker, Onur; Bektaş, İdris; Yazdıç, Ferit Can

This study was conducted to synthesise silver nanoparticles (AgNPs) using Aspergillus floccosus fungal extract and to evaluate the pesticidal efficacy of the resulting nanopesticide product against two harmful organisms (pathogenic fungus and pest) affecting apples. The synthesised AgNPs were subjected to a series of characterisation tests (UV-Vis, FTIR, XRD, SEM, TEM, EDX, Zeta Potential) and, based on the results obtained, the AgNPs synthesis was successfully completed. Within the scope of this study, the first registration process has been carried out for the fungal pathogen (Phoma herbarum) that causes rot disease in apple fruits. The fungicidal efficacy of five concentrations of AgNPs (10, 25, 50, 100, and 200 mg L⁻¹) was evaluated against this pathogen under both in vitro and in vivo conditions. The results showed that AgNPs exhibited a significant inhibition on the mycelial growth of Phoma herbarum in vitro. The 200 mg L⁻¹ concentration showed the highest inhibition percentage (81.5%). Concerning in vivo test, the effect of AgNPs on disease severity index of Phoma herbarum in apple fruits was evaluated. The result of this part showed that the concentration 200 mg L⁻¹ of AgNPs exhibits highest fungicidal efficacy disease reduction rates (100%), Following by 67% for AgNPs 100 mg L⁻¹. The insecticidal effects of AgNPs on fourth-stage nymphs and adults of the pest (Aphis pomi) were evaluated in laboratory and field applications. For this purpose, AgNPs prepared at five different concentrations (30, 60, 90, 120, and 150 mg L⁻¹) were sprayed on the pests. The results showed that the insecticidal efficacy of AgNPs against Aphis pomi was directly related to both the dose and the exposure time. Specifically, the lethal concentration required to kill adults (LC50: 48.9 mg L⁻¹ for laboratory application and 68.4 mg L⁻¹ for orchard application) was higher than the dose required for nymphs (LC50: 32.3 mg L⁻¹ for laboratory and 52.1 mg L⁻¹ for orchard application). A similar trend was observed for lethal time, with adults exhibiting longer required exposure times (LT50: 51.2 h in the lab and 58.4 h in the orchard) compared to nymphs (LT50: 42.0 h in the lab and 45.1 h in the orchard). According to the results obtained, AgNPs synthesised using Aspergillus floccosus fungus have been proven to be highly effective at low doses against two major harmful organisms that cause qualitative and quantitative losses in apples. In conclusion, it has been proven that this silver-based nano pesticide product can be used as an alternative and innovative product in combating factors that cause agricultural damage to protect apple health.

AtıfScopus1·WoS1

İncele

Yazdıç, Ferit Can; Açar, Mıkaıl; Cakilcioglu, Ugur; Tasar, Neslihan; Çelik, İbrahim Seyfettin

Centaurea L. is a genus that is systematically discussed and whose taxonomic issues need to be clarified in the light of molecular techniques developed in recent years. This study aims to contribute taxonomically in molecular terms by studying the morphological and phylogenetic relationships of Centaurea bingoelensis. This limited, endemic species grows naturally in the Bingöl province of Türkiye. A phylogenetic analysis based on the molecular marker ITS, which is the most preferred in evolutionary studies and found in nuclear DNA, has been proposed as a molecular marker of C. bingoelensis , an endemic plant in Türkiye, and has not yet been molecularly identified. For this purpose, PCR amplification of the fragment mentioned above was performed, followed by direct sequencing, analysis of nucleotide variation, and phylogenetic analysis with different species. The Centaurea species identified so far have been shown to have three main distinct major clades and the specific phylogenetic methods used (NJ, ML, MP) and the ITS nucleotide sequences analyzed revealed a close phylogenetic relationship between C. bingoelensis and C. spectabilis. For a more accurate phylogenetic classification of this species within the Asteraceae family, their close relationships were probed using similar sequences from the GenBank Database. Phylogenetic analysis of C. bingoelensis specimens using ITS sequences reveals their position in the Asteraceae family and molecular support for these specimens being new species as proposed. Although morphologically similar to C. fenzlii and C. obtusifolia, the remarkable point of our study is that C. bingoelensis is phylogenetically closer to C. spectabilis. This work has exciting implications for understanding the evolution and diversification of the genus Centaurea. In addition, the results of this study show that the samples identified as Centaurea species in Türkiye are still not entirely determined genetically.

AtıfOpenAlex1

İncele

Yazdıç, Ferit Can; Yazdıç, Fadime; Karaman, Altuğ; Yücel, Halit; Kilic, Sükran

Antibiyotik direnci, yeni antimikrobiyal ajanların keşfini gerektiren, her geçen gün büyüyen küresel bir endişedir. Spor oluşturan gram pozitif bir bakteri olan Bacillus velezensis, lipopeptitler (sürfaktin, fenjisin, iturin) ve poliketidler (difficidin, makrolaktin) gibi biyoaktif bileşikler üretmesiyle bilinmektedir. Bu maddeler geniş spektrumlu antimikrobiyal özellikler göstermekle beraber, bitki patojenlerini baskılar ve bitki büyümesini teşvik eder. Bu çalışmanın amacı, Türkiye'deki endemik Tunceli sarımsağı (Allium tuncelianum (Kollmann) Özhatay, B. Mathew ve Şiraneci) ile ilişkili topraktan B. velezensis'in izolasyonunu, tanımlanmasını ve antimikrobiyal potansiyelini araştırmaktadır. B. velezensis ŞK_B3 suşu, 16S rDNA dizilemesi kullanılarak tanımlandı ve gram pozitif (Staphylococcus aureus, Bacillus subtilis) ve gram negatif (Escherichia coli, Pseudomonas aeruginosa) bakterilere karşı antimikrobiyal aktivite açısından test edildi. Streptomisin ve penisilin gibi standart antibiyotiklere kıyasla orta düzeyde aktivite gösterse de, etkinliği özellikle gram pozitif bakterilere karşı dikkat çekici olduğu tespit edilmiştir. Sonuçlar, özellikle gram pozitif bakterilere karşı orta düzeyde inhibitör aktivitesi olduğunu göstermiştir. Bu da tarımda bir biyokontrol ajanı ve yeni antibiyotik kaynağı olarak potansiyelini vurgulamaktadır. Etkin bileşiklerin aydınlatılması ve antimikrobiyal etkinliğin artırılması için daha ileri çalışmalara ihtiyaç vardır.

İncele

Koçak, Berna; Gürler, Nedim; İpek, Yeliz; Yazdıç, Ferit Can; Karaman, Altuğ

Starch and gelatin offer opportunities for use due to their non-toxicity, biocompatibility, physical and functional properties. In this study, different amounts of nano-zinc borate were added to starch/gelatin composition for biological applications and their properties were studied. The structure of the films was investigated by various techniques. Nanostructured zinc borate was synthesized using a chemical method and particle sizes were determined as 196 nm. The atenolol drug was doped into the polymer composite. The atenolol release was performed at pH 7.4 and in phosphate-buffered saline solution medium. Cumulative drug release was 76% with the inclusion of nano-zinc borate in the polymer mixture. The atenolol release was approximately 50%–70% in films with nano-zinc borate added after 300 min. Furthermore, thermal resistance of the films improved with the addition of nano-zinc borate. The investigated chemical compound exhibited pronounced antibacterial activity against Gram-positive bacteria (Bacillus subtilis and Staphylococcus aureus), with significantly greater potency compared to Gram-negative bacteria (E. coli and Pseudomonas aeruginosa). Notably, the formulation containing 1.5% starch, 0.5% gelatin, and 1% nano-zinc borate demonstrated broad-spectrum efficacy against all tested pathogens, highlighting its potential as a promising antibacterial agent. The observed differential activity against bacterial strains suggests that fine-tuning the concentrations of starch, gelatin, and nano-zinc borate may optimize antibacterial efficacy and broaden the spectrum. The results showed us that non-toxic and biocompatible polymer films can be realized in pharmaceutical industry systems and biomedical applications.

İncele

Kar, Bulent; Bahar, O.Z.; Yazdic, Ferit Can; Karaman, Altug

The myostatin gene (MSTN) is one of the main regulatory genes involved in muscle growth and development in many animals. This study aims to determine the variations in the exon 3 region associated with MSTN expression in Savak Akkaraman sheep and analyze their relationship with growth characteristics. Molecular analyses (RLFP, Real-Time PCR and DNA sequencing) were performed using DNA and RNA isolations from 70 different sheep blood and meat samples. As a result of the study, exon 3 region analysis was performed using NgomIV, AluI, DraI, HaeIII and MspI restriction endonucleases to determine the genetic diversity in Savak Akkaraman sheep breed. Two genotypes (MM and Mm) were detected for MSTN/MspI and a monomorphic mm genotype indicating the conserved exon 3 region for MSTN/HaeIII. Additionally, four new Single Nucleotide Polymorphisms (SNPs) were detected at different positions (164th, 204th, 347th, and 441th) in the working exon region. Two of these SNPs (204th T→G: isoleucine→ methionine and 347th C→A-G: proline→glutamine-arginine) caused amino acid changes. In expression studies, it was determined that MSTN gene expression was higher in female sheep than in male sheep (p<0.05). The MM genotype (MSTN/MspI) was significantly associated with increased weight gain and MSTN expression, while TT genotype at SNP 204 and GG genotype at SNP 347 was found to be associated with meat yield and growth traits (p<0.05). As a result, the genetic differences and functional effects of the new genotypes determined in this study may shed light on breeding strategies aiming to increase meat production.

AtıfScopus3·WoS3·OpenAlex4

İncele

Bektas, Idris; Yazdıc, Ferit Can; Kusek, Mustafa

Apple rot disease, caused by Alternaria alternata, is causing significant losses in apple production, especially in post-harvest periods. Alternaria alternata, was isolated from rotten apple fruit of cv Amasya. Identification of the strain isolated from rotten apple fruit was made by ITS sequence and morphological analysis. In the present study, 58 different endophytic bacteria strains were isolated from apple fruit for use in apple rot disease control. Among the isolated strains, 26 endophyte strains were determined to inhibit the radial growth of mycelia of A. alternata in binary culture in PDA media. Based on 16S rRNA sequencing analysis, these antagonistic endophytic bacteria strains were identified as Bacillus ssp. Bacillus methylotrophicus (ib17) showed the highest significant inhibitory effect on the mycelial growth of A. alternata at a rate of 79.5% in PDA medium. The results of in vivo experiments showed that Bacillus licheniformis (ib20) achieved 100% biocontrol when endophyte bacterial strains were inoculated 24 h before the inoculation of A. alternata. When the three bacteria species and A. alternata were inoculated simultaneously, Bacillus myloliquefaciens (ib1), Bacillus licheniformis (ib21) and the Endophytic bacterium (ib16) showed the highest biocontrol efficacy against A. alternata at 81.8%. Furthermore, when the bacterial strains were inoculated at 24 h after inoculation of A. alternata, B. licheniformis (ib21) showed the highest biocontrol efficacy of 83.3% against the fungal pathogen compared to the controls. The endophytic bacterial strains produced fungal cell wall hydrolysing enzymes such as chitinase, cellulase, amylase and protease. According to the results of this study, apple endophytic bacteria are potential candidates to control apple decay caused by A. alternata through cell wall hydrolysing enzymes and reduce disease severity. However, the efficacy of the biological control was dependent on the applied time of epiphytic bacterial strains. Further research is needed on the biochemical mechanisms underlying the activity of these bacteria against A. alternata.

AtıfScopus7·WoS7·OpenAlex9

İncele

Gedik, Osman; Yazdıç, Ferit Can; Tasar, Neslihan; Karaman, Altuğ

Today, essential oils are considered safe substances and can be used as antibacterial additives. Pimpinella anisum L. (Aniseed) and Foeniculum vulgare Mill. var. dulce (fennel) species are of great economic importance. It is among the medicinal and aromatic plants cultivated in wide areas in our country. In this study, it was aimed to determine the antimicrobial properties of essential oils obtained from Foeniculum vulgare Mill. and Pimpinella anisum L plants. The essential oils of the species were obtained by using the distillation method. The antimicrobial activities of essential oils by hand were studied using the hollow agar method. Known to be medically important in food, cosmetics and pharmaceutical products Enterobacter aerogenes (ATCC 13048), Enterococcus faecalis (ATCC 29212), Salmonella enteritidis (ATCC 13075), Staphylococcus aureus subsp. aureus (ATCC 25923), Escherichia coli (ATCC 25922) and Serratia marcescens (ATCC 13880) evaluated against pathogen and microbial contaminants. While Foeniculum vulgare showed results parallel to the antibiotic used as standard, no antibacterial activity was observed in Pimpinella anisum L.

AtıfOpenAlex2·TR Dizin2

İncele

Gedik, Osman; Yazdıç, Ferit Can; Tasar, Neslihan; Karaman, Altuğ

Bitkilerden elde edilen biyolojik aktif bileşenlerin incelenmesi son zamanlarda en çok araştırılan konular arasındadır. Türkiye florasının çok zengin bir yapıya sahip olması, bu coğrafyada yetişen bitkilerin araştırılmasının önemli olduğunu göstermektedir. Bu çalışmada, kimyasal bileşen olarak eski ve yaygın bir kullanım alanına sahip olan aynı zamanda önemli bir tıbbi bitki olan Hypericum cinsine ait 3 taksondan elde edilen uçucu yağlar antibakteriyel etkileri yönüyle araştırılmıştır. Hypericum spectabile Jaub. &amp; Spach (endemik tür), H. scabrum L., H. venustum Fenzl. türlerinin uçucu yağları distilasyon yöntemi kullanılarak elde edilmiştir. Elde edilen bu yağların antibakteriyel etkileri, in vitro olarak birçok ilaca direnç gösterdiği bilinen; Enterobacter aerogenes (ATCC 13048), Enterococcus faecalis (ATCC 29212), Salmonella enteritidis (ATCC 13075), Staphylococcus aureus subsp. aureus (ATCC 25923), Escherichia coli (ATCC 25922) ve Serratia marcescens (ATCC 13880) patojen bakterileri kullanılarak araştırılmıştır. Türlerin farklı uçucu yağları, çeşitli mikroorganizmalara karşı antibakteriyel aktivite için oyuk agar testi kullanılarak analiz edilmiştir. Tüm uçucu yağların test edilen tüm patojen strainlerine karşı değişen oranlarda (4,80±0,87-27,73±1,27 mm) aktivite gösterdiği gözlenmiştir. Bu türler, literatürde antibakteriyel aktivite açısından yeni değerlendirilen türler arasında gösterilebilir.

AtıfOpenAlex4·TR Dizin3

İncele