Sürdürülebilir Kalkınma Amaçları

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• DüzeltmeAçık Erişim2026Scopus SJRQ3/r/munzur/1491
  Erratum to: Sequence Analysis and Genetic Diversity of ndhF of the Chloroplast DNA (cpDNA) of Chrysophthalmum (Asteraceae) Species in Türkiye

  Sevindik, Emre; Gelir, Seda Nur; Demircan, Şelale; Çiftçi, İbrahim; Paksoy, Mehmet Yavuz

  The article number was incorrectly given as 30 but should have been 29.

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• MakaleYalnız künye2026Scopus SJRQ3/r/munzur/945
  Sequence Analysis and Genetic Diversity of ndhF of the Chloroplast DNA (cpDNA) of Chrysophthalmum (Asteraceae) Species in Türkiye

  Sevindik, Emre; Gelir, Seda Nur; Demircan, Şelale; Çiftçi, İbrahim; Paksoy, Mehmet Yavuz

  Absract: In this study, chloroplast DNA (cpDNA) ndhF sequence analysis was used to determine the sequence analysis and genetic diversity of Chrysophthalmum Schultz Bip. species distributed in Türkiye. Genomic DNA was isolated from green leaves and cpDNA ndhF region was amplified by PCR. The results of the PCR, the forward and reverse sequences were edited using the Sequencher 5.4.6 programme and the contig sequences were obtained. To determine the phylogenetic relationships between species, MEGA 6.0 was used to construct a maximum likelihood (ML) tree. Using the same program, nucleotide composition, phylogenetic trees, genetic distance matrix, and genetic diversity analyses were performed. In addition, the physicochemical properties and 3D structure of ndhF proteins were determined. From the results of the ndhF analyses, the nucleotide length of Chrysophthalmum species was found to vary between 471 and 625. The genetic matrix value was determined to be between 0.000 and 0.009. In the phylogenetic tree constructed using ndhF sequences from Anvillea DC., Pulicaria Gaertn., Limbarda Adans, Inula L., Carpesium L., Pentanema Cass., Dittrichia Greuter, Rhanteriopsis Rauschert and Telekia Baumg species from NCBI, C. montanum was grouped with Inula, Pentanema and Rhanteriopsis species. C. gueneri was grouped with C. dichotomum and Pentanema alanyense. Previous phylogenetic studies were in agreement with our results. In addition, the ndhF results supported that Chrysophthalmum species are not a monophyletic group.

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• DüzeltmeYayıncıda açık erişim2026Scopus SJRQ1/r/munzur/611
  Correction: Comprehensive Biological and Chemical Evaluation of Two Seseli Species (S. gummiferum and S. transcaucasicum) (Antioxidants, (2021), 10, 10, (1510), 10.3390/antiox10101510)

  Zengin, Gokhan; Stojković, Dejan; Mahomoodally, Mohamad Fawzi; Jugreet, Bibi Sharmeen; Paksoy, Mehmet Yavuz; Ivanov, Marija; Gašić, Uroš; Gallo, Monica; Montesano, Domenico

  In the original publication [1], there was a mistake in Figure 1 as published. The figure, as published, did not include the appropriate statistical information. We have revised the figure accordingly, and the corrected version of “Figure 1” is presented below. The authors state that the scientific conclusions are unaffected. This correction was approved by the Academic Editor. The original publication has also been updated.

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• MakaleYalnız künye2025Scopus SJRQ2/r/munzur/1477
  Phylogenetic analysis of the nrDNA ITS and cpDNA rbcL sequences of some endemic Dianthus (Caryophyllaceae) species from Türkiye

  Sevindik, Emre; Güner, Özal; Yolcu, Seher; Başköse, İsa; Paksoy, Mehmet Yavuz; Khadivi, Ali; Tunç, Yazgan; Yaman, Mehmet

  In this study, the phylogenetic relationship of four species of Dianthus genus which are endemic and distributed in Türkiye, including D. zederbaueri Vierch, D. varankii Hamzaoğlu & Koç, D. halisdemirii Hamzaoğlu & Koç, and D. goekayi Kaynak, was determined using nuclear DNA (nrDNA) internal transcribed spacer (ITS) and chloroplast DNA (cpDNA) rbcL regions. After sampling from the plant, DNA was extracted and the ITS (ITS4-ITS5A) and rbcL (rbcLaF-rbcLaR) primers were used to perform PCR amplification. Sequencer 5.4.6. was used to edit the sequences. MEGA 11 software was used to determine the nucleotide ratios, genetic distance matrix, and π = nucleotide diversity. Some species of Dianthus available in the National Center for Biotechnology Information (NCBI) were used to construct maximum likelihood (ML) phylogenetic trees. As a result, based on the ITS analysis π = nucleotide diversity was determined as: 0.001543, and the result of the rbcL analysis π = nucleotide diversity was determined as: 0.000000. In the ITS results, D. halisdemirii, D. superbus, and D. varankii appeared together, while D. zederbaueri and D. aculeatus appeared together. The rbcL results showed that D. zederbaueri and D. varankii were closely related, but the relationship between D. halisdemirii and D. goekayi could not be determined. Furthermore, in the phylogenetic tree constructed by taking the ITS and rbcL sequences of Dianthus, Gypsophila, Silene, Arenaria, Saponaria, Cerastium, Stellaria, Petrorhagia, Minuartia, Agrostemma, and Polycarpon species from NCBI using ITS and rbcL sequences, our endemic Dianthus species appeared in the same group with Petrorhagia, Gypsophila, and Saponaria species. To conclude, our ITS and rbcL results were consistent in determining the phylogenetic relationships of our Dianthus species with other species.

  AtıfScopus1

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• MakaleYalnız künye2025Scopus SJRQ3/r/munzur/1282
  Phylogenetic Analysis of Lisaea Boiss. (Apiaceae) Species in Türkiye Based on Chloroplast DNA (cpDNA) trnL-intron, trnL-F, matK and rbcL Sequences

  Efe, Fadime; Sevindik, Emre; Sevindik, Mustafa; Paksoy, Mehmet Yavuz

  Abstract: In this study, Lisaea heterocarpa,Lisaea papyracea and Lisaea strigosa species belonging to the Lisaea genus distributed in Türkiye phylogenetic analysis was determined chloroplast DNA regions. Plant samples were collected from different provinces of Türkiye and taken to the laboratory for genomic DNA isolation, polymerase chain reaction and bioinformatics analysis. As a result of the study, the lowest π-nucleotide diversity was found in the rbcL analyses (0.000917), while the highest π-nucleotide diversity was found in the trnL-F analysis (0.008700). In the phylogenetic trees constructed using trnL intron, trnL-F,and rbcL sequences, the species L. strigosa and L. papyracea appeared together, while L. heterocarpa appeared close to this group. The matK sequences, L. strigosa and L.heterocarpa appeared together, while L. papyracea appeared close to this group. In addition, the phylogenetic trees constructed using sequences from some Apiaceae species from National Center for Biotechnology Information (NCBI) determined that the genus Lisaea is monophyletic. In the trnL-F and rbcL analyses, Lisaea species appeared together with Torilis,Yabea, Daucus, Cuminum, Pternopetalum and Anthriscus species, while in the matK analysis, Lisaea species appeared in a different group from Anthriscus species.

  AtıfScopus1·WoS1·OpenAlex1

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• MakaleAçık Erişim2024Scopus SJRQ2/r/munzur/2192
  Mattiastrum pulumurense (Cynoglossinae, Boraginaceae), a new endemic species from Türkiye

  Doğru Koca, Aslı; Gökmen, Mustafa; Yilmaz, Gülderen; Paksoy, Mehmet Yavuz

  A new species, Mattiastrum pulumurense, has been described from Tunceli in eastern Türkiye. It is generally distinguished from other species (except M. racemosum var. scabridum) by a sparsely hairy or glabrescent above-ground part. It is most similar morphologically to M. longipes, M. calycinum, and Paracaryum hedgei (P. hedgei is potentially a member of the genus Mattiastrum). However, it differs from M. longipes and M. calycinum by its 3–3.5-mm-long and linear lanceolate scales, 2.5–4.5-mm-long anthers, and 10–15-mm-long styles; it differs from Paracaryum hedgei by its 3–3.5-mm-long scales, 2.5–4.5-mm-long anthers. In addition, this new species differs from M. racemosum var. scabridum by having 3–3.5-mm-long scales and no scale appendages. A description of the new species, an illustration, a comparative Table of morphological characters, detailed photographs, and a distribution map of the new species together with adjacent species were provided. In addition, the evolutionary relationships of these species were calculated using both Bayesian inference and maximum likelihood analyses based on the ribosomal internal transcribed spacer (ITS1-5.8S-ITS2) and combined chloroplast data set (rps16 and trnL genes, trnL-trnF intergenic spacer). According to the phylogeny-based combined chloroplast data set, both populations of Mattiastrum pulumurense generate a monophyletic clade and are closely related to M. longipes, P. hedgei, and M. calycinum. According to ITS-based phylogeny, Mattiastrum pulumurense is closely related to Rindera tetraspis, which is seen in the paraphyletic and nested genera Mattiastrum-Paracaryum-Rindera.

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• MakaleAçık Erişim2024Scopus SJRQ1/r/munzur/2088
  Integrating chemical analysis with in vitro, in silico, and network pharmacology to discover potential functional compounds from Marrubium astracanicum subsp. macrodon

  Avşar, Ömer Kaan; Kasbolat, Sevgi; Ak, Gunes; Nilofar; Caprioli, Giovanni; Santanatoglia, Agnese; Uysal, Ahmet; Uba, Abdullahi Ibrahim; Ponniya, Sathish Kumar M.; Paksoy, Mehmet Yavuz

  The members of the genus Marrubium are of great interest because they contain biologically active compounds. With in this mind, we aimed to examine the chemical profiles and biological activities (antioxidant, enzyme inhibition and antimicrobial effects) of different extracts of Marrubium astracanicum subsp. macrodon. Extractions of the plants were carried out with the solvent n-hexane, acetone, acetone/water (70 %), and water. The antioxidant activity of these extracts was evaluated through six different assays, namely 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), cupric reducing antioxidant capacity (CUPRAC), ferric reducing antioxidant power (FRAP), metal chelating ability (MCA), and phosphomolybdenum (PBD). Additionally, the inhibitory effects of these solvents on five enzymes acetylcholinesterase (AChE), butyrylcholinesterase (BChE), tyrosinase, amylase, and glucosidase were investigated. The study detected 38 compounds in a plant, with the highest content in acetone and acetone/water extracts. The acetone/water extract demonstrated the highest antioxidant activity aligning with its superior total phenolic (51.9 mg gallic acid equivalent (GAE)/g) and flavonoid (31.0 mg rutin equivalent (RE)/g) content, highlighting a direct correlation between bioactive compound concentration and antioxidant potential across various assays. Regarding the enzyme inhibition activity, the acetone/water extract of this plant exhibited significant AChE inhibition measuring 2.5 mg galantamine equivalent (GALAE)/g and anti-glucosidase activity measuring 1.2 mmol acarbose equivalent (ACAE)/g. In antimicrobial evaluation, the acetone extract exhibited good antimicrobial activity against B. cereus at 0.2 mg/ml dose. In molecular docking analysis, delphinidin 3,5 diglucoside showed a good interaction with the active site of AChE active. Through the application of network pharmacology, an in-depth exploration was conducted to unravel the potential of compounds from M. astracanicum against Alzheimer's disease. The study specifically focused on identifying key targets within the Alzheimer's disease pathway, pinpointing crucial proteins such as Glycogen synthase kinase-3 (GSK3), Prostaglandin-endoperoxide synthase 2 (PTGS2), and Alzheimer's-associated amyloid precursor protein (APP). In summary, the plant can serve as a valuable ingredient in the production of functional products within the pharmaceutical, nutraceutical, and cosmeceutical applications.

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• MakaleAçık Erişim2024Scopus SJRQ1/r/munzur/2021
  A broad-spectrum biological activities of Heracleum humile extracts: A first report of the antiviral, anti-cancer and chemical properties

  Ocal, Mustafa; Duran Yelken, Selda; Altunoglu, Yasemin Celik; Baloglu, Mehmet Cengiz; Soomro, Sanam Iram; Zengin, Gokhan; Angeloni, Simone; Mustafa, Ahmed M.; Caprioli, Giovanni; Paksoy, Mehmet Yavuz

  The current work focused on researching the bioactive potential of ethyl acetate (EA), methanol (MeOH), and water extract of H. humile plant, specifically ethyl acetate, methanol extracts were acquired with maceration method, and water extract was obtained by the infusion method. The highest total phenolic ingredient was determined in the water extract, while the highest total flavonoid ingredient was found in the MeOH extract. The water extract displayed the most potent antioxidant activity in the assays used. The ethyl acetate extract showed the highest enzyme inhibition activity in Butyrylcholinesterase inhibition (BChE) and amylase assay. Antibacterial efficiency was analyzed using microdilution analysis. The minimum inhibitory concentration (MIC) amounts ranged from 125 to 500 μg/mL except for water extract. The antiviral potential of the extracts was assessed against Bovine herpes virus 1 (BoHV-1) (Cooper strain). Methanol extract showed more potent antiviral effect. Selectivity indices were calculated for ethyl acetate and methanol extract as 3.32 and 13.39, respectively. All extracts displayed Deoxyribonucleic Acid (DNA) protection activity at approximately 25%–35%. For cell viability evaluation, 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT) test was performed against triple-negative human breast adenocarcinoma cells (MDA-MB-231) and Michigan Cancer Foundation-7 (MCF-7) cells. The most effective results were found in ethyl acetate extract at 48h. The 50% inhibitor concentrations (IC50) were determined for MDA-MB-231 and MCF-7 as 116.7 μg/mL and 247.9 μg/mL, respectively. Based on the bioactive compound content results, extracts of H. humile include valuable compounds that possess significant biological properties. In conclusion, these extracts could offer promising novel plant-derived therapeutics.

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• MakaleAçık Erişim2024Scopus SJRQ4/r/munzur/1742
  MOLECULAR MARKERS ANALYSIS OF ENDEMIC BORNMUELLERA HAUSSKN. SPP. (BRASSICACEAE) IN TÜRKİYE; [ANALIZA MOLEKULARNIH MARKERA ENDEMIČNE VRSTE BORNMUELLERA HAUSSKN. SPP. (BRASSICACEAE) U TURSKOJ]

  Okan, Kemalcan; Özkara, Zekiye; Sevİndİk, Emre; Sevİndİk, Mustafa; Paksoy, Mehmet Yavuz

  Okan K., Z. Özkara, E. Sevindik, M. Sevindik, M. Y. Paksoy (2024). Molecular markers analysis of endemic Bornmuellera hausskn. spp. (Brassıcaceae) ın Türkiye. - Genetika, Vol 56, No.2, 295-304. In this study, molecular characterisation of Türkiye's endemic species Bornmuellera cappadocica (Willd.) Cullen & T.R. Dudley, Bornmuellera glabrescens (Boiss. & Balansa) Cullen & T.R.Dudley, Bornmuellera kiyakii Aytaç & Aksoy and Bornmuellera angustifolia (Hausskn. ex Bornm.) Cullen & T.R.Dudley was carried out using ten RAPD and ten ISSR primers. In RAPD-PCR analysis, 66 bands were obtained and the polymorphism rate was 96.96%. In the ISSR-PCR analysis, 119 bands were obtained and the polymorphism rate was 95.79%. In the UPGMA (Unweighted Pair Group Method with Arithmatic Mean) dendrogram based on RAPD-PCR, B. angustifolia and B. glabrescens were found to be a sister group, and B. kiyakii and B. cappadocica were a sister group. Principal Component Analysis (PCA) analysis based on RAPD-PCR were compatible with the UPGMA dendrogram. In the UPGMA dendrogram based on ISSR-PCR, B. kiyakii and B. glabrescens were found to be sister groups, and B. cappadocica was closely related to this group. PCA analysis based on ISSR-PCR were compatible with the UPGMA dendrogram. As a result, both RAPD and ISSR results a high rate of polymorphism were obtained. The results were compared with previous sequence-based studies, morphological, anatomical and palynological studies.

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• MakaleYalnız künye2024Scopus SJRQ2/r/munzur/1718
  Phylogenetic analysis of the endemic Bornmuellera Hausskn. spp. (Brassicaceae) in Türkiye based on nuclear ITS and chloroplast trnL intron, trnL-F, rbcL and trnQ-rps16 DNA sequences

  Okan, Kemalcan; Sevindik, Emre; Paksoy, Mehmet Yavuz

  In this study, phylogenetic analysis of Turkish endemic Bornmuellera (Brassicaceae) species was conducted based on nuclear ribosomal DNA (ITS) and chloroplast DNA (trnL intron, trnL-F, rbcL and trnQ-rps16 DNA) sequences. In addition, the relationships between the sequences of some Brassicaceae family species retrieved from NCBI, and Bornmuellera species were documented. All of the plant specimens were collected from different regions of Türkiye, and brought to the laboratory. Total genomic DNA was extracted using the GeneMark kit. After polymerase chain reaction (PCR) analyses, DNA sequences obtained were then edited using Sequencher 5.4, Bioedit 7.2.3 and FinchTV 1.4.0, and analyzed using MEGA 6.0 software. Maximum likelihood (ML) and bootstrap trees were constructed in order to identify the relationships among Bornmuellera species. In the study, the highest nucleotide diversity was detected by rps16-trnQ (0.039146) sequence analysis, while the lowest was detected by rbcL (0.004186) sequence analysis. In addition, according to the phylogenetic analysis results obtained with other Brassicaceae species, it is revealed that the Turkish endemic Bornmuellera genus is monophyletic.

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