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In this study, ‘Ak Sakı’ and ‘Kara Sakı’ apple cultivars were collected from different locations in Erzincan province, Türkiye, and genetic diversity was determined using the Start Codon Targeted (SCoT) marker technique. The SCoT marker technique was chosen because its gene targeting, long primer, and high annealing temperature make it more effective than other marker techniques. Using ten SCoT primers, 60 bands were obtained, and 42 of them were polymorphic. The polymorphism rate was determined to be 70%. The UPGMA (Unweighted Pair Group Method with Arithmetic mean) dendrogram created using the PAUP 4.0b10 program consists of two clades. The genetic distance between apple cultivars varies between 0.13462 and 0.45614. Principal Component Analysis (PCA) results were compatible with the UPGMA dendrogram. With the SCoT marker technique, genetic diversity among apple cultivars can be determined in a shorter time and with more reliable results. [ABSTRACT FROM AUTHOR]

In this study, phylogenetic analyses were performed using chloroplast rbcL sequences from Ajuga chamaepitys, Thymbra capitata, Lamium moschatum, Marrubium vulgare, Stachys cretica, Teucrium polium, and Vitex agnus-castus species distributed in Aydın province, Türkiye. After isolating DNA from the samples, PCR amplification was carried out using the rbcLaF and rbcLaR primers. Both forward and reverse sequences were edited using BioEdit 7.2.3, FinchTV 1.4.0, and Sequencher 5.4.6 software. The corrected sequences were converted to protein sequences, and phylogenetic analyses were conducted using MEGA 6.0 software. The rbcL proteins have been motif analysed and their 3D structure revealed. As a result, the phylogenetic tree constructed with sequences obtained from National Center for Biotechnology Information (NCBI) showed that Lamium and Marrubium species formed a clade, while Sideritis and Stachys species formed another one. Additionally, the species of Thymbra, Vitex, Ajuga, and Teucrium each formed distinct groups. In the analyses involving only these seven species, the genetic distance matrix revealed that the closest species were Ajuga chamaepitys and Vitex agnuscastus (0.009), while the most distantly related species were Teucrium polium and Thymbra capitata (0.043). Also, the nucleotide diversity was calculated to be π = 0.025278. Overall, the rbcL sequence results were instrumental in elucidating the phylogenetic relationships within the Lamiaceae family. [ABSTRACT FROM AUTHOR]

Essential oils (EOs) are compounds that are biosynthesized autonomously by aromatic plants as their secondary metabolites. Vitex agnus-castus plant leaves, flowers and fruits are of pharmacological importance. In this study, the chemical composition determination of the essential oils of the Vitex agnus-castus flowers with different colors (white, pink, purple) growing in Aydin ecological conditions was carried out with the extraction using Clevenger hydro-distillation apparatus and then the essential oil composition was determined by Gas Chromatography-Mass Spectrometer (GC-MS). As a result of the study, 'Çakmar' pink-flowered population had the main component (-)-allospathulenol (14.59%), 'Çakmar' purple-flowered and 'Koçarli' purple-flowered populations had the main component pyrrolo (3,2,1-jk) carbazole (14.42% and 14.68%, respectively), while 'Çakmar' white flowered, 'Koçarli' white flowered and 'Koçarli' pink flowered populations had the main component caryophyllene (15.54%, 12.64%, and 19.05 respectively). [ABSTRACT FROM AUTHOR]

In this study, molecular characterization of Dittrichia viscosa (L.) Greuter populations collected from Aydın province was carried out based on ISSR technique and chloroplast DNA trnL intron sequences. 10 ISSR primers were used to determine the molecular characterization among the populations. For cpDNA trnL intron amplification, trnC and trnD primers were used. In ISSR analysis, a total of 70 bands were obtained. The polymorphism rate was determined to be approximately 94.28%. According to the ISSR analysis, the UPGMA dendrogram consisted of three groups. For cpDNA trnL intron sequences, phylogenetic analyses were obtained along with genetic distances. For populations, cpDNA trnL intron sequences were determined between 454 and 472 bases. The maximum likelihood phylogenetic tree consist of two clades. In addition, cpDNA trnL intron sequences of some species (Chrysophthalmum Pulicaria Inula Jasonia Stenachaenium Carpesium Blumea Iphiona Limbarda Rhanterium Lifago Duhaldea Chiliadenus) of Asteraceae family from NCBI with Dittrichia viscosa populations phylogenetic tree was constructed. As a result of the study, it was determined that the polymorphism rate of Dittrichia viscosa populations obtained by ISSR-PCR was higher than the results obtained from trnL intron sequences. [ABSTRACT FROM AUTHOR]

This research was carried out with the aim of revealing the genetic differences of 30 cotton varieties from 14 countries using the iPBS-retrotransposon marker method. Genetic differences were determined by using iPBS marker method in PCR for 30 cotton varieties. According to the genetic distance matrix obtained in the NTSYS-pc 2.10e program, the closest genotypes were determined to be AzGR-11468 (Azerbaijan) and Maydos Yerlisi (India), and the similarity value between them was found to be 0.0318. The most distant genotypes were determined to be Hill Cotton 3 (Bangladesh) and Shazbaz (Pakistan), and the similarity value between them was found to be 0.7572. When the dendrogram generated based on the UPGMA method was examined.30 cotton varieties were divided into 2 clades. According to the PCA made in the JMP program, the graphic results and eigen values obtained on the two-dimensional plane also supported these results. The first 3 eigen values explained 85% of the total variance in the population. Overall results suggest that Hill Cotton 3 (Bangladesh) (Gossypium arboreum) and Shazbaz (Pakistan) (Gossypium hirsutum) cultivars, which are the most distant relatives among 30 cotton genotypes, can be used as breeding cultivars in future cotton breeding studies. [ABSTRACT FROM AUTHOR]

In this study, we performed DNA barcoding and phylogenetic analysis using one nuclear (ITS) and two chloroplast DNA regions (matK and rbcL) of endemic Astragalus nezaketiae A. Duran & Aytaçand Vicia alpestris Stev. subsp. hypoleuca (Boiss.) Davis taxa in Turkey. PCR reactions were performed using universal primers. Sequences of the PCR products were edited using BioEdit and FinchTV software and contigs were obtained. All contigs were Blasted at NCBI and similarities were analysed. Using the MEGA 6.0 program, maximum likelihood trees were constructed including some sequences retrieved from NCBI. For Astragalus nezaketiae; in the ITS analysis, Astragalus nezaketiae appeared separately from other species, and for matK, Astragalus nezaketiae appeared together with Astragalus cicer L. However, rbcL tree was polytomic. For Vicia alpestris subsp. hypoleuca; in ITS, rbcL and matK results Vicia alpestris subsp. hypoleuca were found together with Vicia cracca L., Vicia benghalensis L. and Vicia villosa Roth species. Analysis of the combined data revealed similar results with all barcode regions for Vicia alpestris subsp. hypoleuca while different phylogenetic results were obtained for Astragalus nezaketiae. [ABSTRACT FROM AUTHOR]

In this study, phylogenetic analysis of some fungal species distributed in West Kazakhstan was performed based on ITS sequences. All of the mushroom samples were collected from different regions of West Kazakhstan and brought to the laboratory. Total genomic DNA was extracted using a GeneMark commercial kit. ITS1 and ITS4 primers were used for the amplification of the ITS region in PCR analyses. The resulting DNA sequences were then edited using BioEdit and FinchTV. For phylogenetic analysis used MEGA 6.0 program. As a result of the study, ITS sequences ranged from 532 to 715 nucleotides, while the divergence values of the sequences differed between 0.000 and 0.468. The maximum likelihood tree constructed using ITS sequences consists of two clades. According to the phylogenetic analysis results obtained using other fungal species, ITS results were found to be a good indicator for the differentiation of fungal genera. [ABSTRACT FROM AUTHOR]

In this study, genetic diversity analysis of eight Teucrium polium L. populations distributed in Aydın province of Türkiye was conducted using ten RAPD markers. As a result of the study, a total of 45 bands were obtained, of which eight were monomorphic and 37 were polymorphic. The total polymorphism rate was determined as 82.22%. UPGMA dendrogram consists of two clades. The lowest similarity (-0.100) was observed between the Koçarlı and Hamitler village populations, while the highest coefficient (0.646) was observed with the Çakmar (road) and Hamitler village populations. As a result, RAPD marker technique can be a useful marker for revealing the genetic diversity of Teucrium polium populations. In addition, this results it will be a references for different marker and sequence-based studies in the future. [ABSTRACT FROM AUTHOR]

In this study, phylogenetic analyses of some Eriobotrya japonica (Thunb.) Lindl. populations based on SCoT marker technique and cpDNA trnL intron sequence analysis were performed. Specimens from the populations were collected from the Aegean region of Turkey and brought to the laboratory for genomic DNA isolation. To determine the phylogenetic analysis of Eriobotrya japonica populations, seven SCoT primers were used. In the SCoT analysis, a total of 54 bands were obtained, 49 of which were polymorphic and 5 were monomorphic. In chloroplast trnC intron region, trnC, trnX) primers were used for PCR amplification. Eriobotrya japonica trriC intron sequence lengths were determined to be between 530 and 547 nucleotides. The average nucleotide rate detected as 38.9% for thymine, 18.1% for cytosine, 28.2% for adenine and 14.8% for guanine. Rosaceae family trnL intron sequences belonging to Rhaphiolepis Lindl., Heteromeles M.Roem., Photinia Lindl. Cotoneaster Medik, Sorbus L., Malus Miller, Pyrus L., Prunus L. and Rosa L. were retrieved from NCBI and their phylogenetic relationship with Eriobotrya japonica populations were revealed. As a result of the study, polymorphism rate was determined as 90.74% in SCoT analysis. According to cpDNA trriE intron results, Eriobotrya japonica populations were identified in the same group with Rhaphiolepis in die a, a finding supported by past phylogenetic analyzes. [ABSTRACT FROM AUTHOR]

Cotton belongs to the genus of the Malvaceae family and presents an economically and biologically highly valuable multi-purpose crop grown as a source of fiber, food and feed worldwide. In this study, phylogenetic relationships of cotton genotypes of the thirteen countries (twelve Gossypium hirsutum and one Gossypium barbadense (GIZA 75 Egypt) as outgroup) taken from the Directorate of Nazilli Cotton Research Institute genetic stock were analyzed by using RAPD and ISSR markers. RAPD-PCR analysis obtained total of 53 DNA bands with the highest number of bands for OPA-02 and OPA-13 primers, no bands for OPE-08 primer and rate of polymorphism of 90.56%. ISSR-PCR analysis showed a total of 81 DNA bands, where the highest number of bands was obtained with UBC-811, UBC-834 and UBC836 primers, no bands with UBC-853 primer and rate of polymorphism of 77.77%. Phylogenetic tree was obtained by using the UPGMA algorithm and the tree consisted of two large clades. Analysis of the results suggests that RAPD and ISSR markers are useful tools to demonstrate phylogenetic relationships between cotton genotypes. [ABSTRACT FROM AUTHOR]

In this study, phylogenetic analysis of Turkish Conringia (Brassicaceae) species was conducted based on nuclear ribosomal DNA (nrITS) and chloroplast DNA (trnL-F) sequences. In addition, the relationships between the sequences of some Brassicaceae family species retrieved from NCBI, and Conringia species were documented. All of the plant specimens were collected at their flowering and vegetation periods from different regions of Turkey, and brought to the laboratory. Total genomic DNA was extracted using the GeneMark kit. In PCR analyses, ITS4 and ITS5A primers were used for the amplification of the nrITS region, while thetrnLe and trnLf primers were used for the cpDNA trnL-F region. The DNA sequences obtained were then edited using BioEdit and FinchTV, and analyzed using MEGA 6.0 software. Neighbor joining (NJ) and bootstrap trees were constructed in order to identify the relationships among Conringia taxa. The nrITS sequences ranged between 573 and 672 nucleotides, while the trnL-F sequences ranged between 346 and 764 nucleotides. The divergence values of nrITS sequences differed between 0.177 and 0.00 and divergence values of trnL-F sequences differed between 0.902 and 0.00. NJ tree generated using nrITS and trnL-F sequences consisted of two clades. In trees generated with both the nrITS and trnL-F sequences, C. orientalis, C. grandiflora and C. austriaca appeared within the same group. In addition, according to the phylogenetic analysis results obtained with other Brassicaceae species, it is revealed that the Conringia genus is polyphyletic. [ABSTRACT FROM AUTHOR]

This study was carried out in order to develop an embryo culture technique and to establish breeding lines with this technique. Ovule culture was preferred in the study because the seeds were too small and embryo isolation was difficult. Embryo cultures were done by using populations obtained from producers in Samsun, Denizli, Isparta, Mersin in Turkey and Çameli black cumin variety. Hybridizations were done according to the semi-diallel hybridization method to gain zygotic embryos. LS2.5 and MS (Sigma Aldrich Catalog number: M5519) mediums were used for ovule culture and MSD4 medium was used growing the plants obtained from the ovules. As a result of the research, a total of 2904 ovules were cultured in LS2.5 medium. 148 of them showed callus development; callus formation rate was 5.10%. The highest callus formation rate in the investigated combinations was obtained from Çameli x Denizli combination at 7.26%. Plant regeneration could not be obtained from these calluses. A total of 3526 ovules were cultured in MS medium. Sixty plantlets were obtained from these ovules and plant formation rate was determined as 1.70%. 41 plants from these matured and were harvested. [ABSTRACT FROM AUTHOR]

In this study, genetic diversity and phylogenetic analyzis based on cpDNA trnL intron and trnL-F sequences of L. nobilis L. populations were made. Persea schiedeana and Endiandra wolfei taxa were used as outgroups. Plant samples were collected from various different provinces and districts of the Aegean region and brought to the laboratory. Genomic DNAs were isolated from fresh and green leaves of the plants. trnC and trnD primers were used for the trnL intron region, and trnE and trnF primers were used for the trnL-F region. The obtained DNA sequences were then corrected using BioEdit and FinchTV programs. MEGA 6.0 program was used both phylogenetic analyzis and the detection of genetic distances. For the intron region of the trnL, the mean nucleotide composition was determined as 36.5% T, 20.2% C, 26.4% A and 16.9% G. These values were found as 30.7% T for 15.9% C, 31.9% A and 21.6% G for the trnL-F region. The lowest distance for the trnL intron region was found 0.000 while the highest distance was 0.004. The value was found 0.000 for the trnL-F region. The phylogenetic tree, which was obtained using both trnL intron and trnL-F sequences, consisted of two large branches. As a result, according to the data obtained from trnL intron and trnL-F sequences, the trnL intron sequence found a solvent in the phylogenetic relationship between L. nobilis populations, while the phylogenetic relationship between trnL-F sequence and L. nobilis populations was not found. [ABSTRACT FROM AUTHOR]

The genus Inula belongs to family Asteraceae and it is medicinally important because it possesses cytotoxic, anticancer, hepatoprotective, antibacterial and anti-inflammatory properties. The aim of this research was to explore antioxidant and anti-urease activities of fifteen Inula taxa in Turkey. Ethanol extracts of Inula taxa were obtained by Soxhlet extraction. Antioxidant activity was determined through total antioxidant activity, total phenolic content and copper reducing antioxidant capacity (CUPRAC) analyses. The highest total phenolic content and total antioxidant capacity were found in I. orientalis (158.54±0.002 µg GAE/mL) and I. macrocephala (189.16±0.002 µg AAE/mL). CUPRAC activity increases with the increasing concentration of the extracts and the standard. Moreover, all the tested plants exhibited better anti-urease activity than standard thiourea except for I. anatolica and I. thapsoides subsp. thapsoides. Results obtained from this study demonstrate that Inula species might be utilized as a probable natural source in the pharmaceutical and food industries but further and more specific studies are needed to determine active antioxidative and anti-urease compounds in the extracts. [ABSTRACT FROM AUTHOR]

In this study, genetic diversity and phylogenetic analyzis based on cpDNA trnL intron and trnL-F sequences of L. nobilis L. populations were made. Persea schiedeana and Endiandra wolfei taxa were used as outgroups. Plant samples were collected from various different provinces and districts of the Aegean region and brought to the laboratory. Genomic DNAs were isolated from fresh and green leaves of the plants. trnC and trnD primers were used for the trnL intron region, and trnE and trnF primers were used for the trnL-F region. The obtained DNA sequences were then corrected using BioEdit and FinchTV programs. MEGA 6.0 program was used both phylogenetic analyzis and the detection of genetic distances. For the intron region of the trnL, the mean nucleotide composition was determined as 36.5% T, 20.2% C, 26.4% A and 16.9% G. These values were found as 30.7% T for 15.9% C, 31.9% A and 21.6% G for the trnL-F region. The lowest distance for the trnL intron region was found 0.000 while the highest distance was 0.004. The value was found 0.000 for the trnL-F region. The phylogenetic tree, which was obtained using both trnL intron and trnL-F sequences, consisted of two large branches. As a result, according to the data obtained from trnL intron and trnL-F sequences, the trnL intron sequence found a solvent in the phylogenetic relationship between L. nobilis populations, while the phylogenetic relationship between trnL-F sequence and L. nobilis populations was not found. [ABSTRACT FROM AUTHOR]

Plants display several biological activities as a result of the production of various chemicals inside their metabolic processes. In recent times, the growing prevalence of alternative medicine uses has elevated the significance of plants. The present work aimed to assess the biological activities, phenolic and chemical compositions, applicability, mineral composition, and overall characteristics of Citrullus colocynthis (L.) Schrad. as documented in existing literature. Literature study revealed that it possesses significant antioxidant, antibacterial, and anticancer properties. Furthermore, it has been observed that it may serve as a potential reservoir for the minerals documented inside its structure. It is also thought to be an important source, especially in terms of potassium. From this perspective, it became evident that the fruit components of the plant, in particular, could serve as a significant natural resource for promoting health. [ABSTRACT FROM AUTHOR]

In this study, we performed a genetic diversity analysis using RAPD markers for some Vitex agnus-castus populations grown in Aydin, Turkey. Total genomic DNA isolation from the leaves of Vitex agnus-castus was performed using a commercial kit. Seven RAPD primers (OPA-02, OPA-05, OPA-13, OPA-15, OPA-16, OPA-18, OPA-20) were used to determine genetic diversity among populations. Polymerase Chain Reaction (PCR) was performed with all genomic DNA samples and primers. PCR products were run in agarose gel electrophoresis and visualized under UV light. The amplified products were scored as bands (1) and no bands (0) for all gel images and their matrix files were generated. A total of 36 characters were obtained from the primers. Phylogenetic relationships and genetic distances between the cultivars were calculated by using the PAUP* (Phylogenetic Analysis Using Parsimony and other methods) program. According to PAUP analysis, the closest genetic distances were between Çine pink flower and Çakmar purple flower, and Çakmar pink flower and Çakmar purple flower populations with a value of 0.05556; and the greatest genetic distance was between Çakmar pink flower and Köşk purple flower populations with a value of 0.36111. In the phylogenetic analysis obtained using UPGMA algorithms, the phylogenetic tree consisted of four groups. The results suggest that RAPD markers are useful tools for determining genetic relationships among Vitex agnus-castus genotypes. [ABSTRACT FROM AUTHOR]

The large subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) protein, which plays an important role in the photosynthesis reaction, are encoded by the chloroplast genome. Sideritis L., a medical and aromatic plant group, belongs to Lamiaceae family. In this study, we performed sequence, physicochemical, phylogenetic and three-dimensional (3D) bioinformatic analyses of RuBisCO large subunit (rbcL) proteins in the Sideritis ssp. using various bioinformatics tools. Physicochemical analyzes were performed by ExPASy - ProtParam. The putative phosphorylation sites of the rbcL proteins were determined by NetPhos 2.0 and NetPhos 3.1. Phylogenetic analyses were performed with the MEGA 6.0 software. To estimate 3D protein structures, PyMol program was used. At the end of the study, it was found that the amino acid number of stilbene synthase proteins ranged between 171 and 456, molecular weight ranged between 19002.67 and 50420.44 Da, instability index ranged between 27.30 to 40.70 and GRAVY values ranged between -0.394 to -0.226. While the highest average amino acid rate in the rbcL proteins was Gly (10.00%), the lowest amino acid ratio (1.4%) was determined as Trp. In phylogenetic analyses performed using protein sequences, maximum likelihood (ML) tree consisted of 2 large clades. Pairwise distance analysis based on Sideritis species’ rbcL protein sequences was performed using MEGA 6.0. The lowest pairwise distance was 0.000, while the highest pairwise distance was 0.024. When the estimated 3D structures of the proteins were examined, the Gly residue, which plays an important role in the structure and function of the proteins, was detected as the least in S. libanotica subsp. kurdica species while it was the most abundant residue in S. cretica subsp. spicata. The results of our study provide insights into fundamental characteristics of rbcL proteins in Sideritis taxa. [ABSTRACT FROM AUTHOR]

In the present study, chemical composition determination and in vitro antimicrobial effects of essential oil of Achillea biebersteinii plant grown under Erzincan ecological conditions were evaluated. Extractions were carried out with Clevenger apparatus and essential oil composition was determined by Gas Chromatography-Mass Spectrometry (GC-MS). Microorganisms used for the antimicrobial studies were Salmonella enterica serovar. typhimirium ATCC 14028, Staphylococcus aureus subsp. aureus ATCC 25923, Yersinia pseudotuberculosis ATCC 911, Bacillus cereus 702 ROMA, Enterobacter aerogenes CCM 2531, Bacillus subtilis IMG 22 and Proteus vulgaris FMC 1. As a result, a total of 29 components were detected in Achillea biebersteinii. Among them, 1,8-cineole (20.36%), cyclohexanone (8.39%), 2-cyclohexen-1-one (5.38%) and spathulenol (4.19%) were found as the major components. For the in vitro antimicrobial activity determination of essential oil, disc diffusion method was used in our study. Furthermore, 12-14 mm zone diameters were detected in antimicrobial activity assay. The highest resistance zone was detected against B. subtilis with 14 mm diameter while the least resistance zone was detected against Y. pseudotuberculosis, E. aerogenes and P. vulgaris with 12 mm diameter. Consequently, it was concluded that the essential oil extracted from the A. biebersteinii grown under Erzincan ecological conditions had an inhibitory effects on the pathogenic microorganisms in used method. [ABSTRACT FROM AUTHOR]

In this study, phylogenetic analysis of some Turkish Citrus species was conducted based on chloroplast DNA (trnL intron and trnL-F) sequences. Citrus taxa were plotted on a phylogenetic tree where Zanthoxylum ailanthoides was used as the outgroup. The sequences for trnL intron and trnL-F regions of the outgroup were retrieved from NCBI GenBank. All plant samples were collected from different locations during the inflorescence and vegetation periods, and brought to the laboratory. Genomic DNA was isolated from healthy green leaves using DNAeasy Plant Mini Kit. trnL intron region was amplified using universal primers trnc and trnd, while for the trnL-F region trne and trnf were used. Later obtained DNA sequences were edited using BioEdit 7.0.4.1 and FinchTV. Sequencing data were aligned via ClustalW program and analyzed using MEGA 6.0 software. Maximum Likelihood and bootstrap trees were constructed in order to identify the relationships among Citrus taxa. The trnL intron sequences ranged from 554 to 581 nucleotides. The average nucleotide composition of trnL intron was 26.3% T, 16.8% C, 37.7% A and 19.2% G. The divergence values varied from 0.000 to 0.057. The trnL-F sequences ranged from 392 to 399 nucleotides. Average nucleotide composition was 34.3% T, 21.2% C, 27.4% A and 17.1% G, while the divergence values of trnL-F sequences varied from 0.000 to 0.003. As a result, trees constructed based on trnL intron region have systematically been found to show more reliable and compatible results than those formed based on the trnL-F region. [ABSTRACT FROM AUTHOR]

The aim of this was to assessment chemical composition, antiproliferative of valuable essential oils from Citrus sinensis and Citrus aurantium flowers commonly used in Anatolia. According to the results of the gas chromatography-mass spectrometry analysis, nerolidol (22.13 %), linalool (14.06 %) were found to be highest in the essential oil obtained from C. sinensis. Nerolidol (28.07 %), 2,6,10-dodecatriene-1-ol (15.11 %), were found to be highest in the essential oil obtained from C. aurantium. The antiproliferative activity for both natural products was conducted following the European Pharmacopoeia 8.0 protocol. According to this protocol, we investigated both products for in vitro antiproliferative activity against HeLa, HT29, A549, Hep3B, MCF7 cancer cells and FL normal cells using a cell proliferation assay, cytotoxicity assay (LDH), and phase-contrast microscopic image evaluation techniques. Both essential oils exhibited the strong antiproliferative effect together with low cytotoxicity values at the low and mid concentration (1.9-2.9 Log10 μg/mL). Both samples altered the morphological shape of the cells from being cell shrinkage and rounding to being decreased cell elongation and volume at high concentration (2.9-4.4 Log10 μg/mL). However, these essentials oils caused high cytotoxic effect against FL normal cells compared to that of cancer cells, indicating that these were not promising suitable antiproliferative agents against cells tested. We believe that both essential oils need to be developed by making a more rational research because they have affected normal FL cells. As a conclusion, it seems substantial to continue to improve both essential oils to help the cancer problem further. [ABSTRACT FROM AUTHOR]

This study was carried out with the aim of determining the antifungal effect of the essential oil isolated from Achillea millefolium subsp. millefolium plant against pathogenic fungi. In order to test the antifungal effect of the oil, an analysis was conducted on a total of 4 pathogen fungi which included Candida albicans, Candida tropicalis, Candida parapsilosis and Saccharomyces cerevisiae, and the effect of the essential oil on the growth of these fungi was investigated. The essential oil of A. millefolium ssp. millefolium had varying degrees of effect on the tested fungi. The highest antifungal effect was found against S. cerevisiae; whereas the lowest antifungal effect was found against C. parapsilosis. Nystatin showed a higher activity than the essential oil of A. millefolium subsp. millefolium against the tested fungi. MIC values of the essential oil against the tested fungi ranged from 1.25 µl/ml to 10 µl/ml. The results obtained indicate that essential oil of A. millefolium subsp. millefolium can be used as an alternative to antifungal agents such as amphotericin, ketoconazole, and fluconazole. [ABSTRACT FROM AUTHOR]

In this study, we performed sequence, physicochemical, phylogenetic, and comparative 3D (three-dimensional) analyses of RuBisCO large subunit proteins of the Morus species using various bioinformatics tools. The sequence lengths of the RuBisCO proteins varied between 140 and 475 amino acids with molecular weights (MW) ranging from 15463.40 to 52667.95 Da. The most acidic protein sequences were in M. australis, M. rotundiloba, M. serrata, and M. cathayana (pI=4.77). The extinction coefficients of the proteins at 280 nm ranged from 21430 to 69830 M-1 cm-1, the instability index (II) values ranged from 26.06 to 42.17, and the GRAVY values ranged from -0.355 to -0.215. The most abundant amino acid of RuBisCO proteins was Gly (9.5%) while the least abundant ones were Cys and Trp (1.5%). Based on the phylogenetic analysis, the tree constructed using RuBisCO proteins is composed of three main clades. A RAMPAGE analysis revealed that 96.1% - 98.5% of residues were located in the favored region in RuBisCO proteins. To predict the three dimensional (3D) structures of the RuBisCO proteins PyMOL was used. The highest number of Gly residues was detected in M.mongolica, M. indica, M.notabilis, M. alba var. atropurpurea and M. alba var. multicaulis, while the least Gly residues were detected in M. australis, M.rotundiloba, M. serrata and M.cathayana. The results of our study provide insights into fundamental characteristic of RuBisCO proteins in Morus species. [ABSTRACT FROM AUTHOR]

RuBisCO is an important enzyme for plants to photosynthesize and balance carbon dioxide in the atmosphere. This study aimed to perform sequence, physicochemical, phylogenetic and 3D (three-dimensional) comparative analyses of RuBisCO proteins in the Carthamus ssp. using various bioinformatics tools. The sequence lengths of the RuBisCO proteins were between 166 and 477 amino acids. Their molecular weights (Mw) ranged from 18,711.47 to 52,843.09 Da; the most acidic and basic protein sequences were detected in C. tinctorius (pI = 5.99) and in C. tenuis (pI = 6.92), respectively. The extinction coefficients of RuBisCO proteins at 280 nm ranged from 17,670 to 69,830 M-1 cm-1, the instability index (II) values for RuBisCO proteins ranged from 33.31 to 39.39, while the GRAVY values of RuBisCO proteins ranged from -0.313 to -0.250. The most abundant amino acid in the RuBisCO protein was Gly (9.7%), while the least amino acid ratio was Trp (1.6 %). The putative phosphorylation sites of RuBisCO proteins were determined by NetPhos 2.0. Phylogenetic analysis revealed that RuBisCO proteins formed two main clades. A RAMPAGE analysis revealed that 96.3%-97.6% of residues were located in the favoured region of RuBisCO proteins. To predict the three dimensional (3D) structure of the RuBisCO proteins PyMOL was used. The results of the current study provide insights into fundamental characteristic of RuBisCO proteins in Carthamus ssp. [ABSTRACT FROM AUTHOR]

Walnut (Juglans regia L.) is a deciduous tree of the Juglandaceae family. Beta-amylase (β-amylase, EC 3.2.1.2) is an enzyme that catalyses hydrolysis of glycosidic bonds in polysaccharides. In this study; sequence, physicochemical, and three-dimensional analyses of predicted β-amylase 7-like protein in Juglans regia using various bioinformatic tools were conducted. The physicochemical properties of the predict β-amylase 7-like protein were analyzed by using ExPASy ProtParam tool that revealed the molecular weight (MW), Isoelectric Points (pI), total number of negatively charged residues (Asp + Glu), total number of positively charged residues (Arg + Lys), instability index, aliphatic index and GRAVY (Grand Average of Hydropathy) values. Subcellular localization using CELLO v.2.5, putative phosphorylation sites using NetPhos 3.1 server, domain analysis using Pfam, and secondary structure prediction using SOPMA were accomplished. To predict the 3D structure of the predict β-amylase 7-like protein, homology models were applied using PSIPRED, RAMPAGE and PyMOL programs. The results of our study provide insight into fundamental characteristics of the predicted β-amylase 7-like protein in Juglans regia. [ABSTRACT FROM AUTHOR]

Mentha L., recognized as a medical and aromatic plant, is a general name affiliated to mint species and belongs to Labiatae family. Some species are used as fresh vegetables in the Turkish kitchen and they can also be used in salads. In addition, some species have been used as a spice in food. In this study, chemical composition and antimicrobial activity towards some pathogenics (gram + and gram -) microorganisms of the essential oils Mentha spicata L. subsp. tomentosa (Briq.) Harley, Mentha pulegium L. grown under West Anatolian ecological conditions were investigated. Extractions were carried out with Clevenger apparatus and essential oil composition was determined by Gas Chromatography-Mass Spectrometry (GC-MS). Microorganisms used for the antimicrobial studies were Methicillin-resistant Staphylococcus aureus (MRSA), Staphylococcus aureus ATCC 6538, Pseudomonas aeruginosa, Enterococcus faecium DSM 13590, Escherichia coli Q157:H7 and Bacillus cereus CCM99. As a result, M. pulegium and M. spicata subsp. tomentosa were found to be rich in piperitenone oxide: 72.77% and 25.84%, respectively. Each of the oils was found to possess antimicrobial properties against test microorganisms. Essential oils obtained from Mentha species give positive effect on all microorganisms. [ABSTRACT FROM AUTHOR]

In the current study, sequence analysis of some Turkish Lactuca L. species using nrITS DNA and trnL-F cpDNA sequences were performed to elucidate phylogenetic relationships among the taxa under study. Hieracium umbellatum was used as an outgroup. Different plant materials of Lactuca were collected from different parts of Turkey during excursions of summer 2013. Plant materials were either kept in silica gel or kept fresh for immediate DNA isolation. Both phenol chloroform-isoamyl alcohol method and commercial kits were used to extract genomic DNA for PCR reactions. ITS4 and ITS5A primers were utilized for ITS region, while trnLe and trnLf primers were used to amplify the trnL-F region. Obtained DNA sequences were edited both manually and by using BioEdit 7.0.4.1. Sequencing data were aligned via ClustalW program and analyzed using PAUP 4.01b10 software. nrITS sequences varied from 639 nucleotides to 735 nucleotides. Average nucleotide composition for nrITS was 22.1% (T), 27.9% (C), 23.2% (A) and 26.8% (G). It was also found that divergence values differed between 0.0000 and 0.10290. The trnL-F sequences varied from 296 nucleotides to 385 nucleotides. Average nucleotide composition of trnL-F sequences was 34.1% (T), 18.4% (C), 31.6% (A) and 16.0% (G). It was also found that divergence values differed between 0.0000 and 0.09674. Neighbour Joining (NJ) trees were constructed in order to identify the relationships among Lactuca species. Phylogenetic trees based on ITS region were found to be more useful than phylogenetic trees based on trnL-F region. After analysis of the results obtained, the data suggest that Lactuca contains 2 clades, with clade 1 having 2 subclades. These results support the prior phylogenetic studies on Lactuca and hence provide an up to date review of Turkish Lactuca species. [ABSTRACT FROM AUTHOR]

Simple, fast, low-cost and high throughput protocols are required for DNA isolation of plant species. In this study, phenol chloroform isoamyl alcohol and commercial (Sigma) DNA isolation kit methods were applied on some Inula species that belong to Asteraceae family. Genomic DNA amounts, A260, A280, A260/A230 and purity degrees (A260/A280) that were obtained through both methods were measured through electrophoresis and spectrophotometer. Additionally, PCR amplification was realized by primer pairs specific to nrDNA ITS, cpDNA ndhF (972F-1603R) and trnL-F regions. Results showed that maximum genomic DNA in nanograms obtained by phenol chloroform isoamyl alcohol method. The study also revealed that I. macrocephala had the maximum DNA and I. heterolepis had the minimum DNA amount. A260/A280 purity degrees showed that the highest and lowest purity in gDNAs obtained through phenol-chloroform isoamyl alcohol method were in I.aucheriana and I. salicina, respectively. The highest and lowest purity degrees of gDNAs obtained through commercial kit was observed in I. fragilis and I. macrocephala samples, respectively. PCR amplification results showed that while band profiles of each three regions (ITS, trnL-F and ndhF) did not yield positive results in PCR amplifications using phenol-chloroform isoamyl alcohol method; PCR band profiles obtained through commercial kit yielded positive results. As a result, it is fair to say that the relation of genomic DNA with PCR was found to be more efficient although the maximum amount of genomic DNA was obtained through phenol chloroform isoamyl alcohol method. [ABSTRACT FROM AUTHOR]

In many regions, plants are the sole source of natural medicines. The numerous bioactive substances they contain have significant advantages in the prevention and treatment of many ailments. Determining the therapeutic characteristics of plants requires knowledge about their biological activity and essential oil contents. The mineral, nutritional, essential oil, and biological activity data for the genus Ocimum was gathered in this research. Several members of the genus Ocimum were found to engage in a wide variety of biological processes, as shown by the research findings. It has been discovered that this source may be very useful, particularly for its antioxidant and antibacterial properties. It's also said to contain naturally occurring minerals, nutrients, and essential oils. For this reason, plants belonging to the genus Ocimum are being considered as a potential valuable resource for use in the development of pharmaceuticals. [ABSTRACT FROM AUTHOR]

This research was carried out to determine the in vitro regeneration abilities of tulip leaf explants. In the study, both sterile leaf explants obtained by culturing sterilized onions and leaf explants obtained by sterilizing leaves obtained from the onions germinated in pots were used. For this purpose MS medium containing 2.4-D (2 mg.l-1), TDZ (2 mg.l-1), Kinetin (2 mg.l-1), NAA (2 mg.l-1), 2.4-D+Kinetin (1 mg.l-1+ 1 mg.l-1 and 2 mg.l-1+ 2 mg.l-1), İAA+TDZ (1 mg.l-1+ 1 mg.l-1 and 2 mg.l-1 + 2 mg.l-1), İAA+BAP (1 mg.l-1 + 1 mg.l-1 and 2 mg.l-1 + 2 mg.l-1), NAA+Kinetin (1 mg.l-1+ 1 mg.l-1 and 2 mg.l-1 + 2 mg.l-1), NAA+TDZ (1 mg.l-1 + 1 mg.l-1 and 2 mg.l-1 + 2 mg.l-1) and 2.4-D+TDZ (1 mg.l-1 + 1 mg.l-1 and 2 mg.l-1 + 2 mg.l-1) were used in the study. As a result of subcultures, 6% callus formation was detected in MS medium containing 2.4-D (2 mg.l-1) and NAA (2 mg.l-1) hormone, which is one of the subcultures of leaves formed from the in vitro germination of Purple Prince Tulip bulbs. The highest rate of regeneration was determined as 10% callus formation in the medium containing Kinetin (2 mg.l-1). As a result, while callus regeneration was achieved in 3 different media containing 2.4-D (2 mg.l-1), NAA (2 mg.l-1) and Kinetin (2 mg.l-1) hormones among subcultured media, no regeneration was achieved in the other mediums. [ABSTRACT FROM AUTHOR]

In this study, phylogenetic analysis of some Turkish Prunus armeniaca L. genotypes was conducted based on RAPD-PCR, ISSR-PCR, and chloroplast DNA (trnL-F) sequence analyses. Prunus armeniaca genotypes were obtained from Malatya province, and brought to the laboratory for genomic DNA isolation. Eleven RAPD and fifteen ISSR primers were used to determine molecular characterization of Prunus armeniaca genotypes. For the amplification of the trnL-F region, trne and trnf primers were used in Polymerase Chain Reaction (PCR). A total of 46 and 95 bands were obtained with RAPD and ISSR analysis, respectively. The trnL-F sequences varied from 398 to 403 nucleotides. Average nucleotide composition of trnL-F sequences was 31.0% T, 14.4% C, 37.4% A and 17.2% G. The genetic distance between the five apricot genotypes is 0.00. A maximum likelihood tree was generated to determine genetic relationships among Prunus armeniaca genotypes. Analysis of Prunus armeniaca genotypes based on RAPD, ISSR, and trnL-F sequences revealed that the rate of polymorphism obtained using RAPD and ISSR were higher than those obtained through the trnL-F sequences. [ABSTRACT FROM AUTHOR]

This study aimed to determine the morphological, pomological, biochemical contents, and molecular characterization of 11 cucumber genotypes of Egyptian origin and to reveal their molecular characterization. As a result it was determined that the highest fruit weight, the highest fruit length, and the highest fruit width were in the "Rahaf" genotype (respectively, 337.39 g, 23.25 cm, 53.97 mm). Biochemical analyses of the genotypes revealed that the highest total phenolic content was in the "Madayın" genotype (1938 mg gallic acid equivalent 100 g−1), the highest total antioxidant content was in the "C.5" genotype (59.25% inhibition), and the highest total flavonoid content was in the "Gazir" genotype (752.78 mg catechin equivalent 100 g−1). The highest Chlorophyll (a) content and Chlorophyll (a+b) was in the "Madayın" genotype (respectively, 4.33 mg g−1, 20.92 mg g−1), the highest Chlorophyll (b) content was in the "Iskay" genotype (6.59 mg g−1). It was determined that there were differences between genotypes in terms of other biochemical parameters examined. Using ten Inter Simple Sequence Repeat primers, 119 bands were obtained and the polymorphism rate was determined as 90.75%. [ABSTRACT FROM AUTHOR]

In the study, it was aimed to determine the molecular characterization and genetic relationships of Mentha species obtained from different countries and regions at the molecular level and to ensure the sustainability of these species. For this purpose, ISSR marker technique, which is effective in detecting polymorphism and genetic variation within and between Mentha species, was used. In the study a total of 460 allelic bands were detected, and all bands were found to be 100% polymorphic. The maximum number of bands was produced by the ISSR7 primer (25), but the minimum number of bands was produced by the ISSR12 primer (13). The highest PIC (Polymorphism Information Content) value was detected in the ISSR3 primer (0.521) but the lowest PIC value was determined in the 903 primer (0.203). Molecular datas were analyzed using the NTSYSpc 2.02 software and it was determined that the mint species were divided into two main groups. In the results obtained, it was determined that there was no relationship between the genetic diversity and geographical origins, and the populations from different geographical regions were in the same clusters. In the study, it was concluded that there was a significant molecular diversity among the species, and that some Mentha clones, which are defined by morphological features and still remain taxonomically uncertain, were belong to which species at the molecular level. Therefore, it is insufficient to classify species with morphochemical, morphological and phenotypic characteristics. [ABSTRACT FROM AUTHOR]

Root‐knot nematodes, particularly, Meloidogyne incognita, are among the most destructive endoparasitic nematodes, infecting a diverse range of plant hosts. Nematode‐trapping fungi are known for their potential application as biological control agents against plant parasitic nematodes. In the present study, the nematode‐trapping fungus Arthrobotrys thaumasia was isolated from the rhizosphere soil of tomato plants in the West Mediterranean Region of Türkiye. Two hundred and twenty‐three tomato plant rhizosphere soil samples yielded six nematode‐trapping fungal isolates, giving an occurrence frequency of 2.69%. Using morphology and molecular marker sequences (ITS and β‐tubulin loci), the species of the fungi was confirmed to be A. thaumasia. In vitro, A. thaumasia reduced second‐stage juveniles of M. incognita by 77.5% (isolate I‐Y4‐2) and 72.5% (isolate B‐G5‐1). This is the first report on the isolation and characterization of the nematode‐trapping fungus A. thaumasia from Türkiye. Two isolates of A. thaumasia (I‐Y4‐2 and B‐G5‐1) appear to be promising biological control agents that may be utilized for controlling M. incognita‐caused root‐knot diseases. [ABSTRACT FROM AUTHOR]

This study's objective was to identify the anastomosis groups and pathogenicity of Rhizoctonia species from soil samples in tomato production areas of Antalya, Burdur, and Isparta provinces in the West Mediterranean Region of Türkiye during the 2022 season. Soil samples were gathered from tomato plant rhizospheres in 223 different greenhouses, and isolations were done from the soil using the baiting technique. According to the results of morphological characterization and sequence analysis of the internal transcribed spacers of the ribosomal DNA, 47 Rhizoctonia isolates were defined as binucleate and 21 isolates as multinucleate. The collection of binucleate Rhizoctonia (Ceratobasidium sp.) isolates included representatives of Anastomosis Group‐F (61.76%), AG‐A (1.47%), and an unidentified binucleate Rhizoctonia (Ceratobasidium sp.) (5.88%). Multinucleate R. solani included AG 4 HG‐I (26.47%) and AG 4 HG‐II (4.41%). Pathogenicity tests showed statistically significant differences in virulence between binucleate Rhizoctonia (Ceratobasidium sp.) isolates and multinucleate Rhizoctonia isolates. All R. solani AG 4 HG‐II isolates and most of the AG 4 HG‐I isolates were pathogenic, causing severe necrosis symptoms and damping off in tomato seedlings, but binucleate AG‐A and AG‐F isolates were nonpathogenic. This study is the first detailed report about Rhizoctonia species isolated from the soil of tomato plants grown in greenhouse production areas in Türkiye. [ABSTRACT FROM AUTHOR]

Malpighiales, containing approximately 16,000 species, is one of the largest and most diverse angiosperm orders in plants. Growth-regulating factor (GRF) protein is a putative transcription factor and plays a regulatory role during plant growth and development processes such as stem elongation and cell expansion. The latest available protein data provide an opportunity to compare and understand the critical similarities and differentiation in GRF proteins among Malpighiales members. In the present study we conducted domain, two- and three-dimensional (2D, 3D) comparative, physicochemical, subcellular prediction, and sequence analysis of 87 putative GRF proteins belonging to 4 genera in Malpighiales using different bioinformatic tools. The results showed that QLQ, WRC, TQL, GGPL, RSRKPVE, FDV, and GFG domain motifs are conserved in rates between 34% and 82%. Comparative analysis proved that there is a common triangle-like shape among GRF proteins, and the conserved motifs are localized in similar regions of this triangle. The sequence lengths of GRFs change between 93 and 639 aa, and pH values differ between 5.28 and 10.50. According to subcellular prediction and domain analysis, only 9%-11% of GRFs are localized out of the nuclear region. Additionally, it was determined that 87 GRF proteins have monophyletic phylogeny. The average values of pairwise distance and nucleotide diversity (p) were 2.78 and 0.727, respectively. These results may contribute to an understanding of how structurally similar but functionally diverse GRF proteins execute various functions in different plant parts or in different plant species. [ABSTRACT FROM AUTHOR]