Gülbübü KURMANBEKOVA | Yılmaz KAYA

Article | 2024 | Bioremediation Journal ( Published online: 27 Feb 2024 )

There are mounting concerns over the high concentrations of non-biogenic, toxic halogenated organic compounds being liberated into the ecosystem. Therefore, this study’s isolation of a novel bacterium from a contaminated stream in Fatsa, Ordu, Turkey, adept in degrading 2,2-dichloropropionic (of 2,2-DCP) is a welcome endeavor. The ability of the bacterial isolate to utilize 2,2-DCP as the sole carbon and energy source was discovered when the bacterium was observed to grow well on liquid minimal media containing 20 mM of 2,2-DCP, showing a doubling time of 14.2 h. The following genetic and biochemical characterizations revealed that . . .the 16S rRNA sequence of the fatsa001strain is identical (99) to Pseudomonas fluorescence, after which the sequence was deposited in the NCBI GenBank as Pseudomonas sp. strain fatsa001 (MN098848). The halogen-degrading ability of the P. fluorescens fatsa001 bacterium was again confirmed by the PCR data, which showed the presence of a conserved group of amino acids from the group I dehalogenase gene. It worth mentioning here that this is the first report on a P. fluorescence bacterial strain with the ability to degrade toxic 2,2-DCP. The detoxification ability of this bacterium envisages its practicality as an in situ environmental bioremediation agent. Keyword: dalapon herbicide; dehalogenase; dehalogenation; recalcitran More less

Yılmaz KAYA

Article | 2023 | Journal of Applied Phycology35 ( 2 )

The aim of this study was to isolate and identify Antarctica microalgae collected through the National Antarctic Science Expedition and to examine the growth responses and biochemical contents of Chlorella variabilis under cold and temperate cultivation conditions in growth medium consisting of various nitrogen concentrations under different lighting cycle parameters. In this study, the Antarctic microalgae Chlorella variabilis YTU.ANTARCTIC.001, was cultivated at different temperatures of 4, 13, 20 and 27 °C in modified BG-11 medium with various concentrations of NaNO3 (0, 0.75, 1.5, 2.5 and 3 g L−1) under three photoperiods (8:16, . . . 16:8 and 24:0) to investigate the growth and biochemical compositions. The specific growth rate changed from 0.012 to 0.23 day−1 with an increase in nitrate concentration, temperature and light cycle. The highest specific growth rate was 0.23 day−1 using the growth medium that consisted of 3 g L−1 nitrate at 27 °C under 16:8 h light–dark cycle, while there was no algal growth at 4 °C. Carbohydrate, protein, chlorophyll-a and β-carotene contents of microalgae increased with the increasing concentrations of nitrogen at 20 °C and 27 °C. The highest lipid content was achieved as 66 DW, using the growth medium consisting of 0.75 g L−1 nitrate at 13 °C. This study highlighted that the production of the Antarctic microalgae C. variabilis can be carried out efficiently in temperate conditions by manipulating the growth parameters More less

İbrahim İlker ÖZYİĞİT | Yılmaz KAYA

Review | 2022 | Journal of Natural Fibers19 ( 15 )

Due to its economic worth, cotton (Gossypium hirsutum L.) is grown in almost 70 countries and provides income for more than 250 million people. Therefore, producing cotton with having some desired characteristics that includes extended biotic and abiotic stress tolerance, improved fiber quality, promoted nutritional content and increased yield is the main objective for cotton biotechnology. To achieve this goal, many tissue culture and gene transfer techniques are being developed and used throughout the years. As applications for the gene transfer, the Agrobacterium-mediated, particle bombardment and pollen tube pathway-mediated met . . .hods are most successfully used and in conjunction with this, meristematic shoot tips as explants are efficiently utilized in gene transfer methods. In this study, the main objective was to report an efficient protocol for a greater recovery of transgenic cotton plant using Agrobacterium tumefaciens-mediated transformation. For this, one of the cotton strains (Cukurova 1518) cultivated widely in Turkey was chosen and meristematic shoot tips as explant sources, and GFP and NPTII genes as reporter and marker genes were used, respectively. The effective post co-cultivation conditions were provided via using the selection regime in vitro. Finally, the current results showed highly reproducible protocol developed could be used to produce transgenic cotton plants expressing desired traits or can be utilized as a model system to study the expression of particular genes More less

Yılmaz KAYA

Article | 2021 | Polar Science28 ( Special Issue )

Extreme microorganism has gained interest because of their special contribution to the environmental and industrial biotechnology, particularly psychrophilic microorganisms which can live and thrive at lower temperatures. They produce enzymes with great potential to adapt to extreme conditions. In this study, a novel psychrophilic bacterial strain designated as TaeBurcu001 grew (optimally at 5.C) on a chemically defined medium containing dalapon (refer to as 2,2-dichloropropionic acid, 2,2-DCP) as the sole carbon source. TaeBurcu001 was isolated from Galindez Island, Antarctica. Phylogenetic analysis based on 16S rRNA gene sequence . . .(GeneBank ID MN061637) showed that TaeBurcu001 was closely related to members of the genus Psychrobacter (99? Comparisons of phenotypic and biochemical characteristics between the isolate and the other known Psychrobacter species showed that they are very similar. Chloride ion release was detected using colorimetric assay with maximum value recorded at 0.27 mmol/L in 30 mM of 2,2-DCP. Furthermore, the partial dehalogenase sequence of Psychrobacter TaeBurcu001 (GeneBank ID MW311072) showed a very high similarity (88?to the previously reported 2-haloacid dehalogenase (DehE) from Rhizobium sp. (GeneBank ID CAA75671). To the best of our knowledge, this is the first study reporting on the isolation and characterisation of psychrophilic bacteria able to grow on halogenated compounds as a carbon source. Results are expected to gain new insight for further studies to uncover the full potential of these microorganisms to be applied in environmental processes and the remediation of contaminated ecosystems More less

Yılmaz KAYA

Review | 2023 | Frontiers in Plant Science14

The use of molecular markers has become an essential part of molecular genetics through their application in numerous fields, which includes identification of genes associated with targeted traits, operation of backcrossing programs, modern plant breeding, genetic characterization, and marker-assisted selection. Transposable elements are a core component of all eukaryotic genomes, making them suitable as molecular markers. Most of the large plant genomes consist primarily of transposable elements; variations in their abundance contribute to most of the variation in genome size. Retrotransposons are widely present throughout plant ge . . .nomes, and replicative transposition enables them to insert into the genome without removing the original elements. Various applications of molecular markers have been developed that exploit the fact that these genetic elements are present everywhere and their ability to stably integrate into dispersed chromosomal localities that are polymorphic within a species. The ongoing development of molecular marker technologies is directly related to the deployment of high-throughput genotype sequencing platforms, and this research is of considerable significance. In this review, the practical application to molecular markers, which is a use of technology of interspersed repeats in the plant genome were examined using genomic sources from the past to the present. Prospects and possibilities are also presented. Keywords: molecular markers; interspersed repeats; amplification profiling; inter-retrotransposon amplified polymorphism; transposable elements; retrotransposo More less

Yılmaz KAYA

Article | 2020 | Journal of Biomolecular Structure and Dynamics39 ( 7 )

Literature has shown that oil palm leaves (OPL) can be transformed into nanocellulose (NC) by fungal lignocellulosic enzymes, particularly those produced by the Trichoderma species. However, mechanism of beta-glucosidase and xylanase selectivity to degrade lignin, hemicellulose and cellulose in OPL for NC production remains relatively vague. The study aimed to comprehend this aspect by an in silico approach of molecular docking, molecular dynamics (MD) simulation and Molecular-mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis, to compare interactions between the beta-glucosidase- and xylanase from Trichoderma asperellum UC . . .1 in complex with each substrate. Molecular docking of the enzyme-substrate complex showed residues Glu165-Asp226-Glu423 and Arg155-Glu210-Ser160 being the likely catalytic residues of beta-glucosidase and xylanase, respectively. The binding affinity of beta-glucosidase for the substrates are as follows: cellulose (-8.1 kcal mol(-1)) > lignin (-7.9 kcal mol(-1)) > hemicellulose (-7.8 kcal mol(-1)), whereas, xylanase showed a corresponding preference for; hemicellulose (-6.7 kcal mol(-1)) > cellulose (-5.8 kcal mol(-1)) > lignin (-5.7 kcal mol(-1)). Selectivity of both enzymes was reiterated by MD simulations where interactions between beta-glucosidase-cellulose and xylanase-hemicellulose were the strongest. Notably low free-binding energy (Delta G(bind)) of beta-glucosidase and xylanase in complex with cellulose (-207.23 +/- 47.13 kJ/mol) and hemicellulose (-131.48 +/- 24.57 kJ/mol) were observed, respectively. The findings thus successfully identified the cellulose component selectivity of the polymer-acting beta-glucosidase and xylanase of T. asperellum UC1. Communicated by Ramaswamy H. Sarm More less

Yılmaz KAYA

Letter | 2019 | Journal of Biomolecular Structure and Dynamics38 ( 11 )

KeyWords Plus:ALPHA-HALOALKANOIC ACID; DEHALOGENASE; DEGRADATION

Yılmaz KAYA

Article | 2021 | Biotechnology and Biotechnological Equipment35 ( 1 )

The 16S rRNA amplicon sequencing technique is a key aspect of studies of microbial communities but does not provide direct evidence of a community

Yılmaz KAYA

Article | 2023 | Journal of Animal and Plant Sciences (JAPS)33 ( 5 )

Tomato is one of the best-studied cultivated dicotyledonous plants in molecular studies. Mobile genetic elements constitute large parts of plant genomes. Retrotransposons are mobile genetic elements within the genome and constitute more than 60 of the tomato genome.Transposable elements (TE) or transposons are DNA sequences that can alter their position within a genome, cause mutations and change the genetic identity of the cells and genome size. We aimed to analyze potato specific-P-Tst-1, P-Tst-3 and P-Tst-6 retrotransposon movements in tomatoes at different developmental stages (mature seedling, flowering stage and fruiting stage . . .) under different cultural conditions (organic and conventional) by IRAP(Inter-Retrotransposon Amplified Polymorphism) technique. We found polymorphism rates between 1-100 for P-Tst-1, P-Tst-3 and 0-86 for P-Tst-6. When compared to organically tomatoes, conventionally produced tomatoes showed high polymorphism. Moreover, polymorphism ratios were different at developmental stages. This is the first report to analyze potato-specific retrotransposon movements in tomatoes grown under different conditions. Obtaining findings are expected to understand the evolutionary relationships between tomato and potato, and even the effects of different growing conditions on tomato genome to increase yield in agriculture. Keywords: IRAP; mobile genetic elements; solanum lycopersicu More less

Bermet KIDIRALİYEVA | Nurcamal ÖMÜRZAKOVA | Yılmaz KAYA

Article | 2022 | Frontiers in Life Sciences and Related Technologies3 ( 2 )

Çeltik, Antarktika hariç tüm kıtalarda yetiştirilen dünyanın en değerli gıda ürünleri arasında yer almaktadır. Küresel ölçekte, ekim alanı açısından değerlendirildiğinde buğdaydan sonra ikinci sırada yer almakla birlikte verimi yaklaşık olarak toplam buğday verimine eşittir. Kırgızistan, çeltik yetiştiriciliği bakımından önde gelen ülkeler arasında yer almamakta, bu bölgede sadece yerel ölçekte üretim yapılmaktadır. Kırgızistan’ın güney bölgesi çeltik tarımına elverişli olduğu için son 10 yılda nispeten çeltik ekim alanları ve tüketimi artmıştır. Çeltiğe ilginin artmasına; nüfus artışı, ekonomik olarak getirinin olması, diğer ülkele . . .re ihracat etme durumu gibi birçok faktör neden olmaktadır. Kırgızistan’da çeltik yetiştirilen başlıca bölgeler olan Oş, Calal-Abad ve Batken güney bölgelerinde yer almaktadır. Özgen ve Ak-Turpak çeltik çeşitleri tadı bakımından diğer çeşitlere göre daha üstündür. Araştırmalara göre insanlar için yararlı olan birçok elementleri içermektedir ve diğer çeltiklere kıyasla yüksek protein içeriğine de sahiptir. Bu çalışmada Kırgızistan’daki çeltik tarımının genel özellikleriyle birlikte, Özgen ve Ak-Turpak çeltiklerinin önemi ortaya konulmuştur. Keywords: Ak-Turpak, çeltik, çeltik üretimi, Oryza sp., Özge More less

Yılmaz KAYA

Review | 2023 | Frontiers in Plant Science14

Plants are the sources of many bioactive secondary metabolites which are present in plant organs including leaves, stems, roots, and flowers. Although they provide advantages to the plants in many cases, they are not necessary for metabolisms related to growth, development, and reproduction. They are specific to plant species and are precursor substances, which can be modified for generations of various compounds in different plant species. Secondary metabolites are used in many industries, including dye, food processing and cosmetic industries, and in agricultural control as well as being used as pharmaceutical raw materials by hum . . .ans. For this reason, the demand is high; therefore, they are needed to be obtained in large volumes and the large productions can be achieved using biotechnological methods in addition to production, being done with classical methods. For this, plant biotechnology can be put in action through using different methods. The most important of these methods include tissue culture and gene transfer. The genetically modified plants are agriculturally more productive and are commercially more effective and are valuable tools for industrial and medical purposes as well as being the sources of many secondary metabolites of therapeutic importance. With plant tissue culture applications, which are also the first step in obtaining transgenic plants with having desirable characteristics, it is possible to produce specific secondary metabolites in large-scale through using whole plants or using specific tissues of these plants in laboratory conditions. Currently, many studies are going on this subject, and some of them receiving attention are found to be taken place in plant biotechnology and having promising applications. In this work, particularly benefits of secondary metabolites, and their productions through tissue culture-based biotechnological applications are discussed using literature with presence of current studies. Keywords: tissue culture; gene transfer; bioreactor; hairy root; bioengineerin More less

Yılmaz KAYA

Article | 2020 | Catalysts10 ( 6 )

The indiscriminate use of chemical pesticides alongside the expansion of large-scale industries globally can critically jeopardize marine ecology and the well-being of mankind. This is because the agricultural runoffs and industrial effluents eventually enter waterways before flowing into highly saline environments i.e., oceans. Herein, the study assessed two novel bacterial isolates,Bacillus subtilisstrain H1 andBacillus thuringiensisstrain H2 from the hypersaline Lake Tuz in Turkey to degrade recalcitrant haloalkanoic acids, haloacetates and chlorpyrifos, and consequently, identify their optimal pollutant concentrations, pH and te . . .mperature alongside salt-tolerance thresholds.Bacillusstrains H1 and H2 optimally degraded 2,2-dichloropropionic acid (2,2-DCP) under similar incubation conditions (pH 8.0, 30 degrees C), except the latter preferred a higher concentration of pollutants as well as salinity at 30 mM and 35?respectively, while strain H1 grew well on 20 mM at More less