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Found: 25 Piece 0.001 sn
Publisher : Taylor & Francis ✕Department : Biyoloji Bölümü ✕
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Comparative modeling and enzymatic affinity of novel haloacid dehalogenase from Bacillus megaterium strain BHS1 isolated from alkaline Blue Lake in Turkey

Yılmaz KAYA

This study presents the initial structural model of L-haloacid dehalogenase (DehLBHS1) from Bacillus megaterium BHS1, an alkalotolerant bacterium known for its ability to degrade halogenated environmental pollutants. The model provides insights into the structural features of DehLBHS1 and expands our understanding of the enzymatic mechanisms involved in the degradation of these hazardous pollutants. Key amino acid residues (Arg40, Phe59, Asn118, Asn176, and Trp178) in DehLBHS1 were identified to play critical roles in catalysis and molecular recognition of haloalkanoic acid, essential for effi ...More

Article 2023 Fen Fakültesi Journal of Biomolecular Structure and Dynamics42 ( 3 ) 54 Views
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A 2,2-dichloropropionic acid-degrading novel Pseudomonas fluorescence strain fatsa001: isolation, identification, and characterization

Gülbübü KURMANBEKOVA | Yılmaz KAYA

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 bioc ...More

Article 2024 Fen Fakültesi Bioremediation Journal ( Published online: 27 Feb 2024 ) 5 Views
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Assessment of Cd-induced genotoxic damage in Urtica pilulifera L. using RAPD-PCR analysis

İlhan DOĞAN

Plants can be used as biological indicators in assessing the damage done by bioaccumulation of heavy metals and their negative impact on the environment. In the present research, Roman nettle (Urtica pilulifera L.) was employed as a bioindicator for cadmium (Cd) pollution. The comparisons between unexposed and exposed plant samples revealed inhibition of the root growth (∼25.96% and ∼45.92% after treatment with 100 and 200 µmol/L Cd concentrations, respectively), reduction in the total soluble protein quantities (∼53.92% and ∼66.29% after treatment with 100 and 200 µmol/L Cd concentrations, re ...More

Article 2016 Fen Fakültesi Biotechnology and Biotechnological Equipment30 ( 2 ) 108 Views
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Screening of damage induced by lead (Pb) in rye (Secale cereale L.) – a genetic and physiological approach

İlhan DOĞAN

The fields in which lead (Pb) finds application in the modern world have increased dramatically in recent years. As a consequence of this intensive utilization of Pb, its toxicity tends to pose more and more environmental problems. The aim of this study was to evaluate the genotoxic potential of Pb and to characterize some physiological parameters in Secale cereale under Pb stress. Plants were subjected to different exposure levels of Pb (0, 100, 200 and 400 µmol/L) for two weeks. At the end of the experimental period, the effects of Pb exposure on the photosynthetic pigments content (chloroph ...More

Article 2016 Fen Fakültesi Biotechnology and Biotechnological Equipment30 ( 3 ) 55 Views
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The usability of Juniperus virginiana L. as a biomonitor of heavy metal pollution in Bishkek City, Kyrgyzstan

Zeki SEVEROĞLU | İlhan DOĞAN | Gülbübü KURMANBEKOVA

Uncontrolled and unplanned urbanization and industrialization due to increase of population and rapid industrial development have created severe environmental problems in Kyrgyzstan during the last few decades. In this study, Juniperus virginiana, a dioecious species, was employed in order to make assessment of the heavy metal pollution rate in the area and of the heavy metal pollution impact on the mineral nutrient status of the plant. For this study, leaf (washed and unwashed) and bark samples of J. virginiana, and its co-located soil samples were collected from eight different stations, all ...More

Article 2015 Fen Fakültesi Biotechnology and Biotechnological Equipment29 ( 6 ) 128 Views
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Cotton Biotechnology: An Efficient Gene Transfer Protocol via Agrobacterium tumefaciens for a Greater Transgenic Recovery

İbrahim İlker ÖZYİĞİT | Yılmaz KAYA

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 bombardm ...More

Review 2022 Fen Fakültesi Journal of Natural Fibers19 ( 15 ) 115 Views
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Cotton Agriculture in Turkey and Worldwide Economic Impacts of Turkish Cotton

İbrahim İlker ÖZYİĞİT

Cotton is a product that provides wealth for humanity with its widespread and compulsory usage, and alongside creating employment opportunities in the producer countries. Due to the availability of suitable land for agriculture, seven countries including Turkey produce close to 80% of cotton worldwide. The average cotton yield in Turkey is above the world average, placing the country close to first place among the major producing countries. On the other hand, Turkey is one of the main countries engaged in organic cotton production by using only non-transgenic seeds and therefore, its cotton as ...More

Review 2022 Fen Fakültesi Journal of Natural Fibers19 ( 15 ) 147 Views
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An investigation on environmental pollution due to essential heavy metals: a prediction model through multilayer perceptrons

İbrahim İlker ÖZYİĞİT

This research is to predict heavy metal levels in plants, particularly in Robinia pseudoacacia L., and soils using an effective artificial intelligence approach with some ecological parameters, thereby significantly eliminating common defects such as high cost and seriously tedious and time-consuming laboratory procedures. In this respect, the artificial neural network (ANN) is employed to estimate the concentrations of essential heavy metals such as Fe, Mn and Ni, depending on the Cu and Zn concentrations of plant and soil samples collected from five different locations. The derived relative ...More

Article 2022 Fen Fakültesi International Journal of Phytoremediation25 ( 1 ) 104 Views
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Comparative analyses of phytochelatin synthase (PCS) genes in higher plants

İbrahim İlker ÖZYİĞİT

Plants employ various defence strategies to ameliorate the effects of heavy metal exposures, leading to re-establishment of metal homeostasis. One of the strategies includes the biosynthesis of main heavy metal detoxifying peptides phytochelatins (PCs) by phytochelatin synthase (PCS). In the present study, 14 PCS homologues were identified in the genomes of 10 selected plants. The size of these PCSs was 452-545 amino acid residues, with characteristic phytochelatin and phytochelatin_C domains. The N-terminal site of the proteins is highly conserved, whereas the C-terminal site is less conserve ...More

Article 2019 Fen Fakültesi Biotechnology and Biotechnological Equipment33 ( 1 ) 62 Views
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Biodegradation of 3-chloropropionic acid (3-CP) by Bacillus cereus WH2 and its in silico enzyme-substrate docking analysis

Yılmaz KAYA

KeyWords Plus:ALPHA-HALOALKANOIC ACID; DEHALOGENASE; DEGRADATION

Letter 2019 Fen Fakültesi Journal of Biomolecular Structure and Dynamics38 ( 11 ) 136 Views
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Abiotic stress-induced regulation of antioxidant genes in different Arabidopsis ecotypes: microarray data evaluation

İbrahim İlker ÖZYİĞİT

Although stresses induce generation of reactive oxygen species (ROS), which are highly reactive and toxic, and cause severe damage to cellular components; plants have very efficient enzymatic ROS-scavenging mechanisms. Despite the substantial knowledge produced about these enzymes, we still have limited knowledge regarding their expression patterns in relation to the stress type, duration and strength. Thus, taking advantage of microarray data, this work evaluated the abiotic stresses (salt, cold, heat and light) induced regulation of six antioxidant enzymes, superoxide dismutase (SOD), catala ...More

Article 2019 Fen Fakültesi Biotechnology and Biotechnological Equipment33 ( 1 ) 100 Views
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Haloadaptation: insights from comparative modeling studies between halotolerant and non-halotolerant dehalogenases

Yılmaz KAYA

Halophiles are extremophilic microorganisms that grow optimally at high salt concentrations by producing a myriad of equally halotolerant enzymes. Structural haloadaptation of these enzymes adept to thriving under high-salt environments, though are not fully understood. Herein, the study attempts an in silico investigation to identify and comprehend the evolutionary structural adaptation of a halotolerant dehalogenase, DehHX (GenBank accession number: KR297065) of the halotolerant Pseudomonas halophila, over its non-halotolerant counterpart, DehMX1 (GenBank accession number KY129692) produced ...More

Article 2019 Fen Fakültesi Journal of Biomolecular Structure and Dynamics38 ( 12 ) 113 Views
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