Çimen Atak - Academia.edu (original) (raw)

Papers by Çimen Atak

IntechOpen eBooks, May 18, 2022

The number of approaches related to recombinant protein production in plants is increasing rapidl... more The number of approaches related to recombinant protein production in plants is increasing rapidly day by day. Plant-based expression offers a safe, cost-effective, scalable, and potentially limitless way to rapidly produce recombinant proteins. Plant systems, which have significant advantages over animal and yeast recombinant protein production systems, are particularly promising for the large-scale production of antibodies and therapeutic proteins. Molecular pharming with transgenic plant systems become prominent among other production systems with its low cost, absence of human or animal pathogen contaminants, and the ability to use post-translational modifications such as glycosylation. The ability to produce recombinant pharmaceutical proteins in plant seeds, plant cells and various plant tissues such as hairy roots and leaves, through the stable transformation of the nuclear genome or transient expression, allows for the establishment of different production strategies. In particular, the rapid production of candidate proteins by transient expression, which eliminates the need for lengthy transformation and regeneration procedures, has made plants an attractive bioreactor for the production of pharmaceutical components. This chapter aimsto exhibit the current plant biotechnology applications and transgenic strategies used for the production of recombinant antibodies, antigens, therapeutic proteins and enzymes, which are used especially in the treatment of various diseases.

Genetics and Molecular Research, 2015

Salinity is one of the major problems limiting the yield of agricultural products. Radiation muta... more Salinity is one of the major problems limiting the yield of agricultural products. Radiation mutagenesis is used to improve salttolerant mutant plants. In this study, we aimed to improve salt-tolerant mutants of two oriental tobacco varieties. One thousand seeds of each variety (M 0) were irradiated with 100, 200, 300, and 400 Gy gamma rays by Cs-137 gamma. In the M 1 generation, 2999 single plants were harvested. The next season, these seeds were bulked and planted to obtain M 2 progeny. The seeds of 1900 M 2 plants were picked separately. Salinity tolerance was tested in the M 3 generation. Among M 3 plantlets, 10 salt-tolerant tobacco mutants were selected. According to the results of the selection studies, 100-and 200-Gy gamma radiation doses were the effective doses to obtain the desired mutants. Glutathione reductase enzyme activities of salt-tolerant tobacco mutants were determined biochemically as a stress-tolerance marker. The differences between control and salt-tolerant mutants belonging to the Akhisar 97 and İzmir Özbaş tobacco varieties were evaluated by random amplified polymorphic DNA analysis. The total polymorphism rate was 73.91%.

Genetic Resources and Crop Evolution, Mar 13, 2023

Turkish Journal of Biology, 2012

Th e aim of this study was to compare the salinity tolerances of 2 oriental tobacco varieties (İz... more Th e aim of this study was to compare the salinity tolerances of 2 oriental tobacco varieties (İzmir Özbaş and Akhisar 97). Salinity stress experiments were performed under both in vitro and in vivo conditions. Seedlings of each variety were subjected to 0, 50, 100, 150, 200, 250, 300, and 350 mM NaCl. Photosynthetic pigment levels, lipid peroxidation rate, total protein content, antioxidant enzyme activities, and proline concentrations were determined for seedlings treated with salt for 14 days. Th e Akhisar 97 variety was found to be more sensitive to salinity stress than the İzmir Özbaş variety. Although proline is thought to accumulate in salt-tolerant plants, we found a negative correlation between salinity tolerance and proline accumulation in the plants. According to biochemical analyses, there were no diff erences in SOD, APX, GPX, or CAT activity levels between the 2 varieties, either in vivo or in vitro. However, diff erences in glutathione reductase (GR) activity between control plants and plants under NaCl stress were statistically signifi cant in both varieties, both in vitro and in vivo. Our results support the hypothesis that GR is a key element in the evaluation of salinity tolerance of tobacco varieties.

IntechOpen eBooks, Mar 14, 2023

All life forms, from the simplest to the most complicated, are inevitably exposed to altering env... more All life forms, from the simplest to the most complicated, are inevitably exposed to altering environmental conditions in their natural habitats, gradually depending on their lifestyle. Unfavorable alterations drive these life forms either to avoidance or defense as a response. Most of the essential plant growth-promoting environmental factors can also turn out to be stress factors. Water as the most abundant molecule of all living cells can cause stress either in deficit as drought or in excess as waterlogging. Temperature is important for the maintenance of all biomolecules and metabolic reactions; hence, both low and high temperatures are deleterious stress factors. Even though the plants were exposed to various volcanic origin, heavy metals and pollutants and evolved molecular mechanisms during millions year of evolution, rapid urbanization, and industrial progress introduce brand new pollutants as micro-and nanoplastics as well as nanoparticles to plants like never before. This chapter defines and evaluates major environmental abiotic stress factors with an emphasis on the latest knowledge of molecular effects on plants. In addition, novel stress factors, such as nanoparticles and microplastics, are looked over as hot prospects for the future of plant abiotic stress areas.

IntechOpen eBooks, Sep 28, 2022

Soybean, which has many foods, feed, and industrial raw material products, has relatively limited... more Soybean, which has many foods, feed, and industrial raw material products, has relatively limited genetic diversity due to the domestication practices which mainly focused on higher yield for many centuries. Besides, cleistogamy in soybean plant reduces genetic variations even further. Improving genetic variation in soybean is crucial for breeding applications to improve traits such as higher yield, early maturity, herbicide, and pest resistance, lodging and shattering resistance, seed quality and composition, abiotic stress tolerance and more. In the 21st century, there are numerous alternatives from conventional breeding to biotechnological approaches. Among these, mutation breeding is still a major method to produce new alleles and desired traits within the crop genomes. Physical and chemical mutagen protocols are still improving and mutation breeding proves its value to be fast, flexible, and viable in crop sciences. In the verge of revolutionary genome editing era, induced mutagenesis passed important crossroads successfully with the help of emerging supportive NGS based-methods and non-destructive screening approaches that reduce the timeconsuming labor-intensive selection practices of mutation breeding. Induced mutagenesis will retain its place in crop science in the next decades, especially for plants such as soybean for which cross breeding is limited or not applicable.

IntechOpen eBooks, May 18, 2022

The number of approaches related to recombinant protein production in plants is increasing rapidl... more The number of approaches related to recombinant protein production in plants is increasing rapidly day by day. Plant-based expression offers a safe, cost-effective, scalable, and potentially limitless way to rapidly produce recombinant proteins. Plant systems, which have significant advantages over animal and yeast recombinant protein production systems, are particularly promising for the large-scale production of antibodies and therapeutic proteins. Molecular pharming with transgenic plant systems become prominent among other production systems with its low cost, absence of human or animal pathogen contaminants, and the ability to use post-translational modifications such as glycosylation. The ability to produce recombinant pharmaceutical proteins in plant seeds, plant cells and various plant tissues such as hairy roots and leaves, through the stable transformation of the nuclear genome or transient expression, allows for the establishment of different production strategies. In particular, the rapid production of candidate proteins by transient expression, which eliminates the need for lengthy transformation and regeneration procedures, has made plants an attractive bioreactor for the production of pharmaceutical components. This chapter aimsto exhibit the current plant biotechnology applications and transgenic strategies used for the production of recombinant antibodies, antigens, therapeutic proteins and enzymes, which are used especially in the treatment of various diseases.

Genetics and Molecular Research, 2015

Salinity is one of the major problems limiting the yield of agricultural products. Radiation muta... more Salinity is one of the major problems limiting the yield of agricultural products. Radiation mutagenesis is used to improve salttolerant mutant plants. In this study, we aimed to improve salt-tolerant mutants of two oriental tobacco varieties. One thousand seeds of each variety (M 0) were irradiated with 100, 200, 300, and 400 Gy gamma rays by Cs-137 gamma. In the M 1 generation, 2999 single plants were harvested. The next season, these seeds were bulked and planted to obtain M 2 progeny. The seeds of 1900 M 2 plants were picked separately. Salinity tolerance was tested in the M 3 generation. Among M 3 plantlets, 10 salt-tolerant tobacco mutants were selected. According to the results of the selection studies, 100-and 200-Gy gamma radiation doses were the effective doses to obtain the desired mutants. Glutathione reductase enzyme activities of salt-tolerant tobacco mutants were determined biochemically as a stress-tolerance marker. The differences between control and salt-tolerant mutants belonging to the Akhisar 97 and İzmir Özbaş tobacco varieties were evaluated by random amplified polymorphic DNA analysis. The total polymorphism rate was 73.91%.

Genetic Resources and Crop Evolution, Mar 13, 2023

Turkish Journal of Biology, 2012

Th e aim of this study was to compare the salinity tolerances of 2 oriental tobacco varieties (İz... more Th e aim of this study was to compare the salinity tolerances of 2 oriental tobacco varieties (İzmir Özbaş and Akhisar 97). Salinity stress experiments were performed under both in vitro and in vivo conditions. Seedlings of each variety were subjected to 0, 50, 100, 150, 200, 250, 300, and 350 mM NaCl. Photosynthetic pigment levels, lipid peroxidation rate, total protein content, antioxidant enzyme activities, and proline concentrations were determined for seedlings treated with salt for 14 days. Th e Akhisar 97 variety was found to be more sensitive to salinity stress than the İzmir Özbaş variety. Although proline is thought to accumulate in salt-tolerant plants, we found a negative correlation between salinity tolerance and proline accumulation in the plants. According to biochemical analyses, there were no diff erences in SOD, APX, GPX, or CAT activity levels between the 2 varieties, either in vivo or in vitro. However, diff erences in glutathione reductase (GR) activity between control plants and plants under NaCl stress were statistically signifi cant in both varieties, both in vitro and in vivo. Our results support the hypothesis that GR is a key element in the evaluation of salinity tolerance of tobacco varieties.

IntechOpen eBooks, Mar 14, 2023

All life forms, from the simplest to the most complicated, are inevitably exposed to altering env... more All life forms, from the simplest to the most complicated, are inevitably exposed to altering environmental conditions in their natural habitats, gradually depending on their lifestyle. Unfavorable alterations drive these life forms either to avoidance or defense as a response. Most of the essential plant growth-promoting environmental factors can also turn out to be stress factors. Water as the most abundant molecule of all living cells can cause stress either in deficit as drought or in excess as waterlogging. Temperature is important for the maintenance of all biomolecules and metabolic reactions; hence, both low and high temperatures are deleterious stress factors. Even though the plants were exposed to various volcanic origin, heavy metals and pollutants and evolved molecular mechanisms during millions year of evolution, rapid urbanization, and industrial progress introduce brand new pollutants as micro-and nanoplastics as well as nanoparticles to plants like never before. This chapter defines and evaluates major environmental abiotic stress factors with an emphasis on the latest knowledge of molecular effects on plants. In addition, novel stress factors, such as nanoparticles and microplastics, are looked over as hot prospects for the future of plant abiotic stress areas.

IntechOpen eBooks, Sep 28, 2022

Soybean, which has many foods, feed, and industrial raw material products, has relatively limited... more Soybean, which has many foods, feed, and industrial raw material products, has relatively limited genetic diversity due to the domestication practices which mainly focused on higher yield for many centuries. Besides, cleistogamy in soybean plant reduces genetic variations even further. Improving genetic variation in soybean is crucial for breeding applications to improve traits such as higher yield, early maturity, herbicide, and pest resistance, lodging and shattering resistance, seed quality and composition, abiotic stress tolerance and more. In the 21st century, there are numerous alternatives from conventional breeding to biotechnological approaches. Among these, mutation breeding is still a major method to produce new alleles and desired traits within the crop genomes. Physical and chemical mutagen protocols are still improving and mutation breeding proves its value to be fast, flexible, and viable in crop sciences. In the verge of revolutionary genome editing era, induced mutagenesis passed important crossroads successfully with the help of emerging supportive NGS based-methods and non-destructive screening approaches that reduce the timeconsuming labor-intensive selection practices of mutation breeding. Induced mutagenesis will retain its place in crop science in the next decades, especially for plants such as soybean for which cross breeding is limited or not applicable.