25 results on '"Karakaya H"'
Search Results
2. Molecular mapping of the fasciation mutation in soybean, Glycine max (Leguminosae)
- Author
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Karakaya, H. Caglar, Tang, Yuhong, Cregan, Perry B., and Knap, Halina T.
- Subjects
Soybean -- Genetic aspects ,Plant molecular genetics -- Research ,Biological sciences - Abstract
The spontaneous fasciation mutation generates novel developmental diversity in cultivated soybean, Glycine max (L.) Merrill. An increased apical dominance in the mutant inhibits axillary buds, causes a branchless phenotype, and restricts reproduction to shoot apices. The fasciation mutation is encoded by a recessive (f) allele at a single locus. The mutation, despite its importance in soybean development, has no locus assignment on previously reported molecular maps of soybean. A population of 70 [F.sub.2] progeny was derived from a cross between `Clark 63' and the fasciation mutant. More than 700 molecular markers (amplified restriction fragment length polymorphisms [AFLPs], random amplified polymorphic DNAs [RAPDs], restriction fragment length polymorphisms [RFLPs], and simple sequence repeats [SSRs]) were used in mapping of the fasciation phenotype. Twenty linkage groups (LGs) corresponding to the public soybean molecular map are represented on the Clark 63 x fasciation mutant molecular map that spans 3050 centimorgans (cM). The f locus was mapped on LG D1b+W and linked with two AFLPs and four SSR markers (Satt005, Satt141, Satt600, and Satt703). No linkage was found between the f locus and several cDNA polymorphic loci between the wild type and the mutant. The known map position of the f locus and demonstration of the mutant phenotype from early postembryonic throughout reproductive stages provide an excellent resource for investigations of molecular mechanisms affecting soybean ontogeny. Key words: development; fasciation; Glycine max; Leguminosae; map; molecular markers; mutant; polymorphism; soybean.
- Published
- 2002
3. Ex Vivo Expansion of Human Umbilical Cord Blood Hematopoietic Stem Cells with Valproic Acid or Nicotinamide is Able to Accelerate Engraftment in a NSG Mouse Transplant Model
- Author
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Dilek, Y., Akin, H. Y., Turasan, E., Karakaya, H., Ozisik, M. S., Fadiloglu, E., Tanacan, A., Yurdakul-Mesutoglu, P., Beksac, M., TOBB ETÜ, Tıp Fakültesi, Temel Tıp Bilimleri Bölümü, TOBB ETU, Faculty of Medicine, Department of Basic Medical Sciences, and Mesutoğlu, Pınar Yurdakul
- Subjects
Stem cell transplantation - Abstract
Background: The major obstacle against wider use of cord blood (CB) hematopoietic stem cells (HSC) is low level of HSC counts causing delay in both hematopoietic and immunological recovery. In recent years, HSC expansion strategies with small molecules ie Valproic acid (VPA) or nicotinamide (NAM) have yielded the most promising results. In Ankara University Cord Blood Bank, we have previously demonstrated increase in CD34 content and CFU-GM in the presence of VPA and/or NAM. Aims: To ascertain the functionality of expanded HSCs, we have initiated a mice stem cell transplant model using non-obese diabetic (NOD)Cg-Prkdcscid IL2rgtmWjl stocks of Rag2null mice (NSG mice). Methods: Following consent CD34+ cells were isolated by positive selection using MACS CD34 MicroBead Kit-UltraPure system (Miltenyi Biotec) from fresh CBUs collected at Ankara University or Hacettepe University, Departments of Obstetrics and Gynecology. Subsequently, 3.500 CD34+ cells per ml were plated in StemSpan medium in the presence of cytokine cocktail containing SCF, Flt3L, IL-3 and IL-6 (StemCell Technologies) w/wo VPA (1 mM) and/or NAM (5 mM). VPA, NAM and VPA + NAM added cultures were incubated at 37 °C and 5% CO2 for 8 days, 21 days and either 8 or 21 days, respectively. Following incubation CD34+ cells were washed and evaluated against their colony forming capacities using MethoCult Enriched wo EPO (StemCell Technologies) medium and cell viabilities were detected with 7-AAD and HSC phenotyping were performed by flow cytometry (Beckman Coulter) using labeled CD34 and CD45 monoclonal antibodies. Expanded cells were transplanted to 8- to 12 weeks old NOD.Cg-Prkdcscid IL2rgtmWjl/Sz (NSG) mice, purchased from The Jackson Laboratory and maintained under specific pathogen- free conditions at Laboratory of Animal Research Center in Ankara University. 24 hours prior to transplantation, mice were injected with busulfan through the tail vein (25 mg/kg, 50-100 g per dose). The next day, stem cell harvests (2,5 × 104 - 5 × 105 total nucleated cells (TNC) suspended in 200 ?l PBS) were transplanted by intravenous injection. Following transplantation complete blood count was performed on peripheral blood drawn from the tail vein in every 3-7 days. As control unexpanded CD34 HSCs and cytokine only expanded HSCs were used. Results: Two CBUs were successfully expanded with or without VPA and/or NAM in the presence of cytokine cocktail. All expanded HSCs were found to be competent on CFU-GM assays. Either freshly isolated or expanded HSCs were transplanted into 12 mice in total. One mouse was transplanted with non-expanded HSCs; 2 mice with cytokine-only-expanded HSCs; 2 mice with VPA-expanded HSCs and 2 mice with VPA + NAM expanded HSCs on the 8th day of the expansion. 2 mice with NAM-expanded HSCs and 1 mouse with VPA + NAM expanded HSCs on the 21st day of expansion. WBC counts of mice in different time points are shown in Figure 1. Summary/Conclusion: Our preliminary findings show that expanded CB HSCs are capable of increasing the peripheral WBC counts. VPA and/or NAM mediated expanded HSC led to an increase in WBC counts (>1 × 109/L) earlier than the non-transplanted or unexpanded HSC transplanted mice. Since VPA mediated expansion can be achieved within 8 days, VPA-expanded HSCs seem to be the most rapid way to achieve early engraftment in vivo.
- Published
- 2019
4. Модификации неоднозначных оснований антикодона тРНК и устойчивость дрожжей к борной кислоте: в резистентных к бору делеционных мутантах активирован механизм общего контроля аминокислот и эффлюкс бора
- Author
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Uluisik, İ., primary, Karakaya, H. Caglar, additional, and Koc, A., additional
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- 2020
- Full Text
- View/download PDF
5. PB2385 EX VIVO EXPANSION OF HUMAN UMBILICAL CORD BLOOD HEMATOPOIETIC STEM CELLS WITH VALPROIC ACID OR NICOTINAMIDE IS ABLE TO ACCELERATE ENGRAFTMENT IN A NSG MOUSE TRANSPLANT MODEL
- Author
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Dilek, Y., primary, Akin, H. Y., additional, Turasan, E., additional, Karakaya, H., additional, Ozisik, M. S., additional, Fadiloglu, E., additional, Tanacan, A., additional, Yurdakul-Mesutoglu, P., additional, and Beksac, M., additional
- Published
- 2019
- Full Text
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6. Ex Vivo Expansion of Human Umbilical Cord Blood Hematopoietic Stem Cells with Valproic Acid or Nicotinamide is Able to Accelerate Engraftment in a NSG Mouse Transplant Model
- Author
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Tanacan, A., Dilek, Y., Akın, H. Y., Yurdakul, Mesutoğlu P., Özışık, M. S., Fadiloğlu, E., Karakaya, H., Turasan, E., Beksaç, Mehmet Sinan, Tanacan, A., Dilek, Y., Akın, H. Y., Yurdakul, Mesutoğlu P., Özışık, M. S., Fadiloğlu, E., Karakaya, H., Turasan, E., and Beksaç, Mehmet Sinan
- Abstract
Background: The major obstacle against wider use of cord blood (CB) hematopoietic stem cells (HSC) is low level of HSC counts causing delay in both hematopoietic and immunological recovery. In recent years, HSC expansion strategies with small molecules ie Valproic acid (VPA) or nicotinamide (NAM) have yielded the most promising results. In Ankara University Cord Blood Bank, we have previously demonstrated increase in CD34 content and CFU-GM in the presence of VPA and/or NAM. Aims: To ascertain the functionality of expanded HSCs, we have initiated a mice stem cell transplant model using non-obese diabetic (NOD)Cg-Prkdcscid IL2rgtmWjl stocks of Rag2null mice (NSG mice). Methods: Following consent CD34+ cells were isolated by positive selection using MACS CD34 MicroBead Kit-UltraPure system (Miltenyi Biotec) from fresh CBUs collected at Ankara University or Hacettepe University, Departments of Obstetrics and Gynecology. Subsequently, 3.500 CD34+ cells per ml were plated in StemSpan medium in the presence of cytokine cocktail containing SCF, Flt3L, IL-3 and IL-6 (StemCell Technologies) w/wo VPA (1 mM) and/or NAM (5 mM). VPA, NAM and VPA + NAM added cultures were incubated at 37 °C and 5% CO2 for 8 days, 21 days and either 8 or 21 days, respectively. Following incubation CD34+ cells were washed and evaluated against their colony forming capacities using MethoCult Enriched wo EPO (StemCell Technologies) medium and cell viabilities were detected with 7-AAD and HSC phenotyping were performed by flow cytometry (Beckman Coulter) using labeled CD34 and CD45 monoclonal antibodies. Expanded cells were transplanted to 8- to 12 weeks old NOD.Cg-Prkdcscid IL2rgtmWjl/Sz (NSG) mice, purchased from The Jackson Laboratory and maintained under specific pathogen- free conditions at Laboratory of Animal Research Center in Ankara University. 24 hours prior to transplantation, mice were injected with busulfan through the tail vein (25 mg/kg, 50-100 g per dose). The next day, stem cell harve
- Published
- 2019
7. Ex Vivo Expansion of Human Umbilical Cord Blood Hematopoietic Stem Cells with Valproic Acid or Nicotinamide is Able to Accelerate Engraftment in a NSG Mouse Transplant Model
- Author
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Akın, H. Y., Beksaç, Mehmet Sinan, Yurdakul, Mesutoğlu P., Tanacan, A., Fadiloğlu, E., Özışık, M. S., Karakaya, H., Turasan, E., Dilek, Y., Akın, H. Y., Beksaç, Mehmet Sinan, Yurdakul, Mesutoğlu P., Tanacan, A., Fadiloğlu, E., Özışık, M. S., Karakaya, H., Turasan, E., and Dilek, Y.
- Abstract
Background: The major obstacle against wider use of cord blood (CB) hematopoietic stem cells (HSC) is low level of HSC counts causing delay in both hematopoietic and immunological recovery. In recent years, HSC expansion strategies with small molecules ie Valproic acid (VPA) or nicotinamide (NAM) have yielded the most promising results. In Ankara University Cord Blood Bank, we have previously demonstrated increase in CD34 content and CFU-GM in the presence of VPA and/or NAM. Aims: To ascertain the functionality of expanded HSCs, we have initiated a mice stem cell transplant model using non-obese diabetic (NOD)Cg-Prkdcscid IL2rgtmWjl stocks of Rag2null mice (NSG mice). Methods: Following consent CD34+ cells were isolated by positive selection using MACS CD34 MicroBead Kit-UltraPure system (Miltenyi Biotec) from fresh CBUs collected at Ankara University or Hacettepe University, Departments of Obstetrics and Gynecology. Subsequently, 3.500 CD34+ cells per ml were plated in StemSpan medium in the presence of cytokine cocktail containing SCF, Flt3L, IL-3 and IL-6 (StemCell Technologies) w/wo VPA (1 mM) and/or NAM (5 mM). VPA, NAM and VPA + NAM added cultures were incubated at 37 °C and 5% CO2 for 8 days, 21 days and either 8 or 21 days, respectively. Following incubation CD34+ cells were washed and evaluated against their colony forming capacities using MethoCult Enriched wo EPO (StemCell Technologies) medium and cell viabilities were detected with 7-AAD and HSC phenotyping were performed by flow cytometry (Beckman Coulter) using labeled CD34 and CD45 monoclonal antibodies. Expanded cells were transplanted to 8- to 12 weeks old NOD.Cg-Prkdcscid IL2rgtmWjl/Sz (NSG) mice, purchased from The Jackson Laboratory and maintained under specific pathogen- free conditions at Laboratory of Animal Research Center in Ankara University. 24 hours prior to transplantation, mice were injected with busulfan through the tail vein (25 mg/kg, 50-100 g per dose). The next day, stem cell harve
- Published
- 2019
8. Mutagenesis of the tal gene-encoding Transaldolase in the Cyanobacterium, Anabaena sp. PCC7120
- Author
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Karakaya H., Mann N.H., and Ondokuz Mayıs Üniversitesi
- Subjects
Transaldolase mutant ,tal mutation ,Anabaena ,Glucose-6-phosphate dehydrogenase - Abstract
The transaldolase gene (tal) of Anabaena sp. PCC7120 was interrupted by the insertion of the interposon ?. Transaldolase assays showed that the tal mutant strain possessed the same activity as the wild-type, indicating that the second copy of the gene complements the enzyme activity. Being coded by a gene (zwf) downstream of tal and probably in the same operon, glucose-6-phosphate dehydrogenase (G6PDH) activity was also analysed. Only 34% of wild-type G6PDH activity was retained in the tal mutant strain. This may have due to the polar affect of tal mutation on the transcription of the zwf gene. Growth of the tal mutant was not different than that of the wild-type in the presence of combined nitrogen, but the mutant reached the stationary phase faster than the wild-type in the absence of combined nitrogen. This was probably because of the reduction of G6PDH activity, resulting in less production of reductant and energy in heterocysts, which negatively affects nitrogen fixation and growth. © TÜBİTAK.
- Published
- 2008
9. 5,5-diethylbarbiturate complexes of silver with 2,2 '-bipyridine and 3-(2-pyridyl)propanol: Syntheses, crystal structures, spectroscopic, thermal and antimicrobial activity studies
- Author
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Yilmaz, F., Yilmaz, V. T., Karakaya, H., Büyükgüngör, O., and Ondokuz Mayıs Üniversitesi
- Subjects
crystal structure ,3-(2-pyridyl)propanol ,2,2?-dipyridine ,5,5-diethylbarbiturate ,2,2 '-dipyridine ,silver(I) - Abstract
YILMAZ, Fatih/0000-0002-7711-0975; Karakaya, Haydar/0000-0003-3347-0001; Yilmaz, Veysel/0000-0002-2849-3332 WOS: 000253003200004 Two silver 5,5-diethylbarbiturate (barb) complexes with 2,2'-bipyridine (bpy) and 3-(2-pyridyl) propanol (pypr), [Ag(barb)(bpy)] (1) and [Ag(barb)(pypr)] (2), have been prepared and characterized by elemental analysis, IR spectroscopy, thermal analysis, and single crystal X-ray diffraction. Both complexes crystallize in the triclinic space group P (1) over bar with Z = 2. The barb ligand in 1 is N-coordinated and the bpy ligand acts as a bichelating ligand leading to an AgN3 tricoordination. Crystals of 1 feature a three-dimensional network based on N-H center dot center dot center dot O hydrogen bonding, pi(bpy)center dot center dot center dot pi(bpy), C-H center dot center dot center dot pi(bpy) and pi(bpy)-Ag interactions. In 2, the pypr and barb ligands behave as monodentate ligands through their N atoms, forming a distorted linear AgN2 coordination. Molecules of 2 are doubly bridged by N-H center dot center dot center dot O hydrogen bonds and further connected via O-H center dot center dot center dot O hydrogen bonds and aromatic pi(pypr)center dot center dot center dot pi(pypr) stacking interactions into a supramolecular network. Both complexes exhibit similar thermal decomposition behavior in air. The first stage corresponds to removal of the co-ligands such as bpy or pypr while the degradation of the barb moiety occurs at higher temperatures to give Ag2O. Like the barb, bpy and pypr ligands, 2 does not show any significant antimicrobial activity, but 1 is active against bacteria and fungi.
- Published
- 2008
10. The flora of the subalpine and alpine region of the çambaşi high plateau (Ordu) and its vicinity
- Author
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Karakaya H., Kilinç M., and Ondokuz Mayıs Üniversitesi
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Turkey ,Flora ,Alpine-Subalpine ,Ordu - Abstract
The study area is situated in the western part of the Eastern Black Sea Mountains. From the phytogeographical point of view, it is located in the Euxine province of the Euro-Siberian floristic region. A total of 323 taxa belonging to 58 families and 181 genus from the study area have been determined during this investigation. The distribution of these taxa according to phytogeographic regions is as follows Euro-Siberian, 26.62 %; Euxine, 16.40 %; Hyrcano-Euxine, 3.72 % (Total Euro-Siberian is 46.74 %); IranoTuranien, 4.03 %; and Mediterranean 0.93%. The ratio of unknown floristic regions or pleuriregionals is 48.30 %. The number of endemic taxa is 28, and 15 of these taxa are endemic for the Euxine province and Euro-Siberian region. Endemic taxa make up 8.7 % of the total flora. Seventy-eight taxa are new records from the A6 and A7 squares for the Flora of Turkey.
- Published
- 1996
11. Comparison of caudal ropivacaine and ropivacaine plus neostigmine administration for postoperative analgesia in children
- Author
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Ertugrul, F, primary, Karakaya, H, additional, Ertug, Z, additional, Kanevetci, B, additional, and Sahin, N, additional
- Published
- 2004
- Full Text
- View/download PDF
12. Comparison of caudal ropivacaine and ropivacaine plus tramadol administration for postoperative analgesia in children
- Author
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Ertugrul, F., primary, Karakaya, H., additional, Pürnek, F., additional, Celikbilek, G., additional, Akbas, M., additional, and Titiz, T. A., additional
- Published
- 2004
- Full Text
- View/download PDF
13. Cloning and expression of the pseudomonas KE38 extra-cellular lipase gene in E. coli
- Author
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Karakaş, Fulya, Arslanoğlu, Alper, Karakaya, H. Çağlar, and Biyoteknoloji Ana Bilim Dalı
- Subjects
Pseudomonas ,Escherichia coli ,Lipase ,Biyoteknoloji ,Purification ,Biotechnology ,Cloning - Abstract
Lipazlar uzun zincirli triaçilgliserollerin hem hidroliz hemde sentezlerini katalizleyen serin hidrolazlardır ve endüstrideki yaygın kullanımları nedeniyle büyük öneme sahiptirler. Lipazlar yaşayan tüm organizmalar, yani mikrooraganizmalar (bakteri ve mantarlar), bitkiler ve hayvanlar tarafından üretilmektedirler. Ancak, mikrobiyal lipazlar özellikle bakteri kaynaklı olanlar, birçok önemli ve ayırt edici özelliklerinden dolayı bitki ve hayvan kaynaklı olanlara nazaran daha kullanışlıdırlar. Lipazlar su bulunan ve bulunmayan ortamlarda aktivite gösterebilirler ve bu sebeple biyoteknolojideki kullanım alanları oldukça geniştir.Bu çalışmanın amacı Kayseri Erciyes dağının toprak örneğinden izole edilerek Pseudomonas sp. KE38 olarak adlandırılan bakteriden lipaz geninin elde edilmesi, E. coli bakterisine klonlanması ve yine aynı bakteride rekombinant olarak üretildikten sonra E. coli BL21 bakterisinin en uygun lipaz üretim zamanı belirlenerek recombinant lipazın kısmi saflaştırılmasının yapılmasıdır. SDS-PAGE sonucuna göre rekombinant lipazın molekül ağırlığı yaklaşık olarak 64 kDa olarak belirlenmiş ayrıca E. coli BL21 IPTG ile indüklendikten iki saat sonra lipaz üretimi en üst seviyeye ulaşarak devam eden sekiz saat boyunca herhangi bir değişim gözlemlenmemiştir. Sonuç olarak çalışmada amaç olan Pseudomonas sp. KE38 bakterisinden izole edilen lipaz geninin klonlanması, E. colide ifadelenmesi ve kısmi saflaştırılması gerçekleştirilmiştir. Lipases are serine hydrolases that catalyze both the hydrolysis and synthesis of insoluble or poorly soluble long-chain triacylglycerols with an acyl chain length ? 10 carbon atoms based on the presence or absence of water. Lipases are produced and secreted by all kingdoms of life that are eukaryotes including plants, animals, fungi and prokaryotes including bacteria and archaea. However, microbial lipases, especially from bacteria, more useful than their plant and animal derivatives because of several important properties. Because of their acitivities in both aqueous and nonaqueous environments, lipases have specific applications in industry and medicine.The primary goals of this thesis were to clone and express the extra-cellular lipase gene from Pseudomonas sp. KE38, isolated from soil samples of Erciyes mountain in Kayseri, in E. coli and partial purification of the gene product. To achieve this aim, genome walking technique was used to obtain lipase gene from Pseudomonas sp. KE38, that gene was then cloned into pET28a expression vector and expressed in E. coli. The lipase expression of E. coli BL21 and its activity was screened with olive oil-Rhodamin B plate assay. After expression recombinant lipase was partially purified via inclusion body isolation. Moreover the optimum lipase production time of E. coli BL21 cells were determined and analyzed with SDS-PAGE. According to SDS-PAGE analysis the recombinant lipase was approximately 64 kDa and lipase production reached to the highest level after two hours of IPTG induction.As conclusion, recombinant lipase from Pseudomonas sp. KE38 was cloned into E. coli, expressed and partially purified. 42
- Published
- 2013
14. Biyoteknolojik uygulamalarda kullanılmak üzere bakteriyel amilazın klonlanması, ifadelenmesi ve biyokimyasal karakterizasyonu
- Author
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Burhanoğlu, Tülin, Şanlı Mohamed, Gülşah, Karakaya, H. Çağlar, Biyoteknoloji Ana Bilim Dalı, Şanli Mohamed, Gülşah, and Izmir Institute of Technology. Biotechnology and Bioengineering
- Subjects
Bacillus (Bacteria)--Biotechnology ,Amylases ,Molecular cloning ,Biyoteknoloji ,Microbial biotechnology ,Enzyme purification ,Enzymes ,Biotechnology - Abstract
Thesis (Master)--Izmir Institute of Technology, Biothechnology, Izmir, 2012, Includes bibliographical references (leaves: 47-53), Text in English; Abstract: Turkish and English, xi, 59 leaves, Amylases are the enzymes that act on glycosidic bond of starch and related polysaccarides. They comprise 25% of enzyme utilised in a variety of industry. It is used to obtain maltose, glucose and maltodextrins in various lenghts during industrial processes. Amylases are widely distributed enzymes in bacteria, fungi, higher plants and animals. Thermophilic enzymes are widely demanded in order to be stable at harsh process conditions. Isolating these enzymes from thermophilic microorganism is increasing trend because of ease of enzyme production. In this study α-amylase gene region from a thermophilic Bacillus sp. isolated from Balçova Geotermal region in İzmir was cloned to compotent E. coli BL 21 cells. Additionally protein expression was reinforced with pKJE7 chaperone plasmid. Cloned gene was sequenced and found as 1542 bp in length. Thermophilic amylase that has a 59.9 kD molecular weight was expressed and purified from this recombinant strain. Mass spectrometric analysis were performed and the enzyme was matched with α-amylase family protein of Geobacillus thermodenitrificans NG80-2 using NCBInr database. The aminoacid sequence of this enzyme was seen to be similar 92% with our obtained enzyme. According to the results of characterization studies, the amylase enzyme was seen to have highest activity at pH 8.0 and 60°C. The enzyme was also showed to have resonable activity between pH5 and 9. 85% of the enzyme activity was retained at 70°C. Furthermore, amylase activities at 65 and 85°C were observed to remain stable for 5 and 2 hours, respectively. It was also showed that the activity was stable and pH7 and 9 for 6 hours. The effects of some metal ions, chemical agents and organic solvents on enzyme activity were examined so, Co+2, Mg+2,Ca+2 was determined to be as inducer for the enzyme activity. Conversely the activity was inhibited by Cu+2. Furthermore methanol, DDT and Triton X-100 was found to have no effect on the enzyme activity.
- Published
- 2012
15. Salt stress responsive proteins identification in wild sugar beet (Beta maritima) by mass spectrometry
- Author
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Baydara, Emine Pinar, Yalçin, Talat, TR114633, İzmir Institute of Technology. Chemistry, Yalçın, Talat, Karakaya, H. Çağlar, and Kimya Ana Bilim Dalı
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Chemistry ,SB221 .B356 2008 ,Sugar beet--Breeding ,Mass spectrometry ,Proteomics--Methodology ,Kimya - Abstract
Thesis (Master)--İzmir Institute of Technology, Chemistry, İzmir, 2008, Includes bibliographical references (leaves: 69-75), Text in English; Abstract: Turkish and English, ix, 75 leaves, Salt stress is one of the major abiotic stresses in agriculture worldwide. Seven percent of the land.s surface and five percent of cultivated lands are affected by salinity.Turkey is the fourth in the world and third in Europe in producing sugar beet. It is observed that salt stress affects the sugar beet negatively especially at germination and seedling stages, it limits the productivity of crop plants and affects the quality of plants.In the present study, proteomic approach was used to investigate the salt-stress responsive proteins in wild salt-tolerant beet, Beta maritima. Sugar beet were grown approximately two months. After growing, they were treated with 250 mM NaCl for seven days. Control plants received no salt treatment during this period. Total proteins of leaves and root were extracted. The proteins were fragmented into peptides using insolution digestion technique and liquid chromatography-tandem mass spectrometry (LC-MS/MS) used for identified the proteins. Totally 288 proteins were identified in leave samples and totally 259 proteins were identified in the root samples.Identified protein results were shown that unique of salt leave proteins and upregulated proteins of leave samples were the related to the antioxidant enzymes. On the other hand, active transporter protein of vacular ATP synthase subunit A was identified in the salt responsive of root samples.
- Published
- 2008
16. Effects of Hyperbaric Nitrogen Narcosis on Cognitive Performance in Recreational air SCUBA Divers: An Auditory Event-related Brain Potentials Study.
- Author
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Karakaya H, Aksu S, Egi SM, Aydin S, and Uslu A
- Subjects
- Brain, Cognition, Evoked Potentials, Humans, Diving, Inert Gas Narcosis, Occupational Exposure
- Abstract
Background: The narcotic effect of hyperbaric nitrogen is most pronounced in air-breathing divers because it impairs diver's cognitive and behavioral performance, and limits the depth of dive profiles. We aimed to investigate the cognitive effects of simulated (500 kPa) air environments in recreational SCUBA divers, revealed by auditory event-related potentials (AERPs)., Methods: A total of 18 healthy volunteer recreational air SCUBA divers participated in the study. AERPs were recorded in pre-dive, deep-dive, and post-dive sessions., Results: False-positive score variables were found with significantly higher differences and longer reaction times of hits during deep-dive and post-dive than pre-dive sessions. Also, P3 amplitudes were significantly reduced and peak latencies were prolonged during both deep-dive and post-dive compared with pre-dive sessions., Conclusion: We observed that nitrogen narcosis at 500 kPa pressure in the dry hyperbaric chamber has a mild-to-moderate negative effect on the cognitive performance of recreational air SCUBA divers, which threatened the safety of diving. Although relatively decreased, this effect also continued in the post-dive sessions. These negative effects are especially important for divers engaged in open-sea diving. Our results show crucial implications for the kinds of control measures that can help to prevent nitrogen narcosis and diving accidents at depths up to 40 msw., (© The Author(s) 2021. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.)
- Published
- 2021
- Full Text
- View/download PDF
17. Hyperbaric oxygen therapy for severe blast injury of lower extremity after terrorist attack: case report.
- Author
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Mirasoglu B, Egeren E, Karakaya H, and Aktas S
- Subjects
- Adolescent, Foot blood supply, Humans, Ischemia etiology, Male, Tibial Fractures etiology, Tibial Fractures therapy, Blast Injuries therapy, Hyperbaric Oxygenation, Ischemia therapy, Leg blood supply, Leg Injuries therapy, Terrorism
- Abstract
More blast injuries are encountered in the civilian setting in recent years as terrorist attacks have increased globally. A 17-year-old male patient with severe blast injury of the right lower extremity was admitted to our department on the fifth day after a terrorist bombing attack. Initially he had been admitted to an emergency department with segmental tibia fracture and arterial injury (Gustilo IIIC). An amputation had been foreseen due to ischemia that persisted even after orthopedic fixation and revascularization interventions, followed by fasciotomy incisions. After consultation with our department hyperbaric oxygen (HBO2) therapy was administered twice daily for the first week. Ischemia improved prominently after 10 HBO2 sessions. HBO2 therapy was continued together with antibiotherapy and wound care. The patient underwent a total of 40 HBO2 sessions and two reconstructive operations and healed without amputation. Vascular injuries with concomitant orthopedic trauma cause most of the delayed amputations in bombing attacks since ischemia can persist at the microvascular level even though adequate treatments are applied. HBO2 corrects hypoxia at tissue level and so provides oxygen for the critically ischemic cells in the injured area. HBO2 also enhances host defense and decreases the ischemia reperfusion injury. In this case, HBO2 was effective in survival and functional recovery (salvage) of the extremity together with regular wound care, antibiotherapy and surgical repair., Competing Interests: The authors of this paper declare no conflicts of interest exist with this submission., (Copyright © Undersea and Hyperbaric Medical Society.)
- Published
- 2019
18. Characterisation of an opcA Mutant of the Unicellular Cyanobacterium Synechocystis sp. PCC 6803.
- Author
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Özkul K and Karakaya H
- Subjects
- Cloning, Molecular, Cyanobacteria classification, Cyanobacteria metabolism, Enzyme Activation, Glucosephosphate Dehydrogenase metabolism, Microbial Viability, Phototrophic Processes, Bacterial Proteins genetics, Cyanobacteria genetics, Mutation
- Abstract
The genes opcA and zwf are located close to each other in most of cyanobacterial strains and the mutations in the opcA gene were reported to lose most of G6PDH activity. One of the reasons suggested for this loss was the polar effect of the mutation on expression of the zwf gene in the same operon and the other was absence of the OpcA polypeptide necessary for the catalytic activity of G6PDH. Synechocystis sp. PCC 6803 exhibits a gene organisation in which opcA and zwf are far away from each other and is ideal for analysis of an opcA mutation alone. In this study, an opcA single mutant and an opcA-zwf double mutant were constructed and effects of the opcA mutation on G6PDH activity and dark viability were then investigated. Contrary to the previous observations, no negative effect of the mutation on G6PDH activity was found under the optimal substrate concentrations. However, when one of the substrates, G6P or NADP, was reduced gradually, G6PDH activity in the mutant cells decreased faster than the wild types. Our results indicated that an opcA mutation did not affect G6PDH activity severely when zwf and opcA were in different operons. Similarly, dark viability of the opcA single and the zwf-opcA double mutants did not exhibit meaningful difference from the wild type.
- Published
- 2015
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19. Comparison of ROS formation and antioxidant enzymes in Cleome gynandra (C₄) and Cleome spinosa (C₃) under drought stress.
- Author
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Uzilday B, Turkan I, Sekmen AH, Ozgur R, and Karakaya HC
- Subjects
- Adaptation, Physiological, Antioxidants metabolism, Ascorbate Peroxidases metabolism, Catalase metabolism, Cleome genetics, Gene Expression Regulation, Plant, Glutathione Reductase metabolism, Hydrogen Peroxide chemistry, Lipid Peroxidation, NADPH Oxidases metabolism, Osmotic Pressure, Oxidative Stress, Peroxidase metabolism, Plant Shoots metabolism, Superoxide Dismutase metabolism, Cleome metabolism, Droughts, Reactive Oxygen Species metabolism, Stress, Physiological
- Abstract
Differences between antioxidant responses to drought in C(3) and C(4) plants are rather scanty. Even, we are not aware of any research on comparative ROS formation and antioxidant enzymes in C(3) and C(4) species differing in carboxylation pathway of same genus which would be useful to prevent other differences in plant metabolism. With this aim, relative shoot growth rate, relative water content and osmotic potential, hydrogen peroxide (H(2)O(2)) content and NADPH oxidase (NOX) activity, antioxidant defence system (superoxide dismutase (SOD), catalase (CAT), peroxidase (POX), ascorbate peroxidase (APX), glutathione reductase (GR) enzymes and their isoenzymes), CAT1 mRNA level, and lipid peroxidation in seedlings of Cleome spinosa (C(3)) and Cleome gynandra (C(4)) species of Cleome genus exposed to drought stress for 5 and 10 day (d) were comparatively investigated. Constitutive levels of antioxidant enzymes (except SOD) were consistently higher in C. spinosa than in C. gynandra under control conditions. CAT1 gene expression in C. spinosa was correlated with CAT activity but CAT1 gene expression in C. gynandra at 10 d did not show this correlation. Drought stress caused an increase in POX, CAT, APX and GR in both species. However, SOD activity was slightly decreased in C. gynandra while it was remained unchanged or increased on 5 and 10 d of stress in C. spinosa, respectively. Parallel to results of malon dialdehyde (MDA), H(2)O(2) content was also remarkably increased in C. spinosa as compared to C. gynandra under drought stress. These results suggest that in C. spinosa, antioxidant defence system was insufficient to suppress the increasing ROS production under stress condition. On the other hand, in C. gynandra, although its induction was lower as compared to C. spinosa, antioxidant system was able to cope with ROS formation under drought stress., (Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.)
- Published
- 2012
- Full Text
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20. Tear function and ocular surface findings in premature and term babies.
- Author
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Dogru M, Karakaya H, Baykara M, Ozmen A, Koksal N, Goto E, Matsumoto Y, Kojima T, Shimazaki J, and Tsubota K
- Subjects
- Case-Control Studies, Conjunctival Diseases diagnosis, Corneal Diseases diagnosis, Dry Eye Syndromes diagnosis, Female, Fluorescein, Fluorophotometry, Gestational Age, Humans, Infant, Newborn, Infant, Premature, Diseases diagnosis, Lacrimal Apparatus Diseases diagnosis, Male, Prospective Studies, Staining and Labeling methods, Conjunctival Diseases physiopathology, Corneal Diseases physiopathology, Dry Eye Syndromes physiopathology, Infant, Premature, Diseases physiopathology, Lacrimal Apparatus Diseases physiopathology, Tears physiology
- Abstract
Objective: To describe the ocular surface and tear function findings in premature and term babies., Design: Prospective, case-control study., Participants: Forty-eight eyes of 24 premature babies seen at the Department of Ophthalmology of Uludag University School of Medicine, Bursa, Turkey, from March 2002 through September 2002 and 50 eyes of 25 healthy term babies were studied., Intervention: The subjects underwent routine ophthalmic examinations; corneal sensitivity measurements; Schirmer test with anesthesia, with and without nasal stimulation; primary Jones test; fluorescein staining of the ocular surface; and conjunctival impression cytology., Main Outcome Measures: Premature and term babies were compared for corneal sensitivity, lacrimal drainage system patency, tear function and ocular surface staining parameters, goblet cell density, and squamous metaplasia grade. The relation of these parameters to the status of the ocular surface was also investigated., Results: Mean corneal sensitivity scores were 45+/-5.0 mm and 55+/-4.5 mm in the premature and term babies, respectively (P<0.001). Premature babies had a mean corneal fluorescein staining score of 1.5+/-0.25 points, compared with 0.22+/-0.28 points in the term babies (P<0.001). The mean Schirmer test scores without and with stimulation were 1.5+/-2.5 mm and 4.15+/-2.5 mm in the premature babies, respectively, compared with 15+/-3.5 mm and 18.75+/-4.5 mm in the term babies. The intragroup and intergroup Schirmer test scores were statistically significant (P<0.001). The primary Jones test was positive in 20.8% of the eyes in the premature babies, whereas it was positive in 84% of eyes in the term babies. The premature babies with positive primary Jones test results all had corneal epithelial defects or severe superficial punctuate keratopathy. Mean conjunctival impression cytology squamous metaplasia scores were 1.86+/-1.2 in the premature babies and 0.86+/-0.47 in the term babies (P<0.001). Mean goblet cell densities were 393+/-484 cells/mm(2) and 739+/-503 cells/mm(2) in the premature and term babies, respectively (P<0.001)., Conclusion: Decreased corneal sensitivity, reduced tearing, and lacrimal drainage patency are important determinants of ocular surface disease in premature infants. Premature newborns with low Schirmer test scores and a patent lacrimal system may experience corneal and conjunctival epithelial problems and should be carefully checked for the presence of dry eye complications.
- Published
- 2004
- Full Text
- View/download PDF
21. The inhibitory action of protamine on human internal thoracic artery contractions: the effect of free hemoglobin.
- Author
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Golbasi I, Nacitarhan C, Ozdem S, Turkay C, Karakaya H, Sadan G, and Bayezid O
- Subjects
- Calcium pharmacology, Dose-Response Relationship, Drug, Endothelium, Vascular drug effects, Endothelium, Vascular physiology, Guanylate Cyclase antagonists & inhibitors, Humans, Methylene Blue pharmacology, Muscle Contraction physiology, Muscle, Smooth, Vascular drug effects, Muscle, Smooth, Vascular physiology, NG-Nitroarginine Methyl Ester pharmacology, Nitric Oxide Synthase antagonists & inhibitors, Phenylephrine pharmacology, Potassium Chloride pharmacology, Thoracic Arteries physiology, Vasoconstrictor Agents pharmacology, Hemoglobins metabolism, Muscle Contraction drug effects, Protamines pharmacology, Thoracic Arteries drug effects, Vasodilator Agents pharmacology
- Abstract
Objective: We investigated the mechanism of the protamine action and the effects of free hemoglobin on protamine-induced responses in endothelium-denuded and-intact human internal thoracic artery (ITA) rings precontracted with phenylephrine (PE) or high KCl., Methods: Samples of redundant ITA obtained from patients undergoing a coronary artery bypass graft surgery were cut into 3 mm wide rings and suspended in 20 ml organ baths. Isometric tension was continuously measured with an isometric force transducer connected to a computer-based data acquisition system., Results: Acetylcholine (Ach, 10(-8)-10(-5) M) caused a concentration-dependent relaxation of PE-precontracted ITA rings. Free hemoglobin (0.1 and 0.5 microM) produced a concentration-dependent and significant decrease in sensitivity (pD(2)) and maximal contractility (E(max)) in response to Ach in PE-precontracted ITA rings (P<0.0001). Protamine (50-800 microg/ml), free hemoglobin (0.1 and 0.5 microM), nitric oxide (NO) blocker N(omega)-nitro-L-arginine methyl ester (L-NAME, 100 microM) or soluble guanylate cyclase inhibitor methylene blue (10 microM) administration did not cause a significant alteration on basal tonus of endothelium-intact or -denuded ITA rings. Protamine (50-800 microg/ml) induced concentration-dependent relaxation responses in ITA rings precontracted by either PE or high KCl. There was no difference in sensitivity or maximal response to protamine between the endothelium-intact and -denuded rings. Incubation of endothelium-intact or -denuded ITA rings with L-NAME or free hemoglobin or methylene blue did not cause a significant inhibition on relaxation responses to protamine. ITA ring contractions induced by stepwise addition of calcium to high KCl solution with no calcium were almost completely inhibited by protamine (P<0.0001)., Conclusions: It was suggested that protamine induced relaxation responses in human ITA rings is not NO- or endothelium-dependent but seems to depend on the interactions of protamine with calcium influxes and/or calcium release from intracellular stores in this tissue.
- Published
- 2003
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22. Tear function and ocular surface changes in keratoconus.
- Author
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Dogru M, Karakaya H, Ozçetin H, Ertürk H, Yücel A, Ozmen A, Baykara M, and Tsubota K
- Subjects
- Adolescent, Adult, Case-Control Studies, Cell Count, Child, Conjunctiva pathology, Epithelial Cells pathology, Female, Fluorescein, Goblet Cells pathology, Humans, Male, Metaplasia, Middle Aged, Prospective Studies, Rose Bengal, Sensation Disorders physiopathology, Conjunctival Diseases physiopathology, Corneal Diseases physiopathology, Keratoconus physiopathology, Tears physiology
- Abstract
Purpose: To describe the ocular surface disorder in patients with keratoconus., Design: A prospective, case-controlled study., Participants: Seventy-five eyes of 38 patients with keratoconus seen at Uludag University School of Medicine, Department of Ophthalmology, from March 2000 through April 2001, and 80 eyes of 40 normal control subjects were studied., Intervention: The subjects underwent routine ophthalmic examinations, corneal sensitivity measurements, Schirmer test, tear film breakup time (BUT), fluorescein and rose bengal staining of the ocular surface, and conjunctival impression cytology., Main Outcome Measures: Patients and control subjects were compared for corneal sensitivity, tear function, ocular surface staining parameters, goblet cell density, and squamous metaplasia grade. The relation of these parameters to the severity of keratoconus progression was also investigated., Results: The mean corneal sensitivity was significantly lower in keratoconus patients compared with control subjects (P < 0.001). The BUT values were also significantly lower in the keratoconus group. Patients with keratoconus had significantly higher fluorescein and rose bengal staining scores (P < 0.001). Corneal sensitivity and tear function changes seemed to get worse with advanced stages of keratoconus. Impression cytology showed goblet cell loss and conjunctival squamous metaplasia, both of which again related to the extent of progression of keratoconus., Conclusions: The ocular surface disease in keratoconus is characterized by disorder of tear quality, squamous metaplasia, and goblet cell loss, all of which seem to relate to the extent of keratoconus progression.
- Published
- 2003
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23. Molecular characterization of two soybean homologs of Arabidopsis thaliana CLAVATA1 from the wild type and fasciation mutant.
- Author
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Yamamoto E, Karakaya HC, and Knap HT
- Subjects
- Amino Acid Sequence, Arabidopsis genetics, Base Sequence, Molecular Sequence Data, Mutation, Protein Isoforms genetics, Protein Serine-Threonine Kinases, Receptor Protein-Tyrosine Kinases chemistry, Reverse Transcriptase Polymerase Chain Reaction, Sequence Alignment, Arabidopsis Proteins, Genes, Plant, Plant Proteins genetics, Receptor Protein-Tyrosine Kinases genetics, Glycine max genetics
- Abstract
Arabidopsis thaliana CLAVATA1 (CLV1)-like genes were isolated from the wild type and fasciation mutant of soybean (Glycine max). Two soybean homologs of CLV1, designated GmCLV1A and GmCLV1B, are similar in sequence. No missense mutations in GmCLV1A and GmCLV1B between the wild type and mutant were found. GmCLV1 was mapped at 7. 1 cM from a restriction fragment length polymorphism marker on the linkage group H of the soybean molecular map. DNA fingerprinting using bacterial artificial chromosome clones identified two contigs indicating there are two loci for GmCLV1 in the soybean genome. One locus contains GmCLV1A and the other locus contains GmCLV1A and GmCLV1B. Relative multiplex quantitative reverse transcriptase-polymerase chain reaction analysis indicates that the two genes are transcribed in all organs and at higher levels in floral apices. Differential expression patterns of the two genes suggest that the function of the two genes is slightly different in different organs.
- Published
- 2000
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24. Multiple oligomeric forms of glucose-6-phosphate dehydrogenase in cyanobacteria and the role of OpcA in the assembly process.
- Author
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Sundaram S, Karakaya H, Scanlan DJ, and Mann NH
- Subjects
- Bacterial Proteins chemistry, Blotting, Western, Cyanobacteria genetics, Electrophoresis, Polyacrylamide Gel, Genes, Bacterial genetics, Glucosephosphate Dehydrogenase chemistry, Mutagenesis, Insertional, Polymerase Chain Reaction, Bacterial Proteins analysis, Cyanobacteria enzymology, Glucosephosphate Dehydrogenase analysis
- Abstract
Multiple molecular forms of glucose-6-phosphate dehydrogenase (G6PDH) were detected by activity staining in non-denaturing polyacrylamide gels of cell-free extracts from a range of cyanobacteria including Anabaena sp. PCC 7120, Synechococcus sp. PCC 7942, Plectonema boryanum PCC 73110, Synechocystis sp. PCC 6803, Nostoc sp. MAC PCC 8009 and the marine strain Synechococcus sp. WH7803. In most of the species tested, the profile of G6PDH activities was modulated by the growth of the cells in the presence of exogenous 10 mM glucose. Using an antiserum raised against a fragment of G6PDH from Anabaena sp. PCC 7120, it was shown that the different molecular forms of G6PDH all contained an antigenically related subunit, suggesting that the different forms arose from different quaternary structures involving the same monomer. An insertion mutant of Synechococcus sp. PCC 7942 was constructed in which the opcA gene, adjacent to zwf (encoding G6PDH), was disrupted. Although no reduction in the amount of G6PDH monomers (Zwf) was observed in the opcA mutant, activity staining of native gels indicated that most of this protein is not assembled into one of the active oligomeric forms. The oligomerization of G6PDH in extracts of the opcA mutant was stimulated in vitro by a factor present in crude extracts of the wild-type, suggesting that the product of the opcA gene is involved in the oligomerization and activation of G6PDH.
- Published
- 1998
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25. A comparison of gene organization in the zwf region of the genomes of the cyanobacteria Synechococcus sp. PCC 7942 and Anabaena sp. PCC 7120.
- Author
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Newman J, Karakaya H, Scanlan DJ, and Mann NH
- Subjects
- Amino Acid Sequence, Anabaena enzymology, Cyanobacteria enzymology, Fructose-Bisphosphatase genetics, Gene Expression Regulation, Bacterial genetics, Genes, Bacterial genetics, Glucosephosphate Dehydrogenase genetics, Molecular Sequence Data, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Anabaena genetics, Cyanobacteria genetics
- Abstract
The region of the genome encoding the glucose-6-phosphate dehydrogenase gene zwf was analysed in a unicellular cyanobacterium, Synechococcus sp. PCC 7942, and a filamentous, heterocystous cyanobacterium, Anabaena sp. PCC 7120. Comparison of cyanobacterial zwf sequences revealed the presence of two absolutely conserved cysteine residues which may be implicated in the light/dark control of enzyme activity. The presence in both strains of a gene fbp, encoding fructose-1,6-bisphosphatase, upstream from zwf strongly suggests that the oxidative pentose phosphate pathway in these organisms may function to completely oxidize glucose 6-phosphate to CO2. The amino acid sequence of fructose-1,6-bisphosphatase does not support the idea of its light activation by a thiol/disulfide exchange mechanism. In the case of Anabaena sp. PCC 7120, the tal gene, encoding transaldolase, lies between zwf and fbp.
- Published
- 1995
- Full Text
- View/download PDF
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