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Search Results: 1 - 10 of 151 matches for " Cahid Cakir "
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A Spontaneous Dominant-Negative Mutation within a 35S::AtMYB90 Transgene Inhibits Flower Pigment Production in Tobacco
Jeff Velten,Cahid Cakir,Christopher I. Cazzonelli
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0009917
Abstract: In part due to the ease of visual detection of phenotypic changes, anthocyanin pigment production has long been the target of genetic and molecular research in plants. Specific members of the large family of plant myb transcription factors have been found to play critical roles in regulating expression of anthocyanin biosynthetic genes and these genes continue to serve as important tools in dissecting the molecular mechanisms of plant gene regulation.
Transgene Silencing and Transgene-Derived siRNA Production in Tobacco Plants Homozygous for an Introduced AtMYB90 Construct
Jeff Velten, Cahid Cakir, Eunseog Youn, Junping Chen, Christopher I. Cazzonelli
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0030141
Abstract: Transgenic tobacco (Nicotiana tabacum) lines were engineered to ectopically over-express AtMYB90 (PAP2), an R2–R3 Myb gene associated with regulation of anthocyanin production in Arabidopsis thaliana. Independently transformed transgenic lines, Myb27 and Myb237, accumulated large quantities of anthocyanin, generating a dark purple phenotype in nearly all tissues. After self-fertilization, some progeny of the Myb27 line displayed an unexpected pigmentation pattern, with most leaves displaying large sectors of dramatically reduced anthocyanin production. The green-sectored 27Hmo plants were all found to be homozygous for the transgene and, despite a doubled transgene dosage, to have reduced levels of AtMYB90 mRNA. The observed reduction in anthocyanin pigmentation and AtMYB90 mRNA was phenotypically identical to the patterns seen in leaves systemically silenced for the AtMYB90 transgene, and was associated with the presence of AtMYB90-derived siRNA homologous to both strands of a portion of the AtMYB90 transcribed region. Activation of transgene silencing in the Myb27 line was triggered when the 35S::AtMYB90 transgene dosage was doubled, in both Myb27 homozygotes, and in plants containing one copy of each of the independently segregating Myb27 and Myb237 transgene loci. Mapping of sequenced siRNA molecules to the Myb27 TDNA (including flanking tobacco sequences) indicated that the 3′ half of the AtMYB90 transcript is the primary target for siRNA associated silencing in both homozygous Myb27 plants and in systemically silenced tissues. The transgene within the Myb27 line was found to consist of a single, fully intact, copy of the AtMYB90 construct. Silencing appears to initiate in response to elevated levels of transgene mRNA (or an aberrant product thereof) present within a subset of leaf cells, followed by spread of the resulting small RNA to adjacent leaf tissues and subsequent amplification of siRNA production.
The Irish Potato Famine Pathogen Phytophthora infestans Translocates the CRN8 Kinase into Host Plant Cells
Mireille van Damme,Tolga O. Bozkurt,Cahid Cakir,Sebastian Schornack,Jan Sklenar,Alexandra M. E. Jones,Sophien Kamoun
PLOS Pathogens , 2012, DOI: 10.1371/journal.ppat.1002875
Abstract: Phytopathogenic oomycetes, such as Phytophthora infestans, secrete an arsenal of effector proteins that modulate plant innate immunity to enable infection. We describe CRN8, a host-translocated effector of P. infestans that has kinase activity in planta. CRN8 is a modular protein of the CRN effector family. The C-terminus of CRN8 localizes to the host nucleus and triggers cell death when the protein is expressed in planta. Cell death induction by CRN8 is dependent on its localization to the plant nucleus, which requires a functional nuclear localization signal (NLS). The C-terminal sequence of CRN8 has similarity to a serine/threonine RD kinase domain. We demonstrated that CRN8 is a functional RD kinase and that its auto-phosphorylation is dependent on an intact catalytic site. Co-immunoprecipitation experiments revealed that CRN8 forms a dimer or multimer. Heterologous expression of CRN8 in planta resulted in enhanced virulence by P. infestans. In contrast, in planta expression of the dominant-negative CRN8R469A;D470A resulted in reduced P. infestans infection, further implicating CRN8 in virulence. Overall, our results indicate that similar to animal parasites, plant pathogens also translocate biochemically active kinase effectors inside host cells.
The Adomian Decomposition Method and the Differential Transform Method for Numerical Solution of Multi-Pantograph Delay Differential Equations  [PDF]
Musa Cakir, Derya Arslan
Applied Mathematics (AM) , 2015, DOI: 10.4236/am.2015.68126
Abstract: In this paper, the Adomian Decomposition Method (ADM) and the Differential Transform Method (DTM) are applied to solve the multi-pantograph delay equations. The sufficient conditions are given to assure the convergence of these methods. Several examples are presented to demonstrate the efficiency and reliability of the ADM and the DTM; numerical results are discussed, compared with exact solution. The results of the ADM and the DTM show its better performance than others. These methods give the desired accurate results only in a few terms and in a series form of the solution. The approach is simple and effective. These methods are used to solve many linear and nonlinear problems and reduce the size of computational work.
Dosimetric Comparison of Integral Radiation Dose: Anisotropic Analytical Algorithm and Acuros XB in Breast Radiotherapy  [PDF]
Aydin Cakir, Zuleyha Akgun
International Journal of Medical Physics,Clinical Engineering and Radiation Oncology (IJMPCERO) , 2019, DOI: 10.4236/ijmpcero.2019.82006
Abstract: The impact of the difference between Anisotropic Analytical Algorithm (AAA) and Acuros XB (AXB) in breast radiotherapy is not clearly due to different uses and further research is required to explain this effect. The aim of this study is to investigate the contribution of calculation differences between AAA and AXB to the integral radiation dose (ID) on critical organs. Seven field intensity modulated radiotherapy (IMRT) plans were generated using with AAA and AXB algorithms for twenty patients with early stage left breast cancer after breast conserving surgery. Volumetric and dosimetric differences, as well as, the Dmean, V5, V20 doses of the left and right-sided lung, the Dmean, V10, V20, V30 doses of heart and the Dmean, V5, V10 doses of the contralateral breast were investigated. The mean dose (Dmean), V5, V20 doses of the left-sided lung, the Dmean, V5, V10 doses of right-sided lung, the Dmean, V10, V20, V30 doses of heart and the Dmean, V5, V10 doses of the contralateral breast were found to be significantly higher with AAA. In this research integral dose was also higher in the AAA recalculated plan and the AXB plan with the average dose as follows left lung 2%, heart 2%, contralateral breast 8%, contralateral lung 4% respectively. Our study revealed that the calculation differences between Acuros XB (AXB) and Anisotropic Analytical Algorithm (AAA) in breast radiotherapy caused serious differences on the stored integral doses on critical organs. In addition, AXB plans showed significantly dosimetric improvements in multiple dosimetric parameters.
Stability of Difference Schemes for Fractional Parabolic PDE with the Dirichlet-Neumann Conditions
Zafer Cakir
Abstract and Applied Analysis , 2012, DOI: 10.1155/2012/463746
Abstract: The stable difference schemes for the fractional parabolic equation with Dirichlet and Neumannboundary conditions are presented. Stability estimates and almost coercive stability estimates with ln (1/(
Developing Cultural Awareness In Foreign Language Teaching
Ismail CAKIR
The Turkish Online Journal of Distance Education , 2006,
Abstract: Regardless of different points of view, culture has taken an important place in foreign language teaching and learning studies. It has been widely recognized that culture and language is used as a main medium through which culture is expressed. However, “pure information” is useful but does not necessarily lead learners’ insight; whereas the development of people’s cultural awareness leads them to more critical thinking. Most frequently confronted that students to a great extend know the rules of language, but are not always able to use the language adequately as it requires since they are not knowledgeable enough about the target culture. Bearing all this in mind, the aim of this article has been to provide necessary information for the foreign language teachers and learners so that they can establish a good connection with the target language and its culture.
Water and Salt Metabolism Disorders Following Transsphenoidal Pituitary Surgery
Mehtap Cakir
Turkish Journal of Endocrinology and Metabolism , 2011,
Abstract: Transsphenoidal pituitary surgery is frequently complicated with mild to severe water and electrolyte disturbances in the postoperative period. These disorders are: transient diabetes insipidus, early or delayed hyponatremia, diabetes insipidus followed by hyponatremia (biphasic pattern), diabetes insipidus-hyponatremia-diabetes insipidus (triphasic pattern), permanent diabetes insipidus, and cerebral salt-wasting syndrome. Close monitoring of water intake, urine output, thirst, volume status and serum electrolytes is imperative, and a dynamic treatment plan according to the changing status of the patient is mandatory. This review will focus on the types, course and treatment of water and electrolyte disturbances observed after transsphenoidal pituitary surgery. Turk Jem 2011; 15: 28-32
Searches for Supersymmetry with the CMS Experiment
Altan Cakir
Physics , 2011,
Abstract: After a very successful startup of the LHC in 2010, the CMS experiment has already accumulated significantly more data in 2011. After the successful re-discovery of the Standard Model, the search for signs of new physics has already reached, and in most cases enlarged, the limits from previous experiments. In this conference report I review the recent discovery reach of SUSY searches that will be performed with the 2011 data.
Drawing Particle Symbols and Feynman Diagrams with Office
Orhan Cakir
Physics , 2004,
Abstract: Particle symbols and Feynman diagrams often used in particle physics can be generated by a word document processor. Standard office packages have their built in symbols such as solid-line, dashed-line, arrows, etc. which are also used in particle physics. Three symbols corresponding to photon, gluon and fermion line are not present in the standard office packages. By importing these two symbols and using the built in symbols, tree-level Feynman diagrams can be easily generated in an office program.
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