Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik

Permanent URI for this collectionhttps://hdl.handle.net/11147/9

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Institution Author: search.filters.institutionAuthor.Soyer Dönmez, Ferda

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Now showing 1 - 3 of 3
  • Article
    Citation - WoS: 1
    Citation - Scopus: 3
    Detection of the Contamination Sources of Listeria Monocytogenes in Pickled White Cheese Production Process Line and Genotyping With the Pulsed-Field Gel Electrophoresis Method
    (TUBITAK, 2016) Telli, Nihat; Güner, Ahmet; Soyer Dönmez, Ferda; Özdemir, Özgün Öykü
    This study was conducted to determine the contamination sources, serotyping profiles, and antibiotic resistance patterns of Listeria monocytogenes isolated during the production of pickled white cheese. The genetic-relatedness of the isolates to EGD SLCC (5835) (1/2a, lineage II) and ATCC (13932) (4b, lineage I) reference strains was also determined with pulsed-field gel electrophoresis (PFGE) as a result of digestions with AscI and ApaI enzymes. Samples were collected from 16 different points in the production process of 4 different plants at 3 different times. Among the 192 samples examined, 17 (8.85%) were determined to be contaminated with Listeria spp. Three isolates (3.53%) obtained from raw milk, wall/ground, and press cases were identified as L. monocytogenes via the conventional culture method and confirmed by polymerase chain reaction. These isolates were found to belong to serotype 4b. According to antibiotic resistance testing against 10 antibiotics (ampicillin, gentamicin, erythromycin, tetracycline, chloramphenicol, cefalotin, streptomycin, vancomycin, penicillin, and sulfamethoxazole/trimethoprim), it was determined that isolates from raw milk and press cases were resistant to erythromycin. PPGE band patterns of the isolates displayed indistinguishable with AscI and 80%-94% homology with ApaI. The isolates were observed to display high homology to ATCC (13932) and lower homology to EGD SLCC (5835) obtained by both enzymes.
  • Article
    Citation - WoS: 119
    Citation - Scopus: 121
    Structure of Halothiobacillus Neapolitanus Carboxysomes by Cryo-Electron Tomography
    (Academic Press Inc., 2006) Schmid, Michael F.; Paredes, Angel M.; Khant, Htet A.; Soyer Dönmez, Ferda; Aldrich, Henry C.; Chiu, Wah; Shively, Jessup M.
    Carboxysomes are polyhedral bodies consisting of a proteinaceous shell filled with ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO). They are found in the cytoplasm of all cyanobacteria and some chemoautotrophic bacteria. Previous studies of Halothiobacillus neapolitanus and Nitrobacter agilis carboxysomes suggest that the structures are either icosahedral or dodecahedral. To determine the protein shell structure more definitively, purified H. neapolitanus carboxysomes were re-examined by cryo-electron tomography and scanning transmission electron microscopy (STEM). Due to the limited tilt angles in the electron microscope, the tomographic reconstructions are distorted. Corrections were made in the 3D orientation searching and averaging of the computationally extracted carboxysomes to minimize the missing data effects. It was found that H. neapolitanus carboxysomes vary widely in size and mass as shown by cryo-electron tomography and STEM mass measurements, respectively. We have aligned and averaged carboxysomes in several size classes from the 3D tomographic reconstruction by methods that are not model-biased. The averages reveal icosahedral symmetry of the shell, but not of the density inside it, for all the size classes
  • Article
    Citation - WoS: 50
    Citation - Scopus: 53
    Organization of Carboxysome Genes in the Thiobacilli
    (Springer Verlag, 2003) Cannon, Gordon C.; Baker, Stefanie H.; Soyer Dönmez, Ferda; Johnson, Diana R.; Bradburne, Christopher E.; Mehlman, Jennifer L.; Davies, Paige S.; Jiang, Qinli; Heinhorst, Sabine; Shively, Jessup M.
    The order of genes in the carboxysome gene clusters of four thiobacilli was examined and the possibility of the cluster forming an operon evaluated. Furthermore, carboxysome peptide homologs were compared with respect to similarities in primary sequence, and the unique structural features of the shell protein CsoS2 were described.