Researcher:
Özber, Natali

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Master Student

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Natali

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Özber

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Özber, Natali

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2007 - 20106

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Researcher Of Publications: search.filters.isAuthorOfPublication.52580e3e-4320-472c-995a-3b5c8a7dcc26

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Now showing 1 - 6 of 6
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    The ınteraction of cationic polymers and their bisphosphonate derivatives with hydroxyapatite
    (Wiley-V C H Verlag Gmbh, 2007) Zhang, Sufeng; Wright, Jennifer E. I.; Uludag, Hasan; N/A; Özber, Natali; Master Student; Graduate School of Sciences and Engineering; N/A
    Conjugating proteins with bisphosphonates (BPs), a class of molecules with exceptional affinity to hydroxyapatite (HA), is a feasible means to impart bone affinity to protein-based therapeutic agents. To increase the targeting effectiveness while minimizing protein modification, a polymeric linker containing multiple copies of BPs could be constructed for protein conjugation and targeting to bone. Towards this goal, poly(L-lysine) (PLL) and poly(ethylenimine) (PEI) were utilized as the polymeric backbones to incorporate a BP, namely 2-(3-mercaptopropylsulfanyl) -ethyl-1,1-bisphosphonic acid (thioIBP), by using N-hydroxysuccinimidyl polyethylene glycol maleimide and succinimidyl-4-(N-maleimidomethyl)-cydohexane-1-carboxylate, respectively. In vitro and in vivo mineral affinity of the polymer-BP conjugates were determined in comparison with the unmodified polymers. The in vitro results indicated strong binding of the cationic polymers to HA in their unmodified form. BP conjugation did not enhance the inherent mineral affinity of the polymers; in contrast, certain modifications negatively affected the polymers' binding to the HA. In vivo results from a subcutaneous implant model in rats also showed no significant difference in mineral affinity of the BP modified and unmodified PEI. We conclude that thiolBP conjugation to the cationic polymers PLL and PEI was not beneficial for increasing the mineral affinity of the polymeric molecules. The strong interaction between the cationic polymers and HA may make the polymers suitable for imparting mineral affinity to bone-acting therapeutics.
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    Resonant cantilever bio sensor with integrated grating readout
    (IEEE, 2008) N/A; N/A; N/A; N/A; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Department of Electrical and Electronics Engineering; Ocaklı, Hüseyin İlker; Öztürk, Alibey; Özber, Natali; Kavaklı, İbrahim Halil; Alaca, Burhanettin Erdem; Ürey, Hakan; Master Student; Master Student; Master Student; Faculty Member; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; 40319; 115108; 8579
    Microcantilever based biosensor is fabricated and tested. The main features are the simple single mask fabrication, grating based sensitive optical readout, magnetic thin-film actuation, and suitability for parallel array operation. Sub-picogram mass detection sensitivity demonstrated.
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    A magnetically actuated resonant mass sensor with integrated optical readout
    (Ieee-Inst Electrical Electronics Engineers Inc, 2008) N/A; N/A; Department of Electrical and Electronics Engineering; N/A; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Öztürk, Alibey; Ocaklı, Hüseyin İlker; Özber, Natali; Ürey, Hakan; Kavaklı, İbrahim Halil; Alaca, Burhanettin Erdem; Master Student; Researcher; Master Student; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; 8579; 40319; 115108
    Nickel cantilevers with integrated diffraction gratings are used as resonant mass sensors with a resolution of 500 femtograms. Their applicability to biosensing is demonstrated with human opioid receptors. The device is fabricated through a single-mask lithographic process. The microoptical readout provides a simple measurement platform with one external photodiode. Thanks to its ac operation principle, the device is immune to environmental noise and entails a high tolerance to fabrication defects. Obtained signal-to-noise ratio is comparable to that of a high-end Doppler vibrometer. The device with these aspects for systems integration and microarray technology is a candidate for low-cost portable sensors.
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    Detection of human kappa-opioid antibody using microresonators with integrated optical readout
    (Elsevier advanced Technology, 2010) N/A; N/A; N/A; N/A; Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Department of Electrical and Electronics Engineering; Department of Mechanical Engineering; Timurdoğan, Erman; Özber, Natali; Nargül, Sezin; Yavuz, Serhat; Kılıç, M. Salih; Kavaklı, İbrahim Halil; Ürey, Hakan; Alaca, Burhanettin Erdem; PhD Student; Master Student; PhD Student; Master Student; Resercher; Faculty Member; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Electrical and Electronics Engineering; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; N/A; N/A; 40319; 8579; 115108
    Label-free detection of the interaction between hexahistidine-tagged human kappa-opioid receptor membrane protein and anti-His antibody is demonstrated in liquid by an optical microelectromechanical system utilizing electromagnetically actuated microresonators Shift in resonance frequency due to accretion of mass on the sensitive surface of microresonators is monitored via an integrated optical readout a frequency resolution of 2 Hz is obtained Together with a sensitivity of 7 ppm/(ng/ml)) this leads to a minimum detectable antibody concentration of 57 ng/ml for a 50-kHz device the measurement principle is shown to impart immunity to environmental noise, facilitate operation in liquid media and bring about the prospect for further miniaturization of actuator and readout leading to a portable biochemical sensor.
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    PublicationOpen Access
    Investigation of the interaction between the large and small subunits of potato ADP-glucose pyrophosphorylase
    (Public Library of Science, 2009) Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Barış, İbrahim; Özber, Natali; Keskin, Özlem; Kavaklı, İbrahim Halil; Teaching Faculty; Master Student; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; College of Sciences; College of Engineering; 111629; N/A; N/A; 26605; 40319
    ADP-glucose pyrophosphorylase (AGPase), a key allosteric enzyme involved in higher plant starch biosynthesis, is composed of pairs of large (LS) and small subunits (SS). Current evidence indicates that the two subunit types play distinct roles in enzyme function. Recently the heterotetrameric structure of potato AGPase has been modeled. In the current study, we have applied the molecular mechanics generalized born surface area (MM-GBSA) method and identified critical amino acids of the potato AGPase LS and SS subunits that interact with each other during the native heterotetrameric structure formation. We have further shown the role of the LS amino acids in subunit-subunit interaction by yeast two-hybrid, bacterial complementation assay and native gel. Comparison of the computational results with the experiments has indicated that the backbone energy contribution (rather than the side chain energies) of the interface residues is more important in identifying critical residues. We have found that lateral interaction of the LS-SS is much stronger than the longitudinal one, and it is mainly mediated by hydrophobic interactions. This study will not only enhance our understanding of the interaction between the SS and the LS of AGPase, but will also enable us to engineer proteins to obtain better assembled variants of AGPase which can be used for the improvement of plant yield.
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    PublicationOpen Access
    Identification of two amino acids in the c-terminal domain of mouse CRY2 essential for PER2 interaction
    (BioMed Central, 2010) Department of Chemical and Biological Engineering; Özber, Natali; Barış, İbrahim; Tatlıcı, Gülnaz; Gür, İbrahim; Kılınç, Seda; Ünal, Evrim Besray; Kavaklı, İbrahim Halil; Master Student; Teaching Faculty; PhD Student; Department of Chemical and Biological Engineering; The Center for Computational Biology and Bioinformatics (CCBB); College of Engineering; N/A; 111629; N/A; N/A; N/A; N/A; 40319
    Background: Cryptochromes (CRYs) are a class of flavoprotein blue-light signaling receptors found in plants and animals, and they control plant development and the entrainment of circadian rhythms. They also act as integral parts of the central circadian oscillator in humans and other animals. In mammals, the CLOCK-BMAL1 heterodimer activates transcription of the Per and Cry genes as well as clock-regulated genes. The PER2 proteins interact with CRY and CKI epsilon, and the resulting ternary complexes translocate into the nucleus, where they negatively regulate the transcription of Per and Cry core clock genes and other clock-regulated output genes. Recent studies have indicated that the extended C-termini of the mammalian CRYs, as compared to photolyase proteins, interact with PER proteins. Results: We identified a region on mCRY2 (between residues 493 and 512) responsible for direct physical interaction with mPER2 by mammalian two-hybrid and co immunoprecipitation assays. Moreover, using oligonucleotide-based degenerate PCR, we discovered that mutation of Arg-501 and Lys-503 of mCRY2 within this C-terminal region totally abolishes interaction with PER2. Conclusions: Our results identify mCRY2 amino acid residues that interact with the mPER2 binding region and suggest the potential for rational drug design to inhibit CRYs for specific therapeutic approaches.