Researcher:
Çonkar, Deniz

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PhD Student

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Deniz

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Çonkar

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Çonkar, Deniz

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2014 - 2019112020 - 20233

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Researcher Of Publications: search.filters.isAuthorOfPublication.7212b087-4ffd-41d7-b613-725625049b60

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Now showing 1 - 10 of 14
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    Dynamic recruitment of the retinal degeneration gene product CCDC66 to the centrosome/cilium complex is regulated by satellites and nnicrotubules
    (Amer Soc Cell Biology, 2018) N/A; Department of Molecular Biology and Genetics; N/A; Karalar, Elif Nur Fırat; Çonkar, Deniz; Faculty Member; PhD Student; Department of Molecular Biology and Genetics; College of Sciences; Graduate School of Sciences and Engineering; 206349; N/A
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    3D coffee stains
    (Royal Soc Chemistry, 2017) N/A; N/A; Department of Electrical and Electronics Engineering; N/A; N/A; N/A; Department of Molecular Biology and Genetics; Department of Chemistry; Department of Chemistry; Department of Electrical and Electronics Engineering; Doğru-Yüksel, Itır Bakış; Söz, Çağla Koşak; Press, Daniel Aaron; Melikov, Rustamzhon; Begar, Efe; Çonkar, Deniz; Karalar, Elif Nur Fırat; Yılgör, Emel; Yılgör, İskender; Nizamoğlu, Sedat; PhD Student; PhD Student; Researcher; PhD Student; PhD Student; PhD Student; PhD Student; Faculty Member; Researcher; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Department of Chemistry; Department of Electrical and Electronics Engineering; N/A; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); N/A; N/A; N/A; N/A; N/A; N/A; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; College of Sciences; College of Engineering; N/A; N/A; N/A; N/A; N/A; N/A; 206349; N/A; 24181; 130295
    When a liquid droplet (e.g., coffee, wine, etc.) is splattered on a surface, the droplet dries in a ring-shaped stain. This widely observed pattern in everyday life occurs due to the phenomenon known as a coffee stain (or coffee ring) effect. While the droplet dries, the capillary flow moves and deposits the particles toward the pinned edges, which shows a 2D ring-like structure. Here we demonstrate the transition from a 2D to a 3D coffee stain that has a well-defined and hollow sphere-like structure, when the substrate surface is switched from hydrophilic to superhydrophobic. The 3D stain formation starts with the evaporation of the pinned aqueous colloidal droplet placed on a superhydrophobic surface that facilitates the particle flow towards the liquid-air interface. This leads to spherical skin formation and a cavity in the droplet. Afterwards the water loss in the cavity due to pervaporation leads to bubble nucleation and growth, until complete evaporation of the solvent. In addition to the superhydrophobicity of the surface, the concentration of the solution also has a significant effect on 3D coffee stain formation. Advantageously, 3D coffee stain formation in a pendant droplet configuration enables the construction of all-protein lasers by integrating silk fibroin with fluorescent proteins. No tools, components and/or human intervention are needed after the construction process is initiated; therefore, 3D coffee-stains hold promise for building self-assembled and functional 3D constructs and devices from colloidal solutions.
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    CCDC66 regulates primary cilium length and signaling via interactions with transition zone and axonemal proteins
    (The Company of Biologists, 2023) Frikstad, Kari-Anne M.; Patzke, Sebastian; Department of Molecular Biology and Genetics; Odabaşı, Ezgi; Çonkar, Deniz; Deretic, Jovana; Batman, Umut; Karalar, Elif Nur Fırat; Other; Researcher; Researcher; Master Student; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; N/A; N/A; N/A; N/A; 206349
    The primary cilium is a microtubule-based organelle that serves as a hub for many signaling pathways. It functions as part of the centrosome or cilium complex, which also contains the basal body and the centriolar satellites. Little is known about the mechanisms by which the microtubule-based ciliary axoneme is assembled with a proper length and structure, particularly in terms of the activity of microtubule-associated proteins (MAPs) and the crosstalk between the different compartments of the centrosome or cilium complex. Here, we analyzed CCDC66, a MAP implicated in cilium biogenesis and ciliopathies. Live-cell imaging revealed that CCDC66 compartmentalizes between centrosomes, centriolar satellites, and the ciliary axoneme and tip during cilium biogenesis. CCDC66 depletion in human cells causes defects in cilium assembly, length and morphology. Notably, CCDC66 interacts with the ciliopathy-linked MAPs CEP104 and CSPP1, and regulates axonemal length and Hedgehog pathway activation. Moreover, CCDC66 is required for the basal body recruitment of transition zone proteins and intraflagellar transport B (IFT-B) machinery. Overall, our results establish CCDC66 as a multifaceted regulator of the primary cilium and provide insight into how ciliary MAPs and subcompartments cooperate to ensure assembly of functional cilia.
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    Protein integrated white LEDs for lighting
    (Optica Publishing Group (formerly OSA), 2014) N/A; Department of Electrical and Electronics Engineering; N/A; N/A; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; Press, Daniel Aaron; Melikov, Rustamzhon; Çonkar, Deniz; Karalar, Elif Nur Fırat; Nizamoğlu, Sedat; Researcher; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; N/A; N/A; 206349; 130295
    We demonstrated a new class of white LEDs based on biologically-derived fluorescent proteins. For this we expressed eGFP and mCherry proteins, and integrated them over blue LED chips for cool-, daylight- and warm-white light generation.
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    Microtubule-associated proteins and emerging links to primary cilium structure, assembly, maintenance, and disassembly
    (Wiley, 2021) N/A; Department of Molecular Biology and Genetics; Çonkar, Deniz; Karalar, Elif Nur Fırat; PhD Student; Faculty Member; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of Sciences; N/A; 206349
    The primary cilium is a microtubule-based structure that protrudes from the cell surface in diverse eukaryotic organisms. It functions as a key signaling center that decodes a variety of mechanical and chemical stimuli and plays fundamental roles in development and homeostasis. Accordingly, structural and functional defects of the primary cilium have profound effects on the physiology of multiple organ systems including kidney, retina, and central nervous system. At the core of the primary cilium is the microtubule-based axoneme, which supports the cilium shape and acts as the scaffold for bidirectional transport of cargoes into and out of cilium. Advances in imaging, proteomics, and structural biology have revealed new insights into the ultrastructural organization and composition of the primary cilium, the mechanisms that underlie its biogenesis and functions, and the pathologies that result from their deregulation termed ciliopathies. In this viewpoint, we first discuss the recent studies that identified the three-dimensional native architecture of the ciliary axoneme and revealed that it is considerably different from the well-known '9 + 0' paradigm. Moving forward, we explore emerging themes in the assembly and maintenance of the axoneme, with a focus on how microtubule-associated proteins regulate its structure, length, and stability. This far more complex picture of the primary cilium structure and composition, as well as the recent technological advances, open up new avenues for future research.
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    The centriolar satellite protein Cep109 and Cep290 interact and are required for recruitment of BBS proteins to the cilium
    (Amer Soc Cell Biology, 2016) Rauniyar, N.; Yates, J., I. I. I.; N/A; N/A; N/A; Department of Molecular Biology and Genetics; Çonkar, Deniz; Culfa, Efraim; Odabaşı, Ezgi; Karalar, Elif Nur Fırat; Phd Student; Master Student; Other; Faculty Member; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; N/A; N/A; College of Sciences; N/A; N/A; N/A; 206349
    Defects in centrosome and cilium function are associated with phenotypically related syndromes called ciliopathies. Centriolar satellites are centrosome-associated structures, defined by the protein PCM1, that are implicated in centrosomal protein trafficking. We identify Cep72 as a PCM1-interacting protein required for recruitment of the ciliopathy-associated protein Cep290 to centriolar satellites. Loss of centriolar satellites by depletion of PCM1 causes relocalization of Cep72 and Cep290 from satellites to the centrosome, suggesting that their association with centriolar satellites normally restricts their centrosomal localization. We identify interactions between PCM1, Cep72, and Cep290 and find that disruption of centriolar satellites by overexpression of Cep72 results in specific aggregation of these proteins and the BBSome component BBS4. During ciliogenesis, BBS4 relocalizes from centriolar satellites to the primary cilium. This relocalization occurs normally in the absence of centriolar satellites (PCM1 depletion) but is impaired by depletion of Cep290 or Cep72, resulting in defective ciliary recruitment of the BBSome subunit BBS8. We propose that Cep290 and Cep72 in centriolar satellites regulate the ciliary localization of BBS4, which in turn affects assembly and recruitment of the BBSome. Finally, we show that loss of centriolar satellites in zebrafish leads to phenotypes consistent with cilium dysfunction and analogous to those observed in human ciliopathies.
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    Ultra-efficient and high-quality white light-emitting devices using fluorescent proteins in aqueous medium
    (Wiley, 2020) N/A; N/A; N/A; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; Sadeghi, Sadra; Melikov, Rustamzhon; Çonkar, Deniz; Karalar, Elif Nur Fırat; Nizamoğlu, Sedat; PhD Student; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; 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 Sciences; College of Engineering; N/A; N/A; N/A; 206349; 130295
    The transformation of electronics toward “green” and efficient devices is critical for the environmental sustainability and energy future. So far, majority of efficient lighting devices have been realized by artificial optical materials such as rare-earth-elements-doped phosphors, colloidal quantum dots (QDs) and dyes. In this study, red-emitting mScarlet and green-emitting eGFP fluorescent proteins are determined for high-performance white LEDs, expressed in living Escherichia coli and the purified proteins are integrated in their natural aqueous environment onto blue LED chips. The aqueous integration preserved quantum yield levels of the proteins above 70% in the device architecture and facilitated a high luminous efficiency (LE) of 81 lm W−1 with a color rendering index (CRI) of 83, which is the most efficient eco-friendly white LED reported to date. Moreover, the concentration ratio are also optimized of red- and green-emitting proteins and white protein-based LEDs with a maximum CRI of 92 are demonstrated. This study shows that fluorescent proteins hold great promise for the next generation eco-friendly, efficient and high-quality white light sources.
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    Ecofriendly and efficient luminescent solar concentrators based on fluorescent proteins
    (amer Chemical Soc, 2019) N/A; N/A; N/A; N/A; Department of Electrical and Electronics Engineering; N/A; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; Sadeghi, Sadra; Melikov, Rustamzhon; Jalali, Houman Bahmani; Karatüm, Onuralp; Srivastava, Shashi Bhushan; Çonkar, Deniz; Karalar, Elif Nur Fırat; Nizamoğlu, Sedat; PhD Student; PhD Student; PhD Student; PhD Student; Researcher; PhD Student; Faculty Member, Faculty Member; Department of Molecular Biology and Genetics; Department of Electrical and Electronics 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; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; N/A; N/A; N/A; N/A; N/A; 206349; 130295
    In recent years, luminescent solar concentrators (LSCs) have received renewed attention as a versatile platform for large-area, high-efficiency, and low-cost solar energy harvesting. So far, artificial or engineered optical materials, such as rare-earth ions, organic dyes, and colloidal quantum dots (QDs) have been incorporated into LSCs. Incorporation of nontoxic materials into efficient device architectures is critical for environmental sustainability and clean energy production. Here, we demonstrated LSCs based on fluorescent proteins, which are biologically produced, ecofriendly, and edible luminescent biomaterials along with exceptional optical properties. We synthesized mScarlet fluorescent proteins in Escherichia coli expression system, which is the brightest protein with a quantum yield of 61% in red spectral region that matches well with the spectral response of silicon solar cells. Moreover, we integrated fluorescent proteins in an aqueous medium into solar concentrators, which preserved their quantum efficiency in LSCs and separated luminescence and wave-guiding regions due to refractive index contrast for efficient energy harvesting. Solar concentrators based on mScarlet fluorescent proteins achieved an external LSC efficiency of 2.58%, and the integration at high concentrations increased their efficiency approaching to 5%, which may facilitate their use as “luminescent solar curtains” for in-house applications. The liquid-state integration of proteins paves a way toward efficient and “green” solar energy harvesting.
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    Fluorescent protein integrated white LEDs for displays
    (Iop Publishing Ltd, 2016) N/A; Department of Electrical and Electronics Engineering; N/A; N/A; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; Press, Daniel Aaron; Melikov, Rustamzhon; Çonkar, Deniz; Karalar, Elif Nur Fırat; Nizamoğlu, Sedat; Researcher; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; N/A; N/A; 206349; 130295
    The usage time of displays (e.g., TVs, mobile phones, etc) is in general shorter than their functional life time, which worsens the electronic waste (e-waste) problem around the world. The integration of biomaterials into electronics can help to reduce the e-waste problem. In this study, we demonstrate fluorescent protein integrated white LEDs to use as a backlight source for liquid crystal (LC) displays for the first time. We express and purify enhanced green fluorescent protein (eGFP) and monomeric Cherry protein (mCherry), and afterward we integrate these proteins as a wavelength-converter on a blue LED chip. The protein-integrated backlight exhibits a high luminous efficacy of 248 lm/W-opt and the area of the gamut covers 80% of the NTSC color gamut. The resultant colors and objects in the image on the display can be well observed and distinguished. Therefore, fluorescent proteins show promise for display applications.
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    Single transverse mode eGFP modified silk fibroin laser
    (Optica Publishing Group (formerly OSA), 2018) Min, Kyungtaek; Umar, Muhammad; Kim, Sunghwan; N/A; N/A; N/A; N/A; Department of Molecular Biology and Genetics; Department of Electrical and Electronics Engineering; Doğru-Yüksel, Itır Bakış; Jalali, Houman Bahmani; Begar, Efe; Çonkar, Deniz; Karalar, Elif Nur Fırat; Nizamoğlu, Sedat; PhD Student; PhD Student; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Department of Electrical and Electronics 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 Sciences; College of Engineering; N/A; N/A; N/A; N/A; 206349; 130295
    A single transverse mode distributed feedback laser is reported where the gain medium is composed enhanced green fluorescent protein in silk fibroin matrix. Moreover, optical feedback is increased with a high refractive index TiO<inf>2</inf> layer.