Researcher: Karalar, Elif Nur Fırat
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Karalar, Elif Nur Fırat
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Publication Metadata only Cell scientist to watch - Elif Nur Fırat-Karalar(Company Biologists Ltd, 2019) Breuer, Manuel; N/A; Department of Molecular Biology and Genetics; Karalar, Elif Nur Fırat; N/A; Faculty Member; Department of Molecular Biology and Genetics; N/A; College of Sciences; N/A; 206349N/APublication Metadata only 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/AN/APublication Metadata only 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; 130295When 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.Publication Metadata only 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; 206349The 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.Publication Metadata only The ciliopathy gene product Cep290 is required for primary cilium formation and microtubule network organization(Tubitak Scientific & Technical Research Council Turkey, 2018) N/A; Department of Molecular Biology and Genetics; Karalar, Elif Nur Fırat; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 206349The mammalian centrosome/cilium complex is composed of the centrosome, the primary cilium, and the centriolar satellites, which together function in key cellular processes including signaling. Defective assembly, maintenance, and function of the centrosome/ cilium complex cause the human genetic diseases known as ciliopathies, which are characterized by a multitude of developmental syndromes including retinal degeneration and kidney cysts. The molecular mechanisms underlying pathogenesis in ciliopathies remain poorly understood, which requires structural and functional characterization of the mutated ciliopathy proteins at the cellular level. To this end, we elucidated the function and regulation of Cep290, which is the most frequently mutated gene in ciliopathies and importantly its functions remain poorly understood. First, we generated Cep290-null cells using the CRISPR/Cas9 genome editing approach. Using functional assays, we showed that Cep290-null cells do not ciliate and that they have defects in centriolar satellites dynamics and interphase microtubule organization. I he centriolar satellites were tightly clustered around the centrosome in Cep290-null cells, and the interphase microtubule network lost its radial organization. Our results provide phenotypic insight into the disease mechanisms of Cep290 ciliopathy mutations and also the tools for studying genotype/phenotype relationships in ciliopathies.Publication Metadata only 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; 130295We 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.Publication Metadata only Unraveling the mysteries of centriolar satellites: time to rewrite the textbooks about the centrosome/cilium complex(American Society for Cell Biology, 2020) N/A; Department of Molecular Biology and Genetics; Department of Molecular Biology and Genetics; N/A; Odabaşı, Ezgi; Karalar, Elif Nur Fırat; Batman, Umut; Other; Faculty Member; Master Student; Department of Molecular Biology and Genetics; College of Sciences; College of Sciences; Graduate School of Sciences and Engineering; N/A; 206349; N/ACentriolar satellites are membraneless granules that localize and move around centrosomes and cilia. Once referred to as structures with no obvious function, research in the past decade has identified satellites as key regulators of a wide range of cellular and organismal processes. Importantly, these studies have revealed a substantial overlap between functions, proteomes, and disease links of satellites with centrosomes and cilia. Therefore, satellites are now accepted as the “third component” of the vertebrate centrosome/cilium complex, which profoundly changes the way we think about the assembly, maintenance, and remodeling of the complex at the cellular and organismal levels. In this perspective, we first provide an overview of the cellular and structural complexities of centriolar satellites. We then describe the progress in the identification of the satellite interactome, which have paved the way to a molecular understanding of their mechanism of action and assembly mechanisms. After exploring current insights into their functions as recently described by loss-of-function studies and comparative evolutionary approaches, we discuss major unanswered questions regarding their functional and compositional diversity and their functions outside centrosomes and cilia.Publication Metadata only Probing mammalian centrosome structure using BioID proximity-dependent biotinylation(Elsevier, 2015) Stearns, Tim; Department of Molecular Biology and Genetics; Karalar, Elif Nur Fırat; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 206349Understanding the structure and function of the centrosome will require identification of its constituent components and a detailed characterization of the interactions among these components. Here, we describe the application of proximity-dependent biotin identification (BioID) to identify spatial and temporal relationships among centrosome proteins. The BioID method relies on protein fusions to a promiscuous mutant of the Escherichia coli biotin ligase BirA, which biotinylates proteins that are in a similar to 10 nm labeling radius of the enzyme. The biotinylated proteins are captured by affinity and are identified by mass spectrometry. Proteins identified in this way are referred to as "proximity interactors." Application of BioID to a set of centrosome proteins demonstrated the utility of this approach in overcoming inherent limitations in probing centrosome structure. These studies also demonstrated the potential of BioID for building large-scale proximity interaction maps among centrosome proteins. In this chapter, we describe the work flow for identification of proximity interactions of centrosome proteins, including materials and methods for the generation and characterization of a BirA*-fusion protein expression plasmid, expression of BirA*-fusion proteins in cells, and purification and identification of proximity partners by mass spectrometry.Publication Metadata only A tour de force of primary cilium biogenesis(Nature Portfolio, 2021) N/A; Department of Molecular Biology and Genetics; Karalar, Elif Nur Fırat; Faculty Member; Department of Molecular Biology and Genetics; College of Sciences; 206349N/APublication Metadata only 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; 206349The 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.