Researcher:
Qureshi, Mohammad Haroon

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PhD Student

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Mohammad Haroon

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Qureshi

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Qureshi, Mohammad Haroon

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2015 - 201922020 - 20236

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Now showing 1 - 8 of 8
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    Adaptive tracking algorithm for trajectory analysis of cells and layer-by-layer assessment of motility dynamics
    (Pergamon-Elsevier Science Ltd, 2022) Bayraktar, Halil; N/A; Department of Molecular Biology and Genetics; Qureshi, Mohammad Haroon; PhD Student; Faculty Member; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); N/A; Graduate School of Sciences and Engineering; College of Sciences; N/A; 105301
    Tracking biological objects such as cells or subcellular components imaged with time-lapse microscopy enables us to understand the molecular principles about the dynamics of cell behaviors. However, automatic object detection, segmentation and extracting trajectories remain as a rate-limiting step due to intrinsic challenges of video processing. This paper presents an adaptive tracking algorithm (Adtari) that automatically finds the op-timum search radius and cell linkages to determine trajectories in consecutive frames. A critical assumption in most tracking studies is that displacement remains unchanged throughout the movie and cells in a few frames are usually analyzed to determine its magnitude. Tracking errors and inaccurate association of cells may occur if the user does not correctly evaluate the value or prior knowledge is not present on cell movement. The key novelty of our method is that minimum intercellular distance and maximum displacement of cells between frames are dynamically computed and used to determine the threshold distance. Since the space between cells is highly variable in a given frame, our software recursively alters the magnitude to determine all plausible matches in the trajectory analysis. Our method therefore eliminates a major preprocessing step where a constant distance was used to determine the neighbor cells in tracking methods. Cells having multiple overlaps and splitting events were further evaluated by using the shape attributes including perimeter, area, ellipticity and distance. The features were applied to determine the closest matches by minimizing the difference in their magnitudes. Finally, reporting section of our software were used to generate instant maps by overlaying cell features and trajectories. Adtari was validated by using videos with variable signal-to-noise, contrast ratio and cell density. We compared the adaptive tracking with constant distance and other methods to evaluate performance and its efficiency. Our algorithm yields reduced mismatch ratio, increased ratio of whole cell track, higher frame tracking efficiency and allows layer-by-layer assessment of motility to characterize single-cells. Adaptive tracking provides a reliable, accurate, time efficient and user-friendly open source software that is well suited for analysis of 2D fluorescence microscopy video datasets.
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    Proteomics in cell division
    (Wiley, 2017) N/A; N/A; N/A; N/A; N/A; Department of Molecular Biology and Genetics; Kagiali, Zeynep Cansu Üretmen; Şentürk, Aydanur; Küçük, Nazlı Ezgi Özkan; Qureshi, Mohammad Haroon; PhD Student; PhD Student; Researcher; PhD Student; Faculty Member; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; N/A; 105301
    Cell division requires a coordinated action of the cell cycle machinery, cytoskeletal elements, chromosomes, and membranes. Cell division studies have greatly benefitted from the mass spectrometry (MS)-based proteomic approaches for probing the biochemistry of highly dynamic complexes and their coordination with each other as a cell progresses into division. In this review, the authors first summarize a wide-range of proteomic studies that focus on the identification of sub-cellular components/protein complexes of the cell division machinery including kinetochores, mitotic spindle, midzone, and centrosomes. The authors also highlight MS-based large-scale analyses of the cellular components that are largely understudied during cell division such as the cell surface and lipids. Then, the authors focus on posttranslational modification analyses, especially phosphorylation and the resulting crosstalk with other modifications as a cell undergoes cell division. Combining proteomic approaches that probe the biochemistry of cell division components with functional genomic assays will lead to breakthroughs toward a systems-level understanding of cell division.
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    Refillable anti-icing SBS composite films
    (Elsevier, 2021) N/A; N/A; Department of Chemistry; Department of Chemistry; Department of Chemistry; Department of Chemistry; Ijaz, Aatif; Topçu, Gökhan; Qureshi, Mohammad Haroon; Miko, Annamaria; Demirel, Adem Levent; Researcher; Researcher; PhD Student; Teaching Faculty; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); N/A; College of Sciences; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; N/A; N/A; 163509; 6568
    The lifetime of release-based anti-icing systems can be improved by refilling after the complete release of active agents. A novel swelling mediated consecutive filling of Diatomaceous Earth (DE) loaded Styrene-Butadiene-Styrene (SBS) composite films with PEG for anti-icing applications is reported. The degree of swelling and the diffusion of active agents into the composite was controlled by adjusting the composition of a binary mixture consisting of a non-solvent (acetone) and a good solvent (diethyl ether (DiEt)). Rhodamine 6G was used as a probe to show the extent of diffusion of dissolved molecules into SBS. The reversible loading of PEG-600 as anti-icing agent up to 19% by weight into DE/SBS composites and the complete release in the binary mixture having 30 vol. % DiEt was successfully achieved in consecutive cycles. After the 5th loading cycle, these composite films exhibited similar water contact angles (∼ 64°) and freezing delay times within error bars as those of the 1st loading cycle. At −15 °C, the average freezing delay time of the water droplets on DE/SBS composites filled with PEG in 30 vol. % DiEt was increased by a factor of three to 120 s. The successful refilling of the composites with reversible loading/release cycles and without any deterioration in the anti-icing properties at least up to 5 cycles is a significant contribution to the lifetime of release based functional coatings.
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    Proximal biotinylation-based combinatory approach for isolating integral plasma membrane proteins
    (Amer Chemical Soc, 2020) N/A; Department of Molecular Biology and Genetics; N/A; N/A; N/A; Department of Molecular Biology and Genetics; Akdağ, Mehmet; Yunt, Zeynep Sabahat; Kamacıoğlu, Altuğ; Qureshi, Mohammad Haroon; Akarlar, Büşra; Master Student; Teaching Faculty; Master Student; PhD Student; Other; Faculty Member; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; College of Sciences; N/A; 116178; N/A; N/A; N/A; 105301
    Comprehensive profiling of the cell-surface proteome has been challenging due to the lack of tools for an effective and reproducible way to isolate plasma membrane proteins from mammalian cells. Here we employ a proximity-dependent biotinylation approach to label and isolate plasma membrane proteins without an extra in vitro labeling step, which we call Plasma Membrane-BiolD. The lipid-modified BirA* enzyme (MyrPalm BirA*) was targeted to the inner leaflet of the plasma membrane, where it effectively biotinylated plasma membrane proteins. Biotinylated proteins were then affinity-purified and analyzed by mass spectrometry. Our analysis demonstrates that combining conventional sucrose density gradient centrifugation and Plasma Membrane-BioID is ideal to overcome the inherent limitations of the identification of integral membrane proteins, and it yields highly pure plasma components for downstream proteomic analysis.
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    Quantitative comparison of a human cancer cell surface proteome between interphase and mitosis
    (Wiley, 2015) Toyoda, Yusuke; Renard, Bernhard Y.; Mollaoglu, Gurkan; Poser, Ina; Timm, Wiebke; Hyman, Anthony A.; Mitchison, Timothy J.; Steen, Judith A.; Department of Molecular Biology and Genetics; N/A; N/A; N/A; N/A; Qureshi, Mohammad Haroon; Mollaoğlu, Gürkan; Küçük, Nazlı Ezgi Özkan; Bülbül, Selda; Faculty Member; PhD Student; Master Student; Researcher; Master Student; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; Graduate School of Sciences and Engineering; 105301; N/A; N/A; N/A; N/A
    The cell surface is the cellular compartment responsible for communication with the environment. The interior of mammalian cells undergoes dramatic reorganization when cells enter mitosis. These changes are triggered by activation of the CDK1 kinase and have been studied extensively. In contrast, very little is known of the cell surface changes during cell division. We undertook a quantitative proteomic comparison of cell surface-exposed proteins in human cancer cells that were tightly synchronized in mitosis or interphase. Six hundred and twenty-eight surface and surface-associated proteins in HeLa cells were identified; of these, 27 were significantly enriched at the cell surface in mitosis and 37 in interphase. Using imaging techniques, we confirmed the mitosis-selective cell surface localization of protocadherin PCDH7, a member of a family with anti-adhesive roles in embryos. We show that PCDH7 is required for development of full mitotic rounding pressure at the onset of mitosis. Our analysis provided basic information on how cell cycle progression affects the cell surface. It also provides potential pharmacodynamic biomarkers for anti-mitotic cancer chemotherapy.
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    Biocompatibility and neural stimulation capacity of aluminum antimonide nanocrystals biointerfaces for use in artificial vision
    (Association for Research in Vision and Ophthalmology (ARVO), 2021) N/A; N/A; N/A; N/A; N/A; N/A; N/A; Department of Electrical and Electronics Engineering; N/A; Kesim, Cem; Han, Mertcan; Yıldız, Erdost; Jalali, Houman Bahmani; Qureshi, Mohammad Haroon; Hasanreisoğlu, Murat; Nizamoğlu, Sedat; Şahin, Afsun; Doctor; Master Student; PhD Student; PhD Student; PhD Student; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); N/A; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; School of Medicine; College of Engineering; School of Medicine; Koç University Hospital; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 387367; N/A; N/A; N/A; N/A; 182001; 130295; 71267
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    Cell cycle-dependent palmitoylation of protocadherin 7 by ZDHHC5 promotes successful cytokinesis
    (Company of Biologists Ltd, 2023) N/A; Department of Molecular Biology and Genetics; Department of Physics; N/A; N/A; Kiraz, Alper; Bavili, Nima; Kamacıoğlu, Altuğ; Küçük, Nazlı Ezgi Özkan; Qureshi, Mohammad Haroon; Yapıcı, Gamze Nur; Yiğit, Berfu Nur; Değirmenci, Beste Senem; Faculty Member; Faculty Member; PhD Student; Master Student; Researcher; PhD Student; PhD Student; PhD Student; PhD Student; Department of Molecular Biology and Genetics; Department of Physics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Sciences; College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; N/A; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; 105301; 22542; N/A; N/A; N/A; N/A; N/A; N/A; N/A
    Cell division requires dramatic reorganization of the cell cortex, which is primarily driven by the actomyosin network. We previously reported that protocadherin 7 (PCDH7) gets enriched at the cell surface during mitosis, which is required to build up the full mitotic rounding pressure. Here, we report that PCDH7 interacts with and is palmitoylated by the palmitoyltransferase, ZDHHC5. PCDH7 and ZDHHC5 colocalize at the mitotic cell surface and translocate to the cleavage furrow during cytokinesis. The localization of PCDH7 depends on the palmitoylation activity of ZDHHC5. Silencing PCDH7 increases the percentage of multinucleated cells and the duration of mitosis. Loss of PCDH7 expression correlates with reduced levels of active RhoA and phospho-myosin at the cleavage furrow. This work uncovers a palmitoylation-dependent translocation mechanism for PCDH7, which contributes to the reorganization of the cortical cytoskeleton during cell division.
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    PublicationOpen Access
    Photovoltaic neurointerface based on aluminum antimonide nanocrystals
    (Springer Nature, 2021) Department of Electrical and Electronics Engineering; N/A; Han, Mertcan; Nizamoğlu, Sedat; Jalali, Houman Bahmani; Yıldız, Erdost; Qureshi, Mohammad Haroon; Şahin, Afsun; Master Student; Faculty Member; PhD Student; PhD Student; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Health Sciences; School of Medicine; N/A; 130295; N/A; N/A; N/A; 171267
    Light activated modulation of neural activity is an emerging field for the basic investigation of neural systems and development of new therapeutic methods such as artificial retina. Colloidal inorganic nanocrystals have great potential for neural interfaces due to their adjustable optoelectronic properties via high-level structural, compositional, and size control. However, toxic heavy metal content (e.g., cadmium, mercury), electrochemical coupling to the cells and low photon-to-current efficiency limit their effective use. Here, we introduce the use of aluminum antimonide (AlSb) nanocrystals as the cell interfacing layer for capacitive neural stimulation in the blue spectrum. We demonstrate successful photostimulation of primary hippocampal neurons below ocular safety limits. In addition, our device shows high biocompatibility in vitro and passive accelerated ageing tests indicate a functional lifetime over 3 years showing their feasible use for chronic implants. We demonstrate that nanocrystal biointerfaces hold high promise for future bioelectronics and protheses.