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Phage Display–Selected Peptides: Research and Clinical Applications in Cancer Imaging

Journal of Peptide Science 2025年第7期31卷 e70034页

作者： Cimen, Atike Nur Porsuk, Melis Hazal Kutlu, Ozlem Cetinel, Sibel Sabanci University Nanotechnology Research and Application Center (SUNUM) Istanbul Turkey Molecular Biology Genetics and Bioengineering Program Faculty of Engineering and Natural Sciences Sabanci University Istanbul Turkey

Phage display has emerged as a groundbreaking technique for discovering novel biomolecules with significant applications in cancer diagnosis and therapy. This technique employs genetically engineered bacteriophages to display diverse libraries of peptides on their coat proteins, enabling the identification of candidates through a biopanning process targeting specific cancer markers. Biomolecules identified via phage display are widely used as molecular tools, often labeled with imaging agents or conjugated to nanoparticles for noninvasive tumor imaging. This review provides a comprehensive overview of recent advancements in phage display applications in cancer research over the past 5 years and prominent examples of clinical studies. The analysis underscores the potential of phage display to deliver diagnostic and therapeutic biomolecules, highlighting its promise for future clinical implementation in cancer imaging. © 2025 European Peptide Society and John Wiley & Sons Ltd.

关键词： cancer imaging peptide phage display

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TEM at Millikelvin Temperatures: Observing and Utilizing Superconducting Qubits

arXiv

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arXiv 2022年

作者： Okamoto, Hiroshi Firouzmandi, Reza Miyamura, Ryosuke Sazgari, Vahid Okumura, Shun Uchita, Shota Kaya, Ismet I. Department of Intelligent Mechatronics Akita Prefectural University 84-4 Aza Ebinokuchi Tsuchiya Akita Yurihonjo015-0055 Japan Faculty of Engineering and Natural Sciences Sabancı University Orhanli-Tuzla Istanbul34956 Turkey SUNUM Nanotechnology Research and Application Center Sabanci University Istanbul34956 Turkey

We present a case for developing a millikelvin-temperature transmission electron microscope (TEM). We start by reviewing known reasons for such development, then present new possibilities that have been opened up by recent progress in superconducting quantum circuitry, and finally report on our ongoing experimental effort. Specifically, we first review possibilities to observe a quantum mechanically superposed electromagnetic field around a superconducting qubit. This is followed by a new idea on TEM observation of microwave photons in an unusual quantum state in a resonator. We then proceed to review potential applications of these phenomena, which include low dose electron microscopy beyond the standard quantum limit. Finally, anticipated engineering challenges, as well as the authors' current ongoing experimental effort towards building a millikelvin TEM are described. In addition, we provide a brief introduction to superconducting circuitry in the Appendix for the interested reader who is not familiar with the subject. Copyright © 2022, The Authors. All rights reserved.

关键词： Quantum entanglement

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Numerical study of cavitating flow in orifices and its effect on spray characteristics

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Journal of Hydrodynamics 2018年第5期30卷 908-919页

作者： Morteza Ghorbani Mechatronics Engineering Program Faculty of Engineering and Natural Science Sabanci University Department of Biomedical Engineering and Health Systems KTH Royal Institute of Technology

The bubbly flow regime inside orifices has significant effects on several applications, and studying its trend along an orifice could be helpful in identifying the flow mechanism in various situations. The flow regime inside an orifice depends on the situation which has been specified for the orifice. Orifice geometry has a considerable effect on bubbly flow in injectors. Meanwhile, spray characteristics are influenced by the fuel flow inside an orifice, which has strong effects on the mixture of fuel-air. In this study, spray characteristics are studied for different values of the orifice angle. The cavitation phenomenon which occurs inside an orifice varies in intensity and patterns at different angles of the orifice and consequently has diverse effects on spray characteristics. The governing equations are solved by the SIMPLE algorithm. The spray flow is modeled by the discrete droplet method（DDM）, the droplet breakup is modeled by the WAVE model, and the primary breakup is modeled by the DIESEL BREAK UP model. In order to generate cavitation phenomenon inside orifices and investigate its effect on spray characteristics, the angle of orifice with respect to the injector body is varied and the problem is studied for different angles of orifice.

关键词： Cavitation iinjector angle microchannel spray

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One City, Two Tales: Using Mobility Networks to Understand Neighborhood Resilience and Fragility during the COVID-19 Pandemic

arXiv

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arXiv 2022年

作者： Boz, Hasan Alp Bahrami, Mohsen Balcisoy, Selim Bozkaya, Burcin Mazar, Nina Nichols, Aaron Pentland, Alex Sabanci University Faculty of Engineering and Natural Sciences Istanbul34956 Turkey Massachusetts Institute of Technology Institute for Data Systems and Society CambridgeMA02139 United States New College of Florida The Graduate Program in Applied Data Science 5800 Bay Shore Rd SarasotaFL34243 United States Boston University Questrom School of Business BostonMA02215 United States

What predicts a neighborhood’s resilience and adaptability to essential public health policies and shelter-in-place regulations that prevent the harmful spread of COVID-19? To answer this question, in this paper we present a novel application of human mobility patterns and human behavior in a network setting. We analyze mobility data in New York City over two years, from January 2019 to December 2020, and create weekly mobility networks between Census Block Groups by aggregating Point of Interest level visit patterns. Our results suggest that both the socioeconomic and geographic attributes of neighborhoods significantly predict neighborhood adaptability to the shelter-in-place policies active at that time. That is, our findings and simulation results reveal that in addition to factors such as race, education, and income, geographical attributes such as access to amenities in a neighborhood that satisfy community needs were equally important factors for predicting neighborhood adaptability and the spread of COVID-19. The results of our study provide insights that can enhance urban planning strategies that contribute to pandemic alleviation efforts, which in turn may help urban areas become more resilient to exogenous shocks such as the COVID-19 pandemic. © 2022, CC BY.

关键词： COVID-19

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Small-molecule RNA therapeutics to target prostate cancer

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Cancer Cell 2025年第5期43卷 841-855.e8页

作者： Kuzuoglu-Ozturk, Duygu Nguyen, Hao G. Xue, Lingru Figueredo, Emma Subramanyam, Vishvak Liu, Isabelle Bonitto, Kenya Noronha, Ashish Dabrowska, Adrianna Cowan, Janet E. Oses-Prieto, Juan A. Burlingame, Alma L. Worland, Stephen T. Carroll, Peter R. Ruggero, Davide Department of Urology University of California San Francisco San Francisco CA United States Helen Diller Family Comprehensive Cancer Center University of California San Francisco San Francisco CA United States Faculty of Engineering and Natural Sciences Sabanci University Istanbul Turkey Department of Biochemistry & Biophysics University of California San Francisco San Francisco CA United States Tetrad Graduate Program University of California San Francisco CA United States Department of Pharmaceutical Chemistry University of California San Francisco San Francisco CA United States eFFECTOR Therapeutics San Diego United States Department of Cellular and Molecular Pharmacology University of California San Francisco San Francisco CA United States

Tuning protein expression by targeting RNA structure using small molecules is an unexplored avenue for cancer treatment. To understand whether this vulnerability could be therapeutically targeted in the most lethal form of prostate cancer, castration-resistant prostate cancer (CRPC), we use a clinical small molecule, zotatifin, that targets the RNA helicase and translation factor eukaryotic initiation factor 4A (eIF4A). Zotatifin represses tumorigenesis in patient-derived and xenograft models and prolonged survival in vivo alongside hormone therapy. Genome-wide transcriptome, translatome, and proteomic analysis reveals two important translational targets: androgen receptor (AR), a key oncogene in CRPC, and hypoxia-inducible factor 1A (HIF1A), an essential cancer modulator in hypoxia. We solve the structure of the 5′ UTRs of these oncogenic mRNAs and strikingly observe complex structural remodeling of these select mRNAs by this small molecule. Remarkably, tumors treated with zotatifin become more sensitive to anti-androgen therapy and radiotherapy. Therefore, “translatome therapy” provides additional strategies to treat the deadliest cancers. © 2025 Elsevier Inc.

关键词： 5′ UTR AR combinational therapy eIF4A HIF1A mCRPC prostate cancer RNA structure translational control zotatifin

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Mo-based MXenes: Synthesis, properties, and applications

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Advances in Colloid and Interface Science 2024年 324卷 103077页

作者： Hussain, Iftikhar Amara, Umay Bibi, Faiza Hanan, Abdul Lakhan, Muhammad Nazim Soomro, Irfan Ali Khan, Amjad Shaheen, Irum Sajjad, Uzair Mohana Rani, Gokana Javed, Muhammad Sufyan Khan, Karim Hanif, Muhammad Bilal Assiri, Mohammed A. Sahoo, Sumanta Al Zoubi, Wail Mohapatra, Debananda Zhang, Kaili Department of Mechanical Engineering City University of Hong Kong 83 Tat Chee Avenue Hong Kong Department of Materials Science and Engineering City University of Hong Kong Hong Kong School of Engineering and Technology Sunway University Selangor 47500 Malaysia Applied Chemistry and Environmental Science School of Science STEM College RMIT University MelbourneVIC3000 Australia State Key Laboratory of Chemical Resource Engineering Institute of Computational Chemistry College of Chemistry Beijing University of Chemical Technology Beijing100029 China School of Mechatronics Engineering Korea University of Technology and Education Chungnam Cheonan31253 Korea Republic of Sabanci University SUNUM Nanotechnology Research and Application Center Istanbul Tuzla34956 Turkey Department of Energy and Refrigerating Air-Conditioning Engineering National Taipei University of Technology Taipei10608 Taiwan Department of Materials Science and Engineering National Taiwan University of Science and Technology Keelung Road Taipei10607 Taiwan School of Physical Science and Technology Lanzhou University Lanzhou730000 China School of Electrical Engineering & Intelligentization Dongguan University of Technology Dongguan523808 China Department of Inorganic Chemistry Faculty of Natural Sciences Comenius University Bratislava Bratislava842 15 Slovakia Department of Chemistry Faculty of Science King Khalid University Abha61413 Saudi Arabia School of Chemical Engineering Yeungnam University Gyeongbuk Gyeongsan38541 Korea Republic of Materials Electrochemistry Laboratory School of Materials Science and Engineering Yeungnam University Gyeongsan38541 Korea Republic of Graduate School of Semiconductor Materials and Devices Engineering Ulsan National Institute of Science and Technology 50 UNIST-gil Ulju-gun Ulsan44919 Korea Republic of

Ti-MXene allows a range of possibilities to tune their compositional stoichiometry due to their electronic and electrochemical properties. Other than conventionally explored Ti-MXene, there have been ample opportunities for the non-Ti-based MXenes, especially the emerging Mo-based MXenes. Mo-MXenes are established to be remarkable with optoelectronic and electrochemical properties, tuned energy, catalysis, and sensing applications. In this timely review, we systematically discuss the various organized synthesis procedures, associated experimental tunning parameters, physiochemical properties, structural evaluation, stability challenges, key findings, and a wide range of applications of emerging Mo-MXene over Ti-MXenes. We also critically examined the precise control of Mo-MXenes to cater to advanced applications by comprehensively evaluating the summary of recent studies using artificial intelligence and machine learning tools. The critical future perspectives, significant challenges, and possible outlooks for successfully developing and using Mo-MXenes for various practical applications are highlighted. © 2023

关键词： Electrochemical properties

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Efficiency enhancement in photoelectrochemical water splitting: Defect passivation and boosted charge transfer kinetics of zinc oxide nanostructures via chalcopyrite/chalcogenide mix sensitization

引用

Physical Review Materials 2021年第12期5卷 125403-125403页

作者： Cigdem Tuc Altaf Nazrin Abdullayeva Ozlem Coskun Alihan Kumtepe İpek Deniz Yildirim Emre Erdem Maochang Liu Ali Bozbey Ertan Agar Mehmet Sankir Nurdan Demirci Sankir Micro and Nanotechnology Graduate Program TOBB University of Economics and Technology Sogutozu Caddesi No 43 Sogutozu 06560 Ankara Turkey Faculty of Engineering and Natural Sciences Sabanci University Orhanli Tuzla 34956 Istanbul Turkey International Research Center for Renewable Energy State Key Laboratory of Multiphase Flow in Power Engineering Xi'an Jiaotong University Xi'an Shaanxi 710049 People's Republic of China Department of Electrical and Electronics Engineering TOBB University of Economics and Technology Sogutozu Caddesi No 43 Sogutozu 06560 Ankara Turkey Department of Mechanical Engineering Energy Engineering Graduate Program University of Massachusetts Lowell Lowell Massachusetts 01854 USA Department of Materials Science and Nanotechnology Engineering TOBB University of Economics and Technology Sogutozu Caddesi No 43 Sogutozu 06560 Ankara Turkey

ZnO thin films in nanorod (NR) and nanoflower (NF) morphologies were used as photoelectrode scaffolds for efficient visible-light-driven photoelectrochemical (PEC) water splitting process, where their decoration with copper indium gallium sulfide (CIGS) and indium sulfide (In2S3) layers resulted in significant PEC performance enhancement. ZnO NF/CIGS/In2S3 photoelectrodes exhibited a remarkably high PEC efficiency (∼6.0% applied bias photon-to-current efficiency, 83% incident photon-to-current efficiency) due to the negligible dark current, while ZnO NR/CIGS/In2S3 generated a photocurrent density of ***–2 at 0.4 V (vs Ag/AgCl), being one of the highest performances reported in the literature for copper-based chalcopyrite photoelectrodes so far. The interfacial photoelectrode-electrolyte charge transport dynamics, investigated via intensity-modulated photocurrent spectroscopy, exhibited a sevenfold increase in charge transfer efficiencies with a significant drop in surface recombination kinetics for ZnO NF after CIGS/In2S3 decoration. The obtained results show consistency with numerically modeled electric field distribution profiles and electron paramagnetic resonance results of ZnO NF, rationalizing the enhanced charge transfer rates for decorated samples and confirming the defect passivating nature of CIGS/In2S3.

关键词： Electrochemical properties Photoconductivity

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Highly conductive PDMS/carbon nanotube/graphene nanocomposites and effect of sulfuric acid treatment on conductivity

arXiv

引用

arXiv 2020年

作者： Yetisgin, Abuzer Alp Sakar, Hazal Bermek, Hakan Trabzon, Levent Faculty of Engineering and Natural Sciences Materials Science and Nano-Engineering Program Sabanci University Istanbul34956 Turkey Department of Nanoscience and Nanoengineering Istanbul Technical University Istanbul34469 Turkey Department of Molecular Biology and Genetics Istanbul Technical University Istanbul34469 Turkey Faculty of Mechanical Engineering Istanbul Technical University Istanbul34469 Turkey Nanotechnology Research and Application Center - ITUnano Istanbul Technical University Istanbul Turkey MEMS Research Center Istanbul Technical University Istanbul34469 Turkey

Poly(dimethylsiloxane) (PDMS) is an insulator and it is commonly used in fabrication of micro-structures but there is a need of electrical sonductive pdms. Therefore, this research is mainly focused on producing PDMS nanocomposites with high electrical conductivity. Thus, we produced highly conductive PDMS nanocomposites which were filled with multi-walled carbon nanotubes (MWCNTs) and graphene nanoplatelets (GNPs). Due to the synergistic effect between CNTs and GNPs inside a polymeric matrix, we expected to obtain more conductive nanocomposites than PDMS nanocomposite filled with only CNTs. Additionally, we investigated the effect of sulfuric acid treatment to surface composition and electrical conductivity of prepared PDMS/MWCNT/GNP nanocomposites. Results indicated that electrical conductivity of sulfuric acid-treated samples was significantly higher than untreated samples. The level of conductivity in the range of 270.7 - 1074.9 S/m was obtained, and the higher ones are the samples treated with acid *** Codes 74E30 (Primary) Copyright © 2020, The Authors. All rights reserved.

关键词： Nanocomposites

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Insights into the solution structure of the actin-binding tail domain of metavinculin by small angle X-ray scattering and molecular dynamics simulations

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International journal of biological macromolecules 2025年 144376页

作者： Zeynep Aslıhan Durer Hande İpek İnce Zeynep Şevval Düvenci Emel Timuçin Tobias Gräwert Oya Orun Beki Kan Zehra Sayers School of Medicine Department of Biophysics Acibadem Mehmet Ali Aydinlar University Istanbul Turkey Faculty of Pharmacy Department of Biochemistry Acibadem Mehmet Ali Aydinlar University Istanbul Turkey. Electronic address: zeynep.durer@acibadem.edu.tr. Institute of Health Sciences Department of Biophysics Marmara University Istanbul Turkey. Institute of Health Sciences Department of Biostatistics and Bioinformatics Acibadem Mehmet Ali Aydinlar University Istanbul Turkey. Institute of Health Sciences Department of Biostatistics and Bioinformatics Acibadem Mehmet Ali Aydinlar University Istanbul Turkey School of Medicine Department of Biostatistics and Medical Informatics Acibadem Mehmet Ali Aydinlar University Istanbul Turkey. European Molecular Biology Laboratory - Hamburg Unit Biological Small Angle Scattering Group Hamburg Germany. Institute of Health Sciences Department of Biophysics Marmara University Istanbul Turkey School of Medicine Department of Biophysics Marmara University Istanbul Turkey. School of Medicine Department of Biophysics Acibadem Mehmet Ali Aydinlar University Istanbul Turkey. Faculty of Engineering and Natural Sciences Molecular Biology Genetics and Bioengineering Program Sabanci University İstanbul Turkey.

Vinculin is a ubiquitously expressed focal adhesion protein that plays an important role in cell-matrix and cell-to-cell junctions. Metavinculin, a muscle-specific splice variant of vinculin, contains a 68-amino acid disordered insert region in its actin binding tail domain (MVt). Mutations in this insert are linked to cardiomyopathies. This study investigates the solution structures and structural ensembles of wild-type (WT) and two mutant MVts, ΔLeu954 and R975W, which have been associated with cardiomyopathies, using small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. SAXS analyses revealed subtle differences in the estimated maximum dimensions and corroborated the elongated shape of the MVts. Quantitative comparisons of SAXS profiles indicated similarity between the WT and ΔLeu954, whereas R975W exhibited differences in the small-angle region. MD simulations demonstrated reduced conformational flexibility and greater packing of the insert in WT compared to mutants. Notably, a salt-bridge observed between R975 and D928 in a WT simulation provides a structural basis for the destabilization caused by the R975W mutation. These findings provide insights into the structure and dynamics of WT and mutant MVt, reflecting the promise of SAXS combined with MD simulations to elucidate the structural properties of proteins with structural disorder.

关键词： Metavinculin Molecular dynamics simulations Mutation SAXS Tail domain

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Proteomic Data and Drug Implications for Cerebral Microvascular Endothelial Cells Under Varying Oxygen Levels

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Scientific data 2025年第1期12卷 989页

作者： Sarah Barakat Fan Yang Hayriye Ecem Yelkenci Kıvanç Kök Giovanni E Mann Emrah Eroğlu Regenerative and Restorative Medicine Research Center (REMER) Research Institute for Health Sciences and Technologies (SABITA) Istanbul Medipol University Istanbul 34810 Turkey. sarah.barakat1@medipol.edu.tr. King's British Heart Foundation Centre of Research Excellence School of Cardiovascular and Metabolic Medicine & Sciences Faculty of Life Sciences & Medicine King's College London 150 Stamford Street London SE1 9NH UK. Regenerative and Restorative Medicine Research Center (REMER) Research Institute for Health Sciences and Technologies (SABITA) Istanbul Medipol University Istanbul 34810 Turkey. Regenerative and Restorative Medicine Research Center (REMER) Research Institute for Health Sciences and Technologies (SABITA) Istanbul Medipol University Istanbul 34810 Turkey. guvanch@medipol.edu.tr. Department of Biostatistics and Medical Informatics International School of Medicine Istanbul Medipol University Istanbul 34810 Turkey. guvanch@medipol.edu.tr. Molecular Biology Genetics and Bioengineering Program Faculty of Engineering and Natural Sciences Sabanci University Istanbul 34956 Turkey.

Hyperoxia in standard cell cultures (18 kPa O) imposes cellular oxidative stress, potentially skewing research and drug screening outcomes. Cerebral microvascular endothelial cells (hCMEC/D3) experience no more than 7 kPa O in vivo. In this study, hCMEC/D3 cells were adapted to 5 kPa O for 5 days to optimize an in vitro physiological cell culture model. Using a SYNAPT G2-Si mass spectrometer, we compared the proteomic profiles of cells cultured under 5 kPa versus 18 kPa O. A substantial proteomic shift under hyperoxia highlighted the strong impact of oxygen levels on protein expression. We further investigated the effect of oxygen levels on drug screening using sulforaphane (SFN), an inducer of NRF2-regulated antioxidant defense genes. SFN induced more pronounced changes in proteomic profiles under 18 kPa O compared to 5 kPa, indicating oxygen-dependent cellular drug responses. This dataset offers a valuable resource for analyzing oxygen-sensitive proteomic changes. Comparative studies using different drugs or cell types could further elucidate oxygen-dependent signaling and inform the development of therapies aligned with physiological oxygen levels.

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