Article
Chemistry, Multidisciplinary
Vasilii S. Kolmogorov, Alexander S. Erofeev, Emily Woodcock, Yuri M. Efremov, Aleksei P. Iakovlev, Nikita A. Savin, Anna V. Alova, Svetlana V. Lavrushkina, Igor I. Kireev, Alexandra O. Prelovskaya, Elena V. Sviderskaya, Denis Scaini, Natalia L. Klyachko, Peter S. Timashev, Yasufumi Takahashi, Sergey V. Salikhov, Yuri N. Parkhomenko, Alexander G. Majouga, Christopher R. W. Edwards, Pavel Novak, Yuri E. Korchev, Petr V. Gorelkin
Summary: A high-resolution estimation method for mechanical properties and the possibility of qualitative and quantitative analysis of living cells have been demonstrated in this study. Forces applied using a nanopipette are much smaller than those using atomic force microscopy, with no detectable effect on live cells.
Article
Cell Biology
Vasilii Kolmogorov, Alexander Erofeev, Alexander Vaneev, Lyubov Gorbacheva, Dmitry Kolesov, Natalia Klyachko, Yuri Korchev, Petr Gorelkin
Summary: The mechanical properties of neuronal cells are crucial for various processes such as growth, generation of traction forces, adhesion, and migration. Chemical signaling disruption can lead to diseases, and glutamate excitotoxicity can affect the structural reorganization and mechanical properties of neuronal cells. Scanning ion-conductance microscopy (SICM) is a noncontact and low-stress method that can be used to investigate the mechanical properties of living neuronal cells in the presence of glutamate.
Article
Oncology
Ariana Rostami, Scott Bratman, Kathy Han
Summary: Liquid biopsy approaches for detecting viral DNA play a crucial role in diagnosing virally-associated cancers. The CaptHPV method based on next-generation sequencing is discussed for its potential in detecting plasma HPV DNA in HPV-associated cancers and its potential clinical utility.
CLINICAL CANCER RESEARCH
(2021)
Article
Nanoscience & Nanotechnology
Ryo Yoshihara, Shuta Nomi, Kan Shoji
Summary: Scanning ion conductance microscopy (SICM) using biological nanopores is a powerful analytical tool that provides spatially resolved topography and chemical information. This study proposes a method to prepare lipid bilayers using a hydrogel-filled nanopipette, which improves the lifetime of the lipid bilayer and reduces the translocation speed of analytes through nanopores.
ACS APPLIED NANO MATERIALS
(2022)
Article
Infectious Diseases
Yencheng Chao, Jieyi Li, Ziying Gong, Chun Li, Maosong Ye, Qunying Hong, Xiaokai Zhao, Yonghua Sun, Zhonghai Chen, Shaojie Zhang, Jie Hu, Yong Zhang, Huijun Zhang, Xiaobo Xu, Xinyu Zhang, Dilbar Anwar, Yingyong Hou, Daoyun Zhang, Xin Zhang
Summary: This study established an improved NGS strategy for rapidly distinguishing patients with TB from those with SA, with high sensitivity, specificity, and concordance. The NGS method shows potential clinical benefits in the accurate diagnosis of TB and SA.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Medicine, General & Internal
Cienne Morton, Debashis Sarker, Paul Ross
Summary: Cancers contain numerous mutations, but only a few are critical for malignancy. Targeted therapies and immunotherapy have shown great success in various cancer types. Next-generation sequencing enables the detection of potentially actionable mutations and contributes to the identification of new biomarkers. However, technical challenges and the development of targeted therapies against common genomic aberrations need to be overcome for personalized medicine to become more widely available.
Article
Electrochemistry
Edappalil Satheesan Anupriya, Mei Shen
Summary: The interface between two immiscible electrolyte solutions (ITIES) is a powerful platform for chemical sensing and studying electron/ion transfer reactions. By using the silanization method, micro/nano ITIES interfaces can be formed at the tip of a borosilicate/quartz pipette.
JOURNAL OF THE ELECTROCHEMICAL SOCIETY
(2022)
Review
Biochemistry & Molecular Biology
Sushmaa Chandralekha Selvakumar, K. Auxzilia Preethi, Kehinde Ross, Deusdedit Tusubira, Mohd Wajid Ali Khan, Panagal Mani, Tentu Nageswara Rao, Durairaj Sekar
Summary: Personalized or precision medicine combines genetic information with phenotypic and environmental characteristics to tailor healthcare to individuals, enabled by cancer genome sequencing. The advantages of NGS, such as limited sample requirements and the development of biomarkers, have accelerated personalized medicine.
Review
Oncology
Albrecht Stenzinger, Arndt Vogel, Ulrich Lehmann, Angela Lamarca, Paul Hofman, Luigi Terracciano, Nicola Normanno
Summary: Cholangiocarcinomas are a heterogeneous group of tumors with distinct genomic alterations. Next-generation sequencing is a powerful tool for identifying gene variants and guiding personalized treatment for patients with cholangiocarcinomas. Understanding the use of NGS in molecular profiling is crucial for healthcare professionals to optimize treatment outcomes.
CANCER TREATMENT REVIEWS
(2024)
Article
Medicine, General & Internal
Yifan Guo, Henan Li, Hongbin Chen, Zhenzhong Li, Wenchao Ding, Jun Wang, Yuyao Yin, Longyang Jin, Shijun Sun, Chendi Jing, Hui Wang
Summary: The study established a pipeline for simultaneous detection of pathogens and cancer using Illumina sequencing of lung biopsy tissue, achieving high sensitivity and specificity in infection and cancer diagnosis. The Nanopore platform showed lower sensitivity in pathogen detection compared to Illumina.
Article
Microbiology
Martin Hoenigl, Matthias Egger, Jessica Price, Robert Krause, Juergen Prattes, P. Lewis White
Summary: Timely diagnosis remains an unmet need in non-neutropenic patients at risk for aspergillosis, including those with COVID-19-associated pulmonary aspergillosis (CAPA). Currently available mycological tests show limited sensitivity when testing blood specimens. Metagenomic next-generation sequencing (mNGS) to detect microbial cell-free DNA (mcfDNA) in plasma might overcome some of the limitations of conventional diagnostics.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Review
Oncology
Paul Hofman
Summary: Liquid biopsy (LB) has become the only option to detect molecular targets for first-line treatment in treatment-naive NSCLC patients. Despite not being commonly used in diagnosis currently, Next-Generation Sequencing (NGS) shows the most promise for assessing genetic abnormalities.
Article
Engineering, Biomedical
Yuji Nashimoto, Minori Abe, Ryota Fujii, Noriko Taira, Hiroki Ida, Yasufumi Takahashi, Kosuke Ino, Javier Ramon-Azcon, Hitoshi Shiku
Summary: This study evaluates the role of scanning probe microscopy (SPM) as an analytical tool for microphysiological systems (MPS), providing a new solution for real-time high spatial resolution imaging. A simple vascular model was used for permeability and topographical analysis, paving the way for the application of SPM technology in MPS.
ADVANCED HEALTHCARE MATERIALS
(2021)
Article
Biology
Yumi Yoshii, Shunsuke Okazaki, Masayuki Takeda
Summary: Next-generation sequencing-based comprehensive genome profiling (CGP) testing has been covered by the Japanese national health insurance system, but faces limitations such as deteriorating patient condition during analysis and a limited number of ongoing clinical trials. Despite approval of tumor-agnostic therapies in Japan, performing CGP using DNA derived from tumor tissue poses challenges in cases with insufficient tissue.
Article
Oncology
Masato Kojima, Takanori Harada, Takahiro Fukazawa, Sho Kurihara, Ryo Touge, Isamu Saeki, Shinya Takahashi, Eiso Hiyama
Summary: In this study, single-cell next-generation sequencing of circulating tumor cells (CTCs) from neuroblastoma (NB) patients was performed. The findings showed that the isolation rate of CTCs was associated with disease progression, and single-cell RNA sequencing revealed upregulated genes related to angiogenesis and cell cycle in CTCs. These results indicate the utility of single-cell CTC sequencing in characterizing NB tumor biology and metastasis mechanisms.
Article
Microbiology
Jenny L. Draper, Lori M. Hansen, David L. Bernick, Samar Abedrabbo, Jason G. Underwood, Nguyet Kong, Bihua C. Huang, Allison M. Weis, Bart C. Weimer, Arnoud H. M. van Vliet, Nader Pourmand, Jay V. Solnick, Kevin Karplus, Karen M. Ottemannc
Article
Biochemistry & Molecular Biology
Eszter N. Toth, Akshar Lohith, Manas Mondal, Jia Guo, Akiyoshi Fukamizu, Nader Pourmand
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Chemistry, Multidisciplinary
Rifat Emrah Ozel, Gonca Bulbul, Joanna Perez, Nader Pourmand
Review
Cell Biology
Gonca Bulbul, Gepoliano Chaves, Joseph Olivier, Rifat Emrah Ozel, Nader Pourmand
Article
Multidisciplinary Sciences
Shahid Y. Khan, Muhammad Ali, Firoz Kabir, Ruiqiang Chen, Chan Hyun Na, Mei-Chong W. Lee, Nader Pourmand, Sean F. Hackett, S. Amer Riazuddin
SCIENTIFIC REPORTS
(2018)
Article
Biochemistry & Molecular Biology
Gonca Bulbul, Goksin Liu, Namrata Rao Vithalapur, Canan Atilgan, Zehra Sayers, Nader Pourmand
ACS CHEMICAL NEUROSCIENCE
(2019)
Correction
Microbiology
Magdalena Franco, Michael W. Panas, Nicole D. Marino, Mei-Chong Wendy Lee, Kerry R. Buchholz, Felice D. Kelly, Jeffrey J. Bednarski, Barry P. Sleckman, Nader Pourmand, John C. Boothroyd
Article
Biochemistry & Molecular Biology
Marc Tollis, Jooke Robbins, Andrew E. Webb, Lukas F. K. Kuderna, Aleah F. Caulin, Jacinda D. Garcia, Martine Berube, Nader Pourmand, Tomas Marques-Bonet, Mary J. O'Connell, Per J. Palsboll, Carlo C. Maley
MOLECULAR BIOLOGY AND EVOLUTION
(2019)
Article
Cell Biology
Gepoliano Chaves, John Stanley, Nader Pourmand
Article
Nanoscience & Nanotechnology
John Stanley, Nader Pourmand
Article
Biochemistry & Molecular Biology
Tannia A. Lau, Elmar Mair, Beverley M. Rabbitts, Akshar Lohith, R. Scott Lokey
Summary: In this study, a high-content image-based screen was developed to identify novel anti-inflammatory lead compounds. The screen utilized lipopolysaccharide (LPS) and murine macrophages, and screened a library of bioactive compounds to block the LPS-induced phenotype in macrophages. A deep neural network classifier was trained and optimized using fluorescence microscopy images to distinguish between unstimulated and LPS-stimulated macrophages. The hits from the deep learning classifier were validated using a linear classifier and investigated in a multiplexed cytokine secretion assay. The study identified compounds that modulate the innate immune response to LPS, including allosteric inhibitors of mitogen-activated protein kinase kinase (MEK1/2).
Article
Multidisciplinary Sciences
Gepoliano Chaves, Rifat Emrah Ozel, Namrata Rao, Hana Hadiprodjo, Yvonne Da Costa, Zachary Tokuno, Nader Pourmand
Article
Infectious Diseases
James Heng Chiak Sim, Cynthia Truong, Samuel S. Minot, Nick Greenfield, Indre Budvytiene, Akshar Lohith, Victoria Anikst, Nader Pourmand, Niaz Banaei
DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE
(2017)