Article
Chemistry, Multidisciplinary
Jinyue Zhang, Yu Wang, Yuqin Wang, Panke Zhang, Hong-Yuan Chen, Shuo Huang
Summary: DNA lesions induced by alkylating agents can be directly distinguished by observing the enzymatic stalling kinetics, which is not interfered with by the sequence context.
Article
Chemistry, Multidisciplinary
Filip Boskovic, Ulrich Felix Keyser
Summary: This study presents a three-dimensional molecular construct that allows the identification of RNA transcript isoforms at the single-molecule level using solid-state nanopore microscopy. The newly designed RNA identifiers, which carry a unique sequence of structural colors, enable the simultaneous identification and relative quantification of multiple RNA targets without the need for amplification.
Article
Chemistry, Physical
Angel Diaz Carral, Magnus Ostertag, Maria Fyta
Summary: In this study, machine learning models were trained on experimental data to improve the accuracy of DNA nucleotide sequencing. By reducing the data dimensionality and utilizing deep neural networks, a novel method was proposed to enhance the read-out efficiency, reaching high accuracy levels.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemical Research Methods
Chih-Hsin Shih, Chao-Hui Ke, Chih-Chien Hsiao
Summary: A reversed-phase chromatographic process on a centrifugal platform is developed for separating and collecting water-soluble dyes. A separation column with C18-reversed phase silica gel is used to separate the components, and the eluate is collected by a series of collecting chambers. The purified components can be identified and extracted from the collecting chambers.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Chemistry, Multidisciplinary
Arthur Rand, Philip Zimny, Roland Nagel, Chaitra Telang, Justin Mollison, Aaron Bruns, Emily Leff, Walter W. Reisner, William B. Dunbar
Summary: In this study, an electronic mapping of a bacterial genome using solid-state nanopore technology was presented. The method involves a dual-nano-pore architecture and active control logic to produce single-molecule data and estimate distances between physical tags on double-stranded DNA. Custom analysis methods were developed to generate consensus alignments from multiple scans, and this approach was applied to map the E. coli chromosome. The results showed a significant increase in alignment length with the recapture method, and the intertag resolution was determined to be around 150-166 bp.
Review
Chemistry, Multidisciplinary
Jasper P. Fried, Jacob L. Swett, Binoy Paulose Nadappuram, Jan A. Mol, Joshua B. Edel, Aleksandar P. Ivanov, James R. Yates
Summary: Solid-state nanopore fabrication techniques have advanced significantly, allowing for the rapid and simple creation of nanopores with diameters down to a few nanometres in electrolyte environments, enabling applications in DNA sequencing, protein analysis, and more.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Chemistry, Multidisciplinary
Xiaoyi Wang, Tina-Marie Thomas, Ren Ren, Yu Zhou, Peng Zhang, Jingjing Li, Shenglin Cai, Kai Liu, Aleksandar P. Ivanov, Andreas Herrmann, Joshua B. Edel
Summary: The analysis of proteins and their interactions at the single-molecule level has important implications for understanding biological processes and diseases, especially for proteins found in low copy numbers in biological samples. Nanopore sensing is a label-free detection technique that is well-suited for applications such as studying protein-protein interactions, biomarker screening, drug discovery, and protein sequencing. However, current limitations in protein nanopore sensing pose challenges in controlling protein translocation and relating protein structures and functions to nanopore readouts.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biophysics
Izadora Mayumi Fujinami Tanimoto, Benjamin Cressiot, Nathalie Jarroux, Jean Roman, Gilles Patriarche, Bruno Le Pioufle, Juan Pelta, Laurent Bacri
Summary: Solid-state nanopores provide a powerful tool for single-molecule analysis of nanoparticles and biomolecules. Surface modification with polymers enhances stability and ionic conduction, allowing for control over nanopore diameter and specific interactions with proteins. Factors such as ionic strength and pH are investigated for their effects on the system, improving control over electroosmotic driving force and dynamics.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Biochemical Research Methods
Mitsuki Miyagi, Sotaro Takiguchi, Kazuaki Hakamada, Masafumi Yohda, Ryuji Kawano
Summary: The EXP2 nanopore has been shown to detect poly-L-lysine with single-molecule sensitivity and sufficient resolution to differentiate between two individual PLLs of different molecular weights. Exploring biological nanopores suitable for peptide sensing is key to achieving amino acid sequence determination.
Article
Multidisciplinary Sciences
Zaka Wing-Sze Yuen, Akanksha Srivastava, Runa Daniel, Dennis McNevin, Cameron Jack, Eduardo Eyras
Summary: The study evaluated the performance of multiple tools in detecting CpG methylation from Nanopore sequencing, revealing a tradeoff between false positives and false negatives. The authors proposed a consensus approach, METEORE, to improve prediction accuracy, and provided Snakemake pipelines for reproducibility.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Shuanghong Yan, Liying Wang, Xiaoyu Du, Shanyu Zhang, Sha Wang, Jiao Cao, Jinyue Zhang, Wendong Jia, Yuqin Wang, Panke Zhang, Hong-Yuan Chen, Shuo Huang
Summary: This study has developed an efficient and cost-effective protocol for preparing a variety of MspA mutants for nanopore insertion, sequencing, and other operations, reducing the costs and time associated with human operations.
Article
Multidisciplinary Sciences
Hongxu Ding, Ioannis Anastopoulos, Andrew D. Bailey, Joshua Stuart, Benedict Paten
Summary: This study introduces a deep learning framework that can predict the characteristic ionic currents of nucleotides to enable novel detection of nucleotide modifications, particularly methylated cytosine and guanine, without the need for controls.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Xiaoyu Guan, Zhongnian Li, Yueying Zhou, Wei Shao, Daoqiang Zhang
Summary: Nanopore sequencing, as a high-throughput sequencing technology for DNA, RNA, and proteins, faces the challenge of high labeling costs for the enormous generated data. This study introduces active learning to select samples that need to be labeled, reducing the labeling costs significantly. Experimental results demonstrate that active learning can greatly reduce the labeling amount while achieving the best baseline performance for nanopore data analysis.
Review
Genetics & Heredity
Laura K. White, Jay R. Hesselberth
Summary: This review provides an introduction to nanopore sequencing and its use in direct detection of nucleic acid modifications. Nanopore sequencing, as a third generation sequencing technology, offers advantages in high throughput and direct detection of nucleic acid modifications. Numerous endogenous and synthetic nucleic acid modifications have been studied using nanopore sequencing. Advances in sequencing chemistry and analysis methods are expected to improve the identification and quantification of these epigenetic marks.
FRONTIERS IN GENETICS
(2022)
Article
Physics, Multidisciplinary
Kaikai Chen, Ining Jou, Niklas Ermann, Murugappan Muthukumar, Ulrich F. Keyser, Nicholas A. W. Bell
Summary: Studying polymer translocation through synthetic nanopores reveals a two-stage behavior, where the translocation initially slows before accelerating close to the end of the process, with distinct local velocity correlations observed as the DNA polymer chain passes through the nanopore. Brownian dynamics simulations show that this behavior is associated with tension propagation, providing a non-equilibrium description of the process.
Article
Chemistry, Multidisciplinary
Zeinab Y. Al Subeh, Dakota B. Poschel, Priscilla S. Redd, John D. Klement, Alyssa D. Merting, Dafeng Yang, Megh Mehta, Huidong Shi, Yolonda L. Colson, Nicholas H. Oberlies, Cedric J. Pearce, Aaron H. Colby, Mark W. Grinstaff, Kebin Liu
Summary: Fas ligand (FasL) expressed on activated cytotoxic T lymphocytes (CTLs) binds to the cell surface receptor Fas, initiating a variety of signaling pathways and resulting in anti-tumor effects. Research has shown that Fas is crucial for the efficacy of CAR-T cell immunotherapy. Restoring Fas expression in tumor cells can overcome resistance to T cell cytotoxicity in human melanoma.
Article
Anatomy & Morphology
Deva D. Chan, Maleeha Mashiatulla, Jun Li, Ryan D. Ross, Meghana Pendyala, Amit Patwa, Mark W. Grinstaff, Anna Plaas, D. Rick Sumner
Summary: This study uses contrast-enhanced micro-computed tomography to track the spatiotemporal patterns of cartilage and bone degeneration in a mouse model of osteoarthritis. The findings provide important insights for the development of targeted therapies for osteoarthritis.
ANATOMICAL RECORD-ADVANCES IN INTEGRATIVE ANATOMY AND EVOLUTIONARY BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Aaron H. Colby, Jack Kirsch, Amit N. Patwa, Rong Liu, Beth Hollister, William McCulloch, Joanna E. Burdette, Cedric J. Pearce, Nicholas H. Oberliels, Yolonda L. Colson, Kebin Liu, Mark W. Grinstaff
Summary: The distribution of fluorescently labeled expansile nanoparticles (eNPs) in vivo is crucial for the success of nanoparticle-based drug delivery systems. Quantitative evaluation of eNPs' biodistribution in a murine model of intraperitoneal mesothelioma was conducted using synthesized 14C-labeled eNPs and liquid scintillation counting. The results showed a strong tumor specificity of eNPs, with an overall delivery efficiency of 30% to the tumor tissue, which is higher than other nanoparticle delivery systems. Administration routes had a significant impact on eNPs' targeting strategy, with intraperitoneal administration leading to tumor accumulation while intravenous administration resulted in rapid clearance and low tumor accumulation. These findings lay the foundation for targeting intraperitoneal tumors and exploring alternative delivery routes for nanoparticle therapies.
Article
Cardiac & Cardiovascular Systems
Lillian L. Tsai, Danielle M. Fitzgerald, Rong Liu, Jenny T. Korunes-Miller, Eliza Neal, Yin P. Hung, Samantha Bilton, Aaron Hata, Mark W. Grinstaff, Yolonda L. Colson
Summary: A PDX surgical resection model of non-small cell lung cancer was established in mice, and it was found that intraoperative placement of drug-loaded meshes significantly improved local disease treatment, suggesting a potential improvement in recurrence-free survival for early-stage non-small cell lung cancer patients.
ANNALS OF THORACIC SURGERY
(2023)
Article
Materials Science, Biomaterials
Ismail Altinbasak, Salli Kocak, Aaron H. Colby, Yasin Alp, Rana Sanyal, Mark W. Grinstaff, Amitav Sanyal
Summary: Electrospun nanofibers have numerous advantages as a scaffold for drug delivery devices. A new pH-responsive nanofiber buttress was synthesized via electrospinning. The buttress transforms from a hydrophobic to a hydrophilic state under relevant pH conditions and releases the encapsulated drug. It shows controlled drug release and cytotoxicity to cancer cells.
BIOMATERIALS SCIENCE
(2023)
Article
Nanoscience & Nanotechnology
Danielle M. Fitzgerald, Yolonda L. Colson, Mark W. Grinstaff
Summary: Pressure-sensitive adhesives, commonly found in households, have various applications in everyday life. With advancements in material and polymer science, these adhesives are transitioning from commodity to specialty materials, leading to new clinical uses and improved patient care.
NATURE REVIEWS MATERIALS
(2023)
Article
Multidisciplinary Sciences
Jialiu Zeng, Rebeca Acin-Perez, Essam A. Assali, Andrew Martin, Alexandra J. Brownstein, Anton Petcherski, Lucia Fernandez-del-Rio, Ruiqing Xiao, Chih Hung Lo, Michael Shum, Marc Liesa, Xue Han, Orian S. Shirihai, Mark W. Grinstaff
Summary: Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide. This study synthesizes acid-activated acidifying nanoparticles to restore lysosomal function and reverse fasting hyperglycemia and hepatic steatosis in NAFLD. In high fat diet mouse models, treatment with these nanoparticles restores autophagy and mitochondrial function to lean, healthy levels, showing the potential therapeutic use for NAFLD.
NATURE COMMUNICATIONS
(2023)
Review
Polymer Science
Xingyu Hu, Mark W. Grinstaff
Summary: Millions of individuals undergo gastrointestinal (GI) tract surgeries each year, which often lead to complications such as bleeding, perforation, leakage, and infection. Hydrogel adhesives have shown promise in treating GI tract wounds due to their atraumatic nature, sealing capability, healing properties, and ease of use. However, challenges such as weak underwater adhesive strength and slow gelation need to be addressed. This review summarizes recent advancements in hydrogel adhesives for GI tract wounds, focusing on material designs and compositions to overcome the specific challenges posed by GI injuries.
Article
Biochemistry & Molecular Biology
Chloe Grazon, Elisabeth Garanger, Pierre Lalanne, Emmanuel Ibarboure, James E. Galagan, Mark W. Grinstaff, Sebastien Lecommandoux
Summary: Polymeric micelles based on natural diblocks, such as elastin-like polypeptide (ELP) and oligonucleotide (ON), have advantageous properties in terms of molecular recognition, biocompatibility, and biodegradability. This study reports a straightforward synthesis of ON-b-ELP diblock bioconjugates through copper-catalyzed azide-alkyne cycloaddition. The resulting micelles self-assemble above their critical micelle temperature (CMT) to form stable structures, and they retain their stability and temperature sensitivity when binding with proteins.
Article
Orthopedics
Heta Orava, Petri Paakkari, Jiri Jantti, Miitu K. M. Honkanen, Juuso T. J. Honkanen, Tuomas Viren, Anisha Joenathan, Petri Tanska, Rami K. Korhonen, Mark W. Grinstaff, Juha Toyras, Janne T. A. Makela
Summary: In this study, a triple contrast agent was used to image and segment cadaveric knee joints in CT. The results showed that large BiNPs do not diffuse into cartilage, facilitating straightforward segmentation. The concentration of CA4+ was significantly higher in femoral cartilage than in tibial cartilage, corresponding to the biomechanical differences observed. This suggests that triple contrast agent CT has potential for assessing cartilage morphology and condition in a clinical setting.
JOURNAL OF ORTHOPAEDIC RESEARCH
(2023)
Review
Polymer Science
Danielle M. Fitzgerald, Yolonda L. Colson, Mark W. Grinstaff
Summary: Pressure sensitive adhesives are widely used in everyday products and have the potential for greater use in medicine. The strength of adhesion depends on the chemical and material properties of the adhesive formulation and its interaction with the surface. This review focuses on the structure-property relationships of polymer architecture and pressure sensitive adhesion, specifically in the context of durable, removable, and biocompatible adhesion to wet surfaces like tissue. Challenges in biomedical wound closure are also discussed, along with innovative strategies to address them.
PROGRESS IN POLYMER SCIENCE
(2023)
Article
Polymer Science
Danielle M. M. Fitzgerald, Heng Zhang, Catalina Bordeianu, Yolonda L. L. Colson, Mark W. W. Grinstaff
Summary: This study describes the synthesis of mPEG-b-PGC block copolymers using a cobaltsalen catalyst via the ring-opening polymerization of benzyl glycidyl ether, monomethoxylated polyethylene glycol, and carbon dioxide. The resulting block copolymers exhibit high polymer/cyclic carbonate selectivity (>99%) and random incorporation of oxirane monomers. The diblock mPEG-b-PGC polymer shows promise as a nanocarrier for sustained chemotherapeutic delivery without the need for surfactants.
Review
Oncology
Eric M. Bressler, Sarah Adams, Rong Liu, Yolonda L. Colson, Wilson W. Wong, Mark W. Grinstaff
Summary: The intersection of synthetic biology and biomaterials holds great promise for improving safety and efficacy in novel therapeutics. Recent research has shown that the use of Boolean logic in these fields can lead to the development of new and effective living therapeutics, such as stimuli-responsive drug delivery devices and logic-gated CAR T cells. Collaborations between synthetic biology and biomaterials have resulted in advancements in drug delivery and cell therapy, with potential benefits including enhanced safety and efficacy.
CLINICAL AND TRANSLATIONAL MEDICINE
(2023)
Review
Oncology
Sue Zhang, Kathryn Regan, Julian Najera, Mark W. Grinstaff, Meenal Datta, Hadi T. Nia
Summary: Cancer initiation and progression lead to significant changes in the microenvironment at the interface between healthy and malignant tissue, known as the peritumor. The peritumor is characterized by unique physical and immune attributes, which contribute to tumor progression through interconnected mechanical signaling and immune activity. Understanding and targeting the biomarkers and therapeutic targets in the peritumor is crucial for future cancer research and clinical advancements, particularly in overcoming resistance to immunotherapy.
Review
Chemistry, Multidisciplinary
Maria Varghese, Mark W. Grinstaff
Summary: Ring opening polymerization (ROP) is an efficient method for synthesizing polyamides, with advancements in polymerization techniques and monomer diversity leading to a new era in polyamide chemistry. By controlling the composition and structure, chemists can achieve desired properties and performance. Polyamides synthesized through ROP have various biomedical applications, including as biomaterials and pharmaceuticals.
CHEMICAL SOCIETY REVIEWS
(2022)