Article
Biochemical Research Methods
Jeffrey D. Palumbo, Teresa L. O'Keeffe
Summary: Our laboratory has developed a high-throughput screening method for antifungal phenotypes, which involves transferring bacterial libraries in 96 well format to agar pour plates inoculated with spores of the target fungus. This method improves upon traditional bacterial/fungal coculture plate methods by measuring antifungal activity as inhibition of radial fungal growth.
JOURNAL OF MICROBIOLOGICAL METHODS
(2021)
Article
Biochemical Research Methods
Rong-Rong Xiao, Bolin Jing, Lei Yan, Jiajia Li, Pengfei Tu, Xiaoni Ai
Summary: In this study, a constant-rate perfused array chip (cPAC) was developed to establish a brain endothelium model for screening drug permeability. The cPAC allowed constant-rate and high-throughput flow, and was compatible with a commercial volt-ohm meter for real-time transendothelial electrical resistance (TEER) measurement. The brain endothelium model on the cPAC exhibited superior performance in barrier function, efflux functionality of the transporters, and reversible osmotic opening of the brain endothelium compared to other models. The permeability of model drugs on the cPAC also correlated well with in vivo results. Additionally, the brain endothelium model was cocultured with 3D tumor cells for simultaneous evaluation of drug permeability and brain tumor therapy, which was consistent with clinical findings.
Article
Biochemical Research Methods
Alexander Sotra, Kimia Asadi Jozani, Boyang Zhang
Summary: In order to study colon diseases and develop treatments, it is necessary to create in vitro models with colon-specific physiological features. We have developed a colon epithelium barrier model with vascularized crypts that can replicate relevant cytokine gradients in both healthy and inflammatory conditions. This model integrates colon cells with a patterned scaffold, allowing colon cells to differentiate into epithelial barriers. By incorporating perfusable microvasculature and simulating inflammatory conditions, in vivo-like cytokine gradients and reversals were observed. This model has significant value for emulating colon physiology and advancing disease modeling.
Review
Biotechnology & Applied Microbiology
Hasan Aldewachi, Radhwan N. Al-Zidan, Matthew T. Conner, Mootaz M. Salman
Summary: Neurodegenerative diseases are incurable conditions that cause progressive degeneration or death of nerve cells. Identifying therapeutic targets and new treatments is a major challenge, and high-throughput screening plays a key role in improving drug discovery efficiency.
BIOENGINEERING-BASEL
(2021)
Article
Chemistry, Medicinal
Alexander Neumann, Isaac Attah, Haneen Al-Hroub, Vigneshwaran Namasivayam, Christa E. Mueller
Summary: The human ATP- and UTP-activated P2Y2 receptor plays a role in various pathological conditions. However, the current P2Y2 receptor antagonists have limitations. In this study, researchers utilized virtual screening and molecular docking to discover novel antagonist scaffolds for the P2Y2 receptor. The identified compounds showed similar binding modes with a known potent orthosteric antagonist. This study provides a basis for the development of future drug candidates for the P2Y2 receptor.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Multidisciplinary Sciences
Min-Zhi Jiang, Hai-Zhen Zhu, Nan Zhou, Chang Liu, Cheng-Ying Jiang, Yulin Wang, Shuang-Jiang Liu
Summary: In this study, droplet microfluidics and bar-coding logistics were integrated to achieve high-throughput bacterial isolation and cultivation from environmental samples. The relationships between taxon pairs inferred from microbial co-occurrence networks were experimentally investigated, revealing complex relations including neutralism, competition, and mutualism.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Matz Liebel, Irene Calderon, Nicolas Pazos-Perez, Niek F. van Hulst, Ramon A. Alvarez-Puebla
Summary: Large-scale SERS particle screening (LSSPS) is a fast multiplexed widefield screening approach that quantifies both Raman and Rayleigh scattering simultaneously, allowing for direct quantification of the fraction of SERS-active particles and unprecedented correlation of SERS activity with particle size.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Cell Biology
Boyang Yu, Boye Li, Tian Chen, Jinning Yang, Xiaoli Wang, Bo Peng, Qin Hu
Summary: This study utilized a NF-kappa B luciferase reporter gene system to perform high-throughput screening, identifying four NF-kappa B agonists that can activate NF-kappa B at non-toxic concentrations. The adjuvant effect of these compounds was confirmed on mouse immune cells. Additionally, three compounds that significantly inhibit NF-kappa B at non-toxic doses, including a known NF-kappa B inhibitor, were identified.
Article
Biotechnology & Applied Microbiology
Matthew Rienzo, Shaina J. Jackson, Lawrence K. Chao, Timothy Leaf, Thomas J. Schmidt, Adam H. Navidi, Dana C. Nadler, Maud Ohler, Michael D. Leavell
Summary: Systems metabolic engineering is a challenging task that involves rewiring microbial metabolism to generate high-value molecules from inexpensive feedstocks. High-throughput screening of engineered organism variants for scalable manufacturing potential is necessary, requiring carefully controlled, parallel fermentations and precise analysis of complex mixtures. Strategies to design high-throughput, small-scale fermentation models for predicting improved strain performance at large commercial scale, including microplate and microfluidics-based screening systems, are essential for success.
METABOLIC ENGINEERING
(2021)
Article
Chemistry, Multidisciplinary
Yu-Ting Liu, Xian-Bin Li, Hui Zheng, Nian-Ke Chen, Xue-Peng Wang, Xu-Lin Zhang, Hong-Bo Sun, Shengbai Zhang
Summary: This study reports the largest scale PCM materials searching, starting with 124,515 candidate materials, and eventually screening 158 potential PCM materials using a rational high-throughput screening strategy. Further analyses revealed 52 materials with properties similar to the GST system, some of which show potential for low power consumption and suitability for optical/electrical PCM applications.
ADVANCED FUNCTIONAL MATERIALS
(2021)
Article
Chemistry, Physical
Matthew Bain, Jose L. Godinez Castellanos, Stephen E. Bradforth
Summary: High-repetition-rate lasers have the potential to revolutionize ultrafast spectroscopy by enabling routine analysis for machine learning models in the design of photochemical syntheses. In this study, we combine innovations in line scan cameras and micro-electro-mechanical grating modulators with high-pressure liquid chromatography pumps to develop a transient absorption spectrometer that can characterize photoreactions in minutes. Additionally, we demonstrate the utility of this technique in exploring the effects of conformational modification on excited-state processes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Vei Wang, Gang Tang, Ya-Chao Liu, Ren-Tao Wang, Hiroshi Mizuseki, Yoshiyuki Kawazoe, Jun Nara, Wen Tong Geng
Summary: Two-dimensional materials have attracted attention for their unique physical properties and their ability to meet the demands of nanoscale devices. In this study, we conducted high-throughput calculations and screening to identify 73 direct-gap and 183 indirect-gap 2D nonmagnetic semiconductors based on criteria for thermodynamic, mechanical, dynamic, and thermal stabilities, as well as conductivity type. A database of these materials was created, providing a platform for computational modeling and design of new 2D semiconductors and heterostructures in applications such as photocatalysis and nanoscale devices. Additionally, a linear fitting model was proposed to accurately evaluate band gap, ionization energy, and electron affinity of 2D semiconductors with lower computational cost compared to hybrid DFT methods.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemical Research Methods
Madeline E. McCarthy, William B. Dodd, Xiaoming Lu, Daniel J. Pritko, Nishi D. Patel, Charlotte V. Haskell, Hugo Sanabria, Mark A. Blenner, Marc R. Birtwistle
Summary: We propose a theory for high-throughput genetic interaction screens, which extends the Multiplexing using Spectral Imaging and Combinatorics (MuSIC) approach to create 100,000 spectrally unique MuSIC barcodes. Experimental testing of this theory could revolutionize genetic perturbation technology and knowledge of genetic function. Additionally, a genome-scale spectral barcode library could have widespread applications in genetic screening and lineage tracing.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Chemistry, Physical
Mads Kruse, Urko Petralanda, Morten N. Gjerding, Karsten W. Jacobsen, Kristian S. Thygesen, Thomas Olsen
Summary: We performed a high throughput computational search in the C2DB and identified 63 ferroelectric materials, including 49 with in-plane polarization, 8 with out-of-plane polarization, and 6 with coupled in-plane and out-of-plane polarization. Most known 2D ferroelectrics were recovered and the predicted ones are accessible by direct exfoliation. About 25% of the materials showed a metastable state in the non-polar structure. We also discussed the case of VAgP2Se6, a magnetic pyroelectric material with switchable polarization coupled to magnetic excitation spectrum.
NPJ COMPUTATIONAL MATERIALS
(2023)
Article
Biotechnology & Applied Microbiology
Marshall S. Ma, Subramanian Sundaram, Lihua Lou, Arvind Agarwal, Christopher S. Chen, Thomas G. Bifano
Summary: Three dimensional engineered cardiac tissues (3D ECTs) are crucial in vitro models for assessing drug cardiotoxicity, but the low throughput of current assays limits their efficiency. To overcome this limitation, an innovative mosaic imaging system was developed to measure contractile force of 3D ECTs seeded on a 96-well plate, increasing throughput to 96 samples per measurement.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Review
Materials Science, Biomaterials
Sung-Min Kang, Ji-Hoon Lee, Yun Suk Huh, Shuichi Takayama
Summary: Advances in microscale 3D cell culture systems using alginate hydrogels have provided insights into cellular physiology, stem cell differentiation mechanisms, and cell-cell interactions. Alginate hydrogels offer a simple gelation process without the need for toxic procedures, making them a versatile option for constructing microphysiological cell culture systems. The physicochemical characteristics of alginate hydrogels can be tailored to enhance biocompatibility, porosity, mechanical strength, ligand presentation, and biodegradability, enabling a wide range of cell culture applications.
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Bijean D. Ford, Diego Moncada Giraldo, Camilla Margaroli, Vincent D. Giacalone, Milton R. Brown, Limin Peng, Rabindra Tirouvanziam
Summary: In cystic fibrosis lung disease, the dysfunction of recruited myeloid cells, particularly neutrophils, has been well-studied. This research shows that while monocytes recruited to CF airways do not undergo metabolic activation or significant phenotypic changes, they do exhibit decreased bactericidal activity and differences in immune signaling gene expression compared to healthy controls. These findings highlight the dysregulated bactericidal activity of monocytes in CF airways and provide insights into the immune responses in the CF microenvironment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cell Biology
Daniel R. Laucirica, Craig J. Schofield, Samantha A. McLean, Camilla Margaroli, Patricia Agudelo-Romero, Stephen M. Stick, Rabindra Tirouvanziam, Anthony Kicic, Luke W. Garratt
Summary: This study investigates the population of neutrophils in cystic fibrosis (CF) airways, which is associated with proteolytic lung damage. The study presents a laboratory model to understand the responses of airway epithelium and neutrophils following respiratory infection. The findings suggest that Pseudomonas aeruginosa is a trigger of acute airway inflammation and neutrophil primary granule exocytosis.
IMMUNOLOGY AND CELL BIOLOGY
(2022)
Article
Thermodynamics
Tasdiq Ahmed, Yan Zhang, Ji-Hoon Lee, Mark P. Styczynski, Shuichi Takayama
Summary: This study presents the phase diagram of a PEG 35k-Ficoll 400k-water ATPS in the presence of necessary protocell components. The results show that a mixture of salts and small organic molecules has profound positive effects on ATPS stability and nucleic acid partitioning, which significantly contribute to protocell function. Several new areas of optimization for future protocell engineering are uncovered.
JOURNAL OF CHEMICAL AND ENGINEERING DATA
(2022)
Article
Pediatrics
Vincent D. Giacalone, Diego Moncada-Giraldo, Camilla Margaroli, Milton R. Brown, George L. Silva, Joshua D. Chandler, Limin Peng, Rabindra Tirouvanziam, Lokesh Guglani
Summary: The study found that induced sputum collected from 2-year-olds with CF yields biomarkers of early airway inflammation with good agreement with bronchoalveolar lavage, notably in relation to molecular and cellular outcomes related to neutrophils and monocytes/macrophages.
PEDIATRIC PULMONOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Aurelie Moniot, Julien Braux, Renaud Siboni, Christine Guillaume, Sandra Audonnet, Ingrid Allart-Simon, Janos Sapi, Rabindra Tirouvanziam, Stephane Gerard, Sophie C. Gangloff, Frederic Velard
Summary: In inflammatory diseases, the excessive activation of polymorphonuclear neutrophils (PMNs) can lead to tissue damage. This study investigated the effects of two novel compounds, 4aa and 4ba, on PMNs activation and found that they can reduce the release of inflammatory cytokines, decrease PMNs phagocytic ability, and limit the recruitment of PMNs in tissues. These findings suggest the therapeutic potential of these compounds in the treatment of inflammatory diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Engineering, Biomedical
Eric Parigoris, Ji-Hoon Lee, Amy Yunfan Liu, Xueying Zhao, Shuichi Takayama
Summary: This study demonstrates the development and maintenance of proximal tubule organoids through cellular self-organization. These organoids exhibit higher maturity markers and functional capabilities compared to traditional 2D cultures.
Review
Medicine, General & Internal
Dhruv Atool Amratia, Hannah Viola, Octavian C. Ioachimescu
Summary: This article presents a comprehensive review of the use of immune-modulating corticosteroids (CSs) in respiratory diseases. Although CSs play a critical role in the management of respiratory illnesses, their benefits depend on the underlying pathology and specific risks for each patient.
JOURNAL OF INVESTIGATIVE MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Midori L. L. Wasielewski, Katherine Nguyen, Srilakshmi Yalavarthi, Pallavi Ekbote, Priyan D. D. Weerappuli, Jason S. S. Knight, Shuichi Takayama
Summary: This study analyzed the degradation of millimeter-scale, circular DNA-histone mesostructures (DHMs) by nucleases and serum. It was found that DHMs had a less accessible chromatin structure compared to neutrophil extracellular traps (NETs), as they were degraded well by DNase I but not by micrococcal nuclease (MNase). Moreover, DHMs were degraded by normal human serum at a slower rate than NETs and showed qualitative differences in the degradation process compared to DNase I. Importantly, DHMs mimicked NETs in terms of their susceptibility to degradation by serum from a lupus patient with high disease activity. These findings have implications for the development and use of DHMs in extracellular chromatin-related pathophysiological and diagnostic studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Letter
Allergy
Jocelyn R. Grunwell, Mallory Tidwell, Sydney Zack, Nadine Najjar, Anne M. Fitzpatrick
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE
(2023)
Article
Chemistry, Physical
Ji-Hoon Lee, Joyce Han-Ching Chiu, Nicholas J. J. Ginga, Tasdiq Ahmed, M. D. Thouless, Yifan Liu, Shuichi Takayama
Summary: This study developed a three-layer tunable nanochannel system that enables non-electrophoretic linearization and immobilization of native chromatin. Through careful selection of self-blinking fluorescent dyes and nanochannel design, they achieved super-resolution imaging of the linearized chromatin using direct stochastic optical reconstruction microscopy (dSTORM). This work opens up a new avenue for collecting long-range and high-resolution epigenetic information as well as genetic information.
NANOSCALE HORIZONS
(2023)
Article
Multidisciplinary Sciences
Chak Ming Leung, Pim de Haan, Kacey Ronaldson-Bouchard, Ge-Ah Kim, Jihoon Ko, Hoon Suk Rho, Zhu Chen, Pamela Habibovic, Noo Li Jeon, Shuichi Takayama, Michael L. Shuler, Gordana Vunjak-Novakovic, Olivier Frey, Elisabeth Verpoorte, Yi-Chin Toh
Summary: This article introduces the basic concepts, applications, and development trends of organ-on-chip (OoC) technology, as well as factors to consider when developing application-specific OoCs.
NATURE REVIEWS METHODS PRIMERS
(2022)
