Article
Materials Science, Biomaterials
Zhe Dong, Xizhu Xu, Jing Ni, Yuancheng Li, Kang An, Ling Meng, Han Wu
Summary: A novel aptamer-functionalized cruciate DNA probe has been developed for imaging multiple low-abundance miRNAs in living cells. It offers improved stability, efficient delivery, and amplified signals for sensitive miRNA detection.
JOURNAL OF MATERIALS CHEMISTRY B
(2022)
Article
Chemistry, Multidisciplinary
Hongyu Wu, Chengwen Zhang, Fulin Zhu, Yu Zhu, Xinhui Lu, Ying Wan, Shao Su, Jie Chao, Lianhui Wang, Dan Zhu
Summary: Here, a poly-adenine (polyA)-mediated programmable FRET-nanoflare is presented for ratiometric intracellular ATP imaging with anti-interference capability. The programmable polyA attachment enhances the signal response for ATP, and the FRET-based nanoflare avoids false-positive signals due to probe degradation in complex environments, showing great potential for clinical diagnosis.
CHEMICAL COMMUNICATIONS
(2023)
Article
Medicine, Research & Experimental
Fei Wang, Ling Sum Liu, Pan Li, Hoi Man Leung, Dick Yan Tam, Pik Kwan Lo
Summary: This article presents a TNA-based probe for real-time monitoring of target miRNA levels in cells, highlighting its high specificity, selectivity, and stability.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Article
Engineering, Multidisciplinary
Suresh Neethirajan
Summary: This paper proposes a deep learning-based method for detecting and tracking domesticated chickens in complex backgrounds. The method utilizes multiscale features and Kalman Filter to achieve real-time tracking of multiple chickens in videos, providing accurate counting and trajectory measurements.
Article
Chemistry, Multidisciplinary
Tianwen Li, Liansheng Zhang, Tao Lu, Tongming Zhu, Canbin Feng, Ni Gao, Fei Liu, Jingyu Yu, Kezhu Chen, Junjie Zhong, Qisheng Tang, Quan Zhang, Xiangyang Deng, Junwei Ren, Jun Zeng, Haibo Zhou, Jianhong Zhu
Summary: This study developed an optimized signal peptide and engineered extracellular vesicles for delivering RNA editing tools, and demonstrated their efficacy in inhibiting gene expression and treating acute inflammatory diseases in vitro and in vivo.
Article
Biochemistry & Molecular Biology
So Young Bak, Youngri Jung, Jinho Park, Keewon Sung, Hyeon-Ki Jang, Sangsu Bae, Seong Keun Kim
Summary: This study utilized single-molecule FRET assay to investigate the dynamics of DNA:RNA heteroduplexation for various engineered Cas9 variants, revealing a strong correlation between their conformational structure and nuclease activity. Quantitative analysis showed that these engineered Cas9 variants exhibit a more rapid decrease in cleavage-competent state with increasing base-pair mismatch, leading to enhanced target specificity. The critical specificity enhancement step was found to be activated during DNA:RNA heteroduplexation for some variants, highlighting the importance of conformational dynamics in Cas9 target specificity.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Sushama Telwatte, Holly Anne Martin, Ryan Marczak, Parinaz Fozouni, Albert Vallejo-Gracia, G. Renuka Kumar, Victoria Murray, Sulggi Lee, Melanie Ott, Joseph K. Wong, Steven A. Yukl
Summary: This study describes a novel panel of reverse transcription droplet digital PCR assays that can specifically quantify multiple different subgenomic SARS-CoV-2 transcripts and distinguish them from non-discontinuous transcripts. These assays can be applied to samples from infected patients to better understand the regulation of SARS-CoV-2 transcription and the contribution of different sgRNAs to viral pathogenesis and clinical disease severity.
Article
Biochemistry & Molecular Biology
Yavuz Burak Goc, Jakub Poziemski, Weronika Smolinska, Dominik Suwala, Grzegorz Wieczorek, Dorota Niedzialek
Summary: The aim of this study was to investigate the influence of different single-stranded segments on the stability of RNA G-quadruplexes. Using a software program called NAB-GQ-builder, researchers constructed various two-tetrad G-quadruplex topologies and performed molecular dynamics simulations to study their sequence-morphology-stability relationships. The results offer insights for designing G-quadruplexes with balanced structures and programmable physicochemical properties for biomaterial applications. Additionally, the study examined the drug-targeting potential of single-stranded segments in oncogene promoter G-quadruplexes for future therapeutic strategies. The study also proposed a sequential folding mechanism for G-quadruplex folding based on a thorough quantum mechanical analysis of guanine assemblies triggered by cation coordination.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Andrea Hita, Gilles Brocart, Ana Fernandez, Marc Rehmsmeier, Anna Alemany, Sol Schvartzman
Summary: This paper presents MGcount, a total-RNA-seq quantification tool that addresses the challenges of overlapping transcripts with different lengths and multiple alignments. MGcount is capable of estimating the concentration of various transcript types, including protein-coding, long non-coding, and small non-coding transcripts.
BMC BIOINFORMATICS
(2022)
Article
Environmental Sciences
Nihao Li, Huie Jiang, Lijuan Chen, Zhijian Li, Qingxin Han, Lulu Ning, Zhenjuan Chen, Suqiu Zhao, Xinhua Liu
Summary: In this study, a manufacturing strategy was proposed to convert commonly-used paper into a nano-engineered fluorescent platform. It was integrated with an on-demand self-assembled colorimetric and ratiometric fluorescence sensor for rapid and quantitative detection of ClO- using smartphones. The platform exhibited high selectivity and sensitivity with a low detection limit of 92.6 nM.
Article
Multidisciplinary Sciences
Virginia L. Pimmett, Matthieu Dejean, Carola Fernandez, Antonio Trullo, Edouard Bertrand, Ovidiu Radulescu, Mounia Lagha
Summary: TATA-containing and INR-containing promoters exhibit distinct dynamics in early Drosophila development, requiring one or two separate rate-limiting steps respectively, with TATA-driven promoters requiring more steps. Core promoter elements play an important role in regulating the rate limiting steps of transcription.
NATURE COMMUNICATIONS
(2021)
Article
Materials Science, Biomaterials
Yiting Ze, Ruixin Wang, Hanzhi Deng, Zheqing Zhou, Xiaoju Chen, Linyang Huang, Yang Yao
Summary: Engineered living materials (ELMs) combine principles from synthetic biology and materials science to create multi-scale bulk materials with self-healing and organism adaptability properties. Among various manufacturing methods, 3D bioprinting stands out for its precise control over structure and cell distribution. This review summarizes the progress, cell and material selection, applications, advantages, and limitations of 3D bioprinting for ELMs manufacturing.
BIOMATERIALS ADVANCES
(2022)
Article
Construction & Building Technology
Riccardo Naccarelli, Sara Casaccia, Michela Pirozzi, Gian Marco Revel
Summary: This paper describes a methodology to optimize the home sensor network for measuring the Activities of Daily Living of older people using Machine Learning applied to synthetic data generated via a simulation tool. The authors tested four ML classifiers and conducted optimization analysis to determine the most suitable sensor network configuration.
Article
Engineering, Chemical
Fengpei Qi, Xiuxiu Yue, Yitong Yang, Qin Liang, Ruiren Tang, Xiangzhi Song
Summary: A ratiometric fluorescent probe HBTC-S was developed for rapid, selective, and quantitative profiling of SO32-. The probe exhibited high sensitivity, excellent selectivity, and a low detection limit for SO32-. It was successfully applied for qualitative and quantitative monitoring of SO32- in realistic samples and living cells.
GREEN CHEMICAL ENGINEERING
(2023)
Article
Biology
Amanda N. Henning, Daniel Green, Ryan Baumann, Patrick Grandinetti, Steven L. Highfill, Huizhi Zhou, Valeria De Giorgi
Summary: The study found that RNA quality and RNA-sequencing output were comparable among donor-matched PBMC, whole blood, and B cells following negative selection by immunomagnetic B cell isolation. Transcriptional analysis enabled the development of an 85 gene B cell signature, which effectively clustered isolated B cells from heterogeneous sample types and naive and memory B cells. Furthermore, identification of B cell signature genes with unknown functional roles has opened up avenues for future investigation.
BMC RESEARCH NOTES
(2021)
Article
Chemistry, Multidisciplinary
Elizabeth M. Higbee-Dempsey, Ahmad Amirshaghaghi, Matthew J. Case, Mathilde Bouche, Johoon Kim, David P. Cormode, Andrew Tsourkas
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Chemistry, Multidisciplinary
Sonia Kartha, Lesan Yan, Meagan E. Ita, Ahmad Amirshaghaghi, Lijun Luo, Yulong Wei, Andrew Tsourkas, Beth A. Winkelstein, Zhiliang Cheng
Article
Multidisciplinary Sciences
Brianna F. Moon, Srikant Kamesh Iyer, Eileen Hwuang, Michael P. Solomon, Anya T. Hall, Rishabh Kumar, Nicholas J. Josselyn, Elizabeth M. Higbee-Dempsey, Andrew Tsourkas, Akito Imai, Keitaro Okamoto, Yoshiaki Saito, James J. Pilla, Joseph H. Gorman, Robert C. Gorman, Cory Tschabrunn, Samuel J. Keeney, Estibaliz Castillero, Giovanni Ferrari, Steffen Jockusch, Felix W. Wehrli, Haochang Shou, Victor A. Ferrari, Yuchi Han, Avanti Gulhane, Harold Litt, William Matthai, Walter R. Witschey
NATURE COMMUNICATIONS
(2020)
Article
Biotechnology & Applied Microbiology
Benjamin L. Emert, Christopher J. Cote, Eduardo A. Torre, Ian P. Dardani, Connie L. Jiang, Naveen Jain, Sydney M. Shaffer, Arjun Raj
Summary: Differences in molecular features among individual cells can lead to dramatic differences in cell fate, such as the survival or death of cancer cells upon drug treatment. The Rewind methodology combines genetic barcoding with RNA fluorescence in situ hybridization to capture rare cells that give rise to cellular behaviors of interest. By applying Rewind to BRAF(V600E) melanoma, researchers traced drug-resistant cell fates back to single-cell gene expression differences in their drug-naive precursors, revealing hidden, rare-cell variability that underlies a range of latent phenotypic outcomes upon drug exposure.
NATURE BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
M. Kyle Cromer, Joab Camarena, Renata M. Martin, Benjamin J. Lesch, Christopher A. Vakulskas, Nicole M. Bode, Gavin Kurgan, Michael A. Collingwood, Garrett R. Rettig, Mark A. Behlke, Viktor T. Lemgart, Yankai Zhang, Ankush Goyal, Feifei Zhao, Ezequiel Ponce, Waracharee Srifa, Rasmus O. Bak, Naoya Uchida, Ravindra Majeti, Vivien A. Sheehan, John F. Tisdale, Daniel P. Dever, Matthew H. Porteus
Summary: The study presents a novel genome editing strategy that can restore the balance of beta-globin:alpha-globin in human hematopoietic stem cells from patients with beta-thalassemia, leading to the functional restoration of adult hemoglobin tetramers in patient-derived red blood cells.
Article
Multidisciplinary Sciences
Yulong Wei, Lesan Yan, Lijun Luo, Tao Gui, Biang Jang, Ahmad Amirshaghaghi, Tianyan You, Andrew Tsourkas, Ling Qin, Zhiliang Cheng
Summary: The study found that the enzyme sPLA(2) increases in OA cartilage tissues, and inhibiting its activity could be an effective treatment strategy. By incorporating an sPLA(2) inhibitor into micelles, it improved drug delivery within the joints and showed promising potential as a therapeutic agent for OA.
Article
Biochemical Research Methods
Wendy Yu, Kevin P. Gillespie, Bonirath Chhay, Anne-Sophie Svensson, Per-Ake Nygren, Ian A. Blair, Feifan Yu, Andrew Tsourkas
Summary: ADCs have great therapeutic potential, but the heterogeneous nature of conventional drug conjugation strategies can impact their safety, efficacy, and stability. Site-specific conjugation methods can address these issues without the need for genetic modification or glycan modification.
BIOCONJUGATE CHEMISTRY
(2021)
Article
Biochemical Research Methods
Linghan Mei, Fabiana Zappala, Andrew Tsourkas
Summary: Bispecific antibodies are capable of binding two antigens simultaneously, leading to unique biological effects. Two methods are introduced for rapid assembly of Bispecific antibodies from any two off-the-shelf IgG antibodies, allowing for low-cost, high-throughput production and validation.
BIOCONJUGATE CHEMISTRY
(2022)
Article
Engineering, Biomedical
Tao Gui, Lijun Luo, Bonirath Chhay, Leilei Zhong, Yulong Wei, Lutian Yao, Wei Yu, Jun Li, Charles L. Nelson, Andrew Tsourkas, Ling Qin, Zhiliang Cheng
Summary: Oxidative stress and reactive oxygen species play important roles in the development and progression of osteoarthritis (OA). This study utilized SOD-loaded nanoparticles to deliver antioxidant enzymes to mouse knee joints, demonstrating the accumulation of nanoparticles in the synovium and reduction of oxidative damage. Intra-articular injections of the nanoparticles were effective in attenuating OA initiation and progression, via reduction of reactive oxygen species production and catabolic protease synthesis.
Article
Medicine, Research & Experimental
Alexander Chan, Hejia Henry Wang, Rebecca M. Haley, Cindy Song, David Gonzalez-Martinez, Lukasz Bugaj, Michael J. Mitchell, Andrew Tsourkas
Summary: This study demonstrates the feasibility of using small protein scaffolds with anionic polypeptides to interact with positively charged nonviral lipid-based delivery systems, enabling efficient intracellular delivery. This method can be used to inhibit intracellular proteins that are currently not amenable to small molecule drugs and biologics.
MOLECULAR PHARMACEUTICS
(2022)
Article
Multidisciplinary Sciences
Fabiana Zappala, Elizabeth Higbee-Dempsey, Bian Jang, Joann Miller, Lesan Yan, Nicholas G. Minutolo, Gabriela T. Rosado Gonzalez, Andrew Tsourkas, Burcin Altun Ozdemir
Summary: Researchers have developed a simple method to attach a T cell-redirecting domain to off-the-shelf human immunoglobulin G (IgG) or native IgG, allowing the generation of T cell-redirecting autoantibodies (TRAAbs) without the need for antibody engineering, cloning, or knowledge of the antibody sequence. These TRAAbs preferentially bind tumor tissue over healthy tissue, indicating a previously unexplored therapeutic window. This approach represents a new paradigm in personalized medicine.
Article
Endocrinology & Metabolism
Tao Gui, Yulong Wei, Lijun Luo, Jun Li, Leilei Zhong, Lutian Yao, Frank Beier, Charles L. Nelson, Andrew Tsourkas, X. Sherry Liu, Motomi Enomoto-Iwamoto, Feifan Yu, Zhiliang Cheng, Ling Qin
Summary: This study demonstrates the importance of EGFR signaling in maintaining articular cartilage during PTOA development and explores the development of novel nanomedicines for PTOA treatment.
JOURNAL OF BONE AND MINERAL RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Karun Kiani, Eric M. Sanford, Yogesh Goyal, Arjun Raj
Summary: A major goal in the field of transcriptional regulation is to understand the relationship between transcription factor binding and gene expression changes. This study used ATAC-seq and RNA-seq measurements to examine the concordance between chromatin accessibility changes and expression changes in response to specific perturbations. The results showed that some genes exhibited changes in both accessibility and expression, while others showed changes in expression without corresponding changes in accessibility. The findings suggest that gene expression changes can occur independently of changes in chromatin accessibility.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Nanoscience & Nanotechnology
Rebecca M. Haley, Alexander Chan, Margaret M. Billingsley, Ningqiang Gong, Marshall S. Padilla, Emily H. Kim, Hejia Wang, Dingzi Yin, Kirk J. Wangensteen, Andrew Tsourkas, Michael J. Mitchell
Summary: This study demonstrates the successful delivery of DARPin protein K27-D30 to the cytosol of liver cancer cells using a lipid nanoparticle platform, inhibiting RAS-driven tumor growth and highlighting the potential of K27 as a new cancer therapeutic.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Nanoscience & Nanotechnology
Ahmad Amirshaghaghi, Wen-Chi Chang, Bonirath Chhay, Ariane R. Bartolomeu, Margie L. Clapper, Zhiliang Cheng, Andrew Tsourkas
Summary: The current standard of care for colon cancer surveillance, white light endoscopy, often misses dysplastic lesions that are not visible to the naked eye. Dye-based chromoendoscopy shows promise but lacks accuracy in differentiating tumor tissues from healthy tissues. This study aimed to improve tumor tissue visualization using various phthalocyanine (PC) dye-loaded micelles administered intravenously. Zinc PC (tetra-tert-butyl)-loaded micelles were identified as the optimal formulation, turning tumors dark blue for easy identification. These micelles were also effective in turning colorectal adenomas in mice a dark blue color, aiding in their detection and removal.
ACS APPLIED MATERIALS & INTERFACES
(2023)