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arXiv 2020年

作者： Wei, Haixin Qi, Ruxi Wang, Junmei Cieplak, Piotr Duan, Yong Luo, Ray Departments of Molecular Biology and Biochemistry Chemical and Biomolecular Engineering Materials Science and Engineering and Biomedical Engineering Graduate Program in Chemical and Materials Physics University of California Irvine IrvineCA92697 United States Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center School of Pharmacy University of Pittsburgh PittsburghPA15261 United States SBP Medical Discovery Institute 10901 North Torrey Pines Road San diegoCA92037 United States UC Davis Genome Center Department of Biomedical Engineering University of California Davis One Shields Avenue DavisCA95616 United States

Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing polarizable force fields for handling more complicated biomolecular processes. Here we focus on a recently proposed polarizable Gaussian Multipole (pGM) model for biomolecular simulations. A key benefit of pGM is its screening of all short-range electrostatic interactions in a physically consistent manner, which is critical for stable charge-fitting and is needed to reproduce molecular anisotropy. Another advantage of pGM is that each atom’s multipoles are represented by a single Gaussian function or its derivatives, allowing for more efficient electrostatics than other Gaussian-based models. In this study we present an efficient formulation for the pGM model defined with respect to a local frame formed with a set of covalent basis vectors. The covalent basis vectors are chosen to be along each atom’s covalent bonding directions. The new local frame allows molecular flexibility during molecular simulations and facilitates an efficient formulation of analytical electrostatic forces without explicit torque computation. Subsequent numerical tests show that analytical atomic forces agree excellently with numerical finite-difference forces for the tested system. Finally, the new pGM electrostatics algorithm is interfaced with the PME implementation in Amber for molecular simulations under the periodic boundary conditions. To validate the overall pGM/PME electrostatics, we conducted an NVE simulation for a small water box of 512 water molecules. Our results show that, to achieve energy conservation in the polarizable model, it is important to ensure enough accuracy on both PME and induction iteration. It is hoped that the reformulated pGM model will facilitate the development of future force fields based on the pGM electrostatics for applicatio

关键词： Electrostatics

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Intra-condensate demixing of TDP-43 inside stress granules generates pathological aggregates

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Cell 2025年

作者： Yan, Xiao Kuster, David Mohanty, Priyesh Nijssen, Jik Pombo-García, Karina Garcia Morato, Jorge Rizuan, Azamat Franzmann, Titus M. Sergeeva, Aleksandra Ly, Anh M. Liu, Feilin Passos, Patricia M. George, Leah Wang, Szu-Huan Shenoy, Jayakrishna Danielson, Helen L. Ozguney, Busra Honigmann, Alf Ayala, Yuna M. Fawzi, Nicolas L. Dickson, Dennis W. Rossoll, Wilfried Mittal, Jeetain Alberti, Simon Hyman, Anthony A. Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) Saxony Dresden 01307 Germany Biotechnology Center (BIOTEC) Center for Molecular and Cellular Bioengineering Technische Universität Dresden Saxony Dresden 01307 Germany Artie McFerrin Department of Chemical Engineering Texas A&M University College Station 77843 TX United States Edward Doisy Department of Biochemistry and Molecular Biology Saint Louis University St. Louis 63104 MO United States Department of Molecular Biology Cell Biology & Biochemistry Brown University Providence 02912 RI United States Center for Biomedical Engineering Brown University Providence 02912 RI United States Department of Chemistry Texas A&M University College Station 77843 TX United States Interdisciplinary Graduate Program in Genetics and Genomics Texas A&M University College Station 77843 TX United States Department of Neuroscience Mayo Clinic Jacksonville 32224 FL United States

Cytosolic aggregation of the nuclear protein TAR DNA-binding protein 43 (TDP-43) is associated with many neurodegenerative diseases, but the triggers for TDP-43 aggregation are still debated. Here, we demonstrate that TDP-43 aggregation requires a double event. One is up-concentration in stress granules beyond a threshold, and the other is oxidative stress. These two events collectively induce intra-condensate demixing, giving rise to a dynamic TDP-43-enriched phase within stress granules, which subsequently transition into pathological aggregates. Intra-condensate demixing of TDP-43 is observed in iPS-motor neurons, a disease mouse model, and patient samples. Mechanistically, intra-condensate demixing is triggered by local unfolding of the RRM1 domain for intermolecular disulfide bond formation and by increased hydrophobic patch interactions in the C-terminal domain. By engineering TDP-43 variants resistant to intra-condensate demixing, we successfully eliminate pathological TDP-43 aggregates in cells. We suggest that up-concentration inside condensates followed by intra-condensate demixing could be a general pathway for protein aggregation. © 2025 The Author(s)

关键词： ALS biomolecular condensate FTD intra-condensate demixing neurodegenerative diseases oxidative stress phase separation protein aggregation stress granules TDP-43

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Conceptual design of antifungal and antibacterial herbal ear hygiene product

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AIP Conference Proceedings 2021年第1期2344卷

作者： Matthew Hardhi Delfina Putty Ekadewi Retno Widyati Yuswan Muharam Widodo Wahyu Purwanto Dewi Tristantini Misri Gozan 1Bioprocess Engineering Program Department of Chemical Engineering Faculty of Engineering Universitas Indonesia Depok West Java 16424 Indonesia 2Research Center for Biomedical Engineering Faculty of Engineering Universitas Indonesia Depok West Java 16424 Indonesia

Maintaining good ear hygiene is important, yet currently available ear cleaning products such as cotton buds and ear scoop might lead to internal ear injury when improperly used. This study examines the market competitiveness of a conceptual ear hygiene product based on analyzing consumer needs. This new ear hygiene product is expected to be able to clean the ear properly without exposing users to unnecessary risks, satisfy consumer needs, as well as giving added value in the form of antimicrobial properties. Consumer needs identification and reception toward the product concept were determined through online surveys to 218 respondents. Forty-eight different potential user needs were collected from survey results, which were then transformed into product specifications using the appropriate metrics. A feasibility matrix was made to compare 155 different concepts generated from mind-mapping and brainstorming processes, which results in 13 final product concepts. Further screening stages and benchmarking were applied to select the final product concept. The final concept is a topical, herbal ear hygiene product with antibacterial, antifungal, and earwax solubilization properties with micelle-based solvent in spray form. The active compound of this product is the essential oil of clove oil, also known as eugenol. The testing of the final product concept pointed towards the positive for consumer acceptance.

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CRISPR-Cas Biochemistry and CRISPR-Based Molecular Diagnostics

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Angewandte Chemie 2023年第17期135卷

作者： Zhengyan Weng Zheng You Jie Yang Noor Mohammad Prof. Mengshi Lin Prof. Qingshan Wei Prof. Xue Gao Prof. Yi Zhang Department of Biomedical Engineering University of Connecticut Storrs CT 06269 USA Institute of Materials Science University of Connecticut Storrs CT 06269 USA Department of Chemical and Biomolecular Engineering Rice University Houston TX 77005 USA Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh NC 27695 USA Food Science Program Division of Food Nutrition and Exercise Sciences University of Missouri Columbia MO 65211 USA Department of Bioengineering Rice University Houston TX 77005 USA Department of Chemistry Rice University Houston TX 77005 USA

Polymerase chain reaction (PCR)-based nucleic acid testing has played a critical role in disease diagnostics, pathogen surveillance, and many more. However, this method requires a long turnaround time, expensive equipment, and trained personnel, limiting its widespread availability and diagnostic capacity. On the other hand, the clustered regularly interspaced short palindromic repeats (CRISPR) technology has recently demonstrated capability for nucleic acid detection with high sensitivity and specificity. CRISPR-mediated biosensing holds great promise for revolutionizing nucleic acid testing procedures and developing point-of-care diagnostics. This review focuses on recent developments in both fundamental CRISPR biochemistry and CRISPR-based nucleic acid detection techniques. Four ongoing research hotspots in molecular diagnostics-target preamplification-free detection, microRNA (miRNA) testing, non-nucleic-acid detection, and SARS-CoV-2 detection-are also covered.

关键词： Amplification-Free Detection Biosensors CRISPR-Cas Biochemistry Molecular Diagnostics SARS-Cov-2

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Influence of compatibilizer and carbon nanotubes on mechanical, electrical, and barrier properties of PTT/ABS blends

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Advanced Industrial and engineering Polymer Research 2019年第3期2卷 121-125页

作者： Braga, Natália F. LaChance, Anna Marie Liu, Bin Sun, Luyi Passador, Fabio R. Technology Laboratory of Polymers and Biopolymers Federal University of São Paulo São José dos CamposSP12231-280 Brazil Polymer Program Institute of Materials Science University of Connecticut StorrsCT06269 United States Department of Chemical and Biomolecular Engineering University of Connecticut StorrsCT06269 United States Beijing Key Laboratory of Electrochemical Process and Technology for Materials College of Materials Science and Engineering Beijing University of Chemical Technology Beijing100029 China Department of Biomedical Engineering University of Connecticut StorrsCT06269 United States

Composites based on poly (trimethylene terephthalate) (PTT)/acrylonitrile butadiene styrene (ABS) blend with maleic anhydride grafted PTT (PTT-g-MA) as a compatibilizer and carbon nanotubes (CNTs) as reinforcers were prepared via melt-mixing, and the mechanical, electrical, and barrier properties of the as-fabricated composites were evaluated. Scanning electron microscopy (SEM) characterization of the cross-section of the composites after tensile test showed improved phase stability in the presence of the compatibilizer PTT-g-MA. The toughness of the composites was also improved with the addition of the compatibilizer and CNTs. Electrical conductivity tests were carried out and the results showed that CNT-reinforced composite exhibited significantly increased conductivity. Since barrier properties are very sensitive to structural changes, the oxygen transmission rate (OTR) of the composites was measured and the results showed that the composites possess a much high oxygen barrier compared to that of the neat PTT or ABS. © 2019 Kingfa SCI. & TECH. CO., LTD.

关键词： Carbon nanotubes

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Therapeutic targeting of hepatocellular carcinoma cells with antrocinol, a novel, dual-specificity, small-molecule inhibitor of the KRAS and ERK oncogenic signaling pathways

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Chemico-Biological Interactions 2023年第1期370卷 110329页

作者： Hsu, Chia-Hung Weng, Pei-Wei Chen, Ming-Yao Yeh, Chi-Tai Setiawan, Syahru Agung Yadav, Vijesh Kumar Wu, Alexander T.H. Tzeng, David T.W. Gong, Jian-Xian Yang, Zhen Tzeng, Yew-Min Department of Emergency Medicine Shuang Ho Hospital Taipei Medical University New Taipei City 23561 Taiwan Graduate Institute of Injury Prevention and Control College of Public Health Taipei Medical University Taipei City 11031 Taiwan Department of Emergency Medicine School of Medicine Taipei Medical University Taipei 11031 Taiwan Department of Orthopaedics School of Medicine College of Medicine Taipei Medical University Taipei 11031 Taiwan Department of Orthopaedics Shuang Ho Hospital Taipei Medical University New Taipei City 23561 Taiwan Graduate Institute of Biomedical Materials and Tissue Engineering College of Biomedical Engineering Taipei Medical University Taipei 11031 Taiwan Division of Gastroenterology and Hepatology Department of Internal Medicine Shuang Ho Hospital New Taipei City 23561 Taiwan Division of Gastroenterology and Hepatology Department of Internal Medicine School of Medicine College of Medicine Taipei Medical University Taipei 11031 Taiwan Continuing Education Program of Food Biotechnology Applications College of Science and Engineering National Taitung University Taitung 95092 Taiwan International Ph.D. Program in Medicine College of Medicine Taipei Medical University Taipei 11031 Taiwan Ph.D. Program of Translational Medicine College of Medical Science and Technology Taipei Medical University Taipei 11031 Taiwan School of Life Sciences The Chinese University of Hong Kong 999077 Hong Kong Lifebit London EC2A 2AP United Kingdom Laboratory of Chemical Genomics School of Chemical Biology and Biotechnology Peking University Shenzhen Graduate School Shenzhen 518055 China State Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education and Beijing National Laboratory for Molecular Science College of Chemistry and Molecular Engineering Peking University Beijing 100871 China Shenzhen Bay Laboratory Shenzhen 518055 China Department of Applied Science National Taitung University Taitung

Until recently, sorafenib has been the only treatment approved by the U.S. Food and Drug Administration for patients with advanced hepatocellular carcinoma (HCC). Some patients, however, exhibit resistance to this treatment and subsequently experience cancer progression, recurrence, or death. Therefore, identifying a new alternative treatment for patients with little or no response to sorafenib treatment is vital. In this study, we explored the therapeutic potential and underlying molecular mechanism of antrocinol ((3aS,4R,6aS,10aR)-4-(hydroxymethyl)-7,7-dimethyldecahydro-1H-naphtho[1,8a-c]furan-1-one) in patients with HCC. The results indicated that antrocinol was more therapeutically effective than antrocin, Stivarga, and sorafenib against HCC cell lines. Antrocinol also substantially suppressed the expression of KRAS-GTP, p-MEK1/2, p-ERK1/2, and p-AKT in the Huh7 cell line. Additionally, antrocinol-induced apoptosis in the Huh7 cell line, inhibited the formation of tumorspheres, and suppressed the expression of cancer stem cell markers CD133, KLF4, CD44, OCT4, SOX2, and c-Myc. Animal studies revealed that antrocinol alone considerably suppressed tumor growth in nonobese diabetic/severe combined immunodeficient mice inoculated with Huh7 tumorspheres. It also synergistically enhanced the anticancer effect of sorafenib, resulting in enhanced suppression of tumor growth (p < 0.001) and tumorsphere formation (p < 0.001). In tumor samples resected from mice treated with antrocinol alone or in combination with sorafenib, immunohistochemical analysis revealed an increase in BAX expression and a decrease in ERK and AKT protein expression. To the best of our knowledge, this is the first report of the anti-HCC activity of antrocinol. With its higher therapeutic efficacy than that of sorafenib, antrocinol is a candidate drug for patients with HCC who demonstrate little or no response to sorafenib treatment. © 2022 Elsevier B.V.

关键词： Antrocinol Cancer stemness Hepatocellular carcinoma KRAS/AKT/ERK axis Sorafenib

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An Efficient Near-Infrared Emissive Artificial Supramolecular Light-Harvesting System for Imaging in the Golgi Apparatus

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Advanced Materials 2020年第26期132卷 10579-10583页

作者： Chen, Xu-Man Cao, Qin Bisoyi, Hari Krishna Wang, Meng Yang, Hong Li, Quan Institute of Advanced Materials School of Chemistry and Chemical Engineering Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research State Key Laboratory of Bioelectronics Southeast University Nanjing211189 China Advanced Materials and Liquid Crystal Institute and Chemical Physics Interdisciplinary Program Kent State University KentOH44242 United States

Light-harvesting systems are an important way for capturing, transferring and utilizing light energy. It remains a key challenge to develop highly efficient artificial lightharvesting systems. Herein, we report a supramolecular coassembly based on lower-rim dodecyl-modified sulfonatocalix-[4]arene (SC4AD) and naphthyl-1,8-diphenyl pyridinium derivative (NPS) as a light-harvesting platform. NPS as a donor shows significant aggregation induced emission enhancement (AIEE) after assembling with SC4AD. Upon introduction of Nile blue (NiB) as an acceptor into the NPSSC4AD co-assembly, the light-harvesting system becomes near-infrared (NIR) emissive (675 nm). Importantly, the NIR emitting NPS-SC4AD-NiB system exhibits an ultrahigh antenna effect (33.1) at a high donor/acceptor ratio (250:1). By co-staining PC-3 cells with a Golgi staining reagent, NBD C6-ceramide, NIR imaging in the Golgi apparatus has been demonstrated using these NIR emissive nanoparticles. © 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

关键词： Antennas

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Tribological properties of hydroxyapatite-coated nanorods on Ti-6Al-4V surfaces

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Scientific reports 2025年第1期15卷 19113页

作者： Sarah Akua Osafo Tabiri Asumadu Desmond Klenam Precious Etinosa John David Obayemi Benjamin Agyei-Tuffour Abu Yaya David Dodoo-Arhin Stanley Chijioke Eluu Wole Soboyejo Department of Materials Science and Engineering School of Engineering Sciences College of Basic and Applied Sciences University of Ghana Legon Accra Ghana. Department of Biomaterial Sciences Dental School University of Ghana Korle Bu Campus Accra Ghana. Department of Mechanical Engineering Program in Materials Science and Engineering Worcester Polytechnic Institute 100 Institute Road Worcester MA 01609 USA. Department of Materials Engineering Sunyani Technical University Sunyani Ghana. Global Center of Advanced Materials and Manufacturing Department of Mechanical Engineering College of Engineering State University of New York (SUNY) Polytechnic Institute 100 Seymour Street Utica NY 13502 USA. Next Frontiers in Advanced Material Laboratory School of Chemical and Metallurgical Engineering University of the Witwatersrand 1 Jan Smuts Avenue Johannesburg 2050 South Africa. Department of Biomedical Engineering Worcester Polytechnic Institute Gateway Park Life Sciences and Bioengineering Centre 60 Prescott Street Worcester MA 01609 USA. Department of Biotechnology Ebonyi State University Abakaliki Nigeria. Department of Pharmaceutical Microbiology and Biotechnology Faculty of Pharmaceutical Sciences Nnamdi Azikiwe University Awka Anambra State Nigeria. Department of Mechanical Engineering Program in Materials Science and Engineering Worcester Polytechnic Institute 100 Institute Road Worcester MA 01609 USA. soboyew@sunypoly.edu. Global Center of Advanced Materials and Manufacturing Department of Mechanical Engineering College of Engineering State University of New York (SUNY) Polytechnic Institute 100 Seymour Street Utica NY 13502 USA. soboyew@sunypoly.edu. Department of Biomedical Engineering Worcester Polytechnic Institute Gateway Park Life Sciences and Bioengineering Centre 60 Prescott Street Worcester MA 01609 USA. soboyew@sunypoly.edu.

This paper presents the tribological properties and bioactivity of nanostructured hydroxyapatite (HA) from biowaste sources and coated onto Ti-6Al-4V substrates using a novel pack cementation method. The process introduced HA pillars/nanorods on the surfaces of Ti-6Al-4V to enhance their osseointegration for dental implants. The mechanical and tribological properties were studied with nanoindentation, and pin-on-disk techniques, following the microstructural characterization of the coatings with atomic force microscopy, X-ray diffraction, Raman spectroscopy, scanning electron microscopy, and energy dispersive x-ray spectroscopy. The study also examines the surface bioactivity and elucidates the underlying friction and wear mechanisms of the HA-coated and annealed Ti-6Al-4V surface. The study results show a bone bonding capacity of the biowaste-derived HA-coated substrate with improved hardness and tribological properties. The implications of the study are discussed for the development of nano-structured HA-coated Ti-6Al-4V for dental implants with improved osseointegration for dental and biomedical applications.

关键词： Bioactivity Dental implants Osseointegration Surface modification Titanium alloys Wear resistance

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Frontispiz: Thermo- and Mechanochromic Camouflage and Self-Healing in Biomimetic Soft Actuators Based on Liquid Crystal Elastomers

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Angewandte Chemie 2022年第8期134卷

作者： Zhongcheng Liu Dr. Hari Krishna Bisoyi Yinliang Huang Meng Wang Prof. Hong Yang Prof. Quan Li Institute of Advanced Materials School of Chemistry and Chemical Engineering and Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research Southeast University Nanjing 211189 China Advanced Materials and Liquid Crystal Institute and Chemical Physics Interdisciplinary Program Kent State University Kent OH 44242 USA

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An Artificial Light-Harvesting System with Controllable Efficiency Enabled by an Annulene-Based Anisotropic Fluid

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Angewandte Chemie 2022年第16期134卷

作者： Zhen Yu Dr. Hari Krishna Bisoyi Dr. Xu-Man Chen Zhen-Zhou Nie Dr. Meng Wang Prof. Hong Yang Prof. Quan Li Institute of Advanced Materials School of Chemistry and Chemical Engineering Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research Southeast University Nanjing 211189 China Advanced Materials and Liquid Crystal Institute Chemical Physics Interdisciplinary Program Kent State University Kent OH 44242 USA

The development of controllable artificial light-harvesting systems based on liquid crystal (LC) materials, i.e., anisotropic fluids, remains a challenge. Herein, an annulene-based discotic LC compound 6 with a saddle-shaped cyclooctatetrathiophene core has been synthesized to construct a tunable light-harvesting platform. The LC material shows a typical aggregation-induced emission, which can act as a suitable light-harvesting donor. By loading Nile red (NiR) as an acceptor, an artificial light-harvesting system is achieved. Relying on the thermal-responsive self-assembling ability of 6 with variable molecular order, the efficiency of such 6 -NiR system can be controlled by temperature. This light-harvesting system works sensitively at a high donor/acceptor ratio as 1000 : 1, and exhibits a high antenna effect (39.1) at a 100 : 1 donor/acceptor ratio. This thermochromic artificial light-harvesting LC system could find potential applications in smart devices employing soft materials.

关键词： Aggregation-Induced Emission Light-Harvesting System Liquid Crystal Supramolecular Self-Assembly Tunable Antenna Effect

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