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RSC Applied Polymers 2024年第6期2卷 1147-1156页

作者： Arguien, Meagan N. Kamps, Joshua T. Muth, Sarah A. Trujillo-Lemon, Marianela Bowman, Christopher N. Materials Science & Engineering Program University of Colorado Boulder 80309 CO United States Department of Chemistry University of Colorado Boulder 80309 CO United States Department of Molecular Cellular & Developmental Biology University of Colorado Boulder 80309 CO United States Department of Chemical and Biological Engineering University of Colorado Boulder 80309 CO United States

This work synthesizes poly(ethylene glycol) (PEG) macromers that incorporate a phthalaldehyde moiety located at crosslink junctions. This location facilitates the severing of the polymer network when bond scission of the phthalaldehyde unit occurs with mechanical stimulation. As these networks degrade, the mechanical properties are analyzed to better understand how sonication driven degradation affects a polymer network - specifically looking at the degradation profile in hydrogel systems through the mass loss and storage modulus profiles. Comparison of hydrogels containing phthalaldehyde units with hydrogels that do not have the mechanophore pre- and post-mechanical stimulation provides evidence that the incorporation of the mechanophore at these crosslink junctions reduces the storage modulus by a factor of ten and results in greater than 90% decrease of the gel mass after 15 minutes of probe sonication, leading to breaking the network into soluble daughter fragments. The network degradation conditions of these hydrogels are shown to be compatible with biological component suspension and release for applications such as localized payload release. © 2024 RSC.

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A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH (Jan, 10.1038/s41587-022-01568-9, 2023)

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NATURE BIOTECHNOLOGY 2023年第7期41卷 1027-1027页

作者： Jia, Bojing Blair Jussila, Adam Kern, Colin Zhu, Quan Ren, Bing Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA Medical Scientist Training Program University of California San Diego La Jolla CA USA Department of Cellular and Molecular Medicine Center for Epigenomics University of California San Diego La Jolla CA USA Ludwig Institute for Cancer Research La Jolla CA USA Institute of Genomic Medicine Moores Cancer Center School of Medicine University of California San Diego La Jolla CA USA

Multiplexed fluorescence in situ hybridization (FISH) is a widely used approach for analyzing three-dimensional genome organization, but it is challenging to derive chromosomal conformations from noisy fluorescence signals, and tracing chromatin is not straightforward. Here we report a spatial genome aligner that parses true chromatin signal from noise by aligning signals to a DNA polymer model. Using genomic distances separating imaged loci, our aligner estimates spatial distances expected to separate loci on a polymer in three-dimensional space. Our aligner then evaluates the physical probability observed signals belonging to these loci are connected, thereby tracing chromatin structures. We demonstrate that this spatial genome aligner can efficiently model chromosome architectures from DNA FISH data across multiple scales and be used to predict chromosome ploidies de novo in interphase cells. Reprocessing of previous whole-genome chromosome tracing data with this method indicates the spatial aggregation of sister chromatids in S/G2 phase cells in asynchronous mouse embryonic stem cells and provides evidence for extranumerary chromosomes that remain tightly paired in postmitotic neurons of the adult mouse cortex.

关键词： Gene regulation Image processing

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Rejuvenation of Meropenem by Conjugation with Tilapia Piscidin-4 Peptide Targeting NDM-1 Escherichia coli

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ACS Omega 2024年第27期9卷 29756-29764页

作者： Selvaraj, Sanjay Prasad Lin, Kuan-Hung Lin, Wen-Chun You, Ming-Feng Li, Tsung-Lin Chen, Jyh-Yih Molecular and Biological Agricultural Science Program Taiwan International Graduate Program Academia Sinica Graduate Institute of Biotechnology National Chung Hsing University Genomics Research Center Academia Sinica Marine Research Station Institute of Cellular and Organismic Biology Academia Sinica Biotechnology Center National Chung Hsing University The iEGG and Animal Biotechnology Center and the Rong Hsing Research Center for Translational Medicine National Chung Hsing University

Gram-negative pathogens that produce β-lactamases pose a serious public health threat as they can render β-lactam antibiotics inactive via hydrolysis. This action contributes to the waning effectiveness of clinical antibiotics and creates an urgent need for new antimicrobials. Antimicrobial peptides (AMPs) exhibiting multimodal functions serve as a potential source in spite of a few limitations. Thus, the conjugation of conventional antibiotics with AMPs may be an effective strategy to leverage the advantages of each component. In this study, we conjugated meropenem to the AMP Tilapia piscidin 4 (TP4) using a typical coupling reaction. The conjugate was characterized by using HPLC-MS, HR-MS, and MS-MS fragmentation analysis. It was then evaluated in terms of antibacterial potency, hemolysis, and cytotoxicity toward RAW264.7 and CCD-966SK cell lines. The conjugation of meropenem with TP4 significantly reduced the cytotoxicity compared to TP4. Conjugation of unprotected TP4 with meropenem resulted in cross-linking at the N-terminal and lysine sites. The structural activity relationship of the two isomers of the TP4-meropenem conjugate was investigated. Both the isomers showed notable antibacterial activities against NDM-1 Escherichia coli and reduced red blood cell hemolysis as compared to TP4. Lysine conjugate (TP4-K-Mero) showed lesser hemolysis than the N-terminal conjugate (TP4-N-Mero). molecular modeling further revealed that the conjugates can bind to lipopolysaccharides and inhibit NDM-1 β-lactamase. Together, these data show that conjugation of antibiotics with AMP can be a feasible approach to increase the therapeutic profile and effectively target multidrug-resistant pathogens. Furthermore, antibiotic conjugation at different AMP sites tends to show unique biological properties. © 2024 The Authors. Published by American Chemical Society.

关键词： Antimicrobial agents Show More

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BEAGLE 2.0: A Web Server for RNA Secondary Structure Similarity Detection Leveraging SHAPE-directed RNA Structure Determination

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Journal of molecular biology 2025年第15期437卷

作者： Ballesio, F. Teofani, A. Carrino, C. Catalano, M. Nicolaeasa, M.L. Ausiello, G. Helmer-Citterich, M. Gherardini, P.F. Department of Biology University of Rome “Tor Vergata” Rome Italy Ph.D. Program in Cellular and Molecular Biology Department of Biology University of Rome ’Tor Vergata’ Rome Italy

Recent studies underscore the significant role of RNA secondary structures in various biological and pathological processes. Structural conservation can reveal homologies undetectable by sequence analysis alone, making accurate prediction and comparison of RNA secondary structures crucial. The BEAGLE algorithm enables pairwise alignments of RNA secondary structures through dynamic programming, leveraging the BEAR encoding for RNA secondary structures representation. Initially, BEAGLE was designed to perform pairwise alignments of user-provided RNAs or against a limited number of datasets. We now introduce BEAGLE 2.0, a web server designed to facilitate the search for structural similarities between user-provided RNA molecules and an expanded collection of RNA secondary structure datasets. These datasets include structures derived from SHAPE experiments in Homo sapiens, Mus musculus, Danio rerio, Escherichia coli, Bacillus subtilis, and various viruses, including SARS-CoV-2. It also incorporates predicted structures from the NONCODE database for a wide range of animals and plants, as well as a dataset of structures based on constraints derived from conserved positions within the families present in Rfam. Users can input RNA sequences or a combination of sequences and secondary structures in either dot-bracket or BEAR format. BEAGLE 2.0 outputs pairwise alignments with measures of structural similarity and statistical significance. Additionally, it offers a visual representation of the secondary structures, with structural elements highlighted in different colors. Overall, BEAGLE 2.0 enables searches in RNA structure datasets leveraging experimentally supported data, to identify structural similarities in RNAs of interest. BEAGLE 2.0 is available at https://***. © 2025

关键词： icSHAPE data integration non-coding RNAs (ncRNAs) RNA homology detection RNA secondary structure alignment RNA structural similarity search

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CRISPR-Cas9 engineering of human T regulatory cells – Design and optimization of a manufacturing process

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molecular Immunology 2025年 184卷 13-21页

作者： Shimon, Ortal Dean, Adam M. Cohen, Shoshana Moser, Aiden L. Dacso, Clifford C. Gilad, Yosi Lonard, David M. Department of Molecular and Cellular Biology Baylor College of Medicine Houston TX United States CoRegen Inc. Baylor College of Medicine Houston TX United States SC Bioinformatics Consulting Group Givat Shmuel Israel Nuclear Receptor Transcription and Chromatin Biology Program Dan L. Duncan Cancer Center Baylor College of Medicine Houston TX United States Department of Medicine Baylor College of Medicine Houston TX United States

Regulatory T cells (Tregs) are a subset of CD4 + T cells that comprise 5–10 % of the total CD4 + T cell population. Tregs, which are critically important for the maintenance of immune tolerance and immune homeostasis, are distinguished from other subtypes of CD4 + T cells by the expression of the transcription factor FOXP3. Because of the centrality to immunoregulation, Tregs have gained increasing attention as promising targets for clinical applications in autoimmune diseases, transplant rejection and graft-versus-host disease (GvHD). However, the essential role of Tregs in the complex network of the immune system implies their targeting as a promising therapeutic approach also in other medical indications, such as neurodegenerative diseases and cancer. Our group recently published a study showing that genetically modified Tregs are capable of clearing solid malignancies in various mice models, including an aggressive triple negative breast cancer (TNBC) and prostate cancer, which provides the impetus to develop an adoptive cell therapy using Steroid Receptor Coactivator 3 (SRC-3) knock out (KO) Tregs. It is well known that isolation, genetic editing and the expansion of Tregs as a homogenous and healthy population present specific technical challenges. In this context, here we outline the development of a process for the production of SRC-3 KO human Tregs (hTregs), which can subsequently be adapted for Current Good Manufacturing Practice (cGMP) settings to facilitate clinical-scale production. © 2025 The Authors

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Microfractures in TiO2Enhance the Photoelectrochemical Properties of Photosystem i Bio-Sensitized Solar Cells 5

Microfractures in TiO2Enhance the Photoelectrochemical Prope...

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5th IEEE International Conference on BioInspired Processing, BIP 2023

作者： Flores, Sebastian Castro Araya, Christopher Espinoza Segura, Fabricio Chaverri Pineda, Leslie W. Bruce, Barry D. Villarreal, Claudia C. Cartago Costa Rica Maestria Ingenieria en Dispositivos Medicos Cartago Costa Rica San Jose Costa Rica University of Tennessee Department of Biochemistry Cellular and Molecular Biology Program in Genome Science and Technology KnoxvilleTN United States San Jose Costa Rica

ISBN: (纸本)9798350330052

Climate change, caused by the increasing energy demand from fossil fuels due to population growth and economic expansion, triggers the need for clean, renewable, and sustainable energy sources. The solar energy contributes to approximately 99.9% of the Earth's energy. Therefore, photovoltaic technology is considered a possible substitute for fossil fuels owing to its abundance, but the current silicon and thin film photovoltaic (PV) technologies generate greenhouse gas emissions (GHE) during manufacturing and use scarce and polluting materials. Bio-sensitized solar cells (BSSCs) offer a promising solution using simple, lower energy-demand manufacturing processes and abundant, non-toxic materials. BSSCs are derived from dye-sensitized solar cells (DSSCs) technology by replacing the synthetic dye with biological molecules, such as photosystem I (PSI), into a thin film device. We report a BSSC using PSI as a sensitizer, TiO2 as a wide-bandgap semiconductor, Co-bipyridine compound as a redox mediator in the electrolyte, and PEDOT-CNT composite as the counter electrode. This study investigates how microfractures on the TiO2 thin film induced during thermal sintering affect the photoelectrochemical performance of the BSSCs. Electrochemical characterization of the PSI-BSSCs was performed under a solar simulator using linear sweep voltammetry (LSV), open-circuit voltage decay (OCVD), chronoamperometry, and electrochemical impedance spectroscopy (EIS). SEM micrographs reveal fissures in the photoanode surface induced by the fast heating and cooling during thermal treatments. Surprisingly, the microfractures improved the performance of the solar cells and will be discussed regarding the accessibility of PSI and the mediator to penetrate the nanostructured electrode and enhance the photocurrents generated. The BSSCs improvement due to the microfractures is ascribed to the enabled diffusion of the PSI sensitizer through the nanoporous TiO2, given the significantly larger size o

关键词： bio-sensitized solar cell microfractures photosystem I surface area TiO2 photoanodes

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Direct visualization of translesion DNA synthesis polymerase IV at the replisome

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Proceedings of the National Academy of Sciences of the United States of America 2022年第39期119卷 e2208390119-e2208390119页

作者： Tuan, Pham Minh Gilhooly, Neville S. Marians, Kenneth J. Kowalczykowski, Stephen C. Department of Microbiology and Molecular Genetics University of California Davis 95616 CA United States Department of Molecular and Cellular Biology University of California Davis 95616 CA United States Molecular Biology Program Memorial Sloan Kettering Cancer Center New York 10065 NY United States Institute of Cancer and Genomic Sciences Birmingham Centre for Genome Biology College of Medical and Dental Sciences University of Birmingham Birmingham B15 2TT United Kingdom

In bacterial cells, DNA damage tolerance is manifested by the action of translesion DNA polymerases that can synthesize DNA across template lesions that typically block the replicative DNA polymerase III. It has been suggested that one of these translesion DNA synthesis DNA polymerases, DNA polymerase IV, can either act in concert with the replisome, switching places on the β sliding clamp with DNA polymerase III to bypass the template damage, or act subsequent to the replisome skipping over the template lesion in the gap in nascent DNA left behind as the replisome continues downstream. Evidence exists in support of both mechanisms. Using single-molecule analyses, we show that DNA polymerase IV associates with the replisome in a concentration-dependent manner and remains associated over long stretches of replication fork progression under unstressed conditions. This association slows the replisome, requires DNA polymerase IV binding to the β clamp but not its catalytic activity, and is reinforced by the presence of the γ subunit of the β clamp-loading DnaX complex in the DNA polymerase III holoenzyme. Thus, DNA damage is not required for association of DNA polymerase IV with the replisome. We suggest that under stress conditions such as induction of the SOS response, the association of DNA polymerase IV with the replisome provides both a surveillance/bypass mechanism and a means to slow replication fork progression, thereby reducing the frequency of collisions with template damage and the overall mutagenic potential. © 2022 the Author(s).

关键词： DNA repair DNA replication replisome single-molecule visualization translesion DNA synthesis

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Rapid plasma membrane isolation via intracellular polymerization-mediated biomolecular confinement

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Acta Biomaterialia 2024年 173卷 325-335页

作者： Lin, Chi-Long Fang, Zih-Syun Hsu, Chung-Yao Liu, Yu-Han Lin, Jung-Chen Yao, Bing-Yu Li, Fu-An Yen, Shin-Chwen Bruce Chang, Yuan-Chih Hu, Che-Ming J. Institute of Biomedical Sciences Academia Sinica. 128 Academia Road Sec. 2 Taipei11529 Taiwan Institute of Cellular and Organismic Biology Academia Sinica No. 128 Sec. 2 Taipei11529 Taiwan Research Center for Nanotechnology and Infectious Diseases Taipei Taiwan Taiwan International Graduate Program in Molecular Medicine National Yang Ming Chiao Tung University and Academia Sinica Taipei Taiwan

Plasma membrane isolation is a foundational process in membrane proteomic research, cellular vesicle studies, and biomimetic nanocarrier development, yet separation processes for this outermost layer are cumbersome and susceptible to impurities and low yield. Herein, we demonstrate that cellular cytosol can be chemically polymerized for decoupling and isolation of plasma membrane within minutes. A rapid, non-disruptive in situ polymerization technique is developed with cell membrane-permeable polyethyleneglycol-diacrylate (PEG-DA) and a blue-light-sensitive photoinitiator, lithium phenyl-2,4,6-trimethylbenzoylphosphinate (LAP). The photopolymerization chemistry allows for precise control of intracellular polymerization and tunable confinement of cytosolic molecules. Upon cytosol solidification, plasma membrane proteins and vesicles are rapidly derived and purified as nucleic acids and intracellular proteins as small as 15 kDa are stably entrapped for removal. The polymerization chemistry and membrane derivation technique are broadly applicable to primary and fragile cell types, enabling facile membrane vesicle extraction from shorted-lived neutrophils and human primary CD8 T cells. The study demonstrates tunable intracellular polymerization via optimized live cell chemistry, offers a robust membrane isolation methodology with broad biomedical utility, and reveals insights on molecular crowding and confinement in polymerized cells. Statement of significance: Isolating the minute fraction of plasma membrane proteins and vesicles requires extended density gradient ultracentrifugation processes, which are susceptible to low yield and impurities. The present work demonstrates that the membrane isolation process can be vastly accelerated via a rapid, non-disruptive intracellular polymerization approach that decouples cellular cytosols from the plasma membrane. Following intracellular polymerization, high-yield plasma membrane proteins and vesicles can be derived from lysi

关键词： Cell membranes

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Linear micropatterned epithelial model to study migratory effects of intercellular force transfer 25

Linear micropatterned epithelial model to study migratory ef...

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25th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2021

作者： Dow, Liam P. Kennedy, Reagan Pruitt, Beth L. Biomolecular Science and Engineering Program Molecular Cellular and Developmental Biology Mechanical Engineering University of California Santa Barbara United States

ISBN: (纸本)9781733419031

Mechanical linkages between epithelial cells are critical in regulating collective migration in tissue development and wound repair, but it is unclear how intercellular shear vs. tension forces differently regulate cell behavior and migration. We have developed a linear micropatterned epithelial model that enables the perturbation of shear or tensile forces on local epithelial cells within a tissue. We use this approach to demonstrate how two distinct modes of mechanical force transfer may regulate cellular migration within a developing epithelial tissue. © 2021 MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： Cell adhesion

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PANDA: PAN Cancer Data Analysis Web Tool

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Journal of molecular biology 2025年第15期437卷 169158页

作者： Pepe, G. Notturno Granieri, C. Appierdo, R. Ausiello, G. Helmer-Citterich, M. Gherardini, P.F. Department of Biology University of Rome Tor Vergata Via della Ricerca Scientifica 1 Rome 00133 Italy PhD Program in Cellular and Molecular Biology Department of Biology University of Rome “Tor Vergata” Rome Italy

Cancer research faces challenges due to the genetic diversity within tumors and individual variability. Precision medicine aims to identify genomic and molecular factors linked to clinical outcomes, leveraging large datasets for drug discovery and patient stratification. We introduce PANDA (PAN-cancer Data Analysis web tool) (https://***), a web server designed for analyzing TCGA genomic data. A total of 32 tumor types and 10,711 samples were selected for this analysis. PANDA simplifies complex tasks such as differential expression, survival analysis, and patient stratification, incorporating clinical factors like sex, stage, and treatment history. It also enables the exploration of biological pathways and immune cell type proportion, providing insights into tumor progression. PANDA is user-friendly, designed for researchers with limited informatics expertise, and supports diverse analyses to advance cancer research. © 2025

关键词： cancer biology cancer genomics immune cell deconvolution pan-cancer analysis TCGA patient stratification

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