Multi-Objective Design of DNA-Stabilized Nanoclusters findings published in ACS Publications. DNA-stabilized silver #nanoclusters (AgN-DNAs) exhibit sequence-dependent compositions and fluorescence colors. Recently, high-throughput experiments combined with supervised machine learning have enabled the design of #DNA templates that tune AgN-DNA properties, including near-infrared (NIR) emission, which shows promise for deep tissue bioimaging. Led by?Prof. Stacy Copp,?the IRG2 team and collaborators developed a multiobjective, continuous-property design model for AgN-DNAs using variational autoencoders (VAEs) with automatic feature extraction. This generative model learns both the forward mapping from DNA sequence to AgN-DNA properties and the inverse mapping from properties to sequence. It was trained on experimental data linking DNA sequences to AgN-DNA fluorescence characteristics. Experimental validation demonstrated the model’s ability to design AgN-DNAs with enhanced emission, including bright NIR-emitting AgN-DNAs, which were produced with four times greater abundance than those in the training set. This generative approach can be extended to a variety of biomolecular systems with sequence-dependent properties, facilitating precise design of emerging nanomaterials. The theoretical work was led by MRSEC junior research fellow?Peter Mastracco, who recently earned his Ph.D., in collaboration with?Petko Bogdanov’s experimental group at the University at Albany-SUNY.
Center for Complex and Active Materials MRSEC的动态
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?? Important publication released : Focus on Cryo-FIB Technology in Electron Microscopy?? Cryogenic-Focused Ion Beam (Cryo-FIB) technology is becoming an indispensable tool for high-resolution imaging of cryo-preserved cells and tissues. In scarcely over a decade, it has ascended from a speculative concept to an established sample preparation technique in the cryo-EM repertoire. ???? ?? In this review, The authors Alex Noble and Alex de Marco from New York Structural Biology Center explore the current state-of-the-art capabilities of this technology and its applications in structural cell and tissue biology. https://lnkd.in/es9yfwyP They highlight : ??? Recent advances in instrumentation, imaging modalities, and automation. ???? Sample preparation protocols and targeting techniques. ???? Challenges and future directions to make Cryo-FIB more precise, enable higher throughput, and increase accessibility. These continuous improvements pave the way for revealing intricate molecular architectures across length scales inside cells and tissues. ???? Despite these advancements, persistent challenges remain. However, these can be addressed by: ???? - Enhancing cell culture on grids - Improving sample handling - Developing smart preparation methods that avoid on-grid culturing Thanks to the authors for highlighting the importance of cell culture grids improvements over the last years. The PRIMO SSP (Substrate Sample Preparation) technology from Alvéole is now part of the intricate journey of cryo-ET workflow ! #Science #CryoFIB #CellularImaging #Technology #Research #StructuralBiology #CryoEM #Innovation #Automation #CryoET
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?? Exciting Breakthrough in Molecular Imaging! ?? The Department of Physical Chemistry at the Fritz Haber Institute has just published a remarkable study in Nature Portfolio Nature Communications. Their study, ?Spiral Packing and Chiral Selectivity in Model Membranes Probed by Phase-Resolved Sum-Frequency Generation Microscopy,” marks a significant leap forward in our understanding of biological membranes. https://lnkd.in/df-D2mED Thanks to advancements in Sum-Frequency Generation (SFG) microscopy, scientists can now observe the intricate spiral arrangements of phospholipid molecules within biological membranes. This discovery not only reveals the crucial role of chirality in these structures but also enhances our comprehension of their functions in biological processes. This research sheds light on the complex molecular patterns essential for life, opening new avenues for exploring biological systems and processes at the molecular level. A huge congratulations to the team for their innovative work and for pushing the boundaries of molecular imaging! #Science #Innovation #Research #BiologicalMembranes #MolecularImaging #Chirality #NatureCommunications https://lnkd.in/dQpPUFzh
New Insights into Membrane Structures: Breakthrough in SFG Microscopy
fhi.mpg.de
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We've spent a lot of time during my PhD looking into the issue of extracting high resolution images from a complex sample that is a liver-on-a-chip. We came up with multi-modal labelled and label-free microscopy approaches (2PEF, SHG, THG, SRS) which revealed: a) Distribution of fluorescent anti-sense oligonucleotides (ASOs) from deeeeep within a chip (>150 microns) and confirmed the positive effect of GalNAc moiety on ASO hepatocyte uptake dynamics. b) Intracellular ASO trafficking is likely dependent on hepatocyte morphology. c) Chemical components associated with hepatocyte morphology were discovered potentially making hepatocyte classification and segmentation easier in future studies. This has been recently published in a research paper with the Lab-on-a-Chip journal. https://lnkd.in/gymcgweU Big thanks to everyone involved in the paper, especially to Aneesh Alex
Multimodal imaging of a liver-on-a-chip model using labelled and label-free optical microscopy techniques
pubs.rsc.org
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Researchers from the University of Pennsylvania have demonstrated a new kind of #nanopore platform that consists of two or more nanopores stacked just #nanometers apart, allowing for more precise detection and control of #DNA as it wiggles through. “With current platforms, when molecules like DNA are placed near the nanopores, it’s sort of like having spaghetti in a pot – tangled and difficult to work with, let alone guiding through one hole,” explains Dimitri Monos, one of the scientists involved in this study. “So, typically, researchers need to use proteins to capture, unwind, and straighten it, which, while effective, has many limitations. But with this new design, we’re essentially guiding molecules through two coupled nanopores in the material, providing a controlled, smoother passage of molecules.” https://lnkd.in/eFJvySDf (Work funded by The National Institutes of Health and the National Science Foundation (NSF)) Marija D.
Novel coupled nanopore platform offers greater precision for detecting molecules | Penn Today
penntoday.upenn.edu
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If you have an interest in biomedical fluorescent imaging applications, I highly recommend reading our recent review paper published in the International Journal of Molecular Sciences (#IJMS), titled "High Quantum Yields and Biomedical Fluorescent Imaging Applications of Photosensitized Trivalent Lanthanide Ion-Based Nanoparticles" #Ln3+#ion_based_nanoparticle; #photosensitization; #host_matrix; #organic_ligand; #high_quantum_yield; #biomedical_fluorescent_imaging_application
High Quantum Yields and Biomedical Fluorescent Imaging Applications of Photosensitized Trivalent Lanthanide Ion-Based Nanoparticles
mdpi.com
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ScienceCast Daily Digest: Biophysics Edition ?? Stay ahead in the field of biophysics with our curated daily digest on ScienceCast.org, an arXiv Labs member. Authors can now upload short audio pitches of their work for quick insights. Today's top paper: "Homogeneous large field-of-view and compact iSCAT-TIRF setup for dynamic single molecule measurements" by De Angelis, Francesco Reina et al. This paper provides valuable advancements in single-molecule measurements, crucial for researchers and professionals in biophysics. Dive into the latest research and developments with ScienceCast. #Biophysics #Research #ScienceCast #BiophysicsDigest #Innovation #ScientificResearch https://lnkd.in/ejYYA2TY 4o
Homogeneous large field-of-view and compact iSCAT-TIRF setup for dynamic single molecule measurements
sciencecast.org
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Excited to share our new research on designing DNA polyhedra in a bioRxiv preprint: https://lnkd.in/dHP2GpEE Traditionally, designing these structures relied heavily on DNA origami, limiting flexibility. Arktos is a novel algorithm that allows for designing sequences predicted to fold into a desired structure without the limitations of origami. Arktos empowers researchers with: Simple and user-friendly:?Designs DNA sequences predicted to fold into desired structures. Flexible and customizable:?Caters to diverse research needs by enabling custom DNA polyhedra creation. Validated with success:?We designed and experimentally verified a DNA tetrahedron using Arktos, demonstrating its effectiveness. This research paves the way for: Expanding the toolbox for DNA nanostructure design and developing more diverse and specialized structures for various applications. #bioRxiv #dna #nanotechnology #bioinformatics #DNAorigami #algorithm #biotechnology #computationalbiology #research
Arktos: a simple tool for the design of polyhedral DNA nanostructures
biorxiv.org
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Delve into the secrets of mechanosensory organelles (MO)! ?? https://lnkd.in/gZ2yUFNW MOs are specialized entities which process dedicated structural architectures and function as sensors to detect forces. This innovative protocol by Landi Sun, Jana Meissner,?Jianfeng He, Lihong Cui,?Tobias Fürstenhaupt, and Xin Liang at?Tsinghua University?and?MPI-CBG - Max Planck Institute of Molecular Cell Biology and Genetics utilizes serial section electron tomography to unveil the nanoscopic ultrastructure of fly MOs. ?? This involves cryo-immobilization, freeze-substitution, resin embedding, and dual-axis tilt series imaging to reconstruct the sensory organelles in three dimensions. The approach provides insights into MO function and formation, with potential applicability to various cell and tissue samples. The stunning results of their electron microscopy work got featured on the Bio-protocol issue cover this month (in comments)! We thank Xiaokang W., Rama Reddy Goluguri, and Chen Fan for reviewing the work. #ElectronTomography #SubcellularOrganelles #microscopy Have a protocol that can contribute to scientific clarity and reproducibility ? Visit us at?https://lnkd.in/dt_igxRi?and explore publishing with?Bio-protocol at?https://lnkd.in/dJrqztsf! #openaccess?#reproducibility?#lifesciences?#research
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Quantitative Proteomics & 3D Genome Organization | Strategic Partnerships @ Cube Biotech
?? Cube Biotech's Daily Digest #16 1 - Title: Structure determination by cryoEM at 100 keV 2 - Abstract: A recent study by Greg McMullan and colleagues introduces a breakthrough in electron cryomicroscopy (cryoEM) with a custom-built instrument operating at 100 keV. This innovation significantly reduces the cost and complexity of determining the structures of biological molecules. Traditional cryoEM methods, pivotal for understanding molecular structures, often face limitations due to high costs and technical requirements. This new 100 keV cryoEM microscope overcomes these challenges, providing fast, efficient, and cost-effective structure determination of biological molecules, even allowing for atomic resolution imaging of gold test specimens. 3 - Conclusion: This work marks a pivotal shift in cryoEM technology. By implementing key elements essential for molecular structure determination at a significantly reduced cost, the study demonstrates the ability to conveniently and cost-effectively obtain accurate 3D molecular structures. This advancement is expected to benefit not only biology but also materials science and low-temperature physics, particularly in the imaging of radiation-sensitive specimens. The development of more efficient, less expensive cryoEM instruments paves the way for a broader application of this technology in various scientific fields. 4 - Overall: The study ushers in a new era in cryoEM, showcasing a purpose-built instrument that achieves atomic resolution imaging and molecular structure determination swiftly and affordably. This marks a transformative moment in structural biology, broadening the scope and accessibility of cryoEM for diverse scientific investigations. 5 - Publication: https://lnkd.in/gqaUDUrx Year: 2023 Institute(s): MRC Laboratory of Molecular Biology (LMB), DECTRIS Ltd., JEOL Ltd., YORK PROBE SOURCES LIMITED, KAUST (King Abdullah University of Science and Technology), and Newcastle University. Data: EMPIAR-11752, the eleven reconstructed maps in the EMDB (EMD-17958–EMD-17968), and the eleven refined atomic model coordinates in the PDB (PDB-8PV9–PDB-8PVJ). The code used for converting electron event files to MRC format is available on the author’s website (https://lnkd.in/gi4_PggJ) and deposited in ZENODO (53). --- Cube Biotech's Role: As a leader in providing tools for structural biology, Cube Biotech's range of high-quality products, including reagents, purification kits, and stabilization tools, are perfectly aligned to support the advancements in cryoEM technology. Our products cater to the evolving needs of this field, ensuring that researchers have access to the best resources for their cryoEM studies. ? Products ??https://lnkd.in/gm53hqR8 ? End-to-End Services ??https://lnkd.in/giyc9puN ? Website ??https://cube-biotech.com Message me to learn how?Cube Biotech?can enhance your research! #cubebiotech #cryoEM #structuralbiology #biotechnology #scienceinnovation
Structure determination by cryoEM at 100 keV | Proceedings of the National Academy of Sciences
pnas.org
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The California NanoSystems Institute at UCLA invites you to join us November 15th for a Technology Center Open House! Join researchers, post-docs, students and area stakeholders in learning about the CNSI’s six technology centers which provide UCLA and the greater scientific community with leading technologies, including high-throughput molecular screening to discover novel drug candidates, cryo-electron imaging to reveal atomic structures ranging from new materials to therapeutic targets, super-resolution light microscopy for examining the behavior of single molecules within cells, and nanofabrication facilities for observing and manipulating matter at the nanoscale. https://bit.ly/4dSavOK
CNSI Technology Center Open House
https://cnsi.ucla.edu
