Journal articles: 'Biomolecules visualization'

1

DeVore, Kira, and Po-Lin Chiu. "Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity." Biomolecules 12, no. 5 (April 24, 2022): 628. http://dx.doi.org/10.3390/biom12050628.

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Single-particle cryogenic electron microscopy (cryo-EM) has become an indispensable tool to probe high-resolution structural detail of biomolecules. It enables direct visualization of the biomolecules and opens a possibility for averaging molecular images to reconstruct a three-dimensional Coulomb potential density map. Newly developed algorithms for data analysis allow for the extraction of structural heterogeneity from a massive and low signal-to-noise-ratio (SNR) cryo-EM dataset, expanding our understanding of multiple conformational states, or further implications in dynamics, of the target biomolecule. This review provides an overview that briefly describes the workflow of single-particle cryo-EM, including imaging and data processing, and new methods developed for analyzing the data heterogeneity to understand the structural variability of biomolecules.

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Schatz, Karsten, Michael Krone, Jürgen Pleiss, and Thomas Ertl. "Interactive visualization of biomolecules’ dynamic and complex properties." European Physical Journal Special Topics 227, no. 14 (March 2019): 1725–39. http://dx.doi.org/10.1140/epjst/e2019-800162-y.

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Perlasca, Paolo, Marco Frasca, Cheick Tidiane Ba, Jessica Gliozzo, Marco Notaro, Mario Pennacchioni, Giorgio Valentini, and Marco Mesiti. "Multi-resolution visualization and analysis of biomolecular networks through hierarchical community detection and web-based graphical tools." PLOS ONE 15, no. 12 (December 22, 2020): e0244241. http://dx.doi.org/10.1371/journal.pone.0244241.

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The visual exploration and analysis of biomolecular networks is of paramount importance for identifying hidden and complex interaction patterns among proteins. Although many tools have been proposed for this task, they are mainly focused on the query and visualization of a single protein with its neighborhood. The global exploration of the entire network and the interpretation of its underlying structure still remains difficult, mainly due to the excessively large size of the biomolecular networks. In this paper we propose a novel multi-resolution representation and exploration approach that exploits hierarchical community detection algorithms for the identification of communities occurring in biomolecular networks. The proposed graphical rendering combines two types of nodes (protein and communities) and three types of edges (protein-protein, community-community, protein-community), and displays communities at different resolutions, allowing the user to interactively zoom in and out from different levels of the hierarchy. Links among communities are shown in terms of relationships and functional correlations among the biomolecules they contain. This form of navigation can be also combined by the user with a vertex centric visualization for identifying the communities holding a target biomolecule. Since communities gather limited-size groups of correlated proteins, the visualization and exploration of complex and large networks becomes feasible on off-the-shelf computer machines. The proposed graphical exploration strategies have been implemented and integrated in UNIPred-Web, a web application that we recently introduced for combining the UNIPred algorithm, able to address both integration and protein function prediction in an imbalance-aware fashion, with an easy to use vertex-centric exploration of the integrated network. The tool has been deeply amended from different standpoints, including the prediction core algorithm. Several tests on networks of different size and connectivity have been conducted to show off the vast potential of our methodology; moreover, enrichment analyses have been performed to assess the biological meaningfulness of detected communities. Finally, a CoV-human network has been embedded in the system, and a corresponding case study presented, including the visualization and the prediction of human host proteins that potentially interact with SARS-CoV2 proteins.

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Fenley, Andrew T., Hari S. Muddana, and Michael K. Gilson. "Calculation and Visualization of Atomistic Mechanical Stresses in Biomolecules." Biophysical Journal 106, no. 2 (January 2014): 461a. http://dx.doi.org/10.1016/j.bpj.2013.11.2611.

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Jo, Sunhwan, Miklos Vargyas, Judit Vasko-Szedlar, Benoît Roux, and Wonpil Im. "PBEQ-Solver for online visualization of electrostatic potential of biomolecules." Nucleic Acids Research 36, suppl_2 (May 28, 2008): W270—W275. http://dx.doi.org/10.1093/nar/gkn314.

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Tsujino, Tetsuhiro, Akira Takahashi, Taisuke Watanabe, Kazushige Isobe, Yutaka Kitamura, Kazuhiro Okuda, Koh Nakata, and Tomoyuki Kawase. "Platelet Adhesion on Commercially Pure Titanium Plates in Vitro II. Immunofluorescence Visualization of PDGF-B, TGFβ1, and PPARγ Released from Activated Adherent Platelets." Dentistry Journal 7, no. 4 (November 19, 2019): 109. http://dx.doi.org/10.3390/dj7040109.

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Recent progress in the industrial development of dental implants has improved their surface bio-affinity, while clinical implantologists attempt to improve it through coating with various compounds, including platelet-rich plasma (PRP) in clinical settings. However, it is poorly understood how PRP acts on titanium surfaces. To validate this surface modification method and demonstrate how platelet-derived soluble biomolecules released from the activated adherent platelets act on plain, commercially pure-titanium (cp-Ti) plates, we evaluated the distribution of biomolecules by immunofluorescence. PPARγ, PDGF-B, and TGFβ1 were similarly released at immunofluorescence levels from activated adherent platelets, retained in the surrounding extra-platelet spaces for a while, and did not immediately diffuse away to distant spaces. Exogenously added CaCl2 augmented release and retention of those biomolecules along with activation and aggregation. Taken together with our previous data regarding platelet adhesion, these findings suggest that especially when treated with CaCl2, platelets immediately adhere on cp-Ti plates to release their stored biomolecules in the absence of plasma proteins and that these biomolecules do not diffuse away, but stay longer in extra-platelet spaces around the platelets by newly formed, immature fibrin fiber fragments. Consequently, these retained biomolecules are anticipated to cooperatively stabilize implants by stimulating alveolar bone regeneration and integration.

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Fenley, Andrew T., Hari S. Muddana, and Michael K. Gilson. "Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules." PLoS ONE 9, no. 12 (December 11, 2014): e113119. http://dx.doi.org/10.1371/journal.pone.0113119.

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Tätte, T., K. Saal, I. Kink, A. Kurg, R. Lõhmus, U. Mäeorg, M. Rahi, A. Rinken, and A. Lõhmus. "Preparation of smooth siloxane surfaces for AFM visualization of immobilized biomolecules." Surface Science 532-535 (June 2003): 1085–91. http://dx.doi.org/10.1016/s0039-6028(03)00486-2.

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Shakurov, Ruslan, Svetlana Sizova, Stepan Dudik, Anna Serkina, Mark Bazhutov, Viktorija Stanaityte, Petr Tulyagin, et al. "Dendrimer-Based Coatings on a Photonic Crystal Surface for Ultra-Sensitive Small Molecule Detection." Polymers 15, no. 12 (June 8, 2023): 2607. http://dx.doi.org/10.3390/polym15122607.

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We propose and demonstrate dendrimer-based coatings for a sensitive biochip surface that enhance the high-performance sorption of small molecules (i.e., biomolecules with low molecular weights) and the sensitivity of a label-free, real-time photonic crystal surface mode (PC SM) biosensor. Biomolecule sorption is detected by measuring changes in the parameters of optical modes on the surface of a photonic crystal (PC). We describe the step-by-step biochip fabrication process. Using oligonucleotides as small molecules and PC SM visualization in a microfluidic mode, we show that the PAMAM (poly-amidoamine)-modified chip’s sorption efficiency is almost 14 times higher than that of the planar aminosilane layer and 5 times higher than the 3D epoxy-dextran matrix. The results obtained demonstrate a promising direction for further development of the dendrimer-based PC SM sensor method as an advanced label-free microfluidic tool for detecting biomolecule interactions. Current label-free methods for small biomolecule detection, such as surface plasmon resonance (SPR), have a detection limit down to pM. In this work, we achieved for a PC SM biosensor a Limit of Quantitation of up to 70 fM, which is comparable with the best label-using methods without their inherent disadvantages, such as changes in molecular activity caused by labeling.

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Wolfram, Tobias, Ilia Louban, Joachim P. Spatz, and Joerg Bewersdorf. "High-Resolution Microscopy on Nanostructured Interfaces." Microscopy Today 18, no. 1 (January 2010): 30–33. http://dx.doi.org/10.1017/s1551929510991153.

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Nano- and micro-patterned substrates have become a powerful tool in cell biology in recent years. Although great progress has been made in applying these substrates to cell populations or single cells, visualization of cells in direct contact with nanostructured interfaces remains a challenge. A central question that needs to be addressed by imaging is the number of biomolecules in contact with a single cell.

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Wang, Chunxia, Chujie Xia, Yi Zhu, and Huimin Zhang. "Innovative fluorescent probes for in vivo visualization of biomolecules in living Caenorhabditis elegans." Cytometry Part A 99, no. 6 (February 27, 2021): 560–74. http://dx.doi.org/10.1002/cyto.a.24325.

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Liuzzi, R., S. Gallier, S. Ringler, S. Caserta, and S. Guido. "Visualization of choline-based phospholipids at the interface of oil/water emulsions with TEPC-15 antibody. Immunofluorescence applied to colloidal systems." RSC Advances 6, no. 111 (2016): 109960–68. http://dx.doi.org/10.1039/c6ra13775j.

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Badaczewska-Dawid, Aleksandra E., Vladimir N. Uversky, and Davit A. Potoyan. "BIAPSS: A Comprehensive Physicochemical Analyzer of Proteins Undergoing Liquid–Liquid Phase Separation." International Journal of Molecular Sciences 23, no. 11 (May 31, 2022): 6204. http://dx.doi.org/10.3390/ijms23116204.

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The liquid–liquid phase separation (LLPS) of biomolecules is a phenomenon which is nowadays recognized as the driving force for the biogenesis of numerous functional membraneless organelles and cellular bodies. The interplay between the protein primary sequence and phase separation remains poorly understood, despite intensive research. To uncover the sequence-encoded signals of protein capable of undergoing LLPS, we developed a novel web platform named BIAPSS (Bioinformatics Analysis of LLPS Sequences). This web server provides on-the-fly analysis, visualization, and interpretation of the physicochemical and structural features for the superset of curated LLPS proteins.

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Chen, Qian, Haoxin Bai, Bingchen Che, Tianyun Zhao, Ce Zhang, Kaige Wang, Jintao Bai, and Wei Zhao. "Super-Resolution Reconstruction of Cytoskeleton Image Based on A-Net Deep Learning Network." Micromachines 13, no. 9 (September 13, 2022): 1515. http://dx.doi.org/10.3390/mi13091515.

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To date, live-cell imaging at the nanometer scale remains challenging. Even though super-resolution microscopy methods have enabled visualization of sub-cellular structures below the optical resolution limit, the spatial resolution is still far from enough for the structural reconstruction of biomolecules in vivo (i.e., ~24 nm thickness of microtubule fiber). In this study, a deep learning network named A-net was developed and shows that the resolution of cytoskeleton images captured by a confocal microscope can be significantly improved by combining the A-net deep learning network with the DWDC algorithm based on a degradation model. Utilizing the DWDC algorithm to construct new datasets and taking advantage of A-net neural network’s features (i.e., considerably fewer layers and relatively small dataset), the noise and flocculent structures which originally interfere with the cellular structure in the raw image are significantly removed, with the spatial resolution improved by a factor of 10. The investigation shows a universal approach for exacting structural details of biomolecules, cells and organs from low-resolution images.

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Lentz, Christian S. "What you see is what you get: activity-based probes in single-cell analysis of enzymatic activities." Biological Chemistry 401, no. 2 (February 25, 2020): 233–48. http://dx.doi.org/10.1515/hsz-2019-0262.

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AbstractMolecular imaging methods can provide spatio-temporal information about the distribution of biomolecules or biological processes, such as certain enzymatic activities, in single cells. Within a cell, it is possible to define the subcellular location of a target, its trafficking through the cell, colocalization with other biomolecules of interest and involvement in certain cell biological processes. On the other hand, single-cell imaging promises to distinguish cells that are phenotypically different from each other. The corresponding cellular diversity comprises the presence of functionally distinct cells in a population (‘phenotypic heterogeneity’), as well as dynamic cellular responses to external stimuli (‘phenotypic plasticity’), which is highly relevant, e.g. during cell differentiation, activation (of immune cells), or cell death. This review focuses on applications of a certain class of chemical probes, the so-called activity-based probes (ABPs), for visualization of enzymatic activities in the single-cell context. It discusses the structure of ABPs and other chemical probes, exemplary applications of ABPs in single-cell studies in human, mouse and bacterial systems and considerations to be made with regard to data interpretation.

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Mitra, Alok K. "Visualization of biological macromolecules at near-atomic resolution: cryo-electron microscopy comes of age." Acta Crystallographica Section F Structural Biology Communications 75, no. 1 (January 1, 2019): 3–11. http://dx.doi.org/10.1107/s2053230x18015133.

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Structural biology is going through a revolution as a result of transformational advances in the field of cryo-electron microscopy (cryo-EM) driven by the development of direct electron detectors and ultrastable electron microscopes. High-resolution cryo-EM images of isolated biomolecules (single particles) suspended in a thin layer of vitrified buffer are subjected to powerful image-processing algorithms, enabling near-atomic resolution structures to be determined in unprecedented numbers. Prior to these advances, electron crystallography of two-dimensional crystals and helical assemblies of proteins had established the feasibility of atomic resolution structure determination using cryo-EM. Atomic resolution single-particle analysis, without the need for crystals, now promises to resolve problems in structural biology that were intractable just a few years ago.

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Antina, Elena, Natalia Bumagina, Yuriy Marfin, Galina Guseva, Liliya Nikitina, Dmitry Sbytov, and Felix Telegin. "BODIPY Conjugates as Functional Compounds for Medical Diagnostics and Treatment." Molecules 27, no. 4 (February 18, 2022): 1396. http://dx.doi.org/10.3390/molecules27041396.

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Fluorescent dyes absorbing and emitting in the visible and near-IR regions are promising for the development of fluorescent probes for labeling and bio-visualization of body cells. The ability to absorb and emit in the long-wavelength region increases the efficiency of recording the spectral signals of the probes due to the higher permeability of the skin layers. Compared to other fluorescent dyes, BODIPYs are attractive due to their excellent photophysical properties–narrow absorption and emission, intense fluorescence, simple signal modulation for the practical applications. As part of conjugates with biomolecules, BODIPY could act as a biomarker, but as therapeutic agent, which allows solving several problems at once-labeling or bioimaging and treatment based on the suppression of pathogenic microflora and cancer cells, which provides a huge potential for practical application of BODIPY conjugates in medicine. The review is devoted to the discussion of the recent, promising directions of BODIPY application in the field of conjugation with biomolecules. The first direction is associated with the development of BODIPY conjugates with drugs, including compounds of platinum, paclitaxel, chlorambucil, isoxazole, capsaicin, etc. The second direction is devoted to the labeling of vitamins, hormones, lipids, and other biomolecules to control the processes of their transport, localization in target cells, and metabolism. Within the framework of the third direction, the problem of obtaining functional optically active materials by conjugating BODIPY with other colored and fluorescent particles, in particular, phthalocyanines, is being solved.

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Fukuma, Takeshi. "Subnanometer-scale imaging of nanobio-interfaces by frequency modulation atomic force microscopy." Biochemical Society Transactions 48, no. 4 (August 11, 2020): 1675–82. http://dx.doi.org/10.1042/bst20200155.

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Recently, there have been significant advancements in dynamic-mode atomic force microscopy (AFM) for biological applications. With frequency modulation AFM (FM-AFM), subnanometer-scale surface structures of biomolecules such as secondary structures of proteins, phosphate groups of DNAs, and lipid-ion complexes have been directly visualized. In addition, three-dimensional AFM (3D-AFM) has been developed by combining a high-resolution AFM technique with a 3D tip scanning method. This method enabled visualization of 3D distributions of water (i.e. hydration structures) with subnanometer-scale resolution on various biological molecules such as lipids, proteins, and DNAs. Furthermore, 3D-AFM also allows visualization of subnanometer-scale 3D distributions of flexible surface structures such as thermally fluctuating lipid headgroups. Such a direct local information at nano-bio interfaces can play a critical role in determining the atomic- or molecular-scale model to explain interfacial structures and functions. Here, we present an overview of these recent advancements in the dynamic-mode AFM techniques and their biological applications.

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Rosignoli, Serena, and Alessandro Paiardini. "Boosting the Full Potential of PyMOL with Structural Biology Plugins." Biomolecules 12, no. 12 (November 27, 2022): 1764. http://dx.doi.org/10.3390/biom12121764.

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Over the past few decades, the number of available structural bioinformatics pipelines, libraries, plugins, web resources and software has increased exponentially and become accessible to the broad realm of life scientists. This expansion has shaped the field as a tangled network of methods, algorithms and user interfaces. In recent years PyMOL, widely used software for biomolecules visualization and analysis, has started to play a key role in providing an open platform for the successful implementation of expert knowledge into an easy-to-use molecular graphics tool. This review outlines the plugins and features that make PyMOL an eligible environment for supporting structural bioinformatics analyses.

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Yin, Anxiang, Hao Jing, Zhan Wu, Qiyuan He, Yiliu Wang, Zhaoyang Lin, Yuan Liu, et al. "Quantitative Surface Plasmon Interferometry via Upconversion Photoluminescence Mapping." Research 2019 (September 15, 2019): 1–12. http://dx.doi.org/10.34133/2019/8304824.

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Direct far-field visualization and characterization of surface plasmon polaritons (SPPs) are of great importance for fundamental studies and technological applications. To probe the evanescently confined plasmon fields, one usually requires advanced near-field techniques, which is typically not applicable for real-time, high-throughput detecting or mapping of SPPs in complicated environments. Here, we report the utilization of rare-earth-doped nanoparticles to quantitatively upconvert invisible, evanescently confined SPPs into visible photoluminescence emissions for direct far-field visualization of SPPs in a complicated environment. The observed interference fringes between the SPPs and the coherent incident light at the metal surface provide a quantitative measurement of the SPP wavelength and the SPP propagating length and the local dielectric environments. It thus creates a new signaling pathway to sensitively transduce the local dielectric environment change into interference periodicity variation, enabling a new design of directly measurable, spectrometer-free optical rulers for rapid, ultrasensitive label-free detection of various biomolecules, including streptavidin and prostate-specific antigen, down to the femtomolar level.

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Morii, Takashi, and Takao Okada. "Looking, touching and moving DNA molecules-Knowledge obtained from the method of visualization and measurement of biomolecules." SEIBUTSU BUTSURI KAGAKU 49, no. 1 (2005): 1–3. http://dx.doi.org/10.2198/sbk.49.1.

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Singh, Dhananjaya Pratap, Mansi Singh Bisen, Renu Shukla, Ratna Prabha, Sudarshan Maurya, Yesaru S. Reddy, Prabhakar Mohan Singh, et al. "Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops." International Journal of Molecular Sciences 23, no. 20 (October 11, 2022): 12062. http://dx.doi.org/10.3390/ijms232012062.

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Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.

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T. V., Smitha, Madhura S, Sindhu R, and Brundha R. "A Study on Various Mesh Generation Techniques used for Engineering Applications." Journal of Innovative Image Processing 3, no. 2 (June 2, 2021): 75–84. http://dx.doi.org/10.36548/jiip.2021.2.001.

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In this paper our aim is to provide a survey of mesh generation techniques for some Engineering applications. Mesh generation is a very important requirement to solve any problem by very popular numerical method known as Finite element method (FEM). It has several applications in various fields. One such technique is Automated generation of finite element meshes for aircraft conceptual design. It’s an approach for automated generation of fully connected finite element meshes for all internal structural components, given wing body, geometry model, controlled by a few conceptual level structural layout parameters. Another application where it is used is in the study of biomolecules to generate volumetric mesh of a biomolecule of any size and shape based on its atomic structure. These methods are proved to be a faster method due to the usage of computing techniques. Mesh generator is also used for creating finite element surface and volumetric mesh from 3D binary and gray scale medical images. Some of the applications include volumetric images, surface mesh extraction, surface mesh repairing and many more. It is of great importance in understanding the human brain which is a complex subject. Though 3D visualization is a useful tool available, yet it is inadequate due to its challenging computational problem. This paper also includes the survey on latest tools used for these applications which overcomes many problems associated with the conventional approaches.

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Georgiev, Nikolai I., Ventsislav V. Bakov, Kameliya K. Anichina, and Vladimir B. Bojinov. "Fluorescent Probes as a Tool in Diagnostic and Drug Delivery Systems." Pharmaceuticals 16, no. 3 (March 1, 2023): 381. http://dx.doi.org/10.3390/ph16030381.

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Over the last few years, the development of fluorescent probes has received considerable attention. Fluorescence signaling allows noninvasive and harmless real-time imaging with great spectral resolution in living objects, which is extremely useful for modern biomedical applications. This review presents the basic photophysical principles and strategies for the rational design of fluorescent probes as visualization agents in medical diagnosis and drug delivery systems. Common photophysical phenomena, such as Intramolecular Charge Transfer (ICT), Twisted Intramolecular Charge Transfer (TICT), Photoinduced Electron Transfer (PET), Excited-State Intramolecular Proton Transfer (ESIPT), Fluorescent Resonance Energy Transfer (FRET), and Aggregation-Induced Emission (AIE), are described as platforms for fluorescence sensing and imaging in vivo and in vitro. The presented examples are focused on the visualization of pH, biologically important cations and anions, reactive oxygen species (ROS), viscosity, biomolecules, and enzymes that find application for diagnostic purposes. The general strategies regarding fluorescence probes as molecular logic devices and fluorescence–drug conjugates for theranostic and drug delivery systems are discussed. This work could be of help for researchers working in the field of fluorescence sensing compounds, molecular logic gates, and drug delivery.

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Sung, Jongbaek, Yuna Bae, Hayoung Park, Sungsu Kang, Back Kyu Choi, Joodeok Kim, and Jungwon Park. "Liquid-Phase Transmission Electron Microscopy for Reliable In Situ Imaging of Nanomaterials." Annual Review of Chemical and Biomolecular Engineering 13, no. 1 (June 10, 2022): 167–91. http://dx.doi.org/10.1146/annurev-chembioeng-092120-034534.

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Liquid-phase transmission electron microscopy (LPTEM) is a powerful in situ visualization technique for directly characterizing nanomaterials in the liquid state. Despite its successful application in many fields, several challenges remain in achieving more accurate and reliable observations. We present LPTEM in chemical and biological applications, including studies for the morphological transformation and dynamics of nanoparticles, battery systems, catalysis, biomolecules, and organic systems. We describe the possible interactions and effects of the electron beam on specimens during observation and present sample-specific approaches to mitigate and control these electron-beam effects. We provide recent advances in achieving atomic-level resolution for liquid-phase investigation of structures anddynamics. Moreover, we discuss the development of liquid cell platforms and the introduction of machine-learning data processing for quantitative and objective LPTEM analysis.

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Subramanian, Indhupriya, Srikant Verma, Shiva Kumar, Abhay Jere, and Krishanpal Anamika. "Multi-omics Data Integration, Interpretation, and Its Application." Bioinformatics and Biology Insights 14 (January 2020): 117793221989905. http://dx.doi.org/10.1177/1177932219899051.

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To study complex biological processes holistically, it is imperative to take an integrative approach that combines multi-omics data to highlight the interrelationships of the involved biomolecules and their functions. With the advent of high-throughput techniques and availability of multi-omics data generated from a large set of samples, several promising tools and methods have been developed for data integration and interpretation. In this review, we collected the tools and methods that adopt integrative approach to analyze multiple omics data and summarized their ability to address applications such as disease subtyping, biomarker prediction, and deriving insights into the data. We provide the methodology, use-cases, and limitations of these tools; brief account of multi-omics data repositories and visualization portals; and challenges associated with multi-omics data integration.

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Hatori, Yuta, Takanori Kubo, Yuichiro Sato, Sachiye Inouye, Reiko Akagi, and Toshio Seyama. "Visualization of the Redox Status of Cytosolic Glutathione Using the Organelle- and Cytoskeleton-Targeted Redox Sensors." Antioxidants 9, no. 2 (February 3, 2020): 129. http://dx.doi.org/10.3390/antiox9020129.

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Glutathione is a small thiol-containing peptide that plays a central role in maintaining cellular redox homeostasis. Glutathione serves as a physiologic redox buffer by providing thiol electrons for catabolizing harmful oxidants and reversing oxidative effects on biomolecules. Recent evidence suggests that the balance of reduced and oxidized glutathione (GSH/GSSG) defines the redox states of Cys residues in proteins and fine-tunes their stabilities and functions. To elucidate the redox balance of cellular glutathione at subcellular resolution, a number of redox-sensitive green fluorescent protein (roGFP) variants have been developed. In this study, we constructed and functionally validated organelle- and cytoskeleton-targeted roGFP and elucidated the redox status of the cytosolic glutathione at a subcellular resolution. These new redox sensors firmly established a highly reduced redox equilibrium of cytosolic glutathione, wherein significant deviation was observed among cells. By targeting the sensor to the cytosolic and lumen sides of the Golgi membrane, we identified a prominent redox gradient across the biological membrane at the Golgi body. The results demonstrated that organelle- and cytoskeleton-targeted sensors enable the assessment of glutathione oxidation near the cytosolic surfaces of different organelle membranes.

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More, Lim, Kang, Yun, Yee, and Chang. "Asymmetric and Reduced Xanthene Fluorophores: Synthesis, Photochemical Properties, and Application to Activatable Fluorescent Probes for Detection of Nitroreductase." Molecules 24, no. 17 (September 3, 2019): 3206. http://dx.doi.org/10.3390/molecules24173206.

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Xanthene fluorophores, including fluorescein, rhodol, and rhodamines, are representative classes of fluorescent probes that have been applied in the detection and visualization of biomolecules. “Turn on” activatable fluorescent probes, that can be turned on in response to enzymatic reactions, have been developed and prepared to reduce the high background signal of “always-on” fluorescent probes. However, the development of activity-based fluorescent probes for biological applications, using simple xanthene dyes, is hampered by their inefficient synthetic methods and the difficulty of chemical modifications. We have, thus, developed a highly efficient, versatile synthetic route to developing chemically more stable reduced xanthene fluorophores, based on fluorescein, rhodol, and rhodamine via continuous Pd-catalyzed cross-coupling. Their fluorescent nature was evaluated by monitoring fluorescence with variation in the concentration, pH, and solvent. As an application to activatable fluorescent probe, nitroreductase (NTR)-responsive fluorescent probes were also developed using the reduced xanthene fluorophores, and their fluorogenic properties were evaluated.

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Nieves, Daniel, Katharina Gaus, and Matthew Baker. "DNA-Based Super-Resolution Microscopy: DNA-PAINT." Genes 9, no. 12 (December 11, 2018): 621. http://dx.doi.org/10.3390/genes9120621.

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Super-resolution microscopies, such as single molecule localization microscopy (SMLM), allow the visualization of biomolecules at the nanoscale. The requirement to observe molecules multiple times during an acquisition has pushed the field to explore methods that allow the binding of a fluorophore to a target. This binding is then used to build an image via points accumulation for imaging nanoscale topography (PAINT), which relies on the stochastic binding of a fluorescent ligand instead of the stochastic photo-activation of a permanently bound fluorophore. Recently, systems that use DNA to achieve repeated, transient binding for PAINT imaging have become the cutting edge in SMLM. Here, we review the history of PAINT imaging, with a particular focus on the development of DNA-PAINT. We outline the different variations of DNA-PAINT and their applications for imaging of both DNA origamis and cellular proteins via SMLM. Finally, we reflect on the current challenges for DNA-PAINT imaging going forward.

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Turcan, Alistair, Anna Zivkovic, Dylan Thompson, Lorraine Wong, Lauren Johnson, and Filip Jagodzinski. "CGRAP: A Web Server for Coarse-Grained Rigidity Analysis of Proteins." Symmetry 13, no. 12 (December 12, 2021): 2401. http://dx.doi.org/10.3390/sym13122401.

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Elucidating protein rigidity offers insights about protein conformational changes. An understanding of protein motion can help speed drug development, and provide general insights into the dynamic behaviors of biomolecules. Existing rigidity analysis techniques employ fine-grained, all-atom modeling, which has a costly run-time, particularly for proteins made up of more than 500 residues. In this work, we introduce coarse-grained rigidity analysis, and showcase that it provides flexibility information about a protein that is similar in accuracy to an all-atom modeling approach. We assess the accuracy of the coarse-grained method relative to an all-atom approach via a comparison metric that reasons about the largest rigid clusters of the two methods. The apparent symmetry between the all-atom and coarse-grained methods yields very similar results, but the coarse-grained method routinely exhibits 40% reduced run-times. The CGRAP web server outputs rigid cluster information, and provides data visualization capabilities, including a interactive protein visualizer.

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Usama, Syed Muhammad, Sierra C. Marker, Servando Hernandez Vargas, Solmaz AghaAmiri, Sukhen C. Ghosh, Naruhiko Ikoma, Hop S. Tran Cao, Martin J. Schnermann, and Ali Azhdarinia. "Targeted Dual-Modal PET/SPECT-NIR Imaging: From Building Blocks and Construction Strategies to Applications." Cancers 14, no. 7 (March 23, 2022): 1619. http://dx.doi.org/10.3390/cancers14071619.

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Molecular imaging is an emerging non-invasive method to qualitatively and quantitively visualize and characterize biological processes. Among the imaging modalities, PET/SPECT and near-infrared (NIR) imaging provide synergistic properties that result in deep tissue penetration and up to cell-level resolution. Dual-modal PET/SPECT-NIR agents are commonly combined with a targeting ligand (e.g., antibody or small molecule) to engage biomolecules overexpressed in cancer, thereby enabling selective multimodal visualization of primary and metastatic tumors. The use of such agents for (i) preoperative patient selection and surgical planning and (ii) intraoperative FGS could improve surgical workflow and patient outcomes. However, the development of targeted dual-modal agents is a chemical challenge and a topic of ongoing research. In this review, we define key design considerations of targeted dual-modal imaging from a topological perspective, list targeted dual-modal probes disclosed in the last decade, review recent progress in the field of NIR fluorescent probe development, and highlight future directions in this rapidly developing field.

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Ribrioux, S., G. Kleymann, W. Haase, K. Heitmann, C. Ostermeier, and H. Michel. "Use of nanogold- and fluorescent-labeled antibody Fv fragments in immunocytochemistry." Journal of Histochemistry & Cytochemistry 44, no. 3 (March 1996): 207–13. http://dx.doi.org/10.1177/44.3.8648079.

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Recombinant antibody fragments are emerging as a versatile tool in both basic research and medical therapy. We describe the procedures for direct labeling of engineered antibody fragments (Fv) with fluorescein or nanogold and their use in fluorescence and immunoelectron microscopy, respectively. The Fv fragments were produced in Escherichia coli, purified by one-step Strep tag affinity chromatography, chemically labeled with the marker, and employed in microscopy to localize epitopes on the membrane protein bacteriorhodopsin in purple membranes of Halobacterium halobium and the cytochrome c oxidase of Paracoccus denitrificans. In both cases, methods involving directly labeled antibody fragments show results identical to those in which antibodies or Fv fragments are detected by a secondarily labeled conjugate. The multifunctional design of the recombinant Fv fragments, however, offers more all-around applications in immunocytochemistry. The directly labeled Fv fragments, half the size of an Fab fragment, are at the molecular level the smallest antibody fragments yet described for visualization of biomolecules in microscopy.

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Ohkubo, Tatsunari, Takaaki Shiina, Kayoko Kawaguchi, Daisuke Sasaki, Rena Inamasu, Yue Yang, Zhuoqi Li, et al. "Visualizing Intramolecular Dynamics of Membrane Proteins." International Journal of Molecular Sciences 23, no. 23 (November 22, 2022): 14539. http://dx.doi.org/10.3390/ijms232314539.

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Membrane proteins play important roles in biological functions, with accompanying allosteric structure changes. Understanding intramolecular dynamics helps elucidate catalytic mechanisms and develop new drugs. In contrast to the various technologies for structural analysis, methods for analyzing intramolecular dynamics are limited. Single-molecule measurements using optical microscopy have been widely used for kinetic analysis. Recently, improvements in detectors and image analysis technology have made it possible to use single-molecule determination methods using X-rays and electron beams, such as diffracted X-ray tracking (DXT), X-ray free electron laser (XFEL) imaging, and cryo-electron microscopy (cryo-EM). High-speed atomic force microscopy (HS-AFM) is a scanning probe microscope that can capture the structural dynamics of biomolecules in real time at the single-molecule level. Time-resolved techniques also facilitate an understanding of real-time intramolecular processes during chemical reactions. In this review, recent advances in membrane protein dynamics visualization techniques were presented.

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Chatterjee, Sankar, and Surya Yadav. "The Coevolution of Biomolecules and Prebiotic Information Systems in the Origin of Life: A Visualization Model for Assembling the First Gene." Life 12, no. 6 (June 2, 2022): 834. http://dx.doi.org/10.3390/life12060834.

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Prebiotic information systems exist in three forms: analog, hybrid, and digital. The Analog Information System (AIS), manifested early in abiogenesis, was expressed in the chiral selection, nucleotide formation, self-assembly, polymerization, encapsulation of polymers, and division of protocells. It created noncoding RNAs by polymerizing nucleotides that gave rise to the Hybrid Information System (HIS). The HIS employed different species of noncoding RNAs, such as ribozymes, pre-tRNA and tRNA, ribosomes, and functional enzymes, including bridge peptides, pre-aaRS, and aaRS (aminoacyl-tRNA synthetase). Some of these hybrid components build the translation machinery step-by-step. The HIS ushered in the Digital Information System (DIS), where tRNA molecules become molecular architects for designing mRNAs step-by-step, employing their two distinct genetic codes. First, they created codons of mRNA by the base pair interaction (anticodon–codon mapping). Secondly, each charged tRNA transferred its amino acid information to the corresponding codon (codon–amino acid mapping), facilitated by an aaRS enzyme. With the advent of encoded mRNA molecules, the first genes emerged before DNA. With the genetic memory residing in the digital sequences of mRNA, a mapping mechanism was developed between each codon and its cognate amino acid. As more and more codons ‘remembered’ their respective amino acids, this mapping system developed the genetic code in their memory bank. We compared three kinds of biological information systems with similar types of human-made computer systems.

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Zhang, Delong, Chen Li, Chi Zhang, Mikhail N. Slipchenko, Gregory Eakins, and Ji-Xin Cheng. "Depth-resolved mid-infrared photothermal imaging of living cells and organisms with submicrometer spatial resolution." Science Advances 2, no. 9 (September 2016): e1600521. http://dx.doi.org/10.1126/sciadv.1600521.

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Chemical contrast has long been sought for label-free visualization of biomolecules and materials in complex living systems. Although infrared spectroscopic imaging has come a long way in this direction, it is thus far only applicable to dried tissues because of the strong infrared absorption by water. It also suffers from low spatial resolution due to long wavelengths and lacks optical sectioning capabilities. We overcome these limitations through sensing vibrational absorption–induced photothermal effect by a visible laser beam. Our mid-infrared photothermal (MIP) approach reached 10 μM detection sensitivity and submicrometer lateral spatial resolution. This performance has exceeded the diffraction limit of infrared microscopy and allowed label-free three-dimensional chemical imaging of live cells and organisms. Distributions of endogenous lipid and exogenous drug inside single cells were visualized. We further demonstrated in vivo MIP imaging of lipids and proteins inCaenorhabditis elegans. The reported MIP imaging technology promises broad applications from monitoring metabolic activities to high-resolution mapping of drug molecules in living systems, which are beyond the reach of current infrared microscopy.

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Lomelino, Carrie L., Jacob T. Andring, and Robert McKenna. "Crystallography and Its Impact on Carbonic Anhydrase Research." International Journal of Medicinal Chemistry 2018 (September 13, 2018): 1–21. http://dx.doi.org/10.1155/2018/9419521.

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X-ray and neutron crystallography are powerful techniques utilized to study the structures of biomolecules. Visualization of enzymes in complex with substrate/product and the capture of intermediate states can be related to activity to facilitate understanding of the catalytic mechanism. Subsequent analysis of small molecule binding within the enzyme active site provides insight into mechanisms of inhibition, supporting the design of novel inhibitors using a structure-guided approach. The first X-ray crystal structures were determined for small, ubiquitous enzymes such as carbonic anhydrase (CA). CAs are a family of zinc metalloenzymes that catalyze the hydration of CO2, producing HCO3- and a proton. The CA structure and ping-pong mechanism have been extensively studied and are well understood. Though the function of CA plays an important role in a variety of physiological functions, CA has also been associated with diseases such as glaucoma, edema, epilepsy, obesity, and cancer and is therefore recognized as a drug target. In this review, a brief history of crystallography and its impact on CA research is discussed.

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G.*, Bhusnure O., Gholve V. S., Sugave B. K., Dongre R. C., Gore S. A., and Giram P. S. "3D Printing & Pharmaceutical Manufacturing: Opportunities and Challenges." International Journal of Bioassays 5, no. 01 (January 1, 2016): 4723. http://dx.doi.org/10.21746/ijbio.2016.01.006.

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Many researchers have attempted to use computer-aided design (C.A.D) and computer-aided manufacturing (CAM) to realize a scaffold that provides a three-dimensional (3D) environment for regeneration of tissues and organs. As a result, several 3D printing technologies, including stereolithography, deposition modeling, inkjet-based printing and selective laser sintering have been developed. Because these 3D printing technologies use computers for design and fabrication, and they can fabricate 3D scaffolds as designed; as a consequence, they can be standardized. Growth of target tissues and organs requires the presence of appropriate growth factors, so fabrication of 3Dscaffold systems that release these biomolecules has been explored. A drug delivery system (D.D.S) that administrates a pharmaceutical compound to achieve a therapeutic effect in cells, animals and humans is a key technology that delivers biomolecules without side effects caused by excessive doses. 3D printing technologies and D. D. Ss have been assembled successfully, so new possibilities for improved tissue regeneration have been suggested. If the interaction between cells and scaffold system with biomolecules can be understood and controlled, and if an optimal 3D tissue regenerating environment is realized, 3D printing technologies will become an important aspect of tissue engineering research in the near future. 3D Printing promises to produce complex biomedical devices according to computer design using patient-specific anatomical data. Since its initial use as pre-surgical visualization models and tooling molds, 3D Printing has slowly evolved to create one-of-a-kind devices, implants, scaffolds for tissue engineering, diagnostic platforms, and drug delivery systems. Fuelled by the recent explosion in public interest and access to affordable printers, there is renewed interest to combine stem cells with custom 3D scaffolds for personalized regenerative medicine. Before 3D Printing can be used routinely for the regeneration of complex tissues (e.g. bone, cartilage, muscles, vessels, nerves in the craniomaxillofacial complex), and complex organs with intricate 3D microarchitecture (e.g. liver, lymphoid organs), several technological limitations must be addressed. Until recently, tablet designs had been restricted to the relatively small number of shapes that are easily achievable using traditional manufacturing methods. As 3D printing capabilities develop further, safety and regulatory concerns are addressed and the cost of the technology falls, contract manufacturers and pharmaceutical companies that experiment with these 3D printing innovations are likely to gain a competitive edge. This review compose the basics, types & techniques used, advantages and disadvantages of 3D printing

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Sroyraya, Morakot, Naoko Goto-Inoue, Nobuhiro Zaima, Takahiro Hayasaka, Piyachat Chansela, Supita Tanasawet, Kamlesh Shrivas, Prasert Sobhon, and Mitsutoshi Setou. "Visualization of biomolecules in the eyestalk of the blue swimming crab, Portunus pelagicus , by imaging mass spectrometry using the atmospheric-pressure mass microscope." Surface and Interface Analysis 42, no. 10-11 (June 1, 2010): 1589–92. http://dx.doi.org/10.1002/sia.3571.

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Janus, Łukasz, Julia Radwan-Pragłowska, Marek Piątkowski, and Dariusz Bogdał. "Coumarin-Modified CQDs for Biomedical Applications—Two-Step Synthesis and Characterization." International Journal of Molecular Sciences 21, no. 21 (October 29, 2020): 8073. http://dx.doi.org/10.3390/ijms21218073.

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Waste biomass such as lignin constitutes a great raw material for eco-friendly carbon quantum dots (CQDs) synthesis, which find numerous applications in various fields of industry and medicine. Carbon nanodots, due to their unique luminescent properties as well as water-solubility and biocompatibility, are superior to traditional organic dyes. Thus, obtainment of CQDs with advanced properties can contribute to modern diagnosis and cell visualization method development. In this article, a new type of coumarin-modified CQD was obtained via a hybrid, two-step pathway consisting of hydrothermal carbonization and microwave-assisted surface modification with coumarin-3-carboxylic acid and 7-(Diethylamino) coumarin-3-carboxylate. The ready products were characterized over their chemical structure and morphology. The nanomaterials were confirmed to have superior fluorescence characteristics and quantum yield up to 18.40%. They also possessed the ability of biomolecules and ion detection due to the fluorescence quenching phenomena. Their lack of cytotoxicity to L929 mouse fibroblasts was confirmed by XTT assay. Moreover, the CQDs were proven over their applicability in real-time bioimaging. Obtained results clearly demonstrated that proposed surface-modified carbon quantum dots may become a powerful tool applicable in nanomedicine and pharmacy.

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Ovechkina, Vera S., Suren M. Zakian, Sergey P. Medvedev, and Kamila R. Valetdinova. "Genetically Encoded Fluorescent Biosensors for Biomedical Applications." Biomedicines 9, no. 11 (October 24, 2021): 1528. http://dx.doi.org/10.3390/biomedicines9111528.

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One of the challenges of modern biology and medicine is to visualize biomolecules in their natural environment, in real-time and in a non-invasive fashion, so as to gain insight into their physiological behavior and highlight alterations in pathological settings, which will enable to devise appropriate therapeutic strategies. Genetically encoded fluorescent biosensors constitute a class of imaging agents that enable visualization of biological processes and events directly in situ, preserving the native biological context and providing detailed insight into their localization and dynamics in cells. Real-time monitoring of drug action in a specific cellular compartment, organ, or tissue type; the ability to screen at the single-cell resolution; and the elimination of false-positive results caused by low drug bioavailability that is not detected by in vitro testing methods are a few of the obvious benefits of using genetically encoded fluorescent biosensors in drug screening. This review summarizes results of the studies that have been conducted in the last years toward the fabrication of genetically encoded fluorescent biosensors for biomedical applications with a comprehensive discussion on the challenges, future trends, and potential inputs needed for improving them.

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Chaudhary, Ankita, and Jitender M. Khurana. "Advances in the Synthesis of Xanthenes: An Overview." Current Organic Synthesis 15, no. 3 (April 27, 2018): 341–69. http://dx.doi.org/10.2174/1570179414666171011162902.

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Background: Xanthene is pharmacologically important oxygen containing heterocyclic moeity exhibiting an array of potent biological activities like antibacterial, antiviral, antiinflammatory, antitumor, antioxidant, antiplasmodial etc. Other useful applications of these heterocycles are as fluorescent materials for the visualization of biomolecules and in laser technology. Objective: This review gives an insight of the literature available on the methods for the construction of xanthene nucleus. This review article can be reasonably encouraging for those involved in the synthesis of molecules exhibiting a wide range of biological activities involving xanthene as central nucleus and would provide them assistance in developing new eco-friendly, efficient and economical viable methods. Conclusion: Owing to diverse applications of xanthenes, various synthetic methodologies have been developed, whether to construct this privileged scaffold. Many of the reported methods involve the use of various harsh catalysts/reagents that are not environmentally benign, produce a large amount of waste and need longer reaction times. The sustainable and diversity oriented synthesis of xanthene scaffold which incorporates Green Chemistry tools like multicomponent reaction approach, heterogeneous catalysts, alternate reaction media such as water, ionic liquids, polyethylene glycol etc. has also been developed.

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DOI, Junta. "Biomolecular Visualization." Journal of the Visualization Society of Japan 10, no. 39 (1990): 222–27. http://dx.doi.org/10.3154/jvs.10.222.

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Marcuello, Carlos. "Current and future perspectives of atomic force microscopy to elicit the intrinsic properties of soft matter at the single molecule level." AIMS Bioengineering 9, no. 3 (2022): 293–306. http://dx.doi.org/10.3934/bioeng.2022020.

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<abstract> <p>Soft matter encompasses multitude of systems like biomolecules, living cells, polymers, composites or blends. The increasing interest to better understand their physico-chemical properties has significantly favored the development of new techniques with unprecedented resolution. In this framework, atomic force microscopy (AFM) can act as one main actor to address multitude of intrinsic sample characteristics at the nanoscale level. AFM presents many advantages in comparison to other bulk techniques as the assessment of individual entities discharging thus, ensemble averaging phenomena. Moreover, AFM enables the visualization of singular events that eventually can provide response of some open questions that still remain unclear. The present manuscript aims to make the reader aware of the potential applications in the employment of this tool by providing recent examples of scientific studies where AFM has been employed with success. Several operational modes like AFM imaging, AFM based force spectroscopy (AFM-FS), nanoindentation, AFM-nanoscale infrared spectroscopy (AFM-nanoIR) or magnetic force microscopy (MFM) will be fully explained to detail the type of information that AFM is capable to gather. Finally, future prospects will be delivered to discern the following steps to be conducted in this field.</p> </abstract>

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Di Bella, Maria Antonietta. "Overview and Update on Extracellular Vesicles: Considerations on Exosomes and Their Application in Modern Medicine." Biology 11, no. 6 (May 24, 2022): 804. http://dx.doi.org/10.3390/biology11060804.

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In recent years, there has been a rapid growth in the knowledge of cell-secreted extracellular vesicle functions. They are membrane enclosed and loaded with proteins, nucleic acids, lipids, and other biomolecules. After being released into the extracellular environment, some of these vesicles are delivered to recipient cells; consequently, the target cell may undergo physiological or pathological changes. Thus, extracellular vesicles as biological nano-carriers, have a pivotal role in facilitating long-distance intercellular communication. Understanding the mechanisms that mediate this communication process is important not only for basic science but also in medicine. Indeed, extracellular vesicles are currently seen with immense interest in nanomedicine and precision medicine for their potential use in diagnostic, prognostic, and therapeutic applications. This paper aims to summarize the latest advances in the study of the smallest subtype among extracellular vesicles, the exosomes. The article is divided into several sections, focusing on exosomes’ nature, characteristics, and commonly used strategies and methodologies for their separation, characterization, and visualization. By searching an extended portion of the relevant literature, this work aims to give a quick outline of advances in exosomes’ extensive nanomedical applications. Moreover, considerations that require further investigations before translating them to clinical applications are summarized.

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Isaiev, Mykola, Gauhar Mussabek, Pavlo Lishchuk, Kateryna Dubyk, Nazym Zhylkybayeva, Gulmira Yar-Mukhamedova, David Lacroix, and Vladimir Lysenko. "Application of the Photoacoustic Approach in the Characterization of Nanostructured Materials." Nanomaterials 12, no. 4 (February 21, 2022): 708. http://dx.doi.org/10.3390/nano12040708.

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A new generation of sensors can be engineered based on the sensing of several markers to satisfy the conditions of the multimodal detection principle. From this point of view, photoacoustic-based sensing approaches are essential. The photoacoustic effect relies on the generation of light-induced deformation (pressure) perturbations in media, which is essential for sensing applications since the photoacoustic response is formed due to a contrast in the optical, thermal, and acoustical properties. It is also particularly important to mention that photoacoustic light-based approaches are flexible enough for the measurement of thermal/elastic parameters. Moreover, the photoacoustic approach can be used for imaging and visualization in material research and biomedical applications. The advantages of photoacoustic devices are their compact sizes and the possibility of on-site measurements, enabling the online monitoring of material parameters. The latter has significance for the development of various sensing applications, including biomedical ones, such as monitoring of the biodistribution of biomolecules. To extend sensing abilities and to find reliable measurement conditions, one needs to clearly understand all the phenomena taking place during energy transformation during photoacoustic signal formation. Therefore, the current paper is devoted to an overview of the main measurement principles used in the photoacoustic setup configurations, with a special focus on the key physical parameters.

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Hombu, Ryoma, Sriram Neelamegham, and Sheldon Park. "Cellular and Molecular Engineering of Glycan Sialylation in Heterologous Systems." Molecules 26, no. 19 (September 30, 2021): 5950. http://dx.doi.org/10.3390/molecules26195950.

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Glycans have been shown to play a key role in many biological processes, such as signal transduction, immunogenicity, and disease progression. Among the various glycosylation modifications found on cell surfaces and in biomolecules, sialylation is especially important, because sialic acids are typically found at the terminus of glycans and have unique negatively charged moieties associated with cellular and molecular interactions. Sialic acids are also crucial for glycosylated biopharmaceutics, where they promote stability and activity. In this regard, heterogenous sialylation may produce variability in efficacy and limit therapeutic applications. Homogenous sialylation may be achieved through cellular and molecular engineering, both of which have gained traction in recent years. In this paper, we describe the engineering of intracellular glycosylation pathways through targeted disruption and the introduction of carbohydrate active enzyme genes. The focus of this review is on sialic acid-related genes and efforts to achieve homogenous, humanlike sialylation in model hosts. We also discuss the molecular engineering of sialyltransferases and their application in chemoenzymatic sialylation and sialic acid visualization on cell surfaces. The integration of these complementary engineering strategies will be useful for glycoscience to explore the biological significance of sialic acids on cell surfaces as well as the future development of advanced biopharmaceuticals.

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Chakrabarty, Broto, Varun Naganathan, Kanak Garg, Yash Agarwal, and Nita Parekh. "NAPS update: network analysis of molecular dynamics data and protein–nucleic acid complexes." Nucleic Acids Research 47, W1 (May 20, 2019): W462—W470. http://dx.doi.org/10.1093/nar/gkz399.

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Abstract Network theory is now a method of choice to gain insights in understanding protein structure, folding and function. In combination with molecular dynamics (MD) simulations, it is an invaluable tool with widespread applications such as analyzing subtle conformational changes and flexibility regions in proteins, dynamic correlation analysis across distant regions for allosteric communications, in drug design to reveal alternative binding pockets for drugs, etc. Updated version of NAPS now facilitates network analysis of the complete repertoire of these biomolecules, i.e., proteins, protein–protein/nucleic acid complexes, MD trajectories, and RNA. Various options provided for analysis of MD trajectories include individual network construction and analysis of intermediate time-steps, comparative analysis of these networks, construction and analysis of average network of the ensemble of trajectories and dynamic cross-correlations. For protein–nucleic acid complexes, networks of the whole complex as well as that of the interface can be constructed and analyzed. For analysis of proteins, protein–protein complexes and MD trajectories, network construction based on inter-residue interaction energies with realistic edge-weights obtained from standard force fields is provided to capture the atomistic details. Updated version of NAPS also provides improved visualization features, interactive plots and bulk execution. URL: http://bioinf.iiit.ac.in/NAPS/

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Hun, Tingting, Yi Zhang, Qingmei Xu, Dong Huang, Qi Wang, Zhihong Li, and Wei Wang. "In Situ Electroporation on PERFECT Filter for High-Efficiency and High-Viability Tumor Cell Labeling." Micromachines 13, no. 5 (April 26, 2022): 672. http://dx.doi.org/10.3390/mi13050672.

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Labeling-assisted visualization is a powerful strategy to track circulating tumor cells (CTCs) for mechanism study (e.g., tumor metastasis). Due to the rarity of CTCs in the whole blood, efficient simultaneous enrichment and labeling of CTCs are needed. Hereby, novel in situ electroporation on a previously-developed micropore-arrayed filter (PERFECT filter) is proposed. Benefiting from the ultra-small-thickness and high-porosity of the filter plus high precision pore diameter, target rare tumor cells were enriched with less damage and uniform size distribution, contributing to enhanced molecular delivery efficiency and cell viability in the downstream electroporation. Various biomolecules (e.g., small molecule dyes, plasmids, and functional proteins) were used to verify this in situ electroporation system. High labeling efficiency (74.08 ± 2.94%) and high viability (81.15 ± 3.04%, verified via live/dead staining) were achieved by optimizing the parameters of electric field strength and pulse number, ensuring the labeled tumor cells can be used for further culture and down-stream analysis. In addition, high specificity (99.03 ± 1.67%) probing of tumor cells was further achieved by introducing fluorescent dye-conjugated antibodies into target cells. The whole procedure, including cell separation and electroporation, can be finished quickly (<10 min). The proposed in situ electroporation on the PERFECT filter system has great potential to track CTCs for tumor metastasis studies.

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Hun, Tingting, Yi Zhang, Qingmei Xu, Dong Huang, Qi Wang, Zhihong Li, and Wei Wang. "In Situ Electroporation on PERFECT Filter for High-Efficiency and High-Viability Tumor Cell Labeling." Micromachines 13, no. 5 (April 26, 2022): 672. http://dx.doi.org/10.3390/mi13050672.

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Labeling-assisted visualization is a powerful strategy to track circulating tumor cells (CTCs) for mechanism study (e.g., tumor metastasis). Due to the rarity of CTCs in the whole blood, efficient simultaneous enrichment and labeling of CTCs are needed. Hereby, novel in situ electroporation on a previously-developed micropore-arrayed filter (PERFECT filter) is proposed. Benefiting from the ultra-small-thickness and high-porosity of the filter plus high precision pore diameter, target rare tumor cells were enriched with less damage and uniform size distribution, contributing to enhanced molecular delivery efficiency and cell viability in the downstream electroporation. Various biomolecules (e.g., small molecule dyes, plasmids, and functional proteins) were used to verify this in situ electroporation system. High labeling efficiency (74.08 ± 2.94%) and high viability (81.15 ± 3.04%, verified via live/dead staining) were achieved by optimizing the parameters of electric field strength and pulse number, ensuring the labeled tumor cells can be used for further culture and down-stream analysis. In addition, high specificity (99.03 ± 1.67%) probing of tumor cells was further achieved by introducing fluorescent dye-conjugated antibodies into target cells. The whole procedure, including cell separation and electroporation, can be finished quickly (<10 min). The proposed in situ electroporation on the PERFECT filter system has great potential to track CTCs for tumor metastasis studies.

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Méndez, Lucía, Silvia Muñoz, Bernat Miralles-Pérez, Maria Rosa Nogués, Sara Ramos-Romero, Josep Lluis Torres, and Isabel Medina. "Modulation of the Liver Protein Carbonylome by the Combined Effect of Marine Omega-3 PUFAs and Grape Polyphenols Supplementation in Rats Fed an Obesogenic High Fat and High Sucrose Diet." Marine Drugs 18, no. 1 (December 30, 2019): 34. http://dx.doi.org/10.3390/md18010034.

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Diet-induced obesity has been linked to metabolic disorders such as cardiovascular diseases and type 2 diabetes. A factor linking diet to metabolic disorders is oxidative stress, which can damage biomolecules, especially proteins. The present study was designed to investigate the effect of marine omega-3 polyunsaturated fatty acids (PUFAs) (eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)) and their combination with grape seed polyphenols (GSE) on carbonyl-modified proteins from plasma and liver in Wistar Kyoto rats fed an obesogenic diet, namely high-fat and high-sucrose (HFHS) diet. A proteomics approach consisting of fluorescein 5-thiosemicarbazide (FTSC) labelling of protein carbonyls, visualization of FTSC-labelled protein on 1-DE or 2-DE gels, and protein identification by MS/MS was used for the protein oxidation assessment. Results showed the efficiency of the combination of both bioactive compounds in decreasing the total protein carbonylation induced by HFHS diet in both plasma and liver. The analysis of carbonylated protein targets, also referred to as the ‘carbonylome’, revealed an individual response of liver proteins to supplements and a modulatory effect on specific metabolic pathways and processes due to, at least in part, the control exerted by the supplements on the liver protein carbonylome. This investigation highlights the additive effect of dietary fish oils and grape seed polyphenols in modulating in vivo oxidative damage of proteins induced by the consumption of HFHS diets.

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Journal articles on the topic 'Biomolecules visualization'

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