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1. Mapping Structural Dynamics of Proteins with Femtosecond Stimulated Raman Spectroscopy

   https://doi.org/10.1146/annurev-physchem-071119-040154  

   Fang, Chong ; Tang, Longteng ( April 2020 , Annual Review of Physical Chemistry)

   The structure–function relationships of biomolecules have captured the interest and imagination of the scientific community and general public since the field of structural biology emerged to enable the molecular understanding of life processes. Proteins that play numerous functional roles in cellular processes have remained in the forefront of research, inspiring new characterization techniques. In this review, we present key theoretical concepts and recent experimental strategies using femtosecond stimulated Raman spectroscopy (FSRS) to map the structural dynamics of proteins, highlighting the flexible chromophores on ultrafast timescales. In particular, wavelength-tunable FSRS exploits dynamic resonance conditions to track transient-species-dependent vibrational motions, enabling rational design to alter functions. Various ways of capturing excited-state chromophore structural snapshots in the time and/or frequency domains are discussed. Continuous development of experimental methodologies, synergistic correlation with theoretical modeling, and the expansion to other nonequilibrium, photoswitchable, and controllable protein systems will greatly advance the chemical, physical, and biological sciences. 

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2. Example of Adverse Outcome Pathway Concept Enabling Genome-to-Phenome Discovery in Toxicology

   https://doi.org/10.1093/icb/icaa064  

   Gust, Kurt A ; Ji, Qing ; Luo, Xiao ( June 2020 , Integrative and Comparative Biology)

   Synopsis The following article represents a mini-review of an intensive 10-year progression of genome-to-phenome (G2P) discovery guided by the adverse outcome pathway (AOP) concept. This example is presented as a means to stimulate crossover of this toxicological concept to enhance G2P discovery within the broader biological sciences community. The case study demonstrates the benefits of the AOP approach for establishing causal linkages across multiple levels of biological organization ultimately linking molecular initiation (often at the genomic scale) to organism-level phenotypes of interest. The case study summarizes a US military effort to identify the mechanism(s) underlying toxicological phenotypes of lethargy and weight loss in response to nitroaromatic munitions exposures, such as 2,4,6-trinitrotoluene. Initial key discoveries are described including the toxicogenomic results that nitrotoluene exposures inhibited expression within the peroxisome proliferator activated receptor α (PPARα) pathway. We channeled the AOP concept to test the hypothesis that inhibition of PPARα signaling in nitrotoluene exposures impacted lipid metabolic processes, thus affecting systemic energy budgets, ultimately resulting in body weight loss. Results from a series of transcriptomic, proteomic, lipidomic, in vitro PPARα nuclear signaling, and PPARα knock-out investigations ultimately supported various facets of this hypothesis. Given these results, we next proceeded to develop a formalized AOP description of PPARα antagonism leading to body weight loss. This AOP was refined through intensive literature review and polished through multiple rounds of peer-review leading to final international acceptance as an Organisation for Economic Cooperation and Development-approved AOP. Briefly, that AOP identifies PPARα antagonist binding as the molecular initiating event (MIE) leading to a series of key events including inhibition of nuclear transactivation for genes controlling lipid metabolism and ketogenesis, inhibition of fatty acid beta-oxidation and ketogenesis dynamics, negative energy budget, and ultimately the adverse outcome (AO) of body-weight loss. Given that the PPARα antagonism MIE represented a reliable indicator of AO progression within the pathway, a phylogenetic analysis was conducted which indicated that PPARα amino acid relatedness generally tracked species relatedness. Additionally, PPARα amino acid relatedness analysis using the Sequence Alignment to Predict Across Species Susceptibility predicted susceptibility to the MIE across vertebrates providing context for AOP extrapolation across species. Overall, we hope this illustrative example of how the AOP concept has benefited toxicology sows a seed within the broader biological sciences community to repurpose the concept to facilitate enhanced G2P discovery in biology. 

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3. In Vitro Assay for Single-cell Characterization of Impaired Deformability in Red Blood Cells under Recurrent Episodes of Hypoxia

   https://doi.org/10.1039/D1LC00598G  

   QIANG, YUHAO ; Liu, Jia ; Dao, Ming ; Du, E ( January 2021 , Lab on a Chip)

   null (Ed.)

   Red blood cells (RBCs) are subjected to recurrent changes in shear stress and oxygen tension during blood circulation. The cyclic shear stress has been identified as an important factor that alone can weaken cell mechanical deformability. The effects of cyclic hypoxia on cellular biomechanics have yet to be fully investigated. As the oxygen affinity of hemoglobin plays a key role in the biological function and mechanical performance of RBCs, the repeated transitions of hemoglobin between its R (high oxygen tension) and T (low oxygen tension) states may impact their mechanical behavior. The present study focuses on developing a novel microfluidics-based assay for characterization of the effect of cyclic hypoxia on cell biomechanics. The capability of this assay is demonstrated by a longitudinal study of individual RBCs in health and sickle cell disease subjected to cyclic hypoxia conditions of various durations and levels of low oxygen tension. Viscoelastic properties of cell membranes are extracted from tensile stretching and relaxation processes of RBCs induced by the electrodeformation technique. Results demonstrate that cyclic hypoxia alone can significantly reduce cell deformability, similar to the fatigue damage accumulated through cyclic mechanical loading. RBCs affected by sickle cell disease are less deformable (significantly higher membrane shear modulus and viscosity) than normal RBCs. The fatigue resistance of sickle RBCs to the cyclic hypoxia challenge is significantly inferior to normal RBCs, and this trend is more significant in mature erythrocytes of sickle cells. When oxygen affinity of sickle hemoglobin is enhanced by anti-sickling drug treatment of 5-hydroxymethyl-2-furfural (5-HMF), sickle RBCs show ameliorated resistance to fatigue damage induced by cyclic hypoxia. These results illustrate that an important biophysical mechanism underlying RBC senescence in which cyclic hypoxia challenge alone can lead to mechanical degradation of the RBC membrane. We envision the application of this assay can be further extended to RBCs in other blood diseases and other types of cells. 

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4. Quantifying and controlling bond multivalency for advanced nanoparticle targeting to cells

   https://doi.org/10.1186/s40580-021-00288-1  

   Makhani, Elliot Y. ; Zhang, Ailin ; Haun, Jered B. ( November 2021 , Nano Convergence)

   Nanoparticles have drawn intense interest as delivery agents for diagnosing and treating various cancers. Much of the early success was driven by passive targeting mechanisms such as the enhanced permeability and retention (EPR) effect, but this has failed to lead to the expected clinical successes. Active targeting involves binding interactions between the nanoparticle and cancer cells, which promotes tumor cell-specific accumulation and internalization. Furthermore, nanoparticles are large enough to facilitate multiple bond formation, which can improve adhesive properties substantially in comparison to the single bond case. While multivalent binding is universally believed to be an attribute of nanoparticles, it is a complex process that is still poorly understood and difficult to control. In this review, we will first discuss experimental studies that have elucidated roles for parameters such as nanoparticle size and shape, targeting ligand and target receptor densities, and monovalent binding kinetics on multivalent nanoparticle adhesion efficiency and cellular internalization. Although such experimental studies are very insightful, information is limited and confounded by numerous differences across experimental systems. Thus, we focus the second part of the review on theoretical aspects of binding, including kinetics, biomechanics, and transport physics. Finally, we discuss various computational and simulation studies of nanoparticle adhesion, including advanced treatments that compare directly to experimental results. Future work will ideally continue to combine experimental data and advanced computational studies to extend our knowledge of multivalent adhesion, as well as design the most powerful nanoparticle-based agents to treat cancer.

    

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5. Time-lapse mechanical imaging of neural tube closure in live embryo using Brillouin microscopy

   https://doi.org/10.1038/s41598-023-27456-z  

   Handler, Chenchen ; Scarcelli, Giuliano ; Zhang, Jitao ( January 2023 , Scientific Reports)

   Neural tube closure (NTC) is a complex process of embryonic development involving molecular, cellular, and biomechanical mechanisms. While the genetic factors and biochemical signaling have been extensively investigated, the role of tissue biomechanics remains mostly unexplored due to the lack of tools. Here, we developed an optical modality that can conduct time-lapse mechanical imaging of neural plate tissue as the embryo is experiencing neurulation. This technique is based on the combination of a confocal Brillouin microscope and a modifiedex ovoculturing of chick embryo with an on-stage incubator. With this technique, for the first time, we captured the mechanical evolution of the neural plate tissue with live embryos. Specifically, we observed the continuous increase in tissue modulus of the neural plate during NTC forex ovocultured embryos, which is consistent with the data ofin ovoculture as well as previous studies. Beyond that, we found that the increase in tissue modulus was highly correlated with the tissue thickening and bending. We foresee this non-contact and label-free technique opening new opportunities to understand the biomechanical mechanisms in embryonic development.

    

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