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  1. Calcium ion transporting systems control cytosol Ca2+ levels ([Ca2+]cyt) and generate transient calcium (Ca2+) signatures which are considered to be key to environmental responses. Here, we report an impact of resting [Ca2+]cyt on plants from the functional study of calmodulin regulated Ca2+ pumps or Ca2+-ATPases in Arabidopsis thaliana. The plasma membrane localized pumps ACA8 and ACA10 as well as the vacuole localized pumps ACA4 and ACA11 are found to be critical in maintaining low resting [Ca2+]cyt and be essential for plant survival under chilling and heat-stress conditions. Their loss-of-function mutants aca8 aca10 and aca4 aca11 have autoimmunity at normal temperature, and this deregulated immune activation is enhanced by low temperature leading to chilling lethality. Furthermore, these two mutants have an elevated resting [Ca2+]cyt, and a reduction of external Ca2+ lowers [Ca2+]cyt and represses its autoimmunity and cold susceptibility. The aca8 aca10 and the aca4 aca11 mutants are also susceptible to heat, likely resulting from more closed stomata and higher leaf surface temperature compared to the wild type. These observations support a model in which the regulation of resting [Ca2+]cyt is critical to how plants regulate biotic and abiotic responses.
    Free, publicly-accessible full text available April 1, 2024
  2. Manual labeling of gestures in robot-assisted surgery is labor intensive, prone to errors, and requires ex- pertise or training. We propose a method for automated and explainable generation of gesture transcripts that leverages the abundance of data for image segmentation. Surgical context is detected using segmentation masks by examining the distances and intersections between the tools and objects. Next, context labels are translated into gesture transcripts using knowledge- based Finite State Machine (FSM) and data-driven Long Short Term Memory (LSTM) models. We evaluate the performance of each stage of our method by comparing the results with the ground truth segmentation masks, the consensus context labels, and the gesture labels in the JIGSAWS dataset. Our results show that our segmentation models achieve state-of-the- art performance in recognizing needle and thread in Suturing and we can automatically detect important surgical states with high agreement with crowd-sourced labels (e.g., contact between graspers and objects in Suturing). We also find that the FSM models are more robust to poor segmentation and labeling performance than LSTMs. Our proposed method can significantly shorten the gesture labeling process (∼2.8 times).
    Free, publicly-accessible full text available January 1, 2024
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  6. Dynamic allostery emphasizes a role of entropy change manifested as a sole change in protein fluctuations without structural changes. This kind of entropy-driven effect remains largely understudied. The most significant examples involve protein-ligand interactions, leaving protein-protein interactions, which are critical in signaling and other cellular events, largely unexplored. Here we study an example of how protein-protein interaction (binding of Ras to the Ras binding domain [RBD] of the effector protein Raf) affects a subsequent protein association process (Ras dimerization) by quenching Ras internal motions through dynamic allostery. We also investigate the influence of point mutations or ambient temperature, respectively, on the protein dynamics and interaction of two other systems: in adenylate kinase (ADK) and in the EphA2 SAM:Ship2 SAM complex. Based on these examples, we postulate that there are different ways in which dynamic-change-driven protein interactions are manifested and that it is likely a general biological phenomenon.
    Free, publicly-accessible full text available June 2, 2023
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