Transient absorption imaging of hemeprotein in fresh muscle fibers

2022 Summer.Includes bibliographical references.Mitochondrial diseases affect 1 in 4000 individuals in the U.S. among adults and children of all races and genders. Nevertheless, these diseases are hard to diagnose because they affect each person differently. Meanwhile the gold standard diagnosis methods are usually invasive and time- consuming. Therefore, a non-invasive and in-vivo diagnosis method is highly demanded in this area. Our goal is to develop a non-invasive diagnosis method based on the endogenous nonlinear optical effect of the live tissues. Mitochondrial disease is frequently the result of a defective electron transport chain (ETC). Our goal is to develop a non-invasive way to measure redox within the ETC, specifically, of cytochromes. Cytochromes are iron porphyrins that are essential to the ETC. Their redox states can indicate cellular oxygen consumption and mitochondrial ATP production. So being able to differentiate the redox states of cytochromes will offer us a method to characterize mitochondrial function. Meanwhile, Chergui's group found out that the two redox states of cytochrome c have different pump-probe spectroscopic responses, meaning that the transient absorption (TA) decay lifetime can be a potential molecular contrast for cytochrome redox state discrimination. Their research leads us to utilize the pump-probe spectroscopic idea to develop a time-resolved optical microscopic method to differentiate not only cytochromes from other chemical compounds but also reduced cytochromes from oxidized ones. This dissertation describes groundbreaking experiments where transient absorption is used to reveal excited-state lifetime differences between healthy controls and an animal model of mitochondrial disease, in addition to differences between reduced and oxidized ETC in isolated mitochondria and fresh preparations of muscle fibers. For our initial experiments, we built a pump-probe microscopic system with a fiber laser source, producing 530nm pump and 490nm probe using a 3.5kHz laser scanning rate. The pulse durations of pump and probe are both 800fs. For the preliminary results, we have successfully achieved TA decay contrast between reduced and oxidized cytochromes in solution form. Then we have achieved SNR enhanced pump-probe image of BGO crystal particles with the help of the software- based adaptive filter noise canceling method. We also have installed a FPGA-based adaptive filter to enhance the pump-probe signals of the electrophoresis gels that contain different mitochondrial respiratory chain supercomplexes. However, because the noise floor was still 30 dB higher than shot noise limit, cytochrome imaging in live tissues was still problematic. We then built another pump-probe microscope with a solid- state ultrafast laser source. In that way, we do not need to worry about laser relative intensity noise (RIN) anymore, since the noise floor of the solid-state laser source can reach the shot noise limit at MHz region. One other advantage of the new laser source is that it can provide one tunable laser output that can be directly converted to the probe pulse with tunable center wavelength. Its tunability can cover the entire visible spectrum. We realized a pump-probe microscopy with a 520nm pump pulse and a tunable probe pulse. The tunability on the probe arm allows us to explore better pump-probe contrast between two redox states. What's more, I will introduce my preliminary results of utilizing supercontinuum generation in a photonic crystal fiber (PCF) to realize tunability on pump wavelength. In that way, more possibilities will be unlocked. And the hyperspectral pump-probe microscope will be able to distinguish more molecules

Robustness, dissipations and coherence of the oscillation of circadian clock: potential landscape and flux perspectives

Finding the global probabilistic nature of a non-equilibrium circadian clock is essential for addressing important issues of robustness and function. We have uncovered the underlying potential energy landscape of a simple cyanobacteria biochemical network, and the corresponding flux which is the driving force for the oscillation. We found that the underlying potential landscape for the oscillation in the presence of small statistical fluctuations is like an explicit ring valley or doughnut shape in the three dimensional protein concentration space. We found that the barrier height separating the oscillation ring and other area is a quantitative measure of the oscillation robustness and decreases when the fluctuations increase. We also found that the entropy production rate characterizing the dissipation or heat loss decreases as the fluctuations decrease. In addition, we found that, as the fluctuations increase, the period and the amplitude of the oscillations is more dispersed, and the phase coherence decreases. We also found that the properties from exploring the effects of the inherent chemical rate parameters on the robustness. Our approach is quite general and can be applied to other oscillatory cellular network

Mobility of the imidazolate linkers in neat and confined ZIFs probed by 2H NMR

Significant work is being devoted to the reduction of global energy consumption associated with industrial separations, with increasing attention being focused on membrane technology. In particular, MMMs containing ZIFs are an attractive alternative to conventional thermal separation processes. However, the interaction between the ZIF fillers and polymer matrix remains unclear. We believe that the separation performance of such membranes is highly interplay-dependent, and that proper selection of materials and rational modification of the fabrication procedure will enhance membrane performance. The overarching goal of this research is to understand the polymer confining effects on the motion of imidazolate linker in polymer confined ZIF fillers. The initial work used solid-state NMR to study imidazolate linker motions in ZIF crystals. The second objective directly studied the polymer confinement effects on linker motion in neat and confined ZIF crystals through 2H solid echo line shape analysis and T1 relaxation time analysis. The third objective focused on the experimental demonstration of different transport properties of ZIF crystals in neat and confined environments.M.S

Exploration of Multi-State Conformational Dynamics and Underlying Global Functional Landscape of Maltose Binding Protein

An increasing number of biological machines have been revealed to have more than two macroscopic states. Quantifying the underlying multiple-basin functional landscape is essential for understanding their functions. However, the present models seem to be insufficient to describe such multiple-state systems. To meet this challenge, we have developed a coarse grained triple-basin structure-based model with implicit ligand. Based on our model, the constructed functional landscape is sufficiently sampled by the brute-force molecular dynamics simulation. We explored maltose-binding protein (MBP) which undergoes large-scale domain motion between open, apo-closed (partially closed) and holo-closed (fully closed) states responding to ligand binding. We revealed an underlying mechanism whereby major induced fit and minor population shift pathways co-exist by quantitative flux analysis. We found that the hinge regions play an important role in the functional dynamics as well as that increases in its flexibility promote population shifts. This finding provides a theoretical explanation of the mechanistic discrepancies in PBP protein family. We also found a functional “backtracking” behavior that favors conformational change. We further explored the underlying folding landscape in response to ligand binding. Consistent with earlier experimental findings, the presence of ligand increases the cooperativity and stability of MBP. This work provides the first study to explore the folding dynamics and functional dynamics under the same theoretical framework using our triple-basin functional model

Towards Real-time High-Definition Image Snow Removal: Efficient Pyramid Network with Asymmetrical Encoder-decoder Architecture

In winter scenes, the degradation of images taken under snow can be pretty complex, where the spatial distribution of snowy degradation is varied from image to image. Recent methods adopt deep neural networks to directly recover clean scenes from snowy images. However, due to the paradox caused by the variation of complex snowy degradation, achieving reliable High-Definition image desnowing performance in real time is a considerable challenge. We develop a novel Efficient Pyramid Network with asymmetrical encoder-decoder architecture for real-time HD image desnowing. The general idea of our proposed network is to utilize the multi-scale feature flow fully and implicitly mine clean cues from features. Compared with previous state-of-the-art desnowing methods, our approach achieves a better complexity-performance trade-off and effectively handles the processing difficulties of HD and Ultra-HD images. The extensive experiments on three large-scale image desnowing datasets demonstrate that our method surpasses all state-of-the-art approaches by a large margin both quantitatively and qualitatively, boosting the PSNR metric from 31.76 dB to 34.10 dB on the CSD test dataset and from 28.29 dB to 30.87 dB on the SRRS test dataset

MSP-Former: Multi-Scale Projection Transformer for Single Image Desnowing

Image restoration of snow scenes in severe weather is a difficult task. Snow images have complex degradations and are cluttered over clean images, changing the distribution of clean images. The previous methods based on CNNs are challenging to remove perfectly in restoring snow scenes due to their local inductive biases' lack of a specific global modeling ability. In this paper, we apply the vision transformer to the task of snow removal from a single image. Specifically, we propose a parallel network architecture split along the channel, performing local feature refinement and global information modeling separately. We utilize a channel shuffle operation to combine their respective strengths to enhance network performance. Second, we propose the MSP module, which utilizes multi-scale avgpool to aggregate information of different sizes and simultaneously performs multi-scale projection self-attention on multi-head self-attention to improve the representation ability of the model under different scale degradations. Finally, we design a lightweight and simple local capture module, which can refine the local capture capability of the model. In the experimental part, we conduct extensive experiments to demonstrate the superiority of our method. We compared the previous snow removal methods on three snow scene datasets. The experimental results show that our method surpasses the state-of-the-art methods with fewer parameters and computation. We achieve substantial growth by 1.99dB and SSIM 0.03 on the CSD test dataset. On the SRRS and Snow100K datasets, we also increased PSNR by 2.47dB and 1.62dB compared with the Transweather approach and improved by 0.03 in SSIM. In the visual comparison section, our MSP-Former also achieves better visual effects than existing methods, proving the usability of our method

CurveFormer: 3D Lane Detection by Curve Propagation with Curve Queries and Attention

3D lane detection is an integral part of autonomous driving systems. Previous CNN and Transformer-based methods usually first generate a bird's-eye-view (BEV) feature map from the front view image, and then use a sub-network with BEV feature map as input to predict 3D lanes. Such approaches require an explicit view transformation between BEV and front view, which itself is still a challenging problem. In this paper, we propose CurveFormer, a single-stage Transformer-based method that directly calculates 3D lane parameters and can circumvent the difficult view transformation step. Specifically, we formulate 3D lane detection as a curve propagation problem by using curve queries. A 3D lane query is represented by a dynamic and ordered anchor point set. In this way, queries with curve representation in Transformer decoder iteratively refine the 3D lane detection results. Moreover, a curve cross-attention module is introduced to compute the similarities between curve queries and image features. Additionally, a context sampling module that can capture more relative image features of a curve query is provided to further boost the 3D lane detection performance. We evaluate our method for 3D lane detection on both synthetic and real-world datasets, and the experimental results show that our method achieves promising performance compared with the state-of-the-art approaches. The effectiveness of each component is validated via ablation studies as well