Supplementary document for Influence of static and dynamic ocular aberrations on full-field OCT for in-vivo high resolution retinal imaging - 6783052.pdf

Contribution of each Zernike radial order to the overall static wavefront error

Quantum Mechanical/Molecular Mechanical Elucidation of the Catalytic Mechanism of Leukotriene A4 Hydrolase as an Epoxidase

Leukotriene A4 hydrolase (LTA4H) functions as a mono-zinc bifunctional enzyme with aminopeptidase and epoxidase activities. While the aminopeptidase mechanism is well understood, the epoxidase mechanism remains less clear. In continuation of our prior research, we undertook an in-depth exploration of the LTA4H catalytic role as an epoxidase, employing a combined SCC-DFTB/CHARMM method. In the current work, we found that the conversion of LTA4 to leukotriene B4 (LTB4) involves three successive steps: epoxy ring opening (RO), nucleophilic attack (NA), and proton transfer (PT) reactions at the epoxy oxygen atom. Among these steps, the RO and NA stages constitute the potential rate-limiting step within the entire epoxidase mechanism. Notably, the NA step implicates D375 as the general base catalyst, while the PT step engages protonated E271 as the general acid catalyst. Additionally, we delved into the mechanism behind the formation of the isomer product, Δ6-trans-Δ8-cis-LTB4. Our findings debunked the feasibility of a direct LTB4 to iso-LTB4 conversion. Instead, we highlight the possibility of isomerization from LTA4 to its isomeric conjugate (iso-LTA4), showing comparable energy barriers of 5.1 and 5.5 kcal/mol in aqueous and enzymatic environments, respectively. The ensuing dynamics of iso-LTA4 hydrolysis subsequently yield iso-LTB4 via a mechanism akin to LTA4 hydrolysis, albeit with a heightened barrier. Our computations firmly support the notion that substrate isomerization exclusively takes place prior to or during the initial substrate-binding phase, while LTA4 remains the dominant conformer. Notably, our simulations suggest that irrespective of the active site’s constrained L-shape, isomerization from LTA4 to its isomeric conjugate remains plausible. The mechanistic insights garnered from our simulations furnish a valuable understanding of LTA4H’s role as an epoxidase, thereby facilitating potential advancements in inhibitor design

Influence of static and dynamic ocular aberrations on full-field OCT for in-vivo high resolution retinal imaging

Under spatially incoherent illumination, Time-domain Full-Field Optical Coherence Tomography (FFOCT) offers the possibility to achieve in-vivo retinal imaging at cellular resolution over a wide field-of-view. Such performance is possible albeit the presence of ocular aberrations even without the use of classical Adaptive Optics. While the effect of aberrations in FFOCT has been debated these past years, mostly on low order and static aberrations, we present for the first time a method enabling a quantitative study of the effect of statistically representative static and dynamic ocular aberrations on FFOCT image metrics, such as SNR, resolution, and image similarity. While we show that ocular aberrations can decrease FFOCT SNR and resolution by up to 14 dB and 5-fold, we take advantage of such quantification to discuss different possible compromises between performance gain and Adaptive Optics complexity and speed, to optimize both sensor-based and sensorless FFOCT high-resolution retinal imaging

General Charge Transfer Dipole Model for AMOEBA-Like Force Fields

The development of highly accurate force fields is always an importance aspect in molecular modeling. In this work, we introduce a general damping-based charge transfer dipole (D-CTD) model to describe the charge transfer energy and the corresponding charge flow for H, C, N, O, P, S, F, Cl, and Br elements in common bio-organic systems. Then, two effective schemes to evaluate the charge flow from the corresponding induced dipole moment between the interacting molecules were also proposed and discussed. The potential applicability of the D-CTD model in ion-containing systems was also demonstrated in a series of ion–water complexes including Li+, Na+, K+, Mg2+, Ca2+, Fe2+, Zn2+, Pt2+, F–, Cl–, Br–, and I– ions. In general, the D-CTD model demonstrated good accuracy and good transferability in both charge transfer energy and the corresponding charge flow for a wide range of model systems. By distinguishing the intermolecular charge redistribution (charge transfer) under the influence of an external electric field from the accompanying intramolecular charge redistribution (polarization), the D-CTD model is theoretically consistent with current induced dipole-based polarizable dipole models and hence can be easily implemented and parameterized. Along with our previous work in charge penetration-corrected electrostatics, a bottom-up approach constructed water model was also proposed and demonstrated. The structure-maker and structure-breaker roles of cations and anions were also correctly reproduced using Na+, K+, Cl–, and I– ions in the new water model, respectively. This work demonstrates a cost-effective approach to describe the charge transfer phenomena. The water and ion models also show the feasibility of a modulated development approach for future force fields

General Charge Transfer Dipole Model for AMOEBA-Like Force Fields

The development of highly accurate force fields is always an importance aspect in molecular modeling. In this work, we introduce a general damping-based charge transfer dipole (D-CTD) model to describe the charge transfer energy and the corresponding charge flow for H, C, N, O, P, S, F, Cl, and Br elements in common bio-organic systems. Then, two effective schemes to evaluate the charge flow from the corresponding induced dipole moment between the interacting molecules were also proposed and discussed. The potential applicability of the D-CTD model in ion-containing systems was also demonstrated in a series of ion–water complexes including Li+, Na+, K+, Mg2+, Ca2+, Fe2+, Zn2+, Pt2+, F–, Cl–, Br–, and I– ions. In general, the D-CTD model demonstrated good accuracy and good transferability in both charge transfer energy and the corresponding charge flow for a wide range of model systems. By distinguishing the intermolecular charge redistribution (charge transfer) under the influence of an external electric field from the accompanying intramolecular charge redistribution (polarization), the D-CTD model is theoretically consistent with current induced dipole-based polarizable dipole models and hence can be easily implemented and parameterized. Along with our previous work in charge penetration-corrected electrostatics, a bottom-up approach constructed water model was also proposed and demonstrated. The structure-maker and structure-breaker roles of cations and anions were also correctly reproduced using Na+, K+, Cl–, and I– ions in the new water model, respectively. This work demonstrates a cost-effective approach to describe the charge transfer phenomena. The water and ion models also show the feasibility of a modulated development approach for future force fields

Video_1_Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior.AVI

<p>Magnetotactic bacteria (MTB) are a diverse group of microorganisms capable of using geomagnetic fields for navigation. This magnetotactic behavior can help microorganisms move toward favorable habitats for optimal growth and reproduction. A comprehensive understanding of the magnetotactic mechanism at molecular levels requires highly efficient genomic editing tools, which remain underdeveloped in MTB. Here, we adapted an engineered CRISPR-Cas9 system for efficient inactivation of genes in a widely used MTB model strain, Magnetospirillum magneticum AMB-1. By combining a nuclease-deficient Cas9 (dCas9) and single-guide RNA (sgRNA), a CRISPR interference system was successfully developed to repress amb0994 expression. Furthermore, we constructed an in-frame deletion mutant of amb0994 by developing a CRISPR-Cas9 system. This mutant produces normal magnetosomes; however, its response to abrupt magnetic field reversals is faster than wild-type strain. This behavioral difference is probably a consequence of altered flagella function, as suggested with our dynamics simulation study by modeling M. magneticum AMB-1 cell as an ellipsoid. These data indicate that, Amb0994 is involved in the cellular response to magnetic torque changes via controlling flagella. In summary, this study, besides contributing to a better understanding of magnetotaxis mechanism, demonstrated the CRISPR-(d)Cas9 system as a useful genetic tool for efficient genome editing in MTB.</p

Computational Study of Halide Perovskite-Derived A₂BX₆ Inorganic Compounds: Chemical Trends in Electronic Structure and Structural Stability

The electronic structure and energetic stability of A₂BX₆ halide compounds with the cubic and tetragonal variants of the perovskite-derived K₂PtCl₆ prototype structure are investigated computationally within the frameworks of density-functional-theory (DFT) and hybrid (HSE06) functionals. The HSE06 calculations are undertaken for seven known A₂BX₆ compounds with A = K, Rb, and Cs; and B = Sn, Pd, Pt, Te, and X = I. Trends in band gaps and energetic stability are identified, which are explored further employing DFT calculations over a larger range of chemistries, characterized by A = K, Rb, Cs, B = Si, Ge, Sn, Pb, Ni, Pd, Pt, Se, and Te; and X = Cl, Br, I. For the systems investigated in this work, the band gap increases from iodide to bromide to chloride. Further, variations in the A site cation influences the band gap as well as the preferred degree of tetragonal distortion. Smaller A site cations such as K and Rb favor tetragonal structural distortions, resulting in a slightly larger band gap. For variations in the B site in the (Ni, Pd, Pt) group and the (Se, Te) group, the band gap increases with increasing cation size. However, no observed chemical trend with respect to cation size for band gap was found for the (Si, Sn, Ge, Pb) group. The findings in this work provide guidelines for the design of halide A₂BX₆ compounds for potential photovoltaic applications

POSTN promotes a mesenchymal phenotype in MCF-10A and MCF-7 cells.

<p><b>A.</b> POSTN-overexpressing cells exhibit a mesenchymal-like morphology. <b>B.</b> POSTN promotes cell invasion of human mammary epithelial cells and BCCs as detected by a matrigel-coated transwell invasion assay. <b>C, D.</b> Immunofluorescence analysis revealed that the mesenchymal markers N-cadherin, fibronectin, vimentin and α-SMA in POSTN-expressing cells were increased while the epithelial marker E-cadherin was decreased. <b>E, F.</b> POSTN-expressing cells show increased levels of N-cadherin, fibrnectin, vimentin and α-SMA and decreased E-cadherin. Expression of epithelial and mesenchymal markers was analysed by western blotting.</p

POSTN induces adipogenic and chondrogenic differentiation.

<p><b>A.</b> Following adipogenic differentiation, MCF-10A/POSTN, MCF-7/POSTN cells and hMSCs stained positive with oil red O (top) and fluorescent LipidTox, which stains oil droplets (bottom). <b>B, C.</b> Real-time RT-PCR analysis for the expression of the adipocyte markers <i>PPARγ</i>and <i>ADFP</i> in MCF-10A and MCF-7 cells and their POSTN-overexpressing cells subjected to adipocyte differentiation for 21 days. The data are means ± SD. *P<0.05, **P<0.01. <b>D.</b> Chondrocytic nodules formed by MCF-10A/POSTN cells and hMSCs stained positive with alcian blue 8 GX (left panel). Immunohistochemistry was performed on chondrocyte sections using antibody against collagen II (right panel). MCF-10A/Vector cells, MCF-7/Vector and MCF-7/POSTN cells did not form any chondrocytic nodules under identical conditions.</p

Model of role of POSTN in mammary epithelial neoplasia and metastasis.

<p>POSTN might confer mammary epithelial cells and BCCs with stem cell-like traits and a mesenchymal phenotype, as well as the multipotent potentials of MSCs to promote tumorigenesis and metastasis.</p