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Feb 2022 • Nature communications

Multi-parameter photon-by-photon hidden Markov modeling

Paul David Harris, Alessandra Narducci, Christian Gebhardt, Thorben Cordes, Shimon Weiss, Eitan Lerner

Single molecule Förster resonance energy transfer (smFRET) is a unique biophysical approach for studying conformational dynamics in biomacromolecules. Photon-by-photon hidden Markov modeling (H2MM) is an analysis tool that can quantify FRET dynamics of single biomolecules, even if they occur on the sub-millisecond timescale. However, dye photophysical transitions intertwined with FRET dynamics may cause artifacts. Here, we introduce multi-parameter H2MM (mpH2MM), which assists in identifying FRET dynamics based on simultaneous observation of multiple experimentally-derived parameters. We show the importance of using mpH2MM to decouple FRET dynamics caused by conformational changes from photophysical transitions in confocal-based smFRET measurements of a DNA hairpin, the maltose binding protein, MalE, and the type-III secretion system effector, YopO, from Yersinia species …

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Feb 2022 • Physical Review Applied

Visualizing Current in Superconducting Networks

X Wang, M Laav, I Volotsenko, A Frydman, B Kalisky

We present an experimental study of local magnetic imaging in order to visualize the current flow in superconducting networks. We track the evolution of the spatial distribution of the current flow as the network is driven from fully superconducting to fully normal phases. Our results highlight the factors that contribute to the disordered flow in superconducting networks during their collapse, and demonstrate that the current is never uniformly distributed in the network. These results can assist the design and development of circuits based on superconductors and Josephson junctions.

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Feb 2022 • Biophysical Journal

Single molecule activity assay for SARS-CoV-2 RNA dependent RNA polymerase

SangYoon Chung, Yazan Alhadid, Maya Segal, Jookyung Lee, Sergei Borukhov, Shimon Weiss

Tuesday, February 22, 2022 359a and replication processes. Due to its importance, RdRp is one of the main targets for therapeutic approaches. We developed an in-vitro, single-molecule based assay to detect the polymerization activity of the RdRp complex. Using this assay, we optimized the activity of the minimal SARS-CoV-2 RdRp (composed of nsp12, nsp7, and nsp8) by testing various conditions such as different concentrations of salt, molecular crowding agents, and divalent metal ions. The broad compatibility of our activity assay will enable the study of SARS-CoV-2 transcription and replication mechanisms and will be useful in the development of antiviral agents that inhibit the COVID-19 RdRp and potentially many other viral RdRps.

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Feb 2022 • Biophysical Journal

Bacterial resting membrane potential: a case study with Bacillus subtilis

Debjit Roy, Xavier Michalet, Evan W Miller, Robert P Gunsalus, Robert T Clubb, Shimon Weiss

Bacterial membrane potential changes (Δψ) play an important role in bacterial metabolism and cellular processes as well as cell to cell communications in a biofilm. However, existing tools for reading Δψ quantitatively in individual bacterial cells as well as in bacterial communities are limited. A fluorescence lifetime imaging microscopy (FLIM) technique in combination with photo-induced electron transfer (PeT) based small molecule voltage sensitive dyes have been employed to quantify absolute resting membrane potential for individual Bacillus subtilis cells. The local electrostatic potential affects the relative extent of PeT in these dyes and thus alters fluorescence quantum yield (and hence fluorescence intensity as well as fluorescence lifetime). When localized into the bacterial cell membrane, the extent of PeT gets modulated by the resting membrane potential of the system. The suitability and voltage sensitivity of …

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Feb 2022 • Optics Express

Classification of fluorescent anisotropy decay based on the distance approach in the frequency domain

Gilad Yahav, Yitzchak Weber, Hamootal Duadi, Shweta Pawar, Dror Fixler

Frequency-domain (FD) fluorometry is a widely utilized tool to probe unique features of complex biological structures, which may serve medical diagnostic purposes. The conventional data analysis approaches used today to extract the fluorescence intensity or fluorescence anisotropy (FA) decay data suffer from several drawbacks and are inherently limited by the characteristics and complexity of the decay models. This paper presents the squared distance (D^2) technique, which categorized samples based on the direct frequency response data (FRD) of the FA decay. As such, it improves the classification ability of the FD measurements of the FA decay as it avoids any distortion that results from the challenged translation into time domain data. This paper discusses the potential use of the D^2 approach to classify biological systems. Mathematical formulation of D^2 technique adjusted to the FRD of the FA decay is …

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Feb 2022 • Cancer Research

Abstract PD6-03: Spatio-molecular dissection of the breast cancer metastatic microenvironment

Daniel L Abravanel, Johanna Klughammer, Timothy Blosser, Yury Goltsev, Sizun Jiang, Yunjao Bai, Evan Murray, Shahar Alon, Yi Cui, Daniel R Goodwin, Anubhav Sinha, Ofir Cohen, Michal Slyper, Orr Ashenberg, Danielle Dionne, Judit Jané-Valbuena, Caroline BM Porter, Asa Segerstolpe, Julia Waldman, Sébastien Vigneau, Karla Helvie, Allison Frangieh, Laura DelloStritto, Miraj Patel, Jingyi We, Kathleen Pfaff, Nicole Cullen, Ana Lako, Madison Turner, Isaac Wakiro, Sara Napolitano, Abhay Kanodia, Rebecca Ortiz, Colin MacKichan, Stephanie Inga, Judy Chen, Aaron R Thorner, Asaf Rotem, Scott Rodig, Fei Chen, Edward S Boyden, Garry P Nolan, Xiaowei Zhuang, Orit Rozenblatt-Rosen, Bruce E Johnson, Aviv Regev, Nikhil Wagle

Metastatic breast cancer (MBC) remains incurable due to inevitable development of therapeutic resistance. Although tumor cell intrinsic mechanisms of resistance in MBC are beginning to be elucidated by bulk sequencing studies, the roles of the tumor microenvironment and intratumor heterogeneity in therapeutic resistance remain underexplored due to both technological barriers and limited availability of samples. To comprehensively capture these characteristics we have adapted a research biopsy protocol to collect tissue for an array of single-cell and spatio-molecular assays whose performance we have optimized for MBC, including single-cell and single-nucleus RNA sequencing, Slide-Seq, Multiplexed Error-Robust FISH (MERFISH), Expansion Sequencing (ExSEQ), Co-detection by Indexing (CODEX) and Multiplexed Ion Beam Imaging (MIBI). To date, we have successfully performed single-cell or single …

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Feb 2022 • Biophysical Journal

Controlled membrane interactions by lipid coated quantum dots

Lion Morgenstein, Merav Tsubary, Ayelet Atkins, Asaf Grupi, Shimon Weiss

Quantum Dots (QDs) are being employed in a wide range of biological application due to their superior fluorescence characteristics. Biocompatibility of QDs is usually achieved by exchange of as-synthesized surface ligands with ligands that impart the particle with water solubility properties. An alternative approach for surface functionalization is ligand adsorption. This approach is based on weak interactions between the alkane chains of the as-synthesized surface ligands and a hydrophobic element of an adsorbed ligand with a functional head group/s. There are several advantages for this approach.(i) The photophysical properties stay intact and (ii) the weak association allows for potential adaptive re-distribution of the ligands in response to environment changes. Membrane targeting introduces another layer of complexity and requires precise control of QD’surface properties to control the mode of interaction …

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Feb 2022 • arXiv preprint arXiv:2202.00274

Infinite ergodic theory for three heterogeneous stochastic models with application to subrecoil laser cooling

Takuma Akimoto, Eli Barkai, Günter Radons

We compare ergodic properties of the kinetic energy for three stochastic models of subrecoil-laser-cooled gases. One model is based on a heterogeneous random walk (HRW), another is an HRW with long-range jumps (the exponential model), and the other is a mean-field-like approximation of the exponential model (the deterministic model). All the models show an accumulation of the momentum at zero in the long-time limit, and a formal steady state cannot be normalized, i.e., there exists an infinite invariant density. We obtain the exact form of the infinite invariant density and the scaling function for the exponential and deterministic models and devise a useful approximation for the momentum distribution in the HRW model. While the models are kinetically non-identical, it is natural to wonder whether their ergodic properties share common traits, given that they are all described by an infinite invariant density. We show that the answer to this question depends on the type of observable under study. If the observable is integrable, the ergodic properties such as the statistical behavior of the time averages are universal as they are described by the Darling-Kac theorem. In contrast, for non-integrable observables, the models in general exhibit non-identical statistical laws. This implies that focusing on non-integrable observables, we discover non-universal features of the cooling process, that hopefully can lead to a better understanding of the particular model most suitable for a statistical description of the process. This result is expected to hold true for many other systems, beyond laser cooling.

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Feb 2022 • Journal of The Electrochemical Society

A study of composite solid electrolytes: the effect of inorganic additives on the polyethylene oxide-sodium metal interface

Shaul Bublil, Gayathri Peta, Hadas Alon-Yehezkel, Yuval Elias, Diana Golodnitsky, Miryam Fayena-Greenstein, Doron Aurbach

High electrolyte-electrode interface stability is essential for solid state batteries to avoid side reactions that form interphases and voids, leading to loss of contact and increased impedance. Such detrimental situations increase overvoltage, reduce cycling efficiency, and shorten battery cycle life. While composite solid electrolytes were studied extensively, the effect of inorganic additives in the polymer matrix on the electrolyte-anode interface remains unclear. Here, solid electrolyte was studied for batteries with sodium metal anode based on polyethylene oxide (PEO) polymeric matrix containing ceramic additive. Extensive electrochemical analyses under both AC and DC conditions were performed, and chemical reactions between sodium metal and the PEO matrix, which produce interphases at the electrode-electrolyte interface, were investigated. Addition of sodium beta aluminate in the matrix appears to mitigate …

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Feb 2022 • Measurement

Diamond protection for reusable ZnO coated fiber-optic measurement head in optoelectrochemical investigation of bisphenol A

Małgorzata Szczerska, Monika Kosowska, Paulina Listewnik, Michał Rycewicz, Mikhael Bechelany, Yafit Fleger, Dror Fixler, Paweł Jakóbczyk

Due to the global problem with plastic contaminating the environment, with bisphenol A (BPA) being one of the highest demand, effective monitoring and purification of the pollutants are required. The electrochemical methods constitute a good solution but, due to polymerization of electrochemical oxidation bisphenol A products and their adsorption to the surfaces, measurement head elements are clogged by the formed film. In this research, we propose a nanocrystalline diamond sheet protection for securing elements in direct contact with bisphenol A during electrochemical processes. The solution was presented on the example of a zinc oxide (ZnO) coating deposited on a fiber-optic end-face by Atomic Layer Deposition. Series of optical and electrochemical measurements were performed in a dedicated hybrid setup. The results show that ZnO can be modified during the electrochemistry leading to the drastic …

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Feb 2022 • Advanced Quantum Technologies 5 (2), 2100121, 2022

Geometric phases and the Sagnac effect: Foundational aspects and sensing applications

Ismael L Paiva, Rain Lenny, Eliahu Cohen

Geometric phase is a key player in many areas of quantum science and technology. In this review article, several foundational aspects of quantum geometric phases and their relations to classical geometric phases are outlined. How the Aharonov–Bohm and Sagnac effects fit into this context is then discussed. Moreover, a concise overview of technological applications of the latter, with special emphasis on gravitational sensing, like in gyroscopes and gravitational wave detectors is presented.

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Feb 2022 • The Journal of Chemical Physics 156 (8), 2022

Membrane potential sensing: Material design and method development for single particle optical electrophysiology

Debjit Roy, Zehavit Shapira, Shimon Weiss

We review the development of “single” nanoparticle-based inorganic and organic voltage sensors, which can eventually become a viable tool for “non-genetic optogenetics.” The voltage sensing is accomplished with optical imaging at the fast temporal response and high spatial resolutions in a large field of view. Inorganic voltage nanosensors utilize the Quantum Confined Stark Effect (QCSE) to sense local electric fields. Engineered nanoparticles achieve substantial single-particle voltage sensitivity (∼2% Δλ spectral Stark shift up to ∼30% ΔF/F per 160 mV) at room temperature due to enhanced charge separation. A dedicated home-built fluorescence microscope records spectrally resolved images to measure the QCSE induced spectral shift at the single-particle level. Biomaterial based surface ligands are designed and developed based on theoretical simulations. The hybrid nanobiomaterials satisfy anisotropic …

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Feb 2022 • Physical Review A

Coherence properties of a spin in a squeezed resonator

Inbar Shani, Emanuele G Dalla Torre, Michael Stern

A promising venue for hybrid quantum computation involves the strong coupling between impurity spins and superconducting circuits. This coupling can be controlled and enhanced by preparing superconducting resonators in nonclassical states, such as squeezed states. In this work, we theoretically study the effects of these states on the coherence properties of the spin. We develop an analytic approach based on the Schrieffer-Wolff transformation that allows us to quantitatively predict the dynamics of the spin, and we numerically confirm its validity. We find that squeezing can enhance the coupling between the resonator and the spin. However, at the same time, it amplifies the photon noise and enhances the spin decoherence. Our work demonstrates a major impediment in using squeezing to reach the strong-coupling limit.

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Feb 2022 • Journal of Magnetic Resonance

Shimon Vega in the eyes of his students and postdocs

A Goldbourt, G Goobes, Y Hovav, I Kaminker, V Ladizhansky, M Leskes, PK Madhu, F Mentnik-Vigier, S Pizzanelli, I Sack, D Shimon, J Sunderasan, E Vinogradov

Professor Shimon Vega (1943–2021) of the Weizmann Institute of Science passed away on the 16 th of November. Shimon Vega established theoretical frameworks to develop and explain solid-state nuclear magnetic resonance (NMR) and dynamic nuclear polarization (DNP) techniques and methodologies. His departure left a profound mark on his many students, postdocs, and colleagues. Shortly after his passing, we all assembled spontaneously for an international online meeting to share our reflections and memories of our experiences in Shimon’s lab and how they affected us deeply during that period of time and throughout our scientific careers. These thoughts and feelings were put here into writing.

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Feb 2022 • Molecular Cell

Gene architecture directs splicing outcome in separate nuclear spatial regions

Luna Tammer, Ofir Hameiri, Ifat Keydar, Vanessa Rachel Roy, Asaf Ashkenazy-Titelman, Noélia Custódio, Itay Sason, Ronna Shayevitch, Victoria Rodríguez-Vaello, José Rino, Galit Lev Maor, Yodfat Leader, Doha Khair, Erez Lieberman Aiden, Ran Elkon, Manuel Irimia, Roded Sharan, Yaron Shav-Tal, Maria Carmo-Fonseca, Gil Ast

How the splicing machinery defines exons or introns as the spliced unit has remained a puzzle for 30 years. Here, we demonstrate that peripheral and central regions of the nucleus harbor genes with two distinct exon-intron GC content architectures that differ in the splicing outcome. Genes with low GC content exons, flanked by long introns with lower GC content, are localized in the periphery, and the exons are defined as the spliced unit. Alternative splicing of these genes results in exon skipping. In contrast, the nuclear center contains genes with a high GC content in the exons and short flanking introns. Most splicing of these genes occurs via intron definition, and aberrant splicing leads to intron retention. We demonstrate that the nuclear periphery and center generate different environments for the regulation of alternative splicing and that two sets of splicing factors form discrete regulatory subnetworks for the two …

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Jan 2022 • The CRISPR Journal

High-Throughput Imaging of CRISPR-and Recombinant Adeno-Associated Virus–Induced DNA Damage Response in Human Hematopoietic Stem and Progenitor Cells

Daniel Allen, Lucien E Weiss, Alon Saguy, Michael Rosenberg, Ortal Iancu, Omri Matalon, Ciaran Lee, Katia Beider, Arnon Nagler, Yoav Shechtman, Ayal Hendel

CRISPR-Cas technology has revolutionized gene editing, but concerns remain due to its propensity for off-target interactions. This, combined with genotoxicity related to both CRISPR-Cas9-induced double-strand breaks and transgene delivery, poses a significant liability for clinical genome-editing applications. Current best practice is to optimize genome-editing parameters in preclinical studies. However, quantitative tools that measure off-target interactions and genotoxicity are costly and time-consuming, limiting the practicality of screening large numbers of potential genome-editing reagents and conditions. Here, we show that flow-based imaging facilitates DNA damage characterization of hundreds of human hematopoietic stem and progenitor cells per minute after treatment with CRISPR-Cas9 and recombinant adeno-associated virus serotype 6. With our web-based platform that leverages deep learning for …

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Jan 2022 • arXiv preprint arXiv:2201.09386

Impact of Non-Hermiticity and Nonlinear Interactions on Disordered-Induced Localized Modes

Bhupesh Kumar, Patrick Sebbah

If disorder-induced Anderson localized states have been observed experimentally in optics, their study remains challenging leaving a number of open questions unsolved. Among them, the impact on Anderson localization of non-Hermiticity, optical gain and loss, and more generally, nonlinearities has been the subject of numerous theoretical debates, without yet any conclusive experimental demonstration. Indeed, in systems where localized modes have reasonable spatial extension to be observed and investigated, their mutual interaction and coupling to the sample boundaries make it extremely difficult to isolate them spectrally and investigate them alone. Recently, we successfully exhibited localized lasing modes individually in an active disordered medium, using pump-shaping optimization technique. However, a one-to-one identification of the lasing modes with the eigenmodes of the passive system was not possible, as the impact of non-Hermiticity and nonlinear gain on these localized states was unknown. Here, we apply the pump-shaping method to fully control the non-Hermiticity of an active scattering medium. Direct imaging of the light distribution within the random laser allows us to demonstrate unequivocally that the localized lasing modes are indeed the modes of the passive system. This opens the way to investigate the robustness of localized states in the presence of nonlinear gain and nonlinear modal interactions. We show that, surprisingly, gain saturation and mode competition for gain does not affect the spatial distribution of the modes.

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Jan 2022 • The Journal of Chemical Physics

Gas of sub-recoiled laser cooled atoms described by infinite ergodic theory

Eli Barkai, Günter Radons, Takuma Akimoto

It is well known that for sub-recoiled laser cooled atoms L\'evy statistics and deviations from usual ergodic behaviour come into play.Here we show how tools from infinite ergodic theory describe the cool gas.Specifically, we derive the scaling function and the infinite invariant density of a stochastic model for the momentum of the atoms using two approaches.The first is a direct analysis of the master equation and the second following the analysis of Bertin and Bardou using the lifetime dynamics. The two methods are shown to be identical, but yield different insights into the problem. In the main part of the paper we focus on the case where the laser trapping is strong, namely the rate of escape from the velocity trap is for and .We construct a machinery to investigate the time averages of physical observables and their relationt o ensemble averages. The time averages are given in terms of functionals of the …

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Jan 2022 • bioRxiv

Lytic reactivation of the Kaposi’s sarcoma-associated herpesvirus (KSHV) is accompanied by major nucleolar alterations

Nofar Atari, K Shanmugha Rajan, Vaibhav Chikne, Smadar Cohen-Chalamish, Odelia Orbaum, Avi Jacob, Inna Kalt, Shulamit Michaeli, Ronit Sarid

The nucleolus is a sub-nuclear compartment whose primary function is the biogenesis of ribosomal subunits. Certain viral infections affect the morphology and composition of the nucleolar compartment and influence ribosomal RNA (rRNA) transcription and maturation. However, no description of nucleolar morphology and function during infection with Kaposi’s sarcoma-associated herpesvirus (KSHV) is available to date. Using immunofluorescence microscopy, we documented extensive destruction of the nuclear and nucleolar architecture during lytic reactivation of KSHV. This was manifested by redistribution of key nucleolar proteins, including the rRNA transcription factor, UBF, the essential pre-rRNA processing factor Fibrillarin, and the nucleolar multifunctional phosphoproteins Nucleophosmin (NPM1) and Nucleolin. Distinct delocalization patterns were evident; certain nucleolar proteins remained together whereas others dissociated, implying that nucleolar proteins undergo nonrandom programmed dispersion. Of note, neither Fibrillarin nor UBF colocalized with promyelocytic leukemia (PML) nuclear bodies or with the viral protein LANA-1, and their redistribution was not dependent on viral DNA replication or late viral gene expression. No significant changes in pre-rRNA levels and no accumulation of pre-rRNA intermediates were found by RT-qPCR and Northern blot analysis, respectively. Furthermore, fluorescent in situ hybridization (FISH), combined with immunofluorescence, revealed an overlap between Fibrillarin and internal transcribed spacer 1 (ITS1), which represents the primary product of the pre-rRNA, suggesting that the …

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Jan 2022 • Photonics

Signal-to-Noise Ratio Improvement for Multiple-Pinhole Imaging Using Supervised Encoder–Decoder Convolutional Neural Network Architecture

Eliezer Danan, Nadav Shabairou, Yossef Danan, Zeev Zalevsky

Digital image devices have been widely applied in many fields, such as individual recognition and remote sensing. The captured image is a degraded image from the latent observation, where the degradation processing is affected by some factors, such as lighting and noise corruption. Specifically, noise is generated in the processing of transmission and compression from the unknown latent observation. Thus, it is essential to use image denoising techniques to remove noise and recover the latent observation from the given degraded image. In this research, a supervised encoder–decoder convolution neural network was used to fix image distortion stemming from the limited accuracy of inverse filter methods (Wiener filter, Lucy–Richardson deconvolution, etc.). Particularly, we will correct image degradation that mainly stems from duplications arising from multiple-pinhole array imaging.

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Jan 2022 • ACS Applied Nano Materials

Acoustic Green Synthesis of Graphene-Gallium Nanoparticles and PEDOT: PSS Hybrid Coating for Textile To Mitigate Electromagnetic Radiation Pollution

Poushali Das, Sayan Ganguly, Ilana Perelshtein, Shlomo Margel, Aharon Gedanken

Solid matrix-supported liquid metal nanoparticles have been drawing attention as a nanoadditive in the fabrication of electroconductive flexible and soft materials. The present work reports a facile, green, and sonochemical synthesis approach of gallium (Ga) nanoparticles embedded in reduced graphene oxide (RGO) under ambient conditions for the first time. The as-synthesized ultrasonic energy-irradiated RGO/Ga nanocomposite was studied using SEM, TEM, DSC, XRD, XPS, and solid-state NMR. Because of their electrical conductivity, RGO/Ga nanoparticles have been used as a conducting inclusion for a poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) matrix and coated on cotton fabrics to develop a smart e-textile for electromagnetic (EM) radiation-shielding application. In the X-band (8.2–12.4 GHz) frequency range, the nanocomposites’ EM interference-shielding efficiency was about …

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