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Mar 2022 • Nanoscale Imaging, Sensing, and Actuation for Biomedical Applications XIX …, 2022

Designing a quantifiable detection method for the optimization of gold nanoparticle based gene therapy

Jacqueline Labovitz, Menachem Motiei, Tamar Sadan, Dror Fixler, Rachela Popovtzer

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Mar 2022 • PLoS pathogens

Experimental evolution links post-transcriptional regulation to Leishmania fitness gain

Laura Piel, K Shanmugha Rajan, Giovanni Bussotti, Hugo Varet, Rachel Legendre, Caroline Proux, Thibaut Douché, Quentin Giai-Gianetto, Thibault Chaze, Thomas Cokelaer, Barbora Vojtkova, Nadav Gordon-Bar, Tirza Doniger, Smadar Cohen-Chalamish, Praveenkumar Rengaraj, Céline Besse, Anne Boland, Jovana Sadlova, Jean-François Deleuze, Mariette Matondo, Ron Unger, Petr Volf, Shulamit Michaeli, Pascale Pescher, Gerald F Späth

The protozoan parasite Leishmania donovani causes fatal human visceral leishmaniasis in absence of treatment. Genome instability has been recognized as a driver in Leishmania fitness gain in response to environmental change or chemotherapy. How genome instability generates beneficial phenotypes despite potential deleterious gene dosage effects is unknown. Here we address this important open question applying experimental evolution and integrative systems approaches on parasites adapting to in vitro culture. Phenotypic analyses of parasites from early and late stages of culture adaptation revealed an important fitness tradeoff, with selection for accelerated growth in promastigote culture (fitness gain) impairing infectivity (fitness costs). Comparative genomics, transcriptomics and proteomics analyses revealed a complex regulatory network associated with parasite fitness gain, with genome instability causing highly reproducible, gene dosage-independent and -dependent changes. Reduction of flagellar transcripts and increase in coding and non-coding RNAs implicated in ribosomal biogenesis and protein translation were not correlated to dosage changes of the corresponding genes, revealing a gene dosage-independent, post-transcriptional mechanism of regulation. In contrast, abundance of gene products implicated in post-transcriptional regulation itself correlated to corresponding gene dosage changes. Thus, RNA abundance during parasite adaptation is controled by direct and indirect gene dosage changes. We correlated differential expression of small nucleolar RNAs (snoRNAs) with changes in rRNA modification …

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Mar 2022 • Nanoscale Imaging, Sensing, and Actuation for Biomedical Applications XIX …, 2022

Scattering detection in multi-layer tissue: phantom experiments and in vivo applications

Inbar Yariv, Hamootal Duadi, Dror Fixler

Deep tissue imaging using visible light is challenging due to its turbid nature. Nevertheless, clinical information can be detected by sensing changes in the tissue’s optical properties with low spatial resolution. The most challenging aspect is the spectral dependent scattering, which varies with physiological state and tissue layer. In this paper, we present the multi-layer study of the reflection-based iterative multiplane optical property extraction (IMOPE) technique. The IMOPE is a noninvasive nanophotonics technique that detects medium scattering properties based on the reemitted light phase. The extracted scattering properties are used as indicators of the internal tissue information and the presence of additional nanoparticles (NPs) in it. The technique is a combination of a theoretical model, an experimental setup, and the phase retrieval Gerchberg-Saxton algorithm. The IMOPE experimental setup records light …

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Mar 2022 • Cell

Tumor-reactive antibodies evolve from non-binding and autoreactive precursors

Roei D Mazor, Nachum Nathan, Amit Gilboa, Liat Stoler-Barak, Lihee Moss, Inna Solomonov, Assaf Hanuna, Yalin Divinsky, Merav D Shmueli, Hadas Hezroni, Irina Zaretsky, Michael Mor, Ofra Golani, Gad Sabah, Ariella Jakobson-Setton, Natalia Yanichkin, Meora Feinmesser, Daliah Tsoref, Lina Salman, Effi Yeoshoua, Eyal Peretz, Inna Erlich, Netta Mendelson Cohen, Jonathan M Gershoni, Natalia Freund, Yifat Merbl, Gur Yaari, Ram Eitan, Irit Sagi, Ziv Shulman

The tumor microenvironment hosts antibody-secreting cells (ASCs) associated with a favorable prognosis in several types of cancer. Patient-derived antibodies have diagnostic and therapeutic potential; yet, it remains unclear how antibodies gain autoreactivity and target tumors. Here, we found that somatic hypermutations (SHMs) promote antibody antitumor reactivity against surface autoantigens in high-grade serous ovarian carcinoma (HGSOC). Patient-derived tumor cells were frequently coated with IgGs. Intratumoral ASCs in HGSOC were both mutated and clonally expanded and produced tumor-reactive antibodies that targeted MMP14, which is abundantly expressed on the tumor cell surface. The reversion of monoclonal antibodies to their germline configuration revealed two types of classes: one dependent on SHMs for tumor binding and a second with germline-encoded autoreactivity. Thus, tumor-reactive …

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Feb 2022 • ACS nano

Wafer-Scalable Single-Layer Amorphous Molybdenum Trioxide

Md Hasibul Alam, Sayema Chowdhury, Anupam Roy, Xiaohan Wu, Ruijing Ge, Michael A Rodder, Jun Chen, Yang Lu, Chen Stern, Lothar Houben, Robert Chrostowski, Scott R Burlison, Sung Jin Yang, Martha I Serna, Ananth Dodabalapur, Filippo Mangolini, Doron Naveh, Jack C Lee, Sanjay K Banerjee, Jamie H Warner, Deji Akinwande


Feb 2022 • Biophysical Journal

Dynamical interplay between the human high-affinity copper transporter hCtr1 and its cognate metal ion

Gulshan Walke, Jana Aupič, Hadeel Kashoua, Pavel Janoš, Shelly Meron, Yulia Shenberger, Zena Qasem, Lada Gevorkyan-Airapetov, Alessandra Magistrato, Sharon Ruthstein

Abnormal cellular copper levels have been clearly implicated in genetic diseases, cancer, and neurodegeneration. Ctr1, a high affinity copper transporter, is an homotrimeric integral membrane protein that provides the main route for cellular copper uptake. Together with a sophisticated copper transport system, Ctr1 regulates Cu(I) metabolism in eukaryotes. Despite its pivotal role in normal cell function, the molecular mechanism of copper uptake and transport via Ctr1 remains elusive. In this study, electron paramagnetic resonance (EPR), UV-visible spectroscopy, and all-atom simulations were employed to explore Cu(I) binding to full-length human Ctr1 (hCtr1), thereby elucidating how metal binding at multiple distinct sites affects the hCtr1 conformational dynamics. We demonstrate that each hCtr1 monomer binds up to 5 Cu(I) ions and that progressive Cu(I) binding triggers a marked structural rearrangement in the …

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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 • 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 • Proc. of SPIE Vol 11979, 1197901-1, 2022

Frontiers in Biological Detection: From Nanosensors to Systems XIV

Benjamin L Miller, Sharon M Weiss

The papers in this volume were part of the technical conference cited on the cover and title page. Papers were selected and subject to review by the editors and conference program committee. Some conference presentations may not be available for publication. Additional papers and presentation recordings may be available online in the SPIE Digital Library at SPIEDigitalLibrary. org.

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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 • Global Change Biology

Urbanization comprehensively impairs biological rhythms in coral holobionts

Yaeli Rosenberg, Noa Simon Blecher, Maya Lalzar, Ruth Yam, Aldo Shemesh, Shahar Alon, Gabriela Perna, Anny Cárdenas, Christian R Voolstra, David J Miller, Oren Levy

Coral reefs are in global decline due to climate change and anthropogenic influences (Hughes et al., 2013). Near coastal cities or other densely populated areas, coral reefs face a range of additional challenges. While considerable progress has been made in understanding coral responses to acute individual stressors (Dominoni et al., 2020), the impacts of chronic exposure to varying combinations of sensory pollutants are largely unknown. To investigate the impacts of urban proximity on corals, we conducted a year‐long in‐natura study ‐ incorporating sampling at diel, monthly, and seasonal time points – in which we compared corals from an Urban area to corals from a proximal Non‐Urban area. Here we reveal that despite appearing relatively healthy, natural biorhythms and environmental sensory systems were extensively disturbed in corals from the Urban environment. Transcriptomic data indicated poor …

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Feb 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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Feb 2022 • Optics Express

Analysis of thin layers using surface acoustic wave-photonic devices in silicon-on-insulator

Mirit Hen, Leroy Dokhanian, Etai Grunwald, Matan Slook, Moshe Katzman, Maayan Priel, Olga Girshevitz, Avi Zadok

The analysis of thin layers deposited on various substrates is widely employed in thickness monitoring, materials research and development and quality control. Measurements are often performed based on changes to acoustic resonance frequencies of quartz micro-balance devices. The technique is extremely sensitive, but it is restricted to hundreds of MHz frequencies and requires electrical connectivity. In this work we propose and demonstrate the analysis of elastic properties of thin layers deposited on surface acoustic wave-photonic devices in standard silicon-on-insulator. The devices operate at 2.4 GHz frequency, and their interfaces are fiber-optic. The radio-frequency transfer functions of the devices are modified by sub-percent level changes to the group velocity of surface acoustic waves following deposition of layers. Layers of aluminum oxide and germanium sulfide of thickness between 10-80 nm are characterized. The analysis provides estimates for Young’s modulus of the layers.

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Feb 2022 • Biophysical Journal

Characterization of a large gated SPAD array for widefield NIR fluorescence lifetime imaging in vitro and in vivo

Jason T Smith, Alena Rudkouskaya, Shan Gao, Arin Ulku, Claudio Bruschini, Edoardo Charbon, Shimon Weiss, Margarida MR Barroso, Xavier Intes, Xavier Michalet

Optical imaging (OI) has become the most used alternative imaging tool for pre-clinical studies. Among all molecular imaging modalities, fluorescence optical imaging is central thanks to its high sensitivity, the numerous molecular probes available (either endogenous or exogenous) and its ability to simultaneously image multiple biomarkers or biological processes at various spatio-temporal scales. Especially, fluorescence lifetime imaging (FLI) has become an increasingly popular method, as it provides unique insights into the cellular micro-environment by non-invasively examining numerous intracellular parameters such as metabolic status, reactive oxygen species and intracellular pH. Moreover, FLI’s exploitation of native fluorescent signatures has been extensively investigated for enhanced diagnostic of numerous pathologies. However, to perform such measurements in intact, live specimen, it is required to …

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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 • 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

A novel single molecule fluorescence quenching technique for measuring distances below 3 nm

Benjamin Ambrose, Victoria E Hill, Robert A Shaw, Tristan Johnston-Wood, Matthew Willmott, Callum Johnston, Rebecca Mächtel, Thorben Cordes, Eitan Lerner, JG Hill, Shimon Weiss, Timothy D Craggs

Single-molecule FRET (smFRET) is a powerful biophysical tool for measuring intramolecular distances in biomolecules, however FRET is only effective over a 3-10nm scale. In this work we advance a quenching based method which uses Cy3B and Atto647N, a common dye pair used for smFRET. The quenching effect arising from this dye pair is sensitive to distance changes below 3nm, which is significantly lower than its R0 of 6.2 nm. It has previously been used to measure binary on/off transitions, such as local DNA melting in polymerase complexes. However, by using a series of DNAs labelled at various positions we have shown that we can quantitatively distinguish between slight changes in labelling separation. This quenching method is sufficiently sensitive to distinguish between DNAs labelled with dyes 1bp 3′ of each other from those labelled 5′ of each other. Additionally, this effect has been validated …

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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 Analysis of FI and FA decays and S2. Mathematical formulation of FI and FA decays

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Feb 2022 • Scientific Reports

Author Correction: Picosecond pulsed laser illumination: an ultimate solution for photonic versus thermal processes’ contest in SOI photo-activated modulator

David Glukhov, Zeev Zalevsky, Avi Karsenty

$$\frac {{\partial}^{2}\phi}{\partial {x}^{2}}=-\frac {\partial E}{\partial x}=-\frac {\rho}{\epsilon}\Rightarrow\phi (x)-\phi (0)=-\underset {0}{\overset {x}{\int}} Edx=-\frac {1}{\epsilon}\underset {0}{\overset {x}{\int}}\underset {0}{\overset {{x}^{{\prime}}}{\int}}\rho d {x}^{{\prime}} d {x}^{{\prime}} $$

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Feb 2022 • Analytical Chemistry

Identification of Enantiomers Using Low-Frequency Raman Spectroscopy

Vinayaka Harshothama Damle, Hagit Aviv, Yaakov R Tischler

Distinguishing between d and l enantiomers is of important scientific interest, especially for the pharmaceutical industry. Enantiomeric differentiation in the solid form is repeatedly presented as a challenge in the research community. Raman spectroscopy is a nondestructive tool, widely used for the characterization of different materials by probing their vibrational modes. The low-frequency region of the Raman spectrum reveals lattice-level interactions and global fluctuations in the molecule. Lower frequencies correspond to vibrations arising from weaker bonds and long-range interactions and hence are very susceptible to polarization changes. This work presents low-frequency Raman (LFR) spectroscopy as a facile technique to identify enantiomers. The optical setup of conventional Raman spectroscopy is engineered such that the excitation and collection geometries use an asymmetrical focal cone. In addition, a …

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Feb 2022 • The Journal of Physical Chemistry A

Vibrational Strong Light–Matter Coupling in an Open Microcavity Based on Reflective Germanium Coatings

Rena Yitzhari, Omree Kapon, Yaakov R Tischler

Open microcavities (OMCs) enable tuning of the optical resonances of a system and insertion of different materials between the mirrors. They are of large scientific interest due to their many potential applications. Using OMCs, we can observe strong light–matter coupling while tuning the cavity wavelength. Typically, dielectric Bragg reflectors (DBRs) and Au mirrors are used to form microcavities and observe vibrational strong coupling (VSC) in the middle-infrared (MIR) spectral region. Here, we make the mirrors of the OMC using thin film coatings of the semiconducting material germanium (Ge) and demonstrate VSC in the MIR region. We deposited a uniform coating of poly(methyl methacrylate) (PMMA) on one of the OMC mirrors’ inner surfaces, and then we tuned the cavity to the carbonyl stretch mode resonance at 1731 cm–1. Comparing VSC using Ge mirrors to DBRs or Au mirrors, we achieve enhanced optical …

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