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Jan 2022 • Optics Continuum

Analysis and simulation of optical spectral phase encoding using an array of Fabri-Perot interferometers and code division multiplexing

Shay Yederman, Zeev Zalevsky

This paper proposes a method for a scheme of spectral phase encoding with resolution of up to 10 MHz and addressability of 40GHz, for a typical wide-band optical data carrying signal, by means of optical instruments and prior knowledge about the signal. The setup includes an array of Fabri-Perot Interferometers (FPI) which bypass the grating limitations, and a phase-only spatial light modulator (SLM) to properly encode the diffracted light. Their arrangement along with the method of Optical Code Division Multiple Access (OCDMA) was simulated, and promised fine results for various encoding schemes.

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Jan 2022 • Science advances

Peroxisome function relies on organelle-associated mRNA translation

Noa Dahan, Yury S Bykov, Elizabeth A Boydston, Amir Fadel, Zohar Gazi, Hodaya Hochberg-Laufer, James Martenson, Vlad Denic, Yaron Shav-Tal, Jonathan S Weissman, Naama Aviram, Einat Zalckvar, Maya Schuldiner

Crucial metabolic functions of peroxisomes rely on a variety of peroxisomal membrane proteins (PMPs). While mRNA transcripts of PMPs were shown to be colocalized with peroxisomes, the process by which PMPs efficiently couple translation with targeting to the peroxisomal membrane remained elusive. Here, we combine quantitative electron microscopy with proximity-specific ribosome profiling and reveal that translation of specific PMPs occurs on the surface of peroxisomes in the yeast Saccharomyces cerevisiae. This places peroxisomes alongside chloroplasts, mitochondria, and the endoplasmic reticulum as organelles that use localized translation for ensuring correct insertion of hydrophobic proteins into their membranes. Moreover, the correct targeting of these transcripts to peroxisomes is crucial for peroxisomal and cellular function, emphasizing the importance of localized translation for cellular physiology.

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Jan 2022 • bioRxiv

The association of MEG3 lncRNA with nuclear speckles in living cells

Sarah Hasenson, Ella Alkalay, Mohammad K Atrash, Alon Boocholez, Julianna Gershbaum, Hodaya Hochberg-Laufer, Yaron Shav-Tal

Nuclear speckles are nuclear bodies containing RNA-binding proteins as well as RNAs including long non-coding RNAs (lncRNAs). MEG3 is a nuclear retained lncRNA that was identified to be associated with nuclear speckles. To understand the association dynamics of MEG3 lncRNA with nuclear speckles in living cells we generated a fluorescently-tagged MEG3 transcript that could be detected in real-time. Under regular conditions, transient association of MEG3 with nuclear speckles was observed, including a nucleoplasmic fraction. Conditions under which transcription or splicing were inactive, which are known to affect nuclear speckle structure, showed prominent and increased association of MEG3 lncRNA with the nuclear speckles, specifically forming a ring-like structure around the nuclear speckles. This contrasted with MALAT1 lncRNA that is normally highly associated with nuclear speckles, which was released and dispersed in the nucleoplasm. Under normal conditions MEG3 dynamically associated with the periphery of the nuclear speckles, but under transcription or splicing inhibition, MEG3 could also enter the center of the nuclear speckle. Altogether, using live-cell imaging approaches we find that MEG3 lncRNA is a transient resident of nuclear speckles and that its association with this nuclear body is modulated by the levels of transcription and splicing activities in the cell.

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Jan 2022 • ACS Omega

CVD-Assisted Synthesis of 2D Layered MoSe2 on Mo Foil and Low Frequency Raman Scattering of Its Exfoliated Few-Layer Nanosheets on CaF2 Substrates

Rajashree Konar, Bharathi Rajeswaran, Atanu Paul, Eti Teblum, Hagit Aviv, Ilana Perelshtein, Ilya Grinberg, Yaakov Raphael Tischler, Gilbert Daniel Nessim

Transition-metal dichalcogenides (TMDCs) are unique layered materials with exotic properties. So, examining their structures holds tremendous importance. 2H-MoSe2 (analogous to MoS2; Gr. 6 TMDC) is a crucial optoelectronic material studied extensively using Raman spectroscopy. In this regard, low-frequency Raman (LFR) spectroscopy can probe this material’s structure as it reveals distinct vibration modes. Here, we focus on understanding the microstructural evolution of different 2H-MoSe2 morphologies and their layers using LFR scattering. We grew phase-pure 2H-MoSe2 (with variable microstructures) directly on a Mo foil using a two-furnace ambient-pressure chemical vapor deposition (CVD) system by carefully controlling the process parameters. We analyzed the layers of exfoliated flakes after ultrasonication and drop-cast 2H-MoSe2 of different layer thicknesses by choosing different concentrations of …

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Jan 2022 • bioRxiv

Uncovering cellular processes in HeLa cells using unsupervised machine learning

Tom Maimon, Yaron Trink, Jacob Goldberger, Tomer Kalisky

Gene expression measurements taken over multiple time points are useful for describing dynamic biological phenomena such as tissue development, regeneration, and cancer. However, since these phenomena involve multiple processes occurring in parallel, for example differentiation and proliferation, it is difficult to discern their respective contributions to a measured gene expression profile at any given point in time. Here, we demonstrate the use of un-supervised machine learning techniques to identify and de-convolve processes occurring in parallel in a simple model system. We first downloaded a published dataset of RNAseq measurements from synchronized HeLa cells that were sampled at 14 consecutive time points. We then used Fourier analysis and Topic modeling to identify two concurrent processes: a periodic process, corresponding to cell division, and a transient process related to HeLa cell identity (e.g. cervical cancer), that is presumably required for recovery from cell cycle arrest. This study demonstrates the use of un-supervised machine learning techniques to identify hidden states and processes in the cell.

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Jan 2022 • Journal of Composites Science 6 (1), 15, 2022

A Review on Synthesis Methods of Phyllosilicate-and Graphene-Filled Composite Hydrogels

Sayan Ganguly, Shlomo Margel

This review discusses, in brief, the various synthetic methods of two widely-used nanofillers; phyllosilicate and graphene. Both are 2D fillers introduced into hydrogel matrices to achieve mechanical robustness and water uptake behavior. Both the fillers are inserted by physical and chemical gelation methods where most of the chemical gelation, ie, covalent approaches, results in better physical properties compared to their physical gels. Physical gels occur due to supramolecular assembly, van der Waals interactions, electrostatic interactions, hydrophobic associations, and H-bonding. For chemical gelation, in situ radical triggered gelation mostly occurs.

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Jan 2022 • ACS Applied Materials & Interfaces

Chemical Vapor Deposition of Spherical Amorphous Selenium Mie Resonators for Infrared Meta-Optics

Danveer Singh, Michal Poplinger, Avraham Twitto, Rafi Snitkoff, Pilkhaz Nanikashvili, Ori Azolay, Adi Levi, Chen Stern, Gili Cohen Taguri, Asaf Albo, Doron Naveh, Tomer Lewi

Applying direct growth and deposition of optical surfaces holds great promise for the advancement of future nanophotonic technologies. Here, we report on a chemical vapor deposition (CVD) technique for depositing amorphous selenium (a-Se) spheres by desorption of selenium from Bi2Se3 and re-adsorption on the substrate. We utilize this process to grow scalable, large area Se spheres on several substrates and characterize their Mie-resonant response in the mid-infrared (MIR) spectral range. We demonstrate size-tunable Mie resonances spanning the 2–16 μm spectral range for single isolated resonators and large area ensembles. We further demonstrate strong absorption dips of up to 90% in ensembles of particles in a broad MIR range. Finally, we show that ultra-high-Q resonances arise in the case where Se Mie-resonators are coupled to low-loss epsilon-near-zero (ENZ) substrates. These findings …

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Jan 2022 • New Biotechnology

Microfluidic tool for rapid functional characterization of CRISPR complexes

Dana Peleg-Chen, Guy Shuvali, Lev Brio, Amit Ifrach, Ortal Iancu, Efrat Barbiro-Michaely, Ayal Hendel, Doron Gerber

RNA guided nucleases are regarded as the future genome editing technologies. As such, they need to meet strong safety margins. Two major challenges in incorporating CRISPR technologies into the clinical world are off-target activity and editing efficiency. The common way to tackle such issues is to measure the binding and cleavage kinetics of the CRISPR enzyme. This can be challenging since, for example, DNA is not released from the CAS9 protein post cleavage. Here a promising new microfluidic approach to characterizing Enzymatic Interaction and Function of CRISPR complexes on a microfluidic platform (EnzyMIF) is presented. The method can rapidly detect the kd, koff, km and kcat for various RNA guided nucleases. In this work, two single guide RNAs with significantly different in-cell cleavage efficiency, RAG2 and RAG1, are used as proof-of-concept. The EnzyMIF assay results provide biochemical …

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Jan 2022 • ACS Energy Letters

Stabilizing high-voltage lithium-ion battery cathodes using functional coatings of 2D tungsten diselenide

Sandipan Maiti, Rajashree Konar, Hadar Sclar, Judith Grinblat, Michael Talianker, Maria Tkachev, Xiaohan Wu, Aleksandr Kondrakov, Gilbert Daniel Nessim, Doron Aurbach

Functional surface coatings were applied on high voltage spinel (LiNi0.5Mn1.5O4; LNMO) and Ni-rich (LiNi0.85Co0.1Mn0.05O2; NCM851005) NCM cathode materials using few-layered 2H tungsten diselenide (WSe2). Simple liquid-phase mixing with WSe2 in 2-propanol and low-temperature (130 °C) heat treatment in nitrogen flow dramatically improved electrochemical performance, including stable cycling, high-rate performance, and lower voltage hysteresis in Li coin cells at 30 and 55 °C. Significantly improved capacity retention at 30 °C [Q401/Q9 of 99% vs 38% for LNMO and Q322/Q23 of 64% vs 46% for NCM851005] indicated efficient functionality. TEM and XPS clarified the coating distribution and coordination with the cathode surface, while postcycling studies revealed its sustainability, enabling lower transition metal dissolution and minor morphological deformation/microcrack formation. A modified and …

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Jan 2022 • Scientific Reports

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

David Glukhov, Zeev Zalevsky, Avi Karsenty

The functionality of a nanoscale silicon-based optoelectronic modulator is deeply analyzed while it appears that two competing processes, thermal and photonic, are occurring at the same time, and are preventing the optimization of the electro-optics coupling. While an incident illumination-beam first process is translated into photons, generating pairs of electrons–holes, a second process of thermal generation, creating phonons enables a loss of energy. Complementary studies, combining strong analytical models and numerical simulations, enabled to better understand this competition between photonic and thermal activities, in order to optimize the modulator. Moreover, in order to prevent unnecessary heating effects and to present a proposed solution, a picosecond pulsed laser is suggested and demonstrated as the ultimate solution so no energy will be wasted in heat, and still the photonic energy will be fully …

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Jan 2022 • Journal of Superconductivity and Novel Magnetism

Effect of Focused Ion Beam Irradiation on Superconducting Nanowires

Lior Shani, Avital Fried, Yafit Fleger, Olga Girshevitz, Amos Sharoni, Yosef Yeshurun

Recent advances in focused ion beam (FIB) technology exploit accelerated helium or neon ions, rather than gallium, for maskless fabrication of superconducting nanocomponents. We present a study of the effect of the damage induced by the accelerated ions on the superconducting transition temperature, T c, of a patterned~ 85-nm-wide Nb wire, demonstrating a decrease of T c from~ 5.5 K in the wire patterned by He ions to~ 2.8 and 2.3 K exploiting Ne and Ga ions, respectively. In an effort to gain insight into the origin of these changes in T c, we performed Stopping and Range of Ions in Matter (SRIM) simulations to estimate the damage induced by each type of ion. The simulations show that the lateral distribution of the ion beam and the sputtering rate in using Ne or Ga are significantly larger than those caused by He, consistent with the changes in the measured electrical properties of the nanowire.

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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

Jan 2022 • Elsevier Reference Collection in Chemistry, 1, 2022

Quantum Tunneling in Computational Catalysis and Kinetics: Is it Really Important?

Ashim Nandi, Germán Molpeceres, Prashant K Gupta, Dan T Major, Johannes Kästner, Jan ML Martin, Sebastian Kozuch

Quantum tunneling (QT) is not an effect often considered in chemistry, and rightfully so. However, in many cases it is significant, and in some cases it is even considerable. In this chapter we will describe the basic tenets of QT with a focus on catalysis, followed by some of the most important tools to study and compute them. The chapter goes on to address the title of the chapter by discussing several clear cases of QT for hydrogen-based reactions in organometallic, enzymatic, astrochemical, and organic systems. The insights highlighted in the chapter showcase the importance of QT in specific catalyzed reactions and help uncover the instances that are worth of attention.

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2022 • Methods

CRISPR technology

HJ Chung, YK Kang, PD Hsu, S Konermann, MH Porteus, A Hendel, J Clark, RO Bak, Ryan De, DJ Dellinger, R Kaiser, J Myerson, K Gagnon, M Damha, M Habibian, DT O’Reilly, Z Kartje

Recent patents relating to CRISPR methods and compositions for gene editing and therapeutic use.

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2022 • Energy & Environmental Science

Light-induced beneficial ion accumulation for high-performance quasi-2D perovskite solar cells

Xiaomei Lian, Lijian Zuo, Bowen Chen, Biao Li, Haotian Wu, Shiqi Shan, Gang Wu, Xuegong Yu, Qi Chen, Liwei Chen, Deren Yang, David Cahen, Hongzheng Chen

Ion migration and subsequent accumulation at interfaces, driven by the built-in potential (Vbi), are intrinsic properties of halide perovskite solar cells (PVSCs), which mostly decrease the device performance. To address this issue, we constructed favorable ion accumulation in perovskite solar cells via illumination to improve the performance of the quasi-2D PVSCs. This design dramatically improves the photo-carrier collection and enables significant device performance improvement from 14.6% to 19.05%, one of the best results for quasi-2D PVSCs. We argue that the light-triggered favorable ion accumulation originates from (1) the photo-induced quasi-Fermi level splitting that compensates the Vbi, so as to avoid the ion accumulation that decreases Vbi, and (2) the light-intensity-distribution-induced uneven ion potential further drives the segregation of mobile ions towards favorable ion accumulation, decreasing any …

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2022 • Frontiers in Immunology

A BALB/c IGHV reference set, defined by haplotype analysis of long-read VDJ-c sequences from F1 (BALB/cx C57BL/6) mice

Katherine JL Jackson, Justin T Kos, William Lees, William S Gibson, Melissa Laird Smith, Ayelet Peres, Gur Yaari, Martin Corcoran, Christian E Busse, Mats Ohlin, Corey T Watson, Andrew M Collins

The immunoglobulin genes of inbred mouse strains that are commonly used in models of antibody-mediated human diseases are poorly characterized. This compromises data analysis. To infer the immunoglobulin genes of BALB/c mice, we used long-read SMRT sequencing to amplify VDJ-C sequences from F1 (BALB/cx C57BL/6) hybrid animals. Strain variations were identified in the Ighm and Ighg2b genes, and analysis of VDJ rearrangements led to the inference of 278 germline IGHV alleles. 169 alleles are not present in the C57BL/6 genome reference sequence. To establish a set of expressed BALB/c IGHV germline gene sequences, we computationally retrieved IGHV haplotypes from the IgM dataset. Haplotyping led to the confirmation of 162 BALB/c IGHV gene sequences. A musIGHV398 pseudogene variant also appears to be present in the BALB/cByJ substrain, while a functional musIGHV398 gene is …

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2022 • Physical Chemistry Chemical Physics

The effects of thermal treatment and irradiation on the chemical properties of natural diamonds

Ira Litvak, Avner Cahana, Yaakov Anker, Sharon Ruthstein, Haim Cohen

The modification of nitrogen-contaminated diamonds into color-enhanced diamonds is usually achieved by irradiation and thermal treatment (annealing). These treatments affect nitrogen contamination chemical bonding, vacancy concentration, and atom orientation centers in the diamond lattice. In this study, natural diamonds were subjected to irradiation and thermal annealing color enhancement treatments to produce green, blue, and yellow fancy diamonds. The study followed the changes that occur during treatment relying on visual assessment, fluorescence, UV-vis, FTIR, and EPR spectroscopy to characterize paramagnetic centers. The results indicated that diamonds containing high levels of nitrogen contamination presented a relatively high carbon-centered radical concentration. Two paramagnetic groups with different g-values were found, namely, low g-value centers of 2.0017–2.0027 and high g-value …

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2022 • Materials Advances 3 (11), 4471-4488, 2022

A mini-review focusing on ambient-pressure chemical vapor deposition (AP-CVD) based synthesis of layered transition metal selenides for energy storage applications

Rajashree Konar, Gilbert Daniel Nessim

With high power consumption and energy densities in demand, there has been a surge in researching the next-generation electrochemical energy storage devices (lithium-ion batteries, sodium-ion batteries, and magnesium-ion batteries). 2D layered transition metal selenides (TMSes) are promising in terms of scalability and portability for electronic devices and electric vehicles. Such large-scale applications rely on exploring these TMSes containing high capacity, good cycling stability, and superior rate capability. Their exotic anisotropic properties has pushed their research towards energy storage. Since Chemical vapor deposition (CVD) is an efficient and scalable technique to synthesize these materials, we summarize the synthesis of TMSes using ambient-pressure CVD and highlight their many properties, preparation methods, and applications in LiB, NaB, and MgB. We discuss how tuning surface morphology …

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2022 • Physical Chemistry Chemical Physics

Electron transport via tyrosine-doped oligo-alanine peptide junctions: role of charges and hydrogen bonding

Cunlan Guo, Yulian Gavrilov, Satyajit Gupta, Tatyana Bendikov, Yaakov Levy, Ayelet Vilan, Israel Pecht, Mordechai Sheves, David Cahen

A way of modulating the solid-state electron transport (ETp) properties of oligopeptide junctions is presented by charges and internal hydrogen bonding, which affect this process markedly. The ETp properties of a series of tyrosine (Tyr)-containing hexa-alanine peptides, self-assembled in monolayers and sandwiched between gold electrodes, are investigated in response to their protonation state. Inserting a Tyr residue into these peptides enhances the ETp carried via their junctions. Deprotonation of the Tyr-containing peptides causes a further increase of ETp efficiency that depends on this residue's position. Combined results of molecular dynamics simulations and spectroscopic experiments suggest that the increased conductance upon deprotonation is mainly a result of enhanced coupling between the charged C-terminus carboxylate group and the adjacent Au electrode. Moreover, intra-peptide hydrogen …

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2022 • Chemical Science

Cu (II)-based DNA Labeling Identifies the Structural Link Between Activation and Termination in a Metalloregulator

Joshua Casto, Alysia Mandato, Lukas Hofmann, Idan Yakobov, Shreya Ghosh, Sharon Ruthstein, Sunil Saxena

2022 • Physical Chemistry Chemical Physics

Cu 2+-Induced self-assembly and amyloid formation of a cyclic d, l-α-peptide: structure and function

Daniel Klose, Sahithya Phani Babu Vemulapalli, Michal Richman, Safra Rudnick, Vered Aisha, Meital Abayev, Marina Chemerovski, Meital Shviro, David Zitoun, Katharina Majer, Nino Wili, Gil Goobes, Christian Griesinger, Gunnar Jeschke, Shai Rahimipour

In a wide spectrum of neurodegenerative diseases, self-assembly of pathogenic proteins to cytotoxic intermediates is accelerated by the presence of metal ions such as Cu2+. Only low concentrations of these early transient oligomeric intermediates are present in a mixture of species during fibril formation, and hence information on the extent of structuring of these oligomers is still largely unknown. Here, we investigate dimers as the first intermediates in the Cu2+-driven aggregation of a cyclic D,L-α-peptide architecture. The unique structural and functional properties of this model system recapitulate the self-assembling properties of amyloidogenic proteins including β-sheet conformation and cross-interaction with pathogenic amyloids. We show that a histidine-rich cyclic D,L-α-octapeptide binds Cu2+ with high affinity and selectivity to generate amyloid-like cross-β-sheet structures. By taking advantage of backbone …

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