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Jun 2021 • Nucleic acids research

Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses

Songlei Liu, Sukanya Punthambaker, Eswar PR Iyer, Thomas Ferrante, Daniel Goodwin, Daniel Fürth, Andrew C Pawlowski, Kunal Jindal, Jenny M Tam, Lauren Mifflin, Shahar Alon, Anubhav Sinha, Asmamaw T Wassie, Fei Chen, Anne Cheng, Valerie Willocq, Katharina Meyer, King-Hwa Ling, Conor K Camplisson, Richie E Kohman, John Aach, Je Hyuk Lee, Bruce A Yankner, Edward S Boyden, George M Church

We present barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel insitu analyses (BOLORAMIS), a reverse transcription-free method for spatially-resolved, targeted, in situ RNA identification of single or multiple targets. BOLORAMIS was demonstrated on a range of cell types and human cerebral organoids. Singleplex experiments to detect coding and non-coding RNAs in human iPSCs showed a stem-cell signature pattern. Specificity of BOLORAMIS was found to be 92% as illustrated by a clear distinction between human and mouse housekeeping genes in a co-culture system, as well as by recapitulation of subcellular localization of lncRNA MALAT1. Sensitivity of BOLORAMIS was quantified by comparing with single molecule FISH experiments and found to be 11%, 12% and 35% for GAPDH, TFRC and POLR2A, respectively. To demonstrate BOLORAMIS for multiplexed gene …

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Jun 2021 • Physical Review A

Efimov scenario for overlapping narrow Feshbach resonances

Yaakov Yudkin, Lev Khaykovich

May 2021 • Nucleic acids research

Systematic identification of A-to-I RNA editing in zebrafish development and adult organs

Ilana Buchumenski, Karoline Holler, Lior Appelbaum, Eli Eisenberg, Jan Philipp Junker, Erez Y Levanon

A-to-I RNA editing is a common post transcriptional mechanism, mediated by the Adenosine deaminase that acts on RNA (ADAR) enzymes, that increases transcript and protein diversity. The study of RNA editing is limited by the absence of editing maps for most model organisms, hindering the understanding of its impact on various physiological conditions. Here, we mapped the vertebrate developmental landscape of A-to-I RNA editing, and generated the first comprehensive atlas of editing sites in zebrafish. Tens of thousands unique editing events and 149 coding sites were identified with high-accuracy. Some of these edited sites are conserved between zebrafish and humans. Sequence analysis of RNA over seven developmental stages revealed high levels of editing activity in early stages of embryogenesis, when embryos rely on maternal mRNAs and proteins. In contrast to the other organisms studied so …

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May 2021 • The European Physical Journal D

Roadmap on dynamics of molecules and clusters in the gas phase

Henning Zettergren, Alicja Domaracka, Thomas Schlathölter, Paola Bolognesi, Sergio Díaz-Tendero, Marta Łabuda, Sanja Tosic, Sylvain Maclot, Per Johnsson, Amanda Steber, Denis Tikhonov, Mattea Carmen Castrovilli, Lorenzo Avaldi, Sadia Bari, Aleksandar R Milosavljević, Alicia Palacios, Shirin Faraji, Dariusz G Piekarski, Patrick Rousseau, Daniela Ascenzi, Claire Romanzin, Ewa Erdmann, Manuel Alcamí, Janina Kopyra, Paulo Limão-Vieira, Jaroslav Kočišek, Juraj Fedor, Simon Albertini, Michael Gatchell, Henrik Cederquist, Henning T Schmidt, Elisabeth Gruber, Lars H Andersen, Oded Heber, Yoni Toker, Klavs Hansen, Jennifer A Noble, Christophe Jouvet, Christina Kjær, Steen Brøndsted Nielsen, Eduardo Carrascosa, James Bull, Alessandra Candian, Annemieke Petrignani

This roadmap article highlights recent advances, challenges and future prospects in studies of the dynamics of molecules and clusters in the gas phase. It comprises nineteen contributions by scientists with leading expertise in complementary experimental and theoretical techniques to probe the dynamics on timescales spanning twenty order of magnitudes, from attoseconds to minutes and beyond, and for systems ranging in complexity from the smallest (diatomic) molecules to clusters and nanoparticles. Combining some of these techniques opens up new avenues to unravel hitherto unexplored reaction pathways and mechanisms, and to establish their significance in, eg radiotherapy and radiation damage on the nanoscale, astrophysics, astrochemistry and atmospheric science.

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May 2021 • Nanomaterials

Photocatalytic degradation of organic dyes and antimicrobial activities by polyaniline–nitrogen-doped carbon dot nanocomposite

Moorthy Maruthapandi, Arumugam Saravanan, Priyanka Manohar, John HT Luong, Aharon Gedanken

Nitrogen-doped carbon nanodots ([email protected]) were prepared by hydrothermal processing of bovine serum albumin (Mw: 69,324 with 607 amino acids). A polyaniline ([email protected]) nanocomposite was then synthesized by ultrasonication and used to degrade Congo red (CR), methylene blue (MB), Rhodamine B (RhB), and crystal violet (CV) four common organic dyes. The [email protected] nanocomposite simultaneously adsorbed and concentrated the dye from the bulk solution and degraded the adsorbed dye, resulting in a high rate of dye degradation. The combination of holes (h+), hydroxyl (OH•), and O 2•− was involved in the [email protected] photocatalytic degradation of the dyes. Under visible light illumination at neutral pH, the [email protected] were proven as an efficient adsorbent and photocatalyst for the complete degradation of CR within 20 min. MB and RhB were also degraded but required longer treatment times. These findings supported the design of remediation processes for such dyes and predicted their fate in the environment. The nanocomposite also exhibited antimicrobial activities against Gram-negative bacterium E. coli and Gram-positive bacterium S. aureus. View Full-Text

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May 2021 • Cell reports

PD-L1 recruits phospholipase C and enhances tumorigenicity of lung tumors harboring mutant forms of EGFR

Soma Ghosh, Nishanth Belugali Nataraj, Ashish Noronha, Sushant Patkar, Arunachalam Sekar, Saptaparna Mukherjee, Sabina Winograd-Katz, Lior Kramarski, Aakanksha Verma, Moshit Lindzen, Diana Drago Garcia, Joseph Green, Galit Eisenberg, Hava Gil-Henn, Arkaprabha Basu, Yan Lender, Shimon Weiss, Moshe Oren, Michal Lotem, Benjamin Geiger, Eytan Ruppin, Yosef Yarden

Cancer immunotherapy focuses on inhibitors of checkpoint proteins, such as programmed death ligand 1 (PD-L1). Unlike RAS-mutated lung cancers, EGFR mutant tumors have a generally low response to immunotherapy. Because treatment outcomes vary by EGFR allele, intrinsic and microenvironmental factors may be involved. Among all non-immunological signaling pathways surveyed in patients’ datasets, EGFR signaling is best associated with high PD-L1. Correspondingly, active EGFRs stabilize PD-L1 transcripts and depletion of PD-L1 severely inhibits EGFR-driven tumorigenicity and metastasis in mice. The underlying mechanisms involve the recruitment of phospholipase C-γ1 (PLC-γ1) to a cytoplasmic motif of PD-L1, which enhances PLC-γ1 activation by EGFR. Once stimulated, PLC-γ1 activates calcium flux, Rho GTPases, and protein kinase C, collectively promoting an aggressive phenotype. Anti-PD …

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May 2021

Chemically modified guide rnas for crispr/cas-mediated gene regulation

Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.) 2015-04-06

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May 2021 • The Journal of Physical Chemistry Letters 12 (21), 5138-5149, 2021

Bimetallic phosphides for hybrid supercapacitors

SK Tarik Aziz, Sushil Kumar, Sk Riyajuddin, Kaushik Ghosh, Gilbert Daniel Nessim, Deepak P Dubal

Supercapacitors (SCs) are considered promising energy storage systems because of their high power output and long-term cycling stability; however, they usually exhibit poor energy density. The hybrid supercapacitor (HSC) is an emerging concept in which two dissimilar electrodes with different charge storage mechanisms are paired to deliver high energy without sacrificing power output. This Perspective highlights the features of transition-metal phosphides (TMPs) as the positive electrode in HSCs. In particular, bimetallic nickel cobalt phosphide (NiCoP) with multiple redox sites, excellent electrochemical reversibility, and stability is discussed. We outline how the rational heterostructures, elemental variations, and nanocomposite morphologies tune the electrochemical properties of NiCoP as the positive electrode in HSCs. The Perspective further sheds light on NiCoP-based composites that help in improving the …

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May 2021 • 2021 Conference on Lasers and Electro-Optics (CLEO), 1-2, 2021

Efficient Interaction of X-ray Single Photons with a Beam Splitter

E Strizhevsky, D Borodin, A Schori, S Francoual, R Röhlsberger, S Shwartz

We demonstrate efficient interaction of hard x-ray single photons with a beam splitter for the first time and use it to show the nonclassical behavior of x-ray heralded photons.

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May 2021 • CLEO: Science and Innovations, STu2H. 5, 2021

Integrated discrete-time surface acoustic wave photonic radio-frequency filters with arbitrary tap weights

Moshe Katzman, Dvir Munk, Maayan Priel, Etai Grunwald, Mirit Hen, Avi Zadok

Integrated, discrete time microwave filters are realized in surface acoustic wave photonics over standard silicon on insulator. The magnitude and phase of each tap are adjusted independently. Twelve-tap filters with 5 MHz bandwidth are demonstrated.

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May 2021 • Small

Inelastic Electron Tunneling Spectroscopic Analysis of Bias‐Induced Structural Changes in a Solid‐State Protein Junction

Jerry A Fereiro, Israel Pecht, Mordechai Sheves, David Cahen

A central issue in protein electronics is how far the structural stability of the protein is preserved under the very high electrical field that it will experience once a bias voltage is applied. This question is studied on the redox protein Azurin in the solid‐state Au/protein/Au junction by monitoring protein vibrations during current transport under applied bias, up to ≈1 GV m−1, by electrical detection of inelastic electron transport effects. Characteristic vibrational modes, such as CH stretching, amide (NH) bending, and AuS (of the bonds that connect the protein to an Au electrode), are not found to change noticeably up to 1.0 V. At >1.0 V, the NH bending and CH stretching inelastic features have disappeared, while the AuS features persist till ≈2 V, i.e., the proteins remain Au bound. Three possible causes for the disappearance of the NH and CH inelastic features at high bias, namely, i) resonance transport, ii …

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May 2021 • Trends in Genetics 37 (8), 685-687, 2021

The New RNA-Editing Era–Ethical Considerations

Azgad Gold, Erez Y Levanon, Eli Eisenberg

The characteristics of RNA editing, including the lower risk compared with genome editing, may loosen the ethical barriers that are currently imposed on genetic engineering, thus opening new possibilities for research, therapy, and human enhancement. We should start considering the future ethical and social implications of this new and promising technology.

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May 2021 • Energy Storage Systems Beyond Li-Ion Intercalation Chemistry

Na Na-ion 0.44 MnO Batteries 2

Satyanarayana Maddukuri, Amey Nimkar, Munseok S Chae, Tirupathi Rao Penki, Shalom Luski, Doron Aurbach

Aqueous salt batteries with high concentrations of salt or water in salt aqueous systems have received considerable attention with focus on improving working voltage range and energy density. Here, the effect of NaClO4 salt concentration on the electrochemical performance and stability of tunnel-type Na0. 44MnO2 (NMO) cathodes and organic polyimide (PI) derivative anodes was studied. High capacity retention and 100% coulombic efficiency were shown for NMO/PI full cell in saturated NaClO4 electrolyte. A high, stable capacity of 115 mAh/g was achieved for the PI anode material, and the full cell showed a stable capacity of 41 mAh/g at 2C rate for 430 cycles (calculated for the weight of NMO cathode). Even at a fast 5C rate, a discharge capacity of 33 mAh/g was maintained for 2,400 prolonged cycles with nearly 100% efficiency. The full cell device can achieve an average voltage of 1 V with energy density of 24 Wh/kg. This study highlights concentrated sodium perchlorate as a promising electrolyte solution for stabilization enhancement of electrochemical performance in aqueous media. of electrodes and

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May 2021 • ACS Applied Materials & Interfaces

Toward Efficient Synthesis of Porous All-Carbon-Based Nanocomposites for Enantiospecific Separation

Milena Perovic, Sapir Shekef Aloni, Wuyong Zhang, Yitzhak Mastai, Markus Antonietti, Martin Oschatz

Chiral separation and asymmetric synthesis and catalysis are crucial processes for obtaining enantiopure compounds, which are especially important in the pharmaceutical industry. The efficiency of the separation processes is readily increased by using porous materials as the active material can interact with a larger surface area. Silica, metal–organic frameworks, or chiral polymers are versatile porous materials that are established in chiral applications, but their instability under certain conditions in some cases requires the use of more stable porous materials such as carbons. In addition to their stability, porous carbon materials can be tailored for their ability to adsorb and catalytically activate different chemical compounds from the liquid and the gas phase. The difficulties imposed by the functionalization of carbons with chiral species were tackled in the past by carbonizing chiral ionic liquids (CILs) together with a …

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May 2021 • 2021 Conference on Lasers and Electro-Optics (CLEO), 1-2, 2021

Efficient Interaction of X-ray Single Photons with a Beam Splitter

E Strizhevsky, D Borodin, A Schori, S Francoual, R Röhlsberger, S Shwartz

We demonstrate efficient interaction of hard x-ray single photons with a beam splitter for the first time and use it to show the nonclassical behavior of x-ray heralded photons.

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May 2021 • Journal of Solid State Electrochemistry

The effect of synthesis and zirconium doping on the performance of nickel-rich NCM622 cathode materials for Li-ion batteries

Tirupathi Rao Penki, Sapir Gilady, Prasant Kumar Nayak, Hadar Sclar, Yuval Elias, Judith Grinblat, Michael Talianker, Boris Markovsky, Christoph Erk, Shalom Luski, Doron Aurbach

Among the cathode materials for advanced Li-ion batteries, nickel-rich Ni-Co-Mn (NCM) LiNi x Co y Mn y O 2 (x> 0.5, x+ 2y= 1) attracts great interest as promising materials owing to their high capacity, low cost, good cycling stability, safety and the fact that their stable capacity can be extracted by charging up to 4.3 V vs. Li. In this work, the effect of the synthesis route—freeze-drying, self-combustion, solid state and co-precipitation on the performance of NCM622 (LiNi x Co y Mn y O 2, x= 0.6, y= 0.2) cathodes—in Li cells was thoroughly studied. The material prepared by freeze-drying exhibited superior electrochemical properties. The effect of in situ and ex situ Zr 4+ cations doping on the electrodes’ capacity, stability and average voltage was also studied. Doping via a top–down, ex situ mode improved the performance in terms of capacity stabilization, whereas electrodes comprising materials that were doped via a …

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May 2021 • ECS Meeting Abstracts

Selective Catalysis for Electrocatalytic Hydrogen Oxidation and Evolution Reactions Via Carbon Nanotube Encapsulation and Oxide Nano-Layer Deposition

Samuel Spencer Hardisty, Kobby Saadi, David Zitoun

Catalysts undergo poisoning and degradation during their utilisation in many different fields. Common examples are the CO poisoning of Pt,1 or the degradation of Pt/C catalysts during start-stop procedures,2 both occurring in polymer electrolyte fuel cells (PEMFCs). Another energy technology that features prominent catalyst degradation is the hydrogen bromine redox flow battery (H2-Br2 RFB). H2-Br2 RFBs are a cheap and efficient solution to large scale energy storage.3 The main hinderance of the technology is the poisoning of the hydrogen evolution reaction/hydrogen oxidation reaction (HER/HOR) catalyst by bromine species which have crossed over the proton exchange membrane.4 Without a revolution in membrane development, this crossover appears unpreventable.5,6 Therefore, we sought to protect the catalyst locally. Two possible solutions were found to impart catalyst selectivity: Pt encapsulation …

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May 2021 • Science advances

Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER

Jae Ho Lee, Ahmad Jomaa, SangYoon Chung, Yu-Hsien Hwang Fu, Ruilin Qian, Xuemeng Sun, Hao-Hsuan Hsieh, Sowmya Chandrasekar, Xiaotian Bi, Simone Mattei, Daniel Boehringer, Shimon Weiss, Nenad Ban, Shu-ou Shan

The conserved signal recognition particle (SRP) cotranslationally delivers ~30% of the proteome to the eukaryotic endoplasmic reticulum (ER). The molecular mechanism by which eukaryotic SRP transitions from cargo recognition in the cytosol to protein translocation at the ER is not understood. Here, structural, biochemical, and single-molecule studies show that this transition requires multiple sequential conformational rearrangements in the targeting complex initiated by guanosine triphosphatase (GTPase)–driven compaction of the SRP receptor (SR). Disruption of these rearrangements, particularly in mutant SRP54G226E linked to severe congenital neutropenia, uncouples the SRP/SR GTPase cycle from protein translocation. Structures of targeting intermediates reveal the molecular basis of early SRP-SR recognition and emphasize the role of eukaryote-specific elements in regulating targeting. Our results …

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May 2021 • 2021 Conference on Lasers and Electro-Optics (CLEO), 1-2, 2021

High-resolution x-ray fluorescence imaging using structured illumination

Y Klein, O Sefi, H Schwartz, S Shwartz

We report a proof of principle experiment demonstrating the use of structured illumination and coincidence for x-ray fluorescence imaging at very high spatial resolution and short measurement time with a conventional x-ray tube.

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May 2021 • ECS Meeting Abstracts

Evaluation of Redox Mediator’s Oxidation Stability in Lithium-Oxygen Batteries

Hun Kim, Won-Jin Kwak, Jiwon Park, Doron Aurbach, Hye Ryung Byon, Yang-Kook Sun

Employing organic redox mediators (ORMs) as mobile catalyst into the electrolyte system has been selected as an important strategy to lower the charging overpotentials in lithium-oxygen (Li-O2) batteries. Careful choice of molecular designs of ORMs can also tailor their redox potential and rate of electron-transfer to improve the catalytic efficiency. However, the stability of ORMs in Li–O2 cells was scarcely studied. In here, catalytic efficiency and stability of several important ORMs are assessed through in situ gas analysis and reactivity tests with singlet oxygen. Some well-known ORMs are detrimentally decomposed during the first cycle in Li–O2 cells, whereas nitroxyl-radical-based ORMs bear the most stable and efficient response. Analogous nitroxyl-radical derivatives further increase round-trip energy efficiency and electron-transfer kinetics. This study also emphasizes the evaluation of chemical stability of …

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May 2021 • Science Bulletin

Single-pixel imaging with high-energy electromagnetic radiation and particles

Sharon Shwartz

High-photon-energy electromagnetic radiations in the forms of X-rays and c-rays and particles such as neutrons and electrons are routinely used for various imaging and diffraction modalities with applications ranging from materials science and chemistry to biomedical imaging and industrial imaging. They provide important unique information on the structure and the functionality of the investigated samples that other methods cannot provide. However, despite the extensive efforts, there are several critical challenges that hamper further improvements in the performances of the modalities and thus limit the accessible information. Interestingly, while very different in the way high-photon-energy radiation and particles interact with the sample, imaging modalities that utilize them share similar challenges. Among the major challenges are damage to the sample when it is exposed to the probe beam and the limited resolution of the images (for electrons the resolution can be high but only for small samples). The origin of the damage is the large quanta of energy that is absorbed during the interaction between the probe and the sample. The resolution is limited since magnification and point-to-point imaging are very challenging with high energy photons and particles due to the limited available optics. For some applications, the sensitivity and the slow time response are also obstructive. Traditionally, two approaches for imaging have been utilized. In the first approach, a wide beam irradiates the sample, and a pixelated detector is mounted after the sample to measure the intensity distribution of the transmitted or scattered beam. In the second approach, a …

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