Apr 2023 • Pharmaceutics 15 (5), 1329, 2023
Daniel Allen, Nechama Kalter, Michael Rosenberg, Ayal Hendel
Genome engineering via targeted nucleases, specifically CRISPR-Cas9, has revolutionized the field of gene therapy research, providing a potential treatment for diseases of the blood and immune system. While numerous genome editing techniques have been used, CRISPR-Cas9 homology-directed repair (HDR)-mediated editing represents a promising method for the site-specific insertion of large transgenes for gene knock-in or gene correction. Alternative methods, such as lentiviral/gammaretroviral gene addition, gene knock-out via non-homologous end joining (NHEJ)-mediated editing, and base or prime editing, have shown great promise for clinical applications, yet all possess significant drawbacks when applied in the treatment of patients suffering from inborn errors of immunity or blood system disorders. This review aims to highlight the transformational benefits of HDR-mediated gene therapy and possible solutions for the existing problems holding the methodology back. Together, we aim to help bring HDR-based gene therapy in CD34+ hematopoietic stem progenitor cells (HSPCs) from the lab bench to the bedside.
Show moreApr 2023 • Journal of Functional Biomaterials 14 (4), 215, 2023
Ella Itzhaki, Yuval Elias, Neta Moskovits, Salomon M Stemmer, Shlomo Margel
Proteinoids—simple polymers composed of amino acids—were suggested decades ago by Fox and coworkers to form spontaneously by heat. These special polymers may self-assemble in micrometer structures called proteinoid microspheres, presented as the protocells of life on earth. Interest in proteinoids increased in recent years, in particular for nano-biomedicine. They were produced by stepwise polymerization of 3–4 amino acids. Proteinoids based on the RGD motif were prepared for targeting tumors. Nanocapsules form by heating proteinoids in an aqueous solution and slowly cooling to room temperature. Proteinoid polymers and nanocapsules suit many biomedical applications owing to their non-toxicity, biocompatibility and immune safety. Drugs and/or imaging reagents for cancer diagnostic, therapeutic and theranostic applications were encapsulated by dissolving them in aqueous proteinoid solutions. Here, recent in vitro and in vivo studies are reviewed.
Show moreApr 2023 • Nature Communications
Junbo Zhang, Haikuo Zhang, Suting Weng, Ruhong Li, Di Lu, Tao Deng, Shuoqing Zhang, Ling Lv, Jiacheng Qi, Xuezhang Xiao, Liwu Fan, Shujiang Geng, Fuhui Wang, Lixin Chen, Malachi Noked, Xuefeng Wang, Xiulin Fan
The parasitic reactions at the electrolyte/electrode interfaces inhibit the increase of the charging cut-off voltage and the improvement of energy density. Herein, the authors design multifunctional solvent molecules and propose a practical design principle to stabilize the electrolyte/electrode interfaces for high-voltage Li ion batteries.
Show moreApr 2023 • Solid State Nuclear Magnetic Resonance
Irina Matlahov, Alexey Kulpanovich, Taly Iline-Vul, Merav Nadav-Tsubery, Gil Goobes
Bone construction has been under intensive scrutiny for many years using numerous techniques. Solid-state NMR spectroscopy helped unravel key characteristics of the mineral structure in bone owing to its capability of analyzing crystalline and disordered phases at high-resolution. This has invoked new questions regarding the roles of persistent disordered phases in structural integrity and mechanical function of mature bone as well as regarding regulation of early events in formation of apatite by bone proteins which interact intimately with the different mineral phases to exert biological control. Here, spectral editing tethered to standard NMR techniques is employed to analyze bone-like apatite minerals prepared synthetically in the presence and absence of two non-collagenous bone proteins, osteocalcin and osteonectin. A 1H spectral editing block allows excitation of species from the crystalline and disordered …
Show moreApr 2023 • Journal of Immunology (Baltimore, Md.: 1950)
Easton E Ford, David Tieri, Oscar L Rodriguez, Nancy J Francoeur, Juan Soto, Justin T Kos, Ayelet Peres, William S Gibson, Catherine A Silver, Gintaras Deikus, Elizabeth Hudson, Cassandra R Woolley, Noam Beckmann, Alexander Charney, Thomas C Mitchell, Gur Yaari, Robert P Sebra, Corey T Watson, Melissa L Smith
Current Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) using short-read sequencing strategies resolve expressed Ab transcripts with limited resolution of the C region. In this article, we present the near-full-length AIRR-seq (FLAIRR-seq) method that uses targeted amplification by 5'RACE, combined with single-molecule, real-time sequencing to generate highly accurate (99.99%) human Ab H chain transcripts. FLAIRR-seq was benchmarked by comparing H chain V (IGHV), D (IGHD), and J (IGHJ) gene usage, complementarity-determining region 3 length, and somatic hypermutation to matched datasets generated with standard 5'RACE AIRR-seq using short-read sequencing and full-length isoform sequencing. Together, these data demonstrate robust FLAIRR-seq performance using RNA samples derived from PBMCs, purified B cells, and whole blood, which recapitulated results generated by commonly used methods, while additionally resolving H chain gene features not documented in IMGT at the time of submission. FLAIRR-seq data provide, for the first time, to our knowledge, simultaneous single-molecule characterization of IGHV, IGHD, IGHJ, and IGHC region genes and alleles, allele-resolved subisotype definition, and high-resolution identification of class switch recombination within a clonal lineage. In conjunction with genomic sequencing and genotyping of IGHC genes, FLAIRR-seq of the IgM and IgG repertoires from 10 individuals resulted in the identification of 32 unique IGHC alleles, 28 (87%) of which were previously uncharacterized. Together, these data demonstrate the capabilities of FLAIRR-seq to characterize …
Show moreApr 2023 • PLOS Computational Biology
Tomer D Mann, Eli Kopel, Eli Eisenberg, Erez Y Levanon
Adenosine-to-inosine RNA editing is essential to prevent undesired immune activation. This diverse process alters the genetic content of the RNA and may recode proteins, change splice sites and miRNA targets, and mimic genomic mutations. Recent studies have associated or implicated aberrant editing with pathological conditions, including cancer, autoimmune diseases, and neurological and psychiatric conditions. RNA editing patterns in cardiovascular tissues have not been investigated systematically so far, and little is known about its potential role in cardiac diseases. Some hints suggest robust editing in this system, including the fact that ADARB1 (ADAR2), the main coding-sequence editor, is most highly expressed in these tissues. Here we characterized RNA editing in the heart and arteries and examined a contributory role to the development of atherosclerosis and two structural heart diseases -Ischemic and Dilated Cardiomyopathies. Analyzing hundreds of RNA-seq samples taken from the heart and arteries of cardiac patients and controls, we find that global editing, alongside inflammatory gene expression, is increased in patients with atherosclerosis, cardiomyopathies, and heart failure. We describe a single recoding editing site and suggest it as a target for focused research. This recoding editing site in the IGFBP7 gene is one of the only evolutionary conserved sites between mammals, and we found it exhibits consistently increased levels of editing in these patients. Our findings reveal that RNA editing is abundant in arteries and is elevated in several key cardiovascular conditions. They thus provide a roadmap for basic and …
Show moreApr 2023 • Electrochimica Acta
Sankalpita Chakrabarty, Yuri Glagovsky, Ananya Maddegalla, Natalia Fridman, Dmitry Bravo-Zhivotovski, Doron Aurbach, Ayan Mukherjee, Malachi Noked
The electrochemical response of ethereal solutions containing magnesium organohaloaluminate complexes has drawn great interest in recent decades owing to their relevance to rechargeable magnesium batteries, as demonstrated with solutions containing complexes formed by reacting R2Mg and AlCl2R moieties in ethers like tetrahydrofuran (THF). However, most of previous reports focused on battery related performances, and less on the structure of the active species. Herein, we focus on (1) identifying electroactive species and (2) correlating the electrochemical properties of their solutions to the preparation modes: either through reactions of their precursors in THF, or by dissolving isolated crystallized products in the ether solvent. Specifically, we explore the products of the reaction of the Grignard reagent t-BuMgCl with AlCl3 (1:1) in THF, and how their presence in solutions affect their electrochemical …
Show moreApr 2023 • Journal of Functional Biomaterials 14 (4), 215, 2023
Ella Itzhaki, Yuval Elias, Neta Moskovits, Salomon M Stemmer, Shlomo Margel
Proteinoids—simple polymers composed of amino acids—were suggested decades ago by Fox and coworkers to form spontaneously by heat. These special polymers may self-assemble in micrometer structures called proteinoid microspheres, presented as the protocells of life on earth. Interest in proteinoids increased in recent years, in particular for nano-biomedicine. They were produced by stepwise polymerization of 3–4 amino acids. Proteinoids based on the RGD motif were prepared for targeting tumors. Nanocapsules form by heating proteinoids in an aqueous solution and slowly cooling to room temperature. Proteinoid polymers and nanocapsules suit many biomedical applications owing to their non-toxicity, biocompatibility and immune safety. Drugs and/or imaging reagents for cancer diagnostic, therapeutic and theranostic applications were encapsulated by dissolving them in aqueous proteinoid solutions. Here, recent in vitro and in vivo studies are reviewed.
Show moreApr 2023 • Biomolecular Characterization and Imaging Science Program
Debjit Roy, Shimon Weiss
Precise and calibrated measurements of steady-state RMPs and small changes in RMPs are of crucial importance for energy generation, metabolism, and stress response as well as cell-to-cell communication and coordination among bacteria in a bioflm. However, conventional electrode-based methods are not suitable for recording RMPs from tiny bacterial cells. Optical electrophysiological techniques that utilize fluorescence intensity changes also require rigorous calibration for meaningful quantifcation of RMP changes. Accurate and precise recordings of minute RMP changes require noise-immune optical tools. Here the team has developed a calibrated RMP recording approach that is capable of measuring small changes of bacterial RMPs. Te approach relies on two components:(1) a novel optical transducer that utilizes an intrinsic photoinduced electron transfer (PeT) mechanism to sense RMP changes by fluorescence lifetime changes and (2) a quantitative phasor analysis of the recorded confocal FLIM data using a home-writen code (AlliGator). Tis code provides high-throughput quantifcation of pixel-wise lifetime information. Using this approach, team members have estimated RMPs for Bacillus subtilis under normal culture conditions and RMP changes under perturbing chemical conditions (using RMP modulating ionophores). To improve throughput, researchers are developing and incorporating a time-gated SPAD array imager (SwissSPAD3) and (a TCSPC) SPAD array imager (Piccolo), which will be tested with nonclassical (quantum) and classical light. Te use of nonclassical light in excitation via entangled two-photon absorption …
Show moreApr 2023 • Nature Methods
Ganesh Agam, Christian Gebhardt, Milana Popara, Rebecca Mächtel, Julian Folz, Benjamin Ambrose, Neharika Chamachi, Sang Yoon Chung, Timothy D Craggs, Marijn de Boer, Dina Grohmann, Taekjip Ha, Andreas Hartmann, Jelle Hendrix, Verena Hirschfeld, Christian G Hübner, Thorsten Hugel, Dominik Kammerer, Hyun-Seo Kang, Achillefs N Kapanidis, Georg Krainer, Kevin Kramm, Edward A Lemke, Eitan Lerner, Emmanuel Margeat, Kirsten Martens, Jens Michaelis, Jaba Mitra, Gabriel G Moya Muñoz, Robert B Quast, Nicole C Robb, Michael Sattler, Michael Schlierf, Jonathan Schneider, Tim Schröder, Anna Sefer, Piau Siong Tan, Johann Thurn, Philip Tinnefeld, John van Noort, Shimon Weiss, Nicolas Wendler, Niels Zijlstra, Anders Barth, Claus AM Seidel, Don C Lamb, Thorben Cordes
Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study of biomolecular structure and dynamics in vitro and in vivo. We performed an international blind study involving 19 laboratories to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems with distinct conformational changes and dynamics, we obtained an uncertainty of the FRET efficiency ≤0.06, corresponding to an interdye distance precision of ≤2 Å and accuracy of ≤5 Å. We further discuss the limits for detecting fluctuations in this distance range and how to identify dye perturbations. Our work demonstrates the ability of smFRET experiments to simultaneously measure distances and avoid the averaging of conformational dynamics for realistic …
Show moreApr 2023 • arXiv preprint arXiv:2304.14482
Y Shvartzvald, E Waxman, A Gal-Yam, EO Ofek, S Ben-Ami, D Berge, M Kowalski, R Bühler, S Worm, JE Rhoads, I Arcavi, D Maoz, D Polishook, N Stone, B Trakhtenbrot, M Ackermann, O Aharonson, O Birnholtz, D Chelouche, D Guetta, N Hallakoun, A Horesh, D Kushnir, T Mazeh, J Nordin, A Ofir, S Ohm, D Parsons, A Pe'er, HB Perets, V Perdelwitz, D Poznanski, I Sadeh, I Sagiv, S Shahaf, M Soumagnac, L Tal-Or, J Van Santen, B Zackay, O Guttman, P Rekhi, A Townsend, A Weinstein, I Wold
The Ultraviolet Transient Astronomy Satellite (ULTRASAT) is scheduled to be launched to geostationary orbit in 2026. It will carry a telescope with an unprecedentedly large field of view (204 deg) and NUV (230-290nm) sensitivity (22.5 mag, 5, at 900s). ULTRASAT will conduct the first wide-field survey of transient and variable NUV sources and will revolutionize our ability to study the hot transient universe: It will explore a new parameter space in energy and time-scale (months long light-curves with minutes cadence), with an extra-Galactic volume accessible for the discovery of transient sources that is 300 times larger than that of GALEX and comparable to that of LSST. ULTRASAT data will be transmitted to the ground in real-time, and transient alerts will be distributed to the community in 15 min, enabling a vigorous ground-based follow-up of ULTRASAT sources. ULTRASAT will also provide an all-sky NUV image to 23.5 AB mag, over 10 times deeper than the GALEX map. Two key science goals of ULTRASAT are the study of mergers of binaries involving neutron stars, and supernovae: With a large fraction (50%) of the sky instantaneously accessible, fast (minutes) slewing capability and a field-of-view that covers the error ellipses expected from GW detectors beyond 2025, ULTRASAT will rapidly detect the electromagnetic emission following BNS/NS-BH mergers identified by GW detectors, and will provide continuous NUV light-curves of the events; ULTRASAT will provide early (hour) detection and continuous high (minutes) cadence NUV light curves for hundreds of core-collapse supernovae, including for rarer supernova …
Show moreApr 2023 • Angewandte Chemie
Ori Licht, Darío Barreiro‐Lage, Patrick Rousseau, Alexandre Giuliani, Aleksandar R Milosavljević, Avinoam Isaak, Yitzhak Mastai, Amnon Albeck, Raj Singh, Vy TT Nguyen, Laurent Nahon, Lara Martínez‐Fernández, Sergio Díaz‐Tendero, Yoni Toker
Possible routes for intra‐cluster bond formation (ICBF) in protonated serine dimers have been studied. We found no evidence of ICBF following low energy collision‐induced dissociation (in correspondence with previous works), however, we do observe clear evidence for ICBF following photon absorption in the 4.6–14 eV range. Moreover, the comparison of photon‐induced dissociation measurements of the protonated serine dimer to those of a protonated serine dipeptide provides evidence that ICBF, in this case, involves peptide bond formation (PBF). The experimental results are supported by ab initio molecular dynamics and exploration of several excited state potential energy surfaces, unraveling a pathway for PBF following photon absorption. The combination of experiments and theory provides insight into the PBF mechanisms in clusters of amino acids, and reveals the importance of electronic excited …
Show moreApr 2023 • Optics Continuum
Noam Lhiyani, Abhijit Sanjeev, Avshalom Mor, Yevgeny Beiderman, Javier Garcia, Zeev Zalevsky
This paper aims to present initial proof of concept of a non-invasive early diagnostic tool for Alzheimer disease (AD). The approach is based on the identification using Raman spectroscopy and machine learning algorithms of two proteins that are linked with AD and exist in the cerebrospinal fluid (CSF). As demonstrated in previous studies, the concentration of the proteins amyloid-β and tau may indicate the existence of AD. The proteins’ concentration in the CSF signifies the condition of AD. The current study can contribute to the existing body of knowledge by enabling the development of a non-invasive diagnostic tool that may help with early diagnosis of AD.
Show moreApr 2023 • arXiv preprint arXiv:2304.08834
Lucianno Defaveri, Maike AF dos Santos, David A Kessler, Eli Barkai, Celia Anteneodo
We study non-normalizable quasi-equilibrium states (NNQE) arising from anomalous diffusion. Initially, particles in contact with a thermal bath are released from an asymptotically flat potential well, with dynamics that is described by fractional calculus. For temperatures that are sufficiently low compared to the potential depth, the properties of the system remain almost constant in time. We use the fractional-time Fokker-Planck equation (FTFPE) and continuous-time random walk approaches to calculate the ensemble averages of observables. We obtain analytical estimates of the duration of NNQE, depending on the fractional order, from approximate theoretical solutions of the FTFPE. We study and compare two types of observables, the mean square displacement typically used to characterize diffusion, and the thermodynamic energy. We show that the typical time scales for stagnation depend exponentially on the activation energy in units of temperature multiplied by a function of the fractional exponent.
Show moreApr 2023 • Energies 16 (9), 3659, 2023
Alisa Kozhushner, Qing Li, Lior Elbaz
Polymer Electrolyte Membrane Fuel Cells (PEMFC) are currently considered the most advanced fuel cell technology. However, the industrial implementation of PEMFCs is strongly hindered by deficient durability, especially that of the carbonaceous materials commonly used to support the platinum-based catalyst nanoparticles, which are prone to electrochemical corrosion at the cathode, resulting in a serious performance loss of the entire cell. In the attempt to overcome this issue, many research groups have tried to introduce heteroatoms (N, S, B, P) into the carbon lattice, thus trying to make the electrode corrosion-resistant. Newly developed heteroatom-doped carbons were subjected to corrosion tests in half-cell and single-cell systems to evaluate their stability. This paper reviews the recent studies devoted to corrosion research of heteroatom-doped carbon supports for Pt-based catalysts in PEMFCs. In particular, an overview on N, B, and S dopants and their effects on carbon corrosion is provided.
Show moreApr 2023 • Energy & Fuels
Sengodan Prabhu, Moorthy Maruthapandi, Arulappan Durairaj, John HT Luong, Aharon Gedanken
Capsule-like CuO/CDs (CuO@CDs) with a surface area of 33.12 m2 g–1 were synthesized by the hydrothermal treatment, compared to 19.02 m2 g–1 for pristine CuO. An anode was then fabricated from capsule-like CuO@CDs to form a hybrid solid-state supercapacitor (HSSC) with the activated carbon (AC) cathode and PVA/1M KOH as an electrolyte. Three electrode system offered 1208.88 F/g (specific capacitance at 2 A/g current density) and unveiled a remarkable life cycle (retention) and Coulombic efficiency (CF): 93 and 98% after 5000 charge–discharge cycles at 10 A/g. In terms of performance, the HSSC delivered 1.5 V and 102.60 F/g (50.74 C/g) at 2 A/g, 8437.50 W/kg (power density), and 36.90 Wh/kg (energy density). The HSSC still retained 92% of cyclic stability and 83% of CF after 10,000 cycles.
Show moreApr 2023 • Optics Continuum
Noam Lhiyani, Abhijit Sanjeev, Avshalom Mor, Yevgeny Beiderman, Javier Garcia, Zeev Zalevsky
This paper aims to present initial proof of concept of a non-invasive early diagnostic tool for Alzheimer disease (AD). The approach is based on the identification using Raman spectroscopy and machine learning algorithms of two proteins that are linked with AD and exist in the cerebrospinal fluid (CSF). As demonstrated in previous studies, the concentration of the proteins amyloid-β and tau may indicate the existence of AD. The proteins’ concentration in the CSF signifies the condition of AD. The current study can contribute to the existing body of knowledge by enabling the development of a non-invasive diagnostic tool that may help with early diagnosis of AD.
Show moreApr 2023 • MDPI-Multidisciplinary Digital Publishing Institute, 2023
Indra Pulidindi, Pankaj Sharma, Aharon Gedanken
Biomass—A Renewable Resource for Carbon Materials | MDPI Books Menu MDPI Log in Close Menu Home Books Library Forthcoming Books Publish With Us Advisory Board FAQs Contact Login Register Shopping Cart (0) logo Shopping Cart 0 Cart Log In Login Register Home Books Library Forthcoming Books Publish with Us Book Builder Advisory Board FAQ Search for Books: Biomass—A Renewable Resource for Carbon Materials Open Access Reprint Book Biomass—A Renewable Resource for Carbon Materials Indra Neel Pulidindi, Pankaj Sharma and Aharon Gedanken , Eds. Published: April 2023 Pages: 166 © by the authors ISBN 978-3-0365-7189-8 (hardback); ISBN 978-3-0365-7188-1 (PDF) https://doi.org/10.3390/books978-3-0365-7188-1 (registering DOI) This book is a reprint of the Special Issue Biomass—A Renewable Resource for Carbon Materials that was published in C Download Book PDF …
Show moreApr 2023 • Quantum Reports
Dana Ben Porath, Eliahu Cohen
The Leggett–Garg Inequality (LGI) constrains, under certain fundamental assumptions, the correlations between measurements of a quantity Q at different times. Here, we analyze the LGI and propose similar but somewhat more elaborate inequalities, employing a technique that utilizes the mathematical properties of correlation matrices, which was recently proposed in the context of nonlocal correlations. We also find that this technique can be applied to inequalities that combine correlations between different times (as in LGI) and correlations between different locations (as in Bell inequalities). All the proposed bounds include additional correlations compared to the original ones and also lead to a particular form of complementarity. A possible experimental realization and some applications are briefly discussed.
Show moreApr 2023 • Frontiers in Genome Editing
Ayal Hendel, Rasmus O Bak
Gene editing promises the ultimate cure for genetic diseases by directly correcting disease-causing variants. However, the first clinical trials have chased the “low hanging fruit” using editing strategies that rely on gene disruption by introducing double-strand DNA breaks that lead to insertions and deletions (indels) by the NHEJ pathway. Since NHEJ is constitutively active throughout the cell cycle and the default DNA repair pathway, this is by far the most efficient type of conventional gene editing as opposed to homology-directed repair (HDR). HDR relies on delivery of an exogenous repair template and this pathway is active only in the S and G2 phases of the cell cycle. These two parameters constitute challenges in clinical use of HDR since exogenous DNA is toxic in most therapeutically relevant cell types and since the inherent competition between NHEJ and HDR can be a bottleneck. However, HDR benefits from enabling precise edits to be made to the genome, thereby representing true gene editing with control over the outcome. Still, in both these modalities the DNA breaks are considered a potential source of genotoxicity due to the possibility of off-target edits and chromosomal aberrations such as translocations and chromothripsis. Next-generation gene editing tools like Base and Prime Editing that rely on DNA single strand nicking reduce the risk of such harmful events but are still limited in the scope of the edits they can generate (Anzalone et al., 2020). The newest types of editors based on CRISPR-associated transposases or CRISPR-directed integrases facilitate larger edits but are still under development and immature for clinical …
Show moreApr 2023 • Frontiers in Immunology
Modi Safra, Zvi Tamari, Pazit Polak, Shachaf Shiber, Moshe Matan, Hani Karameh, Yigal Helviz, Adva Levy-Barda, Vered Yahalom, Avi Peretz, Eli Ben-Chetrit, Baruch Brenner, Tamir Tuller, Meital Gal-Tanamy, Gur Yaari
The success of the human body in fighting SARS-CoV2 infection relies on lymphocytes and their antigen receptors. Identifying and characterizing clinically relevant receptors is of utmost importance. We report here the application of a machine learning approach, utilizing B cell receptor repertoire sequencing data from severely and mildly infected individuals with SARS-CoV2 compared with uninfected controls. In contrast to previous studies, our approach successfully stratifies non-infected from infected individuals, as well as disease level of severity. The features that drive this classification are based on somatic hypermutation patterns, and point to alterations in the somatic hypermutation process in COVID-19 patients. These features may be used to build and adapt therapeutic strategies to COVID-19, in particular to quantitatively assess potential diagnostic and therapeutic antibodies. These results constitute a proof of concept for future epidemiological challenges.
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