OPEN Repository

Welcome to OPEN - the Repository of Open Scientific Publications, run by the Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, previously operating as the CeON Repository. The Repository enables Polish researchers from all fields to openly share their articles, books, conference materials, reports, doctoral theses, and other scientific texts.

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A combination treatment based on drug repurposing demonstrates mutation-agnostic efficacy in pre-clinical retinopathy models
(Nature Portfolio, 2024-07-15) Leinonen, Henri; Zhang, Jianye; Occelli, Laurence M.; Seemab, Umair; Choi, Elliot H.; Marinho, Luis Felipe L.P.; Querubin, Janice; Kolesnikov, Alexander V.; Galinska, Anna; Kordecka, Katarzyna; Hoang, Thanh; Lewandowski, Dominik; Lee, Timothy; Einstein, Elliott E.; Einstein, David E.; Dong, Zhiqian; Kiser, Philip D.; Blackshaw, Seth; Kefalov, Vladimir J.; Tabaka, Marcin; Foik, Andrzej T.; Petersen-Jones, Simon M.; Palczewski,  Krzysztof; Zhao Yuan; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland; Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, USA; Small Animal Clinical Sciences, Michigan State University, East Lansing, USA; International Centre for Translational Eye Research, Warsaw, Poland; Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland; Department of Ophthalmology, Department of Cell & Developmental Biology, Ann Arbor, USA; Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, USA; Department of Clinical Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University of California - Irvine, Irvine, USA
Inherited retinopathies are devastating diseases that in most cases lack treatment options. Disease-modifying therapies that mitigate pathophysiology regardless of the underlying genetic lesion are desirable due to the diversity of mutations found in such diseases. We tested a systems pharmacology-based strategy that suppresses intracellular cAMP and Ca2+ activity via G protein-coupled receptor (GPCR) modulation using tamsulosin, metoprolol, and bromocriptine coadministration. The treatment improves cone photoreceptor function and slows degeneration in Pde6βrd10 and RhoP23H/WT retinitis pigmentosa mice. Cone degeneration is modestly mitigated after a 7-month-long drug infusion in PDE6A-/- dogs. The treatment also improves rod pathway function in an Rpe65-/- mouse model of Leber congenital amaurosis but does not protect from cone degeneration. RNA-sequencing analyses indicate improved metabolic function in drug-treated Rpe65-/- and rd10 mice. Our data show that catecholaminergic GPCR drug combinations that modify second messenger levels via multiple receptor actions provide a potential disease-modifying therapy against retinal degeneration.
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Effects of a Multi Scouring Agent on the Pretreatment and Dyeing of different Cellulosic Knitted Fabrics
(Sciendo, 2023-09-01) Khan, Olin; Wasima, Antara; Jahan, Nusrat; Sarkar, Md. Imrul; Das, Shohag Chandra; Department of Wet Process Engineering, Bangladesh University of Textiles, Dhaka, Bangladesh
The study tested the use of Viscobleach as a multi-scouring agent for pretreating cellulosic fabrics (cotton, viscose, and linen) instead of using traditional agents (caustic soda, soda ash, and hydrogen peroxide). The results showed an increase in whiteness and absorbency for viscose and linen fabrics pretreated with Viscobleach. The color strength (K/S) increased for all shades of cotton and for medium and dark shades of viscose and linen. The study also showed that the dye pick-up was higher and dye wastage lower with the Viscobleach pretreatment. The color fastness to wash and rubbing was rated 4-5 for all samples.
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Attenuation Analysis of Polymer Optic Fibres (POF) Manufactured with Different Materials
(Sciendo, 2025-02-25) Esmercan, Can; Doba Kadem, Füsun; Kallweit, Jan; Pätzel, Mark; Gries, Thomas; Department of Textile Engineering-Çukurova University, Adana, Turkey; Institut für Textiltechnik of RWTH Aachen University, Aachen, Germany
An overview of the attenuation analysis of producing polymer optical fibres (POF) with different cladding materials but same diameter is given. Based on a systematic literature review, the melt spinning method was applied in practice and different combinations of POF bobbins manufactured. The production methods are described in detail and their attenuation results discussed.
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Cationic−anionic complexes of Cu(II) and Co(II) with N-scorpionate ligand – structure, spectroscopy, and catecholase activity
(Royal Society of Chemistry, 2025) Zienkiewicz-Machnik, Małgorzata; Luboradzki, Roman; Mech-Piskorz, Justyna; Angulo, Gonzalo; Nogala, Wojciech; Ratajczyk, Tomasz; Aleshkevych, Pavlo; Kubas, Adam; Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
We report structural and physicochemical characterization supported by quantum chemical studies of two novel copper(II) [CuLCl]2[CuCl4] (1) and cobalt(II) [CoLCl][CoL′Cl3] (2) cationic−anionic complexes with N-scorpionate type ligand, N,N,N-tris(3,5-dimethylpyrazol-1-ylmethyl)amine (L), where L′ is 1-methylamine-3,5-dimethylpyrazole. The obtained complexes are the first reported examples of cationic−anionic coordination compounds tested for catecholase activity. Interestingly, only copper complex (1) shows catalytic activity in the oxidation of 3,5-di-tert-butylcatechol (3,5-DTBC), which turned out to be solvent dependent. Here, experimental UV-vis spectroscopy of 1 shows that essential features of the solid-state spectrum are maintained in DMSO and MeOH solvents. In contrast, the build-up of a new feature around 465 nm for 1 in CH3CN was noted, along with negligible activity. According to quantum chemical calculations, this feature could be attributed to ligand-to-metal excitations within the [CuCl4]2− fragment disturbed by adjacent [CuLCl]+ species. The band shifts to lower energies compared to solid-state measurements as the two charged fragments get closer due to Coulomb interactions. In DMSO, the solvent molecule serves as an inert ligand in a [CuLCl]+ fragment and blocks the catalytic center, disturbing the formation of the [catalyst–substrate] complex and decreasing activity, while in MeOH, the solvent effectively stabilizes [CuCl4]2−via a H-bond network and the free coordination site is accessible, thus allowing a substrate molecule to bind. The critical advantage of the investigated complexes, in the context of their possible catalytic activity, was the fact that their usage would not introduce any unnecessary counterions.
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Safer and efficient base editing and prime editing via ribonucleoproteins delivered through optimized lipid-nanoparticle formulations
(Nature Portfolio, 2024-11-28) Hołubowicz, Rafał; Du, Samuel W.; Felgner, Jiin; Smidak, Roman; Choi, Elliot H.; Palczewska, Grazyna; Rodrigues Menezes, Carolline; Dong, Zhiqian; Gao, Fangyuan; Medani, Omar; Yan, Alexander L.; Hołubowicz, Maria W.; Chen, Paul Z.; Bassetto, Marco; Risalit,i Eleonora; Salom, David; Workman, J. Noah; Kiser, Philip D.; Foik, Andrzej T.; Lyon, David C.; Newby, Gregory A.; Liu, David R.; Felgner, Philip L.; Palczewski,  Krzysztof; Cheifet Barbara; Almeida Filipe; Caprettini Valeria; Griffo Alessandra; Haskell Jennifer; Gavin Herbert Eye Institute – Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, USA; Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland; Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA; Adeline Yen Mah Vaccine Center, Department of Physiology and Biophysics, University of California, Irvine, CA, USA; Program in Neuroscience, Amherst College, Amherst, MA, USA; Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Research Service, Tibor Rubin VA Long Beach Medical Center, Long Beach, CA, USA; Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Clinical Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, CA, USA; International Centre for Translational Eye Research (ICTER); Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland; Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA; Department of Chemistry, University of California, Irvine, CA, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
Delivering ribonucleoproteins (RNPs) for in vivo genome editing is safer than using viruses encoding for Cas9 and its respective guide RNA. However, transient RNP activity does not typically lead to optimal editing outcomes. Here we show that the efficiency of delivering RNPs can be enhanced by cell-penetrating peptides (covalently fused to the protein or as excipients) and that lipid nanoparticles (LNPs) encapsulating RNPs can be optimized for enhanced RNP stability, delivery efficiency and editing potency. Specifically, after screening for suitable ionizable cationic lipids and by optimizing the concentration of the synthetic lipid DMG-PEG 2000, we show that the encapsulation, via microfluidic mixing, of adenine base editor and prime editor RNPs within LNPs using the ionizable lipid SM102 can result in in vivo editing-efficiency enhancements larger than 300-fold (with respect to the delivery of the naked RNP) without detectable off-target edits. We believe that chemically defined LNP formulations optimized for RNP-encapsulation stability and delivery efficiency will lead to safer genome editing.

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