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CRISPR Journal
Journals -
Establishing the allosteric mechanism in CRISPR‐Cas9
PublicationAllostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of allosteric communication within CRISPR‐Cas9, a leading genome editing machinery with enormous promises for medicine and biotechnology. MD revealed how allostery intervenes during at least three...
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Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
PublicationAt the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9 introduces site-specific breaks in DNA. However, precise mechanistic information to ameliorate Cas9 function is still missing. Here, multimicrosecond molecular dynamics, free energy and multiscale simulations are combined with solution NMR and DNA cleavage experiments to resolve the catalytic mechanism of target DNA cleavage. We show that the conformation...
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CaZnO-based nanoghosts for the detection of ssDNA, pCRISPR and recombinant SARS-CoV-2 spike antigen and targeted delivery of doxorubicin
PublicationOverexpression of proteins/antigens and other gene-related sequences in the bodies could lead to significant mutations and refractory diseases. Detection and identification of assorted trace concentrations of such proteins/antigens and/or gene-related sequences remain challenging, affecting different pathogens and making viruses stronger. Correspondingly, coronavirus (SARS-CoV-2) mutations/alterations and spread could lead to overexpression...
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A CRISPR/Cas9-Based Mutagenesis Protocol for Brachypodium distachyon and Its Allopolyploid Relative, Brachypodium hybridum
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Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
PublicationCRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum–classical molecular dynamics (MD) and free energy methods are used...
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Headspace liquid phase microextraction for quantitation of hexanal in potato crisps by gas chromatography
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Rapid and sensitive determination of acrylamide in potato crisps using reversed-phase direct immersion single drop microextraction-gas chromatography
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Discrimination of hospital isolates of Acinetobacter baumannii using repeated sequences and whole genome alignment differential analysis
PublicationAn optimized method for bacterial strain differentiation, based on combination of Repeated Sequences and Whole Genome Alignment Differential Analysis (RS&WGADA), is presented in this report. In this analysis, 51 Acinetobacter baumannii multidrug-resistance strains from one hospital environment and patients from 14 hospital wards were classified on the basis of polymorphisms of repeated sequences located in CRISPR region, variation...
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Notatki mikologiczne z okolic Ostrzyc (Kaszubski Park Krajobrazowy)= Mycological notes from the area of Ostrzyce (Kaszubski Landscape Park)
PublicationPrzeprowadzono wstępne badania mikobioty w okolicach Ostrzyc (Północna Polska, Pojerzerze Kaszubskie), podczas których natrafiono na interesujące macromycetes ujęte w poniższym wykazie. Stwierdzono łącznie 117 gatunków, siedem z nich (Strobilomyces strobilaceus, Geastrum fimbriatum, Hericium coralloides, Sparassis crispa, Matinus caninus, Clavariadelphus pistillaris i Polyporus Umbellatus) znajdują się pod ochroną ścisłą, a 23...
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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Polish internet mortgage market: towards fully developed fuzzy model
PublicationThe first part of the paper consists of introduction describing the Polish Internet Mortgage Market. Later there is presented the idea of the rule based model which may be used on this market. Next step consists of fuzzyfication of the model. This process begins with the initial set of variables which was used previously for the rule based model of the same market. As numerous aspects of the market cannot be presented in the crisp...
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Ostoja grzybów wielkoowocnikowych i śluzowców w Lasach Oliwskich (Trójmiejski Park Krajobrazowy)
PublicationBadania grzybów wielkoowocnikowych w Lasach Oliwskich ujawniły niezwykłą ich różnorodność w oddziale 119 leśnictwa Renuszewo. Stwierdzono tam14 gatunków woreczniaków (Ascomycetes) i 99 gatunków podstawczaków (Basidiomycetes). Wśród nich 4 gatunki posiadają status ściśle chronionych; są to siedzuń sosnowy Sparassis crispa, szyszkowiec łuskowaty Strobilomyces strobilaceus, mądziak psi Mutinus caninus oraz ozorek dębowy Fistulina...
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Novel Tools for Comprehensive Functional Analysis of LDLR (Low-Density Lipoprotein Receptor) Variants
PublicationFamilial hypercholesterolemia (FH) is an autosomal-dominant disorder caused mainly by substitutions in the low-density lipoprotein receptor (LDLR) gene, leading to an increased risk of premature cardiovascular diseases. Tremendous advances in sequencing techniques have resulted in the discovery of more than 3000 variants of the LDLR gene, but not all of them are clinically relevant. Therefore, functional studies of selected variants...
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The process of fuzzy model development for the case of polish internet mortgage market
PublicationThe aim of the paper is to present the conceptual description of fuzzy model representing the Polish Internet mortgage market. The first part of the paper consists of assessment and verification of model variables which are important for the Polish Internet Mortgage Market. This process begins with the initial set of variables which was used previously for the rule based model of the same market. As numerous aspects of the market...
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Property sustainable value versus highest and best use analyzes
PublicationThis article proposes the possibility of applying fuzzy logic theory to perform the tasks of determining the market value of agricultural lands. These tasks are of a multi‐criteria character, as multiple factors are taken into consideration during the land value valuation process. The market value of agricultural land plots, calculated using fuzzy logic methods, can provide a basis for further use in the processes that are directly...
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The Implementation of Fuzzy Logic in Forecasting Financial Ratios
PublicationThis paper is devoted to the issue of forecasting financial ratios. The objective of the conducted research is to develop a predictive model with the use of an innovative methodology, i.e., fuzzy logic theory, and to evaluate its effectiveness. Fuzzy logic has been widely used in machinery, robotics and industrial engineering. This paper introduces the use of fuzzy logic for the financial analysis of enterprises. While many current...
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Preliminary Identification of Quantitative Factors Determining the Duration of Court Proceedings in Commercial Cases
PublicationPurpose: The aim of the article was to identify factors that are linear combinations of the variables under scrutiny that affect the duration of court proceedings. Design/Methodology/Approach: This research was conducted on commercial cases, based on the Principal Components Analysis (PCA). The original variables were grouped into factors that are correlated with each other. The Kaiser Criterion (own value >1) was chosen as the...
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Genetyka molekularna - wykład, WCh 2022/23, Biotechnologia II stopień - new
e-Learning CoursesCelem kursu jest zapoznanie się z podstawowymi mechanizmami funkcjonowania genomów, regulacji ich aktywności i dziedziczenia, edycją genomu w oparciu o programowane nukleazy (system CRISPR-Cas i prime-editing), metodami wykorzystywanymi do analizy struktury, funkcji genów, skutków zmian mutacyjnych oraz wyłączania ich aktywności (np. TargeTron gene nockout system) oraz technikami in vitro wykorzystywanymi do wprowadzania biomolekuł...
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Genetyka molekularna - wykład, WCh 2023/24, Biotechnologia II stopień
e-Learning CoursesCelem kursu jest zapoznanie się z podstawowymi mechanizmami funkcjonowania genomów, regulacji ich aktywności i dziedziczenia, edycją genomu w oparciu o programowane nukleazy (system CRISPR-Cas i prime-editing), metodami wykorzystywanymi do analizy struktury, funkcji genów, skutków zmian mutacyjnych oraz wyłączania ich aktywności (np. TargeTron gene nockout system) oraz technikami in vitro wykorzystywanymi do wprowadzania biomolekuł...