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Wyniki wyszukiwania dla: BAGI
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Comparative molecular dynamics simulations of amphotericin B-cholesterol/ergosterol membrane channels
PublikacjaBadania polegały na przeprowadzeniu porównawczej dynamiki molekularnej dla dwóch typów kanałów amfoterycyny B. Obie symulacje różniły się rodzajem sterolu (cholesterol lub ergosterol). Na podstawie wyników przeprowadzonych prac ustalono jakie elementy strukturalne badanych kanałów mogą być odpowiedzialne za selektywne działanie amfoterycyny B.
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Molecular dynamics simulation and MM-PBSA analysis of Oxytricha nova TEBP ternary complex with ssDNA
PublikacjaPraca dotyczy badań metodami chemii obliczeniowej właściwości elektrostatycznych i termodynamicznych kompleksu telomerowego białka TEBP pochodzącego z organizmu Oxytricha z jednoniciowym telomerowym DNA (ssDNA).
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Thermodynamic and electrostatic properties of ternary Oxytricha nova TEBP-DNA complex
PublikacjaZa pomocą metod chemi obliczeniowej badano właściwości molekularne kompleksu telomerowego białka TEBP z Oxytricha nova w kompleksie trójskkładnikowym z DNA o sekwencji telomerowej. Wyliczone wartości energii kompleksowania wskazują specyficznie na jedną z dróg tworzenia kompleksu, gdzie wpierw podjednostka alfa łaczy się z DNA a następnie podjednostka beta dołącza się do takiego dwuskładnikowego kompleksu. Policzone rozkłady molekularnego...
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Adaptative Potential of the Lactococcus Lactis IL594 Strain Encoded in Its 7 Plasmids
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Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives - A molecular dynamics study.
PublikacjaAmphotericin B (AmB) is an effective but very toxic antifungal antibiotic. In our laboratory a series of AmB derivatives of improved selectivity of action was synthesized and tested. To understand molecular basis of this improvement, comparative conformational studies of amphotericin B and its two more selectivederivatives were carried out in an aqueous solution and in a lipid membrane. These molecular simulation studies revealed...
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SiMiSnoRNA: Collection of siRNA, miRNA, and snoRNA database for RNA Interference
PublikacjaObjective:The discovery of sequence specific gene silencing which occurs due to the presence of double-stranded RNAs has considerable impact on biology, revealing an unknown level of regulation of gene expression. This process is known as RNA interference (RNAi) or RNA silencing in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecule. Two types of small RNA molecules - small...
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Molecular docking studies towards development of novel Gly-Phe analogs for potential inhibition of Cathepsin C (dipeptidyl peptidase I).
PublikacjaCathepsin C is a cysteine protease required for activation of various pro-inflammatory serine proteases and, essentially, is of interest as a therapeutic target. Cathepsin C coordinate system was employed as a model to study the interaction of some already available inhibitors of Cathepsin C. Compounds containing Gly-Phe fragment with functional groups at its ends were designed by knowledge based approach. Using AutoDock and...
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COMPUTER-AIDED DESIGN OF ORGANOPHOSPHORUS INHIBITORS OF UREASE
PublikacjaBased on the structure of the most potential inhibitor diamidophosphate, various novel groups of inhibitors were developed by knowledge-based design approach with covalent carbon-phosphorus or carbon-phosphorus-carbon bond to improve hydrolytic stability to inhibit the microbial ureases. Designed compounds were evaluated with 10 (LigScore1, LigScore2, PLP1, PLP2, JAIN, PMF, PMF04, LUDI_1, LUDI_2 and LUDI_3) different scoring functions...
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The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
PublikacjaAmphotericin B (AmB) is an effective but toxic antifungal drug, known to increase the permeability of the cell membrane, presumably by assembling into transmembrane pores in a sterol-dependent manner. The aggregation of AmB molecules in a phospholipid bilayer is, thus, crucial for the drug’s activity. To provide an insight into the molecular nature of this process, here, we report an atomistic molecular dynamics simulation study...
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Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE
PublikacjaThe current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global “one health” perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the...
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Failure analysis of a high-speed induction machine driven by a SiC-inverter and operating on a common shaft with a high-speed generator
PublikacjaDue to ongoing research work, a prototype test rig for testing high-speed motors/generators has been developed. Its design is quite unique as the two high- speed machines share a single shaft with no support bearings between them. A very high maximum operating speed, up to 80,000 rpm, was required. Because of the need to minimise vibration during operation at very high rotational speeds, rolling bearings were used. To eliminate...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublikacjaLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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Submicron inorganic particles as an additional filler in hybrid epoxy matrix composites reinforced with glass fibres
PublikacjaIn this study, the effect of selected submicron metal oxide (zinc oxide, titanium oxide) or non-metal oxide (silicon dioxide) particles on mechanical and thermo-mechanical properties of epoxy/glass composites was investigated. The applied epoxy resin was a diglycidyl ether of bisphenol-A cured with triethylenetetramine. As a reinforcement twill weave E-glass fabric was used. Hybrid composites (contained particulate and fibrous...
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Binding free energy of selected anticancer compounds to DNA - theoreticalcalculations
PublikacjaPraca dotyczy swobodnej energii wiązania z DNA trzech związków o działaniu przeciwnowotworowym (mitoksantronu i dwóch pochodnych pirymidoakrydyny). Obliczenia wykorzystywały metody Poissona-Boltzmanna (udział elektrostatyczny) i metody SASA (udział nieelektrostatyczny). W wyniku badań zaproponowano struktury kompleksów jakie tworzą badane ligandy z DNA.
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Molecular modelling of membrane activity of amphotericin B, a polyene macrolide antifungal antibiotic
PublikacjaPraca dotyczy różnego typu modelowań molekularnych cząsteczki przeciwgrzybowego antybiotyku (amfoterycyny B). Praca przeglądowa obejmuje opis badań nad właściwościami molekularnymi samej cząsteczki antybiotyku, jej oddziaływań z powierzchnią błony oraz struktur kanałowych jakie tworzą cząsteczki amfoterycyny wewnątrz błony lipidowej.
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Genomic and Functional Characterization of the Unusual pLOCK 0919 Plasmid Harboring thespaCBAPili Cluster inLactobacillus caseiLOCK 0919
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Targeting shelterin proteins for cancer therapy.
PublikacjaAs a global health challenge, cancer prompts continuous exploration for innovative therapies that are also based on new targets. One promising avenue is targeting the shelterin protein complex, a safeguard for telomeres crucial in preventing DNA damage. The role of shelterin in modulating ataxia- telangiectasia mutated (ATM) and ataxia-telangiectasia and Rad3-related (ATR) kinases, key players in the DNA damage response (DDR),...
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Life after BEXUS: Stratospheric Balloon Activities at Gdańsk University of Technology
PublikacjaHow do you restart an academic stratospheric balloon programme after taking part in the REXUS/BEXUS programme? How to assemble a new team and share the passion for stratosphere with a new generation of students? In this paper we want to summarise the stratospheric balloon activities at Gdańsk University of Technology held by SimLE Science Club since 2022. We’ll outline the challenges of creating a new team as well as the technical...
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Numerical methods for the assessment of bridge safety barriers
PublikacjaThe paper presents a numerical study of the bus crash test for bridge safety barriers. The analysis is conducted with the use of explicit code LS-DYNA. The problem of hourglass effect in shell elements is discussed. The simulations of bus impact against the barrier show that the analyzed barrier withstands the impact forces and restrains the bus trajectory to the bridge road.
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Membrane Sterols Modulate the Binding Mode of Amphotericin B without Affecting Its Affinity for a Lipid Bilayer
PublikacjaMembrane-active antibiotics are known to selectively target certain pathogens based on cell membrane properties, such as fluidity, lipid ordering, and phase behavior. These are in turn modulated by the composition of a lipid bilayer and in particular by the presence and type of membrane sterols. Amphotericin B (AmB), the golden standard of antifungal treatment, exhibits higher activity toward ergosterol-rich fungal membranes, which...
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Cancer immune escape: the role of antigen presentation machinery
PublikacjaThe mechanisms of antigen processing and presentation play a crucial role in the recognition and targeting of cancer cells by the immune system. Cancer cells can evade the immune system by downregulating or losing the expression of the proteins recognized by the immune cells as antigens, creating an immunosuppressive microenvironment, and altering their ability to process and present antigens. This review focuses on the mechanisms...
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TRF1 and TRF2: pioneering targets in telomere-based cancer therapy
PublikacjaThis article presents an in-depth exploration of the roles of Telomere Repeat-binding Factors 1 and 2 (TRF1 and TRF2), and the shelterin complex, in the context of cancer biology. It emphasizes their emerging significance as potential biomarkers and targets for therapeutic intervention. Central to the shelterin complex, TRF1 and TRF2 are crucial in maintaining telomere integrity and genomic stability, their dysregulation often...
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Stanowisko do badania łożysk foliowych w cyklu start-stop
PublikacjaStreszczenie: W artykule przedstawiono stanowisko do badań typu Start-Stop, które zostało zaprojektowane do testów przydatności materiałów i rozwiązań konstrukcyjnych aerodynamicznych łożysk foliowych. Jest to jeden z modułów stanowiska badawczego wykorzystywanego w badaniach łożysk maszyn szybkoobrotowych opracowywanych w ramach projektu POIG.01.03.01-00-027/08 pt. "Wykorzystanie materiałów i konstrukcji inteligentnych do opracowania...
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Modelowanie i analiza hydrodynamicznych łożysk foliowych
Publikacjastreszczenie: w artykule omówiono zagadnienia związane z modelowaniem i analizą symulacyjną łożysk foliowych. badane łożyska zostały zaprojektowane do pracy w mikroturbinach energetycznych będących kluczowym elementem mikrosiłowni kogeneracyjnych orc. w kolejnych częściach pracy omówiono warunki pracy łożysk foliowych, opracowanie modelu numerycznego oraz analizę łożysk w zakresie obciążeń statycznych i dynamicznych. przedstawiono...
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Stanowisko do badania łożysk foliowych w cyklu start-stop
Publikacjastreszczenie: w artykule przedstawiono stanowisko do badań typu start-stop, które zostało zaprojektowane do testów przydatności materiałów i rozwiązań konstrukcyjnych aerodynamicznych łożysk foliowych. jest to jeden z modułów stanowiska badawczego wykorzystywanego w badaniach łożysk maszyn szybkoobrotowych opracowywanych w ramach projektu poig.01.03.01-00-027/08 pt. "wykorzystanie materiałów i konstrukcji inteligentnych do opracowania...
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Modelowanie i analiza hydrodynamicznych łożysk foliowych
Publikacjastreszczenie: w artykule omówiono zagadnienia związane z modelowaniem i analizą symulacyjną łożysk foliowych. badane łożyska zostały zaprojektowane do pracy w mikroturbinach energetycznych będących kluczowym elementem mikrosiłowni kogeneracyjnych orc. w kolejnych częściach pracy omówiono warunki pracy łożysk foliowych, opracowanie modelu numerycznego oraz analizę łożysk w zakresie obciążeń statycznych i dynamicznych. przedstawiono...
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Theoretical analysis and experimental tests of tilting pad journal bearings with shoes made of polymer material and low-boiling liquid lubrication
PublikacjaSelecting the appropriate bearing system for the rotor requires a good knowledge of the available solutions and the operating conditions of the machine. For newly designed machinery operating in adverse conditions, selecting bearings that ensure correct and long-lasting operation can be extremely challenging. Difficulties in- crease when the machine’s operating parameters are beyond the technical capabilities of available technical solutions....
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From tryptophan to novel mitochondria-disruptive agent, synthesis and biological evaluation of 1,2,3,6-tetrasubstituted carbazoles
PublikacjaMitochondrial targeting plays an important role in anticancer therapy. The Mn(III)-promoted cyclization of 5- (1H-indol-3-yl)-3-oxopentanoic acid allow to obtain novel substituted carbazole derivatives that can act as mitochondria-disruptive agents. The starting materials used for the synthesis of these new aminocarbazoles are oxopentanoate derivatives of tryptophan. The scope and limitation of this method of synthesis are determined...
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MM/PBSA analysis of molecular dynamics simulations of bovine beta-lactoglobulin: free energy gradients in conformational transitions?
PublikacjaPraca dotyczy pH zależnych zmian konformacyjnych EF pętli beta-laktoglobuliny. Zmiany te są śledzone za pomocą metod obliczeniowych chemii (dynamika molekularna oraz metody MM/PBSA).
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Assessment of baby disposable diapers application for urine collection and determination of phthalate metabolites
PublikacjaThe baby disposable diapers were investigated as a sampling material for urine collection and validated for the evaluation of the exposure of children to xenobiotics. Phthalate metabolites detected in urine samples were chosen as proof-of-concept analytes. For the determination of phthalate metabolites in children’s urine samples, high performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS) was used. Two...
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Photosensitive and pH-dependent activity of pyrazine-functionalized carbazole derivative as promising antifungal and imaging agent
PublikacjaCarbazole skeleton plays a significant role as a structural scaffold of many pharmacologically active compounds. Pyrazine-functionalized carbazole derivative was constructed by coupling 2-amino-5-bromo-3-methylaminepyrazine (ABMAP) into 3 and 6 positions of the carbazole ring. Multi-experimental methods were used, e.g., potentiometric, spectroscopic (ATR, UV, XRD powder,1H and13C NMR), electrochemical (cyclic voltammetry), and...
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Research on Linear Actuators for Active Foil Bearings
PublikacjaActive foil bearings are a kind of gas foil bearing. They contain actuators which allow for modification of the bearing sleeve size and the shape of the lubrication gap. Rotor vibrations can be actively controlled by these changes. It is possible, among other things, to reduce the starting torque, control the vibration amplitude at different speeds and improve operational safety. Prototypes of active foil bearings are being developed...
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Możliwości i zasady stosowania hybrydowych urządzeń energochłonnych na przykładzie urządzenia SafeEnd
PublikacjaOd kilku lat na świecie stosowane są urządzenia energochłonne spełniające rolę poduszki zderzeniowej oraz terminala energochłonnego. Urządzenia te stosowane są do osłony zakończeń barier drogowych oraz osłony obiektów znaj-dujących się w strefie bezpieczeństwa drogi. Przykładem takiego urządzenia jest urządzenie energochłonne U-15a SafeEnd (SE) stosowane od niedawna w Polsce, jednakże niektórzy zarządcy dróg zgłaszają obawy do...
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Wytwarzanie i wybrane właściwości kompozycji kauczukowych z regenerowaną celulozą.
PublikacjaCelem niniejszej pracy było zbadanie wpływu regenerowanych włókien wiskozowych (dodanych w ilości 10, 20, 30 phr) jako proekologicznego napełniacza na wybrane właściwości kompozycji na osnowie kauczuku na-turalnego. Dla każdej z wyżej wymienionych proporcji otrzymano materiały wulkanizowane przez 5, 10, 15, 20 minut. Uzyskane materiały poddano statycznej próbie rozciągania, badaniu elastyczności przy odbiciu metodą...
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Triazoloacridone C-1305 impairs XBP1 splicing by acting as a potential IRE1α endoribonuclease inhibitor
PublikacjaInositol requiring enzyme 1 alpha (IRE1α) is one of three signaling sensors in the unfolding protein response (UPR) that alleviates endoplasmic reticulum (ER) stress in cells and functions to promote cell survival. During conditions of irrevocable stress, proapoptotic gene expression is induced to promote cell death. One of the three signaling stressors, IRE1α is an serine/threonine-protein kinase/endoribonuclease (RNase) that...
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Interaction of cisplatin and two potential antitumoral platinum(ii) complexes with a model lipid membrane: a combined NMR and MD study
PublikacjaIn this study, the interaction of cisplatin (1) and two potential antitumoral Pt(II) complexes (2 and 3) with a model DMPC bilayer was investigated by multinuclear NMR spectroscopy and MD simulations in order to understand its implication for the different antitumoral properties shown by the three complexes. In particular, 31P, 13C and 2H solid state NMR experiments were performed to obtain information on the phase structure, phase...
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Novel chalcone-derived pyrazoles as potential therapeutic agents for the treatment of non-small cell lung cancer
PublikacjaLung cancer is considered to account for approximately one-fifth of all malignant tumor-related deaths worldwide and is therefore one of the most lethal malignancies. Pyrazole scaffold possesses a wide range of biological and pharmacological activities, which play important roles in medicinal chemistry. The present study reports the synthesis and in vitro biological characterization of nine pyrazoles derived from chalcones as potential...
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Teloxantron inhibits the processivity of telomerase with preferential DNA damage on telomeres
PublikacjaTelomerase reactivation is one of the hallmarks of cancer, which plays an important role in cellular immortalization and the development and progression of the tumor. Chemical telomerase inhibitors have been shown to trigger replicative senescence and apoptotic cell death both in vitro and in vivo. Due to its upregulation in various cancers, telomerase is considered a potential target in cancer therapy. In this study, we identified...
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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
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Induction of unique structural changes in guanine-rich DNA regions by the triazoloacridone C-1305, a topoisomerase II inhibitor with antitumor activities.
PublikacjaCelem pracy było scharakteryzowanie odziaływania związku C-1305 z DNA w porównaniu do innych inhibitorów topoizomerazy II. Badania pokazują, że C-1305 odziaływuje preferencyjnie z parami CG, interkaluje do DNA i zaburza sąsiednie otoczenie w bardzo charakterystyczny sposób, który nie został zaobserwowany u pozostałych 22 badanych związków.
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Colonization of germ-free mice with a mixture of three lactobacillus strains enhances the integrity of gut mucosa and ameliorates allergic sensitization
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Palindromic carbazole derivatives: unveiling their antiproliferative effect via topoisomerase II catalytic inhibition and apoptosis induction
PublikacjaHuman DNA topoisomerases are essential for crucial cellular processes, including DNA replication, transcription, chromatin condensation, and maintenance of its structure. One of the significant strategies employed in cancer treatment involves the inhibition of a specific type of topoisomerase, known as topoisomerase II (Topo II). Carbazole derivatives, recognised for their varied biological activities, have recently become a significant...
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Mangiferin Affects Melanin Synthesis by an Influence on Tyrosinase: Inhibition, Mechanism of Action and Molecular Docking Studies
PublikacjaMangiferin is a strong antioxidant that presents a wide range of biological activities. The aim of this study was to evaluate, for the first time, the influence of mangiferin on tyrosinase, an enzyme responsible for melanin synthesis and the unwanted browning process of food. The research included both the kinetics and molecular interactions between tyrosinase and mangiferin. The research proved that mangiferin inhibits tyrosinase...
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Combined anticancer therapy with imidazoacridinone analogue C‐1305 and paclitaxel in human lung and colon cancer xenografts—Modulation of tumour angiogenesis
PublikacjaThe acridanone derivative 5-dimethylaminopropylamino- 8- hydroxytriazoloacridinone (C-1305) has been described as a potent inhibitor of cancer cell growth. Its mechanism of action in in vitro conditions was attributed, among others, to its ability to bind and stabilize the microtubule network and subsequently exhibit its tumour- suppressive effects in synergy with paclitaxel (PTX). Therefore, the objective of the present study...
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Cell Density-Dependent Cytological Stage Profile and Its Application for a Screen of Cytostatic Agents Active Toward Leukemic Stem Cells
PublikacjaProliferation and expansion of leukemia is driven by leukemic stem cells (LSCs). Multidrug resistance (MDR) of LSCs is one of the main reasons of failure and relapses in acute myeloid leukemia (AML) treatment. In this study, we show that maintaining HL-60 at low cell culture density or applying a 240-day treatment with anthrapyridazone (BS-121) increased the percentage of primitive cells, which include LSCs determining the overall...
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Relationship between Telomere Length, TERT Genetic Variability and TERT, TP53, SP1, MYC Gene Co-Expression in the Clinicopathological Profile of Breast Cancer
PublikacjaThe molecular mechanisms of telomerase reverse transcriptase (TERT) upregulation in breast cancer (BC) are complex. We compared genetic variability within TERT and telomere length with the clinical data of patients with BC. Additionally, we assessed the expression of the TERT, MYC, TP53 and SP1 genes in BC patients and in BC organoids (3D cell cultures obtained from breast cancer tissues). We observed the same correlation in the...
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[15.03.2023] Information meeting for 4-th year PhD students
Kursy OnlineInformation meeting on 15.03.2023 4th-year PhD students
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Effective Drug Concentration and Selectivity Depends on Fraction of Primitive Cells
PublikacjaPoor efficiency of chemotherapeutics in the eradication of Cancer Stem Cells (CSCs) has been driving the search for more active and specific compounds. In this work, we show how cell density-dependent stage culture profiles can be used in drug development workflows to achieve more robust drug activity (IC50 and EC50) results. Using flow cytometry and light microscopy, we characterized the cytological stage profiles of the HL-60-,...
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Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site
PublikacjaAn important stage in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) life cycle is the binding of the spike (S) protein to the angiotensin converting enzyme-2 (ACE2) host cell receptor. Therefore, to explore conserved features in spike protein dynamics and to identify potentially novel regions for drugging, we measured spike protein variability derived from 791 viral genomes and studied its properties by molecular...
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Polyolefins, commercial and alternative routes toward the world’s most important polymer
Kursy OnlineThe course will consist of lectures followed by discussions. Based on the gained knowledge the Students will be asked to prepare in teams a short essay how to economically produce a selected polyolefin and how to introduce the new product into the market.