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Search results for: molecular biology and genetics
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Generalization of Phylogenetic Matching Metrics with Experimental Tests of Practical Advantages
PublicationThe ability to quantify a dissimilarity of different phylogenetic trees is required in various types of phylogenetic studies, for example, such metrics are used to assess the quality of phylogeny construction methods and to define optimization criteria in supertree building algorithms. In this article, starting from the already described concept of matching metrics, we define three new metrics for rooted phylogenetic trees. One...
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A Proposal for Using Modified Site-specific Recombination Systems for Making Insertions into a Chosen Chromosomal Sitein vivoBased on the Analysis of I Phage Integration
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Reducing the Number of Microlocations in Oligonucleotide Microchip Matrices by the Application of Degenerate Oligonucleotides
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Positive Regulation of Macromolecule Metabolic Process Belongs to the Main Mechanisms Crucial for Porcine Oocytes Maturation
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Does Porcine Oocytes Maturation in Vitro is Regulated by Genes Involved in Transforming Growth Factor Beta Receptor Signaling Pathway?
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Preoperative factors predicting saphenous vein graft occlusion in coronary artery bypass grafting: a multivariate analysis
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Genes Involved in the Processes of Cell Proliferation, Migration, Adhesion, and Tissue Development as New Potential Markers of Porcine Granulosa Cellular Processes In Vitro: A Microarray Approach
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Reactive oxygen species (ROS) production in human peripheral blood neutrophils exposedin vitroto static magnetic field
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“Bone Development” Is an Ontology Group Upregulated in Porcine Oocytes Before In Vitro Maturation: A Microarray Approach
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Genes responsible for proliferation, differentiation, and junction adhesion are significantly up-regulated in human ovarian granulosa cells during a long-term primary in vitro culture
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Expression of genes associated with BMP signaling pathway in porcine oocytes before and after IVM – a microarray approach
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“Cell Migration” Is the Ontology Group Differentially Expressed in Porcine Oocytes Before and After In Vitro Maturation: A Microarray Approach
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The effect of electromagnetic field on reactive oxygen species production in human neutrophilsin vitro
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CD68 expression in aortocoronary saphenous vein bypass grafts
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Immunocytochemical and biochemical detection of EMMPRIN in the rat tooth germ: differentiation-dependent co-expression with MMPs and co-localization with caveolin-1 in membrane rafts of dental epithelial cells
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Expression profiles and genomic organisation of group A protein phosphatase 2C genes inBrassica oleracea
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Kinetic flux vector splitting scheme for solving non-reactive multi-component flows
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Expression of intermediate filaments of podocytes within nephrotic syndrome glomerulopathies in children
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Synthesis and antimicrobial activity of truncated fragments and analogs of citropin 1.1: The solution structure of the SDS micelle-bound citropin-like peptides
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The Arctic mutation alters helix length and type in the 11–28 β-amyloid peptide monomer—CD, NMR and MD studies in an SDS micelle
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Crystal structures of aminotransferases Aro8 and Aro9 from Candida albicans and structural insights into their properties
PublicationAminotransferases catalyze reversibly the transamination reaction by a ping-pong bi-bi mechanism with pyridoxal 5′-phosphate (PLP) as a cofactor. Various aminotransferases acting on a range of substrates have been reported. Aromatic transaminases are able to catalyze the transamination reaction with both aromatic and acidic substrates. Two aminotransferases from C. albicans, Aro8p and Aro9p, have been identified recently, exhibiting...
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Antibiotic-Based Conjugates Containing Antimicrobial HLopt2 Peptide: Design, Synthesis, Antimicrobial and Cytotoxic Activities
PublicationRecent studies have shown that modified human lactoferrin 20−31 fragment, named HLopt2, possesses antibacterial and antifungal activity. Thus, we decided to synthesize and evaluate the biological activity of a series of conjugates based on this peptide and one of the antimicrobials with proven antibacterial (ciprofloxacin, CIP, and levofloxacin, LVX) or antifungal (fluconazole, FLC) activity. The drugs were covalently connected...
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Determinants of the primary stability of cementless acetabular cup implants: A 3D finite element study
PublicationPrimary stability of cementless implants is crucial for the surgical success and long–term stability. However, primary stability is difficult to quantify in vivo and the biomechanical phenomena occurring during the press–fit insertion of an acetabular cup (AC) implant are still poorly understood. The aim of this study is to investigate the influence of the cortical and trabecular bone Young's moduli Ec and Et, the interference...
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Two-step mechanism of J-domain action in driving Hsp70 function
PublicationJ-domain proteins (JDPs), obligatory Hsp70 cochaperones, play critical roles in protein homeostasis. They promote key allosteric transitions that stabilize Hsp70 interaction with substrate polypeptides upon hydrolysis of its bound ATP. Although a recent crystal structure revealed the physical mode of interaction between a J-domain and an Hsp70, the structural and dynamic consequences of J-domain action once bound and how Hsp70s...
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Analysis of the unique structural and physicochemical properties of the DraD/AfaD invasin in the context of its belonging to the family of chaperone/usher type fimbrial subunits
PublicationInwazyna DraD kodowana przez operon dra posiada strukturę charakterystyczną dla białek podjednostkowych fimbrii typu chaperone-usher. Fold-Ig białka DraD posiada dwie charakterystyczne cechy wyróżniające je z pośród rodziny fimbrialnych białek podjednostkowych: 1) zaburzenie struktury beta-beczki w rejonie szczeliny akceptorowej objawiające się układem wiązań wodorowych głównego łańcucha polipeptydowego oraz 2) nietypowo usytuowany...
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Pre-clinical evaluation of 1-nitroacridine derived chemotherapeutic agent that has preferential cytotoxic activity towards prostate cancer
PublicationPraca zawiera wyniki badań przedklinicznych pochodnej 1-nitroakrydyny C-1748 wobec komórek ludzkiego raka prostaty CaP in vitro, jak i przeszczepialnego na zwierzęta. W oparciu o fosforylację histonu H2AX jako markera podwójnych cięć DNA wykazano, że C-1748 jest bardziej aktywny w komórkach CaP niż HL60. Zidentyfikowano poza tym receptor androgenny (AR) jako cel molekularny badanego związku. W doświadczeniach na zwierzętach stwierdzono...
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Comet assay-based methods for measuring DNA repair in vitro; estimates of inter- and intra-individual variation.
PublicationZdolność do naprawy uszkodzeń DNA jest jednym z najważniejszych wyznaczników podatności na choroby nowotworowe. Dlatego też użytecznym staje się możliwość pomiaru stopnia naprawy DNA w próbkach materiału badawczego pobranego od ochotników. Celem pracy było, po pierwsze, opracowanie w warunkach in vitro prostej metody (z wykorzystaniem techniki testu kometowego), w której naprawa DNA odbywa się poprzez wycinanie nukleotydów (NER)....
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Inhibition of HIV‐1 or bacterial activation of macrophages by products of HIV‐1‐resistant human cells
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Tipping point in plant–fungal interactions under severe drought causes abrupt rise in peatland ecosystem respiration
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Ericoid shrub encroachment shifts aboveground–belowground linkages in three peatlands across Europe and Western Siberia
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Transcriptome profiling and environmental linkage to salinity across Salicornia europaea vegetation
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Salt stress vs. salt shock - the case of sugar beet and its halophytic ancestor
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Adapt or die—Response of large herbivores to environmental changes in Europe during the Holocene
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Stigmas of holoparasitic Phelipanche arenaria (Orobanchaceae) – a suitable ephemeric flower habitat for development unique microbiome
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Cold-modulated leaf compounds in winter triticale DH lines tolerant to freezing and
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Expression of cyclin D1 after treatment with doxorubicin in the HL-60 cell line
PublicationIncreased levels of cyclin D1 and amplification of CCND1 gene occur in many types of cancers. We have followed the expression of cyclin D1 after treatment with doxorubicin with reference to cell death and other possible therapeutic implications. The effect of the treatment on the cell cycle, survival, intracellular level (flow cytometry), and intracellular localization of cyclin D1 (fluorescence microscopy) and expression of...
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Anticancer imidazoacridinone C-1311 inhibits hypoxia-inducible factor-1α (HIF-1α), vascular endothelial growth factor (VEGF) and angiogenesis
PublicationAntitumor imidazoacridinone C-1311 is a DNA-reactive topoisomerase II and FLT3 receptor tyrosine kinase inhibitor. Here, we demonstrate the mechanism of C-1311 inhibitory action on novel targets: hypoxia-inducible factor-1α (HIF-1α), vascular-endothelial growth factor (VEGF), and angiogenesis. In a cell-free system, C-1311 prevented HIF-1α binding to an oligonucleotide encompassing a canonical hypoxia-responsive element (HRE),...
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Multivariate evaluation by quality indicators of no-tillage system in Argiudolls of rolling pampa (Argentina)
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Increased water content in bacterial cellulose synthesized under rotating magnetic fields
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A compartment model of alveolar–capillary oxygen diffusion with ventilation–perfusion gradient and dynamics of air transport through the respiratory tract
PublicationThis paper presents a model of alveolar–capillary oxygen diffusion with dynamics of air transport through the respiratory tract. For this purpose electrical model representing the respiratory tract mechanics and differentia equations representing oxygen membrane diffusion are combined. Relevant thermodynamic relations describing the mass of oxygen transported into the human body are proposed as the connection between these models,...
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Wavelet-based denoising method for real phonocardiography signal recorded by mobile devices in noisy environment
PublicationThe main obstacle in development of intelligent autodiagnosis medical systems based on the analysis of phonocardiography (PCG) signals is noise. The noise can be caused by digestive and respiration sounds, movements or even signals from the surrounding environment and it is characterized by wide frequency and intensity spectrum. This spectrum overlaps the heart tones spectrum, which makes the problem of PCG signal filtrating complex....
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A new approach to modeling of selected human respiratory system diseases, directed to computer simulations
PublicationThis paper presents a new versatile approach to model severe human respiratory diseases via computer simulation. The proposed approach enables one to predict the time histories of various diseases via information accessible in medical publications. This knowledge is useful to bioengineers involved in the design and construction of medical devices that are employed for monitoring of respiratory condition. The approach provides the...
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Modulation of CYP3A4 activity and induction of apoptosis, necrosis and senescence by the antitumor imidazoacridinone C-1311 in human hepatoma cells
PublicationThere is increasing evidence that the expression level of drug metabolic enzymes affects the final cellular response following drug treatment. Moreover, anti-tumour agents may modulate enzymatic activity and/or cellular expression of metabolic enzymes in tumour cells. We investigated the influence of CYP3A4 overexpression on the cellular response induced by the anti-tumour agent C-1311 in hepatoma cells. C-1311-mediated CYP3A4...
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Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions
PublicationAbility to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in...
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Human UDP-Glucuronosyltransferases: Effects of altered expression in breast and pancreatic cancer cell lines.
PublicationIncreased aerobic glycolysis and de novo lipid biosynthesis are common characteristics of invasive cancers. UDP-glucuronosyltransferases (UGTs) are phase II drug metabolizing enzymes that in normal cells possess the ability to glucuronidate these lipids and speed their excretion; however, de-regulation of these enzymes in cancer cells can lead to an accumulation of bioactive lipids, which further fuels cancer progression. We hypothesize...
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Ensembling noisy segmentation masks of blurred sperm images
PublicationBackground: Sperm tail morphology and motility have been demonstrated to be important factors in determining sperm quality for in vitro fertilization. However, many existing computer-aided sperm analysis systems leave the sperm tail out of the analysis, as detecting a few tail pixels is challenging. Moreover, some publicly available datasets for classifying morphological defects contain images limited only to the sperm head. This...
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ABSORPCJA, METABOLIZM I ROLA BIOLOGICZNA KWASÓW NUKLEINOWYCH OBECNYCH W ŻYWNOŚCI
PublicationKwasy nukleinowe należą do niedocenianych składników żywności, szczególnie surowej lub nisko przetworzonej. W niniejszej publikacji skupiono się na omówieniu przemian, jakim podlegają kwasy nukleinowe w przewodzie pokarmowym człowieka, procesie absorpcji nukleotydów oraz nukleozydów z przewodu pokarmowego, a także przedstawiono podstawowe etapy ich metabolizmu w komórkach organizmu. Produkty trawienia kwasów nukleinowych stanowią...
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Development of Safirinium dyes for new applications: fluorescent staining of bacteria, human kidney cells, and the horny layer of the epidermis
PublicationLow-molecular synthetic fluorophores are convenient tools in bioimaging applications. Several derivatives of Safirinium dyes as well as their reactive N-hydroxysuccinimide (NHS) esters bearing diverse substituents were synthesized and evaluated experimentally in terms of their lipophilicity by means of reverse-phase and immobilized artificial membrane high-performance liquid chromatography. Subsequently, the selected compounds...
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Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2
PublicationWe combine molecular dynamics, statistical mechanics, and hybrid quantum mechanics/molecular mechanics simulations to describe mechanistically the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp). Our study analyzes the binding mode of both natural triphosphate substrates as well as remdesivir triphosphate (the active form of drug), which is bound preferentially over ATP by RdRp while...
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublicationPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...