Wyniki wyszukiwania dla: genomics
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Cloning and characterization of the dnaK heat shock operon of the marine bacterium Vibrio harveyi
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Regulation of replication of λ phage and λ plasmid DNAs at low temperature
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Professional activity, gender and disease-related emotions: The impact on parents' experiences in caring for children with phenylketonuria
PublikacjaIntroduction: Clinical management of rare diseases often fails to acknowledge the challenges faced by caregivers.Whilst management of phenylketonuria (PKU) may not be considered as dire as other conditions, most studiesprimarily concentrate on clinical issues, dietary adherence, or the quality of life of the PKU patients, leavingcaregivers in the background. The aim of the study was to evaluate the psychosocial...
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Identyfikacja i izolacja genu kodującego zaadaptowaną do zimna β-galaktozydazę Paracoccus sp. = Identification and izolation of the gene encoding cold-active β-galactosidase from paracoccus sp.
PublikacjaZaprezentowane badania były prowadzone u eehi wyizolowania ze środo¬wiska organizmu psychrofilnego, zdolnego do hydrolizy laktozy w niskiej tempe¬raturze, oraz zidentyfikowania genu kodującego (i-galaktozydazę zaadaptowaną do zimna.Poszukiwan gen został w izolowany z psychrofilnego szczepu autarkicz¬nego Paracoccus sp. 321). Na podstawie sekwencji nukleotydowej genu kodują¬cego fS-galaktozdaze ustalono skład aminokwasów),...
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Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
PublikacjaThe molecular mechanism supporting survival at a critical high temperature (CHT) in Escherichia coli was investigated. Genome-wide screening with a single-gene knockout library provided a list of genes indispensable for growth at 47°C, called thermotolerant genes. Genes for which expression was affected by exposure to CHT were identified by DNA chip analysis. Unexpectedly, the former contents did not overlap with the latter except...
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Dominant Pathways of Adenosyl Radical-Induced DNA Damage Revealed by QM/MM Metadynamics
PublikacjaBrominated nucleobases sensitize double stranded DNA to hydrated electrons, one of the dominant genotoxic species produced in hypoxic cancer cells during radiotherapy. Such radiosensitizers can therefore be administered locally to enhance treatment efficiency within the solid tumor while protecting the neighboring tissue. When a solvated electron attaches to 8-bromoadenosine, a potential sensitizer, the dissociation of bromide...
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A new B-D-galactosidase with a low temperature optimum isolated from the Antarctic Arthrobacter sp. 20B: gene cloning, purification and characterization.
PublikacjaA psychrotrophic bacterium producing a coldadaptedB-galactosidase upon growth at low temperatureswas classiWed as Arthrobacter sp. 20B. A genomic DNAlibrary of strain 20B introduced into Escherichia coliTOP10F' and screening on X-Gal (5-bromo-4-chloro-3-indolyl-B-D-galactopyranoside)-containing agar plates ledto the isolation of B-galactosidase gene. The B-galactosidasegene (bgaS) encoding a protein of 1,053 amino acids,with a...
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Real-Time PCR: molecular technique of many applications
PublikacjaReal-Time PCR is a sensitive DNA amplification technique initially applied in genetics and molecular biology. It enables in vivo copying of the selected DNA fragment (flanked by two primers) by the thermostable polymerase (in the presence of magnesium ions and deoxynucleotide triphosphates) and simultaneous measurement of the fluorescence. For one or more specific sequences in a DNA sample, real-time PCR enables both detection...
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Evolving gene regulatory networks controlling foraging strategies of prey and predators in an artificial ecosystem
PublikacjaCo-evolution of predators and prey is an example of an evolutionary arms race, leading in nature to selective pressures in positive feedback. We introduce here an artificial life ecosystem in which such positive feedback can emerge. This ecosystem consists of a 2-dimensional liquid environment and animats controlled by evolving artificial gene regulatory networks encoded in linear genomes. The genes in the genome encode chemical...
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On the Origin of Protein Superfamilies and Superfolds
PublikacjaDistributions of protein families and folds in genomes are highly skewed, having a small number of prevalent superfamiles/superfolds and a large number of families/folds of a small size. Why are the distributions of protein families and folds skewed? Why are there only a limited number of protein families? Here, we employ an information theoretic approach to investigate the protein sequence-structure relationship that leads to...
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Ammonia amendment promotes high rate lactate production and recovery from semi-continuous food waste fermentation
PublikacjaIn this study, a reliable approach using ammonia nitrogen was proposed to increase lactate production during semi-continuous food waste (FW) fermentation under mesophilic conditions. Both free ammonia nitrogen (FAN) and ammonium ion (NH4+-N) were present in mesophilic reactors, with a wide FAN/NH4+-N ratio variation due to the intermittent pH control. The investigation of responsible mechanisms revealed that the increased production...
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Whole-genome sequencing and antimicrobial potential of bacteria isolated from Polish honey
PublikacjaThe aim of this study was the whole-genome analysis and assessment of the antimicrobial potential of bacterial isolates from honey harvested in one geographical location—the north of Poland. In total, 132 strains were derived from three honey samples, and the antimicrobial activity of CFAM (cell-free after-culture medium) was used as a criterion for strain selection and detailed genomic investigation. Two of the tested isolates...
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Enzymes of the lysine biosynthetic pathway as targets for antifungals ?
PublikacjaSystemic infections caused by human pathogenic fungi in immunocompromized patients continue to be one of the important clinical problems. Limited availability of safe and efficacious antifungal chemotherapeutics and emerging resistance to existing drugs stimulates search for novel molecular targets for antifungals. The α-aminoadipate pathway (AAP) of L-lysine biosynthesis is unique in fungi and thus has been so far considered...
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Mechanisms of Damage to DNA Labeled with Electrophilic Nucleobases Induced by Ionizing or UV Radiation
PublikacjaHypoxia—a hallmark of solid tumors—makes hypoxic cells radioresistant. On the other hand, DNA, the main target of anticancer therapy, is not sensitive to the near UV photons and hydrated electrons, one of the major products of water radiolysis under hypoxic conditions. A possible way to overcome these obstacles to the efficient radio- and photodynamic therapy of cancer is to sensitize the cellular DNA to electrons and/or ultraviolet...
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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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Novel staphylococci nucH taxonomical marker used in identification of human-associated Staphylococcus succinus subsp. casei
PublikacjaThe aim of our study was to assess the sequencing of unique nucH gene fragment based on performed bioinformatics analysis as a novel diagnostic method for the identification of difficult to identify staphylococcal human pathogenic strains. Initially, PCR-RFLP-rrn analysis specific to the spacers between 16SrDNA and 23SrDNA followed by HhaI restriction analysis was performed. Further, sequencing of nucH and 16S rDNA genes fragments...
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Lipidomika – strategie analityczne i zastosowania
PublikacjaBioanalityka, to interdyscyplinarna dziedzina wiedzy, która stanowi szybko rozwijający się obecnie dział chemii analitycznej. Bioanaliza zaczyna odgrywać kluczową rolę w szybko rozwijających się dziedzinach współczesnej bionauki w ramach genomiki, proteomiki, metabolomiki, lipidomiki i innych. Umiejętność doboru odpowiednich metod i narzędzi, w zależności od rodzaju podejmowanego problemu, jest niezwykle ważne i często decyduje...
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Association between the NAT1 1095C > A polymorphism and homocysteine concentration
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A new cold-adapted beta-D-galactosidase from the Antarctic Arthrobacter sp. 32c - gene cloning, overexpression, purification and properties
PublikacjaThe development of a new cold-active β-D-galactosidases and microorganisms that efficiently ferment lactose is of high biotechnological interest, particularly for lactose removal in milk and dairy products at low temperatures and for cheese whey bioremediation processes with simultaneous bio-ethanol production. In this article, we present a new β-D-galactosidase as a candidate to be applied in the above mentioned biotechnological...
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Generation and Characterization of a DNA-GCN4 Oligonucleotide-Peptide Conjugate: The Impact DNA/Protein Interactions on the Sensitization of DNA
PublikacjaRadiotherapy, the most common therapy for the treatment of solid tumors, exerts its effects by inducing DNA damage. To fully understand the extent and nature of this damage, DNA models that mimic the in vivo situation should be utilized. In a cellular context, genomic DNA constantly interacts with proteins and these interactions could influence both the primary radical processes (triggered by ionizing radiation) and secondary reactions,...
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More Than just Antioxidants: Redox-Active Components and Mechanisms Shaping Redox Signalling Network
PublikacjasettingsOrder Article Reprints This is an early access version, the complete PDF, HTML, and XML versions will be available soon. Open AccessReview More Than just Antioxidants: Redox-Active Components and Mechanisms Shaping Redox Signalling Network by Monika Kuczyńska,Patrycja Jakubek andAgnieszka Bartoszek *ORCID Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland * Author to whom correspondence should...
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Comprehensive methodology for Staphylococcus aureus lipidomics by liquid chromatography and quadrupole time-of-flight mass spectrometry
PublikacjaStaphylococcus aureus is a common pathogen known to cause relatively minor infections as well as severe disorders in humans. Although there is fair amount of published data concerning various aspects of its biology, epidemiology, genetics, etc., there is still a scarce amount of data presenting reliable and thorough investigations regarding high-throughput analysis of total S. aureus lipid content. Therefore, the aim of this study...
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Conservation and diversity of MutS proteins
PublikacjaThe homologues of MutS, mismatch repair protein, exist in all prokaryotes, with the exception of Actinobacteria, Mollicutes and part of the Archaea. Multiple alignments of 316 MutS amino acid sequences from 169 species revealed conserved residues and sequence motifs distinguishing MutS homologues. All MutS homologues show high conservation within the ATPase domain. MutS1, the homologue responsible for DNA mismatch recognition,...
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Enhancement of photocatalytic-based processes by mono- and bimetallic (CuPd) rutile loaded nanoparticles for antibiotic resistance genes and facultative pathogenic bacteria removal
PublikacjaThe aim of the study was the strong reduction of facultative pathogenic bacteria (FPB), and clinically relevant antibiotic resistance genes (ARGs) from secondary effluent. To evaluate the ARGs removal efficiency comparative study of individual unit processes and combined AOPs has been performed. The present work investigated: i) removal of selected ARGs, namely blaTEM, ermB, qnrS, tetM, five FPB as well as 16S rDNA and the integrase...
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THE GENE CLONING, OVEREXPRESSION, PURIFICATION AND BIOCHEMICAL CHARACTERISATION OF A NEW COLD-ADAPTED β–GALACTOSIDASE FROM ARTHROBACTER SP. VII-4
PublikacjaINTRODUCTION. β-Galactosidase [EC 3.2.1.23] is an enzyme that catalyzes the hydrolysis of O-glycosidic linkages in galactosides. It is commercially used in dairy industry for the production of milk with reduced lactose content. Potentially, the best method for lactose removal under cooling conditions should be carried out with a cold-adapted enzyme. AIM. The aim of this study was to determine the taxonomic affiliation of the isolate...
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The relationship between standard reduction potentials of catechins and biological activities involved in redox control
PublikacjaRedox homeostasis involves factors that ensure proper function of cells. The excess reactive oxygen species (ROS) leads to oxidative stress and increased risk of oxidative damage to cellular components. In contrast, upon reductive stress, insufficient ROS abundance may result in faulty cell signalling. It may be expected that dietary antioxidants, depending on their standard reduction potentials (E°), will affect both scenarios....
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Genotyping Techniques for Determining the Diversity of Microorganisms
PublikacjaTyping of microbial pathogens, or identifying bacteria at the strain level, is particularly important for diagnosis, treatment, and epidemiological surveillance of bacterial infections. This is especially the case for bacteria exhibiting high levels of antibiotic resistance or virulence, and those involved in nosocomial or pandemic infections. Strain typing also has applications in studying bacterial population dynamics. The part...
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PARP inhibition potentiates the cytotoxic activity of C-1305, a selective inhibitor of topoisomerase II, in human BRCA1-positive breast cancer cells
PublikacjaTwo cellular proteins encoded by the breast and ovarian cancer type 1 susceptibility (BRCA1 and BRCA2) tumor suppressor genes are essential for DNA integrity and the maintenance of genomic stability.Approximately 5-10% of breast and ovarian cancers result from inherited alterations or mutations in these genes.Remarkably, BRCA1/BRCA2-deficient cells are hypersensitive to selective inhibition of poly(ADPribose) polymerase 1 (PARP-1),...
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Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70
PublikacjaThe J-domain protein Zuotin is a multi-domain eukaryotic Hsp70 co-chaperone. Though it is primarily ribosome-associated, positioned at the exit of the 60S subunit tunnel where it promotes folding of nascent polypeptide chains, Zuotin also has off-ribosome functions. Domains of Zuotin needed for 60S association and interaction with Hsp70 are conserved in eukaryotes. However, whether the 4-helix bundle (4HB) domain is conserved remains...
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Platelet RNA Sequencing Data Through the Lens of Machine Learning
PublikacjaLiquid biopsies offer minimally invasive diagnosis and monitoring of cancer disease. This biosource is often analyzed using sequencing, which generates highly complex data that can be used using machine learning tools. Nevertheless, validating the clinical applications of such methods is challenging. It requires: (a) using data from many patients; (b) verifying potential bias concerning sample collection; and (c) adding interpretability...
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imPlatelet classifier: image‐converted RNA biomarker profiles enable blood‐based cancer diagnostics
PublikacjaLiquid biopsies offer a minimally invasive sample collection, outperforming traditional biopsies employed for cancer evaluation. The widely used material is blood, which is the source of tumor-educated platelets. Here, we developed the imPlatelet classifier, which converts RNA-sequenced platelet data into images in which each pixel corresponds to the expression level of a certain gene. Biological knowledge from the Kyoto Encyclopedia...
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Małgorzata Pawłowicz dr n. med.
OsobyMałgorzata Pawłowicz MD PhD is a paediatrician and paediatric neurologist (Department of Developmental Neurology; Medical University of Gdańsk, Poland) and a resident in clinical genetics (Genetic Outpatient Clinic, Children's Memorial Health Institute in Warsaw, Poland). She studied medicine and received her Master Degree in Paediatrics and Paediatric Neurology at Medical University of Gdańsk. Dr. Pawłowicz completed her PhD studies...
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Virulence gene profiles in Staphylococcus aureus isolated from cows with subclinical mastitis in eastern Poland
PublikacjaStaphylococcus aureus is arguably the most important pathogen involved in bovine mastitis. The aim of this study was to determine the virulence gene profiles of 124 Staph. aureus isolates from subclinical mastitis in cows in eastern Poland. The presence of 30 virulence genes encoding adhesins, proteases and superantigenic toxins was investigated by PCR. The 17 different combinations of adhesin genes were identified. Occurrence...
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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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Genome-Wide DNA Methylation and Gene Expression in Patients with Indolent Systemic Mastocytosis
PublikacjaMastocytosis is a clinically heterogenous, usually acquired disease of the mast cells with a survival time that depends on the time of onset. It ranges from skin-limited to systemic disease, including indolent and more aggressive variants. The presence of the oncogenic KIT p. D816V gene somatic mutation is a crucial element in the pathogenesis. However, further epigenetic regulation may also affect the expression of genes that...
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Preprzedsiębiorczość
PublikacjaKsiążka składa się z czterech rozdziałów, poprzedzonych wstępem i zwieńczonych częścią podsumowującą całość. Rozdział pierwszy nakreśla tło dla dalszych rozważań. W rozdziale tym wyodrębniono trzy zasadnicze ujęcia: ujęcie ekonomiczne, ujęcie psychologiczne oraz socjologiczno-kulturowe. W dalszej części tego rozdziału przeanalizowano związki między przedsiębiorczością a wzrostem gospodarczym. Wskazano także mniej znane kierunki...
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The essence of marine and coastal space – an interdisciplinary perspective
PublikacjaSea space has been undergoing a profound transformation. Although it retains its inspirational function in arts, literature and philosophy, it has been gaining new anthropogenic dimensions in eco-nomics and urban planning as a source of satisfying human needs i.e. the provision of harmony, beauty, off-shore energy, and biotech substances. Therefore, in this paper marine space is analyzed from a mul-tidimensional perspective of...
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Deep Learning-Based, Multiclass Approach to Cancer Classification on Liquid Biopsy Data
PublikacjaThe field of cancer diagnostics has been revolutionized by liquid biopsies, which offer a bridge between laboratory research and clinical settings. These tests are less invasive than traditional biopsies and more convenient than routine imaging methods. Liquid biopsies allow studying of tumor-derived markers in bodily fluids, enabling the development of more precise cancer diagnostic tests for screening, disease monitoring, and...
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Novel DNA-binding protein from Nanoarchaeum equitans Kin4-M binds all kinds of nucleic acids
PublikacjaNanoarchaeum equitans is the only known representative of Archaea phylum Nanoarchaeota and stands out as one of the tiniest known living organism. What is more it has smallest genome, which is only 490.885 base pairs long. It is also one of the most compact genomes. According to predictions about 95% of the DNA encodes proteins or stable RNA. Nanoarchaeum equitans lacks genes for most vital metabolic pathways including lipid, cofactor,...
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MutS3: a MutS homologue of unknown biological function
PublikacjaThe homologues of MutS proteins are widespread among both Prokaryotes and Eukaryotes. MutS designated as MutS1 is a part of MMR (mismatch repair) system which is responsible for removal of mispaired bases and small insertion/deletion loops in DNA. Initially, the only MutS homologues known were those engaged in mismatch repair and these were later designated as MutS1. Subsequently, the MutS2 homologue was distinguished. MutS2 does...
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Komórki macierzyste nowotworu i ich znaczenie w diagnostyce i terapii przeciwnowotworowej
PublikacjaWedług klasycznej teorii karcinogenezy nowotwór powstaje w wyniku ekspansji klonalnej pojedynczej komórki, która uległa transformacji w wyniku nagromadzenia się w jej genomie zmian genetycznych i epigenetycznych. Jednak w ostatnich latach przywołano do życia inną hipotezę, przedstawioną już ponad 150 lat temu, która mówi, że nowotwór wywodzi się ze stransformowanych komórek posiadających cechy komórek pierwotnych (macierzystych)....
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Биополитика согласно Чеславу Милошу
PublikacjaThe paper shows the origins of the transformation of history into biohistory as well as politics into biopolitics in the writings of Miłosz. It takes into account his view of history when he was a child and his social experiences when he was at school. It proves that the fact that Miłosz comprehends the world within the categories of biopolitics results from projecting Darwinism on the historical past, and then projecting on...