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Department of Microbiology
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Year 2017
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Isolation and Characterization of Phenol-Degrading Psychrotolerant Yeasts
PublicationIn this study, the potential of selected psychrotolerant yeast strains for phenol biodegradation was studied. From 39 strains isolated from soil and water samples from Rucianka peat bog, three psychrotolerant yeast strains: A011, B021 and L012 showed the ability to phenol degradation. The result shows that all three yeast strains could degrade phenol at 500 mg l-1 and 750 mg l-1 concentration, whereas strains A011 and L012 could...
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Izolacja drożdży psychrotolerancyjnych oraz ocena ich zdolności do wykorzystania N-fosfonometyloglicyny jako źródła pierwiastków biogennych
PublicationN-fosfonometyloglicyna (PMG, glifosat) jest substancją aktywną herbicydu Roundup o szerokim spektrum aktywności biologicznej. Mechanizm jego działania opiera się na inhibicji aktywności syntazy 5-enolopirogroniano-szikimowo-3-fosforanowej (EPSP), przez co hamowana jest biosynteza aminokwasów aromatycznych u roślin. Glifosat jest związkiem fosforoorganicznym, w którego budowie wyróżnia się trwałe wiązanie C-P. Szybkość rozkładu...
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Konstrukcja nowych układów do diagnostyki molekularnej zakażeń o etiologii Candida spp.
PublicationDrożdżaki z rodzaju Candida należą do jednych z najczęściej izolowanych czynników etiologicznych zakażeń krwi. Szybka i bezbłędna identyfikacja gatunkowa pozwala na wdrożenie odpowiedniego leczenia i zwiększa szansę na powodzenie terapii. Celem badań była konstrukcja nowych układów wykorzystujących narzędzia diagnostyki molekularnej do specyficznej identyfikacji gatunkowej i rodzajowej drożdżaków Candida. Poszukiwano również nowych...
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Low frequency of itraconazole resistance found among avian Aspergillus fumigatus isolates
PublicationAspergillus fumigatus is the most frequent etiological factor of invasive aspergillosis in human as well as animals, including birds. Aspergillosis caused by drug-resistant strains poses a significant therapeutic issue, especially if resistance pattern includes insensitivity to triazoles, i.e. drugs recommended for the primary therapy purposes. Majority of resistant isolates hold the TR34/L98H...
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Metabolic activity of tree saps of different origin towards cultured human cells in the light of grade correspondence analysis and multiple regression modeling
PublicationTree saps are nourishing biological media commonly used for beverage and syrup production. Although the nutritional aspect of tree saps is widely acknowledged, the exact relationship between the sap composition, origin, and effect on the metabolic rate of human cells is still elusive. Thus, we collected saps from seven different tree species and conducted composition-activity analysis. Saps from trees of Betulaceae, but not from...
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Mikroorganizmy w degradacji celulozy
PublicationCeluloza jest podstawowym składnikiem komórek roślinnych. Włókna celulozowe są bardzo ciasno upakowane w ścianach komórek, przez co utrudniają dostęp enzymom celulolitycznym oraz cząsteczkom wody. Najważniejszą rolę w procesie rozkładu celulozy pełnią celulazy, które należą do rodziny hydrolaz glikozydowych. Zdolność do hydrolizy celulozy i hemicelulozy wykazują mikroorganizmy celulolityczne. Prezentują one dwa różne mechanizmy...
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Modified DNA polymerases for PCR troubleshooting
PublicationPCR has become an essential tool in biological science. However, researchers often encounter problems with difficult targets, inhibitors accompanying the samples, or PCR trouble related to DNA polymerase. Therefore, PCR optimization is necessary to obtain better results. One solution is using modified DNA polymerases with desirable properties for the experiments. In this article, PCR troubleshooting, depending on the DNA polymerase...
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Modyfikacje polimeraz DNA jako rozwiązania problemów w reakcjach PCR
PublicationReakcja PCR już od wielu lat jest podstawowym narzędziem stosowanym w biotechnologii molekularnej. Nadal napotykamy jednak liczne problemy podczas jej przeprowadzania związane z trudnymi matrycami, obecnością inhibitorów itp. Optymalizacja reakcji PCR jest więc niezbędna w celu poprawy wyników. Jednym z rozwiązań tych problemów może być modyfikowanie polimeraz DNA. W powyższym artykule opisano problemy i rozwiązania zależne polimerazy...
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Mushroom Toxins
PublicationToxins and Other Harmful Compounds in Foods provides information on the contents, distribution, chemical properties, and biological activity of toxins and other harmful compounds in foods that are natural components of the raw materials, accumulated due to microbial actions and environmental pollution, or are generated due to processing.
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Neotenic phenomenon in gene expression in the skin of Foxn1- deficient (nude) mice - a projection for regenerative skin wound healing
PublicationMouse fetuses up to 16 day of embryonic development and nude (Foxn1- deficient) mice are examples of animals that undergo regenerative (scar-free) skin healing. The expression of transcription factor Foxn1 in the epidermis of mouse fetuses begins at embryonic day 16.5 which coincides with the transition point from scar-free to scar-forming skin wound healing. In the present study, we tested the hypothesis that Foxn1 expression...
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Polyurethane porous scaffolds (PPS) for soft tissue regenerative medicine applications
PublicationTissue engineering requires suitable polymeric scaffolds, which act as a physical support for regenerated tissue. A promising candidate might be polyurethane (PUR) scaffold, due to the ease of the PUR properties design, which can be adjusted directly to the intended purpose. In this study, we report a successful fabrication of porous polyurethane scaffolds (PPS) using solvent casting/particulate leaching technique combined with...
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Recurrent bowel-blood translocations of Escherichia coli with the unique virulence characteristics over three-year period in the patient with acute myeloid leukaemia – case report
PublicationIn patients with haematological malignancies, the bowel remains the main source of Escherichia coli bloodstream infections. We present the clinical example of recurrent bowel-blood translocations of E. coli with the unique virulence characteristics in a 55-year-old male with the diagnosis of acute myeloid leukaemia. The virulent factors profile of examined strains confirmed that the co-existence of genes papC, sfa, usp and cnf1,...
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Relation of the polymorphism of cyp51A sequence and the susceptibility of Aspergillus fumigatus isolates to triazoles determined by commercial gradient test (Etest) and by reference methods
PublicationThe aim of this study was to evaluate the accuracy of commercial gradient test (Etest) in the detection of triazole resistant Aspergillus fumigatus isolates using reference microdilution methods and the analysis of sequences of the cyp 51A gene. The study was performed on twenty clinical isolates which were identified as Aspergillus fumigatus based on the DNA sequences of the ITS1-2 fragment of ribosomal DNA and the β-tubulin gene,...
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Role of the disulfide bond in stabilizing and folding of the fimbrial protein DraE from uropathogenic Escherichia coli
PublicationDr fimbriae are homopolymeric adhesive organelles of uropathogenic Escherichia coli composed of DraE subunits, responsible for the attachment to host cells. These structures are characterized by enormously high stability resulting from the structural properties of an Ig-like fold of DraE. One feature of DraE and other fimbrial subunits that makes them peculiar among Ig-like domain-containing proteins is a conserved disulfide bond...
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Synthesis and characterization of cycloaliphatic hydrophilic polyurethanes, modified with l-ascorbic acid, as materials for soft tissue regeneration
PublicationIn this paper we described synthesis and characteristic of obtained hydrophilic polyurethanes (PURs) modified with ascorbic acid (commonly known as vitamin C). Such materials may find an application in the biomedical field, for example in the regenerative medicine of soft tissues, according to ascorbic acid wide influence on tissue regeneration Flora (2009), Szymańska-Pasternak et al. (2011), Taikarimi and Ibrahim (2011), Myrvik...
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Transcriptomic responses to wounding: meta-analysis of gene expression microarray data
PublicationBackground A vast amount of microarray data on transcriptomic response to injury has been collected so far. We designed the analysis in order to identify the genes displaying significant changes in expression after wounding in different organisms and tissues. This meta-analysis is the first study to compare gene expression profiles in response to wounding in as different tissues as heart, liver, skin, bones, and spinal cord, and...
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WIELOLEKOOPORNE ZAKAŻENIA CANDIDA - PROBLEM XXI WIEKU!
PublicationW ostatnich latach obserwuje się dramatyczny wzrost zakażeń grzybiczych, których przyczyną są grzyby z rodzaju Candida (C). Większość zakażeń wywoływana jest przez C. albicans, C. glabrata, C. krusei, C. parapsilosis i C. tropicalis. Dotychczas najczęściej stosowanymi lekami przeciwko Candida spp były azole, jednakże ze względu na występowanie naturalnej oporności na te antybiotyki (C. glabrata i C. krusei) coraz częściej azole...
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Zastosowanie immobilizowanego białka MutS do wychwytywania fragmentów DNA zawierających niesparowane zasady
PublicationBiałko MutS wiąże DNA zawierające błędnie sparowane oraz niesparowane zasady w DNA. Podjęto szereg prób wykorzystania tego białka jako narzędzia do detekcji nieznanych mutacji lub zagęszczania frakcji DNA z niesparowaną zasadą. Dotychczas żadna z metod oparta na użyciu białka MutS nie została wdrożona powszechnie do praktyki laboratoryjnej. Głównym powodem takiego stanu rzeczy jest stosunkowo silne powinowactwo MutS do DNA w pełni...
Year 2016
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A Colorimetric Microplate Assay for DNA-Binding Activity of His-Tagged MutS Protein
PublicationA simple microplate method was designed for rapid testing DNA-binding activity of proteins. The principle of the assay involves binding of tested DNA by his-tagged protein immobilized on a nickel-coated ELISA plate, following colorimetric detection of biotinylated DNA with avidin conjugated to horseradish peroxidase. The method was used to compare DNA mismatch binding activities of MutS proteins from three bacterial species. The...
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A new assay for the simultaneous identification and differentiation of Klebsiella oxytoca strains.
PublicationKlebsiella oxytoca is the second most frequently identified species of Klebsiella isolated from hospitalized patients. Klebsiella spp. is difficult to identify using conventional methods and is often misclassified in clinical microbiology laboratories. K. oxytoca is responsible for an increasing number of multi-resistant infections in hospitals because of insufficient detection and identification. In this study, we propose a new...
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A novel chemiluminescent immunoassay for detection of Toxoplasma gondii IgG in human sera
PublicationThis study describes Toxoplasma gondii IgG chemiluminescent immunoassay (CLIA) based on the use of a novel immunochemical reagents in the form of the conjugates of original acridinium ester (AE) labels attached to antibodies and SAG2-GRA1-ROP1L chimeric antigen and shows that this test is useful for diagnostic purposes.
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A simple modification of PCR thermal profile applied to evade persisting contamination
PublicationThe polymerase chain reaction (PCR), one of the most commonly applied methods of diagnostics and molecular biology has a frustrating downside known as the false positive signal or contamination. Several solutions to avoid and to eliminate PCR contaminations have been worked out to date but the implementation of these solutions to laboratory practice may be laborious and time consuming. A simple approach to circumvent the problem...
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A simple modification to improve the accuracy of methylation-sensitive restriction enzyme quantitative polymerase chain reaction
PublicationDNA digestion with endonucleases sensitive to CpG methylation such as HpaII followed by polymerase chain reaction (PCR) quantitation is commonly used in molecular studies as a simple and inexpensive solution for assessment of region-specific DNA methylation. We observed that the results of such analyses were highly overestimated if mock-digested samples were applied as the reference.We determined DNA methylation levels in several...
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Changes in gene methylation patterns in neonatal murine hearts: Implications for the regenerative potential
PublicationBackground The neonatal murine heart is able to regenerate after severe injury; this capacity however, quickly diminishes and it is lost within the first week of life. DNA methylation is an epigenetic mechanism which plays a crucial role in development and gene expression regulation. Under investigation here are the changes in DNA methylation and gene expression patterns which accompany the loss of regenerative potential. Results The...
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Cloning, expression, and biochemical characterization of a coldactive GDSL-esterase of a Pseudomonas sp. S9 isolated from Spitsbergen island soil
PublicationAn estS9 gene, encoding an esterase of the psychrotolerant bacterium Pseudomonas sp. S9 was cloned and sequenced. The deduced sequence revealed a protein of 636 amino acid residues with a molecular mass of 69 kDa.Further amino acid sequence analysis revealed that the EstS9 enzyme contained a G-D-S-L motif centered at a catalytic serine, an N-terminal catalytic domain and a C-terminal autotransporter domain. Two recombinant E. coli...
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Cold-Active beta-Galactosidases: Sources, Biochemical Properties and Their Biotechnological Potential
Publicationbeta-D-Galactosidases have been studied extensively in terms of their application to a variety of industrial technologies. To date, considerable research efforts have been devoted to characterization of new cold-active beta-D-galactosidases which were isolated directly from selected species of bacteria and yeasts, as well as with the use of metagenomic approaches. This chapter will provide a review of current research towards cold-active...
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Correlation between the number of Pro-Ala repeats in the EmrA homologue of Acinetobacter baumannii and resistance to netilmicin, tobramycin, imipenem and ceftazidime
PublicationAcinetobacter baumannii coccobacilli are dangerous to patients in intensive care units because of their multidrug resistance to antibiotics, developed mainly in the past decade. This study aimed to examine whether there is a significant correlation between the number of Pro-Ala repeats in the CAP01997 protein, the EmrA homologue of A. baumannii, and resistance to antibiotics. A total of 79 multidrug-resistant A. baumannii strains...
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Evaluation of the content of inorganic anions in tree saps
PublicationTree saps were once commonly used in the countries of Northern, Central and Eastern Europe. Although once almost forgotten, their popularity has been growing recently as part of an interest in organic food and traditional medicine. Tree saps, tapped mainly from birch and maple trees, are drunk both fresh and fermented or are used as raw material for the production of food products, e.g. syrups. The aim of this study was to determine...
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Expression of a GDSL esterase from Pseudomonas sp. S9 in Pichiapastoris
PublicationCold active lipolytic enzymes are promising to replace the conventional enzymes processes of biotechnological industries. One of the most important feature of the cold-active lipases and esterases is that they offer economic benefits through energy saving. In general, they exhibit high activity at low temperatures and low thermostability at moderate temperatures. Lipolytic enzyme EstS9 was isolated from Pseudomonas sp. S9. A multiple...
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Isolation and characterization of Acid Soluble Collagen from the Skin of African Catfish (Clarias gariepinus), Salmon (Salmo salar) and Baltic cod (Gadus morhua)
PublicationAcid-soluble collagen (ASC) from the fish skin of African catfish (Clarias gariepinus), Salmon (Salmo salar) and Baltic cod (Gadus morhua) was extracted and characterized. The ASC extraction yield was 75%, 73% and 68%, respectively. The denaturation and melting temperatures of African catfish ASC (29.3°C and 100.0°C) were significantly higher than ASC of Salmon and Baltic cod (20.6°C and 90.5°C; 15.2°C and 86.7°C, respectively), assessed...
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Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel disease.
PublicationBACKGROUND: Inflammatory bowel disease (IBD) is a chronic gastrointestinal condition without any known cause or cure. An imbalance in normal gut biota has been identified as an important factor in the inflammatory process. METHODS: Fifty-eight biopsies from Crohn's disease (CD, n = 10), ulcerative colitis (UC, n = 15), and healthy controls (n = 16) were taken from a population-based case-control study. Automated ribosomal intergenic...
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MINERAL CONTENT OF TREE SAP FROM THE SUBCARPATHIAN REGION
Publicationbut also as medicinal substance in folk medicine. Traditionally, it was used to treat various conditions, mostly anaemia and chronic fatigue. This study has been designed to establish the content of metallic elements (sodium, potassium, calcium, magnesium, zinc and copper) in sap collected from eight different species (silver birch, downy birch, hornbeam, Norway maple, boxelder maple, black walnut, black alder and white willow)...
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PCR and real-time PCR approaches to the identification of Arthroderma otae species Microsporum canis and Microsporum audouinii/Microsporum ferrugineum
PublicationObjectives The identification of species in the Arthroderma otae complex is essential to determine the origin of infection and to eliminate the risk of transmission. Microsporum canis is a zoophilic species, whereas Microsporum audouinii and Microsporum ferrugineum are anthropophilic species. In this paper, we propose alternative methods that permit species-specific identification of both anthropophilic and zoophilic members of...
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Principles and applications of Ligation Mediated PCR methods for DNA-based typing of microbial organisms
PublicationA significant number of DNA-based techniques has been introduced into the field of microorganisms’ characterization and taxonomy. These genomic fingerprinting methods were developed to detect DNA sequence polymorphisms by using general principles, such as restriction endonuclease analysis, molecular hybridization, and PCR amplification. In recent years, some alternative techniques based on ligation of oligonucleotide adapters before...
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Rapid Assays for Specific Detection of Fungi of Scopulariopsis and Microascus Genera and Scopulariopsis brevicaulis Species
PublicationPurpose Fungi of Scopulariopsis and Microascus genera cause a wide range of infections, with S. brevicaulis being the most prevalent aetiological agent of mould onychomycosis. Proper identification of these pathogens requires sporulating culture, which considerably delays the diagnosis. So far, sequencing of rDNA regions of clinical isolates has produced ambiguous results due to the lack of reference sequences in publicly available...
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Regulacja epigenetyczna a potencjał regeneracyjny ssaków. Badania globalnych profili metylacji w tkankach dorosłej myszy MRL/MpJ i w sercach noworodków myszy C57BL/6J.
PublicationW pracy tej otrzymano genomowe profile metylacji DNA dla dwóch modeli regeneracji u ssaków: (i) dorosłej myszy MRL/MpJ, która jest zdolna do zamykania otworów w małżowinie usznej oraz wykazuje podwyższone zdolności regeneracyjne w wielu innych narządach oraz (ii) sercach noworodków myszy, u których zachodzi regeneracja rozległych uszkodzeń lewej komory serca. Zidentyfikowano szereg odmiennie metylowanych regionów DNA, regionów DMR,...
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Structural studies of a cold-adapted dimeric Beta-D-galactosidase from Paracoccus sp. 32d
PublicationThe crystal structure of a novel dimeric [beta]-D-galactosidase from Paracoccus sp. 32d (Par[beta]DG) was solved in space group P212121 at a resolution of 2.4 Å by molecular replacement with multiple models using the BALBES software. This enzyme belongs to glycoside hydrolase family 2 (GH2), similar to the tetrameric and hexameric [beta]-D-galactosidases from Escherichia coli and Arthrobacter sp. C2-2, respectively. It is the second...
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Study on a polish peat bog “Rucianka” as a source of yeast strains capable of effective phenol biodegradation
PublicationPhenol is one of the most widely distributed environmental pollutants which can be found in wastewaters and industrial effluents. Due to its toxicity and resistance to self-degradation, it could become even lethal for humans and animals. The treatment of this toxic compound is focused on psychical–chemical methods, although biological treatment of phenol is preferable for economic aspects related to relatively...
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The methylome and transcriptome of fetal skin: implications for scarless healing
PublicationAim: Fetal skin is known to heal without scarring. In mice, the phenomenon is observed until the 16–17 day of gestation – the day of transition from scarless to normal healing. The study aims to identify key methylome and transcriptome changes following the transition. Materials & methods: Methylome and transcriptome profiles were analyzed in murine dorsal skin using microarray approach. Results & conclusion: The genes associated...
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The usefulness of birch saps from the area of Podkarpacie to produce birch syrup
PublicationIn northern European countries, as well as in North America tree saps of maples and birches are used for the production of syrups. Birch syrups are characterized by a specific aromatic taste and can be used as an addition to sweets, desserts, salads and meats. Attention is paid to the health benefits of birch syrups, mainly for high mineral content. The aim of this study was to evaluate the usefulness of birch saps obtained from...
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Use of Escherichia coli Nissle 1917 producing recombinant colicins for treatment of IBD patients
PublicationPatients with Crohn’s Disease and ulcerative colitis infected with Adherent-Invasive Escherichia coli strains constitute the largest group among Inflammatory Bowel Disease subjects, when taking into account all known etiological agents of the disease. A possible link between these pathogenic bacteria and inflammation process has gained the confidence in recently published papers. Observed enteric neuroglial cells apoptosis and...
Year 2015
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A new assay for simultaneous identification and differentiation of Klebsiella oxytoca strains
PublicationBacterial strain typing, 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.
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A new Toxoplasma gondii chimeric antigen containing fragments of SAG2, GRA1, and ROP1 proteins—impact of immunodominant sequences size on its diagnostic usefulness
PublicationThis study presents the first evaluation of new Toxoplasma gondii recombinant chimeric antigens containing three immunodominant regions of SAG2, GRA1, and one of two ROP1 fragments differing in length for the serodiagnosis of human toxoplasmosis. The recombinant chimeric antigens SAG2-GRA1-ROP1L (with large fragment of ROP1, 85-396 amino acid residues) and SAG2-GRA1-ROP1S (with a small fragment of ROP1, 85-250 amino acid residues)...
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A novel method of Mycobacterium tuberculosis complex strain differentiation using polymorphic GC-rich gene sequences.
PublicationTuberculosis is one of the leading infectious diseases. In this work, a new genotyping method of Mycobacterium tuberculosis (Mtb) complex strain is presented. 27 Mtb genomes were analyzed for the presence of length polymorphism within polymorphic GC-rich gene sequences. Four genes, Rv3345c, Rv3507, Rv0747 and Rv3511, showing variation in length depending on the Mtb strain were selected for designing primer sequences flanking variable...
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Characterisation of Escherichia coli isolates from the blood of haematological adult patients with bacteraemia: translocation from gut to blood requires the cooperation of multiple virulence factors
PublicationThe aim of the study was to investigate whether there are unique pathotypes of Escherichia coli capable of transmission from the gastrointestinal tract to the vascular bed. The study included E. coli strains isolated from clinical materials collected from 115 patients suffering from haematologic malignancies diagnosed with bacteraemia. The genotyping techniques established that 89 E. coli isolates from the blood had the same genotype...
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Characterization of a single-stranded DNA-binding-like Protein from Nanoarchaeum equitans - a nucleic acid binding protein with broad substrate specificity
PublicationBackground SSB (single-stranded DNA-binding) proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized,...
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Epigenetyczne i transkryptomiczne podstawy potencjału regeneracyjnego ssaków. Badania na modelach skóry płodowej i dorosłej myszy MRL/MpJ
PublicationRegeneracja jest to zdolność do odbudowy uszkodzonych lub utraconych tkanek, kończyn oraz narządów. Efektywne procesy regeneracji obserwowane są u prymitywnych kręgowców, u których mogą przejawiać się w tak spektakularnych zjawiskach jak odtworzenie całych kończyn po ich amputacji. U wyższych kręgowców zdolności regeneracyjne są znacznie bardziej ograniczone. Rozwój metod umożliwiających badanie globalnych profili ekspresji i metylacji...
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Essential Oils, Silver Nanoparticles and Propolis as Alternative Agents Against Fluconazole Resistant Candida albicans, Candida glabrata and Candida krusei Clinical Isolates
PublicationDevelopment of effective and safe therapeutic treatment of fungal infections remains one of the major challenge for modern medicine. The aim of presented investigation was to analyze the in vitro antifungal activity of selected essential oils, ethanolic extracts of propolis and silver nanoparticles dropped on TiO2 against azole-resistant C. albicans (n = 20), C. glabrata (n = 14) and C. krusei (n = 10) clinical isolates. Among...
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Examination of cyp51A and cyp51B expression level of the first Polish azole resistant clinical Aspergillus fumigatus isolate
PublicationAspergillus fumigatus is one of the most prevalent airborne fungal pathogens causing infections worldwide. Most A. fumigatus strains are susceptible to azoles, which are administered as the first line therapeutics. However, during last decade the acquired resistance to triazoles by these species has been described. There is a number of publications concerning the examination of clinical A. fumigatus strains from different countries,...
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Expression of goose parvovirus whole VP3 protein and its epitopes in Escherichia coli cells
PublicationThe aim of this study was the expression of goose parvovirus capsid protein (VP3) and its epitopes in Escherichia coli cells. Expression of the whole VP3 protein provided an insufficient amount of protein. In contrast, the expression of two VP3 epitopes (VP3ep4, VP3ep6) in E. coli, resulted in very high expression levels. This may suggest that smaller parts of the GPV antigenic determinants are more efficiently expressed than the...