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Comparison of nitrogen and VFA removal pathways in autotrophic and organotrophic anammox reactors
PublicationOrganotrophic anammox is a promising process for treating both nitrogen and organic containing wastewater than that of the traditional autotrophic anammox for sole nitrogen removal. However pathways of nitrogen removal particularly at metagenomic level in both processes are still unknown. Here we report, metabolic pathways of nitrogen removal in two lab-scale sequencing batch reactors (SBR), one autotrophic and another organotrophic...
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Dibutyl phthalate disrupts conserved circadian rhythm in Drosophila and human cells
PublicationPeople are constantly exposed to phthalates, due to their common use in the production of plastics, pharmaceuticals, cosmetics and skin care products. The ability of phthalates to disrupt endocrine signaling, leading to developmental, reproductive and metabolic defects, has been studied, yet how phthalates interfere with these biological functions is still unclear. To uncover DBP interacting molecular pathways, we raised Drosophila...
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The role of epigenetics in regeneration
PublicationComplex changes in chromatin structure and at the transcriptional level occur from the creation of a single parental gamete throughout fertilization, embryo development and the life of an adult organism. Epigenetic changes, such as methylation and hydroxymethylation of DNA or histone methylation and acetylation, are an important part of these processes. Epigenetic regulation has an essential influence on gene expression level. DNA...
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Genome-wide DNA methylation profiling of the regenerative MRL/MpJ mouse and two normal strains
PublicationAims We aimed to identify the pivotal differences in the DNA methylation profiles between the regeneration capable MRL/MpJ mouse and reference mouse strains. Materials and Methods Global DNA methylation profiling was performed in ear pinnae, bone marrow, spleen, liver, heart from uninjured adult females of the MRL/MpJ and C57BL/6J and BALB/c. Results and conclusion A number of differentially methylated regions distinguishing between...
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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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Towards Cancer Patients Classification Using Liquid Biopsy
PublicationLiquid biopsy is a useful, minimally invasive diagnostic and monitoring tool for cancer disease. Yet, developing accurate methods, given the potentially large number of input features, and usually small datasets size remains very challenging. Recently, a novel feature parameterization based on the RNA-sequenced platelet data which uses the biological knowledge from the Kyoto Encyclopedia of Genes and Genomes, combined with a classifier...
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Deep Learning-Based, Multiclass Approach to Cancer Classification on Liquid Biopsy Data
PublicationThe 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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Virulence, antifungal susceptibility and molecular mechanisms of echinocandin resistance among Candida isolates recovered from clinical specimens
PublicationFungi of the genus Candida belong to the natural microflora of healthy individuals. However, they can also be a cause of opportunistic infections especially among patients with an impaired immune system. The first line therapy of Candida infections is based on triazoles. However, in recent years there an increase of azole resistant Candida spp., in particular C. glabrata and C. krusei, has been observed. For this reason, echinocandin...
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Salinity enhances high optically active L-lactate production from co-fermentation of food waste and waste activated sludge: Unveiling the response of microbial community shift and functional profiling
PublicationLactic acid (LA), a versatile platform molecule, can be fermented from organic wastes, such as food waste and waste activated sludge. In this study, an efficient approach using salt, a component of food waste as an additive, was proposed to increase LA production. The LA productivity was increased at 10 g NaCl/L and optical pure L-lactate was obtained at 30 g NaCl/L. The enhancement of LA was in accordance with the increased solubilization...
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Set of Experience and Decisional DNA: Experience-Based Knowledge Structures
PublicationThis chapter presents a description of Set of Experience Knowledge Structure (SOEKS) and Decisional DNA (DDNA), argumentation for a knowledge representation, composition, configuration and metrics. SOEKS is a combination of filtered and amalgamated information obtained from formal decision events. It facilitates effective explicit representation of decisional experience taken from different technologies. SOEKS comprises variables,...
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Molecular Targets for Anticandidal Chemotherapy
PublicationA relatively small number of anticandidal chemotherapeutics used in clinical practice is at least in part consequence of a limited number of their molecular targets: ergosterol in the membrane, lanosterol demethylase, b(1!3) glucan synthase, and DNA/RNA biosynthesis. Much more potential novel targets have been revealed by the comparative genomic studies identifying essential genes unique for Candida albicans or resulted from recognition...
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Ammonia amendment promotes high rate lactate production and recovery from semi-continuous food waste fermentation
PublicationIn 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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Phosphorylation‐mediated regulation of heat shock response in Escherichia coli
PublicationEscherichia coli has two heat shock regulons under the transcriptional control of Esigma(32) and Esigma(E) RNA polymerases. These polymerases control the expression of genes, the products of which are needed for correct folding of proteins in the cytoplasm and the extracytoplasm respectively. In this study, we report that mutations in a tyrosine phosphatase-encoding gene led to decreased activity of these heat shock regulons. The...
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Molecular targets for antifungals in amino acid and protein biosynthetic pathways
PublicationFungi cause death of over 1.5 million people every year, while cutaneous mycoses are among the most common infections in the world. Mycoses vary greatly in severity, there are long-term skin (ringworm), nail or hair infections (tinea capitis), recurrent like vaginal candidiasis or severe, life-threatening systemic, multiorgan infections. In the last few years, increasing importance is attached to the health and economic problems...
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Small regulatory bacterial RNAs regulating the envelope stress response
PublicationMost bacteria encode a large repertoire of RNA-based regulatory mechanisms. Recent discoveries have revealed that the expression of many genes is controlled by a plethora of base-pairing noncoding small regulatory RNAs (sRNAs), regulatory RNA-binding proteins and RNA-degrading enzymes. Some of these RNA-based regulated processes respond to stress conditions and are involved in the maintenance of cellular homeostasis. They achieve...
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Escherichia coli Strains with Virulent Factors Typical for Uropathogens were Isolated from Sinuses from Patients with Chronic Rhinosinusitis—Case Report
PublicationEscherichia coli were isolated from three patients with chronic rhinosinusitis (CRS) by intraoperative sinus tissue biopsy. Taking into account the unusual replicative niche and previous treatment failures, it was decided to focus on the virulence and drug resistance of these bacteria. The strains turned out to be multi-sensitive, but the rich virulence factors profile of bacteria typical for phylogenetic group B2 deserved attention....
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The Effect of Posaconazole, Itraconazole and Voriconazole in the Culture Medium on Aspergillus fumigatus Triazole Resistance
PublicationTriazoles are the only compounds used as antibiotics in both medicine and agriculture. The presence of triazoles in the environment can contribute to the acquisition of azole resistance among isolates of Aspergillus fumigatus. The objective of this study was to investigate the effect of A. fumigatus exposure to triazoles on susceptibility to these compounds. Seventeen triazole-resistant and 21 triazole-sensitive A. fumigatus isolates...
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Pathogenesis of psoriasis in the “omic” era. Part II. Genetic, genomic and epigenetic changes in psoriasis
PublicationPsoriasis is a multifactorial disease in which genetic, environmental and epigenetic factors regulating gene expression play a key role. In the “genomic era”, genome-wide association studies together with target genotyping platforms performed in different ethnic populations have found more than 50 genetic susceptible markers associated with the risk of psoriasis which have been identified so far. Up till now, the strongest association...
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Antimicrobial resistance of Pseudomonas spp. isolated from wastewater and wastewater-impacted marine coastal zone
PublicationIn this study, species distribution and antimicrobial susceptibility of cultivated Pseudomonas spp. were studied in influent (INF), effluent (EFF), and marine outfall (MOut) of wastewater treatment plant (WWTP). The susceptibility was tested against 8 antimicrobial classes, active against Pseudomonas spp.: aminoglycosides, carbapenems, broad-spectrum cephalosporins from the 3rd and 4th generation, extended-spectrum penicillins,...
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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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An MTA-phosphorylase gene discovered in the metagenomic library derived from Antarctic top soil during screening for lipolytic active clones confers strong pink fluorescence in the presence of rhodamine B.
PublicationIn this work, we present the construction of a metagenomic library in Escherichiacoli using the pUC19 vector and environmental DNA directly isolated fromAntarctic topsoil and screened for lipolytic enzymes. Unexpectedly, the screeningon agar supplemented with olive oil and rhodamine B revealed one unusual pinkfluorescent clone (PINKuv) out of 85 000 clones. This clone harbored a plasmid,pPINKuv, which has an insert of 8317 bp that...
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Modulation of CYP1A1, CYP1A2 and CYP1B1 expression by cabbage juices and indoles in human breast cell lines
PublicationEpidemiological studies have shown that consumption of cab- bage and sauerkraut is connected with significant reduction of breast cancer incidences. Estrogens are considered a major breast cancer risk factor and their metabolism by P450 enzymes substan- tially contributes to carcinogenic activity. The aim of this study was to investigate the effect of cabbage and sauerkraut juices of differ- ent origin on the expression profile...
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Nitric Oxide-Dependent Pathways as Critical Factors in the Consequences and Recovery after Brain Ischemic Hypoxia
PublicationBrain ischemia is one of the leading causes of disability and mortality worldwide. Nitric oxide (NO), a molecule that is involved in the regulation of proper blood flow, vasodilation, neuronal and glial activity constitutes the crucial factor that contributes to the development of pathological changes after stroke. One of the early consequences of a sudden interruption in the cerebral blood flow is the massive production of reactive...
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Identification and properties of the psychrophilic bacterium Desulfolatea psychrophila single-stranded DNA binding proteins
PublicationTo study the biochemical properties of SSB from Desulfolatea psychrophila (DpsSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 426 nucleotides encoding SSB protein of 142 amino acids with a calculated molecular mass of 15.6 kDa and it is the smallest known bacterial SSB protein indentified to date. The amino-acid sequence...
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Antibiotic resistance and prevalence of class 1 and 2 integrons in Escherichia coli isolated from two wastewater treatment plants, and their receiving waters (Gulf of Gdansk, Baltic Sea, Poland)
PublicationIn this study, antimicrobial-resistance patterns were analyzed in Escherichia coli isolates from raw (RW) and treated wastewater (TW) of two wastewater treatment plants (WWTPs), their marine outfalls (MOut), and mouth of the Vistula River (VR). Susceptibility of E. coli was tested against different classes of antibiotics. Isolates resistant to at least one antimicrobial agent were PCR tested for the presence of integrons. Ampicillin-resistant...
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Two highly thermostable paralogous single-stranded DNA-binding proteins from Thermoanaerobacter tengcongensis
PublicationThe thermophilic bacterium Thermoanaerobacter tengcongensis has two single-stranded DNA-binding (SSB) proteins, designated TteSSB2 and TteSSB3. In a SSB complementation assay in Escherichia coli, only TteSSB3 took over the in vivo function of EcoSSB. We have cloned the ssb genes obtained by PCR and have developed E. coli overexpression systems. The TteSSB2 and TteSSB3 consist of 153 and 150 amino acids with a calculated molecular...
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Regulation of the First Committed Step in Lipopolysaccharide Biosynthesis Catalyzed by LpxC Requires the Essential Protein LapC (YejM) and HslVU Protease
PublicationWe previously showed that lipopolysaccharide (LPS) assembly requires the essential LapB protein to regulate FtsH-mediated proteolysis of LpxC protein that catalyzes the first committed step in the LPS synthesis. To further understand the essential function of LapB and its role in LpxC turnover, multicopy suppressors of ΔlapB revealed that overproduction of HslV protease subunit prevents its lethality by proteolytic degradation...
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May Staphylococcus lugdunensis Be an Etiological Factor of Chronic Maxillary Sinuses Infection?
PublicationStaphylococcus lugdunensis is an opportunistic pathogen found in the healthy human skin microbiome bacterial community that is able to cause infections of diverse localization, manifestation, and course, including laryngological infections, such as necrotizing sinusitis. Chronic maxillary sinusitis is a disease present in up to one third of European and American populations, and its etiology is not fully described. Within this...
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Antibiotic resistance in wastewater, does the context matter? Poland and Portugal as a case study
PublicationAntibiotic resistance has been considered a major human health threat that may endanger the success of medicine. Recent studies have unveiled worldwide asymmetries of antibiotic resistance occurrence, being factors as diverse as climate, socioeconomic, or antibiotic use possible drivers of such asymmetric distribution. In Europe, where clinical antibiotic resistance is surveyed for more than 20 years, the European Center for Disease...
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Impact of soluble organic matter and particulate organic matter on anammox system: Performance, microbial community and N2O production
PublicationIn this study, the effects of soluble readily biodegradable COD (sCOD) and particulate slowly biodegradable COD (pCOD) on anammox process were investigated. The results of the longterm experiment indicated that a low sCOD/N ratio of 0.5 could accelerate the anammox and denitrification activity, to reach as high as 84.9% ±2.8% TN removal efficiency. Partial denitrification-anammox (PDN/anammox) and denitrification were proposed...
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c-Myc Protein Level Affected by Unsymmetrical Bisacridines Influences Apoptosis and Senescence Induced in HCT116 Colorectal and H460 Lung Cancer Cells
PublicationUnsymmetrical bisacridines (UAs) are highly active antitumor compounds. They contain in their structure the drugs previously synthesized in our Department: C-1311 and C-1748. UAs exhibit different properties than their monomer components. They do not intercalate to dsDNA but stabilize the G-quadruplex structures, particularly those of the MYC and KRAS genes. Since MYC and KRAS are often mutated and constitutively expressed in cancer...
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Anticancer Imidazoacridinone C-1311 is Effective in Androgen-Dependent and Androgen-Independent Prostate Cancer Cells
PublicationAndrogen receptor (AR) plays a crutial role in prostate cancer (PCa) development and metastasis. Here, we reported potent anti-PCa activity of a small molecule imidazoacridinone C-1311. In AR-positive PCa cells, C-1311 was found to inhibit the transcriptional activity of AR uncovering a novel mechanism that may be relevant for its anticancer effect. Mechanistically, C-1311 decreased AR binding to prostate-specific antigen (PSA)...
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Interactions between polyphenolic antioxidants quercetin and naringenin dictate the distinctive redox-related chemical and biological behaviour of their mixtures
PublicationFood synergy concept is suggested to explain observations that isolated antioxidants are less bioactive than real foods containing them. However, mechanisms behind this discrepancy were hardly studied. Here, we demonstrate the profound impact of interactions between two common food flavonoids (individual: aglycones quercetin—Q and naringenin—N− or their glycosides rutin—R and naringin—N+ vs. mixed: QN− and RN+) on their electrochemical...
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Regulated Assembly of LPS, Its Structural Alterations and Cellular Response to LPS Defects
PublicationDistinguishing feature of the outer membrane (OM) of Gram-negative bacteria is its asymmetry due to the presence of lipopolysaccharide (LPS) in the outer leaflet of the OM and phospholipids in the inner leaflet. Recent studies have revealed the existence of regulatory controls that ensure a balanced biosynthesis of LPS and phospholipids, both of which are essential for bacterial viability. LPS provides the essential permeability...
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Occurrence of antimicrobial resistant bacteria in environment and the statistical analysis of this phenomenon
PublicationIntroduction: In this study the occurrence of antimicrobial resistance patterns among fecal indicators (Escherichia coli and Enterococcus spp.) was analyzed in water and wastewater samples. The trends in antimicrobial resistance were analyzed using basic statistical methods. Methods: Samples were obtained from two local watercourses (Oliwski Stream and Reda River) as well as from the wastewater treatment plant (WWTP) Gdansk - Wschod....
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Novel single-stranded DNA-binding protein from psyvhrophilic bacterium Psychrobacter arcticus
PublicationTo study the biochemical properties of SSB from Psychrobacter arcticus (ParSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 642 nucleotides encoding SSB protein of 213 amino acids with a calculated molecular mass of 22.8 kDa. The amino-acid sequence of ParSSB exhibits 49% identity and 57% similarity to Escherichia coli SSB....
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DNA methylation in cancer development, diagnosis and therapy-multiple opportunities for genotoxic agents to act as methylome disruptors or remediators
PublicationThe role of DNA methylation and recently discovered hydroxymethylation in the function of the human epigenome is currently one of the hottest topics in the life sciences. Progress in this field of research has been further accelerated by the discovery that alterations in the methylome are not only associated with key functions of cells and organisms, such as development, differentiation and gene expression, but may underlie a number...
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Population-based case-control study of alpha 1-antitrypsin and SLC11A1 in Crohn's disease and ulcerative colitis.
PublicationBackground: Crohn’s disease (CD) and ulcerative colitis (UC) are chronic inflammatory diseases of the digestive tract. Genetic factors and an abnormal immune response to infections are suspected to be involved in inflammatory bowel diseases. Methods: In the present study 300 blood samples from CD patients (n 100), UC patients (n 100), and healthy controls (n 100) were taken from a population-based case-control study. PCR assays...
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Differential expression profile between amygdala and blood during chronic lithium treatment in a rat model of depression – a pilot study
PublicationLithium is a mood stabilizer widely used in the pharmacotherapy of bipolar disorder and treatment‑resistant depression. Taking into account dysregulated inflammatory activity in depression and the immunomodulatory role of lithium, we hypothesized that genes associated with inflammatory responses may be potential biomarkers of lithium action. We aimed to compare gene expression changes between the brain and the periphery after...
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Platelet RNA Sequencing Data Through the Lens of Machine Learning
PublicationLiquid 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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Checkpoints that regulate balanced biosynthesis of lipopolysaccharide and its essentiality in Escherichia coli
PublicationThe outer membrane (OM) of Gram-negative bacteria, such as Escherichia coli, is essential for their viability. Lipopolysaccharide (LPS) constitutes the major component of OM, providing the permeability barrier, and a tight balance exists between LPS and phospholipids amounts as both of these essential components use a common metabolic precursor. Hence, checkpoints are in place, right from the regulation of the first committed step...
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imPlatelet classifier: image‐converted RNA biomarker profiles enable blood‐based cancer diagnostics
PublicationLiquid 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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Immunophenotyping and transcriptional profiling of in vitro cultured human adipose tissue derived stem cells
PublicationAdipose-derived stem cells (ASCs) have become an important research model in regenerative medicine. However, there are controversies regarding the impact of prolonged cell culture on the ASCs phenotype and their differentiation potential. Hence, we studied 10 clinical ASCs replicates from plastic and oncological surgery patients, in six-passage FBS supplemented cultures. We quantified basic mesenchymal cell surface marker transcripts...
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A vector-enzymatic DNA fragment amplification-expression technology for construction of artificial, concatemeric DNA, RNA and proteins for novel biomaterials, biomedical and industrial applications
PublicationA DNA fragment amplification/expression technology for the production of new generation biomaterials for scientific, industrial and biomedical applications is described. The technology enables the formation of artificial Open Reading Frames (ORFs) encoding concatemeric RNAs and proteins. It recruits the Type IIS SapI restriction endonuclease (REase) for an assembling of DNA fragments in an ordered head-to-tail-orientation. The...
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Epigenetic inhibitor zebularine activates ear pinna wound closure in the mouse
PublicationBackground:Most studies on regenerative medicine focus on cell-based therapies and transplantations.Small-molecule therapeutics, though proved effective in different medical conditions, have not been extensivelyinvestigated in regenerative research. It is known that healing potential decreases with development and devel-opmental changes are driven by epigenetic mechanisms, which suggests epigenetic repression of regenerativecapacity.Methods:We...
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DNA-damaging imidazoacridinone C-1311 induces autophagy followed by irreversible growth arrest and senescence in human lung cancer cells
PublicationImidazoacridinone 5-diethylaminoethylamino-8-hydroxyimidazoacridinone (C-1311) is an antitumor inhibitor of topoisomerase II and FMS-like tyrosine kinase 3 receptor. In this study, we describe the unique sequence of cellular responses to C-1311 in human non-small cell lung cancer (NSCLC) cell lines, A549 and H460. In A549 cells, C-1311 (IC80 = 0.08 µM) induced G1 and G2/M arrests, whereas H460 cells (IC80 = 0.051 µM) accumulated...
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Higher Responsiveness to Rosuvastatin in Polygenic versus Monogenic Hypercholesterolemia: A Propensity Score Analysis
PublicationBackground: The monogenic defect in familial hypercholesterolemia (FH) is detected in ∼40% of cases. The majority of mutation-negative patients have a polygenic cause of high LDL-cholesterol (LDL-C). We sought to investigate whether the underlying monogenic or polygenic defect is associated with the response to rosuvastatin. Methods: FH Individuals were tested for mutations in LDLR and APOB genes. A previously established LDL-C-specific...
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Novel staphylococci nucH taxonomical marker used in identification of human-associated Staphylococcus succinus subsp. casei
PublicationThe 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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Characterization of recombinant homocitrate synthase from Candida albicans
PublicationLYS21 and LYS22 genes from Candida albicans encoding isoforms of homocitrate synthase (HCS), an enzyme catalyzing the first committed step in the L-lysine biosynthetic pathway, were cloned and expressed as NoligoHistagged fusion proteins in Escherichia coli. The purified gene products revealed HCS activity, i.e. catalyzed the condensation of α-ketoglutarate with acetyl-coenzyme A to yield homocitrate. The recombinant enzymes were purified...
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RecA Proteins from Deinococcus geothermalis and Deinococcus murrayi - Cloning, Purification and Biochemical Characterisation
PublicationEscherichia coli RecA plays a crucial role in recombinational processes, the induction of SOS response and mutagenic lesion bypasses. It has also been demonstrated that RecA protein is indispensable when it comes to the reassembly of shattered chromosomes in gamma-irradiated Deinococcus radiodurans, one of the most radiation-resistant organisms known. Moreover, some functional differences between E. coli and D. radiodurans RecA...