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Lactoferrin, an iron-binding glycoprotein, plays a significant role in the innate immune system, with antibacterial, antivirial, antifungal, anticancer, antioxidant and immunomodulatory functions reported. It is worth emphasizing that not only the whole protein but also its derived fragments possess antimicrobial peptide (AMP) activity. Using AmpGram, a top-performing AMP classifier, we generated three novel human lactoferrin (hLF) fragments: hLF 397-412, hLF 448-464 and hLF 668-683, predicted with high probability as AMPs. For comparative studies, we included hLF 1-11, previously confirmed to kill some bacteria. With the four peptides, we treated three Gram-negative and three Gram-positive bacterial strains. Our results indicate that none of the three new lactoferrin fragments have antimicrobial properties for the bacteria tested, but hLF 1-11 was lethal against Pseudomonas aeruginosa. The addition of serine protease inhibitors with the hLF fragments did not enhance their activity, except for hLF 1-11 against P. aeruginosa, which MIC dropped from 128 to 64 µg/mL. Furthermore, we investigated the impact of EDTA with/without serine protease inhibitors and the hLF peptides on selected bacteria. We stress the importance of reporting non-AMP sequences for the development of next-generation AMP prediction models, which suffer from the lack of experimentally validated negative dataset for training and benchmarking.

Because of the close connection between adhesion and many vital cellular functions, the search for new compounds modulating the adhesion of bacteria belonging to the intestinal microbiota is a great challenge and a clinical need. Based on our previous studies, we discovered that O-lkyl naringenin derivatives and their oximes exhibit antimicrobial activity against antibiotic-resistant pathogens. The current study was aimed at determining the modulatory effect of these compounds on the adhesion of selected representatives of the intestinal microbiota: Escherichia coli, a commensal representative of the intestinal microbiota, and Enterococcus faecalis, a bacterium that naturally colonizes the intestines but has disease-promoting potential. To better reflect the variety of real-life scenarios, we performed these studies using two different intestinal cell lines: the physiologically functioning (“healthy”) 3T3-L1 cell line and the disease-mimicking, cancerous HT-29 line. The study was performed in vitro under static and microfluidic conditions generated by the Bioflux system. We detected the modulatory effect of the tested O-alkyl naringenin derivatives on bacterial adhesion, which was dependent on the cell line studied and was more significant for E. coli than for E. faecalis. In addition, it was noticed that this activity was affected by the concentration of the tested compound and its structure (length of the carbon chain). In summary, O-alkyl naringenin derivatives and their oximes possess a promising modulatory effect on the adhesion of selected representatives of the intestinal microbiota.

Naringenin is a 5,7,4′-trihydroxyflavanone naturally occurring mainly in citrus fruits, characterized by a wide spectrum of biological activity. Chemical modifications based on alkylation and oximation in most cases increase its bioactivity. The aim of our research was to evaluate the antiproliferative activity and influence on selected representatives of the human gut microbiota of new synthesized O-alkyl derivatives (A1–A10) and their oximes (B1–B10), which contain hexyl, heptyl, octyl, nonyl and undecyl chains attached to the C-7 or to both the C-7 and C-4′ positions in naringenin. To the best of our knowledge, compounds A3, A4, A6, A8–A10 and B3–B10 have not been described in the scientific literature previously. The anticancer activity was tested on human colon cancer cell line HT-29 and mouse embryo fibroblasts 3T3-L1 using the sulforhodamine B (SRB) and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assays. We also determined the impacts of all compounds on the growth of Gram-positive and Gram-negative bacterial strains, such as Staphylococcus aureus, Enterococcus faecalis and Escherichia coli. The antimicrobial activity was expressed in terms of minimal inhibitory concentrations (MIC) and minimal bactericidal concentrations (MBC) values. For 7,4′-di-O-hexylnaringenin (A2), 7-O-undecylnaringenin (A9) and their oximes (B2, B9), which were safe for microbiota (MIC > 512 µg/mL) and almost all characterized by high cytotoxicity against the HT-29 cell line (A2: IC50 > 100 µg/mL; A9: IC50 = 17.85 ± 0.65 µg/mL; B2: IC50 = 49.76 ± 1.63 µg/mL; B9: IC50 = 11.42 ± 1.17 µg/mL), apoptosis assays were performed to elucidate their mechanisms of action. Based on our results, new compound B9 induced an apoptotic process via caspase 3/7 activation, which proved its potential as an anticancer agent.

The main aim of our research was to investigate antiadhesive and antibiofilm properties of nanocrystalline apatites doped and co-doped with noble metal ions (Ag+, Au+, and Pd2+) against selected drug-resistant strains of Enterococcus faecalis and Staphylococcus aureus. The materials with the structure of apatite (hydroxyapatite, nHAp; hydroxy-chlor-apatites, OH-Cl-Ap) containing 1 mol% and 2 mol% of dopants and co-dopants were successfully obtained by the wet chemistry method. The majority of them contained an additional phase of metallic nanoparticles, in particular, AuNPs and PdNPs, which was confirmed by the XRPD, FTIR, UV–Vis, and SEM–EDS techniques. Extensive microbiological tests of the nanoapatites were carried out determining their MIC, MBC value, and FICI. The antiadhesive and antibiofilm properties of the tested nanoapatites were determined in detail with the use of fluorescence microscopy and computer image analysis. The results showed that almost all tested nanoapatites strongly inhibit adhesion and biofilm production of the tested bacterial strains. Biomaterials have not shown any significant cytotoxic effect on fibroblasts and even increased their survival when co-incubated with bacterial biofilms. Performed analyses confirmed that the nanoapatites doped and co-doped with noble metal ions are safe and excellent antiadhesive and antibiofilm biomaterials with potential use in the future in medical sectors.

Amyloids and antimicrobial peptides (AMPs) have many similarities, e.g., both kill microorganisms by destroying their membranes, form aggregates, and modulate the innate immune system. Given these similarities and the fact that the antimicrobial properties of short amyloids have not yet been investigated, we chose a group of potentially antimicrobial short amyloids to verify their impact on bacterial and eukaryotic cells. We used AmpGram, a best-performing AMP classification model, and selected ten amyloids with the highest AMP probability for our experimental research. Our results indicate that four tested amyloids: VQIVCK, VCIVYK, KCWCFT, and GGYLLG, formed aggregates under the conditions routinely used to evaluate peptide antimicrobial properties, but none of the tested amyloids exhibited antimicrobial or cytotoxic properties. Accordingly, they should be included in the negative datasets to train the next-generation AMP prediction models, based on experimentally confirmed AMP and non-AMP sequences. In the article, we also emphasize the importance of reporting non-AMPs, given that only a handful of such sequences have been officially confirmed.

The main aim of our research was to investigate antiadhesive and antibiofilm properties of nanocrystalline apatites doped and co-doped with noble metal ions (Ag

Amyloid curli fibrils produced by Escherichia coli are well-known virulence factor influencing E. coli adhesion and biofilm formation. However, the impact of curli on intestinal epithelial barrier stimulated with proinflammatory cytokines is unknown. In the study, we examined the effect of curli produced by nonpathogenic E. coli K-12 and wild-type E. coli EC32 strains, and purified CsgA proteins on differentiated Caco-2 cell monolayers stimulated with a mixture of IL-1β, TNF-α, and INFγ cytokines as a model of 'inflamed intestinal epithelial barrier' in vitro. The results of the study indicated that curliated E. coli adhered better to polarized Caco-2 cells than their curli-deficient mutants and the adherence was further augmented by stimulation of epithelial cells with proinflammatory cytokines. Interestingly, curli reduced internalization but enhanced intracellular survival of the wild-type E. coli strain EC32 within intestinal epithelial cells. Curli-expressing E. coli, as well as purified CsgA proteins, attenuated IL-8 secretion by unstimulated Caco-2 cells, although the effect was barely observed on cytokine-stimulated cells. The findings of the study revealed that curli fibrils are an important virulence factor enabling curliated E. coli to effectively colonize intestinal epithelium especially in individuals with inflammatory intestinal disorders.

Background The relationship of diffusely adherent Escherichia coli (DAEC) with pediatric inflammatory bowel disease (IBD) has not been previously studied. Diffusely adherent E. coli are a common cause of long-lasting childhood diarrhea and we postulated that they may induce inflammation of the intestinal mucosa, contributing to the development of IBD in susceptible children. Objectives The aim of the study was to investigate the relationship between DAEC and pediatric IBD, including Crohn's disease (CD) and ulcerative colitis (UC). Diffusely adherent E. coli isolates were also assessed regarding their pathogenicity. Material and methods Diffusely adherent E. coli were screened among 130 E. coli strains isolated from intestinal biopsy specimens from 26 children with IBD using polymerase chain reaction (PCR) with primers specific to the pathotype and adherence assays to HEp-2 cells. Diffusely adherent E. coli were further analyzed for their ability to adhere to and invade polarized Caco-2 cells. The immunomodulatory effect of DAEC on the secretion of tumor necrosis factor α (TNF-α) by human monocyte-derived macrophages (MDM) was assessed using an immunoenzymatic assay. Results Diffusely adherent E. coli were recovered from 18 (69.2%) of the 26 intestinal biopsy specimens from both CD and UC patients. Most DAEC isolates carried AfaE3 adhesin, adhered to and were internalized by Caco-2 cells, and induced secretion of elevated levels of TNF-α. Conclusions The study demonstrated the internalization of DAEC by intestinal epithelial cells and their ability to induce secretion of increased level of TNF-α in a Caco-2/macrophage compartmentalized culture. This indicated that the pathovar should be considered a pathobiont inducing inflammation of the intestinal mucosa in pediatric patients with IBD.

New antimicrobial agents are needed to address infections caused by multidrug-resistant bacteria. Here, we are reporting novel O-alkyl derivatives of naringenin and their oximes, including novel compounds with a naringenin core and O-hexyl chains, showing activity against clinical strains of clarithromycin-resistant Helicobacter pylori, vancomycin-resistant Enterococcus faecalis, methicillin-resistant Staphylococcus aureus, and beta-lactam-resistant Acinetobacter baumannii and Klebsiella pneumoniae. The minimum inhibitory concentrations (MICs), which provide a quantitative measure of antimicrobial activity, were in the low microgram range for the selected compounds. Checkerboard assays for the most active compounds in combination with antibiotics revealed interactions that varied from synergistic to neutral.

Background and Aims. Inflammatory bowel disease pharmacotherapy, despite substantial progress, is still not satisfactory for both patients and clinicians. In view of the chronic and relapsing disease course and not always effective treatment with adverse effects, attempts to search for new, more efficient, and safer substances are essential and reasonable. This study was designed to elucidate the impact of cornelian cherry iridoid-polyphenolic extract (CE) and loganic acid (LA) on adherent-invasive E. coli growth and adhesion in vitro and to assess the effect of pretreatment with CE or LA on the course of intestinal inflammation in rat experimental colitis compared with sulfasalazine. Methods. Antibacterial and antiadhesive activities of CE and LA were assessed using microdilution, Int407 cell adherence, and yeast agglutination assays. The colitis model was induced by 2,4,6-trinitrobenzenesulfonic acid. Studied substances were administered intragastrically for 16 days prior to colitis induction. Body weight loss; colon index; histological injuries; IL-23, IL-17, TNF-α, and chemerin levels; and STAT3, Muc2, and TFF3 mRNA expression were evaluated. Results. Only CE exerted antimicrobial and antiadhesive activities in vitro and alleviated colonic symptoms. CE coadministrated with sulfasalazine was more effective than single compounds in reversing increased concentrations of TNF-α, IL-17, and chemerin and decreased Muc2 mRNA expression. Conclusions. CE exerted a protective effect against experimental colitis via impaired mucosal epithelial barrier restoration and intestinal inflammatory response attenuation and given concomitantly with sulfasalazine counteracted colitis in a more effective way than sulfasalazine alone, which indicates their synergistic interaction. The beneficial effect of CE may also be due to its bacteriostatic and antiadhesive activities.

Objective Genital mycoplasmas are opportunistic pathogens that have been associated with urogenital infections in humans. Only a few groups of antimicrobials are available for treatment of urogenital tract infections caused by genital mycoplasmas. However, emerging resistance of mycoplasmas to antimicrobial agents has been reported worldwide. The aim of the study was a retrospective analysis of the prevalence and antimicrobial susceptibility patterns of M. hominis and Ureaplasma spp. in patients with urogenital tract infections during a twelve-year period between 2003 and 2015. Study design Mycoplasma IST2 test was used for the detection, enumeration, identification and antimicrobial susceptibility testing of genital mycoplasmas in 1182 samples from 778 women and 404 men with genitourinary tract infection. Indicative enumeration in the test determines whether the mycoplasma count in the sample is equal or higher than the threshold set at 104 colony forming units. Results A total of 152 (12.8%) samples were found to be positive for genital mycoplasmas. M. hominis was detected only in three samples and Ureaplasma spp. in 141 samples. Both, M. hominis and Ureaplasma spp. were detected in the remaining eight samples. In the analyzed period between 2003 and 2015, a gradually increasing resistance of ureaplasmas to ciprofloxacin and clarithromycin and decreasing resistance to ofloxacin, erythromycin and tetracycline were observed. Pristinamycin, josamycin and doxycycline were most active against Ureaplasma spp. In contrast, fluoroquinolones had the lowest efficacy against Ureaplasma spp. and as many as 116 (82.3%) and 77 (54.6%) of Ureaplasma spp. isolates were resistant to ciprofloxacin and ofloxacin, respectively. M. hominis isolates were uniformly resistant to azithromycin, clarithromycin and erythromycin but susceptible to josamycin, ofloxacin, doxycycline and pristinamycin. One-third of these isolates were resistant to ciprofloxacin and tetracycline. Conclusion In the study Ureaplasma spp. and M. hominis were detected with relatively low frequency in comparison with other studies however, most of these isolates were resistant to ciprofloxacin indicating the need for better management of ciprofloxacin prescription. Important limitations of Mycoplasma IST2 assay concerning antimicrobial susceptibility testing and divergences between breakpoints in the test and EUCAST guidelines point the need to introduce new methodologies to improve evaluation of resistant strains at our region.

In this research, bacterial cellulose (BC), one of the most promising biopolymers of the recent years, was saturated with thyme, eucalyptus and clove essential oils (EOs) and applied against staphylococcal and pseudomonal biofilms formed on hydroxyapatite (HA). BC dressings were thoroughly analyzed with regard to their physical properties. Moreover, the exact composition and ability of particular EO molecules to adhere to HA was assessed. Additionally, cytotoxicity of oil-containing, cellulose-based dressings towards osteoblasts and fibroblasts as well as their impact on reactive oxygen species (ROS) production by macrophages was assessed. The results revealed the high ability of BC dressings to absorb and subsequently release EOs from within their microstructure; the highest number of compounds able to adhere to HA was found in the thyme EO. The eucalyptus EO displayed low, while thyme and clove EOs displayed high cytotoxicity towards fibroblast and osteoblast cell lines. The clove EO displayed the highest eradication ability toward staphylococcal, while the thyme EO against pseudomonal biofilm. Taken together, the results obtained indicate the suitability of EO-saturated BC dressings to eradicate pseudomonal and staphylococcal biofilm on HA surface and moreover, to not trigger reactive oxygen species production by immune system effector cells. However, due to cytotoxic effects of thyme and clove EOs towards cell lines in vitro, the eucalyptus EO-saturated BC dressing is of highest potential to be further applied.

Amyloids are proteins associated with several clinical disorders, including Alzheimer’s, and Creutzfeldt-Jakob’s. Despite their diversity, all amyloid proteins can undergo aggregation initiated by short segments called hot spots. To find the patterns defining the hot spots, we trained predictors of amyloidogenicity, using n-grams and random forest classifiers. Since the amyloidogenicity may not depend on the exact sequence of amino acids but on their more general properties, we tested 524,284 reduced amino acid alphabets of different lengths (three to six letters) to find the alphabet providing the best performance in cross-validation. The predictor based on this alphabet, called AmyloGram, was benchmarked against the most popular tools for the detection of amyloid peptides using an external data set and obtained the highest values of performance measures (AUC: 0.90, MCC: 0.63). Our results showed sequential patterns in the amyloids which are strongly correlated with hydrophobicity, a tendency to form β-sheets, and lower flexibility of amino acid residues. Among the most informative n-grams of AmyloGram we identified 15 that were previously confirmed experimentally. AmyloGram is available as the web-server: http://smorfland.uni.wroc.pl/shiny/AmyloGram/ and as the R package AmyloGram. R scripts and data used to produce the results of this manuscript are available at http://github.com/michbur/AmyloGramAnalysis.

Background. Mycoplasma pneumoniae is an important cause of upper and lower respiratory tract infections. cough and tracheobronchitis are the commonest features of M. pneumoniae infection but diagnosis based on clinical symptoms that may be due to other respiratory pathogens is impossible. Thus laboratory testing for M. pneumoniae is particularly important. correct and rapid diagnosis of M. pneumoniae infections is of prime importance to introduce appropriate antibiotic treatment. Objectives. evaluation of the incidence of IgM and IgG antibodies specific to M. pneumoniae among children with pneumonia and/or chronic cough. Material and Methods. Serum samples from 148 children with a history of chronic cough (lasting at least one month), recurrent respiratory tract infections, allergic rhinitis, and/or inflammatory changes on X-chest ray. first, all sera were screened for specific anti-M. pneumoniae antibodies using agglutination test following the detection of specific IgM and IgG anti-M. pneumoniae antibodies using immunoenzymatic assays. Results. Out of the 148 serum samples, 57 (38.5%) gave positive screening results. However, the presence of M. pneumoniae-specific IgM and/or IgG antibodies was confirmed by immunoenzymatic assays in only 30 (52.6%) of these 57 positive samples. These results indicated that in as many as 27 (47.4%) out of the 57 serum samples screened, false-positive results occurred. Conclusions. evaluation of acute- and convalescent-phase sera is necessary to make possible accurate interpretation of the serological testing results ( Adv Clin Exp Med 2014, 23, 2, 185–190).

Enteropathogenic Escherichia coli strains (EPEC) carrying the eae gene encoding intimin are divided into typical strains producing bundle forming pili, encoded by the bfpA gene, and atypical strains lacking the gene. In the study typical and atypical EPEC that did not agglutinated with EPEC polyvalent antisera but carrying virulence factors characteristic to other pathogenic E. coli i.e. diffusely adhering and enteroaggregative E. coli were isolated from 24 (43.6%) of 55 children > 10 years old with persistent diarrhea. These results indicated that non-typeable typical and atypical EPEC can contribute to chronic intestinal infections in teenagers.

Amyloids are proteins associated with the number of clinical disorders (e.g., Alzheimer's, Creutzfeldt-Jakob's and Huntington's diseases). Despite their diversity, all amyloid proteins can undergo aggregation initiated by 6- to 15-residue segments, called hot spots. To find the patterns defining the hot-spots, we trained predictors of amyloidogenicity, using n-grams and random forest classifiers, based on data collected in the AmyLoad database. Only the most informative n-grams, selected by our Quick Permutation Test, were considered. Since the amyloidogenicity may not depend on the exact sequence of amino acids but on more general properties of amino acids, we tested 524,284 reduced amino acid alphabets of different lengths (three to six letters) to find the alphabet providing the best performance in cross-validation. The predictor based on this alphabet, called AmyloGram, was benchmarked against the most popular tools for the detection of amyloid peptides using an external data set and obtained the highest values of performance measures (AUC: 0.90, MCC: 0.63). Our results showed sequential patterns in the amyloids, which are strongly correlated with hydrophobicity, a tendency to form ß-sheets and rigidity of amino acid residues. Among the most informative n-grams of AmyloGram we identified 15 that were already confirmed experimentally. AmyloGram is available as a web-server: www.smorfland.uni.wroc.pl/amylogram/. The code and results are publicly available at: www.github.com/michbur/prediction_amyloidogenicity_ngram/.

Arthrobacter is a genus of Gram-positive bacteria widely distributed in soil. The ability to catabolize a variety of xenobiotics has shown their potential as a detoxifying agent. Recently, Arthrobacter has been also recognized as an opportunistic pathogen. Glycolipids from A. scleromae, a clinical isolate, and A. globiformis, from soil, were isolated by chloroform-methanol extraction and subsequently purified using column chromatography and high-performance liquid chromatography. Structural studies were carried out utilizing specific chemical degradation, matrix-assisted laser-desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI FT ICR-MS), and 1D and 2D nuclear magnetic resonance (NMR) spectroscopy. The major glycolipids in A. scleromae and A. globiformis were found to be a diglycosylglycerol with the structure alpha-Manp-(1--3)-alpha-Manp-(1--3)-Gro (Man A-Man B-Gro; G1), and a monoglycosylglycerol with the structure beta-Galp-(1--3)-Gro (G2). Glycolipids were acylated at positions 1 of Gro and 6 of Man B in the case of G1 and at positions 1 and 2 of Gro in the case of G2. The distribution of the fatty acids was different in both species. A. scleromae glycolipids contained heptadecanoic acid while in the A. globiformis glycolipids mainly pentadecanoic acid could be detected. The substitution by hexadecanoic acid was proportionally similar in both species. The taxonomical value of major glycolipids from Arthrobacter is also presented.

The association between Escherichia coli virulence factors and chronic intestinal disorders is mostly unknown. The presented study compared the distribution of virulence genes and phylogroups among E. coli isolated from chronic intestinal disorders such as Crohn's disease and irritable bowel syndrome (IBS) with strains isolated from patients with acute diarrhea as a control group. The presence of 159 virulence genes corresponding to known E. coli pathotypes was determined among 78 E. coli archive strains isolated from IBS, acute diarrhea and Crohn's disease using CGH microarray. E. coli isolated from IBS demonstrated a mosaic of virulence genes specific to enteropathogenic, enterotoxigenic, enterohemorrhagic E. coli strains and Shigella species. In contrast, virulence factors and phylogroups distribution among E. coli isolated from children with acute diarrhea was similar to extraintestinal E. coli strains that probably acquired some virulence genes. The acquisition of virulence genes might have an impact on diarrheagenic potential of these strains. On the other hand, E. coli isolated from children with Crohn's disease seem to be similar to adherent-invasive E. coli strains (AIEC), as it lack most known virulence genes. The presented study showed that these analyzed groups of E. coli strains differed from each other with the respect to the distribution of virulence genes. The differences in gene content support the idea that the participation of E. coli in chronic intestinal diseases is mostly related to virulence potential of these strains.