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- ItemConsensusPrime—A Bioinformatic Pipeline for Ideal Consensus Primer Design(Basel : MDPI, 2022) Collatz, Maximilian; Braun, Sascha D.; Monecke, Stefan; Ehricht, RalfBackground: High-quality oligonucleotides for molecular amplification and detection procedures of diverse target sequences depend on sequence homology. Processing input sequences and identifying homogeneous regions in alignments can be carried out by hand only if they are small and contain sequences of high similarity. Finding the best regions for large and inhomogeneous alignments needs to be automated. Results: The ConsensusPrime pipeline was developed to sort out redundant and technical interfering data in multiple sequence alignments and detect the most homologous regions from multiple sequences. It automates the prediction of optimal consensus primers for molecular analytical and sequence-based procedures/assays. Conclusion: ConsensusPrime is a fast and easy-to-use pipeline for predicting optimal consensus primers that is executable on local systems without depending on external resources and web services. An implementation in a Docker image ensures platform-independent executability and installability despite the combination of multiple programs. The source code and installation instructions are publicly available on GitHub.
- ItemPhenotypic and Molecular Detection of Biofilm Formation in Staphylococcus aureus Isolated from Different Sources in Algeria(Basel : MDPI, 2020) Achek, Rachid; Hotzel, Helmut; Nabi, Ibrahim; Kechida, Souad; Mami, Djamila; Didouh, Nassima; Tomaso, Herbert; Neubauer, Heinrich; Ehricht, Ralf; Monecke, Stefan; El-Adawy, HosnyStaphylococcus aureus is an opportunistic bacterium causing a wide variety of diseases. Biofilm formation of Staphylococcus aureus is of primary public and animal health concern. The purposes of the present study were to investigate the ability of Staphylococcus aureus isolated from animals, humans, and food samples to form biofilms and to screen for the presence of biofilmassociated and regulatory genes. In total, 55 Staphylococcus aureus isolated from sheep mastitis cases (n = 28), humans (n = 19), and from food matrices (n = 8) were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The ability of Staphylococcus aureus for slime production and biofilm formation was determined quantitatively. A DNA microarray examination was performed to detect adhesion genes (icaACD and biofilmassociated protein gene (bap)), genes encoding microbial surface components recognizing adhesive matrix molecules (MSCRAMMs), regulatory genes (accessory gene regulator (agr) and staphylococcal accessory regulator (sarA)), and the staphylococcal cassette chromosome mec elements (SCCmec). Out of 55 Staphylococcus aureus isolates, 39 (71.0%) and 23 (41.8%) were producing slime and biofilm, respectively. All Staphylococcus aureus strains isolated from food showed biofilm formation ability. 52.6% of the Staphylococcus aureus strains isolated from sheep with mastitis, and 17.9% of isolates from humans, were able to form a biofilm. Microarray analysis typed the Staphylococcus aureus into 15 clonal complexes. Among all Staphylococcus aureus isolates, four of the human isolates (21.1%) harbored the mecA gene (SCCmec type IV) typed into 2 clonal complexes (CC22-MRSA-IV and CC80-MRSA-IV) and were considered as methicillin-resistant, while two of them were slime-producing. None of the isolates from sheep with mastitis harbored the cna gene which is associated with biofilm production. The fnbB gene was found in 100%, 60% and 40% of biofilm-producing Staphylococcus aureus isolated from food, humans, and sheep with mastitis, respectively. Three agr groups were present and agr group III was predominant with 43.6%, followed by agr group I (38.2%), and agr group II (18.2%). This study revealed the capacity of Staphylococcus aureus isolates to form biofilms and highlighted the genetic background displayed by Staphylococcus aureus isolates from different sources in Algeria. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
- ItemRelease of Bioactive Molecules from Graphene Oxide-Alginate Hybrid Hydrogels: Effect of Crosslinking Method(Basel : MDPI, 2023) Madeo, Lorenzo Francesco; Curcio, Manuela; Iemma, Francesca; Nicoletta, Fiore Pasquale; Hampel, Silke; Cirillo, GiuseppeTo investigate the influence of crosslinking methods on the releasing performance of hybrid hydrogels, we synthesized two systems consisting of Graphene oxide (GO) as a functional element and alginate as polymer counterpart by means of ionic gelation (physical method, 𝐻𝑃𝐴−𝐺𝑂) and radical polymerization (chemical method, 𝐻𝐶𝐴−𝐺𝑂). Formulations were optimized to maximize the GO content (2.0 and 1.15% for 𝐻𝑃𝐴−𝐺𝑂 and 𝐻𝐶𝐴−𝐺𝑂, respectively) and Curcumin (CUR) was loaded as a model drug at 2.5, 5.0, and 7.5% (by weight). The physico-chemical characterization confirmed the homogeneous incorporation of GO within the polymer network and the enhanced thermal stability of hybrid vs. blank hydrogels. The determination of swelling profiles showed a higher swelling degree for 𝐻𝐶𝐴−𝐺𝑂 and a marked pH responsivity due to the COOH functionalities. Moreover, the application of external voltages modified the water affinity of 𝐻𝐶𝐴−𝐺𝑂, while they accelerated the degradation of 𝐻𝑃𝐴−𝐺𝑂 due to the disruption of the crosslinking points and the partial dissolution of alginate. The evaluation of release profiles, extensively analysed by the application of semi-empirical mathematical models, showed a sustained release from hybrid hydrogels, and the possibility to modulate the releasing amount and rate by electro-stimulation of 𝐻𝐶𝐴−𝐺𝑂.
- ItemHeat Shock Protein 27 Affects Myeloid Cell Activation and Interaction with Prostate Cancer Cells(Basel : MDPI, 2022) Singer, Debora; Ressel, Verena; Stope, Matthias B.; Bekeschus, SanderHeat shock proteins are cytoprotective molecules induced by environmental stresses. The small heat shock protein 27 (Hsp27) is highly expressed under oxidative stress conditions, mediating anti-oxidative effects and blocking apoptosis. Since medical gas plasma treatment subjects cancer cells to a multitude of reactive oxygen species (ROS), inducing apoptosis and immunomodulation, probable effects of Hsp27 should be investigated. To this end, we quantified the extracellular Hsp27 in two prostate cancer cell lines (LNCaP, PC-3) after gas plasma-induced oxidative stress, showing a significantly enhanced release. To investigate immunomodulatory effects, two myeloid cell lines (THP-1 and HL-60) were also exposed to Hsp27. Only negligible effects on viability, intracellular oxidative milieu, and secretion profiles of the myeloid cells were found when cultured alone. Interestingly, prostate cancer-myeloid cell co-cultures showed altered secretion profiles with a significant decrease in vascular endothelial growth factor (VEGF) release. Furthermore, the myeloid surface marker profiles were changed, indicating an enhanced differentiation in co-culture upon Hsp27 treatment. Finally, we investigated morphological changes, proliferation, and interaction with prostate cancer cells, and found significant alterations in the myeloid cells, supporting the tendency to differentiate. Collectively, our results suggest an ambiguous effect of Hsp27 on myeloid cells in the presence of prostate cancer cells which needs to be further investigated.
- ItemThe Anticancer Efficacy of Plasma-Oxidized Saline (POS) in the Ehrlich Ascites Carcinoma Model In Vitro and In Vivo(Basel : MDPI, 2021) Brito, Walison Augusto Silva; Freund, Eric; Nascimento, Thiago Daniel Henrique do; Pasqual-Melo, Gabriella; Sanches, Larissa Juliani; Dionísio, Joyce Hellen Ribeiro; Fumegali, William Capellari; Miebach, Lea; Cecchini, Alessandra Lourenço; Bekeschus, SanderCold physical plasma, a partially ionized gas rich in reactive oxygen species (ROS), is receiving increasing interest as a novel anticancer agent via two modes. The first involves its application to cells and tissues directly, while the second uses physical plasma-derived ROS to oxidize liquids. Saline is a clinically accepted liquid, and here we explored the suitability of plasma-oxidized saline (POS) as anticancer agent technology in vitro and in vivo using the Ehrlich Ascites Carcinoma (EAC) model. EAC mainly grows as a suspension in the peritoneal cavity of mice, making this model ideally suited to test POS as a putative agent against peritoneal carcinomatosis frequently observed with colon, pancreas, and ovarium metastasis. Five POS injections led to a reduction of the tumor burden in vivo as well as in a decline of EAC cell growth and an arrest in metabolic activity ex vivo. The treatment was accompanied by a decreased antioxidant capacity of Ehrlich tumor cells and increased lipid oxidation in the ascites supernatants, while no other side effects were observed. Oxaliplatin and hydrogen peroxide were used as controls and mediated better and worse outcomes, respectively, with the former but not the latter inducing profound changes in the inflammatory milieu among 13 different cytokines investigated in ascites fluid. Modulation of inflammation in the POS group was modest but significant. These results promote POS as a promising candidate for targeting peritoneal carcinomatosis and malignant ascites and suggest EAC to be a suitable and convenient model for analyzing innovative POS approaches and combination therapies.
- ItemCarbon Nanohorns as Effective Nanotherapeutics in Cancer Therapy(Basel : MDPI, 2021) Curcio, M.; Cirillo, G.; Saletta, F.; Michniewicz, F.; Nicoletta, F.; Vittorio, O.; Hampel, S.; Iemma, F.Different carbon nanostructures have been explored as functional materials for the development of effective nanomaterials in cancer treatment applications. This review mainly aims to discuss the features, either strength or weakness, of carbon nanohorn (CNH), carbon conical horn-shaped nanostructures of sp2 carbon atoms. The interest for these materials arises from their ability to couple the clinically relevant properties of carbon nanomaterials as drug carriers with the negligible toxicity described in vivo. Here, we offer a comprehensive overview of the recent advances in the use of CNH in cancer treatments, underlining the benefits of each functionalization route and approach, as well as the biological performances of either loaded and unloaded materials, while discussing the importance of delivery devices.
- ItemCharacterization of Enterococci- and ESBL-Producing Escherichia coli Isolated from Milk of Bovides with Mastitis in Egypt(Basel : MDPI, 2021) Ahmed, Wedad; Neubauer, Heinrich; Tomaso, Herbert; El Hofy, Fatma Ibrahim; Monecke, Stefan; Abd El-Tawab, Ashraf Awad; Hotzel, HelmutThis study aimed to investigate the prevalence and antimicrobial resistance of enterococci- and ESBL-producing E. coli isolated from milk of bovine mastitis cases in Egypt. Fifty milk samples of dairy animals were collected from localities in the Nile Delta region of Egypt. Isolates were identified using MALDI-TOF MS, and antibiotic susceptibility testing was performed by the broth microdilution method. PCR amplifications were carried out, targeting resistance-associated genes. Seventeen Enterococcus isolates and eight coliform isolates could be cultivated. Vancomycin resistance rate was high in Ent. faecalis. The VITEK 2 system confirmed all E. coli isolates as ESBL-producing. All Ent. faecalis isolates harbored erm(B), tetL and aac-aphD genes. The vanA gene was detected in Ent. faecalis isolate, vanB was found in other Enterococcus, while one isolate of E. casseliflavus exhibited the vanA gene. E. coli isolates exhibited high prevalence of erm(B) and tetL. E. coli isolates were analyzed by DNA microarray analysis. Four isolates were determined by O-serotyping as O8 (n = 1), O86 (n = 2) and O157 (n = 1). H-serotyping resulted in H11, H12, H21 (two isolates each) and one was of H16 type. Different virulence-associated genes were detected in E. coli isolates including lpfA, astA, celB, cmahemL, intI1 and intI2, and the iroN gene was identified by DNA microarray analysis.
- ItemFYCO1 Increase and Effect of Arimoclomol–Treatment in Human VCP–Pathology(Basel : MDPI, 2022) Guettsches, Anne-Katrin; Meyer, Nancy; Zahedi, René P.; Evangelista, Teresinha; Muentefering, Thomas; Ruck, Tobias; Lacene, Emmanuelle; Heute, Christoph; Gonczarowska-Jorge, Humberto; Schoser, Benedikt; Krause, Sabine; Hentschel, Andreas; Vorgerd, Matthias; Roos, AndreasDominant VCP–mutations cause a variety of neurological manifestations including inclusion body myopathy with early–onset Paget disease and frontotemporal dementia 1 (IBMPFD). VCP encodes a ubiquitously expressed multifunctional protein that is a member of the AAA+ protein family, implicated in multiple cellular functions ranging from organelle biogenesis to ubiquitin–dependent protein degradation. The latter function accords with the presence of protein aggregates in muscle biopsy specimens derived from VCP–patients. Studying the proteomic signature of VCP–mutant fibroblasts, we identified a (pathophysiological) increase of FYCO1, a protein involved in autophagosome transport. We confirmed this finding applying immunostaining also in muscle biopsies derived from VCP–patients. Treatment of fibroblasts with arimoclomol, an orphan drug thought to restore physiologic cellular protein repair pathways, ameliorated cellular cytotoxicity in VCP–patient derived cells. This finding was accompanied by increased abundance of proteins involved in immune response with a direct impact on protein clearaqnce as well as by elevation of pro–survival proteins as unravelled by untargeted proteomic profiling. Hence, the combined results of our study reveal a dysregulation of FYCO1 in the context of VCP–etiopathology, highlight arimoclomol as a potential drug and introduce proteins targeted by the pre–clinical testing of this drug in fibroblasts.
- ItemSymmetries and Selection Rules of the Spectra of Photoelectrons and High-Order Harmonics Generated by Field-Driven Atoms and Molecules(Basel : MDPI, 2021) Habibović, Dino; Becker, Wilhelm; Milošević, Dejan B.Using the strong-field approximation we systematically investigate the selection rules for high-order harmonic generation and the symmetry properties of the angle-resolved photoelectron spectra for various atomic and molecular targets exposed to one-component and two-component laser fields. These include bicircular fields and orthogonally polarized two-color fields. The selection rules are derived directly from the dynamical symmetries of the driving field. Alternatively, we demonstrate that they can be obtained using the conservation of the projection of the total angular momentum on the quantization axis. We discuss how the harmonic spectra of atomic targets depend on the type of the ground state or, for molecular targets, on the pertinent molecular orbital. In addition, we briefly discuss some properties of the high-order harmonic spectra generated by a few-cycle laser field. The symmetry properties of the angle-resolved photoelectron momentum distribution are also determined by the dynamical symmetry of the driving field. We consider the first two terms in a Born series expansion of the T matrix, which describe the direct and the rescattered electrons. Dynamical symmetries involving time translation generate rotational symmetries obeyed by both terms. However, those that involve time reversal generate reflection symmetries that are only observed by the direct electrons. Finally, we explain how the symmetry properties, imposed by the dynamical symmetry of the driving field, are altered for molecular targets.
- ItemEsr and radiocarbon dating of gut strings from early plucked instruments(Basel : MDPI, 2020) Tsukamoto, Sumiko; Takeuchi, Taro; Tani, Atsushi; Miyairi, Yosuke; Yokoyama, YusukeEarly European plucked instruments have recently experienced a great revival, but a few aspects remain unknown (e.g., the gauge of gut strings). Here we report, for the first time, that the electron spin resonance (ESR) signal intensity of oxidized iron, Fe(III), from gut strings at g = 2 increases linearly with age within a few hundred years. The signal increase in the remaining old strings on early instruments can be used to judge if they are as old as or younger than the instrument. Obtaining the authenticity information of gut strings contributes to the revival of the old instruments and the music. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.