TY - JOUR A1 - Tavasolyzadeh, Zeynab A1 - Tang, Peng A1 - Hahn, Marc Benjamin A1 - Hweidi, Gada A1 - Nordholt, Niclas A1 - Haag, Rainer A1 - Sturm, Heinz A1 - Topolniak, Ievgeniia T1 - 2D and 3D Micropatterning of Mussel‐Inspired Functional Materials by Direct Laser Writing N2 - AbstractThis work addresses the critical need for multifunctional materials and substrate‐independent high‐precision surface modification techniques that are essential for advancing microdevices and sensing elements. To overcome existing limitations, the versatility of mussel‐inspired materials (MIMs) is combined with state‐of‐the‐art multiphoton direct laser writing (DLW) microfabrication. In this way, 2D and 3D MIM microstructures of complex designs are demonstrated with sub‐micron to micron resolution and extensive post‐functionalization capabilities. This study includes polydopamine (PDA), mussel‐inspired linear, and dendritic polyglycerols (MI‐lPG and MI‐dPG), allowing their direct microstructure on the substrate of choice with the option to tailor the patterned topography and morphology in a controllable manner. The functionality potential of MIMs is demonstrated by successfully immobilizing and detecting single‐stranded DNA on MIM micropattern and nanoarray surfaces. In addition, easy modification of MIM microstructure with silver nanoparticles without the need of any reducing agent is shown. The methodology developed here enables the integration of MIMs in advanced applications where precise surface functionalization is essential. KW - Direct laser writing KW - Mussel-inspired materials KW - Polyglycerol KW - Polydopamine KW - Micropatterning PY - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-588778 SN - 1613-6829 SP - 1 EP - 12 PB - Wiley-VCH CY - Weinheim AN - OPUS4-58877 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Bonse, Jörn A1 - Florian, Camilo A1 - Mezera, Marek A1 - Wasmuth, Karsten A1 - Richter, Anja A1 - Schwibbert, Karin A1 - Krüger, Jörg A1 - Müller, F. A. A1 - Gräf, S. T1 - A brief survey on open questions about laser-induced periodic surface structures N2 - The processing of laser-induced periodic surface structures (LIPSS) represents a simple and robust way for the nanostructuring of solids that allows creating a wide range of surface functionalities featuring applications in optics, tribology, medicine, energy technologies, etc. While the currently available laser and scanner technology already allows surface processing rates at the m2/min level, industrial applications of LIPSS are sometimes hampered by the complex interplay between the nanoscale surface topography and the specific surface chemistry. This typically manifests in difficulties to control the processing of LIPSS and in limitations to ensure the long-term stability of the created surface functions. This presentation aims to identify some unsolved scientific problems related to LIPSS, discusses the pending technological limitations, and sketches the current state of theoretical modelling. Hereby, it is intended to stimulate further research and developments in the field of LIPSS for overcoming these limitations and for supporting the transfer of the LIPSS technology into industry. T2 - E-MRS Spring Meeting 2022 CY - Online meeting DA - 30.05.2022 KW - Laser-induced periodic surface structures (LIPSS) KW - Surface functionalization KW - Industrial applications KW - Biofilm growth PY - 2022 AN - OPUS4-54929 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Schulze-Makuch, D. A1 - Haque, S. A1 - Beckles, D. A1 - Schmitt-Kopplin, P. A1 - Harir, M. A1 - Schneider, Beate A1 - Stumpp, C. A1 - Wagner, D. T1 - A chemical and microbial characterization of selected mud volcanoes in Trinidad reveals pathogens introduced by surface water and rain water N2 - Terrestrial mud volcanoes are unique structures driven by tectonic pressure and fluids from the deep subsurface. These structures are mainly found in active tectonic zones, such as the area near the Los Bajos Fault in Trinidad. Here we report a chemical and microbiological characterization of three mud volcanoes, which included analyses of multiple liquid and solid samples from the mud volcanoes. Our study confirms previous suggestions that at least some of the mud volcano fluids are a mixture of deeper salt-rich water and surficial/precipitation water. No apparent water quality differences were found between sampling sites north and south of a major geological fault line. Microbiological analyses revealed diverse communities, both aerobic and anaerobic, including sulfate reducers, methanogens, carbon dioxide fixing and denitrifying bacteria. Several identified species were halophilic and likely derived from the deeper salt-rich subsurface water, while we also cultivated pathogenic species from the Vibrionaceae, Enterobacteriaceae, Shewanellaceae, and Clostridiaceae. These microorganisms were likely introduced into the mud volcano fluids both from surface water or shallow ground-water, and perhaps to a more minor degree by rain water. The identified pathogens are a major health concern that needs to be addressed. KW - Water stable isotope analysis KW - Mud volcanoe fluids KW - Metabolomics PY - 2020 U6 - https://doi.org/10.1016/j.scitotenv.2019.136087 VL - 707 SP - 136087 PB - Elsevier B.V. AN - OPUS4-50499 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Nordholt, Niclas A1 - O'Hara, Kate A1 - Resch-Genger, Ute A1 - Blaskovich, M. A1 - Rühle, Bastian A1 - Schreiber, Frank T1 - A fluorescently labelled quaternary ammonium compound (NBD-DDA) to study resistance mechanisms in bacteria N2 - Quaternary ammonium compounds (QACs) are widely used as active agents in disinfectants, antiseptics, and preservatives. Despite being in use since the 1940s, there remain multiple open questions regarding their detailed mode-of-action and the mechanisms, including phenotypic heterogeneity, that can make bacteria less susceptible to QACs. To facilitate studies on resistance mechanisms towards QACs, we synthesized a fluorescent quaternary ammonium compound, namely N-dodecyl-N,N-dimethyl-[2-[(4-nitro-2,1,3-benzoxadiazol-7-yl)amino]ethyl]azanium-iodide (NBD-DDA). NBD-DDA is readily detected by flow cytometry and fluorescence microscopy with standard GFP/FITC-settings, making it suitable for molecular and single-cell studies. As a proof-of-concept, NBD-DDA was then used to investigate resistance mechanisms which can be heterogeneous among individual bacterial cells. Our results reveal that the antimicrobial activity of NBD-DDA against Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa is comparable to that of benzalkonium chloride (BAC), a widely used QAC, and benzyl-dimethyl-dodecylammonium chloride (BAC12), a mono-constituent BAC with alkyl-chain length of 12 and high structural similarity to NBD-DDA. Characteristic time-kill kinetics and increased tolerance of a BAC tolerant E. coli strain against NBD-DDA suggest that the mode of action of NBD-DDA is similar to that of BAC. As revealed by confocal laser scanning microscopy (CLSM), NBD-DDA is preferentially localized to the cell envelope of E. coli, which is a primary target of BAC and other QACs. Leveraging these findings and NBD-DDA‘s fluorescent properties, we show that reduced cellular accumulation is responsible for the evolved BAC tolerance in the BAC tolerant E. coli strain and that NBD-DDA is subject to efflux mediated by TolC. Overall, NBD-DDA’s antimicrobial activity, its fluorescent properties, and its ease of detection render it a powerful tool to study resistance mechanisms of QACs in bacteria and highlight its potential to gain detailed insights into its mode-of-action. KW - Antimicrobial resistance KW - Bacteria KW - Disinfection KW - Biocides PY - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-563811 SN - 1664-302X IS - 13 SP - 1 EP - 13 PB - Frontiers Media CY - Lausanne AN - OPUS4-56381 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Wen, Keqing A1 - Gorbushina, Anna A. A1 - Schwibbert, Karin A1 - Bell, Jérémy T1 - A microfluidic platform for monitoring biofilm formation in flow under defined hydrodynamic conditions N2 - Bacterial adhesion on surfaces of medical, water and food applications may lead to infections, water or food spoilage and human illness. In comparison to traditional static and macro flow chamber assays for biofilm formation studies, microfluidic chips allow in situ monitoring of biofilm formation under various flow regimes, have better environment control and smaller sample requirements. In this work, a novel microfluidic platform is developed to investigate biofilm adhesion under precisely controlled bacteria concentration, temperature, and flow conditions. This platform central unit is a single-inlet microfluidic flow cell with a 5 mm wide chamber designed and tested to achieve ultra-homogenous flow in the central area of chamber. Within this area, defined microstructures are integrated that will disturb the homogeneity of the flow, thus changing bacterial adhesion pattern. Here we present the monitoring of bacterial biofilm formation in a microfluidic chip equipped with a microstructure known as micro-trap. This feature is based on a 3D bacteria trap designed by Di Giacomo et al. and successfully used to sequester motile bacteria. At first, fluorescent particles similar in size to Escherichia coli (E. coli) are used to simulate bacteria flow inside the flow cell and at the micro-trap. The turbulences induced by the trap are analyzed by imaging and particle tracking velocimetry (PTV). Secondly, the model strain E. coli TG1, ideal and well described for biofilm studies, is used to analyze biofilm formation in the micro-trap. Therefore, a stable fluorescent strain E. coli TG1-MRE-Tn7-141 is constructed by using Tn7 transposon mutagenesis according to the method described by Schlechter et al. Sequestering of E. coli cells within the micro-trap was followed using epifluorescence microscopy. The novel microfluidic platform shows great potential for assessment of bacterial adhesion under various flow regimes. The performance of structural feature with respect to the generation of turbulences that promote or reduce bacterial adhesion can be systematically examined. The combination of flow analysis and fluorescent strain injection into the microfluidic chip shows that the micro-trap is useful for capturing bacteria at defined positions and to study how flow conditions, especially micro-turbulences, can affect biofilm formation. It represents a powerful and versatile tool for studying the relation between topography and bacteria adhesion. T2 - International Conference on Miniaturized Systems for Chemistry and Life Sciences CY - Katowice, Poland DA - 15.10.2023 KW - Biofilm KW - E. coli KW - Microfluidics KW - Velocimetry KW - Fluorescence PY - 2023 AN - OPUS4-59593 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ibrahim, B. A1 - McMahon, Dino Peter A1 - Hufsky, F. A1 - Beer, M. A1 - Ding, L. A1 - Le Mercier, P. A1 - Palmarini, M. A1 - Thiel, V. A1 - Marz, M. T1 - A new era of virus bioinformatics N2 - Despite the recognized excellence of virology and bioinformatics, these two communities have interacted surprisingly sporadically, aside from some pioneering work on HIV-1 and influenza. Bringing together the Expertise of bioinformaticians and virologists is crucial, since very specific but fundamental computational approaches are required for virus research, particularly in an era of big data. Collaboration between virologists and bioinformaticians is necessary to improve existing analytical tools, cloud-based systems, computational resources, data sharing approaches, new diagnostic tools, and bioinformatic training. Here, we highlight current progress and discuss potential avenues for future developments in this promising era of virus bioinformatics. We end by presenting an overview of current technologies, and by outlining some of the Major challenges and Advantages that bioinformatics will bring to the field of virology. KW - Bioinformatics virology viruses software PY - 2018 U6 - https://doi.org/10.1016/j.virusres.2018.05.009 SN - 0168-1702 SN - 1872-7492 VL - 251 SP - 86 EP - 90 PB - Elsevier CY - Amsterdam AN - OPUS4-45880 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Trimpert, J. A1 - Groenke, N. A1 - Kunec, D. A1 - Eschke, K. A1 - He, Shulin A1 - McMahon, Dino Peter A1 - Osterrieder, N. T1 - A proofreading-impaired herpesvirus generates populations with quasispecies-like structure N2 - RNA virus populations are composed of highly diverse individuals that form a cloud of related sequences commonly referred to as a ‘quasispecies’1–3. This diversity arises as a consequence of low-fidelity genome replication4,5. By contrast, DNA Virus populations contain more uniform individuals with similar fitness6. Genome diversity is often correlated with increased Fitness in RNA viruses, while DNA viruses are thought to require more faithful genome replication. During DNA replication, erroneously incorporated bases are removed by a 3′-5′ exonuclease, a highly conserved enzymatic function of replicative DNA but not RNA polymerases. This proofreading process enhances replication fidelity and ensures the genome integrity of DNA organisms, including large DNA viruses7. Here, we show that a herpesvirus can tolerate impaired exonucleolytic proofreading, resulting in DNA virus populations, which, as in RNA viruses8, are composed of highly diverse genotypes of variable individual fitness. This indicates that herpesvirus mutant diversity may compensate for individual Fitness loss. Notably, in vivo infection with diverse virus populations results in a marked increase in virulence compared to genetically homogenous parental virus. While we cannot exclude that the increase in virulence is caused by selection of and/or interactions between individual genotypes, our findings are consistent with quasispecies dynamics. Our results contrast with traditional views of DNA virus replication and evolution, and indicate that a substantial increase in population diversity can lead to higher virulence. KW - Marek's virus KW - Virulence KW - Quasispecies KW - Evolution PY - 2019 U6 - https://doi.org/10.1038/s41564-019-0547-x SN - 2058-5276 N1 - Corrigendum: Nature Microbiology 4 (2019) 2025 VL - 4 SP - 2175 EP - 2183 PB - Nature Publishing Group CY - London AN - OPUS4-48896 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Hobmeier, K. A1 - Cantone, M. A1 - Nguyen, Q. A. A1 - Pflüger-Grau, K. A1 - Kremling, A. A1 - Kunte, Hans-Jörg A1 - Pfeiffer, F. A1 - Marin-Sanguino, A. T1 - Adaptation to varying salinity in Halomonas elongata: Much more than ectoine accumulation N2 - The halophilic γ-proteobacterium Halomonas elongata DSM 2581T thrives at salt concentrations well above 10 % NaCl (1.7 M NaCl). A well-known osmoregulatory mechanism is the accumulation of the compatible solute ectoine within the cell in response to osmotic stress. While ectoine accumulation is central to osmoregulation and promotes resistance to high salinity in halophilic bacteria, ectoine has this effect only to a much lesser extent in non-halophiles. We carried out transcriptome analysis of H. elongata grown on two different carbon sources (acetate or glucose), and low (0.17 M NaCl), medium (1 M), and high salinity (2 M) to identify additional mechanisms for adaptation to high saline environments. To avoid a methodological bias, the transcripts were evaluated by applying two methods, DESeq2 and Transcripts Per Million (TPM). The differentially transcribed genes in response to the available carbon sources and salt stress were then compared to the transcriptome profile of Chromohalobacter salexigens, a closely related moderate halophilic bacterium. Transcriptome profiling supports the notion that glucose is degraded via the cytoplasmic Entner-Doudoroff pathway, whereas the Embden-Meyerhoff-Parnas pathway is employed for gluconeogenesis. The machinery of oxidative phosphorylation in H. elongata and C. salexigens differs greatly from that of non-halophilic organisms, and electron flow can occur from quinone to oxygen along four alternative routes. Two of these pathways via cytochrome bo' and cytochrome bd quinol oxidases seem to be upregulated in salt stressed cells. Among the most highly regulated genes in H. elongata and C. salexigens are those encoding chemotaxis and motility proteins, with genes for chemotaxis and flagellar assembly severely downregulated at low salt concentrations. We also compared transcripts at low and high-salt stress (low growth rate) with transcripts at optimal salt concentration and found that the majority of regulated genes were down-regulated in stressed cells, including many genes involved in carbohydrate metabolism, while ribosome synthesis was up-regulated, which is in contrast to what is known from non-halophiles at slow growth. Finally, comparing the acidity of the cytoplasmic proteomes of non-halophiles, extreme halophiles and moderate halophiles suggests adaptation to an increased cytoplasmic ion concentration of H. elongata. Taken together, these results lead us to propose a model for salt tolerance in H. elongata where ion accumulation plays a greater role in salt tolerance than previously assumed. KW - Ectoine KW - Osmoadaptation PY - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-545608 SN - 1664-302X VL - 13 SP - 1 EP - 19 PB - Frontiers Media CY - Lausanne AN - OPUS4-54560 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Varadarajan, A. A1 - Allan, R. A1 - Valentin, J. A1 - Castañeda Ocampo, O. A1 - Somerville, V. A1 - Buhmann, M. A1 - West, J. A1 - Skipp, Paul A1 - van der Mei, H. A1 - Ren, Q. A1 - Schreiber, Frank A1 - Webb, J. A1 - Pietsch, Franziska A1 - Ahrens, C. T1 - An integrated model system to gain mechanistic insights into biofilm-associated antimicrobial resistance in Pseudomonas aeruginosa MPAO1 N2 - Pseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and biofilm-associated antibiotic resistance. Our model employs a genomics-driven workflow to assemble the complete MPAO1 genome, identify unique and conserved genes by comparative genomics with the PAO1 reference strain and genes missed within existing assemblies by proteogenomics. Among over 200 unique MPAO1 genes, we identified six general essential genes that were overlooked when mapping public Tn-seq data sets against PAO1, including an antitoxin. Genomic data were integrated with phenotypic data from an experimental workflow using a user-friendly, soft lithography-based microfluidic flow chamber for biofilm growth and a screen with the Tn-mutant library in microtiter plates. The screen identified hitherto unknown genes involved in biofilm growth and antibiotic resistance. Experiments conducted with the flow chamber across three laboratories delivered reproducible data on P. aeruginosa biofilms and validated the function of both known genes and genes identified in the Tn-mutant screens. Differential Protein abundance data from planktonic cells versus biofilm confirmed the upregulation of candidates known to affect biofilm formation, of structural and secreted proteins of type VI secretion systems, and provided proteogenomic evidence for some missed MPAO1 genes. This integrated, broadly applicable model promises to improve the mechanistic understanding of biofilm formation, antimicrobial tolerance, and resistance evolution in biofilms. KW - Biofilms PY - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-515108 VL - 6 IS - 1 SP - Article number: 46 PB - Springer Nature CY - Singapore AN - OPUS4-51510 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Schiebel, J. A1 - Noack, J. A1 - Rödiger, S. A1 - Kammel, A. A1 - Menzel, Friederike A1 - Schwibbert, Karin A1 - Weise, Matthias A1 - Weiss, R. A1 - Böhm, A. A1 - Nitschke, J. A1 - Elimport, A. A1 - Roggenbuck, D. A1 - Schierack, P. T1 - Analysis of three-dimensional biofilms on different material surfaces N2 - Biofilms cause complications and high costs in both industry and medicine. Of particular interest are bacterial infections of prosthetic materials, which usually cannot be eliminated due to the high antibiotic resistance known for bacteria forming biofilms. The search for new materials and coatings with lower colonization potential and antibacterial activity is of great importance to reduce biofilm formation. However, there is no standardized procedure to examine the colonization characteristics of bacteria in the Biofilm state in situ. Here, we describe an automated epifluorescence microscopy system for the semi-quantitative analysis of three-dimensional (3D) biofilms on various surfaces. To analyze adherent bacteria, three materials (glass, steel and titanium) were incubated with bacteria in a flow chamber system. After fluorescence staining of the bacteria, automated image capturing, quantification of the bacteria, measurement of the colonized area and determination of the 3D biofilm height were carried out by using novel software. Furthermore, the materials were examined for their surface topography using white light scanning interferometry. Titanium compared to glass showed a significantly higher number of adherent bacteria. We argue that this was due to the higher microroughness of titanium. The colonized area was in accordance with the number of adherent bacteria and was also significantly larger on titanium coupons compared to glass. Maximum 3D biofilm height on glass coupons was significantly lower compared to the ones on steel and titanium. This novel method enables the standardized, automated investigation of the colonization with bacteria on different materials. This approach can considerably support the characterization of new material surfaces and their innovative coatings by analyzing the amount of attached Bacteria and thickness of biofilms in situ and eliminates the need of conventional cultivation. KW - Biofilm KW - Bacterial adhesion KW - Biofilm quantification KW - Automated analysis PY - 2020 U6 - https://doi.org/10.1039/D0BM00455C SP - 1 EP - 11 PB - Royal Society of Chemistry AN - OPUS4-50815 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -