TY - JOUR A1 - Nchiozem-Ngnitedem, Vaderament-Alexe A1 - Sperlich, Eric A1 - Matieta, Valaire Yemene A1 - Kuete, Jenifer Reine Ngnouzouba A1 - Kuete, Victor A1 - Omer, Ejlal A. A. A1 - Efferth, Thomas A1 - Schmidt, Bernd T1 - Synthesis and bioactivity of isoflavones from ficus carica and some non-natural analogues JF - Journal of natural products : Lloydia N2 - FicucariconeD (1) and its 4 '-demethyl congener 2 are isoflavones isolated from fruits of Ficus carica that share a 5,7-dimethoxy-6-prenyl-substituted A-ring. Both naturalproducts were, for the first time, obtained by chemical synthesisin six steps, starting from 2,4,6-trihydroxyacetophenone. Key stepsare a microwave-promoted tandem sequence of Claisen- and Cope-rearrangementsto install the 6-prenyl substituent and a Suzuki-Miyaura crosscoupling for installing the B-ring. By using various boronic acids,non-natural analogues become conveniently available. All compoundswere tested for cytotoxicity against drug-sensitive and drug-resistanthuman leukemia cell lines, but were found to be inactive. The compoundswere also tested for antimicrobial activities against a panel of eightGram-negative and two Gram-positive bacterial strains. Addition ofthe efflux pump inhibitor phenylalanine-arginine-beta-naphthylamide(PA beta N) significantly improved the antibiotic activity in mostcases, with MIC values as low as 2.5 mu M and activity improvementfactors as high as 128-fold. KW - Antimicrobial activity KW - Bacteria KW - Ethers KW - Flavonoids KW - Mixtures Y1 - 2023 U6 - https://doi.org/10.1021/acs.jnatprod.3c00219 SN - 0163-3864 SN - 1520-6025 VL - 86 IS - 6 SP - 1520 EP - 1528 PB - American Chemical Society CY - Washington, DC ER - TY - JOUR A1 - Wurzbacher, Christian A1 - Fuchs, Andrea A1 - Attermeyer, Katrin A1 - Frindte, Katharina A1 - Grossart, Hans-Peter A1 - Hupfer, Michael A1 - Casper, Peter A1 - Monaghan, Michael T. T1 - Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment JF - Microbiome N2 - Background: Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. Methods: We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to Cs-137 dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. Results: Community beta-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. Conclusions: By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper "replacement horizon" is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower "depauperate horizon" is characterized by low taxonomic richness, more stable "low-energy" conditions, and a dominance of enigmatic Archaea. KW - Archaea KW - Eukaryota KW - Bacteria KW - Community KW - Freshwater KW - Lake KW - DNA metabarcoding KW - Beta-diversity KW - Sediment KW - Turnover Y1 - 2017 U6 - https://doi.org/10.1186/s40168-017-0255-9 SN - 2049-2618 VL - 5 PB - BioMed Central CY - London ER - TY - JOUR A1 - Zühlke, Martin A1 - Meiling, Till Thomas A1 - Roder, Phillip A1 - Riebe, Daniel A1 - Beitz, Toralf A1 - Bald, Ilko A1 - Löhmannsröben, Hans-Gerd A1 - Janßen, Traute A1 - Erhard, Marcel A1 - Repp, Alexander T1 - Photodynamic inactivation of E. coli bacteria via carbon nanodots JF - ACS omega / American Chemical Society N2 - The increasing development of antibiotic resistance in bacteria has been a major problem for years, both in human and veterinary medicine. Prophylactic measures, such as the use of vaccines, are of great importance in reducing the use of antibiotics in livestock. These vaccines are mainly produced based on formaldehyde inactivation. However, the latter damages the recognition elements of the bacterial proteins and thus could reduce the immune response in the animal. An alternative inactivation method developed in this work is based on gentle photodynamic inactivation using carbon nanodots (CNDs) at excitation wavelengths λex > 290 nm. The photodynamic inactivation was characterized on the nonvirulent laboratory strain Escherichia coli K12 using synthesized CNDs. For a gentle inactivation, the CNDs must be absorbed into the cytoplasm of the E. coli cell. Thus, the inactivation through photoinduced formation of reactive oxygen species only takes place inside the bacterium, which means that the outer membrane is neither damaged nor altered. The loading of the CNDs into E. coli was examined using fluorescence microscopy. Complete loading of the bacterial cells could be achieved in less than 10 min. These studies revealed a reversible uptake process allowing the recovery and reuse of the CNDs after irradiation and before the administration of the vaccine. The success of photodynamic inactivation was verified by viability assays on agar. In a homemade flow photoreactor, the fastest successful irradiation of the bacteria could be carried out in 34 s. Therefore, the photodynamic inactivation based on CNDs is very effective. The membrane integrity of the bacteria after irradiation was verified by slide agglutination and atomic force microscopy. The method developed for the laboratory strain E. coli K12 could then be successfully applied to the important avian pathogens Bordetella avium and Ornithobacterium rhinotracheale to aid the development of novel vaccines. KW - Bacteria KW - Genetics KW - Fluorescence KW - Photodynamics KW - Irradiation Y1 - 2021 U6 - https://doi.org/10.1021/acsomega.1c01700 SN - 2470-1343 VL - 6 IS - 37 SP - 23742 EP - 23749 PB - ACS Publications CY - Washington, DC ER - TY - JOUR A1 - Unuabonah, Emmanuel I. A1 - Kolawole, Matthew O. A1 - Agunbiade, Foluso O. A1 - Omorogie, Martins O. A1 - Koko, Daniel T. A1 - Ugwuja, Chidinma G. A1 - Ugege, Leonard E. A1 - Oyejide, Nicholas E. A1 - Günter, Christina A1 - Taubert, Andreas T1 - Novel metal-doped bacteriostatic hybrid clay composites for point-of-use disinfection of water JF - Journal of Environmental Chemical Engineering N2 - This study reports the facile microwave-assisted thermal preparation of novel metal-doped hybrid clay composite adsorbents consisting of Kaolinite clay, Carica papaya seeds and/or plantain peels (Musa paradisiaca) and ZnCl2. Fourier Transformed IR spectroscopy, X-ray diffraction, Scanning Electron Microscopy and Brunauer-Emmett-Teller (BET) analysis are employed to characterize these composite adsorbents. The physicochemical analysis of these composites suggests that they act as bacteriostatic rather than bacteriacidal agents. This bacterostactic action is induced by the ZnO phase in the composites whose amount correlates with the efficacy of the composite. The composite prepared with papaya seeds (PS-HYCA) provides the best disinfection efficacy (when compared with composite prepared with Musa paradisiaca peels-PP-HYCA) against gram-negative enteric bacteria with a breakthrough time of 400 and 700 min for the removal of 1.5 x10(6) cfu/mL S. typhi and V. cholerae from water respectively. At 10(3) cfu/mL of each bacterium in solution, 2 g of both composite adsorbents kept the levels the bacteria in effluent solutions at zero for up to 24 h. Steam regeneration of 2 g of bacteria-loaded Carica papaya prepared composite adsorbent shows a loss of ca. 31% of its capacity even after the 3rd regeneration cycle of 25 h of service time. The composite adsorbent prepared with Carica papaya seeds will be useful for developing simple point-of-use water treatment systems for water disinfection application. This composite adsorbent is comparatively of good performance and shows relatively long hydraulic contact times and is expected to minimize energy intensive traditional treatment processes. KW - Kaolinite KW - Composites KW - Bacteria KW - Breakthrough time KW - Regeneration Y1 - 2017 U6 - https://doi.org/10.1016/j.jece.2017.04.017 SN - 2213-3437 VL - 5 SP - 2128 EP - 2141 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Çabuk, Uğur A1 - Ünlü, Ercan Selçuk T1 - A combined de novo assembly approach increases the quality of prokaryotic draft genomes JF - Folia microbiologica : international journal for general, environmental and applied microbiology, and immunology N2 - Next-generation sequencing methods provide comprehensive data for the analysis of structural and functional analysis of the genome. The draft genomes with low contig number and high N50 value can give insight into the structure of the genome as well as provide information on the annotation of the genome. In this study, we designed a pipeline that can be used to assemble prokaryotic draft genomes with low number of contigs and high N50 value. We aimed to use combination of two de novo assembly tools (SPAdes and IDBA-Hybrid) and evaluate the impact of this approach on the quality metrics of the assemblies. The followed pipeline was tested with the raw sequence data with short reads (< 300) for a total of 10 species from four different genera. To obtain the final draft genomes, we firstly assembled the sequences using SPAdes to find closely related organism using the extracted 16 s rRNA from it. IDBA-Hybrid assembler was used to obtain the second assembly data using the closely related organism genome. SPAdes assembler tool was implemented using the second assembly, produced by IDBA-hybrid as a hint. The results were evaluated using QUAST and BUSCO. The pipeline was successful for the reduction of the contig numbers and increasing the N50 statistical values in the draft genome assemblies while preserving the coverage of the draft genomes. KW - De novo assembly KW - Prokaryotes KW - Bacteria KW - NGS KW - Short reads KW - Draft genome Y1 - 2022 U6 - https://doi.org/10.1007/s12223-022-00980-7 SN - 0015-5632 SN - 1874-9356 VL - 67 SP - 801 EP - 810 PB - Springer CY - Dordrecht ER -