Article
Biotechnology & Applied Microbiology
Clarissa Schulze, Maurice Haedrich, Jennifer Borger, Broder Ruehmann, Manuel Doering, Volker Sieber, Felix Thoma, Bastian Blombach
Summary: In this study, a glucose-limited fed-batch fermentation with V. natriegens was established to yield high biomass concentrations. However, it was observed that the viscosity of the culture broth increased due to the formation of exopolysaccharides (EPS). Deletion of cpsR and the cps cluster reduced EPS formation and viscosity, leading to higher succinate production and yield.
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Masoud Norouzi, Sabina Panfilov, Keith Pardee
Summary: Cell-free synthetic biology, an emerging branch of engineered biology, allows for rapid prototyping of biological designs. By incorporating Ter binding sites for DNA-binding protein Tus, linear expression templates could be highly efficiently protected in cell-free systems, showing promising results in both Escherichia coli and Vibrio natriegens extracts.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Felix Thoma, Bastian Blombach
Summary: Vibrio natriegens is emerging as a promising host for biotechnology due to its high growth rate and substrate consumption rate, versatile metabolism, and ease of handling in the lab. Current understanding of its physiological traits and genomic organization is limited, but efforts are being made to overcome obstacles and establish it as an industrial production host.
MICROBIAL CELL FACTORIES-BOOK
(2021)
Article
Cell Biology
Jongoh Shin, Kevin Rychel, Bernhard O. Palsson
Summary: Vibrio natriegens regulates natural competence through the TfoX and QstR transcription factors, involving external DNA capture and transport. By using a machine-learning approach, this study decomposes the transcriptome of Vibrio natriegens into 45 independently modulated sets of genes (iModulons), revealing the repression of two housekeeping iModulons and the activation of six iModulons, including TfoX and QstR, a novel iModulon of unknown function, and three housekeeping iModulons. Phenotypic screening confirms that loss of iModulon function reduces or eliminates competence. These findings provide the genetic basis for understanding the competency in this organism.
Article
Biotechnology & Applied Microbiology
Federica Villa, Francesco Secundo, Fabio Forlani, Cristina Catto, Francesca Cappitelli
Summary: This study evaluated the effectiveness of zosteric acid (ZA) in hindering Escherichia coli biofilm formation on a mineral surface, showing that ZA treatment modified the kinetics of biofilm development, reducing biomass and EPS contents, inhibiting biofilm growth. Comparative proteome analysis revealed that ZA acted as a stress factor on sessile cells, discouraging biomass proliferation.
ANNALS OF MICROBIOLOGY
(2021)
Article
Nanoscience & Nanotechnology
Rushabh M. Shah, Aydin Cihanoglu, Justin Hardcastle, Caitlin Howell, Jessica D. Schiffman
Summary: Antifouling membranes with ultrathin oil layer were demonstrated in this study, offering stable operational lifetimes and long-lasting antifouling properties. The membranes showed stable permeance values and reduced microbial attachment, making them suitable for meeting the growing demand for clean water.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Biotechnology & Applied Microbiology
Peichao Zhang, Jing Gao, Haiyang Zhang, Yongzhen Wang, Zhen Liu, Sang Yup Lee, Xiangzhao Mao
Summary: Metabolically engineered Escherichia coli strains capable of producing Zosteric acid (ZA) from glucose and glycerol were developed. This was achieved by enhancing the availability of the sulfur donor 3'-phosphoadenosine-5'-phospho-sulfate (PAPS), relieving the feedback regulation of L-tyrosine biosynthesis, deleting competing pathway genes, optimizing carbon source, and other measures. The best-performing strain produced 1.52 g L-1 ZA and 1.30 g L-1 p-hydroxycinnamic acid in a fed-batch bioreactor.
METABOLIC ENGINEERING
(2023)
Article
Pharmacology & Pharmacy
Ana Arenas-Vivo, Vanessa Celis Arias, Georgiana Amariei, Roberto Rosal, Isabel Izquierdo-Barba, Tania Hidalgo, Maria Vallet-Regi, Hiram I. Beltran, Sandra Loera-Serna, Patricia Horcajada
Summary: Surface microbial colonization and biofilm formation are major problems causing human infectious diseases, and traditional treatments are often ineffective in eliminating biofilms. This study presents a silver-based metal-organic framework (AgBDC) that has antifouling properties and can prevent bacterial adhesion and surface contamination.
Article
Chemistry, Multidisciplinary
Mingcheng Xu, Yuanchan Luo, Xiaozhen Liu, Peng Fei, Juefeng Lu, Yuying Wang, Hui Wu
Summary: This study successfully utilized engineered V. natriegens to produce 3-hydroxypropionic acid (3-HP) by introducing the heterogeneous malonyl-CoA pathway, optimizing fermentation conditions, adaptive laboratory evolution, and whole-cell biocatalysis. The engineered strain efficiently accumulated 3-HP with a titer of 3.78 g/L and a yield of 0.25 g/g within 24 hours. Furthermore, 2.2 g/L of 3-HP was obtained from syngas-derived acetic acid with a yield of 0.15 g/g. This study provided a novel strategy for producing 3-HP from syngas-derived acetic acid using engineered V. natriegens.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Jing-Guo Xu, Hui-Xue Hu, Jing-Yu Chen, Yan-Song Xue, Bekhzod Kodirkhonov, Bei-Zhong Han
Summary: This study evaluated the inhibitory effects of ferulic acid (FA) and p-coumaric acid (p-CA) on Salmonella Enteritidis biofilm formation and found that they can decrease biofilm formation and bacterial activity while repressing the gene expressions related to biofilm formation. These phenolic acids also showed high antibiofilm efficiency in simulated food processing conditions.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2022)
Article
Infectious Diseases
Weidong Qian, Xinchen Li, Min Yang, Chanchan Liu, Yi Kong, Yongdong Li, Ting Wang, Qian Zhang
Summary: This study investigated the association between biofilm formation and antibiotic resistance in extensively drug-resistant Escherichia coli isolates. The results showed that stronger biofilm formation was correlated with larger proportions of extensively drug-resistant isolates. These findings provide novel insights for the prevention and treatment of E. coli-related infections.
INFECTION AND DRUG RESISTANCE
(2022)
Article
Veterinary Sciences
Elina Tukia, Isa Hallman, Maarit Penttilae, Satu Haenninen, Maria Kareskoski
Summary: Endometritis is a common cause of infertility in mares, often caused by bacteria such as E. coli and beta-haemolytic streptococci. This study aimed to detect the presence and localization of E. coli bacteria in equine endometrial biopsies using a chromogenic RNAscope method. However, no evidence of bacterial invasion was found, regardless of the inflammatory status or previous bacterial culture results. Further research is needed to investigate potential localized infections or biofilm coverings that may have led to undetected bacterial presence.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Khair Bux, Thomas S. Hofer, Syed Tarique Moin
Summary: This study is the first molecular dynamics simulation study on the dimeric form of the LuxS enzyme from Vibrio cholerae, evaluating its structural and dynamical properties, as well as the binding patterns of two inhibitors (RHC and KRI). The results indicate that KRI is a more potent inhibitor than RHC, and the binding patterns of the two inhibitors to the enzyme differ.
Article
Multidisciplinary Sciences
Mona A. El-Zamkan, Ahmed Shaban Ahmed, Hanan H. Abdelhafeez, Hams M. A. Mohamed
Summary: This research aimed to detect Vibrio cholerae and Vibrio parahaemolyticus in raw milk, dairy products, and water samples, and investigated their virulence factors, antibiotic resistance, and biofilm formation. The results showed that Vibrio species were found in 5% of the samples, with Vibrio cholerae and Vibrio parahaemolyticus isolated from 1.25% and 1.5% of the samples, respectively. All strains of Vibrio cholerae and Vibrio parahaemolyticus exhibited resistance to penicillin, and some isolates showed multidrug resistance. Certain virulence genes were detected in a majority of Vibrio cholerae isolates, while only a small percentage of Vibrio parahaemolyticus isolates carried specific virulence genes.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Victoria Ballen, Yaiza Gabasa, Carlos Ratia, Melany Sanchez, Sara Soto
Summary: This study characterized 376 extraintestinal pathogenic E. coli strains collected from hospitals in Catalonia, Spain, between 2016 and 2017. The strains showed high resistance to several antibiotics and varied biofilm formation ability. Various virulence and antimicrobial resistance genes were detected, including the colibactin-encoding genes associated with colorectal cancer. The study also investigated the relationship between colibactin and biofilm formation.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Ecology
Gust Bilcke, Koen Van den Berge, Sam De Decker, Eli Bonneure, Nicole Poulsen, Petra Bulankova, Cristina Maria Osuna-Cruz, Jack Dickenson, Koen Sabbe, Georg Pohnert, Klaas Vandepoele, Sven Mangelinckx, Lieven Clement, Lieven De Veylder, Wim Vyverman
Summary: The study integrates transcriptomic data and reveals significant changes in gene expression during sexual reproduction in diatoms in response to SIP, inhibiting processes like S-phase progression, cell division, mitosis, and inducing upregulation of meiotic genes. The research also uncovers the roles of reactive oxygen species, energy metabolism, and cGMP signaling in early sexual reproduction stages.
Article
Biochemistry & Molecular Biology
Stefanie Liening, Jana Fischer, Hans Jagusch, Georg Pohnert, Oliver Hoecker, Christian Neusuess, Oliver Werz, Gerhard K. E. Scriba, Ulrike Garscha
Summary: In this study, a novel AA-derived GSH conjugate, TOG(10), was identified in human platelets formed via the 12-LOX pathway in combination with a GST. This confirms the involvement of pt12-LOX and suggests a potential new mechanism for the biosynthesis of GSH conjugates in platelets.
PROSTAGLANDINS & OTHER LIPID MEDIATORS
(2021)
Article
Limnology
Frederike Stock, Emilio Cirri, Samarasinghe Gunasekara Liyanage Ishari Nuwanthi, Willem Stock, Nico Ueberschaar, Sven Mangelinckx, Georg Pohnert, Wim Vyverman
Summary: N-acyl homoserine lactones (AHLs) are signaling molecules produced by Gram-negative bacteria for cell-cell communication, influencing marine bacterial processes and interactions with microalgae. Measuring AHL concentrations is challenging but important for ecological research and biofilm control. A novel sampling and analysis method has been developed to detect and quantify AHLs in marine sediment samples efficiently.
LIMNOLOGY AND OCEANOGRAPHY-METHODS
(2021)
Article
Geosciences, Multidisciplinary
Nico Ueberschaar, Katharina Lehmann, Stefanie Meyer, Christian Zerfass, Beate Michalzik, Kai Uwe Totsche, Georg Pohnert
Summary: The passage of surface-sourced organic compounds in infiltrating waters and percolates undergoes transformations through biotic and abiotic processes, leading to changing chemical environments in subsurface compartments. Different types of lysimeters are available for collecting soil solution samples, and solid phase extraction followed by GC-MS analysis can effectively reduce background signals. Multivariate statistics can be used for monitoring chemical differences in various land use sites, allowing for the detection of organic compounds such as sugars, fatty acids, and phenolic acids.
FRONTIERS IN EARTH SCIENCE
(2021)
Article
Oncology
Nazli Mert-Ozupek, Yasemin Basbinar, Tugba Uysal-Kilic, Omer Koz, Hulya Ellidokuz, Levent Cavas
Summary: The study evaluated the antiproliferative effect of Holothuria poli extract on different human cancer cell lines, showing promising results. Mass analysis revealed the presence of Holothurin A in the extract, highlighting the potential for further research on the mechanisms of specific versus mixed saponins for antiproliferation studies.
NUTRITION AND CANCER-AN INTERNATIONAL JOURNAL
(2022)
Article
Environmental Sciences
Nils Meyer, Aljoscha Rydzyk, Georg Pohnert
Summary: This study reveals that diatoms are capable of taking up organic resources from lysates of competing algae, and these resources are partially maintained or undergo metabolic transformation within the cells. This suggests that diatoms have the potential to compete with heterotrophs and may have a significant impact on organic material fluxes in the oceans.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biochemical Research Methods
Batuhan Unver, Gulsen Akin Evingur, Levent Cavas
Summary: This study demonstrates the toxic effects of certain booster biocides on the marine ecosystem, particularly on the fluorescence of GFPs in Anemonia viridis. The results show that different concentrations of irgarol, zinc omadine, and acticide can cause a decrease of over 50% in the fluorescence intensities of GFP proteins. Therefore, the health of the ecosystem should be prioritized when proposing new antifouling paint compositions.
JOURNAL OF FLUORESCENCE
(2022)
Article
Biotechnology & Applied Microbiology
Levent Cavas, Ibrahim Kirkiz
Summary: Although urinary tract infections predominantly occur in women, antibiotic resistance in bacteria has made it a severe health problem. Therefore, discovering new antibiotics is essential. Genome mining of Escherichia coli revealed the presence of effective siderophores, which could be potential targets for pharmaceutical development and compound synthesis in the future.
Article
Environmental Sciences
Runqing Yang, Dong Wei, Georg Pohnert
Summary: This study reveals that a combination of tryptone and urea as organic nitrogen sources can enhance fucoxanthin production in mixotrophic cultivation of Phaeodactylum tricornutum. Among the amino acids present in the medium, arginine has the highest nitrogen utilization rate and promotes cell growth the most. The optimal combination of arginine and urea as nitrogen sources leads to the highest biomass concentration, fucoxanthin content, and productivity. This study provides new insights into the promotion of fucoxanthin biosynthesis and suggests a promising strategy for efficient enhancement of fucoxanthin production.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Vera Nikitashina, Daniel Stettin, Georg Pohnert
Summary: Microalgae respond to salinity stress with common adaptations in the metabolome, such as up-regulation of amino acids and production of saccharides and inositols. However, there are also species-specific dysregulations of metabolites. Several metabolites not previously connected to osmotic stress reactions were identified. This study expands our knowledge about osmoadaptation and highlights the need for further functional characterization of metabolites and pathways in algal stress physiology.
Article
Chemistry, Inorganic & Nuclear
Hacer Kandemir, Levent Cavas
Summary: In this study, silver nanoparticles (AgNPs) were synthesized using the edible marine seaweed Caulerpa lentillifera. The optimal conditions for the synthesis of AgNPs using C. lentillifera were determined as follows: initial biomass concentration of 0.01 g/mL, AgNO3 concentration of 8 mM, pH of 10, temperature of 85 degrees C, and agitation rate of 0 rpm. The synthesized AgNPs had an average particle size of 22.3 nm, which were characterized using UV-Vis spectrophotometry, FT-IR, and XRD. The phytotoxicity of the C. lentillifera-based AgNPs was found to be dose-dependent based on experiments with shallot plants. The results suggest potential industrial applications of these AgNPs in the food, medicine, pharmacy, and agriculture industries, depending on the usage doses.
INORGANIC AND NANO-METAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Franziska A. Klapper, Christine Kiel, Peter Bellstedt, Wim Vyverman, Georg Pohnert
Summary: Diatoms, abundant unicellular microalgae, play a crucial role in global photosynthetic CO2 fixation. However, their sexual reproduction remains poorly understood. In this study, the structure of a sex-inducing pheromone in the diatom Seminavis robusta was elucidated, revealing its mechanism of action and providing important insights into the reproductive process of diatoms.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Agricultural Engineering
Sema Dogmaz, Levent Cavas
Summary: Green synthesized silver nanoparticles were utilized to produce biohydrogen from the biomass of Ulva lactuca, a marine green seaweed. Optimum conditions for silver nanoparticle production and biohydrogen production were determined, and an artificial neural network model was used to analyze these parameters. This study provides recommendations for producing biohydrogen from waste algae and reducing carbon emissions for a better environment and future.
BIORESOURCE TECHNOLOGY
(2023)
Article
Microbiology
Kristy S. Syhapanha, David A. Russo, Yun Deng, Nils Meyer, Remington X. Poulin, Georg Pohnert
Summary: The discovery of an algicidal bacterium and its key protease gene provides insights into the regulation of harmful algal blooms. Transciptomics-guided approach identified a serine protease gene as a critical element in the algicidal activity. This finding opens the possibility of real-time monitoring of the ecological impact of algicidal bacteria in natural phytoplankton blooms.
Article
Computer Science, Artificial Intelligence
Yesim Yilmaz Abeska, Levent Cavas
Summary: This paper investigates the experimental conditions for green synthesis of silver nanoparticles using honey as a medium, and predicts the production yield using artificial neural network modeling. The optimum hidden neuron number is found to be 40 using the Levenberg-Marquardt backpropagation algorithm. The results suggest that neural networks can be a robust alternative approach for estimating the production of silver nanoparticles.
NEURAL NETWORK WORLD
(2022)
