Article
Multidisciplinary Sciences
Behnam Enghiad, Pu Xue, Nilmani Singh, Aashutosh Girish Boob, Chengyou Shi, Vassily Andrew Petrov, Roy Liu, Siddhartha Suryanarayana Peri, Stephan Thomas Lane, Emily Danielle Gaither, Huimin Zhao
Summary: Despite their broad utility, design and construction of plasmids remains laborious and time-consuming. Here the authors report a robust, versatile, and automated end-to-end platform that enables scarless construction of virtually any plasmid.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Wouter Demeester, Jasmine De Baets, Dries Duchi, Marjan De Mey, Brecht De Paepe
Summary: All living organisms have specialized mechanisms to monitor different molecules, which can be used to build cheap, fast, sustainable, portable, self-generating and highly sensitive biological sensors (BioS). However, the lack of standardized and efficient platforms hinders the full potential of BioS. This article introduces a modular, Golden Gate-based construction platform called MoBioS, which allows for the fast creation of transcription factor-based biosensors, demonstrating its potential by creating eight functional and standardized biosensors for different molecules of industrial interest.
Article
Biochemical Research Methods
Zachary P. P. Harmer, Megan N. N. McClean
Summary: Optogenetic systems utilize genetically encoded light-sensitive proteins for cellular control. By combining laboratory automation and modular cloning, high-throughput construction and characterization of optogenetic split transcription factors in Saccharomyces cerevisiae are enabled. This approach allows for the rational design and testing of optimized transcription factors with improved light-sensitive gene expression.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemical Research Methods
Jingyi Cai, Xiaoping Liao, Yufeng Mao, Ruoyu Wang, Haoran Li, Hongwu Ma
Summary: Recent advances in biofoundries have enabled the construction of a large quantity of strains in parallel, accelerating the DBTL cycles for strain development. A method consisting of two complementary algorithms is introduced to optimize genetic manipulation schedules and minimize the total number of manipulations required. The effectiveness of the method is demonstrated through a case study, showing significant reductions in gene manipulations and potential improvements in cost efficiency for developing commercial strains.
BIOTECHNOLOGY JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Carolin Mueller, Patrick J. Bakkes, Patrick Lenz, Vera Waffenschmidt, Laura M. Helleckes, Karl-Erich Jaeger, Wolfgang Wiechert, Andreas Knapp, Roland Freudl, Marco Oldiges
Summary: Automated workflows were developed for heterologous production of cutinase in Corynebacterium glutamicum. The best performing signal peptides for cutinase secretion were identified using enzymatic activity and split GFP assay.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Robotics
Valentin N. Hartmann, Andreas Orthey, Danny Driess, Ozgur S. Oguz, Marc Toussaint
Summary: Robotic construction assembly planning is a parallelizable task and motion planning problem. We propose a planning system that parallelizes complex task and motion planning by solving smaller subproblems. By combining optimization methods and a sampling-based path planner, we can plan cooperative multi-robot manipulation with unknown arrival times. We demonstrate the robustness and scalability of this approach in multiple construction case studies and showcase the feasibility of executing the computed plans in the real world.
IEEE TRANSACTIONS ON ROBOTICS
(2023)
Review
Biotechnology & Applied Microbiology
Jennifer A. Kaczmarek, Kristala L. J. Prather
Summary: Researchers have been developing fast and cost-effective microbial production through recombinant pathways, using biosensors and high throughput methods to improve metabolite production. The effectiveness of biosensor-based methods depends on the specific pathway or strain, and careful consideration is needed when selecting the most suitable approach for high throughput library screening.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2021)
Article
Microbiology
Terence S. Crofts, Alexander G. McFarland, Erica M. Hartmann, Marnix Medema
Summary: Functional metagenomic libraries are essential for exploring metagenomes without prior sequence knowledge or cultivation. The new mosaic ends tagmentation (METa) assembly method significantly increases cloning efficiency, allowing for the preparation of gigabase-sized libraries with minimal input DNA. METa assembly is a streamlined, flexible, and efficient method that enables genetic and biochemical research into low-biomass or scarce microbiomes.
Article
Biochemical Research Methods
Stephanie L. Brumwell, Katherine D. Van Belois, Daniel J. Giguere, David R. Edgell, Bogumil J. Karas
Summary: Deinococcus radiodurans has been established as an attractive microbial platform for extremophile biology and industrial bioproduction. The development of a simple and robust conjugation-based DNA transfer method has improved the genomic manipulation and tractability of this species, allowing for the introduction of stable plasmids and successful cloning of a large megaplasmid.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Engineering, Chemical
Jelena Ochs, Ferdinand Biermann, Tobias Piotrowski, Frederik Erkens, Bastian Niessing, Laura Herbst, Niels Koenig, Robert H. Schmitt
Summary: Laboratory automation is crucial in biotechnology and plays a key role in personalized therapies, enabling cost efficiency and widespread availability of tailored treatments. StemCellDiscovery is a fully automated robotic laboratory for cultivating human mesenchymal stem cells, providing automated confluence estimation and expansion of cell cultures. Simulation modeling shows that StemCellDiscovery is capable of handling over 95 cell culture plates per day under high-throughput conditions.
Article
Pathology
Chiara Lenzi, Giulia Martinelli, Tiziano Camacci, Katia Di Ieso, Emanuele Santoro, Antonella Sechi, Vincenzo Nardini, Angela Pucci
Summary: This study tested the benefits and challenges of routinely using orientation gels in a high throughput pathology laboratory. The results showed that using orientation gels and an automatic embedding system is an efficient way to handle small/thin biopsies, improving workflow and reducing repeat procedures.
ANNALS OF DIAGNOSTIC PATHOLOGY
(2022)
Article
Hematology
Guillaume Nguyen, Manon Lejeune, Mayssa Gaaloul, Isabelle Martin-Toutain, Jean-Pierre Delorme, Yasmine Bourti, Corinne Frere
Summary: The fully automated multiparameter CN-6000 hemostasis analyzer demonstrates equivalent or superior performance compared to the STA-R Max 2 (R) analyzer, with significantly higher throughput. Results obtained from the CN-6000 show strong correlation with those from the STA-R Max 2 (R), and excellent agreement was observed between the two instruments for all assays.
INTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY
(2022)
Article
Biochemical Research Methods
John A. Bryant Jr, Mason Kellinger, Cameron Longmire, Ryan Miller, R. Clay Wright
Summary: As one of the newest fields of engineering, synthetic biology relies upon a trial-and-error Design-Build-Test-Learn (DBTL) approach to simultaneously learn how a function is encoded in biology and attempt to engineer it. Here, we present AssemblyTron, an open-source Python package to integrate j5 DNA assembly design software outputs with build implementation in Opentrons liquid handling robotics with minimal human intervention. AssemblyTron can reduce the time, training, costs and wastes associated with synthetic biology, which, along with open-source and affordable automation, will further foster the accessibility of synthetic biology and accelerate biological research and engineering.
Review
Biotechnology & Applied Microbiology
Vijay Tejwani, Minal Chaudhari, Toyaj Rai, Susan T. Sharfstein
Summary: Mammalian cell line development is a multistep process involving single-cell cloning, monoclonality assurance, productivity and stability screening, which can be labor, time and resource intensive when performed manually. Introduction of automation and miniaturization has reduced manual labor, shortened timelines, and decreased resources required for developing manufacturing cell lines.
BIOTECHNOLOGY PROGRESS
(2021)
Article
Gastroenterology & Hepatology
Lisa Sophie Pflueger, Dominik Noerz, Tassilo Volz, Katja Giersch, Annika Giese, Nora Goldmann, Dieter Glebe, Jan-Hendrik Bockmann, Susanne Pfefferle, Maura Dandri, Julian Schulze Zur Wiesch, Marc Luetgehetmann
Summary: A highly automated PCR assay for HDV detection was developed, showing great consistency and accuracy across all HDV genotypes. The assay demonstrated excellent performance in clinical trials, offering a sensitive new tool for HDV screening and viral load monitoring.
Article
Microbiology
Johanna Wiechert, Andrei Filipchyk, Max Huennefeld, Cornelia Gaetgens, Jannis Brehm, Ralf Heermann, Julia Frunzke
Article
Biochemistry & Molecular Biology
Marc Keppel, Max Huennefeld, Andrei Filipchyk, Ulrike Viets, Cedric-Farhad Davoudi, Aileen Krueger, Christina Mack, Eugen Pfeifer, Tino Polen, Meike Baumgart, Michael Bott, Julia Frunzke
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemical Research Methods
Johanna Wiechert, Cornelia Gaetgens, Astrid Wirtz, Julia Frunzke
ACS SYNTHETIC BIOLOGY
(2020)
Article
Virology
Ael Hardy, Vikas Sharma, Larissa Kever, Julia Frunzke
Article
Virology
Max Huennefeld, Ulrike Viets, Vikas Sharma, Astrid Wirtz, Ael Hardy, Julia Frunzke
Summary: This study provides a comprehensive analysis of the genomic features of phage CL31 and its infection dynamics with the host strain Corynebacterium glutamicum ATCC 13032. The results show that a strain lacking the restriction-modification system is more efficiently infected by CL31, and a prophage-free strain exhibits accelerated amplification of CL31.
Article
Biochemistry & Molecular Biology
Larissa Kever, Max Hunnefeld, Jannis Brehm, Ralf Heermann, Julia Frunzke
Summary: Bacteriophages can be a powerful source for identifying novel antimicrobial proteins by targeting key regulatory hubs of their host. The Gip protein, encoded by CGP3 prophage, was found to interact directly with DNA gyrase subunit A and specifically inhibit the DNA gyrase of Corynebacterium glutamicum, resulting in growth defects and induction of the SOS response. The overexpression of Gip also led to the induction of the cryptic CGP3 prophage, likely caused by topological alterations.
MOLECULAR MICROBIOLOGY
(2021)
Correction
Virology
Ael Hardy, Vikas Sharma, Larissa Kever, Julia Frunzke
Article
Biotechnology & Applied Microbiology
Roberto G. Stella, Christoph G. W. Gertzen, Sander H. J. Smits, Cornelia Gatgens, Tino Polen, Stephan Noack, Julia Frunzke
Summary: Evolutionary engineering is a powerful method to improve microbial cell factory performance, but a new strategy based on transcription factor-based biosensors has been developed to directly couple production to growth, enhancing the production of chemicals. By modulating the intracellular concentration of branched-chain amino acids, specific causal mutations enhancing amino acid production were isolated, with spatial separation identified as a key strategy to limit the selection of 'cheater' strains that escaped evolutionary pressure. This approach can potentially be applied across various microbes, unlocking evolution as a feasible strategy to improve chemical production.
METABOLIC ENGINEERING
(2021)
Article
Microbiology
Vikas Sharma, Ael Hardy, Tom Luthe, Julia Frunzke
Summary: Actinobacteriophages, viruses that infect Actinobacteria species, have highly divergent and mosaic genomes due to gene exchange with their bacterial hosts. This study identified 13 different transcription factor domains in actinobacteriophages, with WhiB and Lsr2 proteins being the most widespread. Phylogenetic analysis showed their origin and evolution within bacterial clades.
MICROBIOLOGY SPECTRUM
(2021)
Article
Virology
Sebastian H. Erdrich, Vikas Sharma, Ulrich Schurr, Borjana Arsova, Julia Frunzke
Summary: This study isolated and characterized seven novel phages infecting Xanthomonas translucens and Xanthomonas campestris. Transmission electron microscopy and genome analysis revealed their characteristics and phylogenetic diversity. These phages are suitable candidates for plant biocontrol and provide important materials for the pathogenic study of X. translucens.
Review
Biochemistry & Molecular Biology
Ael Hardy, Larissa Kever, Julia Frunzke
Summary: Bacterial populations have developed various defense mechanisms against phage infection, most of which are mediated by proteins or RNA complexes at the single-cell level. This review focuses on small molecule based defense strategies, with an emphasis on recently described antiphage molecules. The ability of excreted small molecules to inhibit phage infection highlights the ecological significance of these strategies, as they have the potential to protect entire bacterial communities. With the vast repertoire of bacterial metabolites, it is expected that the list of antiphage small molecules will continue to expand.
TRENDS IN MICROBIOLOGY
(2023)
Review
Microbiology
Tom Luthe, Larissa Kever, Kai Thormann, Julia Frunzke
Summary: Multicellular behavior benefits simple organisms like bacteria in various ways, such as aiding nutrient uptake, enhancing stress resistance, and providing advantages against predation. Recent studies have shown that multicellularity also plays a role in defending against bacteriophages, which are found almost everywhere. This review summarizes the strategies used by multicellular bacteria to protect against phage infection, including the secretion of antiphage molecules or membrane vesicles, the role of quorum sensing, the development of transient phage resistance, and the impact of biofilm components and architecture. These studies expand our understanding of the bacterial immune system and highlight the importance of bacterial multicellular behavior in antiviral defense.
CURRENT OPINION IN MICROBIOLOGY
(2023)
Review
Microbiology
Aileen Krueger, Marc Keppel, Vikas Sharma, Julia Frunzke
Summary: Heme is a versatile molecule that is essential for cellular life, but elevated levels are toxic. The evolution of diverse heme sensor systems has helped regulate heme homeostasis. These systems have various functions, including controlling heme detoxification and uptake, and integrating heme and iron homeostasis. Understanding heme-regulated processes is important for cellular physiology and the development of antibacterial drugs and metabolic engineering strategies.
FEMS MICROBIOLOGY REVIEWS
(2022)
Article
Biotechnology & Applied Microbiology
Roberto Giuseppe Stella, Philipp Baumann, Sophia Lorke, Felix Muenstermann, Astrid Wirtz, Johanna Wiechert, Jan Marienhagen, Julia Frunzke
Summary: The marine bacterium Vibrio natriegens has shown promise as a new host for molecular biology and bioprocesses, with research demonstrating its potential as an amino acid producer. By adapting a biosensor and utilizing fluorescence-activated cell sorting, highly fluorescent producer strains of amino acids were successfully obtained, with insight into the underlying physiology provided through genome sequencing. This study highlights the successful expression and application of transcription factor-based biosensors in V. natriegens, laying a solid foundation for its further development.
METABOLIC ENGINEERING COMMUNICATIONS
(2021)
