5 articles published in JoVE

• Biochemistry

  
  Using Three-color Single-molecule FRET to Study the Correlation of Protein Interactions Markus Götz¹, Philipp Wortmann¹, Sonja Schmid^1,2, Thorsten Hugel^{1 1}Institute of Physical Chemistry, University of Freiburg, ²Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology Here, we present a protocol to obtain three-color smFRET data and its analysis with a 3D ensemble Hidden Markov Model. With this approach, scientists can extract kinetic information from complex protein systems, including cooperativity or correlated interactions.

• Chemistry

  
  Laser-heating and Radiance Spectrometry for the Study of Nuclear Materials in Conditions Simulating a Nuclear Power Plant Accident Dario Manara¹, Luca Soldi^1,2,4, Sara Mastromarino^1,3,5, Kostantinos Boboridis¹, Davide Robba¹, Luka Vlahovic¹, Rudy Konings^{1 1}European Commission, Joint Research Centre, ²Energy Department, Politecnico di Milano, ³Department of Chemical Physics, Sapienza - Università di Roma, ⁴CEA Saclay, ⁵TU Delft We present experiments in which real nuclear fuel, cladding, and containment materials are laser heated to temperatures beyond 3,000 K while their behavior is studied by radiance spectroscopy and thermal analysis. These experiments simulate, on a laboratory scale, the formation of a lava-phase following a nuclear reactor core meltdown.

• Bioengineering

  
  An Experimental and Finite Element Protocol to Investigate the Transport of Neutral and Charged Solutes across Articular Cartilage Vahid Arbabi*^1,2, Behdad Pouran*^1,2, Amir. A. Zadpoor¹, Harrie Weinans^{1,2,3 1}Department of Biomechanical Engineering, Faculty of Mechanical, Maritime, and Materials Engineering, Delft University of Technology (TU Delft), ²Department of Orthopedics, UMC Utrecht, ³Department of Rheumatology, UMC Utrecht We propose a protocol to investigate the transport of charged and uncharged molecules across articular cartilage with the aid of recently developed experimental and numerical methods.

• Biology

  
  Application of an In vitro DNA Protection Assay to Visualize Stress Mediation Properties of the Dps Protein Vlad O. Karas¹, Ilja Westerlaken¹, Anne S. Meyer^{1 1}Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology The DNA-binding protein from starved cells (Dps) plays a crucial role in combating bacterial stress. This article discusses the purification of E. coli Dps and the protocol for an in vitro assay demonstrating Dps-mediated protection of DNA from degradation by reactive oxygen species.

• Bioengineering

  
  A Toolkit to Enable Hydrocarbon Conversion in Aqueous Environments Eva K. Brinkman¹, Kira Schipper¹, Nadine Bongaerts¹, Mathias J. Voges¹, Alessandro Abate², S. Aljoscha Wahl^{1 1}Department of Biotechnology, Delft University of Technology, ²Delft Center for Systems and Control, Delft University of Technology A sustainable auto regulating bacterial system for the remediation of oil pollutions was designed using standard interchangeable DNA parts (BioBricks). An engineered E. coli strain was used to degrade alkanes via β-oxidation in toxic aqueous environments. The respective enzymes from different species showed alkane degradation activity. Additionally, an increased tolerance to n-hexane was achieved by introducing genes from alkane-tolerant bacteria.