Critical review on biofilm methods

Biofilms are widespread in nature and constitute an important strategy implemented by microorganisms to survive in sometimes harsh environmental conditions. They can be beneficial or have a negative impact particularly when formed in industrial settings or on medical devices. As such, research into the formation and elimination of biofilms is important for many disciplines. Several new methodologies have been recently developed for, or adapted to, biofilm studies that have contributed to deeper knowledge on biofilm physiology, structure and composition. In this review, traditional and cutting-edge methods to study biofilm biomass, viability, structure, composition and physiology are addressed. Moreover, as there is a lack of consensus among the diversity of techniques used to grow and study biofilms. This review intends to remedy this, by giving a critical perspective, highlighting the advantages and limitations of several methods. Accordingly, this review aims at helping scientists in finding the most appropriate and up-to-date methods to study their biofilms.The authors would like to acknowledge the support from the EU COST Action BacFoodNet FA1202

Peptide-based microcapsules obtained by self-assembly and microfluidics as controlled environments for cell culture

Funding for this study was provided by the Portuguese Foundation for Science and Technology (FCT, grant PTDC/EBB-BIO/ 114523/2009). D. S. Ferreira gratefully acknowledges FCT for the PhD scholarship (SFRH/BD/44977/2008)

Micro- and nanotechnology for cell biophysics

Procedures and methodologies used in cell biophysics have been improved tremendously with the revolutionary advances witnessed in the micro- and nanotechnology in the last two decades. With the advent of microfluidics it became possible to reduce laboratory-sized equipment to the scale of a microscope slide allowing massive parallelization of measurements with extremely low sample volume at the cellular level. Optical micromanipulation has been used to measure forces or distances or to alter the behavior of biological systems from the level of DNA to organelles or entire organisms. Among the main advantages is its non-invasiveness, giving researchers an invisible micro-hand to “touch” or “feel” the system under study, its freely and very often quickly adjustable experimental parameters such as wavelength, optical power or intensity distribution. Atomic force microscopy (AFM) opened avenues for in vitro biological applications concerning with single molecule imaging, cellular mechanics or morphology. As it can operate in liquid environment and at human body temperature, it became the most reliable and accurate nanoforce-tool in the research of cell biophysics. In this paper we review how the above three techniques help increase our knowledge in biophysics at the cellular level

Microfluidic bacterial traps for simultaneous fluorescence and atomic force microscopy

The atomic force microscope has become an established research tool for imaging microorganisms with unprecedented resolution. However, its use in microbiology has been limited by the difficulty of proper bacterial immobilization. Here, we have developed a microfluidic device that solves the issue of bacterial immobilization for atomic force microscopy under physiological conditions. Our device is able to rapidly immobilize bacteria in well-defined positions and subsequently release the cells for quick sample exchange. The developed device also allows simultaneous fluorescence analysis to assess the bacterial viability during atomic force microscope imaging. We demonstrated the potential of our approach for the immobilization of rod-shaped Escherichia coli and Bacillus subtilis. Using our device, we observed buffer-dependent morphological changes of the bacterial envelope mediated by the antimicrobial peptide CM15. Our approach to bacterial immobilization makes sample preparation much simpler and more reliable, thereby accelerating atomic force microscopy studies at the single-cell level

BioMEMS

As technological advancements widen the scope of applications for biomicroelectromechanical systems (BioMEMS or biomicrosystems), the field continues to have an impact on many aspects of life science operations and functionalities. Because BioMEMS research and development require the input of experts who use different technical languages and come from varying disciplines and backgrounds, scientists and students can avoid potential difficulties in communication and understanding only if they possess a skill set and understanding that enables them to work at the interface of engineering and biosciences. Keeping this duality in mind throughout, BioMEMS: Science and Engineering Perspectives supports and expedites the multidisciplinary learning involved in the development of biomicrosystems. Divided into nine chapters, it starts with a balanced introduction of biological, engineering, application, and commercialization aspects of the field. With a focus on molecules of biological interest, the book explores the building blocks of cells and viruses, as well as molecules that form the self-assembled monolayers (SAMs), linkers, and hydrogels used for making different surfaces biocompatible through functionalization. The book also discusses: Different materials and platforms used to develop biomicrosystems Various biological entities and pathogens (in ascending order of complexity) The multidisciplinary aspects of engineering bioactive surfaces Engineering perspectives, including methods of manufacturing bioactive surfaces and devices Microfluidics modeling and experimentation Device level implementation of BioMEMS concepts for different applications. Because BioMEMS is an application-driven field, the book also highlights the concepts of lab-on-a-chip (LOC) and micro total analysis system (μTAS), along with their pertinence to the emerging point-of-care (POC) and point-of-need (PON) applications

Review of Microfluidic Devices and Imaging Techniques for Fluid Flow Study in Porous Geomaterials

Understanding transport phenomena and governing mechanisms of different physical and chemical processes in porous media has been a critical research area for decades. Correlating fluid flow behaviour at the micro-scale with macro-scale parameters, such as relative permeability and capillary pressure, is key to understanding the processes governing subsurface systems, and this in turn allows us to improve the accuracy of modelling and simulations of transport phenomena at a large scale. Over the last two decades, there have been significant developments in our understanding of pore-scale processes and modelling of complex underground systems. Microfluidic devices (micromodels) and imaging techniques, as facilitators to link experimental observations to simulation, have greatly contributed to these achievements. Although several reviews exist covering separately advances in one of these two areas, we present here a detailed review integrating recent advances and applications in both micromodels and imaging techniques. This includes a comprehensive analysis of critical aspects of fabrication techniques of micromodels, and the most recent advances such as embedding fibre optic sensors in micromodels for research applications. To complete the analysis of visualization techniques, we have thoroughly reviewed the most applicable imaging techniques in the area of geoscience and geo-energy. Moreover, the integration of microfluidic devices and imaging techniques was highlighted as appropriate. In this review, we focus particularly on four prominent yet very wide application areas, namely “fluid flow in porous media”, “flow in heterogeneous rocks and fractures”, “reactive transport, solute and colloid transport”, and finally “porous media characterization”. In summary, this review provides an in-depth analysis of micromodels and imaging techniques that can help to guide future research in the in-situ visualization of fluid flow in porous media

BioMEMS

As technological advancements widen the scope of applications for biomicroelectromechanical systems (BioMEMS or biomicrosystems), the field continues to have an impact on many aspects of life science operations and functionalities. Because BioMEMS research and development require the input of experts who use different technical languages and come from varying disciplines and backgrounds, scientists and students can avoid potential difficulties in communication and understanding only if they possess a skill set and understanding that enables them to work at the interface of engineering and biosciences. Keeping this duality in mind throughout, BioMEMS: Science and Engineering Perspectives supports and expedites the multidisciplinary learning involved in the development of biomicrosystems. Divided into nine chapters, it starts with a balanced introduction of biological, engineering, application, and commercialization aspects of the field. With a focus on molecules of biological interest, the book explores the building blocks of cells and viruses, as well as molecules that form the self-assembled monolayers (SAMs), linkers, and hydrogels used for making different surfaces biocompatible through functionalization. The book also discusses: Different materials and platforms used to develop biomicrosystems Various biological entities and pathogens (in ascending order of complexity) The multidisciplinary aspects of engineering bioactive surfaces Engineering perspectives, including methods of manufacturing bioactive surfaces and devices Microfluidics modeling and experimentation Device level implementation of BioMEMS concepts for different applications. Because BioMEMS is an application-driven field, the book also highlights the concepts of lab-on-a-chip (LOC) and micro total analysis system (μTAS), along with their pertinence to the emerging point-of-care (POC) and point-of-need (PON) applications