Automated single cell sorting and deposition in submicroliter drops

Automated manipulation and sorting of single cells are challenging, when intact cells are needed for further investigations, e.g., RNA or DNA sequencing. We applied a computer controlled micropipette on a microscope admitting 80 PCR (Polymerase Chain Reaction) tubes to be filled with single cells in a cycle. Due to the Laplace pressure, fluid starts to flow out from the micropipette only above a critical pressure preventing the precise control of drop volume in the submicroliter range. We found an anomalous pressure additive to the Laplace pressure that we attribute to the evaporation of the drop. We have overcome the problem of the critical dropping pressure with sequentially operated fast fluidic valves timed with a millisecond precision. Minimum drop volume was 0.4-0.7 μl with a sorting speed of 15-20 s per cell. After picking NE-4C neuroectodermal mouse stem cells and human primary monocytes from a standard plastic Petri dish we could gently deposit single cells inside tiny drops. 94 ± 3% and 54 ± 7% of the deposited drops contained single cells for NE-4C and monocytes, respectively. 7.5 ± 4% of the drops contained multiple cells in case of monocytes. Remaining drops were empty. Number of cells deposited in a drop could be documented by imaging the Petri dish before and after sorting. We tuned the adhesion force of cells to make the manipulation successful without the application of microstructures for trapping cells on the surface. We propose that our straightforward and flexible setup opens an avenue for single cell isolation, critically needed for the rapidly growing field of single cell biology. © 2014 AIP Publishing LLC

Automated single cell sorting and deposition in submicroliter drops

Automated manipulation and sorting of single cells are challenging, when intact cells are needed for further investigations, e.g., RNA or DNA sequencing. We applied a computer controlled micropipette on a microscope admitting 80 PCR (Polymerase Chain Reaction) tubes to be filled with single cells in a cycle. Due to the Laplace pressure, fluid starts to flow out from the micropipette only above a critical pressure preventing the precise control of drop volume in the submicroliter range. We found an anomalous pressure additive to the Laplace pressure that we attribute to the evaporation of the drop. We have overcome the problem of the critical dropping pressure with sequentially operated fast fluidic valves timed with a millisecond precision. Minimum drop volume was 0.4–0.7 ll with a sorting speed of 15–20 s per cell. After picking NE- 4C neuroectodermal mouse stem cells and human primary monocytes from a standard plastic Petri dish we could gently deposit single cells inside tiny drops. 9463% and 5467% of the deposited drops contained single cells for NE-4C and monocytes, respectively. 7.564% of the drops contained multiple cells in case of monocytes. Remaining drops were empty. Number of cells deposited in a drop could be documented by imaging the Petri dish before and after sorting. We tuned the adhesion force of cells to make the manipulation successful without the application of microstructures for trapping cells on the surface. We propose that our straightforward and flexible setup opens an avenue for single cell isolation, critically needed for the rapidly growing field of single cell biology

A centrifugal microfluidic platform for capturing, assaying and manipulation of beads and biological cells

Microfluidics is deemed a field with great opportunities, especially for applications in medical diagnostics. The vision is to miniaturize processes typically performed in a central clinical lab into small, simple to use devices - so called lab-on-a-chip (LOC) systems. A wide variety of concepts for liquid actuation have been developed, including pressure driven flow, electro-osmotic actuation or capillary driven methods. This work is based on the centrifugal platform (lab-on-a-disc). Fluid actuation is performed by the forces induced due to the rotation of the disc, thus eliminating the need for external pumps since only a spindle motor is necessary to rotate the disc and propel the liquids inside of the micro structures. Lab-on-a-disc systems are especially promising for point-of-care applications involving particles or cells due to the centrifugal force present in a rotating system. Capturing, assaying and identification of biological cells and microparticles are important operations for lab-on-a-disc platforms, and the focus of this work is to provide novel building blocks towards an integrated system for cell and particle based assays. As a main outcome of my work, a novel particle capturing and manipulation scheme on a centrifugal microfluidic platform has been developed. To capture particles (biological cells or micro-beads) I designed an array of V-shaped micro cups and characterized it. Particles sediment under stagnant flow conditions into the array where they are then mechanically trapped in spatially well-defined locations. Due to the absence of flow during the capturing process, i.e. particle sedimentation is driven by the artificial gravity field on the centrifugal platform, the capture efficiency of this approach is close to 100% which is notably higher than values reported for typical pressure driven systems. After capturing the particles, the surrounding medium can easily be exchanged to expose them to various conditions such as staining solutions or washing buffers, and thus perform assays on the captured particles. By scale matching the size of the capturing elements to the size of the particles, sharply peaked single occupancy can be achieved. Since all particles are arrayed in the same focal plane in spatially well defined locations, operations such as counting or fluorescent detection can be performed easily. The application of this platform to perform multiplexed bead-based immunoassays as well as the discrimination of various cell types based on intra cellular and membrane based markers using fluorescently tagged antibodies is demonstrated. Additionally, methods to manipulate captured particles either in batch mode or on an individual particle level have been developed and characterized. Batch release of captured particles is performed by a novel magnetic actuator which is solely controlled by the rotation frequency of the disc. Furthermore, the application of this actuator to rapidly mix liquids is shown. Manipulation of individual particles is performed using an optical tweezers setup which has been developed as part of this work. Additionally, this optical module also provides fluorescence detection capabilities. This is the first time that optical tweezers have been combined with a centrifugal microfluidic system. This work presents the core technology for an integrated centrifugal platform to perform cell and particle based assays for fundamental research as well as for point-of- care applications. The key outputs of my specific work are: 1. Design, fabrication and characterization of a novel particle capturing scheme on a centrifugal microfluidic platform (V-cups) with very high capture efficiency (close to 100%) and sharply peaked single occupancy (up to 99.7% single occupancy). 2. A novel rotation frequency controlled magnetic actuator for releasing captured particles as well as for rapidly mixing liquids has been developed, manufactured and characterized. 3. The V-cup platform has successfully been employed to capture cells and perform multi-step antibody staining assays for cell discrimination. 4. An optical tweezers setup has been built and integrated into a centrifugal teststand, and successful manipulation of individual particles trapped in the V-cup array is demonstrated

Microfluidic protein isolation and sample preparation for transmission electron microscopy

The knowledge of atomic structures is essential to understand the mechanics and chemistry of proteins in fundamental research and is often the base for drug development. During the last decades, X-ray crystallography has been the primary method for determining atomic models providing an impressive number of molecular structures. Nevertheless, the technique is limited by the fact that the complexes of interest have to be crystallized. Nuclear magnetic resonance (NMR), which is used as an alternative to solve biomolecules in solution, has the drawback of consuming large amounts of protein, being labour intensive and challenging for large molecules. In recent years, cryogenic electron microscopy (cryo-EM) has evolved as an important tool for protein structure determination. Technical advances in the instrumentation and increased computational power combined with better processing algorithms caused a massive improvement in the resolution of obtained structures. For these achievements Jacques Dubochet, Joachim Frank and Richard Henderson were awarded with a Nobel Prize in 2017. However, sample preparation methods lack behind and did not change a lot. A significant complication is the production of target proteins in sufficient amounts and quality. Although only some thousands to a few million protein particles must be imaged to solve a protein structure, much larger quantities are required to prepare specimens for cryo-EM. Conventional sample preparation methods are very wasteful with proteins and more than 99% of protein is lost during a paper blotting step. Thus, considerable amounts of purified proteins have to be produced using complex and costly procedures usually including several chromatography steps. In this thesis, a novel sample preparation and purification system consuming only minute amounts of biological material is presented. The system allows the purification of proteins and the subsequent preparation of isolated targets for negative stain and cryo-EM. We constructed corresponding hardware and software described in Chapters 1 & 2. The application of the system on biological samples is demonstrated in Chapters 3 & 4. As an example, we purified endogenous human 20S proteasome starting with <1 μL HeLa cytosol and determined it’s 3D structure at a resolution of 3.5Å. In Chapter 5, we show the purification of recombinantly expressed proteins by the use of a novel crosslinker that was developed during the course of this thesis

Lab-on-a-chip platforms for pathogen analysis

Infectious diseases caused by pathogenic microorganisms are a big burden in developed and developing countries. The emergence and rapid global spread of virus and antimicrobial resistant bacteria is a significant threat to patients, healthcare systems and the economy of countries. Early pathogen detection is often hampered by low concentrations present in complex matrices such as food and body fluids.Microfluidic technologies offer new and improved approaches for detection of pathogens on the microscale. Here, two microfluidic platforms for pathogen sorting and molecular identification were investigated: (1) inertial focusing and (2) microscale immiscible filtration. Inertial focusing in two serpentine channel designs etched in glass at different depths was evaluated with different microparticles, bacteria and blood. The shallow design allowed 2.2-fold concentration of Escherichia coli O157 cells, whereas the deep design accomplished recovery of 54% E. coli O157 depleted from 97% red blood cells in 0.81% haematocrit at flowrates of 0.7 mL min-1.A lab-on-a-chip platform based on microscale immiscible filtration was investigated for capture and detection of nucleic acids and bacteria. For nucleic acids, oligo (dT) functionalised magnetic beads or silica paramagnetic particles in GuHCl were used to capture genomic RNA from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and genomic DNA from Neisseria gonorrhoeae, respectively. On-chip amplification and detection were performed via colorimetric loop-mediated isothermal amplification (LAMP). Results showed sensitive and specific detection of targeted nucleic acids (470 RNA copies mL-1 and 5 × 104 DNA copies mL-1) with no cross-reactivity to other RNAs and DNAs tested. The whole workflow was integrated in a single device and time from sample-in to answer-out was within 1h. The platform only required power for a heat source and showed potential for point of care diagnostics in resource-limited settings. For bacteria detection, anti-E. coli O157 functionalised magnetic beads were used to capture cells with > 90% efficiency and on-chip fluorescence in situ hybridisation and a staining assay were explored for bacteria identification.A wide variety of microfluidic approaches for pathogen analysis have been devised in the literature with different advantages and drawbacks. Careful evaluation based on their purpose, integrated steps and end user is critical. Input from stakeholders right from the start of a project and throughout is vital to success. The platforms investigated herein have potential for applications such as sample preparation, pathogen concentration and specific molecular detection of E. coli O157, N. gonorrhoeae DNA, and SARS-CoV-2 RNA. With further development and clinical validation, the widespread use of these systems could facilitate early diagnosis of infectious diseases, allowing timely management of outbreaks and treatment and slowing the incidence of antimicrobial resistance

The NASA SBIR product catalog

The purpose of this catalog is to assist small business firms in making the community aware of products emerging from their efforts in the Small Business Innovation Research (SBIR) program. It contains descriptions of some products that have advanced into Phase 3 and others that are identified as prospective products. Both lists of products in this catalog are based on information supplied by NASA SBIR contractors in responding to an invitation to be represented in this document. Generally, all products suggested by the small firms were included in order to meet the goals of information exchange for SBIR results. Of the 444 SBIR contractors NASA queried, 137 provided information on 219 products. The catalog presents the product information in the technology areas listed in the table of contents. Within each area, the products are listed in alphabetical order by product name and are given identifying numbers. Also included is an alphabetical listing of the companies that have products described. This listing cross-references the product list and provides information on the business activity of each firm. In addition, there are three indexes: one a list of firms by states, one that lists the products according to NASA Centers that managed the SBIR projects, and one that lists the products by the relevant Technical Topics utilized in NASA's annual program solicitation under which each SBIR project was selected

Microdevices and Microsystems for Cell Manipulation

Microfabricated devices and systems capable of micromanipulation are well-suited for the manipulation of cells. These technologies are capable of a variety of functions, including cell trapping, cell sorting, cell culturing, and cell surgery, often at single-cell or sub-cellular resolution. These functionalities are achieved through a variety of mechanisms, including mechanical, electrical, magnetic, optical, and thermal forces. The operations that these microdevices and microsystems enable are relevant to many areas of biomedical research, including tissue engineering, cellular therapeutics, drug discovery, and diagnostics. This Special Issue will highlight recent advances in the field of cellular manipulation. Technologies capable of parallel single-cell manipulation are of special interest

Simulation verification techniques study: Simulation performance validation techniques document

Techniques and support software for the efficient performance of simulation validation are discussed. Overall validation software structure, the performance of validation at various levels of simulation integration, guidelines for check case formulation, methods for real time acquisition and formatting of data from an all up operational simulator, and methods and criteria for comparison and evaluation of simulation data are included. Vehicle subsystems modules, module integration, special test requirements, and reference data formats are also described