Micro-separation toward systems biology

Functional detection of the original generation of hippocampal cells planted on to the micro-fluidic chip with artificial neuronal network using the patch clamp recording technique: a preliminary study

PURPOSE

The design of pattern that limits the hippocampal cells growth is an important explore for realizing a simplified artificial neuronal network in vitro.

MATERIALS AND METHODS

In this study, we examined the pattern in micro-fluidic chip to stipulate the hippocampal cells adhesion, growth and the formation of a functional neuronal network in vitro. Patch clamp recording technique was used to detect the growth situation and biological function of the haippocampal cells on the micro-fluidic chip which could simulate environment in vivo.

RESULTS

We showed that the number of neurons cultured was about 5000-6000 cells on the micro-fluidic chip, which was conductive to the hippocampal cells growth. The result of patch clamp recording technique showed the signals of sodium and potassium channels, meanwhile, it also revealed the signals of synaptic connection.

CONCLUSIONS

These findings involve placing cells in specific locations to create organized structures, and explore the spread function of synaptic on the micro-fluidic chip.

Computer simulation for the study of the liquid chromatographic separation of explosive molecules

The application of high performance liquid chromatography (HPLC) to separate explosive chemicals was investigated by molecular dynamics (MD) simulations. The explosive ingredients including NG, RDX, HMX and TNT were assigned as solutes, while methanol (CH₃OH) and acetonitrile (CH₃CN) were assigned as solvents in the solution system. The polymeric-molecular siloxanes (SiC8) and poly-1,2-methylenedioxy-4-propenyl benzene (PISAF) compounds were treated as stationary phase in the simulation. The simulation results showed that the different species of explosive ingredients were separated successfully in the solutions by each of the constructed stationary phase of SiC8 and PISAF after a total simulation time of 12.0 ps approximately, which were consistent with the experimental analysis of HPLC spectra. The origin for the separation was found due to the electrostatic interactions between polymer and explosives.

Gravity driven deterministic lateral displacement for particle separation in microfluidic devices

We investigate the two-dimensional continuous size-based separation of suspended particles in gravity-driven deterministic lateral displacement (g-DLD) devices. The suspended particles are driven through a periodic array of cylindrical obstacles under the action of gravity. We perform experiments covering the entire range of forcing orientations with respect to the array of obstacles and identify specific forcing angles that would lead to vector separation, in which different particles migrate, on an average, in different directions. A simple model, based on the lateral displacement induced on the trajectory of a particle by irreversible particle-obstacle interactions, accurately predicts the dependence of the migration angle on the forcing direction. The results provide design guidance for the development of g-DLD devices. We observe directional locking, which strongly depends on the size of the particle and suggests that relatively small forcing angles are well suited for size-fractionation purposes. We demonstrate excellent separation resolution for a binary mixture of particles at relatively small forcing angles, that is, forcing angles that are close to but smaller than the first transition angle of the larger particles in the mixture.

Protein analysis-on-chip systems in foodomics

Protein compositional data can address nutritional, packaging, origin/authenticity, processing history, safety and other quality questions. Such data has been time-consuming and expensive to generate until recently but “protein analysis on a chip” systems are now available that can analyze a complex food sample in a few minutes and do not require great protein analytical expertise. We review some of the main new approaches with examples of their application and discuss their advantages and disadvantages.

A simple microfluidic method to select, isolate, and manipulate single-cells in mechanical and biochemical assays

This article describes a simple and low-tech microfluidic method for single-cell experimentation, which permits cell selection without stress, cell manipulation with fine control, and passive self-exclusion of all undesired super-micronic particles. The method requires only conventional soft lithography microfabrication techniques and is applicable to any microfluidic single-cell circuitry. The principle relies on a bypass plugged in parallel with a single-cell assay device and collecting 97% of the flow rate. Cell selection into the single cell device is performed by moving the cell of interest back and forth in the vicinity of the junction between the bypass and the analysis circuitry. Cell navigation is finely controlled by hydrostatic pressure via centimetre-scale actuation of external macroscopic reservoirs connected to the device. We provide successful examples of biomechanical and biochemical assays on living human leukocytes passing through 4 mum wide capillaries. The blebbing process dynamics are monitored by conventional 24 fps videomicroscopy and subcellular cytoskeleton organization is imaged by on-chip immunostaining.

A review of current applications of mass spectrometry for neuroproteomics in epilepsy

The brain is unquestionably the most fascinating organ, and the hippocampus is crucial in memory storage and retrieval and plays an important role in stress response. In temporal lobe epilepsy (TLE), the seizure origin typically involves the hippocampal formation. Despite tremendous progress, current knowledge falls short of being able to explain its function. An emerging approach toward an improved understanding of the complex molecular mechanisms that underlie functions of the brain and hippocampus is neuroproteomics. Mass spectrometry has been widely used to analyze biological samples, and has evolved into an indispensable tool for proteomics research. In this review, we present a general overview of the application of mass spectrometry in proteomics, summarize neuroproteomics and systems biology-based discovery of protein biomarkers for epilepsy, discuss the methodology needed to explore the epileptic hippocampus proteome, and also focus on applications of ingenuity pathway analysis (IPA) in disease research. This neuroproteomics survey presents a framework for large-scale protein research in epilepsy that can be applied for immediate epileptic biomarker discovery and the far-reaching systems biology understanding of the protein regulatory networks. Ultimately, knowledge attained through neuroproteomics could lead to clinical diagnostics and therapeutics to lessen the burden of epilepsy on society.

Metabolic profiling of ultrasmall sample volumes with GC/MS: from microliter to nanoliter samples

Profiling of metabolites is increasingly used to study the functioning of biological systems. For some studies the volume of available samples is limited to only a few microliters or even less, for fluids such as cerebrospinal fluid (CSF) of small animals like mice or the analysis of individual oocytes. Here we present an analytical method using in-liner silylation coupled to gas chromatography/mass spectrometry (GC/MS), that is suitable for metabolic profiling in ultrasmall sample volumes of 2 microL down to 10 nL. Method performance was assessed in various biosamples. Derivatization efficiencies for sugars, organic acids, and amino acids were satisfactory (105-120%), and repeatabilities were generally better than 15%, except for amino acids that had repeatabilities up to about 35-40%. For endogenous sugars and organic acids in fetal bovine serum, the response was linear for aliquots from 10 nL up to at least 1 microL. The developed GC/MS method was applied for the analysis of different sample matrixes, i.e., fetal bovine serum, mouse CSF, and aliquots of the intracellular content of Xenopus laevis oocytes. To the best of our knowledge, we present here the first comprehensive GC/MS metabolite profiles from mouse CSF and from the intracellular content of a single X. laevis oocyte.

Mass spectrometry in systems biology: an overview

As an emerging field, systems biology is currently the talk of the town, which challenges our philosophy in comprehending biology. Instead of the reduction approach advocated in molecular biology, systems biology aims at systems-level understanding of correlations among molecular components. Such comprehensive investigation requires massive information from the "omics" cascade demanding high-throughput screening techniques. Being one of the most versatile analytical methods, mass spectrometry has already been playing a significant role at this early stage of systems biology. In this review, we documented the advances in modern mass spectrometry technologies as well as nascent inventions. Recent applications of mass spectrometry-based techniques and methodologies in genomics, proteomics, transcriptomics and metabolomics will be further elaborated individually. Undoubtedly, more applications of mass spectrometry in systems biology can be expected in the near future.

Microfluidic single-cell analysis of intracellular compounds

Biological analyses traditionally probe cell ensembles in the range of 103-106 cells, thereby completely averaging over relevant individual cell responses, such as differences in cell proliferation, responses to external stimuli or disease onset. In past years, this fact has been realized and increasing interest has evolved for single-cell analytical methods, which could give exciting new insights into genomics, proteomics, transcriptomics and systems biology. Microfluidic or lab-on-a-chip devices are the method of choice for single-cell analytical tools as they allow the integration of a variety of necessary process steps involved in single-cell analysis, such as selection, navigation, positioning or lysis of single cells as well as separation and detection of cellular analytes. Along with this advantageous integration, microfluidic devices confine single cells in compartments near their intrinsic volume, thus minimizing dilution effects and increasing detection sensitivity. This review overviews the developments and achievements of microfluidic single-cell analysis of intracellular compounds in the past few years, from proof-of-principle devices to applications demonstrating a high biological relevance.

Electrokinetic sorting and collection of fractions for preparative capillary electrophoresis on a chip

A microfabricated device capable of selecting and collecting multiple components from a mixture separated by capillary electrophoresis (CE) is described. This collection is automated and can be easily controlled by a set of rules defined by an operator, enabling fast and consistent operation. The device consists of an electrokinetically steered fluidic network that can be divided into three sections: a CE part, a fractions distribution region and a set of storage channels. Sample fractions leave the CE channel and are detected in the interfacial region by fluorescence intensity measurements. If an upcoming peak is detected, separation is withheld and the potentials are reconfigured to force the fraction into one of the collection channels, where they become available for further processing or analysis. The sequence of separation and collection is repeated until all the bands of interest are captured. A mixture of three fluorescent dyes (Rhodamine 6G, Rhodamine B and Fluorescein) was used to demonstrate the principle. The components were repeatedly separated by means of CE and pooled in their respective storage channels. In comparison to previous developments, the system presented in this paper offers automatic collection of all fractions in a single run. Furthermore, it is possible to run the system in a repetitive mode for accumulative pooling if more fractionated sample is required.

Space and time-resolved gene expression experiments on cultured mammalian cells by a single-cell electroporation microarray

Single-cell experiments represent the next frontier for biochemical and gene expression research. Although bulk-scale methods averaging populations of cells have been traditionally used to investigate cellular behavior, they mask individual cell features and can lead to misleading or insufficient biological results. We report on a single-cell electroporation microarray enabling the transfection of pre-selected individual cells at different sites within the same culture (space-resolved), at arbitrarily chosen time points and even sequentially to the same cells (time-resolved). Delivery of impermeant molecules by single-cell electroporation was first proven to be finely tunable by acting on the electroporation protocol and then optimized for transfection of nucleic acids into Chinese Hamster Ovary (CHO-K1) cells. We focused on DNA oligonucleotides (ODNs), short interfering RNAs (siRNAs), and DNA plasmid vectors, thus providing a versatile and easy-to-use platform for time-resolved gene expression experiments in single mammalian cells.

In situ microfluidic flow rate measurement based on near-field heterodyne grating method

The near-field heterodyne grating (NF-HDG) method was applied to flow rate measurements in a microtube. The NF-HDG method is a newly developed optical technique based on photothermal effects. In this technique, pump light is shone on a transmission grating in front of a fluid channel and the inside liquid is heated with a pattern of the grating due to the Talbot effect. Another probe light is similarly shone on the same place as the pump light, and the diffraction by the transmission grating (reference) and the diffraction by the temporally generated thermal grating inside the fluid channel (signal) are mixed and detected (heterodyne detection). Theoretical analysis reveals that the dependence of the heterodyne signal intensity on the flow rate originates from the change in the heterodyne phase difference between the signal and reference, and the experimentally obtained calibration curves can be fitted with the theoretically predicted function. Furthermore, the optical setup was optimized based on the theoretical analysis of the Talbot effect. Flow rates of the order of nl/min were quantitatively measured, and the detection limit of the flow rate was 17 nl/min.

Multiphoton excitation fluorescence: A versatile detection method for capillary electrophoresis

Multiphoton excitation is a relatively old concept in quantum optics. But using multiphoton excitation fluorescence (MPEF) for bioanalysis is still in its infancy. Recently, MPEF has been introduced into the microseparation field, particularly CE, as a novel detection method. In this paper, MPEF detection for CE is reviewed, including MPEF fundamentals, approaches to achieving MPEF, detector configurations and applications in biological and environmental analyses. Emphasis will be placed on some recent advances of CE-MPEF in our laboratory. Challenges and future prospects are also discussed.

Capillary electrophoresis of signaling molecules

The emerging field of quantitative systems biology uses high-throughput bioanalytical measurements to gain a deeper understanding of biological phenomena. With the advent of instrumentation platforms, capillary electrophoresis spans a very wide range of biological applications. This short article focuses on the exploitation of capillary electrophoresis for the systems-level analysis of cell signaling molecules.

Optical molecular imaging for systems biology: from molecule to organism

The development of highly efficient analytical methods capable of probing biological systems at system level is an important task that is required in order to meet the requirements of the emerging field of systems biology. Optical molecular imaging (OMI) is a very powerful tool for studying the temporal and spatial dynamics of specific biomolecules and their interactions in real time in vivo. In this article, recent advances in OMI are reviewed extensively, such as the development of molecular probes that make imaging brighter, more stable and more informative (e.g., FPs and semiconductor nanocrystals, also referred to as quantum dots), the development of imaging approaches that provide higher resolution and greater tissue penetration, and applications for measuring biological events from molecule to organism level, including gene expression, protein and subcellular compartment localization, protein activation and interaction, and low-mass molecule dynamics. These advances are of great significance in the field of biological science and could also be applied to disease diagnosis and pharmaceutical screening. Further developments in OMI for systems biology are also proposed.

Capillary electrophoresis-based separation techniques for the analysis of proteins

CE offers the advantages of high speed, great efficiency, as well as the requirement of minimum amounts of sample and buffer for the analysis of proteins. In this review, we summarize the CE-based techniques coupled with absorption, LIF, and MS detection systems for the analysis of proteins mostly within the past 5 years. The basic principle of each technique and its advantages and disadvantages for protein analysis are discussed in brief. Advanced CE techniques, including on-column concentration techniques and high-efficiency multidimensional separation techniques, for high-throughput protein profiling of complex biological samples and/or of single cells are emphasized. Although the developed techniques provide improved peak capacity, they have not become practical tools for proteomics, mainly because of poor reproducibility, low-sample lading capacity, and low throughput due to ineffective interfaces between two separation dimensions and that between separation and MS systems. In order to identify the complexities and dynamics of the proteomes expressed by cells, tissues, or organisms, techniques providing improved analytical sensitivity, throughput, and dynamic ranges are still demanded.