Analysis of mitochondrial DNA in microfluidic systems

A rapid bioanalytical tool for detection of sequence-specific circular DNA and mitochondrial DNA point mutations

Mutations in mitochondrial DNA (mtDNA) have been an essential cause of numerous diseases, making their identification critically important. The majority of mtDNA screening techniques require polymerase chain reaction (PCR) amplification, enzymatic digestion, and denaturation procedures, which are laborious and costly. Herein, we developed a sensitive PCR-free electrokinetic-based sensor combined with a customized bis-peptide nucleic acid (bis-PNA) and gamma-PNA (γ-PNA) probes immobilized on beads, for the detection of mtDNA point mutations and sequence-specific supercoiled plasmid DNA at the picomolar range. The probes are capable of invading the double-stranded circular DNA and forming a stable triplex structure. Thus, this method can significantly reduce the sample preparation and omit the PCR amplification steps prior to sensing. Further, this bioanalytical tool can open up a new paradigm in clinical settings for the screening of double-stranded circular nucleic acids with a single-base mismatch specificity in a rapid and sensitive manner.

Oxidative stress inhibits axonal transport: implications for neurodegenerative diseases

Background

Reactive oxygen species (ROS) released by microglia and other inflammatory cells can cause axonal degeneration. A reduction in axonal transport has also been implicated as a cause of axonal dystrophies and neurodegeneration, but there is a paucity of experimental data concerning the effects of ROS on axonal transport. We used live cell imaging to examine the effects of hydrogen peroxide on the axonal transport of mitochondria and Golgi-derived vesicles in cultured rat hippocampal neurons.

Results

Hydrogen peroxide rapidly inhibited axonal transport, hours before any detectable changes in mitochondrial morphology or signs of axonal degeneration. Mitochondrial transport was affected earlier and was more severely inhibited than the transport of Golgi-derived vesicles. Anterograde vesicle transport was more susceptible to peroxide inhibition than retrograde transport. Axonal transport partially recovered following removal of hydrogen peroxide and local application of hydrogen peroxide inhibited transport, suggesting that the effects were not simply a result of nerve cell death. Sodium azide, an ATP synthesis blocker, had similar effects on axonal transport, suggesting that ATP depletion may contribute to the transport inhibition due to hydrogen peroxide.

Conclusions

These results indicate that inhibition of axonal transport is an early consequence of exposure to ROS and may contribute to subsequent axonal degeneration.

A microfluidic system for fast detection of mitochondrial DNA deletion

This study reports an integrated microfluidic system capable of automatic extraction and analysis of mitochondrial DNA (mtDNA). Mitochondria are the energy production and metabolism centres of human and animal cells, which supply most of the energy for maintaining physiological functions and play an important role in the process of cell death. Because it lacks an effective repair system, mtDNA suffers much higher oxidative damage and usually harbours more mutations than nuclear DNA. Alterations of mtDNA have been reported to be strongly associated with mitochondrial dysfunction, mitochondria-related diseases, aging, and many important human diseases such as diabetes and cancers. Thus, an effective tool for automatic detection of mtDNA deletion is in great need. This study, therefore, proposed a microfluidic system integrating three enabling modules to perform the entire protocol for the detection of mtDNA deletion. Crucial processes which included mtDNA extraction, nucleic acid amplification, separation and detection of the target genes were automatically performed. When compared with traditional assays, the developed microfluidic system consumed fewer samples and reagents, achieved a higher mtDNA extraction rate, and could automate all the processes within a shorter period of time (150 minutes). It may provide a powerful tool for the analysis of mitochondria mutations in the near future.

Microfabrication and applications of opto-microfluidic sensors

A review of research activities on opto-microfluidic sensors carried out by the research groups in Canada is presented. After a brief introduction of this exciting research field, detailed discussion is focused on different techniques for the fabrication of opto-microfluidic sensors, and various applications of these devices for bioanalysis, chemical detection, and optical measurement. Our current research on femtosecond laser microfabrication of optofluidic devices is introduced and some experimental results are elaborated. The research on opto-microfluidics provides highly sensitive opto-microfluidic sensors for practical applications with significant advantages of portability, efficiency, sensitivity, versatility, and low cost.

Adenine nucleotide translocase 2 is a key mitochondrial protein in cancer metabolism

Adenine nucleotide translocase (ANT), a mitochondrial protein that facilitates the exchange of ADP and ATP across the mitochondrial inner membrane, plays an essential role in cellular energy metabolism. Human ANT presents four isoforms (ANT1-4), each with a specific expression depending on the nature of the tissue, cell type, developmental stage and status of cell proliferation. Thus, ANT1 is specific to muscle and brain tissues; ANT2 occurs mainly in proliferative, undifferentiated cells; ANT3 is ubiquitous; and ANT4 is found in germ cells. ANT1 and ANT3 export the ATP produced by oxidative phosphorylation (OxPhos) from the mitochondria into the cytosol while importing ADP. In contrast, the expression of ANT2, which is linked to the rate of glycolytic metabolism, is an important indicator of carcinogenesis. In fact, cancers are characterized by major metabolic changes that switch cells from the normally dual oxidative and glycolytic metabolisms to an almost exclusively glycolytic metabolism. When OxPhos activity is impaired, ANT2 imports glycolytically produced ATP into the mitochondria. In the mitochondrial matrix, the F1F0-ATPase complex hydrolyzes the ATP, pumping out a proton into the intermembrane space. The reverse operations of ANT2 and F1F0-ATPase under glycolytic conditions contribute to maintaining the mitochondrial membrane potential, ensuring cell survival and proliferation. Unlike the ANT1 and ANT3 isoforms, ANT2 is not pro-apoptotic and may therefore contribute to carcinogenesis. Since the expression of ANT2 is closely linked to the mitochondrial bioenergetics of tumors, it should be taken into account for individualizing cancer treatments and for the development of anticancer strategies.

Fully integrated microfluidic separations systems for biochemical analysis

Over the past decade a tremendous amount of research has been performed using microfluidic analytical devices to detect over 200 different chemical species. Most of this work has involved substantial integration of fluid manipulation components such as separation channels, valves, and filters. This level of integration has enabled complex sample processing on miniscule sample volumes. Such devices have also demonstrated high throughput, sensitivity, and separation performance. Although the miniaturization of fluidics has been highly valuable, these devices typically rely on conventional ancillary equipment such as power supplies, detection systems, and pumps for operation. This auxiliary equipment prevents the full realization of a "lab-on-a-chip" device with complete portability, autonomous operation, and low cost. Integration and/or miniaturization of ancillary components would dramatically increase the capability and impact of microfluidic separations systems. This review describes recent efforts to incorporate auxiliary equipment either as miniaturized plug-in modules or directly fabricated into the microfluidic device.

High resolution DNA separations using microchip electrophoresis

Planar microfluidic devices have emerged as effective tools for the electrophoretic separation of a variety of different DNA inputs. The advancement of this miniaturized platform was inspired initially by demands placed on electrophoretic performance metrics by the human genome project and has provided a viable alternative to slab gel and even capillary formats due to its ability to offer high resolution separations of nucleic acid materials in a fraction of the time associated with its predecessors, consumption of substantially less sample and reagents while maintaining the ability to perform many separations in parallel for realizing ultra-high throughputs. Another compelling advantage of this separation platform is that it offers the potential for integrating front-end sample preprocessing steps onto the separation device eliminating the need for manual sample handling. This review aims to compile a recent survey of various electrophoretic separations using either glass or polymer-based microchips in the areas of genotyping and DNA sequencing as well as those involving the growing field of DNA-based forensics.

Genotyping with microfluidic devices

In the past few years, electrophoresis microchips have been increasingly utilized to interrogate genetic variations in the human and other genomes. Microfluidic devices can be readily applied to speed up existing genotyping protocols, in particular the ones that require electric field-mediated separations in conjunction with restriction fragment analysis, DNA sequencing, hybridization-based techniques, allele-specific amplification, heteroduplex analysis, just to list the most important ones. As a result of recent developments, microfabricated electrophoresis devices offer several advantages over conventional slab-gel electrophoresis, such as small sample volume requirement, low reagent consumption, the option of system integration and easy multiplexing. The analysis speed of microchip electrophoresis is significantly higher than that of any other electric field-mediated separation techniques. State-of-the-art microfluidic bioanalytical devices already claim their place in most molecular biology laboratories. This review summarizes the recent developments in microchip electrophoresis methods of nucleic acids, particularly for rapid genotyping, that will most likely play a significant role in the future of clinical diagnostics.