Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalysed the development of next-generation sequencing (NGS) technologies. The inexpensive production of large volumes of sequence data is the primary advantage over conventional methods. Here, I present a technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments. I also outline the broad range of applications for NGS technologies, in addition to providing guidelines for platform selection to address biological questions of interest.

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Sequencing technologies-the next generation

One of the fastest moving and most exciting interfaces of nanotechnology is the use of quantum dots (QDs) in biology. The unique optical properties of QDs make them appealing as in vivo and in vitro fluorophores in a variety of biological investigations, in which traditional fluorescent labels based on organic molecules fall short of providing long-term stability and simultaneous detection of multiple signals. The ability to make QDs water soluble and target them to specific biomolecules has led to promising applications in cellular labelling, deep-tissue imaging, assay labelling and as efficient fluorescence resonance energy transfer donors. Despite recent progress, much work still needs to be done to achieve reproducible and robust surface functionalization and develop flexible bioconjugation techniques. In this review, we look at current methods for preparing QD bioconjugates as well as presenting an overview of applications. The potential of QDs in biology has just begun to be realized and new avenues will arise as our ability to manipulate these materials improves.

Quantum dot bioconjugates for imaging, labelling and sensing

DNA sequence represents a single format onto which a broad range of biological phenomena can be projected for high-throughput data collection. Over the past three years, massively parallel DNA sequencing platforms have become widely available, reducing the cost of DNA sequencing by over two orders of magnitude, and democratizing the field by putting the sequencing capacity of a major genome center in the hands of individual investigators. These new technologies are rapidly evolving, and near-term challenges include the development of robust protocols for generating sequencing libraries, building effective new approaches to data-analysis, and often a rethinking of experimental design. Next-generation DNA sequencing has the potential to dramatically accelerate biological and biomedical research, by enabling the comprehensive analysis of genomes, transcriptomes and interactomes to become inexpensive, routine and widespread, rather than requiring significant production-scale efforts.

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Next-generation DNA sequencing.

The unprecedented ability of nanometallic (that is, plasmonic) structures to concentrate light into deep-subwavelength volumes has propelled their use in a vast array of nanophotonics technologies and research endeavours. Plasmonic light concentrators can elegantly interface diffraction-limited dielectric optical components with nanophotonic structures. Passive and active plasmonic devices provide new pathways to generate, guide, modulate and detect light with structures that are similar in size to state-of-the-art electronic devices. With the ability to produce highly confined optical fields, the conventional rules for light-matter interactions need to be re-examined, and researchers are venturing into new regimes of optical physics. In this review we will discuss the basic concepts behind plasmonics-enabled light concentration and manipulation, make an attempt to capture the wide range of activities and excitement in this area, and speculate on possible future directions.

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Plasmonics for extreme light concentration and manipulation.

With few exceptions biological tissues strongly scatter light, making high-resolution deep imaging impossible for traditional⎯including confocal⎯fluorescence microscopy. Nonlinear optical microscopy, in particular two photon–excited fluorescence microscopy, has overcome this limitation, providing large depth penetration mainly because even multiply scattered signal photons can be assigned to their origin as the result of localized nonlinear signal generation. Two-photon microscopy thus allows cellular imaging several hundred microns deep in various organs of living animals. Here we review fundamental concepts of nonlinear microscopy and discuss conditions relevant for achieving large imaging depths in intact tissue.

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Deep tissue two-photon microscopy

Optical approaches for observing the dynamics of single molecules have required pico- to nanomolar concentrations of fluorophore in order to isolate individual molecules. However, many biologically relevant processes occur at micromolar ligand concentrations, necessitating a reduction in the conventional observation volume by three orders of magnitude. We show that arrays of zero-mode waveguides consisting of subwavelength holes in a metal film provide a simple and highly parallel means for studying single-molecule dynamics at micromolar concentrations with microsecond temporal resolution. We present observations of DNA polymerase activity as an example of the effectiveness of zero-mode waveguides for performing single-molecule experiments at high concentrations.

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Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations

Although fluorescence microscopy has proven to be one of the most powerful tools in biology, its application to the intact animal has been limited to imaging several hundred micrometers below the surface. The rest of the animal has eluded investigation at the microscopic level without excising tissue or performing extensive surgery. However, the ability to image with subcellular resolution in the intact animal enables a contextual setting that may be critical for understanding proper function. Clinical applications such as disease diagnosis and optical biopsy may benefit from minimally invasive in vivo approaches. Gradient index (GRIN) lenses with needle-like dimensions can transfer high-quality images many centimeters from the object plane. Here, we show that multiphoton microscopy through GRIN lenses enables minimally invasive, subcellular resolution several millimeters in the anesthetized, intact animal, and we present in vivo images of cortical layer V and hippocampus in the anesthetized Thy1-YFP line H mouse. Microangiographies from deep capillaries and blood vessels containing fluorescein-dextran and quantum dot-labeled serum in wild-type mouse brain are also demonstrated.

https://www.physiology.org/doi/pdf/10.1152/jn.01007.2003

In Vivo Multiphoton Microscopy of Deep Brain Tissue

The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

Method for sequencing nucleic acid molecules

The invention is embodied in a method of recording successive holograms in a recording medium, using at least a fan of M waves along at least a first axis with a separation angle between adjacent waves and directing the fan of M waves as a reference beam along a reference beam path onto the recording medium, successively modulating a wave with a succession of images to produce a succession of signal beams along a signal beam path lying at a propagation angle relative to the reference beam path so that the signal and reference beams intersect at a beam intersection lying within the medium, the beam intersection having a size corresponding to beam areas of the reference and signal beams, producing a succession of relative displacements in a direction parallel to the first axis between the recording medium and the beam intersection of the signal and reference beam paths in synchronism with the succession of signal beams, each of the displacements being less than the size of the intersection whereby to record successive holograms partially overlapped along a direction of the displacements.

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Holographic storage using shift multiplexing

Shift multiplexing is a holographic storage method particularly suitable for the implementation of holographic disks. We characterize the performance of shift-multiplexed memories by using a spherical wave as the reference beam. We derive the shift selectivity, the cross talk, the exposure schedule, and the storage density of the method. We give experimental results to verify the theoretical predictions.

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Michael J. Levene

Papers

Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations

In Vivo Multiphoton Microscopy of Deep Brain Tissue

Method for sequencing nucleic acid molecules

Holographic storage using shift multiplexing

Shift multiplexing with spherical reference waves.