Release date: 2014-10-08
A few days ago, Nature Methods magazine launched a special issue on the occasion of the tenth anniversary, commenting on the top ten technologies that have had the most impact on biological research in the past decade. Second-generation sequencing, CRISPR, single-molecule technology, cell reprogramming, optogenetics, and ultra-high-resolution microscopy are on the list.
Second Generation Sequencing Next-generationsequencing
The emergence of second-generation sequencing or massively parallel sequencing has affected almost every corner of the biological field. This technology allows scientists to sequence genomes, assess genetic variation, quantify gene expression, study epigenetic regulation, explore microscopic life, and easily upgrade various analyses and screens. Technological innovations have led to an increase in the quantity and quality of sequencing data, and the construction of sequencing libraries is constantly evolving. It is now possible to detect restricted materials or degraded samples, to flexibly part of the target sequence space, to label a wide variety of molecules in cells, to capture molecular interactions and genomic structures. In addition, the calculation tools have also contributed to the interpretation of the massive data of the second generation of sequencing, revealing the basic information of sequence variation, regulation and evolution.
Genomeengineering
Genomic engineering can make custom changes in cells, patterns, and non-model organisms that are cultured in vitro, and such techniques have greatly facilitated research. Researchers can knock out genes, introduce mutations, or construct fusion genes with the help of these tools. For example, one uses an enzyme to cleave a specific genomic sequence, initiates a cell repair process, and thereby makes the desired sequence change. Meganuclease, zinc finger enzymes and TALEN target the sequence of interest through their respective DNA binding domains. Recently, the CRISPR-Cas9 system has become the new darling of this field. The system uses RNA for nuclease navigation, which is not only easy to design, but also able to rewrite almost any genomic sequence.
Single molecule technology Single-moleculemethods
Studying the behavior of a single molecule (such as a protein or DNA) can reveal important biological mechanisms that are unattainable by averaging molecular studies. In the past decade, some single-molecule technologies have gradually matured. For example, forcespectroscopy can detect molecular binding, folding, or mechanical behavior, while fluorescence microscopy can track single molecules in vitro and in vivo. Emerging single-molecule technologies also include the ability to sequence single-molecule nanopore technology to detect single-molecule optical and plasmonic devices without labeling. The emergence of these tools has enabled people to explore the capabilities of single molecules at unprecedented depths.
Light-cut imaging
The old technology of light-cut imaging has ushered in its second spring, because imaging equipment (including microscopes and cameras), fluorescent probes and image analysis techniques have been greatly improved. Light-cut imaging uses a very thin layer of light to illuminate the sample, rather than by point source or full-field illumination, enabling fast, high-resolution three-dimensional imaging of biological samples while reducing phototoxicity. Researchers in neuroscience and developmental biology are using light-cut imaging in many organisms to study basic biological processes such as embryonic development and brain function.
Mass Spectrometry Based Mass Spectroscopy-Based Mass Spectroscopy–based Proteomics
Ten years ago, proteomics research based on mass spectrometry was a relatively niche area that traditional cell biologists were not familiar with. However, the speed and performance of mass spectrometers have increased rapidly over the past decade, and sample preparation, experimental design, and data analysis have made tremendous advances, and many problems with data repeatability and comprehensiveness have been resolved. These developments have led to a vibrant life in this area. An in-depth quantitative mapping of the proteome of a particular cell state, which used to require the instrument to run for several days, can now be completed in just a few hours. Now, many researchers use mass spectrometry to study the function of proteins at the system level, such as mapping of protein post-translational modifications and protein interactions.
Structural Biology
With the continuous optimization of the structure determination process (from protein expression to crystallization), it has become routine to analyze the atomic structure of soluble small proteins by X-ray crystallography. On this basis, the researchers have analyzed many challenging protein structures, such as membrane proteins and large protein complexes, which are produced in small amounts and are difficult to crystallize. Over the past decade, sample preparation, crystallization, and data analysis of X-ray crystal diffraction have been greatly improved. At the same time, other structural analysis techniques are rapidly evolving, such as nuclear magnetic resonance spectroscopy and single-particle cryo-electron microscopy. Emerging technologies such as X-ray free electron lasers have emerged. These technological advances will help people solve a variety of molecular structures.
Cell reprogramming Cellularreprogramming
iPS technology enables cells to regain pluripotency through reprogramming. The induced pluripotent stem cells (iPSCs) generated by this technique can be amplified, and they can theoretically generate any type of cells for studying diseases and screening drugs. Many laboratories now generate human cells with a specific genetic background through iPS, but people are still exploring better ways to induce iPSC differentiation. The iPS technology boom has also renewed attention to direct reprogramming, which directly converts one terminally differentiated cell into another terminally differentiated cell through an exogenous transcription factor.
Optogenetics Optogenetics
Light-irradiated light-sensitive proteins integrated into cells can non-invasively alter cell behavior. Optogenetics is particularly popular in the field of neurology, and researchers use this technique to activate or inhibit neuronal activity for precise time and space control. The optogenetic tool can be used both in vitro and in vivo to help explore neuronal function, neuronal excitability, and synaptic transmission. In addition, light-sensitive tools can also be used to dimerize proteins or activate transcription. The continuous improvement of existing light-sensitive proteins and the discovery of new light-sensitive proteins are expanding the toolbox of optogenetics. In addition, the luminescence process is also being improved, such as two-photon excitation and patterned illumination stimulation.
Synthetic biology
Designing microbial metabolic pathways to produce drugs and biofuels, building synthetic organisms, and giving new functions to mammalian cells is the goal of synthetic biology. Thanks to improvements in experiments and calculation methods, the above work has made gratifying progress. In terms of gene synthesis and assembly, bacterial genomes and yeast chromosomes have been successfully synthesized. Identifying regulatory elements that control transcription and translation can help people make better loop designs. Researchers are constantly developing predictive models that will lay the foundation for the success of synthetic biology in the next decade.
Ultra High Resolution Microscope Super-resolutionmicroscopy
For centuries, the "diffraction limit" of optical microscopes has been considered unsurpassable. Now people have "breakthrough" this limit from different sources. These technologies are collectively referred to as ultra-high resolution microscopy or nano-microscopy. These technologies have been widely used in the field of biology for nearly a decade. This means that researchers can now distinguish tiny objects (organelles and even macromolecular complexes) within cells, which were previously only obscured points that could not be resolved. Ultra-high resolution microscopy is still evolving rapidly, especially for ultra-high resolution data, which opens up new horizons for scientists studying molecules and cells.
Source: Biopass
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