Miniaturization in functional genomics and proteomics

Abstract

| Proteins are the key components of the cellular machinery responsible for processing changes that are ordered by genomic information. Analysis of most human proteins and nucleic acids is important in order to decode the complex networks that are likely to underlie many common diseases. Significant improvements in current technology are also required to dissect the regulatory processes in high-throughtput and with low cost. Miniaturization of biological assays is an important prerequisite to achieve these goals in the near future. SYSTEMS BIOLOGYThe study of the complex interactions that occur at all levels of biological information -from whole-genome sequence interactions to developmental and biochemical networks -and their functional relationship to organism-level phenotypes. NATURE REVIEWS | GENETICS VOLUME 6 | JUNE 2005 | 465 and concomitantly reducing the complexity of genomic DNA. Although PCR can be used to amplify small numbers of DNA molecules in low microlitre or nanolitre volumes in vitro, problems are associated with the dilution of heterozygous DNA. This could result in incorrect genotyping results (homozygous genotypes) because of the preferential amplification of one of the alleles. Extreme dilution indicates that there is a sufficiently high integrity of the nucleic-acid templates to allow efficient amplification. Furthermore, amplification of low concentrations of nucleic acids requires strict quality control, as it is often associated with contamination problems, which can be problematic in high-throughput applications. In contrast to nucleic-acid manipulation, it is currently impossible to amplify proteins from a biological sample. R E V I E W S Miniaturization in functional genomicsGenome research and functional genomics have catalysed the development of high-throughput and miniaturized approaches for the analysis of biomolecules [5][6][7][8] . Figure 1 | DNA micorarrays. DNA microarrays that are based on non-porous solid supports such as glass have paved the way for highly parallel miniaturized analysis of biomolecules. Using robotic workstations, ~0.25-1 nl of DNA solution are printed on a slide, creating spots that range from 100 to 150 µm in diameter. Successive samples are then spaced to avoid contact between adjacent spots, with approximately 200 µm between each spot 7 . Currently, about 50,000 cDNAs can be robotically spotted onto a microscope slide and hybridized with a fluorescently labelled probe. Using photolithographical masking techniques, arrays that have 400,000 distinct oligonucleotides have been produced, each in its own 20-µm 2 region (today, this can be as small as ~5 µm 2 ) REF. 8. After spotting, nucleic-acid samples can be hybridized on these pre-structured microarrays. Hybridization events are monitored using fluorescence scanners. A typical fluorescence read-out of highly parallel hybridization on a cDNA microarray is shown in the bottom panel. Box 1 | Technological problems in miniaturizationEvery molecular biological method can be miniaturized from microl...

Nanoliter microfluidic hybrid method for simultaneous screening and optimization validated with crystallization of membrane proteins

“…To validate this method using a challenging problem, we demonstrate its compatibility with crystallization of membrane proteins. Small-scale screening and optimization experiments are important for biological assays, chemical screening, and protein crystallization (1)(2)(3). Screening and optimization are usually carried out sequentially.…”

Typing of single nucleotide polymorphisms by MALDI mass spectrometry: Principles and diagnostic applications

“…Future efforts will also include the specific analysis of nucleic acids at the low to sub-zeptomole level in cells or tissues, either in situ or in vivo [11].…”

“…Short reaction sequences become even more important in clinical diagnostics, where rapid analysis can be crucial to save the life of a diseased (e.g., infected) patient. Many of the SNP genotyping techniques are currently being optimized in terms of higher throughput and cost efficiency; however, it seems that the focus is still rather on making SNP genotyping procedures more cost-efficient for fundamental genome research by parallelization and miniaturization of assays [11] rather than simplifying assays for diagnostic routine. While current technology developments thus mainly concentrate on the requirements of research laboratories, in clinics some specific criteria are important that are sketched here: Firstly, a simple and short protocol, which can be easily applied for medium throughput applications, is required.…”

Under-Updated Particle Swarm Optimization for Small Feature Selection Subsets from Large-Scale Datasets

“…The use of feature selection procedures is almost compulsory and complex in biology and medicine because the generation of massive datasets is nowadays common for many stateof-the-art technologies such as transcriptomics, proteomics, metabolomics, and genomics where a single, conventional, and relatively cheap experiment may yield the measurement of several thousands of features per sample (Hieter and Boguski, 1997;Sauer et al, 2005). In such cases, feature selection is used to reduce complexity and large computational costs, as well as to improve pattern recognition accuracy, data interpretability and hypothesis generation (Shen et al, 2008;Vapnik, 1998;Guyon et al, 2002).…”