基因表达差异显示实验

Under exceptional circumstances, it is possible to obtain DNA sequences from samples that are up to hundreds of thousands of years old. These data provide an opportunity to look directly at past genetic diversity, to trace the evolutionary process through time, and to infer demographic and phy ...

Advances in sequencing technologies have dramatically changed the field of ancient DNA (aDNA). It is now possible to generate an enormous quantity of aDNA sequence data both rapidly and inexpensively. As aDNA sequences are generally short in length, damaged, and at low copy number relative to ...

In ancient DNA studies focusing on estimating population histories, genetic markers are sequenced from a large number of samples belonging to the same species. Targeting loci of interest using traditional PCR can be time-consuming, in particular when samples are not well preserved and mu ...

Recent advances in high-throughput DNA sequencing technologies have allowed entire nuclear genomes to be shotgun sequenced from ancient DNA (aDNA) extracts. Nonetheless, targeted analyses of specific genomic loci will remain an important tool for future aDNA studies. DNA capture ...

Here I describe the use of a recently developed technique for targeted high-throughput sequencing of highly degraded DNA by direct multiplex PCR sequencing (DMPS) that was used to amplify 31 near-complete mitochondrial genomes of the extinct cave bear (Ursus spelaeus). DMPS couples mul ...

Entering into the world of ancient DNA research is nontrivial. Because the DNA in most ancient specimens is degraded to some extent, the potential for contamination of ancient samples and DNA extracts with modern DNA is considerable. To minimize the risk associated with working with ancient D ...

Molecular barcoding is an essential tool to use the high throughput of next generation sequencing platforms optimally in studies involving more than one sample. Various barcoding strategies allow for the incorporation of short recognition sequences (barcodes) into sequencing l ...

Next-generation sequencing (NGS) has revolutionized ancient DNA research, especially when combined with high-throughput target enrichment methods. However, attaining high sequencing depth and accuracy from samples often remains problematic due to the damaged state of anc ...

Multiplex PCR allows the simultaneous amplification of up to dozens of target fragments in a single PCR. It is therefore a powerful tool to obtain many kilobases of continuous sequence from minute amounts of ancient DNA (aDNA), which usually must be amplified in multiple short and overlapping f ...

Quantitative real-time PCR (qPCR) is a technique that is widely used in the field of ancient DNA (aDNA). Quantitative PCR can be used to optimize aDNA extraction methodologies, to detect PCR inhibition, and to quantify aDNA libraries for use in high-throughput sequencing. In this chapter, we out ...

PCR amplification of DNA is routine in modern molecular biology. However, the application of PCR to ancient DNA (aDNA) experiments often requires significant modification to standard protocols. The degraded nature of most aDNA fragments requires targeting shorter fragments, per ...

A major challenge for ancient DNA (aDNA) studies using museum specimens is that sampling procedures usually involve at least the partial destruction of each specimen used, such as the removal of skin, pieces of bone, or a tooth. Recently, a nondestructive DNA extraction method was developed for t ...

Natural history museums around the world hold millions of animal and plant specimens that are potentially amenable to genetic analyses. With more and more populations and species becoming extinct, the importance of these specimens for phylogenetic and phylogeographic analyses is r ...

Warm, humid regions are not ideal for long-term DNA preservation. Consequently, little ancient DNA research has been carried out involving taxa that lived in, for example, tropical and subtropical regions. Those studies that have isolated ancient DNA from warm environments have mostly b ...

The principal challenges facing PCR-based analyses of DNA extracted from formalin-fixed materials are fragmentation of the DNA and cross-linked protein–DNA complexes. Here, we present an efficient protocol to extract DNA from formalin-fixed or paraffin-embedded tissues (FFP ...

A variety of protocols for DNA extraction from archaeological and paleobotanical plant specimens have been proposed. This is not surprising given the range of taxa and tissue types that may be preserved and the variety of conditions in which that preservation may take place. Commercially av ...

Comprehensive two-dimensional gas chromatography – time-of-flight mass spectrometry (GC � GC–TOF-MS) is applied to the comparative metabolic fingerprinting of physiological fluids. Stable isotope-labeled internal standards plus norvaline serve as extraction standa ...

The field of metabolomics has become increasingly important in the context of functional genomics. Together with other ”omics“ data, the investigation of the metabolome is an essential part of systems biology. Beside the analysis of human and animal biofluids, the investigation of the mi ...

NMR-based metabolomics is an analytical platform, which has been used to classify and analyze Cannabis sativa L. cell suspension cultures and plants. Diverse groups of primary and secondary metabolites were identified by comparing NMR data with reference compounds and/or by structu ...

In many RNA silencing applications, there is a benefit to expressing multiple interfering RNAs simultaneously. This can be achieved by using a single RNA polymerase II promoter to express multiple micro(mi)RNA-formatted interfering RNAs that are arranged in a polycistronic cluster, ...