Methods in Molecular Biology
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Blood-based assay with secreted Gaussia luciferase to monitor tumor metastasis.
Only a few techniques are currently available for quantifying systemic metastases in preclinical models. Cancer cell expression of naturally secreted Gaussia luciferase (Gluc) provides a useful circulating biomarker that enables the monitoring of metastatic tumor burden and of treatment response fro...
Cell Assessment by At-line Microscopy.
This protocol regards a microscopic application and software for image-guided monitoring of mammalian cells which grow in suspension cultures. It has been developed in order to establish an automated microscopic application for in situ and at-line cell monitoring in bioreactors (Akin et al., Biosens...
Single-copy quantification of HIV-1 in clinical samples.
We describe in detail an assay for HIV-1 RNA with single-copy sensitivity....
Identification and use of fluorescent dyes for plant cell wall imaging using high-throughput screening.
We describe a technique for screening fluorescent compound libraries for enhanced fluorescence upon interaction with plant cell walls, a secondary screening method to identify which cell wall components interact with a given dye, and a protocol for staining and observing Arabidopsis seedlings using...
The use of multidrug approach to uncover new players of the endomembrane system trafficking machinery.
Chemical Biology is a strong tool to perform experimental procedures to study the Endomembrane System (ES) in plant biology. In the last few years, several bioactive compounds and their effects upon protein trafficking as well as organelle distribution, identity, and size in plants and yeast have be...
We provide a brief review of the variations in ChIP assays and a detailed explanation of the basic standard ChIP protocol....
Image analysis: basic procedures for description of plant structures.
This chapter gives examples of basic procedures of quantification of plant structures with the use of image analysis, which are commonly employed to describe differences among experimental treatments or phenotypes of plant material. Tasks are demonstrated with the use of ImageJ, a widely used public...
Soybean, the world's most widely grown seed legume, is an important global source of vegetable oil and protein. Though, complete draft genome sequence of soybean is now available, but functional genomics studies remain in their infancy, as this agricultural legume species exhibits genetic constrains...
Predicting RNA structure: advances and limitations.
We present recent methods to assess the folding kinetics of an RNA via 2D projections of the energy landscape, identification of local minima and energy barriers, or simulation of RNA folding as a Markov process....
Frequency domain fluorometry: theory and application.
Frequency domain fluorometry is a widely utilized tool in the physical, chemical, and biological sciences. This chapter focuses on the theory of the method and the practical aspects required to carry out intensity decay, i.e., lifetime measurements on a modern frequency domain fluorometer. Several c...