Optical molecular imaging for systems biology: from molecule to organism

Abstract

The development of highly efficient analytical methods capable of probing biological systems at system level is an important task that is required in order to meet the requirements of the emerging field of systems biology. Optical molecular imaging (OMI) is a very powerful tool for studying the temporal and spatial dynamics of specific biomolecules and their interactions in real time in vivo. In this article, recent advances in OMI are reviewed extensively, such as the development of molecular probes that make imaging brighter, more stable and more informative (e.g., FPs and semiconductor nanocrystals, also referred to as quantum dots), the development of imaging approaches that provide higher resolution and greater tissue penetration, and applications for measuring biological events from molecule to organism level, including gene expression, protein and subcellular compartment localization, protein activation and interaction, and low-mass molecule dynamics. These advances are of great significance in the field of biological science and could also be applied to disease diagnosis and pharmaceutical screening. Further developments in OMI for systems biology are also proposed.

Imaging the glycome

“…Indeed, when mammalian cell lines are incubated with Ac 4 ManNAz, SiaNAz replaces 4-41% of natural sialic acids (71). Ac 4 ManNAz has been used to visualize sialic acids in a diverse range of cell types (71), as well as living mice (72) and zebrafish (73). Alkynyl ManNAc has been used to visualize sialic acids on human cancer cell lines and for glycoproteomic analysis of labeled glycoproteins (68, 74).…”

“…Per-O-acetylated N-azidoacetylglucosamine (Ac 4 GlcNAz) (78) is modified by the GlcNAc salvage pathway enzymes to form UDP-GlcNAz, which is used as a substrate by the cytosolic O-GlcNAc transferase. Alternatively, Ac 4 GalNAz is metabolized to form UDP-GalNAz, which can be converted to UDP-GlcNAz in situ by an epimerase (79). Ac 4 GlcNAz has been used for the identification of O-GlcNAc-modified proteins in cell lysates (78) and Ac 4 GalNAz has been used to image nuclear O-GlcNAc-modified proteins in cultured cells (M. J. Hangauer and C.R.B., unpublished work).…”

Current standing and future prospects for the technologies proposed to transform toxicity testing in the 21st century

“…But more complex systems, such as differentiated stem cells, primary cells, and non-mammalian organisms are increasingly used because they often provide more relevant information for toxicity predictions (Fernandes et al, 2009 (Morris, 2010). Besides confirming the occurrence of these processes, imaging can provide valuable insight into their spatial and temporal dynamics (Du et al, 2006). Therefore imaging can complement genomics, proteomics, and metabolomics studies, adding valuable information to the systems biology approach (Lee and Li, 2009).…”

Three-dimensional fuse deposition modeling of tissue-simulating phantom for biomedical optical imaging

“…In the wavelength range from ultraviolet to infrared, the primary absorption components in biological tissue include water, hemoglobin, blood sugar, pigment, and lipid; while the primary scattering components include protein, fat, and mitochondria. 1,2 It has been shown that optical phantoms are able to simulate important optical parameters of biological tissues, such as refractive index, absorption coefficient, scattering coefficient, and anisotropy. 3 A typical optical phantom is composed of the base, the scattering, and the absorption materials.…”