Methods and applications of three-color confocal imaging

Global modules robustly emerge from local interactions and smooth gradients

Modular structure and function are ubiquitous in biology, from the organization of animal brains and bodies to the scale of ecosystems. However, the mechanisms of modularity emergence from non-modular precursors remain unclear. Here we introduce the principle of peak selection, a process by which purely local interactions and smooth gradients can drive the self-organization of discrete global modules. The process combines strengths of the positional and Turing pattern-formation mechanisms into a model for morphogenesis. Applied to the grid-cell system of the brain, peak selection results in the self-organization of functionally distinct modules with discretely spaced spatial periods. Applied to ecological systems, it results in discrete multispecies niches and synchronous spawning across geographically distributed coral colonies. The process exhibits self-scaling with system size and 'topological robustness'1, which renders module emergence and module properties insensitive to most parameters. Peak selection ameliorates the fine-tuning requirement for continuous attractor dynamics in single grid-cell modules and it makes a detail-independent prediction that grid module period ratios should approximate adjacent integer ratios, providing a highly accurate match to the available data. Predictions for grid cells at the transcriptional, connectomic and physiological levels promise to elucidate the interplay of molecules, connectivity and function emergence in brains.

Photoperiodic regulation of the orexigenic effects of ghrelin in Siberian hamsters

Animals living in temperate climates with predictable seasonal changes in food availability may use seasonal information to engage different metabolic strategies. Siberian hamsters decrease costs of thermoregulation during winter by reducing food intake and body mass in response to decreasing or short-day lengths (SD). These experiments examined whether SD reduction in food intake in hamsters is driven, at least in part, by altered behavioral responses to ghrelin, a gut-derived orexigenic peptide which induces food intake via NPY-dependent mechanisms. Relative to hamsters housed in long-day (LD) photoperiods, SD hamsters consumed less food in response to i.p. treatment with ghrelin across a range of doses from 0.03 to 3 mg/kg. To determine whether changes in photoperiod alter behavioral responses to ghrelin-induced activation of NPY neurons, c-Fos and NPY expression were quantified in the arcuate nucleus (ARC) via double-label fluorescent immunocytochemistry following i.p. treatment with 0.3 mg/kg ghrelin or saline. Ghrelin induced c-Fos immunoreactivity (-ir) in a greater proportion of NPY-ir neurons of LD relative to SD hamsters. In addition, following ghrelin treatment, a greater proportion of ARC c-Fos-ir neurons were identifiable as NPY-ir in LD relative to SD hamsters. Changes in day length markedly alter the behavioral response to ghrelin. The data also identify photoperiod-induced changes in the ability of ghrelin to activate ARC NPY neurons as a possible mechanism by which changes in day length alter food intake.

Intracellular trafficking and degradation of unassociated proalpha2 chains of collagen type I

Procollagen I is a trimer consisting of two proalpha1(I) chains and one proalpha 2(I) chain. In certain cases of mild osteogenesis imperfecta, abnormal proalpha1(I) chains are degraded very soon after synthesis. As a consequence, the cells produce excess proalpha2(I) chains, which cannot form trimers and are not secreted. The objective of this work was to determine the intracellular fate of unassociated proalpha2(I) chains. Mov13 mouse fibroblasts, which do not synthesize proalpha1(I) mRNA, but do produce proalpha2(I) mRNA, were incubated with radioactive amino acids using pulse-chase protocols, and proteins were analyzed by gel electrophoresis, autoradiography, and Western blotting. Mov13 cells produced proalpha2(I) chains that were degraded intracellularly within 30 min. Degradation was inhibited when cells were treated with brefeldin-A, which blocks transit from endoplasmic reticulum to Golgi. Fixed cells exposed to various immunofluorescence markers and imaged by confocal laser scanning microscopy showed that proalpha2(I) chains colocalized with Golgi and lysosome markers. Degradation was inhibited and chains were secreted when cells were treated with wortmannin, which blocks trafficking to lysosomes. These results demonstrate that unassociated proalpha2(I) chains leave the endoplasmic reticulum, transit the Golgi, and enter lysosomes where they are degraded.

Automated high through-put colocalization analysis of multichannel confocal images

The laser scanning confocal microscope (LSCM) generates images of multiple labelled fluorescent samples. Colocalization of fluorescent labels is frequently examined. Here we present an example where localization of fluorescent analogues of cloned protein were referenced to fluorescent antibodies directed against the proteins of cellular compartments. Colocalization is usually evaluated by visual inspection of signal overlap or by using commercially available software tools, but there are limited possibilities to automate the analysis of large amounts of data. We developed a simple tool using Matlab to automate the colocalization procedure and to exclude the biased estimations resulting from visual inspections of images. The script in Matlab language code automatically imports confocal images and converts them into arrays. The contrast of all images is uniformly set by linearly reassigning the values of pixel intensities to use the full 8-bit range (0-255). Images are binarized on several threshold levels. The area above a certain threshold level is summed for each channel of the image and for colocalized regions. As a result, count of pixels above several threshold levels in any number of images is saved in an ASCII file. In addition Pearson's r correlation coefficient is calculated for fluorescence intensities of both confocal channels. Using this approach quick quantitative analysis of colocalization of hundreds of images is possible. In addition, such automated procedure is not biased by the examiner's subject visualization.

Association of Vpu-binding protein with microtubules and Vpu-dependent redistribution of HIV-1 Gag protein

The efficient exit of HIV-1 particles from cells requires the action of the viral encoded protein Vpu. Vpu-binding protein (Ubp) is a cellular protein that interacts with both Vpu and the major structural component of the viral capsid (Gag) and appears to affect the efficiency of particle exit. Elucidation of the function of Ubp and characterization of the spatial distribution of Ubp may provide information pertinent to understanding the role of Ubp in virus replication. To investigate the subcellular location of Ubp, and to see whether Vpu affects the intracellular distribution of Gag, we carried out immunofluorescence localization in conjunction with confocal microscopy. Based on this analysis Ubp is present in both the nucleus and the cytoplasm. In the cytoplasm, Ubp appeared to be associated with microtubules as evidenced by cofluorescence with tubulin in the absence and in the presence of colchicine. However, cytoskeletal isolation and detergent extraction of cells resulted in association of Ubp with the soluble fractions, indicating that Ubp is not in tight association with microtubules. Moreover, flotation gradient analysis demonstrated that Ubp is cytoplasmic and not stably associated with the plasma membrane. Interestingly, expression of Vpu in cells resulted in redistribution of both Ubp and Gag to a location near the periphery of the cell. The effect of Vpu on both Ubp and Gag protein has implications for Vpu-mediated particle exit from cells.

Localization of procollagen I in the lysosome/endosome system of human fibroblasts

A significant amount of newly synthesized collagen is degraded intracellularly rather than secreted, but there is controversy about whether this process occurs in the lysosomes. We addressed this problem using confocal microscopy and immunofluorescence imaging to study the distribution of procollagen I in the Golgi and the lysosome/endosome system of cultured human fibroblasts. Cells were incubated under basal conditions and then permeabilized and exposed to fluorescently tagged probes for procollagen, Golgi markers (Helix pomatia binding protein or beta-coatamer protein), and lysosome/endosome markers (cathepsin B or LAMP-2). Strong signals for procollagen codistributed with the Golgi and lysosome/endosome markers. Of note, many structures were positive for procollagen and lysosome/endosome markers but not for Golgi markers. When cells were incubated with the proline analog cis-hydroxyproline, which inhibits correct triple helix formation and increases intracellular degradation, the amount of procollagen codistributing with the lysosome/endosome markers increased greatly. Similar results were obtained in I-cells, which do not have functioning lysosomal hydrolases. These findings strongly indicate that the lysosome/endosome system participates in the intracellular degradation of newly synthesized procollagen and that trafficking of procollagen to the lysosome/endosome system does not depend on the cells having active lysosomal hydrolases. We present a model that integrates our findings with other work and resolves inconsistencies in the literature. This model postulates the existence of three separate degradation paths for newly synthesized procollagen. In addition to the endosome/lysosome system, degradation also takes place in the proximal region of the secretory pathway such as the endoplasmic reticulum, cis-Golgi network, or cis-Golgi and in a distal region of the secretory pathway such as the trans-Golgi or trans-Golgi network.

Imaging techniques: picture the world with kaleidoscope dyes

Advances in fluorescence light microscopy have facilitated the production of images from multiply labeled specimens.