Resonance Raman analysis of the Pr and Pfr forms of phytochrome

Resonance Raman vibrational spectra of the Pr and Pfr forms of oat phytochrome have been obtained at room temperature. When Pr is converted to Pfr, new bands appear in the C = C and C = N stretching region at 1622, 1599, and 1552 cm-1, indicating that a major structural change of the chromophore has occurred. The Pr to Pfr conversion results in an 11 cm-1 lowering of the N-H rocking band from 1323 to 1312 cm-1. Normal mode calculations correlate this frequency drop with a Z----E isomerization about the C15 = C16 bond. A line at 803 cm-1 in Pr is replaced by an unusually intense mode at 814 cm-1 in Pfr. Calculations on model tetrapyrrole chromophores suggest that these low-wavenumber modes are hydrogen out-of-plane (HOOP) wagging vibrations of the bridging C15 methine hydrogen and that both the intensity and frequency of the C15 HOOP mode are sensitive to the geometry around the C14-C15 and C15 = C16 bonds. The large intensity of the 814-cm-1 mode in Pfr indicates that the chromophore is highly distorted from planarity around the C15 methine bridge. If the Pr----Pfr conversion does involve a C15 = C16 Z----E isomerization, then the intensity of the C15 HOOP mode in Pfr argues that the chromophore has an E,anti conformation. On the basis of a comparison with the vibrational calculations, the low frequency (803 cm-1) and the reduced intensity of the C15 HOOP mode in Pr suggest that the chromophore in Pr adopts the C15-Z,syn conformation.     

Determining gene expression on a single pair of microarrays

Background  

In microarray experiments the numbers of replicates are often limited due to factors such as cost, availability of sample or poor hybridization. There are currently few choices for the analysis of a pair of microarrays where N = 1 in each condition. In this paper, we demonstrate the effectiveness of a new algorithm called PINC (PINC is Not Cyber-T) that can analyze Affymetrix microarray experiments.     

Vaccinia virus infection and gene transduction in cultured neurons

The study of neurons in culture would benefit from the development of a gene transduction system capable of delivering foreign genes at high efficiency, as transduction of primary neurons with existing systems is inefficient. The efficacy of lytic vaccinia virus (VV) infection of primary retinal cultures and PC12 cells (a model of neuronal differentiation) was examined in order to determine the efficiency of gene transduction using VV in neuronal primary culture. VV was able to infect retinal cells and PC12 cells and express transgenes of Escherichia coli beta-galactosidase (lacZ) and epithelial fatty acid binding protein (E-FABP) in a virus dose-dependent manner. Most (50-100%) of the retinal cells were positive for transgene protein at multiplicities of infection (MOI) between 10 and 100 plaque-forming units (PFU), while over 50% of VV-infected PC12 cells expressed the virus encoded gene at an MOI = 10. The production of foreign mRNA and protein by VV following infection was verified by PCR and Western blot. Because VV is a lytic virus, cytopathic effects were examined. Retinal cultures maintained for 0.5 days in vitro showed greater than 90% survival at 24 h post-infection, while 14-day cultures were equally viable for 48 h. Retinal ganglion cells and differentiated PC12 cells appear to be more protected against lytic VV infection than proliferating glial and undifferentiated PC12 cells. These data suggest that VV may be a useful vector for delivering foreign genes to neuronal cells with an efficient transient transgene expression.