The Arabidopsis sog1-1 (suppressor of gamma response) mutant was originally isolated as a second-site suppressor of the radiosensitive phenotype of seeds defective in the repair endonuclease XPF. Here, we report that SOG1 encodes a putative transcription factor. This gene is a member of the NAC domain [petunia NAM (no apical meristem) and Arabidopsis ATAF1,2 and CUC2] family (a family of proteins unique to land plants). Hundreds of genes are normally up-regulated in Arabidopsis within an hour of treatment with ionizing radiation; the induction of these genes requires the damage response protein kinase ATM, but not the related kinase ATR. Here, we find that SOG1 is also required for this transcriptional up-regulation. In contrast, the SOG1-dependent checkpoint response observed in xpf mutant seeds requires ATR, but does not require ATM. Thus, phenotype of the sog1-1 mutant mimics aspects of the phenotypes of both atr and atm mutants in Arabidopsis, suggesting that SOG1 participates in pathways governed by both of these sensor kinases. We propose that, in plants, signals related to genomic stress are processed through a single, central transcription factor, SOG1.Arabidopsis ͉ ATM ͉ ATR ͉ checkpoint response ͉ XPF
The interactions between biotin and avidin or streptavidin, a prototypical example of a specific biological
ligand−receptor system, were studied by atomic force microscopy (AFM), X-ray photoelectron spectroscopy
(XPS), and time-of-flight secondary ion mass spectrometry (TOF-SIMS). Although this and other ligand−receptor systems have been studied by several techniques, including AFM, in this paper, a statistical
analysis method which makes use of the properties of the Poisson distribution was applied, and the rupture
strength of an individual interaction was obtained from the total adhesion forces measured by the AFM.
Tip- and surface-modification chemistries were investigated by XPS and TOF-SIMS. The magnitudes of
the interactions between biotin−avidin and biotin-streptavidin pairs, as determined by the Poisson method,
were found to be 173 ± 19 and 326 ± 33 pN, respectively, for loading rates between 2 × 105 and 8 × 105
pN·s-1. These values are comparable to the values reported by other groups for the same systems. The
statistical method used in this work has several advantages. It requires no assumptions about the surface
energies or contact area between the AFM tip and the substrate, it is not limited by the force resolution
of the instrument, and the number of measurements required to extract the individual unbinding force
is significantly lower than that required by other methods.
It has been found that a common shipping and packaging material for commercial AFM cantilever tips, poly(dimethylsiloxane) (PDMS), causes a thin layer of silicone oil contamination on AFM cantilever tips. Due to the similarity of elemental compositions between silicone oils and AFM cantilevers (both contain silicon and oxygen), it is difficult to detect such contaminants with the widely used surface characterization technique, X-ray photoelectron spectroscopy (XPS), since XPS provides mainly elemental and short-range chemical information. However, by using static time-of-flight secondary-ion mass spectrometry (TOF-SIMS), a technique that is extremely surface-sensitive, silicone oils on AFM cantilevers can easily be identified by their molecular fragments. A simple dip cleaning procedure using a mixture of concentrated sulfuric acid and hydrogen peroxide (piranha solution) was found to be an easy and effective way to remove organic contamination, including silicone oils, from AFM cantilever tips. It has also been shown, in both XPS and TOF-SIMS spectra, that a small amount of Au is present on the tip side of AFM cantilevers. This is most likely due to thermal diffusion of Au during the deposition of Au on the back side of the cantilevers, placed there to enhance laser reflectivity in the detection system of AFM instruments. No simple dipping approach was found to remove Au contamination on the tip side without also damaging the required Au coating on the back side of the cantilevers.
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