Investigating the cosmic-ray ionization rate in the galactic interstellar medium through observations of H3+

Observations of H3+ in the Galactic diffuse interstellar medium (ISM) have led to various surprising results, including the conclusion that the cosmic-ray ionization rate (zeta_2) is about 1 order of magnitude larger than previously thought. The present survey expands the sample of diffuse cloud sight lines with H3+ observations to 50, with detections in 21 of those. Ionization rates inferred from these detections are in the range (1.7+-1.0)x10^-16 s^-1 < zeta_2 < (10.6+-6.8)x10^-16 s^-1 with a mean value of zeta_2=(3.3+-0.4)x10^-16 s^-1. Upper limits (3sigma) derived from non-detections of H3+ are as low as zeta_2 < 0.4x10^-16 s^-1. These low upper-limits, in combination with the wide range of inferred cosmic-ray ionization rates, indicate variations in zeta_2 between different diffuse cloud sight lines. Calculations of the cosmic-ray ionization rate from theoretical cosmic-ray spectra require a large flux of low-energy (MeV) particles to reproduce values inferred from observations. Given the relatively short range of low-energy cosmic rays --- those most efficient at ionization --- the proximity of a cloud to a site of particle acceleration may set its ionization rate. Variations in zeta_2 are thus likely due to variations in the cosmic-ray spectrum at low energies resulting from the effects of particle propagation. To test this theory, H3+ was observed in sight lines passing through diffuse molecular clouds known to be interacting with the supernova remnant IC 443, a probable site of particle acceleration. Where H3+ is detected, ionization rates of zeta_2=(20+-10)x10^-16 s^-1 are inferred, higher than for any other diffuse cloud. These results support both the concept that supernova remnants act as particle accelerators, and the hypothesis that propagation effects are responsible for causing spatial variations in the cosmic-ray spectrum and ionization rate. Future observations of H3+ near other supernova remnants and in sight lines where complementary ionization tracers (OH+, H2O+, H3O+) have been observed will further our understanding of the subject.

Exploring protein-RNA interactions with site-directed mutagenesis and phage display

The importance of RNA as a mediator of genetic information is widely appreciated. RNA molecules also participate in the regulation of various post-transcriptional activities, such as mRNA splicing, editing, RNA stability and transport. Their regulatory roles for these activities are highly dependent on finely tuned associations with cognate proteins. The RNA recognition motif (RRM) is an ancient RNA binding module that participates in hundreds of essential activities where specific RNA recognition is required. We have applied phage display and site-directed mutagenesis to dissect principles of RRM-controlled RNA recognition. The model systems we are investigating are U1A and CUG-BP1. In this dissertation, the molecular basis of the binding affinity of U1A-RNA beyond individual contacts was investigated. We have identified and evaluated the contributions of the local cooperativity formed by three neighboring residues (Asn15, Asn16 and Glu19) to the stability of the U1A-RNA complex. The localized cooperative network was mapped by double-mutant cycles and explored using phage display. We also showed that a cluster of these residues forms a “hot spot” on the surface of U1A; a single substitution at position 19 with Gln or His can alter the binding properties of U1A to recognize a non-cognate G4U RNA. Finally, we applied a deletion analysis of CUG-BP1 to define the contributions of individual RRMs and RRM combinations to the stability of the complex formed between CUG-BP1 and the GRE sequence. The preliminary results showed RRM3 of CUG-BP1 is a key domain for RNA binding. It possibly binds to the GRE sequence cooperatively with RRM2 of CUG-BP1. RRM1 of CUG-BP1 is not required for GRE recognition, but may be important for maintaining the stability of the full-length CUG-BP1.