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Riboswitches are structured elements located in the 5'-untranslated regions of numerous bacterial mRNAs that serve to regulate gene expression via their ability to specifically bind metabolites. The purine riboswitch ligand-binding domain has emerged as an important model system for investigating the relationship between RNA structure and function. Directed by NMR and crystallographically generated structures of this RNA, a variety of biophysical and biochemical techniques have been utilized to understand its dynamic nature. In this review, we describe these various approaches and what they reveal about the purine riboswitch. Abbreviations 2AP 2-aminopurine; FRET fluorescence resonance energy transfer; J joining region; L loop; NMIA N-methylisatoic anhydride; SHAPE selective 2'-hydroxyl acylation analyzed by primer extension; smFRET single molecule fluorescence reso- nance energy transfer; TPP thiamine pyrophosphate; UTR untranslated region

Riboswitches are highly structured cis-acting elements located in the 5′-untranslated region of messenger RNAs that directly bind small molecule metabolites to regulate gene expression. Structural and biochemical studies have revealed riboswitches experience significant ligand-dependent conformational changes that are coupled to regulation. To monitor the coupling of ligand binding and RNA folding within the aptamer domain of the purine riboswitch, we have chemically probed the RNA with N-methylisatoic anhydride (NMIA) over a broad temperature range. Analysis of the temperature-dependent reactivity of the RNA in the presence and absence of hypoxanthine reveals that a limited set of nucleotides within the binding pocket change their conformation in response to ligand binding. Our data demonstrate that a distal loop–loop interaction serves to restrict the conformational freedom of a significant portion of the three-way junction, thereby promoting ligand binding under physiological conditions.

Riboswitches are recently discovered genetic regulatory elements found in the 5'-untranslated regions of bacterial mRNAs that act through their ability to specifically bind small-molecule metabolites. Binding of the ligand to the aptamer domain of the riboswitch is communicated to a second domain, the expression platform, which directs transcription or translation of the mRNA. To understand this process on a molecular level, structures of three of these riboswitches bound to their cognate ligands have been solved by X-ray crystallography: the purine, thiamine pyrophosphate (TPP), and S-adenosylmethionine (SAM-I) binding aptamer domains. These studies have uncovered three common themes between the otherwise different molecules. First, the natural RNA aptamers recognize directly or indirectly almost every feature of their ligand to achieve extraordinary specificity. Second, all of these RNAs use a complex tertiary architecture to establish the binding pocket. Finally, in each case, ligand binding serves to stabilize a helix that communicates the binding event to the expression platform. Here, we discuss these properties of riboswitches in the context of the purine and SAM-I riboswitches.

Post mortem tissue from stranded marine mammals is met with skepticism when utilized in biochemical assays. Degradation of muscle proteins and enzymes are not well defined. Given the protected nature and value of diving mammal samples, a quantitative analysis of degradation is valuable and presented here., As marine divers, pinnipeds have a high capacity for exercise at depth while holding their breath. With finite access to oxygen, these species need to be capable of extended aerobic exercise and conservation of energy. Pinnipeds must deal with common physiological hurdles, such as hypoxia, exhaustion and acidosis, that are common to all exercising mammals. The physiological mechanisms in marine mammals used for managing oxygen and carbon dioxide have sparked much research, but access to animals and tissues is difficult and requires permits. Deceased animals that are either bycaught or stranded provide one potential source for tissues, but the validity of biochemical data from post-mortem samples has not been rigorously assessed. Tissues collected from stranded diving mammals may be a crucial source to add to our limited knowledge on the physiology of some of these animals and important to the conservation and management of these species. We aim to determine the reliability of biochemical assays derived from post-mortem tissue and to promote the immediate sampling of stranded animals for the purpose of physiological research. In this study, we mapped the temporal degradation of muscle enzymes from biopsied Northern elephant seals (Mirounga angustirostris) and highlight recommendations for storage protocols for the best preservation of tissue. We also compared the enzymatic activity of different muscle groups (pectoral and latissimus dorsi) in relation to locomotion and measured the effects of four freeze–thaw cycles on muscle tissue enzyme function. Results indicate that enzymatic activity fluctuates greatly, especially with varying storage temperature, storage time, species and muscle group being assayed. In contrast, proteins, such as myoglobin, remain relatively continuous in their increase at 4°C for 48 h. Stranded animals can be a valuable source of biochemical data, but enzyme assays should be used only with great caution in post-mortem tissues.

The phenomenon of firm visits by government officials has received almost no scholarly attention. In this paper, we use an event study to examine the stock market returns to firm visits by the Pres...

Combined emission-transmission imaging systems that perform both X-ray CT and SPECT have the potential to correlate anatomical and physical data, and to improve the accuracy of in vivo radiopharmaceutical quantitation. A detection system suitable for the combined CT/SPECT system must achieve both excellent energy resolution at low count rates for radionuclide imaging and must be compatible with the high flux rates and wide dynamic range encountered in X-ray imaging. We therefore are investigating the use of a pixellated CdZnTe for CT/SPECT imaging. Alternative electrode geometries of CdZnTe detectors for SPECT have been investigated with numerical simulation.

Much has been written about the value and use of theory in management and organizational studies. Many have also complained about the lack of clarity associated with a concept so central to our fie...

A medical imaging system providing both x-ray transmission and radionuclide measurements would allow correlation of structural and functional information. We therefore are evaluating a pixellated CdZnTe detector for combined x-ray CT and SPECT imaging with various readout electronics. Gamma-ray spectra of 57Co measured using NIM electronics (2-microsecond(s) shaping time) and multichannel fast photon-counting electronics (50-ns shaping time) produced energy resolutions of 6.5 keV FWHM and 17 keV FWHM respectively at 122 keV. Fast photon-counting electronics achieved linear x-ray count-rate response up to 4 X 105 cps. Dual-mode digital readout electronics are described, which promise to improve SPECT and x-ray CT performance in comparison to the fast-counting electronics. The leakage current and x-ray response with the dual-mode electronics are studied. The leakage current as small as tens of pA is measured, while detector current over 5 orders of magnitude is measured with linearity over 4 orders of magnitude. Results suggest that the CdZnTe detector is capable of performing both x-ray CT and SPECT with the fast photon-counting electronics, and the digital readout electronics can improve the x-ray CT performance.