SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments

Footprinting is a powerful and widely used tool for characterizing the structure, thermodynamics, and kinetics of nucleic acid folding and ligand binding reactions. However, quantitative analysis of the gel images produced by footprinting experiments is tedious and time-consuming, due to the absence of informatics tools specifically designed for footprinting analysis. We have developed SAFA, a semi-automated footprinting analysis software package that achieves accurate gel quantification while reducing the time to analyze a gel from several hours to 15 min or less. The increase in analysis speed is achieved through a graphical user interface that implements a novel methodology for lane and band assignment, called "gel rectification," and an optimized band deconvolution algorithm. The SAFA software yields results that are consistent with published methodologies and reduces the investigator-dependent variability compared to less automated methods. These software developments simplify the analysis procedure for a footprinting gel and can therefore facilitate the use of quantitative footprinting techniques in nucleic acid laboratories that otherwise might not have considered their use. Further, the increased throughput provided by SAFA may allow a more comprehensive understanding of molecular interactions. The software and documentation are freely available for download at http://safa.stanford.edu.     

Regulatory T cell responses: potential role in the control of atherosclerosis

PURPOSE OF REVIEW: Atherosclerosis is an inflammatory disease of the arterial wall where both innate and adaptive Th1-driven immunoinflammatory responses contribute to disease development. Th2-related responses have been shown to be either protective or pathogenic. Thus, it is unclear whether immunoregulatory activity can modulate disease development. RECENT FINDINGS: Novel subtypes of T cells, called the regulatory T cells, have been shown recently to play a critical role in the maintenance of immunological tolerance against self and non-self antigens and prevent the development of various immunoinflammatory diseases. Preliminary studies suggest a potential role for this type of regulatory T cell response in atherosclerosis. SUMMARY: Here we present a novel view of the immunoinflammatory response in atherosclerosis where natural and/or adaptive regulatory T cell responses modulate both Th1 and Th2 pathogenic responses and play a central role in counteracting disease initiation and progression.     

Bienzyme HRP-GOx-modified gold nanoelectrodes for the sensitive amperometric detection of glucose at low overpotentials

Gold nanotubular electrode ensembles were prepared by using electroless deposition of the metal within the pores of polycarbonate track-etched membranes. Mono-enzyme (GOx) and monolayer/bilayer bienzyme (GOx/HRP) bioelectrodes were prepared by immobilizing the enzymes onto gold nanotubes surfaces modified with mercaptoethylamine. Batch amperometric responses to glucose for the different bioelectrodes were determined and compared. The response of the two geometries (monolayer and bilayer) of the bienzyme electrodes was shown to vary with regard to sensitivity at detection potentials above 0V. On the contrary, at detection potentials below 0V, no noticeable influence of the configuration of the bienzyme on the response intensity was observed. The mono-enzyme (650 microAmM-1 in benzoquinone (BQ) at -0.8 V versus Ag/AgCl) and the two bienzyme bioelectrodes (+/-400 microAmM-1 in hydroquinone (H2Q) at -0.2V versus Ag/AgCl) display remarkable sensitivities compared to a classical GOx-modified gold macroelectrode (13 microAmM-1 in BQ at -0.8 V versus Ag/AgCl). A remarkable feature of the bienzyme electrodes is the possibility to detect glucose at very low applied potentials where the noise level and interferences from other electro-oxidizable compounds are minimal. Another important characteristic of the monolayer bienzyme electrode is the possible existence of a direct electronic communication between HRP and the transducer surface.     

Fusogenic Alzheimer's peptide fragment Abeta (29-42) in interaction with lipid bilayers: secondary structure, dynamics, and specific interaction with phosphatidyl ethanolamine polar heads as revealed by solid-state NMR

The interaction of the native Alzheimer's peptide C-terminal fragment Abeta (29-42), and two mutants (G33A and G37A) with neutral lipid bilayers made of POPC and POPE in a 9:1 molar ratio was investigated by solid-state NMR. This fragment and the lipid composition were selected because they represent the minimum requirement for the fusogenic activity of the Alzheimer's peptide. The chemical shifts of alanine methyl isotropic carbon were determined by MAS NMR, and they clearly demonstrated that the major form of the peptide equilibrated in membrane is not in a helical conformation. (2)H NMR, performed with acyl chain deuterated POPC, demonstrated that there is no perturbation of the acyl chain's dynamics and of the lipid phase transition temperature. (2)H NMR, performed with alanine methyl-deuterated peptide demonstrated that the peptide itself has a limited mobility below and above the lipid phase transition temperature (molecular order parameter equal to 0.94). MAS (31)P NMR revealed a specific interaction with POPE polar head as seen by the enhancement of POPE phosphorus nuclei T(2) relaxation. All these results are in favor of a beta-sheet oligomeric association of the peptide at the bilayer interface, preferentially recruiting phosphatidyl ethanolamine polar heads.     

Undistorted structural analysis of soluble proteins by attenuated total reflectance infrared spectroscopy

Water from the solvent very strongly absorbs light in the frequency range of interest for studying protein structure by infrared (IR) spectroscopy. This renders handling of the observation cells painstaking and time consuming, and limits the reproducibility of the measurements when IR spectroscopy is applied to proteins in aqueous solutions. These difficulties are circumvented by the use of an Attenuated Total Reflectance (ATR) accessory. However, when protein solutions are studied, ATR spectroscopy suffers from several drawbacks, the most severe being nonproportionality of the observed absorbance with the protein concentration and spectral distortions that vary from protein to protein and from sample to sample. In this study, we show (1) that the nonproportionality is due to adsorption of the protein on the ATR crystal surface; (2) that the contribution of the crystal-adsorbed protein can easily be taken into account, rendering the corrected absorbance proportional to the protein concentration; (3) that the observed variable base line distortions, likely due to changes in the penetration depth of the light beam in solutions with the refractive index that depends on the protein concentration, can be easily eliminated; and (4) that ATR IR spectra thus corrected for protein adsorption and light penetration can be used to properly analyze the secondary structure of proteins in solution.     

Crossing species' range borders: interspecies gene exchange mediated by hybridogenesis

The distribution of species is limited by their ability to adapt to local environments. For adaptation by selection, genetic variability is crucial. As founder effects reduce genetic variability, extension of species' range borders is usually slow due to the reduced probability of successful colonization. However, the range limit might be extended by incorporating locally adapted genes. In western Palaearctic waterfrogs, interspecies hybrids show hemiclonal gametogenesis, are fertile and reproductively mimic one parental species. Genetic analysis, using allozyme loci, shows that they mediate gene exchange between the two parental species. Selection analysis provides evidence for local adaptation of single locus genotypes. This suggests that hybridogenesis presents a process which increases the number of neoform parental genotypes, exposing these to selection, and thereby revealing locally adapted genotypes which are essential for species range expansion.     

Identification of clustered microRNAs using an <Emphasis Type="Italic">ab initio</Emphasis> prediction method

Background  

MicroRNAs (miRNAs) are endogenous 21 to 23-nucleotide RNA molecules that regulate protein-coding gene expression in plants and animals via the RNA interference pathway. Hundreds of them have been identified in the last five years and very recent works indicate that their total number is still larger. Therefore miRNAs gene discovery remains an important aspect of understanding this new and still widely unknown regulation mechanism. Bioinformatics approaches have proved to be very useful toward this goal by guiding the experimental investigations.