Template-directed interference footprinting for RNA based on inosine-specific cleavage

We report here the development of a Template-directed Interference (TDI) footprinting assay for RNA. The TDI nucleotide analogue inosine (I) lacks the exocyclic amine of G and is a suitable probe for the role of this group in RNA structure and function. Using an I-specific cleavage protocol we identified three functionally significant G residues in the Tetrahymena ribozyme. These residues are proximal to the active site of the folded intron and likely contribute to the positioning of substrates at the catalytic core.     

The impact of carbon footprinting aggregation on realizing emission reduction targets

A variety of activity-based methods exist for estimating the carbon footprint in transportation. For instance, the greenhouse gas protocol suggests a more aggregate estimation method than the Network for Transport and Environment (NTM) method. In this study, we implement a detailed estimation method based on NTM and different aggregate approaches for transportation carbon emissions in the dynamic lot sizing model. Analytical results show the limitations of aggregate models for both accurate estimation of real emissions and risks of compliance with carbon constraints (e.g., carbon caps). Extensive numerical experimentation shows that the magnitude of errors can be substantial. We provide insights under which limited conditions aggregate estimations can be used safely and when more detailed estimates are appropriate.     

Key issues and options in accounting for carbon sequestration and temporary storage in life cycle assessment and carbon footprinting

The International Journal of Life Cycle Assessment - Biological sequestration can increase the carbon stocks of non-atmospheric reservoirs (e.g. land and land-based products). Since this contained...     

Physiological concept for a blood based CFTR test.

We tested the hypothesis that the cystic fibrosis transmembrane conductance regulator (CFTR) could be involved in the volume regulation of human red blood cells (RBC). Experiments were based on two gadolinium (Gd(3+)) sensitive mechanisms, i.e. inhibition of ATP release (thetaATP(i)) and membrane destabilization. RBC of either cystic fibrosis (CF) patients or healthy donors (non-CF) were exposed to KCl buffer containing Gd(3+). A significantly larger quantity of non-CF RBC (2.55 %) hemolyzed as compared to CF RBC (0.89 %). It was found that both of the Gd(3+) mechanisms simultaneously are needed to achieve hemolysis, since either overriding thetaATP(i) by exogenous ATP addition prevented Gd(3+) induced hemolysis, or mimicking thetaATP(i) by apyrase in absence of Gd(3+) could not trigger hemolysis. Additionally, ion driven volume uptake was found to be a prerequisite for Gd3+ induced hemolysis as chloride and potassium channel blockers reduced the Gd(3+) response. The results show that in non-CF RBC Gd(3+) exerts its dual effect leading to hemolysis. On the contrary, in CF RBC, lacking CFTR dependent ATP release, the sole Gd(3+) effect of membrane destabilization is not sufficient to induce hemolysis similar to non-CF. This concept could form the basis of a novel method suitable for testing CFTR function in a blood sample.     

Phylogenetic footprinting: a boost for microbial regulatory genomics

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of homologous regulatory regions, usually collected from multiple species. It does so by identifying the best conserved motifs in those homologous regions. There are two popular sets of methods-alignment-based and motif-based, which are generally employed for phylogenetic methods. However, serious efforts have lacked to develop a tool exclusively for phylogenetic footprinting, based on either of these methods. Nevertheless, a number of software and tools exist that can be applied for prediction of phylogenetic footprinting with variable degree of success. The output from these tools may get affected by a number of factors associated with current state of knowledge, techniques and other resources available. We here present a critical apprehension of various phylogenetic approaches with reference to prokaryotes outlining the available resources and also discussing various factors affecting footprinting in order to make a clear idea about the proper use of this approach on prokaryotes.     

Development of an amperometric assay for phosphate ions in urine based on a chemically modified screen-printed carbon electrode

An amperometric assay for the determination of inorganic phosphate (Pi) in urine has been developed without the need for sample preparation. A screen-printed carbon electrode modified with the electrocatalyst cobalt phthalocyanine (CoPC–SPCE) and covered with a cellulose acetate membrane (CAM) serves as the sensor. The sensor detects hydrogen peroxide (H₂O₂), which is produced as a result of the oxidative decarboxylation of pyruvate, catalyzed by pyruvate oxidase (PyOd), in the presence of Pi, oxygen, and cofactors. Following optimization of solution conditions, and in the presence of a urine sample, a linear range was found to exist between the rate of current increase and phosphate concentration over the range of 2.27 × 10⁻⁵ to 1.81 × 10⁻⁴ M, and the limit of detection was found to be 4.27 × 10⁻⁶ M. The assay was applied to the determination of phosphate ions in the urine of a normal subject, and the mean concentration in unspiked urine was found to be 3.40 × 10⁻⁵ M with a coefficient of variation of 8.0% (n = 5). The mean recovery of phosphate added to urine samples was 98.7% with a coefficient of variation of 5.5% (n = 3). To the authors’ knowledge, this is the first report of an amperometric assay for Pi that incorporates a CoPC–SPCE as the sensing device.     

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.     

PERFILS: a program for the quantitative treatment of footprinting data

PERFILS, a computer program written in Borland TurboPascal,performs quantitative analysis of footprinting experiments usingany IBM PC or compatible microcomputer. The program uses theheight of the bands obtained from densitometric scanning offootprinting autoradiographs to calculate a differential cleavageplot. Such a plot displays, on a logarithmic scale, the differenceof susceptibility of a DNA fragment to DNase I, or any othercleaving agent, in the presence of any ligand versus the sequence.PERFILS calculates the fractional cleavage values for controland ligand, giving a table of values for each internucleotidicbond and rendering the differential cleavage plot in only afew seconds.     

A species concept for bacteria based on adaptive divergence

Bacterial strains are currently grouped into species based on overall genomic similarity and sharing of phenotypes deemed ecologically important. Many believe this polyphasic taxonomy is in need of revision because it lacks grounding in evolutionary theory, and boundaries between species are arbitrary. Recent taxonomy efforts using multilocus sequence typing (MLST) data are based on the identification of distinct phylogenetic clusters. However, these approaches face the problem of deciding the phylogenetic level at which clusters are representative of evolutionary or taxonomically distinct units. In this review, I propose classifying two phylogenetic clusters as separate species only when they have statistically significantly diverged as a result of adaptive evolution. More than a method for classification, the concept of adaptive divergence can be used in a 'reverse ecology' approach to identify lineages that are in the process of speciation or genes involved in initial adaptive divergence.     

Photogeneration of hydroxyl radicals for footprinting.

Hydroxyl radicals yield footprints of DNA-ligand interactions that are uniform in intensity and display single base pair resolution. It is shown here that brief illumination of dilute aqueous solutions of hydrogen peroxide with a standard uv transilluminator can be used to generate hydroxyl radicals for footprinting studies. Photogenerated hydroxyl radicals are used to footprint netropsin, a drug that interacts with the minor groove of DNA. The method presented eliminates two of the reagents used in conventional Fenton-reaction-based hydroxyl radical footprinting. It has the further advantage that the extent of cleavage of the DNA can be precisely regulated by controlling the illumination time. Because light is used to drive the reaction, photogenerated hydroxyl radicals can be used to footprint DNA-ligand interactions under experimental conditions of temperature and pressure inaccessible to Fenton-reaction chemistry.     

Computational methods for defining the allowed conformational space of 16S rRNA based on chemical footprinting data.

Structural models for 16S ribosomal RNA have been proposed based on combinations of crosslinking, chemical protection, shape, and phylogenetic evidence. These models have been based for the most part on independent data sets and different sets of modeling assumptions. In order to evaluate such models meaningfully, methods are required to explicitly model the spatial certainty with which individual structural components are positioned by specific data sets. In this report, we use a constraint satisfaction algorithm to explicitly assess the location of the secondary structural elements of the 16S RNA, as well as the certainty with which these elements can be positioned. The algorithm initially assumes that these helical elements can occupy any position and orientation and then systematically eliminates those positions and orientations that do not satisfy formally parameterized interpretations of structural constraints. Using a conservative interpretation of the hydroxyl radical footprinting data, the positions of the ribosomal proteins as defined by neutron diffraction studies, and the secondary structure of 16S rRNA, the location of the RNA secondary structural elements can be defined with an average precision of 25 A (ranging from 12.8 to 56.3 A). The uncertainty in individual helix positions is both heterogeneous and dependent upon the number of constraints imposed on the helix. The topology of the resulting model is consistent with previous models based on independent approaches. The result of our computation is a conservative upper bound on the possible positions of the RNA secondary structural elements allowed by this data set, and provides a suitable starting point for refinement with other sources of data or different sets of modeling assumptions.     

Support for the shape concept of lipid structure based on a headgroup volume approach.

Headgroup volumes of seven dioleoyl lipid species, calculated from covalent radii, are shown to correlate linearly (r = 0.95) with the ability of those lipids to alter the midpoint temperature of the lamellar to inverted hexagonal phase transition (L alpha-->HII) of a 95 mole fraction percent phosphatidylethanolamine matrix. The results illustrate the utility of the shape concept and basic considerations of headgroup volume as a predictive tool for the determination of lipid structure.     

1,10-Phenanthroline-copper, a footprinting reagent for single-stranded regions of RNAs.

The 1,10-phenanthroline-cuprous complex (OP-Cu) with hydrogen peroxide as a coreactant nicks the single-stranded loops and bulges of RNA stem-loop structures more rapidly than the double-stranded stems. This chemical nuclease is therefore a useful footprinting reagent for these regions and can be used to monitor both intramolecular and intermolecular hybridization of single-stranded domains. The formation of A-form structures characteristic of either RNA-RNA or RNA-DNA duplexes inhibits scission because it blocks the binding site of the coordination complex in single-stranded loops and not because the oxidatively sensitive hydrogens of the ribose moiety are blocked. The C-4' and C-1' hydrogens are accessible to solvent in A-structures.     

Development of a rhenium-186-labeled MAG3-conjugated bisphosphonate for the palliation of metastatic bone pain based on the concept of bifunctional radiopharmaceuticals

Rhenium-186-1-hydroxyethylidene-1,1-diphosphonate (186Re-HEDP) has been used for the palliation of metastatic bone pain. Delayed blood clearance and high gastric uptake of radioactivity have been observed upon injection, due to the instability of (186)Re-HEDP in vivo. In this study, on the basis of the concept of bifunctional radiopharmaceuticals, we designed a stable 186Re-mercaptoacetylglycylglycylglycine (MAG3) complex-conjugated bisphosphonate, [[[[(4-hydroxy-4,4-diphosphonobutyl)carbamoylmethyl]carbamoylmethyl]carbamoylmethyl]carbamoylmethanethiolate]oxorhenium(V) (186Re-MAG3-HBP). As a precursor, [1-hydroxy-1-phosphono-4-[2-[2-[2-(2-tritylmercaptoacetylamino)acetylamino]acetylamino]acetylamino]butyl]phosphonic acid (Tr-MAG3-HBP) was synthesized by the conjugation of N-[(tritylmercapto)acetyl]glycylglycylglycine (Tr-MAG3) with the bisphosphonate analogue. After deprotection of the trityl group of Tr-MAG3-HBP, 186Re-labeling was performed by reacting 186ReO4- with SnCl2 in citrate buffer. After purification by HPLC, 186Re-MAG3-HBP showed a radiochemical purity of over 95%. To compare the stability of 186Re-MAG3-HBP and 186Re-HEDP, these (186)Re complexes were incubated in phosphate buffer. No measurable decomposition of 186Re-MAG3-HBP occurred over a 24-h period, while only approximately 30% of 186Re-HEDP remained intact 24 h postincubation. In biodistribution experiments, the radioactivity level of 186Re-MAG3-HBP in bone was significantly higher than that of (186)Re-HEDP. Blood clearance of 186Re-MAG3-HBP was faster than that of 186Re-HEDP. In addition, the gastric accumulation of 186Re-MAG3-HBP radioactivity was lower than that of 186Re-HEDP. In conclusion, 186Re-MAG3-HBP is expected to be a useful radiopharmaceutical for the palliation of metastatic bone pain.     

Development of biofuel cells based on gold nanoparticle decorated multi-walled carbon nanotubes

This study focused on developing the synthesis of Au nanoparticle-decorated functionalized multi-walled carbon nanotubes (Au-NPs/f-MWCNTs) for monosaccharide (bio-fuel) oxidation reactions and practical application in air-biofuel cells. We developed a scalable and straightforward method to synthesize Au-NPs/f-MWCNTs which allow us to control the loading and size of the Au-NPs. The Au-NPs/f-MWCNTs exhibited better catalytic activities and stability than the Au sheet and subsequently resulted in a threefold increase in the power density of the air-glucose fuel cell with an exceptionally high open circuit voltage (∼1.3 V). The catalytic efficiency was confirmed by high performance liquid chromatography with the superior of the Au-NPs/f-MWCNTs over a bare gold electrode. In addition, the application of this advanced catalyst to other monosaccharide oxidation reactions figured out that the configuration of –OH groups at C₂ and C₃ of the reactants plays an important role in the initial adsorption process, and thus, affects the required activation energy for further oxidation. The different monosaccharides lead to significantly different fuel cell performances in terms of power density, which coherently corresponds to the difference in the configuration of C₂ and C₃. Because two small air-glucose fuel cells using Au-NPs/f-MWCNTs can run a LED lamp, further applications of other monosaccharides as fuel in biofuel cells for equivalent required power devices may be possible.     

Hydroxyl radical footprinting analysis of a human haptoglobin-hemoglobin complex

Methods of structural mass spectrometry have become more popular to study protein structure and dynamics. Among them, fast photochemical oxidation of proteins (FPOP) has several advantages such as irreversibility of modifications and more facile determination of the site of modification with single residue resolution. In the present study, FPOP analysis was applied to study the hemoglobin (Hb) – haptoglobin (Hp) complex allowing identification of respective regions altered upon the complex formation. FPOP footprinting using a timsTOF Pro mass spectrometer revealed structural information for 84 and 76 residues in Hp and Hb, respectively, including statistically significant differences in the modification extent below 0.3%. The most affected residues upon complex formation were Met76 and Tyr140 in Hbα, and Tyr280 and Trp284 in Hpβ. The data allowed determination of amino acids directly involved in Hb – Hp interactions and those located outside of the interaction interface yet affected by the complex formation. Also, previously modeled interaction between Hb βTrp37 and Hp βPhe292 was not confirmed by our data. Data are available via ProteomeXchange with identifier PXD021621.