Top-down characterization of nucleic acids modified by structural probes using high-resolution tandem mass spectrometry and automated data interpretation

A top-down approach based on sustained off-resonance irradiation collision-induced dissociation (SORI-CID) has been implemented on an electrospray ionization (ESI) Fourier transform mass spectrometer (FTMS) to characterize nucleic acid substrates modified by structural probes. Solvent accessibility reagents, such as dimethyl sulfate (DMS), 1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT), and beta-ethoxy-alpha-ketobutyraldehyde (kethoxal, KT) are widely employed to reveal the position of single- vs double-stranded regions and obtain the footprint of bound proteins onto nucleic acids structures. Established methods require end-labeling of the nucleic acid constructs, probe-specific chemistry to produce strand cleavage at the modified nucleotides, and analysis by polyacrylamide gel electrophoresis to determine the position of the susceptible sites. However, these labor-intensive procedures can be avoided when mass spectrometry is used to identify the probe-induced modifications from their characteristic mass signatures. In particular, ESI-FTMS can be directly employed to monitor the conditions of probe application to avoid excessive alkylation, which could induce unwanted distortion or defolding of the substrate of interest. The sequence position of the covalent modifications can be subsequently obtained from classic tandem techniques, which allow for the analysis of individual target adducts present in complex reaction mixtures with no need for separation techniques. Selection and activation by SORI-CID has been employed to reveal the position of adducts in nucleic acid substrates in excess of 6 kDa. The stability of the different covalent modifications under SORI-CID conditions was investigated. Multiple stages of isolation and activation were employed in MS(n)() experiments to obtain the desired sequence information whenever the adduct stability was not particularly favorable, and SORI-CID induced the facile loss of the modified base. A new program called MS2Links was developed for the automated reduction and interpretation of fragmentation data obtained from modified nucleic acids. Based on an algorithm that searches for plausible isotopic patterns, the data reduction module is capable of discriminating legitimate signals from noise spikes of comparable intensity. The fragment identification module calculates the monoisotopic mass of ion products expected from a certain sequence and user-defined covalent modifications, which are finally matched with the signals selected by the data reduction program. Considering that MS2Links can generate similar fragment libraries for peptides and their covalent conjugates with other peptides or nucleic acids, this program provides an integrated platform for the structural investigation of protein-nucleic acid complexes based on cross-linking strategies and top-down ESI-FTMS.     

Metabolite-sensitive holographic biosensors

A new type of biosensor that combines the inexpensiveness and mass-produceability of reflection holograms with the selectivity and specificity of enzymes is described. pH-sensitive holographic sensors were fabricated from ionizable monomers incorporated into thin, polymeric, hydrogel films which were transformed into volume holograms using a diffusion method coupled with holographic recording, using a frequency-doubled Nd:YAG laser (532 nm). These holograms were used as transducer systems to monitor the pH changes associated with specific enzymatic reactions to construct prototype urea- and penicillin-sensitive biosensors. The diffraction wavelength (color) of the holographic biosensors was used to characterize their shrinkage and swelling behavior as a function of analyte concentration. The potential of these sensors for the measurement of the clinically and industrially important metabolites urea and penicillin G is demonstrated.     

Use of the CT images for BNCT calculation: development of BNCT treatment planning system and its applications to dose calculation for voxel phantoms

A BNCT (Boron Neutron Capture Therapy) treatment planning system (BTPS) was developed for BNCT study and treatment planning. Three kinds of CT images, VHP, PINNACLE and DICOM images, were employed to make voxel phantoms for BNCT patient treatment using the BTPS. The thermal neutron, fast neutron, gamma and boron doses are calculated and background, tissue, and tumour doses for idealised standard reactor neutron field (ISRNF) neutron beam were calculated by using BTPS and MCNP code. It was noted that the total computing times needed for BNCT analysis could be greatly reduced since the BTPS system provides a dose analysis tool and a lengthy MCNP input in a short time. It is, thus, expected that the BTPS can significantly contribute the BNCT study for the treatment of patients.     

Incremental penetration depth estimation between convex polytopes using dual-space expansion

We present a fast algorithm to estimate the penetration depth between convex polytopes in 3D. The algorithm incrementally seeks a "locally optimal solution" by walking on the surface of the Minkowski sums. The surface of the Minkowski sums is computed implicitly by constructing a local dual mapping on the Gauss map. We also present three heuristic techniques that are used to estimate the initial features used by the walking algorithm. We have implemented the algorithm and compared its performance with earlier approaches. In our experiments, the algorithm is able to estimate the penetration depth in about a milli-second on an 1 GHz Pentium PC. Moreover, its performance is almost independent of model complexity in environments with high coherence between successive instances.     

Effect of foliar fungicides on aflatoxin, oil and protein content and maturing rate of peanut kernels

Arachis hypogaea L. ‘Tifspan’ and ‘Florunner’ peanuts (groundnuts) were treated with selected foliar fungicides for control of Cercospora leafspot. Peanut fruits were harvested on three different dates and analysed for aflatoxin, oil and protein content and degree of maturity. No significant differences (P = <0.05) in aflatoxin incidence were associated with either fungicide treatments or harvest dates. Significant differences were observed, however, in the percentage protein and oil content of the peanut kernels, depending upon the fungicide treatment. Delayed maturity was caused by specific fungicide treatments.     

Similarity between shock and safe areas during acquisition, transfer, and extinction of escape behavior in rats.

Demonstrated, in 3 experiments with a total of 128 female hooded rats, that performance in escape training was impaired when shock- and safe-box stimuli were similar rather than dissimilar to each other. Prior training with similar shock and safe boxes impaired responding during subsequent training or extinction under the dissimilar shock and safe condition. Prior training under the dissimilar condition did not reliably influence subsequent training or extinction under the similar shock-safe condition. Resistance to extinction under the dissimilar condition was reliably better following training with random presentations to both similar and dissimilar conditions than following training with the dissimilar condition alone. Exp III showed that impairment of escape behavior during training was attributable to response-contingent similarity between shock and safe boxes. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

P-notation: High level description language for software design

The previous three parts of this series have outlined a notation for designing assembly language programs. In this final article the use of the notation is illustrated by designing a fairly large program by the process of stepwise refinement. Emphasis is placed on developing a modular structure by using the procedure and module constructs in order to simplify the design process and to facilitate testing.     

Interactive Graphical Minimax Location of Multiple Facilities with General Constraints

An optimal algorithm for solving constrained minimax location problems has been previously reported, with the major limitation that only a single new service facility is allowed. Algorithmic extensions have now been developed and implemented on an advanced color-graphics system for the location of any number of new facilities to collectively serve the set of existing facilities. The minimax criterion is again considered for the optimization, and nonconvex constraint sets are permitted.     

Creep and drying shrinkage of calcium silicate pastes I. Specimen preparation and mechanical properties

In this first paper of a series dealing with the creep and shrinkage of calcium silicate pastes, the materials, specimen preparation methods, mechanical test procedures and results are discussed. Pastes were prepared with a w/s ratio of 0.4 using C₃S, β-C₂S or a C₃S/C₂S blend. Thin-wall, hollow-cylinder specimens were cast and subjected to various conditions of load and drying. The structural and chemical modifications resulting from these treatments will be covered in subsequence papers.