Explorative data analysis of two-dimensional electrophoresis gels

Methods for classification of two-dimensional (2-DE) electrophoresis gels based on multivariate data analysis are demonstrated. Two-dimensional gels of ten wheat varieties are analyzed and it is demonstrated how to classify the wheat varieties in two qualities and a method for initial screening of gels is presented. First, an approach is demonstrated in which no prior knowledge of the separated proteins is used. Alignment of the gels followed by a simple transformation of data makes it possible to analyze the gels in an automated explorative manner by principal component analysis, to determine if the gels should be further analyzed. A more detailed approach is done by analyzing spot volume lists by principal components analysis and partial least square regression. The use of spot volume data offers a mean to investigate the spot pattern and link the classified protein patterns to distinct spots on the gels for further investigation. The explorative approach in analysis of 2-D gels makes it possible, in a fast and convenient way, to screen many gels in order to determine the protein patterns that form clusters and could be selected for further examination.     

Reactions of (PCP)Ru(CO)(NHPh)(PMe3) (PCP = 2,6-(CH2PtBu2)2C6H3) with substrates that possess polar bonds

The Ru(II) amido complex (PCP)Ru(CO)(PMe(3))(NHPh) (1) (PCP = 2,6-(CH(2)P(t)Bu(2))(2)C(6)H(3)) reacts with compounds that possess polar C=N, C triple bond N, or C=O bonds (e.g., nitriles, carbodiimides, or isocyanates) to produce four-membered heterometallacycles that result from nucleophilic addition of the amido nitrogen to an unsaturated carbon of the organic substrate. Based on studies of the reaction of complex 1 with acetonitrile, the transformations are suggested to proceed by dissociation of trimethylphosphine, followed by coordination of the organic substrate and then intramolecular N-C bond formation. In the presence of ROH (R = H or Me), the fluorinated amidinate complex (PCP)Ru(CO)(N(Ph)C(C(6)F(5))NH) (6) reacts with excess pentafluorobenzonitrile to produce (PCP)Ru(CO)(F)(N(H)C(C(6)F(5))NHPh) (7). The reaction with MeOH also produces o-MeOC(6)F(4)CN (>90%) and p-MeOC(6)F(4)CN (<10%). Details of the solid-state structures of (PCP)Ru(CO)(F)(N(H)C(C(6)F(5))NHPh) (7), (PCP)Ru(CO)[PhNC{NH(hx)}N(hx)] (8), (PCP)Ru(CO){N(Ph)C(NHPh)O} (9), and (PCP)Ru(CO){OC(Ph)N(Ph)} (10) are reported.     

Classification of wheat varieties: use of two-dimensional gel electrophoresis for varieties that can not be classified by matrix assisted laser desorpiton/ionization-time of flight-mass spectrometry and an artificial neural network

Analyzing a gliadin extract by matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) combined with an artificial neural network (ANN) is a suitable method for identification of wheat varieties. However, the ANN can not distinguish between all different wheat varieties. Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) was applied to three pairs of wheat varieties, which can not be classified correctly by ANN. By 2-D PAGE the varieties in the three pairs can be discriminated and these six wheat varieties can be separated from each other, which could not be separated by MALDI-TOF-MS and NN.     

Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures

Fingerprint-based similarity searching is widely used for virtual screening when only a single bioactive reference structure is available. This paper reviews three distinct ways of carrying out such searches when multiple bioactive reference structures are available: merging the individual fingerprints into a single combined fingerprint; applying data fusion to the similarity rankings resulting from individual similarity searches; and approximations to substructural analysis. Extended searches on the MDL Drug Data Report database suggest that fusing similarity scores is the most effective general approach, with the best individual results coming from the binary kernel discrimination technique.     

Synthesis of indeno-fused derivatives of quinolizinium salts, imidazo[1,2-a]pyridine, pyrido[1,2-a]indole, and 4h-quinolizin-4-one via benzannulated enyne-allenes

The benzannulated enediynyl propargylic alcohol 8 was prepared from 1-bromo-2-iodobenzene by two consecutive Sonogashira cross-coupling reactions. The subsequent transformation to mesylate 9 followed by treatment with 4-substituted pyridines 10 then furnished the benzannulated enediynes 11. On exposure of 11 to triethylamine, the indeno-fused quinolizinium salts 15 were produced in quantitative yield. Presumably the reaction proceeded through a 1,3-prototropic rearrangement to form the benzannulated enyne-allenes 12, which then underwent either a concerted Diels-Alder reaction or a two-step process involving a Schmittel cyclization reaction to form biradical 13 followed by an intramolecular radical-radical coupling to afford 14. A subsequent prototropic rearrangement then produced 15. Similarly, 21a and 21b were produced from 19a and 19b, respectively. The use of the Sonogashira reaction for cross-coupling between 1-iodo-2-(phenylethynyl)benzene (7) and 1-(2-propynyl)-1H-imidazole (25) followed by treatment of the resulting adduct with potassium tert-butoxide gave the indeno-fused imidazo[1,2-a]pyridine 24 in 98% yield. Similarly, the indeno-fused pyrido[1,2-a]indole 32 and 4H-quinolizin-4-one 35 were obtained by starting from 7 for cross-coupling with 1-(2-propynyl)-1H-indole (30) and 1-(2-propynyl)-2(1H)-pyridinone (33), respectively, followed by treatment with potassium tert-butoxide.     

Structure of hydrated Na-Nafion polymer membranes

We use molecular dynamics simulations to investigate the structure of the hydrated Na-Nafion membranes. The membrane is "prepared" by starting with the Nafion chains placed on a cylinder having the water inside it. Minimizing the energy of the system leads to a filamentary hydrophilic domain whose structure depends on the degree of hydration. At 5 wt % water the system does not have enough water molecules to solvate all the ions that could be formed by the dissociation of the -SO3Na groups. As a result, the -SO3Na groups aggregate with the water to form very small droplets that do not join into a continuous phase. The size of the droplets is between 5 and 8 A. As the amount of water present in the membrane is increased, the membrane swells, and SO3Na has an increasing tendency to dissociate into ions. Furthermore, a transition to a percolating hydrophilic network is observed. In the percolating structure, the water forms irregular curvilinear channels branching in all directions. The typical dimension of the cross section of these channels is about 10-20 A. Calculated neutron scattering from the simulated system is in qualitative agreement with experiment. In all simulations, the pendant sulfonated perfluorovinyl side chains of the Nafion hug the walls of the hydrophilic channel, while the sulfonate groups point toward the center of the hydrophilic phase. The expulsion of the side chains from the hydrophilic domain is favored because it allows better interaction between the water molecules. We have also examined the probability of finding water molecules around the Na+ and the -SO3(-) ions as well as the probability of finding other water molecules next to a given water molecule. These probabilities are much broader than those found in bulk water or for one ion in bulk water (calculated with the potentials used in the present simulation). This is due to the highly inhomogeneous nature of the material contained in the small hydrophilic pores.     

Factors controlling the drop evaporation constant

In this paper, we discuss the factors affecting drop evaporation. We found that the droplet morphology at a specific temperature was controlled by the physical properties of the liquid itself, such as the molecular weight, density, diffusion coefficient in air, and heat of vaporization. Two processes are included in drop evaporation: diffusion of liquid molecules into the air (diffusion part) and flow of the liquid molecules from inside the drop to the free outer shell liquid layer within the liquid-vapor interface (evaporation part). The diffusion part remained steady during drying and was not sensitive to the variation of temperature. The evaporation part, however, was an active factor and determined the differences in drop evaporation behaviors.     

New FIR laser lines and frequency measurements in CD3OD

Twenty-four new submillimeter laser lines in fully deuterated methyl alcohol (CD₃OD) in the wavelength range from 52 to 328 m have been obtained in a Fabry-Perot FIR resonator by optically pumping the methanol with a cw CO₂ laser. We have made accurate wavelength measurements and have determined the relative polarization of most of the known CD₃OD laser lines. The frequencies of 13 of the strongest lines were also measured.Contribution of the U.S. Government, not subject to copyright.     

Frequencies and wavelengths from a new, efficient FIR lasing gas: CD2F2

We report for the first time wavelength, relative polarization, and frequency measurements for 47 new cw FIR laser lines in the wavelength region from 120 to 1714 m, all obtained by optically pumping CD₂F₂ with a CO₂ laser. Relative output powers were also measured. For comparison, the 189.8 m line pumped by R_I(34) is nearly five times as efficient as the 118.8 m methyl alcohol line.Contribution of the U.S. Government, not subject to copyright.     

Locked nucleic acid (LNA) recognition of RNA: NMR solution structures of LNA:RNA hybrids

Locked nucleic acids (LNAs) containing one or more 2'-O,4'-C-methylene-linked bicyclic ribonucleoside monomers possess a number of the prerequisites of an effective antisense oligonucleotide, e.g. unprecedented helical thermostability when hybridized with cognate RNA and DNA. To acquire a detailed understanding of the structural features of LNA giving rise to its remarkable properties, we have conducted structural studies by use of NMR spectroscopy and now report high-resolution structures of two LNA:RNA hybrids, the LNA strands being d(5'-CTGAT(L)ATGC-3') and d(5'-CT(L)GAT(L)AT(L)GC-3'), respectively, T(L) denoting a modified LNA monomer with a thymine base, along with the unmodified DNA:RNA hybrid. In the structures, the LNA nucleotides are positioned as to partake in base stacking and Watson-Crick base pairing, and with the inclusion of LNA nucleotides, we observe a progressive change in duplex geometry toward an A-like duplex structure. As such, with the inclusion of three LNA nucleotides, the hybrid adopts an almost canonical A-type duplex geometry, and thus it appears that the number of modifications has reached a saturation level with respect to structural changes, and that further incorporations would furnish only minute changes in the duplex structure. We attempt to rationalize the conformational steering induced by the LNA nucleotides by suggesting that the change in electronic density at the brim of the minor groove, introduced by the LNA modification, is causing an alteration of the pseudorotational profile of the 3'-flanking nucleotide, thus shifting this sugar equilibrium toward N-type conformation.