SNPlexing the human Y-chromosome: a single-assay system for major haplogroup screening

SNPs are one of the main sources of DNA variation among humans. Their unique properties make them useful polymorphic markers for a wide range of fields, such as medicine, forensics, and population genetics. Although several high-throughput techniques have been (and are being) developed for the vast typing of SNPs in the medical context, population genetic studies involve the typing of few and select SNPs for targeted research. This results in SNPs having to be typed in multiple reactions, consuming large amounts of time and of DNA. In order to improve the current situation in the area of human Y-chromosome diversity studies, we decided to employ a system based on a multiplex oligo ligation assay/PCR (OLA/PCR) followed by CE to create a Y multiplex capable of distinguishing, in a single reaction, all the major haplogroups and as many subhaplogroups on the Y-chromosome phylogeny as possible. Our efforts resulted in the creation of a robust and accurate 35plex (35 SNPs in a single reaction) that when tested on 165 human DNA samples from different geographic areas, proved capable of assigning samples to their corresponding haplogroup.     

Gain-of-function mutational activation of human tRNA synthetase procytokine

Disease-causing mutations occur in genes for aminoacyl tRNA synthetases. That some mutations are dominant suggests a gain of function. Native tRNA synthetases, such as tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase, catalyze aminoacylation and are also procytokines that are activated by natural fragmentation. In principle, however, gain-of-function phenotypes could arise from mutational activation of synthetase procytokines. From crystal structure analysis, we hypothesized that a steric block of a critical Glu-Leu-Arg (ELR) motif in full-length TyrRS suppresses the cytokine activity of a natural fragment. To test this hypothesis, we attempted to uncover ELR in the procytokine by mutating a conserved tyrosine (Y341) that tethers ELR. Site-specific proteolytic cleavage and small-angle X-ray scattering established subtle opening of the structure by the mutation. Strikingly, four different assays demonstrated mutational activation of cytokine functions. The results prove the possibilities for constitutive gain-of-function mutations in tRNA synthetases.     

Microfluidic HPLC‐Chip devices with integral channels containing methylstyrenic‐based monolithic media

Polyimide HPLC‐Chip devices containing poly(methylstyrene‐bis‐p‐vinylphenyl)ethane (MS/BVPE) stationary phase within the device channels and with wall attachment were prepared by thermally initiated free radical polymerization. The microfluidic devices were coupled to both UV and MS detectors. The potential of the MS/BVPE monolith as an alternative separation media within chip devices was investigated by side‐by‐side comparisons to particulate media within commercial devices. The chromatographic behavior of this stationary phase was comparable to particulate media for separations of proteins as the average peak width at half‐height was equal (6.2 s) for a separation within 8 min under gradient elution conditions. The ability to control the porosity characteristics of the MS/BVPE monolith with changes in polymerization time also extended its utility into small analyte (< 500 Da) applications, although more optimization is needed to match conventional RP media for these applications. The good mechanical stability of the MS/BVPE monolith within the microdevices enabled excellent run‐to‐run repeatability (%RSD retention time (? 0.16) and chip‐to‐chip reproducibility (%RSD retention time (1.4). The use of this material within enrichment channels also shows its potential value in more complex work flows.     

Synthesis,Crystal Structure,Spectral and Thermal Studies of (<Emphasis Type="Italic">E</Emphasis>)-4-Dimethamino[(1-phenylethyl)iminomethyl]benzyne

Abstract  

Schiff-base compound (E)-4-dimethamino[(1-phenylethyl)iminomethyl]benzyne was synthesized and characterized by elemental analyses (CHN), FT-IR and ¹H-NMR spectroscopic techniques and thermogravimetric analyses (TG). Crystal structure of the title compound was obtained by single crystal X-ray diffraction. The title compound crystallizes in the monoclinic space group P2₁ with unit cell parameters: a = 8.5283(2), b = 6.0699(2), c = 13.6997(4) Ǻ, β = 91.471(2)°, V = 708.94(4) Ǻ³ and Z = 2.     

E2(CN)2 (E = S, Se) and related compounds

A synthetic, spectroscopic, and theoretical study of Ex(CN)2 (E = S, Se; x = 1-3) is described. The X-ray structures of Se2(CN)2 and Se3(CN)2 have been determined. Se2(CN)2 crystallizes in a chiral space group with the CN groups approximately gauche.     

The nature of Ru-NO bonds in ruthenium tetraazamacrocycle nitrosyl complexes--a computational study

Ruthenium complexes including nitrosyl or nitrite complexes are particularly interesting because they can not only scavenge but also release nitric oxide in a controlled manner, regulating the NO-level in vivo. The judicious choice of ligands attached to the [RuNO] core has been shown to be a suitable strategy to modulate NO reactivity in these complexes. In order to understand the influence of different equatorial ligands on the electronic structure of the Ru-NO chemical bonding, and thus on the reactivity of the coordinated NO, we propose an investigation of the nature of the Ru-NO chemical bond by means of energy decomposition analysis (EDA), considering tetraamine and tetraazamacrocycles as equatorial ligands, prior to and after the reduction of the {RuNO}(6) moiety by one electron. This investigation provides a deep insight into the Ru-NO bonding situation, which is fundamental in designing new ruthenium nitrosyl complexes with potential biological applications.     

Two new XP(O)[NHC(CH3)3]2 phosphoramidates,with X = (CH3)2N and [(CH3)3CNH]2P(O)(O)

In N,N′‐di‐tert‐butyl‐N′′,N′′‐dimethylphosphoric triamide, C₁₀H₂₆N₃OP, (I), and N,N′,N′′,N′′′‐tetra‐tert‐butoxybis(phosphonic diamide), C₁₆H₄₀N₄O₃P₂, (II), the extended structures are mediated by P(O)...(H—N)₂ interactions. The asymmetric unit of (I) consists of six independent molecules which aggregate through P(O)...(H—N)₂ hydrogen bonds, giving R₂¹(6) loops and forming two independent chains parallel to the a axis. Of the 12 independent tert‐butyl groups, five are disordered over two different positions with occupancies ranging from to . In the structure of (II), the asymmetric unit contains one molecule. P(O)...(H—N)₂ hydrogen bonds give S(6) and R₂²(8) rings, and the molecules form extended chains parallel to the c axis. The structures of (I) and (II), along with similar structures having (N)P(O)(NH)₂ and (NH)₂P(O)(O)P(O)(NH)₂ skeletons extracted from the Cambridge Structural Database, are used to compare hydrogen‐bond patterns in these families of phosphoramidates. The strengths of P(O)[...H—N]_x (x = 1, 2 or 3) hydrogen bonds are also analysed, using these compounds and previously reported structures with (N)₂P(O)(NH) and P(O)(NH)₃ fragments.     

Communication: Probing non-equilibrium vibrational relaxation pathways of highly excited C≡N stretching modes following ultrafast back-electron transfer

Fifth-order nonlinear visible-infrared spectroscopy is used to probe coherent and incoherent vibrational energy relaxation dynamics of highly excited vibrational modes indirectly populated via ultrafast photoinduced back-electron transfer in a trinuclear cyano-bridged mixed-valence complex. The flow of excess energy deposited into four C≡N stretching (ν(CN)) modes of the molecule is monitored by performing an IR pump-probe experiment as a function of the photochemical reaction (τ(vis)). Our results provide experimental evidence that the nuclear motions of the molecule are both coherently and incoherently coupled to the electronic charge transfer process. We observe that intramolecular vibrational relaxation dynamics among the highly excited ν(CN) modes change significantly en route to equilibrium. The experiment also measures a 7 cm(-1) shift in the frequency of a ～57 cm(-1) oscillation reflecting a modulation of the coupling between the probed high-frequency ν(CN) modes for τ(vis) < 500 fs.     

Using integer programming techniques for the solution of an experimental design problem

Latin hypercube sampling is often used to estimate the distribution function of a complicated function of many random variables. In so doing, it is typically necessary to choose a permutation matrix which minimizes the correlation among the cells in the hypercube layout. This problem can be formulated as a generalized, multi-dimensional assignment problem. For the two-dimensional case, we provide a polynomial algorithm. For higher dimensions, we offer effective heuristic and bounding procedures.Supported in part by a grant from the National Institute of Standards and Technology (60NANB9D-0974).Supported in part by grants from the Office of Naval Research (N00014-90-J-1324) and the Air Force Office of Scientific Research (F49 620-90-C-0022).Research partially performed while visiting the Department of Mathematics, Brunel University, Uxbridge, England.     

Kinetics of the bulk polymerization of dioxolane in the presence of water

The polymerization of dioxolane initiated by the ～Si^⊕HSO ion pair is greatly influenced by water which changes the overall polymerization rate. Particularly great changes are brought about at certain higher conversions (whose values are also a function of an initial concentration of water). The polymerization practically stops at these conversions and the system appears to be close to a monomer—polymer equilibrium. It is shown that the equation V_overall = f([H₂O]), which describes the dependence of the overall rate of polymerization on the concentration of water and which was originally derived for the polymerization of trioxane, holds also for the polymerization of dioxolane. The decrease of water concentration during the polymerization was measured and the observed equilibrium was shown to be a kinetic phenomenon.