Approaching real-time molecular diagnostics: single-pair fluorescence resonance energy transfer (spFRET) detection for the analysis of low abundant point mutations in K-ras oncogenes

The aim of this study was to develop new strategies for analyzing molecular signatures of disease states approaching real-time using single pair fluorescence resonance energy transfer (spFRET) to rapidly detect point mutations in unamplified genomic DNA. In addition, the detection process was required to discriminate between normal and mutant (minority) DNAs in heterogeneous populations. The discrimination was carried out using allele-specific primers, which flanked the point mutation in the target gene and were ligated using a thermostable ligase enzyme only when the genomic DNA carried this mutation. The allele-specific primers also carried complementary stem structures with end-labels (donor/acceptor fluorescent dyes, Cy5/Cy5.5, respectively), which formed a molecular beacon following ligation. We coupled ligase detection reaction (LDR) with spFRET to identify a single base mutation in codon 12 of a K-ras oncogene that has high diagnostic value for colorectal cancers. A simple diode laser-based fluorescence system capable of interrogating single fluorescent molecules undergoing FRET was used to detect photon bursts generated from the molecular beacon probes formed upon ligation. LDR-spFRET provided the necessary specificity and sensitivity to detect single-point mutations in as little as 600 copies of human genomic DNA directly without PCR at a level of 1 mutant per 1000 wild type sequences using 20 LDR thermal cycles. We also demonstrate the ability to rapidly discriminate single base differences in the K-ras gene in less than 5 min at a frequency of 1 mutant DNA per 10 normals using only a single LDR thermal cycle of genomic DNA (600 copies). Real-time LDR-spFRET detection of point mutations in the K-ras gene was accomplished in PMMA microfluidic devices using sheath flows.     

Synthese und chemie von 4R-silacyclohexa-2,5-dienen und 4R-silacyclohexa-2,4-dienen

The 1(Z),4(Z)-1,5-dilithium-3R-3-methoxypenta-1,4-dienes, available by cleavage of 1,1-di-n-butyl-4R-4-methoxy-1-stannacyclohexane-2,5-dienes with n-BuLi in ether, react with dichlorosilanes (R′R″ SiCl₂; R′, R″ = H, alkyl, aryl, alkoxy) to give 1R′,1R″,4R-4-methoxy-1-silacyclohexa-2,5-dienes.Claevage of the ether group with BBr₃, BCl₃ or PCl₃ gives 6-chloro(bromo)-1-silacyclohexa-2,4-dienes or 1,5-dichloro-1-silacyclohexane-2,4-dienes, respectively.Ether cleavage of 4R-4-methoxy-1-silacyclohexa-2,5-dienes with sodium results in the formation of 4R-1-silacyclohexadienyl anions, which can be hydrolyzed to give 1-silacyclohexa-2,4-dienes which reach further with trichloromethylsilane to give 6-trimethylsilyl-1-silacyclohexa-2,4-dienes.Phase transfer-catalyzed conversion of 1-chlorosilacyclohexadienes into the fluoro derivatives as well as further substitution reactions of 1-chlorosilacyclohexadienes are described.The ¹H NMR, ¹³C NMR, IR and mass spectra of the silacyclohexadienes are discussed.     

PHOTOREACTIVATION IN THE EXTREME HALOPHILIC ARCHAEBACTERIUM Halobacterium cutirubrum

Abstract— Photoreactivation in the extreme halophilic archaebacterium Halobacterium cutirubrum was studied both in vivo and in vitro. Cells irradiated with ultraviolet (UV)-fluences up to 350 J/m² could be completely photoreactivated, indicating very efficient repair of pyrimidine dimers in UV-irradiated DNA. Dark repair is apparently absent in Halobacterium since liquid holding under non-growth conditions did not influence the survival of UV-irradiated cells, while cells remained completely photoreactivable with no change in the kinetics of photoreactivation. Experiments with Halobacterium isolates of different carotenoid content indicated that carotenoids do not influence either UV-inactivation or photoreactivation. Small differences in the rates of UV-inactivation and photoreactivation could be assigned to the occurrence of gas vesicles. Flash experiments and the temperature dependence of photoreactivation indicated an enzymatical reaction. This was confirmed by in vitro experiments with partially purified photoreactivating enzyme. The in vivo action spectrum of photoreactivation showed a main band in the 400-470 nm region with a maximum at 440 nm. Comparison with action spectra of other microorganisms classified the Halobacterium enzyme as a 8-hydroxy-5-deazaflavin type photoreactivating enzyme.     

金属卟啉催化条件下有机化合物与二氧化碳的电羧化反应Ⅰ. 金属卟啉对苄基氯电羧化催化活性的研究

本文研究了系列金属卟啉对苯基氯(phCH~2Cl)和CO~2电羧化反应的催化活性.用熔点,MS,IR,UV鉴别产物为苯乙酸卟脂,利用高效液相色谱(HPLC)定量分析了羧化产物,选出最佳电羧化电解电位为-1.6v(相对于饱和甘汞电极,vs.SCE,下同). 并对催化活性较高的钴卟啉系列配合物进行了深入研究. 探讨了金属卟啉具有催化活性的原因,认为能形成M(Ⅰ)中间体的金属卟啉配合物.具有较高的催化活性.     

Partons and jets at the LHC

I review some issues related to short distance QCD and its relation to the experimental program of the large hadron collider (LHC) now under construction in Geneva.     

The coherent scattering function of the reptation model: Simulations compared to theory

We present results of Monte Carlo simulations measuring the coherent structure function of a chain moving through an ordered lattice of fixed topological obstacles. Our computer experiments use chains up to 320 beads and cover a large range of wave vectors and a time range exceeding the reptation time. For additional information we also measured the coherent structure function of internal pieces of the chain. We compare our results i) to the predictions of the primitive chain model, ii) to an approximate form resulting from Rouse motion in a coiled tube, and iii) to our recent evaluation of the full reptation model. i) The primitive chain model can fit the data for times , where T ₂ is the Rouse time of the chain. Besides some phenomenological amplitude factor this fit involves the reptation time T ₃ as a second fit parameter. For the chain lengths measured, the asymptotic behavior is not attained. ii) The model of Rouse motion in a tube, which we have criticized before on theoretical grounds, is shown to fail also on the purely phenomenological level. iii) Our evaluation of the full reptation model yields an excellent fit to the data for both total chains and internal pieces and for all wave vectors and all times, provided specific micro-structure effects of the MC dynamics are negligible. Such micro-structure effects show up for wave vectors of the order of the inverse segment size and enforce the introduction of some phenomenological, wave-vector-dependent prefactor. For the dynamics of the total chain our data analysis based on the full reptation model shows the importance of tube length fluctuations. Universal (Rouse-type) internal relaxation, however, is unimportant. It can be observed only in the form of the diffusive motion of a short central subchain in the tube. Finally, we present a fit formula which in a large range of wave vectors and chain lengths reproduces the numerical results of our theory for the scattering from the total chain.Received: 9 July 2003, Published online: 11 November 2003PACS: 83.10.Kn Reptation and tube theories - 82.35.Lr Physical properties of polymers - 83.10.Rs Computer simulation of molecular and particle dynamics     

Antimony by ICP-MS as a marker for sentinel lymph nodes in melanoma patients

A sensitive, accurate and specific method for the analysis of antimony by ICP-MS is presented as a marker of the sentinel lymph node in melanoma patients.     

Large order expansion in perturbation theory

We investigate the large n behavior of the perturbation coefficients E_n for the ground state energy of the anharmonic oscillator, considered as a field theory in one space-time dimension. We combine the saddle point expansion for functional integrals introduced in this context by Lipatov with the dispersion relation (in coupling constant) used by Bender and Wu. The complete Feynman rules for the expansion in $\text{1}\text{n}$ are worked out, and we compute the first two terms, which agree with those computed by Bender and Wu using the WKB approximation. One feature of our analysis is a deformation of the integration contour in function space as one analytically continues in the coupling.     

Petroporphyrins—II: The presence of porphyrins with extended alkyl substituents

The vanadyl porphyrins from Boscan oil (Cretaceous, W. Venezuela) were isolated as 3 fractions, and degraded to maleimides (1H-pyrrole-2,5-diones) by chromic acid. Analysis of the products by GC-MS, using multiple ion detection to enhance sensitivity, revealed a major homologous series of 3-Me components with n-alkyl side chains extending to C₁₁, and a minor series with branched alkyl side chains, the Me branch being at C-1. The origin of the extended alkyl groups is discussed.