8-vinyl-deoxyadenosine, an alternative fluorescent nucleoside analog to 2′-deoxyribosyl-2-aminopurine with improved properties

We report here the synthesis and the spectroscopic characterization of 8-vinyl-deoxyadenosine (8vdA), a new fluorescent analog of deoxyadenosine. 8vdA was found to absorb and emit in the same wavelength range as 2′-deoxyribosyl-2-aminopurine (2AP), the most frequently used fluorescent nucleoside analog. Though the quantum yield of 8vdA is similar to that of 2AP, its molar absorption coefficient is about twice, enabling a more sensitive detection. Moreover, the fluorescence of 8vdA was found to be sensitive to temperature and solvent but not to pH (around neutrality) or coupling to phosphate groups. Though 8vdA is base sensitive and susceptible to depurination, the corresponding phosphoramidite was successfully prepared and incorporated in oligonucleotides of the type d(CGT TTT XNX TTT TGC) where N = 8vdA and X = A, T or C. The 8vdA-labeled oligonucleotides gave more stable duplexes than the corresponding 2AP-labeled sequences when X = A or T, indicating that 8vdA is less perturbing than 2AP and probably adopts an anti conformation to preserve the Watson–Crick H-bonding. In addition, the quantum yield of 8vdA is significantly higher than 2AP in all tested oligonucleotides in both their single strand and duplex states. The steady-state and time-resolved fluorescence parameters of 8vdA and 2AP were found to depend similarly on the nature of their flanking residues and on base pairing, suggesting that their photophysics are governed by similar mechanisms. Taken together, our data suggest that 8vdA is a non perturbing nucleoside analog that may be used with improved sensitivity for the same applications as 2AP

Mechanical testing and comparison of porcine tissue, silicones and 3D-printed materials for cardiovascular phantoms

Background: Cardiovascular phantoms for patient education, pre-operative planning, surgical training, haemodynamic simulation, and device testing may help improve patient care. However, currently used materials may have different mechanical properties compared to biological tissue. Methods/Aim: The aim of this study was to investigate the mechanical properties of 3D-printing and silicone materials in comparison to biological cardiovascular tissues. Uniaxial cyclic tension testing was performed using dumbbell samples from porcine tissue (aorta, pulmonary artery, right and left ventricle). Flexible testing materials included 15 silicone (mixtures) and three 3D-printing materials. The modulus of elasticity was calculated for different deformation ranges. Results: The modulus of elasticity (0%–60%) for the aorta ranged from 0.16 to 0.18 N/mm^2, for the pulmonary artery from 0.07 to 0.09 N/mm^2, and for the right ventricle as well as the left ventricle short-axis from 0.1 to 0.16 N/mm^2. For silicones the range of modulus of elasticity was 0.02–1.16 N/mm^2, and for the 3D-printed materials from 0.85 to 1.02 N/mm^2. The stress-strain curves of all tissues showed a non-linear behaviour in the cyclic tensile testing, with a distinct toe region, followed by exponential strain hardening behaviour towards the peak elongation. The vessel samples showed a more linear behaviour comparted to myocardial samples. The silicones and 3D printing materials exhibited near-linearity at higher strain ranges, with a decrease in stiffness following the initial deformation. All samples showed a deviation between the loading and unloading curves (hysteresis), and a reduction in peak force over the first few cycles (adaptation effect) at constant deformation. Conclusion: The modulus of elasticity of silicone mixtures is more in agreement to porcine cardiovascular tissues than 3D-printed materials. All synthetic materials showed an almost linear behaviour in the mechanical testing compared to the non-linear behaviour of the biological tissues, probably due to fibre recruitment mechanism in the latter

Intermolecular dark resonance energy transfer (DRET): Upgrading fluorogenic DNA sensing

The sensitivity of FRET-based sensing is usually limited by the spectral overlaps of the FRET donor and acceptor, which generate a poor signal-to-noise ratio. To overcome this limitation, a quenched donor presenting a large Stokes shift can be combined with a bright acceptor to perform Dark Resonance Energy Transfer (DRET). The consequent fluorogenic response from the acceptor considerably improves the signal-to-noise ratio. To date, DRET has mainly relied on a donor that is covalently bound to the acceptor. In this context, our aim was to develop the first intermolecular DRET pair for specific sensing of nucleic acid sequences. To this end, we designed DFK, a push-pull probe based on a fluorenyl π-platform that is strongly quenched in water. DFK was incorporated into a series of oligonucleotides and used as a DRET donor with Cy5-labeled complementary sequences. In line with our expectations, excitation of the dark donor in the double-labeled duplex switched on the far-red Cy5 emission and remained free of cross-excitation. The DRET mechanism was supported by time-resolved fluorescence measurements. This concept was then applied with binary probes, which confirmed the distance dependence of DRET as well as its potency in detecting sequences of interest with low background noise

Biology and ecology of biofilms formed by a plant pathogen Phytophthora parasitica: From biochemical ecology to ecological engineering

AbstractIn nature, the organisation of microbial species into biofilms has a great influence on local environments and in human or plant diseases. This important trait of prokaryotes and eukaryotes is poorly understood while the knowledge of the related biological processes could constitute a novel base for controlling diseases. A study is developed on the oomycete Phytophthora parasitica belonging to a major class of eukaryotic plant pathogens to understand molecular and ecological basis of biofilm formation. The identification of signalling molecules and the definition of their spectrum of activity within the biofilm community will improve our understanding of fundamental biological processes, our ability to forecast pathogen behaviour and to elaborate new tools dedicated to plant diseases management with low environmental impact

8-modified-2\u27-deoxyadenosine analogues induce delayed polymerization arrest during HIV-1 reverse transcription

The occurrence of resistant viruses to any of the anti-HIV-1 compounds used in the current therapies against AIDS underlies the urge for the development of new drug targets and/or new drugs acting through novel mechanisms. While all anti-HIV-1 nucleoside analogues in clinical use and in clinical trials rely on ribose modifications for activity, we designed nucleosides with a natural deoxyribose moiety and modifications of position 8 of the adenine base. Such modifications might induce a steric clash with helix &alpha;H in the thumb domain of the p66 subunit of HIV-1 RT at a distance from the catalytic site, causing delayed chain termination. Eleven new 2&prime;-deoxyadenosine analogues modified on position 8 of the purine base were synthesized and tested in vitro and in cell-based assays. In this paper we demonstrate for the first time that chemical modifications on position 8 of 2&prime;-deoxyadenosine induce delayed chain termination in vitro, and also inhibit DNA synthesis when incorporated in a DNA template strand. Furthermore, one of them had moderate anti-HIV-1 activity in cell-culture. Our results constitute a proof of concept indicating that modification on the base moiety of nucleosides can induce delayed polymerization arrest and inhibit HIV-1 replication.<br /

Search for Branons at LEP

We search, in the context of extra-dimension scenarios, for the possible existence of brane fluctuations, called branons. Events with a single photon or a single Z-boson and missing energy and momentum collected with the L3 detector in e^+ e^- collisions at centre-of-mass energies sqrt{s}=189-209$ GeV are analysed. No excess over the Standard Model expectations is found and a lower limit at 95% confidence level of 103 GeV is derived for the mass of branons, for a scenario with small brane tensions. Alternatively, under the assumption of a light branon, brane tensions below 180 GeV are excluded

Search for Charginos with a Small Mass Difference with the Lightest Supersymmetric Particle at \sqrt{s} = 189 GeV

A search for charginos nearly mass-degenerate with the lightest supersymmetric particle is performed using the 176 pb^-1 of data collected at 189 GeV in 1998 with the L3 detector. Mass differences between the chargino and the lightest supersymmetric particle below 4 GeV are considered. The presence of a high transverse momentum photon is required to single out the signal from the photon-photon interaction background. No evidence for charginos is found and upper limits on the cross section for chargino pair production are set. For the first time, in the case of heavy scalar leptons, chargino mass limits are obtained for any \tilde{\chi}^{+-}_1 - \tilde{\chi}^0_1 mass difference

Search for Low Scale Gravity Effects in e+e- Collisions at LEP

Recent theories propose that quantum gravity effects may be observable at LEP energies via gravitons that couple to Standard Model particles and propagate into extra spatial dimensions. The associated production of a graviton and a photon is searched for as well as the effects of virtual graviton exchange in the processes: e+e- -> gamma gamma, ZZ, WW, mu mu, tau tau, qq and ee No evidence for this new interaction is found in the data sample collected by the L3 detector at LEP at centre-of-mass energies up to 183 GeV. Limits close to 1 TeV on the scale of this new scenario of quantum gravity are set

High Resolution Genome-Wide Analysis of Chromosomal Alterations in Burkitt's Lymphoma

Additional chromosomal abnormalities are currently detected in Burkitt's lymphoma. They play major roles in the progression of BL and in prognosis. The genes involved remain elusive. A whole-genome oligonucleotide array CGH analysis correlated with karyotype and FISH was performed in a set of 27 Burkitt's lymphoma-derived cell lines and primary tumors. More than half of the 145 CNAs<2 Mb were mapped to Mendelian CNVs, including GSTT1, glutathione s-transferase and BIRC6, an anti-apoptotic protein, possibly predisposing to some cancers. Somatic cell line-specific CNVs localized to the IG locus were consistently observed with the 244 K aCGH platform. Among 136 CNAs >2 Mb, gains were found in 1q (12/27), 13q (7/27), 7q (6/27), 8q(4/27), 2p (3/27), 11q (2/27) and 15q (2/27). Losses were found in 3p (5/27), 4p (4/27), 4q (4/27), 9p (4/27), 13q (4/27), 6p (3/27), 17p (3/27), 6q (2/27),11pterp13 (2/27) and 14q12q21.3 (2/27). Twenty one minimal critical regions (MCR), (range 0.04–71.36 Mb), were delineated in tumors and cell lines. Three MCRs were localized to 1q. The proximal one was mapped to 1q21.1q25.2 with a 6.3 Mb amplicon (1q21.1q21.3) harboring BCA2 and PIAS3. In the other 2 MCRs, 1q32.1 and 1q44, MDM4 and AKT3 appeared as possible drivers of these gains respectively. The 13q31.3q32.1 <89.58–96.81> MCR contained an amplicon and ABCC4 might be the driver of this amplicon. The 40 Kb 2p16.1 <60.96–61> MCR was the smallest gained MCR and specifically encompassed the REL oncogene which is already implicated in B cell lymphomas. The most frequently deleted MCR was 3p14.1 <60.43–60.53> that removed the fifth exon of FHIT. Further investigations which combined gene expression and functional studies are essential to understand the lymphomagenesis mechanism and for the development of more effective, targeted therapeutic strategies

Search for R-parity Violating Decays of Supersymmetric Particles in e+e−e^+ e^- Collisions at LEP

A search, in $e^+ e^-$ collisions, for chargino, neutralino, scalar lepton and scalar quark pair-production is performed, without assuming R-parity conservation in decays, in the case that only one of the coupling constants $\lambda_{ijk}$ or $\lambda''_{ ijk}$ is non-negligible. No signal is found in data up to a centre-of-mass energy of 208 \GeV. Limits on the production cross sections and on the masses of supersymmetric particles are derived.A search, in e + e − collisions, for chargino, neutralino, scalar lepton and scalar quark pair-production is performed, without assuming R-parity conservation in decays, in the case that only one of the coupling constants λ or λ ″ is non-negligible. No signal is found in data up to a centre-of-mass energy of 208 GeV. Limits on the production cross sections and on the masses of supersymmetric particles are derived.A search, in e^+e^- collisions, for chargino, neutralino, scalar lepton and scalar quark pair-production is performed, without assuming R-parity conservation in decays, in the case that only one of the coupling constants lambda_ijk or lambda''_ijk is non-negligible. No signal is found in data up to a centre-of-mass energy of 208GeV. Limits on the production cross sections and on the masses of supersymmetric particles are derived