Novel DNA probes with low background and high hybridization-triggered fluorescence

Novel fluorogenic DNA probes are described. The probes (called Pleiades) have a minor groove binder (MGB) and a fluorophore at the 5′-end and a non-fluorescent quencher at the 3′-end of the DNA sequence. This configuration provides surprisingly low background and high hybridization-triggered fluorescence. Here, we comparatively study the performance of such probes, MGB-Eclipse probes, and molecular beacons. Unlike the other two probe formats, the Pleiades probes have low, temperature-independent background fluorescence and excellent signal-to-background ratios. The probes possess good mismatch discrimination ability and high rates of hybridization. Based on the analysis of fluorescence and absorption spectra we propose a mechanism of action for the Pleiades probes. First, hydrophobic interactions between the quencher and the MGB bring the ends of the probe and, therefore, the fluorophore and the quencher in close proximity. Second, the MGB interacts with the fluorophore and independent of the quencher is able to provide a modest (2–4-fold) quenching effect. Joint action of the MGB and the quencher is the basis for the unique quenching mechanism. The fluorescence is efficiently restored upon binding of the probe to target sequence due to a disruption in the MGB–quencher interaction and concealment of the MGB moiety inside the minor groove

The Hard Problem of Consciousness in the Light of Onto-Gnoseological Uncertainty

Purpose: The main purpose of this article is to show that the paradigm of viewing the ‘hard problem’ of consciousness in analytic philosophy makes it a pseudo-problem rather than a ‘hard problem’. The objectives of this research included showing the reasons for the authors’ thesis, demonstrating the irreducibility of consciousness as a special layer of reality, and proposing a way to overcome these difficulties. Design/methodology/approach: In this article, the ‘hard problem’ of consciousness is viewed from the standpoints of the transcendental-phenomenological and dialectical approaches and is analyzed through the prism of the principle of onto-gnoseological uncertainty. Findings: It is shown that the way of formulating the ‘hard problem’ in the analytical philosophical tradition inevitably makes it a pseudo-problem. At the same time, with the consistent realization of the principle of onto-gnoseological uncertainty, the antinomy of solutions to the problems of consciousness is eliminated, which opens up a way to a productive solution of problems related to the interpretation of consciousness both in natural sciences and in philosophy. Originality/value: This research reveals the methodological potential of applying the principle of onto-gnoseological uncertainty to the problems that arise in modern philosophy in connection with the achievements of natural sciences

Real-time Monitoring for the Next Core-Collapse Supernova in JUNO

Core-collapse supernova (CCSN) is one of the most energetic astrophysical events in the Universe. The early and prompt detection of neutrinos before (pre-SN) and during the SN burst is a unique opportunity to realize the multi-messenger observation of the CCSN events. In this work, we describe the monitoring concept and present the sensitivity of the system to the pre-SN and SN neutrinos at the Jiangmen Underground Neutrino Observatory (JUNO), which is a 20 kton liquid scintillator detector under construction in South China. The real-time monitoring system is designed with both the prompt monitors on the electronic board and online monitors at the data acquisition stage, in order to ensure both the alert speed and alert coverage of progenitor stars. By assuming a false alert rate of 1 per year, this monitoring system can be sensitive to the pre-SN neutrinos up to the distance of about 1.6 (0.9) kpc and SN neutrinos up to about 370 (360) kpc for a progenitor mass of 30$M_{\odot}$ for the case of normal (inverted) mass ordering. The pointing ability of the CCSN is evaluated by using the accumulated event anisotropy of the inverse beta decay interactions from pre-SN or SN neutrinos, which, along with the early alert, can play important roles for the followup multi-messenger observations of the next Galactic or nearby extragalactic CCSN.Comment: 24 pages, 9 figure

Potential of Core-Collapse Supernova Neutrino Detection at JUNO

JUNO is an underground neutrino observatory under construction in Jiangmen, China. It uses 20kton liquid scintillator as target, which enables it to detect supernova burst neutrinos of a large statistics for the next galactic core-collapse supernova (CCSN) and also pre-supernova neutrinos from the nearby CCSN progenitors. All flavors of supernova burst neutrinos can be detected by JUNO via several interaction channels, including inverse beta decay, elastic scattering on electron and proton, interactions on C12 nuclei, etc. This retains the possibility for JUNO to reconstruct the energy spectra of supernova burst neutrinos of all flavors. The real time monitoring systems based on FPGA and DAQ are under development in JUNO, which allow prompt alert and trigger-less data acquisition of CCSN events. The alert performances of both monitoring systems have been thoroughly studied using simulations. Moreover, once a CCSN is tagged, the system can give fast characterizations, such as directionality and light curve

Detection of the Diffuse Supernova Neutrino Background with JUNO

As an underground multi-purpose neutrino detector with 20 kton liquid scintillator, Jiangmen Underground Neutrino Observatory (JUNO) is competitive with and complementary to the water-Cherenkov detectors on the search for the diffuse supernova neutrino background (DSNB). Typical supernova models predict 2-4 events per year within the optimal observation window in the JUNO detector. The dominant background is from the neutral-current (NC) interaction of atmospheric neutrinos with 12C nuclei, which surpasses the DSNB by more than one order of magnitude. We evaluated the systematic uncertainty of NC background from the spread of a variety of data-driven models and further developed a method to determine NC background within 15\% with {\it{in}} {\it{situ}} measurements after ten years of running. Besides, the NC-like backgrounds can be effectively suppressed by the intrinsic pulse-shape discrimination (PSD) capabilities of liquid scintillators. In this talk, I will present in detail the improvements on NC background uncertainty evaluation, PSD discriminator development, and finally, the potential of DSNB sensitivity in JUNO

Chemistry of Minor Groove Binder–Oligonucleotide Conjugates

Various types of minor groove binders have been attached to synthetic oligodeoxynucleotides, and the interactions of these conjugates (MB‐ODNs) with DNA are reviewed here. MB‐ODNs have enhanced DNA affinity and have improved the hybridization properties of sequence‐specific DNA probes. Short MB‐ODNs hybridize with ssDNA to give more stable DNA duplexes than unmodified ODNs with similar lengths. Mismatch discrimination of short MB‐ODNs is enhanced in comparison to longer unmodified ODNs. The stronger binding of MB‐ODNs allows for more stringent hybridization conditions to be used in DNA probe‐based assays. MB‐ODNs are especially useful in quantitative “real‐time” PCR assays since they bind efficiently during the high‐temperature primer extension cycle. The synthesis and biophysical chemistry of MB‐ODN conjugates are reviewed here. Four published structural classes of MB‐ODNs and their various dsDNA binding modes are discussed, and the well‐characterized DPI3‐type MB‐ODNs and their interactions with ssDNA target strands are described in detail.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153100/1/cpnc0804.pd

Mineralogy of Particulate Suspended Matter of the Severnaya Dvina River (White Sea, Russia)

This paper seeks to generalize the data obtained over 4 years of investigation of the suspended sediment mineral composition in Severnaya Dvina River. The sampling of the river water to isolate suspended particulate matter (SPM) using the method of sedimentation from large water volumes (200–800 L) was carried out at two points of the delta with different hydrological regimes every month for four years. SPM samples weighing 1 g and more allowed us to obtain and preserve for different analytical procedures the grain size fractions from 1.0–0.5 to <0.001 mm (from sands to pelit). The analyses of fractions revealed a sharp prevalence of pelitic fractions (<0.01 mm) (near 90% on average), while the share of silt was 4%–5%. Coarse fractions were found in the SPM of the main stream of the river but were absent in the samples taken at the point near the river–sea boundary. The determinations of clastic, clay, and some other minerals using the method of X-ray diffraction analysis have shown that in the group of clastic minerals, quartz and plagioclase prevail. Among the clay minerals, smectite and illite were present in high quantities, and chlorite and kaolinite were in lower quantitative. The distribution of minerals in the grain size fractions showed that the sum of clastic minerals reached its highest content of up to 84% in silt fractions (0.05–0.01 mm), while the sum of clay minerals in this fraction was minimal (about 15%). Investigations of seasonal variations of clastic and clay minerals during the whole period showed that the contents of minerals in the SPM of the Severnaya Dvina did not change much over the year. As a result of this work, the following trend was established on the behavior of all kinds of minerals: during the periods of high water in spring and autumn, a slightly increased quantity of clastic minerals was detected in comparison to winter and summer, while the variations in the quantities of clay minerals were insignificant

Differential melting curves for the complexes PL1 + C1 (or C2) (), PL2 + C2 (C1) (); EC1 + C1 (or C2) (), EC2 + C2 (C1) (); MB1 + C1 (or C2) (), MB2 + C2 (C1) ()

<p><b>Copyright information:</b></p><p>Taken from "Novel DNA probes with low background and high hybridization-triggered fluorescence"</p><p></p><p>Nucleic Acids Research 2007;35(5):e30-e30.</p><p>Published online 26 Jan 2007</p><p>PMCID:PMC1865069.</p><p>© 2007 The Author(s).</p