A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation

Background: Pyrosequencing techniques allow scientists to perform prokaryotic genome sequencing to achieve the draft genomic sequences within a few days. However, the assemblies with shotgun sequencing are usually composed of hundreds of contigs. A further multiplex PCR procedure is needed to fill all the gaps and link contigs into complete chromosomal sequence, which is the basis for prokaryotic comparative genomic studies. In this article, we study various pyrosequencing strategies by simulated assembling from 100 prokaryotic genomes. Findings. Simulation study shows that a single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) can produce: 1) ∼90% of 100 assemblies with 99.99%; 4) average false gene duplication rate is < 0.7%; 5) average false gene loss rate is < 0.4%. Conclusions: A single end 454 Jr. run combined with a paired end 454 Jr. run (8 kb library) is a cost-effective way for prokaryotic whole genome sequencing. This strategy provides solution to produce high quality draft assemblies for most of prokaryotic organisms within days. Due to the small number of assembled scaffolds, the following multiplex PCR procedure (for gap filling) would be easy. As a result, large scale prokaryotic whole genome sequencing projects may be finished within weeks. © 2012 Jiang et al; BioMed Central Ltd.published_or_final_versio

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

Drug resistance and R-plasmids in salmonellae in Hong Kong

published_or_final_versionMicrobiologyDoctoralDoctor of Philosoph

Functional morphology of Echinocephalus sinensis (Nematoda: Gnathostomatidae), parasite from the oyster and ray in Hong Kong

published_or_final_versionZoologyMasterMaster of Philosoph

Measuring low energy atmospheric neutrino spectra with the JUNO detector

Atmospheric neutrinos are one of the most relevant natural neutrino sources that can be exploited to infer properties about Cosmic Rays and neutrino oscillations. The Jiangmen Underground Neutrino Observatory (JUNO) experiment, a 20 kton liquid scintillator detector with excellent energy resolution is currently under construction in China. JUNO will be able to detect several atmospheric neutrinos per day given the large volume. A study on the JUNO detection and reconstruction capabilities of atmospheric $\nu_e$ and $\nu_\mu$ fluxes is presented in this paper. In this study, a sample of atmospheric neutrinos Monte Carlo events has been generated, starting from theoretical models, and then processed by the detector simulation. The excellent timing resolution of the 3" PMT light detection system of JUNO detector and the much higher light yield for scintillation over Cherenkov allow to measure the time structure of the scintillation light with very high precision. Since $\nu_e$ and $\nu_\mu$ interactions produce a slightly different light pattern, the different time evolution of light allows to discriminate the flavor of primary neutrinos. A probabilistic unfolding method has been used, in order to infer the primary neutrino energy spectrum from the detector experimental observables. The simulated spectrum has been reconstructed between 100 MeV and 10 GeV, showing a great potential of the detector in the atmospheric low energy region

Damping signatures at JUNO, a medium-baseline reactor neutrino oscillation experiment

We study damping signatures at the Jiangmen Underground Neutrino Observatory(JUNO), a medium-baseline reactor neutrino oscillation experiment. These damping signaturesare motivated by various new physics models, including quantum decoherence, 3 decay, neutrinoabsorption, and wave packet decoherence. The phenomenological effects of these models canbe characterized by exponential damping factors at the probability level. We assess how wellJUNO can constrain these damping parameters and how to disentangle these different dampingsignatures at JUNO. Compared to current experimental limits, JUNO can significantly improvethe limits on 3/3 in the 3 decay model, the width of the neutrino wave packet , and theintrinsic relative dispersion of neutrino momentum rel