GenomeFingerprinter and universal genome fingerprint analysis for systematic comparative genomics

How to compare whole genome sequences at large scale has not been achieved via conventional methods based on pair-wisely base-to-base comparison; nevertheless, no attention was paid to handle in-one-sitting a number of genomes crossing genetic category (chromosome, plasmid, and phage) with farther divergences (much less or no homologous) over large size ranges (from Kbp to Mbp). We created a new method, GenomeFingerprinter, to unambiguously produce three-dimensional coordinates from a sequence, followed by one three-dimensional plot and six two-dimensional trajectory projections to illustrate whole genome fingerprints. We further developed a set of concepts and tools and thereby established a new method, universal genome fingerprint analysis. We demonstrated their applications through case studies on over a hundred of genome sequences. Particularly, we defined the total genetic component configuration (TGCC) (i.e., chromosome, plasmid, and phage) for describing a strain as a system, and the universal genome fingerprint map (UGFM) of TGCC for differentiating a strain as a universal system, as well as the systematic comparative genomics (SCG) for comparing in-one-sitting a number of genomes crossing genetic category in diverse strains. By using UGFM, UGFM-TGCC, and UGFM-TGCC-SCG, we compared a number of genome sequences with farther divergences (chromosome, plasmid, and phage; bacterium, archaeal bacterium, and virus) over large size ranges (6Kbp~5Mbp), giving new insights into critical problematic issues in microbial genomics in the post-genomic era. This paper provided a new method for rapidly computing, geometrically visualizing, and intuitively comparing genome sequences at fingerprint level, and hence established a new method of universal genome fingerprint analysis for systematic comparative genomics.Comment: 63 pages, 15 figures, 5 table

Correspondence between Thermal and Quantum Vacuum Transitions around Horizons

Recently, there are comparable revised interests in bubble nucleation seeded by black holes. However, it is debated in the literature that whether one shall interpret a static bounce solution in the Euclidean Schwarzschild spacetime (with periodic Euclidean Schwarzschild time) as describing a false vacuum decay at zero temperature or at finite temperature. In this paper, we show a correspondence that the static bounce solution describes either a thermal transition of vacuum in the static region outside of a Schwarzschild black hole or a quantum transition in a maximally extended Kruskal-Szekeres spacetime, corresponding to the viewpoint of the external static observers or the freely falling observers, respectively. The Matsubara modes in the thermal interpretation can be mapped to the circular harmonic modes from an $O(2)$ symmetry in the tunneling interpretation. The complementary tunneling interpretation must be given in the Kruskal-Szekeres spacetime because of the so-called thermofield dynamics. This correspondence is general for bubble nucleation around horizons. We propose a new paradox related to black holes as a consequence of this correspondence.Comment: 26 pages; v2: typos corrected; v3: references added, discussion on AdS black holes added, to match the published version; v4(v5): Ref [37] updated, footnote [10] added v6: two typos correcte

Fluorescent sensors for biological applications.

Fluorescence is one of the most important analytical methods used in biological studies. In the past decade or two, instrumentation in this field has greatly advanced, and now it is possible to detect single photons or fluorescent molecules [1,2], or break the Abbe diffraction limit to distinguish two points spaced less than 50 nm apart [3]. Concurrently, the development of improved fluorescent probes, which can be coupled with state-of-the-art instruments, has been equally important. This special issue on "fluorescent biosensors" in Sensors reports recent results from eight research groups in the field of sensor development. It includes three review articles, and six research articles reporting original results. [...]