Mechanisms and impact of alternative transposition-induced segmental duplications

Segmental duplications are prevalent in both plant and animal genomes, and have played important roles in genome evolution. The focus of my project is to understand the transposition-mediated mechanisms that lead to the formation of segmental duplications, and the immediate impact of recently generated large (up to 14.6 Mb) tandem duplications in maize. We applied a variety of genetic, molecular, statistical and bioinformatics approaches, including genetic screening, PCR, Southern blotting, qRT-PCR, microarray, mRNA-sequencing, small RNA-sequencing, and a self-developed program (STRAND: Search for Transposon-Induced Tandem Direct Duplications) to study these questions. We discovered new genome rearrangement mechanisms, including transposition of paired DNA transposon termini that can generate tandem direct duplications (TDD) and novel structures termed Composite Insertions. Genomic study revealed that these mechanisms have played an important role in generating TDD in 8 of 22 examined plant genomes. We also found a significant dosage-dependent effect of a 14.6 Mb duplication on phenotypic variation, and expression of mRNA and small RNA transcripts. This work expands our current knowledge of how DNA transposons contribute to rapid genome expansion, extends our understanding of the significance of DNA transposons in altering genome structure, and provides new insight into the transcriptional expression and phenotypic effect of a specific and recent maize duplication

B(s)→SB_{(s)}\to S transitions in the light cone sum rules with the chiral current

$B_{(s)}$ semi-leptonic decays to the light scalar meson, $B_{(s)}\to S l\bar{\nu}_l, S l \bar{l}\,\,(l=e,\mu,\tau)$, are investigated in the QCD light-cone sum rules (LCSR) with chiral current correlator. Having little knowledge of ingredients of the scalar mesons, we confine ourself to the two quark picture for them and work with the two possible Scenarios. The resulting sum rules for the form factors receive no contributions from the twist-3 distribution amplitudes (DA's), in comparison with the calculation of the conventional LCSR approach where the twist-3 parts play usually an important role. We specify the range of the squared momentum transfer $q^2$, in which the operator product expansion (OPE) for the correlators remains valid approximately. It is found that the form factors satisfy a relation consistent with the prediction of soft collinear effective theory (SCET). In the effective range we investigate behaviors of the form factors and differential decay widthes and compare our calculations with the observations from other approaches. The present findings can be beneficial to experimentally identify physical properties of the scalar mesons.Comment: 22 pages,16 figure

Bc(B)→Dlν~B_c(B){\to}D l\tilde{\nu} form factors in Light-Cone Sum Rules and the DD-meson distribution amplitude

In this paper we calculate the weak form factors of the decays $B_c(B)\to Dl\tilde\nu$ by using the chiral current correlator within the framework of the QCD light-cone sum rules (LCSR). The expressions of the form factors only depend on the leading twist distribution amplitude (DA) of the $D$ meson. Three models of the $D$-meson distribution amplitude are employed and the calculated form factor $F_{B_c\to D}(0)$ is given. Our prediction, by using the $D$-meson distribution amplitude with the exponential suppression at the end points, is compatible with other approaches, and favors the three-points sum rules (3PSR) approach with the Coulumb corrections included.Comment: 12 pages, 3 figure

Micro Fourier Transform Profilometry (μ\muFTP): 3D shape measurement at 10,000 frames per second

Recent advances in imaging sensors and digital light projection technology have facilitated a rapid progress in 3D optical sensing, enabling 3D surfaces of complex-shaped objects to be captured with improved resolution and accuracy. However, due to the large number of projection patterns required for phase recovery and disambiguation, the maximum fame rates of current 3D shape measurement techniques are still limited to the range of hundreds of frames per second (fps). Here, we demonstrate a new 3D dynamic imaging technique, Micro Fourier Transform Profilometry ($\mu$FTP), which can capture 3D surfaces of transient events at up to 10,000 fps based on our newly developed high-speed fringe projection system. Compared with existing techniques, $\mu$FTP has the prominent advantage of recovering an accurate, unambiguous, and dense 3D point cloud with only two projected patterns. Furthermore, the phase information is encoded within a single high-frequency fringe image, thereby allowing motion-artifact-free reconstruction of transient events with temporal resolution of 50 microseconds. To show $\mu$FTP's broad utility, we use it to reconstruct 3D videos of 4 transient scenes: vibrating cantilevers, rotating fan blades, bullet fired from a toy gun, and balloon's explosion triggered by a flying dart, which were previously difficult or even unable to be captured with conventional approaches.Comment: This manuscript was originally submitted on 30th January 1

Lamellar phase separation and dynamic competition in La0.23Ca0.77MnO3

We report the coexistence of lamellar charge-ordered (CO) and charge-disordered (CD) domains, and their dynamical behavior, in La0.23Ca0.77MnO3. Using high resolution transmission electron microscopy (TEM), we show that below Tcd~170K a CD-monoclinic phase forms within the established CO-orthorhombic matrix. The CD phase has a sheet-like morphology, perpendicular to the q vector of the CO superlattice (a axis of the Pnma structure). For temperatures between 64K and 130K, both the TEM and resistivity experiments show a dynamic competition between the two phases: at constant T, the CD phase slowly advances over the CO one. This slow dynamics appears to be linked to the magnetic transitions occurring in this compound, suggesting important magnetoelastic effects.Comment: 4 pages, 4 figure