Evolution Of New Duplicate Genes In Arabidopsis Thaliana

Abstract Gene duplication is one of the major mechanisms by which organisms expand their genomes. The material added to the genome can then be acted upon by mutation and natural selection to increase the fitness of the species. By studying these duplicate sequences we can understand the process by which species evolve new functional genes. In a previous paper we identified 100 new duplicate genes through a genome wide comparison between A. thaliana and related species. We selected three of these new duplicate genes and investigated more closely their sequence and expression divergence from their parental gene. The three new duplicate genes selected were AT1G19080, AT1G29410 and AT4G13500 and their parents AT3G55490 AT1G07780 and AT2G05310 respectively. These genes were sequenced using A. thaliana accession lines from a multitude of locations, and the sequences were used in population analyses. The genes were also tested for differential expression patterns. The genes all show evidence of negative selection or a recent population bottleneck. Notably we detected a large number of populations carrying deletions for the new genes. The second set (AT1G07780/ AT1G19080) displayed differential expression, while the third set shows no divergence. The AT4G13500/ AT2G05310 gene family has no known function. In an attempt to discern their function we obtained mutant plants and grew them alongside control plants in an attempt to detect a phenotype for the knockout. We noticed divergent growth patterns between the groups under different light cycles, however they require further testing

CARS-background suppression by phase-controlled nonlinear interferometry.

We have developed a new technique for efficient suppression of the nonresonant background in coherent anti-Stokes Raman scattering (CARS). The advantage of this technique, which is based upon phase-controlled superposition of an appropriately selected reference signal, is presented in theory and demonstrated experimentally by the example of the S(3) (pure rotational) transition of molecular hydrogen

Delta-subunit-containing GABAA-receptors mediate tonic inhibition in paracapsular cells of the mouse amygdala

The intercalated paracapsular cells (pcs) are small GABAergic interneurons that form densely populated clusters surrounding the basolateral (BLA) complex of the amygdala. Their main task in the amygdala circuitry appears to be the control of information flow, as they act as an inhibitory interface between input and output nuclei. Modulation of their activity is thus thought to affect amygdala output and the generation of fear and anxiety. Recent evidence indicates that pcs express benzodiazepine (BZ)-sensitive GABA(A) receptor (GABA(A)R) variants containing the α2- and α3-subunit for transmission of post-synaptic currents, yet little is known about the expression of extrasynaptic GABA(A)Rs, mediating tonic inhibition and regulating neuronal excitability. Here, we show that pcs from the lateral and medial intercalated cell cluster (l- and mITC, respectively) express a tonic GABAergic conductance that could be significantly increased in a concentration-dependent manner by the δ-preferring GABA(A)R agonist THIP (0.5–10 μM), but not by the BZ diazepam (1 μM). The neurosteroid THDOC (300 nM) also increased tonic currents in pcs significantly, but only in the presence of additional GABA (5 μM). Immunohistochemical stainings revealed that both the δ-GABA(A)R and the α4-GABA(A)R subunit are expressed throughout all ITCs, while no staining for the α5-GABA(A)R subunit could be detected. Moreover, 1 μM THIP dampened excitability in pcs most likely by increasing shunting inhibition. In line with this, THIP significantly decreased lITC-generated inhibition in target cells residing in the BLA nucleus by 30%. Taken together these results demonstrate for the first time that pcs express a tonic inhibitory conductance mediated most likely by α4/δ-containing GABA(A)Rs. This data also suggest that δ-GABA(A)R targeting compounds might possibly interfere with pcs-related neuronal processes such as fear extinction

Second harmonic generation in planar optical waveguides.

We study optical second harmonic generation (SHG) in planar waveguide structures composed of several layers with different dielectric constants. We develop a general formalism for the calculation of mode generation by a planar antenna embedded in the waveguide. As an application we consider a monolayer of high second-order susceptibility adsorbed at the interface between two layers of the waveguide structure. Periodic modulation of the nonlinear susceptibility allows phase matching leading to dramatically enhanced second harmonic intensities. We investigate the SHG-efficiency of various experimentally realizable geometries

Divergent Evolutionary and Expression Patterns between Lineage Specific New Duplicate Genes and Their Parental Paralogs in \u3cem\u3eArabidopsis thaliana\u3c/em\u3e

Gene duplication is an important mechanism for the origination of functional novelties in organisms. We performed a comparative genome analysis to systematically estimate recent lineage specific gene duplication events in Arabidopsis thaliana and further investigate whether and how these new duplicate genes (NDGs) play a functional role in the evolution and adaption of A. thaliana. We accomplished this using syntenic relationship among four closely related species, A. thaliana, A. lyrata, Capsella rubella and Brassica rapa. We identified 100 NDGs, showing clear origination patterns, whose parental genes are located in syntenic regions and/or have clear orthologs in at least one of three outgroup species. All 100 NDGs were transcribed and under functional constraints, while 24% of the NDGs have differential expression patterns compared to their parental genes. We explored the underlying evolutionary forces of these paralogous pairs through conducting neutrality tests with sequence divergence and polymorphism data. Evolution of about 15% of NDGs appeared to be driven by natural selection. Moreover, we found that 3 NDGs not only altered their expression patterns when compared with parental genes, but also evolved under positive selection. We investigated the underlying mechanisms driving the differential expression of NDGs and their parents, and found a number of NDGs had different cis-elements and methylation patterns from their parental genes. Overall, we demonstrated that NDGs acquired divergent cis-elements and methylation patterns and may experience sub-functionalization or neo-functionalization influencing the evolution and adaption of A. thaliana

Anisotropic second-order nonlinearities of organic monolayers.

Monolayers prepared from hemicyanine chromophores of high second-order nonlinearity (β=1.3×10−26 esu at resonance) have been used to study anisotropies of the concomitant χ(2)-susceptibility tensor. All components of this third-rank tensor have been determined by Fourier analysis of the anisotropic coverage density Ns(φ) with respect to the angle of rotation about surface normal. Depending on the preparation both Cs and C2v symmetry could be identified

Surface-enhanced optical third-harmonic generation in Ag island films

Surface-enhanced optical third-harmonic generation (THG) is observed in silver island films. The THG intensity from Ag nanoparticles is enhanced by more than two orders of magnitude with respect to the THG intensity from a smooth and homogeneous silver surface. This enhancement is attributed to local plasmon excitation and resonance of the local field at the third-harmonic wavelength. The diffuse and depolarized component of the enhanced THG is associated with the third-order hyper-Rayleigh scattering in a 2-D random array of silver nanoparticles.Comment: 4 pages, 2 figure