Multiple-octave spanning mid-IR supercontinuum generation in bulk quadratic nonlinear crystals

Bright and broadband coherent mid-IR radiation is important for exciting and probing molecular vibrations. Using cascaded nonlinearities in conventional quadratic nonlinear crystal like lithium niobate, self-defocusing near-IR solitons have been demonstrated that led to very broadband supercontinuum generation in the visible, near-IR and short-wavelength mid-IR. Here we conduct an experiment where a mid-IR crystal pumped in the mid-IR gives multiple-octave spanning supercontinua. The crystal is cut for noncritical interaction, so the three-wave mixing of a single mid-IR femtosecond pump source leads to highly phase-mismatched second-harmonic generation. This self-acting cascaded process leads to the formation of a self-defocusing soliton at the mid-IR pump wavelength and after the self-compression point multiple octave-spanning supercontinua are observed (covering 1.6-$7.0~\mu$m). The results were recorded in a commercially available crystal LiInS$_2$ pumped in the 3-$4~\mu$m range, but other mid-IR crystals can readily be used as well.Comment: submitted to APL Photonic

Experimental observation of long-wavelength dispersive wave generation induced by self-defocusing nonlinearity in BBO crystal

We experimentally observe long-wavelength dispersive waves generation in a BBO crystal. A soliton was formed in normal GVD regime of the crystal by a self-defocusing and negative nonlinearity through phase-mismatched quatradic interaction. Strong temporal pulse compression confirmed the formation of soliton during the pulse propagation inside the crystal. Significant dispersive wave radiation was measured in the anomalous GVD regime of the BBO crystal. With the pump wavelengths from 1.24 to 1.4 $\mu$m, tunable dispersive waves are generated around 1.9 to 2.2 $\mu$m. The observed dispersive wave generation is well understood by simulations.Comment: in preparatio

The anisotropic Kerr nonlinear refractive index of the beta-barium borate (\beta-BaB2O4) nonlinear crystal

We study the anisotropic nature of the Kerr nonlinear response in a beta-barium borate (\beta-BaB2O4, BBO) nonlinear crystal. The focus is on determining the relevant $\chi^{(3)}$ cubic tensor components that affect interaction of type I cascaded second-harmonic generation. Various experiments in the literature are analyzed and we correct the data from some of the experiments for contributions from cascading as well as for updated material parameters. We find that the Kerr nonlinear tensor component responsible for self-phase modulation in cascading is considerably larger than what has been used to date. We evaluate the impact of using such a cubic anisotropic response in ultrafast cascading experiments.Comment: Updated version, comments on experiments from the literature welcom

Soliton-induced nonlocal resonances observed through high-intensity tunable spectrally compressed second-harmonic peaks

Experimental data of femtosecond thick-crystal second-harmonic generation shows that when tuning away from phase matching, a dominating narrow spectral peak appears in the second harmonic that can be tuned over 100's of nm by changing the phase-mismatch parameter. Traditional theory explains this as phase matching between a sideband in the broadband pump to its second-harmonic. However, our experiment is conducted under high input intensities and instead shows excellent quantitative agreement with a nonlocal theory describing cascaded quadratic nonlinearities. This theory explains the detuned peak as a nonlocal resonance that arises due to phase-matching between the pump and a detuned second-harmonic frequency, but where in contrast to the traditional theory the pump is assumed dispersion-free. As a soliton is inherently dispersion-free, the agreement between our experiment and the nonlocal theory indirectly proves that we have observed a soliton-induced nonlocal resonance. The soliton exists in the self-defocusing regime of the cascaded nonlinear interaction and in the normal dispersion regime of the crystal, and needs high input intensities to become excited.Comment: submitted, revised versio

Identification and characterization of target genes of RRS1-R, a protein conferring resistance in Arabidopsis thaliana to the pathogenic bacterium Ralstonia solanacearum

Ralstonia solanacearum, agent du flétrissement bactérien, affecte près de 200 espèces végétales. Les gènes RRS1-R confèrent à l'écotype d'A. thaliana Nd-1 une résistance à différentes souches de R. solanacearum. RRS1-R code une protéine de structure modulaire associant les domaines typiques de nombreuses protéines de résistance TIR-NBS-LRR et un domaine signature de facteurs de transcription WRKY. Dans l'écotype sensible Col-0, le gène RRS1-S code pour une protéine qui présente une structure très semblable. Au cours de ce travail, nous avons montré que les gènes RRS1-R et RRS1-S s'expriment essentiellement dans les cellules du péricycle et les cellules de passage de l'endoderme des racines matures et de la base de l'hypocotyle, cellules qui correspondent aux sites de pénétration des bactéries dans le système vasculaire où elles se multiplient. Nous avons montré que les deux domaines WRKY des protéines codées par ces gènes se fixent spécifiquement aux boites W, reconnues par les facteurs de transcription de la famille WRKY. Nous avons par la suite développé une approche DamID (DNA adenine methyltransferase IDentification) visant à identifier les gènes cibles des protéines RRS1-R et RRS1-S in vivo. L'analyse a été focalisée sur l'identification des gènes cibles de RRS1-R, dans le fond génétique résistant Nd-1 exprimant, ou pas, la protéine d'avirulence PopP2 sous contrôle d'un promoteur inductible. Dans chacun des cas le séquençage d'une centaine de FARMs (Fragments Associated to RRS1-driven Methylation) a permis de proposer des cibles potentielles et un modèle de fonctionnement de RRS1-R comme régulateur transcriptionel. Ce travail se poursuit par une analyse globale au niveau du génome, grâce au séquençage haut débit des FARMS et par l'étude de la fonction dans la réponse de la plante et de la régulation transcriptionelle de quelques cibles d'intérêt. Les résultats de ce travail illustrent dans leur ensemble l'importance de RRS1-R pour réguler la réponse des plantes à R.solanacearum.In nature, plants are constantly exposed to microbial pathogens and have evolved an effective and dynamic immune system in order to survive. R. solanacearum, the causing agent of wilt disease, is a soil-borne bacteria pathogenic on more than 200 plant species. Bacteria enter roots, invade xylem vessels and then spread rapidly to aerial parts of the plant through the vasculature. In A. thaliana Nd-1 plants, RRS1-R, with its partner RPS4 allows resistance to strains of R. solanacearum that deliver PopP2, a type III effector, into the plant cells. Previous studies showed that RRS1 and RPS4 are two NBS-LRR receptor proteins involved in the perception of the effector. Interestingly, RRS1 also harbors a WRKY transcription factor domain in its C-terminal end. In a susceptible Arabidopsis ecotype Col 0, RRS1-S is an allelic gene of RRS1-R, which encodes a similar structure. The recognition of bacterial and plant proteins leads to RRS1 protein accumulation in the nucleus, triggering possibly transcriptional gene regulation. Important genomic reprogramming of the infected plant cells has indeed been shown. My work shows that the RRS1-S and RRS1-R genes are expressed mainly in mature roots and basal hypocotyls, in pericycle cells and passage cells from the endoderm. These cells correspond to entry sites of the invading R. solanacearum bacteria within the vascular tissues. We also demonstrated the binding of WRKY domain of RRS1-R and RRS1-S, in vitro, to W boxes which are cis-regulatory elements recognized by WRKY transcription factors. In order to identify the in vivo target sequences of RRS1-R and RRS1-S, a DamID (DNA adenine methyltransferase IDentification) approach, detecting transitory DNA-protein associations was developed. DamID is based on the fusion of a protein of interest to a DNA Adenine Methyl-transferase from E. coli, which will methylate DNA in the vicinity of the binding sites of this protein. The fingerprints can be further mapped by DNA restriction with methylation sensitive enzymes, and cloned or directly sequenced. Analysis was focused on RRS1-R, by cloning FARMs (Fragment Associated to RRS1 driven Methylation) from Nd-1 plants expressing or not an inducible PopP2 gene. This allowed the identification of several putative targets of RRS1-R and led us to propose a model for its function as a transcription factor. High throughput sequencing was then initiated at a whole genome scale analysis. The function and transcriptional regulation of a putative RRS1 target gene was evaluated. Taken together, the results of this study illustrate the important role of RRS1-R in the regulation of the plant response to R. solanacearum

Soliton compression to few-cycle pulses with a high quality factor by engineering cascaded quadratic nonlinearities

We propose an efficient approach to improve few-cycle soliton compression with cascaded quadratic nonlinearities by using an engineered multi-section structure of the nonlinear crystal. By exploiting engineering of the cascaded quadratic nonlinearities, in each section soliton compression with a low effective order is realized, and high-quality few-cycle pulses with large compression factors are feasible. Each subsequent section is designed so that the compressed pulse exiting the previous section experiences an overall effective self-defocusing cubic nonlinearity corresponding to a modest soliton order, which is kept larger than unity to ensure further compression. This is done by increasing the cascaded quadratic nonlinearity in the new section with an engineered reduced residual phase mismatch. The low soliton orders in each section ensure excellent pulse quality and high efficiency. Numerical results show that compressed pulses with less than three-cycle duration can be achieved even when the compression factor is very large, and in contrast to standard soliton compression, these compressed pulses have minimal pedestal and high quality factor