Metagenomic Anlaysis of microsymbiont selection by the legume plant host

Rhizobium leguminosarum bv.viciae is able to establish nitrogen-fixing symbioses with legumes of the genera Pisum, Lens, Lathyrus and Vicia. Classic studies using trap plants (Laguerre et al., Young et al.) provided evidence that different plant hosts are able to select different rhizobial genotypes among those available in a given soil. However, these studies were necessarily limited by the paucity of relevant biodiversity markers. We have now reappraised this problem with the help of genomic tools. A well-characterized agricultural soil (INRA Bretennieres) was used as source of rhizobia. Plants of Pisum sativum, Lens culinaris, Vicia sativa and V. faba were used as traps. Isolates from 100 nodules were pooled, and DNA from each pool was sequenced (BGI-Hong Kong; Illumina Hiseq 2000, 500 bp PE libraries, 100 bp reads, 12 Mreads). Reads were quality filtered (FastQC, Trimmomatic), mapped against reference R. leguminosarum genomes (Bowtie2, Samtools), and visualized (IGV). An important fraction of the filtered reads were not recruited by reference genomes, suggesting that plant isolates contain genes that are not present in the reference genomes. For this study, we focused on three conserved genomic regions: 16S-23S rDNA, atpD and nodDABC, and a Single Nucleotide Polymorphism (SNP) analysis was carried out with meta / multigenomes from each plant. Although the level of polymorphism varied (lowest in the rRNA region), polymorphic sites could be identified that define the specific soil population vs. reference genomes. More importantly, a plant-specific SNP distribution was observed. This could be confirmed with many other regions extracted from the reference genomes (data not shown). Our results confirm at the genomic level previous observations regarding plant selection of specific genotypes. We expect that further, ongoing comparative studies on differential meta / multigenomic sequences will identify specific gene components of the plant-selected genotypes

The Pangenome of the Plant-Selected Rhizobium leguminosarum bv viciae Sub-popuations

Rhizobium leguminosarum bv viciae (Rlv) is a bacterium able to establish effective symbioses with four different legume genera: Pisum, Lens, Lathyrus and Vicia. Classic studies using trap plants have previously shown that, given a choice, different plants prefer specific genotypes of rhizobia, which are adapted to the host (1, 2). In previous work we have performed a Pool-Seq analysis bases on pooled DNA samples from Rlv nodule isolates obtained from Pisum sativum, Lens culinaris, Vicia fava and V. sativa plants, used as rhizobial traps. This experiment allowed us to test the host preference hypothesis: different plant hosts select specific sub-populations of rhizobia from the available population present in a given soil. We have observed that plant-selected sub-populations are different at the single nucleotide polymorphism (SNP) level. We have selected individual isolates from each sub-population (9 fava-bean isolates, 14 pea isolates 9 vetch isolates and 9 lentil isolates) and sequenced their genomes at draft level (ca. 30x, 90 contigs). Genomic analyses have been carried out using J-species and CMG-Biotools. All the isolates had similar genome size (7.5 Mb) and number of genes (7,300). The resulting Average Nucleotide Identity (ANIm) tree showed that Rhizobium leguminosarum bv viciae is a highly diverse group. Each plant-selected subpopulation showed a closed pangenome and core genomes of similar size (11,500 and 4,800 genes, respectively). The addition of all four sub-population results in a larger, closed pangenome of 19,040 genes and a core genome of similar size (4,392 genes). Each sub-population contains a characteristic set of genes but no universal, plant-specific genes were found. The core genome obtained from all four sub-populations is probably a representative core genome for Rhizobium leguminosarum, given that the reference genome (Rhizobium leguminosarum bv. viciae strain 3841) contains most of the core genome. We have also analyzed the symbiotic cluster (nod), and different nod cluster genotypes were found in each sub-population. Supported by MINECO (Consolider-Ingenio 2010, MICROGEN Project, CSD2009-00006).

Ku band transmitarray lens for microwave applications

In this document a microstrip constrained lens device for Ku band, for microwave purpose, is presented. This paper offers an overview of artificial lens-type devices and the proposed transmitarray lens is thoroughly studied in terms of design and manufacturing, with architecture discussion and selection, along with the design, manufacturing and validation of all the forming components of the transmitarray (transmission circuits, radiating elements, etc.). Each element is properly characterized and assembled properly in the complete transmitarray prototype. Eventually, radiation pattern measurements as well as gain and directivity values, are provided to show the proper behaviour of the proposed transmitarray lens.

Solid catadioptric telephoto lens design with SMS method

Two new optical structures are designed using the Simultaneous Multiple Surfaces (SMS) method, comprised of 2 reflecting surfaces and 2 refracting surfaces, 800mm focal length, f/8 (aperture diameter 100 mm) and 1.180 diagonal field of view in the SWIR band. The lens surfaces are rotational symmetric and calculated to have good control of non-paraxial rays. We have achieved designs with excellent performance, and with total system length of less than 60 mm.

Ultra-compact SWIR telephoto lens design with SMS method

In this work, we propose two new optical structures, using the Simultaneous Multiple Surfaces (SMS) method, comprised of 2 reflecting surfaces and 2 refracting surfaces, 800mm focal length, f/8 (aperture diameter 100 mm) and 1.18 0 diagonal field of view in the SWIR band. The lens surfaces are rotational symmetric and calculated to have good control of non-paraxial rays. We have achieved designs with excellent performance, and with total system length of less than 60 mm.

SMS-based optimization strategy for ultra-compact SWIR telephoto lens design: erratum

We report and correct an error in [Opt. Express 20, 9726–9735 (2012)]. The author list has been modified. All other contents are unchanged.

Analytic design method for optimal imaging: coupling three ray sets using two free-form lens profiles

In this work, a new two-dimensional optics design method is proposed that enables the coupling of three ray sets with two lens surfaces. The method is especially important for optical systems designed for wide field of view and with clearly separated optical surfaces. Fermat’s principle is used to deduce a set of functional differential equations fully describing the entire optical system. The presented general analytic solution makes it possible to calculate the lens profiles. Ray tracing results for calculated 15th order Taylor polynomials describing the lens profiles demonstrate excellent imaging performance and the versatility of this new analytic design method.

Analytic free-form lens design in 3D: coupling three ray sets using two lens surfaces

The two-dimensional analytic optics design method presented in a previous paper [Opt. Express 20, 5576–5585 (2012)] is extended in this work to the three-dimensional case, enabling the coupling of three ray sets with two free-form lens surfaces. Fermat’s principle is used to deduce additional sets of functional differential equations which make it possible to calculate the lens surfaces. Ray tracing simulations demonstrate the excellent imaging performance of the resulting free-form lenses described by more than 100 coefficients.

Perfect imaging of three object points with only two analytic lens surfaces in two dimensions

In this work, a new two-dimensional analytic optics design method is presented that enables the coupling of three ray sets with two lens profiles. This method is particularly promising for optical systems designed for wide field of view and with clearly separated optical surfaces. However, this coupling can only be achieved if different ray sets will use different portions of the second lens profile. Based on a very basic example of a single thick lens, the Simultaneous Multiple Surfaces design method in two dimensions (SMS2D) will help to provide a better understanding of the practical implications on the design process by an increased lens thickness and a wider field of view. Fermat?s principle is used to deduce a set of functional differential equations fully describing the entire optical system. The transformation of these functional differential equations into an algebraic linear system of equations allows the successive calculation of the Taylor series coefficients up to an arbitrary order. The evaluation of the solution space reveals the wide range of possible lens configurations covered by this analytic design method. Ray tracing analysis for calculated 20th order Taylor polynomials demonstrate excellent performance and the versatility of this new analytical optics design concept.

Analytic free-form lens design for imaging applications with high aspect ratio

A new three-dimensional analytic optics design method is presented that enables the coupling of three ray sets with only two free-form lens surfaces. Closely related to the Simultaneous Multiple Surface method in three dimensions (SMS3D), it is derived directly from Fermat?s principle, leading to multiple sets of functional differential equations. The general solution of these equations makes it possible to calculate more than 80 coefficients for each implicit surface function. Ray tracing simulations of these free-form lenses demonstrate superior imaging performance for applications with high aspect ratio, compared to conventional rotational symmetric systems.

Aplanatic thin TIR lens

Aplanatic designs present great interest in the optics field since they are free from spherical aberration and linear coma at the axial direction. Nevertheless nowadays it cannot be found on literature any thin aplanatic design based on a lens. This work presents the first aplanatic thin lens (in this case a dome-shaped faceted TIR lens performing light collimation), designed for LED illumination applications. This device, due to its TIR structure (defined as an anomalous microstructure as we will see) presents good color-mixing properties. We will show this by means of raytrace simulations, as well as high optical efficiency.

SMS-based optimization strategy for ultra-compact SWIR telephoto lens design

A new optical design strategy for rotational aspheres using very few parameters is presented. It consists of using the SMS method to design the aspheres embedded in a system with additional simpler surfaces (such as spheres, parabolas or other conics) and optimizing the free-parameters. Although the SMS surfaces are designed using only meridian rays, skew rays have proven to be well controlled within the optimization. In the end, the SMS surfaces are expanded using Forbes series and then a second optimization process is carried out with these SMS surfaces as a starting point. The method has been applied to a telephoto lens design in the SWIR band, achieving ultra-compact designs with an excellent performance.

Silica final lens performance in laser fusion facilities: HiPER and LIFE

Silica final lens performance in laser fusion facilities: HiPER and LIFE

Analytic free-form lens design for tracking integration in concentrating photovoltaics

In this work the concept of tracking integration in concentrating photovoltaics (CPV) is revisited and developed further. With respect to conventional CPV, tracking integration eliminates the clear separation between stationary units of optics and solar cells, and external solar trackers. This approach is capable of further increasing the concentration ratio and makes high concentrating photovoltaics (> 500x) available for single-axis tracker installations. The reduced external solar tracking effort enables possibly cheaper and more compact installations. Our proposed optical system uses two laterally moving plano-convex lenses to achieve high concentration over a wide angular range of ±24°. The lateral movement allows to combine both steering and concentration of the incident direct sun light. Given the specific symmetry conditions of the underlying optical design problem, rotational symmetric lenses are not ideal for this application. For this type of design problems, a new free-form optics design method presented in previous papers perfectly matches the symmetry. It is derived directly from Fermat's principle, leading to sets of functional differential equations allowing the successive calculation of the Taylor series coeficients of each implicit surface function up to very high orders. For optical systems designed for wide field of view and with clearly separated optical surfaces, this new analytic design method has potential application in both fields of nonimaging and imaging optics.

Free-form optics for Fresnel-lens-based photovoltaic concentrators

The Concentrated Photovoltaics (CPV) promise relies upon the use of high-efficiency triple-junction solar cells (with proven efficiencies of over 44%) and upon high-performance optics that allow for high concentration concurrent with relaxed manufacturing tolerances (all key elements for low-cost mass production). Additionally, uniform illumination is highly desirable for efficiency and reliability reasons. All of these features have to be achieved with inexpensive optics containing only a few (in general no more than 2) optical elements. In this paper we show that the degrees of freedom using free-forms allow the introduction of multiple functionalities required for CPV with just 2 optical elements, one of which is a Fresnel lens.