Fast recovery of sparse fringes in unknown freeform surface interferometry.

In the adaptive freeform surface interferometer, the adaptive algorithms were equipped to find the required aberration compensation, making interferogram with dark areas (incomplete interferogram) sparse. However, traditional blind search-based algorithms are limited by convergence rate, time consumption, and convenience. As an alternative, we propose an intelligent approach composed of deep learning and ray tracing technology, which can recover sparse fringes from the incomplete interferogram without iterations. Simulations show that the proposed method has only a few seconds time cost with the failure rate less than 4‰. At the same time, the proposed method is easy to perform because it does not require the manual intervention of internal parameters before execution as in traditional algorithms. Finally, the feasibility of the proposed method was validated in the experiment. We believe that this approach is much more promising in the future.

Adam SPGD algorithm in freeform surface in-process interferometry.

The adaptive interferometer has been recently proposed to realize the metrology of unknown freeform surfaces with several restructured algorithms for feedback control. The adaptive moment estimation (Adam) stochastic parallel gradient descent (SPGD) algorithm is employed in this paper for fringes release. The proposed algorithm makes considerable progress in relieving conflict of the convergence rate, speed, and parameters intervention. Simulations and experiments show its 37% time saving and 99% convergence rate, with arbitrarily configured parameter increment, compared with the SPGD algorithm. It would have great potential in in-process tests in freeform surface fabrication or large-volume testing.

From concept to reality: computing visual vortex beam interferometer for displacement measurement.

In addition to the concept of picometer resolution, we discuss macro displacement measurement with a vortex beam interferometer. Three factors limiting large displacement measurement are resolved. Small topological charge numbers promise both high sensitivity and large displacement measurements. With a computing visual method, a virtual moiré pointer image immune to beam misalignment is proposed to calculate displacements. Interestingly, the absolute benchmark is found for cycle counting in the moiré pointer image of fractional topological charge. The vortex beam interferometer would not stop at the tiny displacement measurement in simulations. We report experimental measurements of nanoscale to hundred millimeter displacement in a vortex beam displacement measurement interferometer (DMI) for the first time, to the best of our knowledge.

Depressed expression of FAE1 and FAD2 genes modifies fatty acid profiles and storage compounds accumulation in Brassica napus seeds.

In plants, the enzymes fatty acid dehydrogenase 2 (FAD2) and fatty acid elongase 1 (FAE1) have been shown in previous studies to play important roles in the de novo biosynthesis of fatty acids. However, the effects of depressed expression of FAD2 and FAE1 on seed storage compounds accumulation remains to be elucidated. In this study, we produced RNA interfering transgenic rapeseeds lines, BnFAD2-Ri, BnFAE1-Ri and BnFAD2/BnFAE1-Ri, which exhibited depressed expression of the BnFAD2 and BnFAE1 genes under the control of seed-specific napin A promoter. These transgenic rapeseeds showed normal growth and development as compared with the wild type (CY2). Depressed expression of BnFAD2 and BnFAE1 genes modified fatty acid profiles, leading to increased oleic acid and decreased erucic acid contents in transgenic seeds. Consistent with these results, the ratios of C18:1/C18:2 and C18:1/C18:3 in C18 unsaturated fatty acids were greatly increased due to increased oleic acid content in transgenic seeds. Moreover, depressed expression of BnFAD2 and BnFAE1 genes resulted in slightly decreased oil contents and increased protein contents in transgenic seeds. Our results demonstrated that depressed expression of BnFAD2 and BnFAE1 greatly improves seed nutritional quality by modulating the fatty acid metabolism and storage products accumulation and that BnFAD2 and BnFAE1 are reliable targets for genetic improvement of rapeseed in seed nutritional quality.

Embryonal Control of Yellow Seed Coat Locus ECY1 Is Related to Alanine and Phenylalanine Metabolism in the Seed Embryo of Brassica napus.

Seed coat color is determined by the type of pigment deposited in the seed coat cells. It is related to important agronomic traits of seeds such as seed dormancy, longevity, oil content, protein content and fiber content. In Brassica napus, inheritance of seed coat color is related to maternal effects and pollen effects (xenia effects). In this research we isolated a mutation of yellow seeded B. napus controlled by a single Mendelian locus, which is named Embryonal Control of Yellow seed coat 1 (Ecy1). Microscopy of transverse sections of the mature seed show that pigment is deposited only in the outer layer of the seed coat. Using Illumina Hisequation 2000 sequencing technology, a total of 12 GB clean data, 116× coverage of coding sequences of B. napus, was achieved from seeds 26 d after pollination (DAP). It was assembled into 172,238 independent transcripts, and 55,637 unigenes. A total of 139 orthologous genes of Arabidopsis transparent testa (TT) genes were mapped in silico to 19 chromosomes of B. napus Only 49 of the TT orthologous genes are transcribed in seeds. However transcription of all orthologs was independent of embryonal control of seed coat color. Only 55 genes were found to be differentially expressed between brown seeds and the yellow mutant. Of these 55, 50 were upregulated and five were downregulated in yellow seeds as compared to their brown counterparts. By KEGG classification, 14 metabolic pathways were significantly enriched. Of these, five pathways: phenylpropanoid biosynthesis, cyanoamino acid metabolism, plant hormone signal transduction, metabolic pathways, and biosynthesis of secondary metabolites, were related with seed coat pigmentation. Free amino acid quantification showed that Ala and Phe were present at higher levels in the embryos of yellow seeds as compared to those of brown seeds. This increase was not observed in the seed coat. Moreover, the excess amount of free Ala was exactly twice that of Phe in the embryo. The pigment substrate chalcone is synthesized from two molecules of Ala and one molecule of Phe. The correlation between accumulation of Ala and Phe, and disappearance of pigment in the yellow seeded mutant, suggests that embryonal control of seed coat color is related with Phe and Ala metabolism in the embryo of B. napus.

RNAi knockdown of fatty acid elongase1 alters fatty acid composition in Brassica napus.

The quality and end-use of oil from oilseed crops is determined by its fatty acid composition. In particular, the relative proportions of erucic and oleic acids are key selection traits for breeders. The goal of our research is to genetically improve the nutritional quality of Brassica napus cultivar CY2, the oil of which is high in erucic acid (about 40%) and low in oleic acid (about 20%). Here, we report the use of a seed-specific napin A promoter to drive the knockdown of BnFAE1 in transgenic CY2. Southern blotting results confirmed the presence of the transgene. RT-PCR analysis showed that the levels of BnFAE1 were greatly decreased in BnFAE1-Ri lines compared with the CY2 cultivar. Knockdown of BnFAE1 sharply decreased the levels of erucic acid (less than 3%), largely increased the contents of oleic acid (more than 60%) and slightly increased the polyunsaturated chain fatty acids. Compared with high erucic acid parents, expression of BnFAE1 was dramatically decreased in developing F1 seeds derived from reciprocally crossed BnFAE1-Ri lines and high erucic acid cultivars. In addition, F1 seeds derived from reciprocal crosses between BnFAE1-Ri lines and high erucic acid cultivars showed significantly increased oleic acid (more than 52%) and sharply decreased erucic acid (less than 4%), demonstrating that the RNAi construct of BnFAE1 can effectively interfere with the target gene in F1 seeds. Taken together, our results demonstrate that BnFAE1 is a reliable target for genetic improvement of rapeseed in seed oil quality promotion.

Identification of a Novel Proline-Rich Antimicrobial Peptide from Brassica napus.

Proline-rich antimicrobial peptides (PR-AMPs) are a group of cationic host defense peptides that are characterized by a high content of proline residues. Up to now, they have been reported in some insects, vertebrate and invertebrate animals, but are not found in plants. In this study, we performed an in silico screening of antimicrobial peptides, which led to discovery of a Brassica napus gene encoding a novel PR-AMP. This gene encodes a 35-amino acid peptide with 13 proline residues, designated BnPRP1. BnPRP1 has 40.5% identity with a known proline-rich antimicrobial peptide SP-B from the pig. BnPRP1 was artificially synthetized and cloned into the prokaryotic expression vector pET30a/His-EDDIE-GFP. Recombinant BnPRP1 was produced in Escherichia coli and has a predicted molecular mass of 3.8 kDa. Analysis of its activity demonstrated that BnPRP1 exhibited strong antimicrobial activity against Gram-positive bacterium, Gram-negative bacterium, yeast and also had strong antifungal activity against several pathogenic fungi, such as Sclerotinia sclerotiorum, Mucor sp., Magnaporthe oryzae and Botrytis cinerea. Circular dichroism (CD) revealed the main secondary structure of BnPRP1 was the random coil. BnPRP1 gene expression detected by qRT-PCR is responsive to pathogen inoculation. At 48 hours after S. sclerotiorum inoculation, the expression of BnPRP1 increased significantly in the susceptible lines while slight decrease occurred in resistant lines. These suggested that BnPRP1 might play a role in the plant defense response against S. sclerotiorum. BnPRP1 isolated from B. napus was the first PR-AMP member that was characterized in plants, and its homology sequences were found in some other Brassicaceae plants by the genome sequences analysis. Compared with the known PR-AMPs, BnPRP1 has the different primary sequences and antimicrobial activity. Above all, this study gives a chance to cast a new light on further understanding about the AMPs' mechanism and application.

Phosphoenolpyruvate Carboxylase in Arabidopsis Leaves Plays a Crucial Role in Carbon and Nitrogen Metabolism.

Phosphoenolpyruvate carboxylase (PEPC) is a crucial enzyme that catalyzes an irreversible primary metabolic reaction in plants.Previous studies have used transgenic plants expressing ectopic PEPC forms with diminished feedback inhibition to examine the role of PEPC in carbon and nitrogen metabolism. To date, the in vivo role of PEPC in carbon and nitrogen metabolism has not been analyzed in plants. In this study, we examined the role of PEPC in plants, demonstrating that PPC1 and PPC2 were highly expressed genes encoding PEPC in Arabidopsis (Arabidopsis thaliana) leaves and that PPC1 and PPC2 accounted for approximately 93% of total PEPC activity in the leaves. A double mutant, ppc1/ppc2, was constructed that exhibited a severe growth-arrest phenotype. The ppc1/ppc2 mutant accumulated more starch and sucrose than wild-type plants when seedlings were grown under normal conditions. Physiological and metabolic analysis revealed that decreased PEPC activity in the ppc1/ppc2 mutant greatly reduced the synthesis of malate and citrate and severely suppressed ammonium assimilation. Furthermore, nitrate levels in the ppc1/ppc2 mutant were significantly lower than those in wild-type plants due to the suppression of ammonium assimilation. Interestingly, starch and sucrose accumulation could be prevented and nitrate levels could be maintained by supplying the ppc1/ppc2 mutant with exogenous malate and glutamate, suggesting that low nitrogen status resulted in the alteration of carbon metabolism and prompted the accumulation of starch and sucrose in the ppc1/ppc2 mutant. Our results demonstrate that PEPC in leaves plays a crucial role in modulating the balance of carbon and nitrogen metabolism in Arabidopsis.

Characterisations of odorant-binding proteins in the tsetse fly Glossina morsitans morsitans.

Odorant-binding proteins (OBPs) play an important role in insect olfaction by mediating interactions between odorants and odorant receptors. We report for the first time 20 OBP genes in the tsetse fly Glossina morsitans morsitans. qRT-PCR revealed that 8 of these genes were highly transcribed in the antennae. The transcription of these genes in the antennae was significantly lower in males than in females and there was a clear correlation between OBP gene transcription and feeding status. Starvation over 72 h post-blood meal (PBM) did not significantly affect the transcription. However, the transcription in the antennae of 10-week-old flies was much higher than in 3-day-old flies at 48 h PBM and decreased sharply after 72 h starvation, suggesting that the OBP gene expression is affected by the insect's nutritional status. Sequence comparisons with OBPs of other Dipterans identified several homologs to sex pheromone-binding proteins and OBPs of Drosophila melanogaster.

[Construction of vectors for expression of cleavable tandem repeat Thanatin fusion protein in plants].

Thanatin, a 21-residue antimicrobial peptide, is an inducible insect peptide with a broad range of activity against bacteria and fungi. It can improve the expression level of the antimicrobial peptide in plants to express the peptide as tandem repeat fusion protein containing multiple Thanatin copies. However, the fusion protein has no antimicrobial activity. To make the fusion protein automatically break into single Thanatin unit with antimicrobial activity, the fused Thanatin was spaced by a linker peptide, which was cleavable in vivo. The soybean (Glysine max L.) chitinase signal peptide was fused to the N end of the fusion protein to induce the antimicrobial peptide accumulated in intercellular space. To construct the vectors for expression of the fusion protein, the overlapped primers were used to clone the antimicrobial peptide gene and the co-adhesive end restriction and ligation strategy was used to add the repeat unit one by one. Vectors containing 1 to 5 repeat units of Thanatin were constructed respectively. These vectors were being used to transform plants to improve plant disease resistance.

RFLP and AFLP analysis of inter- and intraspecific variation of Brassica rapa and B. napus shows that B. rapa is an important genetic resource for B. napus improvement.

Fingerprinting of 29 accessions of oilseed rape, including seven accessions of Brassica napus, and 22 accessions of B. rapa (B. campestris) from Europe, North America, and China was analyzed using RFLP and AFLP markers. In total, 1,477 polymorphic RFLP bands and 183 polymorphic AFLP bands from 166 enzyme-probe combinations and two pairs of AFLP primers, respectively, were scored for the 29 accessions. On average, RFLP analysis showed that the Arabidopsis EST probe detected more polymorphic bands in Brassica than the random genomic probe performed. More polymorphic RFLP markers were detected with the digestion of EcoR I or BamH I than HindIII. According to the number of bands amplified from each accession, the copy numbers of each gene in the genomes of B. rapa and B. napus were estimated. The average copy numbers in B. rapa of China, B. rapa of Europe, and B. napus, were 3.2, 3.1, and 2.9, respectively. Genetic distance based on the AFLP data was well correlated with that based on the RFLP data (r = 0.72, P<0.001), but 0.39 smaller on average. Genetic diversity analysis showed that Chinese B. rapa was more polymorphic than Chinese B. napus and European materials. Some European B. napus accessions were clustered into European B. rapa, which were distinctly different from Chinese B. napus. The larger variations of Chinese accessions of B. rapa suggest that they are valuable in oilseed rape breeding. Novel strategies to use intersubgenomic heterosis between genome of B. rapa (A(r)A(r)) and genome of B. napus (A(n)A(n)C(n)C(n)) were elucidated.

Identification of prior candidate genes for Sclerotinia local resistance in Brassica napus using Arabidopsis cDNA microarray and Brassica-Arabidopsis comparative mapping.

Arabidopsis cDNA arrays were used to screen the local-defense-associated genes in oilseed rape (Brassica napus L.) at the challenge of Sclerotinia sclerotiorum. 61 genes with two-fold expression changes were screened out from the local tissue around the necrosis. Among them, 36 unique genes were up-regulated and 25 unique genes were down-regulated. RT-PCR and Northern blot results were consistent with the array results, suggesting Arabidopsis arrays were useful for transcriptional profiling of B. napus genes. Some of these genes were located in the interval of some QTLs for Sclerotinia resistance in B. napus by Brassica-Arabidopsis comparative mapping. These genes may have priority to be pursued for more intensive research.

[MapDraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data].

MAPMAKER is one of the most widely used computer software package for constructing genetic linkage maps.However, the PC version, MAPMAKER 3.0 for PC, could not draw the genetic linkage maps that its Macintosh version, MAPMAKER 3.0 for Macintosh,was able to do. Especially in recent years, Macintosh computer is much less popular than PC. Most of the geneticists use PC to analyze their genetic linkage data. So a new computer software to draw the same genetic linkage maps on PC as the MAPMAKER for Macintosh to do on Macintosh has been crying for. Microsoft Excel,one component of Microsoft Office package, is one of the most popular software in laboratory data processing. Microsoft Visual Basic for Applications (VBA) is one of the most powerful functions of Microsoft Excel. Using this program language, we can take creative control of Excel, including genetic linkage map construction, automatic data processing and more. In this paper, a Microsoft Excel macro called MapDraw is constructed to draw genetic linkage maps on PC computer based on given genetic linkage data. Use this software,you can freely construct beautiful genetic linkage map in Excel and freely edit and copy it to Word or other application. This software is just an Excel format file. You can freely copy it from ftp://211.69.140.177 or ftp://brassica.hzau.edu.cn and the source code can be found in Excel's Visual Basic Editor.

[Integration of DNA clones related to important economic traits of Brassica napus onto Arabidopsis genetic map].

Arbidopsis thaliana and Brassica oilcrops are closely related species in Brassicae, Cruciferae, and show highly homologous genomes. After a serial important agronomic characteristics of Brassica napus being mapped with probes from EST clones of Arabidopsis and DNA clones of rapeseed, DNA segment sequencing was performed with 25 clones which were found to be closely linked to the CMS restore gene, the boron efficiency gene (BE1), the Sclerotinia resistant QTLs and the characteristic of interspecific biomass heterosis in rapeseed respectively. Highly homologous sequences were found in Arabidopsis genome by searching the relative databases. According to the position of homologous sequences on the chromosomes of Arabidopsis, the 25 clones were integrated into the genetic map of Arabidopsis. Two markers flanking BE1 in B. napus were integrated into a narrow region at the short arm of chromosome 1 of Arabidopsis. One of EST clones, pA24, from this region was used as a probe to map B. napus and consequently been integrated in a position between the two flanking markers of BE1. This event increased the confident for one to map the important characteristics of cultured Brassica species via reciprocal comparative mapping between Arabidopsis and target Brassica crops.