Identification of genes involved in steroid alkaloid biosynthesis in Fritillaria imperialis via de novo transcriptomics

Crown imperial (CI) has been used in traditional medicine. Today it is known that such beneficial effects are due to its richness in steroidal alkaloids (SA). Using de novo transcriptomics, orthologues/paralogues finder, phylogenetic analysis and tissue- and developmental stage-specific expression analysis, we identified ten genes and several TFs involved in the biosynthesis of SA in CI. The comparative analysis of ten genes expression profiles revealed the possibility of their co-regulation, which may imply the possibility of their organization in metabolic gene clusters. Having in mind convergent evolution of steroidal biosynthetic pathways in flowering plants and records of convergent evolution of specific proteins, observed expression patterns open a reasonable interest to investigate the possibility of the existence of genes cluster organization in SA pathway in the family Liliaceae or at least in some species of genus Fritillaria. Obtained results support transcriptomics as useful approach in elucidating genes underlying complex biochemical pathways

Network Meta-Analysis of Chicken Microarray Data following Avian Influenza Challenge-A Comparison of Highly and Lowly Pathogenic Strains

The current bioinformatics study was undertaken to analyze the transcriptome of chicken (Gallus gallus) after influenza A virus challenge. A meta-analysis was carried out to explore the host expression response after challenge with lowly pathogenic avian influenza (LPAI) (H1N1, H2N3, H5N2, H5N3 and H9N2) and with highly pathogenic avian influenza (HPAI) H5N1 strains. To do so, ten microarray datasets obtained from the Gene Expression Omnibus (GEO) database were normalized and meta-analyzed for the LPAI and HPAI host response individually. Different undirected networks were constructed and their metrics determined e.g., degree centrality, closeness centrality, harmonic centrality, subgraph centrality and eigenvector centrality. The results showed that, based on criteria of centrality, the CMTR1, EPSTI1, RNF213, HERC4L, IFIT5 and LY96 genes were the most significant during HPAI challenge, with PARD6G, HMG20A, PEX14, RNF151 and TLK1L having the lowest values. However, for LPAI challenge, ZDHHC9, IMMP2L, COX7C, RBM18, DCTN3, and NDUFB1 genes had the largest values for aforementioned criteria, with GTF3C5, DROSHA, ATRX, RFWD2, MED23 and SEC23B genes having the lowest values. The results of this study can be used as a basis for future development of treatments/preventions of the effects of avian influenza in chicken

Effect of Nano silis elicitor on Anti-inflammatory compound and some morphophysiological characters in saffron

The application of nanotechnology is a novel way of plant nutrition and a valuable technique to reduce environmental hazards by increasing yields in different agricultural sectors. In order to evaluate the content of secondary metabolites and some physiological traits of saffron a completely randomized design with 5 replications was conducted in a greenhouse, under the influence on 2 mM nano elicitor of silica concentration. The results showed that the highest amounts of crocin, picrocrocin, crocetin and safranal were obtained by nano silica treatment with 29.65%, 24.62%, 0.06% and 0.08%, respectively. The most value of inhibitory power of IC50 was due to the application of nano-silica treatment. The highest activity of superoxide dismutase, catalase and ascorbate peroxidase was observed in nano silica and the lowest in control. The highest amount of hydrogen peroxide was observed in 2 mM nano silica treatment with 19.85 (μmol/g). The highest proline content was 57.20 μmol/g and the highest amount of hydrogen peroxide was 68.57% in 2 mM nano silica. The highest amounts of chlorophyll a, b and total were obtained with 9.78, 2.91, and 13.02 mg / g in 2 mM nano silica, respectively. Keywords: antioxidant enzymes, picrocrocin, proline, safranal, photosynthetic pigments, croci

Ratchet effects induced by terahertz radiation in heterostructures with a lateral periodic potential

We report on the observation of terahertz radiation induced photogalvanic currents in semiconductor heterostructures with one-dimensional lateral periodic potential. The potential is produced by etching a grating into the sample surface. The electric current response is well described by phenomenological theory including both the circular and linear photogalvanic effects. Experimental data demonstrate that the inversion asymmetry of the periodic lateral pattern can be varied by means of electron beam lithography to produce classical lateral ratchets. A novel microscopical mechanism for the polarization-dependent photogalvanic effects has been proposed to interpret the experimental findings. The photocurrent generation is based on the combined action of the lateral periodic potential and the modulated in-plane pumping. The latter modulation stems from near-field effects of the radiation propagating through the grating.Comment: 8 pages, 6 figure

Three-dimensional phase-field simulation of microstructural evolution in three-phase materials with different diffusivities

The coarsening behavior of three-phase materials, such as eutectic material systems, is of high technological interest. Microstructure evolution simulations can help to understand the effect of different magnitudes of the diffusivities in the different phases. In this study, the evolution of a 3D three-phase morphology was modeled with equal interfacial energy and volume fraction and similar thermodynamic properties for the three phases, but the diffusion mobilities were taken different. It was observed that the phase with the lowest mobility has the highest growth rate and, on average, a larger number of grain faces, while the other two phases have a nearly equal growth rate and average number of grain faces. The simulation results are compared with results from experiments and simulation studies for single-phase and two-phase materials. © 2014 Springer Science+Business Media New York.status: publishe

Three-dimensional phase-field simulation of microstructural evolution in three-phase materials with different interfacial energies and different diffusivities

The coarsening behavior of three-phase materials, such as eutectic alloys, is of high technological interest. In this study, 3-D ternary three-phase polycrystalline materials were modeled to study the effect of bulk diffusion and phase arrangement on the coarsening kinetics. The diffusion mobilities were defined to be different in the three phases. By varying the phase boundary and grain boundary energies, microstructures with different phase arrangements were obtained, in which the different types of grains had a tendency to alternate or cluster. In all cases, a regime was reached where the average grain size follows a power growth law with growth exponent n = 3, indicating bulk diffusion controlled coarsening. The overall growth rate and that of the individual phases were clearly affected by the phase arrangement, the magnitude of the phase boundary energy and the diffusion mobilities of the different phases. In all cases, the phase with the lowest diffusion mobility showed the highest growth rate and on average a larger number of grain faces. While the average number of grain faces became constant in time in systems with constant grain boundary energy, the average number of grain faces continued to increase during the whole simulation time when the grain boundary energy was misorientation dependent.status: publishe

Three-dimensional phase-field study of grain coarsening and grain shape accommodation in the final stage of liquid-phase sintering

A 3-dimensional phase-field model is implemented to simulate the grain evolution in the final stage of liquid-phase sintering. The model considers a liquid phase and a polycrystalline solid phase. Results for varying ratios of the solid-solid interface energy to solid-liquid interface energy and varying solid volume fractions are presented. A variety of microstructures, from fully connected grain structures with liquid pockets at the grain junctions to individual grains fully wetted by the liquid matrix, is seen. The 3 main mechanisms for particle shape accommodation, namely, contact flattening, Ostwald ripening and particle bonding, are reproduced in the simulations. The solid volume fraction, particle size distribution, contiguity, connectivity, particle-particle contact areas and the number of particle contacts per particle are measured as a function of time. The exponent in the power growth law varies between 2.4, for the fully connected grain structures, and 3, for the completely wetted grains.status: publishe

3D phase-field simulation and characterization of microstructure evolution during Liquid Phase Sintering

status: publishe

In silico identification of transcription factors associated with the biosynthesis of carotenoids in corn ( Zea mays L. )

Carotenoids, a diverse group of colorful pigments, contribute to the development, light harvesting and photoprotection in plants as well as human health. Due to the interesting properties of carotenoids, enhanced carotenoid biosynthesis has been of ongoing interest. Recent advances in computational biology and bioinformatics make it more feasible to understand the transcriptional regulatory network underlying carotenoid biosynthesis. Studies on carotenoid biosynthesis in corn ( Zea mays L. ) have indicated the pivotal role of the phytoene synthase gene PSY1 (accession: GRMZM2G300348) in endosperm color and carotenoid accumulation in corn kernels. Computational approaches such as Genomatix, PlantPAN, PlantCARE, PlantTFDB and IGDE6 have been used for promoter prediction, regulatory features and transcription factor identification, as well as pairwise promoter comparisons. Four transcripts have been identified for the PSY1 gene. Based on Genomatix and PlantPAN, the promoter predicted for GRMZM2G300348_T01 was different from that predicted for the other three transcripts (GRMZM2G300348_T02, GRMZM2G300348_T03 and GRMZM2G300348_T04). The results indiated that the promoter of GRMZM2G300348_T01 has more diverse motifs involved in hormonal/environmental stress responses. The most significant result obtained from this study is the discovery of two transcription factors belonging to the HB family that are co-expressed with all four transcripts of PSY1 under environmental stresses. It is, therefore, likely that these transcription factors may act as critical regulators of PSY1 gene expression in corn. Identification of the proteins acting upstream of PSY1 within corn will shed light on the fine tuning of PSY1 expression regulation. Such an understanding would also contribute to metabolic engineering aimed at enhanced carotenoid biosynthesis

In silico identification of transcription factors associated with the biosynthesis of carotenoids in corn ( Zea mays L. )

Carotenoids, a diverse group of colorful pigments, contribute to the development, light harvesting and photoprotection in plants as well as human health. Due to the interesting properties of carotenoids, enhanced carotenoid biosynthesis has been of ongoing interest. Recent advances in computational biology and bioinformatics make it more feasible to understand the transcriptional regulatory network underlying carotenoid biosynthesis. Studies on carotenoid biosynthesis in corn ( Zea mays L. ) have indicated the pivotal role of the phytoene synthase gene PSY1 (accession: GRMZM2G300348) in endosperm color and carotenoid accumulation in corn kernels. Computational approaches such as Genomatix, PlantPAN, PlantCARE, PlantTFDB and IGDE6 have been used for promoter prediction, regulatory features and transcription factor identification, as well as pairwise promoter comparisons. Four transcripts have been identified for the PSY1 gene. Based on Genomatix and PlantPAN, the promoter predicted for GRMZM2G300348_T01 was different from that predicted for the other three transcripts (GRMZM2G300348_T02, GRMZM2G300348_T03 and GRMZM2G300348_T04). The results indiated that the promoter of GRMZM2G300348_T01 has more diverse motifs involved in hormonal/environmental stress responses. The most significant result obtained from this study is the discovery of two transcription factors belonging to the HB family that are co-expressed with all four transcripts of PSY1 under environmental stresses. It is, therefore, likely that these transcription factors may act as critical regulators of PSY1 gene expression in corn. Identification of the proteins acting upstream of PSY1 within corn will shed light on the fine tuning of PSY1 expression regulation. Such an understanding would also contribute to metabolic engineering aimed at enhanced carotenoid biosynthesis