Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat

BACKGROUND: Bread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets. Therefore each wheat gene potentially exists as a trio of A, B and D homoeoloci, each of which may contribute differentially to wheat phenotypes. We describe a novel approach combining wheat cytogenetic resources (chromosome substitution ‘nullisomic-tetrasomic’ lines) with next generation deep sequencing of gene transcripts (RNA-Seq), to directly and accurately identify homoeologue-specific single nucleotide variants and quantify the relative contribution of individual homoeoloci to gene expression. RESULTS: We discover, based on a sample comprising ~5-10% of the total wheat gene content, that at least 45% of wheat genes are expressed from all three distinct homoeoloci. Most of these genes show strikingly biased expression patterns in which expression is dominated by a single homoeolocus. The remaining ~55% of wheat genes are expressed from either one or two homoeoloci only, through a combination of extensive transcriptional silencing and homoeolocus loss. CONCLUSIONS: We conclude that wheat is tending towards functional diploidy, through a variety of mechanisms causing single homoeoloci to become the predominant source of gene transcripts. This discovery has profound consequences for wheat breeding and our understanding of wheat evolution

HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids

BACKGROUND: The analysis of polyploid genomes is problematic because homeologous subgenome sequences are closely related. This relatedness makes it difficult to assign individual sequences to the specific subgenome from which they are derived, and hinders the development of polyploid whole genome assemblies. RESULTS: We here present a next-generation sequencing (NGS)-based approach for assignment of subgenome-specific base-identity at sites containing homeolog-specific polymorphisms (HSPs): ‘HSP base Assignment using NGS data through Diploid Similarity’ (HANDS). We show that HANDS correctly predicts subgenome-specific base-identity at >90% of assayed HSPs in the hexaploid bread wheat (Triticum aestivum) transcriptome, thus providing a substantial increase in accuracy versus previous methods for homeolog-specific base assignment. CONCLUSION: We conclude that HANDS enables rapid and accurate genome-wide discovery of homeolog-specific base-identity, a capability having multiple applications in polyploid genomics

New Two-Photon Absorbing Fluorene Derivatives: Synthesis And Nonlinear Optical Characterization

(matrix presented). Efficient Pd-catalyzed Heck coupling methodology was employed to provide two new fluorene derivatives with phosphonate (2) and nitro (3) electron-withdrawing functionalities. Both derivatives exhibit two-photon absorption (2PA), as determined by nonlinear absorption measurements using a femtosecond pump/white light continuum probe NLO spectrometer . Both fluorene derivatives have high 2PA cross sections (650 and 1300 × 10-50 cm4 s photon-1 molecule-1 for compounds 2 and 3, respectively)

The gateway pDEST17 expression vector encodes

a 1 ribosomal frameshifting sequenc

Overexpressing the multiple-stress responsive gene At1g74450 reduces plant height and male fertility in Arabidopsis thaliana

A subset of genes in Arabidopsis thaliana is known to be up-regulated in response to a wide range of different environmental stress factors. However, not all of these genes are characterized as yet with respect to their functions. In this study, we used transgenic knockout, overexpression and reporter gene approaches to try to elucidate the biological roles of five unknown multiple-stress responsive genes in Arabidopsis. The selected genes have the following locus identifiers: At1g18740, At1g74450, At4g27652, At4g29780 and At5g12010. Firstly, T-DNA insertion knockout lines were identified for each locus and screened for altered phenotypes. None of the lines were found to be visually different from wildtype Col-0. Secondly, 35S-driven overexpression lines were generated for each open reading frame. Analysis of these transgenic lines showed altered phenotypes for lines overexpressing the At1g74450 ORF. Plants overexpressing the multiple-stress responsive gene At1g74450 are stunted in height and have reduced male fertility. Alexander staining of anthers from flowers at developmental stage 12–13 showed either an absence or a reduction in viable pollen compared to wildtype Col-0 and At1g74450 knockout lines. Interestingly, the effects of stress on crop productivity are most severe at developmental stages such as male gametophyte development. However, the molecular factors and regulatory networks underlying environmental stress-induced male gametophytic alterations are still largely unknown. Our results indicate that the At1g74450 gene provides a potential link between multiple environmental stresses, plant height and pollen development. In addition, ruthenium red staining analysis showed that At1g74450 may affect the composition of the inner seed coat mucilage layer. Finally, C-terminal GFP fusion proteins for At1g74450 were shown to localise to the cytosol

Two-Photon Absorption Cross-Sections Of Common Photoinitiators

Recent interests in and applications of two-photon absorption (2PA) induced photopolymerization have afforded advanced opportunities to perform three-dimensionally resolved polymerization, resulting in intricate microfabrication and imaging. Many of the reported 2PA-induced polymerizations make use of commercially available photoinitiators, and a key parameter to consider is the two-photon absorption cross-section (δ) of the initiator. To date, there has been no comprehensive investigation of two-photon absorptivity of commercial photoinitiators, though a few studies presenting novel photoinitiators for two-photon polymerization have appeared. Herein, we report the 2PA properties of common, commercially available photoinitiators typically utilized in conventional radiation curing science and technologies, and often used in 2PA-based polymerizations. Z-scan and white-light continuum (WLC) pump-probe techniques were utilized to obtain two-photon absorption cross-sections (δ). The results for most compounds were found to yield good agreement between the two methods. Most of the photoinitiators studied possess low δ, except Irgacure OXE01, indicating a need for the development of new photoinitiators with improved properties optimized for 2PA applications. A compound prepared in our laboratories exhibits high 2PA and was useful as a two-photon free-radical photoinitiator. © 2004 Elsevier B.V. All rights reserved

Resonant enhancement of two-photon absorption in substituted fluorene molecules

© 2004 American Institute of Physics. The electronic version of this article is the complete one and can be found at: http://dx.doi.org/10.1063/1.1770726DOI: 10.1063/1.1770726The degenerate and nondegenerate two-photon absorption (2PA) spectra for a symmetric and an asymmetric fluorene derivative were experimentally measured in order to determine the effect of intermediate state resonance enhancement (ISRE) on the 2PA cross section δ. The ability to tune the individual photon energies in the nondegenerate 2PA (ND-2PA) process afforded a quantitative study of the ISRE without modifying the chemical structure of the investigated chromophores. Both molecules exhibited resonant enhancement of the nonlinearity with the asymmetric compound showing as much as a twentyfold increase in δ. Furthermore, the possibility of achieving over a one order of magnitude enhancement of the nonlinearity reveals the potential benefits of utilizing ND-2PA for certain applications. To model ISRE, we have used correlated quantum-chemical methods together with the perturbative sum-over-states (SOS) expression. We find strong qualitative and quantitative correlation between the experimental and theoretical results. Finally, using a simplified three-level model for the SOS expression, we provide intuitive insight into the process of ISRE for ND-2PA