AnnoTALE : bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences

Transcription activator-like effectors (TALEs) are virulence factors, produced by the bacterial plant-pathogen Xanthomonas, that function as gene activators inside plant cells. Although the contribution of individual TALEs to infectivity has been shown, the specific roles of most TALEs, and the overall TALE diversity in Xanthomonas spp. is not known. TALEs possess a highly repetitive DNA-binding domain, which is notoriously difficult to sequence. Here, we describe an improved method for characterizing TALE genes by the use of PacBio sequencing. We present 'AnnoTALE', a suite of applications for the analysis and annotation of TALE genes from Xanthomonas genomes, and for grouping similar TALEs into classes. Based on these classes, we propose a unified nomenclature for Xanthomonas TALEs that reveals similarities pointing to related functionalities. This new classification enables us to compare related TALEs and to identify base substitutions responsible for the evolution of TALE specificities

Removing the major allergen Bra j I from brown mustard (Brassica juncea) by CRISPR/Cas9

Food allergies are a major health issue worldwide. Modern breeding techniques such as genome editing via CRISPR/Cas9 have the potential to mitigate this by targeting allergens in plants. This study addressed the major allergen Bra j I, a seed storage protein of the 2S albumin class, in the allotetraploid brown mustard (Brassica juncea). Cotyledon explants of an Indian gene bank accession (CR2664) and the German variety Terratop were transformed using Agrobacterium tumefaciens harboring binary vectors with multiple single guide RNAs to induce either large deletions or frameshift mutations in both Bra j I homoeologs. A total of 49 T0 lines were obtained with up to 3.8% transformation efficiency. Four lines had large deletions of 566 up to 790 bp in the Bra j IB allele. Among 18 Terratop T0 lines, nine carried indels in the targeted regions. From 16 analyzed CR2664 T0 lines, 14 held indels and three had all four Bra j I alleles mutated. The majority of the CRISPR/Cas9-induced mutations were heritable to T1 progenies. In some edited lines, seed formation and viability were reduced and seeds showed a precocious development of the embryo leading to a rupture of the testa already in the siliques. Immunoblotting using newly developed Bra j I-specific antibodies revealed the amount of Bra j I protein to be reduced or absent in seed extracts of selected lines. Removing an allergenic determinant from mustard is an important first step towards the development of safer food crops

Aging and gate bias effects on TID sensitivity of wide bandgap power devices

The effect of oxide stress on the total ionizing dose (TID) radiation sensitivity of silicon carbide (SiC) power MOSFETS and TID sensitivity of gallium nitride (GaN) power transistor is reported. Difference in TID response for stressed and unstressed devices was observed

The whole and its parts : why and how to disentangle plant communities and synusiae in vegetation classification

Most plant communities consist of different structural and ecological subsets, ranging from cryptogams to different tree layers. The completeness and approach with which these subsets are sampled have implications for vegetation classification. Non‐vascular plants are often omitted or sometimes treated separately, referring to their assemblages as “synusiae” (e.g. epiphytes on bark, saxicolous species on rocks). The distinction of complete plant communities (phytocoenoses or holocoenoses) from their parts (synusiae or merocoenoses) is crucial to avoid logical problems and inconsistencies of the resulting classification systems. We here describe theoretical differences between the phytocoenosis as a whole and its parts, and outline consequences of this distinction for practise and terminology in vegetation classification. To implement a clearer separation, we call for modifications of the International Code of Phytosociological Nomenclature and the EuroVegChecklist. We believe that these steps will make vegetation classification systems better applicable and raise the recognition of the importance of non‐vascular plants in the vegetation as well as their interplay with vascular plants

On the origin of the A1g_{1g} and B1g_{1g} electronic Raman scattering peaks in the superconducting state of YBa2_{2}Cu3_{3}O7−δ_{7-\delta}

The electronic Raman scattering has been investigated in optimally oxygen doped YBa$_{2}$Cu$_{3}$O$_{7-\delta}$ single crystals as well as in crystals with non-magnetic, Zn, and magnetic, Ni, impurities. We found that the intensity of the A$_{1g}$ peak is impurity independent and their energy to $T_{c}$ ratio is almost constant ($2\Delta/k_{B}T_{c}\sim5$). Moreover, the signal at the B$_{1g}$ channel is completely smeared out when non-magnetic Zn impurities are present. These results are qualitatively interpreted in terms of the Zeyher and Greco's theory that relates the electronic Raman scattering in the A$_{1g}$ and B$_{1g}$ channels to \textit{d}-CDW and superconducting order parameters fluctuations, respectively.Comment: Submited to Phys. Rev. Let

Programmable Sequence-Specific Transcriptional Regulation of Mammalian Genome Using Designer TAL Effectors

The ability to direct functional proteins to specific DNA sequences is a long-sought goal in the study and engineering of biological processes. Transcription activator–like effectors (TALEs) from Xanthomonas sp. are site-specific DNA-binding proteins that can be readily designed to target new sequences. Because TALEs contain a large number of repeat domains, it can be difficult to synthesize new variants. Here we describe a method that overcomes this problem. We leverage codon degeneracy and type IIs restriction enzymes to generate orthogonal ligation linkers between individual repeat monomers, thus allowing full-length, customized, repeat domains to be constructed by hierarchical ligation. We synthesized 17 TALEs that are customized to recognize specific DNA-binding sites, and demonstrate that they can specifically modulate transcription of endogenous genes (SOX2 and KLF4) in human cells.Harvard University. Society of FellowsNational Human Genome Research Institute (U.S.) (Center for Excellence in Genomics Science P50 HG003170)United States. Dept. of Energy (Genomes to Life DE-FG02-02ER63445)United States. Defense Advanced Research Projects Agency (W911NF-08-1-0254, G.M.C.)Wyss Institute of Biologically Inspired EngineeringNational Institutes of Health (U.S.) (Transformative R01 (R01 NS073124-01))European School of Molecular Medicine (predoctoral fellowship

Honey bee foraging distance depends on month and forage type

To investigate the distances at which honey bee foragers collect nectar and pollen, we analysed 5,484 decoded waggle dances made to natural forage sites to determine monthly foraging distance for each forage type. Firstly, we found significantly fewer overall dances made for pollen (16.8 %) than for non-pollen, presumably nectar (83.2 %; P < 2.2 × 10−23). When we analysed distance against month and forage type, there was a significant interaction between the two factors, which demonstrates that in some months, one forage type is collected at farther distances, but this would reverse in other months. Overall, these data suggest that distance, as a proxy for forage availability, is not significantly and consistently driven by need for one type of forage over the other

Modern microwave methods in solid state inorganic materials chemistry: from fundamentals to manufacturing

No abstract available