Cloning and characterization of the immunodominant membrane protein of mulberry yellow dwarf phytoplasma

Mulberry yellow dwarf (MYD) disease is a quarantine disease in China and the causal agent is a phytoplasma. The antigenic membrane protein (Amp) of the ‘‘Candidatus Phytoplasma asteris’’ was hypothesized to play an important role in insect transmission specificity. Here, we firstly cloned and characterized Amp gene from the ‘‘Candidatus Phytoplasma asteris’’, MYD strain. The results showed that the MYD Amp gene consisted of 702 nt encoding a predicted protein of 233 aa which was highly similar to Amp of ‘‘Candidatus Phytoplasma asteris’’, sumac witches’-broom phytoplasma (SWB) strain and mulberry dwarf phytoplasma (MD) strain. Prediction of protein structure showed that the MYD-Amp protein possess an N-terminal export leader sequence (Amp-E), a large central hydrophilic domain (Amp-H) and a C-terminal transmembrane domain with a short hydrophilic domain (Amp-T).Key words: Mulberry yellow dwarf phytoplasma, Immunodominant membrane protein

The complete chloroplast genome sequence of Vitis hancockii

In this study, the complete chloroplast genome of Vitis hancockii was assembled for the first time. This genome was 161,205 bp in length, containing a large single copy region (89,397 bp) and a small single copy region (19,100 bp), seperated by two inverted repeat regions. The genome harbored 133 genes, including 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic tree analysis showed that V. hancocikk was the closest related to Vitis ficifolia

The complete chloroplast genome sequence of Vitis yeshanensis strain ‘SJTU004’

This study first released the complete chloroplast genome of Vitis yeshanensis. The circular genome was 161,188 bp in length, composed of a large single-copy region (LSC, 161,100–89,334 bp) and a small single-copy region (SSC, 115,689–134,745 bp), separated by two inverted repeat regions (IRA, 89,335–115,688 bp; IRB, 134,746–161,099 bp). The genome encoded 134 genes, containing 88 protein-coding genes (PCGs), 38 tRNA genes, and 8 rRNA genes. The phylogenetic tree showed a close relationship between V. yeshanensis and V. amurensis

The complete chloroplast genome sequence of Vitis davidii Foex strain ‘SJTU003’

In the present study, the complete chloroplast genome of Vitis davidii Foex strain ‘SJTU003’ was assembled and subjected to phylogenetic analysis. This chloroplast genome of ‘SJTU003’ was 161,335 bp in length, including two inverted repeat regions (IRa and IRb) that were separated by a large single-copy region (89,570 bp) and a small single-copy region (19,059 bp). The genome contained 133 genes, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that V. davidii is most closely related to Vitis flexuosa and Vitis amurensis

High-throughput m6A-seq reveals RNA m6A methylation patterns in the chloroplast and mitochondria transcriptomes of Arabidopsis thaliana.

This study is the first to comprehensively characterize m6A patterns in the Arabidopsis chloroplast and mitochondria transcriptomes based on our open accessible data deposited in NCBI's Gene Expression Omnibus with GEO Series accession number of GSE72706. Over 86% of the transcripts were methylated by m6A in the two organelles. Over 550 and 350 m6A sites were mapped, with ~5.6 to ~5.8 and ~4.6 to ~4.9 m6A sites per transcript, to the chloroplast and mitochondria genome, respectively. The overall m6A methylation extent in the two organelles was greatly higher than that in the nucleus. The m6A motif sequences in the transcriptome of two organelles were similar to the nuclear motifs, suggesting that selection of the m6A motifs for RNA methylation was conserved between the nucleus and organelle transcriptomes. The m6A patterns of rRNAs and tRNAs in the organelle were similar to those in the nucleus. However, the m6A patterns in coding RNAs were distinct between the nucleus and the organelle, suggesting that that regulation of the m6A methylation patterns may be different between the nuclei and the organelles. The extensively methylated transcripts in the two organelles were mainly associated with rRNA, ribosomal proteins, photosystem reaction proteins, tRNA, NADH dehydrogenase and redox. On average, 64% and 79% of the transcripts in the two organelles showed differential m6A methylation across three organs of the leaves, flowers and roots. The m6A methylation extent in the chloroplast was higher than that in the mitochondria. This study provides deep insights into the m6A methylation topology and differentiation in the plant organelle transcriptomes

Molecular Engineering of Quinoxaline-Based Organic Sensitizers for Highly Efficient and Stable Dye-Sensitized Solar Cells

A series of quinoxaline based metal-free organic sensitizers has been designed and synthesized for dye-sensitized solar cells (DSSCs). The absorption, electrochemical, and photovoltaic properties for all sensitizers have been systematically investigated. It is found that the incorporation of quinoxaline unit instead of thienopyrazine unit results in a negative shift of the lowest unoccupied molecular orbital levels for <b>FNE44</b>, <b>FNE45</b>, <b>FNE46</b>, and <b>FNE47</b>, in comparison to <b>FNE32</b>, which induces a remarkable enhancement of the electron injection driving force from the excited organic sensitizers to the TiO₂ semiconductor. Moreover, when the alkyl substituents are removed from the spacer part in <b>FNE44</b> to the donor part in <b>FNE45</b> and <b>FNE46</b>, a more conjugated system and a bathochromically shifted maximum absorption band can be realized, which consequently results in an increased light harvesting efficiency and photogenerated current. In addition, the length of the alkyl substituents on the donor part has a certain influence on the DSSC performance. Combining the three contributions, <b>FNE46</b>-based DSSC with liquid electrolyte displays the highest power conversion efficiency (η) of 8.27%. Most importantly, a η of 7.14% has been achieved for <b>FNE46</b> based quasi-solid-state DSSC and remained at 100% of the initial value after continuous light soaking for 1000 h, which indicates that <b>FNE46</b> is appropriate for promising commercial application. Our findings will facilitate the understanding of the crucial importance of molecular engineering and pave a new path to design novel metal-free organic dyes for highly efficient and stable DSSCs

Facile and Selective Synthesis of Oligothiophene-Based Sensitizer Isomers: An Approach toward Efficient Dye-Sensitized Solar Cells

Two sets of isomeric organic dyes with <i>n</i>-hexyl (<b>DH</b> and <b>AH</b>) or 2-ethylhexyl (<b>DEH</b> and <b>AEH</b>) groups substituted at the spacer part have been designed and straightforwardly synthesized via a facile and selective synthetic route. The structure difference between the isomers stands at the position of the incorporated alkyl chains which are introduced into the terthiophene spacer close to the donor (<b>D</b>) or anchor (<b>A</b>) side. The relationship between the isomeric structures and the optoelectronic properties are systematically investigated. It is found that, in the <b>D</b> series dyes, the alkyl group is much closer to the aromatic donor moiety, which brings about strong steric hindrance and therefore causes a remarkable twist in the molecular skeleton. In contrast, a more planar chemical structure and more effective π-conjugation are realized in the <b>A</b> series dye isomers. Consequently, the <b>A</b> series isomeric dyes demonstrate bathochromically shifted absorption bands, resulting in the improved light-harvesting capability and enhanced photo-generated current. However, the <b>D</b> series isomeric dyes with more twisted molecular skeleton have suppressed the intermolecular interactions and retarded the charge recombination more efficiently, which induces higher open-circuit photovoltage. Combining the two effects on the performance of the fabricated dye-sensitized solar cells (DSSC), the influence from the short-circuit photocurrent plays a more significant role on the power conversion efficiency (η). As a result, isomer <b>AEH</b>-based DSSC with quasi-solid-state electrolyte displays the highest η of 7.10% which remained at 98% of the initial value after continuous light soaking for 1000 h. Promisingly, a η of 8.66% has been achieved for <b>AEH</b>-based DSSC with liquid electrolyte containing Co­(II)/(III) redox couple. This work presents the crucial issue of molecular engineering and paves a way to design organic sensitizers for highly efficient and stable DSSCs

Three groupings of the m⁶A methlylation extent compared to the transcript level in the chloroplast/amyloplast transcriptome of three organs in <i>Arabidopsis</i>.

<p>Three groupings of the m⁶A methlylation extent compared to the transcript level in the chloroplast/amyloplast transcriptome of three organs in <i>Arabidopsis</i>.</p

The transcripts presenting extensive high m⁶A methylation in the <i>Arabidopsis</i> mitochondria.

<p>The transcripts presenting extensive high m⁶A methylation in the <i>Arabidopsis</i> mitochondria.</p

Screenshots from the IGV visualized program present m⁶A topologies in rRNA and tRNAs in the <i>Arabidopsis</i> mitochondria.

<p>Extent of m⁶A methylation, sequencing depth, sequencing fragment alignment, and gene ID of the sequencing data can be clearly visualized by the IGV program [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185612#pone.0185612.ref042" target="_blank">42</a>]. The area in the screenshot indicated by the arrow, “Red leftwards arrow”, presents m⁶A methylation extent across the transcript. The area in the screenshot indicated by the arrow, “Black leftwards arrow”, presents sequencing fragment alignment across the transcript. The area in the screenshot indicated by the arrow, “Black leftwards arrow with tail”, presents gene ID information including gene ID, sequence reading direction, the intron and exon regions. (a) The whole rRNA was highly methylated by m⁶A, representative rRNA, ‘ATMG01390’; (b) The whole tRNA was slightly methylated by m⁶A, representative tRNA, ‘ATMG00380’, expressed for tRNA-Asn. The Trace files of three organs, leaves (the upper), flowers (in the middle) and roots (the lower) were presented within a screenshot.</p