Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae)

<p>Abstract</p> <p>Background</p> <p>The genus <it>Pyrus </it>belongs to the tribe Pyreae (the former subfamily Maloideae) of the family Rosaceae, and includes one of the most important commercial fruit crops, pear. The phylogeny of <it>Pyrus </it>has not been definitively reconstructed. In our previous efforts, the internal transcribed spacer region (ITS) revealed a poorly resolved phylogeny due to non-concerted evolution of nrDNA arrays. Therefore, introns of low copy nuclear genes (LCNG) are explored here for improved resolution. However, paralogs and lineage sorting are still two challenges for applying LCNGs in phylogenetic studies, and at least two independent nuclear loci should be compared. In this work the second intron of <it>LEAFY </it>and the alcohol dehydrogenase gene (<it>Adh</it>) were selected to investigate their molecular evolution and phylogenetic utility.</p> <p>Results</p> <p>DNA sequence analyses revealed a complex ortholog and paralog structure of <it>Adh </it>genes in <it>Pyrus </it>and <it>Malus</it>, the pears and apples. Comparisons between sequences from RT-PCR and genomic PCR indicate that some <it>Adh </it>homologs are putatively nonfunctional. A partial region of <it>Adh1 </it>was sequenced for 18 <it>Pyrus </it>species and three subparalogs representing <it>Adh1-1 </it>were identified. These led to poorly resolved phylogenies due to low sequence divergence and the inclusion of putative recombinants. For the second intron of <it>LEAFY</it>, multiple inparalogs were discovered for both <it>LFY1int2 </it>and <it>LFY2int2</it>. <it>LFY1int2 </it>is inadequate for phylogenetic analysis due to lineage sorting of two inparalogs. <it>LFY2int2-N</it>, however, showed a relatively high sequence divergence and led to the best-resolved phylogeny. This study documents the coexistence of outparalogs and inparalogs, and lineage sorting of these paralogs and orthologous copies. It reveals putative recombinants that can lead to incorrect phylogenetic inferences, and presents an improved phylogenetic resolution of <it>Pyrus </it>using <it>LFY2int2-N</it>.</p> <p>Conclusions</p> <p>Our study represents the first phylogenetic analyses based on LCNGs in <it>Pyrus</it>. Ancient and recent duplications lead to a complex structure of <it>Adh </it>outparalogs and inparalogs in <it>Pyrus </it>and <it>Malus</it>, resulting in neofunctionalization, nonfunctionalization and possible subfunctionalization. Among all investigated orthologs, <it>LFY2int2-N </it>is the best nuclear marker for phylogenetic reconstruction of <it>Pyrus </it>due to suitable sequence divergence and the absence of lineage sorting.</p

LncRNA Expression Profile of Human Thoracic Aortic Dissection by High-Throughput Sequencing

Background/Aims: In this study, the long non-coding RNA (lncRNA) expression profile in human thoracic aortic dissection (TAD), a highly lethal cardiovascular disease, was investigated. Methods: Human TAD (n=3) and normal aortic tissues (NA) (n=3) were examined by high-throughput sequencing. Bioinformatics analyses were performed to predict the roles of aberrantly expressed lncRNAs. Quantitative real-time polymerase chain reaction (qRT-PCR) was applied to validate the results. Results: A total of 269 lncRNAs (159 up-regulated and 110 down-regulated) and 2, 255 mRNAs (1 294 up-regulated and 961 down-regulated) were aberrantly expressed in human TAD (fold-change&#x3e; 1.5, P&#x3c; 0.05). QRT-PCR results of five dysregulated genes were consistent with HTS data. A lncRNA-mRNA coexpression analysis showed positive correlations between the up-regulated lncRNA (ENSG00000269936) and its adjacent up-regulated mRNA (MAP2K6, R=0.940, P&#x3c; 0.01), and between the down-regulated lncRNA_1421 and its down-regulated mRNAs (FBLN5, R=0.950, P&#x3c; 0.01; ACTA2, R=0.96, P&#x3c; 0.01; TIMP3, R=0.96, P&#x3c; 0.05). The lncRNA-miRNA-mRNA network indicated that the up-regulated lncRNA XIST and p21 had similar sequences targeted by has-miR-17-5p. The results of luciferase assay and fluorescence immuno-cytochemistry were consistent with that. And qRT-PCR results showed that lncRNA XIST and p21 were expressed at a higher level and has-miR-17-5p was expressed at a lower level in TAD than in NA. The predicted binding motifs of three up-regulated lncRNAs (ENSG00000248508, ENSG00000226530, and EG00000259719) were correlated with up-regulated RUNX1 (R=0.982, P&#x3c; 0.001; R=0.967, P&#x3c; 0.01; R=0.960, P&#x3c; 0.01, respectively). Conclusions: Our study revealed a set of dysregulated lncRNAs and predicted their multiple potential functions in human TAD. These findings suggest that lncRNAs are novel potential therapeutic targets for human TAD

Climatic and edaphic controls over the elevational pattern of microbial necromass in subtropical forests

The sequestration of soil organic carbon (SOC) in terrestrial ecosystems is determined by the balance between plant- and microbial-derived carbon inputs and losses through soil respiration. However, a consensus on the elevational patterns of soil microbial necromass and its contribution to SOC is rare, and the information on how climatic and edaphic factors affect the accumulation of microbial necromass remains limited. In this study, soil samples were collected with a 50-m interval along an elevational gradient (200-950 m above sea level) to investigate the effects of climatic and edaphic variability associated with elevation and season on microbial necromass in subtropical forests. The concentration of soil amino sugar was measured by high-performance liquid chromatography (HPLC) to characterize soil microbial necromass. Partial least squares path modeling (PLS-PM) was used for testing climatic and edaphic controls over the elevational pattern of microbial necromass. The concentration of soil microbial necromass and its contribution to SOC were affected by elevation and season, with lower concentration and contribution in the wet season than in the dry season. Soil microbial necromass linearly increased or followed a quadratic pattern with elevation, and accounted for 18.9% of SOC on average with a greater contribution from fungal necromass (13.2%) than from bacterial necromass (5.7%). Soil temperature, soil nitrogen and moisture content directly influenced the accumulation of soil microbial necromass with varied effects on fungal and bacterial necromass. Warmer and nutrient-impoverished environments were linked with the depletion of fungal necromass, whereas higher soil moisture and nutrient availability were positively associated with the accumulation of bacterial necromass. Our findings demonstrate that less microbial necromass, especially fungal necromass will accumulate in SOC in response to future climate warming in subtropical forests. Such information is valuable for improving our understanding of the potential impacts of future climatic change on soil carbon cycling in subtropical regions

Forest understory vegetation study: current status and future trends

Understory vegetation accounts for a large proportion of floral diversity. It provides various ecosystem functions and services, such as productivity, nutrient cycling, organic matter decomposition and ecosystem self-regeneration. This review summarizes the available literature on the current status and progress of the ten most studied branches of understory vegetation on both its structural and functional aspects based on global climate change and forest management practices. Future research directions and priorities for each branch is suggested, where understory vegetation in response to the interplay of multiple environmental factors and its long-term monitoring using ground-based surveys combined with more efficient modern techniques is highlighted, although the critical role of understory vegetation in ecosystem processes individually verified in the context of management practices or climate changes have been extensively investigated. In summary, this review provides insights into the effective management of the regeneration and restoration of forest ecosystems, as well as the maintenance of ecosystem multilevel structures, spatial patterns, and ecological functions

A scalable solid-state nanoporous network with atomic-level interaction design for carbon dioxide capture.

Carbon capture and sequestration reduces carbon dioxide emissions and is critical in accomplishing carbon neutrality targets. Here, we demonstrate new sustainable, solid-state, polyamine-appended, cyanuric acid-stabilized melamine nanoporous networks (MNNs) via dynamic combinatorial chemistry (DCC) at the kilogram scale toward effective and high-capacity carbon dioxide capture. Polyamine-appended MNNs reaction mechanisms with carbon dioxide were elucidated with double-level DCC where two-dimensional heteronuclear chemical shift correlation nuclear magnetic resonance spectroscopy was performed to demonstrate the interatomic interactions. We distinguished ammonium carbamate pairs and a mix of ammonium carbamate and carbamic acid during carbon dioxide chemisorption. The coordination of polyamine and cyanuric acid modification endows MNNs with high adsorption capacity (1.82 millimoles per gram at 1 bar), fast adsorption time (less than 1 minute), low price, and extraordinary stability to cycling by flue gas. This work creates a general industrialization method toward carbon dioxide capture via DCC atomic-level design strategies