Conserved DNA sequence analysis reveals the phylogeography and evolutionary events of Akebia trifoliata in the region across the eastern edge of the Tibetan Plateau and subtropical China.

BACKGROUND: The eastern edge of the Qinghai‒Tibet Plateau (QTP) and subtropical China have various regions where plant species originate and thrive, but these regions have been the focus of very few integrative studies. Here, we elucidated the phylogeographic structure of a continuous and widespread Akebia trifoliata population across these two regions. RESULTS: Sixty-one populations consisting of 391 genotypes were examined to assess population diversity and structure via network distribution analysis, maximum likelihood phylogenetic tree reconstruction, divergence time estimation, demographic history inference, and ancestral area reconstruction of both conserved internal transcribed spacer (ITS) and chloroplast (rps16) DNA sequences. The results showed that the ITS region was more variable than the rps16 region and could be suitable for studying intraspecific phylogeography. The A. trifoliata population displayed high genetic diversity, genetic differentiation and obvious phylogeographical structure, possibly originating on the eastern QTP, expanding during the last glacial-interglacial cycle, diverging in the early Pleistocene and middle Pleistocene, and extensively migrating thereafter. The migration route from west to east along rivers could be largely responsible for the long-distance dispersal of this species, while three main refuges (Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) with multiple ice shelters facilitated its wide distribution. CONCLUSIONS: Our results suggested that the from west to east long migration accompanying with the minor short reciprocal migration in the south-north direction, and the three main refuges (the Qinba Mountains, Nanling Mountains and Yunnan-Guizhou Plateau) contributed to the extant geographical distribution of A. trifoliata. In addition, this finding also strongly reduced the discrepancy between glacial contraction and postglacial expansion and the in situ survival hypothesis by simultaneously considering the existence of many similar climate-related ecological niches and migration influences.

Genome-Wide Analysis of the Polygalacturonase Gene Family Sheds Light on the Characteristics, Evolutionary History, and Putative Function of Akebia trifoliata.

Polygalacturonase (PG) is one of the largest families of hydrolytic enzymes in plants. It is involved in the breakdown of pectin in the plant cell wall and even contributes to peel cracks. Here, we characterize PGs and outline their expression profiles using the available reference genome and transcriptome of Akebia trifoliata. The average length and exon number of the 47 identified AktPGs, unevenly assigned on 14 chromosomes and two unassembled contigs, were 5399 bp and 7, respectively. The phylogenetic tree of 191 PGs, including 47, 57, 51, and 36 from A. trifoliata, Durio zibethinus, Actinidia chinensis, and Vitis vinifera, respectively, showed that AktPGs were distributed in all groups except group G and that 10 AktPGs in group E were older, while the remaining 37 AktPGs were younger. Evolutionarily, all AktPGs generally experienced whole-genome duplication (WGD)/segmental repeats and purifying selection. Additionally, the origin of conserved domain III was possibly associated with a histidine residue (H) substitute in motif 8. The results of both the phylogenetic tree and expression profiling indicated that five AktPGs, especially AktPG25, could be associated with the cracking process. Detailed information and data on the PG family are beneficial for further study of the postharvest biology of A. trifoliata.

Spatial characteristics of VOCs and their ozone and secondary organic aerosol formation potentials in autumn and winter in the Guanzhong Plain, China.

As critical precursors of tropospheric ozone (O3) and secondary organic aerosol (SOA), volatile organic compounds (VOCs) largely influence air quality in urban environments. In this study, measurements of 102 VOCs at all five major cities in the Guanzhong Plain (GZP) were conducted during Sep.09-Oct. 13, 2017 (autumn) and Nov. 14, 2017-Jan. 19, 2018 (winter) to investigate the characteristics of VOCs and their roles in O3 and SOA formation. The average concentrations of total VOCs (TVOCs) at Xi'an (XA), Weinan (WN), Xianyang (XY), Tongchuan (TC), and Baoji (BJ) sites were in the range of 55.2-110.2 ppbv in autumn and 42.4-74.3 ppbv in winter. TVOCs concentrations were reduced by 22.4%-43.5% from autumn to winter at XA, WN and BJ. Comparatively low concentrations of TVOCs were observed in XY and TC, ranging from 53.5 to 62.7 ppbv across the sampling period. Alkanes were the major components at all sites, accounting for 26.4%-48.9% of the TVOCs during the sampling campaign, followed by aromatics (4.2%-26.4%). The average concentration of acetylene increased by a factor of up to 4.8 from autumn to winter, indicating the fuel combustion in winter heating period significantly impacted on VOCs composition in the GZP. The OH radical loss rate and maximum incremental reactivity method were employed to determine photochemical reactivities and ozone formation potentials (OFPs) of VOCs, respectively. The VOCs in XA and WN exhibited the highest reactivities in O3 formation, with the OFP of 168-273 ppbv and the OH loss rates of 19.3-40.8 s-1. Alkenes and aromatics primarily related to on-road and industrial emissions contributed 57.8%-76.3% to the total OFP. The contribution of aromatics to the SOA formation at all sites reached 94.1%-98.6%. Considering the potential source-area of VOCs, regional transport of VOCs occurred within the GZP cities.

[Characteristics of VOCs and Formation Potentials of O3 and SOA in Autumn and Winter in Tongchuan, China].

Volatile organic compounds (VOCs) are the main precursors of tropospheric O3 and secondary organic aerosol (SOA), which can enhance atmospheric oxidation, promote the formation of secondary pollutants, and affect regional air quality and human health. In order to gain insights on VOCs characteristics and their potentials for O3 and SOA formation, the volume fraction of 102 VOCs in autumn and winter in the urban area of Tongchuan were monitored using the TH-300B online monitoring system. The maximum incremental reactivity (MIR) coefficient and the fractional aerosol coefficient (FAC) were used to estimate the ozone formation potential (OFP) and SOA formation potential (SOAFP), respectively. The φ(TVOC, total VOCs) were (50.52±16.81)×10-9 in autumn and (63.21±35.24)×10-9 in winter. The OFPs were 138.43×10-9 in autumn and 137.123×10-9 in winter, and the SOAFPs were 3.098 µg·m-3 and 0.612 µg·m-3, respectively. Alkanes (26.19%) and aromatics (26.04%) were the most abundant species in autumn, and alkanes (48.88%) were the most abundant species in winter. Trans-2-pentene, toluene, and m/p-xylene were the most reactive species in terms of OFPs in autumn, and ethylene, acetylene, and propylene were the top three species contributing to the total OFPs in winter. Toluene, m/p-xylene, and ethylbenzene contributed the most to the total SOAFPs in both of autumn and winter. Traffic emissions were considered as the major source of VOCs in both seasons. VOCs from biomass/coal combustion emissions showed seasonal differences, which were more prominent in winter. The results can provide references for the "one city, one policy" to mitigate regional VOCs pollution and improve ambient air quality.

Proteomic analysis of human periodontal ligament cells under hypoxia.

BACKGROUND: The periodontal ligament is essential for homeostasis of periodontal tissue. A hypoxic milieu of the periodontal tissue is generated under periodontitis or during orthodontic treatment, which affects the periodontal and bone remodelling process. Here, we provide a comprehensive proteomic characterization of periodontal ligament cells under hypoxic conditions, aiming to reveal previously unappreciated biological changes and to help advance hypoxia-based therapeutic strategies for periodontal diseases. METHODS: Human periodontal ligament cells (hPDLCs) were characterized using immunohistochemistry (IHC) and flow cytometry (FACS). Successful hypoxia treatment of hPDLCs with 1% O2 was confirmed by qRT-PCR. Proliferation was evaluated using an MTT assay. The proteomic expression profile under hypoxia was studied with the isobaric tags for relative and absolute quantification (iTRAQ) approach followed by protein identification and bioinformatic analysis, and western blot verification was performed. RESULTS: The hPDLCs were positive for vimentin, CD73 and CD105 and negative for keratin, CD34 and CD45. After hypoxia treatment, the mRNA expression of hypoxia-inducible factor 1a (HIF1a) was upregulated. The proliferation rate was elevated during the first 6 h but decreased from 6 h to 72 h. A total of 220 differentially expressed proteins were quantified in hPDLCs under hypoxia (1% O2, 24 h), including 153 upregulated and 67 downregulated proteins, five of which were verified by western blot analysis. The Gene Ontology enriched terms included the energy metabolic process, membrane-bound organelle and vesicle, and protein binding terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated several involved pathways, including glycolysis/gluconeogenesis, biosynthesis of amino acids, the HIF-1 signalling pathway, and focal adhesion. A protein-protein interaction (PPI) network demonstrated the dominant role of autophagy over apoptosis under hypoxia. CONCLUSION: The proteomic profile of hPDLCs under hypoxia was mainly related to energy metabolism, autophagy, and responses to stimuli such as adhesion and inflammation. Previously unrecognized proteins including solute carrier family proteins, heat shock proteins, ubiquitination-related enzymes, collagen and S100 family proteins are involved in adaptive response to hypoxia in hPDLCs and are thus of great research interest in future work.