Transcriptome analysis reveals key transcription factors and pathways of polian vesicle associated with cell proliferation in Vibrio splendidus-challenged Apostichopus japonicus.

Polian vesicle is thought to produce coelomocytes and contribute to the sea cucumber's immune system. Our previous work has indicated that polian vesicle was responsible for cell proliferation at 72 h post pathogenic challenge. However, the transcription factors related to the activation of effector factors and the molecular process behind this remained unknown. In this study, to reveal the early functions of polian vesicle in response to the microbe, a comparative transcriptome sequencing of polian vesicle in V. splendidus-challenged Apostichopus japonicus, including normal group (PV 0 h), pathogen challenging for 6 h (PV 6 h) and 12 h (PV 12 h) was performed. Compared PV 0 h to PV 6 h, PV 0 h to PV 12 h, and PV 6 h to PV 12 h, we found 69, 211, and 175 differentially expressed genes (DEGs), respectively. KEGG enrichment analysis revealed the DEGs, including several transcription factors such as fos, FOS-FOX, ATF2, egr1, KLF2, and Notch3 between PV 6 h and PV 12 h were consistently enriched in MAPK, Apelin and Notch3 signaling pathways related to cell proliferation compared with that in PV 0 h. Important DEGs involved in cell growth were chosen, and their expression patterns were almost the same as the transcriptome profile analysis by qPCR. Protein interaction network analysis indicated that two DEGs of fos and egr1 were probably significant as key candidate genes controlling cell proliferation and differentiation in polian vesicle after pathogenic infection in A. japonicus. Overall, our analysis demonstrates that polian vesicles may play an essential role in regulating proliferation via transcription factors-mediated signaling pathway in A. japonicus and provide new insights into hematopoietic modulation of polian vesicles in response to pathogen infection.

Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax.

All extant core-eudicot plants share a common ancestral genome that has experienced cyclic polyploidizations and (re)diploidizations. Reshuffling of the ancestral core-eudicot genome generates abundant genomic diversity, but the role of this diversity in shaping the hierarchical genome architecture, such as chromatin topology and gene expression, remains poorly understood. Here, we assemble chromosome-level genomes of one diploid and three tetraploid Panax species and conduct in-depth comparative genomic and epigenomic analyses. We show that chromosomal interactions within each duplicated ancestral chromosome largely maintain in extant Panax species, albeit experiencing ca. 100-150 million years of evolution from a shared ancestor. Biased genetic fractionation and epigenetic regulation divergence during polyploidization/(re)diploidization processes generate remarkable biochemical diversity of secondary metabolites in the Panax genus. Our study provides a paleo-polyploidization perspective of how reshuffling of the ancestral core-eudicot genome leads to a highly dynamic genome and to the metabolic diversification of extant eudicot plants.

Genome sequences of five Sitopsis species of Aegilops and the origin of polyploid wheat B subgenome.

Common wheat (Triticum aestivum, BBAADD) is a major staple food crop worldwide. The diploid progenitors of the A and D subgenomes have been unequivocally identified; that of B, however, remains ambiguous and controversial but is suspected to be related to species of Aegilops, section Sitopsis. Here, we report the assembly of chromosome-level genome sequences of all five Sitopsis species, namely Aegilops bicornis, Ae. longissima, Ae. searsii, Ae. sharonensis, and Ae. speltoides, as well as the partial assembly of the Amblyopyrum muticum (synonym Aegilops mutica) genome for phylogenetic analysis. Our results reveal that the donor of the common wheat B subgenome is a distinct, and most probably extinct, diploid species that diverged from an ancestral progenitor of the B lineage to which the still extant Ae. speltoides and Am. muticum belong. In addition, we identified interspecific genetic introgressions throughout the evolution of the Triticum/Aegilops species complex. The five Sitopsis species have various assembled genome sizes (4.11-5.89 Gb) with high proportions of repetitive sequences (85.99%-89.81%); nonetheless, they retain high collinearity with other genomes or subgenomes of species in the Triticum/Aegilops complex. Differences in genome size were primarily due to independent post-speciation amplification of transposons. We also identified a set of Sitopsis genes pertinent to important agronomic traits that can be harnessed for wheat breeding. These newly assembled genome resources provide a new roadmap for evolutionary and genetic studies of the Triticum/Aegilops complex, as well as for wheat improvement.

Evolutionary Contribution of Duplicated Genes to Genome Evolution in the Ginseng Species Complex.

Genes duplicated by whole genome duplication (WGD) and small-scale duplication (SSD) have played important roles in adaptive evolution of all flowering plants. However, it still remains underinvestigated how the distinct models of duplication events and their contending evolutionary patterns have shaped the genome and epigenomes of extant plant species. In this study, we investigated the contribution of the WGD- and SSD-derived duplicate genes to the genome evolution of one diploid and three closely related allotetraploid Panax species based on genome, methylome, and proteome data sets. Our genome-wide comparative analyses revealed that although the ginseng species complex was recently diverged, they have evolved distinct overall patterns of nucleotide variation, cytosine methylation, and protein-level expression. In particular, genetic and epigenetic asymmetries observed in the recent WGD-derived genes are largely consistent across the ginseng species complex. In addition, our results revealed that gene duplicates generated by ancient WGD and SSD mechanisms exhibited distinct evolutionary patterns. We found the ancient WGD-derived genes (i.e., ancient collinear gene) are genetically more conserved and hypomethylated at the cytosine sites. In contrast, some of the SSD-derived genes (i.e., dispersal duplicated gene) showed hypermethylation and high variance in nucleotide variation pattern. Functional enrichment analyses of the duplicated genes indicated that adaptation-related traits (i.e., photosynthesis) created during the distant ancient WGDs are further strengthened by both the more recent WGD and SSD. Together, our findings suggest that different types of duplicated genes may have played distinct but relaying evolutionary roles in the polyploidization and speciation processes in the ginseng species complex.

Three new labdane-type diterpenoids from Callicarpa macrophylla Vahl.

Three new labdane-type diterpenoids, callicapene M3-M5 (1-3) were isolated from the Callicarpa macrophylla Vahl. Their structures were identified by spectroscopic method. The isolated compounds were evaluated for inhibitory activity on NO production in LPS-activated RAW 264.7 macrophage cells by using MTT assays. Compounds 1-3 showed potent inhibitory activity, with IC50 value of 48.15, 46.31 and 38.72 µM respectively.

Three New Abietane-Type Diterpenoids from Callicarpa macrophylla Vahl.

Three new abietane-type diterpenoids, named callicapoic acid M3 (1), callicapoic acid M4 (2) and callicapoic acid M5 (3), were isolated from the Callicarpa macrophylla Vahl. Their structures were established by spectroscopic techniques (IR, UV, MS, 1D and 2D NMR). All the isolated three compounds were evaluated for inhibitory activity on NO production in LPS-activated RAW 264.7 macrophage cells by using MTT assays. Compounds 1, 2 and 3 showed potent inhibitory activity, with inhibition rates of 34.47-40.13%.

Acetylpuerarin increases cell viability and reduces apoptosis in rat hippocampal neurons following oxygen­glucose deprivation/reperfusion.

The effects of acetylpuerarin treatment following oxygen-glucose deprivation/reperfusion (OGD/R) were examined in rat hippocampal neurons in vitro and compared with the effects of acetylpuerarin in normoxic cells to confirm acetylpuerarin's potential neuroprotective effects, including apoptosis inhibition. Wistar rat embryo hippocampal cells (day 18, E18) cultured for 8 days were subjected to 3 h OGD treatment, followed by reperfusion for 12, 24 or 36 h. For each time interval, a group of cells was left untreated (OGD/R-only groups) and treated with 0.1, 0.4 and 1.6 µM acetylpuerarin (OGD/R+acetylpuerarin). Neuron viability, apoptosis and caspase-8 and -3 activities were assessed by the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), 4',6-diamidino-2-phenylindole (DAPI) and terminal deoxynucleotidyl-transferase-mediated dUTP nick end labeling (TUNEL) and spectrophotometric assays, respectively. Fas-ligand (Fas-L), Fas-associated death domain (FADD) and tumor necrosis factor-α (TNF-α) were determined by western blot analysis. Compared with control cells, OCD/R+acetylpuerarin cells treated with 0.1, 0.4 and 1.6 µM doses showed a concentration-dependent increase in hippocampal cell survival and viability by 69.93 ± 2.28%, 81.49 ± 2.13% and 85.28 ± 2.38% at 12 h, 68.59 ± 3.02%, 77.85 ± 2.84% and 85.64 ± 4.39% at 24 h and 69.70 ± 1.70%, 77.21 ± 3.21% and 83.90 ± 2.12% at 36 h (P<0.05). Furthermore, OCD/R+acetylpuerarin cells exhibited a dose-dependent decrease in caspase-8 and -3 activation, TUNEL and DAPI-positive neurons and Fas-L, FADD and TNF-α expression. In conclusion, acetylpuerarin protects against OGD/R-induced neuronal apoptosis predominantly in the first 24 h following ischemia, which may be useful in mediating neuronal apoptosis in ischemic stroke patients.

[Progress of research on TLRs-mediated signaling pathway].

TLRs belong to a family of pattern recognition receptors (PRRs) that recognize highly conserved microbial antigens termed pathogen associated molecular patterns (PAMPs). So far, ten TLRs have been identified in human genome. Each TLR senses a different set of microbial stimuli, and recruits various of adaptors and activates a series of distinct signaling cascades, and drives specific responses against the pathogens. TLRs bridged innate and adaptive immunity. The discoveries of Toll-like receptors guided the field of innate immunity to its present era of accelerated advancement. In this review, we will focus on the recent progresses of TLRs-mediated signaling. A better understanding of the immunological and molecular mechanisms mediated by TLRs will obviously facilitate the exploiting molecular targets of immunotherapy to control TLR-mediated diseases.

[Expression of protooncogene c-jun, p38 and proliferating cell nuclear antigen in intestinal epithelial cells in rats different development stages].

OBJECTIVE: To investigate the expression characteristics of protooncogene c-jun and its related gene p38 in different developmental intestinal epithelial cells in rats, and to explore their biological roles in the intestinal wound healing after injury. METHODS: Immunohistochemical techniques were used to detect the expressions of c-jun, p38 and proliferating cell nuclear antigen (PCNA). RESULTS: The positive expression of c-jun in intestinal epithelial cells at the early development stage (from E14 d to P28 d) was much stronger and more extensive than that in mature rats, and migrated from bottom to top of villus with epithelial cellular development. The positive expression of PCNA was similar with c-jun during the same time, but the distinction between them was location of their expression. The expression of c-jun in mature rat only lay in the top of villus, while the expression of PCNA was limited to intestinal crypts. The expression of p38 during stages of development and mature, mainly was in mitogenic cells. CONCLUSION: The results indicate that the strong expression of tumor gene c-jun at the early development and mature stages of intestinal epithelial cells at the special region is related to cellular differentiation, and p38 is probable correlate with cellular mitogenesis.