The complete chloroplast genome of Pseudotsuga sinensis, a China endemic species.

In this study, we collected plant material from Pseudotsuga sinensis in Guizhou, China, and sequenced it. The complete chloroplast genome consisted of 122,243 bp, including a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat regions like those in P. sinensis var. wilsoniana. The GC content of P. sinensis and P. sinensis var. wilsoniana are 38.7% and 38.8%, respectively. The reconstructed phylogenetic tree reveals that P. sinensis was a sister species to P. sinensis var. wilsoniana. Hence, the availability of the chloroplast genome of P. sinensis will promote further phylogenetic studies of the family Pinaceae.

Prognostic biomarker replication factor C subunit 5 and its correlation with immune infiltrates in acute myeloid leukemia.

OBJECTIVE: To determine the role of replication factor C subunit 5 (RFC5) in acute myeloid leukemia (AML) from four aspects: expression, prognosis, biological functions, and its effects on the immune system. METHODS: The RFC5 gene expression and survival analyses, biological function analyses including functional enrichment analysis of genes co-expressed with RFC5, RFC5-interacted gene network construction, gene set enrichment analysis (GSEA), and immune infiltration analysis were performed using data based on GDC TCGA and GEO. The CIBERSORT algorithm was employed to quantify immune cell fractions. All the statistical analyses were performed in SPSS software, GraphPad Prism, and R software. RESULTS: RFC5 expression was abnormally expressed in AML (P <0.05). Notably, differential RFC5 expression was observed among different FAB AML subtypes and hematopoietic lineages (all P <0.05). More importantly, high RFC5 expression served as an independent prognostic factor for the poor overall survival of AML patients (P <0.001). Enrichment analyses revealed that RFC5 was involved in cell cycle-related pathways in AML. CIBERSORT analysis showed high proportions of M2 macrophages in the high RFC5 expression group. CONCLUSIONS: RFC5 might serve as an effective and robust biomarker for the diagnosis and prognosis of AML. RFC5 might be involved in the AML progression via cell cycle regulation. Moreover, the correlation between RFC5 and immune cells might provide potential assistance for AML treatment.

The complete chloroplast genome of Berberis weiningensis (Berberidaceae), an endemic and traditional Chinese medicinal herb.

Berberis weiningensis is a frequently-used traditional Chinese medicinal herb that included various active alkaloids. In this study, we assembled the complete chloroplast (cp) genome of B. weiningensis. The complete cp genome of B. weiningensis is 166,275 bp in length, and has a typical structure with large single-copy (LSC 73,624 bp) and small single-copy (SSC 18,608 bp) regions separated by a pair of inverted repeats (IRs 37,019 bp) of large size. The B. weiningensis cp genome contains 147 genes, of which 101 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. The phylogenetic analysis revealed that Berberis species closely clustered with Mahonia species, which obviously support that Mahonia and Berberis are not monophyletic.

Identification of Parkinson's disease-related pathways and potential risk factors.

OBJECTIVE: To identify Parkinson's disease (PD)-associated deregulated pathways and genes, to further elucidate the pathogenesis of PD. METHODS: Dataset GSE100054 was downloaded from the Gene Expression Omnibus, and differentially expressed genes (DEGs) in PD samples were identified. Functional enrichment analyses were conducted for the DEGs. The top 10 hub genes in the protein-protein interaction (PPI) network were screened out and used to construct a support vector machine (SVM) model. The expression of the top 10 genes was then validated in another dataset, GSE46129, and a clinical patient cohort. RESULTS: A total of 333 DEGs were identified. The DEGs were clustered into two gene sets that were significantly enriched in 12 pathways, of which 8 were significantly deregulated in PD, including cytokine-cytokine receptor interaction, gap junction, and actin cytoskeleton regulation. The signature of the top 10 hub genes in the PPI network was used to construct the SVM model, which had high performance for predicting PD. Of the 10 genes, GP1BA, GP6, ITGB5, and P2RY12 were independent risk factors of PD. CONCLUSION: Genes such as GP1BA, GP6, P2RY12, and ITGB5 play critical roles in PD pathology through pathways including cytokine-cytokine receptor interaction, gap junctions, and actin cytoskeleton regulation.

Author Correction: Identifying long-term stable refugia for relict plant species in East Asia.

In the original version of this Article, an incorrect sample size was provided for the number of relict species (443 instead of 442) and the number of relict forests (423 instead of 422). These errors have been corrected in both the PDF and HTML versions of the Article.

Identifying long-term stable refugia for relict plant species in East Asia.

Today East Asia harbors many "relict" plant species whose ranges were much larger during the Paleogene-Neogene and earlier. The ecological and climatic conditions suitable for these relict species have not been identified. Here, we map the abundance and distribution patterns of relict species, showing high abundance in the humid subtropical/warm-temperate forest regions. We further use Ecological Niche Modeling to show that these patterns align with maps of climate refugia, and we predict species' chances of persistence given the future climatic changes expected for East Asia. By 2070, potentially suitable areas with high richness of relict species will decrease, although the areas as a whole will probably expand. We identify areas in southwestern China and northern Vietnam as long-term climatically stable refugia likely to preserve ancient lineages, highlighting areas that could be prioritized for conservation of such species.

Potential effects of climate change on geographic distribution of the Tertiary relict tree species Davidia involucrata in China.

This study, using species distribution modeling (involving a new approach that allows for uncertainty), predicts the distribution of climatically suitable areas prevailing during the mid-Holocene, the Last Glacial Maximum (LGM), and at present, and estimates the potential formation of new habitats in 2070 of the endangered and rare Tertiary relict tree Davidia involucrata Baill. The results regarding the mid-Holocene and the LGM demonstrate that south-central and southwestern China have been long-term stable refugia, and that the current distribution is limited to the prehistoric refugia. Given future distribution under six possible climate scenarios, only some parts of the current range of D. involucrata in the mid-high mountains of south-central and southwestern China would be maintained, while some shift west into higher mountains would occur. Our results show that the predicted suitable area offering high probability (0.5‒1) accounts for an average of only 29.2% among the models predicted for the future (2070), making D. involucrata highly vulnerable. We assess and propose priority protected areas in light of climate change. The information provided will also be relevant in planning conservation of other paleoendemic species having ecological traits and distribution ranges comparable to those of D. involucrata.