High-quality genome assembly of Huazhan and Tianfeng,the parents of an elite rice hybrid Tian-you-hua-zhan

High-quality rice reference genomes have accelerated the comprehensive identification of genome-wide variations and research on functional genomics and breeding. Tian-you-hua-zhan has been a leading hybrid in China over the past decade. Here, de novo genome assembly strategy optimization for the rice indica lines Huazhan (HZ) and Tianfeng (TF), including sequencing platforms, assembly pipelines and sequence depth, was carried out. The PacBio and Nanopore platforms for long-read sequencing were utilized, with the Canu, wtdbg2, SMARTdenovo, Flye, Canu-wtdbg2, Canu-SMARTdenovo and Canu-Flye assemblers. The combination of PacBio and Canu was optimal, considering the contig N50 length, contig number, assembled genome size and polishing process. The assembled contigs were scaffolded with Hi-C data, resulting in two “golden quality” rice reference genomes, and evaluated using the scaffold N50, BUSCO, and LTR assembly index. Furthermore, 42,625 and 41,815 non-transposable element genes were annotated for HZ and TF, respectively. Based on our assembly of HZ and TF, as well as Zhenshan97, Minghui63, Shuhui498 and 9311, comprehensive variations were identified using Nipponbare as a reference. The de novo assembly strategy for rice we optimized and the “golden quality” rice genomes we produced for HZ and TF will benefit rice genomics and breeding research, especially with respect to uncovering the genomic basis of the elite traits of HZ and TF.

     

An arabinogalactan isolated from the stems of Cistanche deserticola induces the proliferation of cultured lymphocytes

A purified polysaccharide ACDP-2 was isolated from water extract of the stems of Cistanche deserticola. Chemical and spectroscopic analyses indicated that ACDP-2 is a highly branched arabinogalactan polymer that composes of linked d-galactopyranose and d-glucopyranose, which contains predominantly a branching point at the 6-carbon. The branched side-chains compose of terminal-, 1,5-, and 1,3,5-linked arabinofuranosyl residues. ACDP-2 showed an effect in stimulating the immune response, which when applied onto the cultured mouse lymphocytes induced the cell proliferation in a dose-dependent manner.     

2001—2010年黄河流域生态系统植被净第一性生产力变化及气候因素驱动分析

基于MODIS-NDVI遥感数据,利用CASA模型分析黄河流域2001—2010年植被净第一性生产力（NPP）的空间分布格局,并结合同期气温和降水量数据,分别从不同空间和时间尺度上分析了黄河流域6种生态系统类型区域植被NPP的变化趋势,并对其与气候因素的相关关系进行分析.结果表明： 植被NPP空间分布呈西北低、东南高的分布特征,平均NPP年总量为108.53 Tg C,植被NPP的分布与生态系统类型呈现较高的相关性;2001—2010年,植被NPP总体呈上升趋势但波动较大,55.4%的面积呈现增加趋势,不同生态系统类型区域呈现不同的变化趋势;在年际水平上,黄河流域植被NPP变化与气候因素没有显著相关性,但在月际水平上呈现了较高的相关性,降水量和气温对植被NPP变化的影响作用相当;不同生态系统类型对气候因素呈现不同的相关性质以及时滞效应,草地对降水量的响应存在一定程度的时滞效应,荒漠对气温存在时滞效应.     

PLS3 predicts poor prognosis in pancreatic cancer and promotes cancer cell proliferation via PI3K/AKT signaling

Plastin-3 plays a key role in cancer cell proliferation and invasion, but its prognostic value in pancreatic cancer (PACA) remains poorly defined. In this study, we show that PLS3 messenger RNA is overexpressed in PACA tissue compared with normal tissue. We accumulated 207 cases of PACA specimens to perform immunohistochemical analysis and demonstrated that PLS3 levels correlate with T-classification (p < .001) and pathology (p < .001). Furthermore, overall survival rates (p < .001) in tumors with high PLS3 expression were poor, as assessed through Kaplan–Meier survival analysis. PLS3 was found to be an independent prognostic factor for PACA through multivariate Cox regression analysis. Moreover, we found that PLS3 enhances the proliferation and invasion of tumor cells as assessed through Cell Counting Kit-8, wounding healing assays, and Transwell assays. The upregulation of PLS3 also led to enhanced phosphatidylinositol-3 kinase/protein kinase B signaling in PACA cells. These data suggest that PLS3 is a biomarker to estimate PACA progression and represents a molecular target for PACA therapy.     

Exogenous maltose enhances Zebrafish immunity to levofloxacin-resistant Vibrio alginolyticus

Understanding the interplay between bacterial fitness, antibiotic resistance, host immunity and host metabolism could guide treatment and improve immunity against antibiotic-resistant pathogens. The acquisition of levofloxacin (Lev) resistance affects the fitness of Vibrio alginolyticus in vitro and in vivo. Lev-resistant (Lev-R) V. alginolyticus exhibits slow growth, reduced pathogenicity and greater resistance to killing by the host, Danio rerio (zebrafish), than Lev-sensitive (Lev-S) V. alginolyticus, suggesting that Lev-R V. alginolyticus triggers a weaker innate immune response in D. rerio than Lev-S V. alginolyticus. Differences were detected in the metabolome of D. rerio infected with Lev-S or Lev-R V. alginolyticus. Maltose, a crucial metabolite, is significantly downregulated in D. rerio infected with Lev-R V. alginolyticus, and exogenous maltose enhances the immune response of D. rerio to Lev-R V. alginolyticus, leading to better clearance of the infection. Furthermore, we demonstrate that exogenous maltose stimulates the host production of lysozyme and its binding to Lev-R V. alginolyticus, which depends on bacterial membrane potential. We suggest that exogenous exposure to crucial metabolites could be an effective strategy for treating and/or managing infections with antibiotic-resistant bacteria.