The distribution of coastal fish eDNA sequences in the Anthropocene

Aim

Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio-economic factors.

Location

Tropical, temperate and polar coastal areas.

Time period

Present day.

Major taxa studied

Marine fishes.

Methods

We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio-economic factors on α- and β-diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic α- and β-diversity measured from our barcodes, and phylogenetic but also functional diversity.

Results

We show that fish eDNA MOTU and sequence α- and β-diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity.

Main conclusions

Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions.     

TaTPP-7A positively feedback regulates grain filling and wheat grain yield through T6P-SnRK1 signalling pathway and sugar–ABA interaction

Grain size and filling are two key determinants of grain thousand-kernel weight (TKW) and crop yield, therefore they have undergone strong selection since cereal was domesticated. Genetic dissection of the two traits will improve yield potential in crops. A quantitative trait locus significantly associated with wheat grain TKW was detected on chromosome 7AS flanked by a simple sequence repeat marker of Wmc17 in Chinese wheat 262 mini-core collection by genome-wide association study. Combined with the bulked segregant RNA-sequencing (BSR-seq) analysis of an F₂ genetic segregation population with extremely different TKW traits, a candidate trehalose-6-phosphate phosphatase gene located at 135.0 Mb (CS V1.0), designated as TaTPP-7A, was identified. This gene was specifically expressed in developing grains and strongly influenced grain filling and size. Overexpression (OE) of TaTPP-7A in wheat enhanced grain TKW and wheat yield greatly. Detailed analysis revealed that OE of TaTPP-7A significantly increased the expression levels of starch synthesis- and senescence-related genes involved in abscisic acid (ABA) and ethylene pathways. Moreover, most of the sucrose metabolism and starch regulation-related genes were potentially regulated by SnRK1. In addition, TaTPP-7A is a crucial domestication- and breeding-targeted gene and it feedback regulates sucrose lysis, flux, and utilization in the grain endosperm mainly through the T6P-SnRK1 pathway and sugar–ABA interaction. Thus, we confirmed the T6P signalling pathway as the central regulatory system for sucrose allocation and source–sink interactions in wheat grains and propose that the trehalose pathway components have great potential to increase yields in cereal crops.     

The vacuolar H+-ATPase of Saccharomyces cerevisiae is required for efficient copper detoxification,mitochondrial function,and iron metabolism

Mutations in the GEF2 gene of the yeast Saccharomyces cerevisiae have pleiotropic effects. The gef2 mutants display a petite phenotype. These cells grow slowly on several different carbon sources utilized exclusively or primarily by respiration. This phenotype is suppressed by adding large amounts of iron to the growth medium. A defect in mitochondrial function may be the cause of the petite phenotype: the rate of oxygen consumption by intact gef2 cells and by mitochondrial fractions isolated from gef2 mutants was reduced 60%–75% relative to wild type. Cytochrome levels were unaffected in gef2 mutants, indicating that heme accumulation is not significantly altered in these strains. The gef2 mutants were also more sensitive than wild type to growth inhibition by several divalent cations including Cu. We found that the cup5 mutation, causing Cu sensitivity, is allelic to gef2 mutations. The GEF2 gene was isolated, sequenced, and found to be identical to VMA3, the gene encoding the vacuolar H ⁺-ATPase proteolipid subunit. These genetic and biochemical analyses demonstrate that the vacuolar H ⁺-ATPase plays a previously unknown role in Cu detoxification, mitochondrial function, and iron metabolism.     

L-苹果酸产生菌筛选及高产突变株诱变选育

通过广泛收集和分离,获得根霉属(Rhizopus)、曲霉属(Aspergillus)及裂褶菌属(Schizophyllum)等属菌株897株。产酸指示平板上的变色圈测定结果表明,它们中间628株为产酸菌。通过纸层析对产酸菌发酵液酸谱的分析,获得129株L-苹果酸产生菌,经进一步测定发酵液中L-苹果酸的含量,筛选出以葡萄糖为原料,摇瓶发酵140小时,L-苹果酸产率48．37g／L,对糖转化率48．37×10^-2 的菌株LMO2。经初步鉴定,这一菌株为曲霉(Asper-gillus sp.)以LM02作为出发株,采用亚硝基胍、自然污染细菌、甲基磺酸乙酯及紫外线进行诱变处理,选育出葡萄糖为原料,L-苹果酸产率较高的突变抹N1-14、N1-14、NE1412、NU1416及NU1419。其中N1-14 的L-苹果酸产量最高,比出发株提高46．2×10^-2。N1-14 的菌丝生长速度快,产孢能力强,摇瓶发酵葡萄糖140小时,平均L-苹果酸产率为72．53g／L,对糖转化率53．74×10^-2。全发酵液经薄层层析测定,不含黄曲霉毒素。发酵产物分离提纯后,得到白色粉末状结晶,经纸层析、质谱及红外光谱测定,证明为L-苹果酸。     

尖孢镰孢一新硝酸盐营养突变类型与营养体亲和性

从73个尖孢镰孢(Fusarium oxysporum)不同专化型菌株上获得684个硝酸盐营养突变株(nit mutant)。作相关氮源利用试验及亚硝酸反应后,鉴定出一新硝酸盐营养突变类型:亚硝酸盐还原酶结构基因类型,命名为nit8,占总突变株的6.7%。同时被鉴别的还有nit1、nit3和Nit M三种突变类型,它们分别占突变株总数的81.0%,3.8%和8.5%。此外,首次引入一种亚硝酸反应在这类研究中的应用,还提出了互补指数概念与公式来表示nit突变株营养体之间亲和的能力。     

Inhibitory role of bone marrow mesenchymal stem cells-derived exosome in non-small-cell lung cancer: microRNA-30b-5p,EZH2 and PI3K/AKT pathway

Exosomal microRNA (miRNA) exerts potential roles in non-small-cell lung cancer (NSCLC). The current study elucidated the role of miR-30b-5p shuttled by bone marrow mesenchymal stem cells (BMSCs)-derived exosomes in treating NSCLC. Bioinformatics analysis was performed with NSCLC-related miRNA microarray GSE169587 and mRNA data GSE74706 obtained for collection of the differentially expressed miRNAs and mRNAs. The relationship between miR-30b-5p and EZH2 was predicted and confirmed. Exosomes were isolated from BMSCs and identified. BMSCs-derived exosomes overexpressing miR-30b-5p were used to establish subcutaneous tumorigenesis models to study the effects of miR-30b-5p, EZH2 and PI3K/AKT signalling pathway on tumour growth. A total of 86 BMSC-exo-miRNAs were differentially expressed in NSCLC. Bioinfomatics analysis found that BMSC-exo-miR-30b-5p could regulate NSCLC progression by targeting EZH2, which was verified by in vitro cell experiments. Besides, the target genes of miR-30b-5p were enriched in PI3K/AKT signalling pathway. Animal experiments validated that BMSC-exo-miR-30b-5p promoted NSCLC cell apoptosis and prevented tumorigenesis in nude mice via EZH2/PI3K/AKT axis. Collectively, the inhibitory role of BMSC-derived exosomes-loaded miR-30b-5p in NSCLC was achieved through blocking the EZH2/PI3K/AKT axis.     

靶向RNA的CRISPR-Cas系统研究进展

CRISPR(clustered regularly interspaced short palindromic repeats)-Cas(CRISPR associated proteins)系统是细菌和古细菌抵抗噬菌体、质粒等外源遗传物质的一种适应性免疫系统,该系统利用一种特殊的RNA(CRISPR RNA,crRNA)指导的内切酶来切割与crRNA相互补的外源遗传物质,从而阻碍外源核酸的侵染。根据效应复合物组成形式的不同,CRISPR-Cas系统分为1类(Ⅰ型、Ⅳ型和Ⅲ型)和2类(Ⅱ型、Ⅴ型和Ⅵ型)两大类。目前已发现多个CRISPR-Cas系统具有非常强的特异靶向RNA编辑能力,如Ⅵ型CRISPR-Cas13系统和Ⅲ型CRISPR-Cas7-11系统。随着研究的深入,相关系统在RNA编辑领域应用日渐广泛,使其成为基因编辑的有力工具。本文介绍了靶向RNA的CRISPR-Cas系统的组成、结构、分子机制以及其潜在应用,这为更好地研究该类系统的作用机制奠定基础,也为后期开发为稳定的基因编辑工具提供新的思路。     

大鼠肾髓质活体微循环及观察方法

采用肾乳头暴露方法活体观察Sprague-Dawley大鼠肾髓质微循环。结果发现:正常成年大鼠肾乳头可暴露1.1±0.5mm; 乳头表面直血管数29.8±6.3;升、降支比例3.4:1。升支平均直径13.68±6.13μm,降支10.8±2.57μm。肾乳头连续暴露观察10h,其微循环未发生明显病理性改变。说明这一方法可以用于肾髓质微循环活体研究。     

Multikink quantile regression for longitudinal data with application to progesterone data analysis

Motivated by investigating the relationship between progesterone and the days in a menstrual cycle in a longitudinal study, we propose a multikink quantile regression model for longitudinal data analysis. It relaxes the linearity condition and assumes different regression forms in different regions of the domain of the threshold covariate. In this paper, we first propose a multikink quantile regression for longitudinal data. Two estimation procedures are proposed to estimate the regression coefficients and the kink points locations: one is a computationally efficient profile estimator under the working independence framework while the other one considers the within-subject correlations by using the unbiased generalized estimation equation approach. The selection consistency of the number of kink points and the asymptotic normality of two proposed estimators are established. Second, we construct a rank score test based on partial subgradients for the existence of the kink effect in longitudinal studies. Both the null distribution and the local alternative distribution of the test statistic have been derived. Simulation studies show that the proposed methods have excellent finite sample performance. In the application to the longitudinal progesterone data, we identify two kink points in the progesterone curves over different quantiles and observe that the progesterone level remains stable before the day of ovulation, then increases quickly in 5 to 6 days after ovulation and then changes to stable again or drops slightly.     

催产时鳝卵磷酸酶活性的变化及其与排卵的关系

本实验采用Gomori组织化学法和磷酸苯二钠法,分别检测黄鳝卵ALP、ACP的细胞定位和活性变化。结果表明,催产后72h,ALP活性显著高于临近注射时(Oh),催产后48h和96h(p<0.05);临产前(催产后96h),ACP活性极显著高于试验组其它各时程(p<0.01)。提示ALP和ACP活性增强与卵母细胞成熟、排放有直接关系。本研究为探索排卵机制提供资料。