黄唇鱼(Bahaba flavolabiata)的全基因组测序和基因组特征研究

黄唇鱼(Bahaba flavolabiata)为国家二级重点保护野生动物、IUCN(世界自然保护联盟)红色名录的极度濒危物种(CR)。基于其样本数量极其有限,全基因组研究可以提供大量与重要性状相关的功能基因和分子标记,从而揭示其重要生命现象的遗传机制。采用二代测序技术于2018年5月完成了黄唇鱼基因组精细图的测序,分析结果表明,测序得到约202 Gb的高质量数据,总测序深度约为317×;组装得到的基因组大小为637.43 Mb,Contig N50约为88 Kb,Scaffold N50约为4.65 Mb;重复序列约142.72 Mb,占比22.39%,预测得到23743个基因、920个t RNA、85个rRNA、176个假基因;98.46%的基因可以注释到NR、GO等数据库中;有67个基因家族是黄唇鱼所特有的。本研究从单碱基错误率、核心基因完整性及二代Reads比对分析3个方面对黄唇鱼基因组精细图的组装结果进行了评估,结果显示所组装的基因区的完整性较好。黄唇鱼基因组序列图谱的绘制完成,对于黄唇鱼自然资源的保护和种质资源挖掘具有极其重要的科学意义。     

Quorum sensing regulation confronts the development of a viable but non-culturable state in Vibrio cholerae

Vibrio cholerae can enter a viable but non-culturable (VBNC) state when it encounters unfavourable environments; VBNC cells serve as important reservoirs and still pose threats to public health. The genetic regulation of V. cholerae entering its VBNC state is not well understood. Here, we show a confrontation strategy adapted by V. cholerae O1 in which it utilizes a quorum sensing (QS) system to prevent transition into a VBNC state under low nutrition and temperature conditions. The upregulation of hapR resulted in a prolonged culturable state of V. cholerae in artificial sea water at 4°C, whereas the mutation of hapR led to fast entry into the VBNC state. We also observed that different V. cholerae O1 natural isolates with distinct QS functions present a variety of abilities to maintain culturability during the transition to a VBNC state. The strain groups with higher or constitutive expression of QS genes exhibit a greater tendency to maintain the culturable state during VBNC induction than those lacking QS functional groups. In summary, HapR-mediated QS regulation is associated with the transition to the VBNC state in V. cholerae. HapR expression causes V. cholerae to resist VBNC induction and become dominant over competitors in changing environments.     

Combined use of dbcAMP and IBMX minimizes the damage induced by a long‐term artificial meiotic arrest in mouse germinal vesicle oocytes

Phosphodiesterase (PDE)‐mediated reduction of cyclic adenosine monophosphate (cAMP) activity can initiate germinal vesicle (GV) breakdown in mammalian oocytes. It is crucial to maintain oocytes at the GV stage for a long period to analyze meiotic resumption in vitro. Meiotic resumption can be reversibly inhibited in isolated oocytes by cAMP modulator forskolin, cAMP analog dibutyryl cAMP (dbcAMP), or PDE inhibitors, milrinone (Mil), Cilostazol (CLZ), and 3‐isobutyl‐1‐methylxanthine (IBMX). However, these chemicals negatively affect oocyte development and maturation when used independently. Here, we used ICR mice to develop a model that could maintain GV‐stage arrest with minimal toxic effects on subsequent oocyte and embryonic development. We identified optimal concentrations of forskolin, dbcAMP, Mil, CLZ, IBMX, and their combinations for inhibiting oocyte meiotic resumption. Adverse effects were assessed according to subsequent development potential, including meiotic resumption after washout, first polar body extrusion, early apoptosis, double‐strand DNA breaks, mitochondrial distribution, adenosine triphosphate levels, and embryonic development. Incubation with a combination of 50.0 μM dbcAMP and 10.0 μM IBMX efficiently inhibited meiotic resumption in GV‐stage oocytes, with low toxicity on subsequent oocyte maturation and embryonic development. This work proposes a novel method with reduced toxicity to effectively arrest and maintain mouse oocytes at the GV stage.     

Changes in soil properties and resistance to concentrated flow across a 25‐year passive restoration chronosequence of grasslands on the Chinese Loess Plateau

Revegetation represents an effective measure for preventing soil erosion on the Loess Plateau. However, the effects of revegetation‐induced changes in soil and root properties on soil resistance to concentrated flow erosion (SRC) remain unclear. This study sampled soils and roots across a 25‐year chronosequence from farmland to grasslands of different ages (3, 7, 10, 18, and 25 years) to quantify variations in soil and root properties (soil bulk density, SBD; soil disintegration rate, SDR; saturated hydraulic conductivity, SHC; organic matter content, OMC; water‐stable aggregate, WSA; mean weight diameter, MWD; root mass density, RMD; root length density, RLD; and root surface area density, RSAD) and their effects on SRC. Farmland and grassland SRCs were obtained using a hydraulic flume. Soil properties and root density gradually improved with restoration time. In terms of the comprehensive soil property index calculated via principal component analysis, grassland values were 0.66 to 1.94 times greater than farmland values. Grassland SRCs increased and gradually stabilized (>18 years) over time and were 1.60 to 8.26 times greater than farmland SRC. SRC improvement was significantly related to increases in OMC, SHC, WSA, and MWD and decreases in SBD and SDR over time. SRC was effectively simulated by the Hill curve of RMD, RLD, and RSAD. SDR, SHC, and RMD (0.5–1.0 mm) affected SRC the most. This study scientifically describes how revegetation improves soil quality and soil resistance to flow erosion, and suggests that vegetations rich in 0.5–1.0 mm roots should be preferred during revegetation.     

Platelet‐rich plasma inhibits osteoblast apoptosis and actin cytoskeleton disruption induced by gingipains through upregulating integrin β1

The aim of this study was to explore the effects of platelet‐rich plasma on gingipain‐caused changes in cell morphology and apoptosis of osteoblasts. Mouse osteoblasts MC3T3‐E1 cells were treated with gingipain extracts from Porphyromonas gingivalis in the presence or absence of platelet‐rich plasma. Apoptosis was detected with terminal deoxynucleotidyl transferase‐mediated dUTP nick‐end labeling staining. F‐actin was determined by phalloidin‐fluorescent staining and observed under confocal microscopy. Western blot analysis was used to detect integrin β1, F‐actin, and G‐actin protein expressions. A knocking down approach was used to determine the role of integrin β1. The platelet‐rich plasma protected osteoblasts from gingipain‐induced apoptosis in a dose‐dependent manner, accompanied by upregulation of integrin β1. Platelet‐rich plasma reversed the loss of F‐actin integrity and decrease of F‐actin/G‐actin ratio in osteoblasts in the presence of gingipains. By contrast, the effects of platelet‐rich plasma were abrogated by knockdown of integrin β1. The platelet‐rich plasma failed to reduce cell apoptosis and reorganize the cytoskeleton after knockdown of integrin β1. In conclusion, platelet‐rich plasma inhibits gingipain‐induced osteoblast apoptosis and actin cytoskeleton disruption by upregulating integrin β1 expression.     

Warming counteracts defoliation‐induced mismatch by increasing herbivore‐plant phenological synchrony

Climate change is altering phenology; however, the magnitude of this change varies among taxa. Compared with phenological mismatch between plants and herbivores, synchronization due to climate has been less explored, despite its potential implications for trophic interactions. The earlier budburst induced by defoliation is a phenological strategy for plants against herbivores. Here, we tested whether warming can counteract defoliation‐induced mismatch by increasing herbivore‐plant phenological synchrony. We compared the larval phenology of spruce budworm and budburst in balsam fir, black spruce, and white spruce saplings subjected to defoliation in a controlled environment at temperatures of 12, 17, and 22°C. Budburst in defoliated saplings occurred 6–24 days earlier than in the controls, thus mismatching needle development from larval feeding. This mismatch decreased to only 3–7 days, however, when temperatures warmed by 5 and 10°C, leading to a resynchronization of the host with spruce budworm larvae. The increasing synchrony under warming counteracts the defoliation‐induced mismatch, disrupting trophic interactions and energy flow between forest ecosystem and insect populations. Our results suggest that the predicted warming may improve food quality and provide better growth conditions for larval development, thus promoting longer or more intense insect outbreaks in the future.     

Overexpression of the persimmon abscisic acid β‐glucosidase gene (DkBG1) alters fruit ripening in transgenic tomato

β‐Glucosidases (BG) are present in many plant tissues. Among these, abscisic acid (ABA) β‐glucosidases are thought to take part in the adjustment of cellular ABA levels, however the role of ABA‐BG in fruits is still unclear. In this study, through RNA‐seq analysis of persimmon fruit, 10 full‐length DkBG genes were isolated and were all found to be expressed. In particular, DkBG1 was highly expressed in persimmon fruits with a maximum expression 95 days after full bloom (DAFD). We verified that, in vitro, DkBG1 protein can hydrolyze ABA‐glucose ester (ABA‐GE) to release free ABA. Compared with wild‐type, tomato plants that overexpressed DkBG1 significantly upregulated the expression of ABA receptor PYL3/7 genes and showed typical symptoms of ABA hypersensitivity in fruits. DkBG1 overexpression (DkBG1‐OE) accelerated fruit ripening onset by 3–4 days by increasing ABA levels at the pre‐breaker stage and induced early ethylene release compared with wild‐type fruits. DkBG1‐OE altered the expression of ripening regulator NON‐RIPENING (NOR) and its target genes; this in turn altered fruit quality traits such as coloration. Our results demonstrated that DkBG1 plays an important role in fruit ripening and quality by adjusting ABA levels via hydrolysis of ABA‐GE.