The first chromosome‐level genome for a marine mammal as a resource to study ecology and evolution

Marine mammals are important models for studying convergent evolution and aquatic adaption, and thus reference genomes of marine mammals can provide evolutionary insights. Here, we present the first chromosome‐level marine mammal genome assembly based on the data generated by the BGISEQ‐500 platform, for a stranded female sperm whale (Physeter macrocephalus). Using this reference genome, we performed chromosome evolution analysis of the sperm whale, including constructing ancestral chromosomes, identifying chromosome rearrangement events and comparing with cattle chromosomes, which provides a resource for exploring marine mammal adaptation and speciation. We detected a high proportion of long interspersed nuclear elements and expanded gene families, and contraction of major histocompatibility complex region genes which were specific to sperm whale. Using comparisons with sheep and cattle, we analysed positively selected genes to identify gene pathways that may be related to adaptation to the marine environment. Further, we identified possible convergent evolution in aquatic mammals by testing for positively selected genes across three orders of marine mammals. In addition, we used publicly available resequencing data to confirm a rapid decline in global population size in the Pliocene to Pleistocene transition. This study sheds light on the chromosome evolution and genetic mechanisms underpinning sperm whale adaptations, providing valuable resources for future comparative genomics.     

lncRNA MALAT1 mediated high glucose–induced HK-2 cell epithelial-to-mesenchymal transition and injury

Journal of Physiology and Biochemistry - Epithelial-to-mesenchymal transition (EMT) and injury of tubular cells play critical roles in the pathogenesis of diabetic nephropathy (DN). lncRNA...     

Overview and recommendations for regionalized life cycle impact assessment

The International Journal of Life Cycle Assessment - Regionalized life cycle impact assessment (LCIA) has rapidly developed in the past decade, though its widespread application, robustness, and...     

Soluble CXCL16 promotes TNF‐α‐induced apoptosis in DLBCL via the AMAD10‐NF‐κB regulatory feedback loop

We had previously identified that the co‐expression of transmembrane CXCL16 (TM‐CXCL16) and its receptor CXCR6 is an independent risk factor for poor survival in patients with diffuse large B‐cell lymphoma (DLBCL). However, the impact of the soluble form of CXCL16 (sCXCL16) on the pathogenesis of DLBCL remains unknown. In the present study, the synergistic effect of sCXCL16 and tumor necrosis factor α (TNF‐α) on apoptosis in DLBCL cell lines (OCI‐LY8 and OCI‐LY10) was investigated in vitro. sCXCL16 reinforced TNF‐α‐mediated inhibition of DLBCL cell proliferation, as determined by the cell counting kit‐8 assay. The results of annexin V staining showed that sCXCL16 enhanced TNF‐α‐induced apoptosis in OCI‐LY8 and OCI‐LY10 cells through a death receptor‐caspase signaling pathway. The results of gene microarray suggested a significant upregulation of differentially expressed genes in the TNF signaling pathway. sCXCL16 increased the concentration of extracellular TNF‐α by binding to CXCR6 to activate the nuclear factor‐κB (NF‐κB) signaling pathway. TNF‐α also induced the secretion of sCXCL16 by increasing the expression of ADAM10, which is known to cleave TM‐CXCL16 to yield sCXCL16. Moreover, bioinformatics analysis revealed that elevated TNF‐α and ADAM10 expression levels in tumor tissues predicted better survival in patients with DLBCL. Thus, our study suggests that sCXCL16 enhances TNF‐α‐induced apoptosis of DLBCL cells, which may involve a positive feedback loop consisting of TNF‐α, ADAM10, sCXCL16, and members of the NF‐κB pathway. sCXCL16 and TNF‐α may be used as prognostic markers in the clinic, and their combinational use is a promising approach in the context of DLBCL therapy.     

Surfactin and fengycin contribute to the protection of a Bacillus subtilis strain against grape downy mildew by both direct effect and defence stimulation

Bacillus subtilis GLB191 (hereafter GLB191) is an efficient biological control agent against the biotrophic oomycete Plasmopara viticola, the causal agent of grapevine downy mildew. In this study, we show that GLB191 supernatant is also highly active against downy mildew and that the activity results from both direct effect against the pathogen and stimulation of the plant defences (induction of defence gene expression and callose production). High-performance thin-layer chromatography analysis revealed the presence of the cyclic lipopeptides fengycin and surfactin in the supernatant. Mutants affected in the production of fengycin and/or surfactin were thus obtained and allowed us to show that both surfactin and fengycin contribute to the double activity of GLB191 supernatant against downy mildew. Altogether, this study suggests that GLB191 supernatant could be used as a new biocontrol product against grapevine downy mildew.     

我国稻田氮磷流失现状及影响因素研究进展

水稻是我国主要的粮食作物,分析现阶段我国稻田氮磷流失现状及影响因素,对明确不同区域水稻化肥减施潜力具有重要意义.本研究对我国主要稻区地表径流氮磷流失现状特征和降雨、种植模式、栽培技术、施肥管理、水分管理方式及其他影响因素进行了总结.六大稻区全氮(TN)、全磷(TP)径流损失量范围分别在5.09～21.32和0.70～3.22 kg·hm^-2,均以华南双季稻区最高,TN径流损失量以华北单季稻区最低,TP径流损失量以西南高原单双季稻区最低.各稻区农户习惯施肥的水稻田田面水TN、TP峰值普遍高于径流水.水稻施肥后一周内为氮磷流失高峰期.与优化施肥相比,农户习惯施肥仍具有20%左右的氮磷减施潜力.各因素中,降雨和施肥管理是影响稻田径流氮磷流失的主要因素,而施肥管理和水分管理则最具可控性,具体调控措施包括化肥减量、施用新型肥料、有机肥代替化肥和节水灌溉等.整体上我国稻田氮磷流失风险在南方更突出.应以资源高效利用模式进行水稻种植以降低养分流失风险.未来研究应侧重稻田面源污染监测、氮磷流失风险评估、氮磷流失特征和机理、化肥减施增效新技术等方向.     

长白山温带森林不同演替阶段群落功能性状的空间变化

群落构建机制研究是生态学研究的热点。长白山自然保护区拥有完整的原始阔叶红松林生态系统, 近年来随着物种多样性丧失愈发严重, 对该地区开展群落构建机制研究显得尤为重要。该研究以长白山不同演替阶段的3块5.2 hm ²固定监测样地(次生杨桦林、次生针阔混交林、原始椴树红松林)为研究对象, 通过采集样地内主要树种的6个关键功能性状(叶面积、比叶面积、叶片厚度、叶氮含量、叶磷含量、最大树高), 分析不同空间尺度下(5 m × 5 m, 10 m × 10 m, 20 m × 20 m, 30 m × 30 m, 40 m × 40 m, 50 m × 50 m和60 m × 60 m)及不同演替阶段群落性状空间值的变化, 结合零模型的模拟结果对长白山温带森林演替过程中的群落构建机制进行讨论。结果表明: 种库大小对于研究结果具有重要影响。在较大的种库下, 环境过滤作用影响显著。而在样地水平进行研究时, 演替早期和中期, 群落性状空间值与零模型模拟值无显著差异, 在演替的晚期, 群落性状空间值显著高于零模型模拟值。结合多个群落功能多样性指数分析发现, 环境过滤和竞争作用共同决定该地区顶级群落的物种组成。在演替早期大量物种迁入, 群落内物种间存在强烈的资源竞争, 而随着演替进行, 部分物种逐渐被竞争排除出群落, 群落中的物种呈现明显的生态位分化, 竞争作用是维持物种共存的主要机制。     

未折叠蛋白质的普遍初始热力学亚稳态

探索和理解蛋白质折叠问题一直是分子生物学、结构生物学和生物物理学的终极挑战.未折叠的蛋白质应该存在一种普遍初始热力学亚稳态,否则无法解释蛋白质是如何在剧烈的热振动干扰下完成快速精确折叠的.本文通过分析水溶液环境和蛋白质折叠的相关性,揭示了一种由水分子屏蔽效应引起的未折叠蛋白质的普遍初始热力学亚稳态,该亚稳态的存在是水溶液环境中水分子的物理性质决定,并赋予未折叠蛋白质抵抗热扰动和避免错误折叠的能力.我们通过研究已发表的实验数据和建立分子模型,找到了该初始热力学亚稳态存在的相关证据,并推测了该亚稳态导致蛋白质精确折叠的相关物理学机制.     

白菜PLD基因家族全基因组鉴定及对高温胁迫的响应

膜磷脂是产生胞内信号信使的重要来源,磷脂酶Ds(phospholipase D,PLDs)可以催化磷脂产生信号分子磷脂酸(phosphatidic acid, PA),从而响应不同胁迫信号。该研究利用生物信息学方法对白菜PLD基因家族的基因成员进行鉴定及结构域分析,并采用qRT PCR方法对不结球白菜的18个BrPLD基因的表达进行分析,以探讨不结球白菜的BrPLD基因家族对高温胁迫的响应机制。结果表明：(1)共鉴定到18个白菜PLD基因家族成员,其中有2个成员(BrPLD03和BrPLD09)的C2结构域被替换为PH/PX结构域,另有1个基因(BrPLD12)缺少了其N末端保守结构域,由信号肽代替。(2)根据编码蛋白结构域的不同,18个BrPLD基因分为3个亚类,分别为15个C2 BrPLD、2个PH/PX BrPLD和1个SP BrPLD;氨基酸理化性质分析发现,该基因家族编码蛋白多半为酸性蛋白;18个基因分布在除4号和7号之外的8条染色体,且呈现不均匀分布,并发现了BrPLDs蛋白Ca²⁺配位碱基的缺失。(3)qRT PCR检测发现,高温处理下不结球白菜的BrPLD基因的表达量发生明显变化,各基因在耐热和热敏品种中的表达具有差异。(4)对BrPLD基因家族不同功能顺式响应元件的预测发现,所有家族基因含有光应答有关的作用元件,9个基因含有与低温有关的顺式元件,10个基因含有调控干旱相关元件,18个基因均未预测到热胁迫相关顺式响应元件。