A secreted ribonuclease effector from Verticillium dahliae localizes in the plant nucleus to modulate host immunity

The arms race between fungal pathogens and plant hosts involves recognition of fungal effectors to induce host immunity. Although various fungal effectors have been identified, the effector functions of ribonucleases are largely unknown. Herein, we identified a ribonuclease secreted by Verticillium dahliae (VdRTX1) that translocates into the plant nucleus to modulate immunity. The activity of VdRTX1 causes hypersensitive response (HR)‐related cell death in Nicotiana benthamiana and cotton. VdRTX1 possesses a signal peptide but is unlikely to be an apoplastic effector because its nuclear localization in the plant is necessary for cell death induction. Knockout of VdRTX1 significantly enhanced V. dahliae virulence on tobacco while V. dahliae employs the known suppressor VdCBM1 to escape the immunity induced by VdRTX1. VdRTX1 homologs are widely distributed in fungi but transient expression of 24 homologs from other fungi did not yield cell death induction, suggesting that this function is specific to the VdRTX1 in V. dahliae. Expression of site‐directed mutants of VdRTX1 in N. benthamiana leaves revealed conserved ligand‐binding sites that are important for VdRTX1 function in inducing cell death. Thus, VdRTX1 functions as a unique HR‐inducing effector in V. dahliae that contributes to the activation of plant immunity.     

南京农业大学微生物学虚拟仿真实验教学模式的探索

借助虚拟仿真技术构建的虚实结合的虚拟仿真实验,是提高学生实践动手能力的有力补充和有效途径。本文通过对微生物学实验教学现状的分析,探讨南京农业大学微生物学虚拟仿真实验教学模式建设的意义,重点阐述建设思路、建设方案及教学特点。该仿真实验教学体系主要从基础微生物学和应用微生物学两大模块进行构建,同时将本校的污水生物处理技术、食用菌资源调查与利用等科研成果转化为教学资源,以丰富实验教学内容。     

广竹的生物学特性及栽培技术研究

对广竹的生物学特性及栽培技术研究结果表明:广竹的出笋历期较短且非常集中,出笋高峰期集中在4月上旬,出笋数量占全期出笋总数的62.7%;幼竹高生长及枝条生长曲线均呈"S"形,遵循慢—快—慢的节律;此竹种属于混生竹,可移竹繁殖和埋鞭繁殖,前一方法的繁殖效果较好,成活率可达60%,而埋鞭繁殖效果相对较差,成活率只有38%,最佳繁殖时间宜在12月下旬至次年2月进行;根据其各生长阶段的生长规律、无性繁殖栽培技术以及生产实践,提出了主要栽培技术措施。     

中国近海细鳞鯻线粒体控制区的遗传多样性

通过线粒体控制区序列的分析,研究采自中国南海及东海5个群体102尾细鳞鯻的遗传多样性。发现在962 bp序列中有205个变异位点,其中135个为简约信息位点,共定义102个单倍型。中国近海细鳞鯻总体呈现出较高的遗传多样性特征(Hd=1.000,Pi=0.022),其中博鳌最高(Hd=1.000,Pi=0.028),平潭最低(Hd=1.000,Pi=0.014)。不同地理群体间无明显分化,基因交流频繁(Fst=-0.014—0.041,P0.05);中性检验均为显著负值,推测在16.9万年—5.06万年前,即中-晚更新世出现种群扩张。系统邻接树和单倍型网络图均出现3个显著分化的谱系(谱系间Fst=0.508—0.698,P0.001;净遗传距离Da=0.024—0.031),且各谱系中均有不同地理来源的群体。3个谱系间分歧时间大约在1.07百万年—0.24百万年前,推测可能是更新世冰期边缘海的出现导致群体隔离而产生分化。谱系A(Lineage A)包含85.3%的个体,其总体遗传多样性较高(Hd=1.000,Pi=0.012),其中平潭最高(Hd=1.000,Pi=0.014),合浦最低(Hd=1.000,Pi=0.010);群体间Fst在-0.021—0.068之间,P0.005;AMOVA分析显示只有1.97%的变异来自于种群间,表明群体间也无明显分化;中性检验均为显著负值,推测在25.4万年—7.6万年前出现种群扩张。中国近海细鳞鯻主要受到中-晚更新世海侵和海退的影响而出现种群扩张使得谱系间发生二次接触,最终形成具有显著谱系结构但无地理分化的情况。     

Using all Gene Families Vastly Expands Data Available for Phylogenomic Inference

Traditionally, single-copy orthologs have been the gold standard in phylogenomics. Most phylogenomic studies identify putative single-copy orthologs using clustering approaches and retain families with a single sequence per species. This limits the amount of data available by excluding larger families. Recent advances have suggested several ways to include data from larger families. For instance, tree-based decomposition methods facilitate the extraction of orthologs from large families. Additionally, several methods for species tree inference are robust to the inclusion of paralogs and could use all of the data from larger families. Here, we explore the effects of using all families for phylogenetic inference by examining relationships among 26 primate species in detail and by analyzing five additional data sets. We compare single-copy families, orthologs extracted using tree-based decomposition approaches, and all families with all data. We explore several species tree inference methods, finding that identical trees are returned across nearly all subsets of the data and methods for primates. The relationships among Platyrrhini remain contentious; however, the species tree inference method matters more than the subset of data used. Using data from larger gene families drastically increases the number of genes available and leads to consistent estimates of branch lengths, nodal certainty and concordance, and inferences of introgression in primates. For the other data sets, topological inferences are consistent whether single-copy families or orthologs extracted using decomposition approaches are analyzed. Using larger gene families is a promising approach to include more data in phylogenomics without sacrificing accuracy, at least when high-quality genomes are available.     

Protoplast fusion in Bacillus species produces frequent,unbiased, genome-wide homologous recombination

In eukaryotes, fine-scale maps of meiotic recombination events have greatly advanced our understanding of the factors that affect genomic variation patterns and evolution of traits. However, in bacteria that lack natural systems for sexual reproduction, unbiased characterization of recombination landscapes has remained challenging due to variable rates of genetic exchange and influence of natural selection. Here, to overcome these limitations and to gain a genome-wide view on recombination, we crossed Bacillus strains with different genetic distances using protoplast fusion. The offspring displayed complex inheritance patterns with one of the parents consistently contributing the major part of the chromosome backbone and multiple unselected fragments originating from the second parent. Our results demonstrate that this bias was in part due to the action of restriction–modification systems, whereas genome features like GC content and local nucleotide identity did not affect distribution of recombination events around the chromosome. Furthermore, we found that recombination occurred uniformly across the genome without concentration into hotspots. Notably, our results show that species-level genetic distance did not affect genome-wide recombination. This study provides a new insight into the dynamics of recombination in bacteria and a platform for studying recombination patterns in diverse bacterial species.     

连续两个生长季大气CO2浓度升高对银杏希尔反应活力和叶绿体ATP酶活性的影响

近年来,随着温室气体浓度不断上升,有关CO2浓度升高对植物影响的研究已取得一定进展,但CO2浓度升高对植物光合作用的影响需要从生理生化水平上进一步深入的研究.以沈阳城市森林树种银杏(Ginkgo biloba L.)为研究对象,利用开顶式气室研究连续两个生长季大气CO2浓度升高对银杏光合特性的影响.结果表明,在大气CO2浓度为700μmol·mol-1条件下,与对照相比,第1个生长季CO2处理的银杏叶片净光合速率极显著增加(P<0.01),希尔反应活力极显著增大(P<0.01)、Ca2+/Mg2+-ATP酶活性显著(P<0.05)或极显著增强(P<0.01)、光合产物淀粉的含量极显著增多(P<0.01);第2生长季CO2处理的银杏叶片净光合速率显著增加(P<0.05),希尔反应活力在通气60d时极显著(P<0.01)增大,Ca2+/Mg2+-ATP酶活性在处理30d时显著降低(P<0.05),淀粉含量增多.与第1个生长季相比,第2个生长季CO2处理的银杏叶片净光合速率降低,希尔反应活力减小,Ca2+/Mg2+-ATP酶活性减弱,叶绿素含量增多,淀粉含量减少.试验中出现了光合适应现象.     

荒漠植物梭梭稳定碳同位素组成与环境因子的关系

以广泛分布于新疆荒漠地区的建群种植物——梭梭(Haloxylon ammodendron)为研究对象,通过对23个样地101份梭梭同化枝样品δ~(13)C值的测定,分析了梭梭稳定碳同位素组成的变化特征及其与环境因子(海拔、日照时数、潜在蒸散量、年平均降水量和年平均温度)的关系,并讨论了不同生境下梭梭同化枝δ~(13)C值的变化特征。研究结果显示:(1)梭梭同化枝δ~(13)C平均值为-14.15‰,其在95%置信区间的变化范围为-13.14‰—-15.38‰,表明梭梭是C_4光合途径的植物。(2)梭梭同化枝δ~(13)C值与年平均降水量和年平均温度呈显著负相关关系,而与日照时数、潜在蒸散量和海拔呈显著正相关关系。我们推测梭梭同化枝δ~(13)C值对各环境因子响应趋势的不同,可能是由气孔限制因素造成的,它是梭梭适应干旱荒漠环境的一种策略。(3)在不同生境下,梭梭同化枝的碳同位素组成存在显著差异。当梭梭群落中的主要伴生种为白刺、红砂时,其δ~(13)C值最高,当主要伴生种为沙拐枣和假木贼时,其δ~(13)C值最低。在灰漠土与灰棕漠土样地中的梭梭δ~(13)C值高于棕钙土、风沙土、石质土样地;盆地中梭梭同化枝δ~(13)C值低于平原、山地、丘陵地形条件下的样地。以上结果表明:梭梭水分利用效率在不同环境梯度和生境中,存在着显著不同,表现出显著的适应策略差异。     

Hemin with Peroxidase Activity Can Inhibit the Oxidative Damage Induced by Ultraviolet A

Excessive reactive oxygen species (ROS), a highly reactive substance that contains oxygen, induced by ultraviolet A (UVA) cause oxidative damage to skin. We confirmed that hemin can catalyze the reaction of tyrosine (Tyr) and hydrogen peroxide (H₂O₂). Catalysis was found to effectively reduce or eliminate oxidative damage to cells induced by H₂O₂ or UVA. The scavenging effects of hemin for other free-radical ROS were also evaluated through pyrogallol autoxidation, 1,1-diphenyl-2-picrylhydrazyl radical (DPPH·)-scavenging assays, and phenanthroline–Fe²⁺ assays. The results show that a mixture of hemin and tyrosine exhibits strong scavenging activities for H₂O₂, superoxide anion (O₂⁻·), DPPH·, and the hydroxyl radical (·OH). Furthermore, the inhibition of oxidative damage to human skin keratinocyte (HaCaT) cells induced by H₂O₂ or UVA was evaluated. The results show that catalysis can significantly reduce the ratio of cell apoptosis and death and inhibit the release of lactate dehydrogenase (LDH), as well as accumulation of malondialdehyde (MDA). Furthermore, the resistance to apoptosis was found to be enhanced. These results show that the mixture of hemin and tyrosine has a significantly protective effect against oxidative damage to HaCaT cells caused by UVA, suggesting it as a protective agent for combating UVA damage.     

干旱胁迫对银杏叶片光合系统Ⅱ荧光特性的影响

为了探讨银杏叶片在长期干旱胁迫下光合性能的变化,采用盆栽控水法对银杏幼苗进行干旱处理,并分别在处理后第0、20、30、40、50天,对荧光动力学曲线和荧光参数进行了测定和JIP-test分析.结果表明:随着干旱的加剧,叶片叶绿素含量逐渐递减.由于干旱导致银杏叶片的光合系统Ⅱ(PSⅡ)结构破坏和稳固性减弱,其荧光动力学曲线出现了K相和L相的升高,在干旱处理40 d后升高加剧.PSⅡ结构的变化导致了一系列荧光参数的变化,初始荧光F0逐渐升高,最大荧光Fm逐渐降低;代表单位反应中心活性的参数ABS/RC、ET0/RC、TR0/RC逐渐升高;单位面积捕获的光能TR0/CS0高于对照,单位面积用于电子传递的光能ET0/ CS0后期下降;表示受体侧电子传递活性的参数Sm、Ψ0、(φ)E0逐渐下降,M0、VJ、VI逐渐升高;表示热耗散的参数DI0/RC、DI0/CS0随干旱时间延长而急剧升高;活性反应中心数目RC/CS0减少;代表PSⅡ光合效率的参数Fv/Fm、PIabs逐渐下降;代表PSⅡ供体侧活性的参数Wk随干旱时间延长而逐渐升高,OEC逐渐减少.干旱胁迫导致银杏叶片PSⅡ反应中心失活,能流分配失衡,电子传递受阻,PSⅡ放氧复合体失活和PSⅡ稳固性减弱,从而破坏PSⅡ光合功能.而反应中心失活和受体侧电子QA-的累积是造成PSⅡ电子传递活性减弱的主要原因.干旱条件下,银杏PSⅡ的PIabs比Fv/Fm对干旱的反应更灵敏,可作为银杏叶片受到伤害的指标.