Two-year surveillance of tilapia lake virus (TiLV) reveals its wide circulation in tilapia farms and hatcheries from multiple districts of Bangladesh

Tilapia lake virus (TiLV) is an emerging pathogen in aquaculture, reportedly affecting farmed tilapia in 16 countries across multiple continents. Following an early warning in 2017 that TiLV might be widespread, we executed a surveillance programme on tilapia grow-out farms and hatcheries from 10 districts of Bangladesh in 2017 and 2019. Among farms experiencing unusual mortality, eight out of 11 farms tested positive for TiLV in 2017, and two out of seven tested positive in 2019. Investigation of asymptomatic broodstock collected from 16 tilapia hatcheries revealed that six hatcheries tested positive for TiLV. Representative samples subjected to histopathology confirmed pathognomonic lesions of syncytial hepatitis. We recovered three complete genomes of TiLV from infected fish, one from 2017 and two from 2019. Phylogenetic analyses based on both the concatenated coding sequences of 10 segments and only segment 1 consistently revealed that Bangladeshi TiLV isolates formed a unique cluster within Thai clade, suggesting a close genetic relation. In summary, this study revealed the circulation of TiLV in 10 farms and six hatcheries located in eight districts of Bangladesh. We recommend continuing TiLV-targeted surveillance efforts to identify contaminated sources to minimize the countrywide spread and severity of TiLV infection.     

Effects of different active constituents of Gynostemma pentaphyllum on mitochondrial energy metabolism-related proteins in endothelial cells induced by ox-LDL

AIM To investigate the effects of different components of Gynostemma pentaphyllum ［gypenosides (Gps), gypenoside XLIX (GpXLIX) and ginsenoside Rb3 (GRb3)］ on mitochondrial energy metabolism-related proteins in endothelial cells induced by oxidized low-density lipoprotein (ox-LDL). METHODS EA.hy926 cells were divided into control group, model group, Gps group, GpXLIX group and GRb3 group. The cells in control group were cultured only in DMEM complete medium. The cells in model group were treated with 100 mg/L ox-LDL for 48 h. The cells in Gps group, GpXLIX group and GRb3 group were treated with 100 mg/L ox-LDL for 24 h, and then treated with Gps, GpXLIX and GRb3 at 100 mg/L for another 24 h, respectively. The ATP content in each group was detected by ELISA. The expression levels of mitochondrial energy metabolism-related proteins, cytochrome C oxidase subunit 5a （Cox5a）, NADH:ubiquinone oxidoreductase core subunit S1 （Ndufs1）, ATP synthase F1 subunit alpha (ATP5a) and cytochrome C (Cyt C）, were determined by Wes automatic Western blot quantitative analysis system and Western blot. RESULTS Compared with control group, the ATP content in model group was decreased (P<0.01). After drug intervention, the ATP content increased to different degrees in Gps group, GpXLIX group and GRb3 group (P<0.01). The results of Wes automatic Western blot quantitative analysis system were consistent with those of Western blot. These results showed that compared with control group, the protein expression of Cox5a, Ndufs1 and ATP5a in model group was decreased, and the protein expression of Cyt C was increased (P<0.01). After intervention, the protein expression of Cox5a, Ndufs1 and ATP5a was increased and the protein expression of Cyt C was decreased in Gps group, GpXLIX group and GRb3 group (P<0.05 or P<0.01). Among them, the effect of Gps on the protein expression of Cox5a, Ndufs1 and Cyt C was significantly stronger than those of the 2 monomer components, and the effect of GRb3 was found to be superior in the 2 monomer components. The effect of GpXLIX on ATP5a protein was superior to the other 2 components. CONCLUSION Gynostemma total saponins and related active ingredients protect ox-LDL-induced endothelial cells by affecting mitochondrial energy metabolism-related proteins, thereby preventing and treating atherosclerosis.     

Autophagy induces mitochondrial dysfunction in neurons from neonatal rats with hypoxic ischemic encephalopathy

AIM: To explore the influence of autophagy on the induction of mitochondrial dysfunction in the neurons in a neonatal rat hypoxic ischemic encephalopathy (HIE) model. METHODS: Ten-day-old rat pups (n=30) were randomly divided into sham group and model group. The rats in the latter group were subject to hypoxia-ischemia treatment via unilateral common carotid artery ligation. The rats were sacrificed for brain pathological examination, and the protein levels of cleaved caspase-3 and LC3B-II were detected by immunohistochemical analysis. For the in vitro experiments, the autophagy of primarily cultured rat neurons was observed after hypoxia, and Western blot and mitochondrial function testing were also performed. RESULTS: Compare with sham group, the hypoxia-ischemia treatment caused atrophy and apoptosis of neurons, and ventricular area enlargement of rat brains. Immunohistochemical results demonstrated significantly higher levels of apoptosis- and autophagy-associated proteins, such as cleaved caspase-3 and LC3B-II (P<0.01). In vitro experiments demonstrated that hypoxia induced autophagy and apoptosis in the neurons. Compared with sham group, there were higher levels of reactive oxygen species and mitochondrial superoxide, and lower mitochondrial membrane potential in the model group (P<0.01). CONCLUSION: In neonatal HIE rat model, the hypoxia-induced mitochondrial dysfunction is related to apoptosis and autophagy. It will provide a new idea for administration of autopahgy inducer agents in treatment of HIE.     

Importance of mitochondrial calcium uniporter in high glucose-induced cardiac myocyte apoptosis

AIM: To investigate the role of mitochondrial calcium uniporter (MCU) in high glucose(HG)-induced apoptosis of cardiac myocytes. METHODS: Cardiac myocytes were exposed to normal glucose (5.5 mmol/L glucose+ 19.5 mmol/L mannitol), HG (25 mmol/L glucose), or HG combined with 5 μmol/L spermine for 72 h. Mitochondrial free Ca²⁺ concentration ([Ca²⁺]_m), MCU at mRNA and protein levels, pyruvate dehydrogenase (PDH) activity, mitochondrial membrane potential (Δψ_m), the levels of ATP and reactive oxygen species (ROS), and apoptosis were determined. RESULTS: The [Ca²⁺]_m, the mRNA and protein levels of MCU, PDH activity, ATP levels, and Δψ_m were reduced (P<0.05), while ROS content and the protein levels of caspase-9 and caspase-3 were increased in HG group (P<0.05). Adding 5 μmol/L spermine returned these parameters toward control levels (P<0.05). Moreover, apoptosis was reduced by adding spermine and HG treatment (P<0.05). CONCLUSION: HG-induced cardiac myocyte apoptosis may be associated with the decreased MCU expression and activity, abnormal mitochondrial Ca²⁺ handling, deviant mitochon-drial respiratory chain, and mitochondrial dysfunction.     

大花君子兰叶绿体基因组及其特征

采用Illumina MiSeq测序平台对大花君子兰（Clivia miniata）叶片总DNA进行测序，通过组装获得了其叶绿体基因组（cpDNA）全长序列（158 114 bp）。对其cpDNA注释得到135个基因，包含87个蛋白编码基因、40个tRNA基因和8个rRNA基因。采用生物信息学方法对获得的cpDNA进行简单序列重复（SSR）分析和密码子偏好性分析。结果显示：①大花君子兰cpDNA中共有61个SSR位点，其中单核苷酸、二核苷酸、三核苷酸、四核苷酸、五核苷酸和六核苷酸重复数分别为38、9、2、8、3和1个，多数SSR分布在基因间隔区；②大花君子兰cpDNA密码子偏爱以A或U（T）结尾，亮氨酸使用频率最高，半胱氨酸使用频率最低。基于24种植物的cpDNA全长和23种植物的叶绿体ycf2基因序列进行系统发育分析，结果显示大花君子兰与石蒜科植物在同一分支，显示最近的亲缘关系，支持大花君子兰属于石蒜科。基于叶绿体ycf2的系统发育分析结果与基于cpDNA全长的系统发育分析研究结果大部分相同，支持ycf2基因可以代替cpDNA全长用于植物系统发育分析。     

胡葱黄条病毒吉林毛葱分离物全基因组序列测定与分析

使用RT-PCR方法从吉林省疑似感染胡葱黄条病毒(Shallot yellow stripe virus,SYSV)的分蘖洋葱(毛葱)叶片中获得了SYSV吉林毛葱分离物SYSV-JL(MN607702)的全基因组序列。SYSV-JL的全长序列为10?427 nt,与GenBank已登录的3条SYSV全长或近全长序列在多个基因上保持着较高的序列一致性,但在P1基因上核苷酸和氨基酸序列一致性较低,分别为69.5%～84.2%和60.9%～76.9%,进一步通过变异分析发现,P1基因包含369个变异位点,表现出较为明显的高变异特征。系统发育分析显示,不同SYSV分离物具有较为明显的地区差异,SYSV-JL分离物与多个中国分离物系统发育关系较近。     

棉铃虫膨胀线粒体基因组的鉴定与分析

以已公布的棉铃虫线粒体DNA序列对来自4头棉铃虫雄蛹的DNA的三代测序数据进行筛选,获得了11条与线粒体DNA有同源性的三代read序列,并根据其中的read 66003鉴定出了一种膨胀的线粒体基因组。该线粒体基因组大小为27 113 bp,其保守区域包含13个蛋白编码基因、2个rRNA基因、22个tRNA基因以及1个AT富集区,与已公布的棉铃虫线粒体基因组的结构相似。膨胀区域位于cox1基因编码区内部,大小为11 467 bp,经预测含有一个完整的真核基因(依赖ATP的RNA解旋酶)以及多种转座元件的片段,但与线粒体DNA无同源性,也无I类或Ⅱ类内含子存在的证据。对田间和室内棉铃虫DNA样品的PCR扩增未能检测到膨胀线粒体基因组的存在。以上结果表明膨胀片段可能是细胞核DNA序列通过偶然的水平转移事件而整合到线粒体基因组中的,且该种膨胀方式的发生概率极低。本文报道的膨胀线粒体基因组为日后动物线粒体基因组学的研究提示了一种独特的变异方式。     

扁蓿豆叶绿体基因组密码子偏好性分析

为阐明扁蓿豆（Medicago ruthenica）叶绿体基因组密码子使用模式，以其50条蛋白编码序列（CDS）为对象，利用软件CodonW 1.4.2、Excel以及在线程序对其ENC，RSCU，GC含量、中性绘图、PR2-plot、最优密码子等进行分析得到以下结果：基因组平均GC含量为40.58%，其中GC1>GC2>GC3；ENC的取值介于35.77～56.62之间，表明密码子使用偏好性较弱；基因组中共有30个密码子RSCU>1，其中29个以A/U结尾；ENC-plot绘图分析结果中多数基因分布于标准曲线下方，22个基因ENC比值在—0.05～0.05之间，密码子偏好性主要受选择影响；PR2-plot分析表明碱基T的使用频率大于A，G大于C，说明密码子偏好性还受其他因素影响；该基因组中共有UUU，UUA，ACU等11个最优密码子并均以A/U结尾。以上研究结果可为扁蓿豆叶绿体基因组优良基因利用提供理论与基础。     

利用CRISPR/Cas9技术编辑BADH2-1/BADH2-2创制香米味道玉米新种质

【目的】香味是作物的重要食味品质之一。2-乙酰-1-吡咯啉（2-acetyl-1-pyrroline,2-AP）是主要香味物。BADH2是控制水稻等作物香味性状的关键基因,敲除该基因可以产生香味稻米。利用CRISPR/Cas9基因编辑技术在北京市农林科学院自育的玉米骨干亲本京724上敲除BADH2同源基因,以期获得有香米味道的玉米新种质材料。【方法】利用Ensembl数据库在线BLAST工具,将水稻OsBADH2蛋白序列在拟南芥、水稻和玉米蛋白序列数据库中进行序列比对,获得上述3个物种的BADH基因家族成员,并利用UniProt蛋白数据库中的结构域信息进行验证。进一步使用MEGA软件进行系统进化分析,获得玉米BADH2同源基因作为候选编辑靶标。基于CRISPR/Cas9基因编辑技术的原理,在候选基因的外显子处设计特异性靶点,并构建入CRISPR/Cas9基因编辑载体。再以玉米自交系京724为受体,利用农杆菌介导的遗传转化方法,通过磷酸甘露糖异构酶基因（phosphomannose isomerase,PMI）抗性筛选获得阳性转基因植株。转基因株系经测序明确其在靶基因中产生的突变类型。利用气相色谱质谱联用仪（gas chromatography-mass spectrometry,GC-MS）检测基因编辑株系T₁籽粒中香米主要香味物质2-AP的含量,以确认京724在基因编辑前后2-AP含量的变化。【结果】系统进化分析发现,玉米中存在2个BADH2同源基因,分别命名为ZmBADH2-1和ZmBADH2-2。ZmBADH2-1位于第4染色体,ZmBADH2-2位于第1染色体。2个基因均包含15个外显子和14个内含子,第4外显子间的核苷酸序列高度同源。在2个基因的第4外显子区域设计靶点并构建入CRISPR/Cas9基因编辑载体,通过遗传转化获得28株转基因株系。PCR扩增及测序分析结果显示,其中10株材料的2个ZmBADH2s在靶点区域均发生突变,突变基因型包括双等位突变和多等位突变,突变类型为不同数量的碱基缺失和插入。质谱检测结果显示玉米ZmBADH2双基因突变体籽粒中存在与香稻同样成分的2-AP。随机选取的4个T₁代基因编辑株系籽粒中,2-AP平均含量分别为438.29、404.63、348.65和161.82 μg·kg^-1,而未经过编辑的京724中未检测到2-AP。【结论】利用CRISPR/Cas9技术对玉米ZmBADH2-1和ZmBADH2-2同时进行定点敲除,创制出籽粒中具有香米味道的玉米骨干亲本新种质材料。     

贝母属植物叶绿体基因组候选SNP位点应用分析

贝母属植物是中国中药材的宝库,由于形态上难以区分,在民间应用、临床应用和中药市场中还存在混淆应用、以次充好的现象,急需开发基于新型分子标记位点的精准检测方法。本研究应用多重序列比对、SNP筛选等生物信息学分析手段,对贝母属15种植物28条叶绿体基因组序列进行分析。结果发现,贝母属叶绿体基因组DNA同源性达97.22%,通过分析共发现SNP位点5879个,其中川贝母类鉴别候选位点71个,川贝母鉴别候选位点4个,瓦布贝母鉴别候选位点37个,太白贝母鉴别候选位点147个,浙贝母鉴别候选位点91个,湖北贝母鉴别候选位点271个,平贝母鉴别候选位点1393个,伊贝母鉴别候选位点89个。本研究还对SNP位点在精准鉴定、精确定量应用方面进行了讨论,可为川贝母中药资源鉴定提供技术支撑。