H9N2禽流感病毒全基因组密码子使用偏好性及影响因素分析

【目的】探究H9N2禽流感病毒(AIV)全基因组的密码子使用偏好性及影响因素。【方法】选取2010—2018年国内H9N2 AIV流行毒株的全基因组为研究对象,分析其碱基组成特性、最优密码子、密码子使用偏好性的影响因素以及病毒对宿主密码子使用模式的适应性。【结果】H9N2 AIV的全基因组中AU含量高于GC。大部分最优密码子以A或U结尾,有效密码子数(ENC)平均值为52.86,提示存在密码子使用偏好性但偏好性较低。密码子使用偏好性主要受到突变压力和自然选择的共同作用,其中自然选择(所占比例为61.79%～76.15%)作用大于突变压力(所占比例为23.85%～38.21%)。H9N2 AIV对人Homo sapiens的密码子适应指数平均值为0.739～0.741,提示H9N2AIV禽流感病毒可能已适应人类的密码子使用模式。【结论】本研究为H9N2 AIV的基因进化分析、已有疫苗的密码子优化和新型疫苗(密码子去优化疫苗)研制提供了理论依据。     

菊花ClERF1基因的克隆与表达分析

以甘菊叶片为试验材料,采用RT-PCR和Tail-PCR以及生物信息学的方法,研究了甘菊ClERF1及其启动子序列特征、表达模式,以及甘菊ClERF1在低温胁迫下的响应。以期为进一步研究甘菊ClERF1功能提供参考依据。结果表明:ClERF1基因序列全长1 242 bp,最大开放阅读框(ORF)618 bp,可编码206个氨基酸。经理化性质分析,ClERF1分子量23 631.35 Da,理论等电点5.19,不稳定系数53.84,脂肪指数62.04,平均亲水性-0.786,亚细胞定位在细胞核内。系统进化树表明,ClERF1与拟南芥At3g23240亲缘关系最近,属于ERF亚家族。qRT-PCR分析表明ClERF1在叶片中表达最高,其次在茎段中。该研究克隆了ClERF1启动子序列1 534 bp,主要包括低温反应和乙烯响应元件、生长素和茉莉酸甲酯反应元件等。甘菊低温处理幼苗ClERF1表达量显著高于未低温处理的幼苗,其中5℃时ClERF1相对表达量最高。     

Embryo-mediated genome editing for accelerated genetic improvement of livestock

Selecting beneficial DNA variants is the main goal of animal breeding. However, this process is inherently inefficient because each animal only carries a fraction of all desirable variants. Genome editing technology with its ability to directly introduce beneficial sequence variants offers new opportunities to modernize animal breeding by overcoming this biological limitation and accelerating genetic gains. To realize rapid genetic gain, precise edits need to be introduced into genomically-selected embryos, which minimizes the genetic lag. However, embryo-mediated precision editing by homology-directed repair (HDR) mechanisms is currently an inefficient process that often produces mosaic embryos and greatly limits the numbers of available edited embryos. This review provides a summary of genome editing in bovine embryos and proposes an embryo-mediated accelerated breeding scheme that overcomes the present efficiency limitations of HDR editing in bovine embryos. It integrates embryo-based genomic selection with precise multi-editing and uses embryonic cloning with elite edited blastomeres or embryonic pluripotent stem cells to resolve mosaicism, enable multiplex editing and multiply rare elite genotypes. Such a breeding strategy would enable a more targeted, accelerated approach for livestock improvement that allows stacking of beneficial variants, even including novel traits from outside the breeding population, in the most recent elite genetic background, essentially within a single generation.     

Genome-edited crops: how to move them from laboratory to market

Recent breakthroughs in CRISPR technology allow specific genome manipulation of almost all crops and have initiated a revolution in precision crop breeding. Rationally-based regulation and widespread public acceptance are needed to propel genome-edited crops from laboratory to market and to translate this innovative technology into agricultural productivity.     

我国居民肉类消费特征及趋势判断——基于双对数线性支出模型和LA/AIDS模型

为分析我国城乡居民肉类消费水平及其结构特征,判断居民肉类消费的未来趋势,基于FAO和统计年鉴等相关统计数据,运用双对数线性支出模型和LA/AIDS模型(Linear approximated/Almost ideal deal demand system模型),测算我国及城乡居民肉类消费需求的价格弹性和收入弹性。结果显示我国居民肉类消费量不断增加,且城乡居民肉类消费差距逐步缩小。居民对牛羊肉需求的收入弹性最大,禽肉次之,猪肉最小。其中,农村居民对各项肉类消费需求的收入弹性均显著高于城镇。我国居民的牛羊肉需求对自身价格及其他肉类价格变动较敏感,猪肉需求对自身价格与其他肉类价格变动敏感度较低。由此推断,未来我国居民对牛羊肉消费将呈波动增长态势,而对猪肉的消费呈缓慢增长,但消费量趋于稳定。     

基于YOLO v3与图结构模型的群养猪只头尾辨别方法

在利用视频监控技术对群养猪只进行自动行为监测时,对猪只准确定位并辨别其头尾位置对提高监测水平至关重要,基于此提出一种基于YOLO v3(You only look once v3)模型与图结构模型(Pictorial structure models)的猪只头尾辨别方法。首先,利用基于深度卷积神经网络的YOLO v3目标检测模型,训练猪只整体及其头部和尾部3类目标的检测器,从而在输入图像中获得猪只整体及头尾部所有的检测结果;然后,引入图结构模型,描述猪只的头尾结构特征,对每个猪只整体检测矩形框内的头尾部位组合计算匹配得分,选择最优的部位组合方式;对部分部位漏检的情况,采取阈值分割与前景椭圆拟合的方法,根据椭圆长轴推理出缺失部位。在实际猪场环境下,通过俯拍获得猪舍监控视频,建立了图像数据集,并进行了检测实验。实验结果表明,与直接利用YOLO v3模型相比,本文方法对头尾定位的精确率和召回率均有一定提高。本文方法对猪只头尾辨别精确率达到96.22%,与其他方法相比具有明显优势。     

羊肚菌营养袋制作原料的化学成分分析及配方优化

为优化羊肚菌营养袋的原料组成与配比,以食药用菌栽培基质中常用的4种秸秆及谷壳、麦粒、麦麸,通过主成分分析归纳各原料的营养组成属性,设计出9个营养袋配方进行栽培试验,比较出菇产量,得出高产营养袋原料组合为谷壳和麦粒;再以谷壳与麦粒按11种不同的重量比混合制成营养袋进行栽培试验,综合考量制作成本、出菇产量、经济效益等因素后,最终得到高产高效的羊肚菌营养袋配方(重量比)为谷壳19%、麦粒79%、石灰1%、石膏1%。     

CRISPR/Cas9技术敲除酿酒酵母gpd2基因对产2,3-丁二醇的影响

旨在利用CRISPR/Cas9基因编辑技术敲除酿酒酵母甘油-3-磷酸脱氢酶基因(gpd2),探究其对2,3-丁二醇产量的影响。根据酿酒酵母(Saccharomyces cerevisiae)W5甘油-3-磷酸脱氢酶基因(gpd2)设计供体片段及gRNA片段,将gRNA片段与可表达Cas9蛋白的敲除载体相连,之后将重组质粒及供体DNA片段转化到S. cerevisiae W5细胞中,根据表型筛选及PCR验证获得gpd2基因缺失菌株。结果表明目的基因gpd2敲除成功,基因缺失菌株与原始菌株经发酵实验相比,甘油产量下降22.01%,乙醇产量提高24.65%,2,3-丁二醇产量下降10.60%。gpd2基因的敲除并没有提高2,3-丁二醇的产量,原因可能是逐渐积累的NADH会优先被细胞内大量的乙醇脱氢酶所氧化,作用于乙醇的产生,而不是优先作用于2,3-丁二醇的合成。本实验构建了适用于酿酒酵母的基因敲除系统,该系统对进一步探究酿酒酵母其他代谢产物与2,3-丁二醇合成之间的关系具有实际的借鉴意义。     

Cf-2/Rcr3pim番茄品系对南方根结线虫的抗性测定

Cf-2/Rcr3~(pim)基因型番茄不仅能够抵御番茄叶霉菌的侵染,而且对马铃薯金线虫的寄生也有一定的抑制效果。为挖掘根结线虫的新抗性资源,本研究采用室内人工接种法测定了Cf-0/Rcr3~(pim)、Cf-2/Rcr3-3和Cf-2/Rcr3~(pim)基因型番茄品系对南方根结线虫的抗感性。抗性评价结果显示,Cf-0/Rcr3~(pim)品系对南方根结线虫表现高感,Cf-2/Rcr3-3品系为中感,而Cf-2/Rcr3~(pim)品系则为感病。与Cf-0/Rcr3~(pim)和Cf-2/Rcr3-3基因型相比,Cf-2/Rcr3~(pim)基因型番茄品系虽然对南方根结线虫侵染的敏感性略低,但是不能阻止线虫在根系上的大量繁殖,不适于根结线虫的防控应用。     

Dynamics of apoptosis-related gene expression during follicular development in yak

The potential reproduction power of domestic animals is limited by a complicated follicular atresia process. P53, caspase-9 (Casp9), Bax, Bcl-2 and Fas play a crucial role in the ovarian mitochondrion-dependent apoptosis and death receptor pathway. In accordance with this study, the expression levels of Casp9, Bax, Bcl-2 and Fas were analysed in ovaries and oviducts of yak by immunohistochemistry (IHC). P53 and the above in ovarian granulosa cells (GCs) from atretic (3–6 mm) to healthy follicles (6–8 mm) and in oviducts were examined from the luteal phase to the follicular phase during the oestrous circle by Western blot (WB) and real-time PCR (RT-PCR). Results demonstrated that typical classic apoptotic factors Casp9, Bax, Bcl-2 and Fas were expressed in the cytoplasm and zonal pellucida of oocytes, primordial follicles, primary follicles, ovarian surface epithelium, ovarian GCs, granular lutein cells, surface epithelia in oviduct uterotubal junction and oviduct ampulla during the luteal phase. RT-PCR and WB revealed that P53 and Fas significantly increased in GCs of atretic follicles. P53 and Casp9 increased in oviduct epithelium during the luteal phase, but Fas was unchanged. A contrary tendency was noted in Bcl-2 and Bax expression. Overall, P53 and Fas play an essential role in inducing GC apoptosis, and Bax, Bcl-2, Casp9 and P53 are involved in oviduct epithelial regeneration in yak.