谷子PAL基因家族全基因组的鉴定和表达分析

苯丙氨酸解氢酶(phenylalanine ammonia-lyase,PAL)基因家族参与苯丙烷类代谢过程,通过调控植物抗病次生物质的合成在植物抗逆反应中发挥重要作用。为明确谷子PAL基因家族在逆境胁迫下的表达规律,该研究利用生物信息学方法对谷子PAL基因家族进行鉴定和表达分析。结果表明:谷子具有11个PAL基因,在进化树中可分为3个亚家族,SiPAL7独自进化为一支。通过构建蛋白结构域发现PAL基因家族成员均含有保守的PAL结构域。启动子分析显示,PAL基因含有应答激素、逆境胁迫等多种因子的顺式作用元件,说明PAL基因广泛参与不同生物学调控过程。RT-qPCR结果显示,谷子PAL基因家族多为诱导型表达,不同光照条件下PAL基因表达量变化明显,不同基因具有不同响应模式,说明谷子PAL基因家族在参与光调节反应中发挥重要作用。谷子PAL基因高度保守,广泛响应不同非生物胁迫,具有表达特异性。该研究结果为揭示PAL基因家族在调节谷子抗性及胁迫应答过程中的作用提供了参考。     

白菜CesA基因家族鉴定及表达模式分析

为探究CesA基因家族在白菜生长发育及纤维素合成过程中的作用机制,该文通过生物信息学的方法,以白菜的全基因组序列为研究区域,进行理化特征、基因结构、进化特征、保守基序及结构域、顺式作用元件和组织表达等鉴定分析。结果表明:(1)共鉴定出16个编码纤维素合成酶亚基的CesA基因,该家族成员所编码蛋白的理论等电点为4.76～9.12,相对分子量为17.76～122.67 kD,长度为153～1 089 aa。(2)15个基因不均匀地分布于白菜的7条染色体上,Bra036008定位于scaffold上。(3)大部分成员包含4～14个外显子,1～11个保守基序。(4)该家族具有保守的DDD-QXXRW 保守功能域。(5)该家族编码蛋白主要分布在质膜上,二级结构以无规则卷曲与α-螺旋为主,多数成员都含有CesA蛋白典型的N端、C端和跨膜区。(6)CesA基因在茎中表达量相对较高,其中Bra011865、Bra023952和Bra029874在茎、叶、花中显著表达。该研究结果为后续深入研究CesA基因功能以及白菜生长发育研究奠定了基础。     

Importance of an appropriate visual presentation for avoiding a misconception of the menstrual cycle

Family planning, the prevention of unwanted pregnancy, and women’s reproductive health are topics that have received close attention for decades. It would therefore be fair to assume that there exists a good knowledge of the menstrual cycle. However, it is clear that many people have various misconceptions about the menstrual cycle and fertile days or ovulation, and that this process is still largely taught with the aid of materials and images that have not changed for many years. We investigated the effect of moving away from the usual teaching practice of using a 28-day diagram showing ovulation on the 14th day. A total of 184 students from three different high schools, aged between 17 and 18, participated in this research. The students who were taught using three diagrams showing different durations of the menstrual cycle showed a significantly better adoption of the facts and concepts compared to the students who were taught using a diagram of the average 28-day cycle. Our results confirmed that it is highly important to use appropriate visual displays in the teaching of the menstrual cycle and that it is essential to enhance the visual literacy of students and teachers.     

TrioMDR: Detecting SNP interactions in trio families with model-based multifactor dimensionality reduction

Single nucleotide polymorphism (SNP) interactions can explain the missing heritability of common complex diseases. Many interaction detection methods have been proposed in genome-wide association studies, and they can be divided into two types: population-based and family-based. Compared with population-based methods, family-based methods are robust vs. population stratification. Several family-based methods have been proposed, among which Multifactor Dimensionality Reduction (MDR)-based methods are popular and powerful. However, current MDR-based methods suffer from heavy computational burden. Furthermore, they do not allow for main effect adjustment. In this work we develop a two-stage model-based MDR approach (TrioMDR) to detect multi-locus interaction in trio families (i.e., two parents and one affected child). TrioMDR combines the MDR framework with logistic regression models to check interactions, so TrioMDR can adjust main effects. In addition, unlike consuming permutation procedures used in traditional MDR-based methods, TrioMDR utilizes a simple semi-parameter P-values correction procedure to control type I error rate, this procedure only uses a few permutations to achieve the significance of a multi-locus model and significantly speeds up TrioMDR. We performed extensive experiments on simulated data to compare the type I error and power of TrioMDR under different scenarios. The results demonstrate that TrioMDR is fast and more powerful in general than some recently proposed methods for interaction detection in trios. The R codes of TrioMDR are available at: https://github.com/TrioMDR/TrioMDR.     

Synthetic biology and metabolic engineering of actinomycetes for natural product discovery

Actinomycetes are one of the most valuable sources of natural products with industrial and medicinal importance. After more than half a century of exploitation, it has become increasingly challenging to find novel natural products with useful properties as the same known compounds are often repeatedly re-discovered when using traditional approaches. Modern genome mining approaches have led to the discovery of new biosynthetic gene clusters, thus indicating that actinomycetes still harbor a huge unexploited potential to produce novel natural products. In recent years, innovative synthetic biology and metabolic engineering tools have greatly accelerated the discovery of new natural products and the engineering of actinomycetes. In the first part of this review, we outline the successful application of metabolic engineering to optimize natural product production, focusing on the use of multi-omics data, genome-scale metabolic models, rational approaches to balance precursor pools, and the engineering of regulatory genes and regulatory elements. In the second part, we summarize the recent advances of synthetic biology for actinomycetal metabolic engineering including cluster assembly, cloning and expression, CRISPR/Cas9 technologies, and chassis strain development for natural product overproduction and discovery. Finally, we describe new advances in reprogramming biosynthetic pathways through polyketide synthase and non-ribosomal peptide synthetase engineering. These new developments are expected to revitalize discovery and development of new natural products with medicinal and other industrial applications.     

Nr5a1-Cre-mediated Tspo conditional knockout mice with low growth rate and prediabetes symptoms – A mouse model of stress diabetes

Translocator protein (TSPO) is a high-affinity cholesterol- and drug-binding mitochondrial protein. Nuclear receptor subfamily 5 group A member 1 or steroidogenic factor 1 (Nr5a1)-Cre mice were previously used to generate steroidogenic cell-specific Tspo gene conditional knockout (cKO) mice. TSPO-depleted homozygotes showed no response to adrenocorticotropic hormone (ACTH) in stimulating adrenal cortex corticosterone production but showed increased epinephrine synthesis in the medulla. No other phenotype was observed under normal growth conditions. During these studies, we noted that pairing two cKO mice resulted in the generation of small pups. These pups showed low growth rate at weaning, which has been linked to the development of type 2 diabetes (T2D) in adulthood. Experimental verification of T2D symptoms via blood testing of the adult mice, including glycated hemoglobin and insulin C-peptide measurements, showed that these Tspo cKO mice exhibited sustained hyperglycemia, a sign of prediabetes, likely due to the augmentation of hepatic glucose production mediated by the increased epinephrine. We also observed increased expression of the S100a8 gene, which is upregulated after chronic glucose stimulation. Taken together, the observed prediabetes phenotype and lack of response to ACTH indicate that Tspo cKO mice (Nr5a1-Cre^+/?, Tspo^fl/fl) could provide a useful model to study the link between diabetes and stress.     

杜鹃花TPS基因家族鉴定及与萜类物质代谢的关系分析

萜烯合成酶（terpene synthase,TPS）能催化不同的前体物质生成不同的萜类化合物,是合成萜类物质的关键酶。为探究杜鹃花TPS基因家族成员在萜类物质代谢过程中的表达模式,本文基于杜鹃花基因组数据库,利用生物信息学方法对杜鹃花TPS基因（TPS）进行家族成员鉴定;通过云锦杜鹃和诺娃杜鹃两种不同种高山杜鹃的转录组测序结果,结合qRT-PCR、顶空固相微萃取和气相色谱-质谱联用技术,分析两种杜鹃不同发育时期花瓣中TPS家族成员表达水平和代谢物含量变化关系。结果表明,从杜鹃花基因组数据库中共鉴定获得47个RsTPS成员,RsTPS家族成员长度在591-2 634 bp之间,含有3-12个外显子不等,编码196-877个氨基酸;RsTPS家族成员主要分布在叶绿体和细胞质;系统进化分析结果显示RsTPS基因分为5个亚组。通过分析转录组数据得到7个功能注释为TPS的基因家族成员,发现TPS1、TPS10、TPS12和TPS13的表达量在4个时期中呈现出先上升,到盛开期达到顶峰后再下降的趋势。对基因表达量变化与萜类物质含量变化进行相关性分析,发现TPS1、TPS4、TPS9、TPS10、TPS12和TPS13表达量与云锦杜鹃不同时期花瓣中萜类物质含量变化呈显著性正相关,推测这6个基因家族成员可能是参与云锦杜鹃花香调控的关键基因。     

茉莉酸信号受体COI蛋白家族的分子进化与基因表达分析

茉莉酸(Jasmonic acid,JA)存在于所有高等植物中,是植物对病原微生物和虫害防御反应的关键激素。在茉莉酸信号转导中,COI1(COR-insensitive 1)作为茉莉酸信号受体蛋白在其中发挥关键作用。本研究采用生物信息学方法,从藻类、苔藓类、蕨类、裸子及单、双子叶植物多谱系对COI蛋白家族进行比较基因组学研究,并取得以下结果:(1)同源基因鉴定结果发现,在所选的7种陆生植物中一共鉴定了55个COIs同源基因,然而,在低等的水生植物包括绿藻类(Chlorophytes)、红藻类(Rhodophytes)、硅藻类(Bacillariophytes)、灰胞藻类(Glaucophytes)及褐藻类(Phaeophytes)等基因组中均未发现其同源基因;(2)系统进化树分析表明,植物COI蛋白家族可以分为4个保守的亚家族,且在陆生植物扩增的同时可能已发生功能分化;(3)基因结构分析显示,植物COI家族基因结构表现多样性,主要体现在内含子的数目和长度上;(4)基因表达数据提示,COI基因家族成员参与植物生长发育的多个时期,且在不同组织器官以及不同的胁迫应答反应中发挥不同的作用。以上结果将为植物COI基因家族的深入研究提供参考。     

葡萄BRX基因家族生物信息学分析

BRX基因家族是一类植物特有的转录因子家族,在拟南芥中参与调节根细胞的增殖与伸长。利用生物信息学方法对葡萄基因组中存在的BRX基因家族进行了电子克隆,并对其进行了基因组的定位、蛋白质的结构、理化性质、二级结构及亚细胞定位的预测与分析,并对其与其它植物进化的亲缘关系进行了研究。基因组定位结果发现:葡萄基因组中6个BRX基因集中分布在3条染色体上,其中Vv BRX1和Vv BRX2分布在第2条染色体上,Vv BRX3和Vv BRX4分布在第9条染色体上,Vv BRX5和Vv BRX6分布在第11条染色体上;编码蛋白的氨基酸数目为360~560个,Vv BRX5的相对分子量(61 884.4)和理论等电点(9.38)均最大,而Vv BRX1的相对分子量(40 239.1)和理论等电点(6.23)均最小。研究显示,不同成员间氨基酸数目、氨基酸序列间存在一定的差异,但都为疏水性蛋白;α-螺旋和无规则卷曲为6个BRX氨基酸序列的主要组成部分;均不存在跨膜域及信号肽。基因结构分析表明,6个BRX基因都含有外显子和内含子结构。亚细胞定位分析表明:6个Vv BRX基因均定位于细胞核。系统进化分析结果表明,Vv BRX1、Vv BRX2基因与胡杨的亲缘关系最近,相似性达96%;Vv BRX3、Vv BRX4与蓖麻、麻疯树、柑橘、可可、大豆聚为一类,说明其进化关系较近;Vv BRX5与其它Vv BRX基因明显分开;Vv BRX6基因与莲的亲缘关系最近。试验结果为葡萄BRX基因家族的克隆和功能分析奠定了一定的研究基础。