枸杞SWEET基因家族的鉴定与糖含量关系分析

【目的】糖外排转运蛋白（sugars will eventually be exported transporters, SWEETs）在植物生长发育过程中发挥重要作用,为解析SWEETs基因在枸杞（Lycium barbarum L.）果实发育过程中对糖积累作用,进一步为揭示SWEET基因在枸杞果实发育过程中作用提供参考。【方法】研究基于枸杞基因组数据,采用生物信息学方法对枸杞SWEET基因（LbaSWEET）进行全基因组鉴定,并利用已发表的转录数据分析了LbaSWEETs在果实发育时期的基因表达情况。【结果】结果表明,枸杞SWEET基因家族共有37个成员,随机分布于10条染色体上,分别编码152~621个氨基酸,蛋白质分子量为16.87~69.97 kD,等电点为4.96~9.86。亚细胞定位预测位于叶绿体或质膜,大多数含有7个跨膜螺旋。系统进化分析发现,37个LbaSWEET蛋白可分为4个亚群,每个亚群的基因结构和保守基序组成相似。启动子元件分析发现,LbaSWEET基因启动子富含大量激素响应、逆境胁迫和生长发育响应元件。转录组数据和qRT-PCR分析表明,LbaSWEET9和LbaSWEET29基因表达量随着果实成熟呈现显著增加。相关性分析结果表明,LbaSWEET9和LbaSWEET29基因表达量与果糖含量呈显著正相关。【结论】研究推测LbaSWEET9和LbaSWEET29基因是果糖积累的关键基因。     

荔枝VQ基因家族鉴定及参与非生物胁迫应答的功能分析

【目的】鉴定荔枝（Litchi chinensis）VQ基因家族,并分析其在不同组织的表达模式及在低温、高温、干旱和盐胁迫下的应答。【方法】利用生物信息学方法在荔枝全基因组中鉴定LcVQ基因,并对其理化性质、亚细胞定位、基因结构和保守基序等进行分析;利用MEGA 6.0软件构建系统发育树,分析荔枝、拟南芥和水稻VQ蛋白的系统发育关系;使用实时荧光定量PCR（quantitative real-time PCR,qRT-PCR）技术验证LcVQs对多种非生物胁迫的响应情况。【结果】荔枝中共鉴定获得可聚类为9个亚族的18个VQ基因（LcVQ1-LcVQ18）,依次分布在荔枝的11条染色体上,其编码蛋白的氨基酸数介于111~427 aa之间,分子质量为12.48~45.49 kD;除LcVQ15和LcVQ17定位于细胞质之外,其余LcVQ蛋白均定位于细胞核。顺式作用元件预测分析结果表明,LcVQs启动子区域包含大量植物生长发育响应元件、激素响应元件及逆境响应元件。转录组数据分析结果显示,不同组织中LcVQs的表达量具有明显差异,总体上分为普遍性表达和特异性表达。qRT-PCR结果显示,在低温、高温、干旱和盐胁迫处理下的3 h内,与对照相比分别有4,3,3,4个LcVQs明显上调表达,可快速响应相应胁迫。【结论】荔枝全基因组中有18个VQ家族成员,具有典型VQ保守结构域,能差异化响应多种非生物胁迫,为研究其抗逆机制奠定了基础。     

灵宝杜鹃SBP基因家族的鉴定及非生物胁迫下的表达分析

【目的】 SQUAMOSA启动子结合蛋白（SBP）家族在植物发育和非生物胁迫等方面起重要作用,本研究可为灵宝杜鹃SBP基因家族成员的生物学功能和在非生物胁迫响应的调控功能提供参考,并为灵宝杜鹃物种保护奠定基础。【方法】采用生物信息学方法对灵宝杜鹃（Rhododendron henanense subsp. lingbaoense）SBP基因家族成员进行全基因组鉴定和分析,基于转录组数据分析组织特异性,并利用qRT-PCR方法检测SBP在非生物胁迫下的表达。【结果】结果表明：（1）从灵宝杜鹃基因组中共鉴定出19个含SBP保守结构域SBP成员,依次命名为RhlSBP1- RhlSBP19,基因不均匀分布在8条染色体上,编码的氨基酸长度为179~1 072 aa,分子量为20.26~118.73 kD;蛋白定位于细胞核。（2）系统发育分析将19个RhlSBP分为5个亚族,大部分RhlSBP与拟南芥SPL家族成员聚类。（3）MEME分析表明,所有的RhlSBP共有motif 1、motif 2和motif 4,基因结构显示Ⅳ、Ⅴ亚族内含子数量远多于I、Ⅱ、Ⅲ亚族。（4）顺式作用元件分析表明,RhlSBP启动子中含有大量光响应元件、激素响应元件和环境胁迫响应元件,推测RhlSBP可能在灵宝杜鹃响应光调控、环境胁迫发挥重要作用。（5）物种间的共线性分析显示灵宝杜鹃和羊踟蹰、圆叶杜鹃SBP基因共线性关系与水稻、拟南芥相比更强。（6）转录组数据分析显示,RhlSBP基因亚家族成员具有相似的组织表达模式。（7）qRT-PCR分析表明,RhlSBP基因对非生物胁迫具有响应作用,但不同成员在不同胁迫下的响应程度存在差异。茉莉酸甲酯和低温处理后,基因表达总体呈上调趋势,高盐会抑制RhlSBP基因表达,干旱条件下,RhlSBP基因表达处于先上调再下调趋势,RhlSBP1、RhlSBP8可能是干旱、低温和MeJA诱导关键基因。     

枳LEA基因家族鉴定及其对非生物胁迫的响应

为明确LEA基因在枳非生物胁迫中的作用,研究通过生物信息学方法对枳LEA基因家族进行全基因组的鉴定,并采用qRT-PCR技术分析其在不同非生物胁迫下的表达情况。结果表明:(1)枳基因组中鉴定得到57个LEA基因家族成员,编码蛋白的氨基酸长度在62~945 aa之间,分子质量在6.95~104.98 kD之间。(2)系统进化分析表明,PtrLEA基因可分为8个亚家族,LEA_1~LEA_6、dehydrin和SMP,LEA_2亚族家族成员最多。(3)顺式作用元件分析表明,PtrLEA启动子上存在大量的植物激素、胁迫响应以及生长发育有关的响应元件。(4)转录组数据分析结果显示,LEA基因家族具有组织表达特异性,PtrLEA 15、PtrLEA 17、PtrLEA 23、PtrLEA 51在所有组织中均有高表达,也发现有3个基因在所有组织中不表达。(5)实时荧光定量PCR结果显示:PtrLEA基因在低温、干旱和高盐胁迫处理条件下,与对照相比分别有6、2和6个基因上调表达,推测该基因家族参与多种非生物胁迫应答。     

葡萄中蔗糖转运蛋白家族的序列分析及功能推测

以葡萄中的蔗糖转运蛋白为主要研究对象,结合了功能研究较为深入的拟南芥和水稻蔗糖转运蛋白家族序列,分析讨论了这些基因在启动子区域顺式作用元件的异同,以及这些差异可能对mRNA的转录带来的影响;同时,根据蔗糖转运蛋白氨基酸序列对其家族进行了分类,分析了不同亚类蔗糖转运蛋白基因结构的特点;最后还对蔗糖转运蛋白家族中氨基酸的保守性进行了分析。这些分析将为后续蔗糖转运蛋白功能基因组学的研究以及通过基因工程技术精确调节植物代谢提供一定的依据。     

水稻OsRPL36A基因的表达特性研究

【目的】核糖体蛋白（ribosomal protein,RP）是参与蛋白质合成及基因表达调控的一种重要因子,在植物生长发育和胁迫响应过程中具有重要的作用。研究在水稻中克隆了1个核糖体蛋白家族基因OsRPL36A,并对其生物学功能进行初步研究,为后续OsRPL36A基因功能研究提供理论依据和研究方向。【方法】利用生物信息学技术分析OsRPL36A基因结构、顺式作用元件和演化过程;同时利用实时荧光定量PCR（quantitative real-time PCR,qRT-PCR）技术分析OsRPL36A的组织表达特异性、节律表达模式、及其对不同激素和非生物胁迫的响应情况。【结果】（1）OsRPL36A的编码区全长为297 bp,共编码98个氨基酸,属于核糖体蛋白L36超基因家族。（2）OsRPL36A的启动子区包含3个节律表达相关元件、10个光响应元件、14个激素响应元件和27个环境胁迫响应元件。（3）OsRPL36A在叶片中的表达量相对高于其他组织;具有典型的节律表达模式;且受IAA、高温、低温和渗透胁迫等诱导表达。【结论】OsRPL36A在叶中高表达,具有典型节律表达模式,对IAA显著响应,可能参与热激、低温、盐害和渗透胁迫响应。     

拟南芥GA2ox基因家族启动子分析

赤霉素是一类重要的植物激素,它参与调节植物生长发育的各个阶段。真核基因的表达受多种因素的调控,其中启动子在转录水平上的调节作用至关重要,但是目前对拟南芥GA2ox基因家族上游顺式元件的详细分析较少。本研究分析了AtGA2ox基因家族染色体定位、进化关系、蛋白模体以及顺式元件。分析结果表明：AtGA2ox基因家族分为2个亚类;具有相对集中的染色体分布：具有相似的内含子和外显子结构;AtGA2ox基因家族成员进化关系越相近,模体和顺式元件则越保守且分布位置更接近。PLACE和Plant CARE以及DMB分析显示,AtGA2ox基因家族存在许多保守元件,受多因素的调控,在此家族的上游调控区域普遍存在组织和器官特异性表达元件、光响应元停、激素响应元件以及其他环境响应元件。基因表达谱分析结果表明,在激素诱导下,AtGA2ox基因家族均有响应。这些元件不仅作为正调控元件,诱导部分AtGA2ox基因的表达,而且还能作为负调控元件．抑制其他AtGA2ox基因的表达。     

大豆GATL基因家族结构、进化和表达分析

本研究利用同源检索的方法在大豆数据库中全基因组分析获得18个大豆GATL基因,大豆GATL基因的基因结构保守,其中16个成员不含内含子;其后对其编码蛋白的理化特点、亚细胞定位和信号肽进行了分析;通过邻接法构建了该家族的进化树,以了解GATL家族成员的进化关系;表达模式分析发现,家族成员呈现出各自的表达特点;成员启动子区顺式作用元件分析发现了大量的植物激素和胁迫响应相关元件。本研究为进一步分析基因家族成员的功能提供了理论依据。     

普通丝瓜PYL基因家族鉴定及在果实发育中表达分析

【目的】为了探究普通丝瓜PYL基因在ABA处理下的表达模式。【方法】利用生物信息学方法,分析PYL基因家族在普通丝瓜全基因组中的分布、染色体定位、基因结构、基因共线性、选择压力分析、进化亲缘关系和顺式作用元件,并通过qRT-PCR验证在不同浓度ABA下表达特异性。【结果】在普通丝瓜全基因组中鉴定到11个LcPYL基因,对应CDS长度576-966 bp,均具有典型PYR_PYL_RCAR_like结构;共线性分析发现7对源自于全基因组复制事件,预测具有相似的生物学功能;普通丝瓜PYL基因启动子含多个与植物激素相关的顺式作用元件,其成员的表达具有一定的组织特异性;普通丝瓜果实在不同浓度外源ABA处理下,2 mg/ml ABA处理LcPYLs表达并无显著变化,4 mg/ml ABA处理LcPYL5、LcPYL7、LcPYL11显著上调表达,8 mg/ml ABA处理LcPYL1、LcPYL7开花当天显著表达。【结论】本研究对普通丝瓜PYL家族成员进行了系统的鉴定与分析,明确其分子结构特征和表达模式,其中LcPYL1、LcPYL5、LcPYL7和LcPYL11可能是与内源ABA生物合成密切相关的关键基因。     

陆地棉FAX家族的全基因组鉴定及GhFAX1的功能分析

【目的】脂肪酸转运蛋白（FAX）可介导植物细胞内脂肪酸从质体向外运输,在植物生长发育及响应非生物胁迫等方面发挥重要作用。研究陆地棉FAX家族基因及功能分析,为明确陆地棉油脂积累的分子机制和油脂代谢工程提供新思路。【方法】从全基因组水平对GhFAX基因家族进行鉴定,并对GhFAX1蛋白进行亚细胞定位,通过酵母与烟草遗传转化对GhFAX1进行功能验证。【结果】在陆地棉基因组中共鉴定到12个GhFAXs基因,家族各成员间具有相似的基因结构及蛋白理化性质。序列比对分析发现,GhFAX蛋白仅有少数氨基酸在进化中高度保守,暗示其对功能的重要性;进化树分析表明,GhFAXs基因与亚洲棉、雷蒙德氏棉的亲缘关系较近。转录组数据表明,GhFAXs可能参与陆地棉响应逆境胁迫的调控过程。通过实时荧光定量PCR发现,GhFAX4在花中表达较高,说明其参与花粉发育过程;GhFAX9在茎中表达较高,GhFAX1在陆地棉各个组织表达量均较高。选择GhFAX1进行亚细胞定位分析,证实GhFAX1定位在质体中。构建GhFAX1载体,使GhFAX1在酿酒酵母中过表达,结果显示,GhFAX1过表达酵母总脂提高了3.53%。底...     

A Unique Protease Cleavage Site Predicted in the Spike Protein of the Novel Pneumonia Coronavirus (2019-nCoV) Potentially Related to Viral Transmissibility

正Dear Editor,In December 2019, a novel human coronavirus caused an epidemic of severe pneumonia(Coronavirus Disease 2019,COVID-19) in Wuhan, Hubei, China(Wu et al. 2020; Zhu et al. 2020). So far, this virus has spread to all areas of China and even to other countries. The epidemic has caused 67,102 confirmed infections with 1526 fatal cases     

Curcuminoids as inhibitors of thioredoxin reductase: A receptor based pharmacophore study with distance mapping of the active site

Curcumin is the yellow pigment of turmeric that interacts irreversibly forming an adduct with thioredoxin reductase (TrxR), an enzyme responsible for redox control of cell and defence against oxidative stress. Docking at both the active sites of TrxR was performed to compare the potency of three naturally occurring curcuminoids, namely curcumin, demethoxy curcumin and bis-demethoxy curcumin. Results show that active sites of TrxR occur at the junction of E and F chains. Volume and area of both cavities is predicted. It has been concluded by distance mapping of the most active conformations that Se atom of catalytic residue SeCYS498, is at a distance of 3.56 from C13 of demethoxy curcumin at the E chain active site, whereas C13 carbon atom forms adduct with Se atom of SeCys 498. We report that at least one methoxy group in curcuminoids is necessary for interation with catalytic residues of thioredoxin. Pharmacophore of both active sites of the TrxR receptor for curcumin and demethoxy curcumin molecules has been drawn and proposed for design and synthesis of most probable potent antiproliferative synthetic drugs.     

Comparative morphology of the carpel in the Liliaceae: Hewardieae, Petrosavieae, and Tricyrteae

The young pistils in the melanthioid tribes, Hewardieae, Petrosavieae and Tricyrteae, are uniformly tricarpellate and syncarpous. They lack raphide idioblasts. All are multiovulate, with bitegmic ovules. The Petrosavieae are marked by the presence of septal glands and incomplete syncarpy. Tepals and stamens adhere to the ovary in the Hewardieae and the Petrosavieae but not in the Tricyrteae. Two vascular bundles occur in the stamens of the Hewartlieae and Tricyrtis latifolia. Ventral bundles in the upper part of the ovary of the Hewardieae are continuous with compound septal bundles and placental bundles in the lower part. Putative ventral bundles occur in the alternate position in the Tricyrteae and putative placental bundles in the opposite. position in the Petrosavieae. The dichtomously branched stigma in each carpel of the Tricyrteae is supplied by a bifurcated dorsal bundle.     

Selection with two alleles and complete dominance

For a plant selection model with frequency-independent viabilities, fertilities and selfing rates, it is shown that apart from global fixation, for certain parameter combinations a protected polymorphism and facultative fixation (either allele may become fixed according to initial frequencies) may both occur. Facultative fixation requires different selling rates for the dominant and recessive type. Protection of the polymorphism requires resource allocation for male and female function. In this connection the problem of purely genetically caused population extinction is discussed.
For general frequency dependence and regular segregation, the chances for establishment of a completely recessive gene are compared to those of a completely dominant gene. It is proven that the process of establishment of the recessive gene, despite a fitness advantage, may be considerably endangered by drift effects if random mating prevails. The recessive gene may reach the same effectivity in establishment as a dominant gene, only if the recessive homozygote mates exclusively with its own type during the period of establishment.     

Composition and diversity of bird communities in Swedish farmland–forest mosaic landscapes

CapsuleThe amount of forest (at local and landscape scales) and occurrence of residual habitats at the local scale are shown to be the major factors influencing bird community composition in farmland–forest landscapes in central Sweden.

Aims To investigate the importance of local habitat and landscape structure for breeding birds in farmland–forest landscapes in central Sweden.

Methods Breeding birds were censused at 292 points. A detailed habitat mapping was made within 300 m of the points. Within a 300–600 m radius only two major habitats (forests and arable fields) were identified.

Results Cluster analyses of bird communities identified three site types that also differed in habitat composition: (i) partially forested sites in forested landscapes; (ii) heterogeneous sites with residual habitats in mosaic landscapes; and (iii) field-dominated farmland sites in open landscapes. A total of 19 of 25 farmland bird species (restricted to farmland or using both farmland and forest) had the highest abundance in farmland sites with mosaics of forest and farmland, while only six farmland species had the highest abundance in field-dominated sites. The bird community changed from being dominated by farmland species to being dominated by forest species (common in forest landscapes without farmland) at small proportions (10–20%) of forest at the local scale. A major difference in habitat composition between heterogeneous and field-dominated sites was the occurrence of different residual habitats (e.g. shrubby areas and seminatural grasslands). These habitats seemed to influence bird community composition more than land-use, despite covering <10% of the area. Seminatural grasslands were important for bird community composition and species-richness, but grazing seemed to be less important. Among different land-use types, cereal crops were the least preferred fields. Set-asides with tall vegetation and short rotation coppices were positively associated with species-richness of farmland birds.

Conclusion In general, the composition of the landscape was important for bird community composition, although amount and distribution of forests, occurrence of residual habitats and land-use of fields at the local scale had the strongest influence on bird community composition. The possible implications of these patterns for managing farmland–forest landscapes are discussed.     

Chemical constituents from the fruits of Rhus typhina L. and their chemotaxonomic significance

This work describes the isolation and characterization of twenty-nine compounds from the fruits of Rhus typhina L., including eleven flavonoids (1–11), eleven phenols (12–22), two pentacyclic triterpenes (23–24), two organic acids (25–26), one lumichrome (27), one courmarin (28) and one pyrimidine (29) on the basis of their spectroscopic data. Compounds apigenin (1), daidzein (4), orobol (5), 3′, 5, 5′, 7-tetrahydroxyflavanone (6), naringenin (7), butein (8), (-)-catechin (9), quercetin-3-O-α-L-(3″-O-galloyl)-rhamnoside (11), 2-hydroxybenzoic acid (13), 4-hydroxybenzaldehyde (14), vanillin (15), methyl 3,4-dihydroxybenzoate (16), 3,5-dihydroxybenzamide (18), tyrosol (19), caffeic acid (20), 3-(2,4,6-trihydroxyphenyl)-1-(4-hydroxyphenyl)-propan-1-one (21), phlorizin (22), friedelin (23), oleanolic acid (24), 4,4-dimethyl-heptanedioic acid (25), anthranilic acid (26), lumichrome (27), scoparone (28) and uracil (29) have not been recorded before in this plant. This is the first report on the occurrence of compounds 4–7, 9, 11, 13–14, 16, 18–21, 25–29 from the genus Rhus. Moreover, the chemotaxonomic significance of these isolated compounds was also summarized.