大豆苯丙氨酸代谢途径关键酶基因的挖掘定位及结构分析

利用大豆基因组物理图和遗传图的整合图谱,应用blast软件将基因序列与大豆基因组数据库进行比对,完成了9个大豆天冬氨酸代谢途径中关键酶基因的定位以及结构分析。结果表明:9个基因分别定位在大豆的13个连锁群D1a、B1、N、I、O、C1、C2、F、L、A2、J、D1b以及B2上,并获得了基因所在序列两侧标记。利用大豆的cDNA和gDNA序列信息,获得了9个基因的结构,外显子数目为5～12个,内含子数目为4～11个。     

玉米谷氨酰胺合成酶基因家族的生物信息学分析

谷氨酰胺合成酶(GS,EC6.3.1.2)是氮素代谢途径中的关键酶,对植物的生长和发育至关重要。采用多种生物信息学软件对6个玉米GS基因的可变剪接现象、核苷酸序列、编码蛋白序列、磷酸化位点、基因组结构、同源进化关系以及启动子顺式作用元件进行系统的生物信息学分析。结果表明,5个玉米GS基因存在可变剪接现象,编码蛋白的氨基酸数目为356~423个;6个玉米GS蛋白存在19~38个的磷酸化位点,各成员基因组序列上含有10~15个外显子;玉米GS基因可划分为GS2、GS1-1、GS1-2和GS1-3等4个亚组;6个基因定位到1、4、5、9和10号共5条染色体上,6个成员的启动子区域含有MYB结合位点、水杨酸响应元件和茉莉酸甲酯响应元件等重要的调控元件。     

大豆TPS基因家族全基因组鉴定、分类与表达分析

本研究利用大豆基因组数据库,通过生物信息学分析,鉴定并获得大豆TPS 家族基因所有成员的全序列、基因结构和定位信息。研究还利用序列比对对大豆TPS 家族基因进行进化和分类分析,同时通过soybase大豆发育表达芯片数据库相关信息,对该家族基因成员的组织表达谱进行了检测。研究结果表明,大豆基因组中含有20个TPS家族基因成员。系统发育分析将这些TPS基因分成了两个亚家族。基因定位分析表明,这些成员基因分别分布于大豆的14条染色体上。启动子分析表明,全部大豆TPS 家族基因的启动子区都含有逆境反应顺式作用元件。转录水平芯片数据分析同时显示,大豆TPS家族基因大多在花、根、根瘤等组织中存在优势表达。该研究结果将促进大豆TPS家族基因的功能研究与利用。     

龙眼miRNA合成途径相关基因的鉴定及表达分析

为了解龙眼miRNA合成途径相关基因的生物学功能,本研究依据龙眼第3代基因组数据对龙眼miRNA合成途径相关基因进行了鉴定和生物信息学分析,并利用龙眼转录组对其在体胚发生早期定量表达进行分析。研究结果如下：共鉴定到12条龙眼miRNA合成途径相关基因,分别是DlDDL1、DlDDL2、DlDDL3、DlDCL1、DlSE、DlHYL1a、DlHYL1b、DlHYL1c、DlCBP20、DlCBP80、DlHEN1、DlHASTY。这些基因编码的氨基酸数目400~1000 aa,蛋白分子质量23.92~220.25 kDa;大部分蛋白均为酸性蛋白,所有蛋白均为不稳定蛋白,除DlHASTY外,其余蛋白均为亲水性蛋白;基因结构分析表明,各成员内含子数目差别较大,为2~23个;所有成员均含有保守结构域,数目差别较大,为1~7个;启动子顺式原件分析显示,基因启动子区域均含有大量光反应元件及激素响应元件;蛋白互作预测分析显示龙眼miRNA合成途径相关基因具有较强的互作关系。对龙眼体胚发生早期过程中表达分析显示,各基因在EC阶段具有较高的转录水平。本研究表明：龙眼miRNA合成途径相关基因可能参与龙眼体胚发育早期进程且在EC阶段发挥重要作用,同时响应多种激素应答及非生物胁迫,推测其在生物学功能方面具有多样性和差异性。     

可可泛素结合酶基因家族的生物信息学初步分析

泛素结合酶(E2s)促进底物泛素化或者与E3s链接,是靶蛋白泛素化的关键酶,在泛素-蛋白酶体途径中起重要作用。利用可可(Theobroma cacao L.)全基因组测序数据,共鉴定出45个E2s基因家族成员,包括39个UBC和6个UEV基因。通过生物信息学方法,对可可E2s家族的基本理化性质、基因结构、二级结构预测、亚细胞定位、进化关系等方面进行初步分析。结果表明:可可E2s基因CDS长度在441(Tc UEV3)~3 651 bp(Tc UBC7)之间,对应的编码蛋白氨基酸数目在146(Tc UEV3)~1 216 aa(Tc UBC7)之间,编码蛋白分子量在16.39~134.71 ku之间。E2s基因外显子在1~11之间,多数基因外显子数目在5~7之间。E2s基因在10条染色体上均有分布,1号染色体为7个,数量最多;6号染色体2个基因,数量最少。可可E2s蛋白大多为不稳定蛋白,且均为亲水性蛋白,其二级结构以α-螺旋和无规则卷曲为主要构成元件。大多数可可E2s蛋白定位在细胞核,少数定位在内质网或者细胞质。进化树分析表明:可可E2s蛋白被分为20个亚家族,包括16个UBC亚家族和4个UEV亚家族,第Ⅵ亚家族E2s数目最多为9个;E2s家族蛋白在物种进化过程中具有高度保守性。     

大豆DNA甲基化酶生物信息学分析

植物DNA甲基化酶对建立与维持基因组甲基化,调控基因表达,确保植物快速应对多种逆境具有重要作用。本研究利用多种生物信息学网站和软件初步明确了大豆中四类DNA甲基化酶蛋白及相应基因序列,并分析了进化关系和基因拷贝数,确定了基因在染色体上的物理位置及酶蛋白的理化性质与亚细胞定位,同时揭示了大豆DNA甲基化酶蛋白的结构域和组织表达部位特异性。这些研究结果对全面认知大豆DNA甲基化酶蛋白的特征以及从遗传学上对其展开深入研究和剖析具有重要的理论指导作用。       

大豆PPR基因家族生物信息学分析

为明确大豆PPR基因家族在染色体上的分布、保守结构域、亚族种类、进化关系及表达特征等,采用生物信息学方法,基于Pfam的PPR种子序列模型筛选大豆基因组数据库,获得631个大豆PPR家族基因;利用MEME、ExPASy、TBtools、FigTree等工具对大豆PPR家族基因进行分类,分析各亚族的进化关系和保守结构域差异;筛选各亚族的代表基因,并进一步分析各亚族基因的保守率、等电点、UTR、CDS及基因表达特异性.结果表明:大豆PPR基因家族分为DYW、P、PLS、E/E+亚族以及1个未知亚族,其中DYW亚族为第一大亚族,占总基因数目的57.2％;各亚族基因在染色体上的分布是不均匀的,其内含子数目差异也较大,DYW亚族基因的内含子数目较少,但DYW亚族结构域种类最多,具有在C端出现特有的Motif7和Motif4的显著特征;但大豆PPR家族的各亚族基因表达特异性比较相似,均表现为叶片中高表达,花、根和茎中低表达;而且各亚族中都有大量成员缺失UTR;Glyma.19G095500、Glyma.11G086900、Glyma.02G175900和Glyma.01G158100这4个基因具有独特的Motif8保守结构域,为新的亚族.     

大豆TCP转录因子家族结构域分析及功能预测

利用已知的拟南芥TCP基因和大豆基因组数据库,通过生物信息学方法,鉴定并获得了大豆TCP家族基因序列,基因定位信息。共鉴定大豆TCP基因54个,分布在大豆除14号染色体外的其他19条染色体上。对54个基因进行进化和聚类分析及功能结构域的分析,发现全部具有高度保守的TCP结构域。根据结构域差异和系统发育分析的结果,将大豆TCP转录因子家族分成2个TCP亚家族。以生物信息学手段和已有的其他物种的TCP基因进行了比较分析,大豆TCP基因占总数的3.5%,与拟南芥同源基因比较,序列长度存在相似性。对启动子元件分析显示,TCP基因含有大量与在子叶、根、茎处大量表达有关的元件及对分生组织有作用的元件。     

大豆异黄酮还原酶基因的鉴定及生物信息学分析

异黄酮是大豆生长过程中形成的一类次级代谢产物,是大豆主要的功能活性成分之一。异黄酮还原酶(isoflavone reductase,IFR)是异黄酮分解途径的关键酶之一,在调控异黄酮含量及成分方面起着重要作用。本研究基于大豆全基因组测序数据,利用生物信息学方法鉴定了大豆异黄酮还原酶基因家族成员,并对其基因的序列特征、结构特征和遗传多样性进行了分析。结果表明:大豆异黄酮还原酶(GmIFR)家族含有17个成员,蛋白序列介于191(GmIFR07)和376(GmIFR11)个氨基酸之间,序列相似性为19.59%(Gm IFR07和GmIFR11)~98.43%(Gm IFR12和GmIFR17),结构分析表明这些基因内含子数目差异较大,2~6个不等,不均匀的分布在大豆的1、4、6、9、11、12和16号染色体上。     

大豆CML家族基因的生物信息学分析

CMLs蛋白是一类具有Ca2+结合的EF-hand保守结构域蛋白,广泛参与钙依赖的信号传导途径,在植物生长发育及生物胁迫与非生物胁迫响应中起着重要的作用。通过NCBI和植物基因组注释数据库等筛选并获得了68个大豆GmCML蛋白;分析了所有蛋白的基本特性;通过与拟南芥CMLs基因的进化树分析表明,GmCML家族基因属于8个亚类;对GmCML家族基因进行了染色体定位与重复基因进化关系分析,发现其具有较高的进化速率;序列比对发现GmCML类蛋白含有2~4个保守的EF-hand结构域;利用芯片数据对野生大豆在碱胁迫下的叶和根中的CMLs基因表达模式进行了分析,得到26个GsCML基因在碱胁迫下有显著的差异表达,且在根和叶中的差异表达模式不同,表明这些基因参与植物碱胁迫应答,且具组织表达特异性。     

In vitro reproduction in the annual pasture legumes subterranean clover (Trifolium subterraneum L.) and French serradella (Ornithopus sativus Brot.)

Pasture legumes are important components of both mixed farming rotations and permanent pastures in temperate climates. Breeding of two widely sown pasture legumes, subterranean clover (Trifolium subterraneum L.) and French serradella (Ornithopus sativus Brot.), is constrained by the long generation cycle, typically enabling only one generation per year. We hypothesized manipulation of culture medium and conditions would enable the development of a laboratory‐based protocol for in vitro reproduction in subterranean clover and French serradella. In vitro flowering and viable seed set was induced from both species. For subterranean clover, the most effective treatment was culturing on modified MS medium with 1 μm kinetin and 0·1 m sucrose under a 100 μmol m^?2 s^?1 light intensity and continuous photoperiod. For French serradella, culture on a hormone‐free B5 medium with 5 mm NH₄Cl and 0·1 m sucrose under a 100 μmol m^?2 s^?1 light intensity and 20 h photoperiod was optimum. It is expected this technique will have application in accelerating generation turnover within breeding programs, for the study of factors influencing flowering in pasture legumes, and for the propagation of valuable yet enfeebled plants such as embryo‐rescued hybrids.     

Pharmacokinetics of Marine-Derived Drugs

Marine organisms represent an excellent source of innovative compounds that have the potential for the development of new drugs. The pharmacokinetics of marine drugs has attracted increasing interest in recent decades due to its effective and potential contribution to the selection of rational dosage recommendations and the optimal use of the therapeutic arsenal. In general, pharmacokinetics studies how drugs change after administration via the processes of absorption, distribution, metabolism, and excretion (ADME). This review provides a summary of the pharmacokinetics studies of marine-derived active compounds, with a particular focus on their ADME. The pharmacokinetics of compounds derived from algae, crustaceans, sea cucumber, fungus, sea urchins, sponges, mollusks, tunicate, and bryozoan is discussed, and the pharmacokinetics data in human experiments are analyzed. In-depth characterization using pharmacokinetics is useful for obtaining information for understanding the molecular basis of pharmacological activity, for correct doses and treatment schemes selection, and for more effective drug application. Thus, an increase in pharmacokinetic research on marine-derived compounds is expected in the near future.     

Estimation of lucerne yield stability for enabling effective cultivar selection under rainfed conditions

Evaluation of crop and forage yield stability is of increasing relevance in the context of current and recent environmental changes but, in contrast to other field crops, there are no published systematic analyses among forage crops in Europe. A study of stability performance was conducted with 13 Czech cultivars of lucerne at four locations over a 2‐year period with the following aims: (a) to evaluate yield stability of varieties across different environments and (b) to calculate measurable benefits of variety selection in relation to the specific environment. The cultivar Vlasta was identified as the highest yielding cultivar (annual yield 16.0 t DM/ha), whereas the lowest yielding cv. Magda, Tereza and Oslava averaged around 14.9 t DM/ha. Effect of genotype × environment interaction (G × E) was two times higher than for genotype alone. Additive main effects and the multiplicative interaction (AMMI) model showed that the highest yielding cultivars may not be stable across environments. This study demonstrated further that significant yield improvement could be detected, even among a relatively homogenous group of domestic cultivars, and this was driven mainly by site productivity: the improvement was +10% in low‐yielding sites, compared with +3% in high‐yielding sites. Results highlight that advanced agronomy should also consider stability parameters such as AMMI stability value or superiority measures for forage crops in response to the challenges associated with climate change.     

La pourriture fongique des tubercules de pomme de terre en atmosphère contrôlée

Résumé Fusarium culmorum et, dans une moindre mesure,F. avenaceum, F. sambucinum, Colletotrichum coccodes etCylindrocarpon sp. ont été isolés de tubercules entreposés en atmosphère contr?lée (AC) et atteints de pourriture grave. Des expériences d'inoculation de tubercules avec 10 espèces ou variétés fongiques et conservation en AC à 8 et 10°C ont montré que: 1) les champignons non pathogènes en atmosphère normale (ex.:Cylindrocarpon sp.) le devenaient en AC, 2) ceux qui étaient faiblement pathogènes en atmosphère normale étaient nettement plus virulents en AC (ex.:F. culmorum), 3) les espèces ou variétés virulentes en conditions d'air normales (Fusarium sulphureum etPhoma exigua var.foveata) ne provoquaient pas de pourriture plus grave en AC et leur activité pouvait même être légérement freinée.

---

Summary The extensive rotting of tubers which occurred during storage trials in controlled atmospheres has led to a mycological and pathological study of the rots. The most frequently isolated species wasFusarium culmorum althoughF. avenaceum, F. Sambucinum, Coletotrichum coccodes and aCylindrocarpon sp. were also present. Tubers of cvs Bintje and Ulla were inoculated with 19 isolates of 10 fungal species or varieties associated with rotting of stored tubers (Table 1). The tubers were incubated at 8 or 10°C in normal or controlled (2% O₂:1% CO₂, 2% O₂:6% CO₂, 2% O₂:12% CO₂, 6% O₂:6% CO₂) atmospheres and the extent of rotting was determined a month later (Tables 2 and 3 and Fig. 2). Species which were weakly virulent in a normal atmosphere (variousFusarium spp. andPhoma exigua var.exigua) were clearly more aggressive in the controlled atmosphere and this was especially evident in the case ofF. culmorum. Species ot pathogenic in a normal atmosphere under experimental conditions (Colletotrichum coccodes, Cylindrocarpon sp.,Phoma eupyrena) caused rotting in the controlled atmosphere. The two species which were virulent in a normal atmosphere (F. sulphureum andP. exigua var.foveata) were also virulent in the controlled atmosphere and in some cases the extent of rotting was even less. As a general rule, rotting caused by weakly virulent fungi was greater in both cultivars in the controlled than in a normal atmosphere.

---

Zusammenfassung Eine starke F?ulnis von in Kontrotrollierter Atmosph?re gelagerten Kartoffelknollen veranlasste eine mykologische und pathologische Untersuchung. Der am h?ufigsten isolierte Pilz warFusarium culmorum. F. avenaceum, F. sambucinum, Colletotrichum coccodes undCylindrocarpon sp. wurden ebenfalls bestimmt. Neunzehn St?mme von 10 Pilzsorten oder-Arten welche bei Lagerf?ulnis vorkommen (Tab. 1) wurden auf Knollen der Sorten Bintje und Ulla inokuliert. Die Lagerung wurde bei 8 oder 10°C under Normalbedingungen oder kontrollierter Atmosph?re durchgeführt (2% O₂:1% CO₂, 2% O₂:6% CO₂, 2% O₂:12% CO₂, 6% O₂:6% CO₂). Der F?ulnisgrad (Abb. 1) wurde nach einem Monat bonitiert. Die Ergebnisse sind in den Tabellen 2 und 3 dargestellt und in der Abb. 2 illustriert. Unter in Normalbedingungen nur schwach virulente Arten (verschiedeneFusarien undPhoma exigua var. exigua) waren deutlich aktiver in kontrollierter Atmosph?re. Dies was besonders der Fall fürF. culmorum. Pilze, die im Versuch unter Normalbedingungen nicht pathogen waren (Colletotrichum coccodes, Cylindrocarpon sp., Phoma eupyrena), haben unter kontrollierter Atmosph?re Sch?den verursacht. Hingegen werden die beiden unter Normalbedingungen sehr pathogenen Arten (F. sulphureum undP., exigua var.foveata), durch kontrollierte Atmosph?re wenig beeinflusst. Es wurde sogar in einigen F?llen eine gewisse Verringerung des F?ulnisbefalls beobachtet. Ganz allgemein haben die getesteten kontrollierten Bedingungen die Entwicklung der Pilzf?ulnis an beiden Kartoffelsorten gef?rdert, speziell durch Pilzarten, welche unter Normal-bedingungen wenig Sch?den verursachen.

     

Marine Pharmacology in 2016–2017: Marine Compounds with Antibacterial,Antidiabetic, Antifungal,Anti-Inflammatory,Antiprotozoal, Antituberculosis and Antiviral Activities; Affecting the Immune and Nervous Systems,and Other Miscellaneous Mechanisms of Action

The review of the 2016–2017 marine pharmacology literature was prepared in a manner similar as the 10 prior reviews of this series. Preclinical marine pharmacology research during 2016–2017 assessed 313 marine compounds with novel pharmacology reported by a growing number of investigators from 54 countries. The peer-reviewed literature reported antibacterial, antifungal, antiprotozoal, antituberculosis, and antiviral activities for 123 marine natural products, 111 marine compounds with antidiabetic and anti-inflammatory activities as well as affecting the immune and nervous system, while in contrast 79 marine compounds displayed miscellaneous mechanisms of action which upon further investigation may contribute to several pharmacological classes. Therefore, in 2016–2017, the preclinical marine natural product pharmacology pipeline generated both novel pharmacology as well as potentially new lead compounds for the growing clinical marine pharmaceutical pipeline, and thus sustained with its contributions the global research for novel and effective therapeutic strategies for multiple disease categories.     

Effects of Micronutrient Deficiencies on Human Health: Its Status in South Asia

SUMMARY

Vitamin A, iodine, and iron deficiencies affect large numbers of people worldwide. A deficiency of one or more of these micronutrients adversely affects the physical and mental abilities of humans. South Asia contains a high percentage of these individuals, not just because of its large population, but also the prevalence of deficiency is higher there than in many other parts of the world. The reasons for the high rates of deficiency in South Asia are many, but they include inadequate availability of micronutrient-rich foods, sub-optimal dietary habits, and high rates of infection. Across the region, national plans vary from (a) increasing availability of appropriate foods, (b) introducing new dietary behaviors, (c) improving health status, and (d) directly addressing deficiency through intervention programs. The extent to which each of the countries is making progress toward the goals of these plans can help in understanding the priorities for future efforts to address micronutrient malnutrition. This article discusses the adverse effects of micronutrient deficiencies in humans with special reference to South Asia.     

稻文化的再思考3:稻与社稷——印度、泰国等东南亚、南亚主要国家

东南亚、南亚地区是世界上重要的稻米产区,稻米在民众饮食生活和国家社会政治中占有重要地位,民众生活中也保存了非常悠久和丰富的稻作文化习俗及稻谷起源神话传说。本文分析了水稻在东南亚、南亚主要国家印度、印度尼西亚、泰国、越南、菲律宾、孟加拉国、缅甸的作用、地位、生产、消费、文化等情况,并指出了印度、印度尼西亚稻文化的主要标志。     

Irrigation but not N fertilization enhances seedhead density in plains rough fescue ( F estuca hallii)

Plains rough fescue ( F estuca hallii) is an important forage grass species in western Canada. Seed for use in pastures and ecological restoration is in high demand but supply is limited because F. hallii is an erratic seed producer. Seed producers require an understanding of the factors that influence flowering and seed set in this species. The aim of this study was to assess the effect of irrigation and nitrogen fertilization on the flowering and growth of F. hallii in a native rough fescue prairie in Alberta, Canada. Irrigation had a strong positive effect on seedhead density, whereas fertilization had limited effects on growth and reproduction of F. hallii. These results demonstrate that under field conditions, available moisture is likely to be a key factor driving flowering and seed production in F. hallii.     

Management of Soil Micronutrient Deficiencies in the Rice-Wheat Cropping System

Summary

Within the last three decades, the rice-wheat cropping system has triggered, and with time, aggravated soil micronutrient deficiencies in the Indo-Gangetic Plains (IGP). This has largely been due to the shift from an earlier rice and wheat monoculture with low yielding, long duration indigenous varieties, to an intensive rice-wheat rotation cropping system with short duration modern high yielding varieties on the same piece of land. The problems related to micronutrient deficiency in the IGP are more due to the size of its available pools in the soil rather than its total contents and are greatly influenced by crop management, or rather its mismanagement. Deficiency of zinc is widespread in the IGP, but with the extensive use of zinc sulfate, zinc deficiency has reduced in some areas of the region. Meanwhile, the deficiency of Fe, Mn and B has increased in the IGP. Deficiency of Cu and Mo is location specific and can limit rice and wheat yields. The adoption and spread of the rice-wheat system in permeable coarse textured soils, particularly in the western IGP, not only caused iron deficiency in rice but also resulted in the emergence of manganese deficiency in wheat. In highly calcareous and acidic soils, boron is the next limiting micronutrient in crop production after zinc. Bumper rice and wheat harvests in the past decade, the declining use of organic manures in the region and except for the widespread use of zinc sulfate, a general lack of awareness amongst farmers on micronutrient deficiency problems has contributed to micronutrients limiting rice and wheat yields in the IGP. Approaches to alleviating micronutrient deficiencies include matching the crop removals of the micronutrients with its replenishments through their respective external carriers, supplementation through organic sources and mobilization/utilization through cultivation of micronutrient efficient crop cultivars. Identification of efficient micronutrient carriers and finding the optimum rate, mode and time of its application is important in ameliorating the micronutrient deficiencies. This article reviews the extent of micronutrient deficiency and discusses various management options available to reduce micronutrient deficiency induced crop yield reduction for rice and wheat in the Indo-Gangetic Plains.     

Model of wheat yield response to application of diclofop-methyl to control ryegrass (Lolium rigidum)

A general model of crop yield response to herbicide application is proposed. The model includes three components: the effect of herbicide dosage on weed density, the effect of surviving weed density on crop yield and the effect of herbicide directly on the crop. The model is used to estimate the response of wheat yield to application of diclofop-methyl to control ryegrass (Lolium rigidum) in Australia. It is found that the competitiveness of ryegrass plants surviving treatment is reduced by the treatment and that the proportion of yield loss at a given ryegrass density is not independent of the absolute weed-free yield. The response function is used to calculate economic thresholds and optimal herbicide dosages.