大豆GmMP基因的功能预测及表达分析

通过在大豆基因组数据库中检索拟南芥AtMP(ARF5)在大豆中的同源基因,获得了GmMP基因序列。对GmMP基因编码的氨基酸序列及启动子序列进行生物信息学分析,结果表明:GmMP基因CDS序列全长2 802 bp,编码933个氨基酸。GmMP编码的蛋白为疏水性蛋白。结构域分析表明:GmMP含有B3和AUXIN RESPONSE FACTOR结构域,同时该基因是ARF家族的成员。GmMP预测的启动子区域含有与激素、胁迫、光应答、生物钟调控和转录因子结合相关的顺式作用元件。系统进化分析表明MP在豆科植物进化过程中比较保守。组织特异性表达分析结果显示GmMP在叶片中表达量最低,在茎尖中表达量最高,推测其可能参与生长素的代谢途径。     

茶树Copine家族基因CsBON3的克隆与表达分析

Copine蛋白是一类包含2个C2(N端)和1个vWA(C端)保守域的Ca~(2+)依赖蛋白或磷脂结合蛋白,在胞内信号转导中发挥重要作用。基于序列相似性分析,从茶树转录组数据库中筛选出1条与Copine家族基因高度同源的EST序列。经测序验证该序列包含1 746 bp的完整ORF,编码581个氨基酸。同源比对显示该基因与拟南芥At BON3序列相似度最高(65%),将其命名为CsBON3(Gen Bank登录号为KY435900)。生物信息学分析显示,CsBON3蛋白分子量为63.66 k D,理论等电点为5.48;具有Copine家族蛋白特有的保守结构域;属亲水性蛋白,无信号肽位点,非分泌性蛋白,无跨膜结构域。表达分析表明,CsBON3在茶树花和根系中表达量最高,茎干和成熟叶中表达量最低。低温(4℃)处理茶树1 d后,其表达被显著上调;在生长阶段,该基因表达量高于休眠阶段;同时在接种炭疽菌的茶树叶片中,该基因也被快速上调,表明该基因可能与茶树低温、生长发育及抗病相关。     

大豆病程相关蛋白PR-5及其同源蛋白TPLs的生物信息学分析

大豆病程相关蛋白PR-5又称为类甜蛋白TLPs,广泛分布于高等植物体内,各种生物和非生物胁迫诱导(病原微生物、渗透胁迫,机械损伤和植物激素等)均可诱导其表达。本研究以PR-5编码基因Glyma01g42670.1为目的基因,对该基因及其同源蛋白的结构和功能进行了分析;通过生物信息学的方法,共筛选获得42条大豆TLPs蛋白质序列,并用Mega 4.1软件构建其系统进化树;同时对Soy Base中的大豆TLPs相关的表达数据进行分析。结果表明:大豆病程相关蛋白PR-5的编码基因Glyma01g42670.1编码240个氨基酸的多肽链,p I 6.26,是一种酸性蛋白,属于疏水蛋白,该蛋白质具有典型的TLP家族的保守结构域,具有指导PR-5蛋白的跨膜转移(定位)的N端信号肽序列,PR-5蛋白不含有跨膜螺旋结构,主要存在于质外体中,属于分泌蛋白,推测该蛋白具有内切葡聚糖酶的催化活性,进化分析表明:该编码基因与拟南芥的NP_192902.1基因属于直系同源基因,它们是具有相同功能和共同起源的基因,组织表达特异性分析表明该基因主要在根部和花中表达。     

大豆GmPHD3基因的克隆及逆境表达分析

为探讨大豆PHD-finger转录因子家族编码基因GmPHD3在抵抗中国南方高温高湿非生物胁迫造成种子劣变过程中的调控作用,分离全长GmPHD3基因并进行生物信息学分析、亚细胞定位和转录激活活性分析,以种子劣变抗性品种湘豆3号和不抗品种宁镇1号叶片及不同组织cDNA为材料,通过RT-PCR,进行组织表达模式分析和高温高湿胁迫下的表达模式分析。生物信息学分析结果表明基因CDS序列长度为738 bp,编码246个氨基酸,包含Alfin和PHD-finger 2个结构域。进化树结果表明该基因与木豆ALFIN-Like 3-like(XM_020363358.1)的遗传距离较近。亚细胞定位结果显示该蛋白在细胞核内表达。转录激活试验结果表明基因全长有转录激活活性,激活域为N端Alfin结构域,C端PHD-finger结构域无转录激活活性。组织表达模式分析发现该基因主要在成熟期高表达,且2个品种间存在差异。胁迫下的表达模式分析发现随着胁迫时间的延长,基因的表达量逐渐升高。研究结果为进一步阐明高温高湿胁迫下的调控机制研究奠定一定理论基础。     

大豆MYB转录因子的全基因组鉴定及生物信息学分析

MYB转录因子是植物中最大的转录因子家族之一,近年的研究表明其广泛参与多种生物学过程。MYB转录因子在其N端含有其特有的DNA结合基序(MYB-binding domain),能够与DNA分子大沟结合而调控基因表达。本研究通过生物信息学手段,在全基因组水平上筛选鉴定出了304个大豆MYB类转录因子,并对其进行了分类和保守结构域分析;通过与拟南芥的MYB基因进行系统发生分析,将304个大豆MYB转录因子分为了22个亚类;染色体定位分析表明大豆MYB转录因子在所有染色体上都有分布,部分染色体间的MYB蛋白序列高度相似,表明此类基因在进化上具有相同的来源;利用野生大豆盐、碱胁迫下转录组数据,分析MYB基因的表达模式,发现部分MYB转录因子能够响应盐、碱胁迫的诱导,且在盐、碱胁迫下具有不同的表达模式。     

大豆生长素受体基因家族及组织化学表达模式分析

生长素是调控植物生长的主要激素之一,TIR1/AFB是主要生长素受体基因,参与生长素信号的响应及传递。本研究分析了大豆中生长素受体TIR1/AFB基因家族的各个成员,依据拟南芥生长素受体基因序列比对及系统进化分析,可将大豆生长素受体分为三个聚类,其中I类和II类分别作为ATTIR1/AFB1和ATAFB2/AFB3的同源蛋白均含有FBOX和LRR(Leucine Rich Repeat)结构域,III类作为ATAFB4/AFB5的同源蛋白仅含LC(Low complexity)结构域。基因表达芯片分析结果表明,部分大豆生长素受体基因在不同组织中具有特异性的表达模式,预示着这些基因可能参与相关生物学过程的调控。组织化学表达模式检测结果表明,部分生长素受体在大豆主根及侧根中具有特异表达模式,预示这些基因可能参与大豆主根生长及侧根发生的调控过程。     

大豆GmABCG40基因的功能预测及表达分析

通过在大豆基因组数据库中检索拟南芥At ABCG40在大豆中的同源基因,获得了Gm ABCG40基因序列。通过对Gm ABCG40基因编码的氨基酸序列及启动子序列进行生物信息学分析,结果表明:Gm ABCG40基因CDS序列全长4 284 bp,编码1 427个氨基酸。Gm ABCG40编码的蛋白为疏水性蛋白,具有多个N-糖基化位点、激酶磷酸化位点、N-豆蔻酰化位点、2个ATP/GTP结合位点基序A和1个速激肽家族信号。结构域分析表明Gm ABCG40含有2个核苷酸结合域与2个跨膜结构域,形成NBD1-TMD1-NBD2-TMD2结构,属于ABCG亚家族的成员。Gm ABCG40预测的启动子区域含有与激素、胁迫、光应答、胚乳表达和转录因子结合相关的顺式作用元件。系统进化分析表明Gm ABCG40与菜豆、红豆、木豆、百脉根等豆科植物亲缘关系较近。组织特异性表达分析结果显示Gm DABCG40在叶片中表达量最低,在根中表达量最高,推测其可能参与根中ABA的转运过程。     

大豆Glyma.05G222700.2基因生物信息学与逆境表达分析

为研究Glyma.05G222700.2基因编码的丝氨酸/苏氨酸蛋白激酶在抗非生物胁迫过程的功能和原理,促进大豆抗逆候选基因的开发利用,本研究通过生物信息学方法对大豆Glyma.05G222700.2基因进行同源序列、蛋白结构、进化树和转录组分析,通过qRT-PCR分析盐胁迫下大豆不同组织中该基因的表达情况。结果表明:该基因编码区长2 040 bp,编码697个氨基酸,预测分子量为656.54 kD,pI8.026。多序列比对发现Glyma.05G222700.2蛋白包含1个Pkinase结构域。进化树分析表明该蛋白与野大豆、刺毛黧豆、赤豆一致性较高。转录组数据表明Glyma.05G222700.2基因在大豆各组织中均有表达,其中在种子中表达量最高,在根中表达量最低。qRT-PCR结果发现Glyma.05G222700.2基因在毛状根、茎、叶中均有表达,在茎中表达量最高,在叶中表达量最低;在毛状根中盐胁迫12 h表达量达到极值,盐胁迫24 h表达量下降;在茎中表达量呈上升趋势,在24 h表达量达到极值;在叶中表达量不稳定,盐胁迫2 h该基因不表达,盐胁迫6 h该基因表达量达到极值并高于对照,盐胁迫12和24 h表达量低于对照。推断该基因可能在大豆抵抗盐胁迫过程中起到重要作用。     

大豆GmIDD及其同源基因的生物信息学分析及功能预测

利用NCBI和Phytozome数据库进行GmIDD基因的同源基因检索,获取该基因在大豆不同染色体中5个拷贝的序列信息。通过对功能结构域的分析结果显示GmIDD基因5个拷贝均含有2个C2H2型(72~92 aa、114~142 aa)、2个C2HC型(149~169 aa、176~195 aa)锌指结构域。GmIDD基因cDNA序列全长为1 227 bp,编码408个氨基酸。系统进化树分析结果显示GmIDD基因5个拷贝中除了Glyma.14g10940和Glyma.17G228000外,其它IDD蛋白间进化距离较远,表明不同大豆IDD基因在功能上可能存在一定差异。长短日照处理下GmIDD表达量的分析结果显示GmIDD基因受短日照诱导表达,因此推测GmIDD可能参与大豆开花的调控过程。     

水稻稻曲病菌G蛋白β亚基基因的克隆、表达与序列分析

水稻稻曲病是由稻绿核真菌[Ustilaginoidea virens(Cooke)Tak]引起的一种常见的水稻后期穂部病害。G蛋白可能参与了稻曲病菌的致病过程。为了研究G蛋白在病菌致病过程中的作用,分离并分析了稻曲菌的G蛋白β亚基编码基因。根据丝状真菌G蛋白β亚基编码基因的同源保守序列设计简并引物,采用同源克隆和热不对称交错PCR的方法,分离得到了稻曲菌的G蛋白β亚基全编码基因序列。该序列的长度为2037bp,包含4个内含子,5个外显子和1个编码359个氨基酸的开放阅读框。根据克隆到的UvGβ1设计引物,通过RT-PCR克隆到包含整个开放阅读框的cDNA序列。该基因的DNA序列和cDNA序列在GenBank中注册的登记号分别为GU014921和GU065745。系统进化分析表明该片段与栗疫病菌(Cryphonectria parasitica)的G蛋白β亚基基因亲缘关系最近。将该基因的整个开放阅读框连接于pET-30a构建原核表达载体,通过诱导获得了重组蛋白。     

Comparative Assessment of the Efficacy of Various Nitrogen Fertilizers

Summary

The efficiency of N fertilizers is usually poor; often less than 50% of the applied N is taken up by the crop. This review focuses on various N fertilizers with respect to the significance of different N loss pathways, namely (i) ammonia volatilization, (ii) dinitrogen and nitrogen oxide emissions, and (iii) nitrate leaching. Further, the significance of biological N immobilization, ammonium fixation and, finally, the impact of nitrate vs. ammonium uptake on crop yield are also discussed. The reviewed literature shows that N fertilizers may differ markedly in their susceptibility to losses. There is, however, considerable scope to improve N efficiency of each N source by proper N management practices.     

Studies on natural repellents against potato tuber moth (Phthorimaea operculella Zeller) in country stores

Summary The effects of the leaves of five plant species, one from each of the generaAmbrosia, Anemone, Eupatorium, Eucalyptus andLantana, on potato tuber moth were investigated under indigenous storage conditions at the Central Potato Research Station, Shillong (1800 m above sea level). Their action was compared with that of a biological insecticide (spores ofBacillus thuringiensis), a chemical insecticide (carbaryl), and an untreated control. The data collected after six months storage on tuber damage, sprout damage and the rotting indicated that the leaves ofLantana aculeata provided most protection to the tubers, reducing damage from over 70% in the check to below 5%, and sprout damage from over 45% to below 3%. Next best wasEucalyptus globulus followed byB. thuringiensis. They may be used on tubers stored for table use or for seed as they had no adverse effect on germination or on the yield of a subsequent crop.     

Mineral composition of some traditional Mexican teas

Teas of plant origin traditionally consumed by the Mountain Pima of Chihuahua, Mexico, were analyzed for mineral nutritional content. Fe, Cu, Zn, Ca, and Mg composition was determined for native teas made from shoots ofTagetes lucida, T. filifolia, Elytraria imbricata, andHolodiscus dumosus, and from root xylem ofCeanothus depressus andPhaseolus ritensis. Native uses of these teas are also described.     

Novel food and non-food uses for sorghum and millets

Sorghum and millets have considerable potential in foods and beverages. As they are gluten-free they are suitable for coeliacs. Sorghum is also a potentially important source of nutraceuticals such antioxidant phenolics and cholesterol-lowering waxes. Cakes, cookies, pasta, a parboiled rice-like product and snack foods have been successfully produced from sorghum and, in some cases, millets. Wheat-free sorghum or millet bread remains the main challenge. Additives such as native and pre-gelatinised starches, hydrocolloids, fat, egg and rye pentosans improve bread quality. However, specific volumes are lower than those for wheat bread or gluten-free breads based on pure starches, and in many cases, breads tend to stale faster. Lager and stout beers with sorghum are brewed commercially. Sorghum's high-starch gelatinisation temperature and low beta-amylase activity remain problems with regard to complete substitution of barley malt with sorghum malt . The role of the sorghum endosperm matrix protein and cell wall components in limiting extract is a research focus. Brewing with millets is still at an experimental stage. Sorghum could be important for bioethanol and other bio-industrial products. Bioethanol research has focused on improving the economics of the process through cultivar selection, method development for low-quality grain and pre-processing to recover valuable by-products. Potential by-products such as the kafirin prolamin proteins and the pericarp wax have potential as bioplastic films and coatings for foods, primarily due to their hydrophobicity.     

In vitro antimicrobial activity of different accessions ofSolanum commersonii Dun. from Uruguay

Summary The in vitro antimicrobial activity of extracts from accessions ofSolanum commersonii Dun. collected in the south of Uruguay was investigated against five microorganisms including the pathogenRalstonia solanacearum. A total of 30 extracts corresponding to organic and aqueous extracts were studied. Interestingly, most of the positive results for growth inhibition were againstR. solanacearum. The extracts were also analyzed for the presence of glycoalkaloids and lectins. Six of the ten aqueous extracts showed lectin presence and a wide variation in the type and amounts of glycoalkaloids, was found. Results indicate that there is no clear relationship between the antimicrobial activity against the five microorganisms screened and the presence or amounts of lectins and glycoalkaloids, traditionally regarded as possible antimicrobial metabolites in theSolanum genus, which indicates the presence of as yet unidentified antimicrobial compounds.     

Extreme resistance to infection by potato virus X in genotypes of wild tuber-bearingSolanum species

Summary Clones derived from thirty-one different accessions (nineteen of Argentine origin) belonging to eightSolanum species were screened for resistance to infection by potato virus X strain cp (PVX cp) by mechanical inoculation of plantlets that had been micropropagated in vitro. Estimates of PVX multiplication obtained by enzyme linked immunosorbent assay and slot blot nucleic acid hybridization allowed the identification of resistant clones derived from five accessions belonging toS. commersonii S. oplocense, S. sparsipilum andS. tuberosum andigena. Resistant genotypes supported PVX concentrations 5 to 15 times smaller than did the susceptible control cultivar Spunta. Graft inoculation test confirmed the presence of extreme resistance similar to that conferred by the ‘immunity’ gene X¹ (also called RX_act).     

Cyanobacteria Secondary Metabolites as Biotechnological Ingredients in Natural Anti-Aging Cosmetics: Potential to Overcome Hyperpigmentation,Loss of Skin Density and UV Radiation-Deleterious Effects

The loss of density and elasticity, the appearance of wrinkles and hyperpigmentation are among the first noticeable signs of skin aging. Beyond UV radiation and oxidative stress, matrix metalloproteinases (MMPs) assume a preponderant role in the process, since their deregulation results in the degradation of most extracellular matrix components. In this survey, four cyanobacteria strains were explored for their capacity to produce secondary metabolites with biotechnological potential for use in anti-aging formulations. Leptolyngbya boryana LEGE 15486 and Cephalothrix lacustris LEGE 15493 from freshwater ecosystems, and Leptolyngbya cf. ectocarpi LEGE 11479 and Nodosilinea nodulosa LEGE 06104 from marine habitats were sequentially extracted with acetone and water, and extracts were analyzed for their toxicity in cell lines with key roles in the skin context (HaCAT, 3T3L1, and hCMEC). The non-toxic extracts were chemically characterized in terms of proteins, carotenoids, phenols, and chlorophyll a, and their anti-aging potential was explored through their ability to scavenge the physiological free radical superoxide anion radical (O₂^•−), to reduce the activity of the MMPs elastase and hyaluronidase, to inhibit tyrosinase and thus avoid melanin production, and to block UV-B radiation (sun protection factor, SPF). Leptolyngbya species stood out for anti-aging purposes: L. boryana LEGE 15486 presented a remarkable SPF of 19 (at 200 µg/mL), being among the best species regarding O₂^•− scavenging, (IC₅₀ = 99.50 µg/mL) and also being able to inhibit tyrosinase (IC₂₅ = 784 µg/mL), proving to be promising against UV-induced skin-aging; L. ectocarpi LEGE 11479 was more efficient in inhibiting MMPs (hyaluronidase, IC₅₀ = 863 µg/mL; elastase, IC₅₀ = 391 µg/mL), thus being the choice to retard dermal density loss. Principal component analysis (PCA) of the data allowed the grouping of extracts into three groups, according to their chemical composition; the correlation of carotenoids and chlorophyll a with MMPs activity (p < 0.01), O₂^•− scavenging with phenolic compounds (p < 0.01), and phycocyanin and allophycocyanin with SPF, pointing to these compounds in particular as responsible for UV-B blockage. This original survey explores, for the first time, the biotechnological potential of these cyanobacteria strains in the field of skin aging, demonstrating the promising, innovative, and multifactorial nature of these microorganisms.     

Marine Pharmacology in 2009–2011: 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 peer-reviewed marine pharmacology literature from 2009 to 2011 is presented in this review, following the format used in the 1998–2008 reviews of this series. The pharmacology of structurally-characterized compounds isolated from marine animals, algae, fungi and bacteria is discussed in a comprehensive manner. Antibacterial, antifungal, antiprotozoal, antituberculosis, and antiviral pharmacological activities were reported for 102 marine natural products. Additionally, 60 marine compounds were observed to affect the immune and nervous system as well as possess antidiabetic and anti-inflammatory effects. Finally, 68 marine metabolites were shown to interact with a variety of receptors and molecular targets, and thus will probably contribute to multiple pharmacological classes upon further mechanism of action studies. Marine pharmacology during 2009–2011 remained a global enterprise, with researchers from 35 countries, and the United States, contributing to the preclinical pharmacology of 262 marine compounds which are part of the preclinical pharmaceutical pipeline. Continued pharmacological research with marine natural products will contribute to enhance the marine pharmaceutical clinical pipeline, which in 2013 consisted of 17 marine natural products, analogs or derivatives targeting a limited number of disease categories.