滨麦叶片转录组分析

滨麦（Leymus mollis）是小麦的野生近缘种,具有良好的耐盐抗旱和抗病虫害的能力,是小麦遗传育种的良好资源。为了深入了解和挖掘滨麦的基因信息和优异资源,本研究利用高通量测序技术对生长于滨海沙地的野生滨麦的叶片转录组进行了深度测序并组装,对得到的所有Unigene进行COG、GO和KEGG分类和功能注释,对Na⁺转运相关蛋白基因和氧化胁迫响应基因进行了挖掘,并通过实时荧光定量反转录PCR（qRT-PCR）对随机选取的12个基因的表达模式进行了验证。结果显示,转录组测序共获得112 846条Unigene,其中的59 380条得到功能注释,占总数的52.62%。COG分类结果表明,15 786条Unigene归属于25个类别。GO分类结果表明,20 350条Unigene被注释到三个大类中,其中,属于“生物学过程”的Unigene数量最多,占总数的43.56%。KEGG分析结果表明,18 550条Unigene得到注释,共涉及到128条代谢途径。其中,含Unigene数量最多的类别是“代谢通路”,涉及到的Unigene占总数的27.86%。“植物病原互作”和“植物激素信号转导途径”涉及的Unigene数量也较多,分别为1 367条和861条。对Na⁺转运相关蛋白基因和氧化胁迫响应基因进行挖掘,发现了15条注释为Na⁺/H⁺反向转运蛋白的Unigene和175条响应氧化胁迫的Unigene。随机选取的12个基因的qRT-PCR结果与转录组测序结果基本一致。     

剑麻与烟草疫霉互作过程中的转录组研究

斑马纹病是剑麻的主要病害之一,为了挖掘剑麻斑马纹病抗病相关基因,以斑马纹病抗病品种热麻1号为材料,分别在接种0、24、36、48和72 h进行转录组测序,组装后获得103 326个转录本和70 110个Unigenes,转录本和Unigene的平均长度分别为726 bp和645 bp。其中有33 474个Unigenes被成功注释到NR,NT,KO,Swissport等7个功能数据库中。DEG分析表明,在接种24、36、48、72 h后分别有4 676、3 769、3 308、3 757个Unigenes被诱导差异表达,且PR蛋白,类黄酮生物合成、苯丙素类生物合成、过氧化物酶等基因上调表达明显,而热击蛋白、细胞色素P450和叶绿素a/b结合蛋白等基因明显下调表达。差异基因代谢通路分析表明,参与核糖体、光合作用、苯丙素类生物合成、苯丙氨酸代谢通路、植物激素信号转导途径、类黄酮生物合成途径、脂肪酸生物合成途径等代谢通路明显富集。本研究全面了解剑麻与烟草疫霉互作关系,是为剑麻斑马纹病抗病机制研究提供理论基础。     

基于转录组测序的火龙果果肉不同发育时期淀粉和蔗糖代谢途径相关基因差异表达分析

采用Illumina Novaseq 6000测序技术对火龙果果肉3个时期（幼果期、转色期、成熟期）的样品进行转录组测序,对获得的Unigene进行7大数据库注释,共有3617个Unigene成功注释在所有数据库中,进一步筛选与淀粉和蔗糖代谢途径相关的5个酶基因并进行实时荧光定量PCR（qPCR）基因表达验证。结果表明：转录组测序共得到115 193条转录本和47 855条Unigene,N50为2000。GO功能富集分析结果表明,18 582个Unigene在GO功能注释中被分为生物过程、细胞组成及分子功能3大类。KOG功能分类结果表明,6203个Unigene在KOG注释中被分为25个组,其中翻译后修饰、蛋白质周转、伴侣包含的Unigene最多,共854个。KEGG代谢通路注释结果表明,6554个Unigene获得功能注释,共有119条代谢途径,其中碳水化合物代谢所占比例最高。筛选出UGP2、glgC、glgA、Cluster-12747.5831、Cluster-12747.16617等5个参与淀粉和蔗糖代谢合成途径的关键酶基因,qPCR检测表达水平与转录组测序结果一致。     

软腐病菌侵染下菜心叶片的转录组分析

为探讨软腐病菌侵染下菜心转录组功能基因信息,采用BGISEQ-500高通量测序技术对软腐病菌侵染下菜心叶片进行转录组测序,平均每个样获得47.27 M clean reads,Q20值均大于95%,共检测到表达的Unigene为36 760个,其中已知的有35 327个,预测新Unigene有1 433个;共检测出19 549个新转录本,其长度主要集中在300~2000 nt。功能注释结果显示,有32 047个Unigene在Nr数据库获得注释,其中注释到芸薹属白菜上的Unigene最多;GO功能共注释到12 588个Unigene;KEGG数据库注释到18 583个Unigene,涉及到137个代谢通路。共获得21 776个组间差异表达基因（differential expression genes, DEGs）,其中对照与发病前期组间的DEGs有15 007个,6 137个上调表达,8 870个下调表达;发病前期与发病中期组间DEGs有13 118个,10 278个上调表达,2 840个下调表达;发病中期与发病后期组间DEGs有11 293个,1 790个上调表达,9 503个下调表达。DEGs的Ven图分析显示5 110个基因在每组间均存在差异,DEGs功能分析显示DEGs参与泛素蛋白降解途径、过氧化物酶体途径、光合碳固定途径、糖酵解途径等多种生命活动。本研究结果为深入开展菜心抗软腐病基因组学和分子生物学研究奠定基础。     

茶树叶片响应茶饼病侵染的转录组分析

采用高通量测序技术对被茶饼病病菌侵染的茶树叶片进行转录组测序,筛选得到差异基因359个,其中248个上调表达,111个下调表达。差异基因中有216个获得GO（Gene ontology）数据库功能注释,主要涉及到生物合成过程、催化活性、细胞过程等诸多生理生化过程;KEGG（Kyoto encyclopedia of genes and genomes）数据库富集分析发现,共有106个基因被注释到47个代谢通路中,其中,单萜生物合成、卟啉和叶绿素代谢、核糖体、氮代谢、双萜生物合成、植物病原互作等通路显著富集。有32个差异基因被鉴定为转录因子,分布在16个转录因子家族中。利用实时荧光定量PCR（Real time quantitative PCR,qRT-PCR）验证了随机挑选的差异基因在感病叶片和未感病叶片中的相对表达量,与转录组测序结果的变化趋势一致。结果表明,茶树响应病原菌侵染是一个复杂的过程,大量基因被诱导或抑制表达,与抗病相关的转录因子被大量激活且上调表达。本研究为深入挖掘茶树抗病基因及进一步研究抗病分子机制提供了理论依据。     

大豆胞囊线虫侵染诱导五寨黑豆早期的转录组分析

利用Illumina Hi SeqTM2000对大豆胞囊线虫侵染前后的抗病大豆品种五寨黑豆的转录组进行检测。将测序的两个文库进行拼接,得到长度大于200bp的reads共20 980 831条,总长度约为4.23Gb,筛选到1 045个差异表达基因。Gene ontology功能显著性富集发现差异表达基因在生物过程注释基因最多,共有1 007个差异表达基因。在COG数据库中对基因产物进行直系同源分类,结果表明众多基因参与到碳水化合物及氨基酸的运输和代谢、次生代谢物质合成及信号传导机制过程,并受胞囊线虫侵染的诱导表达。KEGG代谢通路分析显示差异表达基因在苯丙烷类及氧化磷酸化代谢通路显著富集,说明这两个代谢通路在五寨黑豆抗胞囊线虫病中起重要作用。     

丁香假单胞菌变种Pto(AvrB)胁迫下大豆叶片转录组分析

AvrB是丁香假单胞杆菌大豆致病变种分泌的Ⅲ型效应蛋白因子之一,为研究携带异源效应蛋白AvrB的丁香假单胞菌番茄致病变种Pto(AvrB)侵染大豆后的基因转录变化情况,以大豆Williams 82为试验材料,采用RNA-seq技术对不同菌株处理的大豆叶片进行基因表达谱差异分析,探索大豆非寄主病原菌Pseudomonas syringae pv.tomato携带的异源效应蛋白AvrB是否可以增加非寄主病原菌的致病性。结果显示:共得到43 422个序列信息,不同处理间共有序列为37 611个,其中Pto(AvrB)处理组的序列信息最多。根据GO功能分析可以将基因根据功能分为分子功能、细胞成分和生物学过程3类,其差异表达基因涉及信息传递、免疫、次生代谢等过程。KEGG通路富集分析表明,差异表达基因主要富集在植物激素信号转导、异黄酮生物合成、苯丙氨酸代谢、植物-病原体相互作用等通路中。在RT-PCR检测中发现4个随机挑选的差异表达基因的表达量与RNA-Seq的变化趋势一致,说明RNA-Seq的结果可靠。研究结果有助于阐明Ⅲ型效应蛋白因子促进病原菌致病效应的机理,从而为分析AvrB在病原菌与大豆互作过程中的毒性功能研究和培育抗病大豆品种提供依据。     

茉莉酸和乙烯信号转导途径参与花生应答果腐病病原菌侵染的转录组测序分析（英文）

花生果腐病是花生生产上的一种重要病害,对花生的产量和品质构成了严重威胁。本研究以花育20号感病前后籽仁为样品,进行转录组测序,得到Unigene 60 756个,其中表达量上调的基因10 147个,下调的基因4 334个;GO富集分析表明,差异表达基因被分类到24种细胞组分、5种分子功能和23种生物过程中;KEGG富集分析发现有4 291个差异基因被注释到34条代谢通路中。筛选得到多条花生响应果腐病相关的激素信号转导途径,通过分析相关基因的表达图谱,推测花生可能通过JA/ET介导的抗病途径来抵抗果腐病病原菌的侵染。     

水稻WRKY转录因子基因家族响应外源一氧化氮的表达谱分析

一氧化氮(nitric oxide,NO)信号分子与WRKY转录因子均参与植物抗逆、发育与代谢等许多生理过程。采用Agilent水稻全基因组cDNA芯片分析了NO处理后1、6和12h水稻幼苗WRKY转录因子基因的表达谱,鉴定出在1个时间点有两倍或两倍以上表达变化的WRKY基因32个,主要分布在WRKY的Ⅰ和Ⅱ组,其中75%的Ⅱa和45.6%的Ⅱd亚组成员为差异表达基因;鉴定出至少在2个时间点有两倍或两倍以上表达变化的WRKY基因15个,均为早期(1h)应答,且多数(64.2%)持续上调;基因功能预测分析表明,这些基因主要参与生物学过程中的细胞过程、代谢过程和刺激响应,以及分子功能中的转录调节活性和结合;代谢通路分析表明,WRKY24涉及植物与病原菌相互作用代谢通路。实时荧光定量PCR验证结果与芯片杂交结果基本一致,印证了芯片杂交结果的有效性。上述发现提示,NO信号可能参与了WRKY转录因子介导的生物学调控功能,并为这些基因的进一步功能分析奠定基础。     

亚麻芥未成熟胚中磷脂酶基因家族的转录组学分析

为了解磷脂酶基因家族在亚麻芥胚中的表达情况,本研究基于454测序技术对亚麻芥花后10d（DAF10）和花后20d（DAF20）的胚中磷脂酶基因家族进行筛选和分析。测序结果表明,DAF10样本和DAF20样本分别获得有效序列521 507个和310 125个,序列长度主要分布在341~560 bp,序列组装分别获得25 398个和23 678个Unigene,Unigene平均长度分别为630 bp和654 bp。在此基础上,筛选两个样本全部Unigene,共获得磷脂酶基因36个,其中属于磷脂酶A1基因4个、磷脂酶A2基因9个、磷脂酶C基因10个、磷脂酶D基因13个。Pathway基因功能注释显示,PLA1的4个候选基因没有注释到任何代谢通路上;PLA2中只有候选基因Unigene19110被成功注释,它在植物中主要参与甘油磷脂代谢途径和醚酯代谢途径。PLC家族中只有4个候选成员Unigene443、Unigene8071、Unigene8213和Unigene7311被成功注释,它们除参与甘油磷脂代谢和醚酯代谢之外,还在肌醇磷酸代谢途径中发挥重要作用。而PLD家族中除Unigene18630、Unigene17966和Unigene441没有代谢通路注释信息外,其他的10个成员,也都只在甘油磷脂代谢途径和醚酯代谢途径有作用。     

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.     

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.     

Recent Modifications of Chitosan for Adsorption Applications: A Critical and Systematic Review

Chitosan is considered to be one of the most promising and applicable materials in adsorption applications. The existence of amino and hydroxyl groups in its molecules contributes to many possible adsorption interactions between chitosan and pollutants (dyes, metals, ions, phenols, pharmaceuticals/drugs, pesticides, herbicides, etc.). These functional groups can help in establishing positions for modification. Based on the learning from previously published works in literature, researchers have achieved a modification of chitosan with a number of different functional groups. This work summarizes the published works of the last three years (2012–2014) regarding the modification reactions of chitosans (grafting, cross-linking, etc.) and their application to adsorption of different environmental pollutants (in liquid-phase).