沉香叶解剖结构的研究

通过石蜡切片法,光学显微镜观察,研究了沉香叶的解剖结构。结果表明,沉香叶为典型的异面叶,但具有许多旱生特征。表皮由一层排列紧密的形状不规则的表皮细胞组成,细胞外壁角质膜较厚,上表皮角质膜较下表皮的厚3.48μm,下表皮上零星分布着单细胞表皮毛,气孔类型为无规则型,仅分布在下表皮上,微下陷;叶肉组织发达,其间分布着较多的长方晶体,其长轴与表皮垂直;栅栏组织由1～2层圆柱形细胞组成,其外层细胞转化为异细胞,栅栏组织∶海面组织为1∶3.5,下表皮内具有1～2层由异细胞组成的下皮层;主脉发达,有异细胞组成的维管束鞘,具内生韧皮部;叶内具有发达的木质部外纤维。以上特征反映出植物结构与环境的统一性。     

Aquillochin,a coumarinolignan from Aquilaria agallocha

Aquillochin, isolated from the whole plant of Aquilaria agallocha, has been shown to be a coumarinolignan, and a structure has been proposed on the basis of chemical and physical studies.     

REAPR: a universal tool for genome assembly evaluation

Methods to reliably assess the accuracy of genome sequence data are lacking. Currently completeness is only described qualitatively and mis-assemblies are overlooked. Here we present REAPR, a tool that precisely identifies errors in genome assemblies without the need for a reference sequence. We have validated REAPR on complete genomes or de novo assemblies from bacteria, malaria and Caenorhabditis elegans, and demonstrate that 86% and 82% of the human and mouse reference genomes are error-free, respectively. When applied to an ongoing genome project, REAPR provides corrected assembly statistics allowing the quantitative comparison of multiple assemblies. REAPR is available at http://www.sanger.ac.uk/resources/software/reapr/.     

Agarol,a new sesquiterpene from Aquilaria agallocha

The isolation of two sesquiterpenes, gmelofuran and agarol, from Aquilaria agallocha is described Gmelofuran has not been previously reported from this genus and the structure of agarol has been elucidated by physical methods and chemical reactions.     

白木香内生真菌的分离及分子鉴定

对采自广东省信宜市的白木香进行了内生真菌分离培养,共获得50个菌株,通过rDNA中内转录间隔区(ITS)序列鉴定其为20个种,其中确定至种名的有7属8种,仅确定至属名的有8种,不能确定种属的有4种,其中A20菌株(Fimetariella rabenhorstii)为国内首次报道。刺盘孢菌(Colletotrichum)共分离到17株,占分离总数的34%,为白木香优势种群;镰刀菌(Fusarium)共分离到11株,是结香部位的优势种群。白木香内生真菌分布部位的专一性不明显,茎中分离的数量及种类最多,叶中最少;5年龄内生真菌的多样性较好,10月龄的多样性较低。     

Profiling of MicroRNAs under Wound Treatment in Aquilaria sinensis to Identify Possible MicroRNAs Involved in Agarwood Formation

Agarwood, a kind of highly valued non-timber product across Asia, is formed only when its resource trees -- the endangered genus Aquilaria are wounded or infected by some microbes. To promote the efficiency of agarwood production and protect the wild resource of Aquilaria species, we urgently need to reveal the regulation mechanism of agarwood formation. MicroRNAs (miRNAs) are a group of gene expression regulators with overwhelming effects on a large spectrum of biological processes. However, their roles in agarwood formation remain unknown. This work aimed at identifying possible miRNAs involved in the wound induced agarwood formation. In this study, the high-throughput sequencing was adopted to identify miRNAs and monitor their expression under wound treatment in the stems of A. sinensis. The miR171, miR390, miR394, miR2111, and miR3954 families remained at the reduced level two days after the treatment. 131 homologous miRNAs in the 0.5 h library showed over three-fold variation of read number compared with the control library, of which 12 exhibiting strong expression alterations were further confirmed by real-time quantitative PCR. Target prediction and annotation of the miRNAs demonstrated that the binding, metabolic process, catalytic activity, and cellular process are the most common functions of the predicted targets of these newly identified miRNAs in A.sinensis. The cleaveage sites of three newly predicted targets were verified by 5''RACE.     

Effect of cucurbitacins on bilirubin-albumin binding in human plasma

The aim of this study is to investigate the effect of three cucurbitacins (Cuc) E, D and I on the bilirubin-albumin binding, both in human serum albumin (HSA) and in plasma. Bilirubin-HSA solution and plasma free of cucurbitacins were prepared as well as others containing serial concentrations of cucurbitacins. The concentration of unbound bilirubin was determined in bilirubin-HSA solution and the direct and total bilirubin concentrations were measured in plasma (with normal or elevated bilirubinemia) by Jendrassik and Grof method. In the conditions we adopted Cuc E and D (to a lesser extent), decreased the levels of unbound bilirubin in bilirubin-HSA solution and decreased direct bilirubin concentration and total bilirubin concentration in plasma in a dose-dependent manner while Cuc I had no effect. The effect of Cuc is related to the presence of native HSA. Thus, when albumin was absent or has been denatured by heating or by urea, Cuc E did not modify bilirubin levels, suggesting that the native structure of albumin is essential for such activity. The interaction of HSA with Cuc E was investigated by fluorescence spectroscopy. Cuc E increased the intrinsic fluorescence of the protein and the magnitude of fluorescence intensity of bilirubin-albumin complex. We concluded that Cuc E and D produced a rearrangement in the structure of albumin, particularly in the domain-II, resulting in an increase in the binding of bilirubin to albumin regardless to whether it's conjugated to glucuronic acid or unconjugated.     

印度沉香的组织培养和快速繁殖

1植物名称印度沉香(Aquilaria agallocha). 2材料类别种子长成的无菌苗的顶芽. 3培养条件 (1)种子萌发培养基:1/2MS;(2)丛生芽诱导培养基:MS 6-BA 0.1 mg·L-1(单位下同);(3)芽伸长培养基:MS 6-BA 0.05;(4)生根培养基:1/2MS.上述培养基均附加3%蔗糖、0.8%琼脂,pH 5.8.培养温度为(26±1)℃,光照12h·d-1,光照度2 000 lx.     

CGAL: computing genome assembly likelihoods

Assembly algorithms have been extensively benchmarked using simulated data so that results can be compared to ground truth. However, in de novo assembly, only crude metrics such as contig number and size are typically used to evaluate assembly quality. We present CGAL, a novel likelihood-based approach to assembly assessment in the absence of a ground truth. We show that likelihood is more accurate than other metrics currently used for evaluating assemblies, and describe its application to the optimization and comparison of assembly algorithms. Our methods are implemented in software that is freely available at http://bio.math.berkeley.edu/cgal/.     

1株白木香内生真菌中抗肿瘤活性成分的分离纯化和结构鉴定

采用活性追踪的方法对白木香内生真菌螺旋木霉Trichoderma spiraleA17的抗肿瘤活性代谢产物进行了分离纯化和结构鉴定。通过凝胶柱层析和反相硅胶柱层析,从其发酵液的活性组分中分离到2个无色针晶化合物,质谱和核磁共振的鉴定结果表明化合物1是一个八氢萘衍生物,命名为木霉酸(Trichodermic acid),化合物2是酪醇(Tyrosol)。活性实验显示化合物1对SF-268、MCF-7和NCI-H460 3种肿瘤细胞株都具有显著的增殖抑制活性,而化合物2对这3种肿瘤细胞株只有微弱的增殖抑制活性。     

一株源自孔雀的新型支原体的鉴定及其致病性和基因组分析

【背景】Mycoplasma gallinaceum (MGC)是禽源支原体的一种,仅在南非、英国等地发生,我国鲜有报道。【目的】从患呼吸道病的孔雀气管中分离到一株支原体,命名为Peacock20181011,确定其分类、致病性和基因组特征。【方法】利用微生物学常规方法,结合分子生物学检测和基因组序列,对其进行鉴定;通过对Special pathogenic free(SPF)鸡、鸡胚的致病性研究和最小抑菌浓度(minimal inhibitory concentration,MIC)测定,确定其致病性和药敏性。【结果】通过对分离菌的培养、纯化、形态学和染色观察,结合生化试验和16SrRNA基因测序证实,该菌为一株新的MGC,与模式菌株NCTC10183的16S rRNA基因相似性高达99.86%,系统发育树显示该菌与MGC属同一分支;人工感染实验表明该菌对SPF鸡无致病性,但可造成SPF鸡胚发育迟缓,爪部蜷缩;MIC结果显示该菌对单硫酸卡那霉素和氟苯尼考等敏感。基因组序列表明,该菌基因组长度为1 183 913 bp,(G+C)mol%含量为28.7%,含有898个Coding sequences (CDS),拥有4个拷贝的16S rRNA基因和6个质粒,预测有20个毒力因子基因和2个耐药基因。【结论】明确了MGC在我国的存在,丰富了中国禽源支原体的种类,为支原体病的防控提供了依据。     

白木香内生真菌的分离鉴定及其抑菌活性

从白木香Aquilaria sinensis（Lour．）Gilg木质部的树脂形成部位和健康部位中共分离获得42株内生真菌,经初步鉴定,产孢的33株分属于3目4科7属,其余未产孢的9株暂归为无孢菌群。采用杯碟法和MTT法分别测定了各菌株的发酵上清液对3种病原菌的体外抑菌活性和2种肿瘤细胞的体外细胞毒活性。结果表明,白木香木质部健康部位内生真菌以枝顶孢霉属为优势属,而树脂形成部位的内生真菌种类比健康部位要多,且以青霉属为优势属。其中26株至少能抑制一种指示菌,占总数的61．9％;7株对指示瘤株具有细胞毒活性,占总数的16．7％。抑菌活性菌株主要分布在枝顶孢霉属和青霉属。枝顶孢霉属菌株抑菌活性较强,其抗菌活性成分值得进一步研究。     

栽培沉香遗传多样性的ISSR和AFLP分析比较

探讨2种分子标记技术在沉香属药用植物遗传多样性研究中的应用。用ISSR和AFLP分子标记分析了海南、云南、广东、广西等地17份沉香属植物的遗传多样性。14个ISSR引物、8对AFLP引物分别检测到119、919个位点,多态位点百分率分别为73.95%、86.94%。由于AFLP标记具有较高的多态性位点检测效率,AFLP标记分析的遗传多样性参数高于ISSR。虽然基于Nei’s遗传距离的聚类分析结果存在着一定的差异,但用Mantel检测对两种方法检测的遗传一致度进行相关性分析表明,它们之间存在着明显的相关性（r=0.7705,P=0.0003）。ISSR标记与AFLP标记均能应用于沉香属植物的遗传多样性研究。两种标记的研究结果均揭示出沉香属植物具有较高的遗传多样水平。     

白木香树干中的黄酮类成分

从白木香[Aquilaria smensis(Lour.)Gilg]树干的乙醇提取物中分离得到5个黄酮类化合物,经波谱分析,分别鉴定为:洋芹素-7,4'-二甲醚(1)、5-羟基-7,3',4'-三甲氧基黄酮(2)、木犀草素-7,4'-二甲醚p)、芫花素(4)和4',5-二羟基-3',7-二甲氧基黄酮(5).以上化合物均为首次从该种植物树干中分离得到.     

几种提取白木香茎干总RNA方法的比较

目的:通过比较多种RNA提取方法,确定白木香茎干RNA提取的有效手段,为白木香伤害形成沉香药材的分子研究奠定基础。方法:取2年生白木香茎,分别用CTAB法、TRIzol法、异硫氰酸胍-SDS法、Qiagen试剂盒和Nor gen试剂盒法提取总RNA,通过琼脂糖凝胶电泳和紫外分光光度法测定其产量与质量,并通过cDNA合成及小样本克隆测序检查RNA的可用性。结果:异硫氰酸胍-SDS法及Norgen试剂盒法提出的RNA条带清晰,完整性好;D260nm/D280nm值可达2.0左右,纯度较高,其产量足够应用于cDNA合成;其他方法不能提出RNA。结论:异硫氰酸胍-SDS法及Norgen试剂盒法可用于白木香茎干RNA提取。     

白木香内生真菌枝顶孢属两菌株的挥发油成分

采用溶剂萃取法提取白木香内生真菌R1(Acremonium sp.)和R2(Acremonium sp.)的挥发油, 经GC-MS联用技术进行分析, 从R1和R2的挥发油中分别鉴定出20个和16个成分, 均以油酸、亚油酸、棕榈酸等脂肪酸为主要成分, 并且均含有1,8-桉叶油素、姜烯、芳姜黄烯等萜类成分。本研究首次报道白木香内生真菌的挥发油成分。     

Acetone utilization by sulfate-reducing bacteria: draft genome sequence of Desulfococcus biacutus and a proteomic survey of acetone-inducible proteins

Background

The sulfate-reducing bacterium Desulfococcus biacutus is able to utilize acetone for growth by an inducible degradation pathway that involves a novel activation reaction for acetone with CO as a co-substrate. The mechanism, enzyme(s) and gene(s) involved in this acetone activation reaction are of great interest because they represent a novel and yet undefined type of activation reaction under strictly anoxic conditions.

Results

In this study, a draft genome sequence of D. biacutus was established. Sequencing, assembly and annotation resulted in 159 contigs with 5,242,029 base pairs and 4773 predicted genes; 4708 were predicted protein-encoding genes, and 3520 of these had a functional prediction. Proteins and genes were identified that are specifically induced during growth with acetone. A thiamine diphosphate-requiring enzyme appeared to be highly induced during growth with acetone and is probably involved in the activation reaction. Moreover, a coenzyme B₁₂- dependent enzyme and proteins that are involved in redox reactions were also induced during growth with acetone.

Conclusions

We present for the first time the genome of a sulfate reducer that is able to grow with acetone. The genome information of this organism represents an important tool for the elucidation of a novel reaction mechanism that is employed by a sulfate reducer in acetone activation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-584) contains supplementary material, which is available to authorized users.     

白木香遗传多样性研究

用ISSR分子标记技术对白木香(Aquilaria sinensis(Lour.)Gilg)的遗传多样性进行分析.结果表明,白木香物种水平的遗传多样性较高,而居群水平的遗传多样性相对较低,其中广东茂名居群的遗传多样性最高.白木香居群间存在较大的遗传分化,遗传分化系数G_(ST)=0.4425,表明居群内遗传分化大于居群间的分化.UPGMA聚类分析表明白木香分化为两个谱系,其中谱系Ⅰ由广东、福建、海南的5居群组成,谱系Ⅱ由广西、云南的3个居群组成.居群间的基因交流受到阻碍(Nm=0.6633<1),阻碍主要产生于两个谱系间,而谱系内部的居群间在较近的历史时期基因交流频繁(Nm分别为1.4382和1.2333),谱系分化的原因主要是地理因素,两谱系交界处有云开山脉等形成的天然屏障,阻碍物种的扩展和基因交流.