毛壳属真菌所致感染的系统性回顾

目的研究毛壳属真菌所致疾病及其菌种类型,了解其药敏状况。方法通过检索pubmed、万方数据库及中国期刊全文数据库中毛壳属真菌(Chaetomiumspp.)病例报告建立数据库进行描述性分析,时间限定为1983~2013年。结果共获得29篇文献,涉及35例患者。世界各地均有分布,以青中年为主,男性多于女性。侵袭性感染100%有基础疾病或存在诱发因素。感染涉及甲、皮肤、皮下组织、阴道、淋巴结、眼、鼻窦、耳部、肺、脑等组织和器官。浅部感染病程多呈慢性,治疗有效率66.67%。系统性感染预后较差,多数病例对两性霉素B不敏感,死亡率为85.71%。所有病例通过真菌培养确诊,多数病例组织病理中检测到真菌。侵袭性感染主要致病菌种分别为球毛壳(28.57%)、瘤突毛壳(21.43%)、暗褐毛壳(14.29%)及透亮毛壳(14.29%),浅表感染主要菌种为球毛壳(66.67%)。结论毛壳菌引起的感染类型广泛,不同部位毛壳菌感染临床表现不同,组织病理及反复真菌检查对确诊有重要帮助,特殊真菌感染需要引起临床工作者重视。     

球毛壳菌次级代谢产物及其生物活性研究进展

球毛壳菌(Chaetomium globosum)为属子囊菌纲、毛壳目、毛壳科丝状真菌,其在空气、土壤、植物和动物体中均有分布。已有研究表明,球毛壳菌的次生代谢产物种类多样、结构新颖,主要蕴含生物碱类、黄酮类、萜类、酯类等化合物,且多具抗肿瘤、抑菌、抗病毒等生物活性。本文综述了2015年以来所报道的球毛壳菌天然产物及其生物活性,为球毛壳菌真菌天然产物的研究奠定基础。     

葡萄孤儿基因的表达分析和功能推测

孤儿基因为某物种基因组内特有的,在其它物种内没有同源基因存在的特殊基因.对物种孤儿基因的鉴定和分析已成为比较基因组学研究的一个新兴领域.本研究通过生物信息学的分析,着重研究了49个葡萄孤儿基因在各发育阶段和各器官中的特异表达特性、亚细胞定位预测和共表达基因群的生物学过程基因本体论(GO)分析.结果显示,35个基因在NCBI的EST数据库中存在EST表达证据,其中有7个基因具有器官表达特异性,且大部分在生殖器官中特异表达.通过亚细胞定位预测到大部分葡萄孤儿基因为分泌蛋白.GO分析表明葡萄孤儿基因的共表达基因群主要参与寡肽转运和跨膜运输等生物学过程,这与葡萄孤儿基因的亚细胞定位预测结果相一致.本文研究结果将为葡萄孤儿基因的进一步功能分析提供重要研究基础.     

关于保留球毛壳与橄榄色毛壳作为不同种的见解

球毛壳(Chaetomium globosum Kze.)系 Kunze 于1817年报道见于丹麦石竹(Dianthus carthusianorum L.)茎上的毛壳菌属(Chaetomium)的第一个种(模式种)。Cooke and Ellis 在1878年描述了见于飞蓬属(Erigeron L.)腐茎上的橄榄色毛壳(C.oliaceum C.et E.)。在 Chivers(1915)、Skolko and Groves(1953)、Udagawa(1960)、Ames(1963)和 Seth(1972)关于毛壳菌属的专著都曾指出很难划分这两个种的界限。Skolk and Groves(1953)区分此两个种时以橄榄色毛壳具有较大的子囊壳、较宽的顶附属丝和较大的子囊孢子,而 Chivers(1915)则认为橄榄色毛壳是球毛壳的异名,Udagawa(1960)区分此两个种仅根据子囊孢子的长度和宽度,他认为橄榄色毛壳的子囊孢子大于球毛壳的子囊孢子。Seth(1972)在他的专著中虽保留此两个种作为独立种,但他指出限于他镜检过的标本材料及根据 Chivers 专著中的球毛壳的特征辑要概括了橄榄色毛壳的特征,对这两个种的区分界限确实是很难划分的。最近我们在北京采集和分离了来源于不同的植物和动物材料上的毛壳菌种类,以期进行北京地区毛壳菌种类调查研究。我们分离获得许多球毛壳——橄榄色毛壳类的毛壳菌菌株。参考了不同作者对这两个种的子囊壳、顶附属丝、侧附属丝、子囊及子囊孢子的特征记载,对北京的这一类型菌株进行了细致研究,认为球毛壳与橄榄色毛壳确有形态学特征区别,表现在橄榄色毛壳的子囊壳、顶附属丝和子囊孢子较球毛壳的更为粗壮,兼之球毛壳的顶附属丝较橄榄色毛壳的为窄且有分隔和微粗糙,球毛壳的子囊孢子呈浅橄榄褐色至暗橄榄褐色,含两个折光性油滴而橄榄色毛壳的子囊孢子呈暗橄榄褐色,量度亦较大,凭依经验即可鉴别此两个不同种。     

球毛壳菌降解天然木质纤维素能力差异及酶系基因分析

目的:以不同植物中分离到的4株内生球毛壳菌NK102、NK103、NK104和NK105为对象,研究不同生态来源球毛壳菌降解木质素和纤维素的能力。方法:首先采用羧甲基纤维素和纤维素刚果红平板检测各菌株的纤维素降解能力,并利用Bavendamm平板反应检测各菌株的木质素降解能力;将4株菌分别培养在以微晶纤维素、杨树叶和木屑为惟一碳源的液体培养基中,通过检测培养液中纤维素酶和漆酶的酶活力,比较各菌株分解利用天然木质纤维素材料的能力,连续培养12 d后检测培养液中次级代谢产物的合成情况;利用已测序的球毛壳菌CBS148.51的基因组信息,寻找编码木质纤维素降解酶类的基因,为球毛壳菌分解利用木质纤维素提供分子生物学依据。结果:NK102、NK103、NK104和NK105在羧甲基纤维素培养基和纤维素刚果红培养基上都能够生长并形成水解圈;Bavendamm平板反应显示4株菌降解木质素的能力由强到弱依次是NK103、NK102、NK105和NK104。4株菌都能分解利用微晶纤维素、杨树叶和木屑,分泌纤维素酶和漆酶,其中NK102在以木屑为碳源的培养基上纤维素酶活力最强,达到0.76 U/mL发酵液,NK103在以杨树叶为碳源的培养基上漆酶活力最强。与此同时,4株菌在发酵培养过程中都能够稳定地合成球毛壳甲素(ChA),ChA产量受到碳源影响,在以杨树叶为碳源的培养基上,NK104的ChA产量最高,可达到14.88 mg/L发酵液。利用已测序的球毛壳菌CBS148.51的基因组信息,寻找到119个编码纤维素半纤维素酶的基因、8个编码漆酶的基因和2个编码锰过氧化物酶的基因,球毛壳菌具有完整的降解纤维素半纤维素的酶体系,在木质纤维素降解真菌的开发过程中具有重要的研究价值。结论:本研究为球毛壳菌木质纤维素降解过程的研究及该菌种的开发利用奠定了基础。     

利用EST序列构建Mascot本地数据库

对蛋白质质谱数据进行数据库比对和鉴定是蛋白质组学研究技术中的一个重要步骤。由于公共数据库蛋白质数据信息不全,有些蛋白质质谱数据无法得到有效的鉴定。而利用相关物种的EST序列构建专门的质谱数据库则可以增加鉴定未知蛋白的几率。本文介绍了利用EST序列构建Mascot本地数据库的具体方法和步骤,扩展了Mascot检索引擎对蛋白质质谱数据的鉴定范围,从数据库层面提高了对未知蛋白的鉴别几率,为蛋白质组学研究提供了一种较为实用的生物信息学分析技术。     

生物信息学数据库调查分析及其利用研究

从生物信息学数据库利用的角度调查分析生物信息学数据库的现状,为我国科研人员利用网上生物信息学数据库以及生物信息中心的开发提供科学依据和参考价值。研究采用网上调查的方法,对法国生物信息中心Infobiogen建立维护的生物信息学数据库目录DBcat中收录的511个数据库进行调查统计,分析其类型分布、国家分布、更新频率和获取方式;在此基础上。进一步利用欧洲分子生物学信息网(EMBnet)中30个成员国节点对生物信息学数据库利用现状进行统计分析。     

球毛壳菌降解天然木质纤维素能力差异及酶系基因分析简

目的：以不同植物中分离到的4株内生球毛壳菌NK102、NK103、NK104和NK105为对象,研究不同生态来源球毛壳菌降解木质素和纤维素的能力。方法：首先采用羧甲基纤维素和纤维素刚果红平板检测各菌株的纤维素降解能力,并利用Bavendamm平板反应检测各菌株的木质素降解能力;将4株菌分别培养在以微晶纤维素、杨树叶和木屑为惟一碳源的液体培养基中,通过检测培养液中纤维素酶和漆酶的酶活力,比较各菌株分解利用天然木质纤维素材料的能力,连续培养12d后检测培养液中次级代谢产物的合成情况;利用已测序的球毛壳菌CBS148．51的基因组信息,寻找编码木质纤维素降解酶类的基因,为球毛壳菌分解利用木质纤维素提供分子生物学依据。结果：NK102、NK103、NK104和NK105在羧甲基纤维素培养基和纤维素刚果红培养基上都能够生长并形成水解圈;Bavendamm平板反应显示4株菌降解木质素的能力由强到弱依次是NK103、NK102、NK105和NK104。4株菌都能分解利用微晶纤维素、杨树叶和木屑,分泌纤维素酶和漆酶,其中NK102在以木屑为碳源的培养基上纤维素酶活力最强,达到0．76U/mL发酵液,NK103在以杨树叶为碳源的培养基上漆酶活力最强。与此同时,4株菌在发酵培养过程中都能够稳定地合成球毛壳甲素（ChA）,ChA产量受到碳源影响,在以杨树叶为碳源的培养基上,NK104的ChA产量最高,可达到14．88mg/L发酵液。利用已测序的球毛壳菌CBS148．51的基因组信息,寻找到119个编码纤维素半纤维素酶的基因、8个编码漆酶的基因和2个编码锰过氧化物酶的基因,球毛壳菌具有完整的降解纤维素半纤维素的酶体系,在木质纤维素降解真菌的开发过程中具有重要的研究价值。结论：本研究为球毛壳菌木质纤维素降解过程的研究及该菌种的开发利用奠定了基础。     

球毛壳菌循环肽HC-毒素基因的序列分析

为了验证Phrap软件是否适合在EST分析中应用,对球毛壳菌循环肽HC-毒素基因进行了序列分析。根据EST分析的结果,从cDNA文库中挑取循环肽HC-毒素基因的克隆进行了测序并序列分析。结果表明cDNA文库中循环肽HC-毒素基因的克隆插入片断大小为1217bp;用Phrap软件拼接出来的循环肽HC-毒素的表达序列标签拼接序列与实际序列不完全一致,因此Phrap软件不适合在EST分析中应用。     

球毛壳菌对植物病原真菌和根结线虫的生物防治潜力

球毛壳菌(Chaetomium globosum)隶属于子囊菌门、核菌纲、粪壳菌目、毛壳菌科、毛壳菌属真菌,广泛分布于空气、土壤等多种自然环境中,也是植物最常见的内生真菌之一。球毛壳菌能产生种类繁多的次级代谢产物,且其次级代谢产物具有抗真菌和杀线虫等多种生物活性,因而被制作成杀菌剂和杀线虫剂等生物农药,对植物病原真菌和根结线虫(Meloidogyne spp.)有良好的生物防治潜力。本文从球毛壳菌及其次级代谢产物抗植物病原真原菌和杀根结线虫两个方面进行综述,并探讨球毛壳菌对植物病原真菌的生防机制,为植物病原真菌及根结线虫的综合治理和新型生物农药的开发提供参考。     

SimHap GUI: An intuitive graphical user interface for genetic association analysis

Background

The expressed sequence tag (EST) methodology is an attractive option for the generation of sequence data for species for which no completely sequenced genome is available. The annotation and comparative analysis of such datasets poses a formidable challenge for research groups that do not have the bioinformatics infrastructure of major genome sequencing centres. Therefore, there is a need for user-friendly tools to facilitate the annotation of non-model species EST datasets with well-defined ontologies that enable meaningful cross-species comparisons. To address this, we have developed annot8r, a platform for the rapid annotation of EST datasets with GO-terms, EC-numbers and KEGG-pathways.

Results

annot8r automatically downloads all files relevant for the annotation process and generates a reference database that stores UniProt entries, their associated Gene Ontology (GO), Enzyme Commission (EC) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) annotation and additional relevant data. For each of GO, EC and KEGG, annot8r extracts a specific sequence subset from the UniProt dataset based on the information stored in the reference database. These three subsets are then formatted for BLAST searches. The user provides the protein or nucleotide sequences to be annotated and annot8r runs BLAST searches against these three subsets. The BLAST results are parsed and the corresponding annotations retrieved from the reference database. The annotations are saved both as flat files and also in a relational postgreSQL results database to facilitate more advanced searches within the results. annot8r is integrated with the PartiGene suite of EST analysis tools.

Conclusion

annot8r is a tool that assigns GO, EC and KEGG annotations for data sets resulting from EST sequencing projects both rapidly and efficiently. The benefits of an underlying relational database, flexibility and the ease of use of the program make it ideally suited for non-model species EST-sequencing projects.     

Increasing genomic information in bivalves through new EST collections in four species: development of new genetic markers for environmental studies and genome evolution

The generation of EST information is an essential step in the genomic characterisation of species. In the context of the European Network Marine Genomics, a common goal was to significantly increase the amount of ESTs in commercial marine mollusk species and more specifically in the less studied but ecologically and commercially important groups, such as mussel and clam genera. Normalized cDNA libraries were constructed for four different relevant bivalves species (Crassostrea gigas, Mytilus edulis, Ruditapes decussatus and Bathymodiolus azoricus), using numerous tissues and physiological conditions. In this paper, we present the analysis of the 13,013 expressed sequence tags (ESTs) generated. Each EST library was independently assembled and 1300-3000 unique sequences were identified in each species. For the different species, functional categories could be assigned to only about 16 to 27% of ESTs using the GO annotation tool. All sequences have been incorporated into a publicly available database and form the basis for subsequent microarray design, SNP detection and polymorphism analysis, and the placement of novel markers on genetic linkage maps.     

Unix下EST数据库本地化更新及序列预处理分析

利用FreeBSD操作系统的文本过滤命令将NCBI的Genbank数据库的EST序列实现本地化导入到MySQL数据库中并能够进行更新,这利于对不同物种不同组织器官基因表达的分析。以水稻EST数据为例,对EST序列两端出现的polyA/T和载体序列亦进行了鉴别及去除,经过预处理的EST序列数据将为进一步进行EST聚类及基因表达分析提供可靠的保证。     

Mining and comparative survey of EST–SSR markers among members of Euphorbiaceae family

Euphorbiaceae represents flowering plants family of tropical and sub-tropical region rich in secondary metabolites of economic importance. To understand and assess the genetic makeup among the members, this study was undertaken to characterize and compare SSR markers from publicly available ESTs and GSSs of nine selected species of the family. Mining of SSRs was performed by MISA, primer designing by Primer3, while functional annotation, gene ontology (GO) and enrichment analysis were performed by Blast2GO. A total 12,878 number of SSRs were detected from 101,701 number of EST sequences. SSR density ranged from 1 SSR/3.22 kb to 1 SSR/15.65 kb. A total of 1873 primer pairs were designed for the annotated SSR-Contigs. About 77.07% SSR–ESTs could be assigned a significant match to the protein database. 3037 unique SSR–FDM were assigned and IPR003657 (WRKY Domain) was found to be the most dominant FDM among the members. 1810 unique GO terms obtained were further subjected to enrichment analysis to obtain 513 statistically significant GO terms mapped to the SSR containing ESTs. Most frequent enriched GO terms were, GO:0003824 for molecular function, GO:0006350 for biological process and GO:0005886 for cellular component, justifying the richness of defensive secondary metabolites and phytomedicine within the family. The results from this study provides tangible insight to genetic make-up and distribution of SSRs. Functional annotation corresponded many genes of unknown functions which may be considered as novel genes or genes responsible for stress specific secondary metabolites. Further studies are required to understand stress specific genes accountable for leveraging the synthesis of secondary metabolites.     

Gene Ontology term overlap as a measure of gene functional similarity

Background  

The availability of various high-throughput experimental and computational methods allows biologists to rapidly infer functional relationships between genes. It is often necessary to evaluate these predictions computationally, a task that requires a reference database for functional relatedness. One such reference is the Gene Ontology (GO). A number of groups have suggested that the semantic similarity of the GO annotations of genes can serve as a proxy for functional relatedness. Here we evaluate a simple measure of semantic similarity, term overlap (TO).