固定化黄孢原毛平革菌对邻苯二甲酸 二乙酯的降解效果研究

以白腐真菌的模式菌种-黄孢原毛平革菌作为研究对象,探究固定化黄孢原毛平革菌对邻苯二甲酸二乙酯(DEP)的降解效果及其最佳降解条件.研究表明,固定化黄孢原毛平革菌相对于游离态菌体能产生较高活性的木质素过氧化物酶(Li P)和锰过氧化物酶(Mn P).DEP降解效果受固定化菌体接种量、p H值、温度和DEP初始浓度等因素的影响.当p H为6,温度为35℃,DEP初始浓度为10 mg/L时,加入8 g固定化黄孢原毛平革菌时,DEP去除效果最好,其去除率达到94.6%.     

愈创木酚与复合碳源共降解对黄孢原毛平革菌产酶的影响

通过正交实验法,研究愈创木酚与复合碳源共降解对黄孢原毛平革菌产酶的影响,同时探讨不同分子结构对酶催化机制的影响。实验结果表明:同时添加愈创木酚及不同结构的碳源对该菌产酶有显著影响,高浓度的愈创木酚对产酶有明显的促进作用;在培养基中添加愈创木酚2 mmol/L、葡萄糖2.5 g/L和糊精5 g/L,可以显著提高黄孢原毛平革菌的综合产酶能力;黄孢原毛平革菌可以分泌纤维素酶和木聚糖酶,而且二者之间有较好的线性正相关关系。     

真核原核两界细胞融合子SEM形态

报道应用扫描电子显微镜（SEM）、测定跨界融合Fhhh细胞形态的结果。Fhhh由2株真菌真核细胞与1株细菌原核细胞的原生质体融合而成。2株真菌是黄孢原毛平革菌和酿酒酵母，1株细菌是从对苯二甲酸废水活性污泥中筛选获得的土细菌。3个亲株菌体细胞SEM的形态差异极为显，既不同于黄孢原毛平革菌与土细胞的首次跨界融合获得的Fhh，也不同于Fhh与酿酒酵母的2次跨界融合获得的Fhhh。经过350多代的繁殖传代。Fhhh仍然同时含有来自3亲株的基因DNA，具有分子遗传稳定性。研究结果表明，跨界原生质体融合是一种快速有效的构建基因工程菌的生物技术。     

白腐菌相容菌株的筛选及其混合培养产酶

在纤维素筛选培养基中加入了黄孢原毛平革菌稻草固态发酵的浸提液,并用这种培养基直接从自然环境中筛选了与黄孢原毛平革菌相容的菌株,在PDA和MEA平板上进行了进一步的相容性测试,选择出了生长稳定、可以与黄孢原毛平革菌较好共存的6株真菌.然后,对它们进行了固态发酵产酶的研究.对发酵体系中滤纸酶活(FPA)、木素过氧化物酶(L iP)、锰过氧化物酶(MnP)和漆酶(Lac)活力的测定结果表明,这种筛选出来的菌株组合可以部分增强酶的活性,完善体系中胞外酶的组成,其中编号为F05的菌效果最好,它在混合培养时,体系中的FPA和Lac都得到了加强,比单独培养F05和P.C.时的酶活分别提高了55.5%,24.1%和217%,146%.     

培养条件对黄孢原毛平革菌降解稻草的研究

在固态培养条件下研究培养条件对黄孢原毛平革菌降解稻草的影响．实验结果表明：黄孢原毛平革菌降解稻草的最适温度为32℃,最佳时间为24d．通过正交试验确定,对稻草降解影响的营养成分中,苯甲醇最好,使稻草总量降低了0．107％,木质素、纤维素和半纤维素的降解量分别提高了3．285％、0．304％,2．123％;依次为谷氨酸、缓冲液、吐温-80、发酵剂,最后是MnSO4．     

跨界融合子Fhhh降解PTA废水mnp基因转录研究

报道Fhhh的遗传稳定性，及其降解精对苯二甲酸（PTA）废水过程中基因转录的研究结果。聚合酶链式反应PCR的测定结果是，Fhhh同时含有mnp(来自黄孢原毛平革真菌）、FL01（来自酿酒酵母真菌）和16SrDNA(来自土细菌）的3个亲株的基因DNA片断。表明Fhhh具有分子遗传稳定性。反转录－扩增（RT－PCR）的测定表明，Fhhh的黄孢原毛平革菌在降解PTA废水过程，在Mn^2 、Cu^2 、Zn^2 、Se^4 4种金属元素优化水平的条件下，mnp基因均可转录。研究结果为高效处理PTA废水，增添了分子遗传学的调控途径。     

木质纤维原料生产燃料乙醇技术路线研究

分析木质纤维原料转化为燃料乙醇过程存在的障碍。结合国内外最新研究进展,提出杏鲍菇栽培-乙醇生产、黄孢原毛平革菌液态发酵预处理-乙醇生产、白蚁酶降解-乙醇生产3条潜在可行技术路线。     

黄孢原毛平革菌锰过氧化物酶基因（MnP2）的克隆

应用RT-PCR技术,从黄孢原毛平革菌5.766（Phanerochaete chrysosporium）总RNA中成功扩增出预期大小约为1.3 kb的特异性条带,将扩增产物提纯后克隆入PUC19载体,经转化、筛选及酶切鉴定后,获得锰过氧化物酶（MnP2）基因的克隆。序列分析表明,扩增的MnP2基因片段其cDNA长度为1 149 bp,编码358个氨基酸,与其它已发表文献报道的MnP2序列一致,与其同工酶MnP1和MnP3的核苷酸同一性分别为81%和66%。     

鼠李糖脂对两株木质素降解菌产酶能力的影响

研究了生物表面活性剂鼠李糖脂对黄孢原毛平革菌、简青霉产木质素降解酶能力的影响．结果表明,鼠李糖脂对酶活性的影响与鼠李糖脂的浓度、投加形式、菌种及酶的种类有关．0．0065％的鼠李糖脂不同程度地促进了黄孢原毛平革菌产LiP,MnP,简青霉产LiP,漆酶,0．013％的鼠李糖脂可以促进黄孢产LiP,简青霉产漆酶,但却明显抑制了另外两种酶的活性;鼠李糖脂可以使简青霉产MnP的高峰期提前,但不能提高酶活性．通过影响产酶能力,鼠李糖脂使两株菌对木质素的降解率均高于对照样．此外,接种鼠李糖脂产生菌——铜绿假单胞菌的效果达到甚至超过添加鼠李糖脂的促进效果．     

培养条件对甲醇毕赤酵母异源表达木质素过氧化物酶的影响

对含有黄孢原毛平革菌木质素过氧化物酶基因(LipH8)的甲醇毕赤酵母培养基和发酵方法进行了研究．摇瓶培养条件研究结果表明:用11°Bx麦芽汁培养工程菌,然后用高温浸提液置换诱导产酶较好．5 L发酵罐产酶放大实验结果表明,木质素过氧化物酶较稳定,在72 h木质素过氧化物酶酶活达到最高7 568 U/L．     

基于unix的cDNA序列自动分析系统的构建和应用

基于unix/linux操作系统和mysql数据库 ,利用phred/phrap ,stackpack ,blast软件 ,对cDNA和EST序列进行大规模自动分析。它可以完成从测序峰图文件向核酸序列的转化 ,去除载体污染和重复序列 ,序列聚类 ,拼接 ,分析可变剪切 ,数据库搜索进行相似性分析。该系统可以加速大规模EST测序的分析速度。     

Discovery of immune related factors in Fenneropenaeus chinensis by annotation of ESTs

A total of 10446 expressed sequence tags (ESTs) are obtained by a large-scale sequencing of a cDNA library from cephalothorax of adult Fenneropenaeus chinensis.An EST analysis platform was built up based on local computers and bioinformatic techniques were used to annotate these ESTs in order to promptly find possible functional genes, especially for immune related factors.About 4% of the ESTs show similarity to the coding sequences of such factors, including lectin, serine protease, serpin, lysozyme, etc.These ESTs provide a partial profile of the immune system in F.chinensis and useful information for further study on these genes.     

Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates.

Horizontal gene transfer (HGT) has long been recognized as a principal force in the evolution of genomes. Genome sequences of Archaea and Bacteria have revealed the existence of genes whose similarity to loci in distantly related organisms is explained most parsimoniously by HGT events. In most multicellular organisms, such genetic fixation can occur only in the germ line. Therefore, it is notable that the publication of the human genome reports 113 incidents of direct HGT between bacteria and vertebrates, without any apparent occurrence in evolutionary intermediates, that is, non-vertebrate eukaryotes. Phylogenetic analysis arguably provides the most objective approach for determining the occurrence and directionality of HGT. Here we report a phylogenetic analysis of 28 proposed HGT genes, whose presence in the human genome had been confirmed by polymerase chain reaction (PCR). The results indicate that most putative HGT genes are present in more anciently derived eukaryotes (many such sequences available in non-vertebrate EST databases) and can be explained in terms of descent through common ancestry. They are, therefore, unlikely to be examples of direct HGT from bacteria to vertebrates.     

大规模GO注释的生物信息学流程

随着新一代测序技术的不断发展,海量的序列数据将为生物学研究者挖掘基因信息提供巨大的资源.信息挖掘的一项重要工作是对序列进行功能注释,其中最重要的功能注释方式是基因本体论( Gene Ontology,GO)的注释.利用生物信息学方法和软件工具集成了针对EST序列的大规模GO注释流程(large-scale GO annotation pipeline,LSGAP).该流程集合了BLAST、B2g4pipe以及Wego等软件和Swissprot、Nr或Interpro等常用蛋白数据库.用户可以将EST序列通过此流程最终获得可视化的GO分类统计图表,直观地显示基因在不同过程中的参与情况.为了验证LSGAP的准确性,对2007年发表的美洲牡蛎(Crassostrea Virginica)的EST序列进行了LSGAP分析,结果表明GO分析非常准确有效.通过与Blast2go和GoBlast等GO注释软件进行比较,LSGAP流程具有可以本地化运行BLAST、对硬件要求低和运行时间短等诸多优势,因此LSGAP流程是科研人员进行基因功能挖掘的有效工具.     

杨树泛基因组构建与基因组变异分析

【目的】杨树是重要的速生用材、生态防护和碳汇造林树种,也是林木遗传研究的模式树种。开展杨树泛基因组构建与基因组变异分析,可为杨树精准育种和林木泛基因组研究提供理论先导。【方法】 以公开发表的高质量杨树基因组序列为基础,分析不同类型的序列变异,总结变异特征,并构建基于基因和图形结构的杨树泛基因组。【结果】 本研究收集到8个杨属树种和3个二倍体或三倍体杨树杂交品种的基因组序列,3个杂交品种包含7个单倍型亚基因组序列,较好地代表了杨树4个组派的基因组特征。分析结果表明,杨树基因组间存在较多大的结构变异。在基于基因的泛基因组中,共线核心基因、非共线核心基因、次核心基因、非必需基因、特异基因占比分别为12.5%、34.9%、31.4%、16.5%、4.7%。其中,非必需基因在功能上具有较高的多样性。以基因组序列变异为基础构建杨树图形结构泛基因组,大幅提升2代测序数据的变异检测效果。通过泛基因组变异热点分析,鉴定出2个与物候关联的基因位点。【结论】 杨属基因组中存在大量染色体重排,进而增加了基因调控的多样性。杨树组/派间的基因组结构变异可能与物候适应存在关联。基于林木基因组序列的复杂性,在林木泛基因组研究中应注意基因组整合范围与研究目标相匹配,结合基因泛基因组和图形结构泛基因组结果,综合解析林木的遗传变异规律和物种演化特征。     

Numerous potentially functional but non-genic conserved sequences on human chromosome 21

The use of comparative genomics to infer genome function relies on the understanding of how different components of the genome change over evolutionary time. The aim of such comparative analysis is to identify conserved, functionally transcribed sequences such as protein-coding genes and non-coding RNA genes, and other functional sequences such as regulatory regions, as well as other genomic features. Here, we have compared the entire human chromosome 21 with syntenic regions of the mouse genome, and have identified a large number of conserved blocks of unknown function. Although previous studies have made similar observations, it is unknown whether these conserved sequences are genes or not. Here we present an extensive experimental and computational analysis of human chromosome 21 in an effort to assign function to sequences conserved between human chromosome 21 (ref. 8) and the syntenic mouse regions. Our data support the presence of a large number of potentially functional non-genic sequences, probably regulatory and structural. The integration of the properties of the conserved components of human chromosome 21 to the rapidly accumulating functional data for this chromosome will improve considerably our understanding of the role of sequence conservation in mammalian genomes.     

Genome-scale approaches to resolving incongruence in molecular phylogenies

One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets, such as individual genes. To systematically investigate the degree of incongruence, and potential methods for resolving it, we screened the genome sequences of eight yeast species and selected 106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation. Our results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies. By contrast, analyses of the entire data set of concatenated genes yielded a single, fully resolved species tree with maximum support. Comparable results were obtained with a concatenation of a minimum of 20 genes; substantially more genes than commonly used but a small fraction of any genome. These results have important implications for resolving branches of the tree of life.     

Identification of true EST alignments and exon regions of gene sequences

Expressed sequence tags (ESTs), which have piled up considerably so far, provide a valuable resource for finding new genes, disease-relevant genes, and for recognizing alternative splicing variants, SNP sites, etc. The prerequisite for carrying out these researches is to correctly ascertain the gene-sequence-related ESTs. Based on analysis of the alignment results between some known gene sequences and ESTs in public database, several measures including Identity Check, Gap Check, Inclusion Check and Length Check have been introduced to judge whether an EST alignment is related to a gene sequence or not. A computational program EDSAcl.0 has been developed to identify true EST alignments and exon regions of query gene sequences. When tested with human gene sequences in the standard dataset HMR195 and evaluated with the standard measures of gene prediction performance, EDSAel.0 can identify proteincoding regions with specificity of 0.997 and sensitivity of 0.88 at the nucleotide level, which outperform that of the counterpart TAP. A web server of EDSAcl.0 is available at http://infosci.hust.edu.cn.     

水稻基因组中U2snRNA基因连锁的分析

根据Ｕ２ｎＲＮＡ基因的保守性和结构特点设计引物,通过ＰＣＲ法扩增Ｕ２ｓｎＲＮＡ连锁基因间区的ＤＮＡ片段并进行顺序分析,证实在水稻中至少存在一组Ｕ２ｓｎＲＮＡ连锁基因。对水稻总ＤＮＡ的ＰＣＲ分析结果表明,水稻中可能还存在其他形式的连锁基因。ＰＣＲ方法可以有效地应用于结构保守基因的连锁分析中。