聚类分析在黄霉素发酵过程中的应用

【目的】将聚类分析的方法应用于黄霉素摇瓶发酵条件的优化过程中。【方法】通过系统聚类算法、K均值聚类算法和模糊C均值聚类算法对不同批次黄霉素发酵的摇瓶数据的聚类分析进行比较,发现模糊C均值聚类算法优于其他聚类算法,确定了以模糊C均值聚类算法对黄霉素摇瓶发酵数据进行聚类分析。【结果】然后利用模糊C均值聚类算法选取优质组样本,并利用优质样本优化了黄霉素摇瓶发酵的控制参数分布范围。【结论】这充分证明了聚类分析在发酵过程的优化过程中有良好的实用性。     

中国东方蜜蜂的形态分化(英文)

【目的】遗传分化研究是认识蜜蜂形态多样性和适应性进化的重要环节,是确定蜜蜂资源管理单位和保护单位的前提,有助于保护蜜蜂的遗传资源。本研究通过分析形态分化,研究中国东方蜜蜂Apiscerana在中国地理环境下的遗传分化和遗传资源分布。【方法】从我国所有东方蜜蜂分布区102个采样点共采集6 147头东方蜜蜂工蜂,每一采样点10~20群中取60头工蜂进行解剖,测定与翅、个体大小、后足和体色相关的33个形态特征,进行多变量形态统计分析,划分形态类群。同时对分出的不同东方蜜蜂类群的形态特征及分布模式进行分析。【结果】根据判别分析和主成分分析的聚类结果,我国东方蜜蜂分为14个形态类群。有5个类群具有较小的个体大小。海南类群个体最小,其次为滇南类群,台湾类群,南方类群和北方类群。这5个类群之间在吻长、前翅长、前翅第3亚缘室结构、体色和蜡镜长上存在显著差异。长白类群具有最大的肘脉指数、蜡镜和第5背板绒毛带宽。而西藏波密类群具有全国最小的第五背板绒毛带宽。西北类群具有最长的后足。川西高原的5个形态类群具有个体大、体色黑等特点。其中,巴塘类群肘脉指数(3.0169)全国最小,个体大小全国最大。阿坝类群具有仅次于长白类群的肘脉指数,且翅长和第七腹板最大。德荣类群体色最黑。雅江类群具有独特的翅脉角 (A4, N23, E9和J10最小,B4最大)。川滇类群在川西高原个体最小。【结论】本研究在全面收集我国所有东方蜜蜂分布区样本,尤其是西藏波密、台湾省和川西高原的珍贵样本的基础上,进行了东方蜜蜂形态测量学分析。在我国共发现东方蜜蜂14个形态类群：海南类群、滇南类群、长白类群、台湾类群、波密类群、阿坝类群、巴塘类群、德荣类群、雅江类群、川滇类群、川贵类群、西北类群、南方类群以及北方类群。研究结果为中国东方蜜蜂遗传资源的保护和遗传资源的开发利用提供理论基础。     

气孔在四季秋海棠营养器官和繁殖器官上的发育及相关性分析

主要观察了气孔在四季秋海棠营养器官和繁殖器官上的分布和发育情况,并分别对叶片和翅上气孔簇大小、气孔簇密度等指标的相关性进行了研究、结果表明:在叶片的下表皮、雌花和雄花的花被片、苞片、小苞片和翅上有气孔分布,而在茎、花梗上却未见气孔分布.叶片下表皮和翅上气孔通常成簇分布.在叶片的下表皮,气孔簇大小与气孔簇密度呈显著的负相关(P<0.05);气孔簇密度与叶片长度呈极显著的负相关(P<0.01).而翅上的气孔簇密度、气孔簇大小与子房长度无显著相关性(P>0.05).在四季秋海棠中,不同器官表皮的气孔簇大小是不同的,这可能与生理功能的不同有关.     

Asp97 is a crucial residue involved in the ligation of the [Fe4S4] cluster of IscA from Acidithiobacillus ferrooxidans

IscA was proposed to be involved in the ironsulfur cluster assembly encoded by the iscSUA operon, but the role of IscA in the iron-sulfur cluster assembly still remains controversial. In our previous study, the IscA from A. ferrooxidans was successfully expressed in Escherichia coli, and purified to be a [Fe4S4]-cluster-containing protein. Cys35, Cys99, and Cys101 were important residues in ligating with the [Fe4S4] cluster. In this study, Asp97 was found to be another ligand for the iron-sulfur cluster binding according to sitedirected mutagenesis results. Molecular modeling for the IscA also showed that Asp97 was a strong ligand with the [Fe4S4] cluster, which was in good agreement with the experimental results. Thus, the [Fe4S4] cluster in IscA from A. ferrooxidans was ligated by three cysteine residues and one aspartic acid.     

Biochemical characterization of iron-sulfur cluster assembly in the scaffold IscU of Escherichia coli

Iron-sulfur cluster is one of the most common prosthetic groups, and it functions in numerous biological processes. However, little is currently known about the mechanisms of iron-sulfur cluster biosynthesis. In this study, we cloned and purified iron-sulfur cluster assembly proteins from Escherichia coli and assembled the cluster in vitro. The results showed that the assembly of iron-sulfur cluster is completed in about 20 min. Although iron or sulfur binds with IscU equivalently, 2-fold amount of iron or cysteine compared with that of IscU is better for the cluster formation, while high concentrations of IscS (IscS/IscU > 1: 10) do not facilitate the cluster formation. Environmental pH plays an important role in iron-sulfur cluster assembly; the cluster was well assembled at pH 7.6–8.0, but was inhibited at pH less than 7.4. On supply of a catalytic amount of IscS (1/50 of IscU) and excess of other substrates, with increasing each of IscU, iron, or cysteine concentration, the iron-sulfur cluster assembly process developed from first order reaction, mixed order reaction to zero order reaction, and up to 64% of apo-IscU was converted to the [2Fe-2S] cluster-bound IscU under the optimal laboratory conditions.     

Heterologous production of bisucaberin using a biosynthetic gene cluster cloned from a deep sea metagenome

A siderophore biosynthetic gene cluster was cloned from a metagenomic library generated from deep sea sediment. The gene cluster was successfully expressed in Escherichia coli to produce bisucaberin, a siderophore originally reported from the marine bacterium Alteromonas haloplanktis. The cloned bisucaberin biosynthetic gene cluster was moderately similar to that of the known bisucaberin producer Vibrio salmonicida. However, the cloned gene cluster consists of four genes rather than three genes found in the V. salmonicida cluster. The low overall homology of the amino acid and nucleotide sequences with those of other species suggests that the cloned genes were derived from one of the unsequenced bacteria including uncultured species.     

Diverse and unique picocyanobacteria in Chesapeake Bay, revealed by 16S-23S rRNA internal transcribed spacer sequences

rRNA internal transcribed spacer phylogeny showed that Chesapeake Bay is populated with diverse Synechococcus strains, including members of the poorly studied marine cluster B. Marine cluster B prevailed in the upper bay, while marine cluster A was common in the lower bay. Interestingly, marine cluster B Synechococcus included phycocyanin- and phycoerythrin-rich strains.     

对似近分析的一点改进及其拓广

本文给出了似近分析一个重要的改进,并将改进的似近分析推广为m维似近分析,同时给出了两个数学定理及其证明。根据多维似近系数的数学性质,提出了一种新的聚类方法,即逐步多维聚类法。实例分析证明,这种聚类法比二维系数聚类优越,聚类功能强,所获得的结果更为客观。     

The IscA from Acidithiobacillus ferrooxidans is an iron-sulfur protein which assemble the [Fe4S4] cluster with intracellular iron and sulfur

IscA was proposed to be involved in the iron-sulfur cluster assembly in Acidithiobacillus ferrooxidans encoded by the iscSUA operon, but the role of IscA in the iron-sulfur cluster assembly still remains controversial. In this study, the IscA from A. ferrooxidans ATCC 23270 was successfully expressed in Escherichia coli, and purified by affinity chromatography to homogeneity. To our surprise, the purified IscA was observed to be an iron-sulfur protein according to MALDI-TOF-MS and spectra results, which was capable of recruiting intracellular iron and sulfur and hosted a stable [Fe4S4] cluster. Site-directed mutagenesis for the protein revealed that Cys35, Cys99 and Cys101 were in ligating with the [Fe4S4] cluster. The [Fe4S4] cluster could be assembled in apoIscA with Fe2+ and sulfide in vitro. The IscA from A. ferrooxidans may function as a scaffold protein for the pre-assembly of Fe-S cluster and then transfer it to target proteins in A. ferrooxidans.     

Oxidation-reduction properties of the iron-sulfur cluster in Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase

Native Bacillus subtilis glutamine phosphoribosylpyrophosphate amidotransferase contains a [4Fe-4S] cluster in the diamagnetic (+2) state. The cluster is essential for catalytic function, even though amidotransferase does not catalyze a redox reaction. The ability of the Fe-S cluster to undergo oxidation and reduction reactions and the consequences of changes in the redox state of the cluster for enzyme activity were studied. Treatment of the enzyme with oxidants resulted in either no reaction or complete dissolution of the Fe-S cluster and loss of activity. A stable +3 oxidation state was not detected. A small amount of paramagnetic species, probably an oxidized 3Fe cluster, was formed transiently during oxidation. The native cluster was poorly reduced by dithionite, but it could be readily reduced to the +1 state by photoreduction with 5-deazaflavin and oxalate. The reduced enzyme did not display an EPR spectrum typical of [4Fe-4S] ferredoxins in the +1 state, unless it was prepared under denaturing conditions. M?ssbauer spectroscopy of reduced 57Fe-enriched amidotransferase confirmed that the cluster was in the +1 state, but the magnetic properties of the reduced cluster observed at 4.2 K indicated that it is characterized by a ground state spin S greater than or equal to 3/2. The midpoint potential of the +1/+2 couple was too low to measure accurately by conventional techniques, but it was below -600 mV, which is 100 mV more negative than reported for [4Fe-4S] clusters in bacterial ferredoxins. Fully reduced amidotransferase had about 40% of the activity of the native enzyme in glutamine-dependent phosphoribosylamine formation. The fact that both the +1 and +2 forms of the enzyme are active indicates that the cluster does not function as a site of reversible electron transfer during catalysis.     

The urbilaterian Super-Hox cluster

Comparison of whole genome sequences of representative animals enables reconstruction of the ancestral bilaterian genome: the starting point from which most extant animal lineages evolved. The Hox gene cluster patterns the anterior-posterior axis of bilaterians. Here we show that this cluster was embedded within a larger homeobox gene cluster, the Super-Hox cluster, in the ancestral bilaterian. This Super-Hox cluster contained at least eight genes alongside the core Hox genes ('EuHox' genes).     

Characterization of a gene cluster and its putative promoter region for violacein biosynthesis in Pseudoalteromonas sp. 520P1

Violacein, a purple pigment produced by some Gram-negative bacteria, has various physiological properties, such as antitrypanosomal and antitumoral activities. A gene cluster that encodes five enzymes, VioA-VioE, is responsible for synthesizing violacein. The expression of these enzymes is known to be regulated by a quorum sensing mechanism in Chromobacterium violaceum and Pseudoalteromonas sp. 520P1. To clarify the molecular mechanism of regulation of violacein synthesis, we cloned and characterized the gene cluster from Pseudoalteromonas sp. 520P1. A fosmid library of strain 520P1 was constructed and clones containing the gene cluster were isolated. The gene cluster was 7383?bp in length and encoded five enzyme genes, vioA-vioE. A putative promoter sequence was predicted in the upstream region of the cluster. In the promoter region, two contiguous palindromic sequences, a possible quorum sensing regulatory site, were found. However, the isolated Escherichia coli clones harboring the gene cluster and its upstream region were unable to produce violacein probably due to the lack of quorum sensing machinery for expression. To further examine the ability of vioA-vioE genes to synthesize violacein in vivo, the upstream promoter region was removed from the cluster and heterologous expression of the treated cluster was performed in E. coli using a recombinant pET vector with T7 promoter. Purple pigment was expressed, and the pigment was identified to be violacein using ultraviolet and visible light and HPLC analysis. These results will contribute to further studies regarding violacein biosynthesis and its mass production.     

Factors affecting formation of cluster roots in Myrica gale seedlings in water culture

The effect of nutrient deficiency, aeration, phosphorus supply, and nitrogen source on the formation of cluster (proteoid) roots was examined in Myrica gale seedlings growing in water culture. Only the omission of phosphorus resulted in the formation of significant numbers to cluster roots when plants were grown in a number of 1/4 strength Hoagland's solutions, each lacking one mineral nutrient. Aeration shortened the time required for cluster root formation and increased the percentage of plants forming cluster roots. The proportion of the root system comprised of cluster roots decreased as the phosphorus concentration in the solution increased and no cluster roots formed in solutions containing 8 mg P/L. Phosphorus supply also affected total plant biomass, proportion of biomass comprising nitrogen-fixing nodules, shoot:root ratio, phosphorus concentration in the leaves and phosphorus content of the plants. The plants showed luxury consumption of phosphorus and were able to produce large amounts of biomass utilizing only stored phosphorus.Nitrogen source also affected cluster root formation. Urea-fed plants produced cluster roots more quickly and devoted a substantially larger proportion of root growth to cluster roots than did nitrate-fed plants. The longest cluster root axes were produced in nitrate-fed plants supplied with no phosphorus and the shortest were in urea-fed plants at 4 mg P L^–1.Four methods for expressing the extent of cluster root formation were examined and it was concluded that cluster roots as a proportion of total fine root dry weight is preferable in many cases. Formation of cluster roots in response to phosphorus deficiency coupled with previously demonstrated traits allows Myrica gale to adapt to a wide range of soil conditions.     

DIATOM ASSOCIATIONS IN YAQUINA ESTUARY,OREGON: A MULTIVARIATE ANALYSIS1

A cluster analysis and a principal components analysis were performed to examine the degree to which the diatom flora of Yaquina estuary can be partitioned into discrete associations and to relate the composition of the flora to selected physical properties of the estuary. The species composition of the diatom flora during the winter was more closely associated with salinity and intertidal exposure them in the summer. A cluster of freshwater taxa obtained for the winter data was the most conspicuous diatom association defined by the cluster analysis. Although taxa within a cluster had more similar distributions than taxa from different clusters, there was considerable variation in the distributions of marine and brackish water taxa within a multispecies cluster.     

Secreted acid phosphatase is expressed in cluster roots of lupin in response to phosphorus deficiency

The roots of white lupin (Lupinus albus L. cv. Kievskij mutant) secrete acid phosphatase, S-APase, when they grow under conditions of low available phosphorus (P). S-APases hydrolyze organic phosphate compounds in the rhizosphere and supply inorganic phosphate to the plants. Low phosphorus availability also induces vigorous growth of cluster roots. In this study, the function of cluster roots was investigated with reference to S-APase secretion. White lupins were grown in hydroponic culture in a greenhouse under P-deficient and P-sufficient conditions. S-APase in the excised roots after treatment was detected by staining with 4-methylumbelliferone phosphate (MUP). Gene expression of S-APase in cluster and normal roots was also investigated. Activity was greatest in the roots of plants grown under conditions of P -deficiency, particularly in cluster roots. S-APase gene expression was induced by a decrease in internal P concentrations, and was especially high in cluster roots formed under conditions of P -deficiency. It was suggested that decrease of internal P concentration stimulated both of the S-APase expression and cluster root formation.     

Cloning and sequencing of clustered genes involved in fatty acid biosynthesis from the docosahexaenoic acid-producing bacterium, Vibrio marinus strain MP-1

A cluster of genes involved in fatty acid biosynthesis (fab) was isolated from docosahexaenoic acid (DHA)-producing Vibrio marinus strain MP-1. This fab gene cluster included five genes highly homologous to the Escherichia coli counterparts, and their order in the cluster was the same with that of the E. coli fab gene cluster except that the latter included the additional fabH gene. These fab genes should be involved in early steps of DHA biosynthesis in V. marinus strain MP-1.     

基因型值多次聚类法构建作物种质资源核心库

采用合适的遗传模型无偏预测基因型值,用基因型值进行聚类分析,采用马氏距离计算遗传材料间的遗传距离,并用不加权类平均法（ＵＰＧＭＡ）进行聚类,根据树型图,从遗传变异相似的每组二个遗传材料中随机选取一个遗传材料,如组内只有一个遗传材料,则选取该遗传材料,对所取的所有遗传材料再次聚类、取样,直至所取遗传材料的数量为总遗传的２０％￣３０％,这些遗传材料作迷为核心聚类。用方差同质性测验、均值ｔ测验评核心资源