Fermentation analysis by clustering

To supervise, stabilize and optimize antibiotic fermentations in the industrial scale expert systems are presently worked out. For the knowledge acquisition various classifiers are tested using a set of 27 nourseothricin fermentation runs. Two methods are applied: optimal clustering by help of minimum variance criterion and hierarchical clustering by help of dendrograms. The fermentations are classified with respect to the specific material costs as well as the product formation kinetics.List of Symbols a kg/m³ initial value of linearized product kinetics - b kg/(m³ · h) slope of linearized product kinetics - B binary variable (value 0 or 1) - C DM/kg specific costs - d distance - m number of samples - p kg/m³ product concentration - pO₂ % dissolved oxygen concentration - t h fermentation time - T h initial time of linearized product kinetics - n number of fermentation runs     

Proteome-wide analysis of protein function composition reveals the clustering and phylogenetic properties of organisms

A 17-dimensional vector named the proteome vector is defined to represent an organism. The components of the vector reflect the relative contents of protein-encoding genes of the 17 cluster of orthologous groups of proteins (COGs) classes in the whole genome of the relevant organism. Based on the definition of this proteome vector, the fuzzy clustering of 36 completely sequenced organisms (8 archaea, 24 bacteria, and 4 eukarya) was performed and a proteome tree was constructed. Our results show that (1) the 36 organisms can be 100% correctly classified into three clusters corresponding to the three primary kingdoms, (2) our proteome tree is remarkably similar to that derived from 16S rRNA, and (3) the chromosomes and/or plasmids belonging to the same organism have very similar gene composition. Based on these results, we argue that the 17-dimensional proteome vector could be a good criterion for clustering approaches and to a large extent reveals the phylogenetic properties of organisms; the Three Primary Kingdoms Hypothesis is trustworthy although the existence of lateral gene transfer (LGT) brings controversy to the construction of the "universal tree of life."     

Genome phylogenetic analysis based on extended gene contents

With the rapid growth of entire genome data, whole-genome approaches such as gene content become popular for genome phylogeny inference, including the tree of life. However, the underlying model for genome evolution is unclear, and the proposed (ad hoc) genome distance measure may violate the additivity. In this article, we formulate a stochastic framework for genome evolution, which provides a basis for defining an additive genome distance. However, we show that it is difficult to utilize the typical gene content data-i.e., the presence or absence of gene families across genomes-to estimate the genome distance. We solve this problem by introducing the concept of extended gene content; that is, the status of a gene family in a given genome could be absence, presence as single copy, or presence as duplicates, any of which can be used to estimate the genome distance and phylogenetic inference. Computer simulation shows that the new tree-making method is efficient, consistent, and fairly robust. The example of 35 microbial complete genomes demonstrates that it is useful not only to study the universal tree of life but also to explore the evolutionary pattern of genomes.     

Large scale genotype-phenotype correlation analysis based on phylogenetic trees

We provide two methods for identifying changes in genotype that are correlated with changes in a phenotype implied by phylogenetic trees. The first method, VENN, works when the number of branches over which the change occurred are modest. VENN looks for genetic changes that are completely penetrant with phenotype changes on a tree. The second method, CCTSWEEP, allows for a partial matching between changes in phenotypes and genotypes and provides a score for each change using Maddison's concentrated changes test. The mutations that are highly correlated with phenotypic change can be ranked by score. We use these methods to find SNPs correlated with resistance to Bacillus anthracis in inbred mouse strains. Our findings are consistent with the current biological literature, and also suggest potential novel candidate genes.     

菝葜科基于形态学证据的系统发育分析

对全世界范围分布的菝葜科Smilacaceae的79个代表种(包括了全部的属和组), 以分布于南美洲的Philesia Comm. ex Juss.和Lapageria Ruiz &; Pav.属为外类群, 选取包括花粉和染色体性状在内的47个广义的形态学性状进行了分支分类系统发育分析, 同时以表征分类的方法构建了距离树(NJ)辅助分析, 首次对世界分布的菝葜科各属间及属内的系统发育关系作了探讨。(1)Ripogonum与菝葜属Smilax +肖菝葜属Heterosmilax互为姐妹群, 但是距离较远, 支持将类菝葜属(新拟中文名)Ripogonum独立为科的观点; (2)肖菝葜属在菝葜科内处于较为进化的分支上, 并与菝葜属土茯苓组sect. Coilanthus的部分种组成一个具较高支持率(88%)的单系分支, 分析表明肖菝葜属并非是一个好属, 应归入菝葜属; (3)菝葜属6个组的划分大都没有得到支持, 只有东亚北美间断分布的草本菝葜组sect. Nemexia的单系得到很好的支持(93%); (4)分布于南美洲巴西的种类聚为一个单系类群, 表明它们可能有共同的起源, 但由于取样局限, 南美洲种类的系统地位有待进一步研究。     

mdclust--exploratory microarray analysis by multidimensional clustering

MOTIVATION: Unsupervised clustering of microarray data may detect potentially important, but not obvious characteristics of samples, for instance subgroups of diagnoses with distinct gene profiles or systematic errors in experimentation. RESULTS: Multidimensional clustering (mdclust) is a method, which identifies sets of sample clusters and associated genes. It applies iteratively two-means clustering and score-based gene selection. For any phenotype variable best matching sets of clusters can be selected. This provides a method to identify gene-phenotype associations, suited even for settings with a large number of phenotype variables. An optional model based discriminant step may reduce further the number of selected genes.     

A phylogenetic analysis of Dipsacaceae based on four DNA regions

Authors studied the phylogeny of Dipsacaceae using maximum parsimony and Bayesian analyses on sequence data from chloroplast (trnL intron, trnL–trnF intergenic spacer, psbB–psbH gene complex) and nuclear genomes (ITS1 and ITS2). Both data partitions as well as their combination show that Dipsacaceae is a monophyletic group. Topology in tribe Scabioseae is similar to those of other recent studies, except for the position of Pycnocomon, which is nested in Lomelosia. Pycnocomon, the pollen and epicalyx morphologies of which closely resemble those of Lomelosia, is interpreted as a psammophilous morphotype of Lomelosia, and its nomenclature has been revised accordingly. Exclusion of Pseudoscabiosa, Pterocephalidium, Pterocephalodes (and probably Bassecoia), Succisa, Succisella from Scabioseae is confirmed. Pterocephalodes hookeri is the sister group to the rest of the family. Its remoteness from Pterocephalus has been confirmed on molecular grounds. Lack of evident synapomorphies for various clades is interpreted as a possible consequence of fast adaptative radiation.     

多基因系统发育分析竹黄的分类地位

竹黄Shiraia bambusicola是一种重要的药用子囊菌,对其分类归属一直存在不同处理意见,主要原因在于形态分类学难以解释其不同的特征表现.为了对竹黄的分类地位做出更接近自然亲缘关系的解释,本研究以自测的S.bambusicolaS4201菌株基因组为基础,结合Genome Warehouse(GWH)数据库中...     

A phylogenetic analysis based on the gene encoding phosphoglycerate kinase

Summary We have determined the nucleotide sequence of both genomic and complementary DNA (cDNA) for the gene encoding the glycolytic enzyme phosphoglycerate kinase from the ciliated protozoan Tetrahymena thermophila. The amino acid sequence for the enzyme has also been derived from the cDNA sequence. The gene contains an open reading frame of 1260 nucleotides encoding 420 amino acids. Coding sequence in genomic DNA is interrupted by two introns at positions corresponding to introns 3 and 4 in mammalian phosphoglycerate kinase genes. The derived amino acid sequence was used to prepare a phylogeny by aligning the Tetrahymena sequence with 25 other phosphoglycerate kinase amino acid sequences. The Tetrahymena sequence is a typical eukaryotic sequence. There is recognizable and clear homology across species that cover nearly the complete range of life forms. The phylogenetic reconstruction of these sequences generally supports the conclusions that have been reached using rRNA sequences.Offprint requests to: R.E. Pearlman     

基于时间聚类分析和独立成分分析的癫痫fMRI盲分析方法

提出了一种基于时间聚类分析和独立成分分析的癫痫fMRI数据盲分析方法,并将两种方法有效联合,提取发作间期的癫痫fMRI激活时空信息.该方法首先由时间聚类分析得到与激活相关的时间峰度特征曲线,以此特征作为时间参考信息;再由空间独立成分分析分解fMRI信号得到空间独立成分;最后将每个独立成分所对应的时间曲线与参考曲线做相关分析提取相应脑激活图.提出的方法无需任何关于癫痫fMRI的先验假设信息,有效解决了独立成分的排序问题,实现了对数据的盲分析.仿真试验结果阐明了这一方法的有效性及可靠性,对癫痫数据的试验结果显示空间定位准确性优于统计参数图方法.     

A phylogenetic analysis of the arachnid orders based on morphological characters

Morphological evidence for resolving relationships among arachnid orders was surveyed and assembled in a matrix comprising 59 euchelicerate genera (41 extant, 18 fossil) and 202 binary and unordered multistate characters. Parsimony analysis of extant genera recovered a monophyletic Arachnida with the topology (Palpigradi (Acaromorpha (Tetrapulmonata (Haplocnemata, Stomothecata nom. nov. )))), with Acaromorpha containing Ricinulei and Acari, Tetrapulmonata containing Araneae and Pedipalpi (Amblypygi, Uropygi), Haplocnemata (Pseudoscorpiones, Solifugae) and Stomothecata (Scorpiones, Opiliones). However, nodal support and results from exploratory implied weights analysis indicated that relationships among the five clades were effectively unresolved. Analysis of extant and fossil genera recovered a clade, Pantetrapulmonata nom nov. , with the topology (Trigonotarbida (Araneae (Haptopoda (Pedipalpi)))). Arachnida was recovered as monophyletic with the internal relationships (Stomothecata (Palpigradi, Acaromorpha (Haplocnemata, Pantetrapulmonata))). Nodal support and exploratory implied weights indicated that relationships among these five clades were effectively unresolved. Thus, some interordinal relationships were strongly and/or consistently supported by morphology, but arachnid phylogeny is unresolved at its deepest levels. Alternative hypotheses proposed in the recent literature were evaluated by constraining analyses to recover hypothesized clades, an exercise that often resulted in the collapse of otherwise well-supported clades. These results suggest that attempts to resolve specific nodes based on individual characters, lists of similarities, evolutionary scenarios, etc., are problematic, as they ignore broader impacts on homoplasy and analytical effects on non-target nodes.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 221–265.     

PAML 4: phylogenetic analysis by maximum likelihood

PAML, currently in version 4, is a package of programs for phylogeneticanalyses of DNA and protein sequences using maximum likelihood(ML). The programs may be used to compare and test phylogenetictrees, but their main strengths lie in the rich repertoire ofevolutionary models implemented, which can be used to estimateparameters in models of sequence evolution and to test interestingbiological hypotheses. Uses of the programs include estimationof synonymous and nonsynonymous rates (d_N and d_S) between twoprotein-coding DNA sequences, inference of positive Darwinianselection through phylogenetic comparison of protein-codinggenes, reconstruction of ancestral genes and proteins for molecularrestoration studies of extinct life forms, combined analysisof heterogeneous data sets from multiple gene loci, and estimationof species divergence times incorporating uncertainties in fossilcalibrations. This note discusses some of the major applicationsof the package, which includes example data sets to demonstratetheir use. The package is written in ANSI C, and runs underWindows, Mac OSX, and UNIX systems. It is available at http://abacus.gene.ucl.ac.uk/software/paml.html.     

A phylogenetic analysis ofDuguetia (Annonaceae) based on morphological data

In this paper we present a phylogeny based on a study of the general morphology of 61 of the ca. 80 species ofDuguetia. Analyses were performed with PAUP. The resulting phylogeny is compared with the classification ofDuguetia as suggested byFries (1934, 1937, 1939, 1959). The results are partly corresponding withFries's classification. SectionAlcmene includingD. rionegrensis, and sects.Geanthemum, Synsepalantha, andCalothrix withoutD. uniflora, are upheld by this analysis. It is concluded that sect.Xylopipetalum should be united with sect.Duguetia. Before other taxonomic decisions at the section level can be made, more solid data must be available. Most dissimilarities found are considered to be not strong enough to propose alterations.Studies inAnnonaceae XXIII. For 22nd part seeZuilen & Maas (1994).     

A phylogenetic analysis of the emberizid sparrows based on three mitochondrial genes

Previous molecular phylogenetic studies have examined the taxonomic relationships among a number of typical emberizid sparrow genera. To help clarify these relationships, we sequenced a 1673 base pair fragment for the complete sequence of three mitochondrial genes: adenosine triphosphatase (Atp8 and Atp6) and cytochrome oxidase subunit III (COIII) for 38 sparrow species, along with Passerina amoena (Cardinalidae) and Piranga ludoviciana (Thraupidae) which were selected as the outgroups. Our analysis confirms the monophyly of traditional genera such as Junco, Melospiza, and Zonotrichia. Although Calcarius and Plectrophenax are often thought to be putative emberizids, all our analyses placed these genera basal to all other sparrows examined. As observed with Calcarius, Spizella did not form a monophyletic group, with S. arborea being the sister-taxon to Passerella iliaca. Our analyses also suggest that Aimophila ruficeps is probably more closely related to the "brown towhees" (Pipilo aberti, P. crissalis, and P. fuscus) than its putative congeners. The genus Ammodramus was also not monophyletic, since it appears that Passerculus sandwichensis is more closely related to A. henslowii and A. leconteii then either one is related to its congener A. savannarum. Finally, our analyses exhibited other unsuspected associations, such as the sister-taxon relationships between Amphispiza bilineata and the Chondestes grammacus/Calamospiza melanocorys clade, and Amphispiza belli and Pooecetes gramineus.     

Alignment and clustering of phylogenetic markers - implications for microbial diversity studies

Background  

Molecular studies of microbial diversity have provided many insights into the bacterial communities inhabiting the human body and the environment. A common first step in such studies is a survey of conserved marker genes (primarily 16S rRNA) to characterize the taxonomic composition and diversity of these communities. To date, however, there exists significant variability in analysis methods employed in these studies.     

Orthology prediction at scalable resolution by phylogenetic tree analysis

Background  

Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic relations results in inparalogs and outparalogs. For situations with more than two species we lack semantics to specifically describe the phylogenetic relations, let alone to exploit them. Published procedures to extract orthologous groups from phylogenetic trees do not allow identification of orthology at various levels of resolution, nor do they document the relations between the orthologous groups.     

Genetic variations in the chloroplast genome and phylogenetic clustering of Lycoris species

The genus Lycoris of Amaryllidaceae comprises approximately 20 species that are distributed only in the moist warm temperate woodlands of eastern Asia. The objectives of this study were: (1) to clarify the phylogeny of the Lycoris species by using the definitive DNA sequencing method and (2) to examine the possible maternal donor of the hybrid origin Lycoris species and the Japanese triploid strains of Lycoris radiata var. radiata. The nucleotide sequence of the maturase K (matK) gene and the noncoding intergenic spacer (IGS) between the atpB and rbcL genes in the chloroplast genome were determined in a total of 27 strains of 11 species of the genus Lycoris. Variation among taxa was mainly due to nucleotide substitution, although deletions and an insertion were found in the IGS. For two chloroplast regions, the phylogenetic trees showed essentially similar topology, indicating the existence of four clades, I, II, III, and IV. For all the species except L. radiata, intraspecific variation was smaller than interspecific variation. For L. radiata, triploid strains were divided into clades I and II, and diploid strains were divided into clades I and IV. This implies that the diploid species of L. radiata var. pumila is a probable ancestral species. The clustering indicated that the chloroplast genome has not evolved in parallel with the karyotype in genus Lycoris. Regarding the hybrid origin species, the maternal parents of L. squamigara, L. albiflora and L. rosea were revealed to be L. longituba, L. radiata and L. radiata var pumila, respectively. We also suggest that a diploid strain of L. radiata var. pumila in clade I might be a candidate of the maternal donor of the Japanese triploid strains. A possible model of the maternal donor of Lycoris species is proposed.