Functionally diverging molecular quasi-species evolve by crossing two enzymes
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Molecular evolution is frequently portrayed by structural relationships, but delineation of separate functional species is more elusive. We have generated enzyme variants by stochastic recombinations of DNA encoding two homologous detoxication enzymes, human glutathione transferases M1-1 and M2-2, and explored their catalytic versatilities. Sampled mutants were screened for activities with eight alternative substrates, and the activity fingerprints were subjected to principal component analysis. This phenotype characterization clearly identified at least three distributions of substrate selectivity, where one was orthogonal to those of the parent-like distributions. This approach to evolutionary data mining serves to identify emerging molecular quasi-species and indicates potential trajectories available for further protein evolution.Keywords:
Molecular evolution
The article discusses selected problems related to both principal component analysis (PCA) and factor analysis (FA). In particular, both types of analysis were compared. A vector interpretation for both PCA and FA has also been proposed. The problem of determining the number of principal components in PCA and factors in FA was discussed in detail. A new criterion for determining the number of factors and principal components is discussed, which will allow to present most of the variance of each of the analyzed primary variables. An efficient algorithm for determining the number of factors in FA, which complies with this criterion, was also proposed. This algorithm was adapted to find the number of principal components in PCA. It was also proposed to modify the PCA algorithm using a new method of determining the number of principal components. The obtained results were discussed.
Sparse PCA
Factor Analysis
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Component analysis
Sparse PCA
Factor Analysis
Rank (graph theory)
Factor (programming language)
Component (thermodynamics)
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We have isolated a novel enhanced-nodulating mutant astray (Ljsym77) from Lotus japonicus. The name astray derives from the non-symbiotic phenotype of this mutant, agravitropic lateral roots that go “astray” against gravity. In this report we evaluated the symbiotic aspects of this mutant in detail. The astray mutant developed approximately twice the number of nodules on a wider area of roots compared with the wild type. Furthermore, the astray mutant demonstrated early initiation of nodule development, which is an unprecedented symbiotic phenotype. The astray seedlings showed normal sensitivity to the general inhibitors of nodulation such as ethylene and nitrate. These results indicate that the astray mutant is distinct from the hypernodulating mutants reported previously, and that the ASTRAY gene acts as an early and negative regulator in the cascade of nodule development.
Lotus japonicus
Nodule (geology)
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To investigate the architecture of the rolled leaf morphology in rice,the features of phenotype and histological level in 2 reverse rolled leaf mutants derived from rice Ac/Ds transposons insertional mutant library were investingated. The results showed that the number of bulliform cells was reduced in 2 reverse rolled leaf mutants(Ad-mutant:adaxial rolled mutant;Ab-mutant:abaxial rolled mutant) compared with the normal flat leaf in wild type,which may be an important cause of the rolled leaf in rice. And the number of parenchyma also was reduced and dehisced to 2 large air cavities in Abmutant. The cellulose content of leaf and culm in 2 rolled leaf mutant and wild type was measured,and the result showed that the cellulose content of leaf and culm in Ab-mutant was significant reduced compared with Ad-mutant and wild type.But the cellulose content of leaf and culm in Ad-mutant was not significantly different from that of wild type. This result suggested that Ab-mutant and Ad-mutant may be different in mutation of gene loci. In addition,the genetic rule of Abmutant and Ad-mutant was analyzed,and the result showed that both of them were controlled by single recessive gene.
Wild type
Genetic Analysis
Parenchyma
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Using ethylmethansulphonate the chemical mutagenesis of the pea laboratory line SGE was performed. During analysis of 425 families (2069 plants) of Мsub2/sub progeny 45 putative mutants were selected, among them 30 mutants forming ineffective nodules (Fixsup–/sup phenotype), 13 mutantsunable to form nodules (Nodsup–/sup phenotype), and 2 mutants forming a few nodules (Nodsup+/–/sup phenotype). For 1 Nodsup–/sup and 5 Fixsup–/sup mutants monogenic inheritance and recessive phenotype manifestation were demonstrated. For Fixsup– /supmutant SGEFixsup–/sup–9 an additional mutation leading to Nodsup+/–/sup phenotype was shown. Complementation analysis showed that the mutant phenotype of the SGEFixspan style="font-size:11px"sup-/sup - /span5 line is caused by a mutation in the sym33 gene, of theSGEFixsup–/sup–6 linein the sym40 gene, of the SGEFixsup–/sup–7 line in the sym27 gene, and of the SGEFixsup–/sup–8 linein the sym25 gene.
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ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTClassification of Vegetable Oils by Principal Component Analysis of FTIR SpectraDavid A. Rusak , Leah M. Brown , and Scott D. Martin View Author Information Department of Chemistry, University of Scranton, Scranton, PA 18510Cite this: J. Chem. Educ. 2003, 80, 5, 541Publication Date (Web):May 1, 2003Publication History Received3 August 2009Published online1 May 2003Published inissue 1 May 2003https://pubs.acs.org/doi/10.1021/ed080p541https://doi.org/10.1021/ed080p541research-articleACS PublicationsRequest reuse permissionsArticle Views2531Altmetric-Citations42LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Infrared light,Lipids,Mathematical methods,Plant derived food,Principal component analysis Get e-Alerts
Chemometrics
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Cuticle (hair)
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Principal component analysis (PCA) has been widely used for data dimension reduction and process fault detection. However, interpreting the principal components and the outcomes of PCA-based monitoring techniques is a challenging task since each principal component is a linear combination of the original variables which can be numerous in most modern applications. To address this challenge, we first propose the use of sparse principal component analysis (SPCA) where the loadings of some variables in principal components are restricted to zero. This paper then describes a technique to determine the number of non-zero loadings in each principal component. Furthermore, we compare the performance of PCA and SPCA in fault detection. The validity and potential of SPCA are demonstrated through simulated data and a comparative study with the benchmark Tennessee Eastman process.
Sparse PCA
Benchmark (surveying)
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SUMMARY: An investigation was undertaken to determine to what extent the properties of oligosporogenous (Osp) mutants allow them to be considered as a separate class of sporulation mutant, distinct from asporogenous (Sp-) mutants. Of thirty Osp mutants examined, seventeen at least had a phenotype which had previously been identified with a Sp- mutant. The majority of cells in an Osp culture either reached a particular stage in the sporulation process and then stopped, or in some cases went on to produce aberrant forms. Some of these aberrant forms have their counterparts in Sp- mutants described by other authors, but some present new features. The morphological and biochemical sequences were linked so that if the majority of cells were blocked at a certain stage, then the biochemical sequence stopped accordingly. The general similarity in behaviour between the two types of mutant is consistent with the assumption that at least some of the Osp mutants have leaky mutations in genes where mutation can also give rise to Sp- phenotypes. Evidence is presented to suggest that the ability of a cell of an Osp mutant to overcome its block, and so go on to form a spore, is a chance event when that stage in the process is reached. A mutant has been obtained in which the spores are octanol-resistant yet contain no measurable dipicolinate. In several other mutants the spores contained well-developed coat layers, but the cortex was poorly formed or completely missing.
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