gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites

Metabolomes comprise constitutive and non-constitutive metabolites produced due to physiological, genetic or environmental effects. However, finding constitutive metabolites and non-constitutive metabolites in large datasets is technically challenging. We developed gcProfileMakeR, an R package using standard Excel output files from an Agilent Chemstation GC-MS for automatic data analysis using CAS numbers. gcProfileMakeR has two filters for data preprocessing removing contaminants and low-quality peaks. The first function NormalizeWithinFiles, samples assigning retention times to CAS. The second function NormalizeBetweenFiles, reaches a consensus between files where compounds in close retention times are grouped together. The third function getGroups, establishes what is considered as Constitutive Profile, Non-constitutive by Frequency i.e., not present in all samples and Non-constitutive by Quality. Results can be plotted with the plotGroup function. We used it to analyse floral scent emissions in four snapdragon genotypes. These included a wild type, Deficiens nicotianoides and compacta affecting floral identity and RNAi:AmLHY targeting a circadian clock gene. We identified differences in scent constitutive and non-constitutive profiles as well as in timing of emission. gcProfileMakeR is a very useful tool to define constitutive and non-constitutive scent profiles. It also allows to analyse genotypes and circadian datasets to identify differing metabolites.

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Faculty Opinions recommendation of Circadian clock gene LATE ELONGATED HYPOCOTYL directly regulates the timing of floral scent emission in Petunia.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.725599647.793508556 ◽

2015 ◽

Author(s):

Stacey Harmer

Keyword(s):

Circadian Clock ◽

Clock Gene ◽

Floral Scent ◽

Circadian Clock Gene

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Acamprosate-responsive brain sites for suppression of ethanol intake and preference

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.00179.2011 ◽

2011 ◽

Vol 301 (4) ◽

pp. R1032-R1043 ◽

Cited By ~ 10

Author(s):

Allison Brager ◽

Rebecca A. Prosser ◽

J. David Glass

Keyword(s):

Alcohol Intake ◽

Free Choice ◽

Clock Gene ◽

Brain Regions ◽

Ethanol Intake ◽

Mutant Mice ◽

Wild Type ◽

Circadian Clock Gene ◽

Recovering Alcoholics ◽

Brain Reward

Acamprosate suppresses alcohol intake and craving in recovering alcoholics; however, the central sites of its action are unclear. To approach this question, brain regions responsive to acamprosate were mapped using acamprosate microimplants targeted to brain reward and circadian areas implicated in alcohol dependence. mPer2 mutant mice with nonfunctional mPer2, a circadian clock gene that gates endogenous timekeeping, were included, owing to their high levels of ethanol intake and preference. Male wild-type (WT) and mPer2 mutant mice received free-choice (15%) ethanol/water for 3 wk. The ethanol was withdrawn for 3 wk and then reintroduced to facilitate relapse. Four days before ethanol reintroduction, mice received bilateral blank or acamprosate-containing microimplants releasing ∼50 ng/day into reward [ventral tegmental (VTA), peduculopontine tegmentum (PPT), and nucleus accumbens (NA)] and circadian [intergeniculate leaflet (IGL) and suprachiasmatic nucleus (SCN)] areas. The hippocampus was also targeted. Circadian locomotor activity was measured throughout. Ethanol intake and preference were greater in mPer2 mutants than in wild-type (WT) mice (27 g·kg−1·day−1 vs. 13 g·kg−1·day−1 and 70% vs. 50%, respectively; both, P < 0.05). In WTs, acamprosate in all areas, except hippocampus, suppressed ethanol intake and preference (by 40–60%) during ethanol reintroduction. In mPer2 mutants, acamprosate in the VTA, PPT, and SCN suppressed ethanol intake and preference by 20–30%. These data are evidence that acamprosate's suppression of ethanol intake and preference are manifest through actions within major reward and circadian sites.

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The clock gene Period1 regulates innate routine behaviour in mice

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2014.0034 ◽

2014 ◽

Vol 281 (1781) ◽

pp. 20140034 ◽

Cited By ~ 9

Author(s):

Philipp Bechstein ◽

Nils-Jörn Rehbach ◽

Gowzekan Yuhasingham ◽

Christoph Schürmann ◽

Melanie Göpfert ◽

...

Keyword(s):

Clock Gene ◽

Memory Deficits ◽

Nest Building ◽

Partner Choice ◽

Mutant Mice ◽

Spatial Learning And Memory ◽

Wild Type ◽

Circadian Clock Gene ◽

Deficient Mice

Laboratory mice are well capable of performing innate routine behaviour programmes necessary for courtship, nest-building and exploratory activities although housed for decades in animal facilities. We found that in mice inactivation of the clock gene Period1 profoundly changes innate routine behaviour programmes like those necessary for courtship, nest building, exploration and learning. These results in wild-type and Period1 mutant mice, together with earlier findings on courtship behaviour in wild-type and period -mutant Drosophila melanogaster , suggest a conserved role of Period- genes on innate routine behaviour. Additionally, both per -mutant flies and Period1 -mutant mice display spatial learning and memory deficits. The profound influence of Period1 on routine behaviour programmes in mice, including female partner choice, may be independent of its function as a circadian clock gene, since Period1 -deficient mice display normal circadian behaviour.

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Circadian clock gene LATE ELONGATED HYPOCOTYL directly regulates the timing of floral scent emission in Petunia

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1422875112 ◽

2015 ◽

Vol 112 (31) ◽

pp. 9775-9780 ◽

Cited By ~ 46

Author(s):

Myles P. Fenske ◽

Kristen D. Hewett Hazelton ◽

Andrew K. Hempton ◽

Jae Sung Shim ◽

Breanne M. Yamamoto ◽

...

Keyword(s):

Circadian Clock ◽

Clock Gene ◽

Floral Scent ◽

Expression Patterns ◽

Constitutive Expression ◽

Regulatory Elements ◽

Circadian Clock Gene ◽

Volatile Emission ◽

Floral Volatile ◽

Volatile Production

Flowers present a complex display of signals to attract pollinators, including the emission of floral volatiles. Volatile emission is highly regulated, and many species restrict emissions to specific times of the day. This rhythmic emission of scent is regulated by the circadian clock; however, the mechanisms have remained unknown. In Petunia hybrida, volatile emissions are dominated by products of the floral volatile benzenoid/phenylpropanoid (FVBP) metabolic pathway. Here we demonstrate that the circadian clock gene P. hybrida LATE ELONGATED HYPOCOTYL (LHY; PhLHY) regulates the daily expression patterns of the FVBP pathway genes and floral volatile production. PhLHY expression peaks in the morning, antiphasic to the expression of P. hybrida GIGANTEA (PhGI), the master scent regulator ODORANT1 (ODO1), and many other evening-expressed FVBP genes. Overexpression phenotypes of PhLHY in Arabidopsis caused an arrhythmic clock phenotype, which resembles those of LHY overexpressors. In Petunia, constitutive expression of PhLHY depressed the expression levels of PhGI, ODO1, evening-expressed FVBP pathway genes, and FVBP emission in flowers. Additionally, in the Petunia lines in which PhLHY expression was reduced, the timing of peak expression of PhGI, ODO1, and the FVBP pathway genes advanced to the morning. Moreover, PhLHY protein binds to cis-regulatory elements called evening elements that exist in promoters of ODO1 and other FVBP genes. Thus, our results imply that PhLHY directly sets the timing of floral volatile emission by restricting the expression of ODO1 and other FVBP genes to the evening in Petunia.

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Automatic classification of single-molecule charge transport data with an unsupervised machine-learning algorithm

Physical Chemistry Chemical Physics ◽

10.1039/c9cp04496e ◽

2020 ◽

Vol 22 (3) ◽

pp. 1674-1681 ◽

Cited By ~ 9

Author(s):

Feifei Huang ◽

Ruihao Li ◽

Gan Wang ◽

Jueting Zheng ◽

Yongxiang Tang ◽

...

Keyword(s):

Charge Transport ◽

Single Molecule ◽

Learning Algorithm ◽

Analysis Method ◽

Automatic Data ◽

Single Molecule Level ◽

Unsupervised Deep Learning ◽

Automatic Data Analysis ◽

Physical And Chemical

Based on unsupervised deep learning algorithms, an automatic data analysis method for single-molecule charge transport data is developed, which offers an opportunity to reveal more physical and chemical phenomena at the single-molecule level.

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Automatic classification of constitutive and non-constitutive metabolites with gcProfileMakeR

10.1101/2020.02.24.963058 ◽

2020 ◽

Cited By ~ 1

Author(s):

Fernando Pérez-Sanz ◽

Victoria Ruiz-Hernández ◽

Marta Isabel Terry ◽

Sara Arce-Gallego ◽

Julia Weiss ◽

...

Keyword(s):

Data Analysis ◽

Floral Scent ◽

R Package ◽

Targeted Metabolomics ◽

Quality Of Data ◽

Automatic Data ◽

Petal Identity ◽

Volatile Profiles ◽

Major Increase ◽

Standard Output

AbstractData analysis in non-targeted metabolomics is extremely time consuming. Genetic factors and environmental cues affect the composition and quantity of present metabolites i.e. the constitutive and non-constitutive metabolites. We developed gcProfileMakeR, an R package that uses standard output files from GC-MS for automatic data analysis using CAS numbers. gcProfileMakeR produces three outputs: a core or constitutive metabolome, a second list of compounds with high quality matches that is non-constitutive and a third set of compounds with low quality matching to MS libraries. As a proof of concept, we defined the floral scent emission of Antirrhinum majus using wild type plants, the floral identity mutants deficiens and compacta as well as RNAi lines of AmLHY. Loss of petal identity was accompanied by appearance of aldehydes typical of green leaf volatile profiles. Decreased levels of AmLHY caused a major increase in volatile complexity, and activated the synthesis of benzyl acetate, absent in WT. Furthermore, some volatiles emitted in a gated fashion in WT such as methyl 3,5-dimethoxybezoate or linalool became constitutive. Using sixteen volatiles of the constitutive profile, all genotypes were classified by Machine Learning with 0% error. gcProfileMakeR may thus help define core and pan-metabolomes. It enhances the quality of data reported in metabolomic profiles as text outputs rely on CAS numbers. This is especially important for FAIR data implementation.One sentence summarygcProfileMakeR allows the automatic annotation of the core metabolome and non-constitutive metabolites, increasing speed and accuracy of non-targeted metabolomics.

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ABOUT THE PROBLEM OF CLASSIFICATION OF THE CONCEPTS OF INFORMATICS STUDIED AT SECONDARY SCHOOL

Informatics in school ◽

10.32517/2221-1993-2018-17-7-4-7 ◽

2018 ◽

pp. 4-7

Author(s):

S. I. Zenko

Keyword(s):

Secondary School ◽

Foreign Language ◽

Computer Science ◽

Parts Of Speech ◽

The Third ◽

The Cross ◽

Definition Of

The article raises the problem of classification of the concepts of computer science and informatics studied at secondary school. The efficiency of creation of techniques of training of pupils in these concepts depends on its solution. The author proposes to consider classifications of the concepts of school informatics from four positions: on the cross-subject basis, the content lines of the educational subject "Informatics", the logical and structural interrelations and interactions of the studied concepts, the etymology of foreign-language and translated words in the definition of the concepts of informatics. As a result of the first classification general and special concepts are allocated; the second classification — inter-content and intra-content concepts; the third classification — stable (steady), expanding, key and auxiliary concepts; the fourth classification — concepts-nouns, conceptsverbs, concepts-adjectives and concepts — combinations of parts of speech.

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(A review). BRAUN-BLANQUETIA. Recueil de travaux de geobotanique / review of geobotanical monographs. Vol. 46. Centenaire de la phytosociologie. CAMERINO, 2010. 423 p.

Vegetation of Russia ◽

10.31111/vegrus/2011.19.143 ◽

2011 ◽

pp. 143-147

Author(s):

L. G. Naumova ◽

V. B. Martynenko ◽

S. M. Yamalov

Keyword(s):

Plant Association ◽

Northern Asia ◽

The Third ◽

International Botanical ◽

International Botanical Congress ◽

History Of ◽

Definition Of

Date of «birth» of phytosociology (phytocenology) is considered to be 1910, when at the third International Botanical Congress in Brussels adopted the definition of plant association in the wording Including Flaó and K. Schröter (Flahault, Schröter, 1910; Alexandrov, 1969). The centenary of this momentous event in the history of phytocenology devoted to the 46th edition of the Yearbook «Braun-Blanquetia», which began to emerge in 1984 in Camerino (Italy) and it has a task to publish large geobotanical works. During the years of the publication of the Yearbook on its pages were published twice work of the Russian scientists — «The steppes of Mongolia» (Z. V. Karamysheva, V. N. Khramtsov. Vol. 17. 1995), and «Classification of continental hemiboreal forests of Northern Asia» (N. B. Ermakov in collaboration with English colleagues and J. Dring, J. Rodwell. Vol. 28. 2000).

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