Cross-Species Comparison of Metabolomics to Decipher the Metabolic Diversity in Ten Fruits

Fruits provide humans with multiple kinds of nutrients and protect humans against worldwide nutritional deficiency. Therefore, it is essential to understand the nutrient composition of various fruits in depth. In this study, we performed LC-MS-based non-targeted metabolomic analyses with ten kinds of fruit, including passion fruit, mango, starfruit, mangosteen, guava, mandarin orange, grape, apple, blueberry, and strawberry. In total, we detected over 2500 compounds and identified more than 300 nutrients. Although the ten fruits shared 909 common-detected compounds, each species accumulated a variety of species-specific metabolites. Additionally, metabolic profiling analyses revealed a constant variation in each metabolite’s content across the ten fruits. Moreover, we constructed a neighbor-joining tree using metabolomic data, which resembles the single-copy protein-based phylogenetic tree. This indicates that metabolome data could reflect the genetic relationship between different species. In conclusion, our work enriches knowledge on the metabolomics of fruits, and provides metabolic evidence for the genetic relationships among these fruits.

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Deciphering conserved identical sequences of mature miRNAs among six members of great apes

Zoosystematics and Evolution ◽

10.3897/zse.94.28099 ◽

2018 ◽

Vol 94 (2) ◽

pp. 401-408

Author(s):

Aftab Ali Shah ◽

Mushtaq Ahmad ◽

Taqweem Ul-Haq

Keyword(s):

Gene Families ◽

Mature Mirnas ◽

Neighbor Joining ◽

Species Comparison ◽

Rna Molecules ◽

Sequence Identity ◽

Species Specific ◽

Post Transcriptional Regulation ◽

Cross Species Comparison

MicroRNAs (miRNAs) are a group of small RNA molecules which act as negative regulators of gene expression by controlling post-transcriptional regulation through binding to their corresponding mRNAs. Due to their small size, their nucleotide compositions are expected to be similar, but until now, the extent of similarity has not been reported in humans and their six phylogenetically closely related members of hominids. The present study allows direct comparison among six members of hominid species (Homosapiens, Gorillagorilla, Panpaniscus, Pongopygmaeus, Pantroglodytes and Symphalangussyndactylus) in terms of their miRNA repertoire, their evolutionary distance to human, as well as, the categorization of identical species-specific miRNAs. For this purpose, a total of 2694, 370, 157, 673, 590 and 10 mature miRNA sequences of Homosapiens, Gorillagorilla, Panpaniscus, Pongopygmaeus, Pantroglodytes and Symphalangussyndactylus respectively were retrieved from miRbase 22. A total of 12, 4, 4 and 3 conserved clusters with identical miRNA sequences that belong to the same gene families were found in Homosapiens, Gorillagorilla, Pongopygmaeus, Pantroglodytes respectively by neighbor-joining method using MEGA7 software. Interestingly, cross-species comparison has also shown a set of conserved identical miRNA sequences. Homologs of human mature miRNAs with 100% sequence identity are expected to have similar functions in the studied primates. Further in-vitro study is required to investigate common targets for identical miRNAs in the studied primates.

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A cross-species comparison: The efficacy of insect repellents and attractants

10.1603/ice.2016.113020 ◽

2016 ◽

Author(s):

Stacy D. Rodriguez

Keyword(s):

Species Comparison ◽

Insect Repellents ◽

Cross Species Comparison

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Characterization of the Major Antigenic Protein 2 of Ehrlichia canis and Ehrlichia chaffeensis and Its Application for Serodiagnosis of Ehrlichiosis

Clinical and Diagnostic Laboratory Immunology ◽

10.1128/cdli.10.4.520-524.2003 ◽

2003 ◽

Vol 10 (4) ◽

pp. 520-524 ◽

Cited By ~ 7

Author(s):

Tamece T. Knowles ◽

A. Rick Alleman ◽

Heather L. Sorenson ◽

David C. Marciano ◽

Edward B. Breitschwerdt ◽

...

Keyword(s):

Blot Analysis ◽

Single Copy ◽

Ehrlichia Canis ◽

Specific Method ◽

Ehrlichia Chaffeensis ◽

Antigenic Protein ◽

Canine Monocytic Ehrlichiosis ◽

Copy Gene ◽

Species Specific

ABSTRACT Canine monocytic ehrlichiosis, caused by Ehrlichia canis or Ehrlichia chaffeensis, can result in clinical disease in naturally infected animals. Coinfections with these agents may be common in certain areas of endemicity. Currently, a species-specific method for serological diagnosis of monocytic ehrlichiosis is not available. Previously, we developed two indirect enzyme-linked immunosorbent assays (ELISAs) using the major antigenic protein 2 (MAP2) of E. chaffeensis and E. canis. In this study, we further characterized the conservation of MAP2 among various geographic isolates of each organism and determined if the recombinant MAP2 (rMAP2) of E. chaffeensis would cross-react with E. canis-infected dog sera. Genomic Southern blot analysis using digoxigenin-labeled species-specific probes suggested that map2 is a single-copy gene in both Ehrlichia species. Sequences of the single map2 genes of seven geographically different isolates of E. chaffeensis and five isolates of E. canis are highly conserved among the various isolates of each respective ehrlichial species. ELISA and Western blot analysis confirmed that the E. chaffeensis rMAP2 failed to serologically differentiate between E. canis and E. chaffeensis infections.

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Cross-species comparison of fluoxetine metabolism with fish liver microsomes

Chemosphere ◽

10.1016/j.chemosphere.2010.01.058 ◽

2010 ◽

Vol 79 (1) ◽

pp. 26-32 ◽

Cited By ~ 40

Author(s):

Emily M. Smith ◽

Shaogang Chu ◽

Gordon Paterson ◽

Chris D. Metcalfe ◽

Joanna Y. Wilson

Keyword(s):

Liver Microsomes ◽

Species Comparison ◽

Fish Liver ◽

Cross Species Comparison

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Focal Distribution of Baculovirus IE1 Triggered by Its Binding to the hr DNA Elements

Journal of Virology ◽

10.1128/jvi.79.1.39-46.2005 ◽

2005 ◽

Vol 79 (1) ◽

pp. 39-46 ◽

Cited By ~ 17

Author(s):

Toshihiro Nagamine ◽

Yu Kawasaki ◽

Tetsutaro Iizuka ◽

Shogo Matsumoto

Keyword(s):

Fluorescent Protein ◽

Direct Repeat ◽

Single Copy ◽

Targeted Mutagenesis ◽

Homologous Region ◽

Focus Formation ◽

Primary Determinant ◽

Dna Elements ◽

Species Specific ◽

Green Fluorescent

ABSTRACT In BmN cells infected with the baculovirus Bombyx mori nucleopolyhedrovirus (BmNPV), IE1, a principal transcriptional activator, localizes to sites of viral DNA replication. IE1 initially displays focal distribution in BmNPV-infected cells prior to DNA synthesis, whereas the protein expressed by transfection with the ie1 gene is distributed throughout the nucleoplasm instead of localized to discrete subnuclear structures. To identify the inducer of focus formation for IE1, we conducted transfection experiments with an IE1-GFP construct and found that cotransfection with genomic DNA fragments bearing the homologous region (hr) sequences caused the formation of IE1-green fluorescent protein (GFP) foci. The transfection of insect cells with a single plasmid containing exclusively the hr3 sequence and the IE1-GFP gene was sufficient to form IE1-GFP foci. These results suggest that hr elements are a primary determinant of the focal distribution of IE1. An analysis of a series of hr3 deletion mutants showed that a single copy of the direct repeat could induce the formation of IE1 foci. Targeted mutagenesis within the hr-binding domain of IE1-GFP caused impairment of the hr-dependent IE1 localization, suggesting that binding of IE1 to the hr elements is essential for the onset of IE1 focus formation. The observation of BmNPV IE1 foci in non-BmNPV-susceptible cells suggests that no species-specific factors are required for hr-dependent IE1 focus formation.

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