scholarly journals Phyloproteomic Analysis of 11780 Six-Residue-Long Motifs Occurrences

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
O. V. Galzitskaya ◽  
M. Yu. Lobanov
Keyword(s):  
Amino Acids ◽  
Phylogenetic Relationships ◽  
Correlation Coefficients ◽  
Terminal Position ◽  
Phylogenetic Reconstructions ◽  
Eukaryotic Proteomes ◽  
Bacterial Proteomes

How is it possible to find good traits for phylogenetic reconstructions? Here, we present a new phyloproteomic criterion that is an occurrence of simple motifs which can be imprints of evolution history. We studied the occurrences of 11780 six-residue-long motifs consisting of two randomly located amino acids in 97 eukaryotic and 25 bacterial proteomes. For all eukaryotic proteomes, with the exception of the Amoebozoa, Stramenopiles, and Diplomonadida kingdoms, the number of proteins containing the motifs from the first group (one of the two amino acids occurs once at the terminal position) made about 20%; in the case of motifs from the second (one of two amino acids occurs one time within the pattern) and third (the two amino acids occur randomly) groups, 30% and 50%, respectively. For bacterial proteomes, this relationship was 10%, 27%, and 63%, respectively. The matrices of correlation coefficients between numbers of proteins where a motif from the set of 11780 motifs appears at least once in 9 kingdoms and 5 phyla of bacteria were calculated. Among the correlation coefficients for eukaryotic proteomes, the correlation between the animal and fungi kingdoms (0.62) is higher than between fungi and plants (0.54). Our study provides support that animals and fungi are sibling kingdoms. Comparison of the frequencies of six-residue-long motifs in different proteomes allows obtaining phylogenetic relationships based on similarities between these frequencies: the Diplomonadida kingdoms are more close to Bacteria than to Eukaryota; Stramenopiles and Amoebozoa are more close to each other than to other kingdoms of Eukaryota.

scholarly journals Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maria Alejandra Serna-Sánchez ◽  
Oscar A. Pérez-Escobar ◽  
Diego Bogarín ◽  
María Fernanda Torres-Jimenez ◽  
Astrid Catalina Alvarez-Yela ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Times ◽  
Molecular Clocks ◽  
Phylogenetic Placement ◽  
Plastid Genomes ◽  
Phylogenetic Reconstructions ◽  
A Genome ◽  
Tree Models ◽  
Phylogenomic Analyses ◽  
First Time

AbstractRecent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

scholarly journals Evaluation of Different Flax Cultivars in Their Oil, Fatty Acids Protein and Amino Acids and Correlations

2017 ◽  
Vol 27 (1) ◽  
pp. 51-58
Author(s):  
Ahmed Abdullah Bakhashwain Ahmed Abdullah Bakhashwain
Keyword(s):  
Amino Acids ◽  
Fatty Acids ◽  
Amino Acid ◽  
Linolenic Acid ◽  
Correlation Coefficients ◽  
Omega 3 ◽  
Geographical Regions ◽  
Meal Protein ◽  
Omega 6 ◽  
King Abdulaziz University

This study was carried out in the Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University to evaluate 7 flax genotypes from different geographical regions concerning their composition from oil and protein contents, fatty acids and amino acids, besides, calculate the correlation coefficients between the fatty acids and also between the amino acids.The main results showed that Verum cv. had the highest oil content and linolenic acid (Omega-3) while Hiera cv. was the highest in meal protein content and most amino acids. The highest amino acid concentration was proline and it ranged from 27.15% to 30.21%. Linolenic acid (Omega-3) negatively and significantly correlated with Oleic and Linoleic (Omega-6) fatty acids. Lysine amino acid positively and significantly correlated with the amino acids of Glutamine, Aspartic, Leucine, Serine and Isoleucine.

scholarly journals The enzymic degradation of ovalbumin and its glycopeptides

1969 ◽  
Vol 115 (4) ◽  
pp. 717-723 ◽  
Author(s):  
J. Conchie ◽  
A J Hay ◽  
I. Strachan ◽  
G. A. Levvy
Keyword(s):  
Amino Acids ◽  
Aspartic Acid ◽  
Small Proportion ◽  
Carbohydrate Moiety ◽  
Side Chain ◽  
Terminal Position

1. Ovalbumin glycopeptides, freed from all amino acids other than aspartic acid and a small proportion of leucine by repeated digestion with Pronase, were hydrolysed by 1-aspartamido-β-N-acetylglucosamine amidohydrolase (glycoaspartamidase) to the corresponding oligosaccharides. The glycoaspartamidase did not attack ovalbumin itself. 2. Ovalbumin, with mannose/hexosamine ratio 5:4, lost 1·5moles of N-acetylglucosamine and more than 2moles of mannose after incubation with α-mannosidase and β-N-acetylglucosaminidase respectively. 3. In ovalbumin glycopeptides with approximate mannose/hexosamine ratios 5:3 and 5:4, one and two N-acetylglucosamine residues respectively were accessible to the action of β-N-acetylglucosaminidase. 4. A mixture of α-mannosidase and β-N-acetylglucosaminidase, acting on an ovalbumin glycopeptide with mannose/hexosamine ratio 5:3·7, removed nearly 4moles of mannose and 1·5moles of N-acetylglucosamine. 5. α-Mannosidase removed about 1·5moles of mannose from the ovalbumin oligosaccharide with mannose/hexosamine ratio approx. 5:3. The subsequent action of β-N-acetylglucosaminidase liberated less than 1mole of N-acetylglucosamine and made at least 1mole further of mannose accessible to α-mannosidase action. 6. It is concluded that the carbohydrate moiety of ovalbumin is linked through a glycosyl group to asparagine. In a molecule with mannose/hexosamine ratio 5:4, there are two β-N-acetylglucosamine residues linked together in a terminal position, followed by α-mannose. There is also present a side chain containing two α-mannose units.

scholarly journals The tribe Scrophularieae (Scrophulariaceae): A Review of Phylogenetic Studies

Hacquetia ◽  
2019 ◽  
Vol 18 (2) ◽  
pp. 337-347 ◽  
Author(s):  
Mehrshid Riahi ◽  
Farrokh Ghahremaninejad
Keyword(s):  
Phylogenetic Relationships ◽  
Molecular Data ◽  
Morphological Data ◽  
Hybrid Speciation ◽  
The North ◽  
Phylogenetic Studies ◽  
Phylogenetic Reconstructions ◽  
Data Collection And Analysis ◽  
History Of ◽  
Review Reports

Abstract Molecular data have been increasingly used to study the phylogenetic relationships among many taxa, including scrophs. Sometimes they have provided phylogenetic reconstructions that are in conflict with morphological data leading to a re-evaluation of long-standing evolutionary hypotheses. In this paper, we review reports of the recent knowledge of the phylogenetic relationships within Scrophularieae (2011–2017). The results of these analyses led to the following conclusions. (1) Species of Scrophularia have undergone one or more Miocene migration events occurred from eastern Asia to the North America with subsequent long dispersal and diversification in three main directions. (2) Allopolyploid and aneuploid hybrid speciation between Scrophularia species can occur, so hybridization and polyploidy have an important role for history of diversification. (3) The ancestral staminode type for the genus Scrophularia seems to be a large staminode. (4) Monophyly of the genus Verbascum with respect to the genus Scrophularia is strongly supported. (5) Oreosolen, is not monophyletic, because all accessions of Oreosolen were nested within Scrophularia. We discuss methods of data collection and analysis, and we describe the areas of conflict and agreement between molecular phylogenies.

Ozonation by-products issued from the destruction of microorganisms present in wastewaters treated for reuse

2004 ◽  
Vol 50 (2) ◽  
pp. 187-193 ◽  
Author(s):  
M.N. Rojas-Valencia ◽  
M.T. Orta-de-Velásquez ◽  
M. Vaca-Mier ◽  
V. Franco
Keyword(s):  
Amino Acids ◽  
Ascaris Suum ◽  
Correlation Coefficients ◽  
Salmonella Typhi ◽  
Faecal Coliforms ◽  
Excellent Correlation ◽  
Low Concentrations ◽  
Micro Organisms ◽  
By Products ◽  
Cellular Lysis

This work demonstrates the reaction of ozone on the amino acids comprising the covering layer of resistant micro-organisms. A secondary aim was to check the byproducts generated when ozone was applied to synthetic samples (such as Vibrio cholerae NO 01 WFCC-449, Salmonella typhi ATTC-6539, faecal coliforms and Ascaris suum). The ozone was applied at a concentration of 18.4 mgO3/min at pH 3, for different lengths of time. In the case of bacteria, results showed that, at 8 minutes, the number was reduced to the level of the Official Mexican Standards set for treated water destined for irrigation purposes (1,000 MPN/100 mL). Excellent correlation coefficients (0.95 to 0.99) were obtained for microbial concentrations versus ozone contact time. Destruction times required for 100% removal of the initial bacteria population varied between 2 and 14 minutes, while Ascaris suum required 1 hour. When Gram-negative bacteria die due to the effects of ozone, cellular lysis and the liberation of endotoxins (biodegradable) were observed. The ozonation of amino acids in the shell of Ascaris suum eggs, leads to the formation of aldehydes, such as formaldehyde and acetaldehyde, in low concentrations (0.0003 and 0.0005 μg/mL respectively). These levels are not hazardous to human health.

Correlation of the Levels of Several Constituents of Commercial Orange Juices

1968 ◽  
Vol 51 (6) ◽  
pp. 1199-1203 ◽  
Author(s):  
D E Coffin
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Multiple Regression ◽  
Correlation Coefficients ◽  
Titratable Acidity ◽  
The Other ◽  
Regression Equations

Abstract The amino acid, betaine, polyphenolics, ash, and phosphorus contents, and the titratable acidity of 32 samples of commercial orange juices and reconstituted orange juices were determined. Wide variations in the levels of these constituents were found but there were no significant differences between the juices and the reconstituted juices. Highly significant correlations were established between the levels of the amino acids, betaine, polyphenolics, ash, and phosphorus. The titratable acidity levels failed to show any significant correlation to any of the other constituents. Multiple regression equations were developed to express the interrelationships between some of the components, and correlation coefficients of combined distributions were calculated.

The Conservation of Amino Acids in the N-Terminal Position of Ribosomal and Cytosol Proteins from Escherichia coli, Bacillus stearothermophilus, and Halobacterium cutirubrum

1975 ◽  
Vol 53 (12) ◽  
pp. 1323-1327 ◽  
Author(s):  
Alastair T. Matheson ◽  
Makoto Yaguchi ◽  
Louis P. Visentin
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Bacillus Stearothermophilus ◽  
Protein Fractions ◽  
Extreme Halophile ◽  
Terminal Position ◽  
E Coli ◽  
Terminal Residue

Alanine, methionine, and serine are the predominant N-terminal residues in the cytosol and ribosomal protein fractions from the thermophile Bacillus stearothermophilus and the extreme halophile Halobacterium cutirubrum, a similar situation to that previously found in Escherichia coli. In all three bacteria the N-terminal residues of the 30S ribosomal proteins are mainly alanine [Formula: see text] methionine > serine whereas in the 50S ribosomal proteins from E. coli and B. stearothermophilus the predominant residues are methionine > alanine > serine suggesting conservation of specific N-terminal residues in these ribosomal proteins. However, the 50S ribosomal proteins from H. cutirubrum showed serine as the major N-terminal residue.

scholarly journals Aging markers in human urine: A comprehensive, non-targeted LC-MS study

2020 ◽  
Author(s):  
Takayuki Teruya ◽  
Haruhisa Goga ◽  
Mitsuhiro Yanagida
Keyword(s):  
Amino Acids ◽  
Human Subjects ◽  
Endocrine System ◽  
Correlation Coefficients ◽  
Physiological Status ◽  
Healthy Human ◽  
Age Related ◽  
Organ Systems ◽  
Sugar Phosphates ◽  
Highly Correlated

SummaryMetabolites in human biofluids document individual physiological status. We conducted comprehensive, non-targeted, non-invasive metabolomic analysis of urine from 27 healthy human subjects, comprising 13 youths (30±3 yr) and 14 seniors (76±4 yr). Quantitative analysis of 99 metabolites revealed 55 that were linked to aging, displaying significant differences in abundance between the two groups. These include 13 standard amino acids, 5 methylated, 4 acetylated, and 9 other amino acids, 6 nucleosides, nucleobases, and derivatives, 4 sugar derivatives, 5 sugar phosphates, 4 carnitines, 2 hydroxybutyrates, 1 choline, and 1 ethanolamine derivative, and glutathione disulfide. Abundances of 53 compounds decreased, while 2 increased in elderly people. Many age-linked markers were highly correlated; 42 of 55 compounds, showed Pearson’s correlation coefficients larger than 0.70. As metabolite profiles of urine and blood are quite different, age-related information in urine components offer yet more valuable insights into aging mechanisms of endocrine system and related organ systems.

scholarly journals Proposal for practical multi-kingdom classification of eukaryotes based on monophyly and comparable divergence time criteria

2017 ◽  
Author(s):  
Leho Tedersoo
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Classification Systems ◽  
Taxonomic Resolution ◽  
Divergence Times ◽  
Biodiversity Research ◽  
Phylogenetic Reconstructions ◽  
Time Of Divergence ◽  
Comparable Time

SummaryMuch of the ecological, taxonomic and biodiversity research relies on understanding of phylogenetic relationships among organisms. There are multiple available classification systems that all suffer from differences in naming, incompleteness, presence of multiple non-monophyletic entities and poor correspondence of divergence times. These issues render taxonomic comparisons across the main groups of eukaryotes and all life in general difficult at best. By using the monophyly criterion, roughly comparable time of divergence and information from multiple phylogenetic reconstructions, I propose an alternative classification system for the domain Eukarya to improve hierarchical taxonomical comparability for animals, plants, fungi and multiple protist groups. Following this rationale, I propose 32 kingdoms of eukaryotes that are treated in 10 subdomains. These kingdoms are further separated into 43, 115, 140 and 353 taxa at the level of subkingdom, phylum, subphylum and class, respectively (http://dx.doi.org/10.15156/BIO/587483). Most of the names have been used previously or these were deduced from those of the type taxa to be able to unambiguously link genera to higher taxonomic levels. In the era of phylogenomics, understanding about the phylogenetic relationships among organisms is rapidly increasing. Classifications systems must keep pace with this race to serve the research community by consistent improvements in precision in terms of taxonomic resolution and maintaining monophyly of the ingredient taxa.

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