scholarly journals Relationship of diversity and the secondary structure in 16S-23S rDNA internal transcribed spacer: a case in Vibrio parahaemolyticus

2018 ◽  
Vol 365 (17) ◽  
Author(s):  
Jia Yu ◽  
Xi Peng ◽  
Yuxi Wei ◽  
Yue Mi ◽  
Baojie Zhu ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Internal Transcribed Spacer ◽  
Vibrio Parahaemolyticus ◽  
Relationship Of

scholarly journals Relationship of Secondary Structures and Wear Resistance of Antifriction Aluminum Alloys for Journal Bearings from the Point of View of Self-Organization During Friction

Entropy ◽  
2019 ◽  
Vol 21 (11) ◽  
pp. 1048 ◽  
Author(s):  
Gershman ◽  
Mironov ◽  
Podrabinnik ◽  
Kuznetsova ◽  
Gershman ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Organization Theory ◽  
Secondary Structures ◽  
Point Of View ◽  
Self Organization ◽  
Friction Surfaces ◽  
Relationship Of ◽  
The Relationship ◽  
Secondary Structure Composition ◽  
Antifriction Alloys

The paper investigates the relationship between the tribological properties/compositions of new aluminum antifriction alloys and compositions of the secondary structures formed on their friction surfaces. Eight alloys with various compositions have been analyzed. The elemental compositions of the secondary structures on their friction surfaces have been determined. The relationship between the alloy secondary structure compositions with wear rate has been found. An attempt has been made to determine the secondary structure composition patterns based on the non-equilibrium thermodynamics and self-organization theory.

scholarly journals Effect of N- and C-Terminal Amino Acids on the Interfacial Binding Properties of Phospholipase D from Vibrio parahaemolyticus

2018 ◽  
Vol 19 (8) ◽  
pp. 2447
Author(s):  
Fanghua Wang ◽  
Ruixia Wei ◽  
Abdelkarim Abousalham ◽  
Wuchong Chen ◽  
Bo Yang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Secondary Structure ◽  
Phospholipase D ◽  
Vibrio Parahaemolyticus ◽  
Terminal Segment ◽  
Amino Acid Sequences ◽  
Loop Structure ◽  
Binding Properties ◽  
Phospholipid Monolayers ◽  
Terminal Amino

The effects of N-terminal (1–34 amino acids) and C-terminal (434–487 amino acids) amino acid sequences on the interfacial binding properties of Phospholipase D from Vibrio parahaemolyticus (VpPLD) were characterized by using monomolecular film technology. Online tools allowed the prediction of the secondary structure of the target N- and C-terminal VpPLD sequences. Various truncated forms of VpPLD with different N- or C-terminal deletions were designed, based on their secondary structure, and their membrane binding properties were examined. The analysis of the maximum insertion pressure (MIP) and synergy factor “a” indicated that the loop structure (1–25 amino acids) in the N-terminal segment of VpPLD had a positive effect on the binding of VpPLD to phospholipid monolayers, especially to 1,2-dimyristoyl-sn-glycero-3-phosphoserine and 1,2-dimyristoyl-sn-glycero-3-phosphocholine. The deletion affecting the N-terminus loop structure caused a significant decrease of the MIP and synergy factor a of the protein for these phospholipid monolayers. Conversely, the deletion of the helix structure (26–34 amino acids) basically had no influence on the binding of VpPLD to phospholipid monolayers. The deletion of the C-terminal amino acids 434–487 did not significantly change the binding selectivity of VpPLD for the various phospholipid monolayer tested here. However, a significant increase of the MIP value for all the phospholipid monolayers strongly indicated that the three-strand segment (434–469 amino acids) had a great negative effect on the interfacial binding to these phospholipid monolayers. The deletion of this peptide caused a significantly greater insertion of the protein into the phospholipid monolayers examined. The present study provides detailed information on the effect of the N- and C-terminal segments of VpPLD on the interfacial binding properties of the enzyme and improves our understanding of the interactions between this enzyme and cell membranes.

Phylogenetic position of Arabis arenicola and generic limits of Aphragmus and Eutrema (Brassicaceae) based on sequences of nuclear ribosomal DNA

2006 ◽  
Vol 84 (2) ◽  
pp. 269-281 ◽  
Author(s):  
Suzanne I. Warwick ◽  
Ihsan A. Al-Shehbaz ◽  
Connie A. Sauder
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Molecular Data ◽  
The Other ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
New Combinations ◽  
Arabidopsis Lyrata ◽  
Relationship Of

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region of 45 taxa were used to determine the phylogenetic relationship of Arabis arenicola to Arabis , Arabidopsis , Braya , and Eutrema , and that of Eutrema to the purportedly related genera Aphragmus , Lignariella , Neomartinella , Platycraspedum , Taphrospermum , and Thellungiella . Arabis arenicola was originally described as Eutrema in 1830, transferred to Arabis in 1898, and has remained in Arabis to the present, even though it is morphologically more similar to Arabidopsis, Braya, and Eutrema. Sequence data were obtained from representative taxa of Arabis, Arabidopsis, and related Boechera and Catolobus, Braya and Neotorularia, and Eutrema, Aphragmus, Lignariella, Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella. The five Arabis arenicola accessions examined had ITS sequences that were identical to each other and to four Arabidopsis lyrata accessions. In both maximum parsimony and maximum likelihood analyses, Arabis arenicola fell within the Arabidopsis clade and was closely aligned with Arabidopsis lyrata. Two of six purportedly related genera were not closely related to Eutrema. Both analyses placed Lignariella within a separate well-supported clade with Aphragmus, while the other four genera, Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella, fell within a well-supported clade with Eutrema. Morphology and molecular data strongly suggest transferring Arabis arenicola to Arabidopsis, expanding Aphragmus to include Lignariella, and expanding Eutrema to include Neomartinella, Platycraspedum, Taphrospermum, and Thellungiella. New combinations in Arabidopsis and Aphragmus are proposed.

scholarly journals The systematic position of Gradsteinia andicola Ochyra (Donrichardsiaceae, Bryopsida) : evidence from nrDNA internal transcribed spacer sequences

2000 ◽  
Vol 18 (1) ◽  
pp. 75-85
Author(s):  
Michael Stech ◽  
Jan-Peter Frahm
Keyword(s):  
New Zealand ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Systematic Position ◽  
Nuclear Ribosomal Dna ◽  
Maximum Parsimony Tree ◽  
Systematic Relationship ◽  
Parsimony Tree ◽  
Internal Transcribed Spacer Sequences ◽  
Relationship Of

Nuclear ribosomal DNA internal transcribed spacer (ITS) 1/2 sequences of the Colombian endemic Gradsteinia andicola were determined and compared with those of 16 other species of the Hypnales (Amblystegiaceae, Brachytheciaceae, Hypnaceae, Plagiotheciaceae and Rhytidiaceae). In a maximum parsimony tree Gradsteinia andicola belongs to a well supported clade consisting of Amblystegium, Cratoneuron, Cratoneuropsis, Hypnobartlettia and Palustriella, and seems to be closely related to Cratoneuropsis relaxa from New Zealand. Gradsteinia andicola is therefore transferred to Amblystegiaceae, but the genus Gradsteinia is maintained. The systematic relationship of Amblystegiaceae and Donrichardsiaceae is discussed.

scholarly journals Secondary Structure of the Ribosomal Internal Transcribed Spacer (ITS) Region of Hypsizygus marmoreus

2013 ◽  
Vol 23 (10) ◽  
pp. 1260-1266
Author(s):  
Ju-Ri Woo ◽  
Hyeokjun Yoon ◽  
Young-Hyun You ◽  
Chang-Yun Lee ◽  
Won-Sik Kong ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Internal Transcribed Spacer ◽  
Its Region ◽  
Hypsizygus Marmoreus
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