scholarly journals Use of the Codon Table to Quantify the Evolutionary Role of Random Mutations

Algorithms ◽  
2021 ◽  
Vol 14 (9) ◽  
pp. 270
Author(s):  
Mihaly Mezei
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Evolutionary Tree ◽  
Sequence Alignments ◽  
Amino Acid Mutation ◽  
Amino Acid Similarity ◽  
The Subject ◽  
Evolutionary Role ◽  
Intense Research

The various biases affecting RNA mutations during evolution is the subject of intense research, leaving the extent of the role of random mutations undefined. To remedy this lacuna, using the codon table, the number of codons representing each amino acid was correlated with the amino acid frequencies in different branches of the evolutionary tree. The correlations were seen to increase as evolution progressed. Furthermore, the number of RNA mutations that resulted in a given amino acid mutation were found to be correlated with several widely used amino acid similarity tables (used in sequence alignments). These correlations were seen to increase when the observed codon usage was factored in.

scholarly journals Efficient Emission in Halide Layered Double Perovskites: The Role of Sb3+ Substitution in Cs4Cd1–xMnxBi2Cl12 Phosphors

2020 ◽  
Author(s):  
Brenda Vargas ◽  
Eduardo Coutiño-Gonzalez ◽  
Oscar Ovalle-Encinia ◽  
Citlali Sánchez-Aké ◽  
Diego Solis-Ibarra
Keyword(s):  
Optoelectronic Properties ◽  
Double Perovskites ◽  
Spin Orbit Coupling ◽  
Fixed Amount ◽  
Electronic Delocalization ◽  
The Subject ◽  
Halide Perovskites ◽  
Pl Emission ◽  
Intense Research

Layered halide perovskites and double perovskites optoelectronic properties have recently been the subject of intense research. Layered double perovskites represent the merging of both worlds, and as such, have the potential to further expand the already vast space of optoelectronic properties and applications of halide perovskites. Despite having more than 40 known members, to date, only the <111>-oriented layered double perovskites: Cs<sub>4</sub>Cd<sub>1</sub>–<sub>x</sub>Mn<sub>x</sub><b>Bi</b><sub>2</sub>Cl<sub>12</sub>, have shown efficient photoluminescence (PL). In this work, we replaced Bi with Sb to further investigate the electronic structure and PL properties of these materials, resulting in two new families of layered inorganic perovskites alloys with full solubility. The first family, Cs<sub>4</sub>Cd<sub>1</sub>–<sub>x</sub>Mn<b>Sb</b><sub>2</sub>Cl<sub>12</sub>, exhibits a PL emission at 605 nm ascribed to Mn<sup>2+</sup> centers in octahedral coordination, and a maximum photoluminescence quantum yield PLQY of 28.5%. The second family of alloys, also with full solubility, Cs<sub>4</sub>Cd<sub>0.8</sub>Mn<sub>0.2</sub>(Sb<sub>1</sub>–<sub>y</sub>Bi<sub>y</sub>)<sub>2</sub>Cl<sub>12</sub>, contains a fixed amount of Mn<sup>2+</sup> and Cd<sup>2+</sup> cations but different concentrations of the trivalent metals. This variability allows the tuning of the PL emission from 603 nm to 614 nm. We show that the decreased efficiency of the Cs<sub>4</sub>Cd<sub>1</sub>–<sub>x</sub>Mn<sub>x</sub>Sb<sub>2</sub>Cl<sub>12</sub>family compared to Cs<sub>4</sub>Cd<sub>1</sub>–<sub>x</sub>Mn<sub>x</sub><b>Bi</b><sub>2</sub>Cl<sub>12</sub>, is mostly due to a decreased spin-orbit coupling in Sb and the subsequent increased electronic delocalization compared to the Bi alloys, reducing the energy transfer to Mn<sup>2+</sup> centers. This work lays out a roadmap to understand and achieve high photoluminescence efficiencies in layered double perovskites.<p></p>

scholarly journals Phospho-N-Acetyl-Muramyl-Pentapeptide Translocase from Escherichia coli: Catalytic Role of Conserved Aspartic Acid Residues

2004 ◽  
Vol 186 (6) ◽  
pp. 1747-1757 ◽  
Author(s):  
Adrian J. Lloyd ◽  
Philip E. Brandish ◽  
Andrea M. Gilbey ◽  
Timothy D. H. Bugg
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Aspartic Acid ◽  
Catalytic Mechanism ◽  
Partial Purification ◽  
Sequence Alignments ◽  
Structural Environment ◽  
Essential Enzyme ◽  
Covalent Intermediate

ABSTRACT Phospho-N-acetyl-muramyl-pentapeptide translocase (translocase 1) catalyzes the first of a sequence of lipid-linked steps that ultimately assemble the peptidoglycan layer of the bacterial cell wall. This essential enzyme is the target of several natural product antibiotics and has recently been the focus of antimicrobial drug discovery programs. The catalytic mechanism of translocase 1 is believed to proceed via a covalent intermediate formed between phospho-N-acetyl-muramyl-pentapeptide and a nucleophilic amino acid residue. Amino acid sequence alignments of the translocase 1 family and members of the related transmembrane phosphosugar transferase superfamily revealed only three conserved residues that possess nucleophilic side chains: the aspartic acid residues D115, D116, and D267. Here we report the expression and partial purification of Escherichia coli translocase 1 as a C-terminal hexahistidine (C-His6) fusion protein. Three enzymes with the site-directed mutations D115N, D116N, and D267N were constructed, expressed, and purified as C-His6 fusions. Enzymatic analysis established that all three mutations eliminated translocase 1 activity, and this finding verified the essential role of these residues. By analogy with the structural environment of the double aspartate motif found in prenyl transferases, we propose a model whereby D115 and D116 chelate a magnesium ion that coordinates with the pyrophosphate bridge of the UDP-N-acetyl-muramyl-pentapeptide substrate and in which D267 therefore fulfills the role of the translocase 1 active-site nucleophile.

scholarly journals Symbiotic bacteria on the cuticle of the leaf-cutting ant Acromyrmex subterraneus subterraneus protect workers from attack by entomopathogenic fungi

2011 ◽  
Vol 8 (3) ◽  
pp. 461-464 ◽  
Author(s):  
Thalles C. Mattoso ◽  
Denise D. O. Moreira ◽  
Richard I. Samuels
Keyword(s):  
Direct Evidence ◽  
Fungus Garden ◽  
Defensive Strategy ◽  
Fungal Entomopathogen ◽  
Leaf Cutting ◽  
The Subject ◽  
Anti Fungal ◽  
First Time ◽  
Intense Research

Although only discovered in 1999, the symbiotic filamentous actinobacteria present on the integument of certain species of leaf-cutting ants have been the subject of intense research. These bacteria have been shown to specifically suppress fungal garden parasites by secretion of antibiotics. However, more recently, a wider role for these bacteria has been suggested from research revealing their generalist anti-fungal activity. Here we show, for the first time, evidence for a role of these bacteria in the defence of young worker ants against a fungal entomopathogen. Experimental removal of the bacterial bio-film using an antibiotic resulted in a significant increase in susceptibility of worker ants to infection by the entomopathogenic fungus Metarhizium anisopliae . This is the first direct evidence for the advantage of maintaining a bacterial bio-film on the cuticle as a defensive strategy of the ants themselves and not exclusively for protection of the fungus garden.

scholarly journals Efficient Emission in Halide Layered Double Perovskites: The Role of Sb3+ Substitution in Cs4Cd1–xMnxBi2Cl12 Phosphors

2020 ◽  
Author(s):  
Brenda Vargas ◽  
Eduardo Coutiño-Gonzalez ◽  
Oscar Ovalle-Encinia ◽  
Citlali Sánchez-Aké ◽  
Diego Solis-Ibarra
Keyword(s):  
Optoelectronic Properties ◽  
Double Perovskites ◽  
Spin Orbit Coupling ◽  
Fixed Amount ◽  
Electronic Delocalization ◽  
The Subject ◽  
Halide Perovskites ◽  
Pl Emission ◽  
Intense Research

Layered halide perovskites and double perovskites optoelectronic properties have recently been the subject of intense research. Layered double perovskites represent the merging of both worlds, and as such, have the potential to further expand the already vast space of optoelectronic properties and applications of halide perovskites. Despite having more than 40 known members, to date, only the <111>-oriented layered double perovskites: Cs<sub>4</sub>Cd<sub>1</sub>–<sub>x</sub>Mn<sub>x</sub><b>Bi</b><sub>2</sub>Cl<sub>12</sub>, have shown efficient photoluminescence (PL). In this work, we replaced Bi with Sb to further investigate the electronic structure and PL properties of these materials, resulting in two new families of layered inorganic perovskites alloys with full solubility. The first family, Cs<sub>4</sub>Cd<sub>1</sub>–<sub>x</sub>Mn<b>Sb</b><sub>2</sub>Cl<sub>12</sub>, exhibits a PL emission at 605 nm ascribed to Mn<sup>2+</sup> centers in octahedral coordination, and a maximum photoluminescence quantum yield PLQY of 28.5%. The second family of alloys, also with full solubility, Cs<sub>4</sub>Cd<sub>0.8</sub>Mn<sub>0.2</sub>(Sb<sub>1</sub>–<sub>y</sub>Bi<sub>y</sub>)<sub>2</sub>Cl<sub>12</sub>, contains a fixed amount of Mn<sup>2+</sup> and Cd<sup>2+</sup> cations but different concentrations of the trivalent metals. This variability allows the tuning of the PL emission from 603 nm to 614 nm. We show that the decreased efficiency of the Cs<sub>4</sub>Cd<sub>1</sub>–<sub>x</sub>Mn<sub>x</sub>Sb<sub>2</sub>Cl<sub>12</sub>family compared to Cs<sub>4</sub>Cd<sub>1</sub>–<sub>x</sub>Mn<sub>x</sub><b>Bi</b><sub>2</sub>Cl<sub>12</sub>, is mostly due to a decreased spin-orbit coupling in Sb and the subsequent increased electronic delocalization compared to the Bi alloys, reducing the energy transfer to Mn<sup>2+</sup> centers. This work lays out a roadmap to understand and achieve high photoluminescence efficiencies in layered double perovskites.<p></p>

scholarly journals Mutations within the P2 Domain of Norovirus Capsid Affect Binding to Human Histo-Blood Group Antigens: Evidence for a Binding Pocket

2003 ◽  
Vol 77 (23) ◽  
pp. 12562-12571 ◽  
Author(s):  
Ming Tan ◽  
Pengwei Huang ◽  
Jaroslaw Meller ◽  
Weiming Zhong ◽  
Tibor Farkas ◽  
...  
Keyword(s):  
Amino Acid ◽  
Blood Group ◽  
Binding Pocket ◽  
Single Amino Acid ◽  
Blood Group Antigens ◽  
Sequence Alignments ◽  
Amino Acid Mutation ◽  
Multiple Sequence ◽  
Amino Acid Mutations ◽  
Function Relationship

ABSTRACT Noroviruses (NORs) are an important cause of acute gastroenteritis. Recent studies of NOR receptors showed that different NORs bind to different histo-blood group antigens (HBGAs), and at least four distinct binding patterns were observed. To determine the structure-function relationship for NORs and their receptors, two strains representing two of the four binding patterns were studied. Strain VA387 binds to HBGAs of A, B, and O secretors, whereas strain MOH binds to HBGAs of A and B secretors only. Using multiple sequence alignments, homology modeling, and structural analysis of NOR capsids, we identified a plausible “pocket” in the P2 domain that may be responsible for binding to HBGA receptors. This pocket consists of a conserved RGD/K motif surrounded by three strain-specific hot spots (N302, T337, and Q375 for VA387 and N302, N338, and E378 for MOH). Subsequent mutagenesis experiments demonstrated that all four sites played important roles in binding. A single amino acid mutation at T337 (to A) in VA387 or a double amino acid mutation at RN338 (to TT) in MOH abolished binding completely. Change of the entire RGD motif to SAS abolished binding in case of VA387, whereas single amino acid mutations in that motif did not have an apparent effect on binding to A and B antigens but decreased binding to H antigen. Multiple mutations at the RGK motif of MOH (SIRGK to TFRGD) completely knocked out the binding. Mutation of N302 or Q375 in VA387 affected binding to type O HBGA only, while switch mutants with three amino acid changes at either site from MOH to VA387 resulted in a weak binding to type O HBGAs. A further switch mutant with three amino acid changes at E378 from MOH to VA387 diminished the binding to type A HBGA only. Taken together, our data indicate that the binding pocket likely exists on NOR capsids. Direct evidence of this hypothesis requires crystallography studies.

Top-Down Processing and Visual Reorientation Illusions in a Virtual Reality Environment

2004 ◽  
Vol 63 (3) ◽  
pp. 143-149 ◽  
Author(s):  
Fred W. Mast ◽  
Charles M. Oman
Keyword(s):  
Virtual Reality ◽  
Visual Processing ◽  
Line Length ◽  
Perceptual Cues ◽  
Virtual Reality Environment ◽  
Top Down ◽  
Test Conditions ◽  
The Subject ◽  
Processing Mechanisms

The role of top-down processing on the horizontal-vertical line length illusion was examined by means of an ambiguous room with dual visual verticals. In one of the test conditions, the subjects were cued to one of the two verticals and were instructed to cognitively reassign the apparent vertical to the cued orientation. When they have mentally adjusted their perception, two lines in a plus sign configuration appeared and the subjects had to evaluate which line was longer. The results showed that the line length appeared longer when it was aligned with the direction of the vertical currently perceived by the subject. This study provides a demonstration that top-down processing influences lower level visual processing mechanisms. In another test condition, the subjects had all perceptual cues available and the influence was even stronger.

The future role of the psychiatrist in Europe – a UEMS perspective

2014 ◽  
Vol 11 (01) ◽  
pp. 35-42
Author(s):  
M. Hermans
Keyword(s):  
Mental Health ◽  
Mental Health Professionals ◽  
Health Professionals ◽  
General Interest ◽  
Future Role ◽  
Personal Opinion ◽  
The Future ◽  
The Subject ◽  
The Many

SummaryThe author presents his personal opinion inviting to discussion on the possible future role of psychiatrists. His view is based upon the many contacts with psychiatrists all over Europe, academicians and everyday professionals, as well as the familiarity with the literature. The list of papers referred to is based upon (1) the general interest concerning the subject when representing ideas also worded elsewhere, (2) the accessibility to psychiatrists and mental health professionals in Germany, (3) being costless downloadable for non-subscribers and (4) for some geographic aspects (e.g. Belgium, Spain, Sweden) and the latest scientific issues, addressing some authors directly.

Alignment

2016 ◽  
pp. 33-50
Author(s):  
Pier Giuseppe Rossi
Keyword(s):  
Teaching And Learning ◽  
Enactive Approach ◽  
The World ◽  
Strategic Role ◽  
Education Today ◽  
Current Context ◽  
The Subject

The subject of alignment is not new to the world of education. Today however, it has come to mean different things and to have a heuristic value in education according to research in different areas, not least for neuroscience, and to attention to skills and to the alternation framework.This paper, after looking at the classic references that already attributed an important role to alignment in education processes, looks at the strategic role of alignment in the current context, outlining the shared construction processes and focusing on some of the ways in which this is put into effect.Alignment is part of a participatory, enactive approach that gives a central role to the interaction between teaching and learning, avoiding the limits of behaviourism, which has a greater bias towards teaching, and cognitivism/constructivism, which focus their attention on learning and in any case, on that which separates a teacher preparing the environment and a student working in it.

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