scholarly journals Evolution of ribosomal protein network architectures

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Youri Timsit ◽  
Grégoire Sergeant-Perthuis ◽  
Daniel Bennequin
Keyword(s):  
Selective Pressure ◽  
Experimental Studies ◽  
Protein Networks ◽  
Network Architectures ◽  
Mathematical Study ◽  
Remote Communication ◽  
Aromatic Residues ◽  
Peptidyl Transfer ◽  
Exit Tunnel ◽  
Long Range Communication

AbstractTo perform an accurate protein synthesis, ribosomes accomplish complex tasks involving the long-range communication between its functional centres such as the peptidyl transfer centre, the tRNA bindings sites and the peptide exit tunnel. How information is transmitted between these sites remains one of the major challenges in current ribosome research. Many experimental studies have revealed that some r-proteins play essential roles in remote communication and the possible involvement of r-protein networks in these processes have been recently proposed. Our phylogenetic, structural and mathematical study reveals that of the three kingdom’s r-protein networks converged towards non-random graphs where r-proteins collectively coevolved to optimize interconnection between functional centres. The massive acquisition of conserved aromatic residues at the interfaces and along the extensions of the newly connected eukaryotic r-proteins also highlights that a strong selective pressure acts on their sequences probably for the formation of new allosteric pathways in the network.

scholarly journals Molecular Evolution of the Glycosyltransferase 6 Gene Family in Primates

2016 ◽  
Vol 2016 ◽  
pp. 1-6 ◽  
Author(s):  
Eliane Evanovich ◽  
Patricia Jeanne de Souza Mendonça-Mattos ◽  
Maria Lúcia Harada
Keyword(s):  
Gene Family ◽  
Selective Pressure ◽  
Experimental Studies ◽  
Purifying Selection ◽  
Aggressive Periodontitis ◽  
Regulatory Function ◽  
Biological Functions ◽  
Putative Gene ◽  
Functional Potential ◽  
Low Diversity

Glycosyltransferase 6 gene family includes ABO, Ggta1, iGb3S, and GBGT1 genes and by three putative genes restricted to mammals, GT6m6, GTm6, and GT6m7, only the latter is found in primates. GT6 genes may encode functional and nonfunctional proteins. Ggta1 and GBGT1 genes, for instance, are pseudogenes in catarrhine primates, while iGb3S gene is only inactive in human, bonobo, and chimpanzee. Even inactivated, these genes tend to be conversed in primates. As some of the GT6 genes are related to the susceptibility or resistance to parasites, we investigated (i) the selective pressure on the GT6 paralogs genes in primates; (ii) the basis of the conservation of iGb3S in human, chimpanzee, and bonobo; and (iii) the functional potential of the GBGT1 and GT6m7 in catarrhines. We observed that the purifying selection is prevalent and these genes have a low diversity, though ABO and Ggta1 genes have some sites under positive selection. GT6m7, a putative gene associated with aggressive periodontitis, may have regulatory function, but experimental studies are needed to assess its function. The evolutionary conservation of iGb3S in humans, chimpanzee, and bonobo seems to be the result of proximity to genes with important biological functions.

scholarly journals Tomato Leaf Diseases Detection Using Deep Learning Technique

2021 ◽  
Author(s):  
Muhammad E.H. Chowdhury ◽  
Tawsifur Rahman ◽  
Amith Khandakar ◽  
Nabil Ibtehaz ◽  
Aftab Ullah Khan ◽  
...  
Keyword(s):  
Binary Classification ◽  
Experimental Studies ◽  
Tomato Leaf ◽  
Plant Diseases ◽  
Superior Performance ◽  
Disease Monitoring ◽  
World Population ◽  
Network Architectures ◽  
Comparative Performance ◽  
Human Monitoring

Plants are a major source of food for the world population. Plant diseases contribute to production loss, which can be tackled with continuous monitoring. Manual plant disease monitoring is both laborious and error-prone. Early detection of plant diseases using computer vision and artificial intelligence (AI) can help to reduce the adverse effects of diseases and also helps to overcome the shortcomings of continuous human monitoring. In this study, we have extensively studied the performance of the different state-of-the-art convolutional neural networks (CNNs) classification network architectures i.e. ResNet18, MobileNet, DenseNet201, and InceptionV3 on 18,162 plain tomato leaf images to classify tomato diseases. The comparative performance of the models for the binary classification (healthy and unhealthy leaves), six-class classification (healthy and various groups of diseased leaves), and ten-class classification (healthy and various types of unhealthy leaves) are also reported. InceptionV3 showed superior performance for the binary classification using plain leaf images with an accuracy of 99.2%. DenseNet201 also outperform for six-class classification with an accuracy of 97.99%. Finally, DenseNet201 achieved an accuracy of 98.05% for ten-class classification. It can be concluded that deep architectures performed better at classifying the diseases for the three experiments. The performance of each of the experimental studies reported in this work outperforms the existing literature.

Membrane Binding of Peptides Containing Both Basic and Aromatic Residues. Experimental Studies with Peptides Corresponding to the Scaffolding Region of Caveolin and the Effector Region of MARCKS†

Biochemistry ◽  
2000 ◽  
Vol 39 (33) ◽  
pp. 10330-10339 ◽  
Author(s):  
Anna Arbuzova ◽  
Libo Wang ◽  
Jiyao Wang ◽  
Gyöngyi Hangyás-Mihályné ◽  
Diana Murray ◽  
...  
Keyword(s):  
Membrane Binding ◽  
Experimental Studies ◽  
Aromatic Residues

3-D reconstruction and analysis of mammalian mitotic spindle structure

1992 ◽  
Vol 50 (1) ◽  
pp. 578-579
Author(s):  
Kent McDonald ◽  
David Mastronarde ◽  
Rubai Ding ◽  
Eileen O'Toole ◽  
J. Richard McIntosh
Keyword(s):  
Cross Sections ◽  
Mitotic Spindle ◽  
Experimental Studies ◽  
Video Camera ◽  
Three Dimensions ◽  
Mitotic Spindles ◽  
Black And White ◽  
Reconstruction Methods ◽  
Spindle Structure ◽  
Tissue Culture Line

Mammalian spindles are generally large and may contain over a thousand microtubules (MTs). For this reason they are difficult to reconstruct in three dimensions and many researchers have chosen to study the smaller and simpler spindles of lower eukaryotes. Nevertheless, the mammalian spindle is used for many experimental studies and it would be useful to know its detailed structure.We have been using serial cross sections and computer reconstruction methods to analyze MT distributions in mitotic spindles of PtK cells, a mammalian tissue culture line. Images from EM negatives are digtized on a light box by a Dage MTI video camera containing a black and white Saticon tube. The signal is digitized by a Parallax 1280 graphics device in a MicroVax III computer. Microtubules are digitized at a magnification such that each is 10-12 pixels in diameter.

Influence of nascent polypeptide positive charges on translation dynamics

2020 ◽  
Vol 477 (15) ◽  
pp. 2921-2934
Author(s):  
Rodrigo D. Requião ◽  
Géssica C. Barros ◽  
Tatiana Domitrovic ◽  
Fernando L. Palhano
Keyword(s):  
Mrna Decay ◽  
Translation Termination ◽  
Published Data ◽  
Translation Efficiency ◽  
Amino Acid Residues ◽  
High Concentration ◽  
Strong Argument ◽  
Translation Arrest ◽  
Exit Tunnel ◽  
Positively Charged

Protein segments with a high concentration of positively charged amino acid residues are often used in reporter constructs designed to activate ribosomal mRNA/protein decay pathways, such as those involving nonstop mRNA decay (NSD), no-go mRNA decay (NGD) and the ribosome quality control (RQC) complex. It has been proposed that the electrostatic interaction of the positively charged nascent peptide with the negatively charged ribosomal exit tunnel leads to translation arrest. When stalled long enough, the translation process is terminated with the degradation of the transcript and an incomplete protein. Although early experiments made a strong argument for this mechanism, other features associated with positively charged reporters, such as codon bias and mRNA and protein structure, have emerged as potent inducers of ribosome stalling. We carefully reviewed the published data on the protein and mRNA expression of artificial constructs with diverse compositions as assessed in different organisms. We concluded that, although polybasic sequences generally lead to lower translation efficiency, it appears that an aggravating factor, such as a nonoptimal codon composition, is necessary to cause translation termination events.

Effects of Attachment Styles on the Experience of Equity in Heterosexual Couples Relationships

2003 ◽  
Vol 50 (4) ◽  
pp. 298-310 ◽  
Author(s):  
Ina Grau ◽  
Jörg Doll
Keyword(s):  
Attachment Theory ◽  
Attachment Style ◽  
Intimate Relationships ◽  
Attachment Styles ◽  
Experimental Studies ◽  
The Other ◽  
Heterosexual Couples ◽  
Secure Attachment ◽  
Dependent Variables ◽  
Equity Ratio

Abstract. Employing one correlational and two experimental studies, this paper examines the influence of attachment styles (secure, anxious, avoidant) on a person’s experience of equity in intimate relationships. While one experimental study employed a priming technique to stimulate the different attachment styles, the other involved vignettes describing fictitious characters with typical attachment styles. As the specific hypotheses about the single equity components have been developed on the basis of the attachment theory, the equity ratio itself and the four equity components (own outcome, own input, partner’s outcome, partner’s input) are analyzed as dependent variables. While partners with a secure attachment style tend to describe their relationship as equitable (i.e., they give and take extensively), partners who feel anxious about their relationship generally see themselves as being in an inequitable, disadvantaged position (i.e., they receive little from their partner). The hypothesis that avoidant partners would feel advantaged as they were less committed was only supported by the correlational study. Against expectations, the results of both experiments indicate that avoidant partners generally see themselves (or see avoidant vignettes) as being treated equitably, but that there is less emotional exchange than is the case with secure partners. Avoidant partners give and take less than secure ones.

Exneriana – II – The Scientific Legacy of John E. Exner, Jr. 1Part of this paper was presented at the XIXth International Congress of Rorschach and Projective Methods, July 22–26, 2008, Louvain, Belgium.

2008 ◽  
Vol 29 (2) ◽  
pp. 81-107 ◽  
Author(s):  
Anne Andronikof
Keyword(s):  
Clinical Studies ◽  
Experimental Studies ◽  
Scientific Work ◽  
International Congress ◽  
Response Process ◽  
Scientific Legacy ◽  
Projective Test ◽  
Projective Methods ◽  
Comprehensive Picture ◽  
Complex Mechanisms

Based on an analysis of John Exner’s peer-reviewed published work from 1959 to 2007, plus a brief comment for an editorial in Rorschachiana, the author draws a comprehensive picture of the scientific work of this outstanding personality. The article is divided into three sections: (1) the experimental studies on the Rorschach, (2) the clinical studies using the Rorschach, and (3) Exner’s “testament,” which we draw from the last paper he saw published before his death (Exner, 2001/2002). The experimental studies were aimed at better understanding the nature of the test, in particular the respective roles of perception and projection in the response process. These fundamental studies led to a deeper understanding of the complex mechanisms involved in the Rorschach responses and introduced some hypotheses about the intentions of the author of the test. The latter were subsequently confirmed by the preparatory sketches and documents of Hermann Rorschach, which today can be seen at the H. Rorschach Archives and Museum in Bern (Switzerland). Exner’s research has evidenced the notion that the Rorschach is a perceptive-cognitive-projective test.

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