scholarly journals Descent of Bacteria and Eukarya from an archaeal root of life

2019 ◽  
Author(s):  
Xi Long ◽  
Hong Xue ◽  
J. Tze-Fei Wong
Keyword(s):  
Ribosomal Proteins ◽  
Wide Spectrum ◽  
Pyruvate Phosphate Dikinase ◽  
Trna Synthetases ◽  
Bacterial Genes ◽  
The Relationship

AbstractThe three biological domains delineated based on SSU rRNAs are confronted by uncertainties regarding the relationship between Archaea and Bacteria, and the origin of Eukarya. Herein the homologies between the paralogous valyl-tRNA and isoleucyl-tRNA synthetases in a wide spectrum of species revealed vertical gene transmission from an archaeal root of life through a Primitive Archaea Cluster to an Ancestral Bacteria Cluster of species. The higher homologies of the ribosomal proteins (rProts) of eukaryotic Giardia toward archaeal relative to bacterial rProts established that an archaeal-parent rather than a bacterial-parent underwent genome merger with an alphaproteobacterium to generate Eukarya. Moreover, based on the top-ranked homology of the proteins of Aciduliprofundum among archaea toward the Giardia and Trichomonas proteomes and the pyruvate phosphate dikinase of Giardia, together with their active acquisition of exogenous bacterial genes plausibly through foodchain gene adoption, the Aciduliprofundum archaea were identified as leading candidates for the archaeal-parent of Eukarya.

scholarly journals Descent of Bacteria and Eukarya From an Archaeal Root of Life

2020 ◽  
Vol 16 ◽  
pp. 117693432090826
Author(s):  
Xi Long ◽  
Hong Xue ◽  
J Tze-Fei Wong
Keyword(s):  
Genome Evolution ◽  
Ribosomal Proteins ◽  
Bacterial Species ◽  
Small Subunit ◽  
Gene Content ◽  
Ribosomal Rnas ◽  
Trna Synthetases ◽  
Eukaryotic Proteomes ◽  
Methanopyrus Kandleri ◽  
The Relationship

The 3 biological domains delineated based on small subunit ribosomal RNAs (SSU rRNAs) are confronted by uncertainties regarding the relationship between Archaea and Bacteria, and the origin of Eukarya. The similarities between the paralogous valyl-tRNA and isoleucyl-tRNA synthetases in 5398 species estimated by BLASTP, which decreased from Archaea to Bacteria and further to Eukarya, were consistent with vertical gene transmission from an archaeal root of life close to Methanopyrus kandleri through a Primitive Archaea Cluster to an Ancestral Bacteria Cluster, and to Eukarya. The predominant similarities of the ribosomal proteins (rProts) of eukaryotes toward archaeal rProts relative to bacterial rProts established that an archaeal parent rather than a bacterial parent underwent genome merger with bacteria to generate eukaryotes with mitochondria. Eukaryogenesis benefited from the predominantly archaeal accelerated gene adoption (AGA) phenotype pertaining to horizontally transferred genes from other prokaryotes and expedited genome evolution via both gene-content mutations and nucleotidyl mutations. Archaeons endowed with substantial AGA activity were accordingly favored as candidate archaeal parents. Based on the top similarity bitscores displayed by their proteomes toward the eukaryotic proteomes of Giardia and Trichomonas, and high AGA activity, the Aciduliprofundum archaea were identified as leading candidates of the archaeal parent. The Asgard archaeons and a number of bacterial species were among the foremost potential contributors of eukaryotic-like proteins to Eukarya.

scholarly journals Mitochondrial Protein Translation: Emerging Roles and Clinical Significance in Disease

2021 ◽  
Vol 9 ◽  
Author(s):  
Fei Wang ◽  
Deyu Zhang ◽  
Dejiu Zhang ◽  
Peifeng Li ◽  
Yanyan Gao
Keyword(s):  
Ribosomal Proteins ◽  
Large Fraction ◽  
Mitochondrial Protein ◽  
Mitochondrial Diseases ◽  
Protein Translation ◽  
Genetic System ◽  
Mitochondrial Rna ◽  
Trna Synthetases ◽  
Translation Factors ◽  
Genes Encoding

Mitochondria are one of the most important organelles in cells. Mitochondria are semi-autonomous organelles with their own genetic system, and can independently replicate, transcribe, and translate mitochondrial DNA. Translation initiation, elongation, termination, and recycling of the ribosome are four stages in the process of mitochondrial protein translation. In this process, mitochondrial protein translation factors and translation activators, mitochondrial RNA, and other regulatory factors regulate mitochondrial protein translation. Mitochondrial protein translation abnormalities are associated with a variety of diseases, including cancer, cardiovascular diseases, and nervous system diseases. Mutation or deletion of various mitochondrial protein translation factors and translation activators leads to abnormal mitochondrial protein translation. Mitochondrial tRNAs and mitochondrial ribosomal proteins are essential players during translation and mutations in genes encoding them represent a large fraction of mitochondrial diseases. Moreover, there is crosstalk between mitochondrial protein translation and cytoplasmic translation, and the imbalance between mitochondrial protein translation and cytoplasmic translation can affect some physiological and pathological processes. This review summarizes the regulation of mitochondrial protein translation factors, mitochondrial ribosomal proteins, mitochondrial tRNAs, and mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) in the mitochondrial protein translation process and its relationship with diseases. The regulation of mitochondrial protein translation and cytoplasmic translation in multiple diseases is also summarized.

scholarly journals Inflammation in the lungs of patients diagnosed with Cystic Fibrosis: Association with iron deficiency

SURG Journal ◽  
1969 ◽  
Vol 2 (1) ◽  
pp. 3-10
Author(s):  
Dawn Armstrong ◽  
Lindsay Robinson
Keyword(s):  
Cystic Fibrosis ◽  
Iron Deficiency ◽  
Inflammatory Cytokines ◽  
Wide Spectrum ◽  
Iron Status ◽  
Tissue Destruction ◽  
Hypoxic Conditions ◽  
Mediators Of Inflammation ◽  
The Relationship

Cystic Fibrosis (CF) is characterized by a wide spectrum of phenotypic characteristics such as; deep coughing, increased mucous production, and weight loss. However, only recently was the role of inflammation on the etiology of the disease recognized. CF is characterized as a cyclic progression of infective exacerbations and stable periods initiated by the presence of Pseudomonas Aeruginosa (PA). An increase in inflammatory cytokines/mediators and a decrease in anti-inflammatory cytokines contribute to the net inflammation and overall tissue destruction of the lungs. PA is associated with the low iron status that is seen in 60-75% of the CF population, through the presence of iron sequestering siderophores which distract iron from the tissues. Iron deficiency (ID) initiates further symptoms such as; fatigue, tachycardia, weakness, brittle nails etc, in addition to those caused by CF. The colonization of PA may be the cause or a result of increased iron (ferritin) concentrations in the lungs, but independent of the original relationship, results in a decreased iron status. Iron is used by PA under hypoxic conditions such as in the fibrosis lung, as a source of energy. Studies on the relationship between CF and ID contribute a variety of possible causes although currently no direct connection has been discovered. At this stage, further studies in this area are needed. This review will primarily focus on the affects of CF on iron status in humans, and secondarily examine the effect of mediators of inflammation in respects to ID.

Identifying pathogenic determinants of Acidovorax citrulli toward the control of bacterial fruit blotch of cucurbits

2014 ◽  
Author(s):  
Bingyu Zhao ◽  
Saul Burdman ◽  
Ronald Walcott ◽  
Tal Pupko ◽  
Gregory Welbaum
Keyword(s):  
Host Preference ◽  
Biochemical Properties ◽  
Bacterial Fruit Blotch ◽  
Group I ◽  
Experimental Approaches ◽  
Major Factors ◽  
Bacterial Genes ◽  
Relationship Of ◽  
The Relationship

The specific objectives of this BARD proposal were: Use a comparative genomics approach to identify T3Es in group I, II and III strains of A. citrulli. Determine the bacterial genes contributing to host preference. Develop mutant strains that can be used for biological control of BFB. Background to the topic: Bacterial fruit blotch (BFB) of cucurbits, caused by Acidovoraxcitrulli, is a devastating disease that affects watermelon (Citrulluslanatus) and melon (Cucumismelo) production worldwide, including both Israel and USA. Three major groups of A. citrullistrains have been classified based on their virulence on host plants, genetics and biochemical properties. The host selection could be one of the major factors that shape A. citrullivirulence. The differences in the repertoire of type III‐ secreted effectors (T3Es) among the three A. citrulligroups could play a major role in determining host preferential association. Currently, there are only 11 A. citrulliT3Es predicted by the annotation of the genome of the group II strain, AAC00‐1. We expect that new A. citrulliT3Es can be identified by a combination of bioinformatics and experimental approaches, which may help us to further define the relationship of T3Es and host preference of A. citrulli.   Implications, both scientific and agricultural: Enriching the information on virulence and avirulence functions of T3Es will contribute to the understanding of basic aspects of A. citrulli‐cucurbit interactions. In the long term, it will contribute to the development of durable BFB resistance in commercial varieties. In the short term, identifying bacterial genes that contribute to virulence and host preference will allow the engineering of A. citrullimutants that can trigger SAR in a given host. If applied as seed treatments, these should significantly improve the effectiveness and efficacy of BFB management in melon and atermelon production. 

Between Script and Ornament: Delftware Decorated with Pseudo-Chinese Characters, 1680–1720

2020 ◽  
Author(s):  
Willemijn van Noord
Keyword(s):  
Seventeenth Century ◽  
Wide Spectrum ◽  
Chinese Characters ◽  
Semantic Meaning ◽  
The Relationship ◽  
Decorative Design

Abstract In the late seventeenth century, Dutch Delftware manufacturers developed refined ceramics with an entirely new decoration of pseudo-Chinese characters. The application of this extraordinary design did not replicate Chinese porcelain examples and today it is usually dismissed as made up and meaningless. However, illegible script—be it foreign or ‘pseudo’—in any form of art has, if not a specific semantic meaning, a certain agency to evoke particular spheres of authenticity and remoteness and therefore deserves further investigation. Moreover, closer examination of these decorations and their sources of inspiration—both Dutch and Chinese, ceramic and print—reveals that there is a wide spectrum of authenticity and intentionality that ranges between script that appears to have been invented and symbols that show resemblance to actual Chinese characters. This article focusses on the transfer and reinterpretation of script as a decorative design, and how the presence of characters negotiates the relationship between Delftware and Chinese porcelain. By comparing the pseudo-characters on Delftware to pseudo-scripts on other materials, the function of pseudo-script as a design and its relationship to materiality is explored. As characters were appropriated and applied in different contexts, their connotations swayed between Chineseness and foreignness, script and ornament.

scholarly journals Rates of evolution and fossils in phylogenetic analysis: a computer simulation approach

1992 ◽  
Vol 6 ◽  
pp. 140-140
Author(s):  
John P. Huelsenbeck ◽  
David M. Hillis
Keyword(s):  
Phylogenetic Analysis ◽  
Wide Spectrum ◽  
Phylogenetic Reconstruction ◽  
Length Distribution ◽  
Temporal Position ◽  
Rate Of Evolution ◽  
Rates Of Evolution ◽  
Phylogenetic Resolution ◽  
Main Determinants ◽  
The Relationship

Whereas many studies have examined the performance of various character-data sets in phylogenetic analysis, little work has been done on the effect that various classes of taxa have on phylogenetic reconstruction. In particular, the “fossil versus living taxa” debate has concentrated mainly on the effects of fossils in reconstructing vertebrate and plant relationships. While this work has contributed to the understanding of the role that fossils play in systematics, a computer model clarifies the relationship among the main determinants of the fossil-taxa problem. In addition, simulations of phylogenies over a wide spectrum of evolutionary rates clarify the relative efficiencies of various tree-estimation procedures.In this study, computer generated phylogenies were used to examine the relationship between the temporal position and completeness of additional taxa in a phylogenetic analysis and the rate of evolution or, equivalently, the temporal scope of the phylogenetic problem. In the simulations, four fossil taxa of varying temporal position and completeness were added to an analysis that included four living taxa. Additional taxa varied in completeness (25%, 50%, 75%, and 100% completeness) and in temporal position (0%, 33%, 66%, and 100% of the distance from the ancestor to the living time plane). Fifty trees were generated each for low, low intermediate, high intermediate, and high rates of evolution or temporal scope. Because additional taxa that are 100% complete and 100% of the distance to the living time plane are equivalent to the addition of living taxa, this study directly compares the effects of addition of living versus fossil taxa in phylogenetic analysis.The importance of fossil taxa varied depending on their completeness and temporal position and on the rate of evolution under which the phylogeny was generated. In general, high completeness and temporal position near the ancestor of a clade improved phylogenetic resolution as measured by the percentage of the tree-length distribution that contains the real tree. Furthermore, the conditions of completeness and temporal position under which fossil taxa improved phylogenetic resolution over living taxa became less restrictive as the rate of evolution or the temporal scope of the tree increased.

The relationship between the spoT gene, the synthesis of stable RNA, ribosomal proteins, and the ββ′ subunits of RNA polymerase following a nutritional shiftup of Escherichia coli

1978 ◽  
Vol 56 (6) ◽  
pp. 528-533 ◽  
Author(s):  
Stephen M. Boyle ◽  
Frederick Chu ◽  
Nathan Brot ◽  
Bruce H. Sells
Keyword(s):  
Escherichia Coli ◽  
Rna Polymerase ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Rna Synthesis ◽  
Transient Increase ◽  
Spot Gene ◽  
The Relationship

The level of ppGpp and rates of synthesis of stable RNA, ribosomal protein, and the β and β′ subunits of RNA polymerase were measured following a nutritional shiftup in Escherichia coli strains, NF 929 (spoT+) and NF 930 (spoT'−). In the spoT+ strain, ppGpp levels decreased 50% within 2 min following shiftup, and the rates of synthesis of stable RNA, ribosomal proteins, and the β and β′ subunits of RNA polymerase increased with little or no lag. In contrast, in the spoT− strain, ppGpp levels transiently increased 40% during the first 6 min following shiftup. An inhibition in the rate of stable RNA synthesis and a delay in the increased synthesis of ribosomal proteins and β and β′ subunits occurred concurrently with the transient increase in ppGpp. In addition, the DNA-dependent synthesis in vitro of the β and β′ subunits of RNA polymerase was inhibited by physiological levels of ppGpp. Because of the timing and magnitude of the changes in ppGpp levels in the spoT− strain versus the timing when the new rates of stable RNA, ribosomal protein, and β and β′ subunits synthesis are reached, it is concluded that ppGpp is not the sole element regulating the expression of these genes.

A NEW APPROACH TO THE DESCRIPTION OF A BABYLONIAN HYDRAULIC WORK BY HERODOTUS

2013 ◽  
Vol 63 (2) ◽  
pp. 888-891 ◽  
Author(s):  
K.L. Katsifarakis ◽  
I. Avgoloupis
Keyword(s):  
Conference Proceedings ◽  
Scientific Knowledge ◽  
Technological Progress ◽  
Wide Spectrum ◽  
Strong Indication ◽  
New Approach ◽  
The Relationship ◽  
Scientific Fields ◽  
Journal Papers

Herodotus is a fascinating author, not only to scholars of history, but also to a wide spectrum of scientists, such as engineers, who are not usually considered to be relevant to humanistic studies. A strong indication of the persisting interest in Herodotus is the recent proliferation of books, for example those of C. Dewald and J. Marincola and A.M. Bowie, on various aspects of his work. At the same time, there is a remarkable interest in the evolution of knowledge in different scientific fields which promotes the understanding of a) the relationship between socio-economic phenomena and technological progress and b) the process of acquiring and documenting scientific knowledge. In the field of hydraulics and hydrology in particular, this interest is documented by journal papers (for example by L.W. Mays et al. and D. Koutsoyiannis et al.), books (for example by A.K. Biswas, Ö. Wikander), book chapters (for example by A.I. Wilson) and conference proceedings.

Ancient Egyptian architecture

2020 ◽  
pp. 426-440
Author(s):  
Corinna Rossi
Keyword(s):  
Large Scale ◽  
Building Materials ◽  
Wide Spectrum ◽  
Ancient Egypt ◽  
Sources Of Information ◽  
Ancient Egyptian ◽  
Large Scale Analysis ◽  
Ancient Mathematics ◽  
The Relationship ◽  
Egyptian Architecture

Architectural remains represent one of our main sources of information on ancient Egypt, and one of the first aspects of the ancient Egyptian civilization to have captured the attention of the earliest explorers. Since Egyptology was born, and while it developed as a discipline, the study of ancient Egyptian architecture evolved from initial cursory studies on portions of monuments emerging from the sand, to a wide spectrum of investigations, ranging from analyses of the chemical composition of building materials to the ancient mathematics lying at the basis of the ancient projects, and from the detailed study of specific buildings to the large-scale analysis of the relationship between architecture and landscape.

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