*  Archaeoglobus - Wikipedia
Another quarter encodes proteins unique to the archaeal domain. One observation about the genome is that there are many gene ... A quarter of the genome encodes preserved proteins whose functions are not yet determined, but are expressed in other archaeons ... However, the possibility that the shared presence of these signature proteins in these archaeal lineages is due to lateral gene ... Comparative genomic studies on archaeal genomes provide evidence that members of the genus Archaeoglobus are the closest ...
  https://en.wikipedia.org/wiki/Archaeoglobus
*  Thermoplasma volcanium - Wikipedia
Similar genes encoding HU proteins have been discovered in numerous bacterial genomes, as it is a vital component in many ... 2009). "The stability of the archaeal HU histone-like DNA-binding protein from Thermoplasma volcanium". Extremophiles. 13: 1-10 ... helping to better preserve the environment. Through this method, it may also offer insight into reversing the effects of sulfur ... the genome of Thermoplasma volcanium encodes the histone-like DNA-binding protein HU, found on a segment known as huptvo. ...
  https://en.wikipedia.org/wiki/Thermoplasma_volcanium
*  Journal of Cosmology. Origin & Evolution of Life From Other Planets
Indeed, the number of signal transduction and regulatory proteins that are encoded parallel the increasing size of the genome. ... parasitic and symbiotic bacteria and archaeal parasites (e.g., N. equitans) no longer encode or express a variety of protein ... Introns have been preserved often in the same places in the genome, over the course of evolution, be it the genes of Drosophila ... Introns have been preserved often in the same places in the genome, over the course of evolution, be it the genes of Drosophila ...
  http://cosmology.net/Cosmology2.html
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
... gondii by deleting the gene encoding the KU80 protein1,2. The Δku80 strains behave normally during tachyzoite (acute) and ... The Δku80 strains make functional genomic studies feasible on the single gene as well as on the genome scale1-4. Here, we ... We use methanol as the fixative agent to preserve the spatial distribution of cells. Fixed communities are infiltrated with OCT ... have proven useful for observing spatial organization of bacterial and archaeal communities2,3. A combination of confocal ...
  https://www.jove.com/visualize/abstract/24167557/spatial-structure-facilitates-cooperation-social-dilemma-empirical
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
Complex genomes encode at least hundreds of miRNAs, which primarily inhibit the expression of a vast number of target genes ... RISC cleaves the target mRNA thereby reducing the expression of the encoded protein1,2,3. RNAi has become a powerful and widely ... RNA is isolated using a method or reagent that preserves small RNA species, and then labeled with a fluorescence dye. As a ... The interaction of viruses and their prokaryotic hosts shaped the evolution of bacterial and archaeal life. Prokaryotes ...
  https://www.jove.com/visualize/abstract/26147769/assorted-processing-synthetic-trans-acting-sirnas-its-activity
*  Last universal common ancestor - Wikipedia
"The Root of the Universal Tree of Life Inferred from Anciently Duplicated Genes Encoding Components of the Protein-Targeting ... by genetically analyzing 6.1 million protein coding genes from sequenced prokaryotic genomes of various phylogenetic trees, ... Yutin, N.; Makarova K.S.; Mekhedov S.L.; Wolf, Y.I.; Koonin, E.V. (August 2008). "The deep archaeal roots of eukaryotes". ... "Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon". Proceedings of the National Academy of Sciences of the ...
  https://en.wikipedia.org/wiki/Last_universal_common_ancestor
*  Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis...
In addition to the fusions within a single multidomain protein, we identified three groups of HEPN proteins encoded in gene- ... Makarova KS, Wolf YI, Snir S, Koonin EV: Defense islands in bacterial and archaeal genomes and prediction of novel defense ... A subset of the HEPN domains found in these systems preserve the Rx4-6H motif (in large part represented by the DUF86 family in ... and proteins via the DOC toxin. In a similar vein, we found that some PrrC-like proteins are encoded by genomic loci that ...
  https://0-biologydirect-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/1745-6150-8-15
*  Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of...
The main phylogenetic patterns for the predicted proteins encoded in six archaeal genomes. Af, Archaeoglobus fulgidus; Mt, ... As far as annotation is concerned, the purpose of primary sequence databases is to faithfully preserve the description attached ... Not unexpectedly, all newly identified A. pernix genes encode small proteins.. Conservation of the core of archaeal COGs shows ... Aeropyrum pernix has been reported to encode 2,694 putative proteins in a 1.67 megabase (Mb) genome [17]. Of these, 633 ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2000-1-5-research0009
*  Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in...
Of the two genes that co-occur with the pPIWI-RE gene we found the first to encode a protein with a conserved restriction ... suggesting that the stem eukaryotes could have possibly inherited the ancestral PIWI protein directly from their archaeal ... Gene neighborhoods were extracted and analyzed using a custom PERL script that operates on the Genbank genome or whole genome ... critical residues for guide strand-binding and when preserving the nuclease active site also cleaves the target strand. Prior ...
  https://0-biologydirect-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/1745-6150-8-13
*  Functional Subunits of Eukaryotic Chaperonin CCT/TRiC in Protein Folding
Ursic D, Ganetzky B. A Drosophila melanogaster gene encodes a protein homologous to the mouse t complex polypeptide 1. Gene. ... Archaeal chaperonins. Frontiers in Bioscience. 2009;14:1304-1324. [PubMed]. 50. Broadley SA, Hartl FU. The role of molecular ... Genome-wide RNA interference screen identifies previously undescribed regulators of polyglutamine aggregation. Proceedings of ... Clinical, pathological, and neurochemical changes in dementia: a subgroup with preserved mental status and numerous neocortical ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC3268035/?lang=en-ca
*  Publications | Microbial Ecology, University of Vienna
The 5,632,035 bp genome sequence encodes 4914 protein-coding genes and 92 RNA genes. One striking feature of this ... The candidate archaeal phylum 'Aigarchaeota' contains microorganisms from terrestrial and subsurface geothermal ecosystems. The ... Gypsum amendment to rice paddy soil stimulated bacteria involved in sulfur cycling but largely preserved the phylogenetic ... We found an unusually large number of genes encoding proteins with eukaryotic-like domains such as ankyrins, leucine-rich ...
  http://dome.csb.univie.ac.at/publications?id=939
*  The interaction of Nanoarchaeum equitans with Ignicoccus hospitalis: proteins in the contact site between two cells |...
2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci ... Whether this protein, encoded by N. equitans, is involved in protein export or import remains to be determined experimentally. ... The cells were thus preserved in a 'close-to-native' state and permitted a more differentiated view of the contact site. At ... Analysis of archaeal proteins. Cells of I. hospitalis and N. equitans were grown in co-culture as described in [3] under ...
  http://www.biochemsoctrans.org/content/37/1/127
*  The Evolution of Complex Life on Earth
Bacterial and archaeal encoded enzymes catalyze all the major processes involved in global biogeochemical cycling, playing key ... genome expansion, life on Earth, membranes, mitochondria, prokaryotic, protein folds, ribosomes, transition to complex life on ... When sectioned very thinly, fossil stromatolites may be found to contain exquisitely preserved fossil cyanobacteria and algae. ... Eukaryotes invented five times as many protein folds as eubacteria, and ten times as many as archaea. Even median protein ...
  https://sciencepolicyivh.wordpress.com/2015/02/22/the-evolution-of-complex-life-on-earth/
*  Phylogenetic distribution of translational GTPases in bacteria | BMC Genomics | Full Text
267 proteins (from 191 organisms) belong to the EF-Tu family, encoded in 1 to 2 copies of the gene per genome. Most of the ... The gene for CysN/NodQ arose from an archaeal or eukaryotic elongation factor 1 α(EF-1 α) by lateral gene transfer followed by ... where only the core set of genes for the basic processes of gene expression have been preserved. In addition, several other ... Our analysis indicates that 74 genomes code for proteins of the CysN/NodQ subfamily (Figs. 4, 5, 6). In some genomes (Nocardia ...
  https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-8-15
*  ERCC1 - Wikipedia
DNA excision repair protein ERCC-1 is a protein that in humans is encoded by the ERCC1 gene. Together with ERCC4, ERCC1 forms ... Ercc1 mutant mice dietary restriction while delaying aging also attenuates accumulation of genome-wide DNA damage and preserves ... Sgouros J, Gaillard PH, Wood RD (Mar 1999). "A relationship between a DNA-repair/recombination nuclease family and archaeal ... During NER, the ERCC1 protein interacts with the XPA protein to coordinate DNA and protein binding. Mammalian cells with mutant ...
  https://en.wikipedia.org/wiki/ERCC1
*  Visualization of the phylogenetic content of five genomes using dekapentagonal maps | Genome Biology | Full Text
Detection of QuintOPs was analogous to detection of quartets of orthologous proteins [2]. In brief, for each genome in a genome ... The nucleocytoplasm was proposed to have evolved from an archaeal-like ancestor [47, 48]. This archaeal ancestor was either an ... In order to preserve diversity among the individuals as much as possible and prevent premature convergence of the algorithm the ... Schofield JP: Molecular studies on an ancient gene encoding for carbamoyl-phosphate synthetase. Clin Sci (Lond). 1993, 84: 119- ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2004-5-3-r20
*  Antibacterial gene transfer across the tree of life | eLife
Other candidate genes encode proteins involved in nucleotide metabolism, intramembrane proteolysis, or membrane transport, but ... We found no evidence of a GH25 muramidase in 323 sequenced archaeal genomes spanning all the major phyla and sister taxa to A. ... investigated the amino acid sequences for preserved antibacterial action of the transferred lysozymes in nonbacterial genomes. ... A protein diagram for each lysozyme is drawn to scale with the light gray regions highlighting a conserved protein domain. *A. ...
  https://elifesciences.org/articles/04266
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
Genome sequencing projects have ciphered millions of protein sequence, which require knowledge of their structure and function ... Of equal importance are the abilities to extract and use the information encoded in the auditory signal. We refer to these as ... We use methanol as the fixative agent to preserve the spatial distribution of cells. Fixed communities are infiltrated with OCT ... have proven useful for observing spatial organization of bacterial and archaeal communities2,3. A combination of confocal ...
  https://www.jove.com/visualize/abstract/21655211/axelrods-metanorm-games-on-networks
*  Link between sea and land animals found | Page 3 | Sciforums
Genes encoding bacterial proteins involved in structure or assembly of flagella have not been reported in archaeal genomes. If ... and I'm sure the much larger genome of the chromosomes allows for certain select genes, preserved in both lines, to serve as ... FlaA proteins bear no sequence similarity to the FlaB proteins which make up the filament proper. The FlaB proteins have N- and ... They are comprised of FlaA sheath proteins and usually multiple (two to four) FlaB core proteins. The FlaA proteins are made ...
  http://www.sciforums.com/threads/link-between-sea-and-land-animals-found.53866/page-3
*  http://ufdc.ufl.edu/IR00001363/00001
These viruses encode two structural proteins called VP1 and VP2; the latter being the predominant protein of an icosahedral ... A candidate gene for sr2 identified by bioinformatic analysis of linked genes in the maize genome is shown to encode a putative ... CT Two small archaeal modifier proteins (SAMP1and SAMP2) and their activating enzyme, UbaA, were recently described in ... Compared to parental AAV2i8, liver tropism was rescued and muscle transduction was preserved. To address whether unique ...
  http://ufdc.ufl.edu/IR00001363/00001
*  An alternative beads‐on‐a‐string chromatin architecture in Thermococcus kodakarensis | EMBO Reports
Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM (2006) The UCSC archaeal genome browser. Nucleic Acids Res 34:D: 407-410 ... fold proteins [6, 7]. Archaeal histones form dimers in solution [8] and it has been proposed that an archaeal histone tetramer ... which has led to an evolutionary bias in underlying genome sequence, or that the genome sequence itself encodes both chromatin ... Adaptor ligates were size selected on polyacrylamide gels to preserve the size distribution of the fragments before sequencing ...
  http://embor.embopress.org/content/14/8/711
*  http://ufdc.ufl.edu/IR00000755/00001
archaeal genomes sequenced to date co ntain two gene families annotated as tgt encoding TgtA1 and TgtA2. TgtA1 corresponds to ... Although the new pr oteins evolve more rapidly than older proteins, and so do proteins that apparently have been lost, the dist ... Without effective knowledge of scrubland species, we cannot preserve the remaining genetic divers ity of this highly valuable ... The results indicate that a subset of the RNA-binding proteins show evidence of protein-protein interaction, indicating that ...
  http://ufdc.ufl.edu/IR00000755/00001
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
We use methanol as the fixative agent to preserve the spatial distribution of cells. Fixed communities are infiltrated with OCT ... Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion ... The coupling of these approaches provides an overview of both the taxonomical characteristics and the community encoded ... Institutions: San Diego State University, DOE Joint Genome Institute, University of Colorado, University of Colorado. ...
  https://www.jove.com/visualize/abstract/25748024/high-resolution-microbial-community-succession-microbially-induced
*  Frontiers | Microbial Community and Biochemical Dynamics of Biological Soil Crusts across a Gradient of Surface Coverage in the...
454 Tag-Encoded Pyrosequencing. Universal Bacterial primers 28F (5′-GAG TTT GAT CNT GGC TCA G-3′) and 519R (5′-GTN TTA CNG CGG ... 2015). "SILVA Databases," in Encyclopedia of Metagenomics: Genes, Genomes and Metagenomes: Basics, Methods, Databases and Tools ... Cabiscol, E., Tamarit, J., and Ros, J. (2010). Oxidative stress in bacteria and protein damage by reactive oxygen species. Int ... FIGURE 1. Images of black-crusted biological soils crusts (BSCs) in the western section of the Mojave National Preserve showing ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2017.01974/full
*  باستانیان - ویکی‌پدیا، دانشنامهٔ آزاد
... of the proteins encoded by any one archaeal genome being unique to the domain, although most of these unique genes have no ... "Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon" (PDF). Proceedings of the National Academy of Sciences ... The tiny 490,885 base-pair genome of Nanoarchaeum equitans is one-tenth of this size and the smallest archaeal genome known; it ... "Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a ...
  https://fa.wikipedia.org/wiki/%D8%A8%D8%A7%D8%B3%D8%AA%D8%A7%D9%86%DB%8C%D8%A7%D9%86?match=en