An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes. New Archaeal Clusters of Orthologous Genes (arCOGs) were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon) using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for
Researchers often utilize functional genes as a proxy for the potential of microbial communities to mediate specific biochemical and nutrient cycling processes. Metabolic pathways for such processes are, in many cases, composed of multiple steps, requiring more than one protein to function. Genomic data also suggests that pathways can sometimes be incomplete, though it is not well understood what the ecological implications of incomplete pathways might be. The genes for 11 different inorganic nitrogen transformation pathways were thus investigated in 6,384 bacterial and 252 complete archaeal genomes. The analysis aimed to determine how commonly pathways were incomplete, how frequently different pathways co-occur, and how these finding relate to the evolutionary history of microbes. Results from this study indicate that the co-occurrence of different N cycling pathways is infrequent and that pathways are frequently incomplete. These data imply that many microbes specialize in specific metabolic ...
Extreme halophilic, salt-loving, Archaea are members of the third Domain of Life, thriving in hypersaline environments reaching saturating levels of sodium chloride, nine times the salinity of seawater. The unique position of Archaea in the Tree of Life makes these organisms fascinating. Archaea have characteristics of both Bacteria and Eukarya. For example, the archaeal genome structure is more similar to bacteria, while the information transfer macromolecules are eukaryotic-like. With the release of several haloarchaeal genomes I am using comparative genomics to identify haloarchaeal conserved proteins that likely play key roles in these organisms unique environmental adaptations as well as the conservation of the information transfer system of halophilic archaea. ...
The context analysis report aims at understanding drivers and obstacles to the diffusion of Photovoltaic and Building Integrated Photovoltaic solar technologies in the cities involved in the project ...
p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.,/p> ,p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.,/p> ,p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).,/p> ,p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x,sup>64,/sup> + x,sup>4,/sup> + x,sup>3,/sup> + x + 1. The algorithm is described in the ISO 3309 standard. ,/p> ,p class=publication>Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.,br /> ,strong>Cyclic redundancy and other checksums,/strong>,br /> ,a href=http://www.nrbook.com/b/bookcpdf.php>Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993),/a>),/p> Checksum:i ...
Codons consist of six bases and there are six reading frames for each DNA strand, so ... so researchers must evaluate six open reading frames.
The increasing wealth of genomic data from cultured and uncultured microorganisms provides the opportunity to develop a systematic taxonomy based on evolutionary relationships. Here we propose a standardized archaeal taxonomy, as part of the Genome Taxonomy Database (GTDB), derived from a 122 concatenated protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence. The resulting archaeal taxonomy is stable under a range of phylogenetic variables, including marker genes, inference methods, and tree rooting scenarios. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes (ICNP) while taking into account proposals to formally recognise the rank of phylum and to use genome sequences as type material. The taxonomy is based on 2,392 quality screened archaeal genomes, the great majority of which (93.3%) required one or more changes to their existing taxonomy, mostly as a result of incomplete classification. ...
The similarities between essential molecular mechanisms in Archaea and Eukarya make it possible to discover, using comparative genomics, new fundamental mechanisms conserved between these two domains. We are studying a complex of two proteins conserved in Archaea and Eukarya whose precise biological role and biochemical function remain unknown. One of them is a universal protein known as Kae1 (kinase-asociated endopeptidase 1). The second protein is a serine/threonine kinase corresponding to the proteins Bud32 in Saccharomyces cerevisiae and PRPK (p53-related protein kinase) in humans. The genes encoding the archaeal orthologues of Kae1 and PRPK are either contiguous or even fused in many archaeal genomes. In S. cerevisiae, Kae1 and Bud32 (PRPK) belong to a chromatin-associated complex [KEOPS (kinase, endopeptidase and other proteins of small size)/EKC (endopeptidase-like kinase chromatin-associated)] that is essential for telomere elongation and transcription of essential genes. Although Kae1 ...
The ATP-binding cassette (ABC) transporters form one of the largest known protein families, and are widespread in bacteria, archaea, and eukaryotes. They couple ATP hydrolysis to active transport of a wide variety of substrates such as ions, sugars, lipids, sterols, peptides, proteins, and drugs. The structure of a prokaryotic ABC transporter usually consists of three components; typically two integral membrane proteins each having six transmembrane segments, two peripheral proteins that bind and hydrolyze ATP, and a periplasmic (or lipoprotein) substrate-binding protein. Many of the genes for the three components form operons as in fact observed in many bacterial and archaeal genomes. On the other hand, in a typical eukaryotic ABC transporter, the membrane spanning protein and the ATP-binding protein are fused, forming a multi-domain protein with the membrane-spanning domain (MSD) and the nucleotide-binding domain (NBD ...
The ATP-binding cassette (ABC) transporters form one of the largest known protein families, and are widespread in bacteria, archaea, and eukaryotes. They couple ATP hydrolysis to active transport of a wide variety of substrates such as ions, sugars, lipids, sterols, peptides, proteins, and drugs. The structure of a prokaryotic ABC transporter usually consists of three components; typically two integral membrane proteins each having six transmembrane segments, two peripheral proteins that bind and hydrolyze ATP, and a periplasmic (or lipoprotein) substrate-binding protein. Many of the genes for the three components form operons as in fact observed in many bacterial and archaeal genomes. On the other hand, in a typical eukaryotic ABC transporter, the membrane spanning protein and the ATP-binding protein are fused, forming a multi-domain protein with the membrane-spanning domain (MSD) and the nucleotide-binding domain (NBD ...
The forkhead-associated (FHA) domain [(PUBMED:7482699)] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands [(PUBMED:11911881)]. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.. ...
© SJul 20073ISCRAM 2007 User, task, and context analysis Methodology for identifying user- and usage-centered design requirements Identifies different types and critical characteristics of target users, tasks and contexts Usually conducted at the application level
Additional calculations are performed including the search for similarities within or among genus, the search for signal sequence or transmembrane segments, predicted secondary structure and disulfide bonds, and the search for homologs with a known 3D structure in the Protein Databank. As a result, BactPepDB provides insights about candidate peptides in complete prokaryote genomes, and provides information about their conservation, together with some of their expected biological/structural features. A brief overview of the database interface and its functionalities can be found at the bottom of the Help page under the form of a step-by-step tutorial.. As of 08/08/2020, the database contains 1,747,413 Peptides from 557 Genuses, 1,226 Species and 2,240 Strains.. ...
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TY - JOUR. T1 - Diversity of Haloquadratum and other haloarchaea in three, geographically distant, Australian saltern crystallizer ponds. AU - Oh, Dickson. AU - Porter, Kate. AU - Russ, Brendan. AU - Burns, David. AU - Dyall-Smith, Mike. PY - 2010/3. Y1 - 2010/3. N2 - Haloquadratum walsbyi is frequently a dominant member of the microbial communities in hypersaline waters. 16S rRNA gene sequences indicate that divergence within this species is very low but relatively few sites have been examined, particularly in the southern hemisphere. The diversity of Haloquadratum was examined in three coastal, but geographically distant saltern crystallizer ponds in Australia, using both culture-independent and culture-dependent methods. Two 97%-OTU, comprising Haloquadratum- and Halorubrum-related sequences, were shared by all three sites, with the former OTU representing about 40% of the sequences recovered at each site. Sequences 99.5% identical to that of Hqr. walsbyi C23T were present at all three sites ...
The question of which proteins are involved in the interaction cell-cell contact and in transport between these two archaea cannot be addressed, at least presently, by genetics, such as mutagenesis or knockouts. We have therefore chosen the direct approach, by isolating a complex of membrane and membrane-associated proteins, using detergent-induced solubilization, followed by size-exclusion chromatography.. In the analysis of all proteins identified to be present in the detergent-solubilized membranes, approx. 26% of the I. hospitalis proteins, but only 4.2% of the N. equitans proteins belong to the category Transport and metabolism. This reflects the known difference between both organisms in their physiology and genome capacity: whereas I. hospitalis has the ability to grow alone and has a genome with full capacity for all biosynthetic pathways, N. equitans is not able to thrive alone and its genome is very compact and highly reduced; enzymes involved in many biosynthetic pathways cannot be ...
Citation. Ermolaeva, M. D., White, O., Salzberg, S. L.. Prediction of Operons In Microbial Genomes. Nucleic Acids Res. 2001 Mar 01; 29(5): 1216-21.. PubMed Citation. Abstract. Operon structure is an important organization feature of bacterial genomes. Many sets of genes occur in the same order on multiple genomes; these conserved gene groupings represent candidate operons. This study describes a computational method to estimate the likelihood that such conserved gene sets form operons. The method was used to analyze 34 bacterial and archaeal genomes, and yielded more than 7600 pairs of genes that are highly likely (P: ,/= 0.98) to belong to the same operon. The sensitivity of our method is 30-50% for the Escherichia coli genome. The predicted gene pairs are available from our World Wide Web site www.tigr.org/tigr-scripts/operons/operons.cgi.. ...
original description Jolivet, E., LHaridon, S., Corre, E., Forterre, P., and Prieur, D. Thermococcus gammatolerans sp. nov., a hyperthermophilic archaeon from a deep-sea hydrothermal vent that resists ionizing radiation. Int. J. Syst. Evol. Microbiol. (2003) 53:847-851. [details] ...
Arrive with a DNA sample, leave with a genome Course Description This two-week course covers the process of sequencing, assembling and annotating a bacterial or archaeal genome from scratch. It then builds on these skills to train students in further analysis of microbial genomes, such as the prediction of metabolic pathways, comparative genomics, and phylogenomics. This course goes deeper than basic push-button genome assembly and annotation tools - students learn how relevant genomics software tools work and how to make intelligent, situation-dependent decisions when analysing microbial genomes. Students work on real data related to their own research by submitting DNA from an isolate of their choosing several weeks before the course begins. Illumina MiSeq sequencing is then carried out so that sequencing data is ready for students when they arrive. Is this the course for you? If you are a PhD student who would like to answer a research question using a microbial genome but dont know how ...
The DOE Joint Genome Institute (JGI), collaborating with CRDs Biological Data Management and Technology Center (BDMTC), announced last month an upgrade of the metagenome data management and analysis system, IMG/M, on the anniversary of its launch.. Developed by BDMTCs data management and software engineers and scientists of JGIs Genome Biology and Microbial Ecology Programs, IMG/M is a valuable asset for a growing community of biologists. Metagenomics refers to the genomic study of batches of microbes in their natural environments instead of those cultivated individually in lab cultures. IMG/M provides tools for analyzing the capability of microbial communities based on their metagenome sequence-in the context of reference isolate genomes-using a variety of public functional and pathway resources.. Since the release of its initial experimental version in 2006, IMG/M has been used by JGI scientists and their collaborators for analyzing several environmental microbial communities, and has been ...
TY - JOUR. T1 - Human contamination in bacterial genomes has created thousands of spurious proteins. AU - Breitwieser, Florian P.. AU - Pertea, Mihaela. AU - Zimin, Aleksey V.. AU - Salzberg, Steven L.. PY - 2019. Y1 - 2019. N2 - Contaminant sequences that appear in published genomes can cause numerous problems for downstream analyses, particularly for evolutionary studies and metagenomics projects. Our large-scale scan of complete and draft bacterial and archaeal genomes in the NCBI RefSeq database reveals that 2250 genomes are contaminated by human sequence. The contaminant sequences derive primarily from high-copy human repeat regions, which themselves are not adequately represented in the current human reference genome, GRCh38. The absence of the sequences from the human assembly offers a likely explanation for their presence in bacterial assemblies. In some cases, the contaminating contigs have been erroneously annotated as containing protein-coding sequences, which over time have ...
Background: The genetic code is redundant, meaning that most amino acids can be encoded by more than one codon. Highly expressed genes tend to use optimal codons to increase the accuracy and speed of translation. Thus, codon usage biases provide a signature of the relative expression levels of genes, which can, uniquely, be quantified across the domains of life. Results: Here we describe a general statistical framework to exploit this phenomenon and to systematically associate genes with environments and phenotypic traits through changes in codon adaptation. By inferring evolutionary signatures of translation efficiency in 911 bacterial and archaeal genomes while controlling for confounding effects of phylogeny and inter-correlated phenotypes, we linked 187 gene families to 24 diverse phenotypic traits. A series of experiments in Escherichia coli revealed that 13 of 15, 19 of 23, and 3 of 6 gene families with changes in codon adaptation in aerotolerant, thermophilic, or halophilic microbes. ...
I just found this patch of yours that was never screened while cleaning up the rebase state in one of my clones. I have amended the patch to avoid warnings and to avoid running the test when the patch type does not allow coalescing. I think this should go into 2.16 as it clarifies what works with the new rebase implementation. It is of course also valuable to avoid regressions. 1 patch for repository http://darcs.net/screened: patch ba4ca2fb7b6969a24356d36bc4551b43cf7b7e95 Author: Ganesh Sittampalam ,[email protected], Date: Thu May 14 21:29:32 CEST 2020 * test for whether rebase suspend/unsuspend introduces ...
This article explores the beginning of the terrain beyond filing a mechanics lien-the terrain covered by two little Latin words: lis pendens.
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Among the tRNA population of the archaeal parasite Nanoarchaeum equitans are five species assembled from separate 5 and 3 tRNA halves and four species derived from tRNA precursors containing introns. In both groups an intervening sequence element must be removed during tRNA maturation. A bulge-hel …
Strains C23T and HBSQ001 were isolated from solar salterns and are novel square-shaped, aerobic, extremely halophilic members of the domain Archaea and family Halobacteriaceae. Cells stained Gram-negative and grew optimally in media containing 18 % salts at around neutral pH. Mg2+ is not required. The DNA G+C content of both isolates was 46.9 mol% and DNA-DNA cross-hybridization showed a relatedness of 80 %. Their 16S rRNA gene sequences showed only 2 nucleotide differences (99.9 % identity) and phylogenetic tree reconstructions with other recognized members of the Halobacteriaceae indicated that they formed a distinct clade, with the closest relative being Halogeometricum borinquense PR 3T (91.2 % sequence identity). The major polar glycolipid of both isolates was the sulfated diglycosyl diether lipid S-DGD-1. Electron cryomicrosopy of whole cells revealed similar internal structures, such as gas vesicles and polyhydroxyalkanoate granules, but the cell wall of isolate HBSQ001 displayed a more complex S
This list of sequenced eubacterial genomes contains all the eubacteria known to have publicly available complete genome sequences. Most of these sequences have been placed in the International Nucleotide Sequence Database Collaboration, a public database which can be seKarched on the web. A few of the listed genomes may not be in the INSDC database, but in other public databases[verification needed]. Genomes listed as Unpublished are in a database, but not in the peer-reviewed scientific literature. For the genomes of archaea see list of sequenced archaeal genomes. Genome project Human microbiome project List of sequenced eukaryotic genomes List of sequenced archaeal genomes List of sequenced plastomes Entrez Genome Database Search. National Center for Biotechnology Information. Search for details on specific genomes by organism name and strain. Schell MA, et al. (2002). The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. ...
Planchestainer, Matteo and Segaud, Nathalie and Shanmugam, Muralidharan and McMaster, Jonathan and Paradisi, Francesca and Albrecht, Martin (2018) Carbene in cupredoxin protein scaffolds: replacement of a histidine ligand in the active site substantially alters copper redox properties. Angewandte Chemie International Edition, 57 (33). pp. 10677-10682. ISSN 1521-3773 Carucci, Cristina and Bruen, Larah and Gascón, Victoria and Paradisi, Francesca and Magner, Edmond (2018) Significant enhancement of structural stability of the hyperhalophilic ADH from Haloferax volcanii via entrapment on metal organic framework support. Langmuir . ISSN 0743-7463 Contente, Martina L. and Paradisi, Francesca (2018) Self-sustaining closed-loop multienzyme mediated conversion of amines into alcohols in continuous reactions. Nature Catalysis . ISSN 2520-1158 Cassidy, Jennifer and Paradisi, Francesca (2018) Haloquadratum walsbyi yields a versatile, NAD+/NADP+ dual affinity, thermostable, alcohol dehydrogenase (HwADH). ...
RNA degradation can be an essential aspect in the regulation of gene appearance. the examined mRNAs displaying half-lives between 8 and 12 min. The entire mean half-life was 10 min, which is certainly considerably longer compared to the ones within the various other prokaryotes investigated so far. As seen in and NRC-1 previously, is among simply two archaea sequenced to time that are lacking the primary subunits from the archaeal exosome. This complicated orthologous towards the RNA degrading exosome of eukarya is situated in all the archaeal genomes sequenced so far. Fast decay of mRNA allows quick version of microorganisms to adjustments in the surroundings by altering the appearance of chosen genes. The half-lives of specific transcripts as well as transcript sections in a organism show significant variations adding to differential gene appearance. The stabilities of many bacterial transcripts vary in response to exterior factors (analyzed in guide 46); the stabilities of eukaryotic ...
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From: Elijah Newren via GitGitGadget ,[email protected], To: [email protected] Cc: [email protected], [email protected], [email protected], [email protected], [email protected], [email protected], [email protected], Junio C Hamano ,[email protected],, Elijah Newren ,[email protected], Subject: [PATCH v2 12/15] rebase tests: mark tests specific to the am-backend with --am Date: Mon, 23 Dec 2019 18:49:56 +0000 Message-ID: ,c905d[email protected]gmail.com, (raw) In-Reply-To: ,[email protected], From: Elijah Newren ,[email protected], We have many rebase tests in the testsuite, and often the same test is repeated multiple times just testing different backends. For those tests that were specifically trying to test the am backend, add the --am flag. Signed-off-by: Elijah Newren ,[email protected], --- t/t3400-rebase.sh , 10 +++++----- t/t3401-rebase-and-am-rename.sh , 4 ++-- ...
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Arheju šūnu izmēri ir līdzīgi lielākajai prokariotu daļai - vidējais diametrs ap 1 μm. Vissīkākie starp arhejiem ir sugas Nanoarchaeum equitans pārstāvji - 0,4 μm. Šūnu forma ir visdažādākā. Sastopamas ir sfēriskas, iegarenas, spirāliskas, trīsstūra un taisnstūra formas. Daudziem arhejiem ir viciņas, kuru sastāvā, atšķirībā no baktērijām, ietilpst vairāku veidu flagellīni. Arheji nespēj sintezēt sarežģītus hidrolītiskus fermentus, tāpēc tie lielākoties spēj pārstrādāt tikai vienkāršākās organiskās vielas. Tomēr tie spēj eksistēt daudz plašākā ārējās vides diapazonā un ir mazāk no tās atkarīgi.. Bez 16S rRNS arhejiem ir arī citas unikālas īpatnības:. ...
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Some Archaea thrive in extreme places such as in thermal pools, hot vents at the bottom of the sea, extremely salty water, and even in underground oil reserves. This book examines the diverse Archaea kingdom and the division of these organisms by their unusual biology into three main groups. It also explains why little in general is known about them, and why further classification of Archaea is so difficult.
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I am finding that PSAT is 6 MINUTES behind the predictions of the previously provided original Launch TLE : ULTRASat3 1 99993U 15140.67013889 .00040043 00000-0 10235-2 0 00009 2 99993 055.0004 339.9238 0251027 182.3314 074.3075 15.12517086000014 So until I get new ones. Just point at AOS and wait 6 miuntes. Also, I had said not to TX PSK31 on the 10m u plink until you heard the downlink. Well, that was dumb advise, because the transponder does not come up unless it hears PSK31! So the new rule is, Listen first. If not heard, TX anyway. If not heard then, Fix your problem, and try again? We dont know how the power budget will work out. So all we can do is watch. Bob, WB4APR ...
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