Genome sequences and genome assembly data were downloaded for the following eukaryotes: Anopheles gambiae, Apis melifera, A. thaliana, Bos taurus, Canis familiaris, Cavia porcellus, C. brenneri, C. briggsae, C. elegans, C. remanei, Chlamydomonas reinhartdii, Ciona intestinalis, D. melanogaster, Felis catus, Gallus gallus, Giardia lamblia, H. sapiens, Loxodonta africana, Macaca mulatta, Magnoporthe grisea, Neurospora crassa, Ornithorynchus anatinus, Pan troglodytes, Plasmodium falciparum, Populus trichocarpa, S. cerevisiae, S. pombe, T. rubripes, T. gondii, T. spiralis and Xenopus tropicalis (full details of source data and download sites are listed in Supplementary Table S6 ).
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Living Beings
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Amphibian
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Xenopus
Xenopus
Xenopus is a genus of semi-aquatic frogs native to parts of Africa.
These amphibians have become an important model organism in biomedical research, with their large, hardy oocytes and embryos making them well-suited for a variety of experimental techniques.
Xenopus species are widely used in the study of developmental biology, cell biology, and genetics, with their rapid embryonic development and ease of genetic manipulation providing valuable insights.
Researchers leveraging Xenopus models can explore topics ranging from early embryonic patterning to regenerative medicine.
As a well-established and versatile model system, Xenopus continues to play a key role in advancing our understanding of fundamental biological processes.
These amphibians have become an important model organism in biomedical research, with their large, hardy oocytes and embryos making them well-suited for a variety of experimental techniques.
Xenopus species are widely used in the study of developmental biology, cell biology, and genetics, with their rapid embryonic development and ease of genetic manipulation providing valuable insights.
Researchers leveraging Xenopus models can explore topics ranging from early embryonic patterning to regenerative medicine.
As a well-established and versatile model system, Xenopus continues to play a key role in advancing our understanding of fundamental biological processes.
Most cited protocols related to «Xenopus»
Anopheles gambiae
Apis
Bos taurus
Caenorhabditis elegans
Canis familiaris
Cavia porcellus
Chickens
Chlamydomonas
Ciona intestinalis
Drosophila melanogaster
Eukaryota
Felis catus
Genome
Giardia lamblia
Loxodonta
Macaca mulatta
Neurospora crassa
Pan troglodytes
Plasmodium falciparum
Populus
Saccharomyces cerevisiae
Schizosaccharomyces pombe
Xenopus
In HomeoDB2, we used genome sequence data of Homo sapiens Build 37.2 (GRCh37.p2), Mus musculus Build 37.1 (C57BL/6J), Gallus gallus Build 2.1 (Gallus_gallus-2.1), Danio rerio (Zv9), Xenopus (Silurana) tropicalis Build 1.1 (v4.2), Drosophila melanogaster (Release 5.30), Tribolium castaneum (Tcas_3.0), and Apis mellifera (Amel_4.5) from NCBI FTP server (ftp://ftp.ncbi.nih.gov/genomes/ ); Caenorhabditis elegans (WS220) from WormBase (http://www.wormbase.org/ ); Branchiostoma floridae (v2.0) from JGI (http://genome.jgi-psf.org/Brafl1/Brafl1.home.html ). Sequence searches and locus identification followed Zhong and Holland (2011 (link)). The HomeoReg dataset was collected from the literature; models of hybridization were edited from results of RNAhybrid (Rehmsmeier et al. 2004). HomeoDB2 was recoded through an Apache+Perl+MySQL web application technology base on Model-View-Controller design pattern.
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Apis
Branchiostoma floridae
Caenorhabditis elegans
Chickens
Crossbreeding
Drosophila melanogaster
Genome
Genome, Human
Mice, House
Tribolium, monocots
Xenopus
Zebrafish
To test for universality of primers and cycling conditions, we performed parallel experiments in three different laboratories (Berkeley, Cologne, Konstanz) using the same primers but different biochemical products and thermocyclers, and slightly different protocols.
The selected primers for 16S [30 ] amplify a fragment of ca. 550 bp (in amphibians) that has been used in many phylogenetic and phylogeographic studies in this and other vertebrate classes: 16SA-L, 5' - CGC CTG TTT ATC AAA AAC AT - 3'; 16SB-H, 5' - CCG GTC TGA ACT CAG ATC ACG T - 3'.
For COI we tested (1) three primers designed for birds [7 (link)] that amplify a 749 bp region near the 5'-terminus of this gene: BirdF1, 5' - TTC TCC AAC CAC AAA GAC ATT GGC AC - 3', BirdR1, 5' - ACG TGG GAG ATA ATT CCA AAT CCT G - 3', and BirdR2, 5' - ACT ACA TGT GAG ATG ATT CCG AAT CCA G - 3'; and (2) one pair of primers designed for arthropods [2 (link)] that amplify a 658 bp fragment in the same region: LCO1490, 5' - GGT CAA CAA ATC ATA AAG ATA TTG G - 3', and HCO2198, 5'-TAA ACT TCA GGG TGA CCA AAA AAT CA-3'. Sequences of additional primers for COI that had performed well in mammals and fishes were kindly made available by P. D. N. Hebert (personal communication in 2004) and these primers yielded similar results (not shown).
The optimal annealing temperatures for the COI primers were determined using a gradient thermocycler and were found to be 49–50°C; the 16S annealing temperature was 55°C. Successfully amplified fragments were sequenced using various automated sequencers and deposited in Genbank. Accession numbers for the complete data set of adult mantellid sequences used for the assessment of intra- and interspecific divergences (e.g. in Fig.5 ) are AY847959–AY848683. Accession numbers of the obtained COI sequences are AY883978–AY883995.
Nucleotide variability was scored using the software DNAsp [31 (link)] at COI and 16S priming sites of the following complete mitochondrial genomes of nine amphibians and 59 other vertebrates:Cephalochordata: AF098298, Branchiostoma. Myxiniformes: AJ404477, Myxine. Petromyzontiformes: U11880, Petromyzon. Chondrichthyes : AJ310140, Chimaera; AF106038, Raja; Y16067, Scyliorhinus; Y18134, Squalus. Actinopterygii : AY442347, Amia; AB038556, Anguilla; AB034824, Coregonus; M91245, Crossostoma; AP002944, Gasterosteus; AB047553, Plecoglossus; U62532, Polypterus; U12143, Salmo. Dipnoi : L42813, Protopterus. Coelacanthiformes : U82228, Latimeria. Amphibia, Gymnophiona : AF154051, Typhlonectes. Amphibia, Urodela : AJ584639, Ambystoma; AJ492192, Andrias; AF154053, Mertensiella; AJ419960, Ranodon. Amphibia, Anura : AB127977, Buergeria; NC_005794, Bufo; AY158705; Fejervarya; AB043889, Rana; M10217, Xenopus. Testudines : AF069423, NC_000886, Chelonia; Chrysemys; AF366350, Dogania; AY687385, Pelodiscus; AF039066, Pelomedusa. Squamata : NC_005958, Abronia; AB079613, Cordylus; AB008539, Dinodon; AJ278511, Iguana; AB079597, Leptotyphlops; AB079242, Sceloporus; AB080274, Shinisaurus. Crocodilia : AJ404872, Caiman. Aves : AF363031, Anser; AY074885, Arenaria; AF090337, Aythya; AF380305, Buteo; AB026818, Ciconia; AF362763, Eudyptula; AF090338, Falco; AY235571, Gallus; AY074886, Haematopus; AF090339, Rhea; Y12025, Struthio. Mammalia : X83427, Ornithorhynchus; Y10524, Macropus; AJ304826, Vombatus; AF061340, Artibeus; U96639, Canis; AJ222767, Cavia ; AY075116, Dugong; AB099484, Echinops; Y19184, Lama; AJ224821, Loxodonta; AB042432, Mus; AJ001562, Myoxus; AJ001588, Oryctolagus; AF321050, Pteropus; AB061527, Sorex; AF348159, Tarsius; AF217811, Tupaia; AF303111, Ursus (for species names, see Genbank under the respective accession numbers).
16S sequences of a large sample of Madagascan frogs were used to build a database in Bioedit [32 ]. Tadpole sequences were compared with this database using local BLAST searches [33 (link)] as implemented in Bioedit.
The performance of COI and 16S in assigning taxa to inclusive major clades was tested based on gene fragments homologous to those amplified by the primers used herein (see above), extracted from the complete mitochondrial sequences of 68 vertebrate taxa. Sequences were aligned in Sequence Navigator (Applied Biosystems) by a Clustal algorithm with a gap penalty of 50, a gap extend penalty of 10 and a setting of the ktup parameter at 2. PAUP* [34 ] was used with the neighbor-joining algorithm and LogDet distances and excluding pairwise comparisons for gapped sites. We chose these simple phenetic methods instead of maximum likelihood or maximum parsimony approaches because they are computationally more demanding and because the aim of DNA barcoding is a robust and fast identification of taxa rather than an accurate determination of their phylogenetic relationships.
The selected primers for 16S [30 ] amplify a fragment of ca. 550 bp (in amphibians) that has been used in many phylogenetic and phylogeographic studies in this and other vertebrate classes: 16SA-L, 5' - CGC CTG TTT ATC AAA AAC AT - 3'; 16SB-H, 5' - CCG GTC TGA ACT CAG ATC ACG T - 3'.
For COI we tested (1) three primers designed for birds [7 (link)] that amplify a 749 bp region near the 5'-terminus of this gene: BirdF1, 5' - TTC TCC AAC CAC AAA GAC ATT GGC AC - 3', BirdR1, 5' - ACG TGG GAG ATA ATT CCA AAT CCT G - 3', and BirdR2, 5' - ACT ACA TGT GAG ATG ATT CCG AAT CCA G - 3'; and (2) one pair of primers designed for arthropods [2 (link)] that amplify a 658 bp fragment in the same region: LCO1490, 5' - GGT CAA CAA ATC ATA AAG ATA TTG G - 3', and HCO2198, 5'-TAA ACT TCA GGG TGA CCA AAA AAT CA-3'. Sequences of additional primers for COI that had performed well in mammals and fishes were kindly made available by P. D. N. Hebert (personal communication in 2004) and these primers yielded similar results (not shown).
The optimal annealing temperatures for the COI primers were determined using a gradient thermocycler and were found to be 49–50°C; the 16S annealing temperature was 55°C. Successfully amplified fragments were sequenced using various automated sequencers and deposited in Genbank. Accession numbers for the complete data set of adult mantellid sequences used for the assessment of intra- and interspecific divergences (e.g. in Fig.
Nucleotide variability was scored using the software DNAsp [31 (link)] at COI and 16S priming sites of the following complete mitochondrial genomes of nine amphibians and 59 other vertebrates:
16S sequences of a large sample of Madagascan frogs were used to build a database in Bioedit [32 ]. Tadpole sequences were compared with this database using local BLAST searches [33 (link)] as implemented in Bioedit.
The performance of COI and 16S in assigning taxa to inclusive major clades was tested based on gene fragments homologous to those amplified by the primers used herein (see above), extracted from the complete mitochondrial sequences of 68 vertebrate taxa. Sequences were aligned in Sequence Navigator (Applied Biosystems) by a Clustal algorithm with a gap penalty of 50, a gap extend penalty of 10 and a setting of the ktup parameter at 2. PAUP* [34 ] was used with the neighbor-joining algorithm and LogDet distances and excluding pairwise comparisons for gapped sites. We chose these simple phenetic methods instead of maximum likelihood or maximum parsimony approaches because they are computationally more demanding and because the aim of DNA barcoding is a robust and fast identification of taxa rather than an accurate determination of their phylogenetic relationships.
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Abronia
Adult
Ambystoma
Amphibians
Anguilla
Anura
Arthropods
Aves
Bufo
Caimans
Cavia
Cephalochordata
Chimera
Dugong
Echinops
Fishes
Geese
Genes
Genes, vif
Genome, Mitochondrial
Iguanas
Inclusion Bodies
Lancelets
Loxodonta
Macropus
Mammals
Mitochondria
Myxiniformes
Nucleotides
Oligonucleotide Primers
Petromyzon
Petromyzontiformes
Plants, Arenaria
Pteropus
Raja
Rana
Rhea
Salmo salar
Squalus
Tadpole
Tarsius
Tupaia
Urodela
Ursus
Vertebrates
Xenopus
The following genome sequence files were curated from the Genome Bioinformatics Group of University of California, Santa Cruz [25 ]: Human, March 2006 (hg18); Chimpanzee, March 2006 (panTro2); Rhesus, January 2006 (rheMac2); Rat, November 2004 (rn4); Mouse, February 2006 (mm8); Cat, March 2006 (felCat3); Dog, May 2005 (canFam2); Horse, January 2007 (equCab1); Cow, March 2005 (bosTau2); Opossum, January 2006 (monDom4); Chicken, May 2006 (galGal3); Xenopus tropicalis, August 2005 (xenTro2); Zebrafish, March 2006 (danRer4); Tetraodon, February 2004 (tetNig1); Fugu, October 2004 (fr2); Stickleback, February 2006 (gasAcu1); Medaka, April 2006 (oryLat1); D. melanogaster, April 2006 (dm3); D. simulans, April 2005 (droSim1); D. sechellia, October 2005 (droSec1); D. yakuba, November 2005 (droYak2); D. erecta, August 2005 (droEre1); D. ananassae, August 2005 (droAna2); D. pseudoobscura, November 2005 (dp3); D. persimilis, October 2005 (droPer1); D. virilis, August 2005 (droVir2); D. mojavensis, August 2005 (droMoj2); D. grimshawi, August 2005 (droGri1); C. elegans, January 2007 (ce4); C. brenneri, January 2007 (caePb1); C. briggsae, January 2007 (cb3); C. remanei, March 2006 (caeRem2); and P. pacificus, February 2007 (priPac1); The genome sequence files for the Elephant, June 2005; Hedgehog, June 2006 and Armadillo, June 2005 were downloaded from the Broad Institute [26 ].
The following bacteria genome sequence files were curated from the BacMap database of University of Alberta [27 ]: Staphylococcus aureus COL; Staphylococcus aureus MRSA252; Staphylococcus aureus MSSA476, Staphylococcus aureus Mu50; Staphylococcus aureus MW2; Staphylococcus aureus N315; Staphylococcus aureus subsp. aureus NCTC 8325; Staphylococcus aureus RF122; Staphylococcus aureus subsp. aureus USA300; Staphylococcus epidermidis ATCC 12228; Staphylococcus epidermidis RP62; Staphylococcus haemolyticus JCSC1435; Escherichia coli 536; Escherichia coli APEC O1; Escherichia coli CFT073; Escherichia coli O157:H7 EDL933; Escherichia coli K12 MG1655; Escherichia coli W3110; Escherichia coli O157:H7 Sakai; Klebsiella pneumoniae MGH 78578; Salmonella enterica Choleraesuis SC-B67; Salmonella enterica Paratypi A ATCC 9150; Salmonella typhimurium LT2; Salmonella enterica CT18; Salmonella enterica Ty2; Shigella boydii Sb227; Shigella dysenteriae Sd197; Shigella flexneri 2a 2457T; and Shigella flexneri 301. The genome sequence files for Staphylococcus aureus subsp. aureus JH1, Staphylococcus aureus subsp. aureus JH9, Staphylococcus aureus Mu3, and Staphylococcus aureus subsp. aureus str. Newman were curated from the European Bioinformatics Institute of the European Molecular Biology Laboratory [28 ]. The genome sequence file for Escherichia coli UT189 was taken from Enteropathogen Resource Integration Center [29 ], and genome sequence data for Salmonella bongori was downloaded from the Sanger Institute Sequencing Centre [30 (link)].
The mosquito genome sequence files for Aedes aegypti, Anopheles gambiae and Culex pipiens were curated from the VectorBase database [31].
The following bacteria genome sequence files were curated from the BacMap database of University of Alberta [27 ]: Staphylococcus aureus COL; Staphylococcus aureus MRSA252; Staphylococcus aureus MSSA476, Staphylococcus aureus Mu50; Staphylococcus aureus MW2; Staphylococcus aureus N315; Staphylococcus aureus subsp. aureus NCTC 8325; Staphylococcus aureus RF122; Staphylococcus aureus subsp. aureus USA300; Staphylococcus epidermidis ATCC 12228; Staphylococcus epidermidis RP62; Staphylococcus haemolyticus JCSC1435; Escherichia coli 536; Escherichia coli APEC O1; Escherichia coli CFT073; Escherichia coli O157:H7 EDL933; Escherichia coli K12 MG1655; Escherichia coli W3110; Escherichia coli O157:H7 Sakai; Klebsiella pneumoniae MGH 78578; Salmonella enterica Choleraesuis SC-B67; Salmonella enterica Paratypi A ATCC 9150; Salmonella typhimurium LT2; Salmonella enterica CT18; Salmonella enterica Ty2; Shigella boydii Sb227; Shigella dysenteriae Sd197; Shigella flexneri 2a 2457T; and Shigella flexneri 301. The genome sequence files for Staphylococcus aureus subsp. aureus JH1, Staphylococcus aureus subsp. aureus JH9, Staphylococcus aureus Mu3, and Staphylococcus aureus subsp. aureus str. Newman were curated from the European Bioinformatics Institute of the European Molecular Biology Laboratory [28 ]. The genome sequence file for Escherichia coli UT189 was taken from Enteropathogen Resource Integration Center [29 ], and genome sequence data for Salmonella bongori was downloaded from the Sanger Institute Sequencing Centre [30 (link)].
The mosquito genome sequence files for Aedes aegypti, Anopheles gambiae and Culex pipiens were curated from the VectorBase database [31].
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Aedes
Anopheles gambiae
Armadillos
Caenorhabditis elegans
Chickens
Culex
Culicidae
Didelphidae
Drosophila melanogaster
Drosophila simulans
Elephants
Equus caballus
Erinaceidae
Escherichia coli
Escherichia coli K12
Escherichia coli O157
Europeans
Genome
Genome, Bacterial
Homo sapiens
Klebsiella pneumoniae
Macaca mulatta
Mice, House
Oryziinae
Pan troglodytes
Salmonella bongori
Salmonella enterica
Salmonella typhimurium LT2
Shigella boydii
Shigella dysenteriae
Shigella flexneri
Staphylococcus aureus
Staphylococcus aureus subsp. aureus
Staphylococcus epidermidis
Staphylococcus haemolyticus
Sticklebacks
Takifugu
Xenopus
Zebrafish
The Metasequoia seed cone was collected at the Leuven botanical gardens.
The resistor is a 15-kΩ resistor with a tolerance of 5% and has the four band resistor codes: brown, green, red, and gold, purchased from R&S (RS Components GmbH Hessenring 13b, 64546 Mörfelden-Walldorf).
Figurines are from LEGO™ (Billund, Denmark).
The Chrysolina americana sample was collected approximately at 50° 85′ 82.49″ N, 47° 04′ 25.3″ E.
The Drosophila samples were fixed at − 80 °C to maintain the morphology and fluorescence. The fly strain used in Fig.4 a–d expresses GFP in the eyes in a white-eyed background (genotype: y[1] M{vas-int.Dm}ZH-2A w[*]; Bloomington stock center # 24481). Fly strains used in Fig. 4 e–h were Canton-S (CS), Kyoto stock center # 105666, and w; GlaBC/CyO (Bloomington Drosophila stock center # 6662).
Grids were square mesh EM support grids, 400 copper mesh with 26 μm bars (FCF 400 – Cu – SB Electron Microscopy Science) and a finder grid with 17 μm bars (Agar scientific).
Beads were magnetic Dynabeads 500 with iron core with ~ 5 μm size (Thermo Fisher).
A Pollia dorbignyi [56 ] shell was used for the spectral imaging and was obtained at 42° 21′ 49.7″ N, 3° 09′ 47.2″ E.
Samples were mounted using plasticine.
For Additional file13 : Figure S8, a third instar larva was collected from the food of ongoing fly culture and washed in tap water. The wet larva was stuck to the insect pin by adhesion. For imaging, the larva was exposed to an atmosphere of CO2 to stop it from moving during the acquisition. A 0.2 M NaN3 solution for 30 min was used to relax the muscles [57 ].
Xenopus tropicalis embryos were placed in FEP tubes, with 1.6 mm diameter for imaging. Fixed embryos were imaged in PBS, while living ones were kept in 1/9th diluted Modified frog Ringer (MR: 0.1 M NaCl,1.8 mM KCl, 2.0 mM CaCl2, 1.0 MgCl2, 5.0 mM, HEPES-NaOH (pH 7.6), or 300 mg/l NaHCO3) solution. The tube with the frog embryo was submersed in a buffer containing glass cuvette during acquisition. For the live imaging, a crest3-gfp transgenic reporter line was crossed to the F1 generation, and the offspring was imaged (the transgenic Xenopus line is unpublished data from Schmucker’s lab).
The resistor is a 15-kΩ resistor with a tolerance of 5% and has the four band resistor codes: brown, green, red, and gold, purchased from R&S (RS Components GmbH Hessenring 13b, 64546 Mörfelden-Walldorf).
Figurines are from LEGO™ (Billund, Denmark).
The Chrysolina americana sample was collected approximately at 50° 85′ 82.49″ N, 47° 04′ 25.3″ E.
The Drosophila samples were fixed at − 80 °C to maintain the morphology and fluorescence. The fly strain used in Fig.
Grids were square mesh EM support grids, 400 copper mesh with 26 μm bars (FCF 400 – Cu – SB Electron Microscopy Science) and a finder grid with 17 μm bars (Agar scientific).
Beads were magnetic Dynabeads 500 with iron core with ~ 5 μm size (Thermo Fisher).
A Pollia dorbignyi [56 ] shell was used for the spectral imaging and was obtained at 42° 21′ 49.7″ N, 3° 09′ 47.2″ E.
Samples were mounted using plasticine.
For Additional file
Xenopus tropicalis embryos were placed in FEP tubes, with 1.6 mm diameter for imaging. Fixed embryos were imaged in PBS, while living ones were kept in 1/9th diluted Modified frog Ringer (MR: 0.1 M NaCl,1.8 mM KCl, 2.0 mM CaCl2, 1.0 MgCl2, 5.0 mM, HEPES-NaOH (pH 7.6), or 300 mg/l NaHCO3) solution. The tube with the frog embryo was submersed in a buffer containing glass cuvette during acquisition. For the live imaging, a crest3-gfp transgenic reporter line was crossed to the F1 generation, and the offspring was imaged (the transgenic Xenopus line is unpublished data from Schmucker’s lab).
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Agar
Animals, Transgenic
Anura
Atmosphere
Bicarbonate, Sodium
Buffers
Catkins
Copper
Drosophila
Electron Microscopy
Embryo
Fluorescence
Food
Genotype
Gold
HEPES
Immune Tolerance
Insecta
Iron
Larva
Magnesium Chloride
Muscle Tissue
plasticine
Sodium Azide
Sodium Chloride
Strains
Xenopus
Most recents protocols related to «Xenopus»
To investigate the conservation of the ASB9 gene across species, the amino acid sequences of the ASB9 gene from the GRCg7b version of the chicken genome (Gallus gallus) and its homologs in 25 species, including tropical clawed frog (Xenopus tropicalis), wild yak (Bos mutus), human (Homo sapiens), house mouse (Mus musculus), and mallard (Anas platyrhynchos) were downloaded from the NCBI website. Then, ClustalX2.1 was used to conduct multiple sequence alignments of the ASB9 gene proteins from various species (Table S1, Supplementary Materials ), and MEGA 7.0 was used to create phylogenetic trees with 1000 bootstrap repetitions. Finally, an evolutionary tree was constructed using EvolView (https://evolgenius.info//evolview-v2/#login , accessed on 20 September 2022).
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Amino Acid Sequence
Biological Evolution
Chickens
Ducks
Gene Products, Protein
Genes
Genome
Homo sapiens
Mice, House
Sequence Alignment
Trees
Xenopus
Xenopus laevis
To reconstruct the evolutionary history of the p53 domain in animals, the selection of TP53 homologues covering the diversity of the family is necessary.
In this example, the p53 homologues of diverse animals (the cnidarian Hydra vulgaris, four insect species: Drosophila melanogaster, Apis mellifera, Bombus terrestris and Aedes aegyptus, and the tunicate Ciona intestinalis) and the p53, p63, and p73 of diverse vertebrates (the teleost fish Danio rerio, the coelacanth Latimeria chalumnae, the amphibian Xenopus tropicalis, the lizard Anolis carolinensis, the bird Gallus gallus, and the mammals Bos taurus and H. sapiens) were chosen. The p53 of the choanoflagellate Monosiga brevicollis (a protist related to animals), also retrieved from a BLAST search was chosen as outgroup( S1 File ).
In this example, the p53 homologues of diverse animals (the cnidarian Hydra vulgaris, four insect species: Drosophila melanogaster, Apis mellifera, Bombus terrestris and Aedes aegyptus, and the tunicate Ciona intestinalis) and the p53, p63, and p73 of diverse vertebrates (the teleost fish Danio rerio, the coelacanth Latimeria chalumnae, the amphibian Xenopus tropicalis, the lizard Anolis carolinensis, the bird Gallus gallus, and the mammals Bos taurus and H. sapiens) were chosen. The p53 of the choanoflagellate Monosiga brevicollis (a protist related to animals), also retrieved from a BLAST search was chosen as outgroup
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Aedes
Amphibians
Animals
Apis
Aves
Biological Evolution
Bos taurus
Chickens
Choanoflagellata
Ciona intestinalis
Cnidaria
Drosophila melanogaster
Fishes
Hydra
Insecta
Klippel-Feil Syndrome
Lizards
Mammals
Urochordata
Vertebrates
Xenopus
Zebrafish
Wild-type Xenopus laevis were obtained from the European Xenopus Resource Centre (EXRC) at University of Portsmouth, School of Biological Sciences, UK, or Xenopus 1, USA. Frog maintenance and care was conducted according to standard procedures in the AquaCore facility, University Freiburg, Medical Center (RI_00544) and based on recommendations provided by the international Xenopus community resource centers NXR (RRID:SCR_013731) and EXRC as well as by Xenbase (http://www.xenbase.org/ , RRID:SCR_003280)(Nenni et al., 2019 (link)).
Europeans
Rana
Xenopus
Xenopus laevis
The care and handling of the Xenopus model were approved by the National Research and Development Agency (ANID) and by the ethics, Care and Use of Animals committee of the University of Concepción (Fondecyt 11160562). The animals were treated following the ethical protocols established by the United States National Institute of Health (NIH) and the amphibian euthanasia protocol was based on that described by [104 (link)].
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Amphibians
Animals
Euthanasia
Xenopus
A comparison of A. mexicanum V-V intergenic length was made with D. rerio (GRCz11) and H. sapiens (GRCh38.p12). In these cases, coordinate data was obtained from ENSEMBL gff dump (54 (link)). As for X. tropicalis, we performed a new X. tropicalis IGH locus annotation based on the corresponding ENSEMBL annotation (Xenopus_tropicalis_v9.1, GCA_000004195.3), further complemented and refined with sequence data kindly provided by Sibayshi Das (2 (link)), and X. tropicalis liver RNA-seq data (SRR579561) (55 (link)) following the same methodology as for A. mexicanum.
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2'-deoxyuridylic acid
Immunoglobulin Heavy Chain Genes
Liver
RNA-Seq
Xenopus
Top products related to «Xenopus»
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RNA polymerase II is a multi-subunit enzyme responsible for the transcription of protein-coding genes in eukaryotic cells. It catalyzes the synthesis of messenger RNA (mRNA) from a DNA template.
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DMSO is a versatile organic solvent commonly used in laboratory settings. It has a high boiling point, low viscosity, and the ability to dissolve a wide range of polar and non-polar compounds. DMSO's core function is as a solvent, allowing for the effective dissolution and handling of various chemical substances during research and experimentation.
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Alizarin Red S is a chemical compound used as a dye and a stain in laboratory procedures. It is a red-orange powder that is soluble in water and alcohol. Alizarin Red S is commonly used to stain calcium deposits in histological samples, such as bone and cartilage.
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The LSM 710 is a laser scanning microscope developed by Zeiss. It is designed for high-resolution imaging and analysis of biological and materials samples. The LSM 710 utilizes a laser excitation source and a scanning system to capture detailed images of specimens at the microscopic level. The specific capabilities and technical details of the LSM 710 are not provided in this response to maintain an unbiased and factual approach.
More about "Xenopus"
Xenopus, a genus of semi-aquatic frogs native to parts of Africa, has become an essential model organism in biomedical research.
These amphibians, with their large, hardy oocytes and embryos, are well-suited for a variety of experimental techniques, making them invaluable in the study of developmental biology, cell biology, and genetics.
Xenopus species, known for their rapid embryonic development and ease of genetic manipulation, provide researchers with valuable insights into fundamental biological processes, ranging from early embryonic patterning to regenerative medicine.
Researchers leveraging Xenopus models can explore a wide range of topics, including the use of anesthetics like MS-222, hormone treatments like HCG (Chorulon HCG), and molecular techniques like SYBR Green PCR Master Mix and RNA polymerase II.
The versatility of the Xenopus model system is further enhanced by the availability of advanced tools and technologies, such as the Acquity H-class UPLC system for high-performance liquid chromatography and the LSM 710 confocal microscope for detailed imaging.
Additionally, the use of compounds like DMSO and Alizarin Red S can facilitate various experimental procedures and analyses.
PubCompare.ai, an AI-driven platform, empowers researchers to unleash the full potential of Xenopus research.
This innovative tool helps users locate the best protocols from literature, pre-prints, and patents through intelligent comparisons, allowing them to optimize their experimental workflows and enhance reproducibility.
With PubCompare.ai, researchers can discover and refine their Xenopus-based studies, advancing our understanding of fundamental biological processes and driving breakthroughs in fields such as developmental biology, regenerative medicine, and beyond.
These amphibians, with their large, hardy oocytes and embryos, are well-suited for a variety of experimental techniques, making them invaluable in the study of developmental biology, cell biology, and genetics.
Xenopus species, known for their rapid embryonic development and ease of genetic manipulation, provide researchers with valuable insights into fundamental biological processes, ranging from early embryonic patterning to regenerative medicine.
Researchers leveraging Xenopus models can explore a wide range of topics, including the use of anesthetics like MS-222, hormone treatments like HCG (Chorulon HCG), and molecular techniques like SYBR Green PCR Master Mix and RNA polymerase II.
The versatility of the Xenopus model system is further enhanced by the availability of advanced tools and technologies, such as the Acquity H-class UPLC system for high-performance liquid chromatography and the LSM 710 confocal microscope for detailed imaging.
Additionally, the use of compounds like DMSO and Alizarin Red S can facilitate various experimental procedures and analyses.
PubCompare.ai, an AI-driven platform, empowers researchers to unleash the full potential of Xenopus research.
This innovative tool helps users locate the best protocols from literature, pre-prints, and patents through intelligent comparisons, allowing them to optimize their experimental workflows and enhance reproducibility.
With PubCompare.ai, researchers can discover and refine their Xenopus-based studies, advancing our understanding of fundamental biological processes and driving breakthroughs in fields such as developmental biology, regenerative medicine, and beyond.