Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes

Karpinka, J. Brad; Fortriede, Joshua D.; Burns, Kevin A.; James-Zorn, Christina; Ponferrada, Virgilio G.; Lee, Jacqueline; Karimi, Kamran; Zorn, Aaron M.; Vize, Peter D.

doi:10.1093/nar/gku956

Cited by 126 publications

(106 citation statements)

References 23 publications

(19 reference statements)

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“…Each sequence was used to perform second and third TBLASTN and/or PSI-BLAST searches against the Xenopus laevis genomic database. We also checked the Xenbase Release v3.3 (http://www.xenbase.org) (Bowes et al, 2010;Karpinka et al, 2015) used the previous obtained 105 Pak. J. Biol.…”

Section: Methodsmentioning

confidence: 99%

Identification and Bioinformatics Analyses of the Basic Helix-loop-helix Transcription Factors in Xenopus laevis

Liu¹,

Li²

2015

Pakistan J. of Biological Sciences

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A B S T R A C TXenopus laevis is a long established model organism for developmental, behavioral and neurological studies. Herein, an updated genome-wide survey was conducted using the ongoing genome project of Xenopus laevis and 106 non-redundant Basic Helix-Loop-Helix (bHLH) genes were identified in the Xenopus laevis genome databases. Gene Ontology (GO) enrichment statistics showed 51 significant GO annotations of biological processes and molecular functions and 5 significant KEGG pathways and a number of Xenopus laevis bHLH genes play significant role in specific development or special physiology processes like the development processes of muscle and eye and other organs. Furthermore, each sub-group of the bHLH family has its special gene functions except for the common GO term categories. Molecular phylogenetic analyses revealed that among these identified bHLH proteins, 105 sequences could classified into 39 families with 46, 25, 10, 5, 16 and 3 members in the corresponding high-order groups A, B, C, D, E and F, respectively with an addition bHLH member categorized as an orphan. The present study provides much useful information for further researches on Xenopus laevis.

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Section: Methodsmentioning

confidence: 99%

Identification and Bioinformatics Analyses of the Basic Helix-loop-helix Transcription Factors in Xenopus laevis

Liu¹,

Li²

2015

Pakistan J. of Biological Sciences

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“…To create digoxigenin-labeled probes, cDNA/EST and genomic sequence information for X. tropicalis was retrieved from Xenbase (www.xenbase.org; RRID:SCR_003280; Karpinka et al, 2015). Oligonucleotides were designed to PCR amplify an 877 bp fragment of dazl from genomic DNA with a bacteriophage T7 promoter added to the 5′ end of the 'reverse' strand as follows: forward strand, 5′-GGACGATAGTGTGCACCAATTCA-3′; reverse, 5′-GCAGCTAATACGACTCACTATAGGACCACAGATTGCCC-AGTGCT-3′.…”

Section: Whole-mount In Situ Hybridizationsmentioning

confidence: 99%

Leapfrogging: primordial germ cell transplantation permits recovery of CRISPR/Cas9-induced mutations in essential genes

2016

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CRISPR/Cas9 genome editing is revolutionizing genetic loss-offunction analysis but technical limitations remain that slow progress when creating mutant lines. First, in conventional genetic breeding schemes, mosaic founder animals carrying mutant alleles are outcrossed to produce F1 heterozygotes. Phenotypic analysis occurs in the F2 generation following F1 intercrosses. Thus, mutant analyses will require multi-generational studies. Second, when targeting essential genes, efficient mutagenesis of founders is often lethal, preventing the acquisition of mature animals. Reducing mutagenesis levels may improve founder survival, but results in lower, more variable rates of germline transmission. Therefore, an efficient approach to study lethal mutations would be useful. To overcome these shortfalls, we introduce 'leapfrogging', a method combining efficient CRISPR mutagenesis with transplantation of mutated primordial germ cells into a wild-type host. Tested using Xenopus tropicalis, we show that founders containing transplants transmit mutant alleles with high efficiency. F1 offspring from intercrosses between F0 animals that carry embryonic lethal alleles recapitulate loss-of-function phenotypes, circumventing an entire generation of breeding. We anticipate that leapfrogging will be transferable to other species.

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“…We defined stage 46 based on the NF criteria of having two to 2.5 turns of the intestine, slight rounding of the operculum edges, and the presence of the cement gland as a dominant anterior feature in the head (Nieuwkoop and Faber, 1956). Stage 47 encompasses considerable morphological and behavioral changes (Gilbert and Frieden, 1981;Karpinka et al, 2015;McKeown et al, 2013;Miraucourt et al, 2012;Nieuwkoop and Faber, 1956;Sharma and Cline, 2010;Shen et al, 2011), so we further divided stage 47 into early and late substages (Fig. 1B).…”

Section: Nutrient Availability Affects Growth and Developmentmentioning

confidence: 99%

Reversible developmental stasis in response to nutrient availability in theXenopus laevisCNS

McKeown

Thompson

Cline

2016

Journal of Experimental Biology

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Many organisms confront intermittent nutrient restriction (NR), but the mechanisms to cope with nutrient fluctuations during development are not well understood. This is particularly true of the brain, the development and function of which is energy intensive. Here we examine the effects of nutrient availability on visual system development in Xenopus laevis tadpoles. During the first week of development, tadpoles draw nutrients from maternally provided yolk. Upon yolk depletion, animals forage for food. By altering access to external nutrients after yolk depletion, we identified a period of reversible stasis during tadpole development. We demonstrate that NR results in developmental stasis characterized by a decrease in overall growth of the animals, a failure to progress through developmental stages, and a decrease in volume of the optic tectum. During NR, neural progenitors virtually cease proliferation, but tadpoles swim and behave normally. Introducing food after temporary NR increased neural progenitor cell proliferation more than 10-fold relative to NR tadpoles, and cell proliferation was comparable to that of fed counterparts 1 week after delayed feeding. Delayed feeding also rescued NR-induced body length and tectal volume deficits and partially rescued developmental progression defects. Tadpoles recover from developmental stasis if food is provided within the first 9 days of NR, after which access to food fails to increase cell proliferation. These results show that early stages of tadpole brain development are acutely sensitive to fluctuations in nutrient availability and that NR induces developmental stasis from which animals can recover if food becomes available within a critical window.

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Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes

Cited by 126 publications

References 23 publications

Identification and Bioinformatics Analyses of the Basic Helix-loop-helix Transcription Factors in Xenopus laevis

Identification and Bioinformatics Analyses of the Basic Helix-loop-helix Transcription Factors in Xenopus laevis

Leapfrogging: primordial germ cell transplantation permits recovery of CRISPR/Cas9-induced mutations in essential genes

Reversible developmental stasis in response to nutrient availability in theXenopus laevisCNS

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