Database resources of the National Center for Biotechnology

Wheeler, David; Church, Deanna M.; Federhen, Scott; Lash, Alex E.; Madden, Thomas; Pontius, Joan; Schuler, Gregory D.; Schriml, Lynn M.; Sequeira, Edwin; Tatusova, Tatiana; Wagner, Lukas

doi:10.1093/nar/gkg033

Cited by 883 publications

(638 citation statements)

References 27 publications

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“…We matched all loci to the A. carolinensis genome (AnoCar2.0) using Megablast (Zhang, Schwartz, Wagner, & Miller, 2000) implemented in the database resources of the National Center for Biotechnology (NCBI; Wheeler et al., 2003). For each locus, we estimated the average number of pairwise differences between individuals within clades (π; see 3) and an estimate of genetic differentiation (Hudson, Slatkin, & Maddison, 1992) between clades.…”

Section: Methodsmentioning

confidence: 99%

Diversification in wild populations of the model organism Anolis carolinensis: A genome‐wide phylogeographic investigation

Manthey¹,

Tollis

Lemmon

et al. 2016

Ecology and Evolution

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The green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary history in association with morphological, physiological, or reproductive biology studies among sampling localities and necessitate increased effort to resolve evolutionary relationships among natural populations. Here, we used anchored hybrid enrichment of hundreds of genetic markers across the genome of A. carolinensis and identified five strongly supported phylogeographic groups. Using multiple analyses, we produced a fully resolved species tree, investigated relative support for each lineage across all gene trees, and identified mito‐nuclear discordance when comparing our results to previous studies. We found fixed differences in only one clade—southern Florida restricted to the Everglades region—while most polymorphisms were shared between lineages. The southern Florida group likely diverged from other populations during the Pliocene, with all other diversification during the Pleistocene. Multiple lines of support, including phylogenetic relationships, a latitudinal gradient in genetic diversity, and relatively more stable long‐term population sizes in southern phylogeographic groups, indicate that diversification in A. carolinensis occurred northward from southern Florida.

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Section: Methodsmentioning

confidence: 99%

Diversification in wild populations of the model organism Anolis carolinensis: A genome‐wide phylogeographic investigation

Manthey¹,

Tollis

Lemmon

et al. 2016

Ecology and Evolution

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“…This demonstrated that in vivo the human gene was subject to similar control to the mouse gene. Although detailed analysis of the mouse promoter has not been reported, the mouse and human caspase 3 cDNA sequences are 83% identical (HomoloGene database 45 ) while at the protein level they are 87% identical (UniGene database 45 ). Therefore, it is likely that the gene promoters are similar in these two species also.…”

Section: Discussionmentioning

confidence: 99%

“…However in vivo, the human gene and protein appeared to be regulated as normal for their murine counterparts suggesting that caspase activity is tightly regulated under physiological conditions. This is hardly surprising considering the high degree of homology between the human and mouse caspase 3 amino-acid sequences which are 87% identical (UniGene database 45 ).…”

Section: Discussionmentioning

confidence: 99%

Mice overexpressing human caspase 3 appear phenotypically normal but exhibit increased apoptosis and larger lesion volumes in response to transient focal cerebral ischaemia

et al. 2004

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Caspase 3 activation has been implicated in cell death following a number of neurodegenerative insults. To determine whether caspase genes can affect the susceptibility of cells to neurodegeneration, a transgenic mouse line was created, expressing human caspase 3 under control of its own promoter. The human gene was regulated by the murine homeostatic machinery and human procaspase 3 was expressed in the same tissues as mouse caspase 3. These novel transgenic mice appeared phenotypically and developmentally normal and survived in excess of 2 years. Behavioural assessment using the 5-choice serial reaction time task found no differences from wild-type littermates. Caspase activity was found to be tightly regulated under physiological conditions, however, significantly larger lesions were obtained when transgenic mice were subjected to focal cerebral ischaemia/reperfusion injury compared to wildtype littermates. These data demonstrate that mice overexpressing human caspase 3 are essentially normal, however, they have increased susceptibility to degenerative insults.

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“…Open reading frames (ORFs) were identified using GeneWorks software (IntelliGenetics) and ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html) (Wheeler et al, 2003). The criterion for defining an ORF was a size of at least 150 nt (50 aa) with minimal overlap.…”

Section: Methodsmentioning

confidence: 99%

Genomic and host range studies of Maruca vitrata nucleopolyhedrovirus

Chen

Lee

et al. 2008

Journal of General Virology

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The complete genome of the Maruca vitrata nucleopolyhedrovirus (MaviNPV) isolated from the legume pod borer, Maruca vitrata (Lepidoptera: Pyralidae), was sequenced. It was found to be 111 953 bp in length, with an overall 39 % G+C content, and contained 126 open reading frames (ORFs) encoding predicted proteins of over 50 aa. The gene content and gene order of MaviNPV have the highest similarity to those of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) and their shared homologous genes are 100 % collinear. In fact, MaviNPV seems to be a mini-AcMNPV that is native to Taiwan and possesses a smaller genome with fewer auxiliary genes than the AcMNPV type species. Except for one ORF (Mv74), all of the MaviNPV ORFs have homologues in the AcMNPV genome. MaviNPV is the first lepidopteranspecific baculovirus to lack homologues of vfgf and odv-e66. In addition, MaviNPV lacks the baculovirus repeat ORF (bro) gene that corresponds to AcMNPV ORF2. Five homologous regions (hrs) were located within the MaviNPV genome, and these contained a total of 44 imperfect palindromes. Phylogenetic analysis of the whole genome revealed that MaviNPV was separated from the common ancestor of AcMNPV and Bombyx mori nucleopolyhedrovirus before these two viral species diverged from each other. Moreover, replication of MaviNPV in several cell lines and an egfp-MaviNPV infection assay revealed that IPLB-LD-652Y cells are only partially permissive to MaviNPV, which supports our conclusion that MaviNPV is a distinct species of the group I lepidopteran NPVs.

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Database resources of the National Center for Biotechnology

Cited by 883 publications

References 27 publications

Diversification in wild populations of the model organism Anolis carolinensis: A genome‐wide phylogeographic investigation

Diversification in wild populations of the model organism Anolis carolinensis: A genome‐wide phylogeographic investigation

Mice overexpressing human caspase 3 appear phenotypically normal but exhibit increased apoptosis and larger lesion volumes in response to transient focal cerebral ischaemia

Genomic and host range studies of Maruca vitrata nucleopolyhedrovirus

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