FlyBase: anatomical data, images and queries

Grumbling, Gary; Strelets, Victor B.

doi:10.1093/nar/gkj068

Cited by 202 publications

(198 citation statements)

References 9 publications

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“…The ventral-furrow primordium appears as a shallow deepening hollow. Images on the left show ventral views (Grumbling et al, 2006) and those on the right a 2D cross-section . …”

Section: Discussionmentioning

confidence: 99%

“…Experimental evidence shows that the average length of a Drosophila embryo is of 500µm with 2D cross sections almost circular with an average diameter of 180µm (Grumbling et al, 2006); therefore, we used this observation to justify building an exact circular crosssection into the 3D geometry of the model. Since ventral furrow invagination begins just after cellularisation has been completed, we consider the epithelial layer to have uniform thickness, with all of its cells being of the same size (although cells are not specifically modelled).…”

Section: Constructing the 3d Model Of The Embryomentioning

confidence: 99%

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A 3D finite element model of ventral furrow invagination in the Drosophila melanogaster embryo

Conte

Muñoz²,

Miodownik

2008

Journal of the Mechanical Behavior of Biomedical Materials

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Ventral furrow formation is the first large-scale movement in the Drosophila cellular blastoderm which involves the co-ordinated shape change of cells, and as such is an ideal system to use as a proof of principle for simulation methods to study the mechanics of morphogenesis. We have developed a 3D finite element method model of ventral furrow formation by decomposing the total deformation into two parts: an imposed active deformation, and an elastic passive deformation superimposed onto the latter. The model imposes as boundary conditions (i) Vito, C., Muñoz, J.J., Miodownik M., A 3D finite element model of ventral furrow invagination in the Drosophila melanogaster embryo, Journal of the Mechanical Behavior of Biomedical Materials, Vol. 1, Issue 2, pp. 188-198, 2008 compared the model with a 2D model and shown that it exhibits a more robust invagination phenomenon. The 3D model has also revealed that invagination causes a yolk flow from the central region to the anterior and posterior ends of the embryo, causing an accordion-like global compression and expansion wave to move through the embryo. Such phenomenon cannot be described by 2D models.

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“…The ventral-furrow primordium appears as a shallow deepening hollow. Images on the left show ventral views (Grumbling et al, 2006) and those on the right a 2D cross-section . …”

Section: Discussionmentioning

confidence: 99%

Section: Constructing the 3d Model Of The Embryomentioning

confidence: 99%

A 3D finite element model of ventral furrow invagination in the Drosophila melanogaster embryo

Conte

Muñoz²,

Miodownik

2008

Journal of the Mechanical Behavior of Biomedical Materials

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“…Homology search was performed on protein databases of 9 archaea, 53 bacteria, and 8 eukaryotes (for analyzed species, see supplemental Table IV). Databases were retrieved from Swissprot (http://expasy.org) in case of Archaea and Eubacteria, and SGD yeast database (26), FlyBase (27), and IPI (28) in case of eukaryotes. BLAST alignments were classified to be significant if the corresponding BLAST E values were lower than 1E-5.…”

Section: Methodsmentioning

confidence: 99%

Phosphoproteome Analysis of E. coli Reveals Evolutionary Conservation of Bacterial Ser/Thr/Tyr Phosphorylation

Maček

Gnad

Soufi

et al. 2008

Molecular & Cellular Proteomics

387

437

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Protein phosphorylation on serine, threonine, and tyrosine (Ser/Thr/Tyr) is generally considered the major regulatory posttranslational modification in eukaryotic cells. Increasing evidence at the genome and proteome level shows that this modification is also present and functional in prokaryotes. We have recently reported the first indepth phosphorylation site-resolved dataset from the model Gram-positive bacterium, Bacillus subtilis, showing that Ser/Thr/Tyr phosphorylation is also present on many essential bacterial proteins. To test whether this modification is common in Eubacteria, here we use a recently developed proteomics approach based on phosphopeptide enrichment and high accuracy MS to analyze the phosphoproteome of the model Gram-negative bacterium Escherichia coli. We report 81 phosphorylation sites on 79 E. coli proteins, with distribution of Ser/Thr/Tyr phosphorylation sites 68%/23%/9%. Despite their phylogenetic distance, phosphoproteomes of E. coli and B. subtilis show striking similarity in size, classes of phosphorylated proteins, and distribution of Ser/Thr/Tyr phosphorylation sites. By combining the two datasets, we created the largest phosphorylation site-resolved database of bacterial phosphoproteins to date (available at www. phosida.com) and used it to study evolutionary conservation of bacterial phosphoproteins and phosphorylation sites across the phylogenetic tree. We demonstrate that bacterial phosphoproteins and phosphorylated residues are significantly more conserved than their nonphosphorylated counterparts, with a number of potential phosphorylation sites conserved from Archaea to humans. Our results establish Ser/Thr/Tyr phosphorylation as a common posttranslational modification in Eubacteria, present since the onset of cellular life. Molecular & Cellular Proteomics 7:299 -307, 2008.

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“…The six-strain D. simulans alignment was obtained from the Drosophila Population Genomics Project (http:/ /www.dpgp.org), and the release 4.0 D. melanogaster sequence, annotations, and genetic map were obtained from FlyBase (Grumbling and Strelets 2006). All base calls with phred score ,35 were discarded, as was any transcript containing a stop codon in any of the seven sequences.…”

Section: Data Sources and Initial Processingmentioning

confidence: 99%

Genomewide Spatial Correspondence Between Nonsynonymous Divergence and Neutral Polymorphism Reveals Extensive Adaptation in Drosophila

et al. 2007

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The effect of recurrent selective sweeps is a spatially heterogeneous reduction in neutral polymorphism throughout the genome. The pattern of reduction depends on the selective advantage and recurrence rate of the sweeps. Because many adaptive substitutions responsible for these sweeps also contribute to nonsynonymous divergence, the spatial distribution of nonsynonymous divergence also reflects the distribution of adaptive substitutions. Thus, the spatial correspondence between neutral polymorphism and nonsynonymous divergence may be especially informative about the process of adaptation. Here we study this correspondence using genomewide polymorphism data from Drosophila simulans and the divergence between D. simulans and D. melanogaster. Focusing on highly recombining portions of the autosomes, at a spatial scale appropriate to the study of selective sweeps, we find that neutral polymorphism is both lower and, as measured by a new statistic Q S , less homogeneous where nonsynonymous divergence is higher and that the spatial structure of this correlation is best explained by the action of strong recurrent selective sweeps. We introduce a method to infer, from the spatial correspondence between polymorphism and divergence, the rate and selective strength of adaptation. Our results independently confirm a high rate of adaptive substitution ($1/3000 generations) and newly suggest that many adaptations are of surprisingly great selective effect ($1%), reducing the effective population size by $15% even in highly recombining regions of the genome.

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FlyBase: anatomical data, images and queries

Cited by 202 publications

References 9 publications

A 3D finite element model of ventral furrow invagination in the Drosophila melanogaster embryo

A 3D finite element model of ventral furrow invagination in the Drosophila melanogaster embryo

Phosphoproteome Analysis of E. coli Reveals Evolutionary Conservation of Bacterial Ser/Thr/Tyr Phosphorylation

Genomewide Spatial Correspondence Between Nonsynonymous Divergence and Neutral Polymorphism Reveals Extensive Adaptation in Drosophila

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