A PARAMETRIC JOINT MODEL OF DNA-PROTEIN BINDING, GENE EXPRESSION AND DNA SEQUENCE DATA TO DETECT TARGET GENES OF A TRANSCRIPTION FACTOR

AbstractVentral leg patterning in Drosophila is controlled by the expression of the redundant T-box Transcription factors midline (mid) and H15. Here we show that mid represses the Dpp-activated gene Daughters against decapentaplegic (Dad) through a consensus TBE site in the minimal enhancer, Dad13. Mutating the Dad13 DNA sequence results in an increased and broadening of Dad expression. We further demonstrate that the engrailed-homology-1 domain of Mid is critical for regulating the levels of phospho-Mad, a transducer of Dpp-signaling. However, we find that mid does not affect all Dpp-target genes as we demonstrate that brinker (brk) expression is unresponsive to mid. This study further illuminates the interplay between mechanisms involved in determination of cellular fate and the varied roles of mid.Summary statementVentral patterning is controlled in part by the T-box Transcription factor midline blocking Dpp signaling and Dpp-activated genes, though midline does not affect the Dpp-repressed gene brk.

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Caudal counter-represses Hunchback to regulate even-skipped stripe 2 expression in Drosophila embryos

10.1101/226373 ◽

2017 ◽

Cited By ~ 1

Author(s):

Ben J. Vincent ◽

Max V. Staller ◽

Francheska Lopez-Rivera ◽

Meghan D.J. Bragdon ◽

Zeba Wunderlich ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Dna Sequence ◽

Binding Sites ◽

Target Genes ◽

Drosophila Development ◽

Sequence Features ◽

Regulatory Dna ◽

Drosophila Embryos ◽

Direct Activator

AbstractHunchback is a bifunctional transcription factor that can activate and repress gene expression in Drosophila development. We investigated the regulatory DNA sequence features that control Hunchback function by perturbing enhancers for one of its target genes, even-skipped. While Hunchback directly represses the eve stripe 3+7 enhancer, we found that in the eve stripe 2+7 enhancer, Hunchback repression is prevented by Caudal binding—this relationship is called counter-repression. We found evidence that this relationship is conserved by comparing predicted binding sites for Hunchback and Caudal across orthologous eve stripe 2 enhancers. These results alter the textbook view of eve stripe 2 regulation wherein Hb is depicted as a direct activator. Instead, to generate stripe 2, Hunchback repression must be counteracted by Caudal binding. We discuss the implications of this interaction for eve stripe 2 regulation and evolution.

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Using DNA sequence data to investigate the invasive spotted lanternfly's origin, parasitoids, and microbial associates

10.1603/ice.2016.109017 ◽

2016 ◽

Author(s):

Julie M. Urban

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Dna Sequence Data

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DNA sonification for public engagement in bioinformatics

BMC Research Notes ◽

10.1186/s13104-021-05685-7 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Heleen Plaisier ◽

Thomas R. Meagher ◽

Daniel Barker

Keyword(s):

Dna Sequence ◽

Public Engagement ◽

Sequence Data ◽

Sensory Perception ◽

Data Representation ◽

Sequence Information ◽

Dna Sequence Data ◽

Public Events ◽

Dna Base ◽

Alternative Means

Abstract Objective Visualisation methods, primarily color-coded representation of sequence data, have been a predominant means of representation of DNA data. Algorithmic conversion of DNA sequence data to sound—sonification—represents an alternative means of representation that uses a different range of human sensory perception. We propose that sonification has value for public engagement with DNA sequence information because it has potential to be entertaining as well as informative. We conduct preliminary work to explore the potential of DNA sequence sonification in public engagement with bioinformatics. We apply a simple sonification technique for DNA, in which each DNA base is represented by a specific note. Additionally, a beat may be added to indicate codon boundaries or for musical effect. We report a brief analysis from public engagement events we conducted that featured this method of sonification. Results We report on use of DNA sequence sonification at two public events. Sonification has potential in public engagement with bioinformatics, both as a means of data representation and as a means to attract audience to a drop-in stand. We also discuss further directions for research on integration of sonification into bioinformatics public engagement and education.

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When DNA sequence data and morphological results fit together: Phylogenetic position of Crenubiotus within Macrobiotoidea (Eutardigrada) with description of Crenubiotus ruhesteini sp. nov

Journal of Zoological Systematics & Evolutionary Research ◽

10.1111/jzs.12449 ◽

2021 ◽

Author(s):

Roberto Guidetti ◽

Ralph O. Schill ◽

Ilaria Giovannini ◽

Edoardo Massa ◽

Sara Elena Goldoni ◽

...

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Phylogenetic Position ◽

Dna Sequence Data

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A new Liopeltis Fitzinger, 1843 (Squamata: Colubridae) from Pulau Tioman, Peninsular Malaysia

Zootaxa ◽

10.11646/zootaxa.4766.3.6 ◽

2020 ◽

Vol 4766 (3) ◽

pp. 472-484

Author(s):

HANNAH E. SOM ◽

L. LEE GRISMER ◽

PERRY L. JR. WOOD ◽

EVAN S. H. QUAH ◽

RAFE M. BROWN ◽

...

Keyword(s):

Mitochondrial Dna ◽

New Species ◽

Dna Sequence ◽

Rare Species ◽

Sequence Data ◽

Peninsular Malaysia ◽

Tropical Asia ◽

Dna Sequence Data ◽

A New Species ◽

Lines Of Evidence

Liopeltis is a genus of poorly known, infrequently sampled species of colubrid snakes in tropical Asia. We collected a specimen of Liopeltis from Pulau Tioman, Peninsular Malaysia, that superficially resembled L. philippina, a rare species that is endemic to the Palawan Pleistocene Aggregate Island Complex, western Philippines. We analyzed morphological and mitochondrial DNA sequence data from the Pulau Tioman specimen and found distinct differences to L. philippina and all other congeners. On the basis of these corroborated lines of evidence, the Pulau Tioman specimen is described as a new species, L. tiomanica sp. nov. The new species occurs in sympatry with L. tricolor on Pulau Tioman, and our description of L. tiomanica sp. nov. brings the number of endemic amphibians and reptiles on Pulau Tioman to 12.

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