Introduction The causes and identification of transcripts of Neural Tube Defects in Zebrafish (Danio rerio) Cheyanne Wilber, Jennifer Liang University of Wisconsin-Superior McNair Program & Department of Biology, University of Minnesota Duluth, MN “Neurulation | BioNinja.” (Accessed August 6, 2020). https://ib.bioninja.com.au/options/option-a-neurobiology-and/a1-neural-development/neurulation.html. Conclusion Two similar pathways were found between 2 of the 3 developmental stages, which supported my hypothesis. There was no similar pathways associated with the tailbud stage. Future Directions Further research will explore the correlation between these common pathways and neural tube defects in zebrafish and humans. Nature Protocols 2009; 4(1):44 & Nucleic Acids Res. 2009;37(1):1 Nature Protocols 2009; 4(1):44 & Nucleic Acids Res. 2009;37(1):1 The folding process in vertebrate embryos that makes the neural plate into the neural tube, the precursor to the brain and spinal cord. Experimental Design Hypothesis There will be common pathways found between the 3 developmental stages after DAVID analysis is complete. Total Kegg Pathways- 17 Total Kegg Pathways- 12 Examples: - Notch - Wnt - Hedgehog - Retinol Metabolism - TGF-β N/A - Metabolic - RIG-i-like Receptor Examples: - Melanogenesis - Adherens junction - Pyruvate metabolism Examples: - Carbon metabolism - Phagosome - Glycolysis N/A N/A 3,187 RNA transcripts were analyzed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) DAVID was used to group genes into pathways for visualization Found common pathways between stages Figures from: “Laboratory Protocols.” Accessed August 6, 2020. http://www.uoneuro.uoregon.edu/k12/Table%201.html . RIG-i-like Receptors Metabolic Pathway Gilbert, S. (2003). Developmental Biology During development if the neural plate does not properly close it can result in a neural tube defect. Venn Diagram of pathways from DAVID analysis Acknowledgments I would like to thank Kirsta Olson and Mikaela Courrege for all their help and support throughout this project KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction, reaction and relation networks for: Metabolism, Genetic/Environmental Information Processing, Cellular Processes, Organismal Systems, Human Diseases, & Drug Development.” (Assessed August 7, 2020) https://www.genome.jp/kegg/pathway.html#:~:text=KEGG%20PATHWAY%20is%20a%20collection,Amino %20acid%20Other%20amino%20Glycan Neurulation RNA sequencing analyzes the transcriptome (RNA encoded by genes), or all genes expressed at the time RNA is collected. (Kindt, L, et al. (2008) Genesis 56. e23096). Tailbud Stage Total Kegg Pathways- 5 Neural Tube Defects 7-somite Stage Shield Stage Results RNA Sequencing “Over 3,000 transcripts were significantly differentially expressed between embryos that would have closed and open neural tubes.” (Kindt, L, et al. (2008) Genesis 56. e23096).
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Introduction
The causes and identification of transcripts of Neural Tube Defectsin Zebrafish (Danio rerio)
Cheyanne Wilber, Jennifer LiangUniversity of Wisconsin-Superior McNair Program & Department of Biology, University of Minnesota Duluth, MN
“Neurulation | BioNinja.” (Accessed August 6, 2020).https://ib.bioninja.com.au/options/option-a-neurobiology-and/a1-neural-development/neurulation.html.
ConclusionTwo similar pathways were found between 2 of the 3
developmental stages, which supported my hypothesis. There was no similar pathways associated with the tailbud stage.
Future DirectionsFurther research will explore the correlation between these common pathways and neural tube defects in
zebrafish and humans.
Nature Protocols 2009; 4(1):44 & Nucleic Acids Res. 2009;37(1):1
Nature Protocols 2009; 4(1):44 & Nucleic Acids Res. 2009;37(1):1
The folding process in vertebrate embryos that makes the neural plate into the neural tube, the precursor to the brain and spinal cord.
Experimental Design
HypothesisThere will be common pathways found between the 3
developmental stages after DAVID analysis is complete.
Total Kegg Pathways- 17 Total Kegg Pathways- 12
Examples:- Notch - Wnt- Hedgehog- Retinol Metabolism- TGF-β
N/A
- Metabolic- RIG-i-like
Receptor
Examples:- Melanogenesis- Adherens
junction- Pyruvate
metabolism
Examples:- Carbon
metabolism- Phagosome- Glycolysis
N/AN/A
3,187 RNA transcripts were analyzed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID)
DAVID was used to group genes into pathways for visualization
Found common pathways between stages
Figures from: “Laboratory Protocols.” Accessed August 6, 2020. http://www.uoneuro.uoregon.edu/k12/Table%201.html.
RIG-i-like Receptors
Metabolic Pathway
Gilbert, S. (2003). Developmental Biology
During development if the neural plate does not properly close it can result in a neural tube defect.
Venn Diagram of pathways from DAVID analysis
AcknowledgmentsI would like to thank Kirsta Olson and Mikaela Courrege for all their help and
support throughout this project
KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction, reaction and relation networks for: Metabolism, Genetic/Environmental Information Processing, Cellular Processes,
Organismal Systems, Human Diseases, & Drug Development.” (Assessed August 7, 2020) https://www.genome.jp/kegg/pathway.html#:~:text=KEGG%20PATHWAY%20is%20a%20collection,Amino
%20acid%20Other%20amino%20Glycan
Neurulation
RNA sequencing analyzes the transcriptome (RNA encoded by genes), or all genes expressed at the time RNA is collected.
(Kindt, L, et al. (2008) Genesis 56. e23096).
Tailbud StageTotal Kegg Pathways- 5
Neural Tube Defects
7-somite StageShield Stage
Results
RNA Sequencing
“Over 3,000 transcripts were significantly differentially expressed between embryos that would have closed and open neural tubes.” (Kindt, L, et al. (2008) Genesis 56. e23096).
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