Posted: September 2nd, 2015
In this workshop you will explore a database (ToxoDB – https://toxodb.org/toxo/) that draws together genomic, transcriptomic, and proteomic data from the human parasite Toxoplasma gondii (refer to additional papers and the video link on the T. gondii life cycle and invasion – https://www.youtube.com/watch?v=hlKOVvAeq88 .
You are each allocated a novel Toxoplasma gene and you will use the resources of this database
to learn as much as possible about your unknown gene.
Your gene (TGME49_215220 )
You will collate information listed below from the ToxoDB database on your assigned protein. You will then suggest experimental approaches to validate these data and test further any hypotheses about gene function.
Part 1: Deriving the data
Use the genome browser at (https://toxodb.org/toxo/) to derive the following information about your gene. The genome browser also offers tutorials under ‘HELP’ option.
Describe the genomic context (features) of your gene
– intron/exon structure
– the chromosome that it is it on
– best matches of adjacent genes (3 or 4 both sides of your gene); record the distance these are from your gene
List evidence that the bioinformatic prediction for your ‘gene’ is correct and that this gene encodes a protein
– determine whether there is conserved gene order (gene synteny) with other Toxoplasma strains and the other apicomplexan genera, Neospora and Eimeria;
– examine evidence of expression of the gene from looking at proteomic/mass spectrometry data;
• note any evidence of post translational modification, such as phosphorylation, and whether Low Complexity Regions are present. These regions reflect presence of repeated motifs or preponderance of a particular amino acid.
• determine if any Low Complexity Regions have strong biases for the amino acid residues reported in the class of pellicle proteins reported by Gould et al (2011)
-note the predicted molecular weight and other biophysical features (e.g. isoelectric point) of the predicted protein;
– examine evidence of expression of the gene in transcriptome data (Expressed Sequence Tags (ESTs), microarrays or RNA-seq and determine if it is expressed in other Toxoplasma strains.
Determine whether this gene is conserved amongst different apicomplexan parasites and other diverse eukaryotes?
– look at blast results, and also perform your own blast analyses to look for matches in other organisms (protein sequences are available at the bottom of the Toxo DB page, and ‘protein blast’ is available at https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome
– look for known conserved and functional domains such as signal peptides, transmembrane domains.
When and where is the gene expressed?
– what type of information tells you about the expression pattern of this gene relative to the parasite cell cycle or life cycle?
– summarize the expression profile of your gene
Part 2: Writing the report
When you have collected these data, write a report of your findings on your Toxoplasma gondii protein. The report should be written as a scientific paper and should be limited to 1500 words, excluding Tables, figure legends and references. Marks will be deducted if you exceed this limit. State the number of words on the front page of your report.
Avoid the use of tables that are simply screen dumps from the internet. Compile properly constructed tables to support your conclusions. Use Figures where appropriate. Avoid simply cutting and pasting from the internet. Your assignment will be checked for potential plagiarism via Turnitin.
Title: Characterisation of a novel protein of the animal parasite, Toxoplasma gondii
Introduction: Briefly describe the approach that has been taken identify novel proteins of the Toxoplasma pellicle, and the resources at Toxo DB that you have used to gain preliminary insights into these proteins. Outline the approaches that you have used to characterize your protein. (15%)
Present your results in the form of numbered tables and figures and describe these data in the text. Avoid screen dumps of the results of your searches. All tables should be in standard format with a clear heading with footnotes, where necessary to describe the table columns and rows. Figures should be accompanied by figure legends that include a short title followed by a brief description of how the figures were obtained. You must refer to all the Tables and Figures in the text. Only include data in the figures and tables that you describe in the text, and that contribute to your conclusions presented in the Discussion.
Place Tables and Figures at the end of your report. (45%)
Discussion: Discuss your results highlighting the main findings and their implications. Outline some further experiments that could be done to validate the results you have derived from the ToxoDB database, and to learn more of the function, cellular location and behaviour of your protein. You should consider the molecular techniques that have been covered in the lectures to date. Comment on the likelihood that this protein might participate in cell processes that are relevant to the function of the cytoskeleton. (35%)
References: Include a list of references to the bioinformatic tools used in your analyses including website addresses and references to the published literature. References should be cited appropriately in a bibliography using a consistent and scientifically accepted form of referencing. (5%)
How to use the ToxoDB website
Here are the links to online tutorials on how to use the ToxoDB website:
Or check under Education and Tutorials
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