Circadian Biology Exercises |
Learn more about NCBI bioinformatics resources by following the steps taken by a hypothetical researcher interested in circadian biology. |
| Background |
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| A researcher is interested in writing a grant to study circadian
rhythms in mammals. Specifically, she plans to search NCBI resources to
find data on a human sleep disorder that has a genetic basis. The
researcher is familiar with the data obtained on Drosophila: specific
genes including the period gene are known to influence the regular
cycling of gene expression that is coordinated with sleep/wake cycles.
She hopes to use this knowledge of Drosophila circadian rhythms to help
narrow the focus of her research plan. She knows there is a wealth of
information available through NCBI. But she is not familiar with the
molecular biology databases and resources at NCBI. These exercises
guide the researcher through the major NCBI resources. |
| Format of Sequence Records |
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| Entrez |
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Find concise summary of genes pertaining to a specific area of research
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I have received a Request for Proposals on the topic of
circadian rhythms. I'd like to study the regulation of a gene important in circadian rhythms, but I haven't decided which gene to follow. I went to
Entrez Nucleotide, entered "circadian" and found 668 references--too many!
Also, many entries are redundant. How can I get a concise summary of potential
genes to follow?
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| BLAST |
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Identify Gene Involved In Sleep Disorder
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Our research group has obtained the following sequence
data from patients with disturbed sleeping patterns:
Nucleotide sequence: gggtgaacag ccgcacggga gtaggtacgc acctgacctc gctggcactg
ccgggcaagg cagagggtgt ggcgtcgctc accagccagt gcagctacag cagcaccatc gtccatgtgg
gagacaagaa gccgcagccg gagttagaga tggtggaaga tgctgcgagt gggccagaat
AA translation: RTGVGTHLTSLALPGKAEGVASLTSQCSYSSTIVHVGDKKP
What gene might this be?
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Normal vs. Disease Gene
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How does the sequence obtained from patients with sleep
disturbances differ from the normal sequence?
Patient sequence: RTGVGTHLTSLALPGKAEGVASLTSQCSYSSTIVHVGDKKP
Normal sequence: RTGVGTHLTSLALPGKAESVASLTSQCSYSSTIVHVGDKKP
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| Structures |
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View a structure to examine the significance of a conserved domain
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I am looking for a 3D structure that contains a conserved domain
found in the period 2 protein. What conserved domain should I examine? What
structure contains this domain? What can I learn from the structure?
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| Genomes and Maps |
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Find the location of a gene, and download the sequence for the gene plus the promoter region
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I want to examine how cycles of night and day regulate the expression of the PER2 gene. I need the sequence of the per promoter so that I can create a promoter/reporter construct.
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| Genes |
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Gather sequence data and related information
on a particular genetic locus
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In my grant proposal, I plan to focus on the human PER2
gene. I'd like a summary of all the sequence data and related information.
I'd especially like to find any clinically relevant information that would
underscore the importance of studying this particular circadian rhythm gene.
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| Learn More About Circadian Biology |
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Related Educational Websites:
- Howard Hughes Medical Institute Resources on Biological
Clocks
- The Drosophila Molecular Clock Model
Abbreviated Version
Complete Version
- The Mammalian Molecular Clock Model
Complete Version
Part 4 illustrates how a single base
pair substitution in the human Per2 gene results in a shortened
sleep cycle in patients with Familial Advanced Sleep Phase
Syndrome.
References:
- Kay SA. PAS, present, and future: clues to the origins of circadian clocks.
Science. 1997 May 2;276(5313):753-4.
- King DP, Takahashi JS. Molecular genetics of circadian rhythms in mammals.
Annu Rev Neurosci. 2000;23:713-42.
- Toh KL, Jones CR, He Y, Eide EJ, Hinz WA, Virshup DM, Ptacek LJ, Fu YH. An hPer2 phosphorylation site mutation in familial advanced sleep phase syndrome.
Science. 2001 Feb 9;291(5506):1040-3.
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