ALICE: Systems Biology

Intro

The Biomathematics Research Group (BRG) at UGA explores mathematical and computational models that connect genes to ecology. This course is part of ALICE, the Adaptive Learning for Interdisciplinary Learning Environments. You can access the Systems Biology course in ALICE here.

 

Capstone Experiences

Do single cells have clocks?

Often pushing the boundaries of measurement leads to fundamental discoveries. A major boundary to cross is measuring gene expression in single cells.  In no model system has it been demonstrated that single cells have clocks. By a combination of nanotechnology, bioinformatics, and genomics it may be possible to answer this question.

Do circadian rhythms in the host respond to malarial infection?

Real time telemetry data is being collected on primates infected with the malarial parasite, Plasmodium.  Host activityIs a well known circadian trait in mammalian systems. As the immune system is compromised by plasmodium infection, how does the host circadian system respond to this stress?

Malar J. 2016; 15: 410. Published online 2016 Aug 12. doi:  10.1186/s12936-016-1465-5

 

How do we integrate a petabyte of data on the malaria and its host?

Time series on host activity, RNA profiles, lipidomic profiles, cytokine profiles, Protein profiles, and others are being collected on primates infected with Plasmodium.  How do we reliably store and retrieve such information so that scientists engaged in mining this wealth of data do so consistently and repeatably?  There is a compelling need to standardize the data structures on this unique resource so that others can make effective use of it.

 

How are innervation, vasculature, and lymphatic networks organized in the developing postnatal thymus (part of our immune system)?

We seek to establish a phenotypic readout for the normal development of thymus structural networks in order to conduct functional analysis of neural, vasculature, and lymphatic inputs in mutant mouse lines.

Figure from https://en.wikipedia.org/wiki/Thymus

 

How is pattern formation achieved during thymus development?

Understanding pattern formation is a fundamental problem in developmental biology. The thymus and parathyroid organs are critical components of our immune and endocrine systems, respectively. Yet, despite their very different adult functions, the two organs originate from a common embryonic primordium. We know that there are two opposing signaling gradients, SHH and BMP4, in the primordium. It would be interesting to examine how these organs arise under the action of these and other developmental regulators.

 Qiaozhi Wei, Brian G Condie  PLoS ONE: 2011, 6(11);e26795