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    PhD Project: Modeling the gene regulatory network of Chronic Kidney disease of Uncertain Etiology (CKDu) and accelerating model simulation using Field Programmable Gate Array (FPGA).

Details of the project:

In the last two decades, a significant amount of CKD patients has been reported in the North Central province of Sri Lanka. Many people have died from CKD over the past two decades in the North Central Province and the disease is more prevalent among men who are the main working force of Sri Lanka. Because of the late stage identification of the disease, high cost dialysis treatments are required to treat patients, which becomes a big burden to healthcare systems in Sri Lanka.

It is characterized by the absence of high risk factors for CKD such as high blood pressure and diabetes. Therefore, the disease was named as Chronic Kidney Disease of Uncertain Etiology (CKDu). Recently, considering epidemiological and histopathological findings disease is named as Chronic Interstitial Nephritis in Agricultural Communities (CINAC). Not only in Sri Lanka, but the people in several tropical countries such as El Salvador, Nicaragua, Central America, India, and Egypt have been affected by this disease. There is an increasingly urgent need to identify the cause of CKDu in order to prevent and treat the disease and save vulnerable lives.

Currently, the disease is identified as a disease with multifactorial etiology. Some of the identified evidential factors are heavy metals such as Arsenic and Cadmium, heat stress and glyphosate. This research, proposes to construct a gene regulatory network for CKDu. CKDu network would be complex because of the large number of proteins and transcription factors involved in gene regulation. Further, an optimized FPGA implementation of this model would be constructed. This chip would be a stand-alone system on Chip that mimics the behavior of the CKDu network. This system then can be used by medical and biological researchers to extensively study the mechanisms involved in the CKDu pathways and also to study the effects of new drugs on the pathways.


PhD Candidate : Upamalika Samarawikcrama
This is a collaborated project with: Lincoln University, New Zealand and University of Southampton, United Kingdom