Xie Lab
Overview
The research in the lab is not bound by any particular organism or method. Instead, depending on the shared interest of the students and the PI, we work in diverse areas in biology, medicine, and biotechnology. For all the research projects in the lab, we take an interdisciplinary and integrative approach combining molecular data, ecological/environmental studies, and statistical/computational analyses to better address the research question. And we do not always use traditional research methods or follow conventional theoretical framework, particularly when they are inadequate, inappropriate, or cannot really address the research questions. As needed for particular areas of research, we often employ and develop new methods that we think could better address the research questions at hands and explore new research ideas, which often slowly but gradually gain acceptance by the communities.
LATEST RESEARCH PROJECTS
Bioluminescent mushrooms
These mushrooms are not zombies or ghosts! While rare, bioluminescent mushroom do exist in natural habitats on different continents. This NSF-funded project will focus on the bioluminescent mushroom species in Brazil, exploring their diversity and using a comparative genomic and transcriptomic approach to understand the similarity and differences in the bioluminescence pathways of these species, which hopefully will have other practical applications.
Decomposition Microbiomes
Virus Evolution
While most of the research and published studies used the traditional phylogenetic tree analysis to study the evolution of SARS-CoV-2 virus causing the COVID pandemic, the approach is grossly inappropriate and inadequate to study the evolution of this and other RNA viruses. We employ the innovative phylogenetic network approach to study how the viruses evolve and how new variants originate.
Cancer Epigenomics
Cellulosic plant materials are the most abundant biomass on earth and the food for many animals. How cellulose is degraded in natural habitats and in animals is not only important for understanding the nutrient cycling in the ecosystems and animal physiology but also for developing next-generation cellulosic biofuel technology. We are studying the microbes and enzymes involved in such process using metagenomic and biochemical methods.
Phytoplanktons & Environment
Phytoplanktons are the primary producers in aquatic, particularly marine, environments. They are very important for the health of the ecosystem (think about the "red tides"). We are interested in studying how human activities on land and environmental changes affect the dynamics of phytoplanktons in Hawaii and the Cheasapeake Bay on the east coast of the U.S. using a combination of scanning electron microscopy, flow cytometry, and metagenomic methods.
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For too long cancer studies have focused on genetic mutations, particularly at the gene coding region. However, we are taking a different approach to study how chemicals from polluted air, water, smoking, food, beverage, etc. cause epigenetic changes and subsequently gene expressional changes leading to cancer. Our lab is also trying to develop techniques to use CRISPR-based technology as a molecular tool for cancer treatment.
Speciation Genomics
Speciation, or how new species evolve, is a fundamental question in biology. The apple maggot Rhagoletis pomonella has been a model system for the study of speciation. We have expanded the study onto the R. pomonella species complex to examine how the sibling species have diverged from each other both genomically and transcriptomically in order to identify the molecular basis for their adaptive divergence.
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