Biochemistry and Molecular Biology Research Intensives

Novel Genes in Host-microbe Interactions

The Wang lab can host one student.

Plants and animals frequently engage microbes in mutualistic interactions, some of which have significant impacts on human society and the ecosystem.  Because such interactions are complex by nature, we are using one well studied system as an example to probe the molecular mechanisms needed to establish symbiotic relationships in general.  Legumes (beans, peas, etc) play hosts to a class of bacteria called rhizobia, which convert nitrogen in the atmosphere into fertilizers for the plant.  This nitrogen-fixing symbiosis is of great importance to food, nutrition, energy, and the environment, as well as other implications to human health.  Potential projects include discovering novel genes required for this symbiosis, and the effects of specific host proteins on the microbial partner. For more information see http://www.biochem.umass.edu/faculty/dong-wang

 

Learning How Plants Grow and Reproduce

The Cheung and Wu lab can host 1 or 2 students.

We are interested in understanding molecular themes that underlie plant growth and reproduction. In particular, we study how growth-regulating signals are sensed by plant cells and how these signals induce cellular responses that are advantageous to their existence. Although students will be exposed to a wide variety of research questions and approaches, projects that are most appropriate to high school students include (1) those that examine the expression patterns of genes that are important to the biological processes that we study and (2) those that determine the genotype and establish the phenotypes of plants that harbor mutations that affect these processes. Student will learn molecular techniques, such as isolating and characterizing plant nucleic acids (DNA and RNA) and proteins, carry out biochemical assays that measure enzyme activities, analyze simple genetic data to learn basic genetic principles. For further information about the Cheung and Wu lab, see http://www.biochem.umass.edu/faculty/alice-cheung

 

Protein Folding, Misfolding & Aggregation

The Gierasch lab can host one student. 

The failure of proteins to fold into their functional three-dimensional structures has devastating health consequences. Recent research has established the connections between an increasing array of diseases, and defects in the correct folding, assembly, and maturation of proteins. These diseases include cancer, cystic fibrosis and neurodegenerative diseases such as Alzheimer’s and Parkinson’s. The molecular basis of these diseases remains poorly understood, and it is widely agreed that there is a pressing need to better understand the fundamental mechanisms and factors that influence protein homeostasis in the cell. To this end, we are determining the detailed molecular mechanisms of one of the major classes of molecular chaperones, the Hsp70s. Chaperones are proteins that help other proteins to fold. We are also researching the linkages between protein folding, misfolding and aggregation and how molecular chaperones tip the balance towards well-folded, healthy proteins. For more information, see http://www.biochem.umass.edu/faculty/lila-gierasch

 

How do Hosts Control Beneficial Microbes?

The Gershenson Lab/Wang Lab collaboration can host one student.

Symbiotic bacteria can help organisms acquire nutrients, for example by breaking down food in the human intestinal track and by fixing nitrogen in plant roots. For these relationships to succeed, the host organism must control the number of bacteria, since just a few bacteria will not give the host any advantage and too many can result in infections that damage the host. In this project, we are watching the interactions between the host and bacteria by fluorescently tagging proteins in plant root cells and directly observing their motions and interactions using single molecule fluorescence microscopy.

For more information see http://www.biochem.umass.edu/faculty/dong-wang  and http://www.biochem.umass.edu/faculty/anne-gershenson

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Molecular Mechanisms that Control the Excitability of Neurons

The Chase Lab can host one student.

The Chase lab uses C. elegans as a model organism to understand how neurons communicate with each other to control circuit activity and brain function. We are particularly interested in dopamine, which binds to receptors on the surface of neurons to modulate their excitability. Summer projects include: 1) Using fluorescent reporter proteins to determine where the dopamine receptors function in the C. elegans nervous system. 2) Using sophisticated optical techniques to directly measure the effects of dopamine signaling on neural activity in live animals.

For more information see http://www.biochem.umass.edu/faculty/daniel-chase

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Comparative Genomics to Understand Fungal Pathogenicity

The Ma lab can host one student.

Fungi are listed as the most common cause of disease in agricultural crops. A recent survey revealed that fungal pathogens cause widespread population declines and account for 72% and 64% of recent animal and plant extinctions, respectively. It is imperative that we understand the genetic mechanisms that underpin the establishment and manifestation of fungal infections. The Ma lab studies a fungal system, Fusarium oxysporum, an important pathogen that causes severe diseases in humans and over 100 plant species. In silico comparative genomics will be employed to derive the hypothesis and  in vitro pathogenicity assays will be used to test them. For more information, see http://www.biochem.umass.edu/faculty/li-jun-ma

 

 

Nucleic Acid Nanotechnology to Control RNA Folding

The Martin lab can host one student. 

RNA is the “new frontier” of biological macromolecules. No longer seen as just a messenger, encoding proteins, we now know that complex, folded RNAs exist in the cell, carrying out key gene regulatory functions. Genetic riboswitches and many long noncoding RNAs adopt functional structures only when they fold as they are being synthesized (they fold “co-transcriptionally”). Transcriptional pauses are encoded in the DNA to allow time for this folding, but like co-translational protein folding, the process is poorly understood. Indeed, just as in (complex) protein folding, genetic deficiencies in RNA folding are increasingly linked to human disease. Unlike proteins, however, our ability to engineer nucleic acid structures (DNA/RNA origami) is advancing rapidly. These Lego-like tools are being employed in the Martin lab to precisely control the directional release of RNA, mimicking co-transcriptional release. We are engineering site-specific, defined pauses to test specific hypotheses regarding the mechanisms of RNA folding. For more information on the Martin lab, see http://people.chem.umass.edu/cmartin

 

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