Class activity – Lab tours (Part 2) – 2/21/2019

This past week, we were able to visit the lab of Dr. Erin Calipari and Dr. James Crowe. Our first stop was in the laboratory of Dr. Calipari, and we were led by two postdoctoral fellows in her lab, Dr. Lillian Brandy and Dr. Alberto Lopez.

Dr. Brandy obtained her Ph.D. from the University of Alabama at Birmingham (UAB) in the Department of Neurobiology. While at UAB, Dr. Brandy worked with Dr. Lynn Dobrunz, where she studied the role of the dopamine system in the modulation and regulation of inhibitory synaptic transmission and neural circuit function within the hippocampus. Dr. Lopez graduated from Duke University in 2011 with a B.S. in Neuroscience. He worked for two years under Dr. Thomas Kash at UNC-Chapel Hill studying the neural mechanisms behind anxiety and alcoholism and then pursued a graduate degree at UC Irvine in 2013 with Dr. Wood. Within the Calipari lab, as a group are defining the neural dysfunction that underlies psychiatric disease. In particular, they are interested in answering two questions: how do neural circuits integrate experiences with positive and negative stimuli to guide future behavior, and what are the molecular dysregulations that drive maladaptation in these processes?

 

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While touring their laboratory, they showed us the many visual approaches they use to carry out their work. One was a viral transfection technique, and the other was voltammetry. On the Calipari website, they briefly describe both of these techniques (pathway-specific rabies tracing and fast-scan cyclic voltammetry) along with some other techniques they use in the lab. For more information, comment below or email Dr. Brandy or Dr. Lopez at lillian.j.brady@vanderbilt.edu or alberto.lopez@vanderbilt.edu, respectively.

Next, we visited the laboratory of Dr. James Crowe who, as we saw, uses a vast array of techniques, including molecular and cellular biology, state-of-the-art imaging, and flow cytometry, bioinformatics, and bioengineering approaches to study major human pathogens. Dr. Robert Carnahan and Ryan Irving led us through the incredible facilities that make up the Crowe laboratory, which includes over 45 members. Part of the group’s scientific philosophy is using study model systems only when the direct study of the primary pathogen in humans is not feasible. The current research in the Crowe lab includes respiratory syncytial virus, human metapneumovirus, rotavirus, HIV, influenza, and vaccinia virus.

 

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After speaking with Dr. Cinque Soto, it is clear that visuals are needed for external and internal communication of scientific findings. From the recent call for cover art, Eve Moll, a junior here at Vanderbilt, prepared the image below and created the following description of her work. This is a great example of the final projects you are creating. The image is aesthetically attractive, and the message is clearly articulated and carefully created through the written description of the process. In many cases, the written description adds the most value and context on the impact of the work.

Eve Moll - Crowe
The work of Soto et al. demonstrated that the repertoire of each individual contained between 9 and 17 million B cell clonotypes, which is the unique nucleotide sequence that occurs with gene rearrangement of a receptor. In this study, they sequence clonotypes of three individuals and find that between 1% and 6% of B cell heavy-chain clonotypes are shared between two subjects (0.3% of clonotypes shared by all three) and 20% to 34% of l or k light chains are shared between two subjects with 16% or 22% of l or k light chains, respectively, shared by all three. Here, the colored portions between the faces represent the clonotypes. The variety of colors and shapes express the unique way they have been spliced together. Three portraits are shown of the three individuals that took part in this study. The clonotype traces the back of the head of one individual then gives way to the face of another individual, showing the shared nature of the clonotypes for these three people. All three share a portion of the clonotypes and are connected by these lines. The fact that the three individuals share clonotypes was unexpected by the researchers. Further identification of the sequences could enable a fuller understanding of B cell immune repertoires in health and disease but also highlight the highly conserved and shared nature of immunity ((C) Artist: Eve Moll)

Here is another example that I put together with a description:

IMG_0094
Immunogenome. This image is based on the work of Cinque Soto et al. in the laboratory of James Crowe at the Vanderbilt University Medical Center. In the study, they explore the individuality versus shared qualities of the genetic diversity of antigen receptors within the adaptive immune system, specifically B cells. Here, the various colors highlight the unique combination of nucleotide sequences that arise during the gene rearrangement process. This rearrangement of unique heterodimeric receptors can be used in pathogen recognition. As compared to the human genome, which is 99.9% similar, the similarity between individual antigen receptor repositories was between 16% to 22% for l or k light chains between three individuals. These studies raise questions about the individuality and shared nature of B cell receptor repositories. Is this similarity based on the shared environment of the three subjects? Is this similarity shared by all humans? What is the overall diversity, comprising over 78% of the repository, based on? ((C) Artist: Kendra Oliver).

 

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