Integrative Molecular Module

2013_06_13_0400-2MBThe overall objective of the Transcriptomics Phase of the STG Module is to equip students with comprehensive understanding of the relationships between molecular activity in the nervous system and complex behavior. A series of lectures will introduce students to the history and theory of “neuro-molecular-ethology” as well as current research focused on behaviorally relevant patterns of gene expression in the nervous system. We will teach molecular techniques to complement the electrophysiological characterization of identified cells in stomatogastric ganglion. Knowledge and technical skills gained in this module will be widely applicable to research in other model and non-model organisms allowing students to ask questions on multiple levels of biological organization.

We will build on the skills and understanding of the stomatogastric system generated in Cycle II, emphasizing the link between gene expression, neural activity, and behavior.  The module is focused on two key integrated technical approaches – high throughput sequence analysis and qPCR – with the emphasis on single-cell level analyses for both of these approaches.  Students will learn the technical and conceptual advances in modern genomic approaches and apply them to both transcriptome-wide and candidate gene analyses aimed at interrogating the molecular basis of neural network output.

In the first week, students will be introduced to fundamental molecular techniques such as RNA extraction, reverse transcription, RT-PCR, and qPCR design and analysis.  Concomitant with this wet-lab training is an in-depth introduction into the concepts and practical approaches centered around bioinformatics workflow for RNAseq data. The goal is for students to feel confident generating and utilizing raw RNAseq data and establishing a pipeline for assembly and analysis for use in downstream applications. From these bioinformatics data, students will “mine” the sequence data for candidate gene targets that are experimentally relevant to the system at hand. After characterizing the sequence of novel genes of interest, students will design, validate and employ de novo qPCR assays to address specific questions relevant to stomatogastric physiology. The second week of the STG-Integrative Cycle is dedicated to independent projects that integrate the entirety of this new skill set, and address specific principles of activity-dependent gene expression and transcriptome-level neuronal functional identity common across nervous systems. Because the STG is a relatively new system with respect to molecular genetic approaches, these projects are expected to gather new unpublished data and advance the understanding of molecular underpinnings of neural network function both specifically for the STG and generally across systems.

Click here to view the 2016 syllabus and course materials.

This module made its first appearance in 2014 as the Integrative Molecular Module. You can download the 2014 and 2015 manual of exercises here.

 

Faculty and Teaching Assistants

DaveSchulzDavid Schulz
University of Missouri

The general theme of the work in the Schulz lab is a desire to understand the mechanisms underlying neural network function from both the perspective of an individual cell as well as the coordinated activity of the network as a whole. Our model systems are the crustacean stomatogastric ganglion (STG) and cardiac ganglion (CG), as well as the mouse spinal cord. The STG has been at the forefront of electrophysiological questions of neural network function for over 3 decades. Our approach seeks to take this well characterized network to the molecular level to ask detailed questions about the interaction between the genome and the electrophysiogical output of individual cells and the network as a whole. Our goal is to use these model systems to shed light on both the endogenous mechanisms of neural network function, but also responses of these networks in response to injury and other perturbations that challenge the system. David joined the STG faculty in 2015.

 

evaEva Fischer
Harvard University

Dr. Eva Fischer is interested in the mechanisms by which behavioral diversity evolves and is maintained, both within and among species. She uses integrative approaches to understand mechanisms underlying behavioral evolution, including the role of developmental plasticity and phenotypic integration, and whether parallel evolutionary events share common molecular, developmental, and neural substrates.

During her doctoral work, Eva took advantage of Trinidadian guppies to understand how genetic and environmental forces interact to drive behavioral evolution within a single species. Now, during her postdoctoral work in Dr. Lauren O’Connell’s Lab, she is taking advantage of the fantastic variation in behavior (and other traits) in poison frogs to understand inter– as well as intra-specific patterns. Specifically, she is examining to what extent similar parental care behaviors are mediated by similar neural, hormonal, and molecular substrates across individuals and species.

Outside the lab Eva always strives to extend her repertoire of baked goods and scrabble words. Eva joined the integrative faculty in 2016.

 

Hans PictureHans Hofmann
University of Texas at Austin

Hans Hofmann is professor of integrative biology at The University of Texas at Austin. His research interests focus on the neural and molecular mechanisms of social behavior. He received his Ph.D. in biology from the University of Leipzig and the Max-Planck Institute in Seewiesen. As a postdoctoral fellow at Stanford University, he began taking advantage of the astonishing diversity and plasticity of cichlid fishes to study how the social environment regulates brain and behavior. While a Bauer Genome Fellow at Harvard University, he pioneered behavioral genomics in cichlids to analyze and understand the molecular and neural basis of social behavior and its evolution. He developed many of the functional genomics resources for cichlids and has been a co-initiator of the cichlid genome consortium, which successfully completed the sequencing of five cichlid genomes at the Broad Institute. He received the prestigious Alfred P. Sloan Foundation Fellowship (in Neuroscience) and was awarded the Frank A. Beach Early Career Award from the Society for Behavioral Neuroendocrinology. Hans Hofmann has been an NS&B Course Co-director since 2013 and a faculty member of this module since it was formed in 2014.


RaynaHarrisRayna Harris
University of Texas at Austin

Rayna Harris 4th year graduate student in the cellular and molecular biology program at The University of Texas in Austin. She has been a member of Hans Hofmann’s lab since 2009, when I joined as the lab manager. Her research interests focus on the neuromolecular and endocrine mechanisms that regulate social behavior. Rayna has also been a Course Developer since 2013, working to develop tools molecular module for the NS&B and conducting a collaborative research project that unites the expertise of the Hofmann and Fenton Labs.

 

 

clare-diesterClare Diester
University of Missouri

Clare Diester graduated with Honors from the University of Missouri in 2015 with her B.S. in Biological Sciences. While there, she studied the homeostatic regulation of cells in the crustacean stomatogastric ganglion (STG) through an integrated molecular and neurobiological approach in Dr. David Schulz’s lab. This past May she graduated with her M.S. in Forensic Science from Virginia Commonwealth University, where her thesis focused on a novel high-throughput nanopore sequencing device, and will begin VCU’s Pharmacology and Toxicology with a concentration in Molecular Biology and Genetics doctoral program this August. Clare joined the Integrative team in 2017.