Research

C. elegans, engineering, and systems biology

The San Miguel Lab is dedicated to accelerating biological discoveries by incorporating engineering and systems approaches to answer elusive questions in different areas of biology. We focus on applying engineering tools to perform experiments unfeasible with traditional techniques. We use the nematode C. elegans as a model organism and we work in topics such as neuronal aging, synaptic plasticity, noise and stochasticity, genetic networks, and buffering, among others. We incorporate tools that enable large-scale high-content quantitative characterization of phenotypes at various scales: from the subcellular level all the way to whole-organism behavioral outputs. We use custom-built platforms for our experimental studies, which typically incorporate microfluidics, computer vision, statistical data analysis, and integrative automation and control.

Some of our current projects are:

Novel tools for longitudinal, high-resolution monitoring of the aging nervous system in C. elegansSahand Saberi

C. elegans as a model organism has been studied extensively throughout past years. However, conventional techniques used to study these nematodes is low-throughput, labor intensive, and in some cases unable to perform certain experiments such as lifelong imaging. In my project, I am implementing microfluidic devices to address the issues mentioned above. My project is focused on integrating microfluidic device that perform high-resolution, longitudinal imaging with cutting edge image processing techniques to increase the accuracy of the data analysis. I am trying to use various machine learning techniques including Convolutional Neuronal Networks to process the images acquired. Successful integration of these techniques will enable me to segment and process images with complex features and eventually track subtle phenotypes occurring to nematodes as they age. We are currently interested in implementing CNNs in detecting neuronal beading in PVD and track this process quantitatively as nematodes age.

Forward genetic screens for identifying genes that regulate decline with age – Daniel Midkiff

Though nearly every organism naturally undergoes decline with age, the biological mechanisms by which this decline occurs remains largely unknown. In addition to the several signaling pathways which have been found to regulate lifespan, we seek to develop new methods for increasing knowledge about the aging genetic network. We will use the nematode C. elegans as a model organism for studying the aging process due to its short lifespan, well-studied genome, and hermaphroditic self-fertilizing reproduction method. Previously, the insulin signaling pathway and dietary restriction pathways were found to significantly impact lifespan in C. elegans. In our research, we aim to use forward genetic screening techniques to identify mutants in aging phenotypes. We will focus on measuring propensity of proteins to aggregate naturally with age as a biomarker for aging. By identifying mutants that accelerate aggregation with age, we anticipate identifying genes that previously been undiscovered to regulate the aging process. We aim for our research to benefit the scientific community by providing a clearer picture of the aging process, as well as the medical community through improved treatment of age-related decline in humans.

In Vivo Longitudinal Tracking of the C. elegans Aging Network – Javier Huayta  

The activity of gene networks associated with life span and healthspan varies in space and time, and can be perturbed by changes in the environment. It is still unclear how the history of these perturbations, and the responses of aging-associated gene networks determines the healthspan and lifespan of the C. elegans nematode. The longitudinal in vivo tracking of these  live perturbations can be achieved through quantitative imaging processing of endogenous gene network expression. To accomplish this goal, we will combine microfluidics, high throughput imaging, and multi-labeled endogenous gene expression lines (generated through a CRISPR/Cas9 system). A microfluidic device designed ad hoc for in vivo tracking of C. elegans populations will enable quantitative imaging of fluorescent gene expression related to reproduction, dietary restriction, heat shock, oxidative stress, etc. The data sets thus acquired will be used to relate environmental perturbations, longitudinal gene activity, and lifespan and healthspan. Quantitative mathematical models derived with this data will enable elucidating how this lifelong background determines lifespan and healthspan in C. elegans.

In vivo monitoring of head injury cellular damage in Alzheimer’s disease – Rita Tejada 

An important challenge in understanding the links between traumatic brain injury (TBI) and Alzheimer’s disease (AD) is a scarcity of experimental models that enable systematic studies of neuronal injury, while quantifying subsequent damage and its interaction with AD. To elucidate the fundamental mechanistic relationships between injury and AD, and the genetic pathways at play, capturing post-injury in vivo dynamic information of both neurological function and morphology at high-resolution  would be necessary. The nematode C. elegans provides a unique experimental platform to perform quantitative analysis of injury, neurodegeneration, and neuronal function in AD models. Neuronal injury induced by controlled microfluidic devices will enable characterization of morphological and functional defects in an intact nervous system, in vivo. By incorporating a C. elegans AD model, with controlled injury and high-content platforms, this work will enable studies of injury and neurodegeneration.

Quantitative Analysis by Image Processing of Extravillous Cytotrophoblast in Human Embryonic Stem Cell-derived Trophoblast  – Victoria Karakis 

I utilize image analysis techniques to quantitatively asses the effects cytokines have on the differentiation and invasion of human embryonic stem cell-derived extravillous cytotrophoblast cells (EVTs). These cells are a major cell type in the human placenta and play a key role in remodeling uterine spiral arteries to ensure efficient blood flow and fetal nutrition during pregnancy. Improper invasion of these cells can result in life-threatening diseases for the mother and fetus, including pre-eclampsia, where the only known cure is pre-term birth. Therefore, in understanding what effects the invasion of these cells, we can begin to understand and develop therapeutics to combat placental disorders.

Synaptic function and plasticity – Riley Reid and Zachary Crawford

We are trying to understand the connections between neuronal exercise  and synaptic function and plasticity. To answer this question, we are designing and testing a platform to perform controlled optogenetic activation of C. elegans motor neurons by LED illumination. We are working on automating LED flashes, imaging, and data analysis. With this improved platform, we are looking to further study the effect of increased flash length on contractions, lag time between flash and contraction, and muscular response in liquid media. Other areas of interest include: response of uncoordinated C. elegans as well as populations of aging animals. In the future, we will couple these experiments with high-resolution imaging of synaptic patterns. Ultimately, we’re aiming to quantify how plastic synapses are (morphologically and functionally), under different conditions and under various neuronal exercise regimes.

Effects of floxuridine on aging phenotypes of C. elegansHanna Thompson

I am working to understand the effects of floxuridine on aging in C. elegans. Floxuridine is an antimetabolite used to effectively sterilize C. elegans, resulting in an age-synchronized population, but additional effects are unclear. Specifically, I am observing the effects of floxuridine on worm size over the lifespan and the deviations in growth from the norm.