Tag Archives: RF2017-Week3

All Things Poop

Our gut microbiomes have long been known to be critical for immunity, nutrient processing, etc. More recently, research has suggested that gut bacteria play an important bidirectional role in brain development & function, and the modulation of stress response. Major Depressive Disorder (MDD) patients have altered microbial compositions and many metabolites which play a role in depression are byproducts of gut microbiota.

My lab is focusing on the effects of chronic social defeat on the microbiomes of mice (as a pre-clinical model). In short, the social defeat (SD) paradigm involves placing the subject mice into the same cages as aggressive mice, allowing them to fight, and then separating the mice using a divider while but keeping them in close proximity to each other for a day. After the process is repeated 10 times with different aggressive mice, the subjects present with anxiety and depressive symptoms.

The aim is to study changes in microbial richness and diversity, and differences in the relative abundances of gut bacteria at the family and phylum levels between depressed and healthy subjects. This is measured through fecal samples which are collected from the subjects’ cages before the paradigm (a baseline) and after SD. The mice are then treated with electroconvulsive shocks (ECS), and post-treatment samples are taken to examine whether reductions in symptoms are also accompanied by a stabilizing microbiome. Many people don’t realize that ECS is still used today to treat severe depression in humans!

The aggregate sequencing results from a pilot study by Kara McGaughey. Each color represents a bacterial phylum, and the shifts in the microbiomes of the depressed group are easily visible.

I’m involved with comparing two DNA extraction kits using the pre-SD fecal samples to choose the more suitable one for the rest of the experiment. I was initially surprised to learn that there is no ‘gold standard’ in DNA extraction and that the various kits in the market all detect varying species & proportions of bacteria. Although my project has ended up being more about microbiology than neuroscience, learning about the different bacterial DNA extraction and sequencing protocols is definitely cool. I’ve also learnt a ton about the measures used to assess the purity (microplate spectrophotometer), concentration (fluorometer) & quality (TapeStation) of extracted DNA. I’m really looking forward to seeing & comparing the sequencing results!

Spines: what’s the point of it all?

When you hear the word “spine,” your first thought is probably a backbone: that familiar stack of vertebrae running from the base of your skull to your tailbone. At least, that’s what popped into my head when I first discussed my project with my mentor Jacob Harrison, a PhD student in the Patek Lab. However, there’s another type of spine that is often overlooked, one that is far more prevalent in nature than you might think.

Note: drawings are not realistic depictions of species

My research focuses on spines in the spiky sense. For my project, spines are defined as rigid biological structures that come to a point (J. Harrison). Barbs, quills, thorns, spines… these are all different names used across the literature for fundamentally similar structures (J. Harrison). Many of us are aware that spines exist in nature, because we’ve experienced (or tried to avoid) painful run-ins with them. However, until now I never appreciated just how diverse spines are across biology. Some organisms such as sea urchins have conical toothpick-like spines, while other species like stingrays have flattened barbs reminiscent of knife blades. Some spines are smooth, like the stingers of scorpions, while other spines display serrations of varying size, number, and orientation. For instance, while both the sea urchin and stingray have many small serrations on their spines, these serrations run in opposite directions (see Fig. 1)! Furthermore some structures, such as the raptorial appendages of spearing mantis shrimp, contain several spines at once (see Fig. 1).

Aside from being diverse in structure, spines vary widely in their function. Stingrays use their barbs defensively, embedding their spines in the bodies of predators (and sometimes, the feet of unwary beachgoers!). Meanwhile, spearing mantis shrimp use their spines for predation, skewering prey that swim above their sand burrows. This large difference in function occurs, despite the fact that both species utilize the same underlying tool of the spine.   This suggests that small changes to the structure of a spine play a role in how it is used, and ultimately begs the question: how do changes in spine morphology (or structure) influence spine function?

Fig. 1 – The structures of a sea urchin spine, stingray barb, and a spearing mantis shrimp dactyl (foreclaw)

To better understand the relationship between spine form and function, we’ll be investigating how spine structure affects puncture and draw mechanics. We decided to use 3D modeling for this project, because this will allow us to perform more controlled comparisons of changes in spine structure. First, we’ll design a basic underlying spine shape as a control, and then manipulate different aspects of that spine’s morphology (ex. serration number, size and angle) in set increments. After printing the resulting variations using the Patek lab’s 3D printer, we’ll then record the force required for each of the spines to pierce ballistics gel using a Material Testing System (MTS), which measures forces in tension and compression. This will allow us to see whether/how changes in the spine’s morphology affect its puncture/draw mechanics (i.e. how it pierces or retracts from the gel).

Rough idea of a base spine and resulting variations. We chose to model the spine after a stingray barb because 1) it’s an easily replicable shape, and 2) we know that it is definitely used to puncture things that the stingray views as a threat.

Currently I’m in the process of designing prototype spines using the 3D-modeling software 3Ds Max. Below are some printed models!

Feelin a bit like Tony Stark looking at his Hall of Armors

Because these spines aren’t precise replicas of ones found in nature, we have to be careful about what conclusions we can draw about ecological/evolutionary functions. However, the effects we observe with our basic models can still give us insight into the fundamental influences that spine structure can have on function.

The Patek Lab focuses their research on the intersection between physics and evolution, which is an inherent part of my project. I’m really excited to see what we might learn, not only because I am curious about the nature of spines and the organisms that wield them, but because I think our findings could have practical applications to people’s lives. After all, wouldn’t you want to know the structure of a stingray barb if it revealed an easier way to get it out of your foot?

Of course, there’s a lot more to explore, prepare, and test before I can say anything for sure. But still, I’m excited to take a stab at this investigation and see how it goes!

The Game Plan

Anybody who knows me relatively well will know that I am a huge pro-football fan (33 days till Hall of Fame Game Cowboys vs. Cardinals, but who’s counting?) But many fanatics, myself included, often severely overlook the risks that athletes take when they play sports: traumatic brain injury one of many not yet fully understood. Brain injury extends far from sports, however, including military implications and even normal day life—surprisingly, motor vehicles are only the third leading cause of traumatic brain injury (TBI), landing behind ‘falls’ and ‘individual being struck by another object’ (Meaney 2). 

Dr. Bass’ Injury and Orthopaedic Biomechanics Laboratory seeks to dig deeper into different aspects of brain injury; my mentor Chris and I hope to investigate the key mechanism of TBI. Currently, two branches of ideology exist in regards to how mild traumatic brain injury arises; the first believes that mainly direct impacts to the head, linear velocities and accelerations, are the key mechanisms of head injury and the second school conjectures that rotational velocities and accelerations cause head injury. A plethora of experiments (Gennarelli, Euckerhave concluded that head rotation is the greater cause of mild traumatic brain injury, but the exact mechanism of TBI, whether angular velocity or acceleration and whether parameters to measure concussion include shear strain, relative displacement, shear stress, pressure waves, etc. remains to be confirmed. Currently, some of the main parameters used to determine and assess level of brain injury are cumulative strain damage measurements (CSDM), maximum principal strain (MPS), and maximum pressure.

This summer, a twofold process will be used to analyze the true mechanism that is causing shear and strain in the brain. First, a program called LS-DYNA/LS-PrePost will be used to analyze the finite element analysis SIMon model. The SIMon (Simulated Injury Monitor) was made to evaluate injury potential by directly imposing measured responses on a finite element model, which allows deformation and predicts how a product reacts to real world forces.

Using finite element analysis to model reactions to real world forces, such as a ball hitting a plate with a set velocity.

SIMon Model to analyze effects of rotational velocity on the brain

Second, a gel will be used for hands-on experimentation. A built device will allow different accelerations and constant velocities to be manually created and the resulting strain will be reflected in the gel—different colors (similar to figure 4) will appear and can be compared to the strains found from the SIMon model. Although the materials are different (SIMon model set brain material versus brain-like gel), the strains should reflect relatively the same values.

Finally, an experiment will be conducted to attempt to understand the effect of shear shock waves on the brain. Currently, the exact effect of instantaneous pressure waves and energy mounts from shear shock waves (hemorrhages, microcavitations, etc.) is unknown. In order to visualize injury that MRI scans usually cannot pick up on, the same device as the gel experiment will be used to give impact to a pig’s brain. Different boundary conditions will be placed; the pig’s skull will be replaced with a clear, transparent, skull cap in order to visualize the interior of the brain during the impact. Analyzing the effects of shear shock will allow better understanding of how these waves truly contribute to traumatic brain injury. Although the ideas are still preliminary, by the time NFL season rolls around, I hope to have delved deeper into my research project and reaped some interesting results!

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