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Evaluation of tSNE and FlowSOM unsupervised analysis in mouse blood flow cytometry data after an inflammatory challenge

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Traumatic brain injury involves a primary mechanical injury that is followed by a secondary<br/>inflammatory cascade. The inflammatory cascade in the CNS releases cytokines which are<br/>associated with leukocytosis and a systemic immune response. Acute changes to peripheral<br/>immune cell populations post-TBI include a 4.5-fold increase of neutrophils 3 hours post-injury,<br/>and 2.7-fold or…

Traumatic brain injury involves a primary mechanical injury that is followed by a secondary<br/>inflammatory cascade. The inflammatory cascade in the CNS releases cytokines which are<br/>associated with leukocytosis and a systemic immune response. Acute changes to peripheral<br/>immune cell populations post-TBI include a 4.5-fold increase of neutrophils 3 hours post-injury,<br/>and 2.7-fold or higher increase of monocytes 24 hours post-injury. Flow Cytometry is a<br/>technique that integrates fluidics, optics, and electronics to characterize cells based on their light<br/>scatter and antigen expression via monoclonal antibodies conjugated to fluorochromes. Flow<br/>cytometry is a valuable tool in cell characterization however the standard technique for data<br/>analysis, manual gating, is associated with inefficiency, subjectivity, and irreproducibility.<br/>Unsupervised analysis that uses algorithms packaged as plug-ins for flow cytometry analysis<br/>software has been discussed as a solution to the limits of manual gating and as an alternative<br/>method of data visualization and exploration. This investigation evaluated the use of tSNE<br/>(dimensionality reduction algorithm) and FlowSOM (population clustering algorithm)<br/>unsupervised flow cytometry analysis of immune cell population changes in female mice that<br/>have been exposed to a LPS-induced systemic inflammatory challenge, results were compared to<br/>those of manual gating. Flow cytometry data was obtained from blood samples taken prior to and<br/>24 hours after LPS injection. Unsupervised analysis was able to identify populations of<br/>neutrophils and pro-inflammatory/anti-inflammatory monocytes, it also identified several more<br/>populations however further inquiry with a more specific fluorescent panel would be required to<br/>establish the specificity and validity of these populations. Unsupervised analysis with tSNE and<br/>FlowSOM demonstrated the efficient and intuitive nature of the technique, however it also<br/>illustrated the importance of the investigator in preparing data and modulating plug-in settings.
ContributorsDudic, Ahmed (Author) / Stabenfeldt, Sarah (Thesis director) / Lifshitz, Jonathan (Committee member) / Rojas, Luisa (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Remote ischemic conditioning reduces traumatic brain injury induced acute lung injury in an experimental mouse model

Description
Traumatic brain injury (TBI) consists of the primary mechanical forces to the head followed by secondary inflammatory cascades. This inflammatory cascade consists of neuroinflammation characterized by microglial activation as the first line of defense. Another component of secondary inflammation comprises of activation of peripheral immune cells that can infiltrate the…

Traumatic brain injury (TBI) consists of the primary mechanical forces to the head followed by secondary inflammatory cascades. This inflammatory cascade consists of neuroinflammation characterized by microglial activation as the first line of defense. Another component of secondary inflammation comprises of activation of peripheral immune cells that can infiltrate the compromised blood brain barrier and susceptible organs such as the lungs. Acute inflammatory processes in the lungs include a disruption of the epithelial barriers allowing infiltration of neutrophils, and edema build up in the alveoli. This is known as acute lung injury (ALI) and it dampens respiratory function in approximately 20-25% of TBI patients necessitating an intervention. Remote ischemic conditioning (RIC) is an intervention consisting of repeated intervals of cessation and reperfusion of blood flow to a distal limb and has treated ALI, myocardial infarction, and neurological injury. TBI was hypothesized to induce ALI through degradation of alveolar-capillary membrane and infiltration of peripheral leukocytes. Furthermore, RIC was hypothesized to protect the integrity of the alveolar-capillary membrane, reduce infiltration of peripheral immune cells, and reduce microglial activation in the brain through myokine recruitment. Male CD1 mice were subject to either midline fluid percussion or sham injury and further randomized into 4 groups: sham, sham RIC, TBI, TBI RIC. RIC was administered on proximal thigh for 4x5 minutes, with 5-minute reperfusion one hour prior to TBI. One-hour post-injury, brain, lung, BAL fluid, and blood were collected. Lung histopathology showed RIC reduced hydrostatic edema in the alveoli by protecting the alveolar capillary membrane. BAL findings revealed TBI mice had increased neutrophil counts, RIC lowered neutrophil counts. In the brain, RIC increased cortex microglial endpoints were observed with no other significant differences in microglial morphology as well as plasma myokine levels across all sham, sham RIC, TBI, and TBI RIC animals. While underlying mechanisms still have to be further studied, this current study provides evidence that RIC can be used as a therapeutic intervention to ameliorate TBI-induce ALI.
ContributorsChristie, Immaculate (Author) / Newbern, Jason (Thesis director) / Lifshitz, Jonathan (Committee member) / Saber, Maha (Committee member) / School of Life Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
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Time-Lapse Visualization of Microglia Cell Processes using Fluorescent Miniature (Miniscope) Imaging

Description
In the United States, an estimated 2 million cases of traumatic brain injury (TBI) resulting in more than 50,000 deaths occur every year. TBI induces an immediate primary injury resulting in local or diffuse cell death in the brain. Then a secondary injury occurs through neuroinflammation from immune cells in…

In the United States, an estimated 2 million cases of traumatic brain injury (TBI) resulting in more than 50,000 deaths occur every year. TBI induces an immediate primary injury resulting in local or diffuse cell death in the brain. Then a secondary injury occurs through neuroinflammation from immune cells in response to primary injury. Microglia, the resident immune cell of the central nervous system, play a critical role in neuroinflammation following TBI. Microglia make up 10% of all cells in the nervous system and are the fastest moving cells in the brain, scanning the entire parenchyma every several hours. Microglia have roles in both the healthy and injured brain. In the healthy brain, microglia can produce neuroprotective factors, clear cellular debris, and organize neurorestorative processes to recover from TBI. However, microglia mediated neuroinflammation during secondary injury produces pro-inflammatory and cytotoxic mediators contributing to neuronal dysfunction, inhibition of CNS repair, and cell death. Furthermore, neuroinflammation is a prominent feature in many neurodegenerative diseases such as Alzheimer’s, and Parkinson’s disease, of which include overactive microglia function. Microglia cell morphology, activation, and response to TBI is poorly understood. Currently, imaging microglia can only be performed while the animal is stationary and under anesthesia. The Miniscope technology allows for real-time visualization of microglia in awake behaving animals. The Miniscope is a miniature fluorescent microscope that can be implanted over a craniectomy to image microglia. Currently, the goals of Miniscope imaging are to improve image quality and develop time-lapse imaging capabilities. There were five main sub-projects that focused on these goals including surgical nose cone design, surgical holder design, improved GRIN lens setup, improved magnification through achromatic lenses, and time-lapse imaging hardware development. Completing these goals would allow for the visualization of microglia function in the healthy and injured brain, elucidating important immune functions that could provide new strategies for treating brain diseases.
ContributorsNelson, Andrew Frederick (Author) / Stabenfeldt, Sarah (Thesis director) / Lifshitz, Jonathan (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05