Macrophage cellular nibbling

Macrophage cells are on the front lines when the immune system kicks in. They’re a type of white blood cell that phagocytize—or fully engulf—foreign cells. Moreover, scientists have observed another macrophage behavior, in which they “nibble” on pathogens by biting off small chunks at a time. This behavior, called trogocytosis, is quite common in interactions between macrophages and cancer cells. Scientists studying the behavior have identified a potential application to cancer immunotherapy treatments. First-year Biology and English double major Kathleen Zhang worked under UC Santa Barbara faculty member, Meghan Morrissey of the Morrissey Lab, to investigate why macrophage nibbling is only sometimes lethal and how the manipulation of cancer cell gene expression might make them more prone to death from trogocytosis.

Using CRISPR/Cas9 gene editing, Zhang knocked down specific genes to compromise cellular functions and produce internal stress.The induced stress may cause cells to be more prone to death when encountering trogocytosis by macrophages. In order to further investigate this process and its effectiveness, Zhang will be measuring trogocytosis by using time-lapses and fluorescence markers. This will quantify the nibbling done by the macrophages, allowing them to analyze the proportion of cell deaths due to trogocytosis. Because macrophage nibbling has potential to increase cancer cell death, this research has important applications for developing more effective cancer immunotherapy treatments.

Function of neural-like proteins in single-celled eukaryotes

The post-synaptic cells in our neuronal synapses have receptors that are secured in place by a scaffolding protein called postsynaptic density protein 95 (PSD-95). Although single-celled eukaryotes have no nervous system, these organisms also possess the PSD-95 protein. Second-year biology major Riya Nilkant worked with Principal Investigators Kenneth Kosik and Soojin Yi of the Kosik Lab to discover the unknown function of PSD-95 in single-celled eukaryotes and whether it can provide any insight on the origin and evolution of the synapse. 

Nilkant, having found that there are nine amino acid residues involved in binding within PSD-95, produced a matrix by calculating every possible distance between atoms within the binding site. Hydrophobic regions and phi and psi angles were identified to distinguish the protein’s orientation in space. It’s the first known study to quantify the binding pocket of the PSD-95 protein with these methods. Nilkant plans to further observe the function of PSD-95 in the lab. A part of the PSD-95 protein will be inserted into a plasmid, a circular piece of DNA, which will be placed into a neural cell. Comparing areas that fluoresce to PSD-95 protein in its natural state can help determine the protein’s function. This research may have important applications in understanding the neurological basis of conditions such as Alzheimer’s and autism.  

Detection of pathogenic eDNA in soils

Amphibians, like frogs and salamanders, are threatened by a pathogenic fungus called Batrachochytrium dendrobatidis (Bd), a disease caused by zoospores that infect the skin. Bd can be detected through environmental DNA (eDNA), DNA that organisms deposit into the environment. However, eDNA is susceptible to degradation due to different biotic and abiotic factors. Fourth-year EEMB major Kathryn Koo worked with UCSB PhD student Caitlin Nordheim of the Cherie Briggs Lab to investigate whether storage duration at 4°C, soil type, or initial Bd dose affected the detection of Bd eDNA in soil samples.

A “Field-Control Comparison” experiment was conducted where soil from the East Bay, California was cultured with Bd strains from the same site. In the “Methods Validation” experiment, artificial soil was used as the control and the same Bd strain was used. DNA was then extracted from these samples using quantitative polymerase chain reaction, which is a technique used to copy and amplify target sequences of DNA in real time. The method was found to accurately detect the presence of Bd in soil samples but was not sensitive enough to accurately identify the quantity of Bd. The researchers also found that the factors of storage duration, soil type and initial Bd dose did not significantly affect the presence of Bd. For future investigations, Koo and her team recommend that a greater range of initial dosage treatments should be done to gain insight on comparisons of Bd eDNA between field and artificial soil. This research could help develop accurate methods of detecting Bd eDNA in soil and a greater understanding of the spread of Batrachochytrium dendrobatidis.