Oscillations in protein levels or activation state are ubiquitous in eukaryotic signaling pathways, but the function of these oscillations remains unclear. We find that p38α MAPK activation state oscillates at multiple frequencies in response to stress rather than at a singular frequency. Fourier analysis of p38α activation state measured with a novel FRET sensor shows that unique stressors including IL-1β, SARS-CoV-2 Spike protein, and sorbitol induce unique response patterns in the frequency domain. Analysis of statistically over represented frequencies suggests that frequency bins are fixed and organized as harmonics with a fundamental frequency of 0.09 hr−1(p=0.04). Cross spectral dynamics between p38α and a substrate indicate that substrate activation behaves similarly to a forced oscillator system being driven at resonance. We have developed a model that characterizes the MAPK phosphorylation cascade as a chemical resonator that impart multiple frequencies on p38α, allowing the kinase to regulate its substrates through resonance selectivity. Stochastic simulations of substrates being driven on and off-resonance produce spectra comparable to experimental data.

Experiments on E. coli expressing a transposon of the IS200/IS5605 family reveal that expression of transposon protein TnpB leads to a higher excision rate. Furthermore, cells that excise possess TnpB at a significantly higher expression level than cells that don’t, with TnpA expression levels making no discernible difference in excision dynamics.

We present a protocol for purification of SARS-CoV-2 structural proteins using a bacterial expression system, SUMO tags, and affinity purification methods. We further report a method to insert synthesized dimers into a suspended lipid membrane in a homogeneous orientation. AFM and Cryo-EM in tandem with molecular dynamics simulations show membrane thinning around the M protein and a propensity to induce local membrane curvature.

Since the discovery of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), it has allowed for genome editing to be utilized in a way never seen before. Although it can create knockout and point mutations at ease, it can still be difficult to create knockin mutations. In order to combat this issue, GENEWRITE was created utilizing the reverse transcription function of the LINE-1 (long interspersed element-1) and combining it with the commonly used Cas (CRISPR associated proteins). This also worked around the need for CRISPR to silence NHEJ as it can be utilized in the protocol as well. This, however, made it difficult for GENEWRITE to function in organisms such as prokaryotes and archaea which did not already carry a NHEJ pathway. To identify prokaryotes and archaea the GENEWRITE protocol can function in, a bioinformatics analysis was done to identify the known forms of NHEJ in prokaryotes and archaea. Additionally, it was recently found that TnpB, a transposon associated gene from the IS200/IS605 family found in bacteria, is a RNA-guided DNA endonuclease that could be programmed similar to Cas proteins. To verify its potential function within the transposon, a quantitative microscopy study was carried out to observe how TnpB affected transposition in real tim