Biology subjects

Vazquez, F. X.

Publications and source records attributed to Vazquez, F. X..

3 recordsLinked to original sources

bioRxiv2024

A ChatGPT Assisted Reading Protocol for Undergraduate Research Students Engaging with Biophysics Literature

A major challenge for undergraduate students is reading scientific literature. This is especially true in biophysics, where many of the concepts may not have been covered in undergraduate courses. Students can become overwhelmed, which may lead to less overall engagement with the scientific literature. In response, we have developed a guided reading protocol that combines pre-reading strategies, structured notetaking, and ChatGPT to help students clarify unfamiliar concepts in an interactive way. To test the protocol, participants in this study were given an initial survey to determine their experience with reading scientific literature. After this they were given an abridged biophysics paper and the protocol. The ChatGPT transcripts were analyzed using open coding and the students were given a post-study survey. We found most students did not appear to regularly engage with the literature, possibly due to content barriers they encountered. Analyzing their transcripts, we observed that students asked for definitions, explanations, summaries, and simplifications. Overall, students reported that using ChatGPT was a positive experience and they expected to use ChatGPT in the future. From this work, we expect this new protocol may be a way to keep novice students from becoming discouraged when reading scientific papers and keep them engaged with the current literature.

scientific communication and education↗

bioRxiv2024

Expanding salivary biomarker detection by creating a synthetic neuraminic acid sensor via chimeragenesis

Accurate and timely diagnosis of oral squamous cell carcinoma (OSCC) is crucial in preventing its progression to advanced stages with poorer prognosis. As such, the construction of sensors capable of detecting previously established disease biomarkers for the early and non-invasive diagnosis of this and many other conditions has enormous therapeutic potential. In this work, we apply synthetic biology techniques for the development of a whole-cell biosensor (WCB) that leverages the physiology of engineered bacteria in vivo to promote the expression of an observable effector upon detection of a soluble molecule. To this end, we have constructed a bacterial strain expressing a novel chimeric transcription factor (Sphnx) for the detection of N-acetyl-D-neuraminic acid (Neu5Ac), a salivary biomolecule correlated with the onset of OSCC. This WCB serves as the proof-of-concept of a platform that can eventually be applied to clinical screening panels for a multitude of oral and systemic medical conditions whose biomarkers are present in saliva.

synthetic biology↗

bioRxiv2024

Flanking Domains Modulate α-Synuclein Monomer Structure: A Molecular Dynamics Domain Deletion Study

Aggregates of misfolded -synuclein proteins (asyn) are key markers of Parkinsons disease. Asyn proteins have three domains: an N-terminal domain, a hydrophobic NAC core implicated in aggregation, and a proline-rich C-terminal domain. Proteins with truncated C-terminal domains are known to be prone to aggregation and suggest that understanding domain-domain interactions in asyn monomers could help elucidate the role of the flanking domains in modulating protein structure. To this end, we used Gaussian accelerated molecular dynamics (GAMD) to simulate wild-type (WT), N-terminal truncated ({Delta}N), C-terminal truncated ({Delta}C), and isolated NAC domain asyn protein variants (isoNAC). Using clustering and contact analysis, we found that removal of the N-terminal domain led to increased contacts between NAC and C-terminal domains and the formation of interdomain {Delta}-sheets. Removal of either flanking domain also resulted in increased compactness of every domain. We also found that the contacts between flanking domains in the WT protein result in an electrostatic potential (ESP) that may lead to favorable interactions with anionic lipid membranes. Removal of the C-terminal domain disrupts the ESP in a way that could result in over-stabilized protein-membrane interactions. These results suggests that cooperation between the flanking domains may modulate the proteins structure in a way that helps maintain elongation and creates an ESP that may aid favorable interactions with the membrane.

biophysics↗