MaCSBio Science Day 2021

Predicting the effect of contact-tracing apps in epidemic spreading: A multilayer network approach

Numerous countries have relied on contact-tracing (CT) applications as an epidemic control measure against the COVID-19 pandemic. However, limited research has been done to characterise their effectiveness in a dynamic adoption setting.

To this end, we propose the implementation of a multilayer network approach to represent the co-evolution of an epidemic dynamic, modelled using a modified SEIR model, and the CT app adoption process, represented by a threshold dynamic over the same population. The model was initialised to reflect COVID-19 progression and implemented over two populations with different network structures. Two different strategies for the implementation of CT apps were explored, which allowed to characterise the relevance of the time of adoption, number of adopters and level of compliance for the effectiveness of the app.

The results highlighted that an early implementation of the strategy and an adoption by more than 25% of the users is required to ensure a minimal effectiveness (>5% mean peak reduction). Moreover, compliance with the strategy also plays a major role in the app's performance, since even low levels of compliance can result in a moderate effectiveness (>10% mean peak reduction) if high levels of adoption are considered.

The insight obtained from this project was used to study the Spanish CT app in which we identified a bottleneck in the process for reporting an infection. We suggest that the implementation of a more straightforward verification process would increase the compliance with the strategy and cause an increase in its effectiveness.

Deinococcus radiodurans proteome responds rapidly to short-term real microgravity during parabolic flight

As plans for future space exploration are becoming more ambitious, a better understanding of all factors affecting humans, plants, and microorganisms in space is necessary. Microgravity is an important variable in outer space and understanding the short- and long- term effects of microgravity on cellular processes will be important to minimize its negative effects on the physiology of any organism.

Gravitational force has had an important role in the development of life on Earth, and short- and long-term changes in perceived gravitational force can induce notable changes within cells. Deinococcus radiodurans is the gram-positive bacterium that is best known for its extreme resistance to UV-C and gamma radiation, oxidation stress and desiccation, which has led to increased interest in this species in the context of astrobiology.

The present study aimed to elucidate the short-term proteomic response of this species to real microgravity during parabolic flight. Overnight cultures of D.radiodurans were subjected to microgravity during a single parabola, and metabolic activity quenched using methanol on board of parabolic flight. Proteins were extracted and subsequently measured using HPLC ESI MS/MS.

Results indicated multiple affected processes in the cell envelope of D. radiodurans, such as increased peptidoglycan synthesis and altered S-layer activities. Energy metabolism upregulation and increased activity of DNA repair pathways could indicate increased endogenous ROS production that contributes to the stress response.

The present study shows that the D. radiodurans proteome rapidly reacts to real microgravity within 10 2 seconds. Differential expression patterns in response to microgravity show similarities to previously reported stress responses, thus the present results could be used as basis for future research aiming to better understand the complex regulatory processes underpinning stress management in D. radiodurans.

Identifying the key pathways involved in a pearl-necklace like mitochondrial phenotype

Mitochondria are dynamic organelles that are responsible for the production of ATP. Mitochondrial dynamics are processes that allow the organelles to adapt their morphology according to the cellular energy demands.

Fission and fusion are essential processes that regulate the number of healthy mitochondria in the cell. Defects in these processes have been linked to diseases such as Alzheimer and Charot-Marie Tooth. Investigating and identifying key factors involved in mitochondrial dynamics defects will increase our understanding of the organelle’s role in disease. The host research team observed an altered mitochondrial phenotype, resembling a pearl-necklace shape, upon knockdown of fission genes in fibroblast cells that has not been previously reported and did not emerge in HeLa, HEK293T, HUVEC and HepG2 cells.

The current study constitutes a novel computational approach to identify pathways involved in this phenotype. To do so, RNAseq data from the before mentioned cell types were obtained and average gene expression (average FPKM) of each cell type was calculated to compare differences between the cell types in baseline pathway activity level. Moreover, the methodological approach included differentially expressed gene analysis in combination with pathway enrichment and network analysis to compare differences between the cell types in pathway level. Candidate pathways will be selected based on their involvement in the pearl-necklace phenotype. Validation of the candidate pathways will be conducted in the wet lab if Covid-19 measures allow for.

Expected results will confirm the hypothesis that the phenotype is tissue specific, hence provide additional knowledge on the tissue specificity of mitochondrial diseases.