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1. A mysterious disease in Antarctic fish

   DaMommio, C; Postlethwait, John H; Desvignes, Thomas (June 2022, zenodo)

   While conducting research in Antarctica in 2018, scientists were surprised to capture many specimens of two species of fish that had massive skin tumors. In this short graphic novel, “A mysterious disease in Antarctic fish“, Chloe DaMommio, John Postlethwait, and Thomas Desvignes take us on a scientific expedition to Antarctica aboard the US Antarctic Research Vessel Laurence M. Gould to capture those diseased fish, set sail to the isolated Palmer Station to sample them, then back to their laboratory in the States to identify the origin of this mysterious disease and its effects on the fish. The graphic novel is available in English, Spanish, French, German, and Danish! 

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2. Indirect effects in a planktonic disease system

   https://doi.org/10.1016/j.tpb.2019.07.009  

   Rapti, Z.; Stewart-Merrill, T.E.; Mueller-Brennan, L.E.; Caceres, C. (January 2019, Theoretical population biology)

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3. Interacting regional policies in containing a disease

   https://doi.org/10.1073/pnas.2021520118  

   Chandrasekhar, Arun G.; Goldsmith-Pinkham, Paul; Jackson, Matthew O.; Thau, Samuel (April 2021, Proceedings of the National Academy of Sciences)

   Regional quarantine policies, in which a portion of a population surrounding infections is locked down, are an important tool to contain disease. However, jurisdictional governments—such as cities, counties, states, and countries—act with minimal coordination across borders. We show that a regional quarantine policy’s effectiveness depends on whether 1) the network of interactions satisfies a growth balance condition, 2) infections have a short delay in detection, and 3) the government has control over and knowledge of the necessary parts of the network (no leakage of behaviors). As these conditions generally fail to be satisfied, especially when interactions cross borders, we show that substantial improvements are possible if governments are outward looking and proactive: triggering quarantines in reaction to neighbors’ infection rates, in some cases even before infections are detected internally. We also show that even a few lax governments—those that wait for nontrivial internal infection rates before quarantining—impose substantial costs on the whole system. Our results illustrate the importance of understanding contagion across policy borders and offer a starting point in designing proactive policies for decentralized jurisdictions. 

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4. Integrative-omics for discovery of network-level disease biomarkers: a case study in Alzheimer’s disease

   https://doi.org/10.1093/bib/bbab121  

   Xie, Linhui; He, Bing; Varathan, Pradeep; Nho, Kwangsik; Risacher, Shannon L; Saykin, Andrew J; Salama, Paul; Yan, Jingwen (November 2021, Briefings in Bioinformatics)

   Abstract A large number of genetic variations have been identified to be associated with Alzheimer’s disease (AD) and related quantitative traits. However, majority of existing studies focused on single types of omics data, lacking the power of generating a community including multi-omic markers and their functional connections. Because of this, the immense value of multi-omics data on AD has attracted much attention. Leveraging genomic, transcriptomic and proteomic data, and their backbone network through functional relations, we proposed a modularity-constrained logistic regression model to mine the association between disease status and a group of functionally connected multi-omic features, i.e. single-nucleotide polymorphisms (SNPs), genes and proteins. This new model was applied to the real data collected from the frontal cortex tissue in the Religious Orders Study and Memory and Aging Project cohort. Compared with other state-of-art methods, it provided overall the best prediction performance during cross-validation. This new method helped identify a group of densely connected SNPs, genes and proteins predictive of AD status. These SNPs are mostly expression quantitative trait loci in the frontal region. Brain-wide gene expression profile of these genes and proteins were highly correlated with the brain activation map of ‘vision’, a brain function partly controlled by frontal cortex. These genes and proteins were also found to be associated with the amyloid deposition, cortical volume and average thickness of frontal regions. Taken together, these results suggested a potential pathway underlying the development of AD from SNPs to gene expression, protein expression and ultimately brain functional and structural changes. 

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5. Proteolethargy is a pathogenic mechanism in chronic disease

   https://doi.org/10.1016/j.cell.2024.10.051  

   Dall’Agnese, Alessandra; Zheng, Ming M; Moreno, Shannon; Platt, Jesse M; Hoang, An T; Kannan, Deepti; Dall’Agnese, Giuseppe; Overholt, Kalon J; Sagi, Ido; Hannett, Nancy M; et al (January 2025, Cell)

   The pathogenic mechanisms of many diseases are well understood at the molecular level, but there are prevalent syndromes associated with pathogenic signaling, such as diabetes and chronic inflammation, where our understanding is more limited. Here, we report that pathogenic signaling suppresses the mobility of a spectrum of proteins that play essential roles in cellular functions known to be dysregulated in these chronic diseases. The reduced protein mobility, which we call proteolethargy, was linked to cysteine residues in the affected proteins and signaling-related increases in excess reactive oxygen species. Diverse pathogenic stimuli, including hyperglycemia, dyslipidemia, and inflammation, produce similar reduced protein mobility phenotypes. We propose that proteolethargy is an overlooked cellular mechanism that may account for various pathogenic features of diverse chronic diseases. 

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