Jenny Ji

All Publications

• Continuous monitoring of blood-interstitial fluid intercompartmental molecular kinetics in freely moving animals. Science advances Chen, Y., Hu, Q., Kwak, J. W., Zakharian, D., Ji, J., Liu, D., Gopalan, D., Lyons, C., Yates, M., Yee, S., Cui, H., Eisenstein, M., Soh, H. T. 2026; 12 (21): eaed1895

  Abstract

  Accurate health monitoring depends on continuous assessment of biochemical markers across multiple body compartments. While blood remains the clinical gold standard, interstitial fluid (ISF) presents a minimally invasive alternative that reflects local tissue physiology, although its biomarker kinetics often differ from blood. It is currently impossible to achieve simultaneous, continuous monitoring of both compartments, limiting insight into their dynamic relationship. To address this, we present BICEP (blood-ISF continuous-sensing electrochemical probe), a wireless electrochemical platform for continuous dual-compartment monitoring of analytes in blood and ISF. The BICEP system incorporates microfabricated soft sensors with biofouling-resistant aptamer interfaces, paired with a wearable potentiostat for remote configuration and readout. Using this system, we continuously tracked kanamycin signal in both anesthetized and freely moving rats, revealing distinct kinetic profiles and individualized temporal delays between blood and ISF signals. These findings confirm that ISF is not merely a proxy for blood but exhibits unique molecular kinetics influenced by individual variability and physiological state. This platform advances personalized health monitoring by providing integrated, dynamic correlation of blood and ISF biomarkers, deepening understanding of their physiological interplay under real-life conditions and paving the way for broader use of wearable ISF-based biosensors.

  View details for DOI 10.1126/sciadv.aed1895

  View details for PubMedID 42160425

  View details for PubMedCentralID PMC13189097

• A 3D-Printed Scaffolded Hydrogel Microneedle Array Biosensor for Real-Time, Continuous Monitoring. Advanced materials (Deerfield Beach, Fla.) Kwak, J. W., Trinh, T., White, A. D., Chen, Y., Eckman, N., Jain, I., Xu, Y., Nguyen, N., Gopalan, D., Kim, Y. E., Unni Kamat, N., Tumbleston, J. R., Park, C. H., Yoshikawa, A., Ji, J., Dulay, M. T., Eisenstein, M., Appel, E. A., Kim, J., DeSimone, J. M., Soh, H. T. 2026: e73325

  Abstract

  Hydrogel-based biosensors offer a promising platform for designing microneedles capable of continuously tracking biomarkers in real time. However, such biosensors have been limited by the mechanical properties of hydrated hydrogels, which are generally ineffective at penetrating the skin to access interstitial fluid (ISF). As a solution, we have developed a microneedle-array biosensor (MAB) patch that enables continuous, reversible sensing by coupling fluorescent deoxyribonucleic acid (DNA) aptamer switches to a hydrated hydrogel mesh within a 3D-printed scaffold. This scaffold provides essential mechanical support for skin insertion while preserving the apatmer-hydrogel's sensing functionality in the ISF. We demonstrate this design by tuning both aptamer switch design and hydrogel mesh size to detect exogenous levels of stress hormone cortisol and the metabolite adenosine triphosphate. We subsequently incorporated our cortisol-sensing hydrogel into the MAB scaffold and coupled this system to a custom-designed portable optical detector. Following in vitro validation, we demonstrated the biocompatibility and in vivo utility of our system by conducting continuous, real-time measurements of exogenous cortisol in the ISF of live rats. These results demonstrate, for the first time, submicromolar detection using a sensor-embedded hydrogel microneedle system, highlighting the MAB platform as a versatile solution for real-time, continuous in vivo biosensing.

  View details for DOI 10.1002/adma.73325

  View details for PubMedID 42163595

• The gut microbiome promotes mitochondrial respiration in the brain of a Parkinson's disease mouse model NPJ PARKINSONS DISEASE Morais, L. H., Stiles, L., Freeman, M., Oguienko, A. D., Hoang, J. D., Ji, J., Jones, J., Quan, B., Devine, J., Bois, J. S., Chou, T., Trinh, J., Picard, M., Gradinaru, V., Mazmanian, S. K. 2025; 11 (1): 301

  Abstract

  The pathophysiology of Parkinson's disease (PD) involves gene-environment interactions that impair various cellular processes including mitochondrial dysfunction. Mitochondria-associated mutations increase PD risk, respiration is altered in the PD brain, and mitochondria-damaging toxicants cause PD-like motor and gastrointestinal symptoms in animal models. The gut microbiome is altered in PD, representing an environmental risk, however a relationship between mitochondrial function and the microbiome in PD has not been previously established. Herein, we discover that dysregulation of mitochondria-associated genes and hyperactive striatal mitochondria are induced by the microbiome in α-synuclein-overexpressing (Thy1-ASO) mice. Thy1-ASO mice elaborate increased reactive oxygen species in the striatum whereas germ-free counterparts express increased oxygen scavenging proteins. Indeed, treatment with an antioxidant drug improves motor performance in Thy1-ASO mice and blocking oxidant scavenging in germ-free mice enhances motor deficits in an α-synuclein dependent manner. Thus, the gut microbiome promotes motor symptoms in a mouse model of PD via increased mitochondrial respiration and oxidative stress in the brain.

  View details for DOI 10.1038/s41531-025-01142-5

  View details for Web of Science ID 001596233800001

  View details for PubMedID 41115949

  View details for PubMedCentralID PMC12537952

• Regional disparities in US media coverage of archaeology research. Science advances Alex, B., Ji, J., Flad, R. 2025; 11 (27): eadt5435

  Abstract

  Mass media represents a primary avenue for research to reach diverse publics, but relatively few peer-reviewed scientific papers become popular science news. Numerous gatekeepers determine which research manuscripts complete this dissemination pathway, and the resulting media landscape influences public understandings of scientific fields. Here, we compare scientific and popular publishing of archaeology about different geographic regions. Of 1155 archaeology papers in one specialist and six general science journals across 6 years, 32% were reported by at least one of 15 US news sources. Mixed-effects logistic regression models revealed variation across news sources, but overall papers about archaeology in United Kingdom, Israel/Palestine, and Australia were significantly more likely to receive coverage, compared to China/Taiwan. This disparity raises concerns as archaeology influences notions of identity and cultural achievement, and has been misappropriated by racist, nationalist ideologies. We recommend ways for actors in research dissemination to diversify archaeology coverage.

  View details for DOI 10.1126/sciadv.adt5435

  View details for PubMedID 40601722

  View details for PubMedCentralID PMC12219491

• Quantitative SARS-CoV-2 Viral-Load Curves in Paired Saliva Samples and Nasal Swabs Inform Appropriate Respiratory Sampling Site and Analytical Test Sensitivity Required for Earliest Viral Detection JOURNAL OF CLINICAL MICROBIOLOGY Savela, E. S., Winnett, A., Romano, A. E., Porter, M. K., Shelby, N., Akana, R., Ji, J., Cooper, M. M., Schlenker, N. W., Reyes, J. A., Carter, A. M., Barlow, J. T., Tognazzini, C., Feaster, M., Goh, Y., Ismagilov, R. F. 2022; 60 (2): e0178521

  Abstract

  Early detection of SARS-CoV-2 infection is critical to reduce asymptomatic and presymptomatic transmission, curb the spread of variants, and maximize treatment efficacy. Low-analytical-sensitivity nasal-swab testing is commonly used for surveillance and symptomatic testing, but the ability of these tests to detect the earliest stages of infection has not been established. In this study, conducted between September 2020 and June 2021 in the greater Los Angeles County, California, area, initially SARS-CoV-2-negative household contacts of individuals diagnosed with COVID-19 prospectively self-collected paired anterior-nares nasal-swab and saliva samples twice daily for viral-load quantification by high-sensitivity reverse-transcription quantitative PCR (RT-qPCR) and digital-RT-PCR assays. We captured viral-load profiles from the incidence of infection for seven individuals and compared diagnostic sensitivities between respiratory sites. Among unvaccinated persons, testing saliva with a high-analytical-sensitivity assay detected infection up to 4.5 days before viral loads in nasal swabs reached concentrations detectable by low-analytical-sensitivity nasal-swab tests. For most participants, nasal swabs reached higher peak viral loads than saliva but were undetectable or at lower loads during the first few days of infection. High-analytical-sensitivity saliva testing was most reliable for earliest detection. Our study illustrates the value of acquiring early (within hours after a negative high-sensitivity test) viral-load profiles to guide the appropriate analytical sensitivity and respiratory site for detecting earliest infections. Such data are challenging to acquire but critical to designing optimal testing strategies with emerging variants in the current pandemic and to respond to future viral pandemics.

  View details for DOI 10.1128/jcm.01785-21

  View details for Web of Science ID 000765805200010

  View details for PubMedID 34911366

  View details for PubMedCentralID PMC8849374

• Quantitative SARS-CoV-2 viral-load curves in paired saliva and nasal swabs inform appropriate respiratory sampling site and analytical test sensitivity required for earliest viral detection. medRxiv : the preprint server for health sciences Savela, E. S., Winnett, A., Romano, A. E., Porter, M. K., Shelby, N., Akana, R., Ji, J., Cooper, M. M., Schlenker, N. W., Reyes, J. A., Carter, A. M., Barlow, J. T., Tognazzini, C., Feaster, M., Goh, Y., Ismagilov, R. F. 2021

  Abstract

  Early detection of SARS-CoV-2 infection is critical to reduce asymptomatic and pre-symptomatic transmission, curb the spread of variants by travelers, and maximize treatment efficacy. Low-sensitivity nasal-swab testing (antigen and some nucleic-acid-amplification tests) is commonly used for surveillance and symptomatic testing, but the ability of low-sensitivity nasal-swab tests to detect the earliest stages of infection has not been established. In this case-ascertained study, initially-SARS-CoV-2-negative household contacts of individuals diagnosed with COVID-19 prospectively self-collected paired anterior-nares nasal-swab and saliva samples twice daily for viral-load quantification by high-sensitivity RT-qPCR and digital-RT-PCR assays. We captured viral-load profiles from the incidence of infection for seven individuals and compared diagnostic sensitivities between respiratory sites. Among unvaccinated persons, high-sensitivity saliva testing detected infection up to 4.5 days before viral loads in nasal swabs reached the limit of detection of low-sensitivity nasal-swab tests. For most participants, nasal swabs reached higher peak viral loads than saliva, but were undetectable or at lower loads during the first few days of infection. High-sensitivity saliva testing was most reliable for earliest detection. Our study illustrates the value of acquiring early (within hours after a negative high-sensitivity test) viral-load profiles to guide the appropriate analytical sensitivity and respiratory site for detecting earliest infections. Such data are challenging to acquire but critical to design optimal testing strategies in the current pandemic and will be required for responding to future viral pandemics. As new variants and viruses emerge, up-to-date data on viral kinetics are necessary to adjust testing strategies for reliable early detection of infections.

  View details for DOI 10.1101/2021.04.02.21254771

  View details for PubMedID 33851180