Biology subjects

Kim, E. J.

Publications and source records attributed to Kim, E. J..

24 records · Page 2Linked to original sources

bioRxiv2022

Mosaic receptor-binding domain nanoparticles induce protective immunity against SARS-CoV-2 challenges

Recurrent spillovers of - and {beta}-coronaviruses (CoV) such as acute respiratory syndrome (SARS)-CoV, Middle East respiratory syndrome (MERS)-CoV, SARS-CoV-2, and possibly human CoV (NL63, 229E, OC43, and HKU1) have caused serious morbidity and mortality worldwide. Six receptor binding domains (RBDs) derived from - and {beta}-CoV that are considered to have originated from animals and cross-infected humans were linked to proliferating cell nuclear antigen (PCNA) heterotrimeric subunits, PCNA1, PCNA2, and PCNA3. These were used to form a scaffold-based mosaic multivalent antigen, 6RBD-np. Electron microscopic and atomic force microscopic images show a ring-shaped disk with six protruding RBDs, like jewels in a crown, with a size of 40 nm. Prime-boost immunizations with 6RBD-np in BALB/c mice elicited strong, dose-dependent antibody responses. In human angiotensin converting enzyme 2-transgenic mice, the same immunization induced full-protection against SARS-CoV-2 wild type and Delta challenges, resulting in a 100% survival rate. The mosaic 6RBD-np provides a potential platform for developing a pan-CoV vaccine against newly emerging SARS-CoV-2 variants and future CoV spillovers. SignificanceDespite the arsenal of COVID-19 vaccines, hospitalization and mortality associated with SARS-CoV-2 (acute respiratory syndrome coronavirus 2) variants remain high. There is an urgent need to develop next-generation COVID vaccines that provide broad protection against diseases by current and newly emerging SARS-CoV-2 variants. In this study, six receptor binding domains (RBDs) derived from - and {beta}-CoV were linked to proliferating cell nuclear antigen (PCNA) heterotrimeric scaffolds. They assemble to create a stable mosaic multivalent nanoparticle, 6RBD-np, displaying a ring-shaped disk with six protruding antigens. The prime-boost immunization in BALB/c and human angiotensin converting enzyme 2-transgenic mice with the 6RBD-np elicited strong, dose-dependent antibody responses and induced full-protection against both the SARS-CoV-2 wild type (WT) and Delta challenges. This study provides proof-of-concept that the mosaic 6RBD-np induces 100% protection against SARS-CoV-2 WT and Delta. It provides the potential of co-displaying heterologous antigens for novel vaccine designs, which can be deployed countering future pandemics.

bioengineering↗

bioRxiv2021

Pavlovian fear conditioning does not readily occur in rats in naturalistic environments

Pavlovian fear conditioning, which offers the advantage of simplicity in both the control of conditioned and unconditioned stimuli (CS, US) presentation and the analysis of specific conditioned and unconditioned responses (CR, UR) in a controlled laboratory setting, has been the standard model in basic and translational fear research. Despite 100 years of experiments, the utility of fear conditioning has not been trans-situationally validated in real-life contexts. We thus investigated whether fear conditioning readily occurs and guides the animals future behavior in an ecologically-relevant environment. To do so, Long-Evans rats foraging for food in an open arena were presented with a tone CS paired with electric shock US to their dorsal neck/body that instinctively elicited escape UR to the safe nest. On subsequent test days, the tone-shock paired animals failed to exhibit fear CR to the CS. In contrast, animals that encountered a realistic agent of danger (a looming artificial owl) paired with a shock, simulating a realistic predatory strike, instantly fled to the nest when presented with a tone for the first time. These results illustrate the survival function and precedence of a nonassociative process, rather than associative conditioning, in life-threatening situations that animals are likely to encounter in nature.

animal behavior and cognition↗

bioRxiv2021

Antigen identification and high-throughput interaction mapping by reprogramming viral entry

Deciphering immune recognition is critical for understanding a broad range of diseases and for the development of effective vaccines and immunotherapies. Efforts to do so are limited by a lack of technologies capable of simultaneously capturing the complexity of adaptive immune receptor repertoires and the landscape of potential antigens. To address this, we present RAPTR (Receptor-Antigen Pairing by Targeted Retroviruses). RAPTR combines viral pseudotyping and molecular engineering approaches to enable one-pot library on library interaction screens by displaying antigens on the surface of lentiviruses and encoding their identity in the viral genome. Antigen-specific viral infection of cells allows readout of both antigen and receptor identities via single-cell sequencing. The resulting system is modular, scalable, and compatible with any cell type, making it easily implemented. These techniques provide a suite of new tools for targeted viral entry, molecular engineering, and interaction screens with broad potential applications.

immunology↗

bioRxiv2019

Monosynaptic projections to excitatory and inhibitory preBotzinger Complex neurons

The key driver of breathing rhythm is the preBotzinger Complex (preBotC) whose activity is modulated by various categorical inputs, e.g., volitional, physiological, emotional. While the preBotC is highly interconnected with other regions of the breathing central pattern generator (bCPG) in the brainstem, there is no data about the direct projections to either excitatory and inhibitory preBotC subpopulations from other elements of the bCPG or from suprapontine regions. Using modified rabies tracing, we identified neurons throughout the brain that send monosynaptic projections to identified excitatory and inhibitory preBotC neurons. Within the brainstem, neurons from sites in the bCPG, including the contralateral preBotC, Botzinger Complex (BotC), the nucleus of the solitary tract (NTS), parafacial region (pFL/pFV or RTN/pFRG), and parabrachial nuclei, send direct projections to both excitatory and inhibitory preBotC neurons. Suprapontine inputs to the excitatory and inhibitory preBotC neurons include the superior colliculus, red nucleus, amygdala, hypothalamus, and cortex; these projections represent potential direct pathways for volitional, emotional, and physiological control of breathing.

neuroscience↗

bioRxiv2018

Iso-relevance Functions - A Systematic Approach to Ranking Genomic Features by Differential Effect Size

It is common to measure large numbers of features to identify those differing between experimental conditions; for example using RNA-Seq to search for differentially expressed genes. Ranking by p-value allows for statistical control, but has well known issues: unreliability without many replicates; and significance of biologically irrelevant effect sizes. As a result prioritization is typically performed in conjunction with effect size; the canonical one being "fold-change" [Formula]. However fold-change has several issues: division by zero, sensitivity to small values in the denominator, insensitivity to magnitude (1 over 2 equals 100 over 200). To mitigate these problems adding 1 to all values is a widely used heuristic; which we show using real and simulated data is typically highly sub-optimal, while the value 20 is nearly optimal in all cases. From another point of view, adding a fixed "pseudocount" to all values is essentially re-defining effect size from fold-change to something else. To explore this further, we axiomatize the concept of effect size and use this mathematical framework to study the problem in general. We also present the remarkable finding that pseudocounts strike a balance between sorting by fold-change and sorting by difference. Therefore, optimization is equivalent to finding the most harmonious balance between these two extremes. Lastly, the framework is illustrated on a fundamentally different type of problem, that of ranking di-codons by their differential abundance in the ORFeome of different species, where p-values are unavailable and one must solve the problem directly with effect sizes.

bioinformatics↗

bioRxiv2017

Complete Transcriptome Profiling Of Normal And Age-Related Macular Degeneration Eye Tissues Reveals Changes In Regulation Of Non-Coding RNA And Extreme Disregulation Of Anti-Sense Transcription

Strand specific RNA sequencing of retina and RPE-Choroid-Scleara (RCS) in age-related macular degeneration (AMD) and matched normal controls reveals striking impact on anti-sense transcription and changes in the regulation of non-coding RNA that has not previously been reported. Hundreds of genes, which do not express anti-sense transcripts in normal retina and RCS, demonstrate extreme anti-sense expression in AMD. And conversely anti-sense transcription is completely abrogated in many genes which express a high level of anti-sense transcripts in normal retina and RCS. Several pathways are very highly enriched in the upregulated anti-sense transcripts - in particular the EIF2 signaling pathway. These results call for a deeper investigation into anti-sense and noncoding RNA regulation in AMD and their potential as therapeutic targets.

genomics↗