Selected Grantee Publications
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- 14 results found
- Artificial Intelligence/Machine Learning
- Preservation
Establishing the Hybrid Rat Diversity Program: A Resource for Dissecting Complex Traits
Dwinell et al., Mammalian Genome. 2025.
https://pubmed.ncbi.nlm.nih.gov/39907792
Rat models have been extensively used for studying human complex disease mechanisms, behavioral phenotypes, and environmental factors and for discovering and developing drugs. Systems genetics approaches have been used to study the effects of both genetic variation and environmental factors. This approach recognizes the complexity of common disorders and uses intermediate phenotypes to find relationships between genetic variation and clinical traits. This article describes the Hybrid Rat Diversity Program (HDRP) at the Medical College of Wisconsin, which involves 96 inbred rat strains and aims to provide a renewable and reusable resource in terms of the HRDP panel of inbred rat strains, the genomic data derived from the HRDP strains, and banked resources available for additional studies. Supported by ORIP (R24OD024617) and NHLBI.
Pre-Challenge Gut Microbial Signature Predicts RhCMV/SIV Vaccine Efficacy in Rhesus Macaques
Brochu et al., Microbiology Spectrum. 2025.
https://journals.asm.org/doi/10.1128/spectrum.01285-24
Rhesus cytomegalovirus–based simian immunodeficiency virus (RhCMV/SIV) vaccines provide protection against SIV challenge in approximately 60% of vaccinated rhesus macaques. This study assessed the role that gut microbiota play in SIV vaccine efficacy by analyzing the microbiomes of rhesus macaques before and after immunization using novel compositional data analysis techniques and machine-learning strategies. Researchers identified a gut microbial signature that predicted vaccine protection outcomes and correlated with early biomarker changes in the blood (i.e., host immune response to vaccination). This study indicates that the gut microbiome might play a role in vaccine-induced immunity. Supported by ORIP (P51OD011092).
Systematic Multi-trait AAV Capsid Engineering for Efficient Gene Delivery
Eid et al., Nature Communications. 2024.
https://doi.org/10.1038/s41467-024-50555-y
Engineering novel functions into proteins while retaining desired traits is a key challenge for developers of viral vectors, antibodies, and inhibitors of medical and industrial value. In this study, investigators developed Fit4Function, a generalizable machine learning (ML) approach for systematically engineering multi-trait adeno-associated virus (AAV) capsids. Fit4Function was used to generate reproducible screening data from a capsid library that samples the entire manufacturable sequence space. The Fit4Function data were used to train accurate sequence-to-function models, which were combined to develop a library of capsid candidates. Compared to AAV9, top candidates from the Fit4Function capsid library exhibited comparable production yields; more efficient murine liver transduction; up to 1,000-fold greater human hepatocyte transduction; and increased enrichment in a screen for liver transduction in macaques. The Fit4Function strategy enables prediction of peptide-modified AAV capsid traits across species and is a critical step toward assembling an ML atlas that predicts AAV capsid performance across dozens of traits. Supported by ORIP (P51OD011107, U42OD027094), NIDDK, NIMH, and NINDS.
Establishment of a Practical Sperm Cryopreservation Pathway for the Axolotl (Ambystoma mexicanum): A Community-Level Approach to Germplasm Repository Development
Coxe et al., Animals (Basel). 2024.
https://pubmed.ncbi.nlm.nih.gov/38254376/
The axolotl (Ambystoma mexicanum) is an important biomedical research model for organ regeneration, but housing and maintaining live animals is expensive and risky as new transgenic lines are developed. The authors report an initial practical pathway for sperm cryopreservation to support germplasm repository development. They assembled a pathway through the investigation of axolotl sperm collection by stripping, refrigerated storage in various osmotic pressures, cryopreservation in various cryoprotectants, and in vitro fertilization using thawed sperm. This work is the first report of successful production of axolotl offspring with cryopreserved sperm and provides a general framework for pathway development to establish Ambystoma germplasm repositories for future research and applications. Supported by ORIP (R24OD010441, R24OD028443, P40OD019794).
Conduction-Dominated Cryomesh for Organism Vitrification
Guo et al., Advanced Science. 2024.
https://pubmed.ncbi.nlm.nih.gov/38018294/
Vitrification-based cryopreservation via cryomesh is a promising approach for maintaining biodiversity, health care, and sustainable food production via long-term preservation of biological systems. Here, researchers conducted a series of experiments aimed at optimizing the cooling and rewarming rates of cryomesh to increase the viability of various cryopreserved biosystems. They found that vitrification was significantly improved by increasing thermal conductivity, reducing mesh wire diameter and pore size, and minimizing the nitrogen vapor barrier of the conduction-dominated cryomesh. Cooling rates increased twofold to tenfold in a variety of biosystems. The conduction-dominated cryomesh improved the cryopreservation outcomes of coral larvae, Drosophila embryos, and zebrafish embryos by vitrification. These findings suggest that the conduction-dominated cryomesh can improve vitrification in such biosystems for biorepositories, agriculture and aquaculture, and research. Supported by ORIP (R24OD028444, R21OD028758, R24OD034063, R21OD028214), NIDDK, and NIGMS.
The Monarch Initiative in 2024: An Analytic Platform Integrating Phenotypes, Genes and Diseases Across Species
Putman et al., Nucleic Acids Research. 2024.
https://pubmed.ncbi.nlm.nih.gov/38000386/
The Monarch Initiative aims to bridge the gap between the genetic variations, environmental determinants, and phenotypic outcomes critical for translational research. The Monarch app provides researchers access to curated data sets with information on genes, phenotypes, and diseases across species and advanced analysis tools for such diverse applications as variant prioritization, deep phenotyping, and patient profile matching. Researchers describe upgrades to the app, including scalable cloud-based infrastructure, simplified data ingestion and knowledge graph integration systems, enhanced data mapping and integration standards, and a new user interface with novel search and graph navigation features. A customized plugin for OpenAI’s ChatGPT allows the use of large language models to interrogate knowledge in the Monarch graph and increase the reliability of the responses of Monarch’s analytic tools. These upgrades will enhance clinical diagnosis and the understanding of disease mechanisms. Supported by ORIP (R24OD011883), NLM, and NHGRI.
Simian Immunodeficiency Virus and Storage Buffer: Field-Friendly Preservation Methods for RNA Viral Detection in Primate Feces
Wilde et al., mSphere. 2023.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10732032/
Simian immunodeficiency virus (SIV) infects more than 40 nonhuman primate (NHP) species in sub-Saharan Africa, but testing in wild NHP populations can be challenging. Researchers compared methods for SIV RNA preservation and recovery from NHP fecal samples stored in four different buffers. The goal of this work was to identify a robust “field-friendly” method (i.e., without freezing or refrigeration) for this effort, and the samples were collected from a mantled guereza colobus housed at the Columbus Zoo and Aquarium. The authors reported that the DNA/RNA shield is an optimal buffer for preserving SIV RNA in fecal samples in the field. Their findings will inform future fieldwork and facilitate improved approaches for studies of SIV and other RNA viruses. Supported by ORIP (P51OD011132) and NIAID.
Zebrafish as a High Throughput Model for Organ Preservation and Transplantation Research
Da Silveira Cavalcante et al., The FASEB Journal. 2023.
https://faseb.onlinelibrary.wiley.com/doi/10.1096/fj.202300076R
Organ transplantation increases the quality of life and life expectancy of patients with chronic end-stage diseases, but the preservation of organs for transplantation remains a significant barrier. In the current study, researchers demonstrate the value of zebrafish as a high-throughput model organism in the fields of solid-organ preservation and transplantation, with a focus on heart preservation via partial freezing. Their techniques have the potential to advance research in the fields of cryobiology and solid-organ transplantation. Supported by ORIP (R24OD031955) and NHLBI.
Orthotopic Transplantation of the Full-Length Porcine Intestine After Normothermic Machine Perfusion
Abraham et al., Transplantation Direct. 2022.
https://www.doi.org/10.1097/TXD.0000000000001390
Successful intestinal transplantation currently is hindered by graft injury that occurs during procurement and storage, which contributes to postoperative sepsis and allograft rejection. Improved graft preservation could expand transplantable graft numbers and enhance post-transplant outcomes. Superior transplant outcomes recently have been demonstrated in clinical trials using machine perfusion to preserve the liver. The investigators report the development and optimization of machine perfusion preservation of small intestine and successful transplantation of intestinal allografts in a porcine model. Supported by ORIP (K01OD019911), NIAID, and NIDDK.
Rapid Joule Heating Improves Vitrification Based Cryopreservation
Zhan et al., Nature Communications. 2022.
https://www.doi.org/10.1038/s41467-022-33546-9
Cryopreservation by vitrification is an effective approach for long-term preservation of biosystems, but effective vitrification often requires high concentrations of cryoprotective agent (CPA), which can be toxic. The investigators described a joule heating–based platform technology for rapid rewarming of biosystems, which allows the use of low concentrations of CPA. They demonstrated the success of this platform in cryopreservation of three model systems: adherent cells, Drosophila melanogaster embryos, and rat kidney slices with low CPA concentrations. This work provides a general solution to cryopreserve a broad spectrum of cells, tissues, organs, and organisms. Supported by ORIP (R21OD028758), NIDDK, NHLBI, and NIGMS.