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1. Impedance-based biosensor for rapid detection and identification of Salmonella in turkey products

   https://doi.org/10.1117/12.3050876  

   Almalaysha, Mohammed; Allen, Keara; Muhsin, Sura Abd-Alzahra; Bashir_Taas, Kamran; Carlson, Anna; Morey, Amit; Trout, Kate E; Zhang, Shuping; Almasri, Mahmoud F (March 2025, SPIE)

   Rapp, Bastian E; Dalton, Colin (Ed.)

   This study presents the development of a highly sensitive microfluidic-based impedance biosensor designed for rapid detection and identification of Salmonella Infantis in raw turkey samples, with a limit of detection (LOD) as low as 1 CFU/ml in 70 minutes detection time. The biosensor is equipped with novel focusing and trapping regions, significantly enhancing its sensitivity by concentrating and trapping Salmonella cells in the detection region. Salmonella cells labeled with fluorescent dyes were used to validate the functionality of the focusing and trapping mechanism, confirming the biosensor's ability to concentrate and trap Salmonella cells. 

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2. Intracellular Salmonella delivery of an exogenous immunization antigen refocuses CD8 T cells against cancer cells, eliminates pancreatic tumors and forms antitumor immunity

   https://doi.org/10.3389/fimmu.2023.1228532  

   Raman, Vishnu; Howell, Lars M.; Bloom, Shoshana M.; Hall, Christopher L.; Wetherby, Victoria E.; Minter, Lisa M.; Kulkarni, Ashish A.; Forbes, Neil S. (October 2023, Frontiers in Immunology)

   IntroductionImmunotherapies have shown great promise, but are not effective for all tumors types and are effective in less than 3% of patients with pancreatic ductal adenocarcinomas (PDAC). To make an immune treatment that is effective for more cancer patients and those with PDAC specifically, we genetically engineered Salmonella to deliver exogenous antigens directly into the cytoplasm of tumor cells. We hypothesized that intracellular delivery of an exogenous immunization antigen would activate antigen-specific CD8 T cells and reduce tumors in immunized mice. MethodsTo test this hypothesis, we administered intracellular delivering (ID) Salmonella that deliver ovalbumin as a model antigen into tumor-bearing, ovalbumin-vaccinated mice. ID Salmonella delivers antigens by autonomously lysing in cells after the induction of cell invasion. ResultsWe showed that the delivered ovalbumin disperses throughout the cytoplasm of cells in culture and in tumors. This delivery into the cytoplasm is essential for antigen cross-presentation. We showed that co-culture of ovalbumin-recipient cancer cells with ovalbumin-specific CD8 T cells triggered a cytotoxic T cell response. After the adoptive transfer of OT-I CD8 T cells, intracellular delivery of ovalbumin reduced tumor growth and eliminated tumors. This effect was dependent on the presence of the ovalbumin-specific T cells. Following vaccination with the exogenous antigen in mice, intracellular delivery of the antigen cleared 43% of established KPC pancreatic tumors, increased survival, and prevented tumor re-implantation. DiscussionThis response in the immunosuppressive KPC model demonstrates the potential to treat tumors that do not respond to checkpoint inhibitors, and the response to re-challenge indicates that new immunity was established against intrinsic tumor antigens. In the clinic, ID Salmonella could be used to deliver a protein antigen from a childhood immunization to refocus pre-existing T cell immunity against tumors. As an off-the-shelf immunotherapy, this bacterial system has the potential to be effective in a broad range of cancer patients. 

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3. Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire

   Hossein Saghaian, Pavel Skums (October 2023, Lecture notes in bioinformatics)

   Phage display technique has a multitude of applications such as epitope mapping, organ targeting, therapeutic antibody engineering and vaccine design. One area of particular importance is the detection of cancers in early stages, where the discovery of binding motifs and epitopes is critical. While several techniques exist to characterize phages, Next Generation Sequencing (NGS) stands out for its ability to provide detailed insights into antibody binding sites on antigens. However, when dealing with NGS data, identifying regulatory motifs poses significant challenges. Existing methods often lack scalability for large datasets, rely on prior knowledge about the number of motifs, and exhibit low accuracy. In this paper, we present a novel approach for identifying regulatory motifs in NGS data. Our method leverages results from graph theory to overcome the limitations of existing techniques. 

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4. Hierarchical sequence-affinity landscapes shape the evolution of breadth in an anti-influenza receptor binding site antibody

   https://doi.org/10.7554/eLife.83628  

   Phillips, Angela M; Maurer, Daniel P; Brooks, Caelan; Dupic, Thomas; Schmidt, Aaron G; Desai, Michael M (January 2023, eLife)

   Broadly neutralizing antibodies (bnAbs) that neutralize diverse variants of a particular virus are of considerable therapeutic interest. Recent advances have enabled us to isolate and engineer these antibodies as therapeutics, but eliciting them through vaccination remains challenging, in part due to our limited understanding of how antibodies evolve breadth. Here, we analyze the landscape by which an anti-influenza receptor binding site (RBS) bnAb, CH65, evolved broad affinity to diverse H1 influenza strains. We do this by generating an antibody library of all possible evolutionary intermediates between the unmutated common ancestor (UCA) and the affinity-matured CH65 antibody and measure the affinity of each intermediate to three distinct H1 antigens. We find that affinity to each antigen requires a specific set of mutations – distributed across the variable light and heavy chains – that interact non-additively (i.e., epistatically). These sets of mutations form a hierarchical pattern across the antigens, with increasingly divergent antigens requiring additional epistatic mutations beyond those required to bind less divergent antigens. We investigate the underlying biochemical and structural basis for these hierarchical sets of epistatic mutations and find that epistasis between heavy chain mutations and a mutation in the light chain at the V H -V L interface is essential for binding a divergent H1. Collectively, this is the first work to comprehensively characterize epistasis between heavy and light chain mutations and shows that such interactions are both strong and widespread. Together with our previous study analyzing a different class of anti-influenza antibodies, our results implicate epistasis as a general feature of antibody sequence-affinity landscapes that can potentiate and constrain the evolution of breadth. 

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5. Nanoparticle-Supported, Rapid, and Electronic Detection of SARS-CoV-2 Antibodies and Antigens at the Subfemtomolar Level

   https://doi.org/10.1021/acsnano.5c12083  

   Choi, Yeji; Mirjalili, Seyedsina; Ikbal, MD Ashif; McClure, Sean; Mohammadi, Maziyar Kalateh; Clemens, Scott; Solano, Jose; Heggland, John; Zhang, Tingting; Zuo, Jiawei; et al (August 2025, ACS Nano)

   Major challenges remain to precisely detect low-abundance proteins rapidly and cost-effectively from diverse biofluids. Here we present a gold nanoparticle (AuNP)-supported, rapid electronic detection (NasRED) platform with sub-femtomolar sensitivity and high specificity. Surface-functionalized AuNPs act as multivalent detectors to recognize target antigens and antibodies through high-affinity binding, subsequently forming aggregates precipitated in a microcentrifuge tube and producing a solution color change. The residual floating AuNPs’ optical extinction is digitized using customized circuitry incorporating inexpensive optoelectronics and feedback mechanisms for stabilized readout. NasRED introduces active fluidic forces through engineered centrifugation and vortex agitation, effectively promoting low-concentration protein detection and accelerating signal transduction. Using SARS-CoV-2 as a demonstration, NasRED enables detection of both antibodies and antigens from a small sample volume (6 µL), distinguishes the viral antigens from those of human coronaviruses, and delivers test results in <15 min. The limits of detection (LoDs) for antibody detection are approximately 49 aM (7 fg/mL) in phosphate-buffered saline (PBS), or >3,000 times more sensitive than Enzyme-Linked Immunosorbent Assay (ELISA), ~76 aM (11 fg/mL) in human pooled serum and in the femtomolar range in diluted whole blood. For nucleocapsid protein detection, NasRED LoDs are ~190 aM (10 fg/mL) in human saliva and ~2 fM (100 fg/mL) in nasal fluid. Unlike centralized platforms, NasRED is a one-pot, in-solution assay without the needs for washing, labeling, expensive instrumentation or highly trained operators. With low reagent costs and a compact system footprint, this modular digital platform is well-suited for accurate, near-patient diagnosis and screening of a wide range of infectious and chronic diseases. 

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