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Standardized protocols for absolute quantification of potato virus Y (PVY) from potato tissue is critical for host-virus dynamic studies. Here, we developed a standardized protocol using a cloned viral sequence as standards to detect and quantify PVY. Starting with total RNA, concentrated via column-based kit, this protocol is able to detect approximately 50 viral copies/reaction from multiple PVY strains. Validation of this protocol confirmed linearity across 8 orders of magnitude with high repeatability, reproducibility and statistical robustness across three independent runs. This protocol offers reliable PVY quantification to manage potato crop health and enables comparative studies with other viral systems. 

Undergraduate students often have limited access to industry-focused research opportunities. To address this, faculty and students from 10 primarily undergraduate institutions collaborated with Sampling Human, a biotechnology company, to test a biocytometry workflow for single-cell analysis. The project engaged 15 students with varying levels of research experience and demonstrated that prior research expertise was not essential for successfully using the workflow. Participants followed standardized protocols and generated reproducible data comparable to that of PhD-level scientists. Despite some technical challenges, 91.7% of participants completed the study, showcasing the approachability and reliability of the workflow. This collaboration highlights the potential of industry partnerships to expand research opportunities, enhance academic visibility, and foster academic-corporate co-publications. 

The East Palestine, Ohio train derailment released toxic vinyl chloride (VC) and butyl acrylate (BA), which entered the watershed. Streambed sediment, surface water, and private well water samples were collected 128 and 276 days postaccident to assess the natural attenuation potential of VC and BA by quantifying biodegradation biomarker genes and conducting microcosm treatability studies. qPCR detected the aerobic VC degradation biomarkers etnC in ∼40% and etnE in ∼27% of sediments collected in both sampling campaigns in abundances reaching 10e5 gene copies g−1. The 16S rRNA genes of organohalide-respiring Dehalococcoides and Dehalogenimonas were, respectively, detected in 50 and 64% of sediment samples collected 128 days postaccident and in 63 and 88% of sediment samples collected 276 days postaccident, in abundances reaching 10e7 cells g−1. Elevated detection frequencies of VC degradation biomarker genes were measured immediately downstream of the accident site (i.e., Sulphur Run). Aerobic VC degradation occurred in all sediment microcosms and coincided with increases of etnC/etnE genes and Mycobacterium, a genus comprising aerobic VC degraders. The conversion of VC to ethene and an increased abundance of VC reductive dechlorination biomarker genes were observed in microcosms established with sediments collected from Sulphur Run. All anoxic microcosms rapidly degraded BA to innocuous products with intermediate formation of n- butanol and acrylate. The results indicate that microbiomes in the East Palestine watershed have natural attenuation capacity for VC and BA. Recommendations are made to improve first-response actions in future contaminant release accidents of this magnitude. 

Biomedicine today is experiencing a shift towards decentralized data collection, which promises enhanced reproducibility and collaboration across diverse laboratory environments. This inter-laboratory study evaluates the performance of biocytometry, a method utilizing engineered bioparticles for enumerating cells based on their surface antigen patterns. In centralized and aggregated inter-lab studies, biocytometry demonstrated significant statistical power in discriminating numbers of target cells at varying concentrations as low as 1 cell per 100,000 background cells. User skill levels varied from expert to beginner capturing a range of proficiencies. Measurement was performed in a decentralized environment without any instrument cross-calibration or advanced user training outside of a basic instruction manual. The results affirm biocytometry to be a viable solution for immunophenotyping applications demanding sensitivity as well as scalability and reproducibility and paves the way for decentralized analysis of rare cells in heterogeneous samples. 

Abstract Biomedicine today is experiencing a shift towards decentralized data collection, which promises enhanced reproducibility and collaboration across diverse laboratory environments. This inter-laboratory study evaluates the performance of biocytometry, a method utilizing engineered bioparticles for enumerating cells based on their surface antigen patterns. In a decentralized framework, spanning 78 assays conducted by 30 users across 12 distinct laboratories, biocytometry consistently demonstrated significant statistical power in discriminating numbers of target cells at varying concentrations as low as 1 cell per 100,000 background cells. User skill levels varied from expert to beginner capturing a range of proficiencies. Measurement was performed in a decentralized environment without any instrument cross-calibration or advanced user training outside of a basic instruction manual. The results affirm biocytometry to be a viable solution for immunophenotyping applications demanding sensitivity as well as scalability and reproducibility and paves the way for decentralized analysis of rare cells in heterogeneous samples. 

In-person undergraduate research experiences (UREs) promote students’ integration into careers in life science research. In 2020, the COVID-19 pandemic prompted institutions hosting summer URE programs to offer them remotely, raising questions about whether undergraduates who participate in remote research can experience scientific integration and whether they might perceive doing research less favorably (i.e., not beneficial or too costly). To address these questions, we examined indicators of scientific integration and perceptions of the benefits and costs of doing research among students who participated in remote life science URE programs in Summer 2020. We found that students experienced gains in scientific self-efficacy pre- to post-URE, similar to results reported for in-person UREs. We also found that students experienced gains in scientific identity, graduate and career intentions, and perceptions of the benefits of doing research only if they started their remote UREs at lower levels on these variables. Collectively, students did not change in their perceptions of the costs of doing research despite the challenges of working remotely. Yet students who started with low cost perceptions increased in these perceptions. These findings indicate that remote UREs can support students’ self-efficacy development, but may otherwise be limited in their potential to promote scientific integration. 

The COVID-19 pandemic shut down undergraduate research programs across the United States. A group of 23 colleges, universities, and research institutes hosted remote undergraduate research programs in the life sciences during Summer 2020. Given the unprecedented offering of remote programs, we carried out a study to describe and evaluate them. Using structured templates, we documented how programs were designed and implemented, including who participated. Through focus groups and surveys, we identified programmatic strengths and shortcomings as well as recommendations for improvements from students’ perspectives. Strengths included the quality of mentorship, opportunities for learning and professional development, and a feeling of connection with a larger community. Weaknesses included limited cohort building, challenges with insufficient structure, and issues with technology. Although all programs had one or more activities related to diversity, equity, inclusion, and justice, these topics were largely absent from student reports even though programs coincided with a peak in national consciousness about racial inequities and structural racism. Our results provide evidence for designing remote Research Experiences for Undergraduates (REUs) that are experienced favorably by students. Our results also indicate that remote REUs are sufficiently positive to further investigate their affordances and constraints, including the potential to scale up offerings, with minimal concern about disenfranchising students.