Collaboration between clinical and academic laboratories for sequencing SARS-CoV-2 genomes

Genomic sequencing of SARS-CoV-2 continues to provide valuable insight into the ever-changing variant makeup of the COVID-19 pandemic. More than three million SARS-COV-2 genomes have been deposited in GISAID, but contributions from the United States, particularly through 2020, lagged behind the global effort. The primary goal of clinical microbiology laboratories is seldom rooted in epidemiologic or public health testing and many labs do not contain in-house sequencing technology. However, we recognized the need for clinical microbiologists to lend expertise, share specimen resources, and partner with academic laboratories and sequencing cores to assist in SARS-COV-2 epidemiologic sequencing efforts. Here we describe two clinical and academic laboratory collaborations for SARS-COV-2 genomic sequencing. We highlight roles of the clinical microbiologists and the academic labs, outline best practices, describe two divergent strategies in accomplishing a similar goal, and discuss the challenges with implementing and maintaining such programs.

Molecularly Imprinted Polymers (MIPs) in Sensors for Environmental and Biomedical Applications: A Review

Molecular imprinted polymers are custom made materials with specific recognition sites for a target molecule. Their specificity and the variety of materials and physical shapes in which they can be fabricated make them ideal components for sensing platforms. Despite their excellent properties, MIP-based sensors have rarely left the academic laboratory environment. This work presents a comprehensive review of recent reports in the environmental and biomedical fields, with a focus on electrochemical and optical signaling mechanisms. The discussion aims to identify knowledge gaps that hinder the translation of MIP-based technology from research laboratories to commercialization.

Feedback from the Science Café at the 7th European Bioanalysis Forum Young Scientist Symposium

The 7th Young Scientist Symposium, a meeting again organized as a hybrid online event by young scientists for young scientists under the umbrella of the European Bioanalysis Forum and in collaboration with the Universities of Bologna and Ghent, included a variety of interesting presentations on cutting-edge bioanalytical science and processes. On the morning of day 2, the meeting hosted their traditional Science Café around the theme: ‘How has COVID-19 changed our future?’ in which the Young Scientist Symposium organizing committee engaged with the delegates on how the COVID-19 pandemic has impacted the careers of young scientists working in a bioanalytical (industry or academic) laboratory, that is, things they lost, for good or for bad – things they gained, wanted or unwanted, things they learned about themselves and their industry. This manuscript provides feedback from those discussions.

The Code Breaker: Jennifer Doudna, gene editing, and the future of the human race

In this book review and accompanying commentary and Addendum, we focus on 5 principal topics/major themes that are of interest for our readership, with a focus on framing the translation of transformative technology into a platform business model in biopharma. We focus on: 1) the behavioral and personal side of the story of the academic scientist, in this case the principal “code breaker” – Jennifer Doudna; 2) the innovation/technology transfer models, including team building appropriate for successfully translating technology from the academic laboratory into the private sector; 3) the IP considerations needed for broad commercialization and dissemination of pivotal, platform inventions in biopharma; and, 4) framing the issues surrounding the ethical discussion related to use in patients associated with a transformative, gene based technology like CRISPR. We also include an Addendum that covers, 5) Some pertinent, concluding comments on the importance of high–performance, diverse teams for founding, building, and growing successful biotechnology companies.

The cellular response to drug perturbation is limited: comparison of large-scale chemogenomic fitness signatures

BackgroundChemogenomic profiling is a powerful approach towards understanding the genome-wide cellular response to small molecules. Developed in Saccharomyces cerevisiae, chemogenomic screens provide direct, unbiased identification of drug target candidates as well as genes required for drug resistance. While many laboratories have performed chemogenomic fitness assays, they have not been assessed for reproducibility and accuracy. Here we analyze the two largest independent yeast chemogenomic datasets comprising over 35 million gene-drug interactions and more than 6000 unique chemogenomic profiles; the first from our own academic laboratory and the second from the Novartis Institute of Biomedical Research (NIBR).ResultsCombining the datasets revealed robust genetic interaction response signatures that point to common mechanism of action, despite the substantial differences in experimental and analytical pipelines. We previously reported that the cellular response to small molecules is limited and can be described by a network of 45 chemogenomic signatures. In the present study, we show that the majority of these signatures (66%) are also found in the companion dataset, providing further support for their biological relevance as systems-level, small molecule response systems. ConclusionsOur results demonstrate the robustness of chemogenomic fitness profiling in yeast, while offering guidelines for performing other high-dimensional comparisons including parallel CRISPR screens in mammalian cells.

Novel 3D printable powered air purifying respirator for emergency use during PPE shortage of the COVID-19 pandemic: a study protocol and device safety analysis

ObjectivesTo design a low-cost 3D printable powered air-purifying respirator (PAPR) that meets National Institute for Occupational Safety and Health (NIOSH) standard for flow rate and Occupational Safety and Health Administration (OSHA) standard for particle filtration for loose-fitting PAPRs and that can be made with a 3D printer and widely available materials.DesignDetailed description of components, assembly instructions and testing of a novel PAPR design in an academic laboratory following respective protocols. The assembled PAPR must meet NIOSH standards of flow rate, 170 L/min; OSHA fit factor for particle filtration, ≥250 and maintain positive pressure during regular and deep breathing.Main outcome measuresThe PAPR design was run through a series of tests: air flow (L/min), particle filtration (quantitative and qualitative) and positive pressure measured inside the helmet (mm Hg).ResultsFlow rate was 443.32 L/min (NIOSH standard: minimum 170 L/min) and overall fit factor for particle filtration was 1362 (OSHA pass level: ≥500), n=1. The device passed qualitative particle filtration, n=2, and measured peak pressure of 6mm Hg (>0 mm Hg indicates positive pressure) in the helmet, n=1.ConclusionsThe Hygieia PAPR is a low-cost, easily accessible, just-in-time 3D printable PAPR design that meets minimum NIOSH and OSHA standards for flow-rate and particle filtration for loose-fitting PAPR devices to be made and used when industry-made designs are unavailable.

Validation of Roche immunoassay for severe acute respiratory coronavirus 2 in South Africa

Background: Serology testing is an important ancillary diagnostic to the reverse transcriptase polymerase chain reaction (RT-PCR) test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to evaluate the performance of the Roche Elecsys™ chemiluminescent immunoassay (Rotkreuz, Switzerland), that detects antibodies against the SARS-CoV-2 nucleocapsid antigen, at an academic laboratory in South Africa.Methods: Serum samples were collected from 312 donors with confirmed positive SARS-CoV-2 RT-PCR tests, with approval from a large university’s human research ethics committee. Negative controls included samples stored prior to December 2019 and from patients who tested negative for SARS-CoV-2 on RT-PCR and were confirmed negative using multiple serology methods (n = 124). Samples were stored at –80 °C and analysed on a Roche cobas™ 602 autoanalyser.Results: Compared with RT-PCR, our evaluation revealed a specificity of 100% and overall sensitivity of 65.1%. The sensitivity in individuals 14 days’ post-diagnosis was 72.6%, with the highest sensitivity 31–50 days’ post-diagnosis at 88.6%. Results were also compared with in-house serology tests that showed high agreement in majority of categories.Conclusions: The sensitivity at all-time points post-diagnosis was lower than reported in other studies, but sensitivity in appropriate cohorts approached 90% with a high specificity. The lower sensitivity at earlier time points or in individuals without symptomatology may indicate failure to produce antibodies, which was further supported by the comparison against in-house serology tests.

History of Universities: Volume XXXIV/1

This book’s chapters contain a mix of analysis and discussion looking in depth at the history of higher education. This text presents a global history of research education in the nineteenth and twentieth centuries. Chapters cover topics such as how disciplines are formed and research training, the rise of academic laboratory science, research mathematicians circa 1900 and research training in the humanities in British universities from 1870 to 1939. Other subjects include training language scholars between 1920 and 1940, training researchers in Ibero-Amerca, inventing laboratory science in Meiji Japan, and Chinese physics researchers in the period 1927-1941. The book includes an introduction and conclusion by Kevin Chang and Alan Rocke.

The Rise of Academic Laboratory Science

This chapter seeks to understand the context and sequelae of Justus Liebig’s model for university research and teaching. This model was arguably the most important single element in the international rise of graduate education and research, not just in chemistry, but more broadly, over the course of the 19th century, in all academic fields. This chapter avoids hagiography by employing an eclectic approach that places emphasis on contingencies of time, place, and discipline, and briefly examines the results of the story not just in Germany, but also in France, Britain, and the United States.

The current state of safety within the wet laboratories of a Canadian academic institution

Working in an academic laboratory (lab) often involves handling hazardous substances (Shariff & Norazahar, 2012). These substances are dangerous due to their toxic, flammable, explosive, carcinogenic, pathogenic or radioactive properties (Furr, 2000). Therefore, it is crucial that those working in these environments do so safely. Recently, many researchers and students from various universities in the U.S. and globally have suffered severe injuries and fatalities from lab accidents. For example, in 2008 a lab fire at the University of California Los Angeles led to the death of a student(Van Noorden, 2011). Following this and other similar accidents that transpired afterwards, an international study was conducted to understand the state of safety within the wet labs of today’s universities(Van Noorden, 2013a). The findings revealed numerous safety gaps and an overall lack of a strong and positive safety culture within the labs (Benderly, 2013;and Schröder, Huang, Ellis, Gibson, & Wayne, 2016). Since the majority of the accidents and study reports were predominantly from the U.S., it is unknown if the same safety gaps and risks also exist in the wet labs of Canadian universities. Therefore, this research study examined the state of safety within the wet laboratories of a medium-sized Canadian university. This was achieved by: 1) conducting an inventory of the labs’ hazardous substances to identify their labeling and storage conditions, 2) inspecting the labs to identify potential hazards or risky conditions, and 3) surveying lab personnel to understand how safety is perceived and practiced. The results show several safety deficiencies and a negative perception on certain safety elements among the lab personnel. As in universities in the U.S. there is an overall need to enhance thecurrent culture of safety at this Canadian university.