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Luminescence is ubiquitous in biology research and medicine. Conceptually simple, the detection of luminescence nonetheless faces technical challenges because relevant signals can exhibit exceptionally low radiant power densities. Although low light detection is well-established in centralized laboratory settings, the cost, size, and environmental requirements of high-performance benchtop luminometers are not compatible with geographically-distributed global health studies or resource-constrained settings. Here we present the design and application of a ~$700 US handheld, battery-powered luminometer with performance on par with high-end benchtop instruments. By pairing robust and inexpensive Silicon Photomultiplier (SiPM) sensors with a low-profile shutter system, our design compensates for sensor non-idealities and thermal drift, achieving a limit of detection of 1.6E-19 moles of firefly luciferase, or approximately 1fW of radiant optical power. Using these devices, we performed split luciferase serology studies to monitor sars-cov-2 antibodies in a cohort in the United States, as well as a field study in Bangladesh.

BackgroundSARS-CoV-2 rapid antigen tests are an important public health tool.ObjectiveTo evaluate field performance of the BinaxNOW rapid antigen test (Abbott) compared with reverse transcriptase polymerase chain reaction (RT-PCR) for detecting infection with the Omicron variant of SARS-CoV-2.DesignCross-sectional surveillance study.SettingFree, walk-up, outdoor, urban community testing and vaccine site led by Unidos en Salud, serving a predominantly Latinx community highly impacted by COVID-19.ParticipantsPersons seeking COVID-19 testing in January 2022.MeasurementsSimultaneous BinaxNOW and RT-PCR from nasal, cheek, and throat swabs, including cycle threshold (Ct) measures; a lower Ct value is a surrogate for higher amounts of virus.ResultsAmong 731 persons tested with nasal swabs, there were 296 (40.5%) positive results on RT-PCR; 98.9% were the Omicron variant. BinaxNOW detected 95.2% (95% CI, 91% to 98%) of persons who tested positive on RT-PCR with a Ct value below 30, 82.1% (CI, 77% to 87%) of those who tested positive on RT-PCR with a Ct value below 35, and 65.2% (CI, 60% to 71%) of all who were positive on RT-PCR. Among 75 persons with simultaneous nasal and cheek swabs, BinaxNOW using a cheek swab failed to detect 91% (20 of 22) of specimens that were positive on BinaxNOW with a nasal swab. Among persons with simultaneous nasal and throat swabs who were positive on RT-PCR with a Ct value below 30, 42 of 49 (85.7%) were detected by nasal BinaxNOW, 23 of 49 (46.9%) by throat BinaxNOW, and 44 of 49 (89.8%) by either.LimitationParticipants were a cross-sectional sample from a community-based sentinel surveillance site, precluding study of viral or symptom dynamics.ConclusionBinaxNOW detected persons with high SARS-CoV-2 levels during the Omicron surge, enabling rapid responses to positive test results. Cheek or throat swabs should not replace nasal swabs. As currently recommended, high-risk persons with an initial negative BinaxNOW result should have repeated testing.Primary funding sourceUniversity of California, San Francisco.

In 731 persons seeking COVID-19 testing at a walk-up San Francisco community site in January 2022, simultaneous nasal rapid antigen testing (BinaxNOW™) and RT-PCR testing was performed. There were 296 (40.5%) positive tests by RT-PCR; 98.5% of a random sample (N=67) were the omicron variant. Sensitivity of a single antigen test was 95.2% (95% CI 92-98%); 82.1% (95% CI 77-87%) and 65.2% (95% CI 60-71%) for Ct threshold of < 30, < 35 and no threshold, respectively. We also compared BinaxNOW™ to RT-PCR from oral cheek swabs to nasal swabs (N=75); oral cheek specimen was significantly less sensitive than nasal swab. A single BinaxNOW™ oral cheek rapid antigen test failed to detect 91% (20 of 22) of specimens that were BinaxNOW™ positive from the standard nasal sampling. In a separate direct comparison of BinaxNOW™ between specimens collected from nasal or throat (tonsillar) swab (N=115), sensitivity was 97.7% for nasal and 48.8% for throat swabs that were PCR-positive on nasal swab with a Ct threshold < 30. Among persons with either a nasal or throat RT-PCR positive swab with Ct

Author(s): Crawford, Emily D; Acosta, Irene; Ahyong, Vida; Anderson, Erika C; Arevalo, Shaun; Asarnow, Daniel; Axelrod, Shannon; Ayscue, Patrick; Azimi, Camillia S; Azumaya, Caleigh M; Bachl, Stefanie; Bachmutsky, Iris; Bhaduri, Aparna; Brown, Jeremy Bancroft; Batson, Joshua; Behnert, Astrid; Boileau, Ryan M; Bollam, Saumya R; Bonny, Alain R; Booth, David; Borja, Michael Jerico B; Brown, David; Buie, Bryan; Burnett, Cassandra E; Byrnes, Lauren E; Cabral, Katelyn A; Cabrera, Joana P; Caldera, Saharai; Canales, Gabriela; Castaneda, Gloria R; Chan, Agnes Protacio; Chang, Christopher R; Charles-Orszag, Arthur; Cheung, Carly; Chio, Unseng; Chow, Eric D; Citron, Y Rose; Cohen, Allison; Cohn, Lillian B; Chiu, Charles; Cole, Mitchel A; Conrad, Daniel N; Constantino, Angela; Cote, Andrew; Crayton-Hall, Tre'Jon; Darmanis, Spyros; Detweiler, Angela M; Dial, Rebekah L; Dong, Shen; Duarte, Elias M; Dynerman, David; Egger, Rebecca; Fanton, Alison; Frumm, Stacey M; Fu, Becky Xu Hua; Garcia, Valentina E; Garcia, Julie; Gladkova, Christina; Goldman, Miriam; Gomez-Sjoberg, Rafael; Gordon, M Grace; Grove, James CR; Gupta, Shweta; Haddjeri-Hopkins, Alexis; Hadley, Pierce; Haliburton, John; Hao, Samantha L; Hartoularos, George; Herrera, Nadia; Hilberg, Melissa; Ho, Kit Ying E; Hoppe, Nicholas; Hosseinzadeh, Shayan; Howard, Conor J; Hussmann, Jeffrey A; Hwang, Elizabeth; Ingebrigtsen, Danielle; Jackson, Julia R; Jowhar, Ziad M; Kain, Danielle; Kim, James YS; Kistler, Amy; Kreutzfeld, Oriana; Kulsuptrakul, Jessie; Kung, Andrew F

Aging is characterized by a progressive loss of physiological integrity, leading to impaired function and increased vulnerability to death(1). Despite rapid advances over recent years, many of the molecular and cellular processes which underlie progressive loss of healthy physiology are poorly understood(2). To gain a better insight into these processes we have created a single cell transcriptomic atlas across the life span of Mus musculus which includes data from 23 tissues and organs. We discovered cell-specific changes occurring across multiple cell types and organs, as well as age related changes in the cellular composition of different organs. Using single-cell transcriptomic data we were able to assess cell type specific manifestations of different hallmarks of aging, such as senescence(3), genomic instability(4) and changes in the organism’s immune system(2). This Tabula Muris Senis provides a wealth of new molecular information about how the most significant hallmarks of aging are reflected in a broad range of tissues and cell types.

Sequence libraries that cover all k‐mers enable universal and unbiased measurements of binding to both oligonucleotides and peptides. For these measurements, it is desirable to search the largest possible library of k‐mers, as this increases the information content of any returned motif and the ability to predict function in vivo. However, while the number of k‐mers required grows exponentially in k, space on all experimental platforms is limited. The optimal solution makes use of a de Bruijn sequence, which covers all k‐mers in the most compact manner but still requires the explicit occurrence of all k‐mers within the sequence. Here, we introduce a novel advance to shrink k‐mer library sizes further by using joker characters, which represent all characters in the alphabet simultaneously. In this work, we consider the practical problem of generating a minimum‐length sequence that covers each k‐mer at least p times with the caveat that at most one or two joker characters occur in each k‐mer, thereby limiting the potential degeneracy that joker characters could introduce. We present the first algorithmic solution to this problem, JokerCAKE (Joker Covering All K‐mErs). By running our algorithm on a range of parameters and alphabets, we show that JokerCAKE produces sequences that are very close to the theoretical lower bound. Moreover, through comparison with data from hundreds of DNA‐protein binding experiments and direct comparison between experimental results obtained for both standard de Bruijn k‐mer sequences and joker de Bruijn k‐mer sequences, we establish that accurate binding scores can be inferred for high‐affinity k‐mers using JokerCAKE libraries

The Tabula Muris ConsortiumWe have created a compendium of single cell transcriptome data from the model organism Mus musculus comprising more than 100,000 cells from 20 organs and tissues. These data represent a new resource for cell biology, revealing gene expression in poorly characterized cell populations and allowing for direct and controlled comparison of gene expression in cell types shared between tissues, such as T-lymphocytes and endothelial cells from distinct anatomical locations. Two distinct technical approaches were used for most tissues: one approach, microfluidic droplet-based 3’-end counting, enabled the survey of thousands of cells at relatively low coverage, while the other, FACS-based full length transcript analysis, enabled characterization of cell types with high sensitivity and coverage. The cumulative data provide the foundation for an atlas of transcriptomic cell biology.

Microfluidic technologies have been used across diverse disciplines (e.g. high-throughput biological measurement, fluid physics, laboratory fluid manipulation) but widespread adoption has been limited due to the lack of openly disseminated resources that enable non-specialist labs to make and operate their own devices. Here, we report the open-source build of a pneumatic setup capable of operating both single and multilayer (Quake-style) microfluidic devices with programmable scripting automation. This setup can operate both simple and complex devices with 48 device valve control inputs and 18 sample inputs, with modular design for easy expansion, at a fraction of the cost of similar commercial solutions. We present a detailed step-by-step guide to building the pneumatic instrumentation, as well as instructions for custom device operation using our software, Geppetto, through an easy-to-use GUI for live on-chip valve actuation and a scripting system for experiment automation. We show robust valve actuation with near real-time software feedback and demonstrate use of the setup for high-throughput biochemical measurements on-chip. This open-source setup will enable specialists and novices alike to run microfluidic devices easily in their own laboratories. Specifications table

Sequence libraries that cover all k-mers enable universal, unbiased measurements of binding to both oligonucleotides and peptides. While the number of k-mers grows exponentially in k, space on all experimental platforms is limited. Here, we shrink k-mer library sizes by using joker characters, which represent all characters in the alphabet simultaneously. We present the JokerCAKE (joker covering all k-mers) algorithm for generating a short sequence such that each k-mer appears at least p times with at most one joker character per k-mer. By running our algorithm on a range of parameters and alphabets, we show that JokerCAKE produces near-optimal sequences. Moreover, through comparison with data from hundreds of DNA-protein binding experiments and with new experimental results for both standard and JokerCAKE libraries, we establish that accurate binding scores can be inferred for high-affinity k-mers using JokerCAKE libraries. JokerCAKE libraries allow researchers to search a significantly larger sequence space using the same number of experimental measurements and at the same cost. We present a new compact sequence design that covers all k-mers utilizing joker characters and develop an efficient algorithm to generate such designs. We show through simulations and experimental validation that these sequence designs are useful for identifying high-affinity binding sites at significantly reduced cost and space. Keywords: sequence libraries; microarray design; de Bruijn graph, National Institutes of Health (U.S.) (Grant R01GM081871)