An open-source FACS automation system for high-throughput cell biology

Recent advances in gene editing are enabling the engineering of cells with an unprecedented level of scale. To capitalize on this opportunity, new methods are needed to accelerate the different steps required to manufacture and handle engineered cells. Here, we describe the development of an integrated software and hardware platform to automate Fluorescence-Activated Cell Sorting (FACS), a central step for the selection of cells displaying desired molecular attributes. Sorting large numbers of samples is laborious, and, to date, no automated system exists to sequentially manage FACS samples, likely owing to the need to tailor sorting conditions ("gating") to each individual sample. Our platform is built around a commercial instrument and integrates the handling and transfer of samples to and from the instrument, autonomous control of the instrument's software, and the algorithmic generation of sorting gates, resulting in walkaway functionality. Automation eliminates operator errors, standardizes gating conditions by eliminating operator-to-operator variations, and reduces hands-on labor by 93%. Moreover, our strategy for automating the operation of a commercial instrument control software in the absence of an Application Program Interface (API) exemplifies a universal solution for other instruments that lack an API. Our software and hardware designs are fully open-source and include step-by-step build documentation to contribute to a growing open ecosystem of tools for high-throughput cell biology.

Spinal gunshot wounds: A retrospective, multicenter, cohort study

INTRODUCTION AND OBJECTIVE

To describe the demographic and clinical characteristics and treatment of patients with spinal gunshot wounds across Latin America.

MATERIAL AND METHODS

Retrospective, multicenter cohort study of patients treated for gunshot wounds to the spine spanning 12 institutions across Latin America between January 2015 and January 2022. Demographic and clinical data were recorded, including the time of injury, initial assessment, characteristics of the vertebral gunshot injury, and treatment.

RESULTS

Data on 423 patients with spinal gunshot injuries were extracted from institutions in Mexico (82%), Argentina, Brazil, Colombia, and Venezuela. Patients were predominantly male civilians in low-risk-of-violence professions, and of lower/middle social status, and a sizeable majority of gunshots were from low-energy firearms. Vertebral injuries mainly affected the thoracic and lumbar spine. Neurological injury was documented in 320 (76%) patients, with spinal cord injuries in 269 (63%). Treatment was largely conservative, with just 90 (21%) patients treated surgically, principally using posterior open midline approach to the spine (79; 87%). Injury features distinguishing surgical from non-surgical cases were neurological compromise (P = 0.004), canal compromise (P < 0.001), dirty wounds (P < 0.001), bullet or bone fragment remains in the spinal canal (P < 0.001) and injury pattern (P < 0.001). After a multivariate analysis through a binary logistic regression model, the aforementioned variables remained statistically significant except neurological compromise.

CONCLUSIONS

In this multicenter study of spinal gunshot victims, most were treated non-surgically, despite neurological injury in 76% and spinal injury in 63% of patients.

Spinal gunshot wounds: A retrospective, multicenter, cohort study

INTRODUCTION AND OBJECTIVE

To describe the demographic and clinical characteristics and treatment of patients with spinal gunshot wounds across Latin America.

MATERIAL AND METHODS

Retrospective, multicenter cohort study of patients treated for gunshot wounds to the spine spanning 12 institutions across Latin America between January 2015 and January 2022. Demographic and clinical data were recorded, including the time of injury, initial assessment, characteristics of the vertebral gunshot injury, and treatment.

RESULTS

Data on 423 patients with spinal gunshot injuries were extracted from institutions in Mexico (82%), Argentina, Brazil, Colombia, and Venezuela. Patients were predominantly male civilians in low-risk-of-violence professions, and of lower/middle social status, and a sizeable majority of gunshots were from low-energy firearms. Vertebral injuries mainly affected the thoracic and lumbar spine. Neurological injury was documented in n=320 (76%) patients, with spinal cord injuries in 269 (63%). Treatment was largely conservative, with just 90 (21%) patients treated surgically, principally using posterior open midline approach to the spine (n=79; 87%). Injury features distinguishing surgical from non-surgical cases were neurological compromise (p=0.004), canal compromise (p<0.001), dirty wounds (p<0.001), bullet or bone fragment remains in the spinal canal (p<0.001) and injury pattern (p<0.001). After a multivariate analysis through a binary logistic regression model, the aforementioned variables remained statistically significant except neurological compromise.

CONCLUSIONS

In this multicenter study of spinal gunshot victims, most were treated non-surgically, despite neurological injury in 76% and spinal injury in 63% of patients.

OpenCell: Endogenous tagging for the cartography of human cellular organization

Elucidating the wiring diagram of the human cell is a central goal of the postgenomic era. We combined genome engineering, confocal live-cell imaging, mass spectrometry, and data science to systematically map the localization and interactions of human proteins. Our approach provides a data-driven description of the molecular and spatial networks that organize the proteome. Unsupervised clustering of these networks delineates functional communities that facilitate biological discovery. We found that remarkably precise functional information can be derived from protein localization patterns, which often contain enough information to identify molecular interactions, and that RNA binding proteins form a specific subgroup defined by unique interaction and localization properties. Paired with a fully interactive website (opencell.czbiohub.org), our work constitutes a resource for the quantitative cartography of human cellular organization.