Retinal ganglion cell degeneration is topological but not cell type specific in DBA/2J mice

Using a variety of double and triple labeling techniques, we have reevaluated the death of retinal neurons in a mouse model of hereditary glaucoma. Cell-specific markers and total neuron counts revealed no cell loss in any retinal neurons other than the ganglion cells. Within the limits of our ability to define cell types, no group of ganglion cells was especially vulnerable or resistant to degeneration. Retrograde labeling and neurofilament staining showed that axonal atrophy, dendritic remodeling, and somal shrinkage (at least of the largest cell types) precedes ganglion cell death in this glaucoma model. Regions of cell death or survival radiated from the optic nerve head in fan-shaped sectors. Collectively, the data suggest axon damage at the optic nerve head as an early lesion, and damage to axon bundles would cause this pattern of degeneration. However, the architecture of the mouse eye seems to preclude a commonly postulated source of mechanical damage within the nerve head

Protocol for the perioperative outcome risk assessment with computer learning enhancement (Periop ORACLE) randomized study [version 2; peer review: 2 approved]

Background: More than four million people die each year in the month following surgery, and many more experience complications such as acute kidney injury. Some of these outcomes may be prevented through early identification of at-risk patients and through intraoperative risk mitigation. Telemedicine has revolutionized the way at-risk patients are identified in critical care, but intraoperative telemedicine services are not widely used in anesthesiology. Clinicians in telemedicine settings may assist with risk stratification and brainstorm risk mitigation strategies while clinicians in the operating room are busy performing other patient care tasks. Machine learning tools may help clinicians in telemedicine settings leverage the abundant electronic health data available in the perioperative period. The primary hypothesis for this study is that anesthesiology clinicians can predict postoperative complications more accurately with machine learning assistance than without machine learning assistance. Methods: This investigation is a sub-study nested within the TECTONICS randomized clinical trial (NCT03923699). As part of TECTONICS, study team members who are anesthesiology clinicians working in a telemedicine setting are currently reviewing ongoing surgical cases and documenting how likely they feel the patient is to experience 30-day in-hospital death or acute kidney injury. For patients who are included in this sub-study, these case reviews will be randomized to be performed with access to a display showing machine learning predictions for the postoperative complications or without access to the display. The accuracy of the predictions will be compared across these two groups. Conclusion: Successful completion of this study will help define the role of machine learning not only for intraoperative telemedicine, but for other risk assessment tasks before, during, and after surgery. Registration: ORACLE is registered on ClinicalTrials.gov: NCT05042804; registered September 13, 2021

Organotypic Culture of Physiologically Functional Adult Mammalian Retinas

BACKGROUND: The adult mammalian retina is an important model in research on the central nervous system. Many experiments require the combined use of genetic manipulation, imaging, and electrophysiological recording, which make it desirable to use an in vitro preparation. Unfortunately, the tissue culture of the adult mammalian retina is difficult, mainly because of the high energy consumption of photoreceptors. METHODS AND FINDINGS: We describe an interphase culture system for adult mammalian retina that allows for the expression of genes delivered to retinal neurons by particle-mediated transfer. The retinas retain their morphology and function for up to six days— long enough for the expression of many genes of interest—so that effects upon responses to light and receptive fields could be measured by patch recording or multielectrode array recording. We show that a variety of genes encoding pre- and post-synaptic marker proteins are localized correctly in ganglion and amacrine cells. CONCLUSIONS: In this system the effects on neuronal function of one or several introduced exogenous genes can be studied within intact neural circuitry of adult mammalian retina. This system is flexible enough to be compatible with genetic manipulation, imaging, cell transfection, pharmacological assay, and electrophysiological recordings

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data