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  1. Free, publicly-accessible full text available January 1, 2023
  2. Herein, we implement and access machine learning architectures to ascertain models that differentiate healthy from apoptotic cells using exclusively forward (FSC) and side (SSC) scatter flow cytometry information. To generate training data, colorectal cancer HCT116 cells were subjected to miR-34a treatment and then classified using a conventional Annexin V/propidium iodide (PI)-staining assay. The apoptotic cells were defined as Annexin V-positive cells, which include early and late apoptotic cells, necrotic cells, as well as other dying or dead cells. In addition to fluorescent signal, we collected cell size and granularity information from the FSC and SSC parameters. Both parameters are subdivided into area, height, and width, thus providing a total of six numerical features that informed and trained our models. A collection of logistical regression, random forest, k-nearest neighbor, multilayer perceptron, and support vector machine was trained and tested for classification performance in predicting cell states using only the six aforementioned numerical features. Out of 1046 candidate models, a multilayer perceptron was chosen with 0.91 live precision, 0.93 live recall, 0.92 live f value and 0.97 live area under the ROC curve when applied on standardized data. We discuss and highlight differences in classifier performance and compare the results to themore »standard practice of forward and side scatter gating, typically performed to select cells based on size and/or complexity. We demonstrate that our model, a ready-to-use module for any flow cytometry-based analysis, can provide automated, reliable, and stain-free classification of healthy and apoptotic cells using exclusively size and granularity information.« less
  3. Photosynthesis can be challenging for instructors to teach and uninteresting for students to learn, but this shouldn't be the case. An activity developed by middle-school educators and university scientists lets students see how red light emitted from sunlit plants is captured by satellites to measure global photosynthesis. In plants, most of the absorbed light energy is channeled into photosynthesis, and the tiny amount that is emitted as red fluorescence is not visible by naked eye but is detectable by satellites. When chlorophyll is removed from plants into a solution – uncoupled from the photosynthetic apparatus – chlorophyll still is green and absorbs light, but the absorbed light energy has nowhere to go, and a large red glow is visible. In a readily accessible 1-hour middle-school classroom activity, students extract chlorophyll from spinach using rubbing alcohol (91% isopropyl alcohol) and then observe the abundant red fluorescence upon illumination with a flashlight. This simple observation of the red glow (fluorescence) from chlorophyll provides a terrific anchor for teaching photosynthesis in a biological, agricultural and global ecology context, thereby inspiring students to better appreciate the fascinating world of plants.
  4. Here, we report the draft genome sequences of 10 marine Pseudoalteromonas bacteria that were isolated, assembled, and annotated by undergraduate students participating in a marine microbial genomics course. Genomic comparisons suggest that 7 of the 10 strains are novel isolates, providing a resource for future marine microbiology investigations.