The Addition of Transcriptomics to the Bead-Enabled Accelerated Monophasic Multi-Omics Method: A Step toward Universal Sample Preparation
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Engineering topics
Sanders, Claire K.
Publications and source records attributed to Sanders, Claire K..
High-Quality Genome Assembly of Nannochloris desiccata 2437 and Its Associated Bacterial Community
High-quality genome sequences were generated for the nonaxenic marine microalga Nannochloris desiccata UTEX 2437 and eight of its associated environmental bacterial species. N. desiccata UTEX 2437 is diploid, and its 20.738-Mbp nuclear genome sequence is assembled in 29 contigs.
59 BASIC BIOLOGICAL SCIENCES↗
Demonstration of the potential of Picochlorum soloecismus as a microalgal platform for the production of renewable fuels
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Functional and phenotypic flow cytometry characterization of Picochlorum soloecismus
Multiple physiological traits essential for efficient cellular function are important when considering the selection and engineering of algal species for biofuel and bioproduct generation. Bioengineering methods have become more ubiquitous producing several novel algal lines with potentially enhanced traits. Complex metabolic interactions, however, require greater depth in characterizing cellular responses to delineate mechanistic understanding. Here, we have developed fluorescence-based high-throughput flow cytometry protocols to facilitate characterization of cell morphology, membrane permeability, metabolic activity, cell viability, intracellular pH, and reactive oxygen species in isolates derived from the species Picochlorum soloecismus. Flow cytometry parameters were optimized for each assay. This suite of molecular flow cytometry probes and procedures can be utilized for rapid screening of optimal phenotypes in microalgae under various environmental conditions as new technical strategies for improving algae strain productivity are established.
59 BASIC BIOLOGICAL SCIENCES↗
Using flow cytometry and multistage machine learning to discover label-free signatures of algal lipid accumulation
Most applications of flow cytometry or cell sorting rely on the conjugation of fluorescent dyes to specific biomarkers. However, labeled biomarkers are not always available, they can be costly, and they may disrupt natural cell behavior. Label-free quantification based upon machine learning approaches could help correct these issues, but label replacement strategies can be very difficult to discover when applied labels or other modifications in measurements inadvertently modify intrinsic cell properties. Here we demonstrate a new, but simple approach based upon feature selection and linear regression analyses to integrate statistical information collected from both labeled and unlabeled cell populations and to identify models for accurate label-free single-cell quantification. We verify the method’s accuracy to predict lipid content in algal cells (Picochlorum soloecismus) during a nitrogen starvation and lipid accumulation time course. Our general approach is expected to improve label-free single-cell analysis for other organisms or pathways, where biomarkers are inconvenient, expensive, or disruptive to downstream cellular processes.
42 ENGINEERING↗
Correlating light scattering with internal cellular structures
The origins of side scattering from a fibroblast and cervical cell line were determined by comparing side-scatter images with images stained for lysosomes, nuclei, and mitochondria on a cell by cell basis. Lysosomes or nuclei are the most efficient type of scatterer depending on the cell type and incident light polarization. The relative scattering efficiencies of lysosomes and mitochondria were the same for both cell lines, while the scattering efficiencies of the nuclei differed. The percent of 90° scattering from the nucleus, mitochondria, and lysosomes as well as the group of other internal cellular objects was estimated. The nucleus was the largest contributor to side scatter in the cervical carcinoma cells. The contributions of lysosomes, mitochondria, the nucleus, and particles unstained by either Hoechst, LysoSensor or MitoTracker ranges from ~20% to ~30% in fibroblast cells. The contribution of lysosomes to side scatter was much stronger when the incident light was polarized perpendicular to the scattering plane than when the polarization of the side scatter laser was parallel to the scattering plane. This dependence on side scatter polarization indicates that lysosomes contain scattering structures that are much smaller than the wavelength of light used in the measurements (785 nm). In conclusion, mitochondria were not found to be either the most efficient scatterer or to have the largest contribution to scattering in either cell line, in contrast to previous reports. Rather lysosomes, nuclei and unknown particles all have significant contributions to 90° scattering and the contributions of some of these particles can be modulated by changing the polarization of the incident light.
59 BASIC BIOLOGICAL SCIENCES↗