Automated classification of bacterial cell sub-populations with convolutional neural networks.

Quantification of phenotypic heterogeneity present amongst bacterial cells can be a challenging task. Conventionally, classification and counting of bacteria sub-populations is achieved with manual microscopy, due to the lack of alternative, high-throughput, autonomous approaches. In this work, we apply classification-type convolutional neural networks (cCNN) to classify and enumerate bacterial cell sub-populations (B.

Controlling Heterogeneity and Increasing Titer from Riboswitch-Regulated Spores for Time-Delayed Protein Expression Applications.

Sporulated cells have potential as time-delayed expression chassis of proteins for applications such as "on-demand" biologics production, whole cell biosensors, or oral vaccines. However, the desired attributes of high expression rates and low product variances are difficult to maintain from germinated spores. In this work, we study the effect of an integrating vs theta-replicating plasmid in a wild-type and two PolY mutants.

Cell-free supplement mixtures: Elucidating the history and biochemical utility of additives used to support in vitro protein synthesis in E. coli extract.

Cell-free protein synthesis (CFPS) has become an established biotechnology tool for rapid protein expression. Over the past few decades many advances have elevated CFPS from a niche, low-efficiency system to one now capable of biomanufacturing custom proteins. Many research papers and reviews exist on the advances made in CFPS genetic template and cell extract preparation for use in E.

The role of the NADH-dependent nitrite reductase, Nir, from Escherichia coli in fermentative ammonification.

Nitrate and nitrite reduction are of paramount importance for nitrogen assimilation and anaerobic metabolism, and understanding the specific roles of each participating reductase is necessary to describe the biochemical balance that dictates cellular responses to their environments. The soluble, cytoplasmic siroheme NADH-nitrite reductase (Nir) in Escherichia coli is necessary for nitrate/nitrite assimilation but has also been reported to either "detoxify" nitrite, or to carry out fermentative ammonification in support of anaerobic catabolism. Theoretically, nitrite detoxification would be important for anaerobic growth on nitrate, during which excess nitrite would be reduced to ammonium.