Biology subjects

Reuel, N. F.

Publications and source records attributed to Reuel, N. F..

3 recordsLinked to original sources

bioRxiv2020

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. subtilis clusters). Here, we demonstrate that the accuracy of the cCNN developed in this study can be as high as 86% when trained on a relatively small dataset (81 images). We also developed a new image preprocessing algorithm, specific to fluorescent microscope images, which increases the amount of training data available for the neural network by 72 times. By summing the classified cells together, the algorithm provides a total cell count which is on parity with manual counting, but is 10.2 times more consistent and 3.8 times faster. Finally, this work presents a complete solution framework for those wishing to learn and implement cCNN in their synthetic biology work.

synthetic biology↗

bioRxiv2020

Design and Validation of a Frugal, Automated, Solid-Phase Peptide Synthesizer

Solid phase peptide synthesis (SPPS) has enabled widespread use of synthetic peptides in applications ranging from pharmaceuticals to materials science. The demand for synthetic peptides has driven recent efforts to produce automated SPPS synthesizers which utilize fluid-handling components common to chemistry laboratories to drive costs down to several thousand dollars. Herein, we describe the design and validation of a more frugal SPPS synthesizer that uses inexpensive, consumer-grade fluid-handling components to achieve a prototype price point between US$300 and $600. We demonstrated functionality by preparing and characterizing peptides with a variety of distinct properties including binding functionality, nanoscale self-assembly, and oxidation-induced fluorescence. This system yielded micromoles of peptide at a cost of approximately $1/residue, a cost which may be further reduced by optimization and bulk purchasing.

biochemistry↗

bioRxiv2019

One-Pot E. coli Cell-Free Extract for in vitro Expression of Disulfide Bonded Proteins

In vitro expression of proteins from E. coli extract is a useful method for prototyping and production of cytotoxic or unnatural products. However, proteins that have multiple disulfide bonds require custom extract that, to date, requires careful addition of exogenous isomerase enzymes or the use of expensive commercial kits. This cost and complexity currently limit access to some groups who wish to rapidly prototype proteins with disulfide bonds. Herein, we present a simple solution that does not require addition of supplemental enzymes. We use a commercially available SHuffle T7 Express lysY strain of E. coli that expresses both T7 RNAP and DsbC isomerase enzymes. We experimentally determine optimal growth conditions (IPTG induction and harvest times) to balance overall productivity and efficiency of disulfide bond formation using a luciferase (from Gaussia princeps) that contains five disulfide bonds as our reporter protein. We also demonstrate the ability for rapid prototyping by screening the activity of four luciferase candidates against ten luciferin analogues. To display the broad applicability of the extract, three other enzymes containing [≥]3 disulfide bonds (hevamine, endochitinase A, and periplasmic AppA) were also expressed from minimal genetic templates that had undergone rolling circle amplification and confirmed via activity assays.

bioengineering↗