Multi-step processing of single cells using semi-permeable capsules

Leonaviciene, Greta; Leonavicius, Karolis; Meškys, Rolandas; Mažutis, Linas

doi:10.1039/d0lc00660b

Cited by 30 publications

(31 citation statements)

References 58 publications

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“…This result is in agreement with the enhanced growth rate of E . coli observed when encapsulated in capsule particles compared with droplets in oil 24 . The average number of yeast cells in PicoShells is dramatically increased between 24 and 48 hrs after encapsulation to 2900 cells/PicoShell, ~20X higher than the carrying capacity in droplets (~150 cells/droplet).…”

Section: Resultsmentioning

confidence: 99%

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High-throughput selection of microalgae based on biomass accumulation rates in production environments using PicoShell Particles

Rumyan

et al. 2021

Preprint

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Production of high-energy lipids by microalgae may provide a sustainable, renewable energy source that can help tackle climate change. However, microalgae engineered to produce more lipids usually grow slowly, leading to reduced overall yields. Unfortunately, tools that enable the selection of cells based on growth while maintaining high biomass production, such as well-plates, water-in-oil droplet emulsions, and nanowell arrays do not provide production-relevant environments that cells experience in scaled-up cultures (e.g. bioreactors or outdoor cultivation farms). As a result, strains that are developed in the lab often do not exhibit the same beneficial phenotypic behavior when transferred to industrial production. Here we introduce PicoShells, picoliter-scale porous hydrogel compartments, that can enable >100,000 individual cells to be compartmentalized, cultured in production-relevant environments, and selected based on growth and biomass accumulation traits using standard flow cytometers. PicoShells consist of a hollow inner cavity where cells are encapsulated, and a porous outer shell that allows for continuous solution exchange with the external environment so that nutrients, cell-communication factors, and cytotoxic cellular byproducts can transport freely in and out of the inner cavity. PicoShells can also be placed directly into shaking flasks, bioreactors, or other production-relevant environments. We experimentally demonstrate that Chlorella sp. and Saccharomyces cerevisiae grow to significantly larger colony sizes in PicoShells than in water-in-oil droplet emulsions (P < 0.05). We have also demonstrated that PicoShells containing faster biomass accumulating Chlorella clonal colonies can be selected using a fluorescence-activated cell sorter and re-grown. Using the PicoShell process, we select a Chlorella population that accumulates biomass 8% faster than does an un-selected population after a single selection cycle.

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Section: Resultsmentioning

confidence: 99%

“…The molecular weight of the dextran is chosen such that it can diffuse out of the enclosed shell particle following the phase transfer (Figure S3). The mechanism to form such hollow shell or capsule particles using the methods we describe has been adapted from previous work 23,24 .…”

Section: Resultsmentioning

confidence: 99%

High-throughput selection of microalgae based on biomass accumulation rates in production environments using PicoShell Particles

Rumyan

et al. 2021

Preprint

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“…2). This is probably attributable to the enhanced diffusivity of amplified DNA in the sol core 42 . MDA-in-AGM therefore does not require a second round of MDA, which is often necessary in other methods using microfabrication techniques (Supplementary Table 12) 21,24 .…”

Section: Discussionmentioning

confidence: 99%

Agarose Gel Microcapsules Enable Easy-to-prepare, Picolitre-scale Single-cell Genomics, Yielding Near-complete Genome Sequences

Aoki

Yuki

Shimizu

et al. 2022

Preprint

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A novel type of agarose gel microcapsule (AGM), consisting of an alginate picolitre sol core and an agarose gel shell, was developed to obtain high-quality single-cell amplified genomic DNA of bacteria. The AGM is easy to prepare in a stable emulsion with oil of water-equivalent density which prevents AGM aggregation, with only standard laboratory equipment. Single cells from a pure culture of Escherichia coli, a mock community comprising 15 strains of human gut bacteria, and a termite gut bacterial community were encapsulated within AGMs, and their genomic DNA samples were prepared with massively parallel amplifications in a tube. The genome sequencing did not need second-round amplification, and showed an average genome completeness that was much higher than that obtained using a conventional amplification method in microlitre scale, regardless of the genomic guanine-cytosine contents. Our novel method using the AGM allows many researchers to perform single-cell genomics easily and effectively, and can accelerate the genome analysis of yet-uncultured microorganisms.

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“…Additional advantages of the AGM are its physical stability and permeability for small molecules, which have made buffer exchange and physical handling much easier. To increase the uniformity and throughput of single-cell genomics using MDA-in-AGM, microchannels and molecular-barcoding 31 may be adapted, although these approaches decrease the simplicity of the procedure Recently, during our experiments were on going, MDA using a hollow-core hydrogel microcapsule consisting of a crosslinked PEG gel shell and a dextran sol core, a similar capsule structure to AGM, was reported 32 . Although ampli cation bias has not been evaluated, single-cell MDA in the core increases the amount of MDA product when compared with MDA in the gel bead.…”

Section: Discussionmentioning

confidence: 99%

Agarose gel microcapsules enable easy-to-prepare, picolitre-scale single-cell genomics, yielding near-complete genome sequences

Aoki

Yuki

Shimizu

et al. 2021

Preprint

View full text Add to dashboard Cite

A novel type of agarose gel microcapsule (AGM), consisting of an alginate picolitre sol core and an agarose gel shell, was developed to obtain high-quality single-cell amplified genomic DNA of bacteria. The AGM is easy to prepare in a stable emulsion with oil of water-equivalent density which prevents AGM aggregation, with only standard laboratory equipment. Single cells from a pure culture of Escherichia coli, a mock community comprising 15 strains of human gut bacteria, and a termite gut bacterial community were encapsulated within AGMs, and their genomic DNAs were obtained with massively parallel amplifications in a tube. The genome sequencing did not need second-round amplification, and showed an average genome completeness that was much higher than that obtained by the conventional amplification method in microlitre scale, regardless of the genomic guanine-cytosine contents. Our novel method using AGMs allows many researchers to perform single-cell genomics easily and effectively, and can enhance the genome analysis of yet-uncultured microorganisms.

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Multi-step processing of single cells using semi-permeable capsules

Abstract: Semi-permeable capsules offers a powerful approach to isolate and process thousands of single bacterial cells simultaneously.

Cited by 30 publications

References 58 publications

High-throughput selection of microalgae based on biomass accumulation rates in production environments using PicoShell Particles

High-throughput selection of microalgae based on biomass accumulation rates in production environments using PicoShell Particles

Agarose Gel Microcapsules Enable Easy-to-prepare, Picolitre-scale Single-cell Genomics, Yielding Near-complete Genome Sequences

Agarose gel microcapsules enable easy-to-prepare, picolitre-scale single-cell genomics, yielding near-complete genome sequences

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