Pre-cultivation targeted FACS enrichment of aGMDs and abGMDs. (A) Only aGMDs and abGMDs containing algal/bacterial cells were first sorted by size by measuring forward scatter (FSC, x-axis at linear scale) versus side scatter (SSC, y-axis at logarithmic scale). (B) aGMDs and abGMDs were further analyzed by chlorophyll autofluorescence using a 650/50 nm filter (x-axis at logarithmic scale) versus 530/40 nm filter (y-axis at logarithmic scale), to select for GMDs containing algal/bacterial cells. (C) aGMDs and...

Post-cultivation targeted FACS enrichment of abGMDs. Control population of cultivated aGMDs (A) and experimental cultivated population of abGMDs (D) using FSC (x-axis; linear scale) versus SSC (y-axis; log scale). (E) Cultivated abGMDs exhibiting chlorophyll autofluorescence higher than that of the cultivated control aGMDs shown in (B) using a 650/50 nm filter (x-axis at logarithmic scale) versus 530/40 nm filter (y-axis at logarithmic scale). (F) Gated selection of cultivated abGMDs exhibiting higher FSC (to distinguish from...

Schematic for cultivation chamber. The cultivation chamber was fabricated and sterilized as described for the microfluidic droplet generator chip (Figure 2 legend). The microfluidic cultivation chamber was used to microscopically visualize droplets without disturbing them or sacrificing viability, as well as providing an even distribution of light.

Maximum likelihood (ML) tree of sequences from four clinical samples. ML tree of RSV-A and RSV-B sequences obtained from four clinical samples (Sp16, Sp19, Sp8 and Sp9) in this study. The reference sequences were retrieved from GenBank.

Viability is unaffected by short time incubation in high viscosity medium. (A) The number of counted CFU/ml of Pseudomonas putida and Paenibacillus amylolyticus is identical after 45 min. of incubation in PBS and high viscosity liquid (50% glycerol). (B) Similarly, the viability of Xanthomonas retroflexus was unaffected by incubation in high viscosity liquid and did not change over a short time period (N=3, Error bars represent Standard Error (SE)).

Cell input modifications for GMD capture. Bacterial and algal concentrations were adjusted to cell concentrations OD600, OD750 in 1x PBS and 100 µl of the resultant cell suspension (or 50 + 50 µL for abGMDs) was used as cell input for initial capture in the CelGel Matrix prior to sorting. This ratio of bacteria-to-matrix or algae-to-matrix (# cells/GMD) was verified by microscopy; data not presented. “aGMD” = algae only GMDs, “bGMD” = bacteria only GMDs,...

Pre-cultivation targeted FACS enrichment of aGMDs and abGMDs. (A) Only aGMDs and abGMDs containing algal/bacterial cells were first sorted by size by measuring forward scatter (FSC, x-axis at linear scale) versus side scatter (SSC, y-axis at logarithmic scale). (B) aGMDs and abGMDs were further analyzed by chlorophyll autofluorescence using a 650/50 nm filter (x-axis at logarithmic scale) versus 530/40 nm filter (y-axis at logarithmic scale), to select for GMDs containing algal/bacterial cells. (C) aGMDs and...

Comparison of the new mismatch-tolerant RT-qPCR with the assays with only Taq (conventional) and high fidelity (Q5) DNA polymerase. A. Detection of RSV mutants; B. Detection HCoV 229E mutants. The amplified products were detected using 2.5% agarose gel electrophoresis. The arrow highlights the specific product. For other details, please see Figure 3.

Cell input modifications for GMD capture. Bacterial and algal concentrations were adjusted to cell concentrations OD600, OD750 in 1x PBS and 100 µl of the resultant cell suspension (or 50 + 50 µL for abGMDs) was used as cell input for initial capture in the CelGel Matrix prior to sorting. This ratio of bacteria-to-matrix or algae-to-matrix (# cells/GMD) was verified by microscopy; data not presented. “aGMD” = algae only GMDs, “bGMD” = bacteria only GMDs,...

Schematic for cultivation chamber. The cultivation chamber was fabricated and sterilized as described for the microfluidic droplet generator chip (Figure 2 legend). The microfluidic cultivation chamber was used to microscopically visualize droplets without disturbing them or sacrificing viability, as well as providing an even distribution of light.

Maximum likelihood (ML) tree of sequences from four clinical samples. ML tree of RSV-A and RSV-B sequences obtained from four clinical samples (Sp16, Sp19, Sp8 and Sp9) in this study. The reference sequences were retrieved from GenBank.

Post-cultivation targeted FACS enrichment of abGMDs. Control population of cultivated aGMDs (A) and experimental cultivated population of abGMDs (D) using FSC (x-axis; linear scale) versus SSC (y-axis; log scale). (E) Cultivated abGMDs exhibiting chlorophyll autofluorescence higher than that of the cultivated control aGMDs shown in (B) using a 650/50 nm filter (x-axis at logarithmic scale) versus 530/40 nm filter (y-axis at logarithmic scale). (F) Gated selection of cultivated abGMDs exhibiting higher FSC (to distinguish from...

Comparison of the new mismatch-tolerant RT-qPCR with the assays with only Taq (conventional) and high fidelity (Q5) DNA polymerase. A. Detection of RSV mutants; B. Detection HCoV 229E mutants. The amplified products were detected using 2.5% agarose gel electrophoresis. The arrow highlights the specific product. For other details, please see Figure 3.

Viability is unaffected by short time incubation in high viscosity medium. (A) The number of counted CFU/ml of Pseudomonas putida and Paenibacillus amylolyticus is identical after 45 min. of incubation in PBS and high viscosity liquid (50% glycerol). (B) Similarly, the viability of Xanthomonas retroflexus was unaffected by incubation in high viscosity liquid and did not change over a short time period (N=3, Error bars represent Standard Error (SE)).

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