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Bioflo 415

Manufactured by Eppendorf
Sourced in United States

The BioFlo 415 is a benchtop bioreactor system designed for small-scale cell culture and fermentation applications. It features a touchscreen control panel, modular design, and integrated software for monitoring and controlling key process parameters such as temperature, pH, and dissolved oxygen.

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7 protocols using bioflo 415

1

Production of M. carneum Formulations

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To prepare the M. carneum formulation, a preinoculum of the fungus was put into a flask of 1 L with 500 mL of potato dextrose broth (PDB) at a concentration 1 × 106 conidia mL−1. The flask was incubated at 22 °C and at 100 rpm for 72 h. For the liquid formulation, the fungus was reproduced in a BioFlo 415 bioreactor (New Brunswick Scientific, Edison, NJ, USA) with a capacity of 10.5 L (Eppendorf™, Hamburg, Germany) with an oat broth as the growth medium [20 ]; 50 mL of the preinoculum was added to the bioreactor and was incubated for 120 h. Finally, a stabilizer was added to the ferment, which was kept in a hermetically sealed 1 L flask at room temperature. For the powdered formulation, 200 g of sterilized semistarchy rice was impregnated with 25 mL of preinoculum of M. carneum inside a high-density polyethylene bag and was then incubated for 30 days at room temperature (22 ± 2 °C and 60% relative humidity). Afterwards, the rice with the fungus developed was shredded with a food processor (Ninja Intelli-Sense CT680CO2SS, Ninja Kitchen, Newton, MA, USA) at top speed for 20 s. The obtained powder was mixed with 20% of diatom (Dia-Fix™ Zeolitech, Cuernavaca, Mexico). The mixture was then stored in vacuum-sealed bags and kept at room temperature (22 ± 2 °C). At the time of the sealing process, the fermentation suspension had 1.8 × 108 CFU mL−1 and the powder had 1.8 × 107 CFU g−1.
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2

Yeast Cultivation and Oil Extraction

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Yeasts were cultured in 8 l of YM medium supplemented with 1% glucose in a BIOFLO 415 fermenter (New Brunswick Scientific, Edison, NJ, USA) until the stationary phase of growth was reached. Cell pellets were collected by centrifugation at 4000 g at 4 °C for 5 min and were thoroughly washed with distilled water. Oil extraction and analysis were conducted according to the method described by Bligh and Dyer [48 (link)] and the AOAC official method 969.33, which were performed by an external service (ANALAB CHILE S.A., www.analab.cl).
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3

Cloning, Expression, and Purification of FPGS from M. tuberculosis

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The ORF encoding FPGS15 (link) of M. tuberculosis H37Rv was cloned into pYUB28b31 (link) with the resulting construct expressing His6-tagged protein in M. smegmatis mc24517 cells32 (link). The cells were grown in a fermenter (BioFlo®415, New Brunswick Scientific) for 4 days and the protein purified using Ni-NTA and SEC steps, as described for hFPGS, and using a base buffer of 20 mM HEPES pH 8.0, 100 mM KCl, 1 mM MgCl2, 5% glycerol, 2 mM β-mercaptoethanol.
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4

Recombinant WDR5 Protein Purification

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Truncated WDR5 (a.a. 22–334) was cloned into a pET vector with a 6xHis-SUMO tag fused at the N-terminus. The plasmids WDR5 was transformed into E. coli BL21 (DE3) cells. The overnight culture was used to start a 10 L fermentation (BioFlo 415, New Brunswick Scientific) grown at 37 °C. For NMR samples, uniformly 15N-labeled protein was produced in minimal M9 medium, where 15NH4Cl (Cambridge Isotope Laboratories) and D-glucose were used as sole nitrogen and carbon sources. When the cell density reached OD600 = 2.5, the temperature was lowered to 30 °C. The protein was expressed overnight with 1mM isopropyl-β-D-thiogalactoside (IPTG). Myc peptide (DEEEIDVVSVE) was ordered (Genscript) as HPLC purified synthetic polypeptide. It was dissolved in DMSO for further use.
Cell pellets were dissolved in lysis buffer (1XPBS plus 300 mM NaCl, 20 mM imidazole, 5 mM BME, and10% glycerol), and broken by homogenization (APV-2000, APV). The lysate was cleared by centrifugation and filtering, and then applied to an affinity column (140 mL, ProBond, Invitrogen). Bound protein was eluted by an imidazole gradient. The His-SUMO-tag was removed by SUMO protease cleavage during dialysis and the subsequent subtractive second nickel-column. WDR5 protein was then purified by size-exclusion chromatography (HiLoad 26/60, Superdex 75, GE Healthcare) using NMR or crystallization buffer.
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5

Lactic Acid Production from Molasses

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Two fermentation processes were performed, to know batch and fed batch. At the fed batch process, molasses feed were added during the fermentation to increase the final concentration of lactic acid.
A bioreactor (New Brunswick BioFlo 415) with capacity up to 7 L was used. A sterilization procedure was performed for 15 minutes at 121°C with the fermentation medium at the bioreactor before the fermentations started. After cooling, the inoculum was added. The temperature utilized was 43.4°C, the agitation was 200 rmp, and the pH was maintained in 5.0 during the fermentations using a base pump with 4.0 N NaOH. The fermentations were performed under anaerobic conditions.
At the batch process the fermentation was kept until the base pump stopped working, indicating the end of acid production. At the fed batch process three molasses feed were added at 12 hours, 24 hours, and 36 hours, and the fermentation was stopped at 48 h. At both fermentation processes, 4.0 mL samples were taken every 2 hours after the start of fermentation to observe the performance.
The molasses feed volumes were the same as the total samples volume collected until the feeding time, maintaining, in this way, the same total amount of fermentation volume. The concentration determined for the molasses feed was 270 g/L of sucrose, about 10 times more than the initial one.
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6

Purification of Truncated WDR5 Protein

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Truncated WDR5 (a.a. 22–334) was cloned into a pET vector with a 6xHis-SUMO tag fused at the N-terminus. The plasmids WDR5 was transformed into E. coli BL21 (DE3) cells. The overnight culture was used to start a 10 L fermentation (BioFlo 415, New Brunswick Scientific) grown at 37 °C. For NMR samples, uniformly 15N-labeled protein was produced in minimal M9 medium, where 15NH4Cl (Cambridge Isotope Laboratories) and D-glucose were used as sole nitrogen and carbon sources. When the cell density reached OD600 = 2.5, the temperature was lowered to 30 °C. The protein was expressed overnight with 1mM isopropyl-β-D-thiogalactoside (IPTG). M peptide (DEEEIDVVSVE) was ordered (Genscript) as HPLC purified synthetic polypeptide. It was dissolved in DMSO for further use.
Cell pellets were dissolved in lysis buffer (1XPBS plus 300 mM NaCl, 20 mM imidazole, 5 mM BME, and 10% glycerol), and broken by homogenization (APV-2000, APV). The lysate was cleared by centrifugation and filtering, and then applied to an affinity column (140 mL, ProBond, Invitrogen). Bound protein was eluted by an imidazole gradient. The His-SUMO-tag was removed by SUMO protease cleavage during dialysis and the subsequent subtractive second nickel-column. WDR5 protein was then purified by size-exclusion chromatography (HiLoad 26/60, Superdex 75, GE Healthcare) using NMR or crystallization buffer.
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7

Production of M. carneum Formulations

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To prepare the M. carneum formulation, a preinoculum of the fungus was put into a flask of 1 L with 500 mL of potato dextrose broth (PDB) at a concentration 1 × 106 conidia mL−1. The flask was incubated at 22 °C and at 100 rpm for 72 h. For the liquid formulation, the fungus was reproduced in a BioFlo 415 bioreactor (New Brunswick Scientific, Edison, NJ, USA) with a capacity of 10.5 L (Eppendorf™, Hamburg, Germany) with an oat broth as the growth medium [20 ]; 50 mL of the preinoculum was added to the bioreactor and was incubated for 120 h. Finally, a stabilizer was added to the ferment, which was kept in a hermetically sealed 1 L flask at room temperature. For the powdered formulation, 200 g of sterilized semistarchy rice was impregnated with 25 mL of preinoculum of M. carneum inside a high-density polyethylene bag and was then incubated for 30 days at room temperature (22 ± 2 °C and 60% relative humidity). Afterwards, the rice with the fungus developed was shredded with a food processor (Ninja Intelli-Sense CT680CO2SS, Ninja Kitchen, Newton, MA, USA) at top speed for 20 s. The obtained powder was mixed with 20% of diatom (Dia-Fix™ Zeolitech, Cuernavaca, Mexico). The mixture was then stored in vacuum-sealed bags and kept at room temperature (22 ± 2 °C). At the time of the sealing process, the fermentation suspension had 1.8 × 108 CFU mL−1 and the powder had 1.8 × 107 CFU g−1.
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