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9 protocols using 5 bromo 4 chloro 3 indolyl β d galacto pyranoside x gal

1

Whole Cerebral Organoid X-gal Staining

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Whole cerebral organoids were stored at −80 °C and, without thawing, fixed in 2% glutaraldehyde/2% formaldehyde in PBS for 10 min at room temperature. Organoids were incubated in ice-cold citrate phosphate buffer (CPB, pH 4.2) for 20 min, then incubated in X-gal working solution containing 40 mg/ml 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal, Invitrogen, 15520-018), 20 mM K3Fe(CN)6 (Sigma-Aldrich), 20 mM K4Fe(CN)6 (Sigma-Aldrich), 0.02% IGEPAL (Sigma-Aldrich), 0.01% deoxycholic acid (Sigma-Aldrich), and 2 mM MgCl2 (Mallinckrodt) in CPB at 37 °C for 30 min to 2 h. The tissue was rinsed first with CPB and then with PBS, and imaged using a dissecting microscope.
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2

Yeast and Bacterial Growth Protocols

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Except where noted, cultures and colonies were grown at 30 °C for 4 days prior to analysis. Except as noted, all solid media contained 2% Bacto agar. Yeast spot colonies were grown on Sp2% medium (2% potassium acetate (pH, 0.5% yeast extract) or Sp0.5% medium (0.5% potassium acetate (pH 7.0), 0.5% yeast extract) or YLD medium (0.1% glucose, 0.5% yeast extract). Where appropriate, these media also contained 40 μg/ml X-gal. E. coli spot colonies were grown on LBIX medium containing LB (pH 7.0) with 250 μg/ml isopropyl-β-d-thiogalactopyranoside (IPTG, Fisher Scientific), 20 μg/ml 5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside (X-gal, Invitrogen) and 1.5% agar. Standard yeast and bacterial growth media used in this study have been described (Sherman et al. 1974 ; Maniatis et al. 1982 ).
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3

E. coli and H. pylori Culture Conditions

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E. coli cells were grown aerobically in Luria–Bertani (LB) broth or on LB plates at 37 ºC, unless indicated otherwise. Ampicillin (Amp, 100 µg/ml), Chloramphenicol (Cm, 25 µg/ml) and kanamycin (Kan, 30 µg/mL) were added as needed. BACTH screening media include MacConkey (MC) plates (BD-Difco # 281810), supplemented with 1% glucose-free maltose (Mal, BD-Difco #216830), or LB plates supplemented with 20 µg/mL 5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside (X-Gal, Fisher). Both MC-Mal and LB-X-Gal were supplemented with 0.5 mM isopropyl β-d-1-thiogalactopyranoside (IPTG, GoldBio), 0.1 mM FeCl3, 0.5 mM L-cysteine, 100 µg/mL Amp and 30 µg/mL Kan. For BACTH selection experiments, we used a Fe-enriched M63 liquid minimal medium: (NH4)2SO4 (2 g/L), KH2PO4 (13.6 g/L), Thiamine B1 (1 mg/L), 1 mM MgSO4, FeSO4.7H2O (5 mg/L), pH 7. This medium was supplemented with 0.4% Mal, 0.5 mM IPTG, 50 µg/mL Amp and 15 µg/mL Kan. All BACTH growth experiments were carried out at 30 °C in aerobiosis (e.g. exposed to air). H. pylori was routinely grown on Brucella agar plates supplemented with 10% defibrinated sheep blood (BA plates), at 37 ºC under microaerobic conditions (5% CO2, 4% O2 and 91% N2). Cm (25 µg/ml) was added as needed.
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4

Molecular Cloning in Salmonella

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Strains and plasmids used in this study are listed in Table 1. All culture media, antibiotics, and media supplements including sucrose, 5-Bromo-4-chloro-3-indolyl β-D-galactopyranoside (X-Gal), and L-rhamnose were purchased from Fisher Scientific (Pittsburgh, PA, USA). All primers were purchased from Integrated DNA Technologies (Coralville, IA, USA). When needed, antibiotics were added to the media at a final concentration of 20 µg/mL for zeocin, 75 µg/mL for hygromycin B, and 30 µg/mL for nourseothricin and chloramphenicol. Culture media were supplemented with 0.2% L-rhamnose and 30 mg/mL X-Gal as needed. All restriction enzymes, T4 DNA ligase and NEBuilder HiFi DNA Assembly Master Mix (HiFiMix) were purchased from New England Biolabs Inc. (NEB, Ipswich, MA, USA). Strains used in this study were grown in Luria-Bertani (LB) and M9 minimal media as needed. Recombinant plasmids were transformed to Salmonella with a Gene Pulser II (Bio-Rad, Hercules, CA, USA) according to the manufacturer’s guideline.
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5

Chromogenic Screening of Fungal β-Galactosidase

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A chromogenic method was used to screen the fungi for their β-galactosidase activity in Petri plate incubation. The growth medium contained 20% (v/v) malt extract (20 mL/L), lactose (20 g/L), peptone (1 g/L) and agar (20 g/L). After sterilization, the medium was supplemented with 0.5% (v/v) of 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-gal; Thermo Fisher Scientific, Waltham, USA) solution (20 mg/mL in dimethyl-sulfoxide). A volume of 20 µL of spore suspension (106 spores/mL) was added to each agar plate and the cultures were incubated for 10 days at temperatures depending on the culturing requirements of the tested fungus. Visual detection of the plates was performed daily, and the level of the β-galactosidase production was evaluated from the intensity of the blue color developed. The categories of no blue color (NC), light blue color (+), darker blue color (++), blue color (+++), dark blue color (++++) and deep dark blue color (+++++) were defined to evaluate the chromogenic test. Three biological replicates were performed with each tested strain. The qualitative chromogenic assay serves as a preliminary test to screen for enzyme production as reported in other similar studies [12 (link),21 ,22 ,23 (link),24 (link)].
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6

Western Blot Antibodies and Reagents

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Rabbit anti-mouse Rab1a antibodies (cat. no. sc-311) were obtained from Santa Cruz Biotechnology, Inc. and lipopolysaccharide (LPS; from Escherichia coli (E. coli) 055:B5 strain] were purchased from MillliporeSigma. Goat anti-mouse β-actin (cat. no. sc-1615) and horse- radish peroxidase (HRP)-conjugated goat anti-rabbit IgG antibodies (cat. no. sc-2004) were purchased from Santa Cruz Biotechnology, Inc. 5-Bromo-4-chloro-3-indolyl β-D-galactopyranoside (X-gal) was obtained from Thermo Fisher Scientific, Inc.
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7

Cultivation and Storage of Lactococcus and E. coli

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The strains, their derivatives and plasmids used in this study are listed in Table 1. Lactococcus lactis strains were grown in M17 medium (Merck GmbH, Darmstadt, Germany) supplemented with 0.5% glucose (GM17) at 30°C. Escherichia coli strains (DH5α and EC101) were grown in Luria Bertani broth (LB) at 37°C with aeration. To each medium, agar (1.5%; Torlak, Belgrade, Serbia) was added for use as a solid medium. The following antibiotic concentrations were used: ampicillin, 100 μg/ml (E. coli); erythromycin, 10 μg/ml (lactococci) and 300 μg/ml (E. coli); chloramphenicol, 10 μg/ml (lactococci) and 35 μg/ml (E. coli). The 5-bromo-4-chloro-3-indolyl-β-D-galacto-pyranoside (X-Gal) (Fermentas, Vilnius, Lithuania) was added to LB medium plates for blue/white color screening of colonies with cloned fragments at a final concentration of 80 μg/ml (lactococci) and 40 μg/ml (E. coli). Ortho-nitrophenyl-β-galactoside (ONPG) was used for the β-galactosidase assay (Sigma Chemical Co., St. Louis, MO, United States).
All strains carrying constructs were stored in growth medium containing 15% glycerol (Sigma Chemie GmbH, Deisenhofen, Germany) at −80°C.
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8

Antibiotic selection and MIC determination for lactococci

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All strains and derivatives used in this study are listed in Table 1. Lactococcal strains were grown in M17 medium (Merck GmbH, Darmstadt, Germany) supplemented with D-glucose (HiMedia Laboratories, Mumbai, India) (0.5 % w/v) (GM17) at 30 • C. Escherichia coli DH5α was grown aerobically in Luria-Bertani (LB) broth (HiMedia Laboratories, Mumbai, India) at 37 • C. Solid medium was made by adding 1.75 % (w/ v) agar (Torlak, Belgrade, Serbia), to the liquid media. Antibiotics were used at the following concentrations: Erythromycin (SERVA Electrophoresis GmbH, Heidelberg, Germany) was used at 300 μg/mL for E. coli and 10 μg/mL for lactococci for selection and maintaining of transformants. Spectinomycin (Merck KGaA, Darmstadt, Germany) was used at 250 and 500 μg/mL for maintaining of invertants and 50, 100, 150, 200, 250, 300, 350, 400 and 500 μg/mL for determination of MIC values for Spectinomycin of transformants in lactococci. For blue/white colour screening, 5-bromo-4-chloro-3-indolyl-β-D-galacto-pyranoside (X-Gal) (Fermentas, Vilnius, Lithuania) was added to LB medium plates of colonies with cloned fragments at a final concentration of 40 μg/mL.
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9

Isolation and Characterization of Lactococcus raffinolactis from Kajmak

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Lactococcus raffinolactis BGTRK10-1 was isolated from autochthonous sweet kajmak produced from sheep milk without the use of starter cultures in a household of the Vlašić mountain region, central Bosnia and Herzegovina [17 (link)] (Table 1). Preliminary strain classification was done according to its fermentation ability using API 50CHL (Api System SA; Bio-Merieux, Montelieu-Vercieu, France), temperature of growth (30°C, 37°C, and 45°C), growth in the presence of salt (4% and 6.5%), and pH tolerance. Final taxonomic classification of BGTRK10-1 was performed by sequencing of amplified 16S rDNA using primers previously described [18 (link)]. The strain was grown in M17 medium (Merck GmbH, Darmstadt, Germany) supplemented with D-glucose (0.5% w/v) (GM17) at 30°C. Escherichia coli DH5α, HB101, and ER2523 strains were grown aerobically in Luria-Bertani (LB) broth at 37°C, unless otherwise specified. Solid medium was made by adding 1.75% (w/v) agar (Torlak, Belgrade, Serbia), to the liquid media. Antibiotics were used at the following concentrations: erythromycin 300 μg/ml and ampicillin 100 μg/ml for selection and maintaining of transformants. The 5-bromo-4-chloro-3-indolyl-β-D-galacto-pyranoside (X-Gal) (Fermentas, Vilnius, Lithuania) was added to LB medium plates for blue/white colour screening of colonies with cloned fragments at final concentration of 40 μg/ml.
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