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54 protocols using yeast extract

1

Glucose Metabolism Monitoring Protocol

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The average data are presented from 3 independent measurements. The standard errors calculated using Microsoft Excel 2013 do not exceed 3 % (if not mentioned). The validity of the differences between the changes obtained and the controls are estimated by Student P value: if there is no other value, then p < 0.01.
Glucose (Borisov Plant of Medicinal Preparations, Belarus), agar, DCCD (“Sigma”, USA), tryptone, yeast extract, Tris (amino-methane) (“Carl Roth GmbH & Co”, Germany) as well as the other reagents of analytical grade were used in the study.
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2

Antibiotic Susceptibility Profiling

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Double-concentrated half-log dilutions
of reference antibiotics (ampicillin and rifampicin) and test materials
(MAF, MA60, compounds 2, 4, and 7) were prepared in brain-heart-infusion broth or Todd Hewith broth
with yeast extract (all Carl-Roth GmbH) for S. aureus and S. pneumoniae, respectively. A volume of 50
μL of each dilution (duplicates) was dispensed into U-bottomed
96-well sterile plates (Greiner Bio-One GmbH). Then, 50 μL of
bacterial suspension consisting of 2 × 105 CFU/mL40 (link) was inoculated to the antibiotic or test item
dilutions or six wells with antibiotic-free broth for bacterial growth
control. After 24 h of incubation at 37 °C and 5% CO2, the MIC end point was read as the lowest concentration of antibiotic
or test item at which there was no visible growth (n = 3).
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3

Streptococcus pneumoniae 19F Cultivation and Influenza Virus Propagation

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Streptococcus pneumoniae 19F (EF3030), a nasopharynx isolate from a child with frequent episodes of otitis media (90 (link), 91 (link)), was grown on blood agar plates (Oxoid) and cultivated to mid-log phase (optical density at 600 nm [OD600] of 0.35 to 0.40) in Todd-Hewitt broth supplemented with 0.5% (wt/vol) yeast extract (Carl Roth) at 37°C and 5% CO2. Influenza virus A/Bavaria/74/2009 (H1N1) was propagated as described by Eisfeld and colleagues (92 (link)).
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4

Preparation of Standard Media Reagents

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All media were prepared according to standard protocols (Dymond, 2013 (link)). D(+)-Glucose (#HN06, tryptone/peptone (#8952), and yeast extract (#2363) were purchased from Carl Roth. Yeast nitrogen base (YNB) (#CYN0602), agar–agar (#AGA03), and complete supplement mixture (CSM complete) (#DCS0019) were purchased from FORMEDIUM.
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5

Cultivation and Storage of Pathogenic Bacteria

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Staphylococcus aureus (S. aureus, DSM 799) was obtained
from the German
Collection of Microorganisms and Cell Cultures (DSMZ, Braunschweig,
Germany). Aggregatibacter actinomycetemcomitans (A. ac, MCCM 2474) was obtained
from the Microbial Culture Collection Marburg (Marburg, Germany).
The bacteria were stored at −80 °C as glycerol stocks
and precultured for every experiment. S. aureus was cultivated in tryptone soy broth (Oxoid Limited, Hampshire,
UK) supplemented with 10% yeast extract (Carl Roth GmbH + Co. KG,
Karlsruhe, Germany) continuously shaken under aerobic conditions at
37 °C for 16 h. A. ac was cultivated
in Todd Hewitt broth (Oxoid Limited) supplemented with 10% yeast extract
continuously shaken under microaerophilic conditions at 37 °C
for 24 h.
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6

Bacterial Attachment and Biofilm Formation on Nanotopographies

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To analyze bacterial attachment and biofilm formation on nanotopographies,
three individual precultures were centrifuged and resuspended in phosphate-buffered
saline. They were adjusted to an optical density at 600 nm of 0.001
or 0.2 for S. aureus or A. ac, respectively. Test specimens (N = 18 per structure and strain) were incubated with bacterial suspensions
using each preculture in triplicates for 5 h at 37 °C and with
continuous shaking under aerobic (in the case of S.
aureus
) or microaerophilic (5% CO2, in
the case of A. ac) conditions. After
this initial attachment, half of the specimens (N = 9 per structure and strain) were processed for microscopy as described
below.
On the other specimens, the bacterial suspension was
removed and replaced with fresh medium: tryptone soy broth supplemented
with 10% yeast extract and 50 mM glucose (Carl Roth GmbH & Co.
KG) for S. aureus or Schaedler broth
(Oxoid Limited) supplemented with 10 μg/mL vitamin K (Oxoid
Limited) for A. ac. To allow for
biofilm formation of the adhered cells, specimens were further incubated
for a total of 24 h at 37 °C under aerobic conditions and continuous
shaking in the case of S. aureus and
under static microaerophilic conditions (5% CO2) in the
case of A. ac.
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7

Yeast and Fungus Cultivation Protocols

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Yeast liquid cultures were prepared by inoculating a small piece of dried yeast into 10 ml of yeast extract peptone dextrose (YEPD) medium, which contains 1% yeast extract (Carl Roth GmbH), 2% peptone (Carl Roth GmbH), and 2% glucose (Sigma-Aldrich Corp.). The culture was incubated at 30°C while shaking at 300 rpm for ∼18 h.
To cultivate fungus, a potato/dextrose medium was prepared. In brief, 200 g potato was peeled and sliced into small cubes. After boiling those pieces in 1 L distilled water for 1 h, the infusion cleared by sieving, 20 g glucose was added to the infusion and the volume was adjusted to 1 L. Then, a piece of frozen glycerol stock of P. chrysogenum was inoculated in 10 ml of this potato dextrose medium, and the culture was incubated at 24°C while shaking at 300 rpm for 3 days.
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8

Optimizing pDNA Yield and E. coli Biomass

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We screened individual media components, using a Plackett–Burman design with 12 ((n1 + n2) + 1) runs, 9 (n1) factors, and 2 (n2) dummies, to estimate the occurring falsification related to cumulative interaction components, as shown in Table 1. We optimized the process with regard to a maximum specific pDNA yield (ng pDNA/ODV) (OD600 × culture volume = ODV) and the E. coli biomass (determined as OD600). The following components were used for this purpose: LB powder (consists of 10 g/L trypton, 5 g/L yeast extract, 10 g/L NaCl) (Carl Roth), meat peptone (Fluka Analytical), casein peptone (Carl Roth), yeast extract (Carl Roth), glucose (Carl Roth), glycerol (Carl Roth), phosphate (Carl Roth), NaCl (Carl Roth), and MgSO4 (Carl Roth). Experiments were performed in 500 mL shake flasks and harvested and tested after 18 h.
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9

Streptococcus pneumoniae Growth and Preparation

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Streptococcus pneumoniae strains TIGR4 and R6 were streaked on tryptic soy agar plates containing 5% sheep blood (Oxoid) and grown overnight at 37°C and 5% CO2. Strains used are listed in Table EV1. The next day, pre‐cultures were grown in THY medium (to the exception of competence assays, see below) [Todd Hewitt broth (BD Bacto) supplemented with 0.5% yeast extract (Carl Roth)] to an OD600 nm of 0.5 at 37°C without shaking. Subsequently, the pre‐culture was refreshed in THY to a starting OD600 nm of 0.05 and grown at 37°C without shaking to a final OD600 nm of 0.5.
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10

Cultivating Pneumococcal and Staphylococcal Strains

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S. pneumoniae TIGR4Δcps and TIGR4ΔcpsΔply mutant strains were generated as described previously [27 ]. Pneumococci were grown on blood agar plates (Oxoid) overnight and cultivated to mid-log phase (optical density 600 nm, 0.35–0.40) in Todd-Hewitt broth (Carl Roth) supplemented with 0.5% (w/v) yeast extract (Carl Roth) at 37°C and 5% CO2. S. aureus strain LUG2012 was grown overnight at 37°C in casein hydrolysate and yeast extract medium with agitation [28 (link)]. Influenza virus A/Bavaria/74/2009 (H1N1) was propagated as described previously [29 (link)].
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