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6 protocols using glucanase

1

Identifying Binding Components of B. bassiana

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To identify the targeted binding components, B. bassiana spores were treated in the following ways, and then used for binding assays. To remove spore surface proteins, spores were suspended and incubated in the binding buffer containing 0.5 µg/µL Protease K (Roche) at room temperature for 12 h. High concentration of HCl can hydrolyzate proteins (22 (link)). In order to remove all proteins, spores were also incubated in 37% HCl at room temperature for 12 h. To remove chitin component, spores were suspended and incubated in the binding buffer (200 µL) containing 1 µg/µL chitinase (Roche) and 1-mM phenylmethylsulfonyl fluoride (PMSF) (to inhibit protease contamination in this product according to our assay). To remove β-1,3-glucan component, spores were suspended and incubated in 200 µL of 0.2 M of citric acid–sodium citrate buffer (pH 5) containing 10 µg/µL glucanase (Sigma) and 1 mM PMSF at 37°C for 2 h. After these separate treatments (37% HCl, chitinase, and glucanase), spore samples were separated from chemical and washed in binding buffer for three times. Subsequently, the samples were incubated with rPPO1 or rPPO1-GFP as described above. In order to examine the enzyme hydrolysis effect, the dye Calcofluor White (Sigma) was applied for chitin staining (18 (link)), and β-1,3-glucan was detected by using Aniline Blue Fluorochrome (Biosupplies) (23 (link)).
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2

Targeted Gene Silencing in Inonotus obliquus

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RNA interference was used for knockdown of genes. The two complementary cDNA fragments from GSNOR (300 bp), IoTrx1 (200 bp), IoTrx (150 bp) and IoTrx3 (200 bp) were amplified, respectively, using the primers listed in Supplemental Table 1, and inserted to vector pCIT that flanked to the intron (Supplemental Fig. 1A,B) to form silencing construct (Supplemental Fig. 1C). The silencing construct including PtrpC and TtrpC was released by Xho1 and Sac I and subcloned to the sites of Xho1 and Sac I in vector pCH containing hygromycin resistant gene to form pCH-silence plasmids (Supplemental Fig. 1D). For preparing the competent cells, the I. obliquus mycelia were incubated by rotation in 10 ml osmotic medium36 (link) containing lysing enzyme 45 mg (Sigma), yatalase 30 mg (Takara), glucuronidase 50 μl (Sigma), glucanase 20 mg (Sigma) and BSA 50 mg (MP Biomedicals, USA) at 37 °C for 18 h followed by protoplast capture according to the protocols described elsewhere36 (link). Transformation of the plasmids were conducted on an osmotic PDA medium containing 0.1 μg/ml hygromycin B (Sigma) as the procedure previously described36 (link). The positive mutants were further screened using hygromycin B containing PDA medium and used for further experiments.
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3

Fungal Cell Wall Digestion Protocol

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Fixation in formaldehyde was adapted from the protocols described by Bertaux and Wang (Bertaux et al., 2003 (link); Wang et al., 2017 (link)). Fungal cultures grown under varied conditions were fixed in a 4% solution of formaldehyde (w/v, Thermo Fisher Scientific) in PBS overnight at 4°C. Fungal biomass was washed 3× with PBS and then treated with cocktail combinations of cell wall digestive enzymes: 1 mg•ml−1 solution of lysozyme, or 0.5 mg•ml−1 solution of chitinase, and/or 5 mg•ml−1 solution of glucanase (reagents purchased from Sigma-Aldrich) for 1 h at 37°C and washed 3× with PBS. The cultures were then dehydrated with a step-wise series of ethanol treatments: 50%, 75%, 100%, 75%, 50%, and finally replaced with PBS for 3 min between each step.
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4

Qualitative Screening of Microbial Hydrolases

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Selected isolates were inoculated again on the previously mentioned standard media and grown under the described conditions until healthy colonies were visible. Substrate solutions of Glucanase (4-Nitrophenyl Beta-D-glucopyranoside, Sigma, N7006), Xylanase (4-Nitrophenyl Beta-D-xylopyranoside, Sigma, N2132) and Cellobiase (4-Nitrophenyl Beta-D-cellobioside, Sigma, N5759) 0,6% w/v dissolved in 50 mM NaOAc; pH 5 were sprayed on each colony until they were completely covered. The plates were incubated at room temperature for 8 hours and monitored every 15 minutes. Substrate hydrolysis and the consequent liberation of 4-nitrophenyl phosphate (4NP) was shown by yellow coloration; therefore, isolates were scored qualitatively as “0” if no coloration occurred and “3”, “2” or “1” if substrate coloration took place in 1, 2 or more hours, respectively.
These results were incorporated into a matrix to build a heat map (tool available at: http://www.chibi.ubc.ca/matrix2png/bin/matrix2png.cgihttp://www.chibi.ubc.ca/matrix2png/bin/matrix2png.cgi), which was then used to generate a hydrolytic profile of the isolates. Quantitative determination of enzyme activities was not performed.
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5

Enzymatic Lysis of Candida Cells

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Digestive enzymes, including snailase (Takara Biotechnology, China), lyitcase (Sigma, USA), zymolyase (Zymo Research, USA) and glucanase (Sigma, USA), were tested for their capacity to lyse Candida cells. Aliquots of enzyme at different concentrations were prepared according to the manufacturer’s instructions.
The precipitated Candida cells were resuspended in 1 mL of suspension buffer (0.5 M sorbitol, 25 mM EDTA, pH = 8.0) containing 2 μL of β-mercaptoethanol. The different digestive enzymes then were added to each Eppendorf tube at the following concentrations: (1) snailase: 0, 130, 650, 1040 and 2080 μg/mL; (2) lyitcase: 0, 100, 200, 500 and 800 U/mL; (3) zymolyase: 0, 40, 80, 160 and 320 U/mL; and (4) glucanase: 0, 40, 80, 160 and 320 U/mL. All of the digestive reaction systems described above were incubated at the temperatures recommended by the enzymes, which were 35, 30, 30 and 50 °C for snailase, lyitcase, zymolyase and glucanase, respectively. The lysing effects were assessed after 5 h by counting the remaining intact Candida blastospores with a cell counting plate.
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6

Cloning and Expression of Bacillus Glucanase

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Bacterial strains, plasmids and medium. The protein Maker, pMD18-T, T4 DNA ligase and restriction endonucleases EcoRI and BamHI are from Takara Bio.
Raffinose, laminarin and glucanase were purchased from Sigma-Aldrich. All other chemicals were of analytical purity.
Bacillus licheniformis SR01 was kindly supplied by the College of Biological and Chemical Engineering at the Guangxi University of Science and Technology. Vector pMD18-T was used for gene cloning, and plasmid pGEX-4T-3 was used for protein expression. E. coli was used as the host strain for gene cloning and protein expression.
Bacillus licheniformis SR01 was grown on Luria-Bertani (LB) medium at 60∞C. The E. coli strains were grown on LB medium or LB agar plates at 37∞C with ampicillin (100 mg/ml).
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