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Amplifications were carried out in a 25 μl reaction volume for a final concentration of 1.25 U Taq polymerase (Promega), 2.5 mM MgCl2 (Promega), 0.2 mM of each dNTP, 0.2 μM of each primer and about 2 μl of DNA sample and the amount of Taq buffer recommended by the manufacturer.
All other proteases (Table 1) were measured in the buffer recommended by the manufacturer.
RNA sample was treated with DNAse (Roche) in the presence of RNAse inhibitor (Ribolock, Thermo) in the buffer recommended by the manufacturer.
In the case of alkaline phosphatase treatment, [α-P] GTP-labeled product was incubated with 0.5 units of bacterial alkaline phosphatase in a buffer recommended by the manufacturer (Toyobo) at 37°C for 1 hr before nuclease digestion.
The PCR products were subjected to restriction digestion with 4 U of the restriction endonuclease TaqI for 15 μl of PCR sample at 65°C for three hours in the buffer recommended by the manufacturer (MBI Fermentas, USA).
PCRs were carried out in a BIORAD My Cycler tm thermocycler using a reaction volume of 25 μl containing ~ 25 ng genomic DNA, 200 μM each dNTP (Roche Diagnostics), 0.5 μM each primer, 0.625 U Taq DNA polymerase (Roche Diagnostics), the buffer recommended by the polymerase supplier and 2.5 mM MgCl2.
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Restriction endonucleases were purchased from New England Biolabs and used in the buffers recommended by the manufacturer.
Lyophilized stool extracts were dissolved in Tris-buffer saline (TBS) for LL-37 or in appropriate dilution buffer as recommended by the manufacturer for HBD-1, HBD-3 (Alpha diagnostic, Texas, USA), IL-8 and IL-1β (BD Biosciences Pharmingen, California, USA).
We attempted to evaluate the purity of the protein complex es) by eluting the immobilized complex es) from the anti-HA agarose slurry using low pH buffer as recommended by the manufacturer; however, the majority of the proteins were not eluted to the buffer in an amount detectable by Western blot analysis (data not shown).
The saliva was incubated with the lysis buffer at 50°C to release the DNA that was then precipitated by ethanol and dissolved in Tris-EDTA buffer, as recommended by the manufacturer.
Subsequently, they were synthesized by Invitrogen and dissolved in the siRNAs buffer, as recommended by the manufacturer.
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