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Total brains, hippocampi or cultured neurons were homogenized twice for 2 min using metallic beads at a frequency of 20 Hz in RIPA buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% NP-40, 1% NaDC, 2.5 mM Na4 P2O7, 1 mM b-glycerophosphate, 1 mM Na3VO4, 1 μg/ml leupeptin).
A ~4-cm piece of leaf tissue (excluding the midvein) was flash frozen in liquid N2, lysed with two 6-mm glass beads at a frequency of 30 Hz for 30 sec, and then genomic DNA was extracted and purified using a QIAGEN DNeasy Plant Mini kit; we used Tris-EDTA (pH 8.0) heated to 65° to elute DNA rather than the elution buffer provided.
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When DNA coils in high enough concentration are present, the free-bead peak is suppressed in favor of the formation of a new bound-bead peak at a lower frequency.
It is reasonable to assume that the result from measuring on a sample containing both bead sizes would be represented by a peak at a frequency somewhere in between those two values.
Ten milligrams of each of the dried tissues was rubbed for one minute at a frequency of 30 times/second in a FastPrep bead mill (Retsch MM400, Germany).
For no DNA coils present (EC 0, VC 0) a comparably narrow V2' peak is seen at a frequency corresponding to one in-between the two individual free-bead peaks, which could be considered as the sum of the peaks for 250- and 100-nm beads.
Frozen plant material was homogenized to a fine powder with a mixer mill MM301 (Retsch, Haan, Germany) at a frequency of 25 s-1 for 50 s with a single 5 mm diameter steel bead in a 2 ml Eppendorf tube.
By using the straight SPOM technique, we obtained SRS images of 1-μm polystyrene beads at frequency differences of 3051 cm 1 (775 and 1015-nm pulses) and 3333 cm 1 (775 and 1045-nm pulses), as shown in Figs. 8(a) and 8(b).
One ml lysing buffer (Qiazol, Qiagen) and a 5 mm metal bead (Millipore) were added and immediately followed by homogenization in a TissueLyser (Qiagen), with shaking three times for 2 minutes at a frequency of 25 Hz.
The M-S-PB mixture contains PS beads at a volume fraction of 2.0%%.
The 160-μm "quality control" (QC) beads were mixed with 10-μm "screening" beads at a bead stoichiometry of ∼1 20 000 (QC:screening).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com