Journal: ACS nano

Article Title: Stability of Ti 3 C 2 T x MXene Films and Devices under Clinical Sterilization Processes

doi: 10.1021/acsnano.3c01525

Figure Lengend Snippet: (A, B) Left: XRD patterns including pristine control and Parylene-C or textile backgrounds. Right: FWHM of the (002) peak for (A) thin-film devices and (B) MXtrodes (n = 2 for each condition). (C) Raman spectra including pristine controls and Parylene-C background for thin-film devices. (n = 2 samples for each condition). (D) Normalized Gaussian-fitted A1g(C) peak for thin-film devices. (E) Right-shifting Normalized Gaussian-fitted A1g(C) peak for increasingly visually damaged thin-film samples after H2O2 gas plasma sterilization.

Article Snippet: After collection, peak amplitude and FWHM peak values were confirmed using OriginLab, which fitted the peak with a gaussian curve for calculation.

Techniques: Control, Clinical Proteomics

Journal: bioRxiv

Article Title: A gate and clamp regulate sequential DNA strand cleavage by CRISPR-Cas12a

doi: 10.1101/2021.06.18.448962

Figure Lengend Snippet: ( a ) Representation of the magnetic tweezers experiments and DNA protospacer and crRNA spacer sequences used (see main text). ( b ) An example extension time trace (for all data, grey 60 Hz raw data, black 10 Hz filtered) at 0.3 pN showing R-loop formation (IN, blue, at -7 pN nm) and dissociation (OUT, orange, at +7 pN nm) events by WT LbCas12a. ( c ) Example R-loop formation trace at -7 pN nm measured as changes in turns showing hopping between 4 states identified by HMM fitting (red); R-loop states S 2 , S 3 , S 4 and reversible transitions to an R-loop dissociated state (rupture events), S 0 . Gaussian fitting of the histograms gives the average position of each state in agreement with the HMM fitting. ( d ) Example R-loop formation trace at -7 pN nm showing hopping between 5 states including an extended state (blue arrows, S 5 ) that represents pam-distal breathing. ( e ) Example R-loop formation trace at -7 pN nm showing hopping between 4 states, including an additional short R-loop (S 1 ). ( f ) Plot showing the 5 R-loop states identified by HMM analysis and their probability of occupation (P r ) from multiple traces ( N =34), with state positions confirmed from Gaussian fitting. Box width corresponds to the full width at half maximum of each peak. P r Error bars are SD in the turn positions measured by HMM. Errors bars in turn values are s.d from the Gaussian peak fitting. ( g ) Cartoon representation of the R-loops for each state and relative positions of structural features. ( h ) Simple free energy diagram showing sequential hopping between R-loop states. Opening of the Gate residue would lower the energetic barrier to the S 5 state.

Article Snippet: The histograms of turn values of each state were then separately fitted with a gaussian model (in Origin Lab) to extract the state positions.

Techniques: Residue

Journal: bioRxiv

Article Title: A gate and clamp regulate sequential DNA strand cleavage by CRISPR-Cas12a

doi: 10.1101/2021.06.18.448962

Figure Lengend Snippet: ( a ) Example R-loop formation trace at -7 pN nm with W355A Cas12a showing hopping between 5 states identified by HMM fitting (blue); S 2 , S 3 , S 4 and S 5 , and reversible rupture events to S 0 . Gaussian fitting of the histograms gives the average position of each state in agreement with the HMM fitting. ( b ) Example R-loop formation trace at -7 pN nm showing hopping between only 2 states; S 3 and S4. The slower R-loop formation at the start allowed clear identification of S 0 without rupture occurring. ( c ) Example R-loop formation trace at -7 pN nm showing hopping between 3 states; S 3 , S4 and S 5 . As in (b), rupture events were not observed but the initial S 0 could be identified. ( d ) Plot showing the 4 R-loop states identified by HMM analysis and their probability of occupation (P r ) from multiple traces ( N =34), with state positions confirmed from Gaussian fitting. Box width corresponds to the full width at half maximum of each peak. P r Error bars are SD in the turn positions measured by HMM. Errors bars in turn values are the s.d from the Gaussian peak fitting. State S 4 (pink) shows maximum occupation. The downstream DNA breathing events (in blue) show more stability and frequency than observed for Wt Cas12a . ( e ) Pie charts of percentage of traces showing 3, 4 or 5 states for Wt and W355A Cas12a events. ( f ) Cartoon representation of the R-loops for each state. ( g ) Box plots comparing rupture event probability and main R-loop size measured from HMM analysis for WT (red, N=34) and W355A (blue, N=34) Cas12a.

Article Snippet: The histograms of turn values of each state were then separately fitted with a gaussian model (in Origin Lab) to extract the state positions.

Techniques: