Corrigendum: Chromatin structure and context-dependent sequence features control prime editing efficiency

[This corrects the article DOI: 10.3389/fgene.2023.1222112.].

Chromatin structure and context-dependent sequence features control prime editing efficiency

Prime editing (PE) is a highly versatile CRISPR-Cas9 genome editing technique. The current constructs, however, have variable efficiency and may require laborious experimental optimization. This study presents statistical models for learning the salient epigenomic and sequence features of target sites modulating the editing efficiency and provides guidelines for designing optimal PEs. We found that both regional constitutive heterochromatin and local nucleosome occlusion of target sites impede editing, while position-specific G/C nucleotides in the primer-binding site (PBS) and reverse transcription (RT) template regions of PE guide RNA (pegRNA) yield high editing efficiency, especially for short PBS designs. The presence of G/C nucleotides was most critical immediately 5' to the protospacer adjacent motif (PAM) site for all designs. The effects of different last templated nucleotides were quantified and observed to depend on the length of both PBS and RT templates. Our models found AGG to be the preferred PAM and detected a guanine nucleotide four bases downstream of the PAM to facilitate editing, suggesting a hitherto-unrecognized interaction with Cas9. A neural network interpretation method based on nonextensive statistical mechanics further revealed multi-nucleotide preferences, indicating dependency among several bases across pegRNA. Our work clarifies previous conflicting observations and uncovers context-dependent features important for optimizing PE designs.

Chromatin structure and context-dependent sequence features control prime editing efficiency

Prime editor (PE) is a highly versatile CRISPR-Cas9 genome editing technique. The current constructs, however, have variable efficiency and may require laborious experimental optimization. This study presents statistical models for learning the salient epigenomic and sequence features of target sites modulating the editing efficiency and provides guidelines for designing optimal PEs. We found that both regional constitutive heterochromatin and local nucleosome occlusion of target sites impede editing, while position-specific G/C nucleotides in the primer binding site (PBS) and reverse transcription (RT) template regions of PE guide-RNA (pegRNA) yield high editing efficiency, especially for short PBS designs. The presence of G/C nucleotides was most critical immediately 5' to the protospacer adjacent motif (PAM) site for all designs. The effects of different last templated nucleotides were quantified and seen to depend on both PBS and RT template lengths. Our models found AGG to be the preferred PAM and detected a guanine nucleotide four bases downstream of PAM to facilitate editing, suggesting a hitherto-unrecognized interaction with Cas9. A neural network interpretation method based on nonextensive statistical mechanics further revealed multi-nucleotide preferences, indicating dependency among several bases across pegRNA. Our work clarifies previous conflicting observations and uncovers context-dependent features important for optimizing PE designs.

Development of a multi-color gas puff imaging diagnostic on HL-2A tokamak

A Multi-Color (MC) gas puff imaging diagnostic has been developed on HL-2A tokamak. This diagnostic can simultaneously measure two-dimensional (2D, radial, and poloidal) electron density and temperature distributions with a good spatial resolution of 2.5 × 2.5 mm² and a temporal resolution of about 100 µs at best in edge plasmas. The 2D electron density and temperature distributions are inferred from the ratios of intensities of three different neutral helium emission lines; therefore, it is also referred to as helium beam probe or beam emission spectroscopy on thermal helium. A compact light splitter is used to split the inlet visible emission beam into four channels, and the specific neutral helium lines of the wavelengths λ₁ = 587.6 nm, λ₂ = 667.8 nm, λ₃ = 706.5 nm, and λ₄ = 728.1 nm are measured, respectively. This MC diagnostic has been experimentally tested and calibrated on a linear magnetic confinement device Peking University Plasma Test device, and the measured 2D electron density and temperature distributions are compared with the Langmuir probe measurements.

[Therapeutic effect of ginkgo biloba extract on postoperative delirium in aged patients]

Objective: To observe whether Ginkgo biloba extract (EGb761) can improve postoperative delirium in elderly patients. Methods: Eighty elderly patients undergoing tumor surgery at Zhejiang Cancer Hospital and complicated with postoperative delirium(POD) between June 2013 and July 2016 were randomly divided into treatment group (group A) and control group (group B) according to the random number table method. Patients in group A received ginkgo biloba extract (EGb761) drops oral treatment (3 times/d, 80 mg each time) in addition to oxygen inhalation and appeasement treatment. Patients in group B underwent routine oxygen inhalation and appeasement treatment. POD assessment was performed twice between the hours of 8: 00 am and 8: 00 pm daily after the diagnosis of POD. Observed indicators include sex ratio, age, body mass index (BMI), educated level, type of surgery, anesthesia method, duration of surgery, intraoperative mean arterial blood pressure, intraoperative blood loss, type of POD, visual analogue scale (VAS) scores when diagnosis of POD, the onset time of POD, initial RASS scores, duration of POD. Results: A total of 80 patients with POD were enrolled, 23 patients were excluded for did not cooperate with the tests of POD or refused to participate in the study. Finally, 57 elderly patients completed the study, 29 patients in the medication group (A group) and 28 patients in the control group (B group). There was no significant difference in sex ratio, age, BMI, education level, operation type, anesthesia method, operation duration, intraoperative mean arterial pressure, intraoperative blood loss, POD type and VAS score (all P>0.05). There was no significant difference between the two groups in POD onset time and initial RASS score (all P>0.05). The duration of POD in group A and group B was 16 (16)h and 48 (35) h respectively, the difference was statistically significant (U=161.500, P<0.001). Conclusion: Ginkgo biloba extract (EGb761) can shorten the course of POD in elderly patients.

Coiled-coil interactions mediate serine integrase directionality

Serine integrases are bacteriophage enzymes that carry out site-specific integration and excision of their viral genomes. The integration reaction is highly directional; recombination between the phage attachment site attP and the host attachment site attB to form the hybrid sites attL and attR is essentially irreversible. In a recent model, extended coiled-coil (CC) domains in the integrase subunits are proposed to interact in a way that favors the attPxattB reaction but inhibits the attLxattR reaction. Here, we show for the Listeria innocua integrase (LI Int) system that the CC domain promotes self-interaction in isolated Int and when Int is bound to attachment sites. Three independent crystal structures of the CC domain reveal the molecular nature of the CC dimer interface. Alanine substitutions of key residues in the interface support the functional significance of the structural model and indicate that the same interaction is responsible for promoting integration and for inhibiting excision. An updated model of a LI Int•attL complex that incorporates the high resolution CC dimer structure provides insights that help to explain the unusual CC dimer structure and potential sources of stability in Int•attL and Int•attR complexes. Together, the data provide a molecular basis for understanding serine integrase directionality.

Expression of an alfalfa (Medicago sativa L.) peroxidase gene in transgenic Arabidopsis thaliana enhances resistance to NaCl and H2O2

Peroxidases (PODs) are enzymes that play important roles in catalyzing the reduction of H2O2 and the oxidation of various substrates. They function in many different and important biological processes, such as defense mechanisms, immune responses, and pathogeny. The POD genes have been cloned and identified in many plants, but their function in alfalfa (Medicago sativa L.) is not known, to date. Based on the POD gene sequence (GenBank accession No. L36157.1), we cloned the POD gene in alfalfa, which was named MsPOD. MsPOD expression increased with increasing H2O2. The gene was expressed in all of the tissues, including the roots, stems, leaves, and flowers, particularly in stems and leaves under light/dark conditions. A subcellular analysis showed that MsPOD was localized outside the cells. Transgenic Arabidopsis with MsPOD exhibited increased resistance to H2O2 and NaCl. Moreover, POD activity in the transgenic plants was significantly higher than that in wild-type Arabidopsis. These results show that MsPOD plays an important role in resistance to H2O2 and NaCl.

Minimally invasive manipulative reduction with poking k-wire fixation in the treatment of various types of calcaneal fractures

OBJECTIVE

The aim of this study is to investigate the safety and clinical efficacy of minimally invasive manipulative reduction with poking k-wire fixation in the treatment of various types of calcaneal fractures.

PATIENTS AND METHODS

Between July 2012 and July 2014, a prospective parallel controlled study was conducted on 96 patients with closed calcaneal fractures who were admitted to our institution. These patients were randomly divided into two groups, with 48 in each group. Patients in plate group were treated using open reduction and internal fixation, whereas those of manipulation group were treated with minimally invasive manipulative reduction with poking k-wire fixation. All patients were followed up for six months to assess the postoperative recovery and complications. Kerr's scale was adopted to evaluate the functional recovery of fractured calcaneus.

RESULTS

A mean healing duration of 9.48 ± 1.92 weeks was achieved in patients of plate group compared with a healing duration of 9.35 ± 1.66 weeks in those of manipulation group, with no statistical significance (p > 0.05). Complications occurred in 20 cases in plate group versus in seven cases in manipulation group with significant difference (p < 0.05). As for Sanders type II fracture, among patients with compression fracture and tongue type fracture, > 70% of patients achieved with excellent and good outcomes in both groups with no significant difference in clinical efficacy (p > 0.05). The rate of excellent and good outcomes in Sanders type III compression fractures was lower in manipulation group than in plate group (p < 0.05). As for Sanders type II fractures, the Kerr's score of tongue type fractures in manipulation group was higher than that in plate group, and comparison within manipulation group showed that the score of tongue type fractures was significantly higher than that of compression fractures (p < 0.05). However, as for Sanders type III fractures, the score of tongue type fractures in manipulation group was significantly higher than that in plate group, and the score of compression fractures in plate group was significantly higher than that in manipulation group (p < 0.05).

CONCLUSIONS

Minimally invasive manipulative reduction with poking k-wire fixation is suitable for the treatment of Sanders type II tongue type and compression calcaneal fractures, as well as the treatment of Sanders type III tongue type fractures with several advantages, including easy operation, lower cost, fewer complications and favorable recovery.

18F-fluorodeoxyglucose positron emission tomography imaging in brain tumours: the Western Australia positron emission tomography/cyclotron service experience

(18)F-fluorodeoxyglucose positron emission tomography (FDG-PET) scans in the first 49 patients referred with either possible brain tumour or brain tumour recurrence were reviewed. FDG-PET imaging was reported with reference to anatomical imaging. Based on the report the FDG study was classified as either positive or negative for the presence of tumour. Thirty-eight cases were included in the analysis, 21 having pathological data and 17 with diagnostic clinical follow up. Eleven were excluded, as they had inadequate follow-up data. Of the 21 cases with pathology, 18 were shown to have tumour. In this group there were five false-negative scans and two false-positive PET scans. Seventeen cases were assessed by clinical follow up, nine were considered to have been tumour. There were two false negatives with one false positive. The overall sensitivity, specificity and positive and negative predictive values were 74, 73, 87 and 53% respectively. This is similar to figures previously quoted in published work. Despite relatively limited numbers, the utility of FDG PET imaging in our hands is similar to published reports. With a positive predictive value of 87%, a positive FDG study indicates a high likelihood that there is brain tumour present. A negative study does not exclude the presence of tumour.