PAMless SpRY exhibits a preference for the seed region for efficient targeting

Protospacer-adjacent motif (PAM) recognition licenses Cas nucleases for genome engineering applications, thereby restricting gene targeting to PAM-containing regions. Protein engineering has led to PAM-relaxed SpCas9 variants like SpG and SpRY. Given the evolved role of PAMs in facilitating target-searching kinetics, it remains unclear how these variants quickly locate their targets. We show that SpG and SpRY exhibit a preference for the seed region. To compensate for the relaxed PAM recognition, SpRY has evolved a sequence preference for the seed region through interactions with A61R and A1322R. Furthermore, SpCas9 exhibits a significant decrease in target search kinetics on high-PAM-density DNA, slowing down up to three orders of magnitude compared to low-PAM-density DNA, suggesting the necessity for sequence recognition even in PAM-relaxed variants. This underscores the importance of considering Cas9 target-searching kinetics in SpCas9 PAMless engineering, providing valuable insights for further PAMless Cas9 protein engineering efforts.

[Comparison of the clinical efficacy of all-inside arthroscopic lateral ligament augmentation procedure and Broström procedure for the treatment of chronic lateral rotational ankle instability]

Objective: To compare the clinical efficacy of patients with chronic lateral rotational ankle instability(CLRAI) after all-inside arthroscopic lateral ligament augmentation procedure and Broström procedure. Methods: This is a retrospective cohort study. The clinical and imaging data of 106 CLRAI patients were collected at the Xuzhou Central Hospital from January 2021 to December 2022. The patients included 55 males and 51 females with an age of (32.6±8.2) years (range: 16 to 50 years). All patients were treated under all-inside arthroscopic, and were divided into Broström-Gould surgery group (n=54) and Broström surgery group (n=52) according to different ligament repair methods. At 3, 6, and 12 months after surgery, ankle inversion stress tests and anterior drawer tests were used to examine the stability of the ankle joint and observe gait. The American Orthopedic Foot and Ankle Society ankle hindfoot scale (AOFAS-AH) and Karlsson ankle function score (KAFS) were used to assess ankle function; Tegner score was used to assess the patient's level of exercise; the foot and ankle outcome score(FAOS)(including score of symptoms,pain,function, daily living,function, sports and recreational activities (sport); quality of life (QOL)) was used to assess the patient's daily activity ability. Comparisons of data were made using independent sample t test, repeated measures analysis of variance, LSD multiple comparison method, χ2 test or Mann-Whitney U test. Results: All operations were successfully accomplished. All incisions healed by first intention, without evidence of postoperative complications of implant rejection, ligation reaction, and nerve and vessel injury. All patients were followed up at 3, 6, and 12 months after surgery. Ankle varus stress test and anterior drawer test were negative. No evidence supporting lateral ankle instability was obtained. All patients eventually regained normal gait. No patients underwent revision surgery. Repeated measurement analysis of variance showed that AOFAS-AH, Tegner, KAFS and FAOS scores in the Brostrom-Gould group and the Brostrom group were significantly higher than those before surgery (P<0.01). The change trends of Tegner score and FAOS-sport score were significantly different between the two groups (F=18.839, P<0.01; F=8.169, P=0.005). Multiple comparisons revealed that at 3-, 6-and 12-month follow-up, the Tegner scores ((3 months: 3.7±0.5 vs. 3.3±0.5, t=-3.980, P<0.01; 6 months: 4.4±0.6 vs. 3.8±0.7, t=-4.792,P<0.01;12 months: 5.8±0.9 vs. 5.1±1.0, t=-3.889,P<0.01)), sport scores ((3 months: 82.5±3.7 vs. 79.3±3.8, LSD-t=-4.316, P<0.01; 6 months: 88.5±4.9 vs. 85.7±3.8, LSD-t=-3.312,P=0.001;12 months: 90.1±4.3 vs. 88.2±5.1, LSD-t=-2.112,P=0.037)) in the Broström-Gould surgery group were higher than those in the Broström surgery group, with statistical significances. Conclusions: Both Broström-Gould and Broström procedures under all-inside arthroscopic can make ankle stability and improve ankle function in the treatment of CLRAI. However, the former maybe shorten the time to return to exercise and achieve higher motor function.

Recent advances in CRISPR-Cas9-based genome insertion technologies

Programmable genome insertion (or knock-in) is vital for both fundamental and translational research. The continuously expanding number of CRISPR-based genome insertion strategies demonstrates the ongoing development in this field. Common methods for site-specific genome insertion rely on cellular double-strand breaks repair pathways, such as homology-directed repair, non-homologous end-joining, and microhomology-mediated end joining. Recent advancements have further expanded the toolbox of programmable genome insertion techniques, including prime editing, integrase coupled with programmable nuclease, and CRISPR-associated transposon. These tools possess their own capabilities and limitations, promoting tremendous efforts to enhance editing efficiency, broaden targeting scope and improve editing specificity. In this review, we first summarize recent advances in programmable genome insertion techniques. We then elaborate on the cons and pros of each technique to assist researchers in making informed choices when using these tools. Finally, we identify opportunities for future improvements and applications in basic research and therapeutics.

Preoperative CT histogram analysis to predict the expression of Ki-67 in solid pseudopapillary tumours of the pancreas

AIM

To explore the value of preoperative computed tomography (CT) histogram features in predicting the expression status of Ki-67 in patients with solid pseudopapillary pancreatic tumours (SPTP).

MATERIALS AND METHODS

This retrospective study analysed venous phase CT images of 39 patients with SPTP confirmed at surgery and histopathology and measured using the Ki-67 proliferation index from November 2015 to February 2022. According to the Ki-67 proliferation index, they were divided into high expression (Ki-67 ≥ 4%) and low expression (Ki-67 < 4%) groups. The histogram features of quantitative parameters were extracted using MaZda software, and the quantitative parameters of CT histograms were compared between groups. The receiver operating characteristic (ROC) curves of the patients were plotted according to the parameters, with statistically significant differences. The area under the curve (AUC), sensitivity, and specificity were calculated, and the effectiveness of the histogram parameters in predicting Ki-67 expression was analysed and evaluated.

RESULTS

In total, 27 SPTP patients were enrolled, including 11 with high expression of Ki-67 and 16 with low expression. Comparative analysis of the Ki-67 high- and low-expression groups revealed a statistically significant in necrosis and variance (p<0.05). ROC curve analysis showed that the AUC of necrosis and variance predicting Ki-67 expression status were 0.753 and 0.841, the sensitivities were 81.8% and 81.3%, and the specificities were 68.7% and 81.8%, respectively.

CONCLUSION

Preoperative CT histogram features help predict Ki-67 expression status in patients with SPTP.

Dynamic stabilization of ablative Rayleigh-Taylor instability in the presence of a temporally modulated laser pulse

This paper presents a numeric study of the dynamic stabilization of the ablative Rayleigh-Taylor instability (ARTI) in the presence of a temporally modulated laser pulse. The results show that the specially modulated laser produces a dynamically stabilized configuration near the ablation front. The physical features of the relevant laser-driven parameters in the unperturbed ablative flows have been analyzed to reveal the inherent stability mechanism underlying the dynamically stabilized configuration. A single-mode ARTI for the modulated laser pulse is first compared with that of the unmodulated laser pulse. The results show that the modulated laser stabilizes the surface perturbations and reduces the linear growth rate and enhancement of the cutoff wavelength. For multimode perturbations, the dynamic stabilization effect of the modulated laser pulse contributes to suppress the small-scale structure and reduce the width of the mixing layer. Moreover, the results show that the stabilization effect of the modulated laser pulse decreases as the maximum wavelength increases.

Value of spectral CT parameters in predicting the efficacy of neoadjuvant chemotherapy for gastric cancer

AIM

To investigate the value of pre-chemotherapy spectral computed tomography (CT) parameters in predicting neoadjuvant chemotherapy (NAC) response in gastric cancer (GC).

MATERIALS AND METHODS

Sixty patients with GC who received NAC and underwent spectral CT examination before chemotherapy were enrolled retrospectively and divided into a responsive group and a non-responsive group according to the postoperative pathological tumour regression grade. Clinical characteristics were collected. The iodine concentration (IC), water concentration (WC), and effective atomic number (Eff-Z) of the portal venous phases were measured before chemotherapy, and IC was normalised to that of the aorta to provide the normalised IC (NIC). An independent samples t-test, Mann-Whitney U-test, or chi-square test was used to analyse the differences between the two groups, and the receiver operating curve (ROC) was used to evaluate the predictive performance of different variables.

RESULTS

The neutrophil-to-lymphocyte ratio (NLR) was lower in the responsive group than in the non-responsive group (p<0.05). IC, NIC, and Eff-Z values were significantly higher in the responsive group than in the non-responsive group (p<0.01). The areas under the ROC curves for the NLR, IC, NIC, and Eff-Z were 0.694, 0.688, 0.799, and 0.690, respectively. The combination of NIC, Eff-Z, and NLR values showed good diagnostic performance in predicting response to NAC in GC, with an area under the ROC curve of 0.857, 76.92% sensitivity, 80% accuracy, and 85.71% specificity.

CONCLUSION

Spectral CT parameters may serve as non-invasive tools for predicting the response to NAC in patients with GC.

Effects of oleanolic acid on acute liver injury triggered by lipopolysaccharide in broiler chickens

1. Infectious injury caused by lipopolysaccharide (LPS), a metabolite of gram-negative bacteria, can induce stress responses in animals and is a significant cause of morbidity and mortality in young birds. The purpose of this study was to investigate the effects of dietary supplementation with oleanolic acid (OA) on acute liver injury in broiler chickens challenged with LPS.2. In total, 120 broiler chickens were randomly divided into six groups and fed a basal diet containing 0, 50, 100, or 200 mg/kg OA or 100 mg/kg aureomycin. On d 15, broiler chickens were injected with either LPS or an equivalent volume of normal saline. Six hours after LPS injection, two broiler chicks were randomly selected for sampling in each replicate.3. The results indicated that dietary aureomycin was ineffective in alleviating LSP-associated liver injury, but protected broiler chickens from LPS-induced liver damage. This promoted a significant reduction in the levels of malondialdehyde and an increase in the levels of superoxide dismutase in liver. In addition, OA was found to cause significant reductions in the relative expression of IL-1β, IL-6, and TNF-α in broiler liver tissues, whereas the relative expression of IL-10 was significantly increased.4. In conclusion, oleanolic acid can alleviate oxidative stress and injury in the livers of broiler chickens induced by lipopolysaccharide. Consequently, oleanolic acid has potential utility as a novel anti-inflammatory and antioxidant feed additive.

[Effect of hollow compression screw internal fixation in treating McCrory-Bladin type Ⅱ lateral process fracture of the talus: open versus arthroscopy surgery]

In order to explore the clinical efficacy of hollow compression screw internal fixation in the treatment of lateral process fracture of the talus under open surgery versus arthroscopy procedure, a retrospective cohort study was conducted to analyze the clinical data of 33 patients with lateral process fracture of the talus admitted to Xuzhou Central Hospital from January 2019 to December 2021. There were 19 males (19 feet) and 14 females (14 feet), aged 18 to 50 years, with an average age of (32.2±9.3) years. According to the modified McCrory-Bladin classification, all patients were classified as type Ⅱ. Based on the different surgical methods, the patients were divided into the arthroscopy group (21 cases, treated with double-tunnel subtalar arthroscopy combined with hollow compression screw internal fixation) and the open group (12 cases, treated with open reduction and internal fixation with hollow compression screw). The operation time was observed and the surgical effects were evaluated using the visual analogue scale (VAS) of pain, the American Orthopedic Foot and Ankle Society (AOFAS) ankle-hindfoot score, the Foot Function Index (FFI), and the Foot and Ankle Ability Measure (FAAM), which includes the FAAM-ADL (activity of daily living subscale) and the FAAM-S (sport subscale). All the patients of the two groups achieved stage Ⅰ wound healing. On the first day after the operation, the mean VAS score of the arthroscopy group was 2.4±0.7, which was significantly lower than that of the open group (3.4±1.6) (P=0.020). No significant difference was observed in terms of the follow-up time, operation time and AOFAS score between the two groups (all P>0.05). The FFI score of the arthroscopy group was significantly lower than that of the open group, and the FAAM-ADL and FAAM-S scores were significantly higher than those in the open group (all P<0.05). Two cases of dorsal foot numbness occurred in the open group after the operation, and the incidence of complications was not significantly different from that of the arthroscopy group (P=0.054). For McCrory-Bladin type Ⅱ lateral process fracture of the talus, the use of compression screw internal fixation could achieve reliable results, however, compared to open surgery, arthroscopy procedure obtained mini trauma and better functions.

[Long-term trend of gastric cancer survival rate in Qidong, 1972-2016]

Objective: The survival rate of gastric cancer cases in the whole population of Qidong City of Jiangsu Province from 1972 to 2016 was analyzed to provide a data basis for prevention and control of gastric cancer. Methods: The observed survival rate (OSR) was calculated by the life table method, the relative survival rate (RSR) was calculated by SURV 3.01 software, and the trend test was performed by Hakulinen's likelihood ratio test. Age-standardized relative survival rate (ARSR) was calculated using the International Cancer Survival Standard (ICSS). The Joinpoint regression model was used to calculate the average annual percentage change (AAPC) of survival rate, and the trend analysis of the overall survival rate of gastric cancer and the survival rates of different sexes and ages was conducted. The ARIMA model was used to predict the survival rate. Results: From 1972 to 2016, there were 18 067 new cases of gastric cancer in Qidong City. The OSRs at 1, 5, and 10 years were 37.12%, 17.16%, and 12.86%, respectively, and the RSRs at 1, 5, and 10 years were 38.83%, 21.73%, and 21.20%. Dividing 1972-2016 into 9 periods at 5-year intervals, compared with 1972-1976, the 5-year RSR in 2012-2016 increased from 12.53% to 36.26%, and the RSR in the 9 periods increased with statistical significance (χ(2)=747.19, P<0.001). Both OSR and RSR were slightly higher in men than in women, and decreased with age. The AAPC results showed that the AAPC of the 5-year RSR of gastric cancer in Qidong was 2.88%, 2.75% in males and 3.05% in females, and the upward trend was statistically significant (P<0.001). From 1972 to 2016, the 5-year RSR of gastric cancer in all age groups showed an upward trend. Except for the 35-44-year-old group (AAPC=1.07%, t=2.16, P=0.067), the age groups had statistical significance ( AAPC=2.59% in the 45-54-year-old group, AAPC=3.19% in the AAPCs of other 55-64-year-old group, AAPC=3.99% in the 65-74-year-old group, and AAPC=2.97% in the 75-year-old group, all P<0.05). The prediction results of the ARIMA model showed that in 2026, the 5-year OSR of gastric cancer in Qidong will increase to 39.82%, and the 5-year RSR will increase to 49.23%. Conclusion: The overall survival rate of registered gastric cancer cases in Qidong has been greatly improved, but there is still large room for improvement. More attention should be paid to the prevention and treatment of gastric cancer.

Discrimination between microcystic meningioma and atypical meningioma using whole-lesion apparent diffusion coefficient histogram analysis

AIM

To explore the value of whole-lesion apparent diffusion coefficient (ADC) histogram analysis in discriminating microcystic meningioma (MCM) from atypical meningioma (AM).

MATERIALS AND METHODS

Clinical and preoperative MRI data of 20 patients with MCM and 26 patients with AM were analysed retrospectively. Whole-lesion apparent diffusion coefficient (ADC) histogram analysis was performed on each patient's lesion to obtain histogram parameters, including mean, variance, skewness, kurtosis, the 1st (ADCp1), 10th (ADCp10), 50th (ADCp50), 90th (ADCp90), and 99th (ADCp99) percentiles of ADC. The differences between the ADC histogram parameters of the two tumours were compared, and the receiver operating characteristic (ROC) curve was used to assess the diagnostic performance of statistically significant parameters in distinguishing the two tumours.

RESULTS

The mean, ADCp1, ADCp10, ADCp50, and ADCp90 of MCM were greater than those of AM, and significant differences were observed in these parameters between MCM and AM (all p<0.05). ROC analysis showed that the mean had the highest area under the curve value (AUC) in distinguishing the two tumours (AUC = 0.852), when using 120.46 × 10^-6 mm²/s as the optimal threshold, the sensitivity, specificity, accuracy, positive predictive value, and negative predictive value for discriminating the two groups were 84.6%, 75%, 80.4%, 81.5%, and 78.9%, respectively.

CONCLUSION

Histogram analysis based on whole-lesion ADC maps was useful for discriminating between MCM from AM preoperatively, with the mean being the most promising potential parameter.

Bloom helicase mediates formation of large single-stranded DNA loops during DNA end processing

Bloom syndrome (BS) is associated with a profoundly increased cancer risk and is caused by mutations in the Bloom helicase (BLM). BLM is involved in the nucleolytic processing of the ends of DNA double-strand breaks (DSBs), to yield long 3' ssDNA tails that serve as the substrate for break repair by homologous recombination (HR). Here, we use single-molecule imaging to demonstrate that BLM mediates formation of large ssDNA loops during DNA end processing. A BLM mutant lacking the N-terminal domain (NTD) retains vigorous in vitro end processing activity but fails to generate ssDNA loops. This same mutant supports DSB end processing in cells, however, these cells do not form RAD51 DNA repair foci and the processed DSBs are channeled into synthesis-dependent strand annealing (SSA) instead of HR-mediated repair, consistent with a defect in RAD51 filament formation. Together, our results provide insights into BLM functions during homologous recombination.

[Validation of a hyperkalemia prediction model in chronic kidney disease]

Objective: To validate the accuracy and consistency of a previously established prediction model for the occurrence of hyperkalemia in non-dialytic chronic kidney disease (CKD) patients. Methods: All patients diagnosed with CKD from Outpatient Department of Shanghai Changzheng Hospital during the 4th quarter of 2020 were recruited. Demographic data, clinical characteristics and prediction model-related parameters of the patients were collected and analyzed. Receiver operating characteristic (ROC) curve was drawn to evaluate the effectiveness of the model, and the specificity and sensitivity were calculated based on the cut-off value of 4 obtained from the previous model. The improved Hanley method was used to compare the area under the curve (AUC) between the previously established model and current validation dataset. The calibration curve was drawn to verify the model calibration degree. Results: A total of 434 patients diagnosed with non-dialytic CKD were enrolled, among whom 233 were males and 201 were females, with an average age of (55±16) years. According to the measured serum potassium values, the prevalence of hyperkalemia was 7.6%. And 33 patients were allocated to the hyperkalemia group and 401 patients were to the normal potassium group. There was no significant difference in age and sex between the two groups (both P>0.05). A combination of hyperkalemia and heart failure (27.3% vs 3.7%, P<0.001), diabetes (42.4% vs 19.7%, P=0.002), and acidosis (51.5% vs 7.0%, P<0.001) were more frequently in the hyperkalemia group, compared with the normal serum potassium group. Patients in the hyperkalemia group were more likely to have a past history of serum potassium ≥5.0 mmol/L (48.5% vs 2.5%, P<0.001). For the drugs that could increase serum potassium levels, there was a significant correlation between Chinese herbal medicine and the occurrence of hyperkalemia, while renin-angiotensin-aldosterone system inhibitor (RAASi) and potassium supplementation showed no significant difference between the two groups. The results of ROC curve analysis showed that the AUC was 0.914, with the sensitivity of 84.8% and the specificity of 79.8% with the cut-off value of 4. The difference of AUC between the previously established risk assessment model of hyperkalemia in patients with non-dialytic CKD and current validation dataset was not statistically significant (Z=1.924, P=0.054), indicating the good accuracy and consistency of the prediction model. In the calibration curve, when the predicted risk of patients was below 0.4 or above 0.6, the prediction effect of the model was better. Conclusion: The previously-constructed hyperkalemia prediction model in non-dialytic CKD patients had good accuracy and consistency, and could be used to evaluate the risk of hyperkalemia in all stages of non-dialytic CKD patients.

DNA Repair Pathway Choices in CRISPR-Cas9-Mediated Genome Editing

Many clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-based genome editing technologies take advantage of Cas nucleases to induce DNA double-strand breaks (DSBs) at desired locations within a genome. Further processing of the DSBs by the cellular DSB repair machinery is then necessary to introduce desired mutations, sequence insertions, or gene deletions. Thus, the accuracy and efficiency of genome editing are influenced by the cellular DSB repair pathways. DSBs are themselves highly genotoxic lesions and as such cells have evolved multiple mechanisms for their repair. These repair pathways include homologous recombination (HR), classical nonhomologous end joining (cNHEJ), microhomology-mediated end joining (MMEJ) and single-strand annealing (SSA). In this review, we briefly highlight CRISPR-Cas9 and then describe the mechanisms of DSB repair. Finally, we summarize recent findings of factors that can influence the choice of DNA repair pathway in response to Cas9-induced DSBs.

[Establishment of animal models of epidermal growth factor receptor inhibitor-related rashes]

OBJECTIVE

To establish animal models epidermal growth factor receptor inhibitor-related skin rashes using cetuximab, gefitinib or erlotinib.

OBJECTIVE

Female SCID mice were randomly divided into blank control group and high-, moderate-, and low-dose cetuximab groups. The mice in control group received intraperitoneal injection of saline, and those in the 3 cetuximab groups were injected with 80, 40, and 20 mg/kg cetuximab (3 times a week for 4 weeks), respectively. The general skin appearance and skin pathologies of the mice were observed. Female BN rats were randomly divided into blank group, ovalbumin group, gefitinib group and erlotinib group, and in the latter 3 groups, the rats were given ovalbumin (1 mg), gefitinib (37.5 mg/kg), and erlotinib (23.5 mg/kg) by lavage once daily for 45 days, respectively. Skin pathologies of the rats were observed, and serum levels of TNF-α, IL-6 and other inflammatory factors were detected using ELISA.

OBJECTIVE

Intraperitoneal injection of cetuximab did not induce typical skin rashes, scabs or obvious skin inflammation in the mice. In female BN rats, lavage of gefitinib caused obvious skin rashes, scabs and exudation, and obvious inflammatory cell infiltration, keratinosis, spinous layer release and epidermal thickening were observed in the skin. No obvious skin inflammation were observed in the rats in the control, ovalbumin or erlotinib groups. While IgE (P=0.061) and TNF-α concentrations (P=0.057) did not differ significantly among the groups, serum levels of IL-6 was significantly higher in gefitinib group than in the blank control group (P=0.016) but similar between erlotinib group and the blank group (P=0.910).

OBJECTIVE

Intraperitoneal injection of cetuximab can not induce epidermal growth factor receptor inhibitor-related skin rashes in SCID mice. Lavage of gefitinib, but not erlotinib, can be used to establish models of epidermal growth factor receptor inhibitor-related rashes in BN rats.

RADX controls RAD51 filament dynamics to regulate replication fork stability

The RAD51 recombinase forms nucleoprotein filaments to promote double-strand break repair, replication fork reversal, and fork stabilization. The stability of these filaments is highly regulated, as both too little and too much RAD51 activity can cause genome instability. RADX is a single-strand DNA (ssDNA) binding protein that regulates DNA replication. Here, we define its mechanism of action. We find that RADX inhibits RAD51 strand exchange and D-loop formation activities. RADX directly and selectively interacts with ATP-bound RAD51, stimulates ATP hydrolysis, and destabilizes RAD51 nucleofilaments. The RADX interaction with RAD51, in addition to its ssDNA binding capability, is required to maintain replication fork elongation rates and fork stability. Furthermore, BRCA2 can overcome the RADX-dependent RAD51 inhibition. Thus, RADX functions in opposition to BRCA2 in regulating RAD51 nucleofilament stability to ensure the right level of RAD51 function during DNA replication.

Single-molecule visualization of human RECQ5 interactions with single-stranded DNA recombination intermediates

RECQ5 is one of five RecQ helicases found in humans and is thought to participate in homologous DNA recombination by acting as a negative regulator of the recombinase protein RAD51. Here, we use kinetic and single molecule imaging methods to monitor RECQ5 behavior on various nucleoprotein complexes. Our data demonstrate that RECQ5 can act as an ATP-dependent single-stranded DNA (ssDNA) motor protein and can translocate on ssDNA that is bound by replication protein A (RPA). RECQ5 can also translocate on RAD51-coated ssDNA and readily dismantles RAD51-ssDNA filaments. RECQ5 interacts with RAD51 through protein-protein contacts, and disruption of this interface through a RECQ5-F666A mutation reduces translocation velocity by ∼50%. However, RECQ5 readily removes the ATP hydrolysis-deficient mutant RAD51-K133R from ssDNA, suggesting that filament disruption is not coupled to the RAD51 ATP hydrolysis cycle. RECQ5 also readily removes RAD51-I287T, a RAD51 mutant with enhanced ssDNA-binding activity, from ssDNA. Surprisingly, RECQ5 can bind to double-stranded DNA (dsDNA), but it is unable to translocate. Similarly, RECQ5 cannot dismantle RAD51-bound heteroduplex joint molecules. Our results suggest that the roles of RECQ5 in genome maintenance may be regulated in part at the level of substrate specificity.

[Cost-effectiveness of primary prophylaxis with PEG-rhG-CSF in early-stage breast cancer patients receiving chemotherapy in China]

Objective: To evaluate the cost effectiveness of primary prophylaxis (PP) with pegylated recombinant human granulocyte colony stimulating factor (PEG-rhG-CSF), PP with recombinant human granulocyte colony stimulating factor (rhG-CSF) and no prophylaxis in women with early-stage breast cancer in China. Methods: Two phase Markov models were constructed for a hypothetical cohort of patients aged 45 with stage Ⅱ breast cancer. The first phase modelled costs and outcomes of 4 cycles docetaxel combined with cyclophosphamide [TC×4, febrile neutropenia (FN) risk>20%] chemotherapy, which assumptions based on literature reviews, including FN rates [base-case (deterministic sensitivity analysis range), 0.29 (0.24-0.35)] and related events [FN case-fatality, 3.4 (2.7-4.1)]. Second phase modelled the long term survival which was link with the relative dose intensity (RDI) [mortality hazard ratio (HR) of RDI < 85% vs ≥85%, 1.45 (1.00-2.32)]. Clinical effectiveness, therapeutic costs, and economic utilities were estimated from peer-reviewed publications and expert opinions in case of unavailability of published evidences. Results: Compared to rhG-CSF PP and no prophylaxis, the cost of PEG-rhG-CSF PP increased to 5 208.19 RMB and 5 222.73 RMB, respectively. The quality-adjusted life-years (QALYs) enhanced to 0.066 and 0.297, respectively. Accordingly, the incremental cost effectiveness ratios (ICERs) are 79 146.3 RMB and 17 558.77 RMB per QALY, which were both below the willingness to pay (WTP) threshold of three times GDP per capita (18, 000 RMB) recommended by the WHO. Sensitivity analysis suggested that the more clinically effective the primary prophylaxis with PEG-rhG-CSF is, the more cost-effective primary prophylaxis with PEG-rhG-CSF will be. And the lower the mortality HR of RDI<85% vs ≥85% is, the more cost-effective primary prophylaxis with PEG-rhG-CSF will be. Conclusion: Although the cost of PP PEG-rhG-CSF is higher, considering the additional benefits, the administrating of PP PEG-rhG-CSF is likely to be a cost-effective alternative to PP rhG-CSF and no prophylaxis in patients with early stage breast cancer whose FN risks are more than 20% in China.

Human Condensin I and II Drive Extensive ATP-Dependent Compaction of Nucleosome-Bound DNA

Structural maintenance of chromosomes (SMC) complexes are essential for genome organization from bacteria to humans, but their mechanisms of action remain poorly understood. Here, we characterize human SMC complexes condensin I and II and unveil the architecture of the human condensin II complex, revealing two putative DNA-entrapment sites. Using single-molecule imaging, we demonstrate that both condensin I and II exhibit ATP-dependent motor activity and promote extensive and reversible compaction of double-stranded DNA. Nucleosomes are incorporated into DNA loops during compaction without being displaced from the DNA, indicating that condensin complexes can readily act upon nucleosome-bound DNA molecules. These observations shed light on critical processes involved in genome organization in human cells.

DNA Curtains Shed Light on Complex Molecular Systems During Homologous Recombination

Homologous recombination (HR) is important for the repair of double-stranded DNA breaks (DSBs) and stalled replication forks in all organisms. Defects in HR are closely associated with a loss of genome integrity and oncogenic transformation in human cells. HR involves coordinated actions of a complex set of proteins, many of which remain poorly understood. The key aspect of the research described here is a technology called "DNA curtains", a technique which allows for the assembly of aligned DNA molecules on the surface of a microfluidic sample chamber. They can then be visualized by total internal reflection fluorescence microscopy (TIRFM). DNA curtains was pioneered by our laboratory and allows for direct access to spatiotemporal information at millisecond time scales and nanometer scale resolution, which cannot be easily revealed through other methodologies. A major advantage of DNA curtains is that it simplifies the collection of statistically relevant data from single molecule experiments. This research continues to yield new insights into how cells regulate and preserve genome integrity.

Association of Dysplastic Coronoid Process with Long-Face Morphology

Vertical malocclusion is a developmental condition, resulting from complex interactions among multiple etiological factors during the growth period. As a tricky dentofacial deformity clinically, long-face (LF) morphology is characterized by excessive vertical facial growth with severe disarrangement of jaws and teeth. Since the improvement of LF patients on facial profile and occlusion is often difficult and lacks long-term stability, it becomes important to unravel the etiology of LF pattern formation for early prevention and treatment. In the current studies, we identified a transgenic mouse model that exhibited a dysplastic coronoid process and LF morphology. Although the mutant mice exhibited jaw structures and occlusion comparable to controls at birth, they all acquired typical LF morphology with anterior open bite during postnatal growth, resembling clinical features of the selected skeletal class III patients. Since the coronoid process provides an insertion site for the temporalis attachment, we examined the initial development and differentiation of the temporalis and found identical results in both control and mutant mice before E17.5 when the temporal muscle makes attachment to the coronoid process. However, thereafter, we observed altered orientation and reduced size of the cross-sectional area of the temporalis in mutant mice, which persisted to the weaning stage. Biomechanical analysis and simulation modeling further support the idea that altered morphology of the coronoid process may impair the efficiency of the vertical temporalis contraction and appears to correlate with LF formation. Consistently, we present evidence that a dysplastic mandibular coronoid process was also seen in some human patients with skeletal III LF morphology. Taken together, the results presented in this study establish an association of the craniofacial bony structures with vertical patterning, which will have implications in earlier prediction for clinical precaution and intervention.

Single-molecule visualization of human BLM helicase as it acts upon double- and single-stranded DNA substrates

Bloom helicase (BLM) and its orthologs are essential for the maintenance of genome integrity. BLM defects represent the underlying cause of Bloom Syndrome, a rare genetic disorder that is marked by strong cancer predisposition. BLM deficient cells accumulate extensive chromosomal aberrations stemming from dysfunctions in homologous recombination (HR). BLM participates in several HR stages and helps dismantle potentially harmful HR intermediates. However, much remains to be learned about the molecular mechanisms of these BLM-mediated regulatory effects. Here, we use DNA curtains to directly visualize the activity of BLM helicase on single molecules of DNA. Our data show that BLM is a robust helicase capable of rapidly (∼70-80 base pairs per second) unwinding extensive tracts (∼8-10 kilobases) of double-stranded DNA (dsDNA). Importantly, we find no evidence for BLM activity on single-stranded DNA (ssDNA) that is bound by replication protein A (RPA). Likewise, our results show that BLM can neither associate with nor translocate on ssDNA that is bound by the recombinase protein RAD51. Moreover, our data reveal that the presence of RAD51 also blocks BLM translocation on dsDNA substrates. We discuss our findings within the context of potential regulator roles for BLM helicase during DNA replication and repair.

Rad52 Restrains Resection at DNA Double-Strand Break Ends in Yeast

Rad52 is a key factor for homologous recombination (HR) in yeast. Rad52 helps assemble Rad51-ssDNA nucleoprotein filaments that catalyze DNA strand exchange, and it mediates single-strand DNA annealing. We find that Rad52 has an even earlier function in HR in restricting DNA double-stranded break ends resection that generates 3' single-stranded DNA (ssDNA) tails. In fission yeast, Exo1 is the primary resection nuclease, with the helicase Rqh1 playing a minor role. We demonstrate that the choice of two extensive resection pathways is regulated by Rad52. In rad52 cells, the resection rate increases from ∼3-5 kb/h up to ∼10-20 kb/h in an Rqh1-dependent manner, while Exo1 becomes dispensable. Budding yeast Rad52 similarly inhibits Sgs1-dependent resection. Single-molecule analysis with purified budding yeast proteins shows that Rad52 competes with Sgs1 for DNA end binding and inhibits Sgs1 translocation along DNA. These results identify a role for Rad52 in limiting ssDNA generated by end resection.

[Epidemiologic characteristics of fall in the elderly in urban and rural areas in Shanghai]

Objective: To understand the epidemiologic characteristics of fall in the elderly in Shanghai, as well as the differences between urban and rural areas, and provide evidence for targeted fall prevention and intervention. Methods: From January to March in 2017, a questionnaire survey was conducted in the elderly aged 60 or above selected from 7 urban communities and 6 rural communities in Shanghai to understand the epidemiologic characteristics of fall in the elderly and analyze the gender and urban-rural differences. Results: In urban area, a total of 3 386 elderly people were surveyed, in whom 441 (13.0%) had fall and 261 (7.7%) were injured after fall. In rural area, a total of 2 826 elderly people were surveyed, in whom 320 (11.3%) had fall and 169 (6.0%) were injured after fall. Fall risk in women were higher than that in men in both urban and rural areas with OR of 1.62 (95%CI: 1.42-1.86) and 1.16 (95%CI: 1.38-1.98) respectively, but the differences of fall related injury were not significant. Compared with urban areas, fall risk and fall related injury risk were both lower in rural areas with OR of 0.86 (95%CI: 0.73-0.99) and 0.74 (95%CI: 0.56-0.99). Compared with urban areas, men had lower risk for fall, and women had lower risk for fall related injury with OR of 0.68 (95%CI: 0.51-0.90) and 0.66 (95%CI: 0.47-0.93) respectively. Fall mainly occurred at home. Fall in urban area more frequently occurred on stairs, and fall in rural area more frequently occurred during farming. More than 60% of the falls had environmental risk factors. Slippery ground and uneven ground were main reasons. The incidence of fracture resulted from fall was high indicated by 89 fracture cases in urban areas (28.2%) and 64 fracture cases in rural areas (36.1%). Conclusions: The risk for fall in Shanghai had gender and urban-rural differences. Targeted intervention should be conducted according to the characteristics of fall in the elderly.

A heterologous 'prime-boost' anti-PEDV immunization for pregnant sows protects neonatal piglets through lactogenic immunity against PEDV

Abstract

Porcine epidemic diarrhoea virus (PEDV) causes severe diarrhoea in neonatal suckling piglets with a high mortality. Maternal vaccines that can induce lactogenic immunity to protect suckling piglets via colostrums and milk are pivotal for the prevention and control of PEDV infection in neonatal suckling piglets. In this study, a group of pregnant sows were first orally immunized with coated PEDV‐loaded microspheres and boosted with killed PEDV vaccines (heterologous prime‐boost). It has been detected that the levels of PEDV‐specific antibodies (IgG and IgA) in their sera and milks were higher than other negative groups (P < 0·001 or P < 0·05). Furthermore, it has been proved by the neutralization assay that the induced antibodies could significantly inhibit virus infection as compared to other negative groups (P < 0·01 or P < 0·05). Importantly, after PEDV challenge, more than 90% of the suckling piglets delivered by the sows in the heterologous prime‐boost group were completely protected. Overall, the results show that ‘heterologous prime‐boost’ form is an efficient and effective way to provide protection for suckling piglets against PEDV through lactogenic immunity.

Significance and Impact of the Study

As a widespread swine pathogen, PEDV affects the swine industry enormously. It causes enteritis in swine of all ages and is often fatal in neonatal piglets. Our data show that pregnant sows were immunized with ‘coated PEDV‐loaded microspheres + killed PEDV vaccines’ (heterologous prime‐boost immunization) could protect more than 90% suckling piglets delivered by the sows against the virus. These findings provide a new model of developing safe and effective immunizations for newborn animals against established and emerging enteric infections.

[Effects of parthenolide on estradiol-synthesizing enzyme, ER isoforms and VEGF in human endometriotic stromal cells]

Objective: To evaluate the effects of parthenolide on estradiol-synthesizing enzyme, steroidogenic acute regulatory protein (StAR), and ER isoforms,VEGF in human endometriotic stromal cells. Methods: Primary endometriotic stromal cells were treated with different concentrations (1, 5, 10 and 20 μmol/L) of parthenolide. The mRNA of StAR, ER isoforms (ERα and ERβ), PR, vascular endothelial growth factor (VEGF), interleukin-6 (IL-6), tumour necrosis factor-α (TNFα), tumour necrosis factor receptor (TNFR) 1, TNFR2 were measured by real-time PCR. The levels of estradiol and progesterone in the cell supernatant were measured by ELISA. Results: Different concentrations of parthenolide could up-regulate the mRNA of StAR in primary endometriotic stromal cells (F=5.722, P<0.05); the mRNA of StAR in the group of 20 μmol/L was significantly higher than that of the control group [2.6±0.3 versus 1.0, P<0.01]. Different concentrations of parthenolide could down-regulate the mRNA of ERα (F=6.921, P<0.01); the mRNA of ERα in the group of 20 μmol/L and 10 μmol/L were significantly lower than those of the control group [0.2±0.3 versus 0.3±0.3 versus 1.0, all P<0.05]. Different concentrations of parthenolide could down-regulate the ratios of ERα/ERβ mRNA levels (F=4.209, P<0.05). Different concentrations of parthenolide could up-regulate the mRNA of VEGF and TNFR1 (F=10.964, P<0.01; F=7.286, P<0.01). There were no statiscal significances with different concentrations of parthenolide on the mRNA of ERβ, PR, IL-6, TNFα and TNFR2, and the levels of estradiol and progesterone in the cell supernatant (all P>0.05). Conclusions: Parthenolide may regulate the expression of estradiol-synthesizing enzyme, ER isoforms and angiogenesis in endometriotic stromal cells. Parthenolide may promote the development of endometriosis.

The RecQ helicase Sgs1 drives ATP-dependent disruption of Rad51 filaments

DNA helicases of the RecQ family are conserved among the three domains of life and play essential roles in genome maintenance. Mutations in several human RecQ helicases lead to diseases that are marked by cancer predisposition. The Saccharomyces cerevisiae RecQ helicase Sgs1 is orthologous to human BLM, defects in which cause the cancer-prone Bloom's Syndrome. Here, we use single-molecule imaging to provide a quantitative mechanistic understanding of Sgs1 activities on single stranded DNA (ssDNA), which is a central intermediate in all aspects of DNA metabolism. We show that Sgs1 acts upon ssDNA bound by either replication protein A (RPA) or the recombinase Rad51. Surprisingly, we find that Sgs1 utilizes a novel motor mechanism for disrupting ssDNA intermediates bound by the recombinase protein Rad51. The ability of Sgs1 to disrupt Rad51-ssDNA filaments may explain some of the defects engendered by RECQ helicase deficiencies in human cells.

[Studies on the role of chromobox protein homolog 2 in the inhibition of progression of hepatoma]

Objective: To explore chromobox protein homolog 2 (CBX2) expressions in relation to clinical features of patients and elucidate its role in the progression of hepatocellular carcinoma. Methods: Using the Cancer Genome Atlas (TCGA) database, R language was used to analyze the distribution of differentially expressed mRNA in hepatocellular carcinoma. The different expression of CBX2 in HCC and adjacent tissues and its relationship with survival and clinical characteristics of patients were further analyzed. The expression of CBX2 in liver tissues, liver cancer tissue, and L02, HepG2 and SMMC-7721 cell lines was detected by real time-PCR and western blot. The expression of CBX2 was interfered by siRNA in hepatoma cell line. MTT, colony formation, transwell assays, and flow cytometry were used to identify the proliferation, apoptosis, invasion and clone-formation ability of HepG2 and SMMC-7721 cells after CBX2 down-regulation. According to the different data, t-test, ANOVA, chi-square test, and COX regression model were used for statistical analysis. Survival curve was plotted through Kaplan-Meier method. Results: TCGA public database analysis showed that the expression of CBX2 mRNA in hepatocellular carcinoma tissues (7.296 ± 1.6115) was significantly higher than normal liver tissues (4.706 ± 0.940) (P = 0.000). In addition, the overall survival time of patients with low CBX2 mRNA expression was significantly longer than that of patients with high CBX2 mRNA expression [(5.971 ± 0.411) years vs. (4.650 ± 0.503) years, P = 0.001]. The expression level of CBX2 mRNA was correlated with the pathological TNM stage (P = 0.025) and differentiation degree (P < 0.001) of liver cancer. COX regression analysis showed that CBX2 mRNA expression was an independent predictor of patient survival (P = 0.013). siRNA was transfected and compared with the blank control group. The transgenic ability of HepG2 and SMMC-77221 cells decreased significantly at 72h (P < 0.05) and 96h (P < 0.05), and the apoptosis rate (11.430% ± 0.215%) was higher than blank control group (6.6 00% ± 0.170%) (P = 0.003). The number of invasive cells ((both P < 0.05) and relative colony forming cells ((both P < 0.001) were significantly decreased. In 20 cases of tissue samples, the expression of CBX2 protein (relative expression level 3.020 ± 0.269) in liver cancer was higher than that in adjacent tissues (relative expression level 0.886±0.065) (P < 0.001). The overall survival time of patients with low CBX2 expression in liver cancer was longer than that of patients with high expression [(3.670 + 0.576) years vs. (0.834 + 0.153) years, P = 0.004]. Conclusion: An evident high expression of CBX2 is an independent poor prognostic factor in hepatoma. Down-regulation of CBX2 expression can inhibit the progression of liver cancer. Therefore, CBX2 may be a prognostic biomarker and a new target for HCC treatment.

Real-Time Observation of Target Search by the CRISPR Surveillance Complex Cascade

CRISPR-Cas systems defend bacteria and archaea against infection by bacteriophage and other threats. The central component of these systems are surveillance complexes that use guide RNAs to bind specific regions of foreign nucleic acids, marking them for destruction. Surveillance complexes must locate targets rapidly to ensure timely immune response, but the mechanism of this search process remains unclear. Here, we used single-molecule FRET to visualize how the type I-E surveillance complex Cascade searches DNA in real time. Cascade rapidly and randomly samples DNA through nonspecific electrostatic contacts, pausing at short PAM recognition sites that may be adjacent to the target. We identify Cascade motifs that are essential for either nonspecific sampling or positioning and readout of the PAM. Our findings provide a comprehensive structural and kinetic model for the Cascade target-search mechanism, revealing how CRISPR surveillance complexes can rapidly search large amounts of genetic material en route to target recognition.

Fluorescence-based methods for measuring target interference by CRISPR-Cas systems

Type I, II, and V CRISPR-Cas systems are RNA-guided dsDNA targeting defense mechanisms found in bacteria and archaea. During CRISPR interference, Cas effectors use CRISPR-derived RNAs (crRNAs) as guides to bind complementary sequences in foreign dsDNA, leading to the cleavage and destruction of the DNA target. Mutations within the target or in the protospacer adjacent motif can reduce the level of CRISPR interference, although the level of defect is dependent on the type and position of the mutation, as well as the guide sequence of the crRNA. Given the importance of Cas effectors in host defense and for biotechnology tools, there has been considerable interest in developing sensitive methods for detecting Cas effector activity through CRISPR interference. In this chapter, we describe an in vivo fluorescence-based method for monitoring plasmid interference in Escherichia coli. This approach uses a green fluorescent protein reporter to monitor varying plasmid levels within bacterial colonies, or to measure the rate of plasmid-loss in bacterial populations over time. We demonstrate the use of this simple plasmid-loss assay for both chromosomally integrated and plasmid-borne CRISPR-Cas systems.

Multiple eigenmodes of the Rayleigh-Taylor instability observed for a fluid interface with smoothly varying density

In this article, multiple eigen-systems including linear growth rates and eigen-functions have been discovered for the Rayleigh-Taylor instability (RTI) by numerically solving the Sturm-Liouville eigen-value problem in the case of two-dimensional plane geometry. The system called the first mode has the maximal linear growth rate and is just extensively studied in literature. Higher modes have smaller eigen-values, but possess multi-peak eigen-functions which bring on multiple pairs of vortices in the vorticity field. A general fitting expression for the first four eigen-modes is presented. Direct numerical simulations show that high modes lead to appearances of multi-layered spike-bubble pairs, and lots of secondary spikes and bubbles are also generated due to the interactions between internal spikes and bubbles. The present work has potential applications in many research and engineering areas, e.g., in reducing the RTI growth during capsule implosions in inertial confinement fusion.

Altered White Matter Microstructure in the Corpus Callosum and Its Cerebral Interhemispheric Tracts in Adolescent Idiopathic Scoliosis: Diffusion Tensor Imaging Analysis

BACKGROUND AND PURPOSE

Neural system was one of the important contributors to the etiopathogenesis of adolescent idiopathic scoliosis; additionally, the morphology of corpus callosum interconnecting both hemispheres of the brain was found to be altered morphologically. Our aim was to evaluate and compare the microstructural changes of the corpus callosum and its interhemispheric white matter fiber tracts interconnecting both cerebral hemispheres in patients with adolescent idiopathic scoliosis and matched controls using diffusion tensor imaging.

MATERIALS AND METHODS

Brain DTI was performed in 69 patients with adolescent idiopathic scoliosis (female, right thoracic/thoracolumbar curve) and 40 age-matched controls without adolescent idiopathic scoliosis (female). 2D and 3D segmentation of the corpus callosum were performed using a region-growing method, and the corpus callosum was further divided into 6 regions, including the rostrum, genu, anterior and posterior midbodies, isthmus, and splenium. The laterality index was calculated to quantify the asymmetry of the corpus callosum. Interhemispheric fiber tractography were performed using the Brodmann atlas.

RESULTS

2D ROI analysis revealed reduced fractional anisotropy in the genu and splenium (P = .075 and P = .024, respectively). Consistently reduced fractional anisotropy on the left sides of the genu and splenium was also found in 3D ROI analysis (P = .03 and P = .012, respectively). The laterality index analysis revealed a pseudo-right lateralization of the corpus callosum in adolescent idiopathic scoliosis. Interhemispheric fibers via the splenium interconnecting Brodmann 3, 1, and 2; Brodmann 17; and Brodmann 18 (corresponding to the primary somatosensory cortex and primary and secondary visual cortices) were also found to have reduced fractional anisotropy (P ≤ .05).

CONCLUSIONS

Reduced fractional anisotropy was found in the genu and splenium of the corpus callosum and corresponding interhemispheric fiber tracts interconnecting the somatosensory and visual cortices via the splenium. Our results are suggestive of altered white matter microstructure within the brain of those with adolescent idiopathic scoliosis, which could be related to abnormal brain maturation during adolescence in adolescent idiopathic scoliosis and could possibly explain the previously documented somatosensory function impairment and visuo-oculomotor dysfunction in this condition.

Genetic epidemiology of porcine epidemic diarrhoea virus circulating in China in 2012-2017 based on spike gene

A porcine epidemic diarrhoea outbreak first occurred in southern China at the end of 2010 and afterwards the disease spread throughout the country. Spike gene is divergent and important for understanding the genetic relations of porcine epidemic diarrhoea virus field strains, the epidemiological status of the virus and vaccine development. In this study, S1 regions of spike gene of 1,235 selected strains collected from 2012 to 2017 in China were clustered along with 25 references of spike sequences mainly from China. The phylogenetic analysis demonstrates that these sequences of S1 regions were genetically more diverse with time. In all strains, G1a, G1b, G2a and G2b clusters accounted for 1.9%, 9.6%, 32.2% and 56.3%, respectively, namely G2a and G2b were the two most prevalent clusters in China. Furthermore, we made a more detailed classification for G2 group based on phylogenetic tree, in which G2a was divided into two subgroups, and G2b was separated into four subgroups.

Attenuated heart rate recovery predicts risk of incident diabetes: insights from a meta-analysis

AIMS

To assess the association between attenuated heart rate recovery, a non-invasive measure of autonomic dysfunction, and risk of diabetes in the general population.

METHODS

Databases were searched for cohort studies up to May 2017 that reported the association of heart rate recovery with the risk of diabetes. The overall hazard ratios for slowest vs fastest heart rate recovery (the referent) and for every 10-beats-per-min decrement in heart rate recovery were calculated using a random effects meta-analysis model.

RESULTS

Four cohort studies with 430 incident cases of diabetes among a total of 9113 participants during a mean follow-up period of 8.1 years were included. Results showed that the slowest heart rate recovery was associated with a higher risk of diabetes (hazard ratio 1.66, 95% CI 1.16 to 2.38) vs the fastest heart rate recovery, and the hazard ratio of risk of diabetes for every 10-beats-per-min decrement in heart rate recovery was 1.29 (95% CI 1.13 to 1.48). No significant interaction effect was observed regarding the efficacy of 1-min and 2-min heart rate recovery in predicting risk of diabetes (both P_{for interaction} >0.60); however, a linear dose-response relationship existed for overall studies and for studies using 1-min heart rate recovery as the exposure (both P >0.60 for non-linearity).

CONCLUSIONS

Attenuated heart rate recovery is associated with an increased risk of diabetes in a dose-dependent manner, and measurement of heart rate recovery is worth recommending as part of diabetes risk assessment in clinical routines.

Conformational Control of Cascade Interference and Priming Activities in CRISPR Immunity

During type I-E CRISPR-Cas immunity, the Cascade surveillance complex utilizes CRISPR-derived RNAs to target complementary invasive DNA for destruction. When invader mutation blocks this interference activity, Cascade instead triggers rapid primed adaptation against the invader. The molecular basis for this dual Cascade activity is poorly understood. Here we show that the conformation of the Cse1 subunit controls Cascade activity. Using FRET, we find that Cse1 exists in a dynamic equilibrium between "open" and "closed" conformations, and the extent to which the open conformation is favored directly correlates with the attenuation of interference and relative increase in priming activity upon target mutation. Additionally, the Cse1 L1 motif modulates Cascade activity by stabilizing the closed conformation. L1 mutations promote the open conformation and switch immune response from interference to priming. Our results demonstrate that Cascade conformation controls the functional outcome of target recognition, enabling tunable CRISPR immune response to combat invader evolution.