New DNA-hydrolyzing DNAs isolated from an ssDNA library carrying a terminal hybridization stem

DNA-hydrolyzing DNAs represent an attractive type of DNA-processing catalysts distinctive from the protein-based restriction enzymes. The innate DNA property has enabled them to readily join DNA-based manipulations to promote the development of DNA biotechnology. A major in vitro selection strategy to identify these DNA catalysts relies tightly on the isolation of linear DNAs processed from a circular single-stranded (ss) DNA sequence library by self-hydrolysis. Herein, we report that by programming a terminal hybridization stem in the library, other than the previously reported classes (I & II) of deoxyribozymes, two new classes (III & IV) were identified with the old selection strategy to site-specifically hydrolyze DNA in the presence of Zn²⁺. Their representatives own a catalytic core consisting of ∼20 conserved nucleotides and a half-life of ∼15 min at neutral pH. In a bimolecular construct, class III exhibits unique broad generality on the enzyme strand, which can be potentially harnessed to engineer DNA-responsive DNA hydrolyzers for detection of any target ssDNA sequence. Besides the new findings, this work should also provide an improved approach to select for DNA-hydrolyzing deoxyribozymes that use various molecules and ions as cofactors.

Biotechnological production of ssDNA with DNA-hydrolyzing deoxyribozymes

Preparation of long single-stranded (ss)DNA in large quantities with high efficiency and purity remains a synthetic challenge. Here, we present a protocol for using DNA-hydrolyzing DNA enzymes (deoxyribozymes) for efficient biotechnological production of milligrams of ssDNA with a customizable sequence up to a few kilobases. Our protocol provides a convenient yet economical way to store the sequence information of target ssDNA on phages for selective mass production on demand.

For complete details on the use and execution of this protocol, please refer to Jia et al. (2021).

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Storage of target ssDNA on phages for selective mass production on demand

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Controllable release of specific ssDNA targets by trans-cleavage of DNA

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Preparation of long ssDNA in large quantities with high efficiency and purity

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Self-folding of kilo-based long ssDNA into desired nanoshapes

[A cohort study on plasma uric acid levels and the risk of type 2 diabetes mellitus among the oldest old in longevity areas of China]

Objective: To investigate the effect of plasma uric acid level on the incident risk of type 2 diabetes mellitus (T2DM) among the oldest old (those aged ≥80 years). Methods: Participants were recruited from the Healthy Aging and Biomarkers Cohort Study (HABCS), which conducted a baseline survey in 2008-2009 and follow-up of 3 times in 2011-2012, 2014, and 2017-2018, respectively. A total of 2 213 oldest old were enrolled in this study. The general demographic, socioeconomic, lifestyle and disease data of the oldest old were collected, and physical measurements were made for the oldest old. Fasting venous blood was collected for uric acid and blood glucose detection. Information on the incident and death of T2DM were collected through the follow-up. Cox proportional hazard regression model was used to explore the association of hyperuricemia and plasma uric acid level with the incidence of T2DM. Restricted cubic spline (RCS) function was used to explore the dose-response relationship of plasma uric acid levels with the risk of T2DM. Results: The age of participants was (93.2±7.6) years old, and 66.7% of the participants (1 475) were female. The plasma uric acid level at baseline was (289.1±88.0)μmol/L, and the prevalence of hyperuricemia was 13.3% (294 cases). During 9 years of cumulative follow-up of 7 471 person-years (average of 3.38 years for each), 122 new cases of T2DM occurred and the incidence density was 1 632.98/10⁵ person year. Cox proportional hazards regression analysis showed that per 10μmol/L increase in plasma uric acid level, the risk of T2DM increased by 1.1% [HR (95%CI): 1.011 (1.004, 1.017)]. Compared with the participants with the lowest quintile of plasma uric acid (Q₁), the risk of diabetes increased by 20.7 % among the oldest old with uric acid in the highest quintile (Q₅) [HR (95%CI):1.207 (1.029, 1.416)]. The risk of T2DM was 19.2% higher in the hyperuricemia group than that in the oldest old with normal plasma uric acid [HR (95%CI): 1.192 (1.033, 1.377)]. RCS function showed that the risk of T2DM increased with the increase in plasma uric acid levels in a nonlinear dose-response relationship (P=0.016). Conclusion: The incident risk of T2DM increases with the elevates of plasma uric acid levels in the oldest old.

Engineering Allosteric Ribozymes to Detect Thiamine Pyrophosphate in Whole Blood

Thiamine deficiency contributes to several human diseases including Alzheimer's. As its biologically active form, thiamine pyrophosphate (TPP) has been considered as a potential biomarker for Alzheimer's disease (AD) based on several clinical reports that apparently lower blood TPP levels were found in patients with mild cognitive impairment to AD. However, highly sensitive and high-throughput detection of TPP in biological fluids remains an analytical challenge. Here, we report engineering RNA-based sensors to quantitatively measure TPP concentrations in whole blood samples with a detection limit down to a few nM. By fusing a TPP-specific aptamer with the hammerhead ribozyme for in vitro selection, we isolated an allosteric ribozyme with an EC₅₀ value (68 nM) similar to the aptamer's K_D value (50 nM) for TPP, which for the first time demonstrates the possibility to maintain the effector binding affinity of the aptamer in such engineered allosteric RNA constructs. Meanwhile, we developed a new blood sample preparation protocol to be compatible with RNA. By coupling the TPP-induced ribozyme cleavage event with isothermal amplification, we achieved fluorescence monitoring of whole blood TPP levels through the "mix-and-read" operation with high-throughput potential. We expect that the engineered TPP-sensing RNAs will facilitate clinical research on AD as well as other thiamine-related diseases.

Prognosis of patients in prolonged coma after severe carbon monoxide poisoning

BACKGROUND

Late recovery in patients following prolonged coma from carbon monoxide poisoning have been reported, but the probability is unclear. The purpose of this research was to assess the prognosis of patients in prolonged coma after severe carbon monoxide poisoning and related clinical and imaging features.

METHODS

There were 13 patients who had been in a state of coma for >7 days after acute carbon monoxide poisoning in the retrospective observational study, and demographic data, clinical data, laboratory data, complications, and image data were collected. Outcome was assessed by means of the Glasgow outcome scale after 1 year. The relationship between complications and imaging manifestations and prognosis was also analyzed.

RESULTS

One year after severe carbon monoxide poisoning, two patients (15.4%) had died (GOS 1), nine (69.2%) were in a persistent vegetative state (GOS 2), one (7.7%) was moderately disabled (GOS 4), and one (7.7%) achieved a good recovery (GOS 5) with minimal disability.

CONCLUSIONS

Most patients with prolonged coma after severe carbon monoxide poisoning had a poor prognosis, although the younger patients had a better prognosis. Respiratory failure, hypotension and renal failure during the course of the disease were associated with a poor prognosis. The prognosis of patients with injuries in two sites in early CT was poor. Multiple lesions (≥3) and extensive white matter damage (Fazekas grade (PVH or DWMH) = 3) on MRI of chronic phase were also associated with a poor prognosis.

[Association of blood lead level with cognition impairment among elderly aged 65 years and older in 9 longevity areas of China]

Objective: To investigate the association between blood lead concentrations and cognition impairment among Chinese older adults aged 65 or over. Method: Data was collected in 9 longevity areas from Heathy Aging and Biomarkers Cohort Study between 2017 and 2018. This study included 1 684 elderly aged 65 years and older. Information about demographic characteristics, socioeconomic factors, health status and cognitive function score of respondents were collected by questionnaire survey and physical examination. Venous blood of the subjects was collected to detect the blood lead concentration. Subjects were stratified into four groups (Q₁-Q₄) by quartile of blood lead concentration. Multivariate logistic regression model was used to analyze the association between blood lead concentration and cognitive impairment. The linear or non-linear association between blood lead concentration and cognitive impairment were described by restrictive cubic splines (RCS). Results: Among the 1 684 respondents, 843 (50.1%) were female and 191 (11.3%) suffered from cognition impairment. After adjusting for confounding factors, the OR value and 95%CI of cognition impairment was 1.05 (1.01-1.10) for every 10 μg/L increase in blood lead concentration in elderly; Compared with the elderly in Q₁, the elderly with higher blood lead concentration had an increased risk of cognitive impairment. The OR value and 95%CI of Q₂, Q₃ and Q₄ groups were 1.19 (0.69-2.05), 1.45 (0.84-2.51) and 1.92 (1.13-3.27), respectively. Conclusion: Higher blood lead concentration is associated with cognitive impairment among the elderly aged 65 years and older in 9 longevity areas in China.

[Association of blood oxidative stress level with hypertriglyceridemia in the elderly aged 65 years and older in 9 longevity areas of China]

Objective: To investigate the association of blood oxidative stress level with hypertriglyceridemia in the elderly aged 65 years and older in China. Methods: A total of 2 393 participants aged 65 years and older were recruited in 9 longevity areas from Heathy Aging and Biomarkers Cohort Study, during 2017 to 2018. Information on demographics characteristic, life style and health status were collected by questionnaire and physical examination, and venous blood was collected to detect the levels of blood oxidative stress and hypertriglyceridemia. The linear or non-linear association between oxidative stress and hypertriglyceridemia was described by restrictive cubic splines (RCS) fitting multiple linear regression model. The generalized linear mixed effect model was conducted to assess the association between oxidative stress and hypertriglyceridemia. Results: A total of 2 393 participants, mean age was 84.6 years, the youngest was 65 and the oldest was 112, the male was 47.9%(1 145/2 393), the triglyceride level was (1.4±0.8) mmol/L. The hypertriglyceridemia detection rate was 9.99%(239/2 393). The results of multiple linear regression model with restrictive cubic spline fitting showed that MDA level was linear association with triglyceride level; SOD level was nonlinear association with triglyceride level. MDA level had significantly association with hypertriglyceridemia, and the corresponding OR value was 1.063 (95%CI: 1.046,1.081) with 1 nmol/ml increment of blood MDA; SOD level had significantly association with hypertriglyceridemia, and the corresponding OR value was 0.986(95%CI: 0.983,0.989) with 1 U/ml increment of blood SOD. Conclusion: Among the elderly aged 65 and older in 9 longevity areas in China, MDA and SOD levels were associated with the risk of hypertriglyceridemia.

Programming CircLigase Catalysis for DNA Rings and Topologies

Circular single-stranded (ss) DNA is an essential element in rolling circle amplification and many DNA nanotechnology constructions. It is commonly synthesized from linear ssDNA by a ligase, which nevertheless suffers from low and inconsistent efficiency due to the simultaneous formation of concatemeric byproducts. Here, we design an intramolecular terminal hybridization strategy to program the ring formation catalytic process of CircLigase, a thermostable RNA ligase 1 that can ligate ssDNA in an intramolecular fashion. With the enthalpy gained from the programmed hybridization to override disfavored entropic factors associated with end coupling, we broke the limit of natural CircLigase on circularization of ssDNA, realizing over 75% yields of byproduct-free monomeric rings on a series of hundred-to-half-kilo-based linear DNAs. We found that this hybridization strategy can be twisted from intra- to intermolecular to also program CircLigase to efficiently and predominantly join one ssDNA strand to another. We focused on DNA rings premade by CircLigase and demonstrated their utility in elevating the preparation, quantity, and quality of DNA topologies. We expect that the new insights on engineering CircLigase will further promote the development of nucleic acid biotechnology and nanotechnology.

First-phase ejection fraction predicts response to cardiac resynchronization therapy and adverse outcomes

Background

Cardiac Resynchronization Therapy (CRT) is an important therapeutic treatment for chronic heart failure. However, even in carefully selected cases up to 40% of patient fail to respond. First-phase ejection fraction (EF1), the ejection fraction up to the time of maximal ventricular contraction, is a novel and more sensitive echocardiographic measure of early systolic function.

Purpose

We examined the value of EF1, to predict response to CRT and clinical outcomes after CRT.

Methods

We analysed echocardiograms from 197 patients who underwent CRT between 2009 and 2018 and were followed to determine clinical outcomes.

Results

Volumetric response rate (reduction in end-systolic volume ≥15%) was 92.3% vs. 12.1%, for those with EF1 in the highest vs. lowest tertiles (p<0.001). A cut-off value of 11.9% for EF1 had >85% sensitivity and specificity for prediction of response to CRT; on multivariate logistic regression analysis incorporating previously defined predictors, EF1 was the strongest predictor of response (OR: 1.563, 95% CI: 1.371–1.782, p<0.001) (table 1). EF1 was also the strongest predictor of a clinical composite score (OR: 1.115, 95% CI: 1.044–1.191, p=0.001). Improvement in EF1 at 6 months after CRT implantation (6.5±5.8% vs 1.8±4.3% in responders vs. non-responders, p<0.001) was the best predictor of heart failure re-hospitalization and death after median follow-up of 29.2 months (HR: 0.819, 95% CI:0.765–0.876, p<0.001).

Conclusion

EF1 is a promising marker to identify patients likely to respond to CRT and most likely provides a measure of myocardial viability that determines response.

Funding Acknowledgement

Type of funding source: Foundation. Main funding source(s): British Heart Foundation, Wellcome/EPSRC Centre for Medical Engineering

A joint analysis strategy reveals genetic changes associated with artificial selection between egg-type and meat-type ducks

Egg-type ducks and meat-type ducks are predominantly commercial or indigenous and have been subjected to artificial directional selection. These two duck types differ substantially in body shape, production performance and reproductivity. However, the genetic changes associated with phenotypic differences remain unclear. Here, we compared the two duck types at the genomic and transcriptomic levels. We identified a large number of SNPs and genes in genomic divergent regions in terms of F_ST and θπ values. The corresponding genes were mainly enriched in embryonic development function and metabolic pathway. RNA-seq analysis also revealed differential gene expression in the liver and gonads. The differentially expressed genes were functionally associated with signal transmission and substance metabolism respectively. Furthermore, we found that seven genes were related to differentiation between the two types by both g genome and transcriptome analysis and were plausible candidate genes. These genes were annotated to GO categories of cell development and disease immunity. These findings will enable a better understanding of the artificial selection history of meat and egg ducks and provide a valuable resource for future research on the breeding of these two lineages.

LncRNA KCNQ1OT1 delayed fracture healing through the Wnt/β-catenin pathway

OBJECTIVE

The aim of this study was to explore the effect of long non-coding ribonucleic acid (lncRNA) KCNQ1 overlapping transcript 1 (KCNQ1OT1) on fracture healing and its possible mechanism.

PATIENTS AND METHODS

Abnormal lncRNAs were compared between patients with delayed fracture healing and those with normal fracture healing using gene expression profiling method. LncRNA expression in patients was verified by quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR). Subsequently, the model of tibial fracture was successfully established in rabbits. The effect of lncRNA KCNQ1OT1 expression on tibial fracture healing in rabbits was explored. Meanwhile, the effects of lncRNA KCNQ1OT1 on cell proliferation and apoptosis were investigated by knockdown and overexpression experiments with HC-a as a cell model. Furthermore, Western blotting was used to explore the expressions of proteins in signaling pathway affected by lncRNA KCNQ1OT1.

RESULTS

Gene expression profiling and qRT-PCR revealed that lncRNA KCNQ1OT1 was significantly down-regulated in bone tissues of patients with delayed fracture healing. Compared with the control group, knocking down lncRNA KCNQ1OT1 remarkably reduced the serum levels of alkaline phosphatase (ALP) and osteoprotegerin (OPG) in rabbits, and markedly decreased bone trabecular growth index (p<0.05). In HC-a cells, overexpression of lncRNA KCNQ1OT1 activated the Wnt/β-catenin signaling pathway, which could be suppressed by knocking down lncRNA KCNQ1OT1. Cell Counting Kit-8 (CCK-8) assay and 5(6)-carboxyfluorescein diacetate, succinimidyl ester (CFSE) results manifested that lncRNA KCNQ1OT1 remarkably promoted the proliferation and inhibited apoptosis of HC-a cells by activating the Wnt/β-catenin signaling pathway.

CONCLUSIONS

LncRNA KCNQ1OT1 plays a vital role in delayed fracture healing. Moreover, it can induce cell proliferation and inhibit cell apoptosis by activating the Wnt/β-catenin signaling pathway. Therefore, KCNQ1OT1 may be used as a biomarker to predict the occurrence of delayed fracture healing.

[Risk factors for death and the clinical features of different subtypes of patients with pulmonary arterial hypertension related to congenital heart disease]

Objective: To explore the risk factors for death in patients with pulmonary arterial hypertension related to congenital heart disease (PAH-CHD) and the clinical characteristics of different subtypes in patients with PAH-CHD. Methods: It was a retrospective study. A total of 507 PAH-CHD patients, who were hospitalized in the Department of Pediatric Cardiology of Beijing Anzhen Hospital between September 2005 and May 2019, were included. Patients were divided into 4 subgroups: (1) Eisenmenger syndrome(ES) group. (2) PAH associated with prevalent systemic-to-pulmonary shunts(SP) group. (3) PAH associated with small defects(SD) group. (4) PAH after defect correction(CD) group. According to the complexity of cardiac malformation, patients were divided into simple-medium complex malformation group and complex malformation group. According to the location of shunts, patients were divided into pre-tricuspid group, post-tricuspid group, and mixed group or complex deformity group. Baseline clinical data of patients were collected from the electronic medical record system. Demographic data (age, gender, etc.), percutaneous oxygen saturation(SPO(2)), New York Heart Association(NYHA) cardiac function classification, 6 minutes walking distance(6MWD), and B type natriuretic peptide(BNP), systolic pulmonary arterial pressure(sPAP) estimated by echocardiography and mean pulmonary artery pressure (mPAP), mean right atrial pressure(mRAP), cardiac index(CI), and calculated pulmonary vascular resistance (PVR) estimated by right heart catheterization were compared among various groups. The results of regular follow-up of all enrolled patients were collected, including the status of monotherapy or combination of PAH-targeted drugs during the follow-up period, cardiac-related adverse events(hemopysis, syncope, edema, arrhythmia, etc.) and primary endpoint event(all-cause death) were obtained and analyzed. Risk factors for all-cause death were analyzed using univariate and multivariate Cox regression analysis model. Results: The median age at diagnosis was 23.1(13.9,32.1) years, 345 cases(68.0%) were female. Two hunderds and thirty-five cases(46.4%) were diagnosed with ES; 193 cases(38.1%) were diagnosed with CD, 47 cases (9.3%) were diagnosed with SD. Among them, 32 cases(6.3%) were in the SP group. All 507 patients underwent echocardiography examination, there were significant differences in sPAP among different clinical subgroups(P<0.001). A total of 289 patients(57.0%) received right heart catheterization examination, the results showed that the ES group had the highest mPAP and PVR and the lowest mRAP(all P<0.001), the CD group had the highest mRAP and CI(both P<0.001). The 6MWD in the ES group was significantly shorter than that in the SP, SD, and CD groups(all P<0.001). The proportion of patients with NYHA class Ⅲ/Ⅳ was higher in SD group than in SP group(P<0.001), which was similar between SD, ES and CD groups (P values were 0.077 and 0.072, respectively). At admission, the proportion of patients with NYHA class Ⅰ/Ⅱwas the highest in SP group(96.9% (31/32) ), followed by CD group (85.5%(165/193)) and the ES group(85.1%(200/235)), and the SD group(75.0%(35/47)). The BNP level at admission was also higher in SD group than in SP, ES and CD groups(P<0.001). Of the 507 patients, 379(74.8%) patients received PAH-targeted drug therapy at the last follow-up, and the treatment plan was mainly monotherapy(75.7%(287/379)). The median follow-up time was 3.6(2.0, 5.6) years and 37(7.3%) patients died, including 13 in the CD group, 17 in the ES group, and 7 in the SD group. No deaths occurred in the SP group. Right heart failure was the most common cause of death(11(29.7%)), followed by severe hemoptysis dyspnea(7(18.9%)), sudden cardiac death(6(16.2%)), and pulmonary hypertensive crisis(4(10.8%)). Kaplan-Meier curve showed that survival rates of end-point-free events at 1, 3, 5 and 10 years after diagnosis of PAH were 98.0%, 95.4%, 89.9%, and 84.4%, respectively; there were statistically significant differences in survival among the subgroups(P=0.026); there was no significant difference in the survival rate between the ES group and the CD group(P=0.918), and both were higher than the SD group(P values were 0.011 and 0.013, respectively). Univariate Cox regression analysis showed that NYHA class Ⅲ/Ⅳ and BNP>100 ng/L at admission were the risk factors for all-cause death in patients with PAH-CHD(HR=6.452, 95%CI 3.378-12.346, P<0.001, and HR=2.481, 95%CI 1.225-5.025, P=0.012). Multivariate Cox regression analysis showed that NYHA class Ⅲ/Ⅳ was an independent risk factor for all-cause death in patients with PAH-CHD(HR=4.998, 95%CI 1.246-20.055, P=0.023). Conclusions: PAH-CHD patients with different clinical subtypes have different clinical symptoms, cardiac functional class, hemodynamic characteristics, and mid to long-term survival rates. SP patients have the best prognosis, outcome of ES and CD patients is similar, and SD patients have the worst prognosis. NYHA class Ⅲ/Ⅳ is an independent risk factor for all-cause death in patients with PAH-CHD.

[Characteristics of rare diseases in Zhejiang province, 2007-2017]

Objective: To understand the characteristics of 24 388 inpatients with rare diseases in Zhejiang province during 2007-2017 and provide evidence for rare disease prevention and control. Methods: Inpatient data of rare diseases and the number of hospitalization in each year were collected in 10 hospitals of class Ⅲ (A) in Zhejiang province from 2007 to 2017, and descriptive statistical analysis was used. Results: A total of 24 388 cases of rare diseases were found, accounting for 2.69‰ (24 388/9 054 201) of total hospitalized cases. The top 3 types of rare diseases were "diseases of blood and blood-forming organs and certain disorders involving immune mechanism" (32.81%, 8 001/24 388), "congenital malformations, deformations and chromosomal abnormalities" (24.87%, 6 065/24 388) and "diseases of the nervous system" (19.01%, 4 635/24 388). The number of rare disease cases increased year by year from 2007 to 2017 with an average annual growth of 19.69%, however, the proportion of rare disease cases in the annual number of hospitalized cases only showed upward trend during 2016-2017, the time distribution of different types of rare diseases had different characteristics. The male to female ratio of rare diseases cases was 1.35∶1(13 990/10 398), "diseases of the digestive system" (4.45∶1, 1 180/265), "consequences of injury, poisoning and other external causes" (3.51∶1, 281/80) and "diseases of the nervous system" (2.26∶1, 3 213/1 422) had the highest male to female ratio. The distributions of rare disease types and diseases of different types in different age groups varied. The top 10 rare diseases accounted for 53.55% (13 060/24 388) of the total cases, and the top 3 diseases were adult idiopathic neutropenia (14.41%, 3 515/24 388), corticobasal degeneration (7.60%, 1 854/24 388) and henock-schoenlein purpura (6.01%, 1 466/24 388). Conclusion: The analysis on the characteristics of 24 388 rare disease cases in Zhejiang during 2007-2017 provided reference evidence for the promotion of rare disease research, monitoring, building registration database, and development of the prevention and control strategy for rare diseases in China.