Hydrolytic endonucleolytic ribozyme (HYER) is programmable for sequence-specific DNA cleavage.

Ribozymes are catalytic RNAs with diverse functions including self-splicing and polymerization. This work aims to discover natural ribozymes that behave as hydrolytic and sequence-specific DNA endonucleases, which could be repurposed as DNA manipulation tools. Focused on bacterial group II-C introns, we found that many systems without intron-encoded protein propagate multiple copies in their resident genomes. These introns, named HYdrolytic Endonucleolytic Ribozymes (HYERs), cleaved RNA, single-stranded DNA, bubbled double-stranded DNA (dsDNA), and plasmids in vitro. HYER1 generated dsDNA breaks in the mammalian genome. Cryo-electron microscopy analysis revealed a homodimer structure for HYER1, where each monomer contains a Mg2+-dependent hydrolysis pocket and captures DNA complementary to the target recognition site (TRS). Rational designs including TRS extension, recruiting sequence insertion, and heterodimerization yielded engineered HYERs showing improved specificity and flexibility for DNA manipulation.

A systematic review of the quality of reporting and risk of bias for randomized crossover trials in digestive disease journals.

BACKGROUND: The quality of randomized crossover studies on digestive diseases is unclear. We aimed to review crossover trials in digestive disease journals and evaluate their reporting quality and risk of bias. METHODS: We searched the PubMed, Web of Science, and Scopus databases for all crossover trials in 39 digestive journals between January 2011 and September 2021. Reporting adherence was based on the CONSORT 2010 statement: extension to randomized crossover trials published in July 2019. A newly released Cochrane risk of bias tool 2.0 extension for crossover trials was applied to assess the risk of bias. RESULTS: In total, 173 studies were included in the analysis, and 16.2% were published following the CONSORT statement extension. The crossover design was not only widely used in drug efficacy trials (48.6%) but also in endoscopic ultrasound trials (23.7%) and dietary studies (17.9%) in the field of digestive diseases. The overall reporting adherence was 37.6% for full texts and 43.4% for abstracts. The proportions of trials with low, some concerns, and high risk of bias were 13.9%, 15.6%, and 70.5%, respectively. The difference in reporting adherence and high risk of bias between pre- and post-CONSORT was not significant. Having a sample size plan, defining primary end points, and pre-registration showed higher reporting adherence and lower risk of bias than those who did not. CONCLUSION: These findings demonstrated the inadequate quality of randomized crossover trials for digestive diseases. Compliance with the CONSORT extension for crossover trials must be strengthened and improved (PROSPERO CRD: 42021248723).

Clinical impact and quality of randomized controlled trials involving interventions evaluating artificial intelligence prediction tools: a systematic review.

The evidence of the impact of traditional statistical (TS) and artificial intelligence (AI) tool interventions in clinical practice was limited. This study aimed to investigate the clinical impact and quality of randomized controlled trials (RCTs) involving interventions evaluating TS, machine learning (ML), and deep learning (DL) prediction tools. A systematic review on PubMed was conducted to identify RCTs involving TS/ML/DL tool interventions in the past decade. A total of 65 RCTs from 26,082 records were included. A majority of them had model development studies and generally good performance was achieved. The function of TS and ML tools in the RCTs mainly included assistive treatment decisions, assistive diagnosis, and risk stratification, but DL trials were only conducted for assistive diagnosis. Nearly two-fifths of the trial interventions showed no clinical benefit compared to standard care. Though DL and ML interventions achieved higher rates of positive results than TS in the RCTs, in trials with low risk of bias (17/65) the advantage of DL to TS was reduced while the advantage of ML to TS disappeared. The current applications of DL were not yet fully spread performed in medicine. It is predictable that DL will integrate more complex clinical problems than ML and TS tools in the future. Therefore, rigorous studies are required before the clinical application of these tools.

Effects of shikonin on the development of ovarian follicles and female germline stem cells.

OBJECTIVE: To investigate the effects and potential mechanism of action of shikonin (SHK) on the development of ovarian follicles and female germline stem cells (FGSCs). METHODS: Female Kunming adult mice were administered SHK (0, 20 and 50 mg/kg) by oral gavage. Cultures of FGSCs were treated with SHK 32 µmol/l for 24 h. The ovarian index in mouse ovaries was calculated. Numbers of primordial, primary and atretic follicles were counted. Germline stem cell markers and apoptosis were examined. Levels of glutathione (GSH), superoxide dismutase (SOD) and reactive oxygen species (ROS) were measured. RESULTS: Both doses of SHK significantly decreased the ovarian index, the numbers of primordial follicles, primary follicles and antral follicles in mice. SHK significantly increased the numbers of atretic follicles and atretic corpora lutea. SHK promoted apoptosis in vivo and in vitro. SHK significantly decreased the levels of the germline stem cell markers. SHK significantly lowered GSH levels and the activity of SOD in the peripheral blood from mice, whereas SHK significantly elevated cellular ROS content in FGSCs. CONCLUSIONS: These current results suggested that follicular development and FGSCs were suppressed by SHK through the induction of apoptosis and oxidative stress might be involved in this pathological process.

Longitudinal radiomics algorithm of posttreatment computed tomography images for early detecting recurrence of hepatocellular carcinoma after resection or ablation.

OBJECTIVES: To develop a radiomics algorithm, improving the performance of detecting recurrence, based on posttreatment CT images within one month and at suspicious time during follow-up. MATERIALS AND METHODS: A total of 114 patients with 228 images were randomly split (7:3) into training and validation cohort. Radiomics algorithm was trained using machine learning, based on difference-in-difference (DD) features extracted from tumor and liver regions of interest on posttreatment CTs within one month after resection or ablation and when suspected recurrent lesion was observed but cannot be confirmed as HCC during follow-up. The performance was evaluated by area under the receiver operating characteristic curve (AUC) and was compared among radiomics algorithm, change of alpha-fetoprotein (AFP) and combined model of both. Five-folded cross validation (CV) was used to present the training error. RESULTS: A radiomics algorithm was established by 34 DD features selected by random forest and multivariable logistic models and showed a better AUC than that of change of AFP (0.89 [95% CI: 0.78, 1.00] vs 0.63 [95% CI: 0.42, 0.84], P = .04) and similar with the combined model in detecting recurrence in the validation set. Five-folded CV error in the validation cohort was 21% for the algorithm and 26% for the changes of AFP. CONCLUSIONS: The algorithm integrated radiomic features of posttreatment CT showed superior performance to that of conventional AFP and may act as a potential marker in the early detecting recurrence of HCC.

An insight into DNA binding properties of newly designed cationic δ,δ'­diazacarbazoles: Spectroscopy, AFM imaging and living cells staining studies.

Two cationic δ,δ'­diazacarbazoles, 1­Methyl­5H­pyrrolo[3,2­b:4,5­b']dipyridinium iodide (MPDPI) and 1,5­Dimethyl­5H­pyrrolo[3,2­b:4,5­b']dipyridinium iodide (DPDPI), were devised and synthesized. Through characterizations of the interactions between DNA and the two δ,δ'­diazacarbazoles by various spectroscopy means, the strong interactions between the two compounds and double-strand DNA have been observed and the interaction types and mechanisms were explored. UV-Vis and fluorescent data have shown the big changes of DNA in the presence of either of the two compounds, demonstrating that both of the δ,δ'­diazacarbazoles can bind to DNA tightly, and high ionic strength decreased the intercalative interactions. The UV-Vis and fluorescence of dsDNA in the presence of DPDPI showed more profound changes than those in the presence of MPDPI, due to CH3 (in the structure of DPDPI) taking place of H (in the structure of MPDPI) at the position of 5­NH. And the circular dichroism (CD) spectra of CT-DNA and atomic force microscopy (AFM) results indicated more compacted conformation of DNA in the presence of DPDPI than MPDPI, implying that DPDPI has a more significant effect on DNA conformations than MPDPI. Most interestingly, fluorescence enhancement of cationic δ,δ'­diazacarbazoles occurred in the presence of DNA. With ionic strength increasing, the intercalative interactions between δ,δ'­diazacarbazoles and DNA were weakened, but δ,δ'­diazacarbazoles-DNA complexes showed enhanced fluorescence, which indicated that there are other interactions present at high ionic strength. Furthermore, laser confocal fluorescence microscopy results proved that DPDPI was membrane-permeable and stained living cells.

Comparative pharmacokinetics and pharmacodynamics of a PEGylated recombinant human growth hormone and daily recombinant human growth hormone in growth hormone-deficient children.

OBJECTIVE: Recombinant human growth hormone (rhGH) replacement therapy in children generally requires daily subcutaneous (sc) injections, which may be inconvenient for patients. Jintrolong® is a PEGylated rhGH with the purpose of weekly sc injections. The aim of the current study was to examine the pharmacokinetics, pharmacodynamics, safety, and tolerability of multiple sc doses of Jintrolong® vs daily doses of rhGH. DESIGN AND METHODS: Twelve children with growth hormone deficiency participated in this single-center, open-label, crossover Phase I trial. All subjects received daily sc injections of rhGH at 0.0286 mg/kg/d for 7 days, followed by a 4-week washout period and six weekly doses of Jintrolong® at 0.2 mg/kg/w. RESULTS: In comparison with rhGH, sc injection of Jintrolong® produced a noticeably higher C max, significantly longer half-life (t 1/2), and slower plasma clearance, signifying a profile suitable for long-term treatment. The ratio of the area under the concentration vs time curve (AUC) after the seventh and first injections (AUC(0-∞)7th/AUC(0-∞)1st) of rhGH was 1.02, while the AUC(0-∞)6th/AUC(0-∞)1st of Jintrolong ® was 1.03, indicating no accumulation of circulating growth hormone. There was no significant difference in the change in insulin-like growth factor-1 expression produced by 7 days of sc rhGH and weekly Jintrolong® injections. There were no severe adverse events during the trial. CONCLUSION: The elimination rate of Jintrolong® was slower than that of sc rhGH. No progressive serum accumulation of Jintrolong® was found. The changes in insulin-like growth factor-1 expression produced by rhGH and Jintrolong® were comparable, indicating similar pharmacodynamics. Our results demonstrate that Jintrolong® is suitable for long-term growth hormone treatment in children with growth hormone deficiency.

Β-defensin in Nile tilapia (Oreochromis niloticus): Sequence, tissue expression, and anti-bacterial activity of synthetic peptides.

Beta-defensins (ß-defensins) are small cationic amphiphilic peptides that are widely distributed in plants, insects, and vertebrates, and are important for their antimicrobial properties. In this study, the ß-defensin (Onß-defensin) gene of the Nile tilapia (Oreochromis niloticus) was cloned from spleen tissue. Onß-defensin has a genomic DNA sequence of 674 bp and produces a cDNA of 454 bp. Sequence alignments showed that Onß-defensin contains three exons and two introns. Sequence analysis of the cDNA identified an open reading frame of 201 bp, encoding 66 amino acids. Bioinformatic analysis showed that Onß-defensin encodes a cytoplasmic protein molecule containing a signal peptide. The deduced amino acid sequence of this peptide contains six conserved cysteine residues and two conserved glycine residues, and shows 81.82% and 78.33% sequence similarities with ß-defensin-1 of fugu (Takifugu rubripes) and rainbow trout (Oncorhynchus mykiss), respectively. Real-time quantitative PCR showed that the level of Onß-defensin expression was highest in the skin (307.1-fold), followed by the spleen (77.3-fold), kidney (17.8-fold), and muscle (16.5-fold) compared to controls. By contrast, low levels of expression were found in the liver, heart, intestine, stomach, and gill (<3.0-fold). Artificial infection of tilapia with Streptococcus agalactiae (group B streptococcus [GBS] strain) resulted in a significantly upregulated expression of Onß-defensin in the skin, muscle, kidney, and gill. In vitro antimicrobial experiments showed that a synthetic Onß-defensin polypeptide had a certain degree of inhibitory effect on the growth of Escherichia coli DH5α and S. agalactiae. The results indicate that Onß-defensin plays a role in immune responses that suppress or kill pathogens.

[Purification of complicated industrial organic waste gas by complex absorption].

Complicated industrial organic waste gas with the characteristics of low concentration,high wind volume containing inorganic dust and oil was employed the research object by complex absorption. Complex absorption mechanism, process flow, purification equipment and engineering application were studied. Three different surfactants were prepared for the composite absorbent to purify exhaust gas loaded with toluene and butyl acetate, respectively. Results show that the low surface tension of the composite absorbent can improve the removal efficiency of toluene and butyl acetate. With the advantages of the water film, swirl plate and fill absorption device, efficient absorption equipment was developed for the treatment of complicated industrial organic waste gas. It is with superiorities of simple structure, small size, anti-jam and high mass transfer. Based on absorption technology, waste gas treatment process integrated with heating stripping, burning and anaerobic and other processes, so that emissions of waste gas and absorption solution could meet the discharge standards. The technology has been put into practice, such as manufacturing and spraying enterprises.

Development and application of a real-time PCR method for pharmacokinetic and biodistribution studies of recombinant adenovirus.

A replication-deficient recombinant adenovirus (Ad5-LFA-3/IgG(1)) that encodes secreted LFA-3/IgG(1) was constructed for gene therapy treatment of psoriasis. The purpose of this study was to develop a real-time PCR method for pharmacokinetic and biodistribution studies of Ad5-LFA-3/IgG(1) within the circulation and organs. This method showed good specificity, sensitivity and reproducibility over a wide dynamic range of concentrations. Quantitative measurement of recombinant adenoviral DNA suggested that the level of Ad5-LFA-3/IgG(1) DNA in circulating blood peaked within 10 min following intravenous injection in rhesus macaques. Following this peak, the adenoviral DNA level dropped significantly to a very low level. Real-time PCR revealed that Ad5-LFA-3/IgG(1) DNA was enriched in the spleen, lung and liver after injection of the adenovirus into rats through the tail vein. The adenoviral DNA was barely detected in other tissues. These data provide important information for clinical trials of Ad5-LFA-3/IgG(1) and confirm the utility of the real-time PCR assay for monitoring gene therapy trials.