Comparison of the safety and efficacy of Neuroform Atlas stent deployed via Gateway balloon catheter and microcatheter for the treatment of intracranial stenosis

OBJECTIVE

This study aimed to compare the safety and efficacy of the Atlas stent released by the Gateway catheter and microcatheter in the treatment of intracranial stenosis (IS).

METHODS

The primary efficacy and safety outcomes were the in-stent restenosis (ISR) rate and post-procedural stroke or death within one month.

RESULTS

Atlas stents were deployed using the Gateway catheter and microcatheter in 19 (57.6 %) and 14 (42.4 %) procedures, respectively. Follow-up imaging data were available for 26 patients; the incidence of ISR was 15.4 %, and the ISR rate was higher, though not significantly, in the microcatheter group than in the Gateway group (30.0% vs. 6.25 %, P = .39). Clinical follow-up data were available for 30 patients; the post-procedural stroke rate was 3.3 % within one month and 13.3 % from one month to one year. The post-procedural stroke rate within one month was higher, though not significantly, in the microcatheter group than in the Gateway group (7.7% vs. 0 %, P = .43). The Gateway group had a significantly lower rate of post-procedural stroke in the same territory than that of the microcatheter group (0% vs. 30.8 %, P = .026). A higher incidence of residual stenosis <30 % was found in the non-ISR group than in the ISR group (72.2% vs. 0 %, P = .014).

CONCLUSIONS

This study provides preliminary evidence that the Atlas stent is safe and effective for IS treatment. The use of the Gateway catheter to deliver the Atlas stent appears to be safer than using microcatheter. The incidence of ISR may be related to the degree of the residual stenosis.

Cynarin alleviates acetaminophen-induced acute liver injury through the activation of Keap1/Nrf2-mediated lipid peroxidation defense via the AMPK/SIRT3 signaling pathway

Overdose of Acetaminophen (APAP) is a major contributor to acute liver injury (ALI), a complex pathological process with limited effective treatments. Emerging evidence links lipid peroxidation to APAP-induced ALI. Cynarin (Cyn), a hydroxycinnamic acid derivative, exhibits liver protective effects, but whether it mitigates APAP-induced ALI is unclear. Our aim was to verify the protective impact of Cyn on APAP-induced ALI and elucidate the molecular mechanisms governing this process. Herein, the regulation of the Kelch-like ECH-associated protein 1 (Keap1)/nuclear factor erythroid 2-related factor 2 (Nrf2) interaction was determined to be a novel mechanism underlying this protective impact of Cyn against APAP-induced ALI. Nrf2 deficiency increased the severity of APAP-induced ALI and lipid peroxidation and counteracted the protective effect of Cyn against this pathology. Additionally, Cyn promoted the dissociation of Nrf2 from Keap1, enhancing the nuclear translocation of Nrf2 and the transcription of downstream antioxidant proteins, thereby inhibiting lipid peroxidation. Molecular docking demonstrated that Cyn bound competitively to Keap1, and overexpression of Keap1 reversed Nrf2-activated anti-lipid peroxidation. Additionally, Cyn activated the adenosine monophosphate-activated protein kinase (AMPK)/sirtuin (SIRT)3 signaling pathway, which exhibits a protective effect on APAP-induced ALI. These findings propose that Cyn alleviates APAP-induced ALI by enhancing the Keap1/Nrf2-mediated lipid peroxidation defense via activation of the AMPK/SIRT3 signaling pathway.

Beware of atrial pacing-induced ventricular depolarization: A case of lead malfunction

Although ventricular capture during the atrial threshold test is possible, there are rare reports on the insulation defect and inactive leads thereof. In this case, we present a pacemaker-dependent patient with a history of pacemaker generator replacements. The patient experienced ventricular capture induced by atrial pacing due to adhesion of the atrial and ventricular leads with an insulation defect. The atrial lead was abandoned and a new lead was implanted. However, there was a significant decrease in ventricular impedance detected shortly after the new lead was implanted. When observing the phenomenon of atrial pacing-induced ventricular depolarization, one uncommon reason to consider is lead adhesive wear. It is important to pay attention to the contact and bending sites of the leads.

UBDP1 pseudogene and UBD network competitively bind miR‑6072 to promote glioma progression

Increasing evidence suggests that pseudogenes play crucial roles in various cancers, yet their functions and regulatory mechanisms in glioma pathogenesis remain enigmatic. In the present study, a novel pseudogene was identified, UBDP1, which is significantly upregulated in glioblastoma and positively correlated with the expression of its parent gene, UBD. Additionally, high levels of these paired genes are linked with a poor prognosis for patients. In the present study, clinical samples were collected followed by various analyses including microarray for long non‑coding RNAs, reverse transcription‑quantitative PCR, fluorescence in situ hybridization and western blotting. Cell lines were authenticated and cultured then subjected to various assays for proliferation, migration, and invasion to investigate the molecular mechanisms. Bioinformatic tools identified miRNA targets, and luciferase reporter assays validated these interactions. A tumor xenograft model in mice was used for in vivo studies. In vitro and in vivo studies have demonstrated that UBDP1, localized in the cytoplasm, functions as a tumor‑promoting factor influencing cell proliferation, migration, invasion and tumor growth. Mechanistic investigations have indicated that UBDP1 exerts its oncogenic effects by decoying miR‑6072 from UBD mRNA, thus forming a competitive endogenous RNA network, which results in the enhanced oncogenic activity of UBD. The present findings offered new insights into the role of pseudogenes in glioma progression, suggesting that targeting the UBDP1/miR‑6072/UBD network may serve as a potential therapeutic strategy for glioma patients.

Chickpea-Derived Modified Antimicrobial Peptides KTA and KTR Inactivate Staphylococcus aureus via Disrupting Cell Membrane and Interfering with Peptidoglycan Synthesis

The widespread bacterial contamination caused by foodborne pathogens has continuously driven the development of advanced and potent food antimicrobial agents. In this study, two novel antimicrobial peptides (AMPs) named KTA and KTR were obtained by modifying a natural AMP, Leg2, from chickpea storage protein legumin hydrolysates. They were further predicted to be stable hydrophobic cationic AMPs of α-helical structure with no hemolytic toxicity by several online servers. Moreover, the AMPs exerted superior antibacterial activity against two representative Staphylococcus aureus strains thanks to the increased hydrophobicity and positive charge, with minimum inhibition concentration value (4.74-7.41 μM) significantly lower than that of Leg2 (>1158.70 μM). Further, this study sought to elucidate the specific antimicrobial mechanism against Gram-positive bacteria. It was found that the electrostatic interactions of the AMPs with peptidoglycan were vital for peptide activity in combating Gram-positive bacteria. Subsequently, the cell membrane of S. aureus cells was irreversibly disrupted by increasing permeability and impairing membrane components, which led to the massive release of intracellular substances and eventual cell death. Overall, this work demonstrated that KTA and KTR were active against Gram-positive bacteria via peptidoglycan targeting and membrane-disruptive mechanisms and paved the way for expanding their application potential to alleviate food contamination.

Estimation of genetic parameters for fertility traits in Chinese Holstein of south China

Introduction: Chinese Holstein in South China suffer heat stress for a long period, which leads to evolutionary differences from Chinese Holstein in North China. The aim of this study was to estimate the genetic parameters of fertility traits for Chinese Holstein in South China. Methods: A total of 167,840 Chinese Holstein heifers and cows from Guangming Animal Husbandry Co., LTD farms were used in this study. The fertility traits analyzed were calving interval (CI), days open (DO), age of first service (AFS), age of first calving (AFC), calving to first insemination (CTFS), first insemination to conception (FSTC), gestation length (GL), non-return rate to 56 days (NRR), and number of services (NS). Results: The descriptive statistics revealed that the same trait in heifers performed better than in cows, which was consistent with the other studies. The heritabilities of fertility traits in this study ranged from close to 0 (for NS of cows) to 0.2474 (for AFC of heifers). The genetic correlation of NRR between heifers and cows was 0.9993, which indicates that the NRR for heifers and cows could be treated as one trait in this population. Conclusion: The heritabilities of fertility traits in Chinese Holstein in south China were quite different from the heritabilities of fertility traits in North China. NRR56, NS, AFC, and CI were suggested to be included into the selection index to improve fertility performance of Chinsese Holstein of south China. The results of this study could provide genetic parameters for the animal breeding program of Chinese Holstein in the south of China.

Epithelial N-methyl-D-aspartate (NMDA) receptors mediate renal vasodilation by affecting kidney autoregulation

Background

N-methyl-D-aspartate receptor (NMDAR) are amino acid receptors that are well studied in brain physiology; however, their role in kidney is poorly understood. Nonetheless, NMDAR inhibitors can increase serum K+ and reduce GFR, which suggests they have an important physiological role in the kidney. We hypothesized that NMDARs in the distal nephron induce afferent-arteriole vasodilation through the vasodilator mechanism connecting-tubule-glomerular feedback (CNTGF) that involves ENaC activation.

Methods and results

Using a tubule-specific transcriptome database combined with molecular biology and microscopy techniques, we showed kidney expression of NMDAR subunits along the nephron and specifically in ENaC-positive cells. This receptor is expressed in both male and female mice, with higher abundance in females (p=0.02). Microperfusing NMDAR agonists into the connecting tubule induced afferent-arteriole vasodilation (EC50 10.7 vs. 24.5 mM; p<0.001) that was blunted or eliminated with the use of NMDAR blocker MK-801 or with the ENaC inhibitor Benzamil, indicating a dependence on CNTGF of the NMDAR-induced vasodilation. In vivo, we confirmed this CNTGF-associated vasodilation using kidney micropuncture (Stop-flow pressure 37.9±2.6 vs. 28.6±1.9 mmHg, NMDAR agonist vs vehicle; p<0.01). We explored NMDAR and ENaC channel interaction by using mpkCCD cells and split-open connecting tubules. We observed increased amiloride-sensitive current following NMDAR activation that was prevented by MK-801 (1.14 vs. 0.4 μAmp; p=0.03). In split-open tubules, NMDAR activation increased ENaC activity (Npo Vehicle vs. NMDA; p=0.04).

Conclusion

NMDARs are expressed along the nephron, including ENaC-positive cells, with higher expression in females. Epithelial NMDAR mediates renal vasodilation through the connecting-tubule-glomerular feedback, by increasing ENaC activity.

Arm-only combined transarterial and transvenous access for neurointerventional procedures: a double-center retrospective study

OBJECTIVE

This study aims to share our experience with the arm-only combined transarterial and transvenous access approach for neurointerventional procedures and evaluate its efficacy and safety.

METHODS

The arm-only combined transarterial and transvenous access approach was performed using the right/bilateral proximal radial arteries and the right forearm superficial vein system, guided by ultrasonic guidance. Arterial access closure was achieved using a transradial band radial compression device, while manual compression was utilized for venous approach closure.

RESULTS

Thirteen procedures were successfully performed using the arm-only combined transarterial and transvenous access approach, yielding favorable outcomes. The procedures included dural arteriovenous fistula embolization (seven cases), cerebral arteriovenous malformation embolization (four cases), venous sinus thrombosis catheter-directed thrombolysis and intravenous thrombectomy (one case), and cerebral venous sinus stenosis manometry (one case). All procedures were uneventful, allowing patients to ambulate on the same day. At discharge, all patients exhibited modified Rankin scores of 0-2, without any access site or perioperative complications.

CONCLUSION

This double-center study preliminarily demonstrates the feasibility and safety of arm-only combined transarterial and transvenous access applied in neurointerventional procedures for complicated cerebrovascular diseases. The proximal radial artery and forearm superficial vein are recommended as the primary access sites. Unobstructed compression is strongly recommended for radial approach closure.

ADVANCES IN KNOWLEDGE

This study aimed to add evidence and experience on the arm-only combined transarterial and transvenous access, as a new approach, for neurointerventional treatment that required arteriovenous approaches.

Physiochemical characteristics, morphology, and lubricating properties of size-specific whey protein particles by acid or ion aggregation

To investigate the influence of particle characteristics on their lubricating capacity, microparticles of controlled size (~300, ~700, and ~1900 nm) were prepared from whey proteins using two different approaches: reducing the pH and increasing the calcium ion concentration. The physiochemical, morphological, and tribological properties of the two types of particles were determined. Both treatments pronouncedly decreased the absolute value of zeta-potential and surface hydrophobicity of whey proteins, with calcium ions showing a more severe effect on zeta-potential. The viscosity of the particle suspensions increased with particle size, and ion-induced samples showed higher viscosity than acid-induced ones. Morphology investigation revealed that particle aggregation and irregularity increased with particle size increase. Distinct lubricating behaviors were observed for the two particle types within different size ranges. Viscosity played a more important role in lubrication when the particle size was small, while particle characteristics became more dominant for large particles.

Visualization of Hot Carrier Dynamics in a Single CsPbBr3 Perovskite Microplate Using Femtosecond Kerr-Gated Wide-Field Fluorescence Spectroscopy

Lead halide perovskites (LHPs) have excellent semiconductor properties. They have been used in many applications such as solar cells. Recently, the hot carrier dynamics in this type of material have received much attention as they are useful for enhancing the performance of optoelectrical devices fabricated from it. Here, we study the ultrafast hot carrier dynamics of a single CsPbBr3 microplate using femtosecond Kerr-gated wide-field fluorescence spectroscopy. The transient photoluminescence spectra have been measured under a variety of excitation fluences. The temporal evolution of bandgap renormalization and the competition between hot carrier cooling and the recovery of the renormalized bandgap are clearly revealed.

Factors affecting the accuracy of genomic prediction in joint pig populations

Genomic prediction (GP) has greatly advanced animal and plant breeding over the past two decades. GP in joint populations is a feasible method to improve the accuracy of genomic estimated breeding values in small populations. However, there is still a need to understand the factors that influence GP in joint populations. This study used simulated data and real data from Duroc pig populations to examine the impact of linkage disequilibrium (LD), causal variants effect sizes (CVESs), and minor allele frequencies (MAF) of SNPs on the accuracy of genomic prediction in joint populations. Three prediction methods were used: genomic best linear unbiased prediction (GBLUP), single-step GBLUP and multi-trait GBLUP. Results from the simulated datasets showed that the accuracies of GP in joint populations were always higher than those in a single population when only LD inconsistencies existed. However, single-step GBLUP accuracy in joint populations decreased as the correlation of MAF between populations decreased, while the accuracy of GBLUP is consistently higher in joint populations than in a single population. As the correlation of CVES between populations decreased, the accuracy of both GBLUP and single-step GBLUP in joint populations declined. Analysis of real Duroc populations showed low genetic correlation, similar to the simulated relationship between the most distant populations. In most cases in Duroc populations, GP have higher accuracies in joint populations than in individual population. In conclusion, the consistency of CVES plays a more important role in multi-population GP. The genetic relatedness of the Duroc populations is so weak that the prediction accuracy of GP in joint populations is reduced in some traits. Multi-trait GBLUP is a competitive method for the joint breeding evaluation.

Development of a Dihydroquinoline-Pyrazoline GluN2C/2D-Selective Negative Allosteric Modulator of the N-Methyl-d-aspartate Receptor

Subunit-selective inhibition of N-methyl-d-aspartate receptors (NMDARs) is a promising therapeutic strategy for several neurological disorders, including epilepsy, Alzheimer's and Parkinson's disease, depression, and acute brain injury. We previously described the dihydroquinoline-pyrazoline (DQP) analogue 2a (DQP-26) as a potent NMDAR negative allosteric modulator with selectivity for GluN2C/D over GluN2A/B. However, moderate (<100-fold) subunit selectivity, inadequate cell-membrane permeability, and poor brain penetration complicated the use of 2a as an in vivo probe. In an effort to improve selectivity and the pharmacokinetic profile of the series, we performed additional structure-activity relationship studies of the succinate side chain and investigated the use of prodrugs to mask the pendant carboxylic acid. These efforts led to discovery of the analogue (S)-(-)-2i, also referred to as (S)-(-)-DQP-997-74, which exhibits >100- and >300-fold selectivity for GluN2C- and GluN2D-containing NMDARs (IC50 0.069 and 0.035 μM, respectively) compared to GluN2A- and GluN2B-containing receptors (IC50 5.2 and 16 μM, respectively) and has no effects on AMPA, kainate, or GluN1/GluN3 receptors. Compound (S)-(-)-2i is 5-fold more potent than (S)-2a. In addition, compound 2i shows a time-dependent enhancement of inhibitory actions at GluN2C- and GluN2D-containing NMDARs in the presence of the agonist glutamate, which could attenuate hypersynchronous activity driven by high-frequency excitatory synaptic transmission. Consistent with this finding, compound 2i significantly reduced the number of epileptic events in a murine model of tuberous sclerosis complex (TSC)-induced epilepsy that is associated with upregulation of the GluN2C subunit. Thus, 2i represents a robust tool for the GluN2C/D target validation. Esterification of the succinate carboxylate improved brain penetration, suggesting a strategy for therapeutic development of this series for NMDAR-associated neurological conditions.

Genetic variation in ZmWAX2 confers maize resistance to Fusarium verticillioides

Fusarium verticillioides (F. verticillioides) is a widely distributed phytopathogen that incites multiple destructive diseases in maize, posing a grave threat to corn yields and quality worldwide. However, there are few reports of resistance genes to F. verticillioides. Here, we reveal that a combination of two single nucleotide polymorphisms (SNPs) corresponding to ZmWAX2 gene associates with quantitative resistance variations to F. verticillioides in maize through a genome-wide association study. A lack of ZmWAX2 compromises maize resistance to F. verticillioides-caused seed rot, seedling blight and stalk rot by reducing cuticular wax deposition, while the transgenic plants overexpressing ZmWAX2 show significantly increased immunity to F. verticillioides. A natural occurrence of two 7-bp deletions within the promoter increases ZmWAX2 transcription, thus enhancing maize resistance to F. verticillioides. Upon Fusarium stalk rot, ZmWAX2 greatly promotes the yield and grain quality of maize. Our studies demonstrate that ZmWAX2 confers multiple disease resistances caused by F. verticillioides and can serve as an important gene target for the development of F. verticillioides-resistant maize varieties.

Effect of Flaxseed Gum on the Textural, Rheological, and Tribological Properties of Acid-Induced Soy Protein Isolate Gels

This study aimed to investigate the effects of incorporating different concentrations of flaxseed gum (FG) into acid-induced soy protein isolate (SPI) gels. The investigation focused on assessing the effects of FG on the textural, rheological, and tribological properties of the resultant SPI gels. The results showed that adding a small amount of FG (0.05%) to the SPI gel system increased the storage modulus (G') and enhanced gelation while improving textural properties including hardness, viscosity, elasticity, and adhesion. Moreover, these gels exhibited strong water-holding capacity, a desirable property in various food products. However, when the concentration was increased to 0.3%, the WHC of the gel decreased, as did the hardness and cohesiveness. The particle size of the gel also increased with increasing concentration. Tribological investigations revealed that at 0.05-0.2% FG addition, the coefficient of friction (μ) of the composite gel was decreased compared to the pure SPI gel. In the sliding speed range of 1-100 mm/s, the coefficient of friction gradually increased with increasing concentration. When the FG concentration was 0.05%, the μ of the gel system was the lowest. In summary, low concentration of FG (0.05%) was found to play an important role in improving the properties of SPI gel, including enhancing textural, rheological, and lubricating properties.

The feasibility and safety of his-purkinje conduction system pacing in patients with heart failure with severely reduced ejection fraction

Objective

The purpose of this study was to evaluate the feasibility and outcomes of conduction system pacing (CSP) in patients with heart failure (HF) who had a severely reduced left ventricular ejection fraction (LVEF) of less than 30% (HFsrEF).

Methods

Between January 2018 and December 2020, all consecutive HF patients with LVEF < 30% who underwent CSP at our center were evaluated. Clinical outcomes and echocardiographic data [LVEF and left ventricular end-systolic volume (LVESV)], and complications were all recorded. In addition, clinical and echocardiographic (≥5% improvement in LVEF or ≥15% decrease in LVESV) responses were assessed. The patients were classified into a complete left bundle branch block (CLBBB) morphology group and a non-CLBBB morphology group according to the baseline QRS configuration.

Results

Seventy patients (66 ± 8.84 years; 55.7% male) with a mean LVEF of 23.2 ± 3.23%, LVEDd of 67.33 ± 7.47 mm and LVESV of 212.08 ± 39.74 ml were included. QRS configuration at baseline was CLBBB in 67.1% (47/70) of patients and non-CLBBB in 32.9%. At implantation, the CSP threshold was 0.6 ± 0.3 V @ 0.4 ms and remained stable during a mean follow-up of 23.43 ± 11.44 months. CSP resulted in significant LVEF improvement from 23.2 ± 3.23% to 34.93 ± 10.34% (P < 0.001) and significant QRS narrowing from 154.99 ± 34.42 to 130.81 ± 25.18 ms (P < 0.001). Clinical and echocardiographic responses were observed in 91.4% (64/70) and 77.1% (54/70) of patients. Super-response to CSP (≥15% improvement in LVEF or ≥30% decrease in LVESV) was observed in 52.9% (37/70) of patients. One patient died due to acute HF and following severe metabolic disorders. Baseline BNP (odds ratio: 0.969; 95% confidence interval: 0.939-0.989; P = 0.045) was associated with echocardiographic response. The proportions of clinical and echocardiographic responses in the CLBBB group were higher than those in the non-CLBBB group but without significant statistical differences.

Conclusions

CSP is feasible and safe in patients with HFsrEF. CSP is associated with a significant improvement in clinical and echocardiographic outcomes, even for patients with non-CLBBB widened QRS.

Conduction system pacing improves the outcomes on patients with high percentage of ventricular pacing and heart failure with mildly reduced ejection fraction

Aims

This study aimed to investigate the efficacy and safety of CSP in patients with a high percentage of ventricular pacing and heart failure with HFmrEF.

Methods

Patients who underwent CSP for HFmrEF and ventricular pacing >40% were consecutively enrolled from January 2018 to May 2021. All participants were followed up at least 12 months. Clinical data including cardiac performance and lead outcomes were compared before and after the procedure. Left ventricular ejection fraction (LVEF) was measured using the biplane Simpson's method. HFmrEF was defined as heart failure with the LVEF ranging from 41%-49%.

Results

CSP was successfully performed in 64 cases (96.97%), which included 16 cases of left bundle branch pacing (LBBP) and 48 cases of His bundle pacing (HBP). After a mean of 23.12 ± 8.17 months follow-up, NYHA classification (P < 0.001), LVEF (42.45 ± 1.84% vs. 49.97 ± 3.57%, P < 0.001) and left ventricular end diastolic diameter (LVEDD) (55.59 ± 6.17 mm vs. 51.66 ± 3.48 mm, P < 0.001) improved significantly. During follow-up, more than half (39/64,60.9%) of patients returned to normal LVEF and LVEDD with complete reverse remodeling. The pacing threshold in LBBP was lower (0.90 ± 0.27 V@0.4 ms vs. 1.61 ± 0.71 V@0.4 ms, P < 0.001) than that in HBP. No perforation, electrode dislodging, thrombosis or infection was observed during follow-up.

Conclusions

CSP could improve the clinical outcomes in patients with HFmrEF and a high percentage of ventricular pacing. LBBP might be a better choice because of its feasibility and safety, especially in patients with infranodal atrioventricular block.

Comparison and Analysis of Detection Methods for Typhoon-Storm Surges Based on Tide-Gauge Data-Taking Coasts of China as Examples

Global warming is predicted to lead to a new geographic and spatial distribution of storm-surge events and an increase in their activity intensity. Therefore, it is necessary to detect storm-surge events in order to reveal temporal and spatial variations in their activity intensity. This study attempted to detect storm-surge events from the perspective of detecting outliers. Four common outlier-detection methods, the Pauta criterion (PC), Chauvenet criterion (CC), Pareto distribution (PD) and kurtosis coefficient (KC), were used to detect the storm-surge events from the hourly residual water level data of 14 tide gauges along the coasts of China. This paper evaluates the comprehensive ability of the four methods to detect storm-surge events by combining historical typhoon-storm-surge events and deep-learning target-detection-evaluation indicators. The results indicate that (1) all of the four methods are feasible for detecting storm surge events; (2) the PC has the highest comprehensive detection ability for storm-surge events (F1 = 0.66), making it the most suitable for typhoon-storm-surge detection in coastal areas of China; the CC has the highest detection accuracy for typhoon-storm-surge events (precision = 0.89), although the recall of the CC is the lowest (recall = 0.42), as only severe storm surges were detected. This paper therefore evaluates four storm-surge-detection methods in coastal areas of China and provides a basis for the evaluation of storm-surge-detection methods and detection algorithms.

Characterization of isolated starch from Isatis indigotica Fort. root and anhydro-sugars preparation using its decoction residues

Isatis indigotica Fort. root (Ban-lan-gen, IIR), a traditional Chinese medicine (TCM), has an ancient and well-documented history for its medicinal properties. Aside from epigoitrin, indole alkaloids, and their corresponding derivatives as medicinal ingredients, it also contains lots of biomass such as starch. Herein, a new starch was isolated from IIR and the physicochemical properties such as amylose content, moisture content, ash content, morphology, thermal properties, and crystallography were characterized systematically. The amylose content of IIR starch was 19.84 ± 0.85%, and the size and shape of starch granules is ellipsoidal shape with sizes from 2 to 10 μm. IIR starch exhibited a C-type pattern and had 25.92% crystallinity (higher than that of corn starch). The gelatinization temperature of IIR starch was 58.68-75.41 °C, and its gelatinization enthalpy was ΔH gel = 4.33 J/g. After decocting, the IIR's residues can be used to prepare anhydro-sugars in a polar aprotic solvent. The total carbon yield of levoglucosan (LG), levoglucosenone (LGO), 5-hydroxymethylfurfural (HMF), and furfural (FF) could reach 69.81% from IIR's decoction residues in 1,4-dioxane with 15 mM H2SO4 as the catalyst. Further, the residues after dehydration were prepared into biochar by thermochemical conversion and the BET surface area of biochar was 1749.46 m2/g which has good application prospect in soil improvement and alleviates obstacles of IIR continuous cropping.

The effect of high-density genotypic data and different methods on joint genomic prediction: A case study in large white pigs

Joint genomic prediction (GP) is an attractive method to improve the accuracy of GP by combining information from multiple populations. However, many factors can negatively influence the accuracy of joint GP, such as differences in linkage disequilibrium phasing between single nucleotide polymorphisms (SNPs) and causal variants, minor allele frequencies and causal variants' effect sizes across different populations. The objective of this study was to investigate whether the imputed high-density genotype data can improve the accuracy of joint GP using genomic best linear unbiased prediction (GBLUP), single-step GBLUP (ssGBLUP), multi-trait GBLUP (MT-GBLUP) and GBLUP based on genomic relationship matrix considering heterogenous minor allele frequencies across different populations (wGBLUP). Three traits, including days taken to reach slaughter weight, backfat thickness and loin muscle area, were measured on 67 276 Large White pigs from two different populations, for which 3334 were genotyped by SNP array. The results showed that a combined population could substantially improve the accuracy of GP compared with a single-population GP, especially for the population with a smaller size. The imputed SNP data had no effect for single population GP but helped to yield higher accuracy than the medium-density array data for joint GP. Of the four methods, ssGLBUP performed the best, but the advantage of ssGBLUP decreased as more individuals were genotyped. In some cases, MT-GBLUP and wGBLUP performed better than GBLUP. In conclusion, our results confirmed that joint GP could be beneficial from imputed high-density genotype data, and the wGBLUP and MT-GBLUP methods are promising for joint GP in pig breeding.

MiR-484 promotes the malignant progression of glioma by inhibiting CDKN2A expression

INTRODUCTION

Cyclin Dependent Kinase Inhibitor 2A (CDKN2A) is involved in glioma progression, but the specific molecular mechanism of CDKN2A in glioma cell migration and invasion needs to be further explored.

MATERIAL AND METHODS

Data related to CDKN2A expression and glioma overall survival were obtained from The Cancer Genome Atlas (TCGA) database. Then, CDKN2A expression in glioma tissues/cells or paracancer tissues/astrocytes was measured by quantitative reverse transcription polymerase chain reaction (qRT-PCR) or Western blot. Afterwards, Wound healing, Transwell and tube formation assay were performed to identify the invasion, migration and angiogenesis of glioma cells, respectively. TargetScan database predicted the targeted binding between miR-484 and CDKN2A, which was verified by dual luciferase reporter gene assay. Western blot and qRT-PCR were performed to detect the expression of VEGF, E-cadherin, N-cadherin and Vimentin in glioma cells.

RESULTS

CDKN2A was low-expressed in glioma tissue/cells as compared to paracancer tissue/astrocytes, and was strongly associated to the poor prognosis of glioma. Further studies found that down-regulation of CDKN2A could promote migration, invasion and angiogenesis of glioma cells. Besides, miR-484 was high-expressed in glioma cells compared to astrocytes. Up-regulation of miR-484 could enhance migration, invasion and angiogenesis of glioma cells. In addition, up-regulated miR-484 suppressed the expression of E-cadherin, and promoted the expression of N-cadherin, Vimentin and VEGF. However, there was negative regulation of miR-484 and CDKN2A, and CDKN2A could partially offset the effect of miR-484.

CONCLUSIONS

MiR-484 promoted cell migration, invasion and angiogenesis by inhibiting CDKN2A expression.

A novel maize microRNA negatively regulates resistance to Fusarium verticillioides

Although microRNAs (miRNAs) regulate the defence response against multiple pathogenic fungi in diverse plant species, few efforts have been devoted to deciphering the involvement of miRNA in resistance to Fusarium verticillioides, a major pathogenic fungus affecting maize production. In this study, we discovered a novel F. verticillioides-responsive miRNA designated zma-unmiR4 in maize kernels. The expression of zma-unmiR4 was significantly repressed in the resistant maize line but induced in the susceptible lines upon exposure to F. verticillioides exposure, whereas its target gene ZmGA2ox4 exhibited the opposite pattern of expression. Heterologous overexpression of zma-unmiR4 in Arabidopsis resulted in enhanced growth and compromised resistance to F. verticillioides. By contrast, transgenic plants overexpressing ZmGA2ox4 or the homologue AtGA2ox7 showed impaired growth and enhanced resistance to F. verticillioides. Moreover, zma-unmiR4-mediated suppression of AtGA2ox7 disturbed the accumulation of bioactive gibberellin (GA) in transgenic plants and perturbed the expression of a set of defence-related genes in response to F. verticillioides. Exogenous application of GA or a GA biosynthesis inhibitor modulated F. verticillioides resistance in different plants. Taken together, our results suggest that the zma-unmiR4-ZmGA2ox4 module might act as a major player in balancing growth and resistance to F. verticillioides in maize.

Genetic parameters and genome-wide association for milk production traits and somatic cell score in different lactation stages of Shanghai Holstein population

The aim of this study was to investigate the genetic parameters and genetic architectures of six milk production traits in the Shanghai Holstein population. The data used to estimate the genetic parameters consisted of 1,968,589 test-day records for 305,031 primiparous cows. Among the cows with phenotypes, 3,016 cows were genotyped with Illumina Bovine SNP50K BeadChip, GeneSeek Bovine 50K BeadChip, GeneSeek Bovine LD BeadChip v4, GeneSeek Bovine 150K BeadChip, or low-depth whole-genome sequencing. A genome-wide association study was performed to identify quantitative trait loci and genes associated with milk production traits in the Shanghai Holstein population using genotypes imputed to whole-genome sequences and both fixed and random model circulating probability unification and a mixed linear model with rMVP software. Estimated heritabilities (h2) varied from 0.04 to 0.14 for somatic cell score (SCS), 0.07 to 0.22 for fat percentage (FP), 0.09 to 0.27 for milk yield (MY), 0.06 to 0.23 for fat yield (FY), 0.09 to 0.26 for protein yield (PY), and 0.07 to 0.35 for protein percentage (PP), respectively. Within lactation, genetic correlations for SCS, FP, MY, FY, PY, and PP at different stages of lactation estimated in random regression model were ranged from -0.02 to 0.99, 0.18 to 0.99, 0.04 to 0.99, 0.04 to 0.99, 0.01 to 0.99, and 0.33 to 0.99, respectively. The genetic correlations were highest between adjacent DIM but decreased as DIM got further apart. Candidate genes included those related to production traits (DGAT1, MGST1, PTK2, and SCRIB), disease-related (LY6K, COL22A1, TECPR2, and PLCB1), heat stress–related (ITGA9, NDST4, TECPR2, and HSF1), and reproduction-related (7SK and DOCK2) genes. This study has shown that there are differences in the genetic mechanisms of milk production traits at different stages of lactation. Therefore, it is necessary to conduct research on milk production traits at different stages of lactation as different traits. Our results can also provide a theoretical basis for subsequent molecular breeding, especially for the novel genetic loci.

Evaluation and Identification of Resistance Lines and QTLs of Maize to Seedborne Fusarium verticillioides

Internal fungal contamination in cereal grains may affect plant growth and result in health concerns for humans and animals. Fusarium verticillioides is a seedborne fungus that can systemically infect maize. However, few efforts had been devoted to studying the genetics of maize resistance to seedborne F. verticillioides. In this study, we developed a disease evaluation method to identify resistance to seedborne F. verticillioides in maize, by which a set of 121 diverse maize inbred lines were evaluated. A 160 F₁₀-generation recombinant inbred line (RIL) population derived from a cross of the resistant (BT-1) and susceptible (N6) inbred line was further used to identify major quantitative trait loci (QTLs) for seedborne F. verticillioides resistance. Eighteen inbred lines with a high resistance to seedborne F. verticillioides were characterized and could be used as potential germplasm resources for genetic improvement of maize resistance. Six QTLs with high heritability across multiple environments were detected on chromosomes 3, 4, 6, and 10, among which was a major QTL, qISFR4-1. Located on chromosome 4 at the interval of 12922609-13418025, qISFR4-1 could explain 16.63% of the total phenotypic variance. Distinct expression profiles of eight candidate genes in qISFR4-1 between BT-1 and N6 inbred lines suggested their pivotal regulatory roles in seedborne F. verticillioides resistance. Taken together, these results will improve our understanding of the resistant mechanisms of seedborne F. verticillioides and would provide valuable germplasm resources for disease resistance breeding in maize.

Porcine parvovirus triggers autophagy through the AMPK/Raptor/mTOR pathway to promote viral replication in porcine placental trophoblasts

Autophagy has been demonstrated to play important roles in the infection and pathogenesis of many viruses. We previously found that porcine parvovirus (PPV) infection can induce autophagy in porcine placental trophoblast cells (PTCs), but its underlying mechanism has not yet been fully revealed. In this study, we showed that PPV infection inhibited the activation of mTORC1 and promoted the expression of Beclin 1 and LC3II in PTCs. Treatment with a mTOR activator inhibited the expression of Beclin 1 and LC3II, as well as autophagy formation, and reduced viral replication in PPV-infected PTCs. Furthermore, we found that inhibition of AMPK expression, but not the inhibition of PI3K/Akt, p53, or MAPK/ERK1/2 pathway activation, can significantly increase mTOR phosphorylation in PPV-infected PTCs. Then, we found that the regulation of mTOR phosphorylation by AMPK was mediated by Raptor. AMPK expression knockout inhibited the activation of Raptor, decreased the expression of Beclin 1 and LC3II, suppressed the formation of autophagosomes, and reduced viral replication during PPV infection. Together, our results showed that PPV infection induces autophagy to promote viral replication by inhibiting the activation of mTORC1 through activation of the AMPK/Raptor pathway. These findings provide information to understand the molecular mechanisms of PPV-induced autophagy.

Single Crystal Halide Perovskite Film for Nonlinear Resistive Memory with Ultrahigh Switching Ratio

Morre's law is coming to an end only if the memory industry can keep stuffing the devices with new functionality. Halide perovskite acts as a promising candidate for application in next-generation nonvolatile memory. As is well known, the switching ratio is the key device requirement of resistive memory to improve recognition accuracy. Here, the authors introduce an all-inorganic halide perovskite CsPbBr₃ single crystal film (SCF) into resistive memory as an active layer. The Ag/CsPbBr₃ /Ag memory cells exhibit reproducible resistive switching with an ultrahigh switching ratio (over 10⁹ ) and a fast switching speed (1.8 µs). It is studied that the Schottky barrier of metal/CsPbBr₃ SCF contact follows the tendency of Schottky-Mott theory, and the Fermi level pinning effect is effectively reduced. The interface S parameter of metal/CsPbBr₃ SCF contact is 0.50, suggesting a great interface contact is formed. The great interface contact contributes to the steady high resistance state (HRS), and then the steady HRS leads to an ultrahigh resistive switching ratio. This work demonstrates high performance from halide perovskite SCF-based memory. The introduction of halide perovskite SCF in resistive random access memory provides great potential as an alternative in future computing systems.

The construction of a haplotype reference panel using extremely low coverage whole genome sequences and its application in genome-wide association studies and genomic prediction in Duroc pigs

Extremely low coverage whole genome sequencing (lcWGS) is an economical technique to obtain high-density single nucleotide polymorphisms (SNPs). Here, we explored the feasibility of constructing a haplotype reference panel (lcHRP) using lcWGS and evaluated the effects of lcHRP through a genome-wide association study (GWAS) and genomic prediction in pigs. A total of 297 and 974 Duroc pigs were genotyped using lcWGS and a 50 K SNP array, respectively. We obtained 19,306,498 SNPs using lcWGS with an accuracy of 0.984. With the help of lcHRP, the accuracy of imputation from the SNP array to lcWGS was 0.922. Compared to the SNP array findings, those from the imputation-based GWAS identified more signals across four traits. With the integration of the top 1% imputation-based GWAS findings as genomic features, the accuracies of genomic prediction was improved by 6.0% to 13.2%. This study showed the great potential of lcWGS in pigs' molecular breeding.

Identification of biomarkers and ceRNA network in glioblastoma through bioinformatic analysis and evaluation of potential prognostic values

Background

Glioblastoma (GBM) is one of the most common and malignant primary brain tumors in adults, with high mortality rates and limited treatment. Based on bioinformatic analyses, this study aimed to identify biomarkers and relevant molecular pathways that may serve as potential targets for the treatment of GBM.

Methods

Expression profiles were downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database; nine GBM samples and three normal samples were extracted from the GSE104267 dataset. Differentially-expressed messenger RNA (mRNA) and long non-coding RNA (lncRNA) were screened from the preprocessed dataset. The clusterProfiler package in R was used to perform a biological process (BP) analysis of gene ontology (GO), and a Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was performed separately in upregulated and downregulated groups. A competing endogenous RNA (ceRNA) network was constructed using Cytoscape. Based on data downloaded from The Cancer Genome Atlas (TCGA), Kaplan-Meier (K-M) survival curves were established. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to evaluate IL10RB antisense RNA 1 (IL10RB-AS1) expression in GBM tissue compared with that in normal brain tissue.

Results

A total of 253 differentially-expressed genes (DEGs) were obtained. Based on BP and KEGG enrichment annotation analyses, 11 lncRNA-related pathways were identified through function prediction analysis. A competing endogenous RNA (ceRNA) subnetwork, including 21 nodes and 29 regulatory pairs, was then constructed. Based on the clinical data of GBM in TCGA, one survival-related DEG, IL10RB-AS1, was identified using the log-rank statistical test. K-M survival curves of IL10RB-AS1 and expression levels of IL10RB-AS1 in both GBM and normal brain tissue were obtained.

Conclusions

Through the combination of bioinformatic analyses, one survival-related differentially-expressed lncRNA, IL10RB-AS1, was identified. This, along with several related signaling pathways and ceRNA systems that were elucidated in GBM have potential prognostic value and might offer new possibilities for the treatment of GBM.

Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits

Background

Over several decades, a wide range of natural and artificial selection events in response to subtropical environments, intensive pasture and intensive feedlot systems have greatly changed the customary behaviour, appearance, and important economic traits of Shanghai Holstein cattle. In particular, the longevity of the Shanghai Holstein cattle population is generally short, approximately the 2nd to 3rd lactation. In this study, two complementary approaches, integrated haplotype score (iHS) and runs of homozygosity (ROH), were applied for the detection of selection signatures within the genome using genotyping by genome-reduced sequence data from 1092 cows.

Results

In total, 101 significant iHS genomic regions containing selection signatures encompassing a total of 256 candidate genes were detected. There were 27 significant |iHS| genomic regions with a mean |iHS| score > 2. The average number of ROH per individual was 42.15 ± 25.47, with an average size of 2.95 Mb. The length of 78 % of the detected ROH was within the range of 1–2 MB and 2–4 MB, and 99 % were shorter than 8 Mb. A total of 168 genes were detected in 18 ROH islands (top 1 %) across 16 autosomes, in which each SNP showed a percentage of occurrence > 30 %. There were 160 and 167 genes associated with the 52 candidate regions within health-related QTL intervals and 59 candidate regions within reproduction-related QTL intervals, respectively. Annotation of the regions harbouring clustered |iHS| signals and candidate regions for ROH revealed a panel of interesting candidate genes associated with adaptation and economic traits, such as IL22RA1, CALHM3, ITGA9, NDUFB3, RGS3, SOD2, SNRPA1, ST3GAL4, ALAD, EXOSC10, and MASP2. In a further step, a total of 1472 SNPs in 256 genes were matched with 352 cis-eQTLs in 21 tissues and 27 trans-eQTLs in 6 tissues. For SNPs located in candidate regions for ROH, a total of 108 cis-eQTLs in 13 tissues and 4 trans-eQTLs were found for 1092 SNPs. Eighty-one eGenes were significantly expressed in at least one tissue relevant to a trait (P value < 0.05) and matched the 256 genes detected by iHS. For the 168 significant genes detected by ROH, 47 gene-tissue pairs were significantly associated with at least one of the 37 traits.

Conclusions

We provide a comprehensive overview of selection signatures in Shanghai Holstein cattle genomes by combining iHS and ROH. Our study provides a list of genes associated with immunity, reproduction and adaptation. For functional annotation, the cGTEx resource was used to interpret SNP-trait associations. The results may facilitate the identification of genes relevant to important economic traits and can help us better understand the biological processes and mechanisms affected by strong ongoing natural or artificial selection in livestock populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08042-x.

[A multicenter randomized controlled study of bismuth-containing quadruple therapy followed by Jing-Hua-Wei-Kang in the treatment of patients newly diagnosed with Helicobacter pylori infection and dyspepsia]

Objective: To investigate the Helicobacter pylori (H. pylori) eradication rate and improvement of dyspepsia in patients who were newly diagnosed with H. pylori infection and dyspepsia and treated by bismuth-containing quadruple therapy followed by Jing-Hua-Wei-Kang(JHWK). Methods: Patients who were newly diagnosed with dyspepsia and H. pylori infection and treated in 16 medical centers in China between December 1, 2017 and September 30, 2019 were randomly divided into two groups. The experimental group received bismuth-containing quadruple therapy (esomeprazole+amoxicillin+furazolidone+colloidal bismuth pectin capsule, 14 days), followed by JHWK (30 days), and the course of treatment was 44 days in total. In the control group, the administration regimen was bismuth-containing quadruple therapy (esomeprazole+amoxicillin+furazolidone+colloidal bismuth pectin capsule, 14 days). The main outcome measure was H. pylori eradication rate, while the secondary outcome measures were dyspepsia symptom changes and adverse events during the treatment and the 1st month after treatment. Results: A total of 1 054 patients were included in the study. There were 522 cases enrolled in the experimental group, including 224(42.91%) men and 298(57.09%) women, and the age was 53(26, 73) years old; 532 cases enrolled in the control group, including 221(41.54%) men and 311(58.46%) women, and the age was 46(22, 71) years old. Based on PP analysis, it was found that the H. pylori eradication rate in the experimental group was significantly higher than those in the control group (93.85% vs 87.88%, P=0.001). In the group of all enrolled patients, the symptom dyspepsia after H. pylori eradication was significantly improved compared with that before treatment [4(4, 7) vs 15(10, 22), P<0.001], so was the superior and middle abdominal pain [1(1, 4) vs 4(1, 8), P<0.001], the postprandial fullness [1(1, 4) vs 4(4, 9), P<0.001], the early satiety [1(1, 1) vs 4(1, 4), P<0.001], and the heartburn [1(1, 1) vs 1(1, 4), P<0.001]. The symptom dyspepsia after treatment was significantly improved compared with that before treatment in the experimental, the control groups, the successful and the unsuccessful H. pylori eradication groups. The superior and middle abdominal pain after treatment was signifcantly improved than that before treatment [1(1, 2) vs 1(1, 4), P<0.001], so were the postprandial fullness [1(1, 3) vs 1(1, 4), P=0.002] and the dyspepsia[4(4, 7) VS 7(4, 10), P<0.001]. There was no statistically significant difference in the incidence of adverse events between the experimental group and the control group (1.34% vs 0.38%, P=0.09). Conclusions: Compared with bismuth-containing quadruple therapy, bismuth-containing quadruple therapy followed by JHWK significantly improves the H. pylori eradication rate without increasing the incidence of adverse events. H. pylori eradication therapy can improve symptoms of patients with H. pylori infection and dyspepsia.

Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data

Laiwu pigs, distinguished by their high intramuscular fat of 7-9%, is an indigenous pig breed of China, and recent studies also found that Laiwu pigs showed high resistance to Porcine circovirus type 2. However, with the introduction of commercial varieties, the population of Laiwu pigs has declined, and some lineages have disappeared, which could result in inbreeding. Runs of homozygosity (ROH) can be used as a good measure of individual inbreeding status and is also normally used to detect selection signatures so as to map the candidate genes associated with economically important traits. In this study, we used data from Genotyping by Genome Reducing and Sequencing to investigate the number, length, coverage, and distribution patterns of ROH in 93 Chinese Laiwu pigs and identified genomic regions with a high ROH frequency. The average inbreeding coefficient calculated by pedigree was 0.021, whereas that estimated by all detected ROH segments was 0.133. Covering 13.4% of the whole genome, a total of 7,508 ROH segments longer than 1 Mb were detected, whose average length was 3.76 Mb, and short segments (1-5 Mb) dominated. For individuals, the coverage was in the range between 0.56 and 36.86%. For chromosomes, SSC6 had the largest number (n = 688), and the number of ROH in SSC12 was the lowest (n = 215). Thirteen ROH islands were detected in our study, and 86 genes were found within those regions. Some of these genes were correlated with economically important traits, such as meat quality (ECI1, LRP12, NDUFA4L2, GIL1, and LYZ), immunity capacity (IL23A, STAT2, STAT6, TBK1, IFNG, and ITH2), production (DCSTAMP, RDH16, and GDF11), and reproduction (ODF1 and CDK2). A total of six significant Gene Ontology terms and nine significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, most of which were correlated with disease resistance and biosynthesis processes, and one KEGG pathway was related to lipid metabolism. In addition, we aligned all of the ROH islands to the pig quantitative trait loci (QTL) database and finally found eight QTL related to the intramuscular fat trait. These results may help us understand the characteristics of Laiwu pigs and provide insight for future breeding strategies.

Applications of Support Vector Machine in Genomic Prediction in Pig and Maize Populations

Genomic prediction (GP) has revolutionized animal and plant breeding. However, better statistical models that can improve the accuracy of GP are required. For this reason, in this study, we explored the genomic-based prediction performance of a popular machine learning method, the Support Vector Machine (SVM) model. We selected the most suitable kernel function and hyperparameters for the SVM model in eight published genomic data sets on pigs and maize. Next, we compared the SVM model with RBF and the linear kernel functions to the two most commonly used genome-enabled prediction models (GBLUP and BayesR) in terms of prediction accuracy, time, and the memory used. The results showed that the SVM model had the best prediction performance in two of the eight data sets, but in general, the predictions of both models were similar. In terms of time, the SVM model was better than BayesR but worse than GBLUP. In terms of memory, the SVM model was better than GBLUP and worse than BayesR in pig data but the same with BayesR in maize data. According to the results, SVM is a competitive method in animal and plant breeding, and there is no universal prediction model.

Topical photodynamic therapy combined with ablative "light needles" against basal cell carcinoma

Basal cell carcinoma (BCC), a non-melanoma cancer with high morbidity in the elders, is a type of limited skin cancer with a projected appearance. Traditional treatments such as oral or injection administration are likely to result in serious side effects. Here, we developed a strategy that combined photodynamic therapy (PDT) with ablative light "needles" (carbon-dioxide laser) for the treatment of BCC, involving β-Tetra-(4-carboxyl-phenoxy)-zinc phthalocyanine (ZnPC₄) cubic phases with high drug loading, easy preparation, long local retention, good spreading ability and little toxicity. A model of nude mice with BCC was established for the study of pharmacodynamics. The light needles of low energy (53 mJ/cm²) used here could promote transdermal absorption of ZnPC₄ cubic phases while those of high energy (238 mJ/cm²) alone could completely kill tumor cells with no recurrence. However, ZnPC₄ cubic phases alone could not completely inhibit tumor growth, for it was distributed mainly at the topical administration site in the absence of any adjuvant technology. Therefore, the combination of photodynamics and light needles offered a good solution. Especially, the combined use of light needles with high energy and ZnPC₄ cubic phases can treat BCC efficiently with no recurrence. This approach is expected to be a novel and promising medication against BCC.

Synthesis and biological evaluation of 5'-C-methyl nucleotide prodrugs for treating HCV infections

Nucleotide prodrugs are of great clinical interest for treating a variety of viral infections due to their ability to target tissues selectively and to deliver relatively high concentrations of the active nucleotide metabolite intracellularly. However, their clinical successes have been limited, oftentimes due to unwanted in vivo metabolic processes that reduce the quantities of nucleoside triphosphate that reach the site of action. In an attempt to circumvent this, we designed novel nucleosides that incorporate a sterically bulky group at the 5'-carbon of the phosphoester prodrug, which we reasoned would reduce the amounts of non-productive PO bond cleavage back to the corresponding nucleoside by nucleotidases. Molecular docking studies with the NS5B HCV polymerase suggested that a nucleotide containing a 5'-methyl group could be accommodated. Therefore, we synthesized mono- and diphosphate prodrugs of 2',5'-C-dimethyluridine stereoselectively and evaluated their cytotoxicity and anti-HCV activity in the HCV replicon assay. All four prodrugs exhibited anti-HCV activity with IC₅₀ values in the single digit micromolar concentrations, with the 5'(R)-C-methyl prodrug displaying superior potency relative to its 5'(S)-C-methyl counterpart. However, when compared to the unmethylated prodrug, the potency is poorer. The poorer potency of these prodrugs may be due to unfavorable steric interactions of the 5'-C-methyl group in the active sites of the kinases that catalyze the formation of active triphosphate metabolite.

Haplotype Block Analysis Reveals Candidate Genes and QTLs for Meat Quality and Disease Resistance in Chinese Jiangquhai Pig Breed

The Jiangquhai (JQ) pig breed is one of the most widely recognized pig populations in China due to its unique and dominant characteristics. In this study, we examined the extent of Linkage disequilibrium (LD) and haplotype block structure of the JQ pig breed, and scanned the blocks for possible genes underlying important QTLs that could either be responsible for some adaptive features in these pigs or might have undergone some selection pressure. We compared some of our results with other Chinese and Western pig breeds. The results show that the JQ breed had the highest total block length (349.73 Mb ≈ 15% of its genome), and the coverage rate of blocks in most of its chromosomes was larger than those of other breeds except for Sus scrofa chromosome 4 (SSC4), SSC6, SSC7, SSC8, SSC10, SSC12, SSC13, SSC14, SSC17, SSC18, and SSCX. Moreover, the JQ breed had more SNPs that were clustered into haplotype blocks than the other breeds examined in this study. Our shared and unique haplotype block analysis revealed that the Hongdenglong (HD) breed had the lowest percentage of shared haplotype blocks while the Shanzhu (SZ) breed had the highest. We found that the JQ breed had an average r² > 0.2 at SNPs distances 10–20 kb and concluded that about 120,000–240,000 SNPs would be needed for a successful GWAS in the breed. Finally, we detected a total of 88 genes harbored by selected haplotype blocks in the JQ breed, of which only 4 were significantly enriched (p-value ≤ 0.05). These genes were significantly enriched in 2 GO terms (p-value < 0.01), and 2 KEGG pathways (p-value < 0.02). Most of these enriched genes were related to health. Also, most of the overlapping QTLs detected in the haplotype blocks were related to meat and carcass quality, as well as health, with a few of them relating to reproduction and production. These results provide insights into the genetic architecture of some adaptive and meat quality traits observed in the JQ pig breed and also revealed the pattern of LD in the genome of the pig. Our result provides significant guidance for improving the statistical power of GWAS and optimizing the conservation strategy for this JQ pig breed.

Wound healing of laser injured skin with glycerol monooleicate cubic liquid crystal

Laser has found increasingly wider applications in the medical filed, but laser is likely to cause damage to patients' skin. In this experiment, we were surprised to find that glyceryl monooleate (GMO)-based cubic liquid crystal had excellent healing effect on the skin of guinea pigs damaged by laser. Transepidermal water loss (TEWL), H.E. pathology, Masson trichrome dyeing, interleukin-6 (IL-6) levels and the percutaneous depth of fluorescein isothiocyanate (FITC) dyeing were used to evaluate the therapeutic effect of GMO-based cubic liquid crystals against laser damage of different degrees among guinea pigs. GMO-based cubic liquid crystals had an obvious effect in the treatment of slight and moderate laser damage. This finding may provide a effective medical treatment protocols for laser skin damage.

Linkage mapping and genome-wide association reveal candidate genes conferring thermotolerance of seed-set in maize

It is predicted that high-temperature stress will increasingly affect crop yields worldwide as a result of climate change. In order to determine the genetic basis of thermotolerance of seed-set in maize under field conditions, we performed mapping of quantitative trait loci (QTLs) in a recombinant inbred line (RIL) population using a collection of 8329 specifically developed high-density single-nucleotide polymorphism (SNP) markers, combined with a genome-wide association study (GWAS) of 261 diverse maize lines using 259 973 SNPs. In total, four QTLs and 17 genes associated with 42 SNPs related to thermotolerance of seed-set were identified. Among them, four candidate genes were found in both linkage mapping and GWAS. Thermotolerance of seed-set was increased significantly in near-isogenic lines (NILs) that incorporated the four candidate genes in a susceptible parent background. The expression profiles of two of the four genes showed that they were induced by high temperatures in the maize tassel in a tolerant parent background. Our results indicate that thermotolerance of maize seed-set is regulated by multiple genes each of which has minor effects, with calcium signaling playing a central role. The genes identified may be exploited in breeding programs to improve seed-set and yield of maize under heat stress.

MiR-33 may be a Biological Marker for Coronary Heart Disease

BACKGROUND

The main aim of this study was to evaluate the expression and specific role of miR-33 in the progression of coronary heart disease (CAD), thereby evaluating their diagnostic ability and use in treatment in CAD patients.

METHODS

Real time PCR was carried out to explore the level of miR-33 in the plasma of CAD patients and controls. ELISA was performed to analyze the level of placenta growth factor fragment (PLGF). Correlations between miR-33 and PLGF as well as other biochemical parameters were performed with Pearson's correlation analysis.

RESULTS

First, we evaluated the level of plasma miR-33 in CAD patients and healthy controls. Compared with the control group, the level of plasma miR-33 was significantly increased in CAD patients. Furthermore, Spearman's correlation assay showed that plasma miR-33 positively correlated with the Gensini score (r = 0.354, p = 0.003). Meanwhile, plasma miR-33 was significantly enhanced in CAD patients with single- (1 ± 0.48), double- (1.85 ± 0.687), and triple-vessel disease (2.35 ± 0.87). In addition, Spearman's correlation assay demonstrated that plasma miR-33 positively correlated with plasma PLGF level (r = 0.354, p = 0.003). Lastly, ROC analysis showed that plasma miR-33 could screen CAD patients from healthy controls.

CONCLUSIONS

In summary, we showed novel data that enhanced plasma miR-33 may promote the progression of CAD. Furthermore, plasma miR-33 could be used as a potential non-invasive biomarker for CAD patients, which may shed light on the diagnosis and therapy of CAD.

Estimation of genetic parameters for reproductive traits in connectedness groups of Duroc, Landrace and Yorkshire pigs in China

The objective of this study was to estimate group- and breed-specific genetic parameters for reproductive traits in Chinese Duroc, Landrace, and Yorkshire populations. Records for reproductive traits between April 1998 and December 2017 from 92 nucleus pig breeding farms, which were involved in the China Swine Genetic Improvement Program, were analysed. Due to weak genetic connectedness across all farms, connectedness groups consisting of related farms were used. Three, two and four connectedness groups for Duroc, Landrace and Yorkshire were firstly established according to the genetic connectedness rating among farms. For each connectedness group a five-trait animal model was implemented, and via restricted maximum likelihood procedure the genetic parameters were estimated for five reproductive traits i.e., total number born (TNB), number born alive (NBA), litter weight at farrowing (LWF), farrowing interval (FI) and age at first farrowing (AFF). The average of heritabilities among connectedness groups ranged from .01 (for FI in Yorkshire) to .30 (for AFF in Duroc). Estimates of repeatability for litter traits ranged from .14 to .20 and were consistent for each breed, and for FI, the estimates varied from .01 to .11 across breeds and groups. The estimated genetic correlations among litter traits (i.e., TNB, NBA and LWF) were all significantly high (>.56) and similar across breeds. Averaged genetic correlations over three breeds were -.25, -.27, -.18, -.04, -.10, -.02, and .28 for FI-TNB, FI-NBA, FI-LWF, AFF-TNB, AFF-NBA, AFF-LWF and FI-AFF, respectively. The standard errors of the estimates were all very low (<0.01) in most situations. Results from this study suggest that selection based on TNB which is currently used in dam line selection index can improve NBA and LWF simultaneously. However, care should be taken on FI and AFF as they are both greatly influenced by non-genetic factors such as management and measurement.

Ultraflexible and Lightweight Bamboo-Derived Transparent Electrodes for Perovskite Solar Cells

Wearable devices are mainly based on plastic substrates, such as polyethylene terephthalate and polyethylene naphthalate, which causes environmental pollution after use due to the long decomposition periods. This work reports on the fabrication of a biodegradable and biocompatible transparent conductive electrode derived from bamboo for flexible perovskite solar cells. The conductive bioelectrode exhibits extremely flexible and light-weight properties. After bending 3000 times at a 4 mm curvature radius or even undergoing a crumpling test, it still shows excellent electrical performance and negligible decay. The performance of the bamboo-based bioelectrode perovskite solar cell exhibits a record power conversion efficiency (PCE) of 11.68%, showing the highest efficiency among all reported biomass-based perovskite solar cells. It is remarkable that this flexible device has a highly bendable mechanical stability, maintaining over 70% of its original PCE during 1000 bending cycles at a 4 mm curvature radius. This work paves the way for perovskite solar cells toward comfortable and environmentally friendly wearable devices.

Fabrication of Nickel Oxide Nanopillar Arrays on Flexible Electrodes for Highly Efficient Perovskite Solar Cells

Semiconductor nanomaterials with controlled morphologies and architectures are of critical importance for high-performance optoelectronic devices. However, the fabrication of such nanomaterials on polymer-based flexible electrodes is particularly challenging due to degradation of the flexible electrodes at a high temperature. Here we report the fabrication of nickel oxide nanopillar arrays (NiO _x NaPAs) on a flexible electrode by vapor deposition, which enables highly efficient perovskite solar cells (PSCs). The NiO _x NaPAs exhibit an enhanced light transmittance for light harvesting, prohibit exciton recombination, promote irradiation-generated hole transport and collection, and facilitate the formation of large perovskite grains. These advantageous features result in a high efficiency of 20% and 17% for the rigid and flexible PSCs, respectively. Additionally, the NaPAs show no cracking after 500 times of bending, consistent with the mechanic simulation results. This robust fabrication opens a new opportunity for the fabrication of a large area of high-performance flexible optoelectronic devices.

Use of a Bayesian model including QTL markers increases prediction reliability when test animals are distant from the reference population

Relatedness between reference and test animals has an important effect on the reliability of genomic prediction for test animals. Because genomic prediction has been widely applied in practical cattle breeding and bulls have been selected according to genomic breeding value without progeny testing, the sires or grandsires of candidates might not have phenotypic information and might not be in the reference population when the candidates are selected. The objective of this study was to investigate the decreasing trend of the reliability of genomic prediction given distant reference populations, using genomic best linear unbiased prediction (GBLUP) and Bayesian variable selection models with or without including the quantitative trait locus (QTL) markers detected from sequencing data. The data used in this study consisted of 22,242 bulls genotyped using the 54K SNP array from EuroGenomics. Among them, 1,444 Danish bulls born from 2006 to 2010 were selected as test animals. Different reference populations with varying relationships to test animals were created according to pedigree-based relationships. The reference individuals having a relationship with one or more test animals higher than 0.4 (scenario ρ < 0.4), 0.2 (ρ < 0.2), or 0.1 (ρ < 0.1, where ρ = relationship coefficient) were removed from reference sets; these represented the distance between reference and test animals being 2 generations, 3 generations, and 4 generations, respectively. Imputed whole-genome sequencing data of bulls from Denmark were used to conduct a genome-wide association study (GWAS). A small number of significant variants (QTL markers) from the GWAS were added to the array data. To compare the effects of different models, the basic GBLUP model, a Bayesian selection variable model, a GBLUP model with 2 components of genetic effects, and a Bayesian model with pooled array data and QTL markers were used for estimating genomic estimated breeding values (GEBV) of test animals. The reliability of genomic prediction decreased when the test animals were more generations away from the reference population. The reliability of genomic prediction was 0.461 for 1 generation away and 0.396 for 3 generations away, with the same number of individuals in the reference set, using a GBLUP model with chip markers only. The results showed that using the Bayesian method and QTL markers improved the reliability of genomic prediction in all scenarios of relationship between test and reference animals, in a range of 1.3% and 65.1% (4 generations away with only 841 individuals in the reference set). However, most gains were for predictions of milk yield and fat yield. There was little improvement for predictions of protein yield and mastitis, and no improvement for prediction of fertility, except for scenario ρ < 0.1, in which there was a large improvement for predictions of all traits. On the other hand, models including more than 10% polygenic effect decreased prediction reliability when the relationship between test and reference animals was distant.

Genetic analysis of cob resistance to F. verticillioides: another step towards the protection of maize from ear rot

We lay the foundation for further research on maize resistance to Fusarium verticillioides cob rot by identifying a candidate resistance gene. Fusarium verticillioides ear rot is the most common type of maize ear rot in the Huanghuaihai Plain of China. Ear rot resistance includes cob and kernel resistance. Most of the current literature concentrates on kernel resistance, and genetic studies on cob resistance are scarce. We aimed on identifying the QTLs responsible for F. verticillioides cob rot (FCR) resistance. Twenty-eight genes associated with 48 single nucleotide polymorphisms (SNPs) were identified (P < 10^-4) to correlate with FCR resistance using a whole-genome association study. The major quantitative trait locus, qRcfv2, for FCR resistance was identified on chromosome 2 through linkage mapping and was validated in near-isogenic line populations. Two candidate genes associated with two SNPs were detected in the qRcfv2 region with a lower threshold (P < 10^-3). Through real-time fluorescence quantitative PCR, one candidate gene was found to have no expression in the cob but the other was expressed in response to F. verticillioides. These results lay a foundation for research on the resistance mechanisms of cob and provide resources for marker-assisted selection.

Assessment of Autozygosity Derived From Runs of Homozygosity in Jinhua Pigs Disclosed by Sequencing Data

Jinhua pig, a well-known Chinese indigenous breed, has evolved as a pig breed with excellent meat quality, greater disease resistance, and higher prolificacy. The reduction in the number of Jinhua pigs over the past years has raised concerns about inbreeding. Runs of homozygosity (ROH) along the genome have been applied to quantify individual autozygosity to improve the understanding of inbreeding depression and identify genes associated with traits of interest. Here, we investigated the occurrence and distribution of ROH using next-generation sequencing data to characterize autozygosity in 202 Jinhua pigs, as well as to identify the genomic regions with high ROH frequencies within individuals. The average inbreeding coefficient, based on ROH longer than 1 Mb, was 0.168 ± 0.052. In total, 18,690 ROH were identified in all individuals, among which shorter segments (1-5 Mb) predominated. Individual ROH autosome coverage ranged from 5.32 to 29.14% in the Jinhua population. On average, approximately 16.8% of the whole genome was covered by ROH segments, with the lowest coverage on SSC11 and the highest coverage on SSC17. A total of 824 SNPs (about 0.5%) and 11 ROH island regions were identified (occurring in over 45% of the samples). Genes associated with reproduction (HOXA3, HOXA7, HOXA10, and HOXA11), meat quality (MYOD1, LPIN3, and CTNNBL1), appetite (NUCB2) and disease resistance traits (MUC4, MUC13, MUC20, LMLN, ITGB5, HEG1, SLC12A8, and MYLK) were identified in ROH islands. Moreover, several quantitative trait loci for ham weight and ham fat thickness were detected. Genes in ROH islands suggested, at least partially, a selection for economic traits and environmental adaptation, and should be subject of future investigation. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the pig genome.

Improving genomic predictions by correction of genotypes from genotyping by sequencing in livestock populations

Background

Genotyping by sequencing (GBS) is a robust method to genotype markers. Many factors can influence the genotyping quality. One is that heterozygous genotypes could be wrongly genotyped as homozygotes, dependent on the genotyping depths. In this study, a method correcting this type of genotyping error was demonstrated. The efficiency of this correction method and its effect on genomic prediction were assessed using simulated data of livestock populations.

Results

Chip array (Chip) and four depths of GBS data was simulated. After quality control (call rate ≥ 0.8 and MAF ≥ 0.01), the remaining number of Chip and GBS SNPs were both approximately 7,000, averaged over 10 replicates. GBS genotypes were corrected with the proposed method. The reliability of genomic prediction was calculated using GBS, corrected GBS (GBSc), true genotypes for the GBS loci (GBSr) and Chip data. The results showed that GBSc had higher rates of correct genotype calls and higher correlations with true genotypes than GBS. For genomic prediction, using Chip data resulted in the highest reliability. As the depth increased to 10, the prediction reliabilities using GBS and GBSc data approached those using true GBS data. The reliabilities of genomic prediction using GBSc data were 0.604, 0.672, 0.684 and 0.704 after genomic correction, with the improved values of 0.013, 0.009, 0.006 and 0.001 at depth = 2, 4, 5 and 10, respectively.

Conclusions

The current study showed that a correction method for GBS data increased the genotype accuracies and, consequently, improved genomic predictions. These results suggest that a correction of GBS genotype is necessary, especially for the GBS data with low depths.

Electronic supplementary material

The online version of this article (10.1186/s40104-019-0315-z) contains supplementary material, which is available to authorized users.