Genetic diversity and characterization of rhinoviruses from Chinese clinical samples with a global perspective

IMPORTANCE

Based on clinical samples collected in China, we detected and reported 22 types for the first time in China, as well as three types for the first time in Asia, and reported their genetic characteristics and diversity. We identified a novel type of Rhinovirus (RV), A110, highlighting its unique genetic features. We annotated the genomic structure and serotype of all the existing RV sequences in the database, and four novel RV types were identified and their genetic diversity reported. Combined with the sequence annotation, we constructed a complete VP1 data set of RV and conducted the first large-scale evolutionary dynamics analysis of RV. Based on a high-quality data set, we conducted a comprehensive analysis of the guanine-cytosine (GC) content variations among serotypes of RVs. This study provides crucial theoretical support and valuable data for understanding RV's genetic diversity and developing antiviral strategies.

Development and validation of a novel nomogram predicting clinically significant prostate cancer in biopsy-naive men based on multi-institutional analysis

BACKGROUND

Prediction of clinically significant prostate cancer (csPCa) is essential to select biopsy-naive patients for prostate biopsy. This study was to develop and validate a nomogram based on clinicodemographic parameters and exclude csPCa using prostate-specific antigen density (PSAD) stratification.

METHODS

Independent predictors were determined via univariate and multivariate logistic analysis and adopted for developing a predictive nomogram, which was assessed in terms of discrimination, calibration, and net benefit. Different PSAD thresholds were used for deciding immediate biopsies in patients with Prostate Imaging-Reporting and Data System (PI-RADS) 3 lesions.

RESULTS

A total of 932 consecutive patients who underwent ultrasound-guided transperineal cognitive biopsy were enrolled in our study. In the development cohort, age (odds ratio [OR], 1.075; 95% confidence interval [CI], 1.036-1.114), PSAD (OR, 6.003; 95% CI, 2.826-12.751), and PI-RADS (OR, 3.419; 95% CI, 2.453-4.766) were significant predictors for csPCa. On internal and external validation, this nomogram showed high areas under the curve of 0.943, 0.922, and 0.897, and low Brier scores of 0.092, 0.102, and 0.133 and insignificant unreliability tests of 0.713, 0.490, and 0.859, respectively. Decision curve analysis revealed this model could markedly improve clinical net benefit. The probability of excluding csPCa was 98.51% in patients with PI-RADS 3 lesions and PSAD <0.2 ng/ml2 .

CONCLUSION

This novel nomogram including age, PSAD, and PI-RADS could be applied to accurately predict csPCa, and 44.08% of patients with equivocal imaging findings plus PSAD <0.2 ng/ml2 could safely forgo biopsy.

Fertility and prognosis assessment between bleomycin/etoposide/cisplatin and paclitaxel/carboplatin chemotherapy regimens in the conservative treatment of malignant ovarian germ cell tumors: a multicenter and retrospective study

OBJECTIVE

To evaluate the impact of bleomycin/etoposide/cisplatin (BEP) and paclitaxel/carboplatin (PC) chemotherapy regimens on the fertility and prognostic outcomes in malignant ovarian germ cell tumor (MOGCT) patients who underwent fertility-sparing surgery (FSS).

METHODS

A propensity score matching algorithm was performed between the BEP and PC groups. The χ² test and the Kaplan-Meier method were used to compare the fertility outcome, disease-free survival (DFS) and overall survival (OS). The Cox proportional hazards regression analysis was used to identify risk factor of DFS.

RESULTS

We included 213 patients, 185 (86.9%) underwent BEP chemotherapy, and 28 (13.1%) underwent PC chemotherapy. The median age was 22 years (range, 8-44 years), and the median follow-up period was 63 months (range, 2-191 months). Fifty-one (29.3%) patients had a pregnancy plan, and 35 (85.4%) delivered successfully. In the before and after propensity score matching cohorts, there were no significant differences in spontaneous abortion, selective termination of pregnancy, during-pregnancy status, and live birth between the BEP and PC groups (p>0.05). Fourteen (6.6%) patients experienced recurrence, including 11 (5.9%) in the BEP group and 3 (10.7%) in the PC group. Four (1.9%) patients in the BEP group died. Kaplan-Meier analysis revealed no significant differences in DFS (p=0.328) and OS (p=0.446) between the BEP and PC groups, and the same survival results were observed in the after matching cohort.

CONCLUSION

The PC regimen is as safe as the BEP regimen for MOGCT patients with fertility preservation treatment, and no differences were observed in fertility and clinical prognosis.

An ultrasound-driven immune-boosting molecular machine for systemic tumor suppression

Exploring facile and effective therapeutic modalities for synergistically controlling primary tumor and metastasis remains a pressing clinical need. Sonodynamic therapy (SDT) offers the possibility of noninvasively eradicating local solid tumors, but lacks antimetastatic activity because of its limited ability in generating systemic antitumor effect. Here, we exploited a previously unidentified ultrasound-driven “molecular machine,” DYSP-C34 (C34 for short), with multiple attractive features, emerging from preferential tumor accumulation, potent ultrasound-triggered cytotoxicity, and intrinsic immune-boosting capacity. Driven by the ultrasound, C34 functioned not only as a tumor cell killing reagent but also as an immune booster that could potentiate robust adaptive antitumor immunity by directly stimulating dendritic cells, resulting in the eradication of the primary solid tumor along with the inhibition of metastasis. This molecular machine, C34, rendered great promise to achieve systemic treatment against cancer via unimolecule-mediated SDT.

Response analysis of the nodes of pipe networks under seismic load

Transient ground displacement (TGD) that is caused by earthquakes can damage underground pipes. This damage is especially critical for the joints, elbows and tees of the pipes which play an important role in the operation of a pipe network. In this study, a scale pipe network with both elbows and tees, as well as some components of the pipe network with only tees or elbows, has been investigated. The response of the nodes of a pipe network, when installed in non-uniform geology, was analyzed using the shaking table test and ABAQUS finite element simulation. This paper has firstly introduced the preparation of the test and the developed finite element model. Then the system response in terms of strain, the friction, the bending deformation, the node deformation amplification coefficient and the pipe-soil relative displacement along the pipe axis of the pipe network and two pipe network components have been analyzed explaining the correlation between these responses. Finally, the influence of elbows and tees on the pipe network was analyzed, and the conclusions that have been reached about how tees and elbows can change the response of a pipe network during an earthquake can provide theoretical support for the seismic design and layout of an underground pipe network.

Novel variants in DNAH9 lead to nonsyndromic severe asthenozoospermia

BACKGROUND

Asthenozoospermia is one of the most common causes of male infertility, and its genetic etiology is poorly understood. DNAH9 is a core component of outer dynein arms in cilia and flagellum. It was reported that variants of DNAH9 (OMIM: 603330) might cause primary ciliary dyskinesia (PCD). However, variants in DNAH9 lead to nonsyndromic severe asthenozoospermia have yet to be reported.

METHODS

Whole exome sequencing (WES) was performed for two individuals with nonsyndromic severe asthenozoospermia from two non-consanguineous families, and Sanger sequencing was performed to verify the identified variants and parental origins. Sperm routine analysis, sperm vitality rate and sperm morphology analysis were performed according the WHO guidelines 2010 (5th edition). Transmission electron microscopy (TEM, TECNAI-10, 80 kV, Philips, Holland) was used to observe ultrastructures of sperm tail. Quantitative realtime-PCR and immunofluorescence staining were performed to detect the expression of DNAH9-mRNA and location of DNAH9-protein. Furthermore, assisted reproductive procedures were applied.

RESULTS

By WES and Sanger sequencing, compound heterozygous DNAH9 (NM_001372.4) variants were identified in the two individuals with nonsyndromic severe asthenozoospermia (F1 II-1: c.302dupT, p.Leu101fs*47 / c.6956A > G, p.Asp2319Gly; F2 II-1: c.6294 T > A, p.Phe2098Leu / c.10571 T > A, p.Leu3524Gln). Progressive rates less than 1% with normal sperm morphology rates and normal vitality rates were found in both of the two subjects. No respiratory phenotypes, situs inversus or other malformations were found by detailed medical history, physical examination and lung CT scans etc. Moreover, the expression of DNAH9-mRNA was significantly decreased in sperm from F1 II-1. And expression of DNAH9 is lower in sperm tail by immunofluorescence staining in F1 II-1 compared with normal control. Notably, by intracytoplasmic sperm injection (ICSI), F1 II-1 and his partner successfully achieved clinical pregnancy.

CONCLUSIONS

We identified DNAH9 as a novel pathogenic gene for nonsyndromic severe asthenospermia, and ICSI can contribute to favorable pregnancy outcomes for these patients.

Molecular typing and characterization of a novel genotype of EV-B93 isolated from Tibet, China

EV-B93 is a novel serotype within the Enterovirus B species and is uncommon worldwide. Currently, only one full-length genomic sequence (the prototype strain) has been deposited in the GenBank database. In this study, three EV-B93 were identified, including one from an acute flaccid paralysis (AFP) patient (named 99052/XZ/CHN/1999, hereafter XZ99052) and two from healthy children (named 99096/XZ/CHN/1999 and 99167/XZ/CHN/1999, hereafter XZ99096 and XZ99167, respectively) from Tibet in 1999 during the polio eradication program. The identity between the nucleotide and amino acid sequences of the Tibet EV-B93 strain and the EV-B93 prototype strain is 83.2%–83.4% and 96.8%–96.9%, respectively. The Tibet EV-B93 strain was found to have greater nucleotide sequence identity in the P3 region to another enterovirus EV-B107 as per a phylogenetic tree analysis, which revealed that recombination occurred. Seroepidemiology data showed that EV-B93 has not produced an epidemic in Tibet and there may be susceptible individuals. The three Tibet EV-B93 strains are temperature-resistant with prognosticative virulence, suggesting the possibility of a potential large-scale outbreak of EV-B93. The analyzed EV-B93 strains enrich our knowledge about this serotype and provide valuable information on global EV-B93 molecular epidemiology. What is more, they permit the appraisal of the serotype's potential public health impact and aid in understanding the role of recombination events in the evolution of enteroviruses.

Surrounded catalysts prepared by ion-exchange inverse loading

The supported catalyst featuring highly dispersed active phase on support is the most important kind of industrial catalyst. Extensive research has demonstrated the critical role (in catalysis) of the interfacial interaction/perimeter sites between the active phase and support. However, the supported catalyst prepared by traditional methods generally presents low interface density because of limit contact area. Here, an ion-exchange inverse loading (IEIL) method has been developed, in which the precursor of support is controllably deposited onto the precursor of active phase by ion-exchange reaction, leading to an active core surrounded (by support) catalyst with various structures. The unique surrounded structure presents not only high interface density and mutually changed interface but also high stability due to the physical isolation of active phase, revealing superior catalytic performances to the traditional supported catalysts, suggesting the great potential of this new surrounded catalyst as the upgrade of supported catalyst in heterogeneous catalysis.

Improvement of the catalytic activity and thermostability of a hyperthermostable endoglucanase by optimizing N-glycosylation sites

BACKGROUND

Endoglucanase has been extensively employed in industrial processes as a key biocatalyst for lignocellulosic biomass degradation. Thermostable endoglucanases with high catalytic activity at elevated temperatures are preferred in industrial use. To improve the activity and thermostability, site-directed mutagenesis was conducted to modify the N-glycosylation sites of the thermostable β-1,4-endoglucanase CTendo45 from Chaetomium thermophilum.

RESULTS

In this study, structure-based rational design was performed based on the modification of N-glycosylation sites in CTendo45. Eight single mutants and one double mutant were constructed and successfully expressed in Pichia pastoris. When the unique N-glycosylation site of N88 was eliminated, a T90A variant was active, and its specific activity towards CMC-Na and β-d-glucan was increased 1.85- and 1.64-fold, respectively. The mutant R67S with an additional N-glycosylation site of N65 showed a distinct enhancement in catalytic efficiency. Moreover, T90A and R67S were endowed with extraordinary heat endurance after 200 min of incubation at different temperatures ranging from 30 to 90 °C. Likewise, the half-lives (t _1/2) indicated that T90A and R67S exhibited improved enzyme thermostability at 80 °C and 90 °C. Notably, the double-mutant T90A/R67S possessed better hydrolysis activity and thermal stability than its single-mutant counterparts and the wild type.

CONCLUSIONS

This study provides initial insight into the biochemical function of N-glycosylation in thermostable endoglucanases. Moreover, the design approach to the optimization of N-glycosylation sites presents an effective and feasible strategy to improve enzymatic activity and thermostability.

Effects of drought stress on photosynthesis and photosynthetic electron transport chain in young apple tree leaves

In our study, the effects of water stress on photosynthesis and photosynthetic electron transport chain (PETC) were studied in several ways, including monitoring the change of gas exchange parameters, modulated chlorophyll fluorescence, rapid fluorescence induction kinetics, reactive oxygen species (ROS), antioxidant enzyme activities and D1 protein levels in apple leaves. Our results show that when leaf water potential (ψ w) is above -1.5 MPa, the stomatal limitation should be the main reason for a drop of photosynthesis. In this period, photosynthetic rate (P N), stomatal conductance (G s), transpiration rate (E) and intercellular CO2 concentration (C i) all showed a strong positive correlation with ψ w Modulated chlorophyll fluorescence parameters related to photosynthetic biochemistry activity including maximum photochemical efficiency (Fv/Fm), actual photochemical efficiency of PSII (ΦPSII), photochemical quenching coefficient (q P) and coefficient of photochemical fluorescence quenching assuming interconnected PSII antennae (q L) also showed a strong positive correlation as ψ w gradually decreased. On the other hand, in this period, Stern-Volmer type non-photochemical quenching coefficient (NPQ) and quantum yield of light-induced non-photochemical fluorescence quenching [Y (NPQ)] kept going up, which shows an attempt to dissipate excess energy to avoid damage to plants. When ψ w was below -1.5 MPa, P N continued to decrease linearly, while C i increased and a 'V' model presents the correlation between C i and ψ w by polynomial regression. This implies that, in this period, the drop in photosynthesis activity might be caused by non-stomatal limitation. Fv/Fm, ΦPSII, q P and q L in apple leaves treated with water stress were much lower than in control, while NPQ and Y (NPQ) started to go down. This demonstrates that excess energy might exceed the tolerance ability of apple leaves. Consistent with changes of these parameters, excess energy led to an increase in the production of ROS including H2O2 and O2 •- Although the activities of antioxidant enzymes like catalase (CAT), superoxide dismutase (SOD) and peroxidase (POD) increased dramatically and ascorbate peroxidase (APX) decreased in apple leaves with drought stress, it was still not sufficient to scavenge ROS. Consequently, the accumulation of ROS triggered a reduction of net D1 protein content, a core protein in the PSII reaction center. As D1 is responsible for the photosynthetic electron transport from plastoquinone A (QA) to plastoquinone B (QB), the capacity of PETC between QA and QB was considerably downregulated. The decline of photosynthesis and activity of PETC may result in the shortage of adenosine triphosphate (ATP) and limitation the regeneration of RuBP (J max), a key enzyme in CO2 assimilation. These are all non-stomatal factors and together contributed to decreased CO2 assimilation under severe water stress.

Identical anthropometric characteristics of impaired fasting glucose combined with impaired glucose tolerance and newly diagnosed type 2 diabetes: anthropometric indicators to predict hyperglycaemia in a community-based prospective cohort study in southwest China

OBJECTIVES

To assess the anthropometric characteristics of normoglycaemic individuals who subsequently developed hyperglycaemia, and to evaluate the validity of these measures to predict prediabetes and diabetes.

DESIGN

A community-based prospective cohort study.

PARTICIPANTS

In total, 1885 residents with euglycaemia at baseline from six communities were enrolled.

SETTING

Sichuan, southwest China.

PRIMARY OUTCOME MEASURES

The incidences of prediabetes and diabetes were the primary outcomes.

METHODS

The waist-to-height ratio (WHtR), body mass index (BMI), waist circumference (WC) and waist-to-hip ratio (WHR) of all participants were measured at baseline and during follow-up. A 75 g glucose oral glucose tolerance test was conducted at each survey.

RESULTS

During a median of 3.00 (IQR: 2.92-4.17) years follow-up, the cumulative incidence of isolated impaired fasting glucose (IFG), isolated impaired glucose tolerance (IGT), IFG combined with IGT (IFG+IGT), and newly diagnosed diabetes mellitus (NDDM) were 8.44%, 18.14%, 8.06% and 13.79%, respectively. WHtR, BMI, WC and WHR were significantly different among subjects who subsequently progressed to isolated IFG or IGT, IFG+IGT or NDDM (p<0.05). The anthropometric characteristics of IFG+IGT subjects were similar to those of the NDDM population (p>0.005). All the baseline anthropometric measurements were useful for the prediction of future prediabetes and NDDM (p<0.05). The optimal thresholds for the four measurements were calculated for the prediction of hyperglycaemia, with a WHtR value of 0.52 performing best to identify isolated IFG or IGT, IFG+IGT and NDDM.

CONCLUSIONS

Anthropometric measures, especially WHtR, could be used to predict hyperglycaemia 3 years in advance. Distinct from isolated IFG and IGT, the individuals who developed combined IFG+IGT had identical anthropometric profiles to those who progressed to NDDM.

Signaling protein signature predicts clinical outcome of non-small-cell lung cancer

BACKGROUND

Non-small-cell lung cancer (NSCLC) is characterized by abnormalities of numerous signaling proteins that play pivotal roles in cancer development and progression. Many of these proteins have been reported to be correlated with clinical outcomes of NSCLC. However, none of them could provide adequate accuracy of prognosis prediction in clinical application.

METHODS

A total of 384 resected NSCLC specimens from two hospitals in Beijing (BJ) and Chongqing (CQ) were collected. Using immunohistochemistry (IHC) staining on stored formalin-fixed paraffin-embedded (FFPE) surgical samples, we examined the expression levels of 75 critical proteins on BJ samples. Random forest algorithm (RFA) and support vector machines (SVM) computation were applied to identify protein signatures on 2/3 randomly assigned BJ samples. The identified signatures were tested on the remaining BJ samples, and were further validated with CQ independent cohort.

RESULTS

A 6-protein signature for adenocarcinoma (ADC) and a 5-protein signature for squamous cell carcinoma (SCC) were identified from training sets and tested in testing sets. In independent validation with CQ cohort, patients can also be divided into high- and low-risk groups with significantly different median overall survivals by Kaplan-Meier analysis, both in ADC (31 months vs. 87 months, HR 2.81; P <  0.001) and SCC patients (27 months vs. not reached, HR 9.97; P <  0.001). Cox regression analysis showed that both signatures are independent prognostic indicators and outperformed TNM staging (ADC: adjusted HR 3.07 vs. 2.43, SCC: adjusted HR 7.84 vs. 2.24). Particularly, we found that only the ADC patients in high-risk group significantly benefited from adjuvant chemotherapy (P = 0.018).

CONCLUSIONS

Both ADC and SCC protein signatures could effectively stratify the prognosis of NSCLC patients, and may support patient selection for adjuvant chemotherapy.

Comparative analysis of miRNA and mRNA abundance in determinate cucumber by high-throughput sequencing

Determinate cucumber is a type of short vines, fewer nodes, and terminal flowers, it is suitable for high-density planting and available harvesting in field cultivation, whereas the indeterminate cucumber is preferred to cultivate in greenhouses. However, many biotic or abiotic stresses could lead indeterminate cucumber to be determinate in greenhouse cultivation, which may decrease yield and fruit quality. Therefore, it is urgent and essential to investigate the key factors forming determinate and terminal flowering in cucumber. In this study, two close background inbred lines were selected and conducted the miRNA and mRNA high throughput sequencing. Interestingly, ethylene-associated miRNAs and mRNAs were intensively obtained, indicating that the plant hormone ethylene is a key factor impacting determinate and terminal flowering in cucumber. The ethylene metabolites analysis showed that significant higher ethylene was observed in determinate line than that in the indeterminate line. The RT-qPCR validation of ethylene related miRNAs Cas-miR172, Cas-miR396, and Cas-miR414 and their target mRNAs showed a significant negative correlation. These data suggested that ethylene-associated miRNAs might affect determinate and terminal flower phenotypes by regulating their target genes expression. This study not only provides a potential molecular mechanism for determinate formation in cucumber but also establishes a method to demonstrate important physiological processes through the comprehensive association of miRNA and mRNA high-throughput sequencing.

Influences of dietary protein sources and crude protein levels on intracellular free amino acid profile in the longissimus dorsi muscle of finishing gilts

BACKGROUND

The current study was carried out to determine effects of dietary protein source and crude protein (CP) level on carcass characteristics, meat quality, and muscle amino acid (AA) profile in finishing gilts. The experiment was designed as a 2 × 2 factorial arrangement with two sources of dietary proteins (cottonseed meal, CSM vs. soybean meal, SBM) and two levels of CP (12 % vs. 14 %, as-fed basis). Seventy-two crossbred gilts (89.5 ± 0.9 kg) were allotted to one of four dietary treatments in a randomized complete block design for a period of 28 d. All diets were formulated to be isoenergetic and similar concentrations of standardized ileal digestible essential AA covering the nutrient requirements of pigs.

RESULTS

Growth, carcass characteristics and meat quality were not affected by dietary protein source nor crude protein level (P > 0.10) except that average daily feed intake was increased by CSM diets (P = 0.03). Gilts offered reduced protein diets had lower muscle pH45min (P < 0.05). Neither dietary protein source nor crude protein level influenced N deposition. However, reduced protein diets decreased N intake, N excretion, and serum urea nitrogen content, whilst improved N efficiency (P < 0.01). CSM diets increased N intake (P = 0.04), but did not depress N efficiency. The concentrations of phenylalanine, tryptophan, cysteine and tyrosine (P < 0.05) of the longissimus muscle were decreased when gilts offered CSM diets, while muscle intracellular free valine concentration was increased (P = 0.03). The gilts offered reduced protein diets had greater intracellular concentrations of free methionine, lysine, and total AA in muscle (P < 0.05).

CONCLUSION

These results suggest that CSM could replace SBM as a primary protein source in finishing pig diets in terms of performance, N efficiency, carcass characteristics, and meat quality, but decrease the concentrations of muscle specific AA. Furthermore, the reduced protein diet played an important role in increasing muscle intracellular concentrations of specific free amino acids (FAA), and in reducing the relative ratios of specific FAA to lysine in longissimus dorsi muscle of pig, whose biological meaning needs further studies.