The 6-Month Antibody Durability of Heterologous Convidecia Plus CoronaVac and Homologous CoronaVac Immunizations in People Aged 18-59 Years and over 60 Years Based on Two Randomized Controlled Trials in China.

Previous reports have shown that heterologous boosting with the AD5-vectored COVID-19 vaccine Convidecia based on a primary series of two doses of inactivated vaccine induces increasing immune responses. However, the immune persistence until 6 months after the heterologous prime-boost immunization was limited. Participants were from two single-center, randomized, controlled, observer-blinded trials, which involved individuals of 18-59 years of age and over 60 years of age. Eligible participants who previously primed with one dose or two doses of CoronaVac were stratified and randomly assigned to inoculate a booster dose of Convidecia or CoronaVac. Neutralizing antibodies against a live SARS-CoV-2 prototype virus and Delta and Omicron (B.1.1.529) variants, pseudovirus neutralizing antibodies against Omicron BA.4/5 variants, and anti-SARS-CoV-2 RBD antibodies at month 6 were detected, and the fold decreases and rate difference were calculated by comparing the levels of antibodies at month 6 with the peak levels at month 1. The neutralizing antibody titers against prototype SARS-CoV-2, RBD-specific IgG antibodies, and the Delta variant in the heterologous regimen of the CoronaVac plus Convidecia groups were significantly higher than those of the homologous prime-boost groups. In three-dose regimen groups, the geometric mean titers (GMTs) of neutralizing antibodies against prototype SARS-CoV-2 were 30.6 (95% CI: 25.1; 37.2) in the heterologous boosting group versus 6.9 (95% CI: 5.6; 8.6) in the homologous boosting group (p < 0.001) at month 6 in participants aged 18-59 years, and in the two-dose regimen, the neutralizing antibody GMTs were 8.5 (95% CI: 6.2; 11.7) and 2.7 (2.3 to 3.1) (heterologous regimen group versus CoronaVac regimen group, p < 0.001). Participants aged over 60 years had similar levels of neutralizing antibodies against the prototype, with GMTs of 49.1 (38.0 to 63.6) in the group receiving two doses of CoronaVac plus one dose of Convidecia versus 9.4 (7.7 to 11.4) in the group receiving three doses of CoronaVac (p < 0.001) and 11.6 (8.4 to 16.0) in the group receiving one dose of CoronaVac and one dose of Convidecia versus 3.3 (2.7 to 4.0) in the group receiving two doses of CoronaVac (p < 0.001). Compared with day 14, over sixfold decreases in neutralizing antibody GMTs were observed in the heterologous groups of the three- or two-dose regimen groups of younger and elderly participants, while in the homologous regimen groups, the GMTs of neutralizing antibodies decreased about fivefold in the two age groups. The heterologous prime-boost regimen with two doses of CoronaVac and one dose of Convidecia was persistently more immunogenic than the regimen of the homologous prime-boost with three doses of CoronaVac.

Epigenetic regulation during cancer transitions across 11 tumour types.

Chromatin accessibility is essential in regulating gene expression and cellular identity, and alterations in accessibility have been implicated in driving cancer initiation, progression and metastasis1-4. Although the genetic contributions to oncogenic transitions have been investigated, epigenetic drivers remain less understood. Here we constructed a pan-cancer epigenetic and transcriptomic atlas using single-nucleus chromatin accessibility data (using single-nucleus assay for transposase-accessible chromatin) from 225 samples and matched single-cell or single-nucleus RNA-sequencing expression data from 206 samples. With over 1 million cells from each platform analysed through the enrichment of accessible chromatin regions, transcription factor motifs and regulons, we identified epigenetic drivers associated with cancer transitions. Some epigenetic drivers appeared in multiple cancers (for example, regulatory regions of ABCC1 and VEGFA; GATA6 and FOX-family motifs), whereas others were cancer specific (for example, regulatory regions of FGF19, ASAP2 and EN1, and the PBX3 motif). Among epigenetically altered pathways, TP53, hypoxia and TNF signalling were linked to cancer initiation, whereas oestrogen response, epithelial-mesenchymal transition and apical junction were tied to metastatic transition. Furthermore, we revealed a marked correlation between enhancer accessibility and gene expression and uncovered cooperation between epigenetic and genetic drivers. This atlas provides a foundation for further investigation of epigenetic dynamics in cancer transitions.

Predictive models for sepsis in children with Staphylococcus aureus bloodstream infections: a retrospective cohort study.

BACKGROUND: The presence of Staphylococcus aureus in the bloodstream can lead to the development of sepsis; however, the severity and risk factors of the systemic inflammatory response to Staphylococcus aureus bloodstream infections were unclear. This study is aimed to build a model to predict the risk of sepsis in children with Staphylococcus aureus bloodstream infections. METHODS: A retrospective analysis of hospitalized pediatric patients diagnosed with Staphylococcus aureus bloodstream infections was performed between January 2013 and December 2019. Each patient was assessed using the pediatric version of the Sequential Organ Failure Assessment score (pSOFA) within 24 h of blood culture collection. A nomogram based on logistic regression models was constructed to predict the risk factors for sepsis in children with Staphylococcus aureus bloodstream infections. It was validated using the area under the receiver-operating characteristic curve (AUC). RESULTS: Of the 94 patients included in the study, 35 cases (37.2%) developed sepsis. The pSOFA scores ranged from 0 to 8, with 35 patients having a pSOFA score of ≥ 2. Six children (6.4%) died within 30 days, who were all from the sepsis group and had different pSOFA scores. The most common organs involved in sepsis in children with staphylococcal bloodstream infections were the neurologic system (68.6%), respiratory system (48.6%), and coagulation system (45.7%). Hospital-acquired infections (adjusted odds ratio [aOR], 3.0; 95% confidence interval [CI], 1.3-7.2), implanted catheters (aOR, 10.4; 95% CI, 3.8-28.4), procalcitonin level ≥ 1.7 ng/mL (aOR, 15.4; 95% CI, 2.7-87.1), and underlying diseases, especially gastrointestinal malformations (aOR, 14.0; 95% CI, 2.9-66.7) were associated with Staphylococcus aureus sepsis. However, methicillin-resistant Staphylococcus aureus infection was not a risk factor for sepsis. The nomogram had high predictive accuracy for the estimation of sepsis risk, with an AUC of 0.85. CONCLUSIONS: We developed a predictive model for sepsis in children with Staphylococcus aureus infection.

Integrated metabolomics and network pharmacology revealing the mechanism of arsenic-induced hepatotoxicity in mice.

Endemic arsenic (As) poisoning is a severe biogeochemical disease that endangers human health. Epidemiological investigations and animal experiments have confirmed the damaging effects of As on the liver, but there is an urgent need to investigate the underlying mechanisms. This study adopted a metabolomic approach using UHPLC-QE/MS to identify the different metabolites and metabolic mechanisms associated with As-induced hepatotoxicity in mice. A network pharmacology approach was applied to predict the potential target of As-induced hepatotoxicity. The predicted targets of differential metabolites were subjected to a deep matching for elucidating the integration mechanisms. The results demonstrate that the levels of ALT and AST in plasma significantly increased in mice after As exposure. In addition, the liver tissue showed disorganized liver lobules, lax cytoplasm and inflammatory cell infiltration. Metabolomic analysis revealed that As exposure caused disturbance to 40 and 75 potential differential metabolites in plasma and liver, respectively. Further investigation led to discovering five vital metabolic pathways, including phenylalanine, tyrosine, and tryptophan biosynthesis and nicotinate and nicotinamide metabolism pathways. These pathways may responded to As-induced hepatotoxicity primarily through lipid metabolism, apoptosis, and deoxyribonucleic acid damage. The network pharmacology suggested that As could induce hepatotoxicity in mice by acting on targets including Hsp90aa1, Akt2, Egfr, and Tnf, which regulate PI3K Akt, HIF-1, MAPK, and TNF signaling pathways. Finally, the integrated metabolomics and network pharmacology revealed eight key targets associated with As-induced hepatoxicity, namely DNMT1, MAOB, PARP1, MAOA, EPHX2, ANPEP, XDH, and ADA. The results also suggest that nicotinic acid and nicotinamide metabolisms may be involved in As-induced hepatotoxicity. This research identified the metabolites, targets, and mechanisms of As-induced hepatotoxicity, offering meaningful insights and establishing the groundwork for developing antidotes for widespread As poisoning.

Immunogenicity and safety of heterologous immunisation with Ad5-nCOV in healthy adults aged 60 years and older primed with an inactivated SARS-CoV-2 vaccine (CoronaVac): a phase 4, randomised, observer-blind, non-inferiority trial.

Background: People over 60 have been found to develop less protection after two doses of inactivated COVID-19 vaccines than younger people. Heterologous immunisation could potentially induce more robust immune responses compared to homologous immunisation. We aimed to assess the immunogenicity and safety of a heterologous immunisation with an adenovirus type 5-vectored vaccine (Ad5-nCOV, Convidecia) among elderly who were primed with an inactivated vaccine (CoronaVac) previously. Methods: We did a randomised, observer-blinded, non-inferiority trial in healthy adults aged 60 years and older in Lianshui County (Jiangsu, China) between August 26, 2021 and May 15, 2022. 199 eligible participants who had received two doses of CoronaVac in the past 3-6 months were randomised (1:1) to receive a third dose of Convidecia (group A, n = 99) or CoronaVac (group B, n = 100), while 100 participants primed with one dose of CoronaVac in the past 1-2 months were randomised equally to receive a second dose of Convidecia (group C, n = 50) or CoronaVac (group D, n = 50). Participants and investigators were masked to the vaccine received. Primary outcomes were the geometric mean titers (GMTs) of neutralising antibodies against live SARS-CoV-2 virus 14 days after boosting and 28-day adverse reactions. This study was registered with ClinicalTrials.govNCT04952727. Findings: A heterologous third dose of Convidecia resulted in a 6.2-fold (GMTs: 286.4 vs 48.2), 6.3-fold (45.9 vs 7.3) and 7.5-fold (32.9 vs 4.4) increase in neutralising antibodies against SARS-CoV-2 wild-type, delta (B.1.617.2) and omicron (BA.1.1) 14 days post boosting, respectively, compared with the homologous boost. The heterologous booster with Convidecia induced significantly higher neutralsing activities, with up to 91% inhibition in binding of Spike to ACE2 for BA.4 and BA.5 variants, compared with 35% inhibition induced by three doses of CoronaVac. For participants primed with one dose of CoronaVac, a heterologous dose of Convidecia induced higher neutralising antibodies against wild-type than two doses of CoronaVac (GMTs: 70.9 vs 9.3, p < 0.0001), but not for that against variants of concern (GMTs against delta: 5.0 vs 4.0, p = 0.4876; GMTs against omicron: 4.8 vs 3.7, p = 0.4707). Adverse reactions were reported by 8 (8.1%) participants in group A and 4 (4.0%) in group B (p ＞ 0.05), and 8 (16.0%) in group C and 1 (2.0%) in group D (p = 0.031). Interpretation: In elderly individuals primed with two doses of CoronaVac, the heterologous immunisation with Convidecia induced strong antibodies against SARS-CoV-2 wildtype and variants of concern, which could be an alternative regimen for enhancing protection in this vulnerable population. Funding: National Natural Science Foundation of China, Jiangsu Provincial Key Research and Development Program, and Jiangsu Science Fund for Distinguished Young Scholars Program.

Locating the propagation source in complex networks with observers-based similarity measures and direction-induced search.

Locating the propagation source is one of the most important strategies to control the harmful diffusion process on complex networks. Most existing methods only consider the infection time information of the observers, but the diffusion direction information of the observers is ignored, which is helpful to locate the source. In this paper, we consider both of the diffusion direction information and the infection time information to locate the source. We introduce a relaxed direction-induced search (DIS) to utilize the diffusion direction information of the observers to approximate the actual diffusion tree on a network. Based on the relaxed DIS, we further utilize the infection time information of the observers to define two kinds of observers-based similarity measures, including the Infection Time Similarity and the Infection Time Order Similarity. With the two kinds of similarity measures and the relaxed DIS, a novel source locating method is proposed. We validate the performance of the proposed method on a series of synthetic and real networks. The experimental results show that the proposed method is feasible and effective in accurately locating the propagation source.

Diffusion characteristics classification framework for identification of diffusion source in complex networks.

The diffusion phenomena taking place in complex networks are usually modelled as diffusion process, such as the diffusion of diseases, rumors and viruses. Identification of diffusion source is crucial for developing strategies to control these harmful diffusion processes. At present, accurately identifying the diffusion source is still an opening challenge. In this paper, we define a kind of diffusion characteristics that is composed of the diffusion direction and time information of observers, and propose a neural networks based diffusion characteristics classification framework (NN-DCCF) to identify the source. The NN-DCCF contains three stages. First, the diffusion characteristics are utilized to construct network snapshot feature. Then, a graph LSTM auto-encoder is proposed to convert the network snapshot feature into low-dimension representation vectors. Further, a source classification neural network is proposed to identify the diffusion source by classifying the representation vectors. With NN-DCCF, the identification of diffusion source is converted into a classification problem. Experiments are performed on a series of synthetic and real networks. The results show that the NN-DCCF is feasible and effective in accurately identifying the diffusion source.

Descriptions of Three New Species of the Genus Acerataspis Uchida, 1934 (Hymenoptera, Ichneumonidae, Metopiinae), with an Illustrated Identification Key to Extant Species.

The Asian genus Acerataspis Uchida, 1934 is reviewed based on both morphology and DNA barcodes. Ten species are recognized in total, of which three species from Yunnan Province of China are described as new: Acerataspis maliae sp. nov., A. seperata sp. nov. and A. similis sp. nov. The male of A. fukienensis Chao, 1957 is described and illustrated for the first time. The genus is recorded from Thailand and Southeast Asia for the first time. An illustrated key to all known extant species is provided. With the supplement of DNA barcodes, a few diagnostic morphological characters are found useful in species identification.

Safety and immunogenicity of aerosolised Ad5-nCoV, intramuscular Ad5-nCoV, or inactivated COVID-19 vaccine CoronaVac given as the second booster following three doses of CoronaVac: a multicentre, open-label, phase 4, randomised trial.

BACKGROUND: Aerosolised Ad5-nCoV is the first approved mucosal respiratory COVID-19 vaccine to be used as a booster after the primary immunisation with COVID-19 vaccines. This study aimed to evaluate the safety and immunogenicity of aerosolised Ad5-nCoV, intramuscular Ad5-nCoV, or inactivated COVID-19 vaccine CoronaVac given as the second booster. METHODS: This is an open-label, parallel-controlled, phase 4 randomised trial enrolling healthy adult participants (≥18 years) who had completed a two-dose primary immunisation and a booster immunisation with inactivated COVID-19 vaccines (CoronaVac only) at least 6 months before, in Lianshui and Donghai counties, Jiangsu Province, China. We recruited eligible participants from previous trials in China (NCT04892459, NCT04952727, and NCT05043259) as cohort 1 (with the serum before and after the first booster dose available), and from eligible volunteers in Lianshui and Donghai counties, Jiangsu Province, as cohort 2. Participants were randomly assigned at a ratio of 1:1:1, using a web-based interactive response randomisation system, to receive the fourth dose (second booster) of aerosolised Ad5-nCoV (0·1 mL of 1·0 × 1011 viral particles per mL), intramuscular Ad5-nCoV (0·5 mL of 1·0 × 1011 viral particles per mL), or inactivated COVID-19 vaccine CoronaVac (0·5 mL), respectively. The co-primary outcomes were safety and immunogenicity of geometric mean titres (GMTs) of serum neutralising antibodies against prototype live SARS-CoV-2 virus 28 days after the vaccination, assessed on a per-protocol basis. Non-inferiority or superiority was achieved when the lower limit of the 95% CI of the GMT ratio (heterologous group vs homologous group) exceeded 0·67 or 1·0, respectively. This study was registered with ClinicalTrials.gov, NCT05303584 and is ongoing. FINDINGS: Between April 23 and May 23, 2022, from 367 volunteers screened for eligibility, 356 participants met eligibility criteria and received a dose of aerosolised Ad5-nCoV (n=117), intramuscular Ad5-nCoV (n=120), or CoronaVac (n=119). Within 28 days of booster vaccination, participants in the intramuscular Ad5-nCoV group reported a significantly higher frequency of adverse reactions than those in the aerosolised Ad5-nCoV and intramuscular CoronaVac groups (30% vs 9% and 14%, respectively; p<0·0001). No serious adverse events related to the vaccination were reported. The heterologous boosting with aerosolised Ad5-nCoV triggered a GMT of 672·4 (95% CI 539·7-837·7) and intramuscular Ad5-nCoV triggered a serum neutralising antibody GMT of 582·6 (505·0-672·2) 28 days after the booster dose, both of which were significantly higher than the GMT in the CoronaVac group (58·5 [48·0-71·4]; p<0·0001). INTERPRETATION: A heterologous fourth dose (second booster) with either aerosolised Ad5-nCoV or intramuscular Ad5-nCoV was safe and highly immunogenic in healthy adults who had been immunised with three doses of CoronaVac. FUNDING: National Natural Science Foundation of China, Jiangsu Provincial Science Fund for Distinguished Young Scholars, and Jiangsu Provincial Key Project of Science and Technology Plan.

A differential correction based shadow removal method for real-time monitoring.

Shadow removal is an important issue in the field of motion object surveillance and automatic control. Although many works are concentrated on this issue, the diverse and similar motion patterns between shadows and objects still severely affect the removal performance. Constrained by the computational efficiency in real-time monitoring, the pixel feature based methods are still the main shadow removal methods in practice. Following this idea, this paper proposes a novel and simple shadow removal method based on a differential correction calculation between the pixel values of Red, Green and Blue channels. Specifically, considering the fact that shadows are formed because of the occlusion of light by objects, all the reflected light will be attenuated. Hence there will be a similar weakening trends in all Red, Green and Blue channels of the shadow areas, but not in the object areas. These trends can be caught by differential correction calculation and distinguish the shadow areas from object areas. Based on this feature, our shadow removal method is designed. Experiment results verify that, compared with other state-of-the-art shadow removal methods, our method improves the average of object and shadow detection accuracies by at least 10% in most of the cases.

Impact of Environmental Uncertainties and Strategic Flexibility in Innovation Activities on NEV Battery Recycling Firms in China.

Due to the popularization and development of new energy vehicles (NEVs) worldwide, power batteries that have been used are being retired and replaced. In China's battery recycling industry, the legal NEV battery recycling enterprises are at a negative financial performance. Based on theory of organizational adaptation, the key to innovation performance and sustainable development is recognition of the environment and strengthening organizational flexibility. This study empirically explores the bidirectional dynamic relationships among heterogeneous environmental uncertainties, innovation activities, firm growth and strategic flexibility in Chinese NEV battery recycling firms. A total of 1040 sample data were collected from 2015 to 2021. The research results demonstrate that environmental uncertainty (EU), strategic flexibility (SF) and innovation activities (INNO) all had impacts on firm growth (FG). Specifically, INNO had strongly negative effects in the short term, and in the long term, it will bring a positive effect to FG; the impact of EPU was more important than market uncertainty (MU) to FG and innovation activities. This could be due to the dependence of the Chinese NEV battery recycling industry on government policy. However, MU has a strong impact on SF. Moreover, the levels of SF should be reasonable, otherwise it could be a burden to enterprises. There also exists the bidirectional dynamic relationships between FG and INNO. This study contributes a non-core perspective to strategic flexibility research by revealing the complex environmental mechanism, and to the Chinese NEV battery recycling industry we provide a theoretical basis and practical guidance for government and firms on how to apply SF to promote innovation and realize growth in the present business environment.

Terminalia bellirica ethanol extract ameliorates nonalcoholic fatty liver disease in mice by amending the intestinal microbiota and faecal metabolites.

ETHNOPHARMACOLOGICAL RELEVANCE: Terminalia bellirica (Gaertn.) Roxb. (TB) is a traditional Tibetan medicine used to treat hepatobiliary diseases. However, modern pharmacological evidence of the activities and potential mechanisms of TB against nonalcoholic fatty liver disease (NAFLD) are still unknown. AIM OF THE STUDY: This study aimed to evaluate the anti-NAFLD effect of ethanol extract of TB (ETB) and investigate whether its ameliorative effects are associated with the regulation of intestinal microecology. MATERIALS AND METHODS: In this study, the curative effects of ETB on NAFLD were evaluated in mice fed a choline-deficient, L-amino acid defined, high fat diet (CDAHFD). Biochemical markers and hepatic histological alterations were detected. Gut microbiota and faecal metabolites were analyzed by 16S rRNA gene sequencing and liquid chromatograph mass spectrometer (LC‒MS) profiling. RESULTS: The results showed that oral treatment with middle- and high-dose ETB significantly improved features of NAFLD, reducing the levels of TG, LDL-C, ALT and AST, and increasing the level of HDL-C. Liver histopathologic examination demonstrated that ETB attenuated lipid accumulation and hepatocellular necrosis. ETB treatment restored the structural disturbances of gut microbiota induced by CDAHFD, reduced the levels of Intestinimonas, Lachnoclostridium, and Lachnospirace-ae_FCS020_group, and increased Akkermansia and Bifidobacterium. Moreover, untargeted metabolomics analysis revealed that ETB could restore the disrupted taurine and hypotaurine metabolism, glycine, serine and threonine metabolism, and glutathione metabolism of the intestinal bacterial community in NAFLD mice. CONCLUSIONS: ETB was effective in ameliorating the NAFLD, possibly by remodelling the gut microbiota composition and modulating the faecal metabolism metabolites of the host, highlighting the potential of TB as a resource for the development of anti-NAFLD drugs.

DNA Barcoding Unveils New Species of the Sexually Dimorphic Genus Anteon Jurine (Hymenoptera, Dryinidae) from China.

Species of Anteon Jurine, 1807 are a large group of parasitoids attacking leafhoppers, which are important insect pests. Despite their great potential in pest biological control, the taxonomy and biology of these parasitoids are far from clear. Sexual dimorphism is extreme in Anteon species and has hampered the taxonomy of these parasitoids, resulting in many species described based on a single sex. In this paper, we employed an integrated taxonomic approach for delimitating species, combining morphological examinations with DNA barcoding, to investigate Anteon species from China. In total, 53 COI sequences representing 29 species of Anteon were obtained and analyzed. On the basis of both morphology and DNA barcoding, five new species of Anteon were discovered and described: A. clariclypeum sp. nov., A. maguanense sp. nov., A. parafidum sp. nov., A. shaanxianum sp. nov., and A. shandonganum sp. nov. The neotype of A. claricolle Kieffer is designated. The sexual association of six species was confirmed by DNA barcoding, which led to the synonymy of Anteon liui Xu, Olmi & He 2010, new syn., under Anteon meifenganum Olmi, 1991. Keys to species of Anteon from the Oriental and Eastern Palaearctic are updated to contain the five new species. Our study demonstrates that DNA barcoding is a potent tool for tackling the taxonomic challenges in parasitoids with extreme sexual dimorphism.

A Facile machine learning multi-classification model for Streptococcus agalactiae clonal complexes.

BACKGROUND: The clinical significance of group B streptococcus (GBS) was different among different clonal complexes (CCs), accurate strain typing of GBS would facilitate clinical prognostic evaluation, epidemiological investigation and infection control. The aim of this study was to construct a practical and facile CCs prediction model for S. agalactiae. METHODS: A total of 325 non-duplicated GBS strains were collected from clinical samples in Xinhua Hospital, Shanghai, China. Multilocus sequence typing (MLST) method was used for molecular classification, the results were analyzed to derive CCs by Bionumeric 8.0 software. Antibiotic susceptibility test was performed using Vitek-2 Compact system combined with K-B method. Multiplex PCR method was used for serotype identification. A total of 45 virulence genes associated with adhesion, invasion, immune evasion were detected by PCR method and electrophoresis. Three types of features, including antibiotic susceptibility (A), serotypes (S) and virulence genes (V) tests, and XGBoost algorithm was established to develop multi-class CCs identification models. The performance of proposed models was evaluated by the receiver operating characteristic curve (ROC). RESULTS: The 325 GBS were divided into 47 STs, and then calculated into 7 major CCs, including CC1, CC10, CC12, CC17, CC19, CC23, CC24. A total of 18 features in three kinds of tests (A, S, V) were significantly different from each CC. The model based on all the features (S&A&V) performed best with AUC 0.9536. The model based on serotype and antibiotic resistance (S&A) only enrolled 5 weighed features, performed well in predicting CCs with mean AUC 0.9212, and had no statistical difference in predicting CC10, CC12, CC17, CC19, CC23 and CC24 when compared with S&A&V model (all p > 0.05). CONCLUSIONS: The S&A model requires least parameters while maintaining a high accuracy and predictive power of CCs prediction. The established model could be used as a promising tool to classify the GBS molecular types, and suggests a substantive improvement in clinical application and epidemiology surveillance in GBS phenotyping.

Evaluation of the resistance to Chinese predominant races of Puccinia triticina and analysis of effective leaf rust resistance genes in wheat accessions from the U.S. National Plant Germplasm System.

Puccinia triticina, which is the causative agent of wheat leaf rust, is widely spread in China and most other wheat-planting countries around the globe. Cultivating resistant wheat cultivars is the most economical, effective, and environmentally friendly method for controlling leaf rust-caused yield damage. Exploring the source of resistance is very important in wheat resistance breeding programs. In order to explore more effective resistance sources for wheat leaf rust, the resistance of 112 wheat accessions introduced from the U.S. National Plant Germplasm System were identified using a mixture of pathogenic isolates of THTT, THTS, PHTT, THJT and THJS which are the most predominant races in China. As a result, all of these accessions showed high resistance at seedling stage, of which, ninety-nine accessions exhibited resistance at adult plant stage. Eleven molecular markers of eight effective leaf rust resistance genes in China were used to screen the 112 accessions. Seven effective leaf rust resistance genes Lr9, Lr19, Lr24, Lr28, Lr29, Lr38 and Lr45 were detected, except Lr47. Twenty-three accessions had only one of those seven effective leaf rust resistance gene. Eleven accessions carried Lr24+Lr38, and 7 accessions carried Lr9+Lr24+Lr38, Lr24+Lr38+Lr45, Lr24+Lr29+Lr38 and Lr19+Lr38+Lr45 respectively. The remaining seventy-one accessions had none of those eight effective leaf rust resistance genes. This study will provide theoretical guidance for rational utilization of these introduted wheat accessions directly or for breeding the resistant wheat cultivars.

Mapping QTL for Adult-Plant Resistance to Stripe Rust in a Chinese Wheat Landrace.

Wheat stripe (yellow) rust is a worldwide disease that seriously reduces wheat grain yield and quality. Adult-plant resistance (APR) to stripe rust is generally more durable but usually controlled by multiple genes with partial resistance. In this study, a recombinant inbred line population was developed from a cross between a Chinese wheat landrace, Tutoumai, with APR to stripe rust, and a highly susceptible wheat cultivar, Siyang 936. The population was genotyped by genotyping-by-sequencing and phenotyped for APR to stripe rust in four consecutive field experiments. Three QTLs, QYr.sdau-1BL, QYr.sdau-5BL, and QYr.sdau-6BL, were identified for APR to stripe rust, and explained 8.0-21.2%, 10.1-22.7%, and 11.6-18.0% of the phenotypic variation, respectively. QYr.sdau-1BL was further mapped to a 21.6 Mb region using KASP markers derived from SNPs identified by RNA-seq of the two parents. In the QYr.sdau-1BL region, 13 disease-resistance-related genes were differently expressed between the two parents, and therefore were considered as the putative candidates of QYr.sdau-1BL. This study provides favorable gene/QTL and high-throughput markers to breeding programs for marker-assisted selection of the wheat stripe rust APR genes.

Evaluation of in vivo antibacterial drug efficacy using Caenorhabditis elegans infected with carbapenem-resistant Klebsiella pneumoniae as a model host.

Objective: This study was developed to assess the in vivo antimicrobial activity of specific drugs using a model system consisting of Caenorhabditis elegans (C. elegans) infected with Carbapenem-resistant Klebsiella pneumoniae (CRKP) in an effort to identify promising drugs for CRKP-infected patient treatment. Methods: A C. elegans-CRKP liquid assay platform was developed and used to conduct limited in vivo screening for antimicrobial agents with potential activity against CRKP. Time curves for 10 different concentrations of tested antimicrobial agents were tested in this model system at 0, 2, 6, 8, and 12 h after treatment. The protective effects of these different antimicrobial agents were compared at different time points. Furthermore, ten CRKP strains samples were isolated from clinical specimens to demonstrate the applicability of the nematode model method, and two typical clinical cases are presented. Results: CRKP bacteria were sufficient to induce C. elegans death in a dose- and time-dependent fashion, while effective antimicrobial agents improved the survival of these nematodes in a dose-dependent manner. Notably, PB and TGC exhibited robust antibacterial protection within 12 h even at low tested concentrations, and clear efficacy remained evident for high doses of CAZ at this same time point as mediators of improved nematode survival. The results of C. elegans model method were well consistent with that using the Kirby-Bauer method in 10 CRKP strains samples, and two typical clinical cases showed applicability, reliability and efficacy of C. elegans model method. Conclusion: Overall, nematode models in drug sensitivity testing have shown advantages in clinical settings. Our results highlight the value of C. elegans model systems as tools for the simultaneous screening of different agents for in vivo antibacterial efficacy and are deserved further study.

Fitness effects of CRISPR endonucleases in Drosophila melanogaster populations.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 provides a highly efficient and flexible genome editing technology with numerous potential applications ranging from gene therapy to population control. Some proposed applications involve the integration of CRISPR/Cas9 endonucleases into an organism's genome, which raises questions about potentially harmful effects to the transgenic individuals. One example for which this is particularly relevant are CRISPR-based gene drives conceived for the genetic alteration of entire populations. The performance of such drives can strongly depend on fitness costs experienced by drive carriers, yet relatively little is known about the magnitude and causes of these costs. Here, we assess the fitness effects of genomic CRISPR/Cas9 expression in Drosophila melanogaster cage populations by tracking allele frequencies of four different transgenic constructs that allow us to disentangle 'direct' fitness costs due to the integration, expression, and target-site activity of Cas9, from fitness costs due to potential off-target cleavage. Using a maximum likelihood framework, we find that a model with no direct fitness costs but moderate costs due to off-target effects fits our cage data best. Consistent with this, we do not observe fitness costs for a construct with Cas9HF1, a high-fidelity version of Cas9. We further demonstrate that using Cas9HF1 instead of standard Cas9 in a homing drive achieves similar drive conversion efficiency. These results suggest that gene drives should be designed with high-fidelity endonucleases and may have implications for other applications that involve genomic integration of CRISPR endonucleases.

Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer.

Pancreatic ductal adenocarcinoma is a lethal disease with limited treatment options and poor survival. We studied 83 spatial samples from 31 patients (11 treatment-naïve and 20 treated) using single-cell/nucleus RNA sequencing, bulk-proteogenomics, spatial transcriptomics and cellular imaging. Subpopulations of tumor cells exhibited signatures of proliferation, KRAS signaling, cell stress and epithelial-to-mesenchymal transition. Mapping mutations and copy number events distinguished tumor populations from normal and transitional cells, including acinar-to-ductal metaplasia and pancreatic intraepithelial neoplasia. Pathology-assisted deconvolution of spatial transcriptomic data identified tumor and transitional subpopulations with distinct histological features. We showed coordinated expression of TIGIT in exhausted and regulatory T cells and Nectin in tumor cells. Chemo-resistant samples contain a threefold enrichment of inflammatory cancer-associated fibroblasts that upregulate metallothioneins. Our study reveals a deeper understanding of the intricate substructure of pancreatic ductal adenocarcinoma tumors that could help improve therapy for patients with this disease.