NIN is essential for development of symbiosomes, suppression of defence and premature senescence in Medicago truncatula nodules

NIN (NODULE INCEPTION) is a transcription factor that plays a key role during root nodule initiation. However, its role in later nodule developmental stages is unclear. Both NIN mRNA and protein accumulated at the highest level in the proximal part of the infection zone in Medicago truncatula nodules. Two nin weak allele mutants, nin-13/16, form a rather normal nodule infection zone, whereas a fixation zone is not formed. Instead, a zone with defence responses and premature senescence occurred and symbiosome development gets arrested. Mutations in nin-13/16 resulted in a truncated NIN lacking the conserved PB1 domain. However, this did not cause the nodule phenotype as nin mutants expressing NIN_ΔPB1 formed wild-type-like nodule. The phenotype is likely to be caused by reduced NIN mRNA levels in the cytoplasm. Transcriptome analyses of nin-16 nodules showed that expression levels of defence/senescence-related genes are markedly increased, whereas the levels of defence suppressing genes are reduced. Although defence/senescence seems well suppressed in the infection zone, the transcriptome is already markedly changed in the proximal part of infection zone. In addition to its function in infection and nodule organogenesis, NIN also plays a major role at the transition from infection to fixation zone in establishing a functional symbiosis.

Prediction of CRISPR/Cas9 single guide RNA cleavage efficiency and specificity by attention-based convolutional neural networks

CRISPR/Cas9 is a preferred genome editing tool and has been widely adapted to ranges of disciplines, from molecular biology to gene therapy. A key prerequisite for the success of CRISPR/Cas9 is its capacity to distinguish between single guide RNAs (sgRNAs) on target and homologous off-target sites. Thus, optimized design of sgRNAs by maximizing their on-target activity and minimizing their potential off-target mutations are crucial concerns for this system. Several deep learning models have been developed for comprehensive understanding of sgRNA cleavage efficacy and specificity. Although the proposed methods yield the performance results by automatically learning a suitable representation from the input data, there is still room for the improvement of accuracy and interpretability. Here, we propose novel interpretable attention-based convolutional neural networks, namely CRISPR-ONT and CRISPR-OFFT, for the prediction of CRISPR/Cas9 sgRNA on- and off-target activities, respectively. Experimental tests on public datasets demonstrate that our models significantly yield satisfactory results in terms of accuracy and interpretability. Our findings contribute to the understanding of how RNA-guide Cas9 nucleases scan the mammalian genome. Data and source codes are available at https://github.com/Peppags/CRISPRont-CRISPRofft.

Effectiveness assessment of improvement measures in physical protection system monitoring center

The optimization measures in the physical protection system monitoring center of a nuclear power plant include the prioritization of alarm signals, optimization of sound and light alarm form, improvement of the layout of video monitor screen, security training, and strengthening of organizational management. Based on the fuzzy analytic hierarchy process, the influence of these factors on the probability of alert assessment and guard’s respond time in the EASI method are quantitatively analyzed. Making full use of the measures for prioritization of alarm signals can effectively promote the improvement of human-computer interaction efficiency. The degree of influence of the four factors (guarder’s status, decision strategy, guarder’s training and organization management) on guard’s decision-making is roughly the same.

The clinical value of serum sirtuin-1 in the diagnosis of rheumatoid arthritis: a pilot study

Introduction: Cell biology studies, animal models and other data suggest a role for sirtuin-1 in the pathogenesis of rheumatoid arthritis (RA). We hypothesized the clinical significance of serum sirtuin-1 in this disease.Methods: Serum was obtained from 141 RA patients, 144 non-RA patients and 88 healthy controls. Sirtuin-1, anti-mutant citrulline vimentin antibody (anti-MCV), anti-cyclic citrulline polypeptide antibody (anti-CCP), rheumatoid factor and C-reactive protein were measured by immunological methods, and erythrocyte sedimentation rate was determined by the Westergren method.Results: All markers were higher in the RA group than in the non-RA group and the healthy control group (P < 0.01). The specificity of sirtuin-1 for the diagnosis of RA was 97% (the highest among all markers), sensitivity was 71%. In ROC curve analysis, the AUCs (95% CI) of sirtuin-1, anti-CCP and anti-MCV were 0.87 (0.82-0.91), 0.91 (0.88-0.94) and 0.92 (0.89-0.95) respectively (all p < 0.01). The combination of sirtuin-1and anti-MCV gave the highest Youden index of 0.79, whilst Cox regression showed sirtuin-1 and rheumatoid factor were the strongest independent predictors of RA.Conclusions: Serum sirtuin-1 is increased in RA, and may have a place is the diagnosis of this disease when combined with other markers.

The DNA replication regulator MCM6: An emerging cancer biomarker and target

MCM6 is a significant DNA replication regulator that plays a crucial role in sustaining the cell cycle. In many cancer cells, MCM6 expression is enhanced. For example, persistently increased expression of MCM6 promotes the formation, development and progression of hepatocellular carcinoma (HCC). Up- and down-regulation studies have indicated that MCM6 regulates cell cycle, proliferation, metastasis, immune response and the maintenance of the DNA replication system. MCM6 can also regulate downstream signaling such as MEK/ERK thus promoting carcinogenesis. Accordingly, MCM6 may represent a sensitive and specific biomarker to predict adverse progression and poor outcome. Furthermore, inhibition of MCM6 may be an effective cancer treatment. The present review summarizes the latest results on the inactivating and activating functions of MCM6, underlining its function in carcinogenesis. Further studies of the carcinogenic functions of MCM6 may provide novel insight into cancer biology and shed light on new approaches for cancer diagnosis and treatment.

Overexpression of the long noncoding RNA NEAT1 protects against As2O3-induced injury of cardiomyocyte by inhibiting the miR-124/NF-κB signaling pathway

OBJECTIVE

Arsenic trioxide (As2O3) an evident effect in the treatment of acute promyelocytic leukemia and other malignant tumors in recent years. However, more and more studies have found that the cardiac toxicity of As2O3 was increased, limiting its wide clinical application. This study aims to explore the molecule mechanisms of As2O3 on cardiomyocyte injury.

MATERIALS AND METHODS

The cardiomyocyte injury under As2O3 was detected by MTT assay. The levels of NEAT1 and miR-124 were examined by RT-PCR. The functions of NEAT1 and miR-124 at H9c2 cell injury under As2O3 were detected by cell transfection of the overexpression or repression. The expression levels of inflammation factors, apoptosis genes and NF-κB signals were measured by Western blot in H9c2 cell lines under As2O3. The luciferase assay detected the direct interaction between NEAT1 and miR-124.

RESULTS

The overexpression of NEAT1 decreased the H9c2 cells injury under As2O3. The levels of IL-1β, IL-6, TNF-α were upregulated after NEAT1 overexpression. Moreover, the luciferase assay results showed NEAT1 was directly interacting with miR-124. Silencing of miR-124 significantly increased the H9c2 cell survival under As2O3 by repressing NF-κB signaling pathway. Furthermore, the overexpression of NEAT1 markedly increased H9c2 cells survival under As2O3, while the miR-124 could reverse the effects. Finally, NEAT1 regulated the H9c2 cells As2O3 injury by repressing the miR-124, NF-kappa B expressions and inflammatory response.

CONCLUSIONS

According to the results, we found that long non-coding RNA NEAT1 regulated the expression of inflammatory factors to protect cardiomyocytes from As2O3 damage by inhibiting miR-124/NF-kappa B signaling pathway. It provides a novel potential treatment strategy for As2O3 cardiomyocytes injury.

Pattern-recognition receptors in duck (Anas platyrhynchos): identification, expression and function analysis of toll-like receptor 3

1. Innate immunity provides the first line of defence against pathogenic organisms through a myriad of germline encoded receptors called pattern-recognition receptors (PRRs). Toll-like receptor (TLR) 3, as an important member of PRRs, is indispensable for host defence against viral infection by recognising virus-derived RNAs. However, little is known about the structure and function of TLR3 in ducks (Anas platyrhynchos), a natural host for the avian influenza virus.2. This study cloned the full-length cDNA of duck TLR3 using reverse transcription polymerase chain reaction (RT-PCR) with rapid amplification of cDNA ends (RACE). The cDNA sequence of duck TLR3 was 4046 bp in length and encoded 895 amino acids. Multiple sequence alignment showed that duck TLR3 shared high similarity with that from other vertebrates.3. Quantitative real-time PCR (qRT-PCR) analysis suggested that TLR3 mRNA was constitutively expressed in all tissues tested, having higher levels in the kidney, liver, breast muscle, ovary and heart. After stimulation with viral- or bacterial-mimics, including LPS, poly(I:C), pam3CSK4, FLS-1, FLA-ST and R848, the TLR3 transcript was significantly upregulated. Meanwhile, overexpression of duck TLR3 significantly promoted the transcription of IFN-β, IRF7, TRIF, Mx, STAT1 and STAT2 mRNA after stimulation with poly(I:C).4. These results suggested that TLR3 play an important role in resistance against viral and bacterial infections in ducks.

The Relationship of Lymphocyte to High-Density Lipoprotein Ratio with Pulmonary Function in COPD

Purpose

This study aimed to explore the relation between lymphocyte to high-density lipoprotein ratio (LHR) and pulmonary function of chronic obstructive pulmonary disease (COPD) patients compared with neutrophil–lymphocyte ratio (NLR) and platelet–lymphocyte ratio (PLR).

Patients and Methods

In total, 154 participants (n = 77 with COPD and n = 77 without COPD) were recruited. LHR, NLR, PLR, lung function and other data were collected and compared. Pearson’s correlation test and the receiver operating characteristics curves were used to compare the utility of LHR, NLR and PLR. Besides, univariate and multivariate logistic regression analyses were conducted.

Results

COPD patients with poorer lung function had a lower LHR level (P < 0.001). In low LHR group, more patients underwent greater airflow limitation than the other group (P = 0.006). LHR positively correlated with forced expiratory volume in 1 second in percent of the predicted value (FEV₁%) (r = 0.333, P = 0.003). At a cut-off value of 2.08, the sensitivity and specificity of LHR in predicting FEV₁% < 50 were 93.2% and 55.6%, respectively, with an AUC of 0.770 (P = 0.001) better than NLR and PLR. Based on logistic regression analyses, it was proved that LHR was associated with decreased risk of FEV₁ <50% predicted in COPD patients (odds ratio = 0.198, 95% CI: 0.048–0.811, P = 0.024).

Conclusion

In contrast with NLR and PLR, LHR has higher accuracy for predicting pulmonary function in COPD; lower LHR level is independently associated with poorer pulmonary function.

Association between polymorphism near the MC4R gene and cancer risk: A meta-analysis

OBJECTIVE

Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) near the melanocortin 4 receptor (MC4R), gene which are associated with risk of obesity. Since obesity is an established risk factor of cancer, several studies have examined the association between SNPs near the MC4R gene and cancer risk, but the findings are inconsistent. The present study aimed to perform a meta-analysis to clarify the association between SNPs near MC4R and cancer risk.

METHODS

The PubMed and Embase databases were searched for potentially eligible publications. All studies that evaluated the association between MC4R rs17782313 SNP (or its proxy rs12970134) and cancer risk were included. The pooled odds ratios with 95% confidence intervals (CIs) were calculated using the random-effects model. And subgroup analysis by cancer type (colorectal cancer, endometrial cancer and breast cancer) was conducted for further investigate the association.

RESULTS

A total of 6 eligible studies (6517 cases and 16,886 controls) were included in the present meta-analysis. The results indicated that MC4R rs17782313 SNP was moderately associated with cancer risk (odds ratio = 1.12, 95% CI = 1.01-1.24). However, the subgroup analysis between different cancer types shows that rs17782313 is only associated with colorectal cancer but not the endometrial cancer and breast cancer. Risk factor in colorectal cancer was both significantly associated with rs17782313 with and without adjustment for body mass index; while the risk factor of the endometrial cancer and breast cancer were both not associated with the rs17782313 with and without adjustment for body mass index. There was no publication bias for the association between MC4R rs17782313 and cancer risk.

CONCLUSION

The present meta-analysis confirmed the moderate association between MC4R rs17782313 and cancer risk.

Quantifying the sharing of foliar fungal pathogens by the invasive plant Ageratina adenophora and its neighbours

Local pathogens can accumulate as asymptomatic endophytes, making it difficult to detect the impacts of invasive species as propagators of disease in the invaded range. We used the invasive plant Ageratina adenophora to assess such accumulation. We intensively collected foliar fungal endophytes and leaf spot pathogens of A. adenophora and co-occurring neighbours and performed an inoculation experiment to evaluate their pathogenicity and host range. Ageratina adenophora harboured diverse necrotrophic pathogens; its communities of endophytes and leaf spot pathogens were different in composition and shared only a small number of fungal species. In the pathogen communities of local plant hosts, 21% of the operational taxonomic units (OTUs), representing 50% of strains, also occurred as leaf spot pathogens and/or endophytes of A. adenophora. The local pathogen community was more similar to the endophytes than to the pathogens of A. adenophora. The inoculation experiment showed that local pathogens could infect A. adenophora leaves asymptomatically and that local plant hosts were susceptible to both A. adenophora endophytes and pathogens. Ageratina adenophora is a highly competent host for local pathogens, and its asymptomatic latent pathogens are fungi primarily shared with local neighbours. This poses challenges for understanding the long-term ecological consequences of plant invasion.

Propofol‑induced miR‑125a‑5p inhibits the proliferation and metastasis of ovarian cancer by suppressing LIN28B

Propofol, a commonly used intravenous anesthetic agent during surgery, has relatively widespread pharmacological actions. Previous studies have reported that propofol may act as an antitumor drug in several cancer types, such as pancreatic cancer, lung cancer and gastric cancer. However, the underlying mechanism in ovarian cancer remain unknown. Therefore, the present study investigated the pharmacological effect of propofol on microRNAs (miRNAs) in ovarian cancer treatment. Propofol (1, 5 or 10 µg/ml) was used to treat A2780 and SKOV3 ovarian cancer cells for 1, 2, 3, 4 or 5 days. The MTT assay was used to detect cell viability, while wound healing and Transwell assays were utilized to assess the invasive and migratory abilities. The bioinformatics prediction approach identified differentially expressed miRNAs (miRs) that were used in Gene Ontology, Gene Set Enrichment Analysis and Kyoto Encyclopedia of Genes and Genomes analyses. The expression levels of miR‑125a‑5p and lin‑28 homolog B (LIN28B) were evaluated by reverse transcription‑quantitative PCR (RT‑qPCR). A luciferase assay was performed to identify the relationship between miR‑125a‑5p and LIN28B. Western blotting was conducted to measure the protein expression of LIN28B. It was demonstrated that propofol significantly upregulated miR‑125a‑5p to exert its antitumor activity. RT‑qPCR results suggested that propofol could upregulate miR‑125a‑5p and LIN28B expression levels in ovarian cancer cell lines. Western blot analysis also indicated that propofol could enhance the expression of LIN28B in ovarian cancer cell lines. The luciferase assay identified that miR‑125a‑5p could directly inhibit the expression of LIN28B to suppress proliferation and metastasis in ovarian cancer. In conclusion, these results suggested that propofol inhibited ovarian cancer proliferation and metastasis by enhancing miR‑125a‑5p, which targets LIN28B.

Iron-Catalyzed Diastereoselective Synthesis of Disubstituted Morpholines via C–O or C–N Bond Formation

The diastereoselective synthesis of 2,6- and 3,5-disubstituted morpholines was achieved from 1,2-amino ethers and 1,2-hydroxy amines substituted by an allylic alcohol using an iron(III) catalyst. The morpholines were obtained either by C–O or C–N bond formation. A plausible mechanism is suggested, involving a thermodynamic equilibrium to explain the formation of the cis diastereoisomer as the major product.

[Clinical and immunological characteristics of a case with activated phosphoinositide 3-kinase δ syndrome 2]

Objective: To analyze the clinical and immunological characteristics of a patient with activated phosphoinositide 3-kinase δ syndrome 2 (APDS2). Methods: A retrospective analysis of clinical data, immune-related gene sequencing, imaging and laboratory findings of a patient with APDS2 admitted to Children's Hospital of Chongqing Medical University was performed. The absolute and relative numbers of peripheral lymphocyte subsets, immune cell subsets and phenotypes were detected by flow cytometry with the age matched healthy child or the patient's father as a control. Results: A female patient aged 6 years and 4 months old was firstly admitted due to paleness over one month and cough for 7 days in June 2017. The IgA (<0.067 g/L) decreased while the IgM (2.55 g/L) increased. The abdominal ultrasound found hepatomegaly (subcostal 1.7 cm) and splenomegaly (subcostal 3.6 cm), and gene sequencing revealed a heterozygous mutation in the PIK3R1 gene c.1425+1G>A. After the treatment with prednisone which was initiated with a dose of 10 mg/times, 3 times/d and continued and tapered over 7 months, the IgM decreased to normal (1.72 g/L), and the hepatomegaly (subcostal 0 cm) and splenomegaly (subcostal 0.5 cm) were improved. The patient was readmitted due to pale and sallow complexion for half a month in July 2019. The percentage of naive CD4(+)T (0.386) and naive CD8(+)T cells (0.271) were decreased while the percentage of terminally differentiated effector memory CD8(+)T cells (0.377) and transitional B cells (0.223) were increased. The mean fluorescence intensity (MFI) of phosphorylated protein kinase B (AKT) in CD3(+)T, CD4(+)T and CD8(+)T cells were higher in the patient (4 125, 5 213, 3 497) than those in her father (3 434, 3 312, 3 058). The percentage of follicular helper T cell (Tfh) (0.299), Th1 (0.491) and Th1-like cells (0.438) in the patient were higher than those in the healthy control (0.156,0.313,0.303), while the percentage of Th17 (0.126) and Th17-like cells (0.188) were lower than those in the healthy control (0.198, 0.315). And the percentage of CD57 in the patient (0.306) was also higher than that in the healthy control (0.246). Conclusions: The humoral immunity and cellular immunity of APDS2 patient are impaired to varying degrees. The steroid can improve the lymphoproliferation and autoimmune hemolytic anemia in this case.

Transition-Metal-Catalyzed 1,2-Carboboration of Alkenes: Strategies, Mechanisms, and Stereocontrol

During the past decade, many research groups have described catalytic methods for 1,2-carboboration, allowing access to structurally complex organoboronates from alkenes. Various transition metals, especially copper, palladium, and nickel, have been widely used in these reactions. This review summarizes advances in this field, with a special focus on the catalytic cycles involved in different metal-catalyzed carboboration reactions, as well as the regio- and stereochemical consequences of the underlying mechanisms. 1,2-Carboboration of other unsaturated systems, such as alkynes and allenes, are outside of the scope of this review.

Intestinal responses of the oriental fruit fly Bactrocera dorsalis (Hendel) after ingestion of an entomopathogenic bacterium strain

BACKGROUND

Bactrocera dorsalis (Hendel) is the main fruit fly pest of tropical and subtropical countries. The application of insecticides to manage this pest has led to serious resistance problems; therefore, new ways to control B. dorsalis are required. Pathogenic bacteria are sources of biocontrol agents for pest management.

RESULTS

We determined that a pathogenic bacterial strain, Serratia marcescens PS-1, isolated from a moribund striped flea beetle (Phyllotreta striolata), was lethal to B. dorsalis adults following ingestion. Histological analyses revealed that PS-1 damaged the intestinal epithelium, resulting in cell death within 24 h. We then generated a gut transcriptomic data set using RNA-Seq at two time points (6 and 24 h) after PS-1 infection. We found that genes encoding the peritrophic matrix constituent were down-regulated, whereas genes involved in lipid and glycan metabolism, and renewal of the gut epithelium, along with genes encoding digestive enzymes and stress response factors, were up-regulated. In addition, 14 cecropin genes were identified and cloned from B. dorsalis. To our knowledge, the number of cecropins identified in the present study is greater than that reported in the insects of earlier studies. Moreover, some of the cecropins identified were significantly down-regulated after PS-1 treatment.

CONCLUSION

Our findings provide new insights into the insect gut response to pathogenic bacterial invasion and may aid the development of new strategies for the biological control of B. dorsalis. © 2019 Society of Chemical Industry.

Immunological role and underlying mechanisms of B7-H6 in tumorigenesis

B7 homolog 6 (B7-H6) has been identified as involved in tumorigenesis. Elucidating its role and potential mechanism of action is essential for understanding tumorigenesis and the potential development of an effective clinical strategy. Abnormal overexpression of B7-H6 in various types of tumors was reported to be linked with poor prognosis. B7-H6 suppresses the initiation of the "caspase cascade" and induces anti-apoptosis by STAT3 pathway activation to provoke tumorigenesis. B7-H6 facilitates tumor proliferation and cell cycle progression by regulating apoptosis suppressors. B7-H6 induces cellular cytotoxicity, secretion of TNF-α and IFN-γ and B7-H6-specific BiTE triggers T cells to accelerate tumorigenesis. B7-H6 induces abnormal immunological progression by HER2-scFv mediated ADCC and NKp30 immune escape to promote tumorigenesis. B7-H6 promotes tumorigenesis via apoptosis inhibition, proliferation and immunological progression. B7-H6 may a valuable potential biomarker and therapeutic strategy for diagnostics, prognostics and treatment in cancer.

A lysin motif effector subverts chitin-triggered immunity to facilitate arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal (AM) fungi greatly improve mineral uptake by host plants in nutrient-depleted soil and can intracellularly colonize root cortex cells in the vast majority of higher plants. However, AM fungi possess common fungal cell wall components such as chitin that can be recognized by plant chitin receptors to trigger immune responses, raising the question as to how AM fungi effectively evade chitin-triggered immune responses during symbiosis. In this study, we characterize a secreted lysin motif (LysM) effector identified from the model AM fungal species Rhizophagus irregularis, called RiSLM. RiSLM is one of the highest expressed effector proteins in intraradical mycelium during the symbiosis. In vitro binding assays show that RiSLM binds chitin-oligosaccharides and can protect fungal cell walls from chitinases. Moreover, RiSLM efficiently interferes with chitin-triggered immune responses, such as defence gene induction and reactive oxygen species production in Medicago truncatula. Although RiSLM also binds to symbiotic (lipo)chitooligosaccharides it does not interfere significantly with symbiotic signalling in Medicago. Host-induced gene silencing of RiSLM greatly reduces fungal colonization levels. Taken together, our results reveal a key role for AM fungal LysM effectors to subvert chitin-triggered immunity in symbiosis, pointing to a common role for LysM effectors in both symbiotic and pathogenic fungi.

CRISPR/Cas9-mediated knockout of the eye pigmentation gene white leads to alterations in colour of head spots in the oriental fruit fly, Bactrocera dorsalis

The intensely studied white gene is widely used as a genetic marker in Drosophila melanogaster. Here, we cloned and characterized the white gene in an important pest of the fruit industry, Bactrocera dorsalis, to understand its functional role in pigmentation. We obtained BdWhite knockout strains, based on the wild-type strain, using the CRISPR/Cas9 genome editing system, and found that mutants lost pigmentation in the compound eye and their black head spots. We then examined differences in the expression levels of genes associated with melanin pigmentation between mutants and the wild-type strain using quantitative reverse transcription PCR. We found that transcription levels of the Bd-yellow1 were lower in the head of mutants than in the wild-type strain, and there were no significant differences in expression of the other six genes between mutants and the wild type. Since yellow is critical for melanin biosynthesis (Heinze et al., Scientific Reports. 2017;7:4582), the lower levels of expression of Bd-yellow1 in mutants led to reduced dark pigmentation in head spots. Our results provide the first evidence, to our knowledge, that white may play a functional role in cuticle pigmentation by affecting the expression of yellow.