PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components.

The genetic compensation response (GCR) has recently been proposed as a possible explanation for the phenotypic discrepancies between gene-knockout and gene-knockdown1,2; however, the underlying molecular mechanism of the GCR remains uncharacterized. Here, using zebrafish knockdown and knockout models of the capn3a and nid1a genes, we show that mRNA bearing a premature termination codon (PTC) promptly triggers a GCR that involves Upf3a and components of the COMPASS complex. Unlike capn3a-knockdown embryos, which have small livers, and nid1a-knockdown embryos, which have short body lengths2, capn3a-null and nid1a-null mutants appear normal. These phenotypic differences have been attributed to the upregulation of other genes in the same families. By analysing six uniquely designed transgenes, we demonstrate that the GCR is dependent on both the presence of a PTC and the nucleotide sequence of the transgene mRNA, which is homologous to the compensatory endogenous genes. We show that upf3a (a member of the nonsense-mediated mRNA decay pathway) and components of the COMPASS complex including wdr5 function in GCR. Furthermore, we demonstrate that the GCR is accompanied by an enhancement of histone H3 Lys4 trimethylation (H3K4me3) at the transcription start site regions of the compensatory genes. These findings provide a potential mechanistic basis for the GCR, and may help lead to the development of therapeutic strategies that treat missense mutations associated with genetic disorders by either creating a PTC in the mutated gene or introducing a transgene containing a PTC to trigger a GCR.

Deciphering the tumour microenvironment of clear cell renal cell carcinoma: Prognostic insights from programmed death genes using machine learning.

Clear cell renal cell carcinoma (ccRCC), a prevalent kidney cancer form characterised by its invasiveness and heterogeneity, presents challenges in late-stage prognosis and treatment outcomes. Programmed cell death mechanisms, crucial in eliminating cancer cells, offer substantial insights into malignant tumour diagnosis, treatment and prognosis. This study aims to provide a model based on 15 types of Programmed Cell Death-Related Genes (PCDRGs) for evaluating immune microenvironment and prognosis in ccRCC patients. ccRCC patients from the TCGA and arrayexpress cohorts were grouped based on PCDRGs. A combination model using Lasso and SuperPC was constructed to identify prognostic gene features. The arrayexpress cohort validated the model, confirming its robustness. Immune microenvironment analysis, facilitated by PCDRGs, employed various methods, including CIBERSORT. Drug sensitivity analysis guided clinical treatment decisions. Single-cell data enabled Programmed Cell Death-Related scoring, subsequent pseudo-temporal and cell-cell communication analyses. A PCDRGs signature was established using TCGA-KIRC data. External validation in the arrayexpress cohort underscored the model's superiority over traditional clinical features. Furthermore, our single-cell analysis unveiled the roles of PCDRG-based single-cell subgroups in ccRCC, both in pseudo-temporal progression and intercellular communication. Finally, we performed CCK-8 assay and other experiments to investigate csf2. In conclusion, these findings reveal that csf2 inhibit the growth, infiltration and movement of cells associated with renal clear cell carcinoma. This study introduces a PCDRGs prognostic model benefiting ccRCC patients while shedding light on the pivotal role of programmed cell death genes in shaping the immune microenvironment of ccRCC patients.

A designer rice NLR immune receptor confers resistance to the rice blast fungus carrying noncorresponding avirulence effectors.

Plant nucleotide-binding and leucine-rich repeat (NLR) receptors recognize avirulence effectors directly through their integrated domains (IDs) or indirectly via the effector-targeted proteins. Previous studies have succeeded in generating designer NLR receptors with new recognition profiles by engineering IDs or targeted proteins based on prior knowledge of their interactions with the effectors. However, it is yet a challenge to design a new plant receptor capable of recognizing effectors that function by unknown mechanisms. Several rice NLR immune receptors, including RGA5, possess an integrated heavy metal-associated (HMA) domain that recognizes corresponding Magnaporthe oryzae Avrs and ToxB-like (MAX) effectors in the rice blast fungus. Here, we report a designer rice NLR receptor RGA5HMA2 carrying an engineered, integrated HMA domain (RGA5-HMA2) that can recognize the noncorresponding MAX effector AvrPib and confers the RGA4-dependent resistance to the M. oryzae isolates expressing AvrPib, which originally triggers the Pib-mediated blast resistance via unknown mechanisms. The RGA5-HMA2 domain is contrived based on the high structural similarity of AvrPib with two MAX effectors, AVR-Pia and AVR1-CO39, recognized by cognate RGA5-HMA, the binding interface between AVR1-CO39 and RGA5-HMA, and the distinct surface charge of AvrPib and RAG5-HMA. This work demonstrates that rice NLR receptors with the HMA domain can be engineered to confer resistance to the M. oryzae isolates noncorresponding but structurally similar MAX effectors, which manifest cognate NLR receptor-mediated resistance with unknown mechanisms. Our study also provides a practical approach for developing rice multilines and broad race spectrum-resistant cultivars by introducing a series of engineered NLR receptors.

A tRNAModification-based strategy for Identifying amiNo acid Overproducers (AMINO).

Amino acids have a multi-billion-dollar market with rising demand, prompting the development of high-performance microbial factories. However, a general screening strategy applicable to all proteinogenic and non-proteinogenic amino acids is still lacking. Modification of the critical structure of tRNA could decrease the aminoacylation level of tRNA catalyzed by aminoacyl-tRNA synthetases. Involved in a two-substrate sequential reaction, amino acids with increased concentration could elevate the reduced aminoacylation rate caused by specific tRNA modification. Here, we developed a selection system for overproducers of specific amino acids using corresponding engineered tRNAs and marker genes. As a proof-of-concept, overproducers of five amino acids such as L-tryptophan were screened out by growth-based and/or fluorescence-activated cell sorting (FACS)-based screening from random mutation libraries of Escherichia coli and Corynebacterium glutamicum, respectively. This study provided a universal strategy that could be applied to screen overproducers of proteinogenic and non-proteinogenic amino acids in amber-stop-codon-recoded or non-recoded hosts.

Salipaludibacillus daqingensis sp. nov., a moderately halophilic bacterium isolated from an oilfield.

A novel alkaliphilic, Gram-stain-positive, moderately halophilic, rod-shaped, endospore-forming, motile, facultatively anaerobic bacterium (DQ-9T) was isolated from a sediment sample collected from Daqing oilfield in China, and characterized by a polyphasic taxonomic approach. Strain DQ-9T formed yellow pigment and grew occurred at salinities of 1-12 % (w/v) NaCl (optimum, 8 %) and at 10-40 °C (optimum, 30-35 °C), at pH 7.5-10.5 (optimum, pH 9.0-9.5). It was catalase-positive, but oxidase-negative. Based on the analysis of 16S rRNA gene sequences, DQ-9T was classified into the genus Salipaludibacillus and exhibited the highest similarities (98.37 %) to Salipaludibacillus neizhouensis JSM 071004T. Digital DNA-DNA hybridization and average nucleotide identity values between strain DQ-9T and the most closely related strain, S. neizhouensis DSM 19794T, were determined to be 72.0 and 21.6 %, respectively. The polar lipids were constituted by diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids (>5 %) comprised anteiso-C15 : 0, anteiso-C17 : 0, iso-C17 : 0, iso-C15 : 0 and C16 : 0. The cell-wall peptidoglycan contained meso-diaminopimelic acid, and menaquinone-7 was identified as the primary respiratory quinone. The DNA G+C content was 37.5 mol%. Through chemotaxonomic, physiological, and biochemical characterization, strain DQ-9T could be clearly distinguished from the closest Salipaludibacillus species. Based on provided data, strain DQ-9T is proposed to represent a novel species, Salipaludibacillus daqingensis sp. nov., within the genus Salipaludibacillus. The type strain is DQ-9T (=ACCC 60415T=KCTC 33936T).

Use of portable air purifiers to reduce aerosols in hospital settings and cut down the clinical backlog.

SARS-CoV-2 has severely affected capacity in the National Health Service (NHS), and waiting lists are markedly increasing due to downtime of up to 50 min between patient consultations/procedures, to reduce the risk of infection. Ventilation accelerates this air cleaning, but retroactively installing built-in mechanical ventilation is often cost-prohibitive. We investigated the effect of using portable air cleaners (PAC), a low-energy and low-cost alternative, to reduce the concentration of aerosols in typical patient consultation/procedure environments. The experimental setup consisted of an aerosol generator, which mimicked the subject affected by SARS-CoV-19, and an aerosol detector, representing a subject who could potentially contract SARS-CoV-19. Experiments of aerosol dispersion and clearing were undertaken in situ in a variety of rooms with two different types of PAC in various combinations and positions. Correct use of PAC can reduce the clearance half-life of aerosols by 82% compared to the same indoor-environment without any ventilation, and at a broadly equivalent rate to built-in mechanical ventilation. In addition, the highest level of aerosol concentration measured when using PAC remains at least 46% lower than that when no mitigation is used, even if the PAC's operation is impeded due to placement under a table. The use of PAC leads to significant reductions in the level of aerosol concentration, associated with transmission of droplet-based airborne diseases. This could enable NHS departments to reduce the downtime between consultations/procedures.

Immune-related effects of compound astragalus polysaccharide and sulfated epimedium polysaccharide on newborn piglets.

This study aimed to evaluate the immune effects of compound astragalus polysaccharide and sulfated epimedium polysaccharide (APS-sEPS) on the peripheral blood lymphocyte and intestinal mucosa in newborn piglets. A total of 40 newborn piglets were randomly divided into four groups during a 25-day experiment, including APS-sEPS, APS, sEPS and control group. The results showed that supplementation with APS-sEPS to newborn piglets remarkably increased the physiological parameters, especially the WBC. In peripheral blood, piglets that received APS-sEPS showed the highest proliferation of T lymphocytes, the percentage of CD3 + CD4+ and CD3 + CD8+ cells were the highest on days 15 and 25 (p < 0.05). The serum concentrations of IFN-γ on days 7 and 15, and IL-4, IL-10, sIgA on days 7, 15 and 25 in APS-sEPS group were significantly higher than those in the control group (p < 0.05). Furthermore, the villus length and the ratio of villus length to crypt depth in APS-sEPS group were both significantly increased compared to that of control group (p < 0.05). In the duodenum, jejunum and illume, the concentrations of IFN-γ, IL-10, total IgG and sIgA in APS-sEPS group were all significantly higher than that in control group (p < 0.05). In intestinal mucosa, APS-sEPS significantly increased the expression of NF-κB and IRF-3 mRNA in each section of small intestine of piglets. Nevertheless, in the illume segment, the effect of APS-sEPS was more significant than that of APS and sEPS (p < 0.05). The expression of TLR4 was more significant than that of control group in duodenum only. The results from the present research provide evidence that the suckling piglets administered with APS-sEPS supplement exhibited enhanced immune function of peripheral blood lymphocyte and expression of specific antibodies, and ameliorated intestinal morphological development and increased activities of humoral immune response in the small intestine, which would be related to the activation of the TLR4-NF-κB signaling pathway and IRF3.

Characterization of a Root-Knot Nematode Infecting Aconitum carmichaelii in Southwest China.

Growth of the Chinese herbal medicine industry has resulted in several new pests and diseases. China is one of the world largest producers of monkshood (Aconitum carmichaelii Debx.), but an unidentified root-knot nematode has become a significant pest in the southwestern provinces of Yunnan and Sichuan. Morphological characteristics and the ribosomal DNA-internal transcribed spacer and D2-D3 region of the 28S ribosomal RNA gene sequences were used to identify the nematode as Meloidogyne hapla. Through investigation, this is the first report of M. hapla infecting monkshood in Yunnan and Sichuan Provinces.

A new Panax notoginseng Leaf Spot Caused by Boeremia linicola in Yunnan, China.

Panax notoginseng-also known as Tianqi and Sanqi-is one of the most highly valued medicinal perennial herbs in the world (Wang et al. 2016). In August 2021, leaf spot was observed on P. notoginseng leaves in Lincang sanqi base (23º43´10˝N, 100º7´32˝E, 13.33 hm2). Symptoms expanded from water soaked areas on the leaves to form irregular round or oval leaf spots with transparent or grayish-brown centers containing black granular matter, with an incidence of 10 to 20%. To identify the causal agent, ten symptomatic leaves were randomly selected from ten P. notoginseng plants. Symptomatic leaves were cut into small pieces (5 mm2) with asymptomatic tissue margins, disinfected in 75% ethanol for 30s and in 2% sodium hypochlorite for 3 min, and rinsed three times with sterile distilled water. The tissue portions were placed on potato dextrose agar (PDA) plates incubated at 20℃ with a 12 h light/dark photoperiod. Seven pure isolates were obtained with similar colony morphology, dark gray (top view) or taupe (back view) coloration, with flat and villous surfaces. Pycnidia were globose to subglobose, glabrous or with few mycelial outgrowths, dark brown to black, 22.46 to 155.94 (av. 69.57) µm × 18.20 to 130.5 (av. 57.65) µm (n=50) in size. Conidia were ellipsoidal to cylindrical, thinwalled, smooth, hyaline, aseptate, and measured 1.47 to 6.81 (av. 4.29) µm long and 1.01 to 2.97 (av. 1.98) µm thick (n=100). The isolated strains were preliminarily identified as Boeremia sp. based on the morphological characteristics of colonies and conidia. (Aveskamp et al. 2010; Schaffrath et al. 2021). To confirm pathogen identity, the total genomic DNA of two isolates (LYB-2 and LYB-3) was extracted using the T5 Direct PCR kit. The internal transcribed spacer (ITS), 28S large subunit nrRNA gene (LSU), and ß-tubulin (TUB2) gene regions were PCR-amplified using primers ITS1/ITS4, LR0Rf/LR5r, and BT2F/BT4R (Chen et al. 2015), respectively. Sequences have been deposited in GenBank (ON908942-ON908943 for ITS, ON908944-ON908945 for LSU, ON929285-ON929286 for TUB2). BLASTn searches of generated DNA sequences from 2 purified isolates (LYB-2 and LYB-3) against GenBank showed high similarity (>99%) with the sequences of Boeremia linicola. Moreover, a phylogenetic tree was constructed based on the neighbor-joining method in MEGA-X (Kumar et al. 2018) and revealed that the 2 isolates were closest to B. linicola (CBS 116.76). Pathogenicity tests were conducted with the 2 isolates (LYB-2 and LYB-3) as described by Cai et al. (2009) with slight modifications. Each isolate was inoculated with three healthy annual P. notoginseng plants, and each leaf was inoculated with three drops of conidia suspension (106 spores/mL). Three P. notoginseng plants inoculated with sterile water were used as controls. All plants were covered with plastic bags incubated in a greenhouse (20℃, 90%RH, 12 h light/dark photoperiod). Fifteen days post-inoculation, all inoculated leaves showed similar lesions, and the symptoms were identical to those in the field. The pathogen was reisolated from symptomatic leaf spots, and the colony characteristics were identical to the original isolates. Control plants remained healthy, and no fungus was re-isolated. Morphological characteristics, sequence alignment and pathogenicity tests confirmed that B. linicola was the cause of P. notoginseng leaf spot disease. This is the first report of B. linicola causing leaf spot on P. notoginseng in Yunnan, China. The identification of B. linicola as the causal agent of the observed leaf spot on P. notoginseng is critical to the prevention and control of this disease in the future.

Effects of different soil moisture on the growth, quality, and root rot disease of organic Panax notoginseng cultivated under pine forests.

The under-forest economy in the agroforestry system can improve land use efficiency, protect ecological environment, and promote arable land sustainable development. However, the effects of soil moisture in the forest and irrigation strategies on the healthy growth of intercropping crops are still incomplete. Here, considering the organic Panax notoginseng cultivated under pine forests (PPF) as the research object, we explored the effects of different soil moisture on the physiological state, yield, quality and disease occurrence of PPF. Our results suggested that 80-85% and 95-100% field capacity (FC) treatments were more conducive to increased photosynthetic rate and biomass accumulation of PPF, but 50-55% and 65-70% FC treatments were more conducive to the accumulation of saponins in PPF leaves. Notably, the root rot index of PPF was highest under 95-100% FC (19.51) treatment, significantly higher than that under 65-70% FC (8.44) and 80-85% FC (10.21) treatments. Further, the rhizosphere microorganisms of PPF under different soil moisture treatments were sequenced, and the sequencing data analysis revealed that high soil moisture (95-100% FC) could destroy the microbial diversity balance and cause the accumulation of pathogens (Fusarium oxysporum and Ilyonectria radicicola), leading to a high incidence of root rot. The incidence of PPF root rot was negatively correlated with rhizosphere microbial diversity. Overall, our results highlight that the quantitative irrigation (80-85% FC) is conducive to maintaining the balance between yield, saponin content and disease occurrence of PPF, providing a practical basis for PPF irrigation strategy and promoting the sustainable development of PPF agroforestry system.

Volatile Organic Compounds of Bacillus velezensis GJ-7 against Meloidogyne hapla through Multiple Prevention and Control Modes.

The Bacillus velezensis GJ-7 strain isolated from the rhizosphere soil of Panax notoginseng showed high nematicidal activity and therefore has been considered a biological control agent that could act against the root-knot nematode Meloidogyne hapla. However, little was known about whether the GJ-7 strain could produce volatile organic compounds (VOCs) that were effective in biocontrol against M. hapla. In this study, we evaluated the nematicidal activity of VOCs produced by the fermentation of GJ-7 in three-compartment Petri dishes. The results revealed that the mortality rates of M. hapla J2s were 85% at 24 h and 97.1% at 48 h after treatment with the VOCs produced during GJ-7 fermentation. Subsequently, the VOCs produced by the GJ-7 strain were identified through solid-phase micro-extraction gas chromatography mass spectrometry (SPME-GC/MS). Six characteristic VOCs from the GJ-7 strain fermentation broth were identified, including 3-methyl-1-butanol, 3-methyl-2-pentanone, 5-methyl-2-hexanone, 2-heptanone, 2,5-dimethylpyrazine, and 6-methyl-2-heptanone. The in vitro experimental results from 24-well culture plates showed that the six volatiles had direct-contact nematicidal activity against M. hapla J2s and inhibition activity against egg hatching. In addition, 3-methyl-1-butanol and 2-heptanone showed significant fumigation effects on M. hapla J2s and eggs. Furthermore, all six of the VOCs repelled M. hapla J2 juveniles in 2% water agar Petri plates. The above data suggested that the VOCs of B. velezensis GJ-7 acted against M. hapla through multiple prevention and control modes (including direct-contact nematicidal activity, fumigant activity, and repellent activity), and therefore could be considered as potential biocontrol agents against root-knot nematodes.

Tetraspanin 7 promotes osteosarcoma cell invasion and metastasis by inducing EMT and activating the FAK-Src-Ras-ERK1/2 signaling pathway.

BACKGROUND: Tetraspanins are members of the 4-transmembrane protein superfamily (TM4SF) that function by recruiting many cell surface receptors and signaling proteins into tetraspanin-enriched microdomains (TEMs) that play vital roles in the regulation of key cellular processes including adhesion, motility, and proliferation. Tetraspanin7 (Tspan7) is a member of this superfamily that plays documented roles in hippocampal neurogenesis, synaptic transmission, and malignant transformation in certain tumor types. How Tspan7 influences the onset or progression of osteosarcoma (OS), however, remains to be defined. Herein, this study aimed to explore the relationship between Tspan7 and the malignant progression of OS, and its underlying mechanism of action. METHODS: In this study, the levels of Tspan7 expression in human OS cell lines were evaluated via qRT-PCR and western blotting. The effect of Tspan7 on proliferation was examined using CCK-8 and colony formation assays, while metastatic role of Tspan7 was assessed by functional assays both in vitro and in vivo. In addition, mass spectrometry and co-immunoprecipitation were performed to verify the interaction between Tspan7 and ß1 integrin, and western blotting was used to explore the mechanisms of Tspan7 in OS progresses. RESULTS: We found that Tspan7 is highly expressed in primary OS tumors and OS cell lines. Downregulation of Tspan7 significantly suppressed OS growth, metastasis, and attenuated epithelial-mesenchymal transition (EMT), while its overexpression had the opposite effects in vitro. Furthermore, it exhibited reduced OS pulmonary metastases in Tspan7-deleted mice comparing control mice in vivo. Additionally, we proved that Tspan7 interacted with ß1 integrin to facilitate OS metastasis through the activation of integrin-mediated downstream FAK-Src-Ras-ERK1/2 signaling pathway. CONCLUSION: In summary, this study demonstrates for the first time that Tspan7 promotes OS metastasis via interacting with ß1 integrin and activating the FAK-Src-Ras-ERK1/2 pathway, which could provide rationale for a new therapeutic strategy for OS.

Alteribacter keqinensis sp. nov., a moderately halophilic bacterium isolated from a soda lake.

A Gram-stain-positive, aerobic, endospore-forming and rod-shaped bacterium (KQ-3T), which grew at 10-45 °C (optimum 35 °C), pH 8.0-10.5 (optimum pH 9.0) and in the presence of 0-16 % (w/v) NaCl (optimum 3.0 %), was isolated from a soda lake and identified as representing a novel species using a polyphasic taxonomic approach. Strain KQ-3T was catalase-positive, oxidase-negative and non-motile. Phylogenetic analysis based on 16S rRNA gene sequence affiliated KQ-3T to the genus Alteribacter and showed the highest similarities to Alteribacter natronophilus M30T (97.90 %), Alteribacter aurantiacus K1-5T (97.84 %) and Alteribacter populi FJAT-45347T (97.22 %). Digital DNA-DNA hybridization and average nucleotide identity analyses revealed that KQ-3T displayed 21.4 and 72.81% genomic DNA relatedness with the most closely related strain, A. natronophilus M30T, respectively. KQ-3T contained all of the conserved signature indels that are specific for members of the genus Alteribacter. The DNA G+C content was 45.03 mol%. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid. The predominant menaquinone was MK-7 (100%) and the major fatty acids (>10 %) comprised anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0. Based on the data from the current polyphasic studies, KQ-3T represents a novel species of the genus Alteribacter, for which the name Alteribacter keqinensis sp. nov. is proposed. The type strain is KQ-3T (=ACCC 61799T=KCTC 33933T).

Effects of sulfated ß-glucan from Saccharomyces cerevisiae on growth performance, antioxidant ability, nonspecific immunity, and intestinal flora of the red swamp crayfish (Procambarus clarkii).

The aim of this study was to examine the combined effects of sulfated ß-Glucan from Saccharomyces cerevisiae (sGSC) on growth performance, antioxidant ability, nonspecific immunity, and intestinal flora of the red swamp crayfish (Procambarus clarkii). Four experimental diets (sGSC25, sGSC50, sGSC100 and sGSC200) with different levels of sGSC (0.025%, 0.05%, 0.1% and 0.2% in diet, respectively) were fed to juvenile crayfish (average weight: 2.5 ± 0.5 g) for 8 weeks. The control diet was given with 2000 mg/kg GSC (GSC200 group). The based control diet was given without sGSC or GSC (blank group). Each group had 3 parallel test pools, 20 crayfish were reared in each pool. At the end of the growth trial, adding dietary 0.025%-0.1% sGSC could significantly improve the growth performance, antioxidant capacity and immunity of crayfish. Compared with GSC, sGSC had a better effect at lower concentration. Higher concentration of sGSC (>0.1%) would cause some side effects. sGSC also could improve the structure of the intestinal flora and optimize the function of the flora. sGSC would increase the abundances of probiotics such as Hafnia and Acinetobacter, and decreases the abundances of maleficent bacteria such as Enterobacteriaceae. Higher concentration of sGSC (>0.1%) would increase the abundance of Aeromonas. To conclude, 0.025%-0.1% sGSC can be used as a supplement in crayfish feed to increase growth, immunity, and antioxidant capacity and improve the structure of intestinal flora. These results provided a theoretical basis for the application of sGSC instead of GSC in crayfish breeding. It will be necessary to further study the optimal concentration of sGSC in feed additives in different growth stages of crayfish in the future.

First Report of Leaf Spot on Panax notoginseng Caused by Caryophylloseptoria pseudolychnidis in Yunnan, China.

Panax notoginseng is a unique traditional medicinal plant in China, which has the effects of improving myocardial ischemia, protecting liver and preventing cardiovascular diseases (Jiang, 2020). In July 2021, gray-brown round spots were found on the leaves of P. notoginseng in the plantations of Lincang City (23º43´10˝N, 100º7´32˝E). By September, the symptoms were observed on more P. notoginseng plants, with incidence reaching 31%. Initial symptoms on leaves were small, brown spots that expanded, with black granular bulges on the lesions, often surrounded with yellow halo. As the disease progressed, multiple lesions merged, leaves became yellow, and abscission occurred. To isolate the causal pathogen, twelve symptomatic leaves were randomly obtained from twelve P. notoginseng plants. Small pieces of infected leaf tissues (about 5 mm2) were disinfected with 75% ethanol for 30 s, soaked in 2% sodium hypochlorite for 3 min, and then rinsed 3 times with sterile water and blotted dry. Sample tissues were plated on potato dextrose agar (PDA) plates incubated at 25℃ for 5 days with 12 h light/dark photoperiod. Hyphal-tips from the growing edge of colonies were transferred to fresh PDA to obtain pure cultures. Eight isolates were obtained with similar colony morphology, gray (top view) or black (back view) coloration, with a villous surface, and slow-growing on PDA. Conidia were hyaline, slender and obtuse to subobtuse at both ends, 10.3 to 52.62 (av. 25.2) µm × 1.4 to 4.0 (av. 2.4) µm (n=200) in size. Characteristics of the colonies and conidia were consistent with Caryophylloseptoria pseudolychnidis as described by Quaedvlieg et al. (2013) and Verkley et al. (2013). Genomic DNA of three representative isolates (LINC-4 to LINC-6) was extracted, and the rDNA-ITS region, ACT, and LSU gene regions were amplified and sequenced using the primer pairs ITS4/ITS5, 512F/783R, and LSU1Fd/LR5, respectively. Sequences have been deposited in GenBank (OK614104-OK614106 for ITS, OK614109-OK614111 for LSU, OK628350-OK628352 for ACT). BLAST search showed that all sequences were 98% to 100% homology with the corresponding sequences of C. pseudolychnidis. ITS sequences of the three isolates (LINC-4 to LINC-6) showed 99.21% identity (500/504 bp) to C. pseudolychnidis strain CBS 128630 (GenBank accession no. NR156266). LSU sequences of the three isolates showed 99.76% identity (823/825 bp) to C. pseudolychnidis strain CBS 128630 (MH876481). For ACT sequences, LINC-4 and LINC-5 showed 98.53% identity (201/204 bp) to C. pseudolychnidis strain 128614 (KF253599); LINC-6 showed 99.02% identity (202/204 bp) to C. pseudolychnidis strain 128614 (KF253599). Further, the neighbor-joining and maximum-likelihood method were used for multilocus phylogenetic analysis of the obtained sequences using MEGA-X (Kumar et al. 2018). The three isolates were clustered in the same clade with two C. pesudolychidis from database. Three isolates (LINC-4 to LINC-6) were tested for pathogenicity to confirm Koch's postulates. Annual potted P. notoginseng was inoculated with spore suspension (105 spores.mL-1). Each isolate was inoculated onto two leaves each of five P. notoginseng plants. The controls were similarly mock-inoculated with sterile water. To maintain high humidity (>90% RH), all plants were placed in transparent plastic boxes in a greenhouse at 25℃ with a 12 h light/dark photoperiod. Fifteen days post-inoculation, inoculated leaves showed similar symptoms to those observed in the field, and control plants remained healthy. The pathogen were reisolated from symptomatic leaf spots, and the colony characteristics were the same as those of the original isolates. Morphological characteristics, molecular data, and Koch's postulates tests confirmed C. pseudolychnidis as the cause of P. notoginseng leaf spot disease. To our knowledge, this is the first report of C. pseudolychnidis causing leaf spot on P. notoginseng in Yunnan, China. The spread of this disease might pose a serious threat to the production of P. notoginseng. The occurrence and spread of this pathogen should be further studied in order to formulate reasonable control measures.

Preliminary study on the application of renal ultrasonography radiomics in the classification of glomerulopathy.

BACKGROUND: The aim of this study was to investigate the potential use of renal ultrasonography radiomics features in the histologic classification of glomerulopathy. METHODS: A total of 623 renal ultrasound images from 46 membranous nephropathy (MN) and 22 IgA nephropathy patients were collected. The cases and images were divided into a training group (51 cases with 470 images) and a test group (17 cases with 153 images). A total of 180 dimensional features were designed and extracted from the renal parenchyma in the ultrasound images. Least absolute shrinkage and selection operator (LASSO) logistic regression was then applied to these normalized radiomics features to select the features with the highest correlations. Four machine learning classifiers, including logistic regression, a support vector machine (SVM), a random forest, and a K-nearest neighbour classifier, were deployed for the classification of MN and IgA nephropathy. Subsequently, the results were assessed according to accuracy and receiver operating characteristic (ROC) curves. RESULTS: Patients with MN were older than patients with IgA nephropathy. MN primarily manifested in patients as nephrotic syndrome, whereas IgA nephropathy presented mainly as nephritic syndrome. Analysis of the classification performance of the four classifiers for IgA nephropathy and MN revealed that the random forest achieved the highest area under the ROC curve (AUC) (0.7639) and the highest specificity (0.8750). However, logistic regression attained the highest accuracy (0.7647) and the highest sensitivity (0.8889). CONCLUSIONS: Quantitative radiomics imaging features extracted from digital renal ultrasound are fully capable of distinguishing IgA nephropathy from MN. Radiomics analysis, a non-invasive method, is helpful for histological classification of glomerulopathy.

Specific recognition of two MAX effectors by integrated HMA domains in plant immune receptors involves distinct binding surfaces.

The structurally conserved but sequence-unrelated MAX (Magnaporthe oryzae avirulence and ToxB-like) effectors AVR1-CO39 and AVR-PikD from the blast fungus M. oryzae are recognized by the rice nucleotide-binding domain and leucine-rich repeat proteins (NLRs) RGA5 and Pikp-1, respectively. This involves, in both cases, direct interaction of the effector with a heavy metal-associated (HMA) integrated domain (ID) in the NLR. Here, we solved the crystal structures of a C-terminal fragment of RGA5 carrying the HMA ID (RGA5_S), alone, and in complex with AVR1-CO39 and compared it to the structure of the Pikp1HMA/AVR-PikD complex. In both complexes, HMA ID/MAX effector interactions involve antiparallel alignment of ß-sheets from each partner. However, effector-binding occurs at different surfaces in Pikp1HMA and RGA5HMA, indicating that these interactions evolved independently by convergence of these two MAX effectors to the same type of plant target proteins. Interestingly, the effector-binding surface in RGA5HMA overlaps with the surface that mediates RGA5HMA self-interaction. Mutations in the HMA-binding interface of AVR1-CO39 perturb RGA5HMA-binding, in vitro and in vivo, and affect the recognition of M. oryzae in a rice cultivar containing Pi-CO39 Our study provides detailed insight into the mechanisms of effector recognition by NLRs, which has substantial implications for future engineering of NLRs to expand their recognition specificities. In addition, we propose, as a hypothesis for the understanding of effector diversity, that in the structurally conserved MAX effectors the molecular mechanism of host target protein-binding is conserved rather than the host target proteins themselves.

First report of Meloidogyne arenaria infecting Maidong (Ophiopogon japonicus) in China.

Maidong (Ophiopogon japonicus) is a perennial evergreen plant of the Asparagaceae, occurring mainly in China, Japan, Vietnam, and India. It grows in the damp place on the hillside below 2000 meters above sea level, under the forest or beside the stream;It has been widely cultivated in the Sichuan ofhina for medicinal uses; and it is included in the Chinese Pharmacopoeia. During April 2019, Maidong plants exhibiting symptoms of stunting, leaf wilting, and multiple galls in the roots associated with root-knot nematode (Meloidogyne sp.) were detected in a commercial field in near the city of Mianyang (N105°42', E30°93'), Sichuan, China. The second-stage juveniles (J2) were collected from the soil in the root zone, and adult females were dissected from roots. Population densities of J2 ranged from 190 to 255 per 100 cm3. Subsequently, individual females (n=20) were extracted from root samples and submitted to Meloidogyne species identification by perineal pattern morphological analysis (n=20), and morphometric measurements of second stage juveniles (J2) (n = 20). The J2 showed the following morphometric characters：body length = 475.5 ± 24.2 µm, tail length = 55.2 ± 6.43µm, stylet length = 12.4 ± 1.56 µm and distance from dorsal esophageal gland opening to the stylet knot (DGO) = 2.97 ± 0.44 µm; perineal patterns of females showed a low dorsal arch, with lateral field marked by forked and broken striae, no punctate markings between anus and tail terminus were observed. These morphological characteristics are consistent with Meloidogyne arenaria (Neves et al. 2016). In addition, to confirm species identification, DNA was extracted from females (Blok, et al. 1997) and D2/D3 fragments of the 28S rRNA was amplified using the universal primers D2A/D3B. The DNA fragment obtained showed a 754 bp length (GenBank accession no. MW965614) that was sequenced and analyzed, sequences were 99.8% identical to the MH359158, KX151138 and EU364889 M. arenaria sequences. Furthermore, species-specific SCAR primers Far/Rar were used as described by Zijlstra et al. 2000. The PCR produced approximately 420 bp sequences, which was identical to that previously reported for M. arenaria (Zijlstra et al. 2000). Morphological and molecular characterization supports the identification of the isolate found on Ophiopogon japonicus as M. arenaria. To verify the nematode pathogenicity on Maidong plants, Maidong seed were planted in 20-cm diameter, 10-cm deep plastic pots containing 1000 cm3 sterilized soil and infested with 2000 M. arenaria J2 per seedling, using a sterilized micropipette. Plants were maintained at 20-25°C in a greenhouse. Control plants received sterile water, and the pathogenicity test was repeated three times. After 60 days, all inoculated plants showed reduced growth compared with control. The symptoms were similar to those observed in the field, a large number of galls (38.5 ± 2.4) and egg masses (18.5 ± 0.2) were found on each root system. Maidong was considered a good host for M. arenaria in Mianyang. M. arenaria is one of the most important plant parasitic nematode with a wide geographic distribution and causes great losses in many crops around the world (Perry et al. 2009). Through investigation, this is the first report worldwide of M. arenaria infecting Ophiopogon japonicus.

Efficient long fragment editing technique enables large-scale and scarless bacterial genome engineering.

Bacteria are versatile living systems that enhance our understanding of nature and enable biosynthesis of valuable chemicals. Long fragment editing techniques are of great importance for accelerating bacterial genome engineering to obtain desirable and genetically stable strains. However, the existing genome editing methods cannot meet the needs of engineers. We herein report an efficient long fragment editing method for large-scale and scarless genome engineering in Escherichia coli. The method enabled us to insert DNA fragments up to 12 kb into the genome and to delete DNA fragments up to 186.7 kb from the genome, with positive rates over 95%. We applied this method for E. coli genome simplification, resulting in 12 individual deletion mutants and four cumulative deletion mutants. The simplest genome lost a total of 370.6 kb of DNA sequence containing 364 open reading frames. Additionally, we applied this technique to metabolic engineering and obtained a genetically stable plasmid-independent isobutanol production strain that produced 1.3 g/L isobutanol via shake-flask fermentation. These results suggest that the method is a powerful genome engineering tool, highlighting its potential to be applied in synthetic biology and metabolic engineering. KEY POINTS: • This article reports an efficient genome engineering tool for E. coli. • The tool is advantageous for the manipulations of long DNA fragments. • The tool has been successfully applied for genome simplification. • The tool has been successfully applied for metabolic engineering.

Metabolic engineering of E. coli for producing phloroglucinol from acetate.

Phloroglucinol is a three-hydroxyl phenolic compound and has diverse physiological and pharmacological activities such as antivirus and anti-inflammatory activities. Chemical synthesis of phloroglucinol suffered from many drawbacks such as high cost and environmental pollution. To avoid the above issues, microbial phloroglucinol biosynthesis was successfully accomplished in this study, while the abundant and low-cost acetate was used as the main carbon source. Firstly, the toxicity of phloroglucinol was tested, and E. coli BL21(DE3) could tolerate 5 g/L phloroglucinol. The ability of phloroglucinol synthase (PhlD) for catalyzing malonyl-CoA to phloroglucinol was confirmed, and E. coli BL21(DE3) expressing PhlD and acetyl-CoA carboxylase (ACCase) could produce 1107 ± 12 mg/L phloroglucinol from glucose. Then, E. coli BL21(DE3) was engineered to utilize acetate to produce 228 ± 15 mg/L phloroglucinol. Then, the endogenous citrate synthase (GltA) which could catalyze oxaloacetate and acetyl-CoA generated from acetate to citrate was knocked down by CRISPRi system in order to enhance the carbon flux for phloroglucinol production, and the titer was improved to 284 ± 8 mg/L. This work demonstrated that acetate could be used as low-cost substrate to achieve the biosynthesis of phloroglucinol and provided an example of effective utilization of acetate.