Formation of NPR1 Condensates Promotes Cell Survival during the Plant Immune Response.

In plants, pathogen effector-triggered immunity (ETI) often leads to programmed cell death, which is restricted by NPR1, an activator of systemic acquired resistance. However, the biochemical activities of NPR1 enabling it to promote defense and restrict cell death remain unclear. Here we show that NPR1 promotes cell survival by targeting substrates for ubiquitination and degradation through formation of salicylic acid-induced NPR1 condensates (SINCs). SINCs are enriched with stress response proteins, including nucleotide-binding leucine-rich repeat immune receptors, oxidative and DNA damage response proteins, and protein quality control machineries. Transition of NPR1 into condensates is required for formation of the NPR1-Cullin 3 E3 ligase complex to ubiquitinate SINC-localized substrates, such as EDS1 and specific WRKY transcription factors, and promote cell survival during ETI. Our analysis of SINCs suggests that NPR1 is centrally integrated into the cell death or survival decisions in plant immunity by modulating multiple stress-responsive processes in this quasi-organelle.

Pervasive downstream RNA hairpins dynamically dictate start-codon selection.

Translational reprogramming allows organisms to adapt to changing conditions. Upstream start codons (uAUGs), which are prevalently present in mRNAs, have crucial roles in regulating translation by providing alternative translation start sites1-4. However, what determines this selective initiation of translation between conditions remains unclear. Here, by integrating transcriptome-wide translational and structural analyses during pattern-triggered immunity in Arabidopsis, we found that transcripts with immune-induced translation are enriched with upstream open reading frames (uORFs). Without infection, these uORFs are selectively translated owing to hairpins immediately downstream of uAUGs, presumably by slowing and engaging the scanning preinitiation complex. Modelling using deep learning provides unbiased support for these recognizable double-stranded RNA structures downstream of uAUGs (which we term uAUG-ds) being responsible for the selective translation of uAUGs, and allows the prediction and rational design of translating uAUG-ds. We found that uAUG-ds-mediated regulation can be generalized to human cells. Moreover, uAUG-ds-mediated start-codon selection is dynamically regulated. After immune challenge in plants, induced RNA helicases that are homologous to Ded1p in yeast and DDX3X in humans resolve these structures, allowing ribosomes to bypass uAUGs to translate downstream defence proteins. This study shows that mRNA structures dynamically regulate start-codon selection. The prevalence of this RNA structural feature and the conservation of RNA helicases across kingdoms suggest that mRNA structural remodelling is a general feature of translational reprogramming.

Fate of contaminants of emerging concern in two wastewater treatment plants after retrofitting tertiary treatment for reduction of nitrogen discharge.

More and more previously designed wastewater treatment plants (WWTPs) are upgraded to tertiary treatment to meet the higher effluent discharge standards of conventional pollutants. Contaminants of emerging concern (CECs) can cause adverse effects on organisms and usually flow into WWTPs along with urban sewage. How the retrofitted WWTPs targeting conventional pollutants will influence the treatment efficiency of CECs is seldom discussed. This study investigates the removal of CECs in two full-scale newly retrofitted WWTPs (CD and JM WWTPs), containing high-efficiency sedimentation tank and denitrification deep bed filter for enhancing total nitrogen removal. The overall CEC removal efficiencies in the CD and JM WWTPs were 73.79 % and 93.63 %, respectively. Mass balance results indicated that CD WWTP and JM WWTP release a total of 36.89 and 88.58 g/d of CECs into the environment through effluent and excess sludge, respectively. Analysis of the concentration of CECs along the treatment process revealed most CECs were removed in the biological treatment units. The incorporation of newly constructed tertiary treatment proved beneficial for CEC removal and removed 2.93 % and 2.36 % CECs, corresponding to CEC removal of 2.92 and 27.49 g/d in the CD and JM WWTPs, respectively. The data of this study were further used to evaluate the suitability of the SimpleTreat model for simulating the fate of CECs in WWTPs. The predicted fraction of CECs discharged through the biological treatment effluent were generally within ten-fold difference from the measured results, highlighting its potential for estimating CEC removal in WWTPs.

Plant NLR immune receptor Tm-22 activation requires NB-ARC domain-mediated self-association of CC domain.

The nucleotide-binding, leucine-rich repeat-containing (NLR) class of immune receptors of plants and animals recognize pathogen-encoded proteins and trigger host defenses. Although animal NLRs form oligomers upon pathogen recognition to activate downstream signaling, the mechanisms of plant NLR activation remain largely elusive. Tm-22 is a plasma membrane (PM)-localized coiled coil (CC)-type NLR and confers resistance to Tobacco mosaic virus (TMV) by recognizing its viral movement protein (MP). In this study, we found that Tm-22 self-associates upon recognition of MP. The CC domain of Tm-22 is the signaling domain and its function requires PM localization and self-association. The nucleotide-binding (NB-ARC) domain is important for Tm-22 self-interaction and regulates activation of the CC domain through its nucleotide-binding and self-association. (d)ATP binding may alter the NB-ARC conformation to release its suppression of Tm-22 CC domain-mediated cell death. Our findings provide the first example of signaling domain for PM-localized NLR and insight into PM-localized NLR activation.

Cotton Leaf Curl Multan virus C4 protein suppresses both transcriptional and post-transcriptional gene silencing by interacting with SAM synthetase.

Gene silencing is a natural antiviral defense mechanism in plants. For effective infection, plant viruses encode viral silencing suppressors to counter this plant antiviral response. The geminivirus-encoded C4 protein has been identified as a gene silencing suppressor, but the underlying mechanism of action has not been characterized. Here, we report that Cotton Leaf Curl Multan virus (CLCuMuV) C4 protein interacts with S-adenosyl methionine synthetase (SAMS), a core enzyme in the methyl cycle, and inhibits SAMS enzymatic activity. By contrast, an R13A mutation in C4 abolished its capacity to interact with SAMS and to suppress SAMS enzymatic activity. Overexpression of wild-type C4, but not mutant C4R13A, suppresses both transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS). Plants infected with CLCuMuV carrying C4R13A show decreased levels of symptoms and viral DNA accumulation associated with enhanced viral DNA methylation. Furthermore, silencing of NbSAMS2 reduces both TGS and PTGS, but enhanced plant susceptibility to two geminiviruses CLCuMuV and Tomato yellow leaf curl China virus. These data suggest that CLCuMuV C4 suppresses both TGS and PTGS by inhibiting SAMS activity to enhance CLCuMuV infection in plants.

Antiviral Resistance Protein Tm-22 Functions on the Plasma Membrane.

The tomato Tobacco mosaic virus resistance-22 (Tm-22 ) gene encodes a coiled-coil-nucleotide binding site-Leu-rich repeat protein lacking a conventional plasma membrane (PM) localization motif. Tm-22 confers plant extreme resistance against tobamoviruses including Tobacco mosaic virus (TMV) by recognizing the avirulence (Avr) viral movement protein (MP). However, the subcellular compartment where Tm-22 functions is unclear. Here, we demonstrate that Tm-22 interacts with TMV MP to form a protein complex at the PM We show that both inactive and active Tm-22 proteins are localized to the PM When restricted to PM by fusing Tm-22 to the S-acylated PM association motif, the Tm-22 fusion protein can still induce a hypersensitive response cell death, consistent with its activation at the PM Through analyses of viral MP mutants, we find that the plasmodesmata (PD) localization of the Avr protein MP is not required for Tm-22 function. These results suggest that Tm-22-mediated resistance takes place on PM without requirement of its Avr protein to be located to PD.

Foxtail Mosaic Virus-Induced Gene Silencing in Monocot Plants.

Virus-induced gene silencing (VIGS) is a powerful technique to study gene function in plants. However, very few VIGS vectors are available for monocot plants. Here we report that Foxtail mosaic virus (FoMV) can be engineered as an effective VIGS system to induce efficient silencing of endogenous genes in monocot plants including barley (Hordeum vulgare L.), wheat (Triticum aestivum) and foxtail millet (Setaria italica). This is evidenced by FoMV-based silencing of phytoene desaturase (PDS) and magnesium chelatase in barley, of PDS and Cloroplastos alterados1 in foxtail millet and wheat, and of an additional gene IspH in foxtail millet. Silencing of these genes resulted in photobleached or chlorosis phenotypes in barley, wheat, and foxtail millet. Furthermore, our FoMV-based gene silencing is the first VIGS system reported for foxtail millet, an important C4 model plant. It may provide an efficient toolbox for high-throughput functional genomics in economically important monocot crops.

Endoscopic optical coherence tomography with a focus-adjustable probe.

We present a focus-adjustable endoscopic probe for optical coherence tomography (OCT), which is able to acquire images with different focal planes and overcome depth-of-focus limitations by image fusing. The use of a two-way shape-memory-alloy spring enables the probe to adjust working distance over 1.5 mm, providing a large scanning range with high resolution and no sensitivity loss. Equipped with a homemade hollow-core ultrasonic motor, the probe is capable of performing an unobstructed 360 deg field-of-view distal scanning. Both the axial resolution and the best lateral resolution are ∼4 µm, with a sensitivity of 100.3 dB. Spectral-domain OCT imaging of phantom and biological tissues with the probe is also demonstrated.

Type I J-domain NbMIP1 proteins are required for both Tobacco mosaic virus infection and plant innate immunity.

Tm-2² is a coiled coil-nucleotide binding-leucine rich repeat resistance protein that confers durable extreme resistance against Tomato mosaic virus (ToMV) and Tobacco mosaic virus (TMV) by recognizing the viral movement protein (MP). Here we report that the Nicotiana benthamiana J-domain MIP1 proteins (NbMIP1s) associate with tobamovirus MP, Tm-2² and SGT1. Silencing of NbMIP1s reduced TMV movement and compromised Tm-2²-mediated resistance against TMV and ToMV. Furthermore, silencing of NbMIP1s reduced the steady-state protein levels of ToMV MP and Tm-2². Moreover, NbMIP1s are required for plant resistance induced by other R genes and the nonhost pathogen Pseudomonas syringae pv. tomato (Pst) DC3000. In addition, we found that SGT1 associates with Tm-2² and is required for Tm-2²-mediated resistance against TMV. These results suggest that NbMIP1s function as co-chaperones during virus infection and plant immunity.

Relative Orientation and Position Detections Based on an RGB-D Sensor and Dynamic Cooperation Strategies for Jumping Sensor Nodes Recycling.

This paper presents relative orientation and position detection methods for jumping sensor nodes (JSNs) recycling. The methods are based on motion captures of the JSNs by an RGB-D sensor mounted on a carrier robot and the dynamic cooperation between the carrier and the JSNs. A disc-like label with two different colored sides is mounted on the top of the JSNs. The RGB-D sensor can detect the motion of the label to calculate the orientations and positions of the JSNs and the carrier relative to each other. After the orientations and positions have been detected, the JSNs jump into a cabin mounted on the carrier in dynamic cooperation with the carrier for recycling. The performances of the proposed methods are tested with a prototype system. The results show that the carrier can detect a JSN from up to 2 m away and sense its relative orientation and position successfully. The errors of the JSN's orientation and position detections relative to the carrier could be reduced to the values smaller than 1° and 1 cm, respectively, by using the dynamic cooperation strategies. The proposed methods in this paper could also be used for other kinds of mobile sensor nodes and multi-robot systems.

Linear-in-wavenumber swept laser with an acousto-optic deflector for optical coherence tomography.

We report a novel linear-in-wavenumber (k-linear) swept laser source based on an acousto-optic deflector (AOD). The AOD-based optical filter includes an acousto-optic deflector and a reflection grating. The laser may tune k linearly in wavenumber over time due to its appropriate configuration and is favorable for fast imaging because it avoids data resampling and recalibration, as are required in conventional swept source optical coherence tomography (SS-OCT). We achieved k-linearity with Pearson's r correlation coefficients of 0.99995 without and 0.99997 with optimization. The laser has a tuning range of 50 nm, a 3 dB swept range of 42 nm (FWHM), output power of 2.56 mW, 6 dB sensitivity roll-off depth of 0.941 mm, and central wavelength of 1064 nm at a scanning rate of ∼20 kHz. Scanning rate as high as ∼400 kHz is also achieved for this laser with the tuning range 49 nm, swept linearity of 0.99990, output power of 2.30 mW, and a 6 dB sensitivity roll-off depth 0.550 mm. SS-OCT imaging with linear-in-wavenumber swept laser is also demonstrated.

Out-of-set association analysis of lung cancer drugs and symptoms based on clinical case data mining.

BACKGROUND: There are 1.8 million lung cancer deaths worldwide, accounting for 18% of global cancer deaths, including 710,000 in China, accounting for 23.8% of all cancer deaths in China. OBJECTIVE: To explore the out-of-set association rules of lung cancer symptoms and drugs through text mining of traditional Chinese medicine (TCM) treatment of lung cancer, and form medical case analysis to analyze the experience of TCM syndrome differentiation in its treatment. METHODS: The medical records of all patients diagnosed with lung cancer in Nanjing Chest Hospital from January to December 2018 were collected, and the out-of-set association analysis was performed using the MedCase v5.2 TCM clinical scientific research auxiliary platform based on the frequent pattern growth enhanced association analysis algorithm. RESULTS: In terms of TCM treatment of lung cancer, the clinical symptoms with high correlation included cough, expectoration, chest distress, and white phlegm; and the drugs with high correlation included Pinellia ternata, licorice root, white Atractylodes rhizome, and Radix Ophiopogonis; with the prescriptions based on Erchen and Maimendong decoctions. CONCLUSION: This analytical study of the medical cases of TCM treatment for lung cancer was performed using data mining techniques, and the out-of-set association rules between clinical symptoms and drugs were analyzed, including the understanding of lung cancer in TCM. Moreover, the essence of experience in drug use was gathered, providing significant scientific guidance for the clinical treatment of lung cancer.

GJA4 expressed on cancer associated fibroblasts (CAFs)-A 'promoter' of the mesenchymal phenotype.

BACKGROUND: Colorectal cancer (CRC) is the third most common cancer worldwide. Connexin is a transmembrane protein involved in gap junctions (GJs) formation. Our previous study found that connexin 37 (Cx37), encoded by gap junction protein alpha 4 (GJA4), expressed on fibroblasts acts as a promoter of CRC and is closely related to epithelial-mesenchymal transition (EMT) and tumor immune microenvironment. However, to date, the mechanism concerning the malignancy of GJA4 in tumor stroma has not been studied. METHODS: Hematoxylin-eosin (HE) and immunohistochemical (IHC) staining were used to validate the expression and localization of GJA4. Using single-cell analysis, enrichment analysis, spatial transcriptomics, immunofluorescence staining (IF), Sirius red staining, wound healing and transwell assays, western blotting (WB), Cell Counting Kit-8 (CCK8) assay and in vivo experiments, we investigated the possible mechanisms of GJA4 in promoting CRC. RESULTS: We discovered that in CRC, GJA4 on fibroblasts is involved in promoting fibroblast activation and promoting EMT through a fibroblast-dependent pathway. Furthermore, GJA4 may act synergistically with M2 macrophages to limit T cell infiltration by stimulating the formation of an immune-excluded desmoplasic barrier. Finally, we found a significantly correlation between GJA4 and pathological staging (P < 0.0001) or D2 dimer (R = 0.03, P < 0.05). CONCLUSION: We have identified GJA4 expressed on fibroblasts is actually a promoter of the tumor mesenchymal phenotype. Our findings suggest that the interaction between GJA4+ fibroblasts and M2 macrophages may be an effective target for enhancing tumor immunotherapy.

Self-Assembled BiGaSeAs Composite Superlattice-Structured Nanowire for Broad-Band Photodetection.

Photodetectors with a broad-band response range are widely used in many fields and are regarded as pivotal components of the modern miniaturized electronics industry. However, commercial broad-band photodetectors composed of traditional bulk semiconductor materials are still limited by complex preparation techniques, high costs, and a lack of mechanical strength and flexibility, which are difficult to satisfy the increasing demand for flexible and wearable optoelectronics. Therefore, researchers have been devoted to finding new strategies to obtain flexible, stable, and high-performance broad-band photodetectors. In this work, a novel self-assembled BiGaSeAs composite superlattice-structured nanowire was developed with a simple chemical vapor deposition method for easy fabrication. After the device assembling, the photodetector showed outstanding performance in terms of obvious Ion/Ioff (13.9), broad-band photoresponse (365-940 nm), excellent responsivity (1007.67 A/W), high detectivity (9.38 × 109 Jones), and rapid response (21 and 23 ms). The formation of microheterojunctions among various materials inside the nanowires also contributed to their extended broad-spectrum response and outstanding detection ability. These results indicate that the BiGaSeAs nanowires have potential applications in the field of flexible and wearable electronics.

H2O2 sulfenylates CHE linking local infection to establishment of systemic acquired resistance.

In plants, a local infection can lead to systemic acquired resistance (SAR) through increased production of salicylic acid (SA). For 30 years, the identity of the mobile signal and its direct transduction mechanism for systemic SA synthesis in initiating SAR have been hotly debated. We found that, upon pathogen challenge, the cysteine residue of transcription factor CHE undergoes sulfenylation in systemic tissues, enhancing its binding to the promoter of SA-synthesis gene, ICS1, and increasing SA production. This occurs independently of previously reported pipecolic acid (Pip) signal. Instead, H2O2 produced by NADPH oxidase, RBOHD, is the mobile signal that sulfenylates CHE in a concentration-dependent manner. This modification serves as a molecular switch that activates CHE-mediated SA-increase and subsequent Pip-accumulation in systemic tissues to synergistically induce SAR.

Global translational induction during NLR-mediated immunity in plants is dynamically regulated by CDC123, an ATP-sensitive protein.

The recognition of pathogen effectors by their cognate nucleotide-binding leucine-rich repeat (NLR) receptors activates effector-triggered immunity (ETI) in plants. ETI is associated with correlated transcriptional and translational reprogramming and subsequent death of infected cells. Whether ETI-associated translation is actively regulated or passively driven by transcriptional dynamics remains unknown. In a genetic screen using a translational reporter, we identified CDC123, an ATP-grasp protein, as a key activator of ETI-associated translation and defense. During ETI, an increase in ATP concentration facilitates CDC123-mediated assembly of the eukaryotic translation initiation factor 2 (eIF2) complex. Because ATP is required for the activation of NLRs as well as the CDC123 function, we uncovered a possible mechanism by which the defense translatome is coordinately induced during NLR-mediated immunity. The conservation of the CDC123-mediated eIF2 assembly suggests its possible role in NLR-mediated immunity beyond plants.

Analysis of the cluster efficacy and prescription characteristics of traditional Chinese medicine intervention for non-small cell lung cancer based on a clustering algorithm.

BACKGROUND: In recent years, malignant tumors have gradually become one of the main causes of death for Chinese residents, of which lung cancer ranks first in both the incidence and mortality in China. OBJECTIVE: To mine the text of traditional Chinese medicine (TCM) clinical medical cases after data cleaning, analyze it, and study the experience of TCM doctors in treating non-small cell lung cancer (NSCLC). METHODS: The applied approach was based on the data mining methods of decentralized and hierarchical system clustering of data from a drug and prescription database. This study involved 215 patients, 287 cases, and 147 types of clinical drugs. RESULTS: The data analysis of the clinical treatment of NSCLC in TCM showed that Erchen Decoction was the main method for the treatment of non-small cell lung cancer in clinical treatment of non-small cell lung cancer. Junjian recipes were close to each other, with Banzhilian, Lobelia, Shanci Mushroom, Hedyotis diffusa to anticancer and detoxify. CONCLUSION: This study analyzed the core TCM prescription for NSCLC by collecting the empirical essence and characteristics of specific medications. It has some guiding scientific significance for the clinical treatment of lung cancer.

Efficient Doping Induced by Charge Transfer at the Hetero-Interface to Enhance Photocatalytic Performance.

The construction of heterojunction photocatalysts is an effective method to improve photocatalytic efficiency since the potential gradient and built-in electron field established at the junction could enhance the efficiency of charge separation and interfacial charge transfer. Nevertheless, heterojunction photocatalysts with strong built-in electron fields remain difficult to build since the two adjacent constitutes must be satisfied with an appropriate band alignment, redox potential, and carrier concentration gradient. Here, an efficient charge transfer-induced doping strategy is proposed to enhance the heterojunction built-in electron field for stable and efficient photocatalytic performance. Carrier transfer tests show that the rectification ratio of the n-TiO2-X/n-BiOI heterojunction is significantly enhanced after being coated with graphene oxide (GO). Consequently, both the hydrogen production and photodegradation performance of the GO composite heterojunction are considerably enhanced compared with pure TiO2-X, BiOI, and n-TiO2-X/n-BiOI. This work provides a facile method to prepare heterojunction photocatalysts with a high catalytic activity.

Spectral-domain optical coherence tomography with a Fresnel spectrometer.

We propose a novel spectral-domain optical coherence tomography (SD-OCT) equipped with a Fresnel spectrometer, which utilizes a Fresnel zone plate (FZP) as both dispersion and focusing optics and thus spreads the spectral interferogram evenly in wavenumber domain because of the proportional relation between the focal length of the FZP and the wavenumber. With no need of the conversion calculation from wavelength to wavenumber in conventional SD-OCT, this new design is favorable for fast imaging with high resolution. As only a FZP and CCD are used, the Fresnel spectrometer is simple and compact. It is experimentally shown that its performance is as good as that of numerical interpolation in conventional SD-OCT. Imaging of bio-tissue by Fresnel SD-OCT is also demonstrated.

Compressed sensing with linear-in-wavenumber sampling in spectral-domain optical coherence tomography.

We propose a novel method called compressed sensing with linear-in-wavenumber sampling (k-linear CS) to retrieve an image for spectral-domain optical coherence tomography (SD-OCT). An array of points that is evenly spaced in wavenumber domain is sampled from an original interferogram by a preset k-linear mask. Then the compressed sensing based on l1 norm minimization is applied on these points to reconstruct an A-scan data. To get an OCT image, this method uses less than 20% of the total data as required in the typical process and gets rid of the spectral calibration with numerical interpolation in traditional CS-OCT. Therefore k-linear CS is favorable for high speed imaging. It is demonstrated that the k-linear CS has the same axial resolution performance with ~30 dB higher signal-to-noise ratio (SNR) as compared with the numerical interpolation. Imaging of bio-tissue by SD-OCT with k-linear CS is also demonstrated.